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value | path stringlengths 12 229 | size int64 23 843k | source_encoding stringclasses 9
values | md5 stringlengths 32 32 | text stringlengths 23 843k |
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github | HelmchenLabSoftware/OCIA-master | preprocLickData.m | .m | OCIA-master/caImgAnalysis/utils/preprocLickData.m | 3,089 | utf_8 | 3f4c637d9aa39cc0464e87a71cae95d2 | function lickRateUS = preprocLickData(lickDataCell, lickThreshHard, sampRate, doPlots)
lickRateBinSize = 0.05; % in s (e.g. 0.05 for 50 ms bins)
for n = 1 : numel(lickDataCell);
lickV = lickDataCell{n};
t = (1 : numel(lickV)) ./ sampRate;
try
% filter the lick vector
lickVfil... |
github | HelmchenLabSoftware/OCIA-master | eventDetector.m | .m | OCIA-master/caImgAnalysis/utils/eventDetection/eventDetector.m | 9,591 | utf_8 | 66349ac972c2fcdf425e9e2ba5603434 | function eventDetection = eventDetector(ROIStats, stim, eventDetectMethod, frameRate, psConfig, saveName)
%[eventMatAllRuns, instFiringRateAllRuns, residuals, models] = testingEventDetector(ROIStats, stim, eventDetectMethod, frameRate, psConfig, saveName)
% event detection function - wrapper to different event dete... |
github | HelmchenLabSoftware/OCIA-master | PeelingOptimizeSpikeTimesSaturation.m | .m | OCIA-master/caImgAnalysis/utils/eventDetection/PeelingOptimizeSpikeTimesSaturation.m | 4,465 | utf_8 | 82892eced9f5fb70e0d8ad3f544df164 | function [spkTout,output] = PeelingOptimizeSpikeTimesSaturation(dff,spkTin,lowerT,upperT,...
ca_amp,ca_gamma,ca_onsettau,ca_rest, ca_kappas, kd, conc, dffmax, frameRate, dur, optimMethod,maxIter,doPlot)
% optimization of spike times found by Peeling algorithm
% minimize the sum of the residual squared
% while sever... |
github | HelmchenLabSoftware/OCIA-master | PeelingOptimizeSpikeTimes.m | .m | OCIA-master/caImgAnalysis/utils/eventDetection/PeelingOptimizeSpikeTimes.m | 4,159 | utf_8 | 61e419a2e0808657c62b39f38bc0fb60 | function [spkTout,output] = PeelingOptimizeSpikeTimes(dff,spkTin,lowerT,upperT,...
rate,tauOn,A1,tau1,optimMethod,maxIter,doPlot)
% optimization of spike times found by Peeling algorithm
% minimize the sum of the residual squared
% while several optimization algorithms are implemented (see below), we have only used... |
github | HelmchenLabSoftware/OCIA-master | Peeling.m | .m | OCIA-master/caImgAnalysis/utils/eventDetection/Peeling.m | 9,395 | utf_8 | 87cff27352caf1bd8056e60c2e4c81cf | function [ca_p, peel_p, data] = Peeling(dff, rate, varargin)
% this is the main routine of the peeling algorithm
%
% Peeling algorithm was developed by Fritjof Helmchen
% Brain Research Institute
% University of Zurich
% Switzerland
%
% Matlab implementation and spike timing optimization by Henry Luetcke & Fritjof Helm... |
github | HelmchenLabSoftware/OCIA-master | eventDetector_OLDBalazs.m | .m | OCIA-master/caImgAnalysis/utils/eventDetection/eventDetector_OLDBalazs.m | 15,137 | utf_8 | 826457af3667681b47d959443193ceeb | function varargout = eventDetector(ROIStats, stim, ROISet, eventDetectMethod, frameRate, bpfilter, psConfig, saveName)
% event detection function - wrapper to different event detection algorithms
% input: structure created by GetRoiStats (*_RoiStats)
dbgLevel = 2;
% required folders
%folderList = {'Projects/EventDetect... |
github | HelmchenLabSoftware/OCIA-master | CalciumDecay.m | .m | OCIA-master/caImgAnalysis/utils/eventDetection/CalciumDecay.m | 1,116 | utf_8 | 67138b4224a9d6e8edefa5aa8b387b8e | function [t,X] = CalciumDecay(p_gamma,p_carest,p_cacurrent,p_kappas,p_kd,p_conc,tspan)
% Uses ODE45 to solve Single-compartment model differential equation
%
% Fritjof Helmchen (helmchen@hifo.uzh.ch)
% Brain Research Institute,University of Zurich, Switzerland
% created: 7.10.2013, last update: 25.10.2013 fh
options... |
github | HelmchenLabSoftware/OCIA-master | extractPSTrace.m | .m | OCIA-master/caImgAnalysis/utils/periStim/extractPSTrace.m | 3,041 | utf_8 | d3b2e3521d07d12854cf69d00e9ef54d | function PSCaTraces = extractPSTrace(caTraces, stims, PSFrames, varargin)
if numel(varargin) > 0 && isnumeric(varargin{1}) && numel(varargin{1}) == 1;
nMaxStimPerTrial = varargin{1};
else
nMaxStimPerTrial = 10;
end;
if numel(varargin) > 1 && islogical(varargin{2}) && varargin{2};
useROIParFor = true;
else... |
github | HelmchenLabSoftware/OCIA-master | PsPlotAnalysisCellArray.m | .m | OCIA-master/caImgAnalysis/utils/periStim/PsPlotAnalysisCellArray.m | 4,374 | utf_8 | 5d32da67e5de7c730620b9a5b3198cce | function PSData = PsPlotAnalysisCellArray(ROIStatsData, stimCell, psFrames)
% dataCell ... cell array with roi time-series (nROIs x nReps), each cell is a matrix of 1 x nFrames
% stimCell ... cell array of stim vectors (1 x nReps), each cell is a matrix of 1 x nFrames
% config ... peri-stimulus config ... |
github | HelmchenLabSoftware/OCIA-master | GetRoiStatsRaps.m | .m | OCIA-master/caImgAnalysis/ROIStats/GetRoiStatsRaps.m | 14,428 | utf_8 | c3e91f2c80c771821e60bb7a2d4530ef | function varargout = GetRoiStatsRaps(config)
% get ROI timecourses from images, with support for muliple ROIs and runs
% returns structure data, info and stimulus fields
% data field contains a cell array with ROI timecourses for different cells
% in rows and different runs in columns:
% [cell1_run1] [cell1_run2] ... [... |
github | HelmchenLabSoftware/OCIA-master | GetRoiStatsLineScan.m | .m | OCIA-master/caImgAnalysis/ROIStats/GetRoiStatsLineScan.m | 10,400 | utf_8 | 14f4dec618b5d5152ce43b50f448cbac | function varargout = GetRoiStatsLineScan(config)
% get ROI timecourses from images, with support for muliple ROIs and runs
% returns structure data, info and stimulus fields
% data field contains a cell array with ROI timecourses for different cells
% in rows and different runs in columns:
% [cell1_run1] [cell1_run2] .... |
github | HelmchenLabSoftware/OCIA-master | ConvertRawData_legacy.m | .m | OCIA-master/caImgAnalysis/ROIStats/ConvertRawData_legacy.m | 12,315 | utf_8 | 54a3f3e6134c4f0dd99acd8f124d9fc8 | function varargout = ConvertRawData(varargin)
% inputs: no need to specify any inputs --> GUI-based file selection
