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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/isetbio-master | computeConeEfficiencyCorrectionFactors.m | .m | isetbio-master/isettools/cones/deprecated/@coneMosaicHex/computeConeEfficiencyCorrectionFactors.m | 6,910 | utf_8 | ffe20ee77b534ac05274548566b56173 | function [correctionFactors, outerSegmentLengthAttenationFactors, innerSegmentDiameterBoostFactors] = computeConeEfficiencyCorrectionFactors(obj, triggerFunctionName, varargin)
% Static method for computing ecc-based absorption correction factors
%
% Syntax:
% correctionFactors = COMPUTECONEEFFICIENCYCORRECTIONFACTOR... |
github | isetbio/isetbio-master | visualizeActivationMaps.m | .m | isetbio-master/isettools/cones/deprecated/@coneMosaicHex/visualizeActivationMaps.m | 23,311 | utf_8 | 618230b15bc2cec2e59880bf17ede624 | function hFig = visualizeActivationMaps(obj, activation, varargin)
% Separately visualize mosaic activations for each submosaic and the whole
%
% Syntax:
% hFig = visualizeActivationMaps(obj, activation, varargin)
%
% Description:
% Visualize mosaic activations separately for each submosaic and for the
% entire... |
github | isetbio/isetbio-master | plotMosaicProgression.m | .m | isetbio-master/isettools/cones/deprecated/@coneMosaicHex/plotMosaicProgression.m | 11,564 | utf_8 | df6133494ea23257cba4b7866f7cd3f1 | function hFig = plotMosaicProgression(obj, varargin)
% Plot the mosaic progression
%
% Syntax:
% hFig = plotMosaicProgression(obj, [varargin])
%
% Description:
% Plot the mosaic progression
%
% Inputs:
% obj - the cone mosaic hex object
%
% Outputs:
% hFig - The figure handle
%
% Optional key/value pairs:
% ... |
github | isetbio/isetbio-master | demosaicConeTypeActivationFromFullActivation.m | .m | isetbio-master/isettools/cones/deprecated/@coneMosaicHex/demosaicConeTypeActivationFromFullActivation.m | 5,969 | utf_8 | dedfe9a8c02ccc8d2239fa3d4f5611fe | function [demosaicedResponseMap, spatialSupportDegs, coneResponses, coneXlocsDegs, coneYlocsDegs] = ...
demosaicConeTypeActivationFromFullActivation(obj, coneType,...
theFullPatternResponse, demosaicingSampleSpacingMicrons, varargin)
% Obtain a demosaiced map of the activation for a single cone type from
% th... |
github | isetbio/isetbio-master | renderActivationMap.m | .m | isetbio-master/isettools/cones/deprecated/@coneMosaicHex/renderActivationMap.m | 14,583 | utf_8 | 42dcaa82d21e7dea591c5652582ccf3f | function activationMetaData = renderActivationMap(obj, axesHandle, activation, varargin)
% Render (in the passed axesHandle) an activation map for the hex mosaic
%
% Syntax:
% renderActivationMap(obj, axesHandle, activation, [varargin])
%
% Description:
% Render (draw) an activation map for the hex mosaic on the p... |
github | isetbio/isetbio-master | reassignConeIdentities.m | .m | isetbio-master/isettools/cones/deprecated/@coneMosaicHex/reassignConeIdentities.m | 8,516 | utf_8 | 4ec70ffdbfd7b429a5a081906eca9dc9 | function reassignConeIdentities(obj, varargin)
% Reassign the cone identities of the cone mosaic hex object
%
% Syntax:
% reassignConeIdentities(obj, [varargin])
%
% Description:
% Reassign the cone identities of the provided cone mosaic hex.
%
% Inputs:
% obj - The ... |
github | isetbio/isetbio-master | coneMosaicHex.m | .m | isetbio-master/isettools/cones/deprecated/@coneMosaicHex/coneMosaicHex.m | 24,823 | utf_8 | e6db9b296f29bdca8c9a5ce3f2f80956 | classdef coneMosaicHex < coneMosaic
% Create a hexagonal cone mosaic class
%
% Syntax:
% cMosaicHex = coneMosaicHex(resamplingFactor, [varargin]);
%
% Description:
% The cone mosaic HEX is a subclass of coneMosaic. It differs because
% the array of cones is placed on a hexagonal, rather than rectangular,
% g... |
github | isetbio/isetbio-master | geometryStruct.m | .m | isetbio-master/isettools/cones/deprecated/@coneMosaicHex/geometryStruct.m | 2,690 | utf_8 | 4db4585a9e1bd406b293cb228d219e88 | function cmStruct = geometryStruct(obj)
% % Return a struct with the mosaic geometry
%
% Syntax:
% cmStruct = geometryStruct(obj)
%
% Description:
% Return a struct with the mosaic geometry (cone positions, Delaunay
% triangles, and cone aperture sizes)
%
%
% Inputs:
% obj - The cone mosaic hex obje... |
github | isetbio/isetbio-master | plot.m | .m | isetbio-master/isettools/cones/rectangular/@coneMosaic/plot.m | 26,319 | utf_8 | c27713137c42c3f1f385ebe825a23bc4 | function [uData, hf] = plot(obj, plotType, varargin)
% Plot function for @conemmsaic base class
%
% Syntax:
% [uData, hf] = plot(obj, plotType, varargin)
%
% Description:
% There is a specialized plot method for the coneMosaicHex class that
% calls this function.
%
% When the plot type string begins with 'o... |
github | isetbio/isetbio-master | computeForOISequence.m | .m | isetbio-master/isettools/cones/rectangular/@coneMosaic/computeForOISequence.m | 37,499 | utf_8 | d85aec187040e793d5105dcf92ee407f | function [absorptions, photocurrents, LMSfilters, meanCur] = ...
computeForOISequence(obj, oiSequence, varargin)
% Compute cone absorptions and optionally photocurrents for a @oiSequence
%
% Syntax:
% [absorptions, photocurrents, LMSfilters] = ...
% computeForOISequence(obj, oiSequence, varargin)
%
% Descr... |
github | isetbio/isetbio-master | lowPassMosaicResponse.m | .m | isetbio-master/isettools/cones/rectangular/@coneMosaic/lowPassMosaicResponse.m | 4,169 | utf_8 | d87531c6401b27bd38c303c65727fbaa | function [lowPassedResponse, Lmap, Mmap, Smap] = ...
lowPassMosaicResponse(obj, absorptions, spaceConstants)
% Low pass filter mosaic isomerizations
%
% Syntax:
% [lowPassedResponse, Lmap, Mmap, Smap] = ...
% lowPassMosaicResponse(obj, response, spaceConstants)
%
% Description:
% Spatially low pass fi... |
github | isetbio/isetbio-master | importExternalConeData.m | .m | isetbio-master/isettools/cones/@cMosaic/importExternalConeData.m | 6,270 | utf_8 | 7be4c795372276ffd14887de8d4c70db | function importExternalConeData(obj, coneData)
% Validate coneData struct
validateInput(coneData);
% Flag indicating that the mosaic was generated via imported cone data
obj.employsImportedConeData = true;
% Import cone positions
switch (coneData.positionUnits)
case 'microns'
... |
github | isetbio/isetbio-master | plot.m | .m | isetbio-master/isettools/cones/@cMosaic/plot.m | 10,002 | utf_8 | dfa966af60200a507413564b4ff93f47 | function [uData, hdl] = plot(cmosaic,plotType, allE, varargin)
% plot methods for the cMosaic
%
% Syopsis
% [uData, hdl] = plot(cmosaic, plotType, allE, varargin)
%
% Inputs
% cmosaic - cMosaic class
% plotType - See below. Many.
