# end of user parameters #
##########################
#################################################
# Initialize paths, detector, setup and logfile #
#################################################
kwargs = dict() # create dictionnary
try:
kwargs['is_series'] = is_series
except NameError: # is_series not declared
pass
detector = exp.Detector(name=detector, datadir='', template_imagefile=template_imagefile, binning=pre_binning, **kwargs)
setup = exp.SetupPreprocessing(beamline=beamline, rocking_angle=rocking_angle, distance=sdd, energy=energy,
beam_direction=beam_direction, sample_inplane=sample_inplane,
sample_outofplane=sample_outofplane,
offset_inplane=0) # no need to worry about offsets, work relatively to the Bragg peak
print('\nScan', scan)
print('Setup: ', setup.beamline)
print('Detector: ', detector.name)
print('Pixel sizes after pre_binning (vertical, horizontal): ', detector.pixelsize_y, detector.pixelsize_x, '(m)')
print('Scan type: ', setup.rocking_angle)
print('Sample to detector distance: ', setup.distance, 'm')
print('Energy:', setup.energy, 'ev')
if simulation:
detector.datadir = root_folder
detector.savedir = root_folder
else:
if setup.beamline != 'P10':
except NameError: # nb_pixel_y not declared
pass
try:
kwargs['is_series'] = is_series
except NameError: # is_series not declared
pass
detector = exp.Detector(name=detector, datadir='', template_imagefile=template_imagefile, roi=roi_detector,
binning=binning, **kwargs)
####################
# Initialize setup #
####################
setup = exp.SetupPreprocessing(beamline=beamline, energy=energy, rocking_angle=rocking_angle, distance=sdd,
beam_direction=beam_direction, sample_inplane=sample_inplane,
sample_outofplane=sample_outofplane, offset_inplane=offset_inplane,
custom_scan=custom_scan, custom_images=custom_images, sample_offsets=sample_offsets,
custom_monitor=custom_monitor, custom_motors=custom_motors)
#############################################
# Initialize geometry for orthogonalization #
#############################################
if rocking_angle == "energy":
use_rawdata = False # you need to interpolate the data in QxQyQz for energy scans
print("Energy scan: defaulting use_rawdata to False, the data will be interpolated using xrayutilities")
if not use_rawdata:
qconv, offsets = pru.init_qconversion(setup)
detector.offsets = offsets
hxrd = xu.experiment.HXRD(sample_inplane, sample_outofplane, qconv=qconv) # x downstream, y outboard, z vertical
# first two arguments in HXRD are the inplane reference direction along the beam and surface normal of the sample
cch1 = cch1 - detector.roi[0] # take into account the roi if the image is cropped
#######################
# Initialize detector #
#######################
detector = exp.Detector(name=detector,
datadir='',
template_imagefile=template_imagefile,
roi=roi_detector)
####################
# Initialize setup #
####################
setup = exp.SetupPreprocessing(beamline=beamline,
energy=energy,
rocking_angle=rocking_angle,
distance=sdd,
beam_direction=beam_direction,
sample_inplane=sample_inplane,
sample_outofplane=sample_outofplane,
offset_inplane=offset_inplane)
#############################################
# Initialize geometry for orthogonalization #
#############################################
qconv, offsets = pru.init_qconversion(setup)
detector.offsets = offsets
hxrd = xrayutilities.experiment.HXRD(
sample_inplane, sample_outofplane,
qconv=qconv) # x downstream, y outboard, z vertical
# first two arguments in HXRD are the inplane reference direction along the beam and surface normal of the sample
cch1 = cch1 - detector.roi[
0] # take into account the roi if the image is cropped
plt.ion()
#######################
# Initialize detector #
#######################
detector = exp.Detector(name=detector,
datadir='',
template_imagefile=template_imagefile,
roi=roi_detector)
####################
# Initialize setup #
####################
setup_pre = exp.SetupPreprocessing(beamline=beamline,
rocking_angle=rocking_angle,
distance=sdd,
energy=energy,
beam_direction=beam_direction)
if setup_pre.beamline != 'P10':
homedir = root_folder + sample_name + str(scan) + '/'
detector.datadir = homedir + "data/"
else:
specfile_name = specfile_name % scan
homedir = root_folder + specfile_name + '/'
detector.datadir = homedir + 'e4m/'
template_imagefile = specfile_name + template_imagefile
detector.template_imagefile = template_imagefile
print('\nScan', scan)
print('Setup: ', setup_pre.beamline)
detector = exp.Detector(name=detector,
