Tested parsing on IKZ and PDI examples

FAIRmat-NFDI · Jan 13, 2024 · 712e384 · 712e384
1 parent bd4edec
commit 712e384
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Showing 8 changed files with 278 additions and 69 deletions.
diff --git a/debug/spctrscpy.batch.sh b/debug/spctrscpy.batch.sh
@@ -1,11 +1,15 @@
 #!/bin/bash
 
-datasource="../../../../paper_paper_paper/scidat_nomad_ebsd/bb_analysis/data/development_spctrscpy/pdi/"
+datasource="../../../../../paper_paper_paper/scidat_nomad_ebsd/bb_analysis/data/development_spctrscpy/pdi/"
+datasource="../../../../../paper_paper_paper/scidat_nomad_ebsd/bb_analysis/data/development_spctrscpy/ikz/"
+
 
 # apex examples ikz, pdi
 # examples="ikz/VInP_108_L2.h5 ikz/GeSn_13.h5 pynx/46_ES-LP_L1_brg.bcf pynx/1613_Si_HAADF_610_kx.emd pynx/EELS_map_2_ROI_1_location_4.dm3 pynx/H5OINA_examples_Specimen_1_Map_EDS_+_EBSD_Map_Data_2.h5oina"
-examples="ikz/VInP_108_L2.h5"
-examples="InGaN_nanowires_spectra.edaxh5"
+examples="AlGaO.nxs"
+examples="GeSi.nxs"
+examples="VInP_108_L2.h5"
+#examples="InGaN_nanowires_spectra.edaxh5"
 
 for example in $examples; do
 	echo $example

diff --git a/debug/spctrscpy.dev.ipynb b/debug/spctrscpy.dev.ipynb
diff --git a/pynxtools/dataconverter/readers/em/concepts/nxs_image_r_set.py b/pynxtools/dataconverter/readers/em/concepts/nxs_image_r_set.py
@@ -65,9 +65,9 @@ def __init__(self):
         self.tmp: Dict = {}
         self.tmp["source"] = None
         for entry in NX_IMAGE_REAL_SPACE_SET_HDF_PATH:
-            if entry.endswith("-field") is True:
+            if entry.endswith("-field"):
                 self.tmp[entry[0:len(entry) - len("-field")]] = NxObject(eqv_hdf="dataset")
-            elif entry.endswith("-attribute") is True:
+            elif entry.endswith("-attribute"):
                 self.tmp[entry[0:len(entry) - len("-attribute")]] = NxObject(eqv_hdf="attribute")
             else:
                 self.tmp[entry[0:len(entry) - len("-group")]] = NxObject(eqv_hdf="group")
diff --git a/pynxtools/dataconverter/readers/em/concepts/nxs_object.py b/pynxtools/dataconverter/readers/em/concepts/nxs_object.py
@@ -28,7 +28,7 @@ class NxObject:
     def __init__(self,
                  name: str = None,
                  unit: str = None,
-                 dtype=str,
+                 dtype=None,
                  value=None,
                  **kwargs):
         if (name is not None) and (name == ""):
@@ -44,10 +44,9 @@ def __init__(self,
         # use special values "unitless" for NX_UNITLESS (e.g. 1) and
         # "dimensionless" for NX_DIMENSIONLESS (e.g. 1m / 1m)
         self.dtype = dtype  # use np.dtype if possible
-        if value is None or dtype is str:
+        if value is None or isinstance(dtype, str):
             self.unit = "unitless"
-        if value is not None:
-            self.value = value
+        self.value = value
         # value should be a numpy scalar, tensor, or string if possible
         self.eqv_hdf = None
         if "eqv_hdf" in kwargs:
@@ -58,4 +57,4 @@ def __init__(self,
 
