[TEST] adding unit tests for 08MQ

narps_open/pipelines/team_08MQ.py

@@ -390,29 +390,23 @@ def get_subject_information(event_file):
 
             for line in file:
                 info = line.strip().split()
-
-                for condition in condition_names:
-                    if condition == 'gain':
-                        onsets[condition].append(float(info[0]))
-                        durations[condition].append(float(info[4])) # TODO : change to info[1] (= 4) ?
-                        amplitudes[condition].append(float(info[2]))
-                    elif condition == 'loss':
-                        onsets[condition].append(float(info[0]))
-                        durations[condition].append(float(info[4])) # TODO : change to info[1] (= 4) ?
-                        amplitudes[condition].append(float(info[3]))
-                    elif condition == 'event':
-                        onsets[condition].append(float(info[0]))
-                        durations[condition].append(float(info[1]))
-                        amplitudes[condition].append(1.0)
-                    elif condition == 'response':
-                        onsets[condition].append(float(info[0]))
-                        durations[condition].append(float(info[1])) # TODO : change to info[4] (= RT) ?
-                        if 'accept' in info[5]:
-                            amplitudes[condition].append(1.0)
-                        elif 'reject' in info[5]:
-                            amplitudes[condition].append(-1.0)
-                        else:
-                            amplitudes[condition].append(0.0)
+                onsets['event'].append(float(info[0]))
+                durations['event'].append(float(info[1]))
+                amplitudes['event'].append(1.0)
+                onsets['gain'].append(float(info[0]))
+                durations['gain'].append(float(info[4])) # TODO : change to info[1] (= 4) ?
+                amplitudes['gain'].append(float(info[2]))
+                onsets['loss'].append(float(info[0]))
+                durations['loss'].append(float(info[4])) # TODO : change to info[1] (= 4) ?
+                amplitudes['loss'].append(float(info[3]))
+                onsets['response'].append(float(info[0]))
+                durations['response'].append(float(info[1])) # TODO : change to info[4] (= RT) ?
+                if 'accept' in info[5]:
+                    amplitudes['response'].append(1.0)
+                elif 'reject' in info[5]:
+                    amplitudes['response'].append(-1.0)
+                else:
+                    amplitudes['response'].append(0.0)
 
         return [
             Bunch(
@@ -433,17 +427,12 @@ def get_run_level_contrasts():
         Returns:
             - contrasts: list of tuples, list of contrasts to analyze
         """
-        # List of condition names
         conditions = ['gain', 'loss']
 
-        # Return contrast list
         return [
-            # Positive parametric effect of gain
-            ('positive_effect_gain', 'T', conditions, [1, 0]),
-            # Positive parametric effect of loss
-            ('positive_effect_loss', 'T', conditions, [0, 1]),
-            # Negative parametric effect of loss.
-            ('negative_effect_loss', 'T', conditions, [0, -1])
+            ('positive_effect_gain', 'T', conditions, [1, 0]), # Positive parametric effect of gain
+            ('positive_effect_loss', 'T', conditions, [0, 1]), # Positive parametric effect of loss
+            ('negative_effect_loss', 'T', conditions, [0, -1]) # Negative parametric effect of loss
         ]
 
     def get_run_level_analysis(self):
@@ -689,63 +678,46 @@ def get_subgroups_contrasts(copes, varcopes, subject_list: list, participants_fi
           in the equalIndifference group
         - copes_equal_range : a subset of copes corresponding to subjects
           in the equalRange group
-        - copes_global : a list of all copes
         - varcopes_equal_indifference : a subset of varcopes corresponding to subjects
           in the equalIndifference group
         - varcopes_equal_range : a subset of varcopes corresponding to subjects
           in the equalRange group
         - equal_indifference_ids : a list of subject ids in the equalIndifference group
         - equal_range_ids : a list of subject ids in the equalRange group
-        - varcopes_global : a list of all varcopes
         """
 
-        equal_range_ids = []
-        equal_indifference_ids = []
+        subject_list_sub_ids = [] # ids as written in the participants file
+        equal_range_ids = [] # ids as 3-digit string
+        equal_indifference_ids = [] # ids as 3-digit string
+        equal_range_sub_ids = [] # ids as written in the participants file
+        equal_indifference_sub_ids = [] # ids as written in the participants file
 
