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annotate clip_image.xml @ 1:eb5a84e77beb draft default tip

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/clip_image/ commit e9a49428eb8424b1e2b80093e6b3f924f98f2d14
author imgteam
date Sun, 04 Jan 2026 22:20:07 +0000
parents 969840610383
children
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1
eb5a84e77beb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/clip_image/ commit e9a49428eb8424b1e2b80093e6b3f924f98f2d14
imgteam
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1 <tool id="clip_image" name="Clip image intensities" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="25.1">
0
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2 <description>with giatools</description>
969840610383 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/clip_image/ commit ae489da900083dcea56c4d4822592efb3225ab31
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3 <macros>
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4 <import>creators.xml</import>
969840610383 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/clip_image/ commit ae489da900083dcea56c4d4822592efb3225ab31
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5 <import>tests.xml</import>
969840610383 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/clip_image/ commit ae489da900083dcea56c4d4822592efb3225ab31
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6 <token name="@TOOL_VERSION@">0.7.3</token>
969840610383 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/clip_image/ commit ae489da900083dcea56c4d4822592efb3225ab31
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7 <token name="@VERSION_SUFFIX@">0</token>
969840610383 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/clip_image/ commit ae489da900083dcea56c4d4822592efb3225ab31
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8 <xml name="bound" tokens="name,label,help">
1
eb5a84e77beb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/clip_image/ commit e9a49428eb8424b1e2b80093e6b3f924f98f2d14
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9 <param name="@NAME@" type="float" optional="true" label="@LABEL@" help="@HELP@"/>
0
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10 </xml>
969840610383 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/clip_image/ commit ae489da900083dcea56c4d4822592efb3225ab31
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11 </macros>
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12 <creator>
969840610383 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/clip_image/ commit ae489da900083dcea56c4d4822592efb3225ab31
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13 <expand macro="creators/bmcv"/>
969840610383 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/clip_image/ commit ae489da900083dcea56c4d4822592efb3225ab31
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14 <expand macro="creators/kostrykin"/>
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15 </creator>
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16 <edam_operations>
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17 <edam_operation>operation_3443</edam_operation>
969840610383 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/clip_image/ commit ae489da900083dcea56c4d4822592efb3225ab31
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18 </edam_operations>
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19 <xrefs>
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20 <xref type="bio.tools">galaxy_image_analysis</xref>
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21 <xref type="bio.tools">giatools</xref>
969840610383 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/clip_image/ commit ae489da900083dcea56c4d4822592efb3225ab31
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22 <xref type="bio.tools">numpy</xref>
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23 </xrefs>
969840610383 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/clip_image/ commit ae489da900083dcea56c4d4822592efb3225ab31
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24 <requirements>
969840610383 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/clip_image/ commit ae489da900083dcea56c4d4822592efb3225ab31
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25 <requirement type="package" version="@TOOL_VERSION@">giatools</requirement>
969840610383 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/clip_image/ commit ae489da900083dcea56c4d4822592efb3225ab31
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26 <requirement type="package" version="0.12.2">ome-zarr</requirement>
969840610383 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/clip_image/ commit ae489da900083dcea56c4d4822592efb3225ab31
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27 </requirements>
969840610383 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/clip_image/ commit ae489da900083dcea56c4d4822592efb3225ab31
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28 <required_files>
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29 <include type="literal" path="clip_image.py"/>
969840610383 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/clip_image/ commit ae489da900083dcea56c4d4822592efb3225ab31
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30 </required_files>
969840610383 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/clip_image/ commit ae489da900083dcea56c4d4822592efb3225ab31
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31 <command detect_errors="aggressive"><![CDATA[
969840610383 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/clip_image/ commit ae489da900083dcea56c4d4822592efb3225ab31
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32
969840610383 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/clip_image/ commit ae489da900083dcea56c4d4822592efb3225ab31
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33 python '$__tool_directory__/clip_image.py'
969840610383 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/clip_image/ commit ae489da900083dcea56c4d4822592efb3225ab31
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34
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35 #if $input.extension == "zarr"
969840610383 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/clip_image/ commit ae489da900083dcea56c4d4822592efb3225ab31
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36 --input '$input.extra_files_path/$input.metadata.store_root'
969840610383 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/clip_image/ commit ae489da900083dcea56c4d4822592efb3225ab31
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37 #else
969840610383 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/clip_image/ commit ae489da900083dcea56c4d4822592efb3225ab31
