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rename from lmt-analysis/LMT/lmtanalysis/BuildEventNight.py
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diff --git a/lmt-analysis/LMT/lmtanalysis/BuildEventObjectSniffingNor.py b/EMT/lmtanalysis/BuildEventObjectSniffingNor.py
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rename from lmt-analysis/LMT/lmtanalysis/BuildEventObjectSniffingNor.py
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rename from lmt-analysis/LMT/lmtanalysis/BuildEventObjectSniffingNorAcquisitionWithConfig.py
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diff --git a/lmt-analysis/LMT/lmtanalysis/BuildEventObjectSniffingNorTestWithConfig.py b/EMT/lmtanalysis/BuildEventObjectSniffingNorTestWithConfig.py
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rename from lmt-analysis/LMT/lmtanalysis/BuildEventObjectSniffingNorTestWithConfig.py
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diff --git a/lmt-analysis/LMT/lmtanalysis/BuildEventOnHouse.py b/EMT/lmtanalysis/BuildEventOnHouse.py
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rename from lmt-analysis/LMT/lmtanalysis/BuildEventOnHouse.py
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diff --git a/lmt-analysis/LMT/lmtanalysis/BuildEventOralGenitalContact.py b/EMT/lmtanalysis/BuildEventOralGenitalContact.py
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rename from lmt-analysis/LMT/lmtanalysis/BuildEventOralGenitalContact.py
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diff --git a/lmt-analysis/LMT/lmtanalysis/BuildEventOralOralContact.py b/EMT/lmtanalysis/BuildEventOralOralContact.py
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rename from lmt-analysis/LMT/lmtanalysis/BuildEventOralOralContact.py
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diff --git a/lmt-analysis/LMT/lmtanalysis/BuildEventOralSideSequence.py b/EMT/lmtanalysis/BuildEventOralSideSequence.py
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rename from lmt-analysis/LMT/lmtanalysis/BuildEventOralSideSequence.py
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rename from lmt-analysis/LMT/lmtanalysis/BuildEventOtherContact.py
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diff --git a/lmt-analysis/LMT/lmtanalysis/BuildEventPassiveAnogenitalSniff.py b/EMT/lmtanalysis/BuildEventPassiveAnogenitalSniff.py
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rename from lmt-analysis/LMT/lmtanalysis/BuildEventPassiveAnogenitalSniff.py
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rename from lmt-analysis/LMT/lmtanalysis/BuildEventRear5.py
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diff --git a/lmt-analysis/LMT/lmtanalysis/BuildEventRearCenterPeriphery.py b/EMT/lmtanalysis/BuildEventRearCenterPeriphery.py
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rename from lmt-analysis/LMT/lmtanalysis/BuildEventRearCenterPeriphery.py
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rename from lmt-analysis/LMT/lmtanalysis/BuildEventSAP.py
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diff --git a/lmt-analysis/LMT/lmtanalysis/BuildEventSideBySide.py b/EMT/lmtanalysis/BuildEventSideBySide.py
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rename from lmt-analysis/LMT/lmtanalysis/BuildEventSideBySide.py
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diff --git a/lmt-analysis/LMT/lmtanalysis/BuildEventSideBySideOpposite.py b/EMT/lmtanalysis/BuildEventSideBySideOpposite.py
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rename from lmt-analysis/LMT/lmtanalysis/BuildEventSideBySideOpposite.py
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diff --git a/lmt-analysis/LMT/lmtanalysis/BuildEventSideWalk.py b/EMT/lmtanalysis/BuildEventSideWalk.py
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rename from lmt-analysis/LMT/lmtanalysis/BuildEventSideWalk.py
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diff --git a/lmt-analysis/LMT/lmtanalysis/BuildEventSocialApproach.py b/EMT/lmtanalysis/BuildEventSocialApproach.py
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rename from lmt-analysis/LMT/lmtanalysis/BuildEventSocialApproach.py
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diff --git a/lmt-analysis/LMT/lmtanalysis/BuildEventSocialEscape.py b/EMT/lmtanalysis/BuildEventSocialEscape.py
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rename from lmt-analysis/LMT/lmtanalysis/BuildEventSocialEscape.py
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diff --git a/lmt-analysis/LMT/lmtanalysis/BuildEventStop.py b/EMT/lmtanalysis/BuildEventStop.py
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rename from lmt-analysis/LMT/lmtanalysis/BuildEventStop.py
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diff --git a/lmt-analysis/LMT/lmtanalysis/BuildEventTrain2.py b/EMT/lmtanalysis/BuildEventTrain2.py
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rename from lmt-analysis/LMT/lmtanalysis/BuildEventTrain2.py
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rename from lmt-analysis/LMT/lmtanalysis/BuildEventTrain3.py
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rename from lmt-analysis/LMT/lmtanalysis/BuildEventTrain4.py
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diff --git a/lmt-analysis/LMT/lmtanalysis/BuildEventWallJump.py b/EMT/lmtanalysis/BuildEventWallJump.py
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rename from lmt-analysis/LMT/lmtanalysis/BuildEventWallJump.py
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diff --git a/lmt-analysis/LMT/lmtanalysis/BuildEventWallJump_oldv.py b/EMT/lmtanalysis/BuildEventWallJump_oldv.py
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rename from lmt-analysis/LMT/lmtanalysis/BuildEventWallJump_oldv.py
