From 83c48bd8b34562815b473cc937710c58f3a55f4a Mon Sep 17 00:00:00 2001
From: kgerb <ki-facebook@freenet.de>
Date: Tue, 21 Apr 2026 23:21:57 +0200
Subject: [PATCH 1/9] Update 3Dtrees SmartTile tool to version 2.0.1, adding
 support for a new output option for resolution 2 as COPC. Adjusted default
 settings and updated center of mass for output preview.

---
 tools/3dtrees_smart_tile/smart_tile.xml | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/tools/3dtrees_smart_tile/smart_tile.xml b/tools/3dtrees_smart_tile/smart_tile.xml
index d348121d44..c80e3cc901 100644
--- a/tools/3dtrees_smart_tile/smart_tile.xml
+++ b/tools/3dtrees_smart_tile/smart_tile.xml
@@ -1,7 +1,7 @@
 <tool id="3dtrees_smart_tile" name="3DTrees: SmartTile" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="24.2">
     <description>Create COPC tiles, subsample outputs, filter border overlap, and remap prediction dimensions</description>
     <macros>
-        <token name="@TOOL_VERSION@">2.0.0</token>
+        <token name="@TOOL_VERSION@">2.0.1</token>
         <token name="@VERSION_SUFFIX@">0</token>
         <xml name="produce_merged_file_param">
             <param argument="--produce-merged-file" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Also write one merged output (LAZ)" help="If enabled (default), produce a single merged LAZ in addition to the per-file outputs."/>
@@ -59,6 +59,7 @@
                 --resolution-1 '$operation.resolution_1'
                 --resolution-2 '$operation.resolution_2'
                 --output-copc-res1 $operation.output_copc_res1
+                --output-copc-res2 $operation.output_copc_res2
                 --dimension-reduction $operation.dimension_reduction
                 --chunk-size '$operation.chunk_size'
                 --num-spatial-chunks \${GALAXY_SLOTS:-4}
@@ -229,6 +230,7 @@
                 <param argument="--resolution-1" type="float" min="0.001" max="1.0" value="0.01" label="Subsample resolution 1 (m)" help="First subsampling resolution, in meters."/>
                 <param argument="--resolution-2" type="float" min="0.001" max="1.0" value="0.1" label="Subsample resolution 2 (m)" help="Second subsampling resolution, in meters."/>
                 <param argument="--output-copc-res1" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Write resolution 1 as COPC (.copc.laz)" help="If enabled (default), the first subsampled output collection is written as COPC LAZ (`*.copc.laz`). If disabled, it is written as standard LAZ (`*.laz`). This does not affect the internal COPC-normalized source cache."/>
+                <param argument="--output-copc-res2" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Write resolution 2 as COPC (.copc.laz)" help="If enabled, the second subsampled output collection is written as COPC LAZ (`*.copc.laz`). If disabled (default), it is written as standard LAZ (`*.laz`). This matches the new SmartTile res2 COPC output option."/>
                 <param argument="--dimension-reduction" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Reduce dimensions in subsampled outputs" help="If enabled (default), subsampled outputs are written with a minimal LAS schema (smaller files). The initial source-to-COPC normalization step still preserves all input dimensions."/>
                 <param argument="--chunk-size" type="integer" min="100000" max="200000000" value="20000000" label="Chunk size (points)" help="Performance knob. Controls chunked reads used during COPC normalization and later spatial slicing steps."/>
             </when>
@@ -363,7 +365,7 @@
             <output_collection name="output_subsampled_res2" type="list" count="1"/>
             <output name="output_tiling_preview">
                 <assert_contents>
-                    <has_image_center_of_mass center_of_mass="1813, 1768" eps="100"/>
+                    <has_image_center_of_mass center_of_mass="1974, 1785" eps="100"/>
                 </assert_contents>
             </output>
             <output name="output_tile_bounds_json">
@@ -449,6 +451,7 @@
 - It then creates overlapping tiles and writes two subsampled output collections.
 - `Reduce dimensions in subsampled outputs` only affects the subsampled outputs, not the internal COPC cache.
 - `Write resolution 1 as COPC (.copc.laz)` only affects the first subsampled output collection (default: enabled).
+- `Write resolution 2 as COPC (.copc.laz)` only affects the second subsampled output collection (default: disabled).
 
 **Filter**
 

From 6ea2b3c20bae4ecc4a8303fea53ed84ab250ec98 Mon Sep 17 00:00:00 2001
From: kgerb <ki-facebook@freenet.de>
Date: Wed, 22 Apr 2026 08:47:35 +0200
Subject: [PATCH 2/9] change boolean to select

---
 tools/3dtrees_smart_tile/smart_tile.xml | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/tools/3dtrees_smart_tile/smart_tile.xml b/tools/3dtrees_smart_tile/smart_tile.xml
index c80e3cc901..42774718de 100644
--- a/tools/3dtrees_smart_tile/smart_tile.xml
+++ b/tools/3dtrees_smart_tile/smart_tile.xml
@@ -4,7 +4,10 @@
         <token name="@TOOL_VERSION@">2.0.1</token>
         <token name="@VERSION_SUFFIX@">0</token>
         <xml name="produce_merged_file_param">
-            <param argument="--produce-merged-file" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Also write one merged output (LAZ)" help="If enabled (default), produce a single merged LAZ in addition to the per-file outputs."/>
+            <param name="produce_merged_file" type="select" label="Also write one merged output (LAZ)" help="If enabled (default), produce a single merged LAZ in addition to the per-file outputs.">
+                <option value="False">No</option>
+                <option value="True" selected="true">Yes</option>
+            </param>
         </xml>
         <xml name="merge_enrichment_conditional">
             <conditional name="merge_enrichment_mode">

