Mercurial > repos > bgruening > cp_measure_image_quality

annotate measure_image_quality.xml @ 5:73ec291048a5 draft default tip

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 7d7a519c3a2cc612d38695b335d0f6c75a099de3"
author bgruening
date Fri, 26 Feb 2021 13:57:30 +0000
parents e4fad0ecf376
children
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1 <tool id="cp_measure_image_quality" name="MeasureImageQuality" version="@CP_VERSION@+galaxy@VERSION_SUFFIX@">
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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>
5
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6 <token name="@VERSION_SUFFIX@">0</token>
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7 <xml name="macro_calc_threshold">
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8 <conditional name="con_use_all_methods">
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9 <param name="use_all_methods" type="select" display="radio" label="Use all thresholding methods?">
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10 <help>
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11 <![CDATA[
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12 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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13 <br> - Otsu: Thresholds for all combinations of class number, minimization parameter and middle class assignment are computed.
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14 <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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15 See the IdentifyPrimaryObjects module for more information on thresholding methods.
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16 ]]>
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17 </help>
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18 <option value="Yes">Yes</option>
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19 <option value="No">No</option>
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20 </param>
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21 <when value="Yes" />
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22 <when value="No">
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23 <repeat name="rpt_threshold_method" title="new threshold method" min="1">
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24 <conditional name="con_threshold_methods">
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25 <param name="select_threshold_method" type="select" label="Select a thresholding method">
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26 <help>
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27 This setting allows you to apply automatic thresholding methods used in the Identify modules.
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28 Only the global methods are applied. For more help on thresholding, see the Identify modules.
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29 </help>
0
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30 <option value="Otsu">Otsu</option>
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31 <option value="MoG">MoG</option>
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32 <option value="Background">Background</option>
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33 <option value="RobustBackground">Robust background</option>
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34 <option value="RidlerCalvard">Ridler Calvard</option>
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35 <option value="Kapur">Kapur</option>
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36 <option value="MCT">MCT</option>
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37 </param>
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38 <when value="Otsu">
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39 <expand macro="otsu_method" />
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40 </when>
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41 <when value="MoG">
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42 <expand macro="mog_method" />
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43 </when>
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44 <when value="Background" />
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45 <when value="RobustBackground" />
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46 <when value="RidlerCalvard" />
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47 <when value="Kapur" />
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48 <when value="MCT" />
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49 </conditional>
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50 </repeat>
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51 </when>
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52 </conditional>
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53 </xml>
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54
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55 <xml name="otsu_method">
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56 <param name="otsu_weighted_entropy" label="Minimize the weighted variance or the entropy?" type="select">
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57 <option value="Weighted variance">Weighted variance</option>
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58 <option value="Entropy">Entropy</option>
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59 </param>
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60 <conditional name="con_threshold_classes">
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61 <param name="threshold_classes" label="Two-class or three-class thresholding?" type="select">
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62 <help>
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63 Select Two classes if the grayscale levels are readily distinguishable into foreground (i.e., objects) and background.
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64 Select Three classes if there is a middle set of grayscale levels that belongs to neither the foreground nor background.
