Mercurial > repos > bgruening > cp_mask_image

annotate mask_image.xml @ 4:3a05117669cf draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
author bgruening
date Sat, 06 Feb 2021 10:02:20 +0000
parents ca1421f7e3ed
children b178453ea8d1
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1 <tool id="cp_mask_image" name="MaskImage" version="@CP_VERSION@">
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2 <description>hide portions of an image based on previously identified objects</description>
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4 <macros>
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5 <import>macros.xml</import>
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6 </macros>
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8 <expand macro="py_requirements"/>
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9 <expand macro="cmd_modules" />
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11 <configfiles>
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12 <inputs name="inputs"/>
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13 <configfile name="script_file">
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14 import json
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15 import sys
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16 import os
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18 FOURSPACES=@SPACES@
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20 input_json_path = sys.argv[1]
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21 input_pipeline= sys.argv[2]
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23 params = json.load(open(input_json_path, "r"))
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25 def writemi():
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26 _str = "\nMaskImage:[module_num:%d|svn_version:\\'Unknown\\'|variable_revision_number:3|show_window:False|notes:\\x5B\'Keep only nucleoli inside the nuclei\\'\\x5D|batch_state:array(\\x5B\\x5D, dtype=uint8)|enabled:True|wants_pause:False]\n" % new_count
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28 _str += FOURSPACES + "Select the input image:%s\n" % params['input_image']
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29 _str += FOURSPACES + "Name the output image:%s\n" % params['name_output_image']
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31 img_obj = params['con_img_obj']['img_obj']
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33 _str += FOURSPACES + "Use objects or an image as a mask?:%s\n" % params['con_img_obj']['img_obj']
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35 if img_obj == "Objects":
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36 _str += FOURSPACES + "Select object for mask:%s\n" % params['con_img_obj']['select_obj']
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37 _str += FOURSPACES + "Select image for mask:None\n"
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38 else:
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39 _str += FOURSPACES + "Select object for mask:None\n"
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40 _str += FOURSPACES + "Select image for mask:%s\n" % params['con_img_obj']['select_img']
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42 _str += FOURSPACES + "Invert the mask?:%s\n" % params['invert_mask']
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44 return _str
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46 with open(input_pipeline) as fin:
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47 lines = fin.readlines()
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49 k, v = lines[4].strip().split(':')
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51 module_count = int(v)
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52 new_count = module_count + 1
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53 lines[4] = k + ":%d\n" % new_count
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54
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55 with open("output.cppipe", "w") as f:
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56 f.writelines(lines)
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57 f.write(writemi())
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58
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59 f.close()
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60 </configfile>
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61 </configfiles>
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63 <inputs>
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64
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65 <expand macro="input_pipeline_param" />
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66 <param name="input_image" label="Enter the name of the input image" type="text">
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67 <expand macro="text_validator" />
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68 </param>
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69
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70 <param name="name_output_image" type="text" label="Enter the name of the resulting image">
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71 <expand macro="text_validator" />
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72 </param>
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74 <conditional name="con_img_obj">
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75 <param name="img_obj" label="Use objects or an image as a mask?" type="select">
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76 <help>
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77 <![CDATA[
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78 You can mask an image in two ways:
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79 <br> - Objects: Using objects created by another module (for instance IdentifyPrimaryObjects).
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80 The module will mask out all parts of the image that are not within one of the objects (unless you invert the mask).
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81 <br> - Image: Using a binary image as the mask, where black portions of the image (false or zero-value pixels) will be masked out.
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82 If the image is not binary, the module will use all pixels whose intensity is greater than 0.5 as the mask’s foreground (white area).
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83 You can use Threshold instead to create a binary image with finer control over the intensity choice.
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84 ]]>
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85 </help>
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86 <option value="Objects">Objects</option>
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87 <option value="Image">Image</option>
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88 </param>
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89 <when value="Objects">
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90 <param name="select_obj" label="Enter the name objects to mask the input image" type="text"/>
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91 </when>
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92 <when value="Image">
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93 <param name="select_img" label="Select image for mask" type="text"/>
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94 </when>
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95 </conditional>
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96 <param name="invert_mask" label="Invert the mask?" type="select" display="radio">
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97 <help>
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98 <![CDATA[
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99 This option reverses the foreground/background relationship of the mask.
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100 <br> - Select "No" to produce the mask from the foreground (white portion) of the masking image or the area within the masking objects.
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101 <br> - Select "Yes" to instead produce the mask from the background (black portions) of the masking image or the area outside the masking objects.
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102 ]]>
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103 </help>
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104 <option value="Yes">Yes</option>
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105 <option value="No">No</option>
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106 </param>
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107 </inputs>
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108
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109 <outputs>
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110 <expand macro="output_pipeline_param" />
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111 </outputs>
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112
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113 <tests>
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114 <test>
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115 <expand macro="test_input_pipeline_param"/>
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116 <param name="input_image" value="DNAdarkholes" />
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117 <param name="name_output_image" value="MaskDNAdarkholes" />
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118 <conditional name="con_img_obj">
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119 <param name="img_obj" value="Objects" />
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120 <param name="select_obj" value="Nuclei" />
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121 </conditional>
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122 <param name="invert_mask" value="No" />
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123 <expand macro="test_out_file" file="mask_image.cppipe" />
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124 </test>
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125 </tests>
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126
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127 <help>
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128 <![CDATA[
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129 .. class:: infomark
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130
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131 **What it does**
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132
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133 This tool masks an image so you can use the mask downstream in the pipeline.
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134 The masked image is based on the original image and the masking object or image that is selected.
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135 If using a masking image, the mask is composed of the foreground (white portions);
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136 if using a masking object, the mask is composed of the area within the object.
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137 Note that the image created by this tool for further processing downstream is grayscale.
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138 If a binary mask is desired in subsequent tools, use the Threshold tool instead of MaskImage.
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139
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140 @COMMON_HELP@
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141 ]]>
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142 </help>
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143
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144 <expand macro="citations" />
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145
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146 </tool>