datadir='',
template_imagefile=template_imagefile,
roi=roi_detector)
####################
# Initialize setup #
####################
setup = exp.SetupPreprocessing(beamline=beamline,
energy=energy,
rocking_angle=rocking_angle,
distance=sdd,
beam_direction=beam_direction,
sample_inplane=sample_inplane,
sample_outofplane=sample_outofplane,
sample_offsets=(offset_chi, offset_phi,
offset_eta),
offset_inplane=offset_inplane,
custom_scan=custom_scan,
custom_images=custom_images,
custom_monitor=custom_monitor,
custom_motors=custom_motors,
filtered_data=filtered_data,
is_orthogonal=is_orthogonal)
#############################################
# Initialize geometry for orthogonalization #
#############################################
qconv, offsets = pru.init_qconversion(setup)
detector.offsets = offsets
hxrd = xu.experiment.HXRD(sample_inplane, sample_outofplane,
qconv=qconv) # x downstream, y outboard, z vertical
pass
detector = exp.Detector(name=detector,
datadir='',
template_imagefile=template_imagefile,
roi=roi_detector,
sum_roi=normalize_roi,
binning=binning,
**kwargs)
####################
# Initialize setup #
####################
setup = exp.SetupPreprocessing(beamline=beamline,
energy=energy,
rocking_angle=rocking_angle,
distance=sdd,
direct_beam=direct_beam)
############################################
# Initialize values for callback functions #
############################################
flag_mask = False
flag_aliens = False
plt.rcParams["keymap.quit"] = [
"ctrl+w", "cmd+w"
] # this one to avoid that q closes window (matplotlib default)
############################
# start looping over scans #
############################
my_cmap = colormap.cmap
plt.ion()
#################################################
# initialize detector, setup, paths and logfile #
#################################################
kwargs = dict() # create dictionnary
kwargs['is_series'] = is_series
detector = exp.Detector(name=detector,
datadir='',
template_imagefile=template_imagefile,
sum_roi=sum_roi,
binning=[1, binning[0], binning[1]],
**kwargs)
setup = exp.SetupPreprocessing(beamline=beamline)
if setup.beamline == 'P10':
specfile_name = sample_name + '_{:05d}'.format(scan)
homedir = root_folder + specfile_name + '/'
detector.datadir = homedir + 'e4m/'
template_imagefile = specfile_name + template_imagefile
detector.template_imagefile = template_imagefile
elif setup.beamline == 'SIXS_2018' or setup.beamline == 'SIXS_2019':
homedir = root_folder
detector.datadir = homedir + "align/"
else:
homedir = root_folder + sample_name + str(scan) + '/'
detector.datadir = homedir + "data/"
if savedir == '':
bad_color = '1.0' # white background
colormap = gu.Colormap(bad_color=bad_color)
my_cmap = colormap.cmap
plt.ion()
#################################################
# Initialize detector, setup, paths and logfile #
#################################################
detector = exp.Detector(name=detector,
datadir='',
template_imagefile=template_imagefile,
is_series=is_series)
setup = exp.SetupPreprocessing(beamline=beamline,
rocking_angle=rocking_angle,
custom_scan=custom_scan,
custom_images=custom_images,
custom_monitor=custom_monitor,
custom_motors=custom_motors)
if setup.beamline == 'P10':
specfile_name = specfile_name % scan
homedir = root_folder + specfile_name + '/'
detector.datadir = homedir + 'e4m/'
template_imagefile = specfile_name + template_imagefile
detector.template_imagefile = template_imagefile
elif setup.beamline == 'SIXS_2018' or setup.beamline == 'SIXS_2019':
homedir = root_folder
detector.datadir = homedir + "align/"
else:
homedir = root_folder + sample_name + str(scan) + '/'
detector.datadir = homedir + "data/"
# Initialize detector #
#######################
detector = exp.Detector(name=detector,
datadir='',
template_imagefile=template_imagefile,
roi=roi_detector,
is_series=is_series)
####################
# Initialize setup #
####################
setup_pre = exp.SetupPreprocessing(beamline=beamline,
rocking_angle=rocking_angle,
distance=sdd,
energy=energy,
beam_direction=beam_direction,
custom_scan=custom_scan,
custom_images=custom_images,
custom_monitor=custom_monitor,
custom_motors=custom_motors)
if setup_pre.beamline != 'P10':
homedir = root_folder + sample_name + str(scan) + '/'
detector.datadir = homedir + "data/"
else:
specfile_name = specfile_name % scan
homedir = root_folder + specfile_name + '/'
detector.datadir = homedir + 'e4m/'
template_imagefile = specfile_name + template_imagefile
detector.template_imagefile = template_imagefile