Orthomosaic Phenotyping Through FIELDimageR

This is SOP specific to the scripts I have created and stored in my Flood_Tolerance repository. My goal streamline their use for others within the lab. For a more in depth tutorial the FIELDimageR tutorial from OpenDroneMap is what my work is based on.

LINK: https://github.com/OpenDroneMap/FIELDimageR

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Creating the File System:

1. Create a folder titled "Name of Field_Data_Extraction"

2. Within this folder, there should be subfolders labeled "Date of Imaging_DE" (This folder will turn into the working directory for the script)

This folder will need to contain the following:

• A copy of the RGB .tif file

• A copy of the RGB dsm .tif file

• A copy of all Multispectral .tif files

• A copy of all the files in the originals folder 

  • 01_Phenotype_Extraction

  • 02_Data_Cleaning

  • 03_Phenotype_Graphs

  • 6 Rollins5_grid_NEW files 

  • Rollins_Field_Map_NEW.csv

  • 210604_m2pro_Rollins5_Pix4D_dsm.tif

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Running the 01_Phenotype_Extraction Script:

1. Once the script is open the assigned variables will need to be changed in accordance with the new working directory and flight date

Variable Naming System:

• wd = pathway to the working directory ("Date of Imaging_DE" folder)

• x = file name of the grid

• y = file name of the RGB tif

• z = name of the final indices values file (will be exported to wd)

• b = name of the final LAI values file (will be exported to wd)

• c = digital surface model of the DSM

• d = reference DEM with no plants

• e = the final file name of the plant height values

2. Click the green run triangle in the top right corner of each r chunk in the script…some steps will take a while to run

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Running the 02_Data_Cleaning Script:

1. Once the script is open the assigned variables will need to be changed in accordance with the new working directory and flight date

Variable Naming System:

• wd = pathway to the working directory ("Date of Imaging_DE" folder)

• x = name of the final indices csv file

• y =  name of the final height values csv file

• z = name of the final LAI values csv file

• m = the name of the column and row csv file from planting 

• a = the name of the new condensed file

2. Click the green run triangle in the top right corner of each r chunk in the script…some steps will take a while to run

3. After this step, I like to organize all the files in the folder

   1. Originals = all the files copies from the originals folder

   2. 210701 or the date = all the tiffs from that specific date

   3. Height

   4. LAI

   5. Indices

   6. Leave the All_Data in the working directory folder