Metadata-Version: 2.1
Name: tomni
Version: 1.9.0
Summary: Tomni is a collection of image analysis functions usefull for CytoSmart solution.
Home-page: https://github.com/cytosmart-bv/tomni
Author: Tom Nijhof
License: UNKNOWN
Keywords: tomni
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Science/Research
Classifier: Natural Language :: English
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Description-Content-Type: text/markdown
License-File: LICENSE

Tomni
=====

Tomni is a python package that contains a collection of helper functions based on OpenCV and NumPy. It can be used for any python based computer vision or image analysis problem. The package simplifies the code and takes care of edge cages, everything from simplifying code like img_dim to compute optimization like labels2contours or illumination correction image processing. Tomni uses the image coordinates (same as OpenCV). 

Tomni is created by [CytoSMART](https://cytosmart.com).

The package was developed in-house to centralize the helper function for computer vision problems. In 2021, CytoSMART engineers turned it to open source, enabling researchers and educators to use it for free.

## Getting Tomni

``` cmd
pip install tomni
```

## License

Tomni is free for academic and educational use.

For commercial use please contact [CytoSMART](https://cytosmart.com/contact).

## The name

The name Tomni is a combination of creator (Tom) and other CytoSMART product he was working on, [the Omni](https://cytosmart.com/products/omni). Tomni name was proposed by Denissa Daroţi, a former CytoSMART intern, who won a bet with her mentor by getting a (well deserved) 9/10 for her internship. 



## Features

* Bounding box fitting (bbox fitting)
  * Center bounding box fit
  * Custom location box fit
* Illumination correction 
  * Brightfield
  * Fluorescence
* Json operation
  * Add circularity property
  * Scale object
  * Translate object
* Make a mask
  * Ellipse
  * Polygon
* Shape fitting
  * Rect around ellipse
* Transformers of data format
  * Contours to json
  * Ellipse to json
  * Json 2 contours
  * Json 2 label
  * Labels 2 contours
  * Labels 2 lists of points

## Credits
Sorted alphabetically

- Coenraad Stijne
- Denisa Daroţi
- Hristo Atanasov
- Jelle van Kerkvoorde
- Kirsten Koopman
- Manon van Erp
- Marina Tzenkova
- Tom de Vries
- Tom Nijhof

# History
1.9.0 (2021-10-01)
------------------
- add mask2bbox
- add contour2bbox
- add check_overlap_bbox

1.8.0 (2021-09-01)
------------------
- add mask2json
- add json2mask

1.7.4 (2021-07-02)
------------------
Upgrade/change requirements to work with python 3.9
Opencv needed fuzzy requirments
Remove scikit-image from requirements by replacing the function with numpy function

1.7.3 (2021-06-23)
------------------
speedup positions2contour by replacing for-loop with numpy slicing

1.7.2 (2021-04-21)
------------------
Migrate to github

1.7.1 (2020-12-23)
------------------
updated setup file simplification<0.6

1.7.0 (2020-12-03)
------------------
added new functions
- add_area
- summary_json 
- json2dict

1.6.4 (2020-11-26)
------------------
- add  missing requirements in setup file

1.6.3 (2020-11-25)
------------------
- bug fix. cropping now with deepcopy

1.6.2 (2020-11-10)
------------------
-add fluo_tophat background subtraction

1.6.1 (2020-11-04)
------------------
-add accuracy to json2vgg

1.6.0 (2020-11-03)
------------------
- add json2vgg

1.5.2
------------------
- add ellipse to vgg2json
1.5.1
------------------
- fix rotation, flipping, crop import

1.5.0
------------------
add json_operations
- add crop list of jsons
- add flipping json
- add rotation json

1.4.0
------------------
- add get center point contour
- add get center point json
- add vgg2json

1.3.0
------------------
Updating of relative illumination correction.
- add (optional) smoothing step
- add (optional) resize step
- add (optional) normalization 

1.2.0 (2020-07-02)
------------------
- Add translation of json functions

1.1.0 (2020-03-11)
------------------
Updating of illumination correction.
Splitting into two illumination correction:
- absolute difference
- relative difference

1.0.0 (2020-03-06)
------------------
(new function)
- add_circularity

1.0.0 (2020-02-28)
------------------
Restructuring of tomni:
- Migrated Visualization to cytoBoom
- Migrated validation to manVal
- Made sure every function followed:
    function_name
    - __init__.py 
    - main.py
    - test_function_name
- removed following function:
-- channel_selecting (was only used for old cell counter)
-- select_labels (complete replaceable by transformers.labels2listsOfPoints
- Added docstring to all functions
- Added typing to all functions
- Renamed everything to pep8

0.4.0 (2019-09-30)
------------------
Add transformer as category
- Add labels 2 list of points as function

0.3.3 (2019-09-17)
------------------
Draw_json (draw_json_mask_onto_image):
- rename it from draw_json_mask_onto_image to draw_json
- Make the Visualization of json shapes more dynamic.
- Callable directly from Visualization
- it return an image rather than manipulating it
- converts the color to the color type of input

0.2.1 (2019-07-24)
------------------
Remove f strings to prevent conflicts on python 3.5

0.2.0 (2019-07-09)
------------------
Visualization is now part of tomni.

STRUCTURE:
BGR: All colors are Gray, BGR or BGRA. This because tomni is mostly combined with openCV usage.

FUNCTION:
- Add color converter
- Add circle draw function that works with the input of the cell counter


0.1.8 (2019-02-21)
------------------
- imdim: Function what gives the dimensions of an image from a numpy.ndarray
- ellipse_mask: creates an ellipse at a given position, with given radius length but a fixed rotation

0.0.1 (2018-10-15)
------------------
- First release on PyPI.


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Initially written by Andras Varga (public domain) for OMNeT++ https://omnetpp.org/intro/license, 
adapted by CytoSMART TECHNOLOGIES BV. The adaptation is licensed under CC0 1.0 (Public Domain Dedication).

