Mercurial > repos > thomaswollmann > detection_viz
view detection_viz.py @ 0:629d9e8ca64c draft
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit a0ba841e8b3aee770a3243155bedfac0adf9a5a6
author | thomaswollmann |
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date | Wed, 12 Dec 2018 04:37:59 -0500 |
parents | |
children | ff66bae1f7f8 |
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import argparse import sys import os import csv import matplotlib matplotlib.use('Agg') import matplotlib.pyplot as plt import skimage.io def plot_circles(file_name, ax, color, stroke_size, radius): resfile = open(file_name, 'rb') rd = csv.reader(resfile, delimiter=',') for row in rd: circ = plt.Circle((int(row[1]), int(row[0])), lw=stroke_size, radius=radius, color=color, fill=False) ax.add_patch(circ) resfile.close() def detection_viz(input_file, output_file, tp=None, fn=None, fp=None, stroke_size=3, circle_radius=50): img = skimage.io.imread(input_file) fig = plt.figure(figsize=(40, 40)) ax = fig.add_axes([0, 0, 1, 1]) ax.axis('off') plt.imshow(img) if tp is not None: plot_circles(tp, ax, '#00FF00', stroke_size, circle_radius) if fn is not None: plot_circles(fn, ax, 'red', stroke_size, circle_radius) if fp is not None: plot_circles(fp, ax, 'darkorange', stroke_size, circle_radius) fig.canvas.print_png("tmp.png", dpi=1800) os.rename("tmp.png", output_file) if __name__ == "__main__": parser = argparse.ArgumentParser() parser.add_argument('input_file', type=argparse.FileType('r'), help='original file') # output file should not be of type argparse.FileType('w') sine it is created immediately in this case which leads to an error in renaming parser.add_argument('out_file_str', type=str, help='string of output file name') parser.add_argument('--tp', dest='input_tp_file', type=argparse.FileType('r'), help='input TP file') parser.add_argument('--fn', dest='input_fn_file', type=argparse.FileType('r'), help='input FN file') parser.add_argument('--fp', dest='input_fp_file', type=argparse.FileType('r'), help='input FP file') parser.add_argument('--stroke_size', dest='thickness', default=3, type=float, help='stroke thickness') parser.add_argument('--circle_radius', dest='circle_radius', type=float, default=50, help='circle radius') args = parser.parse_args() tp=None if args.input_tp_file: tp=args.input_tp_file.name fn=None if args.input_fn_file: fn=args.input_fn_file.name fp=None if args.input_fp_file: fp=args.input_fp_file.name detection_viz(args.input_file.name, args.out_file_str, tp=tp, fn=fn, fp=fp, stroke_size=args.thickness, circle_radius=args.circle_radius)