listOfShapes = []
for kk in range(len(listOfArrays)):
listOfShapes.append(np.shape(fileContent[0]))
# use the two differential data
n_files -= 1
print(listOfFiles)
del listOfFiles[2]
# %% define what to do, use of ini file
if 'Height' in headers[-1]:
what2do = 'Height response function'
else:
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)
vlim10 = np.max(np.abs(diffPhase10))
# ==========================================================================
# %% Integration
# ==========================================================================
if easyqt.get_yes_or_no('New Crop for Integration?\n' +
"(If 'No', the values from last run are used)"):
idx4crop = ''
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
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]
plt.show(block=False)
plt.pause(.1)
else:
plt.close()
return outFilesList, allShifts
# %%
inifname = '.align_many_imgs_and_save.ini'
# %%
idx4crop = list(
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)