def main(): file_name = '/local/dataraid/databank/dataExchange/microCT/Elettra.h5' file_name_out = 'tmp/projection_' mydata = dx.Import() # Read series of images data, white, dark, theta = mydata.xtomo_raw(file_name, data_type='h5', projections_start=0, projections_end=16) # Save data mydata = ex.Export() mydata.xtomo_tiff(data=data, output_file=file_name_out, axis=0) file_name = '/local/dataraid/databank/dataExchange/microCT/Elettra.h5' file_name_out = 'tmp/sinogram_' # Load data mydata = dx.Import() # Read series of images data, white, dark, theta = mydata.xtomo_raw(file_name, data_type='h5', slices_start=0, slices_end=16) # Save data mydata = ex.Export() mydata.xtomo_tiff(data=data, output_file=file_name_out, axis=1)
def main(): file_name = '/local/dataraid/databank/CHESS/Dummy001_.tif' hdf5_file_name = '/local/dataraid/databank/dataExchange/microCT/CHESS_01.h5' sample_name = 'Dummy' projections_start = 1 projections_end = 181 white_start = 0 white_end = 10 white_step = 1 dark_start = 0 dark_end = 10 dark_step = 1 mydata = dx.Import() # Read series of images data, white, dark, theta = mydata.series_of_images( file_name, projections_start=projections_start, projections_end=projections_end, sample_name=sample_name, projections_digits=4, projections_zeros=True, log='INFO') mydata = ex.Export() # Create minimal data exchange hdf5 file mydata.xtomo_exchange(data=data, data_white=white, data_dark=dark, theta=theta, hdf5_file_name=hdf5_file_name, data_exchange_type='tomography_raw_projections')
def main(): file_name = '/local/dataraid/databank/APS_13_BM/NC/Dorthe_F_.nc' hdf5_file_name = '/local/dataraid/databank/dataExchange/tmp/APS_13_BM_netCDF.h5' white_start = 1 white_end = 4 white_step = 2 projections_start = 2 projections_end = 3 projections_step = 1 mydata = dx.Import() # Read series of images data, white, dark, theta = mydata.xtomo_raw( file_name, projections_start=projections_start, projections_end=projections_end, projections_step=projections_step, white_start=white_start, white_end=white_end, white_step=white_step, projections_digits=3, data_type='nc', log='INFO') mydata = ex.Export() # Create minimal data exchange hdf5 file mydata.xtomo_exchange(data=data, data_white=white, data_dark=dark, theta=theta, hdf5_file_name=hdf5_file_name, data_exchange_type='tomography_raw_projections')
def main(): file_name = '/local/dataraid/databank/TXM_26_ID/20130731_004_Stripe_Solder_Sample_Tip1_TomoScript_181imgs_p1s_b1.txrm' # white is saturated .... white_file_name = '/local/dataraid/databank/TXM_26_ID/20130731_001_Background_Reference_20imgs_p5s_b1.xrm' hdf5_file_name = '/local/dataraid/databank/dataExchange/tmp/APS_26_ID_xradia.h5' sample_name = '20130731_004_Stripe_Solder_Sample_Tip1' mydata = dx.Import() # Read series of images data, white, dark, theta = mydata.xtomo_raw( file_name, white_file_name=white_file_name, data_type='xradia', log='INFO') mydata = ex.Export() # Create minimal data exchange hdf5 file mydata.xtomo_exchange(data=data, data_white=white, data_dark=dark, theta=theta, hdf5_file_name=hdf5_file_name, data_exchange_type='tomography_raw_projections', sample_name=sample_name)
def main(): file_name = '/local/dataraid/databank/ESRF/scan.edf' dark_file_name = '/local/dataraid/databank/ESRF/dark.edf' white_file_name = '/local/dataraid/databank/ESRF/flat.edf' hdf5_file_name = '/local/dataraid/databank/dataExchange/microCT/ESRF_test_06.h5' sample_name = 'esrf' # set to convert slices between slices_start and slices_end # if omitted all data set will be converted slices_start = 300 slices_end = 304 mydata = dx.Import() # Read series of images data, white, dark, theta = mydata.series_of_images( file_name, white_file_name=white_file_name, dark_file_name=dark_file_name, sample_name=sample_name, slices_start=slices_start, slices_end=slices_end, data_type='edf', log='INFO') mydata = ex.Export() # Create minimal data exchange hdf5 file mydata.xtomo_exchange(data=data, data_white=white, data_dark=dark, theta=theta, hdf5_file_name=hdf5_file_name, data_exchange_type='tomography_raw_projections')