%
% Optional key/val pairs
% roi
% cone type
% hdl - Figure han... |
github | isetbio/isetbio-master | computeMPBoostFactors.m | .m | isetbio-master/isettools/cones/@cMosaic/computeMPBoostFactors.m | 3,532 | utf_8 | e7738e93f94575efa982bb131efd1418 | % Since this correction is applied on the optical image we need to compute
% correction factors at each emPosition because the relative position
% between the optical image and the mosaic varies during the emPath
function macularPigmentDensityBoostFactors = computeMPBoostFactors(obj, oiPositionsDegs, emPositionDegs, oi... |
github | isetbio/isetbio-master | distanceMicronsToDistanceDegreesForCmosaic.m | .m | isetbio-master/isettools/cones/@cMosaic/distanceMicronsToDistanceDegreesForCmosaic.m | 779 | utf_8 | 17ef8b4a063c2ceac5f8f32c675ce6ff | % Method to transform a DISTANCE specified in units of visual
% degrees to DISTANCE in units of retinal microns based on the @cMosaic configuration
function degrees = distanceMicronsToDistanceDegreesForCmosaic(obj, microns)
if (~isempty(obj.micronsPerDegreeApproximation))
% Linear transformation based on a... |
github | isetbio/isetbio-master | generateApertureKernel.m | .m | isetbio-master/isettools/cones/@cMosaic/generateApertureKernel.m | 6,712 | utf_8 | cab3a884f30b05f59fae7f9b8f750a3d | function apertureKernel = generateApertureKernel(obj, blurApertureDiameterMicrons, oiResMicrons, lowOpticalImageResolutionWarning)
% Compute convolution kernel size in pixels - make it big here, we'll
% trim at the end
apertureSamples = ceil(blurApertureDiameterMicrons*2 / oiResMicrons);
if (apert... |
github | isetbio/isetbio-master | apertureBlurSigmaMicronsOfConeFromItsBlurZone.m | .m | isetbio-master/isettools/cones/@cMosaic/apertureBlurSigmaMicronsOfConeFromItsBlurZone.m | 736 | utf_8 | b150787060c804b37310881a5fa914fa | % Blur sigma (in microns) of a cone with index theConeIndex, from its blur zone
function apertureBlurSigmaMicrons = apertureBlurSigmaMicronsOfConeFromItsBlurZone(obj, theConeIndex)
apertureBlurSigmaMicrons = [];
if (isempty(obj.coneApertureModifiers))
return;
end
foundZoneOfCone = false;
for... |
github | isetbio/isetbio-master | semiTransparentContourPlot.m | .m | isetbio-master/isettools/cones/@cMosaic/semiTransparentContourPlot.m | 2,124 | utf_8 | f0dc43482a337efbc5b0d291c3694f7a | % Function to generate a semitransparent controur plot
function semiTransparentContourPlot(axesHandle, xSupport, ySupport, zData, zLevels, cmap, alpha, contourLineColor, varargin)
p = inputParser;
p.addParameter('lineWidth', 1.0, @isscalar);
p.addParameter('edgeAlpha', 0.5, @isscalar);
p.parse(vara... |
github | isetbio/isetbio-master | computeConeApertureRodIntrusionInducedShrinkageFactors.m | .m | isetbio-master/isettools/cones/@cMosaic/computeConeApertureRodIntrusionInducedShrinkageFactors.m | 2,425 | utf_8 | de733e67bab7eec3bdd1cf252ca9a579 | function computeConeApertureRodIntrusionInducedShrinkageFactors(obj)
% Compute radial eccDegs of all cones
coneEccentricityDegs = sqrt((obj.coneRFpositionsDegs(:,1)).^2 + (obj.coneRFpositionsDegs(:,2)).^2);
% Compute shrinkage at eccentricities
obj.coneApertureRodIntrusionInducedShrinkageFactors = ... |
github | isetbio/isetbio-master | distanceDegreesToDistanceMicronsForCmosaic.m | .m | isetbio-master/isettools/cones/@cMosaic/distanceDegreesToDistanceMicronsForCmosaic.m | 767 | utf_8 | 4b000c2ad530a5c4c3c64a0f5c87c1d1 | % Method to transform a DISTANCE specified in units of retinal
% microns to DISTANCE in units of visual degrees based on the @cMosaic configuration
function microns = distanceDegreesToDistanceMicronsForCmosaic(obj, degrees)
if (~isempty(obj.micronsPerDegreeApproximation))
% Linear transformation based on a... |
github | isetbio/isetbio-master | sizeMicronsToSizeDegreesForCmosaic.m | .m | isetbio-master/isettools/cones/@cMosaic/sizeMicronsToSizeDegreesForCmosaic.m | 1,890 | utf_8 | 213e85cddf740121ed986edfd31ff214 | % Method to transform a SIZE specified in units of retinal microns at a
% given eccentricity (also specified in microns) to a SIZE in units of
% visual degrees based on the @cMosaic configuration
function sizeDegrees = sizeMicronsToSizeDegreesForCmosaic(obj, sizeMicrons, eccentricityMicrons)
if (~isempty(obj.micro... |
github | isetbio/isetbio-master | assignConeTypes.m | .m | isetbio-master/isettools/cones/@cMosaic/assignConeTypes.m | 7,224 | utf_8 | 88314b3c3425977131476a912bdded36 | function assignConeTypes(obj, src, ~)
% Needs comments from NC. Not sure why 'src' is here.
%
% Called by the cMosaic constructor
% Looks like the cone positions are calculated by
% regenerateConePositions or initializeConePositions
%
% This routine then 'colors' each of the positions with a cone type.
%
% See also
%... |
github | isetbio/isetbio-master | sizeDegreesToSizeMicronsForCmosaic.m | .m | isetbio-master/isettools/cones/@cMosaic/sizeDegreesToSizeMicronsForCmosaic.m | 1,927 | utf_8 | 409fca10b2813bcb3158b94713bbd37e | % Method to transform a SIZE specified in units of visual degrees at a
% given eccentricity (also specified in degrees) to a SIZE in units of
% retinal microns based on the @cMosaic configuration
function sizeMicrons = sizeDegreesToSizeMicronsForCmosaic(obj, sizeDegrees, eccentricityDegrees)
if (~isempty(obj.micr... |
github | isetbio/isetbio-master | visualizeFullAbsorptionsDensity.m | .m | isetbio-master/isettools/cones/@cMosaic/visualizeFullAbsorptionsDensity.m | 3,422 | utf_8 | afac3a6546c3bfdb1704300c82b2b9ae | function visualizeFullAbsorptionsDensity(obj, figNo)
% Create an image that shows ... Nicolas???
