This web app is intended to provide users with an overview of the anatomy of a Helium Nanodroplet Isolation Spectrometer and to allow users to experiment with changing parameters such as the nozzle temperature to better understand the effect of these parameters on the spectra collected by the instrument. The user can simulate collecting spectra at a variety of nozzle temperatures ranging between 13.5 and 20 K.
A demo of this application is currently hosted at http://virtual-hendi.isaac-j-miller.com.
In order to view a tooltip about a component of the instrument, hover your mouse over it. In order to view inside the instrument, click the "See inside the instrument" button in the top right corner. To run a spectrum, specify the wavelength range and the temperature using the controls and then click the "Run Spectrum" button. A spectrum should appear after a few seconds. If you wish to change the parameters, do so and then click "Run Spectrum" again, as it does not update automatically. Once the spectrum is loaded, you may download the spectrum as a .csv file. You may interact with the spectrum in a few ways:
- Zoom in on a section by pressing down the left mouse button, dragging across the section, and then releasing.
- Scrub the spectrum by pressing down the left mouse button and dragging across the spectrum while pressing the "shift" key
- Reset the view by double-clicking on the spectrum.
To run the application locally, after cloning the repository, cd into the root directory (i.e. virtual-hendi/) and run scripts/check-env. This ensures that all the necessary tools are installed. Then, run scripts/start-local. This builds the frontend and starts the server, which listens on port 3000. Once this script is running, you may visit the site locally at http://localhost:3000.
If you make changes to the front end while running the site in this way, you must re-build the frontend by running scripts/rebuild-front.
If running in a non-ubuntu environment, you may have to make changes to the scripts/check-env script, as it uses apt to install the necessary packages. The script does the following:
- install Python 3.8
- create a virtual environment in
back/src/python/env - activate
env - install python modules using
python -m pip install requirements.txt, whererequirements.txtis inback/src/python - install nodejs, npm
- cd into
frontand runnpm installto install the node modules there - cd into
backand runnpm installto install the node modules there Also, if running on windows, be sure to use git bash, rather than powershell or cmd.
This application requires Ubuntu 20.04 to run. An older or newer version might work, but it has only been tested on 20.04. After instantiating the server, run scripts/user-data in the # directory (sudo -i). Since the repo has not been cloned yet, you will need to copy the contents of this script to the server and then run it. This script clones the repo and configures the server to host the site. It configures nginx to listen on port 80 and redirect traffic to port 3000 so that the web app can be accessed from the server's public IP.
To update the version on the server, ssh into the server and sudo -i. Then run scripts/update-reload. I have had some issues with the process not properly stopping, so it may be necessary to determine the PID of the process using port 3000 and manually kill it before running scripts/update-reload.
If you would like to make changes to this repo, please submit a pull request. I will review it in as timely a manner as possible and then update the server that I'm using to host the demo at http://virtual-hendi.isaac-j-miller.com to reflect the changes if I decide to merge the pull request.