migrate test to unit tests

cleanup and fixes

unit_tests/test_ereg.py

@@ -0,0 +1,130 @@
+import logging
+import os
+import tempfile
+import unittest
+
+import yaml
+from ereg.cli.run import main
+from ereg.functional import registration_function, resample_function
+from ereg.registration import RegistrationClass
+from ereg.utils.io import read_image_and_cast_to_32bit_float
+
+
+class TestEReg(unittest.TestCase):
+
+    def setUp(self):
+        # While this is already set within eReg it is necessary to specify it as well in the test environment
+        # else pytest will overwrite it with its own logging configuration (level WARNING)
+        logging.getLogger().setLevel(logging.DEBUG)
+
+        test_data_dir = "data"
+        atlas_data_dir = "atlases"
+        self.moving_image = os.path.join(test_data_dir, "tcia_aaac_t1ce.nii.gz")
+        self.atlas_sri = os.path.join(atlas_data_dir, "sri24", "image.nii.gz")
+        self.test_config_file = os.path.join(test_data_dir, "test_config.yaml")
+
+        test_config = {"initialization": "moments"}
+        with open(self.test_config_file, "w") as f:
+            yaml.dump(test_config, f)
+
+    # Helper function
+    def _image_sanity_check(self, image1, image2):
+        image_1 = read_image_and_cast_to_32bit_float(image1)
+        image_2 = read_image_and_cast_to_32bit_float(image2)
+        assert image_1.GetSize() == image_2.GetSize(), "Image sizes do not match."
+        assert (
+            image_1.GetSpacing() == image_2.GetSpacing()
+        ), "Image spacings do not match."
+        assert image_1.GetOrigin() == image_2.GetOrigin(), "Image origins do not match."
+        assert (
+            image_1.GetDirection() == image_2.GetDirection()
+        ), "Image directions do not match."
+
+    ###### TESTS ######
+
+    def test_cli_run_main(self):
+
+        with tempfile.TemporaryDirectory() as temp_dir:
+            output_image = os.path.join(temp_dir, "reg.nii.gz")
+            transform_file = os.path.join(temp_dir, "trans.mat")
+            main(
+                [
+                    "--movingImg",
+                    self.moving_image,
+                    "--targetImg",
+                    self.atlas_sri,
+                    "--output",
+                    output_image,
+                    "--transfile",
+                    transform_file,
+                    "--config",
+                    self.test_config_file,
+                ]
+            )
+            self._image_sanity_check(self.atlas_sri, output_image)
+
+    def test_registration_function(self):
+        test_config = {"initialization": "moments", "bias": True}
+        with tempfile.TemporaryDirectory() as temp_dir:
+            output_image = os.path.join(temp_dir, "reg.nii.gz")
+            transform_file = os.path.join(temp_dir, "trans.mat")
+            log_file = os.path.join(temp_dir, "reg.log")
+            registration_function(
+                target_image=self.atlas_sri,
+                moving_image=self.moving_image,
+                output_image=output_image,
+                transform_file=transform_file,
+                configuration=test_config,
+                log_file=log_file,
+            )
+
+            self._image_sanity_check(self.atlas_sri, output_image)
+
+            assert os.path.exists(transform_file), "Transform file not created."
+            assert os.path.exists(log_file), "Log file not created."
+            # check if log_file is empty
+            assert os.path.getsize(log_file) > 0, "Log file is empty."
+
+    def test_registration_and_resampling_function(self):
+        test_config = {"initialization": "moments", "bias": True}
+        with tempfile.TemporaryDirectory() as temp_dir:
+            reg_output_image = os.path.join(temp_dir, "reg.nii.gz")
+            transform_file = os.path.join(temp_dir, "trans.mat")
+            reg_log_file = os.path.join(temp_dir, "reg.log")
+
+            registration_function(
+                target_image=self.atlas_sri,
+                moving_image=self.moving_image,
+                output_image=reg_output_image,
+                transform_file=transform_file,
+                configuration=test_config,
+                log_file=reg_log_file,
+            )
+
+            self._image_sanity_check(self.atlas_sri, reg_output_image)
+
+            assert os.path.exists(transform_file), "Transform file not created."
+            assert os.path.exists(reg_log_file), "Registration log file not created."
+            assert os.path.getsize(reg_log_file) > 0, "Registration log file is empty."
+
+            ## Resample
+            resample_log_file = os.path.join(temp_dir, "resample.log")
+            resample_output_image = os.path.join(temp_dir, "resample.nii.gz")
+            resample_function(
+                target_image=self.atlas_sri,
+                moving_image=self.moving_image,
+                output_image=resample_output_image,
+                transform_file=transform_file,
+                configuration=test_config,
+                log_file=resample_log_file,
+            )
+
+            self._image_sanity_check(self.atlas_sri, resample_output_image)
+            assert os.path.exists(transform_file), "Transform file not created"
+            assert os.path.exists(resample_log_file), "Resample log file not created"
+            assert os.path.getsize(resample_log_file) > 0, "Resample log file is empty"
+
+    def test_bias_correct_image(self):
+        register_obj = RegistrationClass()
+        moving_bias = register_obj._bias_correct_image(self.moving_image)
+        self._image_sanity_check(self.moving_image, moving_bias)