def _intial_gui_setup(sys_argv):
global inifname # name of .ini file
inifname = os.curdir + '/.' + os.path.basename(__file__).replace(
'.py', '.ini')
for i, argv in enumerate(sys_argv):
print('arg {}: '.format(i) + argv)
if len(sys_argv) == 1:
default_ini = wpu.load_ini_file(inifname)
foldername = default_ini['Files']['Folder Name']
if easyqt.get_yes_or_no('Select new folder?\n' +
'[ESC load folder of previous run]'):
foldername = easyqt.get_directory_name(title='Select Folder that' +
'\ncontains *csv files')
elif len(sys_argv) == 2:
foldername = sys_argv[1]
else:
print('ERROR: wrong number of inputs: {} \n'.format(len(argv) - 1) +
'Usage: \n'
'\n' + os.path.basename(__file__) +
' : (no inputs) load dialogs \n'
'\n' + os.path.basename(__file__) + ' [args] \n'
'\n'
'arg1: folder that contains the *csv files\n'
'\n')
exit(-1)
wpu.set_at_ini_file(inifname, 'Files', 'Folder Name', foldername)
list_of_files = sorted(glob.glob(foldername + '/*csv'))
nfiles = len(list_of_files)
data, header_list = wpu.load_csv_file(list_of_files[0])
wpu.print_blue('MESSAGE: Header of data files:')
wpu.print_blue(header_list)
ncurves = data.shape[1] - 1
label_list = [
fname.rsplit('_', 1)[1].split('.')[0] for fname in list_of_files
]
#[fname.rsplit('/', 1)[1].split('_Y_integrated')[0]
# for fname in list_of_files]
return list_of_files, nfiles, ncurves, label_list, header_list
# %%
if len(sys.argv) == 1:
dirName = easyqt.get_directory_name('Directory to the data:')
else:
dirName = sys.argv[1]
# here the response function initialization file
inifname = '.Revise_response_func.ini'
defaults = wpu.load_ini_file(inifname)
if dirName == '':
dirName = defaults['Files'].get('Folder with csv files')
else:
wpu.set_at_ini_file(inifname, 'Files', 'Folder with csv files', dirName)
print(dirName)
'''
Here use the cap to wavesensor data transfer function to generate the same structure
data file with the wavefront measurement curve. The file is generated in the dir_name path
'''
listOfFiles = glob.glob(dirName + '/*.csv')
listOfFiles.sort()
n_files = len(listOfFiles)
# %% Load data
listOfArrays = []
listOfShapes = []
what2do = wpu.get_from_ini_file(inifname, 'Parameters', 'what2do')
if 'DPC' in what2do:
choices = [
'DPC response function',
'Curvature response function from diff data'
]
else:
choices = [
'Curvature response function from diff data',
'DPC response function'
]
what2do = easyqt.get_choice('Pick one', choices=choices)
wpu.set_at_ini_file(inifname, 'Parameters', 'what2do', what2do)
# %%
listInterpFunc = []
npoints_interp = 460
xnew = np.linspace(listOfArrays[0][0, 0], listOfArrays[0][-1, 0],
npoints_interp)
# %%
from scipy.ndimage import gaussian_filter1d
if 'Curvature' in what2do:
def _intial_gui_setup(sys_argv):
global inifname # name of .ini file
inifname = os.curdir + '/.' + os.path.basename(__file__).replace(
'.py', '.ini')
for i, argv in enumerate(sys_argv):
print('arg {}: '.format(i) + argv)
