ChessAnalysisPipeline 0.0.13__py3-none-any.whl → 0.0.14__py3-none-any.whl

CHAP/common/reader.py

@@ -12,7 +12,6 @@ from os.path import (
     splitext,
 )
 from sys import modules
-from time import time
 
 # Third party modules
 import numpy as np
@@ -40,7 +39,7 @@ class BinaryFileReader(Reader):
 class H5Reader(Reader):
     """Reader for h5 files.
     """
-    def read(self, filename, h5path='/'):
+    def read(self, filename, h5path='/', idx=None):
         """Return the data object stored at `h5path` in an h5-file.
 
         :param filename: The name of the h5-file to read from.
@@ -55,6 +54,8 @@ class H5Reader(Reader):
         from h5py import File
 
         data = File(filename, 'r')[h5path]
+        if idx is not None:
+            data = data[tuple(idx)]
         return data
 
 
@@ -142,8 +143,8 @@ class MapReader(Reader):
                 attrs={'long_name': f'{dim.label} ({dim.units})',
                        'data_type': dim.data_type,
                        'local_name': dim.name})
-            if map_config.map_type == 'structured':
-                nxentry.data.attrs[f'{dim.label}_indices'] = i
+#            if map_config.map_type == 'structured':
+#                nxentry.data.attrs[f'{dim.label}_indices'] = i
 
         # Create empty NXfields for all scalar data present in the
         # provided map configuration
@@ -167,15 +168,13 @@ class MapReader(Reader):
         # Create empty NXfields of appropriate shape for raw
         # detector data
         for detector_name in detector_names:
+            if not isinstance(detector_name, str):
+                detector_name = str(detector_name)
             detector_data = map_config.get_detector_data(
                 detector_name, (0,) * len(map_config.shape))
             nxentry.data[detector_name] = NXfield(value=np.zeros(
                 (*map_config.shape, *detector_data.shape)),
                 dtype=detector_data.dtype)
-#            data_shape = list(map_config.shape)+list(detector_data.shape)
-#            nxentry.data[detector_name] = NXfield(
-#                value=np.zeros(data_shape), shape=data_shape,
-#                dtype=detector_data.dtype)
 
         # Read and fill in maps of raw data
         if len(map_config.all_scalar_data) > 0 or len(detector_names) > 0:
@@ -184,6 +183,8 @@ class MapReader(Reader):
                     nxentry.data[data.label][map_index] = map_config.get_value(
                         data, map_index)
                 for detector_name in detector_names:
+                    if not isinstance(detector_name, str):
+                        detector_name = str(detector_name)
                     nxentry.data[detector_name][map_index] = \
                         map_config.get_detector_data(detector_name, map_index)
 

CHAP/common/writer.py

@@ -136,7 +136,7 @@ class ExtractArchiveWriter(Writer):
         and write the extracted archive to files.
 
         :param data: The data to write to archive.
-        :type data: CHAP.pipeline.PipelineData
+        :type data: list[PipelineData]
         :param filename: The name of the directory to write the archive
             files to.
         :type filename: str
@@ -162,7 +162,7 @@ class FileTreeWriter(Writer):
         directory tree stuctured like the NeXus tree.
 
         :param data: The data to write to disk.
-        :type data: CHAP.pipeline.PipelineData
+        :type data: list[PipelineData]
         :param outputdir: The name of the directory to write to.
         :type outputdir: str
         :param force_overwrite: Flag to allow data to be overwritten
@@ -211,7 +211,7 @@ class MatplotlibAnimationWriter(Writer):
         contained in `data` to file.
 
         :param data: The matplotlib animation.
-        :type data: CHAP.pipeline.PipelineData
+        :type data: list[PipelineData]
         :param filename: The name of the file to write to.
         :type filename: str
         :param fps: Movie frame rate (frames per second),
@@ -224,7 +224,7 @@ class MatplotlibAnimationWriter(Writer):
         extension = os_path.splitext(filename)[1]
         if not extension:
             data.save(f'{filename}.gif', fps=fps)
-        elif extension in '.gif':
+        elif extension == '.gif':
             data.save(filename, fps=fps)
         elif extension == '.mp4':
             data.save(filename, writer='ffmpeg', fps=fps)
@@ -239,7 +239,7 @@ class MatplotlibFigureWriter(Writer):
         file.
 
         :param data: The matplotlib figure
-        :type data: CHAP.pipeline.PipelineData
+        :type data: list[PipelineData]
         :param filename: The name of the file to write to.
         :type filename: str
         :param savefig_kw: Keyword args to pass to
@@ -265,7 +265,7 @@ class NexusWriter(Writer):
         """Write the NeXus object contained in `data` to file.
 
