Package: tomni
TomniTomni 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 byCytoSMART.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 Tomnipip install tomniLicenseTomni is free for academic and educational use.For commercial use please contactCytoSMART.The nameThe 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.FeaturesBounding box fitting (bbox fitting)Center bounding box fitCustom location box fitImage helpersGet image dimensionsConvert color of an imageIllumination correctionBrightfieldFluorescenceContour operationsGet centerApproximate circle by areaGet roundnessGet circularityCytoSMART data formatTbaJson operationAdd circularity propertyScale objectTranslate objectMake a maskEllipsePolygonPolygon downsamplingiterative downsamplingShape fittingRect around ellipseTransformers of data formatContours to jsonEllipse to jsonJson 2 contoursJson 2 labelJson 2 bboxLabels 2 contoursLabels 2 lists of pointsBinary 2 contoursExamplesDiameter vs radiusMost geometric operation use functions from OpenCVSome of these function return diameter and some radius of the circle. This is not consistent.For example, the functioncv2.minEnclosingCirclereturns the center and radius of the circle. The functioncv2.fitEllipsereturns the center and the major and minor axes of the ellipse.Min enclosing circle exampleimportcv2importmathimportnumpyasnppoints=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 70.71067811865476Fit ellipse exampleimportcv2importmathimportnumpyasnp# Generate some example pointspoints=np.array([[0,0],[100,0],[100,100],[0,100],[0,0]],dtype=np.float32)# Fit an ellipse to the pointsellipse=cv2.fitEllipse(points)# Extract ellipse parameterscenter,axes,angle=ellipsediameter=math.sqrt(50**2+50**2)*2print("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: 141.4213562373095Example is related to the following functions in the packageCreditsSorted alphabeticallyBram van der VeldenCoenraad StijneDenisa DaroţiHristo AtanasovJan-Niklas SchneiderJelle van KerkvoordeKirsten KoopmanLisa KoolenManon van ErpMarina TzenkovaTom de VriesTom NijhofHistory2.2.0 (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 points2.0.0-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_maskChanged variable name inellipseclass from r1/r2 to diameter_1/diameter_2 etc for naming clarity.BUGFIX: Multiplied minor axis and major axis by 2 inellipseclass, which was currently calculated as radii instead of diameters.BUGFIX: Fixed average diameter inellipseclass, which was calculated with radii instead of diameters.BUGFIX: removed assert, which took over half the time of the entirefrom_binary_mask.BUGFIX: Fixed unittest labels2listsOfPoints2.0.0-b2 (2023-08-04)Moved feature_multiplier and metric_unit to to_dict() from from_dict().Added inner contours optionsadded binary2contourschange parameters for from_binary_maskmade contours2polygon2.0.0-b1 (2023-07-06)AnnotationManager function from_dict is called with an optional list of featuresChanged Polygon and Ellipse classes to include the list of features initialized by AnnotationManagerto_dict function now only returns features in the dictionary that were asked for in the feature listAddedfeature_multiplierandmetric_unitas inputs to apply to the features' name and value outputs.Added all features toellipseandpolygon.Features are now in camelCasing when outputto_dict2.0.0-b0 (2022-11-29)CDF-Main: Implementfilterto allow filtering of annotations by feature values (aka gating).CDF-Main: Implementfrom_contours.CDF-Main: Implementto_contours.CDF-Main: Implementfrom_dict.CDF-Main: Implementto_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 pointAdd ellipse annotation class.CDF-ellipse: Implement__eq__CDF-ellipse: Set all rotations between 0 and 90, flip radii if neededRenamedCytoSmartDataFormattoAnnotationManagerAddis_in_maskforEllipseandPolygonAddmin_overlap-parameter into_dictto apply masks to filter annotationsAddto_binary_maskandto_labeled_maskforAnnotationManager,EllipseandPolygonAdd init-functionfrom_binary_maskandfrom_labeled_masktoAnnotationManagerBugfix: Fixed a bug wheresimplify_linereturns empty list when passing two points.Add option to to compress polygons into_dict().
