source_dir = './merge_images/'
infiles = glob.glob(os.path.join(source_dir, pattern + '.npy'))
infiles.sort()
# Analysis to perform
########################################
load_args = {
'calibration': calibration,
'mask': mask,
}
run_args = {
'verbosity': 3,
}
process = Protocols.ProcessorXS(load_args=load_args, run_args=run_args)
thumb_merged = Protocols.thumbnails(crop=None,
resize=1,
blur=None,
cmap=cmap_vge_hdr,
ztrim=[0.1, 0.002])
thumb_merged.name = 'thumbnails_merged'
q_images_merged = Protocols.q_image(cmap=cmap_vge,
plot_range=[-0.1, 7.0, 0, 5.5],
xticks=[0, 2, 4, 6],
yticks=[0, 2, 4],
plot_buffers=[0.2, 0.05, 0.15, 0.05],
ztrim=[0.3, 0.001])
q_images_merged.name = 'q_images_merged'
infiles = glob.glob(os.path.join(source_dir, pattern + '.tiff'))
infiles.sort()
# Analysis to perform
########################################
load_args = {
'calibration': calibration,
'mask': mask,
}
run_args = {
'verbosity': 3,
}
process = Protocols.ProcessorXS(load_args=load_args, run_args=run_args)
# Examples:
#protocols = [ Protocols.circular_average_q2I(plot_range=[0, 0.2, 0, None]) ]
#protocols = [ Protocols.linecut_angle(q0=0.01687, dq=0.00455*1.5, show_region=False) ]
#protocols = [ Protocols.q_image(blur=1.0, bins_relative=0.5, plot_range=[-0.1, 3.0, 0, 3.0], _xticks=[0, 1.0, 2.0, 3.0], ztrim=[0.2, 0.01]) ]
#protocols = [ Protocols.qr_image(blur=1.0, bins_relative=0.5, plot_range=[-0.1, 3.0, 0, 3.0], _xticks=[0, 1.0, 2.0, 3.0], zmin=1010., ztrim=[None, 0.01]) ]
#protocols = [ Protocols.qr_image(blur=None, bins_relative=0.8, plot_range=[-0.1, 3.0, 0, 3.0], _xticks=[0, 1.0, 2.0, 3.0], ztrim=[0.38, 0.002], dezing_fill=True) ]
#protocols = [ Protocols.q_phi_image(bins_relative=0.25, plot_range=[0, 3.0, 0, +90]) ]
protocols = [
#Protocols.calibration_check(show=False, AgBH=True, q0=1.369*0.25, dq=0.002, num_rings=10, ztrim=[0.2, 0.01], dpi=300) ,
#Protocols.circular_average(ylog=False, plot_range=[0, 3.5, None, None]) ,
Protocols.thumbnails(crop=None,
blur=None,
resize=1.0,
# Analysis to perform
########################################
load_args = {
'calibration': calibration,
'mask': mask,
#'background' : source_dir+'empty*saxs.tiff',
#'transmission_int': '../../data/Transmission_output.csv', # Can also specify an float value.
