def write_example(filename):
# --- prepare data ---
# Generate fake raw data
rawdata = np.ones(180 * 256 * 256, np.uint16).reshape(180, 256, 256)
rawdata_white = np.ones(2 * 256 * 256, np.uint16).reshape(2, 256, 256)
rawdata_dark = np.zeros(10 * 256 * 256, np.uint16).reshape(10, 256, 256)
# Generate fake normalized data
normalizeddata = np.ones(180 * 256 * 256, \
np.float64).reshape(180, 256, 256)
# Generate fake reconstructed data
reconstructeddata = np.ones(256 * 256 * 256, \
np.float64).reshape(256, 256, 256)
# x, y and z ranges
x = np.arange(128)
y = np.arange(128)
z = np.arange(180);
# Fabricated theta values
theta = (z / float(180)) * 180.0
theta_white = (0.0, 180.0)
theta_dark = (0.0, 0.0, 0.0, 0.0, 0.0, 180.0, 180.0, 180.0, 180.0, 180.0)
# Fabricated data_shift_x and data_shift_y value
data_shift_x = np.random.randint(-100, 100, size=180)
data_shift_y = np.random.randint(-100, 100, size=180)
# --- create file ---
print filename
# Open DataExchange file
f = DataExchangeFile(filename, mode='w')
# Create core HDF5 dataset in exchange group for 180 deep stack
# of x,y images /exchange/data
f.add_entry( DataExchangeEntry.data(data={'value': rawdata, 'units':'counts', 'description': 'transmission', 'axes':'theta:y:x',
'dataset_opts': {'compression': 'gzip', 'compression_opts': 4} })
)
f.add_entry( DataExchangeEntry.data(title={'value': 'tomography_raw_projections'}))
f.add_entry( DataExchangeEntry.data(data_dark={'value':rawdata_dark, 'units':'counts', 'axes':'theta_dark:y:x',
'dataset_opts': {'compression': 'gzip', 'compression_opts': 4} })
)
f.add_entry( DataExchangeEntry.data(data_white={'value': rawdata_white, 'units':'counts', 'axes':'theta_white:y:x',
'dataset_opts': {'compression': 'gzip', 'compression_opts': 4} })
)
f.add_entry( DataExchangeEntry.data(theta={'value': theta, 'units':'degrees'}))
f.add_entry( DataExchangeEntry.data(theta_dark={'value': theta_dark, 'units':'degrees'}))
f.add_entry( DataExchangeEntry.data(theta_white={'value': theta_white, 'units':'degrees'}))
f.add_entry( DataExchangeEntry.data(data_shift_x={'value': data_shift_x}))
f.add_entry( DataExchangeEntry.data(data_shift_y={'value': data_shift_y}))
# Exchange HDF5 group
# /exchange_2
# this will be the out_put of the normalization process
f.add_entry( DataExchangeEntry.data(root='exchange_2', title={'value': 'tomography normalized projections'}) )
f.add_entry( DataExchangeEntry.data(root='exchange_2', data={'value': normalizeddata, 'units':'counts', 'axes':'theta:y:x',
'dataset_opts': {'compression': 'gzip', 'compression_opts': 4} })
)
f.add_entry( DataExchangeEntry.data(root='exchange_2', theta={'value': theta, 'units':'degrees'}))
# Exchange HDF5 group
# /exchange_3
# this will be the out_put of the reconstruction process
f.add_entry( DataExchangeEntry.data(root='exchange_3', title={'value': 'tomography reconstructions'}) )
f.add_entry( DataExchangeEntry.data(root='exchange_3', data={'value': reconstructeddata, 'units':'density', 'axes':'z:y:x',
'dataset_opts': {'compression': 'gzip', 'compression_opts': 4} })
)
# Create HDF5 group measurement
# /measuremen
f.add_entry( DataExchangeEntry.instrument(name={'value': 'APS 2-BM'}) )
# Create HDF5 subgroup
# /measurement/instrument/source
f.add_entry( DataExchangeEntry.source(name={'value': 'APS'},
date_time={'value': "2012-07-31T21:15:23+0600"},
beamline={'value': "2-BM"},
