diff filter.xml @ 5:1b7e67168732 draft

planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit a6fd77be465068f709a71d377900da99becf94d8

--- a/filter.xml	Wed Apr 24 08:12:03 2024 +0000
+++ b/filter.xml	Fri Dec 12 21:18:21 2025 +0000
@@ -1,81 +1,136 @@
-<tool id="ip_filter_standard" name="Filter 2-D image" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05">
+<tool id="ip_filter_standard" name="Apply 2-D image filter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05">
     <description>with scipy</description>
     <macros>
         <import>creators.xml</import>
         <import>tests.xml</import>
-        <token name="@TOOL_VERSION@">1.12.0</token>
-        <token name="@VERSION_SUFFIX@">1</token>
+        <token name="@TOOL_VERSION@">1.16.3</token>
+        <token name="@VERSION_SUFFIX@">0</token>
+        <xml name="select_axis">
+            <param name="axis" type="select" label="Direction">
+                <option value="1" selected="true">Horizontal</option>
+                <option value="0">Vertical</option>
+            </param>
+        </xml>
     </macros>
     <creator>
-        <expand macro="creators/bmcv" />
+        <expand macro="creators/bmcv"/>
+        <expand macro="creators/kostrykin"/>
     </creator>
     <edam_operations>
         <edam_operation>operation_3443</edam_operation>
     </edam_operations>
     <xrefs>
+        <xref type="bio.tools">galaxy_image_analysis</xref>
         <xref type="biii">scipy</xref>
     </xrefs>
     <requirements>
         <requirement type="package" version="@TOOL_VERSION@">scipy</requirement>
-        <requirement type="package" version="1.26.4">numpy</requirement>
-        <requirement type="package" version="0.22.0">scikit-image</requirement>
-        <requirement type="package" version="2024.2.12">tifffile</requirement>
-        <requirement type="package" version="0.1">giatools</requirement>
+        <requirement type="package" version="2.3.5">numpy</requirement>
+        <requirement type="package" version="0.25.2">scikit-image</requirement>
+        <requirement type="package" version="2025.10.16">tifffile</requirement>
+        <requirement type="package" version="0.5.2">giatools</requirement>
     </requirements>
     <command detect_errors="aggressive"><![CDATA[
 
-        python '$__tool_directory__/filter_image.py'
+        python '$__tool_directory__/filter.py'
 
         '$input'
         '$output'
-
-        $filter_type
-        $size
+        '$params'
 
