LICENSE
README.md
setup.cfg
setup.py
zebrazoom/GUIAllPy.py
zebrazoom/__init__.py
zebrazoom/__main__.py
zebrazoom/_subcommands.py
zebrazoom/clusteringAnalysis.py
zebrazoom/clusteringAnalysisPerFrame.py
zebrazoom/extractZZParametersFromTailAngle.py
zebrazoom/getTailExtremityFirstFrame.py
zebrazoom/kinematicParametersAnalysis.py
zebrazoom/kinematicParametersAnalysisCenterOfMassOnlyNoBoutsDetection.py
zebrazoom/recreateSuperStruct.py
zebrazoom/version.txt
zebrazoom/zebraZoomVideoAnalysis.py
zebrazoom.egg-info/PKG-INFO
zebrazoom.egg-info/SOURCES.txt
zebrazoom.egg-info/dependency_links.txt
zebrazoom.egg-info/requires.txt
zebrazoom.egg-info/top_level.txt
zebrazoom/ZZoutput/example1/configUsed.json
zebrazoom/ZZoutput/example1/example1.avi
zebrazoom/ZZoutput/example1/intermediaryWellPosition.txt
zebrazoom/ZZoutput/example1/results_example1.txt
zebrazoom/ZZoutput/example2/configUsed.json
zebrazoom/ZZoutput/example2/example2.avi
zebrazoom/ZZoutput/example2/intermediaryWellPosition.txt
zebrazoom/ZZoutput/example2/results_example2.txt
zebrazoom/ZZoutput/example3/configUsed.json
zebrazoom/ZZoutput/example3/example3.avi
zebrazoom/ZZoutput/example3/intermediaryWellPosition.txt
zebrazoom/ZZoutput/example3/results_example3.txt
zebrazoom/ZZoutput/standardValueFreelySwimZebrafishLarvae/parametersUsedForCalculation.json
zebrazoom/ZZoutput/standardValueFreelySwimZebrafishLarvae/standardValueFreelySwimZebrafishLarvae.pkl
zebrazoom/code/__init__.py
zebrazoom/code/adjustHyperparameters.py
zebrazoom/code/checkConsistencyOfParameters.py
zebrazoom/code/createSuperStruct.py
zebrazoom/code/createValidationVideo.py
zebrazoom/code/detectMovementWithRawVideo.py
zebrazoom/code/extractParameters.py
zebrazoom/code/findWells.py
zebrazoom/code/getHyperparameters.py
zebrazoom/code/paths.py
zebrazoom/code/popUpAlgoFollow.py
zebrazoom/code/popUpAlgoFollowOldVersion.py
zebrazoom/code/preprocessImage.py
zebrazoom/code/util.py
zebrazoom/code/vars.py
zebrazoom/code/GUI/GUI_InitialClasses.py
zebrazoom/code/GUI/GUI_InitialFunctions.py
zebrazoom/code/GUI/__init__.py
zebrazoom/code/GUI/adjustParameterInsideAlgo.py
zebrazoom/code/GUI/adjustParameterInsideAlgoFunctions.py
zebrazoom/code/GUI/automaticallyFindOptimalParameters.py
zebrazoom/code/GUI/automaticallyFindOptimalParametersFunctions.py
zebrazoom/code/GUI/blobCenter.png
zebrazoom/code/GUI/blobExtremity.png
zebrazoom/code/GUI/centerOfMassAnyAnimal.png
zebrazoom/code/GUI/centerOfMassAnyAnimal2.png
zebrazoom/code/GUI/configFilePrepare.py
zebrazoom/code/GUI/configFilePrepareFunctions.py
zebrazoom/code/GUI/configFileROI.png
zebrazoom/code/GUI/configFileZebrafish.py
zebrazoom/code/GUI/configFileZebrafishFunctions.py
zebrazoom/code/GUI/dataAnalysisGUI.py
zebrazoom/code/GUI/dataAnalysisGUIFunctions.py
zebrazoom/code/GUI/freelySwimming.png
zebrazoom/code/GUI/getCoordinates.py
zebrazoom/code/GUI/gridSystem.png
zebrazoom/code/GUI/headEmbedded.png
zebrazoom/code/GUI/leftborder.png
zebrazoom/code/GUI/no1.png
zebrazoom/code/GUI/no2.png
zebrazoom/code/GUI/ok1.png
zebrazoom/code/GUI/readValidationVideo.py
zebrazoom/code/GUI/rightborder.png
zebrazoom/code/GUI/rolloverAnalysis.py
zebrazoom/code/GUI/runtimeROI.png
zebrazoom/code/GUI/savedjustincase.png
zebrazoom/code/GUI/screen.png
