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value | path stringlengths 12 229 | size int64 23 843k | source_encoding stringclasses 9
values | md5 stringlengths 32 32 | text stringlengths 23 843k |
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github | johnnychien85/seq2map-master | emat2mot.m | .m | seq2map-master/scripts/matlab/math/emat2mot.m | 1,374 | utf_8 | d86c81c2fbcddbbcc3488a3aefc0b807 | % M = EMAT2MOT(E,x1,x2) decomposes essential matrix E into rotation and translation
% elements that together form the motion matrix M. Optional normalised point
% correspondences x1 and x2 are given to return only the valid geometric configuration
% out of all the four possible solutions.
function M = emat2mot(E,x1,x2)... |
github | johnnychien85/seq2map-master | im2mot.m | .m | seq2map-master/scripts/matlab/math/im2mot.m | 1,205 | utf_8 | 5d27a7cb75b58c37db2cc0d7ae356deb | % IM2MOT finds relative pose from two images.
function M = im2mot(I1,I2,K1,K2,epsilon,confidence,iter)
if nargin < 4, K2 = K1; end
if nargin < 5, epsilon = 0.05; end
if nargin < 6, confidence = 0.99; end
if nargin < 7, iter = 1000; end
x1 = detectFASTFeatures(I1);... |
github | johnnychien85/seq2map-master | mot2emat.m | .m | seq2map-master/scripts/matlab/math/mot2emat.m | 603 | utf_8 | bfc35dac3fc85a76207fcbb07353f3fb | % MOT2EMAT converts pose matrix M = [R,t] to essential matrix
% E = tx * R, where tx is the skew-symmetry form of vector t.
%
% Use mot2fmat instead for calibrated camera(s) to obtain the
% fundamental matrix that directly applies to unormalised image
% coordinates.
%
% See also mot2fmat
%
function E = mot2emat(M)
... |
github | johnnychien85/seq2map-master | vec2mot.m | .m | seq2map-master/scripts/matlab/math/vec2mot.m | 362 | utf_8 | 28fd61e9522acae2b86c3de735089aa2 | % restore pose matrix from it's vector representation
function M = vec2mot(x,angleAxis)
if nargin < 2, angleAxis = false; end
t = x(4:6); % * 100;
if angleAxis
n = norm(x(1:3));
r = [x(1:3)/n;n];
R = vrrotvec2mat(r);
else
r = deg2rad(x(1:3));
R = angle2dcm(r(1),r... |
github | johnnychien85/seq2map-master | bisect2.m | .m | seq2map-master/scripts/matlab/math/bisect2.m | 1,234 | utf_8 | 226b54ed105358f37a987db1985d17a9 | % BISECT2 cuts through a given matrix along columns to achieve
% minimal cost specified by the matrix itself while maintaining
% desired smoothness. The minimisation is based on the Viterbi
% algorithm, a dynamic programming technique.
%
% By Hsiang-Jen (Johnny) Chien (jchien@aut.ac.nz) from Centre of Robotics and
% Vi... |
github | johnnychien85/seq2map-master | undistort.m | .m | seq2map-master/scripts/matlab/math/undistort.m | 391 | utf_8 | 447a231a074044972e47850dc567a443 | % undistort transforms points from an distorted image plane to an ideal one
function x = undistort(x,cam)
if isa(cam.ParamsObject,'cameraParameters')
x = undistortPoints(x,cam.ParamsObject); % use the built-in function
else
% TODO: finish this for undistortion without the help of
% Comp... |
github | johnnychien85/seq2map-master | transformCovariance.m | .m | seq2map-master/scripts/matlab/math/transformCovariance.m | 93 | utf_8 | 96e9a7de44525dbbff2f21d66d61b66b | % Ci = Ai * cov_i * Ai'
function cov = transformCovariance(cov,A)
[d0,d1] = size(A);
end |
github | johnnychien85/seq2map-master | mot2fmat.m | .m | seq2map-master/scripts/matlab/math/mot2fmat.m | 530 | utf_8 | 813f47851af5c3abd72a8eba96fd7078 | % MOT2FMAT converts pose matrix M = [R,t] to fundamental matrix F
% with respect to cameras K1 and K2. For corresponding image points
% (x1,x2) it holds x2'*F*x1 = 0. Optionally the epipoles are returned
% by the second and third outputs.
%
% See also mot2emat, invcam
%
function [F,e1,e2] = mot2fmat(M,K1,K2)
if nar... |
github | johnnychien85/seq2map-master | pts2image.m | .m | seq2map-master/scripts/matlab/math/pts2image.m | 3,157 | utf_8 | 42b8548a4b526f2f5fcd69903e7ae1bd | function [x2d, inRange, idx, im] = pts2image(x3d, cam, im, varargin)
po = parseArgs(varargin{:});
if nargin < 3
lim = [-inf,-inf,-inf;inf,inf,inf];
im = [];
po.Quiet = true;
elseif ndims(im) == 2 && all(size(im) == [2,3])
lim = im;
im = [];
else
lim = ... |
github | johnnychien85/seq2map-master | epimatch.m | .m | seq2map-master/scripts/matlab/math/epimatch.m | 2,531 | utf_8 | 21c79445fa7defec509626a15c7c6a78 | % EPIMATCH performs exhaustive search for each
% image point in pts2d following the corresponding
% epipolar lines in I2 to find the best match.
function D = epimatch(I1,I2,M12,K1,K2,pts2d)
[F,~,e2] = mot2fmat(M12,K1,K2); % find the fundamental matrix between I1 and I2 and the epipole in I2
x1 = pts2d + 1;
... |
github | johnnychien85/seq2map-master | fullsymmat.m | .m | seq2map-master/scripts/matlab/math/fullsymmat.m | 341 | utf_8 | d3c4fba433155d8fd27d0eb4205a0b95 | function B = fullsymmat(A,m)
B = zeros(m,m,size(A,1),'like',A);
for i = 1 : m
for j = 1 : m
B(i,j,:) = reshape(A(:,sub2symind(i-1,j-1,m)+1),1,1,[]);
end
end
end
function ind = sub2symind(i,j,m)
if i < j, ind = i*m - (i-1) * i/2 + j - i;
else ind = j*m - (j-1) * j/2... |
github | johnnychien85/seq2map-master | imwarpdp.m | .m | seq2map-master/scripts/matlab/math/imwarpdp.m | 1,791 | utf_8 | 9ae13760520b5aa1b104f4540acf7158 | % I0 = IMWARPDP(It,D01) warps image I1 to I0 via disparity map D01 following
% I0(x,y) = I1(x-D01(x,y),y).
