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annotate detection_viz.py @ 2:f46f64f9590d draft

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit a47299b0f9de530b7501f72fae2dd43d4e7700ba
author imgteam
date Mon, 22 Jul 2019 11:22:03 -0400
parents ec1ca4d62192
children cb2d9de888a1
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3f738d5d91bf planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
1 import argparse
3f738d5d91bf planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
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2 import sys
3f738d5d91bf planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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3 import os
3f738d5d91bf planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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4 import csv
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ec1ca4d62192 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit b2acc1845a25828181597fe5b6982fe116a7796d
imgteam
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3f738d5d91bf planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
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6 import matplotlib
3f738d5d91bf planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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7 matplotlib.use('Agg')
3f738d5d91bf planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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8 import matplotlib.pyplot as plt
3f738d5d91bf planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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3f738d5d91bf planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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10 import skimage.io
3f738d5d91bf planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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3f738d5d91bf planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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12 def plot_circles(file_name, ax, color, stroke_size, radius):
3f738d5d91bf planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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13 resfile = open(file_name, 'rb')
3f738d5d91bf planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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14 rd = csv.reader(resfile, delimiter=',')
3f738d5d91bf planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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15 for row in rd:
3f738d5d91bf planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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16 circ = plt.Circle((int(row[1]), int(row[0])), lw=stroke_size, radius=radius, color=color, fill=False)
3f738d5d91bf planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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17 ax.add_patch(circ)
3f738d5d91bf planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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18 resfile.close()
3f738d5d91bf planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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3f738d5d91bf planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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20 def detection_viz(input_file, output_file, tp=None, fn=None, fp=None, stroke_size=3, circle_radius=50):
3f738d5d91bf planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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21 img = skimage.io.imread(input_file)
3f738d5d91bf planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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3f738d5d91bf planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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23 fig = plt.figure(figsize=(40, 40))
3f738d5d91bf planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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24 ax = fig.add_axes([0, 0, 1, 1])
3f738d5d91bf planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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25 ax.axis('off')
3f738d5d91bf planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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3f738d5d91bf planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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27 plt.imshow(img)
3f738d5d91bf planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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28 if tp is not None:
3f738d5d91bf planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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29 plot_circles(tp, ax, '#00FF00', stroke_size, circle_radius)
3f738d5d91bf planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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30 if fn is not None:
3f738d5d91bf planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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31 plot_circles(fn, ax, 'red', stroke_size, circle_radius)
3f738d5d91bf planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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32 if fp is not None:
3f738d5d91bf planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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33 plot_circles(fp, ax, 'darkorange', stroke_size, circle_radius)
3f738d5d91bf planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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3f738d5d91bf planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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35 fig.canvas.print_png(output_file, dpi=1800)
3f738d5d91bf planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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3f738d5d91bf planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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37 if __name__ == "__main__":
3f738d5d91bf planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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38 parser = argparse.ArgumentParser()
3f738d5d91bf planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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39 parser.add_argument('input_file', type=argparse.FileType('r'), help='original file')
3f738d5d91bf planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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40 # 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
3f738d5d91bf planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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41 parser.add_argument('out_file_str', type=str, help='string of output file name')
3f738d5d91bf planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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42 parser.add_argument('--tp', dest='input_tp_file', type=argparse.FileType('r'), help='input TP file')
3f738d5d91bf planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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43 parser.add_argument('--fn', dest='input_fn_file', type=argparse.FileType('r'), help='input FN file')
3f738d5d91bf planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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44 parser.add_argument('--fp', dest='input_fp_file', type=argparse.FileType('r'), help='input FP file')
3f738d5d91bf planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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45 parser.add_argument('--stroke_size', dest='thickness', default=3, type=float, help='stroke thickness')
3f738d5d91bf planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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46 parser.add_argument('--circle_radius', dest='circle_radius', type=float, default=50, help='circle radius')
3f738d5d91bf planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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47 args = parser.parse_args()
3f738d5d91bf planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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48
3f738d5d91bf planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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49 tp=None
3f738d5d91bf planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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50 if args.input_tp_file:
3f738d5d91bf planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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51 tp=args.input_tp_file.name
3f738d5d91bf planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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52 fn=None
3f738d5d91bf planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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53 if args.input_fn_file:
3f738d5d91bf planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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54 fn=args.input_fn_file.name
3f738d5d91bf planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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55 fp=None
3f738d5d91bf planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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56 if args.input_fp_file:
3f738d5d91bf planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
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57 fp=args.input_fp_file.name
3f738d5d91bf planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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58
3f738d5d91bf planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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59 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)