Changelog

Changelog

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.

Unreleased

0.2.2

Fixed

• Resolved a bug where the clear processing step unintentionally replaced stack.data with an invalid or uninitialised array, causing corrupted or excessively large Z-values in processed frames. The clear step now correctly clears only the current mask and returns the current working array (arr) without modifying image data.

• Incorrect mapping of centroid_x and centroid_y in feature flattening logic. Centroids returned by regionprops were interpreted as (row, col) but incorrectly assigned as (x, y).

• RuntimeWarning caused by invalid value casting during Z-scaling normalization in GIF export. Improved robustness of GIF frame generation when AFM data contains missing or extreme Z-values.

Changed

• Normalization step now uses np.nan_to_num and np.clip to ensure all values are within the valid range before casting.

• Updated centroid assignment:

  • centroid_x = centroid[1] (column → x)

  • centroid_y = centroid[0] (row → y)

Added

• Safe normalization logic for GIF export in create_gif_with_scale_and_timestamp to handle NaN, inf, and out-of-range values before casting to np.uint8.

• Pytest coverage for:

  • Centroid coordinate mapping

  • Autodetection of object key (tracks vs clusters)

  • Handling of out-of-range indices

  • Column presence

0.2.1

Changed

• Package renames to all lowercase playnano to follow PEP8 and prevent cross-platform issues with case-sensitivity.

• The import path is now playnano (lowercase). Update your code: import playnano instead of import playNano.

• Backward‑compatibility: import playNano still works in v0.2.1 via a shim and emits a DeprecationWarning. The playNano path will be removed in a future release.

• CLI unchanged: Keep using playnano on the command line.

• Docs: Versioned documentation with main, stable, and tags; API reference updated to playnano.*.

0.2.0

This release introduces video processing, stack editing, multi-version documentation, and major CLI enhancements.

Added

• Documentation

  • New Exporting Data page (docs/exporting.rst) covering OME-TIFF, NPZ, HDF5, and GIF export formats with CLI and Python examples.

  • New Processing Operations Reference page (docs/processing-operations-reference.rst) listing all built-in filters, masks, and stack/video operations with parameters.

  • Added version-switcher support for Sphinx with:

    • docs/_static/version-switcher.js and version-switcher.css.

    • Sidebar template docs/_templates/sidebar/versions.html.

  • New versions.json generation and “stable” alias logic in docs build workflow.

  • Support for multi-version documentation builds via sphinx-multiversion.

  • Added project version/commit metadata injection to Sphinx conf.py.

• Codebase

  • AFMImageStack now registers and resolves new processing groups:

    • video_processing and stack_edit modules added.

  • Added internal state backup mechanism (state_backups attribute) for preserving origonal metadata.

  • Moved the versioning module for funcitons from the processing subpakage to the utils subpackage.

• Docs Generation

  • Automatic inclusion of playNano.analysis.utils.loader, playNano.processing.video_processing, and playNano.processing.stack_edit in the API reference.

• GitHub

  • Issue templates added for bug reports and feature requests.

Changed

• Documentation

  • Documents and docstrings updated to correct typos address sphinx build warnings.

  • Instructions for installation from PyPi to the user docs.

  • Clearer instruction for the installation procedure to use notebooks added.

  • Major re-write of processing.rst:

    • Expanded explanation of pipeline structure, operation types, and provenance tracking.

    • Improved CLI/GUI examples, programmatic usage, and plugin registration guidance.

    • index.rst, introduction.rst, gui.rst, and quickstart.rst updated with links to new Exporting and Processing Operations Reference pages.

    • analysis.rst fixed Sphinx link formatting.

    • Improved generated module list formatting for analysis modules.

    • Updated Sphinx conf.py to:

      • Support multi-version builds, version detection, and sidebar switcher.

      • Move src path resolution to a relative form.

      • Reorganize theme and HTML sidebar configuration.

    • Added sphinx-multiversion to pyproject.toml under [project.optional-dependencies.docs].

• GitHub Actions

  • Overhauled docs.yaml workflow:

    • Builds and deploys versioned docs on main and release tags.

    • Adds PR preview artifact upload.

    • Generates versions.json and root redirect index.

    • Creates “stable” alias for latest release.

  • Renamed job to “Build and Deploy Docs”.

  • Notebooks

    • Added a root search function so hard coded paths to demo data from the tests folder can be accessed whereever jupyter is launched from.

Fixed

• Documentation

  • Corrected malformed Sphinx links and build warnings across multiple pages.

  • Improved auto-generated module list formatting and spacing.

0.1.0.post1 - 2025-10-14

Changed

• GitHub

  • Add workflows for pypi publishing

• Documentation

  • Add badges for tests, PyPi python versino and PyPi relases.

  • Added links to the documentation and user guide on github pages.

  • Added a PyPi installation guide to the README and user guide.

  • Some general rewriting and improvements

0.1.0 - 2025-09-17

Added

• First public release 🎉

• AFM data loading & playback

  • Load HS‑AFM videos from .h5-jpk and .asd files and folders of .spm and .jpk files.

  • Time‑aware frame navigation and consistent pixel/scale metadata.

• Processing pipeline with masks & full provenance

  • Sequential filters and masks (e.g., plane removal, row/median alignment, polynomial flatten, Gaussian filtering).

  • Each step is recorded with index, name, parameters, timestamps, and environment details under stack.provenance.

  • Processed snapshots and masks are stored with ordered keys like step_<n>_<name> for reliable inspection and re‑use.

• Reproducible export & re‑import (analysis‑ready)

  • Save the current stack state (with stages, masks, and provenance) to HDF5 (.h5) or NumPy bundles (.npz).

  • Re‑load bundles later to continue processing and run analyses with the full history intact.

  • Export to OME‑TIFF for interoperability and to GIF (with optional scale bars) for quick sharing and presentation.

• Interactive GUI (PySide6) for exploration

  • Real‑time playback, frame seeking, and snapshot previews.

  • Z‑range control (auto or manual) to maintain consistent height scaling across frames.

  • Annotations/overlays (i.e. timestamps, raw data label, scale bar) rendered on top of frames.

  • Built‑in dark theme stylesheet for high‑contrast analysis.

• Analysis framework

  • Build analysis pipelines from built-in and pluggable analysis modules.

  • Built-in analysis modules (e.g., LoG blob detection, DBSCAN/K‑Means/X‑Means clustering, particle tracking).

  • Produces labeled masks, per‑feature properties (area, min/max/mean, bbox, centroid), and summary statistics.

  • Analysis outputs are keyed and traced in provenance for reproducibility.

• Command Line Interface (CLI)

  • playnano entrypoint to run processing pipelines, export bundles (TIFF/NPZ/HDF5), and create GIFs from the shell.

• Notebooks

  • Jupyter notebooks included to demonstrate programmatic workflow.

  • Overview notebook covers the whole loading, processing, analysis and export workflow.

  • Processing notebook focuses on processing and export of loaded data.

• Documentation:

  • Created a Sphinx documentation site on GitHub Pages.

  • User Guide covering installation, quick start, GUI and CLI usage, processing, analysis and exports.

  • API Reference generated with sphinx-autoapi for all packages.

  • CLI reference with examples and typical workflows.

  • Furo theme and MyST Markdown configuration for a clean, consistent look.

Changed

• N/A (initial public release).

Fixed

• N/A (initial public release).