From f064f3f1f61cb1a21d0b674a4f3558669805e5e3 Mon Sep 17 00:00:00 2001
From: kgerb <ki-facebook@freenet.de>
Date: Sat, 16 May 2026 00:16:12 +0200
Subject: [PATCH 3/9] tools: add 3dtrees metadata wrapper

---
 tools/3dtrees_metadata/.shed.yml              |  12 ++
 tools/3dtrees_metadata/metadata.xml           | 141 ++++++++++++++++++
 .../test-data/collection_summary.json         |   8 +
 .../test-data/gadm_fixture.geojson            |  35 +++++
 .../test-data/wwf_ecoregions_fixture.geojson  |  34 +++++
 5 files changed, 230 insertions(+)
 create mode 100644 tools/3dtrees_metadata/.shed.yml
 create mode 100644 tools/3dtrees_metadata/metadata.xml
 create mode 100644 tools/3dtrees_metadata/test-data/collection_summary.json
 create mode 100644 tools/3dtrees_metadata/test-data/gadm_fixture.geojson
 create mode 100644 tools/3dtrees_metadata/test-data/wwf_ecoregions_fixture.geojson

diff --git a/tools/3dtrees_metadata/.shed.yml b/tools/3dtrees_metadata/.shed.yml
new file mode 100644
index 0000000000..24eac2fc91
--- /dev/null
+++ b/tools/3dtrees_metadata/.shed.yml
@@ -0,0 +1,12 @@
+name: 3dtrees_metadata
+owner: bgruening
+description: Extract administrative metadata for 3Dtrees collections from GADM boundaries.
+homepage_url: https://github.com/3dTrees-earth/tool_metadata
+long_description: |
+  Extracts administrative context for a 3Dtrees collection summary by computing
+  the collection centroid from collection_summary.json and intersecting it with a
+  supplied GADM vector dataset.
+remote_repository_url: https://github.com/bgruening/galaxytools/tree/master/tools/3dtrees_metadata
+type: unrestricted
+categories:
+- "Geo Science"
diff --git a/tools/3dtrees_metadata/metadata.xml b/tools/3dtrees_metadata/metadata.xml
new file mode 100644
index 0000000000..d419dd9aa8
--- /dev/null
+++ b/tools/3dtrees_metadata/metadata.xml
@@ -0,0 +1,141 @@
+<tool id="3dtrees_metadata" name="3Dtrees: Metadata" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="24.2">
+    <description>Extract administrative and ecoregion metadata for a point-cloud collection</description>
+    <macros>
+        <token name="@TOOL_VERSION@">1.0.0</token>
+        <token name="@VERSION_SUFFIX@">0</token>
+    </macros>
+    <requirements>
+        <container type="docker">ghcr.io/3dtrees-earth/tool_metadata:@TOOL_VERSION@</container>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+        ln -s '$collection_summary' collection_summary.json &&
+        #if str($metadata_layers).find('gadm') != -1:
+            #set $gadm_name = 'gadm.' + str($gadm_path.ext)
+            ln -s '$gadm_path' '$gadm_name' &&
+        #end if
+        #if str($metadata_layers).find('ecoregion') != -1:
+            #set $wwf_name = 'wwf_ecoregions.' + str($wwf_ecoregions_path.ext)
+            ln -s '$wwf_ecoregions_path' '$wwf_name' &&
+        #end if
+        python -u /src/run.py
+        --collection-summary collection_summary.json
+        #if str($metadata_layers).find('gadm') != -1:
+            --gadm-path '$gadm_name'
+            #if $gadm_layer:
+                --gadm-layer '$gadm_layer'
+            #end if
+        #end if
+        #if str($metadata_layers).find('ecoregion') != -1:
+            --wwf-ecoregions-path '$wwf_name'
+            #if $wwf_ecoregions_layer:
+                --wwf-ecoregions-layer '$wwf_ecoregions_layer'
+            #end if
+        #end if
+        --output-file additional_metadata.json
+        2>&1
+    ]]></command>
+    <inputs>
+        <param name="collection_summary" type="data" format="json" label="Collection summary" help="collection_summary.json from the 3Dtrees: LAS/LAZ Standardization collection mode."/>
+        <param name="metadata_layers" type="select" multiple="true" display="checkboxes" min="1" label="Metadata layers to extract" help="Choose at least one metadata layer. Both are selected by default.">
+            <option value="gadm" selected="true">GADM administrative boundaries</option>
+            <option value="ecoregion" selected="true">WWF Terrestrial Ecoregions v2.0</option>
+        </param>
+        <param name="gadm_path" type="data" format="data,geojson" optional="true" label="GADM vector dataset" help="Required when GADM administrative boundaries are selected. Typically a GeoPackage (.gpkg) or GeoJSON export. The dataset is supplied at runtime because GADM data is not bundled with the container."/>
+        <param argument="--gadm-layer" type="text" value="" optional="true" label="GADM layer" help="Optional layer name. Leave empty to check all layers and select the deepest matching administrative level.">
+            <validator type="regex" message="Only letters, numbers, dots, underscores, and dashes are allowed">^[A-Za-z0-9._-]*$</validator>
+        </param>
+        <param name="wwf_ecoregions_path" type="data" format="data,geojson" optional="true" label="WWF Terrestrial Ecoregions v2.0 dataset" help="Optional WWF terrestrial ecoregions vector dataset, typically wwf_terr_ecos.shp or a GeoJSON export."/>
+        <param argument="--wwf-ecoregions-layer" name="wwf_ecoregions_layer" type="text" value="" optional="true" label="WWF ecoregions layer" help="Optional layer name for the WWF ecoregions dataset. Leave empty to check all layers.">
+            <validator type="regex" message="Only letters, numbers, dots, underscores, and dashes are allowed">^[A-Za-z0-9._-]*$</validator>
+        </param>
+    </inputs>
+    <outputs>
+        <data name="additional_metadata" format="json" label="additional_metadata" from_work_dir="additional_metadata.json"/>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="collection_summary" value="collection_summary.json" ftype="json"/>
+            <param name="metadata_layers" value="gadm,ecoregion"/>
+            <param name="gadm_path" value="gadm_fixture.geojson" ftype="geojson"/>
+            <param name="wwf_ecoregions_path" value="wwf_ecoregions_fixture.geojson" ftype="geojson"/>
+            <output name="additional_metadata" ftype="json">
+                <assert_contents>
+                    <has_text text='"matched": true'/>
