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redo ExtractROI #47

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redo ExtractROI #47

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040708f
rename roi_file with new basename
yibeichan May 9, 2023
d0df719
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] May 9, 2023
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6 changes: 3 additions & 3 deletions pydra/tasks/fsl/utils/extractroi.py
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Original file line number Diff line number Diff line change
Expand Up @@ -20,7 +20,7 @@
"help_string": "output file",
"argstr": "{roi_file}",
"position": 1,
"output_file_template": "{in_file}_trim",
"output_file_template": "{in_file}_roi",
},
),
("x_min", int, {"help_string": "", "argstr": "{x_min}", "position": 2}),
Expand Down Expand Up @@ -48,9 +48,9 @@ class ExtractROI(ShellCommandTask):
>>> task.inputs.in_file = "test.nii.gz"
>>> task.inputs.t_min = 0
>>> task.inputs.t_size = 3
>>> task.inputs.roi_file = "test_trim.nii.gz"
>>> task.inputs.roi_file = "test_roi.nii.gz"
>>> task.cmdline
'fslroi test.nii.gz test_trim.nii.gz 0 3'
'fslroi test.nii.gz test_roi.nii.gz 0 3'
"""

input_spec = ExtractROI_input_spec
Expand Down
16 changes: 15 additions & 1 deletion pydra/tasks/fsl/utils/tests/test_run_extractroi.py
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Expand Up @@ -6,7 +6,21 @@
@pytest.mark.xfail("FSLDIR" not in os.environ, reason="no FSL found", raises=FileNotFoundError)
@pytest.mark.parametrize(
"inputs, outputs",
[({"in_file": "test.nii.gz", "t_min": 0, "t_size": 1}, ["roi_file"])],
[
({"in_file": "test.nii.gz", "t_min": 0, "t_size": 1}, ["roi_file"]),
(
{
"in_file": "test.nii.gz",
"x_min": 0,
"x_size": 1,
"y_min": 20,
"y_size": 1,
"z_min": 10,
"z_size": 1,
},
["roi_file"],
),
],
)
def test_ExtractROI(test_data, inputs, outputs):
if inputs is None:
Expand Down
16 changes: 15 additions & 1 deletion pydra/tasks/fsl/utils/tests/test_spec_extractroi.py
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Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,21 @@

@pytest.mark.parametrize(
"inputs, outputs",
[({"in_file": "test.nii.gz", "t_min": 0, "t_size": 1}, ["roi_file"])],
[
({"in_file": "test.nii.gz", "t_min": 0, "t_size": 1}, ["roi_file"]),
(
{
"in_file": "test.nii.gz",
"x_min": 0,
"x_size": 1,
"y_min": 20,
"y_size": 1,
"z_min": 10,
"z_size": 1,
},
["roi_file"],
),
],
)
def test_ExtractROI(test_data, inputs, outputs):
if inputs is None:
Expand Down
14 changes: 11 additions & 3 deletions specs/fsl_utils_param.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -90,21 +90,29 @@ ExtractROI:
output_requirements:
roi_file: [in_file]
output_templates:
roi_file: "{in_file}_trim"
roi_file: "{in_file}_roi"
inputs_drop:
- crop_list
doctest:
in_file: test.nii.gz
t_min: 0
t_size: 3
roi_file: test_trim.nii.gz
cmdline: fslroi test.nii.gz test_trim.nii.gz 0 3
roi_file: test_roi.nii.gz
cmdline: fslroi test.nii.gz test_roi.nii.gz 0 3
tests_inputs:
- in_file: test.nii.gz
t_min: 0
t_size: 1
- in_file: test.nii.gz
x_min: 0
x_size: 1
y_min: 20
y_size: 1
z_min: 10
z_size: 1
tests_outputs:
- roi_file
- roi_file

FilterRegressor:
output_requirements:
Expand Down