Mercurial > repos > imgteam > overlay_images

changeset 9:66fe62b96281 draft default tip

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/overlay_images/ commit a11042fbd0da4bfcc54522b31919aa5efb862f3d
author imgteam
date Fri, 28 Nov 2025 08:41:02 +0000
parents ca362a9bfa20
children
files creators.xml overlay_images.py overlay_images.xml test-data/mask1.tif test-data/mask1.tiff test-data/mask1r.tif test-data/mask1r.tiff test-data/mask2.tif test-data/mask2.tiff test-data/mask3.tiff test-data/sample1_uint16.tif test-data/sample1_uint16.tiff test-data/sample1_uint8.tif test-data/sample1_uint8.tiff test-data/sample2.tiff test-data/sample3.tiff test-data/test1.tif test-data/test1.tiff test-data/test10.png test-data/test2.tif test-data/test2.tiff test-data/test6.png test-data/test7.png test-data/test8.png test-data/test9.png
diffstat 25 files changed, 223 insertions(+), 45 deletions(-) [+]
line wrap: on
line diff
--- a/creators.xml	Mon Sep 23 10:26:26 2024 +0000
+++ b/creators.xml	Fri Nov 28 08:41:02 2025 +0000
@@ -5,6 +5,11 @@
         <yield />
     </xml>
 
+    <xml name="creators/kostrykin">
+        <person givenName="Leonid" familyName="Kostrykin"/>
+        <yield/>
+    </xml>
+
     <xml name="creators/rmassei">
         <person givenName="Riccardo" familyName="Massei"/>
         <yield/>
@@ -24,5 +29,15 @@
         <person givenName="Till" familyName="Korten"/>
         <yield/>
     </xml>
-    
+
+    <xml name="creators/pavanvidem">
+        <person givenName="Pavan" familyName="Videm"/>
+        <yield/>
+    </xml>
+
+    <xml name="creators/tuncK">
+        <person givenName="Tunc" familyName="Kayikcioglu"/>
+        <yield/>
+    </xml>
+
 </macros>
--- a/overlay_images.py	Mon Sep 23 10:26:26 2024 +0000
+++ b/overlay_images.py	Fri Nov 28 08:41:02 2025 +0000
@@ -30,15 +30,42 @@
         return img
 
 
-def get_rgb8_copy(img):
+def get_rgb8_copy(img, fp_lower, fp_upper):
     img = np.squeeze(img)
     assert img.ndim == 2 or (img.ndim == 3 and img.shape[-1] in (3, 4))
+    assert fp_lower == 'min' or abs(float(fp_lower)) < np.inf  # 'min' or number
+    assert fp_upper == 'max' or abs(float(fp_upper)) < np.inf  # 'max' or number
+
+    # Convert from floating point
     if str(img.dtype).startswith('float'):
+        a = img.min() if fp_lower == 'min' else float(fp_lower)
+        b = img.max() if fp_upper == 'max' else float(fp_upper)
+
+        if a > b:
+            raise ValueError(
+                f'Lower bound ({a:g}) must be less than upper bound ({b:g}).'
+            )
+        if a == b:
+            raise ValueError(
+                'Floating point conversion is undefined'
+                ' because lower and upper bounds are identical.'
