canObsR aims at streamlining, standardizing and facilitating processing of repetead UAV surveys from R. It focuses 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).
To cite ‘canObsR’, please use citation(‘canObsR’).
library(devtools)
install_github("https://github.com/umr-amap/canObsR.git")In addition to the usual R package documentation, we also have extensive docs and examples here
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(canObsR)# Python env creation
env_name <- "canObsR_env" # use the name you want for your environment
environment = file.path( system.file(package="canObsR"), 'PYTHON/environment.yaml') # use the environment.yaml file included in the package
conda_create(env_name, environment = environment)
use_condaenv(env_name)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)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 canObs_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 !
One of the main functions of the package is to generate orthomosaics and to align them in R, using Metashape and AROSICS. To guide you step by step into the workflow, you should download the test dataset and follow the article.
Generate orthomosaics
