Merge pull request #639 from AlexVCaron/moc_test_bilateral_filter

[ENH] POC : Use mocking to get faster execution of tests

.gitignore

@@ -67,3 +67,6 @@ target/
 
 # VS Code
 .vscode/
+
+# Virtualenv
+venv/

requirements.txt

@@ -30,6 +30,7 @@ coloredlogs==10.0.*
 nilearn==0.6.*
 pytest==5.3.*
 pytest_console_scripts==0.2.*
+pytest-mock==3.10.*
 requests==2.23.*
 bctpy==0.5.*
 statsmodels==0.11.*

scilpy/io/fetcher.py

@@ -68,7 +68,10 @@ def get_testing_files_dict():
              'bcc21835cf0bf7210bdc99ba5d8df44b'],
             'anatomical_filtering.zip':
             ['1Li8DdySnMnO9Gich4pilhXisjkjz1-Dy',
-             '6f0eff5154ff0973a3dc26db00e383ea']}
+             '6f0eff5154ff0973a3dc26db00e383ea'],
+            'fodf_filtering.zip':
+            ['1iyoX2ltLOoLer-v-49LHOzopHCFZ_Tv6',
+             'e79c4291af584fdb25814aa7b403a6ce']}
 
 
 def fetch_data(files_dict, keys=None):

scripts/tests/test_execute_angle_aware_bilateral_filtering.py

@@ -1,54 +1,112 @@
 #!/usr/bin/env python3
 # -*- coding: utf-8 -*-
 
+import nibabel as nib
+import numpy as np
 import os
+import pytest
 import tempfile
 
 from scilpy.io.fetcher import get_testing_files_dict, fetch_data, get_home
 
 
 # If they already exist, this only takes 5 seconds (check md5sum)
-fetch_data(get_testing_files_dict(), keys=['processing.zip'])
+fetch_data(get_testing_files_dict(), keys=['fodf_filtering.zip'])
+data_path = os.path.join(get_home(), 'fodf_filtering')
 tmp_dir = tempfile.TemporaryDirectory()
 
 
+@pytest.fixture
+def mock_filtering(mocker, out_fodf):
+    def _mock(*args, **kwargs):
+        img = nib.load(out_fodf)
+        return img.get_fdata().astype(np.float32)
+
+    script = 'scil_execute_angle_aware_bilateral_filtering'
+    filtering_fn = "angle_aware_bilateral_filtering"
+    return mocker.patch("scripts.{}.{}".format(script, filtering_fn),
+                        side_effect=_mock, create=True)
+
+
 def test_help_option(script_runner):
     ret = script_runner.run('scil_execute_angle_aware_bilateral_filtering.py',
                             '--help')
     assert ret.success
 
 
-def test_asym_basis_output(script_runner):
+@pytest.mark.parametrize("in_fodf,out_fodf",
+    [[os.path.join(data_path, 'fodf_descoteaux07_sub.nii.gz'),
+      os.path.join(data_path, 'fodf_descoteaux07_sub_full.nii.gz')]])
+def test_asym_basis_output(script_runner, mock_filtering, in_fodf, out_fodf):
     os.chdir(os.path.expanduser(tmp_dir.name))
-    in_fodf = os.path.join(get_home(), 'processing',
-                           'fodf_descoteaux07_sub.nii.gz')
 
-    # We use a low resolution sphere to reduce execution time
     ret = script_runner.run('scil_execute_angle_aware_bilateral_filtering.py',
-                            in_fodf, 'out_0.nii.gz',
-                            '--sphere', 'repulsion100')
+                            in_fodf,
+                            'out_fodf1.nii.gz',
+                            '--sphere', 'repulsion100',
+                            '--sigma_angular', '1.0',
+                            '--sigma_spatial', '1.0',
+                            '--sigma_range', '1.0',
+                            '--sh_basis', 'descoteaux07',
+                            '--processes', '1', '-f',
+                            print_result=True, shell=True)
+
     assert ret.success
+    mock_filtering.assert_called_once()
 