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rename from lmt-analysis/LMT/lmtanalysis/BuildEventWaterPoint.py
rename to EMT/lmtanalysis/BuildEventWaterPoint.py
diff --git a/lmt-analysis/LMT/lmtanalysis/CheckWrongAnimal.py b/EMT/lmtanalysis/CheckWrongAnimal.py
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rename from lmt-analysis/LMT/lmtanalysis/CheckWrongAnimal.py
rename to EMT/lmtanalysis/CheckWrongAnimal.py
diff --git a/lmt-analysis/LMT/lmtanalysis/Chronometer.py b/EMT/lmtanalysis/Chronometer.py
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rename from lmt-analysis/LMT/lmtanalysis/Chronometer.py
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diff --git a/lmt-analysis/LMT/lmtanalysis/CorrectDetectionIntegrity.py b/EMT/lmtanalysis/CorrectDetectionIntegrity.py
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rename from lmt-analysis/LMT/lmtanalysis/CorrectDetectionIntegrity.py
rename to EMT/lmtanalysis/CorrectDetectionIntegrity.py
diff --git a/lmt-analysis/LMT/lmtanalysis/Detection.py b/EMT/lmtanalysis/Detection.py
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rename from lmt-analysis/LMT/lmtanalysis/Detection.py
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diff --git a/lmt-analysis/LMT/lmtanalysis/Event.py b/EMT/lmtanalysis/Event.py
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rename from lmt-analysis/LMT/lmtanalysis/Event.py
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rename from lmt-analysis/LMT/lmtanalysis/EventTimeLineCache.py
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diff --git a/lmt-analysis/LMT/lmtanalysis/FileUtil.py b/EMT/lmtanalysis/FileUtil.py
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rename from lmt-analysis/LMT/lmtanalysis/FileUtil.py
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diff --git a/lmt-analysis/LMT/lmtanalysis/Mask.py b/EMT/lmtanalysis/Mask.py
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rename from lmt-analysis/LMT/lmtanalysis/Mask.py
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diff --git a/lmt-analysis/LMT/lmtanalysis/Measure.py b/EMT/lmtanalysis/Measure.py
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rename from lmt-analysis/LMT/lmtanalysis/Measure.py
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rename from lmt-analysis/LMT/lmtanalysis/MeasureOld.py
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diff --git a/lmt-analysis/LMT/lmtanalysis/Parameters.py b/EMT/lmtanalysis/Parameters.py
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rename from lmt-analysis/LMT/lmtanalysis/Parameters.py
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rename from lmt-analysis/LMT/lmtanalysis/ParametersMouse.py
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rename from lmt-analysis/LMT/lmtanalysis/ParametersRat.py
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diff --git a/lmt-analysis/LMT/lmtanalysis/Point.py b/EMT/lmtanalysis/Point.py
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rename from lmt-analysis/LMT/lmtanalysis/Point.py
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diff --git a/lmt-analysis/LMT/lmtanalysis/Rectangle.py b/EMT/lmtanalysis/Rectangle.py
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rename from lmt-analysis/LMT/lmtanalysis/Rectangle.py
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diff --git a/lmt-analysis/LMT/lmtanalysis/Settings.py b/EMT/lmtanalysis/Settings.py
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rename from lmt-analysis/LMT/lmtanalysis/Settings.py
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diff --git a/lmt-analysis/LMT/lmtanalysis/TaskLogger.py b/EMT/lmtanalysis/TaskLogger.py
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rename from lmt-analysis/LMT/lmtanalysis/TaskLogger.py
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diff --git a/lmt-analysis/LMT/lmtanalysis/Util.py b/EMT/lmtanalysis/Util.py
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rename from lmt-analysis/LMT/lmtanalysis/Util.py
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diff --git a/lmt-analysis/LMT/lmtanalysis/__init__.py b/EMT/lmtanalysis/__init__.py
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rename from lmt-analysis/LMT/lmtanalysis/__init__.py
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diff --git a/lmt-analysis/LMT/lmtanalysis/split_database.py b/EMT/lmtanalysis/split_database.py
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rename from lmt-analysis/LMT/lmtanalysis/split_database.py
rename to EMT/lmtanalysis/split_database.py
diff --git a/lmt-analysis/LMT/scripts/AddFileInfo.py b/EMT/scripts/AddFileInfo.py
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rename from lmt-analysis/LMT/scripts/AddFileInfo.py
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diff --git a/lmt-analysis/LMT/scripts/AlterColBase.py b/EMT/scripts/AlterColBase.py
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rename from lmt-analysis/LMT/scripts/AlterColBase.py
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diff --git a/lmt-analysis/LMT/scripts/AutoNightInput.ipynb b/EMT/scripts/AutoNightInput.ipynb
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rename from lmt-analysis/LMT/scripts/AutoNightInput.ipynb
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diff --git a/lmt-analysis/LMT/scripts/BehaviouralSequences/.idea/BehaviouralSequences.iml b/EMT/scripts/BehaviouralSequences/.idea/BehaviouralSequences.iml
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rename from lmt-analysis/LMT/scripts/BehaviouralSequences/.idea/BehaviouralSequences.iml
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rename from lmt-analysis/LMT/scripts/BehaviouralSequences/.idea/modules.xml
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rename from lmt-analysis/LMT/scripts/BehaviouralSequences/.idea/workspace.xml