+                    <has_text text='"selected_level": 1'/>
+                    <has_text text='"name": "Baden-Wuerttemberg"'/>
+                    <has_text text='"ecoregion_name": "Black Forest"'/>
+                    <has_text text='"biome_name": "Temperate Broadleaf &amp; Mixed Forests"'/>
+                    <has_text text='"is_forest_biome": true'/>
+                </assert_contents>
+            </output>
+        </test>
+        <test expect_num_outputs="1">
+            <param name="collection_summary" value="collection_summary.json" ftype="json"/>
+            <param name="metadata_layers" value="gadm"/>
+            <param name="gadm_path" value="gadm_fixture.geojson" ftype="geojson"/>
+            <output name="additional_metadata" ftype="json">
+                <assert_contents>
+                    <has_text text='"admin"'/>
+                    <has_text text='"selected_level": 1'/>
+                    <has_text text='"name": "Baden-Wuerttemberg"'/>
+                    <not_has_text text='"ecoregion"'/>
+                </assert_contents>
+            </output>
+        </test>
+        <test expect_num_outputs="1">
+            <param name="collection_summary" value="collection_summary.json" ftype="json"/>
+            <param name="metadata_layers" value="ecoregion"/>
+            <param name="wwf_ecoregions_path" value="wwf_ecoregions_fixture.geojson" ftype="geojson"/>
+            <output name="additional_metadata" ftype="json">
+                <assert_contents>
+                    <has_text text='"ecoregion_name": "Black Forest"'/>
+                    <has_text text='"is_forest_biome": true'/>
+                    <not_has_text text='"admin"'/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help format="markdown"><![CDATA[
+**What it does**
+
+This tool reads a 3Dtrees `collection_summary.json`, computes the WGS84 centroid
+from `collection.multipolygon_wkt`, and intersects that point with supplied
+reference vector datasets. GADM provides administrative context; optional WWF
+Terrestrial Ecoregions v2.0 data provides ecoregion, realm, and biome context.
+
+-----
+
+**Input**
+
+- **Collection summary**: `collection_summary.json` produced by the 3Dtrees
+  standardization tool in collection mode.
+- **GADM vector dataset**: A GADM boundary file supplied at runtime. GeoPackage
+  and GeoJSON inputs are the intended formats.
+- **GADM layer**: Optional layer name. If omitted, the tool checks all available
+  layers and selects the deepest matching administrative level.
+- **WWF Terrestrial Ecoregions v2.0 dataset**: Optional ecoregions vector file.
+- **WWF ecoregions layer**: Optional layer name for the WWF dataset.
+
+-----
+
+**Output**
+
+The tool writes `additional_metadata.json` with:
+
+- GADM source details and checked layers
+- Collection centroid longitude/latitude in EPSG:4326
+- Whether the centroid matched a GADM feature
+- Selected administrative level and hierarchy
+- Raw matched GADM fields for downstream metadata enrichment
+- Optional WWF ecoregion name/id, realm, biome code/name, and forest-biome flag
+    ]]></help>
+    <creator>
+        <person name="Kilian Gerberding" email="kilian.gerberding@geosense.uni-freiburg.de" url="https://orcid.org/0009-0002-5001-2571"/>
+        <organization name="3Dtrees-Team, University of Freiburg" url="https://github.com/3dTrees-earth"/>
+    </creator>
+    <citations>
+        <citation type="bibtex">
+            @misc{3dtrees_metadata, title = {3Dtrees: Metadata}, author = {3Dtrees Project}, year = {2026}}
+        </citation>
+    </citations>
+</tool>
diff --git a/tools/3dtrees_metadata/test-data/collection_summary.json b/tools/3dtrees_metadata/test-data/collection_summary.json
new file mode 100644
index 0000000000..d3db2a25a9
--- /dev/null
+++ b/tools/3dtrees_metadata/test-data/collection_summary.json
@@ -0,0 +1,8 @@
+{
+  "collection": {
+    "multipolygon_wkt": "MULTIPOLYGON(((7.84 47.98, 7.86 47.98, 7.86 48.00, 7.84 48.00, 7.84 47.98)))"
+  },
+  "n_tiles": 2,
+  "homogeneous_crs": true,
+  "homogeneous_attribute_names": true
+}
diff --git a/tools/3dtrees_metadata/test-data/gadm_fixture.geojson b/tools/3dtrees_metadata/test-data/gadm_fixture.geojson
new file mode 100644
index 0000000000..80656cdc6b
--- /dev/null
+++ b/tools/3dtrees_metadata/test-data/gadm_fixture.geojson
@@ -0,0 +1,35 @@
+{
+  "type": "FeatureCollection",
+  "name": "gadm_fixture",
+  "crs": {
+    "type": "name",
+    "properties": {
+      "name": "urn:ogc:def:crs:OGC:1.3:CRS84"
+    }
+  },
+  "features": [
+    {
+      "type": "Feature",
+      "properties": {
+        "GID_0": "DEU",
+        "COUNTRY": "Germany",
+        "GID_1": "DEU.1_1",
+        "NAME_1": "Baden-Wuerttemberg",
+        "TYPE_1": "Land",
+        "ENGTYPE_1": "State"
+      },
+      "geometry": {
+        "type": "Polygon",
+        "coordinates": [
+          [
+            [7.70, 47.80],
+            [8.00, 47.80],
+            [8.00, 48.20],
+            [7.70, 48.20],
+            [7.70, 47.80]
+          ]
+        ]
+      }
+    }
+  ]
+}
diff --git a/tools/3dtrees_metadata/test-data/wwf_ecoregions_fixture.geojson b/tools/3dtrees_metadata/test-data/wwf_ecoregions_fixture.geojson
new file mode 100644
index 0000000000..0c4b464112
--- /dev/null
+++ b/tools/3dtrees_metadata/test-data/wwf_ecoregions_fixture.geojson
@@ -0,0 +1,34 @@
+{
+  "type": "FeatureCollection",
+  "name": "wwf_ecoregions_fixture",
+  "crs": {
+    "type": "name",
+    "properties": {
+      "name": "urn:ogc:def:crs:OGC:1.3:CRS84"
+    }
+  },
+  "features": [
+    {
+      "type": "Feature",
+      "properties": {
+        "ECO_NAME": "Black Forest",
+        "ECO_ID": "PA0414",
+        "REALM": "PA",
+        "BIOME": 4,
+        "BIOME_DESC": "Temperate Broadleaf & Mixed Forests"
+      },
+      "geometry": {
+        "type": "Polygon",
+        "coordinates": [
+          [
+            [7.70, 47.80],
+            [8.00, 47.80],
+            [8.00, 48.20],
+            [7.70, 48.20],
+            [7.70, 47.80]
+          ]
+        ]
+      }
+    }
+  ]
+}

