CD Spectra Batch Import and Visualization Script

This Python script automates the import, pruning, and visualization of multiple circular dichroism (CD) spectrum .txt files. It is designed for researchers who need to extract the data section from many files, combine them into a single Excel sheet (wide format), and visualize all spectra together.

Features

• Batch Import: Reads all .txt files in a specified folder.
• Header Skipping: Only imports the data section after the XYDATA marker in each file.
• Wide Format Output: Combines all spectra into a single Excel file, with each file's CD_mdeg values as a separate column aligned by wavelength.
• Automated Plotting: Plots all spectra together, with each curve labeled by filename.
• Customizable: Axis limits and plot appearance can be easily adjusted in the script.

How to Use

1. Install dependencies:

   pip install pandas matplotlib openpyxl
   

2. Edit the script:

   • Set the folder variable near the top of the script to the path containing your CD .txt files.

3. Run the script:

   python cd_spectra_wide.py
   

4. Results:

   • cd_spectra_wide.xlsx will appear in your data folder, containing all spectra in wide format.
   • A plot window will display all spectra for visual comparison.

File Format Assumptions

• Each .txt file contains metadata, followed by a line with XYDATA, then tab-delimited data columns:

  (metadata lines)
  XYDATA
  260.0   4.5   0.1   0.02
  261.0   4.3   0.1   0.02
  ...
  

• Columns are assumed to be: Wavelength, CD_mdeg, HT_V, Absorbance.

Customization

• To adjust axis ranges, uncomment and edit the plt.xlim() and plt.ylim() lines in the script.
• To further process or normalize data, modify the pandas DataFrame operations as needed.

How This Script Evolved

This script was developed in response to a real-world need to automate the batch import and analysis of CD spectrum data, as discussed in detail here . It is designed for robust, reproducible scientific data processing and visualization.

License

MIT License

Contributions

Pull requests and suggestions are welcome!

Acknowledgment

If you find this script useful in your research or work, a citation or acknowledgment to this GitHub repository (vinodksubramani/cd-spectrum-utils) would be appreciated, but is not required.

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Contact:
For questions or improvements, please open an issue or contact the maintainer.