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Merge remote-tracking branch 'upstream/main' into fix-collection
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@tsalo
tsalo committed Sep 8, 2023
2 parents fdc0ff5 + fadeca3 commit b96be01
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Showing 6 changed files with 117 additions and 125 deletions.
1 change: 0 additions & 1 deletion xcp_d/tests/test_workflows_anatomical.py
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Original file line number Diff line number Diff line change
Expand Up @@ -90,7 +90,6 @@ def test_postprocess_anat_wf(ds001419_data, tmp_path_factory):
t1w_available=True,
t2w_available=True,
target_space="MNI152NLin2009cAsym",
dcan_qc=False,
omp_nthreads=1,
mem_gb=0.1,
name="postprocess_anat_wf",
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44 changes: 20 additions & 24 deletions xcp_d/workflows/anatomical.py
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Original file line number Diff line number Diff line change
Expand Up @@ -47,7 +47,6 @@ def init_postprocess_anat_wf(
t1w_available,
t2w_available,
target_space,
dcan_qc,
omp_nthreads,
mem_gb,
name="postprocess_anat_wf",
Expand All @@ -69,7 +68,6 @@ def init_postprocess_anat_wf(
t1w_available=True,
t2w_available=True,
target_space="MNI152NLin6Asym",
dcan_qc=True,
omp_nthreads=1,
mem_gb=0.1,
name="postprocess_anat_wf",
Expand All @@ -85,7 +83,6 @@ def init_postprocess_anat_wf(
True if a preprocessed T2w is available, False if not.
target_space : :obj:`str`
Target NIFTI template for T1w.
%(dcan_qc)s
%(omp_nthreads)s
%(mem_gb)s
%(name)s
Expand Down Expand Up @@ -287,33 +284,32 @@ def init_postprocess_anat_wf(
])
# fmt:on

if dcan_qc:
execsummary_anatomical_plots_wf = init_execsummary_anatomical_plots_wf(
t1w_available=t1w_available,
t2w_available=t2w_available,
output_dir=output_dir,
name="execsummary_anatomical_plots_wf",
)
execsummary_anatomical_plots_wf = init_execsummary_anatomical_plots_wf(
t1w_available=t1w_available,
t2w_available=t2w_available,
output_dir=output_dir,
name="execsummary_anatomical_plots_wf",
)

# fmt:off
workflow.connect([
(inputnode, execsummary_anatomical_plots_wf, [("template", "inputnode.template")]),
])
# fmt:on

if t1w_available:
# fmt:off
workflow.connect([
(inputnode, execsummary_anatomical_plots_wf, [("template", "inputnode.template")]),
(ds_t1w_std, execsummary_anatomical_plots_wf, [("out_file", "inputnode.t1w")]),
])
# fmt:on

if t1w_available:
# fmt:off
workflow.connect([
(ds_t1w_std, execsummary_anatomical_plots_wf, [("out_file", "inputnode.t1w")]),
])
# fmt:on

if t2w_available:
# fmt:off
workflow.connect([
(ds_t2w_std, execsummary_anatomical_plots_wf, [("out_file", "inputnode.t2w")]),
])
# fmt:on
if t2w_available:
# fmt:off
workflow.connect([
(ds_t2w_std, execsummary_anatomical_plots_wf, [("out_file", "inputnode.t2w")]),
])
# fmt:on

return workflow

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1 change: 0 additions & 1 deletion xcp_d/workflows/base.py
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Original file line number Diff line number Diff line change
Expand Up @@ -520,7 +520,6 @@ def init_subject_wf(
t1w_available=t1w_available,
t2w_available=t2w_available,
target_space=target_space,
dcan_qc=dcan_qc,
omp_nthreads=omp_nthreads,
mem_gb=1,
name="postprocess_anat_wf",
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39 changes: 19 additions & 20 deletions xcp_d/workflows/bold.py
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Original file line number Diff line number Diff line change
Expand Up @@ -570,27 +570,26 @@ def init_postprocess_nifti_wf(
# fmt:on

# executive summary workflow
if dcan_qc:
execsummary_functional_plots_wf = init_execsummary_functional_plots_wf(
preproc_nifti=bold_file,
t1w_available=t1w_available,
t2w_available=t2w_available,
output_dir=output_dir,
layout=layout,
name="execsummary_functional_plots_wf",
)
execsummary_functional_plots_wf = init_execsummary_functional_plots_wf(
preproc_nifti=bold_file,
t1w_available=t1w_available,
t2w_available=t2w_available,
output_dir=output_dir,
layout=layout,
name="execsummary_functional_plots_wf",
)

# fmt:off
workflow.connect([
# Use inputnode for executive summary instead of downcast_data
# because T1w is used as name source.
(inputnode, execsummary_functional_plots_wf, [
("boldref", "inputnode.boldref"),
("t1w", "inputnode.t1w"),
("t2w", "inputnode.t2w"),
]),
])
# fmt:on
# fmt:off
workflow.connect([
# Use inputnode for executive summary instead of downcast_data
# because T1w is used as name source.
(inputnode, execsummary_functional_plots_wf, [
("boldref", "inputnode.boldref"),
("t1w", "inputnode.t1w"),
("t2w", "inputnode.t2w"),
]),
])
# fmt:on

return workflow

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39 changes: 19 additions & 20 deletions xcp_d/workflows/cifti.py
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Original file line number Diff line number Diff line change
Expand Up @@ -544,29 +544,28 @@ def init_postprocess_cifti_wf(
# fmt:on

