Mercurial > repos > imgteam > points2binaryimage

comparison points2binaryimage.py @ 0:dd513c9f5230 draft

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2binaryimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
author imgteam
date Sat, 09 Feb 2019 14:43:25 -0500
parents
children 90385ec28b34
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-1:000000000000 0:dd513c9f5230
1 import argparse
2 import sys
3 import numpy as np
4 import skimage.io
5 import pandas as pd
6 import os
7 import warnings
8
9
10 def points2binaryimage(point_file, out_file, shape=[500, 500], has_header=False, invert_xy=False):
11
12 img = np.zeros(shape, dtype=np.int16)
13 if os.path.exists(point_file) and os.path.getsize(point_file) > 0:
14 if has_header:
15 df = pd.read_csv(point_file, skiprows=1, header=None, delimiter="\t")
16 else:
17 df = pd.read_csv(point_file, header=None, delimiter="\t")
18
19 for i in range(0, len(df)):
20 a_row = df.iloc[i]
21 if int(a_row[0]) < 0 or int(a_row[1]) < 0:
22 raise IndexError("Point {},{} is out of image with bounds {},{}.".format(int(a_row[0]), int(a_row[1]), shape[0], shape[1]))
23
24 if invert_xy:
25 if img.shape[0]<=int(a_row[0]) or img.shape[1]<=int(a_row[1]):
26 raise IndexError("Point {},{} is out of image with bounds {},{}.".format(int(a_row[0]), int(a_row[1]), shape[0], shape[1]))
27 else:
28 img[int(a_row[1]), int(a_row[0])] = 32767
29 else:
30 if img.shape[0]<=int(a_row[1]) or img.shape[1]<=int(a_row[0]):
31 raise IndexError("Point {},{} is out of image with bounds {},{}.".format(int(a_row[1]), int(a_row[0]), shape[0], shape[1]))
32 else:
33 img[int(a_row[0]), int(a_row[1])] = 32767
34 else:
35 raise Exception("{} is empty or does not exist.".format(point_file)) # appropriate built-in error?
36
37 with warnings.catch_warnings():
38 warnings.simplefilter("ignore")
39 skimage.io.imsave(out_file, img, plugin='tifffile') # otherwise we get problems with the .dat extension
40
41 if __name__ == "__main__":
42 parser = argparse.ArgumentParser()
43 parser.add_argument('point_file', type=argparse.FileType('r'), help='label file')
44 parser.add_argument('out_file', type=str, help='out file (TIFF)')
45 parser.add_argument('shapex', type=int, help='shapex')
46 parser.add_argument('shapey', type=int, help='shapey')
47 parser.add_argument('--has_header', dest='has_header', default=False, help='set True if CSV has header')
48 parser.add_argument('--invert_xy', dest='invert_xy', default=False, help='invert x and y in CSV')
49
50 args = parser.parse_args()
51
52 #TOOL
53 points2binaryimage(args.point_file.name, args.out_file, [args.shapey, args.shapex], has_header=args.has_header, invert_xy=args.invert_xy)