Mercurial > repos > bgruening > 3dtrees_smart_tile

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/3dtrees_smart_tile commit fe65e773176a1e35cb4ba32ce9e038e95e780d4c
author bgruening
date Tue, 27 Jan 2026 13:22:53 +0000
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53ee54da7150 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/3dtrees_smart_tile commit fe65e773176a1e35cb4ba32ce9e038e95e780d4c
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1 <tool id="3dtrees_smart_tile" name="3DTrees: SmartTile" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="24.2">
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2 <description>Subsampling, tiling, merging and matching of (multiple) point clouds</description>
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3 <macros>
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4 <token name="@TOOL_VERSION@">1.0.0</token>
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5 <token name="@VERSION_SUFFIX@">0</token>
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6 </macros>
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7 <requirements>
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8 <container type="docker">ghcr.io/3dtrees-earth/3dtrees_smart_tile:@TOOL_VERSION@</container>
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9 </requirements>
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10 <command detect_errors="exit_code"><![CDATA[
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11 ## Create output directory
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12 mkdir -p output_dir &&
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13
53ee54da7150 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/3dtrees_smart_tile commit fe65e773176a1e35cb4ba32ce9e038e95e780d4c
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14 ## Task-specific input setup and command execution
53ee54da7150 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/3dtrees_smart_tile commit fe65e773176a1e35cb4ba32ce9e038e95e780d4c
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15 #if $operation.task == 'tile':
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16 ## Create input directory and symlink files
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17 mkdir -p input_dir &&
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18 #for $f in $operation.input_files:
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19 ln -s '$f' input_dir/'${f.element_identifier}.laz' &&
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20 #end for
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21
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22 ## Run tile task
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23 python -u /src/run.py
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24 --task tile
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25 --input-dir input_dir
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26 --output-dir output_dir
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27 --tile-length '$operation.tile_length'
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28 --tile-buffer '$operation.tile_buffer'
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29 #if $operation.tiling_threshold:
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30 --tiling-threshold '$operation.tiling_threshold'
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31 #end if
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32 --resolution-1 '$operation.resolution_1'
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33 --resolution-2 '$operation.resolution_2'
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34 --skip-dimension-reduction '$operation.skip_dimension_reduction'
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35 --num-spatial-chunks \${GALAXY_SLOTS:-4}
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36 --workers '$operation.workers'
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37 --threads \${GALAXY_SLOTS:-4}
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38
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39 #elif $operation.task == 'merge':
53ee54da7150 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/3dtrees_smart_tile commit fe65e773176a1e35cb4ba32ce9e038e95e780d4c
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40 ## Create input directories and symlink files
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41 mkdir -p input_segmented &&
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42 #for $f in $operation.input_segmented:
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43 ln -s '$f' input_segmented/'${f.element_identifier}.laz' &&
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44 #end for
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45
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46 mkdir -p input_res1 &&
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47 #for $f in $operation.input_res1:
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48 ln -s '$f' input_res1/'${f.element_identifier}.laz' &&
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49 #end for
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50
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51 #if $operation.input_original:
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52 mkdir -p input_original &&
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53 #for $f in $operation.input_original:
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54 ln -s '$f' input_original/'${f.element_identifier}.laz' &&
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55 #end for
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56 #end if
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57
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58 ## Run merge task
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59 python -u /src/run.py
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60 --task merge
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61 --subsampled-segmented-folder input_segmented
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62 --subsampled-target-folder input_res1
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63 #if $operation.input_original:
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64 --original-input-dir input_original
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65 #end if
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66 --output-tiles-folder output_dir/output_tiles
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67 --buffer '$operation.buffer'
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68 --overlap-threshold '$operation.overlap_threshold'
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69 --max-centroid-distance '$operation.max_centroid_distance'
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70 --correspondence-tolerance '$operation.correspondence_tolerance'
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71 --max-volume-for-merge '$operation.max_volume_for_merge'
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72 --min-cluster-size '$operation.min_cluster_size'
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73 --border-zone-width '$operation.border_zone_width'
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74 $operation.disable_matching
