Merge branch 'main' into B23O_repro

narps_open/pipelines/__init__.py

@@ -27,7 +27,7 @@
     '43FJ': None,
     '46CD': None,
     '4SZ2': None,
-    '4TQ6': None,
+    '4TQ6': 'PipelineTeam4TQ6',
     '50GV': None,
     '51PW': 'PipelineTeam51PW',
     '5G9K': None,
@@ -58,8 +58,8 @@
     'L7J7': 'PipelineTeamL7J7',
     'L9G5': None,
     'O03M': None,
-    'O21U': None,
-    'O6R6': None,
+    'O21U': 'PipelineTeamO21U',
+    'O6R6': 'PipelineTeamO6R6',
     'P5F3': None,
     'Q58J': None,
     'Q6O0': 'PipelineTeamQ6O0',

narps_open/utils/correlation/__main__.py

@@ -19,7 +19,7 @@ def main():
     parser = ArgumentParser(description = 'Compare reproduced files to original results.')
     parser.add_argument('-t', '--team', type = str, required = True,
         help = 'the team ID', choices = get_implemented_pipelines())
-    subjects.add_argument('-n', '--nsubjects', type=str, required = True,
+    parser.add_argument('-n', '--nsubjects', type=int, required = True,
         help='the number of subjects to be selected')
     arguments = parser.parse_args()
 

tests/pipelines/test_team_4TQ6.py

@@ -0,0 +1,96 @@
+#!/usr/bin/python
+# coding: utf-8
+
+""" Tests of the 'narps_open.pipelines.team_4TQ6' module.
+
+Launch this test with PyTest
+
+Usage:
+======
+    pytest -q test_team_4TQ6.py
+    pytest -q test_team_4TQ6.py -k <selected_test>
+"""
+from os.path import join, exists, abspath
+from filecmp import cmp
+
+from pytest import helpers, mark
+from nipype import Workflow, Node, Function
+from nipype.interfaces.base import Bunch
+
+from narps_open.utils.configuration import Configuration
+from narps_open.pipelines.team_4TQ6 import PipelineTeam4TQ6
+
+class TestPipelinesTeam4TQ6:
+    """ A class that contains all the unit tests for the PipelineTeam4TQ6 class."""
+
+    @staticmethod
+    @mark.unit_test
+    def test_create():
+        """ Test the creation of a PipelineTeam4TQ6 object """
+
+        pipeline = PipelineTeam4TQ6()
+
+        # 1 - check the parameters
+        assert pipeline.fwhm == 6.0
+        assert pipeline.team_id == '4TQ6'
+
+        # 2 - check workflows
+        assert pipeline.get_preprocessing() is None
+        assert isinstance(pipeline.get_run_level_analysis(), Workflow)
