29 generate contributed defs

.gitignore

@@ -3,3 +3,6 @@
 # Microsoft VSCode
 settings.json
 launch.json
+
+#pyCharm
+.idea

autogenerated_examples/nxdl/python_scripts/h5py/ex_h5py_NXarchive.py

@@ -57,11 +57,11 @@
 root['/entry/entry_identifier'].attrs['type'] = 'NX_CHAR'
 root['/entry/entry_identifier'].attrs['EX_required'] = 'true'
 
-root['/entry'].create_dataset(name='start_time', data='2021-03-29T15:51:33.227367', maxshape=None)
+root['/entry'].create_dataset(name='start_time', data='2022-03-04T14:56:32.205127', maxshape=None)
 root['/entry/start_time'].attrs['type'] = 'NX_DATE_TIME'
 root['/entry/start_time'].attrs['EX_required'] = 'true'
 
-root['/entry'].create_dataset(name='end_time', data='2021-03-29T15:51:33.233370', maxshape=None)
+root['/entry'].create_dataset(name='end_time', data='2022-03-04T14:56:32.220782', maxshape=None)
 root['/entry/end_time'].attrs['type'] = 'NX_DATE_TIME'
 root['/entry/end_time'].attrs['EX_required'] = 'true'
 

autogenerated_examples/nxdl/python_scripts/h5py/ex_h5py_NXarpes.py

@@ -45,7 +45,7 @@
 root['/entry/title'].attrs['type'] = 'NX_CHAR'
 root['/entry/title'].attrs['EX_required'] = 'true'
 
-root['/entry'].create_dataset(name='start_time', data='2021-03-29T15:51:33.838489', maxshape=None)
+root['/entry'].create_dataset(name='start_time', data='2022-03-04T14:56:32.376970', maxshape=None)
 root['/entry/start_time'].attrs['type'] = 'NX_DATE_TIME'
 root['/entry/start_time'].attrs['EX_required'] = 'true'
 