+            )
+
+        # Perform linear mapping to [0, 1]
+        img = img.clip(a, b)
+        img = (img - a) / (b - a)
+
+        # Convert to uint8
         img = np.round(img * 255).astype(np.uint8)
+
+    # Convert from uint16
     elif img.dtype == np.uint16:
         img = (img // 256).astype(np.uint8)
+
+    # Other dtypes than float, uint8, uint16 are not supported
     elif img.dtype != np.uint8:
         raise ValueError(f'unknown dtype: {img.dtype}')
+
     if img.ndim == 2:
         result = np.dstack([img] * 3).copy()
     else:
@@ -72,11 +99,11 @@
         skimage.io.imsave(out_fn, out_im.astype(im1.dtype))  # format of output is the same as input
 
 
-def seg_contour(im1_fn, im2_fn, out_fn, linewidth, color='#ff0000', show_label=False, label_color='#ffff00'):
+def seg_contour(im1_fn, im2_fn, out_fn, fp_lower, fp_upper, linewidth, color='#ff0000', show_label=False, label_color='#ffff00'):
     img = giatools.io.imread(im1_fn)
     labels = giatools.io.imread(im2_fn)
 
-    result = get_rgb8_copy(img)
+    result = get_rgb8_copy(img, fp_lower, fp_upper)
     cp = ContourPaint(labels, linewidth, where='center')
     color_rgb = np.multiply(255, matplotlib.colors.to_rgb(color))
 
@@ -106,6 +133,8 @@
     parser.add_argument("im2", help="The second image")
     parser.add_argument("out", help="Output image")
     parser.add_argument('--method', dest='method', default='coloc_vis', help='How to overlay images')
+    parser.add_argument('--fp_lower', default='0', type=str, help='Lower bound for floating point conversion')
+    parser.add_argument('--fp_upper', default='1', type=str, help='Upper bound for floating point conversion')
     parser.add_argument('--alpha', dest='alpha', default=0.5, type=float, help='Blending weight')
     parser.add_argument('--thickness', dest='thickness', default=2, type=int, help='Contour thickness')
     parser.add_argument('--color', dest='color', default='#FF0000', help='Contour color')
@@ -118,8 +147,14 @@
     elif args.method == 'blending':
         blending(args.im1, args.im2, args.out, alpha=args.alpha)
     elif args.method == 'seg_contour':
-        seg_contour(args.im1, args.im2, args.out,
-                    linewidth=args.thickness,
-                    color=args.color,
-                    show_label=args.show_label,
-                    label_color=args.label_color)
+        seg_contour(
+            args.im1,
+            args.im2,
+            args.out,
+            fp_lower=args.fp_lower,
+            fp_upper=args.fp_upper,
+            linewidth=args.thickness,
+            color=args.color,
+            show_label=args.show_label,
+            label_color=args.label_color,
+        )
--- a/overlay_images.xml	Mon Sep 23 10:26:26 2024 +0000
+++ b/overlay_images.xml	Fri Nov 28 08:41:02 2025 +0000
@@ -1,13 +1,13 @@
-<tool id="ip_overlay_images" name="Overlay images" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05">
+<tool id="ip_overlay_images" name="Overlay images" version="@TOOL_VERSION@" profile="20.05">
     <description></description>
     <macros>
         <import>creators.xml</import>
         <import>tests.xml</import>
-        <token name="@TOOL_VERSION@">0.0.4</token>
-        <token name="@VERSION_SUFFIX@">4</token>
+        <token name="@TOOL_VERSION@">0.0.5</token>
     </macros>
     <creator>
         <expand macro="creators/bmcv"/>
+        <expand macro="creators/kostrykin"/>
         <expand macro="creators/thawn"/>
     </creator>
     <edam_operations>
@@ -17,7 +17,7 @@
         <xref type="bio.tools">galaxy_image_analysis</xref>
     </xrefs>
     <requirements>
-        <requirement type="package" version="0.18.1">scikit-image</requirement> 
+        <requirement type="package" version="0.18.1">scikit-image</requirement>
         <requirement type="package" version="3.3.4">matplotlib</requirement>
         <requirement type="package" version="2020.10.1">tifffile</requirement>
         <requirement type="package" version="1.21">numpy</requirement>
@@ -31,12 +31,14 @@
         #if $method_option.method == "seg_contour"
             ./output.png
         #else
-            ./output.tif
+            ./output.tiff
         #end if
         --method $method_option.method
         #if $method_option.method == "blending"
             --alpha $method_option.alpha
         #elif $method_option.method == "seg_contour"
+            --fp_lower '${method_option.fp_conversion.lower}'
+            --fp_upper '${method_option.fp_conversion.upper}'
             --thickness $method_option.thickness
             --color '$method_option.color'
