annotate imagej2_find_maxima.xml @ 1:f00fd3aa6472 draft default tip

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8ea6a4271431c05c82b09c0d3e629b13e6ea7936
author iuc
date Fri, 22 Jul 2016 23:12:48 -0400
parents 802c21d935e7
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
802c21d935e7 planemo upload commit 378c3ecfbaed0330faf197811d379431b0f9e92c-dirty
iuc
parents:
diff changeset
1 <?xml version='1.0' encoding='UTF-8'?>
802c21d935e7 planemo upload commit 378c3ecfbaed0330faf197811d379431b0f9e92c-dirty
iuc
parents:
diff changeset
2 <tool id="imagej2_find_maxima" name="Find maxima" version="@WRAPPER_VERSION@.0">
802c21d935e7 planemo upload commit 378c3ecfbaed0330faf197811d379431b0f9e92c-dirty
iuc
parents:
diff changeset
3 <description></description>
802c21d935e7 planemo upload commit 378c3ecfbaed0330faf197811d379431b0f9e92c-dirty
iuc
parents:
diff changeset
4 <macros>
802c21d935e7 planemo upload commit 378c3ecfbaed0330faf197811d379431b0f9e92c-dirty
iuc
parents:
diff changeset
5 <import>imagej2_macros.xml</import>
802c21d935e7 planemo upload commit 378c3ecfbaed0330faf197811d379431b0f9e92c-dirty
iuc
parents:
diff changeset
6 </macros>
802c21d935e7 planemo upload commit 378c3ecfbaed0330faf197811d379431b0f9e92c-dirty
iuc
parents:
diff changeset
7 <expand macro="fiji_requirements" />
802c21d935e7 planemo upload commit 378c3ecfbaed0330faf197811d379431b0f9e92c-dirty
iuc
parents:
diff changeset
8 <command>
802c21d935e7 planemo upload commit 378c3ecfbaed0330faf197811d379431b0f9e92c-dirty
iuc
parents:
diff changeset
9 <![CDATA[
802c21d935e7 planemo upload commit 378c3ecfbaed0330faf197811d379431b0f9e92c-dirty
iuc
parents:
diff changeset
10 python $__tool_directory__/imagej2_find_maxima.py
802c21d935e7 planemo upload commit 378c3ecfbaed0330faf197811d379431b0f9e92c-dirty
iuc
parents:
diff changeset
11 --input "$input"
802c21d935e7 planemo upload commit 378c3ecfbaed0330faf197811d379431b0f9e92c-dirty
iuc
parents:
diff changeset
12 --input_datatype $input.ext
802c21d935e7 planemo upload commit 378c3ecfbaed0330faf197811d379431b0f9e92c-dirty
iuc
parents:
diff changeset
13 --scale_when_converting $scale_when_converting
802c21d935e7 planemo upload commit 378c3ecfbaed0330faf197811d379431b0f9e92c-dirty
iuc
parents:
diff changeset
14 --weighted_rgb_conversions $weighted_rgb_conversions
802c21d935e7 planemo upload commit 378c3ecfbaed0330faf197811d379431b0f9e92c-dirty
iuc
parents:
diff changeset
15 --noise_tolerance $noise_tolerance
802c21d935e7 planemo upload commit 378c3ecfbaed0330faf197811d379431b0f9e92c-dirty
iuc
parents:
diff changeset
16 --output_type $output_type
802c21d935e7 planemo upload commit 378c3ecfbaed0330faf197811d379431b0f9e92c-dirty
iuc
parents:
diff changeset
17 --exclude_edge_maxima $exclude_edge_maxima
802c21d935e7 planemo upload commit 378c3ecfbaed0330faf197811d379431b0f9e92c-dirty
iuc
parents:
diff changeset
18 --light_background $light_background
1
f00fd3aa6472 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8ea6a4271431c05c82b09c0d3e629b13e6ea7936
iuc
parents: 0
diff changeset
19 --jython_script $__tool_directory__/imagej2_find_maxima_jython_script.py
0
802c21d935e7 planemo upload commit 378c3ecfbaed0330faf197811d379431b0f9e92c-dirty
iuc
parents:
diff changeset
20 #if str( $output_type ) == "List" or str( $output_type ) == "Count":