autogenerated_examples/nxdl/python_scripts/h5py/ex_h5py_NXcxi_ptycho.py

@@ -0,0 +1,179 @@
+
+import numpy as np
+import datetime
+import h5py
+import os
+
+# Note this example script was generated by nxdl_to_hdf5.py using the current 
+# installed version of the NEXUS definitions ver[v2020.10] 
+
+root = h5py.File('NXcxi_ptycho.h5', 'w')
+
+# Create the GROUPS 
+
+root.create_group('entry_1')
+root['/entry_1'].attrs['NX_class'] = 'NXentry'
+root['/entry_1'].attrs['EX_required'] = 'false'
+
+root['/entry_1/'].create_group('instrument_1')
+root['/entry_1/instrument_1'].attrs['NX_class'] = 'NXinstrument'
+root['/entry_1/instrument_1'].attrs['EX_required'] = 'true'
+
+root['/entry_1/instrument_1/'].create_group('source_1')
+root['/entry_1/instrument_1/source_1'].attrs['NX_class'] = 'NXsource'
+root['/entry_1/instrument_1/source_1'].attrs['EX_required'] = 'true'
+
+root['/entry_1/instrument_1/'].create_group('beam_1')
+root['/entry_1/instrument_1/beam_1'].attrs['NX_class'] = 'NXbeam'
+root['/entry_1/instrument_1/beam_1'].attrs['EX_required'] = 'true'
+
+root['/entry_1/instrument_1/'].create_group('detector_1')
+root['/entry_1/instrument_1/detector_1'].attrs['NX_class'] = 'NXdetector'
+root['/entry_1/instrument_1/detector_1'].attrs['EX_required'] = 'true'
+
+root['/entry_1/instrument_1/detector_1/'].create_group('transformations')
+root['/entry_1/instrument_1/detector_1/transformations'].attrs['NX_class'] = 'NXtransformations'
+root['/entry_1/instrument_1/detector_1/transformations'].attrs['EX_required'] = 'false'
+
+root['/entry_1/instrument_1/'].create_group('monitor')
+root['/entry_1/instrument_1/monitor'].attrs['NX_class'] = 'NXmonitor'
+root['/entry_1/instrument_1/monitor'].attrs['EX_required'] = 'false'
+
+# Create the FIELDS 
+
+root['/entry_1'].create_dataset(name='title', data='SAMPLE-CHAR-DATA', maxshape=None)
+root['/entry_1/title'].attrs['type'] = 'NX_CHAR'
+root['/entry_1/title'].attrs['EX_required'] = 'false'
+
+root['/entry_1'].create_dataset(name='start_time', data='2022-03-04T14:56:23.795988', maxshape=None)
+root['/entry_1/start_time'].attrs['type'] = 'NX_DATE_TIME'
+root['/entry_1/start_time'].attrs['EX_required'] = 'false'
+
+root['/entry_1'].create_dataset(name='end_time', data='2022-03-04T14:56:23.795988', maxshape=None)
+root['/entry_1/end_time'].attrs['type'] = 'NX_DATE_TIME'
+root['/entry_1/end_time'].attrs['EX_required'] = 'false'
+
+# Valid enumeration values for root['/entry_1']['definition'] are: 
+#	 NXcxi_ptycho
+
+root['/entry_1'].create_dataset(name='definition', data='NXcxi_ptycho', maxshape=None)
+root['/entry_1/definition'].attrs['type'] = 'NX_CHAR'
+root['/entry_1/definition'].attrs['EX_required'] = 'true'
+
+root['/entry_1/instrument_1/source_1'].create_dataset(name='name', data='SAMPLE-CHAR-DATA', maxshape=None)
+root['/entry_1/instrument_1/source_1/name'].attrs['type'] = 'NX_CHAR'
+root['/entry_1/instrument_1/source_1/name'].attrs['EX_required'] = 'true'
+
+root['/entry_1/instrument_1/source_1'].create_dataset(name='energy', data=1.0, maxshape=None)
+root['/entry_1/instrument_1/source_1/energy'].attrs['type'] = 'NX_FLOAT'
+root['/entry_1/instrument_1/source_1/energy'].attrs['EX_required'] = 'true'
+
+root['/entry_1/instrument_1/source_1'].create_dataset(name='probe', data=1.0, maxshape=None)
+root['/entry_1/instrument_1/source_1/probe'].attrs['type'] = 'NX_FLOAT'
+root['/entry_1/instrument_1/source_1/probe'].attrs['EX_required'] = 'true'
+
+root['/entry_1/instrument_1/source_1'].create_dataset(name='type', data=1.0, maxshape=None)