         :param data: The data to write to file.
-        :type data: CHAP.pipeline.PipelineData
+        :type data: list[PipelineData]
         :param filename: The name of the file to write to.
         :param force_overwrite: Flag to allow data in `filename` to be
             overwritten if it already exists, defaults to `False`.
@@ -275,7 +275,21 @@ class NexusWriter(Writer):
         :return: The data written to file.
         :rtype: nexusformat.nexus.NXobject
         """
+        from nexusformat.nexus import (
+            NXentry,
+            NXroot,
+        )
         data = self.unwrap_pipelinedata(data)[-1]
+        nxclass = data.nxclass
+        nxname = data.nxname
+        if nxclass == 'NXentry':
+            data = NXroot(data)
+            data[nxname].set_default()
+        elif nxclass != 'NXroot':
+            data = NXroot(NXentry(data))
+            if nxclass == 'NXdata':
+                data.entry[nxname].set_default()
+            data.entry.set_default()
         write_nexus(data, filename, force_overwrite)
 
         return data

CHAP/edd/__init__.py

@@ -3,8 +3,10 @@ processing workflows.
 """
 # from CHAP.edd.reader import
 from CHAP.edd.processor import (DiffractionVolumeLengthProcessor,
+                                LatticeParameterRefinementProcessor,
                                 MCACeriaCalibrationProcessor,
                                 MCADataProcessor,
+                                MCAEnergyCalibrationProcessor,
                                 StrainAnalysisProcessor)
 # from CHAP.edd.writer import
 

CHAP/edd/models.py

@@ -38,43 +38,70 @@ class MCAElementConfig(BaseModel):
     :type detector_name: str
     :ivar num_bins: Number of MCA channels.
     :type num_bins: int, optional
-    :ivar include_bin_ranges: List of MCA channel index ranges whose
-        data should be included after applying a mask (the bounds are
-        inclusive), defaults to `[]`
-    :type include_bin_ranges: list[[int, int]], optional
+    :ivar include_energy_ranges: List of MCA channel energy ranges
+        whose data should be included after applying a mask (the
+        bounds are inclusive), defaults to `[[50,150]]`
+    :type include_energy_ranges: list[[float, float]], optional
     """
     detector_name: constr(strip_whitespace=True, min_length=1) = 'mca1'
     num_bins: Optional[conint(gt=0)]
-    include_bin_ranges: conlist(
+    max_energy_kev: confloat(gt=0) = 200
+    include_energy_ranges: conlist(
         min_items=1,
         item_type=conlist(
-            item_type=conint(ge=0),
+            item_type=confloat(ge=0),
             min_items=2,
-            max_items=2)) = []
+            max_items=2)) = [[50,150]]
 
-    @validator('include_bin_ranges', each_item=True)
-    def validate_include_bin_range(cls, value, values):
-        """Ensure that no bin ranges are outside the boundary of the
+    @validator('include_energy_ranges', each_item=True)
+    def validate_include_energy_range(cls, value, values):
+        """Ensure that no energy ranges are outside the boundary of the
         detector.
 
-        :param value: Field value to validate (`include_bin_ranges`).
+        :param value: Field value to validate (`include_energy_ranges`).
         :type values: dict
         :param values: Dictionary of previously validated field values.
         :type values: dict
-        :return: The validated value of `include_bin_ranges`.
+        :return: The validated value of `include_energy_ranges`.
         :rtype: dict
         """
-        num_bins = values.get('num_bins')
-        if num_bins is not None:
-            value[1] = min(value[1], num_bins-1)
-        if value[0] >= value[1]:
-            raise ValueError('Invalid bin range in include_bin_ranges '
-                             f'({value})')
+        max_energy_kev = values.get('max_energy_kev')
+        value.sort()
+        if value[1] > max_energy_kev:
+            value[1] = max_energy_kev
         return value
 
+    @property
+    def include_bin_ranges(self):
+        """Return the value of `include_energy_ranges` represented in
+        terms of channel indices instead of channel energies.
+        """
+        from CHAP.utils.general import index_nearest_down, index_nearest_upp
+
+        include_bin_ranges = []
+        energies = np.linspace(0, self.max_energy_kev, self.num_bins)
+        for e_min, e_max in self.include_energy_ranges:
+            include_bin_ranges.append(
+                [index_nearest_down(energies, e_min),
+                 index_nearest_upp(energies, e_max)])
+        return include_bin_ranges
+
+    def get_energy_ranges(self, bin_ranges):
+        """Given a list of channel index ranges, return the
+        correspongin list of channel energy ranges.
+
+        :param bin_ranges: A list of channel bin ranges to convert to
+            energy ranges.
+        :type bin_ranges: list[list[int]]
+        :returns: Energy ranges
+        :rtype: list[list[float]]
+        """
+        energies = np.linspace(0, self.max_energy_kev, self.num_bins)
+        return [[energies[i] for i in range_] for range_ in bin_ranges]
+
     def mca_mask(self):
         """Get a boolean mask array to use on this MCA element's data.
-        Note that the bounds of self.include_bin_ranges are inclusive.
+        Note that the bounds of self.include_energy_ranges are inclusive.
 
