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Commit message:
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit 787ebcc8daa1834214bc92c201c921c704ef2d1f |
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scale_image.py scale_image.xml test-data/out.png test-data/out2.png test-data/sample1.png |
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| diff -r 000000000000 -r 2d69cbf0f2d2 scale_image.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/scale_image.py Mon Jan 07 05:39:54 2019 -0500 |
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| @@ -0,0 +1,44 @@ +import argparse +import sys +import skimage.io +import skimage.transform +import scipy.misc +import warnings +import os +from PIL import Image + + +def scale_image(input_file, output_file, scale, order=1): + with warnings.catch_warnings(): + warnings.simplefilter("ignore") + Image.MAX_IMAGE_PIXELS = 50000*50000 + img_in = skimage.io.imread(input_file) + if order == 0: + interp = 'nearest' + elif order == 1: + interp = 'bilinear' + elif order == 2: + interp = 'bicubic' + + if ',' in scale: + scale = scale[1:-1].split(',') + scale.reverse() + scale = [int(i) for i in scale] + elif '.' in scale: + scale = float(scale) + else: + scale = int(scale) + + res = scipy.misc.imresize(img_in, scale, interp=interp) + skimage.io.imsave(output_file, res) + + +if __name__ == "__main__": + parser = argparse.ArgumentParser() + parser.add_argument('input_file', type=argparse.FileType('r'), default=sys.stdin, help='input file') + parser.add_argument('out_file', type=argparse.FileType('w'), default=sys.stdin, help='out file (PNG)') + parser.add_argument('scale', type=str, help='fraction scaling factor(float), percentage scaling factor(int), output size(tuple(height,width))') # integer option not implemented in galaxy wrapper + parser.add_argument('order', type=int, default=1, help='interpolation method') + args = parser.parse_args() + + scale_image(args.input_file.name, args.out_file.name, args.scale, args.order) \ No newline at end of file |
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| diff -r 000000000000 -r 2d69cbf0f2d2 scale_image.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/scale_image.xml Mon Jan 07 05:39:54 2019 -0500 |
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| @@ -0,0 +1,59 @@ +<tool id="scale_image" name="Scale Image" version="0.2"> + <description>Scales image</description> + <requirements> + <requirement type="package" version="0.14.0">scikit-image</requirement> + <requirement type="package" version="1.1.0">scipy</requirement> + </requirements> + <command> + <![CDATA[ + python '$__tool_directory__/scale_image.py' '$input' ./out.png + #if $use_scale_option.use_scale == 'true' + $use_scale_option.scale + #else if $use_scale_option.use_scale == 'false' + '[$use_scale_option.scale_x, $use_scale_option.scale_y]' + #end if + $order + + && + mv ./out.png '$output' + ]]> + </command> + <inputs> + <param name="input" type="data" format="png" label="Image file"/> + <conditional name="use_scale_option"><!--a third option (using one integer as percentage scaling) could still be implemented--> + <param label="Lock scaling between image dimensions" name="use_scale" type="select"> + <option selected="true" value="true">Lock</option> + <option value="false">Individual scales</option> + </param> + <when value="true"> + <param name="scale" size="4" type="float" value="1.0" label="Scaling factor" /> + </when> + <when value="false"> + <param name="scale_x" size="4" type="integer" value="100" label="New height of the image in pixels" /> + <param name="scale_y" size="4" type="integer" value="100" label="New width of the image in pixels" /> + </when> + </conditional> + <param name="order" type="select" label="Interpolation method"> + <option value="0">Nearest-neighbor</option> + <option value="1" selected="true">Bi-linear</option> + <option value="2">Bi-cubic</option> + </param> + </inputs> + <outputs> + <data format="png" name="output"/> + </outputs> + <tests> + <test> + <param name="input" value="sample1.png"/> <!--continue here--> + <param name="use_scale_option.use_scale" value="false"/> + <param name="use_scale_option.scale_x" value="200"/> + <param name="use_scale_option.scale_y" value="150"/> + <param name="order" value="0"/> + <output name="output" value="out2.png" ftype="png" compare="sim_size"/> + </test> + </tests> + <help>This tool scales an image using the scaling factor.</help> + <citations> + <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation> + </citations> +</tool> |
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