Update scale_image tool (not finished yet)

macros/tests.xml

@@ -21,7 +21,11 @@
         token_metric="iou"
         token_eps="0.01">
 
-        <output name="@NAME@" value="@VALUE@" ftype="@FTYPE@" compare="image_diff" metric="@METRIC@" eps="@EPS@"/>
+        <output name="@NAME@" value="@VALUE@" ftype="@FTYPE@" compare="image_diff" metric="@METRIC@" eps="@EPS@">
+            <assert_contents>
+                <yield/>
+            </assert_contents>
+        </output>
 
     </xml>
 
@@ -31,7 +35,11 @@
         token_metric="rms"
         token_eps="0.01">
 
-        <output name="@NAME@" value="@VALUE@" ftype="@FTYPE@" compare="image_diff" metric="@METRIC@" eps="@EPS@"/>
+        <output name="@NAME@" value="@VALUE@" ftype="@FTYPE@" compare="image_diff" metric="@METRIC@" eps="@EPS@">
+            <assert_contents>
+                <yield/>
+            </assert_contents>
+        </output>
 
     </xml>
 

tools/2d_simple_filter/filter.xml

@@ -102,6 +102,9 @@
 
         **Applies a standard filter to a single-channel 2-D image.**
 
+        Note that this operation can change the range of the values of the image intensities in the image.
+        This is necessary, for example, to preserve the brightness of the image after filtering.
+
     </help>
     <citations>
        <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation>

tools/scale_image/creators.xml

@@ -0,0 +1 @@
+../../macros/creators.xml

tools/scale_image/scale_image.py

@@ -1,38 +1,50 @@
 import argparse
 import sys
 
-import scipy.misc
+import numpy as np
 import skimage.io
 import skimage.transform
+import skimage.util
 from PIL import Image
 
 
-def scale_image(input_file, output_file, scale, order=1):
+def scale_image(input_file, output_file, scale, order, antialias):
     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'
+    im = skimage.io.imread(input_file)
+
+    # Parse `--scale` argument
     if ',' in scale:
-        scale = scale[1:-1].split(',')
-        scale = [int(i) for i in scale]
-    elif '.' in scale:
-        scale = float(scale)
+        scale = [float(s.strip()) for s in scale.split(',')]
+        assert len(scale) <= im.ndim, f'Image has {im.ndim} axes, but scale factors were given for {len(scale)} axes.'
+        scale = scale + [1] * (im.ndim - len(scale))
+
     else:
-        scale = int(scale)
-    res = scipy.misc.imresize(img_in, scale, interp=interp)
+        scale = float(scale)
+
+    # Do the scaling
+    res = skimage.transform.rescale(im, scale, order, anti_aliasing=antialias)
+
+    # Convert `res` to the same dtype as `im`,
+    # it is important to preserve the dtype so that both brightness and range of values is preserved
+    if res.dtype != im.dtype:
+        src_max_value = skimage.util.dtype_limits(res)[1]
+        dst_max_value = skimage.util.dtype_limits(im)[1]
+        res = (res / src_max_value) * dst_max_value
+        if np.issubdtype(im.dtype, np.integer):
+            res = res.round()
+        res = res.astype(im.dtype)
+
+    # Save result
     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')
+    parser.add_argument('input_file', type=argparse.FileType('r'), default=sys.stdin)
+    parser.add_argument('out_file', type=argparse.FileType('w'), default=sys.stdin)
+    parser.add_argument('--scale', type=str, required=True)
+    parser.add_argument('--order', type=int, required=True)
+    parser.add_argument('--antialias', default=False, action='store_true')
     args = parser.parse_args()
 
-    scale_image(args.input_file.name, args.out_file.name, args.scale, args.order)
+    scale_image(args.input_file.name, args.out_file.name, args.scale, args.order, args.antialias)

