Execute a darfix workflow without GUI

import os

from orangecontrib.darfix import tutorials

from CLI using ewoks

You can execute darfix workflows as any ewoks workflow using the ewoks execute command. Parameter values can be provided with the --parameter options (or the -p alias). For example, we want to execute a workflow named my_darfix_workflow.ows by setting two parameters: the detector HDF5 dataset and the HDF5 positioner dataset (aka metadata). For this, we can use the following command:

ewoks execute src/orangecontrib/darfix/tutorials/darfix_example1.ows --parameter raw_input_file=/data/scisoft/darfix/datasets/bliss_hdf5/Silicon_111_reflection_0003/Silicon_111_reflection_0003.h5 --parameter raw_detector_data_path=/1.1/instrument/pco_ff/data --parameter raw_metadata_path=/1.1/instrument/positioners

Warning: the HDF5 dataset must be provided as silx URL

From Python

step 1: Define task arguments which are not defined in the workflow

in this example we will focus about HDF5 dataset.

root_dir = "/tmp/darfix"
os.makedirs(root_dir, exist_ok=True)
hdf5_file = os.path.join(tutorials.__path__[0], "hdf5_dataset", "strain.hdf5")
assert os.path.exists(hdf5_file)

step2: Execute the workflow

For more information on executing ewoks workflows: https://workflow.gitlab-pages.esrf.fr/ewoks/ewoks/

from ewoks import execute_graph

graph = os.path.join(tutorials.__path__[0], "darfix_example_hdf.ows")
results = execute_graph(
    graph,
    inputs=[
        {
            "name": "raw_input_file",
            "value": hdf5_file,
        },
        {
            "name": "raw_detector_data_path",
            "value": "/1.1/instrument/my_detector/data",
        },
        {"name": "raw_metadata_path", "value": "/1.1/instrument/positioners"},
    ],
    output_tasks=True,
)

WARNING:/home/docs/checkouts/readthedocs.org/user_builds/darfix/envs/stable/lib/python3.12/site-packages/darfix/tasks/roi.py:Cannot apply a ROI if origin ([]) or size ([]) is empty. Dataset is unchanged.
Noise removal operation: 100%|██████████| 2/2 [00:00<00:00, 26800.66it/s]
Compute Skewness and Kurtosis...: 100%|██████████| 3/3 [00:04<00:00,  1.48s/it]

Inspect the results

for node_id, task in results.items():
    assert task.succeeded, f"task {node_id} failed"
    print(task.get_output_values())

{'dataset': <darfix.dtypes.Dataset object at 0x7443c7cfa510>}
{}
{'dataset': <darfix.dtypes.Dataset object at 0x7443c76473e0>}
{'dataset': <darfix.dtypes.Dataset object at 0x7443c7647bc0>}
{'dataset': <darfix.dtypes.Dataset object at 0x7443c7647bc0>}
{'dataset': <darfix.dtypes.Dataset object at 0x7443c7647bc0>}
{'zsum': array([[[178, 214, 218, ..., 217, 208, 221],
        [215, 219, 212, ..., 227, 225, 222],
        [377, 223, 221, ..., 217, 217, 211],
        ...,
        [167, 188, 197, ..., 191, 199, 190],
        [185, 184, 181, ..., 178, 183, 191],
        [176, 198, 203, ..., 181, 195, 187]]],
      shape=(1, 512, 512), dtype=uint64)}
{'dataset': <darfix.dtypes.Dataset object at 0x7443c7647bc0>}