plateform stringclasses 1
value | repo_name stringlengths 13 113 | name stringlengths 3 74 | ext stringclasses 1
value | path stringlengths 12 229 | size int64 23 843k | source_encoding stringclasses 9
values | md5 stringlengths 32 32 | text stringlengths 23 843k |
|---|---|---|---|---|---|---|---|---|
github | shayo/Kofiko-master | fnLoadForceChoiceNewDesignFile.m | .m | Kofiko-master/Paradigms/TouchParadigms/TouchForceChoice/fnLoadForceChoiceNewDesignFile.m | 29,897 | utf_8 | 6606b02a5e857d5365b50a8f8b93cf3e | function strctDesign = fnLoadForceChoiceNewDesignFile(strDesignXML,iMaxImagesToHoldInMemory)
%% Parse XML file
try
strctXML = fnMyXMLToStruct(strDesignXML,false);
catch
fprintf('Error parsing XML file %s.\n',strDesignXML);
strctDesign = [];
return;
end
if ~isfield(strctXML,'Media')
... |
github | shayo/Kofiko-master | fnParadigmTouchForceChoiceGUI.m | .m | Kofiko-master/Paradigms/TouchParadigms/TouchForceChoice/fnParadigmTouchForceChoiceGUI.m | 15,257 | utf_8 | 19edba5a0ec54d699199166b63b2d0ca | function fnParadigmTouchForceChoiceGUI()
%
% Copyright (c) 2008 Shay Ohayon, California Institute of Technology.
% This file is a part of a free software. you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation (see GPL.txt)
global g_... |
github | shayo/Kofiko-master | fnParadigmTouchScreenCycle.m | .m | Kofiko-master/Paradigms/TouchParadigms/TouchScreenTraining/fnParadigmTouchScreenCycle.m | 9,081 | utf_8 | 27e08eaac8739e28bab5504bbe92a449 | function [strctOutput] = fnParadigmTouchScreenCycle(strctInputs)
%
% Copyright (c) 2008 Shay Ohayon, California Institute of Technology.
% This file is a part of a free software. you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation (... |
github | shayo/Kofiko-master | fnParadigmTargetDetectionDrawCycle.m | .m | Kofiko-master/Paradigms/TargetDetection/fnParadigmTargetDetectionDrawCycle.m | 4,603 | utf_8 | c1200120881869ffb0bde234dbe0ff96 | function fnParadigmTargetDetectionDrawCycle(acInputFromKofiko)
%
% Copyright (c) 2008 Shay Ohayon, California Institute of Technology.
% This file is a part of a free software. you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation (se... |
github | shayo/Kofiko-master | fnParadigmTargetDetectionCallbacks.m | .m | Kofiko-master/Paradigms/TargetDetection/fnParadigmTargetDetectionCallbacks.m | 6,493 | utf_8 | 4dd97e66b9439f1e12ee9ee0b77f163c | function fnParadigmTargetDetectionCallbacks(strCallback,varargin)
%
% Copyright (c) 2008 Shay Ohayon, California Institute of Technology.
% This file is a part of a free software. you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation ... |
github | shayo/Kofiko-master | fnParadigmTargetDetectionCycle.m | .m | Kofiko-master/Paradigms/TargetDetection/fnParadigmTargetDetectionCycle.m | 23,290 | utf_8 | 4706d74de63184367a6951b4269b5047 | function [strctOutput] = fnParadigmTargetDetectionCycle(strctInputs)
%
% Copyright (c) 2008 Shay Ohayon, California Institute of Technology.
% This file is a part of a free software. you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundati... |
github | shayo/Kofiko-master | fnParadigmForcedChoiceCallbacks.m | .m | Kofiko-master/Paradigms/ForcedChoice/fnParadigmForcedChoiceCallbacks.m | 4,850 | utf_8 | 96cf3984f097b89102ed82ae4d355153 | function fnParadigmForcedChoiceCallbacks(strCallback,varargin)
%
% Copyright (c) 2008 Shay Ohayon, California Institute of Technology.
% This file is a part of a free software. you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation (se... |
github | shayo/Kofiko-master | fnParadigmForcedChoiceCycle.m | .m | Kofiko-master/Paradigms/ForcedChoice/fnParadigmForcedChoiceCycle.m | 22,434 | utf_8 | bda70c2659093ee29aec7de1d297b456 | function [strctOutput] = fnParadigmForcedChoiceCycle(strctInputs)
%
% Copyright (c) 2008 Shay Ohayon, California Institute of Technology.
% This file is a part of a free software. you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation ... |
github | shayo/Kofiko-master | fnParadigmForcedChoiceDrawCycle.m | .m | Kofiko-master/Paradigms/ForcedChoice/fnParadigmForcedChoiceDrawCycle.m | 10,886 | utf_8 | d40c7655734626eaee0f6f92a12882f1 | function fnParadigmForcedChoiceDrawCycle(acInputFromKofiko)
%
% Copyright (c) 2008 Shay Ohayon, California Institute of Technology.
% This file is a part of a free software. you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation (see G... |
github | shayo/Kofiko-master | fnParadigmBlockDesignNewCycle.m | .m | Kofiko-master/Paradigms/BlockDesignNew/fnParadigmBlockDesignNewCycle.m | 14,450 | utf_8 | d604ce797023842bce5ca805875bedde | function [strctOutput] = fnParadigmBlockDesignNewCycle(strctInputs)
%
% Copyright (c) 2008 Shay Ohayon, California Institute of Technology.
% This file is a part of a free software. you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundatio... |
github | shayo/Kofiko-master | fnParadigmBlockDesignNewDrawCycle.m | .m | Kofiko-master/Paradigms/BlockDesignNew/fnParadigmBlockDesignNewDrawCycle.m | 6,998 | utf_8 | 5c7b809b91002cb64b19e98325c5be3d | function fnParadigmBlockDesignNewDrawCycle(acInputFromKofiko)
%
% Copyright (c) 2008 Shay Ohayon, California Institute of Technology.
% This file is a part of a free software. you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation (see... |
github | shayo/Kofiko-master | fnPrepareStimuliTimingFromBlockDesign.m | .m | Kofiko-master/Paradigms/BlockDesignNew/fnPrepareStimuliTimingFromBlockDesign.m | 6,678 | utf_8 | 9c44f05281f97568a51f0ac5c237dae4 | function strctRun = fnPrepareStimuliTimingFromBlockDesign()
%
% Copyright (c) 2008 Shay Ohayon, California Institute of Technology.
% This file is a part of a free software. you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation (see G... |
github | shayo/Kofiko-master | fnParadigmBlockDesignNewCallbacks.m | .m | Kofiko-master/Paradigms/BlockDesignNew/fnParadigmBlockDesignNewCallbacks.m | 8,051 | utf_8 | 092950776fefe6d251150da4f03c9aeb | function fnParadigmBlockDesignNewCallbacks(strCallback,varargin)
%
% Copyright (c) 2008 Shay Ohayon, California Institute of Technology.
% This file is a part of a free software. you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation (... |
github | shayo/Kofiko-master | fnParadigmBlockDesignCycle.m | .m | Kofiko-master/Paradigms/BlockDesign/fnParadigmBlockDesignCycle.m | 12,723 | utf_8 | 6f72cd4c2886fbaee10f57b8c18fd8ab | function [strctOutput] = fnParadigmBlockDesignCycle(strctInputs)
%
% Copyright (c) 2008 Shay Ohayon, California Institute of Technology.
% This file is a part of a free software. you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation (... |
github | shayo/Kofiko-master | fnParadigmBlockDesignCallbacks.m | .m | Kofiko-master/Paradigms/BlockDesign/fnParadigmBlockDesignCallbacks.m | 16,977 | utf_8 | eb7eee2743bd22365e87cba2e45eb598 | function fnParadigmBlockDesignCallbacks(strCallback,varargin)
%
% Copyright (c) 2008 Shay Ohayon, California Institute of Technology.
