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 | satoshi-hirose/MVPC_toolbox-master | islr.m | .m | MVPC_toolbox-master/Algorithms/islr.m | 6,335 | utf_8 | 801ef52c6502a23182e80bcc48be0638 | function [errTable_tr,errTable_te,model] = islr(xtrain,ttrain,xtest,ttest,repn,classification)
% number of features
n_feat = size(xtrain,2);
% initialization
esti_curr_te_prob = ones(length(unique(ttrain)),length(ttest));
esti_curr_tr_prob = ones(length(unique(ttrain)),length(ttrain));
% iterative training and test
... |
github | satoshi-hirose/MVPC_toolbox-master | save_raw_image.m | .m | MVPC_toolbox-master/Save_Image_iSLR/save_raw_image.m | 2,430 | utf_8 | 10c4146a40beaeae4d2703b85562a5fe | % Save image (.img) and header files representing the weights.
%
function save_raw_image(MY_VAR)
load(fullfile(MY_VAR.figure_dir,'results_fig.mat'),'Spatial_ROI','Temporal_ROI','Param_search','Method_info')
for methodn = 1:length(MY_VAR.method)
method_id(methodn) = 0;
for decoding_methodn = 1:length(Method_i... |
github | satoshi-hirose/MVPC_toolbox-master | my_normalization.m | .m | MVPC_toolbox-master/Save_Image_iSLR/my_normalization.m | 732 | utf_8 | 3d5d43a7ec092b14f33ccd75122b05b9 | % template: Normalze parameter file ('T1_sn.mat')
% fname: cell structure of files.
function my_normalization(fname,template)
%% normalization
% set parameters
jobs{1}.spatial{1}.normalise{1}.write.subj(1).matname{1} = template;
jobs{1}.spatial{1}.normalise{1}.write... |
github | satoshi-hirose/MVPC_toolbox-master | cross_valid_leave_two_out.m | .m | MVPC_toolbox-master/Cross_Validation/cross_valid_leave_two_out.m | 1,005 | utf_8 | 617cad216f87d7f5c307da1c017e2e6a | % Leave-two-run-out cross-validation.
% 2010/June/3 SH
% 2010/June/10 IN modified
% 2010/June/11 SH
function cross_valid_leave_two_out(MY_VAR)
% Subject loop
for sub = 1:length(MY_VAR.subnames)
%% start cross validation and save results
for cros_valid = 1: length(MY_VAR.sessions{sub})
... |
github | satoshi-hirose/MVPC_toolbox-master | cross_valid.m | .m | MVPC_toolbox-master/Cross_Validation/cross_valid.m | 10,037 | utf_8 | f292b12c0a5da8a6fa23ca1e40e0f53d | % Run leave-one-run-out cross validation
% (number of spatial ROI) x (number of temporal ROI) times.
% script 'clsfy.m' is used.
%
% input:
% MY_VAR
% .analyze_dir :string('/home/dcn/hirose/analyze/tapping_decoding/analysis_folder')
% .subnames :1 x N_sub cell array({'US','SH','YS... |
github | satoshi-hirose/MVPC_toolbox-master | add_num.m | .m | MVPC_toolbox-master/Subfunctions/add_num.m | 290 | utf_8 | fe5c80c3aa8bdfacee5017ee424a3868 | % adds the number to avoid file-overwrite
function filename = add_num(dirn,filen_pre,filen_post)
file_num=1;
while exist(fullfile(dirn,[filen_pre,int2str(file_num),filen_post]),'file')
file_num = file_num+1;
end
filename = fullfile(dirn,[filen_pre,int2str(file_num),filen_post]);
|
github | satoshi-hirose/MVPC_toolbox-master | write_text.m | .m | MVPC_toolbox-master/Subfunctions/write_text.m | 431 | utf_8 | 208430489fe9bfc5b0ff74c201870c51 |
function [end_line str] = write_text(str,start_line)
temp = start_line;
str_curr = deblank(str);
for j = 1:ceil(length(str_curr)/100)
if j == ceil(length(str_curr)/100)
str_write = str_curr((j-1)*100+1:end);
else
str_write = str_curr((j-1)*100+1:j*100);
end
text(0.01,0.99-0.03*tem... |
github | satoshi-hirose/MVPC_toolbox-master | rename_for_load.m | .m | MVPC_toolbox-master/Subfunctions/rename_for_load.m | 1,067 | utf_8 | a7d4285e2f07c40f866f523bf8512166 | % rename file path. Useful when analysis file server is changed
% (ex. move your file to new directory).
% input: fname
% output: fname_new
%
% 2013/04/11 SH edited
function fname_new = rename_for_load(fname)
ex_check = { '/home/nobita/hirose', '/Volumes/nobita/hirose' , '/project/doraemon/jaian/hirose/nobita'}... |
github | satoshi-hirose/MVPC_toolbox-master | norm2sub.m | .m | MVPC_toolbox-master/Subfunctions/norm2sub.m | 476 | utf_8 | b82ecfd24a929630cc4f816a73e5f032 | % 2010/June/8 SH
function sub_XYZmm = norm2sub(sn_mat,norm_XYZmm)
P=sn_mat; % select y_deformation_sn.nii
P=[repmat(P,3,1) [',1,1';',1,2';',1,3']];
V=spm_vol(P);
norm_vox = V(1).mat\[norm_XYZmm; ones(1,size(norm_XYZmm,2))];
sub_XYZmm(1,:) = spm_sample_vol(V(1),norm_vox(1,:),norm_vox(2,:),norm_vox(3,:),1);
sub_XYZmm(... |
github | satoshi-hirose/MVPC_toolbox-master | assign_tempo_ROI.m | .m | MVPC_toolbox-master/Subfunctions/assign_tempo_ROI.m | 2,410 | utf_8 | b826b4b394ed0f37eb43ff372c9fb8af | % Temporal ROI assinment
% temporal normalization (divide with mean, dividde with sd)
% and averaging are also performed.
