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 | isetbio/ISETBioCSF-master | plotLCA.m | .m | ISETBioCSF-master/paperfigs/CSFpaper/plotLCA.m | 1,935 | utf_8 | 784719bff7194f43753aa4df92e0ad1c | function plotLCA
lambda = 400:10:700;
lambdaFocus = 550;
defocus = 633.46 * (1/(lambdaFocus - 214.1) - 1./(lambda-214.1));
xLims = [lambda(1) lambda(end)];
yLims = [-1.6 0.6];
xTicks = 400:50:700;
yTicks = -2:0.2:1;
localDir = strrep(isetRootPath, 'toolboxes/isetbio/isettools',... |
github | isetbio/ISETBioCSF-master | plotAberrationMapAndPSF.m | .m | ISETBioCSF-master/paperfigs/CSFpaper/plotAberrationMapAndPSF.m | 7,564 | utf_8 | 6f6a551e48fb82429504d0c17340b504 | function plotAberrationMapAndPSF
opticsModels = availableCustomWvfOpticsModels();
visualizedOpticsModelIndex = 7;
visualizedOpticsModel = opticsModels{visualizedOpticsModelIndex};
targetWavelengths = 550 + [0 -70 70];
calcPupilDiametersMM = [2 3];
localDir = strrep(isetRootPath, 'tool... |
github | isetbio/ISETBioCSF-master | plotSVMdemoFig.m | .m | ISETBioCSF-master/paperfigs/CSFpaper/plotSVMdemoFig.m | 3,940 | utf_8 | e6ba3234ed2a9b6ef22281be3b0a48c0 | function plotSVMdemoFig
N = 100;
rng default % For reproducibility
mu = [1 3];
sigma = [4 1.0; 5.5 3];
sigma = (sigma.' + sigma) / 2;
% Generate data
features1 = mvnrnd(mu,sigma,N);
class1Indices = 1:N;
% Add some covariance
mu = [-3 3];
sigma = [4 .1; 0.3 8];
... |
github | isetbio/ISETBioCSF-master | visualizeOptics.m | .m | ISETBioCSF-master/paperfigs/CSFpaper/visualizeOptics.m | 7,721 | utf_8 | a46071d8e48d29c8ba48468c0215ccf7 | function visualizeOptics
opticsModels = availableCustomWvfOpticsModels();
visualizedOpticsModelIndex = 7;
visualizedOpticsModel = opticsModels{visualizedOpticsModelIndex};
targetWavelengths = [450 550 650];
showPupilRayMap = true;
calcPupilDiameterMM = 3;
umPerDegree = 300;
wa... |
github | isetbio/ISETBioCSF-master | predictTrialsToOptimalPerformance.m | .m | ISETBioCSF-master/paperfigs/CSFpaper/predictTrialsToOptimalPerformance.m | 2,382 | utf_8 | 9f0bb9397532b89bd744e99c755ad265 | function predictTrialsToOptimalPerformance
load('/Users/nicolas/Desktop/theData8.mat', 'theData')
[trialsLog8, mlpt8, svmPCA8, svmPool8] = analyzeData(theData);
load('/Users/nicolas/Desktop/theData16.mat', 'theData')
[trialsLog16, mlpt16, svmPCA16, svmPool16] = analyzeData(theData);
l... |
github | isetbio/ISETBioCSF-master | plotLensTransmittance.m | .m | ISETBioCSF-master/paperfigs/CSFpaper/plotLensTransmittance.m | 2,603 | utf_8 | 813b83bfa5e75c519aec233e853818a7 | function plotLensAndMacularPigmentTransmittance
lens = Lens();
lambda = lens.wave;
idx = find(lambda == 460);
lensTransmittance = lens.transmittance;
xLims = [lambda(1) lambda(end)];
yLims = [0 1];
xTicks = 400:50:850;
yTicks = 0:0.1:1;
localDir = strrep(isetRootPath, 'too... |
github | isetbio/ISETBioCSF-master | plotConeQuantalEfficiencies.m | .m | ISETBioCSF-master/paperfigs/CSFpaper/plotConeQuantalEfficiencies.m | 2,642 | utf_8 | 1a92bed0318f8535bcc1e03b5c06cd82 | function plotConeQuantalEfficiencies
c = coneMosaic;
lambda = c.wave;
efficienciesAtCornea = true;
if (efficienciesAtCornea)
l = Lens();
quantalEfficiencies(:,1) = c.qe(:,1) .* l.transmittance;
quantalEfficiencies(:,2) = c.qe(:,2) .* l.transmittance;
quantalE... |
github | isetbio/ISETBioCSF-master | generateFigureForPaper.m | .m | ISETBioCSF-master/paperfigs/CSFpaper/generateFigureForPaper.m | 17,010 | utf_8 | bc48504688f7f5a147ec0b969dbd6538 | function hFig = generateFigureForPaper(theFigData, variedParamLegends, variedParamName, fixedParamName, varargin)
p = inputParser;
p.addParameter('figureType', 'CSF', @ischar);
p.addParameter('figDataIndicesToDisplay', [], @isnumeric);
p.addParameter('showBanksPaperIOAcurves', false, @islogical);
p... |
github | isetbio/ISETBioCSF-master | generateFig1Components.m | .m | ISETBioCSF-master/paperfigs/CSFpaper/Figure1Resources/script/generateFig1Components.m | 10,404 | utf_8 | 054d2054c245baa11cd17606734f68cd | function generateFig1Components
[rootPath,~] = fileparts(which(mfilename));
rootPath = strrep(rootPath, 'script', 'isetbio_resources');
generateDisplayFig(rootPath);
mosaicFOV = 0.6;
theConeMosaic = generateMosaicFig(rootPath, mosaicFOV);
sceneFOV = 20;
visualizedSceneFractio... |
github | isetbio/ISETBioCSF-master | generateMosaicWithPSFsuperimposedFig.m | .m | ISETBioCSF-master/paperfigs/CSFpaper/Figure1Resources/script/generateMosaicWithPSFsuperimposedFig.m | 3,285 | utf_8 | 5de5f36e7312a7ed1a1efe5d49067462 | function generateMosaicWithPSFsuperimposedFig
[rootPath,~] = fileparts(which(mfilename));
rootPath = strrep(rootPath, 'script', 'isetbio_resources');
mosaicFOV = 0.6;
load(fullfile(rootPath, sprintf('coneMosaic_%1.2fdegFOV.mat', mosaicFOV)), 'theConeMosaic');
hFig = figure(4); clf
set... |
github | isetbio/ISETBioCSF-master | figGenerateMosaicConstruction.m | .m | ISETBioCSF-master/paperfigs/CSFpaper/MosaicGeneration/figGenerateMosaicConstruction.m | 32,546 | utf_8 | bbcf285a8c73e1c76e3b6bbd42754d7f | function figGenerateMosaicConstruction()
% cd to wherver this script resides
[localDir,~] = fileparts(which(mfilename()));
cd(localDir)
% Set random seed to obtain replicable results
rng(1235);
params.fovDegs = [0.6 0.6]; % [1.15 1.15]; % [0.75 0.4]; % FOV in degrees ([width height], default: 0.25x0.25
makeNewMosai... |
github | isetbio/ISETBioCSF-master | examineGridMethod.m | .m | ISETBioCSF-master/paperfigs/CSFpaper/MosaicGeneration/examineGridMethod.m | 22,167 | utf_8 | 5f9a85406ef6c7c509dca13a29a86d35 | function examineGridMethod
load('s.mat')
params.latticeAdjustmentPositionalToleranceF = s.positionalToleranceF/8;
params.latticeAdjustmentDelaunayToleranceF = s.DelaunayToleranceF/8;
params.maxGridAdjustmentIterations = s.maxGridAdjustmentIterations*8;
params.saveLatticeAdjustmentProgression = true;... |
github | isetbio/ISETBioCSF-master | compareLattices.m | .m | ISETBioCSF-master/paperfigs/CSFpaper/MosaicGeneration/mosaic_analyses/compareLattices.m | 5,958 | utf_8 | 3b83f5ec9d835e5c467ff02a7fe58157 | function compareLattices
coneLocsDegsISETBio = loadISETBioMosaic();
maxEcc = max(abs(coneLocsDegsISETBio(:)));
coneLocsDegsBradley = loadBradleyMosaic(maxEcc);
qDistISETBio = computeQuality(coneLocsDegsISETBio);
qDistBradley = computeQuality(coneLocsDegsBradley);
hFig = figure(1); clf;... |
github | isetbio/ISETBioCSF-master | create_GC_mosaic.m | .m | ISETBioCSF-master/paperfigs/CSFpaper/MosaicGeneration/mosaic_analyses/0_BradleyGeisler/retina_V1_model/create_GC_mosaic.m | 10,218 | utf_8 | 7662256386c16e0c2541053875ebebed | function out = create_GC_mosaic(sizeXY)
%create_GC_mosaic creates a ganglion cell mosaic that fully covers a square with edge length sizeXY, in degrees. The
%fovea is at the center of this square. The ganglion cell mosaic represents the locations of ganglion cells in the right
%eye. The distributions are governed by t... |
github | isetbio/ISETBioCSF-master | compareMosaics.m | .m | ISETBioCSF-master/paperfigs/CSFpaper/MosaicGeneration/mosaic_analyses/0_BradleyGeisler/retina_V1_model/compareMosaics.m | 8,580 | utf_8 | 9923d82688cfe491d3d86a6d2fa31305 | function compareMosaics
p = getpref('IBIOColorDetect');
IBIOColorDetectOutputBaseDir = p.outputBaseDir;
load(fullfile(IBIOColorDetectOutputBaseDir,'[c_BanksEtAlPhotocurrentAndEyeMovements]/M_hexPacking_coneSizeUm1.5797_coneSepUmNaN_VariedConeEff_rotationDegs0_eccentricityDegs0.00_LMSdensities0.60_0.30_... |
github | isetbio/ISETBioCSF-master | IBIOColorDetectLocalHookTemplate.m | .m | ISETBioCSF-master/configuration/IBIOColorDetectLocalHookTemplate.m | 5,110 | utf_8 | e3d8f1e420bc5a4994c725d29080b611 | function IBIOColorDetectLocalHook
% IBIOColorDetectLocalHook
%
% Configure things for working on the IBIOColorDetect project.
