def writer(self, h5parent, writer, scan, nxclass=None, *args, **kws):
'''Describe how to store this data in an HDF5 NeXus file'''
# consider putting this info under NXsample or NXentry/metadata
if hasattr(scan, 'TEMP_SP'):
write_dataset(h5parent, "TEMP_SP", scan.TEMP_SP, description='temperature set point')
if hasattr(scan, 'DEGC_SP'):
write_dataset(h5parent, "DEGC_SP", scan.DEGC_SP, units='C', description='temperature set point (C)')
def test_makeExternalLink(self):
external = eznx.makeFile('external.h5', creator='eznx', default='entry')
eznx.write_dataset(external, "text", "some text")
root = eznx.makeFile('test.h5', creator='eznx', default='entry')
nxentry = eznx.makeGroup(root, 'entry', 'NXentry', default='data')
eznx.makeExternalLink(root, 'external.h5', "/text", nxentry.name + "/external_text")
# check the external file first
with h5py.File("external.h5", "r") as hp:
root = hp["/"]
self.assertTrue("text" in root)
ds = root["text"]
value = ds[()] # ds.value deprecated in h5py
self.assertEqual(value, [b"some text"])
# check the file with the external link
with h5py.File("test.h5", "r") as hp:
root = hp["/"]
nxentry = root["entry"]
self.assertTrue("external_text" in nxentry)
value = eznx.read_nexus_field(nxentry, "external_text")
self.assertEqual(value, b"some text")
value = eznx.read_nexus_field(nxentry, "external_text", astype=str)
self.assertEqual(value, "some text")
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'):
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'):
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, *args, **kws):
'''Describe how to store this data in an HDF5 NeXus file'''
desc = 'SPEC scan with constant counting time'
write_dataset(h5parent, "counting_basis", desc)
write_dataset(h5parent,
"T",
float(scan.T),
units='s',
description=desc)
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 test_write_dataset_existing(self):
root = eznx.makeFile('test.h5', creator='eznx', default='entry')
nxentry = eznx.makeGroup(root, 'entry', 'NXentry', default='data')
eznx.write_dataset(nxentry, "text", "some text")
eznx.write_dataset(nxentry, "text", "replacement text")
with h5py.File("test.h5", "r") as hp:
root = hp["/"]
nxentry = root["entry"]
self.assertTrue("text" in nxentry)
value = eznx.read_nexus_field(nxentry, "text", astype=str)
self.assertEqual(value, "replacement text")
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, header, nxclass=None, *args, **kws):
'''Describe how to store this data in an HDF5 NeXus file'''
if not hasattr(header, 'positioner_xref'):
header.counter_xref = {} # mnemonic:name
desc = 'cross-reference SPEC positioner mnemonics and names'
comment = 'keys are SPEC positioner mnemonics, values are SPEC positioner names'
if nxclass is None:
nxclass = CONTAINER_CLASS
group = makeGroup(h5parent, "positioner_cross_reference", nxclass,
description=desc, comment=comment)
for key, value in sorted(header.positioner_xref.items()):
write_dataset(group, key, value)
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'''
# consider putting this info under NXsample or NXentry/metadata
if hasattr(scan, 'TEMP_SP'):
write_dataset(h5parent,
"TEMP_SP",
scan.TEMP_SP,
description='temperature set point')
if hasattr(scan, 'DEGC_SP'):
write_dataset(h5parent,
"DEGC_SP",
scan.DEGC_SP,
units='C',
description='temperature set point (C)')
def writer(self, h5parent, writer, header, nxclass=None, *args, **kws):
'''Describe how to store this data in an HDF5 NeXus file'''
if not hasattr(header, 'positioner_xref'):
header.counter_xref = {} # mnemonic:name
desc = 'cross-reference SPEC positioner mnemonics and names'
comment = 'keys are SPEC positioner mnemonics, values are SPEC positioner names'
if nxclass is None:
nxclass = CONTAINER_CLASS
group = makeGroup(h5parent,
"positioner_cross_reference",
nxclass,
description=desc,
comment=comment)
for key, value in sorted(header.positioner_xref.items()):
write_dataset(group, key, value)
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 test_read_nexus_field_alternatives(self):
root = eznx.makeFile('test.h5', creator='eznx', default='entry')
nxentry = eznx.makeGroup(root, 'entry', 'NXentry', default='data')
eznx.write_dataset(nxentry, "text", "some text")
