lavlab-shell 0.2.0__tar.gz → 0.3.0__tar.gz

lavlab_shell-0.3.0/.github/workflows/build.yml

@@ -0,0 +1,54 @@
+name: Build Wheel using Hatch
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+
+jobs:
+  build-wheel:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: '3.12'
+
+      - name: Install build tools
+        run: |
+          python -m pip install --upgrade pip setuptools wheel
+          python -m pip install "virtualenv==20.23.1"
+          python -m pip install --upgrade hatch
+
+      - name: Build wheel with hatch
+        run: hatch build
+      - name: Upload wheel
+        uses: actions/upload-artifact@v4
+        with:
+          name: wheel
+          path: dist/*.whl
+
+              - uses: actions/checkout@v4
+
+              - name: Build Docker image (hatch stage)
+                uses: docker/build-push-action@v4
+                with:
+                  context: .
+                  file: ./Dockerfile
+                  target: hatch
+                  tags: shell-ci:latest
+
+              - name: Run build inside Docker container
+                run: |
+                  docker run --rm \
+                    -v "${{ github.workspace }}:/app" \
+                    -w /app \
+                    shell-ci:latest build
+
+              - name: Upload wheel
+                uses: actions/upload-artifact@v4
+                with:
+                  name: wheel
+                  path: dist/*.whl

{lavlab_shell-0.2.0 → lavlab_shell-0.3.0}/.github/workflows/publish.yml

@@ -17,17 +17,20 @@ jobs:
       - name: Checkout
         uses: actions/checkout@v4
 
-      - name: Set up Python 3.12
-        uses: actions/setup-python@v5
+      - name: Build Docker image (hatch stage)
+        uses: docker/build-push-action@v4
         with:
-          python-version: "3.12"
+          context: .
+          file: ./Dockerfile
+          target: hatch
+          tags: shell-ci:latest
 
-      - name: Install build tools
+      - name: Build wheel and sdist inside Docker
         run: |
-          python -m pip install --upgrade pip setuptools wheel hatch
-
-      - name: Build wheel and sdist
-        run: hatch build
+          docker run --rm \
+            -v "${{ github.workspace }}:/app" \
+            -w /app \
+            shell-ci:latest build
 
       - name: Publish to PyPI
         uses: pypa/gh-action-pypi-publish@release/v1

{lavlab_shell-0.2.0 → lavlab_shell-0.3.0}/.github/workflows/pytest.yml

@@ -10,11 +10,19 @@ jobs:
     steps:
       - uses: actions/checkout@v4
 
-      - name: Build Docker image
-        run: docker build --target hatch -t shell:hatch .
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: '3.12'
+
+      - name: Install test dependencies
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install pytest pytest-cov coverage[toml]>=6.2
 
       - name: Run pytest and generate coverage report
-        run: docker run --rm -e HATCH_ENV=test -v "${{ github.workspace }}:/app" shell:hatch cov
+        run: |
+          pytest --cov=src --cov-report=xml:coverage.xml
 
       - name: Upload coverage artifact
         uses: actions/upload-artifact@v4

{lavlab_shell-0.2.0 → lavlab_shell-0.3.0}/Dockerfile

@@ -22,7 +22,9 @@ COPY src/ src/
 RUN chown -R vscode:vscode /app
 
 FROM base AS hatch
-RUN pip3 install --no-cache-dir hatch uv
+RUN pip3 install --no-cache-dir --upgrade pip setuptools wheel
+RUN pip3 install --no-cache-dir 'virtualenv<21'
+RUN pip3 install --no-cache-dir --upgrade hatch hatch-uv
 ENV HATCH_ENV=default
 ENTRYPOINT ["hatch", "run"]
 
@@ -32,7 +34,7 @@ COPY requirements.txt ./
 COPY tests/ tests/
 COPY docs/ docs/
 COPY mkdocs.yml ./
-RUN pip3 install --no-cache-dir hatch \
+RUN pip3 install --no-cache-dir hatch hatch-uv \
     && hatch build \
     && pip3 install --no-cache-dir $(find /app -name 'requirement*.txt' -exec echo -n '-r {} ' \;)
 USER vscode

