def gui_list_data_phase_stepping(directory=''):
'''
TODO: Write Docstring
'''
originalDir = os.getcwd()
if directory != '':
if os.path.isdir(directory):
os.chdir(directory)
else:
wpu.print_red("WARNING: Directory " + directory +
" doesn't exist.")
wpu.print_blue("MESSAGE: Using current working directory " +
originalDir)
samplef1 = easyqt.get_file_names("Choose one of the scan " +
"files with sample")
if len(samplef1) == 3:
[samplef1, samplef2, samplef3] = samplef1
else:
samplef1 = samplef1[0]
os.chdir(samplef1.rsplit('/', 1)[0])
samplef2 = easyqt.get_file_names("File name with Reference")[0]
samplef3 = easyqt.get_file_names("File name with Dark Image")
if len(samplef3) == 1:
samplef3 = samplef3[0]
else:
samplef3 = ''
wpu.print_red('MESSAGE: You choosed to not use dark images')
wpu.print_blue('MESSAGE: Sample files directory: ' +
samplef1.rsplit('/', 1)[0])
samplef1.rsplit('/', 1)[0]
listf1 = load_files_scan(samplef1)
listf2 = load_files_scan(samplef2)
listf3 = load_files_scan(samplef3)
listf1.sort()
listf2.sort()
listf3.sort()
return listf1, listf2, listf3
def gui_load_data_finename(directory='', title="File name with Data"):
originalDir = os.getcwd()
if directory != '':
if os.path.isdir(directory):
os.chdir(directory)
else:
wpu.print_red("WARNING: Directory " + directory +
" doesn't exist.")
wpu.print_blue("MESSAGE: Using current working directory " +
originalDir)
fname1 = easyqt.get_file_names(title)
if len(fname1) == 0:
fname_last = None
else:
fname_last = fname1[0]
os.chdir(originalDir)
return fname_last
unFilterSize=unFilterSize)
# =============================================================================
# %% Script starts
# =============================================================================
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')
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
return data2save, headerdic
# %%
if __name__ == '__main__':
argv = sys.argv
if len(argv) == 4:
data, headerdic = save_profile_from_sdf(argv[1],
nprofiles=int(argv[2]),
direction=argv[3])
else:
data, headerdic = save_profile_from_sdf(easyqt.get_file_names()[0],
nprofiles=easyqt.get_int('Number of profiles'),
direction=easyqt.get_choice(choices=['Vertical', 'Horizontal']))
# %%
plt.figure()
for i in range(1, data.shape[1]):
plt.plot(data[:,0], data[:,i]+1e-9)
plt.show()
]
what2do = easyqt.get_choice('Pick one', choices=choices)
wpu.set_at_ini_file(inifname, 'Parameters', 'what2do', what2do)
# %% Target
# Target file is the shape wanted for the correction.
if len(sys.argv) > 2 or easyqt.get_yes_or_no(
'Do you want to load a target file?'):
if len(sys.argv) > 2:
targetName = sys.argv[2]
else:
targetName = easyqt.get_file_names('the target file directory:')
if targetName == []:
targetName = defaults['Files'].get('target file')
else:
wpu.set_at_ini_file(inifname, 'Files', 'target file', targetName[0])
temp_Data = wpu.load_csv_file(targetName[0])[0]
lim_xnew = np.min(
(np.abs(listOfArrays[0][0, 0]), np.abs(listOfArrays[0][-1, 0]),
np.abs(temp_Data[0, 0]), np.abs(temp_Data[-1, 0])))
else:
temp_Data = None
lim_xnew = np.min(
(np.abs(listOfArrays[0][0, 0]), np.abs(listOfArrays[0][-1, 0])))
import os
import sys
import matplotlib.pyplot as plt
from skimage.restoration import unwrap_phase
import numpy as np
from mpl_toolkits.mplot3d import Axes3D
if len(sys.argv) != 1:
os.chdir(sys.argv[1])
os.chdir('/home/grizolli/work/spectra/tempresults/')
data = np.loadtxt(open(easyqt.get_file_names("Data File to Plot")[0], 'rb'),
skiprows=11)
# %%
nx = len(set(data[:, 0]))
ny = len(set(data[:, 1]))
xxGrid = np.reshape(data[:, 0]*1e-3, (nx, ny))
yyGrid = np.reshape(data[:, 1]*1e-3, (nx, ny))
field_x = np.reshape(data[:, 2] + 1j*data[:, 3], (nx, ny))
field_y = np.reshape(data[:, 4] + 1j*data[:, 5], (nx, ny))
phase_x = -unwrap_phase(np.angle(field_x))
]
what2do = easyqt.get_choice('Pick one', choices=choices)
wpu.set_at_ini_file(inifname, 'Parameters', 'what2do', what2do)