}
run_args = {
'verbosity': 3,
#'save_results' : ['xml', 'plots', 'txt', 'hdf5'],
}
process = Protocols.ProcessorXS(load_args=load_args, run_args=run_args)
#process.connect_databroker('cms') # Access databroker metadata
patterns = [
['theta', '.+_th(\d+\.\d+)_.+'],
['x_position', '.+_x(-?\d+\.\d+)_.+'],
['y_position', '.+_yy(-?\d+\.\d+)_.+'],
#['anneal_time', '.+_anneal(\d+)_.+'] ,
#['cost', '.+_Cost(\d+\.\d+)_.+'] ,
['annealing_temperature', '.+_T(\d+\.\d\d\d)C_.+'],
#['annealing_time', '.+_(\d+\.\d)s_T.+'] ,
#['annealing_temperature', '.+_localT(\d+\.\d)_.+'] ,
#['annealing_time', '.+_clock(\d+\.\d\d)_.+'] ,
#['o_position', '.+_opos(\d+\.\d+)_.+'] ,
#['l_position', '.+_lpos(\d+\.\d+)_.+'] ,
['exposure_time', '.+_(\d+\.\d+)s_\d+_saxs.+'],
infiles.sort()
# Analysis to perform
########################################
load_args = {
'calibration': calibration,
'mask': mask,
#'rot180' : False,
}
run_args = {
'verbosity': 3,
}
process = Protocols.ProcessorXS(load_args=load_args, run_args=run_args)
protocols = [
#Protocols.export_STL( stl_zscale=150, stl_pedestal=8, blur=1.0, resize=1.0, crop_GI=700, logo_file='logo.png', logo_resize=0.5),
Protocols.export_STL(stl_zscale=150,
stl_pedestal=8,
blur=1.0,
resize=1.0,
crop_beam=[900, 900],
logo_file='logo.png',
logo_resize=0.5),
]
# Run
########################################
print('Processing {} infiles...'.format(len(infiles)))
infiles = glob.glob(os.path.join(source_dir, pattern + '.tiff'))
infiles.sort()
# Analysis to perform
########################################
load_args = {
'calibration': calibration,
'mask': mask,
}
run_args = {
'verbosity': 4,
#'save_results' : ['xml', 'plots', 'txt', 'npz', 'hdf5'],
}
process = Protocols.ProcessorXS(load_args=load_args, run_args=run_args)
# Examples:
#protocols = [ Protocols.q_image(q_max=0.14, blur=2.0, bins_relative=0.25, xticks=[-.1, 0, .1], ztrim=[0.01, 0.001])]
#protocols = [ Protocols.linecut_angle(q0=0.01687, dq=0.00455*1.5, show_region=False) ]
q0, qw = 0.0259, 0.0015
#q0, qw = 0.0313, 0.0008
protocols = [
#Protocols.calibration_check(show=False, AgBH=True, q0=0.010, num_rings=4, ztrim=[0.05, 0.05], ) ,
#Protocols.circular_average(ylog=True, plot_range=[0, 0.12, None, None]) ,
#Protocols.thumbnails(name='thumbnails_hdr_goldish', cmap=cmap_hdr_goldish, blur=None, crop=None, resize=1),
#Protocols.thumbnails(name='thumbnails_jet', crop=None, blur=None, resize=1) ,
#Protocols.thumbnails(crop=None, resize=1.0, blur=None, cmap=cmap_vge, ztrim=[0.01, 0.001]) ,
#Protocols.q_image(blur=None, cmap='jet', plot_range=[-0.05, 0.05, 0, 0.1], ztrim=[0.05, 0.002], colorbar=False, plot_buffers=[0.25, 0.06, 0.2, 0.05], xticks=[-0.04, 0, 0.04]),
Protocols.linecut_qz_fit(
infiles = glob.glob(os.path.join(source_dir, pattern + '.tiff'))
infiles.sort()
# Analysis to perform
########################################
load_args = {
'calibration': calibration,
'mask': mask,
}
run_args = {
'verbosity': 3,
#'save_results' : ['xml', 'plots', 'txt', 'npz', 'hdf5'],
}
process = Protocols.ProcessorXS(load_args=load_args, run_args=run_args)
# Examples:
#protocols = [ Protocols.q_image(q_max=0.14, blur=2.0, bins_relative=0.25, xticks=[-.1, 0, .1], ztrim=[0.01, 0.001])]
