The package
This R package aims at streamlining, standardizing and facilitating processing of repetead UAV surveys from R. It focuses (for now) on RGB data. It notably allows generating 3D and 4D mosaics & mosaics spatial alignment using state-of-the-art approaches, provides tools to generate reference labels, segment crowns (not now) and classify crown phenophases (not now).
Documentation
In addition to the usual R package documentation, we also have extensive docs and examples here
How to use managecrownsdata
Python environment
First, make sure you have python>3.9 and anaconda / miniconda installed on your device. If not, you can download them using the following links :
https://www.python.org/downloads/ https://www.anaconda.com/download/
After completing the installation steps, you can create your own python environment that will contain everything you need to call this package’s functions.
# Imports
library(reticulate)
library(managecrownsdata)
# Python env creation
env_name <- "managecrownsdata_env" # use the name you want for your environment
environment = file.path( system.file(package="managecrownsdata"), 'PYTHON/environment.yaml') # use the environment.yaml file included in the package
conda_create(env_name, environment = environment)
use_condaenv(env_name)Metashape
The environment you just created contains already all necessary dependences but the Metashape python API, which is required to align photos using TimeSIFT. To install it, you first need to download a file from the Metashape website : https://www.agisoft.com/downloads/installer/. Go to the “Python 3 module” section and click on the link corresponding to your operating system. This should download a file named “Metashape[…].whl”. Then, copy the path to the downloaded .whl file below
# Add metashape API to env
path_to_whl_file <- "MYPATH/Metashape-2.1.3-cp37.cp38.cp39.cp310.cp311-none-win_amd64.whl" #replace with your path
py_install(path_to_whl_file, envname = env_name, pip=TRUE)Metashape license activation
Your python environment should be ready for use now. However, Agisoft Metashape requires a paid license in order to access all its features. It is not necessary to have the Metashape application installed on your device in order for the python API to work, but whether or not the application is installed and/or activated, the API still needs to be activated using a license key (it can be the same used for the application if it is already installed).
To activate the key, follow these steps :
- Open an anaconda command prompt
- Activate the environnement you just created : $ conda activate managecrownsdata_env
- start python and activate the licence : $ python >>> import Metashape >>> Metashape.license.activate(“AAAA-BBBB-CCCC-DDDD”) # replace with your license key
If that works, you can close the command prompt. You should be good to go !