             $method_option.show_label
@@ -46,32 +48,50 @@
     </command>
     <inputs>
         <conditional name="method_option">
+
             <param name="method" type="select" label="Type of the overlay">
                 <option value="coloc_vis" selected="True">Colocalization</option>
                 <option value="blending">Linear blending</option>
                 <option value="seg_contour">Segmentation contours over image</option>
             </param>
+
             <when value="coloc_vis">
                 <param name="im1" type="data" format="tiff,png" label="Image 1 (red channel)" />
                 <param name="im2" type="data" format="tiff,png" label="Image 2 (green channel)" />
             </when>
+
             <when value="blending">
                 <param name="im1" type="data" format="tiff,png" label="Image 1" />
                 <param name="im2" type="data" format="tiff,png" label="Image 2" />
                 <param name="alpha" type="float" value="0.5" min="0.0" max="1.0" label="The weight for blending: result = (1 - weight) * image1 + weight * image2." />
             </when>
+
             <when value="seg_contour">
                 <param name="im1" type="data" format="tiff,png" label="Intensity image" />
+
+                <section name="fp_conversion" title="Intensity image floating point conversion" expanded="false" help="This is only used if the values of the intensity image have a floating point format. Overlay images are created as PNG files, that do not support floating point values (but only integer values between 0 and 255). Conversion of floating point intensity values to integer values via linear mapping is generally ambiguous and can be adapted here.">
+                    <param name="lower" type="select" label="Lower bound conversion" help="Choose which floating point intensity value will be mapped to 0 (i.e. black if grayscale).">
+                        <option value="0" selected="True">0</option>
+                        <option value="-1">-1</option>
+                        <option value="min">Minimum value of the image</option>
+                    </param>
+                    <param name="upper" type="select" label="Upper bound conversion" help="Choose which floating point intensity value will be mapped to 255 (i.e. white if grayscale).">
+                        <option value="1" selected="True">1</option>
+                        <option value="max">Maximum value of the image</option>
+                    </param>
+                </section>
+
                 <param name="im2" type="data" format="tiff,png" label="Label map" />
                 <param name="thickness" type="integer" value="2" min="1" label="Contour thickness (in pixels)" />
                 <param name="color" type="color" value="#ff0000" label="Contour color"/>
                 <param argument="--show_label" type="boolean" checked='false' truevalue="--show_label" falsevalue="" label="Show labels" />
                 <param name="label_color" type="color" value="#ffff00" label="Label color"/>
             </when>
+
         </conditional>
     </inputs>
     <outputs>
-        <data format="tiff" name="out_tiff" from_work_dir="output.tif" label="${tool.name} on ${on_string} output:tiff">
+        <data format="tiff" name="out_tiff" from_work_dir="output.tiff" label="${tool.name} on ${on_string} output:tiff">
             <filter>method_option['method'] != 'seg_contour'</filter>
         </data>
         <data format="png" name="out_png" from_work_dir="output.png" label="${tool.name} on ${on_string} output:png">
@@ -80,51 +100,159 @@
     </outputs>
     <tests>
         <test expect_num_outputs="1">
-            <param name="im1" value="mask1.tif"/>
-            <param name="im2" value="mask1r.tif"/>
-            <param name="method" value="coloc_vis"/>
-            <expand macro="tests/intensity_image_diff" name="out_tiff" value="test1.tif" ftype="tiff"/>
+            <conditional name="method_option">
+                <param name="method" value="coloc_vis"/>
+                <param name="im1" value="mask1.tiff"/>
+                <param name="im2" value="mask1r.tiff"/>
+            </conditional>
+            <expand macro="tests/intensity_image_diff" name="out_tiff" value="test1.tiff" ftype="tiff"/>
         </test>
         <test expect_num_outputs="1">
-            <param name="im1" value="mask1.tif"/>
-            <param name="im2" value="mask1r.tif"/>
-            <param name="method" value="blending"/>
-            <param name="alpha" value="0.3"/>
-            <expand macro="tests/intensity_image_diff" name="out_tiff" value="test2.tif" ftype="tiff"/>