if len(sys_argv) == 1:
default_ini = wpu.load_ini_file(inifname)
p0 = float(default_ini['Parameters']['Photon Energy [eV]'])
p1 = float(default_ini['Parameters']['grazing angle [mrad]'])
p2 = int(default_ini['Parameters']['n profiles'])
p3 = int(default_ini['Parameters']['filter width'])
p4 = float(default_ini['Parameters']['projection From Divergence'])
if easyqt.get_yes_or_no('Load new files?\n' +
'[ESC load file(s) of previous run]'):
fnameH = easyqt.get_file_names(title='Select DPC Horizontal\n' +
'(and Vertical if you want)')
fnameV = None
if len(fnameH) == 1:
fnameH = fnameH[0]
wpu.print_blue('MESSAGE: Horiz DPC: Loading ' + fnameH)
elif len(fnameH) == 0:
fnameH = None
elif len(fnameH) == 2:
[fnameH, fnameV] = fnameH
wpu.print_blue('MESSAGE: Horiz DPC: Loading ' + fnameH)
wpu.print_blue('MESSAGE: Vert DPC: Loading ' + fnameV)
if fnameV is None:
fnameV = easyqt.get_file_names(title='Select DPC Vertical')
if len(fnameV) == 1:
fnameV = fnameV[0]
wpu.print_blue('MESSAGE: Vert DPC: Loading ' + fnameV)
elif len(fnameV) == 0:
fnameV = None
else:
fnameH = default_ini['Files']['dpc H']
fnameV = default_ini['Files']['dpc V']
wpu.print_blue('MESSAGE: Horiz DPC: Loading ' + fnameH)
wpu.print_blue('MESSAGE: Vert DPC: Loading ' + fnameV)
if fnameH == 'None':
fnameH = None
if fnameV == 'None':
fnameV = None
phenergy = easyqt.get_float("Enter Photon Energy [KeV]",
title='Experimental Values',
default_value=p0 * 1e-3) * 1e3
grazing_angle = easyqt.get_float(
'Grazing angle [mrad]\n' + '[0.0 to ignore projection]',
title='Experimental Values',
default_value=p1) * 1e-3
projectionFromDiv = easyqt.get_float('projection From Divergence\n' +
'[Multiplication factor]',
title='Experimental Values',
default_value=p4)
nprofiles = easyqt.get_int("Number of profiles to plot",
title='Experimental Values',
default_value=p2)
filter_width = easyqt.get_int("Width fo uniform filter [pixels]",
title='Experimental Values',
default_value=p3)
remove2ndOrder = easyqt.get_yes_or_no("Remove 2nd Order?",
title='Experimental Values')
elif len(sys_argv) == 8:
if 'none' in sys_argv[1].lower():
fnameH = None
else:
fnameH = sys_argv[1]
if 'none' in sys_argv[2].lower():
fnameV = None
else:
fnameV = sys_argv[2]
phenergy = float(sys_argv[3]) * 1e3
nprofiles = int(sys_argv[4])
filter_width = int(sys_argv[5])
grazing_angle = float(sys_argv[6]) * 1e-3
projectionFromDiv = float(sys_argv[7])
else:
print(
'ERROR: wrong number of inputs: {} \n'.format(len(argv) - 1) +
'Usage: \n'
'\n' + os.path.basename(__file__) +
' : (no inputs) load dialogs \n'
'\n' + os.path.basename(__file__) + ' [args] \n'
'\n'
'arg1: file name DPC Horiz (type "None" '
' to ignore it)\n'
'arg2: file name DPC Vert (type "None" '
' to ignore it)\n'
'arg3: Photon Energy [KeV]\n'
'arg4: Number of profiles to plot\n'
'arg5: Width of uniform filter [pixels]\n'
'arg6: Grazing angle to project coordinates to mirror [mrad], use zero to ignore\n'
