Utility

This section contains links to python code examples to generate a simple.py and a full.py data-exchange file using the DXfile class.

dump_dxfile.py allows to print the list of Groups/Datasets names and values contained in a DataExchange hdf file. Using > is possible to save this script output to a text file. The script has also an option to convert a DataExchange file into a stack of tiff files.

Usage:

python dump_dxfile.py -h
usage: dump_dxfile.py [-h] [--tiff] fname


positional arguments:
        fname       directory containing multiple dxfiles or a single DataExchange
            file: /data/ or /data/sample.h5

optional arguments:
        -h, --help      show this help message and exit
        --tiff          convert a single DataExchange file to a stack of tiff files

Example:

python dump_dxfile.py test01/ | grep "start_date"

    test01/001_test.h5 /process/acquisition/start_date = ['May 29, 2019 19:20:21']
    test01/002_test.h5 /process/acquisition/start_date = ['May 29, 2019 19:23:26']
    test01/003_test.h5 /process/acquisition/start_date = ['May 29, 2019 19:26:51']
    test01/004_test.h5 /process/acquisition/start_date = ['May 29, 2019 19:30:17']
    test01/005_test.h5 /process/acquisition/start_date = ['May 29, 2019 19:33:42']
    test01/006_test.h5 /process/acquisition/start_date = ['May 29, 2019 19:37:07']
    ...


python dump_dxfile.py test01/ | grep "data array"
    data array test01/001_test.h5 /exchange/data (1500, 2048, 2448)
    data array test01/002_test.h5 /exchange/data (1500, 2048, 2448)
    data array test01/003_test.h5 /exchange/data (1500, 2048, 2448)
    data array test01/004_test.h5 /exchange/data (1500, 2048, 2448)
    data array test01/005_test.h5 /exchange/data (1500, 2048, 2448)
    data array test01/006_test.h5 /exchange/data (1500, 2048, 2448)
    ...

    python dump_dxfile.py /tomobank/tomo_00001.h5 > experiment_log.txt
    python dump_dxfile.py /tomobank/tomo_00001.h5 --tiff