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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit cd908933bd7bd8756c213af57ea6343a90effc12
author imgteam
date Sat, 13 Dec 2025 22:11:13 +0000
parents ba2b1a6f1b84
children
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3
ba2b1a6f1b84 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit c55311bbe4c3d7e0039c77785509a150864bb272
imgteam
parents: 2
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1 <tool id="ip_scale_image" name="Scale image" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05">
ba2b1a6f1b84 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit c55311bbe4c3d7e0039c77785509a150864bb272
imgteam
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2 <description>with scikit-image</description>
ba2b1a6f1b84 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit c55311bbe4c3d7e0039c77785509a150864bb272
imgteam
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3 <macros>
ba2b1a6f1b84 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit c55311bbe4c3d7e0039c77785509a150864bb272
imgteam
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4 <import>creators.xml</import>
ba2b1a6f1b84 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit c55311bbe4c3d7e0039c77785509a150864bb272
imgteam
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5 <import>tests.xml</import>
4
5122286b700e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit cd908933bd7bd8756c213af57ea6343a90effc12
imgteam
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6 <token name="@TOOL_VERSION@">0.25.2</token>
5122286b700e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit cd908933bd7bd8756c213af57ea6343a90effc12
imgteam
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7 <token name="@VERSION_SUFFIX@">0</token>
5122286b700e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit cd908933bd7bd8756c213af57ea6343a90effc12
imgteam
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8 <xml name="factor_input" tokens="name,label">
5122286b700e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit cd908933bd7bd8756c213af57ea6343a90effc12
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9 <param name="@NAME@" type="float" min="0.01" max="10" value="1" label="@LABEL@ scaling factor"
5122286b700e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit cd908933bd7bd8756c213af57ea6343a90effc12
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10 help="Values less than 1 will down-sample the image data. Values greater than 1 will up-sample the image data."/>
5122286b700e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit cd908933bd7bd8756c213af57ea6343a90effc12
imgteam
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11 </xml>
5122286b700e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit cd908933bd7bd8756c213af57ea6343a90effc12
imgteam
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12 <xml name="anti_alias_input">
5122286b700e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit cd908933bd7bd8756c213af57ea6343a90effc12
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13 <param name="anti_alias" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Enable anti-aliasing"
5122286b700e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit cd908933bd7bd8756c213af57ea6343a90effc12
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14 help="Disable this when processing binary images or label maps."/>
5122286b700e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit cd908933bd7bd8756c213af57ea6343a90effc12
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15 </xml>
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imgteam
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16 </macros>
ba2b1a6f1b84 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit c55311bbe4c3d7e0039c77785509a150864bb272
imgteam
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17 <creator>
4
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18 <expand macro="creators/bmcv"/>
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19 <expand macro="creators/kostrykin"/>
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ba2b1a6f1b84 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit c55311bbe4c3d7e0039c77785509a150864bb272
imgteam
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20 </creator>
ba2b1a6f1b84 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit c55311bbe4c3d7e0039c77785509a150864bb272
imgteam
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21 <edam_operations>
ba2b1a6f1b84 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit c55311bbe4c3d7e0039c77785509a150864bb272
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22 <edam_operation>operation_3443</edam_operation>
ba2b1a6f1b84 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit c55311bbe4c3d7e0039c77785509a150864bb272
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23 </edam_operations>
ba2b1a6f1b84 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit c55311bbe4c3d7e0039c77785509a150864bb272
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24 <xrefs>
4
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25 <xref type="bio.tools">galaxy_image_analysis</xref>
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ba2b1a6f1b84 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit c55311bbe4c3d7e0039c77785509a150864bb272
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26 <xref type="bio.tools">scikit-image</xref>
ba2b1a6f1b84 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit c55311bbe4c3d7e0039c77785509a150864bb272
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27 <xref type="biii">scikit-image</xref>
ba2b1a6f1b84 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit c55311bbe4c3d7e0039c77785509a150864bb272
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28 </xrefs>
0
8b187dfeb541 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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29 <requirements>
3
ba2b1a6f1b84 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit c55311bbe4c3d7e0039c77785509a150864bb272
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30 <requirement type="package" version="@TOOL_VERSION@">scikit-image</requirement>
4
