Execute a darfix workflow without GUI#

[1]:
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 /home/esrf/payno/Documents/my_darfix_workflow.ows --parameter filenames=silx:///data/scisoft/darfix/datasets/bliss_hdf5/Silicon_111_reflection_0003/Silicon_111_reflection_0003.h5?path=/1.1/instrument/pco_ff/data --parameter metadata_url=silx:///data/scisoft/darfix/datasets/bliss_hdf5/Silicon_111_reflection_0003/Silicon_111_reflection_0003.h5?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.

[2]:
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/

[3]:
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_positioners_group_path", "value": "/1.1/instrument/positioners"},
        {"name": "in_memory", "value": False,},
    ],
    output_tasks=True,
)
WARNING:/usr/local/lib/python3.9/site-packages/darfix/tasks/roi.py:Cannot apply a ROI if origin ([]) or size ([]) is empty. Dataset is unchanged.
Computing moments |████████████████████████████████████████████████████████████████████████████████████████████████████| 100.0%

Inspect the results#

[4]:
for node_id, task in results.items():
    assert task.succeeded, f"task {node_id} failed"
    print(task.get_output_values())
{'dataset': Dataset(dataset=<darfix.core.dataset.ImageDataset object at 0x7fc3bc09c670>, indices=None, bg_indices=None, bg_dataset=None)}
{}
{'dataset': Dataset(dataset=<darfix.core.dataset.ImageDataset object at 0x7fc3bc09c670>, indices=None, bg_indices=None, bg_dataset=None)}
{'dataset': Dataset(dataset=<darfix.core.dataset.ImageDataset object at 0x7fc3bc09c670>, indices=None, bg_indices=None, bg_dataset=None)}
{'dataset': Dataset(dataset=<darfix.core.dataset.ImageDataset object at 0x7fc3bc09c670>, indices=None, bg_indices=None, bg_dataset=None)}
{'dataset': Dataset(dataset=<darfix.core.dataset.ImageDataset object at 0x7fc3bc09c670>, indices=None, bg_indices=None, bg_dataset=None)}
{'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.]])}
{'dataset': Dataset(dataset=<darfix.core.dataset.ImageDataset object at 0x7fc3bc09c670>, indices=None, bg_indices=None, bg_dataset=None)}

Note#

The same can be done for EDF datasets. In this case the, metadata_url parameter should be omitted and the filenames parameter will contain the list of the EDF image paths:

from glob import glob
root_dir = "/tmp/darfix"
os.makedirs(root_dir, exist_ok=True)
filenames = glob(os.path.join(tutorials.__path__[0], "*.edf"))
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