Testing registrator

brainles_preprocessing/modality.py

@@ -94,11 +94,11 @@ def register(
         registered_log = os.path.join(registration_dir, f"{moving_image_name}.log")
 
         registrator.register(
-            fixed_image=fixed_image_path,
-            moving_image=self.current,
+            fixed_image_path=fixed_image_path,
+            moving_image_path=self.current,
             transformed_image=registered,
-            matrix=registered_matrix,
-            log_file=registered_log,
+            matrix_path=registered_matrix,
+            log_file_path=registered_log,
         )
         self.current = registered
         return registered_matrix
@@ -133,11 +133,11 @@ def transform(
         transformed_log = os.path.join(registration_dir, f"{moving_image_name}.log")
 
         registrator.transform(
-            fixed_image=fixed_image_path,
-            moving_image=self.current,
-            transformed_image=transformed,
-            matrix=transformation_matrix,
-            log_file=transformed_log,
+            fixed_image_path=fixed_image_path,
+            moving_image_path=self.current,
+            transformed_image_path=transformed,
+            matrix_path=transformation_matrix,
+            log_file_path=transformed_log,
         )
         self.current = transformed
 

brainles_preprocessing/registration/niftyreg.py

@@ -42,25 +42,25 @@ def __init__(
 
     def register(
         self,
-        fixed_image,
-        moving_image,
-        transformed_image,
-        matrix,
-        log_file,
+        fixed_image_path: str,
+        moving_image_path: str,
+        transformed_image_path: str,
+        matrix_path: str,
+        log_file_path: str,
     ):
         """
         Register images using NiftyReg.
 
         Args:
-            fixed_image (str): Path to the fixed image.
-            moving_image (str): Path to the moving image.
-            transformed_image (str): Path to the transformed image (output).
-            matrix (str): Path to the transformation matrix (output).
-            log_file (str): Path to the log file.
+            fixed_image_path (str): Path to the fixed image.
+            moving_image_path (str): Path to the moving image.
+            transformed_image_path (str): Path to the transformed image (output).
+            matrix_path (str): Path to the transformation matrix (output).
+            log_file_path (str): Path to the log file.
         """
         runner = ScriptRunner(
             script_path=self.registration_script,
-            log_path=log_file,
+            log_path=log_file_path,
         )
 
         niftyreg_executable = str(
@@ -69,10 +69,10 @@ def register(
 
         input_params = [
             turbopath(niftyreg_executable),
-            turbopath(fixed_image),
-            turbopath(moving_image),
-            turbopath(transformed_image),
-            turbopath(matrix),
+            turbopath(fixed_image_path),
+            turbopath(moving_image_path),
+            turbopath(transformed_image_path),
+            turbopath(matrix_path),
         ]
 
         # Call the run method to execute the script and capture the output in the log file
@@ -85,25 +85,25 @@ def register(
 
     def transform(
         self,
-        fixed_image,
-        moving_image,
-        transformed_image,
-        matrix,
-        log_file,
+        fixed_image_path: str,
+        moving_image_path: str,
+        transformed_image_path: str,
+        matrix_path: str,
+        log_file_path: str,
     ):
         """
         Apply a transformation using NiftyReg.
 
         Args:
-            fixed_image (str): Path to the fixed image.
-            moving_image (str): Path to the moving image.
-            transformed_image (str): Path to the transformed image (output).
-            matrix (str): Path to the transformation matrix.
-            log_file (str): Path to the log file.
+            fixed_image_path (str): Path to the fixed image.
+            moving_image_path (str): Path to the moving image.
+            transformed_image_path (str): Path to the transformed image (output).
+            matrix_path (str): Path to the transformation matrix.
+            log_file_path (str): Path to the log file.
         """
         runner = ScriptRunner(
             script_path=self.transformation_script,
-            log_path=log_file,
+            log_path=log_file_path,
         )
 
         niftyreg_executable = str(
@@ -112,10 +112,10 @@ def transform(
 
         input_params = [
             turbopath(niftyreg_executable),
-            turbopath(fixed_image),
-            turbopath(moving_image),
-            turbopath(transformed_image),
-            turbopath(matrix),
+            turbopath(fixed_image_path),
+            turbopath(moving_image_path),
+            turbopath(transformed_image_path),
+            turbopath(matrix_path),
         ]
 
         # Call the run method to execute the script and capture the output in the log file

brainles_preprocessing/registration/registrator.py

@@ -1,29 +1,56 @@
-# TODO add typing and docs
 from abc import ABC, abstractmethod
+from typing import Any
 
 
 class Registrator(ABC):
-    def __init__(self, backend):
-        self.backend = backend
+    # TODO probably the init here should be removed?
+    # def __init__(self, backend):
+    #     self.backend = backend
 
