Mercurial > repos > imgteam > imagej2_find_maxima

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
author imgteam
date Tue, 17 Sep 2019 16:57:59 -0400
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2395ccf9ccc1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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1 <?xml version='1.0' encoding='UTF-8'?>
2395ccf9ccc1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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2 <tool id="imagej2_find_maxima" name="Find maxima" version="@WRAPPER_VERSION@.0">
2395ccf9ccc1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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3 <description></description>
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4 <macros>
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5 <import>imagej2_macros.xml</import>
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6 </macros>
2395ccf9ccc1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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7 <expand macro="fiji_requirements" />
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8 <command>
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9 <![CDATA[
2395ccf9ccc1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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10 python $__tool_directory__/imagej2_find_maxima.py
2395ccf9ccc1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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11 --input "$input"
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12 --input_datatype $input.ext
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13 --scale_when_converting $scale_when_converting
2395ccf9ccc1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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14 --weighted_rgb_conversions $weighted_rgb_conversions
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15 --noise_tolerance $noise_tolerance
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16 --output_type $output_type
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17 --exclude_edge_maxima $exclude_edge_maxima
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18 --light_background $light_background
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19 --jython_script $__tool_directory__/imagej2_find_maxima_jython_script.py
2395ccf9ccc1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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20 #if str( $output_type ) == "List" or str( $output_type ) == "Count":
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21 --output "$results"
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22 --output_datatype "tabular"
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23 #else:
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24 --output "$output"
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25 --output_datatype $output.ext
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26 #end if
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27 ]]>
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28 </command>
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29 <inputs>
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30 <param format="bmp,eps,gif,jpg,pcx,pgm,png,psd,tiff" name="input" type="data" label="Select image"/>
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31 <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."/>
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32 <param name="output_type" type="select" label="Output type">
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33 <option value="Single_Points" selected="True">Single Points</option>
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34 <option value="Maxima_Within_Tolerance">Maxima Within Tolerance</option>
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35 <option value="Segmented_Particles">Segmented Particles</option>
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36 <!--
2395ccf9ccc1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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37 This version of Fiji does not produce the same resultsTable
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38 as the previous version, so eliminating these options until
2395ccf9ccc1 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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39 there is time to investigate
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40 <option value="List">List</option>
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41 <option value="Count">Count</option>
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42 -->
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43 </param>
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44 <param name="exclude_edge_maxima" type="select" label="Exclude edge maxima?">
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45 <option value="no" selected="True">No</option>
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46 <option value="yes">Yes</option>
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47 </param>
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48 <param name="light_background" type="select" label="Light background?">
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49 <option value="no" selected="True">No</option>
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50 <option value="yes">Yes</option>
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51 </param>
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52 <param name="scale_when_converting" type="select" label="Scale when converting?" help="Applies only to 24-bit (RGB) images, ignored for other types.">
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53 <option value="yes" selected="True">Yes</option>
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54 <option value="no">No</option>
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55 </param>
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56 <param name="weighted_rgb_conversions" type="select" label="Weighted RGB conversions?" help="Applies only to 24-bit (RGB) images, ignored for other types.">
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57 <option value="no" selected="True">No</option>
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58 <option value="yes">Yes</option>
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59 </param>
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60 </inputs>
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61 <outputs>
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62 <data name="output" format_source="input" label="${tool.name} on ${on_string}: ${output_type}">
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63 <filter>output_type != "List" and output_type != "Count"</filter>
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64 </data>
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65 <data name="results" format="tabular" label="${tool.name} on ${on_string}: ${output_type}">
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66 <filter>output_type == "List" or output_type == "Count"</filter>
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67 </data>
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68 </outputs>
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69 <tests>
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70 <test>
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71 <param name="input" value="blobs.gif" />
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72 <output name="output" file="blobs_single_points.gif" compare="sim_size" />
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73 </test>
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74 <test>
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75 <param name="input" value="blobs.gif" />
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76 <param name="noise_tolerance" value="13" />
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77 <param name="output_type" value="Maxima_Within_Tolerance" />
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78 <output name="output" file="blobs_tolerance.gif" compare="sim_size" />
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79 </test>
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80 <test>
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81 <param name="input" value="blobs.gif" />
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82 <param name="noise_tolerance" value="16" />
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83 <param name="output_type" value="Segmented_Particles" />
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84 <param name="exclude_edge_maxima" value="yes" />
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85 <output name="output" file="blobs_segmented.gif" compare="sim_size" />
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86 </test>
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87 <!--
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88 This version of Fiji does not produce the same resultsTable
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89 as the previous version, so eliminating these options until
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90 there is time to investigate
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91 <test>
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92 <param name="input" value="blobs.gif" />
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93 <param name="output_type" value="List" />
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94 <output name="output" file="blobs_list.tabular" />
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95 </test>
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96 <test>
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97 <param name="input" value="blobs.gif" />
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98 <param name="output_type" value="Count" />
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99 <output name="output" file="blobs_count.tabular" />
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100 </test>
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101 -->
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102 </tests>
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103 <help>
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104
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105 **What it does**
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106
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107 Determines the local maxima in an image and creates a binary (mask-like) image of the same size with the
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108 maxima (or one segmented particle per maximum) marked. For RGB images, maxima of luminance are selected
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109 with the luminance defined as the weighted or unweighted average of the colors depending on the **Scale
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110 when converting** and **Weighted RGB conversions** settings.
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111
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112 - **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.
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113
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114 - **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.
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115
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116 - **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.
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117
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118 - **Output Type** can be:
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119
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120 - **Single Points** - Produces an image with one single point per maximum.
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121
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122 - **Maxima Within Tolerance** - Produces an image with all points within the "Noise Tolerance" for each maximum.
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123
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124 - **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.
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125
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126 - **List** - Produces the list x, y of maxima in the image.
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127
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128 - **Count** - Produces the number of maxima in the image.
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129
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130 - **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).
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131
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132 - **Light Background** - Select "yes" if the image background is brighter than the objects you want to find.
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133
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134 </help>
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135 <expand macro="fiji_headless_citations" />
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136 </tool>