Mercurial > repos > imgteam > coordinates_of_roi

changeset 2:24d9bd16c953 draft

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/coordinates_of_roi/ commit bfae746780819634a014388ea4671a49fc5c178d
author imgteam
date Wed, 20 Mar 2019 09:18:06 -0400
parents ee045a6bbdef
children 02a686fc1654
files coordinates_of_roi.py coordinates_of_roi.xml test-data/.gitignore test-data/newtable.tsv test-data/newtable2.tsv
diffstat 5 files changed, 22 insertions(+), 7 deletions(-) [+]
line wrap: on
line diff
--- a/coordinates_of_roi.py	Fri Feb 22 17:11:28 2019 -0500
+++ b/coordinates_of_roi.py	Wed Mar 20 09:18:06 2019 -0400
@@ -16,11 +16,11 @@
         for i in range(img_height):
             if white_obj == False:
                 if data[i,j] <= threshold:
-                    x.append(j + offset[0])
-                    y.append(img_height-(i+1) + offset[1])
+                    x.append(i + offset[0])
+                    y.append(j + offset[1])
             elif data[i,j] >= threshold:
-                    x.append(j + offset[0])
-                    y.append(img_height-(i+1) + offset[1])
+                    x.append(i + offset[0])
+                    y.append(j + offset[1])
                     
     df = pd.DataFrame()
     df['x'] = x
--- a/coordinates_of_roi.xml	Fri Feb 22 17:11:28 2019 -0500
+++ b/coordinates_of_roi.xml	Wed Mar 20 09:18:06 2019 -0400
@@ -1,4 +1,4 @@
-<tool id="ip_coordinates_of_roi" name="Coordinates of ROI" version="0.0.3">
+<tool id="ip_coordinates_of_roi" name="Coordinates of ROI" version="0.0.4">
     <description></description>
     <requirements>
         <requirement type="package" version="0.14.2">scikit-image</requirement>
@@ -29,14 +29,14 @@
         <test>
             <param name="im" value="test.png"/>
             <param name="white_obj" value="true"/>
-            <output name="pixel_table" value="table.tsv" ftype="tabular"/>
+            <output name="pixel_table" value="newtable.tsv" ftype="tabular"/>
         </test>
         <test>
             <param name="im" value="test.png"/>
             <param name="white_obj" value="true"/>
             <param name="offset_x" value="1"/>
             <param name="offset_y" value="2"/>
-            <output name="pixel_table" value="table2.tsv" ftype="tabular"/>
+            <output name="pixel_table" value="newtable2.tsv" ftype="tabular"/>
         </test>
     </tests>
     <help>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/.gitignore	Wed Mar 20 09:18:06 2019 -0400
@@ -0,0 +1,1 @@
+/test2.png
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/newtable.tsv	Wed Mar 20 09:18:06 2019 -0400
@@ -0,0 +1,7 @@
+x	y
+5	4
+5	5
+5	6
+5	7
+5	8
+5	9
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/newtable2.tsv	Wed Mar 20 09:18:06 2019 -0400
@@ -0,0 +1,7 @@
+x	y
+6	6
+6	7
+6	8
+6	9
+6	10
+6	11