handle symlinked slides dirs

fixes #214

Author: kaczmarj

tests/test_all.py

@@ -532,3 +532,28 @@ def test_issue_203(tiff_image: Path) -> None:
         img = oslide.read_region((w, h), level=0, size=(256, 256))
         assert img.size == (256, 256)
         assert np.allclose(np.array(img), 0)
+
+
+def test_issue_214(tmp_path: Path, tiff_image: Path) -> None:
+    """Test that symlinked slides don't mess things up."""
+    link = tmp_path / "forlinks" / "arbitrary-link-name.tiff"
+    link.parent.mkdir(parents=True)
+    link.symlink_to(tiff_image)
+
+    runner = CliRunner()
+    results_dir = tmp_path / "inference"
+    result = runner.invoke(
+        cli,
+        [
+            "run",
+            "--wsi-dir",
+            str(link.parent),
+            "--results-dir",
+            str(results_dir),
+            "--model",
+            "breast-tumor-resnet34.tcga-brca",
+        ],
+    )
+    assert result.exit_code == 0
+    assert (results_dir / "patches" / link.with_suffix(".h5").name).exists()
+    assert (results_dir / "model-outputs-csv" / link.with_suffix(".csv").name).exists()

wsinfer/cli/convert_csv_to_sbubmi.py

@@ -249,21 +249,17 @@ def get_color(row: pd.Series) -> tuple[float, float, float]:
 @click.command()
 @click.argument(
     "results_dir",
-    type=click.Path(
-        exists=True, file_okay=False, dir_okay=True, path_type=Path, resolve_path=True
-    ),
+    type=click.Path(exists=True, file_okay=False, dir_okay=True, path_type=Path),
 )
 @click.argument(
     "output",
-    type=click.Path(exists=False, path_type=Path, resolve_path=True),
+    type=click.Path(exists=False, path_type=Path),
 )
 @click.option(
     "--wsi-dir",
     required=True,
     help="Directory with whole slide images.",
-    type=click.Path(
-        exists=True, file_okay=False, dir_okay=True, path_type=Path, resolve_path=True
-    ),
+    type=click.Path(exists=True, file_okay=False, dir_okay=True, path_type=Path),
 )
 @click.option("--execution-id", required=True, help="Unique execution ID for this run.")
 @click.option("--study-id", required=True, help="Study ID, like TCGA-BRCA.")

wsinfer/cli/infer.py

@@ -188,15 +188,15 @@ def get_stdout(args: list[str]) -> str:
 @click.option(
     "-i",
     "--wsi-dir",
-    type=click.Path(exists=True, file_okay=False, path_type=Path, resolve_path=True),
+    type=click.Path(exists=True, file_okay=False, path_type=Path),
     required=True,
     help="Directory containing whole slide images. This directory can *only* contain"
     " whole slide images.",
 )
 @click.option(
     "-o",
     "--results-dir",
-    type=click.Path(file_okay=False, path_type=Path, resolve_path=True),
+    type=click.Path(file_okay=False, path_type=Path),
     required=True,
     help="Directory to store results. If directory exists, will skip"
     " whole slides for which outputs exist.",
@@ -212,7 +212,7 @@ def get_stdout(args: list[str]) -> str:
 @click.option(
     "-c",
     "--config",
-    type=click.Path(exists=True, dir_okay=False, path_type=Path, resolve_path=True),
+    type=click.Path(exists=True, dir_okay=False, path_type=Path),
     help=(
         "Path to configuration for the trained model. Use this option if the"
         " model weights are not registered in wsinfer. Mutually exclusive with"
@@ -222,7 +222,7 @@ def get_stdout(args: list[str]) -> str:
 @click.option(
     "-p",
     "--model-path",
-    type=click.Path(exists=True, dir_okay=False, path_type=Path, resolve_path=True),
+    type=click.Path(exists=True, dir_okay=False, path_type=Path),
     help=(
         "Path to the pretrained model. Use only when --config is passed. Mutually "
         "exclusive with --model."
@@ -349,9 +349,6 @@ def run(
             "--config and --model-path must both be set if one is set."
         )
 