%
% Inputs
% obj - cMosaic object
% figNo - Optional figure number. If not passed then figure() is called
%
% Buglet: You need to run compute before this to fill in the
% absorptionsDensitySpatialSupportMic... |
github | isetbio/isetbio-master | computeOuterSegmentLengthEccVariationAttenuationFactors.m | .m | isetbio-master/isettools/cones/@cMosaic/computeOuterSegmentLengthEccVariationAttenuationFactors.m | 3,722 | utf_8 | 019ee921625230c7ee22daf5971e3d47 | function computeOuterSegmentLengthEccVariationAttenuationFactors(obj, varargin)
% Parse input
p = inputParser;
p.addParameter('useParfor', true, @islogical);
p.parse(varargin{:});
useParfor = p.Results.useParfor;
% Compute radial eccDegs of all cones
coneEccentricityDegs = sqrt((obj.co... |
github | isetbio/isetbio-master | compute.m | .m | isetbio-master/isettools/cones/@cMosaic/compute.m | 24,492 | utf_8 | c208653cdae0b6826e75cbb8bbbfc65b | function [noiseFreeAbsorptionsCount, noisyAbsorptionInstances, ...
photoCurrents, photoCurrentInstances, responseTemporalSupport] = ...
compute(obj, oi, varargin)
% Compute the cone absorptions, possibly for multiple instances
%
% Syntax:
% [absorptions, current, interpFilters, meanCur] = compute(obj, oi);
% ... |
github | isetbio/isetbio-master | computeConeApertures.m | .m | isetbio-master/isettools/cones/@cMosaic/computeConeApertures.m | 14,544 | utf_8 | 96c4beaee985277c40e19fdef9612f17 | function computeConeApertures(obj, lowOpticalImageResolutionWarning)
% Compute unsmoothed spacings from positions
[obj.coneRFspacingsMicrons, nearbyConeIndices] = RGCmodels.Watson.convert.positionsToSpacings(obj.coneRFpositionsMicrons);
% Retrieve number of cones
nConesNum = size(obj.coneRFpositio... |
github | isetbio/isetbio-master | eccentricitiesForRetinaMeridianInEye.m | .m | isetbio-master/isettools/cones/@cMosaic/eccentricitiesForRetinaMeridianInEye.m | 2,087 | utf_8 | 0d48a45bb90f5c50b50f66e5bf677c8b | % Static method to return signed horizontal and vertical
% eccentricities corresponding to radial eccentricities specified
% on one of the 4 principal retinal meridians and eye
function [horizontalEcc, verticalEcc] = eccentricitiesForRetinaMeridianInEye(...
radialEcc, retinaMeridian, whichEye)
temporal... |
github | isetbio/isetbio-master | visualize.m | .m | isetbio-master/isettools/cones/@cMosaic/visualize.m | 53,347 | utf_8 | 8c9d206141dc145506bc838dad369bea | function visualizationParams = visualize(obj, varargin)
% Visualize different aspects of a @cMosaic or its activation
%
% Syntax:
% cm = cMosaic(); cm.visualize();
%
% % Return the various settable params
% pStruct = cm.visualize('params')
%
% % Display the various settable params and info about them
% cm.vis... |
github | isetbio/isetbio-master | suggestedScenePixelSizeDegs.m | .m | isetbio-master/isettools/cones/@cMosaic/suggestedScenePixelSizeDegs.m | 741 | utf_8 | 0a76d5e290f56f81f496db19e8c60155 | % Method for suggesting an optimal pixel size for the input scene
% depending on the aperture size of the mosaic's cones and whether
% the computation is done using ecc-dependent blur mode
function minScenePixelSizeDegs = suggestedScenePixelSizeDegs(obj, eccVaryingConeBlur)
% Compute cone aperture diameters based ... |
github | isetbio/isetbio-master | electricallyCoupleConeResponses.m | .m | isetbio-master/isettools/cones/@cMosaic/electricallyCoupleConeResponses.m | 6,693 | utf_8 | d05803f24a0dec9053a7faf2a3f62e0f | function electricallyCoupledResponses = electricallyCoupleConeResponses(obj, responses)
% Compute neighoring cone indices and coupling weights with those
% neighbors for each cone.
if (obj.coneCouplingLambda < 0)
% the 6 closest neigbors, but will only keep the closest one that is not an S-con... |
github | isetbio/isetbio-master | ISO12233.m | .m | isetbio-master/isettools/metrics/ISO12233.m | 27,694 | utf_8 | ecd3446df29c40279e9e59257472cd2b | function [results, fitme, esf, h] = ISO12233(barImage, deltaX, weight, plotOptions)
% ISO 12233 (slanted bar) spatial frequency response (SFR) analysis.
%
% Syntax
% [results, fitme, esf, h] = ISO12233(barImage, deltaX, weight,plotOptions);
%
% Description
% Slanted-edge and color mis-registration analysis.
%
% Input... |
github | isetbio/isetbio-master | oiCreate.m | .m | isetbio-master/isettools/opticalimage/oiCreate.m | 8,453 | utf_8 | 6b90b5c04399d80fd7ff4873f0dd585d | function oi = oiCreate(oiType, varargin)
% Create an optical image structure
%
% Syntax:
% oi = oiCreate(oiType, [varargin])
%
% Description:
% The optical image represents the spectral irradiance at the sensor.
% The irradiance is computed from the scene radiance, using the
% information in the optics struc... |
github | isetbio/isetbio-master | microLens.m | .m | isetbio-master/isettools/opticalimage/optics/microLens.m | 17,851 | utf_8 | 7c19107d9828f10857a3e94b93f3bf2d | function varargout = microLens(varargin)
% M-file for microLens.fig
%
% Syntax:
% varargout = microLens([varargin])
%
% Description:
% Calling microlens, by itself, creates a new MICROLENS or raises the
% existing singleton*.
%
% H = MICROLENS returns the handle to a new MICROLENS or the handle to
% the e... |
github | isetbio/isetbio-master | opticsCreate.m | .m | isetbio-master/isettools/opticalimage/optics/opticsCreate.m | 13,173 | utf_8 | d7b90a1dcf7f8235ee61bb9ec71e8fcf | function [optics, wvfP] = opticsCreate(opticsType, varargin)
% Create an optics structure
%
% Syntax:
% [optics, wvf] = OPTICSCREATE(opticsType, [varargin])
%
% Description:
% This function is typically called through oiCreate. The optics
% structure is attached to the oi and manipulated by oiSet and oiGet.
%
%... |
github | isetbio/isetbio-master | opticsOTF.m | .m | isetbio-master/isettools/opticalimage/optics/opticsOTF.m | 6,115 | utf_8 | b3aed121a8d2e9fe96747b650c319323 | function oi = opticsOTF(oi, scene)
% Apply the opticalImage OTF to the photon data
%
% Syntax:
% oi = opticsOTF(oi, scene);
%
% Description:
% The optical transform function (OTF) associated with the optics in the
% OI is calculated and applied to the scene data. This function is
% called for shift-invariant... |
github | isetbio/isetbio-master | oiWindow.m | .m | isetbio-master/isettools/opticalimage/oigui/oiWindow.m | 85,113 | utf_8 | 87a1b903af577728b4fb9b16263ed67c | function varargout = oiWindow(varargin)
% Optical image window
%
% Syntax:
% [varargout] = oiWindow([varargin])
%
% Description:
% Graphical user interface to manage the ISET OPTICALIMAGE properties.
%
% OIWINDOW, by itself, creates a new OIWINDOW or raises the existing
% singleton*.
%
% H = OIWINDOW retu... |
github | isetbio/isetbio-master | oiSetEditsAndButtons.m | .m | isetbio-master/isettools/opticalimage/oigui/oiSetEditsAndButtons.m | 7,568 | utf_8 | 98015ee7fbe67c73cfae513a4abe0e9e | function oiSetEditsAndButtons(handles)
% Refresh the buttons and edit fields in the optical image window
%
% Syntax:
% oiSetEditsAndButtons(handles)
%
% Description:
% Refresh the current optical image window. If there is no optical
% image, then a default oi is created.
