User Manual The_Tropical_River control software

Writing a protocol

Two mains protocol writing styles are available:

• Relative time: instructions separated by waiting times in milliseconds.

• Absolute time: instructions executed at a given time in seconds since the start of the protocol.

Serials

The Tropical River comes with build-in serial devices integrated into the UI:

• heater: control the river temperature via a PID.
• river: temperature sensor and peristaltic pump control.
• valves: switches valves to inject products or water in the injector.
• fl1: control the flow rate inside The Tropical River.

Any Arduino device that follows the sketch standard (see below) can be connected add-on. Get the list of all Arduino devices connected by port series by taping in the serial terminal panel:

ls serial

To communicate directly with the device types:

device::command:value

Protocol standard

General commands

1. To print a message in the status bar: print::Your message

2. To control the camera: camera::start camera::stop

3. To control a serial device: serialId::command:value

4. To create a directory to save images, protocol, and parameter files:

   data::create directory

Write a protocol with relative time

Instructions are separated by a wait time in milliseconds:

camera::start
fl1::setFlow:10
wait::1000
fl1::setFlow:20
wait::1000
fl1::stop

In this protocol, the camera will start, then the flow rate is set to 10, 1 second later it is set to 20, and then 1 second later it will stop.

Write protocol with absolute time

The time in seconds (since the beginning of the protocol) at which the instruction must be executed is indicated before the instruction as time->instruction.

0->camera::start
0->fl1::setFlow:10
1->fl1::setFlow:20
2->fl1::stop

Notes

Do not mix the two writing styles!

Example

For example, if you want to record an experiment where the flow rate is set to 1 L/s for 6 seconds:

# Example protocol in relative time
print::Starting protocol...

# Create a directory and save parameter and protocol files
data::create directory

# Start images recording
camera::start

#Set flow rate of fl device to 1
fl::setFlow:1

# Wait
wait::6000

fl::stop

# Stop images recording
camera::stop
print::Protocol ended

# Example protocol in absolute time
t0->print::Starting protocol...

# Create a directory and save parameter and protocol files
t0->data::create directory

# Start images recording
t0->camera::start

# Set flow rate of fl device to 1
t0->fl::setFlow:1

# Stop flow rate
t6->fl:stop

# Stop images recording
t6->camera:stop
t6->print:Protocol ended

Add a device by serial port

Arduino device

The connection of an Arduino device is automatic if it follows this guideline:

1. The Arduino serial server has to have a getId method that gives an id to the device.
2. The Arduino serial server has to accept input as command:value or command if no value is needed.

Non-Arduino device

A non-Arduino device's connection has to be manually added in the source code (see, for example, the Neslab_Rte class).

Serial terminal

A console to talk to devices (only Arduino automatically detected) is available in the terminal panel. You can list connected devices by taping ls serial. All commands allowed by the devices are available. For example, if you want to set the flow rate of a device named fl that has a setFlowRate method, just type:

fl::setFlowRate:20

Todo

• Temperature manual control without PID.
• Offset in the PID temperature.
• Camera display widget auto-resize but conserving the aspect ratio.