#protocols = [ Protocols.linecut_angle(q0=0.01687, dq=0.00455*1.5, show_region=False) ]
protocols = [
#Protocols.HDF5(save_results=['hdf5'])
#Protocols.calibration_check(show=False, AgBH=True, q0=0.010, num_rings=4, ztrim=[0.05, 0.05], ) ,
#Protocols.circular_average(ylog=True, plot_range=[0, 0.15, None, None], show=False) ,
#Protocols.circular_average_q2I_fit(ylog=False, plot_range=[0, 0.15, None, None], show=False, label_filename=False) ,
#Protocols.linecut_angle(q0=0.108, dq=0.005, show_region=False) ,
Protocols.q_image(q_max=0.14,
blur=2.0,
bins_relative=0.25,
xticks=[-.1, 0, .1],
# Analysis to perform
########################################
load_args = {
'calibration': calibration,
'mask': mask,
#'rot180' : False,
#'flip' : True, # PSCCD
}
run_args = {
'verbosity': 3,
#'save_results' : ['xml', 'plots', 'txt', 'hdf5'],
}
process = Protocols.ProcessorXS(load_args=load_args, run_args=run_args)
#process.connect_databroker('cms') # Access databroker metadata
# Examples:
# Protocols.circular_average_q2I(plot_range=[0, 0.2, 0, None])
# Protocols.sector_average(angle=-70, dangle=25, show_region=False)
# Protocols.linecut_q(chi0= 90+70, dq= .5, gridlines=True, label_filename=True, save_results = [ 'hdf5' ] )
# Protocols.linecut_angle(q0=0.01687, dq=0.00455*1.5, show_region=False)
# Protocols.q_image(blur=1.0, bins_relative=0.5, plot_range=[-0.1, 3.0, 0, 3.0], _xticks=[0, 1.0, 2.0, 3.0], ztrim=[0.2, 0.01])
# Protocols.qr_image(blur=1.0, bins_relative=0.5, plot_range=[-0.1, 3.0, 0, 3.0], _xticks=[0, 1.0, 2.0, 3.0], zmin=1010., ztrim=[None, 0.01])
# Protocols.qr_image(blur=None, bins_relative=0.8, plot_range=[-0.1, 3.0, 0, 3.0], _xticks=[0, 1.0, 2.0, 3.0], ztrim=[0.38, 0.002], dezing_fill=True)
# Protocols.qr_image(blur=None, colorbar=True, save_data=False, transparent=False, label_filename=True)
# Protocols.q_phi_image(bins_relative=0.25, plot_range=[0, 3.0, 0, +90])
protocols = [
#Protocols.HDF5(save_results=['hdf5'])
infiles.sort()
#infiles = [infiles[0]]
#infiles = [infiles[-1]]
# Analysis to perform
########################################
load_args = {
'calibration': calibration,
'mask': mask,
}
run_args = {
'verbosity': 3,
}
process = Protocols.ProcessorXS(load_args=load_args, run_args=run_args)
protocols = [
Protocols.calibration_check(show=False, AgBH=True, q0=0.015, num_rings=2)
]
#protocols = [ Protocols.thumbnails(crop=0.8)] # mini
#protocols = [ Protocols.thumbnails(crop=None, resize=1.0, blur=None, file_extension='.png') ] # full-size
#protocols = [ Protocols.thumbnails(crop=None, resize=1.0, blur=None, cmap=cmap_vge, ztrim=[0, 0.001], file_extension='.png') ] # custom
#protocols = [ Protocols.q_image(q_max=0.14, blur=2.0, bins_relative=0.25, xticks=[-.1, 0, .1], ztrim=[0.01, 0.001])]
#protocols = [ Protocols.circular_average(ylog=True, plot_range=[0, 0.2, None, None]) ]
#protocols = [ Protocols.circular_average_q2I(plot_range=[0, 0.2, 0, None]) ]
#protocols = [ circular_average_q2I_fit(plot_range=[0, 0.2, 0, None]) ] # local protocol
calibration = Calibration()
calibration.set_energy(8.8984) # CHX
#calibration.set_image_size(512, 512)
calibration.set_image_size(619, 487)
calibration.set_pixel_size(pixel_size_um=75.0)
calibration.set_distance(0.5944)
calibration.set_beam_position(150.18, 390.59)
mask_dir = './'