%
% Perhaps we should have a flag to ... |
github | isetbio/isetbio-master | isetbioLocalHookTemplate.m | .m | isetbio-master/configuration/isetbioLocalHookTemplate.m | 5,048 | utf_8 | 3cc93d5eafe72d36c970153308adf94e | function isetbioLocalHookTemplate
% Method to set ISETBIO-specific preferences.
%
% Syntax:
% isetbioLocalHookTemplate
%
% Description:
% Generally, this function should be edited for your website and then
% run once.
%
% You should be able just to use this template version without editing
% for both fu... |
github | isetbio/isetbio-master | unitTestFigure10.m | .m | isetbio-master/calculators/@WatsonRGCModel/unitTestFigure10.m | 3,242 | utf_8 | e1bc1e369b955e62b24bafdd5b51b1bf | function plotlabOBJ = unitTestFigure10(varargin)
% Generate Figure 10 of Watson (2014) which plots the mRGC RF spacing as a function
% of eccentricity.
% Parse input
p = inputParser;
p.addParameter('plotlabOBJ', [], @(x)(isempty(x) || isa(x, 'plotlab')));
p.parse(varargin{:});
plotlabOBJ = p.Result... |
github | isetbio/isetbio-master | unitTestFigure1.m | .m | isetbio-master/calculators/@WatsonRGCModel/unitTestFigure1.m | 3,535 | utf_8 | 74c5716b37346b069ff84164c0a6bed9 | function plotlabOBJ = unitTestFigure1(varargin)
% Generate Figure 1 of Watson (2014) which plots cone density as a function
% of eccentricity using Curcio's 1990 data.
% Parse input
p = inputParser;
p.addParameter('plotlabOBJ', [], @(x)(isempty(x) || isa(x, 'plotlab')));
p.parse(varargin{:});
plotl... |
github | isetbio/isetbio-master | unitTestFigure9.m | .m | isetbio-master/calculators/@WatsonRGCModel/unitTestFigure9.m | 3,585 | utf_8 | e402a43f50e2d2bd7c6038b174084139 | function plotlabOBJ = unitTestFigure9(varargin)
% Generate Figure 9 of Watson (2014) which plots the mRGC RF density as a function
% of eccentricity.
% Parse input
p = inputParser;
p.addParameter('plotlabOBJ', [], @(x)(isempty(x) || isa(x, 'plotlab')));
p.parse(varargin{:});
plotlabOBJ = p.Results.... |
github | isetbio/isetbio-master | unitTestFigure11.m | .m | isetbio-master/calculators/@WatsonRGCModel/unitTestFigure11.m | 3,723 | utf_8 | 706648bbeef4e69bf0609eddc7231a01 | function plotlabOBJ = unitTestFigure11(varargin)
% Generate Figure 10 of Watson (2014) which plots the mRGC RF spacing as a function
% of eccentricity (0-10 degs).
% Parse input
p = inputParser;
p.addParameter('plotlabOBJ', [], @(x)(isempty(x) || isa(x, 'plotlab')));
p.parse(varargin{:});
plotlabOB... |
github | isetbio/isetbio-master | unitTestFigureA1.m | .m | isetbio-master/calculators/@WatsonRGCModel/unitTestFigureA1.m | 5,323 | utf_8 | 863788234f111a2599540df5c4e369d1 | function plotlabOBJ = unitTestFigureA1(varargin)
% Generate Figure A1 of Watson (2014) which plots the relationshi between
% retinal distance in mm and retinal distance in degrees.
% Parse input
p = inputParser;
p.addParameter('plotlabOBJ', [], @(x)(isempty(x) || isa(x, 'plotlab')));
p.parse(varargin{:... |
github | isetbio/isetbio-master | unitTestFigure5.m | .m | isetbio-master/calculators/@WatsonRGCModel/unitTestFigure5.m | 3,560 | utf_8 | 56f0483432fbcfb3105994062d64d22e | function plotlabOBJ = unitTestFigure5(varargin)
% Generate Figure 5 of Watson (2014) which plots total RGC RF density as a function
% of eccentricity.
% Parse input
p = inputParser;
p.addParameter('plotlabOBJ', [], @(x)(isempty(x) || isa(x, 'plotlab')));
p.parse(varargin{:});
plotlabOBJ = p.Results... |
github | isetbio/isetbio-master | unitTestFigure14.m | .m | isetbio-master/calculators/@WatsonRGCModel/unitTestFigure14.m | 3,385 | utf_8 | 0af3c945d2699fcdd7f993623eb7df89 | function plotlabOBJ = unitTestFigure14(varargin)
% Generate Figure 14 of Watson (2014) which plots the ratio of mRGC RFs to cones
% as a function of eccentricity.
% Parse input
p = inputParser;
p.addParameter('plotlabOBJ', [], @(x)(isempty(x) || isa(x, 'plotlab')));
p.parse(varargin{:});
plotlabOBJ... |
github | isetbio/isetbio-master | unitTestRFDensity2D.m | .m | isetbio-master/calculators/@WatsonRGCModel/unitTestRFDensity2D.m | 9,999 | utf_8 | a3d46f35fee984d32dd9c22ce3784130 | function unitTestRFDensity2D()
eccMinDegs = 1/60;
eccMaxDegs = 2.5;
eccSamplesNum = 32;
eccDegs = logspace(log10(eccMinDegs), log10(eccMaxDegs), eccSamplesNum);
obj = WatsonRGCModel();
theView = 'right eye visual field';
theView = 'left eye retina';
[coneDensity2DMap, coneMeri... |
github | isetbio/isetbio-master | unitTestSmoothGrid.m | .m | isetbio-master/calculators/@WatsonRGCModel/unitTestSmoothGrid.m | 45,962 | utf_8 | b8580788c1e7074d99535c983544b58a | function unitTestSmoothGrid()
% Generate or view saved mosaic
generateNewMosaic = true;
% Visualize mosaic and progress
visualizeProgress = generateNewMosaic;
% Size of mosaic to generate
mosaicFOVDegs = 20; %30;
% Type of mosaic to generate
neuronalType = 'cone';
n... |
github | isetbio/isetbio-master | unitTestRetinalSizeToVisualSize.m | .m | isetbio-master/calculators/@WatsonRGCModel/unitTestRetinalSizeToVisualSize.m | 5,798 | utf_8 | ed0525ab6d37d02d7c6e6d9beb1e55e0 | function plotlabOBJ = unitTestRetinalSizeToVisualSize(varargin)
% Plot the correspondence of a constant retinal size (in microns) to the visual
% size (in degrees), and conversely, the correspondence of a constant visual size
% (in degrees) to retinal size (in microns), both as a function of eccentricity
% Parse i... |
github | isetbio/isetbio-master | analyzeThibosOptics.m | .m | isetbio-master/calculators/opticsAssessment/analyzeThibosOptics.m | 9,382 | utf_8 | d9e2d734214bea8a176718baed68249c | function analyzeThibosOptics(reAnalyzeData)
% Get directory
[directory,~] = fileparts(which(mfilename()));
exportsDir = fullfile(directory, 'exports');
if (reAnalyzeData)
reAnalyze('left eye', exportsDir);
reAnalyze('right eye', exportsDir);
else
doRankAnalysis = true;
... |
github | isetbio/isetbio-master | analyzeArtalOptics.m | .m | isetbio-master/calculators/opticsAssessment/analyzeArtalOptics.m | 23,051 | utf_8 | 7382369a7187bd78293e92344da5866c | function analyzeArtalOptics(reAnalyzeData)
