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 | yzliao/cs229mario-master | plotQvalues.m | .m | cs229mario-master/MarioAI/plotQvalues.m | 1,478 | utf_8 | e718b48fc843f8c0da694d124b0f17d7 | % The state numbers and corresponding descriptions:
% 0: small, nothing present
% 1: big, nothing present
% 2: fire, nothing present
% +8: jump height 1
% +16: jump height 2
% +24: jump height 3
% +32: enemy in ABOVE
% +64: enemy FRONT_ABOVE
% +128: enemy FRONT
% +256: enemy FRONT_BELOW
% +512: enemy BELOW
% +1024: ene... |
github | SheffieldML/collab-master | computePredictionsErrorWeak.m | .m | collab-master/matlab/computePredictionsErrorWeak.m | 625 | utf_8 | 2cebae9bb711876ad1a62e1a9640a98d |
function [mu_T] = computePredictionsErrorWeak(model,Y,Ytest)
%
% [error_L2,error_NMAE,error_NMAE_round] = computePredictionsErrorWeak(model,Y,Ytest)
val_L2 = 0;
tot_L2 = 0;
val_NMAE = 0;
tot_NMAE = 0;
val_round_NMAE = 0;
tot_round_NMAE = 0;
accum = [];
mu_T = [];
for i = 1:size(Y, 2)
ind = find(Ytest(:, ... |
github | SheffieldML/collab-master | PlotResultsMovielensMarlinWeak.m | .m | collab-master/matlab/PlotResultsMovielensMarlinWeak.m | 2,911 | utf_8 | 3edd1f0df55232df63472ad5edcd1c06 | function [L2_error_T,NMAE_error_T,NMAE_round_error_T] = PlotResultsMovielensMarlinWeak(substract_mean,partNo_v,latentDim_v, iters, type, inverted, kernel_type, new_iters)
%
% [L2_error,NMAE_error,NMAE_round_error] = PlotResultsMovielensMarlinWeak(substract_mean,partNo_v,latentDim_v, iters, type, inverted, kernel_type... |
github | SheffieldML/collab-master | PlotResultsEachMovieMarlinWeak.m | .m | collab-master/matlab/PlotResultsEachMovieMarlinWeak.m | 2,628 | utf_8 | f2aecb19c2ce0d061783146941d1fb49 | function [L2_error_T,NMAE_error_T,NMAE_round_error_T] = PlotResultsEachMovieMarlinWeak(substract_mean,partNo_v,latentDim_v, iters, type, inverted, kern_type)
%
% [L2_error,NMAE_error,NMAE_round_error] = PlotResultsEachMovieMarlinWeak(substract_mean,partNo_v,latentDim_v, iters, kern_type)
%
% substract_mean --> bool i... |
github | SheffieldML/collab-master | PlotResultsMovielensWeak.m | .m | collab-master/matlab/PlotResultsMovielensWeak.m | 2,210 | utf_8 | f7f0d7ad0139a8d8b074176305f67157 | function [L2_error_T,NMAE_error_T,NMAE_round_error_T] = PlotResultsMovielensWeak(substract_mean,partNo_v,latentDim_v, iters, type)
%
% [L2_error,NMAE_error,NMAE_round_error] = PlotResultsMovielensWeak(substract_mean,partNo_v,latentDim_v, iters)
%
% substract_mean --> bool if substract the mean
% partNo_v --> vector w... |
github | SheffieldML/collab-master | PlotResultsMovielens.m | .m | collab-master/matlab/PlotResultsMovielens.m | 5,503 | utf_8 | 8a46a7d38ef5947219a5041e7f274310 | function [L2_error_T,NMAE_error_T,NMAE_round_error_T] = PlotResultsMovielens(perc_train_v,substract_mean,partNo_v,latentDim_v, iters, if_plot, if_print)
%
% [L2_error_T,NMAE_error,NMAE_round_error] = PlotResultsMovielens(perc_train,substract_mean,partNo_v,latentDim_v, iters, if_plot, if_print)
%
% perc_train_v -> per... |
github | SheffieldML/collab-master | PlotResultsEachMovieMarlinCompareKernels.m | .m | collab-master/matlab/PlotResultsEachMovieMarlinCompareKernels.m | 3,540 | utf_8 | 6b7cdc561efa6a710a27505f68a23a8f | function [] = PlotResultsEachMovieMarlinCompareKernels(substract_mean, partNo_v, latentDim_v, iters, type, inverted, directories, if_plot, if_print)
%
%function [] = PlotResultsEachMovieMarlinCompareKernels(substract_mean, partNo_v, latentDim_v, iters, type, inverted, directories, if_plot, if_print)
if strcmp(type... |
github | SheffieldML/collab-master | PlotResultsMovielensMarlinCompareKernels.m | .m | collab-master/matlab/PlotResultsMovielensMarlinCompareKernels.m | 3,643 | utf_8 | 9a1e6b85fbeb33eaa6da08b551988d2e | function [] = PlotResultsMovielensMarlinCompareKernels(substract_mean, partNo_v, latentDim_v, iters, type, inverted, directories, if_plot, if_print, new_iters)
%
%function [] = PlotResultsMovielensMarlinCompareKernels(substract_mean, partNo_v, latentDim_v, iters, type, inverted, directories, if_plot, if_print, new_it... |
github | PythonOptimizers/pysparse-master | poisson2d.m | .m | pysparse-master/examples/poisson_test/poisson2d.m | 405 | utf_8 | d4ca262e2c61fd0ccb588307b8a4429a | % Create sparse 2D Poisson matrix
%
% Used for benchmarking element-wise assignment to sparse matrices in Matlab.