tools/scale_image/scale_image.xml

@@ -1,5 +1,14 @@
-<tool id="ip_scale_image" name="Scale image" version="0.4-2"> 
+<tool id="ip_scale_image" name="Scale image" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05"> 
     <description>with scikit-image</description>
+    <macros>
+        <import>creators.xml</import>
+        <import>tests.xml</import>
+        <token name="@TOOL_VERSION@">0.18.3</token>
+        <token name="@VERSION_SUFFIX@">0</token>
+    </macros>
+    <creator>
+        <expand macro="creators/bmcv" />
+    </creator>
     <edam_operations>
         <edam_operation>operation_3443</edam_operation>
     </edam_operations>
@@ -8,64 +17,85 @@
         <xref type="biii">scikit-image</xref>
     </xrefs>
     <requirements>
-        <requirement type="package" version="6.1.0">pillow</requirement>
-        <requirement type="package" version="0.14.2">scikit-image</requirement>
-        <requirement type="package" version="1.15.4">numpy</requirement>
-        <requirement type="package" version="1.1.0">scipy</requirement>
-        <requirement type="package" version="0.15.1">tifffile</requirement>
+        <requirement type="package" version="@TOOL_VERSION@">scikit-image</requirement>
+        <requirement type="package" version="10.0.1">pillow</requirement>
+        <requirement type="package" version="1.24.4">numpy</requirement>
+        <requirement type="package" version="2021.7.2">tifffile</requirement>
     </requirements> 
-    <command detect_errors="aggressive">
-        <![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 detect_errors="aggressive"><![CDATA[
 
-        ]]>
-    </command>
+        python '$__tool_directory__/scale_image.py' '$input'
+
+        ./output.${input.ext}
+
+        --scale '$scale'
+        --order  $order
+        $antialias
+
+        && mv ./output.${input.ext} ./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" 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">
+        <param argument="--scale" type="text" value="1" label="Scaling factor" help="Use either a single scaling factor (uniform scaling), or a comma-separated list of scaling factors (anistropic scaling). For a 2-D single-channel or RGB image, the first scaling factor corresponds to the image width and the second corresponds to the image height."/>
+        <param argument="--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>
+        <param name="antialias" type="boolean" truevalue="--antialias" falsevalue="" checked="true" label="Enable anti-aliasing" help="This should only be used for down-scaling."/>
     </inputs>
     <outputs>
-        <data format="png" name="output" from_work_dir="out.png"/>
+        <data format="png" name="output" from_work_dir="output"/>
     </outputs>
     <tests>
+        <!-- Test PNG, without antialias -->
         <test>
-            <param name="input" value="sample1.png"/> <!--continue here-->
-            <conditional name="use_scale_option">
-                <param name="use_scale" value="false"/>
-                <param name="scale_x" value="200"/>
-                <param name="scale_y" value="150"/>
-            </conditional>
+            <param name="input" value="input1_binary_rgb.png"/>
+            <param name="scale" value="0.5"/>
+            <param name="antialias" value="false"/>
             <param name="order" value="0"/>
-            <output name="output" value="out2.png" ftype="png" compare="sim_size"/>
+            <expand macro="tests/binary_image_diff" name="output" value="uniform_binary.png" ftype="png"/>
+        </test>
+        <!-- Test PNG, uniform scaling -->
+        <test>
+            <param name="input" value="input1_binary_rgb.png"/>
+            <param name="scale" value="0.5"/>
+            <expand macro="tests/intensity_image_diff" name="output" value="uniform.png" ftype="png"/>
+        </test>
+        <!-- Test PNG, anistropic scaling -->
+        <test>
+            <param name="input" value="input1_binary_rgb.png"/>
+            <param name="scale" value="0.5, 0.8"/>
+            <expand macro="tests/intensity_image_diff" name="output" value="anisotropic.png" ftype="png"/>
+        </test>
+        <test>
+            <param name="input" value="input1_binary_rgb.png"/>
+            <param name="scale" value="0.5, 0.8, 1"/>
+            <expand macro="tests/intensity_image_diff" name="output" value="anisotropic.png" ftype="png"/>
+        </test>
+        <!-- Test TIFF, normalized -->
+        <test>
+            <param name="input" value="input2_normalized.tiff"/>
+            <param name="scale" value="0.5"/>
+            <output name="output" value="normalized.tiff" ftype="tiff" compare="sim_size" delta_frac="0.01"/><!-- Looks like pillow cannot read float TIFFs -->
+        </test>
+        <!-- Test TIFF, not normalized -->
+        <test>
+            <param name="input" value="input3_not_normalized.tiff"/>
+            <param name="scale" value="0.5"/>
+            <output name="output" value="not_normalized.tiff" ftype="tiff" compare="sim_size" delta_frac="0.01"/><!-- Looks like pillow cannot read float TIFFs -->
         </test>
     </tests>
     <help>
-    **What it does**
 
-    This tool scales an image using the scaling factor.
+        **Scales an image using one or more scaling factors.**
+
+        The image is rescaled uniformly along all axes, or anistropically if multiple scale factors are given.
+
+        Note that this operation can change the range of the values of the image intensities in the image.
+        This is necessary, for example, to preserve the brightness of the image after scaling.
+
     </help>
     <citations>
         <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation>

tools/scale_image/tests.xml

@@ -0,0 +1 @@
+../../macros/tests.xml