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75 --workers 2
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76 #end if
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77 ]]></command>
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78 <inputs>
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79 <conditional name="operation">
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80 <param name="task" type="select" label="Task">
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81 <option value="tile">Tile</option>
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82 <option value="merge">Merge</option>
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83 </param>
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84 <when value="tile">
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85 <param name="input_files" type="data" format="laz,las" multiple="true" label="Input LAZ/LAS files" help="Collection of point cloud files to tile and subsample"/>
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86 <param argument="--tile-length" type="integer" min="1" max="10000" value="300" label="Tile Length" help="Size of tiles in meters (default: 300m)"/>
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87 <param argument="--tile-buffer" type="integer" min="1" max="10000" value="20" label="Tile Buffer" help="Overlap/buffer between tiles in meters (default: 20m)"/>
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88 <param argument="--tiling-threshold" type="float" min="0.1" max="50000" value="10000" optional="true" label="Tiling Threshold (MB)" help="File size threshold in MB. If input folder has single file below this size, skip tiling (optional)"/>
53ee54da7150 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/3dtrees_smart_tile commit fe65e773176a1e35cb4ba32ce9e038e95e780d4c
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89 <param argument="--resolution-1" type="float" min="0.001" max="1.0" value="0.01" label="Resolution 1 (m)" help="First subsampling resolution in meters (default: 0.02 = 2cm)"/>
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90 <param argument="--resolution-2" type="float" min="0.001" max="1.0" value="0.1" label="Resolution 2 (m)" help="Second subsampling resolution in meters (default: 0.1 = 10cm)"/>
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91 <param argument="--skip-dimension-reduction" type="boolean" truevalue="--skip-dimension-reduction" falsevalue="" checked="true" label="Skip Dimension Reduction" help="Keep all point dimensions instead of reducing to XYZ-only. Set to False only for raw pre-segmentation data (default: True)"/>
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92 <param argument="--workers" type="hidden" min="1" max="10" value="2" label="Workers" help="Number of workers for parallel processing (default: 2)"/>
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93 </when>
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94 <when value="merge">
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95 <param name="input_segmented" type="data" format="laz" multiple="true" label="Segmented files (e.g.10cm)" help="Collection of subsampled LAZ files with predictions (PredInstance/PredSemantic dimensions)"/>
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96 <param name="input_res1" type="data" format="laz" multiple="true" label="Subsampled target files (e.g. 1cm)" help="Collection of subsampled LAZ files at target resolution (for remapping)"/>
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97 <param name="input_original" type="data" format="laz,las" multiple="true" optional="true" label="Original input files (optional)" help="Optional collection of original input LAZ files for final remap to original resolution"/>
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98 <param argument="--buffer" type="float" min="0" max="100" value="30.0" label="Buffer Distance (m)" help="Buffer distance for filtering in meters (default: 10.0m)"/>
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99 <param argument="--overlap-threshold" type="float" min="0" max="1" value="0.3" label="Overlap Threshold" help="Overlap ratio threshold for instance matching (0.3 = 30%)"/>
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100 <param argument="--max-centroid-distance" type="float" min="0" max="100" value="3.0" label="Max Centroid Distance (m)" help="Maximum centroid distance to merge instances in meters (default: 3.0m)"/>
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101 <param argument="--max-volume-for-merge" type="float" min="0" max="100" value="4.0" label="Max Volume for Merge (m³)" help="Max convex hull volume for small instance merging in m³ (default: 4.0m³)"/>
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102 <param argument="--min-cluster-size" type="integer" min="1" max="10000" value="300" label="Minimum Cluster Size" help="Minimum cluster size in points for reassignment (default: 300)"/>
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103 <param argument="--border-zone-width" type="float" min="0" max="100" value="10.0" label="Border Zone Width (m)" help="Width of border zone beyond buffer for instance matching in meters (default: 10.0m)"/>
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104 <param argument="--correspondence-tolerance" type="float" min="0" max="1" value="0.05" label="Correspondence Tolerance (m)" help="Max distance for point correspondence in meters - should be small ~5cm (default: 0.05m)"/>
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105 <param argument="--disable-matching" type="boolean" truevalue="--disable-matching" falsevalue="" checked="false" label="Disable Matching" help="Disable cross-tile instance matching (default: False)"/>
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106 <param argument="--workers" type="hidden" min="1" max="10" value="2" label="Workers" help="Number of workers for parallel processing (default: 2)"/>
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107 </when>
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108 </conditional>
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109 </inputs>
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110 <outputs>
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111 <!-- Tile task outputs: collection of all output files -->
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112 <collection name="Subsampled_Resolution_1" type="list" label="${tool.name}: Subsampled ${operation.resolution_1}m">
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113 <filter>operation['task'] == "tile"</filter>
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114 <discover_datasets pattern="__name_and_ext__" directory="output_dir/subsampled_res1" format="laz" recurse="false"/>
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115 </collection>
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116 <collection name="Subsampled_Resolution_2" type="list" label="${tool.name}: Subsampled ${operation.resolution_2}m">
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117 <filter>operation['task'] == "tile"</filter>
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118 <discover_datasets pattern="__name_and_ext__" directory="output_dir/subsampled_res2" format="laz" recurse="false"/>
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119 </collection>