{lavlab_shell-0.2.0 → lavlab_shell-0.3.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: lavlab-shell
-Version: 0.2.0
+Version: 0.3.0
 Summary: SHELL Highlights Epithelium and Lumen Locations — whole-slide H&E segmentation
 Project-URL: Documentation, https://github.com/laviolette-lab/shell#readme
 Project-URL: Issues, https://github.com/laviolette-lab/shell/issues
@@ -21,6 +21,7 @@ Requires-Dist: monai
 Requires-Dist: numpy
 Requires-Dist: openslide-python
 Requires-Dist: pyvips
+Requires-Dist: scikit-image
 Requires-Dist: scipy
 Requires-Dist: torch
 Provides-Extra: omero

{lavlab_shell-0.2.0 → lavlab_shell-0.3.0}/pyproject.toml

@@ -33,6 +33,7 @@ dependencies = [
     "pyvips",
     "openslide-python",
     "macenko-pca",
+    "scikit-image",
 ]
 
 [project.optional-dependencies]
@@ -53,27 +54,25 @@ path = "src/shell/__about__.py"
 [tool.hatch.build.targets.wheel]
 packages = ["src/shell"]
 
-[tool.hatch.env]
-requires = ["hatch-pip-compile"]
-
 [tool.hatch.envs.default]
-type = "pip-compile"
-pip-compile-resolver = "uv"
-pip-compile-hashes = false
-pip-compile-args = ["--allow-unsafe", "--universal"]
-dependencies = ["setuptools==82.0.0"]
+dependencies = ["setuptools>=82.0.0"]
 
 [tool.hatch.envs.default.scripts]
 build = "hatch build && chmod -R 777 dist/*"
 
 [tool.hatch.envs.test]
-dependencies = ["pytest", "pytest-cov", "coverage[toml]>=6.2", "setuptools==82.0.0"]
+dependencies = [
+    "pytest",
+    "pytest-cov",
+    "coverage[toml]>=6.2",
+    "setuptools>=82.0.0",
+]
 [tool.hatch.envs.test.scripts]
 test = "pytest {args:tests}"
 cov = "pytest --cov=src --cov-report=term-missing --cov-report=xml {args:tests}"
 
 [tool.hatch.envs.lint]
-dependencies = ["ruff>=0.4.0", "setuptools==82.0.0"]
+dependencies = ["ruff>=0.4.0", "setuptools>=82.0.0"]
 [tool.hatch.envs.lint.scripts]
 check = "ruff check src tests"
 format = "ruff format src tests"
@@ -82,7 +81,7 @@ fix = "ruff check --fix src tests"
 all = ["format", "fix", "check"]
 
 [tool.hatch.envs.types]
-dependencies = ["mypy>=1.0.0", "setuptools==82.0.0"]
+dependencies = ["mypy>=1.0.0", "setuptools>=82.0.0"]
 [tool.hatch.envs.types.scripts]
 check = "mypy --install-types --non-interactive {args:src/shell tests}"
 
@@ -95,7 +94,7 @@ dependencies = [
     "mkdocs-minify-plugin",
     "mkdocs-material-extensions",
     "mkdocs-git-revision-date-localized-plugin",
-    "setuptools==82.0.0",
+    "setuptools>=82.0.0",
 ]
 [tool.hatch.envs.docs.scripts]
 build-docs = "mkdocs build"

{lavlab_shell-0.2.0 → lavlab_shell-0.3.0}/src/shell/__about__.py

@@ -3,4 +3,4 @@
 # SPDX-License-Identifier: MIT
 """Version information for shell."""
 
