Metadata-Version: 2.1
Name: multifocal-stitching
Version: 0.2.1
Summary: Algorithms and tools for stitching microscopy images taken at different focal lengths
Author-email: Chenyang Yuan <yuanchenyang@gmail.com>
Maintainer-email: Chenyang Yuan <yuanchenyang@gmail.com>
License: Copyright 2023 Chenyang Yuan
        
        Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
        
        The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
        
        THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
        
Project-URL: Homepage, https://github.com/yuanchenyang/multifocal-stitching
Project-URL: Bug Tracker, https://github.com/yuanchenyang/multifocal-stitching/issues
Project-URL: Documentation, https://github.com/yuanchenyang/multifocal-stitching
Project-URL: Source, https://github.com/yuanchenyang/multifocal-stitching
Classifier: Development Status :: 3 - Alpha
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 3
Classifier: Operating System :: OS Independent
Requires-Python: >=3.7
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: numpy
Requires-Dist: scipy
Requires-Dist: scikit-learn
Requires-Dist: opencv-python
Requires-Dist: Pillow
Provides-Extra: dev
Requires-Dist: build ; extra == 'dev'
Requires-Dist: twine ; extra == 'dev'
Provides-Extra: test
Requires-Dist: pytest ; extra == 'test'
Requires-Dist: pytest-cov ; extra == 'test'
Provides-Extra: webapp
Requires-Dist: gradio ; extra == 'webapp'
Requires-Dist: matplotlib ; extra == 'webapp'

Multifocal Image Stitching
---------------
| **Documentation** | **Build Status** |
|:-----------------:|:----------------:|
| [![][docs-latest-img]][docs-latest-url] | [![Build Status][build-img]][build-url] |

This package aims to:
- Accurately compute translation parameters between two images taken with a
  translation and focus change
- Be tolerant of high levels of noise and blurriness caused by the focus change

This package does not:
- Account for other non-translational camera models
- Calculate subpixel-level stitching coordinates
- Perform focus stacking or blending of images in any manner

### Examples

Matching using low-frequency features:

<img src="assets/image1.png" width="90%"/>

Matching using high-frequency features:

<img src="assets/image2.png" width="90%"/>

### Installation

To install from [pypi](https://pypi.org/project/multifocal-stitching/):

```
pip install multifocal-stitching
```

### Usage
Ensure the images to be stitched are sequentially named in `<dir>`, then run:

```
python -m multifocal_stitching <dir>
```

Most images can be stitched successfully with the default settings. To fine-tune
settings with the CLI:

```
python -m multifocal_stitching -h
usage: __main__.py [-h] [-v] [--ext EXT] [--imgs IMGS [IMGS ...]] [--no_merge] [--workers WORKERS]
                   [--min_overlap MIN_OVERLAP] [--early_term_thresh EARLY_TERM_THRESH]
                   [--use_wins USE_WINS [USE_WINS ...]] [--peak_cutoff_std PEAK_CUTOFF_STD]
                   [--peaks_dist_threshold PEAKS_DIST_THRESHOLD]
                   [--filter_radii FILTER_RADII [FILTER_RADII ...]]
                   [--stitching_result STITCHING_RESULT] [--result_dir RESULT_DIR]
                   [--resize_factor RESIZE_FACTOR] [--save_gif]
                   dir

positional arguments:
  dir                   Base directory

options:
  -h, --help            show this help message and exit
  -v, --verbose         Increase output verbosity (default: False)
  --ext EXT             Filename extension of images (default: .jpg)
  --imgs IMGS [IMGS ...]
                        Stitch only provided images in provided order, otherwise will run in batch
                        mode over all images in directory (default: None)
  --no_merge            Disable generating merged images (default: False)
  --workers WORKERS     Number of CPU threads to use in FFT (default: 2)
  --min_overlap MIN_OVERLAP
                        Set lower limit for overlapping region as a fraction of total image area
                        (default: 0.125)
  --early_term_thresh EARLY_TERM_THRESH
                        Stop searching when correlation is above this value (default: 0.7)
  --use_wins USE_WINS [USE_WINS ...]
                        Whether to try using Hanning window (default: (0,))
  --peak_cutoff_std PEAK_CUTOFF_STD
                        Number of standard deviations below max value to use for peak finding
                        (default: 1)
  --peaks_dist_threshold PEAKS_DIST_THRESHOLD
                        Distance to consider as part of same cluster when finding peak centroid
                        (default: 25)
  --filter_radii FILTER_RADII [FILTER_RADII ...]
                        Low-pass filter radii to try, smaller matches coarser/out-of-focus features
                        (default: (100, 50, 20))
  --stitching_result STITCHING_RESULT
                        Stitching result csv file (default: stitching_result.csv)
  --result_dir RESULT_DIR
                        Directory to save merged files (default: merged)
  --resize_factor RESIZE_FACTOR
                        Whether to resize the images saved by a factor (default: 1)
  --save_gif            Whether to save a gif alternating between the merged files (default: False)
```

[docs-latest-img]: https://img.shields.io/badge/docs-latest-blue.svg
[docs-latest-url]: https://github.com/yuanchenyang/multifocal-stitching
[build-img]: https://github.com/yuanchenyang/multifocal-stitching/workflows/CI/badge.svg?branch=master
[build-url]: https://github.com/yuanchenyang/multifocal-stitching/actions?query=workflow%3ACI