% This file is a part of a free software. you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation (see... |
github | shayo/Kofiko-master | fnParadigmBlockDesignDrawCycle.m | .m | Kofiko-master/Paradigms/BlockDesign/fnParadigmBlockDesignDrawCycle.m | 6,881 | utf_8 | 7010992811f0ee9e5da98eb82d735413 | function fnParadigmBlockDesignDrawCycle(acInputFromKofiko)
%
% Copyright (c) 2008 Shay Ohayon, California Institute of Technology.
% This file is a part of a free software. you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation (see GP... |
github | shayo/Kofiko-master | fnLoadMRIStyleBlockList.m | .m | Kofiko-master/Paradigms/BlockDesign/fnLoadMRIStyleBlockList.m | 2,057 | utf_8 | 60eeb833992271cad2464393a5c853aa | function [acImageIndices, acBlockNames] = fnLoadMRIStyleBlockList(strBlockList)
%
% Copyright (c) 2008 Shay Ohayon, California Institute of Technology.
% This file is a part of a free software. you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Softwa... |
github | shayo/Kofiko-master | fnParadigmFiveDotCycle.m | .m | Kofiko-master/Paradigms/FiveDot/fnParadigmFiveDotCycle.m | 7,776 | utf_8 | 38bb7ee2c88b9961bba8ff325e0e84ca | function [strctOutput] = fnParadigmFiveDotCycle(strctInputs)
%
% Copyright (c) 2008 Shay Ohayon, California Institute of Technology.
% This file is a part of a free software. you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation (see ... |
github | shayo/Kofiko-master | fnInitializeTexturesAux.m | .m | Kofiko-master/Paradigms/CommonFunctions/fnInitializeTexturesAux.m | 3,150 | utf_8 | ece44e88b5b912030d4dfcffdef61c8c | function [ahTextures,a2iTextureSize,abIsMovie,aiApproxNumFrames, afMovieLengthSec,acImages] = fnInitializeTexturesAux(acFileNames, bShowWhileLoading, bPing)
%
% Copyright (c) 2008 Shay Ohayon, California Institute of Technology.
% This file is a part of a free software. you can redistribute it and/or modify
% it under ... |
github | shayo/Kofiko-master | fnPassiveFixationPrepareTrial.m | .m | Kofiko-master/Paradigms/PassiveFixationNew/fnPassiveFixationPrepareTrial.m | 12,418 | utf_8 | 202d06837fad33d966f06d3e53b6795c | function strctTrial = fnPassiveFixationPrepareTrial()
%
% Copyright (c) 2008 Shay Ohayon, California Institute of Technology.
% This file is a part of a free software. you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation (see GPL.txt... |
github | shayo/Kofiko-master | fnParadigmPassiveFixationDrawNew.m | .m | Kofiko-master/Paradigms/PassiveFixationNew/fnParadigmPassiveFixationDrawNew.m | 20,700 | utf_8 | 50a0a354b3e57b811ad1a9a88d652391 | function fnParadigmPassiveFixationDrawNew()
%
% Copyright (c) 2008 Shay Ohayon, California Institute of Technology.
% This file is a part of a free software. you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation (see GPL.txt)
global... |
github | shayo/Kofiko-master | fnParsePassiveFixationDesignMediaFiles.m | .m | Kofiko-master/Paradigms/PassiveFixationNew/fnParsePassiveFixationDesignMediaFiles.m | 15,894 | utf_8 | f830985a216629343c9993546b6f4d6e | function [strctDesign, bStereoRequired] = fnParsePassiveFixationDesignMediaFiles(strDesignXML, bVerifyExistance, bMessages)
strctDesign = [];
bStereoRequired = false;
%% Load the XML
try
fprintf('Parsing XML, please wait...');
strctXML = fnMyXMLToStruct(strDesignXML,false,true);
fprintf('Done!\n');
... |
github | shayo/Kofiko-master | fnParadigmPassiveFixationCallbacksNew.m | .m | Kofiko-master/Paradigms/PassiveFixationNew/fnParadigmPassiveFixationCallbacksNew.m | 23,788 | utf_8 | ac4ed8d97e6c3cb5ef4db04c72b2ce68 | function fnParadigmPassiveFixationCallbacksNew(strCallback,varargin)
%
% Copyright (c) 2008 Shay Ohayon, California Institute of Technology.
% This file is a part of a free software. you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundati... |
github | shayo/Kofiko-master | fnLoadPassiveFixationDesignAux.m | .m | Kofiko-master/Paradigms/PassiveFixationNew/fnLoadPassiveFixationDesignAux.m | 6,013 | utf_8 | 0d97d443dbe1eda86f7af027be069add | function strctDesign = fnLoadPassiveFixationDesignAux(strDesignFile)
%
% Copyright (c) 2008 Shay Ohayon, California Institute of Technology.
% This file is a part of a free software. you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundati... |
github | shayo/Kofiko-master | fnParadigmPassiveFixationDrawCycleNew.m | .m | Kofiko-master/Paradigms/PassiveFixationNew/fnParadigmPassiveFixationDrawCycleNew.m | 27,146 | utf_8 | e3ac6029e5b0463608579a0cdc7cd112 | function fnParadigmPassiveFixationDrawCycleNew(acInputFromKofiko)
%
% Copyright (c) 2008 Shay Ohayon, California Institute of Technology.
% This file is a part of a free software. you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation ... |
github | shayo/Kofiko-master | fnInitializeTexturesAuxPing.m | .m | Kofiko-master/Paradigms/PassiveFixationNew/fnInitializeTexturesAuxPing.m | 2,499 | utf_8 | 22e5da0eab4770df57926dc5fbc4f9ab | function [ahTextures,a2iTextureSize,abIsMovie,aiApproxNumFrames, afMovieLengthSec,acImages] = fnInitializeTexturesAuxPing(acFileNames)
%
% Copyright (c) 2008 Shay Ohayon, California Institute of Technology.
% This file is a part of a free software. you can redistribute it and/or modify
% it under the terms of the GNU G... |
github | shayo/Kofiko-master | fnEntryPoint_OptogeneticsFEF_Behavior_New.m | .m | Kofiko-master/AnalysisScripts/ScriptsForPaperGeneration/fnEntryPoint_OptogeneticsFEF_Behavior_New.m | 46,653 | utf_8 | 873e89dc401a09825b901cad70d6c765 | function fnEntryPoint_OptogeneticsFEF_Behavior_New()
% This block loads the data from disk (or uses the cache if data was
% already loaded
global g_acData
%strPopulationList = 'D:\Data\Doris\Data For Publications\FEF Opto\Bert_Memory_Saccade_Task_All.mat';
% {'D:\Data\Doris\Electrophys\Julien\Optogenetics\120227\RAW\... |
github | shayo/Kofiko-master | fnEntryPoint_OptogeneticsFEF_MappingSaccades.m | .m | Kofiko-master/AnalysisScripts/ScriptsForPaperGeneration/fnEntryPoint_OptogeneticsFEF_MappingSaccades.m | 5,982 | utf_8 | ed63709ce9bc8e08507ff3d961ca81ff | function fnEntryPoint_OptogeneticsFEF_MappingSaccades
fPIX_TO_VISUAL_ANGLE_OldRig = 28.8/800;
fPIX_TO_VISUAL_ANGLE_NewRig = 28.8 / 1920;
strctRawBertChR2 = load('D:\Data\Doris\Electrophys\Bert\Optogenetics\120514\RAW\..\Processed\ElectricalMicrostim\Bert-14-May-2012_14-51-29_ElectricalMicrostim_Channel1.mat');
strctR... |
github | shayo/Kofiko-master | fnReanalyzeSaccadeTrials.m | .m | Kofiko-master/AnalysisScripts/ScriptsForPaperGeneration/fnReanalyzeSaccadeTrials.m | 18,649 | utf_8 | 59b17609f964f9fd8e8e29a62afbe460 | function acTrials=fnReanalyzeSaccadeTrials(acTrials,strRawFolder,strSession,strctSync,strctKofiko,a2fTargetCenter,fFixationRadius,fChoiceRadius,abTrialTypesWithStimulation)
iNumTrials = length(acTrials);
pt2fScreenCenter = strctKofiko.g_strctStimulusServer.m_aiScreenSize(3:4)/2;
strSessionPrefix = [strRawFolder,filese... |
github | shayo/Kofiko-master | fnCollectClassificationImageUnitStats.m | .m | Kofiko-master/AnalysisScripts/OldPipelines/ClassificationImage/fnCollectClassificationImageUnitStats.m | 34,110 | utf_8 | ff957d792f472d466809092e507004c5 | function acUnitsStat = fnCollectClassificationImageUnitStats(strctKofiko, strctPlexon, strctSession,iSessionIter, strctConfig)
%strctStatParams
% Computes various statistics about the recorded units in a given recorded session
%
% Copyright (c) 2008 Shay Ohayon, California Institute of Technology.
