nxtomomill.app.h52nx#
Application to convert a bliss-hdf5 tomography dataset to Nexus - NXtomo (hdf5) format
usage: nxtomomill h52nx [-h] [--file-extension FILE_EXTENSION] [--single-file] [--overwrite] [--debug] [--entries ENTRIES] [--ignore-sub-entries IGNORE_SUB_ENTRIES] [--raises-error]
[--field-of-view FIELD_OF_VIEW] [--no-input] [--data-copy] [--x_trans_keys X_TRANS_KEYS] [--y_trans_keys Y_TRANS_KEYS] [--z_trans_keys Z_TRANS_KEYS]
[--sample-detector-distance-paths SAMPLE_DETECTOR_DISTANCE_PATHS] [--valid_camera_names VALID_CAMERA_NAMES] [--rot_angle_keys ROT_ANGLE_KEYS] [--acq_expo_time_keys ACQ_EXPO_TIME_KEYS]
[--x_pixel_size_key X_PIXEL_SIZE_KEY] [--y_pixel_size_key Y_PIXEL_SIZE_KEY] [--init_titles INIT_TITLES] [--init_zserie_titles INIT_ZSERIE_TITLES] [--dark_titles DARK_TITLES]
[--ref_titles REF_TITLES] [--proj_titles PROJ_TITLES] [--align_titles ALIGN_TITLES] [--set-params [SET_PARAMS [SET_PARAMS ...]]] [--format FORMAT] [--config CONFIG]
[input_file] [output_file]
convert data acquired as hdf5 from bliss to nexus `NXtomo` classes. For `zseries` it will create one entry per `z`
positional arguments:
input_file master file of the acquisition
output_file output .nx or .h5 file
optional arguments:
-h, --help show this help message and exit
--file-extension FILE_EXTENSION, --file_extension FILE_EXTENSION
extension of the output file. Valid values are .h5/.hdf5/.nx
--single-file merge all scan sequence to the same output file. By default create one file per sequence and group all sequence in the output file
--overwrite Do not ask for user permission to overwrite output files
--debug Set logs to debug mode
--entries ENTRIES Specify (root) entries to be converted. By default it will try to convert all existing entries.
--ignore-sub-entries IGNORE_SUB_ENTRIES
Specify (none-root) sub entries to ignore.
--raises-error Raise errors if some data are not met instead of providing some default values
--field-of-view FIELD_OF_VIEW
Force the output to be `Half` or `Full` acquisition. Otherwise parse raw data to find this information.
--no-input, --no-input-for-missing-information
The user won't be ask for any inputs
--data-copy, --copy-data
Force data duplication of frames. This will permit to have an 'all-embed' file. Otherwise the detector/data dataset will haves links to other files.
--x_trans_keys X_TRANS_KEYS, --x-trans-keys X_TRANS_KEYS
x translation key in bliss HDF5 file
--y_trans_keys Y_TRANS_KEYS, --y-trans-keys Y_TRANS_KEYS
y translation key in bliss HDF5 file
--z_trans_keys Z_TRANS_KEYS, --z-trans-keys Z_TRANS_KEYS
z translation key in bliss HDF5 file
--sample-detector-distance-paths SAMPLE_DETECTOR_DISTANCE_PATHS, --distance SAMPLE_DETECTOR_DISTANCE_PATHS
sample detector distance
--valid_camera_names VALID_CAMERA_NAMES, --valid-camera-names VALID_CAMERA_NAMES
Valid NXDetector dataset name to be considered. Otherwise willtry to deduce them from NX_class attibute (value should beNXdetector) or from instrument group child structure.
--rot_angle_keys ROT_ANGLE_KEYS, --rot-angle-keys ROT_ANGLE_KEYS
Valid dataset name for rotation angle
--acq_expo_time_keys ACQ_EXPO_TIME_KEYS, --acq-expo-time-keys ACQ_EXPO_TIME_KEYS
Valid dataset name for acquisition exposure time
--x_pixel_size_key X_PIXEL_SIZE_KEY, --x-pixel-size-key X_PIXEL_SIZE_KEY
X pixel size key to read
--y_pixel_size_key Y_PIXEL_SIZE_KEY, --y-pixel-size-key Y_PIXEL_SIZE_KEY
Y pixel size key to read
--init_titles INIT_TITLES, --init-titles INIT_TITLES
Titles corresponding to init scans
--init_zserie_titles INIT_ZSERIE_TITLES, --init-zserie-titles INIT_ZSERIE_TITLES
Titles corresponding to zserie init scans
--dark_titles DARK_TITLES, --dark-titles DARK_TITLES
Titles corresponding to dark scans
--flat_titles --flat-titles --ref_titles REF_TITLES, --ref-titles FLAT_TITLES
Titles corresponding to ref scans
--proj_titles PROJ_TITLES, --proj-titles PROJ_TITLES
Titles corresponding to projection scans
--align_titles ALIGN_TITLES, --align-titles ALIGN_TITLES
Titles corresponding to alignment scans
--set-params [SET_PARAMS [SET_PARAMS ...]]
Allow manual definition of some parameters. Valid parameters (and expected input unit) are: energy (kev), x_pixel_size (m), y_pixel_size (m). Should be added at the end of the command
line because will try to cover all text set after this option.
--format FORMAT Input format. Standard by default. Should be 'xrd-ct' otherwise
--config CONFIG, --config-file CONFIG, --configuration CONFIG, --configuration-file CONFIG
file containing the full configuration to convert from h5 bliss to nexus
For a complete tutorial you can have a look at: h52nx tutorial
Functions
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