Mercurial > repos > bgruening > cp_measure_image_quality

annotate measure_image_quality.xml @ 3:08a2cf887a44 draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
author bgruening
date Mon, 11 May 2020 07:46:58 -0400
parents 4dcd464c22ff
children 6f4715b8540a
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1 <tool id="cp_measure_image_quality" name="MeasureImageQuality" version="@CP_VERSION@">
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2 <description>measure features that indicate image quality</description>
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3
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4 <macros>
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5 <import>macros.xml</import>
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6 <xml name="macro_calc_threshold">
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7 <conditional name="con_use_all_methods">
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8 <param name="use_all_methods" type="select" display="radio" label="Use all thresholding methods?">
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9 <help>
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10 <![CDATA[
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11 Select 'Yes' to calculate thresholds using all the available methods. Only the global methods are used. While most methods are straightfoward, some methods have additional parameters that require special handling:
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12 <br> - Otsu: Thresholds for all combinations of class number, minimization parameter and middle class assignment are computed.
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13 <br> - Mixture of Gaussians (MoG): Thresholds for image coverage fractions of 0.05, 0.25, 0.75 and 0.95 are computed.
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14 See the IdentifyPrimaryObjects module for more information on thresholding methods.
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15 ]]>
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16 </help>
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17 <option value="Yes">Yes</option>
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18 <option value="No">No</option>
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19 </param>
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20 <when value="Yes" />
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21 <when value="No">
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22 <repeat name="rpt_threshold_method" title="new threshold method" min="1">
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23 <conditional name="con_threshold_methods">
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24 <param name="select_threshold_method" type="select" label="Select a thresholding method">
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25 <help>
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26 This setting allows you to apply automatic thresholding methods used in the Identify modules.
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27 Only the global methods are applied. For more help on thresholding, see the Identify modules.
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28 </help>
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29 <option value="Otsu">Otsu</option>
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30 <option value="MoG">MoG</option>
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31 <option value="Background">Background</option>
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32 <option value="RobustBackground">Robust background</option>
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33 <option value="RidlerCalvard">Ridler Calvard</option>
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34 <option value="Kapur">Kapur</option>
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35 <option value="MCT">MCT</option>
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36 </param>
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37 <when value="Otsu">
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38 <expand macro="otsu_method" />
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39 </when>
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40 <when value="MoG">
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41 <expand macro="mog_method" />
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42 </when>
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43 <when value="Background" />
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44 <when value="RobustBackground" />
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45 <when value="RidlerCalvard" />
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46 <when value="Kapur" />
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47 <when value="MCT" />
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48 </conditional>
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49 </repeat>
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50 </when>
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51 </conditional>
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52 </xml>
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53
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54 <xml name="otsu_method">
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55 <param name="otsu_weighted_entropy" label="Minimize the weighted variance or the entropy?" type="select">
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56 <option value="Weighted variance">Weighted variance</option>
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57 <option value="Entropy">Entropy</option>
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58 </param>
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59 <conditional name="con_threshold_classes">
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60 <param name="threshold_classes" label="Two-class or three-class thresholding?" type="select">
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61 <help>
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62 Select Two classes if the grayscale levels are readily distinguishable into foreground (i.e., objects) and background.
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63 Select Three classes if there is a middle set of grayscale levels that belongs to neither the foreground nor background.
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64 For example, three-class thresholding may be useful for images in which you have nuclear staining along with a low-intensity non-specific cell staining.
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65 Where two-class thresholding might incorrectly assign this intermediate staining to the nuclei objects, three-class thresholding allows you to assign it to the foreground or background as desired.
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66 However, in extreme cases where either there are almost no objects or the entire field of view is covered with objects, three-class thresholding may perform worse than two-class.