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diff --git a/lmt-analysis/LMT/scripts/BehaviouralSequences/CheckEventsForSequences.py b/EMT/scripts/BehaviouralSequences/CheckEventsForSequences.py
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rename from lmt-analysis/LMT/scripts/BehaviouralSequences/CheckEventsForSequences.py
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diff --git a/lmt-analysis/LMT/scripts/BehaviouralSequences/CompareProfileInitialExclusiveEvents.py b/EMT/scripts/BehaviouralSequences/CompareProfileInitialExclusiveEvents.py
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rename from lmt-analysis/LMT/scripts/BehaviouralSequences/CompareProfileInitialExclusiveEvents.py
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diff --git a/lmt-analysis/LMT/scripts/BehaviouralSequences/ComputeTransitionsBetweenEvents.py b/EMT/scripts/BehaviouralSequences/ComputeTransitionsBetweenEvents.py
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rename from lmt-analysis/LMT/scripts/BehaviouralSequences/ComputeTransitionsBetweenEvents.py
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diff --git a/lmt-analysis/LMT/scripts/BehaviouralSequences/ExclusivePattern.py b/EMT/scripts/BehaviouralSequences/ExclusivePattern.py
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rename from lmt-analysis/LMT/scripts/BehaviouralSequences/ExclusivePattern.py
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diff --git a/lmt-analysis/LMT/scripts/BehaviouralSequences/ExtractEventTableFromDatabase.py b/EMT/scripts/BehaviouralSequences/ExtractEventTableFromDatabase.py
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rename from lmt-analysis/LMT/scripts/BehaviouralSequences/ExtractEventTableFromDatabase.py
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diff --git a/lmt-analysis/LMT/scripts/BehaviouralSequences/__init__.py b/EMT/scripts/BehaviouralSequences/__init__.py
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rename from lmt-analysis/LMT/scripts/BehaviouralSequences/__init__.py
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diff --git a/lmt-analysis/LMT/scripts/BehaviouralSequences/mygraph.html b/EMT/scripts/BehaviouralSequences/mygraph.html
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rename from lmt-analysis/LMT/scripts/BehaviouralSequences/mygraph.html
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diff --git a/lmt-analysis/LMT/scripts/BuildDataBaseIndex.py b/EMT/scripts/BuildDataBaseIndex.py
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rename from lmt-analysis/LMT/scripts/BuildDataBaseIndex.py
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diff --git a/lmt-analysis/LMT/scripts/Check_Experiment_Reliability.py b/EMT/scripts/Check_Experiment_Reliability.py
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rename from lmt-analysis/LMT/scripts/Check_Experiment_Reliability.py
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diff --git a/lmt-analysis/LMT/scripts/ComputeMeanSpeedPerEvent.py b/EMT/scripts/ComputeMeanSpeedPerEvent.py
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rename from lmt-analysis/LMT/scripts/ComputeMeanSpeedPerEvent.py
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diff --git a/lmt-analysis/LMT/scripts/ComputeMeasuresIdentityProfileOneMouseAuto.ipynb b/EMT/scripts/ComputeMeasuresIdentityProfileOneMouseAuto.ipynb
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rename from lmt-analysis/LMT/scripts/ComputeMeasuresIdentityProfileOneMouseAutomatic.py
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rename from lmt-analysis/LMT/scripts/ComputeMeasuresIdentityProfileOneMouseAutomaticPerIndividual.py
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diff --git a/lmt-analysis/LMT/scripts/Compute_Contact_Out_Of_Nest_Zone.py b/EMT/scripts/Compute_Contact_Out_Of_Nest_Zone.py
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rename from lmt-analysis/LMT/scripts/Compute_Contact_Out_Of_Nest_Zone.py
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diff --git a/lmt-analysis/LMT/scripts/Compute_Distance_Lg_Term_Timebin.py b/EMT/scripts/Compute_Distance_Lg_Term_Timebin.py
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rename from lmt-analysis/LMT/scripts/Compute_Distance_Lg_Term_Timebin.py
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rename from lmt-analysis/LMT/scripts/Compute_Event_Duration_Distribution.py
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diff --git a/lmt-analysis/LMT/scripts/Compute_Individual_Profiles_Mixed_Genotypes.py b/EMT/scripts/Compute_Individual_Profiles_Mixed_Genotypes.py
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rename from lmt-analysis/LMT/scripts/Compute_Individual_Profiles_Mixed_Genotypes.py
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diff --git a/lmt-analysis/LMT/scripts/Compute_Link_Make_Break_Group3.py b/EMT/scripts/Compute_Link_Make_Break_Group3.py
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rename from lmt-analysis/LMT/scripts/Compute_Link_Make_Break_Group3.py
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rename from lmt-analysis/LMT/scripts/Compute_Link_Make_Break_Group4.py
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diff --git a/lmt-analysis/LMT/scripts/Compute_Make_Break_Group3.py b/EMT/scripts/Compute_Make_Break_Group3.py
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rename from lmt-analysis/LMT/scripts/Compute_Make_Break_Group3.py
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rename from lmt-analysis/LMT/scripts/Compute_Make_Break_Group4.py
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diff --git a/lmt-analysis/LMT/scripts/Compute_Manual_Validation.py b/EMT/scripts/Compute_Manual_Validation.py