         # Reading file containing participants IDs and groups
         with open(participants_file, 'rt') as file:
             next(file)  # skip the header
 
             for line in file:
                 info = line.strip().split()
-
-                # Checking for each participant if its ID was selected
-                # and separate people depending on their group
-                if info[0][-3:] in subject_list and info[1] == 'equalIndifference':
-                    equal_indifference_ids.append(info[0][-3:])
-                elif info[0][-3:] in subject_list and info[1] == 'equalRange':
-                    equal_range_ids.append(info[0][-3:])
-
-        copes_equal_indifference = []
-        copes_equal_range = []
-        copes_global = []
-        varcopes_equal_indifference = []
-        varcopes_equal_range = []
-        varcopes_global = []
-
-        # Checking for each selected file if the corresponding participant was selected
-        # and add the file to the list corresponding to its group
-        for cope, varcope in zip(copes, varcopes):
-            sub_id = cope.split('/')
-            if sub_id[-2][-3:] in equal_indifference_ids:
-                copes_equal_indifference.append(cope)
-            elif sub_id[-2][-3:] in equal_range_ids:
-                copes_equal_range.append(cope)
-            if sub_id[-2][-3:] in subject_list:
-                copes_global.append(cope)
-
-            sub_id = varcope.split('/')
-            if sub_id[-2][-3:] in equal_indifference_ids:
-                varcopes_equal_indifference.append(varcope)
-            elif sub_id[-2][-3:] in equal_range_ids:
-                varcopes_equal_range.append(varcope)
-            if sub_id[-2][-3:] in subject_list:
-                varcopes_global.append(varcope)
-
-        return copes_equal_indifference, copes_equal_range,\
-               varcopes_equal_indifference, varcopes_equal_range,\
-               equal_indifference_ids, equal_range_ids,\
-               copes_global, varcopes_global
+                subject_id = info[0][-3:]
+                subject_group = info[1]
+
+                # Check if the participant ID was selected and sort depending on group
+                if subject_id in subject_list:
+                    subject_list_sub_ids.append(info[0])
+                    if subject_group == 'equalIndifference':
+                        equal_indifference_ids.append(subject_id)
+                        equal_indifference_sub_ids.append(info[0])
+                    elif subject_group == 'equalRange':
+                        equal_range_ids.append(subject_id)
+                        equal_range_sub_ids.append(info[0])
+
+        # Reurn sorted selected copes and varcopes by group, and corresponding ids
+        return \
+            [c for c in copes if any(i in c for i in equal_indifference_sub_ids)],\
+            [c for c in copes if any(i in c for i in equal_range_sub_ids)],\
+            [v for v in varcopes if any(i in v for i in equal_indifference_sub_ids)],\
+            [v for v in varcopes if any(i in v for i in equal_range_sub_ids)],\
+            equal_indifference_ids, equal_range_ids
 
     def get_one_sample_t_test_regressors(subject_ids: list) -> dict:
         """
@@ -850,9 +822,7 @@ def get_group_level_analysis_sub_workflow(self, method):
                     'varcopes_equal_indifference',
                     'varcopes_equal_range',
                     'equal_indifference_ids',
-                    'equal_range_ids',
-                    'copes_global',
-                    'varcopes_global'
+                    'equal_range_ids'
                 ]
             ),
             name = 'get_contrasts',

tests/pipelines/__init__.py

@@ -0,0 +1,31 @@
+#!/usr/bin/python
+# coding: utf-8
+
+"""
+Configuration for testing of the narps_open.pipelines modules.
+"""
+
+from pytest import helpers
+
+@helpers.register
+def mock_event_data(mocker):
+    """ Mocks the retrun of the open function with the contents of a fake event file """
+
+    fake_event_data = 'onset duration\tgain\tloss\tRT\tparticipant_response\n'
+    fake_event_data += '4.071\t4\t14\t6\t2.388\tweakly_accept\n'
+    fake_event_data += '11.834\t4\t34\t14\t2.289\tstrongly_accept\n'
+
+    mocker.patch('builtins.open', mocker.mock_open(read_data = fake_event_data))
+
+
+@helpers.register
+def mock_participants_data(mocker):
+    """ Mocks the retrun of the open function with the contents of a fake participants file """
+
+    fake_participants_data = 'participant_id\tgroup\tgender\tage\n'
+    fake_participants_data += 'sub-001\tequalIndifference\tM\t24\n'
+    fake_participants_data += 'sub-002\tequalRange\tM\t25\n'
+    fake_participants_data += 'sub-003\tequalIndifference\tF\t27\n'
+    fake_participants_data += 'sub-004\tequalRange\tM\t25\n'
+
+    mocker.patch('builtins.open', mocker.mock_open(read_data = fake_participants_data))

tests/pipelines/test_team_08MQ.py

@@ -13,6 +13,7 @@
 
 from pytest import helpers, mark
 from nipype import Workflow
+from nipype.interfaces.base import Bunch
 
 from narps_open.pipelines.team_08MQ import PipelineTeam08MQ
 
@@ -63,34 +64,59 @@ def test_outputs():
 
     @staticmethod
     @mark.unit_test
-    def test_subject_information():
+    def test_subject_information(mocker):
         """ Test the get_subject_information method """
 
