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… xray line identification
FAIRmat-NFDI · Jan 15, 2024 · bc2dc04 · bc2dc04
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commit bc2dc04
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Showing 6 changed files with 258 additions and 108 deletions.
diff --git a/debug/spctrscpy.batch.sh b/debug/spctrscpy.batch.sh
@@ -1,15 +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/ikz/"
+#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="AlGaO.nxs"
 examples="GeSi.nxs"
 examples="VInP_108_L2.h5"
-#examples="InGaN_nanowires_spectra.edaxh5"
+examples="InGaN_nanowires_spectra.edaxh5"
 
 for example in $examples; do
 	echo $example

diff --git a/pynxtools/dataconverter/readers/em/concepts/nxs_em_eds_indexing.py b/pynxtools/dataconverter/readers/em/concepts/nxs_em_eds_indexing.py
@@ -22,23 +22,21 @@
 from pynxtools.dataconverter.readers.em.concepts.nxs_object import NxObject
 
 
-NX_EM_EDS_INDEXING_HDF_PATH = ["indexing-group",
-                               "indexing/element_names-field",
-                               "indexing/IMAGE_R_SET-group",
+NX_EM_EDS_INDEXING_HDF_PATH = ["indexing/element_names-field",
                                "indexing/IMAGE_R_SET/PROCESS-group",
                                "indexing/IMAGE_R_SET/PROCESS/peaks-field",
+                               "indexing/IMAGE_R_SET/description-field",
+                               "indexing/IMAGE_R_SET/iupac_line_candidates-field",
                                "indexing/IMAGE_R_SET/PROCESS/weights-field",
-                               "indexing/PEAK-group",
-                               "indexing/PEAK/ION-group",
+                               "indexing/IMAGE_R_SET/PROCESS/weights-field",
+                               "indexing/IMAGE_R_SET/image_twod/axis_x-field",
+                               "indexing/IMAGE_R_SET/image_twod/axis_x@long_name-attribute",
+                               "indexing/IMAGE_R_SET/image_twod/axis_y-field",
+                               "indexing/IMAGE_R_SET/image_twod/axis_y@long_name-attribute",
+                               "indexing/IMAGE_R_SET/image_twod/intensity-field",
                                "indexing/PEAK/ION/energy-field",
                                "indexing/PEAK/ION/energy_range-field",
-                               "indexing/PEAK/ION/iupac_line_names-field",
-                               "indexing/PROGRAM-group",
-                               "indexing/summary-group",
-                               "indexing/summary/axis_energy-field",
-                               "indexing/summary/axis_energy@long_name-attribute",
-                               "indexing/summary/intensity-field",
-                               "indexing/summary/intensity@long_name-attribute"]
+                               "indexing/PEAK/ION/iupac_line_names-field"]
 
 
 class NxEmEdsIndexing():

diff --git a/pynxtools/dataconverter/readers/em/concepts/nxs_object.py b/pynxtools/dataconverter/readers/em/concepts/nxs_object.py
@@ -19,6 +19,8 @@
 
 # pylint: disable=no-member,too-few-public-methods
 
+import numpy as np
+
 from typing import Dict
 
 
@@ -57,4 +59,4 @@ def __init__(self,
 
     def __repr__(self):
         """Report values."""
-        return f"Name: {self.name}, unit: {self.unit}, dtype: {self.dtype}, value: {self.value}, eqv_hdf: {self.eqv_hdf}"
+        return f"Name: {self.name}, unit: {self.unit}, dtype: {self.dtype}, np.shape(value): {np.shape(self.value)}, eqv_hdf: {self.eqv_hdf}"