%
function assigned_data = assign_tempo_ROI(rawdata,tempo_ROI,normalization_method)
assigned_data = rawdata;
for sess = 1:length(tempo_ROI)
% data massage & ... |
github | jonprivate/burstImageDenoising-master | discretizeAndGroupImageHomography.m | .m | burstImageDenoising-master/include/discretizeAndGroupImageHomography.m | 1,455 | utf_8 | fc72845fdbe982fb0d602ef99a6a4663 | function homographyFlow = discretizeAndGroupImageHomography(homographySet, nodeRows, nodeCols, imageRows, imageCols)
% Discretize and group image node homographies to form the homography flow
homographyFlow = zeros(imageRows, imageCols, 2);
rowsPerNode = floor(imageRows / nodeRows);
colsPerNode = floor(imageCols / node... |
github | jonprivate/burstImageDenoising-master | getHomographyPyramid.m | .m | burstImageDenoising-master/include/getHomographyPyramid.m | 3,472 | utf_8 | 8f835f19cecbf5c24d51adfb81d9206c | function homographyPyramid = getHomographyPyramid(pyramid, matchedPoints1, matchedPoints2)
% Compute homography pyramid from matched feature points
featuredPyramid1 = getFeaturedPyramid(pyramid, matchedPoints1);
featuredPyramid2 = getFeaturedPyramidWithRef(pyramid, matchedPoints2, featuredPyramid1);
[~, layerNum] = siz... |
github | bigjun/slam-optim-matlab-master | Chol_ela.m | .m | slam-optim-matlab-master/Utils/Math/Chol_ela.m | 827 | utf_8 | 7b9ff9f4f24f1b3d651531b50f26591f |
function Chol_ela
A=[1, 0 0 0 0 0 0
-1, 1, 0 0 0 0 0
0 -1, 1, 0 0 0 0
1, 0 0 -1, 0 0 0
0 0 -1 1 0 0 0
0 1 0 0 -1 0 0
0 0 0 0 -1 1 0
0 0 0 0 0 -1 1];
%A=[1 0 0 0;-1 1 0 0 ;0 -1 1 0; 0 0 -1 1;1 0 0 -1];
Lambda=A'*A;
sL=size(Lambda,1);
R=zeros(sL,sL);
for j=1:sL
j
for i=1:sL
i
if (R(... |
github | bigjun/slam-optim-matlab-master | covTest.m | .m | slam-optim-matlab-master/Utils/Math/CovRecovery/covTest.m | 2,030 | utf_8 | e7e9af836fec2be7b919ed590d884c0a | function covTest
clear all
dof = 3;
% test incremental update
[A49,rows49,cols49,entries49,rep49,field49,symm49] = mmread('lambda_049.mtx');
[A50,rows50,cols50,entries50,rep50,field50,symm50] = mmread('lambda_050.mtx');
R49=chol(A49);
R50=chol(A50);
% ground truth
S49=inv(R49);
S50=inv(R50);
C49=S49 * S49';
C50... |
github | bigjun/slam-optim-matlab-master | pi2pi.m | .m | slam-optim-matlab-master/Utils/SE3/pi2pi.m | 292 | utf_8 | d6b6adb3f8df8c1f1c879049a943dbbb |
% Moves an angle to the -pi,pi range.
%
% Ensures that the given angles are all in the -pi, pi range.
function angle=pi2pi(angle)
dp=2*pi;
ang=(angle<=-dp)||(angle>=dp);
angle(ang)=mod(angle(ang),dp);
ang=angle>=pi;
angle(ang)=angle(ang)-2*pi;
ang=angle<=-pi;
angle(ang)=angle(ang)+2*pi; |
github | bigjun/slam-optim-matlab-master | separateTreeConstraintsFromMatrix.m | .m | slam-optim-matlab-master/Graph/separateTreeConstraintsFromMatrix.m | 531 | utf_8 | d1726d970aab8e0351889994b8c53227 |
function [Graph,System]=separateTreeConstraintsFromMatrix(subgraph,Graph,System)
[rows,cols] = find(subgraph);
n=size(Graph.F,1);
ind=1;
System.A1=[];
System.A2=[];
while ind<n
RowCol=Graph.F(ind).RowCol;
%factorR=Graph.F(ind);
rowA=Graph.F(ind).ndxA;
if ismember(RowCol,[rows,cols],'rows')
%Gr... |
github | bigjun/slam-optim-matlab-master | separateTreeConstraints.m | .m | slam-optim-matlab-master/Graph/separateTreeConstraints.m | 303 | utf_8 | bebd445c9c0fcb00fc8329acb269de5b |
function [tree_edges,cnstr_edges]=separateTreeConstraints(tree,ed)
% Separate the tree a
tree = tree + tree';
% tree
[rows,cols] = find(tree);
%
treeIndices = ismember(ed(:,1:2)+1,[rows,cols],'rows');
tree_edges = full(ed(treeIndices, :));
if nargout > 1
cnstr_edges=full(ed(~treeIndices,:));
end |
github | bigjun/slam-optim-matlab-master | linearSystemROslamBA.m | .m | slam-optim-matlab-master/Tests/RangeOnly/linearSystemROslamBA.m | 832 | utf_8 | f67ce896302d73f887d1a73ca1844314 |
function [J,d] = linearSystemROslamBA(nd, dim, dimb, poses,buoy, range, RInit, RObs)
I3 = eye(3);
O3 = zeros(3,1);
nb = 4;
m = nb*nd + dim;
n = nb*dimb + nd*dim;
J = zeros(m,n);
d = zeros (m,1);
row = 1:dim;
col = 1:dim;
%
% poses = reshape(x(1:end-12),nd,dim);
% buoy = reshape(x((end-11):end),4,dimb);
% % st... |
github | bigjun/slam-optim-matlab-master | generateData.m | .m | slam-optim-matlab-master/Tests/RangeOnly/generateData.m | 4,360 | utf_8 | b51274c6aa15e5e293d399521ed58891 | %generate data
function [range,vd,buoy,sigInit,sigState,sigObs,dt,nd,A, diver]=generateData
close all
range_type = 1 ; % 0-range; 1-pseudorange
I6 = eye(6);
I3 = eye(3);
O33 = zeros(3,3);
O3 = zeros(3,1);
randn('seed', 12345);
%
buoy = [ -1.3, -1.2, -0.01;
1.1, -1.1, 0.02;
1.2, 1.2, -0.01;
-1.2, ... |
github | bigjun/slam-optim-matlab-master | linearSystemPseudoRange.m | .m | slam-optim-matlab-master/Tests/RangeOnly/linearSystemPseudoRange.m | 2,887 | utf_8 | 90a2b0b3481165196659603ba2d9056d |
function [J,d] = linearSystemPseudoRange(range,poses,buoy,RInit,RState,RBias,RObs,dim,dimb,A,nd,nb)
I6 = eye(6);
Idimb = eye(dimb);
%nb = (size(x,1)-nd*dim) / dimb;
m = nb*nd + nd*dim;
n = nb*dimb + nd*dim;
J = zeros(m,n);
d = zeros (m,1);
col = 1:dim;
%poses = reshape(x(1:end-12),dim,nd)';
%buoy = reshape(x... |
github | bigjun/slam-optim-matlab-master | generateDataPseudoRange.m | .m | slam-optim-matlab-master/Tests/RangeOnly/generateDataPseudoRange.m | 2,046 | utf_8 | 32eedc78e07919801be8e03f5d856027 | %generate data
function [range,vertices,buoy,sigInit,sigState,sigBias,sigObs,dt,A]=generateDataPseudoRange
close all
range_type = 1 ; % 0-range; 1-pseudorange
I6 = eye(6);
I3 = eye(3);
O33 = zeros(3,3);
O3 = zeros(3,1);
randn('seed', 12345);
%
buoy = [ -1.3, -1.2, -0.01;
1.1, -1.1, 0.02;
1.2, 1.2, -0.... |
github | bigjun/slam-optim-matlab-master | linearSystemROslam.m | .m | slam-optim-matlab-master/Tests/RangeOnly/linearSystemROslam.m | 1,577 | utf_8 | 0d077e4246cba0d6215500aebcaf3b90 |
function [J,d] = linearSystemROslam(nd, dim, dimb, A, poses,buoy, range, RInit, RState, RObs)
I6 = eye(6);
I3 = eye(3);
%nb = (size(x,1)-nd*dim) / dimb;
nb = 4;
m = nb*nd + nd*dim;
n = nb*dimb + nd*dim;
J = zeros(m,n);
d = zeros (m,1);
col = 1:dim;
%poses = reshape(x(1:end-12),dim,nd)';
%buoy = reshape(x((end-... |