'arg7: Projection From Divergence, use 1 to ignore'
'\n')
exit(-1)
wpu.set_at_ini_file(inifname, 'Files', 'DPC H', fnameH)
wpu.set_at_ini_file(inifname, 'Files', 'DPC V', fnameV)
wpu.set_at_ini_file(inifname, 'Parameters', 'Photon Energy [eV]', phenergy)
wpu.set_at_ini_file(inifname, 'Parameters', 'grazing angle [mrad]',
grazing_angle * 1e3)
wpu.set_at_ini_file(inifname, 'Parameters', 'projection From Divergence',
projectionFromDiv)
wpu.set_at_ini_file(inifname, 'Parameters', 'n profiles', nprofiles)
wpu.set_at_ini_file(inifname, 'Parameters', 'filter width', filter_width)
wpu.set_at_ini_file(inifname, 'Parameters', 'Remove 2nd Order',
remove2ndOrder)
return (fnameH, fnameV, phenergy, grazing_angle, projectionFromDiv,
nprofiles, remove2ndOrder, filter_width)
def _intial_gui_setup(sys_argv):
global inifname # name of .ini file
pwd, inifname = sys_argv[0].rsplit('/', 1)
inifname = pwd + '/.' + inifname.replace('.py', '.ini')
for i, argv in enumerate(sys_argv):
print('arg {}: '.format(i) + argv)
if len(sys_argv) == 1:
default_ini = wpu.load_ini_file(inifname)
p0 = float(default_ini['Parameters']['Photon Energy [eV]'])
p1 = float(default_ini['Parameters']['grazing angle [mrad]'])
p2 = int(default_ini['Parameters']['n profiles'])
p3 = int(default_ini['Parameters']['filter width'])
p4 = float(default_ini['Parameters']['projection From Divergence'])
if easyqt.get_yes_or_no('Load new files?\n' +
'[ESC load file(s) of previous run]'):
fnameH = easyqt.get_file_names(title='Select DPC Horizontal\n' +
'(and Vertical if you want)')
fnameV = None
if len(fnameH) == 1:
fnameH = fnameH[0]
wpu.print_blue('MESSAGE: Horiz DPC: Loading ' + fnameH)
elif len(fnameH) == 0:
fnameH = None
elif len(fnameH) == 2:
[fnameH, fnameV] = fnameH
wpu.print_blue('MESSAGE: Horiz DPC: Loading ' + fnameH)
wpu.print_blue('MESSAGE: Vert DPC: Loading ' + fnameV)
if fnameV is None:
fnameV = easyqt.get_file_names(title='Select DPC Vertical')
if len(fnameV) == 1:
fnameV = fnameV[0]
wpu.print_blue('MESSAGE: Vert DPC: Loading ' + fnameV)
elif len(fnameV) == 0:
fnameV = None
else:
fnameH = default_ini['Files']['dpc H']
fnameV = default_ini['Files']['dpc V']
wpu.print_blue('MESSAGE: Horiz DPC: Loading ' + fnameH)
wpu.print_blue('MESSAGE: Vert DPC: Loading ' + fnameV)
if fnameH == 'None':
fnameH = None
if fnameV == 'None':
fnameV = None
phenergy = easyqt.get_float("Enter Photon Energy [KeV]",
title='Experimental Values',
default_value=p0*1e-3)*1e3
grazing_angle = easyqt.get_float('Grazing angle [mrad]\n' +
'[0.0 to ignore projection]',
title='Experimental Values',
default_value=p1)*1e-3
projectionFromDiv = easyqt.get_float('projection From Divergence\n' +
'[Multiplication factor]',
title='Experimental Values',
default_value=p4)
nprofiles = easyqt.get_int("Number of profiles to plot",
title='Experimental Values',
default_value=p2)
filter_width = easyqt.get_int("Width fo uniform filter [pixels]",
