dd-hebert / agilent-uvvis-to-csv

A simple script to convert Agilent 845x Chemstation UV-Vis files (.KD or .SD formats) to .csv format. Fast and easy!

uv2csv

A simple script for converting Agilent 845x Chemstation UV-vis binary files (.KD or .SD formats) to .csv format.

Do you have .KD or .SD UV-vis files but no access to the Agilent 845x UV-vis Chemstation software? Do you have large .KD files that contain thousands of spectra? This script will automatically convert your .KD or .SD files to .csv format (and it's significantly faster than the Agilent Chemstation software!). Exports thousands of spectra in seconds!

Currently supports .KD and .SD UV-vis binary file types.

Using This Script

To use this script, simply run it from the command line:

python uv2csv.py

Then provide a file path when prompted.

How It Works

This script works by searching a .KD or .SD file for a unique byte string which precedes the absorbance data (see disclaimer). The absorbance data that follows this byte string are encoded as little-endian double precision floats, which the script unpacks into a pandas DataFrame.

Export Location for .CSV Files

You can locate the exported .csv files in the same directory as the original .KD or .SD binary file.

• Files with Multiple Spectra: .csv files are exported into a folder within the same directory as the binary file.
• Files with a Single Spectrum: A single .csv file is exported to the same directory as the binary file.

Note: If the .SD file you are parsing contains sample names, the sample names will be included in the file names of the exported .csv files. Please be aware that sample names are not currently supported for .KD files.

Changing The Wavelength Range

By default, the script assumes your spectrometer captures data from 190 nm to 1100 nm. If the range of wavelengths your spectrometer records is different than this, you can set the wavelength range by adding a single keyword argument wavelength_range to the UVvisFile object constructor at the bottom of the script:

if __name__ == '__main__':
    PATH = os.path.normpath(input('Enter a file path or "q" to quit: '))
    UV_FILE = UVvisFile(PATH, export_csv=True, wavelength_range=(min, max))

Requirements

You must have the pandas python package installed to use this script.

Disclaimer

This script has only been tested on files from a small number of different versions of the Agilent UV-vis Chemstation software. Therefore, binary files from other versions of UV-vis Chemstation, different spectrometer setups, or custom methods may not work.

Known Supported Chemstation Versions:

• B.05.02 [16]
• A.08.03 [71]

If you encounter an bug or problem, please submit an issue so I can improve this script!

agilent-uvvis-to-csv's Issues

Sample Names

Hello again! This time I came not with a bug, but with a proposal. Is it possible to decode from SD files not only the absorption spectrum itself, but also the names of the samples? When reading SD files, I can find the approximate location of the sample names, but I have trouble decoding them. This would be quite useful, especially if you need to open some old files when no one remembers what specific position the required spectra were in

UnicodeDecodeError

Hi I talked to you a while ago about other of this errors, and it's happening again with a teacher's file that I'm converting.

So the error was UnicodeDecodeError: 'ascii' codec can't decode byte 0xd3 in position 1: ordinal not in range(128)

I will send the data that wasn't working with one that works (chlorphyll), sorry to bother again.
srry.zip

UnicodeDecodeError: 'ascii' codec can't decode byte 0xf0 in position 0: ordinal not in range(128)

Hi i'm not much of a programmer but i've been using this to plot some spectra, usually go well but for these specific samples this error has ocurred, what can i do to correct it?

Agilent Chemstation 8453

Hello! Looking for tips on how to open Agilent files i came across your script that allows convert SD files to CSV. However, when I try to use it on my existing files (Agilent 8453), I get an attribute error. I've only recently started learning python, so I didn't delve into your code, but would like to ask for help. An example of few of these files is attached.

SSP.zip