Mercurial > repos > imgteam > concat_channels

annotate concat_channels.xml @ 3:01c1d5af33be draft default tip

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/concat_channels/ commit a94f04c109c545a9f892a6ce7a5ffef152253201
author imgteam
date Fri, 12 Dec 2025 21:15:44 +0000
parents ad1caf2331c6
children
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3
01c1d5af33be planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/concat_channels/ commit a94f04c109c545a9f892a6ce7a5ffef152253201
imgteam
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1 <tool id="ip_concat_channels" name="Concatenate images or channels" version="0.5" profile="20.05">
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2 <description></description>
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3 <macros>
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4 <import>creators.xml</import>
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5 <import>tests.xml</import>
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6 </macros>
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7 <creator>
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8 <expand macro="creators/bmcv"/>
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9 <expand macro="creators/kostrykin"/>
2
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10 </creator>
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11 <edam_operations>
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12 <edam_operation>operation_3443</edam_operation>
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13 </edam_operations>
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14 <xrefs>
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15 <xref type="bio.tools">galaxy_image_analysis</xref>
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16 </xrefs>
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17 <requirements>
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18 <requirement type="package" version="0.25.2">scikit-image</requirement>
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19 <requirement type="package" version="2.3.5">numpy</requirement>
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20 <requirement type="package" version="2025.10.16">tifffile</requirement>
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21 <requirement type="package" version="0.5.2">giatools</requirement>
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22 </requirements>
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23 <command detect_errors="aggressive"><![CDATA[
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25 python '$__tool_directory__/concat_channels.py'
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26
0
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27 #for $input in $inputs
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28 '$input'
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29 #end for
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31 '$output'
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32 '$axis'
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34 $mode
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35
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36 #if $sort_by != ""
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37 --sort_by '$sort_by'
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38 #end if
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39
2
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40 ]]></command>
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41 <inputs>
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42 <param name="inputs" type="data" multiple="true" format="tiff,png" label="Images to concatenate"/>
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43 <param name="axis" type="select" label="Concatenation axis" help="The images will be concatenated along this axis.">
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44 <option value="X">X-axis (concatenate images or image sequences horizontally)</option>
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45 <option value="Y">Y-axis (concatenate images or image sequences vertically)</option>
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46 <option value="T">T-axis (concatenate images as frames of a temporal image sequence)</option>
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47 <option value="Z">Z-axis (concatenate images as slices of a 3-D image or image sequence)</option>
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48 <option value="C" selected="true">C-axis (concatenate the channels/samples of images or image sequences)</option>
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49 <option value="Q">Q-axis (concatenate along other or unknown axis)</option>
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50 </param>
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51 <param name="mode" type="select" label="Scaling of values" help="If the brightness is to be preserved (default), then the values will be scaled between 0 and 1, and a floating point pixel data type will be used.">
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52 <option value="" selected="true">Preserve brightness</option>
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53 <option value="--preserve_values">Preserve range of values</option>
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54 </param>
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55 <param name="sort_by" type="select" label="Sort images before concatenating">
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56 <option value="" selected="true">Do not sort (keep the order of the datasets)</option>
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57 <option value="z_position">Sort images by their position along the Z-axis</option>
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58 </param>
0
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59 </inputs>
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60 <outputs>
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61 <data format="tiff" name="output"/>
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62 </outputs>
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63 <tests>
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64 <!-- Test with "preserve brightness", vertical concatenation -->
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65 <test>
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66 <param name="inputs" value="input1_uint8.png,input2_float.tiff"/>
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67 <param name="axis" value="Y"/>
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68 <param name="mode" value=""/>
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69 <param name="sort_by" value=""/>
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70 <expand macro="tests/intensity_image_diff" name="output" value="res_preserve_brightness.tiff" ftype="tiff"/>
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71 <assert_stdout>
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72 <has_line line="Output TIFF shape: (238, 119, 4)"/>
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73 <has_line line="Output TIFF axes: YXC"/>
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74 <has_line line="Output TIFF resolution: (1.0, 1.0)"/>
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75 </assert_stdout>
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76 </test>
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77 <!-- Test with "preserve range of values", vertical concatenation -->
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78 <test>
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79 <param name="inputs" value="input1_uint8.png,input2_float.tiff"/>
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80 <param name="axis" value="Y"/>
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81 <param name="mode" value="--preserve_values"/>
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82 <param name="sort_by" value=""/>
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83 <expand macro="tests/intensity_image_diff" name="output" value="res_preserve_values.tiff" ftype="tiff">
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84 <!--
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85
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86 The input files have values ranging between 0 and 255.