% optional input arguments, specified as 'property' 'value' pair in
% arbitrary order, e.g. 'zoom',1.07 OR as a structure with properties as
% field names and values, e.g. config.zoom = 1.07
% for a full l... |
github | HelmchenLabSoftware/OCIA-master | registerImages_MIRT.m | .m | OCIA-master/caImgAnalysis/ROIStats/registerImages_MIRT.m | 3,661 | utf_8 | a9d34819b9b436f37f06ed9e5e7bdb43 | function [tranformMatrix,newImage] = registerImages_MIRT(refim, im, varargin)
% wrapper for MIRT registration tools
% For the MIRT info visit the project website at
% https://sites.google.com/site/myronenko/research/mirt
% it is safer to add MIRT dynamicaly to the path because the toolbox
% shadows some native ML func... |
github | HelmchenLabSoftware/OCIA-master | ConvertRawData.m | .m | OCIA-master/caImgAnalysis/ROIStats/ConvertRawData.m | 23,529 | utf_8 | 09b72a006a2b553e3c3efd8e14720406 | function varargout = ConvertRawData(varargin)
% inputs: no need to specify any inputs --> GUI-based file selection
% optional input arguments, specified as 'property' 'value' pair in
% arbitrary order, e.g. 'zoom',1.07 OR as a structure with properties as
% field names and values, e.g. config.zoom = 1.07
% for a full l... |
github | HelmchenLabSoftware/OCIA-master | GetRoiStats.m | .m | OCIA-master/caImgAnalysis/ROIStats/GetRoiStats.m | 30,729 | utf_8 | 40f7e00ec7f7217d038af19be260c737 | function varargout = GetRoiStats(config)
% get ROI timecourses from images, with support for muliple ROIs and runs
% returns structure data, info and stimulus fields
% data field contains a cell array with ROI timecourses for different cells
% in rows and different runs in columns:
% [cell1_run1] [cell1_run2] ... [cell... |
github | HelmchenLabSoftware/OCIA-master | roiStatsSingleDay.m | .m | OCIA-master/caImgAnalysis/ROIStats/roiStatsSingleDay.m | 8,667 | utf_8 | c684320eb5799d0a156ee487373b3ffb | function configCell = roiStatsSingleDay(spotList, doAddRois, config)
roiStatsSingleDayTic = tic; % for performance timing purposes
% add folders to path
folderList = {'Projects/2PIanalyzer','Projects/CalciumSim',...
'Projects/EventDetect'};
addFolders2Path(folderList,1);
dbgLevel = 1;
o('#roiStatsSingleDay(): %d ... |
github | HelmchenLabSoftware/OCIA-master | extractSummaryInfoForSpots.m | .m | OCIA-master/caImgAnalysis/ROIStats/extractSummaryInfoForSpots.m | 8,614 | utf_8 | 85d821b91cc6f7df9c0da703f4792edb | function extractSummaryInfoForSpots(animalID)
dbgLevel = 4;
extractAllTic = tic; % for performance timing purposes
%% Get days with spots
year = '2013'; % leave this as a string, not a number
rawDataRootPath = 'W:\Neurophysiology\RawData\Balazs_Laurenczy\';
analysisRootPath = 'W:\Neurophysiology\Projects\Auditory\Anal... |
github | HelmchenLabSoftware/OCIA-master | GetRoiStatsFrameJ90.m | .m | OCIA-master/caImgAnalysis/ROIStats/GetRoiStatsFrameJ90.m | 19,099 | utf_8 | 018f54858f295d12e1a279c84d8700c4 | function varargout = GetRoiStatsFrameJ90(config)
% get ROI timecourses from images, with support for muliple ROIs and runs
% returns structure data, info and stimulus fields
% data field contains a cell array with ROI timecourses for different cells
% in rows and different runs in columns:
% [cell1_run1] [cell1_run2] .... |
github | HelmchenLabSoftware/OCIA-master | henry_analyzeHDF5_singleDay.m | .m | OCIA-master/caImgAnalysis/analysisHDF5/henry_analyzeHDF5_singleDay.m | 8,844 | utf_8 | 594a225ffaaef1c7c4dd24f7b2b9e09b | function S = henry_analyzeHDF5_singleDay(id, doSave, doDecode)
% id ... date string for the HDF5 file (e.g. 14011001) or Matlab structure from previous run
config.doSave = doSave;
config.doDecode = doDecode;
if ~isstruct(id)
fileName = sprintf('%s.h5',id);
animalID = sprintf('mou_bl_%s_%s',id(1:6),id(7:8));
... |
github | HelmchenLabSoftware/OCIA-master | henry_analyzeHDF5_multiDay.m | .m | OCIA-master/caImgAnalysis/analysisHDF5/henry_analyzeHDF5_multiDay.m | 11,569 | utf_8 | 74a90237433029f9bab1d1ffc0de5844 | function S = henry_analyzeHDF5_multiDay(id, config)
% id ... date string for the HDF5 file (e.g. 14011001) or Matlab structure from previous run
% ADD ANALYSIS OF DECODING WITH LABELING OF WHICH PHASE IT IS ('NAIVE', 'LEARNING', 'EXPERT')
% SEE IF TRAINING DATA SET ON EXPERT CAN ALSO PREDICT IN LEARNING
% TRY TO PRED... |
github | HelmchenLabSoftware/OCIA-master | analyseStimulusTuning.m | .m | OCIA-master/caImgAnalysis/postAnalysis/analyseStimulusTuning.m | 9,135 | utf_8 | 9c894bb7f270ae312885d479465bfde5 | function multiCompTuningPairs = analyseStimulusTuning(multiComparisonStats, stimIDs, multiCompareThresh, saveName, plotLimits, doSaveTuningPlot, doSavePairedTuningPlot)
% By using the results obtained by multiStimComparison this function
% plots the significance levels for different comparison metric (every
... |
github | HelmchenLabSoftware/OCIA-master | doROIRGBPlot.m | .m | OCIA-master/caImgAnalysis/postAnalysis/plotting/doROIRGBPlot.m | 2,018 | utf_8 | ee970a4efdf6e6b9c9d7596a4dd7e72a | %% Function - doROIRGBPlot
function figH = doROIRGBPlot(axeH, imgDims, ROISet, leftImg, meanImage, fileID, alphaVal)
% created by B. Laurenczy - 2013
% 2D matrix for the alpha transparency of each ROI on the final image
alphaMat = ones(imgDims(1), imgDims(2));
% 3D matrix for the RGB values of each ROI
ROIRGB = zeros... |
github | HelmchenLabSoftware/OCIA-master | PlotRoiTimecourse.m | .m | OCIA-master/caImgAnalysis/postAnalysis/plotting/PlotRoiTimecourse.m | 7,108 | utf_8 | 5d58dabaf73fc2b72e2636360675e780 | function varargout = PlotRoiTimecourse(varargin)
% plot timecourses of Rois in RoiSet
% in1 ... fcs-file / cell-array of tiff-files (max. 2)
% in2 ... RoiSet
% returns structure with fields time (adjusted by Roi location), stats type
% and value and roi ID
% return time axis in varargout{1}
% return timeseries as cell ... |
github | HelmchenLabSoftware/OCIA-master | doPSAveragePlotForROI.m | .m | OCIA-master/caImgAnalysis/postAnalysis/plotting/doPSAveragePlotForROI.m | 1,893 | utf_8 | 2ba38f9d133c145dfca2444bc537918b | %% Function - doPSAveragePlot
function [fig, fig2] = doPSAveragePlotForROI(iROI, ROIID, PSROIStatsData, uniqueStims,...