+            <conditional name="method_option">
+                <param name="method" value="blending"/>
+                <param name="im1" value="mask1.tiff"/>
+                <param name="im2" value="mask1r.tiff"/>
+                <param name="alpha" value="0.3"/>
+            </conditional>
+            <expand macro="tests/intensity_image_diff" name="out_tiff" value="test2.tiff" ftype="tiff"/>
         </test>
         <test expect_num_outputs="1">
-            <param name="im1" value="sample1_uint8.tif"/>
-            <param name="im2" value="mask1.tif"/>
-            <param name="method" value="seg_contour"/>
-            <param name="thickness" value="2"/>
-            <param name="color" value="#ff0000"/>
-            <param name="show_label" value="--show_label"/>
+            <conditional name="method_option">
+                <param name="method" value="seg_contour"/>
+                <param name="im1" value="sample1_uint8.tiff"/>
+                <param name="im2" value="mask1.tiff"/>
+                <param name="thickness" value="2"/>
+                <param name="color" value="#ff0000"/>
+                <param name="label_color" value="#ffff00"/>
+                <param name="show_label" value="true"/>
+            </conditional>
             <expand macro="tests/intensity_image_diff" name="out_png" value="test3.png" ftype="png"/>
         </test>
         <test expect_num_outputs="1"><!-- segmentation overlay, 8bit test -->
-            <param name="im1" value="sample1_uint8.tif"/>
-            <param name="im2" value="mask2.tif"/>
-            <param name="method" value="seg_contour"/>
-            <param name="thickness" value="2"/>
-            <param name="color" value="#ff0000"/>
+            <conditional name="method_option">
+                <param name="method" value="seg_contour"/>
+                <param name="im1" value="sample1_uint8.tiff"/>
+                <param name="im2" value="mask2.tiff"/>
+                <param name="thickness" value="2"/>
+                <param name="color" value="#ff0000"/>
+                <param name="label_color" value="#ffff00"/>
+            </conditional>
             <expand macro="tests/intensity_image_diff" name="out_png" value="test4.png" ftype="png"/>
         </test>
         <test expect_num_outputs="1"><!-- segmentation overlay, 16bit test -->
-            <param name="im1" value="sample1_uint16.tif"/>
-            <param name="im2" value="mask2.tif"/>
-            <param name="method" value="seg_contour"/>
-            <param name="thickness" value="2"/>
-            <param name="color" value="#ff0000"/>
+            <conditional name="method_option">
+                <param name="method" value="seg_contour"/>
+                <param name="im1" value="sample1_uint16.tiff"/>
+                <param name="im2" value="mask2.tiff"/>
+                <param name="thickness" value="2"/>
+                <param name="color" value="#ff0000"/>
+                <param name="label_color" value="#ffff00"/>
+            </conditional>
             <expand macro="tests/intensity_image_diff" name="out_png" value="test4.png" ftype="png" eps="1"/>
         </test>
         <test expect_num_outputs="1"><!-- segmentation overlay, 8bit RGB test -->
-            <param name="im1" value="sample1_uint8_rgb.png"/>
-            <param name="im2" value="mask2.tif"/>
-            <param name="method" value="seg_contour"/>
-            <param name="thickness" value="2"/>
-            <param name="color" value="#ff0000"/>
+            <conditional name="method_option">
+                <param name="method" value="seg_contour"/>
+                <param name="im1" value="sample1_uint8_rgb.png"/>
+                <param name="im2" value="mask2.tiff"/>
+                <param name="thickness" value="2"/>
+                <param name="color" value="#ff0000"/>
+                <param name="label_color" value="#ffff00"/>
+            </conditional>
             <expand macro="tests/intensity_image_diff" name="out_png" value="test5.png" ftype="png"/>
         </test>
+        <test expect_num_outputs="1"><!-- segmentation overlay, floating point conversion test 0/1 -->
+            <conditional name="method_option">
+                <param name="method" value="seg_contour"/>
+                <param name="im1" value="sample2.tiff"/>
+                <param name="im2" value="mask3.tiff"/>
+                <param name="thickness" value="1"/>
+                <param name="color" value="#ff0000"/>
+                <param name="label_color" value="#ffff00"/>