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rename from lmt-analysis/LMT/scripts/Compute_Manual_Validation.py
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diff --git a/lmt-analysis/LMT/scripts/Compute_Measures_Identity_Profile.py b/EMT/scripts/Compute_Measures_Identity_Profile.py
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rename from lmt-analysis/LMT/scripts/Compute_Measures_Identity_Profile.py
rename to EMT/scripts/Compute_Measures_Identity_Profile.py
diff --git a/lmt-analysis/LMT/scripts/Compute_Measures_Identity_Profile_Dyadic.py b/EMT/scripts/Compute_Measures_Identity_Profile_Dyadic.py
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rename from lmt-analysis/LMT/scripts/Compute_Measures_Identity_Profile_Dyadic.py
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diff --git a/lmt-analysis/LMT/scripts/Compute_Measures_Identity_Profile_Mixed_Geno_Groups.py b/EMT/scripts/Compute_Measures_Identity_Profile_Mixed_Geno_Groups.py
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rename from lmt-analysis/LMT/scripts/Compute_Measures_Identity_Profile_Mixed_Geno_Groups.py
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diff --git a/lmt-analysis/LMT/scripts/Compute_Measures_Identity_Profile_OneMouse.py b/EMT/scripts/Compute_Measures_Identity_Profile_OneMouse.py
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rename from lmt-analysis/LMT/scripts/Compute_Measures_Identity_Profile_OneMouse.py
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diff --git a/lmt-analysis/LMT/scripts/Compute_Measures_Identity_Profile_OneMouse_During_Night.py b/EMT/scripts/Compute_Measures_Identity_Profile_OneMouse_During_Night.py
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rename from lmt-analysis/LMT/scripts/Compute_Measures_Identity_Profile_OneMouse_During_Night.py
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diff --git a/lmt-analysis/LMT/scripts/Compute_Measures_Identity_Profile_Pairs.py b/EMT/scripts/Compute_Measures_Identity_Profile_Pairs.py
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rename from lmt-analysis/LMT/scripts/Compute_Measures_Identity_Profile_Pairs.py
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diff --git a/lmt-analysis/LMT/scripts/Compute_Measures_Identity_Profile_Single_Object_Explo.py b/EMT/scripts/Compute_Measures_Identity_Profile_Single_Object_Explo.py
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rename from lmt-analysis/LMT/scripts/Compute_Measures_Identity_Profile_Single_Object_Explo.py
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diff --git a/lmt-analysis/LMT/scripts/Compute_Measures_Identity_Profile_Social_Recognition.py b/EMT/scripts/Compute_Measures_Identity_Profile_Social_Recognition.py
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rename from lmt-analysis/LMT/scripts/Compute_Measures_Identity_Profile_Social_Recognition.py
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diff --git a/lmt-analysis/LMT/scripts/Compute_OnHouseStats.py b/EMT/scripts/Compute_OnHouseStats.py
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rename from lmt-analysis/LMT/scripts/Compute_OnHouseStats.py
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diff --git a/lmt-analysis/LMT/scripts/Compute_OnHouseTimelines.py b/EMT/scripts/Compute_OnHouseTimelines.py
similarity index 100%
rename from lmt-analysis/LMT/scripts/Compute_OnHouseTimelines.py
rename to EMT/scripts/Compute_OnHouseTimelines.py
diff --git a/lmt-analysis/LMT/scripts/Compute_Proportions_Group3.py b/EMT/scripts/Compute_Proportions_Group3.py
similarity index 100%
rename from lmt-analysis/LMT/scripts/Compute_Proportions_Group3.py
rename to EMT/scripts/Compute_Proportions_Group3.py
diff --git a/lmt-analysis/LMT/scripts/ExportAnimalListFromJsonResultFile.py b/EMT/scripts/ExportAnimalListFromJsonResultFile.py
similarity index 100%
rename from lmt-analysis/LMT/scripts/ExportAnimalListFromJsonResultFile.py
rename to EMT/scripts/ExportAnimalListFromJsonResultFile.py
diff --git a/lmt-analysis/LMT/scripts/ExportResultsDyadicToCSV.py b/EMT/scripts/ExportResultsDyadicToCSV.py
similarity index 100%
rename from lmt-analysis/LMT/scripts/ExportResultsDyadicToCSV.py
rename to EMT/scripts/ExportResultsDyadicToCSV.py
diff --git a/lmt-analysis/LMT/scripts/ExportResultsOpenField.py b/EMT/scripts/ExportResultsOpenField.py
similarity index 100%
rename from lmt-analysis/LMT/scripts/ExportResultsOpenField.py
rename to EMT/scripts/ExportResultsOpenField.py
diff --git a/lmt-analysis/LMT/scripts/ExportResultsToCSV.py b/EMT/scripts/ExportResultsToCSV.py
similarity index 100%
rename from lmt-analysis/LMT/scripts/ExportResultsToCSV.py
rename to EMT/scripts/ExportResultsToCSV.py
diff --git a/lmt-analysis/LMT/scripts/Inter animal interaction matrix.py b/EMT/scripts/Inter animal interaction matrix.py
similarity index 100%
rename from lmt-analysis/LMT/scripts/Inter animal interaction matrix.py
rename to EMT/scripts/Inter animal interaction matrix.py
diff --git a/lmt-analysis/LMT/scripts/ManualNightInput.ipynb b/EMT/scripts/ManualNightInput.ipynb
similarity index 100%
rename from lmt-analysis/LMT/scripts/ManualNightInput.ipynb
rename to EMT/scripts/ManualNightInput.ipynb
diff --git a/lmt-analysis/LMT/scripts/ManualNightInput.py b/EMT/scripts/ManualNightInput.py
similarity index 100%
rename from lmt-analysis/LMT/scripts/ManualNightInput.py
rename to EMT/scripts/ManualNightInput.py
diff --git a/lmt-analysis/LMT/scripts/Novel_Object_Recognition_Test/ComputeActivityHabituationNorOpenfield.py b/EMT/scripts/Novel_Object_Recognition_Test/ComputeActivityHabituationNorOpenfield.py
similarity index 100%
rename from lmt-analysis/LMT/scripts/Novel_Object_Recognition_Test/ComputeActivityHabituationNorOpenfield.py
rename to EMT/scripts/Novel_Object_Recognition_Test/ComputeActivityHabituationNorOpenfield.py
