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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
author imgteam
date Wed, 25 Sep 2024 16:16:10 +0000
parents 756e062741dc
children
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2:756e062741dc 3:73cc4e6a741d
1 <tool id="imagej2_noise" name="Add or remove noise" version="@WRAPPER_VERSION@.1"> 1 <tool id="imagej2_noise" name="Add or remove noise" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.0">
2 <description>with ImageJ2</description> 2 <description>with ImageJ2</description>
3 <macros> 3 <macros>
4 <import>imagej2_macros.xml</import> 4 <import>imagej2_macros.xml</import>
5 <xml name="insertion_select">
6 <param name="insertion" type="select" label="Insertion">
7 <option value="additive" selected="True">Additive</option>
8 <option value="multiplicative">Multiplicative</option>
9 </param>
10 </xml>
11 </macros> 5 </macros>
12 <edam_operations> 6 <edam_operations>
13 <edam_operation>operation_3443</edam_operation> 7 <edam_operation>operation_3443</edam_operation>
14 </edam_operations> 8 </edam_operations>
15 <xrefs> 9 <xrefs>
17 <xref type="biii">imagej2</xref> 11 <xref type="biii">imagej2</xref>
18 </xrefs> 12 </xrefs>
19 <expand macro="fiji_requirements"/> 13 <expand macro="fiji_requirements"/>
20 <command detect_errors="exit_code"><![CDATA[ 14 <command detect_errors="exit_code"><![CDATA[
21 #import os 15 #import os
22 #set error_log = 'output_log.txt'
23 #if str($noise_cond.noise) == 'randomj':
24 #set randomj_value = $noise_cond.randomj_cond.randomj
25 #else:
26 #set randomj_value = None
27 #end if
28 #set input_sans_ext = $os.path.splitext($os.path.basename($input.file_name))[0] 16 #set input_sans_ext = $os.path.splitext($os.path.basename($input.file_name))[0]
29 #set input_with_ext = '.'.join([input_sans_ext, $input.ext]) 17 #set input_with_ext = './' + '.'.join([input_sans_ext, $input.ext])
30 ln -s '$input.file_name' '$input_with_ext' && 18 ln -s '$input.file_name' '$input_with_ext' &&
31 #set output_filename = '.'.join(['output', $input.ext]) 19 #set output_filename = '.'.join(['output', $input.ext])
32 touch '$output_filename' && 20 touch '$output_filename' &&
33 touch '$error_log' &&
34 ImageJ --ij2 --headless --debug 21 ImageJ --ij2 --headless --debug
35 --jython '$__tool_directory__/imagej2_noise_jython_script.py' 22 --jython '$__tool_directory__/imagej2_noise_jython_script.py'
36 '$error_log'
37 '$input_with_ext' 23 '$input_with_ext'
38 '$input.ext' 24 '$input.ext'
39 '$noise_cond.noise' 25 '$noise_cond.noise'
40 #if $noise_cond.noise == 'add_specified_noise': 26 #if $noise_cond.noise == 'add_specified_noise':
41 $noise_cond.standard_deviation 27 $noise_cond.standard_deviation
49 #else: 35 #else:
50 'None' 36 'None'
51 'None' 37 'None'
52 'None' 38 'None'
53 #end if 39 #end if
54 '$randomj_value'
55 #if $randomj_value == 'randomj_binomial':
56 $noise_cond.randomj_cond.trials
57 $noise_cond.randomj_cond.probability
58 #else:
59 'None'
60 'None'
61 #end if
62 #if $randomj_value == 'randomj_exponential':
63 $noise_cond.randomj_cond.lammbda
64 #else:
65 'None'
66 #end if
67 #if $randomj_value == 'randomj_gamma':
68 $noise_cond.randomj_cond.order
69 #else:
70 'None'
71 #end if
72 #if $randomj_value in['randomj_gaussian', 'randomj_poisson']:
73 $noise_cond.randomj_cond.mean
74 #if $randomj_value == 'randomj_gaussian':
75 $noise_cond.randomj_cond.sigma
76 #else:
77 'None'
78 #end if
79 #else:
80 'None'
81 'None'
82 #end if
83 #if $randomj_value == 'randomj_uniform':
84 $noise_cond.randomj_cond.min
85 $noise_cond.randomj_cond.max
86 #else:
87 'None'
88 'None'
89 #end if
90 #if str($randomj_value) != 'None':
91 '$noise_cond.randomj_cond.insertion'
92 #else:
93 'None'
94 #end if
95 '$output_filename' 40 '$output_filename'
96 &>'$error_log'; 41 && mv '$output_filename' '$output';
97 if [[ $? -ne 0 ]]; then
98 cat '$error_log' >&2;
99 else
100 mv '$output_filename' '$output';
101 fi
102 ]]></command> 42 ]]></command>
103 <inputs> 43 <inputs>
104 <expand macro="param_input"/> 44 <expand macro="param_input"/>
105 <conditional name="noise_cond"> 45 <conditional name="noise_cond">
