Mercurial > repos > iuc > imagej2_make_binary

annotate imagej2_macros.xml @ 0:66d9e595dff2 draft

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planemo upload commit 98c34e070343a117019ffd25a3af117808159bf5-dirty
author iuc
date Tue, 04 Aug 2015 13:20:29 -0400
parents
children d26f11339f08
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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1 <?xml version='1.0' encoding='UTF-8'?>
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2 <macros>
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3 <xml name="fiji_20141125_requirements">
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4 <requirements>
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5 <requirement type="package" version="20141125">fiji</requirement>
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6 </requirements>
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7 </xml>
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8 <xml name="python_bioformats_104_requirements">
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9 <requirements>
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10 <requirement type="package" version="20141125">fiji</requirement>
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11 <requirement type="package" version="1.0.11">javabridge</requirement>
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12 <requirement type="package" version="1.9">numpy</requirement>
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13 <requirement type="package" version="1.0.4">python_bioformats</requirement>
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14 </requirements>
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15 </xml>
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16 <xml name="stdio">
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17 <stdio>
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18 <exit_code range="1:"/>
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19 <exit_code range=":-1"/>
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20 <regex match="Error:"/>
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21 <regex match="Exception:"/>
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22 </stdio>
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23 </xml>
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24 <xml name="image_type">
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25 <param name="image_type" type="select" label="Image type">
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26 <option value="8-bit_white" selected="True">8-bit white</option>
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27 <option value="8-bit_black">8-bit black</option>
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28 <option value="8-bit_random">8-bit random</option>
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29 <option value="8-bit_ramp">8-bit ramp</option>
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30 <option value="16-bit_white">16-bit white</option>
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31 <option value="16-bit_black">16-bit black</option>
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32 <option value="16-bit_random">16-bit random</option>
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33 <option value="16-bit_ramp">16-bit ramp</option>
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34 <option value="32-bit_white">32-bit white</option>
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35 <option value="32-bit_black">32-bit black</option>
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36 <option value="32-bit_random">32-bit random</option>
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37 <option value="32-bit_ramp">32-bit ramp</option>
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38 <option value="RGB_white">RGB white</option>
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39 <option value="RGB_black">RGB black</option>
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40 <option value="RGB_random">RGB random</option>
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41 <option value="RGB_ramp">RGB ramp</option>
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42 </param>
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43 </xml>
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44 <xml name="make_binary_params">
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45 <param name="iterations" type="integer" value="1" min="1" max="100" label="Iterations" help="The number of times (1-100) erosion, dilation, opening, and closing are performed."/>
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46 <param name="count" type="integer" value="1" min="1" max="8" label="Count" help="The number of adjacent background pixels necessary (1-8) for erosion or dilation."/>
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47 <param name="black_background" type="select" label="Black background" help="If Yes, the background is black and the foreground is white (no implies the opposite).">
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48 <option value="no" selected="True">No</option>
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49 <option value="yes">Yes</option>
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50 </param>
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51 <param name="pad_edges_when_eroding" type="select" label="Pad edges when eroding" help="If Yes, eroding does not erode from the edges of the image.">
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52 <option value="no" selected="True">No</option>
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53 <option value="yes">Yes</option>
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54 </param>
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55 </xml>
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56 <token name="@make_binary_args@">
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57 --iterations $iterations
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58 --count $count
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59 --black_background $black_background
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60 --pad_edges_when_eroding $pad_edges_when_eroding
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61 </token>
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62 <xml name="max_heap_size_type_conditional">
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63 <conditional name="set_max_heap_size">
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64 <param name="max_heap_size_type" type="select" label="Maximum size of the memory allocation pool used by the JVM" help="This value must be a multiple of 1024 or it will be ignored and the system default will be used.">
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65 <option value="default" selected="True">Do not set</option>
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66 <option value="megabytes">Set in megabytes</option>
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67 <option value="gigabytes">Set in gigabytes</option>
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68 </param>
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69 <when value="default" >
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70 <param name="max_heap_size" type="integer" value="0" hidden="true" label="Do not set" help="Use system default"/>
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71 </when>
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72 <when value="megabytes">
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73 <param name="max_heap_size" type="integer" value="512" min="256" label="Maximum size, in megabytes, of the memory allocation pool" help="Examples: 256, 512, etc."/>
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74 </when>
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75 <when value="gigabytes">
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76 <param name="max_heap_size" type="integer" value="1" min="1" label="Maximum size, in gigabytes, of the memory allocation pool" help="Examples: 1, 2, etc."/>
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77 </when>
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78 </conditional>
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79 </xml>
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80 <token name="@max_heap_size_args@">
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81 --max_heap_size_type $set_max_heap_size.max_heap_size_type
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82 --max_heap_size $set_max_heap_size.max_heap_size
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83 </token>
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84 <xml name="image_datatypes">
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85 <option value="bmp">bmp</option>
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86 <option value="gif">gif</option>
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87 <option value="jpg">jpg</option>
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88 <option value="png" selected="true">png</option>
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89 <option value="tiff">tiff</option>
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90 </xml>
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91 <xml name="bunwarpj_citations">
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92 <citations>
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93 <citation type="bibtex">
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94 @InProceedings(Arganda-Carreras2006,
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95 author = "Ignacio Arganda-Carreras and
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96 Carlos Oscar S{\'a}nchez Sorzano and
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97 Roberto Marabini and
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98 Jos{\'e} Mar\'{\i}a Carazo and
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99 Carlos Ortiz-de-Solorzano and
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100 Jan Kybic",
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101 title = "Consistent and Elastic Registration of Histological Sections Using Vector-Spline Regularization",
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102 publisher = "Springer Berlin / Heidelberg",
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103 booktitle = "Computer Vision Approaches to Medical Image Analysis",
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104 series = "Lecture Notes in Computer Science",
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105 year = "2006",
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106 volume = "4241",
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107 pages = "85-95",
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108 month = "May",
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109 city = "Graz, Austria")
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110 </citation>
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111 <citation type="doi">10.1038/nmeth.2019</citation>
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112 </citations>
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113 </xml>
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114 <xml name="fiji_headless_citations">
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115 <citations>
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116 <citation type="doi">10.1038/nmeth.2102</citation>
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117 </citations>
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118 </xml>
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119 <xml name="bioformats_fiji_javabridge_citations">
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120 <citations>
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121 <citation type="doi">10.1038/nmeth.2102</citation>
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122 <citation type="doi">10.1038/nmeth.2019</citation>
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123 <citation type="doi">10.1083/jcb.201004104</citation>
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124 </citations>
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125 </xml>
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126 </macros>