# %% Target
# Target file is the shape wanted for the correction.
if len(sys.argv) > 2 or easyqt.get_yes_or_no(
'Do you want to load a target file?'):
if len(sys.argv) > 2:
targetName = sys.argv[2]
else:
targetName = easyqt.get_file_names('the target file directory:')
# use one image as the current state
if easyqt.get_yes_or_no(
'Do you want to load the refence file for target?'):
ref_name = easyqt.get_file_names('the reference file directory:')
else:
ref_name = []
if targetName == []:
targetName = defaults['Files'].get('target file')
else:
wpu.set_at_ini_file(inifname, 'Files', 'target file', targetName[0])
if use_cap:
if ref_name == []:
# =============================================================================
originalDir = os.getcwd()
try:
os.chdir('/data/share/BeamtimeData/')
except FileNotFoundError:
try:
os.chdir('~/workspace/pythonWorkspace/data')
except:
pass
samplefileName = easyqt.get_file_names("Choose one of the scan files")[0]
listOfDataFiles = glob.glob(samplefileName.rsplit('_' ,1)[0] + '*.tif')
data_dir = samplefileName.rsplit('/', 1)[0]
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)
curves.append(np.asarray(fig.axes[0].lines[i].get_data()))
return curves
# %%
if __name__ == '__main__':
# if len(sys.argv) != 1:
# os.chdir(sys.argv[1])
if len(sys.argv) == 1:
flist = easyqt.get_file_names("Pickle File to Plot")
fname = flist[0]
else:
fname = sys.argv[1]
results = _load_data_from_pickle(fname)
# %%
zvec = results[0][0] * 1e-3
contrastV = results[0][1] * 1e-2
contrastH = results[1][1] * 1e-2
if zvec[-1] - zvec[0] < 0:
"""
from wavepy.utils import easyqt
import dxchange
import sys
import numpy as np
import wavepy.utils as wpu
if len(sys.argv) != 1:
fname = sys.argv[1]
else:
fname = easyqt.get_file_names("Data File to Plot")[0]
data = dxchange.read_tiff(fname)
data = wpu.crop_graphic_image(data, kargs4graph={'cmap': 'rainbow'})[0]
# %%
nx, ny = np.shape(data)
stride = 1
if nx > 200 or ny > 200:
stride = easyqt.get_int(
'Number of points: {} x {}.'.format(nx, ny) +
' Enter value for stride:', 'Enter Value', 2, 1, 101)
@author: Walan Grizolli
Hint: make the file executable and add to a directory in the PATH
to make executable in linux:
>>> chmod +x FILENAME
"""
import pickle
from wavepy.utils import easyqt
import matplotlib.pyplot as plt
figx = pickle.load(open(easyqt.get_file_names("Pickle File to Plot")[0],'rb'))
plt.show(block=False) # this lines keep the script alive to see the plot
figx2 = pickle.load(open(easyqt.get_file_names("Pickle File to Plot")[0],'rb'))
plt.show(block=True) # this lines keep the script alive to see the plot
# %% Example of how to get the data from a graph
import numpy as np
# %%
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)
optionRef = easyqt.get_choice(
'Align images to reference ot to previous image?',
title='Title',
choices=['Reference', 'Previous', 'Manual'])
fixRef = (optionRef == 'Reference')
if optionRef != 'Manual':
def main_terminal(data_dir,
zvec_from,
startDist,
step_z_scan,
image_per_point,
strideFile,
pixelSize=0.65e-6,
gratingPeriod=4.8e-6,
pattern='Diagonal',
sourceDistanceV=-1,
sourceDistanceH=32,
unFilterSize=1,
searchRegion=20,
idx4crop=[0, -1, 0, -1],
darkRegionSelctionFlag=True):
'''
*** all unit in [m]
data_dir: data folder path
zvec_from: distance type:
'Calculated'
'Tabled'
startDist: started distance postion
step_z_scan: step size
image_per_point: images number for every distance
strideFile: Stride (Use only every XX files)
pixelSize: Pixel Size
gratingPeriod: CB Grating Period
pattern: grating pattern
'Diagonal' or 'Edge']
sourceDistanceV: Distance to Source
in the VERTICAL [m]
sourceDistanceH: Distance to Source
in the Horizontal [m]
unFilterSize: Size for Uniform Filter [Pixels]
default_value 1
searchRegion: Size of Region for Searching
the Peak [in Pixels]
default_value=20
idx4crop: crop area
[low_y, high_y, low_x, high_x ]
darkRegionSelctionFlag: use dark region [0, 20, 0, 20]?