%
function I0 = imwarpdp(I1,D01,c0,c1,cj)
[m,n,k] = size(I1);
assert(size(D01,1) == m && size(D01,2) == n);
if nargin > 2
assert(nargin == 5);
rectified = checkCanonical(c0,c1);
else
... |
github | johnnychien85/seq2map-master | triangulatePoints.m | .m | seq2map-master/scripts/matlab/math/triangulatePoints.m | 930 | utf_8 | cfb256f944133ad06bac1df1e7115b51 | % borrowed from triangulateMidPoint in cameraPose.m
function [g,e,k,rpe] = triangulatePoints(x0,x1,P0,P1)
if size(x0,2) == 2, x0 = eucl2homo(x0); end
if size(x1,2) == 2, x1 = eucl2homo(x1); end
assert(numel(x0) == numel(x1));
[KR0,c0] = pmat2krc(P0);
[KR1,c1] = pmat2krc(P1);
% normalised image coordinate... |
github | johnnychien85/seq2map-master | dp2el.m | .m | seq2map-master/scripts/matlab/math/dp2el.m | 3,843 | utf_8 | 40bd4a0292b8ced0a109e12d117e5f5c | % DP2EL identifies road manifold using DP2STX in the first frame and uses it to
% build a digital elevation map (DEM) by accumulating transformed 3D points for
% each disparity map.
function [el,zgrid,xgrid,rcs] = dp2el(dp,cam0,cam1,mot,varargin)
po = parseArgs(dp,cam0,cam1,mot,varargin{:});
frames = size(dp,3)... |
github | johnnychien85/seq2map-master | ransac.m | .m | seq2map-master/scripts/matlab/math/ransac.m | 848 | utf_8 | 91d8dbf533cdcd6aed6942358e0152dc | % a generic RANSAC subroutine
function [x_bst,d_bst,inliers] = ransac(m,n,f_est,f_eval,epsilon,confidence,iter,acceptance)
x_bst = [];
d_bst = [];
i_bst = [];
n_bst = 0;
inliers = false(m,1);
k = 0;
while k < iter
idx = drawSamples(m,n);
x_est = f_est(idx);
d_est = f_eval(x_est);
... |
github | johnnychien85/seq2map-master | pts2mot.m | .m | seq2map-master/scripts/matlab/math/pts2mot.m | 586 | utf_8 | 4f56090e3e4568fb78c716a2ec2e6eb7 | function M = pts2mot(x1,x2,K)
E = estimateEssentialMatrix(x1,x2,K,K);
M = emat2mot(E,eucl2cano(x1,K),eucl2cano(x2,K));
end
%{
function [M,E] = pts2mot(x1,x2,K)
F = estimateFundamentalMatrix(x0,x1);
E = K'*F*K;
M = chieralityCheck(emat2mot(E),x0,x1,K);
end
function M = chieralityCheck(M,x0,x1,K)
numPosK = ... |
github | johnnychien85/seq2map-master | rigid.m | .m | seq2map-master/scripts/matlab/math/rigid.m | 965 | utf_8 | a6b94d139ebc2a595b332ebbff77262c | % y = M * x
function M = rigid(x,y)
u = mean(x,1);
v = mean(y,1);
M = bsxfun(@minus,x,u)' * bsxfun(@minus,y,v);
[Sxx,Syx,Szx,Sxy,Syy,Szy,Sxz,Syz,Szz] = dealr(M(:));
N = [Sxx+Syy+Szz, Syz-Szy, Szx-Sxz, Sxy-Syx;...
Syz-Szy, Sxx-Syy-Szz, Sxy+Syx, Szx+Sxz;...
... |
github | johnnychien85/seq2map-master | mot2vec.m | .m | seq2map-master/scripts/matlab/math/mot2vec.m | 333 | utf_8 | cb607cdff3bc48c6f388dbce9357ab13 | % convert post matrix to a 6-vector
function x = mot2vec(M,angleAxis)
if nargin < 2, angleAxis = false; end
R = M(1:3,1:3);
t = M(1:3,4);
if angleAxis
r = vrrotmat2vec(R)';
r = norm(r(1:3)) * r(1:3);
else
[r1,r2,r3] = dcm2angle(R);
r = rad2deg([r1,r2,r3])';
end
x... |
github | johnnychien85/seq2map-master | dp2mot.m | .m | seq2map-master/scripts/matlab/math/dp2mot.m | 11,183 | utf_8 | ce63f2978c513f10e502098c13982d53 | % DP2MOT implements a scoped Visual Odometry algorithm based on direct intensity
% matching or optionally a feature-based descriptor matching technique.
%
% See also: epnp
function [mot,x2d] = dp2mot(dp,im,cam0,cam1,varargin)
% some preliminary processing..
dp(find(dp < 0 | ~isfinite(dp))) = 0;
dp = double(... |
github | johnnychien85/seq2map-master | estimateEssentialMatrix.m | .m | seq2map-master/scripts/matlab/math/estimateEssentialMatrix.m | 1,027 | utf_8 | 95660b61f79f6f202471db77f7b5f78e | % ESTIMATEESSENTIALMATRIX finds an essential matrix from 2D point correspondences given
% camera matrices. The outliers are rejected using RANSAC.
function [E,inliers,err] = estimateEssentialMatrix(x1,x2,K1,K2,epsilon,confidence,iter)
K1_inv = inv(K1);
K2_inv = inv(K2);
vec2emat = @(x) mot2emat(vec2mot(x));
[E,er... |
github | johnnychien85/seq2map-master | solveEgomo.m | .m | seq2map-master/scripts/matlab/math/solveEgomo.m | 3,410 | utf_8 | 23c80ed8c890dbd16b0f4e5fcea026c8 | function [M,epi,rpe] = solveEgomo(egomo,alpha,M,im,dryrun)
if nargin < 3, M = []; end
if nargin < 4, im = []; end
if nargin < 5, dryrun = false; end
extended = true;
n_epi = numel(egomo.epi.uid);
n_pnp = numel(egomo.pnp.uid);
a_epi = 1 / (1 + n_epi/n_pnp*(1/alpha-1)); %* (n_epi + n_pnp) / n_epi / 2;
a_rpe... |
github | johnnychien85/seq2map-master | invcam.m | .m | seq2map-master/scripts/matlab/math/invcam.m | 551 | utf_8 | 613dbfc3693da7be598639997cada0e8 | % INVCAM finds the inverse of an upper triangular 3-by-3 camera matrix
% K = [a,b,c; 0,d,e; 0,0,1]. The computation is slightly faster than using inv(K).
function K_inv = invcam(K)
K_inv = [ ...
1/K(1,1), -K(1,2)/K(1,1)/K(2,2), K(2,3)*K... |
github | johnnychien85/seq2map-master | featureShow.m | .m | seq2map-master/scripts/matlab/unused/featureShow.m | 2,133 | utf_8 | cc65d6921cf798a60a9f1bd79bc20b21 | function featureShow(cam,out)
fps = 30;
scantime = 1;
locktime = 1;
showtime = 2;
radius0 = 32;
radius1 = 2;
im = loadImage(cam,1,'greyscale');
out = vision.VideoFileWriter(out,'FrameRate',fps);
fig = vision.VideoPlayer();
scanframes = scantime * fps;
y0 = 1;
h = round(size(im,1) / scanframes);
mask = z... |
github | johnnychien85/seq2map-master | coaxflow.m | .m | seq2map-master/scripts/matlab/unused/coaxflow.m | 2,986 | utf_8 | 3d88007757fc157bda997ae37e5755ec | function [D,G1] = coaxflow(I0,I1,M,K)
[m,n,~] = size(I1);
[T0,T1,R1] = estimateCoaxTransforms(K,M(1:3,1:3),M(1:3,4));
R1i = R1';
%figure, imshow(imwarp(I0,T0));
%figure, imshow(imwarp(I1,T1));
ref2d = imref2d([m,n]);
W0 = imwarp(I0,T0,'Outputview',ref2d);
W1 = imwarp(I1,T1,'Outputview',ref2d);
[P0,A0,R0] = ... |
github | johnnychien85/seq2map-master | pts2edges.m | .m | seq2map-master/scripts/matlab/unused/pts2edges.m | 1,231 | utf_8 | f6e9aa63f95c539ce30c4d2042f062ef | function dst = points2edges(x3d,useConvexity)
if nargin < 2, useConvexity = true; end
% kdt = KDTreeSearcher(x3d);
% nn2 = knnsearch(kdt,x3d,'K',3); % search for 2 nearest neighbors for each point
% nn2 = nn2(:,2:3);
[T,P,R] = cart2sph(x3d(:,1),x3d(:,2),x3d(:,3));
kdt = KDTreeSearcher([T,P]);
... |
github | johnnychien85/seq2map-master | rmat2angles.m | .m | seq2map-master/scripts/matlab/unused/rmat2angles.m | 356 | utf_8 | 1d00d26c3dde62f16a9dd71e195e818d | % RMAT2ANGLES converts a rotation matrix to euler angles which define three
% consequent rotations respectively about x-, y-, and z-axis.