diff --git a/lmt-analysis/LMT/scripts/Novel_Object_Recognition_Test/ComputeActivityHabituationNorTest.py b/EMT/scripts/Novel_Object_Recognition_Test/ComputeActivityHabituationNorTest.py
similarity index 100%
rename from lmt-analysis/LMT/scripts/Novel_Object_Recognition_Test/ComputeActivityHabituationNorTest.py
rename to EMT/scripts/Novel_Object_Recognition_Test/ComputeActivityHabituationNorTest.py
diff --git a/lmt-analysis/LMT/scripts/Novel_Object_Recognition_Test/ComputeActivityHabituationNorTestRedCage.py b/EMT/scripts/Novel_Object_Recognition_Test/ComputeActivityHabituationNorTestRedCage.py
similarity index 100%
rename from lmt-analysis/LMT/scripts/Novel_Object_Recognition_Test/ComputeActivityHabituationNorTestRedCage.py
rename to EMT/scripts/Novel_Object_Recognition_Test/ComputeActivityHabituationNorTestRedCage.py
diff --git a/lmt-analysis/LMT/scripts/Novel_Object_Recognition_Test/ComputeNORAnalysis.py b/EMT/scripts/Novel_Object_Recognition_Test/ComputeNORAnalysis.py
similarity index 100%
rename from lmt-analysis/LMT/scripts/Novel_Object_Recognition_Test/ComputeNORAnalysis.py
rename to EMT/scripts/Novel_Object_Recognition_Test/ComputeNORAnalysis.py
diff --git a/lmt-analysis/LMT/scripts/Novel_Object_Recognition_Test/ComputeNORAnalysisGenotypeComparison.py b/EMT/scripts/Novel_Object_Recognition_Test/ComputeNORAnalysisGenotypeComparison.py
similarity index 100%
rename from lmt-analysis/LMT/scripts/Novel_Object_Recognition_Test/ComputeNORAnalysisGenotypeComparison.py
rename to EMT/scripts/Novel_Object_Recognition_Test/ComputeNORAnalysisGenotypeComparison.py
diff --git a/lmt-analysis/LMT/scripts/Novel_Object_Recognition_Test/ComputeNORAnalysisObjectComparisons.py b/EMT/scripts/Novel_Object_Recognition_Test/ComputeNORAnalysisObjectComparisons.py
similarity index 100%
rename from lmt-analysis/LMT/scripts/Novel_Object_Recognition_Test/ComputeNORAnalysisObjectComparisons.py
rename to EMT/scripts/Novel_Object_Recognition_Test/ComputeNORAnalysisObjectComparisons.py
diff --git a/lmt-analysis/LMT/scripts/Novel_Object_Recognition_Test/ComputeObjectRecognition.py b/EMT/scripts/Novel_Object_Recognition_Test/ComputeObjectRecognition.py
similarity index 100%
rename from lmt-analysis/LMT/scripts/Novel_Object_Recognition_Test/ComputeObjectRecognition.py
rename to EMT/scripts/Novel_Object_Recognition_Test/ComputeObjectRecognition.py
diff --git a/lmt-analysis/LMT/scripts/Novel_Object_Recognition_Test/ComputeObjectRecognitionNorRedCage.py b/EMT/scripts/Novel_Object_Recognition_Test/ComputeObjectRecognitionNorRedCage.py
similarity index 100%
rename from lmt-analysis/LMT/scripts/Novel_Object_Recognition_Test/ComputeObjectRecognitionNorRedCage.py
rename to EMT/scripts/Novel_Object_Recognition_Test/ComputeObjectRecognitionNorRedCage.py
diff --git a/lmt-analysis/LMT/scripts/Novel_Object_Recognition_Test/ConfigurationNOR.py b/EMT/scripts/Novel_Object_Recognition_Test/ConfigurationNOR.py
similarity index 100%
rename from lmt-analysis/LMT/scripts/Novel_Object_Recognition_Test/ConfigurationNOR.py
rename to EMT/scripts/Novel_Object_Recognition_Test/ConfigurationNOR.py
diff --git a/lmt-analysis/LMT/scripts/Novel_Object_Recognition_Test/checkObjectPreference.py b/EMT/scripts/Novel_Object_Recognition_Test/checkObjectPreference.py
similarity index 100%
rename from lmt-analysis/LMT/scripts/Novel_Object_Recognition_Test/checkObjectPreference.py
rename to EMT/scripts/Novel_Object_Recognition_Test/checkObjectPreference.py
diff --git a/lmt-analysis/LMT/scripts/Novel_Object_Recognition_Test/computeManualScoringNOR.py b/EMT/scripts/Novel_Object_Recognition_Test/computeManualScoringNOR.py
similarity index 100%
rename from lmt-analysis/LMT/scripts/Novel_Object_Recognition_Test/computeManualScoringNOR.py
rename to EMT/scripts/Novel_Object_Recognition_Test/computeManualScoringNOR.py
diff --git a/lmt-analysis/LMT/scripts/Plot Heat Map.ipynb b/EMT/scripts/Plot Heat Map.ipynb
similarity index 100%
rename from lmt-analysis/LMT/scripts/Plot Heat Map.ipynb
rename to EMT/scripts/Plot Heat Map.ipynb
diff --git a/lmt-analysis/LMT/scripts/PlotFigurePairsBothSexes.py b/EMT/scripts/PlotFigurePairsBothSexes.py
similarity index 100%
rename from lmt-analysis/LMT/scripts/PlotFigurePairsBothSexes.py
rename to EMT/scripts/PlotFigurePairsBothSexes.py
diff --git a/lmt-analysis/LMT/scripts/PlotFigureProfilesAuto.py b/EMT/scripts/PlotFigureProfilesAuto.py
similarity index 100%
rename from lmt-analysis/LMT/scripts/PlotFigureProfilesAuto.py
rename to EMT/scripts/PlotFigureProfilesAuto.py
diff --git a/lmt-analysis/LMT/scripts/PlotSensorData.py b/EMT/scripts/PlotSensorData.py
similarity index 100%
rename from lmt-analysis/LMT/scripts/PlotSensorData.py
rename to EMT/scripts/PlotSensorData.py
diff --git a/lmt-analysis/LMT/scripts/PlotTimeLineActivity.py b/EMT/scripts/PlotTimeLineActivity.py
similarity index 100%
rename from lmt-analysis/LMT/scripts/PlotTimeLineActivity.py
rename to EMT/scripts/PlotTimeLineActivity.py
diff --git a/lmt-analysis/LMT/scripts/PlotTimeLineActivityAutomatic.ipynb b/EMT/scripts/PlotTimeLineActivityAutomatic.ipynb
similarity index 100%
rename from lmt-analysis/LMT/scripts/PlotTimeLineActivityAutomatic.ipynb
rename to EMT/scripts/PlotTimeLineActivityAutomatic.ipynb
diff --git a/lmt-analysis/LMT/scripts/PlotTimeLineActivityAutomatic.py b/EMT/scripts/PlotTimeLineActivityAutomatic.py
similarity index 100%
rename from lmt-analysis/LMT/scripts/PlotTimeLineActivityAutomatic.py
rename to EMT/scripts/PlotTimeLineActivityAutomatic.py
diff --git a/lmt-analysis/LMT/scripts/PlotTimeLineCumulativeWaterPoint.py b/EMT/scripts/PlotTimeLineCumulativeWaterPoint.py
similarity index 100%
rename from lmt-analysis/LMT/scripts/PlotTimeLineCumulativeWaterPoint.py
rename to EMT/scripts/PlotTimeLineCumulativeWaterPoint.py
diff --git a/lmt-analysis/LMT/scripts/Plot_Activity_Interlab_Study_First_4h.py b/EMT/scripts/Plot_Activity_Interlab_Study_First_4h.py
