def main():
file_name = '/local/dataraid/databank/templates/esrf_ID19/tomo.edf'
dark_file_name = '/local/dataraid/databank/templates/esrf_ID19/dark.edf'
white_file_name = '/local/dataraid/databank/templates/esrf_ID19/flat.edf'
hdf5_file_name = '/local/dataraid/databank/templates/dataExchange/tmp/ESRF.h5'
sample_name = 'edf test'
# Read raw data
read = xtomo_imp.Import()
data, white, dark, theta = read.xtomo_raw(file_name,
white_file_name=white_file_name,
dark_file_name=dark_file_name,
data_type='edf',
log='INFO')
# Save data as dataExchange
write = xtomo_exp.Export()
write.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')
def main():
file_name = '/local/dataraid/databank/templates/sls_tomcat/sample_name.tif'
log_file = '/local/dataraid/databank/templates/sls_tomcat/sample_name.log'
hdf5_file_name = '/local/dataraid/databank/templates/dataExchange/tmp/SLS.h5'
sample_name = 'Hornby_b'
#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
projections_angle_end = 180 + angular_step
# Read raw data
read = xtomo_imp.Import()
data, white, dark, theta = read.xtomo_raw(
file_name,
projections_start=projections_start,
projections_end=projections_end,
projections_angle_end=projections_angle_end,
projections_digits=4,
white_start=white_start,
white_end=white_end,
dark_start=dark_start,
dark_end=dark_end,
log='INFO')
# Save data as dataExchange
write = xtomo_exp.Export()
write.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')
def main():
file_name = '/local/dataraid/databank/templates/elettra_SYRMEP/tomo_.tif'
dark_file_name = '/local/dataraid/databank/templates/elettra_SYRMEP/dark_.tif'
white_file_name = '/local/dataraid/databank/templates/elettra_SYRMEP/flat_.tif'
hdf5_file_name = '/local/dataraid/databank/templates/dataExchange/tmp/Elettra.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'
# Read raw data
read = xtomo_imp.Import()
data, white, dark, theta = read.xtomo_raw(
file_name,
projections_start=projections_start,
projections_end=projections_end,
projections_digits=4,
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',
projections_zeros=True,
white_zeros=False,
dark_zeros=False,
log='INFO')
# Save data as dataExchange
write = xtomo_exp.Export()
write.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')
def main():
file_name = '/local/dataraid/databank/templates/australian_micro-tomography/SAMPLE_T_.tif'
dark_file_name = '/local/dataraid/databank/templates/australian_micro-tomography/DF__BEFORE_.tif'
white_file_name = '/local/dataraid/databank/templates/australian_micro-tomography/BG__BEFORE_.tif'
hdf5_file_name = '/local/dataraid/databank/templates/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
# Read raw data
read = xtomo_imp.Import()
data, white, dark, theta = read.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'
)
# Save data as dataExchange
write = xtomo_exp.Export()
write.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'
)
def main():
# oster: pj: from 0 -> 1440; bf from 0 -> 19; df from 0 -> 19
file_name = '/local/dataraid/databank/templates/petraIII_P05/sample_name00_0000/scan_0002/ccd/pco01/ccd_.tif'
dark_file_name = '/local/dataraid/databank/templates/petraIII_P05/sample_name00_0000/scan_0000/ccd/pco01/ccd_.tif'
white_file_name = '/local/dataraid/databank/templates/petraIII_P05/sample_name00_0000/scan_0001/ccd/pco01/ccd_.tif'
hdf5_file_name = '/local/dataraid/databank/templates/dataExchange/tmp/PetraIII.h5'
projections_start = 0
projections_end = 1441
white_start = 0
white_end = 20
white_step = 1
dark_start = 0
dark_end = 20
dark_step = 1
sample_name = 'oster02_0001'
# Read raw data
read = xtomo_imp.Import()
data, white, dark, theta = read.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,
projections_zeros=True,
log='INFO')
# Save data as dataExchange
write = xtomo_exp.Export()
write.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')
def main():
file_name = '/local/dataraid/databank/templates/anka_topo-tomo/radios/image_.tif'
dark_file_name = '/local/dataraid/databank/templates/anka_topo-tomo/darks/image_.tif'