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38 --input '$input'
969840610383 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/clip_image/ commit ae489da900083dcea56c4d4822592efb3225ab31
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39 #end if
969840610383 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/clip_image/ commit ae489da900083dcea56c4d4822592efb3225ab31
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40
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41 --output 'output.tiff'
969840610383 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/clip_image/ commit ae489da900083dcea56c4d4822592efb3225ab31
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42 --params '$params'
969840610383 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/clip_image/ commit ae489da900083dcea56c4d4822592efb3225ab31
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43 --verbose
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44
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45 ]]></command>
969840610383 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/clip_image/ commit ae489da900083dcea56c4d4822592efb3225ab31
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46 <configfiles>
969840610383 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/clip_image/ commit ae489da900083dcea56c4d4822592efb3225ab31
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47 <configfile name="params"><![CDATA[
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48 {
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49
1
eb5a84e77beb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/clip_image/ commit e9a49428eb8424b1e2b80093e6b3f924f98f2d14
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50 #if str($lower_bound) != ""
eb5a84e77beb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/clip_image/ commit e9a49428eb8424b1e2b80093e6b3f924f98f2d14
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51 "lower_bound": $lower_bound,
0
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52 #end if
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53
1
eb5a84e77beb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/clip_image/ commit e9a49428eb8424b1e2b80093e6b3f924f98f2d14
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54 #if str($upper_bound) != ""
eb5a84e77beb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/clip_image/ commit e9a49428eb8424b1e2b80093e6b3f924f98f2d14
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55 "upper_bound": $upper_bound,
0
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56 #end if
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57
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58 "": null
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59 }
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60 ]]></configfile>
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61 </configfiles>
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62 <inputs>
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63 <param name="input" type="data" format="tiff,zarr,png,jpg" label="Input image"/>
1
eb5a84e77beb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/clip_image/ commit e9a49428eb8424b1e2b80093e6b3f924f98f2d14
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64 <expand macro="bound" name="lower_bound" label="Lower bound"
eb5a84e77beb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/clip_image/ commit e9a49428eb8424b1e2b80093e6b3f924f98f2d14
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65 help="Image intensities below this value will be set to this value."/>
eb5a84e77beb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/clip_image/ commit e9a49428eb8424b1e2b80093e6b3f924f98f2d14
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66 <expand macro="bound" name="upper_bound" label="Upper bound"
eb5a84e77beb planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/clip_image/ commit e9a49428eb8424b1e2b80093e6b3f924f98f2d14
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67 help="Image intensities above this value will be set to this value."/>
0
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68 </inputs>
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69 <outputs>
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70 <data format="tiff" name="output" from_work_dir="output.tiff"/>
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71 </outputs>
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72 <tests>
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73 <test>
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74 <param name="input" value="input/input4_float16.tiff"/>
1
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75 <param name="lower_bound" value="0.5"/>
0
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76 <expand macro="tests/intensity_image_diff" name="output" value="output/input4.tiff" ftype="tiff"/>
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77 <assert_stdout>
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78 <has_line line="[input] Input image axes: ZYX"/>
969840610383 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/clip_image/ commit ae489da900083dcea56c4d4822592efb3225ab31
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79 <has_line line="[input] Input image shape: (10, 15, 18)"/>
969840610383 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/clip_image/ commit ae489da900083dcea56c4d4822592efb3225ab31
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80 <has_line line="[input] Input image dtype: float16"/>
969840610383 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/clip_image/ commit ae489da900083dcea56c4d4822592efb3225ab31
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81 <has_line line="[input] Input image resolution=(2.0, 1.0), unit='inch', z_spacing=2.0"/>
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82 <has_line line="Applying clipping: [0.5, inf]"/>
969840610383 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/clip_image/ commit ae489da900083dcea56c4d4822592efb3225ab31
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83 <has_line line="[output] Output image axes: ZYX"/>
969840610383 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/clip_image/ commit ae489da900083dcea56c4d4822592efb3225ab31
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84 <has_line line="[output] Output image shape: (10, 15, 18)"/>
969840610383 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/clip_image/ commit ae489da900083dcea56c4d4822592efb3225ab31
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85 <has_line line="[output] Output image dtype: float16"/>
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86 <has_line line="[output] Output image resolution=(2.0, 1.0), unit='inch', z_spacing=2.0"/>
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87 </assert_stdout>