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87
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88 Below, we use an assertion in addition to the `image_diff` comparison, to ensure that the range of
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89 values is preserved. The motiviation behind this is that the expectation images are usually checked
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90 visually, which means that the `image_diff` comparison is likely to ensure that the brightness of
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91 the image is correct, thus it's good to double-check the range of values.
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92
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93 -->
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94 <has_image_mean_intensity min="0" max="255"/>
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95 </expand>
3
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96 <assert_stdout>
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97 <has_line line="Output TIFF shape: (238, 119, 4)"/>
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98 <has_line line="Output TIFF axes: YXC"/>
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99 <has_line line="Output TIFF resolution: (1.0, 1.0)"/>
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100 </assert_stdout>
2
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101 </test>
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102 <!-- Test concatenation of channels (axis *exists* in both images) -->
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103 <test>
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104 <param name="inputs" value="input1_uint8.png,input2_float.tiff"/>
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105 <param name="axis" value="C"/>
3
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106 <param name="sort_by" value=""/>
2
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107 <output name="output" ftype="tiff">
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108 <assert_contents>
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109 <has_image_width width="119"/>
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110 <has_image_height height="119"/>
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111 <has_image_depth depth="1"/>
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112 <has_image_channels channels="8"/>
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113 <has_image_frames frames="1"/>
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114 </assert_contents>
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115 </output>
3
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116 <assert_stdout>
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117 <has_line line="Output TIFF shape: (119, 119, 8)"/>
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118 <has_line line="Output TIFF axes: YXC"/>
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119 <has_line line="Output TIFF resolution: (1.0, 1.0)"/>
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120 </assert_stdout>
2
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121 </test>
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122 <!-- Test concatenation of frames (axis *does not* exist in both images) -->
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123 <test>
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124 <param name="inputs" value="input1_uint8.png,input2_float.tiff"/>
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125 <param name="axis" value="T"/>
3
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126 <param name="sort_by" value=""/>
2
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127 <output name="output" ftype="tiff">
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128 <assert_contents>
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129 <has_image_width width="119"/>
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130 <has_image_height height="119"/>
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131 <has_image_depth depth="1"/>
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132 <has_image_channels channels="4"/>
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133 <has_image_frames frames="2"/>
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134 </assert_contents>
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135 </output>
3
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136 <assert_stdout>
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137 <has_line line="Output TIFF shape: (2, 119, 119, 4)"/>
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138 <has_line line="Output TIFF axes: TYXC"/>
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139 <has_line line="Output TIFF resolution: (1.0, 1.0)"/>
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140 </assert_stdout>
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141 </test>
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142 <!-- Test concatenation of z-slices with metadata -->
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143 <test>
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144 <param name="inputs" value="heart_ct_4043.tiff,heart_ct_3983.tiff,heart_ct_3953.tiff,heart_ct_3923.tiff"/>
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145 <param name="axis" value="Z"/>
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146 <param name="mode" value="--preserve_values"/>
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147 <param name="sort_by" value=""/>
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148 <output name="output" ftype="tiff">
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149 <assert_contents>
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150 <has_image_width width="512"/>
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151 <has_image_height height="512"/>
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152 <has_image_depth depth="4"/>
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153 <has_image_channels channels="1"/>
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154 <has_image_frames frames="1"/>
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155 <has_image_center_of_mass slice="0" center_of_mass="254.83911700, 251.72483820" eps="1e-8"/><!-- 4043 -->
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156 <has_image_center_of_mass slice="1" center_of_mass="254.94356937, 251.88178729" eps="1e-8"/><!-- 3983 -->
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157 <has_image_center_of_mass slice="2" center_of_mass="254.95107235, 252.04425222" eps="1e-8"/><!-- 3953 -->
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158 <has_image_center_of_mass slice="3" center_of_mass="254.91235475, 252.24777978" eps="1e-8"/><!-- 3923 -->
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159 </assert_contents>
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160 </output>
