changeset 1:f38f42d55813 draft default tip

planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/binaryimage2points/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
author imgteam
date Mon, 13 Nov 2023 22:10:37 +0000
parents cb1eaebdb4c4
children
files binaryimage2points.py binaryimage2points.xml
diffstat 2 files changed, 35 insertions(+), 32 deletions(-) [+]
line wrap: on
line diff
--- a/binaryimage2points.py	Sat Feb 09 14:31:13 2019 -0500
+++ b/binaryimage2points.py	Mon Nov 13 22:10:37 2023 +0000
@@ -1,53 +1,49 @@
 import argparse
-import sys
+import warnings
+
+import numpy as np
 import pandas as pd
 import skimage.io
-from skimage.measure import label
-from skimage.data import checkerboard
-import numpy as np
-import warnings 
-
 
 
 def binaryimage2points(input_file):
     # ignore warnings that arise when importing a package that was compiled against an older version of numpy than installed; https://github.com/numpy/numpy/pull/432
-    warnings.filterwarnings("ignore") 
+    warnings.filterwarnings("ignore")
+
+    img_in = skimage.io.imread(input_file, plugin='tifffile')
 
-    img_in = skimage.io.imread(input_file, plugin='tifffile') 
-    
-    #make label image
+    # make label image
     label = skimage.measure.label(img_in)
-    
-    #amount of regions
+
+    # amount of regions
     amount_label = np.max(label)
-    
+
     # iterate over all regions in order to calc center of mass
     center_mass = []
-    for i in range(1,amount_label+1):    
-        #get coordinates of region
-        coord = np.where(label==i)
+    for i in range(1, amount_label + 1):
+        # get coordinates of region
+        coord = np.where(label == i)
         # be carefull with x,y coordinates
-        center_mass.append([np.mean(coord[1]),np.mean(coord[0])])
+        center_mass.append([np.mean(coord[1]), np.mean(coord[0])])
 
-    #make data frame of detections
+    # make data frame of detections
     out_dataFrame = pd.DataFrame(center_mass)
 
-
-    #return
-    return(out_dataFrame)
+    # return
+    return out_dataFrame
 
 
 if __name__ == "__main__":
     parser = argparse.ArgumentParser()
     parser.add_argument('input_file', help='input file')
     parser.add_argument('out_file', help='out file (TSV)')
-    
-    args        = parser.parse_args()
-    input_file  = args.input_file
-    out_file    = args.out_file
-    
-    #TOOL
+
+    args = parser.parse_args()
+    input_file = args.input_file
+    out_file = args.out_file
+
+    # TOOL
     out_dataFrame = binaryimage2points(input_file)
-    
-    #Print to csv file
+
+    # Print to csv file
     out_dataFrame.to_csv(out_file, index=False, header=False, sep="\t")
--- a/binaryimage2points.xml	Sat Feb 09 14:31:13 2019 -0500
+++ b/binaryimage2points.xml	Mon Nov 13 22:10:37 2023 +0000
@@ -1,9 +1,16 @@
-<tool id="ip_binaryimage_to_points" name="Binary To Points" version="0.1">
-    <description>Converts Binary Image to Points</description>
+<tool id="ip_binaryimage_to_points" name="Convert binary image to points (center of masses)" version="0.1-2">
+    <description></description>
+    <edam_operations>
+        <edam_operation>operation_3443</edam_operation>
+    </edam_operations>
+    <xrefs>
+        <xref type="bio.tools">galaxy_image_analysis</xref>
+    </xrefs>
     <requirements>
         <requirement type="package" version="1.15.4">numpy</requirement><!--https://github.com/numpy/numpy/pull/432 -->
-        <requirement type="package" version="0.14.2">scikit-image</requirement>
+        <requirement type="package" version="0.14.2">scikit-image</requirement> 
         <requirement type="package" version="0.23.4">pandas</requirement>
+        <requirement type="package" version="0.15.1">tifffile</requirement>
     </requirements>
     <command>
         <![CDATA[