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65 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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66 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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67 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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68 </help>
0
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69 <option value="Two classes">Two classes</option>
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70 <option value="Three classes">Three classes</option>
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71 </param>
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72 <when value="Three classes">
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73 <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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74 <option value="Foreground">Foreground</option>
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75 <option value="Background">Background</option>
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76 </param>
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77 </when>
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78 <when value="Two classes" />
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79 </conditional>
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80 </xml>
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81
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82 <xml name="mog_method">
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83 <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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84 </xml>
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85 </macros>
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86
0
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87 <expand macro="py_requirements"/>
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88 <expand macro="cmd_modules" />
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89
03766f122074 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
90 <configfiles>
03766f122074 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
91 <inputs name="inputs" />
03766f122074 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
92
03766f122074 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
93 <configfile name="script_file">
03766f122074 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
94 import json
03766f122074 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
95 import sys
03766f122074 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
96 import os
03766f122074 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
97
03766f122074 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
98 FOURSPACES=@SPACES@
03766f122074 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
99
03766f122074 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
100 input_json_path = sys.argv[1]
03766f122074 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
101 input_pipeline= sys.argv[2]
03766f122074 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
102
03766f122074 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
103 params = json.load(open(input_json_path, "r"))
03766f122074 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
104
03766f122074 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
105 def writemiq():
03766f122074 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
106 _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
03766f122074 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
107
03766f122074 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
108 for_images = params['calc_for_images']
03766f122074 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
109 selected_images = ""
03766f122074 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
110
03766f122074 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
111 if for_images == "All loaded images":
03766f122074 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
112 _str += FOURSPACES + "Calculate metrics for which images?:%s\n" % for_images
03766f122074 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
113 else:
03766f122074 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
114 _str += FOURSPACES + "Calculate metrics for which images?:Select...\n"
03766f122074 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
115 selected_images = params['calc_for_images']
03766f122074 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
116
03766f122074 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
117 image_count = 1
03766f122074 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
118 _str += FOURSPACES + "Image count:%d\n" % image_count
03766f122074 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
119
03766f122074 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
120 if 'rpt_blur_measurements' in params['con_calc_blur_metrics']:
03766f122074 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
121 scale_count = len(params['con_calc_blur_metrics']['rpt_blur_measurements'])
03766f122074 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
122 else:
03766f122074 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
123 scale_count = 1
03766f122074 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
124
03766f122074 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
125 _str += FOURSPACES + "Scale count:%d\n" % scale_count
03766f122074 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
126
03766f122074 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
127 calc_threshold = params['con_calc_threshold']['calc_threshold']
03766f122074 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
128 if calc_threshold == "No":
03766f122074 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
129 threshold_count = 1
03766f122074 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
130 all_method = "No"
03766f122074 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
131 else:
03766f122074 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
132 all_method = params['con_calc_threshold']['con_use_all_methods']['use_all_methods']
3
e4fad0ecf376 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
133 if all_method == "No":
e4fad0ecf376 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
134 threshold_count = 1
e4fad0ecf376 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
135 else:
e4fad0ecf376 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
136 threshold_count = len(params['con_calc_threshold']['con_use_all_methods']['rpt_threshold_method'])
0
03766f122074 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
137
03766f122074 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
138 _str += FOURSPACES + "Threshold count:%d\n" % threshold_count
03766f122074 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
139
03766f122074 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
140 _str += FOURSPACES + "Select the images to measure:%s\n" % selected_images
03766f122074 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
141
03766f122074 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
142 include_rescaling = params['include_rescaling_value']
03766f122074 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
143 _str += FOURSPACES + "Include the image rescaling value?:%s\n" % include_rescaling
03766f122074 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
144
03766f122074 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
145 calc_blur_metrics = params['con_calc_blur_metrics']['calc_blur_metrics']
03766f122074 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
146 _str += FOURSPACES + "Calculate blur metrics?:%s\n" % calc_blur_metrics
03766f122074 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
147
03766f122074 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
148 if calc_blur_metrics == "Yes" and 'rpt_blur_measurements' in params['con_calc_blur_metrics']:
03766f122074 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
149 for bm in params['con_calc_blur_metrics']['rpt_blur_measurements']:
03766f122074 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
150 _str += FOURSPACES + "Spatial scale for blur measurements:%d\n" % bm['blur_measurements']
03766f122074 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
151
03766f122074 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
152 calc_saturation = params['calc_saturation_metrics']