5122286b700e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit cd908933bd7bd8756c213af57ea6343a90effc12
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31 <requirement type="package" version="2.3.5">numpy</requirement>
5122286b700e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit cd908933bd7bd8756c213af57ea6343a90effc12
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32 <requirement type="package" version="0.5.2">giatools</requirement>
5122286b700e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit cd908933bd7bd8756c213af57ea6343a90effc12
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33 <requirement type="package" version="2025.10.16">tifffile</requirement>
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34 </requirements>
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35 <command detect_errors="aggressive"><![CDATA[
0
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36
4
5122286b700e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit cd908933bd7bd8756c213af57ea6343a90effc12
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37 python '$__tool_directory__/scale_image.py'
3
ba2b1a6f1b84 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit c55311bbe4c3d7e0039c77785509a150864bb272
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38
4
5122286b700e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit cd908933bd7bd8756c213af57ea6343a90effc12
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39 '$input'
5122286b700e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit cd908933bd7bd8756c213af57ea6343a90effc12
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40 ./output.${input.ext}
5122286b700e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit cd908933bd7bd8756c213af57ea6343a90effc12
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41 '$params'
3
ba2b1a6f1b84 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit c55311bbe4c3d7e0039c77785509a150864bb272
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42
ba2b1a6f1b84 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit c55311bbe4c3d7e0039c77785509a150864bb272
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43 && mv ./output.${input.ext} ./output
ba2b1a6f1b84 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit c55311bbe4c3d7e0039c77785509a150864bb272
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44
ba2b1a6f1b84 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit c55311bbe4c3d7e0039c77785509a150864bb272
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45 ]]></command>
4
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46 <configfiles>
5122286b700e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit cd908933bd7bd8756c213af57ea6343a90effc12
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47 <configfile name="params"><![CDATA[
5122286b700e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit cd908933bd7bd8756c213af57ea6343a90effc12
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48 {
5122286b700e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit cd908933bd7bd8756c213af57ea6343a90effc12
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49
5122286b700e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit cd908933bd7bd8756c213af57ea6343a90effc12
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50 #if $scale.mode == "uniform"
5122286b700e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit cd908933bd7bd8756c213af57ea6343a90effc12
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51 "axes": "$scale.axes",
5122286b700e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit cd908933bd7bd8756c213af57ea6343a90effc12
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52 "factor": $scale.factor,
5122286b700e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit cd908933bd7bd8756c213af57ea6343a90effc12
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53
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54 #elif $scale.mode == "explicit"
5122286b700e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit cd908933bd7bd8756c213af57ea6343a90effc12
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55 "factor_x": $scale.factor_x,
5122286b700e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit cd908933bd7bd8756c213af57ea6343a90effc12
imgteam
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56 "factor_y": $scale.factor_y,
5122286b700e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit cd908933bd7bd8756c213af57ea6343a90effc12
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57 "factor_z": $scale.factor_z,
5122286b700e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit cd908933bd7bd8756c213af57ea6343a90effc12
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58 "factor_t": $scale.factor_t,
5122286b700e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit cd908933bd7bd8756c213af57ea6343a90effc12
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59 "factor_q": $scale.factor_q,
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60
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61 #elif $scale.mode == "isotropy"
5122286b700e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit cd908933bd7bd8756c213af57ea6343a90effc12
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62 "sample": "$scale.sample",
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63
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64 #end if
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65 "mode": "$scale.mode",
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66 "order": $interpolation.order,
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67 "anti_alias": $interpolation.anti_alias
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68
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69 }
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70 ]]></configfile>
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71 </configfiles>
0
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72 <inputs>
4
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73 <param name="input" type="data" format="png,tiff" label="Input image"/>
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74 <conditional name="scale">
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75 <param name="mode" type="select" label="How to scale?"