802c21d935e7 planemo upload commit 378c3ecfbaed0330faf197811d379431b0f9e92c-dirty
iuc
parents:
diff changeset
21 --output "$results"
802c21d935e7 planemo upload commit 378c3ecfbaed0330faf197811d379431b0f9e92c-dirty
iuc
parents:
diff changeset
22 #else:
802c21d935e7 planemo upload commit 378c3ecfbaed0330faf197811d379431b0f9e92c-dirty
iuc
parents:
diff changeset
23 --output "$output"
802c21d935e7 planemo upload commit 378c3ecfbaed0330faf197811d379431b0f9e92c-dirty
iuc
parents:
diff changeset
24 #end if
802c21d935e7 planemo upload commit 378c3ecfbaed0330faf197811d379431b0f9e92c-dirty
iuc
parents:
diff changeset
25 --output_datatype $output.ext
802c21d935e7 planemo upload commit 378c3ecfbaed0330faf197811d379431b0f9e92c-dirty
iuc
parents:
diff changeset
26 ]]>
802c21d935e7 planemo upload commit 378c3ecfbaed0330faf197811d379431b0f9e92c-dirty
iuc
parents:
diff changeset
27 </command>
802c21d935e7 planemo upload commit 378c3ecfbaed0330faf197811d379431b0f9e92c-dirty
iuc
parents:
diff changeset
28 <inputs>
802c21d935e7 planemo upload commit 378c3ecfbaed0330faf197811d379431b0f9e92c-dirty
iuc
parents:
diff changeset
29 <param format="bmp,eps,gif,jpg,pcx,pgm,png,psd,tiff" name="input" type="data" label="Select image"/>
802c21d935e7 planemo upload commit 378c3ecfbaed0330faf197811d379431b0f9e92c-dirty
iuc
parents:
diff changeset
30 <param name="noise_tolerance" type="integer" value="10" min="0" label="Noise tolerance" help="Maxima are ignored if they do not stand out from the surroundings by more than this value."/>
802c21d935e7 planemo upload commit 378c3ecfbaed0330faf197811d379431b0f9e92c-dirty
iuc
parents:
diff changeset
31 <param name="output_type" type="select" label="Output type">
802c21d935e7 planemo upload commit 378c3ecfbaed0330faf197811d379431b0f9e92c-dirty
iuc
parents:
diff changeset
32 <option value="Single_Points" selected="True">Single Points</option>
802c21d935e7 planemo upload commit 378c3ecfbaed0330faf197811d379431b0f9e92c-dirty
iuc
parents:
diff changeset
33 <option value="Maxima_Within_Tolerance">Maxima Within Tolerance</option>
802c21d935e7 planemo upload commit 378c3ecfbaed0330faf197811d379431b0f9e92c-dirty
iuc
parents:
diff changeset
34 <option value="Segmented_Particles">Segmented Particles</option>
802c21d935e7 planemo upload commit 378c3ecfbaed0330faf197811d379431b0f9e92c-dirty
iuc
parents:
diff changeset
35 <option value="List">List</option>
802c21d935e7 planemo upload commit 378c3ecfbaed0330faf197811d379431b0f9e92c-dirty
iuc
parents:
diff changeset
36 <option value="Count">Count</option>
802c21d935e7 planemo upload commit 378c3ecfbaed0330faf197811d379431b0f9e92c-dirty
iuc
parents:
diff changeset
37 </param>
802c21d935e7 planemo upload commit 378c3ecfbaed0330faf197811d379431b0f9e92c-dirty
iuc
parents:
diff changeset
38 <param name="exclude_edge_maxima" type="select" label="Exclude edge maxima?">
802c21d935e7 planemo upload commit 378c3ecfbaed0330faf197811d379431b0f9e92c-dirty
iuc
parents:
diff changeset
39 <option value="no" selected="True">No</option>
802c21d935e7 planemo upload commit 378c3ecfbaed0330faf197811d379431b0f9e92c-dirty
iuc
parents:
diff changeset
40 <option value="yes">Yes</option>
802c21d935e7 planemo upload commit 378c3ecfbaed0330faf197811d379431b0f9e92c-dirty
iuc
parents:
diff changeset
41 </param>
802c21d935e7 planemo upload commit 378c3ecfbaed0330faf197811d379431b0f9e92c-dirty
iuc
parents:
diff changeset
42 <param name="light_background" type="select" label="Light background?">
802c21d935e7 planemo upload commit 378c3ecfbaed0330faf197811d379431b0f9e92c-dirty
iuc
parents:
diff changeset
43 <option value="no" selected="True">No</option>
802c21d935e7 planemo upload commit 378c3ecfbaed0330faf197811d379431b0f9e92c-dirty
iuc
parents:
diff changeset
44 <option value="yes">Yes</option>
802c21d935e7 planemo upload commit 378c3ecfbaed0330faf197811d379431b0f9e92c-dirty
iuc
parents:
diff changeset
45 </param>
802c21d935e7 planemo upload commit 378c3ecfbaed0330faf197811d379431b0f9e92c-dirty
iuc
parents:
diff changeset
46 <param name="scale_when_converting" type="select" label="Scale when converting?" help="Applies only to 24-bit (RGB) images, ignored for other types.">
802c21d935e7 planemo upload commit 378c3ecfbaed0330faf197811d379431b0f9e92c-dirty
iuc
parents:
diff changeset
47 <option value="yes" selected="True">Yes</option>
802c21d935e7 planemo upload commit 378c3ecfbaed0330faf197811d379431b0f9e92c-dirty
iuc
parents:
diff changeset
48 <option value="no">No</option>
802c21d935e7 planemo upload commit 378c3ecfbaed0330faf197811d379431b0f9e92c-dirty
iuc
parents:
diff changeset
49 </param>
802c21d935e7 planemo upload commit 378c3ecfbaed0330faf197811d379431b0f9e92c-dirty
iuc
parents:
diff changeset
50 <param name="weighted_rgb_conversions" type="select" label="Weighted RGB conversions?" help="Applies only to 24-bit (RGB) images, ignored for other types.">
802c21d935e7 planemo upload commit 378c3ecfbaed0330faf197811d379431b0f9e92c-dirty
iuc
parents:
diff changeset
51 <option value="no" selected="True">No</option>
802c21d935e7 planemo upload commit 378c3ecfbaed0330faf197811d379431b0f9e92c-dirty
iuc
parents:
diff changeset
52 <option value="yes">Yes</option>
802c21d935e7 planemo upload commit 378c3ecfbaed0330faf197811d379431b0f9e92c-dirty
iuc
parents:
diff changeset
53 </param>
802c21d935e7 planemo upload commit 378c3ecfbaed0330faf197811d379431b0f9e92c-dirty
iuc
parents:
diff changeset
54 </inputs>
802c21d935e7 planemo upload commit 378c3ecfbaed0330faf197811d379431b0f9e92c-dirty
iuc
parents:
diff changeset
55 <outputs>
802c21d935e7 planemo upload commit 378c3ecfbaed0330faf197811d379431b0f9e92c-dirty
iuc
parents:
diff changeset
56 <data name="output" format_source="input" label="${tool.name} on ${on_string}: ${output_type}">
802c21d935e7 planemo upload commit 378c3ecfbaed0330faf197811d379431b0f9e92c-dirty
iuc
parents:
diff changeset
57 <filter>output_type != "List" and output_type != "Count"</filter>
802c21d935e7 planemo upload commit 378c3ecfbaed0330faf197811d379431b0f9e92c-dirty
iuc
parents:
diff changeset
58 </data>
802c21d935e7 planemo upload commit 378c3ecfbaed0330faf197811d379431b0f9e92c-dirty
iuc
parents:
diff changeset
59 <data name="results" format="tabular" label="${tool.name} on ${on_string}: ${output_type}">
802c21d935e7 planemo upload commit 378c3ecfbaed0330faf197811d379431b0f9e92c-dirty
iuc
parents:
diff changeset
60 <filter>output_type == "List" or output_type == "Count"</filter>
802c21d935e7 planemo upload commit 378c3ecfbaed0330faf197811d379431b0f9e92c-dirty
iuc
parents:
diff changeset
61 </data>