github | bigjun/slam-optim-matlab-master | generateDataDoubleDifference.m | .m | slam-optim-matlab-master/Tests/RangeOnly/generateDataDoubleDifference.m | 1,928 | utf_8 | d9d5081ace0875360ccd052c3e3b9b78 | %generate data
function [doubleDiff,vd,buoys,sigInit,sigState,sigObs,dt,A]=generateDataDoubleDifference
close all
I3 = eye(3);
O33 = zeros(3,3);
randn('seed', 12345);
%
buoys = [ -1.3, -1.2, -0.01;
1.1, -1.1, 0.02;
1.2, 1.2, -0.01;
-1.2, 1.2, 0.01];
%test
nb = size(buoys,1);
timeDive = 15; % div... |
github | bigjun/slam-optim-matlab-master | linearSystemDoubleDifference.m | .m | slam-optim-matlab-master/Tests/RangeOnly/linearSystemDoubleDifference.m | 1,578 | utf_8 | 381ab75c4a29b8b6120de0c976788830 |
function [J,d] = linearSystemDoubleDifference(meas,poses,buoy,RInit,RState,RObs,dim,dimb,A,nd,nb)
I6 = eye(6);
I3 = eye(3);
%nb = (size(x,1)-nd*dim) / dimb;
nb = 4;
m = nb*nd + nd*dim;
n = nb*dimb + nd*dim;
J = zeros(m,n);
d = zeros (m,1);
col = 1:dim;
%poses = reshape(x(1:end-12),dim,nd)';
%buoy = reshape(x((... |
github | bigjun/slam-optim-matlab-master | linearSystemROslam_old.m | .m | slam-optim-matlab-master/Tests/RangeOnly/linearSystemROslam_old.m | 1,404 | utf_8 | cc6b2a13906d00960220342f4a98f493 |
function [J,d] = linearSystemROslam_old(nd, dim, dimb, A, poses,buoy, range, RInit, RState, RObs)
I6 = eye(6);
O3 = zeros(3,1);
%nb = (size(x,1)-nd*dim) / dimb;
nb = 4;
m = nb*nd + nd*dim;
n = nb*dimb + nd*dim;
J = zeros(m,n);
d = zeros (m,1);
row = 1:dim;
col = 1:dim;
%poses = reshape(x(1:end-12),dim,nd)';
%bu... |
github | bigjun/slam-optim-matlab-master | AbsoluteBuoy2DD.m | .m | slam-optim-matlab-master/Tests/RangeOnly/AbsoluteBuoy2DD.m | 593 | utf_8 | 6306c8ef0716609fb2c9c1ba756c1330 | function [dd,range,vect] = AbsoluteBuoy2DD(pose, buoys)
%returns a vector of size (nb x 1) of double differences (column vector)
nb = length(buoys);
dd = [];
range = [];
vect = [];
pivot = buoys(1,:); % set pivot
[r_pivot,v] = getRange(pose,pivot); % pseudo range
if (nargout >1)
range = [range;r_pivot];
vect... |
github | bigjun/slam-optim-matlab-master | pi2pi.m | .m | slam-optim-matlab-master/Config/pi2pi.m | 292 | utf_8 | d6b6adb3f8df8c1f1c879049a943dbbb |
% Moves an angle to the -pi,pi range.
%
% Ensures that the given angles are all in the -pi, pi range.
function angle=pi2pi(angle)
dp=2*pi;
ang=(angle<=-dp)||(angle>=dp);
angle(ang)=mod(angle(ang),dp);
ang=angle>=pi;
angle(ang)=angle(ang)-2*pi;
ang=angle<=-pi;
angle(ang)=angle(ang)+2*pi; |
github | bigjun/slam-optim-matlab-master | LevenbergMarquardtOptimization.m | .m | slam-optim-matlab-master/Optimization/NonlinearOptimization/LevenbergMarquardtOptimization.m | 3,984 | utf_8 | 4c127e9f686a82d2fc9d17934142c163 | function [Config,System,Solver]=LevenbergMarquardtOptimization(Config,System,Graph,Solver,Plot)
% [Config,System]=LevenbergMarquardtOptimization(Config,System,Graph,Solver,Plot)
% The script applyes Levenberg-Marquardt nonlinear optimization to a Graph SLAM problem
% Returns a new configuraton: Config and the relinear... |
github | bigjun/slam-optim-matlab-master | GaussNewtonOptimizationCHOL.m | .m | slam-optim-matlab-master/Optimization/NonlinearOptimization/GaussNewtonOptimizationCHOL.m | 1,690 | utf_8 | 0d71c3a70c70d538cd203342368d8e13 | function [Config,System]=GaussNewtonOptimizationCHOL(Config,System,Graph,Solver,Plot)
% [Config,System]=GaussNewtonOptimization(Config,System,Graph,Solver,Plot)
% The script applyes Gauss-Newton nonlinear optimization to a Graph SLAM problem
% Returns a new configuraton: Config and the relinearized system: System
% Au... |
github | bigjun/slam-optim-matlab-master | ArotMat.m | .m | slam-optim-matlab-master/SEJacobians/utils/ArotMat.m | 664 | utf_8 | 8c891b5db8927bbbff9bded5a1a6d4df |
function Ln=ArotMat(varargin)
if nargin==1
rd11=varargin{1}(1,1);
rd12=varargin{1}(1,2);
rd13=varargin{1}(1,3);
rd21=varargin{1}(2,1);
rd22=varargin{1}(2,2);
rd23=varargin{1}(2,3);
rd31=varargin{1}(3,1);
rd32=varargin{1}(3,2);
rd33=varargin{1}(3,3);
else
rd11=varargin{1... |
github | bigjun/slam-optim-matlab-master | ExpSE3.m | .m | slam-optim-matlab-master/SEJacobians/utils/ExpSE3.m | 335 | utf_8 | 1b9e037b12f516b6cd754db227abd35d |
function T = ExpSE3(a)
td = a(1:3);
rd = a(4:6);
I3 = eye(3);
th = sqrt(rd' * rd);
%rd = rd/th;
cd =cos(th);
sd = sin(th);
rx=skew_symmetric(rd);
%Rd = I3 + rx * sd + (1 - cd) * rx^2;
Rd = I3 + rx * sd/th + ((1 - cd)/th^2) * rx^2;
V = (I3 - ((1 - cd)/(th^2)) * rx + ((th - sd) / (th^3) ) * rx^2);
td = V * td;... |
github | bigjun/slam-optim-matlab-master | LogSE3.m | .m | slam-optim-matlab-master/SEJacobians/utils/LogSE3.m | 1,031 | utf_8 | c3e059ed231e5dfbe2c0f160ed0a8182 |
function Ln = LogSE3(T)
% %debug only
% syms r11 r12 r13 t1 r21 r22 r23 t2 r31 r32 r33 t3 real
% T = [ r11 r12 r13 t1; r21 r22 r23 t2; r31 r32 r33 t3; 0 0 0 1];
R = T(1:3,1:3);
t = T(1:3,4);
%tr = rd11 + rd22 + rd33;
tr = trace(R);
cd = (tr-1)/2;
th = acos(cd);
sd = sqrt(1 - cd^2);
%% Rotation
b = th/(2*sd);
r=[R(... |
github | bigjun/slam-optim-matlab-master | A2RJacobiansSymsHauke.m | .m | slam-optim-matlab-master/SEJacobians/OldTry/A2RJacobiansSymsHauke.m | 2,400 | utf_8 | 2ff6d75fa9a9265bcaaa60074eb2c40f |
function [Ju , Jv] = A2RJacobiansSymsHauke
I6 = eye(6);
O33 = zeros(3,3);
syms xu yu zu a1u a2u a3u xv yv zv a1v a2v a3v real
ut = [xu yu zu]';
ua = [a1u a2u a3u]';
vt = [xv yv zv]';
va = [a1v a2v a3v]';
u=[ut; ua];
v=[vt; va];
[Ru, tu, Rv, tv]=RotMat(u,v);
td = Ru'*(tv - tu);
Rd= Ru'*Rv;
%Rd= Ru\Rv;
[ a1d, ... |
github | bigjun/slam-optim-matlab-master | A2RJacobiansSyms.m | .m | slam-optim-matlab-master/SEJacobians/Lie/A2RJacobiansSyms.m | 215 | utf_8 | 4581f4a6787f0970837344d3f63987f6 |
function [Td, JTu, JTv]=A2RJacobiansSyms(Ru,tu,Rv,tv)
td = Ru'*(tv - tu);
Rd= Ru'*Rv;
%Rd= Ru\Rv;
Tu=[Ru, tu];
Tv=[Rv, tv];
Td=[Rd, td];
% Jacobian in rotation space
JTu=jacobian(Td,Tu);
JTv=jacobian(Td,Tv);
|
github | rock-perception/perception-libelas-master | process.m | .m | perception-libelas-master/matlab/process.m | 3,129 | utf_8 | 7e01c4630417629ddc540f207d624229 | % Copyright 2011. All rights reserved.
