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annotate orientationpy.xml @ 1:df211f6b5cf2 draft

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy commit c045f067a57e8308308cf6329060c7ccd3fc372f
author imgteam
date Thu, 04 Apr 2024 15:25:49 +0000
parents 214f548481eb
children cc8fe984ec3e
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214f548481eb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy commit fa4501fb81c17f0b56889f250cf92396804295d1
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1 <tool id="orientationpy" name="Compute image orientation" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.0">
214f548481eb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy commit fa4501fb81c17f0b56889f250cf92396804295d1
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2 <description>with OrientationPy</description>
214f548481eb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy commit fa4501fb81c17f0b56889f250cf92396804295d1
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3 <macros>
1
df211f6b5cf2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy commit c045f067a57e8308308cf6329060c7ccd3fc372f
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4 <import>creators.xml</import>
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214f548481eb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy commit fa4501fb81c17f0b56889f250cf92396804295d1
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5 <token name="@TOOL_VERSION@">0.2.0.4</token>
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df211f6b5cf2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy commit c045f067a57e8308308cf6329060c7ccd3fc372f
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6 <token name="@VERSION_SUFFIX@">1</token>
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214f548481eb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy commit fa4501fb81c17f0b56889f250cf92396804295d1
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7 </macros>
1
df211f6b5cf2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy commit c045f067a57e8308308cf6329060c7ccd3fc372f
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8 <creator>
df211f6b5cf2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy commit c045f067a57e8308308cf6329060c7ccd3fc372f
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9 <expand macro="creators/bmcv"/>
df211f6b5cf2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy commit c045f067a57e8308308cf6329060c7ccd3fc372f
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10 </creator>
0
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11 <edam_operations>
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12 <edam_operation>operation_3443</edam_operation>
214f548481eb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy commit fa4501fb81c17f0b56889f250cf92396804295d1
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13 </edam_operations>
214f548481eb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy commit fa4501fb81c17f0b56889f250cf92396804295d1
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14 <xrefs>
214f548481eb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy commit fa4501fb81c17f0b56889f250cf92396804295d1
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15 <xref type="biii">orientationj</xref>
214f548481eb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy commit fa4501fb81c17f0b56889f250cf92396804295d1
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16 </xrefs>
214f548481eb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy commit fa4501fb81c17f0b56889f250cf92396804295d1
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17 <requirements>
1
df211f6b5cf2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy commit c045f067a57e8308308cf6329060c7ccd3fc372f
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18 <requirement type="package" version="@TOOL_VERSION@">orientationpy</requirement>
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214f548481eb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy commit fa4501fb81c17f0b56889f250cf92396804295d1
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19 <requirement type="package" version="0.22.0">scikit-image</requirement>
214f548481eb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy commit fa4501fb81c17f0b56889f250cf92396804295d1
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20 </requirements>
214f548481eb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy commit fa4501fb81c17f0b56889f250cf92396804295d1
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21 <command><![CDATA[
214f548481eb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy commit fa4501fb81c17f0b56889f250cf92396804295d1
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214f548481eb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy commit fa4501fb81c17f0b56889f250cf92396804295d1
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23 ## Inputs
214f548481eb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy commit fa4501fb81c17f0b56889f250cf92396804295d1
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214f548481eb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy commit fa4501fb81c17f0b56889f250cf92396804295d1
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25 python '$__tool_directory__/orientationpy-cli.py' '$image'
214f548481eb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy commit fa4501fb81c17f0b56889f250cf92396804295d1
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26 --mode $mode
214f548481eb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy commit fa4501fb81c17f0b56889f250cf92396804295d1
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27 --sigma $sigma
214f548481eb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy commit fa4501fb81c17f0b56889f250cf92396804295d1
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28 --min_energy $min_energy
214f548481eb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy commit fa4501fb81c17f0b56889f250cf92396804295d1
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29 --min_coherency $min_coherency
214f548481eb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy commit fa4501fb81c17f0b56889f250cf92396804295d1
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30 --max_precision $max_precision
214f548481eb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy commit fa4501fb81c17f0b56889f250cf92396804295d1
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31
214f548481eb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy commit fa4501fb81c17f0b56889f250cf92396804295d1
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32 ## Outputs
214f548481eb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy commit fa4501fb81c17f0b56889f250cf92396804295d1
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214f548481eb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy commit fa4501fb81c17f0b56889f250cf92396804295d1
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34 --output_angle_tsv '$output_angle_tsv'
214f548481eb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy commit fa4501fb81c17f0b56889f250cf92396804295d1
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35
214f548481eb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy commit fa4501fb81c17f0b56889f250cf92396804295d1
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36 ]]>
214f548481eb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy commit fa4501fb81c17f0b56889f250cf92396804295d1
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37 </command>
214f548481eb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy commit fa4501fb81c17f0b56889f250cf92396804295d1
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38 <inputs>
214f548481eb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy commit fa4501fb81c17f0b56889f250cf92396804295d1
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39 <param name="image" type="data" format="png,tiff" label="Input image" />
214f548481eb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy commit fa4501fb81c17f0b56889f250cf92396804295d1
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40 <param argument="--mode" type="select" label="Gradient computation">
214f548481eb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy commit fa4501fb81c17f0b56889f250cf92396804295d1