zebrazoom/code/GUI/troubleshooting.py
zebrazoom/code/GUI/troubleshootingFunction.py
zebrazoom/code/GUI/wholeVideo.png
zebrazoom/code/GUI/tracking/__init__.py
zebrazoom/code/GUI/tracking/_base.py
zebrazoom/code/GUI/tracking/fasterMultiprocessing.py
zebrazoom/code/GUI/tracking/fasterMultiprocessing2.py
zebrazoom/code/GUI/tracking/tracking.py
zebrazoom/code/GUI/tracking/customTrackingImplementations/__init__.py
zebrazoom/code/GUI/tracking/customTrackingImplementations/examples/example.py
zebrazoom/code/GUI/tracking/customTrackingImplementations/fastFishTracking/tracking.py
zebrazoom/code/dataPostProcessing/__init__.py
zebrazoom/code/dataPostProcessing/computeEyesHeadingPlot.py
zebrazoom/code/dataPostProcessing/createPandasDataFrameOfParameters.py
zebrazoom/code/dataPostProcessing/dataPostProcessing.py
zebrazoom/code/dataPostProcessing/findSleepVsMoving.py
zebrazoom/code/dataPostProcessing/generateAllTimeTailAngleGraph.py
zebrazoom/code/dataPostProcessing/perBoutOutput.py
zebrazoom/code/dataPostProcessing/tailAnglesHeatmap.py
zebrazoom/code/deepLearningFunctions/__init__.py
zebrazoom/code/deepLearningFunctions/labellingFunctions.py
zebrazoom/code/deepLearningFunctions/loadDLmodel.py
zebrazoom/code/deepLearningFunctions/PyTorchFunctions/__init__.py
zebrazoom/code/deepLearningFunctions/PyTorchFunctions/coco_eval.py
zebrazoom/code/deepLearningFunctions/PyTorchFunctions/coco_utils.py
zebrazoom/code/deepLearningFunctions/PyTorchFunctions/engine.py
zebrazoom/code/deepLearningFunctions/PyTorchFunctions/transforms.py
zebrazoom/code/deepLearningFunctions/PyTorchFunctions/utils.py
zebrazoom/code/tracking/__init__.py
zebrazoom/code/tracking/_base.py
zebrazoom/code/tracking/_baseZebraZoom.py
zebrazoom/code/tracking/_centerOfMassTailTracking.py
zebrazoom/code/tracking/_computeHeading.py
zebrazoom/code/tracking/_eyeTracking.py
zebrazoom/code/tracking/_fasterMultiprocessingBase.py
zebrazoom/code/tracking/_getBackground.py
zebrazoom/code/tracking/_getImages.py
zebrazoom/code/tracking/_headEmbeddedTailTracking.py
zebrazoom/code/tracking/_headEmbeddedTailTrackingForImage.py
zebrazoom/code/tracking/_headEmbeddedTailTrackingTeresaNicolson.py
zebrazoom/code/tracking/_headTrackingHeadingCalculation.py
zebrazoom/code/tracking/_tailExtremityTracking.py
zebrazoom/code/tracking/_tailTracking.py
zebrazoom/code/tracking/_tailTrackingBase.py
zebrazoom/code/tracking/_tailTrackingBlobDescent.py
zebrazoom/code/tracking/_tailTrackingDifficultBackground.py
zebrazoom/code/tracking/_updateBackgroundAtInterval.py
zebrazoom/code/tracking/fasterMultiprocessing.py
zebrazoom/code/tracking/fasterMultiprocessing2.py
zebrazoom/code/tracking/tracking.py
zebrazoom/code/tracking/customTrackingImplementations/__init__.py
zebrazoom/code/tracking/customTrackingImplementations/examples/exampleDummyHeadAndTailTracking.py
zebrazoom/code/tracking/customTrackingImplementations/examples/exampleTrackingMethod.py
zebrazoom/code/tracking/customTrackingImplementations/fastFishTracking/animalDetectionBackToWholeImage.py
zebrazoom/code/tracking/customTrackingImplementations/fastFishTracking/backgroundSubtractionOnWholeImage.py
zebrazoom/code/tracking/customTrackingImplementations/fastFishTracking/backgroundSubtractionOnlyOnROIs.py