%
% $Id$
function L = poisson2d(n)
L = spalloc(n*n, n*n, 5*n*n);
for i = 1:n
for j = 1:n
k = i + n*(j-1);
L(k,k) = 4;
if i > 1, L(k,k-1) = -1; end
if i < n, L(k,k+1) = -1; end... |
github | PythonOptimizers/pysparse-master | poisson.m | .m | pysparse-master/pysparse/tools/poisson.m | 873 | utf_8 | 6175c8266c7f175ab86f555b4efebe2c | function poisson(n)
%fprintf('poisson2d ');
%tic;
% poisson2d(n);
%toc;
%fprintf('poisson2d_blk ');
%tic;
% poisson2d_blk(n);
%toc;
fprintf('poisson2d_kron ');
tic;
poisson2d_kron(n);
toc;
return;
function L = poisson2d(n)
L = sparse(n*n);
for i = 1:n
for j = 1:n
k = i + n*(j-1);
L(k,k) = 4;
... |
github | petteriTeikari/twoPhotonVessels-master | analyze_getSDFvalues.m | .m | twoPhotonVessels-master/analyze_getSDFvalues.m | 3,378 | utf_8 | 4557767935ab558cf1bc7fd3ec524769 | % Uses command-line CGAL implementation of SHAPE DIAMETER FUNCTION (SDF)
function [diameterVals, segmentIDs] = analyze_getSDFvalues(fileNameForMesh, options)
if nargin == 2
disp('"options" is a lazy placeholder if we need to pass some parameters eventually')
elseif nargin == 1
options = [];
... |
github | petteriTeikari/twoPhotonVessels-master | import_checkQuality.m | .m | twoPhotonVessels-master/import_checkQuality.m | 1,313 | utf_8 | 1eff8d143544ff64a58a4181ebecbf2f | % Check for NaN and Inf values
function imageMatrixStack = import_checkQuality(imageMatrixStack, path, options)
if nargin == 0
load testQuality.mat
else
% save testQuality.mat
end
% check the quality of the input image
nanIndices = find(isnan(imageMatrixStack) == 1);... |
github | petteriTeikari/twoPhotonVessels-master | export_figureToDisk.m | .m | twoPhotonVessels-master/export_figureToDisk.m | 2,324 | utf_8 | bac1254d1c86cd7fa31f2c4c4e261ba4 | % Export figures to disk using some 3rd party writers
function export_figureToDisk(fig, fileNameOut, format, resolution, antiAliasLevel, options)
%% INPUT CHECKING
if ispc % Windows
splitFilePath = strsplit(fileNameOut, '\');
elseif isunix || ismac % LINUX/UNIX and MAC
... |
github | petteriTeikari/twoPhotonVessels-master | import_checkImportedData.m | .m | twoPhotonVessels-master/import_checkImportedData.m | 702 | utf_8 | 523cee81944bd3d853ea59d407b6d945 | % check that the import was okay
function options = import_checkImportedData(data, metadata, extraString, options)
options.imageSize = size(data{1, 1}{1, 1});
options.numberOfStacks = size(data{1}, 1);
options.numberOf_tPlanes = 6; % fixed now, maybe from metadata at some point
options.numberOf_zStack... |
github | petteriTeikari/twoPhotonVessels-master | denoise_demoGuidedFilter_iterations.m | .m | twoPhotonVessels-master/demos/denoise_demoGuidedFilter_iterations.m | 7,919 | utf_8 | 255b75968c9693ad0bae2d6f31accf41 | % Testing whether the quality improves if the filter is iterated
function denoise_demoGuidedFilter_iterations()
%% Import test data
load(fullfile('..', 'debugMATs', 'testSlices.mat'))
% z-slices of 9-11 from first time point of:
% "CP-20150323-TR70-mouse2-1-son.oib" from Charissa
... |
