Implement inference test

Author: constantinpape

test/test_cli.py

@@ -12,6 +12,7 @@
 from synapse_net.sample_data import get_sample_data
 
 
+@unittest.skipIf(platform.system() == "Windows", "CLI does not work on Windows")
 class TestCLI(unittest.TestCase):
     tmp_dir = "tmp"
 
@@ -72,17 +73,10 @@ def test_segmentation_cli_with_scale(self):
     def test_segmentation_cli_with_checkpoint(self):
         cache_dir = os.path.expanduser(pooch.os_cache("synapse-net"))
         model_path = os.path.join(cache_dir, "models", "vesicles_2d")
-        if platform.system() == "Windows":
-            cmd = [
-                sys.executable, "-m", "synapse_net.run_segmentation",
-                "-i", self.data_path, "-o", self.tmp_dir, "-m", "vesicles_2d",
-                "-c", model_path,
-            ]
-        else:
-            cmd = [
-                "synapse_net.run_segmentation", "-i", self.data_path, "-o", self.tmp_dir, "-m", "vesicles_2d",
-                "-c", model_path,
-            ]
+        cmd = [
+            "synapse_net.run_segmentation", "-i", self.data_path, "-o", self.tmp_dir, "-m", "vesicles_2d",
+            "-c", model_path,
+        ]
         run(cmd)
         self.check_segmentation_result()
 

test/test_inference.py

@@ -0,0 +1,51 @@
+import os
+import unittest
+from functools import partial
+from shutil import rmtree
+
+import imageio.v3 as imageio
+from synapse_net.file_utils import read_mrc
+from synapse_net.sample_data import get_sample_data
+
+
+class TestInference(unittest.TestCase):
+    tmp_dir = "tmp"
+    model_type = "vesicles_2d"
+    tiling = {"tile": {"z": 1, "y": 512, "x": 512}, "halo": {"z": 0, "y": 32, "x": 32}}
+
+    def setUp(self):
+        self.data_path = get_sample_data("tem_2d")
+        os.makedirs(self.tmp_dir, exist_ok=True)
+
+    def tearDown(self):
+        try:
+            rmtree(self.tmp_dir)
+        except OSError:
+            pass
+
+    def test_run_segmentation(self):
+        from synapse_net.inference import run_segmentation, get_model
+
+        image, _ = read_mrc(self.data_path)
+        model = get_model(self.model_type)
+        seg = run_segmentation(image, model, model_type=self.model_type, tiling=self.tiling)
+        self.assertEqual(image.shape, seg.shape)
+
+    def test_segmentation_with_inference_helper(self):
+        from synapse_net.inference import run_segmentation, get_model
+        from synapse_net.inference.util import inference_helper
+
+        model = get_model(self.model_type)
+        segmentation_function = partial(
+            run_segmentation, model=model, model_type=self.model_type, verbose=False, tiling=self.tiling,
+        )
+        inference_helper(self.data_path, self.tmp_dir, segmentation_function, data_ext=".mrc")
+        expected_output_path = os.path.join(self.tmp_dir, "tem_2d_prediction.tif")
+        self.assertTrue(os.path.exists(expected_output_path))
+        seg = imageio.imread(expected_output_path)
+        image, _ = read_mrc(self.data_path)
+        self.assertEqual(image.shape, seg.shape)
+
+
+if __name__ == "__main__":
+    unittest.main()