zebrazoom/code/tracking/customTrackingImplementations/fastFishTracking/detectMovementWithRawVideoInsideTracking.py
zebrazoom/code/tracking/customTrackingImplementations/fastFishTracking/detectMovementWithTrackedDataAfterTracking.py
zebrazoom/code/tracking/customTrackingImplementations/fastFishTracking/dualDirectionTailDetection.py
zebrazoom/code/tracking/customTrackingImplementations/fastFishTracking/getListOfWellsOnWhichToRunTheTracking.py
zebrazoom/code/tracking/customTrackingImplementations/fastFishTracking/getNewFrameROI.py
zebrazoom/code/tracking/customTrackingImplementations/fastFishTracking/removeAnimalJustTrackedFromFrame.py
zebrazoom/code/tracking/customTrackingImplementations/fastFishTracking/tailTrackFindNextPoint.py
zebrazoom/code/tracking/customTrackingImplementations/fastFishTracking/tailTrackTry4InitialPerpendicularDirections.py
zebrazoom/code/tracking/customTrackingImplementations/fastFishTracking/trackTail.py
zebrazoom/code/tracking/customTrackingImplementations/fastFishTracking/tracking.py
zebrazoom/code/tracking/customTrackingImplementations/fastFishTracking/utilities.py
zebrazoom/code/tracking/customTrackingImplementations/multipleCenterOfMassTracking/_headTrackingHeadingCalculation.py
zebrazoom/code/tracking/customTrackingImplementations/multipleCenterOfMassTracking/multipleCenterOfMassTracking.py
zebrazoom/configuration/4wellsZebrafishLarvaeEscapeResponses.json
zebrazoom/configuration/__init__.py
zebrazoom/configuration/fliesInTube.json
zebrazoom/configuration/headEmbeddedZebrafishLarva.json
zebrazoom/configuration/invertBlackWhiteOnImages.json
zebrazoom/configuration/invertColorsForHeadEmbeddedEyeTracking.json
zebrazoom/configuration/noPreProcessingOfImageForBoutDetection.json
zebrazoom/configuration/screenFastTrackingConfigFileTemplate.json
zebrazoom/configuration/testThresholdsForFastScreen.json
zebrazoom/configuration/toCreateConfigFileForBarelyMovingAnimals.json
zebrazoom/dataAPI/__init__.py
zebrazoom/dataAPI/_calculateAndStoreCurvature.py
zebrazoom/dataAPI/_calculateAndStoreTailAngleHeatmap.py
zebrazoom/dataAPI/_createSuperStructFromH5.py
zebrazoom/dataAPI/_openResultsFile.py
zebrazoom/dataAPI/applyMedianFilterOnCurvature.py
zebrazoom/dataAPI/createDistanceBetweenFramesExcelFile.py
zebrazoom/dataAPI/createExcelFileWithRawData.py
zebrazoom/dataAPI/deleteAutomaticallyCalculatedKinematicParameters.py
zebrazoom/dataAPI/getConfigurationFileUsed.py
zebrazoom/dataAPI/getCurvaturePerBout.py
zebrazoom/dataAPI/getCurvaturePerTimeInterval.py
zebrazoom/dataAPI/getDataPerBout.py
zebrazoom/dataAPI/getDataPerTimeInterval.py
zebrazoom/dataAPI/getFPSandPixelSize.py
zebrazoom/dataAPI/getFirstAndLastFrame.py
zebrazoom/dataAPI/getKinematicParametersPerBout.py
zebrazoom/dataAPI/getKinematicParametersPerInterval.py
zebrazoom/dataAPI/getNbOscAndTBFPerBoutFromManualClassification.py
zebrazoom/dataAPI/getSingleFrameDistanceToAxis.py
zebrazoom/dataAPI/getSingleFrameTrackingAndCurvatureForFolder.py
zebrazoom/dataAPI/getSingleFrameTrackingAndDistanceToAxisForFolder.py
zebrazoom/dataAPI/getTailAngleHeatmapPerBout.py
zebrazoom/dataAPI/getTailAngleHeatmapPerTimeInterval.py
zebrazoom/dataAPI/listAllBouts.py
zebrazoom/dataAPI/plotCurvatureYaxisApproximate.py
zebrazoom/dataAPI/plotCurvatureYaxisExact.py
