🐛 Create missing space-bold_desc-brain_mask on-demand

[shnizzedy]

Fixes

Fixes #2248 by @shnizzedy
Fixes #2257 by @shnizzedy
Fixes #2258 by @shnizzedy
Related to #2225 by @shnizzedy
Related to #2215 by @birajstha

Description

If space-bold_desc-brain_mask is missing when needed for nuisance generation, create it by transforming space-template_desc-bold_mask or space-template_desc-brain_mask to native BOLD space.

Technical details

C-PAC/CPAC/nuisance/nuisance.py

Lines 2523 to 2545 in 0ec8206

	brain_mask = (
	strat_pool.node_data("space-bold_desc-brain_mask")
	if strat_pool.check_rpool("space-bold_desc-brain_mask")
	else NodeData()
	)
	if space == "T1w":
	prefixes[0] = ""
	if strat_pool.check_rpool("from-template_to-T1w_mode-image_desc-linear_xfm"):
	reg_tool = strat_pool.reg_tool(
	"from-template_to-T1w_mode-image_desc-linear_xfm"
	)
	if brain_mask.node is NotImplemented:
	if reg_tool and strat_pool.check_rpool(
	["space-template_desc-bold_mask", "space-template_desc-brain_mask"]
	):
	outputs["space-bold_desc-brain_mask"] = (
	transform_bold_mask_to_native(
	wf, strat_pool, cfg, pipe_num, reg_tool
	)
	)
	brain_mask.node, brain_mask.out = outputs[
	"space-bold_desc-brain_mask"
	]

C-PAC/CPAC/nuisance/utils/xfm.py

Lines 30 to 71 in 0ec8206

	def transform_bold_mask_to_native(
	wf: Workflow,
	strat_pool: ResourcePool,
	cfg: Configuration,
	pipe_num: int,
	reg_tool: Literal["ants", "fsl"],
	) -> tuple[Workflow, str]:
	"""Transform a template-space BOLD mask to native space."""
	num_cpus = cast(
	int, cfg["pipeline_setup", "system_config", "max_cores_per_participant"]
	)
	num_ants_cores = cast(
	int, cfg["pipeline_setup", "system_config", "num_ants_threads"]
	)
	apply_xfm = apply_transform(
	f"xfm_from-template_to-bold_mask_{pipe_num}",
	reg_tool,
	time_series=True,
	num_cpus=num_cpus,
	num_ants_cores=num_ants_cores,
	)
	apply_xfm.inputs.inputspec.interpolation = cfg[
	"registration_workflows",
	"functional_registration",
	"func_registration_to_template",
	f"{'ANTs' if reg_tool == 'ants' else 'FNIRT'}_pipelines",
	"interpolation",
	]
	sbref = strat_pool.node_data("sbref")
	bold_mask = strat_pool.node_data(
	["space-template_desc-bold_mask", "space-template_desc-brain_mask"]
	)
	xfm = strat_pool.node_data("from-template_to-bold_mode-image_xfm")
	wf.connect(
	[
	(bold_mask.node, apply_xfm, [(bold_mask.out, "inputspec.input_image")]),
	(sbref.node, apply_xfm, [(sbref.out, "inputspec.reference")]),
	(xfm.node, apply_xfm, [(xfm.out, "inputspec.transform")]),
	]
	)
	return apply_xfm, "outputspec.output_image"

Tests

Adds an abcd-options smoke test (just one human subject) to the unit test suite:

C-PAC/CPAC/pipeline/test/test_connect_pipeline.py

Lines 47 to 116 in 0ec8206

	@pytest.mark.parametrize("preconfig", ["abcd-options"])
	def test_config(
	caplog: pytest.LogCaptureFixture, preconfig: str, tmp_path: Path
	) -> None:
	"""Run 'test_config' analysis level."""
	caplog.set_level(INFO)
	data_config_file = tmp_path / "data_config.yaml"
	with data_config_file.open("w") as _f:
	yaml.dump(
	[
	{
	"anat": "s3://fcp-indi/data/Projects/ADHD200/RawDataBIDS/KKI/sub-1019436/ses-1/anat/sub-1019436_ses-1_run-1_T1w.nii.gz",
	"func": {
	"rest_acq-1_run-1": {
	"scan": "s3://fcp-indi/data/Projects/ADHD200/RawDataBIDS/KKI/sub-1019436/ses-1/func/sub-1019436_ses-1_task-rest_acq-1_run-1_bold.nii.gz",
	"scan_parameters": "s3://fcp-indi/data/Projects/ADHD200/RawDataBIDS/KKI/task-rest_acq-1_bold.json",
	}
	},
	"site": "KKI",
	"subject_id": "1019436",
	"unique_id": "1",
	}
	],
	_f,
	)
	# output in tmp_path/outputs
	pipeline = Preconfiguration(preconfig)
	output_dir = tmp_path / "outputs"
	output_dir.mkdir(parents=True, exist_ok=True)
	pipeline["pipeline_setup", "log_directory", "path"] = str(output_dir / "log")
	pipeline["pipeline_setup", "output_directory", "path"] = str(output_dir / "out")
	pipeline["pipeline_setup", "working_directory", "path"] = str(
	output_dir / "working"
	)
	pipeline_file = tmp_path / "pipe_config.yaml"
	with pipeline_file.open("w") as _f:
	_f.write(create_yaml_from_template(pipeline, preconfig, preconfig, True))
	plugin = "MultiProc"
	plugin_args: dict[str, int | bool | Callable] = {
	"n_procs": 2,
	"memory_gb": 10,
	"raise_insufficient": True,
	"status_callback": log_nodes_cb,
	}
	tracking = False
	exitcode = run(
	str(data_config_file),
	str(pipeline_file),
	plugin=plugin,
	plugin_args=plugin_args,
	tracking=tracking,
	test_config=True,
	)
	if exitcode != 0:
	records = list(caplog.records)
	msg: str
	msg = str(records[-1])
	if hasattr(records[-1], "exc_info"):
	exc_info = records[-1].exc_info
	if (
	exc_info
	and exc_info[0]
	and exc_info[1]
	and hasattr(exc_info[1], "args")
	):
	msg = exc_info[1].args[0]
	raise exc_info[0](exc_info[1])
	raise AssertionError(msg)