% Get directory
[directory,~] = fileparts(which(mfilename()));
exportsDir = fullfile(directory, 'exports');
plotEachPosition = ~true;
if (reAnalyzeData)
reAnalyze('left eye', plotEachPosition, exportsDir);
reAnalyze('right eye'... |
github | isetbio/isetbio-master | analyzePolansOptics.m | .m | isetbio-master/calculators/opticsAssessment/analyzePolansOptics.m | 22,384 | utf_8 | 25e3baead8d4edc93059dcb1ea667800 | function analyzePolansOptics(reAnalyzeData)
% Get directory
[directory,~] = fileparts(which(mfilename()));
exportsDir = fullfile(directory, 'exports');
if (reAnalyzeData)
reAnalyze(exportsDir);
% Rank subjects
rankStrategy = 'resolution'; % Choose from {'resolution', '... |
github | isetbio/isetbio-master | demoConeMosaicAliasing.m | .m | isetbio-master/calculators/opticsAssessment/demoConeMosaicAliasing.m | 20,644 | utf_8 | da14b737b64f440a4af28d297f580ed6 | function demoConeMosaicAliasing()
% Get directory
[directory,~] = fileparts(which(mfilename()));
exportsDir = fullfile(directory, 'exports');
whichEye = 'right eye';
zernikeDataBase = 'Polans2015'; % choose between {'Polans2015', and 'Artal2012'}
subjectID = 4;
% Mosai... |
github | isetbio/isetbio-master | contrastPolansToArtal.m | .m | isetbio-master/calculators/opticsAssessment/contrastPolansToArtal.m | 4,338 | utf_8 | 0e1ddaae5cc22f98ececf66a22e0bc27 | function contrastPolansToArtal
% Get directory
[directory,~] = fileparts(which(mfilename()));
exportsDir = fullfile(directory, 'exports');
[PolansZcoeffs, horizontalEccPolans] = loadPolansZCoeffs(exportsDir);
[ArtalZcoeffs, horizontalEccArtal] = loadArtalZCoeffs(exportsDir);
rowsNum ... |
github | isetbio/isetbio-master | analyzeLattice.m | .m | isetbio-master/calculators/latticeGenerator/analyzeLattice.m | 10,071 | utf_8 | 37ba264f3edba002d6c7dbe44425f7b8 | function analyzeLattice
% Size of mosaic to generate
mosaicFOVDegs = 20;
% Type of mosaic to generate
%neuronalType = 'cone';
neuronalType = 'mRGC';
% Which eye
whichEye = 'right';
% Samples of eccentricities to tabulate spacing on
% Precompute cone spacing for a grid... |
github | isetbio/isetbio-master | generateLattice.m | .m | isetbio-master/calculators/latticeGenerator/generateLattice.m | 4,586 | utf_8 | bb3c25f2c3e91a9262edf887cb8d4c9d | function generateLattice
% Size of mosaic to generate
mosaicFOVDegs = 40.0;
% Type of mosaic to generate
neuronalType = 'cone';
%neuronalType = 'mRGC';
% Which eye
whichEye = 'right';
% Samples of eccentricities to tabulate spacing on
% Precompute cone spacing for a ... |
github | isetbio/isetbio-master | illustrateDifferenceInConeDensityBetweenISETBioAndWatson.m | .m | isetbio-master/calculators/latticeGenerator/illustrateDifferenceInConeDensityBetweenISETBioAndWatson.m | 3,439 | utf_8 | 5395449051ea8cc70250b300c5e6a6f8 | function illustrateDifferenceInConeDensityBetweenISETBioAndWatson
obj = WatsonRGCModel();
obj.dc0
eccentricities = logspace(log10(0.01), log10(60), 64); eccUnits = 'deg';
densityUnits = 'mm^2';
rightEyeVisualFieldMeridianName = 'superior meridian';
[~, coneDensityISETBio] =... |
github | isetbio/isetbio-master | generateInitialRFpositions.m | .m | isetbio-master/calculators/latticeGenerator/generateInitialRFpositions.m | 1,539 | utf_8 | 8ee66aaeba50a6e1d31c7ae21ec6a724 | function [rfPositions, lambdaMicrons] = generateInitialRFpositions(mosaicWidthDegs, neuronalType)
% Determine the mosaics
[mosaicRadiusRetinalMicrons, lambdaMicrons] = determineMosaicWidthAndLambda(mosaicWidthDegs, neuronalType);
% Generate a mosaic that is 20% larger to minimize edge effects
margin =... |
github | isetbio/isetbio-master | iterativelySmoothLattice.m | .m | isetbio-master/calculators/latticeGenerator/iterativelySmoothLattice.m | 12,578 | utf_8 | 6d892245399d3d4c52632ef138928ada | function [rfPositions, rfPositionsHistory, maxMovements, iteration, terminationReason] = iterativelySmoothLattice(rfPositions, tabulatedSpacing, tabulatedEcc, iterativeParams, lambda, domain, visualizationParams)
% Initiate state
iteration = 0;
lastTriangularizationIteration = 0;
desiredSpringLengths =... |
github | isetbio/isetbio-master | generateConeMosaicResponsesToDriftingSinewaves.m | .m | isetbio-master/demoapps/RGCSFTuningSimulator/Resources/generateConeMosaicResponsesToDriftingSinewaves.m | 9,437 | utf_8 | 143f72ec684a7ed3c56d299741086a31 | function generateConeMosaicResponsesToDriftingSinewaves
% Generate the data used by the RGCSFTuningSimulator
%
% History:
% 08/01/21 NPC ISETBIO Team, Copyright 2021 Wrote it.
% Eccentricities examined
mosaicEccentricities = [...
0 0; ...
0.2 0; ...
1.0 0];
% Correspondin... |
github | isetbio/isetbio-master | runCSFGeneratorMultipleSubjects.m | .m | isetbio-master/demoapps/CSFgenerator2/scripts/runCSFGeneratorMultipleSubjects.m | 5,965 | utf_8 | 02d2f2890412ffa2a72ec526eeae955a | function runCSFGeneratorMultipleSubjects
compute = true;
if (compute)
computeCSF()
else
visualizeCSF()
end
end
function visualizeCSF()
load('subjectsData.mat', 'sfSupport', ...
'constantSizeWatsonPyradidOfVisbility', ...
'constantCyclesWatsonPyradidOfVisbility'... |
github | isetbio/isetbio-master | gratingSceneEngine.m | .m | isetbio-master/demoapps/CSFgenerator2/+CSFGeneratorApp/+generate/gratingSceneEngine.m | 1,719 | utf_8 | 6735368072df57b884c75ed218578bf9 | % CSFapp support method to generate the gratingSceneEngine and test/null stimuli.
function [theSceneSequence, theNullStimulusScene, statusReport, theGratingSceneEngine] = gratingSceneEngine(sParams, theGratingSceneEngine)
if (isempty(theGratingSceneEngine))
theGratingSceneEngine = createGratingScene(sParams... |
github | isetbio/isetbio-master | stimParamsStructForGratingSceneEngine.m | .m | isetbio-master/demoapps/CSFgenerator2/+CSFGeneratorApp/+generate/stimParamsStructForGratingSceneEngine.m | 2,806 | utf_8 | f1448c4ba64c27e7a3de418e4546a2a0 | function [sParams, coneMosaicIsTooSmall] = stimParamsStructForGratingSceneEngine(app, currentSpatialFrequency)
% Form sParams struct
sParams = struct(...
