diff wsi_extract_top_view.py @ 2:3bd767eee603 draft default tip

planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/wsi_extract_top_view/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf

--- a/wsi_extract_top_view.py	Wed Dec 18 05:03:44 2019 -0500
+++ b/wsi_extract_top_view.py	Mon Nov 13 22:12:44 2023 +0000
@@ -1,14 +1,14 @@
 import argparse
+
+import numpy as np
 import openslide
-import os
-import fnmatch
 import skimage.io
-import numpy as np
- 
+
+
 def wsi_extract_top_view(input_path, out_path):
     img_raw = openslide.OpenSlide(input_path)
-    top_size = img_raw.level_dimensions[len(img_raw.level_dimensions)-1]
-    img_area = img_raw.read_region((0,0), len(img_raw.level_dimensions)-1, top_size)
+    top_size = img_raw.level_dimensions[len(img_raw.level_dimensions) - 1]
+    img_area = img_raw.read_region((0, 0), len(img_raw.level_dimensions) - 1, top_size)
     img_area = np.asarray(img_area, dtype=np.uint8)
     skimage.io.imsave(out_path, img_area, plugin="tifffile")
 
@@ -18,5 +18,5 @@
     parser.add_argument('input_file', type=argparse.FileType('r'), help='input file')
     parser.add_argument('out_file', help='out file')
     args = parser.parse_args()
- 
+
     wsi_extract_top_view(args.input_file.name, args.out_file)