Clean up

lazyslide/__init__.py

@@ -1,10 +1,7 @@
 """Working with whole slide imaging"""
 __version__ = "0.1.0"
 
-from .wsi import WSI, create_tiles_coords, filter_tiles
-from .readers.utils import get_crop_left_top_width_height
-from .cv_mods import TissueDetectionHE
-from .h5 import H5File
+from .wsi import WSI
 from .utils import get_reader
 
 

lazyslide/h5.py

@@ -2,14 +2,12 @@
 from pathlib import Path
 
 import h5py
-import numpy as np
 
 from .utils import TileOps
 
 
 class H5File:
     """A class that handle storage and reading of h5 file"""
-    # TODO: Add options to save contours and holes
 
     COORDS_KEY = "coords"
     MASKS_KEY = "masks"

lazyslide/utils.py

@@ -1,11 +1,19 @@
 from dataclasses import dataclass, field
+from itertools import tee
 from typing import Type
 
 from .readers.base import ReaderBase
 from .readers.vips import VipsReader
 from .readers.openslide import OpenSlideReader
 
 
+def pairwise(iterable):
+    # pairwise('ABCDEFG') --> AB BC CD DE EF FG
+    a, b = tee(iterable)
+    next(b, None)
+    return zip(a, b)
+
+
 def get_reader(reader="auto") -> Type[ReaderBase]:
     """Return an available backend"""
 

lazyslide/wsi.py

@@ -1,7 +1,6 @@
 from __future__ import annotations
 
 import warnings
-from itertools import tee
 from numbers import Integral
 from pathlib import Path
 from typing import Iterable
@@ -11,20 +10,12 @@
 from matplotlib import pyplot as plt
 from matplotlib.collections import PatchCollection
 from matplotlib.patches import Rectangle
-from numba import njit, prange
+from numba import njit
 
 from .cv_mods import TissueDetectionHE
 from .h5 import H5File
 from .readers.base import ReaderBase
-from .torch_dataset import WSIDataset
-from .utils import get_reader, TileOps
-
-
-def pairwise(iterable):
-    # pairwise('ABCDEFG') --> AB BC CD DE EF FG
-    a, b = tee(iterable)
-    next(b, None)
-    return zip(a, b)
+from .utils import pairwise, get_reader, TileOps
 
 
 @njit
@@ -576,9 +567,8 @@ def plot_mask(self,
             fig.savefig(savefig, **save_kws)
         return ax
 
-    def to_dataset(self, transform=None, run_pretrained=False, **kwargs):
-        # TODO: Allow resize transform on-the-fly to fit into different models
-        return WSIDataset(self, transform=transform, run_pretrained=run_pretrained, **kwargs)
+    # def to_dataset(self, transform=None, run_pretrained=False, **kwargs):
+    #     return WSIDataset(self, transform=transform, run_pretrained=run_pretrained, **kwargs)
 
     def get_patch(self, left, top, width, height, level=0, **kwargs):
         return self.reader.get_patch(left, top, width, height, level=level, **kwargs)

pyproject.toml

@@ -30,6 +30,9 @@ dependencies = [
 vips = [
     "pyvips",
 ]
+all = [
+    "ncls"
+]
 dev = [
     "flit",
     "pytest >=2.7.3",