stimNames, frameRate, baseFrames)
figName = sprintf('PSPlot %s', ROIID);
fig = figure('Name', figName, 'NumberTitle', 'off');
hold all;
% setup subplot
if numel(uniqueStims) > 3;
M = ceil(sq... |
github | HelmchenLabSoftware/OCIA-master | glmAnalysis2P.m | .m | OCIA-master/caImgAnalysis/Decoding_2PI/glmAnalysis2P.m | 6,600 | utf_8 | 3db4ec3701a3383bb6d15241bffd2e87 | function glmAnalysis2P
% GLM analysis function for two-photon imaging data
% input: structure created by GetRoiStats (*_RoiStats)
% make GLM design matrix
if config.doGLMstats
onsettau = 0.05;
tau = 0.5;
tAxis_singleRun = (1:numel(config.stim{1}))./config.frameRate{1};
modelTransient = spkTimes2Calciu... |
github | HelmchenLabSoftware/OCIA-master | analyzeHDF5.m | .m | OCIA-master/caImgAnalysis/Decoding_2PI/analyzeHDF5.m | 8,349 | utf_8 | fb7db0df66962b7b174a9a468b6386ab | function S = analyzeHDF5(id)
% id ... date string for the HDF5 file (e.g. 14011001) or Matlab structure from previous run
doSave = 1;
if ~isstruct(id)
fileName = sprintf('%s.h5',id);
animalID = sprintf('mou_bl_%s_%s',id(1:6),id(7:8));
datasetID = ['/' animalID];
% load HDF5 and convert to data structu... |
github | HelmchenLabSoftware/OCIA-master | treeBaggerClassifier.m | .m | OCIA-master/caImgAnalysis/Decoding_2PI/regressionClassifier/treeBaggerClassifier.m | 4,908 | utf_8 | 49f4179317c4ba59e28b5720c576ef65 | function [rmse_true,rmse_shuf,pVal] = ...
treeBaggerClassifier(neuronData,stimData)
% neuronData ... trial x neuron cell array of calcium data
% each calcium timeseries must be column vector
% stimData ... trial x 1 cell array of stimulus data for each trial
% stim vector must be at frame rate and column vector
nt... |
github | HelmchenLabSoftware/OCIA-master | treeBaggerClassifier.m | .m | OCIA-master/caImgAnalysis/Decoding_2PI/AwakeWhisk_Tina/treeBaggerClassifier.m | 4,923 | utf_8 | 4869515cb11a96bbbae85e3de0522e59 | function [rmse_true,rmse_shuf,pVal] = ...
treeBaggerClassifier(neuronData,stimData)
% neuronData ... trial x neuron cell array of calcium data
% each calcium timeseries must be column vector
% stimData ... trial x 1 cell array of stimulus data for each trial
% stim vector must be at frame rate and column vector
nt... |
github | HelmchenLabSoftware/OCIA-master | treeBaggerClassifierTrainTest.m | .m | OCIA-master/caImgAnalysis/Decoding_2PI/AwakeWhisk_Tina/treeBaggerClassifierTrainTest.m | 7,127 | utf_8 | 02182e3a0bb5570bd5f6b45cac09cf18 | function [mseTrue, mseShuf] = treeBaggerClassifierTrainTest(neuronTrain,neuronTest,stimTrain,stimTest)
% in this file, train and test data sets are explicitely specified (e.g. for chronic analysis across
% sessions)
% neuronTrain ... trial x neuron cell array of training calcium data
% neuronTest ... trial x neuron cel... |
github | HelmchenLabSoftware/OCIA-master | treeBaggerClassifier2.m | .m | OCIA-master/caImgAnalysis/Decoding_2PI/AwakeWhisk_Tina/treeBaggerClassifier2.m | 7,070 | utf_8 | 718e6cc19869446a49a17adf092dde6e | function varargout = treeBaggerClassifier2(neuronData,stimData)
% neuronData ... trial x neuron cell array of calcium data
% each calcium timeseries must be column vector
% stimData ... trial x 1 cell array of stimulus data for each trial
% stim vector must be at frame rate and column vector
f = 7.81;
maxTrials = Inf... |
github | HelmchenLabSoftware/OCIA-master | importData_textureDisc.m | .m | OCIA-master/caImgAnalysis/Decoding_2PI/TextureDisc_Jerry/importData_textureDisc.m | 1,991 | utf_8 | 9965ffb89b724ddee6083c3d90aa97cf | function Sout = importData_textureDisc(matfile)
load(matfile)
roiLabel = Ca.roiLabel;
% animal / session ID
id = roiLabel{1,1};
idx = strfind(id,'-');
Sout.info.animal = id(1:idx(1)-1);
Sout.info.session = str2num(id(idx(1)+1:idx(2)-1));
Sout.info.sample_rate = Ca.sample_rate;
Sout.info.roiLabel = roiLabel;
trialID... |
github | HelmchenLabSoftware/OCIA-master | textureDisc_dimensionReduce.m | .m | OCIA-master/caImgAnalysis/Decoding_2PI/TextureDisc_Jerry/textureDisc_dimensionReduce.m | 1,799 | utf_8 | 6db53e071307051e42d0481f251ad5b6 | function S = textureDisc_dimensionReduce(S)
% S is a data structure returned by importData_textureDisc
% this file written by Henry Luetcke (hluetck@gmail.com)
animalID = S.info.animal;
sessionID = S.info.session;
rate = S.info.sample_rate;
roiLabel = S.info.roiLabel;
% roi labels without session ID
roiLabel = strre... |
github | HelmchenLabSoftware/OCIA-master | strucdisp.m | .m | OCIA-master/utils/misc/strucdisp.m | 18,695 | utf_8 | d5a885d0bc1cb649b355669e25a49853 | function strucdisp(Structure, depth, printValues, maxArrayLength, fileName)
%STRUCDISP display structure outline
%
% STRUCDISP(STRUC, DEPTH, PRINTVALUES, MAXARRAYLENGTH, FILENAME) displays
% the hierarchical outline of a structure and its substructures.
