Add logging infrastructure with debug output for scaled processing plugins

[Copilot]

Adds library-style logging to zarrnii that can be easily controlled by calling scripts (e.g., Snakemake). Includes detailed debug output for scaled_processing plugins to help diagnose memory issues by exposing zarr chunking and dask graph details.

Changes

• New zarrnii/logging.py module

  • get_logger(name) - hierarchical loggers under zarrnii.* namespace
  • configure_logging(level, format_string, handler, stream) - one-liner setup for calling scripts
  • Uses NullHandler by default per Python library conventions

• Debug logging in apply_scaled_processing()

  • Zarr shapes, chunks, dtype at each step
  • Dask graph layers and task counts
  • Intermediate OME-Zarr paths
  • Lowres array memory footprint

• Debug logging in scaled processing plugins

  • GaussianBiasFieldCorrection, N4BiasFieldCorrection, SegmentationCleaner
  • Input/output shapes, processing parameters, array statistics

Usage

import logging
from zarrnii import configure_logging, ZarrNii

# Enable debug output
configure_logging(level=logging.DEBUG)

# Or write to file
configure_logging(level=logging.DEBUG, handler=logging.FileHandler("zarrnii.log"))

# Scaled processing will now emit detailed debug logs
result = znii.apply_scaled_processing(plugin, downsample_factor=4)

Example debug output:

2025-11-25 23:48:27 - zarrnii.core - INFO - Starting scaled processing with plugin: Gaussian Bias Field Correction (downsample_factor=4)
2025-11-25 23:48:27 - zarrnii.core - DEBUG - Input zarr - shape: (1, 256, 256, 256), chunks: (1, 64, 64, 64), dtype: float32
2025-11-25 23:48:27 - zarrnii.core - DEBUG - Upsampled dask graph layers: 3, total tasks: 125

Original prompt

Can yoh add logging to zarrnii, in such a way that it is easily controlled by calling scripts (like the snakemake script logging in spimquant). Also add some debug level output that can be enabled, specifically want this adddd for the scaled_processing plugins, giving info on the zarrs being used (chunking) and the dask graphs, tryibg to debug some memroy issues

---

💬 We'd love your input! Share your thoughts on Copilot coding agent in our 2 minute survey.