%
% For use with the ToolboxToolbox.
%
% If you 'git clone' IBIOColorDetect into your ToolboxToolbox "projectRoot"
% folder, then run in MATLAB
% tbUseProject('IBIOColorDetect')
% ToolboxToolb... |
github | isetbio/ISETBioCSF-master | IBIOCDDeleteValidationFile.m | .m | ISETBioCSF-master/validations/IBIOCDDeleteValidationFile.m | 1,863 | utf_8 | 91604fd3cee5ee741ff670eda78f969c | function IBIOCDDeleteValidationFile
% IBIOCDDeleteValidationFile
%
%% Utility to remove one validation ground truth data set (both fast and full)
% Which project
thisProject = 'IBIOColorDetect';
validationFileToBeDeleted = selectValidationFile(thisProject);
list = rdtListLocalArtifacts(...
getpref(thisProject, '... |
github | isetbio/ISETBioCSF-master | v_BanksEtAlReplicate.m | .m | ISETBioCSF-master/validations/scripts/compute/v_BanksEtAlReplicate.m | 10,122 | utf_8 | cdbe7fb38c434dcc9ca84e150a8a7079 | function varargout = v_BanksEtAlReplicate(varargin)
% varargout = v_BanksEtAlReplicate(varargin)
%
% Works by running t_coneIsomerizationsMovie with various arguments and comparing
% results with those stored.
varargout = UnitTest.runValidationRun(@ValidationFunction, nargout, varargin);
end
%% Checks
%
% 1) - Qu... |
github | isetbio/ISETBioCSF-master | v_IBIOCDConeIsomerizationsMovie.m | .m | ISETBioCSF-master/validations/scripts/basic/v_IBIOCDConeIsomerizationsMovie.m | 913 | utf_8 | ceb569c2169bbec14fb2d774bc609483 | function varargout = v_IBIOCDConeIsomerizationsMovie(varargin)
% varargout = v_IBIOCDConeIsomerizationsMovie(varargin)
%
% Works by running t_coneIsomerizationsMovie with various arguments and comparing
% results with those stored.
varargout = UnitTest.runValidationRun(@ValidationFunction, nargout, varargin);
end
... |
github | isetbio/ISETBioCSF-master | v_IBIOCD2ColorDetectFindPerformance.m | .m | ISETBioCSF-master/validations/scripts/basic/v_IBIOCD2ColorDetectFindPerformance.m | 1,344 | utf_8 | faf2ba364d560ad8e60cb0144967a7bd | function varargout = v_IBIOCD2ColorDetectFindPerformance(varargin)
% varargout = v_IBIOCDC2olorDetectFindPerformance(varargin)
%
% Works by running t_colorDetectFindPerformance with various arguments and comparing
% results with those stored.
%
% The 2 in the filename is to make sure that's gets run in the right order
... |
github | isetbio/ISETBioCSF-master | v_IBIOCDColorGabor.m | .m | ISETBioCSF-master/validations/scripts/basic/v_IBIOCDColorGabor.m | 803 | utf_8 | 1b937ff047157f10addb8199a2051da7 | function varargout = v_IBIOCDColorGabor(varargin)
% varargout = v_IBIOCDColorGabor(varargin)
%
% Works by running t_colorGabor with various arguments and comparing
% results with those stored.
varargout = UnitTest.runValidationRun(@ValidationFunction, nargout, varargin);
end
%% Function implementing the isetbio v... |
github | isetbio/ISETBioCSF-master | v_IBIOCD1ConeCurrentEyeMovementsResponseInstances.m | .m | ISETBioCSF-master/validations/scripts/basic/v_IBIOCD1ConeCurrentEyeMovementsResponseInstances.m | 4,373 | utf_8 | 3a3075f4db1339d8f99c97eeee88bc66 | function varargout = v_IBIOCD1ConeCurrentEyeMovementsResponseInstances(varargin)
% varargout = v_IBIOCD1ConeCuurentEyeMovementsResponseInstances(varargin)
%
% Works by running t_coneCurrentEyeMovementsResponseInstances with various arguments and comparing
% results with those stored.
%
% The 1 in the filename is to mak... |
github | isetbio/ISETBioCSF-master | c_DavilaGeislerReplicateEyeMovements.m | .m | ISETBioCSF-master/compute/c_DavilaGeislerReplicateEyeMovements.m | 29,278 | utf_8 | 240e9400138258bd19c98178236c6e0d | function varargout = c_DavilaGeislerReplicateEyeMovements(varargin)
% c_DavilaGeislerReplicate(varargin)
%
% Compute thresholds to replicate spatial summation calculations of Davila and Geisler, more or less.
%
% This looks at thresholds as a function of spot size. Our stimuli are
% monochromatic rather than monitor ... |
github | isetbio/ISETBioCSF-master | c_AdaptiveMethodTraining.m | .m | ISETBioCSF-master/compute/c_AdaptiveMethodTraining.m | 22,988 | utf_8 | 07b8e1b6c7214dc84c0b3127e227871c | function c_AdaptiveMethodTraining(varargin)
% c_AdaptiveMethodTraining(varargin)
%
% Explore learning classifier in the context of adaptive psychophysical
% methods.
