Merge branch 'main' into dev_rolf

CHAP/edd/__init__.py

@@ -18,5 +18,6 @@
     SetupNXdataReader,
     UpdateNXdataReader,
     NXdataSliceReader,
+    SliceNXdataReader,
 )
 # from CHAP.edd.writer import

CHAP/edd/reader.py

@@ -699,6 +699,59 @@ def read(self, filename, dataset_id, detectors=None):
         return {'coords': coords, 'signals': signals,
                 'attrs': attrs, 'data_points': data_points}
 
+class SliceNXdataReader(Reader):
+    """A reader class to load and slice an NXdata field from a NeXus
+    file.  This class reads EDD (Energy Dispersive Diffraction) data
+    from an NXdata group and slices all fields according to the
+    provided slicing parameters.
+    """
+    def read(self, filename, scan_number, inputdir=None):
+        """Reads an NXdata group from a NeXus file and slices the
+        fields within it based on the provided scan number.
+
+        :param filename: The name of the NeXus file to read.
+        :type filename: str
+        :param scan_number: The scan number to use for slicing the
+            data.
+        :type scan_number: int
+        :param inputdir: The directory containing the input file,
+            defaults to None.
+        :type inputdir: str, optional
+
+        :return: The root object of the NeXus file with sliced NXdata
+            fields.
+        :rtype: NXroot
+
+        :raises ValueError: If no NXdata group is found in the file.
+        """
+        import os
+        import numpy as np
+        from nexusformat.nexus import NXentry, NXfield
+
+        from CHAP.common import NexusReader
+        from CHAP.utils.general import nxcopy
+
+        reader = NexusReader()
+        nxroot = nxcopy(reader.read(os.path.join(inputdir, filename)))
+        nxdata = None
+        for nxname, nxobject in nxroot.items():
+            if isinstance(nxobject, NXentry):
+                nxdata = nxobject.data
+        if nxdata is None:
+            msg = 'Could not find NXdata group'
+            self.logger.error(msg)
+            raise ValueError(msg)
+
+        indices = np.argwhere(nxdata.SCAN_N.nxdata == 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,
+                )
+
+        return nxroot
 
 class UpdateNXdataReader(Reader):
     """Companion to `edd.SetupNXdataReader` and

CHAP/edd/utils.py

@@ -1398,6 +1398,7 @@ def get_spectra_fits(spectra, energies, peak_locations, detector):
         numpy.ndarray, numpy.ndarray, numpy.ndarray, numpy.ndarray,
         numpy.ndarray]
     """
+    from os import getpid
     # Third party modules
     from nexusformat.nexus import NXdata, NXfield
 
@@ -1432,6 +1433,7 @@ def get_spectra_fits(spectra, energies, peak_locations, detector):
 #        'method': 'trf',
         'method': 'leastsq',
 #        'method': 'least_squares',
+        'memfolder': f'/tmp/{getpid()}_joblib_memmap',
     }
 
     # Perform uniform fit

CHAP/utils/fit.py

@@ -2084,7 +2084,7 @@ def __init__(self, nxdata, config):
         self._best_values = None
         self._inv_transpose = None
         self._max_nfev = None
-        self._memfolder = None
+        self._memfolder = config.memfolder
         self._new_parameters = None
         self._num_func_eval = None
         self._out_of_bounds = None
@@ -2319,7 +2319,6 @@ def freemem(self):
             return
         try:
             rmtree(self._memfolder)
-            self._memfolder = None
         except:
             logger.warning('Could not clean-up automatically.')
 
@@ -2514,7 +2513,6 @@ def fit(self, config=None, **kwargs):
                     np.zeros(self._map_dim, dtype=np.float64)
                     for _ in range(num_new_parameters)]
         else:
-            self._memfolder = 'joblib_memmap'
             try:
                 mkdir(self._memfolder)
             except FileExistsError:

CHAP/utils/models.py

@@ -568,6 +568,7 @@ class FitConfig(BaseModel):
     num_proc: conint(gt=0) = 1
     plot: StrictBool = False
     print_report:  StrictBool = False
+    memfolder: str = 'joblib_memmap'
 
     @field_validator('method')
     @classmethod