From f6fe291d363c408c609ecbfb1f52f187698fd1b0 Mon Sep 17 00:00:00 2001
From: Keara Soloway <kls286@cornell.edu>
Date: Wed, 25 Mar 2026 10:30:25 -0400
Subject: [PATCH 01/76] bump: pydantify NexusValuesWriter

---
 CHAP/common/writer.py | 13 ++++++++++---
 1 file changed, 10 insertions(+), 3 deletions(-)

diff --git a/CHAP/common/writer.py b/CHAP/common/writer.py
index da33beda..2e09febc 100755
--- a/CHAP/common/writer.py
+++ b/CHAP/common/writer.py
@@ -536,8 +536,15 @@ def write(self, data):
 
 
 class NexusValuesWriter(Writer):
-    """Writer for updating values in an existing NeXus file."""
-    def write(self, data, filename, path_prefix=''):
+    """Writer for updating values in an existing NeXus file.
+
+    :ivar path_prefix: Prefix to use for all paths in input `data`,
+        defaults to `''`.
+    :vartype path_prefix: str, optional
+    """
+    path_prefix: str = ''
+
+    def write(self, data, filename):
         """Write new values specified in `data` to the exising NeXus
         file `filename`.
 
@@ -561,7 +568,7 @@ def write(self, data, filename, path_prefix=''):
             with NXFile(filename, 'a') as nxroot:
                 self.nxs_writer(
                     nxroot=nxroot,
-                    path=os.path.join(path_prefix, d['path']),
+                    path=os.path.join(self.path_prefix, d['path']),
                     idx=d['idx'],
                     data=d['data']
                 )

From 2832f19f57750ff1dbd9c4bc5d03dc807b27a50d Mon Sep 17 00:00:00 2001
From: Keara Soloway <kls286@cornell.edu>
Date: Wed, 25 Mar 2026 12:46:29 -0400
Subject: [PATCH 02/76] add: NexusValuesWriter.resize_axis

If `False`, same behavior as before.
If an `int`, use it as the axis to resize the NXfield along (only if
the target slice shape does not match the data shape).
---
 CHAP/common/writer.py | 36 +++++++++++++++++++++++++++++-------
 1 file changed, 29 insertions(+), 7 deletions(-)

diff --git a/CHAP/common/writer.py b/CHAP/common/writer.py
index 2e09febc..d6c6f1e3 100755
--- a/CHAP/common/writer.py
+++ b/CHAP/common/writer.py
@@ -7,7 +7,11 @@
 
 # System modules
 import os
-from typing import Optional
+from typing import (
+    Literal,
+    Optional,
+    Union,
+)
 
 # Third party modules
 import numpy as np
@@ -541,8 +545,14 @@ class NexusValuesWriter(Writer):
     :ivar path_prefix: Prefix to use for all paths in input `data`,
         defaults to `''`.
     :vartype path_prefix: str, optional
+    :ivar resize_axis: `False` OR the axis along which the dataset
+        should be resized if the target slice shape does not match the
+        data shape. If `False`, any mismatching shapes will just raise
+        an error. Defaults to `False`.
+    :vartype resize_axis: Union[int, Literal[False]], optional
     """
     path_prefix: str = ''
+    resize_axis: Union[int, Literal[False]] = False
 
     def write(self, data, filename):
         """Write new values specified in `data` to the exising NeXus
@@ -552,7 +562,7 @@ def write(self, data, filename):
         -- `'path'` identifying the location of the `NXfield` object
         to which values will be written, `'data'` identifying the data
         to be written, and `'idx'` identifying the index / indicies of
-        the `NXfield` to which the data will be written.
+         the `NXfield` to which the data will be written.
         :type data: list[PipelineData]
         :param filename: Name of an existing NeXus file to update.
         :type filename: str
@@ -586,8 +596,8 @@ def nxs_writer(self, nxroot, path, idx, data):
         :type nxroot: nexusformat.nexus.NXroot
         :param path: Path to the dataset inside the NeXus file.
         :type path: str
-        :param idx: Index or slice where the data should be written.
-        :type idx: tuple or int
+        :param idx: Slice where the data should be written.
+        :type idx: slice
         :param data: Data to be written to the specified slice in the
             dataset.
         :type data: numpy.ndarray or compatible array-like object
@@ -607,9 +617,21 @@ def nxs_writer(self, nxroot, path, idx, data):
         # Check that the slice shape matches the data shape
         data = np.asarray(data)
         if dataset[idx].shape != data.shape:
-            raise ValueError(
-                f'Data shape {data.shape} does not match the target slice '
-                f'shape {dataset[idx].shape}.')
+            if self.resize_axis is not False:
+                # Resize along the specified axis
+                start = idx.start or 0
+                stop = start + data.shape[0]
+                newshape = max(dataset.shape[self.resize_axis], stop)
+                self.logger.debug(
+                    f'Resizing {path} {dataset.shape} -> {newshape} '
+                    + f'along axis {self.resize_axis}'
+                )
+
+                dataset.resize(newshape, axis=self.resize_axis)
+            else:
+                raise ValueError(
+                    f'Data shape {data.shape} does not match the target slice '
+                    f'shape {dataset[idx].shape}.')
 
         # Write the data to the specified slice
         dataset[idx] = data

From 0c1e7143f88aef0881f9598a1f58a96a55e93012 Mon Sep 17 00:00:00 2001
From: Keara Soloway <kls286@cornell.edu>
Date: Wed, 25 Mar 2026 12:52:32 -0400
Subject: [PATCH 03/76] fix: list access typo

---
 CHAP/pipeline.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/CHAP/pipeline.py b/CHAP/pipeline.py
index c7e63512..522bc772 100755
--- a/CHAP/pipeline.py
+++ b/CHAP/pipeline.py
@@ -352,7 +352,7 @@ def get_pipelinedata_item(data, index=-1, remove=False):
         if isinstance(data, list):
             if remove:
                 return data.pop(index)['data']
-            return data.get(index)['data']
+            return data[index]['data']
         return data
 
     def execute(self, data):

From f02dd10d4cfbb45d355864690cb2e5bfbbe28841 Mon Sep 17 00:00:00 2001
From: Keara Soloway <kls286@cornell.edu>
Date: Wed, 25 Mar 2026 12:54:33 -0400
Subject: [PATCH 04/76] add: expandable first dimension for all NXfields in
 result of MapProcessor

---
 CHAP/common/processor.py | 20 ++++++++++++++++----
 1 file changed, 16 insertions(+), 4 deletions(-)

diff --git a/CHAP/common/processor.py b/CHAP/common/processor.py
index 172b120e..ee230b56 100755
--- a/CHAP/common/processor.py
+++ b/CHAP/common/processor.py
@@ -1272,7 +1272,10 @@ def linkdims(nxgroup, nxdata_source):
                         attrs={'units': dim.units,
                                'long_name': f'{dim.label} ({dim.units})',
                                'data_type': dim.data_type,
-                               'local_name': dim.name})
+                               'local_name': dim.name},
+                        maxshape= (None, *independent_dimensions[i].shape[1:]),
+                        chunks=(1, *independent_dimensions[i].shape[1:])
+                    )
         else:
             nxentry.independent_dimensions.index = NXfield(
                 np.arange(independent_dimensions[0].size), 'index')
@@ -1291,7 +1294,10 @@ def linkdims(nxgroup, nxdata_source):
                 units=dim.units,
                 attrs={'long_name': f'{dim.label} ({dim.units})',
                        'data_type': dim.data_type,
-                       'local_name': dim.name}))
+                       'local_name': dim.name},
+                maxshape=(None, *all_scalar_data[i].shape[1:]),
+                chunks=(1, *all_scalar_data[i].shape[1:])
+            ))
         if (self.config.experiment_type == 'EDD'
                 and not placeholder_data is False):
             scalar_signals.append('placeholder_data_used')
@@ -1308,7 +1314,10 @@ def linkdims(nxgroup, nxdata_source):
                     attrs={'units': dim.units,
                            'long_name': f'{dim.label} ({dim.units})',
                            'data_type': dim.data_type,
-                           'local_name': dim.name}))
+                           'local_name': dim.name},
+                    maxshape=(None, *independent_dimensions[i].shape[1:]),
+                    chunks=(1, *independent_dimensions[i].shape[1:])
+                ))
                 self.config.all_scalar_data.append(
                     PointByPointScanData(**dim.model_dump()))
                 self.config.independent_dimensions.remove(dim)
@@ -1336,7 +1345,10 @@ def linkdims(nxgroup, nxdata_source):
         for i, detector in enumerate(self.detector_config.detectors):
             nxdata[detector.get_id()] = NXfield(
                 value=data[i],
-                attrs={**detector.attrs, 'min': min_[i], 'max': max_[i]})
+                attrs={**detector.attrs, 'min': min_[i], 'max': max_[i]},
+                maxshape=(None, *data[i].shape[1:]),
+                chunks=(1, *data[i].shape[1:])
+            )
             detector_ids.append(detector.get_id())
         linkdims(nxdata, nxentry.independent_dimensions)
         if len(self.detector_config.detectors) == 1:

From 2ef093628aa9b31fe9e96806e9067f83c0bc4f1e Mon Sep 17 00:00:00 2001
From: Keara Soloway <kls286@cornell.edu>
Date: Thu, 26 Mar 2026 12:32:58 -0400
Subject: [PATCH 05/76] add: reminder comment

---
 CHAP/edd/processor.py | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/CHAP/edd/processor.py b/CHAP/edd/processor.py
index 7aa412bc..7ea2d660 100755
--- a/CHAP/edd/processor.py
+++ b/CHAP/edd/processor.py
@@ -2666,6 +2666,9 @@ def process(self, data):
         nxdata = nxentry[nxentry.default]
 
         # Load the validated calibration configuration
+        # FIX make this a class field and add to pipeline_fields too?
+        #     NB: be sure that adding this field does not mess up
+        #     self.detector_config during pydantic validation
         calibration_config = self.get_config(
             data, schema='edd.models.MCATthCalibrationConfig', remove=False)
 

From a318c74327b231210902066c8d39095dd7697ee2 Mon Sep 17 00:00:00 2001
From: Keara Soloway <kls286@cornell.edu>
Date: Thu, 26 Mar 2026 13:40:04 -0400
Subject: [PATCH 06/76] fix: slice stop indices in MapSliceProcessor

---
 CHAP/common/map_utils.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/CHAP/common/map_utils.py b/CHAP/common/map_utils.py
index 7ae1f35e..eb15bebc 100644
--- a/CHAP/common/map_utils.py
+++ b/CHAP/common/map_utils.py
@@ -106,13 +106,13 @@ def process(self, data, #spec_file, scan_number,
         # Get spec scan indices to process
         scan_indices = range(npts_scan)[slice(
             idx_slice.get('start', 0),
-            idx_slice.get('stop', npts_scan + 1),
+            idx_slice.get('stop', npts_scan),
             idx_slice.get('step', 1)
         )]
         # Get map indices to write to
         map_indices = slice(
             idx_slice.get('start', 0) + index_offset,
-            idx_slice.get('stop', npts_scan + 1) + index_offset,
+            idx_slice.get('stop', npts_scan) + index_offset,
             idx_slice.get('step', 1)
         )
 

From b0c2e105699daf793878e3c60a4e6e316129cd65 Mon Sep 17 00:00:00 2001
From: Keara Soloway <kls286@cornell.edu>
Date: Thu, 26 Mar 2026 13:40:51 -0400
Subject: [PATCH 07/76] fix: support oddball EDD get_detector_data return
 values

---
 CHAP/common/map_utils.py | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

diff --git a/CHAP/common/map_utils.py b/CHAP/common/map_utils.py
index eb15bebc..3987207d 100644
--- a/CHAP/common/map_utils.py
+++ b/CHAP/common/map_utils.py
@@ -129,12 +129,18 @@ def process(self, data, #spec_file, scan_number,
             }
             for s_d in self.map_config.all_scalar_data
         ]
+        if self.map_config.experiment_type == 'EDD':
+            def get_detector_data(detector, index):
+                return scan.get_detector_data(detector.get_id(), index)[0]
+        else:
+            def get_detector_data(detector, index):
+                return scan.get_detector_data(detector.get_id(), index)
         data_points.extend(
             [
                 {
                     'path': f'{self.map_config.title}/data/{det.get_id()}',
                     'data': np.asarray([
-                        scan.get_detector_data(det.get_id(), i)
+                        get_detector_data(det, i)
                         for i in scan_indices
                     ]),
                     'idx': map_indices

From 9fa6985716976146387289c87d49c84841408f8a Mon Sep 17 00:00:00 2001
From: Keara Soloway <kls286@cornell.edu>
Date: Thu, 26 Mar 2026 16:35:04 -0400
Subject: [PATCH 08/76] add: support for finding SCAN_N datasets in groups
 other than "data"

---
 CHAP/edd/reader.py | 16 +++++++++++++++-
 1 file changed, 15 insertions(+), 1 deletion(-)

diff --git a/CHAP/edd/reader.py b/CHAP/edd/reader.py
index 8ff854a7..8bad0f6a 100755
--- a/CHAP/edd/reader.py
+++ b/CHAP/edd/reader.py
@@ -750,7 +750,7 @@ class SliceNXdataReader(Reader):
     provided slicing parameters.
  
     :param scan_number: Number of the SPEC scan.
-    :type scan_number: int
+    :vartype scan_number: int
     """
     scan_number: conint(ge=0)
 
@@ -772,14 +772,28 @@ def read(self):
 
         reader = NexusReader(**self.model_dump())
         nxroot = nxcopy(reader.read())
+        nxentry = None
         nxdata = None
         for nxname, nxobject in nxroot.items():
             if isinstance(nxobject, NXentry):
+                nxentry = nxobject
                 nxdata = nxobject.data
         if nxdata is None:
             msg = 'Could not find NXdata group'
             self.logger.error(msg)
             raise ValueError(msg)
+        if 'SCAN_N' not in nxdata:
+            self.logger.warning(f'SCAN_N not in {nxdata}')
+            scan_n_found = False
+            for k, v in nxentry.items():
+                if 'SCAN_N' in v:
+                    nxdata = v
+                    scan_n_found = True
+                    self.logger.warning(f'Using SCAN_N dataset in {nxdata}')
+            if not scan_n_found:
+                msg = 'Cannot find SCAN_N dataset'
+                self.logger.error(msg)
+                raise ValueError(msg)
 
         indices = np.argwhere(
             nxdata.SCAN_N.nxdata == self.scan_number).flatten()

From 4fcdda1235786ecc383d2f620460878bebc48be5 Mon Sep 17 00:00:00 2001
From: Keara Soloway <kls286@cornell.edu>
Date: Wed, 1 Apr 2026 12:18:22 -0400
Subject: [PATCH 09/76] fix: add independent_dimensions to results of
 MapSliceProcessor

---
 CHAP/common/map_utils.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/CHAP/common/map_utils.py b/CHAP/common/map_utils.py
index 3987207d..2b71c3d0 100644
--- a/CHAP/common/map_utils.py
+++ b/CHAP/common/map_utils.py
@@ -59,7 +59,7 @@ class MapSliceProcessor(Processor):
     spec_file: FilePath
     scan_number: conint(gt=0)
 
-    def process(self, data, #spec_file, scan_number,
+    def process(self, data,
                 idx_slice={'start': 0, 'step': 1}):
         """Aggregate partial spec and detector data from one scan in a
         map, returning results in a format suitable for writing to the
@@ -128,6 +128,7 @@ def process(self, data, #spec_file, scan_number,
                 'idx': map_indices
             }
             for s_d in self.map_config.all_scalar_data
+                       + self.map_config.independent_dimensions
         ]
         if self.map_config.experiment_type == 'EDD':
             def get_detector_data(detector, index):

From 9ed9e017871e61fc6ed15b0cae94b9b19de8cf01 Mon Sep 17 00:00:00 2001
From: Keara Soloway <kls286@cornell.edu>
Date: Wed, 1 Apr 2026 12:19:21 -0400
Subject: [PATCH 10/76] fix: EDD-specific modifications for MapSliceProcessor

---
 CHAP/common/map_utils.py | 15 ++++++++++++++-
 1 file changed, 14 insertions(+), 1 deletion(-)

diff --git a/CHAP/common/map_utils.py b/CHAP/common/map_utils.py
index 2b71c3d0..7b4c1034 100644
--- a/CHAP/common/map_utils.py
+++ b/CHAP/common/map_utils.py
@@ -131,8 +131,21 @@ def process(self, data,
                        + self.map_config.independent_dimensions
         ]
         if self.map_config.experiment_type == 'EDD':
+            data_points.extend(
+                [
+                    {
+                        'path': f'{self.map_config.title}/independent_dimensions/index',
+                        'data': [
+                            i for i in range(
+                                map_indices.start, map_indices.stop
+                            )
+                        ],
+                        'idx': map_indices
+                    }
+                ]
+            )
             def get_detector_data(detector, index):
-                return scan.get_detector_data(detector.get_id(), index)[0]
+                return scan.get_detector_data(detector.get_id(), index)[0][0]
         else:
             def get_detector_data(detector, index):
                 return scan.get_detector_data(detector.get_id(), index)

From 76a9a611f36aee2297b143ed62d9ad67bd12ef48 Mon Sep 17 00:00:00 2001
From: Keara Soloway <kls286@cornell.edu>
Date: Wed, 1 Apr 2026 12:21:59 -0400
Subject: [PATCH 11/76] fix: some missing resizable NXfields for MapProcessor

---
 CHAP/common/processor.py | 13 ++++++++++---
 1 file changed, 10 insertions(+), 3 deletions(-)

diff --git a/CHAP/common/processor.py b/CHAP/common/processor.py
index ee230b56..31f11a3c 100755
--- a/CHAP/common/processor.py
+++ b/CHAP/common/processor.py
@@ -1273,12 +1273,15 @@ def linkdims(nxgroup, nxdata_source):
                                'long_name': f'{dim.label} ({dim.units})',
                                'data_type': dim.data_type,
                                'local_name': dim.name},
-                        maxshape= (None, *independent_dimensions[i].shape[1:]),
+                        maxshape=(None, *independent_dimensions[i].shape[1:]),
                         chunks=(1, *independent_dimensions[i].shape[1:])
                     )
         else:
             nxentry.independent_dimensions.index = NXfield(
-                np.arange(independent_dimensions[0].size), 'index')
+                np.arange(independent_dimensions[0].size), 'index',
+                maxshape=(None,),
+                chunks=(1,)
+            )
 
         # Set up scalar data NeXus NXdata group
         # (add the constant independent dimensions)
@@ -1298,6 +1301,7 @@ def linkdims(nxgroup, nxdata_source):
                 maxshape=(None, *all_scalar_data[i].shape[1:]),
                 chunks=(1, *all_scalar_data[i].shape[1:])
             ))
+
         if (self.config.experiment_type == 'EDD'
                 and not placeholder_data is False):
             scalar_signals.append('placeholder_data_used')
@@ -1305,7 +1309,10 @@ def linkdims(nxgroup, nxdata_source):
                 value=all_scalar_data[-1],
                 attrs={'description':
                     'Indicates whether placeholder data may be present for'
-                    'the corresponding frames of detector data.'}))
+                    'the corresponding frames of detector data.'},
+                maxshape=(None, *all_scalar_data[-1].shape[1:]),
+                chunks=(1, *all_scalar_data[-1].shape[1:])
+            ))
         for i, dim in enumerate(deepcopy(self.config.independent_dimensions)):
             if i in constant_dim:
                 scalar_signals.append(dim.label)

From a68706cd0b881f07d65caa1854100192e00d519d Mon Sep 17 00:00:00 2001
From: Keara Soloway <kls286@cornell.edu>
Date: Wed, 1 Apr 2026 12:38:48 -0400
Subject: [PATCH 12/76] fix: independent_dimensions paths in MapSliceProcessor
 results

---
 CHAP/common/map_utils.py | 30 ++++++++++++++++--------------
 1 file changed, 16 insertions(+), 14 deletions(-)

diff --git a/CHAP/common/map_utils.py b/CHAP/common/map_utils.py
index 7b4c1034..541c0d70 100644
--- a/CHAP/common/map_utils.py
+++ b/CHAP/common/map_utils.py
@@ -128,22 +128,24 @@ def process(self, data,
                 'idx': map_indices
             }
             for s_d in self.map_config.all_scalar_data
-                       + self.map_config.independent_dimensions
         ]
+        data_points.extend(
+            [
+                {
+                    'path': f'{self.map_config.title}/independent_dimensions/{dim.label}',
+                    'data': np.asarray([
+                        dim.get_value(
+                            scans, self.scan_number, i,
+                            scalar_data=self.map_config.scalar_data
+                        )
+                        for i in scan_indices
+                    ]),
+                    'idx': map_indices,
+                }
+                for dim in self.map_config.independent_dimensions
+            ]
+        )
         if self.map_config.experiment_type == 'EDD':
-            data_points.extend(
-                [
-                    {
-                        'path': f'{self.map_config.title}/independent_dimensions/index',
-                        'data': [
-                            i for i in range(
-                                map_indices.start, map_indices.stop
-                            )
-                        ],
-                        'idx': map_indices
-                    }
-                ]
-            )
             def get_detector_data(detector, index):
                 return scan.get_detector_data(detector.get_id(), index)[0][0]
         else:

From 4d689979fa7100fa37f4d0109d6f562b153b6cb0 Mon Sep 17 00:00:00 2001
From: Keara Soloway <kls286@cornell.edu>
Date: Mon, 6 Apr 2026 11:35:53 -0400
Subject: [PATCH 13/76] add: common.models.IndexSliceConfig

---
 CHAP/common/models/__init__.py |  1 +
 CHAP/common/models/common.py   | 19 +++++++++++++++++++
 2 files changed, 20 insertions(+)

diff --git a/CHAP/common/models/__init__.py b/CHAP/common/models/__init__.py
index d95277f7..062ef9ba 100755
--- a/CHAP/common/models/__init__.py
+++ b/CHAP/common/models/__init__.py
@@ -5,5 +5,6 @@
 from CHAP.common.models.common import (
     BinarizeConfig,
     ImageProcessorConfig,
+    IndexSliceConfig,
     UnstructuredToStructuredConfig,
 )
diff --git a/CHAP/common/models/common.py b/CHAP/common/models/common.py
index c24b9178..b2a9b486 100755
--- a/CHAP/common/models/common.py
+++ b/CHAP/common/models/common.py
@@ -129,6 +129,25 @@ def validate_vrange(cls, vrange):
                 for i in index_range]
 
 
+class IndexSliceConfig(CHAPBaseModel):
+    """Configuration for a python `sslice` object.
+
+    :ivar start: A `start` parameter for `slice()`, defaults to 0.
+    :vartype start: int, optional
+    :ivar stop: A `stop` parameter for `slice()`, defaults to -1.
+    :vartype stop: int, optional
+    :ivar step: A `step` parameter for `slice()`, defaults to 1.
+    :vartype step: int, optional
+    """
+    start: Optional[int] = 0
+    stop: Optional[int] = -1
+    step: Optional[int] = 1
+
+    @property
+    def _slice(self):
+        return slice(self.start, self.stop, self.step)
+
+
 class UnstructuredToStructuredConfig(CHAPBaseModel):
     """Configuration class to reshape data in an NXdata from an
     "unstructured" to a "structured" representation.

From 0ec1f60f935f6e0cf41c5ff6da5748ee7a03dc9d Mon Sep 17 00:00:00 2001
From: Keara Soloway <kls286@cornell.edu>
Date: Mon, 6 Apr 2026 11:44:32 -0400
Subject: [PATCH 14/76] add: NexusValuesWriter.idx_slice

---
 CHAP/common/writer.py | 29 +++++++++++++++++++++++------
 1 file changed, 23 insertions(+), 6 deletions(-)

diff --git a/CHAP/common/writer.py b/CHAP/common/writer.py
index d6c6f1e3..b2b6b714 100755
--- a/CHAP/common/writer.py
+++ b/CHAP/common/writer.py
@@ -25,6 +25,7 @@
 from CHAP import Writer
 from CHAP.pipeline import PipelineItem
 from CHAP.writer import validate_writer_model
+from CHAP.common.models import IndexSliceConfig
 
 
 def validate_model(model):
@@ -550,9 +551,16 @@ class NexusValuesWriter(Writer):
         data shape. If `False`, any mismatching shapes will just raise
         an error. Defaults to `False`.
     :vartype resize_axis: Union[int, Literal[False]], optional
+    :ivar idx_slice: Configuration for a slice object that will be
+        used to select the slice of the target array to write to. Used
+        only if the `"idx"` key is not present for an item in the
+        newest `PipelineData` item in `data`. Defaults to
+        `IndexSliceConfig()`.
+    :vartype idx_slice: CHAP.common.models.IndexSliceConfig, optional
     """
     path_prefix: str = ''
     resize_axis: Union[int, Literal[False]] = False
+    idx_slice: Optional[IndexSliceConfig] = IndexSliceConfig()
 
     def write(self, data, filename):
         """Write new values specified in `data` to the exising NeXus
@@ -576,12 +584,15 @@ def write(self, data, filename):
         data = self.get_pipelinedata_item(data, remove=self.remove)
         for d in data:
             with NXFile(filename, 'a') as nxroot:
-                self.nxs_writer(
-                    nxroot=nxroot,
-                    path=os.path.join(self.path_prefix, d['path']),
-                    idx=d['idx'],
-                    data=d['data']
-                )
+                try:
+                    self.nxs_writer(
+                        nxroot=nxroot,
+                        path=os.path.join(self.path_prefix, d['path']),
+                        idx=d.get('idx', self.idx_slice._slice),
+                        data=d['data']
+                    )
+                except Exception as exc:
+                    self.logger.error(exc)
 
     def nxs_writer(self, nxroot, path, idx, data):
         """Write data to a specific NeXus file.
@@ -613,9 +624,15 @@ def nxs_writer(self, nxroot, path, idx, data):
 
         # Access the specified dataset
         dataset = nxroot[path]
+        self.logger.debug(
+            f'chunks, maxshape = {dataset.chunks}, {dataset.maxshape}'
+        )
 
         # Check that the slice shape matches the data shape
         data = np.asarray(data)
+        self.logger.debug(
+            f'data shape, target shape = {data.shape}, {dataset[idx].shape}'
+        )
         if dataset[idx].shape != data.shape:
             if self.resize_axis is not False:
                 # Resize along the specified axis

From 8fd846bbb8bf0925478a9cfffd1d06cf911546e9 Mon Sep 17 00:00:00 2001
From: Keara Soloway <kls286@cornell.edu>
Date: Mon, 6 Apr 2026 11:48:28 -0400
Subject: [PATCH 15/76] add: MapProcessor.remove_constant_dims

---
 CHAP/common/processor.py | 14 ++++++++++----
 1 file changed, 10 insertions(+), 4 deletions(-)

diff --git a/CHAP/common/processor.py b/CHAP/common/processor.py
index 31f11a3c..70f924ad 100755
--- a/CHAP/common/processor.py
+++ b/CHAP/common/processor.py
@@ -891,15 +891,20 @@ class MapProcessor(Processor):
         instance of common.models.map.MapConfig. Any values in
         `'config'` supplant their corresponding values obtained from
         the pipeline data configuration.
-    :type config: Union[dict, common.models.map.MapConfig]
+    :vartype config: Union[dict, common.models.map.MapConfig]
     :ivar detector_config: Detector configurations of the detectors to
         include raw data for in the returned NeXus NXentry object
         (overruling detector info in the pipeline data, if present).
-    :type detector_config: Union[
+    :vartype detector_config: Union[
         dict, common.models.map.DetectorConfig]
     :ivar num_proc: Number of processors used to read map,
         defaults to `1`.
-    :type num_proc: int, optional
+    :vartype num_proc: int, optional
+    :ivar remove_constant_dims: Flag to indicate that any
+        `independent_dimension`s in the map whose values are constant
+        across the map should be exluded from the output
+        `NXentry`. Defaults to `True`.
+    :vartype remove_constant_dims: bool, optional
     """
     pipeline_fields: dict = Field(
         default = {
@@ -909,6 +914,7 @@ class MapProcessor(Processor):
     config: MapConfig
     detector_config: DetectorConfig = DetectorConfig(detectors=[])
     num_proc: Optional[conint(gt=0)] = 1
+    remove_constant_dims: Optional[bool] = True
 
     @field_validator('num_proc')
     @classmethod
@@ -1266,7 +1272,7 @@ def linkdims(nxgroup, nxdata_source):
         nxentry.independent_dimensions = NXdata()
         if len(constant_dim) < len(self.config.independent_dimensions):
             for i, dim in enumerate(self.config.independent_dimensions):
-                if i not in constant_dim:
+                if i not in constant_dim or not self.remove_constant_dims:
                     nxentry.independent_dimensions[dim.label] = NXfield(
                         independent_dimensions[i], dim.label,
                         attrs={'units': dim.units,

From 3205a4c6f6cadbed389ff108f10dd299a32e041f Mon Sep 17 00:00:00 2001
From: Keara Soloway <kls286@cornell.edu>
Date: Mon, 6 Apr 2026 11:58:00 -0400
Subject: [PATCH 16/76] fix: include independent_dimensions.index in results of
 MapSliceProcessor just in case all configured ind_dims were constant across
 the map and removed from the NXentry by MapProcessor

---
 CHAP/common/map_utils.py | 27 +++++++++++++++++++--------
 1 file changed, 19 insertions(+), 8 deletions(-)

diff --git a/CHAP/common/map_utils.py b/CHAP/common/map_utils.py
index 541c0d70..5515d358 100644
--- a/CHAP/common/map_utils.py
+++ b/CHAP/common/map_utils.py
@@ -118,17 +118,28 @@ def process(self, data,
 
         data_points = [
             {
-                'path': f'{self.map_config.title}/scalar_data/{s_d.label}',
-                'data': np.asarray([
-                    s_d.get_value(
-                        scans, self.scan_number, i,
-                        scalar_data=self.map_config.scalar_data)
-                    for i in scan_indices
-                ]),
+                'path': f'{self.map_config.title}/independent_dimensions/index',
+                'data': np.asarray(
+                    [i for i in range(index_offset, index_offset + npts_scan)]
+                ),
                 'idx': map_indices
             }
-            for s_d in self.map_config.all_scalar_data
         ]
+        data_points.extend(
+            [
+                {
+                    'path': f'{self.map_config.title}/scalar_data/{s_d.label}',
+                    'data': np.asarray([
+                        s_d.get_value(
+                            scans, self.scan_number, i,
+                            scalar_data=self.map_config.scalar_data)
+                        for i in scan_indices
+                    ]),
+                    'idx': map_indices
+                }
+                for s_d in self.map_config.all_scalar_data
+            ]
+        )
         data_points.extend(
             [
                 {

From 3791322b570f6a6b5a673a61ee1c9be13df85048 Mon Sep 17 00:00:00 2001
From: Keara Soloway <kls286@cornell.edu>
Date: Mon, 6 Apr 2026 12:25:12 -0400
Subject: [PATCH 17/76] fix: bug with MapProcessor.remove_constant_dims

---
 CHAP/common/processor.py | 89 +++++++++++++++++++++++-----------------
 1 file changed, 52 insertions(+), 37 deletions(-)

diff --git a/CHAP/common/processor.py b/CHAP/common/processor.py
index 70f924ad..b9693364 100755
--- a/CHAP/common/processor.py
+++ b/CHAP/common/processor.py
@@ -1263,31 +1263,45 @@ def linkdims(nxgroup, nxdata_source):
             **self.config.sample.model_dump())
 
         # Set up independent dimensions NeXus NXdata group
-        # (squeeze out constant dimensions)
-        constant_dim = []
-        for i, dim in enumerate(self.config.independent_dimensions):
-            unique = np.unique(independent_dimensions[i])
-            if unique.size == 1:
-                constant_dim.append(i)
         nxentry.independent_dimensions = NXdata()
-        if len(constant_dim) < len(self.config.independent_dimensions):
+        if self.remove_constant_dims:
+            # (squeeze out constant dimensions)
+            constant_dim = []
             for i, dim in enumerate(self.config.independent_dimensions):
-                if i not in constant_dim or not self.remove_constant_dims:
-                    nxentry.independent_dimensions[dim.label] = NXfield(
-                        independent_dimensions[i], dim.label,
-                        attrs={'units': dim.units,
-                               'long_name': f'{dim.label} ({dim.units})',
-                               'data_type': dim.data_type,
-                               'local_name': dim.name},
-                        maxshape=(None, *independent_dimensions[i].shape[1:]),
-                        chunks=(1, *independent_dimensions[i].shape[1:])
-                    )
+                unique = np.unique(independent_dimensions[i])
+                if unique.size == 1:
+                    constant_dim.append(i)
+            if len(constant_dim) < len(self.config.independent_dimensions):
+                for i, dim in enumerate(self.config.independent_dimensions):
+                    if i not in constant_dim or not self.remove_constant_dims:
+                        nxentry.independent_dimensions[dim.label] = NXfield(
+                            independent_dimensions[i], dim.label,
+                            attrs={'units': dim.units,
+                                   'long_name': f'{dim.label} ({dim.units})',
+                                   'data_type': dim.data_type,
+                                   'local_name': dim.name},
+                            maxshape=(None,
+                                      *independent_dimensions[i].shape[1:]),
+                            chunks=(1, *independent_dimensions[i].shape[1:])
+                        )
+            else:
+                nxentry.independent_dimensions.index = NXfield(
+                    np.arange(independent_dimensions[0].size), 'index',
+                    maxshape=(None,),
+                    chunks=(1,)
+                )
         else:
-            nxentry.independent_dimensions.index = NXfield(
-                np.arange(independent_dimensions[0].size), 'index',
-                maxshape=(None,),
-                chunks=(1,)
-            )
+            for i, dim in enumerate(self.config.independent_dimensions):
+                nxentry.independent_dimensions[dim.label] = NXfield(
+                    independent_dimensions[i], dim.label,
+                    attrs={'units': dim.units,
+                           'long_name': f'{dim.label} ({dim.units})',
+                           'data_type': dim.data_type,
+                           'local_name': dim.name},
+                    maxshape=(None,
+                              *independent_dimensions[i].shape[1:]),
+                    chunks=(1, *independent_dimensions[i].shape[1:])
+                )
 
         # Set up scalar data NeXus NXdata group
         # (add the constant independent dimensions)
@@ -1319,21 +1333,22 @@ def linkdims(nxgroup, nxdata_source):
                 maxshape=(None, *all_scalar_data[-1].shape[1:]),
                 chunks=(1, *all_scalar_data[-1].shape[1:])
             ))
-        for i, dim in enumerate(deepcopy(self.config.independent_dimensions)):
-            if i in constant_dim:
-                scalar_signals.append(dim.label)
-                scalar_data.append(NXfield(
-                    independent_dimensions[i], dim.label,
-                    attrs={'units': dim.units,
-                           'long_name': f'{dim.label} ({dim.units})',
-                           'data_type': dim.data_type,
-                           'local_name': dim.name},
-                    maxshape=(None, *independent_dimensions[i].shape[1:]),
-                    chunks=(1, *independent_dimensions[i].shape[1:])
-                ))
-                self.config.all_scalar_data.append(
-                    PointByPointScanData(**dim.model_dump()))
-                self.config.independent_dimensions.remove(dim)
+        if self.remove_constant_dims:
+            for i, dim in enumerate(deepcopy(self.config.independent_dimensions)):
+                if i in constant_dim:
+                    scalar_signals.append(dim.label)
+                    scalar_data.append(NXfield(
+                        independent_dimensions[i], dim.label,
+                        attrs={'units': dim.units,
+                               'long_name': f'{dim.label} ({dim.units})',
+                               'data_type': dim.data_type,
+                               'local_name': dim.name},
+                        maxshape=(None, *independent_dimensions[i].shape[1:]),
+                        chunks=(1, *independent_dimensions[i].shape[1:])
+                    ))
+                    self.config.all_scalar_data.append(
+                        PointByPointScanData(**dim.model_dump()))
+                    self.config.independent_dimensions.remove(dim)
         if scalar_signals:
             nxentry.scalar_data = NXdata()
             for k, v in zip(scalar_signals, scalar_data):

From 6ad40220755281ed6dd34e708bd2db7b152ea9c2 Mon Sep 17 00:00:00 2001
From: Keara Soloway <kls286@cornell.edu>
Date: Mon, 6 Apr 2026 13:09:11 -0400
Subject: [PATCH 18/76] add: link to all scalar_data fields from main
 <map_nxentry>.data NXdata group

---
 CHAP/common/processor.py | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/CHAP/common/processor.py b/CHAP/common/processor.py
index b9693364..29792425 100755
--- a/CHAP/common/processor.py
+++ b/CHAP/common/processor.py
@@ -1257,6 +1257,7 @@ def linkdims(nxgroup, nxdata_source):
                 NXfield(value=scans.scan_numbers,
                         dtype='int8',
                         attrs={'spec_file': str(scans.spec_file)})
+        nxentry.data = NXdata()
 
         # Add sample metadata
         nxentry[self.config.sample.name] = NXsample(
@@ -1353,6 +1354,7 @@ def linkdims(nxgroup, nxdata_source):
             nxentry.scalar_data = NXdata()
             for k, v in zip(scalar_signals, scalar_data):
                 nxentry.scalar_data[k] = v
+                nxentry.data.makelink(nxentry.scalar_data[k])
             if 'SCAN_N' in scalar_signals:
                 nxentry.scalar_data.attrs['signal'] = 'SCAN_N'
             else:
@@ -1361,8 +1363,7 @@ def linkdims(nxgroup, nxdata_source):
             nxentry.scalar_data.attrs['auxiliary_signals'] = scalar_signals
 
         # Add detector data
-        nxdata = NXdata()
-        nxentry.data = nxdata
+        nxdata = nxentry.data
         nxentry.data.set_default()
         detector_ids = []
         for k, v in self.config.attrs.items():

From 59979381cae2d4555bf4c9d7b60a3e00b9795bed Mon Sep 17 00:00:00 2001
From: Keara Soloway <kls286@cornell.edu>
Date: Mon, 6 Apr 2026 13:46:19 -0400
Subject: [PATCH 19/76] fix: add data type check/conversion to
 NexusValuesWriter

---
 CHAP/common/writer.py | 10 +++++++++-
 1 file changed, 9 insertions(+), 1 deletion(-)

diff --git a/CHAP/common/writer.py b/CHAP/common/writer.py
index b2b6b714..b426d60e 100755
--- a/CHAP/common/writer.py
+++ b/CHAP/common/writer.py
@@ -628,8 +628,16 @@ def nxs_writer(self, nxroot, path, idx, data):
             f'chunks, maxshape = {dataset.chunks}, {dataset.maxshape}'
         )
 
-        # Check that the slice shape matches the data shape
         data = np.asarray(data)
+
+        # Check the datatype
+        if data.dtype != dataset.dtype:
+            self.logger.warning(
+                f'Converting new data (type: {data.dtype}) to {dataset.dtype}'
+            )
+            data = data.astype(dataset.dtype)
+
+        # Check the shape
         self.logger.debug(
             f'data shape, target shape = {data.shape}, {dataset[idx].shape}'
         )

From 06ce58fcf0708d651447f447f8f15481cd6cd52e Mon Sep 17 00:00:00 2001
From: Keara Soloway <kls286@cornell.edu>
Date: Mon, 6 Apr 2026 14:00:14 -0400
Subject: [PATCH 20/76] fix: peak_fit_info in StrainAnalysisProcessor when
 setup is True

---
 CHAP/edd/processor.py | 16 +++++++++++++---
 1 file changed, 13 insertions(+), 3 deletions(-)

diff --git a/CHAP/edd/processor.py b/CHAP/edd/processor.py
index 7ea2d660..c1bb5534 100755
--- a/CHAP/edd/processor.py
+++ b/CHAP/edd/processor.py
@@ -2814,8 +2814,12 @@ def _add_fit_nxcollection(self, nxdetector, fit_type, hkls, peak_fit_info):
         nxdata.best_fit = NXfield(shape=shape, dtype=np.float64)
         nxdata.included_peaks = NXfield(
             shape=[shape[0], len(hkls)], dtype=bool)
-        nxdata.included_peaks.attrs['hkls'] = dumps(peak_fit_info['hkls'])
-        nxdata.included_peaks.attrs['use_peaks'] = peak_fit_info['use_peaks']
+        nxdata.included_peaks.attrs['hkls'] = dumps(
+            peak_fit_info.get('hkls', '')
+        )
+        nxdata.included_peaks.attrs['use_peaks'] = peak_fit_info.get(
+            'use_peaks'
+        )
         nxdata.residual = NXfield(shape=shape, dtype=np.float64)
         nxdata.redchi = NXfield(shape=[shape[0]], dtype=np.float64)
         nxdata.success = NXfield(shape=[shape[0]], dtype='bool')
@@ -2862,7 +2866,7 @@ def _add_fit_nxcollection(self, nxdetector, fit_type, hkls, peak_fit_info):
             nxcollection[hkl_name].sigmas.errors = NXfield(
                 shape=[shape[0]], dtype=np.float64)
             nxcollection[hkl_name].sigmas.attrs['signal'] = 'values'
-            if peak_fit_info['peak_models'] == 'pvoigt':
+            if peak_fit_info.get('peak_models') == 'pvoigt':
                 # Report HKL peak fractions
                 nxcollection[hkl_name].fractions = NXdata()
                 self._linkdims(
@@ -3020,6 +3024,12 @@ def _get_nxroot(self, nxentry, calibration_config):
         nxprocess.strain_analysis_config = \
             self.config.model_dump_json()
 
+        if len(self._peak_fit_info) == 0:
+            # FIX this is a temporary fix to be able to run update
+            # after setup.
+            self._peak_fit_info = [{}] * len(self.detector_config.detectors)
+            self.logger.warning('Missing peak_fit_info')
+
         # Loop over the detectors to fill in the nxprocess
         for energies, mask, nxdata, detector, peak_fit_info in zip(
                 self._energies, self._masks, self._nxdata_detectors,

From 3cbcb31022d082600e568a450dd3841a3fb37983 Mon Sep 17 00:00:00 2001
From: Keara Soloway <kls286@cornell.edu>
Date: Mon, 6 Apr 2026 14:12:04 -0400
Subject: [PATCH 21/76] add: make all NXfields resizable in
 StrainAnalysisProcessor results

---
 CHAP/edd/processor.py | 109 +++++++++++++++++++++++++++++++-----------
 1 file changed, 82 insertions(+), 27 deletions(-)

diff --git a/CHAP/edd/processor.py b/CHAP/edd/processor.py
index c1bb5534..9d7f8e60 100755
--- a/CHAP/edd/processor.py
+++ b/CHAP/edd/processor.py
@@ -2811,18 +2811,32 @@ def _add_fit_nxcollection(self, nxdetector, fit_type, hkls, peak_fit_info):
         nxcollection.results = NXdata()
         nxdata = nxcollection.results
         self._linkdims(nxdata, det_nxdata)
-        nxdata.best_fit = NXfield(shape=shape, dtype=np.float64)
+        nxdata.best_fit = NXfield(
+            shape=shape, dtype=np.float64,
+            maxshape=(None, *shape[1:]), chunks=(1, *shape[1:])
+        )
         nxdata.included_peaks = NXfield(
-            shape=[shape[0], len(hkls)], dtype=bool)
+            shape=[shape[0], len(hkls)], dtype=bool,
+            maxshape=(None, *shape[1:]), chunks=(1, *shape[1:])
+        )
         nxdata.included_peaks.attrs['hkls'] = dumps(
             peak_fit_info.get('hkls', '')
         )
         nxdata.included_peaks.attrs['use_peaks'] = peak_fit_info.get(
             'use_peaks'
         )
-        nxdata.residual = NXfield(shape=shape, dtype=np.float64)
-        nxdata.redchi = NXfield(shape=[shape[0]], dtype=np.float64)
-        nxdata.success = NXfield(shape=[shape[0]], dtype='bool')
+        nxdata.residual = NXfield(
+            shape=shape, dtype=np.float64,
+            maxshape=(None, *shape[1:]), chunks=(1, *shape[1:])
+        )
+        nxdata.redchi = NXfield(
+            shape=[shape[0]], dtype=np.float64,
+            maxshape=(None,), chunks=(1,)
+        )
+        nxdata.success = NXfield(
+            shape=[shape[0]], dtype='bool',
+            maxshape=(None,), chunks=(1,)
+        )
 
         # Peak-by-peak results
         for hkl in hkls:
@@ -2842,9 +2856,13 @@ def _add_fit_nxcollection(self, nxdetector, fit_type, hkls, peak_fit_info):
                 nxcollection[hkl_name].amplitudes, det_nxdata,
                 skip_field_dims=['energy'])
             nxcollection[hkl_name].amplitudes.values = NXfield(
-                shape=[shape[0]], dtype=np.float64, attrs={'units': 'counts'})
+                shape=[shape[0]], dtype=np.float64, attrs={'units': 'counts'},
+                maxshape=(None,), chunks=(1,)
+            )
             nxcollection[hkl_name].amplitudes.errors = NXfield(
-                shape=[shape[0]], dtype=np.float64)
+                shape=[shape[0]], dtype=np.float64,
+                maxshape=(None,), chunks=(1,)
+            )
             nxcollection[hkl_name].amplitudes.attrs['signal'] = 'values'
             # Report HKL peak centers
             nxcollection[hkl_name].centers = NXdata()
@@ -2852,9 +2870,13 @@ def _add_fit_nxcollection(self, nxdetector, fit_type, hkls, peak_fit_info):
                 nxcollection[hkl_name].centers, det_nxdata,
                 skip_field_dims=['energy'])
             nxcollection[hkl_name].centers.values = NXfield(
-                shape=[shape[0]], dtype=np.float64, attrs={'units': 'keV'})
+                shape=[shape[0]], dtype=np.float64, attrs={'units': 'keV'},
+                maxshape=(None,), chunks=(1,)
+            )
             nxcollection[hkl_name].centers.errors = NXfield(
-                shape=[shape[0]], dtype=np.float64)
+                shape=[shape[0]], dtype=np.float64,
+                maxshape=(None,), chunks=(1,)
+            )
             nxcollection[hkl_name].centers.attrs['signal'] = 'values'
             # Report HKL peak FWHMs
             nxcollection[hkl_name].sigmas = NXdata()
@@ -2862,9 +2884,13 @@ def _add_fit_nxcollection(self, nxdetector, fit_type, hkls, peak_fit_info):
                 nxcollection[hkl_name].sigmas, det_nxdata,
                 skip_field_dims=['energy'])
             nxcollection[hkl_name].sigmas.values = NXfield(
-                shape=[shape[0]], dtype=np.float64, attrs={'units': 'keV'})
+                shape=[shape[0]], dtype=np.float64, attrs={'units': 'keV'},
+                maxshape=(None,), chunks=(1,)
+            )
             nxcollection[hkl_name].sigmas.errors = NXfield(
-                shape=[shape[0]], dtype=np.float64)
+                shape=[shape[0]], dtype=np.float64,
+                maxshape=(None,), chunks=(1,)
+            )
             nxcollection[hkl_name].sigmas.attrs['signal'] = 'values'
             if peak_fit_info.get('peak_models') == 'pvoigt':
                 # Report HKL peak fractions
@@ -2873,9 +2899,13 @@ def _add_fit_nxcollection(self, nxdetector, fit_type, hkls, peak_fit_info):
                     nxcollection[hkl_name].fractions, det_nxdata,
                     skip_field_dims=['energy'])
                 nxcollection[hkl_name].fractions.values = NXfield(
-                    shape=[shape[0]], dtype=np.float64)
+                    shape=[shape[0]], dtype=np.float64,
+                    maxshape=(None,), chunks=(1,)
+                )
                 nxcollection[hkl_name].fractions.errors = NXfield(
-                    shape=[shape[0]], dtype=np.float64)
+                    shape=[shape[0]], dtype=np.float64,
+                    maxshape=(None,), chunks=(1,)
+                )
                 nxcollection[hkl_name].fractions.attrs['signal'] = 'values'
             # Report HKL peak strains (unconstrained only)
             if fit_type == 'unconstrained':
@@ -2885,11 +2915,17 @@ def _add_fit_nxcollection(self, nxdetector, fit_type, hkls, peak_fit_info):
                     skip_field_dims=['energy'])
                 values = np.full(shape=[shape[0]], fill_value=np.nan)
                 nxcollection[hkl_name].strains.values = NXfield(
-                    value=values, shape=[shape[0]], dtype=np.float64)
+                    value=values, shape=[shape[0]], dtype=np.float64,
+                    maxshape=(None,), chunks=(1,)
+                )
                 nxcollection[hkl_name].strains.errors = NXfield(
-                    value=values, shape=[shape[0]], dtype=np.float64)
+                    value=values, shape=[shape[0]], dtype=np.float64,
+                    maxshape=(None,), chunks=(1,)
+                )
                 nxcollection[hkl_name].strains.residuals = NXfield(
-                    value=values, shape=[shape[0]], dtype=np.float64)
+                    value=values, shape=[shape[0]], dtype=np.float64,
+                    maxshape=(None,), chunks=(1,)
+                )
                 nxcollection[hkl_name].strains.attrs['signal'] = 'values'
 
 
@@ -3061,35 +3097,54 @@ def _get_nxroot(self, nxentry, calibration_config):
                 value=energies[mask], attrs={'units': 'keV'})
             det_nxdata.norm = NXfield(
                 dtype=np.float64,
-                shape=(num_points,))
+                shape=(num_points,),
+                maxshape=(None,), chunks=(1,)
+            )
             det_nxdata.tth = NXfield(
                 dtype=np.float64,
                 shape=(num_points,),
-                attrs={'units':'degrees', 'long_name': '2\u03B8 (degrees)'})
+                attrs={'units':'degrees', 'long_name': '2\u03B8 (degrees)'},
+                maxshape=(None,), chunks=(1,),
+            )
             det_nxdata.uniform_strain = NXfield(
                 dtype=np.float64,
                 shape=(num_points,),
-                attrs={'long_name': 'Strain from uniform fit (\u03B5)'})
-                #attrs={'long_name': 'Strain from uniform fit (\u03BC\u03B5)'})
+                attrs={'long_name': 'Strain from uniform fit (\u03B5)'},
+                # attrs={'long_name': 'Strain from uniform fit (\u03BC\u03B5)'}
+                maxshape=(None,), chunks=(1,)
+            )
+
             det_nxdata.unconstrained_strain = NXfield(
                 dtype=np.float64,
                 shape=(num_points,),
                 attrs={'long_name':
-                           'Strain from unconstrained fit (\u03B5)'})
-                           #'Strain from unconstrained fit (\u03BC\u03B5)'})
+                           'Strain from unconstrained fit (\u03B5)'},
+                           #'Strain from unconstrained fit (\u03BC\u03B5)'},
+                maxshape=(None,), chunks=(1,)
+            )
             det_nxdata.unconstrained_strain_stdev = NXfield(
                 dtype=np.float64,
                 shape=(num_points,),
                 attrs={'long_name':
                            'Standard deviation in strain from unconstrained '
-                           'fit (\u03B5)'})
-                           #'fit (\u03BC\u03B5)'})
+                           'fit (\u03B5)'},
+                           #'fit (\u03BC\u03B5)'}
+                maxshape=(None,), chunks=(1,)
+            )
 
             # Add the detector data
+            _intensity=np.asarray(
+                [
+                    data[i].astype(np.float64)[mask]
+                    for i in range(num_points)
+                ]
+            )
             det_nxdata.intensity = NXfield(
-                value=np.asarray([data[i].astype(np.float64)[mask]
-                                  for i in range(num_points)]),
-                attrs={'units': 'counts'})
+                value=_intensity,
+                attrs={'units': 'counts'},
+                maxshape=(None,*_intensity.shape[1:]),
+                chunks=(1,*_intensity.shape[1:])
+            )
             det_nxdata.attrs['signal'] = 'intensity'
 
             # Get the unique HKLs and lattice spacings for the strain

From f13a81b6be493e4054510057b941254fc7d2dfd5 Mon Sep 17 00:00:00 2001
From: Keara Soloway <kls286@cornell.edu>
Date: Fri, 10 Apr 2026 12:17:38 -0400
Subject: [PATCH 22/76] temporary: add OrnlStrainAnalysisProcessor