def main(): # read a series of tiff # oster: pj: from 0 -> 1440; bf from 0 -> 19; df from 0 -> 19 file_name = '/local/dataraid/databank/PetraIII/2011_KW16_oster/oster02_0001/scan_0002/ccd/pco01/ccd_.tif' dark_file_name = '/local/dataraid/databank/PetraIII/2011_KW16_oster/oster02_0001/scan_0000/ccd/pco01/ccd_.tif' white_file_name = '/local/dataraid/databank/PetraIII/2011_KW16_oster/oster02_0001/scan_0001/ccd/pco01/ccd_.tif' projections_start = 0 projections_end = 1441 white_start = 0 white_end = 20 white_step = 1 dark_start = 0 dark_end = 20 dark_step = 1 # to reconstruct slices from slices_start to slices_end # if omitted all data set is recontructed slices_start = 1000 slices_end = 1004 mydata = dx.Import() # Read series of images data, white, dark, theta = mydata.xtomo_raw( file_name, projections_start=projections_start, projections_end=projections_end, slices_start=slices_start, slices_end=slices_end, #projections_angle_range=360, white_file_name=white_file_name, white_start=white_start, white_end=white_end, white_step=white_step, dark_file_name=dark_file_name, dark_start=dark_start, dark_end=dark_end, dark_step=dark_step, projections_digits=4, projections_zeros=True, log='INFO') # TomoPy xtomo object creation and pipeline of methods. d = tomopy.xtomo_dataset(log='debug') d.dataset(data, white, dark, theta) d.normalize() d.correct_drift() #d.optimize_center() #d.phase_retrieval(pixel_size=0.9e-4, dist=6.9, energy=15.25) #d.correct_drift() d.center = 1872.87890625 d.gridrec() # Write to stack of TIFFs. mydata = ex.Export() mydata.xtomo_tiff(data=d.data_recon, output_file='tmp/PetraIII_tiff_2_tomoPy_', axis=0)
def main(): # read a series of tiff file_name = '/local/dataraid/databank/AS/Mayo_tooth_AS/SAMPLE_T_.tif' dark_file_name = '/local/dataraid/databank/AS/Mayo_tooth_AS/DF__BEFORE_.tif' white_file_name = '/local/dataraid/databank/AS/Mayo_tooth_AS/BG__BEFORE_.tif' sample_name = 'Teeth' projections_start = 0 projections_end = 1801 white_start = 0 white_end = 10 white_step = 1 dark_start = 0 dark_end = 10 dark_step = 1 # to reconstruct slices from slices_start to slices_end # if omitted all data set is recontructed slices_start = 290 slices_end = 294 mydata = dx.Import() # Read series of images data, white, dark, theta = mydata.xtomo_raw(file_name, projections_start = projections_start, projections_end = projections_end, slices_start = slices_start, slices_end = slices_end, white_file_name = white_file_name, white_start = white_start, white_end = white_end, white_step = white_step, dark_file_name = dark_file_name, dark_start = dark_start, dark_end = dark_end, dark_step = dark_step, projections_digits = 4, white_digits = 2, dark_digits = 2, projections_zeros = True, log='INFO' ) # TomoPy xtomo object creation and pipeline of methods. d = tomopy.xtomo_dataset(log='debug') d.dataset(data, white, dark, theta) d.normalize() d.correct_drift() #d.optimize_center() #d.phase_retrieval() #d.correct_drift() d.center=1184.0 d.gridrec() # Write to stack of TIFFs. mydata = ex.Export() mydata.xtomo_tiff(data = d.data_recon, output_file = 'tmp/Australian_tiff_2_tomoPy_', axis=0)
def main(): file_name = '/local/dataraid/databank/SLS_2011/Ashley/3e_final_2_.tif' log_file = '/local/dataraid/databank/SLS_2011/Ashley/3e_final_2_.log' hdf5_file_name = '/local/dataraid/databank/dataExchange/microCT/Ashley_SLS.h5' #Read SLS log file data file = open(log_file, 'r') for line in file: if 'Number of darks' in line: NumberOfDarks = re.findall(r'\d+', line) if 'Number of flats' in line: NumberOfFlats = re.findall(r'\d+', line) if 'Number of projections' in line: NumberOfProjections = re.findall(r'\d+', line) if 'Number of inter-flats' in line: NumberOfInterFlats = re.findall(r'\d+', line) if 'Inner scan flag' in line: InnerScanFlag = re.findall(r'\d+', line) if 'Flat frequency' in line: FlatFrequency = re.findall(r'\d+', line) if 'Rot Y min' in line: RotYmin = re.findall(r'\d+.\d+', line) if 'Rot Y max' in line: RotYmax = re.findall(r'\d+.\d+', line) if 'Angular step' in line: AngularStep = re.findall(r'\d+.\d+', line) file.close() dark_start = 1 dark_end = int(NumberOfDarks[0]) + 1 white_start = dark_end white_end = white_start + int(NumberOfFlats[0]) projections_start = white_end projections_end = projections_start + int(NumberOfProjections[0]) mydata = dx.Import() # Read series of images data, white, dark, theta = mydata.series_of_images( file_name, projections_start=projections_start, projections_end=projections_end, projections_digits=4, white_start=white_start, white_end=white_end, dark_start=dark_start, dark_end=dark_end, log='INFO') mydata = ex.Export() # Create minimal data exchange hdf5 file mydata.xtomo_exchange(data=data, data_white=white, data_dark=dark, theta=theta, hdf5_file_name=hdf5_file_name, data_exchange_type='tomography_raw_projections')