% Institute of Measurement and Control Systems
% Karlsruhe Institute of Technology, Germany
% This file is part of libelas.
% Authors: Andreas Geiger
% libelas is free software; you can redistribute it and/or modify it under the
% terms of the GNU General Public License as publi... |
github | hyiltiz/altruism-master | genTrials.m | .m | altruism-master/genTrials.m | 3,144 | utf_8 | 709c5e69fd318cb7ce0a5ced4723ad35 | function trials=genTrials(withinblock_repetitions, withinblock_factors, betweenblock_repetitions, betweenblock_factors)
% Generating randomized trials based repetition and factors
% syntax: genTrials(withinblock_repetition, betweenblock_repetition, withinblock_factors, [ betweenblock_factors])
% eg: genTrials(2, 10, [2... |
github | hyiltiz/altruism-master | BitsPlusPlus.m | .m | altruism-master/BitsPlusPlus.m | 82,974 | utf_8 | 76d85c9bd505dd9a9b7d4b2bb6ed91fe | function [win, winRect] = BitsPlusPlus(cmd, arg, dummy, varargin)
% BitsPlusPlus(cmd [, arg1][, arg2, ...]) -- Psychtoolbox interface to
% Cambridge Research Systems Bits++ and Bits# boxes for high precision
% stimulus output to analog displays via 14 bit video converters.
%
% This function is used to set up and interf... |
github | hyiltiz/altruism-master | option_zili.m | .m | altruism-master/option_zili.m | 2,801 | utf_8 | 7edf8dcd35d73081378d9c8718d04f98 | function option_zili(wptr, ziti_size, xcenter, left_center, right_center, up_center, down_center, options, msg1)
%% option zili
% 150315
<<<<<<< HEAD
function option_zili(wptr, ziti_size, xcenter, left_center, right_center, up_center, down_center, xuhao, init_item_num)
=======
>>>>>>> 1394a75... re-ordered the whole ... |
github | hyiltiz/altruism-master | oneAl_Zili_Trial.m | .m | altruism-master/oneAl_Zili_Trial.m | 657 | utf_8 | bc4973786e61d191477f736f17a15c7f |
function oneAl_Zili_Trial(wptr, ziti_size, xcenter, ycenter, wrect, options, msg1)
left_center = xcenter - 12*ziti_size;
right_center = xcenter + 1*ziti_size;
up_center = ycenter - 2*ziti_size;
down_center = ycenter + 1*ziti_size;
if rand < 0.5
altruismRight = 0; % altruism option on the left
else
altruismRi... |
github | hyiltiz/altruism-master | option_al.m | .m | altruism-master/option_al.m | 3,037 | utf_8 | c669355952374461c5c69299694c6ef9 | <<<<<<< HEAD
<<<<<<< HEAD
%% option
% 150315
function option_al(wptr, ziti_size, xcenter, left_center, right_center, up_center, down_center, xuhao, init_item_num)
=======
function option_al(wptr, ziti_size, xcenter, left_center, right_center, up_center, down_center,options)
>>>>>>> 1394a75... re-ordered the whole pro... |
github | spunt/barpatch-master | barpatch.m | .m | barpatch-master/barpatch.m | 24,571 | utf_8 | 1e76915f16b4d864a09bc00b70659187 | function h = barpatch(data, varargin)
% BARPATCH Create bar graph with error bars using patch and line objects
%
% This function will create a grouped bar graph with error bars without
% using the standard plotting functions BAR and ERRORBAR. It uses PATCH to
% create the bars and LINE to construct the error bars.
%
... |
github | DylanMuir/MappedTensor-master | arrayfun2.m | .m | MappedTensor-master/@MappedTensor/arrayfun2.m | 11,800 | utf_8 | c8ab1dcea0ce26f24085f74204b55ff4 | function [mtNewVar] = arrayfun2(mtVar1, mtVar2, fhFunction, varargin)
% ARRAYFUN2 Apply a function on two similar arrays, in slices.
% ARRAYFUN2(M1, M2, FUN, ...) applies the function specified by FUN.
% Each slice is passed individually to FUN, along with the slice index and
% any trailing arguments (..... |
github | DylanMuir/MappedTensor-master | plot.m | .m | MappedTensor-master/@MappedTensor/plot.m | 5,696 | utf_8 | 1f3197bfc1ea2acd3502ccc11c505ab2 | function h = plot(a, varargin)
% PLOT Plot an array.
% H = PLOT(M) plots the array M as a vector, matrix/surface, or volume.
% Higher dimension tensors plot a projection.
%
% Example: h=plot(MappedTensor(rand(100))); close(gcf); 1
h = [];
% handle ndims > 3
if ndims(a) > 3
for n=4:ndims(a)
signal = sum(sign... |
github | DylanMuir/MappedTensor-master | version.m | .m | MappedTensor-master/@MappedTensor/version.m | 6,763 | utf_8 | 4f2f1ed322022b787064b28b3a72b5ae | function [b, vers, info] = version(a,long_request)
% VERSION Return class version
% VERSION(s) return the version of the class
%
% VERSION(s, 'long') returns the full version with all contributors.
%
% [str, ver, info] = VERSION(s) returns as well the short version name
% 'ver', and additional information: memo... |
github | DylanMuir/MappedTensor-master | runtest.m | .m | MappedTensor-master/@MappedTensor/runtest.m | 10,975 | utf_8 | 738878653ae50d67cc4eb504da8c74ff | function r = runtest(s, m, option)
% RUNTEST runs a set of tests on object methods
% RUNTEST(s) checks all object methods. In deployed versions, only the 'test'
% functions can be used, whereas from Matlab, the header Example: lines can be
% used for testing. The test functions must be named 'test_<class>_<method... |
github | DylanMuir/MappedTensor-master | pack.m | .m | MappedTensor-master/@MappedTensor/pack.m | 8,503 | utf_8 | ce4e17d7de4d56f557a71c04ec1dca88 | function ret = pack(mtVar, method)
% PACK Compress the mapped file.