%
% Source of formula: http://planning.cs.uiuc.edu/node103.html
%
function [x,y,z] = rmat2angles(R)
z = atan( R(2,1) / R(1,1));
y = atan(-R(3,1) / sqrt(R(3,2)^2+R(3,3)^2));
... |
github | johnnychien85/seq2map-master | rio.m | .m | seq2map-master/scripts/matlab/unused/rio.m | 9,651 | utf_8 | 890fe8de23d103e6486225d1628a05ca | function rio(seq)
cam = seq.cam(1);
if ~isfield(cam,'Features')
error 'Image features are not available; use findSequenceFeatures first.';
end
t0 = 1;
tn = numel(cam.ImageFiles);
frames = tn - t0;
% initialise motion matrix stack
M = zeros(4,4,tn);
M(:,:,1) = eye(4);
% initialise features' 3D coord... |
github | johnnychien85/seq2map-master | vrrotvec2mat.m | .m | seq2map-master/scripts/matlab/unused/vrrotvec2mat.m | 2,293 | utf_8 | 96e508992a531c5e5681098ac407fc0c | function m = vrrotvec2mat(r, options)
%VRROTVEC2MAT Convert rotation from axis-angle to matrix representation.
% M = VRROTVEC2MAT(R) returns a matrix representation of rotation
% defined by the axis-angle rotation vector R.
%
% M = VRROTVEC2MAT(R, OPTIONS) returns a matrix representation of rotation
% defined... |
github | johnnychien85/seq2map-master | loadCalibrationCamToCam.m | .m | seq2map-master/3rdparties/kitti/devkit_raw_data/matlab/loadCalibrationCamToCam.m | 1,894 | utf_8 | 88db832a2338f205ea36b1a9f6231aed | function calib = loadCalibrationCamToCam(filename)
% open file
fid = fopen(filename,'r');
if fid<0
calib = [];
return;
end
% read corner distance
calib.cornerdist = readVariable(fid,'corner_dist',1,1);
% read all cameras (maximum: 100)
for cam=1:100
% read variables
S_ = readVariable(fid,['S_' num2s... |
github | johnnychien85/seq2map-master | loadCalibrationRigid.m | .m | seq2map-master/3rdparties/kitti/devkit_raw_data/matlab/loadCalibrationRigid.m | 855 | utf_8 | 9148661cd7335b41dace4f57bd25b3a4 | function Tr = loadCalibrationRigid(filename)
% open file
fid = fopen(filename,'r');
if fid<0
error(['ERROR: Could not load: ' filename]);
end
% read calibration
R = readVariable(fid,'R',3,3);
T = readVariable(fid,'T',3,1);
Tr = [R T;0 0 0 1];
% close file
fclose(fid);
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%... |
github | johnnychien85/seq2map-master | Ematrix5pt_v2.m | .m | seq2map-master/3rdparties/fivepoints/Ematrix5pt_v2.m | 2,159 | utf_8 | 005c1de626bca8b9445662be031f7598 |
function EMatrices = Ematrix5pt_v2 (q, qp)
% Computes possible E-matrices from matches
% Call as follows: E = Ematrix5pt_v2(q1, q2)
% where both q1 and q2 are of dimension (3, 5).
% This version uses polyeig to solve.
% Copyright Richard Hartley: 2010
%-----------------------------------------... |
github | johnnychien85/seq2map-master | Ematrix6pt.m | .m | seq2map-master/3rdparties/fivepoints/Ematrix6pt.m | 10,082 | utf_8 | dddd76b2c83c12396e79f374931dd9ef |
function [EMatrices, flengths, A] = Ematrix6pt (q, qp)
% Computes possible E-matrices and focal lengths from six matches
% Call as follows: [E, f] = Ematrix6pt(q1, q2)
% where both q1 and q2 are of dimension (3, 6).
% Copyright Richard Hartley: 2010
%----------------------------------------------... |
github | johnnychien85/seq2map-master | Ematrix5pt_v3.m | .m | seq2map-master/3rdparties/fivepoints/Ematrix5pt_v3.m | 2,778 | utf_8 | 76329a564c86adb16d1f6bf5dd87acc2 |
function Ematrices = Ematrix5pt_v3 (q, qp)
% Computes possible E-matrices from matches
% Call as follows: E = Ematrix5-t(q1, q2)
% where both q1 and q2 are of dimension (3, 5).
% This version uses polyeig to solve.
% Copyright Richard Hartley: 2010
%--------------------------------------------... |
github | johnnychien85/seq2map-master | Ematrix6pt_v2.m | .m | seq2map-master/3rdparties/fivepoints/Ematrix6pt_v2.m | 2,225 | utf_8 | 9487a5e97a324bb84d165c27605cf2c7 |
function [EMatrices, flengths] = Ematrix6pt_v2 (q, qp)
% Computes possible E-matrices and focal lengths from matches
% Call as follows: [E, f] = Ematrix6pt_v2(q1, q2)
% where both q1 and q2 are of dimension (3, 6).
% This version uses polyeig to solve.
% Copyright Richard Hartley: 2010
%------... |
github | johnnychien85/seq2map-master | Ematrix5pt.m | .m | seq2map-master/3rdparties/fivepoints/Ematrix5pt.m | 8,261 | utf_8 | 596d25b93cc7d28f3fa271682e9491b7 |
function EMatrices = Ematrix5pt (q, qp)
% Computes possible E-matrices from matches
% Call as follows: E = Ematrix5-t(q1, q2)
% where both q1 and q2 are of dimension (3, 5).
% Copyright Richard Hartley: 2010
%--------------------------------------------------------------------------
% LICENSE ... |
github | zhoupc/OASIS_matlab-master | deconvolveCa.m | .m | OASIS_matlab-master/deconvolveCa.m | 14,012 | utf_8 | eb64220833e8877ca018cf2444f5f5d4 | function [c, s, options] = deconvolveCa(y, varargin)
%% infer the most likely discretized spike train underlying an fluorescence trace
%% Solves mutliple formulation of the problem
% 1) FOOPSI,
% mininize_{c,s} 1/2 * norm(y-c,2)^2 + lambda * norm(s,1)
% subject to c>=0, s>=0, s=Gc
% 2) constrained FOOPSI... |
github | zhoupc/OASIS_matlab-master | constrained_oasisAR2.m | .m | OASIS_matlab-master/packages/oasis/constrained_oasisAR2.m | 7,946 | utf_8 | c8e60c17c59fcd3a3d6987960dd2b38c | function [c, s, b, g, lam, active_set] = constrained_oasisAR2(y, g, sn, optimize_b,...
optimize_g, decimate, maxIter)
%% Infer the most likely discretized spike train underlying an AR(2) fluorescence trace
% Solves the sparse non-negative deconvolution problem
% min lam |s|_1
% subject to |y-c|_2^2 <= sn^2*T
%% ... |
github | zhoupc/OASIS_matlab-master | constrained_oasisAR1.m | .m | OASIS_matlab-master/packages/oasis/constrained_oasisAR1.m | 8,276 | utf_8 | 842b905d790770bdf2f2eafcbdbf50e0 | function [c, s, b, g, lam, active_set] = constrained_oasisAR1(y, g, sn, optimize_b,...
