Mercurial > repos > imgteam > wsi_extract_top_view

changeset 2:3bd767eee603 draft default tip

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/wsi_extract_top_view/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
author imgteam
date Mon, 13 Nov 2023 22:12:44 +0000
parents cfe88c6041e9
children
files wsi_extract_top_view.py wsi_extract_top_view.xml
diffstat 2 files changed, 13 insertions(+), 10 deletions(-) [+]
line wrap: on
line diff
--- 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)
--- a/wsi_extract_top_view.xml	Wed Dec 18 05:03:44 2019 -0500
+++ b/wsi_extract_top_view.xml	Mon Nov 13 22:12:44 2023 +0000
@@ -1,5 +1,8 @@
-<tool id="ip_wsi_extract_top_view" name="Extract top view" version="0.2"> 
-    <description>from whole-slice image</description>
+<tool id="ip_wsi_extract_top_view" name="Extract top view from whole-slide image" version="0.2-2"> 
+    <description>with OpenSlide</description>
+    <edam_operations>
+        <edam_operation>operation_3443</edam_operation>
+    </edam_operations>
     <requirements>  
         <requirement type="package" version="0.14.2">scikit-image</requirement>
         <requirement type="package" version="1.15.4">numpy</requirement>
@@ -27,7 +30,7 @@
     <help>
     **What it does**
 
-    Extracts the top view from a whole-slice image, also known as virtual slide, which are high-resolution images used in digital pathology.
+    Extracts the top view from a whole-slide image, also known as virtual slide, which are high-resolution images used in digital pathology.
     </help>
     <citations>
         <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation>