VPalm IDE

Introduction

VPalm IDE is used to compute architectural parameters from field data, call the VPalm automaton using those parameters and to build 3D plant mock-ups arranged in a scene. The output files are in OPF (Open Plant Format) and OPS (OPen Scene) format.

The data preparation, the models and all details are described in the PhD of R. Perez and the subsequent articles (Perez et al. 2016; Perez 2017; Perez, Costes, et al. 2018; Perez, Dauzat, et al. 2018; Perez et al. 2017)

Program details

VPalm IDE is an R Shiny application bundled in an Electron application. This method was used following the work of Katie Sasso on this repository, and improved to add an installer for windows users.

Install

User

To install VPALM_IDE, simply download this repository wherever you want, and download the data folder. The data folder is available to PT-SMART partners only, or upon request (need clearance from PT-SMART + CIRAD). For partners, just download the “0-data” folder from Alfresco, and put it at the root of this folder.

Developer

To build the electron app, you need to download and install node.js, and to restart your computer. Then, you need to download R-portable so your application does not depends on external ressources. You can also follow this link that points to the latest release of the project.

Then, clone this repository:

# Clone this repository
git clone https://github.com/PalmStudio/VPALM_IDE
# Go into the repository
cd VPALM_IDE

Unzip the R-portable archive into the root of the project.

And now you can install the app and run it for the first time following these steps:

# Install dependencies
npm install
# Run the app
npm start

The installation adds a new folder called node_modules into your project.

Build

Windows

If the app is running with no issue, then you can build the electron application:

npm run package-win

Linux

npm run package-linux

Mac

npm run package-mac

All at once

npm run package-all

NB: not tested yet.

Issues

If it does not work, it is probably because the packager is not installed. try to run this command, and re-run the previous one:

npm install -g electron-packager

run

A new folder called builds appeared on the project. The electron application you just built is in there. To start the application, find the corresponding execution file (e.g. the windows .exe file) and start it. That’s it ! The folder were the executable lies is a standalone Shiny application.

Share

You can share the application just by copy/pasting it into a USB key or by deploying it on the cloud. You might want to compress it beforehand though.

Build Windows installer

To build windows installer, we use the windows-installer app. Simply follow these instructions to build it:

Install the package if not already done:

 npm install --save-dev electron-winstaller
 npm install --save electron-squirrel-startup

And build the installer using node:

 node build.js

Remember to first build the app (npm run package-win) before building the installer.

NB: Several interesting build options are available for the installer, see the project repository for more details. These options should be added to the settings variable in build.js.

Automatic updates

It is possible to add automatic updates to the app by using a remote repository. To set it up, we can add the option remoteReleases (see here for more details) and remoteToken if necessary. The link should point the releases folders i.e. the installer-x64 folder for our example. Then electron will check for any updates automatically, dowload them and install them if necessary. Further details are available on the Squirrel.Windows documentation. Also see this and this.

Summary

To update the application and the installer, simply run these commands:

npm install
npm run package-win
node build.js

References

Perez, Raphaël. 2017. “Analyzing and Modelling the Genetic Variability of Aerial Architecture and Light Interception of Oil Palm (Elaeis Guineensis Jacq).” Thesis.

Perez, Raphaël, Evelyne Costes, Frédéric Théveny, Sébastien Griffon, Jean-Pierre Caliman, and Jean Dauzat. 2018. “3D Plant Model Assessed by Terrestrial Lidar and Hemispherical Photographs: A Useful Tool for Comparing Light Interception Among Oil Palm Progenies.” Agricultural and Forest Meteorology 249: 250–63. DOI.

Perez, Raphaël, Jean Dauzat, Benoît Pallas, Julien Lamour, Philippe Verley, Jean-Pierre Caliman, Evelyne Costes, and Robert Faivre. 2018. “Designing Oil Palm Architectural Ideotypes for Optimal Light Interception and Carbon Assimilation Through a Sensitivity Analysis of Leaf Traits.” Journal Article. Annals of Botany 121 (5): 909–26. DOI: 10.1093/aob/mcx161.

Perez, Raphaël, Benoît Pallas, Gilles Le Moguédec, Hervé Rey, Griffon Sébastien, Jean-Pierre Caliman, Evelyne Costes, and Jean Dauzat. 2016. “Integrating Mixed-Effect Models into an Architectural Plant Model to Simulate Inter-and Intra-Progeny Variability: A Case Study on Oil Palm (Elaeis Guineensis Jacq.).” Journal of Experimental Botany 67 (June): erw203. DOI: 10.1093/jxb/erw203.

Perez, Raphaël, Benoît Pallas, Griffon Sébastien, Hervé Rey, J.P. Caliman, G Le Moguédec, Jean Dauzat, and Evelyne Costes. 2017. “Reconstructing Three-Dimensional Oil Palm Architecture from Allometric Relationships.” Acta Horticulturae 1160 (May): 11–18. DOI.