You need first to have a workflow set-up.
For this example we will pick the one from examples -> Simple user case -> simple slice reconstruction
For this example we will tune the following:
- cor to use the 'radio sliding_window' and lock it
- Paganin to use activate it
then save the workflow under my_workflow.ows
This is this saved file that we can execute with ewoks using ewoks execute and ewoks submit
local exuection using ewoks execute¶
To provide the dataset to be executed you can provide it using the --parameter data={my_dataset} to the interface like
ewoks execute processing_data.json --parameter data=hdf5:scan:bambou_hercules_0001.nx?path=entry0000
Scan and volume must be provided as unique identifiers For now other parameters (reconstruction parameters, cor algorithm...) must be provided from the GUI.
example of execution
gpu4-02:/tmp_14_days/payno/test_training/test_ewoks % ewoks execute my_workflow.ows --parameter data=hdf5:scan:bambou_hercules_0001.nx?path=entry0000
###################################
# Execute workflow 'my_workflow.ows'
###################################
/scisoft/tomotools/x86_64/cuda11/2024_02_26/lib/python3.8/site-packages/pyqtgraph/colors/palette.py:1: RuntimeWarning: PyQtGraph supports Qt version >= 5.15, but 5.12.8 detected.
from ..Qt import QtGui
/scisoft/tomotools/x86_64/cuda11/2024_02_26/lib/python3.8/site-packages/pyopencl/cache.py:495: CompilerWarning: Non-empty compiler output encountered. Set the environment variable PYOPENCL_COMPILER_OUTPUT=1 to see more.
_create_built_program_from_source_cached(
/scisoft/tomotools/x86_64/cuda11/2024_02_26/lib/python3.8/site-packages/pyopencl/cache.py:499: CompilerWarning: Non-empty compiler output encountered. Set the environment variable PYOPENCL_COMPILER_OUTPUT=1 to see more.
prg.build(options_bytes, devices)
2 errors generated.
2024-02-27 08:52:12,316 - tomwer.core.process.reconstruction.darkref.darkrefs - PROCESS_STARTED - start dark and ref for NXtomo scan(master_file: test_training/test_ewoks/bambou_hercules_0001.nx, entry: entry0000)
2024-02-27 08:52:18,092 - tomwer.core.process.reconstruction.darkref.darkrefs - PROCESS_SUCCEED - Dark and flat reduction succeeded for NXtomo scan(master_file: test_training/test_ewoks/bambou_hercules_0001.nx, entry: entry0000)
Loaded darks from /mnt/multipath-shares/tmp_14_days/payno/test_training/test_ewoks/bambou_hercules_0001_darks.hdf5
Loaded flats from /mnt/multipath-shares/tmp_14_days/payno/test_training/test_ewoks/bambou_hercules_0001_flats.hdf5
2024-02-27 08:52:20,343 - tomwer.core.process.reconstruction.axis.axis - PROCESS_SUCCEED - axis calculation defined for /mnt/multipath-shares/tmp_14_days/payno/test_training/test_ewoks: 780.3473938218999 (using radios-sliding-window)
2024-02-27 08:52:30,687 - tomwer.core.process.reconstruction.nabu.nabuslices - PROCESS_SUCCEED - Slices computed for NXtomo scan(master_file: test_training/test_ewoks/bambou_hercules_0001.nx, entry: entry0000).
FINISHED
And then we can find the reconstructed slice
See also tomwer ewoks tutorial and ewoks official tutorials.
- This is style some fresh feature and some bug might remain. So please double check your result and let us know if you encounter some troubles with it.
- For now the settings must be tune from the GUI, not much can be provided from the CLI. This should improve in the future