eznx.write_dataset(nxentry, "number", 42)
eznx.write_dataset(nxentry, "array", [[1,2,3], [4,5,6]])
# check the file with the external link
with h5py.File("test.h5", "r") as hp:
root = hp["/"]
nxentry = root["entry"]
value = eznx.read_nexus_field(nxentry, "key_error")
self.assertEqual(value, None)
value = eznx.read_nexus_field(nxentry, "text")
self.assertEqual(value, b"some text")
value = eznx.read_nexus_field(nxentry, "text", astype=str)
self.assertEqual(value, "some text")
value = eznx.read_nexus_field(nxentry, "number")
self.assertEqual(value, 42)
value = eznx.read_nexus_field(nxentry, "number", astype=float)
self.assertEqual(value, 42)
value = eznx.read_nexus_field(nxentry, "number", astype=str)
self.assertEqual(value, "42")
ds = nxentry["array"]
value = ds[()] # ds.value deprecated in h5py
expected = numpy.array([[1,2,3], [4,5,6]])
self.assertTrue((value == expected).any())
with self.assertRaises(RuntimeError) as context:
value = eznx.read_nexus_field(nxentry, "array")
received = str(context.exception)
expected = "unexpected 2-D data"
self.assertTrue(received.startswith(expected))
def writer(self, h5parent, writer, scan, *args, **kws):
'''Describe how to store this data in an HDF5 NeXus file'''
desc = 'SPEC scan with constant counting time'
write_dataset(h5parent, "counting_basis", desc)
write_dataset(h5parent, "T", float(scan.T), units='s', description = desc)
def writer(self, h5parent, writer, scan, *args, **kws):
'''Describe how to store this data in an HDF5 NeXus file'''
desc = 'hkl at start of scan'
write_dataset(h5parent, "Q", scan.Q, description = desc)
def writer(self, h5parent, writer, scan, *args, **kws):
'''Describe how to store this data in an HDF5 NeXus file'''
desc = 'hkl at start of scan'
write_dataset(h5parent, "Q", scan.Q, description=desc)
def writer(self, h5parent, writer, scan, *args, **kws):
'''Describe how to store this data in an HDF5 NeXus file'''
write_dataset(h5parent, "comments", '\n'.join(map(str, scan.comments)))
def writer(self, h5parent, writer, scan, *args, **kws):
'''Describe how to store this data in an HDF5 NeXus file'''
write_dataset(h5parent, "date", iso8601(scan.date) )
def writer(self, h5parent, writer, scan, *args, **kws):
'''Describe how to store this data in an HDF5 NeXus file'''
write_dataset(h5parent, "date", iso8601(scan.date))
root = eznx.makeFile(TARGET_FILE, default='entry') nxentry = eznx.makeGroup(root, 'entry', 'NXentry', default='data') nxdata = eznx.makeGroup(nxentry, 'data', 'NXdata', signal='frames', ) nxinstrument = eznx.makeGroup(nxentry, 'instrument', 'NXinstrument') nxdetector = eznx.makeGroup(nxinstrument, 'detector', 'NXdetector') nxsource = eznx.makeGroup(nxinstrument, 'source', 'NXsource') nxmonochromator = eznx.makeGroup(nxinstrument, 'monochromator', 'NXmonochromator') nxcollimator = eznx.makeGroup(nxinstrument, 'collimator', 'NXcollimator') nxgeometry_slit = eznx.makeGroup(nxcollimator, 'geometry', 'NXgeometry') nxshape_slit = eznx.makeGroup(nxgeometry_slit, 'shape', 'NXshape') nxsample = eznx.makeGroup(nxinstrument, 'sample', 'NXsample') nxmonitor = eznx.makeGroup(nxinstrument, 'control', 'NXmonitor') # various metadata eznx.addAttributes(root, creator=h5.attrs['creator'] + ' and spec2nexus.eznx') eznx.write_dataset(nxentry, 'title', 'NeXus NXsas example') eznx.write_dataset(nxentry, 'definition', 'NXsas', URL='http://download.nexusformat.org/doc/html/classes/applications/NXsas.html') eznx.write_dataset(nxentry, 'start_time', h5_files[0].attrs['file_time']) eznx.write_dataset(nxentry, 'end_time', h5_files[-1].attrs['file_time']) eznx.write_dataset(nxdetector, 'frame_files', '\n'.join(names)) eznx.write_dataset(nxinstrument, 'name', 'APS 9-ID-C USAXS pinSAXS') eznx.write_dataset(nxsource, 'type', 'Synchrotron X-ray Source') eznx.write_dataset(nxsource, 'name', 'Advanced Photon Source Undulator A, sector 9ID-C') eznx.write_dataset(nxsource, 'probe', 'x-ray') eznx.write_dataset(nxsource, 'current', h5['/entry/EPICS_PV_metadata/SRcurrent'], units='mA') eznx.write_dataset(nxsource, 'energy', float(7), units='GeV') eznx.write_dataset(nxmonochromator, 'energy', h5['/entry/instrument/monochromator/energy'], units='keV') eznx.write_dataset(nxmonochromator, 'wavelength', h5['/entry/EPICS_PV_metadata/wavelength'], units='Angstroms') eznx.write_dataset(nxmonochromator, 'wavelength_spread', h5['/entry/EPICS_PV_metadata/wavelength_spread'], units='Angstroms/Angstroms') eznx.write_dataset(nxshape_slit, 'shape', 'nxbox') # next four are not defined in the NXsas specification