+    ret_fodf = nib.load("out_fodf1.nii.gz")
+    test_fodf = nib.load(out_fodf)
+    assert np.allclose(ret_fodf.get_fdata(), test_fodf.get_fdata())
 
-def test_sym_basis_output(script_runner):
+
+@pytest.mark.parametrize("in_fodf,out_fodf,sym_fodf",
+    [[os.path.join(data_path, "fodf_descoteaux07_sub.nii.gz"),
+      os.path.join(data_path, "fodf_descoteaux07_sub_full.nii.gz"),
+      os.path.join(data_path, "fodf_descoteaux07_sub_sym.nii.gz")]])
+def test_sym_basis_output(
+    script_runner, mock_filtering, in_fodf, out_fodf, sym_fodf):
     os.chdir(os.path.expanduser(tmp_dir.name))
-    in_fodf = os.path.join(get_home(), 'processing',
-                           'fodf_descoteaux07_sub.nii.gz')
 
-    # We use a low resolution sphere to reduce execution time
     ret = script_runner.run('scil_execute_angle_aware_bilateral_filtering.py',
-                            in_fodf, 'out_1.nii.gz', '--out_sym',
-                            'out_sym.nii.gz', '--sphere', 'repulsion100')
+                            in_fodf,
+                            'out_fodf2.nii.gz',
+                            '--out_sym', 'out_sym.nii.gz',
+                            '--sphere', 'repulsion100',
+                            '--sigma_angular', '1.0',
+                            '--sigma_spatial', '1.0',
+                            '--sigma_range', '1.0',
+                            '--sh_basis', 'descoteaux07',
+                            '--processes', '1', '-f',
+                            print_result=True, shell=True)
+
     assert ret.success
+    mock_filtering.assert_called_once()
 
+    ret_sym_fodf = nib.load("out_sym.nii.gz")
+    test_sym_fodf = nib.load(sym_fodf)
+    assert np.allclose(ret_sym_fodf.get_fdata(), test_sym_fodf.get_fdata())
 
-def test_asym_input(script_runner):
+
+@pytest.mark.parametrize("in_fodf,out_fodf",
+    [[os.path.join(data_path, "fodf_descoteaux07_sub_full.nii.gz"),
+      os.path.join(data_path, "fodf_descoteaux07_sub_twice.nii.gz")]])
+def test_asym_input(script_runner, mock_filtering, in_fodf, out_fodf):
     os.chdir(os.path.expanduser(tmp_dir.name))
-    in_fodf = os.path.join(get_home(), 'processing',
-                           'fodf_descoteaux07_sub_full.nii.gz')
 
-    # We use a low resolution sphere to reduce execution time
     ret = script_runner.run('scil_execute_angle_aware_bilateral_filtering.py',
-                            in_fodf, 'out_2.nii.gz',
-                            '--sphere', 'repulsion100', '-f')
+                            in_fodf,
+                            'out_fodf3.nii.gz',
+                            '--sphere', 'repulsion100',
+                            '--sigma_angular', '1.0',
+                            '--sigma_spatial', '1.0',
+                            '--sigma_range', '1.0',
+                            '--sh_basis', 'descoteaux07',
+                            '--processes', '1', '-f',
+                            print_result=True, shell=True)
+
     assert ret.success
+    mock_filtering.assert_called_once()
+
+    ret_fodf = nib.load("out_fodf3.nii.gz")
+    test_fodf = nib.load(out_fodf)
+    assert np.allclose(ret_fodf.get_fdata(), test_fodf.get_fdata())

setup.py

@@ -68,7 +68,11 @@ def run(self):
             ext_modules=get_extensions(),
             setup_requires=['cython', 'numpy'],
             install_requires=external_dependencies,
-            scripts=SCRIPTS,
+            entry_points={
+                'console_scripts': ["{}=scripts.{}:main".format(
+                    os.path.basename(s),
+                    os.path.basename(s).split(".")[0]) for s in SCRIPTS]
+            },
             data_files=[('data/LUT',
                          ["data/LUT/freesurfer_desikan_killiany.json",
                           "data/LUT/freesurfer_subcortical.json",