Pneumatron

This dashboard was developed with the aiming to create a more user-friendly interface to use pneumatron. Pneumatron is an apparatus develop by Pereira et al. 2020 to automatically generate xylem embolism vulnerability curve from pneumatic-method (Pereira et al. 2016). With this dashboard, you will be able to track currently running curves and analyze your experiments.

Instructions

Installation

Required

The user needs to have Arduino IDE, R and R Studio installed.

Setting up ESP8266 on Arduino IDE

In order for your computer to read the ESP8266 through a communication port, it is necessary to install the ESP8266 board in the Arduino IDE. Here are the steps to do this:

1. Open the Arduino IDE.
2. Go to File > Preferences.
3. In the "Additional Board Manager URLs" field, enter the following JSON link: http://arduino.esp8266.com/stable/package_esp8266com_index.json.
4. Click OK to save your changes and return to the main screen.
5. Now go to Tools > Board > Board Manager.
6. Look for the option "esp8266 by ESP8266 Community" and click the Install button.
7. After the installation, your computer will automatically create a communication port for ESP8266 boards.

Steps

1. Clone/Download this repository to your local machine.
2. Open the file pneumatron.Rproj, them you will be at R Studio interface.
3. Within R Studio platform open the R Script Run.R.
4. Execute line #1 source("scripts/required_libs.R") to install all dependent libraries and to create sub folders.

Experiments

For all next instructions, please these steps first:

1. Open the file pneumatron.Rproj, them you will be at R Studio interface.
2. Within R Studio platform open the R Script Run.R.

Data Acquisition

1. Execute line #5 serial::listPorts() to discover your Pneumatron/receiver COM port. Tip: first execute this line with your device unattached from USB port, then attached again and execute this line one more time. The port's name from your device appears only when it is connected.
2. In line #7 specify your device(s) COM port name. Ex: c("COM1") or c("COM1", "COM2").
3. Execute line #7.
4. In line #8 specify your database file name. This is where your raw data will be saved. You can leave it as suggested or specify a name for each experiment.
5. Execute line #8.
6. Execute line #11.

Now your receiver is collecting data. When you turn on your Pneumatron, data will be automatically saved on a specified database file. There is also a python3 script in scripts/00-py_read_pneumatron.py that you could use to acquire your data.

Dashboard

1. Execute line #14
2. A message containing a web address will be displayed. Ex: Listening on http://127.0.0.1:6098.
3. Access the address displayed in that message in your preferred web browser. All next steps will be in your browser.
4. In Databases tab, press File Select to select your database file. This file name was specified in data acquisition step 4, and is saved inside raw_pneumatron folder.
5. Go to Running Experiments tab to track your current data.