+                <section name="fp_conversion">
+                    <param name="lower" value="0"/>
+                    <param name="upper" value="1"/>
+                </section>
+            </conditional>
+            <expand macro="tests/intensity_image_diff" name="out_png" value="test6.png" ftype="png"/>
+        </test>
+        <test expect_num_outputs="1"><!-- segmentation overlay, floating point conversion test -1/1 -->
+            <conditional name="method_option">
+                <param name="method" value="seg_contour"/>
+                <param name="im1" value="sample2.tiff"/>
+                <param name="im2" value="mask3.tiff"/>
+                <param name="thickness" value="1"/>
+                <param name="color" value="#ff0000"/>
+                <param name="label_color" value="#ffff00"/>
+                <section name="fp_conversion">
+                    <param name="lower" value="-1"/>
+                    <param name="upper" value="1"/>
+                </section>
+            </conditional>
+            <expand macro="tests/intensity_image_diff" name="out_png" value="test7.png" ftype="png"/>
+        </test>
+        <test expect_num_outputs="1"><!-- segmentation overlay, floating point conversion test min/1 -->
+            <conditional name="method_option">
+                <param name="method" value="seg_contour"/>
+                <param name="im1" value="sample2.tiff"/>
+                <param name="im2" value="mask3.tiff"/>
+                <param name="thickness" value="1"/>
+                <param name="color" value="#ff0000"/>
+                <param name="label_color" value="#ffff00"/>
+                <section name="fp_conversion">
+                    <param name="lower" value="min"/>
+                    <param name="upper" value="1"/>
+                </section>
+            </conditional>
+            <expand macro="tests/intensity_image_diff" name="out_png" value="test8.png" ftype="png"/>
+        </test>
+        <test expect_num_outputs="1"><!-- segmentation overlay, floating point conversion test 0/max -->
+            <conditional name="method_option">
+                <param name="method" value="seg_contour"/>
+                <param name="im1" value="sample2.tiff"/>
+                <param name="im2" value="mask3.tiff"/>
+                <param name="thickness" value="1"/>
+                <param name="color" value="#ff0000"/>
+                <param name="label_color" value="#ffff00"/>
+                <section name="fp_conversion">
+                    <param name="lower" value="0"/>
+                    <param name="upper" value="max"/>
+                </section>
+            </conditional>
+            <expand macro="tests/intensity_image_diff" name="out_png" value="test9.png" ftype="png"/>
+        </test>
+        <test expect_num_outputs="1"><!-- segmentation overlay, floating point conversion test min/max -->
+            <conditional name="method_option">
+                <param name="method" value="seg_contour"/>
+                <param name="im1" value="sample2.tiff"/>
+                <param name="im2" value="mask3.tiff"/>
+                <param name="thickness" value="1"/>
+                <param name="color" value="#ff0000"/>
+                <param name="label_color" value="#ffff00"/>
+                <section name="fp_conversion">
+                    <param name="lower" value="min"/>
+                    <param name="upper" value="max"/>
+                </section>
+            </conditional>
+            <expand macro="tests/intensity_image_diff" name="out_png" value="test10.png" ftype="png"/>
+        </test>
+        <test expect_failure="true"><!-- segmentation overlay, floating point conversion test with illegal settings -->
+            <conditional name="method_option">
+                <param name="method" value="seg_contour"/>
+                <param name="im1" value="sample3.tiff"/>
+                <param name="im2" value="mask3.tiff"/>
+                <param name="thickness" value="1"/>
+                <param name="color" value="#ff0000"/>
+                <param name="label_color" value="#ffff00"/>
+                <section name="fp_conversion">
+                    <param name="lower" value="0"/>
+                    <param name="upper" value="max"/>
+                </section>
+            </conditional>
+            <assert_stderr>
+                <has_text text="Lower bound (0) must be less than upper bound (-10)." />
+            </assert_stderr>
+        </test>
     </tests>
     <help><![CDATA[
 
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