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 | xyza11808/MATLAB-master | DIRT_Precomputation.m | .m | MATLAB-master/alignment/dirt/DIRT_Precomputation.m | 15,279 | utf_8 | 4d0d580de562775f1514e3b37e5e38ea | function pre = DIRT_Precomputation(sI, varargin)
% pre = DIRT_Precomputation(sI, ...)
%
% Do some precomputations for image alignment using the DIRT_Registration
% function.
%
% Mandatory inputs:
% - sI [image]
% The source image
%
% Optional inputs (properties):
% - 'ROI' [struct from the DIRT_Mask2ROI functio... |
github | xyza11808/MATLAB-master | DIRT_FM_Registration.m | .m | MATLAB-master/alignment/dirt/DIRT_FM_Registration.m | 2,749 | utf_8 | 96862857a3ffd780c1b26d3d2732cf76 | function reg_FM = DIRT_FM_Registration(tI, pre_FM, tR, tC, varargin)
% reg_FM = DIRT_FM_Registration(tI, pre_FM, tR, tC, varargin)
%
% Compute the SSD and OptSSD between the points in the source image in pre_FM
% and the points (tR,tC) in the target image.
%
% Mandatory inputs:
% - tI [image]
% The source image... |
github | xyza11808/MATLAB-master | DIRT_FM_Precomputation.m | .m | MATLAB-master/alignment/dirt/DIRT_FM_Precomputation.m | 2,514 | utf_8 | bcbdd3a7c94000f185b6d5c867e50183 | function pre_FM = DIRT_FM_Precomputation(sI, sR, sC, varargin)
% pre_FM = DIRT_FM_Precomputation(sI, sR, sC, varargin)
%
% Do some precomputations for two-image feature matching using the
% DIRT_FM_Registration function.
%
% Mandatory inputs:
% - sI [image]
% The source image
% - sR, sC [column vectors]
% ... |
github | xyza11808/MATLAB-master | iat_dense_sift.m | .m | MATLAB-master/alignment/nonrigid/siftflow/iat_dense_sift.m | 6,593 | utf_8 | f62616f37431ec9d79b88479d166ce62 | function [siftImage, gridX, gridY] = iat_dense_sift(im, patch_size, grid_spacing, varargin)
% [SIFTIMAGE, GRIDX,GRIDY] = IAT_DENSE_SIFT(IMAGE, PS, GSPACING)
% IAT_DENSE_SIFT creates SIFTIMAGE from IMAGE, when the pixels of latter
% are replaced by SIFT descriptors [1] that describe their surrounding
% area od size PSxP... |
github | xyza11808/MATLAB-master | launchNeuronRasterViewer.m | .m | MATLAB-master/steinmetz-et-al-2019-master/launchNeuronRasterViewer.m | 818 | utf_8 | f51ceb208ef22f40dc51f389be3f6601 |
function launchNeuronRasterViewer()
rootDir = uigetdir(pwd, 'Select folder containing the downloaded sessions');
if ~isempty(rootDir)
d = dir(fullfile(rootDir, '*'));
d = d([d.isdir]);
sessionNames = {d.name};
sessionNames = sessionNames(~strcmp(sessionNames, '.') & ~strcmp(sessionNames,'..'));
... |
github | xyza11808/MATLAB-master | launchRasterViewer.m | .m | MATLAB-master/steinmetz-et-al-2019-master/launchRasterViewer.m | 812 | utf_8 | 8fb1985e0fa9a31b605b433b5a7ec828 |
function launchRasterViewer()
rootDir = uigetdir(pwd, 'Select folder containing the downloaded sessions');
if ~isempty(rootDir)
d = dir(fullfile(rootDir, '*'));
d = d([d.isdir]);
sessionNames = {d.name};
sessionNames = sessionNames(~strcmp(sessionNames, '.') & ~strcmp(sessionNames,'..'));
in... |
github | xyza11808/MATLAB-master | choiceProbShuf.m | .m | MATLAB-master/steinmetz-et-al-2019-master/ccCP/choiceProbShuf.m | 1,388 | utf_8 | 3d587d237dcac3d78b382cce5597c047 |
function [cp, p, cpSummary] = choiceProbShuf(spikeCounts, trialChoice, trialCondition, shufLabels)
% Returns choice probability for a set of trials by combining across
% conditions with a decomposed mann-whitney u-stat.
%
% spikeCounts, trialChoice, trialCondition are all vectors of the same
% length.
%
% trialChoice... |
github | xyza11808/MATLAB-master | mannWhitneyUshuf.m | .m | MATLAB-master/steinmetz-et-al-2019-master/ccCP/mannWhitneyUshuf.m | 548 | utf_8 | b7551ba736c34a1f2aa81fee29f29afa |
function numer = mannWhitneyUshuf(x,y,shufLabels)
% function numer = mannWhitneyUshuf(x,y,shufLabels)
%
% numer is the number of instances for which x>y, of all possible
% comparisons. Divide by nx*ny for mannWhitney u statistic.
%
% shufLabels is ny x nshuf, each column a random permutation of integers
% from 1:nx. ... |
github | xyza11808/MATLAB-master | colorForAcr.m | .m | MATLAB-master/steinmetz-et-al-2019-master/plotting/colorForAcr.m | 152 | utf_8 | 59b19f3cb5772fbd826d02a18e5d2267 |
function c = colorForAcr(acr, g)
c = [0 0 0];
for q = 1:numel(g)
if any(cellfun(@(x)strcmp(acr,x), g(q).acr))
c = g(q).color;
end
end |
github | xyza11808/MATLAB-master | plotMJ2frame.m | .m | MATLAB-master/steinmetz-et-al-2019-master/plotting/plotMJ2frame.m | 369 | utf_8 | 02946296e0186bd8e7c323bf1d7aeb35 |
function plotMJ2frame(ax, currTime, myData)
vr = myData{1};
t = myData{2};
thisFrame = find(t>currTime, 1);
if ~isempty(thisFrame)
img = read(vr, thisFrame);
imHand = get(ax, 'Children');
if isempty(imHand)
imagesc(img);
colormap(gca, 'gray');
axis off
axis image
el... |
github | xyza11808/MATLAB-master | plotRecLocsMapByColor3A.m | .m | MATLAB-master/steinmetz-et-al-2019-master/plotting/plotRecLocsMapByColor3A.m | 3,474 | utf_8 | 74ece0497c1eca97643f80946b0d919d | function OverAllNotShow = plotRecLocsMapByColor3A(sagAx, topdownAx, sagAx2, uacr, colors, st, av, tpidx)
% sagAx2
% st = loadStructureTree();
if ~exist('tpidx', 'var')
[tpidx, tp] = makeSTtree(st);
end
% steps:
% 4. choose a few slices
% coronal
% avs = squeeze(av(850,:,:));
% avs = avs(:,1:size(avs,2)/2);
% ... |
github | xyza11808/MATLAB-master | plotAllNeurons.m | .m | MATLAB-master/steinmetz-et-al-2019-master/plotting/plotAllNeurons.m | 1,145 | utf_8 | 2e9671aed05aac6535836c4b30d72548 |
function sepHands = plotAllNeurons(dat, acr, sortBy, acrOrder, xbins, ax, showN)
% function plotAllNeurons(dat, acr, sortBy, acrOrder, xbins)
% sortBy is a vector to be sorted ascending
if nargin<7; showN = true; end
plotDat = zeros(size(dat));
n = 0;
nTick = zeros(1, numel(acrOrder));
txt = {};
for q = 1:numel(acr... |
github | xyza11808/MATLAB-master | popRasterWrapper.m | .m | MATLAB-master/steinmetz-et-al-2019-master/plotting/popRasterWrapper.m | 7,355 | utf_8 | 1869d7b227d3fb86d2545cb975d9f397 |
function popRasterWrapper(s, vidPath)
r = struct();
% Spikes
% inclCID = find(s.clusters.probes==nProbe-1)-1;
% inclSpikes = ismember(s.spikes.clusters, inclCID);
% r.st = s.spikes.times(inclSpikes);
% r.clu = double(s.spikes.clusters(inclSpikes))+1;
