Mercurial > repos > imgteam > points2binaryimage
changeset 0:dd513c9f5230 draft
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2binaryimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
| author | imgteam |
|---|---|
| date | Sat, 09 Feb 2019 14:43:25 -0500 |
| parents | |
| children | 90385ec28b34 |
| files | __pycache__/points2binaryimage.cpython-36.pyc points2binaryimage.py points2binaryimage.xml test-data/out.tiff test-data/points.tsv |
| diffstat | 5 files changed, 105 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/points2binaryimage.py Sat Feb 09 14:43:25 2019 -0500 @@ -0,0 +1,53 @@ +import argparse +import sys +import numpy as np +import skimage.io +import pandas as pd +import os +import warnings + + +def points2binaryimage(point_file, out_file, shape=[500, 500], has_header=False, invert_xy=False): + + img = np.zeros(shape, dtype=np.int16) + if os.path.exists(point_file) and os.path.getsize(point_file) > 0: + if has_header: + df = pd.read_csv(point_file, skiprows=1, header=None, delimiter="\t") + else: + df = pd.read_csv(point_file, header=None, delimiter="\t") + + for i in range(0, len(df)): + a_row = df.iloc[i] + if int(a_row[0]) < 0 or int(a_row[1]) < 0: + raise IndexError("Point {},{} is out of image with bounds {},{}.".format(int(a_row[0]), int(a_row[1]), shape[0], shape[1])) + + if invert_xy: + if img.shape[0]<=int(a_row[0]) or img.shape[1]<=int(a_row[1]): + raise IndexError("Point {},{} is out of image with bounds {},{}.".format(int(a_row[0]), int(a_row[1]), shape[0], shape[1])) + else: + img[int(a_row[1]), int(a_row[0])] = 32767 + else: + if img.shape[0]<=int(a_row[1]) or img.shape[1]<=int(a_row[0]): + raise IndexError("Point {},{} is out of image with bounds {},{}.".format(int(a_row[1]), int(a_row[0]), shape[0], shape[1])) + else: + img[int(a_row[0]), int(a_row[1])] = 32767 + else: + raise Exception("{} is empty or does not exist.".format(point_file)) # appropriate built-in error? + + with warnings.catch_warnings(): + warnings.simplefilter("ignore") + skimage.io.imsave(out_file, img, plugin='tifffile') # otherwise we get problems with the .dat extension + +if __name__ == "__main__": + parser = argparse.ArgumentParser() + parser.add_argument('point_file', type=argparse.FileType('r'), help='label file') + parser.add_argument('out_file', type=str, help='out file (TIFF)') + parser.add_argument('shapex', type=int, help='shapex') + parser.add_argument('shapey', type=int, help='shapey') + parser.add_argument('--has_header', dest='has_header', default=False, help='set True if CSV has header') + parser.add_argument('--invert_xy', dest='invert_xy', default=False, help='invert x and y in CSV') + + args = parser.parse_args() + + #TOOL + points2binaryimage(args.point_file.name, args.out_file, [args.shapey, args.shapex], has_header=args.has_header, invert_xy=args.invert_xy)
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/points2binaryimage.xml Sat Feb 09 14:43:25 2019 -0500 @@ -0,0 +1,43 @@ +<tool id="ip_points_to_binaryimage" name="Points to Binary Image" version="0.1"> + <description>Converts points to a binary image</description> + <requirements> + <requirement type="package" version="0.14.2">scikit-image</requirement> + <requirement type="package" version="1.15.4">numpy</requirement> + <requirement type="package" version="0.23.4">pandas</requirement> + <requirement type="package" version="2018.7">pytz</requirement><!--pandas seems to have additional requirements that are not automatically installed--> + <requirement type="package" version="2.4.1">dateutil</requirement> + </requirements> + <command> + <![CDATA[ + python '$__tool_directory__/points2binaryimage.py' '$input' '$output' $shapex $shapey $has_header $invert_xy + ]]> + </command> + <inputs> + <param name="input" type="data" format="tabular" label="CSV point file"/> + <param name="shapex" type="integer" value="500" optional="true" min="1" max="2000" label="Width of output image" /> + <param name="shapey" type="integer" value="500" optional="true" min="1" max="2000" label="Height of output image" /> + <param name="has_header" type="boolean" checked="false" truevalue="--has_header True" falsevalue="" optional="true" label="Does point file contain header?" /> + <param name="invert_xy" type="boolean" checked="false" falsevalue="" truevalue="--invert_xy True" optional="true" label="Inverts x and y in CSV point file" /> + </inputs> + <outputs> + <data name="output" format="tiff" /> + </outputs> + <tests> + <test> + <param name="input" value="points.tsv" /> + <param name="shapex" value="20" /> + <param name="shapey" value="30" /> + <param name="has_header" value="false" /> + <param name="invert_xy" value="true" /> + <output name="output" ftype="tiff" file="out.tiff" compare="sim_size"/> + </test> + </tests> + <help> + **What it does** + + Converts CSV point file to binary image. + </help> + <citations> + <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation> + </citations> +</tool>