def writer(self, h5parent, writer, scan, nxclass=None, *args, **kws):
'''Describe how to store this data in an HDF5 NeXus file'''
if hasattr(scan, 'MCA'):
if hasattr(scan.MCA, 'ROI'):
mca_group = openGroup(h5parent, 'MCA', nxclass, description='MCA metadata')
roi_group = openGroup(mca_group, 'ROI', nxclass, description='Regions Of Interest')
roi_dict = scan.MCA['ROI']
for key, roi in roi_dict.items():
dataset = [roi['first_chan'], roi['last_chan']]
desc = 'first_chan, last_chan'
write_dataset(roi_group, key, dataset, description=desc, units='channel')
def writer(self, h5parent, writer, scan, nxclass=None, *args, **kws):
'''Describe how to store this data in an HDF5 NeXus file'''
if hasattr(scan, 'MCA'):
mca_group = openGroup(h5parent, 'MCA', nxclass, description='MCA metadata')
mca = scan.MCA
for key in ('preset_time elapsed_live_time elapsed_real_time'.split()):
if key in mca:
write_dataset(mca_group, key, mca[key], units='s')
def writer(self, h5parent, writer, scan, nxclass=None, *args, **kws):
'''Describe how to store this data in an HDF5 NeXus file'''
if hasattr(scan, 'MCA'):
mca_group = openGroup(h5parent, 'MCA', nxclass, description='MCA metadata')
mca = scan.MCA
for key in ('number_saved first_saved last_saved reduction_coef'.split()):
if key in mca:
write_dataset(mca_group, key, mca[key])
def writer(self, h5parent, writer, scan, nxclass=None, *args, **kws):
'''Describe how to store this data in an HDF5 NeXus file'''
if hasattr(scan, 'MCA'):
if 'CALIB' in scan.MCA:
mca_group = openGroup(h5parent, 'MCA', nxclass, description='MCA metadata')
calib_dict = scan.MCA['CALIB']
for key in ('a b c'.split()):
if key in calib_dict:
write_dataset(mca_group, 'calib_' + key, calib_dict[key])
def writer(self, h5parent, writer, scan, nxclass=None, *args, **kws):
'''Describe how to store this data in an HDF5 NeXus file'''
if hasattr(scan, 'MCA'):
mca_group = openGroup(h5parent,
'MCA',
nxclass,
description='MCA metadata')
mca = scan.MCA
for key in ('preset_time elapsed_live_time elapsed_real_time'.
split()):
if key in mca:
write_dataset(mca_group, key, mca[key], units='s')
def writer(self, h5parent, writer, scan, nxclass=None, *args, **kws):
'''Describe how to store this data in an HDF5 NeXus file'''
if hasattr(scan, 'MCA'):
mca_group = openGroup(h5parent,
'MCA',
nxclass,
description='MCA metadata')
mca = scan.MCA
for key in ('number_saved first_saved last_saved reduction_coef'
.split()):
if key in mca:
write_dataset(mca_group, key, mca[key])
def writer(self, h5parent, writer, scan, nxclass=None, *args, **kws):
'''Describe how to store this data in an HDF5 NeXus file'''
if hasattr(scan, 'MCA'):
if hasattr(scan.MCA, 'ROI'):
mca_group = openGroup(h5parent,
'MCA',
nxclass,
description='MCA metadata')
roi_group = openGroup(mca_group,
'ROI',
nxclass,
description='Regions Of Interest')
roi_dict = scan.MCA['ROI']
for key, roi in roi_dict.items():
dataset = [roi['first_chan'], roi['last_chan']]
desc = 'first_chan, last_chan'
write_dataset(roi_group,
key,
dataset,
description=desc,
units='channel')
def writer(self, h5parent, writer, scan, nxclass=None, *args, **kws):
'''Describe how to store this data in an HDF5 NeXus file'''
if hasattr(scan, 'MCA'):
if 'CALIB' in scan.MCA:
mca_group = openGroup(h5parent,
'MCA',
nxclass,
description='MCA metadata')
calib_dict = scan.MCA['CALIB']
for key in ('a b c'.split()):
if key in calib_dict:
write_dataset(mca_group, 'calib_' + key,
calib_dict[key])
def save(self, hfile=None, key=None):
'''
save the reduced data group to an HDF5 file, return filename or None if not written
:param str hfile: output HDF5 file name (default: input HDF5 file)
:param str key: name of reduced data set (default: nothing will be saved)
By default, save to the input HDF5 file.
To override this, specify the output HDF5 file name when calling this method.
* If the file exists, this will not overwrite any input data.
* Full, reduced :math:`R(Q)` goes into NXdata group::
/entry/flyScan_reduced_full
* any previous full reduced :math:`R(Q)` will be replaced.
