Move test to correct module.

Author: AlexVCaron

scilpy/tests/checks.py

@@ -3,15 +3,37 @@
 import numpy as np
 
 
+def _nd_array_match(_arr1, _arr2, _rtol=1E-05, _atol=1E-8):
+    return np.allclose(_arr1, _arr2, rtol=_rtol, atol=_atol)
+
+
+def _mse_metrics(_arr1, _arr2):
+    _mse = (_arr1 - _arr2) ** 2.
+    return np.mean(_mse), np.max(_mse)
+
+
 def assert_images_close(img1, img2):
     dtype = img1.header.get_data_dtype()
 
     assert np.allclose(img1.affine, img2.affine), "Images affines don't match"
 
-    assert np.allclose(
-        img1.get_fdata(dtype=dtype), img2.get_fdata(dtype=dtype)), \
+    assert _nd_array_match(img1.get_fdata(dtype=dtype),
+                           img2.get_fdata(dtype=dtype)), \
         "Images data don't match. MSE : {} | max SE : {}".format(
-            np.mean((img1.get_fdata(dtype=dtype) -
-                     img2.get_fdata(dtype=dtype)) ** 2.),
-            np.max((img1.get_fdata(dtype=dtype) -
-                    img2.get_fdata(dtype=dtype)) ** 2.))
+            *_mse_metrics(img1.get_fdata(dtype=dtype),
+                          img2.get_fdata(dtype=dtype)))
+
+
+
+def assert_images_not_close(img1, img2, affine_must_match=True):
+    dtype = img1.header.get_data_dtype()
+
+    if affine_must_match:
+        assert np.allclose(img1.affine, img2.affine), \
+            "Images affines don't match"
+
+    assert not _nd_array_match(img1.get_fdata(dtype=dtype),
+                           img2.get_fdata(dtype=dtype)), \
+        "Images data should not match. MSE : {} | max SE : {}".format(
+            *_mse_metrics(img1.get_fdata(dtype=dtype),
+                          img2.get_fdata(dtype=dtype)))

scripts/tests/test_execute_angle_aware_bilateral_filtering.py

@@ -8,6 +8,7 @@
 import tempfile
 
 from scilpy.io.fetcher import get_testing_files_dict, fetch_data, get_home
+from scilpy.tests.checks import assert_images_close, assert_images_not_close
 
 
 # If they already exist, this only takes 5 seconds (check md5sum)
@@ -16,53 +17,50 @@
 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_sh_to_aodf'
-    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_sh_to_aodf.py', '--help')
     assert ret.success
 
 
-@pytest.mark.parametrize("in_fodf,out_fodf",
+@pytest.mark.parametrize("in_fodf,expected_results",
     [[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.path.join(data_path, 'fodf_descoteaux07_sub_full.nii.gz')]],
+    scope='function')
+def test_asym_basis_output(script_runner, in_fodf, expected_results,
+                           mock_collector):
+
     os.chdir(os.path.expanduser(tmp_dir.name))
+    _mocks = mock_collector(["bilateral_filtering"], "scripts.scil_sh_to_aodf")
 
     ret = script_runner.run('scil_sh_to_aodf.py',
                             in_fodf, 'out_fodf1.nii.gz',
                             '--sphere', 'repulsion100',
                             '--sigma_angular', '1.0',
                             '--sigma_spatial', '1.0',
                             '--sigma_range', '1.0',
-                            '--sh_basis', 'descoteaux07', '-f',
+                            '--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())
+    if _mocks["bilateral_filtering"]:
+        _mocks["bilateral_filtering"].assert_called_once()
+
+    assert_images_close(nib.load(expected_results),
+                        nib.load("out_fodf1.nii.gz"))
 
 
-@pytest.mark.parametrize("in_fodf,out_fodf,sym_fodf",
+@pytest.mark.parametrize("in_fodf,expected_results,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.path.join(data_path, "fodf_descoteaux07_sub_sym.nii.gz")]],
+    scope='function')
+def test_sym_basis_output(script_runner, in_fodf, expected_results, sym_fodf,
+                          mock_collector):
+
     os.chdir(os.path.expanduser(tmp_dir.name))
+    _mocks = mock_collector(["bilateral_filtering"], "scripts.scil_sh_to_aodf")
 
     ret = script_runner.run('scil_sh_to_aodf.py',
                             in_fodf,
@@ -72,22 +70,26 @@ def test_sym_basis_output(
                             '--sigma_angular', '1.0',
                             '--sigma_spatial', '1.0',
                             '--sigma_range', '1.0',
-                            '--sh_basis', 'descoteaux07', '-f',
+                            '--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())
+    if _mocks["bilateral_filtering"]:
+        _mocks["bilateral_filtering"].assert_called_once()
+
+    assert_images_close(nib.load(sym_fodf), nib.load("out_sym.nii.gz"))
 
 
-@pytest.mark.parametrize("in_fodf,out_fodf",
+@pytest.mark.parametrize("in_fodf,expected_results",
     [[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.path.join(data_path, "fodf_descoteaux07_sub_twice.nii.gz")]],
+    scope='function')
+def test_asym_input(script_runner, in_fodf, expected_results, mock_collector):
+
     os.chdir(os.path.expanduser(tmp_dir.name))
+    _mocks = mock_collector(["bilateral_filtering"], "scripts.scil_sh_to_aodf")
 
     ret = script_runner.run('scil_sh_to_aodf.py',
                             in_fodf,
@@ -96,39 +98,38 @@ def test_asym_input(script_runner, mock_filtering, in_fodf, out_fodf):
                             '--sigma_angular', '1.0',
                             '--sigma_spatial', '1.0',
                             '--sigma_range', '1.0',
-                            '--sh_basis', 'descoteaux07', '-f',
+                            '--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())
 
+    if _mocks["bilateral_filtering"]:
+        _mocks["bilateral_filtering"].assert_called_once()
+
+    assert_images_close(nib.load(expected_results),
+                        nib.load("out_fodf3.nii.gz"))
 
-@pytest.mark.parametrize("in_fodf,out_fodf",
+
+@pytest.mark.parametrize("in_fodf,expected_results",
     [[os.path.join(data_path, 'fodf_descoteaux07_sub.nii.gz'),
       os.path.join(data_path, 'fodf_descoteaux07_sub_full.nii.gz')]])
-def test_cosine_method(script_runner, mock_filtering, in_fodf, out_fodf):
+def test_cosine_method(script_runner, in_fodf, expected_results):
+
     os.chdir(os.path.expanduser(tmp_dir.name))
+    # method cosine is fast and not mocked
 
     ret = script_runner.run('scil_sh_to_aodf.py',
                             in_fodf, 'out_fodf1.nii.gz',
                             '--sphere', 'repulsion100',
                             '--method', 'cosine',
                             '--sh_basis', 'descoteaux07',
-                            '-f',
+                            '--processes', '1', '-f',
                             print_result=True, shell=True)
 
     assert ret.success
 
-    # method cosine is fast and not mocked
-    mock_filtering.assert_not_called()
-
-    ret_fodf = nib.load("out_fodf1.nii.gz")
-    test_fodf = nib.load(out_fodf)
-
     # We expect the output to be different from the
     # one obtained with angle-aware bilateral filtering
-    assert not np.allclose(ret_fodf.get_fdata(), test_fodf.get_fdata())
+    assert_images_not_close(nib.load(expected_results),
+                            nib.load("out_fodf1.nii.gz"))