5122286b700e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit cd908933bd7bd8756c213af57ea6343a90effc12
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76 help='Using the "Scale to spatially isotropic pixels/voxels" option requires that the real-world resolution is available from the metadata of the input image.'>
5122286b700e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit cd908933bd7bd8756c213af57ea6343a90effc12
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77 <option value="uniform" selected="true">Uniform scaling factor</option>
5122286b700e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit cd908933bd7bd8756c213af57ea6343a90effc12
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78 <option value="explicit">Explicit scaling factors</option>
5122286b700e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit cd908933bd7bd8756c213af57ea6343a90effc12
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79 <option value="isotropy">Scale to spatially isotropic pixels/voxels</option>
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80 </param>
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81 <when value="uniform">
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82 <param name="axes" type="select" label="Axes to be scaled">
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83 <option value="spatial" selected="true">All spatial axes (X, Y, Z)</option>
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84 <option value="all">All axes except channels (X, Y, Z, T, Q)</option>
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85 </param>
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86 <expand macro="factor_input" name="factor" label="Uniform"/>
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87 </when>
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88 <when value="explicit">
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89 <expand macro="factor_input" name="factor_x" label="Horizontal (X)"/>
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90 <expand macro="factor_input" name="factor_y" label="Vertical (Y)"/>
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91 <expand macro="factor_input" name="factor_z" label="Depth axis (Z)"/>
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92 <expand macro="factor_input" name="factor_t" label="Temporal (T)"/>
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93 <expand macro="factor_input" name="factor_q" label="Other axis (Q)"/>
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94 </when>
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95 <when value="isotropy">
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96 <param name="sample" type="select" label="Method">
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97 <option value="up">Up-sample (enlarges the image data)</option>
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98 <option value="down" selected="true">Down-sample (might lose information)</option>
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99 </param>
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100 </when>
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101 </conditional>
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102 <conditional name="interpolation">
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103 <param name="order" type="select" label="Interpolation method">
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104 <option value="0">Nearest-neighbor (good for binary images and label maps)</option>
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105 <option value="1" selected="true">Linear (better preserves the intensity values)</option>
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106 <option value="2">Cubic (yields visually superior results)</option>
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107 </param>
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108 <when value="0">
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109 <param name="anti_alias" type="hidden" value="false"/>
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110 </when>
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111 <when value="1">
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112 <expand macro="anti_alias_input"/>
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113 </when>
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114 <when value="2">
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115 <expand macro="anti_alias_input"/>
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116 </when>
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117 </conditional>
0
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118 </inputs>
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119 <outputs>
3
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120 <data name="output" from_work_dir="output" format_source="input" metadata_source="input"/>
0
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121 </outputs>
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122 <tests>
4
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123 <!-- Test PNG, uniform scaling, nearest neighbor interpolation (without anti-alias) -->
0
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124 <test>
4
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125 <param name="input" value="inputs/binary_rgba.png"/>
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126 <conditional name="scale">
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127 <param name="mode" value="uniform"/>
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128 <param name="factor" value="0.7"/>
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129 </conditional>
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130 <conditional name="interpolation">
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131 <param name="order" value="0"/>
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132 </conditional>
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133 <expand macro="tests/binary_image_diff" name="output" value="outputs/binary_rgba_uniform_down_nn.png" ftype="png"/>
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134 <assert_stdout>
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135 <has_line line="Input axes: YXC"/>
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136 <has_line line="Input has no metadata"/>
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137 <has_line line="Output axes: YXC"/>
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138 <has_line line="Output resolution: (0.7, 0.7), z_spacing: 1.0"/>
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139 <has_line line="scale: (1, 1, 1, 0.7, 0.7)"/>
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140 <has_line line="order: 0"/>
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141 <has_line line="anti_aliasing: False"/>