% r.cids = inclCID+1;
% r.cgs = s.clusters.x_phy_annotation(... |
github | xyza11808/MATLAB-master | plotAllGLMData.m | .m | MATLAB-master/steinmetz-et-al-2019-master/plotting/plotAllGLMData.m | 2,154 | utf_8 | deea0c5abdb2be7f6c9413e78f94f218 |
function plotAllGLMData(mdl, dataTab, names, modelSampVals, dataBinVals, outputIdx, outputName)
n = numel(names);
varNames = dataTab.Properties.VariableNames;
isSq = find(cellfun(@(x)x(end)=='2', varNames));
outVar = dataTab.(varNames{outputIdx});
plotIdx = 1:numel(varNames);
plotIdx([isSq outputIdx]) = [];
nPl... |
github | xyza11808/MATLAB-master | eventRasters.m | .m | MATLAB-master/steinmetz-et-al-2019-master/plotting/eventRasters.m | 2,731 | utf_8 | f1d04568fdd620dff3d782ddfd84ff3f |
function eventRasters(s, nProbe)
% Wrapper for evRastersGUI from /cortex-lab/spikes
%
% Inputs:
% - s - is a struct created with loadSession
% - nProbe - is an index of which probe to include (1-indexed, i.e. cannot
% be zero)
%
% Example usage:
% >> s = loadSession('Muller_2017-01-07');
% >> eventRasters(s)
... |
github | xyza11808/MATLAB-master | addAxisAcronyms.m | .m | MATLAB-master/steinmetz-et-al-2019-master/plotting/addAxisAcronyms.m | 1,395 | utf_8 | 5e7e402f3b0e11492e1d2d9be962d7c8 |
function sepHands = addAxisAcronyms(ax, whichAxis, acrInOrder, pars)
if nargin<4
pars = struct();
end
tickLocs = getOr(pars, 'tickLocs', (1:numel(acrInOrder))');
addSep = getOr(pars, 'addSep', []);
extraText = getOr(pars, 'extraText', {});
xVal = getOr(pars, 'xVal', []);
g = getOr(pars, 'g', brainRegionGroups())... |
github | xyza11808/MATLAB-master | plotRecLocsMapByColor.m | .m | MATLAB-master/steinmetz-et-al-2019-master/plotting/plotRecLocsMapByColor.m | 3,230 | utf_8 | ed406a94ed269bd91dc4c0ae20fffbab |
function OverAllNotShow = plotRecLocsMapByColor(sagAx, topdownAx, uacr, colors, st, av, tpidx)
% sagAx2
% st = loadStructureTree();
if ~exist('tpidx', 'var')
[tpidx, tp] = makeSTtree(st);
end
% steps:
% 4. choose a few slices
% coronal
% avs = squeeze(av(850,:,:));
% avs = avs(:,1:size(avs,2)/2);
% horiz
% ... |
github | xyza11808/MATLAB-master | movieWithTracesSpikesWrapper.m | .m | MATLAB-master/steinmetz-et-al-2019-master/plotting/movieWithTracesSpikesWrapper.m | 3,824 | utf_8 | 4686e85bf0adf5bef356b22c41f8202c |
function movieWithTracesSpikesWrapper(s, nProbe)
tInd=1;
t = s.eye.timestamps; tr = s.eye.area;
tVec = interp1(t(:,1), t(:,2), 0:numel(tr)-1);
traces(tInd).t = tVec;
traces(tInd).v = tr;
traces(tInd).name = 'eye.area';
eyeInTr = tr(tVec>min(s.trials.intervals(:)) & tVec<max(s.trials.intervals(:)));
traces(tInd).... |
github | xyza11808/MATLAB-master | brainRegionGroups.m | .m | MATLAB-master/steinmetz-et-al-2019-master/utils/brainRegionGroups.m | 13,840 | utf_8 | 5f34a11ed240d7ed9d925d7708ab1089 |
function groups = brainRegionGroups(style)
% co = get(gca, 'ColorOrder');
co = [ 0 0.4470 0.7410;...
0.8500 0.3250 0.0980;...
0.9290 0.6940 0.1250;...
0.4940 0.1840 0.5560;...
0.4660 0.6740 0.1880;...
0.3010 0.7450 0.9330;...
0.6350 0.0780 0.1... |
github | xyza11808/MATLAB-master | areaOrdering.m | .m | MATLAB-master/steinmetz-et-al-2019-master/utils/areaOrdering.m | 1,704 | utf_8 | 4a4decc6124c41827fe2eddf9521ed02 |
function manOrder = areaOrdering(type)
manOrder = {};
switch type
case 'manualByLatency'
manOrder = {'SCs', 'VISp', 'LP', 'VISl', 'VISpm', 'VISam','VISrl', ...
'VISa', 'LD','CP', ...
'ACA', 'MOs','PL','GPe', 'SCm','MRN','SNr', ...
'ZI', 'APN','ORB', 'ILA', 'ACB'... |
github | xyza11808/MATLAB-master | roc.m | .m | MATLAB-master/steinmetz-et-al-2019-master/utils/roc.m | 152 | utf_8 | e123fcf1fa10a4aac38aab7379d8436f |
function r = roc(x,y)
nx = numel(x); ny = numel(y);
t = tiedrank([x(:); y(:)]);
numer = sum(t(1:nx))-nx*(nx+1)/2;
denom = nx*ny;
r = numer/denom; |
github | xyza11808/MATLAB-master | binAndNorm.m | .m | MATLAB-master/steinmetz-et-al-2019-master/utils/binAndNorm.m | 299 | utf_8 | 6ddf4b62898a96f4fc4858dcc68b7ec2 |
function [allba, mnNorm, bins, mn] = binAndNorm(st, clu, evt, binSize, win, bsl, mgw, trAvg)
[allba, bins] = makeAllBA(st, clu, evt, binSize, win);
allba = allba./binSize; % Hz
if isempty(bsl)
bsl = mean(mean(allba(:,:,bins<0),3),2);
end
[mnNorm, mn] = avgAndNorm(allba, bsl, mgw, trAvg);
end |
github | xyza11808/MATLAB-master | jPECC.m | .m | MATLAB-master/steinmetz-et-al-2019-master/jPECC/jPECC.m | 3,213 | utf_8 | 72e34a5f16873efd7cff413cbbfb2ac7 |
function [jPECC_val, jPECC_p] = jPECC(sp1, sp2, kfold, lambda, maxNpc)
% function [jPECC_val, jPECC_p] = jPECC(sp1, sp2, kfold, lambda)
%
% Inputs:
% - sp1 and sp2 are size [trials, neurons, timebins] and contain spike counts
% aligned to an event, from neurons in area 1 and area 2. The third
% dimension (number of ... |
github | xyza11808/MATLAB-master | kernelRegFit.m | .m | MATLAB-master/steinmetz-et-al-2019-master/reducedRankRegression/kernelRegFit.m | 157 | utf_8 | b277207d0cf44c585b0a35c267194613 |
function fitK = kernelRegFit(bs, A, b, lambda, opts)
fit = glmnet(A*b, bs, 'gaussian', opts);
this_a = glmnetCoef(fit, lambda);
fitK = this_a(2:end)';
|
github | xyza11808/MATLAB-master | kernelRegEval.m | .m | MATLAB-master/steinmetz-et-al-2019-master/reducedRankRegression/kernelRegEval.m | 108 | utf_8 | a21feb8193979526dcfd28a7e3d003c2 |
function cvVarExpl = kernelRegEval(trueBS, predBS)
cvVarExpl = 1 - ( var(trueBS-predBS) ./ var(trueBS) ); |
github | xyza11808/MATLAB-master | kmDummy.m | .m | MATLAB-master/steinmetz-et-al-2019-master/reducedRankRegression/kmDummy.m | 637 | utf_8 | b260269b256fdb11aca0f98b311ee93f |
function kmd = kmDummy(modelkm, win, stimID, moveDir, simRT)
% moveDir is -1 for left, 0 for nogo, 1 for right
n=1;
tN = win(1):modelkm.timeBinSize:win(end);
kmd = KernelModel('toeplitz', tN, 1);
kmd.eventSeries = modelkm.eventSeries;
kmd.timeBinSize = modelkm.timeBinSize;
evs = kmd.eventSeries;
for e = 1:numel(evs)
... |
github | xyza11808/MATLAB-master | kernelFitBasic.m | .m | MATLAB-master/steinmetz-et-al-2019-master/reducedRankRegression/kernelFitBasic.m | 9,263 | utf_8 | de821e3e41f7264c900b79fda8e6a8cf |
function [km, binnedSpikes, inclU, inclTimes, trNum, cweA, cwtA, pvals, bslMeans, effectSizes] = ...