From f82e16895cd10c0182a2190c153594c259253253 Mon Sep 17 00:00:00 2001
From: kgerb <ki-facebook@freenet.de>
Date: Sat, 16 May 2026 00:23:30 +0200
Subject: [PATCH 4/9] tools: rename 3dtrees metadata wrapper XML

---
 tools/3dtrees_metadata/.shed.yml                      | 11 ++++++-----
 .../{metadata.xml => 3dtrees_metadata.xml}            |  0
 2 files changed, 6 insertions(+), 5 deletions(-)
 rename tools/3dtrees_metadata/{metadata.xml => 3dtrees_metadata.xml} (100%)

diff --git a/tools/3dtrees_metadata/.shed.yml b/tools/3dtrees_metadata/.shed.yml
index 24eac2fc91..d25107b342 100644
--- a/tools/3dtrees_metadata/.shed.yml
+++ b/tools/3dtrees_metadata/.shed.yml
@@ -1,12 +1,13 @@
 name: 3dtrees_metadata
 owner: bgruening
-description: Extract administrative metadata for 3Dtrees collections from GADM boundaries.
+description: Extract administrative and ecoregion metadata for 3Dtrees collections.
 homepage_url: https://github.com/3dTrees-earth/tool_metadata
 long_description: |
-  Extracts administrative context for a 3Dtrees collection summary by computing
-  the collection centroid from collection_summary.json and intersecting it with a
-  supplied GADM vector dataset.
-remote_repository_url: https://github.com/bgruening/galaxytools/tree/master/tools/3dtrees_metadata
+  Extracts administrative and ecoregion context for a 3Dtrees collection summary
+  by computing the collection centroid from collection_summary.json and
+  intersecting it with selected GADM and WWF Terrestrial Ecoregions v2.0 vector
+  datasets.
+remote_repository_url: https://github.com/3dTrees-earth/galaxytools/tree/3dtrees_metadata_v1_0_0/tools/3dtrees_metadata
 type: unrestricted
 categories:
 - "Geo Science"
diff --git a/tools/3dtrees_metadata/metadata.xml b/tools/3dtrees_metadata/3dtrees_metadata.xml
similarity index 100%
rename from tools/3dtrees_metadata/metadata.xml
rename to tools/3dtrees_metadata/3dtrees_metadata.xml

From 32e0fd0423ef2f346797f7b99460f1ead0b90251 Mon Sep 17 00:00:00 2001
From: kgerb <ki-facebook@freenet.de>
Date: Sat, 16 May 2026 09:51:04 +0200
Subject: [PATCH 5/9] tools: update metadata tool repository URL

