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add auto-tiling and fix weighting after merging #7

Merged
merged 23 commits into from
Dec 14, 2021
Merged

add auto-tiling and fix weighting after merging #7

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5351226
add auto-tiling and fix weighting after merging
renerichter Sep 27, 2021
fdc38c8
add minimal overlap
renerichter Sep 29, 2021
6db742e
Merge remote-tracking branch 'origin/master' into renerichter-rl
the-lay Nov 8, 2021
c10c04c
Code linting
the-lay Nov 9, 2021
a14beea
Added ndarray types; Throw an exception in case of non-matching data.…
the-lay Nov 18, 2021
ab58cd3
Removing flattop window since it has negative values
the-lay Nov 18, 2021
46e948b
Code linting
the-lay Nov 19, 2021
a6e56e4
Added dtype keyword to Merger that specifies dtype of data buffer
the-lay Dec 10, 2021
4474666
Added apply_padding method; overlap now can be given as a numpy array
the-lay Dec 10, 2021
3640e2d
Small documentation fixes
the-lay Dec 10, 2021
ae79a80
Saving Merger data_visits is now optional
the-lay Dec 10, 2021
ebac20a
Fixed data visits check
the-lay Dec 10, 2021
51cc98c
Added an uncovered edge case test
the-lay Dec 11, 2021
5eee24b
Added test for Merger with disabled save_visits
the-lay Dec 11, 2021
aa86420
Refactored normalization by weights in merging
the-lay Dec 11, 2021
69ab5c9
Fixed explicit padding for odd data shapes
the-lay Dec 11, 2021
d0a559e
Hiding division by zero warning when normalizing by weight
the-lay Dec 11, 2021
f0b1f9b
Code linting
the-lay Dec 11, 2021
bd1cd9e
Updated documentation
the-lay Dec 11, 2021
f032b09
Fixing trying to submit coveralls on pull requests
the-lay Dec 11, 2021
054b5d7
Teaser image generated script now actually tiles and merges the image :)
the-lay Dec 11, 2021
a02c0c6
Merger buffer dtypes are now hardcoded, optional casting to specified…
the-lay Dec 11, 2021
c230be4
Refactored extra padding system and updated examples
the-lay Dec 12, 2021
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Small documentation fixes
  • Loading branch information
@the-lay
the-lay committed Dec 10, 2021
commit 3640e2dfc5e395f140f1b604f63932da93983ba5
7 changes: 5 additions & 2 deletions .github/CONTRIBUTING.md
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@@ -1,8 +1,10 @@
## Bug reports
Please be as specific as you can, ideally with code to recreate the issue.
Please include:
1. Which version you are using (`python -c "import tiler; print(tiler.__version__)"`)
2. A minimal code example to recreate the issue


# Code contribution workflow
## Code contribution
First off, thanks for taking the time!
Please feel free to contact me with questions.

Expand Down Expand Up @@ -30,3 +32,4 @@ cd misc
5. Once you want to share what you've changed, please commit, push make a pull request to the main repo.

6. Github will run lint and tests, but please don't rely on that and test before pull request :)

11 changes: 6 additions & 5 deletions README.md
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Expand Up @@ -15,7 +15,8 @@ _________________
⚠️ **Please note: work in progress, things will change and/or break!** ⚠️
_________________

This python package provides functions for tiling/patching and subsequent merging of NumPy arrays.
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
Expand All @@ -24,12 +25,12 @@ such as semantic segmentation in deep learning, especially in domains where imag

Features
-------------
- N-dimensional *(note: currently tile shape must have the same number of dimensions as the array)*
- N-dimensional
- Optional in-place tiling
- Optional channel dimension, dimension that is not tiled
- Optional batching
- Optional channel dimension (dimension that is not tiled)
- Optional tile batching
- Tile overlapping
- Access individual tiles with iterator or a getter
- Access individual tiles with an iterator or a getter
- Tile merging, with optional window functions/tapering


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