+root['/entry_1/instrument_1/source_1/type'].attrs['type'] = 'NX_FLOAT'
+root['/entry_1/instrument_1/source_1/type'].attrs['EX_required'] = 'true'
+
+root['/entry_1/instrument_1/beam_1'].create_dataset(name='energy', data=1.0, maxshape=None)
+root['/entry_1/instrument_1/beam_1/energy'].attrs['type'] = 'NX_FLOAT'
+root['/entry_1/instrument_1/beam_1/energy'].attrs['EX_required'] = 'true'
+
+root['/entry_1/instrument_1/beam_1'].create_dataset(name='extent', data=1.0, maxshape=None)
+root['/entry_1/instrument_1/beam_1/extent'].attrs['type'] = 'NX_FLOAT'
+root['/entry_1/instrument_1/beam_1/extent'].attrs['EX_required'] = 'false'
+
+root['/entry_1/instrument_1/beam_1'].create_dataset(name='incident_beam_divergence', data=1.0, maxshape=None)
+root['/entry_1/instrument_1/beam_1/incident_beam_divergence'].attrs['type'] = 'NX_FLOAT'
+root['/entry_1/instrument_1/beam_1/incident_beam_divergence'].attrs['EX_required'] = 'false'
+
+root['/entry_1/instrument_1/beam_1'].create_dataset(name='incident_beam_energy', data=1.0, maxshape=None)
+root['/entry_1/instrument_1/beam_1/incident_beam_energy'].attrs['type'] = 'NX_FLOAT'
+root['/entry_1/instrument_1/beam_1/incident_beam_energy'].attrs['EX_required'] = 'true'
+
+root['/entry_1/instrument_1/beam_1'].create_dataset(name='incident_energy_spread', data=1.0, maxshape=None)
+root['/entry_1/instrument_1/beam_1/incident_energy_spread'].attrs['type'] = 'NX_FLOAT'
+root['/entry_1/instrument_1/beam_1/incident_energy_spread'].attrs['EX_required'] = 'true'
+
+root['/entry_1/instrument_1/detector_1/transformations'].create_dataset(name='vector', data=1.0, maxshape=None)
+root['/entry_1/instrument_1/detector_1/transformations/vector'].attrs['type'] = 'NX_NUMBER'
+root['/entry_1/instrument_1/detector_1/transformations/vector'].attrs['EX_required'] = 'true'
+
+root['/entry_1/instrument_1/detector_1'].create_dataset(name='translation', data=1.0, maxshape=None)
+root['/entry_1/instrument_1/detector_1/translation'].attrs['type'] = 'NX_FLOAT'
+root['/entry_1/instrument_1/detector_1/translation'].attrs['EX_required'] = 'true'
+root['/entry_1/instrument_1/detector_1/translation'].attrs['units'] = 'NX_LENGTH'
+
+root['/entry_1/instrument_1/detector_1'].create_dataset(name='data', data=1, maxshape=None)
+root['/entry_1/instrument_1/detector_1/data'].attrs['type'] = 'NX_INT'
+root['/entry_1/instrument_1/detector_1/data'].attrs['EX_required'] = 'true'
+root['/entry_1/instrument_1/detector_1/data'].attrs['signal'] = '1'
+
+root['/entry_1/instrument_1/detector_1'].create_dataset(name='x_pixel_size', data=1.0, maxshape=None)
+root['/entry_1/instrument_1/detector_1/x_pixel_size'].attrs['type'] = 'NX_FLOAT'
+root['/entry_1/instrument_1/detector_1/x_pixel_size'].attrs['EX_required'] = 'true'
+root['/entry_1/instrument_1/detector_1/x_pixel_size'].attrs['units'] = 'NX_LENGTH'
+
+root['/entry_1/instrument_1/detector_1'].create_dataset(name='y_pixel_size', data=1.0, maxshape=None)
+root['/entry_1/instrument_1/detector_1/y_pixel_size'].attrs['type'] = 'NX_FLOAT'
+root['/entry_1/instrument_1/detector_1/y_pixel_size'].attrs['EX_required'] = 'true'
+root['/entry_1/instrument_1/detector_1/y_pixel_size'].attrs['units'] = 'NX_LENGTH'
+
+root['/entry_1/instrument_1/detector_1'].create_dataset(name='distance', data=1.0, maxshape=None)
+root['/entry_1/instrument_1/detector_1/distance'].attrs['type'] = 'NX_FLOAT'
+root['/entry_1/instrument_1/detector_1/distance'].attrs['EX_required'] = 'true'
+root['/entry_1/instrument_1/detector_1/distance'].attrs['units'] = 'NX_LENGTH'
+
