Mercurial > repos > thomaswollmann > detection_viz
changeset 0:629d9e8ca64c draft
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/detection_viz/ commit a0ba841e8b3aee770a3243155bedfac0adf9a5a6
| author | thomaswollmann |
|---|---|
| date | Wed, 12 Dec 2018 04:37:59 -0500 |
| parents | |
| children | ff66bae1f7f8 |
| files | detection_viz.py detection_viz.xml test-data/out.png test-data/out.tif test-data/sample.png |
| diffstat | 5 files changed, 93 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/detection_viz.py Wed Dec 12 04:37:59 2018 -0500 @@ -0,0 +1,60 @@ +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)
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/detection_viz.xml Wed Dec 12 04:37:59 2018 -0500 @@ -0,0 +1,33 @@ +<tool id="detection_viz" name="Detection Visualization" version="0.1"> + <description>Detection Visualization</description> + <requirements> + <requirement type="package" version="0.14.1" >scikit-image</requirement> + <requirement type="package" version="3.0.2" >matplotlib</requirement> + </requirements> + <command> + <![CDATA[ + python '$__tool_directory__/detection_viz.py' '$input' '$output' --stroke_size $thickness --circle_radius $circle_radius $tp $fn $fp +]]> + </command> + <inputs> + <param name="input" type="data" format="tiff,png,jpg,bmp" label="Binary Image File"/> + <param name="tp" type="boolean" checked="false" falsevalue="" truevalue="--tp"/> + <param name="fn" type="boolean" checked="false" falsevalue="" truevalue="--fn"/> + <param name="fp" type="boolean" checked="false" falsevalue="" truevalue="--fp"/> + <param name="thickness" type="float" value="3.0" label="Stroke thickness"/> + <param name="circle_radius" type="float" value="50.0" label="Circle radius"/> + </inputs> + <outputs> + <data format="png" name="output"/> + </outputs> + <tests> + <test> + <param name="input" value="sample.png"/> + <output name="output" value="out.png" ftype="png"/> + </test> + </tests> + <help>Draws circles of different colors around detected true positives, false negatives and false positives.</help> + <citations> + <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation> + </citations> +</tool>