---
 tools/3dtrees_metadata/.shed.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tools/3dtrees_metadata/.shed.yml b/tools/3dtrees_metadata/.shed.yml
index d25107b342..b644d6ea25 100644
--- a/tools/3dtrees_metadata/.shed.yml
+++ b/tools/3dtrees_metadata/.shed.yml
@@ -1,7 +1,7 @@
 name: 3dtrees_metadata
 owner: bgruening
 description: Extract administrative and ecoregion metadata for 3Dtrees collections.
-homepage_url: https://github.com/3dTrees-earth/tool_metadata
+homepage_url: https://github.com/3dTrees-earth/3dtrees_metadata
 long_description: |
   Extracts administrative and ecoregion context for a 3Dtrees collection summary
   by computing the collection centroid from collection_summary.json and

From 8bbb0de21280e87cc2266d73fccee07257dbdc1d Mon Sep 17 00:00:00 2001
From: kgerb <ki-facebook@freenet.de>
Date: Sat, 16 May 2026 10:04:44 +0200
Subject: [PATCH 6/9] tools: use 3dtrees metadata container

---
 tools/3dtrees_metadata/3dtrees_metadata.xml | 14 +++-----------
 1 file changed, 3 insertions(+), 11 deletions(-)

diff --git a/tools/3dtrees_metadata/3dtrees_metadata.xml b/tools/3dtrees_metadata/3dtrees_metadata.xml
index d419dd9aa8..3681aa060b 100644
--- a/tools/3dtrees_metadata/3dtrees_metadata.xml
+++ b/tools/3dtrees_metadata/3dtrees_metadata.xml
@@ -5,28 +5,20 @@
         <token name="@VERSION_SUFFIX@">0</token>
     </macros>
     <requirements>
-        <container type="docker">ghcr.io/3dtrees-earth/tool_metadata:@TOOL_VERSION@</container>
+        <container type="docker">ghcr.io/3dtrees-earth/3dtrees_metadata:@TOOL_VERSION@</container>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
         ln -s '$collection_summary' collection_summary.json &&
-        #if str($metadata_layers).find('gadm') != -1:
-            #set $gadm_name = 'gadm.' + str($gadm_path.ext)
-            ln -s '$gadm_path' '$gadm_name' &&
-        #end if
-        #if str($metadata_layers).find('ecoregion') != -1:
-            #set $wwf_name = 'wwf_ecoregions.' + str($wwf_ecoregions_path.ext)
-            ln -s '$wwf_ecoregions_path' '$wwf_name' &&
-        #end if
         python -u /src/run.py
         --collection-summary collection_summary.json
         #if str($metadata_layers).find('gadm') != -1:
-            --gadm-path '$gadm_name'
+            --gadm-path '$gadm_path'
             #if $gadm_layer:
                 --gadm-layer '$gadm_layer'
             #end if
         #end if
         #if str($metadata_layers).find('ecoregion') != -1:
-            --wwf-ecoregions-path '$wwf_name'
+            --wwf-ecoregions-path '$wwf_ecoregions_path'
             #if $wwf_ecoregions_layer:
                 --wwf-ecoregions-layer '$wwf_ecoregions_layer'
             #end if

From ab902417ad697448336196439cf8a5345b9a4621 Mon Sep 17 00:00:00 2001
From: kgerb <ki-facebook@freenet.de>
Date: Sat, 16 May 2026 10:24:36 +0200
Subject: [PATCH 7/9] Update metadata tool to use internal reference layers

---
 tools/3dtrees_metadata/3dtrees_metadata.xml | 39 ++++-----------------
 1 file changed, 6 insertions(+), 33 deletions(-)