%
% This looks at L+M detection thrsholds, by default at a moderate spatial frequency (10
% cpd). The stimulus size is inversely proportional to spatial ... |
github | isetbio/ISETBioCSF-master | c_BanksEtAlPhotocurrentAndEyeMovements.m | .m | ISETBioCSF-master/compute/c_BanksEtAlPhotocurrentAndEyeMovements.m | 34,642 | utf_8 | cd7aaf79740dcb7ad02384aeb14160e9 | function varargout = c_BanksEtAlPhotocurrentAndEyeMovements(varargin)
%% Parse input
p = inputParser;
% ----- cBanksEtAl params -----
p.addParameter('employStandardHostComputerResources', false, @islogical);
p.addParameter('useScratchTopLevelDirName', false, @islogical);
p.addParameter('nTrainingSamples',500,@isnume... |
github | isetbio/ISETBioCSF-master | c_PoirsonAndWandell96RunSession.m | .m | ISETBioCSF-master/compute/c_PoirsonAndWandell96RunSession.m | 10,709 | utf_8 | 0d903a51da10f26b4697bb99c0a835e0 | function detectionThresholdData = c_PoirsonAndWandell96RunSession(runConfigID, nTrainingSamples, performanceClassifierTrainingSamples, ...
computeMosaic, computeResponses, findPerformances, visualizeResponses, visualizePerformances, ...
visualizeMosaic, visualizeSpatialScheme, classifierSignalList, classifierTy... |
github | isetbio/ISETBioCSF-master | c_PoirsonAndWandell96VisualizeResponses.m | .m | ISETBioCSF-master/compute/c_PoirsonAndWandell96VisualizeResponses.m | 47,218 | utf_8 | e4deb588432958aa56f64344a6809f16 | function c_PoirsonAndWandell96VisualizeResponses
% c_PoirsonAndWandell96VisualizeResponses
%
% Compute color detection thresholds to replicate the Poirson & Wandell 1996
close all
% Export video (takes a long time).
exportMosaic2DActivationStillsAndVideo = true;
exportPhotoCurrentsVideo =... |
github | isetbio/ISETBioCSF-master | getOtfPsfData.m | .m | ISETBioCSF-master/toolbox/oi/getOtfPsfData.m | 1,200 | utf_8 | e3035bf91a6618fd18c25f930859242f | % Method to get the OTF and the PSF for a particular wavelength (as well as the microns/degree factor) from an oi
function [otf, otf_fxCyclesPerDeg, otf_fyCyclesPerDeg, psf, psf_xMinutes, psf_yMinutes, micronsPerDegree] = getOtfPsfData(theOI, selectedWavelength)
% Get OTF
theOptics = oiGet(theOI, 'optics');
... |
github | isetbio/ISETBioCSF-master | availableCustomWvfOpticsModels.m | .m | ISETBioCSF-master/toolbox/oi/availableCustomWvfOpticsModels.m | 892 | utf_8 | 5795b9cc7a56ee71a7515cf0fea89e0a | %availableCustomWvfOpticsModels Return cell array with names of available custom wvf optic
% availableCustomWvfOpticsModels()
%
% Also see: oiWithCustomOptics
%
% 6/20/17 npc Wrote it.
function opticsModels = availableCustomWvfOpticsModels
% Available custom wvf optics models
opticsModels = {...
... |
github | isetbio/ISETBioCSF-master | rankThibosSubjects.m | .m | ISETBioCSF-master/toolbox/oi/wavefrontutils/rankThibosSubjects.m | 24,425 | utf_8 | 1e9db04410f03c751312c7f2083b9e99 | function rankThibosSubjects()
% Recompute or load previously computed OTFs/PSFs for all 200 Thibos subjects
recomputeOTFdata = ~true;
[d,wavelengthsListToCompute, focusWavelength] = generateMultiSpectralOTFs(recomputeOTFdata);
% Generate spectral weights for the PSF residuals
psfSpectralWeight... |
github | isetbio/ISETBioCSF-master | renderNullTestComboResponse.m | .m | ISETBioCSF-master/toolbox/visualization/renderNullTestComboResponse.m | 4,963 | utf_8 | 317d2373b4bd9e26969fde38cc001052 | function timeAxisLimits = renderNullTestComboResponse(ax1, ax2, signalSource, noStimResponses, stimResponses, noStimResponsesNoiseFree, stimResponsesNoiseFree, responseLevels, timeAxis, plotType, row, col, rows)
comboResponses = cat(2, noStimResponses, stimResponses);
if ((isempty(noStimResponsesNoiseFree)... |
github | isetbio/ISETBioCSF-master | visualizeResponseInstances.m | .m | ISETBioCSF-master/toolbox/visualization/visualizeResponseInstances.m | 71,278 | utf_8 | c86fce3b63a4da32fc16ad4910d2eb46 | function hFigsInfo = visualizeResponseInstances(theMosaic, ...
stimData, noStimData, visualizeOuterSegmentFilters, ...
condIndex, condsNum)
instancesNum = size(stimData.responseInstanceArray.theMosaicIsomerizations,1);
if (instancesNum < 1)
return;
end
timeAxis = 1000*noStimData.re... |
github | isetbio/ISETBioCSF-master | visualizeBestRespondingLMSResponseInstancesAndNoiseFreeResponse.m | .m | ISETBioCSF-master/toolbox/visualization/visualizeBestRespondingLMSResponseInstancesAndNoiseFreeResponse.m | 5,291 | utf_8 | 7e24f7cb1ed3b841323ec3210518d61e | function hFig = visualizeBestRespondingLMSResponseInstancesAndNoiseFreeResponse(...
timeAxis, noStimResponseInstances, stimResponseInstances, ...
noStimNoiseFreeResponse, stimNoiseFreeResponse, responseRange, instancesPercentRange, ...
signalSource, yAxisLabel, figNo)
dt = timeAxis(2)-timeAxis(1);
... |
github | isetbio/ISETBioCSF-master | plotQuantizedWeights.m | .m | ISETBioCSF-master/toolbox/visualization/plotQuantizedWeights.m | 1,815 | utf_8 | 72c7c0461abc056d5911b95d7668d906 | function plotQuantizedWeights(axesHandle, quantizedWeights, quantizationLevels, coneLocsInDegs, pixelOutline)
quantizedWeights(quantizedWeights > 1) = 1;
quantizedWeights(quantizedWeights < -1) = -1;
faceColorsNormalizedValues = 0.5*(1+quantizedWeights);
xCoords = coneLocsInDegs(:,1);
yCoords = c... |
github | isetbio/ISETBioCSF-master | visualizeSubMosaicResponseSequence.m | .m | ISETBioCSF-master/toolbox/visualization/visualizeSubMosaicResponseSequence.m | 6,892 | utf_8 | 3db918b0df339f41c66fa01b43d2dcd5 | function visualizeSubMosaicResponseSequence(rwObject,parentParamsList,theProgram, ...
signalName, mosaicResponseSequence, eyeMovementSequence, coneTypes, timeAxis, mosaicSize, mosaicFOV, integrationTimeInSeconds, movieName)
% visualizeMosaicResponseSequence(rwObject,parentParamsList,theProgram, ...
% signalName,... |
github | isetbio/ISETBioCSF-master | visualizeDisplayProperties.m | .m | ISETBioCSF-master/toolbox/visualization/visualizeDisplayProperties.m | 11,143 | utf_8 | 5377b24855aee0a8856e4edc1d989836 | function hFig = visualizeDisplayProperties(theDisplay, backgroundParams, stimulusScene)
hFig = figure(); clf;
formatFigureForPaper(hFig, 'figureType', 'DISPLAY_PROPERTIES');
subplotPosVectors = NicePlot.getSubPlotPosVectors(...
'rowsNum', 2, ...
'colsNum', 3, ...