def writer(self, h5parent, writer, scan, *args, **kws):
'''Describe how to store this data in an HDF5 NeXus file'''
write_dataset(h5parent, "comments", '\n'.join(map(str, scan.comments)))
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
def test_example(self):
root = eznx.makeFile('test.h5', creator='eznx', default='entry')
nxentry = eznx.makeGroup(root, 'entry', 'NXentry', default='data')
ds = eznx.write_dataset(nxentry, 'title', 'simple test data')
nxdata = eznx.makeGroup(nxentry, 'data', 'NXdata', signal='counts', axes='tth', tth_indices=0)
ds = eznx.write_dataset(nxdata, 'tth', [10.0, 10.1, 10.2, 10.3], units='degrees')
ds = eznx.write_dataset(nxdata, 'counts', [1, 50, 1000, 5], units='counts', axes="tth")
root.close()
"""
Test the data file for this structure::
test.h5:NeXus data file
@creator = eznx
@default = 'entry'
entry:NXentry
@NX_class = NXentry
@default = 'data'
title:NX_CHAR = simple test data
data:NXdata
@NX_class = NXdata
@signal = 'counts'
@axes = 'tth'
@axes_indices = 0
counts:NX_INT64[4] = [1, 50, 1000, 5]
@units = counts
@axes = tth
tth:NX_FLOAT64[4] = [10.0, 10.1, 10.199999999999999, 10.300000000000001]
@units = degrees
"""
self.assertTrue(os.path.exists("test.h5"))
with h5py.File("test.h5", "r") as hp:
root = hp["/"]
self.assertEqual(root.attrs.get("creator"), "eznx")
self.assertEqual(root.attrs.get("default"), "entry")
nxentry = root["entry"]
self.assertEqual(nxentry.attrs.get("NX_class"), "NXentry")
self.assertEqual(nxentry.attrs.get("default"), "data")
self.assertEqual(
eznx.read_nexus_field(nxentry, "title").decode('utf8'),
"simple test data")
nxdata = nxentry["data"]
self.assertEqual(nxdata.attrs.get("NX_class"), "NXdata")
self.assertEqual(nxdata.attrs.get("signal"), "counts")
self.assertEqual(nxdata.attrs.get("axes"), "tth")
self.assertEqual(nxdata.attrs.get("tth_indices"), 0)
# test the HDF5 structure
counts = nxdata["counts"]
self.assertEqual(counts.attrs.get("units"), "counts")
self.assertEqual(counts.attrs.get("axes"), "tth")
tth = nxdata["tth"]
self.assertEqual(tth.attrs.get("units"), "degrees")
# test the data
fields = eznx.read_nexus_group_fields(nxentry, "data", "counts tth".split())
counts = fields["counts"]
self.assertEqual(len(counts), 4)
self.assertEqual(counts[2], [1, 50, 1000, 5][2])
tth = fields["tth"]
self.assertEqual(len(tth), 4)
self.assertEqual(tth[2], [10.0, 10.1, 10.2, 10.3][2])
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
signal='frames',
)
nxinstrument = eznx.makeGroup(nxentry, 'instrument', 'NXinstrument')
nxdetector = eznx.makeGroup(nxinstrument, 'detector', 'NXdetector')
nxsource = eznx.makeGroup(nxinstrument, 'source', 'NXsource')
nxmonochromator = eznx.makeGroup(nxinstrument, 'monochromator',
'NXmonochromator')
nxcollimator = eznx.makeGroup(nxinstrument, 'collimator', 'NXcollimator')
nxgeometry_slit = eznx.makeGroup(nxcollimator, 'geometry', 'NXgeometry')
nxshape_slit = eznx.makeGroup(nxgeometry_slit, 'shape', 'NXshape')
nxsample = eznx.makeGroup(nxinstrument, 'sample', 'NXsample')
nxmonitor = eznx.makeGroup(nxinstrument, 'control', 'NXmonitor')
# various metadata
eznx.addAttributes(root, creator=h5.attrs['creator'] + ' and spec2nexus.eznx')
eznx.write_dataset(nxentry, 'title', 'NeXus NXsas example')
eznx.write_dataset(
nxentry,
'definition',
'NXsas',
URL=
'http://download.nexusformat.org/doc/html/classes/applications/NXsas.html')
eznx.write_dataset(nxentry, 'start_time', h5_files[0].attrs['file_time'])
eznx.write_dataset(nxentry, 'end_time', h5_files[-1].attrs['file_time'])
eznx.write_dataset(nxdetector, 'frame_files', '\n'.join(names))
eznx.write_dataset(nxinstrument, 'name', 'APS 9-ID-C USAXS pinSAXS')
eznx.write_dataset(nxsource, 'type', 'Synchrotron X-ray Source')
eznx.write_dataset(nxsource, 'name',
'Advanced Photon Source Undulator A, sector 9ID-C')
eznx.write_dataset(nxsource, 'probe', 'x-ray')
eznx.write_dataset(nxsource,