+        helpers.mock_event_data(mocker)
+
+        information = PipelineTeam08MQ.get_subject_information('fake_event_file_path')[0]
+
+        assert isinstance(information, Bunch)
+        assert information.amplitudes == [[1.0, 1.0], [14.0, 34.0], [6.0, 14.0], [1.0, 1.0]]
+        assert information.durations == [[4.0, 4.0], [2.388, 2.289], [2.388, 2.289], [4.0, 4.0]]
+        assert information.conditions == ['event', 'gain', 'loss', 'response']
+        assert information.onsets == [
+        [4.071, 11.834], [4.071, 11.834], [4.071, 11.834], [4.071, 11.834]
+        ]
+
     @staticmethod
     @mark.unit_test
     def test_run_level_contrasts():
         """ Test the get_run_level_contrasts method """
-        contrasts = PipelineTeam08MQ.get_run_level_contrasts()
 
+        contrasts = PipelineTeam08MQ.get_run_level_contrasts()
         assert contrasts[0] == ('positive_effect_gain', 'T', ['gain', 'loss'], [1, 0])
-        assert contrasts[0] == ('positive_effect_loss', 'T', ['gain', 'loss'], [0, 1])
-        assert contrasts[0] == ('negative_effect_loss', 'T', ['gain', 'loss'], [0, -1])
+        assert contrasts[1] == ('positive_effect_loss', 'T', ['gain', 'loss'], [0, 1])
+        assert contrasts[2] == ('negative_effect_loss', 'T', ['gain', 'loss'], [0, -1])
 
     @staticmethod
     @mark.unit_test
-    def test_subgroups_contrasts():
+    def test_subgroups_contrasts(mocker):
         """ Test the get_subgroups_contrasts method """
 
-        #contrasts = PipelineTeam08MQ().get_subgroups_contrasts()
-        #copes, varcopes, subject_list: list, participants_file: str
+        helpers.mock_participants_data(mocker)
+
+        cei, cer, vei, ver, eii, eri = PipelineTeam08MQ.get_subgroups_contrasts(
+            ['sub-001/_contrast_id_1/cope1.nii.gz', 'sub-001/_contrast_id_2/cope1.nii.gz', 'sub-002/_contrast_id_1/cope1.nii.gz', 'sub-002/_contrast_id_2/cope1.nii.gz', 'sub-003/_contrast_id_1/cope1.nii.gz', 'sub-003/_contrast_id_2/cope1.nii.gz', 'sub-004/_contrast_id_1/cope1.nii.gz', 'sub-004/_contrast_id_2/cope1.nii.gz'], # copes
+            ['sub-001/_contrast_id_1/varcope1.nii.gz', 'sub-001/_contrast_id_2/varcope1.nii.gz', 'sub-002/_contrast_id_1/varcope1.nii.gz', 'sub-002/_contrast_id_2/varcope1.nii.gz', 'sub-003/_contrast_id_1/varcope1.nii.gz', 'sub-003/_contrast_id_2/varcope1.nii.gz', 'sub-004/_contrast_id_1/varcope1.nii.gz', 'sub-004/_contrast_id_2/varcope1.nii.gz'], # varcopes
+            ['001', '002', '003', '004'], # subject_list
+            ['fake_participants_file_path'] # participants file
+            )
+
+        assert cei == ['sub-001/_contrast_id_1/cope1.nii.gz', 'sub-001/_contrast_id_2/cope1.nii.gz', 'sub-003/_contrast_id_1/cope1.nii.gz', 'sub-003/_contrast_id_2/cope1.nii.gz']
+        assert cer == ['sub-002/_contrast_id_1/cope1.nii.gz', 'sub-002/_contrast_id_2/cope1.nii.gz', 'sub-004/_contrast_id_1/cope1.nii.gz', 'sub-004/_contrast_id_2/cope1.nii.gz']
+        assert vei == ['sub-001/_contrast_id_1/varcope1.nii.gz', 'sub-001/_contrast_id_2/varcope1.nii.gz', 'sub-003/_contrast_id_1/varcope1.nii.gz', 'sub-003/_contrast_id_2/varcope1.nii.gz']
+        assert ver == ['sub-002/_contrast_id_1/varcope1.nii.gz', 'sub-002/_contrast_id_2/varcope1.nii.gz', 'sub-004/_contrast_id_1/varcope1.nii.gz', 'sub-004/_contrast_id_2/varcope1.nii.gz']
+        assert eii == ['001', '003']
+        assert eri == ['002', '004']
 
     @staticmethod
     @mark.unit_test
     def test_one_sample_t_test_regressors():
         """ Test the get_one_sample_t_test_regressors method """
 
         regressors = PipelineTeam08MQ.get_one_sample_t_test_regressors(['001', '002'])
-        assert regressors == [1, 1]
+        assert regressors == {'group_mean': [1, 1]}
 
     @staticmethod
     @mark.unit_test