diff --git a/tools/3dtrees_metadata/3dtrees_metadata.xml b/tools/3dtrees_metadata/3dtrees_metadata.xml
index 3681aa060b..696bbb0e20 100644
--- a/tools/3dtrees_metadata/3dtrees_metadata.xml
+++ b/tools/3dtrees_metadata/3dtrees_metadata.xml
@@ -11,18 +11,7 @@
         ln -s '$collection_summary' collection_summary.json &&
         python -u /src/run.py
         --collection-summary collection_summary.json
-        #if str($metadata_layers).find('gadm') != -1:
-            --gadm-path '$gadm_path'
-            #if $gadm_layer:
-                --gadm-layer '$gadm_layer'
-            #end if
-        #end if
-        #if str($metadata_layers).find('ecoregion') != -1:
-            --wwf-ecoregions-path '$wwf_ecoregions_path'
-            #if $wwf_ecoregions_layer:
-                --wwf-ecoregions-layer '$wwf_ecoregions_layer'
-            #end if
-        #end if
+        --metadata-layers '$metadata_layers'
         --output-file additional_metadata.json
         2>&1
     ]]></command>
@@ -32,14 +21,6 @@
             <option value="gadm" selected="true">GADM administrative boundaries</option>
             <option value="ecoregion" selected="true">WWF Terrestrial Ecoregions v2.0</option>
         </param>
-        <param name="gadm_path" type="data" format="data,geojson" optional="true" label="GADM vector dataset" help="Required when GADM administrative boundaries are selected. Typically a GeoPackage (.gpkg) or GeoJSON export. The dataset is supplied at runtime because GADM data is not bundled with the container."/>
-        <param argument="--gadm-layer" type="text" value="" optional="true" label="GADM layer" help="Optional layer name. Leave empty to check all layers and select the deepest matching administrative level.">
-            <validator type="regex" message="Only letters, numbers, dots, underscores, and dashes are allowed">^[A-Za-z0-9._-]*$</validator>
-        </param>
-        <param name="wwf_ecoregions_path" type="data" format="data,geojson" optional="true" label="WWF Terrestrial Ecoregions v2.0 dataset" help="Optional WWF terrestrial ecoregions vector dataset, typically wwf_terr_ecos.shp or a GeoJSON export."/>
-        <param argument="--wwf-ecoregions-layer" name="wwf_ecoregions_layer" type="text" value="" optional="true" label="WWF ecoregions layer" help="Optional layer name for the WWF ecoregions dataset. Leave empty to check all layers.">
-            <validator type="regex" message="Only letters, numbers, dots, underscores, and dashes are allowed">^[A-Za-z0-9._-]*$</validator>
-        </param>
     </inputs>
     <outputs>
         <data name="additional_metadata" format="json" label="additional_metadata" from_work_dir="additional_metadata.json"/>
@@ -48,8 +29,6 @@
         <test expect_num_outputs="1">
             <param name="collection_summary" value="collection_summary.json" ftype="json"/>
             <param name="metadata_layers" value="gadm,ecoregion"/>
-            <param name="gadm_path" value="gadm_fixture.geojson" ftype="geojson"/>
-            <param name="wwf_ecoregions_path" value="wwf_ecoregions_fixture.geojson" ftype="geojson"/>
             <output name="additional_metadata" ftype="json">
                 <assert_contents>
                     <has_text text='"matched": true'/>
@@ -64,7 +43,6 @@
         <test expect_num_outputs="1">
             <param name="collection_summary" value="collection_summary.json" ftype="json"/>
             <param name="metadata_layers" value="gadm"/>
-            <param name="gadm_path" value="gadm_fixture.geojson" ftype="geojson"/>
             <output name="additional_metadata" ftype="json">
                 <assert_contents>
                     <has_text text='"admin"'/>
@@ -77,7 +55,6 @@
         <test expect_num_outputs="1">
             <param name="collection_summary" value="collection_summary.json" ftype="json"/>
             <param name="metadata_layers" value="ecoregion"/>
-            <param name="wwf_ecoregions_path" value="wwf_ecoregions_fixture.geojson" ftype="geojson"/>
             <output name="additional_metadata" ftype="json">
                 <assert_contents>
                     <has_text text='"ecoregion_name": "Black Forest"'/>
@@ -91,9 +68,9 @@
 **What it does**
 
 This tool reads a 3Dtrees `collection_summary.json`, computes the WGS84 centroid
-from `collection.multipolygon_wkt`, and intersects that point with supplied
-reference vector datasets. GADM provides administrative context; optional WWF
-Terrestrial Ecoregions v2.0 data provides ecoregion, realm, and biome context.
+from `collection.multipolygon_wkt`, and intersects that point with the selected
+reference layers. GADM provides administrative context; WWF Terrestrial
+Ecoregions v2.0 data provides ecoregion, realm, and biome context.
 
 -----
 
@@ -101,12 +78,8 @@ Terrestrial Ecoregions v2.0 data provides ecoregion, realm, and biome context.
 
 - **Collection summary**: `collection_summary.json` produced by the 3Dtrees
   standardization tool in collection mode.
-- **GADM vector dataset**: A GADM boundary file supplied at runtime. GeoPackage
-  and GeoJSON inputs are the intended formats.
-- **GADM layer**: Optional layer name. If omitted, the tool checks all available
-  layers and selects the deepest matching administrative level.
-- **WWF Terrestrial Ecoregions v2.0 dataset**: Optional ecoregions vector file.
-- **WWF ecoregions layer**: Optional layer name for the WWF dataset.
+- **Metadata layers to extract**: one or more internal reference layers. The tool
+  reads the selected reference datasets from the Docker image.
 
 -----
 

From eb7b9532fe99ab9fd3aabfa6dccfb9d228464da1 Mon Sep 17 00:00:00 2001
From: kgerb <ki-facebook@freenet.de>
Date: Sat, 16 May 2026 12:12:23 +0200
Subject: [PATCH 8/9] tools: align metadata layer argument

---
 tools/3dtrees_metadata/3dtrees_metadata.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tools/3dtrees_metadata/3dtrees_metadata.xml b/tools/3dtrees_metadata/3dtrees_metadata.xml
index 696bbb0e20..4236516eff 100644
--- a/tools/3dtrees_metadata/3dtrees_metadata.xml
+++ b/tools/3dtrees_metadata/3dtrees_metadata.xml
@@ -17,7 +17,7 @@
     ]]></command>
     <inputs>
         <param name="collection_summary" type="data" format="json" label="Collection summary" help="collection_summary.json from the 3Dtrees: LAS/LAZ Standardization collection mode."/>
-        <param name="metadata_layers" type="select" multiple="true" display="checkboxes" min="1" label="Metadata layers to extract" help="Choose at least one metadata layer. Both are selected by default.">
+        <param argument="--metadata-layers" type="select" multiple="true" display="checkboxes" min="1" label="Metadata layers to extract" help="Choose at least one metadata layer. Both are selected by default.">
             <option value="gadm" selected="true">GADM administrative boundaries</option>
             <option value="ecoregion" selected="true">WWF Terrestrial Ecoregions v2.0</option>
         </param>