'''
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/' + 'zscan'
# wpu.print_blue('MESSAGE: Loading files ' +
# samplefileName.rsplit('_', 1)[0] + '*.tif')
wpu.print_blue('MESSAGE: Loading files ' + data_dir + '/*.tif')
# listOfDataFiles = glob.glob(samplefileName.rsplit('_', 2)[0] + '*.tif')
listOfDataFiles = glob.glob(os.path.join(data_dir, '*.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]')
print(darkRegionSelctionFlag)
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 folder: ' + data_dir, preffname=fname2save)
wpu.log_this('\nNumber of files : ' + str(nfiles))
wpu.log_this('Stride : ' + str(strideFile))
print(zvec_from)
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 - 2)
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)
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)
# %% Target
if len(sys.argv) > 2 or easyqt.get_yes_or_no('Do you want to load a target file?'):
if len(sys.argv) > 2:
targetName = sys.argv[2]
else:
targetName = easyqt.get_file_names(title='select target CSV')
if targetName == []:
targetName = defaults['Files'].get('target file')
else:
wpu.set_at_ini_file(inifname,
'Files',
'target file', targetName[0])
#temp_Data = wpu.load_csv_file(targetName[0])[0]
temp_Data = load_csv_new(targetName[0])[0]
lim_xnew = np.min((np.abs(listOfArrays[0][0, 0]),
np.abs(listOfArrays[0][-1, 0]),
np.abs(temp_Data[0, 0]),
np.abs(temp_Data[-1, 0])))
else:
Hint: make the file executable and add to a directory in the PATH
to make executable in linux:
>>> chmod +x FILENAME
"""
import pickle
from wavepy.utils import easyqt
import os
import sys
import matplotlib.pyplot as plt
fname = easyqt.get_file_names("Pickle File to Plot")[0]
figx = pickle.load(open(fname, 'rb'))
plt.show(block=False) # this lines keep the script alive to see the plot
label1 = fname.rsplit('.')[0].rsplit('/')[-1]
fname = easyqt.get_file_names("Pickle File to Plot")[0]
figx2 = pickle.load(open(fname, 'rb'))
plt.show(block=False) # this lines keep the script alive to see the plot
label2 = fname.rsplit('.')[0].rsplit('/')[-1]
fname = easyqt.get_file_names("Pickle File to Plot")[0]
figx3 = pickle.load(open(fname, 'rb'))
plt.show(block=False) # this lines keep the script alive to see the plot
label3 = fname.rsplit('.')[0].rsplit('/')[-1]
fname = easyqt.get_file_names("Pickle File to Plot")[0]
@author: grizolli
"""
# %%
import numpy as np
import matplotlib.pyplot as plt
from mpl_toolkits.mplot3d import Axes3D
import wavepy.utils as wpu
from wavepy.utils import easyqt
import h5py
# %%
fname_dpc_h5 = easyqt.get_file_names("DPC Files")[0]
fh5 = h5py.File(fname_dpc_h5)
# %%
dpc_x = np.array(fh5['dpcHorizontal'])
dpc_y = np.array(fh5['dpcVertical'])
phase = np.array(fh5['phase'])
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)
import sys
from wavepy.utils import _fwhm_xy
plt.rc('axes', prop_cycle=(cycler('linestyle', ['-', '--', '-.', ':']) *
cycler('color', ['k', 'r', 'g', 'b', 'm', 'c'])))
# %% Select data File
if len(sys.argv) != 1:
listFiles = sys.argv[1:]
else:
listFiles = easyqt.get_file_names("File name with Data")
figname = listFiles[0].rsplit('/', 1)[1].rsplit('.', 1)[0]
f = open(listFiles[0], 'r')
text = f.readlines()[0:11]
f.close()
print('### FILE HEADER')
for item in text:
print('###' + item[:-1])
# %% Select which collum to plot
quantity = text[8].split()
zmin = np.nanmin(z)
zmax = np.nanmax(z)
colorIndex = np.rint(inverse * ((z - zmin) / (zmax - zmin))**power *
(nColours - 1)).astype(int)
colorIndex[np.isnan(z)] = 1
colorMap = jet_vals[colorIndex[:, :]]
return colorMap
if __name__ == '__main__':
# %%
dataFilename = easyqt.get_file_names()
if len(dataFilename) == 1:
dataFilename = dataFilename[0]
dataZ, pixelSize, headerdic = wpu.load_sdf_file(dataFilename)
else:
y, x = np.mgrid[-1:1:100j, -1:1:100j]
dataZ = np.sinc(10 * x**2) * np.exp(-y**2 / .5**2)
pixelSize = [1 / 2, 1]
# %%
plot_surf_fast(dataZ,
pixelSize,