---
 CHAP/edd/processor.py | 439 ++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 439 insertions(+)

diff --git a/CHAP/edd/processor.py b/CHAP/edd/processor.py
index 9d7f8e60..cad34d02 100755
--- a/CHAP/edd/processor.py
+++ b/CHAP/edd/processor.py
@@ -3523,6 +3523,445 @@ def _strain_analysis(self):
 
         return points
 
+class OrnlStrainAnalysisProcessor(StrainAnalysisProcessor):
+    """Processor that handles strain analysis in the middle of
+    autonomously driven experients."""
+
+    def process(self, data):
+        """Setup the strain analysis and/or return the strain analysis
+        results as a list of updated points or a
+        `nexusformat.nexus.NXroot` object.
+
+        :param data: Input data containing configurations for a map,
+            completed energy/tth calibration, and (optionally)
+            parameters for the strain analysis.
+        :type data: list[PipelineData]
+        :raises RuntimeError: Unable to get a valid strain analysis
+            configuration.
+        :return: The strain analysis setup or results, a list of
+            byte stream representions of Matplotlib figures and an
+            animation of the fit results.
+        :rtype: Union[list[dict[str, object]],
+            nexusformat.nexus.NXroot], PipelineData, PipelineData
+        """
+        # Third party modules
+        from nexusformat.nexus import (
+            NXentry,
+            NXroot,
+        )
+
+        # Local modules
+        from CHAP.utils.general import list_to_string
+
+        if not (self.setup or self.update):
+            raise RuntimeError('Illegal combination of setup and update')
+        if not self.update:
+            if self.interactive:
+                self.logger.warning('Interactive option disabled during setup')
+                self.interactive = False
+            if self.save_figures:
+                self.logger.warning(
+                    'Saving figures option disabled during setup')
+                self.save_figures = False
+        self._animation = []
+
+        # Load the pipeline input data
+        try:
+            nxobject = self.get_data(data)
+            if isinstance(nxobject, NXroot):
+                nxroot = nxobject
+            elif isinstance(nxobject, NXentry):
+                nxroot = NXroot()
+                nxroot[nxobject.nxname] = nxobject
+                nxobject.set_default()
+            else:
+                raise RuntimeError
+        except Exception as exc:
+            raise RuntimeError(
+                'No valid input in the pipeline data') from exc
+
+        # Load the detector data
+        # FIX set rel_height_cutoff
+        nxentry = self.get_default_nxentry(nxroot)
+        for k, v in nxentry.scalar_data.items():
+            self.logger.debug(f'{k}.chunks = {v.chunks}')
+            self.logger.debug(f'{k}.maxshape = {v.maxshape}')
+
+        nxdata = nxentry[nxentry.default]
+
+        # Load the validated calibration configuration
+        # FIX make this a class field and add to pipeline_fields too?
+        #     NB: be sure that adding this field does not mess up
+        #     self.detector_config during pydantic validation
+        calibration_config = self.get_config(
+            data, schema='edd.models.MCATthCalibrationConfig', remove=False)
+
+        # Load the validated calibration detector configurations
+        calibration_detector_config = self.get_data(
+            data, schema='edd.models.MCATthCalibrationConfig')
+        calibration_detectors = [
+            MCADetectorCalibration(**d)
+            for d in calibration_detector_config.get('detectors', [])]
+        calibration_detector_ids = [d.get_id() for d in calibration_detectors]
+
+        # Check for available raw detector data and for the available
+        # calibration data
+        if not self.detector_config.detectors:
+            self.detector_config.detectors = [
+                MCADetectorStrainAnalysis(
+                    id=id_, processor_type='strainanalysis')
+                for id_ in nxentry.detector_ids]
+            self.detector_config.update_detectors()
+        skipped_detectors = []
+        sskipped_detectors = []
+        detectors = []
+        for detector in self.detector_config.detectors:
+            detector_id = detector.get_id()
+            if detector_id not in nxdata:
+                skipped_detectors.append(detector_id)
+            elif detector_id not in calibration_detector_ids:
+                sskipped_detectors.append(detector_id)
+            else:
+                raw_detector_data = nxdata[detector_id].nxdata
+                if raw_detector_data.ndim != 2:
+                    self.logger.warning(
+                        f'Skipping detector {detector_id} (Illegal data shape '
+                        f'{raw_detector_data.shape})')
+                elif raw_detector_data.sum():
+                    for k, v in nxdata[detector_id].attrs.items():
+                        detector.attrs[k] = v.nxdata
+                    if self.config.rel_height_cutoff is not None:
+                        detector.rel_height_cutoff = \
+                            self.config.rel_height_cutoff
+                    detector.add_calibration(
+                        calibration_detectors[
+                            int(calibration_detector_ids.index(detector_id))])
+                    detectors.append(detector)
+                else:
+                    self.logger.warning(
+                        f'Skipping detector {detector_id} (zero intensity)')
+        if len(skipped_detectors) == 1:
+            self.logger.warning(
+                f'Skipping detector {skipped_detectors[0]} '
+                '(no raw data)')
+        elif skipped_detectors:
+            skipped_detectors = [int(d) for d in skipped_detectors]
+            self.logger.warning(
+                'Skipping detectors '
+                f'{list_to_string(skipped_detectors)} (no raw data)')
+        if len(sskipped_detectors) == 1:
+            self.logger.warning(
+                f'Skipping detector {sskipped_detectors[0]} '
+                '(no raw data)')
+        elif sskipped_detectors:
+            skipped_detectors = [int(d) for d in sskipped_detectors]
+            self.logger.warning(
+                'Skipping detectors '
+                f'{list_to_string(skipped_detectors)} (no calibration data)')
+        self.detector_config.detectors = detectors
+        if not self.detector_config.detectors:
+            raise ValueError('No valid data or unable to match an available '
+                             'calibrated detector for the strain analysis')
+
+        # Load the raw MCA data and compute the detector bin energies
+        # and the mean spectra
+        self._setup_detector_data(
+            nxentry[nxentry.default],
+            strain_analysis_config=self.config, update=self.update)
+
+        # Apply the energy mask
+        self._apply_energy_mask()
+
+        # Get the mask and HKLs used in the strain analysis
+        self._get_mask_hkls()
+
+        # Apply the combined energy ranges mask
+        self._apply_combined_mask()
+
+        # Setup and/or run the strain analysis
+        points = []
+        if self.update:
+            points = self._strain_analysis()
+            values = self._get_values(nxroot, points)
+        if self.setup:
+            nxprocess = self._get_nxprocess(nxentry, calibration_config)
+            if points:
+                self.logger.info(f'Adding {len(points)} points')
+                self.add_points(nxprocess, points, logger=self.logger)
+                self.logger.info(f'... done')
+            else:
+                self.logger.warning('Skip adding points')
+            if not (self._figures or self._animation):
+                return nxprocess
+            ret = [nxprocess]
+        else:
+            if not (self._figures or self._animation):
+                return values
+            ret = [values]
+        if self._figures:
+            ret.append(
+                PipelineData(
+                    name=self.__name__, data=self._figures,
+                    schema='common.write.ImageWriter'))
+        if self._animation:
+            ret.append(
+                PipelineData(
+                    name=self.__name__, data=self._animation,
+                    schema='common.write.ImageWriter'))
+        return tuple(ret)
+
+    def _get_nxprocess(self, nxentry, calibration_config):
+        """Return a standalone NXprocess for the strain analysis
+        results & metadata.
+
+        :param nxentry: Strain analysis map, including the raw
+            MCA data.
+        :type nxentry: nexusformat.nexus.NXentry
+        :param calibration_config: 2&theta calibration configuration.
+        :type calibration_config:
+            CHAP.edd.models.MCATthCalibrationConfig
+        :return: Strain analysis results & associated metadata.
+        :rtype: nexusformat.nexus.NXprocess
+        """
+        # Third party modules
+        # pylint: disable=no-name-in-module
+        from nexusformat.nexus import (
+            NXdetector,
+            NXfield,
+            NXprocess,
+            NXroot,
+        )
+        # pylint: enable=no-name-in-module
+
+        # Third party modules
+        from json import dumps
+
+        # Local modules
+        from CHAP.edd.utils import get_unique_hkls_ds
+        from CHAP.utils.general import nxcopy
+
+        if not self.interactive and not self.config.materials:
+            raise ValueError(
+                'No material provided. Provide a material in the '
+                'StrainAnalysis Configuration, or re-run the pipeline with '
+                'the --interactive flag.')
+
+        nxprocess = NXprocess()
+        nxprocess.calibration_config = \
+            calibration_config.model_dump_json()
+        nxprocess.strain_analysis_config = \
+            self.config.model_dump_json()
+
+        if len(self._peak_fit_info) == 0:
+            # FIX this is a temporary fix to be able to run update
+            # after setup.
+            self._peak_fit_info = [{}] * len(self.detector_config.detectors)
+            self.logger.warning('Missing peak_fit_info')
+
+        # Loop over the detectors to fill in the nxprocess
+        for energies, mask, nxdata, detector, peak_fit_info in zip(
+                self._energies, self._masks, self._nxdata_detectors,
+                self.detector_config.detectors, self._peak_fit_info):
+
+            # Get the current data object
+            data = nxdata.nxsignal
+            num_points = data.shape[0]
+
+            # Setup the NXdetector object for the current detector
+            self.logger.debug(
+                f'Setting up NXdetector group for {detector.get_id()}')
+            nxdetector = NXdetector()
+            nxprocess[detector.get_id()] = nxdetector
+            nxdetector.local_name = detector.get_id()
+            nxdetector.detector_config = detector.model_dump_json()
+            nxdetector.peak_fit_info = dumps(peak_fit_info)
+            nxdetector.data = nxcopy(nxdata, exclude_nxpaths='detector_data')
+            det_nxdata = nxdetector.data
+            if 'axes' in det_nxdata.attrs:
+                if isinstance(det_nxdata.attrs['axes'], str):
+                    det_nxdata.attrs['axes'] = [
+                        det_nxdata.attrs['axes'], 'energy']
+                else:
+                    det_nxdata.attrs['axes'].append('energy')
+            else:
+                det_nxdata.attrs['axes'] = ['energy']
+            det_nxdata.energy = NXfield(
+                value=energies[mask], attrs={'units': 'keV'})
+            det_nxdata.norm = NXfield(
+                dtype=np.float64,
+                shape=(num_points,),
+                maxshape=(None,), chunks=(1,)
+            )
+            det_nxdata.tth = NXfield(
+                dtype=np.float64,
+                shape=(num_points,),
+                attrs={'units':'degrees', 'long_name': '2\u03B8 (degrees)'},
+                maxshape=(None,), chunks=(1,),
+            )
+            det_nxdata.uniform_strain = NXfield(
+                dtype=np.float64,
+                shape=(num_points,),
+                attrs={'long_name': 'Strain from uniform fit (\u03B5)'},
+                # attrs={'long_name': 'Strain from uniform fit (\u03BC\u03B5)'}
+                maxshape=(None,), chunks=(1,)
+            )
+
+            det_nxdata.unconstrained_strain = NXfield(
+                dtype=np.float64,
+                shape=(num_points,),
+                attrs={'long_name':
+                           'Strain from unconstrained fit (\u03B5)'},
+                           #'Strain from unconstrained fit (\u03BC\u03B5)'},
+                maxshape=(None,), chunks=(1,)
+            )
+            det_nxdata.unconstrained_strain_stdev = NXfield(
+                dtype=np.float64,
+                shape=(num_points,),
+                attrs={'long_name':
+                           'Standard deviation in strain from unconstrained '
+                           'fit (\u03B5)'},
+                           #'fit (\u03BC\u03B5)'}
+                maxshape=(None,), chunks=(1,)
+            )
+
+            # Add the detector data
+            _intensity=np.asarray(
+                [
+                    data[i].astype(np.float64)[mask]
+                    for i in range(num_points)
+                ]
+            )
+            det_nxdata.intensity = NXfield(
+                value=_intensity,
+                attrs={'units': 'counts'},
+                maxshape=(None,*_intensity.shape[1:]),
+                chunks=(1,*_intensity.shape[1:])
+            )
+            det_nxdata.attrs['signal'] = 'intensity'
+
+            # Get the unique HKLs and lattice spacings for the strain
+            # analysis materials
+            hkls, _ = get_unique_hkls_ds(
+                self.config.materials, tth_max=detector.tth_max,
+                tth_tol=detector.tth_tol)
+
+            # Get the HKLs and lattice spacings that will be used for
+            # fitting
+            hkls_fit = np.asarray([hkls[i] for i in detector.hkl_indices])
+
+            # Add the uniform fit nxcollection
+            self._add_fit_nxcollection(
+                nxdetector, 'uniform', hkls_fit, peak_fit_info)
+
+            # Add the unconstrained fit nxcollection
+            self._add_fit_nxcollection(
+                nxdetector, 'unconstrained', hkls_fit, peak_fit_info)
+
+            # Add the strain fields
+            tth_map = detector.get_tth_map((num_points,))
+            det_nxdata.tth.nxdata = tth_map
+
+        return nxprocess
+
+    def _linkdims(
+            self, nxgroup, nxdata_source, add_field_dims=None,
+            skip_field_dims=None, oversampling_axis=None):
+        """Link the dimensions for a 'nexusformat.nexus.NXgroup`
+        object.
+        """
+        # Third party modules
+        from nexusformat.nexus import NXfield, NXroot
+        from nexusformat.nexus.tree import NXlinkfield
+
+        if not isinstance(nxgroup.nxroot, NXroot):
+            self.logger.warning(
+                'Skipping linkdims -- type(nxgroup.nxroot) = '
+                + f'{type(nxgroup.nxroot)}'
+            )
+            return
+        super()._linkdims(
+            nxgroup, nxdata_source, add_field_dims=add_field_dims,
+            skip_field_dims=skip_field_dims, oversampling_axis=skip_field_dims
+        )
+
+    def _get_values(self, nxroot, points):
+        """Return list of dictionaries with new srtain results values
+        suitable for writing with `common.NexusValuesWriter`.
+
+        :param nxroot:
+        :type nxroot:
+        :param points:
+        :type points:
+        :returns:
+        :rtype:
+        """
+        # pylint: disable=no-name-in-module
+        from nexusformat.nexus import (
+            NXdetector,
+            NXprocess
+        )
+        # pylint: enable=no-name-in-module
+
+        nxprocess = None
+        for nxobject in nxroot.values():
+            if isinstance(nxobject, NXprocess):
+                nxprocess = nxobject
+                break
+        if nxprocess is None:
+            raise RuntimeError('Unable to find the strainanalysis object')
+
+        nxdata_detectors = []
+        for nxobject in nxprocess.values():
+            if isinstance(nxobject, NXdetector):
+                nxdata_detectors.append(nxobject.data)
+        if not nxdata_detectors:
+            raise RuntimeError(
+                'Unable to find detector data in strainanalysis object')
+        axes = get_axes(nxdata_detectors[0], skip_axes=['energy'])
+
+        values = []
+        if axes:
+            coords = np.asarray(
+                [nxdata_detectors[0][a].nxdata for a in axes]).T
+
+            def get_matching_indices(all_coords, point_coords, decimals=None):
+                if isinstance(decimals, int):
+                    all_coords = np.round(all_coords, decimals=decimals)
+                    point_coords = np.round(point_coords, decimals=decimals)
+                coords_match = np.all(all_coords == point_coords, axis=1)
+                index = np.where(coords_match)[0]
+                return index
+
+            # FIX: can we round to 3 decimals right away in general?
+            # FIX: assumes points contains a sorted and continous
+            # slice of updates
+            i_0 = get_matching_indices(
+                coords,
+                np.asarray([points[0][a] for a in axes]), decimals=3)[0]
+            i_f = get_matching_indices(
+                coords,
+                np.asarray([points[-1][a] for a in axes]), decimals=3)[0]
+            slices = {k: np.asarray([p[k] for p in points]) for k in points[0]}
+            for k, v in slices.items():
+                values.append(
+                    {
+                        'data': v,
+                        'path': k,
+                    }
+                )
+        else:
+            values.extend(
+                [
+                    {
+                        'data': v,
+                        'path': k,
+                    }
+                    for k, v in points[0].items()
+                ]
+            )
+
+        return values
+
 
 if __name__ == '__main__':
     # Local modules

From 00f8b587c78b0b185564363696ca0153f1d17593 Mon Sep 17 00:00:00 2001
From: Keara Soloway <kls286@cornell.edu>
Date: Fri, 10 Apr 2026 14:54:37 -0400
Subject: [PATCH 23/76] optimize: NexusValuesWriter loop order

---
 CHAP/common/writer.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/CHAP/common/writer.py b/CHAP/common/writer.py
index b426d60e..aad605c1 100755
--- a/CHAP/common/writer.py
+++ b/CHAP/common/writer.py
@@ -582,8 +582,8 @@ def write(self, data, filename):
         from nexusformat.nexus import NXFile
 
         data = self.get_pipelinedata_item(data, remove=self.remove)
-        for d in data:
-            with NXFile(filename, 'a') as nxroot:
+        with NXFile(filename, 'a') as nxroot:
+            for d in data:
                 try:
                     self.nxs_writer(
                         nxroot=nxroot,

From a2ad853a2f20e94fc4dee60235cb81d8681f0b14 Mon Sep 17 00:00:00 2001
From: Keara Soloway <kls286@cornell.edu>
Date: Tue, 21 Apr 2026 11:08:57 -0400
Subject: [PATCH 24/76] add: StrainAnalysisProcessor.standalone

---
 CHAP/edd/processor.py | 797 ++++++++++++------------------------------
 1 file changed, 216 insertions(+), 581 deletions(-)

diff --git a/CHAP/edd/processor.py b/CHAP/edd/processor.py
index cad34d02..230d0a25 100755
--- a/CHAP/edd/processor.py
+++ b/CHAP/edd/processor.py
@@ -5,7 +5,6 @@
 Author     : Keara Soloway, Rolf Verberg
 Description: Module for Processors used only by EDD experiments
 """
-
 # System modules
 from copy import deepcopy
 import os
@@ -2514,6 +2513,16 @@ class StrainAnalysisProcessor(BaseStrainProcessor):
         results as a list of updated points or update the result
         from the `setup` stage, defaults to `True`.
     :type update: bool, optional
+    :ivar standalone: Return results in standalone format suitable
+        for autonomous/streaming experiments, defaults to `False`.
+        When `True`, setup returns a standalone
+        `nexusformat.nexus.NXprocess` (not wrapped in an
+        `nexusformat.nexus.NXroot`), and update returns a list of
+        ``{'data': array, 'path': str}`` dicts suitable for writing
+        with ``common.NexusValuesWriter``. When both `setup` and
+        `update` are `True` the standalone `NXprocess` and the
+        values list are returned together as a tuple.
+    :type standalone: bool, optional
     """
     pipeline_fields: dict = Field(
         default = {
@@ -2527,6 +2536,7 @@ class StrainAnalysisProcessor(BaseStrainProcessor):
     detector_config: MCADetectorConfig
     setup: Optional[bool] = True
     update: Optional[bool] = True
+    standalone: Optional[bool] = False
 
     @model_validator(mode='before')
     @classmethod
@@ -2755,24 +2765,36 @@ def process(self, data):
         self._apply_combined_mask()
 
         # Setup and/or run the strain analysis
-        points = []
+        results = {}
         if self.update:
-            points = self._strain_analysis()
+            results = self._strain_analysis()
         if self.setup:
-            nxroot = self._get_nxroot(nxentry, calibration_config)
-            if points:
-                self.logger.info(f'Adding {len(points)} points')
-                self.add_points(nxroot, points, logger=self.logger)
-                self.logger.info(f'... done')
+            if self.standalone:
+                nxsetup = self._get_nxprocess(nxentry, calibration_config)
             else:
-                self.logger.warning('Skip adding points')
-            if not (self._figures or self._animation):
-                return nxroot
-            ret = [nxroot]
+                nxsetup = self._get_nxroot(nxentry, calibration_config)
+            if not self.standalone:
+                points = self._get_points(results)
+                if points:
+                    self.logger.info(f'Adding {len(points)} points')
+                    self.add_points(nxsetup, points, logger=self.logger)
+                    self.logger.info(f'... done')
+                else:
+                    self.logger.warning('Skip adding points')
+            if self.standalone and self.update:
+                # Return nxprocess structure and values separately for writer
+                values = self._get_values(results)
+                ret = [nxsetup, values]
+            else:
+                if not (self._figures or self._animation):
+                    return nxsetup
+                ret = [nxsetup]
         else:
+            result = self._get_values(results) if self.standalone \
+                     else self._get_points(results)
             if not (self._figures or self._animation):
-                return points
-            ret = [points]
+                return result
+            ret = [result]
         if self._figures:
             ret.append(
                 PipelineData(
@@ -3014,9 +3036,38 @@ def animate(i):
                 f'{detector_id}_strainanalysis_unconstrained_fits'))
         plt.close()
 
-    def _get_nxroot(self, nxentry, calibration_config):
-        """Return a `nexusformat.nexus.NXroot` object initialized for
-        the stress analysis.
+    def _get_points(self, results):
+        """Convert strain analysis results to list-of-dicts format
+        expected by `add_points`.
+
+        :param results: Strain analysis results, mapping NeXus path
+            strings to arrays with leading axis = num_points.
+        :type results: dict[str, numpy.ndarray]
+        :return: One dict per map coordinate, each containing all
+            result values at that coordinate.
+        :rtype: list[dict[str, object]]
+        """
+        if not results:
+            return []
+        num_points = next(iter(results.values())).shape[0]
+        return [{k: v[i] for k, v in results.items()}
+                for i in range(num_points)]
+
+    def _get_values(self, results):
+        """Convert strain analysis results to a list of value dicts
+        suitable for writing with ``common.NexusValuesWriter``.
+
+        :param results: Strain analysis results, mapping NeXus path
+            strings to arrays with leading axis = num_points.
+        :type results: dict[str, numpy.ndarray]
+        :return: List of ``{'data': array, 'path': str}`` dicts.
+        :rtype: list[dict[str, object]]
+        """
+        return [{'data': v, 'path': k} for k, v in results.items()]
+
+    def _get_nxprocess(self, nxentry, calibration_config):
+        """Return a standalone NXprocess for the strain analysis
+        results & metadata.
 
         :param nxentry: Strain analysis map, including the raw
             MCA data.
@@ -3024,8 +3075,8 @@ def _get_nxroot(self, nxentry, calibration_config):
         :param calibration_config: 2&theta calibration configuration.
         :type calibration_config:
             CHAP.edd.models.MCATthCalibrationConfig
-        :return: Strain analysis results & associated metadata..
-        :rtype: nexusformat.nexus.NXroot
+        :return: Strain analysis results & associated metadata.
+        :rtype: nexusformat.nexus.NXprocess
         """
         # Third party modules
         # pylint: disable=no-name-in-module
@@ -3033,7 +3084,6 @@ def _get_nxroot(self, nxentry, calibration_config):
             NXdetector,
             NXfield,
             NXprocess,
-            NXroot,
         )
         # pylint: enable=no-name-in-module
 
@@ -3050,11 +3100,7 @@ def _get_nxroot(self, nxentry, calibration_config):
                 'StrainAnalysis Configuration, or re-run the pipeline with '
                 'the --interactive flag.')
 
-        # Create the NXroot object
-        nxroot = NXroot()
-        nxroot[nxentry.nxname] = nxentry
-        nxroot[f'{nxentry.nxname}_strainanalysis'] = NXprocess()
-        nxprocess = nxroot[f'{nxentry.nxname}_strainanalysis']
+        nxprocess = NXprocess()
         nxprocess.calibration_config = \
             calibration_config.model_dump_json()
         nxprocess.strain_analysis_config = \
@@ -3169,6 +3215,30 @@ def _get_nxroot(self, nxentry, calibration_config):
             tth_map = detector.get_tth_map((num_points,))
             det_nxdata.tth.nxdata = tth_map
 
+        return nxprocess
+
+    def _get_nxroot(self, nxentry, calibration_config):
+        """Return a `nexusformat.nexus.NXroot` object initialized for
+        the strain analysis.
+
+        :param nxentry: Strain analysis map, including the raw
+            MCA data.
+        :type nxentry: nexusformat.nexus.NXentry
+        :param calibration_config: 2&theta calibration configuration.
+        :type calibration_config:
+            CHAP.edd.models.MCATthCalibrationConfig
+        :return: Strain analysis results & associated metadata.
+        :rtype: nexusformat.nexus.NXroot
+        """
+        # Third party modules
+        # pylint: disable=no-name-in-module
+        from nexusformat.nexus import NXroot
+        # pylint: enable=no-name-in-module
+
+        nxroot = NXroot()
+        nxroot[nxentry.nxname] = nxentry
+        nxprocess = self._get_nxprocess(nxentry, calibration_config)
+        nxroot[f'{nxentry.nxname}_strainanalysis'] = nxprocess
         return nxroot
 
     def _linkdims(
@@ -3178,9 +3248,16 @@ def _linkdims(
         object.
         """
         # Third party modules
-        from nexusformat.nexus import NXfield
+        from nexusformat.nexus import NXfield, NXroot
         from nexusformat.nexus.tree import NXlinkfield
 
+        if not isinstance(nxgroup.nxroot, NXroot):
+            self.logger.warning(
+                'Skipping linkdims -- type(nxgroup.nxroot) = '
+                + f'{type(nxgroup.nxroot)}'
+            )
+            return
+
         if skip_field_dims is None:
             skip_field_dims = []
         if oversampling_axis is None:
@@ -3232,7 +3309,13 @@ def _linkdims(
             nxgroup.attrs['unstructured_axes'] = unstructured_axes
 
     def _strain_analysis(self):
-        """Perform the strain analysis on the full or partial map."""
+        """Perform the strain analysis on the full or partial map.
+
+        :return: Strain analysis results mapping NeXus path strings to
+            arrays with leading axis = num_points. Returns an empty
+            dict when no valid peaks are found.
+        :rtype: dict[str, numpy.ndarray]
+        """
         # Third party modules
         from nexusformat.nexus import NXfield
 
@@ -3254,25 +3337,23 @@ def _strain_analysis(self):
                 f'{self.detector_config.detectors[0].get_id()}_'
                     'strainanalysis_material_config'))
 
-        # Setup the points list with the map axes values
+        # Setup the results dict with the map axes values
         nxdata_ref = self._nxdata_detectors[0]
         axes = get_axes(nxdata_ref)
         if axes:
-            points = [
-                {a: nxdata_ref[a].nxdata[i] for a in axes}
-                for i in range(nxdata_ref[axes[0]].size)]
+            num_points = nxdata_ref[axes[0]].size
+            results = {a: nxdata_ref[a].nxdata for a in axes}
         else:
             axes = ['index']
-            points = [
-                {'index': i}
-                for i in range(np.prod(nxdata_ref.nxsignal.shape[:-1]))]
+            num_points = int(np.prod(nxdata_ref.nxsignal.shape[:-1]))
+            results = {'index': np.arange(num_points)}
             for nxdata in self._nxdata_detectors:
                 nxdata.attrs['axes'] = axes
                 nxdata.index = NXfield(
-                    np.arange(np.prod(nxdata_ref.nxsignal.shape[:-1])),
+                    np.arange(num_points),
                     'index')
 
-        # Loop over the detectors to fill in the nxprocess
+        # Loop over the detectors to fill in the results dict
         for energies, mask, mean_data, nxdata, detector in zip(
                 self._energies, self._masks, self._mean_data,
                 self._nxdata_detectors, self.detector_config.detectors):
@@ -3341,7 +3422,7 @@ def _strain_analysis(self):
                 self.logger.warning(
                     'No matching peaks with heights above the threshold, '
                     f'skipping the fit for detector {detector.get_id()}')
-                return []
+                return {}
             self._peak_fit_info.append({
                 'hkls': ["".join(map(str, hkl)) for hkl in hkls_fit],
                 'nominal_peak_centers': peak_locations.tolist(),
@@ -3354,7 +3435,7 @@ def _strain_analysis(self):
                 np.squeeze(intensities), energies[mask],
                 peak_locations[use_peaks], detector,
                 num_proc=self.config.num_proc, **self.run_config)
-            if intensities.shape[0] == 1:
+            if num_points == 1:
                 uniform_results = {k: [v] for k, v in uniform_results.items()}
                 unconstrained_results = {
                     k: [v] for k, v in unconstrained_results.items()}
@@ -3373,8 +3454,7 @@ def _strain_analysis(self):
 
             self.logger.info('... done')
 
-            # Add the fit results to the list of points
-            num_points = len(points)
+            # Compute the strain analysis results for all map points
             tth_map = detector.get_tth_map((nxdata.shape[0],))
             nominal_centers = np.asarray(
                 [get_peak_locations(d0, tth_map)
@@ -3410,109 +3490,103 @@ def _strain_analysis(self):
                 unconstrained_amplitudes_vary, insert_peak_indices, [False],
                 axis=-1)
 
-            # Add points
-            for i, point in enumerate(points):
-                point.update({
-                    f'{detector.get_id()}/data/intensity': intensities[i],
-                    f'{detector.get_id()}/data/norm': intensity_norms[i],
-                    f'{detector.get_id()}/data/uniform_strain':
-                        uniform_strain[i],
-                    f'{detector.get_id()}/data/unconstrained_strain':
-                        unconstrained_strain[i],
-                    f'{detector.get_id()}/data/unconstrained_strain_stdev':
-                        unconstrained_strain_stdev[i],
-                    f'{detector.get_id()}/uniform_fit/results/best_fit':
-                        uniform_results['best_fits'][i],
-                    f'{detector.get_id()}/uniform_fit/results/included_peaks':
-                        uniform_amplitudes_vary[i],
-                    f'{detector.get_id()}/uniform_fit/results/residual':
-                        uniform_results['residuals'][i],
-                    f'{detector.get_id()}/uniform_fit/results/redchi':
-                        uniform_results['redchis'][i],
-                    f'{detector.get_id()}/uniform_fit/results/success':
-                        uniform_results['success'][i],
-                    f'{detector.get_id()}/unconstrained_fit/results/best_fit':
-                        unconstrained_results['best_fits'][i],
-                    f'{detector.get_id()}/unconstrained_fit/results/'
-                        'included_peaks': unconstrained_amplitudes_vary[i],
-                    f'{detector.get_id()}/unconstrained_fit/results/residual':
-                        unconstrained_results['residuals'][i],
-                    f'{detector.get_id()}/unconstrained_fit/results/redchi':
-                        unconstrained_results['redchis'][i],
-                    f'{detector.get_id()}/unconstrained_fit/results/success':
-                        unconstrained_results['success'][i],
+            # Store results as full arrays (leading axis = num_points)
+            det_id = detector.get_id()
+            results.update({
+                f'{det_id}/data/intensity': intensities,
+                f'{det_id}/data/norm': intensity_norms,
+                f'{det_id}/data/uniform_strain': uniform_strain,
+                f'{det_id}/data/unconstrained_strain': unconstrained_strain,
+                f'{det_id}/data/unconstrained_strain_stdev':
+                    unconstrained_strain_stdev,
+                f'{det_id}/uniform_fit/results/best_fit':
+                    np.asarray(uniform_results['best_fits']),
+                f'{det_id}/uniform_fit/results/included_peaks':
+                    uniform_amplitudes_vary,
+                f'{det_id}/uniform_fit/results/residual':
+                    np.asarray(uniform_results['residuals']),
+                f'{det_id}/uniform_fit/results/redchi':
+                    np.asarray(uniform_results['redchis']),
+                f'{det_id}/uniform_fit/results/success':
+                    np.asarray(uniform_results['success']),
+                f'{det_id}/unconstrained_fit/results/best_fit':
+                    np.asarray(unconstrained_results['best_fits']),
+                f'{det_id}/unconstrained_fit/results/included_peaks':
+                    unconstrained_amplitudes_vary,
+                f'{det_id}/unconstrained_fit/results/residual':
+                    np.asarray(unconstrained_results['residuals']),
+                f'{det_id}/unconstrained_fit/results/redchi':
+                    np.asarray(unconstrained_results['redchis']),
+                f'{det_id}/unconstrained_fit/results/success':
+                    np.asarray(unconstrained_results['success']),
+            })
+            for j, hkl in enumerate(hkls_fit[use_peaks]):
+                hkl_name = '_'.join(str(hkl)[1:-1].split(' '))
+                uniform_fit_path = f'{det_id}/uniform_fit/{hkl_name}'
+                unconstrained_fit_path = \
+                    f'{det_id}/unconstrained_fit/{hkl_name}'
+                results.update({
+                    f'{uniform_fit_path}/amplitudes/values':
+                        np.asarray(uniform_results['amplitudes'][j]),
+                    f'{uniform_fit_path}/amplitudes/errors':
+                        np.asarray(uniform_results['amplitudes_errors'][j]),
+                    f'{uniform_fit_path}/centers/values':
+                        uniform_centers[j],
+                    f'{uniform_fit_path}/centers/errors':
+                        np.asarray(uniform_results['centers_errors'][j]),
+                    f'{uniform_fit_path}/sigmas/values':
+                        np.asarray(uniform_results['sigmas'][j]),
+                    f'{uniform_fit_path}/sigmas/errors':
+                        np.asarray(uniform_results['sigmas_errors'][j]),
+                    f'{unconstrained_fit_path}/amplitudes/values':
+                        np.asarray(unconstrained_results['amplitudes'][j]),
+                    f'{unconstrained_fit_path}/amplitudes/errors':
+                        np.asarray(
+                            unconstrained_results['amplitudes_errors'][j]),
+                    f'{unconstrained_fit_path}/centers/values':
+                        unconstrained_centers[j],
+                    f'{unconstrained_fit_path}/centers/errors':
+                        np.asarray(
+                            unconstrained_results['centers_errors'][j]),
+                    f'{unconstrained_fit_path}/sigmas/values':
+                        np.asarray(unconstrained_results['sigmas'][j]),
+                    f'{unconstrained_fit_path}/sigmas/errors':
+                        np.asarray(unconstrained_results['sigmas_errors'][j]),
                 })
-                for j, hkl in enumerate(hkls_fit[use_peaks]):
-                    hkl_name = '_'.join(str(hkl)[1:-1].split(' '))
-                    uniform_fit_path = \
-                        f'{detector.get_id()}/uniform_fit/{hkl_name}'
-                    unconstrained_fit_path = \
-                        f'{detector.get_id()}/unconstrained_fit/{hkl_name}'
-                    point.update({
-                        f'{uniform_fit_path}/amplitudes/values':
-                            uniform_results['amplitudes'][j][i],
-                        f'{uniform_fit_path}/amplitudes/errors':
-                            uniform_results['amplitudes_errors'][j][i],
-                        f'{uniform_fit_path}/centers/values':
-                            uniform_centers[j][i],
-                        f'{uniform_fit_path}/centers/errors':
-                            uniform_results['centers_errors'][j][i],
-                        f'{uniform_fit_path}/sigmas/values':
-                            uniform_results['sigmas'][j][i],
-                        f'{uniform_fit_path}/sigmas/errors':
-                            uniform_results['sigmas_errors'][j][i],
-                        f'{unconstrained_fit_path}/amplitudes/values':
-                            unconstrained_results['amplitudes'][j][i],
-                        f'{unconstrained_fit_path}/amplitudes/errors':
-                            unconstrained_results['amplitudes_errors'][j][i],
-                        f'{unconstrained_fit_path}/centers/values':
-                            unconstrained_centers[j][i],
-                        f'{unconstrained_fit_path}/centers/errors':
-                            unconstrained_results['centers_errors'][j][i],
-                        f'{unconstrained_fit_path}/sigmas/values':
-                            unconstrained_results['sigmas'][j][i],
-                        f'{unconstrained_fit_path}/sigmas/errors':
-                            unconstrained_results['sigmas_errors'][j][i],
+                if detector.peak_models == 'pvoigt':
+                    results.update({
+                        f'{uniform_fit_path}/fractions/values':
+                            np.asarray(uniform_results['fractions'][j]),
+                        f'{uniform_fit_path}/fractions/errors':
+                            np.asarray(
+                                uniform_results['fractions_errors'][j]),
+                        f'{unconstrained_fit_path}/fractions/values':
+                            np.asarray(
+                                unconstrained_results['fractions'][j]),
+                        f'{unconstrained_fit_path}/fractions/errors':
+                            np.asarray(
+                                unconstrained_results['fractions_errors'][j]),
                     })
-                    if detector.peak_models == 'pvoigt':
-                        point.update({
-                            f'{uniform_fit_path}/fractions/values':
-                                uniform_results['fractions'][j][i],
-                            f'{uniform_fit_path}/fractions/errors':
-                                uniform_results['fractions_errors'][j][i],
-                            f'{unconstrained_fit_path}/fractions/values':
-                                unconstrained_results['fractions'][j][i],
-                            f'{unconstrained_fit_path}/fractions/errors':
-                                unconstrained_results['fractions_errors'][j][i],
-                        })
-                    if unconstrained_centers[j][i]:
-                        point.update({
-                            f'{unconstrained_fit_path}/strains/values':
-                                unconstrained_strains[j][i],
-                            f'{unconstrained_fit_path}/strains/residuals':
-                                unconstrained_strain[i] -
-                                    unconstrained_strains[j][i],
-                        })
-                        if (unconstrained_results['centers_errors'][j][i]
-                                is None):
-                            point.update({
-                                f'{unconstrained_fit_path}/strains/errors':
-                                    None,
-                            })
-                        else:
-                            point.update({
-                                f'{unconstrained_fit_path}/strains/errors':
-                                    unconstrained_results[
-                                        'centers_errors'][j][i] /
-                                    unconstrained_centers[j][i],
-                            })
-                    else:
-                        point.update({
-                            f'{unconstrained_fit_path}/strains/values': None,
-                            f'{unconstrained_fit_path}/strains/errors': None,
-                            f'{unconstrained_fit_path}/strains/residuals':
-                                None,
-                        })
+                # Strain values: NaN where unconstrained center is zero
+                has_center = unconstrained_centers[j].astype(bool)
+                centers_errors_j = unconstrained_results['centers_errors'][j]
+                strain_errors_raw = np.asarray([
+                    (e / c if e is not None else np.nan)
+                    for e, c in zip(centers_errors_j,
+                                    unconstrained_centers[j])
+                ])
+                results.update({
+                    f'{unconstrained_fit_path}/strains/values':
+                        np.where(has_center, unconstrained_strains[j],
+                                 np.nan),
+                    f'{unconstrained_fit_path}/strains/errors':
+                        np.where(has_center, strain_errors_raw, np.nan),
+                    f'{unconstrained_fit_path}/strains/residuals':
+                        np.where(
+                            has_center,
+                            unconstrained_strain - unconstrained_strains[j],
+                            np.nan),
+                })
 
             # Create an animation of the fit points
             if (not self.config.skip_animation
@@ -3521,446 +3595,7 @@ def _strain_analysis(self):
                     nxdata, energies[mask], intensities, intensity_norms,
                     unconstrained_results['best_fits'], detector.get_id())
 
-        return points
-
-class OrnlStrainAnalysisProcessor(StrainAnalysisProcessor):
-    """Processor that handles strain analysis in the middle of
-    autonomously driven experients."""
-
-    def process(self, data):
-        """Setup the strain analysis and/or return the strain analysis
-        results as a list of updated points or a
-        `nexusformat.nexus.NXroot` object.
-
-        :param data: Input data containing configurations for a map,
-            completed energy/tth calibration, and (optionally)
-            parameters for the strain analysis.
-        :type data: list[PipelineData]
-        :raises RuntimeError: Unable to get a valid strain analysis
-            configuration.
-        :return: The strain analysis setup or results, a list of
-            byte stream representions of Matplotlib figures and an
-            animation of the fit results.
-        :rtype: Union[list[dict[str, object]],
-            nexusformat.nexus.NXroot], PipelineData, PipelineData
-        """
-        # Third party modules
-        from nexusformat.nexus import (
-            NXentry,
-            NXroot,
-        )
-
-        # Local modules
-        from CHAP.utils.general import list_to_string
-
-        if not (self.setup or self.update):
-            raise RuntimeError('Illegal combination of setup and update')
-        if not self.update:
-            if self.interactive:
-                self.logger.warning('Interactive option disabled during setup')
-                self.interactive = False
-            if self.save_figures:
-                self.logger.warning(
-                    'Saving figures option disabled during setup')
-                self.save_figures = False
-        self._animation = []
-
-        # Load the pipeline input data
-        try:
-            nxobject = self.get_data(data)
-            if isinstance(nxobject, NXroot):
-                nxroot = nxobject
-            elif isinstance(nxobject, NXentry):
-                nxroot = NXroot()
-                nxroot[nxobject.nxname] = nxobject
-                nxobject.set_default()
-            else:
-                raise RuntimeError
-        except Exception as exc:
-            raise RuntimeError(
-                'No valid input in the pipeline data') from exc
-
-        # Load the detector data
-        # FIX set rel_height_cutoff
-        nxentry = self.get_default_nxentry(nxroot)
-        for k, v in nxentry.scalar_data.items():
-            self.logger.debug(f'{k}.chunks = {v.chunks}')
-            self.logger.debug(f'{k}.maxshape = {v.maxshape}')
-
-        nxdata = nxentry[nxentry.default]
-
-        # Load the validated calibration configuration
-        # FIX make this a class field and add to pipeline_fields too?
-        #     NB: be sure that adding this field does not mess up
-        #     self.detector_config during pydantic validation
-        calibration_config = self.get_config(
-            data, schema='edd.models.MCATthCalibrationConfig', remove=False)
-
-        # Load the validated calibration detector configurations
-        calibration_detector_config = self.get_data(
-            data, schema='edd.models.MCATthCalibrationConfig')
-        calibration_detectors = [
-            MCADetectorCalibration(**d)
-            for d in calibration_detector_config.get('detectors', [])]
-        calibration_detector_ids = [d.get_id() for d in calibration_detectors]
-
-        # Check for available raw detector data and for the available
-        # calibration data
-        if not self.detector_config.detectors:
-            self.detector_config.detectors = [
-                MCADetectorStrainAnalysis(
-                    id=id_, processor_type='strainanalysis')
-                for id_ in nxentry.detector_ids]
-            self.detector_config.update_detectors()
-        skipped_detectors = []
-        sskipped_detectors = []
-        detectors = []
-        for detector in self.detector_config.detectors:
-            detector_id = detector.get_id()
-            if detector_id not in nxdata:
-                skipped_detectors.append(detector_id)
-            elif detector_id not in calibration_detector_ids:
-                sskipped_detectors.append(detector_id)
-            else:
-                raw_detector_data = nxdata[detector_id].nxdata
-                if raw_detector_data.ndim != 2:
-                    self.logger.warning(
-                        f'Skipping detector {detector_id} (Illegal data shape '
-                        f'{raw_detector_data.shape})')
-                elif raw_detector_data.sum():
-                    for k, v in nxdata[detector_id].attrs.items():
-                        detector.attrs[k] = v.nxdata
-                    if self.config.rel_height_cutoff is not None:
-                        detector.rel_height_cutoff = \
-                            self.config.rel_height_cutoff
-                    detector.add_calibration(
-                        calibration_detectors[
-                            int(calibration_detector_ids.index(detector_id))])
-                    detectors.append(detector)
-                else:
-                    self.logger.warning(
-                        f'Skipping detector {detector_id} (zero intensity)')
-        if len(skipped_detectors) == 1:
-            self.logger.warning(
-                f'Skipping detector {skipped_detectors[0]} '
-                '(no raw data)')
-        elif skipped_detectors:
-            skipped_detectors = [int(d) for d in skipped_detectors]
-            self.logger.warning(
-                'Skipping detectors '
-                f'{list_to_string(skipped_detectors)} (no raw data)')
-        if len(sskipped_detectors) == 1:
-            self.logger.warning(
-                f'Skipping detector {sskipped_detectors[0]} '
-                '(no raw data)')
-        elif sskipped_detectors:
-            skipped_detectors = [int(d) for d in sskipped_detectors]
-            self.logger.warning(
-                'Skipping detectors '
-                f'{list_to_string(skipped_detectors)} (no calibration data)')
-        self.detector_config.detectors = detectors
-        if not self.detector_config.detectors:
-            raise ValueError('No valid data or unable to match an available '
-                             'calibrated detector for the strain analysis')
-
-        # Load the raw MCA data and compute the detector bin energies
-        # and the mean spectra
-        self._setup_detector_data(
-            nxentry[nxentry.default],
-            strain_analysis_config=self.config, update=self.update)
-
-        # Apply the energy mask
-        self._apply_energy_mask()
-
-        # Get the mask and HKLs used in the strain analysis
-        self._get_mask_hkls()
-
-        # Apply the combined energy ranges mask
-        self._apply_combined_mask()
-
-        # Setup and/or run the strain analysis
-        points = []
-        if self.update:
-            points = self._strain_analysis()
-            values = self._get_values(nxroot, points)
-        if self.setup:
-            nxprocess = self._get_nxprocess(nxentry, calibration_config)
-            if points:
-                self.logger.info(f'Adding {len(points)} points')
-                self.add_points(nxprocess, points, logger=self.logger)
-                self.logger.info(f'... done')
-            else:
-                self.logger.warning('Skip adding points')
-            if not (self._figures or self._animation):
-                return nxprocess
-            ret = [nxprocess]
-        else:
-            if not (self._figures or self._animation):
-                return values
-            ret = [values]
-        if self._figures:
-            ret.append(
-                PipelineData(
-                    name=self.__name__, data=self._figures,
-                    schema='common.write.ImageWriter'))
-        if self._animation:
-            ret.append(
-                PipelineData(
-                    name=self.__name__, data=self._animation,
-                    schema='common.write.ImageWriter'))
-        return tuple(ret)
-
-    def _get_nxprocess(self, nxentry, calibration_config):
-        """Return a standalone NXprocess for the strain analysis
-        results & metadata.
-
-        :param nxentry: Strain analysis map, including the raw
-            MCA data.
-        :type nxentry: nexusformat.nexus.NXentry
-        :param calibration_config: 2&theta calibration configuration.
-        :type calibration_config:
-            CHAP.edd.models.MCATthCalibrationConfig
-        :return: Strain analysis results & associated metadata.
-        :rtype: nexusformat.nexus.NXprocess
-        """
-        # Third party modules
-        # pylint: disable=no-name-in-module
-        from nexusformat.nexus import (
-            NXdetector,
-            NXfield,
-            NXprocess,
-            NXroot,
-        )
-        # pylint: enable=no-name-in-module
-
-        # Third party modules
-        from json import dumps
-
-        # Local modules
-        from CHAP.edd.utils import get_unique_hkls_ds
-        from CHAP.utils.general import nxcopy
-
-        if not self.interactive and not self.config.materials:
-            raise ValueError(
-                'No material provided. Provide a material in the '
-                'StrainAnalysis Configuration, or re-run the pipeline with '
-                'the --interactive flag.')
-
-        nxprocess = NXprocess()
-        nxprocess.calibration_config = \
-            calibration_config.model_dump_json()
-        nxprocess.strain_analysis_config = \
-            self.config.model_dump_json()
-
-        if len(self._peak_fit_info) == 0:
-            # FIX this is a temporary fix to be able to run update
-            # after setup.
-            self._peak_fit_info = [{}] * len(self.detector_config.detectors)
-            self.logger.warning('Missing peak_fit_info')
-
-        # Loop over the detectors to fill in the nxprocess
-        for energies, mask, nxdata, detector, peak_fit_info in zip(
-                self._energies, self._masks, self._nxdata_detectors,
-                self.detector_config.detectors, self._peak_fit_info):
-
-            # Get the current data object
-            data = nxdata.nxsignal
-            num_points = data.shape[0]
-
-            # Setup the NXdetector object for the current detector
-            self.logger.debug(
-                f'Setting up NXdetector group for {detector.get_id()}')
-            nxdetector = NXdetector()
-            nxprocess[detector.get_id()] = nxdetector
-            nxdetector.local_name = detector.get_id()
-            nxdetector.detector_config = detector.model_dump_json()
-            nxdetector.peak_fit_info = dumps(peak_fit_info)
-            nxdetector.data = nxcopy(nxdata, exclude_nxpaths='detector_data')
-            det_nxdata = nxdetector.data
-            if 'axes' in det_nxdata.attrs:
-                if isinstance(det_nxdata.attrs['axes'], str):
-                    det_nxdata.attrs['axes'] = [
-                        det_nxdata.attrs['axes'], 'energy']
-                else:
-                    det_nxdata.attrs['axes'].append('energy')
-            else:
-                det_nxdata.attrs['axes'] = ['energy']
-            det_nxdata.energy = NXfield(
-                value=energies[mask], attrs={'units': 'keV'})
-            det_nxdata.norm = NXfield(
-                dtype=np.float64,
-                shape=(num_points,),
-                maxshape=(None,), chunks=(1,)
-            )
-            det_nxdata.tth = NXfield(
-                dtype=np.float64,
-                shape=(num_points,),
-                attrs={'units':'degrees', 'long_name': '2\u03B8 (degrees)'},
-                maxshape=(None,), chunks=(1,),
-            )
-            det_nxdata.uniform_strain = NXfield(
-                dtype=np.float64,
-                shape=(num_points,),
-                attrs={'long_name': 'Strain from uniform fit (\u03B5)'},
-                # attrs={'long_name': 'Strain from uniform fit (\u03BC\u03B5)'}
-                maxshape=(None,), chunks=(1,)
-            )
-
-            det_nxdata.unconstrained_strain = NXfield(
-                dtype=np.float64,
-                shape=(num_points,),
-                attrs={'long_name':
-                           'Strain from unconstrained fit (\u03B5)'},
-                           #'Strain from unconstrained fit (\u03BC\u03B5)'},
-                maxshape=(None,), chunks=(1,)
-            )
-            det_nxdata.unconstrained_strain_stdev = NXfield(
-                dtype=np.float64,
-                shape=(num_points,),
-                attrs={'long_name':
-                           'Standard deviation in strain from unconstrained '
-                           'fit (\u03B5)'},
-                           #'fit (\u03BC\u03B5)'}
-                maxshape=(None,), chunks=(1,)
-            )
-
-            # Add the detector data
-            _intensity=np.asarray(
-                [
-                    data[i].astype(np.float64)[mask]
-                    for i in range(num_points)
-                ]
-            )
-            det_nxdata.intensity = NXfield(
-                value=_intensity,
-                attrs={'units': 'counts'},
-                maxshape=(None,*_intensity.shape[1:]),
-                chunks=(1,*_intensity.shape[1:])
-            )
-            det_nxdata.attrs['signal'] = 'intensity'
-
-            # Get the unique HKLs and lattice spacings for the strain
-            # analysis materials
-            hkls, _ = get_unique_hkls_ds(
-                self.config.materials, tth_max=detector.tth_max,
-                tth_tol=detector.tth_tol)
-
-            # Get the HKLs and lattice spacings that will be used for
-            # fitting
-            hkls_fit = np.asarray([hkls[i] for i in detector.hkl_indices])
-
-            # Add the uniform fit nxcollection
-            self._add_fit_nxcollection(
-                nxdetector, 'uniform', hkls_fit, peak_fit_info)
-
-            # Add the unconstrained fit nxcollection
-            self._add_fit_nxcollection(
-                nxdetector, 'unconstrained', hkls_fit, peak_fit_info)
-
-            # Add the strain fields
-            tth_map = detector.get_tth_map((num_points,))
-            det_nxdata.tth.nxdata = tth_map
-
-        return nxprocess
-
-    def _linkdims(
-            self, nxgroup, nxdata_source, add_field_dims=None,
-            skip_field_dims=None, oversampling_axis=None):
-        """Link the dimensions for a 'nexusformat.nexus.NXgroup`
-        object.
-        """
-        # Third party modules
-        from nexusformat.nexus import NXfield, NXroot
-        from nexusformat.nexus.tree import NXlinkfield
-
-        if not isinstance(nxgroup.nxroot, NXroot):
-            self.logger.warning(
-                'Skipping linkdims -- type(nxgroup.nxroot) = '
-                + f'{type(nxgroup.nxroot)}'
-            )
-            return
-        super()._linkdims(
-            nxgroup, nxdata_source, add_field_dims=add_field_dims,
-            skip_field_dims=skip_field_dims, oversampling_axis=skip_field_dims
-        )
-
-    def _get_values(self, nxroot, points):
-        """Return list of dictionaries with new srtain results values
-        suitable for writing with `common.NexusValuesWriter`.
-
-        :param nxroot:
-        :type nxroot:
-        :param points:
-        :type points:
-        :returns:
-        :rtype:
-        """
-        # pylint: disable=no-name-in-module
-        from nexusformat.nexus import (
-            NXdetector,
-            NXprocess
-        )
-        # pylint: enable=no-name-in-module
-
-        nxprocess = None
-        for nxobject in nxroot.values():
-            if isinstance(nxobject, NXprocess):
-                nxprocess = nxobject
-                break
-        if nxprocess is None:
-            raise RuntimeError('Unable to find the strainanalysis object')
-
-        nxdata_detectors = []
-        for nxobject in nxprocess.values():
-            if isinstance(nxobject, NXdetector):
-                nxdata_detectors.append(nxobject.data)
-        if not nxdata_detectors:
-            raise RuntimeError(
-                'Unable to find detector data in strainanalysis object')
-        axes = get_axes(nxdata_detectors[0], skip_axes=['energy'])
-
-        values = []
-        if axes:
-            coords = np.asarray(
-                [nxdata_detectors[0][a].nxdata for a in axes]).T
-
-            def get_matching_indices(all_coords, point_coords, decimals=None):
-                if isinstance(decimals, int):
-                    all_coords = np.round(all_coords, decimals=decimals)
-                    point_coords = np.round(point_coords, decimals=decimals)
-                coords_match = np.all(all_coords == point_coords, axis=1)
-                index = np.where(coords_match)[0]
-                return index
-
-            # FIX: can we round to 3 decimals right away in general?
-            # FIX: assumes points contains a sorted and continous
-            # slice of updates
-            i_0 = get_matching_indices(
-                coords,
-                np.asarray([points[0][a] for a in axes]), decimals=3)[0]
-            i_f = get_matching_indices(
-                coords,
-                np.asarray([points[-1][a] for a in axes]), decimals=3)[0]
-            slices = {k: np.asarray([p[k] for p in points]) for k in points[0]}
-            for k, v in slices.items():
-                values.append(
-                    {
-                        'data': v,
-                        'path': k,
-                    }
-                )
-        else:
-            values.extend(
-                [
-                    {
-                        'data': v,
-                        'path': k,
-                    }
-                    for k, v in points[0].items()
-                ]
-            )
-
-        return values
+        return results
 
 
 if __name__ == '__main__':