From 6cf6b13e917b94207c7326c01613294577f7f830 Mon Sep 17 00:00:00 2001
From: kgerb <ki-facebook@freenet.de>
Date: Mon, 1 Jun 2026 11:49:46 +0200
Subject: [PATCH 9/9] test: cover standardization collection centroid

---
 tools/3dtrees_standardization/standard.xml    |  54 +++++++++++++++++-
 .../test-data/mikro2_no_crs.laz               | Bin 0 -> 847 bytes
 .../test-data/mikro_no_crs.laz                | Bin 0 -> 833 bytes
 3 files changed, 53 insertions(+), 1 deletion(-)
 create mode 100644 tools/3dtrees_standardization/test-data/mikro2_no_crs.laz
 create mode 100644 tools/3dtrees_standardization/test-data/mikro_no_crs.laz

diff --git a/tools/3dtrees_standardization/standard.xml b/tools/3dtrees_standardization/standard.xml
index 72d9dd5d5f..176cba2645 100644
--- a/tools/3dtrees_standardization/standard.xml
+++ b/tools/3dtrees_standardization/standard.xml
@@ -1,7 +1,7 @@
 <tool id="3dtrees_standardization" name="3DTrees: LAS/LAZ Standardization" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="24.2">
     <description>Standardize LAS/LAZ files or validate collections for consistency</description>
     <macros>
-        <token name="@TOOL_VERSION@">1.1.0</token>
+        <token name="@TOOL_VERSION@">1.2.0</token>
         <token name="@VERSION_SUFFIX@">0</token>
     </macros>
     <requirements>
@@ -27,6 +27,12 @@
             --dataset-path ./input_files/
             --output-dir ./
             --method collection
+            #if $mode.approx_lon is not None:
+                --approx-lon '$mode.approx_lon'
+            #end if
+            #if $mode.approx_lat is not None:
+                --approx-lat '$mode.approx_lat'
+            #end if
         #end if
     ]]></command>
 
@@ -49,6 +55,12 @@
             <when value="collection">
                 <param name="input_collection" type="data" format="laz" multiple="true" label="Point Cloud Collection" 
                        help="Multiple LAZ/LAS files to validate for consistency (CRS homogeneity, attribute consistency, overlaps)"/>
+                <param argument="--approx-lon" type="float" optional="true" min="-180" max="180"
+                       label="Approximate longitude"
+                       help="Optional WGS84 longitude that overrides the calculated collection centroid when paired with approximate latitude."/>
+                <param argument="--approx-lat" type="float" optional="true" min="-90" max="90"
+                       label="Approximate latitude"
+                       help="Optional WGS84 latitude that overrides the calculated collection centroid when paired with approximate longitude."/>
             </when>
         </conditional>
     </inputs>
@@ -90,16 +102,55 @@
                 </assert_contents>
             </output>
         </test>
+        <test expect_num_outputs="1">
+            <conditional name="mode">
+                <param name="task" value="collection"/>
+                <param name="input_collection" value="mikro_no_crs.laz,mikro2_no_crs.laz" ftype="laz"/>
+                <param name="approx_lon" value="7.85"/>
+                <param name="approx_lat" value="47.99"/>
+            </conditional>
+            <output name="collection_summary" ftype="json">
+                <assert_contents>
+                    <has_json_property_with_value property="n_tiles" value="2"/>
+                    <has_json_property_with_value property="homogeneous_crs" value="true"/>
+                    <has_json_property_with_value property="homogeneous_attribute_names" value="true"/>
+                    <has_json_property_with_value property="longitude" value="7.85"/>
+                    <has_json_property_with_value property="latitude" value="47.99"/>
+                    <has_json_property_with_text property="crs" text="EPSG:4326"/>
+                    <has_json_property_with_text property="source" text="approximate_input"/>
+                    <has_json_property_with_value property="available" value="true"/>
+                    <has_json_property_with_text property="multipolygon_crs" text="LOCAL_OR_UNKNOWN"/>
+                    <has_json_property_with_text property="multipolygon_source" text="source"/>
+                    <has_json_property_with_value property="multipolygon_available" value="true"/>
+                    <has_json_property_with_value property="multipolygon_wgs84_available" value="false"/>
+                    <has_json_property_with_text property="concave_hull_crs" text="LOCAL_OR_UNKNOWN"/>
+                    <has_json_property_with_text property="concave_hull_source" text="source"/>
+                </assert_contents>
+            </output>
+        </test>
         <test expect_num_outputs="1">
             <conditional name="mode">
                 <param name="task" value="collection"/>
                 <param name="input_collection" value="mikro.laz,mikro2.laz" ftype="laz"/>
+                <param name="approx_lon" value="7.86"/>
+                <param name="approx_lat" value="48.01"/>
             </conditional>
             <output name="collection_summary" ftype="json">
                 <assert_contents>
                     <has_json_property_with_value property="n_tiles" value="2"/>
                     <has_json_property_with_value property="homogeneous_crs" value="true"/>
                     <has_json_property_with_value property="homogeneous_attribute_names" value="true"/>
+                    <has_json_property_with_value property="longitude" value="7.86"/>
+                    <has_json_property_with_value property="latitude" value="48.01"/>
+                    <has_json_property_with_text property="crs" text="EPSG:4326"/>
+                    <has_json_property_with_text property="source" text="approximate_input"/>
+                    <has_json_property_with_value property="available" value="true"/>
+                    <has_json_property_with_text property="multipolygon_crs" text="EPSG:4326"/>
+                    <has_json_property_with_text property="multipolygon_source" text="wgs84_transform"/>
+                    <has_json_property_with_value property="multipolygon_available" value="true"/>
+                    <has_json_property_with_value property="multipolygon_wgs84_available" value="true"/>
+                    <has_json_property_with_text property="concave_hull_crs" text="EPSG:4326"/>
+                    <has_json_property_with_text property="concave_hull_source" text="wgs84_transform"/>
                 </assert_contents>
             </output>
         </test>
@@ -134,6 +185,7 @@ Validates consistency of multiple LAS/LAZ files:
 - **Tile Geometry**: Detects overlaps and gaps between tiles
 - **Global Statistics**: Computes aggregated statistics across all files
 - **Removeable Attributes**: Identifies attributes that are all-NA or constant-zero
+- **Collection Centroid**: Computes a WGS84 centroid from valid collection geometry, or uses optional approximate longitude/latitude as a trusted override when provided
 