+        assert isinstance(pipeline.get_subject_level_analysis(), Workflow)
+        group_level = pipeline.get_group_level_analysis()
+        assert len(group_level) == 3
+        for sub_workflow in group_level:
+            assert isinstance(sub_workflow, Workflow)
+
+    @staticmethod
+    @mark.unit_test
+    def test_outputs():
+        """ Test the expected outputs of a PipelineTeam4TQ6 object """
+
+        pipeline = PipelineTeam4TQ6()
+
+        # 1 - 1 subject outputs
+        pipeline.subject_list = ['001']
+        helpers.test_pipeline_outputs(pipeline, [0, 4*1*2*4, 4*2*1 + 2*1, 6*2*2 + 3*2, 18])
+
+        # 2 - 4 subjects outputs
+        pipeline.subject_list = ['001', '002', '003', '004']
+        helpers.test_pipeline_outputs(pipeline, [0, 4*4*2*4, 4*2*4 + 2*4, 6*2*2 + 3*2, 18])
+
+    @staticmethod
+    @mark.unit_test
+    def test_subject_information():
+        """ Test the get_subject_information method """
+
+        # Get test files
+        test_file = join(Configuration()['directories']['test_data'], 'pipelines', 'events.tsv')
+
+        # Prepare several scenarii
+        info_missed = PipelineTeam4TQ6.get_subject_information(test_file)
+
+        # Compare bunches to expected
+        bunch = info_missed[0]
+        assert isinstance(bunch, Bunch)
+        assert bunch.conditions == ['trial', 'gain', 'loss']
+        helpers.compare_float_2d_arrays(bunch.onsets, [
+            [4.071, 11.834, 19.535, 27.535, 36.435],
+            [4.071, 11.834, 19.535, 27.535, 36.435],
+            [4.071, 11.834, 19.535, 27.535, 36.435]
+            ])
+        helpers.compare_float_2d_arrays(bunch.durations, [
+            [4.0, 4.0, 4.0, 4.0, 4.0],
+            [4.0, 4.0, 4.0, 4.0, 4.0],
+            [4.0, 4.0, 4.0, 4.0, 4.0]
+            ])
+        helpers.compare_float_2d_arrays(bunch.amplitudes, [
+            [1.0, 1.0, 1.0, 1.0, 1.0],
+            [14.0, 34.0, 38.0, 10.0, 16.0],
+            [6.0, 14.0, 19.0, 15.0, 17.0]
+            ])
+
+    @staticmethod
+    @mark.pipeline_test
+    def test_execution():
+        """ Test the execution of a PipelineTeam4TQ6 and compare results """
+        helpers.test_pipeline_evaluation('4TQ6')