802c21d935e7 planemo upload commit 378c3ecfbaed0330faf197811d379431b0f9e92c-dirty
iuc
parents:
diff changeset
62 </outputs>
802c21d935e7 planemo upload commit 378c3ecfbaed0330faf197811d379431b0f9e92c-dirty
iuc
parents:
diff changeset
63 <tests>
802c21d935e7 planemo upload commit 378c3ecfbaed0330faf197811d379431b0f9e92c-dirty
iuc
parents:
diff changeset
64 <test>
802c21d935e7 planemo upload commit 378c3ecfbaed0330faf197811d379431b0f9e92c-dirty
iuc
parents:
diff changeset
65 <param name="input" value="blobs.gif" />
802c21d935e7 planemo upload commit 378c3ecfbaed0330faf197811d379431b0f9e92c-dirty
iuc
parents:
diff changeset
66 <output name="output" file="blobs_single_points.gif" compare="sim_size" />
802c21d935e7 planemo upload commit 378c3ecfbaed0330faf197811d379431b0f9e92c-dirty
iuc
parents:
diff changeset
67 </test>
802c21d935e7 planemo upload commit 378c3ecfbaed0330faf197811d379431b0f9e92c-dirty
iuc
parents:
diff changeset
68 <test>
802c21d935e7 planemo upload commit 378c3ecfbaed0330faf197811d379431b0f9e92c-dirty
iuc
parents:
diff changeset
69 <param name="input" value="blobs.gif" />
802c21d935e7 planemo upload commit 378c3ecfbaed0330faf197811d379431b0f9e92c-dirty
iuc
parents:
diff changeset
70 <param name="noise_tolerance" value="13" />
802c21d935e7 planemo upload commit 378c3ecfbaed0330faf197811d379431b0f9e92c-dirty
iuc
parents:
diff changeset
71 <param name="output_type" value="Maxima_Within_Tolerance" />
802c21d935e7 planemo upload commit 378c3ecfbaed0330faf197811d379431b0f9e92c-dirty
iuc
parents:
diff changeset
72 <output name="output" file="blobs_tolerance.gif" compare="sim_size" />
802c21d935e7 planemo upload commit 378c3ecfbaed0330faf197811d379431b0f9e92c-dirty
iuc
parents:
diff changeset
73 </test>
802c21d935e7 planemo upload commit 378c3ecfbaed0330faf197811d379431b0f9e92c-dirty
iuc
parents:
diff changeset
74 <test>
802c21d935e7 planemo upload commit 378c3ecfbaed0330faf197811d379431b0f9e92c-dirty
iuc
parents:
diff changeset
75 <param name="input" value="blobs.gif" />
802c21d935e7 planemo upload commit 378c3ecfbaed0330faf197811d379431b0f9e92c-dirty
iuc
parents:
diff changeset
76 <param name="noise_tolerance" value="16" />
802c21d935e7 planemo upload commit 378c3ecfbaed0330faf197811d379431b0f9e92c-dirty
iuc
parents:
diff changeset
77 <param name="output_type" value="Segmented_Particles" />
802c21d935e7 planemo upload commit 378c3ecfbaed0330faf197811d379431b0f9e92c-dirty
iuc
parents:
diff changeset
78 <param name="exclude_edge_maxima" value="yes" />
802c21d935e7 planemo upload commit 378c3ecfbaed0330faf197811d379431b0f9e92c-dirty
iuc
parents:
diff changeset
79 <output name="output" file="blobs_segmented.gif" compare="sim_size" />
802c21d935e7 planemo upload commit 378c3ecfbaed0330faf197811d379431b0f9e92c-dirty
iuc
parents:
diff changeset
80 </test>
802c21d935e7 planemo upload commit 378c3ecfbaed0330faf197811d379431b0f9e92c-dirty
iuc
parents:
diff changeset
81 <test>
802c21d935e7 planemo upload commit 378c3ecfbaed0330faf197811d379431b0f9e92c-dirty
iuc
parents:
diff changeset
82 <param name="input" value="blobs.gif" />
802c21d935e7 planemo upload commit 378c3ecfbaed0330faf197811d379431b0f9e92c-dirty
iuc
parents:
diff changeset
83 <param name="output_type" value="List" />
802c21d935e7 planemo upload commit 378c3ecfbaed0330faf197811d379431b0f9e92c-dirty