03766f122074 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
153 _str += FOURSPACES + "Calculate saturation metrics?:%s\n" % calc_saturation
03766f122074 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
154
03766f122074 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
155 calc_intensity = params['calc_intensity_metrics']
03766f122074 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
156 _str += FOURSPACES + "Calculate intensity metrics?:%s\n" % calc_intensity
03766f122074 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
157
03766f122074 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
158 calc_threshold = params['con_calc_threshold']['calc_threshold']
03766f122074 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
159 _str += FOURSPACES + "Calculate thresholds?:%s\n" % calc_threshold
03766f122074 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
160 _str += FOURSPACES + "Use all thresholding methods?:%s\n" % all_method
03766f122074 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
161
03766f122074 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
162 if all_method == "No":
03766f122074 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
163 for method in params['con_calc_threshold']['con_use_all_methods']['rpt_threshold_method']:
03766f122074 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
164 _str += FOURSPACES + "Select a thresholding method:%s\n" % method['con_threshold_methods']['select_threshold_method']
3
e4fad0ecf376 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
165
e4fad0ecf376 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
166 fraction_cover = method['con_threshold_methods']['mog_fraction_cover'] if 'mog_fraction_cover' in method['con_threshold_methods'] else 0.1
0
03766f122074 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
167
3
e4fad0ecf376 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
168 tt_classes = method['con_threshold_methods']['con_threshold_classes']['threshold_classes'] if 'con_threshold_classes' in method['con_threshold_methods'] else 'Two classes'
0
03766f122074 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
169
3
e4fad0ecf376 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
170 minimize = method['con_threshold_methods']['otsu_weighted_entropy'] if 'otsu_weighted_entropy' in method['con_threshold_methods'] else 'Entropy'
0
03766f122074 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
171
03766f122074 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
172 if tt_classes == "Three classes":
3
e4fad0ecf376 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
bgruening
parents: 2
diff changeset
173 pixel_intensity = method['con_threshold_methods']['con_threshold_classes']['pixel_foreground_or_background']
0
03766f122074 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
174 else:
03766f122074 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
175 pixel_intensity = "Foreground"
03766f122074 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
176
03766f122074 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
177 _str += FOURSPACES + "Typical fraction of the image covered by objects:%.1f\n" % fraction_cover
03766f122074 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
178
03766f122074 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
179 _str += FOURSPACES + "Two-class or three-class thresholding?:%s\n" % tt_classes
03766f122074 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
bgruening
parents:
diff changeset
180
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181 _str += FOURSPACES + "Minimize the weighted variance or the entropy:%s\n" % minimize
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182
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183 _str += FOURSPACES + "Assign pixels in the middle intensity class to the foreground or the background?:%s\n" % pixel_intensity
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184
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185 return _str
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186
03766f122074 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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187 with open(input_pipeline) as fin:
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188 lines = fin.readlines()
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189
03766f122074 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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190 k, v = lines[4].strip().split(':')
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191
03766f122074 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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192 module_count = int(v)
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193 new_count = module_count + 1
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194 lines[4] = k + ":%d\n" % new_count
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195
3
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196 with open("output.cppipe", "w") as f:
0
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197 f.writelines(lines)
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198 f.write(writemiq())
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199
3
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200 f.close()
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201 </configfile>
0
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202 </configfiles>
3
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203
0
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204 <inputs>
3
e4fad0ecf376 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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205 <expand macro="input_pipeline_param" />
0
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206 <param name="calc_for_images" type="text" label="Calculate metrics for which images?" value="All loaded images">
3
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207 <help>
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208 Image names are separated by comma and correspond to the values in the section NameAndType of the 'Starting module' tool.
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209
e4fad0ecf376 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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210 </help>
0
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211 <expand macro="text_validator" />
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212 </param>
3
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213
e4fad0ecf376 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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214 <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
03766f122074 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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215 <option value="Yes">Yes</option>
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216 <option value="No">No</option>
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217 </param>
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218
03766f122074 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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219 <conditional name="con_calc_blur_metrics">
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220 <param name="calc_blur_metrics" type="select" display="radio" label="Calculate blur metrics?">
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221 <option value="Yes">Yes</option>
3
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222 <option value="No" selected="True">No</option>
0
03766f122074 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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223 </param>
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224 <when value="Yes">
3
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225 <repeat name="rpt_blur_measurements" title="new scale" min="1">
e4fad0ecf376 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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226 <param name="blur_measurements" label="Spatial scale for blur measurements" type="integer" value="20">
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227 <help>
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bgruening
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228 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.