% Compress tensor storage with ZIP, TAR, GZIP, LZ4, ZSTD, BZIP2, XZ, LZO, ...
% M = PACK(M) compresses the mapped data files for given tensor.
% Unpacking is done transparently when data is accessed, or can be forced with
% UNPACK(M).
%
% ... |
github | DylanMuir/MappedTensor-master | make_complex.m | .m | MappedTensor-master/@MappedTensor/private/make_complex.m | 1,055 | utf_8 | 619bd6673a8015055fb1db7f1720ba92 | %% make_complex - PROTECTED METHOD Convert tensor to complex storage
function make_complex(mtVar)
% - test to see if we can store complex values in the desired
% representation
switch (mtVar.Format)
case {'char', 'logical'}
error('MappedTensor:NoConversionComplexToClass', ...
... |
github | DylanMuir/MappedTensor-master | unary.m | .m | MappedTensor-master/@MappedTensor/private/unary.m | 4,125 | utf_8 | b55858f05cb7abeaffc771aaddd4b6c2 | function b = unary(a, op, varargin)
% UNARY handles unary operations
% UNARY(M, op, ...) applies unary operator OP onto array M. OP must be given
% as a string.
%
% Operations that keep data order:
% abs acosh acos asinh asin atanh atan ceil conj cosh cos del2 exp
% floor imag isfinite isinf isnan log10 log not... |
github | DylanMuir/MappedTensor-master | ConvertColonsCheckLims.m | .m | MappedTensor-master/@MappedTensor/private/ConvertColonsCheckLims.m | 1,706 | utf_8 | 5cb2c03525406b1aa4ba41814b5b0bb5 | % ConvertColonCheckLims - FUNCTION Convert colon referencing to subscript indices; check index limits
function [vnLinearIndices, vnDataSize] = ConvertColonsCheckLims(cRefs, vnLims, hRepSumFunc)
% - Fill trailing referenced dimension limits
vnLims(end+1:numel(cRefs)) = 1;
% - Handle linear indexing
if (... |
github | DylanMuir/MappedTensor-master | binary.m | .m | MappedTensor-master/@MappedTensor/private/binary.m | 2,599 | utf_8 | f4c6a34def6f00708449c4537cda2cc9 | function c = binary(a, b, op, varargin)
% UNARY handles unary operations
% UNARY(M, op, ...) applies unary operator OP onto array M. OP must be given
% as a string.
%
% binary operator may be:
% eq ge gt ldivide le lt and or xor
% minus mldivide mpower mrdivide mtimes ne plus power rdivide times
% isequal
% ... |
github | DylanMuir/MappedTensor-master | str2struct.m | .m | MappedTensor-master/@MappedTensor/private/str2struct.m | 4,559 | utf_8 | 4e3c86e98135614fef03550dafad5768 | function s=str2struct(string)
% s=str2struct(string) Create a structure from string lines
% This function creates a structure from string containing <name> <value> pairs
% Structure member must be separated by ';' or end-of-lines.
% The member assignation can be specified with spaces, '=' and ':'
% Values of ty... |
github | DylanMuir/MappedTensor-master | SplitFileChunks.m | .m | MappedTensor-master/@MappedTensor/private/SplitFileChunks.m | 1,778 | utf_8 | d70eaa3276f3585dc6b78c49512a17bf | % SplitFileChunks - FUNCTION Split a set of indices into contiguous chunks
% (with a consistent skip step within a chunk)
function [mnFileChunkIndices] = SplitFileChunks(vnLinearIndices, hChunkLengthFunc)
% - Handle degenerate cases
switch (numel(vnLinearIndices))
case 1
% - Single element
... |
github | DylanMuir/MappedTensor-master | private_load_npy.m | .m | MappedTensor-master/@MappedTensor/private/private_load_npy.m | 3,576 | UNKNOWN | 73285cc861a812b973be4bc16f12968d | function [Descr,args,s] = private_load_npy(filename)
% PRIVATE_LOAD_NPY Reads a single NumPy array (binary format).
% Read a Python Numpy array '.npy' file.
% can handle: 'uint8','uint16','uint32','uint64
% 'int8','int16','int32','int64'
% 'single','double', 'logical'
%
% To generate a... |
github | DylanMuir/MappedTensor-master | isvalidsubscript.m | .m | MappedTensor-master/@MappedTensor/private/isvalidsubscript.m | 721 | utf_8 | 72409edbd78678fb2cf6f7c20e950182 | % isvalidsubscript - FUNCTION Test whether a vector contains valid entries
% for subscript referencing
function isvalidsubscript(oRefs)
try
% - Test for colon
if (iscolon(oRefs))
return;
end
if (islogical(oRefs))
% - Test for logical indexing
... |
github | DylanMuir/MappedTensor-master | mt_write_all.m | .m | MappedTensor-master/@MappedTensor/private/mt_write_all.m | 818 | utf_8 | 6e258b5976ef016959dc7549b711395d | % mt_write_all - FUNCTION Write the entire stack
function mt_write_all(hDataFile, vnTensorSize, Format, Offset, tData, ~)
% - Do we need to replicate the data?
if (isscalar(tData) && prod(vnTensorSize) > 1)
tData = repmat(tData, prod(vnTensorSize), 1);
elseif (numel(tData) ~= prod(vnTensorSize))
... |
github | DylanMuir/MappedTensor-master | private_load_edf.m | .m | MappedTensor-master/@MappedTensor/private/private_load_edf.m | 4,396 | utf_8 | 92c335c3135f73f7e0dfd6fefc2edfee | function [Descr, args, header] = private_load_edf(filename)
% PRIVATE_LOAD_EDF Read an ESRF Data Format file (EDF)
%
% Only reads the first block/image
%
% Using: pmedf_read and pmedfwrite by Petr Mikulik, Masaryk University, Brno, 11.8.2010
% <http://www.sci.muni.cz/~mikulik/Soft4Synchro.html>
Descr=''; args = {}; f... |
github | DylanMuir/MappedTensor-master | unique_accel.m | .m | MappedTensor-master/@MappedTensor/private/unique_accel.m | 1,807 | utf_8 | 2de79d0a6c3f5031a4476de2872b285e | % unique_accel - FUNCTION Accelerated version of 'unique', for the
% particular usage required here
function [c,indA,indC] = unique_accel(a)
numelA = numel(a);
% - Short-cut for vectors that are already unique
[bIsUnique, sortA, indSortA] = isunique(a);
if (bIsUnique)
c = sortA;
indA ... |
github | DylanMuir/MappedTensor-master | isunique.m | .m | MappedTensor-master/@MappedTensor/private/isunique.m | 434 | utf_8 | dfcf368805f556ede076813e8c97c16f | % isunique - FUNCTION Determine whether the elements of a vector are unique
function [bIsUnique, aSorted, vnASortedIndices] = isunique(a)
% - Check for a sorted vector, or sort it
if issorted(a)
aSorted = a;
vnASortedIndices = 1:numel(a);
else
[aSorted, vnASortedIndices] = sort(a);
... |
github | DylanMuir/MappedTensor-master | my_subsref.m | .m | MappedTensor-master/@MappedTensor/private/my_subsref.m | 4,673 | utf_8 | aa00e58b0b4756b65e60a94f63c7d308 | % my_subsref - Standard array referencing
function [tfData] = my_subsref(mtVar, S)
% - Test for valid subscripts
cellfun(@isvalidsubscript, S.subs);
% - Re-order reference indices
nNumDims = numel(S.subs);
nNumTotalDims = numel(mtVar.vnDimensionOrder);
vnReferencedTensorSize = size(mtVar);
... |
github | DylanMuir/MappedTensor-master | iscolon.m | .m | MappedTensor-master/@MappedTensor/private/iscolon.m | 148 | utf_8 | e09fdd9a954f80fe9345a938f305de84 | % iscolon - FUNCTION Test whether a reference is equal to ':'
function bIsColon = iscolon(ref)
bIsColon = ischar(ref) && isequal(ref, ':');
end
|
github | DylanMuir/MappedTensor-master | compare_single_tensor.m | .m | MappedTensor-master/@MappedTensor/private/compare_single_tensor.m | 944 | utf_8 | 6bfbbf88b584fe5b742b29c8a1e991fb | % compare_single_tensor - FUNCTION Comparison function along a single tensor
function [tfResult, tnIndices] = compare_single_tensor(mtVarA, nDim, fhCompare)
% - Determine size of slice
vnSliceSize = size(mtVarA);
vnSliceSize(nDim) = 1;
% - Make a referencing structure
sSubs = substruct('()', repmat... |
github | DylanMuir/MappedTensor-master | mt_read_all.m | .m | MappedTensor-master/@MappedTensor/private/mt_read_all.m | 439 | utf_8 | c0b512b95c0969316a08e44ca0f51cd9 | % mt_read_all - FUNCTION Read the entire stack
function [tData] = mt_read_all(hDataFile, vnTensorSize, Format, Offset, ~)
% - Allocate data
[~, strStorageClass] = ClassSize(Format);
% tData = zeros(vnTensorSize, strStorageClass);
% - Seek file to beginning of data
fseek(hDataFile, Offset, 'bof')... |
github | DylanMuir/MappedTensor-master | GetLinearIndicesForRefs.m | .m | MappedTensor-master/@MappedTensor/private/GetLinearIndicesForRefs.m | 2,479 | utf_8 | 57565eab46b2ad01621bc39d013e274b | % GetLinearIndicesForRefs - FUNCTION Convert a set of multi-dimensional indices directly into linear indices
function [vnLinearIndices, vnDimRefSizes] = GetLinearIndicesForRefs(cRefs, vnLims, hRepSumFunc)
% - Find colon references
vbIsColon = cellfun(@iscolon, cRefs);
% - Fill trailing referenced dimensio... |
github | DylanMuir/MappedTensor-master | compare_dual_tensor.m | .m | MappedTensor-master/@MappedTensor/private/compare_dual_tensor.m | 2,903 | utf_8 | 5e12bee913edbe0c1a23ac695b6feb23 | % compare_dual_tensor - FUNCTION Comparison function between two tensors, or a tensor and scalar
function [tfResult, tnIndices] = compare_dual_tensor(oVarA, oVarB, nDim, fhCompare)
% -- Check arguments
% - Make sure we have a double scalar
vbScalarArgs = false(1, 2);
if (isscalar(oVarA))
oVarA ... |
github | DylanMuir/MappedTensor-master | private_load_mrc.m | .m | MappedTensor-master/@MappedTensor/private/private_load_mrc.m | 17,667 | utf_8 | fb7279877f41d2e0736c44153635064d | function [Descr, args, Data] = private_load_mrc(filename)
% PRIVATE_LOAD_MRC MRC/CCP4/MAP electronic density map file.
%
% Format definition:
% <http://en.wikipedia.org/wiki/MRC_%28file_format%29>
%
% Get EM data files at EMDB Data base <https://www.emdataresource.org/index.html>
%
% References:
% tom_mrcread from Wolf... |
github | DIDSR/eeDAP-master | ExtractROI_BIO.m | .m | eeDAP-master/utilities/After_the_fact_registration/ExtractROI_BIO.m | 8,106 | utf_8 | f4656808717a46b1e3bce8c1a91117f3 |
% ##########################################################################
%% ########################## EXTRACT ROI ###################################
% ##########################################################################
function success = ExtractROI_BIO(...
wsi_info,... % WSI inf... |
github | DIDSR/eeDAP-master | Load_Output_File.m | .m | eeDAP-master/utilities/After_the_fact_registration/Load_Output_File.m | 16,362 | utf_8 | 0cc9826f7a20242381b47c8d1ff9b962 | % ##########################################################################
%% ######################### LOAD INPUT FILE ################################
% ##########################################################################
function succeed = Load_Output_File(handles)
try
%---------------------------... |
github | DIDSR/eeDAP-master | Registration_after_work.m | .m | eeDAP-master/utilities/After_the_fact_registration/Registration_after_work.m | 44,306 | utf_8 | 8b0ebbbb80ab7642a6f55d5f44c909a8 | function varargout = Registration_after_work(varargin)
gui_Singleton = 1;
gui_State = struct('gui_Name', mfilename, ...
'gui_Singleton', gui_Singleton, ...
'gui_OpeningFcn', @Registration_after_work_OpeningFcn, ...
'gui_OutputFcn', @R... |
github | DIDSR/eeDAP-master | Register_ROI.m | .m | eeDAP-master/utilities/After_the_fact_registration/Register_ROI.m | 8,057 | utf_8 | c202be25803f1b069257d96e20817cd6 | % ##########################################################################
%% ############################ REGISTER ROI ################################
% ##########################################################################
function Register_ROI(handles)
try
%-----------------------------------------... |
github | DIDSR/eeDAP-master | bfCheckJavaPath.m | .m | eeDAP-master/utilities/After_the_fact_registration/bfmatlab/bfCheckJavaPath.m | 3,347 | utf_8 | 10338284140f806a8da0a37de50a6664 | function [status, version] = bfCheckJavaPath(varargin)
% bfCheckJavaPath check Bio-Formats is included in the Java class path
%
% SYNOPSIS bfCheckJavaPath()
% status = bfCheckJavaPath(autoloadBioFormats)
% [status, version] = bfCheckJavaPath()
%
% Input
%
% autoloadBioFormats - Optional. A boole... |
github | DIDSR/eeDAP-master | createMinimalOMEXMLMetadata.m | .m | eeDAP-master/utilities/After_the_fact_registration/bfmatlab/createMinimalOMEXMLMetadata.m | 4,094 | utf_8 | d749a8ce7895da8405a789d7b6a0c754 | function metadata = createMinimalOMEXMLMetadata(I, varargin)
% CREATEMINIMALOMEXMLMETADATA Create an OME-XML metadata object from an input matrix
%
% createMinimalOMEXMLMetadata(I) creates an OME-XML metadata object from
% an input 5-D array. Minimal metadata information is stored such as the
% pixels dimensio... |
github | DIDSR/eeDAP-master | bfsave.m | .m | eeDAP-master/utilities/After_the_fact_registration/bfmatlab/bfsave.m | 5,285 | utf_8 | 1caba8d6ea3e021cc71f100929200dcc | function bfsave(varargin)
% BFSAVE Save a 5D matrix into an OME-TIFF using Bio-Formats library
%
% bfsave(I, outputPath) writes the input 5D matrix into a new file
% specified by outputPath.
