[TEST] adding tests for 98BT

narps_open/pipelines/team_98BT.py

@@ -419,8 +419,8 @@ def get_subject_information(event_file: str):
         condition_names = ['gamble']
 
         # Create empty lists
-        onset = []
-        duration = []
+        onsets = []
+        durations = []
         weights_gain = []
         weights_loss = []
         answers = []
@@ -444,8 +444,8 @@ def get_subject_information(event_file: str):
         # Create Bunch
         return Bunch(
             conditions = ['gamble'],
-            onsets = onsets,
-            durations = durations,
+            onsets = [onsets],
+            durations = [durations],
             amplitudes = None,
             tmod = None,
             pmod = [

tests/conftest.py

@@ -12,6 +12,7 @@
 
 from pytest import helpers
 from pathvalidate import is_valid_filepath
+from numpy import isclose
 
 from narps_open.pipelines import Pipeline
 from narps_open.runner import PipelineRunner
@@ -23,6 +24,15 @@
 # Init configuration, to ensure it is in testing mode
 Configuration(config_type='testing')
 
+@helpers.register
+def compare_float_2d_arrays(array_1, array_2):
+    """ Assert array_1 and array_2 are close enough """
+
+    assert len(array_1) == len(array_2)
+    for reference_array, test_array in zip(array_1, array_2):
+        assert len(reference_array) == len(test_array)
+        assert isclose(reference_array, test_array).all()
+
 @helpers.register
 def test_pipeline_outputs(pipeline: Pipeline, number_of_outputs: list):
     """ Test the outputs of a Pipeline.

tests/pipelines/test_team_98BT.py

@@ -11,11 +11,26 @@
     pytest -q test_team_98BT.py -k <selected_test>
 """
 
-from pytest import helpers, mark
+from os.path import join
+
+from pytest import helpers, mark, fixture
 from nipype import Workflow
+from nipype.interfaces.base import Bunch
 
+from narps_open.utils.configuration import Configuration
 from narps_open.pipelines.team_98BT import PipelineTeam98BT
 
+TEMPORARY_DIR = join(Configuration()['directories']['test_runs'], 'test_98BT')
+
+@fixture
+def remove_test_dir():
+    """ A fixture to remove temporary directory created by tests """
+
+    rmtree(TEMPORARY_DIR, ignore_errors = True)
+    mkdir(TEMPORARY_DIR)
+    yield # test runs here
+    rmtree(TEMPORARY_DIR, ignore_errors = True)
+
 class TestPipelinesTeam98BT:
     """ A class that contains all the unit tests for the PipelineTeam98BT class."""
 
@@ -58,7 +73,7 @@ def test_outputs():
         helpers.test_pipeline_outputs(pipeline, [0,0,36,84,18])
 
     @staticmethod
-    @mark.pipeline_test
+    @mark.unit_test
     def test_fieldmap_info():
         """ Test the get_fieldmap_info method """
 
@@ -67,29 +82,69 @@ def test_fieldmap_info():
         filedmap_file_2 = join(
             Configuration()['directories']['test_data'], 'pipelines', 'phasediff_2.json')
 
-        pipeline = PipelineTeam98BT()
-        test_result = pipeline.get_fieldmap_info(filedmap_file_1, ['magnitude_1', 'magnitude_2'])
-        assert test_result[0] == [0.0, 0.0]
-        assert test_result[1] == 'magnitude_2'
-        test_result = pipeline.get_fieldmap_info(filedmap_file_2, ['magnitude_1', 'magnitude_2'])
-        assert test_result[0] == [0.0, 0.0]
+        test_result = PipelineTeam98BT.get_fieldmap_info(
+            filedmap_file_1, ['magnitude_1', 'magnitude_2'])
+        assert test_result[0] == (0.00492, 0.00738)
         assert test_result[1] == 'magnitude_1'
+        test_result = PipelineTeam98BT.get_fieldmap_info(
+            filedmap_file_2, ['magnitude_1', 'magnitude_2'])
+        assert test_result[0] == (0.00492, 0.00738)
+        assert test_result[1] == 'magnitude_2'
 
     @staticmethod
-    @mark.pipeline_test
-    def test_fieldmap_info():
-        """ Test the get_fieldmap_info method """
-
-    @staticmethod
-    @mark.pipeline_test
-    def test_parameters_files():
+    @mark.unit_test
+    def test_parameters_files(remove_test_dir):
         """ Test the get_parameters_files method """
+        """
+        parameters_file = join(
+            Configuration()['directories']['test_data'], 'pipelines', 'confounds.tsv')
+        reference_file = join(
+            Configuration()['directories']['test_data'], 'pipelines', 'team_98BT', 'parameters.tsv')
+
+        # Get new parameters file
+        PipelineTeam98BT.get_parameters_file(
+            parameters_file, wc2_file, motion_corrected_files, 'sid', TEMPORARY_DIR)
+
+        # Check parameters file was created
+        created_parameters_file = join(
+            TEMPORARY_DIR, 'parameters_files', 'parameters_file_sub-sid.tsv')
+        assert exists(created_parameters_file)
+
+        # Check contents
+        assert cmp(reference_file, created_confounds_file)
+        """
 
     @staticmethod
-    @mark.pipeline_test
+    @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')
+
+        bunch = PipelineTeam98BT.get_subject_information(test_file)
+
+        # Compare bunches to expected
+        assert isinstance(bunch, Bunch)
+        assert bunch.conditions == ['gamble']
+        helpers.compare_float_2d_arrays(bunch.onsets, [
+            [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]])
+        assert bunch.amplitudes == None
+        assert bunch.tmod == None
+        assert bunch.regressor_names == None
+        assert bunch.regressors == None
+        pmod = bunch.pmod[0]
+        assert isinstance(pmod, Bunch)
+        assert pmod.name == ['gain', 'loss', 'answer']
+        assert pmod.poly == [1, 1, 1]
+        helpers.compare_float_2d_arrays(pmod.param, [
+            [14.0, 34.0, 38.0, 10.0, 16.0],
+            [6.0, 14.0, 19.0, 15.0, 17.0],
+            [1, 1, 0, 0, 0]
+            ])
+
     @staticmethod
     @mark.pipeline_test
     def test_execution():

tests/test_conftest.py

@@ -239,6 +239,30 @@ def download(self):
 class TestConftest:
     """ A class that contains all the unit tests for the conftest module."""
 
+    @staticmethod
+    @mark.unit_test
+    def test_compare_float_2d_arrays():
+        """ Test the compare_float_2d_arrays helper """
+
+        array_1 = [[5.0, 0.0], [1.0, 2.0]]
+        array_2 = [[5.0, 0.0], [1.0]]
+        with raises(AssertionError):
+            helpers.compare_float_2d_arrays(array_1, array_2)
+
+        array_1 = [[6.0, 0.0], [1.0]]
+        array_2 = [[6.0, 0.0], [1.0, 2.0]]
+        with raises(AssertionError):
+            helpers.compare_float_2d_arrays(array_1, array_2)
+
+        array_1 = [[7.10001, 0.0], [1.0, 2.0]]
+        array_2 = [[7.10001, 0.0], [1.0, 2.00003]]
+        with raises(AssertionError):
+            helpers.compare_float_2d_arrays(array_1, array_2)
+
+        array_1 = [[10.0000200, 15.10], [1.0, 2.0]]
+        array_2 = [[10.00002, 15.10000], [1.0, 2.000003]]
+        helpers.compare_float_2d_arrays(array_1, array_2)
+
     @staticmethod
     @mark.unit_test
     def test_test_outputs(set_test_directory):