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()
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', default_value=1) listOfDataFiles = listOfDataFiles[0::strideFile] zvec = zvec[0::strideFile] elif zvec_from == 'Tabled':
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)
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) 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)
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) yyGrid, xxGrid = np.mgrid[0:nx:stride, 0:ny:stride] # %% wpu.plot_profile(xxGrid, yyGrid, data[::stride, ::stride], title=fname)
option = easyqt.get_choice('Crop or Pad?', title='Title', choices=['Pad', 'Crop']) else: samplefileName = sys.argv[1] option = sys.argv[2] fixRef = ('Ref' in sys.argv[2]) displayPlots = False # %% if optionRef == 'Manual': totalShift_i = easyqt.get_int('Total Vertical Shift', title='Title', default_value=0) totalShift_j = easyqt.get_int('Total Horizontal Shift', title='Title', default_value=0) _, allShifts = align_many_imgs_linearshifts( samplefileName, totalShift=[-totalShift_i, -totalShift_j]) else: img_ref = dxchange.read_tiff(samplefileName) if easyqt.get_yes_or_no('New Crop?'): [colorlimit, cmap] = wpu.plot_slide_colorbar(
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)