%
% STRUC is a structure datatype with unknown field conte... |
github | HelmchenLabSoftware/OCIA-master | client.m | .m | OCIA-master/utils/socket_communication/client.m | 1,728 | utf_8 | c1e65f4b0d1315930638729cb9769c5e | % CLIENT connect to a server and read a message
%
% Usage - message = client(host, port, number_of_retries)
function message = client(host, port, number_of_retries)
import java.net.Socket
import java.io.*
if (nargin < 3)
number_of_retries = 20; % set to -1 for infinite
end
retry ... |
github | HelmchenLabSoftware/OCIA-master | makeMMNexperiment_duration.m | .m | OCIA-master/utils/soundGen/makeMMNexperiment_duration.m | 2,993 | utf_8 | 92bdcf7093f7ef7456e1a169108f5e79 | function makeMMNexperiment_duration(durVector,f,sf)
% in1 ... duration vector
% in2 ... pure tone frequency (Hz)
% in3 ... sampling frequency
% this file written by Henry Luetcke (hluetck@gmail.com)
% some fixed parameters
duty = 0.5; % duty cycle in s
runs = 2; % no. of runs
% (must be even, half the runs f1 is stan... |
github | HelmchenLabSoftware/OCIA-master | makePureTone.m | .m | OCIA-master/utils/soundGen/makePureTone.m | 1,803 | utf_8 | 4775e6038bf3aba14c55af3dbc971624 | function s = makePureTone(freqs,duration,varargin)
% generate a pure tone
% in1 ... carrier frequency in Hz
% in2 ... duration in s
% in3 ... sampling frequency in Hz {44100}
% in4 ... rampDur in fraction of total duration {0.05}
% in5 ... play tone {0}; 0 or 1
% in6 ... save wav file {[]}; filename of wav file
% out1 ... |
github | HelmchenLabSoftware/OCIA-master | makeOmittedStimExperimentNoise.m | .m | OCIA-master/utils/soundGen/makeOmittedStimExperimentNoise.m | 3,099 | utf_8 | f608ebec790c4a07c4e0772436893523 | function makeOmittedStimExperimentNoise(fCellArray,sf)
% fCellArray ... {[lower1 upper1],[lower2 upper2]}
% sf ... sampling frequency
% if f2 = 0, this will create an omitted stimulus paradigm
% this file written by Henry Luetcke (hluetck@gmail.com)
% some fixed parameters
dur = 0.2; % tone duration in s
runs = 10; %... |
github | HelmchenLabSoftware/OCIA-master | makeMMNexperiment.m | .m | OCIA-master/utils/soundGen/makeMMNexperiment.m | 3,040 | utf_8 | 1c64717c6c6d44304d01eeced947ad07 | function makeMMNexperiment(fVector,sf)
% fVector ... [freq1 freq2]
% sf ... sampling frequency
% if freq2 = 0, this will create an omitted stimulus paradigm
% this file written by Henry Luetcke (hluetck@gmail.com)
% some fixed parameters
dur = 0.2; % tone duration in s
runs = 10; % no. of runs
% (must be even, half t... |
github | HelmchenLabSoftware/OCIA-master | makeNoiseTone.m | .m | OCIA-master/utils/soundGen/makeNoiseTone.m | 1,583 | utf_8 | c793c5a273c13f3af3f81b914137b260 | function s = makeNoiseTone(freqs,duration,varargin)
% generate a pure tone
% in1 ... band-limiting frequencies in Hz [lower upper]
% in2 ... duration in s
% in3 ... sampling frequency in Hz {44100}
% in4 ... play tone {0}; 0 or 1
% in5 ... rd
% out1 ... the sound vector s
% this file written by Henry Luetcke (hluetck@... |
github | HelmchenLabSoftware/OCIA-master | xyerrorbar.m | .m | OCIA-master/utils/plotting/xyerrorbar.m | 1,618 | utf_8 | bbdb1d7c67cfdc53de32740db8e3dbd1 | % xyerrorbar.m
% (c) Nils Sjoberg 07-09-2004 Sweden
% xyerrorbar(x,y,errx,erry,s) plots the data in y vs x with errorbars for
% both y and x-data. Variables errx and erry are arrays of length=length(x and y) containing the
% error in each and every datapoint.
% s contains drawing-options for the plot and th... |
github | HelmchenLabSoftware/OCIA-master | displayData.m | .m | OCIA-master/utils/plotting/displayData.m | 9,061 | utf_8 | 8f602663bd107c33523766f80b676ca0 | function varargout = displayData(varargin)
% this file written by Henry Luetcke
if nargin
S = varargin{1}; % parameter structure
else
S = struct;
end
tic
S = parseInputs(S);
%% load data
[FilePath,FileName,FileType] = fileparts(S.RawFiles{1});
fullInfile = fullfile(FilePath,[FileName FileType]);
if exist(ful... |
github | HelmchenLabSoftware/OCIA-master | patchline.m | .m | OCIA-master/utils/plotting/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 | HelmchenLabSoftware/OCIA-master | makePrettyFigure.m | .m | OCIA-master/utils/plotting/makePrettyFigure.m | 1,030 | utf_8 | 4025d23131e4c264865ded9bcedc5c31 | function figOut = makePrettyFigure(varargin)
% for a given figure, apply some operations to make it look nicer
if nargin == 0;
fig = gcf;
else
fig = varargin{1};
end;
figOut = fig;
% a cell array of default axis properties (column 1 is the property name,
% column 2 is the property value)
defaultProps = { ...... |
github | HelmchenLabSoftware/OCIA-master | PsPlot2Raster.m | .m | OCIA-master/utils/plotting/PsPlot2Raster.m | 7,798 | utf_8 | 50a24bc695620bf37df86f36fba74d0b | function varargout = PsPlot2Raster(varargin)
% plot different columns (stims) in ps_plot_cell in different subplots
% in1 ... psPlot cell array (roi x stim), each cell contains trial x
% timepoints ps-matrix
% in2 ... sampling frequency
% in3 ... offset (frame of stimulus presentation)
% in4 ... optional cellstring wit... |
github | HelmchenLabSoftware/OCIA-master | adjustSubplotAxes.m | .m | OCIA-master/utils/plotting/adjustSubplotAxes.m | 1,602 | utf_8 | 0fd6cc79ba5adfbf3fc307b09b8e87bd | function adjustSubplotAxes(h,varargin)
% adjust axis of all subplots in figure h
% specify axis by string / value combination, e.g.:
% 'X',[-5 10] sets all x-limits to [-5 10]
% 'Y',[] sets y-limits to Min / Max
% unlisted axes are left untouched
% varargin{1} ... the axis limits to be set (default: Min / Max)
inargs ... |
github | HelmchenLabSoftware/OCIA-master | groupedErrBar.m | .m | OCIA-master/utils/plotting/groupedErrBar.m | 5,106 | utf_8 | 94caedf9ae477f0d7de99a816ae21638 | function h = groupedErrBar(dataCell,varargin)
% plot multiple data sets in groups with errorbar and (optionally) individual data points
% dataCell ... cell array with 1 vector per cell containing n observations
% cells in the same row will be grouped, cells in different rows will be different groups (similar
% to bar f... |
github | HelmchenLabSoftware/OCIA-master | nfb_errorbar.m | .m | OCIA-master/utils/plotting/nfb_errorbar.m | 7,945 | utf_8 | 90c8e91005ce42d017454ea42ffb2e73 | % nfb_errorbar is a generic function which produces a bar chart with error
% bars
% its main advantage is that it readily plots each bar and errorbar
% separately, making it easy to change colours, filling etc for each bar
% individually later on
%
% USAGE:
% [out1] = nfb_errorbar(in1, in2)
%
% Comulsory input argument... |
github | HelmchenLabSoftware/OCIA-master | fig2m.m | .m | OCIA-master/utils/plotting/fig2m.m | 19,924 | utf_8 | 857a1a6daef974fc98a2e735071bb6e8 | function varargout = fig2m(guiName,outputDir,syscolorfig,cb_gen)
% FIG2M - Generate programmatic GUI M-File from a FIG-File
%
% Version : 1.0
% Created : 10/05/2006
% Modified: 14/04/2010
% Author : Thomas Montagnon (The MathWorks France)
%
% >> outputFile = fig2m(guiName,outputDir,syscolorfig,cb_gen);
%
% guiName ... |
github | HelmchenLabSoftware/OCIA-master | sigstar.m | .m | OCIA-master/utils/plotting/sigstar.m | 9,019 | utf_8 | 9e111a96ba442eee144d7eaac47163c8 | function varargout=sigstar(groups,stats,nosort,putStarsUnder)
% SIGSTAR Add significance stars to bar charts, boxplots, line charts, etc,
%
% H = SIGSTAR(GROUPS,STATS,NSORT)
%
% Purpose
% Add stars and lines highlighting significant differences between pairs of groups.
