diff binaryimage2points.py @ 0:c983b2d2cdd7 draft default tip

planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/binaryimage2points/ commit 27a6350188f687411bdd6bfe0d569c0803389ca0

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/binaryimage2points.py	Wed Dec 12 04:49:24 2018 -0500
@@ -0,0 +1,55 @@
+import argparse
+import sys
+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") 
+
+    img_in = skimage.io.imread(input_file, plugin='tifffile') 
+    
+    #make label image
+    label = skimage.measure.label(img_in)
+    
+    #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)
+        # be carefull with x,y coordinates
+        center_mass.append([np.mean(coord[1]),np.mean(coord[0])])
+
+    #make data frame of detections
+    out_dataFrame = pd.DataFrame(center_mass)
+
+
+    #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 (CSV)')
+    
+    args        = parser.parse_args()
+    input_file  = args.input_file
+    out_file    = args.out_file
+    
+    #TOOL
+    out_dataFrame = binaryimage2points(input_file)
+    
+    #Print to csv file
+    out_dataFrame.to_csv(out_file,index=False,header=False)