kernelFitBasic(sp, cweA, cwtA, moveData)
%% load some data
% r = listInclRecs();
% n = 9;
% mouseName = r(n).mouseName; thisDate = r(n).thisDate;
% tags = getEphysTags(mouseName, thisDate);
% [sp, cweA, c... |
github | xyza11808/MATLAB-master | makeCosReg.m | .m | MATLAB-master/steinmetz-et-al-2019-master/reducedRankRegression/makeCosReg.m | 860 | utf_8 | 8fe76ec7137a96824d3e20340e202378 |
function [Acos,newPredInds] = makeCosReg(km, cosSep, A, trNum)
% make cos function
% cosSep = 0.05; % sec, from Park & Pillow
cosF = 1/(cosSep*4); % Hz
cosSep = cosSep/km.timeBinSize;
cosSamps = 1/cosF/km.timeBinSize;
cosFcn = (1-cos(linspace(0, 2*pi, cosSamps)))/2;
% figure out which columns of the toeplitz are our... |
github | xyza11808/MATLAB-master | predictResidualsWith.m | .m | MATLAB-master/steinmetz-et-al-2019-master/reducedRankRegression/predictResidualsWith.m | 8,423 | utf_8 | 2dbf6db15839eadffdb072c0f6f723df |
function [ExKFitRes, bExK] = predictResidualsWith(name, thesePredInds, residName, ...
allBSresidExK, r, allR, excl, evalWins)
% evalWins: 2x1 cell array, giving the time around visual stimulus, and
% time around movement onset, over which to evaluate the prediction
nCompExK = 18;
opts.alpha = 0.5;
opts = glmnet... |
github | xyza11808/MATLAB-master | kernelRegPredict.m | .m | MATLAB-master/steinmetz-et-al-2019-master/reducedRankRegression/kernelRegPredict.m | 78 | utf_8 | 248a2fe68a093397d08f7c6c5bd64645 |
function predBS = kernelRegPredict(testA, b, fitK)
predBS = testA*(b*fitK'); |
github | xyza11808/MATLAB-master | computeRegTraces.m | .m | MATLAB-master/steinmetz-et-al-2019-master/reducedRankRegression/computeRegTraces.m | 940 | utf_8 | eaf05111c5b21dd06bb160e162a5c5d0 |
function [winSamps, bsByTr, bsByTrP, bsByTrR] = computeRegTraces(...
bs, residBS, predBs, win, bsBinSize, inclTimes, km, bsl, evTimes)
% compute firing rate from BS, and prediction from kernel reg
% rbs is the prediction we must have had at the beginning, to get
% these residuals
rbs = bs-residBS;
% A = r... |
github | xyza11808/MATLAB-master | kernelRegFitOne.m | .m | MATLAB-master/steinmetz-et-al-2019-master/reducedRankRegression/kernelRegFitOne.m | 3,665 | utf_8 | 824e6231c85f7f856ce7c413b470e6dd |
function fitRes = kernelRegFitOne(bs, A, b, trNum, nComp, nfold, useCVG, lambda, opts, toEval, predInds)
if isempty(nComp)
skipComp = true; nComp = 1;
else
skipComp = false;
end
nTrials = max(trNum);
trInds = 1:nTrials;
% do cross-validation by trial, not by time point
cvp = cvpartition(nTrials,'KFold',nfo... |
github | xyza11808/MATLAB-master | determineResidualsWithout.m | .m | MATLAB-master/steinmetz-et-al-2019-master/reducedRankRegression/determineResidualsWithout.m | 2,097 | utf_8 | f29e8aa05046c5a03facb4402a3774d2 |
function [allBSresidExK, noExKfitRes, bNoExK] = determineResidualsWithout(...
name, thesePredInds, r, basicFitRes)
% see script crossValExcludingK for usage
nComp = 75; % for the fit without these
%%
fprintf(1, 'fit without %s\n', name);
tic
allBS = {r.bs};
allA = {};
allPredInds = unique(r(1).km.predictor... |
github | xyza11808/MATLAB-master | CanonCor2all.m | .m | MATLAB-master/steinmetz-et-al-2019-master/reducedRankRegression/CanonCor2all.m | 2,642 | utf_8 | 2c48b4a1a8913364136e723b523062db |
function [a, b, R2] = CanonCor2all(Y, X)
% [a, b, R2] = CanonCor2all(Y, X)
%
% Version of CanonCor2 (see original doc below) that accepts cell arrays of
% Y and X which represent different instances of the mapping from the same
% X variables to different Y's.
%
% The intended application is for doing a reduced-rank ... |
github | xyza11808/MATLAB-master | findMoveTimes.m | .m | MATLAB-master/steinmetz-et-al-2019-master/behavior/findMoveTimes.m | 1,511 | utf_8 | 341008f7df6902cc8b7a4930ae5d1f96 |
function [moveTimeUse, firstMoveType, firstMoveTime, hasNoMoveInWin] = ...
findMoveTimes(...
