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N-dimensional NumPy array tiling and merging with overlapping, padding and tapering

Project description

tiler_baby_logo tiler

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⚠️ Please note: work in progress, things will change and/or break! ⚠️


This python package provides consistent and user-friendly functions for tiling/patching and subsequent merging of NumPy arrays.

Such tiling is often required for various heavy image-processing tasks such as semantic segmentation in deep learning, especially in domains where images do not fit into GPU memory (e.g., hyperspectral satellite images, whole slide images, videos, tomography data).

Please see Quick start section.
If you want to use tiler interactively, I highly recommend napari and napari-tiler plugin.

Features

  • N-dimensional
  • Optional in-place tiling
  • Optional channel dimension (dimension that is not tiled)
  • Optional tile batching
  • Tile overlapping
  • Access individual tiles with an iterator or a getter
  • Tile merging, with optional window functions/tapering

Quick start

You can find more examples in examples.
For more Tiler and Merger functionality, please check documentation.

import numpy as np
from tiler import Tiler, Merger

image = np.random.random((3, 1920, 1080))

# Setup tiling parameters
tiler = Tiler(data_shape=image.shape,
              tile_shape=(3, 250, 250),
              channel_dimension=0)

## Access tiles:
# 1. with an iterator
for tile_id, tile in tiler.iterate(image):
   print(f'Tile {tile_id} out of {len(tiler)} tiles.')
# 1b. the iterator can also be accessed through __call__
for tile_id, tile in tiler(image):
   print(f'Tile {tile_id} out of {len(tiler)} tiles.')
# 2. individually
tile_3 = tiler.get_tile(image, 3)
# 3. in batches
tiles_in_batches = [batch for _, batch in tiler(image, batch_size=10)]

# Setup merging parameters
merger = Merger(tiler)

## Merge tiles:
# 1. one by one
for tile_id, tile in tiler(image):
   merger.add(tile_id, some_processing_fn(tile))
# 2. in batches
merger.reset()
for batch_id, batch in tiler(image, batch_size=10):
   merger.add_batch(batch_id, 10, batch)

# Final merging: applies tapering and optional unpadding
final_image = merger.merge(unpad=True)  # (3, 1920, 1080)

Installation

The latest release is available through pip:

pip install tiler

Alternatively, you can clone the repository and install it manually:

git clone git@github.com:the-lay/tiler.git
cd tiler
pip install

If you are planning to contribute, please take a look at the contribution instructions.

Motivation & other packages

I work on semantic segmentation of patched 3D data and I often found myself reusing tiling functions that I wrote for the previous projects. No existing libraries listed below fit my use case, so that's why I wrote this library.

However, other libraries/examples might fit you better:

Moreover, some related approaches have been described in the literature:

Frequently asked questions

This section is a work in progress.

How do I create tiles with less dimensions than the data array?

Tiler expects tile_shape to have less than or the same number of elements as data_shape. If tile_shape has less elements than data_shape, tile_shape will be prepended with ones to match the size of data_shape.
For example, if you want to get 2d tiles out from 3d array you can initialize Tiler like this: Tiler(data_shape=(128,128,128), tile_shape=(128, 128)) and it will be equivalent to Tiler(data_shape=(128,128,128), tile_shape=(1, 128, 128)).

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