optimize_g, decimate, maxIter, tau_range)
%% Infer the most likely discretized spike train underlying an AR(1) fluorescence trace
% Solves the sparse non-negative deconvolution problem
% min 1/2|c-y|^2 + lam |s|_1 subject to s_t... |
github | zhoupc/OASIS_matlab-master | thresholded_oasisAR2.m | .m | OASIS_matlab-master/packages/oasis/thresholded_oasisAR2.m | 9,443 | utf_8 | 5f79de90da526c696fa1a6edc58e6248 | function [c, s, b, g, smin, active_set] = thresholded_oasisAR2(y, g, sn, smin, optimize_b,...
optimize_g, decimate, maxIter, thresh_factor)
%% Infer the most likely discretized spike train underlying an AR(2) fluorescence trace
% Solves the sparse non-negative deconvolution problem
% min 1/2|c-y|^2 + lam |s|_1 sub... |
github | zhoupc/OASIS_matlab-master | thresholded_nnls.m | .m | OASIS_matlab-master/packages/oasis/thresholded_nnls.m | 6,354 | utf_8 | 1e8c174df6516a34c3555337e00adc9f | function [c, s] = thresholded_nnls(y, g, sn, smin, shift, win, tol, maxIter, mask, thresh_factor)
%% Infer the most likely discretized spike train underlying an AR(2) fluorescence trace
% Solves the sparse non-negative deconvolution problem
% min 1/2|Ks-y|^2 + lam * |s|_1 subject to s_t = c_t-g c_{t-1} >= 0
%% inputs... |
github | zhoupc/OASIS_matlab-master | foopsi_oasisAR1.m | .m | OASIS_matlab-master/packages/oasis/foopsi_oasisAR1.m | 5,966 | utf_8 | 41c045bd8710676bf341c8989ed13192 | function [c, s, b, g, active_set] = foopsi_oasisAR1(y, g, lam, smin, optimize_b,...
optimize_g, decimate, maxIter, tau_range, gmax)
%% Infer the most likely discretized spike train underlying an AR(1) fluorescence trace
% Solves the sparse non-negative deconvolution problem
% min 1/2|c-y|^2 + lam |s|_1 subject to ... |
github | zhoupc/OASIS_matlab-master | onnls.m | .m | OASIS_matlab-master/packages/oasis/onnls.m | 6,281 | utf_8 | c9f35b277ec6f6569add4901501d5f7a | function [c, s] = onnls(y, g, lam, shift, win, tol, maxIter, mask, smin)
%% Infer the most likely discretized spike train underlying an AR(2) fluorescence trace
% Solves the sparse non-negative deconvolution problem
% min 1/2|Ks-y|^2 + lam * |s|_1 subject to c = Ks >= 0
%% inputs:
% y: T*1 vector, vth dimensional ... |
github | zhoupc/OASIS_matlab-master | foopsi_oasisAR2.m | .m | OASIS_matlab-master/packages/oasis/foopsi_oasisAR2.m | 5,559 | utf_8 | f0aad72d74a7bb37f2f3e71f147fd343 | function [c, s, b, g, active_set] = foopsi_oasisAR2(y, g, lam, smin, optimize_b,...
optimize_g, decimate, maxIter)
%% Infer the most likely discretized spike train underlying an AR(2) fluorescence trace
% Solves the sparse non-negative deconvolution problem
% min 1/2|c-y|^2 + lam |s|_1 subject to s_t = c_t-g_1 c_{... |
github | zhoupc/OASIS_matlab-master | thresholded_oasisAR1.m | .m | OASIS_matlab-master/packages/oasis/thresholded_oasisAR1.m | 8,686 | utf_8 | ef1f954920ceb24238a011e171e498b2 | function [c, s, b, g, smin, active_set] = thresholded_oasisAR1(y, g, sn, optimize_b,...
optimize_g, decimate, maxIter, thresh_factor, p_noise, tau_range)
%% Infer the most likely discretized spike train underlying an AR(1) fluorescence trace
% Solves the sparse non-negative deconvolution problem
% min 1/2|c-y|^2 ... |
github | zhoupc/OASIS_matlab-master | deconvCa.m | .m | OASIS_matlab-master/packages/oasis/deconvCa.m | 11,612 | utf_8 | 54f929ab3540e783c4822ea127e20a93 | function [c, s, kernel, iter] = deconvCa(y, kernel, smin, fit_gt, debug_on, sn, maxIter, theta, lambda)
%% deconvolve calcium traces to infer spike counts
%% inputs:
% y: 1*T vector, observed calcium traces
% kernel: struct variable with two fields {'fhandle', 'pars', nMax}. kernel
% deterines the convolution ke... |
github | zhoupc/OASIS_matlab-master | lars_regression_noise.m | .m | OASIS_matlab-master/packages/constrained-foopsi/lars_regression_noise.m | 7,310 | utf_8 | 57b6188ceb2fc027c7e65b5a96aac472 | function [Ws, lambdas, W_lam, lam, flag] = lars_regression_noise(Y, X, positive, noise)
% run LARS for regression problems with LASSO penalty, with optional positivity constraints
% Author: Eftychios Pnevmatikakis. Adapted code from Ari Pakman
% Input Parameters:
% Y: Y(:,t) is the observed data at time ... |
github | zhoupc/OASIS_matlab-master | deconvCa.m | .m | OASIS_matlab-master/packages/oasis_kernel/deconvCa.m | 11,706 | utf_8 | ca3322ab3646d22465e5fbb0509a2e84 | function [c, s, kernel, iter] = deconvCa(y, kernel, smin, fit_gt, debug_on, sn, maxIter, theta, lambda)
%% deconvolve calcium traces to infer spike counts
%% inputs:
% y: 1*T vector, observed calcium traces
% kernel: struct variable with two fields {'fhandle', 'pars', nMax}. kernel
% deterines the convolution ke... |
github | zhoupc/OASIS_matlab-master | cvx_version.m | .m | OASIS_matlab-master/packages/cvx/cvx_version.m | 14,459 | utf_8 | 64d0f08cf9bf3c75fcad41acaf35a8c0 | function varargout = cvx_version( varargin )
% CVX_VERSION Returns version and environment information for CVX.
%
% When called with no arguments, CVX_VERSION prints out version and
% platform information that is needed when submitting CVX bug reports.
%
% This function is also used internally to return use... |
github | zhoupc/OASIS_matlab-master | cvx_grbgetkey.m | .m | OASIS_matlab-master/packages/cvx/cvx_grbgetkey.m | 19,096 | utf_8 | 080162e4fd27b14ea8387362148db7d1 | function success = cvx_grbgetkey( kcode, overwrite )
% CVX_GRBGETKEY Retrieves and saves a Gurobi/CVX license.
%
% This function is used to install Gurobi license keys for use in CVX. It
% is called with your Gurobi license code as a string argument; e.g.
%
% cvx_grbgetkey xxxxxxxx-xxxx-xxxx-xxxx-xxxxxxxxxxxx
% ... |
github | zhoupc/OASIS_matlab-master | HSDNTcorr.m | .m | OASIS_matlab-master/packages/cvx/sdpt3/HSDSolver/HSDNTcorr.m | 1,001 | utf_8 | c42eba1c6bae660b88921b7c8747490e | %%************************************************************************
%% HSDNTcorr: corrector step for the NT direction.
