diff points2binaryimage.py @ 0:dd513c9f5230 draft

planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2binaryimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/points2binaryimage.py	Sat Feb 09 14:43:25 2019 -0500
@@ -0,0 +1,53 @@
+import argparse
+import sys
+import numpy as np
+import skimage.io
+import pandas as pd
+import os
+import warnings
+
+
+def points2binaryimage(point_file, out_file, shape=[500, 500], has_header=False, invert_xy=False):
+
+    img = np.zeros(shape, dtype=np.int16)
+    if os.path.exists(point_file) and os.path.getsize(point_file) > 0:
+        if has_header:
+            df = pd.read_csv(point_file, skiprows=1, header=None, delimiter="\t")
+        else:
+            df = pd.read_csv(point_file, header=None, delimiter="\t")
+
+        for i in range(0, len(df)):
+            a_row = df.iloc[i]
+            if int(a_row[0]) < 0 or int(a_row[1]) < 0:
+                raise IndexError("Point {},{} is out of image with bounds {},{}.".format(int(a_row[0]), int(a_row[1]), shape[0], shape[1]))
+
+            if invert_xy:
+                if img.shape[0]<=int(a_row[0]) or img.shape[1]<=int(a_row[1]):
+                    raise IndexError("Point {},{} is out of image with bounds {},{}.".format(int(a_row[0]), int(a_row[1]), shape[0], shape[1]))
+                else:
+                    img[int(a_row[1]), int(a_row[0])] = 32767
+            else:
+                if img.shape[0]<=int(a_row[1]) or img.shape[1]<=int(a_row[0]):
+                    raise IndexError("Point {},{} is out of image with bounds {},{}.".format(int(a_row[1]), int(a_row[0]), shape[0], shape[1]))
+                else:
+                    img[int(a_row[0]), int(a_row[1])] = 32767
+    else:
+        raise Exception("{} is empty or does not exist.".format(point_file)) # appropriate built-in error?
+
+    with warnings.catch_warnings():
+        warnings.simplefilter("ignore")
+        skimage.io.imsave(out_file, img, plugin='tifffile') # otherwise we get problems with the .dat extension
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser()
+    parser.add_argument('point_file', type=argparse.FileType('r'), help='label file')
+    parser.add_argument('out_file', type=str, help='out file (TIFF)')
+    parser.add_argument('shapex', type=int, help='shapex')
+    parser.add_argument('shapey', type=int, help='shapey')
+    parser.add_argument('--has_header', dest='has_header', default=False, help='set True if CSV has header')
+    parser.add_argument('--invert_xy', dest='invert_xy', default=False, help='invert x and y in CSV')
+
+    args = parser.parse_args()
+
+    #TOOL
+    points2binaryimage(args.point_file.name, args.out_file, [args.shapey, args.shapex], has_header=args.has_header, invert_xy=args.invert_xy)