[REFAC] using narps_open.core functions [TEST] events data in a file

narps_open/pipelines/team_08MQ.py

@@ -28,6 +28,7 @@
 from narps_open.data.task import TaskInformation
 from narps_open.data.participants import get_group
 from narps_open.core.common import remove_file, list_intersection, elements_in_string, clean_list
+
 # Setup FSL
 FSLCommand.set_default_output_type('NIFTI_GZ')
 
@@ -45,29 +46,6 @@ def __init__(self):
             ('negative_effect_loss', 'T', ['gain', 'loss'], [0, -1])
         ]
 
-    def remove_files(_, files):
-        """
-        This method is used in a Function node to fully remove
-        files generated by a Node, once they aren't needed anymore.
-
-        Parameters:
-        - _: Node input only used for triggering the Node
-        - files: str or list, a single filename or a list of filenames to remove
-        """
-        from os import remove
-
-        if isinstance(files, str):
-            files = [files]
-
-        try:
-            for file in files:
-                remove(file)
-        except OSError as error:
-            print(error)
-        else:
-            print('The following files were successfully deleted.')
-            print(files)
-
     def get_preprocessing(self):
         """ Return a Nipype workflow describing the prerpocessing part of the pipeline """
 
@@ -237,35 +215,35 @@ def get_preprocessing(self):
         compute_confounds.inputs.repetition_time = TaskInformation()['RepetitionTime']
 
         # Function Nodes remove_files - Remove sizeable files once they aren't needed
-        remove_func_0 = Node(Function(
-            function = self.remove_files,
-            input_names = ['_', 'files'],
+        remove_func_0 = MapNode(Function(
+            function = remove_file,
+            input_names = ['_', 'file'],
             output_names = []
-            ), name = 'remove_func_0')
+            ), name = 'remove_func_0', iterfield = 'file')
 
-        remove_func_1 = Node(Function(
-            function = self.remove_files,
-            input_names = ['_', 'files'],
+        remove_func_1 = MapNode(Function(
+            function = remove_file,
+            input_names = ['_', 'file'],
             output_names = []
-            ), name = 'remove_func_1')
+            ), name = 'remove_func_1', iterfield = 'file')
 
-        remove_func_2 = Node(Function(
-            function = self.remove_files,
-            input_names = ['_', 'files'],
+        remove_func_2 = MapNode(Function(
+            function = remove_file,
+            input_names = ['_', 'file'],
             output_names = []
-            ), name = 'remove_func_2')
+            ), name = 'remove_func_2', iterfield = 'file')
 
-        remove_func_3 = Node(Function(
-            function = self.remove_files,
-            input_names = ['_', 'files'],
+        remove_func_3 = MapNode(Function(
+            function = remove_file,
+            input_names = ['_', 'file'],
             output_names = []
-            ), name = 'remove_func_3')
+            ), name = 'remove_func_3', iterfield = 'file')
 
-        remove_func_4 = Node(Function(
-            function = self.remove_files,
-            input_names = ['_', 'files'],
+        remove_func_4 = MapNode(Function(
+            function = remove_file,
+            input_names = ['_', 'file'],
             output_names = []
-            ), name = 'remove_func_4')
+            ), name = 'remove_func_4', iterfield = 'file')
 
         preprocessing = Workflow(base_dir = self.directories.working_dir, name = 'preprocessing')
         preprocessing.config['execution']['stop_on_first_crash'] = 'true'
@@ -326,15 +304,15 @@ def get_preprocessing(self):
             (alignment_func_to_mni, data_sink, [('output_image', 'preprocessing.@output_image')]),
 
             # File removals
-            (motion_correction, remove_func_0, [('out_file', 'files')]),
+            (motion_correction, remove_func_0, [('out_file', 'file')]),
             (data_sink, remove_func_0, [('out_file', '_')]),
-            (slice_time_correction, remove_func_1, [('slice_time_corrected_file', 'files')]),
+            (slice_time_correction, remove_func_1, [('slice_time_corrected_file', 'file')]),
             (data_sink, remove_func_1, [('out_file', '_')]),
-            (smoothing, remove_func_2, [('smoothed_file', 'files')]),
+            (smoothing, remove_func_2, [('smoothed_file', 'file')]),
             (data_sink, remove_func_2, [('out_file', '_')]),
-            (alignment_func_to_anat, remove_func_3, [('out_file', 'files')]),
+            (alignment_func_to_anat, remove_func_3, [('out_file', 'file')]),
             (data_sink, remove_func_3, [('out_file', '_')]),
-            (alignment_func_to_mni, remove_func_4, [('output_image', 'files')]),
+            (alignment_func_to_mni, remove_func_4, [('output_image', 'file')]),
             (data_sink, remove_func_4, [('out_file', '_')])
         ])
 

tests/pipelines/test_team_08MQ.py

@@ -10,11 +10,14 @@
     pytest -q test_team_08MQ.py
     pytest -q test_team_08MQ.py -k <selected_test>
 """
+from os.path import join
 
 from pytest import helpers, mark
+from numpy import isclose
 from nipype import Workflow
 from nipype.interfaces.base import Bunch
 
+from narps_open.utils.configuration import Configuration
 from narps_open.pipelines.team_08MQ import PipelineTeam08MQ
 
 class TestPipelinesTeam08MQ:
@@ -70,20 +73,44 @@ def test_outputs():
 
     @staticmethod
     @mark.unit_test
-    def test_subject_information(mocker):
+    def test_subject_information():
         """ Test the get_subject_information method """
 
-        helpers.mock_event_data(mocker)
-
-        information = PipelineTeam08MQ.get_subject_information('fake_event_file_path')[0]
+        information = PipelineTeam08MQ.get_subject_information(join(
+            Configuration()['directories']['test_data'],
+            'pipelines',
+            'events.tsv'
+            ))[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]
+
+        reference_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],
+            [1.0, 1.0, 0.0, -1.0, -1.0]
+            ]
+        for reference_array, test_array in zip(reference_amplitudes, information.amplitudes):
+            assert isclose(reference_array, test_array).all()
+
+        reference_durations = [
+            [4.0, 4.0, 4.0, 4.0, 4.0],
+            [2.388, 2.289, 0.0, 2.08, 2.288],
+            [2.388, 2.289, 0.0, 2.08, 2.288],
+            [4.0, 4.0, 4.0, 4.0, 4.0]
+            ]
+        for reference_array, test_array in zip(reference_durations, information.durations):
+            assert isclose(reference_array, test_array).all()
+
+        reference_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],
+            [4.071, 11.834, 19.535, 27.535, 36.435]
         ]
+        for reference_array, test_array in zip(reference_onsets, information.onsets):
+            assert isclose(reference_array, test_array).all()
 
     @staticmethod
     @mark.unit_test

tests/test_data/pipelines/events.tsv

@@ -0,0 +1,6 @@
+onset	duration	gain	loss	RT	participant_response
+4.071	4	14	6	2.388	weakly_accept
+11.834	4	34	14	2.289	strongly_accept
+19.535	4	38	19	0	NoResp
+27.535	4	10	15	2.08	strongly_reject
+36.435	4	16	17	2.288	weakly_reject