calc mpp with openslide tiff tags (#166)

SBU-BMI · Jul 24, 2023 · 8dbb90f · 8dbb90f
1 parent 0338d76
commit 8dbb90f
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Showing 2 changed files with 41 additions and 2 deletions.
diff --git a/tests/test_all.py b/tests/test_all.py
@@ -293,8 +293,13 @@ def test_convert_to_sbu():
     ["patch_size", "patch_spacing"],
     [(256, 0.25), (256, 0.50), (350, 0.25), (100, 0.3), (100, 0.5)],
 )
+@pytest.mark.parametrize("backend", ["openslide", "tiffslide"])
 def test_patch_cli(
-    patch_size: int, patch_spacing: float, tmp_path: Path, tiff_image: Path
+    patch_size: int,
+    patch_spacing: float,
+    backend: str,
+    tmp_path: Path,
+    tiff_image: Path,
 ):
     """Test of 'wsinfer patch'."""
     orig_slide_size = 4096
@@ -305,6 +310,8 @@ def test_patch_cli(
     result = runner.invoke(
         cli,
         [
+            "--backend",
+            backend,
             "patch",
             "--wsi-dir",
             str(tiff_image.parent),
@@ -342,7 +349,7 @@ def test_patch_cli(
     assert np.array_equal(expected_coords, coords)
 
 
-# FIXME: parametrize thie test across our models.
+# FIXME: parametrize this test across our models.
 def test_jit_compile():
     w = get_registered_model("breast-tumor-resnet34.tcga-brca")
     model = get_pretrained_torch_module(w)

diff --git a/wsinfer/wsi.py b/wsinfer/wsi.py
@@ -126,6 +126,38 @@ def _get_mpp_openslide(slide_path: str | Path) -> tuple[float, float]:
                 return mppx, mppy
             except Exception as err:
                 logger.debug(f"Exception caught while converting to float: {err}")
+    elif (
+        "tiff.ResolutionUnit" in slide.properties
+        and "tiff.XResolution" in slide.properties
+        and "tiff.YResolution" in slide.properties
+    ):
+        logger.debug("Attempting to read spacing using openslide and tiff tags")
+        resunit = slide.properties["tiff.ResolutionUnit"].lower()
+        if resunit not in {"millimeter", "centimeter", "cm", "inch"}:
+            raise CannotReadSpacing(f"unknown resolution unit: '{resunit}'")
+        scale = {
+            "inch": 25400.0,
+            "centimeter": 10000.0,
+            "cm": 10000.0,
+            "millimeter": 1000.0,
+        }.get(resunit, None)
+
+        x_resolution = float(slide.properties["tiff.XResolution"])
+        y_resolution = float(slide.properties["tiff.YResolution"])
+
+        if scale is not None:
+            try:
+                mpp_x = scale / x_resolution
+                mpp_y = scale / y_resolution
+                return mpp_x, mpp_y
+            except ArithmeticError as err:
+                raise CannotReadSpacing(
+                    f"error in math {scale} / {x_resolution}"
+                    f" or {scale} / {y_resolution}"
+                ) from err
+        else:
+            raise CannotReadSpacing()
+
     else:
         logger.debug(
             "Properties of the OpenSlide object does not contain keys"