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120 <data name="output_png" format="png" label="${tool.name}: Tiling preview" from_work_dir="output_dir/overview_copc_tiles.png">
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121 <filter>operation['task'] == "tile"</filter>
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122 </data>
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123
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124 <!-- Merge task outputs: collection of per-tile files + optional merged file -->
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125 <collection name="output_merge_tiles" type="list" label="${tool.name}: Original with added dimensions">
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126 <filter>operation['task'] == "merge"</filter>
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127 <discover_datasets pattern="__name_and_ext__" directory="output_dir/original_with_predictions" format="laz"/>
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128 </collection>
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129 <data name="output_merged_laz" format="laz" label="${tool.name}: Merged LAZ file" from_work_dir="merged.laz">
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130 <filter>operation['task'] == "merge"</filter>
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131 </data>
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132
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133 </outputs>
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134 <tests>
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135 <test expect_num_outputs="3">
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136 <conditional name="operation">
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137 <param name="task" value="tile"/>
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138 <param name="input_files" value="mikro.laz"/>
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139 <param name="tile_length" value="50"/>
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140 <param name="tile_buffer" value="20"/>
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141 <param name="tiling_threshold" value="3"/>
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142 <param name="resolution_1" value="0.01"/>
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143 <param name="resolution_2" value="0.1"/>
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144 </conditional>
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145 <output_collection name="Subsampled_Resolution_1" type="list" count="1"/>
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146 <output_collection name="Subsampled_Resolution_2" type="list" count="1"/>
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147 <output name="output_png" file="mikro_preview.png" compare="image_diff">
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148 <assert_contents>
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149 <has_image_center_of_mass center_of_mass="1732,1785" eps="100"/>
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150 </assert_contents>
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151 </output>
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152 </test>
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153 <test expect_num_outputs="2">
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154 <conditional name="operation">
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155 <param name="task" value="merge"/>
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156 <param name="input_segmented" value="mikro_segmented.laz"/>
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157 <param name="input_res1" value="mikro_res1.laz"/>
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158 <param name="input_original" value="mikro.laz"/>
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159 </conditional>
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160 <output_collection name="output_merge_tiles" type="list" count="1"/>
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161 <output name="output_merged_laz">
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162 <assert_contents>
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163 <has_size value="47500" delta="1000"/>
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164 </assert_contents>
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165 </output>
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166 </test>
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167 </tests>
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168 <help format="markdown">
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169 **What it does**
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170
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171 This tool processes 3D point cloud data for tree segmentation with four task modes:
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172
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173 1. **Tile**: Subsample input point clouds and create overlapping tiles for processing
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174 3. **Merge**: Remaps predictions to target resolution and merge tiles with instance matching
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175
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176 **Tile Task**
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177
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178 Processes input LAZ/LAS files through tiling and subsampling pipeline:
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179 - Converts to COPC format
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180 - Creates overlapping tiles
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181 - Generates two subsampled resolutions (default: 2cm and 10cm)
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182
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183 *Parameters:*
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184 - Tile Length: Size of tiles in meters (default: 100m)
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185 - Tile Buffer: Overlap between tiles in meters (default: 5m)
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186 - Tiling Threshold: File size threshold in MB - files below this skip tiling (optional)
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187 - Resolution 1: First subsampling resolution in meters (default: 0.02 = 2cm)
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188 - Resolution 2: Second subsampling resolution in meters (default: 0.1 = 10cm)
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189 - Skip Dimension Reduction: Keep all point dimensions (default: True)
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190
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191 *Outputs:* Collection of tiled and subsampled LAZ files organized in subdirectories
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192
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193 **Remap Task**
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194
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195 Remaps predictions from source files to target resolution files using KDTree nearest neighbor matching.