     def __repr__(self):
         """Report values."""
-        return f"Name: {self.name}, unit: {self.unit}, dtype: {self.dtype}, eqv_hdf: {self.eqv_hdf}"
+        return f"Name: {self.name}, unit: {self.unit}, dtype: {self.dtype}, value: {self.value}, eqv_hdf: {self.eqv_hdf}"
diff --git a/pynxtools/dataconverter/readers/em/concepts/nxs_spectrum_set.py b/pynxtools/dataconverter/readers/em/concepts/nxs_spectrum_set.py
@@ -34,19 +34,16 @@
                                   "PROCESS/mode-field",
                                   "PROCESS/PROGRAM-group",
                                   "PROCESS/source-group",
-                                  "spectrum_zerod-group",
                                   "spectrum_zerod/axis_energy-field",
                                   "spectrum_zerod/axis_energy@long_name-attribute",
                                   "spectrum_zerod/intensity-field",
                                   "spectrum_zerod/intensity@long_name-attribute",
-                                  "spectrum_oned-group",
                                   "spectrum_oned/axis_energy-field",
                                   "spectrum_oned/axis_energy@long_name-attribute",
                                   "spectrum_oned/axis_x-field",
                                   "spectrum_oned/axis_x@long_name-attribute",
                                   "spectrum_oned/intensity-field",
                                   "spectrum_oned/intensity@long_name-attribute",
-                                  "spectrum_threed-group",
                                   "spectrum_threed/axis_energy-field",
                                   "spectrum_threed/axis_energy@long_name-attribute",
                                   "spectrum_threed/axis_x-field",
@@ -57,7 +54,6 @@
                                   "spectrum_threed/axis_z@long_name-attribute",
                                   "spectrum_threed/intensity-field",
                                   "spectrum_threed/intensity@long_name-attribute",
-                                  "spectrum_twod-group",
                                   "spectrum_twod/axis_energy-field",
                                   "spectrum_twod/axis_energy@long_name-attribute",
                                   "spectrum_twod/axis_x-field",

diff --git a/pynxtools/dataconverter/readers/em/reader.py b/pynxtools/dataconverter/readers/em/reader.py
@@ -23,9 +23,9 @@
 
 from pynxtools.dataconverter.readers.base.reader import BaseReader
 # from pynxtools.dataconverter.readers.em.concepts.nxs_concepts import NxEmAppDef
-# from pynxtools.dataconverter.readers.em.subparsers.nxs_mtex import NxEmNxsMTexSubParser
-# from pynxtools.dataconverter.readers.em.subparsers.nxs_pyxem import NxEmNxsPyxemSubParser
-# from pynxtools.dataconverter.readers.em.subparsers.nxs_imgs import NxEmImagesSubParser
+from pynxtools.dataconverter.readers.em.subparsers.nxs_mtex import NxEmNxsMTexSubParser
+from pynxtools.dataconverter.readers.em.subparsers.nxs_pyxem import NxEmNxsPyxemSubParser
+from pynxtools.dataconverter.readers.em.subparsers.nxs_imgs import NxEmImagesSubParser
 from pynxtools.dataconverter.readers.em.subparsers.nxs_nion import NxEmZippedNionProjectSubParser
 from pynxtools.dataconverter.readers.em.utils.default_plots import NxEmDefaultPlotResolver
 # from pynxtools.dataconverter.readers.em.geometry.convention_mapper import NxEmConventionMapper
@@ -119,18 +119,18 @@ def read(self,
 
         # add further with resolving cases
         # if file_path is an HDF5 will use hfive parser
-        # sub_parser = "nxs_pyxem"
-        # subparser = NxEmNxsPyxemSubParser(entry_id, file_paths[0])
-        # subparser.parse(template)
+        sub_parser = "nxs_pyxem"
+        subparser = NxEmNxsPyxemSubParser(entry_id, file_paths[0])
+        subparser.parse(template)
         # TODO::check correct loop through!
 
         # sub_parser = "image_tiff"
         # subparser = NxEmImagesSubParser(entry_id, file_paths[0])
         # subparser.parse(template)
 
         # sub_parser = "zipped_nion_project"
-        subparser = NxEmZippedNionProjectSubParser(entry_id, file_paths[0])
-        subparser.parse(template, verbose=True)
+        # subparser = NxEmZippedNionProjectSubParser(entry_id, file_paths[0])
+        # subparser.parse(template, verbose=True)
 
         # for dat_instance in case.dat_parser_type:
         #     print(f"Process pieces of information in {dat_instance} tech partner file...")