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142 </assert_stdout>
3
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143 </test>
4
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144 <test>
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145 <param name="input" value="inputs/binary_rgba.png"/>
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146 <conditional name="scale">
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147 <param name="mode" value="uniform"/>
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148 <param name="factor" value="1.5"/>
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149 </conditional>
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150 <conditional name="interpolation">
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151 <param name="order" value="0"/>
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152 </conditional>
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153 <expand macro="tests/binary_image_diff" name="output" value="outputs/binary_rgba_uniform_up_nn.png" ftype="png"/>
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154 <assert_stdout>
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155 <has_line line="Input axes: YXC"/>
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156 <has_line line="Input has no metadata"/>
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157 <has_line line="Output axes: YXC"/>
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158 <has_line line="Output resolution: (1.5, 1.5), z_spacing: 1.0"/>
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159 <has_line line="scale: (1, 1, 1, 1.5, 1.5)"/>
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160 <has_line line="order: 0"/>
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161 <has_line line="anti_aliasing: False"/>
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162 </assert_stdout>
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163 </test>
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164 <!-- Test PNG, uniform scaling, linear interpolation with anti-alias -->
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165 <test>
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166 <param name="input" value="inputs/rgb.png"/>
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167 <conditional name="scale">
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168 <param name="mode" value="uniform"/>
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169 <param name="factor" value="0.7"/>
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170 </conditional>
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171 <conditional name="interpolation">
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172 <param name="order" value="1"/>
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173 <param name="anti_alias" value="true"/>
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174 </conditional>
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175 <expand macro="tests/intensity_image_diff" name="output" value="outputs/rgb_uniform_down_linear_aa.png" ftype="png"/>
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176 <assert_stdout>
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177 <has_line line="Input axes: YXC"/>
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178 <has_line line="Input has no metadata"/>
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179 <has_line line="Output axes: YXC"/>
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180 <has_line line="Output resolution: (0.7, 0.7), z_spacing: 1.0"/>
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181 <has_line line="scale: (1, 1, 1, 0.7, 0.7)"/>
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182 <has_line line="order: 1"/>
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183 <has_line line="anti_aliasing: True"/>
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184 <has_line_matching expression="anti_aliasing_sigma: \(0, 0, 0, 0.214[0-9]+, 0.214[0-9]+, 0\)"/>
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185 </assert_stdout>
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186 </test>
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187 <test>
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188 <param name="input" value="inputs/rgb.png"/>
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189 <conditional name="scale">
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190 <param name="mode" value="uniform"/>
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191 <param name="factor" value="1.5"/>
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192 </conditional>
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193 <conditional name="interpolation">
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194 <param name="order" value="1"/>
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195 <param name="anti_alias" value="true"/>
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196 </conditional>
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197 <expand macro="tests/intensity_image_diff" name="output" value="outputs/rgb_uniform_up_linear_aa.png" ftype="png"/>
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198 <assert_stdout>
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199 <has_line line="Input axes: YXC"/>
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200 <has_line line="Input has no metadata"/>
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201 <has_line line="Output axes: YXC"/>
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202 <has_line line="Output resolution: (1.5, 1.5), z_spacing: 1.0"/>
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203 <has_line line="scale: (1, 1, 1, 1.5, 1.5)"/>
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204 <has_line line="order: 1"/>
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205 <has_line line="anti_aliasing: False"/>
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206 </assert_stdout>
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207 </test>
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208 <!-- Test PNG, explicit scaling, cubic interpolation with anti-alias -->
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209 <test>
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210 <param name="input" value="inputs/binary_rgba.png"/>
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211 <conditional name="scale">
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212 <param name="mode" value="explicit"/>
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213 <param name="factor_x" value="1.5"/>
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214 <param name="factor_y" value="0.7"/>
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215 <param name="factor_z" value="1.0"/>
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216 <param name="factor_t" value="1.0"/>
