UtilityΒΆ
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