% The user specifies the groups and associated p... |
github | HelmchenLabSoftware/OCIA-master | barerrorbar.m | .m | OCIA-master/utils/plotting/barerrorbar.m | 6,065 | utf_8 | d18f6c7caa4b5acbe0a3a5d61dc73f31 | function varargout = barerrorbar(varargin)
% BARERRORBAR Create a bar plot with error bars. BARERRORBAR() uses the
% MATLAB functions BAR() and ERRORBAR() and changes the 'XData' property
% of the errorbar plot so that the error bars are plotted at the center
% of each bar. This does not support "stack" bar pl... |
github | HelmchenLabSoftware/OCIA-master | pdftops.m | .m | OCIA-master/utils/plotting/export_fig/pdftops.m | 3,574 | utf_8 | 92ff676904575e16046dfff010b4e145 | function varargout = pdftops(cmd)
%PDFTOPS Calls a local pdftops executable with the input command
%
% Example:
% [status result] = pdftops(cmd)
%
% Attempts to locate a pdftops executable, finally asking the user to
% specify the directory pdftops was installed into. The resulting path is
% stored for future refere... |
github | HelmchenLabSoftware/OCIA-master | crop_borders.m | .m | OCIA-master/utils/plotting/export_fig/crop_borders.m | 3,666 | utf_8 | ebb9c61581b6f0d4a2db2fd1d9e30685 | function [A, vA, vB, bb_rel] = crop_borders(A, bcol, padding)
%CROP_BORDERS Crop the borders of an image or stack of images
%
% [B, vA, vB, bb_rel] = crop_borders(A, bcol, [padding])
%
%IN:
% A - HxWxCxN stack of images.
% bcol - Cx1 background colour vector.
% padding - scalar indicating how much padding to ha... |
github | HelmchenLabSoftware/OCIA-master | isolate_axes.m | .m | OCIA-master/utils/plotting/export_fig/isolate_axes.m | 4,721 | utf_8 | 253cd7b7d8fc7cb00d0cc55926f32de5 | function fh = isolate_axes(ah, vis)
%ISOLATE_AXES Isolate the specified axes in a figure on their own
%
% Examples:
% fh = isolate_axes(ah)
% fh = isolate_axes(ah, vis)
%
% This function will create a new figure containing the axes/uipanels
% specified, and also their associated legends and colorbars. The objects
%... |
github | HelmchenLabSoftware/OCIA-master | im2gif.m | .m | OCIA-master/utils/plotting/export_fig/im2gif.m | 6,048 | utf_8 | 5a7437140f8d013158a195de1e372737 | %IM2GIF Convert a multiframe image to an animated GIF file
%
% Examples:
% im2gif infile
% im2gif infile outfile
% im2gif(A, outfile)
% im2gif(..., '-nocrop')
% im2gif(..., '-nodither')
% im2gif(..., '-ncolors', n)
% im2gif(..., '-loops', n)
% im2gif(..., '-delay', n)
%
% This function converts a mu... |
github | HelmchenLabSoftware/OCIA-master | read_write_entire_textfile.m | .m | OCIA-master/utils/plotting/export_fig/read_write_entire_textfile.m | 924 | utf_8 | 779e56972f5d9778c40dee98ddbd677e | %READ_WRITE_ENTIRE_TEXTFILE Read or write a whole text file to/from memory
%
% Read or write an entire text file to/from memory, without leaving the
% file open if an error occurs.
%
% Reading:
% fstrm = read_write_entire_textfile(fname)
% Writing:
% read_write_entire_textfile(fname, fstrm)
%
%IN:
% fname - Pathn... |
github | HelmchenLabSoftware/OCIA-master | pdf2eps.m | .m | OCIA-master/utils/plotting/export_fig/pdf2eps.m | 1,471 | utf_8 | a1f41f0c7713c73886a2323e53ed982b | %PDF2EPS Convert a pdf file to eps format using pdftops
%
% Examples:
% pdf2eps source dest
%
% This function converts a pdf file to eps format.
%
% This function requires that you have pdftops, from the Xpdf suite of
% functions, installed on your system. This can be downloaded from:
% http://www.foolabs.com/xpdf ... |
github | HelmchenLabSoftware/OCIA-master | print2array.m | .m | OCIA-master/utils/plotting/export_fig/print2array.m | 9,369 | utf_8 | ca18a1e6c5a944b591a0557bd69f1c2c | function [A, bcol] = print2array(fig, res, renderer, gs_options)
%PRINT2ARRAY Exports a figure to an image array
%
% Examples:
% A = print2array
% A = print2array(figure_handle)
% A = print2array(figure_handle, resolution)
% A = print2array(figure_handle, resolution, renderer)
% A = print2array(figure_handle... |
github | HelmchenLabSoftware/OCIA-master | append_pdfs.m | .m | OCIA-master/utils/plotting/export_fig/append_pdfs.m | 2,678 | utf_8 | 949c7c4ec3f5af6ff23099f17b1dfd79 | %APPEND_PDFS Appends/concatenates multiple PDF files
%
% Example:
% append_pdfs(output, input1, input2, ...)
% append_pdfs(output, input_list{:})
% append_pdfs test.pdf temp1.pdf temp2.pdf
%
% This function appends multiple PDF files to an existing PDF file, or
% concatenates them into a PDF file if the output fi... |
github | HelmchenLabSoftware/OCIA-master | using_hg2.m | .m | OCIA-master/utils/plotting/export_fig/using_hg2.m | 1,002 | utf_8 | b1620dd31f4d0b8acea2723e354a3518 | %USING_HG2 Determine if the HG2 graphics engine is used
%
% tf = using_hg2(fig)
%
%IN:
% fig - handle to the figure in question.
%
%OUT:
% tf - boolean indicating whether the HG2 graphics engine is being used
% (true) or not (false).
% 19/06/2015 - Suppress warning in R2015b; cache result for improved per... |
github | HelmchenLabSoftware/OCIA-master | eps2pdf.m | .m | OCIA-master/utils/plotting/export_fig/eps2pdf.m | 8,355 | utf_8 | 3b82818a1bc7c7e39c8491ce325b2235 | function eps2pdf(source, dest, crop, append, gray, quality, gs_options)
%EPS2PDF Convert an eps file to pdf format using ghostscript
%
% Examples:
% eps2pdf source dest
% eps2pdf(source, dest, crop)
% eps2pdf(source, dest, crop, append)
% eps2pdf(source, dest, crop, append, gray)
% eps2pdf(source, dest, crop... |
github | HelmchenLabSoftware/OCIA-master | ghostscript.m | .m | OCIA-master/utils/plotting/export_fig/ghostscript.m | 7,706 | utf_8 | 92dbafb8d4fb243cae8716c6ecb0bbe5 | function varargout = ghostscript(cmd)
%GHOSTSCRIPT Calls a local GhostScript executable with the input command
%
% Example:
% [status result] = ghostscript(cmd)
%
% Attempts to locate a ghostscript executable, finally asking the user to
% specify the directory ghostcript was installed into. The resulting path
% is s... |
github | HelmchenLabSoftware/OCIA-master | fix_lines.m | .m | OCIA-master/utils/plotting/export_fig/fix_lines.m | 6,290 | utf_8 | 8437006b104957762090e3d875688cb6 | %FIX_LINES Improves the line style of eps files generated by print
%
% Examples:
% fix_lines fname
% fix_lines fname fname2
% fstrm_out = fixlines(fstrm_in)
%
% This function improves the style of lines in eps files generated by
% MATLAB's print function, making them more similar to those seen on
% screen. Grid ... |
github | HelmchenLabSoftware/OCIA-master | notBoxPlot.m | .m | OCIA-master/utils/plotting/notBoxPlot/notBoxPlot.m | 6,618 | utf_8 | bce98cc92bdab9639cc0a40da6e039e3 | function varargout=notBoxPlot(y,x,jitter,style)
% notBoxPlot - Doesn't plot box plots!
