Merge pull request #6 from sumanthratna/master

Fix svs2dask_array

pathflowai/utils.py

@@ -84,40 +84,49 @@ def df2sql(df, sql_file, patch_size, mode='replace'):
 
 # https://github.com/qupath/qupath/wiki/Supported-image-formats
 def svs2dask_array(svs_file, tile_size=1000, overlap=0, remove_last=True, allow_unknown_chunksizes=False):
-	"""Convert SVS, TIF or TIFF to dask array.
-
-	Parameters
-	----------
-	svs_file:str
-		Image file.
-	tile_size:int
-		Size of chunk to be read in.
-	overlap:int
-		Do not modify, overlap between neighboring tiles.
-	remove_last:bool
-		Remove last tile because it has a custom size.
-	allow_unknown_chunksizes: bool
-		Allow different chunk sizes, more flexible, but slowdown.
-
-	Returns
-	-------
-	dask.array
-		Dask Array.
-
-	>>> arr=svs2dask_array(svs_file, tile_size=1000, overlap=0, remove_last=True, allow_unknown_chunksizes=False)
-	>>> arr2=arr.compute()
-	>>> arr3=to_pil(cv2.resize(arr2, dsize=(1440,700), interpolation=cv2.INTER_CUBIC))
-	>>> arr3.save(test_image_name)"""
-	img=openslide.open_slide(svs_file)
-	gen=deepzoom.DeepZoomGenerator(img, tile_size=tile_size, overlap=overlap, limit_bounds=True)
-	max_level = len(gen.level_dimensions)-1
-	n_tiles_x, n_tiles_y = gen.level_tiles[max_level]
-	get_tile = lambda i,j: np.array(gen.get_tile(max_level,(i,j))).transpose((1,0,2))
-	sample_tile = get_tile(0,0)
-	sample_tile_shape = sample_tile.shape
-	dask_get_tile = dask.delayed(get_tile, pure=True)
-	arr=da.concatenate([da.concatenate([da.from_delayed(dask_get_tile(i,j),sample_tile_shape,np.uint8) for j in range(n_tiles_y - (0 if not remove_last else 1))],allow_unknown_chunksizes=allow_unknown_chunksizes,axis=1) for i in range(n_tiles_x - (0 if not remove_last else 1))],allow_unknown_chunksizes=allow_unknown_chunksizes)#.transpose([1,0,2])
-	return arr
+    """Convert SVS, TIF or TIFF to dask array.
+    Parameters
+    ----------
+    svs_file : str
+            Image file.
+    tile_size : int
+            Size of chunk to be read in.
+    overlap : int
+            Do not modify, overlap between neighboring tiles.
+    remove_last : bool
+            Remove last tile because it has a custom size.
+    allow_unknown_chunksizes : bool
+            Allow different chunk sizes, more flexible, but slowdown.
+    Returns
+    -------
+    arr : dask.array.Array
+            A Dask Array representing the contents of the image file.
+    >>> arr = svs2dask_array(svs_file, tile_size=1000, overlap=0, remove_last=True, allow_unknown_chunksizes=False)
+    >>> arr2 = arr.compute()
+    >>> arr3 = to_pil(cv2.resize(arr2, dsize=(1440, 700), interpolation=cv2.INTER_CUBIC))
+    >>> arr3.save(test_image_name)
+    """
+    # https://github.com/jlevy44/PathFlowAI/blob/master/pathflowai/utils.py
+    img = openslide.open_slide(svs_file)
+    if type(img) is openslide.OpenSlide:
+        gen = deepzoom.DeepZoomGenerator(
+            img, tile_size=tile_size, overlap=overlap, limit_bounds=True)
+        max_level = len(gen.level_dimensions) - 1
+        n_tiles_x, n_tiles_y = gen.level_tiles[max_level]
+
+        @dask.delayed(pure=True)
+        def get_tile(level, column, row):
+            tile = gen.get_tile(level, (column, row))
+            return np.array(tile).transpose((1, 0, 2))
+
+        sample_tile_shape = get_tile(max_level, 0, 0).shape.compute()
+        rows = range(n_tiles_y - (0 if not remove_last else 1))
+        cols = range(n_tiles_x - (0 if not remove_last else 1))
+        arr = da.concatenate([da.concatenate([da.from_delayed(get_tile(max_level, col, row), sample_tile_shape, np.uint8) for row in rows],
+                                             allow_unknown_chunksizes=allow_unknown_chunksizes, axis=1) for col in cols], allow_unknown_chunksizes=allow_unknown_chunksizes).transpose([1, 0, 2])
+        return arr
+    else:  # img is instance of openslide.ImageSlide
+        return dask_image.imread.imread(svs_file)
 
 def img2npy_(input_dir,basename, svs_file):
 	"""Convert SVS, TIF, TIFF to NPY.