current={'value': 101.199, 'units': 'mA', 'dataset_opts': {'dtype': 'd'}},
energy={'value': 7.0, 'units':'GeV', 'dataset_opts': {'dtype': 'd'}},
mode={'value':'TOPUP'}
)
)
# Create HDF5 subgroup
# /measurement/instrument/attenuator
f.add_entry( DataExchangeEntry.attenuator(thickness={'value': 1e-3, 'units': 'm', 'dataset_opts': {'dtype': 'd'}},
type={'value': 'Al'}
)
)
# Create HDF5 subgroup
# /measurement/instrument/monochromator
f.add_entry( DataExchangeEntry.monochromator(type={'value': 'Multilayer'},
energy={'value': 19.26, 'units': 'keV', 'dataset_opts': {'dtype': 'd'}},
energy_error={'value': 1e-3, 'units': 'keV', 'dataset_opts': {'dtype': 'd'}},
mono_stripe={'value': 'Ru/C'},
)
)
# Create HDF5 subgroup
# /measurement/instrument/detector
f.add_entry( DataExchangeEntry.detector(manufacturer={'value':'CooKe Corporation'},
model={'value': 'pco dimax'},
serial_number={'value': '1234XW2'},
bit_depth={'value': 12, 'dataset_opts': {'dtype': 'd'}},
x_pixel_size={'value': 6.7e-6, 'dataset_opts': {'dtype': 'f'}},
y_pixel_size={'value': 6.7e-6, 'dataset_opts': {'dtype': 'f'}},
x_dimensions={'value': 2048, 'dataset_opts': {'dtype': 'i'}},
y_dimensions={'value': 2048, 'dataset_opts': {'dtype': 'i'}},
x_binning={'value': 1, 'dataset_opts': {'dtype': 'i'}},
y_binning={'value': 1, 'dataset_opts': {'dtype': 'i'}},
operating_temperature={'value': 270, 'units':'K', 'dataset_opts': {'dtype': 'f'}},
exposure_time={'value': 170, 'units':'ms', 'dataset_opts': {'dtype': 'd'}},
frame_rate={'value': 3, 'dataset_opts': {'dtype': 'i'}},
output_data={'value':'/exchange'}
)
)
f.add_entry( DataExchangeEntry.roi(name={'value':'Center Third'},
x1={'value':256, 'dataset_opts': {'dtype': 'i'}},
x2={'value':1792, 'dataset_opts': {'dtype': 'i'}},
y1={'value':256, 'dataset_opts': {'dtype': 'i'}},
y2={'value':1792, 'dataset_opts': {'dtype': 'i'}},
)
)
f.add_entry(DataExchangeEntry.objective(manufacturer={'value':'Zeiss'},
model={'value':'Plan-NEOFLUAR 1004-072'},
magnification={'value':20, 'dataset_opts': {'dtype': 'd'}},
numerical_aperture={'value':0.5, 'dataset_opts': {'dtype': 'd'}},
)
)
f.add_entry(DataExchangeEntry.scintillator(manufacturer={'value':'Crytur'},
serial_number={'value':'12'},
name={'value':'YAG polished'},
type={'value':'YAG on YAG'},
scintillating_thickness={'value':5e-6, 'dataset_opts': {'dtype': 'd'}},
substrate_thickness={'value':1e-4, 'dataset_opts': {'dtype': 'd'}},
)
)
# Create HDF5 subgroup
# /measurement/sample
f.add_entry( DataExchangeEntry.sample( name={'value':'Hornby_b'},
description={'value':'test sample'},
preparation_date={'value':'2011-07-31T21:15:23+0600'},
chemical_formula={'value':'unknown'},
mass={'value':0.25, 'units':'g', 'dataset_opts': {'dtype': 'd'}},
enviroment={'value':'air'},
temperature={'value':120.0, 'units':'Celsius', 'dataset_opts': {'dtype': 'd'}},
temperature_set={'value':130.0, 'units':'Celsius', 'dataset_opts': {'dtype': 'd'}},
)
)
# Create HDF5 subgroup
# /measurement/sample/geometry/translation
f.add_entry( DataExchangeEntry.translation(root='/measurement/sample/geometry',
distances={'value':[0,0,0],'axes':'z:y:x', 'units':'m', 'dataset_opts': {'dtype': 'd'}}
)
)
# Create HDF5 subgroup
# /measurement/experimenter
f.add_entry( DataExchangeEntry.experimenter(name={'value':"John Doe"},
role={'value':"Project PI"},
affiliation={'value':"University of California, Berkeley"},