-__version__ = "0.2.0"
+__version__ = "0.3.0"

{lavlab_shell-0.2.0 → lavlab_shell-0.3.0}/src/shell/cli.py

@@ -98,12 +98,6 @@ def build_parser() -> argparse.ArgumentParser:
         default=None,
         help="Optional: also save the intermediate EHO image.",
     )
-    infer_p.add_argument(
-        "--stain-downsample",
-        type=int,
-        default=4,
-        help="Downsample factor for stain parameter estimation.",
-    )
     infer_p.add_argument(
         "--device",
         type=str,
@@ -138,7 +132,6 @@ def build_parser() -> argparse.ArgumentParser:
         default=1.0,
         help="Desired output resolution (um/pixel)",
     )
-    omero_p.add_argument("--max-dim", type=int, default=None)
     omero_p.add_argument(
         "--model-path",
         type=str,
@@ -283,7 +276,6 @@ def main(argv: list[str] | None = None) -> int:
             target_mpp=args.target_mpp,
             mpp=args.mpp,
             save_eho=args.save_eho,
-            stain_downsample=args.stain_downsample,
             device=args.device,
         )
 
@@ -311,7 +303,6 @@ def main(argv: list[str] | None = None) -> int:
             model_version=args.model_version,
             output_path=args.output,
             target_mpp=args.target_mpp,
-            max_dim=args.max_dim,
             group_id=args.group_id,
             save_eho=args.save_eho,
             no_tissue_crop=args.no_tissue_crop,

{lavlab_shell-0.2.0 → lavlab_shell-0.3.0}/src/shell/infer_omero_wsi.py

@@ -1095,7 +1095,6 @@ def infer_omero_wsi(
     model_path: str | None = None,
     output_path: str,
     target_mpp: float = 1.0,
-    max_dim: int | None = None,
     group_id: int | None = None,
     save_eho: str | None = None,
     no_tissue_crop: bool = False,
@@ -1146,8 +1145,6 @@ def infer_omero_wsi(
         Where to save the prediction image (format from extension).
     target_mpp : float
         Desired microns-per-pixel.
-    max_dim : int or None
-        Clamp the longest output dimension.
     group_id : int or None
         OMERO group to switch to.
     save_eho : str or None
@@ -1267,13 +1264,6 @@ def infer_omero_wsi(
         out_w = max(1, round(best_lsz_x * sx))
         out_h = max(1, round(best_lsz_y * sy))
 
-        if max_dim is not None and (out_w > max_dim or out_h > max_dim):
-            clamp = min(max_dim / out_w, max_dim / out_h)
-            out_w = max(1, round(out_w * clamp))
-            out_h = max(1, round(out_h * clamp))
-            sx *= clamp
-            sy *= clamp
-
         # Native tile size at best level
         probe2 = conn.c.sf.createRawPixelsStore()  # type: ignore[union-attr]
         try:

{lavlab_shell-0.2.0 → lavlab_shell-0.3.0}/src/shell/infer_wsi.py

@@ -23,9 +23,9 @@ import gc
 import logging
 import os
 import warnings
+from types import ModuleType
 
 import numpy as np
-import openslide
 
 # shell.inference and shell.model load torch at their module level.
 # pyvips must come *after* them so PyTorch initialises its thread-pool
@@ -34,17 +34,16 @@ import openslide
 # own the same OpenMP/GCD thread infrastructure.
 from shell.inference import run_inference
 from shell.model import build_model
-from shell.preprocessing import (
-    apply_eho_chunked,
-    detect_background,
-    estimate_stain_params,
-)
+from shell.transforms import EHOd, TissueMaskd
 
 # pyvips intentionally after torch-loading shell imports above (macOS safety)
 import pyvips  # isort: skip
 
 log = logging.getLogger(__name__)
 