def main(): file_name = '/local/dataraid/databank/Elettra/Volcanic_rock/tomo_.tif' dark_file_name = '/local/dataraid/databank/Elettra/Volcanic_rock/dark_.tif' white_file_name = '/local/dataraid/databank/Elettra/Volcanic_rock/flat_.tif' hdf5_file_name = '/local/dataraid/databank/dataExchange/microCT/Elettra_test.h5' projections_start = 1 projections_end = 1441 white_start = 1 white_end = 11 white_step = 1 dark_start = 1 dark_end = 11 dark_step = 1 sample_name = 'Volcanic_rock' # set to convert slices between slices_start and slices_end # if omitted all data set will be converted slices_start = 150 slices_end = 154 mydata = dx.Import() # Read series of images data, white, dark, theta = mydata.series_of_images( file_name, projections_start=projections_start, projections_end=projections_end, projections_digits=4, slices_start=slices_start, slices_end=slices_end, white_file_name=white_file_name, white_start=white_start, white_end=white_end, white_step=white_step, dark_file_name=dark_file_name, dark_start=dark_start, dark_end=dark_end, dark_step=dark_step, data_type='compressed_tiff', # comment this line if regular tiff projections_zeros=True, white_zeros=False, dark_zeros=False, sample_name=sample_name, log='INFO') mydata = ex.Export() # Create minimal data exchange hdf5 file mydata.xtomo_exchange(data=data, data_white=white, data_dark=dark, theta=theta, hdf5_file_name=hdf5_file_name, data_exchange_type='tomography_raw_projections')
def main(): file_name = '/local/dataraid/databank/SLS_2011/Hornby_SLS/Hornby_b.tif' log_file = '/local/dataraid/databank/SLS_2011/Hornby_SLS/Hornby.log' hdf5_file_name = '/local/dataraid/databank/dataExchange/tmp/SLS.h5' #Read SLS log file data file = open(log_file, 'r') for line in file: linelist = line.split() if len(linelist) > 1: if (linelist[0] == "Number" and linelist[2] == "darks"): number_of_darks = int(linelist[4]) elif (linelist[0] == "Number" and linelist[2] == "flats"): number_of_flats = int(linelist[4]) elif (linelist[0] == "Number" and linelist[2] == "projections"): number_of_projections = int(linelist[4]) elif (linelist[0] == "Rot" and linelist[2] == "min"): rotation_min = float(linelist[6]) elif (linelist[0] == "Rot" and linelist[2] == "max"): rotation_max = float(linelist[6]) elif (linelist[0] == "Angular" and linelist[1] == "step"): angular_step = float(linelist[4]) file.close() dark_start = 1 dark_end = number_of_darks + 1 white_start = dark_end white_end = white_start + number_of_flats projections_start = white_end projections_end = projections_start + number_of_projections mydata = dx.Import() # Read series of images data, white, dark, theta = mydata.xtomo_raw( file_name, projections_start=projections_start, projections_end=projections_end, projections_digits=4, white_start=white_start, white_end=white_end, dark_start=dark_start, dark_end=dark_end, log='INFO') mydata = ex.Export() # Create minimal data exchange hdf5 file mydata.xtomo_exchange(data=data, data_white=white, data_dark=dark, theta=theta, hdf5_file_name=hdf5_file_name, data_exchange_type='tomography_raw_projections')
def main(): file_name = '/local/dataraid/databank/AS/Mayo_tooth_AS/SAMPLE_T_.tif' dark_file_name = '/local/dataraid/databank/AS/Mayo_tooth_AS/DF__AFTER_.tif' white_file_name = '/local/dataraid/databank/AS/Mayo_tooth_AS/BG__BEFORE_.tif' hdf5_file_name = '/local/dataraid/databank/dataExchange/microCT/Australian_test.h5' sample_name = 'Teeth' projections_start = 0 projections_end = 1801 white_start = 0 white_end = 10 white_step = 1 dark_start = 0 dark_end = 10 dark_step = 1 # set to convert slices between slices_start and slices_end # if omitted all data set will be converted slices_start = 290 slices_end = 294 mydata = dx.Import() # Read series of images data, white, dark, theta = mydata.series_of_images( file_name, projections_start=projections_start, projections_end=projections_end, slices_start=slices_start, slices_end=slices_end, white_file_name=white_file_name, white_start=white_start, white_end=white_end, white_step=white_step, dark_file_name=dark_file_name, dark_start=dark_start, dark_end=dark_end, dark_step=dark_step, sample_name=sample_name, projections_digits=4, white_digits=2, dark_digits=2, projections_zeros=True, log='INFO') mydata = ex.Export() # Create minimal data exchange hdf5 file mydata.xtomo_exchange(data=data, data_white=white, data_dark=dark, theta=theta, hdf5_file_name=hdf5_file_name, data_exchange_type='tomography_raw_projections')
