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.

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

pip install tomni

License

Tomni is free for academic and educational use.

For commercial use please contact CytoSMART.

The name

The name Tomni is a combination of creator (Tom) and other CytoSMART product he was working on, the 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
• Image helpers
  • Get image dimensions
  • Convert color of an image
• Illumination correction
  • Brightfield
  • Fluorescence
• Contour operations
  • Get center
  • Approximate circle by area
  • Get roundness
  • Get circularity
• CytoSMART data format
  • Tba
• Json operation
  • Add circularity property
  • Scale object
  • Translate object
• Make a mask
  • Ellipse
  • Polygon
• Polygon downsampling
  • iterative downsampling
• Shape fitting
  • Rect around ellipse
• Transformers of data format
  • Contours to json
  • Ellipse to json
  • Json 2 contours
  • Json 2 label
  • Json 2 bbox
  • Labels 2 contours
  • Labels 2 lists of points
  • Binary 2 contours

Examples

Diameter vs radius

Most geometric operation use functions from OpenCV

Some of these function return diameter and some radius of the circle. This is not consistent.

For example, the function cv2.minEnclosingCircle returns the center and radius of the circle. The function cv2.fitEllipse returns the center and the major and minor axes of the ellipse.

Min enclosing circle example

import cv2
import math
import numpy as np

points = np.array([[0, 0], [100, 0], [100, 100], [0, 100], [0, 0]], dtype=np.float32)

center, radius = cv2.minEnclosingCircle(points)
diameter = math.sqrt(50**2 + 50**2) 

print("Center:", center)
print("Major and Minor Axes:", radius)
print("Diameter calculated with Pythagoras formula", diameter)

this results in the following output:

Center: (50.0, 50.0)
Major and Minor Axes: 70.71077728271484
Diameter calculated with Pythagoras formula 70.71067811865476

Fit ellipse example

import cv2
import math
import numpy as np

# Generate some example points
points = np.array([[0, 0], [100, 0], [100, 100], [0, 100], [0, 0]], dtype=np.float32)

# Fit an ellipse to the points
ellipse = cv2.fitEllipse(points)

# Extract ellipse parameters
center, axes, angle = ellipse

diameter = math.sqrt(50**2 + 50**2) * 2

print("Center:", center)
print("Major and Minor Axes:", axes)
print("Diameter calculated with Pythagoras formula", diameter)

this results in the following output:

Center: (50.0, 49.95212173461914)
Major and Minor Axes: (141.43260192871094, 141.5462188720703)
Diameter: 141.4213562373095

Example is related to the following functions in the package

Credits

Sorted alphabetically

• Bram van der Velden
• Coenraad Stijne
• Denisa Daroţi
• Hristo Atanasov
• Jan-Niklas Schneider
• Jelle van Kerkvoorde
• Kirsten Koopman
• Lisa Koolen
• Manon van Erp
• Marina Tzenkova
• Tom de Vries
• Tom Nijhof

History

2.2.0 (2023-11-10)

• function add_area subtracts the inner area when inner points are present.
• function flipping now flips the inner contours as well.
• function rotation now rotates inner contours.
• function scale_json now scales inner contours.

2.1.0 (2023-10-04)

• translation_json function can now also translate the inner points

2.0.0-b3 (2023-09-08)

• Added check for rectangled contours.
  • Adds extra point if rectangle.
  • This allows us to initialize masks (of wells) that only consist of 4 points if required in the future.
• Added unittests for empty and full masks from binary_mask and from_labeled_mask
• Changed variable name in ellipse class from r1/r2 to diameter_1/diameter_2 etc for naming clarity.
• BUGFIX: Multiplied minor axis and major axis by 2 in ellipse class, which was currently calculated as radii instead of diameters.
• BUGFIX: Fixed average diameter in ellipse class, which was calculated with radii instead of diameters.
• BUGFIX: removed assert, which took over half the time of the entire from_binary_mask.
• BUGFIX: Fixed unittest labels2listsOfPoints

2.0.0-b2 (2023-08-04)

• Moved feature_multiplier and metric_unit to to_dict() from from_dict().
• Added inner contours options
• added binary2contours
• change parameters for from_binary_mask
• made contours2polygon

2.0.0-b1 (2023-07-06)

• AnnotationManager function from_dict is called with an optional list of features
• Changed Polygon and Ellipse classes to include the list of features initialized by AnnotationManager
• to_dict function now only returns features in the dictionary that were asked for in the feature list
• Added feature_multiplier and metric_unit as inputs to apply to the features' name and value outputs.
• Added all features to ellipse and polygon.
• Features are now in camelCasing when output to_dict

2.0.0-b0 (2022-11-29)

• CDF-Main: Implement filter to allow filtering of annotations by feature values (aka gating).
• CDF-Main: Implement from_contours.
• CDF-Main: Implement to_contours.
• CDF-Main: Implement from_dict.
• CDF-Main: Implement to_dict. Includes rounding.
• CDF-Main: Implement __len__.
• CDF-Main: Implement __iter__ and __next__.
• Add polygon annotation class.
• CDF-polygon: Implement __eq__
• CDF-polygon: Remove useless point
• Add ellipse annotation class.
• CDF-ellipse: Implement __eq__
• CDF-ellipse: Set all rotations between 0 and 90, flip radii if needed
• Renamed CytoSmartDataFormat to AnnotationManager
• Add is_in_mask for Ellipse and Polygon
• Add min_overlap-parameter in to_dict to apply masks to filter annotations
• Add to_binary_mask and to_labeled_mask for AnnotationManager, Ellipse and Polygon
• Add init-function from_binary_mask and from_labeled_mask to AnnotationManager
• Bugfix: Fixed a bug where simplify_line returns empty list when passing two points.
• Add option to to compress polygons in to_dict(). 1.17.0 (2023-07-26)
• Add binary2contours

1.16.1 (2023-05-10)

• make it possible to set n_iter to 0.

1.16.0 (2023-05-08)

• Add iterative_downsampling for downsampling polygon points in 'naive' way

1.15.0 (2022-12-05)

• Add json2bbox for ellipse with angle of rotation

1.14.0 (2022-11-11)

• Add convert to color

1.13.0 (2022-10-24)

• Add json2bbox for polygon and ellipse

1.12.1 (2022-10-06)

• Update Json-circularity with circularity calculation from contour ops.

1.12.0 (2022-04-15)

• BUGFIX: Import approximate_circle_by_area
• Add roundness
• Add contour operation circularity

1.11.0 (2022-04-11)

• Add inner contours to labels2contours
• Add inner contours to mask2json

1.10.0 (2022-02-17)

• Add approximate_circle_by_area to contour operations
• BUGFIX: Change type np.array to np.ndarray
• DEPRECATE: Remove simplification so python 3.8+ can be used

1.9.2 (2022-01-03)

• BUGFIX: Bufferoverflow make_mask_ellipse (again/still) remove times 2 for all values in the function

1.9.1 (2021-10-26)

• add ellipse to json2mask
• BUGFIX: Bufferoverflow make_mask_ellipse
• BUGFIX: Make make_mask_ellipse accept floats

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).