Speedup normalize

[ternaus]

Summary by Sourcery

Simplify the image normalization module by removing batch-based normalization, restricting LUT-based optimization to standard 3D images, and updating the package version.

Enhancements:

• Restrict uint8 LUT-based normalization to 3D images for improved performance.

Tests:

• Remove tests for the deprecated batch normalization function, retaining only per-image normalization tests.

Chores:

• Remove the normalize_per_image_batch function and its associated imports.
• Bump the package version to 0.0.30.

[sourcery-ai]

Reviewer's Guide

This PR optimizes per-image normalization by narrowing the LUT path to 3-channel uint8 images, removes the standalone batch normalization function and its tests to simplify the API, and increments the package version.

Class diagram for normalization function changes

classDiagram
    class functions {
        +normalize_per_image(img: np.ndarray, normalization: NormalizationType) np.ndarray
        -normalize_per_image_batch(images: np.ndarray, normalization: NormalizationType, spatial_axes: tuple[int, ...]) np.ndarray
        +to_float_numpy(img: np.ndarray, max_value: float | None = None) np.ndarray
    }
    functions : -normalize_per_image_batch removed
    functions : +normalize_per_image updated
    functions : +to_float_numpy unchanged

Loading

File-Level Changes

Change	Details	Files
Restrict LUT-based normalization to 3D images	Added img.ndim == 3 check to the uint8 LUT-based branch in normalize_per_image	albucore/functions.py
Remove batch normalization utility	Deleted normalize_per_image_batch function and its docstring Removed its import and all related tests	albucore/functions.py tests/test_normalize_per_image.py
Bump package version	Updated version from 0.0.29 to 0.0.30	pyproject.toml

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[Copilot]

Pull Request Overview

This PR aims to speed up image normalization by refining the normalization path for single images and deprecating the batch normalization API. Key changes include:

• Removal of the batch normalization test and its implementation.
• Update of the normalization condition in functions.py to restrict LUT-based normalization to 3D uint8 images.
• Version bump in pyproject.toml from 0.0.29 to 0.0.30.

Reviewed Changes

Copilot reviewed 3 out of 3 changed files in this pull request and generated no comments.

File	Description
tests/test_normalize_per_image.py	Removed tests for the deprecated batch normalization method.
pyproject.toml	Updated version to reflect the new release.
albucore/functions.py	Updated LUT normalization condition and removed batch normalization.

Comments suppressed due to low confidence (2)

tests/test_normalize_per_image.py:138

• The batch normalization test and its corresponding functionality have been removed. Please update the public API documentation to reflect this change if the removal was intentional.

def test_normalize_per_image_constant(shape, normalization, dtype):

albucore/functions.py:712

• [nitpick] The updated condition limits LUT normalization to 3D images; please update the function's docstring to clarify that non-3D images will be handled by the OpenCV implementation.

    if img.dtype == np.uint8 and normalization != "image_per_channel" and img.ndim == 3:

[sourcery-ai]

Hey @ternaus - I've reviewed your changes and they look great!

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[codecov-commenter]

Codecov Report

All modified and coverable lines are covered by tests ✅

Please upload report for BASE (main@ccd12b9). Learn more about missing BASE report.

Additional details and impacted files

@@           Coverage Diff           @@
##             main      #60   +/-   ##
=======================================
  Coverage        ?   93.97%           
=======================================
  Files           ?       17           
  Lines           ?     1793           
  Branches        ?        0           
=======================================
  Hits            ?     1685           
  Misses          ?      108           
  Partials        ?        0           

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[cursor]

Bug: Grayscale Image Normalization Performance Issue

The img.ndim == 3 condition added in the normalize_per_image function (line 712) unnecessarily restricts the fast LUT optimization path. This forces 2D uint8 grayscale images (shape (H, W)) to use the slower OpenCV normalization method instead of the faster normalize_per_image_lut function, causing a performance regression. The normalize_per_image_lut function is capable of handling 2D inputs.

albucore/functions.py#L711-L712

albucore/albucore/functions.py

Lines 711 to 712 in 0228681

	"""
	if img.dtype == np.uint8 and normalization != "image_per_channel" and img.ndim == 3:

Fix in Cursor

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