Removed functionality that is no longer useful.

test/ibsi_2_feature_test.py

@@ -13,9 +13,6 @@
 # Find path to the test directory. This is because we need to read datafiles stored in subdirectories.
 CURRENT_DIR = os.path.dirname(os.path.abspath(__file__))
 
-PERTURB_IMAGES = False
-WRITE_TEMP_FILES = True
-
 
 def within_tolerance(ref, tol, x):
     # Read from pandas Series
@@ -57,19 +54,9 @@ def _get_default_settings(
         resegmentation_intensity_range=[-1000.0, 400.0]
     )
 
-    if PERTURB_IMAGES:
-        perturbation_settings = ImagePerturbationSettingsClass(
-            crop_around_roi=False,
-            perturbation_rotation_angles=[-15.0, -10.0, 5.0, 0.0, 5.0, 10.0, 15.0],
-            perturbation_translation_fraction=[0.00, 0.25, 0.50, 0.75],
-            perturbation_roi_adapt_size=[-2.0, 0.0, 2.0],
-            perturbation_roi_adapt_type="distance"
-        )
-
-    else:
-        perturbation_settings = ImagePerturbationSettingsClass(
-            crop_around_roi=False
-        )
+    perturbation_settings = ImagePerturbationSettingsClass(
+        crop_around_roi=False
+    )
 
     feature_computation_parameters = FeatureExtractionSettingsClass(
         by_slice=by_slice,
@@ -84,8 +71,8 @@ def _process_experiment(
         configuration_id: str,
         by_slice: bool,
         image_transformation_settings: ImageTransformationSettingsClass,
-        tmp_path: str | os.PathLike,
-        base_feature_families: str = "none"):
+        base_feature_families: str = "none"
+):
 
     # Get default settings.
     general_settings, image_interpolation_settings, feature_computation_parameters, resegmentation_settings, \
@@ -116,20 +103,10 @@ def _process_experiment(
 
     data = data[0]
 
-    if WRITE_TEMP_FILES:
-        file_name = "_".join([configuration_id, "perturb", "features.csv"] if PERTURB_IMAGES else [configuration_id, "features.csv"])
-
-        data.to_csv(
-            tmp_path / file_name,
-            sep=";",
-            decimal=".",
-            index=False
-        )
-
     return data
 
 
-def test_ibsi_2_config_none(tmp_path):
+def test_ibsi_2_config_none():
     """
     Compare computed feature values with reference values for configurations 1A and 1B of IBSI 2 phase 2.
     """
@@ -147,7 +124,6 @@ def test_ibsi_2_config_none(tmp_path):
         configuration_id="1.A",
         by_slice=True,
         image_transformation_settings=image_transformation_settings,
-        tmp_path=tmp_path,
         base_feature_families="statistics"
     )
 
@@ -183,7 +159,6 @@ def test_ibsi_2_config_none(tmp_path):
         configuration_id="1.B",
         by_slice=False,
         image_transformation_settings=image_transformation_settings,
-        tmp_path=tmp_path,
         base_feature_families="statistics"
     )
 
@@ -207,7 +182,7 @@ def test_ibsi_2_config_none(tmp_path):
     assert (within_tolerance(52600, 2800, data["stat_var"]))
 
 
-def test_ibsi_2_config_mean_filter(tmp_path):
+def test_ibsi_2_config_mean_filter():
     """
     Compare computed feature values with reference values for configurations 2A and 2B of IBSI 2 phase 2.
     """
@@ -226,7 +201,6 @@ def test_ibsi_2_config_mean_filter(tmp_path):
         configuration_id="2.A",
         by_slice=True,
         image_transformation_settings=image_transformation_settings,
-        tmp_path=tmp_path
     )
 
     data.columns = [column_name.replace("mean_d_5_", "") for column_name in data.columns]
@@ -264,7 +238,6 @@ def test_ibsi_2_config_mean_filter(tmp_path):
         configuration_id="2.B",
         by_slice=False,
         image_transformation_settings=image_transformation_settings,
-        tmp_path=tmp_path,
     )
 
     data.columns = [column_name.replace("mean_d_5_", "") for column_name in data.columns]
@@ -289,7 +262,7 @@ def test_ibsi_2_config_mean_filter(tmp_path):
     assert (within_tolerance(44400, 2300, data["stat_var"]))
 