white_file_name = '/local/dataraid/databank/templates/anka_topo-tomo/flats/image_.tif'
hdf5_file_name = '/local/dataraid/databank/templates/dataExchange/tmp/Anka.h5'
projections_start = 0
projections_end = 3167
white_start = 0
white_end = 100
dark_start = 0
dark_end = 100
sample_name = 'insect'
# Read raw data
read = xtomo_imp.Import()
data, white, dark, theta = read.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')
# Save data as dataExchange
write = xtomo_exp.Export()
write.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')
def main():
file_name = '/local/dataraid/databank/templates/aps_13-BM/SPE/sample_name_.SPE'
hdf5_file_name = '/local/dataraid/databank/templates/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
sample_name = 'run2_soln1_2'
# Read raw data
read = xtomo_imp.Import()
data, white, dark, theta = read.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_zeros=False,
white_zeros=False,
dark_zeros=False,
projections_digits=1,
data_type='spe',
log='INFO')
# Save data as dataExchange
write = xtomo_exp.Export()
write.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')
def main():
file_name = '/local/dataraid/databank/templates/diamond_JEEP/tiff/sample_name/im_.tif'
white_file_name = '/local/dataraid/databank/templates/diamond_JEEP/tiff/sample_name/flat_.tif'
hdf5_file_name = '/local/dataraid/databank/templates/dataExchange/tmp/Diamond.h5'
sample_name = 'waterflow'
white_start = 0
white_end = 1
projections_start = 1000
projections_end = 2440
#print "Dark", dark_start, dark_end
print "White", white_start, white_end
print "Projection", projections_start, projections_end
# Read series of images
read = xtomo_imp.Import()
data, white, dark, theta = read.xtomo_raw(
file_name,
projections_start=projections_start,
projections_end=projections_end,
projections_angle_end=360,
projections_digits=6,
white_file_name=white_file_name,
white_start=white_start,
white_end=white_end,
log='INFO')
write = xtomo_exp.Export()
# Create minimal data exchange hdf5 file
write.xtomo_exchange(data=data,
data_white=white,
data_dark=dark,
theta=theta,
sample_name=sample_name,
hdf5_file_name=hdf5_file_name,
data_exchange_type='tomography_raw_projections')
def main():
file_name = '/local/dataraid/databank/templates/diamond_JEEP/sample_name_subx.nxs'
hdf5_file_name = '/local/dataraid/databank/dataExchange/tmp/Diamond.h5'
# Read raw data
# set slice_start and slice_end to full size. 1600-1610 is for testing only
read = xtomo_imp.Import()
data, white, dark, theta = read.xtomo_raw(file_name,
data_type='nxs',
slices_start=1600,
slices_end=1610,
slices_step=1,
log='INFO')
# Save data as dataExchange
write = xtomo_exp.Export()
write.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/templates/aps_13-BM/NC/sample_name_.nc'
hdf5_file_name = '/local/dataraid/databank/templates/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
sample_name = 'Dorthe_F'
# Read raw data
read = xtomo_imp.Import()
data, white, dark, theta = read.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'
)
# Save data as dataExchange
write = xtomo_exp.Export()
write.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'
)
def main():
file_name = '/local/dataraid/databank/templates/aps_1-ID/data_.tif'
log_file = '/local/dataraid/databank/templates/aps_1-ID/TomoStillScan.dat'
hdf5_file_name = '/local/dataraid/databank/templates/dataExchange/tmp/APS_1_ID.h5'
#Read APS 1-ID log file data
file = open(log_file, 'r')
for line in file:
linelist = line.split()
if len(linelist) > 1:
if (linelist[0] == "First" and linelist[1] == "image"):
projections_start = int(linelist[4])
elif (linelist[0] == "Last" and linelist[1] == "image"):
projections_end = int(linelist[4])
elif (linelist[0] == "Dark" and linelist[1] == "field"):
dark_start = int(linelist[6])
elif (linelist[0] == "Number" and linelist[2] == "dark"):
number_of_dark = int(linelist[5])
elif (linelist[0] == "White" and linelist[1] == "field"):
white_start = int(linelist[6])
elif (linelist[0] == "Number" and linelist[2] == "white"):
number_of_white = int(linelist[5])
file.close()