From b0c9ae5ffb126881eff899d97df0d9279f600133 Mon Sep 17 00:00:00 2001
From: Keara Soloway <kls286@cornell.edu>
Date: Tue, 21 Apr 2026 11:26:17 -0400
Subject: [PATCH 25/76] optimize: edd.SliceNXdataReader

---
 CHAP/edd/reader.py | 83 +++++++++++++++++++++++++++++-----------------
 1 file changed, 52 insertions(+), 31 deletions(-)

diff --git a/CHAP/edd/reader.py b/CHAP/edd/reader.py
index 8bad0f6a..ad4eb757 100755
--- a/CHAP/edd/reader.py
+++ b/CHAP/edd/reader.py
@@ -770,43 +770,64 @@ def read(self):
         from CHAP.common import NexusReader
         from CHAP.utils.general import nxcopy
 
+        # Read NXroot
         reader = NexusReader(**self.model_dump())
-        nxroot = nxcopy(reader.read())
-        nxentry = None
-        nxdata = None
-        for nxname, nxobject in nxroot.items():
-            if isinstance(nxobject, NXentry):
-                nxentry = nxobject
-                nxdata = nxobject.data
+        nxroot = reader.read()
+
+        # Locate NXentry
+        nxentry = next(
+            (obj for obj in nxroot.values() if isinstance(obj, NXentry)),
+            None,
+        )
+        if nxentry is None:
+            raise ValueError('Could not find NXentry group')
+        nxentry_nxpath = nxentry.nxpath
+        self.logger.info(f'Using NXentry at: {nxentry_nxpath}')
+
+        # Make a copy of the NXroot, excluding everything but the
+        # NXentry of interest. Do this so we can just slice the
+        # NXfields in place in the copy (because copy is not tied to
+        # the original input file).
+        exclude_nxpaths = []
+        for v in nxroot.values():
+            if v.nxpath != nxentry_nxpath:
+                exclude_nxpaths.append(v.nxpath)
+        nxroot = nxcopy(nxroot, exclude_nxpaths=exclude_nxpaths)
+        nxentry = nxroot[nxentry_nxpath]
+
+        # Locate NXdata containining the "SCAN_N" NXfield
+        nxdata = getattr(nxentry, 'data', None)
         if nxdata is None:
-            msg = 'Could not find NXdata group'
-            self.logger.error(msg)
-            raise ValueError(msg)
-        if 'SCAN_N' not in nxdata:
-            self.logger.warning(f'SCAN_N not in {nxdata}')
-            scan_n_found = False
-            for k, v in nxentry.items():
-                if 'SCAN_N' in v:
+            self.logger.warning('NXdata group missing — searching fallback')
+
+            for v in nxentry.values():
+                if hasattr(v, 'SCAN_N'):
                     nxdata = v
-                    scan_n_found = True
-                    self.logger.warning(f'Using SCAN_N dataset in {nxdata}')
-            if not scan_n_found:
-                msg = 'Cannot find SCAN_N dataset'
-                self.logger.error(msg)
-                raise ValueError(msg)
-
-        indices = np.argwhere(
-            nxdata.SCAN_N.nxdata == self.scan_number).flatten()
-        for nxname, nxobject in nxdata.items():
-            if isinstance(nxobject, NXfield):
-                nxdata[nxname] = NXfield(
-                    value=nxobject.nxdata[indices],
-                    dtype=nxdata[nxname].dtype,
-                    attrs=nxdata[nxname].attrs,
-                )
+                    break
+
+            if nxdata is None:
+                raise ValueError('Cannot find SCAN_N dataset')
+        self.logger.info(f'Using NXdata at: {nxdata.nxpath}')
+
+        # Get indicies of SCAN_N that match self.scan_number
+        scan_field = nxdata['SCAN_N'].nxdata
+        indices = np.flatnonzero(scan_field == self.scan_number)
+
+        if indices.size == 0:
+            self.logger.warning(
+                f'scan_number {self.scan_number} not found in SCAN_N'
+            )
+        self.logger.info(f'Slicing NXfields with: {indices}')
+
+        # Slice only NXfields
+        for name, obj in list(nxdata.items()):
+            if isinstance(obj, NXfield):
+                self.logger.info(f'Slicing NXfield at: {obj.nxpath}')
+                nxdata[name] = obj[indices]
 
         return nxroot
 
+
 class UpdateNXdataReader(Reader):
     """Companion to `edd.SetupNXdataReader` and
     `common.UpdateNXDataProcessor`. Constructs a list of data points

From 23ba5d3fa7d53a977d363c3ae5bcfdf56b8b4a6b Mon Sep 17 00:00:00 2001
From: Rolf Verberg <rv43@cornell.edu>
Date: Tue, 28 Apr 2026 12:50:53 -0400
Subject: [PATCH 26/76] add: added peak fit results to the EDD calibration
 output yamls

---
 CHAP/edd/processor.py | 72 ++++++++++++++++++++++++++++++++-----------
 1 file changed, 54 insertions(+), 18 deletions(-)

diff --git a/CHAP/edd/processor.py b/CHAP/edd/processor.py
index 2309ff78..733ec448 100755
--- a/CHAP/edd/processor.py
+++ b/CHAP/edd/processor.py
@@ -1185,6 +1185,8 @@ class MCAEnergyCalibrationProcessor(_BaseEddProcessor):
     config: MCAEnergyCalibrationConfig
     detector_config: MCADetectorConfig
 
+    _peak_fit_results: dict = PrivateAttr(default={})
+
     @model_validator(mode='before')
     @classmethod
     def validate_mcaenergycalibrationprocessor_before(cls, data):
@@ -1309,6 +1311,10 @@ def process(self, data):
             **self.config.model_dump(),
             'detectors': [d.model_dump(exclude_defaults=True)
                           for d in self.detector_config.detectors]}
+        # Add the fit results to the detector fields
+        for i, d in enumerate(self.detector_config.detectors):
+            configs['detectors'][i].update(
+                {'peak_fit_results': self._peak_fit_results[d.get_id()]})
         return configs, PipelineData(
             name=self.__name__, data=self._figures,
             schema='common.write.ImageWriter')
@@ -1369,7 +1375,9 @@ def _calibrate(self):
                 self._energies, self._masks, self._mean_data,
                 self._mask_index_ranges, self.detector_config.detectors):
 
-            self.logger.info(f'Calibrating detector {detector.get_id()}')
+            id_ = detector.get_id()
+
+            self.logger.info(f'Calibrating detector {id_}')
 
             bins = low + np.arange(energies.size, dtype=np.int16)
 
@@ -1378,13 +1386,11 @@ def _calibrate(self):
                              for energy in peak_energies]
             buf, initial_peak_indices = self._get_initial_peak_positions(
                 mean_data*np.asarray(mask).astype(np.int32), low,
-                detector.mask_ranges, input_indices, max_peak_index,
-                detector.get_id(), return_buf=self.save_figures)
+                detector.mask_ranges, input_indices, max_peak_index, id_,
+                return_buf=self.save_figures)
             if self.save_figures:
                 self._figures.append(
-                    (buf,
-                     f'{detector.get_id()}'
-                         '_energy_calibration_initial_peak_positions'))
+                    (buf, f'{id_}_energy_calibration_initial_peak_positions'))
 
             # Construct the fit model and perform the fit
             models = []
@@ -1409,17 +1415,24 @@ def _calibrate(self):
 
             # Extract the fit results for the peaks
             fit_peak_amplitudes = sorted([
-                mean_data_fit.best_values[f'peak{i+1}_amplitude']
+                mean_data_fit.best_values[f'peak{i+1}_amplitude'].tolist()
                 for i in range(len(initial_peak_indices))])
             self.logger.debug(f'Fit peak amplitudes: {fit_peak_amplitudes}')
             fit_peak_indices = sorted([
-                mean_data_fit.best_values[f'peak{i+1}_center']
+                mean_data_fit.best_values[f'peak{i+1}_center'].tolist()
                 for i in range(len(initial_peak_indices))])
             self.logger.debug(f'Fit peak center indices: {fit_peak_indices}')
-            fit_peak_fwhms = sorted([
-                2.35482*mean_data_fit.best_values[f'peak{i+1}_sigma']
+            fit_peak_sigmas = sorted([
+                mean_data_fit.best_values[f'peak{i+1}_sigma'].tolist()
                 for i in range(len(initial_peak_indices))])
-            self.logger.debug(f'Fit peak fwhms: {fit_peak_fwhms}')
+            self.logger.debug(f'Fit peak sigmas: {fit_peak_sigmas}')
+            self._peak_fit_results[id_] = {
+                'amplitudes': fit_peak_amplitudes,
+                'centers': fit_peak_indices,
+                'sigmas': fit_peak_sigmas,
+                'independent_dimension': {
+                    'name': 'Detector Channel', 'unit': '-'}
+            }
 
             # FIX for now stick with a linear energy correction
             fit = FitProcessor(**self.run_config)
@@ -1446,8 +1459,7 @@ def _calibrate(self):
 
                 bins_masked = bins[mask]
                 fig, axs = plt.subplots(1, 2, figsize=(11, 4.25))
-                fig.suptitle(
-                    f'Detector {detector.get_id()} energy calibration')
+                fig.suptitle(f'Detector {id_} energy calibration')
                 # Left plot: raw MCA data and best fit of peaks
                 axs[0].set_title('MCA spectrum peak fit')
                 axs[0].set_xlabel('Detector Channel (-)')
@@ -1488,8 +1500,7 @@ def _calibrate(self):
 
                 if self.save_figures:
                     self._figures.append(
-                        (fig_to_iobuf(fig),
-                         f'{detector.get_id()}_energy_calibration_fit'))
+                        (fig_to_iobuf(fig), f'{id_}_energy_calibration_fit'))
                 if self.interactive:
                     plt.show()
                 plt.close()
@@ -1740,6 +1751,8 @@ class MCATthCalibrationProcessor(_BaseEddProcessor):
     config: MCATthCalibrationConfig
     detector_config: MCADetectorConfig
 
+    _peak_fit_results: dict = PrivateAttr(default={})
+
     @model_validator(mode='before')
     @classmethod
     def validate_mcatthcalibrationprocessor_before(cls, data):
@@ -1875,6 +1888,10 @@ def process(self, data):
             **self.config.model_dump(),
             'detectors': [d.model_dump(exclude_defaults=True)
                           for d in self.detector_config.detectors]}
+        # Add the fit results to the detector fields
+        for i, d in enumerate(self.detector_config.detectors):
+            configs['detectors'][i].update(
+                {'peak_fit_results': self._peak_fit_results[d.get_id()]})
         return configs, PipelineData(
             name=self.__name__, data=self._figures,
             schema='common.write.ImageWriter')
@@ -2128,7 +2145,26 @@ def _direct_bragg_peak_fit(
         residual = result.residual
 
         # Extract the Bragg peak indices from the fit
-        i_bragg_fit = np.asarray(
+        fit_peak_amplitudes = [
+            result.best_values[f'peak{i+1}_amplitude'].tolist()
+            for i in range(len(e_bragg))]
+        self.logger.debug(f'Fit peak amplitudes: {fit_peak_amplitudes}')
+        fit_peak_indices = [
+            result.best_values[f'peak{i+1}_center'].tolist()
+            for i in range(len(e_bragg))]
+        self.logger.debug(f'Fit peak center indices: {fit_peak_indices}')
+        fit_peak_sigmas = [
+            result.best_values[f'peak{i+1}_sigma'].tolist()
+            for i in range(len(e_bragg))]
+        self.logger.debug(f'Fit peak sigmas: {fit_peak_sigmas}')
+        self._peak_fit_results[detector.get_id()] = {
+            'amplitudes': fit_peak_amplitudes,
+            'centers': fit_peak_indices,
+            'sigmas': fit_peak_sigmas,
+            'independent_dimension': {
+                'name': 'Detector Channel', 'unit': '-'}
+        }
+        fit_peak_indices = np.asarray(
             [result.best_values[f'peak{i+1}_center']
              for i in range(len(e_bragg))])
 
@@ -2140,7 +2176,7 @@ def _direct_bragg_peak_fit(
             model = 'linear'
         fit = FitProcessor(**self.run_config)
         result = fit.process(
-            NXdata(NXfield(e_bragg, 'y'), NXfield(i_bragg_fit, 'x')),
+            NXdata(NXfield(e_bragg, 'y'), NXfield(fit_peak_indices, 'x')),
             {'models': [{'model': model}]})
         if quadratic_energy_calibration:
             a_fit = result.best_values['a']
@@ -2151,7 +2187,7 @@ def _direct_bragg_peak_fit(
             b_fit = result.best_values['slope']
             c_fit = result.best_values['intercept']
         e_bragg_unconstrained = (
-            (a_fit*i_bragg_fit + b_fit) * i_bragg_fit + c_fit)
+            (a_fit*fit_peak_indices + b_fit) * fit_peak_indices + c_fit)
 
         return {
             'best_fit_unconstrained': best_fit,

From 5d229a8ae53be23d3d98bafe81c32f9b9c86a733 Mon Sep 17 00:00:00 2001
From: Keara Soloway <kls286@cornell.edu>
Date: Tue, 28 Apr 2026 14:13:11 -0400
Subject: [PATCH 27/76] fix: YAMLWriter can write lists as well as dicts

---
 CHAP/common/writer.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/CHAP/common/writer.py b/CHAP/common/writer.py
index aad605c1..89ddea98 100755
--- a/CHAP/common/writer.py
+++ b/CHAP/common/writer.py
@@ -772,7 +772,7 @@ def write(self, data):
         from CHAP.models import CHAPBaseModel
 
         def get_dict(data):
-            if isinstance(data, dict):
+            if isinstance(data, dict) or isinstance(data, list):
                 return data
             if isinstance(data, (BaseModel, CHAPBaseModel)):
                 try:

From 4f85f99c599e794a225f4a6e302a145fc0d394fb Mon Sep 17 00:00:00 2001
From: Keara Soloway <kls286@cornell.edu>
Date: Tue, 28 Apr 2026 14:14:13 -0400
Subject: [PATCH 28/76] add: JSONWriter

---
 CHAP/common/writer.py | 16 ++++++++++++++++
 1 file changed, 16 insertions(+)

diff --git a/CHAP/common/writer.py b/CHAP/common/writer.py
index 89ddea98..62c983ec 100755
--- a/CHAP/common/writer.py
+++ b/CHAP/common/writer.py
@@ -418,6 +418,22 @@ def write(self, data):
             raise ValueError(f'Invalid image input type {type(image_data)}')
 
 
+class JSONWriter(Writer):
+    """Writer for JSON data.
+
+    :ivar index: Index of ``PipelineData`` item in input ``data`` list
+        that should be written to the JSON file. Defaults to ``-1``.
+    :vartpe index: int, Optional.
+    """
+    index: int = -1
+    def write(self, data):
+        """Write the last """
+        import json
+        _data = self.get_pipelinedata_item(data, remove=self.remove)
+        with open(self.filename, 'w') as outf:
+            json.dump(_data, outf)
+
+
 class MatplotlibAnimationWriter(Writer):
     """Writer for saving matplotlib animations.
 

From b81e6c0f0d967286ca6b90e94eddc94f215a8b34 Mon Sep 17 00:00:00 2001
From: Keara Soloway <kls286@cornell.edu>
Date: Tue, 28 Apr 2026 14:17:48 -0400
Subject: [PATCH 29/76] add: StrainAnalysisProcessor.json_results

---
 CHAP/edd/processor.py | 13 +++++++++++--
 1 file changed, 11 insertions(+), 2 deletions(-)

diff --git a/CHAP/edd/processor.py b/CHAP/edd/processor.py
index 230d0a25..be95381f 100755
--- a/CHAP/edd/processor.py
+++ b/CHAP/edd/processor.py
@@ -2523,6 +2523,11 @@ class StrainAnalysisProcessor(BaseStrainProcessor):
         `update` are `True` the standalone `NXprocess` and the
         values list are returned together as a tuple.
     :type standalone: bool, optional
+    :ivar json_results: If updating, return an additional minimal
+        dictionary of results that can be written to .json file for
+        easier access by autonomous feedback experiment
+        drivers. Defaults to `False`.
+    :vartype json_results: bool, optional
     """
     pipeline_fields: dict = Field(
         default = {
@@ -2537,6 +2542,7 @@ class StrainAnalysisProcessor(BaseStrainProcessor):
     setup: Optional[bool] = True
     update: Optional[bool] = True
     standalone: Optional[bool] = False
+    json_results: Optional[bool] = False
 
     @model_validator(mode='before')
     @classmethod
@@ -2792,9 +2798,12 @@ def process(self, data):
         else:
             result = self._get_values(results) if self.standalone \
                      else self._get_points(results)
-            if not (self._figures or self._animation):
-                return result
             ret = [result]
+            if self.json_results:
+                json_results = {k: v.tolist() for k, v in results.items()}
+                ret.append(json_results)
+            if not (self._figures or self._animation):
+                return tuple(ret)
         if self._figures:
             ret.append(
                 PipelineData(

From 925f136a5fa53f4753b183f026f1e3e079b46328 Mon Sep 17 00:00:00 2001
From: Keara Soloway <kls286@cornell.edu>
Date: Wed, 29 Apr 2026 10:29:06 -0400
Subject: [PATCH 30/76] add: scan_number option for
 PointByPointScanData.data_type

---
 CHAP/common/models/map.py | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/CHAP/common/models/map.py b/CHAP/common/models/map.py
index 52afbf40..65bbfb98 100755
--- a/CHAP/common/models/map.py
+++ b/CHAP/common/models/map.py
@@ -370,8 +370,8 @@ class PointByPointScanData(CHAPBaseModel):
     units: constr(strip_whitespace=True, min_length=1)
     data_type: Literal[
         'spec_motor', 'spec_motor_absolute', 'spec_motor_static',
-        'scan_column', 'scan_start_time', 'smb_par', 'expression',
-        'detector_log_timestamps', 'scan_step_index'
+        'scan_column', 'scan_number', 'scan_start_time', 'smb_par',
+        'expression', 'detector_log_timestamps', 'scan_step_index'
     ]
     name: constr(strip_whitespace=True, min_length=1)
     ndigits: Optional[conint(ge=0)] = None
@@ -557,6 +557,8 @@ def get_value(
                 return scan_step_index
             scanparser = get_scanparser(spec_scans.spec_file, scan_number)
             return [i for i in range(scanparser.spec_scan_npts)]
+        if self.data_type == 'scan_number':
+            return scan_number
         return None
 
 @cache

From 58b40a4f1d86441f3077b7b6ec9eda46129e2bd8 Mon Sep 17 00:00:00 2001
From: Keara Soloway <kls286@cornell.edu>
Date: Wed, 29 Apr 2026 11:02:45 -0400
Subject: [PATCH 31/76] fix: allow MapConfig.scalar_data to contain items with
 data_type==expression

---
 CHAP/common/models/map.py | 16 +++++++++++++++-
 1 file changed, 15 insertions(+), 1 deletion(-)

diff --git a/CHAP/common/models/map.py b/CHAP/common/models/map.py
index 65bbfb98..97ee496f 100755
--- a/CHAP/common/models/map.py
+++ b/CHAP/common/models/map.py
@@ -766,7 +766,9 @@ def _validate_data_source_for_map_config(data_source, info):
         if data_source is not None:
             values = info.data
             if data_source.data_type == 'expression':
-                data_source.validate_for_scalar_data(values['scalar_data'])
+                if 'scalar_data' in values:
+                    data_source.validate_for_scalar_data(
+                        values['scalar_data'])
             else:
                 import_scanparser(
                     values['station'], values['experiment_type'])
@@ -1126,6 +1128,18 @@ def validate_before(cls, data):
             data['attrs'] = {}
         return data
 
+    @model_validator(mode='after')
+    def validate_scalar_data_expressions(self):
+        """Validate any expression-type items in scalar_data against
+        the complete scalar_data list. This deferred check is necessary
+        because field validation of scalar_data runs before the list is
+        fully constructed.
+        """
+        for data_source in self.scalar_data:
+            if data_source.data_type == 'expression':
+                data_source.validate_for_scalar_data(self.scalar_data)
+        return self
+
     #RV maybe better to use model_validator, see v2 docs?
     @field_validator('attrs')
     @classmethod

From f868c510652dc264056b089f4b0c882856a132ab Mon Sep 17 00:00:00 2001
From: Keara Soloway <kls286@cornell.edu>
Date: Wed, 29 Apr 2026 14:55:18 -0400
Subject: [PATCH 32/76] fix: allow 1d detector shapes in DetectorConfig

---
 CHAP/common/models/map.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/CHAP/common/models/map.py b/CHAP/common/models/map.py
index 97ee496f..5d159fe8 100755
--- a/CHAP/common/models/map.py
+++ b/CHAP/common/models/map.py
@@ -65,7 +65,7 @@ class Detector(CHAPBaseModel):
     :type attrs: dict, optional
     """
     id_: constr(min_length=1) = Field(alias='id')
-    shape: Optional[tuple[int, int]] = None
+    shape: Optional[Union[tuple[int, int], tuple[int]]] = None
     attrs: Optional[Annotated[dict, Field(validate_default=True)]] = {}
 
     @field_validator('id_', mode='before')

From 519f989979f2925e2dd054f816f186730cb8333b Mon Sep 17 00:00:00 2001
From: Keara Soloway <kls286@cornell.edu>
Date: Thu, 30 Apr 2026 08:47:05 -0400
Subject: [PATCH 33/76] feat: support 0-scan MapConfigs

---
 CHAP/common/models/map.py | 10 ++++++++--
 CHAP/common/processor.py  | 38 ++++++++++++++++++++++++++++++++------
 2 files changed, 40 insertions(+), 8 deletions(-)

diff --git a/CHAP/common/models/map.py b/CHAP/common/models/map.py
index 5d159fe8..597385a6 100755
--- a/CHAP/common/models/map.py
+++ b/CHAP/common/models/map.py
@@ -159,7 +159,7 @@ class SpecScans(CHAPBaseModel):
     """
     spec_file: FilePath
     scan_numbers: Union[
-        constr(min_length=1), conlist(item_type=conint(gt=0), min_length=1)]
+        constr(min_length=1), conlist(item_type=conint(gt=0))]
     par_file: Optional[FilePath] = None
 
     @field_validator('spec_file')
@@ -1157,13 +1157,17 @@ def validate_attrs(cls, attrs, info):
         """
         # Get the map's scan_type for EDD experiments
         values = info.data
+        if not values['validate_data_present']:
+            return attrs
         station = values['station']
         experiment_type = values['experiment_type']
         if station in ['id1a3', 'id3a'] and experiment_type == 'EDD':
             scan_type = cls.get_smb_par_attr(values, 'scan_type')
             if scan_type is not None:
                 attrs['scan_type'] = scan_type
-            attrs['config_id'] = cls.get_smb_par_attr(values, 'config_id')
+            config_id = cls.get_smb_par_attr(values, 'config_id')
+            if config_id is not None:
+                attrs['config_id'] = config_id
             dataset_id = cls.get_smb_par_attr(
                 values, 'dataset_id', unique=False)
             if dataset_id is not None:
@@ -1215,6 +1219,8 @@ def get_smb_par_attr(
 #                        f'{scans.spec_file}.')
                     values.append(None)
         values = list(set(values))
+        if not values:
+            return None
         if len(values) == 1:
             return values[0]
         if unique:
diff --git a/CHAP/common/processor.py b/CHAP/common/processor.py
index 29792425..2d2f591c 100755
--- a/CHAP/common/processor.py
+++ b/CHAP/common/processor.py
@@ -1001,7 +1001,7 @@ def _process(
             spec_scans = self.config.spec_scans[0]
             scan_numbers = spec_scans.scan_numbers
             num_scan = len(scan_numbers)
-            if num_scan < self.num_proc:
+            if 0 < num_scan < self.num_proc:
                 self.logger.warning(
                     f'Requested number of processors ({self.num_proc}) exceeds '
                     f'the number of scans ({num_scan}): reset it to {num_scan}')
@@ -1085,7 +1085,16 @@ def _process(
                 offset = common_comm.scatter(offsets, root=0)
 
             # Read the raw data
-            if self.config.experiment_type == 'EDD':
+            if num_scan == 0:
+                num_id = len(self.config.independent_dimensions)
+                num_sd = len(self.config.all_scalar_data)
+                num_det = len(self.detector_config.detectors)
+                if placeholder_data is not False:
+                    num_sd += 1
+                data = np.empty((num_det, 0))
+                independent_dimensions = np.empty((num_id, 0))
+                all_scalar_data = np.empty((num_sd, 0))
+            elif self.config.experiment_type == 'EDD':
                 data, independent_dimensions, all_scalar_data = \
                     self._read_raw_data_edd(
                         common_comm, num_scan, offset, placeholder_data)
@@ -1093,7 +1102,8 @@ def _process(
                 data, independent_dimensions, all_scalar_data = \
                     self._read_raw_data(common_comm, num_scan, offset)
             if not rank:
-                self.logger.debug(f'Data shape: {data.shape}')
+                self.logger.debug(
+                    f'Data shape: {data.shape if data is not None else None}')
                 if independent_dimensions is not None:
                     self.logger.debug('Independent dimensions shape: '
                                       f'{independent_dimensions.shape}')
@@ -1142,6 +1152,11 @@ def _process(
             all_scalar_data = np.empty(
                 (len(self.config.all_scalar_data), map_len))
             if len(self.detector_config.detectors) > 0:
+                if det_shapes is False:
+                    det_shapes = {}
+                    for det in self.detector_config.detectors:
+                        if det.shape is not None:
+                            det_shapes[det.get_id()] = det.shape
                 data = np.empty(
                     (len(self.detector_config.detectors),
                      map_len,
@@ -1253,7 +1268,14 @@ def linkdims(nxgroup, nxdata_source):
             nxentry.attrs[k] = v
         nxentry.spec_scans = NXcollection()
         for scans in self.config.spec_scans:
-            nxentry.spec_scans[scans.scanparsers[0].scan_name] = \
+            if len(scans.scanparsers) > 0:
+                key = scans.scanparsers[0].scan_name
+            else:
+                if str(scans.spec_file).endswith('spec.log'):
+                    key = str(scans.spec_file).split('/')[-2]
+                else:
+                    key = str(scans.spec_file).split('/')[-1]
+            nxentry.spec_scans[key] = \
                 NXfield(value=scans.scan_numbers,
                         dtype='int8',
                         attrs={'spec_file': str(scans.spec_file)})
@@ -1369,8 +1391,12 @@ def linkdims(nxgroup, nxdata_source):
         for k, v in self.config.attrs.items():
             nxdata.attrs[k] = v
         if data is not None:
-            min_ = np.min(data, axis=tuple(range(1, data.ndim)))
-            max_ = np.max(data, axis=tuple(range(1, data.ndim)))
+            if data.size > 0:
+                min_ = np.min(data, axis=tuple(range(1, data.ndim)))
+                max_ = np.max(data, axis=tuple(range(1, data.ndim)))
+            else:
+                min_ = np.full(len(self.detector_config.detectors), np.nan)
+                max_ = np.full(len(self.detector_config.detectors), np.nan)
         for i, detector in enumerate(self.detector_config.detectors):
             nxdata[detector.get_id()] = NXfield(
                 value=data[i],

From 168f0bbb406d189b4082e96632f86b6bf82339c8 Mon Sep 17 00:00:00 2001
From: Keara Soloway <kls286@cornell.edu>
Date: Thu, 30 Apr 2026 09:33:50 -0400
Subject: [PATCH 34/76] add: JSONWriter.update and JSONWriter.extend

---
 CHAP/common/writer.py | 44 +++++++++++++++++++++++++++++++++++++++++--
 1 file changed, 42 insertions(+), 2 deletions(-)

diff --git a/CHAP/common/writer.py b/CHAP/common/writer.py
index 62c983ec..4e775ff9 100755
--- a/CHAP/common/writer.py
+++ b/CHAP/common/writer.py
@@ -424,14 +424,54 @@ class JSONWriter(Writer):
     :ivar index: Index of ``PipelineData`` item in input ``data`` list
         that should be written to the JSON file. Defaults to ``-1``.
     :vartpe index: int, Optional.
+    :ivar update: Update an existing file with new values, overwriting
+        the existing file's values. Defaults to ``False``.
+    :vartype update: bool, optional
+    :ivar extend: Extend the values in an existing file, adding to the
+        existing file's value lists. Defaults to ``False``.
+    :vartype extend: bool, optional
     """
     index: int = -1
+    update: Optional[bool] = False
+    extend: Optional[bool] = False
+
     def write(self, data):
         """Write the last """
         import json
-        _data = self.get_pipelinedata_item(data, remove=self.remove)
+
+        _data = self.get_pipelinedata_item(
+            data,
+            index=self.index,
+            remove=self.remove,
+        )
+
+        write_data = _data
+        if self.update:
+            try:
+                with open(self.filename, 'r') as inf:
+                    write_data = json.load(inf)
+            except:
+                self.logger.warning(f'Could not load JSON from {self.filename}')
+                write_data = {}
+            if self.extend:
+                for k, v in _data.items():
+                    if k in write_data:
+                        if not isinstance(write_data[k], list):
+                            write_data[k] = [write_data[k]]
+                        write_data[k].extend(v)
+                    else:
+                        write_data[k] = v
+            else:
+                write_data.update(_data)
+
         with open(self.filename, 'w') as outf:
-            json.dump(_data, outf)
+            json.dump(write_data, outf)
+
+    @model_validator(mode='after')
+    def validate_modes(self):
+        if self.extend and not self.update:
+            self.update = True
+        return self
 
 
 class MatplotlibAnimationWriter(Writer):

From e8ff4e3958c48b476aeb052b9fcea17b875cb773 Mon Sep 17 00:00:00 2001
From: Rolf Verberg <rv43@cornell.edu>
Date: Thu, 30 Apr 2026 11:52:31 -0400
Subject: [PATCH 35/76] test: Updated tomo_one_plane.py to use the hollow_cube
 example

---
 examples/tomo/tomo_one_plane.py | 182 ++++++++++++++++++++++----------
 1 file changed, 124 insertions(+), 58 deletions(-)

diff --git a/examples/tomo/tomo_one_plane.py b/examples/tomo/tomo_one_plane.py
index 353d760b..90770b31 100644
--- a/examples/tomo/tomo_one_plane.py
+++ b/examples/tomo/tomo_one_plane.py
@@ -1,11 +1,19 @@
 #!/usr/bin/env python3
 # -*- coding: utf-8 -*-
 
+"""Choose the path to your CHESS repo."""
 import sys
 #sys.path.append(
 #    '/home/rv43/Documents/Programs/repos/CHESSComputing/ChessAnalysisPipeline')
 sys.path.append(
-    '/nfs/chess/sw/CHESS-software-releases/repos/prod/ChessAnalysisPipeline')
+    '/home/rv43/Documents/Programs/repos/CHESSComputing/ChessAnalysisPipeline_main')
+#sys.path.append(
+#    '/nfs/chess/sw/CHESS-software-releases/repos/prod/ChessAnalysisPipeline')
+
+# System modules
+import os
+from pprint import pprint
+from tempfile import NamedTemporaryFile
 
 # Third party modules
 import matplotlib.pyplot as plt
@@ -29,74 +37,80 @@
 # Start user input
 #------------------------------------------------------------------------------#
 
+"""Select run_type from
+'normal':     Full regular reconstruction
+              (like running the default hollow_cube in CHAP)
+'one_plane':  Reconstruction of two planes only
+'two_planes': Reconstruction of one plane only
+'roi':        Reconstruction for a subset or rows
+              (find center at first and last row)
+"""
+#run_type = 'normal'
+#run_type = 'one_plane'
+#run_type = 'two_planes'
+run_type = 'roi'
+
 interactive = True
+outputdir = 'output'
 construct_chess_map = True
-map_name = 'output/map.nxs'
-chess_map_name = 'output/chess_map.nxs'
-load_converted_map = True
-img_row_bounds = [600, 606] # None, [80, 2080] or [1050, 1251]
-recon_layer_index = [600, 1400] # One or two values
-                                # ignored when using img_row_bounds
 reduce_data = True
-reduced_data_name = 'output/reduced_data.nxs'
+find_center = True
+reconstruct_data = True
+
+map_name = f'{outputdir}/map.nxs'
+chess_map_name = f'{outputdir}/chess_map.nxs'
+reduced_data_name = f'{outputdir}/reduced_data.nxs'
 reduce_config = {
-    'remove_stripe': {'remove_all_stripe': {}},
-    'img_row_bounds': img_row_bounds,
+#    'remove_stripe': {'remove_all_stripe': {}},
 }
-find_center = True
-find_center_name = 'output/find_center.yaml'
+find_center_name = f'{outputdir}/find_center.yaml'
 find_center_config = {
-    'gaussian_sigma': 0.75,
+    'gaussian_sigma': 0.05,
 #    'remove_stripe_sigma': None,
-    'ring_width': 5,
+    'ring_width': 1,
 }
-reconstruct_data = True
-reconstructed_data_name = 'output/reconstructed_data.nxs'
+reconstructed_data_name = f'{outputdir}/reconstructed_data.nxs'
 reconstruct_config = {
-    'x_bounds': [90, 2470],
-    'y_bounds': [600, 2000],
-    'secondary_iters:': 25,
-    'gaussian_sigma': 0.75,
-    'remove_stripe_sigma': None,
-    'ring_width': 5,
+    'x_bounds': [15, 390],
+    'y_bounds': [25, 380],
+    'secondary_iters': 10,
+#    'gaussian_sigma': 0.75,
+#    'remove_stripe_sigma': None,
+    'ring_width': 1,
 }
 tdf_scan_numbers = 1
 tbf_scan_numbers = 2
 map_config = {
-    'title': 'badran-4510-b',
+    'title': 'hollow_cube',
     'station': 'id3b',
     'experiment_type': 'TOMO',
-    'sample': {'name': 'sample_190-1-Edge'},
+    'sample': {'name': 'hollow_cube'},
     'spec_scans': [
-        {'spec_file': 'data/sample_190-1-Edge/refine_1',
+        {'spec_file': 'raw/hollow_cube/hollow_cube',
          'scan_numbers': 3}
     ],
     'independent_dimensions': [
         {'label': 'rotation_angles',
          'units': 'degrees',
          'data_type': 'scan_column',
-         'name': 'GI_samphi'},
+         'name': 'theta'},
         {'label': 'x_translation',
          'units': 'mm',
          'data_type': 'spec_motor',
-         'name': 'saxx'},
+         'name': 'GI_samx'},
         {'label': 'z_translation',
          'units': 'mm',
          'data_type': 'spec_motor',
-         'name': 'saxz'}
+         'name': 'GI_samz'}
     ],
-    'presample_intensity': {
-        'data_type': 'scan_column',
-        'name': 'ic1'
-    }
 }
-detector_config = {'detectors': [{'id': 'andor2'}],}
+detector_config = {'detectors': [{'id': 'sim'}],}
 detector_setup = {
-    'prefix': 'andor2',
-    'rows': 2160,
-    'columns': 2560,
-    'pixel_size': [0.0065, 0.0065],
-    'lens_magnification': 5.0,
+    'prefix': 'sim',
+    'rows': 40,
+    'columns': 400,
+    'pixel_size': [0.05, 0.005],
+    'lens_magnification': 1.0,
 }
 remove_stripe_corrections = [
 #    'remove_all_stripe',
@@ -111,34 +125,86 @@
 #    'remove_stripe_ti',
 ]
 
+#------------------------------------------------------------------------------#
+# Optional user input
+#------------------------------------------------------------------------------#
+
+if run_type == 'normal':
+    img_row_bounds = [3, 35]
+    recon_layer_indices = [11, 28]
+elif run_type == 'one_plane':
+    img_row_bounds = None
+    recon_layer_indices = 15
+elif run_type == 'two_planes':
+    img_row_bounds = None
+    recon_layer_indices = [11, 20]
+elif run_type == 'roi':
+    img_row_bounds = None
+    recon_layer_indices = [11, 20]
+else:
+    print('Pick valid values for img_row_bounds and recon_layer_indices')
+    img_row_bounds = None       # list[int, int], optional
+    recon_layer_indices = None  # int | list[int, int], optional
+                                # ignored when using img_row_bounds
+
 #------------------------------------------------------------------------------#
 # End user input
 #------------------------------------------------------------------------------#
 
+if not os.path.isdir(outputdir):
+    os.makedirs(outputdir)
+try:
+    NamedTemporaryFile(dir=outputdir)
+except Exception as exc:
+    raise OSError(
+        'Output directory not accessible for writing ({outputdir})') from exc
+
+if isinstance(recon_layer_indices, int):
+    recon_layer_indices = [recon_layer_indices]
 if img_row_bounds is None:
-    if len(recon_layer_index)== 1:
+    center_rows = None
+    if len(recon_layer_indices)== 1:
         detector_config['roi'] = [
-            {'start': recon_layer_index,
-             'end': recon_layer_index+1,
+            {'start': recon_layer_indices[0],
+             'end': recon_layer_indices[0]+1,
              'step': None},
             None]
-    elif len(recon_layer_index) == 2:
+    elif len(recon_layer_indices) == 2:
         detector_config['roi'] = [
-            {'start': recon_layer_index[0],
-             'end': recon_layer_index[1],
-             'step': recon_layer_index[1]-recon_layer_index[0]-1},
+            {'start': recon_layer_indices[0],
+             'end': recon_layer_indices[1]},
             None]
+        if run_type == 'two_planes':
+            detector_config['roi'][0]['step'] = \
+                recon_layer_indices[1]-recon_layer_indices[0]-1
+        else:
+            detector_config['roi'][0]['step'] = None
     else:
-        print('Invalid value for recon_layer_index ({recon_layer_index})')
-        exit()
+        raise RuntimeError('Invalid value for recon_layer_indices ({recon_layer_indices})')
 else:
     assert len(img_row_bounds) == 2
-    recon_layer_index = []
-    detector_config['roi'] = [
-        {'start': img_row_bounds[0],
-         'end': img_row_bounds[1],
-         'step': 1},
-        None]
+    center_rows = recon_layer_indices
+    recon_layer_indices = []
+
+reduce_config['img_row_bounds'] = img_row_bounds
+find_center_config['center_rows'] = center_rows
+
+#------------------------------------------------------------------------------#
+
+if construct_chess_map:
+    print(f'\nmap_config:')
+    pprint(map_config)
+if reduce_data:
+    print(f'\nreduce_config:')
+    pprint(reduce_config)
+if find_center:
+    print(f'\nfind_center_config:')
+    pprint(find_center_config)
+if reconstruct_data:
+    print(f'\nreconstruct_config:')
+    pprint(reconstruct_config)
+print(f'\ndetector_config:')
+pprint(detector_config)
 
 # Construct the CHESS style tomo map
 if not construct_chess_map:
@@ -197,9 +263,7 @@
 if not reduce_data:
     nxroot = nxload(reduced_data_name)
 else:
-    # Load as needed
-    if load_converted_map:
-        nxroot = nxload(chess_map_name)
+    nxroot = nxload(chess_map_name)
     # Reduce the data with remove_all_stripe
     data = [
         PipelineData(name='TomoCHESSMapConverter', data=nxroot, schema=None)]
@@ -222,7 +286,7 @@
     image_slice = nxdata.nxsignal[0,:,0,:]
     vmin = image_slice.min()
     vmax = image_slice.max()
-    if len(recon_layer_index):
+    if len(recon_layer_indices):
         quick_imshow(
             image_slice,
             title=f'Slice {detector_config["roi"][0]["start"]}',
@@ -231,7 +295,7 @@
             vmin=vmin, vmax=vmax,
             save_fig=True,
             block=True)
-    if len(recon_layer_index) == 2:
+    if len(recon_layer_indices) == 2:
         quick_imshow(
             image_slice,
             title=f'Slice {detector_config["roi"][0]["end"]}',
@@ -300,6 +364,8 @@
 #            name='TomoFindCenterProcessor', data=center_config,
 #            schema='tomo.models.TomoFindCenterConfig')
     ]
+    from pprint import pprint
+    pprint(reconstruct_config)
     tomo = TomoReconstructProcessor(
         config=reconstruct_config,
         center_config=center_config,

From 7610912b5fc4142810ebdc3071a1cd0bd6d2d0ed Mon Sep 17 00:00:00 2001
From: Rolf Verberg <rv43@cornell.edu>
Date: Thu, 30 Apr 2026 11:56:10 -0400
Subject: [PATCH 36/76] test: renamed tomo script consistent with CHAP pipeline
 version

---
 examples/tomo/{tomo_one_plane.py => tomo_script_id3b.py} | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 rename examples/tomo/{tomo_one_plane.py => tomo_script_id3b.py} (100%)

diff --git a/examples/tomo/tomo_one_plane.py b/examples/tomo/tomo_script_id3b.py
similarity index 100%
rename from examples/tomo/tomo_one_plane.py
rename to examples/tomo/tomo_script_id3b.py

From a27102a0ac17cc6a716c10ef2b132405ef1b67ea Mon Sep 17 00:00:00 2001
From: Keara Soloway <kls286@cornell.edu>
Date: Thu, 30 Apr 2026 12:06:24 -0400
Subject: [PATCH 37/76] feat: support processing multiple scans with
 MapSliceProcessor

---
 CHAP/common/map_utils.py | 287 +++++++++++++++++++++++++++------------
 1 file changed, 200 insertions(+), 87 deletions(-)

diff --git a/CHAP/common/map_utils.py b/CHAP/common/map_utils.py
index 5515d358..531a2157 100644
--- a/CHAP/common/map_utils.py
+++ b/CHAP/common/map_utils.py
@@ -3,9 +3,11 @@
 from pydantic import (
     conint,
     conlist,
+    model_validator,
     Field,
     FilePath,
 )
+from typing import Optional
 
 # Local modules
 from CHAP import Processor
@@ -45,9 +47,9 @@ class MapSliceProcessor(Processor):
     :ivar spec_file: SPEC file containing scan from which to read a
         slice of raw data.
     :type spec_file: pydantic.FilePath
-    :ivar scan_number: Number of scan from which to read a slice of
+    :ivar scan_numbers: Numbers of scans from which to read slices of
         raw data.
-    :type scan_number: int
+    :type scan_numbers: list[int]
     """
     pipeline_fields: dict = Field(
         default={
@@ -57,23 +59,29 @@ class MapSliceProcessor(Processor):
     map_config: MapConfig
     detectors: conlist(item_type=Detector, min_length=1)
     spec_file: FilePath
-    scan_number: conint(gt=0)
+    scan_number: Optional[conint(gt=0)] = None
+    scan_numbers: Optional[conlist(item_type=conint(gt=0))] = None
 
     def process(self, data,
                 idx_slice={'start': 0, 'step': 1}):
-        """Aggregate partial spec and detector data from one scan in a
-        map, returning results in a format suitable for writing to the
-        full map container with `common.NexusValuesWriter` or
-        `common.ZarrValuesWriter`.
+        """Aggregate partial spec and detector data from one or more
+        scans in a map, returning results in a format suitable for
+        writing to the full map container with
+        `common.NexusValuesWriter` or `common.ZarrValuesWriter`.
+
+        When all scans are adjacent in the map and `idx_slice` covers
+        each scan in full, data_points entries for the same path are
+        consolidated into a single array + slice, avoiding redundant
+        write calls.
 
         :param data: Result of `Reader.read` where at least one item
             has the value `'common.models.map.MapConfig'` for the
             `'schema'` key.
         :type data: list[PipelineData]
-        :type idx_slice: Parameters for the slice of the scan to
+        :param idx_slice: Parameters for the slice of each scan to
             process (slice parameters are the usual for the python
-            `slice` object: `'start'`, `'stop'`, and
-            `'step'`). Defaults to `{'start': 0, 'step': '1'}`.
+            `slice` object: `'start'`, `'stop'`, and `'step'`).
+            Defaults to `{'start': 0, 'step': 1}`.
         :type idx_slice: dict[str, int], optional
         :return: Slice of map data, ready to be written to a map
              container.
@@ -81,102 +89,207 @@ def process(self, data,
         """
         import numpy as np
         import os
-        from chess_scanparsers import choose_scanparser
-
         from CHAP.common.models.map import SpecScans
 
-        ScanParser = choose_scanparser(
-            self.map_config.station, self.map_config.experiment_type)
-        scans = SpecScans(
-            spec_file=self.spec_file, scan_numbers=[self.scan_number])
-        scan = scans.get_scanparser(self.scan_number)
+        scans_obj = SpecScans(
+            spec_file=self.spec_file, scan_numbers=self.scan_numbers)
+        self_spec_file_abs = os.path.abspath(str(self.spec_file))
+
+        if self.map_config.experiment_type == 'EDD':
+            def get_detector_data(scan, detector, index):
+                return scan.get_detector_data(detector.get_id(), index)[0][0]
+        else:
+            def get_detector_data(scan, detector, index):
+                return scan.get_detector_data(detector.get_id(), index)
 
-        # Get index offset for this data slice within the map
-        npts_scan = int(scan.spec_scan_npts)
-        nscans_prev = 0
-        for scans in self.map_config.spec_scans:
-            for scan_n in scans.scan_numbers:
-                if (os.path.abspath(self.spec_file) == \
-                    os.path.abspath(self.spec_file)
-                    and scan_n == self.scan_number):
+        # Build flat ordered list of (abs_spec_file, scan_number) for
+        # all scans in the map to determine each scan's map position
+        map_scan_order = []
+        for spec_scans_item in self.map_config.spec_scans:
+            sf_abs = os.path.abspath(str(spec_scans_item.spec_file))
+            for sn in spec_scans_item.scan_numbers:
+                map_scan_order.append((sf_abs, sn))
+        scan_positions = {}
+        for sn in self.scan_numbers:
+            for pos, (sf, n) in enumerate(map_scan_order):
+                if sf == self_spec_file_abs and n == sn:
+                    scan_positions[sn] = pos
                     break
-                nscans_prev += 1
-        index_offset = nscans_prev * npts_scan
 
-        # Get spec scan indices to process
-        scan_indices = range(npts_scan)[slice(
-            idx_slice.get('start', 0),
-            idx_slice.get('stop', npts_scan),
-            idx_slice.get('step', 1)
-        )]
-        # Get map indices to write to
-        map_indices = slice(
-            idx_slice.get('start', 0) + index_offset,
-            idx_slice.get('stop', npts_scan) + index_offset,
-            idx_slice.get('step', 1)
+        # Process scans in map order
+        sorted_scan_numbers = sorted(
+            self.scan_numbers, key=lambda sn: scan_positions[sn])
+
+        slice_start = idx_slice.get('start', 0)
+        slice_step = idx_slice.get('step', 1)
+
+        # Collect per-scan metadata; assumes uniform npts across scans
+        # for index_offset calculation (index_offset = map_pos * npts)
+        per_scan = []
+        for sn in sorted_scan_numbers:
+            scan = scans_obj.get_scanparser(sn)
+            npts_scan = int(scan.spec_scan_npts)
+            index_offset = scan_positions[sn] * npts_scan
+            # Cap stop at npts_scan so map_indices and data stay in sync
+            slice_stop = min(idx_slice.get('stop', npts_scan), npts_scan)
+            scan_indices = range(npts_scan)[
+                slice(slice_start, slice_stop, slice_step)]
+            map_indices = slice(
+                slice_start + index_offset,
+                slice_stop + index_offset,
+                slice_step,
+            )
+            per_scan.append({
+                'sn': sn, 'scan': scan, 'npts_scan': npts_scan,
+                'index_offset': index_offset,
+                'scan_indices': scan_indices,
+                'map_indices': map_indices,
+                'full': (slice_start == 0
+                         and slice_step == 1
+                         and slice_stop == npts_scan),
+            })
+
+        # Consolidate into single data_points entries when all scans
+        # are adjacent in the map and idx_slice covers each scan fully
+        sorted_positions = [scan_positions[sn] for sn in sorted_scan_numbers]
+        scans_are_adjacent = all(
+            sorted_positions[i + 1] == sorted_positions[i] + 1
+            for i in range(len(sorted_positions) - 1)
+        )
+        can_consolidate = (
+            len(per_scan) > 1
+            and scans_are_adjacent
+            and all(ps['full'] for ps in per_scan)
         )
 
-        data_points = [
-            {
-                'path': f'{self.map_config.title}/independent_dimensions/index',
-                'data': np.asarray(
-                    [i for i in range(index_offset, index_offset + npts_scan)]
+        if can_consolidate:
+            first, last = per_scan[0], per_scan[-1]
+            merged_idx = slice(
+                first['index_offset'],
+                last['index_offset'] + last['npts_scan'],
+                1,
+            )
+            data_points = [{
+                'path': (f'{self.map_config.title}'
+                         f'/independent_dimensions/index'),
+                'data': np.arange(
+                    first['index_offset'],
+                    last['index_offset'] + last['npts_scan'],
                 ),
-                'idx': map_indices
-            }
-        ]
-        data_points.extend(
-            [
-                {
-                    'path': f'{self.map_config.title}/scalar_data/{s_d.label}',
+                'idx': merged_idx,
+            }]
+            for s_d in self.map_config.all_scalar_data:
+                data_points.append({
+                    'path': (f'{self.map_config.title}'
+                             f'/scalar_data/{s_d.label}'),
+                    'data': np.concatenate([
+                        np.asarray([
+                            s_d.get_value(
+                                scans_obj, ps['sn'], i,
+                                scalar_data=self.map_config.scalar_data)
+                            for i in ps['scan_indices']
+                        ])
+                        for ps in per_scan
+                    ]),
+                    'idx': merged_idx,
+                })
+            for dim in self.map_config.independent_dimensions:
+                data_points.append({
+                    'path': (f'{self.map_config.title}'
+                             f'/independent_dimensions/{dim.label}'),
+                    'data': np.concatenate([
+                        np.asarray([
+                            dim.get_value(
+                                scans_obj, ps['sn'], i,
+                                scalar_data=self.map_config.scalar_data)
+                            for i in ps['scan_indices']
+                        ])
+                        for ps in per_scan
+                    ]),
+                    'idx': merged_idx,
+                })
+            for det in self.detectors:
+                data_points.append({
+                    'path': (f'{self.map_config.title}'
+                             f'/data/{det.get_id()}'),
+                    'data': np.concatenate([
+                        np.asarray([
+                            get_detector_data(ps['scan'], det, i)
+                            for i in ps['scan_indices']
+                        ])
+                        for ps in per_scan
+                    ]),
+                    'idx': merged_idx,
+                })
+        else:
+            data_points = []
+            for ps in per_scan:
+                data_points.append({
+                    'path': (f'{self.map_config.title}'
+                             f'/independent_dimensions/index'),
+                    'data': np.asarray(
+                        [ps['index_offset'] + i for i in ps['scan_indices']]
+                    ),
+                    'idx': ps['map_indices'],
+                })
+                data_points.extend([{
+                    'path': (f'{self.map_config.title}'
+                             f'/scalar_data/{s_d.label}'),
                     'data': np.asarray([
                         s_d.get_value(
-                            scans, self.scan_number, i,
+                            scans_obj, ps['sn'], i,
                             scalar_data=self.map_config.scalar_data)
-                        for i in scan_indices
+                        for i in ps['scan_indices']
                     ]),
-                    'idx': map_indices
-                }
-                for s_d in self.map_config.all_scalar_data
-            ]
-        )
-        data_points.extend(
-            [
-                {
-                    'path': f'{self.map_config.title}/independent_dimensions/{dim.label}',
+                    'idx': ps['map_indices'],
+                } for s_d in self.map_config.all_scalar_data])
+                data_points.extend([{
+                    'path': (f'{self.map_config.title}'
+                             f'/independent_dimensions/{dim.label}'),
                     'data': np.asarray([
                         dim.get_value(
-                            scans, self.scan_number, i,
-                            scalar_data=self.map_config.scalar_data
-                        )
-                        for i in scan_indices
+                            scans_obj, ps['sn'], i,
+                            scalar_data=self.map_config.scalar_data)
+                        for i in ps['scan_indices']
                     ]),
-                    'idx': map_indices,
-                }
-                for dim in self.map_config.independent_dimensions
-            ]
-        )
-        if self.map_config.experiment_type == 'EDD':
-            def get_detector_data(detector, index):
-                return scan.get_detector_data(detector.get_id(), index)[0][0]
-        else:
-            def get_detector_data(detector, index):
-                return scan.get_detector_data(detector.get_id(), index)
-        data_points.extend(
-            [
-                {
-                    'path': f'{self.map_config.title}/data/{det.get_id()}',
+                    'idx': ps['map_indices'],
+                } for dim in self.map_config.independent_dimensions])
+                data_points.extend([{
+                    'path': (f'{self.map_config.title}'
+                             f'/data/{det.get_id()}'),
                     'data': np.asarray([
-                        get_detector_data(det, i)
-                        for i in scan_indices
+                        get_detector_data(ps['scan'], det, i)
+                        for i in ps['scan_indices']
                     ]),
-                    'idx': map_indices
-                }
-                for det in self.detectors
-            ]
-        )
+                    'idx': ps['map_indices'],
+                } for det in self.detectors])
         return data_points
 
+    @model_validator(mode='before')
+    @classmethod
+    def fill_scan_numbers(cls, data):
+        if not isinstance(data, dict):
+            return data
+        if 'scan_numbers' not in data or data['scan_numbers'] is None:
+            if data.get('scan_number') is not None:
+                data['scan_numbers'] = [data['scan_number']]
+        elif isinstance(data['scan_numbers'], int):
+            data['scan_numbers'] = [data['scan_numbers']]
+        elif isinstance(data['scan_numbers'], str):
+            from CHAP.utils.general import string_to_list
+            data['scan_numbers'] = string_to_list(data['scan_numbers'])
+        return data
+
+    @model_validator(mode='after')
+    def validate_scan_numbers(self):
+        if self.scan_numbers is None:
+            raise ValueError(
+                'scan_numbers is required; alternatively, provide scan_number')
+        if self.scan_number is not None \
+           and self.scan_number not in self.scan_numbers:
+            self.scan_numbers.append(self.scan_number)
+        return self
+
 
 class SpecScanToMapConfigProcessor(Processor):
     """Processor to get the `CHAP.common.models.map.MapConfig`

From 9cf6b798fb8dec8c4e734b4a22d47b2656556155 Mon Sep 17 00:00:00 2001
From: Keara Soloway <kls286@cornell.edu>
Date: Thu, 30 Apr 2026 12:07:52 -0400
Subject: [PATCH 38/76] add: support reading data from multiple scans with
 edd.SliceNXdataReader

---
 CHAP/edd/reader.py | 35 +++++++++++++++++++++++++++++++----
 1 file changed, 31 insertions(+), 4 deletions(-)

diff --git a/CHAP/edd/reader.py b/CHAP/edd/reader.py
index ad4eb757..db3cf934 100755
--- a/CHAP/edd/reader.py
+++ b/CHAP/edd/reader.py
@@ -15,6 +15,7 @@
     conlist,
     constr,
     field_validator,
+    model_validator,
 )
 
 # Local modules
@@ -749,10 +750,12 @@ class SliceNXdataReader(Reader):
     from an NXdata group and slices all fields according to the
     provided slicing parameters.
  