similarity index 100%
rename from lmt-analysis/LMT/scripts/Plot_Activity_Interlab_Study_First_4h.py
rename to EMT/scripts/Plot_Activity_Interlab_Study_First_4h.py
diff --git a/lmt-analysis/LMT/scripts/Plot_Figure_Activity_NOR_habituation_group_monitoring.py b/EMT/scripts/Plot_Figure_Activity_NOR_habituation_group_monitoring.py
similarity index 100%
rename from lmt-analysis/LMT/scripts/Plot_Figure_Activity_NOR_habituation_group_monitoring.py
rename to EMT/scripts/Plot_Figure_Activity_NOR_habituation_group_monitoring.py
diff --git a/lmt-analysis/LMT/scripts/Plot_Trajectory_Single_Object_Explo.py b/EMT/scripts/Plot_Trajectory_Single_Object_Explo.py
similarity index 100%
rename from lmt-analysis/LMT/scripts/Plot_Trajectory_Single_Object_Explo.py
rename to EMT/scripts/Plot_Trajectory_Single_Object_Explo.py
diff --git a/lmt-analysis/LMT/scripts/Rebuild all events.ipynb b/EMT/scripts/Rebuild all events.ipynb
similarity index 100%
rename from lmt-analysis/LMT/scripts/Rebuild all events.ipynb
rename to EMT/scripts/Rebuild all events.ipynb
diff --git a/lmt-analysis/LMT/scripts/Rebuild_All_Events.py b/EMT/scripts/Rebuild_All_Events.py
similarity index 100%
rename from lmt-analysis/LMT/scripts/Rebuild_All_Events.py
rename to EMT/scripts/Rebuild_All_Events.py
diff --git a/lmt-analysis/LMT/scripts/Rebuild_All_Exclusive_Contact_Events.py b/EMT/scripts/Rebuild_All_Exclusive_Contact_Events.py
similarity index 100%
rename from lmt-analysis/LMT/scripts/Rebuild_All_Exclusive_Contact_Events.py
rename to EMT/scripts/Rebuild_All_Exclusive_Contact_Events.py
diff --git a/lmt-analysis/LMT/scripts/Rebuild_All_Profile_Relative.py b/EMT/scripts/Rebuild_All_Profile_Relative.py
similarity index 100%
rename from lmt-analysis/LMT/scripts/Rebuild_All_Profile_Relative.py
rename to EMT/scripts/Rebuild_All_Profile_Relative.py
diff --git a/lmt-analysis/LMT/scripts/Rebuild_All_Profile_deprecated.py b/EMT/scripts/Rebuild_All_Profile_deprecated.py
similarity index 100%
rename from lmt-analysis/LMT/scripts/Rebuild_All_Profile_deprecated.py
rename to EMT/scripts/Rebuild_All_Profile_deprecated.py
diff --git a/lmt-analysis/LMT/scripts/Rebuild_info_mice.py b/EMT/scripts/Rebuild_info_mice.py
similarity index 100%
rename from lmt-analysis/LMT/scripts/Rebuild_info_mice.py
rename to EMT/scripts/Rebuild_info_mice.py
diff --git a/lmt-analysis/LMT/scripts/SemiAutomaticNightInput.py b/EMT/scripts/SemiAutomaticNightInput.py
similarity index 100%
rename from lmt-analysis/LMT/scripts/SemiAutomaticNightInput.py
rename to EMT/scripts/SemiAutomaticNightInput.py
diff --git a/lmt-analysis/LMT/scripts/SetGenotype.ipynb b/EMT/scripts/SetGenotype.ipynb
similarity index 100%
rename from lmt-analysis/LMT/scripts/SetGenotype.ipynb
rename to EMT/scripts/SetGenotype.ipynb
diff --git a/lmt-analysis/LMT/scripts/Show Sensor Data.ipynb b/EMT/scripts/Show Sensor Data.ipynb
similarity index 100%
rename from lmt-analysis/LMT/scripts/Show Sensor Data.ipynb
rename to EMT/scripts/Show Sensor Data.ipynb
diff --git a/lmt-analysis/LMT/scripts/ShowLog.py b/EMT/scripts/ShowLog.py
similarity index 100%
rename from lmt-analysis/LMT/scripts/ShowLog.py
rename to EMT/scripts/ShowLog.py
diff --git a/lmt-analysis/LMT/scripts/__init__.py b/EMT/scripts/__init__.py
similarity index 100%
rename from lmt-analysis/LMT/scripts/__init__.py
rename to EMT/scripts/__init__.py
diff --git a/lmt-analysis/LMT/scripts/checkMove.py b/EMT/scripts/checkMove.py
similarity index 100%
rename from lmt-analysis/LMT/scripts/checkMove.py
rename to EMT/scripts/checkMove.py
diff --git a/lmt-analysis/LMT/scripts/checkTimeLine.py b/EMT/scripts/checkTimeLine.py
similarity index 100%
rename from lmt-analysis/LMT/scripts/checkTimeLine.py
rename to EMT/scripts/checkTimeLine.py
diff --git a/lmt-analysis/LMT/scripts/fix_RFID.py b/EMT/scripts/fix_RFID.py
similarity index 100%
rename from lmt-analysis/LMT/scripts/fix_RFID.py
rename to EMT/scripts/fix_RFID.py
diff --git a/lmt-analysis/LMT/scripts/nightInputFromSensor.py b/EMT/scripts/nightInputFromSensor.py
similarity index 100%
rename from lmt-analysis/LMT/scripts/nightInputFromSensor.py
rename to EMT/scripts/nightInputFromSensor.py
diff --git a/lmt-analysis/LMT/scripts/sensor/__init__.py b/EMT/scripts/sensor/__init__.py
similarity index 100%
rename from lmt-analysis/LMT/scripts/sensor/__init__.py
rename to EMT/scripts/sensor/__init__.py
diff --git a/lmt-analysis/LMT/scripts/sensor/plotSensorData.py b/EMT/scripts/sensor/plotSensorData.py
similarity index 100%
rename from lmt-analysis/LMT/scripts/sensor/plotSensorData.py
rename to EMT/scripts/sensor/plotSensorData.py
diff --git a/lmt-analysis/LMT/scripts/tools/RecoverFrame.py b/EMT/scripts/tools/RecoverFrame.py
similarity index 100%
rename from lmt-analysis/LMT/scripts/tools/RecoverFrame.py
rename to EMT/scripts/tools/RecoverFrame.py
diff --git a/lmt-analysis/LMT/scripts/tools/__init__.py b/EMT/scripts/tools/__init__.py
similarity index 100%
rename from lmt-analysis/LMT/scripts/tools/__init__.py
rename to EMT/scripts/tools/__init__.py
diff --git a/lmt-analysis/LMT/setup.py b/EMT/setup.py
similarity index 100%
rename from lmt-analysis/LMT/setup.py
rename to EMT/setup.py
diff --git a/lmt-analysis/LICENSE b/LICENSE
similarity index 100%
rename from lmt-analysis/LICENSE
rename to LICENSE
diff --git a/lmt-analysis/README.md b/README.md
similarity index 92%
rename from lmt-analysis/README.md
rename to README.md
index b583af7e28dcea002bf4a085bbdb072cc777f175..797631f8295f8ee937aad13c44a07c8383f39758 100644
--- a/lmt-analysis/README.md
+++ b/README.md
@@ -3,7 +3,7 @@
 Enhanced Mouse Tracker is an evolution of the Live Mouse Tracker Analysis.
 It is a new toolbox with an improved pipeline to reconstruct LMT events with faster, more precise and more robust algorithms.