 
-def test_ibsi_2_config_laplacian_of_gaussian_filter(tmp_path):
+def test_ibsi_2_config_laplacian_of_gaussian_filter():
     """
     Compare computed feature values with reference values for configurations 3A and 3B of IBSI 2 phase 2.
     """
@@ -309,7 +282,6 @@ def test_ibsi_2_config_laplacian_of_gaussian_filter(tmp_path):
         configuration_id="3.A",
         by_slice=True,
         image_transformation_settings=image_transformation_settings,
-        tmp_path=tmp_path,
     )
 
     data.columns = [column_name.replace("log_s_1.5_", "") for column_name in data.columns]
@@ -348,7 +320,6 @@ def test_ibsi_2_config_laplacian_of_gaussian_filter(tmp_path):
         configuration_id="3.B",
         by_slice=False,
         image_transformation_settings=image_transformation_settings,
-        tmp_path=tmp_path,
     )
 
     data.columns = [column_name.replace("log_s_1.5_", "") for column_name in data.columns]
@@ -373,7 +344,7 @@ def test_ibsi_2_config_laplacian_of_gaussian_filter(tmp_path):
     assert (within_tolerance(720, 33, data["stat_var"]))
 
 
-def test_ibsi_2_config_laws_filter(tmp_path):
+def test_ibsi_2_config_laws_filter():
     """
     Compare computed feature values with reference values for configurations 4A and 4B of IBSI 2 phase 2.
     """
@@ -396,7 +367,6 @@ def test_ibsi_2_config_laws_filter(tmp_path):
         configuration_id="4.A",
         by_slice=True,
         image_transformation_settings=image_transformation_settings,
-        tmp_path=tmp_path,
     )
 
     data.columns = [column_name.replace("laws_l5e5_energy_delta_7_invar_", "") for column_name in data.columns]
@@ -438,7 +408,6 @@ def test_ibsi_2_config_laws_filter(tmp_path):
         configuration_id="4.B",
         by_slice=False,
         image_transformation_settings=image_transformation_settings,
-        tmp_path=tmp_path,
     )
 
     data.columns = [column_name.replace("laws_l5e5e5_energy_delta_7_invar_", "") for column_name in data.columns]
@@ -463,7 +432,7 @@ def test_ibsi_2_config_laws_filter(tmp_path):
     assert (within_tolerance(11100, 300, data["stat_var"]))
 
 
-def test_ibsi_2_config_gabor_filter(tmp_path):
+def test_ibsi_2_config_gabor_filter():
     """
     Compare computed feature values with reference values for configurations 5A and 5B of IBSI 2 phase 2.
     """
@@ -489,7 +458,6 @@ def test_ibsi_2_config_gabor_filter(tmp_path):
         configuration_id="5.A",
         by_slice=True,
         image_transformation_settings=image_transformation_settings,
-        tmp_path=tmp_path,
     )
 
     data.columns = [column_name.replace("gabor_s_5.0_g_1.5_l_2.0_2D_", "") for column_name in data.columns]
@@ -534,7 +502,6 @@ def test_ibsi_2_config_gabor_filter(tmp_path):
         configuration_id="5.B",
         by_slice=False,
         image_transformation_settings=image_transformation_settings,
-        tmp_path=tmp_path,
     )
 
     data.columns = [column_name.replace("gabor_s_5.0_g_1.5_l_2.0_3D_invar_", "") for column_name in data.columns]
@@ -559,7 +526,7 @@ def test_ibsi_2_config_gabor_filter(tmp_path):
     assert (within_tolerance(231, 2, data["stat_var"]))
 