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67 </help>
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68 <option value="Two classes">Two classes</option>
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69 <option value="Three classes">Three classes</option>
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70 </param>
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71 <when value="Three classes">
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72 <param name="pixel_foreground_or_background" label="Assign pixels in the middle intensity class to the foreground or the background?" type="select">
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73 <option value="Foreground">Foreground</option>
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74 <option value="Background">Background</option>
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75 </param>
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76 </when>
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77 <when value="Two classes" />
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78 </conditional>
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79 </xml>
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80
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81 <xml name="mog_method">
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82 <param name="mog_fraction_cover" label="Typical fraction of the image covered by objects" type="float" value="0.1" min="0.0" max="1.0"/>
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83 </xml>
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84 </macros>
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85
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86 <expand macro="py_requirements"/>
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87 <expand macro="cmd_modules" />
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88
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89 <configfiles>
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90 <inputs name="inputs" />
26945c55ddff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
91
26945c55ddff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
92 <configfile name="script_file">
26945c55ddff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
93 import json
26945c55ddff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
94 import sys
26945c55ddff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
95 import os
26945c55ddff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
96
26945c55ddff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
97 FOURSPACES=@SPACES@
26945c55ddff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
98
26945c55ddff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
99 input_json_path = sys.argv[1]
26945c55ddff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
100 input_pipeline= sys.argv[2]
26945c55ddff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
101
26945c55ddff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
102 params = json.load(open(input_json_path, "r"))
26945c55ddff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
103
26945c55ddff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
104 def writemiq():
26945c55ddff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
105 _str = "\nMeasureImageQuality:[module_num:%d|svn_version:\\'Unknown\\'|variable_revision_number:5|show_window:False|notes:\\x5B\\x5D|batch_state:array(\\x5B\\x5D, dtype=uint8)|enabled:True|wants_pause:False]\n" % new_count
26945c55ddff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
106
26945c55ddff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
107 for_images = params['calc_for_images']
26945c55ddff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
108 selected_images = ""
26945c55ddff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
109
26945c55ddff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
110 if for_images == "All loaded images":
26945c55ddff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
111 _str += FOURSPACES + "Calculate metrics for which images?:%s\n" % for_images
26945c55ddff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
112 else:
26945c55ddff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
113 _str += FOURSPACES + "Calculate metrics for which images?:Select...\n"
26945c55ddff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
114 selected_images = params['calc_for_images']
26945c55ddff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
115
26945c55ddff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
116 image_count = 1
26945c55ddff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
117 _str += FOURSPACES + "Image count:%d\n" % image_count
26945c55ddff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
118
26945c55ddff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
119 if 'rpt_blur_measurements' in params['con_calc_blur_metrics']:
26945c55ddff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
120 scale_count = len(params['con_calc_blur_metrics']['rpt_blur_measurements'])
26945c55ddff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
121 else:
26945c55ddff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
122 scale_count = 1
26945c55ddff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
123
26945c55ddff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
124 _str += FOURSPACES + "Scale count:%d\n" % scale_count
26945c55ddff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
125
26945c55ddff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
126 calc_threshold = params['con_calc_threshold']['calc_threshold']
26945c55ddff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
127 if calc_threshold == "No":
26945c55ddff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
128 threshold_count = 1
26945c55ddff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
129 all_method = "No"
26945c55ddff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
130 else:
26945c55ddff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
131 all_method = params['con_calc_threshold']['con_use_all_methods']['use_all_methods']
3
08a2cf887a44 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
132 if all_method == "No":
08a2cf887a44 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
133 threshold_count = 1
08a2cf887a44 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
134 else:
08a2cf887a44 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
135 threshold_count = len(params['con_calc_threshold']['con_use_all_methods']['rpt_threshold_method'])
0
26945c55ddff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
136
26945c55ddff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
137 _str += FOURSPACES + "Threshold count:%d\n" % threshold_count
26945c55ddff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
138
26945c55ddff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
139 _str += FOURSPACES + "Select the images to measure:%s\n" % selected_images
26945c55ddff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
140
26945c55ddff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
141 include_rescaling = params['include_rescaling_value']
26945c55ddff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
142 _str += FOURSPACES + "Include the image rescaling value?:%s\n" % include_rescaling
26945c55ddff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
143
26945c55ddff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
144 calc_blur_metrics = params['con_calc_blur_metrics']['calc_blur_metrics']
26945c55ddff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
145 _str += FOURSPACES + "Calculate blur metrics?:%s\n" % calc_blur_metrics
26945c55ddff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
146
26945c55ddff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
147 if calc_blur_metrics == "Yes" and 'rpt_blur_measurements' in params['con_calc_blur_metrics']:
26945c55ddff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
148 for bm in params['con_calc_blur_metrics']['rpt_blur_measurements']:
26945c55ddff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
149 _str += FOURSPACES + "Spatial scale for blur measurements:%d\n" % bm['blur_measurements']
26945c55ddff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
150
26945c55ddff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
151 calc_saturation = params['calc_saturation_metrics']
26945c55ddff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
152 _str += FOURSPACES + "Calculate saturation metrics?:%s\n" % calc_saturation
26945c55ddff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
153
26945c55ddff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
154 calc_intensity = params['calc_intensity_metrics']
26945c55ddff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
