def intial_setup():
[list_sample_files, list_ref_files,
list_dark_files] = wpu.gui_list_data_phase_stepping()
for fname in list_sample_files + list_ref_files + list_dark_files:
wpu.print_blue('MESSAGE: Loading ' + fname.rsplit('/')[-1])
pixelSize = easyqt.get_float("Enter Pixel Size [um]",
title='Experimental Values',
default_value=.65) * 1e-6
stepSize = easyqt.get_float("Enter scan step size [um]",
title='Experimental Values',
default_value=.2) * 1e-6
return (list_sample_files, list_ref_files, list_dark_files, pixelSize,
stepSize)
def intial_setup():
[list_sample_files,
list_ref_files,
list_dark_files] = wpu.gui_list_data_phase_stepping()
for fname in list_sample_files + list_ref_files + list_dark_files:
wpu.print_blue('MESSAGE: Loading ' + fname.rsplit('/')[-1])
pixelSize = easyqt.get_float("Enter Pixel Size [um]",
title='Experimental Values',
default_value=.65)*1e-6
stepSize = easyqt.get_float("Enter scan step size [um]",
title='Experimental Values',
default_value=.2)*1e-6
return (list_sample_files, list_ref_files, list_dark_files,
pixelSize, stepSize)
dark_im = dxchange.read_tiff(listOfDataFiles[0]) * 0.0
img = dxchange.read_tiff(listOfDataFiles[0]) - dark_im
# %%
#exit()
# =============================================================================
# %% Experimental parameters
# =============================================================================
from scipy import constants
hc = constants.value('inverse meter-electron volt relationship') # hc
wavelength = hc / easyqt.get_float("Photon Energy [KeV]",
title='Experimental Values',
default_value=25.0) * 1e-3
pixelSize = easyqt.get_float("Enter Pixel Size [um]",
title='Experimental Values',
default_value=.65) * 1e-6
gratingPeriod = easyqt.get_float("Enter CB Grating Period [um]",
title='Experimental Values',
default_value=3.4) * 1e-6
pattern = easyqt.get_choice(message='Select CB Grating Pattern',
title='Title',
choices=['Diagonal', 'Edge'])
if pattern == 'Diagonal':
'*.tif')
listOfDataFiles = glob.glob(samplefileName.rsplit('_', 2)[0] + '*.tif')
listOfDataFiles.sort()
nfiles = len(listOfDataFiles)
zvec_from = easyqt.get_choice(
message='z distances is calculated or from table?',
title='Title',
choices=['Calculated', 'Tabled'])
# %%
if zvec_from == 'Calculated':
startDist = easyqt.get_float(
'Starting distance scan [mm]', title='Title', default_value=10) * 1e-3
step_z_scan = easyqt.get_float(
'Step size scan [mm]', title='Title', default_value=2) * 1e-3
image_per_point = easyqt.get_int('Number of images by step',
title='Title',
default_value=1)
zvec = np.linspace(
startDist, startDist + step_z_scan * (nfiles / image_per_point - 1),
int(nfiles / image_per_point))
zvec = zvec.repeat(image_per_point)
strideFile = easyqt.get_int('Stride (Use only every XX files)',
title='Title',
def _intial_gui_setup():
# global inifname # name of .ini file
# pwd, inifname = argvzero.rsplit('/', 1)
# inifname = pwd + '/.' + inifname.replace('.py', '.ini')
defaults = wpu.load_ini_file(inifname)
fname = easyqt.get_file_names("File to Plot (Pickle or sdf)")
if fname == []:
fname = defaults['Files'].get('file with thickness')
else:
fname = fname[0]
defaults['Files']['file with thickness'] = fname
wpu.print_blue('MESSAGE: Loading File: ' + fname)
with open(inifname, 'w') as configfile:
defaults.write(configfile)
if defaults is None:
p1 = ''
p2 = 100e-6
else:
p1 = defaults['Parameters'].get('String for Titles')
p2 = float(defaults['Parameters'].get('Nominal Radius For Fitting'))
p3 = defaults['Parameters']['Diameter of active area for fitting']
p4 = defaults['Parameters']['Lens Geometry']
str4title = easyqt.get_string('String for Titles', 'Enter String', p1)
if str4title != '':
defaults['Parameters']['String for Titles'] = str4title
wpu.print_blue('MESSAGE: Loading Pickle: ' + fname)
if p4 == '2D Lens Stigmatic Lens':
menu_choices4lensmode = [
'2D Lens Stigmatic Lens', '1Dx Horizontal focusing',