iuc
parents:
diff changeset
84 <output name="output" file="blobs_list.tabular" />
802c21d935e7 planemo upload commit 378c3ecfbaed0330faf197811d379431b0f9e92c-dirty
iuc
parents:
diff changeset
85 </test>
802c21d935e7 planemo upload commit 378c3ecfbaed0330faf197811d379431b0f9e92c-dirty
iuc
parents:
diff changeset
86 <test>
802c21d935e7 planemo upload commit 378c3ecfbaed0330faf197811d379431b0f9e92c-dirty
iuc
parents:
diff changeset
87 <param name="input" value="blobs.gif" />
802c21d935e7 planemo upload commit 378c3ecfbaed0330faf197811d379431b0f9e92c-dirty
iuc
parents:
diff changeset
88 <param name="output_type" value="Count" />
802c21d935e7 planemo upload commit 378c3ecfbaed0330faf197811d379431b0f9e92c-dirty
iuc
parents:
diff changeset
89 <output name="output" file="blobs_count.tabular" />
802c21d935e7 planemo upload commit 378c3ecfbaed0330faf197811d379431b0f9e92c-dirty
iuc
parents:
diff changeset
90 </test>
802c21d935e7 planemo upload commit 378c3ecfbaed0330faf197811d379431b0f9e92c-dirty
iuc
parents:
diff changeset
91 </tests>
802c21d935e7 planemo upload commit 378c3ecfbaed0330faf197811d379431b0f9e92c-dirty
iuc
parents:
diff changeset
92 <help>
802c21d935e7 planemo upload commit 378c3ecfbaed0330faf197811d379431b0f9e92c-dirty
iuc
parents:
diff changeset
93
802c21d935e7 planemo upload commit 378c3ecfbaed0330faf197811d379431b0f9e92c-dirty
iuc
parents:
diff changeset
94 **What it does**
802c21d935e7 planemo upload commit 378c3ecfbaed0330faf197811d379431b0f9e92c-dirty
iuc
parents:
diff changeset
95
802c21d935e7 planemo upload commit 378c3ecfbaed0330faf197811d379431b0f9e92c-dirty
iuc
parents:
diff changeset
96 Determines the local maxima in an image and creates a binary (mask-like) image of the same size with the
802c21d935e7 planemo upload commit 378c3ecfbaed0330faf197811d379431b0f9e92c-dirty
iuc
parents:
diff changeset
97 maxima (or one segmented particle per maximum) marked. For RGB images, maxima of luminance are selected
802c21d935e7 planemo upload commit 378c3ecfbaed0330faf197811d379431b0f9e92c-dirty
iuc
parents:
diff changeset
98 with the luminance defined as the weighted or unweighted average of the colors depending on the **Scale
802c21d935e7 planemo upload commit 378c3ecfbaed0330faf197811d379431b0f9e92c-dirty
iuc
parents:
diff changeset
99 when converting** and **Weighted RGB conversions** settings.
802c21d935e7 planemo upload commit 378c3ecfbaed0330faf197811d379431b0f9e92c-dirty
iuc
parents:
diff changeset
100
802c21d935e7 planemo upload commit 378c3ecfbaed0330faf197811d379431b0f9e92c-dirty
iuc
parents:
diff changeset
101 - **Scale when converting** (RGB images only) - If "yes", the tool will scale from min--max to 0--255 when converting from 16-bit or 32-bit to 8-bit or to scale from min--max to 0--65535 when converting from 32-bit to 16-bit.
802c21d935e7 planemo upload commit 378c3ecfbaed0330faf197811d379431b0f9e92c-dirty
iuc
parents:
diff changeset
102
802c21d935e7 planemo upload commit 378c3ecfbaed0330faf197811d379431b0f9e92c-dirty
iuc
parents:
diff changeset
103 - **Weighted RGB conversions** (RGB images only) - If "yes", the formula gray = 0.299 × red + 0.587 × green + 0.114 × blue is used to convert RGB images to grayscale. If "no", the formula gray = (red + green + blue) ⁄ 3 is used.