-    :param scan_number: Number of the SPEC scan.
-    :vartype scan_number: int
+    :ivar scan_numbers: Numbers of scans from which to read slices of
+        raw data.
+    :type scan_numbers: list[int]
     """
-    scan_number: conint(ge=0)
+    scan_number: Optional[conint(gt=0)] = None
+    scan_numbers: Optional[conlist(item_type=conint(gt=0))] = None
 
     def read(self):
         """Reads an NXdata group from a NeXus file and slices the
@@ -811,7 +814,7 @@ def read(self):
 
         # Get indicies of SCAN_N that match self.scan_number
         scan_field = nxdata['SCAN_N'].nxdata
-        indices = np.flatnonzero(scan_field == self.scan_number)
+        indices = np.flatnonzero(np.isin(scan_field, self.scan_numbers))
 
         if indices.size == 0:
             self.logger.warning(
@@ -827,6 +830,30 @@ def read(self):
 
         return nxroot
 
+    @model_validator(mode='before')
+    @classmethod
+    def fill_scan_numbers(cls, data):
+        if not isinstance(data, dict):
+            return data
+        if 'scan_numbers' not in data or data['scan_numbers'] is None:
+            if data.get('scan_number') is not None:
+                data['scan_numbers'] = [data['scan_number']]
+        elif isinstance(data['scan_numbers'], int):
+            data['scan_numbers'] = [data['scan_numbers']]
+        elif isinstance(data['scan_numbers'], str):
+            from CHAP.utils.general import string_to_list
+            data['scan_numbers'] = string_to_list(data['scan_numbers'])
+        return data
+
+    @model_validator(mode='after')
+    def validate_scan_numbers(self):
+        if self.scan_numbers is None:
+            raise ValueError(
+                'scan_numbers is required; alternatively, provide scan_number')
+        if self.scan_number is not None \
+           and self.scan_number not in self.scan_numbers:
+            self.scan_numbers.append(self.scan_number)
+        return self
 
 class UpdateNXdataReader(Reader):
     """Companion to `edd.SetupNXdataReader` and

From 9fba14e627b999f7014bc1c0bc412252bea06d43 Mon Sep 17 00:00:00 2001
From: Rolf Verberg <rv43@cornell.edu>
Date: Thu, 30 Apr 2026 20:34:01 -0400
Subject: [PATCH 39/76] add: simplified script based calling and added an EDD
 calib script

Also update the tomo script to the new CHAP calling style
---
 CHAP/common/processor.py               |   2 +-
 CHAP/common/reader.py                  |   9 +-
 CHAP/models.py                         |   6 +-
 CHAP/pipeline.py                       |  71 ++++++++++-
 CHAP/utils/fit.py                      |  24 ++--
 CHAP/utils/general.py                  |   8 +-
 CHAP/utils/models.py                   |   4 +-
 examples/edd/edd_calibration_script.py | 158 +++++++++++++++++++++++++
 examples/tomo/tomo_script_id3b.py      | 118 +++++++++---------
 9 files changed, 306 insertions(+), 94 deletions(-)
 create mode 100644 examples/edd/edd_calibration_script.py

diff --git a/CHAP/common/processor.py b/CHAP/common/processor.py
index 0d198c11..0665b101 100755
--- a/CHAP/common/processor.py
+++ b/CHAP/common/processor.py
@@ -2422,7 +2422,7 @@ def process(
         :type npt: int
         :param mask_file: File to use for masking the input data.
         :type mask_file: str, optional
-        :param integrate1d_kwargs: Optional dictionary of keywords
+        :param integrate1d_kwargs: Optional dictionary of keywords.
         :type integrate1d_kwargs: Optional[dict]
         :returns: Azimuthal integration results as a dictionary of
             numpy arrays.
diff --git a/CHAP/common/reader.py b/CHAP/common/reader.py
index 398fe189..8d6042bc 100755
--- a/CHAP/common/reader.py
+++ b/CHAP/common/reader.py
@@ -550,7 +550,7 @@ class PandasReader(Reader):
     `pandas <https://pandas.pydata.org/docs/index.html>`__
     """
 
-    def read(self, filename, method='read_csv', comment='#', kwargs=None):
+    def read(self, filename, method='read_csv', comment='#', **kwargs):
         """Return a `pandas.DataFrame` read from the given file.
 
         :param filename: Name of file to read from.
@@ -561,9 +561,9 @@ def read(self, filename, method='read_csv', comment='#', kwargs=None):
         :param comment: Character to identify comment lines in the
             input file, defaults to `'#'`.
         :type comment: str, optional
-        :param kwargs: Additional keyword arguments to supply to the
+        :param \*\*kwargs: Additional keyword arguments to supply to the
             `pandas` reader.
-        :param kwargs: dict, optional.
+        :type: dict, optional.
         :rtype: `pandas.DataFrame`
         """
         # Third party modules
@@ -575,8 +575,6 @@ def read(self, filename, method='read_csv', comment='#', kwargs=None):
             raise ValueError(
                 f'{method} is not a callable pandas reader method')
 
-        if kwargs is None:
-            kwargs = {}
         if not isinstance(kwargs, dict):
             raise TypeError(
                 f'Invalid kwargs type ({type(kwargs)}, should be dict)')
@@ -921,7 +919,6 @@ def read(self):
                             detector_roi=[
                                self.detector_config.roi[0].toslice(),
                                self.detector_config.roi[1].toslice()]
-                        print(f'\n\ndetector_roi: {detector_roi}\n\n')
                         nxdata[detector.get_id()] = NXfield(
                            value=scanparser.get_detector_data(
                                detector.get_id(),
diff --git a/CHAP/models.py b/CHAP/models.py
index 7a7df819..9b4ad36c 100755
--- a/CHAP/models.py
+++ b/CHAP/models.py
@@ -34,7 +34,7 @@ def dict(self, *args, **kwargs):
         """Dump the class implemention to a dictionary.
 
         :param \*\*kwargs: Arbitrary keyword arguments.
-        :type: dict
+        :type: dict, optional
         :keyword exclude: Class variable(s) to omit from the output
             dictionary.
         :type exclude: dict or set, optional
@@ -50,7 +50,7 @@ def model_dump(self, *args, **kwargs):
         """Dump the class implemention to a dictionary.
 
         :param \*\*kwargs: Arbitrary keyword arguments.
-        :type: dict
+        :type: dict, optional
         :keyword exclude: Class variable(s) to omit from the output
             dictionary.
         :type exclude: dict or set, optional
@@ -71,7 +71,7 @@ def model_dump_json(self, *args, **kwargs):
         """Dump the class implemention to a JSON string.
 
         :param \*\*kwargs: Arbitrary keyword arguments.
-        :type: dict
+        :type: dict, optional
         :keyword exclude: Class variable(s) to omit from the output
             dictionary.
         :type exclude: dict or set, optional
diff --git a/CHAP/pipeline.py b/CHAP/pipeline.py
index ce854e1f..47df472d 100755
--- a/CHAP/pipeline.py
+++ b/CHAP/pipeline.py
@@ -444,18 +444,17 @@ def unwrap_pipelinedata(data):
             unwrapped_data = [data]
         return unwrapped_data
 
-    def execute(self, data):#, metadata, provenance):
+    def execute(self, data=None):#, metadata, provenance):
         """Execute the appropriate method of the object and return the
         result.
 
         :param data: Input data.
-        :type data: list[PipelineData]
+        :type data: list[PipelineData], optional
         :return: Wrapped result of executing read, process, or write.
         :rtype: PipelineData | tuple[PipelineData]
         """
 #        self._metadata = metadata
 #        self._provenance = provenance
-
         if 'data' in self._allowed_args:
             self._args['data'] = data
         t0 = time()
@@ -467,6 +466,72 @@ def execute(self, data):#, metadata, provenance):
             f'Finished "{self._method}" in {time()-t0:.0f} seconds\n')
         return data
 
+    @classmethod
+    def run(cls, **kwargs):
+        """Execute the appropriate method of the object and return the
+        result.
+
+        This class method gets and executes the appropriate method
+        (process, read or write) from the pipeline item it's called
+        from.  It is intended to be called from a script or notebook
+        only and should not be called from other CHAP Processors,
+        Readers or Writers.
+
+        The method expects the same parameters as those used to
+        instantiate its class object and run the process, read or
+        write method, in addition to any run time parameter in the
+        pipeline file config dictionary (see:
+        :class:`~CHAP.models.RunConfig)`.
+
+        :param \*\*kwargs: Arbitrary keyword arguments, including:
+        :type: dict, optional
+        :keyword config: Initialization parameters for an instance
+            of the pipeline item this method is called from (often
+            used by Readers and Processors).
+        :type config: dict, optional
+        :keyword data: Input data (required for any Processor, but
+            is allowed to be `None` or `[]`).
+        :type data: list[PipelineData], optional
+        :keyword filename: Name of file to read (required for most
+            Readers and Writers).
+        :type filename: str, optional
+        :keyword force_overwrite: Flag to allow data in `filename`
+            to be overwritten if it already exists, defaults to
+            `False` (optional for Writers).
+        :type force_overwrite: bool, optional
+        :keyword remove: Flag to remove the dictionary from `data`,
+            defaults to `False` (optional for Writers).
+        :type remove: bool, optional
+        :return: Returned result from executing the underlying read,
+            process, or write method.
+        :rtype: Any
+        """
+        # System modules
+        from importlib import import_module
+        from inspect import isclass
+        from pkgutil import walk_packages
+
+        def _find_class_in_package(package_name, class_name):
+            package = import_module(package_name)
+            # Recursively walk through all submodules
+            for _, module_name, _ in walk_packages(
+                    package.__path__, package.__name__ + "."):
+                try:
+                    module = import_module(module_name)
+                    # Check if the class exists in this module
+                    if hasattr(module, class_name):
+                        cls = getattr(module, class_name)
+                        if isclass(cls) and cls.__module__ == module_name:
+                            return cls
+                except ImportError:
+                    continue
+            return None
+
+        cls_name = cls.__name__
+        mmc = _find_class_in_package('CHAP', cls_name)
+        item = mmc(modelmetaclass=mmc, **kwargs)
+        return item.execute(kwargs.get('data'))
+
 
 class Pipeline(CHAPBaseModel):
     """Class representing a full `Pipeline` object.
diff --git a/CHAP/utils/fit.py b/CHAP/utils/fit.py
index c626b74b..6f65c6ed 100755
--- a/CHAP/utils/fit.py
+++ b/CHAP/utils/fit.py
@@ -1258,9 +1258,9 @@ def fit(self, config=None, **kwargs):
 
         :param config: Fit configuration.
         :type config: CHAP.utils.models.FitConfig, optional
-        :param kwargs: Additional key, value pairs to pass on directly
-            to the core fit routine.
-        :type kwargs: dict
+        :param \*\*kwargs: Additional key, value pairs to pass on
+            directly to the core fit routine.
+        :type: dict, optional
         """
         # Check input parameters
         if self._model is None:
@@ -1359,9 +1359,9 @@ class attribute.
         :type plot_residual: bool, optional
         :param plot_masked_data:
         :type plot_masked_data: bool, optional
-        :param kwargs: Additional key, value pairs to pass on directly
-            to the Matplotlib plot function.
-        :type kwargs: dict
+        :param \*\*kwargs: Additional key, value pairs to pass on
+            directly to the Matplotlib plot function.
+        :type: dict, optional
         """
         if result is None:
             result = self._result
@@ -2645,9 +2645,9 @@ def plot(
         :type plot_residual: bool, optional
         :param plot_masked_data:
         :type plot_masked_data: bool, optional
-        :param kwargs: Additional key, value pairs to pass on directly
-            to the Matplotlib plot function.
-        :type kwargs: dict
+        :param \*\*kwargs: Additional key, value pairs to pass on
+            directly to the Matplotlib plot function.
+        :type: dict, optional
         """
         # Third party modules
         from lmfit.models import ExpressionModel
@@ -2720,9 +2720,9 @@ def fit(self, config=None, **kwargs):
 
         :param config: Fit configuration.
         :type config: CHAP.utils.models.FitConfig, optional
-        :param kwargs: Additional key, value pairs to pass on directly
-            to the core fit routine.
-        :type kwargs: dict
+        :param \*\*kwargs: Additional key, value pairs to pass on
+            directly to the core fit routine.
+        :type: dict, optional
         """
         # Check input parameters
         if self._model is None:
diff --git a/CHAP/utils/general.py b/CHAP/utils/general.py
index 6a717336..4c9f8c02 100755
--- a/CHAP/utils/general.py
+++ b/CHAP/utils/general.py
@@ -2735,9 +2735,9 @@ def quick_imshow(
     :type grid_linewidth: int, optional
     :param colorbar: Include a colorbar, defaults to `False`.
     :type colorbar: bool, optional
-    :param kwargs: Any additional keyword parameters to pass on to
+    :param \*\*kwargs: Any additional keyword parameters to pass on to
         `matplotlib.pyplot.imshow <https://matplotlib.org/stable/api/_as_gen/matplotlib.pyplot.imshow.html>`__.
-    :type kwargs: dict, optional
+    :type: dict, optional
     :raise: ValueError for invalid input data or parameters. 
     :return: In-memory object as a byte stream represention if
         `return_fig` is set.
@@ -2853,9 +2853,9 @@ def quick_plot(
     :type save_only: bool, optional
     :param block: Wait for the image to be closed before returning.
     :type block: bool, optional
-    :param kwargs: Any additional keyword parameters to pass on to
+    :param \*\*kwargs: Any additional keyword parameters to pass on to
         `matplotlib.pyplot.plot <https://matplotlib.org/stable/api/_as_gen/matplotlib.pyplot.plot.html>`__
-    :type kwargs: dict, optional
+    :type: dict, optional
     :raise: ValueError for invalid input data or parameters. 
     """
     #FIX: Update with return_buf
diff --git a/CHAP/utils/models.py b/CHAP/utils/models.py
index 99d8a714..ebdeb88a 100755
--- a/CHAP/utils/models.py
+++ b/CHAP/utils/models.py
@@ -300,7 +300,7 @@ def validate_parameters(parameters, info):
     :rtype: list[FitParameter]
     """
     # System imports
-    import inspect
+    from inspect import signature
 
     if 'model' in info.data:
         model = info.data['model']
@@ -308,7 +308,7 @@ def validate_parameters(parameters, info):
         model = None
     if model is None or model == 'expression':
         return parameters
-    sig = dict(inspect.signature(models[model]['name']).parameters.items())
+    sig = dict(signature(models[model]['name']).parameters.items())
     sig.pop('x')
 
     # Check input model parameter validity
diff --git a/examples/edd/edd_calibration_script.py b/examples/edd/edd_calibration_script.py
new file mode 100644
index 00000000..fc3e25ff
--- /dev/null
+++ b/examples/edd/edd_calibration_script.py
@@ -0,0 +1,158 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+"""A python script version of the CHAP pipeline version of the 
+calibration example.
+
+Modify any user choices in the "Start user input" and "Optional user
+input" blocks below.
+
+In particular:
+
+* Choose the path to your CHAP repo by setting sys.path.
+"""
+
+# System modules
+import os
+from pprint import pprint
+import sys
+from tempfile import NamedTemporaryFile
+
+# Third party modules
+import yaml
+
+# Local modules
+from CHAP.pipeline import PipelineData
+from CHAP.common.reader import SpecReader
+from CHAP.edd.processor import (
+    MCAEnergyCalibrationProcessor,
+    MCATthCalibrationProcessor,
+)
+
+#------------------------------------------------------------------------------#
+# Start user input
+#------------------------------------------------------------------------------#
+
+# Choose the path to your CHAP repo
+sys.path.append(
+    '/home/rv43/Documents/Programs/repos/CHESSComputing/ChessAnalysisPipeline_main')
+#sys.path.append(
+#    '/nfs/chess/sw/CHESS-software-releases/repos/prod/ChessAnalysisPipeline')
+
+root = None #'examples/edd'
+interactive = True
+outputdir = 'output'
+energy_calib = True
+tth_calib = True
+
+if root is None:
+    root = os.getcwd()
+if outputdir is None:
+    outputdir = '.'
+if not os.path.isabs(outputdir):
+    outputdir = os.path.normpath(
+        os.path.realpath(os.path.join(root, outputdir)))
+
+energy_name = f'{outputdir}/energy_calibration_result.yaml'
+tth_name = f'{outputdir}/tth_calibration_result.yaml'
+spec_file = f'{root}/data/ceo2-5deg-80um-calib/spec.log'
+scan_numbers = 1
+detector_ids = [0, 21]
+
+#------------------------------------------------------------------------------#
+# Optional user input
+#------------------------------------------------------------------------------#
+
+spec_config = {
+    'station': 'id3a',
+    'experiment_type': 'EDD',
+    'spec_scans': [
+        {'spec_file': spec_file,
+         'scan_numbers': scan_numbers}
+    ],
+}
+energy_config = {
+    'peak_energies': [34.276, 34.717, 39.255, 40.231],
+    'max_peak_index': 1,
+    'materials': [
+        {'material_name': 'CeO2',
+         'lattice_parameters': 5.41153,
+         'sgnum': 225}
+    ],
+}
+energy_detector_config = {
+    'baseline': True,
+    'mask_ranges': [[650, 850]],
+}
+if detector_ids is not None:
+    energy_detector_config['detectors'] = [{'id':id_} for id_ in detector_ids]
+tth_config = {'tth_initial_guess': 5.2}
+tth_detector_config = {
+    'energy_mask_ranges': [[65, 155]],
+}
+
+#------------------------------------------------------------------------------#
+# End user input
+#------------------------------------------------------------------------------#
+
+if not os.path.isdir(outputdir):
+    os.makedirs(outputdir)
+try:
+    NamedTemporaryFile(dir=outputdir)
+except Exception as exc:
+    raise OSError(
+        'Output directory not accessible for writing ({outputdir})') from exc
+
+#------------------------------------------------------------------------------#
+
+print(f'\nspec_config:')
+pprint(spec_config)
+if energy_calib:
+    print(f'\nenergy_config:')
+    pprint(energy_config)
+    print(f'\nenergy_detector_config:')
+    pprint(energy_detector_config)
+if tth_calib:
+    print(f'\ntth_config:')
+    pprint(tth_config)
+    print(f'\ntth_detector_config:')
+    pprint(tth_detector_config)
+
+# Perform the energy calibration
+if energy_calib:
+    # Read the calibration data
+    spec_reader = SpecReader(config=spec_config)
+    nxroot = spec_reader.read()
+
+    # Perform the energy calibration
+    data = [PipelineData(name='SpecReader', data=nxroot)]
+    energy_calib_config, images = MCAEnergyCalibrationProcessor.run(
+        data=data, config=energy_config, detector_config=energy_detector_config,
+        interactive=interactive)
+
+    # Write the energy calibration results
+    with open(energy_name, 'w', encoding='utf-8') as f:
+        yaml.dump(energy_calib_config, f, sort_keys=False)
+
+# Perform the tth calibration
+if tth_calib:
+    # Read the energy calibration results
+    with open(energy_name, encoding='utf-8') as f:
+        energy_calib_config = yaml.safe_load(f)
+
+    # Read the calibration data
+    spec_reader = SpecReader(config=spec_config)
+    nxroot = spec_reader.read()
+
+    # Perform the tth calibration
+    data = [
+        PipelineData(
+            data=energy_calib_config,
+            schema='edd.models.MCAEnergyCalibrationConfig'),
+        PipelineData(name='SpecReader', data=nxroot),
+    ]
+    tth_calib_config, images = MCATthCalibrationProcessor.run(
+        data=data, config=tth_config, detector_config=tth_detector_config,
+        interactive=interactive)
+    with open(tth_name, 'w', encoding='utf-8') as f:
+        yaml.dump(tth_calib_config, f, sort_keys=False)
+
diff --git a/examples/tomo/tomo_script_id3b.py b/examples/tomo/tomo_script_id3b.py
index 90770b31..c6eed623 100644
--- a/examples/tomo/tomo_script_id3b.py
+++ b/examples/tomo/tomo_script_id3b.py
@@ -1,24 +1,36 @@
 #!/usr/bin/env python3
 # -*- coding: utf-8 -*-
+"""A python script version of the CHAP pipeline version of the id3b
+example.
 
-"""Choose the path to your CHESS repo."""
-import sys
-#sys.path.append(
-#    '/home/rv43/Documents/Programs/repos/CHESSComputing/ChessAnalysisPipeline')
-sys.path.append(
-    '/home/rv43/Documents/Programs/repos/CHESSComputing/ChessAnalysisPipeline_main')
-#sys.path.append(
-#    '/nfs/chess/sw/CHESS-software-releases/repos/prod/ChessAnalysisPipeline')
+Modify any user choices in the "Start user input" and "Optional user
+input" blocks below.
+
+In particular:
+
+* Choose the path to your CHAP repo by setting sys.path.
+
+* Select the run_type below from:
+      ===========  ==============================================
+      run_type     Description
+      ===========  ==============================================
+      'normal'     Full regular reconstruction
+                   (like running the default hollow_cube in CHAP)
+      'one_plane'  Reconstruction of two planes only
+      'two_planes' Reconstruction of one plane only
+      'roi'        Reconstruction for a subset or rows
+                   (find center at first and last row)
+      ===========  ==============================================
+"""
 
 # System modules
 import os
 from pprint import pprint
+import sys
 from tempfile import NamedTemporaryFile
 
 # Third party modules
-import matplotlib.pyplot as plt
 from nexusformat.nexus import nxload
-from PIL import Image
 import yaml
 
 # Local modules
@@ -37,14 +49,13 @@
 # Start user input
 #------------------------------------------------------------------------------#
 
-"""Select run_type from
-'normal':     Full regular reconstruction
-              (like running the default hollow_cube in CHAP)
-'one_plane':  Reconstruction of two planes only
-'two_planes': Reconstruction of one plane only
-'roi':        Reconstruction for a subset or rows
-              (find center at first and last row)
-"""
+# Choose the path to your CHAP repo
+#sys.path.append(
+#    '/home/rv43/Documents/Programs/repos/CHESSComputing/ChessAnalysisPipeline_main')
+sys.path.append(
+    '/nfs/chess/sw/CHESS-software-releases/repos/prod/ChessAnalysisPipeline')
+
+# Select run_type
 #run_type = 'normal'
 #run_type = 'one_plane'
 #run_type = 'two_planes'
@@ -206,44 +217,40 @@
 print(f'\ndetector_config:')
 pprint(detector_config)
 
-# Construct the CHESS style tomo map
+# Construct the CHAP style tomo map
 if not construct_chess_map:
     nxroot = nxload(chess_map_name)
 else:
     # Create the map for the tomo stack
-    tomo_map = MapProcessor(config=map_config, detector_config=detector_config)
-
-    # Read the map for the tomo stack
-    tomofields = tomo_map.process(data=None)
+    tomofields = MapProcessor.run(
+        config=map_config, detector_config=detector_config)
     tomofields.save(map_name, mode='w')
 
     # Read the dark field
-    tdf_spec_reader = SpecReader(
+    darkfield = SpecReader.run(
         config={
-            'station': tomo_map.config.station,
-            'experiment_type': tomo_map.config.experiment_type,
-            'sample': tomo_map.config.sample,
+            'station': map_config['station'],
+            'experiment_type': map_config['experiment_type'],
+            'sample': map_config['sample'],
             'spec_scans': [
-                {'spec_file': tomo_map.config.spec_scans[0].spec_file,
+                {'spec_file': map_config['spec_scans'][0].spec_file,
                  'scan_numbers': tdf_scan_numbers}],
         },
         detector_config=detector_config)
-    darkfield = tdf_spec_reader.read()
 
     # Read the bright field
-    tbf_spec_reader = SpecReader(
+    brightfield = SpecReader.run(
         config={
-            'station': tomo_map.config.station,
-            'experiment_type': tomo_map.config.experiment_type,
-            'sample': tomo_map.config.sample,
+            'station': map_config['station'],
+            'experiment_type': map_config['experiment_type'],
+            'sample': map_config['sample'],
             'spec_scans': [
-                {'spec_file': tomo_map.config.spec_scans[0].spec_file,
+                {'spec_file': map_config['spec_scans'][0].spec_file,
                  'scan_numbers': tbf_scan_numbers}],
         },
         detector_config=detector_config)
-    brightfield = tbf_spec_reader.read()
 
-    # Convert to CHESS style tomography map
+    # Convert to CHAP style tomography map
     data = [
         PipelineData(
             name='MapProcessor', data=tomofields, schema='tomofields'),
@@ -254,8 +261,7 @@
             name='YAMLReader', data=detector_setup,
             schema='tomo.models.Detector')
     ]
-    chess_map = TomoCHESSMapConverter()
-    _, _, nxroot = chess_map.process(data=data)
+    _, _, nxroot = TomoCHESSMapConverter.run(data=data)
     nxroot = nxroot['data']
     nxroot.save(chess_map_name, mode='w')
 
@@ -267,26 +273,17 @@
     # Reduce the data with remove_all_stripe
     data = [
         PipelineData(name='TomoCHESSMapConverter', data=nxroot, schema=None)]
-    tomo = TomoReduceProcessor(
-        config=reduce_config, interactive=interactive)
-    (metadata, provenance, images, reduced_data) = tomo.process(data)
+    _, _, _, reduced_data = TomoReduceProcessor.run(
+        data=data, config=reduce_config, interactive=interactive)
     reduced_data = reduced_data['data']
     reduced_data.save(reduced_data_name, mode='w')
 
-#    for (buf, ext), name in images.get('data', []):
-#        buf.seek(0)
-#        plt.imshow(Image.open(buf))
-#        plt.axis('off')
-#        plt.tight_layout()
-#        plt.show(block=True)
-#        buf.close()
-#        plt.close()
     nxentry = reduced_data[reduced_data.default]
     nxdata = nxentry[nxentry.default]
     image_slice = nxdata.nxsignal[0,:,0,:]
     vmin = image_slice.min()
     vmax = image_slice.max()
-    if len(recon_layer_indices):
+    if recon_layer_indices:
         quick_imshow(
             image_slice,
             title=f'Slice {detector_config["roi"][0]["start"]}',
@@ -310,10 +307,10 @@
 
         data = [PipelineData(
             name='TomoCHESSMapConverter', data=nxroot, schema=None)]
-        tomo = TomoReduceProcessor(
+        _, _, _, reduced_data = TomoReduceProcessor.run(
+            data=data,
             config=reduce_config.update({'remove_stripe': {method: {}}}),
             interactive=interactive)
-        (metadata, provenance, images, reduced_data) = tomo.process(data)
         reduced_data = reduced_data['data']
         reduced_data.save(f'reduced_data_{method}.nxs', mode='w')
 
@@ -338,11 +335,10 @@
 
     data = [PipelineData(
         name='TomoCHESSMapConverter', data=reduced_data, schema=None)]
-    tomo = TomoFindCenterProcessor(
-        interactive=interactive, config=find_center_config)
-    (metadata, provenance, images, center_config) = tomo.process(data)
+    _, _, _, center_config = TomoFindCenterProcessor.run(
+        data=data, config=find_center_config, interactive=interactive)
     center_config = center_config['data']
-    with open(find_center_name, 'w') as f:
+    with open(find_center_name, 'w', encoding='utf-8') as f:
         yaml.dump(center_config, f, sort_keys=False)
 
 # Reconstruct
@@ -351,7 +347,7 @@
     pass
 else:
     reduced_data = nxload(reduced_data_name)
-    with open(find_center_name) as f:
+    with open(find_center_name, encoding='utf-8') as f:
         center_config = yaml.safe_load(f)
 
     data = [
@@ -364,12 +360,8 @@
 #            name='TomoFindCenterProcessor', data=center_config,
 #            schema='tomo.models.TomoFindCenterConfig')
     ]
-    from pprint import pprint
-    pprint(reconstruct_config)
-    tomo = TomoReconstructProcessor(
-        config=reconstruct_config,
-        center_config=center_config,
+    _, _, _, reconstructed_data = TomoReconstructProcessor.run(
+        data=data, config=reconstruct_config, center_config=center_config,
         interactive=interactive)
-    (metadata, provenance, images, reconstructed_data) = tomo.process(data)
     reconstructed_data = reconstructed_data['data']
     reconstructed_data.save(reconstructed_data_name, mode='w')

From 4f4ce623dc01648644a6b4cb06ad068c44f34fea Mon Sep 17 00:00:00 2001
From: Rolf Verberg <rv43@cornell.edu>
Date: Thu, 30 Apr 2026 21:02:55 -0400
Subject: [PATCH 40/76] docs: cleaned up kwargs docstrings

---
 CHAP/common/reader.py | 1 -
 CHAP/models.py        | 9 +++------
 CHAP/pipeline.py      | 3 +--
 CHAP/utils/fit.py     | 4 ----
 CHAP/utils/general.py | 2 --
 5 files changed, 4 insertions(+), 15 deletions(-)

diff --git a/CHAP/common/reader.py b/CHAP/common/reader.py
index 8d6042bc..de9b78a9 100755
--- a/CHAP/common/reader.py
+++ b/CHAP/common/reader.py
@@ -563,7 +563,6 @@ def read(self, filename, method='read_csv', comment='#', **kwargs):
         :type comment: str, optional
         :param \*\*kwargs: Additional keyword arguments to supply to the
             `pandas` reader.
-        :type: dict, optional.
         :rtype: `pandas.DataFrame`
         """
         # Third party modules
diff --git a/CHAP/models.py b/CHAP/models.py
index 9b4ad36c..435c2b57 100755
--- a/CHAP/models.py
+++ b/CHAP/models.py
@@ -33,8 +33,7 @@ class CHAPBaseModel(BaseModel):
     def dict(self, *args, **kwargs):
         """Dump the class implemention to a dictionary.
 
-        :param \*\*kwargs: Arbitrary keyword arguments.
-        :type: dict, optional
+        :param \*\*kwargs: Optional keyword arguments, including:
         :keyword exclude: Class variable(s) to omit from the output
             dictionary.
         :type exclude: dict or set, optional
@@ -49,8 +48,7 @@ class variables that have an alias., defaults to `True`.
     def model_dump(self, *args, **kwargs):
         """Dump the class implemention to a dictionary.
 
-        :param \*\*kwargs: Arbitrary keyword arguments.
-        :type: dict, optional
+        :param \*\*kwargs: Optional keyword arguments, including:
         :keyword exclude: Class variable(s) to omit from the output
             dictionary.
         :type exclude: dict or set, optional
@@ -70,8 +68,7 @@ class variables that have an alias., defaults to `True`.
     def model_dump_json(self, *args, **kwargs):
         """Dump the class implemention to a JSON string.
 
-        :param \*\*kwargs: Arbitrary keyword arguments.
-        :type: dict, optional
+        :param \*\*kwargs: Optional keyword arguments, including:
         :keyword exclude: Class variable(s) to omit from the output
             dictionary.
         :type exclude: dict or set, optional
diff --git a/CHAP/pipeline.py b/CHAP/pipeline.py
index 47df472d..802a9b38 100755
--- a/CHAP/pipeline.py
+++ b/CHAP/pipeline.py
@@ -483,8 +483,7 @@ def run(cls, **kwargs):
         pipeline file config dictionary (see:
         :class:`~CHAP.models.RunConfig)`.
 
-        :param \*\*kwargs: Arbitrary keyword arguments, including:
-        :type: dict, optional
+        :param \*\*kwargs: Optional keyword arguments, including:
         :keyword config: Initialization parameters for an instance
             of the pipeline item this method is called from (often
             used by Readers and Processors).
diff --git a/CHAP/utils/fit.py b/CHAP/utils/fit.py
index 6f65c6ed..56489ab8 100755
--- a/CHAP/utils/fit.py
+++ b/CHAP/utils/fit.py
@@ -1260,7 +1260,6 @@ def fit(self, config=None, **kwargs):
         :type config: CHAP.utils.models.FitConfig, optional
         :param \*\*kwargs: Additional key, value pairs to pass on
             directly to the core fit routine.
-        :type: dict, optional
         """
         # Check input parameters
         if self._model is None:
@@ -1361,7 +1360,6 @@ class attribute.
         :type plot_masked_data: bool, optional
         :param \*\*kwargs: Additional key, value pairs to pass on
             directly to the Matplotlib plot function.
-        :type: dict, optional
         """
         if result is None:
             result = self._result
@@ -2647,7 +2645,6 @@ def plot(
         :type plot_masked_data: bool, optional
         :param \*\*kwargs: Additional key, value pairs to pass on
             directly to the Matplotlib plot function.
-        :type: dict, optional
         """
         # Third party modules
         from lmfit.models import ExpressionModel
@@ -2722,7 +2719,6 @@ def fit(self, config=None, **kwargs):
         :type config: CHAP.utils.models.FitConfig, optional
         :param \*\*kwargs: Additional key, value pairs to pass on
             directly to the core fit routine.
-        :type: dict, optional
         """
         # Check input parameters
         if self._model is None:
diff --git a/CHAP/utils/general.py b/CHAP/utils/general.py
index 4c9f8c02..5b9cfb5a 100755
--- a/CHAP/utils/general.py
+++ b/CHAP/utils/general.py
@@ -2737,7 +2737,6 @@ def quick_imshow(
     :type colorbar: bool, optional
     :param \*\*kwargs: Any additional keyword parameters to pass on to
         `matplotlib.pyplot.imshow <https://matplotlib.org/stable/api/_as_gen/matplotlib.pyplot.imshow.html>`__.
-    :type: dict, optional
     :raise: ValueError for invalid input data or parameters. 
     :return: In-memory object as a byte stream represention if
         `return_fig` is set.
@@ -2855,7 +2854,6 @@ def quick_plot(
     :type block: bool, optional
     :param \*\*kwargs: Any additional keyword parameters to pass on to
         `matplotlib.pyplot.plot <https://matplotlib.org/stable/api/_as_gen/matplotlib.pyplot.plot.html>`__
-    :type: dict, optional
     :raise: ValueError for invalid input data or parameters. 
     """
     #FIX: Update with return_buf

From d46b27d7f1fc1bc08f195b86260ad6faea4ac6cd Mon Sep 17 00:00:00 2001
From: Rolf Verberg <rv43@cornell.edu>
Date: Fri, 1 May 2026 11:01:19 -0400
Subject: [PATCH 41/76] fix: fixed pipelineitem.run for duplicate class names

---
 CHAP/pipeline.py                       | 19 ++++++++++++++++---
 examples/edd/edd_calibration_script.py |  6 ++----
 2 files changed, 18 insertions(+), 7 deletions(-)

diff --git a/CHAP/pipeline.py b/CHAP/pipeline.py
index 802a9b38..1b206945 100755
--- a/CHAP/pipeline.py
+++ b/CHAP/pipeline.py
@@ -510,9 +510,13 @@ def run(cls, **kwargs):
         from inspect import isclass
         from pkgutil import walk_packages
 
+        # Local modules
+        from CHAP.utils.general import input_menu
+
         def _find_class_in_package(package_name, class_name):
             package = import_module(package_name)
             # Recursively walk through all submodules
+            found_classes = []
             for _, module_name, _ in walk_packages(
                     package.__path__, package.__name__ + "."):
                 try:
@@ -520,11 +524,20 @@ def _find_class_in_package(package_name, class_name):
                     # Check if the class exists in this module
                     if hasattr(module, class_name):
                         cls = getattr(module, class_name)
-                        if isclass(cls) and cls.__module__ == module_name:
-                            return cls
+                        if (isclass(cls) and cls.__module__ == module_name
+                                and cls not in found_classes):
+                            found_classes.append(cls)
                 except ImportError:
                     continue
-            return None
+            if not found_classes:
+                raise ImportError(f'Unable to find {class_name} in CHAP')
+            if len(found_classes) == 1:
+                return found_classes[0]
+            index = input_menu(
+                [v.__module__ for v in found_classes],
+                header=f'\nFound multiple classes named {class_name} in '
+                       f'CHAP\nUse {class_name} from:')
+            return found_classes[index]
 
         cls_name = cls.__name__
         mmc = _find_class_in_package('CHAP', cls_name)
diff --git a/examples/edd/edd_calibration_script.py b/examples/edd/edd_calibration_script.py
index fc3e25ff..b8ed5b9d 100644
--- a/examples/edd/edd_calibration_script.py
+++ b/examples/edd/edd_calibration_script.py
@@ -120,8 +120,7 @@
 # Perform the energy calibration
 if energy_calib:
     # Read the calibration data
-    spec_reader = SpecReader(config=spec_config)
-    nxroot = spec_reader.read()
+    nxroot = SpecReader.run(config=spec_config)
 
     # Perform the energy calibration
     data = [PipelineData(name='SpecReader', data=nxroot)]
@@ -140,8 +139,7 @@
         energy_calib_config = yaml.safe_load(f)
 
     # Read the calibration data
-    spec_reader = SpecReader(config=spec_config)
-    nxroot = spec_reader.read()
+    nxroot = SpecReader.run(config=spec_config)
 
     # Perform the tth calibration
     data = [

From 661e81d8e62e97183c0217f8956e937d5b51cc72 Mon Sep 17 00:00:00 2001
From: Keara Soloway <kls286@cornell.edu>
Date: Fri, 1 May 2026 13:55:29 -0400
Subject: [PATCH 42/76] feat: support 0-scan maps in
 edd.StrainAnalysisProcessor with setup=True and update=False

---
 CHAP/edd/processor.py | 59 ++++++++++++++++++++++++++++++++++++-------
 1 file changed, 50 insertions(+), 9 deletions(-)

diff --git a/CHAP/edd/processor.py b/CHAP/edd/processor.py
index be95381f..146a28ae 100755
--- a/CHAP/edd/processor.py
+++ b/CHAP/edd/processor.py
@@ -2719,6 +2719,17 @@ def process(self, data):
                     self.logger.warning(
                         f'Skipping detector {detector_id} (Illegal data shape '
                         f'{raw_detector_data.shape})')
+                elif raw_detector_data.size == 0 and self.setup:
+                    # 0-scan map: no spectra yet, include for setup
+                    for k, v in nxdata[detector_id].attrs.items():
+                        detector.attrs[k] = v.nxdata
+                    if self.config.rel_height_cutoff is not None:
+                        detector.rel_height_cutoff = \
+                            self.config.rel_height_cutoff
+                    detector.add_calibration(
+                        calibration_detectors[
+                            int(calibration_detector_ids.index(detector_id))])
+                    detectors.append(detector)
                 elif raw_detector_data.sum():
                     for k, v in nxdata[detector_id].attrs.items():
                         detector.attrs[k] = v.nxdata
@@ -2770,9 +2781,16 @@ def process(self, data):
         # Apply the combined energy ranges mask
         self._apply_combined_mask()
 
+        # Populate _peak_fit_info when there are no spectra (0-scan setup)
+        no_raw_data = (
+            bool(self._nxdata_detectors)
+            and self._nxdata_detectors[0].nxsignal.shape[0] == 0)
+        if no_raw_data:
+            self._populate_peak_fit_info()
+
         # Setup and/or run the strain analysis
         results = {}
-        if self.update:
+        if self.update and not no_raw_data:
             results = self._strain_analysis()
         if self.setup:
             if self.standalone:
@@ -2959,6 +2977,30 @@ def _add_fit_nxcollection(self, nxdetector, fit_type, hkls, peak_fit_info):
                 )
                 nxcollection[hkl_name].strains.attrs['signal'] = 'values'
 
+    def _populate_peak_fit_info(self):
+        """Populate _peak_fit_info with all configured HKLs for each
+        detector, with all peaks marked as used.
+
+        Called when no raw detector spectra are present (e.g. a 0-scan
+        setup run), so that the resulting NXprocess contains entries for
+        every HKL that could be encountered in a subsequent update run.
+        """
+        # Local modules
+        from CHAP.edd.utils import get_peak_locations, get_unique_hkls_ds
+
+        for detector in self.detector_config.detectors:
+            hkls, ds = get_unique_hkls_ds(
+                self.config.materials, tth_max=detector.tth_max,
+                tth_tol=detector.tth_tol)
+            hkls_fit = np.asarray([hkls[i] for i in detector.hkl_indices])
+            ds_fit = np.asarray([ds[i] for i in detector.hkl_indices])
+            peak_locations = get_peak_locations(ds_fit, detector.tth_calibrated)
+            self._peak_fit_info.append({
+                'hkls': [''.join(map(str, hkl)) for hkl in hkls_fit],
+                'nominal_peak_centers': peak_locations.tolist(),
+                'peak_models': detector.peak_models,
+                'use_peaks': np.ones(len(hkls_fit), dtype=bool).tolist(),
+            })
 
     def _create_animation(
             self, nxdata, energies, intensities, intensity_norms, best_fits,
@@ -3188,17 +3230,16 @@ def _get_nxprocess(self, nxentry, calibration_config):
             )
 
             # Add the detector data
-            _intensity=np.asarray(
-                [
-                    data[i].astype(np.float64)[mask]
-                    for i in range(num_points)
-                ]
-            )
+            num_energy_bins = mask.sum()
+            _intensity = np.empty(
+                (num_points, num_energy_bins), dtype=np.float64)
+            for i in range(num_points):
+                _intensity[i] = data[i].astype(np.float64)[mask]
             det_nxdata.intensity = NXfield(
                 value=_intensity,
                 attrs={'units': 'counts'},
-                maxshape=(None,*_intensity.shape[1:]),
-                chunks=(1,*_intensity.shape[1:])
+                maxshape=(None, num_energy_bins),
+                chunks=(1, num_energy_bins)
             )
             det_nxdata.attrs['signal'] = 'intensity'
 

From fc796f0db681ba57da382c6fff1faf0246e00eee Mon Sep 17 00:00:00 2001
From: Keara Soloway <kls286@cornell.edu>
Date: Fri, 1 May 2026 14:29:58 -0400
Subject: [PATCH 43/76] cut: exclude spectra-like data from JSON results of
 StrainAnalysisProcessor

---
 CHAP/edd/processor.py | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

diff --git a/CHAP/edd/processor.py b/CHAP/edd/processor.py
index 146a28ae..ca0d9f94 100755
--- a/CHAP/edd/processor.py
+++ b/CHAP/edd/processor.py
@@ -2818,7 +2818,13 @@ def process(self, data):
                      else self._get_points(results)
             ret = [result]
             if self.json_results:
-                json_results = {k: v.tolist() for k, v in results.items()}
+                json_results = {
+                    k: v.tolist()
+                    for k, v in results.items()
+                    if not k.endswith('intensity') # exclude raw detector data
+                       and not k.endswith('best_fit') # exlude best_fit spectra
+                       and not k.endswith('residual')
+                }
                 ret.append(json_results)
             if not (self._figures or self._animation):
                 return tuple(ret)

From 02eae4190bc78cc0f60a3ed504a5e5f62a17ee47 Mon Sep 17 00:00:00 2001
From: Keara Soloway <kls286@cornell.edu>
Date: Fri, 1 May 2026 14:30:55 -0400
Subject: [PATCH 44/76] add: include placeholder values for unused peaks in
 JSON results of StrainAnalysisProcessor

---
 CHAP/edd/processor.py | 23 +++++++++++++++++++++++
 1 file changed, 23 insertions(+)

diff --git a/CHAP/edd/processor.py b/CHAP/edd/processor.py
index ca0d9f94..620c0b2c 100755
--- a/CHAP/edd/processor.py
+++ b/CHAP/edd/processor.py
@@ -3644,6 +3644,29 @@ def _strain_analysis(self):
                             np.nan),
                 })
 
+            if self.json_results:
+                # Include placeholder values for unused peaks in results
+                placeholder = np.full(num_points, np.nan)
+                for j, hkl in enumerate(hkls_fit[~use_peaks]):
+                    hkl_name = '_'.join(str(hkl)[1:-1].split(' '))
+                    for fitmode in ('unconstrained', 'uniform'):
+                        fitparams = ('amplitudes', 'centers', 'sigmas')
+                        if detector.peak_models == 'pvoigt':
+                            fitparams = (*fitparams, 'fractions')
+                        if fitmode == 'unconstrained':
+                            fitparams = (*fitparams, 'strains')
+                        for fitparam in fitparams:
+                            fitquants = ('values', 'errors')
+                            if fitmode == 'unconstrained' \
+                               and fitparam == 'strains':
+                                fitquants = (*fitquants, 'residuals')
+                            for fitquant in fitquants:
+                                key = str(
+                                    f'{det_id}/{fitmode}_fit/{hkl_name}/'
+                                    f'{fitparam}/{fitquant}'
+                                )
+                                results.update({key: placeholder})
+
             # Create an animation of the fit points
             if (not self.config.skip_animation
                     and (self.interactive or self.save_figures)):

From 266086e4d69ecf766e2ef4d897b2f7c41f76438c Mon Sep 17 00:00:00 2001
From: Rolf Verberg <rv43@cornell.edu>
Date: Tue, 5 May 2026 13:50:19 -0400
Subject: [PATCH 45/76] fix: peak fit results for the EDD calibration in
 channel energies

---
 CHAP/edd/processor.py | 71 ++++++++++++++++++++++++-------------------
 1 file changed, 39 insertions(+), 32 deletions(-)

diff --git a/CHAP/edd/processor.py b/CHAP/edd/processor.py
index 733ec448..102c554c 100755
--- a/CHAP/edd/processor.py
+++ b/CHAP/edd/processor.py
@@ -1413,26 +1413,20 @@ def _calibrate(self):
                     NXfield(mean_data[mask], 'y'), NXfield(bins[mask], 'x')),
                 {'models': models, 'method': 'trf'})
 
+
             # Extract the fit results for the peaks
-            fit_peak_amplitudes = sorted([
-                mean_data_fit.best_values[f'peak{i+1}_amplitude'].tolist()
+            fit_peak_amplitudes = np.asarray([
+                mean_data_fit.best_values[f'peak{i+1}_amplitude']
                 for i in range(len(initial_peak_indices))])
             self.logger.debug(f'Fit peak amplitudes: {fit_peak_amplitudes}')
-            fit_peak_indices = sorted([
-                mean_data_fit.best_values[f'peak{i+1}_center'].tolist()
+            fit_peak_indices = np.asarray([
+                mean_data_fit.best_values[f'peak{i+1}_center']
                 for i in range(len(initial_peak_indices))])
             self.logger.debug(f'Fit peak center indices: {fit_peak_indices}')
-            fit_peak_sigmas = sorted([
-                mean_data_fit.best_values[f'peak{i+1}_sigma'].tolist()
+            fit_peak_sigmas = np.asarray([
+                mean_data_fit.best_values[f'peak{i+1}_sigma']
                 for i in range(len(initial_peak_indices))])
             self.logger.debug(f'Fit peak sigmas: {fit_peak_sigmas}')
-            self._peak_fit_results[id_] = {
-                'amplitudes': fit_peak_amplitudes,
-                'centers': fit_peak_indices,
-                'sigmas': fit_peak_sigmas,
-                'independent_dimension': {
-                    'name': 'Detector Channel', 'unit': '-'}
-            }
 
             # FIX for now stick with a linear energy correction
             fit = FitProcessor(**self.run_config)
@@ -1505,6 +1499,17 @@ def _calibrate(self):
                     plt.show()
                 plt.close()
 
+            # Collect the fit results for the peaks
+            # FIX assume Gaussian peaks for now and a=0
+            self._peak_fit_results[id_] = {
+                'heights': (fit_peak_amplitudes /
+                            (np.sqrt(2*np.pi)*fit_peak_sigmas)).tolist(),
+                'centers': (b*fit_peak_indices + c).tolist(),
+                'fwhm': (b*fit_peak_sigmas*np.sqrt(8*np.log(2))).tolist(),
+                'independent_dimension': {
+                    'name': 'Energy', 'unit': '-'},
+            }
+
     def _get_initial_peak_positions(
             self, y, low, index_ranges, input_indices, input_max_peak_index,
             detector_id, reset_flag=0, return_buf=False):
@@ -2145,28 +2150,18 @@ def _direct_bragg_peak_fit(
         residual = result.residual
 
         # Extract the Bragg peak indices from the fit
-        fit_peak_amplitudes = [
-            result.best_values[f'peak{i+1}_amplitude'].tolist()
-            for i in range(len(e_bragg))]
+        fit_peak_amplitudes = np.asarray([
+            result.best_values[f'peak{i+1}_amplitude']
+            for i in range(len(e_bragg))])
         self.logger.debug(f'Fit peak amplitudes: {fit_peak_amplitudes}')
-        fit_peak_indices = [
-            result.best_values[f'peak{i+1}_center'].tolist()
-            for i in range(len(e_bragg))]
+        fit_peak_indices = np.asarray([
+            result.best_values[f'peak{i+1}_center']
+            for i in range(len(e_bragg))])
         self.logger.debug(f'Fit peak center indices: {fit_peak_indices}')
-        fit_peak_sigmas = [
-            result.best_values[f'peak{i+1}_sigma'].tolist()
-            for i in range(len(e_bragg))]
+        fit_peak_sigmas = np.asarray([
+            result.best_values[f'peak{i+1}_sigma']
+            for i in range(len(e_bragg))])
         self.logger.debug(f'Fit peak sigmas: {fit_peak_sigmas}')
-        self._peak_fit_results[detector.get_id()] = {
-            'amplitudes': fit_peak_amplitudes,
-            'centers': fit_peak_indices,
-            'sigmas': fit_peak_sigmas,
-            'independent_dimension': {
-                'name': 'Detector Channel', 'unit': '-'}
-        }
-        fit_peak_indices = np.asarray(
-            [result.best_values[f'peak{i+1}_center']
-             for i in range(len(e_bragg))])
 
         # Fit a line through zero strain peak energies vs detector
         # energy bins
@@ -2189,6 +2184,18 @@ def _direct_bragg_peak_fit(
         e_bragg_unconstrained = (
             (a_fit*fit_peak_indices + b_fit) * fit_peak_indices + c_fit)
 