dark_end = dark_start + number_of_dark
white_end = white_start + number_of_white
# to fix a data collection looging bug ?
white_start = white_start + 1
dark_start = dark_start + 1
projections_start = projections_start + 11
projections_end = projections_end - 9
## # these are correct per Peter discussion
## projections_start = 943
## projections_end = 1853
## white_start = 1844
## white_end = 1853
## dark_start = 1854
## dark_end = 1863
sample_name = 'CAT4B_2'
# Read raw data
read = xtomo_imp.Import()
data, white, dark, theta = read.xtomo_raw(
file_name,
projections_start=projections_start,
projections_end=projections_end,
white_start=white_start,
white_end=white_end,
dark_start=dark_start,
dark_end=dark_end,
projections_digits=6,
log='INFO')
# Save data as dataExchange
write = xtomo_exp.Export()
write.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')
def main():
file_name = '/local/dataraid/databank/templates/als_beamline_8.3.2/sample_name_0000_.tif'
dark_file_name = '/local/dataraid/databank/templates/als_beamline_8.3.2/sample_namedrk_.tif'
white_file_name = '/local/dataraid/databank/templates/als_beamline_8.3.2/sample_namebak_.tif'
log_file = '/local/dataraid/databank/templates/als_beamline_8.3.2/sample_name.sct'
hdf5_file_name = '/local/dataraid/databank/templates/dataExchange/tmp/ALS.h5'
verbose = True
# Read ALS log file data
file = open(log_file, 'r')
for line in file:
if '-scanner' in line:
Source = re.sub(r'-scanner ', "", line)
if verbose: print 'Facility', Source
if '-object' in line:
Sample = re.sub(r'-object ', "", line)
if verbose: print 'Sample', Sample
if '-senergy' in line:
Energy = re.findall(r'\d+.\d+', line)
if verbose: print 'Energy', Energy[0]
if '-scurrent' in line:
Current = re.findall(r'\d+.\d+', line)
if verbose: print 'Current', Current[0]
if '-nangles' in line:
Angles = re.findall(r'\d+', line)
if verbose: print 'Angles', Angles[0]
if '-num_bright_field' in line:
WhiteEnd = re.findall(r'\d+', line)
if '-num_dark_fields' in line:
DarkEnd = re.findall(r'\d+', line)
file.close()
dark_start = 0
dark_end = int(DarkEnd[0])
dark_step = 1
white_start = 0
white_end = int(WhiteEnd[0])
white_step = 1
projections_start = 0
projections_end = int(Angles[0])
#projections_end = 18
print dark_end, white_end, projections_end
# Read raw data
read = xtomo_imp.Import()
data, white, dark, theta = read.xtomo_raw(
file_name=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=4,
#data_type='tiff',
log='INFO')
# Save data as dataExchange
write = xtomo_exp.Export()
write.xtomo_exchange(data=data,
data_white=white,
data_dark=dark,
theta=theta,
hdf5_file_name=hdf5_file_name,
sample_name=Sample,
data_exchange_type='tomography_raw_projections')
def main():
file_name = '/local/dataraid/databank/templates/xradia_dtu/sample_name.txrm'
hdf5_file_name = '/local/dataraid/databank/templates/dataExchange/tmp/DTU_103.h5'
sample_name = 'halvmaane_150kV-HE6-20X-60s'
experimenter_name = "Martin Skovgaard Andersen"
experimenter_affiliation = "Technical University of Denmark"
experimenter_email = "*****@*****.**"
instrument_comment = "Xradia Versa micro CT scanner"
image_exposure_time = read_meta_txm(file_name, 'ImageInfo/ExpTimes')
image_datetime = read_meta_txm(file_name, 'ImageInfo/Date')
image_theta = read_meta_txm(file_name, 'ImageInfo/Angles')
sample_image_shift_x = read_meta_txm(file_name, 'Alignment/X-Shifts')
sample_image_shift_y = read_meta_txm(file_name, 'Alignment/Y-Shifts')
sample_position_x = read_meta_txm(file_name, 'ImageInfo/XPosition')
sample_position_y = read_meta_txm(file_name, 'ImageInfo/YPosition')
sample_position_z = read_meta_txm(file_name, 'ImageInfo/ZPosition')