'contrast', 1.0, ...
'chromaDir', [app.stimParams.LconeContrast app.stimParams.MconeContrast app.stimParams.SconeContrast]/100... |
github | isetbio/isetbio-master | stimulus.m | .m | isetbio-master/demoapps/CSFgenerator2/+CSFGeneratorApp/+generate/stimulus.m | 2,187 | utf_8 | 0db4d7afb25605728e11f7861e676696 | function stimulus(app, dialog)
deleteProgressBar = isempty(dialog);
if (deleteProgressBar)
% Open progressbar
dialogBox = uiprogressdlg(app.mainView,'Title','Please Wait',...
'Message','Generating stimulus ...');
dialogBox.Value = 0.2;
end
% Generate stimParams stru... |
github | isetbio/isetbio-master | psychometricFunctionView.m | .m | isetbio-master/demoapps/CSFgenerator2/+CSFGeneratorApp/+render/psychometricFunctionView.m | 4,731 | utf_8 | 95db08442e98883e2d5615bbddfb9c6c | function psychometricFunctionView(app, mode, varargin)
p = inputParser;
p.addParameter('withData', []);
p.parse(varargin{:});
psychometricData = p.Results.withData;
switch (mode)
case 'initialize'
initializePsychometricFunctionView(app);
case 'update'
... |
github | isetbio/isetbio-master | csfView.m | .m | isetbio-master/demoapps/CSFgenerator2/+CSFGeneratorApp/+render/csfView.m | 3,698 | utf_8 | cbdb6cc432c6a805ac759e33128678be | function csfView(app, mode, varargin)
p = inputParser;
p.addParameter('withData', []);
p.parse(varargin{:});
csfData = p.Results.withData;
switch (mode)
case 'initialize'
initializeCSFView(app);
case 'update'
updateCSFViewWithNewData(app, csfData... |
github | isetbio/isetbio-master | stimulusView.m | .m | isetbio-master/demoapps/CSFgenerator2/+CSFGeneratorApp/+render/stimulusView.m | 1,510 | utf_8 | 297fef166996bfeff95486546769bb8b | function stimulusView(app, mode)
switch (mode)
case 'initialize'
initializeStimulusView(app);
case 'update'
updateStimulusViewWithNewData(app);
end
end
function initializeStimulusView(app)
app.stimulusPlotHandle = image(app.stimulusView, [-0.01 0.01], [-0.01 0.01], ... |
github | isetbio/isetbio-master | coneMosaicView.m | .m | isetbio-master/demoapps/CSFgenerator2/+CSFGeneratorApp/+render/coneMosaicView.m | 16,754 | utf_8 | 1b14c91b7bfb4827b1c1be0b946282e2 | function coneMosaicView(app, mode)
switch (mode)
case 'initialize'
initializeConeMosaicView(app);
case 'update'
updateConeMosaicViewWithNewData(app);
end
end
function initializeConeMosaicView(app)
set(app.coneMosaicView, 'LineWidth', 0.5);
box(app.coneMosaicView... |
github | isetbio/isetbio-master | roiView.m | .m | isetbio-master/demoapps/CSFgenerator2/+CSFGeneratorApp/+render/roiView.m | 6,366 | utf_8 | ce6e9932813a1df3b55fbf12a4c0bc0b | function roiView(app, mode)
switch (mode)
case 'initialize'
initializeROIView(app);
case 'update'
updateROIViewWithNewData(app);
end
end
function initializeROIView(app)
% Plot the crosshairs
plot(app.roiView, app.roiParams.maxEcc*2*[-1 1], [0 0], 'k-', 'LineWidt... |
github | isetbio/isetbio-master | opticsView.m | .m | isetbio-master/demoapps/CSFgenerator2/+CSFGeneratorApp/+render/opticsView.m | 3,846 | utf_8 | c3c2a1c1066724c013af1753a1c8dd4e | function opticsView(app, mode)
switch (mode)
case 'initialize'
initializeOpticsView(app);
case 'update'
updateOpticsViewWithNewData(app);
end
end
function initializeOpticsView(app)
cla(app.opticsView);
cMap = brewermap(512, '*spectral');
colormap(app.optics... |
github | isetbio/isetbio-master | guiComponents.m | .m | isetbio-master/demoapps/CSFgenerator2/+CSFGeneratorApp/+initialize/guiComponents.m | 12,799 | utf_8 | 98009d4d327182e130c5d60d5dc21413 | function guiComponents(app)
% Initialize colors for different aspects of the app
initializeColors(app);
% Initialize the status fields
initializeStatusFields(app);
% Initialize the region of interest GUI components
initializeROIGUIComponents(app);
% Initialize the stimulus GUI com... |
github | isetbio/isetbio-master | t_opticsRefractiveError.m | .m | isetbio-master/tutorials/t_optics/t_opticsRefractiveError.m | 8,795 | utf_8 | 0b23883d1f968dd9ec8ccbb9607f9d4d | % Examine the effect of refractive error the on retinal image
%
% Description:
% Generates an ISETBio scene from a jpg file. Passes the scene via
% optics in which the user controls the additional refractive error.
%
% History:
% 08/24/21 NPC Wrote it. Copyright, ISETBIO Team, 2021
% 01/12/23 N... |
github | isetbio/isetbio-master | t_diffractionAcrossWavelengthPsfAndOtf.m | .m | isetbio-master/tutorials/t_optics/advancedTutorials_optics/t_diffractionAcrossWavelengthPsfAndOtf.m | 8,491 | utf_8 | 1f660f3cb3df9e6aa1d174a2b0c1ead5 | function t_diffractionAcrossWavelengthPsfAndOtf
% Test different ways of getting diffraction limited optics with defocus
%
% Syntax:
% t_diffractionAcrossWavelengthPsfAndOtf
%
% Description:
% Shows how to get diffraction limited optics plus the effect of defocus
% across wavelengths.
%
% Also illustrates th... |
github | isetbio/isetbio-master | t_mRGCMosaicBasic.m | .m | isetbio-master/tutorials/t_mRGCMosaic/t_mRGCMosaicBasic.m | 11,449 | utf_8 | a3e39c4f16004b1a861fb6d7d04671f4 | %% Introduction to the midget RGC mosaic (mRGCMosaic) object.
%
% Description:
% Demonstrates
% - creation o a midget RGC mosaic,
% - how to compute with it, and
% - how to visualize different aspects of the mRGCMosaic
% - how to visualize its response
%
% History:
% 01/27/23 NPC I... |
github | isetbio/isetbio-master | t_dynamicStimulusToPhotocurrent.m | .m | isetbio-master/tutorials/t_recipes/t_dynamicStimulusToPhotocurrent.m | 55,684 | utf_8 | 3fd323d778b08f1000dd2ca58f8ddf5d | function t_dynamicStimulusToPhotocurrent
% Illustrates how to compute photocurrent responses to a dynamic stimulus.