     ]]></command>
+    <configfiles>
+        <configfile name="params"><![CDATA[
+            {
+
+            ## =====================================================================
+            #if $filter.filter_type == "gaussian"
+                "sigma": $filter.sigma,
+                "order": $filter.derivative.order,
+
+                #if $filter.derivative.order != "0"
+                    "axis": $filter.derivative.axis,
+                #end if
+
+            ## =====================================================================
+            #elif $filter.filter_type == "uniform"
+                "size": $filter.size,
+
+            ## =====================================================================
+            #elif $filter.filter_type == "median"
+                "radius": $filter.radius,
+
+            ## =====================================================================
+            #elif $filter.filter_type == "prewitt" or $filter.filter_type == "sobel"
+                "axis": $filter.axis,
+
+            ## =====================================================================
+            #end if
+
+                "filter_type": "$filter.filter_type"
+
+            }
+        ]]></configfile>
+    </configfiles>
     <inputs>
-        <param name="input" type="data" format="tiff,png" label="Input image" />
+        <param name="input" type="data" format="tiff,png" label="Input image"/>
         <conditional name="filter">
             <param name="filter_type" type="select" label="Filter type">
                 <option value="gaussian" selected="True">Gaussian</option>
+                <option value="uniform">Box filter (uniform filter)</option>
                 <option value="median">Median</option>
-                <option value="prewitt_h">Prewitt horizontal</option>
-                <option value="prewitt_v">Prewitt vertical</option>
-                <option value="sobel_h">Sobel horizontal</option>
-                <option value="sobel_v">Sobel vertical</option>
+                <option value="prewitt">Prewitt</option>
+                <option value="sobel">Sobel</option>
             </param>
             <when value="gaussian">
-                <param name="size" type="float" value="3" min="0.1" label="Sigma" help="The half width of the Gaussian bell (in pixels)." />
+                <param name="sigma" type="float" value="3" min="0.1" label="Sigma"
+                       help="The half width of the Gaussian bell (in pixels)."/>
+                <conditional name="derivative">
+                    <param name="order" type="select" label="Use a derivative?">
+                        <option value="0">No derivative (mean filter)</option>
+                        <option value="1">1st-order derivative</option>
+                        <option value="2">2nd-order derivative</option>
+                    </param>
+                    <when value="0">
+                    </when>
+                    <when value="1">
+                        <expand macro="select_axis"/>
+                    </when>
+                    <when value="2">
+                        <expand macro="select_axis"/>
+                    </when>
+                </conditional>
+            </when>
+            <when value="uniform">
+                <param name="size" type="integer" min="2" value="3" label="Size"
+                       help="Edge length of the neighborhood (square, in pixels)."/>
             </when>
             <when value="median">
-                <param name="size" type="integer" value="3" label="Radius" help="Radius of the neighborhood (in pixels)." />
-            </when>
-            <when value="prewitt_h">
-                <param name="size" type="hidden" value="0" />
+                <param name="radius" type="integer" min="2" value="3" label="Radius"
+                       help="Radius of the neighborhood (circle, in pixels)." />
             </when>
-            <when value="prewitt_v">
-                <param name="size" type="hidden" value="0" />
+            <when value="prewitt">
+                <expand macro="select_axis"/>
             </when>
-            <when value="sobel_h">
-                <param name="size" type="hidden" value="0" />
-            </when>
-            <when value="sobel_v">
-                <param name="size" type="hidden" value="0" />
+            <when value="sobel">
+                <expand macro="select_axis"/>
             </when>
         </conditional>
     </inputs>
     <outputs>
        <data format="tiff" name="output" />
-    </outputs> 
+    </outputs>
     <tests>
         <!-- Tests with uint8 TIFF input image -->
         <test>
-            <param name="input" value="input1_uint8.tif" />
-            <param name="filter_type" value="gaussian" />
-            <expand macro="tests/intensity_image_diff" name="output" value="input1_gaussian.tif" ftype="tiff">
+            <param name="input" value="input1_uint8.tiff"/>
+            <conditional name="filter">
+                <param name="filter_type" value="gaussian"/>
+            </conditional>
+            <expand macro="tests/intensity_image_diff" name="output" value="input1_gaussian.tiff" ftype="tiff">
                 <!--
 
-                The input file `input1_uint8.tif` has values ranging between 23 and 254, with a mean value of 63.67.
+                The input file `input1_uint8.tiff` has values ranging between 23 and 254, with a mean value of 63.67.
 