% This file is a part... |
github | shayo/Kofiko-master | fnAnalyzeOddOneOutBehaviorStatistics.m | .m | Kofiko-master/AnalysisScripts/OldPipelines/OddOneOut/fnAnalyzeOddOneOutBehaviorStatistics.m | 5,155 | utf_8 | fa2cf2cbc4904c61eade02f9d00cddb0 | function acUnitsStat = fnAnalyzeOddOneOutBehaviorStatistics(strctKofiko,strctConfig)
acUnitsStat = [];
fnWorkerLog('Collecting data for Odd One Out paradigm...');
iParadigmIndex = fnFindParadigmIndex(strctKofiko,'Touch Odd One Out');
if isempty(iParadigmIndex)
return;
end;
acstrNumDesignsUsed = unique(strctKofik... |
github | shayo/Kofiko-master | fnAnalyzeForceChoiceParadigm.m | .m | Kofiko-master/AnalysisScripts/OldPipelines/ForceChoice/fnAnalyzeForceChoiceParadigm.m | 16,749 | utf_8 | 84fc57df66227b6c4db25cd91f68baf6 | function acUnitsStat = fnAnalyzeForceChoiceParadigm(strctKofiko, strctPlexon, strctSession,iSessionIter, strctConfig)
if isfield(strctConfig,'m_acSpecificAnalysis') && ~iscell(strctConfig.m_acSpecificAnalysis)
strctConfig.m_acSpecificAnalysis = {strctConfig.m_acSpecificAnalysis};
end
% This function will analyze ... |
github | shayo/Kofiko-master | fnAnalyzeForceChoiceParadigmNewFormat.m | .m | Kofiko-master/AnalysisScripts/OldPipelines/ForceChoice/fnAnalyzeForceChoiceParadigmNewFormat.m | 19,355 | utf_8 | 9ffe8badc50280e7000d2343d4ac35ac | function acUnitsStat = fnAnalyzeForceChoiceParadigmNewFormat(strctKofiko, strctSync, strctConfig, strctInterval)
if isfield(strctConfig,'m_acSpecificAnalysis') && ~iscell(strctConfig.m_acSpecificAnalysis)
strctConfig.m_acSpecificAnalysis = {strctConfig.m_acSpecificAnalysis};
end
fStartTS_PTB_Kofiko = fnTimeZoneCh... |
github | shayo/Kofiko-master | fnAnalyzeForceChoiceBehaviorStatistics.m | .m | Kofiko-master/AnalysisScripts/OldPipelines/ForceChoice/fnAnalyzeForceChoiceBehaviorStatistics.m | 7,639 | utf_8 | 1da2ca98631782a2a122617af468f1d0 | function acUnitsStat = fnAnalyzeForceChoiceBehaviorStatistics(strctKofiko,strctConfig)
% This function will analyze ALL trials, but will call special analysis
% functions per design.
if isfield(strctConfig,'m_acSpecificAnalysis') && ~iscell(strctConfig.m_acSpecificAnalysis)
strctConfig.m_acSpecificAnalysis = {strc... |
github | shayo/Kofiko-master | fnGetUniqueExperimentCode.m | .m | Kofiko-master/AnalysisScripts/OldPipelines/PassiveFixation/fnGetUniqueExperimentCode.m | 3,873 | utf_8 | e4b2fbc8759194a60674de04621f69e0 | function [a2iCodes,strctCodeIndex, acSubjects,acLists, a2iListToIndex, strctQuality] = fnGetUniqueExperimentCode(acEntries)
% returns a 5xN matrix.
% First column is subject index
% second column is experiment date
% third column is experiment recorded index
% forth column is recorded channel
% fifth column is recorded... |
github | shayo/Kofiko-master | fnGetAccurateStimulusTSusingFlipTime.m | .m | Kofiko-master/AnalysisScripts/OldPipelines/PassiveFixation/fnGetAccurateStimulusTSusingFlipTime.m | 7,654 | utf_8 | 84fdd9383d2f1b35fbe27a3d29282db3 | function [aiStimulusIndex,afModifiedStimulusON_TS_Plexon,afModifiedStimulusOFF_TS_Plexon,bFailed] = ...
fnGetAccurateStimulusTSusingFlipTime(strctKofiko, strctSession,iParadigmIndex)
%
% Copyright (c) 2008 Shay Ohayon, California Institute of Technology.
% This file is a part of a free software. you can redistribut... |
github | shayo/Kofiko-master | fnCollectPassiveFixationUnitStatsAux.m | .m | Kofiko-master/AnalysisScripts/OldPipelines/PassiveFixation/fnCollectPassiveFixationUnitStatsAux.m | 28,045 | utf_8 | 19f6f8597cb69bf8266b5a64bef4d5ee | function acUnitsStat = fnCollectPassiveFixationUnitStatsAux(strctKofiko, strctPlexon, strctSession,iExperimentIndex, strctConfig,iParadigmIndex)
%
% Copyright (c) 2008 Shay Ohayon, California Institute of Technology.
% This file is a part of a free software. you can redistribute it and/or modify
% it under the terms o... |
github | shayo/Kofiko-master | fnFindValidTrials.m | .m | Kofiko-master/AnalysisScripts/OldPipelines/PassiveFixation/fnFindValidTrials.m | 16,506 | utf_8 | 854f1c1f8ebe7b535d494175c3e8f74d | function strctValidTrials = fnFindValidTrials(strctKofiko, strctPlexon, strctSession,iParadigmIndex,fFixationPercThreshold, ...
aiStimulusIndex,afModifiedStimulusON_TS_Plexon,afModifiedStimulusOFF_TS_Plexon,strctSpecialAnalysis)
%
% Copyright (c) 2008 Shay Ohayon, California Institute of Technology.
% This file is ... |
github | shayo/Kofiko-master | fnCollectPassiveFixationUnitStatsAuxMultList.m | .m | Kofiko-master/AnalysisScripts/OldPipelines/PassiveFixation/fnCollectPassiveFixationUnitStatsAuxMultList.m | 29,079 | utf_8 | 5dc4dd53bd7f6084813ff951f23d06d4 | function acUnitsStat = fnCollectPassiveFixationUnitStatsAuxMultList(strctKofiko, strctPlexon, strctSession,iExperimentIndex, strctConfig,iParadigmIndex)
%
% Copyright (c) 2008 Shay Ohayon, California Institute of Technology.
% This file is a part of a free software. you can redistribute it and/or modify
% it under the... |
github | shayo/Kofiko-master | fnGetAccurateStimulusTSusingPhotodiode.m | .m | Kofiko-master/AnalysisScripts/OldPipelines/PassiveFixation/fnGetAccurateStimulusTSusingPhotodiode.m | 12,569 | utf_8 | eb36678dd4c4ff32b40250413d128b6c | function [aiStimulusIndex,afModifiedStimulusON_TS_Plexon,afModifiedStimulusOFF_TS_Plexon] = ...
fnGetAccurateStimulusTSusingPhotodiode(strctKofiko, strctPlexon, strctSession,iParadigmIndex)
%
% Copyright (c) 2008 Shay Ohayon, California Institute of Technology.