 **Outputs (collection mode):**
 - ``collection_summary.json`` containing collection-level checks and flags, per-file metadata (CRS, attributes, point counts, convex hulls), and suggested removeable attributes for standardization
diff --git a/tools/3dtrees_standardization/test-data/mikro2_no_crs.laz b/tools/3dtrees_standardization/test-data/mikro2_no_crs.laz
new file mode 100644
index 0000000000000000000000000000000000000000..2ae852ef6ff2fd7ebf21276b116eb923d1d35295
GIT binary patch
literal 847
zcmeZq40dB+U}QiCj4bFP==`Fb#A1aYg@VN7?8Nj`bXf+52@J2;%NcJ2jRu+Cu7aro
zDpD=7&i!Fki#<9GlKxX9=?J781k*x5Gy{V{jRV*9#RVe8l8!*i_8(9_XouWYVW9k*
zz#VxYbzpPuLDbor)i{9lp%EfbKFpT_X!5k??p_59y{gOth19&{{FKxb28KOhdJIXG
z3Q*zvGzA~W;FA3OoMHtHBO^mYBMVIi24<kMm{~w114F=J28RD=fQf;NK@O;jn}H2T
zIzbdNTm**yEg-uasEeOL5lBva0WyKxF-&KdBSQj10fRj#JOY7O86*J(;y{`Y#sSjW
zK<o{~8frR^4%o{F^81)xPtxZwoVV@Pa~{u4lO5+&KRob`nNu-(TZ{emJv_;;r*UY@
zhrLn#bU5(ZVuuaE4|wLv&-tyMtuo13dhNkZN#kE#>IFapT^9X!nf2n(<Y_0X=YKcU
z+WvO$i$@ParEha;hiE*gyXps2l03`&yuQwXE?&DG3a=7X7ruRXJqRe=WUTP=!`=nO
zH;=Lbc_LalC%?^DVler;L+?71Z)(4-e$Mb_FHLTK(5g{cnejR)<?_-M%nJ8_O0Q1T
z+&brC!{(IiGDF45d;8<J%nRgIa#VTX#ajRM+MN9b8?JiqNmEMdt2rLDaATL(%)62&
kj?37I_}a%z=Kr>BvinknDEq7%VL+om02smy-f}<!0Dp|sfdBvi

literal 0
HcmV?d00001

diff --git a/tools/3dtrees_standardization/test-data/mikro_no_crs.laz b/tools/3dtrees_standardization/test-data/mikro_no_crs.laz
new file mode 100644
index 0000000000000000000000000000000000000000..70219f70d290a7c70f4b5e195f31e8385cfeb14c
GIT binary patch
literal 833
zcmeZq40dB+U}QiCj4bFP==`Fb#A1aYg@VN7?8Nj`bXf+52@J2;%NcJ2jRu+Cu7aro
zDpD=7&i!Fki#<9GlD<$R=?J0)(?Y;BgF=nN4!PFXPk`bNt3=ja0@B9D#+O0zOA2hc
zKy(@ibV1Yw0@Z``qXQAB05g;pL{~s#{_a)4(5uQUP)N;7&QD2AVPM!3rpJ&}sQ?wu
zPgC%53@*vf&nZ^WFfuYUG_ufSU;w$6nFZqJfWr(7|Iq*w0~doFP!%@=8;~@CdafE6
z{y@bHQb4T60P^Xp=RjhDflZjsE=L9(26F~AP<VI%u?!HyfEbX$3*!K3T_E-aVuOgK
zn{szZDxTg^{$zc~gXHtKELXnf4nJ~u`sx=+)uG=%?JDM;Vds3g`0i)D(B!+?dymg4
z(2e!}e@b{0_bY3?n;#uT`M(3rk<+vKW768SzU|jX&i=ie&MBWHj~t$}yS4%-r&Sa`
zn|1SEw$L9X&e1*Z%n!Gn0*W>{=`6XJeEq>K4IoENuGqN5>FZqox9g|>*`?xK@-1w!
z4DZC!^$qh<%{b!kZI@Krcs=B}(TQxJ;w#NH-`6bF;0a7FDCaqR)sVku)xv8xr*7Y7
zt)405JXg+Q-bGQ<)7#Qk9oScUM7S~Edvo*i0FKLk3k&>e<0X1eJSx_?`g=|0%r|8~
N!$1I(roBMH2mrU-(F6bh

literal 0
HcmV?d00001