+        # Collect the fit results for the peaks
+        # FWHM to first order (i.e. ignore non-zero a)
+        # FIX assume Gaussian peaks for now
+        self._peak_fit_results[detector.get_id()] = {
+            'heights': (fit_peak_amplitudes /
+                (np.sqrt(2*np.pi)*fit_peak_sigmas)).tolist(),
+            'centers': e_bragg_unconstrained.tolist(),
+            'fwhm': (b_fit*fit_peak_sigmas*np.sqrt(8*np.log(2))).tolist(),
+            'independent_dimension': {
+                'name': 'Energy', 'unit': 'keV'},
+        }
+
         return {
             'best_fit_unconstrained': best_fit,
             'residual_unconstrained': residual,

From d248941db7b6360e34eb2958f142cb225b62856a Mon Sep 17 00:00:00 2001
From: CHESS MSNC <chess_msnc@lnx201.classe.cornell.edu>
Date: Tue, 12 May 2026 22:11:54 -0400
Subject: [PATCH 46/76] fix: missing call to import_scanparser in MapConfig
 validation

---
 CHAP/common/models/map.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHAP/common/models/map.py b/CHAP/common/models/map.py
index fa463f6b..2d4b0ca5 100755
--- a/CHAP/common/models/map.py
+++ b/CHAP/common/models/map.py
@@ -1201,6 +1201,7 @@ def validate_experiment_type(cls, experiment_type, info):
                 f'For station {station}, allowed experiment types are '
                 f'{", ".join(allowed_experiment_types)}. '
                 f'Supplied experiment type {experiment_type} is not allowed.')
+        import_scanparser(station, experiment_type)
         return experiment_type
 
 

From 3b760679e0c0e021894cbd86e16c78970bb6abec Mon Sep 17 00:00:00 2001
From: Rolf Verberg <rv43@cornell.edu>
Date: Tue, 12 May 2026 22:19:32 -0400
Subject: [PATCH 47/76] fix: missing call to import_scanparser in MapConfig
 validation

---
 CHAP/common/models/map.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHAP/common/models/map.py b/CHAP/common/models/map.py
index fa463f6b..2d4b0ca5 100755
--- a/CHAP/common/models/map.py
+++ b/CHAP/common/models/map.py
@@ -1201,6 +1201,7 @@ def validate_experiment_type(cls, experiment_type, info):
                 f'For station {station}, allowed experiment types are '
                 f'{", ".join(allowed_experiment_types)}. '
                 f'Supplied experiment type {experiment_type} is not allowed.')
+        import_scanparser(station, experiment_type)
         return experiment_type
 
 

From 278eb49ebd46ccf8322506516dd955ae34c10664 Mon Sep 17 00:00:00 2001
From: Keara Soloway <kls286@cornell.edu>
Date: Thu, 14 May 2026 10:19:07 -0400
Subject: [PATCH 48/76] fix: saxswaxs processor imports & docstring typo

---
 CHAP/saxswaxs/processor.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/CHAP/saxswaxs/processor.py b/CHAP/saxswaxs/processor.py
index f2933d86..5c8621ef 100755
--- a/CHAP/saxswaxs/processor.py
+++ b/CHAP/saxswaxs/processor.py
@@ -745,7 +745,7 @@ def process(self, data):
         # pylint: enable=import-error
 
         # Local modules
-        from CHAP.common import (
+        from CHAP.common.processor import (
             MapProcessor,
             NexusToZarrProcessor,
         )
@@ -1238,7 +1238,7 @@ def process(self, data, idx_slice=None):
         import os
 
         # Local modules
-        from CHAP.common import MapSliceProcessor
+        from CHAP.common.map_utils import MapSliceProcessor
         from CHAP.pipeline import PipelineData
         #from CHAP.saxswaxs.processor import PyfaiIntegrationProcessor
 
@@ -1278,7 +1278,7 @@ def set_logger(pipeline_item):
         ).process(None, idx_slice=idx_slice)
 
         def _get_detector_data(values, name):
-            "Get the detector data."""
+            """Get the detector data."""
             for v in values:
                 if os.path.basename(v['path']) == name:
                     return v['data']

From 8d4d5a4c27b4c3d19616d9c56a6c7ee5b929c774 Mon Sep 17 00:00:00 2001
From: Keara Soloway <kls286@cornell.edu>
Date: Thu, 14 May 2026 10:33:09 -0400
Subject: [PATCH 49/76] fix: erroneous in-place modification of pipeline data
 in UpdateValuesProcessor

---
 CHAP/saxswaxs/processor.py | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/CHAP/saxswaxs/processor.py b/CHAP/saxswaxs/processor.py
index 5c8621ef..88202735 100755
--- a/CHAP/saxswaxs/processor.py
+++ b/CHAP/saxswaxs/processor.py
@@ -1234,6 +1234,7 @@ def process(self, data, idx_slice=None):
         # Pass detector data to PyfaiIntegration processor
         # Concatenate & return results
         # System modules
+        from copy import deepcopy
         import logging
         import os
 
@@ -1242,6 +1243,7 @@ def process(self, data, idx_slice=None):
         from CHAP.pipeline import PipelineData
         #from CHAP.saxswaxs.processor import PyfaiIntegrationProcessor
 
+        _data = deepcopy(data)
         def set_logger(pipeline_item):
             """Set the logger and logging handler for given pipeline
             item.
@@ -1286,7 +1288,7 @@ def _get_detector_data(values, name):
 
         # Use raw detector data as input to integration
         for d in self.detectors:
-            data.append(
+            _data.append(
                 PipelineData(
                     name=d.get_id(),
                     data=_get_detector_data(raw_values, d.get_id()),
@@ -1295,7 +1297,7 @@ def _get_detector_data(values, name):
         # Get integrated data
         processed_values = set_logger(
             PyfaiIntegrationProcessor(config=self.pyfai_config)
-        ).process(data, idx_slices=[idx_slice])
+        ).process(_data, idx_slices=[idx_slice])
 
         if self.raw_data:
             return raw_values + processed_values

From c75303e47c1a347437f355e9f416f4f58e865491 Mon Sep 17 00:00:00 2001
From: Keara Soloway <kls286@cornell.edu>
Date: Thu, 14 May 2026 11:37:23 -0400
Subject: [PATCH 50/76] fix: typo

---
 CHAP/edd/utils.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/CHAP/edd/utils.py b/CHAP/edd/utils.py
index f4d7a836..12c0e49f 100755
--- a/CHAP/edd/utils.py
+++ b/CHAP/edd/utils.py
@@ -1523,8 +1523,8 @@ def get_spectra_fits(
             'amplitudes': uniform_fit_amplitudes,
             'amplitudes_errors': uniform_fit_amplitudes_errors,
             'amplitudes_vary': uniform_fit_amplitudes_vary,
-            'sigmas': uniform_fit_fractions,
-            'sigmas_errors': uniform_fit_fractions_errors,
+            'sigmas': uniform_fit_sigmas,
+            'sigmas_errors': uniform_fit_sigmas_errors,
             'best_fits': uniform_fit.best_fit,
             'residuals': uniform_fit.residual,
             'redchis': uniform_fit.redchi,

From acf8b1dbafd5972bae31f80c9fab2f17171a6c20 Mon Sep 17 00:00:00 2001
From: Keara Soloway <kls286@cornell.edu>
Date: Fri, 15 May 2026 14:51:40 -0400
Subject: [PATCH 51/76] fix: module path to IndexSliceConfig

---
 CHAP/common/writer.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/CHAP/common/writer.py b/CHAP/common/writer.py
index 04d6e84b..64b35be5 100755
--- a/CHAP/common/writer.py
+++ b/CHAP/common/writer.py
@@ -26,7 +26,7 @@
     Writer,
     validate_writer_model,
 )
-from CHAP.common.models import IndexSliceConfig
+from CHAP.common.models.common import IndexSliceConfig
 
 
 
@@ -640,7 +640,7 @@ class NexusValuesWriter(Writer):
         only if the `"idx"` key is not present for an item in the
         newest `PipelineData` item in `data`. Defaults to
         `IndexSliceConfig()`.
-    :vartype idx_slice: CHAP.common.models.IndexSliceConfig, optional
+    :vartype idx_slice: CHAP.common.models.common.IndexSliceConfig, optional
     """
     path_prefix: str = ''
     resize_axis: Union[int, Literal[False]] = False

From f9e9cfb2df32799ab42871442cc71f3e80834431 Mon Sep 17 00:00:00 2001
From: Keara Soloway <kls286@cornell.edu>
Date: Fri, 15 May 2026 14:55:05 -0400
Subject: [PATCH 52/76] add: ZarrValuesWriter.resize_axis and
 ZarrValuesWriter.idx_slice

---
 CHAP/common/writer.py | 70 +++++++++++++++++++++++++++++++++----------
 1 file changed, 55 insertions(+), 15 deletions(-)

diff --git a/CHAP/common/writer.py b/CHAP/common/writer.py
index 64b35be5..d951e533 100755
--- a/CHAP/common/writer.py
+++ b/CHAP/common/writer.py
@@ -906,12 +906,24 @@ class ZarrValuesWriter(Writer):
     """Writer for updating values in arrays of an existing
     `Zarr <https://zarr.readthedocs.io/en/stable/>`__ file.
 
-    :ivar path_prefix: Prefix to prepend to all "path" fields in
-        `data` before writing. Defaults to `""`.
+    :ivar path_prefix: Prefix to use for all paths in input `data`,
+        defaults to `''`.
     :vartype path_prefix: str, optional
+    :ivar resize_axis: `False` OR the axis along which the dataset
+        should be resized if the target slice shape does not match the
+        data shape. If `False`, any mismatching shapes will just raise
+        an error. Defaults to `False`.
+    :vartype resize_axis: Union[int, Literal[False]], optional
+    :ivar idx_slice: Configuration for a slice object that will be
+        used to select the slice of the target array to write to. Used
+        only if the `"idx"` key is not present for an item in the
+        newest `PipelineData` item in `data`. Defaults to
+        `IndexSliceConfig()`.
+    :vartype idx_slice: CHAP.common.models.common.IndexSliceConfig, optional
     """
-
     path_prefix: Optional[str] = ''
+    resize_axis: Union[int, Literal[False]] = False
+    idx_slice: Optional[IndexSliceConfig] = IndexSliceConfig()
 
     def write(self, data):
         """Write values to specific paths and slices in an existing
@@ -931,11 +943,16 @@ def write(self, data):
 
         # Get list of PyfaiIntegrationProcessor results to write
         for d in self.get_pipelinedata_item(data, remove=self.remove):
-            self.zarr_writer(
-                zarrfile=zarrfile,
-                path=os.path.join(self.path_prefix, d['path']),
-                idx=d['idx'],
-                data=d['data'])
+            try:
+                self.logger.info(f'd = {d}')
+                self.zarr_writer(
+                    zarrfile=zarrfile,
+                    path=os.path.join(self.path_prefix, d['path']),
+                    idx=d.get('idx', self.idx_slice._slice),
+                    data=d['data']
+                )
+            except Exception as exc:
+                self.logger.error(exc)
 
     def zarr_writer(self, zarrfile, path, idx, data):
         """Write data to a specific dataset.
@@ -963,18 +980,41 @@ def zarr_writer(self, zarrfile, path, idx, data):
         # Check if the dataset exists
         if path not in zarrfile:
             raise ValueError(
-                f'Dataset "{path}" does not exist in the Zarr file.')
+                f'Dataset "{path}" does not exist in the Zarr file.'
+            )
 
         # Access the specified dataset
         dataset = zarrfile[path]
+        self.logger.debug(
+            f'chunks = {dataset.chunks}'
+        )
 
-        # Check that the slice shape matches the data shape
-        if dataset[idx].shape != data.shape and data.shape[0] == 1:
-            data = np.squeeze(data, axis=0)
+        data = np.asarray(data)
+
+        # Check the shape
+        self.logger.info(
+            f'data shape, target shape = {data.shape}, {dataset[idx].shape}'
+        )
         if dataset[idx].shape != data.shape:
-            raise ValueError(
-                f'Data shape {data.shape} does not match the target slice '
-                f'shape {dataset[idx].shape}.')
+            if self.resize_axis is not False:
+                # Resize along the specified axis
+                start = idx.start or 0
+                stop = start + data.shape[0]
+                newshape_axis = max(dataset.shape[self.resize_axis], stop)
+                oldshape = dataset.shape
+                newshape = (
+                    *oldshape[0:self.resize_axis],
+                    newshape_axis,
+                    *oldshape[self.resize_axis + 1:]
+                )
+                self.logger.info(
+                    f'Resizing {path} {oldshape} -> {newshape}'
+                )
+                dataset.resize(newshape)
+            else:
+                raise ValueError(
+                    f'Data shape {data.shape} does not match the target slice '
+                    f'shape {dataset[idx].shape}.')
 
         # Write the data to the specified slice
         dataset[idx] = data

From d665f2f28bde26296aeed31c0b240b26bae84728 Mon Sep 17 00:00:00 2001
From: Keara Soloway <kls286@cornell.edu>
Date: Fri, 15 May 2026 16:29:25 -0400
Subject: [PATCH 53/76] fix: preserve NXlinks when passing through
 NexusToZarrProcessor and ZarrToNexusProcessor

---
 CHAP/common/processor.py | 33 +++++++++++++++++++++++++++++----
 1 file changed, 29 insertions(+), 4 deletions(-)

diff --git a/CHAP/common/processor.py b/CHAP/common/processor.py
index cd5d48f7..1a1ff447 100755
--- a/CHAP/common/processor.py
+++ b/CHAP/common/processor.py
@@ -2209,6 +2209,7 @@ def process(self, data, chunks='auto'):
         from nexusformat.nexus import (
             NXfield,
             NXgroup,
+            NXlink,
         )
         # pylint: disable=import-error
         import zarr
@@ -2241,9 +2242,19 @@ def copy_group(nexus_group, zarr_group):
                 else:
                     zarr_group.attrs[attr_key] = attr_value.nxvalue
 
-            # Copy datasets and sub-groups
+            # Copy datasets, sub-groups, and links
+            nxlinks = {}
             for key, item in nexus_group.items():
-                if isinstance(item, NXfield):
+                if isinstance(item, NXlink):
+                    self.logger.info(f'Recording link {item.nxpath}')
+                    if item.nxfilename is not None:
+                        nxlinks[key] = {
+                            'target': item.nxtarget,
+                            'file': item.nxfilename,
+                        }
+                    else:
+                        nxlinks[key] = item.nxtarget
+                elif isinstance(item, NXfield):
                     if isinstance(item.nxdata, np.ndarray):
                         try:
                             # Determine chunks
@@ -2278,6 +2289,8 @@ def copy_group(nexus_group, zarr_group):
                     # Recursively copy subgroup
                     zarr_subgroup = zarr_group.create_group(key)
                     copy_group(item, zarr_subgroup)
+            if nxlinks:
+                zarr_group.attrs['__nxlinks__'] = nxlinks
 
         copy_group(nexus_group, zarr_group)
         return zarr_group
@@ -3514,9 +3527,10 @@ def copy_group(zarr_group, nexus_group):
                 :type: nexusformat.nexus.NXgroup
                 """
                 self.logger.info(f'Copying {zarr_group.path}')
-                # Copy attributes
+                # Copy attributes (skip the internal link-metadata key)
                 for attr_key, attr_value in zarr_group.attrs.items():
-                    nexus_group.attrs[attr_key] = attr_value
+                    if attr_key != '__nxlinks__':
+                        nexus_group.attrs[attr_key] = attr_value
 
                 # Copy datasets and sub-groups
                 for key, item in zarr_group.members():
@@ -3538,6 +3552,17 @@ def copy_group(zarr_group, nexus_group):
                         nexus_subgroup = nexus_group.create_group(key)
                         copy_group(item, nexus_subgroup)
 
+                # Recreate NXlinks
+                for link_name, link_target in \
+                        zarr_group.attrs.get('__nxlinks__', {}).items():
+                    self.logger.info(
+                        f'Creating link {zarr_group.path}/{link_name}')
+                    if isinstance(link_target, dict):
+                        nexus_group[link_name] = h5py.ExternalLink(
+                            link_target['file'], link_target['target'])
+                    else:
+                        nexus_group[link_name] = h5py.SoftLink(link_target)
+
             # Start copying from the root group
             copy_group(zarr_file, nexus_file)
 

From 72cc37190844cb4364e2e25bee2cc52aecc01009 Mon Sep 17 00:00:00 2001
From: Keara Soloway <kls286@cornell.edu>
Date: Fri, 15 May 2026 16:31:49 -0400
Subject: [PATCH 54/76] bump: pydantify idx_slice parameter in
 common.map_utils.MapSliceProcessor and saxswaxs.UpdateValuesProcessor

---
 CHAP/common/map_utils.py   | 20 ++++++++++----------
 CHAP/saxswaxs/processor.py | 12 ++++++------
 2 files changed, 16 insertions(+), 16 deletions(-)

diff --git a/CHAP/common/map_utils.py b/CHAP/common/map_utils.py
index 08551fa0..b29139f5 100755
--- a/CHAP/common/map_utils.py
+++ b/CHAP/common/map_utils.py
@@ -13,6 +13,7 @@
 from typing import Optional
 
 # Local modules
+from CHAP.common.models.common import IndexSliceConfig
 from CHAP.common.models.map import (
     Detector,
     MapConfig,
@@ -65,6 +66,9 @@ class MapSliceProcessor(Processor):
     :ivar scan_numbers: Numbers of scans from which to read slices of
         raw data.
     :vartype scan_numbers: list[int]
+    :ivar idx_slice: Parameters for the slice of each scan to process
+        Defaults to `IndexSliceConfig()`.
+    :vartype idx_slice: CHAP.common.models.common.IndexSliceConfig, optional
     """
 
     pipeline_fields: dict = Field(
@@ -77,9 +81,9 @@ class MapSliceProcessor(Processor):
     spec_file: FilePath
     scan_number: Optional[conint(gt=0)] = None
     scan_numbers: Optional[conlist(item_type=conint(gt=0))] = None
+    idx_slice: Optional[IndexSliceConfig] = IndexSliceConfig()
 
-    def process(self, data,
-                idx_slice={'start': 0, 'step': 1}):
+    def process(self, data):
 
         """Aggregate partial spec and detector data from one or more
         scans in a map, returning results in a format suitable for
@@ -96,11 +100,6 @@ def process(self, data,
             has the value `'common.models.map.MapConfig'` for the
             `'schema'` key.
         :type data: list[PipelineData]
-        :param idx_slice: Parameters for the slice of each scan to
-            process (slice parameters are the usual for the python
-            `slice` object: `'start'`, `'stop'`, and `'step'`).
-            Defaults to `{'start': 0, 'step': 1}`.
-        :type idx_slice: dict[str, int], optional
         :return: Slice of map data, ready to be written to a map
              container.
         :rtype: list[dict[str, Any]]
@@ -143,8 +142,8 @@ def get_detector_data(scan, detector, index):
         sorted_scan_numbers = sorted(
             self.scan_numbers, key=lambda sn: scan_positions[sn])
 
-        slice_start = idx_slice.get('start', 0)
-        slice_step = idx_slice.get('step', 1)
+        slice_start = self.idx_slice._slice.start
+        slice_step = self.idx_slice._slice.step
 
         # Collect per-scan metadata; assumes uniform npts across scans
         # for index_offset calculation (index_offset = map_pos * npts)
@@ -154,7 +153,8 @@ def get_detector_data(scan, detector, index):
             npts_scan = int(scan.spec_scan_npts)
             index_offset = scan_positions[sn] * npts_scan
             # Cap stop at npts_scan so map_indices and data stay in sync
-            slice_stop = min(idx_slice.get('stop', npts_scan), npts_scan)
+            slice_stop = min(self.idx_slice._slice.stop, npts_scan) \
+                if self.idx_slice._slice.stop > 0 else npts_scan
             scan_indices = range(npts_scan)[
                 slice(slice_start, slice_stop, slice_step)]
             map_indices = slice(
diff --git a/CHAP/saxswaxs/processor.py b/CHAP/saxswaxs/processor.py
index 88202735..232db427 100755
--- a/CHAP/saxswaxs/processor.py
+++ b/CHAP/saxswaxs/processor.py
@@ -22,6 +22,7 @@
 import numpy as np
 
 # Local modules
+from CHAP.common.models.common import IndexSliceConfig
 from CHAP.common.models.map import (
     Detector,
     MapConfig,
@@ -1211,8 +1212,9 @@ class UpdateValuesProcessor(Processor):
     scan_number: conint(gt=0)
     detectors: conlist(item_type=Detector, min_length=1)
     raw_data: Optional[bool] = True
+    idx_slice: Optional[IndexSliceConfig] = IndexSliceConfig()
 
-    def process(self, data, idx_slice=None):
+    def process(self, data):
         """Processes a slice of data for updating values in an existing
         container for a SAXS/WAXS experiment.
 
@@ -1266,18 +1268,16 @@ def set_logger(pipeline_item):
             pipeline_item.logger.addHandler(handler)
             return pipeline_item
 
-        if idx_slice is None:
-            idx_slice = {'start':0, 'step': 1}
-
         # Read in slice of raw data
         raw_values = set_logger(
             MapSliceProcessor(
                 map_config=self.map_config,
                 detectors=self.detectors,
                 spec_file=str(self.spec_file),
-                scan_number=self.scan_number,
+                scan_numbers=[self.scan_number],
+                idx_slice=self.idx_slice
             )
-        ).process(None, idx_slice=idx_slice)
+        ).process(None)
 
         def _get_detector_data(values, name):
             """Get the detector data."""

From a5d616ae58fb7aae0bdd420b2620fb2eeb279c8b Mon Sep 17 00:00:00 2001
From: Keara Soloway <kls286@cornell.edu>
Date: Fri, 15 May 2026 16:35:55 -0400
Subject: [PATCH 55/76] rm: idx_slices parameter for
 saxswaxs.PyfaiIntegrationProcessor

---
 CHAP/saxswaxs/processor.py | 13 ++-----------
 1 file changed, 2 insertions(+), 11 deletions(-)

diff --git a/CHAP/saxswaxs/processor.py b/CHAP/saxswaxs/processor.py
index 232db427..ac92125e 100755
--- a/CHAP/saxswaxs/processor.py
+++ b/CHAP/saxswaxs/processor.py
@@ -499,7 +499,7 @@ class PyfaiIntegrationProcessor(Processor):
         init_var=True)
     config: PyfaiIntegrationConfig
 
-    def process(self, data, idx_slices=None):
+    def process(self, data):
         """Perform a set of integrations on 2D detector data.
 
         :param data: Input data.
@@ -516,19 +516,11 @@ def process(self, data, idx_slices=None):
         # System modules
         import time
 
-        if idx_slices is None:
-            idx_slices = [{'start':0, 'step': 1}]
-
         # Organize input for integrations
         input_data = {d['name']: d['data']
             for d in [d for d in data if isinstance(d['data'], np.ndarray)]}
         ais = {ai.get_id(): ai for ai in self.config.azimuthal_integrators}
 
-        # Finalize idx slice for results
-        idx = tuple(slice(idx_slice.get('start'),
-                     idx_slice.get('stop'),
-                     idx_slice.get('step')) for idx_slice in idx_slices)
-
         # Perform integration(s), package results for ZarrResultsWriter
         results = []
         nframes = len(input_data[list(input_data.keys())[0]])
@@ -544,7 +536,6 @@ def process(self, data, idx_slices=None):
                 [
                     {
                         'path': f'{integration.name}/data/I',
-                        'idx': idx,
                         'data': np.asarray(result['intensities']),
                     },
                 ]
@@ -1297,7 +1288,7 @@ def _get_detector_data(values, name):
         # Get integrated data
         processed_values = set_logger(
             PyfaiIntegrationProcessor(config=self.pyfai_config)
-        ).process(_data, idx_slices=[idx_slice])
+        ).process(_data)
 
         if self.raw_data:
             return raw_values + processed_values

From 140104452f3e340459a865cef73f47d8df2a0033 Mon Sep 17 00:00:00 2001
From: Keara Soloway <kls286@cornell.edu>
Date: Fri, 15 May 2026 16:37:50 -0400
Subject: [PATCH 56/76] feat: support 0-sized setup arrays in
 saxswaxs.SetupProcessor

---
 CHAP/saxswaxs/processor.py | 19 ++++++++-----------
 1 file changed, 8 insertions(+), 11 deletions(-)

diff --git a/CHAP/saxswaxs/processor.py b/CHAP/saxswaxs/processor.py
index ac92125e..deaf1dcf 100755
--- a/CHAP/saxswaxs/processor.py
+++ b/CHAP/saxswaxs/processor.py
@@ -575,7 +575,7 @@ class SetupResultsProcessor(Processor):
         },
         init_var=True)
     config: PyfaiIntegrationConfig
-    dataset_shape: conlist(item_type=conint(gt=0), min_length=1)
+    dataset_shape: conlist(item_type=conint(ge=0), min_length=1)
     dataset_chunks: Optional[
         Union[
             Literal['auto'],
@@ -704,9 +704,9 @@ class SetupProcessor(Processor):
     # Pipeline to pass validation.
     map_config: MapConfig = None
     pyfai_config: PyfaiIntegrationConfig
-    detectors: conlist(item_type=Detector, min_length=1)
+    detectors: conlist(item_type=Detector, min_length=0)
     dataset_shape: Optional[
-        conlist(item_type=conint(gt=0), min_length=1)] = None
+        conlist(item_type=conint(ge=0), min_length=1)] = None
     dataset_chunks: Optional[
         Union[
             Literal['auto'],
@@ -768,7 +768,8 @@ def set_logger(pipeline_item):
 
         # Get NXroot container for raw data map
         map_processor_kwargs = {
-            'config': self.map_config
+            'config': self.map_config,
+            'remove_constant_dims': False,
         }
         if self.raw_data:
             map_processor_kwargs['detector_config'] = {
@@ -778,13 +779,9 @@ def set_logger(pipeline_item):
             map_processor_kwargs['detector_config'] = {
                 'detectors': []
             }
-        setup_map_processor = set_logger(
-            MapProcessor(
-                **map_processor_kwargs
-                # config=self.map_config,
-                # detector_config={'detectors': self.detectors},
-            )
-        )
+            self.map_config.spec_scans[0].scan_numbers = []
+
+        setup_map_processor = set_logger(MapProcessor(**map_processor_kwargs))
         ddata = [
             PipelineData(
                 data=setup_map_processor.process(

From eb06d7b335ada7d8c8b30f25787fe1f7a60570ec Mon Sep 17 00:00:00 2001
From: Keara Soloway <kls286@cornell.edu>
Date: Mon, 18 May 2026 08:26:23 -0400
Subject: [PATCH 57/76] fix: do not duplicate log handlers for PipelineItems
 with the same name

---
 CHAP/pipeline.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/CHAP/pipeline.py b/CHAP/pipeline.py
index 1b206945..2f606d37 100755
--- a/CHAP/pipeline.py
+++ b/CHAP/pipeline.py
@@ -88,7 +88,7 @@ def validate_pipelineitem_after(self):
             log_handler.setFormatter(logging.Formatter(
                 '{asctime}: {name:20}: {levelname}: {message}',
                 datefmt='%Y-%m-%d %H:%M:%S', style='{'))
-            self.logger.addHandler(log_handler)
+            self.logger.handlers = [log_handler]
         self.logger.setLevel(self.log_level)
         # Optinal, but it's already available in the 'name' field
         #if self.get_schema() is None:

From d6587dd6e0ea5414f053757c032f74928a263431 Mon Sep 17 00:00:00 2001
From: Keara Soloway <kls286@cornell.edu>
Date: Mon, 18 May 2026 08:26:58 -0400
Subject: [PATCH 58/76] style: include lineno in log formatters

---
 CHAP/pipeline.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/CHAP/pipeline.py b/CHAP/pipeline.py
index 2f606d37..ba843ca3 100755
--- a/CHAP/pipeline.py
+++ b/CHAP/pipeline.py
@@ -86,7 +86,7 @@ def validate_pipelineitem_after(self):
             self.logger.propagate = False
             log_handler = logging.StreamHandler()
             log_handler.setFormatter(logging.Formatter(
-                '{asctime}: {name:20}: {levelname}: {message}',
+                '{asctime}: {name:20} (L{lineno}): {levelname}: {message}',
                 datefmt='%Y-%m-%d %H:%M:%S', style='{'))
             self.logger.handlers = [log_handler]
         self.logger.setLevel(self.log_level)

From 47b24e0a420a426ee872f09bc106357f3175e825 Mon Sep 17 00:00:00 2001
From: Keara Soloway <kls286@cornell.edu>
Date: Thu, 21 May 2026 15:46:53 -0400
Subject: [PATCH 59/76] add: support detector_config in addition to detectors
 field in MapSliceProcessor

---
 CHAP/common/map_utils.py | 24 +++++++++++++++++++++---
 1 file changed, 21 insertions(+), 3 deletions(-)

diff --git a/CHAP/common/map_utils.py b/CHAP/common/map_utils.py
index b29139f5..91c57e85 100755
--- a/CHAP/common/map_utils.py
+++ b/CHAP/common/map_utils.py
@@ -15,6 +15,7 @@
 # Local modules
 from CHAP.common.models.common import IndexSliceConfig
 from CHAP.common.models.map import (
+    DetectorConfig,
     Detector,
     MapConfig,
 )
@@ -74,10 +75,12 @@ class MapSliceProcessor(Processor):
     pipeline_fields: dict = Field(
         default={
             'map_config': 'common.models.map.MapConfig',
+            'detector_config': 'common.models.map.DetectorConfig'
         },
         init_var=True)
     map_config: MapConfig
-    detectors: conlist(item_type=Detector, min_length=1)
+    detector_config: DetectorConfig
+    detectors: Optional[conlist(item_type=Detector)] = None
     spec_file: FilePath
     scan_number: Optional[conint(gt=0)] = None
     scan_numbers: Optional[conlist(item_type=conint(gt=0))] = None
@@ -231,7 +234,7 @@ def get_detector_data(scan, detector, index):
                     ]),
                     'idx': merged_idx,
                 })
-            for det in self.detectors:
+            for det in self.detector_config.detectors:
                 data_points.append({
                     'path': (f'{self.map_config.title}'
                              f'/data/{det.get_id()}'),
@@ -285,7 +288,7 @@ def get_detector_data(scan, detector, index):
                         for i in ps['scan_indices']
                     ]),
                     'idx': ps['map_indices'],
-                } for det in self.detectors])
+                } for det in self.detector_config.detectors])
         return data_points
 
     @model_validator(mode='before')
@@ -313,6 +316,21 @@ def validate_scan_numbers(self):
             self.scan_numbers.append(self.scan_number)
         return self
 
+    @model_validator(mode='before')
+    def fill_detector_config(cls, data):
+        if not isinstance(data, dict):
+            return data
+        if 'detector_config' not in data or data['detector_config'] is None:
+            if data.get('detectors') is not None:
+                data['detector_config'] = DetectorConfig(
+                    detectors=data['detectors']
+                )
+            else:
+                raise ValueError(
+                    'detector_config is required; alternatively, provide detectors'
+                )
+        return data
+
 
 class SpecScanToMapConfigProcessor(Processor):
     """Processor to get the

From ea2510cea9dff44ef7007a994db5a9301d35cbba Mon Sep 17 00:00:00 2001
From: Keara Soloway <kls286@cornell.edu>
Date: Thu, 21 May 2026 15:49:11 -0400
Subject: [PATCH 60/76] feat: in zarr_tree methods of pyFAI integration
 configs, support adding attributes that will result in NXlinks when converted
 to NeXus format

---
 CHAP/common/models/integration.py | 69 ++++++++++++++++++++++++-------
 1 file changed, 54 insertions(+), 15 deletions(-)

diff --git a/CHAP/common/models/integration.py b/CHAP/common/models/integration.py
index fd88bb48..1bce0d24 100755
--- a/CHAP/common/models/integration.py
+++ b/CHAP/common/models/integration.py
@@ -634,17 +634,37 @@ def integrate(self, azimuthal_integrators, data):
 
         return results
 
-    def zarr_tree(self, dataset_shape, dataset_chunks='auto'):
+    def zarr_tree(self, dataset_shape, dataset_chunks='auto', nxlinks=None):
         """Return a dictionary representing a `zarr.group` that can be
         used to contain results from this integration.
 
-        :return: A `zarr.group` that can be used to contain the
-            integration results.
+        :param dataset_shape: Shape of the measurement (scan) dimensions
+            of the output dataset, excluding the integration dimensions.
+        :type dataset_shape: tuple[int, ...]
+        :param dataset_chunks: Chunk shape along the scan dimensions, or
+            ``'auto'``, defaults to ``'auto'``.
+        :type dataset_chunks: list[int] or str, optional
+        :param nxlinks: NeXus path(s) to link into the ``data`` group.
+            When the zarr tree is written to a ``.zarr`` file and
+            converted to ``.nxs`` with
+            :class:`~CHAP.common.processor.ZarrToNexusProcessor`, each
+            path produces an ``NXlink`` whose name is
+            ``os.path.basename(path)``.  Accepts a single path string or
+            a list of path strings.
+        :type nxlinks: str or list[str], optional
+        :returns: Nested dict representing the zarr group tree for this
+            integration.
         :rtype: dict
         """
         # Third party modules
         #import json
 
+        if isinstance(nxlinks, str):
+            nxlinks = [nxlinks]
+        data_attrs = {**self.get_axes_indices(len(dataset_shape))}
+        if nxlinks:
+            data_attrs['__nxlinks__'] = {
+                os.path.basename(p): p for p in nxlinks}
         tree = {
             # NXprocess
             'attributes': {
@@ -654,10 +674,7 @@ def zarr_tree(self, dataset_shape, dataset_chunks='auto'):
             'children': {
                 'data': {
                     # NXdata
-                    'attributes': {
-                        # 'axes': self.result_axes(),
-                        **self.get_axes_indices(len(dataset_shape))
-                    },
+                    'attributes': data_attrs,
                     'children': {
                         'I': {
                             # NXfield
@@ -732,28 +749,50 @@ def validate_config(cls, data):
                 data['azimuthal_integrators'] = ais
         return data
 
-    def zarr_tree(self, dataset_shape, dataset_chunks='auto'):
+    def zarr_tree(self, dataset_shape, dataset_chunks='auto', nxlinks=None):
         """Return a dictionary representing a `zarr.group` that can be
         used to contain results from
         :class:`~CHAP.saxswaxs.PyfaiIntegrationProcessor`.
 
-        :return: A `zarr.group` that can be used to contain the
-            integration results.
+        Each integration defined in :attr:`integrations` gets its own
+        sub-group keyed by the integration's ``name``.  See
+        :meth:`PyfaiIntegratorConfig.zarr_tree` for the structure of
+        each sub-group.
+
+        :param dataset_shape: Shape of the measurement (scan) dimensions
+            of the output dataset, excluding the integration dimensions.
+        :type dataset_shape: tuple[int, ...]
+        :param dataset_chunks: Chunk shape along the scan dimensions, or
+            ``'auto'``, defaults to ``'auto'``.
+        :type dataset_chunks: list[int] or str, optional
+        :param nxlinks: NeXus links to inject into each integration's
+            ``data`` group.  May be a single path string or list of path
+            strings (forwarded to every integration), or a dict keyed by
+            integration name mapping each integration to its own path(s).
+            See :meth:`PyfaiIntegratorConfig.zarr_tree` for details on
+            how individual paths are handled.
+        :type nxlinks: str or list[str] or dict[str, str or list[str]],
+            optional
+        :returns: Nested dict representing the zarr group tree for all
+            integrations.
         :rtype: dict
         """
         ais = {ai.get_id(): ai for ai in self.azimuthal_integrators}
         for integration in self.integrations:
             integration.init_placeholder_results(ais)
+        if not isinstance(nxlinks, dict):
+            nxlinks = {intg.name: nxlinks for intg in self.integrations}
         tree = {
             'root': {
                 'attributes': {
                     'description': 'Container for processed SAXS/WAXS data'
                 },
-                'children': {
-                    integration.name: integration.zarr_tree(
-                        dataset_shape, dataset_chunks)
-                    for integration in self.integrations
-                }
+            },
+            'children': {
+                integration.name: integration.zarr_tree(
+                    dataset_shape, dataset_chunks,
+                    nxlinks=nxlinks.get(integration.name))
+                for integration in self.integrations
             }
         }
         return tree

From 740072ba2f6549c449653f7f617515d7368623cc Mon Sep 17 00:00:00 2001
From: Keara Soloway <kls286@cornell.edu>
Date: Thu, 21 May 2026 15:54:21 -0400
Subject: [PATCH 61/76] doc: update MapSliceProcessor docstring

---
 CHAP/common/map_utils.py | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/CHAP/common/map_utils.py b/CHAP/common/map_utils.py
index 91c57e85..384aabd4 100755
--- a/CHAP/common/map_utils.py
+++ b/CHAP/common/map_utils.py
@@ -58,9 +58,8 @@ class MapSliceProcessor(Processor):
 
     :ivar map_config: Map configuration.
     :vartype map_config: MapConfig
-    :ivar detectors: Detector configurations.
-    :vartype detectors:
-        list[:class:`~CHAP.common.models.map.Detector`]
+    :ivar detector_config: Detector configurations.
+    :vartype detector_config: :class:`~CHAP.common.models.map.DetectorConfig`
     :ivar spec_file: SPEC file containing scan from which to read a
         slice of raw data.
     :vartype spec_file: pydantic.FilePath

From 1fda1d39e91fd72ce9a07865bdc55c5fbdee04eb Mon Sep 17 00:00:00 2001
From: Keara Soloway <kls286@cornell.edu>
Date: Thu, 21 May 2026 15:57:53 -0400
Subject: [PATCH 62/76] feat: support slicewise processing for corrected data

---
 CHAP/saxswaxs/models.py    | 356 ++++++++++++++++++++++++++
 CHAP/saxswaxs/processor.py | 496 ++++++++++++++++++++++---------------
 CHAP/saxswaxs/utils.py     |  60 +++++
 3 files changed, 709 insertions(+), 203 deletions(-)
 create mode 100644 CHAP/saxswaxs/models.py
 create mode 100644 CHAP/saxswaxs/utils.py

diff --git a/CHAP/saxswaxs/models.py b/CHAP/saxswaxs/models.py
new file mode 100644
index 00000000..86df7a9a
--- /dev/null
+++ b/CHAP/saxswaxs/models.py
@@ -0,0 +1,356 @@
+"""Models to help construct containers for results of
+``saxswaxs.*CorrectionProcessor`` tools."""
+
+# System modules
+from functools import cached_property
+import os
+import re
+from typing import Literal, Optional, Union
+
+# Third party modules
+from pydantic import (
+    confloat,
+    conlist,
+    model_validator,
+)
+
+# Local modules
+from CHAP import version as chap_version
+from CHAP.models import CHAPBaseModel
+from CHAP.common.models.common import IndexSliceConfig
+from CHAP.common.models.map import SpecScans
+
+
+class Background(SpecScans):
+    """Configuration for background scan data associated with a
+    correction.
+
+    Extends :class:`~CHAP.common.models.map.SpecScans` with an
+    optional index slice so that only a subset of scan steps is used
+    when reading background images.
+
+    :ivar idx_slice: Index slice selecting which scan steps of the
+        background scan(s) to read and average.  Defaults to all steps.
+    :vartype idx_slice: IndexSliceConfig
+    """
+
+    idx_slice: IndexSliceConfig = IndexSliceConfig()
+
+    def zarr_arrays(self, integration_shape):
+        """Return a dictionary describing the zarr array that will hold
+        the averaged integrated background intensity.
+
+        :param integration_shape: Shape of one frame of integration
+            results, as returned by
+            :attr:`~CHAP.common.models.integration.PyfaiIntegratorConfig.result_shape`.
+        :type integration_shape: tuple[int, ...]
+        :returns: Dict mapping the array name ``'I_background'`` to a
+            zarr array specification (``dtype``, ``shape``, and
+            ``attributes`` keys) compatible with
+            :func:`~CHAP.saxswaxs.utils.dict_to_zarr`.
+        :rtype: dict
+        """
+        return {
+            'I_background': {
+                'attributes': {
+                    'long_name': 'Intensity (a.u)',
+                    'units': 'a.u,'
+                },
+                'dtype': 'float64',
+                'shape': integration_shape,
+            }
+        }
+
+
+class CorrectionConfig(CHAPBaseModel):
+    """Base configuration for a single SAXS/WAXS correction step.
+
+    Describes one correction (flux, flux+absorption, or
+    flux+absorption+background) to be applied to azimuthally integrated
+    detector data.  Subclasses pin ``correction_type`` and may require
+    additional fields such as ``background``.
+
+    :ivar correction_type: Identifies the correction algorithm.
+        One of ``'flux'``, ``'flux_absorption'``, or
+        ``'flux_absorption_background'``.
+    :vartype correction_type: str
+    :ivar name: Human-readable name used as the key for this
+        correction's group in the output zarr / NeXus tree.
+    :vartype name: str
+    :ivar uncorrected_data_name: Name of the
+        :class:`~CHAP.common.models.integration.PyfaiIntegratorConfig`
+        integration whose output serves as the uncorrected input for
+        this correction.  Must match the ``name`` field of one of the
+        integrations in the associated
+        :class:`~CHAP.common.models.integration.PyfaiIntegrationConfig`.
+    :vartype uncorrected_data_name: str
+    :ivar presample_intensity_reference_rate: Fixed reference counting
+        rate for the pre-sample beam intensity monitor.  When ``None``
+        the rate is computed from the scan data as
+        ``nanmean(presample_intensity / dwell_time_actual)``.
+    :vartype presample_intensity_reference_rate: float, optional
+    :ivar background: Background scan configuration.  Required for
+        ``'flux_absorption'`` and ``'flux_absorption_background'``
+        correction types.
+    :vartype background: Background, optional
+    """
+
+    correction_type: Literal['flux', 'flux_absorption',
+                             'flux_absorption_background']
+    name: str
+    uncorrected_data_name: str
+    presample_intensity_reference_rate: Optional[float] = None
+    background: Optional[Background] = None
+
+    def zarr_tree(self, dataset_shape, dataset_chunks, integration_shape,
+                  nxlinks=None):
+        """Return a dictionary representing the zarr tree for this
+        correction's output container.
+
+        The returned tree is compatible with
+        :func:`~CHAP.saxswaxs.utils.dict_to_zarr` and, after conversion
+        with :class:`~CHAP.common.processor.ZarrToNexusProcessor`,
+        produces an ``NXprocess`` group containing a ``data`` sub-group
+        with an ``I_corrected`` dataset and, when a ``background`` is
+        configured, an ``I_background`` dataset.
+
+        :param dataset_shape: Shape of the measurement (scan) dimensions
+            of the output dataset, excluding the integration dimensions.
+        :type dataset_shape: tuple[int, ...]
+        :param dataset_chunks: Chunk shape along the scan dimensions, or
+            ``'auto'``.
+        :type dataset_chunks: list[int] or str
+        :param integration_shape: Shape of one frame of integration
+            results for the integration named by
+            ``uncorrected_data_name``.
+        :type integration_shape: tuple[int, ...]
+        :param nxlinks: NeXus path(s) to link into the ``data`` group.
+            When the zarr tree is written to a ``.zarr`` file and
+            converted to ``.nxs`` with
+            :class:`~CHAP.common.processor.ZarrToNexusProcessor`, each
+            path produces an ``NXlink`` whose name is
+            ``os.path.basename(path)``.  Accepts a single path string or
+            a list of path strings.  All links must be explicit; none are
+            auto-generated.
+        :type nxlinks: str or list[str], optional
+        :returns: Nested dict representing the zarr group tree for this
+            correction.
+        :rtype: dict
+        """
+        if isinstance(nxlinks, str):
+            nxlinks = [nxlinks]
+        data_attrs = {}
+        if nxlinks:
+            data_attrs['__nxlinks__'] = {
+                os.path.basename(p): p for p in nxlinks
+            }
+        if self.background is None:
+            background_arrays = {}
+        else:
+            background_arrays = self.background.zarr_arrays(integration_shape)
+            data_attrs['background'] = str(self.background.model_dump())
+        return {
+            # NXprocess
+            'attributes': {
+                'correction_type': self.correction_type,
+                'default': 'data',
+            },
+            'children': {
+                'program': 'CHAP.saxswaxs',
+                'version': chap_version,
+                'data': {
+                    # NXdata
+                    'attributes': data_attrs,
+                    'children': {
+                        'I_corrected': {
+                            'attributes': {
+                                'long_name': 'Intensity (a.u)',
+                                'units': 'a.u,'
+                            },
+                            'dtype': 'float64',
+                            'shape': (*dataset_shape, *integration_shape),
+                        },
+                        **background_arrays,
+                    }
+                }
+            }
+        }
+
+    @cached_property
+    def processor_name(self):
+        """Name of the processor class that implements this correction.
+
+        Derived from ``correction_type`` by capitalising each
+        ``'_'``-separated word and appending ``'CorrectionProcessor'``
+        (e.g. ``'flux_absorption'`` →
+        ``'FluxAbsorptionCorrectionProcessor'``).
+
+        :type: str
+        """
+        return ''.join(
+            [x.capitalize() for x in self.correction_type.split('_')] +
+            ['CorrectionProcessor']
+        )
+
+    @cached_property
+    def processor_module(self):
+        """Module object containing the processor class for this
+        correction.
+
+        :type: module
+        """
+        return __import__('CHAP.saxswaxs.processor',
+                          fromlist=[self.processor_name])
+
+    @cached_property
+    def processor_class(self):
+        """Processor class that implements this correction.
+
+        :type: type
+        """
+        return getattr(self.processor_module, self.processor_name)
+
+    @property
+    def processor(self):
+        """A new instance of the processor class for this correction,
+        initialised with the current configuration.
+
+        :type: Processor
+        """
+        return self.processor_class(config=self.model_dump())
+
+
+class CorrectionsConfig(CHAPBaseModel):
+    """Configuration container for an ordered list of SAXS/WAXS
+    correction steps to apply to integrated detector data.
+
+    :ivar corrections: Ordered list of correction configurations.
+    :vartype corrections: list[CorrectionConfig]
+    """
+
+    corrections: conlist(item_type=CorrectionConfig)
+
+    def zarr_tree(self, dataset_shape, dataset_chunks,
+                  integration_shapes, nxlinks=None):
+        """Return a dictionary representing the zarr tree for all
+        corrections in this configuration.
+
+        Each correction gets its own sub-group keyed by
+        :attr:`CorrectionConfig.name`.  See
+        :meth:`CorrectionConfig.zarr_tree` for the structure of each
+        sub-group.
+
+        :param dataset_shape: Shape of the measurement (scan) dimensions,
+            excluding integration dimensions.
+        :type dataset_shape: tuple[int, ...]
+        :param dataset_chunks: Chunk shape along the scan dimensions, or
+            ``'auto'``.
+        :type dataset_chunks: list[int] or str
+        :param integration_shapes: Mapping from integration name to the
+            shape of one integration result frame.  Used to look up the
+            ``integration_shape`` for each correction via
+            :attr:`CorrectionConfig.uncorrected_data_name`.
+        :type integration_shapes: dict[str, tuple[int, ...]]
+        :param nxlinks: NeXus links to inject into each correction's
+            ``data`` group.  May be a single path string or list of path
+            strings (forwarded to every correction), or a dict keyed by
+            correction name mapping each correction to its own path(s).
+            See :meth:`CorrectionConfig.zarr_tree` for details on how
+            individual paths are handled.
+        :type nxlinks: str or list[str] or dict[str, str or list[str]],
+            optional
+        :returns: Nested dict representing the zarr group tree for all
+            corrections.
+        :rtype: dict
+        """
+        if not isinstance(nxlinks, dict):
+            nxlinks = {corr.name: nxlinks for corr in self.corrections}
+        return {
+            'root': {
+                'attributes': {},
+            },
+            'children': {
+                corr.name: corr.zarr_tree(
+                    dataset_shape, dataset_chunks,
+                    integration_shapes.get(
+                        corr.uncorrected_data_name, None
+                    ),
+                    nxlinks=nxlinks.get(corr.name),
+                )
+                for corr in self.corrections
+            }
+        }
+
+
+class FluxCorrectionConfig(CorrectionConfig):
+    """Correction configuration for flux-only correction.
+
+    Applies a flux correction that normalises the measured intensity by
+    the pre-sample beam monitor counts, referenced to a fixed counting
+    rate.  No background scan is required.
+    """
+
+    correction_type: Literal['flux'] = 'flux'
+
+
+class FluxAbsorptionCorrectionConfig(FluxCorrectionConfig):
+    """Correction configuration for combined flux and absorption
+    correction.
+
+    Extends :class:`FluxCorrectionConfig` with a required background
+    scan used to determine the sample transmission.
+
+    :ivar background: Background scan configuration used to compute
+        the sample transmission term.
+    :vartype background: Background
+    """
+
+    correction_type: Literal['flux_absorption'] = 'flux_absorption'
+    background: Background
+
+
+class FluxAbsorptionBackgroundCorrectionConfig(
+        FluxAbsorptionCorrectionConfig):
+    """Correction configuration for combined flux, absorption, and
+    background-subtraction correction with optional thickness
+    normalisation.
+
+    Extends :class:`FluxAbsorptionCorrectionConfig` with an integrated
+    background subtraction step and an optional sample thickness or
+    linear attenuation coefficient for thickness normalisation.  At
+    most one of ``sample_thickness_cm`` and ``sample_mu_inv_cm`` may be
+    provided.
+
+    :ivar background: Background scan configuration.
+    :vartype background: Background
+    :ivar sample_thickness_cm: Sample thickness in centimetres.  When
+        provided, corrected intensities are divided by this value.
+        Mutually exclusive with ``sample_mu_inv_cm``.
+    :vartype sample_thickness_cm: float, optional
+    :ivar sample_mu_inv_cm: Sample linear attenuation coefficient in
+        inverse centimetres.  When provided, the effective thickness is
+        derived from the measured transmission.  Mutually exclusive with
+        ``sample_thickness_cm``.
+    :vartype sample_mu_inv_cm: float, optional
+    """
+
+    correction_type: Literal[
+        'flux_absorption_background'] = 'flux_absorption_background'
+    background: Background
+    sample_thickness_cm: Optional[confloat(gt=0)]
+    sample_mu_inv_cm: Optional[confloat(gt=0)]
+
+    @model_validator(mode='after')
+    def validate_thickness(self):
+        """Ensure ``sample_thickness_cm`` and ``sample_mu_inv_cm`` are
+        not both specified.
+
+        :raises ValueError: If both fields are set.
+        :returns: The validated model instance.
+        :rtype: FluxAbsorptionBackgroundCorrectionConfig
+        """
+        if self.sample_thickness_cm and self.sample_mu_inv_cm:
+            raise ValueError(
+                'Use sample_thickness_cm OR sample_mu_inv_cm, not both.'
+            )
+        return self
diff --git a/CHAP/saxswaxs/processor.py b/CHAP/saxswaxs/processor.py
index deaf1dcf..4f8872e1 100755
--- a/CHAP/saxswaxs/processor.py
+++ b/CHAP/saxswaxs/processor.py
@@ -24,12 +24,21 @@
 # Local modules
 from CHAP.common.models.common import IndexSliceConfig
 from CHAP.common.models.map import (
+    DetectorConfig,
     Detector,
     MapConfig,
 )
 from CHAP.common.models.integration import PyfaiIntegrationConfig
 from CHAP.common.processor import ExpressionProcessor
 from CHAP.processor import Processor
+from CHAP.pipeline import PipelineData
+from CHAP.saxswaxs.models import (
+    CorrectionsConfig,
+    FluxCorrectionConfig,
+    FluxAbsorptionCorrectionConfig,
+    FluxAbsorptionBackgroundCorrectionConfig,
+)
+from CHAP.saxswaxs.utils import dict_to_zarr
 
 
 class CfProcessor(Processor):
@@ -216,7 +225,7 @@ def process(
 
 class FluxCorrectionProcessor(ExpressionProcessor):
     """Processor for flux correction."""
-
+    config: FluxCorrectionConfig
     def process(
             self, data, presample_intensity_reference_rate=None,
             nxprocess=False):
@@ -252,7 +261,7 @@ def process(
             data, name='presample_intensity',
         )
         intensity = self.get_data(
-            data, name='intensity',
+            data, name=self.config.uncorrected_data_name,
         )
         # nxfieldtable = {
         #     'intensity': intensity,
@@ -287,7 +296,7 @@ def process(
 
 class FluxAbsorptionCorrectionProcessor(ExpressionProcessor):
     """Processor for flux and absorption correction."""
-
+    config: FluxAbsorptionCorrectionConfig
     def process(
             self, data, presample_intensity_reference_rate=None,
             nxprocess=False):
@@ -316,7 +325,7 @@ def process(
         :rtype: Any
         """
         intensity = self.get_data(
-            data, name='intensity',
+            data, name=self.config.uncorrected_data_name, #'intensity',
         )
 
         if presample_intensity_reference_rate is None:
@@ -366,7 +375,7 @@ def process(
 class FluxAbsorptionBackgroundCorrectionProcessor(ExpressionProcessor):
     """Processor for flux, absorption, and background correction as
     well as optional thickness correction."""
-
+    config: FluxAbsorptionBackgroundCorrectionConfig
     def process(
             self, data, presample_intensity_reference_rate=None,
             sample_thickness_cm=None, sample_mu_inv_cm=None, nxprocess=False):
@@ -414,7 +423,7 @@ def process(
             ))
 
         intensity = self.get_data(
-            data, name='intensity',
+            data, name=self.config.uncorrected_data_name,
         )
 
         if presample_intensity_reference_rate is None:
@@ -543,119 +552,6 @@ def process(self, data):
         return results
 