%
% bfsave(I, outputPath, dimensionOrder) specifies the dimension order of
% the input matrix. Default valuse is XYZC... |
github | DIDSR/eeDAP-master | Image_Information.m | .m | eeDAP-master/utilities/View_WSI_information/Image_Information.m | 8,381 | utf_8 | 020d8fac717c56e5f031aad73b88ea07 | function varargout = Image_Information(varargin)
% IMAGE_INFORMATION MATLAB code for Image_Information.fig
% IMAGE_INFORMATION, by itself, creates a new IMAGE_INFORMATION or raises the existing
% singleton*.
%
% H = IMAGE_INFORMATION returns the handle to a new IMAGE_INFORMATION or the handle to
% t... |
github | DIDSR/eeDAP-master | ExtractROI_BIO.m | .m | eeDAP-master/utilities/View_WSI_information/ExtractROI_BIO.m | 8,106 | utf_8 | f4656808717a46b1e3bce8c1a91117f3 |
% ##########################################################################
%% ########################## EXTRACT ROI ###################################
% ##########################################################################
function success = ExtractROI_BIO(...
wsi_info,... % WSI inf... |
github | DIDSR/eeDAP-master | bfCheckJavaPath.m | .m | eeDAP-master/utilities/View_WSI_information/bfmatlab/bfCheckJavaPath.m | 3,347 | utf_8 | 10338284140f806a8da0a37de50a6664 | function [status, version] = bfCheckJavaPath(varargin)
% bfCheckJavaPath check Bio-Formats is included in the Java class path
%
% SYNOPSIS bfCheckJavaPath()
% status = bfCheckJavaPath(autoloadBioFormats)
% [status, version] = bfCheckJavaPath()
%
% Input
%
% autoloadBioFormats - Optional. A boole... |
github | DIDSR/eeDAP-master | createMinimalOMEXMLMetadata.m | .m | eeDAP-master/utilities/View_WSI_information/bfmatlab/createMinimalOMEXMLMetadata.m | 4,094 | utf_8 | d749a8ce7895da8405a789d7b6a0c754 | function metadata = createMinimalOMEXMLMetadata(I, varargin)
% CREATEMINIMALOMEXMLMETADATA Create an OME-XML metadata object from an input matrix
%
% createMinimalOMEXMLMetadata(I) creates an OME-XML metadata object from
% an input 5-D array. Minimal metadata information is stored such as the
% pixels dimensio... |
github | DIDSR/eeDAP-master | bfsave.m | .m | eeDAP-master/utilities/View_WSI_information/bfmatlab/bfsave.m | 5,285 | utf_8 | 1caba8d6ea3e021cc71f100929200dcc | function bfsave(varargin)
% BFSAVE Save a 5D matrix into an OME-TIFF using Bio-Formats library
%
% bfsave(I, outputPath) writes the input 5D matrix into a new file
% specified by outputPath.
%
% bfsave(I, outputPath, dimensionOrder) specifies the dimension order of
% the input matrix. Default valuse is XYZC... |
github | DIDSR/eeDAP-master | stage_move.m | .m | eeDAP-master/utilities/Camera_stage_review/stage_move.m | 1,515 | utf_8 | 24c3dfbc218e2c88feb5af41a9508eb6 | % ##########################################################################
%% ###################### MOVE STAGE SEQUENCE ###############################
% ##########################################################################
function stage=stage_move(stage, target_pos, h_stage)
%---------------------------... |
github | DIDSR/eeDAP-master | stage_close.m | .m | eeDAP-master/utilities/Camera_stage_review/stage_close.m | 627 | utf_8 | 17bec92b6137d4d7789aa10f96b950cb | % ##########################################################################
%% ######################## CLOSE SERIAL PORT ###############################
% ##########################################################################
function status=stage_close(S)
%--------------------------------------------... |
github | DIDSR/eeDAP-master | Camera_stage_review.m | .m | eeDAP-master/utilities/Camera_stage_review/Camera_stage_review.m | 19,578 | utf_8 | 7deabc9bb416bfdd03c6c4a7db310814 | function varargout = Camera_stage_review(varargin)
% CAMERA_STAGE_REVIEW MATLAB code for Camera_stage_review.fig
% CAMERA_STAGE_REVIEW, by itself, creates a new CAMERA_STAGE_REVIEW or raises the existing
% singleton*.
%
% H = CAMERA_STAGE_REVIEW returns the handle to a new CAMERA_STAGE_REVIEW or the hand... |
github | DIDSR/eeDAP-master | stage_set_origin.m | .m | eeDAP-master/utilities/Camera_stage_review/stage_set_origin.m | 805 | utf_8 | 9484a59090ec8a5c4b0b7a935816a2d4 | % ##########################################################################
%% ###################### MOVE STAGE SEQUENCE ###############################
% ##########################################################################
function stage = stage_set_origin(stage,h_stage)
try
stage_label = stage.labe... |
github | DIDSR/eeDAP-master | stage_get_joy_speed.m | .m | eeDAP-master/utilities/Camera_stage_review/stage_get_joy_speed.m | 625 | utf_8 | 629e052beaad82ebe8f10fd48af18a25 | % ##########################################################################
%% ###################### MOVE STAGE SEQUENCE ###############################
% ##########################################################################
function stage = stage_get_joy_speed(stage,h_stage)
try
stage_label = stage.l... |
github | DIDSR/eeDAP-master | stage_set_joy_speed.m | .m | eeDAP-master/utilities/Camera_stage_review/stage_set_joy_speed.m | 664 | utf_8 | 470c68947e77b1dc70820f10a8344d76 | % ##########################################################################
%% ###################### MOVE STAGE SEQUENCE ###############################
% ##########################################################################
function stage = stage_set_joy_speed(stage,target_speed,h_stage)
try
stage_la... |
github | DIDSR/eeDAP-master | stage_open.m | .m | eeDAP-master/utilities/Camera_stage_review/stage_open.m | 242 | utf_8 | a4b0002042b0e3bd4b80ee71400374ba |
function stage = stage_open(label)
try
if strcmp(label(end-4:end),'Prior')
stage = stage_open_prior(label);
else
stage = stage_open_Ludl(label);
end
catch ME
error_show(ME)
end
end |
github | DIDSR/eeDAP-master | stage_move_Ludl.m | .m | eeDAP-master/utilities/Camera_stage_review/stages/Ludl/stage_move_Ludl.m | 3,706 | utf_8 | bff21c99c6f9dd3b2bdba03b5a220408 | % ##########################################################################
%% ###################### MOVE STAGE SEQUENCE ###############################
% ##########################################################################
function stage=stage_move_Ludl(stage, target_pos, h_stage)
%----------------------... |
github | DIDSR/eeDAP-master | stage_open_Ludl.m | .m | eeDAP-master/utilities/Camera_stage_review/stages/Ludl/stage_open_Ludl.m | 3,032 | utf_8 | b5b96e93fa669ab7f7c04cf807e53b60 |
function stage = stage_open_Ludl(label)
try
% instrfind returns the instrument object array
% objects = instrfind
% each entry includes the type, status, and name as follows
% Index: Type: Status: Name:
% 1 serial closed Serial-COM4
%
% objects can be ... |
