Plant Height from LiDAR
This analytic automatically estimates plant height from LiDAR Data in field trials.
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- This task requires a specific Alteia platform license. Please contact your Sales Representative for more information.
- If during the lidar data acquisition a RGB or Multispectral sensor was embedded on the drone, we recommend to first upload and process the RGB or multispectral images and then process the Lidar Data. It will facilitate the microplot boundaries adjustment.
- Imported Lidar data (LAS file) have to be initially co registered with Ground Control Points. When tagging the GCPs in the
- Lidar Software, each drone axis have to be tagged separately.
1. Inputs
- Point Cloud in LAS format*
- Microplots vector file*
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IMPORTANT
- Format: Shape File or Geojson
- For Shape file format:
- The following extensions are required: .dbf, .shp, .shx (.prj is optional).
- The extensions have to be located in a compressed folder (.zip)
- We recommend to have the same CRS for the Shape File and project
- The plot id must be unique
- If the plot dimensions (width and/or length) have to be changed within this task (to evaluate only certain rows of the microplot for example), the final plot dimensions (final_width and final_length attributes) have to be indicated in the vector file attribute table. You can use the “Joint attributes” tool to add these information (Join attributes to a vector file)
- Deliverables suffix
- Field trial start*: A point annotation made in Alteia platform defining the field trial start
- Minimum Height: Minimum plant height to be used in the statistics computation
- Maximum Height: Maximum plant height to be used in the statistics computation
*Mandatory
2. Deliverables
- Plant height statistics CSV + suffix .csv: CSV file with plant height statistics at microplot level
- Plant height statistics +suffix .geojson: Vector file with plant height statistics at microplot level*
- Plant height +suffix .tif: Raster file with plant height at pixel level
- DTM.tif: Digital Terrain Model
- DSM.tif: Digital Surface Model
*Other format are available if needed (Shape file…)
3. Attributes
“Plant height statistics geojson output:
- Attributes from the input vector file (parent_id, block_plot_id,… if the vector is from Alteia)
- max: Maximum plant height
- mean: Average plant height
- median: Median
- min: Minimum plant height
- count: Number of pixel in the polygon
- std-dev: Standard deviation
- var: Variance
- decile_1: decile 1
- decile_2: decile 2
- decile_3: decile 3
- decile_7: decile 7
- decile_8: decile 8
- decile_9: decile 9
- percentile_1: percentile 1
- percentile_5: percentile 5
- percentile_95: percentile 95
- percentile_99: percentile 99
“Plant height statistics CSV output:
- Attributes from the input vector file (parent_id, block_plot_id,… if the vector is from Alteia)
- max-out_plant_height-b1: Maximum plant height
- mean-out_plant_height-b1: Average plant height
- min-out_plant_height-b1: Minimum plant height
- count-out_plant_height-b1: Number of pixel in the polygon
- std-dev-out_plant_height-b1: Standard deviation
- var-out_plant_height-b1: Variance
- decile_1-out_plant_height-b1: decile 1
- decile_2-out_plant_height-b1: decile 2
- decile_3-out_plant_height-b1: decile 3
- decile_7-out_plant_height-b1: decile 7
- decile_8-out_plant_height-b1: decile 8
- decile_9-out_plant_height-b1: decile 9
- percentile_1-out_plant_height-b1: percentile 1
- percentile_5-out_plant_height-b1: percentile 5
- percentile_95-out_plant_height-b1: percentile 95
- percentile_99-out_plant_height-b1: percentile 99
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The unit of length attributes is meter
Example for the deciles and percentiles:
- Decile 1 has 10% of the data points below it and has 90% of the data points above it.
- Decile 2 has 20% of the data points below it and has 80% of the data points above it…
- Percentile_1 has 1% of the data points below it and has 99% of the data points above it.
- Percentile_5 has 5% of the data points below it and has 95 % of the data points above it…
4. Workflow
Upload the point cloud (LAS file)
- Create a new Site if there is no existing one (see here for more information on new site creation)
- Click on UPLOAD FILES
- Select a new survey or select an existing one if any.
- In the next page, the Type “Point Cloud” is normally selected by default. Select “None” in Category.
- Define the CRS
- Click on upload
- Once the upload is complete, the file is visible in the download section and in the 3D view:
Delete- To visualise the x, y and z position, hide the left panel (see bellow)
- We recommend to select the Elevation in Material for optimal visualisation
- Use the right and left click of the mouse to navigate in the point cloud.
Upload the microplot vector file
- Click on UPLOAD FILES
- Select the same survey as the point cloud and click on “next”
- Select Vector in Type and Microplos / Plots in Category
- If not automatically defined, select the CRS of the microplot file and click on Upload.
- Once the upload is complete, the microplot file is visible in the download section and in the 2D view
Definition of the field trial start
Case 1: a RGB map (or NDVI / VARI Index) is available in the survey
- Display the 2D map
- Select the Point annotation tool
- Add a point at the corner of the first plot of the trial.
- Change the name of the annotation (Field trial start - “first plot name”) then click on Enter to validate
- You can change the icon (green flag for example)
Case 2: I only have a point cloud and a microplot vector file (no 2D map available).
- Display the point cloud in the 3D view, select “Elevation” in Material (cf above)
- Select the Point annotation tool
- Add a point at the corner of the first plot of the trial.
- Change the name of the annotation (Field trial start - “first plot name”) then click on Enter to validate
- Back to 2D view
Adding custom attributes to the microplot file (optional)
Please read the following article for more information: Join attributes to a vector file
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In particular, if the plot dimensions have to be changed, you can add the final plot dimensions information to the vector attribute tableusing the Custom attributes tool.
Launch the analytic
In the analytic section, select the “Plant height from LiDAR” analytic and click on LAUNCH.
Select the Point Cloud and de Microplot vector.
In the next page, add a suffix for the deliverables (optional) and indicate the Minimum height and Maximum height to be used in the statistics computation. Then click on launch.
Once the task is finished, the results will be available in the 2D view and Export section
5. How to value the results
The 2 main outputs are the “Plant Height map” and “Plant Height statistics”
- If "Plant height" layer is displayed, a map with a color scale appears: the highest vegetation is displayed in green. Low vegetation tends towards yellow or red. Clicking on “Value at point” gives the vegetation height in a specific location of the field
- If "Plant height statistics" layer is displayed, the microplot vector appears. Clicking on a microplot gives statistics associated to this microplot.
Other color scale can also be displayed such as Mean, Min, Max…
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For more information about data export: Exporting Data