cweA, cwtA, moveData, win, winNoMove)
% determine the movement times to use, including choosing a suitable null
if nargin<4
win = [0.075 0.4];
winNoMove = [-0.1 0.4];
elseif nargin<5
winNoMove = [-0.1 0.4... |
github | xyza11808/MATLAB-master | getIncludedUnits.m | .m | MATLAB-master/steinmetz-et-al-2019-master/behavior/inclusionData/getIncludedUnits.m | 215 | utf_8 | cc4ae0724771c39457d41e0b13a60246 |
function inclU = getIncludedUnits(sessionName)
mfpath = mfilename('fullpath');
inclUnitsPath = fullfile(fileparts(mfpath), 'neurons');
inclU = readNPY(fullfile(inclUnitsPath, [sessionName '_inclNeurons.npy']));
|
github | xyza11808/MATLAB-master | getIncludedTrials.m | .m | MATLAB-master/steinmetz-et-al-2019-master/behavior/inclusionData/getIncludedTrials.m | 363 | utf_8 | 7974c91dba42f570467782b658ec559a |
function [hasL, hasR, hasNone] = getIncludedTrials(sessionName)
mfpath = mfilename('fullpath');
inclTrPath = fullfile(fileparts(mfpath), 'trials');
hasL = readNPY(fullfile(inclTrPath, [sessionName '_hasLeft.npy']));
hasR = readNPY(fullfile(inclTrPath, [sessionName '_hasRight.npy']));
hasNone = readNPY(fullfile(i... |
github | xyza11808/MATLAB-master | surface2volume.m | .m | MATLAB-master/3d_reconstruction/surface2volume.m | 9,259 | utf_8 | 82feb716651726145cbe8a9de2151397 | function outputVolume = surface2volume(inputPatches, inputGrid, verboseOutput)
%SURFACE2VOLUME convert a surface volume to a solid volume
% OV = surface2volume(fv) creates a volume block (logical) in which every
% voxel which is inside the given surface fv is set to 1. The
% structure fv defines the surface by ve... |
github | xyza11808/MATLAB-master | sliceomatic.m | .m | MATLAB-master/3d_reconstruction/sliceomatic/sliceomatic.m | 45,173 | utf_8 | a6c61d18b7e44f84ce50fb0b3a843a8d | function sliceomatic(p1,p2,xmesh,ymesh,zmesh)
% SLICEOMATIC - Slice and isosurface volume exploration GUI
%
% SLICEOMATIC(DATA) - Use 3D double matrix DATA as a volume data
%
% Example:
%
% [x,y,z] = meshgrid(-2:.2:2, -2:.25:2, -2:.16:2);
% v = x .* exp(-x.^2 - y.^2 - z.^2);
% sliceomatic(v)
%
% Using... |
github | xyza11808/MATLAB-master | blinnblob.m | .m | MATLAB-master/3d_reconstruction/sliceomatic/blinnblob.m | 1,004 | utf_8 | 239fa67f6c48a03641f3f1a6df023f87 | function v=blinnblob(centers,nx,ny,nz)
% Blinn's blobs
%
% Make something vaguely benzene like as follows:
%
% centers=[20+8*cos(theta);20+8*sin(theta);20+zeros(1,6)]'
% v=blob(centers,40,40,40)
% isosurface(v,.125)
% Written by Mike Garrity
% Copyright 2000, 2001, 2002, 2003, 2004, 2005 The MathWorks Inc
%
% From ACM... |
github | xyza11808/MATLAB-master | sliceomatic1p0.m | .m | MATLAB-master/3d_reconstruction/sliceomatic/sliceomatic-1.0/sliceomatic1p0.m | 34,558 | utf_8 | dcf318c09849ed1323836bb59725bb3c | function sliceomatic1p0(p1,p2,p3,p4,p5)
% SLICEOMATIC - Slice and isosurface volume exploration GUI
%
% SLICEOMATIC(DATA) - Use 3D double matrix DATA as a volume data
% SLICEOMATIC(X,Y,Z,DATA) - Use 3d double matrix DATA as a volume
% Set the volume dimensions as X, Y, and Z.
% (Not currently used.)
%
% Exa... |
github | xyza11808/MATLAB-master | activelabel.m | .m | MATLAB-master/3d_reconstruction/sliceomatic/private/activelabel.m | 531 | utf_8 | a7db5ca0c16cf6bd4123d6d2d5b25a19 | function activelabel(label, string)
% ACTIVELABEL(LABEL, STRING) - Create a label on GCA which is
% active. LABEL is the property of GCA whose label you are
% setting. STRING is the initial text string for the label.
% Copyright 2000, 2001, 2002, 2003, 2004, 2005 The MathWorks Inc
l = get(gca,label);
... |
github | xyza11808/MATLAB-master | slowset.m | .m | MATLAB-master/3d_reconstruction/sliceomatic/private/slowset.m | 1,890 | utf_8 | 25154d50f242b5f4fc08f7c08502b2f8 | function slowset(handle, prop, value, increment)
% SLOWSET(H, 'PROPERTY', VALUE)
%
% Like SET, except that the property is set against the original
% value over several steps such that the value morphs from the
% starting value to the end value.
%
% H can be a vector of handles, but they must all accept PROPERTY.
%
% O... |
github | xyza11808/MATLAB-master | figmenus.m | .m | MATLAB-master/3d_reconstruction/sliceomatic/private/figmenus.m | 20,391 | utf_8 | 9d31c5bc53fe1498ae9d2aa0b405713e | function outd = figmenus(d)
% Set up sliceomatic's gui menus within structure D
% Copyright 2000, 2001, 2002, 2003, 2004, 2005 The MathWorks Inc
%%% 2/18/05 RAB part in 3 parts %%%
% Main Figure Menu
set(gcf,'menubar','none');
% File menu
d.filemenu = uimenu(gcf,'label','File');
d.fcopy = uimenu(d.fileme... |
github | xyza11808/MATLAB-master | viewer3d.m | .m | MATLAB-master/3d_reconstruction/viewer_3d/viewer3d.m | 242,127 | utf_8 | 54313e095ad9115e782e9c7c86fd600b | function varargout = viewer3d(varargin)
% VIEWER3D is a Matlab GUI for fast shearwarp volume rendering. It also
% allows segmentation and measurements in the imagedata.
%
%
% Just start with
% VIEWER3D
%
% Or to display one or more matlab volumes
%
% VIEWER3D(V); VIEWER3D(V1,V2,V3 ....);
%
%
% inputs,... |
github | xyza11808/MATLAB-master | render.m | .m | MATLAB-master/3d_reconstruction/viewer_3d/render.m | 39,420 | utf_8 | 862781f2513a29b297d0f3ad03c4d348 | function render_image = render(volume,options)
% Function RENDER will volume render a image of a 3D volume,
% with transperancy, shading and ColorTable.
%
% I = RENDER(VOLUME,OPTIONS);
%
% outputs,
% I: The rendered image
%
% inputs,
% VOLUME : Input image volume (Data of type double has short render
% times uin... |
github | xyza11808/MATLAB-master | ReadData3D.m | .m | MATLAB-master/3d_reconstruction/viewer_3d/ReadData3D/ReadData3D.m | 14,704 | utf_8 | 0cf98e0452dcfacfd88336aba55fe9aa | function varargout = ReadData3D(varargin)
% This function ReadData3D allows the user to open medical 3D files. It
% supports the following formats :
%
% Dicom Files ( .dcm , .dicom )
% V3D Philips Scanner ( .v3d )
% GIPL Guys Image Processing Lab ( .gipl )
% HDR/IMG Analyze ( .hdr )
% ISI Files ( .isi )
% N... |
github | xyza11808/MATLAB-master | dicom_folder_info.m | .m | MATLAB-master/3d_reconstruction/viewer_3d/ReadData3D/dicom/dicom_folder_info.m | 8,202 | utf_8 | 26efe1095d5d56ab2f0385376e40facd | function datasets=dicom_folder_info(link,subfolders)
% Function DICOM_FOLDER_INFO gives information about all Dicom files
% in a certain folder (and subfolders), or of a certain dataset
%
% datasets=dicom_folder_info(link,subfolders)
%
% inputs,
% link : A link to a folder like "C:\temp" or a link to the first
% ... |
github | xyza11808/MATLAB-master | dicom_write_volume.m | .m | MATLAB-master/3d_reconstruction/viewer_3d/ReadData3D/dicom/dicom_write_volume.m | 2,148 | utf_8 | ec91c6935829e990ed10a5df29fbc7f5 | function dicom_write_volume(Volume,filename,volscale,info)
% This function DICOM_WRITE_VOLUME will write a Matlab 3D volume as
% a stack of 2D slices in separate dicom files.