address={'value':"EPS UC Berkeley CA 94720 4767 USA"},
phone={'value':"+1 123 456 0000"},
email={'value':"*****@*****.**"},
facility_user_id={'value':"a123456"},
)
)
# Create HDF5 subgroup
# /measurement/experiment
f.add_entry( DataExchangeEntry.experiment( proposal={'value':"1234"},
activity={'value':"e11218"},
safety={'value':"9876"},
)
)
# --- All done ---
f.close()
def main():
##file_name = '/local/data/databank/SLS_2011/Blakely_SLS/Blakely.tif'
##log_file = '/local/data/databank/SLS_2011/Blakely_SLS/Blakely.log'
##
##hdf5_file_name = '/local/data/databank/dataExchange/microCT/Blakely_SLS_2011.h5'
file_name = '/local/data/databank/SLS_2011/Hornby_SLS/Hornby_b.tif'
log_file = '/local/data/databank/SLS_2011/Hornby_SLS/Hornby.log'
hdf5_file_name = '/local/data/databank/dataExchange/microCT/Hornby_SLS_2011.h5'
verbose = True
if verbose: print file_name
if verbose: print log_file
if verbose: print hdf5_file_name
#Read input SLS data
file = open(log_file, 'r')
if verbose: print '###############################'
for line in file:
if 'Number of darks' in line:
NumberOfDarks = re.findall(r'\d+', line)
if verbose: print 'Number of Darks', NumberOfDarks[0]
if 'Number of flats' in line:
NumberOfFlats = re.findall(r'\d+', line)
if verbose: print 'Number of Flats', NumberOfFlats[0]
if 'Number of projections' in line:
NumberOfProjections = re.findall(r'\d+', line)
if verbose: print 'Number of Projections', NumberOfProjections[0]
if 'Number of inter-flats' in line:
NumberOfInterFlats = re.findall(r'\d+', line)
if verbose: print 'Number of inter-flats', NumberOfInterFlats[0]
if 'Inner scan flag' in line:
InnerScanFlag = re.findall(r'\d+', line)
if verbose: print 'Inner scan flag', InnerScanFlag[0]
if 'Flat frequency' in line:
FlatFrequency = re.findall(r'\d+', line)
if verbose: print 'Flat frequency', FlatFrequency[0]
if 'Rot Y min' in line:
RotYmin = re.findall(r'\d+.\d+', line)
if verbose: print 'Rot Y min', RotYmin[0]
if 'Rot Y max' in line:
RotYmax = re.findall(r'\d+.\d+', line)
if verbose: print 'Rot Y max', RotYmax[0]
if 'Angular step' in line:
AngularStep = re.findall(r'\d+.\d+', line)
if verbose: print 'Angular step', AngularStep[0]
if verbose: print '###############################'
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])
if verbose: print dark_start, dark_end
if verbose: print white_start, white_end
if verbose: print projections_start, projections_end
dark_start = 1
dark_end = 21
white_start = 21
white_end = 221
projections_start = 221
projections_end = 1662
### if testing uncomment
##dark_end = 4
##white_end = 24
##projections_end = 224
mydata = Convert()
# Create minimal hdf5 file
mydata.series_of_images(file_name,
hdf5_file_name,
projections_start,
projections_end,
white_start = white_start,
white_end = white_end,
dark_start = dark_start,
dark_end = dark_end,
verbose = False
)
# Add extra metadata if available
# Open DataExchange file
f = DataExchangeFile(hdf5_file_name, mode='a')
# Create HDF5 subgroup
# /measurement/instrument
f.add_entry( DataExchangeEntry.instrument(name={'value': 'Tomcat'}) )
# Create HDF5 subgroup
# /measurement/instrument/source
f.add_entry( DataExchangeEntry.source(name={'value': 'Swiss Light Source'},
date_time={'value': "2010-11-08T14:51:56+0100"},
beamline={'value': "Tomcat"},
current={'value': 401.96, 'units': 'mA', 'dataset_opts': {'dtype': 'd'}},
)
)