Checklist

• My pull request has a descriptive title (not a vague title like Update index.md).
• My pull request targets the develop branch of the repository.
• My commit messages follow best practices.
• My code follows the established code style of the repository.
• I added tests for the changes I made (if applicable).
• I updated the changelog.
• I added or updated documentation (if applicable).
• I tried running the project locally and verified that there are no visible errors.

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(a) The contribution was created in whole or in part by me and I
    have the right to submit it under the open source license
    indicated in the file; or

(b) The contribution is based upon previous work that, to the best
    of my knowledge, is covered under an appropriate open source
    license and I have the right under that license to submit that
    work with modifications, whether created in whole or in part
    by me, under the same open source license (unless I am
    permitted to submit under a different license), as indicated
    in the file; or

(c) The contribution was provided directly to me by some other
    person who certified (a), (b) or (c) and I have not modified
    it.

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    are public and that a record of the contribution (including all
    personal information I submit with it, including my sign-off) is
    maintained indefinitely and may be redistributed consistent with
    this project or the open source license(s) involved.

[codecov]

Codecov Report

Attention: Patch coverage is 82.32323% with 35 lines in your changes missing coverage. Please review.

Project coverage is 33.8%. Comparing base (8596775) to head (6e501cc).
Report is 53 commits behind head on develop.

Files with missing lines	Patch %	Lines
CPAC/pipeline/test/test_connect_pipeline.py	71.1%	12 Missing and 1 partial ⚠️
CPAC/utils/monitoring/monitoring.py	69.0%	5 Missing and 4 partials ⚠️
CPAC/utils/datasource.py	53.8%	4 Missing and 2 partials ⚠️
CPAC/func_preproc/func_preproc.py	62.5%	2 Missing and 1 partial ⚠️
CPAC/utils/test_resources.py	83.3%	2 Missing ⚠️
...PAC/distortion_correction/distortion_correction.py	50.0%	1 Missing ⚠️
CPAC/nuisance/nuisance.py	92.3%	0 Missing and 1 partial ⚠️

Additional details and impacted files

@@            Coverage Diff            @@
##           develop   #2256     +/-   ##
=========================================
+ Coverage     28.4%   33.8%   +5.4%     
=========================================
  Files          230     232      +2     
  Lines        26052   26300    +248     
  Branches      4092    4130     +38     
=========================================
+ Hits          7397    8886   +1489     
+ Misses       18024   16687   -1337     
- Partials       631     727     +96     

Files with missing lines	Coverage Δ
CPAC/nuisance/utils/xfm.py	100.0% <100.0%> (ø)
CPAC/pipeline/cpac_runner.py	25.0% <100.0%> (+1.7%)	⬆️
CPAC/registration/registration.py	43.6% <100.0%> (+23.3%)	⬆️
CPAC/utils/monitoring/draw_gantt_chart.py	10.2% <ø> (ø)
CPAC/utils/tests/test_datasource.py	100.0% <100.0%> (+74.2%)	⬆️
...PAC/distortion_correction/distortion_correction.py	7.5% <50.0%> (+<0.1%)	⬆️
CPAC/nuisance/nuisance.py	25.9% <92.3%> (+1.8%)	⬆️
CPAC/utils/test_resources.py	69.7% <83.3%> (+64.4%)	⬆️
CPAC/func_preproc/func_preproc.py	25.9% <62.5%> (+15.5%)	⬆️
CPAC/utils/datasource.py	32.7% <53.8%> (+5.2%)	⬆️
... and 2 more

... and 15 files with indirect coverage changes

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[sgiavasis]

I like the handling of the outputs, and that new pipeline connection test 👍