-    wsi_dir = wsi_dir.resolve()
-    results_dir = results_dir.resolve()
-
     if not wsi_dir.exists():
         raise FileNotFoundError(f"Whole slide image directory not found: {wsi_dir}")
 

wsinfer/cli/patch.py

@@ -11,15 +11,15 @@
 @click.option(
     "-i",
     "--wsi-dir",
-    type=click.Path(exists=True, file_okay=False, path_type=Path, resolve_path=True),
+    type=click.Path(exists=True, file_okay=False, path_type=Path),
     required=True,
     help="Directory containing whole slide images. This directory can *only* contain"
     " whole slide images.",
 )
 @click.option(
     "-o",
     "--results-dir",
-    type=click.Path(file_okay=False, path_type=Path, resolve_path=True),
+    type=click.Path(file_okay=False, path_type=Path),
     required=True,
     help="Directory to store patch results. If directory exists, will skip"
     " whole slides for which outputs exist.",
@@ -32,41 +32,41 @@
     help="Physical spacing of the patch in micrometers per pixel.",
 )
 @click.option(
-    "--thumbsize",
+    "--seg-thumbsize",
     default=(2048, 2048),
     type=(int, int),
     help="The size of the slide thumbnail (in pixels) used for tissue segmentation."
     " The aspect ratio is preserved, and the longest side will have length"
     " max(thumbsize).",
 )
 @click.option(
-    "--median-filter-size",
+    "--seg-median-filter-size",
     default=7,
     type=click.IntRange(min=3),
     help="The kernel size for median filtering. Must be greater than 1 and odd.",
 )
 @click.option(
-    "--binary-threshold",
+    "--seg-binary-threshold",
     default=7,
     type=click.IntRange(min=1),
     help="The threshold for image binarization.",
 )
 @click.option(
-    "--closing-kernel-size",
+    "--seg-closing-kernel-size",
     default=6,
     type=click.IntRange(min=1),
     help="The kernel size for binary closing (morphological operation).",
 )
 @click.option(
-    "--min-object-size-um2",
+    "--seg-min-object-size-um2",
     default=200**2,
     type=click.FloatRange(min=0),
     help="The minimum size of an object to keep during tissue detection. If a"
     " contiguous object is smaller than this area, it replaced with background."
     " The default is 200um x 200um. The units of this argument are microns squared.",
 )
 @click.option(
-    "--min-hole-size-um2",
+    "--seg-min-hole-size-um2",
     default=190**2,
     type=click.FloatRange(min=0),
     help="The minimum size of a hole to keep as a hole. If a hole is smaller than this"
@@ -78,23 +78,23 @@ def patch(
     results_dir: str,
     patch_size_px: int,
     patch_spacing_um_px: float,
-    thumbsize: tuple[int, int],
-    median_filter_size: int,
-    binary_threshold: int,
-    closing_kernel_size: int,
-    min_object_size_um2: float,
-    min_hole_size_um2: float,
+    seg_thumbsize: tuple[int, int],
+    seg_median_filter_size: int,
+    seg_binary_threshold: int,
+    seg_closing_kernel_size: int,
+    seg_min_object_size_um2: float,
+    seg_min_hole_size_um2: float,
 ) -> None:
     """Patch a directory of whole slide iamges."""
     segment_and_patch_directory_of_slides(
         wsi_dir=wsi_dir,
         save_dir=results_dir,
         patch_size_px=patch_size_px,
         patch_spacing_um_px=patch_spacing_um_px,
-        thumbsize=thumbsize,
-        median_filter_size=median_filter_size,
-        binary_threshold=binary_threshold,
-        closing_kernel_size=closing_kernel_size,
-        min_object_size_um2=min_object_size_um2,
-        min_hole_size_um2=min_hole_size_um2,
+        thumbsize=seg_thumbsize,
+        median_filter_size=seg_median_filter_size,
+        binary_threshold=seg_binary_threshold,
+        closing_kernel_size=seg_closing_kernel_size,
+        min_object_size_um2=seg_min_object_size_um2,
+        min_hole_size_um2=seg_min_hole_size_um2,
     )

wsinfer/patchlib/__init__.py

@@ -85,8 +85,8 @@ def segment_and_patch_one_slide(
     None
     """
 
-    save_dir = Path(save_dir).resolve()
-    slide_path = Path(slide_path).resolve()
+    save_dir = Path(save_dir)
+    slide_path = Path(slide_path)
     slide_prefix = slide_path.stem
 
     logger.info(f"Segmenting and patching slide {slide_path}")