# Create HDF5 subgroup
# /measurement/instrument/monochromator
f.add_entry( DataExchangeEntry.monochromator(type={'value': 'Multilayer'},
energy={'value': 19.260, 'units': 'keV', 'dataset_opts': {'dtype': 'd'}},
mono_stripe={'value': 'Ru/C'},
)
)
# Create HDF5 subgroup
# /measurement/experimenter
f.add_entry( DataExchangeEntry.experimenter(name={'value':"Federica Marone"},
role={'value':"Project PI"},
affiliation={'value':"Swiss Light Source"},
phone={'value':"+41 56 310 5318"},
email={'value':"*****@*****.**"},
)
)
# Create HDF5 subgroup
# /measurement/instrument/detector
f.add_entry( DataExchangeEntry.detector(manufacturer={'value':'CooKe Corporation'},
model={'value': 'pco dimax'},
serial_number={'value': '1234XW2'},
bit_depth={'value': 12, 'dataset_opts': {'dtype': 'd'}},
x_pixel_size={'value': 6.7e-6, 'dataset_opts': {'dtype': 'f'}},
y_pixel_size={'value': 6.7e-6, 'dataset_opts': {'dtype': 'f'}},
x_dimensions={'value': 2048, 'dataset_opts': {'dtype': 'i'}},
y_dimensions={'value': 2048, 'dataset_opts': {'dtype': 'i'}},
x_binning={'value': 1, 'dataset_opts': {'dtype': 'i'}},
y_binning={'value': 1, 'dataset_opts': {'dtype': 'i'}},
operating_temperature={'value': 270, 'units':'K', 'dataset_opts': {'dtype': 'f'}},
exposure_time={'value': 170, 'units':'ms', 'dataset_opts': {'dtype': 'd'}},
frame_rate={'value': 3, 'dataset_opts': {'dtype': 'i'}},
output_data={'value':'/exchange'}
)
)
f.add_entry(DataExchangeEntry.objective(magnification={'value':10, 'dataset_opts': {'dtype': 'd'}},
)
)
f.add_entry(DataExchangeEntry.scintillator(name={'value':'LuAg '},
type={'value':'LuAg'},
scintillating_thickness={'value':20e-6, 'dataset_opts': {'dtype': 'd'}},
)
)
# Create HDF5 subgroup
# /measurement/experiment
f.add_entry( DataExchangeEntry.experiment( proposal={'value':"e11218"},
)
)
f.close()
if verbose: print "Done converting ", file_name
def main():
##file_name = '/local/data/databank/APS_2_BM/Sam18_hornby/raw/Hornby_19keV_10x_.hdf'
##log_file = '/local/data/databank/APS_2_BM/Sam18_hornby/raw/Hornby.log'
##
##hdf5_file_name = '/local/data/databank/dataExchange/microCT/Hornby_APS_2011.h5'
file_name = '/local/data/databank/APS_2_BM/Sam19_blakely/raw/Blakely_19keV_10x_.hdf'
log_file = '/local/data/databank/APS_2_BM/Sam19_blakely/raw/Blakely.log'
hdf5_file_name = '/local/data/databank/dataExchange/microCT/Blakely_APS_2011.h5'
verbose = True
if verbose: print file_name
if verbose: print log_file
if verbose: print hdf5_file_name
#Read input SLS data
file = open(log_file, 'r')
if verbose: print '###############################'
for line in file:
if 'Number of darks' in line:
NumberOfDarks = re.findall(r'\d+', line)
if verbose: print 'Number of Darks', NumberOfDarks[0]
if 'Number of flats' in line:
NumberOfFlats = re.findall(r'\d+', line)
if verbose: print 'Number of Flats', NumberOfFlats[0]
if 'Number of projections' in line:
NumberOfProjections = re.findall(r'\d+', line)
if verbose: print 'Number of Projections', NumberOfProjections[0]
if 'Number of inter-flats' in line:
NumberOfInterFlats = re.findall(r'\d+', line)
if verbose: print 'Number of inter-flats', NumberOfInterFlats[0]
if 'Inner scan flag' in line:
InnerScanFlag = re.findall(r'\d+', line)
if verbose: print 'Inner scan flag', InnerScanFlag[0]
if 'Flat frequency' in line:
FlatFrequency = re.findall(r'\d+', line)
if verbose: print 'Flat frequency', FlatFrequency[0]
if 'Rot Y min' in line:
RotYmin = re.findall(r'\d+.\d+', line)
if verbose: print 'Rot Y min', RotYmin[0]
if 'Rot Y max' in line:
RotYmax = re.findall(r'\d+.\d+', line)
if verbose: print 'Rot Y max', RotYmax[0]
if 'Angular step' in line:
AngularStep = re.findall(r'\d+.\d+', line)
if verbose: print 'Angular step', AngularStep[0]
if verbose: print '###############################'
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])
if verbose: print dark_start, dark_end
if verbose: print white_start, white_end
if verbose: print projections_start, projections_end
dark_start = 1504
dark_end = 1505
white_start = 1
white_end = 2
projections_start = 2
projections_end = 1503
### if testing uncomment
##dark_start = 1
##dark_end = 3
##white_start = 10
##white_end = 12
##projections_start = 20
##projections_end = 23
if verbose: print dark_start, dark_end
if verbose: print white_start, white_end
if verbose: print projections_start, projections_end
mydata = Convert()
# Create minimal hdf5 file
mydata.series_of_images(file_name,
hdf5_file_name,
projections_start,
projections_end,
white_start = white_start,
white_end = white_end,
dark_start = dark_start,
dark_end = dark_end,
projections_digits = 5,
data_type = 'hdf4',
#verbose = False
)
# Add extra metadata if available
# Open DataExchange file
f = DataExchangeFile(hdf5_file_name, mode='a')
# Create HDF5 subgroup
# /measurement/instrument
f.add_entry( DataExchangeEntry.instrument(name={'value': 'APS 2-BM'}) )
f.add_entry( DataExchangeEntry.source(name={'value': 'Advanced Photon Source'},
date_time={'value': "2012-07-31T21:15:23+0600"},
beamline={'value': "2-BM"},
current={'value': 101.199, 'units': 'mA', 'dataset_opts': {'dtype': 'd'}},
energy={'value': 7.0, 'units':'GeV', 'dataset_opts': {'dtype': 'd'}},
mode={'value':'TOPUP'}
)
)
# Create HDF5 subgroup
# /measurement/instrument/attenuator
f.add_entry( DataExchangeEntry.attenuator(thickness={'value': 1e-3, 'units': 'm', 'dataset_opts': {'dtype': 'd'}},
type={'value': 'Al'}
)
)
# Create HDF5 subgroup
# Create HDF5 subgroup
# /measurement/instrument/monochromator
f.add_entry( DataExchangeEntry.monochromator(type={'value': 'Multilayer'},
energy={'value': 19.26, 'units': 'keV', 'dataset_opts': {'dtype': 'd'}},
energy_error={'value': 1e-3, 'units': 'keV', 'dataset_opts': {'dtype': 'd'}},
mono_stripe={'value': 'Ru/C'},
)
)
# Create HDF5 subgroup
# /measurement/experimenter
f.add_entry( DataExchangeEntry.experimenter(name={'value':"Jane Waruntorn"},
role={'value':"Project PI"},
affiliation={'value':"University of California"},
facility_user_id={'value':"64924"},
)
)
f.add_entry(DataExchangeEntry.objective(manufacturer={'value':'Zeiss'},
model={'value':'Plan-NEOFLUAR 1004-072'},
magnification={'value':5, 'dataset_opts': {'dtype': 'd'}},
numerical_aperture={'value':0.5, 'dataset_opts': {'dtype': 'd'}},
)
)
f.add_entry(DataExchangeEntry.scintillator(manufacturer={'value':'Crytur'},
serial_number={'value':'12'},
name={'value':'LuAg '},
type={'value':'LuAg'},
scintillating_thickness={'value':50e-6, 'dataset_opts': {'dtype': 'd'}},
substrate_thickness={'value':50e-6, 'dataset_opts': {'dtype': 'd'}},
)
)
# Create HDF5 subgroup
# /measurement/experiment
f.add_entry( DataExchangeEntry.experiment( proposal={'value':"GUP-34353"},
activity={'value':"32-IDBC-2013-106491"},
safety={'value':"106491-49734"},
)
)
f.close()
if verbose: print "Done converting ", file_name