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Update unit references to use NXdata for datasets, include optional a… #307

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Merged
briantoby merged 1 commit into from
Feb 16, 2026
Merged

Update unit references to use NXdata for datasets, include optional a… #307

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46 changes: 36 additions & 10 deletions GSASII/imports/G2pwd_HDF5.py
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Original file line number Diff line number Diff line change
Expand Up @@ -54,7 +54,8 @@ def ContentsValidator(self, filename):
if definition == 'NXazint1d':
fileItems = {
'I':('NXdata','I'),
'unit':('NXparameters','unit'),
'unit':('NXdata','radial_axis','units'),
# 'unit':('NXparameters','unit'),
}
buffer = {}
if not self.readInNeXus(filename,buffer,fileItems,'NXazint1d-validate'):
Expand All @@ -67,7 +68,7 @@ def ContentsValidator(self, filename):
if definition == 'NXazint2d':
fileItems = {
'I':('NXdata','I'),
'unit':('NXparameters','unit'),
'unit':('NXdata','radial_axis','units'),
'azimuthal_axis':('NXdata','azimuthal_axis'),
}
buffer = {}
Expand Down Expand Up @@ -176,6 +177,7 @@ def readNXazint1d(self, filename, fpbuffer={}, entry=None):

see https://nxazint-hdf5-nexus-3229ecbd09ba8a773fbbd8beb72cace6216dfd5063e1.gitlab-pages.esrf.fr/classes/contributed_definitions/NXazint1d.html
'''
# key: (NeXus section, dataset name, optional attribute name)
fileItems = {
# arrays
'radial_axis':('NXdata','radial_axis'),
Expand All @@ -186,9 +188,13 @@ def readNXazint1d(self, filename, fpbuffer={}, entry=None):
'polarization_factor':('NXparameters','polarization_factor'),
# strings
'instrument/name':('NXinstrument','name'),
'unit':('NXparameters','unit'),
'unit':('NXdata','radial_axis','units'),
# 'unit':('NXparameters','unit'),
'sample/name':('NXsample','name'),
'source/name':('NXsource','name'),
# bools
'polarization_applied':('NXentry', 'polarization_applied'),

}
# test if we have what we need in the buffer and if not read it in
if not self.readInNeXus(filename,fpbuffer,fileItems,'NXazint1d',entry): return False
Expand All @@ -207,6 +213,10 @@ def readNXazint1d(self, filename, fpbuffer={}, entry=None):
self.powderentry[2] = self.blknum # bank number
self.idstring = f'#{self.blknum} {os.path.split(filename)[1][:60]}'
self.instdict['wave'] = fpbuffer['wavelength']
# if the data are already corrected for polarization, set the polarization factor
# to 0.5 (unpolarized)
if fpbuffer['polarization_applied']:
self.instdict['Polariz.'] = [0.5,0.5,False]
# if not, are there more [selected] images that after this to be read?
self.repeat = False
if self.blknum < self.numbanks-1:
Expand All @@ -232,6 +242,7 @@ def readNXazint2d(self, filename, fpbuffer={}, entry=None):
see https://nxazint-hdf5-nexus-3229ecbd09ba8a773fbbd8beb72cace6216dfd5063e1.gitlab-pages.esrf.fr/classes/contributed_definitions/NXazint2d.html
'''
self.comments = []
# key: (NeXus section, dataset name, optional attribute name)
fileItems = {
# arrays
'radial_axis':('NXdata','radial_axis'),
Expand All @@ -243,15 +254,19 @@ def readNXazint2d(self, filename, fpbuffer={}, entry=None):
'polarization_factor':('NXparameters','polarization_factor'),
# strings
'instrument/name':('NXinstrument','name'),
'unit':('NXparameters','unit'),
'azimuth_bins':('NXparameters','azimuth_bins'),
# 'azimuth_bins':('NXparameters','azimuth_bins'),
'sample/name':('NXsample','name'),
'source/name':('NXsource','name'),
# bools
'polarization_applied':('NXentry', 'polarization_applied'),
# from attributes
'unit':('NXdata','radial_axis','units'),
}
# test if we have what we need in the buffer and if not read it in
if not self.readInNeXus(filename,fpbuffer,fileItems,'NXazint2d',entry): return False
# now pull the selected dataset from the buffer
self.numazimuth = fpbuffer['azimuth_bins']
self.numazimuth = fpbuffer['azimuthal_axis'].size
# self.numazimuth = fpbuffer['azimuth_bins']
self.numbanks = self.numparams * self.numazimuth
# group by parametric variable
numScan = self.blknum // self.numazimuth
Expand All @@ -271,6 +286,10 @@ def readNXazint2d(self, filename, fpbuffer={}, entry=None):
self.powderentry[2] = self.blknum # bank number
self.idstring = f'#{numScan} Azm={self.Sample["Azimuth"]} {os.path.split(filename)[1][:60]}'
self.instdict['wave'] = fpbuffer['wavelength']
# if the data are already corrected for polarization, set the polarization factor
# to 0.5 (unpolarized)
if fpbuffer['polarization_applied']:
self.instdict['Polariz.'] = [0.5,0.5,False]
# if not, are there more [selected] images that after this to be read?
self.repeat = False
if self.blknum < self.numbanks-1:
Expand Down Expand Up @@ -318,11 +337,18 @@ def readInNeXus(self,filename,fpbuffer,fileItems,fmt,entry=None):
if nexusDict[loc[0]] is None:
fpbuffer[k] = None
continue
key = '/'.join((nexusDict[loc[0]],)+loc[1:])
key = '/'.join((nexusDict[loc[0]],)+loc[1:2])
savedKeys.append(key)
if key not in fp:
fpbuffer[k] = None
continue
# check if the value should be read from a dataset attribute rather
# than the dataset itself
if len(loc) > 2: # attribute
val = fp[key].attrs[loc[2]]
val = val.decode() if isinstance(val, bytes) else val
fpbuffer[k] = val
continue
val = fp[key]
if val.shape:
fpbuffer[k] = np.array(val)
Expand All @@ -332,9 +358,9 @@ def readInNeXus(self,filename,fpbuffer,fileItems,fmt,entry=None):
elif 'int' in str(val.dtype):
fpbuffer[k] = int(val[()])
else:
fpbuffer[k] = val[()].decode()
fpbuffer[k] = val[()].decode() if isinstance(val[()], bytes) else val[()]
self.comments.append(f'{k}={fpbuffer[k]}')
if fpbuffer['unit'] != '2th':
if fpbuffer['unit'] not in ['degrees','deg','2th', '2theta']:
print(f'{fmt} HDF5 file has units',fpbuffer['unit'])
self.errors = f'{fmt} only can be read with 2theta units'
return False
Expand Down Expand Up @@ -379,7 +405,7 @@ def readInNeXus(self,filename,fpbuffer,fileItems,fmt,entry=None):
else:
self.blknum = min(self.selections)
return True

def FillInParametics(self,fpbuffer,count):
'''put changing parametric variables into the top of the comments
'''
Expand Down