         :return: Boolean mask array.
         :rtype: numpy.ndarray
@@ -94,9 +121,9 @@ class MCAElementConfig(BaseModel):
         :rtype: dict
         """
         d = super().dict(*args, **kwargs)
-        d['include_bin_ranges'] = [
-            list(d['include_bin_ranges'][i]) \
-            for i in range(len(d['include_bin_ranges']))]
+        d['include_energy_ranges'] = [
+            [float(energy) for energy in d['include_energy_ranges'][i]]
+            for i in range(len(d['include_energy_ranges']))]
         return d
 
 
@@ -172,7 +199,7 @@ class MCAScanDataConfig(BaseModel):
     def validate_detectors(cls, values):
         """Fill in values for _scanparser / _parfile (if applicable).
         Fill in each detector's num_bins field, if needed.
-        Check each detector's include_bin_ranges field against the
+        Check each detector's include_energy_ranges field against the
         flux file, if available.
 
         :param values: Dictionary of previously validated field values.
@@ -212,20 +239,21 @@ class MCAScanDataConfig(BaseModel):
             )
             flux = np.loadtxt(flux_file)
             flux_file_energies = flux[:,0]/1.e3
-            energy_range = (flux_file_energies.min(), flux_file_energies.max())
+            flux_e_min = flux_file_energies.min()
+            flux_e_max = flux_file_energies.max()
             for detector in detectors:
                 mca_bin_energies = np.linspace( 
                     0, detector.max_energy_kev, detector.num_bins)
-                e_min = index_nearest_upp(mca_bin_energies, energy_range[0])
-                e_max = index_nearest_down(mca_bin_energies, energy_range[1])
-                for i, (min_, max_) in enumerate(
-                        deepcopy(detector.include_bin_ranges)):
-                    if min_ < e_min or max_ > e_max:
-                        bin_range = [max(min_, e_min), min(max_, e_max)]
-                        print(f'WARNING: include_bin_ranges[{i}] out of range '
-                              f'({detector.include_bin_ranges[i]}): adjusted '
-                              f'to {bin_range}')
-                        detector.include_bin_ranges[i] = bin_range
+                for i, (det_e_min, det_e_max) in enumerate(
+                        deepcopy(detector.include_energy_ranges)):
+                    if det_e_min < flux_e_min or det_e_max > flux_e_max:
+                        energy_range = [min(det_e_min, flux_e_min),
+                                        max(det_e_max, flux_e_max)]
+                        print(
+                            f'WARNING: include_energy_ranges[{i}] out of range'
+                            f' ({detector.include_energy_ranges[i]}): adjusted'
+                            f' to {energy_range}')
+                        detector.include_energy_ranges[i] = energy_range
 
         return values
 
@@ -381,6 +409,8 @@ class MCAElementCalibrationConfig(MCAElementConfig):
     :ivar hkl_indices: List of unique HKL indices to fit peaks for in
         the calibration routine, defaults to `[]`.
     :type hkl_indices: list[int], optional
+    :ivar background: Background model for peak fitting.
+    :type background: str, list[str], optional
     :ivar tth_initial_guess: Initial guess for 2&theta,
         defaults to `5.0`.
     :type tth_initial_guess: float, optional
@@ -394,7 +424,7 @@ class MCAElementCalibrationConfig(MCAElementConfig):
     :type tth_calibrated: float, optional
     :ivar slope_calibrated: Calibrated value for detector channel
         energy correction linear slope.
-    :type  slope_calibrated: float, optional
+    :type slope_calibrated: float, optional
     :ivar intercept_calibrated: Calibrated value for detector channel
         energy correction y-intercept.
     :type intercept_calibrated: float, optional
@@ -403,6 +433,7 @@ class MCAElementCalibrationConfig(MCAElementConfig):
     tth_max: confloat(gt=0, allow_inf_nan=False) = 90.0
     hkl_tth_tol: confloat(gt=0, allow_inf_nan=False) = 0.15
     hkl_indices: Optional[conlist(item_type=conint(ge=0), min_items=1)] = []
+    background: Optional[Union[str, list]]
     tth_initial_guess: confloat(gt=0, le=tth_max, allow_inf_nan=False) = 5.0
     slope_initial_guess: float = 1.0
     intercept_initial_guess: float = 0.0
@@ -435,10 +466,19 @@ class MCAElementDiffractionVolumeLengthConfig(MCAElementConfig):
     :ivar dvl_measured: Placeholder for the measured diffraction
         volume length before writing the data to file.
     :type dvl_measured: float, optional
+    :ivar fit_amplitude: Placeholder for amplitude of the gaussian fit.
+    :type fit_amplitude: float, optional
+    :ivar fit_center: Placeholder for center of the gaussian fit.
+    :type fit_center: float, optional
+    :ivar fit_sigma: Placeholder for sigma of the gaussian fit.
+    :type fit_sigma: float, optional
     """
     measurement_mode: Optional[Literal['manual', 'auto']] = 'auto'
     sigma_to_dvl_factor: Optional[Literal[3.5, 2.0, 4.0]] = 3.5
     dvl_measured: Optional[confloat(gt=0)] = None
+    fit_amplitude: Optional[float] = None
+    fit_center: Optional[float] = None
+    fit_sigma: Optional[float] = None
 