 
-<img src=./LMT/images/view_coherence.gif alt="drawing" width="500"/>
+<img src=./EMT/images/view_coherence.gif alt="drawing" width="500"/>
 
 ## Improvements
 
@@ -24,15 +24,15 @@ To do so type this command when you are in your working python evironment at thi
     pip install -e .
 
 You can use either the jupyter notebooks, to run each processing separately, or you can use the python script to run the full pipeline in a once.
-Notebooks are in `./LMT/EMT/EMT_notebooks/`.
-Scripts are in `./LMT/EMT/EMT_scripts/`.
+Notebooks are in `./EMT/EMT_notebooks/`.
+Scripts are in `./EMT/EMT_scripts/`.
 In order to use the jupyter notebooks you just have to follow the given instructions. All the parameters you may modify to adapt the functionality to your need are in one of the first cells of the notebook, check it.
 To use the python scripts, you can run the `run_EMT_pipeline.py` which will run all the functions in a once. It will rebuild all LMT events with the new algorithms and paramenters, it will also plot the cage conditions registered throughout the experiment and it will compute the traveled distance in 1h intervals, the timeleine of the stops (> 1s) of each animal and the post-processing of the events, outputing filtered events in either csv files, time graphics and/or sqlite databases.
 Although this processing is long (for a 3-day database it will take a whole day to fully process), it is relatively lightweight and ou may process many databases in parallel, if your machine is powerful enough (An Intel i9 with 64 GB RAM can handle up to 8 databases simultaneously without much effort.)
 
 ### Using script to detect drinking and eating
 
-If you have feeders/drinkers in the cage, ou can detect the contact of the animals with these structures by setting up the coordinates of the contours of the structure in a file named `feeders.txt` (a model can be found at `./LMT/images/`) to be put on the same directory of the database (sqlite file). The original script expects to find the coordinates of 1 drinker and 4 feeders, but you can adapt it easily four your needs by manipulating the script. Each object can have an arbitrary number of coordinates to set up the contour.
+If you have feeders/drinkers in the cage, ou can detect the contact of the animals with these structures by setting up the coordinates of the contours of the structure in a file named `feeders.txt` (a model can be found at `./EMT/images/`) to be put on the same directory of the database (sqlite file). The original script expects to find the coordinates of 1 drinker and 4 feeders, but you can adapt it easily four your needs by manipulating the script. Each object can have an arbitrary number of coordinates to set up the contour.
 
 ### Processing sequences of events
 
@@ -47,7 +47,7 @@ Live Mouse Tracker analysis
 
 lmt-analysis provides all the analysis tools needed to extract information from the tracking performed by [live mouse tracker](https://livemousetracker.org).
 
-![Alt text](./LMT/images/lmt-mice-tracking.jpg?raw=true "live mouse tracker")
+![Alt text](./EMT/images/lmt-mice-tracking.jpg?raw=true "live mouse tracker")
 This view shows the basic output of live mouse tracker, and this package let you get the juice of it :)
 
 With this package, you can
@@ -58,7 +58,7 @@ With this package, you can
 - access your lmt .sqlite database files and query them to get the graph or output you need
 - compute the following events (and create your own)
 
-![Alt text](./LMT/images/events.jpg?raw=true "live mouse tracker events")
+![Alt text](./EMT/images/events.jpg?raw=true "live mouse tracker events")
 
 ### Tutorial
 
diff --git a/lmt-analysis/.idea/.gitignore b/lmt-analysis/.idea/.gitignore
deleted file mode 100644
index 26d33521af10bcc7fd8cea344038eaaeb78d0ef5..0000000000000000000000000000000000000000
--- a/lmt-analysis/.idea/.gitignore
+++ /dev/null
@@ -1,3 +0,0 @@
-# Default ignored files
-/shelf/
-/workspace.xml
diff --git a/lmt-analysis/.idea/codestream.xml b/lmt-analysis/.idea/codestream.xml
deleted file mode 100644
index 4c83dd346335c92a045fd59abf5afcbda116041c..0000000000000000000000000000000000000000
--- a/lmt-analysis/.idea/codestream.xml
+++ /dev/null
@@ -1,6 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<project version="4">
-  <component name="CodeStream">
-    <option name="webViewContext" value="{&quot;chatProviderAccess&quot;:&quot;strict&quot;,&quot;newPostEntryPoint&quot;:&quot;JB Commit Detected&quot;,&quot;currentTeamId&quot;:&quot;6391e6a1d578ac141251fbf7&quot;,&quot;currentStreamId&quot;:&quot;&quot;,&quot;pullRequestCheckoutBranch&quot;:false,&quot;isRepositioning&quot;:false,&quot;onboardStep&quot;:0,&quot;panelStack&quot;:[&quot;landing-redirect&quot;],&quot;hasFocus&quot;:true,&quot;channelFilter&quot;:&quot;all&quot;,&quot;channelsMuteAll&quot;:false,&quot;codemarkFileFilter&quot;:&quot;all&quot;,&quot;codemarkTypeFilter&quot;:&quot;all&quot;,&quot;codemarkTagFilter&quot;:&quot;all&quot;,&quot;codemarkBranchFilter&quot;:&quot;all&quot;,&quot;codemarkAuthorFilter&quot;:&quot;all&quot;,&quot;codemarksFileViewStyle&quot;:&quot;inline&quot;,&quot;codemarksShowArchived&quot;:false,&quot;codemarksShowResolved&quot;:false,&quot;codemarksWrapComments&quot;:false,&quot;showFeedbackSmiley&quot;:true,&quot;route&quot;:{&quot;name&quot;:&quot;newUserEntry&quot;,&quot;params&quot;:{}},&quot;spatialViewShowPRComments&quot;:false,&quot;currentPullRequestNeedsRefresh&quot;:{&quot;needsRefresh&quot;:false,&quot;providerId&quot;:&quot;&quot;,&quot;pullRequestId&quot;:&quot;&quot;},&quot;__teamless__&quot;:{&quot;selectedRegion&quot;:&quot;us&quot;},&quot;sessionStart&quot;:1676036216924,&quot;isFirstPageview&quot;:false,&quot;currentReviewOptions&quot;:{&quot;includeLatestCommit&quot;:true},&quot;currentReviewId&quot;:&quot;&quot;}" />