# Example of SLS multiple scan meta data
size = image_theta.shape[0]
scan_index = np.zeros(size)
image_number = np.arange(0, size)
time_stamp = np.arange(0, size * 20000000, 20000000)
image_exposure_time = np.random.random_integers(10000000, 10005000, size)
image_is_complete = np.ones(size)
today = datetime.datetime.today()
today = today.isoformat()
today = '2014-08-08T16:00:00'
scan_datetime = range(0, size)
scan_datetime = [today for i in scan_datetime]
# Read raw data
read = xtomo_imp.Import()
data, white, dark, theta = read.xtomo_raw(file_name,
projections_angle_start=-180,
projections_angle_end=180,
data_type='xradia',
log='INFO')
# Save data as dataExchange
write = xtomo_exp.Export()
write.xtomo_exchange(data=data,
data_white=white,
data_dark=dark,
theta=theta,
hdf5_file_name=hdf5_file_name,
experimenter_name=experimenter_name,
experimenter_affiliation=experimenter_affiliation,
experimenter_email=experimenter_email,
instrument_comment=instrument_comment,
sample_name=sample_name,
sample_position_x=sample_position_x,
sample_position_y=sample_position_y,
sample_position_z=sample_position_z,
sample_image_shift_x=sample_image_shift_x,
sample_image_shift_y=sample_image_shift_y,
image_exposure_time=image_exposure_time,
image_datetime=image_datetime,
image_theta=image_theta,
scan_index=scan_index,
scan_datetime=scan_datetime,
time_stamp=time_stamp,
image_number=image_number,
image_is_complete=image_is_complete,
data_exchange_type='tomography_raw_projections')
def main():
top_dir = '/local/carmen/lorentz/stu/'
tray = 'tray03'
sample = 'Sam20'
sample_name = 'Plesio_hor_2'
log_file = top_dir + tray + '/exp.log'
# create an exp.log file as:
# Number of projections : 1500
# Number of darks : 1
# Number of flats : 2
# Rot Y min position [deg] : 0.000
# Rot Y max position [deg] : 180.000
# Angular step [deg] : 0.12
hdf5_file_name = top_dir + tray + '/hdf5/' + sample + '.h5'
file_name = top_dir + tray + '/' + sample + '/raw/' + sample_name + '_.h5'
source_name = "Advanced Photon Source"
source_mode = "top-up"
beamline = "2-BM"
experimenter_name = "Stuart R Stock"
experimenter_affiliation = "Northwestern University Feinberg School of Medicine"
experimenter_email = "*****@*****.**"
instrument_comment = "Francesco De Carlo at [email protected]"
#Read exp 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()
white_start = 1
white_end = 2
projections_start = 2
projections_end = projections_start + (int)(
(rotation_max - rotation_min) / angular_step) + 1
dark_start = projections_end + 1
dark_end = dark_start + number_of_darks
projections_angle_end = 180 + angular_step
print "DARK", dark_start, dark_end
print "WHITE", white_start, white_end
print projections_start, projections_end
print projections_angle_end
print file_name
print log_file
# Read raw data
read = xtomo_imp.Import()
data, white, dark, theta = read.xtomo_raw(
file_name,
projections_start=projections_start,
projections_end=projections_end,
projections_angle_end=projections_angle_end,
projections_digits=5,
white_start=white_start,
white_end=white_end,
dark_start=dark_start,
dark_end=dark_end,
data_type='hdf5',
log='INFO')
# Save data as dataExchange
write = xtomo_exp.Export()
write.xtomo_exchange(data=data,
data_white=white,
data_dark=dark,
theta=theta,
hdf5_file_name=hdf5_file_name,
source_name=source_name,
source_mode=source_mode,
beamline=beamline,
experimenter_name=experimenter_name,
experimenter_affiliation=experimenter_affiliation,
experimenter_email=experimenter_email,
instrument_comment=instrument_comment,
sample_name=sample_name,
data_exchange_type='tomography_raw_projections')