Mercurial > repos > imgteam > imagecoordinates_flipaxis
changeset 0:5a210baa2ff1 draft
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/imagecoordinates_flipaxis/ commit 67eaf2b9a9ee1bfed14afba33007ef595890400c
| author | imgteam |
|---|---|
| date | Wed, 20 Mar 2019 12:06:07 -0400 |
| parents | |
| children | d0960e1b25a8 |
| files | imagecoordinates_flipaxis.py imagecoordinates_flipaxis.xml test-data/out2.tsv test-data/table.tsv |
| diffstat | 4 files changed, 67 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/imagecoordinates_flipaxis.py Wed Mar 20 12:06:07 2019 -0400 @@ -0,0 +1,23 @@ +import argparse +import pandas as pd + + +def imagecoordinates_flipyaxis(input_file, output_file, image_height): + df = pd.read_csv(input_file, sep='\t') + + x = df.copy().y # create copy instead of view + df.y = image_height-(df.x + 1) # since maximal y index = height-1 + df.x = x + df.to_csv(output_file, sep="\t", index=False) + + + +if __name__ == "__main__": + parser = argparse.ArgumentParser() + parser.add_argument('input_file', type=argparse.FileType('r'), help='original file') + parser.add_argument('out_file_str', type=str, help='string of output file name') + # parser.add_argument('image_height', help='height of image') + parser.add_argument('image_height', type=int, help='height of image') + args = parser.parse_args() + imagecoordinates_flipyaxis(args.input_file.name, args.out_file_str, args.image_height) + # imagecoordinates_flipyaxis(args.input_file.name, args.out_file_str, int(args.image_height))
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/imagecoordinates_flipaxis.xml Wed Mar 20 12:06:07 2019 -0400 @@ -0,0 +1,30 @@ +<tool id="imagecoordinates_flipaxis" name="Switch axis coordinates" version="0.1"> + <description>Switches the axes of an image and flips the y axis.</description> + <requirements> + <requirement type="package" version="0.23.4" >pandas</requirement> + </requirements> + <command detect_errors="aggressive"> + <![CDATA[ + python "$__tool_directory__/imagecoordinates_flipaxis.py" '$input' '$output' $img_height + ]]> + </command> + <inputs> + <param name="input" type="data" format="tabular" label="File with image coordinates"/> + <param name="img_height" type="integer" value="100" label="Height of the corresponding image"/> + </inputs> + <outputs> + <data name="output" format="tabular"/> + </outputs> + <tests> + <test> + <param name="input" value="table.tsv" /> + <param name="img_height" value="500"/> + <output name="output" value="out2.tsv" ftype="tabular" /> + </test> + </tests> + <help>Makes x the horizontal axis (left to right) and y the vertical axis (bottom to top), + like in a coordinate system.</help> + <citations> + <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation> + </citations> +</tool>