%
% function notBoxPlot(y,x,jitter,style)
%
%
% Purpose
% An alternative to a box plot, where the focus is on showing raw
% data. Plots columns of y as different groups located at points
% along the x axis defined by the optional vec... |
github | HelmchenLabSoftware/OCIA-master | importResonanceFolder.m | .m | OCIA-master/utils/importExport/importResonanceFolder.m | 2,264 | utf_8 | 17b8b7e3b8ac097566672757e58f4ca8 | function imgStruct = importResonanceFolder(dataPath) %#ok<STOUT,INUSD>
error('importResonanceFolder:Deprecated', 'DEPRECATED: use loadData instead');
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Intrinsic image analyser %
% Originally created on 28 / 11 / 2013 %
% Written by B.... |
github | HelmchenLabSoftware/OCIA-master | ReadEphys.m | .m | OCIA-master/utils/importExport/ReadEphys.m | 1,245 | utf_8 | 07f7cdadb5d8e096e0e9a910fd033ee4 | function [ephys,FrameClock] = ReadEphys(varargin)
% read binary data files written by LabView E-phys acquisition program in
% H45
% requires file name of file to read and number of timepoints
% returns e-phys trace and frame clock
% this file written by Henry Luetcke (hluetck@gmail.com)
if nargin == 2
filename = v... |
github | HelmchenLabSoftware/OCIA-master | ij_RoiSetSeedPointSegment.m | .m | OCIA-master/utils/importExport/imageJROI/ij_RoiSetSeedPointSegment.m | 4,975 | utf_8 | 8d601794c01445d79037f07f2ec57d22 | function ij_RoiSetSeedPointSegment(varargin)
% segment cell Rois from ImageJ single point RoiSet and save as new ImageJ
% RoiSet
% in1 ... configuration structure for this program
% may be called without input arguments --> GUI file selection and default
% parameters (c.f. below)
% uses ActiveModel segmentation pr... |
github | HelmchenLabSoftware/OCIA-master | loadDataFromHDF5.m | .m | OCIA-master/utils/importExport/HDF5/loadDataFromHDF5.m | 7,865 | utf_8 | 4d3a9dea75580223eebd08fa81693430 | function data = loadDataFromHDF5(filePath, datasetPath)
% data = loadDataFromHDF5(filePath, datasetPath)
% Wrapper for the h5readAsStruct function that reads out the content of the HDF5 file as a structure and reshapes it
% to a more usable format.
%
% Written on 2014-04-07 by B. Laurenczy (blaurenczy@gmail.com)
% rea... |
github | HelmchenLabSoftware/OCIA-master | h5createIntermediateGroup.m | .m | OCIA-master/utils/importExport/HDF5/h5createIntermediateGroup.m | 1,120 | utf_8 | 5ba2a52ce40089c79f3c43287ca89493 | % creates an intermediate group in the HDF5 file so that group exists whenever an attribute needs to be attached to it
function h5createIntermediateGroup(fileName, groupPath)
% if file does not exist, create a new file using the default properties
if ~exist(fileName, 'file');
fID = H5F.create(fileName, 'H5F_ACC_TR... |
github | HelmchenLabSoftware/OCIA-master | h5read_wrapper.m | .m | OCIA-master/utils/importExport/HDF5/h5read_wrapper.m | 9,682 | utf_8 | 1e980dce42de30109767710808bce2c5 | function data = h5read_wrapper(filePath, datasetPath, h5readArgs)
% data = h5read_wrapper(fileName, datasetPath, h5readArgs)
% Wrapper for the h5read function that also handles cell-array, structures and struct-arrays.
% Recursively reads the data from the HDF5 file "fileName" from the dataset path "datasetPath".
% Arg... |
github | HelmchenLabSoftware/OCIA-master | h5exists.m | .m | OCIA-master/utils/importExport/HDF5/h5exists.m | 1,057 | utf_8 | 1db0c46a2621b643d377b487c7574545 | % delete a group in the HDF5 file
function doesExist = h5exists(fileName, groupPath)
% check if the file exists
if ~exist(fileName, 'file');
doesExist = false;
return;
end;
doesExist = true;
fileID = H5F.open(fileName);
pathParts = regexp(groupPath, '/', 'split');
iPart = 2;
while iPart < numel(pathParts);
... |
github | HelmchenLabSoftware/OCIA-master | loadDataFromHDF5_old.m | .m | OCIA-master/utils/importExport/HDF5/loadDataFromHDF5_old.m | 4,559 | utf_8 | b3d2b1533fb9d314c711a71eefa2fff5 | function data = loadDataFromHDF5_old(filePath, datasetPath)
% data = loadDataFromHDF5(filePath, datasetPath)
% Wrapper for the h5readAsStruct function that reads out the content of the HDF5 file as a structure and reshapes it
% to a more usable format.
%
% Written on 2014-04-07 by B. Laurenczy (blaurenczy@gmail.com)
%... |
github | HelmchenLabSoftware/OCIA-master | h5createwrite_wrapper.m | .m | OCIA-master/utils/importExport/HDF5/h5createwrite_wrapper.m | 16,544 | utf_8 | 9489ee1b4d18ac50e7741d3b0080da0f | function h5createwrite_wrapper(fileName, datasetPath, data, h5createArgs, h5writeArgs)
% h5createwrite_wrapper(fileName, datasetPath, data, h5createArgs, h5writeArgs)
% Wrapper for the h5create and h5write functions that also handles cell-array, structures and struct-arrays.
% Recursively creates and/or writes the data... |
github | HelmchenLabSoftware/OCIA-master | h5deleteGroup.m | .m | OCIA-master/utils/importExport/HDF5/h5deleteGroup.m | 762 | utf_8 | 8ef76eb11513fb6fff7cba395bdaa02c | % delete a group in the HDF5 file
function h5deleteGroup(fileName, groupPath)
% if file does not exist, create a new file using the default properties
if ~exist(fileName, 'file');
fID = H5F.create(fileName, 'H5F_ACC_TRUNC', 'H5P_DEFAULT', 'H5P_DEFAULT');
% if file exists, open it using the default properties
else
... |
github | HelmchenLabSoftware/OCIA-master | xcorr_mc.m | .m | OCIA-master/utils/stat/xcorr_mc.m | 1,122 | utf_8 | bb01c55ef67edb3bbe21ccc25ae74ecb | function [cc,p,cc_mc] = xcorr_mc(x,y,maxlags,n)
% monte-carlo cross-correlation of x and y
% Input
% x ... input vector 1 (will be shuffled)
% y ... input vector 2 (will NOT be shuffled)
% lag ... lag for xcorr
% n ... number of samples for shuffled data
% Output
% cc ... the true cross-correlation between x and y
% p ... |
github | HelmchenLabSoftware/OCIA-master | sparseness.m | .m | OCIA-master/utils/stat/sparseness.m | 1,021 | utf_8 | 9e7d0a6350274c815488872e8005f081 | function k = sparseness(varargin)
% calculate sparseness measure k for response vector r (in1) with method
% (in2)
% methods:
% {'kurtosis'}
% 'treves_rolls'
% 'willmore_tolhurst'
% this file written by Henry Luetcke (hluetck@gmail.com)
if nargin == 1
r = varargin{1};
method = 'kurtosis';
elseif nargin == 2
... |
github | HelmchenLabSoftware/OCIA-master | fit_fminsearch.m | .m | OCIA-master/utils/matlabExtend/fit_fminsearch.m | 1,098 | utf_8 | aba55d992c51d5e7750b6453a19ddde2 | function fit_fminsearch
% simulate a double-peaked Gaussian
a = normrnd(1,0.5,[10000,1]);
a = [a; normrnd(3,0.5,[10000,1])];
[count,xout] = hist(a,sqrt(numel(a)));
figure('Name','Fit fun figure','NumberTitle','off')
stairs(xout,count,'k-'), hold on
%% fit with curve fitting toolbox
% fit double-peaked gaussian to his... |
github | HelmchenLabSoftware/OCIA-master | mydepfun.m | .m | OCIA-master/utils/matlabExtend/mydepfun.m | 3,300 | utf_8 | 4b01dad21c371327373768234c3dc9be | function filelist = mydepfun(fn,recursive)
%MYDEPFUN - Variation on depfun which skips toolbox files
%
% filelist = mydepfun(fn)
% filelist = mydepfun(fn,recursive)
%
% Returns a list of files which are required by the specified
% function, omitting any which are inside $matlabroot/toolbox.