106 <param name="noise" type="select" label="Noise"> 46 <param name="noise" type="select" label="Noise">
109 <option value="salt_and_pepper">Salt and Pepper</option> 49 <option value="salt_and_pepper">Salt and Pepper</option>
110 <option value="despeckle">Despeckle</option> 50 <option value="despeckle">Despeckle</option>
111 <option value="remove_outliers">Remove Outliers</option> 51 <option value="remove_outliers">Remove Outliers</option>
112 <option value="remove_nans">Remove NaNs</option> 52 <option value="remove_nans">Remove NaNs</option>
113 <option value="rof_denoise">ROF Denoise</option> 53 <option value="rof_denoise">ROF Denoise</option>
114 <option value="randomj">RandomJ</option>
115 </param> 54 </param>
116 <when value="add_noise"/> 55 <when value="add_noise"/>
117 <when value="add_specified_noise"> 56 <when value="add_specified_noise">
118 <param name="standard_deviation" type="float" value="25.0" label="Standard deviation" help="Floating point number"/> 57 <param name="standard_deviation" type="float" value="25.0" label="Standard deviation" help="Floating point number"/>
119 </when> 58 </when>
121 <when value="despeckle"/> 60 <when value="despeckle"/>
122 <when value="remove_outliers"> 61 <when value="remove_outliers">
123 <param name="radius" type="float" value="2.0" label="Radius" help="pixels"/> 62 <param name="radius" type="float" value="2.0" label="Radius" help="pixels"/>
124 <param name="threshold" type="float" value="50.0" label="Threshold"/> 63 <param name="threshold" type="float" value="50.0" label="Threshold"/>
125 <param name="which_outliers" type="select" label="Which Outliers"> 64 <param name="which_outliers" type="select" label="Which Outliers">
126 <option value="bright" selected="True">Bright</option> 65 <option value="Bright" selected="True">Bright</option>
127 <option value="dark">Dark</option> 66 <option value="Dark">Dark</option>
128 </param> 67 </param>
129 </when> 68 </when>
130 <when value="remove_nans"/> 69 <when value="remove_nans"/>
131 <when value="rof_denoise"/> 70 <when value="rof_denoise"/>
132 <when value="randomj">
133 <conditional name="randomj_cond">
134 <param name="randomj" type="select" label="RandomJ">
135 <option value="randomj_binomial" selected="True">RandomJ Binomial</option>
136 <option value="randomj_exponential">RandomJ Exponential</option>
137 <option value="randomj_gamma">RandomJ Gamma</option>
138 <option value="randomj_gaussian">RandomJ Gaussian</option>
139 <option value="randomj_poisson">RandomJ Poisson</option>
140 <option value="randomj_uniform">RandomJ Uniform</option>
141 </param>
142 <when value="randomj_binomial">
143 <param name="trials" type="float" value="1.0" label="Trials"/>
144 <param name="probability" type="float" value="0.5" label="Probability"/>
145 <expand macro="insertion_select"/>
146 </when>
147 <when value="randomj_exponential">
148 <param name="lammbda" type="float" value="0.5" label="Lambda"/>
149 <expand macro="insertion_select"/>
150 </when>
151 <when value="randomj_gamma">
152 <param name="order" type="integer" value="1" label="Order"/>
153 <expand macro="insertion_select"/>
154 </when>
155 <when value="randomj_gaussian">
156 <param name="mean" type="float" value="0.0" label="Mean"/>
157 <param name="sigma" type="float" value="1.0" label="Sigma"/>
158 <expand macro="insertion_select"/>
159 </when>
160 <when value="randomj_poisson">
161 <param name="mean" type="float" value="1.0" label="Mean"/>
162 <expand macro="insertion_select"/>
163 </when>
164 <when value="randomj_uniform">
165 <param name="min" type="float" value="0.0" label="Min"/>
166 <param name="max" type="float" value="1.0" label="Max"/>
167 <expand macro="insertion_select"/>
168 </when>
169 </conditional>
170 </when>
171 </conditional> 71 </conditional>
172 </inputs> 72 </inputs>
173 <outputs> 73 <outputs>
174 <data name="output" format_source="input"/> 74 <data name="output" format_source="input"/>
175 </outputs> 75 </outputs>
176 <tests> 76 <tests>
177 <test> 77 <test>
178 <param name="input" value="blobs.gif"/> 78 <param name="input" value="blobs.gif"/>
179 <param name="noise" value="add_specified_noise"/> 79 <param name="noise" value="add_specified_noise"/>