* It may replace the rebinned, reduced :math:`R(Q)`
if a NXdata group of the same number of bins exists.
* Rebinned, reduced :math:`R(Q)` goes into NXdata group::
/entry/flyScan_reduced_<N>
where ``<N>`` is the number of bins, such as (for 500 bins)::
/entry/flyScan_reduced_500
:see: http://download.nexusformat.org/doc/html/classes/base_classes/NXentry.html
:see: http://download.nexusformat.org/doc/html/classes/base_classes/NXdata.html
'''
# TODO: save with NXprocess/NXdata structure
# TODO: link that NXdata up to NXentry level
# TODO: change /NXentry@default to point to best NXdata reduced
# TODO: What about NXcanSAS?
key = str(key)
if key not in self.reduced:
return
nxname = 'flyScan_reduced_' + key
hfile = hfile or self.hdf5_file_name
ds = self.reduced[key]
with h5py.File(hfile, 'a') as hdf:
if 'default' not in hdf.attrs:
hdf.attrs['default'] = 'entry'
nxentry = eznx.openGroup(hdf, 'entry', 'NXentry')
if 'default' not in nxentry.attrs:
nxentry.attrs['default'] = nxname
nxdata = eznx.openGroup(
nxentry,
nxname,
'NXdata',
signal='R',
axes='Q',
Q_indices=0,
timestamp=calc.iso8601_datetime(),
)
for key in sorted(ds.keys()):
try:
_ds = eznx.write_dataset(nxdata, key, ds[key])
if key in self.units:
eznx.addAttributes(_ds, units=self.units[key])
except RuntimeError as e:
pass # TODO: reporting
return hfile
def save(self, hfile = None, key = None):
'''
save the reduced data group to an HDF5 file, return filename or None if not written
:param str hfile: output HDF5 file name (default: input HDF5 file)
:param str key: name of reduced data set (default: nothing will be saved)
By default, save to the input HDF5 file.
To override this, specify the output HDF5 file name when calling this method.
* If the file exists, this will not overwrite any input data.
* Full, reduced :math:`R(Q)` goes into NXdata group::
/entry/areaDetector_reduced_full
* any previous full reduced :math:`R(Q)` will be replaced.
* It may replace the rebinned, reduced :math:`R(Q)`
if a NXdata group of the same number of bins exists.
* Rebinned, reduced :math:`R(Q)` goes into NXdata group::
/entry/areaDetector_reduced_<N>
where ``<N>`` is the number of bins, such as (for 500 bins)::
/entry/areaDetector_reduced_500
:see: http://download.nexusformat.org/doc/html/classes/base_classes/NXentry.html
:see: http://download.nexusformat.org/doc/html/classes/base_classes/NXdata.html
'''
key = str(key)
if key not in self.reduced:
return
nxname = 'areaDetector_reduced_' + key
hfile = hfile or self.hdf5_file_name
ds = self.reduced[key]
try:
hdf = h5py.File(hfile, 'a')
except IOError as _exc:
# FIXME: some h5py problem in <h5py>/_hl/files.py, line 101
# this fails: fid = h5f.open(name, h5f.ACC_RDWR, fapl=fapl)
# with IOError that is improperly caught on next and then:
# fid = h5f.create(name, h5f.ACC_EXCL, fapl=fapl, fcpl=fcpl) fails with IOError
# since the second call has "name" with all lower case
#
# real problem is that these HDF5 files have the wrong uid/gid, as set by the Pilatus computer
# TODO: fix each Pilatus and this problem will go away
# TODO: change uid/gid on all the acquired HDF5 files (*.h5, *.hdf) under usaxscontrol:/share1/USAXS_data/2*
# Files should be owned by usaxs:usaxs (1810:2026), but are owned by tomo2:usaxs (500:2026) as seen by usaxs@usaxscontrol
# not enough to change the "umask" on the det@dec1122 computer, what else will fix this?
pvwatch.logMessage( "Problem writing reduced data back to file: " + hfile )
return
if 'default' not in hdf.attrs:
hdf.attrs['default'] = 'entry'
nxentry = eznx.openGroup(hdf, 'entry', 'NXentry')
if 'default' not in nxentry.attrs:
nxentry.attrs['default'] = nxname
nxdata = eznx.openGroup(nxentry,
nxname,
'NXdata',
signal='R',
axes='Q',
Q_indices=0,
timestamp=calc.iso8601_datetime(),
)
for key in sorted(ds.keys()):
try:
_ds = eznx.write_dataset(nxdata, key, ds[key])
if key in self.units:
eznx.addAttributes(_ds, units=self.units[key])
except RuntimeError as e:
pass # TODO: reporting
hdf.close()
return hfile