title='Experimental Values',
default_value=p3, max_=1e6)
remove1stOrderDPC = easyqt.get_yes_or_no("Remove 1st Order DPC?",
title='Experimental Values')
remove2ndOrder = easyqt.get_yes_or_no("Remove 2nd Order?",
title='Experimental Values')
elif len(sys_argv) == 10:
if 'none' in sys_argv[1].lower():
fnameH = None
else:
fnameH = sys_argv[1]
if 'none' in sys_argv[2].lower():
fnameV = None
else:
fnameV = sys_argv[2]
phenergy = float(sys_argv[3])*1e3
nprofiles = int(sys_argv[4])
filter_width = int(sys_argv[5])
grazing_angle = float(sys_argv[6])*1e-3
projectionFromDiv = float(sys_argv[7])
remove1stOrderDPC = bool(int(argv[8]))
remove2ndOrder = bool(int(argv[9]))
else:
print('ERROR: wrong number of inputs: {} \n'.format(len(argv)-1) +
'Usage: \n'
'\n' +
sys_argv[0].rsplit('/')[-1] + ' : (no inputs) load dialogs \n'
'\n' +
sys_argv[0].rsplit('/')[-1] + ' [args] \n'
'\n'
'arg1: file name DPC Horiz (type "None" '
' to ignore it)\n'
'arg2: file name DPC Vert (type "None" '
' to ignore it)\n'
'arg3: Photon Energy [KeV]\n'
'arg4: Number of profiles to plot\n'
'arg5: Width of uniform filter [pixels]\n'
'arg6: Grazing angle to project coordinates to mirror [mrad], use zero to ignore\n'
'arg7: Projection From Divergence, use 1 to ignore'
'\n')
exit(-1)
wpu.set_at_ini_file(inifname, 'Files', 'DPC H', fnameH)
wpu.set_at_ini_file(inifname, 'Files', 'DPC V', fnameV)
wpu.set_at_ini_file(inifname, 'Parameters', 'Photon Energy [eV]', phenergy)
wpu.set_at_ini_file(inifname, 'Parameters',
'grazing angle [mrad]', grazing_angle*1e3)
wpu.set_at_ini_file(inifname, 'Parameters',
'projection From Divergence', projectionFromDiv)
wpu.set_at_ini_file(inifname, 'Parameters', 'n profiles', nprofiles)
wpu.set_at_ini_file(inifname, 'Parameters', 'filter width', filter_width)
wpu.set_at_ini_file(inifname, 'Parameters', 'Remove 1st Order DPC', remove1stOrderDPC)
wpu.set_at_ini_file(inifname, 'Parameters', 'Remove 2nd Order', remove2ndOrder)
return (fnameH, fnameV,
phenergy, grazing_angle, projectionFromDiv,
nprofiles, remove1stOrderDPC, remove2ndOrder, filter_width)
def main_single_gr_Talbot(img, imgRef,
phenergy, pixelsize, distDet2sample,
period_harm, saveFileSuf,
unwrapFlag=True,
plotFlag=True,
saveFigFlag=False):
global inifname # name of .ini file
[period_harm_Vert, period_harm_Hor] = period_harm
# img, imgRef = wpu.align_two_images(img, imgRef)
# Crop
img_size_o = np.shape(img)
# take index from ini file
idx4crop = list(map(int, (wpu.get_from_ini_file(inifname, 'Parameters',
'Crop').split(','))))
# Plot Real Image wiht default crop
tmpImage = wpu.crop_matrix_at_indexes(img, idx4crop)
plt.figure()
plt.imshow(tmpImage,
cmap='viridis',
extent=wpu.extent_func(tmpImage, pixelsize)*1e6)
plt.xlabel(r'$[\mu m]$')
plt.ylabel(r'$[\mu m]$')
plt.colorbar()
plt.title('Raw Image with initial Crop', fontsize=18, weight='bold')
plt.pause(.1)
# ask if the crop need to be changed
newCrop = easyqt.get_yes_or_no('New Crop?')
