Merge branch 'main' into B5I6_repro

CODE_OF_CONDUCT.md

@@ -5,7 +5,7 @@
 We as members, contributors, and leaders pledge to make participation in our
 community a harassment-free experience for everyone, regardless of age, body
 size, visible or invisible disability, ethnicity, sex characteristics, gender
-identity and expression, level of experience, education, socio-economic status,
+identity and expression, level of experience, education, socioeconomic status,
 nationality, personal appearance, race, caste, color, religion, or sexual
 identity and orientation.
 

narps_open/pipelines/__init__.py

@@ -26,7 +26,7 @@
     '3TR7': 'PipelineTeam3TR7',
     '43FJ': None,
     '46CD': None,
-    '4SZ2': None,
+    '4SZ2': 'PipelineTeam4SZ2',
     '4TQ6': 'PipelineTeam4TQ6',
     '50GV': None,
     '51PW': 'PipelineTeam51PW',
@@ -42,6 +42,8 @@
     'AO86': None,
     'B23O': None,
     'B5I6': 'PipelineTeamB5I6',
+    'B23O': 'PipelineTeamB23O',
+    'B5I6': 'PipelineTeamB5I6',
     'C22U': None,
     'C88N': 'PipelineTeamC88N',
     'DC61': None,

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())
-    parser.add_argument('-n', '--nsubjects', type=int, 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_4SZ2.py

@@ -0,0 +1,106 @@
+#!/usr/bin/python
+# coding: utf-8
+
+""" Tests of the 'narps_open.pipelines.team_4SZ2' module.
+
+Launch this test with PyTest
+
+Usage:
+======
+    pytest -q test_team_4SZ2.py
+    pytest -q test_team_4SZ2.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_4SZ2 import PipelineTeam4SZ2
+
+class TestPipelinesTeam4SZ2:
+    """ A class that contains all the unit tests for the PipelineTeam4SZ2 class."""
+
+    @staticmethod
+    @mark.unit_test
+    def test_create():
+        """ Test the creation of a PipelineTeam4SZ2 object """
+
+        pipeline = PipelineTeam4SZ2()
+
+        # 1 - check the parameters
+        assert pipeline.fwhm == 5.0
+        assert pipeline.team_id == '4SZ2'
+
+        # 2 - check workflows
+        assert pipeline.get_preprocessing() is None
+        assert isinstance(pipeline.get_run_level_analysis(), Workflow)
+        assert pipeline.get_subject_level_analysis() is None
+        assert isinstance(pipeline.get_group_level_analysis(), Workflow)
+
+    @staticmethod
+    @mark.unit_test
+    def test_outputs():
+        """ Test the expected outputs of a PipelineTeam4SZ2 object """
+
+        pipeline = PipelineTeam4SZ2()
+
+        # 1 - 1 subject outputs
+        pipeline.subject_list = ['001']
+        helpers.test_pipeline_outputs(pipeline, [0, 2*4*1*4, 0, 2*9, 18])
+
+        # 2 - 4 subjects outputs
+        pipeline.subject_list = ['001', '002', '003', '004']
+        helpers.test_pipeline_outputs(pipeline, [0, 2*4*4*4, 0, 2*9, 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 = PipelineTeam4SZ2.get_subject_information(test_file)
+
+        # Compare bunches to expected
+        bunch = info_missed[0]
+        assert isinstance(bunch, Bunch)
+        assert bunch.conditions == ['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]
+            ])
+        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]
+            ])
+        helpers.compare_float_2d_arrays(bunch.amplitudes, [
+            [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_get_group_level_regressors():
+        """ Test the get_group_level_regressors method """
+
+        regressors = PipelineTeam4SZ2.get_group_level_regressors(
+            ['001', '002', '003', '004'],
+            ['01', '02'])
+
+        for k1, k2 in zip(regressors.keys(), ['equalIndifference', 'equalRange', 'age', 'gender']):
+            assert k1 == k2
+        assert regressors['equalIndifference'] == [1, 1, 0, 0, 1, 1, 0, 0]
+        assert regressors['equalRange'] == [0, 0, 1, 1, 0, 0, 1, 1]
+        assert regressors['age'] == [24, 24, 25, 25, 27, 27, 25, 25]
+        assert regressors['gender'] == [0, 0, 0, 0, 1, 1, 0, 0]
+
+    @staticmethod
+    @mark.pipeline_test
+    def test_execution():
+        """ Test the execution of a PipelineTeam4SZ2 and compare results """
+        helpers.test_pipeline_evaluation('4SZ2')

tests/pipelines/test_team_B23O.py

@@ -0,0 +1,127 @@
+#!/usr/bin/python
+# coding: utf-8
+
+""" Tests of the 'narps_open.pipelines.team_B23O' module.
+
+Launch this test with PyTest
+
+Usage:
+======
+    pytest -q test_team_B23O.py
+    pytest -q test_team_B23O.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_B23O import PipelineTeamB23O
+
+class TestPipelinesTeamB23O:
+    """ A class that contains all the unit tests for the PipelineTeamB23O class."""
+
+    @staticmethod
+    @mark.unit_test
+    def test_create():
+        """ Test the creation of a PipelineTeamB23O object """
+
+        pipeline = PipelineTeamB23O()
+
+        # 1 - check the parameters
+        assert pipeline.team_id == 'B23O'
+
+        # 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 PipelineTeamB23O object """
+
+        pipeline = PipelineTeamB23O()
+
+        # 1 - 1 subject outputs
+        pipeline.subject_list = ['001']
+        helpers.test_pipeline_outputs(pipeline, [0, 4*2*4*1, 4*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*2*4*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 = PipelineTeamB23O.get_subject_information(test_file)
+
+        # Compare bunches to expected
+        bunch = info[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 = join(
+            Configuration()['directories']['test_data'], 'pipelines', 'confounds.tsv')
+        reference_file = join(
+            Configuration()['directories']['test_data'],
+            'pipelines', 'team_B23O', 'confounds.tsv')
+
+        # Create new confounds file
+        confounds_node = Node(Function(
+            input_names = ['filepath', 'subject_id', 'run_id'],
+            output_names = ['confounds_file'],
+            function = PipelineTeamB23O.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 PipelineTeamB23O and compare results """
+        helpers.test_pipeline_evaluation('B23O')

tests/test_data/pipelines/team_B23O/confounds.tsv

@@ -0,0 +1,3 @@
+6551.281999999999	6476.4653	9874.576	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	0.0	1.0	0.0	0.0	0.0	0.0	-0.0	0.0
+6484.7285	6473.4890000000005	9830.212	0.0263099209	-0.0673065879	0.0934882554	-0.0079328884	0.0338007737	-0.0114910839999999	-0.0424113470999999	0.0277364229	0.0453303087	-0.0702260949	0.0963618709	-0.0200867957	0.0665186088	0.0665174038	0.0665153954	0.0665125838	0.0665089688	0.0665045505999999	0.0	-0.00996895	-0.0313444	-3.00931e-06	0.00132687	-0.000384193	-0.00016819
+6441.5337	6485.7256	9821.212	-0.0404820317	0.034150583	0.1366118421	0.0745358691	-0.0054829985999999	-0.0217322686	0.0462141151999999	0.005774624	-0.0439093598	-0.075619539	0.1754689153999999	-0.0345256763	0.0665153954	0.0665045505999999	0.0664864771999999	0.0664611772	0.0664286533	0.0663889091	0.0	-2.56954e-05	-0.00923735	0.0549667	0.000997278	-0.00019745	-0.000398988