add basic tests for EXTRACTSegmentation

Author: weiglszonja

src/pynwb/tests/test_extract.py

@@ -0,0 +1,85 @@
+from datetime import datetime
+from pathlib import Path
+from shutil import rmtree
+from tempfile import mkdtemp
+
+import numpy as np
+from hdmf.testing import TestCase
+from numpy.testing import assert_array_equal
+from pynwb import NWBFile, NWBHDF5IO
+
+from ndx_extract import EXTRACTSegmentation
+
+
+class TestExtractSegmentation(TestCase):
+    @classmethod
+    def setUpClass(cls):
+        cls.file_path = "extract_public_output.mat"
+        cls.output_struct_name = "output"
+
+        cls.session_start_time = datetime.now().astimezone()
+
+        cls.image_segmentation_name = "ExtractSegmentation"
+
+    def setUp(self):
+        self.nwbfile = NWBFile(
+            session_description="session_description",
+            identifier="file_id",
+            session_start_time=self.session_start_time,
+        )
+
+        self.tmpdir = Path(mkdtemp())
+        self.nwbfile_path = self.tmpdir / "test_nwb.nwb"
+
+    def tearDown(self):
+        rmtree(self.tmpdir)
+
+    def test_extract_defaults(self):
+        image_segmentation = EXTRACTSegmentation()
+        self.assertEqual(image_segmentation.name, "ImageSegmentation")
+
+    def test_extract_name_propagates(self):
+        image_segmentation = EXTRACTSegmentation(name=self.image_segmentation_name)
+        self.assertEqual(image_segmentation.name, self.image_segmentation_name)
+
+    def test_extract_roundtrip(self):
+        image_segmentation = EXTRACTSegmentation(
+            name="test_name",
+            version="1.1.0",
+            preprocess=True,
+            movie_mask=np.ones((15, 15)),
+        )
+
+        ophys_module = self.nwbfile.create_processing_module(
+            name="ophys",
+            description="optical physiology processed data",
+        )
+
+        ophys_module.add(image_segmentation)
+
+        with NWBHDF5IO(self.nwbfile_path, mode="w") as io:
+            io.write(self.nwbfile)
+
+        with NWBHDF5IO(self.nwbfile_path, mode="r") as io:
+            nwbfile_in = io.read()
+
+            movie_mask = (
+                nwbfile_in.processing["ophys"]
+                .data_interfaces["test_name"]
+                .movie_mask[:]
+            )
+
+            assert_array_equal(
+                movie_mask,
+                np.ones((15, 15)),
+            )
+
+        self.assertEqual(
+            nwbfile_in.processing["ophys"].data_interfaces["test_name"].version,
+            "1.1.0",
+        )
+
+        self.assertEqual(
+            nwbfile_in.processing["ophys"].data_interfaces["test_name"].preprocess,
+            True,
+        )