'1Dy Vertical focusing'
]
elif p4 == '1Dx Horizontal focusing':
menu_choices4lensmode = [
'1Dx Horizontal focusing', '1Dy Vertical focusing',
'2D Lens Stigmatic Lens'
]
elif p4 == '1Dy Vertical focusing':
menu_choices4lensmode = [
'1Dy Vertical focusing', '1Dx Horizontal focusing',
'2D Lens Stigmatic Lens'
]
lensGeometry = easyqt.get_choice(message='Lens Geometry',
title='Input Parameter',
choices=menu_choices4lensmode)
nominalRadius = easyqt.get_float(
'Nominal Curvature Radius' + ' for Fitting [um]',
title='Input Parameter',
default_value=p2 * 1e6) * 1e-6
diameter4fit_str = easyqt.get_string(
'Diameter of active area for fitting [um]',
title='Input Parameter',
default_response=p3)
diameter4fit_list = [float(a) * 1e-6 for a in diameter4fit_str.split(',')]
defaults['Parameters']['Nominal Radius For Fitting'] = str(nominalRadius)
defaults['Parameters'][
'Diameter of active area for fitting'] = diameter4fit_str
defaults['Parameters']['Lens Geometry'] = lensGeometry
with open(inifname, 'w') as configfile:
defaults.write(configfile)
return fname, str4title, nominalRadius, diameter4fit_list, lensGeometry
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)
os.chdir(data_dir)
listOfDataFiles.sort()
wpu.print_blue('MESSAGE: Loading files ' + \
samplefileName.rsplit('_',1)[0] + '*.tif')
#fname_dark = easyqt.get_file_names("Dark File")[0]
os.chdir(originalDir)
strideFile = easyqt.get_int('Stride', default_value=1)
startDist = easyqt.get_float('Starting distance scan [mm]',
default_value=10)*1e-3
step_z_scan = strideFile*easyqt.get_float('Step size scan [mm]',
default_value=2)*1e-3
listOfDataFiles = listOfDataFiles[0::strideFile]
nfiles = len(listOfDataFiles)
#dark_im = dxchange.read_tiff(fname_dark)
dark_im = dxchange.read_tiff(listOfDataFiles[0])*0.0
img = dxchange.read_tiff(listOfDataFiles[0]) - dark_im
# =============================================================================
def main():
wpu._mpl_settings_4_nice_graphs()
# =============================================================================
# %% Load Image
# =============================================================================
originalDir = os.getcwd()
samplefileName = easyqt.get_file_names("Choose one of the scan files")[0]
data_dir = samplefileName.rsplit('/', 1)[0]
os.chdir(data_dir)
try:
os.mkdir(data_dir + '/output/')
except:
pass
fname2save = data_dir + '/output/' + samplefileName.rsplit(
'_', 1)[0].rsplit('/', 1)[1]
wpu.print_blue('MESSAGE: Loading files ' +
samplefileName.rsplit('_', 1)[0] + '*.tif')
listOfDataFiles = glob.glob(samplefileName.rsplit('_', 2)[0] + '*.tif')
listOfDataFiles.sort()
nfiles = len(listOfDataFiles)
zvec_from = easyqt.get_choice(
message='z distances is calculated or from table?',
title='Title',
choices=['Calculated', 'Tabled'])
# %%
if zvec_from == 'Calculated':
startDist = easyqt.get_float('Starting distance scan [mm]',
title='Title',
default_value=20) * 1e-3
step_z_scan = easyqt.get_float(
'Step size scan [mm]', title='Title', default_value=5) * 1e-3
image_per_point = easyqt.get_int('Number of images by step',
title='Title',
default_value=1)
zvec = np.linspace(
startDist,
startDist + step_z_scan * (nfiles / image_per_point - 1),
int(nfiles / image_per_point))
zvec = zvec.repeat(image_per_point)
strideFile = easyqt.get_int('Stride (Use only every XX files)',
title='Title',
default_value=1)
listOfDataFiles = listOfDataFiles[0::strideFile]
zvec = zvec[0::strideFile]
print(zvec)
elif zvec_from == 'Tabled':
zvec = np.loadtxt(
easyqt.get_file_names("Table with the z distance values in mm")
[0]) * 1e-3
step_z_scan = np.mean(np.diff(zvec))
if step_z_scan > 0:
pass
else:
listOfDataFiles = listOfDataFiles[::-1]
zvec = zvec[::-1]
img = dxchange.read_tiff(listOfDataFiles[0])
# =============================================================================
# %% Experimental parameters
# =============================================================================
pixelSize = easyqt.get_float("Enter Pixel Size [um]",