% This file is a part of a free software. you can redi... |
github | shayo/Kofiko-master | fnFiringRateNumberOfCorrectRatios.m | .m | Kofiko-master/AnalysisScripts/OldPipelines/PassiveFixation/CBCL/fnFiringRateNumberOfCorrectRatios.m | 2,424 | utf_8 | 93cd1f08f4c7c22599c9ceb3b132fe0d | function [afResFace, afResNonFace,afResFaceMax, afResNonFaceMax,dPrime,fPerecentCorrect,afStdFace,afStdNonFace] =...
fnFiringRateNumberOfCorrectRatios(strctUnit, aiNumCorrectSinhaInFaces,aiNumCorrectSinhaInNonFaces,bNorm,bSubtractBaseline)
afNumRatio = [aiNumCorrectSinhaInFaces; aiNumCorrectSinhaInNonFaces];
abFace... |
github | shayo/Kofiko-master | fnCBCLPopulationAnalysis.m | .m | Kofiko-master/AnalysisScripts/OldPipelines/PassiveFixation/CBCL/fnCBCLPopulationAnalysis.m | 15,294 | utf_8 | f3fdb34e60139c9f71610bf1c1375bb3 | function fnCBCLPopulationAnalysis(acUnits,strctConfig)
if 0
for iUnitIter=1:length(acUnits)
fprintf('%d out of %d\n',iUnitIter,length(acUnits));
strctUnit = acUnits{iUnitIter};
if ~isfield(strctUnit.m_strctStatParams,'m_iAfterMS')
strctUnit.m_strctStatParams.m_iAfterMS = strctUnit.m_strctStatParams... |
github | shayo/Kofiko-master | fnMetaAnalysis.m | .m | Kofiko-master/AnalysisScripts/OldPipelines/PassiveFixation/MetaAnalysis_CBCL_VJ_Sinha_FOB/fnMetaAnalysis.m | 11,215 | utf_8 | e7b44be2c10601b4b04fccb358350231 | function fnMetaAnalysis(acEntries,strctConfig,handles)
iNumEntries = length(acEntries);
acEntriesIDs = cell(0);
aiEntryToUnitIndex = zeros(1,iNumEntries);
astrctUnits = [];
iUnitIndex = 0;
for iIter=1:iNumEntries
strctEntry = acEntries{iIter};
strUniqueID = [strctEntry.m_strRecordedTimeDate, ' Exp ',num2str(str... |
github | shayo/Kofiko-master | fnFOB_Inv_PopulationAnalysis.m | .m | Kofiko-master/AnalysisScripts/OldPipelines/PassiveFixation/ContrastInversion/fnFOB_Inv_PopulationAnalysis.m | 14,377 | utf_8 | c2bfdf3811f1210467a4a164a1df83b0 | function fnFOB_Inv_PopulationAnalysis(acUnits,strctConfig)
[a2iCodes,strctCodeIndex, acSubjects,acLists, a2iListToIndex, strctQuality] = fnGetUniqueExperimentCode(acUnits);
iListIndexInsEqHist = find(ismember(acLists,'StandardFOB_v4_Inv_Cropped_HistEq'));
iListIndexFOB = find(ismember(acLists,'StandardFOB_v5_Inv_Ed... |
github | shayo/Kofiko-master | fnPopulationInvertedContrastControl.m | .m | Kofiko-master/AnalysisScripts/OldPipelines/PassiveFixation/ContrastInversion/fnPopulationInvertedContrastControl.m | 30,314 | utf_8 | 15212f8d9f2ca1a4f722e3a5d7a3d041 | function fnPopulationInvertedContrastControl(acEntries,strctConfig)
% This script will accumulate the statistics from several different lists.
% It will display the PSTH for faces, cropped faces, cropped histogram
% equated faces, cropped external contours, and their inverted contrast
% versions.
%
% Questions :
% 1.... |
github | shayo/Kofiko-master | fnSinhaPopulationAnalysisJustGraph.m | .m | Kofiko-master/AnalysisScripts/OldPipelines/PassiveFixation/Sinha/fnSinhaPopulationAnalysisJustGraph.m | 67,323 | utf_8 | 6098d27d89dd0acf34ce7bb0a4af0109 | function fnSinhaPopulationAnalysisJustGraph(acUnits,strctConfig)
for iUnitIter=1:length(acUnits)
strctUnit = acUnits{iUnitIter};
aiPeriStimulusRangeMS = strctUnit.m_strctStatParams.m_iBeforeMS:strctUnit.m_strctStatParams.m_iAfterMS;
iStartAvg = find(aiPeriStimulusRangeMS>=strctUnit.m_strctStatParams.m_iStartAvgMS... |
github | shayo/Kofiko-master | fnSinhaEdgePopulationAnalysis.m | .m | Kofiko-master/AnalysisScripts/OldPipelines/PassiveFixation/Sinha/fnSinhaEdgePopulationAnalysis.m | 17,053 | utf_8 | f9fa96c69d7d42ee5c3cb395c0a371bd | function fnSinhaEdgePopulationAnalysis(acUnits,strctConfig)
%% Face Selectivity Index
[aiFaceSelectivityIndex] = fnComputeFaceSelecitivyIndex(acUnits);
aiSubSet=1:length(acUnits);
[afH,afX]= hist(aiFaceSelectivityIndex,-1:0.1:1);
figure(1);
clf
bar(afX,afH);
hold on;
plot([0.3 0.3],[0 max(afH)],'g');
xlabel('Face Sel... |
github | shayo/Kofiko-master | fnSinhaBestStimulusPopulation.m | .m | Kofiko-master/AnalysisScripts/OldPipelines/PassiveFixation/Sinha/fnSinhaBestStimulusPopulation.m | 58,009 | utf_8 | 6bea299275d04fdbbe957c52703dd5c1 | function fnSinhaPopulationAnalysis(acUnits,strctConfig)
%%
warning off
for k=1:15
try
close(k)
catch
end
end
warning on
%% Face Selectivity Index
bUseStandardParamOnly = true;
bAnalyzeOnlySubSet = true;
fQuality = 0.5; %1.2
aiNumSpikes = zeros(1,length(acUnits));
afMUA = zeros(1,length(acUnits))... |
github | shayo/Kofiko-master | fnDisplaySinhaAnalysis.m | .m | Kofiko-master/AnalysisScripts/OldPipelines/PassiveFixation/Sinha/fnDisplaySinhaAnalysis.m | 5,910 | utf_8 | 31f9652f8b1a0b0dac387979b346fbcd | function fnDisplaySinhaAnalysis(ahPanels, strctUnit)
%
% Copyright (c) 2008 Shay Ohayon, California Institute of Technology.
% This file is a part of a free software. you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation (see GPL.txt)... |
github | shayo/Kofiko-master | fnSinhaAnalysis.m | .m | Kofiko-master/AnalysisScripts/OldPipelines/PassiveFixation/Sinha/fnSinhaAnalysis.m | 19,488 | utf_8 | f1b559ebb3472a90933d5abb1b5ab8e0 | function strctUnit = fnSinhaAnalysis(strctUnit,iStimOffset,iCatOffset,a2iPerm,acPartNames,a2iCorrectPairALargerB,strctConfig)
% What type of analysis do we want here?
acPlot0 = fnComputeFaceSelecitivyIndex(strctUnit);
% 1. Part- Intensity plot, Part-Part intensity plot
acPlot1 = fnGeneratePartIntensityPlot(a2iPerm... |
github | shayo/Kofiko-master | fnSinhaProfilePopulationAnalysis.m | .m | Kofiko-master/AnalysisScripts/OldPipelines/PassiveFixation/Sinha/fnSinhaProfilePopulationAnalysis.m | 14,043 | utf_8 | 2bdd0ab74ad4426bf61352bfe84e7e7c | function fnSinhaProfilePopulationAnalysis(acUnits,strctConfig)
%% Face Selectivity Index
bUseStandardParamOnly = true;
bAnalyzeOnlySubSet = true;
aiNumSpikes = zeros(1,length(acUnits));
for k=1:length(acUnits)
aiNumSpikes(k) = length(acUnits{k}.m_afSpikeTimes);
end
acUnits = acUnits(aiNumSpikes > 500);
[aiFaceSel... |
github | shayo/Kofiko-master | fnSinhaPopulationAnalysisTimeToPeak.m | .m | Kofiko-master/AnalysisScripts/OldPipelines/PassiveFixation/Sinha/fnSinhaPopulationAnalysisTimeToPeak.m | 87,389 | utf_8 | 23ebc5f59b0083b31527c91694bc9d85 | function fnSinhaPopulationAnalysis(acUnits,strctConfig)
%%
warning off
for j=0:100:600
for k=1:15
try
close(k+j)
catch
end
end
end
warning on
%% Face Selectivity Index
bUseStandardParamOnly = true;
bAnalyzeOnlySubSet = true;
fQuality = 0.5; %1.2
fMUAThres = 3.5;
aiNumSpikes = zeros(1,length(acUn... |
github | shayo/Kofiko-master | fnSinhaPopulationAnalysis.m | .m | Kofiko-master/AnalysisScripts/OldPipelines/PassiveFixation/Sinha/fnSinhaPopulationAnalysis.m | 112,056 | utf_8 | 5f49359f180f4a93854eae429daad942 | function fnSinhaPopulationAnalysis(acUnits,strctConfig)
%% statistics for Winrich..