def main(): # read a series of SPE file_name = '/local/dataraid/databank/APS_13_BM/SPE/run2_soln1_2_.SPE' white_start = 1 white_end = 8 white_step = 2 projections_start = 2 projections_end = 7 projections_step = 2 # set to convert slices between slices_start and slices_end # if omitted all data set will be converted slices_start = 100 slices_end = 104 mydata = dx.Import() # Read series of images data, white, dark, theta = mydata.xtomo_raw( file_name, projections_start=projections_start, projections_end=projections_end, projections_step=projections_step, slices_start=slices_start, slices_end=slices_end, white_start=white_start, white_end=white_end, white_step=white_step, projections_zeros=False, white_zeros=False, dark_zeros=False, projections_digits=1, data_type='spe', log='INFO') # TomoPy xtomo object creation and pipeline of methods. d = tomopy.xtomo_dataset(log='debug') d.dataset(data, white, dark, theta) d.normalize() d.correct_drift() #d.optimize_center() #d.phase_retrieval() #d.correct_drift() d.center = 705 d.gridrec() # Write to stack of TIFFs. mydata = ex.Export() mydata.xtomo_tiff(data=d.data_recon, output_file='tmp/APS_13_BM_spe_2_tomoPy_', axis=0)
def main(): # only used to locate the wavelenght.dpt and angle.dpt files raw_tiff_base_name = "/local/dataraid/databank/dataExchange/microCT/SRC/raw/FPA_16_18_18_TOMO_243_Fiber_2500_50_50_" hdf5_base_name = "/local/dataraid/databank/dataExchange/microCT/SRC/dx/FPA_16_18_18_TOMO_243_Fiber_2500_50_50_" log_file = raw_tiff_base_name + "wavelength.dpt" angle_file = raw_tiff_base_name + "angle.dpt" dir_name = os.path.dirname(hdf5_base_name) sample_name_prefix = os.path.basename(hdf5_base_name) print dir_name print sample_name_prefix file = open(log_file, 'r') for line in file: linelist=line.split(",") hdf5_file_name = hdf5_base_name+linelist[0]+"cm-1.h5" sample_name = hdf5_base_name+linelist[0]+"cm-1" # set to read slices between slices_start and slices_end # if omitted all data set will be converted slices_start = 30 slices_end = 36 # to create a data exchange file use convert_SRC.py module, data, white, dark, theta = tomopy.xtomo_reader(hdf5_file_name, slices_start=slices_start, slices_end=slices_end) # TomoPy xtomo object creation and pipeline of methods. d = tomopy.xtomo_dataset(log='debug') d.dataset(data, white, dark, theta) d.normalize() d.correct_drift() #d.optimize_center() #d.phase_retrieval() #d.correct_drift() d.center=64 d.gridrec() # Write to stack of TIFFs. rec_name = dir_name + "/rec/" + sample_name_prefix + linelist[0] + "cm-1" # Write to stack of TIFFs. mydata = ex.Export() mydata.xtomo_tiff(data = d.data_recon, output_file = rec_name, axis=0) file.close()
def main(): # read a series of tiff file_name = '/local/dataraid/databank/Anka/radios/image_.tif' dark_file_name = '/local/dataraid/databank/Anka/darks/image_.tif' white_file_name = '/local/dataraid/databank/Anka/flats/image_.tif' projections_start = 0 projections_end = 3167 white_start = 0 white_end = 100 dark_start = 0 dark_end = 100 sample_name = 'Anka' # to reconstruct slices from slices_start to slices_end # if omitted all data set is recontructed slices_start = 800 slices_end = 804 mydata = dx.Import() # Read series of images data, white, dark, theta = mydata.xtomo_raw(file_name, projections_start = projections_start, projections_end = projections_end, slices_start = slices_start, slices_end = slices_end, white_file_name = white_file_name, white_start = white_start, white_end = white_end, dark_file_name = dark_file_name, dark_start = dark_start, dark_end = dark_end, projections_digits = 5, log='INFO' ) # TomoPy xtomo object creation and pipeline of methods. d = tomopy.xtomo_dataset(log='debug') d.dataset(data, white, dark, theta) d.normalize() d.correct_drift() #d.optimize_center() #d.phase_retrieval() #d.correct_drift() d.center=993.825 d.gridrec() # Write to stack of TIFFs. mydata = ex.Export() mydata.xtomo_tiff(data = d.data_recon, output_file = 'tmp/Anka_tiff_2_tomoPy_', axis=0)