title='Experimental Values',
default_value=.6500,
decimals=5) * 1e-6
gratingPeriod = easyqt.get_float("Enter CB Grating Period [um]",
title='Experimental Values',
default_value=4.8) * 1e-6
pattern = easyqt.get_choice(message='Select CB Grating Pattern',
title='Title',
choices=['Diagonal', 'Edge'])
# choices=['Edge', 'Diagonal'])
sourceDistanceV = easyqt.get_float(
"Enter Distance to Source\n in the VERTICAL [m]",
title='Experimental Values',
default_value=-0.73)
sourceDistanceH = easyqt.get_float(
"Enter Distance to Source\n in the Horizontal [m]",
title='Experimental Values',
default_value=34.0)
unFilterSize = easyqt.get_int("Enter Size for Uniform Filter [Pixels]\n" +
" (Enter 1 to NOT use the filter)",
title='Experimental Values',
default_value=1)
searchRegion = easyqt.get_int(
"Enter Size of Region for Searching\n the Peak [in Pixels]",
title='Experimental Values',
default_value=20)
os.chdir(originalDir)
# =============================================================================
# %% Crop
# =============================================================================
idx4crop = [0, -1, 0, -1]
[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.print_blue("MESSAGE: idx for cropping")
wpu.print_blue(idx4crop)
# =============================================================================
# %% Dark indexes
# =============================================================================
darkRegionSelctionFlag = easyqt.get_yes_or_no(
'Do you want to select ' + 'region for dark calculation?\n' +
'Press ESC to use [0, 20, 0, 20]')
if darkRegionSelctionFlag:
idx4cropDark = wpu.graphical_roi_idx(img,
verbose=True,
kargs4graph={
'cmap': cmap,
'vmin': colorlimit[0],
'vmax': colorlimit[1]
})
else:
idx4cropDark = [0, 20, 0, 20]
# dark_im = dxchange.read_tiff(listOfDataFiles[0])*0.0 + avgDark
img = wpu.crop_matrix_at_indexes(img, idx4crop)
# ==============================================================================
# %% Harmonic Periods
# ==============================================================================
if pattern == 'Diagonal':
period_harm_Vert = np.int(
np.sqrt(2) * pixelSize / gratingPeriod * img.shape[0])
period_harm_Horz = np.int(
np.sqrt(2) * pixelSize / gratingPeriod * img.shape[1])
elif pattern == 'Edge':
period_harm_Vert = np.int(2 * pixelSize / gratingPeriod * img.shape[0])
period_harm_Horz = np.int(2 * pixelSize / gratingPeriod * img.shape[1])
# Obtain harmonic periods from images
(period_harm_Vert,
_) = wgi.exp_harm_period(img, [period_harm_Vert, period_harm_Horz],
harmonic_ij=['1', '0'],
searchRegion=40,
isFFT=False,
verbose=True)
(_, period_harm_Horz) = wgi.exp_harm_period(
img, [period_harm_Vert, period_harm_Horz],
harmonic_ij=['0', '1'],
searchRegion=40,
isFFT=False,
verbose=True)
wpu.log_this('Input files: ' + samplefileName.rsplit('_', 1)[0] + '*.tif',
preffname=fname2save)
wpu.log_this('\nNumber of files : ' + str(nfiles))
wpu.log_this('Stride : ' + str(strideFile))
wpu.log_this('Z distances is ' + zvec_from)
if zvec_from == 'Calculated':
wpu.log_this('Step zscan [mm] : {:.4g}'.format(step_z_scan * 1e3))
wpu.log_this('Start point zscan [mm] : {:.4g}'.format(startDist * 1e3))
wpu.log_this('Pixel Size [um] : {:.4g}'.format(pixelSize * 1e6))
wpu.log_this('Grating Period [um] : {:.4g}'.format(gratingPeriod * 1e6))
wpu.log_this('Grating Pattern : ' + pattern)
wpu.log_this('Crop idxs : ' + str(idx4crop))
wpu.log_this('Dark idxs : ' + str(idx4cropDark))
wpu.log_this('Vertical Source Distance: ' + str(sourceDistanceV))
wpu.log_this('Horizontal Source Distance: ' + str(sourceDistanceH))
wpu.log_this('Uniform Filter Size : {:d}'.format(unFilterSize))
wpu.log_this('Search Region : {:d}'.format(searchRegion))