1.17.0 (2023-07-26)Add binary2contours1.16.1 (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' way1.15.0 (2022-12-05)Add json2bbox for ellipse with angle of rotation1.14.0 (2022-11-11)Add convert to color1.13.0 (2022-10-24)Add json2bbox for polygon and ellipse1.12.1 (2022-10-06)Update Json-circularity with circularity calculation from contour ops.1.12.0 (2022-04-15)BUGFIX: Import approximate_circle_by_areaAdd roundnessAdd contour operation circularity1.11.0 (2022-04-11)Add inner contours to labels2contoursAdd inner contours to mask2json1.10.0 (2022-02-17)Add approximate_circle_by_area to contour operationsBUGFIX: Change type np.array to np.ndarrayDEPRECATE: Remove simplification so python 3.8+ can be used1.9.2 (2022-01-03)BUGFIX: Bufferoverflow make_mask_ellipse (again/still)
remove times 2 for all values in the function1.9.1 (2021-10-26)add ellipse to json2maskBUGFIX: Bufferoverflow make_mask_ellipseBUGFIX: Make make_mask_ellipse accept floats1.9.0 (2021-10-01)add mask2bboxadd contour2bboxadd check_overlap_bbox1.8.0 (2021-09-01)add mask2jsonadd json2mask1.7.4 (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 function1.7.3 (2021-06-23)speedup positions2contour by replacing for-loop with numpy slicing1.7.2 (2021-04-21)Migrate to github1.7.1 (2020-12-23)updated setup file simplification<0.61.7.0 (2020-12-03)added new functionsadd_areasummary_jsonjson2dict1.6.4 (2020-11-26)add  missing requirements in setup file1.6.3 (2020-11-25)bug fix. cropping now with deepcopy1.6.2 (2020-11-10)-add fluo_tophat background subtraction1.6.1 (2020-11-04)-add accuracy to json2vgg1.6.0 (2020-11-03)add json2vgg1.5.2add ellipse to vgg2json
1.5.1fix rotation, flipping, crop import1.5.0add json_operationsadd crop list of jsonsadd flipping jsonadd rotation json1.4.0add get center point contouradd get center point jsonadd vgg2json1.3.0Updating of relative illumination correction.add (optional) smoothing stepadd (optional) resize stepadd (optional) normalization1.2.0 (2020-07-02)Add translation of json functions1.1.0 (2020-03-11)Updating of illumination correction.
Splitting into two illumination correction:absolute differencerelative difference1.0.0 (2020-03-06)(new function)add_circularity1.0.0 (2020-02-28)Restructuring of tomni:Migrated Visualization to cytoBoomMigrated validation to manValMade sure every function followed:
function_nameinit.pymain.pytest_function_nameremoved following function:
-- channel_selecting (was only used for old cell counter)
-- select_labels (complete replaceable by transformers.labels2listsOfPointsAdded docstring to all functionsAdded typing to all functionsRenamed everything to pep80.4.0 (2019-09-30)Add transformer as categoryAdd labels 2 list of points as function0.3.3 (2019-09-17)Draw_json (draw_json_mask_onto_image):rename it from draw_json_mask_onto_image to draw_jsonMake the Visualization of json shapes more dynamic.Callable directly from Visualizationit return an image rather than manipulating itconverts the color to the color type of input0.2.1 (2019-07-24)Remove f strings to prevent conflicts on python 3.50.2.0 (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 converterAdd circle draw function that works with the input of the cell counter0.1.8 (2019-02-21)imdim: Function what gives the dimensions of an image from a numpy.ndarrayellipse_mask: creates an ellipse at a given position, with given radius length but a fixed rotation0.0.1 (2018-10-15)First release on PyPI.ACADEMIC PUBLIC LICENSE
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