%%
%% SDPT3: version 3.1
%% Copyright (c) 1997 by
%% K.C. Toh, M.J. Todd, R.H. Tutuncu
%% Last Modified: 16 Sep 2004
%%************************************************************************
f... |
github | zhoupc/OASIS_matlab-master | HSDHKMdirfun.m | .m | OASIS_matlab-master/packages/cvx/sdpt3/HSDSolver/HSDHKMdirfun.m | 1,551 | utf_8 | 1034e25e48a42d2fa143f93f47961fe9 | %%*******************************************************************
%% HSDHKMdirfun: compute (dX,dZ), given dy, for the HKM direction.
%%
%% SDPT3: version 3.1
%% Copyright (c) 1997 by
%% K.C. Toh, M.J. Todd, R.H. Tutuncu
%% Last Modified: 16 Sep 2004
%%****************************************************************... |
github | zhoupc/OASIS_matlab-master | HSDsqlp.m | .m | OASIS_matlab-master/packages/cvx/sdpt3/HSDSolver/HSDsqlp.m | 11,860 | utf_8 | 00b8311a8efbee36662ca9288870a1cd | %%*****************************************************************************
%% HSDsqlp: solve an semidefinite-quadratic-linear program
%% by infeasible path-following method on the homogeneous self-dual model.
%%
%% [obj,X,y,Z,info,runhist] =
%% HSDsqlp(blk,At,C,b,OPTIONS,X0,y0,Z0);
%%
%% Input: blk: a cel... |
github | zhoupc/OASIS_matlab-master | HSDsortA.m | .m | OASIS_matlab-master/packages/cvx/sdpt3/HSDSolver/HSDsortA.m | 2,577 | utf_8 | 0a74ddbb8a0c79bf22592d780d865e06 | %%*********************************************************************
%% sortA: sort columns of At{p} in ascending order according to the
%% number of nonzero elements.
%%
%% [At,C,b,X0,Z0,permA,permZ] = sortA(blk,At,C,b,X0,Z0);
%%
%% SDPT3: version 3.1
%% Copyright (c) 1997 by
%% K.C. Toh, M.J. Todd, R.H. Tut... |
github | zhoupc/OASIS_matlab-master | HSDHKMrhsfun.m | .m | OASIS_matlab-master/packages/cvx/sdpt3/HSDSolver/HSDHKMrhsfun.m | 2,666 | utf_8 | 16409ae4672f80ef54a33c31ef30000f | %%*******************************************************************
%% HSDHKMrhsfun: compute the right-hand side vector of the
%% Schur complement equation for the HKM direction.
%%
%% SDPT3: version 3.1
%% Copyright (c) 1997 by
%% K.C. Toh, M.J. Todd, R.H. Tutuncu
%% Last Modified: 16 Sep 2004
%%*****... |
github | zhoupc/OASIS_matlab-master | HSDsqlpcheckconvg.m | .m | OASIS_matlab-master/packages/cvx/sdpt3/HSDSolver/HSDsqlpcheckconvg.m | 6,249 | utf_8 | a579e4972fd77d5cc3e11b72bf56d3a9 | %%*****************************************************************************
%% HSDsqlpcheckconvg: check convergence.
%%
%% ZpATynorm, AX, normX, normZ are with respect to the
%% original variables, not the HSD variables.
%%
%% SDPT3: version 3.1
%% Copyright (c) 1997 by
%% K.C. Toh, M.J. Todd, R.H. Tutuncu
%% Last ... |
github | zhoupc/OASIS_matlab-master | HSDNTdirfun.m | .m | OASIS_matlab-master/packages/cvx/sdpt3/HSDSolver/HSDNTdirfun.m | 1,459 | utf_8 | a045827a3ca1adcf8806cfd8234ad5e4 | %%*******************************************************************
%% HSDNTdirfun: compute (dX,dZ), given dy, for the NT direction.
%%
%% SDPT3: version 3.1
%% Copyright (c) 1997 by
%% K.C. Toh, M.J. Todd, R.H. Tutuncu
%% Last Modified: 16 Sep 2004
%%******************************************************************... |
github | zhoupc/OASIS_matlab-master | HSDNTrhsfun.m | .m | OASIS_matlab-master/packages/cvx/sdpt3/HSDSolver/HSDNTrhsfun.m | 3,424 | utf_8 | 02348c55d691a53b023639b8103757be | %%*******************************************************************
%% HSDNTrhsfun: compute the right-hand side vector of the
%% Schur complement equation for the NT direction.
%%
%% SDPT3: version 3.1
%% Copyright (c) 1997 by
%% K.C. Toh, M.J. Todd, R.H. Tutuncu
%% Last Modified: 16 Sep 2004
%%*********... |
github | zhoupc/OASIS_matlab-master | HSDHKMpred.m | .m | OASIS_matlab-master/packages/cvx/sdpt3/HSDSolver/HSDHKMpred.m | 2,644 | utf_8 | 81b89c36e0d0bad30836c551264a6a05 | %%*******************************************************************
%% HSDHKMpred: Compute (dX,dy,dZ) for the H..K..M direction.
%%
%% SDPT3: version 3.1
%% Copyright (c) 1997 by
%% K.C. Toh, M.J. Todd, R.H. Tutuncu
%% Last Modified: 16 Sep 2004
%%*******************************************************************
f... |
github | zhoupc/OASIS_matlab-master | HSDsqlpmain.m | .m | OASIS_matlab-master/packages/cvx/sdpt3/HSDSolver/HSDsqlpmain.m | 28,301 | utf_8 | df880652075e1e6d94eefd6ddfe38c64 | %%*****************************************************************************
%% HSDsqlp: solve an semidefinite-quadratic-linear program
%% by infeasible path-following method on the homogeneous self-dual model.
%%
%% [obj,X,y,Z,info,runhist] =
%% HSDsqlp(blk,At,C,b,OPTIONS,X0,y0,Z0,kap0,tau0,theta0);
%%
%% ... |
github | zhoupc/OASIS_matlab-master | HSDlinsysolve.m | .m | OASIS_matlab-master/packages/cvx/sdpt3/HSDSolver/HSDlinsysolve.m | 6,495 | utf_8 | 0644ae75443d221edcf585f5a5736fe5 | %%***************************************************************
%% linsysolve: solve linear system to get dy, and direction
%% corresponding to unrestricted variables.
%%
%% [xx,coeff,L,resnrm] = linsysolve(schur,UU,EE,Bmat,rhs);
%%
%% child functions: mybicgstable.m
%%
%% SDPT3: version 3.1
%% Copyright ... |
github | zhoupc/OASIS_matlab-master | HSDsqlpmisc.m | .m | OASIS_matlab-master/packages/cvx/sdpt3/HSDSolver/HSDsqlpmisc.m | 3,299 | utf_8 | f36316ddff8099a74241fa1590fc584a | %%*****************************************************************************
%% HSDsqlpmisc:
%% produce infeasibility certificates if appropriate
%%
%% Input: X,y,Z are the original variables, not the HSD variables.
%%
%% SDPT3: version 3.1
%% Copyright (c) 1997 by
%% K.C. Toh, M.J. Todd, R.H. Tutuncu
%% Last Modifi... |
github | zhoupc/OASIS_matlab-master | HSDbicgstab.m | .m | OASIS_matlab-master/packages/cvx/sdpt3/HSDSolver/HSDbicgstab.m | 3,084 | utf_8 | 96ee9f939e0b2527113539aa0b633ffc | %%*************************************************************************
%% HSDbicgstab
%%
%% [xx,resnrm,flag] = HSDbicgstab(A,b,M1,tol,maxit)
%%
%% iterate on bb - (M1)*AA*x
%%
%% r = b-A*xtrue;
%%
%%*************************************************************************
function [xx,resnrm,flag] = HSDbicgstab(... |
github | zhoupc/OASIS_matlab-master | HSDHKMcorr.m | .m | OASIS_matlab-master/packages/cvx/sdpt3/HSDSolver/HSDHKMcorr.m | 985 | utf_8 | 1e1983a66956f1d3e4e8e279b1dbe2d0 | %%*****************************************************************
%% HSDHKMcorr: corrector step for the HKM direction.