180 <output name="output" file="add_specified_noise.gif"/> 80 <param name="standard_deviation" value="5" />
81 <!-- Cannot use image_diff as the noise is random -->
82 <output name="output" file="add_specified_noise.gif" compare="sim_size"/>
181 </test> 83 </test>
182 <test> 84 <test>
183 <param name="input" value="blobs.gif"/> 85 <param name="input" value="blobs.gif"/>
184 <param name="noise" value="despeckle"/> 86 <param name="noise" value="despeckle"/>
185 <output name="output" file="despeckle.gif"/> 87 <output name="output" file="despeckle.gif" compare="image_diff"/>
186 </test> 88 </test>
187 <test> 89 <test>
188 <param name="input" value="blobs.gif"/> 90 <param name="input" value="blobs.gif"/>
189 <param name="noise" value="remove_outliers"/> 91 <param name="noise" value="remove_outliers"/>
190 <output name="output" file="remove_outliers.gif"/> 92 <param name="radius" value="10.0"/>
93 <param name="threshold" value="1"/>
94 <param name="which_outliers" value="Bright"/>
95 <output name="output" file="remove_outliers.gif" compare="image_diff"/>
96 </test>
97 <test expect_failure="true">
98 <param name="input" value="blobs.gif"/>
99 <param name="noise" value="remove_nans"/>
191 </test> 100 </test>
192 </tests> 101 </tests>
193 <help> 102 <help>
194 **What it does** 103 **What it does**
195 104
200 - **Add Specified Noise** - Adds Gaussian noise with a mean of zero and a chosen standard deviation. 109 - **Add Specified Noise** - Adds Gaussian noise with a mean of zero and a chosen standard deviation.
201 - **Salt and Pepper** - Adds salt and pepper noise to the image by randomly replacing 2.5% of the pixels with black pixels and 2.5% with white pixels. This command only works with 8-bit images. 110 - **Salt and Pepper** - Adds salt and pepper noise to the image by randomly replacing 2.5% of the pixels with black pixels and 2.5% with white pixels. This command only works with 8-bit images.
202 - **Despeckle** - Replaces each pixel with the median value in its 3 × 3 neighborhood. This is a time consuming operation because for each pixel, the nine pixels in the 3 × 3 neighborhood must be sorted and the center pixel replaced with the median value (the fifth). 111 - **Despeckle** - Replaces each pixel with the median value in its 3 × 3 neighborhood. This is a time consuming operation because for each pixel, the nine pixels in the 3 × 3 neighborhood must be sorted and the center pixel replaced with the median value (the fifth).
203 - **Remove Outliers** - Replaces a pixel by the median of the pixels in the surrounding if it deviates from the median by more than a certain value (the threshold). 112 - **Remove Outliers** - Replaces a pixel by the median of the pixels in the surrounding if it deviates from the median by more than a certain value (the threshold).
204 - **Remove NaNs** - Replaces NaN (Not-a-Number) pixels in 32-bit images by the median of the neighbors inside the circular kernel area defined by Radius. It does not remove patches of NaNs larger than the kernel size, however. 113 - **Remove NaNs** - Replaces NaN (Not-a-Number) pixels in 32-bit images by the median of the neighbors inside the circular kernel area defined by Radius. It does not remove patches of NaNs larger than the kernel size, however.
205 - **RandonJ Binomial** - Contaminates image with random numbers generated using a binomial random variable
206 - **RandonJ Exponential** - Contaminates image with random numbers generated using an exponential random variable.
207 - **RandonJ Gamma** - Contaminates image with random numbers generated using a gamma random variable.
208 - **RandonJ Gaussian** - Contaminates image with random numbers generated using a Gaussian random variable.
209 - **RandonJ Poisson** - Contaminates image with random numbers generated using a Poisson random variable.
210 - **RandonJ Uniform** - Contaminates image with random numbers generated using a uniform random variable.
211 ]]> 114 ]]>
212 </help> 115 </help>
213 <expand macro="fiji_headless_citations"/> 116 <expand macro="fiji_headless_citations"/>
214 </tool> 117 </tool>