github | petteriTeikari/twoPhotonVessels-master | denoise_demoMethods.m | .m | twoPhotonVessels-master/demos/denoise_demoMethods.m | 22,137 | utf_8 | 6b17de8162d13e26f229668aedb8ff1c | % These depend on the 3rd party toolboxes
% TODO: Add toolboxes to github
function denoise_demoMethods()
%% Import test data
load(fullfile('..', 'debugMATs', 'testSlices.mat'))
% z-slices of 9-11 from first time point of:
% "CP-20150323-TR70-mouse2-1-son.oib" from Charissa
... |
github | petteriTeikari/twoPhotonVessels-master | asets_demoWrapper_3D.m | .m | twoPhotonVessels-master/demos/segmentationDemo/asets_demoWrapper_3D.m | 19,875 | utf_8 | dc7fb871ad97cb39fea3a45e7017cd0b | function region = asets_demoWrapper_3D(img, vessel, edges, sliceIndex, visualize3D, visualizeON, fileOutBase)
%% Tutorial 02: Time-implicit level set segmentation
% Martin Rajchl, Imperial College London, 2015
%
% [1] Rajchl, M.; Baxter, JSH.; Bae, E.; Tai, X-C.; Fenster, A.;
% Peters, TM... |
github | petteriTeikari/twoPhotonVessels-master | asets_demoWrapper_3D_v3.m | .m | twoPhotonVessels-master/demos/segmentationDemo/asets_demoWrapper_3D_v3.m | 23,188 | utf_8 | c3dfa03732b97d6b1360d96ca456d7cf | function region = asets_demoWrapper_3D_v3(img, vessel, edges, region, ...
maxLevelSetIterations, tau, w1, w2, w3, pars, ...
regWeight1, regWeight2, regWeight3, ...
secondPass, sliceIndex, visualize... |
github | petteriTeikari/twoPhotonVessels-master | asets_demoWrapper_3D_v2.m | .m | twoPhotonVessels-master/demos/segmentationDemo/asets_demoWrapper_3D_v2.m | 20,897 | utf_8 | 5b473d15a3379240a801830762fe937b | function region = asets_demoWrapper_3D_v2(img, vessel, edges, sliceIndex, visualize3D, visualizeON, fileOutBase)
%% Tutorial 02: Time-implicit level set segmentation
% Martin Rajchl, Imperial College London, 2015
%
% [1] Rajchl, M.; Baxter, JSH.; Bae, E.; Tai, X-C.; Fenster, A.;
% Peters,... |
github | petteriTeikari/twoPhotonVessels-master | pdftops.m | .m | twoPhotonVessels-master/3rdParty/export_fig/pdftops.m | 3,053 | utf_8 | 6eb261c6107aedd03ceace4ccbce285c | function varargout = pdftops(cmd)
%PDFTOPS Calls a local pdftops executable with the input command
%
% Example:
% [status result] = pdftops(cmd)
%
% Attempts to locate a pdftops executable, finally asking the user to
% specify the directory pdftops was installed into. The resulting path is
% stored for futur... |
github | petteriTeikari/twoPhotonVessels-master | isolate_axes.m | .m | twoPhotonVessels-master/3rdParty/export_fig/isolate_axes.m | 3,529 | utf_8 | b552c5f50835b27b0cec7cb0198d4d18 | %ISOLATE_AXES Isolate the specified axes in a figure on their own
%
% Examples:
% fh = isolate_axes(ah)
% fh = isolate_axes(ah, vis)
%
% This function will create a new figure containing the axes specified, and
% also their associated legends and colorbars. The axes specified must all
% be in the same figur... |
github | petteriTeikari/twoPhotonVessels-master | pdf2eps.m | .m | twoPhotonVessels-master/3rdParty/export_fig/pdf2eps.m | 1,524 | utf_8 | 037f9109e96ab4385d13019a29db4639 | %PDF2EPS Convert a pdf file to eps format using pdftops
%
% Examples:
% pdf2eps source dest
%
% This function converts a pdf file to eps format.