%%
%% SDPT3: version 3.1
%% Copyright (c) 1997 by
%% K.C. Toh, M.J. Todd, R.H. Tutuncu
%% Last Modified: 16 Sep 2004
%%*****************************************************************
function [par... |
github | zhoupc/OASIS_matlab-master | HSDNTpred.m | .m | OASIS_matlab-master/packages/cvx/sdpt3/HSDSolver/HSDNTpred.m | 2,034 | utf_8 | e194daf53d375b24154b1caf94b7646d | %%**********************************************************************
%% HSDNTpred: Compute (dX,dy,dZ) for NT direction.
%%
%% compute SVD of Xchol*Zchol via eigenvalue decompostion of
%% Zchol * X * Zchol' = V * diag(sv2) * V'.
%% compute W satisfying W*Z*W = X.
%% W = G'*G, where G = diag(sqrt(sv)) * (inv... |
github | zhoupc/OASIS_matlab-master | HSDsqlpCpert.m | .m | OASIS_matlab-master/packages/cvx/sdpt3/HSDSolver/HSDsqlpCpert.m | 2,263 | utf_8 | 326ec0065ebb155fab5ee8b4670ec0db | %%*****************************************************************************
%% HSDsqlpCpert: perturb C.
%%
%%*****************************************************************************
function [At,Cpert] = HSDsqlpCpert(blk,At,par,C,X,Cpert,runhist)
iter = length(runhist.pinfeas);
prim_infeas = runhist.pinfeas(... |
github | zhoupc/OASIS_matlab-master | cheby0.m | .m | OASIS_matlab-master/packages/cvx/sdpt3/Examples/cheby0.m | 2,576 | utf_8 | a31e95ee5e80694cd1c3f2ceb594d369 | %%**********************************************************
%% cheby0:
%%
%% minimize || p(d) ||_infty
%% p = polynomial of degree <= m such that p(0) = 1.
%%
%% Here d = n-vector
%%----------------------------------------------------------
%% [blk,Avec,C,b,X0,y0,Z0,objval,p] = cheby0(d,m,solve);
%%
%% d ... |
github | zhoupc/OASIS_matlab-master | randmat.m | .m | OASIS_matlab-master/packages/cvx/sdpt3/Solver/randmat.m | 811 | utf_8 | 483225eceeb882378d1a6fc61914a4be | %%******************************************************
%% randmat: generate an mxn matrix using matlab's
%% rand or randn functions using state = k.
%%
%%******************************************************
function v = randmat(m,n,k,randtype)
try
s = rng;
rng(k);
if strcmp(randtype,... |
github | zhoupc/OASIS_matlab-master | skron.m | .m | OASIS_matlab-master/packages/cvx/sdpt3/Solver/skron.m | 1,389 | utf_8 | 3aba6bed9dc50b45f766b4a8620c4ac3 | %%***********************************************************************
%% skron: Find the matrix presentation of
%% symmetric kronecker product skron(A,B), where
%% A,B are symmetric.
%%
%% Important: A,B are assumed to be symmetric.
%%
%% K = skron(blk,A,B);
%%
%% blk: a cell array specifying the b... |
github | zhoupc/OASIS_matlab-master | NTcorr.m | .m | OASIS_matlab-master/packages/cvx/sdpt3/Solver/NTcorr.m | 1,315 | utf_8 | 458c52ec6bf00d3507df137889a53c7e | %%************************************************************************
%% NTcorr: corrector step for the NT direction.
%%
%% SDPT3: version 3.1
%% Copyright (c) 1997 by
%% K.C. Toh, M.J. Todd, R.H. Tutuncu
%% Last Modified: 16 Sep 2004
%%************************************************************************
func... |
github | zhoupc/OASIS_matlab-master | HKMcorr.m | .m | OASIS_matlab-master/packages/cvx/sdpt3/Solver/HKMcorr.m | 1,313 | utf_8 | ff69a87fe927bf7f964fd55cbf7ec718 | %%*****************************************************************
%% HKMcorr: corrector step for the HKM direction.
%%
%% SDPT3: version 3.1
%% Copyright (c) 1997 by
%% K.C. Toh, M.J. Todd, R.H. Tutuncu
%% Last Modified: 16 Sep 2004
%%*****************************************************************
function [dX,dy,... |
github | zhoupc/OASIS_matlab-master | steplength.m | .m | OASIS_matlab-master/packages/cvx/sdpt3/Solver/steplength.m | 5,590 | utf_8 | 2b52f7d5b9712cf17885f9ca3eaeb666 | %%***************************************************************************
%% steplength: compute xstep such that X + xstep*dX >= 0.
%%
%% [xstep] = steplength(blk,X,dX,Xchol,invXchol);
%%
%% SDPT3: version 3.1
%% Copyright (c) 1997 by
%% K.C. Toh, M.J. Todd, R.H. Tutuncu
%% Last Modified: 16 Sep 2004
%%***********... |
github | zhoupc/OASIS_matlab-master | SDPT3data_SEDUMIdata.m | .m | OASIS_matlab-master/packages/cvx/sdpt3/Solver/SDPT3data_SEDUMIdata.m | 3,843 | utf_8 | 26106829dfa4c0fbb1ca8c4aa9839fa8 | %%**********************************************************
%% SDPT3data_SEDUMIdata: convert SQLP data in SDPT3 format to
%% SeDuMi format
%%
%% [At,b,c,K] = SDPT3data_SEDUMIdata(blk,AAt,CC,bb);
%%
%% SDPT3: version 3.1
%% Copyright (c) 1997 by
%% K.C. Toh, M.J. Todd, R.H. Tutuncu
%% Last Modifie... |
github | zhoupc/OASIS_matlab-master | schurmat_sblk.m | .m | OASIS_matlab-master/packages/cvx/sdpt3/Solver/schurmat_sblk.m | 4,549 | utf_8 | f992891144a934ab4edffde2a692e435 | %%*******************************************************************
%% schurmat_sblk: compute Schur complement matrix corresponding to
%% SDP blocks.
%%
%% symm = 0, HKM
%% = 1, NT
%%
%% SDPT3: version 3.1
%% Copyright (c) 1997 by
%% K.C. Toh, M.J. Todd, R.H. Tutuncu
%% Last Modified: 16 Sep 2004
... |
github | zhoupc/OASIS_matlab-master | blktrace.m | .m | OASIS_matlab-master/packages/cvx/sdpt3/Solver/blktrace.m | 2,084 | utf_8 | 6a5c3d9ff74073a8e864c246727eaa86 | %%**********************************************************************
%% blktrace: compute <X1,Z1> + ... + <Xp,Zp>
%%
%% SDPT3: version 3.1
%% Copyright (c) 1997 by
%% K.C. Toh, M.J. Todd, R.H. Tutuncu
%% Last Modified: 16 Sep 2004
%%**********************************************************************
function tr... |
github | zhoupc/OASIS_matlab-master | sqlpu2lblk.m | .m | OASIS_matlab-master/packages/cvx/sdpt3/Solver/sqlpu2lblk.m | 3,099 | utf_8 | 1a67e45c349d19614e890521aed11db5 | %%***************************************************************************
%% sqlpu2lblk: decide whether to convert ublk to lblk
%%
%% SDPT3: version 3.1
%% Copyright (c) 1997 by
%% K.C. Toh, M.J. Todd, R.H. Tutuncu
%% Last Modified: 10 Jul 2007
%%*********************************************************************... |
github | zhoupc/OASIS_matlab-master | Prod3.m | .m | OASIS_matlab-master/packages/cvx/sdpt3/Solver/Prod3.m | 1,677 | utf_8 | 2ee9f0d732e5ea1f326bfcf275b0da3c | %%************************************************************
%% Prod3: compute the entries of Q = A*B*C specified in
%% nzlistQ.
