Advanced Photon Source

At synchrotron facilities using the EPICS [B1] software for area detectors [B12] with the NDFileHDF5 plugin [B11], is possible to save Data Exchange files by properly configure the detector and the HDF schema attribute files to obtain txm.h5

Here are the templates in use at the Advanced Photon Source:

• 2-BM-A/B

  • Micro Tomography Instrument: hdf_schema.xml plus A_station_detector_attributes.xml or B_station_detector_attributes.xml

• 6-BM

  • Micro Tomography Instrument: TomoScanLayout.xml and TomoScanDetectorAttributes.xml

• 7-BM

  • Fast Micro Tomography Instrument: mct_hdf_schema.xml and mct_detector_attribute.xml

• 13-BM

  • Micro-tomography system at 13-BM-D using PG cameras: tomoLayout.xml and tomoDetectorAttributes.xml

• 32-ID

  • Transmission X-Ray Microscope: hdf_schema.xml and txm_detector_attribute.xml.

  • Micro Tomography Instrument: mct_hdf_schema.xml and mct_detector_attribute.xml.

XML

To check that the areadetector attributes and layout XML contain a set of matching names run:

$ bash
usertxm@txmtwo$ grep -oP 'name=\"\K[^\"]+' TomoScanDetectorAttributes.xml | while read -r line ; do echo -n "$line " ; grep -q "$line" TomoScanLayout.xml && echo true || echo false ; done | grep false
usertxm@txmtwo$ grep -oP 'ndattribute=\"\K[^\"]+' TomoScanLayout.xml | while read -r line; do echo -n "$line "; grep -q "$line" TomoScanDetectorAttributes.xml && echo true || echo false ; done |grep false

To visualize the meta data and the layout of the hdf file use meta cli

View the hdf tree

To view the data tree contained in a generic hdf file:

$ meta tree --file-name data/base_file_name_001.h5

View the meta data

To view the meta data contained in a generic hdf file:

$ meta show --file-name data/base_file_name_001.h5

View a subset meta data

To view a subset of the meta data contained in a generic hdf file:

$ meta show --file-name data/base_file_name_001.h5 --key energy

Replace an hdf entry value

To replace the value of an entry:

$ meta set --file-name data/base_file_name_001.h5 --key /process/acquisition/rotation/rotation_start --value 10

Meta data rst table

To generate a meta data rst table compatible with sphinx/readthedocs:

$ meta docs --file-name data/base_file_name_001.h5
2022-02-09 12:30:16,983 - Please copy/paste the content of ./log_2020-05.rst in your rst docs file

The content of the generated rst file will publish in a sphinx/readthedocs document as:

2022-05

decarlo

	value	unit
000/measurement/instrument/monochromator/energy	30.0	keV
000/measurement/instrument/sample_motor_stack/setup/x	0.0	mm
000/measurement/instrument/sample_motor_stack/setup/y	0.4000116247000278	mm
000/measurement/sample/experimenter/email	decarlof@gmail.com

Note

when using the docs option –file-name can be also a folder, e.g. –file-name data/ in this case all hdf files in the folder will be processed.

to list of all available options:

$ meta  -h