Mercurial > repos > imgteam > points2binaryimage

comparison points2binaryimage.py @ 1:90385ec28b34 draft

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2binaryimage/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
author imgteam
date Mon, 13 Nov 2023 22:11:42 +0000
parents dd513c9f5230
children
comparison
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0:dd513c9f5230 1:90385ec28b34
1 import argparse 1 import argparse
2 import sys
3 import numpy as np
4 import skimage.io
5 import pandas as pd
6 import os 2 import os
7 import warnings 3 import warnings
4
5 import numpy as np
6 import pandas as pd
7 import skimage.io
8 8
9 9
10 def points2binaryimage(point_file, out_file, shape=[500, 500], has_header=False, invert_xy=False): 10 def points2binaryimage(point_file, out_file, shape=[500, 500], has_header=False, invert_xy=False):
11 11
12 img = np.zeros(shape, dtype=np.int16) 12 img = np.zeros(shape, dtype=np.int16)
20 a_row = df.iloc[i] 20 a_row = df.iloc[i]
21 if int(a_row[0]) < 0 or int(a_row[1]) < 0: 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])) 22 raise IndexError("Point {},{} is out of image with bounds {},{}.".format(int(a_row[0]), int(a_row[1]), shape[0], shape[1]))
23 23
24 if invert_xy: 24 if invert_xy:
25 if img.shape[0]<=int(a_row[0]) or img.shape[1]<=int(a_row[1]): 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])) 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: 27 else:
28 img[int(a_row[1]), int(a_row[0])] = 32767 28 img[int(a_row[1]), int(a_row[0])] = 32767
29 else: 29 else:
30 if img.shape[0]<=int(a_row[1]) or img.shape[1]<=int(a_row[0]): 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])) 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: 32 else:
33 img[int(a_row[0]), int(a_row[1])] = 32767 33 img[int(a_row[0]), int(a_row[1])] = 32767
34 else: 34 else:
35 raise Exception("{} is empty or does not exist.".format(point_file)) # appropriate built-in error? 35 raise Exception("{} is empty or does not exist.".format(point_file)) # appropriate built-in error?
36 36
37 with warnings.catch_warnings(): 37 with warnings.catch_warnings():
38 warnings.simplefilter("ignore") 38 warnings.simplefilter("ignore")
39 skimage.io.imsave(out_file, img, plugin='tifffile') # otherwise we get problems with the .dat extension 39 skimage.io.imsave(out_file, img, plugin='tifffile') # otherwise we get problems with the .dat extension
40
40 41
41 if __name__ == "__main__": 42 if __name__ == "__main__":
42 parser = argparse.ArgumentParser() 43 parser = argparse.ArgumentParser()
43 parser.add_argument('point_file', type=argparse.FileType('r'), help='label file') 44 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('out_file', type=str, help='out file (TIFF)')
47 parser.add_argument('--has_header', dest='has_header', default=False, help='set True if CSV has header') 48 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 parser.add_argument('--invert_xy', dest='invert_xy', default=False, help='invert x and y in CSV')
49 50
50 args = parser.parse_args() 51 args = parser.parse_args()
51 52
52 #TOOL 53 # TOOL
53 points2binaryimage(args.point_file.name, args.out_file, [args.shapey, args.shapex], has_header=args.has_header, invert_xy=args.invert_xy) 54 points2binaryimage(args.point_file.name, args.out_file, [args.shapey, args.shapex], has_header=args.has_header, invert_xy=args.invert_xy)