# =============================================================================
# %% Calculate everything
# =============================================================================
# =============================================================================
# %% multiprocessing
# =============================================================================
ncpus = cpu_count()
wpu.print_blue("MESSAGE: %d cpu's available" % ncpus)
tzero = time.time()
p = Pool(ncpus - 5)
indexes = range(len(listOfDataFiles))
parameters = []
for i in indexes:
parameters.append([
i, listOfDataFiles, zvec, idx4cropDark, idx4crop, period_harm_Vert,
sourceDistanceV, period_harm_Horz, sourceDistanceH, searchRegion,
unFilterSize
])
res = p.map(_func, parameters)
p.close()
wpu.print_blue('MESSAGE: Time spent: {0:.3f} s'.format(time.time() -
tzero))
'''
res = []
for i in range(len(listOfDataFiles)):
res.append(_func(i))
print(res)
'''
# =============================================================================
# %% Sorting the data
# =============================================================================
contrastV = np.asarray([x[0] for x in res])
contrastH = np.asarray([x[1] for x in res])
p0 = np.asarray([x[2] for x in res])
pv = np.asarray([x[3] for x in res])
ph = np.asarray([x[4] for x in res])
pattern_period_Vert_z = pixelSize / (pv[:, 0] - p0[:, 0]) * img.shape[0]
pattern_period_Horz_z = pixelSize / (ph[:, 1] - p0[:, 1]) * img.shape[1]
# =============================================================================
# %% Save csv file
# =============================================================================
outputfname = wpu.get_unique_filename(fname2save, 'csv')
wpu.save_csv_file(np.c_[zvec.T, contrastV.T, contrastH.T,
pattern_period_Vert_z.T, pattern_period_Horz_z.T],
outputfname,
headerList=[
'z [m]', 'Vert Contrast', 'Horz Contrast',
'Vert Period [m]', 'Horz Period [m]'
])
wpu.log_this('\nOutput file: ' + outputfname)
# =============================================================================
# %% Plot
# =============================================================================
# contrast vs z
fig = plt.figure(figsize=(10, 7))
plt.plot(zvec * 1e3, contrastV * 100, '-ko', label='Vert')
plt.plot(zvec * 1e3, contrastH * 100, '-ro', label='Hor')
plt.xlabel(r'Distance $z$ [mm]', fontsize=14)
plt.ylabel(r'Visibility $\times$ 100 [%]', fontsize=14)
plt.title('Visibility vs detector distance', fontsize=14, weight='bold')
plt.legend(fontsize=14, loc=0)
wpu.save_figs_with_idx(fname2save)
plt.show(block=False)
# =============================================================================
# %% Plot Harmonic position and calculate source distance
# =============================================================================
# from wavepytools.diag.coherence.fit_singleGratingCoherence_z_scan import fit_period_vs_z
#xshi 20190719
from fit_singleGratingCoherence_z_scan import fit_period_vs_z
(sourceDistance_from_fit_V,
patternPeriodFromData_V) = fit_period_vs_z(zvec,
pattern_period_Vert_z,
contrastV,
direction='Vertical',
threshold=.002,
fname4graphs=fname2save)
(sourceDistance_from_fit_H,
patternPeriodFromData_H) = fit_period_vs_z(zvec,
pattern_period_Horz_z,
contrastH,
direction='Horizontal',
threshold=0.0005,
fname4graphs=fname2save)
arg2: Grating Period [µm]
arg3: CB Grating Orientation: 'Edge' or 'Diagonal'
arg4: Source distance [meters]
arg5: file name [.pickle]
"""
if len(sys.argv) == 1:
flist = easyqt.get_file_names("Pickle File to Plot")
fname = flist[0]
wavelength = hc/easyqt.get_float("Photon Energy [KeV]",
title='Experimental Values',
default_value=8.0)*1e-3
grPeriod = easyqt.get_float("Enter CB Grating Period [um]",
title='Experimental Values',
default_value=4.8)*1e-6
pattern = easyqt.get_choice(message='Select CB Grating Pattern',
title='Experimental Values',
choices=['Edge', 'Diagonal'])
# choices=['Diagonal', 'Edge'])
sourceDistance = easyqt.get_float("Enter Distance to Source [m]",
title='Experimental Values',
default_value=34)