github | DIDSR/eeDAP-master | stage_send_com_Ludl.m | .m | eeDAP-master/utilities/Camera_stage_review/stages/Ludl/stage_send_com_Ludl.m | 2,237 | utf_8 | 61c55a96d2eaed4a5ad24ca158a74516 | % ##########################################################################
%% ########################## SEND COMMAND ##################################
% ##########################################################################
function ST_answer=stage_send_com_Ludl (S, CommandStr)
%----------------------... |
github | DIDSR/eeDAP-master | stage_set_origin_Ludl.m | .m | eeDAP-master/utilities/Camera_stage_review/stages/Ludl/stage_set_origin_Ludl.m | 3,453 | utf_8 | 87ad7ca6e638c2b36538cb28aa26fa02 | % ##########################################################################
%% ###################### MOVE STAGE SEQUENCE ###############################
% ##########################################################################
function stage = stage_set_origin_Ludl(stage,h_stage)
try
% If communic... |
github | DIDSR/eeDAP-master | stage_get_pos_prior.m | .m | eeDAP-master/utilities/Camera_stage_review/stages/Prior/stage_get_pos_prior.m | 1,885 | utf_8 | 558915c55ba5f3fa39c7ea135c4f7200 |
%% ################# GET STAGE POSITION SEQUENCE FOR PRIOR ##########################
function stage=stage_get_pos_prior(stage,h_stage)
% instrfind returns the instrument object array
% objects = instrfind
% each entry includes the type, status, and name as follows
% Index: Type: Status: Name:
% 1 ... |
github | DIDSR/eeDAP-master | stage_move_prior.m | .m | eeDAP-master/utilities/Camera_stage_review/stages/Prior/stage_move_prior.m | 4,079 | utf_8 | aa900775635216b43aa51c76db08e876 | % ##########################################################################
%% ################# MOVE STAGE SEQUENCE FOR PRIOR ##########################
% ##########################################################################
function stage=stage_move_prior(stage, target_pos, h_stage)
%---------------------... |
github | DIDSR/eeDAP-master | stage_open_prior.m | .m | eeDAP-master/utilities/Camera_stage_review/stages/Prior/stage_open_prior.m | 2,331 | utf_8 | ac8589da9b02334ceb353c16e47f6385 |
function stage = stage_open_prior(label)
try
% instrfind returns the instrument object array
% objects = instrfind
% each entry includes the type, status, and name as follows
% Index: Type: Status: Name:
% 1 serial closed Serial-COM4
%
% objects can be... |
github | DIDSR/eeDAP-master | stage_send_com_prior.m | .m | eeDAP-master/utilities/Camera_stage_review/stages/Prior/stage_send_com_prior.m | 1,939 | utf_8 | c61f5be107cb1eb97a382969223cd00c | % ##########################################################################
%% ########################## SEND COMMAND ##################################
% ##########################################################################
function ST_answer=stage_send_com_prior (S, CommandStr)
%---------------------... |
github | DIDSR/eeDAP-master | stage_check_busy_prior.m | .m | eeDAP-master/utilities/Camera_stage_review/stages/Prior/stage_check_busy_prior.m | 320 | utf_8 | a00e2ede69fd8d3b16ec3e5460ff9482 |
%% ################# CHECK STAGE STATUS FOR PRIOR ##########################
function busy = stage_check_busy_prior(S)
try
status=stage_send_com_prior (S, '#');
if isempty(status)
busy = 1;
return
end
busy = str2num(status);
catch ME
error_show(ME)
end
end |
github | DIDSR/eeDAP-master | stage_set_origin_prior.m | .m | eeDAP-master/utilities/Camera_stage_review/stages/Prior/stage_set_origin_prior.m | 2,593 | utf_8 | ced089681bdcb4533c7262f729fffb46 | % ##########################################################################
%% ################# MOVE STAGE SEQUENCE FOR PORIOR##########################
% ##########################################################################
function stage = stage_set_origin_prior(stage,h_stage)
try
% If communi... |
github | DIDSR/eeDAP-master | ExtractROI_BIO.m | .m | eeDAP-master/utilities/WSI_to_WSI_registration/ExtractROI_BIO.m | 8,106 | utf_8 | f4656808717a46b1e3bce8c1a91117f3 |
% ##########################################################################
%% ########################## EXTRACT ROI ###################################
% ##########################################################################
function success = ExtractROI_BIO(...
wsi_info,... % WSI inf... |
github | DIDSR/eeDAP-master | WSIregistration.m | .m | eeDAP-master/utilities/WSI_to_WSI_registration/WSIregistration.m | 45,207 | utf_8 | a3f4dea6bd74427a3f55a04ef872e641 | function varargout = WSIregistration(varargin)
% WSIREGISTRATION MATLAB code for WSIregistration.fig
% WSIREGISTRATION, by itself, creates a new WSIREGISTRATION or raises the existing
% singleton*.
%
% H = WSIREGISTRATION returns the handle to a new WSIREGISTRATION or the handle to
% the existing si... |
github | DIDSR/eeDAP-master | Register_Two_WSI_ROI.m | .m | eeDAP-master/utilities/WSI_to_WSI_registration/Register_Two_WSI_ROI.m | 7,250 | utf_8 | faaea265bf8baf19d98e063a6114aa82 | % ##########################################################################
%% ############################ REGISTER ROI ################################
% ##########################################################################
function Register_Two_WSI_ROI(handles)
try
%---------------------------------... |
github | DIDSR/eeDAP-master | bfCheckJavaPath.m | .m | eeDAP-master/utilities/WSI_to_WSI_registration/bfmatlab/bfCheckJavaPath.m | 3,347 | utf_8 | 10338284140f806a8da0a37de50a6664 | function [status, version] = bfCheckJavaPath(varargin)
% bfCheckJavaPath check Bio-Formats is included in the Java class path
%
% SYNOPSIS bfCheckJavaPath()
% status = bfCheckJavaPath(autoloadBioFormats)
% [status, version] = bfCheckJavaPath()
%
% Input
%
% autoloadBioFormats - Optional. A boole... |
github | DIDSR/eeDAP-master | createMinimalOMEXMLMetadata.m | .m | eeDAP-master/utilities/WSI_to_WSI_registration/bfmatlab/createMinimalOMEXMLMetadata.m | 4,094 | utf_8 | d749a8ce7895da8405a789d7b6a0c754 | function metadata = createMinimalOMEXMLMetadata(I, varargin)
% CREATEMINIMALOMEXMLMETADATA Create an OME-XML metadata object from an input matrix
%
% createMinimalOMEXMLMetadata(I) creates an OME-XML metadata object from
% an input 5-D array. Minimal metadata information is stored such as the
% pixels dimensio... |
github | DIDSR/eeDAP-master | bfsave.m | .m | eeDAP-master/utilities/WSI_to_WSI_registration/bfmatlab/bfsave.m | 5,285 | utf_8 | 1caba8d6ea3e021cc71f100929200dcc | function bfsave(varargin)
% BFSAVE Save a 5D matrix into an OME-TIFF using Bio-Formats library
%
% bfsave(I, outputPath) writes the input 5D matrix into a new file
% specified by outputPath.
%
% bfsave(I, outputPath, dimensionOrder) specifies the dimension order of
% the input matrix. Default valuse is XYZC... |
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