def main(): file_name = '/local/dataraid/databank/VirginiaTech/test_sample_Diplo_4/Diplodocus_1_200mm_4_.tif' dark_file_name = '/local/dataraid/databank/VirginiaTech/test_sample_Diplo_4/Diplodocus_1_200mm_4postDark_.tif' white_file_name = '/local/dataraid/databank/VirginiaTech/test_sample_Diplo_4/Diplodocus_1_200mm_4postFlat_.tif' hdf5_file_name = '/local/dataraid/databank/dataExchange/microCT/VirginiaTech_test.h5' sample_name = 'Diplodocus_1_200mm_' projections_start = 1 # projection 0 is dark so we skip it projections_end = 1500 white_start = 0 white_end = 10 white_step = 1 dark_start = 0 dark_end = 10 dark_step = 1 # set to convert slices between slices_start and slices_end # if omitted all data set will be converted slices_start = 600 slices_end = 604 mydata = dx.Import() # Read series of images data, white, dark, theta = mydata.series_of_images( file_name, projections_start=projections_start, projections_end=projections_end, slices_start=slices_start, slices_end=slices_end, white_file_name=white_file_name, white_start=white_start, white_end=white_end, white_step=white_step, dark_file_name=dark_file_name, dark_start=dark_start, dark_end=dark_end, dark_step=dark_step, sample_name=sample_name, projections_digits=5, projections_zeros=True, log='INFO') mydata = ex.Export() # Create minimal data exchange hdf5 file mydata.xtomo_exchange(data=data, data_white=white, data_dark=dark, theta=theta, hdf5_file_name=hdf5_file_name, data_exchange_type='tomography_raw_projections')
def main(): # read a series of netCDF file_name = '/local/dataraid/databank/APS_13_BM/NC/Dorthe_F_.nc' white_start = 1 white_end = 4 white_step = 2 projections_start = 2 projections_end = 3 projections_step = 1 # set to convert slices between slices_start and slices_end # if omitted all data set will be converted slices_start = 300 slices_end = 304 mydata = dx.Import() # Read series of images data, white, dark, theta = mydata.xtomo_raw( file_name, projections_start=projections_start, projections_end=projections_end, projections_step=projections_step, slices_start=slices_start, slices_end=slices_end, white_start=white_start, white_end=white_end, white_step=white_step, projections_digits=3, data_type='nc', log='INFO') # TomoPy xtomo object creation and pipeline of methods. d = tomopy.xtomo_dataset(log='debug') d.dataset(data, white, dark, theta) d.normalize() d.correct_drift() #d.optimize_center() #d.phase_retrieval() #d.correct_drift() d.center = 484.5 d.gridrec() # Write to stack of TIFFs. mydata = ex.Export() mydata.xtomo_tiff(data=d.data_recon, output_file='tmp/APS_13_BM_netCDF_2_tomoPy_', axis=0)
def main(): file_name = '/local/dataraid/databank/Anka/radios/image_.tif' dark_file_name = '/local/dataraid/databank/Anka/darks/image_.tif' white_file_name = '/local/dataraid/databank/Anka/flats/image_.tif' hdf5_file_name = '/local/dataraid/databank/dataExchange/microCT/Anka_test.h5' projections_start = 0 projections_end = 3167 white_start = 0 white_end = 100 dark_start = 0 dark_end = 100 sample_name = 'Anka' # set to convert slices between slices_start and slices_end # if omitted all data set will be converted slices_start = 800 slices_end = 804 mydata = dx.Import() # Read series of images data, white, dark, theta = mydata.series_of_images( file_name, projections_start=projections_start, projections_end=projections_end, slices_start=slices_start, slices_end=slices_end, white_file_name=white_file_name, white_start=white_start, white_end=white_end, dark_file_name=dark_file_name, dark_start=dark_start, dark_end=dark_end, sample_name=sample_name, projections_digits=5, log='INFO') mydata = ex.Export() # Create minimal data exchange hdf5 file mydata.xtomo_exchange(data=data, data_white=white, data_dark=dark, theta=theta, hdf5_file_name=hdf5_file_name, data_exchange_type='tomography_raw_projections')
