Python Project Development for Spectroscopy (part 2)- Technote

Posted on: May 27th, 2020

This post is part of a series on “Creating a Python Spectroscopy Project”

Developing a customized Python project application to integrate with Avantes Spectrometers is easier than you might expect. Join Justin Spott, regional sales engineer, with a new series of “tech notes” that explores this topic in greater detail.

Part 1: Installing the AvaSpec library

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Python is becoming very popular with scientists (the author included) because of its readability, ease of use, and availability. In this tutorial, I will walk you through connecting to and taking data with your Avantes spectrometer. This tutorial assumes you have already installed the AvaSpec library and Python. I will be using Anaconda and its IDE Spyder.

Python Project File/Folder Structure

We will start by creating a project directory. This folder needs to contain the avaspec.dll or avaspecx64.dll library. We will also need a python wrapper.  Both the library and wrapper can be found in the AvaSpec-DLL install directory. The default install directory is  C:\AvaSpec-DLL_<version_nr> for the 32-bit version and  C:\AvaSpecX64-DLL_<version_nr> for the 64-bit version of the Library.

mkdir PySpec
cd PySpec
copy C:\AvaSpecX64-DLL_9.9.3.0\examples\PyQt5\avaspecx64.dll
copy C:\AvaSpecX64-DLL_9.9.3.0\examples\PyQt5\avaspec.py

Connecting to the Spectrometer

Connecting to the spectrometer is done in three steps: initializing the library, asking for information on the spectrometers available to the library, and retrieving the spectrometer-specific handle from the library.

First, AVS_Init initializes the library with the a_Port parameter by looking for USB devices (0) Ethernet devices (256), or both (-1). AVS_GetNrOfDevices can be called at any time to refresh the device list in the library.

>>> AVS_Init(0) 
1
>>> ret = AVS_GetNrOfDevices() 
>>> ret
1

AvsIdentityType is a simple structure that contains 3 attributes: the serial number, status, and user friendly name of the spectrometer.  We use AvsIdentityType and the number of devices and to build the buffer a_pList required by AVS_GetList.  AVS_GetList also requires the size of the buffer a_pList – 75 bytes times the number of devices. GetList returns a tuple containing the size required for the deviceList buffer (position 0), and an  AvsIdentityType for every spectrometer.

>>> req = 75*ret
>>> a_pList = AvsIdentityType * ret 
>>> AVS_GetList(req,req,a_pList)
(75, <avaspec.AvsIdentityType at 0x1b25d99cf48>)
>>> ret[1].SerialNumber, ret[1].Status
(b'1709195M1', b'\x01')

Passing an AvsIdentityType to AVS_Activate, gives back an AvsHandle to be used in subsequent function calls.

>>> handle = AVS_Activate(ret[1])

Configuring the Spectrometer

With the handle, we can now prepare the spectrometer to collect data. We call AVS_GetParameter to retrieve configuration information about the spectrometer in the form of a DeviceConfigType. From here we retrieve the number of pixels, which we’ll use to get the wavelength data and later plot the spectrum. Next, use AVS_GetLambda to retrieve the wavelength calibration for each pixel – we’ll iterate through and store the values for later.

>>> config = DeviceConfigType
>>> ret = AVS_GetParameter(handle, 63484, 63484, config)
>>> pixels = ret[1].m_Detector_m_NrPixels
>>> wavelengths = []
>>> ret = AVS_GetLambda(handle,wavelengths)
>>> for pixel in range(pixels):
>>>     wavelengths.append(ret[1][pixel])

Create a MeasConfigType to hold the acquisition data. Here is a brief overview of these settings; always contact your Avantes salesperson for any further questions about these:

• m_StartPixel and m_StopPixellet you retrieve a smaller portion of the spectrum. This can increase framerate; but generally you’ll want to collect the entire spectrum.
• m_IntegrationTimeis the acquisition time for each spectrum, in milliseconds.
• m_IntegrationDelay allows you to set a delay before the sensor starts collecting data. This is useful for filtering out noise from an experiment like in the LIBS experiment described here.
• m_NrAveragesallows you to perform on-spectrometer averaging, increasing sensitvity.
• m_CorDynDark_m_Enable and m_CorDynDark_m_ForgetPercentage are part of the DarkCorrectionType, settings for the Correct for Dynamic Dark [link] setting.
• m_Smooting_m_SmoothPix and m_Smoothing_m_SmoothModel enable smoothing settings.
• m_SaturationDetection controls the saturation detection feature.
• The next three settings are part of the TriggerType. m_Trigger_m_Mode, m_Trigger_m_Source, and m_Trigger_m_SourceType control the triggering.
• The final five settings are part of the ControlType. These settings change how the spectrometer interacts with light sources.

>>> measconfig = MeasConfigType 
>>> measconfig.m_StartPixel = 0 
>>> measconfig.m_StopPixel = pixels - 1 
>>> measconfig.m_IntegrationTime = 50 
>>> measconfig.m_IntegrationDelay = 0 
>>> measconfig.m_NrAverages = 1 
>>> measconfig.m_CorDynDark_m_Enable = 0 
>>> measconfig.m_CorDynDark_m_ForgetPercentage = 100 
>>> measconfig.m_Smoothing_m_SmoothPix = 0 
>>> measconfig.m_Smoothing_m_SmoothModel = 0 
>>> measconfig.m_SaturationDetection = 0 
>>> measconfig.m_Trigger_m_Mode = 0 
>>> measconfig.m_Trigger_m_Source = 0 
>>> measconfig.m_Trigger_m_SourceType = 0 
>>> measconfig.m_Control_m_StrobeControl = 0 
>>> measconfig.m_Control_m_LaserDelay = 0 
>>> measconfig.m_Control_m_LaserWidth = 0 
>>> measconfig.m_Control_m_LaserWaveLength = 0.0 
>>> measconfig.m_Control_m_StoreToRam = 0

Finally, we can send the configuration to the spectrometer!

>>> AVS_PrepareMeasure(handle, measconfig)
0

Collecting and displaying spectral data

Now we can have the spectrometer begin taking data.

scans = 1
AVS_Measure(handle, 0, scans)

A 50 ms exposure time and single scan will complete quickly. Longer experiments may require us to wait for the collection to finish – so we’ll add a small check to see if the spectral data is ready.

import time

dataready = False
while not dataready:
    dataready = AVS_PollScan(handle)
    time.sleep(measconfig.m_IntegrationTime/1000)

And now its time to grab the data!

timestamp = 0
spectraldata = []
ret = AVS_GetScopeData(handle, timestamp, spectraldata)
timestamp = ret[0]
for i,pix in enumerate(wavelengths):
    spectraldata.append(ret[1][i])

Finally, we can plot with matplotlib.

>>> import matplotlib.pyplot as plt
>>> plt.plot(wavelengths,spectraldata)

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