%
% dicom_write_volume(Volume,Filename,Scales,Info)
%
% inputs,
% Volume: The 3D Matlab volume
% Filename: The name of the dicom files
% Sc... |
github | xyza11808/MATLAB-master | choose_from_list.m | .m | MATLAB-master/3d_reconstruction/viewer_3d/ReadData3D/dicom/choose_from_list.m | 1,062 | utf_8 | 9a5736ab8c4022c2092521054615df27 | function [id,name] = choose_from_list(varargin)
%
% example :
%
% c{1}='apple'
% c{2}='orange'
% c{3}='berries'
% [id,name]=choose_from_list(c,'Select a Fruit');
%
if(strcmp(varargin{1},'press'))
handles=guihandles;
id=get(handles.listbox1,'Value');
setMyData(id);
uiresume
return
end
% listbox1 Positio... |
github | xyza11808/MATLAB-master | mha_read_volume.m | .m | MATLAB-master/3d_reconstruction/viewer_3d/ReadData3D/mha/mha_read_volume.m | 2,558 | utf_8 | b988be7c56d4b9bf113deb6947527f3f | function V = mha_read_volume(info)
% Function for reading the volume of a Insight Meta-Image (.mha, .mhd) file
%
% volume = tk_read_volume(file-header)
%
% examples:
% 1: info = mha_read_header()
% V = mha_read_volume(info);
% imshow(squeeze(V(:,:,round(end/2))),[]);
%
% 2: V = mha_read_volume('test.mha');
if(~... |
github | xyza11808/MATLAB-master | raw_read_header.m | .m | MATLAB-master/3d_reconstruction/viewer_3d/ReadData3D/raw/raw_read_header.m | 19,605 | utf_8 | 4012e947c5ae87248c1a2034fb83864e | function varargout = raw_read_header(varargin)
% function for reading header of raw volume file
%
% info = raw_read_header(filename);
%
% examples:
% 1, info=raw_read_header()
% 2, info=raw_read_header('volume.raw');
% Edit the above text to modify the response to help raw_read_header
% Last Modified by GUIDE v2.5 ... |
github | xyza11808/MATLAB-master | par_read_header.m | .m | MATLAB-master/3d_reconstruction/viewer_3d/ReadData3D/par/par_read_header.m | 9,018 | utf_8 | 3c5c69964c5a28cad0efe6a75824f403 | function info =par_read_header(filename)
% Function for reading the header of a Philips Par / Rec MR V4.* file
%
% info = par_read_header(filename);
%
% examples:
% 1, info=par_read_header()
% 2, info=par_read_header('volume.par');
if(exist('filename','var')==0)
[filename, pathname] = uigetfile('*.par', 'Read... |
github | xyza11808/MATLAB-master | hdr_read_volume.m | .m | MATLAB-master/3d_reconstruction/viewer_3d/ReadData3D/hdr/hdr_read_volume.m | 1,378 | utf_8 | fb7909dc79b89134c95a7cea8a22da3a | function V=hdr_read_volume(info)
% function for reading volume of HDR/IMG Analyze ( .hdr ) volume file
%
% volume = hdr_read_volume(file-header)
%
% examples:
% 1: info = hdr_read_volume(()
% V = hdr_read_volume(info);
% imshow(squeeze(V(:,:,round(end/2))),[]);
%
% 2: V = hdr_read_volume(('test.hdr');
%
if(~isst... |
github | xyza11808/MATLAB-master | hdr_read_header.m | .m | MATLAB-master/3d_reconstruction/viewer_3d/ReadData3D/hdr/hdr_read_header.m | 4,576 | utf_8 | 0f22557f8c44e3654f7b85480334066d | function info=hdr_read_header(filename)
% function for reading header of HDR/IMG Analyze ( .hdr ) volume file
%
% info = hdr_read_header(filename);
%
% examples:
% 1, info=hdr_read_header()
% 2, info=hdr_read_header('volume.hdr');
if(exist('filename','var')==0)
[filename, pathname] = uigetfile('*.hdr', 'Read hdr... |
github | xyza11808/MATLAB-master | ErrorData3D.m | .m | MATLAB-master/3d_reconstruction/viewer_3d/ReadData3D/subfunctions/ErrorData3D.m | 3,246 | utf_8 | 66924055ba5a507e5363c6d4666bdac8 | function varargout = ErrorData3D(varargin)
% ERRORDATA3D M-file for ErrorData3D.fig
% ERRORDATA3D, by itself, creates a new ERRORDATA3D or raises the existing
% singleton*.
%
% H = ERRORDATA3D returns the handle to a new ERRORDATA3D or the handle to
% the existing singleton*.
%
% ERRORDATA3D('C... |
github | xyza11808/MATLAB-master | InfoData3D.m | .m | MATLAB-master/3d_reconstruction/viewer_3d/ReadData3D/subfunctions/InfoData3D.m | 3,553 | utf_8 | da6f4f6491166d601be56e443974a131 | function varargout = InfoData3D(varargin)
% INFODATA3D M-file for InfoData3D.fig
% INFODATA3D, by itself, creates a new INFODATA3D or raises the existing
% singleton*.
%
% H = INFODATA3D returns the handle to a new INFODATA3D or the handle to
% the existing singleton*.
%
% INFODATA3D('CALLBACK'... |
github | xyza11808/MATLAB-master | render_color.m | .m | MATLAB-master/3d_reconstruction/viewer_3d/Old_Viewer3D_with_c_code/render_color.m | 15,415 | utf_8 | c18a598b1bf6ce37891ab8c0d1a7749c | function render_image = render_color(V, image_size, Mview,alphatable,colortable)
% Function RENDER_COLOR will volume render a Image of a 3D volume with
% transperancy and colortable.
%
% I = RENDER_COLOR(V, SIZE, Mview, ALPHATABLE, COLORTABLE);
%
% inputs,
% V: Input image volume
% SIZE: Sizes (height and length) of... |
github | xyza11808/MATLAB-master | viewer3d_histogram.m | .m | MATLAB-master/3d_reconstruction/viewer_3d/Old_Viewer3D_with_c_code/viewer3d_histogram.m | 4,424 | utf_8 | 04cc06c842af8e3042d6ea77f91aedfb | function varargout = viewer3d_histogram(varargin)
% This function is part of VIEWER3D
%
% color and alpha maps can be changed on the fly by dragging and creating
% new color/alpha markers with the left mouse button.
%
% Function is written by D.Kroon University of Twente (October 2008)
% Edit the above text to modify ... |
github | xyza11808/MATLAB-master | makeViewMatrix.m | .m | MATLAB-master/3d_reconstruction/viewer_3d/Old_Viewer3D_with_c_code/makeViewMatrix.m | 1,147 | utf_8 | 539ba4b4ad9b1b04837ff97b17d7838d | function Mview=makeViewMatrix(r,s,t)
% function makeViewMatrix construct a 4x4 transformation matrix from
% rotation, resize and translation variables.
%
% Mview=makeViewMatrix(R,S,T)
%
% inputs,
% R: Rotation vector [Rx, Ry, Rz];
% S: Resize vector [Sx, Sy, Sz];
% T: Translation vector [Tx, Ty, Tz];
%
% outputs,
%... |
github | xyza11808/MATLAB-master | render_shaded.m | .m | MATLAB-master/3d_reconstruction/viewer_3d/Old_Viewer3D_with_c_code/render_shaded.m | 18,881 | utf_8 | 9c4b0161ecba5d23aaf2897462cb4fe4 | function render_image = render_shaded(V, image_size, Mview,alphatable,colortable,LVector,VVector,shadingtype)
% Function RENDER_SHADED will volume render a shaded Image of a 3D volume,
% with transperancy and colortable.
%
% I = RENDER_SHADED(V, SIZE, Mview, ALPHATABLE, COLORTABLE,LightVector,ViewerVector,SHADINGMATERI... |
github | xyza11808/MATLAB-master | viewer3d.m | .m | MATLAB-master/3d_reconstruction/viewer_3d/Old_Viewer3D_with_c_code/viewer3d.m | 39,153 | utf_8 | 9fa9fa60946c257acdeb09c113487637 | function varargout = viewer3d(varargin)
% VIEWER3D a Matlab 3D volume renderer using the fast shearwarp algorithm.