for k=1:length(acUnits)
afMeanFaceRes(k) = mean(acUnits{k}.m_afAvgFirintRate_Stimulus(1:16));
afMeanObjRes(k) = mean(acUnits{k}.m_afAvgFirintRate_Stimulus(17:96));
afMaxSinha(k) = max(acUnits{k}.m_afAvgFirintRate_Stimul... |
github | shayo/Kofiko-master | fnAnalyzeTargetDetectionBehaviorStatistics.m | .m | Kofiko-master/AnalysisScripts/OldPipelines/TargetDetection/fnAnalyzeTargetDetectionBehaviorStatistics.m | 7,269 | utf_8 | b0d5f5d71b20f9cfecef13a1170df25e | function acUnitsStat = fnAnalyzeTargetDetectionBehaviorStatistics(strctKofiko,strctConfig)
if isfield(strctConfig,'m_acSpecificAnalysis') && ~iscell(strctConfig.m_acSpecificAnalysis)
strctConfig.m_acSpecificAnalysis = {strctConfig.m_acSpecificAnalysis};
end
iParadigmIndex = fnFindParadigmIndex(strctKofiko, 'Targe... |
github | shayo/Kofiko-master | fnPlotExperiment.m | .m | Kofiko-master/AnalysisScripts/OldPipelines/BlockDesign/fnPlotExperiment.m | 3,325 | utf_8 | 2ad08cc42ecd210a82f5973986018738 | function [strctUnit, bOverride] = fnPlotExperiment(strctUnit)
%%
% Plexon time
bOverride = true;
if ~strcmp(strctUnit.m_strParadigm,'Passive Fixation')
return;
end;
iSelectedStimulus = 12;
hFig = figure;
clf;
hold on;
title(sprintf('%s Exp %d, Ch %d, Unit %d',...
strctUnit.m_strRecordedTimeDate,strctUnit.m_iR... |
github | shayo/Kofiko-master | fnPipelinePassiveFixation_v2.m | .m | Kofiko-master/AnalysisScripts/Pipelines/PassiveFixationV2/fnPipelinePassiveFixation_v2.m | 8,132 | utf_8 | 64eeaf22de234c891bbe5596a0daffe2 | function fnPipelinePassiveFixation_v2(strctInputs)
clear global g_acDesignCache
strDataRootFolder = strctInputs.m_strDataRootFolder;
strConfigFolder = strctInputs.m_strConfigFolder;
strSession = strctInputs.m_strSession;
if strDataRootFolder(end) ~= filesep()
strDataRootFolder(end+1) = filesep();
end;
fn... |
github | shayo/Kofiko-master | fnPipelinePassiveFixation_v3.m | .m | Kofiko-master/AnalysisScripts/Pipelines/PassiveFixationV2/fnPipelinePassiveFixation_v3.m | 9,542 | utf_8 | 4f915e477f3554dc4eccf8a4f47d92c3 | function fnPipelinePassiveFixation_v3(strctInputs)
clear global g_acDesignCache
strDataRootFolder = strctInputs.m_strDataRootFolder;
strConfigFolder = strctInputs.m_strConfigFolder;
strSession = strctInputs.m_strSession;
if strDataRootFolder(end) ~= filesep()
strDataRootFolder(end+1) = filesep();
end;
fn... |
github | shayo/Kofiko-master | fnPipelinePassiveFixation_v4.m | .m | Kofiko-master/AnalysisScripts/Pipelines/PassiveFixationV2/fnPipelinePassiveFixation_v4.m | 9,593 | utf_8 | 83027757ff66354903b52444f0563eee | function fnPipelinePassiveFixation_v3(strctInputs)
clear global g_acDesignCache
strDataRootFolder = strctInputs.m_strDataRootFolder;
strConfigFolder = strctInputs.m_strConfigFolder;
strSession = strctInputs.m_strSession;
if strDataRootFolder(end) ~= filesep()
strDataRootFolder(end+1) = filesep();
end;
fn... |
github | shayo/Kofiko-master | fnPipelineOptogeneticsMicrostim_v1.m | .m | Kofiko-master/AnalysisScripts/Pipelines/OptoeneticsMicrostim/fnPipelineOptogeneticsMicrostim_v1.m | 18,847 | utf_8 | 49c7440ecfc5364219ca59c6c74ac85d | function fnPipelineOptogeneticsMicrostim_v1(strctInputs)
clear global g_acDesignCache
strDataRootFolder = strctInputs.m_strDataRootFolder;
strConfigFolder = strctInputs.m_strConfigFolder;
strSession = strctInputs.m_strSession;
if strDataRootFolder(end) ~= filesep()
strDataRootFolder(end+1) = filesep();
e... |
github | shayo/Kofiko-master | fnOpticalStimulationEyeMovementPopulationAnalysisControl.m | .m | Kofiko-master/AnalysisScripts/Pipelines/OptoeneticsMicrostim/fnOpticalStimulationEyeMovementPopulationAnalysisControl.m | 8,774 | utf_8 | 476d9ea52ae468001c1a07d5d5cb375d | function fnOpticalStimulationEyeMovementPopulationAnalysisControl(acDataEntries)
%global g_acDataCache
% This block loads the data from disk (or uses the cache if data was
% already loaded
% It is comments out because I can no longer hold all data in memory :(
% if ~isempty(g_acDataCache) && length(g_acDataCache) == le... |
github | shayo/Kofiko-master | fnPipelineOptogeneticsMicrostim_v2.m | .m | Kofiko-master/AnalysisScripts/Pipelines/OptoeneticsMicrostim/fnPipelineOptogeneticsMicrostim_v2.m | 18,409 | utf_8 | 380259624fff14a25fcac85c4984a554 | function fnPipelineOptogeneticsMicrostim_v2(strctInputs)
clear global g_acDesignCache
strDataRootFolder = strctInputs.m_strDataRootFolder;
strConfigFolder = strctInputs.m_strConfigFolder;
strSession = strctInputs.m_strSession;
if strDataRootFolder(end) ~= filesep()
strDataRootFolder(end+1) = filesep();
e... |
github | shayo/Kofiko-master | fnStandardTrainAnalysis.m | .m | Kofiko-master/AnalysisScripts/Pipelines/OptoeneticsMicrostim/fnStandardTrainAnalysis.m | 27,213 | utf_8 | 2687ba5bb970227d2cb065ce72858f80 | function fnStandardTrainAnalysis(strSubject, strTimeDate,strctChannelInfo,strctUnitInterval, strctAdvancerInformation, strTrainFile,strTrainFile2,strAnalogChannelFile,strOutputFolder,strOpsin,...
strEyeXFile,strEyeYFile,strctKofiko,strctSync)
if isempty(strctUnitInterval.m_afTimestamps)
return;
end;
[strctTra... |
github | shayo/Kofiko-master | fnStandardTrainAnalysis_v2.m | .m | Kofiko-master/AnalysisScripts/Pipelines/OptoeneticsMicrostim/fnStandardTrainAnalysis_v2.m | 12,508 | utf_8 | 0d3a55ad8ee4f880e3008c32d701d271 | function fnStandardTrainAnalysis_v2(strSubject, strTimeDate,strctChannelInfo,strctUnitInterval, strctAdvancerInformation, strTrainFile,strAnalogChannelFile,strOutputFolder,strOpsin,...
