Add parser for parsing saved Mark objects from MATLAB files

packages/scratch-core/src/conversion/export/mark.py

@@ -8,8 +8,9 @@
 from pathlib import Path
 from typing import Annotated, Any
 
+import numpy as np
 from pydantic import Field
-
+from scipy.io import loadmat
 from container_models.base import ConfigBaseModel
 from container_models.scan_image import ScanImage
 from conversion.data_formats import Mark, MarkType
@@ -50,6 +51,22 @@ def save_mark(mark: Mark, path: Path) -> None:
     save_as_compressed_binary(array=mark.scan_image.data, file_path=path)
 
 
+def load_mark_from_mat_file(path: Path) -> Mark:
+    """Load a `Mark` object from a .mat file."""
+    parsed = loadmat(str(path))
+    container = parsed["data_struct"][0, 0]
+    mark = Mark(
+        scan_image=ScanImage(
+            data=np.asarray(container["depth_data"], dtype=np.float64),
+            scale_x=float(container["xdim"][0]),
+            scale_y=float(container["ydim"][0]),
+        ),
+        mark_type=MarkType(str(container["mark_type"][0]).lower()),
+        # TODO: Parse `center` and `meta_data` from data struct
+    )
+    return mark
+
+
 def load_mark_from_path(path: Path, stem: str) -> Mark:
     """
     Load a Mark object from JSON and NPZ files.

packages/scratch-core/tests/conftest.py

@@ -50,6 +50,12 @@ def baseline_images_dir() -> Path:
     return TEST_ROOT / "resources" / "baseline_images"
 
 
+@pytest.fixture(scope="session")
+def matlab_marks_dir() -> Path:
+    """Path to `Mark` instances saved as .mat file."""
+    return TEST_ROOT / "resources" / "matlab_marks"
+
+
 @pytest.fixture(scope="session")
 def scan_image_array(baseline_images_dir: Path) -> DepthData:
     """Build a fixture with ground truth image data."""

packages/scratch-core/tests/conversion/export/test_mark.py

@@ -1,13 +1,18 @@
 import json
-from pathlib import PosixPath
+from pathlib import PosixPath, Path
 
 import numpy as np
 import pytest
 from scipy.constants import micro
 
 from container_models.scan_image import ScanImage
 from conversion.data_formats import Mark, MarkType
-from conversion.export.mark import ExportedMarkData, load_mark_from_path, save_mark
+from conversion.export.mark import (
+    ExportedMarkData,
+    load_mark_from_path,
+    save_mark,
+    load_mark_from_mat_file,
+)
 
 
 @pytest.fixture()
@@ -264,3 +269,16 @@ def test_multiple_marks_in_directory(
         assert loaded_mark2.mark_type == MarkType.CHAMBER_IMPRESSION
         assert loaded_mark1.meta_data["id"] == 1
         assert loaded_mark2.meta_data["id"] == 2
+
+    def test_load_mark_from_mat_file(self, tmp_path: PosixPath, matlab_marks_dir: Path):
+        """Test that we can build a `Mark` instance from a .mat file."""
+        # Arrange
+        path = matlab_marks_dir / "processed.mat"
+        # Act
+        mark = load_mark_from_mat_file(path)
+        # Asserts
+        assert mark.mark_type == MarkType.BREECH_FACE_IMPRESSION
+        assert mark.scan_image.scale_x == pytest.approx(3.5e-6)
+        assert mark.scan_image.scale_y == pytest.approx(3.5e-6)
+        assert (mark.scan_image.width, mark.scan_image.height) == (1060, 1060)
+        assert np.any(mark.scan_image.valid_mask)