mask = Mask()
mask.load(mask_dir + 'mask.png')
load_args = {'calibration': calibration, 'mask': mask}
run_args = {'verbosity': 4}
process = Protocols.ProcessorXS(load_args=load_args, run_args=run_args)
protocols = [main_peak()]
startreg = time.clock()
process.run(infiles, protocols, output_dir=output_dir, force=True)
print('Reg time', time.clock() - startreg)
startpar = time.clock()
Parallel(n_jobs=4, backend='threading')(delayed(
process.run
)(infiles=[infile], protocols=protocols, output_dir=output_dir, force=True)
for infile in infiles)
# Analysis to perform
########################################
load_args = {
'calibration': calibration,
'mask': mask,
'format': 'tiff',
'full_name': True, # Don't truncate at a decimal point
}
run_args = {
'verbosity': 3,
#'save_results' : ['xml', 'plots', 'txt', 'hdf5'],
}
process = Protocols.ProcessorXS(load_args=load_args, run_args=run_args)
# Examples:
#protocols = [ Protocols.q_image(q_max=0.14, blur=2.0, bins_relative=0.25, xticks=[-.1, 0, .1], ztrim=[0.01, 0.001])]
#protocols = [ Protocols.linecut_angle(q0=0.01687, dq=0.00455*1.5, show_region=False) ]
q0, dq0, qp = 0.0136, 0.005, 0.05
protocols = [
#Protocols.calibration_check(show=False, AgBH=True, q0=0.010, num_rings=4, ztrim=[0.05, 0.005], ) ,
#Protocols.circular_average(ylog=True, plot_range=[0, 0.12, None, None]) ,
Protocols.q_image(plot_range=[-qp, +qp, 0, 2 * qp],
plot_buffers=[0.28, 0.07, 0.25, 0.05]),
Protocols.linecut_qr_fit(qz=0.033,
dq=0.005,
show_region=False,
q0=q0,
plot_range=[0, qp / 2, 0, None],
infiles = glob.glob(os.path.join(source_dir, pattern + '.tiff'))
infiles.sort()
# Analysis to perform
########################################
load_args = {
'calibration': calibration,
'mask': mask,
}
run_args = {
'verbosity': 3,
}
process = Protocols.ProcessorXS(load_args=load_args, run_args=run_args)
patterns = [
['theta', '.+_th(\d+\.\d+)_.+'],
['x_position', '.+_x(-?\d+\.\d+)_.+'],
['y_position', '.+_yy(-?\d+\.\d+)_.+'],
['cost', '.+_Cost(\d+\.\d+)_.+'],
['annealing_temperature', '.+_T(\d+\.\d\d\d)C_.+'],
['annealing_time', '.+_(\d+\.\d)s_T.+'],
['exposure_time', '.+_(\d+\.\d+)c_\d+_saxs.+'],
['sequence_ID', '.+_(\d+)_saxs.+'],
]
protocols = [
#Protocols.thumbnails(name='thumbnails2', crop=None, resize=1.0, blur=None, cmap=cmap_vge, ztrim=[0.0, 0.01])
#circular_average_q2I_fit(show=False, q0=None, plot_range=[0, 0.025, 0, None], fit_range=[0.010, 0.022], vary=True) ,
infiles.sort()
# Analysis to perform
########################################
load_args = {
'calibration': calibration,
'mask': mask,
'rotCCW': True,
}
run_args = {
'verbosity': 3,
}
process = Protocols.ProcessorXS(load_args=load_args, run_args=run_args)
# Examples:
protocols = [
#Protocols.calibration_check(show=False, AgBH=True, q0=0.010, num_rings=4, ztrim=[0.05, 0.005], ) ,
#Protocols.circular_average(ylog=True, plot_range=[0, 0.12, None, None]) ,
Protocols.thumbnails(crop=None,
resize=0.5,
blur=None,
cmap=cmap_vge_hdr,
ztrim=[0.1, 0.002]),
]
# Run
########################################
infiles = glob.glob(os.path.join(source_dir, pattern + '.tiff'))
infiles.sort()
# Analysis to perform
########################################
load_args = {
'calibration': calibration,
'mask': mask,
}
run_args = {