+_OPENSLIDE_MODULE: ModuleType | None = None
+_OPENSLIDE_IMPORT_FAILED: bool = False
+
 # ---------------------------------------------------------------------------
 # Default parameters
 # ---------------------------------------------------------------------------
@@ -54,12 +53,34 @@ TARGET_MPP: float = 1.0
 # ---------------------------------------------------------------------------
 # Helpers
 # ---------------------------------------------------------------------------
+def _get_openslide() -> ModuleType | None:
+    """Import and cache the ``openslide`` module lazily.
+
+    Returns ``None`` when openslide is unavailable.
+    """
+    global _OPENSLIDE_MODULE, _OPENSLIDE_IMPORT_FAILED
+    if _OPENSLIDE_IMPORT_FAILED:
+        return None
+    if _OPENSLIDE_MODULE is None:
+        try:
+            import openslide
+        except Exception:
+            _OPENSLIDE_IMPORT_FAILED = True
+            return None
+        _OPENSLIDE_MODULE = openslide
+    return _OPENSLIDE_MODULE
+
+
 def _read_mpp_from_openslide(image_path: str) -> tuple[float, float] | None:
     """Try to extract um/px from OpenSlide metadata.
 
     Returns ``(mpp_x, mpp_y)`` or ``None`` if the format is unsupported
     or the metadata is missing.
     """
+    openslide = _get_openslide()
+    if openslide is None:
+        return None
+
     try:
         slide = openslide.OpenSlide(image_path)
     except (
@@ -98,6 +119,15 @@ def _load_image(
         log.info("pyvips could not open %s; falling back to OpenSlide.", image_path)
 
     # --- attempt 2: openslide ---
+    openslide = _get_openslide()
+    if openslide is None:
+        msg = (
+            f"pyvips could not open '{image_path}', and OpenSlide is not available. "
+            "Install openslide-python (and OpenSlide runtime) or use a format "
+            "supported by pyvips."
+        )
+        raise ValueError(msg)
+
     try:
         slide = openslide.OpenSlide(image_path)
         dims = slide.dimensions  # (width, height)
@@ -129,6 +159,47 @@ def _vips_to_rgb_numpy(vips_img: pyvips.Image) -> np.ndarray:
     return vips_img.numpy()
 
 
+def _read_image_size(image_path: str) -> tuple[int, int]:
+    """Return ``(height, width)`` for *image_path*."""
+    try:
+        vips_img = pyvips.Image.new_from_file(image_path, access="sequential")
+        return int(vips_img.height), int(vips_img.width)
+    except pyvips.Error:
+        pass
+
+    openslide = _get_openslide()
+    if openslide is None:
+        msg = f"Could not determine image size for '{image_path}'."
+        raise ValueError(msg)
+
+    try:
+        slide = openslide.OpenSlide(image_path)
+        width, height = slide.dimensions
+        slide.close()
+        return int(height), int(width)
+    except (
+        openslide.OpenSlideUnsupportedFormatError,
+        openslide.OpenSlideError,
+    ) as exc:
+        msg = f"Could not determine image size for '{image_path}'."
+        raise ValueError(msg) from exc
+
+
+def _resize_label_map_nearest(
+    label_map: np.ndarray,
+    out_h: int,
+    out_w: int,
+) -> np.ndarray:
+    """Resize a label map to ``(out_h, out_w)`` using nearest-neighbour."""
+    in_h, in_w = label_map.shape[:2]
+    if in_h == out_h and in_w == out_w:
+        return label_map
+
+    y_idx = np.clip((np.arange(out_h) * in_h / out_h).astype(np.int64), 0, in_h - 1)
+    x_idx = np.clip((np.arange(out_w) * in_w / out_w).astype(np.int64), 0, in_w - 1)
+    return label_map[y_idx[:, None], x_idx[None, :]]
+
+
 # ---------------------------------------------------------------------------
 # Public API
 # ---------------------------------------------------------------------------
@@ -137,19 +208,23 @@ def preprocess_wsi(
     *,
     target_mpp: float = TARGET_MPP,
     mpp: float | None = None,
-    stain_downsample: int = 4,
-) -> np.ndarray:
+) -> tuple[np.ndarray, np.ndarray]:
     """Read a raw RGB image, scale to *target_mpp*, and produce an EHO image.
 