 
-class SetupResultsProcessor(Processor):
-    """Processor for creating an intital
-    `Zarr group <https://zarr.readthedocs.io/en/stable/api/zarr/group/#zarr.Group>`__
-    object with empty datasets for filling in by
-    :class:`~CHAP.saxswaxs.PyfaiIntegrationProcessor` and
-    :class:`~CHAP.common.ZarrValuesWriter`.
-
-    :ivar config: Initialization parameters for an instance of
-        :class:`~CHAP.common.models.integration.PyfaiIntegrationConfig`.
-    :vartype config: dict
-    :ivar dataset_shape: Shape of the completed dataset that will be
-        processed later on (shape of the measurement itself, _not_
-        including the dimensions of any signals collected at each point
-        in that measurement).
-    :vartype dataset_shape: int or list[int]
-    :ivar dataset_chunks: Extent of chunks along each dimension of the
-        completed dataset / measurement. Choose this according to how
-        you will process your data -- for example, if your
-        `dataset_shape` is `[m, n]`, and you are planning to process
-        each of the `m` rows as chunks, `dataset_chunks` should be
-        `[1, n]`. But if you plan to process each of the `n` columns as
-        chunks, `dataset_chunks` should be `[m, 1]`,
-        defaults to `"auto"`.
-    :vartype dataset_chunks: list[int] or Literal["auto"], optional
-    """
-
-    pipeline_fields: dict = Field(
-        default={
-            'config': 'common.models.integration.PyfaiIntegrationConfig'
-        },
-        init_var=True)
-    config: PyfaiIntegrationConfig
-    dataset_shape: conlist(item_type=conint(ge=0), min_length=1)
-    dataset_chunks: Optional[
-        Union[
-            Literal['auto'],
-            conlist(item_type=conint(gt=0), min_length=1)
-        ]] = 'auto'
-
-    def process(self, data):
-        """Create and return a
-        `Zarr group <https://zarr.readthedocs.io/en/stable/api/zarr/group/#zarr.Group>`__
-        object to hold processed SAXS/WAXS data processed
-        by :class:`~CHAP.saxswaxs.PyfaiIntegrationProcessor`.
-
-        :param data: Input data.
-        :type data: list[PipelineData]
-        :return: Empty structure for filling in SAXS/WAXS data.
-        :rtype: zarr.Group
-        """
-
-        # Get Zarr tree as dict from the PyfaiIntegrationConfig
-        tree = self.config.zarr_tree(self.dataset_shape, self.dataset_chunks)
-
-        # Construct & return the root Zarr group
-        return self.zarr_setup(tree)
-
-    def zarr_setup(self, tree):
-        """Create a
-        `Zarr group <https://zarr.readthedocs.io/en/stable/api/zarr/group/#zarr.Group>`__
-        object based on a dictionary representing a Zarr tree of groups
-        and arrays.
-
-        :param tree: Nested dictionary representing a Zarr tree of
-            groups and arrays.
-        :type tree: dict[str, Any]
-        :return: Zarr group corresponding to the contents of `tree`.
-        :rtype: zarr.Group
-        """
-        # Third party modules
-        # pylint: disable=import-error
-        import zarr
-        from zarr.storage import MemoryStore
-
-        def create_group_or_dataset(node, zarr_parent, indent=0):
-            """Create and return a
-            `Zarr group <https://zarr.readthedocs.io/en/stable/api/zarr/group/#zarr.Group>`__
-            `Zarr dataset <https://zarr.readthedocs.io/en/stable/api/zarr/array/#zarr.Array>`__.
-
-            :param node: Child Zarr tree group.
-            :type node: zarr.Group or zarr.Array
-            :param zarr_parent: Parent Zarr tree group.
-            :type zarr_parent: zarr.Group
-            :param indent: Indentation level, defaults to 0.
-            :type indent: int, optional
-            """
-            # Set attributes if present
-            if 'attributes' in node:
-                for key, value in node['attributes'].items():
-                    zarr_parent.attrs[key] = value
-            # Create children (groups or datasets)
-            if 'children' in node:
-                for name, child in node['children'].items():
-                    if 'shape' in child or 'data' in child:
-                        # It's a dataset
-                        self.logger.debug(f'Adding dset: {name}')
-                        zarr_parent.create_dataset(
-                            name,
-                            **child,
-                        )
-                        # Set dataset attributes
-                        if 'attributes' in child:
-                            for key, value in child['attributes'].items():
-                                zarr_parent[name].attrs[key] = value
-                    else:
-                        # It's a group
-                        group = zarr_parent.create_group(name)
-                        create_group_or_dataset(child, group, indent=indent+2)
-        results = zarr.create_group(store=MemoryStore({}))
-        create_group_or_dataset(tree['root'], results)
-        return results
-
-
 class SetupProcessor(Processor):
     """Convenience Processor for setting up a container for SAXS/WAXS
     experiments.
@@ -666,13 +562,13 @@ class SetupProcessor(Processor):
     :ivar pyfai_config: Initialization parameters for an instance of
         :class:`~CHAP.common.models.integration.PyfaiIntegrationConfig`.
     :vartype pyfai_config: dict, optional
-    :ivar detectors: Detector configurations.
-    :vartype detectors: DetectorConfig
+    :ivar detector_config: Detector configurations.
+    :vartype detector_config: DetectorConfig
     :ivar dataset_shape: Shape of the completed dataset that will be
         processed later on (shape of the measurement itself, _not_
         including the dimensions of any signals collected at each point
-        in that measurement).
-    :vartype dataset_shape: int or list[int]
+        in that measurement). Defaults to `[0]`.
+    :vartype dataset_shape: int or list[int], optional
     :ivar dataset_chunks: Extent of chunks along each dimension of the
         completed dataset / measurement. Choose this according to how
         you will process your data -- for example, if your
@@ -695,7 +591,9 @@ class SetupProcessor(Processor):
     pipeline_fields: dict = Field(
         default={
             'map_config': 'common.models.map.MapConfig',
-            'pyfai_config': 'common.models.integration.PyfaiIntegrationConfig'
+            'detector_config': 'common.models.map.DetectorConfig',
+            'pyfai_config': 'common.models.integration.PyfaiIntegrationConfig',
+            'correction_config': 'saxswaxs.models.CorrectionsConfig',
         },
         init_var=True)
     # map_config needs a default value because the map configuration
@@ -704,9 +602,10 @@ class SetupProcessor(Processor):
     # Pipeline to pass validation.
     map_config: MapConfig = None
     pyfai_config: PyfaiIntegrationConfig
-    detectors: conlist(item_type=Detector, min_length=0)
+    detector_config: DetectorConfig = DetectorConfig(detectors=[])
+    correction_config: CorrectionsConfig
     dataset_shape: Optional[
-        conlist(item_type=conint(ge=0), min_length=1)] = None
+        conlist(item_type=conint(ge=0), min_length=1)] = [0]
     dataset_chunks: Optional[
         Union[
             Literal['auto'],
@@ -742,46 +641,19 @@ def process(self, data):
             NexusToZarrProcessor,
         )
         from CHAP.pipeline import PipelineData
-        #from CHAP.saxswaxs.processor import SetupResultsProcessor
-
-        def set_logger(pipeline_item):
-            """Set the logger and logging handler for given pipeline
-            item.
-
-            :param pipeline_item: Pipeline item.
-            :type pipeline_item: PipelineItem
-            :return: Input Pipeline item, with updated logger and
-                logging handler.
-            :rtype: PipelineItem
-            """
-            pipeline_item.logger = self.logger
-            pipeline_item.logger.name = pipeline_item.__class__.__name__
-            handler = logging.StreamHandler()
-            handler.setFormatter(logging.Formatter(
-                '{asctime}: {name:20} (from '+ self.__class__.__name__
-                + '): {levelname}: {message}',
-                datefmt='%Y-%m-%d %H:%M:%S', style='{'))
-            pipeline_item.logger.removeHandler(
-                pipeline_item.logger.handlers[0])
-            pipeline_item.logger.addHandler(handler)
-            return pipeline_item
 
         # Get NXroot container for raw data map
         map_processor_kwargs = {
             'config': self.map_config,
+            'detector_config': self.detector_config,
             'remove_constant_dims': False,
         }
-        if self.raw_data:
-            map_processor_kwargs['detector_config'] = {
-                'detectors': self.detectors
-            }
-        else:
-            map_processor_kwargs['detector_config'] = {
-                'detectors': []
-            }
+        if not self.raw_data:
             self.map_config.spec_scans[0].scan_numbers = []
 
-        setup_map_processor = set_logger(MapProcessor(**map_processor_kwargs))
+        setup_map_processor = self.setup_pipelineitem(
+            MapProcessor(**map_processor_kwargs)
+        )
         ddata = [
             PipelineData(
                 data=setup_map_processor.process(
@@ -813,18 +685,124 @@ def set_logger(pipeline_item):
             self.dataset_chunks = [self.dataset_chunks]
 
         # Convert raw data map container to Zarr format
-        ddata_converter = set_logger(NexusToZarrProcessor())
+        ddata_converter = self.setup_pipelineitem(NexusToZarrProcessor())
         zarr_map = ddata_converter.process(ddata, chunks=self.dataset_chunks)
 
-        # Get Zarr container for integration results
-        setup_results_processor = set_logger(
-            SetupResultsProcessor(
-                config=self.pyfai_config,
-                dataset_shape=self.dataset_shape,
-                dataset_chunks=self.dataset_chunks,
+        # Get paths to independent_dimension arrays
+        dim_paths = [
+            f'{self.map_config.title}/independent_dimensions/{dim.label}'
+            for dim in self.map_config.independent_dimensions
+        ]
+
+        # Get Zarr container for pyfai integrations
+        zarr_pyfai_tree = self.pyfai_config.zarr_tree(
+            self.dataset_shape, self.dataset_chunks,
+            nxlinks=dim_paths
+        )
+        zarr_pyfai = dict_to_zarr(zarr_pyfai_tree, logger=self.logger)
+
+
+        # Get zarr container for corrected datasets
+        integration_shapes = {
+            integration.name: integration.result_shape
+            for integration in self.pyfai_config.integrations
+        }
+        intg_by_name = {
+            intg.name: intg for intg in self.pyfai_config.integrations
+        }
+        corr_nxlinks = {
+            corr.name: (
+                dim_paths
+                + [f'{corr.uncorrected_data_name}/data/I']
+                + [
+                    f'{corr.uncorrected_data_name}/data/{coord}'
+                    for coord in intg_by_name[
+                        corr.uncorrected_data_name].result_coords
+                ]
             )
+            for corr in self.correction_config.corrections
+        }
+        zarr_corr = dict_to_zarr(
+            self.correction_config.zarr_tree(
+                self.dataset_shape, self.dataset_chunks,
+                integration_shapes,
+                nxlinks=corr_nxlinks,
+            ),
+            logger=self.logger,
         )
-        zarr_results = setup_results_processor.process(data)
+
+        # For corrections that include a background, read and integrate
+        # that background data and store it in zarr_corr
+        for corr_cfg in self.correction_config.corrections:
+            if corr_cfg.background is None:
+                continue
+            if not self.detector_config.detectors:
+                self.logger.warning(
+                    f'No detectors configured; skipping background '
+                    f'processing for correction "{corr_cfg.name}"')
+                continue
+            # Read in background raw detector data
+            self.logger.info(
+                f'Reading background data for correction "{corr_cfg.name}"')
+            idx_slice = corr_cfg.background.idx_slice
+            bg_det_images = {
+                d.get_id(): [] for d in self.detector_config.detectors}
+            for scan_number in corr_cfg.background.scan_numbers:
+                scanparser = corr_cfg.background.get_scanparser(scan_number)
+                npts = int(scanparser.spec_scan_npts)
+                slice_stop = (
+                    min(idx_slice._slice.stop, npts)
+                    if idx_slice._slice.stop > 0 else npts
+                )
+                scan_indices = range(npts)[
+                    slice(idx_slice._slice.start, slice_stop,
+                          idx_slice._slice.step)]
+                for i in scan_indices:
+                    for det in self.detector_config.detectors:
+                        bg_det_images[det.get_id()].append(
+                            scanparser.get_detector_data(det.get_id(), i))
+            # Average all background data to a single frame before
+            # processing with appropriate integration
+            for det_id in bg_det_images:
+                bg_det_images[det_id] = np.mean(
+                    bg_det_images[det_id], axis=0, keepdims=True)
+            self.logger.info(
+                f'Integrating background data for correction '
+                f'"{corr_cfg.name}"')
+            bg_pyfai_input = [
+                PipelineData(name=det_id, data=imgs)
+                for det_id, imgs in bg_det_images.items()
+            ]
+            bg_pyfai_config = self.pyfai_config.model_copy(
+                update={'integrations': [
+                    intg for intg in self.pyfai_config.integrations
+                    if intg.name == corr_cfg.uncorrected_data_name
+                ]}
+            )
+            bg_integrated = self.setup_pipelineitem(
+                PyfaiIntegrationProcessor(config=bg_pyfai_config)
+            ).process(bg_pyfai_input)[0]
+            # Read background scalar data
+            bg_presample = self.map_config.presample_intensity.get_value(
+                corr_cfg.background, scan_number, -1,
+                self.map_config.scalar_data
+            )[idx_slice._slice]
+            bg_postsample = self.map_config.postsample_intensity.get_value(
+                corr_cfg.background, scan_number, -1,
+                self.map_config.scalar_data
+            )[idx_slice._slice]
+            # Fill in placeholder zarr arrays with real background
+            # data
+            data_group = zarr_corr[corr_cfg.name]['data']
+            data_group['I_background'][:] = bg_integrated['data']
+            bg_presample_arr = data_group.create_array(
+                'background_presample_intensity',
+                shape=bg_presample.shape, dtype=bg_presample.dtype)
+            bg_presample_arr[:] = bg_presample
+            bg_postsample_arr = data_group.create_array(
+                'background_postsample_intensity',
+                shape=bg_postsample.shape, dtype=bg_postsample.dtype)
+            bg_postsample_arr[:] = bg_postsample
 
         # Assemble containers for raw & processed data
         zarr_root = zarr.create_group(store=MemoryStore({}))
@@ -842,10 +820,34 @@ async def copy_zarr_store(source_store, dest_store):
                 buf = await source_store.get(
                     k, prototype=default_buffer_prototype())
                 await dest_store.set(k, buf)
-        asyncio.run(copy_zarr_store(zarr_map.store, zarr_root.store))
-        asyncio.run(copy_zarr_store(zarr_results.store, zarr_root.store))
+        for zarr_group in (zarr_map, zarr_pyfai, zarr_corr):
+            asyncio.run(copy_zarr_store(zarr_group.store, zarr_root.store))
         return zarr_root
 
+    def setup_pipelineitem(self, pipeline_item):
+        """Convenience method to use a nice logger when this
+        ``Processor`` calls on another ``PipelineItem``. Set the
+        logger and logging handler for given pipeline item.
+
+        :param pipeline_item: Pipeline item.
+        :type pipeline_item: PipelineItem
+        :return: Input Pipeline item, with updated logger and
+            logging handler.
+        :rtype: PipelineItem
+        """
+        import logging
+
+        pipeline_item.logger = logging.getLogger(
+            pipeline_item.__class__.__name__,
+        )
+        handler = logging.StreamHandler()
+        handler.setFormatter(logging.Formatter(
+            '{asctime}: {name:20} (from '+ self.__class__.__name__
+            + ') (L{lineno}): {levelname}: {message}',
+            datefmt='%Y-%m-%d %H:%M:%S', style='{'))
+        pipeline_item.logger.handlers = [handler]
+        return pipeline_item
+
 
 class UnstructuredToStructuredProcessor(Processor):
     """Processor to aggregate "unstructured" data into a single NeXus
@@ -1176,18 +1178,19 @@ class UpdateValuesProcessor(Processor):
     :ivar scan_number: Scan number from which to read and process a
         slice of raw data.
     :vartype scan_number: int
-    :ivar detectors: Detector configurations.
-    :vartype detectors: list[CHAP.common.models.map.Detector]
+    :ivar detector_config: Detector configurations.
+    :vartype detector_config: :class:`~CHAP.common.models.map.DetectorConfig`
     :ivar raw_data: Flag to indicate wether or not space for raw
         detector data should be included in the values returned,
         defaults to `True`.
     :vartype raw_data: bool, optional
     """
-
     pipeline_fields: dict = Field(
-        default={
+        {
             'map_config': 'common.models.map.MapConfig',
-            'pyfai_config': 'common.models.integration.PyfaiIntegrationConfig'
+            'detector_config': 'common.models.map.DetectorConfig',
+            'pyfai_config': 'common.models.integration.PyfaiIntegrationConfig',
+            'correction_config': 'saxswaxs.models.CorrectionsConfig',
         },
         init_var=True)
     # map_config needs a default value because the map configuration
@@ -1196,9 +1199,11 @@ class UpdateValuesProcessor(Processor):
     # Pipeline to pass validation.
     map_config: MapConfig = None
     pyfai_config: PyfaiIntegrationConfig
+    detector_config: DetectorConfig = DetectorConfig(detectors=[])
+    correction_config: CorrectionsConfig
     spec_file: FilePath
     scan_number: conint(gt=0)
-    detectors: conlist(item_type=Detector, min_length=1)
+    filename: Optional[str] = None
     raw_data: Optional[bool] = True
     idx_slice: Optional[IndexSliceConfig] = IndexSliceConfig()
 
@@ -1231,36 +1236,17 @@ def process(self, data):
         # Local modules
         from CHAP.common.map_utils import MapSliceProcessor
         from CHAP.pipeline import PipelineData
-        #from CHAP.saxswaxs.processor import PyfaiIntegrationProcessor
 
+        # Use a copy of input data so we can append to it inside this
+        # Processor without modifying the actual Pipeline's data
+        # unecessarily.
         _data = deepcopy(data)
-        def set_logger(pipeline_item):
-            """Set the logger and logging handler for given pipeline
-            item.
-
-            :param pipeline_item: Pipeline item.
-            :type pipeline_item: PipelineItem
-            :return: Input Pipeline item, with updated logger and
-                logging handler.
-            :rtype: PipelineItem
-            """
-            pipeline_item.logger = self.logger
-            pipeline_item.logger.name = pipeline_item.__class__.__name__
-            handler = logging.StreamHandler()
-            handler.setFormatter(logging.Formatter(
-                '{asctime}: {name:20} (from '+ self.__class__.__name__
-                + '): {levelname}: {message}',
-                datefmt='%Y-%m-%d %H:%M:%S', style='{'))
-            pipeline_item.logger.removeHandler(
-                pipeline_item.logger.handlers[0])
-            pipeline_item.logger.addHandler(handler)
-            return pipeline_item
 
         # Read in slice of raw data
-        raw_values = set_logger(
+        raw_values = self.setup_pipelineitem(
             MapSliceProcessor(
                 map_config=self.map_config,
-                detectors=self.detectors,
+                detector_config=self.detector_config,
                 spec_file=str(self.spec_file),
                 scan_numbers=[self.scan_number],
                 idx_slice=self.idx_slice
@@ -1275,7 +1261,7 @@ def _get_detector_data(values, name):
             return None
 
         # Use raw detector data as input to integration
-        for d in self.detectors:
+        for d in self.detector_config.detectors:
             _data.append(
                 PipelineData(
                     name=d.get_id(),
@@ -1283,19 +1269,123 @@ def _get_detector_data(values, name):
                 )
             )
         # Get integrated data
-        processed_values = set_logger(
+        processed_values = self.setup_pipelineitem(
             PyfaiIntegrationProcessor(config=self.pyfai_config)
         ).process(_data)
 
+        # Get corrected data
+        corrected_values = [
+            {
+                'data': self.setup_pipelineitem(
+                    corr_cfg.processor
+                ).process(
+                    self.get_corrections_input_data(
+                        raw_values, processed_values, corr_cfg
+                    ),
+                    nxprocess=False,
+                ),
+                'path': f'{corr_cfg.name}/data/I_corrected'
+            }
+            for corr_cfg in self.correction_config.corrections
+        ]
+
         if self.raw_data:
-            return raw_values + processed_values
+            return raw_values + processed_values + corrected_values
 
-        detector_ids = [d.get_id() for d in self.detectors]
+        detector_ids = [d.get_id() for d in self.detector_config.detectors]
         scalar_values = [
             d for d in raw_values
             if not os.path.basename(d['path']) in detector_ids
         ]
-        return scalar_values + processed_values
+        return scalar_values + processed_values + corrected_values
+
+    def get_corrections_input_data(self, raw_values, processed_values,
+                                   corr_cfg):
+        corr_data = []
+        for x in ('dwell_time_actual', 'presample_intensity',
+                  'postsample_intensity'):
+            for d in raw_values:
+                if d['path'].endswith(x):
+                    corr_data.append(
+                        PipelineData(data=d['data'], name=x)
+                    )
+                    break
+        for d in processed_values:
+            if d['path'].startswith(f'{corr_cfg.uncorrected_data_name}/'):
+                corr_data.append(
+                    PipelineData(
+                        data=d['data'],
+                        name=corr_cfg.uncorrected_data_name,
+                    )
+                )
+        if corr_cfg.background is not None:
+            if self.filename is None:
+                self.logger.warning(
+                    f'No filename configured; cannot read background '
+                    f'intensities for correction "{corr_cfg.name}"')
+            else:
+                # System modules
+                import os
+                pre_path = (f'{corr_cfg.name}/data/'
+                            'background_presample_intensity')
+                post_path = (f'{corr_cfg.name}/data/'
+                             'background_postsample_intensity')
+                if os.path.splitext(self.filename)[1] in ('.nxs', '.h5',
+                                                          '.hdf5'):
+                    import h5py
+                    with h5py.File(self.filename, 'r') as f:
+                        for path, name in (
+                                (pre_path,
+                                 'background_presample_intensity'),
+                                (post_path,
+                                 'background_postsample_intensity')):
+                            if path in f:
+                                corr_data.append(PipelineData(
+                                    data=np.asarray(f[path]),
+                                    name=name,
+                                ))
+                            else:
+                                self.logger.warning(
+                                    f'{path} not found in {self.filename}')
+                else:
+                    import zarr
+                    zarrfile = zarr.open(self.filename, mode='r')
+                    for path, name in (
+                            (pre_path, 'background_presample_intensity'),
+                            (post_path, 'background_postsample_intensity')):
+                        try:
+                            corr_data.append(PipelineData(
+                                data=np.asarray(zarrfile[path]),
+                                name=name,
+                            ))
+                        except KeyError:
+                            self.logger.warning(
+                                f'{path} not found in {self.filename}')
+        return corr_data
+
+    def setup_pipelineitem(self, pipeline_item):
+        """Convenience method to use a nice logger when this
+        ``Processor`` calls on another ``PipelineItem``. Set the
+        logger and logging handler for given pipeline item.
+
+        :param pipeline_item: Pipeline item.
+        :type pipeline_item: PipelineItem
+        :return: Input Pipeline item, with updated logger and
+            logging handler.
+        :rtype: PipelineItem
+        """
+        import logging
+
+        pipeline_item.logger = logging.getLogger(
+            pipeline_item.__class__.__name__,
+        )
+        handler = logging.StreamHandler()
+        handler.setFormatter(logging.Formatter(
+            '{asctime}: {name:20} (from '+ self.__class__.__name__
+            + ') (L{lineno}): {levelname}: {message}',
+            datefmt='%Y-%m-%d %H:%M:%S', style='{'))
+        pipeline_item.logger.handlers = [handler]
+        return pipeline_item
 
 
 if __name__ == '__main__':
diff --git a/CHAP/saxswaxs/utils.py b/CHAP/saxswaxs/utils.py
new file mode 100644
index 00000000..4a9cdfb7
--- /dev/null
+++ b/CHAP/saxswaxs/utils.py
@@ -0,0 +1,60 @@
+import zarr
+
+from CHAP.runner import set_logger
+
+logger, _ = set_logger(log_level='DEBUG')
+
+def dict_to_zarr(tree, logger=logger):
+    """Create a
+    `Zarr group <https://zarr.readthedocs.io/en/stable/api/zarr/group/#zarr.Group>`__
+    object based on a dictionary representing a Zarr tree of groups
+    and arrays.
+
+    :param tree: Nested dictionary representing a Zarr tree of
+        groups and arrays.
+    :type tree: dict[str, Any]
+    :return: Zarr group corresponding to the contents of `tree`.
+    :rtype: zarr.Group
+    """
+    # Third party modules
+    # pylint: disable=import-error
+    import zarr
+    from zarr.storage import MemoryStore
+
+    def create_group_or_dataset(node, zarr_parent, indent=0):
+        """Create and return a
+        `Zarr group <https://zarr.readthedocs.io/en/stable/api/zarr/group/#zarr.Group>`__
+        `Zarr dataset <https://zarr.readthedocs.io/en/stable/api/zarr/array/#zarr.Array>`__.
+
+        :param node: Child Zarr tree group.
+        :type node: zarr.Group or zarr.Array
+        :param zarr_parent: Parent Zarr tree group.
+        :type zarr_parent: zarr.Group
+        :param indent: Indentation level, defaults to 0.
+        :type indent: int, optional
+        """
+        # Set attributes if present
+        if 'attributes' in node:
+            for key, value in node['attributes'].items():
+                zarr_parent.attrs[key] = value
+        # Create children (groups or datasets)
+        if 'children' in node:
+            for name, child in node['children'].items():
+                if 'shape' in child or 'data' in child:
+                    # It's a dataset
+                    logger.debug(f'Adding dset: {name}')
+                    zarr_parent.create_dataset(
+                        name,
+                        **child,
+                    )
+                    # Set dataset attributes
+                    if 'attributes' in child:
+                        for key, value in child['attributes'].items():
+                            zarr_parent[name].attrs[key] = value
+                else:
+                    # It's a group
+                    group = zarr_parent.create_group(name)
+                    create_group_or_dataset(child, group, indent=indent+2)
+    results = zarr.create_group(store=MemoryStore({}))
+    create_group_or_dataset(tree, results)
+    return results

From 8fc3d6efda37e961c995ced3b5846eacb988f535 Mon Sep 17 00:00:00 2001
From: Keara Soloway <kls286@cornell.edu>
Date: Thu, 21 May 2026 15:59:14 -0400
Subject: [PATCH 63/76] fix: set logger handlers instead of using addHandler
 (avoids duplicate logging messages when scripting)

---
 CHAP/runner.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/CHAP/runner.py b/CHAP/runner.py
index 9e191d16..b7045658 100755
--- a/CHAP/runner.py
+++ b/CHAP/runner.py
@@ -227,9 +227,9 @@ def set_logger(log_level='INFO'):
     logger.setLevel(log_level)
     log_handler = logging.StreamHandler()
     log_handler.setFormatter(logging.Formatter(
-        '{asctime}: {name:20}: {levelname}: {message}',
+        '{asctime}: {name:20} (L{lineno}): {levelname}: {message}',
         datefmt='%Y-%m-%d %H:%M:%S', style='{'))
-    logger.addHandler(log_handler)
+    logger.handlers = [log_handler]
     return logger, log_handler
 
 def run(

From f899e7c3bbea03dcadcce8a0e989c9ae5334c998 Mon Sep 17 00:00:00 2001
From: Rolf Verberg <rv43@cornell.edu>
Date: Fri, 22 May 2026 13:39:31 -0400
Subject: [PATCH 64/76] feat: added create_copy to NexusReader to avoid linked
 data issues

---
 CHAP/common/reader.py | 21 ++++++++++++++++++---
 1 file changed, 18 insertions(+), 3 deletions(-)

diff --git a/CHAP/common/reader.py b/CHAP/common/reader.py
index de9b78a9..5fc45067 100755
--- a/CHAP/common/reader.py
+++ b/CHAP/common/reader.py
@@ -584,6 +584,9 @@ def read(self, filename, method='read_csv', comment='#', **kwargs):
 class NexusReader(Reader):
     """Reader for `NeXus <https://www.nexusformat.org>`__ files.
 
+    :ivar create_copy: Return a copy of the selected data, resolving
+        any and all linked NeXus objects, defaults to `False`..
+    :vartype create_copy: bool, optional
     :ivar nxpath: Path to a specific location in the NeXus file tree
         to read from, defaults to `'/'`.
     :vartype nxpath: str, optional
@@ -595,10 +598,11 @@ class NexusReader(Reader):
     :vartype nxmemory: int, optional
     """
 
-    nxpath: Optional[constr(strip_whitespace=True, min_length=1)] = '/'
+    create_copy: Optional[bool] = False
     idx: Optional[conint(ge=0)] = None
     mode: Literal['r', 'rw', 'r+', 'w', 'a'] = 'r'
     nxmemory: Optional[conint(gt=0)] = None
+    nxpath: Optional[constr(strip_whitespace=True, min_length=1)] = '/'
 
     def read(self):
         """Return the NeXus Style
@@ -617,11 +621,22 @@ def read(self):
             nxsetconfig,
         )
 
+        # Local modules
+        from CHAP.utils.general import nxcopy
+
         if self.nxmemory is not None:
             nxsetconfig(memory=self.nxmemory)
         if self.idx is not None:
-            return nxload(self.filename, mode=self.mode)[self.nxpath][self.idx]
-        return nxload(self.filename, mode=self.mode)[self.nxpath]
+            nxobject = nxload(
+                self.filename, mode=self.mode)[self.nxpath][self.idx]
+            if self.create_copy:
+                return nxcopy(nxobject)
+            return nxobject
+            #return nxload(self.filename, mode=self.mode)[self.nxpath][self.idx]
+        nxobject = nxload(self.filename, mode=self.mode)[self.nxpath]
+        if self.create_copy:
+            nxobject = nxcopy(nxobject)
+        return nxobject
 
 
 class NXdataReader(Reader):

From 0b0f2f43bc667a78d3488a1c9349644eca9498e3 Mon Sep 17 00:00:00 2001
From: Keara Soloway <kls286@cornell.edu>
Date: Fri, 22 May 2026 13:52:58 -0400
Subject: [PATCH 65/76] fix: squeeze empty first dim out of I_background before
 putting in zarr source

---
 CHAP/saxswaxs/processor.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/CHAP/saxswaxs/processor.py b/CHAP/saxswaxs/processor.py
index 4f8872e1..b9f486b0 100755
--- a/CHAP/saxswaxs/processor.py
+++ b/CHAP/saxswaxs/processor.py
@@ -794,7 +794,9 @@ def process(self, data):
             # Fill in placeholder zarr arrays with real background
             # data
             data_group = zarr_corr[corr_cfg.name]['data']
-            data_group['I_background'][:] = bg_integrated['data']
+            data_group['I_background'][:] = np.squeeze(
+                bg_integrated['data'], axis=0
+            )
             bg_presample_arr = data_group.create_array(
                 'background_presample_intensity',
                 shape=bg_presample.shape, dtype=bg_presample.dtype)

From afc02798e948a05510431ce2159966f40ca6d677 Mon Sep 17 00:00:00 2001
From: Keara Soloway <kls286@cornell.edu>
Date: Fri, 22 May 2026 13:54:24 -0400
Subject: [PATCH 66/76] feat: alias old CorrectionConfig field names

---
 CHAP/saxswaxs/models.py | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/CHAP/saxswaxs/models.py b/CHAP/saxswaxs/models.py
index 86df7a9a..79bfd101 100644
--- a/CHAP/saxswaxs/models.py
+++ b/CHAP/saxswaxs/models.py
@@ -12,6 +12,8 @@
     confloat,
     conlist,
     model_validator,
+    Field,
+    AliasChoices,
 )
 
 # Local modules
@@ -97,8 +99,9 @@ class CorrectionConfig(CHAPBaseModel):
 
     correction_type: Literal['flux', 'flux_absorption',
                              'flux_absorption_background']
-    name: str
-    uncorrected_data_name: str
+    name: str = Field(validation_alias=AliasChoices('name', 'title'))
+    uncorrected_data_name: str = Field(validation_alias=AliasChoices(
+        'uncorrected_data_name', 'uncorrected_data_title'))
     presample_intensity_reference_rate: Optional[float] = None
     background: Optional[Background] = None
 

From 6fe7c82d5d2d4f97755fe2d4fd263c51d2a1599d Mon Sep 17 00:00:00 2001
From: Keara Soloway <kls286@cornell.edu>
Date: Fri, 22 May 2026 14:10:47 -0400
Subject: [PATCH 67/76] fix: add default values for optional fields
 sample_thickness_cm and sample_mu_inv_cm

---
 CHAP/saxswaxs/models.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/CHAP/saxswaxs/models.py b/CHAP/saxswaxs/models.py
index 79bfd101..af0c5a3b 100644
--- a/CHAP/saxswaxs/models.py
+++ b/CHAP/saxswaxs/models.py
@@ -340,8 +340,8 @@ class FluxAbsorptionBackgroundCorrectionConfig(
     correction_type: Literal[
         'flux_absorption_background'] = 'flux_absorption_background'
     background: Background
-    sample_thickness_cm: Optional[confloat(gt=0)]
-    sample_mu_inv_cm: Optional[confloat(gt=0)]
+    sample_thickness_cm: Optional[confloat(gt=0)] = None
+    sample_mu_inv_cm: Optional[confloat(gt=0)] = None
 
     @model_validator(mode='after')
     def validate_thickness(self):

From dc3d5f94833e4de10b8d8bf31f705addaa984257 Mon Sep 17 00:00:00 2001
From: Keara Soloway <kls286@cornell.edu>
Date: Fri, 22 May 2026 14:22:59 -0400
Subject: [PATCH 68/76] fix: swap old method args for new config fields in
 saxswaxs.*CorrectionProcessors

---
 CHAP/saxswaxs/models.py    |   2 +-
 CHAP/saxswaxs/processor.py | 218 +++++++++++++++++++------------------
 2 files changed, 115 insertions(+), 105 deletions(-)

diff --git a/CHAP/saxswaxs/models.py b/CHAP/saxswaxs/models.py
index af0c5a3b..48667db9 100644
--- a/CHAP/saxswaxs/models.py
+++ b/CHAP/saxswaxs/models.py
@@ -80,7 +80,7 @@ class CorrectionConfig(CHAPBaseModel):
         correction's group in the output zarr / NeXus tree.
     :vartype name: str
     :ivar uncorrected_data_name: Name of the
-        :class:`~CHAP.common.models.integration.PyfaiIntegratorConfig`
+        :class:`~CHAP.common.models.integration.PyfaiIntegrationConfig`
         integration whose output serves as the uncorrected input for
         this correction.  Must match the ``name`` field of one of the
         integrations in the associated
diff --git a/CHAP/saxswaxs/processor.py b/CHAP/saxswaxs/processor.py
index b9f486b0..03c731fe 100755
--- a/CHAP/saxswaxs/processor.py
+++ b/CHAP/saxswaxs/processor.py
@@ -224,36 +224,41 @@ def process(
 
 
 class FluxCorrectionProcessor(ExpressionProcessor):
-    """Processor for flux correction."""
+    """Processor for applying a flux correction to azimuthally
+    integrated SAXS/WAXS intensity data.
+
+    Normalises the measured intensity by the pre-sample beam monitor
+    counts, referenced to a fixed counting rate configured via
+    :attr:`config`.
+
+    :ivar config: Correction configuration.
+    :vartype config: FluxCorrectionConfig
+    """
     config: FluxCorrectionConfig
-    def process(
-            self, data, presample_intensity_reference_rate=None,
-            nxprocess=False):
-        """Given input data for `'intensity'`, `'presample_intensity'`,
-        and `'dwell_time_actual'`, compute the flux corrected intensity
-        signal.
-
-        :param data: Input data list containing items with names
-            `'intensity'`, `'presample_intensity'`, and
-            `'dwell_time_actual'` (if
-            `presample_intensity_reference_rate` is not specified).
+    def process(self, data, nxprocess=False):
+        """Compute the flux-corrected intensity.
+
+        Requires input data items named ``'intensity'`` (the raw
+        integrated signal) and ``'presample_intensity'`` (beam monitor
+        counts).  When
+        :attr:`~saxswaxs.models.FluxCorrectionConfig.presample_intensity_reference_rate`
+        is not pre-configured in :attr:`config`, an additional item
+        named ``'dwell_time_actual'`` is also required and the
+        reference rate is computed on the fly as
+        ``np.nanmean(presample_intensity / dwell_time_actual)``.
+
+        :param data: Input data list.
         :type data: list[PipelineData]
-        :param presample_intensity_reference_rate: Reference counting
-            rate for the `'presample_intensity'` signal. If not
-            specified, it will  set to
-            `'numpy.nanmean(presample_intensity /
-            dwell_time_actual)'`.
-        :type presample_intensity_reference_rate: float, optional
-        :param nxprocess: Flag to indicate the flux corrected data
-            should be returned as a NeXus style
+        :param nxprocess: Return the result as a NeXus
             `NXobject <https://manual.nexusformat.org/classes/base_classes/NXobject.html#index-0>`__
-            object. Defaults to `False`.
+            object.  Defaults to ``False``.
         :type nxprocess: bool, optional
-        :returns: Flux corrected version of input `'intensity'` data.
-        :rtype: Any
+        :returns: Flux-corrected intensity array (or NXobject when
+            ``nxprocess`` is ``True``).
+        :rtype: numpy.ndarray or nexusformat.nexus.NXobject
         """
-        if presample_intensity_reference_rate is None:
-            presample_intensity_reference_rate = super().process(
+        if self.config.presample_intensity_reference_rate is None:
+            self.config.presample_intensity_reference_rate = super().process(
                 data,
                 'np.nanmean(presample_intensity / dwell_time_actual)'
             )
@@ -280,7 +285,7 @@ def process(
             )
         symtable = {
             'presample_intensity_reference_rate':
-                presample_intensity_reference_rate,
+                self.config.presample_intensity_reference_rate,
             'intensity': intensity,
             'presample_intensity': presample_intensity
         }
@@ -295,41 +300,47 @@ def process(
 
 
 class FluxAbsorptionCorrectionProcessor(ExpressionProcessor):
-    """Processor for flux and absorption correction."""
+    """Processor for applying combined flux and absorption correction
+    to azimuthally integrated SAXS/WAXS intensity data.
+
+    In addition to flux normalisation (see
+    :class:`FluxCorrectionProcessor`), divides by the sample
+    transmission, which is estimated from the ratio of post-sample to
+    pre-sample intensities for both the sample and a background scan.
+
+    :ivar config: Correction configuration.
+    :vartype config: FluxAbsorptionCorrectionConfig
+    """
     config: FluxAbsorptionCorrectionConfig
-    def process(
-            self, data, presample_intensity_reference_rate=None,
-            nxprocess=False):
-        """Given input data for `'intensity'`, `'presample_intensity'`,
-        `'postsample_intensity'`, `'background_presample_intensity'`,
-        `'background_postsample_intensity'`, and
-        `'dwell_time_actual'`, compute the flux and absorption
-        corrected intensity signal.
-
-        :param data: Input data list containing all necessary data
-            labelled with their proper names.
+    def process(self, data, nxprocess=False):
+        """Compute the flux- and absorption-corrected intensity.
+
+        Requires input data items named ``'intensity'``,
+        ``'presample_intensity'``, ``'postsample_intensity'``,
+        ``'background_presample_intensity'``, and
+        ``'background_postsample_intensity'``.  When
+        :attr:`~saxswaxs.models.FluxAbsorptionCorrectionConfig.presample_intensity_reference_rate`
+        is not pre-configured in :attr:`config`, an additional item
+        named ``'dwell_time_actual'`` is also required and the
+        reference rate is computed on the fly as
+        ``np.nanmean(presample_intensity / dwell_time_actual)``.
+
+        :param data: Input data list.
         :type data: list[PipelineData]
-        :param presample_intensity_reference_rate: Reference counting
-            rate for the `'presample_intensity'` signal. If not
-            specified, it will be calculated with
-            `'numpy.nanmean(presample_intensity /
-            dwell_time_actual)'`.
-        :type presample_intensity_reference_rate: float, optional
-        :param nxprocess: Flag to indicate the flux and absorption
-            corrected data should be returned as a NeXus style
+        :param nxprocess: Return the result as a NeXus
             `NXobject <https://manual.nexusformat.org/classes/base_classes/NXobject.html#index-0>`__
-            object. Defaults to `False`.
+            object.  Defaults to ``False``.
         :type nxprocess: bool, optional
-        :returns: Flux and absorption corrected version of input
-            `'intensity'` data.
-        :rtype: Any
+        :returns: Flux- and absorption-corrected intensity array (or
+            NXobject when ``nxprocess`` is ``True``).
+        :rtype: numpy.ndarray or nexusformat.nexus.NXobject
         """
         intensity = self.get_data(
             data, name=self.config.uncorrected_data_name, #'intensity',
         )
 
-        if presample_intensity_reference_rate is None:
-            presample_intensity_reference_rate = super().process(
+        if self.config.presample_intensity_reference_rate is None:
+            self.config.presample_intensity_reference_rate = super().process(
                 data,
                 'np.nanmean(presample_intensity / dwell_time_actual)'
             )
@@ -356,7 +367,7 @@ def process(
 
         symtable = {
             'presample_intensity_reference_rate':
-                presample_intensity_reference_rate,
+                self.config.presample_intensity_reference_rate,
             'intensity': intensity,
             'presample_intensity': presample_intensity,
             'tt': tt
@@ -373,61 +384,60 @@ def process(
 
 
 class FluxAbsorptionBackgroundCorrectionProcessor(ExpressionProcessor):
-    """Processor for flux, absorption, and background correction as
-    well as optional thickness correction."""
+    """Processor for applying combined flux, absorption, and
+    background-subtraction correction to azimuthally integrated
+    SAXS/WAXS intensity data, with optional thickness normalisation.
+
+    Extends :class:`FluxAbsorptionCorrectionProcessor` by subtracting
+    an integrated background signal after flux and absorption
+    correction.  Thickness normalisation is applied when
+    :attr:`~saxswaxs.models.FluxAbsorptionBackgroundCorrectionConfig.sample_thickness_cm`
+    or
+    :attr:`~saxswaxs.models.FluxAbsorptionBackgroundCorrectionConfig.sample_mu_inv_cm`
+    is set in :attr:`config`.
+
+    :ivar config: Correction configuration.
+    :vartype config: FluxAbsorptionBackgroundCorrectionConfig
+    """
     config: FluxAbsorptionBackgroundCorrectionConfig
-    def process(
-            self, data, presample_intensity_reference_rate=None,
-            sample_thickness_cm=None, sample_mu_inv_cm=None, nxprocess=False):
-        """Given input data for `'intensity'`, `'presample_intensity'`,
-        `'postsample_intensity'`, `'background_presample_intensity'`,
-        `'background_postsample_intensity'`, `'background_intensity'`,
-        and `'dwell_time_actual'`, return flux, absorption and
-        background corrected intensity signal.
-
-        :param data: Input data list containing all necessary data
-            labelled with their proper names.
+    def process(self, data, nxprocess=False):
+        """Compute the flux-, absorption-, and background-corrected
+        intensity, with optional thickness normalisation.
+
+        Requires input data items named ``'intensity'``,
+        ``'presample_intensity'``, ``'postsample_intensity'``,
+        ``'background_presample_intensity'``,
+        ``'background_postsample_intensity'``, and
+        ``'background_intensity'``.  When
+        :attr:`~saxswaxs.models.FluxAbsorptionBackgroundCorrectionConfig.presample_intensity_reference_rate`
+        is not pre-configured in :attr:`config`, an additional item
+        named ``'dwell_time_actual'`` is also required and the
+        reference rate is computed on the fly as
+        ``np.nanmean(presample_intensity / dwell_time_actual)``.
+
+        Thickness normalisation is controlled by :attr:`config`: if
+        ``config.sample_thickness_cm`` is set the corrected signal is
+        divided by that value; if ``config.sample_mu_inv_cm`` is set
+        the effective thickness is derived from the measured
+        transmission; otherwise no thickness normalisation is applied.
+
+        :param data: Input data list.
         :type data: list[PipelineData]
-        :param presample_intensity_reference_rate: Reference counting
-            rate for the `'presample_intensity'` signal. If not
-            specified, it will be calculated with
-            `'numpy.nanmean(presample_intensity /
-            dwell_time_actual)'`.
-        :type presample_intensity_reference_rate: float, optional
-        :param sample_thickness_cm: Sample thickness in
-            centimeters. If specified, this processor will
-            additionally perform thickness correction. Use of this
-            parameter is mutualy exclusive with
-            use of `sample_mu_inv_cm`.
-        :type sample_thickness_cm: float, optional
-        :param sample_mu_inv_cm: Sample linear attenuation coefficient
-            in inverse centimeters. If specified, this processor will
-            additionally perform thickness correction. Use of this
-            parameter is mutualy exclusive with use of
-            `sample_thickness_cm`.
-        :type sample_mu_inv_cm: float, optional
-        :param nxprocess: Flag to indicate the flux, absorption, and
-            background corrected data should be returned as a Nexus
-            style
+        :param nxprocess: Return the result as a NeXus
             `NXobject <https://manual.nexusformat.org/classes/base_classes/NXobject.html#index-0>`__
-            object. Defaults to `False`.
+            object.  Defaults to ``False``.
         :type nxprocess: bool, optional
-        :returns: Flux, absorption and background corrected version of
-            input `'intensity'` data.
-        :rtype: Any
+        :returns: Flux-, absorption-, and background-corrected
+            intensity array (or NXobject when ``nxprocess`` is
+            ``True``).
+        :rtype: numpy.ndarray or nexusformat.nexus.NXobject
         """
-        if sample_thickness_cm is not None and sample_mu_inv_cm is not None:
-            raise ValueError((
-                'Cannot use sample_thickness_cm and sample_mu_inv_cm'
-                ' at the same time'
-            ))
-
         intensity = self.get_data(
             data, name=self.config.uncorrected_data_name,
         )
 
-        if presample_intensity_reference_rate is None:
-            presample_intensity_reference_rate = super().process(
+        if self.config.presample_intensity_reference_rate is None:
+            self.config.presample_intensity_reference_rate = super().process(
                 data,
                 'np.nanmean(presample_intensity / dwell_time_actual)'
             )
@@ -460,17 +470,17 @@ def process(
         background_intensity = np.broadcast_to(
             background_intensity, intensity.shape)
 
-        if sample_thickness_cm is not None:
-            t = sample_thickness_cm
-        elif sample_mu_inv_cm is not None:
-            t = -np.log(tt / sample_mu_inv_cm)
+        if self.config.sample_thickness_cm is not None:
+            t = self.config.sample_thickness_cm
+        elif self.config.sample_mu_inv_cm is not None:
+            t = -np.log(tt / self.config.sample_mu_inv_cm)
         else:
             t = 1
 
         symtable = {
             't': t,
             'presample_intensity_reference_rate':
-                presample_intensity_reference_rate,
+                self.config.presample_intensity_reference_rate,
             'intensity': intensity,
             'presample_intensity': presample_intensity,
             'tt': tt,

From 1fb4b1f506f5290664983937063fa4c726fff77b Mon Sep 17 00:00:00 2001
From: Keara Soloway <kls286@cornell.edu>
Date: Fri, 22 May 2026 14:23:49 -0400
Subject: [PATCH 69/76] fix: include background intensities in input data for
 correction Processors that need them

---
 CHAP/saxswaxs/processor.py | 11 +++++++----
 1 file changed, 7 insertions(+), 4 deletions(-)

diff --git a/CHAP/saxswaxs/processor.py b/CHAP/saxswaxs/processor.py
index 03c731fe..aa4be885 100755
--- a/CHAP/saxswaxs/processor.py
+++ b/CHAP/saxswaxs/processor.py
@@ -611,9 +611,9 @@ class SetupProcessor(Processor):
     # the case, then map_config needs SOME value in order for the
     # Pipeline to pass validation.
     map_config: MapConfig = None
-    pyfai_config: PyfaiIntegrationConfig
+    pyfai_config: PyfaiIntegrationConfig = None
     detector_config: DetectorConfig = DetectorConfig(detectors=[])
-    correction_config: CorrectionsConfig
+    correction_config: CorrectionsConfig = CorrectionsConfig(corrections=[])
     dataset_shape: Optional[
         conlist(item_type=conint(ge=0), min_length=1)] = [0]
     dataset_chunks: Optional[
@@ -1342,6 +1342,7 @@ def get_corrections_input_data(self, raw_values, processed_values,
                             'background_presample_intensity')
                 post_path = (f'{corr_cfg.name}/data/'
                              'background_postsample_intensity')
+                intens_path = f'{corr_cfg.name}/data/I_background'
                 if os.path.splitext(self.filename)[1] in ('.nxs', '.h5',
                                                           '.hdf5'):
                     import h5py
@@ -1350,7 +1351,8 @@ def get_corrections_input_data(self, raw_values, processed_values,
                                 (pre_path,
                                  'background_presample_intensity'),
                                 (post_path,
-                                 'background_postsample_intensity')):
+                                 'background_postsample_intensity'),
+                                (intens_path, 'background_intensity')):
                             if path in f:
                                 corr_data.append(PipelineData(
                                     data=np.asarray(f[path]),
@@ -1364,7 +1366,8 @@ def get_corrections_input_data(self, raw_values, processed_values,
                     zarrfile = zarr.open(self.filename, mode='r')
                     for path, name in (
                             (pre_path, 'background_presample_intensity'),
-                            (post_path, 'background_postsample_intensity')):
+                            (post_path, 'background_postsample_intensity'),
+                            (intens_path, 'background_intensity')):
                         try:
                             corr_data.append(PipelineData(
                                 data=np.asarray(zarrfile[path]),

From e8f16c9701766d406e8eda90931b7cf548518b25 Mon Sep 17 00:00:00 2001
From: Rolf Verberg <rv43@cornell.edu>
Date: Thu, 28 May 2026 12:54:12 -0400
Subject: [PATCH 70/76] add: Added a max # func evals for option for the fit
 processor

Applied its use to the EDD workflow.
---
 CHAP/common/writer.py |  3 +--
 CHAP/edd/models.py    |  7 +++++--
 CHAP/edd/processor.py |  5 +++--
 CHAP/edd/reader.py    |  2 +-
 CHAP/edd/utils.py     |  4 +++-
 CHAP/utils/fit.py     | 21 ++++++++++++++-------
 6 files changed, 27 insertions(+), 15 deletions(-)

diff --git a/CHAP/common/writer.py b/CHAP/common/writer.py
index 04d6e84b..a118ba22 100755
--- a/CHAP/common/writer.py
+++ b/CHAP/common/writer.py
@@ -26,8 +26,7 @@
     Writer,
     validate_writer_model,
 )
-from CHAP.common.models import IndexSliceConfig
-
+from CHAP.common.models.common import IndexSliceConfig
 
 
 def validate_model(model):
diff --git a/CHAP/edd/models.py b/CHAP/edd/models.py
index d224a69e..0ad7dabe 100755
--- a/CHAP/edd/models.py
+++ b/CHAP/edd/models.py
@@ -883,15 +883,17 @@ class StrainAnalysisConfig(MCACalibrationConfig):
         the maximum mean intensity for that detector. Defaults to `0`
         in which case this step is ignored.
     :vartype find_peak_cutoff: float, optional
+    :ivar max_nfev: Maximum number of function evaluations in the
+        the strain analysis peak fitting routine.
+    :vartype max_nfev: int, optional
     :ivar num_proc: Number of processors to be used by the strain
         analysis peak fitting routine.
-    :vartype num_proc: int
+    :vartype num_proc: int, optional
     :ivar rel_height_cutoff: Used to excluded peaks based on the
         `find_peak` parameter as well as for peak fitting exclusion
         of the individual detector spectra (see the strain detector
         configuration
         :class:`~CHAP.edd.models.MCADetectorStrainAnalysis`).
-        Defaults to `None`.
     :vartype rel_height_cutoff: float, optional
     :ivar skip_animation: Skip the animation and plotting of
         the strain analysis fits, defaults to `False`.
@@ -904,6 +906,7 @@ class StrainAnalysisConfig(MCACalibrationConfig):
     #:vartype oversampling: FIX
 
     find_peak_cutoff: Optional[confloat(ge=0.0, allow_inf_nan=False)] = 0.0
+    max_nfev: Optional[conint(gt=0)] = None
     num_proc: Optional[conint(gt=0)] = max(1, os.cpu_count()//4)
     #oversampling: dict = {'num': 10}
     rel_height_cutoff: Optional[
diff --git a/CHAP/edd/processor.py b/CHAP/edd/processor.py
index db685bbe..971aef78 100755
--- a/CHAP/edd/processor.py
+++ b/CHAP/edd/processor.py
@@ -3377,7 +3377,7 @@ def _linkdims(
         from nexusformat.nexus.tree import NXlinkfield
 
         if not isinstance(nxgroup.nxroot, NXroot):
-            self.logger.warning(
+            self.logger.debug(
                 'Skipping linkdims -- type(nxgroup.nxroot) = '
                 + f'{type(nxgroup.nxroot)}'
             )
@@ -3561,7 +3561,8 @@ def _strain_analysis(self):
             uniform_results, unconstrained_results = get_spectra_fits(
                 np.squeeze(intensities), energies[mask],
                 peak_locations[use_peaks], detector,
-                num_proc=self.config.num_proc, **self.run_config)
+                num_proc=self.config.num_proc,
+                max_nfev=self.config.max_nfev, **self.run_config)
             if num_points == 1:
                 uniform_results = {k: [v] for k, v in uniform_results.items()}
                 unconstrained_results = {
diff --git a/CHAP/edd/reader.py b/CHAP/edd/reader.py
index e813ee03..4a89b18d 100755
--- a/CHAP/edd/reader.py
+++ b/CHAP/edd/reader.py
@@ -785,7 +785,7 @@ def read(self):
         from nexusformat.nexus import NXentry, NXfield
 