%
% This function requires that you have pdftops, from the Xpdf suite of
% functions, installed on your system. This can be downloaded from:
% http://www.foolabs.c... |
github | petteriTeikari/twoPhotonVessels-master | print2array.m | .m | twoPhotonVessels-master/3rdParty/export_fig/print2array.m | 3,731 | utf_8 | 6f18d0ebdd7fa8e2ecf9a0b75e07c40a | %PRINT2ARRAY Exports a figure to an image array
%
% Examples:
% A = print2array
% A = print2array(figure_handle)
% A = print2array(figure_handle, resolution)
% A = print2array(figure_handle, resolution, renderer)
%
% This function outputs a bitmap image of the given figure, at the desired
% resolution... |
github | petteriTeikari/twoPhotonVessels-master | eps2pdf.m | .m | twoPhotonVessels-master/3rdParty/export_fig/eps2pdf.m | 4,321 | utf_8 | 0cf21e6015693f00b403681bbcada6e0 | %EPS2PDF Convert an eps file to pdf format using ghostscript
%
% Examples:
% eps2pdf source dest
% eps2pdf(source, dest, crop)
% eps2pdf(source, dest, crop, append)
% eps2pdf(source, dest, crop, append, gray)
% eps2pdf(source, dest, crop, append, gray, quality)
%
% This function converts an eps file... |
github | petteriTeikari/twoPhotonVessels-master | user_string.m | .m | twoPhotonVessels-master/3rdParty/export_fig/user_string.m | 2,339 | utf_8 | f9b2326571e9d13eccc99ce441efd788 | %USER_STRING Get/set a user specific string
%
% Examples:
% string = user_string(string_name)
% saved = user_string(string_name, new_string)
%
% Function to get and set a string in a system or user specific file. This
% enables, for example, system specific paths to binaries to be saved.
%
% IN:
% string_name - ... |
github | petteriTeikari/twoPhotonVessels-master | export_fig.m | .m | twoPhotonVessels-master/3rdParty/export_fig/export_fig.m | 24,629 | utf_8 | 2ebd1f96ee9cd175a6ca7f5c6caf11cf | %EXPORT_FIG Exports figures suitable for publication
%
% Examples:
% im = export_fig
% [im alpha] = export_fig
% export_fig filename
% export_fig filename -format1 -format2
% export_fig ... -nocrop
% export_fig ... -native
% export_fig ... -m<val>
% export_fig ... -r<val>
% export_fig ... ... |
github | petteriTeikari/twoPhotonVessels-master | ghostscript.m | .m | twoPhotonVessels-master/3rdParty/export_fig/ghostscript.m | 3,909 | utf_8 | 1052b6816638b0e6f59b471bf25dd055 | function varargout = ghostscript(cmd)
%GHOSTSCRIPT Calls a local GhostScript executable with the input command
%
% Example:
% [status result] = ghostscript(cmd)
%
% Attempts to locate a ghostscript executable, finally asking the user to
% specify the directory ghostcript was installed into. The resulting path... |
github | petteriTeikari/twoPhotonVessels-master | print2eps.m | .m | twoPhotonVessels-master/3rdParty/export_fig/print2eps.m | 1,846 | utf_8 | b35c00359f5f3745c0ab843d7ed7e269 | %PRINT2EPS Prints figures to eps with improved line styles
%
% Examples:
% print2eps filename
% print2eps(filename, fig_handle)
% print2eps(filename, fig_handle, options)
%
% This function saves a figure as an eps file, and improves the line style,
% making dashed lines more like those on screen and givi... |
github | petteriTeikari/twoPhotonVessels-master | metchgui_one.m | .m | twoPhotonVessels-master/3rdParty/metch/metchgui_one.m | 44,038 | utf_8 | 93c0b0c49efb410cbf67f8af71186b36 | function varargout = metchgui_one(varargin)
% alldata = metchgui_one(node,elem,points) or metchgui_one(volume,points)
%
% A GUI to register a point cloud to a mesh or volumetric image
%
% author: Qianqian Fang <fangq at nmr.mgh.harvard.edu>
% date: 12/16/2008
%
% parameters:
% node: node coord... |
github | petteriTeikari/twoPhotonVessels-master | metchgui.m | .m | twoPhotonVessels-master/3rdParty/metch/metchgui.m | 15,913 | utf_8 | 16764d1eb4e0d31371670214808417c8 | function varargout = metchgui(varargin)