     @abstractmethod
     def register(
         self,
-        fixed_image,
-        moving_image,
-        transformed_image,
-        matrix,
-        log_file,
-    ):
+        fixed_image_path: Any,
+        moving_image_path: Any,
+        transformed_image_path: Any,
+        matrix_path: Any,
+        log_file_path: str,
+    ) -> None:
+        """
+        Abstract method for registering images.
+
+        Args:
+            fixed_image_path (Any): The fixed image for registration.
+            moving_image_path (Any): The moving image to be registered.
+            transformed_image_path (Any): The resulting transformed image after registration.
+            matrix_path (Any): The transformation matrix applied during registration.
+            log_file_path (str): The path to the log file for recording registration details.
+
+        Returns:
+            None
+        """
         pass
 
     @abstractmethod
     def transform(
         self,
-        fixed_image,
-        moving_image,
-        transformed_image,
-        matrix,
-        log_file,
-    ):
+        fixed_image_path: Any,
+        moving_image_path: Any,
+        transformed_image_path: Any,
+        matrix: Any,
+        log_file: str,
+    ) -> None:
+        """
+        Abstract method for transforming images.
+
+        Args:
+            fixed_image_path (Any): The fixed image to be transformed.
+            moving_image_path (Any): The moving image to be transformed.
+            transformed_image_path (Any): The resulting transformed image.
+            matrix_path (Any): The transformation matrix applied during transformation.
+            log_file_path (str): The path to the log file for recording transformation details.
+
+        Returns:
+            None
+        """
         pass

tests/test_brain_extractor.py → tests/test_hdbet_brain_extractor.py

@@ -11,12 +11,14 @@ class TestHDBetExtractor(unittest.TestCase):
     def setUp(self):
         test_data_dir = turbopath(__file__).parent + "/test_data"
         input_dir = test_data_dir + "/input"
-        self.output_dir = test_data_dir + "/temp_output"
+        self.output_dir = test_data_dir + "/temp_output_hdbet"
         os.makedirs(self.output_dir, exist_ok=True)
 
         self.brain_extractor = HDBetExtractor()
+
         self.input_image_path = input_dir + "/tcia_example_t1c.nii.gz"
         self.input_brain_mask_path = input_dir + "/bet_tcia_example_t1c_mask.nii.gz"
+
         self.masked_image_path = self.output_dir + "/bet_tcia_example_t1c.nii.gz"
         self.brain_mask_path = self.output_dir + "/bet_tcia_example_t1c_mask.nii.gz"
         self.masked_again_image_path = (
@@ -30,9 +32,8 @@ def tearDown(self):
         # Clean up created files if they exist
         shutil.rmtree(self.output_dir)
 
-
     def test_extract_creates_output_files(self):
-        # we try to run the fastest possible skullstripping on GPU
+        # we try to run the fastest possible skullstripping on CPU
         self.brain_extractor.extract(
             input_image_path=self.input_image_path,
             masked_image_path=self.masked_image_path,

tests/test_niftyreg_registrator.py

@@ -0,0 +1,56 @@
+import os
+import shutil
+import unittest
+
+from auxiliary.turbopath import turbopath
+
+from brainles_preprocessing.registration.niftyreg import NiftyRegRegistrator
+
+
+class TestNiftyRegRegistrator(unittest.TestCase):
+    def setUp(self):
+        test_data_dir = turbopath(__file__).parent + "/test_data"
+        input_dir = test_data_dir + "/input"
+        self.output_dir = test_data_dir + "/temp_output_niftyreg"
+        os.makedirs(self.output_dir, exist_ok=True)
+
+        self.registrator = NiftyRegRegistrator()
+
+        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"
+
+    def tearDown(self):
+        # Clean up created files if they exist
+        shutil.rmtree(self.output_dir)
+
+    def test_register_creates_output_files(self):
+        # we try to run the fastest possible skullstripping on GPU
+        self.registrator.register(
+            fixed_image_path=self.fixed_image,
+            moving_image_path=self.moving_image,
+            transformed_image_path=self.transformed_image,
+            matrix_path=self.matrix,
+            log_file_path=self.log_file,
+        )
+
+        self.assertTrue(
+            os.path.exists(self.transformed_image),
+            "transformed file was not created.",
+        )
+
+        self.assertTrue(
+            os.path.exists(self.matrix),
+            "matrix file was not created.",
+        )
+
+        self.assertTrue(
+            os.path.exists(self.log_file),
+            "log file was not created.",
+        )
+
+
+# TODO also test transform