strEyeXFile,strEyeYFile,strctKofiko,strctSync)
if isempty(strctUnitInterval.m_afTimestamps)
return;
end;
[strctTrain, afTrain... |
github | shayo/Kofiko-master | fnTouchForceChoiceBehaviorAnalysis.m | .m | Kofiko-master/AnalysisScripts/Pipelines/TouchForceChoice/fnTouchForceChoiceBehaviorAnalysis.m | 14,340 | utf_8 | 4d36a5d490e80639282709cd1d76388d | function fnTouchForceChoiceBehaviorAnalysis(strctKofiko,strRawFolder,strSession,strctSync, strOutputFolder)
%
strSubject = strctKofiko.g_strctAppConfig.m_strctSubject.m_strName;
strTimeDate = strctKofiko.g_strctAppConfig.m_strTimeDate;
strTimeDate(strTimeDate == ':') = '-';
strTimeDate(strTimeDate == ' ') = '_';
acPar... |
github | shayo/Kofiko-master | fnPipelineTouchForceChoice_v1.m | .m | Kofiko-master/AnalysisScripts/Pipelines/TouchForceChoice/fnPipelineTouchForceChoice_v1.m | 7,304 | utf_8 | e21d18198bb29855818c3798b1965a3d | function fnPipelineTouchForceChoice_v1(strctInputs)
strDataRootFolder = strctInputs.m_strDataRootFolder;
strConfigFolder = strctInputs.m_strConfigFolder;
strSession = strctInputs.m_strSession;
if strDataRootFolder(end) ~= filesep()
strDataRootFolder(end+1) = filesep();
end;
fnWorkerLog('Starting force ch... |
github | shayo/Kofiko-master | fnDefaultForceChoiceNeuralDisplay.m | .m | Kofiko-master/AnalysisScripts/Pipelines/TouchForceChoice/fnDefaultForceChoiceNeuralDisplay.m | 5,117 | utf_8 | dbc4d794279db525b5d7f52069c2eb50 | function fnDefaultForceChoiceNeuralDisplay(ahPanels, strctUnit)
a2cTrialsOfInterest= ...
{'SaccadeTaskRight','MicrostimSaccadeTaskRight';... %1
'SaccadeTaskLeft','MicrostimSaccadeTaskLeft';... %2
'SaccadeTaskUp','MicrostimSaccadeTaskUp';... ... |
github | shayo/Kofiko-master | fnPipelineTouchForceChoice_v2.m | .m | Kofiko-master/AnalysisScripts/Pipelines/TouchForceChoice/fnPipelineTouchForceChoice_v2.m | 2,352 | utf_8 | 118903b95cbb66a21cd8d156c5e13d58 | function fnPipelineTouchForceChoice_v2(strctInputs)
strDataRootFolder = strctInputs.m_strDataRootFolder;
strConfigFolder = strctInputs.m_strConfigFolder;
strSession = strctInputs.m_strSession;
if strDataRootFolder(end) ~= filesep()
strDataRootFolder(end+1) = filesep();
end;
fnWorkerLog('Starting force ch... |
github | shayo/Kofiko-master | fnOpticalStimulationBehaviorPopulationAnalysis.m | .m | Kofiko-master/AnalysisScripts/Pipelines/TouchForceChoice/PopulationScripts/fnOpticalStimulationBehaviorPopulationAnalysis.m | 19,310 | utf_8 | e29dc00689885734dca500fa8212bdb5 | function fnOpticalStimulationBehaviorPopulationAnalysis(acDataEntries)
%global g_acDataCache
% This block loads the data from disk (or uses the cache if data was
% already loaded
% It is comments out because I can no longer hold all data in memory :(
% if ~isempty(g_acDataCache) && length(g_acDataCache) == length(acDat... |
github | shayo/Kofiko-master | fnOpticalStimulationEyeMovementPopulationAnalysis.m | .m | Kofiko-master/AnalysisScripts/Pipelines/TouchForceChoice/PopulationScripts/fnOpticalStimulationEyeMovementPopulationAnalysis.m | 9,977 | utf_8 | e3cca2e236bfd561b563e831df32b54d | function fnOpticalStimulationEyeMovementPopulationAnalysis(acDataEntries)
%global g_acDataCache
% This block loads the data from disk (or uses the cache if data was
% already loaded
% It is comments out because I can no longer hold all data in memory :(
% if ~isempty(g_acDataCache) && length(g_acDataCache) == length(ac... |
github | shayo/Kofiko-master | fnTouchForceChoicePopulationBehavior.m | .m | Kofiko-master/AnalysisScripts/Pipelines/TouchForceChoice/PopulationScripts/fnTouchForceChoicePopulationBehavior.m | 10,735 | utf_8 | 427771aa6c7da556bd121c6de2868a8c | function fnTouchForceChoicePopulationBehavior(acDataEntries)
global g_acDataCache
% This block loads the data from disk (or uses the cache if data was
% already loaded
if ~isempty(g_acDataCache) && length(g_acDataCache) == length(acDataEntries)
fprintf('Loading Data from cache...');
acData = g_acDataCache;
... |
github | shayo/Kofiko-master | fnSaccadeMemoryTaskAnalysis.m | .m | Kofiko-master/AnalysisScripts/Pipelines/TouchForceChoice/SaccadeMemoryTaskSpecialScript/fnSaccadeMemoryTaskAnalysis.m | 19,194 | utf_8 | 22cc7739c5dc66970cf1890eaa2f12b0 | function fnSaccadeMemoryTaskAnalysis(strctKofiko,strRawFolder,strSession,strctSync, strOutputFolder)
%
strSubject = strctKofiko.g_strctAppConfig.m_strctSubject.m_strName;
strTimeDate = strctKofiko.g_strctAppConfig.m_strTimeDate;
strTimeDate(strTimeDate == ':') = '-';
strTimeDate(strTimeDate == ' ') = '_';
acParadigms ... |
github | shayo/Kofiko-master | fnMidSaccadeStimSpecialScript.m | .m | Kofiko-master/AnalysisScripts/Pipelines/TouchForceChoice/MidSaccadeStimSpecialScript/fnMidSaccadeStimSpecialScript.m | 18,186 | utf_8 | c3c8f5c779f9bef447395dd79096ee39 | function fnSaccadeMemoryTaskAnalysis(strctKofiko,strRawFolder,strSession,strctSync, strOutputFolder)
%
strSubject = strctKofiko.g_strctAppConfig.m_strctSubject.m_strName;
strTimeDate = strctKofiko.g_strctAppConfig.m_strTimeDate;
strTimeDate(strTimeDate == ':') = '-';
strTimeDate(strTimeDate == ' ') = '_';
acParadigms ... |
github | shayo/Kofiko-master | fnPipelineForceChoice_v2.m | .m | Kofiko-master/AnalysisScripts/Pipelines/ForceChoice/fnPipelineForceChoice_v2.m | 10,024 | utf_8 | 1edd469b7fdc03c8ee04a3a8c5ec4f89 | function fnPipelineForceChoice_v2(strctInputs)
strDataRootFolder = strctInputs.m_strDataRootFolder;
strConfigFolder = strctInputs.m_strConfigFolder;
strSession = strctInputs.m_strSession;
if strDataRootFolder(end) ~= filesep()
strDataRootFolder(end+1) = filesep();
end;
fnWorkerLog('Starting force choice ... |
github | shayo/Kofiko-master | fnCollectForceChoiceStats.m | .m | Kofiko-master/AnalysisScripts/Pipelines/ForceChoice/fnCollectForceChoiceStats.m | 20,701 | utf_8 | 33b5e0f9c82aaca4d7340fab85e08b18 | function acUnitsStat = fnCollectForceChoiceStats(strRawFolder,strSession,strctKofiko, strctSync, strctConfig, strctInterval, strOutputFolder,strTrainFile1,strTrainFile2)
% Computes various statistics about the recorded units in a given recorded session
%
% Copyright (c) 2008 Shay Ohayon, California Institute of Technol... |
github | shayo/Kofiko-master | fnPipelineForceChoice_v3_Saccades.m | .m | Kofiko-master/AnalysisScripts/Pipelines/ForceChoice/fnPipelineForceChoice_v3_Saccades.m | 10,698 | utf_8 | 30040f561716c40db509a247807ddea8 | function fnPipelineForceChoice_v3_Saccades(strctInputs)
strDataRootFolder = strctInputs.m_strDataRootFolder;
strConfigFolder = strctInputs.m_strConfigFolder;
strSession = strctInputs.m_strSession;
if strDataRootFolder(end) ~= filesep()
strDataRootFolder(end+1) = filesep();
end;
fnWorkerLog('Starting forc... |
github | shayo/Kofiko-master | fnCollectForceChoiceStats_Saccades.m | .m | Kofiko-master/AnalysisScripts/Pipelines/ForceChoice/fnCollectForceChoiceStats_Saccades.m | 18,791 | utf_8 | 28d3aee3ca24223c644c46852a5a4df2 | function acUnitsStat = fnCollectForceChoiceStats_Saccades(strctKofiko, strctSync, strctConfig, strctInterval, strOutputFolder)
% Computes various statistics about the recorded units in a given recorded session
%
% Copyright (c) 2008 Shay Ohayon, California Institute of Technology.