def main(): file_name = '/local/dataraid/databank/CHESS/scan1/scan1_.tiff' dark_file_name = '/local/dataraid/databank/CHESS/scan1/scan1_dark_.tiff' white_file_name = '/local/dataraid/databank/CHESS/scan1/scan1_white_.tiff' projections_start = 1 projections_end = 361 white_start = 0 white_end = 1 white_step = 1 dark_start = 0 dark_end = 1 dark_step = 1 # set to convert slices between slices_start and slices_end # if omitted all data set will be converted slices_start = 400 slices_end = 404 mydata = dx.Import() # Read series of images data, white, dark, theta = mydata.xtomo_raw(file_name, projections_start = projections_start, projections_end = projections_end, slices_start = slices_start, slices_end = slices_end, projections_digits = 3, projections_zeros = True, log='INFO' ) # Xtomo object creation and pipeline of methods. d = tomopy.xtomo_dataset(log='debug') d.dataset(data, white, dark, theta) d.normalize() d.correct_drift() #d.optimize_center() #d.phase_retrieval() #d.correct_drift() d.center=1160.5 d.gridrec() # Write to stack of TIFFs. mydata = ex.Export() mydata.xtomo_tiff(data = d.data_recon, output_file = 'tmp/CHESS_tiff_2_tomoPy_', axis=0)
def main(): file_name = '/local/dataraid/databank/AS/Mayo_tooth_AS/SAMPLE_T_.tif' dark_file_name = '/local/dataraid/databank/AS/Mayo_tooth_AS/DF__BEFORE_.tif' white_file_name = '/local/dataraid/databank/AS/Mayo_tooth_AS/BG__BEFORE_.tif' hdf5_file_name = '/local/dataraid/databank/dataExchange/tmp/Australian.h5' sample_name = 'Teeth' projections_start = 0 projections_end = 1801 white_start = 0 white_end = 10 white_step = 1 dark_start = 0 dark_end = 10 dark_step = 1 mydata = dx.Import() # Read series of images data, white, dark, theta = mydata.xtomo_raw( file_name, projections_start=projections_start, projections_end=projections_end, white_file_name=white_file_name, white_start=white_start, white_end=white_end, white_step=white_step, dark_file_name=dark_file_name, dark_start=dark_start, dark_end=dark_end, dark_step=dark_step, projections_digits=4, white_digits=2, dark_digits=2, projections_zeros=True, log='INFO') mydata = ex.Export() # Create minimal data exchange hdf5 file mydata.xtomo_exchange(data=data, data_white=white, data_dark=dark, theta=theta, hdf5_file_name=hdf5_file_name, data_exchange_type='tomography_raw_projections', sample_name=sample_name)
def main(): file_name = '/local/dataraid/databank/APS_13_BM/SPE/run2_soln1_2_.SPE' hdf5_file_name = '/local/dataraid/databank/dataExchange/microCT/APS_13_BM_test_07.h5' white_start = 1 white_end = 8 white_step = 2 projections_start = 2 projections_end = 7 projections_step = 2 # set to convert slices between slices_start and slices_end # if omitted all data set will be converted slices_start = 100 slices_end = 104 mydata = dx.Import() # Read series of images data, white, dark, theta = mydata.series_of_images(file_name, projections_start = projections_start, projections_end = projections_end, projections_step = projections_step, slices_start = slices_start, slices_end = slices_end, white_start = white_start, white_end = white_end, white_step = white_step, projections_zeros=False, white_zeros=False, dark_zeros=False, projections_digits = 1, data_type='spe', log='INFO' ) mydata = ex.Export() # Create minimal data exchange hdf5 file mydata.xtomo_exchange(data = data, data_white = white, data_dark = dark, theta = theta, hdf5_file_name = hdf5_file_name, data_exchange_type = 'tomography_raw_projections' )
def main(): file_name = '/local/dataraid/databank/dataExchange/microCT/Elettra.h5' file_name_out = '/local/dataraid/databank/dataExchange/microCT/Elettra_out.h5' mydata = dx.Import() # Read series of images data, white, dark, theta = mydata.xtomo_raw(file_name, data_type='h5', log='INFO') mydata = ex.Export() # Create minimal data exchange hdf5 file mydata.xtomo_exchange(data=data, data_white=white, data_dark=dark, theta=theta, hdf5_file_name=file_name_out, data_exchange_type='tomography_raw_projections')
