dash-ocean-optics

Introduction

dash-ocean-optics is an app created to control and read data from Ocean Optics spectrometers. Try the app out yourself at dash-gallery and learn more about this app from our blog entry!

Absorption Spectroscopy

Certain wavelengths of electromagnetic radiation correspond to frequencies that allow the electrons in certain atoms to transition to higher or lower energy levels; as these wavelengths are absorbed by the sample, the resulting spectrum can yield insight into the chemical composition of the sample. Read more about spectroscopy here.

dash-daq

Dash DAQ is a data acquisition and control package built on top of Plotly's Dash.

Requirements

It is advisable to create a separate conda environment running Python 3 for the app and install all of the required packages there. To do so, run (any version of Python 3 will work):

conda create -n	[your environment name] python=3.4

source activate [your environment name]

To install all of the required packages to this conda environment, simply run:

pip install -r requirements.txt
conda install -c poehlmann python-seabreeze

and all of the required pip packages, as well as the python-seabreeze package, will be installed, and the app will be able to run.

How to use the app

Run the app with:

python3 app.py

If you would like to run the app in demo mode, then run:

python3 app.py demo

Then, navigate to localhost:8050 in your browser and you should see something like this:

The controls are all disabled until the "on" button is pressed:

Then, the live spectrometer data should appear on the plot, and the model of the spectrometer should appear above the plot. Note that the "autoscale" feature is on by default. To improve the speed and animations of the graph, it is necessary to turn this feature off.

The controls below the plot will allow you to change parameters of the spectrometer. The dial labelled "light intensity" to the right of the plot will allow you to adjust the intensity of the light source selected below. Note that the dial is disabled until a light source is selected from the appropriate dropdown menu.

Controls

• int. time (us) - The integration time, in microseconds.
• number of scans - The number of scans to average over.
• strobe - Enables/disables the continuous strobe.
• strobe pd. (us) - The period of the continuous strobe, in microseconds.
• light source - The light source to be used.

Once they have been changed to the appropriate settings, the "update" button to the right of the plot should be pressed, and each of the settings will be sent to the spectrometer one-by-one. The window below the "update" button displays the commands that failed, with the associated error messages, and the commands that succeeded, with the new values.

Note that the window below the update button is scrollable!

Advanced

Configuring the colours

The colours for all of the Dash and Dash-DAQ components are loaded from colors.txt. Note that if you want to change the appearance of other components on the page, you'll have to link a different CSS file in app.py.

Adding your own controls

In order to add a control yourself, you must:

• Create a new Control object in app.py; note that the component_attr dictionary must have the key id in order for the callbacks to be properly triggered.
• Append this new object to the list controls within app.py.
• Add the key-value pair "[dash component id]", "[function object associated with control]" to the dictionary self._controlFunctions in the PhysicalSpectrometer and DemoSpectrometer class definitions (if you don't want this control to have any effect in the demo mode, then set the value to "empty_control_demo").

Adding your own spectrometers

Although this app was created for Ocean Optics spectrometers, it is possible to use it to interface with other types of spectrometers. The abstract base class DashOceanOpticsSpectrometer contains a set of methods and properties that are necessary for the spectrometer to properly interface with the app. Please note that you should be using the communication and spectrometer locks as necessary to avoid issues with two different callbacks trying to modify/read the same thing concurrently.