% This file is a part of a free softwa... |
github | shayo/Kofiko-master | fnPipelineElectricalMicrostim_v4.m | .m | Kofiko-master/AnalysisScripts/Pipelines/ElectricalMicrostim/fnPipelineElectricalMicrostim_v4.m | 29,551 | utf_8 | bd7816985117006b70b741933e3efdf2 | function fnPipelineElectricalMicrostim_v4(strctInputs)
% Used for detecting antidromic spikes
clear global g_acDesignCache
strDataRootFolder = strctInputs.m_strDataRootFolder;
strConfigFolder = strctInputs.m_strConfigFolder;
strSession = strctInputs.m_strSession;
if strDataRootFolder(end) ~= filesep()
st... |
github | shayo/Kofiko-master | fnPipelineElectricalMicrostim_v2.m | .m | Kofiko-master/AnalysisScripts/Pipelines/ElectricalMicrostim/fnPipelineElectricalMicrostim_v2.m | 22,516 | utf_8 | eddcd3b637903eb8928bef39dc4830ab | function fnPipelineElectricalMicrostim_v2(strctInputs)
clear global g_acDesignCache
strDataRootFolder = strctInputs.m_strDataRootFolder;
strConfigFolder = strctInputs.m_strConfigFolder;
strSession = strctInputs.m_strSession;
if strDataRootFolder(end) ~= filesep()
strDataRootFolder(end+1) = filesep();
end... |
github | shayo/Kofiko-master | fnPipelineElectricalMicrostim_v3.m | .m | Kofiko-master/AnalysisScripts/Pipelines/ElectricalMicrostim/fnPipelineElectricalMicrostim_v3.m | 20,602 | utf_8 | 4771ea7e9d0f1df4651a593e0a75ffce | function fnPipelineElectricalMicrostim_v3(strctInputs)
clear global g_acDesignCache
strDataRootFolder = strctInputs.m_strDataRootFolder;
strConfigFolder = strctInputs.m_strConfigFolder;
strSession = strctInputs.m_strSession;
if strDataRootFolder(end) ~= filesep()
strDataRootFolder(end+1) = filesep();
end... |
github | shayo/Kofiko-master | fnPipelineElectricalMicrostim_v1.m | .m | Kofiko-master/AnalysisScripts/Pipelines/ElectricalMicrostim/fnPipelineElectricalMicrostim_v1.m | 12,888 | utf_8 | 035469bbfb9b2ac84d4f8b5ae5f45fd9 | function fnPipelineElectricalMicrostim_v1(strctInputs)
clear global g_acDesignCache
strDataRootFolder = strctInputs.m_strDataRootFolder;
strConfigFolder = strctInputs.m_strConfigFolder;
strSession = strctInputs.m_strSession;
if strDataRootFolder(end) ~= filesep()
strDataRootFolder(end+1) = filesep();
end... |
github | shayo/Kofiko-master | fnReadDumpAnalogFile.m | .m | Kofiko-master/AnalysisScripts/Pipelines/Common/fnReadDumpAnalogFile.m | 8,674 | utf_8 | d321e05bb9481d26f83714db0968b413 | function [strctAnalog, afTime] = fnReadDumpAnalogFile(strInputFile, varargin)
bReadHeaderOnly = false;
bReadInterval = false;
iParamCount = 0;
strReadMode = 'Normal';
while iParamCount < length(varargin)
iParamCount=iParamCount+1;
switch lower(varargin{iParamCount})
case 'readheaderonly'
bRe... |
github | shayo/Kofiko-master | fnTimeZoneChange.m | .m | Kofiko-master/AnalysisScripts/Pipelines/Common/fnTimeZoneChange.m | 7,049 | utf_8 | 5f7619e7ba59c22374a37c19cd80fc29 | function afNewTS = fnTimeZoneChange(afTS, strctSync, strZoneFrom, strZoneTo)
switch lower(strZoneFrom)
case 'kofiko'
switch lower(strZoneTo)
case 'plexon'
% Kofiko To Plexon
afNewTS = fnApplyTransform(afTS, strctSync.m_strctKofikoToPlexon);
case 'stats... |
github | shayo/Kofiko-master | fnReadDumpSpikeFile.m | .m | Kofiko-master/AnalysisScripts/Pipelines/Common/fnReadDumpSpikeFile.m | 6,406 | utf_8 | e6959c1620daabfd24fda782cc409c8e | function [astrctUnits,strctChannelInfo] = fnReadDumpSpikeFile(strInputFile, varargin)
strctOpt=fnParseParams(varargin{:});
hFileID = fopen(strInputFile,'rb+');
strHeader = fread(hFileID, 13,'char=>char'); % Identifier...
if all(strHeader' == 'KOFIKO_v1.01S')
astrctUnits = fnRead101Version(hFileID,strctOpt);
st... |
github | shayo/Kofiko-master | parseXML.m | .m | Kofiko-master/AnalysisScripts/OpenEphys/parseXML.m | 1,992 | utf_8 | 8a71dd3adffd7429abb78309d5e4a29b | function theStruct = parseXML(filename)
% PARSEXML Convert XML file to a MATLAB structure.
try
tree = xmlread(filename);
catch
error('Failed to read XML file %s.',filename);
end
% Recurse over child nodes. This could run into problems
% with very deeply nested trees.
theStruct = parseChildNodes(tree);
... |
github | shayo/Kofiko-master | load_events_version_0_31.m | .m | Kofiko-master/AnalysisScripts/OpenEphys/load_events_version_0_31.m | 21,152 | utf_8 | 4558a06b1f9a4e87e010eb583d85d3d6 | function [strctDataFromEvents] = load_events_version_0_31(filename, verbose)
%
% [data, timestamps, info] = load_open_ephys_data(filename)
%
% parses the event file saved by PSTH module
%
% Inputs:
%
% filename: path to file
%
%
% Outputs:
%
%
% strctDataFromEvents, contains the following fields:
%
% strct... |
github | shayo/Kofiko-master | fnTimeZoneChangeOpenEphys.m | .m | Kofiko-master/AnalysisScripts/OpenEphys/fnTimeZoneChangeOpenEphys.m | 1,898 | utf_8 | f8de7b951a6adeff4ac98b57498cb39d | function targetTS = fnTimeZoneChangeOpenEphys(strctSync, strFrom, strTo, sourceTS)
if strcmpi(strFrom,'Software')
if strcmpi(strTo,'Hardware')
targetTS = fnTimeZoneChangeOpenEphysAux(strctSync.strctSoftwareHardwareSync, sourceTS);
elseif strcmpi(strTo,'Kofiko')
targetTS = fnTimeZoneChangeOpenEp... |
github | shayo/Kofiko-master | load_continuous_data.m | .m | Kofiko-master/AnalysisScripts/OpenEphys/load_continuous_data.m | 4,647 | utf_8 | 3e2b3deb57c3343e7be0d61bbc1d8143 | function [data, timestamps, info] = load_continuous_data(filename)
if ~exist(filename,'file')
fprintf('File does not exit!\n');
data = [];
timestamps = [];
info = [];
return
end
fid = fopen(filename,'rb+');
filesize = getfilesize(fid);
index = 0;
NUM_HEADER_BYTES = 1024;
SAMPLES_PER_RECORD = 1024;
... |
github | shayo/Kofiko-master | parseXMLstructure.m | .m | Kofiko-master/AnalysisScripts/OpenEphys/parseXMLstructure.m | 1,441 | utf_8 | a32b2d9d84fe865d1df6010a6416155a | function allFields = parseXMLstructure(node)
% make the tree "flat" and return the path to each leaf.