def main(): raw_tiff_base_name = "/local/dataraid/databank/dataExchange/microCT/SRC/raw/FPA_16_18_18_TOMO_243_Fiber_2500_50_50_" hdf5_base_name = "/local/dataraid/databank/dataExchange/tmp/SRC_" log_file = raw_tiff_base_name + "wavelength.dpt" angle_file = raw_tiff_base_name + "angle.dpt" # Determine projection angle end file = open(angle_file, 'r') lines = file.readlines() projections_angle_end = float(lines[0]) + float(lines[1]) file.close() file = open(log_file, 'r') for line in file: linelist = line.split(",") file_name = raw_tiff_base_name+linelist[0]+"cm-1.dpt" sample_name = raw_tiff_base_name+linelist[0]+"cm-1" hdf5_file_name = hdf5_base_name+linelist[0]+"cm-1.h5" mydata = dx.Import() # Read series of images from a single dpt file data, white, dark, theta = mydata.xtomo_raw(file_name, data_type='dpt', projections_angle_end = projections_angle_end, log='INFO' ) mydata = ex.Export() # Create minimal data exchange hdf5 file mydata.xtomo_exchange(data = data, data_white = white, data_dark = dark, theta = theta, hdf5_file_name = hdf5_file_name, sample_name = sample_name, data_exchange_type = 'tomography_raw_projections' ) file.close()
def main(): file_name = '/local/dataraid/databank/APS_13_BM/NC/Dorthe_F_.nc' hdf5_file_name = '/local/dataraid/databank/dataExchange/microCT/APS_13_BM_NC_test_02.h5' white_start = 1 white_end = 4 white_step = 2 projections_start = 2 projections_end = 3 projections_step = 1 # set to convert slices between slices_start and slices_end # if omitted all data set will be converted slices_start = 300 slices_end = 304 mydata = dx.Import() # Read series of images data, white, dark, theta = mydata.series_of_images( file_name, projections_start=projections_start, projections_end=projections_end, projections_step=projections_step, slices_start=slices_start, slices_end=slices_end, white_start=white_start, white_end=white_end, white_step=white_step, projections_digits=3, data_type='nc', sample_name='Stripe_Solder_Sample_Tip1', log='INFO') mydata = ex.Export() # Create minimal data exchange hdf5 file mydata.xtomo_exchange(data=data, data_white=white, data_dark=dark, theta=theta, hdf5_file_name=hdf5_file_name, data_exchange_type='tomography_raw_projections')
def main(): file_name = '/local/dataraid/databank/Anka/radios/image_.tif' dark_file_name = '/local/dataraid/databank/Anka/darks/image_.tif' white_file_name = '/local/dataraid/databank/Anka/flats/image_.tif' hdf5_file_name = '/local/dataraid/databank/dataExchange/tmp/Anka.h5' projections_start = 0 projections_end = 3167 white_start = 0 white_end = 100 dark_start = 0 dark_end = 100 sample_name = 'Anka' mydata = dx.Import() # Read series of images data, white, dark, theta = mydata.xtomo_raw( file_name, projections_start=projections_start, projections_end=projections_end, white_file_name=white_file_name, white_start=white_start, white_end=white_end, dark_file_name=dark_file_name, dark_start=dark_start, dark_end=dark_end, projections_digits=5, log='INFO') mydata = ex.Export() # Create minimal data exchange hdf5 file mydata.xtomo_exchange(data=data, data_white=white, data_dark=dark, theta=theta, hdf5_file_name=hdf5_file_name, data_exchange_type='tomography_raw_projections', sample_name=sample_name)
def main(): file_name = '/local/dataraid/2013_11/Vincent_201311/GA_exp/92_2_01/rad_0400ms_.tiff' white_file_name = '/local/dataraid/2013_11/Vincent_201311/GA_exp/92_2_01/ff_0350ms_.tiff' hdf5_file_name = '/local/dataraid/databank/dataExchange/microCT/NSLS.h5' white_start = 0 white_end = 2580 white_step = 30 projections_start = 0 projections_end = 2600 # set to convert slices between slices_start and slices_end # if omitted all data set will be converted slices_start = 800 slices_end = 804 mydata = dx.Import() # Read series of images data, white, dark, theta = mydata.series_of_images( file_name, projections_start=projections_start, projections_end=projections_end, projections_digits=4, slices_start=slices_start, slices_end=slices_end, white_file_name=white_file_name, white_start=white_start, white_end=white_end, white_step=white_step, log='INFO') mydata = ex.Export() # Create minimal data exchange hdf5 file mydata.xtomo_exchange(data=data, data_white=white, data_dark=dark, theta=theta, hdf5_file_name=hdf5_file_name, data_exchange_type='tomography_raw_projections')