     def dict(self, *args, **kwargs):
         """Return a representation of this configuration in a
@@ -452,6 +492,8 @@ class MCAElementDiffractionVolumeLengthConfig(MCAElementConfig):
         d = super().dict(*args, **kwargs)
         if self.measurement_mode == 'manual':
             del d['sigma_to_dvl_factor']
+        for param in ('amplitude', 'center', 'sigma'):
+            d[f'fit_{param}'] = float(d[f'fit_{param}'])
         return d
 
 
@@ -460,10 +502,15 @@ class DiffractionVolumeLengthConfig(MCAScanDataConfig):
     volume length calculation for an EDD setup using a steel-foil
     raster scan.
 
+    :ivar sample_thickness: Thickness of scanned foil sample. Quantity
+        must be provided in the same units as the values of the
+        scanning motor.
+    :type sample_thickness: float
     :ivar detectors: Individual detector element DVL
         measurement configurations
     :type detectors: list[MCAElementDiffractionVolumeLengthConfig]
     """
+    sample_thickness: float
     detectors: conlist(min_items=1,
                        item_type=MCAElementDiffractionVolumeLengthConfig)
 
@@ -481,18 +528,6 @@ class DiffractionVolumeLengthConfig(MCAScanDataConfig):
                 scan_numbers=self._parfile.good_scan_numbers())
         return self.scanparser.spec_scan_motor_vals[0]
 
-    @property
-    def scanned_dim_lbl(self):
-        """Return a label for plot axes corresponding to the scanned
-        dimension.
-
-        :return: Name of scanned motor.
-        :rtype: str
-        """
-        if self._parfile is not None:
-            return self.scan_column
-        return self.scanparser.spec_scan_motor_mnes[0]
-
 
 class CeriaConfig(MaterialConfig):
     """Model for the sample material used in calibrations.
@@ -629,6 +664,8 @@ class MCAElementStrainAnalysisConfig(MCAElementConfig):
     :type hkl_indices: list[int], optional
     :ivar background: Background model for peak fitting.
     :type background: str, list[str], optional
+    :ivar num_proc: Number of processors used for peak fitting.
+    :type num_proc: int, optional
     :ivar peak_models: Peak model for peak fitting,
         defaults to `'gaussian'`.
     :type peak_models: Literal['gaussian', 'lorentzian']],
@@ -656,7 +693,8 @@ class MCAElementStrainAnalysisConfig(MCAElementConfig):
     tth_max: confloat(gt=0, allow_inf_nan=False) = 90.0
     hkl_tth_tol: confloat(gt=0, allow_inf_nan=False) = 0.15
     hkl_indices: Optional[conlist(item_type=conint(ge=0), min_items=1)] = []
-    background: Optional[str]
+    background: Optional[Union[str, list]]
+    num_proc: Optional[conint(gt=0)] = os.cpu_count()
     peak_models: Union[
         conlist(item_type=Literal['gaussian', 'lorentzian'], min_items=1),
         Literal['gaussian', 'lorentzian']] = 'gaussian'
@@ -667,6 +705,13 @@ class MCAElementStrainAnalysisConfig(MCAElementConfig):
     tth_calibrated: Optional[confloat(gt=0, allow_inf_nan=False)]
     slope_calibrated: Optional[confloat(allow_inf_nan=False)]
     intercept_calibrated: Optional[confloat(allow_inf_nan=False)]
+    calibration_bin_ranges: Optional[
+        conlist(
+            min_items=1,
+            item_type=conlist(
+                item_type=conint(ge=0),
+                min_items=2,
+            max_items=2))]
     tth_file: Optional[FilePath]
     tth_map: Optional[np.ndarray] = None
 
@@ -696,6 +741,7 @@ class MCAElementStrainAnalysisConfig(MCAElementConfig):
                       'intercept_calibrated', 'num_bins', 'max_energy_kev']
         for field in add_fields:
             setattr(self, field, getattr(calibration, field))
+        self.calibration_bin_ranges = calibration.include_bin_ranges
 
     def get_tth_map(self, map_config):
         """Return a map of 2&theta values to use -- may vary at each