%
% Syntax:
% t_dynamicStimulusToPhotocurrent
%
% Description:
% Demonstrates how to compute photocurrent responses to a dynamic
% stimulus whose contrast is modulated against an adapting ... |
github | isetbio/isetbio-master | t_generateConeSpecificStimuli.m | .m | isetbio-master/tutorials/t_recipes/t_generateConeSpecificStimuli.m | 13,899 | utf_8 | a59ca5dffd4cdf68d0ea1c7473992db6 | function t_generateConeSpecificStimuli
% Illustrate how to generate scenes depicting various cone-specific stimuli
%
% Syntax:
% t_generateConeSpecificStimuli
%
% Description:
% Simple script that demonstrates how to generate scenes depicting
% various superimposed cone-specific stimuli on a specific backgroun... |
github | isetbio/isetbio-master | t_computingWithCustomPSFs.m | .m | isetbio-master/tutorials/t_recipes/t_computingWithCustomPSFs.m | 11,454 | utf_8 | 205a47075d3416a148432b5059f2a982 | function t_computingWithCustomPSFs()
% Illustrate generate optics using custom PSFs
%
% Syntax:
% t_computingWithCustomPSFs
%
% Description:
% Script that demonstrates how to compute cone excitations using optics
% derived from a set of custom PSFs measured/computed at a set of wavelengths
% Also illustrates... |
github | isetbio/isetbio-master | t_fixationalEyeMovementsTypes.m | .m | isetbio-master/tutorials/t_eyemovement/t_fixationalEyeMovementsTypes.m | 7,105 | utf_8 | 7b06a64a097db89b40356d78a1ebfd0e | function t_fixationalEyeMovementsTypes(varargin)
% Examine eye movement paths using different 'microSaccadeType' parameters.
%
% Syntax:
% t_fixationalEyeMovementsTypes
%
% Description:
% The fixation maps are a bit different for microsaccades that are
% generated using the 'heatmap/fixation based' strategy vs.... |
github | isetbio/isetbio-master | t_fixationalEyeMovementsCharacterize.m | .m | isetbio-master/tutorials/t_eyemovement/t_fixationalEyeMovementsCharacterize.m | 14,582 | utf_8 | 4b57b7b8296d32179ef1b4fdefe6b1a8 | function t_fixationalEyeMovementsCharacterize
% Explore how micro-saccade strategies affect emPath of a fixationalEM.
%
% Syntax:
% t_fixationalEyeMovementsCharacterize
%
% Description:
% Computes key characteristics of emPaths and explores how these differ
% for different micro-saccade strategies the @fixation... |
github | isetbio/isetbio-master | t_fixationalEyeMovementsFeedbackGainAndControlGainDependence.m | .m | isetbio-master/tutorials/t_eyemovement/t_fixationalEyeMovementsFeedbackGainAndControlGainDependence.m | 26,608 | utf_8 | 67a806bf2c9df04b00144b325f2e1a29 | function t_fixationalEyeMovementsFeedbackGainAndControlGainDependence
% Explore how fixationalEM drift parameters affect emPath characteristics
%
% Syntax:
% t_fixationalEyeMovementsFeedbackGainAndControlGainDependence
%
% Description:
% Explore how the following key characteristics of emPaths
% (i) velocity... |
github | isetbio/isetbio-master | t_coneQuantalEfficiencyChangesWithMacularPigmentAndLens.m | .m | isetbio-master/tutorials/t_cones/t_coneQuantalEfficiencyChangesWithMacularPigmentAndLens.m | 5,945 | utf_8 | f140c5a1bf52aee0ed4dfda76c8b7fa9 | % Illustrate cone quantal efficiency changes with macular pigment and lens
%
% Description:
% This tutorial illustrates how to use machinery built into the @cMosaic
% object to calculate how the cone quantal efficiency changes with
% eccentricity due to changes in MP density with eccentricity. The effect
% of t... |
github | isetbio/isetbio-master | t_cMosaicEccDependentAbsorptionEfficacy.m | .m | isetbio-master/tutorials/t_cones/t_cMosaicEccDependentAbsorptionEfficacy.m | 10,248 | utf_8 | b91fb51acf07d54ec2cc3f9ac3135457 | % Demostrate different ecc-dependent capabilties of the new @cMosaic object
%
% Description:
% Shows how to set different ecc-dependent properties of the @cMosaic,
% and demonstrates their effect on the computed mean response.
% The following ecc-dependent properties are examined:
% - eccVaryingConeApertur... |
github | isetbio/isetbio-master | t_cMosaicCustomConeData.m | .m | isetbio-master/tutorials/t_cones/t_cMosaicCustomConeData.m | 4,291 | utf_8 | 0570762a9762807d0de53ac807b6ce81 | % Demo usage of computing and using custom cone mosaics
%
% Description:
% Shows how to generate a completely custom @cMosaic object in which the
% position, type, and aperture size of each and every cone is specified
% by the user. This functionality enables the modeling of real mosaics,
% for example mosa... |
github | isetbio/isetbio-master | t_mapConeRF.m | .m | isetbio-master/tutorials/t_cones/t_mapConeRF.m | 14,628 | utf_8 | 35bb07e22f404f1ea8cee5a80bbd78b5 | % Demo usage of RF mapping using the subspace RF mapping method
%
% Description:
% Shows how to use the rfMappingStimulusGenerator package to map
% the visual spatial RFs of cones using the subspace RF mapping method.
%
% History:
% 09/28/22 NPC ISETBIO Team, Copyright 2022 Wrote it.
function t_mapConeRF... |
github | isetbio/isetbio-master | t_cMosaicBenchMark.m | .m | isetbio-master/tutorials/t_cones/t_cMosaicBenchMark.m | 15,296 | utf_8 | a4c117abeb8a3176a117e3b903e4a8fc | % Benchmark the new @cMosaic object vs the old @coneMosaicHex
%
% Description:
% Shows how to generate a @cMosaic object that is completely equivalent
% to a @coneMosaicHex, computes the noise-free responses of the @cMosaic and
% of the original @coneMosaicHex to two scenes, and contrasts the
% responses, t... |
github | isetbio/isetbio-master | t_cMosaicRodIntrusion.m | .m | isetbio-master/tutorials/t_cones/t_cMosaicRodIntrusion.m | 9,018 | utf_8 | 0b403019042d8b8ff0859bf13f1eacf1 | % Demo usage of rodIntrusionAdjustedConeAperture flag in new @cMosaic object
%
% Description:
% Shows how to generate @cMosaics in which the cone aperture takes into
% account rod intrusion as a function of eccentricity. Also compares the
% generated mosaics with those of Curcio 1990. (Fig 3).
%
% History:
% ... |
github | isetbio/isetbio-master | t_cMosaicSinewaveStimuli.m | .m | isetbio-master/tutorials/t_cones/t_cMosaicSinewaveStimuli.m | 10,224 | utf_8 | 96e0eb7c6551230631ddbae26be89e1b | % Demo computing off-axis responses to sinewave stimuli
%
% Description:
% Demonstrate usage of @cMosaic, +PolansOptics to compute cone excitations
% to sinewave stimuli and display the cone mosaic, the PSF and the mosaic
% cone excitations and modulations
%
% See Also:
% t_cMosaicOffAxisDistortion
% t_cMosa... |
github | isetbio/isetbio-master | t_cMosaicSinewaveStimulus.m | .m | isetbio-master/tutorials/t_cones/t_cMosaicSinewaveStimulus.m | 11,230 | utf_8 | 9b7bc659e3e7cde31ee9181750128e51 | % Demo computing off-axis responses to sinewave stimuli
%
% Description:
% Demonstrate usage of @cMosaic, +PolansOptics to compute cone excitations
% to sinewave stimuli and display the cone mosaic, the PSF and the mosaic
% cone excitations and modulations
%
% See Also:
% t_cMosaicOffAxisDistortion
% t_cMosa... |
github | isetbio/isetbio-master | t_conesEyeSensitivity.m | .m | isetbio-master/tutorials/t_cones/t_conesEyeSensitivity.m | 9,588 | utf_8 | e354fa24240aafd9d1b86f546343b74d | function t_eyeSensitivity
%% Illustrate how eye parameters affect isomerizations.
