Add new sample data and test for file utils

Author: constantinpape

synaptic_reconstruction/file_utils.py

@@ -59,7 +59,6 @@ def read_voxel_size(path: str) -> Dict[str, float] | None:
     return voxel_size
 
 
-# TODO: double check axis ordering with elf
 def read_mrc(path: str) -> Tuple[np.ndarray, Dict[str, float]]:
     """Read data and voxel size from mrc/rec file.
 
@@ -73,11 +72,8 @@ def read_mrc(path: str) -> Tuple[np.ndarray, Dict[str, float]]:
     with mrcfile.open(path, permissive=True) as mrc:
         voxel_size = _parse_voxel_size(mrc.voxel_size)
         data = np.asarray(mrc.data[:])
+    assert data.ndim in (2, 3)
 
     # Transpose the data to match python axis order.
-    if data.ndim == 3:
-        data = np.flip(data, axis=1)
-    else:
-        data = np.flip(data, axis=0)
-
+    data = np.flip(data, axis=1) if data.ndim == 3 else np.flip(data, axis=0)
     return data, voxel_size

synaptic_reconstruction/napari.yaml

@@ -27,6 +27,9 @@ contributions:
     - id: synaptic_reconstruction.sample_data_tem_2d
       python_name: synaptic_reconstruction.sample_data:sample_data_tem_2d
       title: Load TEM 2D sample data
+    - id: synaptic_reconstruction.sample_data_tem_tomo
+      python_name: synaptic_reconstruction.sample_data:sample_data_tem_tomo
+      title: Load TEM Tomo sample data
 
   readers:
     - command: synaptic_reconstruction.file_reader
@@ -50,3 +53,6 @@ contributions:
     - command: synaptic_reconstruction.sample_data_tem_2d
       display_name: TEM 2D Sample Data
       key: synapse-net-tem-2d
+    - command: synaptic_reconstruction.sample_data_tem_tomo
+      display_name: TEM Tomo Sample Data
+      key: synapse-net-tem-tomo

synaptic_reconstruction/sample_data.py

@@ -8,16 +8,18 @@ def get_sample_data(name: str) -> str:
     """Get the filepath to SynapseNet sample data, stored as mrc file.
 
     Args:
-        name: The name of the sample data. Currently, we only provide the 'tem_2d' sample data.
+        name: The name of the sample data. Currently, we only provide 'tem_2d' and 'tem_tomo'.
 
     Returns:
         The filepath to the downloaded sample data.
     """
     registry = {
         "tem_2d.mrc": "3c6f9ff6d7673d9bf2fd46c09750c3c7dbb8fa1aa59dcdb3363b65cc774dcf28",
+        "tem_tomo.mrc": "24af31a10761b59fa6ad9f0e763f8f084304e4f31c59b482dd09dde8cd443ed7",
     }
     urls = {
         "tem_2d.mrc": "https://owncloud.gwdg.de/index.php/s/5sAQ0U4puAspcHg/download",
+        "tem_tomo.mrc": "https://owncloud.gwdg.de/index.php/s/NeP7gOv76Vj26lm/download",
     }
     key = f"{name}.mrc"
 
@@ -36,9 +38,17 @@ def get_sample_data(name: str) -> str:
     return file_path
 
 
-def sample_data_tem_2d():
-    file_path = get_sample_data("tem_2d")
+def _sample_data(name):
+    file_path = get_sample_data(name)
     data, voxel_size = read_mrc(file_path)
     metadata = {"file_path": file_path, "voxel_size": voxel_size}
-    add_image_kwargs = {"name": "tem_2d", "metadata": metadata, "colormap": "gray"}
+    add_image_kwargs = {"name": name, "metadata": metadata, "colormap": "gray"}
     return [(data, add_image_kwargs)]
+
+
+def sample_data_tem_2d():
+    return _sample_data("tem_2d")
+
+
+def sample_data_tem_tomo():
+    return _sample_data("tem_tomo")

test/test_file_utils.py

@@ -0,0 +1,46 @@
+import unittest
+
+import numpy as np
+from elf.io import open_file
+from synaptic_reconstruction.sample_data import get_sample_data
+
+
+class TestFileUtils(unittest.TestCase):
+
+    def test_read_mrc_2d(self):
+        from synaptic_reconstruction.file_utils import read_mrc
+
+        file_path = get_sample_data("tem_2d")
+        data, voxel_size = read_mrc(file_path)
+
+        with open_file(file_path, "r") as f:
+            data_exp = f["data"][:]
+
+        self.assertTrue(data.shape, data_exp.shape)
+        self.assertTrue(np.allclose(data, data_exp))
+
+        resolution = 0.592
+        self.assertTrue(np.isclose(voxel_size["x"], resolution))
+        self.assertTrue(np.isclose(voxel_size["y"], resolution))
+        self.assertTrue(np.isclose(voxel_size["z"], 0.0))
+
+    def test_read_mrc_3d(self):
+        from synaptic_reconstruction.file_utils import read_mrc
+
+        file_path = get_sample_data("tem_tomo")
+        data, voxel_size = read_mrc(file_path)
+
+        with open_file(file_path, "r") as f:
+            data_exp = f["data"][:]
+
+        self.assertTrue(data.shape, data_exp.shape)
+        self.assertTrue(np.allclose(data, data_exp))
+
+        resolution = 1.554
+        self.assertTrue(np.isclose(voxel_size["x"], resolution))
+        self.assertTrue(np.isclose(voxel_size["y"], resolution))
+        self.assertTrue(np.isclose(voxel_size["z"], resolution))
+
+
+if __name__ == "__main__":
+    unittest.main()