-  </component>
-</project>
\ No newline at end of file
diff --git a/lmt-analysis/.idea/lmt-analysis.iml b/lmt-analysis/.idea/lmt-analysis.iml
deleted file mode 100644
index a71721b3ab138897c345fc214a2497d147e80fef..0000000000000000000000000000000000000000
--- a/lmt-analysis/.idea/lmt-analysis.iml
+++ /dev/null
@@ -1,18 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<module type="PYTHON_MODULE" version="4">
-  <component name="NewModuleRootManager">
-    <content url="file://$MODULE_DIR$">
-      <sourceFolder url="file://$MODULE_DIR$" isTestSource="false" />
-      <sourceFolder url="file://$MODULE_DIR$/LMT" isTestSource="false" />
-      <sourceFolder url="file://$MODULE_DIR$/LMT/experimental" isTestSource="false" />
-      <sourceFolder url="file://$MODULE_DIR$/LMT/lmtanalysis" isTestSource="false" />
-      <sourceFolder url="file://$MODULE_DIR$/LMT/scripts" isTestSource="false" />
-    </content>
-    <orderEntry type="jdk" jdkName="Python 3.8 (lmt-analysis)" jdkType="Python SDK" />
-    <orderEntry type="sourceFolder" forTests="false" />
-  </component>
-  <component name="PyDocumentationSettings">
-    <option name="format" value="PLAIN" />
-    <option name="myDocStringFormat" value="Plain" />
-  </component>
-</module>
\ No newline at end of file
diff --git a/lmt-analysis/.idea/misc.xml b/lmt-analysis/.idea/misc.xml
deleted file mode 100644
index 8e9e65eb586fe20d60e36e1e606ca681bd56e9f4..0000000000000000000000000000000000000000
--- a/lmt-analysis/.idea/misc.xml
+++ /dev/null
@@ -1,4 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<project version="4">
-  <component name="ProjectRootManager" version="2" project-jdk-name="Python 3.8 (lmt-analysis)" project-jdk-type="Python SDK" />
-</project>
\ No newline at end of file
diff --git a/lmt-analysis/.idea/modules.xml b/lmt-analysis/.idea/modules.xml
deleted file mode 100644
index e3f28c08144a6d93e2e63e701fddee6a9fc47ade..0000000000000000000000000000000000000000
--- a/lmt-analysis/.idea/modules.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<project version="4">
-  <component name="ProjectModuleManager">
-    <modules>
-      <module fileurl="file://$PROJECT_DIR$/.idea/lmt-analysis.iml" filepath="$PROJECT_DIR$/.idea/lmt-analysis.iml" />
-    </modules>
-  </component>
-</project>
\ No newline at end of file
diff --git a/lmt-analysis/.idea/vcs.xml b/lmt-analysis/.idea/vcs.xml
deleted file mode 100644
index 94a25f7f4cb416c083d265558da75d457237d671..0000000000000000000000000000000000000000
--- a/lmt-analysis/.idea/vcs.xml
+++ /dev/null
@@ -1,6 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<project version="4">
-  <component name="VcsDirectoryMappings">
-    <mapping directory="$PROJECT_DIR$" vcs="Git" />
-  </component>
-</project>
\ No newline at end of file
diff --git a/lmt-analysis/.project b/lmt-analysis/.project
deleted file mode 100644
index b66a0922992c802417802fba556f19d78a14e88d..0000000000000000000000000000000000000000
--- a/lmt-analysis/.project
+++ /dev/null
@@ -1,18 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<projectDescription>
-	<name>lmt-analysis</name>
-	<comment></comment>
-	<projects>
-		<project>USV-analysis</project>
-	</projects>
-	<buildSpec>
-		<buildCommand>
-			<name>org.python.pydev.PyDevBuilder</name>
-			<arguments>
-			</arguments>
-		</buildCommand>
-	</buildSpec>
-	<natures>
-		<nature>org.python.pydev.pythonNature</nature>
-	</natures>
-</projectDescription>
diff --git a/lmt-analysis/.pydevproject b/lmt-analysis/.pydevproject
deleted file mode 100644
index f1a73a7b236a9e081199dc2ef75bcb64289bcf39..0000000000000000000000000000000000000000
--- a/lmt-analysis/.pydevproject
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8" standalone="no"?>
-<?eclipse-pydev version="1.0"?><pydev_project>
-        
-    <pydev_property name="org.python.pydev.PYTHON_PROJECT_INTERPRETER">Default</pydev_property>
-        
-    <pydev_property name="org.python.pydev.PYTHON_PROJECT_VERSION">python interpreter</pydev_property>
-    
-    <pydev_pathproperty name="org.python.pydev.PROJECT_SOURCE_PATH">
-        <path>/${PROJECT_DIR_NAME}/LMT</path>
-        <path>/${PROJECT_DIR_NAME}</path>
-    </pydev_pathproperty>
-</pydev_project>
diff --git a/lmt-analysis/.settings/org.eclipse.core.resources.prefs b/lmt-analysis/.settings/org.eclipse.core.resources.prefs
deleted file mode 100644
index 4d92ab903753cf7688263cafd234d13012a2094d..0000000000000000000000000000000000000000
--- a/lmt-analysis/.settings/org.eclipse.core.resources.prefs
+++ /dev/null
@@ -1,5 +0,0 @@
-eclipse.preferences.version=1
-encoding//LMT/lmtanalysis/AnimalType.py=UTF-8
-encoding//LMT/lmtanalysis/Parameters.py=UTF-8
-encoding//LMT/scripts/Novel_Object_Recognition_Test/ComputeActivityHabituationNorTestRedCage.py=UTF-8
-encoding/<project>=UTF-8
diff --git a/lmt-analysis/LMT/scripts/BehaviouralSequences/.idea/inspectionProfiles/profiles_settings.xml b/lmt-analysis/LMT/scripts/BehaviouralSequences/.idea/inspectionProfiles/profiles_settings.xml
deleted file mode 100644
index 105ce2da2d6447d11dfe32bfb846c3d5b199fc99..0000000000000000000000000000000000000000
--- a/lmt-analysis/LMT/scripts/BehaviouralSequences/.idea/inspectionProfiles/profiles_settings.xml
+++ /dev/null
@@ -1,6 +0,0 @@
-<component name="InspectionProjectProfileManager">
-  <settings>
-    <option name="USE_PROJECT_PROFILE" value="false" />
-    <version value="1.0" />
-  </settings>
-</component>
\ No newline at end of file