if saveFigFlag and not newCrop:
wpu.save_figs_with_idx(saveFileSuf + '_Talbot_image')
plt.close(plt.gcf())
if newCrop:
[colorlimit,
cmap] = wpu.plot_slide_colorbar(img,
title='SELECT COLOR SCALE,\n' +
'Raw Image, No Crop',
xlabel=r'x [$\mu m$ ]',
ylabel=r'y [$\mu m$ ]',
extent=wpu.extent_func(img,
pixelsize)*1e6)
idx4crop = wpu.graphical_roi_idx(img, verbose=True,
kargs4graph={'cmap': cmap,
'vmin': colorlimit[0],
'vmax': colorlimit[1]})
wpu.set_at_ini_file(inifname, 'Parameters', 'Crop',
'{}, {}, {}, {}'.format(idx4crop[0], idx4crop[1],
idx4crop[2], idx4crop[3]))
img = wpu.crop_matrix_at_indexes(img, idx4crop)
# Plot Real Image AFTER crop
plt.imshow(img, cmap='viridis',
extent=wpu.extent_func(img, pixelsize)*1e6)
plt.xlabel(r'$[\mu m]$')
plt.ylabel(r'$[\mu m]$')
plt.colorbar()
plt.title('Raw Image with New Crop', fontsize=18, weight='bold')
if saveFigFlag:
wpu.save_figs_with_idx(saveFileSuf + '_Talbot_image')
plt.show(block=True)
else:
img = tmpImage
imgRef = wpu.crop_matrix_at_indexes(imgRef, idx4crop)
# calculate harmonic position after crop
period_harm_Vert = int(period_harm_Vert*(idx4crop[1] - idx4crop[0]) /
img_size_o[0])
period_harm_Hor = int(period_harm_Hor*(idx4crop[3] - idx4crop[2]) /
img_size_o[1])
# Obtain harmonic periods from images
(period_harm_Vert,
_) = wgi.exp_harm_period(img, [period_harm_Vert,
period_harm_Hor],
harmonic_ij=['1', '0'],
searchRegion=20,
isFFT=False, verbose=True)
(_,
period_harm_Horz) = wgi.exp_harm_period(img, [period_harm_Vert,
period_harm_Hor],
harmonic_ij=['0', '1'],
searchRegion=20,
isFFT=False, verbose=True)
# Calculate everything
harmPeriod = [period_harm_Vert, period_harm_Hor]
[int00, int01, int10,
darkField01, darkField10,
phaseFFT_01,
phaseFFT_10] = wgi.single_2Dgrating_analyses(img, imgRef,
harmonicPeriod=harmPeriod,
plotFlag=plotFlag,
unwrapFlag=unwrapFlag,
verbose=True)
virtual_pixelsize = [0, 0]
virtual_pixelsize[0] = pixelsize[0]*img.shape[0]/int00.shape[0]
virtual_pixelsize[1] = pixelsize[1]*img.shape[1]/int00.shape[1]
diffPhase01 = phaseFFT_01*virtual_pixelsize[1]/distDet2sample/hc*phenergy
diffPhase10 = phaseFFT_10*virtual_pixelsize[0]/distDet2sample/hc*phenergy
return [int00, int01, int10,
darkField01, darkField10,
diffPhase01, diffPhase10,
virtual_pixelsize]
else:
idx4crop = list(map(int,
(wpu.get_from_ini_file(inifname,
'Parameters',
'crop integration').split(','))))
phase, idx4crop = wgi.dpc_integration(diffPhase01, diffPhase10,
virtual_pixelsize,
idx4crop=idx4crop,
saveFileSuf=saveFileSuf,
plotErrorIntegration=True,
shifthalfpixel=True)
wpu.set_at_ini_file(inifname, 'Parameters', 'crop integration',
'{}, {}, {}, {}'.format(idx4crop[0], idx4crop[1],
idx4crop[2], idx4crop[3]))
phase -= np.mean(phase) # apply here your favorite offset
# %%
ax = wgi.plot_integration(1/2/np.pi*phase, virtual_pixelsize,
titleStr=r'WF $[\lambda$ units $]$',
saveFigFlag=True, saveFileSuf=saveFileSuf)
plt.pause(.2)
# ==========================================================================
map(int,
(wpu.get_from_ini_file(inifname, 'Parameters', 'Crop').split(','))))
defaults = wpu.load_ini_file(inifname)
deafaultfileName = defaults['Files'].get('Reference')
# %% Load
if len(sys.argv) == 1:
samplefileName = easyqt.get_file_names("Choose the reference file " +
"for alignment")
if samplefileName == []:
samplefileName = deafaultfileName
else:
samplefileName = samplefileName[0]
wpu.set_at_ini_file(inifname, 'Files', 'reference', samplefileName)
optionRef = easyqt.get_choice(
'Align images to reference ot to previous image?',
title='Title',
choices=['Reference', 'Previous', 'Manual'])
fixRef = (optionRef == 'Reference')
if optionRef != 'Manual':
option = easyqt.get_choice('Crop or Pad?',
title='Title',
choices=['Pad', 'Crop'])
else:
samplefileName = sys.argv[1]
option = sys.argv[2]