% alldata = metchgui(node,elem,points) or metchgui(volume,points)
%
% A GUI to register a point cloud to a mesh or volumetric image
%
% author: Qianqian Fang <fangq at nmr.mgh.harvard.edu>
% date: 12/16/2008
%
% parameters:
% node: node coordinate of the... |
github | petteriTeikari/twoPhotonVessels-master | fastflux3.m | .m | twoPhotonVessels-master/3rdParty/SphericalFluxComputation/fastflux3.m | 8,585 | UNKNOWN | 08a0a4cbb802a16840ba1fd326e33ef7 | function outputfeature = fastflux3( image, ranges, sigma, pixelspacing)
% Compute the analytical 3D multi-radii spherical flux responses for
% curvilinear structure segmentation. Offer up to 1000 times speed up
% compared to spatial domain implementation. Support GPU computation for
% further speed improvement. ... |
github | petteriTeikari/twoPhotonVessels-master | minimize_point_to_plane.m | .m | twoPhotonVessels-master/3rdParty/fastICP/minimize_point_to_plane.m | 610 | utf_8 | d2c3b115033ade43a811b33bb39c8113 |
% Minimize the point to plane metric according to
% Kok Lim Low : Linear Least Squares Optimization for Point-to-Plane
% ICP Surface Registration
% Also check
% Ef?cient Variants of the ICP Algorithm by Szymon Rusinkiewicz
%
% Author: Tolga Birdal
%
function [x]=minimize_point_to_plane(Src, Dst, Normals)
... |
github | petteriTeikari/twoPhotonVessels-master | icp_mod_point_plane_pyr.m | .m | twoPhotonVessels-master/3rdParty/fastICP/icp_mod_point_plane_pyr.m | 9,934 | utf_8 | ab9f58993f37801955222fbb01825b20 |
%% icp_mod_point_plane_pyr
% by Tolga Birdal
% This file is an attempt towards fast and robust ICP. Here I combine many
% of the proposed variants into a single implementation to make ICP a
% practical tool for matching, pose refinement, SLAM etc.
% The the details are explained in more detailed in ICP.pdf, but... |
github | petteriTeikari/twoPhotonVessels-master | get_transform_mat.m | .m | twoPhotonVessels-master/3rdParty/fastICP/get_transform_mat.m | 445 | utf_8 | 3c0b6b8fd045820c164ac0cbb4181494 |
% Given the parameters as [\theta_x, \theta_y, \theta_z, t_x, t_y, t_z]
% Returns the pose matrix [R | t]
% Author: Tolga Birdal
%
function M=get_transform_mat(par)
r=par(1:3);
t=par(4:6);
Rx=[1 0 0 ;
0 cos(r(1)) -sin(r(1)) ;
0 sin(r(1)) cos(r(1)) ];
Ry=[cos(r(2)) 0 sin(r(2)) ;
0 1 0;
... |
github | petteriTeikari/twoPhotonVessels-master | get_duplicates.m | .m | twoPhotonVessels-master/3rdParty/fastICP/get_duplicates.m | 372 | utf_8 | 208ef7628b2da56c142c5143d8c491de |
% Returns the duplicates of a vector
%
% Author: Tolga Birdal
function duplicates = get_duplicates(X)
%[uniqueX i j] = unique(X,'first');
% duplicates = 1:length(X);
% duplicates(i) = [];
%duplicates = find(not(ismember(1:numel(X),i)));
uniqueX = unique(X);
countOfX = hist(X,uniqueX);
index = (countOfX~=... |
github | petteriTeikari/twoPhotonVessels-master | test_icp_p_pl.m | .m | twoPhotonVessels-master/3rdParty/fastICP/test_icp_p_pl.m | 1,712 | utf_8 | 7948258767066973147535ac14b50d03 |
% Test function for efficient ICP registration
% Author: Tolga Birdal
function []=test_icp_p_pl()
close all;
% Generate a tough random transformation
t=[0.1,1.2,1.1];
R1 = deg2rad(14);
R2 = deg2rad(23);
R3 = deg2rad(-37);
x=[R1 R2 R3 t];
PoseGT = get_transform_mat(x);
disp('Ground truth pose: ');
Po... |
github | petteriTeikari/twoPhotonVessels-master | sample_pc_uniform.m | .m | twoPhotonVessels-master/3rdParty/fastICP/sample_pc_uniform.m | 325 | utf_8 | 49b10c7bc3417a234325ba4d8818b6bc |
% by Tolga Birdal
% Uniform sampling of point clouds
function [SrcSample, SrcSampleNormals]=sample_pc_uniform(Src, NormalsSrc, numPoints)
n = length(Src);
% Really sample them.