'hei... |
github | isetbio/ISETBioCSF-master | visualizeSceneOpticalImageAndMeanResponses.m | .m | ISETBioCSF-master/toolbox/visualization/visualizeSceneOpticalImageAndMeanResponses.m | 8,434 | utf_8 | a583832ba05edf5f1645869db0399d4d | function visualizeSceneOpticalImageAndMeanResponses(modulatedScene, oiModulated, theMosaic, noiseFreeIsomerizations, noiseFreePhotocurrents, paramsList)
sceneXYZ = sceneGet(modulatedScene, 'xyz');
oiXYZ = oiGet(oiModulated, 'xyz');
[sceneSRGB, ~, ~] = xyz2srgb(sceneXYZ);
[oiSRGB, ~, ~] = xyz2srgb(oiXYZ... |
github | isetbio/ISETBioCSF-master | visualizeSceneAndOpticalImage.m | .m | ISETBioCSF-master/toolbox/visualization/visualizeSceneAndOpticalImage.m | 9,490 | utf_8 | 9ddfc1be750422ad3c9d6397a221f197 | function visualizeSceneAndOpticalImage(backgroundScene, modulatedScene, oiBackground, oiModulated, paramsList)
% Wether to separate plots into different figures
separatePlotsForImageAndProfile = true;
sceneLMS = sceneGet(modulatedScene, 'lms');
sceneXYZ = sceneGet(modulatedScene, 'xyz');
oiLMS... |
github | isetbio/ISETBioCSF-master | generateV1FilterBank.m | .m | ISETBioCSF-master/toolbox/utility/generateV1FilterBank.m | 9,731 | utf_8 | 2d03e79dc97f92d4b5246a735d992ea2 | function [V1filterBank, hFig] = generateV1FilterBank(spatialParams, mosaicParams, topLevelDirParams, visualizeSpatialScheme, thresholdParams, paramsList)
% Filter width
filterWidthInDegrees = spatialParams.fieldOfViewDegs;
if (isfield(thresholdParams,'poolingTemplateWidthInDegrees'))
filterWidt... |
github | isetbio/ISETBioCSF-master | squareTemporalWindowCreate.m | .m | ISETBioCSF-master/toolbox/utility/squareTemporalWindowCreate.m | 3,051 | utf_8 | 81b7a1569fc7f2b91f84d30b4066fb35 | function [sampleTimes, squareTemporalWindow, rasterModulation] = squareTemporalWindowCreate(temporalParams)
%
% Special case where we generate a temporal window with a singe time sample
if (temporalParams.stimulusDurationInSeconds == temporalParams.stimulusSamplingIntervalInSeconds) && ...
(temporalParams.singleBinT... |
github | isetbio/ISETBioCSF-master | renameOutputDirs.m | .m | ISETBioCSF-master/toolbox/utility/renameOutputDirs.m | 14,523 | utf_8 | ea9c9775073b049b90f09a061aa5e01b | % Utility to rename outputDirs.
function renameOutputDirs()
% Get baseOutputDir
p = getpref('IBIOColorDetect');
rootDir = uigetdir(p.outputBaseDir);
srcPattern = '[CONE_MODULATION]'; destPattern = 'CM';
renameDirs(rootDir, srcPattern, destPattern);
srcPattern = '[LM_PLANE]'; destPattern ... |
github | isetbio/ISETBioCSF-master | removePhotocurrentDataFromResponseInstancesFile.m | .m | ISETBioCSF-master/toolbox/utility/removePhotocurrentDataFromResponseInstancesFile.m | 1,787 | utf_8 | 0eb5c0b7a59af28c7a9fd766103f7659 | function removePhotocurrentDataFromResponseInstancesFile()
conditionDir = 'CM_L71_M71_S0_con0.05000_wls_380_4_780';
updateFile(conditionDir);
end
function updateFile(conditionDir)
dropboxDir = '/home/isetbio/Data';
experimentDir = '[c_BanksEtAlPhotocurrentAndEyeMovements]';
mosaicDi... |
github | isetbio/ISETBioCSF-master | generateGaussianPoolingEnsemble.m | .m | ISETBioCSF-master/toolbox/utility/generateGaussianPoolingEnsemble.m | 4,415 | utf_8 | d3bcac27ab9239f891f3dbbbd0aac8c0 | function [GaussianPoolingEnsemble, hFig] = generateGaussianPoolingEnsemble(GaussianPoolingSigmaArcMin, mosaicParams, topLevelDirParams, visualizeSpatialScheme, thresholdParams, paramsList)
% Load the mosaic
coneParamsList = {topLevelDirParams, mosaicParams};
theProgram = 't_coneCurrentEyeMovementsResponse... |
github | isetbio/ISETBioCSF-master | generateSpatialPoolingKernel.m | .m | ISETBioCSF-master/toolbox/utility/generateSpatialPoolingKernel.m | 5,423 | utf_8 | 504ca829306cfdfc7af845ec985d249c | function [spatialPoolingFilter, hFig] = generateSpatialPoolingKernel(spatialParams, mosaicParams, topLevelDirParams, visualizeSpatialScheme, thresholdParams, paramsList)
% Load the mosaic
coneParamsList = {topLevelDirParams, mosaicParams};
theProgram = 't_coneCurrentEyeMovementsResponseInstances';
rwOb... |
github | isetbio/ISETBioCSF-master | transformDataWithV1FilterBank.m | .m | ISETBioCSF-master/toolbox/classifier/transformDataWithV1FilterBank.m | 8,763 | utf_8 | 2f3fde2b7644efa0ff1088d11a4f8028 | function [noStimData, stimData] = transformDataWithV1FilterBank(noStimData, stimData, thresholdParams, paramsList, visualizeTheTransformedSignals)
% [noStimData, stimData] = transformDataWithV1FilterBank(noStimData, stimData, thresholdParams)
% Compute from the raw signal responses (isomerizations/photocurrents) the
% ... |
github | isetbio/ISETBioCSF-master | visualizeGaussianPooledSignals.m | .m | ISETBioCSF-master/toolbox/classifier/visualizeGaussianPooledSignals.m | 5,840 | utf_8 | a0813356b0c9cbe055ed63af7255397f | function hFigs = visualizeGaussianPooledSignals(spatialPoolingKernel, timeAxis, noStimResponseInstances, stimResponseInstances, signalSource, stimContrast, spatialFilterName)
if (strcmp(signalSource, 'isomerizations'))
plotType = 'density';
else
plotType = 'line';
end
r... |
github | isetbio/ISETBioCSF-master | transformDataWithV1FilterEnsemble.m | .m | ISETBioCSF-master/toolbox/classifier/transformDataWithV1FilterEnsemble.m | 8,538 | utf_8 | f893f8081d752b46438218d73708c7e6 | function [noStimData, stimData] = transformDataWithV1FilterEnsemble(noStimData, stimData, thresholdParams, paramsList, visualizeTheTransformedSignals, parforWorkersNum)
% [noStimData, stimData] = transformDataWithV1FilterEnsemble(noStimData, stimData, thresholdParams)
% Compute from the raw signal responses (isomerizat... |
github | isetbio/ISETBioCSF-master | visualizeTransformedEnsembleSignals.m | .m | ISETBioCSF-master/toolbox/classifier/visualizeTransformedEnsembleSignals.m | 4,503 | utf_8 | 2e42215beaaeacfaaae912dadf1f583d | function hFigs = visualizeTransformedEnsembleSignals(V1filterEnsemble, timeAxis, noStimResponseInstances, stimResponseInstances, signalSource, stimContrast, spatialFilterName)
if (strcmp(signalSource, 'isomerizations'))
plotType = 'density';
else
plotType = 'line';
end
resp... |
github | isetbio/ISETBioCSF-master | transformDataWithGaussianPooling.m | .m | ISETBioCSF-master/toolbox/classifier/transformDataWithGaussianPooling.m | 5,480 | utf_8 | 8d7d9bd3848ebd08d4bf689f22b33a92 | function [noStimData, stimData] = transformDataWithGaussianPooling(noStimData, stimData, thresholdParams, paramsList, visualizeTheTransformedSignals, parforWorkersNum)
% [noStimData, stimData] = transformDataWithGaussPooling(noStimData, stimData, thresholdParams)
% Replace each cone's output with the spatially-pooled ... |
github | isetbio/ISETBioCSF-master | LoadDigitizedBanksFigure2.m | .m | ISETBioCSF-master/toolbox/thresholds/LoadDigitizedBanksFigure2.m | 2,985 | utf_8 | f38776e0c1b0efe36a74c94a51906846 |
function [A,B,C,D,E] = LoadDigitizedBanksFigure2
% These are the curves from Banks Et Al. Figure 2, digitized.