%
% VIEWER3D(V, RENDERTYPE, SCALES);
%
% inputs,
% V : 3D Input image volume, of type double, single, uint8, uint16 or
% uint32
% (the render process uses only double calculations)
% RENDERTYPE... |
github | xyza11808/MATLAB-master | render_bw.m | .m | MATLAB-master/3d_reconstruction/viewer_3d/Old_Viewer3D_with_c_code/render_bw.m | 14,470 | utf_8 | 3f240d23513941e1acf530df31489f4f | function render_image = render_bw(V, image_size, Mview,alphatable)
% Function RENDER_BW will volume render a Image of a 3D volume with
% a transperancy table.
%
% I = RENDER_MIP(V, SIZE, Mview, ALPHAtable);
%
% inputs,
% V: Input image volume
% SIZE: Sizes (height and length) of output image
% Mview: Viewer (Transf... |
github | xyza11808/MATLAB-master | viewer3d_error.m | .m | MATLAB-master/3d_reconstruction/viewer_3d/Old_Viewer3D_with_c_code/viewer3d_error.m | 3,313 | utf_8 | abc306910c64efef252c1762e396a06b | function varargout = viewer3d_error(varargin)
% VIEWER3D_ERROR M-file for viewer3d_error.fig
% VIEWER3D_ERROR, by itself, creates a new VIEWER3D_ERROR or raises the existing
% singleton*.
%
% H = VIEWER3D_ERROR returns the handle to a new VIEWER3D_ERROR or the handle to
% the existing singleton*.
%
... |
github | xyza11808/MATLAB-master | viewer3d_about.m | .m | MATLAB-master/3d_reconstruction/viewer_3d/Old_Viewer3D_with_c_code/viewer3d_about.m | 2,927 | utf_8 | 9e977443451bfd53ee2b650fe96f2246 | function varargout = viewer3d_about(varargin)
% VIEWER3D_ABOUT M-file for viewer3d_about.fig
% VIEWER3D_ABOUT, by itself, creates a new VIEWER3D_ABOUT or raises the existing
% singleton*.
%
% H = VIEWER3D_ABOUT returns the handle to a new VIEWER3D_ABOUT or the handle to
% the existing singleton*.
%
... |
github | xyza11808/MATLAB-master | render_mip.m | .m | MATLAB-master/3d_reconstruction/viewer_3d/Old_Viewer3D_with_c_code/render_mip.m | 13,775 | utf_8 | 87dc82c11a0e26770c0a35d3010baa37 | function render_image = render_mip(V, image_size, Mview)
% Function RENDER_MIP will render a Maximum Intensity Image of a 3D volume
%
% I = RENDER_MIP(V, SIZE, Mview);
%
% inputs,
% V: Input image volume
% SIZE: Sizes (height and length) of output image
% Mview: Transformation matrix
%
% outputs,
% I: The maximum ... |
github | xyza11808/MATLAB-master | bitmaptext.m | .m | MATLAB-master/3d_reconstruction/viewer_3d/SubFunctions/bitmaptext.m | 100,292 | utf_8 | bd8772fcaf2502542ecd038a976c1616 | function I=bitmaptext(lines,I,pos,options)
% The function BITMAPTEXT will insert textline(s) on the specified position
% in the image.
%
% I=bitmaptext(Text,Ibackground,Position,options)
%
% inputs,
% Text : Cell array with text lines
% Ibackground: the bitmap used as background when a m x n x 3 matrix
% colo... |
github | xyza11808/MATLAB-master | viewer3d_qualityspeed.m | .m | MATLAB-master/3d_reconstruction/viewer_3d/SubFunctions/viewer3d_qualityspeed.m | 6,060 | utf_8 | b56938bc38cf2f4eccdd0ba38ff93d0a | function varargout = viewer3d_qualityspeed(varargin)
% VIEWER3D_QUALITYSPEED M-file for viewer3d_qualityspeed.fig
% VIEWER3D_QUALITYSPEED, by itself, creates a new VIEWER3D_QUALITYSPEED or raises the existing
% singleton*.
%
% H = VIEWER3D_QUALITYSPEED returns the handle to a new VIEWER3D_QUALITYSPEED or... |
github | xyza11808/MATLAB-master | viewer3d_voxelsize.m | .m | MATLAB-master/3d_reconstruction/viewer_3d/SubFunctions/viewer3d_voxelsize.m | 8,989 | utf_8 | 05035f45cf682370f5de14ad000e1ffa | function varargout = viewer3d_voxelsize(varargin)
% VIEWER3D_VOXELSIZE M-file for viewer3d_voxelsize.fig
% VIEWER3D_VOXELSIZE, by itself, creates a new VIEWER3D_VOXELSIZE or raises the existing
% singleton*.
%
% H = VIEWER3D_VOXELSIZE returns the handle to a new VIEWER3D_VOXELSIZE or the handle to
% ... |
github | xyza11808/MATLAB-master | viewer3d_lightvector.m | .m | MATLAB-master/3d_reconstruction/viewer_3d/SubFunctions/viewer3d_lightvector.m | 6,223 | utf_8 | 15bbf1983818b61fcb3e2747adea2fe1 | function varargout = viewer3d_lightvector(varargin)
% VIEWER3D_LIGHTVECTOR M-file for viewer3d_lightvector.fig
% VIEWER3D_LIGHTVECTOR, by itself, creates a new VIEWER3D_LIGHTVECTOR or raises the existing
% singleton*.
%
% H = VIEWER3D_LIGHTVECTOR returns the handle to a new VIEWER3D_LIGHTVECTOR or the ha... |
github | xyza11808/MATLAB-master | viewer3d_histogram.m | .m | MATLAB-master/3d_reconstruction/viewer_3d/SubFunctions/viewer3d_histogram.m | 4,955 | utf_8 | 707fcbdb2a3d383b3de6cfbb144169d0 | function varargout = viewer3d_histogram(varargin)
% This function is part of VIEWER3D
%
% color and alpha maps can be changed on the fly by dragging and creating
% new color/alpha markers with the left mouse button.
%
% Function is written by D.Kroon University of Twente (October 2008)
% Edit the above text to modify ... |
github | xyza11808/MATLAB-master | makeViewMatrix.m | .m | MATLAB-master/3d_reconstruction/viewer_3d/SubFunctions/makeViewMatrix.m | 1,147 | utf_8 | 539ba4b4ad9b1b04837ff97b17d7838d | function Mview=makeViewMatrix(r,s,t)
% function makeViewMatrix construct a 4x4 transformation matrix from
% rotation, resize and translation variables.
%
% Mview=makeViewMatrix(R,S,T)
%
% inputs,
% R: Rotation vector [Rx, Ry, Rz];
% S: Resize vector [Sx, Sy, Sz];
% T: Translation vector [Tx, Ty, Tz];
%
% outputs,
%... |
github | xyza11808/MATLAB-master | viewer3d_console.m | .m | MATLAB-master/3d_reconstruction/viewer_3d/SubFunctions/viewer3d_console.m | 4,231 | utf_8 | c358c82f26d26886a33ea68845e6cfb0 | function varargout = viewer3d_console(varargin)
% VIEWER3D_CONSOLE M-file for viewer3d_console.fig
% VIEWER3D_CONSOLE, by itself, creates a new VIEWER3D_CONSOLE or raises the existing
% singleton*.
%
% H = VIEWER3D_CONSOLE returns the handle to a new VIEWER3D_CONSOLE or the handle to
% the existing ... |
github | xyza11808/MATLAB-master | viewer3d_error.m | .m | MATLAB-master/3d_reconstruction/viewer_3d/SubFunctions/viewer3d_error.m | 3,313 | utf_8 | abc306910c64efef252c1762e396a06b | function varargout = viewer3d_error(varargin)
% VIEWER3D_ERROR M-file for viewer3d_error.fig
% VIEWER3D_ERROR, by itself, creates a new VIEWER3D_ERROR or raises the existing
% singleton*.