802c21d935e7 planemo upload commit 378c3ecfbaed0330faf197811d379431b0f9e92c-dirty
iuc
parents:
diff changeset
104
802c21d935e7 planemo upload commit 378c3ecfbaed0330faf197811d379431b0f9e92c-dirty
iuc
parents:
diff changeset
105 - **Noise Tolerance** - Maxima are ignored if they do not stand out from the surroundings by more than this value (calibrated units for calibrated images). In other words, a threshold is set at the maximum value minus noise tolerance and the contiguous area around the maximum above the threshold is analyzed. For accepting a maximum, this area must not contain any point with a value higher than the maximum. Only one maximum within this area is accepted.
802c21d935e7 planemo upload commit 378c3ecfbaed0330faf197811d379431b0f9e92c-dirty
iuc
parents:
diff changeset
106
802c21d935e7 planemo upload commit 378c3ecfbaed0330faf197811d379431b0f9e92c-dirty
iuc
parents:
diff changeset
107 - **Output Type** can be:
802c21d935e7 planemo upload commit 378c3ecfbaed0330faf197811d379431b0f9e92c-dirty
iuc
parents:
diff changeset
108
802c21d935e7 planemo upload commit 378c3ecfbaed0330faf197811d379431b0f9e92c-dirty
iuc
parents:
diff changeset
109 - **Single Points** - Produces an image with one single point per maximum.
802c21d935e7 planemo upload commit 378c3ecfbaed0330faf197811d379431b0f9e92c-dirty
iuc
parents:
diff changeset
110
802c21d935e7 planemo upload commit 378c3ecfbaed0330faf197811d379431b0f9e92c-dirty
iuc
parents:
diff changeset
111 - **Maxima Within Tolerance** - Produces an image with all points within the "Noise Tolerance" for each maximum.
802c21d935e7 planemo upload commit 378c3ecfbaed0330faf197811d379431b0f9e92c-dirty
iuc
parents:
diff changeset
112
802c21d935e7 planemo upload commit 378c3ecfbaed0330faf197811d379431b0f9e92c-dirty
iuc
parents:
diff changeset
113 - **Segmented Particles** - Assumes that each maximum belongs to a particle and segments the image by a watershed algorithm applied to the values of the image.
802c21d935e7 planemo upload commit 378c3ecfbaed0330faf197811d379431b0f9e92c-dirty
iuc
parents:
diff changeset
114
802c21d935e7 planemo upload commit 378c3ecfbaed0330faf197811d379431b0f9e92c-dirty
iuc
parents:
diff changeset
115 - **List** - Produces the list x, y of maxima in the image.
802c21d935e7 planemo upload commit 378c3ecfbaed0330faf197811d379431b0f9e92c-dirty
iuc
parents:
diff changeset
116
802c21d935e7 planemo upload commit 378c3ecfbaed0330faf197811d379431b0f9e92c-dirty
iuc
parents:
diff changeset
117 - **Count** - Produces the number of maxima in the image.
802c21d935e7 planemo upload commit 378c3ecfbaed0330faf197811d379431b0f9e92c-dirty
iuc
parents:
diff changeset
118
802c21d935e7 planemo upload commit 378c3ecfbaed0330faf197811d379431b0f9e92c-dirty
iuc
parents:
diff changeset
119 - **Exclude Edge Maxima** - Excludes maxima if the area within the noise tolerance surrounding a maximum touches the edge of the image (edge of the selection does not matter).
802c21d935e7 planemo upload commit 378c3ecfbaed0330faf197811d379431b0f9e92c-dirty
iuc
parents:
diff changeset
120
802c21d935e7 planemo upload commit 378c3ecfbaed0330faf197811d379431b0f9e92c-dirty
iuc
parents:
diff changeset
121 - **Light Background** - Select "yes" if the image background is brighter than the objects you want to find.
802c21d935e7 planemo upload commit 378c3ecfbaed0330faf197811d379431b0f9e92c-dirty
iuc
parents:
diff changeset
122
802c21d935e7 planemo upload commit 378c3ecfbaed0330faf197811d379431b0f9e92c-dirty
iuc
parents:
diff changeset
123 </help>
802c21d935e7 planemo upload commit 378c3ecfbaed0330faf197811d379431b0f9e92c-dirty
iuc
parents:
diff changeset
124 <expand macro="fiji_headless_citations" />
802c21d935e7 planemo upload commit 378c3ecfbaed0330faf197811d379431b0f9e92c-dirty
iuc
parents:
diff changeset
125 </tool>