%%
%% Q = Prod3(blk,A,B,C,sym,nzlistQ)
%% Important: (a) A is assumed to be symmetric if nzlistQ
%% has 2 columns (since mexProd2nz computes A'*B).
%% (b) T... |
github | zhoupc/OASIS_matlab-master | sqlptermcode.m | .m | OASIS_matlab-master/packages/cvx/sdpt3/Solver/sqlptermcode.m | 1,230 | utf_8 | 40b494719c3c614b6196dd9846778c4c | %%*************************************************************************
%% sqlptermcode.m: explains the termination code in sqlp.m
%%
%%
%% SDPT3: version 3.1
%% Copyright (c) 1997 by
%% K.C. Toh, M.J. Todd, R.H. Tutuncu
%% Last Modified: 16 Sep 2004
%%***************************************************************... |
github | zhoupc/OASIS_matlab-master | AXfun.m | .m | OASIS_matlab-master/packages/cvx/sdpt3/Solver/AXfun.m | 1,869 | utf_8 | e816cba65d629a72167375f9a7697b2f | %%*************************************************************************
%% AXfun: compute AX(k) = <Ak,X>, k = 1:m
%%
%% AX = AXfun(blk,At,permA,X);
%%
%% Note: permA may be set to [] if no permutation is neccessary.
%%
%% SDPT3: version 3.1
%% Copyright (c) 1997 by
%% K.C. Toh, M.J. Todd, R.H. Tutuncu
%% Last Mod... |
github | zhoupc/OASIS_matlab-master | NTpred.m | .m | OASIS_matlab-master/packages/cvx/sdpt3/Solver/NTpred.m | 1,963 | utf_8 | 3a2374e8ffa4806b637e50e551b9c17c | %%**********************************************************************
%% NTpred: Compute (dX,dy,dZ) for NT direction.
%%
%% compute SVD of Xchol*Zchol via eigenvalue decompostion of
%% Zchol * X * Zchol' = V * diag(sv2) * V'.
%% compute W satisfying W*Z*W = X.
%% W = G'*G, where G = diag(sqrt(sv)) * (invZch... |
github | zhoupc/OASIS_matlab-master | sqlp.m | .m | OASIS_matlab-master/packages/cvx/sdpt3/Solver/sqlp.m | 11,506 | utf_8 | d4acdbc7a5a1c0fd270f5d3de302c545 | %%*****************************************************************************
%% sqlp: solve an semidefinite-quadratic-linear program
%% by infeasible path-following method.
%%
%% [obj,X,y,Z,info,runhist] = sqlp(blk,At,C,b,OPTIONS,X0,y0,Z0);
%%
%% Input: blk: a cell array describing the block diagonal structu... |
github | zhoupc/OASIS_matlab-master | infeaspt.m | .m | OASIS_matlab-master/packages/cvx/sdpt3/Solver/infeaspt.m | 5,422 | utf_8 | ed7ce61d1094307a576ad8ddfd42bd30 | %%********************************************************************
%% infeaspt: generate an initial point for sdp.m
%%
%% [X0,y0,Z0] = infeaspt(blk,At,C,b,options,scalefac);
%%
%% options = 1 if want X0,Z0 to be scaled identity matrices
%% = 2 if want X0,Z0 to be scalefac*(identity matrices).
%%
%% SDP... |
github | zhoupc/OASIS_matlab-master | Arrow.m | .m | OASIS_matlab-master/packages/cvx/sdpt3/Solver/Arrow.m | 933 | utf_8 | 4a1803a8a960eba5462879d0ae4cbb78 | %%********************************************************
%% Arrow:
%%
%% Fx = Arrow(pblk,f,x,options);
%%
%% if options == 0;
%% Fx = Arr(F)*x
%% if options == 1;
%% Fx = Arr(F)^{-1}*x
%%
%% SDPT3: version 3.1
%% Copyright (c) 1997 by
%% K.C. Toh, M.J. Todd, R.H. Tutuncu
%% Last Modified: 16 Sep 2004
%%********... |
github | zhoupc/OASIS_matlab-master | mybicgstab.m | .m | OASIS_matlab-master/packages/cvx/sdpt3/Solver/mybicgstab.m | 3,536 | utf_8 | 7ae20f5d14c6533fd9a50b23a1e5c8b3 | %%*************************************************************************
%% mybicgstab
%%
%% [xx,resnrm,flag] = mybicgstab(A,b,M1,tol,maxit)
%%
%% iterate on bb - (M1)*AA*x
%%
%% r = b-A*xtrue;
%%
%%*************************************************************************
function [xx,resnrm,flag] = mybicgstab(A,b... |
github | zhoupc/OASIS_matlab-master | degeneracy.m | .m | OASIS_matlab-master/packages/cvx/sdpt3/Solver/degeneracy.m | 5,175 | utf_8 | 52287ec83b17f60c33554d7a25764672 | %%***************************************************************
%% degeneracy: determine if an SDP problem is non-degenerate.
%%
%% [ddx,ddz,B1,B2,sig1,sig12] = degeneracy(blk,At,X,y,Z);
%%
%% Assume that strict complementarity holds:
%% for primal non-degeneracy, we need rank([B1 B2]) = m
%% for dual non-degeneracy,... |
github | zhoupc/OASIS_matlab-master | mytime.m | .m | OASIS_matlab-master/packages/cvx/sdpt3/Solver/mytime.m | 557 | utf_8 | 2d076b8ed1091521bbe986194c6e2b84 | %%*********************************************
%% mytime:
%%
%% SDPT3: version 3.1
%% Copyright (c) 1997 by
%% K.C. Toh, M.J. Todd, R.H. Tutuncu
%% Last Modified: 16 Sep 2004
%%*********************************************
function [hh,mm,ss] = mytime(t)
t = round(t);
h = floor(t/3600);
m = floor(rem(t,3600)/60);
s ... |
github | zhoupc/OASIS_matlab-master | validate.m | .m | OASIS_matlab-master/packages/cvx/sdpt3/Solver/validate.m | 7,427 | utf_8 | 60774ce6b3bd16bde97e4078d89db39b | %%***********************************************************************
%% validate: validate data
%%
%%
%% SDPT3: version 3.1
%% Copyright (c) 1997 by
%% K.C. Toh, M.J. Todd, R.H. Tutuncu
%% Last Modified: 16 Sep 2004
%%***********************************************************************
function [blk,At,C,b,di... |
github | zhoupc/OASIS_matlab-master | svec.m | .m | OASIS_matlab-master/packages/cvx/sdpt3/Solver/svec.m | 2,027 | utf_8 | 43bbe7c274d2d1bfb1014fc2000f47e3 | %*********************************************************
%% svec: compute the vector svec(M),
%%
%% x = svec(blk,M,isspx);
%%
%% SDPT3: version 3.1
%% Copyright (c) 1997 by
%% K.C. Toh, M.J. Todd, R.H. Tutuncu
%% Last Modified: 16 Sep 2004
%%**********************************************************
function x = s... |
github | zhoupc/OASIS_matlab-master | read_sedumi.m | .m | OASIS_matlab-master/packages/cvx/sdpt3/Solver/read_sedumi.m | 7,265 | utf_8 | 2035885c053fc9de89cf19fa667603d2 | %%*******************************************************************
%% Read in a problem in SeDuMi format.