+root['/entry_1/instrument_1/detector_1'].create_dataset(name='beam_center_x', data=1.0, maxshape=None)
+root['/entry_1/instrument_1/detector_1/beam_center_x'].attrs['type'] = 'NX_FLOAT'
+root['/entry_1/instrument_1/detector_1/beam_center_x'].attrs['EX_required'] = 'false'
+root['/entry_1/instrument_1/detector_1/beam_center_x'].attrs['units'] = 'NX_LENGTH'
+
+root['/entry_1/instrument_1/detector_1'].create_dataset(name='beam_center_y', data=1.0, maxshape=None)
+root['/entry_1/instrument_1/detector_1/beam_center_y'].attrs['type'] = 'NX_FLOAT'
+root['/entry_1/instrument_1/detector_1/beam_center_y'].attrs['EX_required'] = 'false'
+root['/entry_1/instrument_1/detector_1/beam_center_y'].attrs['units'] = 'NX_LENGTH'
+
+root['/entry_1/instrument_1/monitor'].create_dataset(name='data', data=1.0, maxshape=None)
+root['/entry_1/instrument_1/monitor/data'].attrs['type'] = 'NX_FLOAT'
+root['/entry_1/instrument_1/monitor/data'].attrs['EX_required'] = 'false'
+
+# Create the LINKS 
+root['/entry_1/instrument_1/detector_1/data_1'] = h5py.SoftLink('/entry_1/title')
+root['/entry_1/instrument_1/detector_1/data_1/'].attrs['target'] = '/entry/instrument/detector/data'
+
+# Create the DOC strings 
+root['/entry_1/definition'].attrs['EX_doc'] = 'Official NeXus NXDL schema to which this file conforms '
+root['/entry_1/instrument_1/source_1/energy'].attrs['EX_doc'] = 'This is the energy of the machine, not the beamline. '
+root['/entry_1/instrument_1/detector_1/translation'].attrs['EX_doc'] = 'This is an array of shape (npts_x*npts_y, 3) and can be a Virtual Dataset of x and y '
+root['/entry_1/instrument_1/detector_1/data_1'].attrs['EX_doc'] = 'This data must always have shape (npts_x*npts_y, frame_size_x, frame_size_y) regardless   of the scan pattern. Use hdf5 virtual dataset to achieve this. '
+root['/entry_1/instrument_1/detector_1/distance'].attrs['EX_doc'] = 'The distance between the detector and the sample '
+
+
+# Create the ATTRIBUTES 
+root['/entry_1/instrument_1/beam_1/energy'].attrs['units'] = 'SAMPLE-CHAR-DATA'
+root['/entry_1/instrument_1/beam_1/extent'].attrs['units'] = 'SAMPLE-CHAR-DATA'
+root['/entry_1/instrument_1/beam_1/incident_beam_divergence'].attrs['units'] = 'SAMPLE-CHAR-DATA'
+root['/entry_1/instrument_1/beam_1/incident_beam_energy'].attrs['units'] = 'SAMPLE-CHAR-DATA'
+root['/entry_1/instrument_1/beam_1/incident_energy_spread'].attrs['units'] = 'SAMPLE-CHAR-DATA'
+root['/entry_1/instrument_1/detector_1'].attrs['axes'] = 'SAMPLE-CHAR-DATA'
+root['/entry_1/instrument_1/detector_1'].attrs['signal'] = 'SAMPLE-CHAR-DATA'
+root['/entry_1/instrument_1/detector_1/translation'].attrs['units'] = 'SAMPLE-CHAR-DATA'
+root['/entry_1/instrument_1/detector_1/translation'].attrs['axes'] = 'SAMPLE-CHAR-DATA'
+root['/entry_1/instrument_1/detector_1/translation'].attrs['interpretation'] = 'SAMPLE-CHAR-DATA'
+root['/entry_1/instrument_1/detector_1/x_pixel_size'].attrs['units'] = 'SAMPLE-CHAR-DATA'
+root['/entry_1/instrument_1/detector_1/y_pixel_size'].attrs['units'] = 'SAMPLE-CHAR-DATA'
+root['/entry_1/instrument_1/detector_1/distance'].attrs['units'] = 'SAMPLE-CHAR-DATA'
+root['/entry_1/instrument_1/detector_1/beam_center_x'].attrs['units'] = 'SAMPLE-CHAR-DATA'
+root['/entry_1/instrument_1/detector_1/beam_center_y'].attrs['units'] = 'SAMPLE-CHAR-DATA'
+root['/'].attrs['default'] = 'entry_1'
+root.attrs['file_name'] = os.path.abspath('NXcxi_ptycho')
+root.attrs['file_time'] = datetime.datetime.now().isoformat()
+root.attrs['h5py_version'] = h5py.version.version
+root.attrs['HDF5_Version'] = h5py.version.hdf5_version
+
+# Close the file
+root.close()
+
+