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217 <param name="factor_q" value="1.0"/>
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218 </conditional>
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219 <conditional name="interpolation">
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220 <param name="order" value="2"/>
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221 <param name="anti_alias" value="true"/>
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222 </conditional>
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223 <expand macro="tests/intensity_image_diff" name="output" value="outputs/binary_rgba_explicit_cubic_aa.png" ftype="png"/>
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224 <assert_stdout>
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225 <has_line line="Input axes: YXC"/>
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226 <has_line line="Input has no metadata"/>
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227 <has_line line="Output axes: YXC"/>
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228 <has_line line="Output resolution: (1.5, 0.7), z_spacing: 1.0"/>
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229 <has_line line="scale: (1.0, 1.0, 1.0, 0.7, 1.5)"/>
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230 <has_line line="order: 2"/>
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231 <has_line line="anti_aliasing: True"/>
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232 <has_line_matching expression="anti_aliasing_sigma: \(0, 0, 0, 0.214[0-9]+, 0, 0\)"/>
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233 </assert_stdout>
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234 </test>
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235 <test>
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236 <param name="input" value="inputs/binary_rgba.png"/>
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237 <conditional name="scale">
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238 <param name="mode" value="explicit"/>
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239 <param name="factor_x" value="1.5"/>
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240 <param name="factor_y" value="0.7"/>
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241 <param name="factor_z" value="1.0"/>
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242 <param name="factor_t" value="0.1"/>
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243 <param name="factor_q" value="1.0"/>
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244 </conditional>
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245 <conditional name="interpolation">
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246 <param name="order" value="2"/>
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247 <param name="anti_alias" value="true"/>
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248 </conditional>
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249 <expand macro="tests/intensity_image_diff" name="output" value="outputs/binary_rgba_explicit_cubic_aa.png" ftype="png"/>
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250 <assert_stdout>
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251 <has_line line="Input axes: YXC"/>
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252 <has_line line="Input has no metadata"/>
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253 <has_line line="Output axes: YXC"/>
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254 <has_line line="Output resolution: (1.5, 0.7), z_spacing: 1.0"/>
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255 <has_line line="scale: (1.0, 0.1, 1.0, 0.7, 1.5)"/>
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256 <has_line line="order: 2"/>
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257 <has_line line="anti_aliasing: True"/>
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258 <has_line_matching expression="anti_aliasing_sigma: \(0, 4.5, 0, 0.214[0-9]+, 0, 0\)"/>
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259 </assert_stdout>
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260 </test>
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261 <test expect_failure="true">
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262 <param name="input" value="inputs/binary_rgba.png"/>
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263 <conditional name="scale">
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264 <param name="mode" value="explicit"/>
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265 <param name="factor_x" value="1.5"/>
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266 <param name="factor_y" value="0.7"/>
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267 <param name="factor_z" value="2.0"/>
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268 <param name="factor_t" value="0.1"/>
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269 <param name="factor_q" value="1.0"/>
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270 </conditional>
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271 <conditional name="interpolation">
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272 <param name="order" value="2"/>
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273 <param name="anti_alias" value="true"/>
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274 </conditional>
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275 <assert_stderr>
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276 <has_line line='Cannot write PNG file with axes "ZYXC"'/>
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277 </assert_stderr>
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278 </test>
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279 <!-- Test TIFF, explicit scaling, cubic interpolation with anti-alias -->
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280 <test>
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281 <param name="input" value="inputs/binary_c0.tiff"/>
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282 <conditional name="scale">
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283 <param name="mode" value="explicit"/>
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284 <param name="factor_x" value="1.5"/>
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285 <param name="factor_y" value="0.7"/>
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286 <param name="factor_z" value="2.0"/>
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287 <param name="factor_t" value="0.1"/>
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288 <param name="factor_q" value="1.0"/>
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289 </conditional>
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290 <conditional name="interpolation">
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291 <param name="order" value="2"/>