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88 </test>
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89 <test>
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90 <param name="input" value="input/input5.jpg"/>
1
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91 <param name="upper_bound" value="100.5"/>
0
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92 <expand macro="tests/intensity_image_diff" name="output" value="output/input5.tiff" ftype="tiff"/>
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93 <assert_stdout>
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94 <has_line line="[input] Input image axes: YXC"/>
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95 <has_line line="[input] Input image shape: (10, 10, 3)"/>
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96 <has_line line="[input] Input image dtype: uint8"/>
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97 <has_line line="Applying clipping: [-inf, 100.5]"/>
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98 <has_line line="[output] Output image axes: YXC"/>
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99 <has_line line="[output] Output image shape: (10, 10, 3)"/>
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100 <has_line line="[output] Output image dtype: uint8"/>
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101 </assert_stdout>
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102 </test>
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103 <test expect_failure="true">
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104 <param name="input" value="input/input5.jpg"/>
1
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105 <param name="lower_bound" value="60"/>
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106 <param name="upper_bound" value="50"/>
0
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107 <assert_stderr>
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108 <has_line line="Lower bound (60) must be less or equal compared to the upper bound (50)."/>
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109 </assert_stderr>
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110 </test>
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111 <test>
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112 <param name="input" value="input/input6_yx.zarr"/>
1
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113 <param name="lower_bound" value="-21.5"/>
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114 <param name="upper_bound" value="101.5"/>
0
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115 <expand macro="tests/intensity_image_diff" name="output" value="output/input6.tiff" ftype="tiff"/>
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116 <assert_stdout>
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117 <has_line line="[input] Input image axes: YX"/>
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118 <has_line line="[input] Input image shape: (200, 200)"/>
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119 <has_line line="[input] Input image dtype: float64"/>
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120 <has_line line="[input] Input image resolution=(1.0, 1.0), unit='um'"/>
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121 <has_line line="Applying clipping: [-21.5, 101.5]"/>
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122 <has_line line="[output] Output image axes: YX"/>
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123 <has_line line="[output] Output image shape: (200, 200)"/>
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124 <has_line line="[output] Output image dtype: float64"/>
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125 <has_line line="[output] Output image resolution=(1.0, 1.0), unit='um'"/>
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126 </assert_stdout>
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127 </test>
1
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128 <test>
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129 <param name="input" value="input/input4_float16.tiff"/>
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130 <expand macro="tests/intensity_image_diff" name="output" value="input/input4_float16.tiff" ftype="tiff"/>
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131 <assert_stdout>
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132 <has_line line="[input] Input image axes: ZYX"/>
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133 <has_line line="[input] Input image shape: (10, 15, 18)"/>
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134 <has_line line="[input] Input image dtype: float16"/>
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135 <has_line line="[input] Input image resolution=(2.0, 1.0), unit='inch', z_spacing=2.0"/>
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136 <has_line line="Applying clipping: [-inf, inf]"/>
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137 <has_line line="[output] Output image axes: ZYX"/>
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138 <has_line line="[output] Output image shape: (10, 15, 18)"/>
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139 <has_line line="[output] Output image dtype: float16"/>
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140 <has_line line="[output] Output image resolution=(2.0, 1.0), unit='inch', z_spacing=2.0"/>
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141 </assert_stdout>
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142 </test>
0
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143 </tests>
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144 <help>
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145
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146 **Applies intensity clipping to an image.**
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147
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148 Supports 2-D and 3-D images, single-channel and multi-channel images, and arbitrary series of images (e.g., temporal image sequences).
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149
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150 This tool preserves the image pixel data type and—subject to clipping—the image brightness and the range of values.
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151
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152 </help>
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153 <citations>
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154 <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation>
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155 </citations>
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156 </tool>