annotate points2label.py @ 0:dcc8c1d6af48 draft

planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
author imgteam
date Sat, 09 Feb 2019 14:44:10 -0500
parents
children 9bd039f46843
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
dcc8c1d6af48 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
1 import argparse
dcc8c1d6af48 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
2 import sys
dcc8c1d6af48 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
3 import numpy as np
dcc8c1d6af48 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
4 import skimage.io
dcc8c1d6af48 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
5 import pandas as pd
dcc8c1d6af48 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
6 import warnings
dcc8c1d6af48 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
7
dcc8c1d6af48 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
8 def points2label(labels, shape, output_file=None, has_header=False, is_TSV=True):
dcc8c1d6af48 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
9 labelimg = np.zeros([shape[0], shape[1]], dtype=np.int32)
dcc8c1d6af48 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
10
dcc8c1d6af48 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
11 if is_TSV:
dcc8c1d6af48 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
12 if has_header:
dcc8c1d6af48 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
13 df = pd.read_csv(labels, sep='\t', skiprows=1, header=None)
dcc8c1d6af48 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
14 else:
dcc8c1d6af48 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
15 df = pd.read_csv(labels, sep='\t', header=None)
dcc8c1d6af48 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
16 else:
dcc8c1d6af48 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
17 if has_header:
dcc8c1d6af48 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
18 df = pd.read_csv(labels, skiprows=1, header=None)
dcc8c1d6af48 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
19 else:
dcc8c1d6af48 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
20 df = pd.read_csv(labels, header=None)
dcc8c1d6af48 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
21
dcc8c1d6af48 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
22 for i in range(0, len(df)):
dcc8c1d6af48 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
23 a_row = df.iloc[i]
dcc8c1d6af48 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
24 labelimg[a_row[0], a_row[1]] = i+1
dcc8c1d6af48 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
25
dcc8c1d6af48 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
26 if output_file is not None:
dcc8c1d6af48 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
27 with warnings.catch_warnings():
dcc8c1d6af48 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
28 warnings.simplefilter("ignore")
dcc8c1d6af48 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
29 skimage.io.imsave(output_file, labelimg, plugin='tifffile')
dcc8c1d6af48 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
30 else:
dcc8c1d6af48 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
31 return labelimg
dcc8c1d6af48 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
32
dcc8c1d6af48 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
33 if __name__ == "__main__":
dcc8c1d6af48 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
34 parser = argparse.ArgumentParser()
dcc8c1d6af48 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
35 parser.add_argument('label_file', type=argparse.FileType('r'), default=sys.stdin, help='label file')
dcc8c1d6af48 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
36 parser.add_argument('out_file', type=argparse.FileType('w'), default=sys.stdin, help='out file')
dcc8c1d6af48 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
37 parser.add_argument('org_file', type=argparse.FileType('r'), default=sys.stdin, help='input original file')
dcc8c1d6af48 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
38 parser.add_argument('--has_header', dest='has_header', type=bool, default=False, help='label file has header')
dcc8c1d6af48 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
39 parser.add_argument('--is_tsv', dest='is_tsv', type=bool, default=True, help='label file is TSV')
dcc8c1d6af48 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
40 args = parser.parse_args()
dcc8c1d6af48 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
41
dcc8c1d6af48 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
42 original_shape = skimage.io.imread(args.org_file.name, plugin='tifffile').shape
dcc8c1d6af48 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
43
dcc8c1d6af48 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2labelimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
44 points2label(args.label_file.name, original_shape, args.out_file.name, args.has_header, args.is_tsv)