tests/pipelines/test_team_O21U.py

@@ -0,0 +1,128 @@
+#!/usr/bin/python
+# coding: utf-8
+
+""" Tests of the 'narps_open.pipelines.team_O21U' module.
+
+Launch this test with PyTest
+
+Usage:
+======
+    pytest -q test_team_O21U.py
+    pytest -q test_team_O21U.py -k <selected_test>
+"""
+from os.path import join, exists, abspath
+from filecmp import cmp
+
+from pytest import helpers, mark
+from nipype import Workflow, Node, Function
+from nipype.interfaces.base import Bunch
+
+from narps_open.utils.configuration import Configuration
+from narps_open.pipelines.team_O21U import PipelineTeamO21U
+
+class TestPipelinesTeamO21U:
+    """ A class that contains all the unit tests for the PipelineTeamO21U class."""
+
+    @staticmethod
+    @mark.unit_test
+    def test_create():
+        """ Test the creation of a PipelineTeamO21U object """
+
+        pipeline = PipelineTeamO21U()
+
+        # 1 - check the parameters
+        assert pipeline.fwhm == 5.0
+        assert pipeline.team_id == 'O21U'
+
+        # 2 - check workflows
+        assert pipeline.get_preprocessing() is None
+        assert isinstance(pipeline.get_run_level_analysis(), Workflow)
+        assert isinstance(pipeline.get_subject_level_analysis(), Workflow)
+        group_level = pipeline.get_group_level_analysis()
+        assert len(group_level) == 3
+        for sub_workflow in group_level:
+            assert isinstance(sub_workflow, Workflow)
+
+    @staticmethod
+    @mark.unit_test
+    def test_outputs():
+        """ Test the expected outputs of a PipelineTeamO21U object """
+
+        pipeline = PipelineTeamO21U()
+
+        # 1 - 1 subject outputs
+        pipeline.subject_list = ['001']
+        helpers.test_pipeline_outputs(pipeline, [0, 4*1*2*4, 4*2*1 + 2*1, 6*2*2 + 3*2, 18])
+
+        # 2 - 4 subjects outputs
+        pipeline.subject_list = ['001', '002', '003', '004']
+        helpers.test_pipeline_outputs(pipeline, [0, 4*4*2*4, 4*2*4 + 2*4, 6*2*2 + 3*2, 18])
+
+    @staticmethod
+    @mark.unit_test
+    def test_subject_information():
+        """ Test the get_subject_information method """
+
+        # Get test files
+        test_file = join(Configuration()['directories']['test_data'], 'pipelines', 'events.tsv')
+
+        # Prepare several scenarii
+        info_missed = PipelineTeamO21U.get_subject_information(test_file)
+
+        # Compare bunches to expected
+        bunch = info_missed[0]
+        assert isinstance(bunch, Bunch)
+        assert bunch.conditions == ['trial', 'gain', 'loss']
+        helpers.compare_float_2d_arrays(bunch.onsets, [
+            [4.071, 11.834, 19.535, 27.535, 36.435],
+            [4.071, 11.834, 19.535, 27.535, 36.435],
+            [4.071, 11.834, 19.535, 27.535, 36.435]
+            ])
+        helpers.compare_float_2d_arrays(bunch.durations, [
+            [4.0, 4.0, 4.0, 4.0, 4.0],
+            [4.0, 4.0, 4.0, 4.0, 4.0],
+            [4.0, 4.0, 4.0, 4.0, 4.0]
+            ])
+        helpers.compare_float_2d_arrays(bunch.amplitudes, [
+            [1.0, 1.0, 1.0, 1.0, 1.0],
+            [14.0, 34.0, 38.0, 10.0, 16.0],
+            [6.0, 14.0, 19.0, 15.0, 17.0]
+            ])
+
+    @staticmethod
+    @mark.unit_test
+    def test_confounds_file(temporary_data_dir):
+        """ Test the get_confounds_file method """
+
+        # Get input and reference output file
+        confounds_file = abspath(join(
+            Configuration()['directories']['test_data'], 'pipelines', 'confounds.tsv'))
+        reference_file = abspath(join(
+            Configuration()['directories']['test_data'],
+            'pipelines', 'team_O21U', 'confounds.tsv'))
+
+        # Create new confounds file
+        confounds_node = Node(Function(
+            input_names = ['filepath', 'subject_id', 'run_id'],
+            output_names = ['confounds_file'],
+            function = PipelineTeamO21U.get_confounds_file),
+            name = 'confounds_node')
+        confounds_node.base_dir = temporary_data_dir
+        confounds_node.inputs.filepath = confounds_file
+        confounds_node.inputs.subject_id = 'sid'
+        confounds_node.inputs.run_id = 'rid'
+        confounds_node.run()
+
+        # Check confounds file was created
+        created_confounds_file = abspath(join(
+            temporary_data_dir, confounds_node.name, 'confounds_file_sub-sid_run-rid.tsv'))
+        assert exists(created_confounds_file)
+
+        # Check contents
+        assert cmp(reference_file, created_confounds_file)
+
+    @staticmethod
+    @mark.pipeline_test
+    def test_execution():
+        """ Test the execution of a PipelineTeamO21U and compare results """
+        helpers.test_pipeline_evaluation('O21U')