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161 <assert_stdout>
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162 <has_line line="Output TIFF shape: (4, 512, 512)"/>
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163 <has_line line="Output TIFF axes: ZYX"/>
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164 <has_line line="Output TIFF resolution: (1.137778101526753, 1.137778101526753), unit: mm, z_position: -219.860001, z_spacing: 2.5"/>
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165 </assert_stdout>
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166 </test>
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167 <!-- Test concatenation of z-slices with metadata + sorting by `z_position` (inputs in wrong order) -->
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168 <test>
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169 <param name="inputs" value="heart_ct_3953.tiff,heart_ct_3983.tiff,heart_ct_4043.tiff,heart_ct_3923.tiff"/>
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170 <param name="axis" value="Z"/>
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171 <param name="mode" value="--preserve_values"/>
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172 <param name="sort_by" value="z_position"/>
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173 <output name="output" ftype="tiff">
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174 <assert_contents>
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175 <has_image_width width="512"/>
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176 <has_image_height height="512"/>
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177 <has_image_depth depth="4"/>
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178 <has_image_channels channels="1"/>
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179 <has_image_frames frames="1"/>
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180 <has_image_center_of_mass slice="0" center_of_mass="254.83911700, 251.72483820" eps="1e-8"/><!-- 4043 -->
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181 <has_image_center_of_mass slice="1" center_of_mass="254.94356937, 251.88178729" eps="1e-8"/><!-- 3983 -->
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182 <has_image_center_of_mass slice="2" center_of_mass="254.95107235, 252.04425222" eps="1e-8"/><!-- 3953 -->
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183 <has_image_center_of_mass slice="3" center_of_mass="254.91235475, 252.24777978" eps="1e-8"/><!-- 3923 -->
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184 </assert_contents>
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185 </output>
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186 <assert_stdout>
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187 <has_line line="Output TIFF shape: (4, 512, 512)"/>
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188 <has_line line="Output TIFF axes: ZYX"/>
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189 <has_line line="Output TIFF resolution: (1.137778101526753, 1.137778101526753), unit: mm, z_position: -219.860001, z_spacing: 2.5"/>
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190 </assert_stdout>
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191 </test>
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192 <!-- Test concatenation of z-slices with a missing slice in between (`z_position` must increase) -->
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193 <test>
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194 <param name="inputs" value="heart_ct_4043.tiff,heart_ct_3983.tiff,heart_ct_3923.tiff"/>
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195 <param name="axis" value="Z"/>
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196 <param name="mode" value="--preserve_values"/>
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197 <param name="sort_by" value=""/>
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198 <output name="output" ftype="tiff">
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199 <assert_contents>
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200 <has_image_width width="512"/>
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201 <has_image_height height="512"/>
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202 <has_image_depth depth="3"/>
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203 <has_image_channels channels="1"/>
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204 <has_image_frames frames="1"/>
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205 <has_image_center_of_mass slice="0" center_of_mass="254.83911700, 251.72483820" eps="1e-8"/><!-- 4043 -->
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206 <has_image_center_of_mass slice="1" center_of_mass="254.94356937, 251.88178729" eps="1e-8"/><!-- 3983 -->
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207 <has_image_center_of_mass slice="2" center_of_mass="254.91235475, 252.24777978" eps="1e-8"/><!-- 3923 -->
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208 </assert_contents>
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209 </output>
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210 <assert_stdout>
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211 <has_line line="Output TIFF shape: (3, 512, 512)"/>
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212 <has_line line="Output TIFF axes: ZYX"/>
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213 <has_line line="Output TIFF resolution: (1.137778101526753, 1.137778101526753), unit: mm, z_position: -220.27666766666667, z_spacing: 3.75"/>
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214 </assert_stdout>
0
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215 </test>
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216 </tests>
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217 <help>
2
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218
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219 **Concatenates images along arbitrary axes.**
0
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220
2
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221 This can be used, for example, to spatially concatenate images, or along their channels.
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222
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223 This tool either preserves the image brightness, or the range of values.
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224 In general, both cannot be preserved when concatenating images of different pixel types (e.g., uint8 and uint16).
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225
0
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226 </help>
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227 <citations>
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228 <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation>
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229 </citations>
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230 </tool>