%
% "fn" is a string specif... |
github | HelmchenLabSoftware/OCIA-master | smoothn.m | .m | OCIA-master/utils/matlabExtend/smoothn.m | 3,357 | utf_8 | 880f4a892aa0f80387fc54388891b162 | function Y = smoothn(X,sz,filt,std)
%SMOOTHN Smooth N-D data
% Y = SMOOTHN(X, SIZE) smooths input data X. The smoothed data is
% retuirned in Y. SIZE sets the size of the convolution kernel
% such that LENGTH(SIZE) = NDIMS(X)
%
% Y = SMOOTHN(X, SIZE, FILTER) Filter can be 'gaussian' or 'box' (default)
... |
github | HelmchenLabSoftware/OCIA-master | DataHash.m | .m | OCIA-master/utils/matlabExtend/DataHash.m | 15,429 | utf_8 | e725a80cb9180de1eb03e47b850a95dc | function Hash = DataHash(Data, Opt)
% DATAHASH - Checksum for Matlab array of any type
% This function creates a hash value for an input of any type. The type and
% dimensions of the input are considered as default, such that UINT8([0,0]) and
% UINT16(0) have different hash values. Nested STRUCTs and CELLs are parsed
%... |
github | HelmchenLabSoftware/OCIA-master | gencode_rvalue.m | .m | OCIA-master/utils/matlabExtend/gencode/gencode_rvalue.m | 4,540 | utf_8 | 461c5aa9248a9962253bec5ce7d36038 | function [str, sts] = gencode_rvalue(item)
% GENCODE_RVALUE Code for right hand side of MATLAB assignment
% Generate the right hand side for a valid MATLAB variable
% assignment. This function is a helper to GENCODE, but can be used on
% its own to generate code for the following types of variables:
% * scalar, 1D or... |
github | HelmchenLabSoftware/OCIA-master | gencode.m | .m | OCIA-master/utils/matlabExtend/gencode/gencode.m | 8,361 | utf_8 | 7355f9b9b8500373a07c87da2f3deab7 | function [str, tag, cind] = gencode(item, tag, tagctx)
% GENCODE Generate code to recreate any MATLAB struct/cell variable.
% For any MATLAB variable, this function generates a .m file that
% can be run to recreate it. Classes can implement their class specific
% equivalent of gencode with the same calling syntax. By... |
github | HelmchenLabSoftware/OCIA-master | profile_history.m | .m | OCIA-master/utils/matlabExtend/profile_history/profile_history.m | 21,451 | utf_8 | 09cf826e21a726826828395761ce3c13 | function profile_history(profData, initialDetail, varargin)
% profile_history - display profiling data as a timeline history
%
% profile_history analyzes the latest profiling session and displays the
% function-call timings and durations in a graphical timeline. The function
% labels and timeline bars are clickable, li... |
github | HelmchenLabSoftware/OCIA-master | parseXML.m | .m | OCIA-master/utils/file/parseXML.m | 2,298 | utf_8 | 2872d6a03a9a0534868ee63adbb29a11 | 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);
return
t... |
github | HelmchenLabSoftware/OCIA-master | depfunFast.m | .m | OCIA-master/utils/file/depfunFast.m | 3,341 | utf_8 | e1a987535066e28a1e99c5fce821bdda | function filelist = depfunFast(fn,recursive)
% Variation on the built-in depfun function, which skips toolbox files
%
% filelist = mydepfun(fn)
% filelist = mydepfun(fn,recursive)
%
% Returns a list of files which are required by the specified
% function, omitting any which are inside $matlabroot/toolbox.
%
%... |
github | HelmchenLabSoftware/OCIA-master | showByteSize.m | .m | OCIA-master/utils/file/showByteSize.m | 991 | utf_8 | 0a61a86db4a2ae5060ab4797b40d0d11 | function showByteSize(in, fid) %#ok<INUSL>
% BYTESIZE writes the memory usage of the provide variable to the given file
% identifier. Output is written to screen if fid is 1, empty or not provided.
if nargin == 1 || isempty(fid)
fid = 1;
end
s = whos('in');
fprintf(fid,[Bytes2str(s.bytes) '\n']);
end
function st... |
github | HelmchenLabSoftware/OCIA-master | exportMfiles.m | .m | OCIA-master/utils/file/exportMfiles.m | 3,841 | utf_8 | 367bfa75d006163523b8208a9c631218 | function exportMfiles(funcname,doPcode,doZip,saveDir)
% find dependencies for function funcname
% copy all dependencies to saveDir
% create zip-archive saveDir.zip
% optionally, pcode
% this file written by Henry Luetcke (hluetck@gmail.com)
if ~iscell(funcname)
funcname = {funcname};
end
if isempty(funcname)
... |
github | HelmchenLabSoftware/OCIA-master | tiffread2.m | .m | OCIA-master/utils/file/tiffread2.m | 19,177 | utf_8 | 1eab6091d5c0b85e5ab70139f0d580c3 | function [stack, img_read] = tiffread2(filename, img_first, img_last, funUpdateWaitBar)
% tiffread, version 2.4
%
% [stack, nbImages] = tiffread;
% [stack, nbImages] = tiffread(filename);
% [stack, nbImages] = tiffread(filename, imageIndex);
% [stack, nbImages] = tiffread(filename, firstImageIndex, lastImageIndex);
%
%... |
github | HelmchenLabSoftware/OCIA-master | spikeTimeAnalyzer.m | .m | OCIA-master/utils/spike/spikeTimeAnalyzer.m | 5,911 | utf_8 | 40a546c18226484564e906b605c8c857 | function varargout = spikeTimeAnalyzer( s, psthT, evokedT, method, doPlot )
% inputs (all compulsory):
% s ... cell array of spike times per trial
% psthTime ... time bins relative to stim onset (=0)
% evokedT ... time to count as evoked; used for counting evoked spikes; either n x 2 matrix with
% different tStart and ... |
github | HelmchenLabSoftware/OCIA-master | concatanateSegments.m | .m | OCIA-master/other/functions_widefield/whisker_tracking/concatanateSegments.m | 1,464 | utf_8 | 768b37514426be26a3cc94efe0113aa4 | %dirname='F:\data tetrodes\th_8\th_8_2014_10_28_a';
function f= concatanateSegments(dirname)
list = dir(dirname);
i=3;
oldExpName='Experiment';
whiskingAll = [];
mkdir(fullfile(dirname,'whiskByTrial'));
count = 0;
for i=3:length(list)
fname = list(i).name;
ind=strfind(fname,'_Whisker_Tracking');
if(~is... |
github | HelmchenLabSoftware/OCIA-master | wt_keyboard_shortcuts.m | .m | OCIA-master/other/functions_widefield/whisker_tracking/wt_knutsen/wt_keyboard_shortcuts.m | 887 | utf_8 | 80026debb0b351752a721eab3a1cdda9 | % WT_SHOW_KEYBOARD_SHORTCUTS
% Show keyboard shortcuts.
function wt_keyboard_shortcuts
cShortcuts = { ...