+    Uses the MONAI transform pipeline (``TissueMaskd`` → ``EHOd``) from
+    :mod:`shell.transforms`.
+
     :param image_path: path to an RGB image (TIFF, PNG, JPEG, etc.).
     :param target_mpp: desired microns-per-pixel.
     :param mpp: manual override for the source image um/px.  When
         ``None`` the value is read from slide metadata; if metadata is
         unavailable (e.g. plain PNG) a warning is emitted and scaling is
         skipped (the image is assumed to already be at *target_mpp*).
-    :param stain_downsample: downsample factor for stain parameter estimation.
-    :return: (H, W, 3) uint8 EHO image.
+    :return: tuple of (H, W, 3) uint8 EHO image and (H, W) bool tissue mask.
     """
+    from monai.data import MetaTensor
+    from monai.transforms import Compose
+
     # 1. Determine MPP
     if mpp is not None:
         mpp_x = mpp_y = float(mpp)
@@ -194,20 +269,26 @@ def preprocess_wsi(
             image_np = _vips_to_rgb_numpy(vips_tmp)
             del vips_tmp
 
-    # 4. Estimate stain parameters on a down-sampled copy
-    ds = stain_downsample
-    rgb_small = image_np[::ds, ::ds]
-    bg_small = detect_background(rgb_small)
-    sp = estimate_stain_params(rgb_small, bg_mask=bg_small)
-    del rgb_small, bg_small
+    # 4. Run MONAI transform pipeline: TissueMask → EHO
+    pipeline = Compose(
+        [
+            TissueMaskd(keys=["image"]),
+            EHOd(
+                keys=["image"],
+                tissue_mask_keys=["image_tissue_mask"],
+            ),
+        ]
+    )
+    data = pipeline({"image": MetaTensor(image_np)})
+    del image_np
     gc.collect()
 
-    # 5. Apply EHO colour transform (chunked)
-    eho = apply_eho_chunked(image_np, **sp)
-    del image_np, sp
-    gc.collect()
+    # EHOd outputs (3, H, W) MetaTensor — convert back to (H, W, 3) uint8
+    eho = data["image"].numpy().transpose(1, 2, 0).astype(np.uint8)
+    tissue_mask = data["image_tissue_mask"].numpy().squeeze() > 0
+    del data
 
-    return eho
+    return eho, tissue_mask
 
 
 def infer_wsi(
@@ -219,7 +300,6 @@ def infer_wsi(
     target_mpp: float = TARGET_MPP,
     mpp: float | None = None,
     save_eho: str | None = None,
-    stain_downsample: int = 4,
     device: str = "auto",
 ) -> np.ndarray:
     """Full pipeline: preprocess -> model -> label image.
@@ -234,9 +314,8 @@ def infer_wsi(
     :param mpp: manual source um/px override.  See
         :func:`preprocess_wsi` for details.
     :param save_eho: optional path to save the intermediate EHO image.
-    :param stain_downsample: downsample factor for stain estimation.
     :param device: ``"auto"``, ``"cpu"``, or ``"cuda"``.
-    :return: (H, W) uint8 label map.
+    :return: (H, W) uint8 label map at the original input resolution.
     """
     import torch
 
@@ -249,11 +328,10 @@ def infer_wsi(
             device = "cpu"
 
     # 1. Preprocess
-    eho = preprocess_wsi(
+    eho, tissue_mask = preprocess_wsi(
         input_path,
         target_mpp=target_mpp,
         mpp=mpp,
-        stain_downsample=stain_downsample,
     )
 
     if save_eho:
@@ -262,11 +340,20 @@ def infer_wsi(
 
     # 2. Load model + inference
     model = build_model(model_path, device, model_version=model_version)
-    label_map = run_inference(eho, model, device)
-    del eho, model
+    label_map = run_inference(
+        eho,
+        model,
+        device,
+        tissue_mask=tissue_mask,
+    )
+    del eho, model, tissue_mask
     gc.collect()
 
-    # 3. Save
+    # 3. Always return/save at original input resolution.
+    input_h, input_w = _read_image_size(input_path)
+    label_map = _resize_label_map_nearest(label_map, input_h, input_w)
+
+    # 4. Save
     os.makedirs(os.path.dirname(output_path) or ".", exist_ok=True)
     pyvips.Image.new_from_array(label_map).write_to_file(output_path)