e4fad0ecf376 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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229 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.
e4fad0ecf376 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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230 </help>
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231 </param>
0
03766f122074 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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232 </repeat>
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233 </when>
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234 <when value="No" />
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235 </conditional>
3
e4fad0ecf376 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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236
0
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237 <param name="calc_intensity_metrics" type="select" display="radio" label="Calculate intensity metrics?">
3
e4fad0ecf376 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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238 <help>
e4fad0ecf376 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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239 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.
e4fad0ecf376 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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240 </help>
0
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241 <option value="Yes">Yes</option>
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242 <option value="No">No</option>
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243 </param>
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244 <param name="calc_saturation_metrics" type="select" display="radio" label="Calculate saturation metrics">
3
e4fad0ecf376 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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245 <help>
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246 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.
e4fad0ecf376 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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247 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.
e4fad0ecf376 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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248 </help>
0
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249 <option value="Yes">Yes</option>
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250 <option value="No">No</option>
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251 </param>
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252
03766f122074 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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253 <conditional name="con_calc_threshold">
03766f122074 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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254 <param name="calc_threshold" type="select" display="radio" label="Calculate thresholds?">
3
e4fad0ecf376 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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255 <help>
e4fad0ecf376 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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256 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.
e4fad0ecf376 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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257 </help>
0
03766f122074 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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diff changeset
258 <option value="Yes">Yes</option>
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259 <option value="No">No</option>
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260 </param>
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261 <when value="Yes">
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262 <expand macro="macro_calc_threshold" />
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263 </when>
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264 <when value="No" />
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265 </conditional>
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266
03766f122074 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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diff changeset
267 </inputs>
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268
03766f122074 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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269 <outputs>
3
e4fad0ecf376 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
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270 <expand macro="output_pipeline_param" />
0
03766f122074 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 6d73056a625002d0275b5a9a90a9fae329ce47f1"
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271 </outputs>
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272
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273 <tests>
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274 <test>
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275 <expand macro="test_input_pipeline_param" />
3
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276
0
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277 <param name="calc_for_images" value="All loaded images" />
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278 <param name="include_rescaling_value" value="Yes" />
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279
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280 <conditional name="con_calc_blur_metrics">
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281 <param name="calc_blur_metrics" value="Yes" />
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282 <repeat name="rpt_blur_measurements">
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283 <param name="blur_measurements" value="20" />
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284 </repeat>
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285 </conditional>
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286
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287 <param name="calc_intensity_metrics" value="Yes" />
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288 <param name="calc_saturation_metrics" value="Yes" />
3
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289 <conditional name="con_calc_threshold">
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290 <param name="calc_threshold" value="Yes" />
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291 </conditional>
0
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292
3
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293 <conditional name="con_use_all_methods">
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294 <param name="use_all_methods" value="No" />
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295 <repeat name="rpt_threshold_method">
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296 <conditional name="con_threshold_methods">
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297 <param name="select_threshold_method" value="Otsu" />
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298 <param name="otsu_weighted_entropy" value="Weighted variance" />
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299 <conditional name="con_threshold_classes">
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300 <param name="threshold_classes" value="Two classes" />
0
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301 </conditional>
3
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302 </conditional>
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303 </repeat>
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304 </conditional>
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305
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306 <expand macro="test_out_file" file="measure_image_quality.cppipe" />
0
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307 </test>
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308 </tests>
3
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309
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310 <help>
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311 <![CDATA[
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312
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313 .. class:: infomark
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314
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315 **What it does**
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316
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317 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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318 Details and guidance for each of these measures is provided in the settings help.
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319 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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320
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321 @COMMON_HELP@
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322 ]]>
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323 </help>
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324
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325 <expand macro="citations" />
0
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326 </tool>