1. Description

The "Plant Height" analytic automatically estimates plant height for field trials, production fields, and plantations and forestry. The calculation can be done in two ways.

• The first is by subtracting a “survey 1 DSM with bare soil” from “survey 2 DSM with vegetation”.
                                                                                                 
• The second is by subtracting an “Estimated Terrain Elevation (DTM)” from a “survey DSM with vegetation”.
  

Both methods are explained below.

2. Inputs

• Required inputs for the "plant height for field trial" analytic are:

  Required Inputs	Description
  Digital Surface Model (DSM)	Provided through the photogrammetry process
  DSM from bare soil survey (DTM)	Can be an estimated DTM from the bare soil model estimation analytic. If the bare soil model estimation is used, areas of bare soil must be visible in the survey, such as alleys or tracks, in order to estimate the DTM.
  Microplots vector	Can come from either the Microplot Designer‍ or can be imported into Alteia
  Optional Inputs	Description
  Deliverables suffix
  Minimum height	Minimum plant height to be used in the statistics computation (plants should be taller than 30cm)
  Maximum height	Maximum plant height to be used in the statistics computation

• Required inputs for the "plant height for production field and plantation/forestry" analytic are:

  Required Inputs	Description
  Digital Surface Model (DSM)	Provided through the photogrammetry process
  DSM from bare soil survey (DTM)	Can be an estimated DTM from the bare soil model estimation analytic. If the bare soil model estimation is used, areas of bare soil must be visible in the survey, such as alleys or tracks, in order to estimate the DTM.
  Field Boundaries	Read more at How to create a Field Boundaries‍
  Optional Inputs	Description
  Grid size
  Deliverables suffix
  Minimum height	Minimum plant height to be used in the statistics computation (plants should be taller than 30cm)
  Maximum height	Maximum plant height to be used in the statistics computation

3. Workflow

3.1 DTM Estimation

Note: If you do not have a bare soil map (DTM) on a specific survey, you can estimate it with the analytic “bare soil model estimation”. If you already have a bare soil map, skip paragraph 3.1.

Step 1 - To begin, select the category depending on your project (Field Experiment, Plantation & Forestry, or Production Field) and then click on “Bare soil model estimation" analytic.

Step 2 - Launch the analytic and select the DSM of the survey in which you want to estimate the bare soil (1).

Step 3 - Select an associated scouting map (RGB or Multispectral) (2).

Step 4 - Depending on the type of project, select the “microplots” or, if running the production field analytic select a vector file for “field boundaries" (3).

Step 5 - Click on "LAUNCH BARE SOIL MODEL ESTIMATION".

After following the above steps, the estimated DTM is available in the map view (the operation may take a few minutes).

3.2 Launching Plant Height Analytic

Step 1 - From the analytics panel list, select the corresponding "plant height analytic", either "Field Experiment", "Plantation & Forestry", or "Production Field". Then, select "Launch".
Step 2 - Select the DSM of the survey in which you want to measure the height (1).

Step 3 - Select the DTM (DSM) coming from a bare soil acquisition or generated by the Bare soil model estimation task (see step 1) (2).

Step 4 - Depending on the type of field, select the “microplot” or “field boundaries” vector (3).

Note: For Production field projects, field boundaries need to be a vector file.

Step 5 - Click on "NEXT STEP".

Step 6 - Select a grid size (in meters) [For Production Field only] (1).

Step 7 - Add a suffix for the deliverables (optional for Field Experiment) (2).

Step 8 - Indicate the Minimum height and Maximum height to be used in the statistics computation (optional for Field Experiment) (3) + (4).

Step 9 - Launch the analytic.

4. Results

The two main outputs for the plant height analytic are the “Plant height" map and “Plant height statistics”.

4.1 Plant Height Map

If the "Plant height" map is displayed, a map with a color scale appears: the highest vegetation is displayed in green. Low vegetation is represented as yellow or red.

If you click on the name of the map, the right panel will appear with advanced visualization features:

• “Value at point”: gives the vegetation height in a specific location of the field.
• Color chart option
• Plant height distribution:

Height value distributions can be displayed with these modes.

4.2 Plant Height Statistics

If the "Plant height statistics" map is displayed, the microplot or field vector appears.

• Different styles are available by default: mean, max...

If needed you can customize the styles (see Vector Layers Styling)‍. 

• Click on a specific microplot or tile to view the statistics associated with this microplot or tile.

5. Deliverables

The deliverables are available in the below formats with their corresponding attributes. Note that for all attributes the unit of measurement is in meters.

5.1 For Field Trial

5.1.1 Plant height statistics + suffix .csv

This deliverable is a .csv file with plant height statistics at a microplot or tile level for a production field. Below are the attributes from the input vector file (parent_id, block_plot_id, etc.) if the vector file is generated from Alteia.

• max-clipped_plant_height_[ID_PROJECT]-b1: Maximum plant height
• mean-clipped_plant_height_[ID_PROJECT]-b1: Average plant height
• median-clipped_plant_height_[ID_PROJECT]-b1: Median
• min-clipped_plant_height_[ID_PROJECT]-b1: Minimum plant height
• count-clipped_plant_height_[ID_PROJECT]-b1: Number of pixel in the polygon
• std-dev-clipped_plant_height_[ID_PROJECT]-b1: Standard deviation
• var-clipped_plant_height_[ID_PROJECT]-b1: Variance
• decile_1-clipped_plant_height_[ID_PROJECT]-b1: decile 1
• decile_2-clipped_plant_height_[ID_PROJECT]-b1: decile 2
• decile_3-clipped_plant_height_[ID_PROJECT]-b1: decile 3
• decile_7-clipped_plant_height_[ID_PROJECT]-b1: decile 7
• decile_8-clipped_plant_height_[ID_PROJECT]-b1: decile 8
• decile_9-clipped_plant_height_[ID_PROJECT]-b1: decile 9
• percentile_1-clipped_plant_height_[ID_PROJECT]-b1: percentile 1
• percentile_5-clipped_plant_height_[ID_PROJECT]-b1: percentile 5
• percentile_95-clipped_plant_height_[ID_PROJECT]-b1: percentile 95
• percentile_99-clipped_plant_height_[ID_PROJECT]-b1: percentile 99

5.1.2 Plant height statistics + suffix .geojson

This deliverable is a vector file with plant height statistics at a microplot or tile level for a production field. Below are the attributes from the input vector file (parent_id, block_plot_id, etc.) if the vector file is generated 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

5.1.3 Plant height + suffix .tiff

This deliverable is a raster file with plant height values at the pixel level.

5.2 For production field and plantation/forestry

For production field and plantation/forestry, the plant height statistics .csv or .geojson output has the same attributes as the above, plus the following:

• id_x: column number
• id_y: row number

The Plant Height + suffix .tiff is also identical to 5.1.3.