zebrazoom/dataAPI/plotKinematicParametersHist.py
zebrazoom/dataAPI/plotManualVsAutomaticBendLocations.py
zebrazoom/dataAPI/plotSingleFrameTrackingPoints.py
zebrazoom/dataAPI/plotTailAngleHeatmap.py
zebrazoom/dataAPI/setFPSandPixelSize.py
zebrazoom/dataAnalysis/__init__.py
zebrazoom/dataAnalysis/cluster_1a_UsageExample.py
zebrazoom/dataAnalysis/cluster_1b_UsageExampleReloadClassifier.py
zebrazoom/dataAnalysis/populationCompare_UsageExample.py
zebrazoom/dataAnalysis/createCustomDataStructure/__init__.py
zebrazoom/dataAnalysis/createCustomDataStructure/createDistanceBetweenFramesExcelFile.py
zebrazoom/dataAnalysis/createCustomDataStructure/createDistanceSpeedHeadingDeltaHeadingExcelFile.py
zebrazoom/dataAnalysis/createCustomDataStructure/filterLatencyAndMergeBoutsInSameTrials.py
zebrazoom/dataAnalysis/createCustomDataStructure/removeLargeInstantaneousDistanceData.py
zebrazoom/dataAnalysis/dataanalysis/__init__.py
zebrazoom/dataAnalysis/dataanalysis/activeLearning.py
zebrazoom/dataAnalysis/dataanalysis/applyClustering.py
zebrazoom/dataAnalysis/dataanalysis/applyClusteringPerFrame.py
zebrazoom/dataAnalysis/dataanalysis/createSuperClusterVideo.py
zebrazoom/dataAnalysis/dataanalysis/outputValidationVideo.py
zebrazoom/dataAnalysis/dataanalysis/populationComparaison.py
zebrazoom/dataAnalysis/dataanalysis/readValidationVideoDataAnalysis.py
zebrazoom/dataAnalysis/dataanalysis/reapplyClustering.py
zebrazoom/dataAnalysis/dataanalysis/visualizeClusters.py
zebrazoom/dataAnalysis/datasetcreation/__init__.py
zebrazoom/dataAnalysis/datasetcreation/createDataFrame.py
zebrazoom/dataAnalysis/datasetcreation/createDataFramePerFrame.py
zebrazoom/dataAnalysis/datasetcreation/createDatasetsForExperiments.py
zebrazoom/dataAnalysis/datasetcreation/gatherInitialRawData.py
zebrazoom/dataAnalysis/datasetcreation/generatePklDataFileForVideo.py
zebrazoom/dataAnalysis/datasetcreation/getDeltaHead.py
zebrazoom/dataAnalysis/datasetcreation/getDynamicParameters.py
zebrazoom/dataAnalysis/datasetcreation/getGlobalParameters.py
zebrazoom/dataAnalysis/datasetcreation/getInstaHeadingDiff.py
zebrazoom/dataAnalysis/datasetcreation/getInstaHorizontalDisplacement.py
zebrazoom/dataAnalysis/datasetcreation/getInstaMaxTailBendPos.py
zebrazoom/dataAnalysis/datasetcreation/getInstaSpeed.py
zebrazoom/dataAnalysis/datasetcreation/getTailAngleRecalculated.py
zebrazoom/dataAnalysis/datasetcreation/getTailAngleRecalculated2.py
zebrazoom/dataAnalysis/datasetcreation/getTailAngles.py
zebrazoom/dataAnalysis/datasetcreation/getTailLength.py
zebrazoom/dataAnalysis/datasetcreation/getTailLength2.py
zebrazoom/dataAnalysis/experimentOrganizationExcel/example.xlsx
zebrazoom/dataAnalysis/postProcessingFromCommandLine/__init__.py
zebrazoom/dataAnalysis/postProcessingFromCommandLine/postProcessingFromCommandLine.py
zebrazoom/otherScripts/__init__.py
zebrazoom/otherScripts/alternativeKinematicParameterCalculation.py
zebrazoom/otherScripts/launchActiveLearning.py
zebrazoom/otherScripts/launchOptimalClusterNumberSearch.py
zebrazoom/otherScripts/launchReapplyClustering.py
zebrazoom/rolloverDetectionConfiguration/rolloverDetection.json
zebrazoom/videoFormatConversion/__init__.py
zebrazoom/videoFormatConversion/seq_to_avi.py
zebrazoom/videoFormatConversion/zzVideoReading.py