Mercurial > repos > imgteam > imagecoordinates_flipaxis
changeset 1:d0960e1b25a8 draft
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/imagecoordinates_flipaxis/ commit da043bdec956714abb0fa82f278931bbe1a6d41d
| author | imgteam |
|---|---|
| date | Mon, 25 Mar 2019 11:15:54 -0400 |
| parents | 5a210baa2ff1 |
| children | f8f1100d0701 |
| files | imagecoordinates_flipaxis.py imagecoordinates_flipaxis.xml test-data/out.tsv test-data/out2.tsv test-data/out_offset.tsv |
| diffstat | 5 files changed, 32 insertions(+), 14 deletions(-) [+] |
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--- a/imagecoordinates_flipaxis.py Wed Mar 20 12:06:07 2019 -0400 +++ b/imagecoordinates_flipaxis.py Mon Mar 25 11:15:54 2019 -0400 @@ -2,12 +2,12 @@ import pandas as pd -def imagecoordinates_flipyaxis(input_file, output_file, image_height): +def imagecoordinates_flipyaxis(input_file, output_file, image_height, offset=[0,0]): 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.y = image_height-(df.x + 1) + offset[1] # since maximal y index = height-1 + df.x = x + offset[0] df.to_csv(output_file, sep="\t", index=False) @@ -16,8 +16,9 @@ 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') + parser.add_argument('offset_x', type=int, help='offset in x direction (width)', default=0) + parser.add_argument('offset_y', type=int, help='offset in y direction (height)', default=0) 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, args.image_height, [args.offset_x, args.offset_y]) # imagecoordinates_flipyaxis(args.input_file.name, args.out_file_str, int(args.image_height))
--- a/imagecoordinates_flipaxis.xml Wed Mar 20 12:06:07 2019 -0400 +++ b/imagecoordinates_flipaxis.xml Mon Mar 25 11:15:54 2019 -0400 @@ -6,20 +6,30 @@ <command detect_errors="aggressive"> <![CDATA[ python "$__tool_directory__/imagecoordinates_flipaxis.py" '$input' '$output' $img_height + $offset_x $offset_y ]]> </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> + <param name="offset_x" type="integer" value="0" label="Added offset in x direction (=width direction)" /> + <param name="offset_y" type="integer" value="0" label="Added offset in y direction (=height direction)" /> + </inputs> <outputs> <data name="output" format="tabular"/> </outputs> <tests> <test> <param name="input" value="table.tsv" /> + <output name="output" value="out.tsv" ftype="tabular" /> <param name="img_height" value="500"/> - <output name="output" value="out2.tsv" ftype="tabular" /> + </test> + <test> + <param name="input" value="table.tsv" /> + <output name="output" value="out_offset.tsv" ftype="tabular" /> + <param name="img_height" value="500"/> + <param name="offset_x" value="1"/> + <param name="offset_y" value="2"/> </test> </tests> <help>Makes x the horizontal axis (left to right) and y the vertical axis (bottom to top),
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out.tsv Mon Mar 25 11:15:54 2019 -0400 @@ -0,0 +1,7 @@ +x y +4 495 +104 494 +204 493 +34 492 +4 491 +4 490