%
% A - Quantal fluctuations, 340 cd/m2
% B - Quantal + cone aperture, 340 cd/m2
% C - Quantal + cone aperture + optical blur, 340 cd/m2
% D - Quantal + cone aperture + optical blur, 34 cd/m2
% E - Quantal + ... |
github | isetbio/ISETBioCSF-master | importColorMaterialISETbioData.m | .m | ISETBioCSF-master/sideprojects/colorMaterial/scripts/importColorMaterialISETbioData.m | 9,918 | utf_8 | 2c2ccc46422dcd8acc795842c44e5c2b | function importColorMaterialISETbioData
% Loads the isomerization responses to the set of the 13 images employed
% in the the color-material paper and displays them.
%
% History
% 2/8/18 NPC Wrote it.
%
close all;
% Choose whether to render images of the data or not
renderIsomerizationMaps = ~true;
... |
github | isetbio/ISETBioCSF-master | colorMaterialSettingsImageToConeIsomerizations.m | .m | ISETBioCSF-master/sideprojects/colorMaterial/scripts/colorMaterialSettingsImageToConeIsomerizations.m | 19,336 | utf_8 | 128dd6ca3539851bb1895e00053c7117 | function colorMaterialSettingsImageToConeIsomerizations
% Loads a set of images in RGB settings (the 13 images used in the
% color-material paper) and the employed display calibration file and generates
% ISETbio scenes for that display. Then passes the scenes via a
% typical ISETbio processing pipeline to compute i... |
github | isetbio/ISETBioCSF-master | computeOpticalImages.m | .m | ISETBioCSF-master/sideprojects/BLilluminationUpdatedOpticsMosaic/computeOpticalImages.m | 5,565 | utf_8 | 9c27d9fe181a900bf6199aa91b0e4d8f | function computeOpticalImages
% visualizePSF = true;
% horizontalFOV = 16;
% pupilDiamMM = 6;
% generateOI(horizontalFOV, pupilDiamMM, visualizePSF);
% return;
ibioDataDir = '/Volumes/DropBoxDisk/Dropbox/Dropbox (Aguirre-Brainard Lab)/IBIO_data';
%ibioDataDir = '/Volumes/SamsungT3/Drop... |
github | isetbio/ISETBioCSF-master | generateMosaicForBLIllumination.m | .m | ISETBioCSF-master/sideprojects/BLilluminationUpdatedOpticsMosaic/generateMosaicForBLIllumination.m | 4,650 | utf_8 | 85662e3548677271cba705b2a040d8dc | function generateMosaicForBLIllumination()
mosaicFOV = 1.1;
integrationTime = 50/1000;
resamplingFactor = 7;
c = coneMosaicHex(7);
if (1==2)
coneMosaic = coneMosaicHex(resamplingFactor, ...
'fovDegs', mosaicFOV*[1 1], ...
'wave', SToWls([380 8 51]), ..... |
github | isetbio/ISETBioCSF-master | testImagePipeline.m | .m | ISETBioCSF-master/sideprojects/DebugImagePipeline/testImagePipeline.m | 5,705 | utf_8 | dbd6169cfd846ce007d90a382d4ba2cc | function testImagePipeline
theRetina = makeRetina();
imageStbize = [128, 128, 3];
input = ones(imageSize) * 1;
[theRetina, ~, ~, ~, coneVec] = retinaCompute(theRetina, input);
%
%% Linearity test
% Run N images with only one pixel set to a value of 1
nInput = 10;
coneR... |
github | isetbio/ISETBioCSF-master | visualizeSpatialPoolingKernelsAndStimuli.m | .m | ISETBioCSF-master/sideprojects/RucciSimulations/visualizeSpatialPoolingKernelsAndStimuli.m | 4,333 | utf_8 | 71d28e303c6f2d61a7d4cfdcc4d8f388 | function visualizeSpatialPoolingKernelsAndStimuli(spatialPoolingKernels, ...
lowFrequencyScene, lowFrequencySceneOrtho, ...
highFrequencyScene, highFrequencySceneOrtho, spatialSupportDegs, contrastLevelForScene)
hFig = figure(333); clf;
set(hFig, 'Position', [10 10 1640 910], 'Color', [1 1 1]);
... |
github | isetbio/ISETBioCSF-master | visualizeOpticalImages.m | .m | ISETBioCSF-master/sideprojects/RucciSimulations/visualizeOpticalImages.m | 2,782 | utf_8 | d160fba09b69d9bfb55cd47625d6fd47 | function visualizeOpticalImages(nullSceneOI, lowFrequencyOIs, highFrequencyOIs, lowFrequencyOIsOrtho, highFrequencyOIsOrtho, contrastLevels, analyzedNoiseInstance)
lumMapRange = [0 0.8];
subplotPosVectors = NicePlot.getSubPlotPosVectors(...
'rowsNum', numel(contrastLevels)+1, ...
'... |
github | isetbio/ISETBioCSF-master | simulateRucciExperiment.m | .m | ISETBioCSF-master/sideprojects/RucciSimulations/simulateRucciExperiment.m | 12,943 | utf_8 | 983088b455e88a57160b7bda8dcb0d2d | function simulateRucciExperiment
% Determine resources
[rootDir,~] = fileparts(which(mfilename));
[resourcesDir, parforWorkers, localHostName] = determineResources(rootDir);
addpath(genpath(rootDir));
% Actions
analyzeStimulusSpatioTemporalSpectra = true;
generateScenes = ~true;
... |
github | isetbio/ISETBioCSF-master | visualizePoolingKernel.m | .m | ISETBioCSF-master/sideprojects/RucciSimulations/visualizePoolingKernel.m | 2,129 | utf_8 | 7e801d9120a2d25bd4c945eb1d7bc3c6 | function visualizePoolingKernel(ax, coneLocsDegs, coneAperture, poolingWeights, spatialSupportDegs, showXLabel)
poolingWeights = poolingWeights / max(abs(poolingWeights));
quantizationLevels = 1024;
cmap = brewermap(quantizationLevels, '*RdBu');
faceColorsNormalizedValues = round(quantization... |
github | isetbio/ISETBioCSF-master | computeSpatialPoolingMechanismOutputs.m | .m | ISETBioCSF-master/sideprojects/RucciSimulations/computeSpatialPoolingMechanismOutputs.m | 7,748 | utf_8 | c2343159b99579b137ddd0abd739dc3b | function computeSpatialPoolingMechanismOutputs(spatialPoolingKernels, stimDescriptor, contrastLevels, analyzedNoiseInstance, nTrials, eyePosition, parforWorkers, resourcesDir)
% Load responses to null (zero contrast) stimulus
fName = fullfile(resourcesDir, sprintf('%s_nTrials_%d.mat', 'zeroContrast', nTri... |
github | isetbio/ISETBioCSF-master | analyzeStabilizedAndDynamicSpectra.m | .m | ISETBioCSF-master/sideprojects/RucciSimulations/analyzeStabilizedAndDynamicSpectra.m | 5,481 | utf_8 | 3c1815bb7c9f483cd2192e4a9161042e | function analyzeStabilizedAndDynamicSpectra(stimulusTypes, stimulusSizeDegs, fixationDurationSeconds, noiseInstances, reComputeSpectralAnalyses)
noiseNorm = nan;
oriDegs = 0;
contrastLevels = [1];
if (reComputeSpectralAnalyses)
% Generate fixational eye movmeents
nTrials = noiseInst... |
github | isetbio/ISETBioCSF-master | visualizeStabilizedAndDynamicsSpectra.m | .m | ISETBioCSF-master/sideprojects/RucciSimulations/visualizeStabilizedAndDynamicsSpectra.m | 11,341 | utf_8 | 7746010356432e378f9a7b71212bf1eb | function visualizeStabilizedAndDynamicsSpectra(xtSpectralDensityStabilized, xtSpectralDensityDynamic, sfSupport, tfSupport, figNo)
% Limits
sfLims = [0.2 50];
tfLims = [0 200];
dbRange = [0 90]; % [-60 45]; % in dB
hFig = figure(figNo+100); clf;
plotSummarySlices(xtSpectralDensityStabiliz... |
github | isetbio/ISETBioCSF-master | estimatePerformanceForStimulus.m | .m | ISETBioCSF-master/sideprojects/RucciSimulations/estimatePerformanceForStimulus.m | 11,035 | utf_8 | 25ccc91e061c9d193addcb67ec593dd4 | function estimatePerformanceForStimulus(stimDescriptor, analyzedNoiseInstance, nTrials, eyePosition, contrastLevels, resourcesDir, figNo)
% Load energy mechanism responses to the standard orientation stimulus
fName = energyResponsesDataFileName(stimDescriptor, analyzedNoiseInstance, nTrials, eyePositio... |
github | isetbio/ISETBioCSF-master | visualizeAllResponses.m | .m | ISETBioCSF-master/sideprojects/RucciSimulations/visualizeAllResponses.m | 7,603 | utf_8 | 53a925fed0ac6d8bca63707d9ab6a52e | function visualizeAllResponses(stimDescriptor, theMosaic, contrastLevel, theInstance, nTrials, eyePosition, trialNo, resourcesDir, figNo)
if (strcmp(stimDescriptor, 'zeroContrast'))
fName = fullfile(resourcesDir, sprintf('zeroContrast_nTrials_%d.mat', nTrials));
else
fName = coneMosaicResp... |
github | isetbio/ISETBioCSF-master | visualizeEnergyResponses.m | .m | ISETBioCSF-master/sideprojects/RucciSimulations/visualizeEnergyResponses.m | 5,312 | utf_8 | b4c7397cf62dbfb99a07c017d3c1ada9 | function visualizeEnergyResponses(stimDescriptor, signalName, ...