'verbosity': 3,
}
process = Protocols.ProcessorXS(load_args=load_args, run_args=run_args)
thumb2 = Protocols.thumbnails(crop=None,
resize=1.0,
blur=None,
cmap=cmap_vge,
ztrim=[0.0, 0.01])
thumb2.name = 'thumbnails2'
L0 = 48 # nm
q0 = 0.1 * 2 * np.pi / (L0)
print(q0)
patterns = [
['theta', '.+_th(\d+\.\d+)_.+'],
['x_position', '.+_x(-?\d+\.\d+)_.+'],
mask_file = glob.glob(os.path.join(source_dir, pattern+'mask.png'))
mask = Mask(mask_file[0])
# Analysis to perform
########################################
load_args = { 'calibration' : calibration,
'mask' : mask,
}
run_args = { 'verbosity' : 3,
}
process = Protocols.ProcessorXS(load_args=load_args, run_args=run_args)
protocols = [
#Protocols.calibration_check(show=False, AgBH=True, q0=0.010, num_rings=4, ztrim=[0.05, 0.005], zmin=0) ,
#Protocols.circular_average(ylog=True, plot_range=[0, 5.5, None, None]) ,
Protocols.q_image(name='q_images_merged', cmap=cmap_vge, plot_range=[-0.1, 3, 0, 3], xticks=[0, 2, 4, 6], yticks=[0, 2, 4], plot_buffers=[0.2, 0.05, 0.15, 0.05], ztrim=[0.3, 0.001])
Protocols.thumbnails(name='thumbnails_merged', crop=None, resize=1, blur=None, cmap=cmap_vge_hdr, ztrim=[0.1, 0.002])
]
# Run
########################################
process.run(infiles, protocols, output_dir=output_dir, force=1)
# Loop
#infiles = glob.glob(os.path.join(source_dir, 'AgBH_5m_th0.000_10.00s_20323_saxs.tiff'))
infiles.sort()
# Analysis to perform
########################################
load_args = {
'calibration': calibration,
'mask': mask,
}
run_args = {
'verbosity': 3,
}
process = Protocols.ProcessorXS(load_args=load_args, run_args=run_args)
protocols = [
#Protocols.calibration_check(show=False, AgBH=True, q0=0.010, num_rings=4, ztrim=[0.05, 0.05], ) ,
Protocols.circular_average(ylog=True, plot_range=[0, 0.12, None, None]),
#Protocols.sector_average(angle=0, dangle=20, ylog=True, plot_range=[0, 0.3, None, None], show_region=True) ,
#Protocols.linecut_angle(q0=0.094, dq=0.015, show_region=False) ,
#Protocols.q_image(blur=1.0, bins_relative=0.5, plot_range=[-0.1, 3.0, 0, 3.0], _xticks=[0, 1.0, 2.0, 3.0], ztrim=[0.2, 0.01]) ,
#Protocols.qr_image(blur=None, bins_relative=0.8, plot_range=[-0.1, 3.0, 0, 3.0], _xticks=[0, 1.0, 2.0, 3.0], ztrim=[0.38, 0.002], dezing_fill=True) ,
#Protocols.q_phi_image(bins_relative=0.25, plot_range=[0, 3.0, 0, +90]) ,
Protocols.thumbnails(crop=None,
resize=1.0,
blur=None,
cmap=cmap_vge,
ztrim=[0.0, 0.01]),
]
calibration.set_image_size(2070, 2167) # Eiger 4M
calibration.set_pixel_size(pixel_size_um=75.0)
calibration.set_distance(4.755)
calibration.set_beam_position(838.5, 1833.4) # Approximate
mask_dir = '/home/kyager/current/code/SciAnalysis/main/SciAnalysis/XSAnalysis/masks/'
mask = Mask()
#mask.load(mask_dir+'Eiger4M_all_gaps-mask.png')
#mask.load(mask_dir+'CHX_Eiger4M-bad_flatfield_10percent-mask.png')
mask.load(mask_dir + 'CHX_Eiger4M-bad_flatfield_05percent-mask.png')
mask.load(mask_dir + 'CHX_pipe-2015Oct-mask.png')
#mask.load(mask_dir+'CHX_bs_streaks-2015Oct-mask.png')
from SciAnalysis.XSAnalysis import Protocols
process = Protocols.ProcessorXS(calibration=calibration, mask=mask)
protocols = [Protocols.thumbnails(crop=1.3)]
#protocols = [ Protocols.circular_average(ylog=True) ]