 
-def test_ibsi_2_config_daubechies_filter(tmp_path):
+def test_ibsi_2_config_daubechies_filter():
     """
     Compare computed feature values with reference values for configurations 6A, 6B, 7A and 7B of IBSI 2 phase 2.
     """
@@ -582,7 +549,6 @@ def test_ibsi_2_config_daubechies_filter(tmp_path):
         configuration_id="6.A",
         by_slice=True,
         image_transformation_settings=image_transformation_settings,
-        tmp_path=tmp_path,
     )
 
     data.columns = [column_name.replace("wavelet_db3_lh_level_1_invar_", "") for column_name in data.columns]
@@ -624,7 +590,6 @@ def test_ibsi_2_config_daubechies_filter(tmp_path):
         configuration_id="6.B",
         by_slice=False,
         image_transformation_settings=image_transformation_settings,
-        tmp_path=tmp_path,
     )
 
     data.columns = [column_name.replace("wavelet_db3_llh_level_1_invar_", "") for column_name in data.columns]
@@ -666,7 +631,6 @@ def test_ibsi_2_config_daubechies_filter(tmp_path):
         configuration_id="7.A",
         by_slice=True,
         image_transformation_settings=image_transformation_settings,
-        tmp_path=tmp_path,
     )
 
     data.columns = [column_name.replace("wavelet_db3_hh_level_2_invar_", "") for column_name in data.columns]
@@ -708,7 +672,6 @@ def test_ibsi_2_config_daubechies_filter(tmp_path):
         configuration_id="7.B",
         by_slice=False,
         image_transformation_settings=image_transformation_settings,
-        tmp_path=tmp_path,
     )
 
     data.columns = [column_name.replace("wavelet_db3_hhh_level_2_invar_", "") for column_name in data.columns]
@@ -733,7 +696,7 @@ def test_ibsi_2_config_daubechies_filter(tmp_path):
     assert (within_tolerance(422, 11, data["stat_var"]))
 
 
-def test_ibsi_2_config_simoncelli_filter(tmp_path):
+def test_ibsi_2_config_simoncelli_filter():
     """
     Compare computed feature values with reference values for configurations 8A, 8B, 9A and 9B of IBSI 2 phase 2.
     """
@@ -753,7 +716,6 @@ def test_ibsi_2_config_simoncelli_filter(tmp_path):
         configuration_id="8.A",
         by_slice=True,
         image_transformation_settings=image_transformation_settings,
-        tmp_path=tmp_path,
     )
 
     data.columns = [column_name.replace("wavelet_simoncelli_level_1_", "") for column_name in data.columns]
@@ -792,7 +754,6 @@ def test_ibsi_2_config_simoncelli_filter(tmp_path):
         configuration_id="8.B",
         by_slice=False,
         image_transformation_settings=image_transformation_settings,
-        tmp_path=tmp_path,
     )
 
     data.columns = [column_name.replace("wavelet_simoncelli_level_1_", "") for column_name in data.columns]
@@ -830,7 +791,6 @@ def test_ibsi_2_config_simoncelli_filter(tmp_path):
         configuration_id="9.A",
         by_slice=True,
         image_transformation_settings=image_transformation_settings,
-        tmp_path=tmp_path,
     )
 
     data.columns = [column_name.replace("wavelet_simoncelli_level_2_", "") for column_name in data.columns]
@@ -869,7 +829,6 @@ def test_ibsi_2_config_simoncelli_filter(tmp_path):
         configuration_id="9.B",
         by_slice=False,
         image_transformation_settings=image_transformation_settings,
-        tmp_path=tmp_path,
     )
 
     data.columns = [column_name.replace("wavelet_simoncelli_level_2_", "") for column_name in data.columns]