def main(): file_name = '/local/dataraid/databank/APS_15_ID/AluminaStick_0A_fullRunRenamed/AluminaStick_.hdf' projections_start = 1 projections_end = 361 # to reconstruct a subset of slices set slices_start and slices_end # if omitted the full data set is recontructed slices_start = 800 slices_end = 804 mydata = dx.Import() # Read series of images data, white, dark, theta = mydata.xtomo_raw( file_name, projections_start=projections_start, projections_end=projections_end, slices_start=slices_start, slices_end=slices_end, projections_digits=4, data_type='hdf5', log='INFO') # TomoPy xtomo object creation and pipeline of methods. d = tomopy.xtomo_dataset(log='debug') d.dataset(data, white, dark, theta) d.normalize() d.correct_drift() #d.optimize_center() d.phase_retrieval(pixel_size=0.9e-4, dist=8.1, energy=17) #d.correct_drift() d.center = 772.2 d.gridrec() # Write to stack of TIFFs. mydata = ex.Export() mydata.xtomo_tiff(data=d.data_recon, output_file='tmp/AluminaStick_0A_', axis=0)
def main(): file_name = '/local/dataraid/databank/APS_13_BM/SPE/run2_soln1_2_.SPE' hdf5_file_name = '/local/dataraid/databank/dataExchange/tmp/APS_13_BM_spe.h5' white_start = 1 white_end = 8 white_step = 2 projections_start = 2 projections_end = 7 projections_step = 2 mydata = dx.Import() # Read series of images data, white, dark, theta = mydata.xtomo_raw(file_name, projections_start = projections_start, projections_end = projections_end, projections_step = projections_step, # slices_start = slices_start, # slices_end = slices_end, white_start = white_start, white_end = white_end, white_step = white_step, projections_zeros=False, white_zeros=False, dark_zeros=False, projections_digits = 1, data_type='spe', log='INFO' ) mydata = ex.Export() # Create minimal data exchange hdf5 file mydata.xtomo_exchange(data = data, data_white = white, data_dark = dark, theta = theta, hdf5_file_name = hdf5_file_name, data_exchange_type = 'tomography_raw_projections' )
def main(): file_name = '/local/dataraid/databank/Diamond/13429_subx.nxs' hdf5_file_name = '/local/dataraid/databank/dataExchange/tmp/Diamond_04.h5' mydata = dx.Import() # Read series of images data, white, dark, theta = mydata.xtomo_raw(file_name, data_type='nxs', slices_start=1600, slices_end=1610, slices_step=1, log='INFO') mydata = ex.Export() # Create minimal data exchange hdf5 file mydata.xtomo_exchange(data=data, data_white=white, data_dark=dark, theta=theta, hdf5_file_name=hdf5_file_name, data_exchange_type='tomography_raw_projections')
def main(): # read a series of tiff file_name = '/local/dataraid/databank/dataExchange/microCT/Sangid_ShortFiber.h5' file_name = '/local/dataraid/databank/dataExchange/tmp/Elettra.h5' # to reconstruct slices from slices_start to slices_end # if omitted all data set is recontructed # slices_start = 1365 # slices_end = 1367 slices_start = 150 slices_end = 154 mydata = dx.Import() # Read series of images data, white, dark, theta = mydata.xtomo_raw(file_name, slices_start = slices_start, slices_end = slices_end, data_type='h5', log='INFO' ) # TomoPy xtomo object creation and pipeline of methods. d = tomopy.xtomo_dataset(log='debug') d.dataset(data, white, dark, theta) d.normalize() #d.correct_drift() d.optimize_center() #d.phase_retrieval() #d.correct_drift() #d.center=1096.375 d.gridrec() # Write to stack of TIFFs. mydata = ex.Export() mydata.xtomo_tiff(data = d.data_recon, output_file = 'tmp/Elettra_DataExchange_2_tomoPy_', axis=0)
def main(): # HN-MR-002-1.0kPa/ HN-MR-002-2.0kPa/ HN-MR-002-3.0kPa/ ## file_name = '/local/dataraid/databank/GrenobleGranularData/Tomo/HN-MR-002-1_0kPa/Radios_original/HN-MR-002-SAT_.tif' ## hdf5_file_name = '/local/dataraid/databank/dataExchange/microCT/HN-MR-002-SAT.h5' ## sample_name = 'HN-MR-002-SAT' file_name = '/local/dataraid/databank/GrenobleGranularData/Tomo/HN-MR-002-2_0kPa/Radios_original/HN-MR-002-2KPA_.tif' hdf5_file_name = '/local/dataraid/databank/dataExchange/microCT/HN-MR-002-2KPA.h5' sample_name = 'HN-MR-002-2KPA' ## file_name = '/local/dataraid/databank/GrenobleGranularData/Tomo/HN-MR-002-3_0kPa/Radios_original/HN-MR-002-3_0KPA_.tif' ## hdf5_file_name = '/local/dataraid/databank/dataExchange/microCT/HN-MR-002-3_0KPA.h5' ## sample_name = 'HN-MR-002-3_0KPA' projections_start = 1 projections_end = 1201 mydata = dx.Import() # Read series of images data, white, dark, theta = mydata.series_of_images( file_name, projections_start=projections_start, projections_end=projections_end, sample_name=sample_name, projections_digits=5, projections_zeros=True, log='INFO') mydata = ex.Export() # Create minimal data exchange hdf5 file mydata.xtomo_exchange(data=data, data_white=white, data_dark=dark, theta=theta, hdf5_file_name=hdf5_file_name, data_exchange_type='tomography_raw_projections')