'Ctr+P Open parameters window' ...
'Ctr+D Dump current view to printer, file or clipboard' ...
'Ctr+S Save data' ... |
github | HelmchenLabSoftware/OCIA-master | wt_find_nose.m | .m | OCIA-master/other/functions_widefield/whisker_tracking/wt_knutsen/wt_find_nose.m | 932 | utf_8 | 975914d45d66953aedf8d6b290311c4d | % WT_FIND_NOSE Finds the nose in image, given eye positions.
%
% Whisker Tracker (WT)
%
% Authors: Per Magne Knutsen, Dori Derdikman
%
% (c) Copyright 2004 Yeda Research and Development Company Ltd.,
% Rehovot, Israel
%
% This software is protected by copyright and patent law. Any unauthorized
% use, reproduction o... |
github | HelmchenLabSoftware/OCIA-master | wt_change_whisker_width.m | .m | OCIA-master/other/functions_widefield/whisker_tracking/wt_knutsen/wt_change_whisker_width.m | 507 | utf_8 | 42e2a89228861c394eea10f3855e1ff8 | %%%% WT_CHANGE_WHISKER_WIDTH %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Open dialog window and allow user to select width of displayed whiskers
% in pixels.
function wt_change_whisker_width
global g_tWT
sAns = inputdlg('Set whisker width in pixels', 'WT');
% Exceptions
if isempty(sAns), return; end
if g_tWT.W... |
github | HelmchenLabSoftware/OCIA-master | wt_reset_all.m | .m | OCIA-master/other/functions_widefield/whisker_tracking/wt_knutsen/wt_reset_all.m | 1,679 | utf_8 | 1226ca71091a23a6f1f8303cb5f55ec0 | % WT_RESET_ALL
% Reset all movie and tracking parameters
%
% Whisker Tracker (WT)
%
% Authors: Per Magne Knutsen, Dori Derdikman
%
% (c) Copyright 2004 Yeda Research and Development Company Ltd.,
% Rehovot, Israel
%
% This software is protected by copyright and patent law. Any unauthorized
% use, reproduction or di... |
github | HelmchenLabSoftware/OCIA-master | wt_clean_splines.m | .m | OCIA-master/other/functions_widefield/whisker_tracking/wt_knutsen/wt_clean_splines.m | 7,905 | utf_8 | 2e17634243b0ca52ef2135a4c7ca49a8 | % WT_CLEAN_SPLINES
%
% Clean splinepoints by removing movements of certain amplitude and
% duration. Also included is an optional low-pass filter (mainly intended
% to filter head-movements before tracking whiskers). Note that all
% changes made are permanent
%
% Syntax: wt_clean_splines(W, OPT), where
% W is... |
github | HelmchenLabSoftware/OCIA-master | wt_graphs.m | .m | OCIA-master/other/functions_widefield/whisker_tracking/wt_knutsen/wt_graphs.m | 37,590 | utf_8 | e8c936d149d617165a414402eb0796d8 | function wt_graphs( varargin )
% WT_GRAPHS
% Organize and create graphs
%
% Usage:
% wt_graphs
% wt_graphs(CMD)
% wt_graphs(VAR, TGL)
%
% Inputs:
% CMD close
% refresh
% VAR angle
% curvature
% TGL Toggle parameter ON/OFF
%
if length(varargin) == 2
varargin{1}... |
github | HelmchenLabSoftware/OCIA-master | wt_wizard_ctrl.m | .m | OCIA-master/other/functions_widefield/whisker_tracking/wt_knutsen/wt_wizard_ctrl.m | 10,146 | utf_8 | 875f79eadaf0ebadb41e2143ca2195c3 | function wt_wizard_ctrl(sName, sStateVector, sFuncVector)
%
% Whisker Tracker (WT)
%
% Authors: Per Magne Knutsen, Dori Derdikman
% The code in this script was contributed by Aharon Sheer.
%
% (c) Copyright 2004 Yeda Research and Development Company Ltd.,
% Rehovot, Israel
%
% This software is protected by... |
github | HelmchenLabSoftware/OCIA-master | wt_image_preprocess.m | .m | OCIA-master/other/functions_widefield/whisker_tracking/wt_knutsen/wt_image_preprocess.m | 1,643 | utf_8 | 8206eeba9fb64b5ae81978e901201c64 | function [mImgOut, mImgOutCroppedOnly] = wt_image_preprocess( mImgIn )
% IM = WT_IMAGE_PREPROCESS(IM)
% Pre-processes movie frames during tracking:
% (1) Crop
% (2) Rotate
% (3) Invert contrast
%
global g_tWT
bDebug = g_tWT.VerboseMode;
mImgOut = mImgIn; % assign original image
%%% DEBUG ONLY
if bDebug % origi... |
github | HelmchenLabSoftware/OCIA-master | wt_set_parameters.m | .m | OCIA-master/other/functions_widefield/whisker_tracking/wt_knutsen/wt_set_parameters.m | 9,886 | utf_8 | f5dbb32b1dbc879034399099bdb6a129 | function wt_set_parameters(varargin)
% wt_set_parameters
global g_tWT
% If no movie is loaded, do not open Parameters dialog
bMovieLoaded = 0;
if isfield(g_tWT.MovieInfo, 'Filename')
if ~isempty(g_tWT.MovieInfo.Filename)
bMovieLoaded = 1;
end
end
if ~bMovieLoaded, return, end
% Execute sub-function
i... |
github | HelmchenLabSoftware/OCIA-master | wt_toggle_imageshow.m | .m | OCIA-master/other/functions_widefield/whisker_tracking/wt_knutsen/wt_toggle_imageshow.m | 1,038 | utf_8 | b9f1e7badee6073df78f3a1350acbcfa | %%%% WT_TOGGLE_IMAGESHOW %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% Whisker Tracker (WT)
%
% Authors: Per Magne Knutsen, Dori Derdikman
%
% (c) Copyright 2004 Yeda Research and Development Company Ltd.,
% Rehovot, Israel
%
% This software is protected by copyright and patent law. Any unauthorized
% use, reproduction... |
github | HelmchenLabSoftware/OCIA-master | wt_select_file.m | .m | OCIA-master/other/functions_widefield/whisker_tracking/wt_knutsen/wt_select_file.m | 668 | utf_8 | 09d3aee4c8195babda4f43a86ff08344 | % WT_SELECT_FILE
function sMovies = wt_select_file
global g_tWT
[sFilename, sFilepath] = uigetfile({'*.avi', 'AVI-files (*.avi)'; '*.mat', 'MAT-files (*.mat)';'*.*', 'All File (*.*)'}, 'Select file');
% Return immeditaley if user cancelled this action
if ~sFilename return; end
% Build list of files
g_tWT.Movies = ... |
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