registration and transformation tests

Signed-off-by: neuronflow <[email protected]>

tests/test_registrators.py

@@ -6,66 +6,101 @@
 from auxiliary.turbopath import turbopath
 
 from brainles_preprocessing.registration.ANTs.ANTs import ANTsRegistrator
-from brainles_preprocessing.registration.niftyreg.niftyreg import \
-    NiftyRegRegistrator
+from brainles_preprocessing.registration.niftyreg.niftyreg import NiftyRegRegistrator
 
 
-class TestRegistratorBase(unittest.TestCase):
+class RegistratorBase:
     @abstractmethod
     def get_registrator(self):
         pass
 
+    @abstractmethod
+    def get_method_and_extension(self):
+        pass
+
     def setUp(self):
+        self.registrator = self.get_registrator()
+        self.method_name, self.matrix_extension = self.get_method_and_extension()
+
         test_data_dir = turbopath(__file__).parent + "/test_data"
         input_dir = test_data_dir + "/input"
-        self.output_dir = test_data_dir + "/temp_output_niftyreg"
+        self.output_dir = test_data_dir + f"/temp_output_{self.method_name}"
         os.makedirs(self.output_dir, exist_ok=True)
 
-        self.registrator = self.get_registrator()
-
         self.fixed_image = input_dir + "/tcia_example_t1c.nii.gz"
         self.moving_image = input_dir + "/bet_tcia_example_t1c_mask.nii.gz"
 
-        self.transformed_image = self.output_dir + "/transformed_image.nii.gz"
-        self.matrix = self.output_dir + "/matrix.txt"
-        self.log_file = self.output_dir + "/registration.log"
+        self.matrix = self.output_dir + "/matrix"
+        self.transform_matrix = f"{self.matrix}.{self.matrix_extension}"
 
     def tearDown(self):
         # Clean up created files if they exist
         shutil.rmtree(self.output_dir)
 
     def test_register_creates_output_files(self):
+        transformed_image = self.output_dir + "/registered_image.nii.gz"
+        log_file = self.output_dir + "/registration.log"
+
         self.registrator.register(
             fixed_image_path=self.fixed_image,
             moving_image_path=self.moving_image,
-            transformed_image_path=self.transformed_image,
+            transformed_image_path=transformed_image,
             matrix_path=self.matrix,
-            log_file_path=self.log_file,
+            log_file_path=log_file,
         )
 
         self.assertTrue(
-            os.path.exists(self.transformed_image),
+            os.path.exists(transformed_image),
             "transformed file was not created.",
         )
 
         self.assertTrue(
-            os.path.exists(self.matrix),
+            os.path.exists(f"{self.matrix}.{self.matrix_extension}"),
             "matrix file was not created.",
         )
 
         self.assertTrue(
-            os.path.exists(self.log_file),
+            os.path.exists(log_file),
+            "log file was not created.",
+        )
+
+    def test_transform_creates_output_files(self):
+        transformed_image = self.output_dir + "/transformed_image.nii.gz"
+        log_file = self.output_dir + "/transformation.log"
+
+        self.registrator.transform(
+            fixed_image_path=self.fixed_image,
+            moving_image_path=self.moving_image,
+            transformed_image_path=transformed_image,
+            matrix_path=self.transform_matrix,
+            log_file_path=log_file,
+        )
+
+        self.assertTrue(
+            os.path.exists(transformed_image),
+            "transformed file was not created.",
+        )
+
+        self.assertTrue(
+            os.path.exists(log_file),
             "log file was not created.",
         )
 
 
 # TODO also test transform
 
 
-class TestANTsRegistratorBase(TestRegistratorBase):
+class TestANTsRegistrator(RegistratorBase, unittest.TestCase):
     def get_registrator(self):
         return ANTsRegistrator()
 
-class TestNiftyRegRegistratorRegistratorBase(TestRegistratorBase):
+    def get_method_and_extension(self):
+        return "ants", "mat"
+
+
+class TestNiftyRegRegistratorRegistrator(RegistratorBase, unittest.TestCase):
     def get_registrator(self):
         return NiftyRegRegistrator()
+
+    def get_method_and_extension(self):
+        return "niftyreg", "txt"