Clean up

lazyslide/__init__.py

@@ -2,12 +2,7 @@
 
 __version__ = "0.1.0"
 
-subpackages = [
-    "pp",
-    "tl",
-    "pl",
-    "get",
-]
+subpackages = ["pp", "tl", "pl", "get", "models"]
 
 
 __getattr__, __dir__, __all__ = lazy.attach(

lazyslide/__main__.py

@@ -1,39 +1,53 @@
-from typer import Typer
-from lazyslide import WSI
-
 import warnings
-import logging
-from rich.logging import RichHandler
+from typing import Optional
 
-FORMAT = "%(message)s"
-logging.basicConfig(
-    level="NOTSET", format=FORMAT, datefmt="[%X]", handlers=[RichHandler()]
-)
+from rich import print
+from typer import Typer, Argument, Option
+
+from lazyslide import WSI
 
-log = logging.getLogger("LAZYSLIDE")
-log.setLevel(logging.INFO)
 warnings.filterwarnings("ignore", category=UserWarning)
 
 app = Typer(pretty_exceptions_show_locals=False)
 
+# Define shared parameters
+SLIDE = Argument(..., help="The slide file to process")
+OUTPUT = Option(
+    None,
+    "--output",
+    "-o",
+    help="By default will write to a zarr file with the same name as the slide file",
+)
+
 
 @app.command()
-def tissue(slide: str):
+def tissue(
+    slide: str = SLIDE,
+    output: Optional[str] = OUTPUT,
+):
     from lazyslide.pp import find_tissue
 
-    log.info(f"Read slide file {slide}")
+    print(f"Read slide file {slide}")
     wsi = WSI(slide)
     find_tissue(wsi)
-    wsi.write()
-    log.info(f"Write to {wsi.file}")
+    wsi.write(output)
+    print(f"Write to {wsi.file}")
 
 
 @app.command()
-def tile(slide: str, tile_px: int, mpp: float):
+def tile(
+    slide: str = SLIDE,
+    tile_px: int = Argument(..., help="The size of the tile in pixels"),
+    stride_px: int = Option(
+        None, help="The stride of the tile in pixels, by default equal to tile_px"
+    ),
+    mpp: float = Option(None, help="The microns per pixel"),
+    output: Optional[str] = OUTPUT,
+):
     from lazyslide.pp import tiles
 
-    log.info(f"Read slide file {slide}")
+    print(f"Read slide file {slide}")
     wsi = WSI(slide)
-    tiles(wsi, tile_px=tile_px, mpp=mpp)
-    wsi.write()
-    log.info(f"Write to {wsi.file}")
+    tiles(wsi, tile_px=tile_px, stride_px=stride_px, mpp=mpp)
+    wsi.write(output)
+    print(f"Write to {wsi.file}")

lazyslide/tl/__init__.py

@@ -1,2 +1,4 @@
 from .features import feature_extraction
 from .tissue_props import tissue_props
+from .domain import anatomical_domain
+from .annotate import annotate

pyproject.toml

@@ -18,6 +18,7 @@ dependencies = [
     "numba",
     "opencv-python",
     "openslide-python",
+    "tiffslide",
     "matplotlib",
     "legendkit",
     "anndata",
@@ -40,15 +41,12 @@ all = [
     "torchstain",
 ]
 dev = [
-    "flit",
-    "pytest >=2.7.3",
-    "pytest-cov",
-    "pre-commit",
-    "ruff",
-    "mkdocs",
-    "mkdocs-material",
-    "mkdocstrings",
-    "mkdocstrings-python",
+    "hatchling",
+    "sphinx",
+    "sphinxawesome-theme",
+    "numpydoc",
+    "sphinx_design",
+    "sphinx_copybutton",
 ]
 
 # Define entry points