standardOriStimulusResponse, standardOriStimulusOrthoResponse, ...
orthogonalOriStimulusResponse, orthogonalOriStimulusOrthoResponse, ...
contrastLevels, timeAxis, figNo)
hFig = figure(figNo); clf;
set(hFig, 'Position', [61 22 2500 7... |
github | isetbio/ISETBioCSF-master | generateAllMosaicResponses.m | .m | ISETBioCSF-master/sideprojects/RucciSimulations/generateAllMosaicResponses.m | 11,246 | utf_8 | f9c323b3c940754baae5bdb3d6898996 | function generateAllMosaicResponses(theMosaic, nullSceneOI, lowFrequencyOIs, highFrequencyOIs, ...
lowFrequencyOIsOrtho, highFrequencyOIsOrtho, mosaicIntegrationTimeSeconds, fixationDurationSeconds, warmupTimeSeconds, ...
contrastLevels, analyzedNoiseInstance, nTrials, eyePosition, parfo... |
github | isetbio/ISETBioCSF-master | generateSpatiotemporalStimulusSequenceDueToFixationalEM.m | .m | ISETBioCSF-master/sideprojects/RucciSimulations/stimGeneration/generateSpatiotemporalStimulusSequenceDueToFixationalEM.m | 8,493 | utf_8 | ad0db4adaec44944456bbd8ea01bce15 | function sData = generateSpatiotemporalStimulusSequenceDueToFixationalEM(timeAxis, emPosArcMin, stimulus)
instancesNum = size(emPosArcMin,1);
timeBins = size(emPosArcMin,2);
extraBins = 0; % max([0 round((1024-timeBins)/2)]); % bins for zero padding in time domain
totalTimeBins = timeBins+extraBins*2;
... |
github | isetbio/ISETBioCSF-master | generateGratingInNoiseSpatialModulationPattern.m | .m | ISETBioCSF-master/sideprojects/RucciSimulations/stimGeneration/generateGratingInNoiseSpatialModulationPattern.m | 11,850 | utf_8 | 9eb44765078c1059dc9fed9d949350c5 | % Generate noise with spectrum f^{alpha}
function [stimulus, noiseNorm] = generateGratingInNoiseSpatialModulationPattern(stimSizeArcMin, pixelSizeArcMin, gratingParams, noiseParams, noiseNorm, instancesNum, figNo)
N = round(stimSizeArcMin / pixelSizeArcMin);
if (mod(N,2) == 1)
N = N + 1;
end
... |
github | isetbio/ISETBioCSF-master | generateAllScenes.m | .m | ISETBioCSF-master/sideprojects/RucciSimulations/stimGeneration/generateAllScenes.m | 7,138 | utf_8 | 99c2115f2a6e21a8f100db07100daf8f | function generateAllScenes(noiseInstances, stimulusSizeDegs, meanLuminanceCdPerM2, contrastLevels, resourcesDir)
viewingDistance = 75/100;
% Generate stimulus spatial modulations
noiseNorm = nan;
nContrasts = numel(contrastLevels);
oriDegs = 0;
[lowFrequencySpatialModulations, ... |
github | isetbio/ISETBioCSF-master | testSVM.m | .m | ISETBioCSF-master/sideprojects/SVMdemo/testSVM.m | 7,842 | utf_8 | 5a089463b4b89cee420caaaf26e1917b | % Examine SVM performance as a function of trialsNum
function testSVM
clear; close all;
% Stimulus spatial frequency
testSF = 2.0;
% Stimulus size (inversely proportional to SF)
sizeDegs = 2.0/testSF;
theMosaic = coneMosaicTreeShrewCreate(75, ...% theOI.optics.micronsPerDegree, ... |
github | isetbio/ISETBioCSF-master | pupilSizeForAnasExperiment.m | .m | ISETBioCSF-master/sideprojects/playground/pupilSizeForAnasExperiment.m | 2,182 | utf_8 | df42f674ef64862c90869765532d09be | function pupilSizeForAnasExperiment
% fraction of stimulus area to background (entire display) area
fraction = 0.288;
scene.xDegs = 20;
scene.yDegs = 16.7;
scene.luminance = 17.25;
background.xDegs = scene.xDegs/sqrt(fraction);
background.yDegs = scene.yDegs/sqrt(fraction);
background... |
github | isetbio/ISETBioCSF-master | macularPigmentCalcs.m | .m | ISETBioCSF-master/sideprojects/playground/macularPigmentCalcs.m | 3,496 | utf_8 | 47cab89feaca8a310163410f474d6bb5 | function macularPigmentCalcs
wavelength = 380:5:780;
mDefault = Macular('wave', wavelength);
densityAtEcc = Macular.eccDensity(0);
mPeriphery = Macular('wave', wavelength, 'density', densityAtEcc);
x = -2:0.1:2;
xCenter = (numel(x)-1)/2
y = x;
[X,Y] = meshgrid(x,y);
eccDeg... |
github | isetbio/ISETBioCSF-master | testOI.m | .m | ISETBioCSF-master/sideprojects/playground/testOI.m | 4,078 | utf_8 | fcb0c8e195589836e6db8fdb698e2ffb | function testOI
rParams = responseParamsGenerate;
rParams.backgroundParams.backgroundxyY = [0.31 0.31 10];
rParams.colorModulationParams.coneContrasts = [0.5 0.5 0.5];
rParams.spatialParams.row = 256;
rParams.spatialParams.col = 256;
rParams.spatialParams.fieldOfViewDegs = 0.3;
rParams.s... |
github | isetbio/ISETBioCSF-master | testSmoothGrid.m | .m | ISETBioCSF-master/sideprojects/MosaicGenerator/testSmoothGrid.m | 10,534 | utf_8 | d0ef6a18e2f81558e221dd209a403930 | function testSmoothGrid
load('cp0.5degs.mat', 'conePositions');
% Termination conditions
dTolerance = 1.0e-3;
maxIterations = 500;
visualizeProgress = true;
conePositions = smoothGrid(conePositions, dTolerance, maxIterations, visualizeProgress);
end
function conePositions = smoo... |
github | isetbio/ISETBioCSF-master | generateRGCmosaicFromConeMosaic.m | .m | ISETBioCSF-master/sideprojects/MosaicGenerator/generateRGCmosaicFromConeMosaic.m | 7,295 | utf_8 | 57466a9779a5f4b4211225fff857e8e4 | function generateRGCmosaicFromConeMosaic()
% Instantiate a WatsonRGCModel object. Set the 'generateAllFigures' flag
% to true to generate several figures of the Watson 2014 paper
WatsonRGCCalc = WatsonRGCModel('generateAllFigures', false);
meridians = {'superior', 'inferior', 'nasal', 'temporal'}... |
github | isetbio/ISETBioCSF-master | visualizeLargeMosaic.m | .m | ISETBioCSF-master/sideprojects/MosaicGenerator/visualizeLargeMosaic.m | 4,388 | utf_8 | d0581d4d56b0472c3f215b0764914c18 | function visualizeLargeMosaic()
load('HexConeMosaic15DegsBest.mat', 'theMosaic');
geomStruct = theMosaic.geometryStruct();
% Visualize only part of the mosaic X(degs): [0 7], Y(degs): [-0.25 0.25]
visualizedFOV = struct('xo', 3.5, 'yo', 0.0, 'width', 7., 'height', 0.4);
WatsonRGCCalc = Wat... |
github | isetbio/ISETBioCSF-master | exploreMosaic.m | .m | ISETBioCSF-master/sideprojects/MosaicGenerator/exploreMosaic.m | 8,415 | utf_8 | 74233c562de4d1f7ce7016ea5819f420 | function exploreMosaic
[rootPath0,~] = fileparts(which(mfilename));
rootPath = strrep(rootPath0, 'sideprojects/MosaicGenerator', 'FVM2018Scripts/resources');
mosaicFOV = 20;
mosaicFileName = sprintf('ConeMosaic_%2.1fDegs.mat', mosaicFOV);
%load(mosaicFileName, 'theConeMosaic');
load('/Volu... |
github | isetbio/ISETBioCSF-master | generateFigureDorDavidsCappadociaTalk.m | .m | ISETBioCSF-master/sideprojects/DavidCappadociaTalk/generateFigureDorDavidsCappadociaTalk.m | 3,828 | utf_8 | ca3df96ba8467f9073a8b2cd8560a08b | function generateFigureDorDavidsCappadociaTalk
generateFig1()
generateFig2()
end
function generateFig2()
load('Fig2')
expData.x = Fig2(:,1)
expData.y = Fig2(:,2)
expData.errorBar = (Fig2(:,4)-expData.y)*0.7;
poolingData.x = Fig2(:,5);
poolingData.y = Fig2(:,6);
tmp= [.... |
github | isetbio/ISETBioCSF-master | run_c_DavilaGeislerReplicateEyeMovementsJob.m | .m | ISETBioCSF-master/bashscripts/forLocalMachine/run_c_DavilaGeislerReplicateEyeMovementsJob.m | 5,180 | utf_8 | 6df8e0f21ab4bd4e1086c3e8c1157a9c | function run_c_DavilaGeislerReplicateEyeMovementsJob
% What to do ?
