CALOA

CALOA project Summary :

Licence

CALOA is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

CALOA is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with CALOA. If not, see here.

Installation

Requires admin privileges.

Installation of CALOA is simple but there is some really important steps that have to be carefully taken. Installation is done by an installer which runs all third-party installers useful to run CALOA. If Python 3 is already installed on your computer, it is recommended to
uninstall it to use Anaconda Python 3 instead. Anaconda provides a wide selection of scientific python libraries. An uninstaller is provided with CALOA Installer to allow you to easily uninstall Python 3. Python 2 does not need to be uninstalled. Installation can be split in 4 parts.

Connect the spectrometer and the BNC via USB-to-Serial to the computer

to be used for installation and operating.

Installing Python

Python 3.6 environment (env. 0.5 Gb disk space required) was used to write the CALOA application, and is used during installation and execution. During installation, an Python installer window will pop up. Here is a really important step which have to be taken to use CALAO and successfully run installation. During Python installation, while encountering Advanced Installation Options, select "Add Python to the PATH environment variable", if this step is not taken, installation will not be complete and CALOA will not be usable. Appearance of cmd.exe window is is normal, they will be closed afterwards.

In the end of installation, after VSCode installation is prompted, install it. This will need an internet connection, if you do not have one, there is an installer along with

Installing libraries

Many libraries are used by CALOA to complete its role. They will be be installed automatically, as long as, all previous steps has been followed correctly.

Installing FTDI CDM Drivers

FTDI CDM Drivers is needed for USB-to-Serial interfacing. A new installation window will pop-up, simply follow the steps given by the installer.

Installing CALOA

This is the program that pilots communication with both BNC generator and Avantes fiber spectrometers. Installation will be done automatically.

If all went right, you can choose to start the application

Using CALOA

Starting CALOA

To start CALOA, simply double click on the CALOA short-cut. Then a console will run, don't close this console manually, this will cause CALOA to crash. In this console, some information will be written, please DO NOT interact with the console while it is starting, wait for GUI to appear.

Interface overview

On the top of the frame, below menu bar, you can choose your "mode" between "Normal" and "Advanced".

Normal mode

Normal mode interface can be split in 3 parts :

BNC channel setter

This part of the interface is the lefter one. Here we can divide interface in 8 similar labeled boxes. Each one of this boxes corresponds to one of the BNC Channels (often named Pulse). A box contains many informations :

Pulse state (check box) : whether you want the pulse to be active or not.
Pulse Label (text) : the name you want to give to the Pulse.
Pulse width (floating point number) : width of the real TTL pulse in sec
Pulse phase (floating point number) : delay between trigger and TTL pulse in sec
Pulse phase variation (floating point number) : delay variation in sec
Pulse phase base (floating point number) : delay increment base

Observation management frame

Here again, interface can be split in three parts :

Experiment management

In this part, you can fix your experiment parameters :

Total time : total time your observation will take (i.e. the time between two triggers).
Observation time : integration time of the spectrometers.
Averaging number : Averaging number of the spectrometers.
Delay number : number of delays you want to do.

Interpolation management

In this part you can set you interpolation parameters.

Starting wavelength : the wavelength you want the spectra to start with
Ending wavelength : the wavelength you want the spectra to end with
Points number : number of points you want between starting and ending wavelengths.

Reference channel selector

Here is the useful part to manage absorbance reference spectrum, select here the AvaSpec channel used as reference.

Scope Display

Here you can select which scope you want to see, note that absorbance scope will not be displayed before you've selected a reference channel. It is composed of multiple panes clearly identified.

Advanced mode

This is really not useful to interact with BNC using this mode. But if you want some fine tunes of BNC, you should use this interface. More informations about how to use and program BNC are given in his own documentation, given along this file.

Starting an observation

CALOA is used to perform spectrometry over time using a generator and Avantes spectrometers.

Enter experiment parameters

First of all you will have to enter your parameters in the application. Enter the total observation time (this is the time between two triggers) in the Entry labeled "Total time" in milliseconds. Then enter the integration time of the spectrometers, be careful, a minimal integration time of 1.1 ms is needed. Then enter the number of averages and number of delays. Averaging number corresponds to the number of averages for a single delay number. Delay number corresponds to the number of times CALOA will delay all instruments.

Enter generator parameters

You now have to set all parameters for all 8 generator channels. In each channel cell, as previously mentionned, you can set 5 parameters. Label can be set to whatever value you want, it is used as a human readable identification. Channel parameters will be send to the generator only if State is enabled, if not, for the sake of time saving other parameters will be skipped.

Set black and white

By observation

You will now need to set Black and White. Your hardware setup needs to be set for each of them, for example, after setting your hardware to a "Black"-mode, hit "Set Black" button, this will set black spectra. Then proceed in the same order to set white.

From a file

After observation of black (or white), you can save spectra in files.

To do this :

Select, in the menu, "Spectra"
Click on the button corresponding to the spectrum you want to save
Then click on "Save"

You will then be asked to selected a file to save selected spectra.

After that, you can load this files instead of observing.

If you have already observed Black and White spectra and exited the application, they will be saved and loaded automatically.

Select the reference

Now, select a reference channel, it will be used to compute absorbance during the experiment.

Run experiment

After that you can hit "Start experiment" to run the observation. CALOA will proceed as such :

Set width and delay for each channel
Prepare measures on spectrometers
Trigger generator (which trigger all instruments in the determined order)
Go to Step 3 for a total of of times.
Recover spectra, store them, and display them
Increment delay of phase variation for each channel
Go to step 3 for a total of of time

Step 6 can be fine tuned, using Phase Base parameter. If this entry is set to 1, incrementation of delay will be done linearly, if a number is entered, this will be used to compute an exponential increment thet is : (base)^i * (phase variation) instead of i * (phase variation).

Save observed data

After that, you will be asked for a folder where you want to save datas. Datas will be saved in a predetermined organization :

  selected_folder :
  |-save[TIMESTAMP] :
    |
    |-raw :
    | |
    | |- [A FILE FOR EACH CHANNEL]
    | |- ...
    |
    |-interp :
    | |
    | |- [A FILE FOR EACH CHANNEL]
    | |- ...
    |
    |-cosmetic :
    | |
    | |- [A FILE FOR EACH CHANNEL]
    | |- ...
    |
    |-config.txt
    |- time_table.txt

In each file (except config.txt), datas will be organized in lines as follows :

LAMBDAS	BLACK	WHITE	Spectrum 1	Spectrum 2	...

Folder raw will contain raw datas, interp interpolated datas, and cosmetic smoothed datas.

config.txt contains an explicit and exhaustive list of all entered parameters.

time_table.txt contains a table of delays for each generator channel.

Updates

CALOA updates (or releases) can be split in two categories with diverse characteristics and consequences on CALOA. These characteristics are summed up in the hereinbelow table :

Characteristics	Stable	Pre-Release
Stability	High	Low
Bug report	Optionnal	Forced
Change rate	Low	High

To custom your update management, you will have to open the config file named "config.py" in a raw text editor (like Notepad). This file is located in the installation folder. To find it, just search for "CALOA" in the file explorer.

After opening this file, you will see many variable names of the form MAJ_WORD = (True or False), each of these MAJ_WORD corresponds to a degree of modification of the application. For each of them, a quick help is written above and a proper documentation is written to know how to do. But for short, to enable a functionality write True after the = to disable it, write False. Be carefull case is important.

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