                 Below, we use an assertion in addition to the `image_diff` comparison, to ensure that the range of
                 values is preserved. The motiviation behind this is that the expectation images are usually checked
@@ -88,48 +143,106 @@
             </expand>
         </test>
         <test>
-            <param name="input" value="input1_uint8.tif" />
-            <param name="filter_type" value="median" />
-            <expand macro="tests/intensity_image_diff" name="output" value="input1_median.tif" ftype="tiff">
+            <param name="input" value="input1_uint8.tiff"/>
+            <conditional name="filter">
+                <param name="filter_type" value="median"/>
+            </conditional>
+            <expand macro="tests/intensity_image_diff" name="output" value="input1_median.tiff" ftype="tiff">
                 <!-- See note for Gaussian filter above. -->
                 <has_image_mean_intensity mean_intensity="63.67" eps="10"/>
             </expand>
         </test>
         <test>
-            <param name="input" value="input1_uint8.tif" />
-            <param name="filter_type" value="prewitt_h" />
-            <expand macro="tests/intensity_image_diff" name="output" value="input1_prewitt_h.tif" ftype="tiff"/>
+            <param name="input" value="input1_uint8.tiff"/>
+            <conditional name="filter">
+                <param name="filter_type" value="prewitt"/>
+                <param name="axis" value="1"/>
+            </conditional>
+            <expand macro="tests/intensity_image_diff" name="output" value="input1_prewitt_h.tiff" ftype="tiff"/>
         </test>
         <test>
-            <param name="input" value="input1_uint8.tif" />
-            <param name="filter_type" value="prewitt_v" />
-            <expand macro="tests/intensity_image_diff" name="output" value="input1_prewitt_v.tif" ftype="tiff"/>
+            <param name="input" value="input1_uint8.tiff"/>
+            <conditional name="filter">
+                <param name="filter_type" value="prewitt"/>
+                <param name="axis" value="0"/>
+            </conditional>
+            <expand macro="tests/intensity_image_diff" name="output" value="input1_prewitt_v.tiff" ftype="tiff"/>
         </test>
         <test>
-            <param name="input" value="input1_uint8.tif" />
-            <param name="filter_type" value="sobel_h" />
-            <expand macro="tests/intensity_image_diff" name="output" value="input1_sobel_h.tif" ftype="tiff"/>
+            <param name="input" value="input1_uint8.tiff"/>
+            <conditional name="filter">
+                <param name="filter_type" value="sobel"/>
+                <param name="axis" value="1"/>
+            </conditional>
+            <expand macro="tests/intensity_image_diff" name="output" value="input1_sobel_h.tiff" ftype="tiff"/>
         </test>
         <test>
-            <param name="input" value="input1_uint8.tif" />
-            <param name="filter_type" value="sobel_v" />
-            <expand macro="tests/intensity_image_diff" name="output" value="input1_sobel_v.tif" ftype="tiff"/>
+            <param name="input" value="input1_uint8.tiff"/>
+            <conditional name="filter">
+                <param name="filter_type" value="sobel"/>
+                <param name="axis" value="0"/>
+            </conditional>
+            <expand macro="tests/intensity_image_diff" name="output" value="input1_sobel_v.tiff" ftype="tiff"/>
         </test>
         <!-- Tests with float TIFF input image -->
         <test>
-            <param name="input" value="input2_float.tif" />
-            <param name="filter_type" value="gaussian" />
-            <expand macro="tests/intensity_image_diff" name="output" value="input2_gaussian.tif" ftype="tiff">
+            <param name="input" value="input2_float.tiff"/>
+            <conditional name="filter">
+                <param name="filter_type" value="gaussian"/>
+            </conditional>
+            <expand macro="tests/intensity_image_diff" name="output" value="input2_gaussian.tiff" ftype="tiff">
                 <!-- See note for Gaussian filter above. -->
                 <has_image_mean_intensity mean_intensity="0.25" eps="0.01"/>
             </expand>
         </test>
+        <test>
+            <param name="input" value="input2_float.tiff"/>
+            <conditional name="filter">
+                <param name="filter_type" value="uniform"/>
+                <param name="size" value="4"/>
+            </conditional>
+            <expand macro="tests/intensity_image_diff" name="output" value="input2_uniform.tiff" ftype="tiff">
+                <!-- See note for Gaussian filter above. -->
+                <has_image_mean_intensity mean_intensity="0.25" eps="0.01"/>
+            </expand>
+        </test>
+        <!-- Tests with multi-channel image (RGB) -->
+        <test>
+            <param name="input" value="scikit-image/retina.png"/>
+            <conditional name="filter">
+                <param name="filter_type" value="gaussian"/>
+                <param name="sigma" value="5"/>
+                <conditional name="derivative">
+                    <param name="order" value="0"/>
+                </conditional>
+            </conditional>
+            <expand macro="tests/intensity_image_diff" name="output" value="retina_gaussian_order0.tiff" ftype="tiff"/>
+        </test>
+        <test>
+            <param name="input" value="scikit-image/retina.png"/>
+            <conditional name="filter">
+                <param name="filter_type" value="gaussian"/>
+                <param name="sigma" value="3"/>
+                <conditional name="derivative">
+                    <param name="order" value="2"/>
+                    <param name="axis" value="0"/>
+                </conditional>
+            </conditional>
+            <expand macro="tests/intensity_image_diff" name="output" value="retina_gaussian_order2_axis0.tiff" ftype="tiff"/>
+        </test>
     </tests>
     <help>
 
-        **Applies a standard filter to a single-channel 2-D image.**
+        **Applies a standard, general-purpose 2-D filter to an image.**
+
+        Support for different image types:
 
-        Mean filters like the Gaussian filter or the median filter preserve both the brightness of the image, and the range of values.
+        - For 3-D images, the filter is applied to all z-slices of the image.
+        - For multi-channel images, the filter is applied to all channels of the image.
+        - For time-series images, the filter is also applied for all time steps.
+
+        Mean filters like the Gaussian filter, the box filter, or the median filter preserve both the brightness of the image, and
+        the range of values. This does not hold for the derivative variants of the Gaussian filter, which may produce negative values.
 
     </help>
     <citations>