changeset 0:c4c76f1ebad2 draft

planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/scale_image.py	Sat Feb 09 14:46:03 2019 -0500
@@ -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

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/scale_image.xml	Sat Feb 09 14:46:03 2019 -0500
@@ -0,0 +1,61 @@
+<tool id="ip_scale_image" name="Scale Image" version="0.2">
+    <description>Scales image</description>
+    <requirements>
+        <requirement type="package" version="0.14.2">scikit-image</requirement>
+        <requirement type="package" version="1.15.4">numpy</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
+
+        ]]>
+    </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" type="float" value="1.0" label="Scaling factor" />
+            </when>
+            <when value="false">
+                <param name="scale_x" type="integer" value="100" label="New height of the image in pixels" />
+                <param name="scale_y" 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" from_work_dir="out.png"/>
+    </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>
+    **What it does**
+
+    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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