pyAthina 0.1.1

A photoelectron microspectroscopy/spectromicroscopy data analysis package

pyAthina

A lightweight PyQt6 + pyqtgraph skeleton for PEEM-style image-stack workflows.

Install

pip install -r requirements.txt

Run

Any of these should work from the extracted project folder:

python -m pyAthina.main

python -m pyAthina

python run_pyAthina.py

If you cd into the pyAthina/ subfolder itself, you can also run:

python main.py

Alignment modes

• Phase correlation: translation-only drift correction with sub-pixel shift estimation.
• Image registration: ECC-based registration on the ROI, with the estimated transform applied to the full image.
  • default: sub-pixel translation
  • optional: rotation
  • optional: scale
  • optional: skew

When scale or skew is enabled, the registration model becomes affine.

Z profile improvements

• live ROI-driven z-profile updates while moving or resizing the ROI
• standalone popup plot window
• plot styling controls (grid, markers, line width)
• export z-profile as TXT (x, y columns)
• export plot as PNG

Line profile

• Click Line profile using line ROI.
• Then press and drag on the image to draw the line.
• The popup profile updates when you move the line endpoints or change stack layer with the slider.
• The profile width is controlled by Profile width (px) in the Profiles dock.

Xarray-backed import and axis metadata

The stack import layer creates an xarray.DataArray with dims (z, y, x).

No sample data or synthetic coordinate ranges are enabled by default. When file metadata is missing, pyAthina falls back to:

• x: pixel index (0 .. nx-1)
• y: pixel index (0 .. ny-1)
• z: layer index (0 .. nz-1)

HDF5 metadata parsing helpers are included, but the final mapping of file metadata into domain-specific xarray attrs is intentionally left as a placeholder for user customization. Commented debug snippets remain in the codebase so synthetic data can be re-enabled temporarily when needed.

Multi-core alignment and headless cluster use

The alignment backend can now use multiple worker processes.

• In the GUI, set Worker processes to 1 for the original serial path, or a larger value to use a process pool.
• For headless cluster jobs, use:

python -m pyAthina.batch_align input.h5 aligned_stack.tif \
  --dataset-path /root/entry/instrument/tvips/data \
  --workers 8 \
  --reference-index 0 \
  --method image_registration

phase_correlation is also available with --method phase_correlation.