         # Local modules
-        from CHAP.common import NexusReader
+        from CHAP.common.reader import NexusReader
         from CHAP.utils.general import nxcopy
 
         # Read NXroot
diff --git a/CHAP/edd/utils.py b/CHAP/edd/utils.py
index 8079d4b5..82f8b625 100755
--- a/CHAP/edd/utils.py
+++ b/CHAP/edd/utils.py
@@ -1311,7 +1311,8 @@ def get_spectra_fits(
     # Local modules
     from CHAP.utils.fit import FitProcessor
 
-    num_proc = kwargs.get('num_proc', 1)
+    num_proc = kwargs.pop('num_proc', 1)
+    max_nfev = kwargs.pop('max_nfev', 64000)
     rel_height_cutoff = detector.rel_height_cutoff
     num_peak = len(peak_locations)
     nxdata = NXdata(NXfield(spectra, 'y'), NXfield(energies, 'x'))
@@ -1341,6 +1342,7 @@ def get_spectra_fits(
         'models': models,
 #        'plot': True,
         'num_proc': num_proc,
+        'max_nfev': max_nfev,
         'rel_height_cutoff': rel_height_cutoff,
 #        'method': 'trf',
         'method': 'leastsq',
diff --git a/CHAP/utils/fit.py b/CHAP/utils/fit.py
index 56489ab8..af4fc1a4 100755
--- a/CHAP/utils/fit.py
+++ b/CHAP/utils/fit.py
@@ -106,9 +106,9 @@ def process(self, data, config=None):
             # Refit/continue the fit with possibly updated parameters
             fit = data
             if isinstance(data, FitMap):
-                fit.fit(config=fit_config)
+                fit.fit(config=fit_config, max_nfev=config.get('max_nfev'))
             else:
-                fit.fit(config=fit_config)
+                fit.fit(config=fit_config, max_nfev=config.get('max_nfev'))
                 if fit_config is not None:
                     if fit_config.print_report:
                         fit.print_fit_report()
@@ -145,7 +145,7 @@ def process(self, data, config=None):
             # Instantiate the Fit or FitMap object and fit the data
             if np.squeeze(nxdata.nxsignal).ndim == 1:
                 fit = Fit(nxdata, fit_config, self.logger)
-                fit.fit()
+                fit.fit(max_nfev=config.get('max_nfev'))
                 if fit_config.print_report:
                     fit.print_fit_report()
                 if fit_config.plot:
@@ -154,8 +154,9 @@ def process(self, data, config=None):
                 fit = FitMap(nxdata, fit_config, self.logger)
                 fit.fit(
                     rel_height_cutoff=fit_config.rel_height_cutoff,
-                    num_proc=fit_config.num_proc, plot=fit_config.plot,
-                    print_report=fit_config.print_report)
+                    max_nfev=config.get('max_nfev'),
+                    num_proc=fit_config.num_proc,
+                    plot=fit_config.plot, print_report=fit_config.print_report)
         else:
             raise ValueError(f'Invalid input data ({type(data)}: {data})')
 
@@ -2087,12 +2088,12 @@ def _fit_nonlinear_model(self, x, y, **kwargs):
                 'gtol': 10*FLOAT_EPS,
             }
             if self._method == 'leastsq':
-                lskws['maxfev'] = 64000
+                lskws['maxfev'] = kwarg.get('max_nfev', 64000)
                 result = leastsq(
                     self._residual, pars_init, args=(x, y), full_output=True,
                     **lskws)
             else:
-                lskws['max_nfev'] = 64000
+                lskws['max_nfev'] = kwarg.get('max_nfev', 64000)
                 result = least_squares(
                     self._residual, pars_init, bounds=bounds,
                     method=self._method, args=(x, y), **lskws)
@@ -3089,6 +3090,9 @@ def _fit(self, n, current_best_values, return_result=False, **kwargs):
 
         # Regular full fit
         result = self._fit_with_bounds_check(n, current_best_values, **kwargs)
+        if result.nfev == kwargs.get('max_nfev'):
+            self._logger.info(
+                f'Hit max_nfev limit for n={n}\n\tnfev: {result.nfev}')
 
         if self._rel_height_cutoff is not None:
             # Check for low heights peaks and refit without them
@@ -3123,6 +3127,9 @@ def _fit(self, n, current_best_values, return_result=False, **kwargs):
                     # Reset fixed amplitudes back to default
                     self._parameters = deepcopy(parameters_save)
                     self._parameter_bounds = deepcopy(parameters_bounds_save)
+                    if result.nfev == kwargs.get('max_nfev'):
+                        self._logger.info(
+                        f'\nHit max_nfev limit again after refit for n={n}')
 
         if result.redchi >= self._redchi_cutoff:
             result.success = False

From 580d5964e4a8aff0a838280ee53931b7ed98e9bc Mon Sep 17 00:00:00 2001
From: Rolf Verberg <rv43@cornell.edu>
Date: Fri, 29 May 2026 13:38:10 -0400
Subject: [PATCH 71/76] fix: bug in max_nfev kwargs for scipy fitting

---
 CHAP/common/writer.py | 2 +-
 CHAP/utils/fit.py     | 7 +++++--
 2 files changed, 6 insertions(+), 3 deletions(-)

diff --git a/CHAP/common/writer.py b/CHAP/common/writer.py
index a118ba22..ceb3c661 100755
--- a/CHAP/common/writer.py
+++ b/CHAP/common/writer.py
@@ -897,7 +897,7 @@ def get_dict(data):
         self.status = 'written' # Right now does nothing yet, but could
                                 # add a sort of modification flag later
 
-       # Return provenance with the output file name added
+        # Return provenance with the output file name added
         return self._update_provenance(data)
 
 
diff --git a/CHAP/utils/fit.py b/CHAP/utils/fit.py
index af4fc1a4..4b15d05e 100755
--- a/CHAP/utils/fit.py
+++ b/CHAP/utils/fit.py
@@ -2087,13 +2087,16 @@ def _fit_nonlinear_model(self, x, y, **kwargs):
                 'xtol': 1.49012e-08,
                 'gtol': 10*FLOAT_EPS,
             }
+            max_nfev = kwargs.get('max_nfev')
             if self._method == 'leastsq':
-                lskws['maxfev'] = kwarg.get('max_nfev', 64000)
+                if max_nfev is not None:
+                    lskws['maxfev'] = max_nfev
                 result = leastsq(
                     self._residual, pars_init, args=(x, y), full_output=True,
                     **lskws)
             else:
-                lskws['max_nfev'] = kwarg.get('max_nfev', 64000)
+                if max_nfev is not None:
+                    lskws['max_nfev'] = max_nfev
                 result = least_squares(
                     self._residual, pars_init, bounds=bounds,
                     method=self._method, args=(x, y), **lskws)

From 6e0bc658c5da85db22cbb618b1e44e357f99367d Mon Sep 17 00:00:00 2001
From: Keara Soloway <kls286@cornell.edu>
Date: Mon, 1 Jun 2026 09:23:12 -0400
Subject: [PATCH 72/76] fix: add CHAP.saxswaxs.models.Background.idx_slice

---
 CHAP/saxswaxs/models.py | 47 +++++++++++++++++++++++++++++++++++++++++
 1 file changed, 47 insertions(+)

diff --git a/CHAP/saxswaxs/models.py b/CHAP/saxswaxs/models.py
index 48667db9..25d30d22 100644
--- a/CHAP/saxswaxs/models.py
+++ b/CHAP/saxswaxs/models.py
@@ -31,12 +31,59 @@ class Background(SpecScans):
     optional index slice so that only a subset of scan steps is used
     when reading background images.
 
+    Accepts either ``idx_slice`` (a :class:`~CHAP.common.models.common.IndexSliceConfig`
+    dict) or the convenience field ``scan_step_indices`` (a list of
+    integers or a compact string such as ``"0-4, 6"``), but not both.
+    When ``scan_step_indices`` is given it is converted to the
+    equivalent ``idx_slice``; the indices must form a uniformly-spaced
+    sequence expressible as a Python :class:`slice`.
+
     :ivar idx_slice: Index slice selecting which scan steps of the
         background scan(s) to read and average.  Defaults to all steps.
     :vartype idx_slice: IndexSliceConfig
+    :ivar scan_step_indices: Convenience alternative to ``idx_slice``.
+        A list of integer step indices (or a compact string such as
+        ``"0-4, 6"``) that are converted to an ``idx_slice`` during
+        validation.  The indices must be uniformly spaced.  Mutually
+        exclusive with ``idx_slice``.
+    :vartype scan_step_indices: list[int] or str, optional
     """
 
     idx_slice: IndexSliceConfig = IndexSliceConfig()
+    scan_step_indices: Optional[Union[list[int], str]] = None
+
+    @model_validator(mode='before')
+    @classmethod
+    def fill_idx_slice(cls, data):
+        scan_step_indices = data.get('scan_step_indices')
+        idx_slice = data.get('idx_slice')
+        if scan_step_indices is not None and idx_slice is not None:
+            raise ValueError(
+                'Specify idx_slice or scan_step_indices, not both.')
+        if scan_step_indices is not None:
+            if isinstance(scan_step_indices, str):
+                from CHAP.utils.general import string_to_list
+                scan_step_indices = string_to_list(scan_step_indices)
+            # scan_step_indices is now list[int]; derive a uniform slice
+            indices = sorted(scan_step_indices)
+            if len(indices) == 1:
+                start, step = indices[0], 1
+            else:
+                step = indices[1] - indices[0]
+                if step <= 0:
+                    raise ValueError(
+                        'scan_step_indices must contain distinct, '
+                        'positive-step values.')
+                diffs = [indices[i+1] - indices[i]
+                         for i in range(len(indices) - 1)]
+                if len(set(diffs)) != 1:
+                    raise ValueError(
+                        'scan_step_indices must be uniformly spaced so '
+                        'they can be expressed as a slice.')
+                start = indices[0]
+            stop = indices[-1] + step
+            data['idx_slice'] = {'start': start, 'stop': stop, 'step': step}
+        return data
 
     def zarr_arrays(self, integration_shape):
         """Return a dictionary describing the zarr array that will hold

From ad7de50c0b51def6bdc9785932e6ed1e328931f1 Mon Sep 17 00:00:00 2001
From: Rolf Verberg <rv43@cornell.edu>
Date: Tue, 2 Jun 2026 09:21:05 -0400
Subject: [PATCH 73/76] fix: changed config to FitProcessor class field, change
 input data type for fit

---
 CHAP/edd/processor.py  |  66 +++++------
 CHAP/edd/utils.py      |   8 +-
 CHAP/pipeline.py       |   2 +-
 CHAP/tomo/processor.py |  10 +-
 CHAP/utils/fit.py      | 261 +++++++++++++++++++++--------------------
 5 files changed, 175 insertions(+), 172 deletions(-)

diff --git a/CHAP/edd/processor.py b/CHAP/edd/processor.py
index db685bbe..c2258031 100755
--- a/CHAP/edd/processor.py
+++ b/CHAP/edd/processor.py
@@ -735,11 +735,10 @@ def _measure_dvl(self, scanned_vals):
                         models.append({'model': model, 'prefix': f'{model}_'})
             models.append({'model': 'gaussian'})
             self.logger.debug('Fitting mean spectrum')
-            fit = FitProcessor(**self.run_config)
-            result = fit.process(
-                NXdata(
-                    NXfield(masked_sum, 'y'), NXfield(x, 'x')),
-                    {'models': models, 'method': 'trf'})
+            result = FitProcessor.run(
+                data={'x': x, 'y': masked_sum},
+                config={'models': models, 'method': 'trf'},
+                **self.run_config)
 
             # Calculate / manually select diffraction volume length
             detector.dvl = float(
@@ -1406,12 +1405,10 @@ def _calibrate(self):
                  'fwhm_min': detector.fwhm_min,
                  'fwhm_max': detector.fwhm_max})
             self.logger.debug('Fitting spectrum')
-            fit = FitProcessor(**self.run_config)
-            mean_data_fit = fit.process(
-                NXdata(
-                    NXfield(mean_data[mask], 'y'), NXfield(bins[mask], 'x')),
-                {'models': models, 'method': 'trf'})
-
+            mean_data_fit = FitProcessor.run(
+                data={'x': bins[mask], 'y': mean_data[mask]},
+                config={'models': models, 'method': 'trf'},
+                **self.run_config)
 
             # Extract the fit results for the peaks
             fit_peak_amplitudes = np.asarray([
@@ -1428,12 +1425,10 @@ def _calibrate(self):
             self.logger.debug(f'Fit peak sigmas: {fit_peak_sigmas}')
 
             # FIX for now stick with a linear energy correction
-            fit = FitProcessor(**self.run_config)
-            energy_fit = fit.process(
-                    NXdata(
-                        NXfield(peak_energies, 'y'),
-                        NXfield(fit_peak_indices, 'x')),
-                    {'models': [{'model': 'linear'}]})
+            energy_fit = FitProcessor.run(
+                data={'x': fit_peak_indices, 'y': peak_energies},
+                config={'models': [{'model': 'linear'}]},
+                **self.run_config)
             a = 0.0
             b = float(energy_fit.best_values['slope'])
             c = float(energy_fit.best_values['intercept'])
@@ -2141,10 +2136,10 @@ def _direct_bragg_peak_fit(
              'fwhm_max': detector.fwhm_max})
 
         # Perform an unconstrained fit in terms of MCA bin index
-        fit = FitProcessor(**self.run_config)
-        result = fit.process(
-            NXdata(NXfield(mean_data[mask], 'y'), NXfield(bins[mask], 'x')),
-            {'models': models, 'method': 'trf'})
+        result = FitProcessor.run(
+            data={'x': bins[mask], 'y': mean_data[mask]},
+            config={'models': models, 'method': 'trf'},
+            **self.run_config)
         best_fit = result.best_fit
         residual = result.residual
 
@@ -2168,10 +2163,10 @@ def _direct_bragg_peak_fit(
             model = 'quadratic'
         else:
             model = 'linear'
-        fit = FitProcessor(**self.run_config)
-        result = fit.process(
-            NXdata(NXfield(e_bragg, 'y'), NXfield(fit_peak_indices, 'x')),
-            {'models': [{'model': model}]})
+        result = FitProcessor.run(
+            data={'x': fit_peak_indices, 'y': e_bragg},
+            config={'models': [{'model': model}]},
+            **self.run_config)
         if quadratic_energy_calibration:
             a_fit = result.best_values['a']
             b_fit = result.best_values['b']
@@ -2298,10 +2293,11 @@ def _direct_fit_tth_ecc(
                     {'name': 'sigma', 'min': sig_min, 'max': sig_max}]})
 
         # Perform the fit
-        fit = FitProcessor(**self.run_config)
-        result = fit.process(
-            NXdata(NXfield(mean_data[mask], 'y'), NXfield(bins[mask], 'x')),
-            {'parameters': parameters, 'models': models, 'method': 'trf'})
+        result = FitProcessor.run(
+            data={'x': bins[mask], 'y': mean_data[mask]},
+            config={
+                'parameters': parameters, 'models': models, 'method': 'trf'},
+            **self.run_config)
 
         # Extract values of interest from the best values
         tth_fit = np.degrees(result.best_values['tth'])
@@ -2333,14 +2329,10 @@ def _direct_fit_tth_ecc(
             'centers_range': b_fit * detector.centers_range,
             'fwhm_min': b_fit * detector.fwhm_min,
             'fwhm_max': b_fit * detector.fwhm_max}]
-        result = fit.process(
-            NXdata(NXfield(mean_data[mask], 'y'), NXfield(bins[mask], 'x')),
-            {'parameters': parameters, 'models': models, 'method': 'trf'})
-        fit = FitProcessor(**self.run_config)
-        result = fit.process(
-            NXdata(NXfield(mean_data[mask], 'y'),
-            NXfield(energies[mask], 'x')),
-            {'models': models, 'method': 'trf'})
+        result = FitProcessor.run(
+            data={'x': energies[mask], 'y': mean_data[mask]},
+            config={'models': models, 'method': 'trf'},
+            **self.run_config)
         e_xrf_unconstrained = np.sort(
             [result.best_values[f'peak{i+1}_center']
              for i in range(num_xrf)])
diff --git a/CHAP/edd/utils.py b/CHAP/edd/utils.py
index 8079d4b5..7a1537ef 100755
--- a/CHAP/edd/utils.py
+++ b/CHAP/edd/utils.py
@@ -1314,7 +1314,6 @@ def get_spectra_fits(
     num_proc = kwargs.get('num_proc', 1)
     rel_height_cutoff = detector.rel_height_cutoff
     num_peak = len(peak_locations)
-    nxdata = NXdata(NXfield(spectra, 'y'), NXfield(energies, 'x'))
 
     # Construct the fit model
     models = []
@@ -1350,8 +1349,8 @@ def get_spectra_fits(
 
     # Perform uniform fit
     # FIX make more generic for fit parameters
-    fit = FitProcessor(**kwargs)
-    uniform_fit = fit.process(nxdata, config)
+    uniform_fit = FitProcessor.fit(
+        data={'x': energies, 'y': spectra}, config=config, **kwargs)
     uniform_success = uniform_fit.success
     if spectra.ndim == 1:
         if uniform_success:
@@ -1518,7 +1517,8 @@ def get_spectra_fits(
 
     # Perform unconstrained fit
     config['models'][-1]['fit_type'] = 'unconstrained'
-    unconstrained_fit = fit.process(uniform_fit, config)
+    fit.config = config
+    unconstrained_fit = fit.process(uniform_fit)
     unconstrained_success = unconstrained_fit.success
     if spectra.ndim == 1:
         if unconstrained_success:
diff --git a/CHAP/pipeline.py b/CHAP/pipeline.py
index ba843ca3..91800b24 100755
--- a/CHAP/pipeline.py
+++ b/CHAP/pipeline.py
@@ -416,7 +416,7 @@ def get_pipelinedata_item(data, index=-1, remove=False):
         :return: Matching data item.
         :rtype: Any
         """
-        if isinstance(data, list):
+        if isinstance(data, list) and isinstance(data[index], PipelineData):
             if remove:
                 return data.pop(index)['data']
             return data[index]['data']
diff --git a/CHAP/tomo/processor.py b/CHAP/tomo/processor.py
index 18993aa5..9d794348 100755
--- a/CHAP/tomo/processor.py
+++ b/CHAP/tomo/processor.py
@@ -1627,7 +1627,6 @@ def _set_detector_bounds(
                 # Try to get a fit from the bright field
                 row_sum = np.sum(tbf, 1)
                 num = len(row_sum)
-                fit = FitProcessor(**self.run_config)
                 model = {'model': 'rectangle',
                          'parameters': [
                              {'name': 'amplitude',
@@ -1641,11 +1640,10 @@ def _set_detector_bounds(
                               'min': 0.0, 'max': num},
                              {'name': 'sigma2', 'value': num/7.0,
                               'min': sys.float_info.min}]}
-                bounds_fit = fit.process(
-                    data=NXdata(
-                        NXfield(row_sum, 'y'),
-                        NXfield(np.array(range(num)), 'x')),
-                    config={'models': [model], 'method': 'trf'})
+                bounds_fit = FitProcessor.run(
+                    data={'x': np.array(range(num)), 'y':row_sum},
+                    config={'models': [model], 'method': 'trf'},
+                    **self.run_config)
                 parameters = bounds_fit.best_values
                 row_low_fit = parameters.get('center1', None)
                 row_upp_fit = parameters.get('center2', None)
diff --git a/CHAP/utils/fit.py b/CHAP/utils/fit.py
index 56489ab8..86f810c4 100755
--- a/CHAP/utils/fit.py
+++ b/CHAP/utils/fit.py
@@ -14,6 +14,7 @@
 from shutil import rmtree
 from sys import float_info
 #from time import time
+from typing import Optional
 
 # Third party modules
 try:
@@ -24,8 +25,8 @@
     HAVE_JOBLIB = True
 except ImportError:
     HAVE_JOBLIB = False
-from nexusformat.nexus import NXdata
 import numpy as np
+from pydantic import Field
 
 # Local modules
 from CHAP.processor import Processor
@@ -35,6 +36,7 @@
     index_nearest,
     quick_plot,
 )
+from CHAP.utils.models import FitConfig
 
 FLOAT_MIN = float_info.min
 FLOAT_MAX = float_info.max
@@ -60,104 +62,93 @@
 
 
 class FitProcessor(Processor):
-    """A processor to perform a fit on a data set or data map. """
+    """A processor to perform a fit on a data set or data map.
 
-    def process(self, data, config=None):
+    :ivar config: Initialization parameters for an instance of
+        :class:`~CHAP.utils.models.FitConfig`.
+    :vartype config: dict, optional
+    """
+
+    pipeline_fields: dict = Field(
+        default = {
+            'config': 'CHAP.utils.models.FitConfig'}, init_var=True)
+    config: Optional[FitConfig] = None
+
+    def process(self, data):
         """Fit the data and return a :class:`~CHAP.utils.fit.Fit` or
         :class:`~CHAP.utils.fit.FitMap` object depending on the
-        dimensionality of the input data. The input data should be or
-        contain a NeXus style
-        `NXdata <https://manual.nexusformat.org/classes/base_classes/NXdata.html#index-0>`__ 
-        object, with properly defined signal and axis, or a
-        :class:`~CHAP.utils.fit.Fit` or :class:`~CHAP.utils.fit.FitMap`
-        object from a previous fit.
-
-        :param data: Input data containing the
-            nexusformat.nexus.NXdata object to fit.
-        :type data: list[PipelineData] or Fit or FitMap or
-            nexusformat.nexus.NXdata
-        :param config: Fit configuration.
-        :type config: dict, optional
-        :raises ValueError: Invalid input or configuration parameter.
+        dimensionality of the input data. The input data should be an
+        array-like object (tuple, list or numpy.ndarray) or a
+        dictionary with at least a `"y"` field with a value equal to
+        one or a :class:`~CHAP.utils.fit.Fit` or
+        :class:`~CHAP.utils.fit.FitMap` object from a previous fit.
+
+        :param data: Input data containing the data object to fit.
+        :type data: list[PipelineData] or Fit or FitMap or array-like
         :return: The fitted data object.
         :rtype: Fit or FitMap
         """
         # Local modules
-        from CHAP.utils.models import (
-            FitConfig,
-            Multipeak,
-        )
+        from CHAP.utils.models import Multipeak
 
-        # Unwrap the PipelineData if called as a Pipeline Processor
-        if (not isinstance(data, (Fit, FitMap))
-                and not isinstance(data, NXdata)):
-            data = self.get_pipelinedata_item(data)
-
-        # Get the validated fit configuration
-        fit_config = None
-        if config is not None:
-            try:
-                fit_config = FitConfig(**config)
-            except Exception as exc:
-                raise RuntimeError from exc
+#        # Unwrap the PipelineData if called as a Pipeline Processor
+#        data = self.get_pipelinedata_item(data)
 
         if isinstance(data, (Fit, FitMap)):
 
             # Refit/continue the fit with possibly updated parameters
             fit = data
             if isinstance(data, FitMap):
-                fit.fit(config=fit_config)
+                fit.fit(config=self.config)
             else:
-                fit.fit(config=fit_config)
-                if fit_config is not None:
-                    if fit_config.print_report:
+                fit.fit(config=self.config)
+                if self.config is not None:
+                    if self.config.print_report:
                         fit.print_fit_report()
-                    if fit_config.plot:
+                    if self.config.plot:
                         fit.plot(skip_init=True)
 
-        elif isinstance(data, NXdata):
+        else:
 
-            # Get the default NXdata object
+            # Test for the correct input data type
             try:
-                nxdata = data.get_default()
-                assert nxdata is not None
-            except (AssertionError, ValueError) as exc:
-                if nxdata is None or nxdata.nxclass != 'NXdata':
-                    raise ValueError(
-                        'Invalid default pathway to an NXdata '
-                        f'object in ({data})') from exc
+                if isinstance(data, dict):
+                    x = np.asarray(data.get('x'))
+                    y = np.asarray(data.get('y'))
+                else:
+                    y = np.asarray(data)
+            except (ValueError, TypeError) as exc:
+                raise ValueError(f'Invalid input data ({type(data)}\n{data})')
 
             # Expand multipeak model if present
             found_multipeak = False
-            for i, model in enumerate(deepcopy(fit_config.models)):
+            for i, model in enumerate(deepcopy(self.config.models)):
                 if isinstance(model, Multipeak):
                     if found_multipeak:
                         raise ValueError(
-                            f'Invalid parameter models ({fit_config.models}) '
+                            f'Invalid parameter models ({self.config.models}) '
                             '(multiple instances of multipeak not allowed)')
                     parameters, models = self.create_multipeak_model(model)
                     if parameters:
-                        fit_config.parameters += parameters
-                    fit_config.models += models
-                    fit_config.models.pop(i)
+                        self.config.parameters += parameters
+                    self.config.models += models
+                    self.config.models.pop(i)
                     found_multipeak = True
 
             # Instantiate the Fit or FitMap object and fit the data
-            if np.squeeze(nxdata.nxsignal).ndim == 1:
-                fit = Fit(nxdata, fit_config, self.logger)
+            if np.squeeze(y).ndim == 1:
+                fit = Fit(data, self.config, self.logger)
                 fit.fit()
-                if fit_config.print_report:
+                if self.config.print_report:
                     fit.print_fit_report()
-                if fit_config.plot:
+                if self.config.plot:
                     fit.plot(skip_init=True)
             else:
-                fit = FitMap(nxdata, fit_config, self.logger)
+                fit = FitMap(data, self.config, self.logger)
                 fit.fit(
-                    rel_height_cutoff=fit_config.rel_height_cutoff,
-                    num_proc=fit_config.num_proc, plot=fit_config.plot,
-                    print_report=fit_config.print_report)
-        else:
-            raise ValueError(f'Invalid input data ({type(data)}: {data})')
+                    rel_height_cutoff=self.config.rel_height_cutoff,
+                    num_proc=self.config.num_proc, plot=self.config.plot,
+                    print_report=self.config.print_report)
 
         return fit
 
@@ -577,11 +568,11 @@ def fit_report(self, show_correl=False):
 class Fit:
     """Wrapper class for scipy/lmfit."""
 
-    def __init__(self, nxdata, config, logger):
+    def __init__(self, data, config, logger):
         """Initialize Fit.
 
-        :param nxdata: The input data.
-        :type nxdata: nexusformat.nexus.NXdata
+        :param data: The input data.
+        :type data: array-like, or dict
         :param config: Fit configuration.
         :type config: CHAP.utils.models.FitConfig, optional
         :param logger: A python Logger object.
@@ -633,20 +624,20 @@ def __init__(self, nxdata, config, logger):
 #                raise ValueError(
 #                    'Invalid value of keyword argument try_linear_fit '
 #                    f'({self._try_linear_fit})')
-        if nxdata is not None:
-            if isinstance(nxdata.attrs['axes'], str):
-                dim_x = nxdata.attrs['axes']
-            else:
-                dim_x = nxdata.attrs['axes'][-1]
-            self._x = np.asarray(nxdata[dim_x])
-            self._y = np.squeeze(nxdata.nxsignal)
-            if self._x.ndim != 1:
-                raise ValueError(
-                    f'Invalid x dimension ({self._x.ndim})')
-            if self._x.size != self._y.size:
+        if data is not None:
+            try:
+                if isinstance(data, dict):
+                    self._x = np.asarray(data.get('x'))
+                    self._y = np.squeeze(data.get('y'))
+                    assert self._x.size == self._y.size
+                else:
+                    self._y = np.squeeze(data)
+                    self._x = np.arange(self._y.size)
+            except (ValueError, TypeError) as exc:
+                raise ValueError(f'Invalid input data ({type(data)}\n{data})')
+            if self._y.ndim != 1:
                 raise ValueError(
-                    f'Inconsistent x and y dimensions ({self._x.size} vs '
-                    f'{self._y.size})')
+                    f'Invalid input data dimension ({self._y.ndim})')
 #            if 'mask' in kwargs:
 #                self._mask = kwargs.pop('mask')
             if True: #self._mask is None:
@@ -928,14 +919,6 @@ def var_names(self):
             return None
         return getattr(self._result, 'var_names', None)
 
-    @property
-    def x(self):
-        """Return the input x-coordinates.
-
-        :type: numpy.ndarray
-        """
-        return self._x
-
     @property
     def y(self):
         """Return the input y-coordinates.
@@ -1216,8 +1199,7 @@ def add_model(self, model, prefix):
             if name not in new_parameters:
                 name = pprefix+name
                 if name not in new_parameters:
-                    raise ValueError(
-                        f'Unable to match parameter {name}')
+                    raise ValueError(f'Unable to match parameter {name}')
             if parameter.expr is None:
                 self._parameters[name].set(
                     value=parameter.value, min=parameter.min,
@@ -1331,11 +1313,13 @@ def fit(self, config=None, **kwargs):
         return None
 
     def plot(
-            self, y=None, *, y_title=None, title=None, result=None,
+            self, x=None, y=None, *, y_title=None, title=None, result=None,
             skip_init=False, plot_comp=True, plot_comp_legends=False,
             plot_residual=False, plot_masked_data=True, **kwargs):
         """Plot the best fit.
 
+        :param x: x-coordinates.
+        :type x: array-like, optional
         :param y: y-coordinates.
         :type y: array-like, optional
         :param y_title: y-axis label.
@@ -1372,34 +1356,45 @@ class attribute.
             plot_masked_data = False
         else:
             mask = self._mask
+        if x is not None:
+            if not isinstance(x, (tuple, list, np.ndarray)):
+                self._logger.warning(
+                    'Ignoring invalid parameter x ({type(x)})')
+            if len(x) != len(self._x):
+                self._logger.warning(
+                    'Ignoring parameter x in plot (wrong dimension)')
+                x = None
+        if x is None:
+            x = self._x
         if y is not None:
             if not isinstance(y, (tuple, list, np.ndarray)):
-                self._logger.warning('Ignorint invalid parameter y ({y}')
-            if len(y) != len(self._x):
+                self._logger.warning(
+                    'Ignoring invalid parameter y ({type(y)})')
+            if len(y) != len(x):
                 self._logger.warning(
                     'Ignoring parameter y in plot (wrong dimension)')
                 y = None
         if y is not None:
             if y_title is None or not isinstance(y_title, str):
                 y_title = 'data'
-            plots += [(self._x, y, '.')]
+            plots += [(x, y, '.')]
             legend += [y_title]
         if self._y is not None:
-            plots += [(self._x, np.asarray(self._y), 'b.')]
+            plots += [(x, np.asarray(self._y), 'b.')]
             legend += ['data']
             if plot_masked_data:
-                plots += [(self._x[mask], np.asarray(self._y)[mask], 'bx')]
+                plots += [(x[mask], np.asarray(self._y)[mask], 'bx')]
                 legend += ['masked data']
         if isinstance(plot_residual, bool) and plot_residual:
-            plots += [(self._x[~mask], result.residual, 'r-')]
+            plots += [(x[~mask], result.residual, 'r-')]
             legend += ['residual']
-        plots += [(self._x[~mask], result.best_fit, 'k-')]
+        plots += [(x[~mask], result.best_fit, 'k-')]
         legend += ['best fit']
         if not skip_init and hasattr(result, 'init_fit'):
-            plots += [(self._x[~mask], result.init_fit, 'g-')]
+            plots += [(x[~mask], result.init_fit, 'g-')]
             legend += ['init']
         if plot_comp:
-            components = result.eval_components(x=self._x[~mask])
+            components = result.eval_components(x=x[~mask])
             num_components = len(components)
             if 'tmp_normalization_offset_' in components:
                 num_components -= 1
@@ -1413,8 +1408,8 @@ class attribute.
                     if len(modelname) > 20:
                         modelname = f'{modelname[0:16]} ...'
                     if isinstance(y_comp, (int, float)):
-                        y_comp *= np.ones(self._x[~mask].size)
-                    plots += [(self._x[~mask], y_comp, '--')]
+                        y_comp *= np.ones(x[~mask].size)
+                    plots += [(x[~mask], y_comp, '--')]
                     if plot_comp_legends:
                         if modelname[-1] == '_':
                             legend.append(modelname[:-1])
@@ -2311,11 +2306,11 @@ def _residual(self, pars, x, y):
 class FitMap(Fit):
     """Wrapper to the Fit class to fit data on a N-dimensional map."""
 
-    def __init__(self, nxdata, config, logger):
+    def __init__(self, data, config, logger):
         """Initialize FitMap.
 
-        :param nxdata: The input data.
-        :type nxdata: nexusformat.nexus.NXdata
+        :param data: The input data.
+        :type data: array-like, or dict
         :param config: Fit configuration.
         :type config: CHAP.utils.models.FitConfig, optional
         :param logger: A python Logger object.
@@ -2345,16 +2340,16 @@ def __init__(self, nxdata, config, logger):
         # At this point the fastest index should always be the signal
         #     dimension so that the slowest ndim-1 dimensions are the
         #     map dimensions
-        self._x = np.asarray(nxdata[nxdata.attrs['axes'][-1]])
-        self._ymap = np.asarray(nxdata.nxsignal)
-
-        # Check input parameters
-        if self._x.ndim != 1:
-            raise ValueError(f'Invalid x dimension ({self._x.ndim})')
-        if self._x.size != self._ymap.shape[-1]:
-            raise ValueError(
-                f'Inconsistent x and y dimensions ({self._x.size} vs '
-                f'{self._ymap.shape[-1]})')
+        try:
+            if isinstance(data, dict):
+                self._x = np.asarray(data.get('x'))
+                self._ymap = np.asarray(data.get('y'))
+                assert self._x.size == self._ymap.shape[-1]
+            else:
+                self._ymap = np.asarray(data)
+                self._x = np.arange(self._ymap.shape[-1])
+        except (ValueError, TypeError) as exc:
+            raise ValueError(f'Invalid input data ({type(data)}\n{data})')
 
         # Flatten the map
         # Store the flattened map in self._ymap_norm
@@ -2385,7 +2380,7 @@ def __init__(self, nxdata, config, logger):
         self._y_range = ymap_max-ymap_min
         if self._y_range > 0.0:
             self._norm = (ymap_min, self._y_range)
-            self._ymap_norm = (self._ymap_norm-self._norm[0]) / self._norm[1]
+            self._ymap_norm = (self._ymap_norm-self._norm[0])/self._norm[1]
         else:
             self._redchi_cutoff *= self._y_range**2
 
@@ -2588,7 +2583,12 @@ def best_parameters(self, dims=None):
         :rtype: list[str] or dict
         """
         if dims is None:
-            return self._best_parameters
+            parameters_dict = {}
+            for i, name in enumerate(self._best_parameters):
+                parameters_dict[name] = {
+                    'values': self._best_values[i],
+                    'errors': self._best_errors[i]}
+            return parameters_dict
         if (not isinstance(dims, (list, tuple))
                 or len(dims) != len(self._map_shape)):
             raise ValueError('Invalid parameter dims ({dims})')
@@ -2627,10 +2627,12 @@ def freemem(self):
             self._logger.warning('Could not clean-up automatically.')
 
     def plot(
-            self, dims=None, *, y_title=None, plot_comp_legends=False,
+            self, x=None, dims=None, *, y_title=None, plot_comp_legends=False,
             plot_residual=False, plot_masked_data=True, **kwargs):
         """Plot the best fits.
 
+        :param x: x-coordinates.
+        :type x: array-like, optional
         :param dims: Map indices of the data point to plot,
             defaults to `None` which will plot the first data point.
         :type dims: list or tuple, optional
@@ -2649,6 +2651,16 @@ def plot(
         # Third party modules
         from lmfit.models import ExpressionModel
 
+        if x is not None:
+            if not isinstance(x, (tuple, list, np.ndarray)):
+                self._logger.warning(
+                    'Ignoring invalid parameter x ({type(x)})')
+            if len(x) != len(self._x):
+                self._logger.warning(
+                    'Ignoring parameter x in plot (wrong dimension)')
+                x = None
+        if x is None:
+            x = self._x
         if dims is None:
             dims = [0]*len(self._map_shape)
         if (not isinstance(dims, (list, tuple))
@@ -2663,20 +2675,20 @@ def plot(
         if y_title is None or not isinstance(y_title, str):
             y_title = 'data'
         if self._mask is None:
-            mask = np.zeros(self._x.size).astype(bool)
+            mask = np.zeros(x.size).astype(bool)
             plot_masked_data = False
         else:
             mask = self._mask
-        plots = [(self._x, np.asarray(self._ymap[dims]), 'b.')]
+        plots = [(x, np.asarray(self._ymap[dims]), 'b.')]
         legend = [y_title]
         if plot_masked_data:
             plots += \
-                [(self._x[mask], np.asarray(self._ymap)[(*dims,mask)], 'bx')]
+                [(x[mask], np.asarray(self._ymap)[(*dims,mask)], 'bx')]
             legend += ['masked data']
-        plots += [(self._x[~mask], self.best_fit[dims], 'k-')]
+        plots += [(x[~mask], self.best_fit[dims], 'k-')]
         legend += ['best fit']
         if plot_residual:
-            plots += [(self._x[~mask], self.residual[dims], 'r--')]
+            plots += [(x[~mask], self.residual[dims], 'r--')]
             legend += ['residual']
         # Create current parameters
         parameters = deepcopy(self._parameters)
@@ -2703,10 +2715,10 @@ def plot(
                     modelname = f'{component._name}'
             if len(modelname) > 20:
                 modelname = f'{modelname[0:16]} ...'
-            y = component.eval(params=parameters, x=self._x[~mask])
+            y = component.eval(params=parameters, x=x[~mask])
             if isinstance(y, (int, float)):
-                y *= np.ones(self._x[~mask].size)
-            plots += [(self._x[~mask], y, '--')]
+                y *= np.ones(x[~mask].size)
+            plots += [(x[~mask], y, '--')]
             if plot_comp_legends:
                 legend.append(modelname)
         quick_plot(
@@ -3092,6 +3104,7 @@ def _fit(self, n, current_best_values, return_result=False, **kwargs):
 
         if self._rel_height_cutoff is not None:
             # Check for low heights peaks and refit without them
+            # FIX make sure to add "height" and "fwhm" to peak-like models
             heights = []
             names = []
             for component in result.components:

From 372c6152e777f1a3d426a8a1ddb667bb6111ccb9 Mon Sep 17 00:00:00 2001
From: Keara Soloway <kls286@cornell.edu>
Date: Tue, 2 Jun 2026 10:03:56 -0400
Subject: [PATCH 74/76] fix: merge commit bug

---
 CHAP/utils/fit.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/CHAP/utils/fit.py b/CHAP/utils/fit.py
index d09599f7..a834d46d 100755
--- a/CHAP/utils/fit.py
+++ b/CHAP/utils/fit.py
@@ -99,9 +99,9 @@ def process(self, data):
             # Refit/continue the fit with possibly updated parameters
             fit = data
             if isinstance(data, FitMap):
-                fit.fit(config=self.config, max_nfev=config.get('max_nfev'))
+                fit.fit(config=self.config, max_nfev=self.config.max_nfev)
             else:
-                fit.fit(config=self.config, max_nfev=config.get('max_nfev'))
+                fit.fit(config=self.config, max_nfev=self.config.max_nfev)
                 if self.config is not None:
                     if self.config.print_report:
                         fit.print_fit_report()

From 3de02faaab39788cc1f4d55cc20971a1cc1fea93 Mon Sep 17 00:00:00 2001
From: Rolf Verberg <rv43@cornell.edu>
Date: Tue, 2 Jun 2026 11:26:06 -0400
Subject: [PATCH 75/76] fix: merge more fit processor commit bug

---
 CHAP/edd/utils.py    |  6 +++---
 CHAP/utils/fit.py    | 23 ++++++++++++----------
 CHAP/utils/models.py | 46 ++++++++++++++++++++++++++------------------
 3 files changed, 43 insertions(+), 32 deletions(-)

diff --git a/CHAP/edd/utils.py b/CHAP/edd/utils.py
index 837bc4d5..dceb4a78 100755
--- a/CHAP/edd/utils.py
+++ b/CHAP/edd/utils.py
@@ -1351,7 +1351,7 @@ def get_spectra_fits(
 
     # Perform uniform fit
     # FIX make more generic for fit parameters
-    uniform_fit = FitProcessor.fit(
+    uniform_fit = FitProcessor.run(
         data={'x': energies, 'y': spectra}, config=config, **kwargs)
     uniform_success = uniform_fit.success
     if spectra.ndim == 1:
@@ -1519,8 +1519,8 @@ def get_spectra_fits(
 
     # Perform unconstrained fit
     config['models'][-1]['fit_type'] = 'unconstrained'
-    fit.config = config
-    unconstrained_fit = fit.process(uniform_fit)
+    unconstrained_fit = FitProcessor.run(
+        data=uniform_fit, config=config, **kwargs)
     unconstrained_success = unconstrained_fit.success
     if spectra.ndim == 1:
         if unconstrained_success:
diff --git a/CHAP/utils/fit.py b/CHAP/utils/fit.py
index a834d46d..c4671cf8 100755
--- a/CHAP/utils/fit.py
+++ b/CHAP/utils/fit.py
@@ -136,7 +136,7 @@ def process(self, data):
                     found_multipeak = True
 
             # Instantiate the Fit or FitMap object and fit the data
-            if np.squeeze(data.nxsignal).ndim == 1:
+            if np.squeeze(y).ndim == 1:
                 fit = Fit(data, self.config, self.logger)
                 fit.fit(max_nfev=self.config.max_nfev)
                 if self.config.print_report:
@@ -149,9 +149,8 @@ def process(self, data):
                     rel_height_cutoff=self.config.rel_height_cutoff,
                     max_nfev=self.config.max_nfev,
                     num_proc=self.config.num_proc,
-                    plot=self.config.plot, print_report=self.config.print_report)
-        else:
-            raise ValueError(f'Invalid input data ({type(data)}: {data})')
+                    plot=self.config.plot,
+                    print_report=self.config.print_report)
 
         return fit
 
@@ -2589,12 +2588,16 @@ def best_parameters(self, dims=None):
         :rtype: list[str] or dict
         """
         if dims is None:
-            parameters_dict = {}
-            for i, name in enumerate(self._best_parameters):
-                parameters_dict[name] = {
-                    'values': self._best_values[i],
-                    'errors': self._best_errors[i]}
-            return parameters_dict
+            return self._best_parameters
+# FIX use something else, self._best_parameters is "reserved" to get the
+# parameters in the EDD strain analysis and must return the order of the
+# parameters in self.best_values and self.best_errors
+#            parameters_dict = {}
+#            for i, name in enumerate(self._best_parameters):
+#                parameters_dict[name] = {
+#                    'values': self._best_values[i],
+#                    'errors': self._best_errors[i]}
+#            return parameters_dict
         if (not isinstance(dims, (list, tuple))
                 or len(dims) != len(self._map_shape)):
             raise ValueError('Invalid parameter dims ({dims})')
diff --git a/CHAP/utils/models.py b/CHAP/utils/models.py
index ebdeb88a..e63b7e30 100755
--- a/CHAP/utils/models.py
+++ b/CHAP/utils/models.py
@@ -768,46 +768,54 @@ class FitConfig(CHAPBaseModel):
     :ivar code: Specifies is lmfit is used to perform the fit or if
         the scipy fit method is called directly, default to `'lmfit'`.
     :vartype code: Literal['lmfit', 'scipy'], optional
-    :ivar parameters: Fit model parameters in addition to those
-        implicitly defined through the build-in model functions,
-        defaults to `[]`'
-    :vartype parameters:
-        list[:class:`~CHAP.utils.models.FitParameter`], optional
+    :ivar max_nfev: Maximum number of function evaluations in the
+        the strain analysis peak fitting routine.
+    :vartype max_nfev: int, optional
+    :ivar memfolder: Folder name for the temporary memory map if
+        multiple processors are used, defaults to `'joblib_memmap'`.
+    :vartype memfolder: str, optional
+    :ivar method: SciPy non-linear fit method, defaults to
+        `"leastsq"`.
+    :vartype method: Literal[
+        'leastsq', 'trf', 'dogbox', 'lm', 'least_squares']
     :ivar models: The component(s) of the (composite) fit model.
     :vartype models:
         list[:attr:`~CHAP.utils.models.FitConfig.models`]
-    :ivar rel_height_cutoff: Relative peak height cutoff for
-        peak fitting (any peak with a height smaller than
-        `rel_height_cutoff` times the maximum height of all peaks 
-        gets removed from the fit model).
-    :vartype rel_height_cutoff: float, optional
     :ivar num_proc: The number of processors used in fitting a map
         of data, defaults to `1`.
     :vartype num_proc: int, optional
+    :ivar parameters: Fit model parameters in addition to those
+        implicitly defined through the build-in model functions,
+        defaults to `[]`'
+    :vartype parameters:
+        list[:class:`~CHAP.utils.models.FitParameter`], optional
     :ivar plot: Whether a plot of the fit result is generated,
         defaults to `False`.
     :vartype plot: bool, optional.
     :ivar print_report:  Whether to generate a fit result printout,
         defaults to `False`.
     :vartype print_report: bool, optional.
-    :ivar memfolder: Folder name for the temporary memory map if
-        multiple processors are used, defaults to `'joblib_memmap'`.
-    :vartype memfolder: str, optional
+    :ivar rel_height_cutoff: Relative peak height cutoff for
+        peak fitting (any peak with a height smaller than
+        `rel_height_cutoff` times the maximum height of all peaks 
+        gets removed from the fit model).
+    :vartype rel_height_cutoff: float, optional
     """
 
     code: Literal['lmfit', 'scipy'] = 'scipy'
-    parameters: conlist(item_type=FitParameter) = []
+    max_nfev: Optional[conint(gt=0)] = None
+    memfolder: str = 'joblib_memmap'
+    method: Literal[
+        'leastsq', 'trf', 'dogbox', 'lm', 'least_squares'] = 'leastsq'
     models: conlist(item_type=Union[
         Constant, Linear, Quadratic, Exponential, Gaussian, Lorentzian,
         PseudoVoigt, Rectangle, Expression, Multipeak], min_length=1)
-    method: Literal[
-        'leastsq', 'trf', 'dogbox', 'lm', 'least_squares'] = 'leastsq'
-    rel_height_cutoff: Optional[
-        confloat(gt=0, lt=1.0, allow_inf_nan=False)] = None
     num_proc: conint(gt=0) = 1
+    parameters: conlist(item_type=FitParameter) = []
     plot: StrictBool = False
     print_report:  StrictBool = False
-    memfolder: str = 'joblib_memmap'
+    rel_height_cutoff: Optional[
+        confloat(gt=0, lt=1.0, allow_inf_nan=False)] = None
 
     @field_validator('method')
     @classmethod

From cf1e0887935b706eb1c11425dc09d85cb919c7e4 Mon Sep 17 00:00:00 2001
From: Rolf Verberg <rv43@cornell.edu>
Date: Tue, 9 Jun 2026 15:26:04 -0400
Subject: [PATCH 76/76] refactor: change valid input data types of FitProcessor
 and Fit/FitMap

---
 CHAP/pipeline.py     |   2 +-
 CHAP/utils/fit.py    | 542 ++++++++++++++++++++++---------------------
 CHAP/utils/models.py | 447 ++++++++++++++++-------------------
 3 files changed, 486 insertions(+), 505 deletions(-)

diff --git a/CHAP/pipeline.py b/CHAP/pipeline.py
index 91800b24..ba046a68 100755
--- a/CHAP/pipeline.py
+++ b/CHAP/pipeline.py
@@ -269,7 +269,7 @@ def get_data(data, name=None, schema=None, remove=True):
         `NXobject <https://manual.nexusformat.org/classes/base_classes/NXobject.html#index-0>`__
         object or matches a given name or schema. Pick the last item for which
         the `'name'` key matches `name` if set or the `'schema'` key matches
-        `schema` if set, pick the last match for a `NXobjecta` object
+        `schema` if set, pick the last match for a `NXobject` object
         otherwise. Return the data object.
 
         :param data: Input data.
diff --git a/CHAP/utils/fit.py b/CHAP/utils/fit.py
index c4671cf8..019608af 100755
--- a/CHAP/utils/fit.py
+++ b/CHAP/utils/fit.py
@@ -74,56 +74,91 @@ class FitProcessor(Processor):
             'config': 'CHAP.utils.models.FitConfig'}, init_var=True)
     config: Optional[FitConfig] = None
 
+    def _get_pipelinedata_item(self, data, remove=True):
+        """Retrieve the input data to :meth:`process` from the list of
+        PipelineData items.
+
+        :param data: Input data.
+        :type data: list[PipelineData]
+        :param remove: If there is a matching entry in `data`, remove
+            it from the list, defaults to `True`.
+        :type remove: bool, optional
+        :return: Matching data item(s).
+        :rtype: Any
+        """
+        # Retrieve the data to (re)fit from the pipeline
+        for i, d in reversed(list(enumerate(data))):
+            ddata = d.get('data')
+            if isinstance(ddata, (Fit, FitMap)):
+                if remove:
+                    data.pop(i)
+                return ddata
+            if d.get('name') == 'signal':
+                if remove:
+                    data.pop(i)
+                break
+        else:
+            raise ValueError(
+                f'Unable to extract suitable fit input data from {data}')
+
+        # Retrieve the optional coordinates from the pipeline
+        try:
+            y = np.asarray(ddata)
+            for i, d in reversed(list(enumerate(data))):
+                if d.get('name') == 'coordinates':
+                    x = np.asarray(d.get('data'))
+                    if remove:
+                        data.pop(i)
+                    assert x.size == y.shape[-1]
+                    break
+            else:
+                x = None
+        except (ValueError, TypeError) as exc:
+            raise ValueError(
+                f'Unable to extract suitable fit input data from {data}')
+        return x, y
+
     def process(self, data):
         """Fit the data and return a :class:`~CHAP.utils.fit.Fit` or
         :class:`~CHAP.utils.fit.FitMap` object depending on the
-        dimensionality of the input data. The input data should be an
-        array-like object (tuple, list or numpy.ndarray) or a
-        dictionary with at least a `"y"` field with a value equal to
-        one or a :class:`~CHAP.utils.fit.Fit` or
-        :class:`~CHAP.utils.fit.FitMap` object from a previous fit.
-
-        :param data: Input data containing the data object to fit.
-        :type data: list[PipelineData] or Fit or FitMap or array-like
+        dimensionality of the input data. The input data should be a
+        list of PipelineData items containing either one with a `data`
+        field of type :class:`~CHAP.utils.fit.Fit` or
+        :class:`~CHAP.utils.fit.FitMap` (to refit or continue a
+        previous fit), or one with the `name` of `signal` and an
+        array-like `data` field. In the latter case, optional
+        x-coordinates can be supplied by a second PipelineData item
+        with the `name` of `coordinates` and again an array-like
+        `data` field.
+
+        :param data: Input data.
+        :type data: list[PipelineData]
         :return: The fitted data object.
         :rtype: Fit or FitMap
         """
         # Local modules
-        from CHAP.utils.models import Multipeak
+        from CHAP.utils.models import MultipeakModel
 
-#        # Unwrap the PipelineData if called as a Pipeline Processor
-#        data = self.get_pipelinedata_item(data)
+        # Unwrap the PipelineData
+        data = self._get_pipelinedata_item(data)
 
         if isinstance(data, (Fit, FitMap)):
 
             # Refit/continue the fit with possibly updated parameters
             fit = data
-            if isinstance(data, FitMap):
-                fit.fit(config=self.config, max_nfev=self.config.max_nfev)
-            else:
-                fit.fit(config=self.config, max_nfev=self.config.max_nfev)
-                if self.config is not None:
-                    if self.config.print_report:
-                        fit.print_fit_report()
-                    if self.config.plot:
-                        fit.plot(skip_init=True)
+            fit.fit(config=self.config, max_nfev=self.config.max_nfev)
+            if self.config is not None and not isinstance(data, FitMap):
+                if self.config.print_report:
+                    fit.print_fit_report()
+                if self.config.plot:
+                    fit.plot(skip_init=True)
 
         else:
 
-            # Test for the correct input data type
-            try:
-                if isinstance(data, dict):
-                    x = np.asarray(data.get('x'))
-                    y = np.asarray(data.get('y'))
-                else:
-                    y = np.asarray(data)
-            except (ValueError, TypeError) as exc:
-                raise ValueError(f'Invalid input data ({type(data)}\n{data})')
-
             # Expand multipeak model if present
             found_multipeak = False
             for i, model in enumerate(deepcopy(self.config.models)):
-                if isinstance(model, Multipeak):
+                if isinstance(model, MultipeakModel):
                     if found_multipeak:
                         raise ValueError(
                             f'Invalid parameter models ({self.config.models}) '
@@ -136,15 +171,15 @@ def process(self, data):
                     found_multipeak = True
 
             # Instantiate the Fit or FitMap object and fit the data
-            if np.squeeze(y).ndim == 1:
-                fit = Fit(data, self.config, self.logger)
+            if np.squeeze(data[1]).ndim == 1:
+                fit = Fit(data[1], self.config, self.logger, x=data[0])
                 fit.fit(max_nfev=self.config.max_nfev)
                 if self.config.print_report:
                     fit.print_fit_report()
                 if self.config.plot:
                     fit.plot(skip_init=True)
             else:
-                fit = FitMap(data, self.config, self.logger)
+                fit = FitMap(data[1], self.config, self.logger, x=data[0])
                 fit.fit(
                     rel_height_cutoff=self.config.rel_height_cutoff,
                     max_nfev=self.config.max_nfev,
@@ -155,66 +190,65 @@ def process(self, data):
         return fit
 
     @staticmethod
-    def create_multipeak_model(model_config):
+    def create_multipeak_model(model):
         """Create a multipeak model.
 
