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] [--sample_x_keys SAMPLE_X_KEYS] [--sample_y_keys SAMPLE_Y_KEYS] [--translation_z_keys TRANSLATION_Z_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.
  --sample_x_keys SAMPLE_X_KEYS, --sample-x-keys SAMPLE_X_KEYS
                        sample x translation key in bliss HDF5 file (direction is independent of the rotation angle)
  --sample_y_keys SAMPLE_Y_KEYS, --sample-y-keys SAMPLE_Y_KEYS
                        sample y translation key in bliss HDF5 file (direction is independent of the rotation angle)
  --translation_z_keys TRANSLATION_Z_KEYS, --translation-z-keys TRANSLATION_Z_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 will try to deduce them from NX_class attribute (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.
  --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

main(argv)