computeMosaic = ~true;
visualizeMosaic = ~true;
computeResponses = ~true;
visualizeResponses = ~true;
visualizeSpatialScheme = true;
findPerformance = true;
visualizePerformance = true;
visualizeTransformedSignal... |
github | isetbio/ISETBioCSF-master | t_colorDetectFindPerformance.m | .m | ISETBioCSF-master/tutorials/basic/t_colorDetectFindPerformance.m | 28,583 | utf_8 | 620d6d57597a80b893246ee5eec79089 | function [validationData,extraData] = t_colorDetectFindPerformance(varargin)
% [validationData,extraData] = t_colorDetectFindPerformance(varargin)
%
% Classify data generated by
% t_coneCurrentEyeMovementsResponseInstances.
% That tutorial generates multiple noisy instances of responses for color
% Gabors and saves t... |
github | isetbio/ISETBioCSF-master | t_coneCurrentEyeMovementsResponseInstances.m | .m | ISETBioCSF-master/tutorials/basic/t_coneCurrentEyeMovementsResponseInstances.m | 44,393 | utf_8 | 224507a9387430aa6fe928ab9f6b0969 | function [validationData, extraData, varargout] = t_coneCurrentEyeMovementsResponseInstances(varargin)
% T_CONECURRENTEYEMOVEMENTRESPONSES Generate response instances for a given stimulus condition.
% [validationData, extraData, varargout] = T_CONECURRENTEYEMOVEMENTRESPONSES(varargin)
%
% Show how to generate... |
github | isetbio/ISETBioCSF-master | run_adaptiveOpticsCSFunderSpatialSummation.m | .m | ISETBioCSF-master/paperscripts/SpatialPoolingAdaptiveOptics/run_adaptiveOpticsCSFunderSpatialSummation.m | 5,768 | utf_8 | 7b24ca93f47988d7842a87592e85c6e5 | function run_adaptiveOpticsCSFunderSpatialSummation
% Compute and contrast performance at the level of isomerizations
% under AO conditions with and without spatial pooling
%
% Syntax:
% run_adaptiveOpticsCSFunderSpatialSummation
%
% Description:
%
%
% Inputs:
% None.
%
% Outputs:
% None.
%
% Optional key/valu... |
github | isetbio/ISETBioCSF-master | run_paper2PupilEffect.m | .m | ISETBioCSF-master/paperscripts/CSFpaper2/run_paper2PupilEffect.m | 6,185 | utf_8 | 9a645db0f90e4ad776ae97e3444c4b67 | function run_paper2PupilEffect
% Contrast performance for 2 vs 3 mm pupils
%
% Syntax:
% run_paper2PupilEffect
%
% Description:
% Compute and contrast performance for 2 vs 3 mm pupils
% This is done in the absence of eye movements using the SVM-Template-Linear inference
%
% The computation is done via the ec... |
github | isetbio/ISETBioCSF-master | run_paper2FixationalEyeMovementsVsNone.m | .m | ISETBioCSF-master/paperscripts/CSFpaper2/run_paper2FixationalEyeMovementsVsNone.m | 8,465 | utf_8 | eb8e514a804fab1b1326df489850fb20 | function run_paper2FixationalEyeMovementsVsNone
% Compute and contrast performance for fixational eye movements vs no EM.
%
% Syntax:
% run_paper2FixationalEyeMovementsVsNone
%
% Description:
% Compute and contrast performance for fixational eye movements vs no EM
%
% The computation is done via the ecc-based c... |
github | isetbio/ISETBioCSF-master | run_paper2InferenceEngine.m | .m | ISETBioCSF-master/paperscripts/CSFpaper2/run_paper2InferenceEngine.m | 15,058 | utf_8 | 2aa4aac105576e2d6f834015fbcef0eb | function run_paper2InferenceEngine
% Compute and contrast performance via different inference engines.
%
% Syntax:
% run_paper2InferenceEngine
%
% Description:
% Compute and contrast performance via different inference engines.
%
% The computation is done via the ecc-based cone efficiency & macular pigment
% ... |
github | isetbio/ISETBioCSF-master | run_paper2_ComboFemAndPcurrent.m | .m | ISETBioCSF-master/paperscripts/CSFpaper2/run_paper2_ComboFemAndPcurrent.m | 8,685 | utf_8 | b0b177b3fbcdc9823b689406e8d0aebc | function run_paper2_ComboFemAndPcurrent
% Compute and contrast performance via different inference engines.
%
% Syntax:
% run_paper2_FinalConditionsUsing2mmPupil
%
% Description:
% Compute and contrast performance via different inference engines.
%
% The computation is done via the ecc-based cone efficiency & m... |
github | isetbio/ISETBioCSF-master | run_paper2InferenceEngineMultiTemplates.m | .m | ISETBioCSF-master/paperscripts/CSFpaper2/run_paper2InferenceEngineMultiTemplates.m | 16,340 | utf_8 | 9307ee6db58861651e8af1514e44b393 | function run_paper2InferenceEngineMultiTemplates
% Compute and contrast performance via different inference engines.
%
% Syntax:
% run_paper2InferenceEngine
%
% Description:
% Compute and contrast performance via different inference engines.
