Refactor

src/lazyslide/__init__.py

@@ -1,7 +1,10 @@
 """Efficient and Scalable Whole Slide Image (WSI) processing library."""
 __version__ = "0.1.0"
 
-from wsi_data import open_wsi
-import lazyslide.pp as pp
-import lazyslide.tl as tl
-import lazyslide.pl as pl
+from . import preprocess as pp
+from . import tools as tl
+from . import plotting as pl
+from . import models as models
+
+# Re-export
+from wsidata import open_wsi, agg_wsi

src/lazyslide/__main__.py

@@ -126,7 +126,7 @@ def feature(
     wsi = zs.open_wsi(slide, backed_file=output)
     print(f"Read slide file {slide}")
     print(f"Extract features using model {model}")
-    zs.tl.feature_extraction(wsi, model, slide_encoder=slide_encoder, device=device)
+    zs.tl.feature_extraction(wsi, model, slide_agg=slide_encoder, device=device)
     wsi.save()
     print(f"Write to {wsi.sdata.path}")
 
@@ -136,7 +136,7 @@ def agg_wsi(
     slide_table: Path = Argument(..., help="The slide table file"),
     output: Optional[str] = OUTPUT,
 ):
-    from wsi_data import agg_wsi
+    from wsidata import agg_wsi
 
     print(f"Read slide table {slide_table}")
     slides_table = pd.read_csv(slide_table)

src/lazyslide_cv/scorer/base.py → src/lazyslide/_cv/scorer/base.py

@@ -1,6 +1,6 @@
 from collections import namedtuple
 
-ScoreResult = namedtuple("Score", ["scores", "qc"])
+ScoreResult = namedtuple("ScoreResult", ["scores", "qc"])
 
 
 class ScorerBase:

src/lazyslide/utils.py → src/lazyslide/_utils.py

@@ -1,3 +1,8 @@
+from rich.console import Console
+
+console = Console()
+
+
 def get_torch_device():
     """Automatically get the torch device"""
     import torch
@@ -27,6 +32,7 @@ def default_pbar(disable=False):
         TaskProgressColumn(),
         TimeRemainingColumn(compact=True, elapsed_when_finished=True),
         disable=disable,
+        console=console,
     )
 
 

src/lazyslide/plotting/__init__.py

@@ -0,0 +1,2 @@
+from ._api import tissue, tiles
+from ._report import qc_summary

src/lazyslide/pl/api.py → src/lazyslide/plotting/_api.py

@@ -1,7 +1,7 @@
 import matplotlib.pyplot as plt
 
-from wsi_data import WSIData
-from .viewer import SlideViewer
+from wsidata import WSIData
+from ._viewer import SlideViewer
 from .._const import Key
 
 
@@ -14,6 +14,7 @@ def tissue(
     show_contours=True,
     show_origin=True,
     show_id=True,
+    show_bbox=None,
     render_size=1000,
     scale_bar=True,
     ax=None,
@@ -51,9 +52,9 @@ def tissue(
         :context: close-figs
 
         >>> import lazyslide as zs
-        >>> wsi = zs.WSI("https://github.com/camicroscope/Distro/raw/master/images/sample.svs")
-        >>> zs.pp.find_tissue(wsi)
-        >>> zs.pl.tissue(wsi)
+        >>> wsi = zs.open_wsi("https://github.com/camicroscope/Distro/raw/master/images/sample.svs")
+        >>> zs.preprocess.find_tissue(wsi)
+        >>> zs.plotting.tissue(wsi)
 
     """
     if ax is None:
@@ -71,8 +72,10 @@ def tissue(
         slide.add_origin(ax=ax)
     if show_id:
         slide.add_tissue_id(ax=ax)
-    if show_contours:
-        slide.add_contours_holes(ax=ax)
+        if show_bbox is None:
+            show_bbox = True
+    if show_contours or show_bbox:
+        slide.add_contours_holes(ax=ax, show_bbox=show_bbox, show_shape=show_contours)
     slide.add_title(title, ax=ax)
 
 
@@ -91,6 +94,7 @@ def tiles(
     show_contours=True,
     show_origin=True,
     show_id=False,
+    show_bbox=None,
     render_size=1000,
     alpha=0.9,
     marker="o",
@@ -172,11 +176,11 @@ def tiles(
         :context: close-figs
 
         >>> import lazyslide as zs
-        >>> wsi = zs.WSI("https://github.com/camicroscope/Distro/raw/master/images/sample.svs")
-        >>> zs.pp.find_tissue(wsi)
-        >>> zs.pp.tiles(wsi, 256, mpp=0.5)
-        >>> zs.pp.tiles_qc(wsi, scorers=["contrast"])
-        >>> zs.pl.tiles(wsi, tissue_id=0, show_grid=True, color='contrast')
+        >>> wsi = zs.open_wsi("https://github.com/camicroscope/Distro/raw/master/images/sample.svs")
+        >>> zs.preprocess.find_tissue(wsi)
+        >>> zs.preprocess.tiles(wsi, 256, mpp=0.5)
+        >>> zs.preprocess.tiles_qc(wsi, scorers=["contrast"])
+        >>> zs.plotting.tiles(wsi, tissue_id=0, show_grid=True, color='contrast')
 
     """
     if ax is None:
@@ -196,8 +200,10 @@ def tiles(
         slide.add_origin(ax=ax)
     if show_id:
         slide.add_tissue_id(ax=ax)
-    if show_contours:
-        slide.add_contours_holes(ax=ax)
+        if show_bbox is None:
+            show_bbox = True
+    if show_contours or show_bbox:
+        slide.add_contours_holes(ax=ax, show_bbox=show_bbox, show_shape=show_contours)
     if show_point:
         slide.add_points(
             feature_key=feature_key,