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41 <option value="finite_difference" selected="True">Finite differences</option>
214f548481eb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy commit fa4501fb81c17f0b56889f250cf92396804295d1
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42 <option value="gaussian">Gaussian</option>
214f548481eb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy commit fa4501fb81c17f0b56889f250cf92396804295d1
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43 <option value="splines">Splines</option>
214f548481eb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy commit fa4501fb81c17f0b56889f250cf92396804295d1
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44 </param>
214f548481eb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy commit fa4501fb81c17f0b56889f250cf92396804295d1
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45 <param argument="--sigma" type="float" label="Spatial scale (in pixels)" value="2" />
214f548481eb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy commit fa4501fb81c17f0b56889f250cf92396804295d1
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46 <param argument="--min_energy" type="float" label="Minimum energy" value="0.1" min="0" max="1" />
214f548481eb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy commit fa4501fb81c17f0b56889f250cf92396804295d1
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47 <param argument="--min_coherency" type="float" label="Minimum coherency" value="0.2" min="0" max="1" />
214f548481eb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy commit fa4501fb81c17f0b56889f250cf92396804295d1
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48 <param argument="--max_precision" type="integer" label="Maximum possible precision (in decimals)" value="3" min="0" max="8" help="Governs the histogram bin size (increasing maximum possible precision leads to smaller bin sizes). Note that increasing the maximum possible precision too far may actually decrease the actual precision, because the bin size becomes too small." />
214f548481eb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy commit fa4501fb81c17f0b56889f250cf92396804295d1
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49 </inputs>
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50 <outputs>
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51 <data format="tabular" name="output_angle_tsv" from_work_dir="output_angle.tsv" />
214f548481eb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy commit fa4501fb81c17f0b56889f250cf92396804295d1
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52 </outputs>
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53 <tests>
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54 <!-- Test negative angle -->
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55 <test>
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56 <param name="image" value="input1.tif" />
214f548481eb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy commit fa4501fb81c17f0b56889f250cf92396804295d1
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57 <param name="mode" value="finite_difference" />
214f548481eb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy commit fa4501fb81c17f0b56889f250cf92396804295d1
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58 <param name="sigma" value="2" />
214f548481eb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy commit fa4501fb81c17f0b56889f250cf92396804295d1
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59 <param name="min_energy" value="0.1" />
214f548481eb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy commit fa4501fb81c17f0b56889f250cf92396804295d1
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60 <param name="min_coherency" value="0.2" />
214f548481eb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy commit fa4501fb81c17f0b56889f250cf92396804295d1
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61 <param name="max_precision" value="1" />
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62 <output name="output_angle_tsv">
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63 <assert_contents>
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64 <has_line line="Angle" />
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65 <has_line line="-45.0" />
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66 <has_n_lines n="2" />
214f548481eb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy commit fa4501fb81c17f0b56889f250cf92396804295d1
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67 <has_n_columns n="1" />
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68 </assert_contents>
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69 </output>
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70 </test>
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71 <!-- Test positive angle -->
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72 <test>
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73 <param name="image" value="input2.tif" />
214f548481eb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy commit fa4501fb81c17f0b56889f250cf92396804295d1
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74 <param name="mode" value="finite_difference" />
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75 <param name="sigma" value="2" />
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76 <param name="min_energy" value="0.1" />
214f548481eb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy commit fa4501fb81c17f0b56889f250cf92396804295d1
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77 <param name="min_coherency" value="0.2" />
214f548481eb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy commit fa4501fb81c17f0b56889f250cf92396804295d1
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78 <param name="max_precision" value="1" />
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79 <output name="output_angle_tsv">
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80 <assert_contents>
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81 <has_line line="Angle" />
214f548481eb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy commit fa4501fb81c17f0b56889f250cf92396804295d1
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82 <has_line line="45.0" />
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83 <has_n_lines n="2" />
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84 <has_n_columns n="1" />
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85 </assert_contents>
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86 </output>
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87 </test>
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88 </tests>
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89 <help>
1
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90
df211f6b5cf2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/orientationpy commit c045f067a57e8308308cf6329060c7ccd3fc372f
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91 **Computes the orientation of 2-D images in degrees using OrientationPy.**
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92
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93 OrientationPy is the pythonic successor to the well-loved OrientationJ Fiji Plugin.
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94 It is a library that takes in images and computes the orientation of the greylevels.
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95 A key step is the computation of image gradients, for a number of different techniques is supported.
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96
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97 For more information on ``--min_energy`` and ``--min_coherency`` see: https://epfl-center-for-imaging.gitlab.io/orientationpy/orientationpy_examples/plot_fibres_2d.html#plot-hsv-composition
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98
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99 </help>
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100 <citations>
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101 <citation type="doi">10.1007/s10237-011-0325-z</citation>
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102 </citations>
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103 </tool>