155 _str += FOURSPACES + "Calculate intensity metrics?:%s\n" % calc_intensity
26945c55ddff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
156
26945c55ddff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
157 calc_threshold = params['con_calc_threshold']['calc_threshold']
26945c55ddff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
158 _str += FOURSPACES + "Calculate thresholds?:%s\n" % calc_threshold
26945c55ddff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
159 _str += FOURSPACES + "Use all thresholding methods?:%s\n" % all_method
26945c55ddff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
160
26945c55ddff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
161 if all_method == "No":
26945c55ddff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
162 for method in params['con_calc_threshold']['con_use_all_methods']['rpt_threshold_method']:
26945c55ddff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
163 _str += FOURSPACES + "Select a thresholding method:%s\n" % method['con_threshold_methods']['select_threshold_method']
3
08a2cf887a44 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
164
08a2cf887a44 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
165 fraction_cover = method['con_threshold_methods']['mog_fraction_cover'] if 'mog_fraction_cover' in method['con_threshold_methods'] else 0.1
0
26945c55ddff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
166
3
08a2cf887a44 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
167 tt_classes = method['con_threshold_methods']['con_threshold_classes']['threshold_classes'] if 'con_threshold_classes' in method['con_threshold_methods'] else 'Two classes'
0
26945c55ddff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
168
3
08a2cf887a44 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
169 minimize = method['con_threshold_methods']['otsu_weighted_entropy'] if 'otsu_weighted_entropy' in method['con_threshold_methods'] else 'Entropy'
0
26945c55ddff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
170
26945c55ddff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
171 if tt_classes == "Three classes":
3
08a2cf887a44 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
172 pixel_intensity = method['con_threshold_methods']['con_threshold_classes']['pixel_foreground_or_background']
0
26945c55ddff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
173 else:
26945c55ddff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
174 pixel_intensity = "Foreground"
26945c55ddff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
175
26945c55ddff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
176 _str += FOURSPACES + "Typical fraction of the image covered by objects:%.1f\n" % fraction_cover
26945c55ddff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
177
26945c55ddff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
178 _str += FOURSPACES + "Two-class or three-class thresholding?:%s\n" % tt_classes
26945c55ddff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
179
26945c55ddff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
180 _str += FOURSPACES + "Minimize the weighted variance or the entropy:%s\n" % minimize
26945c55ddff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
181
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182 _str += FOURSPACES + "Assign pixels in the middle intensity class to the foreground or the background?:%s\n" % pixel_intensity
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183
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184 return _str
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185
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186 with open(input_pipeline) as fin:
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187 lines = fin.readlines()
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188
26945c55ddff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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189 k, v = lines[4].strip().split(':')
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190
26945c55ddff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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191 module_count = int(v)
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192 new_count = module_count + 1
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193 lines[4] = k + ":%d\n" % new_count
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194
3
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195 with open("output.cppipe", "w") as f:
0
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196 f.writelines(lines)
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197 f.write(writemiq())
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198
3
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199 f.close()
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200 </configfile>
0
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201 </configfiles>
3
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202
0
26945c55ddff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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203 <inputs>
3
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204 <expand macro="input_pipeline_param" />
0
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205 <param name="calc_for_images" type="text" label="Calculate metrics for which images?" value="All loaded images">
3
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206 <help>
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207 Image names are separated by comma and correspond to the values in the section NameAndType of the 'Starting module' tool.
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208
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209 </help>
0
26945c55ddff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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210 <expand macro="text_validator" />
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211 </param>
3
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212
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213 <param name="include_rescaling_value" type="select" display="radio" label="Include the image rescaling value?" help="Select 'Yes' to add the image’s rescaling value as a quality control metric. This value is recorded only for images loaded using the Input modules. This is useful in confirming that all images are rescaled by the same value, given that some acquisition device vendors may output this value differently. ">
0
26945c55ddff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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214 <option value="Yes">Yes</option>
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215 <option value="No">No</option>
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216 </param>
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217
26945c55ddff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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218 <conditional name="con_calc_blur_metrics">
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219 <param name="calc_blur_metrics" type="select" display="radio" label="Calculate blur metrics?">
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220 <option value="Yes">Yes</option>
3
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bgruening
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221 <option value="No" selected="True">No</option>
0
26945c55ddff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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222 </param>
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223 <when value="Yes">
3
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bgruening
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224 <repeat name="rpt_blur_measurements" title="new scale" min="1">
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225 <param name="blur_measurements" label="Spatial scale for blur measurements" type="integer" value="20">
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226 <help>
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bgruening
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diff changeset
227 Enter an integer for the window size N, in units of pixels. The LocalFocusScore is measured within an N × N pixel window applied to the image, and the Correlation of a pixel is measured with respect to its neighbors N pixels away.
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228 A higher number for the window size N measures larger patterns of image blur whereas smaller numbers measure more localized patterns of blur. We suggest selecting a window size that is on the order of the feature of interest (e.g., the object diameter). You can measure these metrics for multiple window sizes by selecting additional scales for each image.