-        :param model_config: A Multipeak fit model class.
-        :type model_config: :class:`~CHAP.utils.models.Multipeak`
+        :param model: A Multipeak fit model class.
+        :type model: :class:`~CHAP.utils.models.MultipeakModel`
         :return: The fit parameters and fit model classes.
         :rtype: list[:attr:`~CHAP.utils.models.FitParameter`],
             list[:attr:`~CHAP.utils.models.FitConfig.models`]
         """
         # Local modules
         from CHAP.utils.models import (
+            PEAK_LIKE_MODELS,
             FitParameter,
-            models,
         )
 
-        peak_model_name = model_config.peak_models
-        peak_model_class = models[peak_model_name]['class']
+        peak_model_class = PEAK_LIKE_MODELS[model.peak_models]
         parameters = []
         peak_models = []
-        num_peak = len(model_config.centers)
-        if num_peak == 1 and model_config.fit_type == 'uniform':
-            model_config.fit_type = 'unconstrained'
+        num_peak = len(model.centers)
+        if num_peak == 1 and model.fit_type == 'uniform':
+            model.fit_type = 'unconstrained'
 
         sig_min = FLOAT_MIN
         sig_max = np.inf
-        if (model_config.fwhm_min is not None
-                or model_config.fwhm_max is not None):
+        if (model.fwhm_min is not None
+                or model.fwhm_max is not None):
             # Third party modules
             from asteval import Interpreter
 
             ast = Interpreter()
 
-            if model_config.fwhm_min is not None:
-                ast(f'fwhm = {model_config.fwhm_min}')
-                sig_min = ast(fwhm_factor[model_config.peak_models])
-            if model_config.fwhm_max is not None:
-                ast(f'fwhm = {model_config.fwhm_max}')
-                sig_max = ast(fwhm_factor[model_config.peak_models])
+            if model.fwhm_min is not None:
+                ast(f'fwhm = {model.fwhm_min}')
+                sig_min = ast(fwhm_factor[model.peak_models])
+            if model.fwhm_max is not None:
+                ast(f'fwhm = {model.fwhm_max}')
+                sig_max = ast(fwhm_factor[model.peak_models])
 
         prefix = ''
-        if model_config.fit_type == 'uniform':
+        if model.fit_type == 'uniform':
             parameters.append(FitParameter(
                 name='scale_factor', value=1.0, min=FLOAT_MIN))
-            for i, cen in enumerate(model_config.centers):
+            for i, cen in enumerate(model.centers):
                 if num_peak > 1:
                     prefix = f'peak{i+1}_'
                 peak_models.append(peak_model_class(
-                    model=peak_model_name,
+                    model_type=model.peak_models,
                     prefix=prefix,
                     parameters=[
                          {'name': 'amplitude', 'min': FLOAT_MIN},
                          {'name': 'center', 'expr': f'scale_factor*{cen}'},
                          {'name': 'sigma', 'min': sig_min, 'max': sig_max}]))
         else:
-            for i, cen in enumerate(model_config.centers):
+            for i, cen in enumerate(model.centers):
                 if num_peak > 1:
                     prefix = f'peak{i+1}_'
-                if model_config.centers_range == 0:
+                if model.centers_range == 0:
                     peak_models.append(peak_model_class(
-                        model=peak_model_name,
+                        model_type=model.peak_models,
                         prefix=prefix,
                         parameters=[
                              {'name': 'amplitude', 'min': FLOAT_MIN},
@@ -222,14 +256,14 @@ def create_multipeak_model(model_config):
                              {'name': 'sigma', 'min': sig_min, 'max': sig_max}
                         ]))
                 else:
-                    if model_config.centers_range is None:
+                    if model.centers_range is None:
                         cen_min = None
                         cen_max = None
                     else:
-                        cen_min = cen - model_config.centers_range
-                        cen_max = cen + model_config.centers_range
+                        cen_min = cen - model.centers_range
+                        cen_max = cen + model.centers_range
                     peak_models.append(peak_model_class(
-                        model=peak_model_name,
+                        model_type=model.peak_models,
                         prefix=prefix,
                         parameters=[
                              {'name': 'amplitude', 'min': FLOAT_MIN},
@@ -253,12 +287,15 @@ def __init__(self, model, prefix=''):
         :type prefix: str, optional
         """
         # Local modules
-        from CHAP.utils.models import models
+        #from CHAP.utils.models import MODEL_TYPE_TO_CLASS
 
-        self.func = models[model.model]['name']
+        self.func = model.func #MODEL_TYPE_TO_CLASS[model.model_type]
+        self.func_args = model._func_args #MODEL_TYPE_TO_CLASS[model.model_type]
         self.param_names = [f'{prefix}{par.name}' for par in model.parameters]
         self.prefix = prefix
-        self._name = model.model
+        self._name = model.model_type
+        names = [f'{par.name}' for par in model.parameters]
+        self.func_args_indices = [names.index(arg) for arg in self.func_args]
 
 
 class Components(dict):
@@ -284,24 +321,6 @@ def components(self):
         """
         return self.values()
 
-    def add(self, model, prefix=''):
-        """Add a model to the model fit components dictionary.
-
-        :param model: A fit model class.
-        :type model: :attr:`~CHAP.utils.models.FitConfig.models`
-        :param prefix: Model prefix.
-        :type prefix: str, optional
-        """
-        # Local modules
-        from CHAP.utils.models import model_classes
-
-        if not isinstance(model, model_classes):
-            raise ValueError(f'Invalid parameter model ({model})')
-        if not isinstance(prefix, str):
-            raise ValueError(f'Invalid parameter prefix ({prefix})')
-        name = f'{prefix}{model.model}'
-        self.__setitem__(name, Component(model, prefix))
-
 
 class Parameters(dict):
     """A dictionary of FitParameter objects, mimicking the
@@ -357,7 +376,7 @@ class ModelResult():
     """
 
     def __init__(
-            self, model, parameters, x=None, y=None, method=None, ast=None,
+            self, model, parameters, *, x=None, y=None, method=None, ast=None,
             res_par_exprs=None, res_par_indices=None, res_par_names=None,
             result=None):
         """Initialize SetNumexprThreads.
@@ -498,7 +517,9 @@ def eval_components(self, x=None, parameters=None):
                 name = component._name
             else:
                 name = component.prefix
-            result[name] = component.func(x, *par_values)
+            ppar_values = tuple(
+                par_values[i] for i in component.func_args_indices)
+            result[name] = component.func(x, *ppar_values)
         return result
 
     def fit_report(self, show_correl=False):
@@ -570,22 +591,24 @@ def fit_report(self, show_correl=False):
 class Fit:
     """Wrapper class for scipy/lmfit."""
 
-    def __init__(self, data, config, logger):
+    def __init__(self, y, config, logger, x=None):
         """Initialize Fit.
 
-        :param data: The input data.
-        :type data: array-like, or dict
+        :param y: Input signal data.
+        :type y: array-like
         :param config: Fit configuration.
-        :type config: CHAP.utils.models.FitConfig, optional
+        :type config: CHAP.utils.models.FitConfig
         :param logger: A python Logger object.
         :type logger: logging.Logger
+        :param x: Input coordinate data.
+        :type x: array-like, optional
         """
         self._code = config.code
         for model in config.models:
-            if model.model == 'expression' and self._code != 'lmfit':
+            if model.model_type == 'expression' and self._code != 'lmfit':
                 self._code = 'lmfit'
-                logger.warning('Using lmfit instead of scipy with '
-                                    'an expression model')
+                logger.warning('Using lmfit instead of scipy with an '
+                               'expression model')
         if self._code == 'scipy':
             # Local modules
             from CHAP.utils.fit import Parameters
@@ -626,20 +649,16 @@ def __init__(self, data, config, logger):
 #                raise ValueError(
 #                    'Invalid value of keyword argument try_linear_fit '
 #                    f'({self._try_linear_fit})')
-        if data is not None:
-            try:
-                if isinstance(data, dict):
-                    self._x = np.asarray(data.get('x'))
-                    self._y = np.squeeze(data.get('y'))
-                    assert self._x.size == self._y.size
-                else:
-                    self._y = np.squeeze(data)
-                    self._x = np.arange(self._y.size)
-            except (ValueError, TypeError) as exc:
-                raise ValueError(f'Invalid input data ({type(data)}\n{data})')
+        if y is not None:
+            self._y = np.squeeze(y)
             if self._y.ndim != 1:
                 raise ValueError(
-                    f'Invalid input data dimension ({self._y.ndim})')
+                    f'Invalid input signal dimension ({self._y.ndim})')
+            if x is None:
+                self._x = np.arange(self._y.size)
+            else:
+                self._x = x
+                assert self._x.size == self._y.size
 #            if 'mask' in kwargs:
 #                self._mask = kwargs.pop('mask')
             if True: #self._mask is None:
@@ -995,12 +1014,10 @@ def add_model(self, model, prefix):
                 RectangleModel,
         )
 
-        if model.model == 'expression':
+        if model.model_type == 'expression':
             expr = model.expr
         else:
             expr = None
-        parameters = model.parameters
-        model_name = model.model
 
         if prefix is None:
             pprefix = ''
@@ -1008,149 +1025,147 @@ def add_model(self, model, prefix):
             pprefix = prefix
         if self._code == 'scipy':
             new_parameters = []
-            for par in deepcopy(parameters):
+            for par in deepcopy(model.parameters):
+                name = par.name
                 self._parameters.add(par, pprefix)
                 if self._parameters[par.name].expr is None:
                     self._parameters[par.name].set(value=par.default)
                 new_parameters.append(par.name)
-            self._res_num_pars += [len(parameters)]
+                if name in model.LINEAR_PARAMETERS:
+                    self._linear_parameters.append(par.name)
+                elif name not in model.MODEL_PARAMETERS:
+                    self._nonlinear_parameters.append(par.name)
+            self._res_num_pars += [len(model.parameters)]
 
-        if model_name == 'constant':
-            # Par: c
-            if self._code == 'lmfit':
+        if self._code == 'lmfit':
+            if model.model_type == 'constant':
+                # Par: c
                 newmodel = ConstantModel(prefix=prefix)
-            self._linear_parameters.append(f'{pprefix}c')
-        elif model_name == 'linear':
-            # Par: slope, intercept
-            if self._code == 'lmfit':
+                self._linear_parameters.append(f'{pprefix}c')
+            elif model.model_type == 'linear':
+                # Par: slope, intercept
                 newmodel = LinearModel(prefix=prefix)
-            self._linear_parameters.append(f'{pprefix}slope')
-            self._linear_parameters.append(f'{pprefix}intercept')
-        elif model_name == 'quadratic':
-            # Par: a, b, c
-            if self._code == 'lmfit':
+                self._linear_parameters.append(f'{pprefix}slope')
+                self._linear_parameters.append(f'{pprefix}intercept')
+            elif model.model_type == 'parabolic':
+                # Par: a, b, c
                 newmodel = QuadraticModel(prefix=prefix)
-            self._linear_parameters.append(f'{pprefix}a')
-            self._linear_parameters.append(f'{pprefix}b')
-            self._linear_parameters.append(f'{pprefix}c')
-#        elif model_name == 'polynomial':
-#            # Par: c0, c1,..., c7
-#            degree = kwargs.get('degree')
-#            if degree is not None:
-#                kwargs.pop('degree')
-#            if degree is None or not is_int(degree, ge=0, le=7):
-#                raise ValueError(
-#                    'Invalid parameter degree for build-in step model '
-#                    f'({degree})')
-#            if self._code == 'lmfit':
+                self._linear_parameters.append(f'{pprefix}a')
+                self._linear_parameters.append(f'{pprefix}b')
+                self._linear_parameters.append(f'{pprefix}c')
+#            elif model.model_type == 'polynomial':
+#                # Par: c0, c1,..., c7
+#                degree = kwargs.get('degree')
+#                if degree is not None:
+#                    kwargs.pop('degree')
+#                if degree is None or not is_int(degree, ge=0, le=7):
+#                    raise ValueError(
+#                        'Invalid parameter degree for build-in step model '
+#                        f'({degree})')
 #                newmodel = PolynomialModel(degree=degree, prefix=prefix)
-#            for i in range(degree+1):
-#                self._linear_parameters.append(f'{pprefix}c{i}')
-        elif model_name == 'exponential':
-            # Par: amplitude, decay
-            if self._code == 'lmfit':
+#                for i in range(degree+1):
+#                    self._linear_parameters.append(f'{pprefix}c{i}')
+            elif model.model_type == 'exponential':
+                # Par: amplitude, decay
                 newmodel = ExponentialModel(prefix=prefix)
-            self._linear_parameters.append(f'{pprefix}amplitude')
-            self._nonlinear_parameters.append(f'{pprefix}decay')
-        elif model_name == 'gaussian':
-            # Par: amplitude, center, sigma (fwhm, height)
-            if self._code == 'lmfit':
+                self._linear_parameters.append(f'{pprefix}amplitude')
+                self._nonlinear_parameters.append(f'{pprefix}decay')
+            elif model.model_type == 'gaussian':
+                # Par: amplitude, center, sigma (fwhm, height)
                 newmodel = GaussianModel(prefix=prefix)
                 # parameter norms for height and fwhm are needed to
                 #   get correct errors
-            self._linear_parameters.append(f'{pprefix}amplitude')
-            self._nonlinear_parameters.append(f'{pprefix}center')
-            self._nonlinear_parameters.append(f'{pprefix}sigma')
-        elif model_name == 'lorentzian':
-            # Par: amplitude, center, sigma (fwhm, height)
-            if self._code == 'lmfit':
+                self._linear_parameters.append(f'{pprefix}amplitude')
+                self._nonlinear_parameters.append(f'{pprefix}center')
+                self._nonlinear_parameters.append(f'{pprefix}sigma')
+            elif model.model_type == 'lorentzian':
+                # Par: amplitude, center, sigma (fwhm, height)
                 newmodel = LorentzianModel(prefix=prefix)
                 # parameter norms for height and fwhm are needed to
                 #   get correct errors
-            self._linear_parameters.append(f'{pprefix}amplitude')
-            self._nonlinear_parameters.append(f'{pprefix}center')
-            self._nonlinear_parameters.append(f'{pprefix}sigma')
-        elif model_name == 'pvoigt':
-            # Par: amplitude, center, sigma (fwhm, height), fraction
-            if self._code == 'lmfit':
+                self._linear_parameters.append(f'{pprefix}amplitude')
+                self._nonlinear_parameters.append(f'{pprefix}center')
+                self._nonlinear_parameters.append(f'{pprefix}sigma')
+            elif model.model_type == 'pvoigt':
+                # Par: amplitude, center, sigma (fwhm, height), fraction
                 newmodel = PseudoVoigtModel(prefix=prefix)
                 # parameter norms for height and fwhm are needed to
                 #   get correct errors
-            self._linear_parameters.append(f'{pprefix}amplitude')
-            self._linear_parameters.append(f'{pprefix}fraction')
-            self._nonlinear_parameters.append(f'{pprefix}center')
-            self._nonlinear_parameters.append(f'{pprefix}sigma')
-#        elif model_name == 'step':
-#            # Par: amplitude, center, sigma
-#            form = kwargs.get('form')
-#            if form is not None:
-#                kwargs.pop('form')
-#            if (form is None or form not in
-#                    ('linear', 'atan', 'arctan', 'erf', 'logistic')):
-#                raise ValueError(
-#                    'Invalid parameter form for build-in step model '
-#                    f'({form})')
-#            if self._code == 'lmfit':
+                self._linear_parameters.append(f'{pprefix}amplitude')
+                self._linear_parameters.append(f'{pprefix}fraction')
+                self._nonlinear_parameters.append(f'{pprefix}center')
+                self._nonlinear_parameters.append(f'{pprefix}sigma')
+#            elif model.model_type == 'step':
+#                # Par: amplitude, center, sigma
+#                form = kwargs.get('form')
+#                if form is not None:
+#                    kwargs.pop('form')
+#                if (form is None or form not in
+#                        ('linear', 'atan', 'arctan', 'erf', 'logistic')):
+#                    raise ValueError(
+#                        'Invalid parameter form for build-in step model '
+#                        f'({form})')
 #                newmodel = StepModel(prefix=prefix, form=form)
-#            self._linear_parameters.append(f'{pprefix}amplitude')
-#            self._nonlinear_parameters.append(f'{pprefix}center')
-#            self._nonlinear_parameters.append(f'{pprefix}sigma')
-        elif model_name == 'rectangle':
-            # Par: amplitude, center1, center2, sigma1, sigma2
-            form = 'atan' #kwargs.get('form')
-            #if form is not None:
-            #    kwargs.pop('form')
-            # RV: Implement and test other forms when needed
-            if (form is None or form not in
-                    ('linear', 'atan', 'arctan', 'erf', 'logistic')):
-                raise ValueError(
-                    'Invalid parameter form for build-in rectangle model '
-                    f'({form})')
-            if self._code == 'lmfit':
+#                self._linear_parameters.append(f'{pprefix}amplitude')
+#                self._nonlinear_parameters.append(f'{pprefix}center')
+#                self._nonlinear_parameters.append(f'{pprefix}sigma')
+            elif model.model_type == 'rectangle':
+                # Par: amplitude, center1, center2, sigma1, sigma2
+                form = 'atan' #kwargs.get('form')
+                #if form is not None:
+                #    kwargs.pop('form')
+                # RV: Implement and test other forms when needed
+                if (form is None or form not in
+                        ('linear', 'atan', 'arctan', 'erf', 'logistic')):
+                    raise ValueError(
+                        'Invalid parameter form for build-in rectangle model '
+                        f'({form})')
                 newmodel = RectangleModel(prefix=prefix, form=form)
-            self._linear_parameters.append(f'{pprefix}amplitude')
-            self._nonlinear_parameters.append(f'{pprefix}center1')
-            self._nonlinear_parameters.append(f'{pprefix}center2')
-            self._nonlinear_parameters.append(f'{pprefix}sigma1')
-            self._nonlinear_parameters.append(f'{pprefix}sigma2')
-        elif model_name == 'expression' and self._code == 'lmfit':
-            # Third party modules
-            from asteval import (
-                Interpreter,
-                get_ast_names,
-            )
+                self._linear_parameters.append(f'{pprefix}amplitude')
+                self._nonlinear_parameters.append(f'{pprefix}center1')
+                self._nonlinear_parameters.append(f'{pprefix}center2')
+                self._nonlinear_parameters.append(f'{pprefix}sigma1')
+                self._nonlinear_parameters.append(f'{pprefix}sigma2')
+            elif model.model_type == 'expression':
+                # FIX move to a validator
+                # Third party modules
+                from asteval import (
+                    Interpreter,
+                    get_ast_names,
+                )
 
-            for par in parameters:
-                if par.expr is not None:
-                    raise KeyError(
-                        f'Invalid "expr" key ({par.expr}) in '
-                        f'parameter ({par}) for an expression model')
-            ast = Interpreter()
-            expr_parameters = [
-                name for name in get_ast_names(ast.parse(expr))
-                if (name != 'x' and name not in self._parameters
-                    and name not in ast.symtable)]
-            if prefix is None:
-                newmodel = ExpressionModel(expr=expr)
-            else:
-                for name in expr_parameters:
-                    expr = sub(rf'\b{name}\b', f'{prefix}{name}', expr)
+                for par in model.parameters:
+                    if par.expr is not None:
+                        raise KeyError(
+                            f'Invalid "expr" key ({par.expr}) in '
+                            f'parameter ({par}) for an expression model')
+                ast = Interpreter()
                 expr_parameters = [
-                    f'{prefix}{name}' for name in expr_parameters]
-            newmodel = ExpressionModel(expr=expr, name=model_name)
-            # Remove already existing names
-            for name in newmodel.param_names.copy():
-                if name not in expr_parameters:
-                    newmodel._func_allargs.remove(name)
-                    newmodel._param_names.remove(name)
-        else:
-            raise ValueError(f'Unknown fit model ({model_name})')
+                    name for name in get_ast_names(ast.parse(expr))
+                    if (name != 'x' and name not in self._parameters
+                        and name not in ast.symtable)]
+                if prefix is None:
+                    newmodel = ExpressionModel(expr=expr)
+                else:
+                    for name in expr_parameters:
+                        expr = sub(rf'\b{name}\b', f'{prefix}{name}', expr)
+                    expr_parameters = [
+                        f'{prefix}{name}' for name in expr_parameters]
+                newmodel = ExpressionModel(expr=expr, name=model.model_type)
+                # Remove already existing names
+                for name in newmodel.param_names.copy():
+                    if name not in expr_parameters:
+                        newmodel._func_allargs.remove(name)
+                        newmodel._param_names.remove(name)
+            else:
+                raise ValueError(f'Unknown fit model ({model.model_type})')
 
         # Add the new model to the current one
         if self._code == 'scipy':
             if self._model is None:
                 self._model = Components()
-            self._model.add(model, prefix)
+            self._model |= {
+                f'{prefix}{model.model_type}': Component(model, prefix)}
         else:
             if self._model is None:
                 self._model = newmodel
@@ -1186,17 +1201,23 @@ def add_model(self, model, prefix):
                             value = par.value
                         _min = par.min
                         _max = par.max
-                        if not (model_name == 'pvoigt' and 'fraction' in name):
-                            if value is not None:
-                                value *= self._norm[1]
-                            if not np.isinf(_min) and abs(_min) != FLOAT_MIN:
-                                _min *= self._norm[1]
-                            if not np.isinf(_max) and abs(_max) != FLOAT_MIN:
-                                _max *= self._norm[1]
+#                        if not (model.model_type == 'pvoigt' and 'fraction' in name):
+#                            if value is not None:
+#                                value *= self._norm[1]
+#                            if not np.isinf(_min) and abs(_min) != FLOAT_MIN:
+#                                _min *= self._norm[1]
+#                            if not np.isinf(_max) and abs(_max) != FLOAT_MIN:
+#                                _max *= self._norm[1]
+                        if value is not None:
+                            value *= self._norm[1]
+                        if not np.isinf(_min) and abs(_min) != FLOAT_MIN:
+                            _min *= self._norm[1]
+                        if not np.isinf(_max) and abs(_max) != FLOAT_MIN:
+                            _max *= self._norm[1]
                         par.set(value=value, min=_min, max=_max)
 
         # Initialize the model parameters
-        for parameter in deepcopy(parameters):
+        for parameter in deepcopy(model.parameters):
             name = parameter.name
             if name not in new_parameters:
                 name = pprefix+name
@@ -1538,7 +1559,7 @@ def _create_prefixes(self, models):
         names = []
         prefixes = []
         for model in models:
-            names.append(f'{model.prefix}{model.model}')
+            names.append(f'{model.prefix}{model.model_type}')
             prefixes.append(model.prefix)
         counts = Counter(names)
         for model, count in counts.items():
@@ -1651,10 +1672,10 @@ def _setup_fit(self, config, guess=False):
         # Add constant offset for a normalized model
         if self._result is None and self._norm is not None and self._norm[0]:
             # Local modules
-            from CHAP.utils.models import Constant
+            from CHAP.utils.models import ConstantModel
 
-            model = Constant(
-                model='constant',
+            model = ConstantModel(
+                model_type='constant',
                 parameters=[{
                     'name': 'c',
                     'value': -self._norm[0],
@@ -1667,14 +1688,14 @@ def _setup_fit(self, config, guess=False):
             # Local modules
             from CHAP.utils.models import (
                 FitConfig,
-                Multipeak,
+                MultipeakModel,
             )
 
             # Expand multipeak model if present
             scale_factor = None
             for i, model in enumerate(deepcopy(config.models)):
                 found_multipeak = False
-                if isinstance(model, Multipeak):
+                if isinstance(model, MultipeakModel):
                     if found_multipeak:
                         raise ValueError(
                             f'Invalid parameter models ({config.models}) '
@@ -1758,10 +1779,9 @@ def _setup_fit(self, config, guess=False):
                 if par.expr:
                     self._res_par_exprs.append(
                         {'expr': par.expr, 'index': i})
-                else:
-                    if par.vary:
-                        self._res_par_indices.append(i)
-                        self._res_par_names.append(name)
+                elif par.vary:
+                    self._res_par_indices.append(i)
+                    self._res_par_names.append(name)
 
         # Check for uninitialized parameters
         for name, par in self._parameters.items():
@@ -2077,7 +2097,6 @@ def _fit_nonlinear_model(self, x, y, **kwargs):
             else:
                 bounds = (-np.inf, np.inf)
             init_params = deepcopy(self._parameters)
-#            t0 = time()
             lskws = {
                 'ftol': 1.49012e-08,
                 'xtol': 1.49012e-08,
@@ -2096,12 +2115,11 @@ def _fit_nonlinear_model(self, x, y, **kwargs):
                 result = least_squares(
                     self._residual, pars_init, bounds=bounds,
                     method=self._method, args=(x, y), **lskws)
-#            t1 = time()
-#            print(f'\n\nFitting took {1000*(t1-t0):.3f} ms\n\n')
             model_result = ModelResult(
-                self._model, self._parameters, x, y, self._method, self._ast,
-                self._res_par_exprs, self._res_par_indices,
-                self._res_par_names, result)
+                self._model, self._parameters, x=x, y=y, method=self._method,
+                ast=self._ast, res_par_exprs=self._res_par_exprs,
+                res_par_indices=self._res_par_indices,
+                res_par_names=self._res_par_names, result=result)
             model_result.init_params = init_params
             model_result.init_values = {}
             for name, par in init_params.items():
@@ -2111,12 +2129,9 @@ def _fit_nonlinear_model(self, x, y, **kwargs):
             fit_kws = {}
 #            if 'Dfun' in kwargs:
 #                fit_kws['Dfun'] = kwargs.pop('Dfun')
-#            t0 = time()
             model_result = self._model.fit(
                 y, self._parameters, x=x, method=self._method, fit_kws=fit_kws,
                 **kwargs)
-#            t1 = time()
-#            print(f'\n\nFitting took {1000*(t1-t0):.3f} ms\n\n')
 
         return model_result
 
@@ -2302,8 +2317,11 @@ def _residual(self, pars, x, y):
                     self._ast.eval(expr['expr'])
         for component, num_par in zip(
                 self._model.components, self._res_num_pars):
+            values = self._res_par_values[n_par:n_par+num_par]
+            vvalues = [values[i] for i in component.func_args_indices]
             res += component.func(
-                x, *tuple(self._res_par_values[n_par:n_par+num_par]))
+#                x, *tuple(self._res_par_values[n_par:n_par+num_par]))
+                x, *tuple(vvalues))
             n_par += num_par
         return res - y
 
@@ -2311,15 +2329,17 @@ def _residual(self, pars, x, y):
 class FitMap(Fit):
     """Wrapper to the Fit class to fit data on a N-dimensional map."""
 
-    def __init__(self, data, config, logger):
+    def __init__(self, y, config, logger, x=None):
         """Initialize FitMap.
 
-        :param data: The input data.
-        :type data: array-like, or dict
+        :param y: Input signal data.
+        :type y: array-like
         :param config: Fit configuration.
-        :type config: CHAP.utils.models.FitConfig, optional
+        :type config: CHAP.utils.models.FitConfig
         :param logger: A python Logger object.
         :type logger: logging.Logger
+        :param x: Input coordinate data.
+        :type x: array-like, optional
         """
         super().__init__(None, config, logger)
         self._best_errors = None
@@ -2345,16 +2365,12 @@ def __init__(self, data, config, logger):
         # At this point the fastest index should always be the signal
         #     dimension so that the slowest ndim-1 dimensions are the
         #     map dimensions
-        try:
-            if isinstance(data, dict):
-                self._x = np.asarray(data.get('x'))
-                self._ymap = np.asarray(data.get('y'))
-                assert self._x.size == self._ymap.shape[-1]
-            else:
-                self._ymap = np.asarray(data)
-                self._x = np.arange(self._ymap.shape[-1])
-        except (ValueError, TypeError) as exc:
-            raise ValueError(f'Invalid input data ({type(data)}\n{data})')
+        self._ymap = y
+        if x is None:
+            self._x = np.arange(self._ymap.shape[-1])
+        else:
+            self._x = x
+            assert self._x.size == self._ymap.shape[-1]
 
         # Flatten the map
         # Store the flattened map in self._ymap_norm
diff --git a/CHAP/utils/models.py b/CHAP/utils/models.py
index e63b7e30..657265a3 100755
--- a/CHAP/utils/models.py
+++ b/CHAP/utils/models.py
@@ -4,6 +4,7 @@
 
 # System modules
 from typing import (
+    ClassVar,
     Literal,
     Optional,
     Union,
@@ -19,6 +20,7 @@
     confloat,
     constr,
     field_validator,
+    model_validator,
 )
 from typing_extensions import Annotated
 import numpy as np
@@ -27,9 +29,6 @@
 from CHAP.models import CHAPBaseModel
 from CHAP.utils.general import not_zero, tiny
 
-# pylint: disable=no-member
-tiny = np.finfo(np.float64).resolution
-# pylint: enable=no-member
 s2pi = np.sqrt(2*np.pi)
 s2ln2 = np.sqrt(2*np.log(2))
 
@@ -39,7 +38,7 @@ def constant(x, c=0.0):
 
     :param c: Constant, defaults to `0`.
     :type c: float, optional
-    :returns: The function evaluations.
+    :returns: Function evaluations.
     :rtype: numpy.ndarray
 
     .. math::
@@ -58,7 +57,7 @@ def linear(x, slope=1.0, intercept=0.0):
     :type slope: float, optional
     :param intercept: Intercept, defaults to `0`.
     :type intercept: float, optional
-    :returns: The function evaluations.
+    :returns: Function evaluations.
     :rtype: numpy.ndarray
 
     .. math::
@@ -71,8 +70,8 @@ def linear(x, slope=1.0, intercept=0.0):
     return slope * x + intercept
 
 
-#def quadratic(x, a=0.5, b=0.4, c=0.1):
-def quadratic(x, a=0.0, b=0.0, c=0.0):
+#def parabolic(x, a=0.5, b=0.4, c=0.1):
+def parabolic(x, a=0.0, b=0.0, c=0.0):
     r"""Return a parabolic function.
 
     :param a: Quadratic polynomial coefficient, defaults to an
@@ -84,7 +83,7 @@ def quadratic(x, a=0.0, b=0.0, c=0.0):
     :param c: Constant polynomial coefficient, defaults to an
         initial value of `0`.
     :type c: float, optional
-    :returns: The function evaluations.
+    :returns: Function evaluations.
     :rtype: numpy.ndarray
 
     .. math::
@@ -104,7 +103,7 @@ def exponential(x, amplitude=1.0, decay=1.0):
     :type amplitude: float, optional
     :param decay: Exponential decay, defaults to `1`.
     :type decay: float, optional
-    :returns: The function evaluations.
+    :returns: Function evaluations.
     :rtype: numpy.ndarray
 
     .. math::
@@ -128,7 +127,7 @@ def gaussian(x, amplitude=1.0, center=0.0, sigma=1.0):
     :type center: float, optional
     :param sigma: Standard deviation, defaults to `1`.
     :type sigma: float, optional
-    :returns: The function evaluations.
+    :returns: Function evaluations.
     :rtype: numpy.ndarray
 
     .. math::
@@ -160,7 +159,7 @@ def lorentzian(x, amplitude=1.0, center=0.0, sigma=1.0):
     :type center: float, optional
     :param sigma: Standard deviation, defaults to `1`.
     :type sigma: float, optional
-    :returns: The function evaluations.
+    :returns: Function evaluations.
     :rtype: numpy.ndarray
 
     .. math::
@@ -196,7 +195,7 @@ def pvoigt(x, amplitude=1.0, center=0.0, sigma=1.0, fraction=0.5):
     :param fraction: Relative weight of the Gaussian and Lorentzian
         components, defaults to `0.5`.
     :type fraction: float, optional
-    :returns: The function evaluations.
+    :returns: Function evaluations.
     :rtype: numpy.ndarray
 
     .. math::
@@ -248,7 +247,7 @@ def rectangle(
         - ``'logistic'``: Sigmoidal (logistic function) transitions.
     :type form: str, optional
 
-    :returns: The evaluated rectangle function values.
+    :returns: Evaluated rectangle function values.
     :rtype: float or numpy.ndarray
 
     .. note::
@@ -289,53 +288,6 @@ def rectangle(
     return amplitude*rect
 
 
-def validate_parameters(parameters, info):
-    """Validate the parameters.
-
-    :param parameters: Fit model parameters.
-    :type parameters: list[FitParameter]
-    :param info: Model parameter validation information.
-    :type info: pydantic.ValidationInfo
-    :return: List of fit model parameters.
-    :rtype: list[FitParameter]
-    """
-    # System imports
-    from inspect import signature
-
-    if 'model' in info.data:
-        model = info.data['model']
-    else:
-        model = None
-    if model is None or model == 'expression':
-        return parameters
-    sig = dict(signature(models[model]['name']).parameters.items())
-    sig.pop('x')
-
-    # Check input model parameter validity
-    for par in parameters:
-        if par.name not in sig:
-            raise ValueError('Invalid parameter {par.name} in {model} model')
-
-    # Set model parameters
-    output_parameters = []
-    for sig_name, sig_par in sig.items():
-        if model == 'rectangle' and sig_name == 'form':
-            continue
-        for par in parameters:
-            if sig_name == par.name:
-                break
-        else:
-            par = FitParameter(name=sig_name)
-        if sig_par.default != sig_par.empty:
-            par._default = sig_par.default
-        if model == 'pvoigt' and sig_name == 'fraction':
-            par.min = 0.0
-            par.max = 1.0
-        output_parameters.append(par)
-
-    return output_parameters
-
-
 class FitParameter(CHAPBaseModel):
     """Class representing a specific fit parameter for the fit
     processor.
@@ -489,232 +441,271 @@ def set(self, value=None, min=None, max=None, vary=None, expr=None):
                 self.value = self.min
             self.expr = None
 
-class Constant(CHAPBaseModel):
+
+class ConstantModel(CHAPBaseModel):
     """Class representing a Constant model component.
 
-    :ivar model: The model component base name (a prefix will be added
-        if multiple identical model components are added).
-    :vartype model: Literal['constant']
+    :ivar model_type: Model component base name (a prefix will be
+        added if multiple identical model components are added).
+    :vartype model_type: Literal['constant']
     :ivar parameters: Function parameters, defaults to those auto
         generated from the function signature (excluding the
         independent variable).
     :vartype parameters: list[FitParameter], optional
-    :ivar prefix: The model prefix, defaults to `''`.
+    :ivar prefix: Model prefix, defaults to `''`.
     :vartype prefix: str, optional
     """
 
-    model: Literal['constant']
+    LINEAR_PARAMETERS: ClassVar[list[str]] = ['c']
+    MODEL_PARAMETERS: ClassVar[list[str]] = []
+    MODEL_IDENTIFIERS: ClassVar[list[str]] = []
+    model_type: Literal['constant']
     parameters: Annotated[
         conlist(item_type=FitParameter),
         Field(validate_default=True)] = []
     prefix: Optional[str] = ''
 
-    _validate_parameters_parameters = field_validator(
-        'parameters')(validate_parameters)
+    _func: PrivateAttr
+    _func_args: PrivateAttr
+
+    @model_validator(mode='after')
+    def validate_model_after(self):
+        """Validate the model configuration and initialize the
+        appropriate parameters from the model function signature.
+
+        :return: Validated and initialized configuration.
+        :rtype: Model
+        """
+        # System imports
+        from inspect import signature
+
+        if self.model_type == 'expression':
+            return self
+        self._func = globals()[self.model_type]
+        sig = dict(signature(self._func).parameters)
+        sig.pop('x')
+        self._func_args = list(sig.keys())
+
+        # Check input model parameter validity
+        par_names = []
+        for par in self.parameters:
+            if par.name not in sig:
+                raise ValueError(
+                    'Invalid parameter {par.name} in {self.model_type} model '
+                    f'valid function arguments: {list(sig.keys())}')
+            par_names.append(par.name)
+
+        # Set model parameters
+        for sig_name, sig_par in sig.items():
+            if sig_name in self.MODEL_IDENTIFIERS or sig_name in par_names:
+#            if ((self.model_type == 'rectangle' and sig_name == 'form')
+#                    or sig_name in par_names):
+                continue
+            par = FitParameter(name=sig_name)
+            if sig_par.default != sig_par.empty:
+                par._default = sig_par.default
+            self.parameters.append(par)
+            par_names.append(par.name)
+
+        # Perform any additional validation of model parameters
+        if hasattr(self, '_validate_parameters'):
+            self._validate_parameters()
+        return self
 
+    @property
+    def func(self):
+        """Return the model function
 
-class Linear(CHAPBaseModel):
+        :type: function
+        """
+        if hasattr(self, '_func'):
+            return self._func
+        return None
+
+
+class LinearModel(ConstantModel):
     """Class representing a Linear model component.
 
-    :ivar model: The model component base name (a prefix will be added
-        if multiple identical model components are added).
-    :vartype model: Literal['linear']
-    :ivar parameters: Function parameters, defaults to those auto
-        generated from the function signature (excluding the
-        independent variable).
-    :vartype parameters: list[FitParameter], optional
-    :ivar prefix: The model prefix, defaults to `''`.
-    :vartype prefix: str, optional
+    :ivar model_type: Model component base name (a prefix will be
+        added if multiple identical model components are added).
+    :vartype model_type: Literal['linear']
     """
 
-    model: Literal['linear']
-    parameters: Annotated[
-        conlist(item_type=FitParameter),
-        Field(validate_default=True)] = []
-    prefix: Optional[str] = ''
+    LINEAR_PARAMETERS: ClassVar[list[str]] = ['slope', 'intercept']
+    model_type: Literal['linear']
 
-    _validate_parameters_parameters = field_validator(
-        'parameters')(validate_parameters)
 
-
-class Quadratic(CHAPBaseModel):
+class QuadraticModel(ConstantModel):
     """Class representing a Quadratic model component.
 
-    :ivar model: The model component base name (a prefix will be added
-        if multiple identical model components are added).
-    :vartype model: Literal['quadratic']
-    :ivar parameters: Function parameters, defaults to those auto
-        generated from the function signature (excluding the
-        independent variable).
-    :vartype parameters: list[FitParameter], optional
-    :ivar prefix: The model prefix, defaults to `''`.
-    :vartype prefix: str, optional
+    :ivar model_type: Model component base name (a prefix will be
+        added if multiple identical model components are added).
+    :vartype model_type: Literal['parabolic']
     """
 
-    model: Literal['quadratic']
-    parameters: Annotated[
-        conlist(item_type=FitParameter),
-        Field(validate_default=True)] = []
-    prefix: Optional[str] = ''
-
-    _validate_parameters_parameters = field_validator(
-        'parameters')(validate_parameters)
+    LINEAR_PARAMETERS: ClassVar[list[str]] = ['a', 'b', 'c']
+    model_type: Literal['parabolic']
 
 
-class Exponential(CHAPBaseModel):
+class ExponentialModel(ConstantModel):
     """Class representing an Exponential model component.
 
-    :ivar model: The model component base name (a prefix will be added
-        if multiple identical model components are added).
-    :vartype model: Literal['exponential']
-    :ivar parameters: Function parameters, defaults to those auto
-        generated from the function signature (excluding the
-        independent variable).
-    :vartype parameters: list[FitParameter], optional
-    :ivar prefix: The model prefix, defaults to `''`.
-    :vartype prefix: str, optional
+    :ivar model_type: Model component base name (a prefix will be
+        added if multiple identical model components are added).
+    :vartype model_type: Literal['exponential']
     """
 
-    model: Literal['exponential']
-    parameters: Annotated[
-        conlist(item_type=FitParameter),
-        Field(validate_default=True)] = []
-    prefix: Optional[str] = ''
-
-    _validate_parameters_parameters = field_validator(
-        'parameters')(validate_parameters)
+    LINEAR_PARAMETERS: ClassVar[list[str]] = ['amplitude']
+    model_type: Literal['exponential']
 
 
-class Gaussian(CHAPBaseModel):
+class GaussianModel(ConstantModel):
     """Class representing a Gaussian model component.
 
-    :ivar model: The model component base name (a prefix will be added
-        if multiple identical model components are added).
-    :vartype model: Literal['gaussian']
-    :ivar parameters: Function parameters, defaults to those auto
-        generated from the function signature (excluding the
-        independent variable).
-    :vartype parameters: list[FitParameter], optional
-    :ivar prefix: The model prefix, defaults to `''`.
-    :vartype prefix: str, optional
+    :ivar model_type: Model component base name (a prefix will be
+        added if multiple identical model components are added).
+    :vartype model_type: Literal['gaussian']
     """
 
-    model: Literal['gaussian']
-    parameters: Annotated[
-        conlist(item_type=FitParameter),
-        Field(validate_default=True)] = []
-    prefix: Optional[str] = ''
+    LINEAR_PARAMETERS: ClassVar[list[str]] = ['amplitude']
+    model_type: Literal['gaussian']
 
-    _validate_parameters_parameters = field_validator(
-        'parameters')(validate_parameters)
+    def _validate_parameters(self):
+        """Validate the model parameters."""
+        for par in self.parameters:
+            if par.name == 'sigma':
+                par.min = 0.0
 
 
-class Lorentzian(CHAPBaseModel):
+class LorentzianModel(ConstantModel):
     """Class representing a Lorentzian model component.
 
-    :ivar model: The model component base name (a prefix will be added
-        if multiple identical model components are added).
-    :vartype model: Literal['lorentzian']
-    :ivar parameters: Function parameters, defaults to those auto
-        generated from the function signature (excluding the
-        independent variable).
-    :vartype parameters: list[FitParameter], optional
-    :ivar prefix: The model prefix, defaults to `''`.
-    :vartype prefix: str, optional
+    :ivar model_type: Model component base name (a prefix will be
+        added if multiple identical model components are added).
+    :vartype model_type: Literal['lorentzian']
     """
 
-    model: Literal['lorentzian']
-    parameters: Annotated[
-        conlist(item_type=FitParameter),
-        Field(validate_default=True)] = []
-    prefix: Optional[str] = ''
+    LINEAR_PARAMETERS: ClassVar[list[str]] = ['amplitude']
+    model_type: Literal['lorentzian']
 
-    _validate_parameters_parameters = field_validator(
-        'parameters')(validate_parameters)
+    def _validate_parameters(self):
+        """Validate the model parameters."""
+        for par in self.parameters:
+            if par.name == 'sigma':
+                par.min = 0.0
 
 
-class PseudoVoigt(CHAPBaseModel):
+class PseudoVoigtModel(ConstantModel):
     """Class representing a PseudoVoigt model component.
 
-    :ivar model: The model component base name (a prefix will be added
-        if multiple identical model components are added).
-    :vartype model: Literal['pvoigt']
-    :ivar parameters: Function parameters, defaults to those auto
-        generated from the function signature (excluding the
-        independent variable).
-    :vartype parameters: list[FitParameter], optional
-    :ivar prefix: The model prefix, defaults to `''`.
-    :vartype prefix: str, optional
+    :ivar model_type: Model component base name (a prefix will be
+        added if multiple identical model components are added).
+    :vartype model_type: Literal['pvoigt']
     """
 
-    model: Literal['pvoigt']
-    parameters: Annotated[
-        conlist(item_type=FitParameter),
-        Field(validate_default=True)] = []
-    prefix: Optional[str] = ''
+    LINEAR_PARAMETERS: ClassVar[list[str]] = ['amplitude']
+    MODEL_PARAMETERS: ClassVar[list[str]] = ['fraction']
+    model_type: Literal['pvoigt']
 
-    _validate_parameters_parameters = field_validator(
-        'parameters')(validate_parameters)
+    def _validate_parameters(self):
+        """Validate the model parameters."""
+        for par in self.parameters:
+            if par.name == 'fraction':
+                par.min = 0.0
+                par.max = 1.0
+            elif par.name == 'sigma':
+                par.min = 0.0
 
 
-class Rectangle(CHAPBaseModel):
+class RectangleModel(ConstantModel):
     """Class representing a Rectangle model component.
 
-    :ivar model: The model component base name (a prefix will be added
-        if multiple identical model components are added).
-    :vartype model: Literal['rectangle']
-    :ivar parameters: Function parameters, defaults to those auto
-        generated from the function signature (excluding the
-        independent variable).
-    :vartype parameters: list[FitParameter], optional
-    :ivar prefix: The model prefix, defaults to `''`.
-    :vartype prefix: str, optional
+    :ivar model_type: Model component base name (a prefix will be
+        added if multiple identical model components are added).
+    :vartype model_type: Literal['rectangle']
     """
 
-    model: Literal['rectangle']
-    parameters: Annotated[
-        conlist(item_type=FitParameter),
-        Field(validate_default=True)] = []
-    prefix: Optional[str] = ''
-
-    _validate_parameters_parameters = field_validator(
-        'parameters')(validate_parameters)
+    LINEAR_PARAMETERS: ClassVar[list[str]] = ['amplitude']
+    MODEL_IDENTIFIERS: ClassVar[list[str]] = ['form']
+    model_type: Literal['rectangle']
 
+    def _validate_parameters(self):
+        """Validate the model parameters."""
+        for par in self.parameters:
+            if par.name == 'form':
+                assert form in ('linear', 'atan', 'arctan', 'erf', 'logistic')
 
-class Expression(CHAPBaseModel):
+class ExpressionModel(ConstantModel):
     """Class representing an Expression model component.
 
-    :ivar model: The model component base name (a prefix will be added
-        if multiple identical model components are added).
-    :vartype model: Literal['expression']
+    :ivar model_type: The model component base name (a prefix will be
+        added if multiple identical model components are added).
+    :vartype model_type: Literal['expression']
     :ivar expr: Mathematical expression to represent the model
         component.
     :vartype expr: str
-    :ivar parameters: Function parameters, defaults to those auto
-        generated from the model expression (excluding the
-        independent variable).
-    :vartype parameters: list[FitParameter], optional
-    :ivar prefix: The model prefix, defaults to `''`.
-    :vartype prefix: str, optional
     """
 
-    model: Literal['expression']
+    model_type: Literal['expression']
     expr: constr(strip_whitespace=True, min_length=1)
-    parameters: Annotated[
-        conlist(item_type=FitParameter),
-        Field(validate_default=True)] = []
-    prefix: Optional[str] = ''
 
-    _validate_parameters_parameters = field_validator(
-        'parameters')(validate_parameters)
+
+# Available models for components of the fitting function
+#MODEL_CLASSES = [
+#    ConstantModel,
+#    LinearModel,
+#    QuadraticModel,
+#    ExponentialModel,
+#    GaussianModel,
+#    LorentzianModel,
+#    PseudoVoigtModel,
+#    RectangleModel,
+#    ExpressionModel,
+#]
+
+# Reusable Discriminator Union for supported fit model components.
+Model = Annotated[
+# FIX for Python 3.11+    Union[*MODEL_CLASSES],
+    Union[
+        ConstantModel,
+        LinearModel,
+        QuadraticModel,
+        ExponentialModel,
+        GaussianModel,
+        LorentzianModel,
+        PseudoVoigtModel,
+        RectangleModel,
+        ExpressionModel,
+    ],
+    Field(discriminator='model_type')
+]
+
+# Peak-like models: with amplitude, center and sigma as their
+# function arguments
+PEAK_LIKE_MODELS = {
+    'gaussian': GaussianModel,
+    'lorentzian': LorentzianModel,
+    'pvoigt': PseudoVoigtModel,
+}
+
+#MODEL_TYPE_TO_CLASS = {#v.model_type:v for v in MODEL_CLASSES}
+#    'constant': constant,
+#    'linear': linear,
+#    'parabolic': parabolic,
+#    'exponential': exponential,
+#    'gaussian': gaussian,
+#    'lorentzian': lorentzian,
+#    'pvoigt': pvoigt,
+#    'rectangle': rectangle,
+#}
 
 
-class Multipeak(CHAPBaseModel):
+class MultipeakModel(CHAPBaseModel):
     """Class representing a multipeak model.
 
-    :ivar model: The model component base name (a prefix will be added
-        if multiple identical model components are added).
-    :vartype model: Literal['expression']
+    :ivar model_type: The model component base name (a prefix will be
+        added if multiple identical model components are added).
+    :vartype model_type: Literal['expression']
     :ivar centers: Peak centers.
     :vartype center: list[float]
     :ivar centers_range: Range of peak centers around their centers.
@@ -730,7 +721,7 @@ class Multipeak(CHAPBaseModel):
         optional.
     """
 
-    model: Literal['multipeak']
+    model_type: Literal['multipeak']
     centers: conlist(item_type=confloat(allow_inf_nan=False), min_length=1)
     centers_range: Optional[confloat(allow_inf_nan=False)] = None
     fit_type: Optional[Literal['uniform', 'unconstrained']] = 'unconstrained'
@@ -739,29 +730,6 @@ class Multipeak(CHAPBaseModel):
     peak_models: Literal['gaussian', 'lorentzian', 'pvoigt'] = 'gaussian'
 
 
-models = {
-    'constant': {'name': constant, 'class': Constant},
-    'linear': {'name': linear, 'class': Linear},
-    'quadratic': {'name': quadratic, 'class': Quadratic},
-    'exponential': {'name': exponential, 'class': Exponential},
-    'gaussian': {'name': gaussian, 'class': Gaussian},
-    'lorentzian': {'name': lorentzian, 'class': Lorentzian},
-    'pvoigt': {'name': pvoigt, 'class': PseudoVoigt},
-    'rectangle': {'name': rectangle, 'class': Rectangle},
-}
-
-model_classes = (
-    Constant,
-    Linear,
-    Quadratic,
-    Exponential,
-    Gaussian,
-    Lorentzian,
-    PseudoVoigt,
-    Rectangle,
-)
-
-
 class FitConfig(CHAPBaseModel):
     """Class representing the configuration for the fit processor.
 
@@ -779,8 +747,7 @@ class FitConfig(CHAPBaseModel):
     :vartype method: Literal[
         'leastsq', 'trf', 'dogbox', 'lm', 'least_squares']
     :ivar models: The component(s) of the (composite) fit model.
-    :vartype models:
-        list[:attr:`~CHAP.utils.models.FitConfig.models`]
+    :vartype models: list[Model, MultipeakModel]
     :ivar num_proc: The number of processors used in fitting a map
         of data, defaults to `1`.
     :vartype num_proc: int, optional
@@ -807,9 +774,7 @@ class FitConfig(CHAPBaseModel):
     memfolder: str = 'joblib_memmap'
     method: Literal[
         'leastsq', 'trf', 'dogbox', 'lm', 'least_squares'] = 'leastsq'
-    models: conlist(item_type=Union[
-        Constant, Linear, Quadratic, Exponential, Gaussian, Lorentzian,
-        PseudoVoigt, Rectangle, Expression, Multipeak], min_length=1)
+    models: conlist(item_type=Union[Model, MultipeakModel], min_length=1)
     num_proc: conint(gt=0) = 1
     parameters: conlist(item_type=FitParameter) = []
     plot: StrictBool = False