#protocols = [ Protocols.fit_calibration(ylog=True) ]
process.run(infiles, protocols, output_dir=output_dir, force=True)
if False:
root_dir = '/media/extend/CHX/'
data_dir = 'LDRD_Meso_correlation/2015_10Oct-ref_patterns/21/'
source_dir = root_dir + 'data/' + data_dir
output_dir = root_dir + 'analysis/' + data_dir
import glob
#infiles = glob.glob(source_dir+'AgBH_series_24_master.h5')
infiles = glob.glob(os.path.join(source_dir, pattern+'.tiff'))
infiles.sort()
# Analysis to perform
########################################
load_args = { 'calibration' : calibration,
'mask' : mask,
#'rot180' : False,
#'flip' : True, # PSCCD
}
run_args = { 'verbosity' : 3,
}
process = Protocols.ProcessorXS(load_args=load_args, run_args=run_args)
# Examples:
#protocols = [ Protocols.circular_average_q2I(plot_range=[0, 0.2, 0, None]) ]
#protocols = [ Protocols.linecut_angle(q0=0.01687, dq=0.00455*1.5, show_region=False) ]
#protocols = [ Protocols.q_image(blur=1.0, bins_relative=0.5, plot_range=[-0.1, 3.0, 0, 3.0], _xticks=[0, 1.0, 2.0, 3.0], ztrim=[0.2, 0.01]) ]
#protocols = [ Protocols.qr_image(blur=1.0, bins_relative=0.5, plot_range=[-0.1, 3.0, 0, 3.0], _xticks=[0, 1.0, 2.0, 3.0], zmin=1010., ztrim=[None, 0.01]) ]
#protocols = [ Protocols.qr_image(blur=None, bins_relative=0.8, plot_range=[-0.1, 3.0, 0, 3.0], _xticks=[0, 1.0, 2.0, 3.0], ztrim=[0.38, 0.002], dezing_fill=True) ]
#protocols = [ Protocols.q_phi_image(bins_relative=0.25, plot_range=[0, 3.0, 0, +90]) ]
protocols = [
#Protocols.calibration_check(show=False, AgBH=True, q0=1.369*0.25, dq=0.002, num_rings=10, ztrim=[0.2, 0.01], dpi=300) ,
Protocols.circular_average(ylog=True, dq = .001, plot_range=[0.0, 1.5, None, None], gridlines=True, save_results = [ 'hdf5' ] ) ,
#Protocols.thumbnails(crop=None, resize=0.5, cmap=cmap_vge, ztrim=[0.06, 0.001], zmin=1000.0) , # PSCCD
#Protocols.linecut_q(chi0= 90+0, dq=.5, ylog=True, gridlines=True, plot_range=[0.0, 1.5, None, None] ) ,
infiles.sort()
# Analysis to perform
########################################
load_args = {
'calibration': calibration,
'mask': mask,
'flip': True,
}
run_args = {
'verbosity': 3,
}
process = Protocols.ProcessorXS(load_args=load_args, run_args=run_args)
# Examples:
#protocols = [ Protocols.calibration_check(show=False, AgBH=True, q0=0.010, num_rings=4) ]
#protocols = [ Protocols.thumbnails(crop=0.8)] # mini
#protocols = [ Protocols.thumbnails(crop=None, resize=1.0, blur=None, file_extension='.png') ] # full-size
#protocols = [ Protocols.thumbnails(crop=None, resize=1.0, blur=None, cmap=cmap_vge, ztrim=[0, 0.001], file_extension='.png') ] # custom
#protocols = [ Protocols.q_image(q_max=0.14, blur=2.0, bins_relative=0.25, xticks=[-.1, 0, .1], ztrim=[0.01, 0.001])]
#protocols = [ Protocols.circular_average(ylog=True, plot_range=[0, 0.2, None, None]) ]
#protocols = [ Protocols.circular_average_q2I(plot_range=[0, 0.2, 0, None]) ]
#protocols = [ circular_average_q2I_fit(plot_range=[0, 0.2, 0, None]) ] # local protocol
#protocols = [ Protocols.linecut_angle(q0=0.01687, dq=0.00455*1.5, show_region=False) ]
#protocols = [ linecut_angle_fit(dq=0.00455*1.5) ]
protocols = [
#Protocols.calibration_check(show=False, AgBH=True, q0=1.369*0.25, dq=0.002, num_rings=10, ztrim=[0.2, 0.01], dpi=300) ,