08a2cf887a44 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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229 </help>
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230 </param>
0
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231 </repeat>
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232 </when>
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233 <when value="No" />
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234 </conditional>
3
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235
0
26945c55ddff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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236 <param name="calc_intensity_metrics" type="select" display="radio" label="Calculate intensity metrics?">
3
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237 <help>
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238 Select 'Yes' to calculate image-based intensity measures, namely the mean, maximum, minimum, standard deviation and median absolute deviation of pixel intensities. These measures are identical to those calculated by MeasureImageIntensity.
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bgruening
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239 </help>
0
26945c55ddff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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240 <option value="Yes">Yes</option>
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241 <option value="No">No</option>
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242 </param>
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243 <param name="calc_saturation_metrics" type="select" display="radio" label="Calculate saturation metrics">
3
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244 <help>
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245 Select 'Yes' to calculate the saturation metrics PercentMaximal and PercentMinimal, i.e., the percentage of pixels at the upper or lower limit of each individual image.
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246 For this calculation, the hard limits of 0 and 1 are not used because images often have undergone some kind of transformation such that no pixels ever reach the absolute maximum or minimum of the image format. Given the noise typical in images, both these measures should be a low percentage but if the images were saturated during imaging, a higher than usual PercentMaximal will be observed, and if there are no objects, the PercentMinimal value will increase.
08a2cf887a44 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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247 </help>
0
26945c55ddff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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248 <option value="Yes">Yes</option>
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249 <option value="No">No</option>
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250 </param>
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251
26945c55ddff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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252 <conditional name="con_calc_threshold">
26945c55ddff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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253 <param name="calc_threshold" type="select" display="radio" label="Calculate thresholds?">
3
08a2cf887a44 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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254 <help>
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255 Automatically calculate a suggested threshold for each image. One indicator of image quality is that these threshold values lie within a typical range. Outlier images with high or low thresholds often contain artifacts.
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256 </help>
0
26945c55ddff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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257 <option value="Yes">Yes</option>
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258 <option value="No">No</option>
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259 </param>
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260 <when value="Yes">
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diff changeset
261 <expand macro="macro_calc_threshold" />
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262 </when>
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263 <when value="No" />
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264 </conditional>
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265
26945c55ddff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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266 </inputs>
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267
26945c55ddff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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268 <outputs>
3
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diff changeset
269 <expand macro="output_pipeline_param" />
0
26945c55ddff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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270 </outputs>
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271
26945c55ddff "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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272 <tests>
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273 <test>
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274 <expand macro="test_input_pipeline_param" />
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275
0
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276 <param name="calc_for_images" value="All loaded images" />
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277 <param name="include_rescaling_value" value="Yes" />
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278
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279 <conditional name="con_calc_blur_metrics">
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280 <param name="calc_blur_metrics" value="Yes" />
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281 <repeat name="rpt_blur_measurements">
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282 <param name="blur_measurements" value="20" />
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283 </repeat>
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284 </conditional>
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285
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286 <param name="calc_intensity_metrics" value="Yes" />
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287 <param name="calc_saturation_metrics" value="Yes" />
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288 <conditional name="con_calc_threshold">
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289 <param name="calc_threshold" value="Yes" />
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290 </conditional>
0
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291
3
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292 <conditional name="con_use_all_methods">
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293 <param name="use_all_methods" value="No" />
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294 <repeat name="rpt_threshold_method">
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295 <conditional name="con_threshold_methods">
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296 <param name="select_threshold_method" value="Otsu" />
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297 <param name="otsu_weighted_entropy" value="Weighted variance" />
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298 <conditional name="con_threshold_classes">
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299 <param name="threshold_classes" value="Two classes" />
0
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300 </conditional>
3
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301 </conditional>
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302 </repeat>
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303 </conditional>
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304
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305 <expand macro="test_out_file" file="measure_image_quality.cppipe" />
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306 </test>
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307 </tests>
3
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308
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309 <help>
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310 <![CDATA[
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311
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312 .. class:: infomark
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313
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314 **What it does**
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315
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316 This tool collects measurements indicating possible image aberrations, e.g., blur (poor focus), intensity, saturation (i.e., the percentage of pixels in the image that are at/near the maximum possible value, and at/near the minimum possible value).
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317 Details and guidance for each of these measures is provided in the settings help.
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318 Please note that for best results, this module should be applied to the original raw images, rather than images that have already been corrected for illumination.
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319
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320 @COMMON_HELP@
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321 ]]>
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322 </help>
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323
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324 <expand macro="citations" />
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325 </tool>