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196 Files are matched by spatial bounds.
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197
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198 *Parameters:*
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199 - Source files: LAZ files with predictions (e.g., segmented 10cm files)
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200 - Target files: LAZ files at target resolution (e.g., 2cm subsampled files)
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201 - Tolerance: Bounds matching tolerance in meters (default: 5.0m)
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202
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203 *Outputs:* Collection of remapped LAZ files with predictions transferred to target resolution
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204
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205 **Merge Task**
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206
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207 Complete merge workflow:
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208 1. Remaps 10cm predictions to target resolution (default: 2cm)
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209 2. Merges overlapping tiles with cross-tile instance matching
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210 3. Optionally remaps to original input resolution
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211
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212 *Parameters:*
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213 - Input: Collection of 10cm subsampled LAZ files with predictions (PredInstance/PredSemantic)
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214 - Target Resolution: Resolution for remapping (default: 2cm)
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215 - Buffer: Buffer distance for filtering in meters (default: 10.0m)
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216 - Overlap Threshold: Ratio for instance matching, 0-1 (default: 0.3 = 30%)
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217 - Max Centroid Distance: Max distance to merge instances (default: 3.0m)
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218 - Correspondence Tolerance: Point matching tolerance (default: 0.05m = 5cm)
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219 - Max Volume for Merge: Max volume for small instance merging (default: 4.0m³)
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220 - Min Cluster Size: Minimum points per cluster (default: 300)
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221 - Border Zone Width: Width of border zone for matching (default: 10.0m)
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222 - Retile Buffer: Buffer expansion during retiling (fixed: 2.0m)
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223
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224 *Outputs:*
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225 - Collection of per-tile segmented LAZ files
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226 - Single merged LAZ file (if not skipped)
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227
53ee54da7150 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/3dtrees_smart_tile commit fe65e773176a1e35cb4ba32ce9e038e95e780d4c
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228 **Remap and Merge Task**
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229
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230 Combined remap + merge workflow:
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231 1. Remaps predictions from source to target files
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232 2. Merges tiles with instance matching
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233 3. Optionally remaps to original input resolution
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234
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235 Uses same parameters as separate remap and merge tasks.
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236
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237 *Outputs:*
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238 - Collection of per-tile segmented LAZ files
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239 - Single merged LAZ file (if not skipped)
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240
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241 **Processing Notes**
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242
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243 - All tasks use parallel processing with configurable workers (defaults to Galaxy job slots)
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244 - Tiling uses spatial chunks aligned to voxel grid to prevent duplicate points
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245 - Merge identifies whole trees, reassigns small clusters, and handles cross-tile instances
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246 - Remap uses cKDTree for efficient nearest neighbor queries
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247 </help>
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248 <creator>
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249 <person name="Kilian Gerberding" email="kilian.gerberding@geosense.uni-freiburg.de" identifier="0009-0002-5001-2571"/>
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250 <organization name="3Dtrees-Team, University of Freiburg" url="https://github.com/3dTrees-earth"/>
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251 </creator>
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252 <citations>
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253 <citation type="bibtex">
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254 @misc{3dtrees_tile_merge, title = {3D Trees Tile and Merge Tool}, author = {3D Trees Project}, year = {2025}}
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255 </citation>
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256 </citations>
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257 </tool>