tests/pipelines/test_team_O6R6.py

@@ -0,0 +1,116 @@
+#!/usr/bin/python
+# coding: utf-8
+
+""" Tests of the 'narps_open.pipelines.team_O6R6' module.
+
+Launch this test with PyTest
+
+Usage:
+======
+    pytest -q test_team_O6R6.py
+    pytest -q test_team_O6R6.py -k <selected_test>
+"""
+from os.path import join, exists, abspath
+from filecmp import cmp
+
+from pytest import helpers, mark
+from nipype import Workflow, Node, Function
+from nipype.interfaces.base import Bunch
+
+from narps_open.utils.configuration import Configuration
+from narps_open.pipelines.team_O6R6 import PipelineTeamO6R6
+
+class TestPipelinesTeamO6R6:
+    """ A class that contains all the unit tests for the PipelineTeamO6R6 class."""
+
+    @staticmethod
+    @mark.unit_test
+    def test_create():
+        """ Test the creation of a PipelineTeamO6R6 object """
+
+        pipeline = PipelineTeamO6R6()
+
+        # 1 - check the parameters
+        assert pipeline.team_id == 'O6R6'
+
+        # 2 - check workflows
+        assert pipeline.get_preprocessing() is None
+        assert isinstance(pipeline.get_run_level_analysis(), Workflow)
+        assert isinstance(pipeline.get_subject_level_analysis(), Workflow)
+        group_level = pipeline.get_group_level_analysis()
+        assert len(group_level) == 3
+        for sub_workflow in group_level:
+            assert isinstance(sub_workflow, Workflow)
+
+    @staticmethod
+    @mark.unit_test
+    def test_outputs():
+        """ Test the expected outputs of a PipelineTeamO6R6 object """
+
+        pipeline = PipelineTeamO6R6()
+
+        # 1 - 1 subject outputs
+        pipeline.subject_list = ['001']
+        helpers.test_pipeline_outputs(pipeline, [0, 2*1*4*4, 2*4*1 + 2*1, 6*2*2 + 3*2, 18])
+
+        # 2 - 4 subjects outputs
+        pipeline.subject_list = ['001', '002', '003', '004']
+        helpers.test_pipeline_outputs(pipeline, [0, 2*4*4*4, 2*4*4 + 2*4, 6*2*2 + 3*2, 18])
+
+    @staticmethod
+    @mark.unit_test
+    def test_subject_information():
+        """ Test the get_subject_information method """
+
+        # Get test files
+        test_file = join(Configuration()['directories']['test_data'], 'pipelines', 'events.tsv')
+
+        # Prepare several scenarii
+        info_ei = PipelineTeamO6R6.get_subject_information(test_file, 'equalIndifference')
+        info_er = PipelineTeamO6R6.get_subject_information(test_file, 'equalRange')
+
+        # Compare bunches to expected
+        bunch = info_ei[0]
+        assert isinstance(bunch, Bunch)
+        assert bunch.conditions == ['trial', 'gain_trial', 'loss_trial']
+        helpers.compare_float_2d_arrays(bunch.onsets, [
+            [4.071, 11.834, 27.535, 36.435],
+            [4.071, 11.834],
+            [27.535, 36.435]
+            ])        
+        helpers.compare_float_2d_arrays(bunch.durations, [
+            [2.388, 2.289, 2.08, 2.288],
+            [2.388, 2.289],
+            [2.08, 2.288]
+            ])
+        helpers.compare_float_2d_arrays(bunch.amplitudes, [
+            [1.0, 1.0, 1.0, 1.0],
+            [3.0, 13.0],
+            [3.5, 4.5]
+            ])
+
+        # Compare bunches to expected
+        bunch = info_er[0]
+        assert isinstance(bunch, Bunch)
+        assert bunch.conditions == ['trial', 'gain_trial', 'loss_trial']
+        helpers.compare_float_2d_arrays(bunch.onsets, [
+            [4.071, 11.834, 27.535, 36.435],
+            [4.071, 11.834],
+            [27.535, 36.435]
+            ])
+        helpers.compare_float_2d_arrays(bunch.durations, [
+            [2.388, 2.289, 2.08, 2.288],
+            [2.388, 2.289],
+            [2.08, 2.288]
+            ])
+        helpers.compare_float_2d_arrays(bunch.amplitudes, [
+            [1.0, 1.0, 1.0, 1.0],
+            [10.0, 30.0],
+            [11.0, 13.0]
+            ])
+
+    @staticmethod
+    @mark.pipeline_test
+    def test_execution():
+        """ Test the execution of a PipelineTeamO6R6 and compare results """
+        helpers.test_pipeline_evaluation('O6R6')

tests/test_data/pipelines/team_O21U/confounds.tsv

@@ -0,0 +1,3 @@
+0.0	0.0	0.0	0.0	0.0	-0.0	0.0
+0.1352790093099999	-0.00996895	-0.0313444	-3.00931e-06	0.00132687	-0.000384193	-0.00016819
+0.12437666391	-2.56954e-05	-0.00923735	0.0549667	0.000997278	-0.00019745	-0.000398988