# executive summary workflow
if dcan_qc:
execsummary_functional_plots_wf = init_execsummary_functional_plots_wf(
preproc_nifti=run_data["nifti_file"],
t1w_available=t1w_available,
t2w_available=t2w_available,
output_dir=output_dir,
layout=layout,
name="execsummary_functional_plots_wf",
)
execsummary_functional_plots_wf = init_execsummary_functional_plots_wf(
preproc_nifti=run_data["nifti_file"],
t1w_available=t1w_available,
t2w_available=t2w_available,
output_dir=output_dir,
layout=layout,
name="execsummary_functional_plots_wf",
)

# Use inputnode for executive summary instead of downcast_data
# because T1w is used as name source.
# fmt:off
workflow.connect([
# Use inputnode for executive summary instead of downcast_data
# because T1w is used as name source.
# fmt:off
workflow.connect([
# Use inputnode for executive summary instead of downcast_data
# because T1w is used as name source.
(inputnode, execsummary_functional_plots_wf, [
("boldref", "inputnode.boldref"),
("t1w", "inputnode.t1w"),
("t2w", "inputnode.t2w"),
]),
])
# fmt:on
(inputnode, execsummary_functional_plots_wf, [
("boldref", "inputnode.boldref"),
("t1w", "inputnode.t1w"),
("t2w", "inputnode.t2w"),
]),
])
# fmt:on

return workflow

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118 changes: 59 additions & 59 deletions xcp_d/workflows/plotting.py
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Original file line number Diff line number Diff line change
Expand Up @@ -358,75 +358,75 @@ def init_qc_report_wf(
])
# fmt:on

# Generate preprocessing and postprocessing carpet plots.
plot_execsummary_carpets_dcan = pe.Node(
QCPlotsES(TR=TR, standardize=params == "none"),
name="plot_execsummary_carpets_dcan",
mem_gb=mem_gb,
n_procs=omp_nthreads,
)
# Generate preprocessing and postprocessing carpet plots.
plot_execsummary_carpets_dcan = pe.Node(
QCPlotsES(TR=TR, standardize=params == "none"),
name="plot_execsummary_carpets_dcan",
mem_gb=mem_gb,
n_procs=omp_nthreads,
)

# fmt:off
workflow.connect([
(inputnode, plot_execsummary_carpets_dcan, [
("preprocessed_bold", "preprocessed_bold"),
("uncensored_denoised_bold", "uncensored_denoised_bold"),
("interpolated_filtered_bold", "interpolated_filtered_bold"),
("filtered_motion", "filtered_motion"),
("run_index", "run_index"),
]),
])
# fmt:on

if not cifti:
# fmt:off
workflow.connect([
(inputnode, plot_execsummary_carpets_dcan, [
("preprocessed_bold", "preprocessed_bold"),
("uncensored_denoised_bold", "uncensored_denoised_bold"),
("interpolated_filtered_bold", "interpolated_filtered_bold"),
("filtered_motion", "filtered_motion"),
("run_index", "run_index"),
(inputnode, plot_execsummary_carpets_dcan, [("bold_mask", "mask")]),
(warp_dseg_to_bold, plot_execsummary_carpets_dcan, [
("output_image", "seg_data"),
]),
])
# fmt:on

if not cifti:
# fmt:off
workflow.connect([
(inputnode, plot_execsummary_carpets_dcan, [("bold_mask", "mask")]),
(warp_dseg_to_bold, plot_execsummary_carpets_dcan, [
("output_image", "seg_data"),
]),
])
# fmt:on

ds_preproc_execsummary_carpet_dcan = pe.Node(
DerivativesDataSink(
base_directory=output_dir,
dismiss_entities=["den"],
datatype="figures",
desc="preprocESQC",
),
name="ds_preproc_execsummary_carpet_dcan",
run_without_submitting=True,
)
ds_preproc_execsummary_carpet_dcan = pe.Node(
DerivativesDataSink(
base_directory=output_dir,
dismiss_entities=["den"],
datatype="figures",
desc="preprocESQC",
),
name="ds_preproc_execsummary_carpet_dcan",
run_without_submitting=True,
)

# fmt:off
workflow.connect([
(inputnode, ds_preproc_execsummary_carpet_dcan, [("name_source", "source_file")]),
(plot_execsummary_carpets_dcan, ds_preproc_execsummary_carpet_dcan, [
("before_process", "in_file"),
]),
])
# fmt:on
# fmt:off
workflow.connect([
(inputnode, ds_preproc_execsummary_carpet_dcan, [("name_source", "source_file")]),
(plot_execsummary_carpets_dcan, ds_preproc_execsummary_carpet_dcan, [
("before_process", "in_file"),
]),
])
# fmt:on

ds_postproc_execsummary_carpet_dcan = pe.Node(
DerivativesDataSink(
base_directory=output_dir,
dismiss_entities=["den"],
datatype="figures",
desc="postprocESQC",
),
name="ds_postproc_execsummary_carpet_dcan",
run_without_submitting=True,
)
ds_postproc_execsummary_carpet_dcan = pe.Node(
DerivativesDataSink(
base_directory=output_dir,
dismiss_entities=["den"],
datatype="figures",
desc="postprocESQC",
),
name="ds_postproc_execsummary_carpet_dcan",
run_without_submitting=True,
)

# fmt:off
workflow.connect([
(inputnode, ds_postproc_execsummary_carpet_dcan, [("name_source", "source_file")]),
(plot_execsummary_carpets_dcan, ds_postproc_execsummary_carpet_dcan, [
("after_process", "in_file"),
]),
])
# fmt:on
# fmt:off
workflow.connect([
(inputnode, ds_postproc_execsummary_carpet_dcan, [("name_source", "source_file")]),
(plot_execsummary_carpets_dcan, ds_postproc_execsummary_carpet_dcan, [
("after_process", "in_file"),
]),
])
# fmt:on

if not cifti:
# fmt:off
Expand Down

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