%
% Description:
% Demonstrate how changing the focal length, the pupil diameter and the
% inner segment aperture affect retinal illuminance/photoreceptor
% isomerization rate computed by ISETBio, and compare this with the
% a... |
github | isetbio/isetbio-master | t_cMosaicAccelerationScaling.m | .m | isetbio-master/tutorials/t_cones/cMosaic_supportTutorials/t_cMosaicAccelerationScaling.m | 6,459 | utf_8 | b247291d242d51ae2cc3c886ebf2f5b0 | % Examine how computation time scales with mosaic size for the new @cMosaic
%
% Description:
% Examine compute times for @cMosaic vs @coneMosaicHex, as a function of
% mosaic field of view. This one takes a long time to run and requires at
% least 32 GB RAM to run.
%
% See Also:
% t_cMosaicBasic
% t_cMosai... |
github | isetbio/isetbio-master | t_cMosaicBenchMark.m | .m | isetbio-master/tutorials/t_cones/cMosaic_supportTutorials/t_cMosaicBenchMark.m | 15,140 | utf_8 | 384957ac853ebbaa2212075cd6417275 | % Benchmark the new @cMosaic object vs the old @coneMosaicHex
%
% Description:
% Shows how to generate a @cMosaic object that is completely equivalent
% to a @coneMosaicHex, computes the noise-free responses of the @cMosaic and
% of the original @coneMosaicHex to two scenes, and contrasts the
% responses, t... |
github | isetbio/isetbio-master | t_conesMosaicAbsorptionsEccBased.m | .m | isetbio-master/tutorials/t_cones/coneMosaic_old/t_conesMosaicAbsorptionsEccBased.m | 18,017 | utf_8 | 5ac64778213db85e34e0816e4c27cb81 | function t_conesMosaicAbsorptionsEccBased
% Demonstrate applying ecc-based efficiency correction on static stimulus.
%
% Syntax:
% t_conesMosaicAbsorptionEccBased
%
% Description:
% Demonstrates the effect of applying eccentricity-based cone efficiency
% correction for a static (e.g., not modulated over time) s... |
github | isetbio/isetbio-master | t_wavefrontSampling.m | .m | isetbio-master/tutorials/t_wavefront/advancedTutorials_wavefront/t_wavefrontSampling.m | 12,488 | utf_8 | 4d7fabc27cc73e3548c61eabfc9d3ca3 | function t_wavefrontSampling
% Show how PSF and OTF are effected by different wavelength sampling params
%
% Syntax:
% t_wavefrontSampling
%
% Description
% Examine the effects of different sampling parameters in a wavefront on
% the resulting PSF and the OTF.
%
% (1) Shows that by increasing the 'spatial sa... |
github | isetbio/isetbio-master | t_linearFilters.m | .m | isetbio-master/tutorials/t_outersegment/t_linearFilters.m | 11,586 | utf_8 | 888b7e23bd13887421bf815669a81e6c | function t_linearFilters
% Compute the photocurrent at different mean field levels
%
% Syntax:
% t_linearFilters
%
% Description:
% Computes L-, M- and S-cone outer segment photocurrent responses to
% luminance step stimuli of fixed height presented on different
% backgrounds. Visualizes isomerization respon... |
github | isetbio/isetbio-master | t_osTimeStep.m | .m | isetbio-master/tutorials/t_outersegment/advancedTutorials_os/t_osTimeStep.m | 29,961 | utf_8 | a7171e293aa56617b25adb012a91ea01 | function t_osTimeStep
% Show how to change timebase of os calculation.
%
% Syntax:
% t_osTimeStep
%
% Description:
% Demonstrate simulations using three different timebases, one for
% stimuli (based on stimulus refresh rate), one for absorptions and eye
% movements (based on coneMosaic.integrationTime), and ... |
github | isetbio/isetbio-master | t_osCurrentsVsLuminanceLevel.m | .m | isetbio-master/tutorials/t_outersegment/underDevelopment_os/t_osCurrentsVsLuminanceLevel.m | 15,413 | utf_8 | 54255dd135d9fddb497643b9adfbde32 | function t_osCurrentsVsLuminanceLevel
% [DHB NOTE: NEEDS COMMENTING. WHAT DOES IT SHOW?]
% [DHB NOTE: THIS HAD TOO MANY CASES. I SHORTENED TO TWO.]
% [DHB NOTE: HOW DOES THIS RELATE TO t_linearFilters?
% Define the time axis for the simulation
stimulusSamplingInterval = 1/1000; % 50/1000
oiTi... |
github | isetbio/isetbio-master | csfTreeShrewFromPaper.m | .m | isetbio-master/data/dataroutines/treeshrew/csfTreeShrewFromPaper.m | 1,783 | utf_8 | 89f0d77fab1ab730d17ec899cf3092d7 | % Return a struct with treeshrew csfData from a particular paper
function csfData = csfTreeShrewFromPaper(paperName)
switch (paperName)
case 'casagrande84'
csfData = Casagrande84CSFdata();
otherwise
error('Unknown paper: ''%s''.', paperName);
end
end
function csfData = Casagrande84CSFdata()
... |
github | isetbio/isetbio-master | mtfTreeShrewFromPaper.m | .m | isetbio-master/data/dataroutines/treeshrew/mtfTreeShrewFromPaper.m | 1,146 | utf_8 | 4b37892ffddff564ec140059a387a168 | % Return a struct with treeshrew csfData from a particular paper
function mtfData = mtfTreeShrewFromPaper(paperName)
switch (paperName)
case 'SaidakEtAl_2019'
mtfData = SaidakEtAl2019MTFdata();
otherwise
error('Unknown paper: ''%s''.', paperName);
end
end
% Want to replace this eventually wit... |
github | isetbio/isetbio-master | demoOIwindowIssue.m | .m | isetbio-master/validation/demoOIwindowIssue.m | 2,998 | utf_8 | 99658cfc598c0300c74fdee0b8317c7a | function demoOIwindowIssue
% please uncomment one of the following 5 conditions
conditionIndex = 'FAIL_1';
% conditionIndex = 'FAIL_2';
% conditionIndex = 'SUCCESS_1';
% conditionIndex = 'SUCCESS_2';
% conditionIndex = 'SUCCESS_3';
switch conditionIndex
case 'FAIL_1'
% ... |
github | isetbio/isetbio-master | ieDeleteLocalValidationFile.m | .m | isetbio-master/validation/ieDeleteLocalValidationFile.m | 1,250 | utf_8 | 27bd809323bd58a876355b238c373e05 | % Utility to remove one local validation ground truth data set (both fast and full)
%
% Usage: ieDeleteValidationFile('osBiophysObject')
% ieDeleteValidationFile('oi')
function ieDeleteLocalValidationFile(validationFileToBeDeleted)
list = rdtListLocalArtifacts(...
getpref('isetbio', 'remoteDataTool... |
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