%
% H = VIEWER3D_ERROR returns the handle to a new VIEWER3D_ERROR or the handle to
% the existing singleton*.
%
... |
github | xyza11808/MATLAB-master | viewer3d_about.m | .m | MATLAB-master/3d_reconstruction/viewer_3d/SubFunctions/viewer3d_about.m | 2,931 | utf_8 | b00f2eccc530dd07ac25d2285ef08012 | function varargout = viewer3d_about(varargin)
% VIEWER3D_ABOUT M-file for viewer3d_about.fig
% VIEWER3D_ABOUT, by itself, creates a new VIEWER3D_ABOUT or raises the existing
% singleton*.
%
% H = VIEWER3D_ABOUT returns the handle to a new VIEWER3D_ABOUT or the handle to
% the existing singleton*.
%
... |
github | xyza11808/MATLAB-master | viewer3d_workspacevars.m | .m | MATLAB-master/3d_reconstruction/viewer_3d/SubFunctions/viewer3d_workspacevars.m | 4,426 | utf_8 | 7a77a2a3833854c6146fc182b03521b8 | function varargout = viewer3d_workspacevars(varargin)
% VIEWER3D_WORKSPACEVARS M-file for viewer3d_workspacevars.fig
% VIEWER3D_WORKSPACEVARS, by itself, creates a new VIEWER3D_WORKSPACEVARS or raises the existing
% singleton*.
%
% H = VIEWER3D_WORKSPACEVARS returns the handle to a new VIEWER3D_WORKSPACE... |
github | xyza11808/MATLAB-master | viewer3d_dicominfo.m | .m | MATLAB-master/3d_reconstruction/viewer_3d/SubFunctions/viewer3d_dicominfo.m | 3,768 | utf_8 | 799dc4c250afac440206ca300c785cf9 | function varargout = viewer3d_dicominfo(varargin)
% VIEWER3D_DICOMINFO M-file for viewer3d_dicominfo.fig
% VIEWER3D_DICOMINFO, by itself, creates a new VIEWER3D_DICOMINFO or raises the existing
% singleton*.
%
% H = VIEWER3D_DICOMINFO returns the handle to a new VIEWER3D_DICOMINFO or the handle to
% ... |
github | xyza11808/MATLAB-master | interpcontour.m | .m | MATLAB-master/3d_reconstruction/viewer_3d/SubFunctions/interpcontour.m | 668 | utf_8 | 5f0e5a0717eb56a6b0d97b319d67ae05 | function [x,y,z]=interpcontour(x,y,z,s)
% [x,y,z]=interpcontour(x,y,z,s)
%
pos=[x(:) y(:) z(:)];
[t,ind]=unique(pos,'rows');
pos=pos(sort(ind),:);
x=pos(:,1); y=pos(:,2); z=pos(:,3);
[x,y,z]=interpcontour1(x,y,z,1);
[x,y,z]=interpcontour1(x,y,z,s);
function [x,y,z]=interpcontour1(x,y,z,s)
i1=(length(x)+1);
i2=(leng... |
github | xyza11808/MATLAB-master | menubar.m | .m | MATLAB-master/3d_reconstruction/viewer_3d/SubFunctions/menubar.m | 21,801 | utf_8 | 33906f75ca5f7c38c5d456382bb9bc86 | function menubar(varargin)
% This function MenuBar, allows the user to create menu's anywhere in a figure
% it replaces UIcontextmenu of UIpanels by real menu bars.
%
% menubar(figure_handle) or menubar
%
% Mouse hover, and window-resize updates can be enabled by
%
% menubar('start',figure_handle) o... |
github | xyza11808/MATLAB-master | bitmapplot.m | .m | MATLAB-master/3d_reconstruction/viewer_3d/SubFunctions/bitmapplot.m | 8,845 | utf_8 | 772ffb858faea1fb602ebf2370d65c09 | function I=bitmapplot(x,y,Ibackground,options)
% BITMAPPLOT, Linear plot in bitmap.
%
% Iplot=bitmapplot(x,y,Ibackground,options)
%
% inputs,
% x : a vector with x values
% y : a vector with y values, with same length as x
% Ibackground: the bitmap used as background when a m x n x 3 matrix
% color plots a... |
github | xyza11808/MATLAB-master | viewer3d_segment.m | .m | MATLAB-master/3d_reconstruction/viewer_3d/SubFunctions/viewer3d_segment.m | 10,723 | utf_8 | 7b38f76dbd5d9b62bc3cdb6a3b682bc5 | function varargout = viewer3d_segment(varargin)
% VIEWER3D_SEGMENT MATLAB code for viewer3d_segment.fig
% VIEWER3D_SEGMENT, by itself, creates a new VIEWER3D_SEGMENT or raises the existing
% singleton*.
%
% H = VIEWER3D_SEGMENT returns the handle to a new VIEWER3D_SEGMENT or the handle to
% the exis... |
github | xyza11808/MATLAB-master | viewer3d_contrast.m | .m | MATLAB-master/3d_reconstruction/viewer_3d/SubFunctions/viewer3d_contrast.m | 8,521 | utf_8 | 23f75c7fe9be514aa92a196006737ece | function varargout = viewer3d_contrast(varargin)
% VIEWER3D_CONTRAST M-file for viewer3d_contrast.fig
% VIEWER3D_CONTRAST, by itself, creates a new VIEWER3D_CONTRAST or raises the existing
% singleton*.
%
% H = VIEWER3D_CONTRAST returns the handle to a new VIEWER3D_CONTRAST or the handle to
% the ex... |
github | xyza11808/MATLAB-master | structfind.m | .m | MATLAB-master/3d_reconstruction/viewer_3d/SubFunctions/structfind.m | 2,901 | utf_8 | 51470c4dc239dc604683c60f4f742e8e | function index=structfind(a,field,value)
% StructFind, Find the index of a certain string or value in a struct
%
% index=structfind(a,field,value)
%
% inputs,
% a : A Matlab struct, for example a(1).name='red', a(2).name='blue';
% field : The name of the field which is searched, for example 'name'
% ... |
github | xyza11808/MATLAB-master | SnakeInternalForceMatrix3D.m | .m | MATLAB-master/3d_reconstruction/viewer_3d/SubFunctions/BasicSnake_version2d/SnakeInternalForceMatrix3D.m | 1,378 | utf_8 | ca47306c4d20736868edd2baa262a662 | function B=SnakeInternalForceMatrix3D(FV,alpha,beta,gamma)
%
% B=SnakeInternalForceMatrix3D(F,alpha,beta,gamma)
%
% inputs,
% FV : Struct (Patch) with the triangulated surface
% alpha : membrame energy (first order)
% beta : thin plate energy (second order)
% gamma : Step Size (Time)
%
% outputs,
% B : The S... |
github | xyza11808/MATLAB-master | MakeContourClockwise3D.m | .m | MATLAB-master/3d_reconstruction/viewer_3d/SubFunctions/BasicSnake_version2d/MakeContourClockwise3D.m | 1,030 | utf_8 | 11bb54c730373b9ac5d01947f140e490 | function FV=MakeContourClockwise3D(FV)
% This function MakeContourClockwise will make a surface clockwise
% contour clockwise. This is done by calculating the volume inside the
% surface, if it is negative we change the surface orientation.
%
% FV=MakeContourClockwise2D(FV);
%
% input/output,
% FV : Triangulated... |
github | xyza11808/MATLAB-master | SeparateKernel.m | .m | MATLAB-master/3d_reconstruction/viewer_3d/SubFunctions/BasicSnake_version2d/SeparateKernel.m | 8,336 | utf_8 | 0cbb1b55e85e0caddafeea123997195b | function [K1 KN ERR]=SeparateKernel(H)
% This function SEPARATEKERNEL will separate ( do decomposition ) any
% 2D, 3D or nD kernel into 1D kernels. Ofcourse only a sub-set of Kernels
% are separable such as a Gaussian Kernel, but it will give least-squares
% sollutions for non-separatable kernels.