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292 <param name="anti_alias" value="true"/>
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293 </conditional>
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294 <expand macro="tests/intensity_image_diff" name="output" value="outputs/binary_c0_explicit_cubic_aa.tiff" ftype="tiff"/>
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295 <assert_stdout>
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296 <has_line line="Input axes: YX"/>
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297 <has_line line="Input resolution: (1.0, 1.0)"/>
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298 <has_line line="Output axes: ZYX"/>
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299 <has_line line="Output resolution: (1.5, 0.7), z_spacing: 0.5"/>
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300 <has_line line="scale: (1.0, 0.1, 2.0, 0.7, 1.5)"/>
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301 <has_line line="order: 2"/>
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302 <has_line line="anti_aliasing: True"/>
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303 <has_line_matching expression="anti_aliasing_sigma: \(0, 4.5, 0, 0.214[0-9]+, 0, 0\)"/>
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304 </assert_stdout>
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305 </test>
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306 <!-- Test TIFF, isotropy scaling, linear interpolation (without anti-alias) -->
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307 <test>
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308 <param name="input" value="inputs/binary_c2_z10.tiff"/>
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309 <conditional name="scale">
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310 <param name="mode" value="isotropy"/>
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311 <param name="sample" value="up"/>
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312 </conditional>
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313 <conditional name="interpolation">
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314 <param name="order" value="1"/>
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315 <param name="anti_alias" value="false"/>
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316 </conditional>
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317 <expand macro="tests/intensity_image_diff" name="output" value="outputs/binary_c2_z10_isotropy_linear.tiff" ftype="tiff"/>
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318 <assert_stdout>
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319 <has_line line="Input axes: ZYXC"/>
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320 <has_line_matching expression="Input resolution: \(0.1[0-9]*, 0.05[0-9]*\), unit: um, z_spacing: 40.0"/>
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321 <has_line line="Output axes: ZYXC"/>
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322 <has_line_matching expression="Output resolution: \(0.1[0-9]*, 0.1[0-9]*\), unit: um, z_spacing: (?:9.999[0-9]+|10.0[0-9]*)"/>
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323 <has_line_matching expression="scale: \(1, 1, 4.0[0-9]*, 2.0, 1.0\)"/>
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324 <has_line line="order: 1"/>
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325 <has_line line="anti_aliasing: False"/>
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326 </assert_stdout>
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327 </test>
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328 <test>
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329 <param name="input" value="inputs/binary_c2.tiff"/>
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330 <conditional name="scale">
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331 <param name="mode" value="isotropy"/>
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332 <param name="sample" value="up"/>
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333 </conditional>
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334 <conditional name="interpolation">
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335 <param name="order" value="1"/>
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336 <param name="anti_alias" value="false"/>
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337 </conditional>
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338 <expand macro="tests/intensity_image_diff" name="output" value="outputs/binary_c2_isotropy_linear.tiff" ftype="tiff"/>
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339 <assert_stdout>
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340 <has_line line="Input axes: YXC"/>
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341 <has_line_matching expression="Input resolution: \(0.1[0-9]*, 0.05[0-9]*\), unit: um, z_spacing: 40.0"/>
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342 <has_line line="Output axes: YXC"/>
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343 <has_line_matching expression="Output resolution: \(0.1[0-9]*, 0.1[0-9]*\), unit: um, z_spacing: 40.0"/>
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344 <has_line line="scale: (1, 1, 1, 2.0, 1.0)"/>
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345 <has_line line="order: 1"/>
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346 <has_line line="anti_aliasing: False"/>
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347 </assert_stdout>
0
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348 </test>
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349 </tests>
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350 <help>
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351
4
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352 **Scales an image by re-sampling the image data.**
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353
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354 The image is rescaled uniformly along all axes, or anisotropically if multiple scale factors are given.
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355 In addition, the metadata of an image can be used to automatically rescale the image to obtain isotropic pixels or voxels.
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357 This operation preserves both the brightness of the image, and the range of values.
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358
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359 </help>
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360 <citations>
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361 <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation>
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362 </citations>
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363 </tool>