allFields = parseXMLstructureRecursive(node, node.Name,cell(0));
function allFields = parseXMLstructureRecursive(node, rootName,allFields)
if length(node.Children) == 1 && strcmp(node.Children.Name,'#text')
% lea... |
github | shayo/Kofiko-master | SpikeDetectThresholdSelectGUI.m | .m | Kofiko-master/AnalysisScripts/OpenEphys/SpikeDetectThresholdSelectGUI.m | 4,437 | utf_8 | fc4e7021340f29d46a288a435b3edfec | function varargout = SpikeDetectThresholdSelectGUI(varargin)
% SPIKEDETECTTHRESHOLDSELECTGUI MATLAB code for SpikeDetectThresholdSelectGUI.fig
% SPIKEDETECTTHRESHOLDSELECTGUI, by itself, creates a new SPIKEDETECTTHRESHOLDSELECTGUI or raises the existing
% singleton*.
%
% H = SPIKEDETECTTHRESHOLDSELECTGUI... |
github | shayo/Kofiko-master | patchline.m | .m | Kofiko-master/AnalysisScripts/Common/patchline.m | 3,694 | utf_8 | 7e03ec713dc3b5ed750f273f9a944d50 | function p = patchline(xs,ys,varargin)
% Plot lines as patches (efficiently)
%
% SYNTAX:
% patchline(xs,ys)
% patchline(xs,ys,zs,...)
% patchline(xs,ys,zs,'PropertyName',propertyvalue,...)
% p = patchline(...)
%
% PROPERTIES:
% Accepts all parameter-values accepted by PATCH.
%
% DESCRIPTION:
% ... |
github | shayo/Kofiko-master | arrow.m | .m | Kofiko-master/AnalysisScripts/Common/arrow.m | 55,316 | utf_8 | a9fba6cb870e440f70d88c6a4849cb63 | function [h,yy,zz] = arrow(varargin)
% ARROW Draw a line with an arrowhead.
%
% ARROW(Start,Stop) draws a line with an arrow from Start to Stop (points
% should be vectors of length 2 or 3, or matrices with 2 or 3
% columns), and returns the graphics handle of the arrow(s).
%
% ARROW uses the mouse (cl... |
github | shayo/Kofiko-master | xml2struct.m | .m | Kofiko-master/AnalysisScripts/Common/xml2struct.m | 2,163 | utf_8 | 89d5349cc31971f9e87b90624eac5df5 | function theStruct = xml2struct(filename)
% XML2STRUCT Convert an XML file into a MATLAB structure.
% Copyright 2003-2007 The MathWorks, Inc.
% $Revision: 1.1.4.3 $ $Date: 2007/06/04 21:04:28 $
% Based on an idea by Douglas M. Schwarz, Eastman Kodak Company
try
tree = xmlread(filename);
catch
error('B... |
github | shayo/Kofiko-master | fnReadPlexonFile.m | .m | Kofiko-master/AnalysisScripts/Common/fnReadPlexonFile.m | 7,749 | utf_8 | b806719c2153d6a837db89b7e487a9dd | function strctPlexon = fnReadPlexonFile(strInputFile, acAnalogInputsRequired, acAnalogStructNames, bReadSpikes)
%
% Copyright (c) 2008 Shay Ohayon, California Institute of Technology.
% This file is a part of a free software. you can redistribute it and/or modify
% it under the terms of the GNU General Public License a... |
github | shayo/Kofiko-master | myaa.m | .m | Kofiko-master/AnalysisScripts/Common/myaa.m | 11,141 | utf_8 | a66dd7fc188c3f6a1a0a0c07623cf831 | function [varargout] = myaa(varargin)
%MYAA Render figure with anti-aliasing.
% MYAA
% Anti-aliased rendering of the current figure. This makes graphics look
% a lot better than in a standard matlab figure, which is useful for
% publishing results on the web or to better see the fine details in a
% complex... |
github | shayo/Kofiko-master | fnReadPlexonFileAllCh.m | .m | Kofiko-master/AnalysisScripts/Common/fnReadPlexonFileAllCh.m | 9,234 | utf_8 | 89a16a32f263131d1a325070c432557a | function strctPlexon = fnReadPlexonFileAllCh(strInputFile, strctNameConversion)
%
% Copyright (c) 2008 Shay Ohayon, California Institute of Technology.
% This file is a part of a free software. you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Softwa... |
github | shayo/Kofiko-master | fnCondorQueue.m | .m | Kofiko-master/AnalysisScripts/Distributed/fnCondorQueue.m | 1,795 | utf_8 | 332aff69e801e5472d88d6672790175b | function astrctQueue = fnCondorQueue()
strTempFileName = tempname;
strTempFileName2 = tempname;
system(['condor_q -xml >',strTempFileName]);
hFileID = fopen(strTempFileName);
hFileID2 = fopen(strTempFileName2,'w+');
while (1)
strLine = fgetl(hFileID);
if length(strLine) == 1 && strLine(1) == -1
break;
... |
github | shayo/Kofiko-master | fnWorker.m | .m | Kofiko-master/AnalysisScripts/Distributed/fnWorker.m | 4,254 | utf_8 | 137794d4922b589dbed50994525c8857 | function acFilesToTransferBack = fnWorker(strInputFile,strLogFileName,strOutputFile)
global g_hLogFileID
g_hLogFileID = fopen(strLogFileName,'w+');
acFilesToTransferBack = [];
try
fnWorkerLog(sprintf('Worker started on machine %s at %s',getenv('COMPUTERNAME'),fnDoubleSlash(pwd())));
strctTmp = load(strInputFile... |
github | shayo/Kofiko-master | SubmitJobGUI.m | .m | Kofiko-master/AnalysisScripts/Distributed/SubmitJobGUI.m | 15,287 | utf_8 | 844c9b5e90cd35c2ecfd11a8daed9721 | function varargout = SubmitJobGUI(varargin)
% SUBMITJOBGUI M-file for SubmitJobGUI.fig
% SUBMITJOBGUI, by itself, creates a new SUBMITJOBGUI or raises the existing
% singleton*.
%
% H = SUBMITJOBGUI returns the handle to a new SUBMITJOBGUI or the handle to
% the existing singleton*.
%
% SUBMITJ... |
github | shayo/Kofiko-master | fnCondorStatus.m | .m | Kofiko-master/AnalysisScripts/Distributed/fnCondorStatus.m | 1,645 | utf_8 | a6fa803d6cb40d697e8bf6b4b73af461 | function astrctMachines = fnCondorStatus()
astrctMachines = [];
strTempFileName = tempname;
strTempFileName2 = tempname;
system(['condor_status -xml >',strTempFileName]);
hFileID = fopen(strTempFileName);
hFileID2 = fopen(strTempFileName2,'w+');
bFileEmpty = true;
while (1)
strLine = fgetl(hFileID);
if length(... |
github | shayo/Kofiko-master | fnSinhaControlAnalysisCartoon.m | .m | Kofiko-master/AnalysisScripts/NewAnalysisPipeline/Sinha/fnSinhaControlAnalysisCartoon.m | 16,514 | utf_8 | 8c10712cc7c412e7b845e8ad9ad97994 | function strctUnit = fnSinhaControlAnalysisCartoon(strctUnit, strctKofiko, strctInterval,strctConfig,aiTrialIndices)
% load('C:\DeleteMeUnit.mat');
% figure;
% imagesc(strctUnit.m_aiPeriStimulusRangeMS, 1:strctUnit.m_iNumStimuli, fnMyColorMap(strctUnit.m_a2fAvgFirintRate_Stimulus))
% Add quality information about the... |
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