def command_line_interface():
'''standard command-line interface'''
cmd_args = get_user_options()
if len(cmd_args.output_file) > 0:
output_filename = cmd_args.output_file
else:
output_filename = cmd_args.hdf5_file
s_num_bins = str(cmd_args.num_bins)
needs_calc = {}
pvwatch.logMessage("Reading USAXS FlyScan data file: " +
cmd_args.hdf5_file)
scan = UsaxsFlyScan(cmd_args.hdf5_file)
# 2015-06-08,prj: no need for archives now
#if cmd_args.no_archive:
# print ' skipping check for archived original file'
#else:
# afile = scan.make_archive()
# if afile is not None:
# print ' archived original file to ' + afile
pvwatch.logMessage(' checking for previously-saved R(Q)')
scan.read_reduced()
needs_calc['full'] = not scan.has_reduced('full')
if cmd_args.recompute_full:
needs_calc['full'] = True
needs_calc[s_num_bins] = not scan.has_reduced(s_num_bins)
if cmd_args.recompute_rebinned:
needs_calc[s_num_bins] = True
# needs_calc['250'] = True # FIXME: developer only
if needs_calc['full']:
pvwatch.logMessage(' reducing FlyScan to R(Q)')
scan.reduce()
if 'full' not in scan.reduced:
pvwatch.logMessage(
' no reduced R(Q) when checking for previously-saved ' +
output_filename)
return
pvwatch.logMessage(' saving reduced R(Q) to ' + output_filename)
scan.save(cmd_args.hdf5_file, 'full')
needs_calc[s_num_bins] = True
if needs_calc[s_num_bins]:
pvwatch.logMessage(' rebinning R(Q) (from %d) to %d points' %
(scan.reduced['full']['Q'].size, cmd_args.num_bins))
scan.rebin(cmd_args.num_bins)
pvwatch.logMessage(' saving rebinned R(Q) to ' + output_filename)
scan.save(cmd_args.hdf5_file, s_num_bins)
return scan
def reduce_area_detector_data(hdf5_file,
num_bins,
recompute_full=False,
recompute_rebinned=False,
output_filename=None):
'''
reduce areaDetector image data to R(Q)
:param str hdf5_file: name of HDF5 file with AD image data
:param int num_bins: number of bins in rebinned data set
:param bool recompute_full: set True to force recompute,
even if reduced data already in data file (default: False)
:param bool recompute_rebinned: set True to force recompute,
even if reduced data already in data file (default: False)
:param str output_filename: name of file to write reduced data
if None, use hdf5_file (default: None)
'''
needs_calc = {}
pvwatch.logMessage( "Area Detector data file: " + hdf5_file )
scan = AD_ScatteringImage(hdf5_file) # initialize the object
s_num_bins = str(num_bins)
output_filename = output_filename or hdf5_file
pvwatch.logMessage( ' checking for previously-saved R(Q)' )
scan.read_reduced()
needs_calc['full'] = not scan.has_reduced('full')
if recompute_full:
needs_calc['full'] = True
needs_calc[s_num_bins] = not scan.has_reduced(s_num_bins)
if recompute_rebinned:
needs_calc[s_num_bins] = True
if needs_calc['full']:
pvwatch.logMessage(' reducing Area Detector image to R(Q)')
scan.reduce()
pvwatch.logMessage( ' saving reduced R(Q) to ' + output_filename)
scan.save(hdf5_file, 'full')
needs_calc[s_num_bins] = True
if needs_calc[s_num_bins]:
msg = ' rebinning R(Q) (from %d) to %d points'
msg = msg % (scan.reduced['full']['Q'].size, num_bins)
pvwatch.logMessage( msg )
scan.rebin(num_bins)
pvwatch.logMessage( ' saving rebinned R(Q) to ' + output_filename )
scan.save(hdf5_file, s_num_bins)
return scan
scan = reduceFlyData.command_line_interface()
plotfile = os.path.join(
path, 'test_reduceFly__' + os.path.basename(hdf5_file) + '_.png')
plot_mpl.spec_plot(
scan.reduced['full']['Q'],
scan.reduced['full']['R'],
plotfile,
xtitle='Q',
ytitle='R',
ylog=True,
)
plotfile = os.path.join(
path, 'test_reduceFly_USAXS_' + os.path.basename(hdf5_file) + '_.png')
ds_full = plot_mpl.Plottable_USAXS_Dataset()
ds_full.label = 'full data'
ds_full.Q = scan.reduced['full']['Q']
ds_full.I = scan.reduced['full']['R']
ds_250 = plot_mpl.Plottable_USAXS_Dataset()
ds_250.label = 'rebinned (250) data'
ds_250.Q = scan.reduced['250']['Q']
ds_250.I = scan.reduced['250']['R']
pvwatch.logMessage(' plotting to ' + plotfile)
plot_mpl.livedata_plot([ds_full, ds_250], plotfile,
'test: ' + os.path.basename(hdf5_file))
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