%
% Separating a 3D... |
github | xyza11808/MATLAB-master | Events.m | .m | MATLAB-master/nstat/Events.m | 7,434 | utf_8 | 5ee03e27e754e757b26643fe55614e07 | classdef Events
% EVENTS Events represent times of importance during an experiment that
% need to be highlighted in figures or used to identify certain epochs
% in the data.
%
% e = Events(eventTimes, eventLabels)
% e = Events(eventTimes, eventLabels,eventColor)
% eventTimes: a vector of times at which certain events... |
github | xyza11808/MATLAB-master | CovColl.m | .m | MATLAB-master/nstat/CovColl.m | 37,578 | utf_8 | 43fc126c84f794a4c211452f83fc2f15 | classdef CovColl <handle
% COVCOLL a collection of covariates. Allows multiple covariates that were
% recorded simultaneously to be treated as single unit. Operations such
% as resampling, setting time windows, etc can then be performed on the
% collection as a whole.
%
% When covariates are accessed through the getC... |
github | xyza11808/MATLAB-master | SignalObj.m | .m | MATLAB-master/nstat/SignalObj.m | 99,937 | utf_8 | d38fa44a5241053bdaf3fc7efa7e3e3d | classdef SignalObj < handle
%SIGNALOBJ Class representing a signal abstraction
% SignalObj consist of data that is indexed by time (as a default). The
% indexing variable can be any other type of data and the x-axis labels
% modified to represent this change.
%
% A SignalObj can be multivariate in that the da... |
github | xyza11808/MATLAB-master | Analysis.m | .m | MATLAB-master/nstat/Analysis.m | 59,375 | utf_8 | c5e848faa0f4e2cf29c5cb66720ef6ff | classdef Analysis
% ANALYSIS Collection of functions (static methods) used for GLM analysis
% of point process data.
% <a href="matlab: methods('Analysis')">methods</a>
% <a href="matlab:web('AnalysisExamples.html', '-helpbrowser')">Analysis Examples</a>
%
% see also <a href="matlab:help('Trial')">Trial</a>, <a
% href... |
github | xyza11808/MATLAB-master | vsdload.m | .m | MATLAB-master/WagenaarMBL/vsdload.m | 15,731 | utf_8 | 01f23ff18e868c250d510195742c154b | function dat=vsdload(ifn,wht,frmno,camno)
% VSDLOAD - Load data from vsdscope
% dat = VSDLOAD(ifn) loads data from a single trial from vsdscope.
% IFN may be an "-analog.dat" file, a "-digital.dat" file, or a
% "-ccd.dat" file, in which case raw data is read.
% Alternatively, IFN may be a ".xml" file, in w... |
github | xyza11808/MATLAB-master | selspktrace.m | .m | MATLAB-master/WagenaarMBL/selspktrace.m | 9,954 | utf_8 | 6fd829a6552682af33ef1d8aa9249e9e | function gdspk = selspk_trace(spk,dat,tt)
% SELSPKTRACE - Interactive posthoc spike classification
% gdspk = SELSPKTRACE(spk,dat,tt) starts user interaction for selecting
% spikes based on previous DETECTSPIKE output SPK.
% gdspk = SELSPKTRACE(dat,tt) calls DETECTSPIKE internally with standard
% parameters.... |
github | xyza11808/MATLAB-master | readabf.m | .m | MATLAB-master/WagenaarMBL/readabf.m | 19,972 | utf_8 | db303de9147d56940f9f9effbc001d72 | function [dat,aux] = readabf(ifn, epi, offset, limit)
% READABF - Read ABF files from pClamp 10 into Matlab
% dat = READABF(ifn) simply reads the data and returns values in mV or nA.
% [dat,aux] = READABF(ifn) also returns a structure with auxiliary
% information, which includes:
% CHANNELNAME: cell arra... |
github | xyza11808/MATLAB-master | selectspike.m | .m | MATLAB-master/WagenaarMBL/selectspike.m | 11,158 | utf_8 | 2c960695497ffd24a203fe8aa954f120 | function gdspk = selectspike(spk)
% SELECTSPIKE - Interactive posthoc spike classification
% gdspk = SELECTSPIKE(spk) plots a raster of the spikes in SPK (previously
% detected using SUC2SPIKE) and lets the user interactively select
% which spikes belong to the neuron of interest.
%
% Place the green and bl... |
github | xyza11808/MATLAB-master | physfit.m | .m | MATLAB-master/WagenaarMBL/physfit.m | 11,101 | utf_8 | 4a659d86e0db28e601dd136011de8440 | function [fit,yfit] = physfit(fform,x,y,sy,sx,p0,sxy)
%PHYSFIT Function fitting using errors on both X and Y
% fit = PHYSFIT(fform,x,y,sy,sx) fits the data (X+-SX,Y+-SY) to the
% given functional form FFORM.
% It returns a struct array:
%
% fit(1) is for fitting to (X, Y);
% fit(2) is for fitting to (X, ... |
github | xyza11808/MATLAB-master | mousemove.m | .m | MATLAB-master/WagenaarMBL/mousemove.m | 2,232 | utf_8 | 6f559214f770586c23eb338a968d488d | function [xy0,xy1] = mousemove(foo,varargin)
% MOUSEMOVE Repeatedly call a function until mouse is released
% xy1 = MOUSEMOVE(foo,args,...) repeatedly calls FOO (a function
% handle) with arguments H, XY0, XY1, ARGS, until the mouse is released.
% XY0 is the mouse position at the start of the drag, XY1 is the c... |
github | xyza11808/MATLAB-master | dfdp.m | .m | MATLAB-master/WagenaarMBL/dfdp.m | 2,221 | utf_8 | 11a3dcf6a438c80734ac7230a81d8d91 | % Copyright (C) 1992-1994 Richard Shrager
% Copyright (C) 1992-1994 Arthur Jutan
% Copyright (C) 1992-1994 Ray Muzic
%
% This program is free software; you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation; either version 2 of the Lic... |
github | xyza11808/MATLAB-master | CaSignal_ROI_GUI_NP_Mat.m | .m | MATLAB-master/Matlab_Codes/CaSignal_ROI_GUI_NP_Mat.m | 121,402 | utf_8 | 58fc8ef83abde6b5e849e34322ceae74 | function varargout = CaSignal_ROI_GUI_NP_Mat(varargin)
% CaSignal_ROI_GUI_NP_extract M-file for CaSignal_ROI_GUI_NP_extract.fig
% CaSignal_ROI_GUI_NP_extract, by itself, creates a new CaSignal_ROI_GUI_NP_extract or raises the existing
% singleton*.
%
% H = CaSignal_ROI_GUI_NP_extract returns the handle t... |
github | xyza11808/MATLAB-master | tfagui.m | .m | MATLAB-master/tfa/tfagui.m | 9,813 | utf_8 | 1964dd8433aa912eb0ee7f3204487278 | %AOK TFR 2.0
%Deming Zhang
%deming.zhang@gmail.com
%
function varargout = tfagui(varargin)
% Begin initialization code - DO NOT EDIT
gui_Singleton = 1;
gui_State = struct('gui_Name', mfilename, ...
'gui_Singleton', gui_Singleton, ...
'gui_OpeningFcn', @TFA_OpeningFcn, ...... |
github | xyza11808/MATLAB-master | MultiROI.m | .m | MATLAB-master/ROI/MultiROI.m | 11,887 | utf_8 | 848db38d1e440d6aaeb5aa9790e00e18 | function roi = multiROI(img, nroi)
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% 1) Goal: Draw & process multiple ROIs interactively on an image. %
%% %
%% 2) Usage:... |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.