autogenerated_examples/nxdl/python_scripts/h5py/ex_h5py_NXdirecttof.py

@@ -53,7 +53,7 @@
 root['/entry/title'].attrs['type'] = 'NX_CHAR'
 root['/entry/title'].attrs['EX_required'] = 'true'
 
-root['/entry'].create_dataset(name='start_time', data='2021-03-29T15:51:37.033456', maxshape=None)
+root['/entry'].create_dataset(name='start_time', data='2022-03-04T14:56:33.860983', maxshape=None)
 root['/entry/start_time'].attrs['type'] = 'NX_DATE_TIME'
 root['/entry/start_time'].attrs['EX_required'] = 'true'
 

autogenerated_examples/nxdl/python_scripts/h5py/ex_h5py_NXfluo.py

@@ -49,7 +49,7 @@
 root['/entry/title'].attrs['type'] = 'NX_CHAR'
 root['/entry/title'].attrs['EX_required'] = 'true'
 
-root['/entry'].create_dataset(name='start_time', data='2021-03-29T15:51:37.263456', maxshape=None)
+root['/entry'].create_dataset(name='start_time', data='2022-03-04T14:56:33.985974', maxshape=None)
 root['/entry/start_time'].attrs['type'] = 'NX_DATE_TIME'
 root['/entry/start_time'].attrs['EX_required'] = 'true'
 

autogenerated_examples/nxdl/python_scripts/h5py/ex_h5py_NXindirecttof.py

@@ -49,7 +49,7 @@
 root['/entry/title'].attrs['type'] = 'NX_CHAR'
 root['/entry/title'].attrs['EX_required'] = 'true'
 
-root['/entry'].create_dataset(name='start_time', data='2021-03-29T15:51:37.731456', maxshape=None)
+root['/entry'].create_dataset(name='start_time', data='2022-03-04T14:56:34.220274', maxshape=None)
 root['/entry/start_time'].attrs['type'] = 'NX_DATE_TIME'
 root['/entry/start_time'].attrs['EX_required'] = 'true'
 

autogenerated_examples/nxdl/python_scripts/h5py/ex_h5py_NXlauetof.py

@@ -134,6 +134,9 @@
 
 
 # Create the ATTRIBUTES 
+
+# Valid enumeration values for root['/entry/instrument/detector/data']['signal'] are: 
+#	 1
 root['/entry/instrument/detector/data'].attrs['signal'] = '1'
 root['/'].attrs['default'] = 'entry'
 root['/entry'].attrs['default'] = 'name'

autogenerated_examples/nxdl/python_scripts/h5py/ex_h5py_NXmonopd.py

@@ -49,7 +49,7 @@
 root['/entry/title'].attrs['type'] = 'NX_CHAR'
 root['/entry/title'].attrs['EX_required'] = 'true'
 
-root['/entry'].create_dataset(name='start_time', data='2021-03-29T15:51:38.596455', maxshape=None)
+root['/entry'].create_dataset(name='start_time', data='2022-03-04T14:56:34.657669', maxshape=None)
 root['/entry/start_time'].attrs['type'] = 'NX_DATE_TIME'
 root['/entry/start_time'].attrs['EX_required'] = 'true'
 
@@ -135,8 +135,8 @@
 root['/entry/monitor/mode'].attrs['EX_doc'] = 'Count to a preset value based on either clock time (timer) or received monitor counts (monitor). '
 root['/entry/monitor/preset'].attrs['EX_doc'] = 'preset value for time or monitor '
 root['/entry/monitor/integral'].attrs['EX_doc'] = 'Total integral monitor counts '
-root['/entry/data/polar_angle'].attrs['EX_doc'] = 'Link to polar angle in /NXentry/NXinstrument/NXdetector '
-root['/entry/data/data'].attrs['EX_doc'] = 'Link to data in /NXentry/NXinstrument/NXdetector '
+root['/entry/data/polar_angle'].attrs['EX_doc'] = 'NXdetector '
+root['/entry/data/data'].attrs['EX_doc'] = 'NXdetector '
 
 
 # Create the ATTRIBUTES