better tests

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

tests/registrator_base.py

@@ -0,0 +1,93 @@
+import os
+import shutil
+import unittest
+from abc import ABC, abstractmethod
+
+from auxiliary.turbopath import turbopath
+
+
+class RegistratorBase(unittest.TestCase):
+
+    @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 + f"/temp_output_{self.method_name}"
+        os.makedirs(self.output_dir, exist_ok=True)
+
+        self.fixed_image = input_dir + "/tcia_example_t1c.nii.gz"
+        self.moving_image = input_dir + "/tcia_example_t1.nii.gz"
+
+        self.matrix = self.output_dir + f"/{self.method_name}_matrix"
+        self.transform_matrix = (
+            input_dir + f"/{self.method_name}_matrix.{self.matrix_extension}"
+        )
+
+    def tearDown(self):
+        # Clean up created files if they exist
+        # shutil.rmtree(self.output_dir)
+        pass
+
+    def test_register_creates_output_files(self):
+        transformed_image = (
+            self.output_dir + f"/{self.method_name}_registered_image.nii.gz"
+        )
+        log_file = self.output_dir + f"/{self.method_name}_registration.log"
+
+        self.registrator.register(
+            fixed_image_path=self.fixed_image,
+            moving_image_path=self.moving_image,
+            transformed_image_path=transformed_image,
+            matrix_path=self.matrix,
+            log_file_path=log_file,
+        )
+
+        self.assertTrue(
+            os.path.exists(transformed_image),
+            "transformed file was not created.",
+        )
+
+        self.assertTrue(
+            os.path.exists(f"{self.matrix}.{self.matrix_extension}"),
+            "matrix file was not created.",
+        )
+
+        self.assertTrue(
+            os.path.exists(log_file),
+            "log file was not created.",
+        )
+
+    def test_transform_creates_output_files(self):
+        transformed_image = (
+            self.output_dir + f"/{self.method_name}_transformed_image.nii.gz"
+        )
+        log_file = self.output_dir + f"/{self.method_name}_transformation.log"
+
+        print("tf m:", self.transform_matrix)
+        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.",
+        )

tests/test_data/input/niftyreg_matrix.txt

@@ -0,0 +1,4 @@
+0.9888756 0.1354215 0.06153017 -1.314461
+-0.1397797 0.9874795 0.07311541 -1.147088
+-0.05085838 -0.08090271 0.9954236 2.731441
+0 0 0 1

tests/test_registrators.py

@@ -1,96 +1,10 @@
-import os
-import shutil
-import unittest
-from abc import abstractmethod
-
-from auxiliary.turbopath import turbopath
+from registrator_base import RegistratorBase
 
 from brainles_preprocessing.registration.ANTs.ANTs import ANTsRegistrator
 from brainles_preprocessing.registration.eReg.eReg import eRegRegistrator
 from brainles_preprocessing.registration.niftyreg.niftyreg import NiftyRegRegistrator
 
 
-class RegistratorBase(unittest.TestCase):
-    @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 + f"/temp_output_{self.method_name}"
-        os.makedirs(self.output_dir, exist_ok=True)
-
-        self.fixed_image = input_dir + "/tcia_example_t1c.nii.gz"
-        self.moving_image = input_dir + "/bet_tcia_example_t1c_mask.nii.gz"
-
-        self.matrix = self.output_dir + "/matrix"
-        self.transform_matrix = input_dir + f"/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=transformed_image,
-            matrix_path=self.matrix,
-            log_file_path=log_file,
-        )
-
-        self.assertTrue(
-            os.path.exists(transformed_image),
-            "transformed file was not created.",
-        )
-
-        self.assertTrue(
-            os.path.exists(f"{self.matrix}.{self.matrix_extension}"),
-            "matrix file was not created.",
-        )
-
-        self.assertTrue(
-            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 TestANTsRegistrator(RegistratorBase):
     def get_registrator(self):
         return ANTsRegistrator()