Solutions Rename filenames by folder names

Importance of the Topic

Effective management of chromatographic data exports is critical in modern analytical laboratories. When Agilent ChemStation exports chromatograms in AIA (*.cdf) format, it generates a deep folder hierarchy with generic file names. Standardizing file names based on chromatogram identifiers and consolidating them into a single directory enables reliable automation, reduces manual errors, and streamlines downstream import into Clarity or other LIMS platforms.

Objectives and Overview

This application note presents a practical, Windows-based solution for renaming and organizing AIA-exported chromatogram files. The primary goals are to:

• Rename individual signal files (signal01.cdf, signal02.cdf) to include the parent folder (chromatogram) name.
• Consolidate all renamed files into a single output folder.
• Optionally remove now-empty source folders to maintain a clean directory structure.

The approach relies on a batch script (rename-aia.bat) that leverages the command-line version of Bulk Rename Utility (BRC).

Methodology and Instrumentation

The workflow uses a simple batch file in combination with BRC to perform four main tasks:

• Detect the operating system architecture (32-bit or 64-bit) to select the appropriate BRC executable.
• Traverse the exported AIA folder tree and rename each *.cdf file, prefixing the parent folder name and appending a sequential index.
• Move all renamed files into a single designated output folder.
• Remove any empty directories left behind in the source folder (optional steps can be commented out if undesired).

Users configure the script by editing two folder path variables (INFOLDER and OUTFOLDER) and specifying the location of the BRC executable files. The batch file can be downloaded along with demo data from DataApex.

Main Findings and Discussion

Testing with the provided demo dataset demonstrates that the script reliably transforms:

• chrom-A.AIA/signal01.cdf into chromA_01.cdf
• chrom-A.AIA/signal02.cdf into chromA_02.cdf
• chrom-B.AIA/signal01.cdf into chromB_01.cdf
• chrom-B.AIA/signal02.cdf into chromB_92.cdf

All files are relocated to the output folder, preserving a clear naming convention aligned with chromatogram identifiers. Optional cleanup steps successfully remove empty subfolders, ensuring a tidy file system.

Benefits and Practical Applications

• Reduced manual intervention and risk of naming errors when importing large batches of chromatograms.
• Consistent, descriptive file names improve traceability and audit readiness in regulated environments.
• Script-based solution can be integrated into existing data pipelines or scheduled tasks for automated processing.

Future Trends and Opportunities

• Tight integration of renaming utilities within chromatography data systems to eliminate post-export processing.
• Cross-platform scripting (PowerShell, Python) for greater flexibility and metadata-driven naming schemes.
• Cloud-based data management workflows that automatically ingest and tag chromatogram files upon export.

Conclusion

The rename-aia.bat script coupled with Bulk Rename Utility offers a straightforward, configurable approach to standardizing AIA exports from ChemStation. By automating file renaming, consolidation, and folder cleanup, laboratories can accelerate Clarity imports, minimize errors, and maintain a clean data structure.

References

• DataApex. rename-aia.bat batch script and demo data archive (cdfstore.zip). Code/Version: D145/EN03-20240314.