%%
%% [blk,A,C,b,perm] = read_sedumi(fname,b,c,K)
%%
%% Input: fname.mat = name of the file containing SDP data in
%% SeDuMi format.
%%
%% Important note: Sedumi's notation for free variab... |
github | zhoupc/OASIS_matlab-master | qprod.m | .m | OASIS_matlab-master/packages/cvx/sdpt3/Solver/qprod.m | 655 | utf_8 | 2d6550b139b2dfcf3d134f61deec3686 | %%***************************************************
%% qprod:
%%
%% Input: A = [A1 A2 ... An]
%% x = [x1; x2; ...; xn]
%% Output: [A1*x1 A2*x2 ... An*xn]
%%
%% SDPT3: version 3.1
%% Copyright (c) 1997 by
%% K.C. Toh, M.J. Todd, R.H. Tutuncu
%% Last Modified: 16 Sep 2004
%%**************************************... |
github | zhoupc/OASIS_matlab-master | nzlist.m | .m | OASIS_matlab-master/packages/cvx/sdpt3/Solver/nzlist.m | 5,014 | utf_8 | 1225b63fe9e00df09546243f60599dc2 | %%***********************************************************************
%% nzlist: find the combined list of non-zero elements
%% of Aj, j = 1:k, for each k,
%% assuming that the Aj's are permuted such that
%% A1 has the fewest nonzero elements, followed by A2, and so on.
%%
%% [isspA,nzlistA,... |
github | zhoupc/OASIS_matlab-master | detect_lblk.m | .m | OASIS_matlab-master/packages/cvx/sdpt3/Solver/detect_lblk.m | 4,228 | utf_8 | a69e3486a171d0169d9b62b749ed6cd8 | %%*******************************************************************
%% detect_lblk: detect diagonal blocks in the SDP data.
%%
%% [blk,At,C,diagblkinfo,blockchange,parbarrier,X,Z] = ...
%% detect_lblk(blk,At,C,b,parbarrier,X,Z);
%%
%% SDPT3: version 3.1
%% Copyright (c) 1997 by
%% K.C. Toh, M.J. Todd, R.H. ... |
github | zhoupc/OASIS_matlab-master | gdcomp.m | .m | OASIS_matlab-master/packages/cvx/sdpt3/Solver/gdcomp.m | 5,041 | utf_8 | 798f2741f8133bfe774e59417201fb41 | %%*********************************************************************
%% gdcomp: Compute gd = 1/td in Equation (15) of the paper:
%%
%% R.M. Freund, F. Ordonez, and K.C. Toh,
%% Behavioral measures and their correlation with IPM iteration counts
%% on semi-definite programming problems,
%% Mathematical Programm... |
github | zhoupc/OASIS_matlab-master | blkbarrier.m | .m | OASIS_matlab-master/packages/cvx/sdpt3/Solver/blkbarrier.m | 1,795 | utf_8 | 77a6eb1f1708aa69217000d27735efa0 | %%********************************************************************
%% blkbarrier: calculate
%% [-v(p)*logdet(X{p}), v(p)*logdet(Z{p}) + n*v(p)*(1-log(v(p)))]
%% [-v(p)*log(gam(X{p})), v(p)*log(gam(Z{p})) + v(p)]
%% [-v(p)*log(X{p}), v(p)*log(Z{p}) + n*v(p)*(1-log(v(p)))]
%%***********************************... |
github | zhoupc/OASIS_matlab-master | sqlpmain.m | .m | OASIS_matlab-master/packages/cvx/sdpt3/Solver/sqlpmain.m | 29,812 | utf_8 | 97c549fe923480dc73e59887089d5656 | %%*************************************************************************
%% sqlp: main solver
%%
%%*************************************************************************
%% SDPT3: version 3.1
%% Copyright (c) 1997 by
%% K.C. Toh, M.J. Todd, R.H. Tutuncu
%% Last Modified: 16 Sep 2004
%%****************************... |
github | zhoupc/OASIS_matlab-master | HKMpred.m | .m | OASIS_matlab-master/packages/cvx/sdpt3/Solver/HKMpred.m | 2,818 | utf_8 | da0e8d9efacd9a7cebaae5ea2ad63de9 | %%*******************************************************************
%% HKMpred: Compute (dX,dy,dZ) for the H..K..M direction.
%%
%% SDPT3: version 3.1
%% Copyright (c) 1997 by
%% K.C. Toh, M.J. Todd, R.H. Tutuncu
%% Last Modified: 16 Sep 2004
%%*******************************************************************
func... |
github | zhoupc/OASIS_matlab-master | read_sdpa.m | .m | OASIS_matlab-master/packages/cvx/sdpt3/Solver/read_sdpa.m | 7,591 | utf_8 | 211ea10474df1ffe50a0c5456e1cbe41 | %%*******************************************************************
%% Read in a problem in SDPA sparse format.
%%
%% [blk,At,C,b] = read_sdpa(fname)
%%
%% Input: fname = name of the file containing SDP data in
%% SDPA foramt.
%% Important: the data is assumed to contain only
%% semide... |
github | zhoupc/OASIS_matlab-master | sortA.m | .m | OASIS_matlab-master/packages/cvx/sdpt3/Solver/sortA.m | 2,639 | utf_8 | c998ea7df87432b78f6c001d0bbc5318 | %%*********************************************************************
%% sortA: sort columns of At{p} in ascending order according to the
%% number of nonzero elements.
%%
%% [At,C,b,X0,Z0,permA,permZ] = sortA(blk,At,C,b,X0,Z0);
%%
%% SDPT3: version 3.1
%% Copyright (c) 1997 by
%% K.C. Toh, M.J. Todd, R.H. Tut... |
github | zhoupc/OASIS_matlab-master | blkeig.m | .m | OASIS_matlab-master/packages/cvx/sdpt3/Solver/blkeig.m | 2,412 | utf_8 | 97da97f8165585de45eae52a86e0f127 | %%***************************************************************************
%% blkeig: compute eigenvalue decomposition of a cell array
%% whose contents are square matrices or the diagonal
%% of a diagonal matrix.
%%
%% [d,V] = blkeig(blk,X);
%%
%% SDPT3: version 3.1
%% Copyright (c) 1997 by
%% K.C. ... |
github | zhoupc/OASIS_matlab-master | HKMrhsfun.m | .m | OASIS_matlab-master/packages/cvx/sdpt3/Solver/HKMrhsfun.m | 3,358 | utf_8 | b1e6a8305128af799634b9ef7324cfeb | %%*******************************************************************
%% HKMrhsfun: compute the right-hand side vector of the
%% Schur complement equation for the HKM direction.
%%
%% SDPT3: version 3.1
%% Copyright (c) 1997 by
%% K.C. Toh, M.J. Todd, R.H. Tutuncu
%% Last Modified: 16 Sep 2004
%%***********... |
github | zhoupc/OASIS_matlab-master | linsysolve.m | .m | OASIS_matlab-master/packages/cvx/sdpt3/Solver/linsysolve.m | 7,741 | utf_8 | 2091e9d1c0858acfd5c4e07842ed787d | %%***************************************************************
%% linsysolve: solve linear system to get dy, and direction
%% corresponding to unrestricted variables.
%%
%% [xx,coeff,L,resnrm] = linsysolve(schur,UU,Afree,EE,rhs);
%%
%% child functions: symqmr.m, mybicgstable.m, linsysolvefun.m
%%
%% SDPT... |
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