%
% The computation is done via the ecc-based cone efficiency & macula... |
github | isetbio/ISETBioCSF-master | run_paper2_CrowellBanksUnpublishedExperimentVisualize.m | .m | ISETBioCSF-master/paperscripts/CSFpaper2/run_paper2_CrowellBanksUnpublishedExperimentVisualize.m | 10,202 | utf_8 | c5f6c7130aef570ed7597f84b9c267c1 | function run_paper2_CrowellBanksUnpublishedExperimentVisualize
% Visualize responses from experiment 3 of Crowell & Banks
%exit
% Syntax:
% run_paper2_CrowellBanksUnpublishedExperiment
%
% Description:
% Compute simulated responses to experiment 3 (spatial summation experiment)
% of Crowell & Banks (unpublishe... |
github | isetbio/ISETBioCSF-master | run_paper2EffectOfBackgroundLuminance.m | .m | ISETBioCSF-master/paperscripts/CSFpaper2/run_paper2EffectOfBackgroundLuminance.m | 6,833 | utf_8 | 532624b1d20d84af4dc2ee35e4b74067 | function run_paper2EffectOfBackgroundLuminance
% Compute and contrast performance at the level of photocurrents for
% different background luminance levels
%
% Syntax:
% run_paper2EffectOfBackgroundLuminance
%
% Description:
% Compute and contrast performance at the different background luminance
% levels in th... |
github | isetbio/ISETBioCSF-master | run_paper2_CrowellBanksUnpublishedExperimentTest.m | .m | ISETBioCSF-master/paperscripts/CSFpaper2/run_paper2_CrowellBanksUnpublishedExperimentTest.m | 13,139 | utf_8 | 92b493a7a067b18b6ddf48cfd00b75f0 | function run_paper2_CrowellBanksUnpublishedExperimentTest
% Simulate experiment 3 of Crowell & Banks
%
% Syntax:
% run_paper2_CrowellBanksUnpublishedExperiment
%
% Description:
% Simulate experiment 3 (spatial summation experiment) of Crowell &
% Banks (unpublished data)
%
%
% Inputs:
% None.
%
% Outputs:
%... |
github | isetbio/ISETBioCSF-master | run_paper2_FinalConditionsUsing2mmPupil.m | .m | ISETBioCSF-master/paperscripts/CSFpaper2/run_paper2_FinalConditionsUsing2mmPupil.m | 10,261 | utf_8 | 4d968916b0d28b1d1caea05a9a8e5af4 | function run_paper2_FinalConditionsUsing2mmPupil
% Compute and contrast performance via different inference engines.
%
% Syntax:
% run_paper2_FinalConditionsUsing2mmPupil
%
% Description:
% Compute and contrast performance via different inference engines.
%
% The computation is done via the ecc-based cone effic... |
github | isetbio/ISETBioCSF-master | run_paper2FixationalEyeMovementsVsNoneNew.m | .m | ISETBioCSF-master/paperscripts/CSFpaper2/run_paper2FixationalEyeMovementsVsNoneNew.m | 8,483 | utf_8 | 848e687fc5b212f44b5fab3c3b4a7e46 | function run_paper2FixationalEyeMovementsVsNoneNew
% Compute and contrast performance for fixational eye movements vs no EM.
%
% Syntax:
% run_paper2FixationalEyeMovementsVsNone
%
% Description:
% Compute and contrast performance for fixational eye movements vs no EM
%
% The computation is done via the ecc-base... |
github | isetbio/ISETBioCSF-master | run_paper2EffectOfPulseDuration.m | .m | ISETBioCSF-master/paperscripts/CSFpaper2/run_paper2EffectOfPulseDuration.m | 8,456 | utf_8 | 6e136cc82bcdc23f146edca9e2dab555 | function run_paper2EffectOfPulseDuration
% Compute and contrast performance at the level of photocurrents for
% different pulse durations
%
% Syntax:
% run_paper2EffectOfPulseDuration
%
% Description:
% Compute and contrast performance at the different pulse durations
%
% The computation is done via the ecc-bas... |
github | isetbio/ISETBioCSF-master | run_paper2IsomerizationsVsPhotocurrents.m | .m | ISETBioCSF-master/paperscripts/CSFpaper2/run_paper2IsomerizationsVsPhotocurrents.m | 6,595 | utf_8 | 67dbb4f1bc6ecb8b7b540b18afdb90f8 | function run_paper2IsomerizationsVsPhotocurrents
% Compute and contrast performance at the level of isomerizations vs
% photocurrents.m
%
% Syntax:
% run_paper2IsomerizationsVsPhotocurrents
%
% Description:
% Compute and contrast performance at the level of isomerizations vs photocurrents.
% This is done in the... |
github | isetbio/ISETBioCSF-master | makePhotocurrentFigure.m | .m | ISETBioCSF-master/paperscripts/CSFpaper2/makePhotocurrentFigure.m | 3,996 | utf_8 | d3df2ce0966d4f6a32dc37aaf3c04da4 | function makePhotocurrentFigure
% Define background luminace levels examined & the pedestal step (cd/m2)
backgroundLuminances = [34];
lumStep = 20;
stimulusSamplingInterval = 20 / 1000;
oiTimeAxis = -0.5:stimulusSamplingInterval:1;
stimDuration = 500/1000;
mosaicSize = nan;
i... |
github | isetbio/ISETBioCSF-master | run_paper2_CrowellBanksUnpublishedExperiment.m | .m | ISETBioCSF-master/paperscripts/CSFpaper2/run_paper2_CrowellBanksUnpublishedExperiment.m | 12,310 | utf_8 | 5f4f5fd60f4620213b7f349a01946914 | function run_paper2_CrowellBanksUnpublishedExperiment
% Simulate experiment 3 of Crowell & Banks
%
% Syntax:
% run_paper2_CrowellBanksUnpublishedExperiment
%
% Description:
% Simulate experiment 3 (spatial summation experiment) of Crowell &
% Banks (unpublished data)
%
%
% Inputs:
% None.
%
% Outputs:
% ... |
github | isetbio/ISETBioCSF-master | photocurrentAdaptationModelDemo.m | .m | ISETBioCSF-master/paperscripts/CSFpaper2/photocurrentAdaptationModelDemo.m | 20,328 | utf_8 | 3c61356f43966f09fabc5c0c880bc46f | function photocurrentAdaptationModelDemo
% The Rieke et al os model is constructed from responses to
% isomerization rates in the range [500 20000] R*/cone/sec
validIsomerizationRateRange = [300 20000];
% Duration of flash in seconds
flashDurationSeconds = 1000/1000;
% Different flash... |
github | isetbio/ISETBioCSF-master | makeFixationalEyeMovementFigure.m | .m | ISETBioCSF-master/paperscripts/CSFpaper2/fixationalEMDemoFig/makeFixationalEyeMovementFigure.m | 8,517 | utf_8 | 660d9faa3858508b9caa32b12284f0e9 | function makeFixationalEyeMovementFigure()
% Generate 512 3-second emPaths with a sample time of 1 msec
emDurationSeconds = 3;
sampleTimeSeconds = 1.0 / 1000;
nTrials = 1024;
microSaccadeType = 'none'; % , 'heatmap/fixation based', 'none'
fixEMobj = fixationalEM();
fixEMobj.randomS... |
github | isetbio/ISETBioCSF-master | computeNoisyReponseSNRs.m | .m | ISETBioCSF-master/paperscripts/CSFpaper2/pCurrentModelDemos/computeNoisyReponseSNRs.m | 10,213 | utf_8 | b025793070de11fc84e018de60f30e90 | function [timeAxis, photoCurrents, noisyPhotoCurrentsInstance, ...
timeAxisConeExcitations, coneExcitationRates, noisyConeExcitationRateInstance, ...
photocurrentSNR, coneExcitationSNR, legends] = ...
computeNoisyReponseSNRs(adaptationPhotonRates, pulseWeberContrasts, ...
pulseDurationSeconds, s... |
github | isetbio/ISETBioCSF-master | plotOnOffResponses.m | .m | ISETBioCSF-master/paperscripts/CSFpaper2/pCurrentModelDemos/plotOnOffResponses.m | 9,061 | utf_8 | 782ecae892ef35ccc1f9e177b4151c23 | function plotOnOffResponses(timeAxis, stepResponses, modelResponses, adaptationPhotonRates, stepWeberConstants, negativePulseDelay, figNo)
% Plot the photocurrent responses for the examined On/OFF stimuli
%
% Syntax:
% plotStepResponses(timeAxis, stepResponses, adaptationPhotonRates, stepWeberConstants, legends, fig... |
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