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]
[--with-master-file] [--overwrite] [--debug]
[--entries ENTRIES]
[--sub-entries-to-ignore SUB_ENTRIES_TO_IGNORE]
[--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-keys SAMPLE_DETECTOR_DISTANCE_KEYS]
[--valid_camera_names VALID_CAMERA_NAMES]
[--rotation_angle_keys ROTATION_ANGLE_KEYS]
[--exposure_time_keys EXPOSURE_TIME_KEYS]
[--sample-x-pixel-size_keys SAMPLE_X_PIXEL_SIZE_KEYS]
[--sample-y-pixel-size_keys SAMPLE_Y_PIXEL_SIZE_KEYS]
[--init_titles INIT_TITLES]
[--zseries-init-titles ZSERIES_INIT_TITLES]
[--multitomo-init-titles MULTITOMO_INIT_TITLES]
[--back-and-forth-init-titles BACK_AND_FORTH_INIT_TITLES]
[--dark-titles DARK_TITLES]
[--flat-titles FLAT_TITLES]
[--projection_titles PROJECTION_TITLES]
[--alignment-titles ALIGNMENT_TITLES]
[--set-params [SET_PARAMS ...]]
[--config-file CONFIG_FILE]
[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
options:
-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/.nxs
--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
--with-master-file Creates a master file linking all .nx files
--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.
--sub-entries-to-ignore SUB_ENTRIES_TO_IGNORE, --ignore-sub-entries SUB_ENTRIES_TO_IGNORE
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
x translation key in bliss HDF5 file
--sample_y_keys SAMPLE_Y_KEYS, --sample-y-keys SAMPLE_Y_KEYS
y translation key in bliss HDF5 file
--translation_z_keys TRANSLATION_Z_KEYS, --translation-z-keys TRANSLATION_Z_KEYS
z translation key in bliss HDF5 file
--sample-detector-distance-keys SAMPLE_DETECTOR_DISTANCE_KEYS, --sample-detector-distance-paths SAMPLE_DETECTOR_DISTANCE_KEYS, --distance-paths SAMPLE_DETECTOR_DISTANCE_KEYS
sample detector distance paths
--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.
--rotation_angle_keys ROTATION_ANGLE_KEYS, --rotation-angle-keys ROTATION_ANGLE_KEYS, --rot-angle-keys ROTATION_ANGLE_KEYS, --rot_angle_keys ROTATION_ANGLE_KEYS
Valid dataset name for rotation angle
--exposure_time_keys EXPOSURE_TIME_KEYS, --exposure-time-keys EXPOSURE_TIME_KEYS, --acq_expo_time_keys EXPOSURE_TIME_KEYS, --acq-expo-time-keys EXPOSURE_TIME_KEYS
Valid dataset name for acquisition exposure time
--sample-x-pixel-size_keys SAMPLE_X_PIXEL_SIZE_KEYS, --sample_x_pixel_size_keys SAMPLE_X_PIXEL_SIZE_KEYS
X pixel size key to read
--sample-y-pixel-size_keys SAMPLE_Y_PIXEL_SIZE_KEYS, --sample_y_pixel_size_keys SAMPLE_Y_PIXEL_SIZE_KEYS
Y pixel size key to read
--init_titles INIT_TITLES, --init-titles INIT_TITLES
Titles corresponding to init scans
--zseries-init-titles ZSERIES_INIT_TITLES, --zseries_init_titles ZSERIES_INIT_TITLES, --z_series_init_titles ZSERIES_INIT_TITLES, --z-series_init_titles ZSERIES_INIT_TITLES, --init_zserie_titles ZSERIES_INIT_TITLES, --init-zserie-titles ZSERIES_INIT_TITLES
Titles corresponding to zserie init scans
--multitomo-init-titles MULTITOMO_INIT_TITLES, --multitomo_init_titles MULTITOMO_INIT_TITLES, --multi-tomo-init-titles MULTITOMO_INIT_TITLES, --multi_tomo_init_titles MULTITOMO_INIT_TITLES, --init-multi-tomo-titles MULTITOMO_INIT_TITLES, --init-pcotomo-titles MULTITOMO_INIT_TITLES
Titles corresponding to multi-tomo init scans
--back-and-forth-init-titles BACK_AND_FORTH_INIT_TITLES, --back_and_forth_init_titles BACK_AND_FORTH_INIT_TITLES, --init-back-and-forth-titles BACK_AND_FORTH_INIT_TITLES, --init_back_and_forth_titles BACK_AND_FORTH_INIT_TITLES
Titles corresponding to back-and-forth init scans
--dark-titles DARK_TITLES, --dark_titles DARK_TITLES
Titles corresponding to dark scans
--flat-titles FLAT_TITLES, --flat_titles FLAT_TITLES, --ref_titles FLAT_TITLES, --ref-titles FLAT_TITLES
Titles corresponding to ref scans
--projection_titles PROJECTION_TITLES, --proj_titles PROJECTION_TITLES, --proj-titles PROJECTION_TITLES
Titles corresponding to projection scans
--alignment-titles ALIGNMENT_TITLES, --alignment_titles ALIGNMENT_TITLES, --align_titles ALIGNMENT_TITLES, --align-titles ALIGNMENT_TITLES
Titles corresponding to alignment scans
--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),
detector_sample_distance (m). Should be added at the
end of the command line because will try to cover all
text set after this option.
--config-file CONFIG_FILE, --config CONFIG_FILE, --configuration CONFIG_FILE, --configuration-file CONFIG_FILE
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
|