sampledIndices=1:fix(n/numPoints):n;
SrcSample = Src(sampledIndices, :);
SrcSampleNormals = NormalsSrc(sampledIndices, :);
... |
github | petteriTeikari/twoPhotonVessels-master | ICP_finite.m | .m | twoPhotonVessels-master/3rdParty/fastICP/ICP_finite.m | 13,545 | utf_8 | 8ef62873a65267fd922b3fec50813297 | function [Points_Moved,M]=ICP_finite(Points_Static, Points_Moving, Options)
% This function ICP_FINITE is an kind of Iterative Closest Point
% registration algorithm for point clouds (vertice data) using finite
% difference methods.
%
% Normal ICP solves translation and rotation with analytical equations.
% ... |
github | petteriTeikari/twoPhotonVessels-master | Poisson_denoising_Anscombe_exact_unbiased_inverse.m | .m | twoPhotonVessels-master/3rdParty/invansc_v203/Poisson_denoising_Anscombe_exact_unbiased_inverse.m | 4,285 | UNKNOWN | 3d7174487bb1a68da5feb16839dbee81 | % Denoise Poisson images using the Anscombe variance-stabilizing transformation, BM3D filter, and the exact unbiased inverse of the Anscombe transformation
%
% [y_hat, PSNR_y_hat, NMISE_y_hat] = Poisson_denoising_Anscombe_exact_unbiased_inverse(noisy, original)
%
% the input D is the filtered (e.g., denoised) s... |
github | petteriTeikari/twoPhotonVessels-master | qslim.m | .m | twoPhotonVessels-master/3rdParty/ToolboxGraph/qslim.m | 13,152 | utf_8 | 2ab54ac7408e720642cbe21d8b6927bd | function [NFV,smf_fname] = qslim(FV,varargin);
%QSLIM - Mesh simplification, wrapper function for Garland's QSLIM executable program
% function [NFV,smf_fname] = qslim(FV,varargin);
% varargin should be entered in pairs '<option>','<arg>'.
% Valid pairs used in this wrapper are:
%
% '-t', <n>
%
% Specify the desired... |
github | petteriTeikari/twoPhotonVessels-master | perform_triangle_flipping.m | .m | twoPhotonVessels-master/3rdParty/ToolboxGraph/perform_triangle_flipping.m | 1,848 | utf_8 | b6a78203795416882735031895a76703 | function face = perform_triangle_flipping(face, flips, options)
% perform_triangle_flipping - apply a sequence of flips to a triangulation
%
% face = perform_triangle_flipping(face, flips, options);
%
% Flip that are not topologically valid (either on a boundary edge or a
% flip that creates a double face) are s... |
github | petteriTeikari/twoPhotonVessels-master | perform_point_picking.m | .m | twoPhotonVessels-master/3rdParty/ToolboxGraph/perform_point_picking.m | 4,121 | utf_8 | 9c43a474845c0bc92e5d215f6eda9a88 | function perform_point_picking( PointCloud, face )
% function perform_point_picking( PointCloud, face );
%
% This function shows a 3D point cloud or a mesh and lets the user click select one
% of the points by clicking on it. The selected point will be highlighted
% and its index in the point cloud will be... |
github | petteriTeikari/twoPhotonVessels-master | select3d.m | .m | twoPhotonVessels-master/3rdParty/ToolboxGraph/select3d.m | 10,864 | utf_8 | 64f6b58cf8db75c3508f68035be9892e | function [pout, vout, viout, facevout, faceiout] = select3d(obj)
%SELECT3D(H) Determines the selected point in 3-D data space.
% P = SELECT3D determines the point, P, in data space corresponding
% to the current selection position. P is a point on the first
% patch or surface face intersected along the selection ... |
github | petteriTeikari/twoPhotonVessels-master | compute_parameterization.m | .m | twoPhotonVessels-master/3rdParty/ToolboxGraph/compute_parameterization.m | 7,948 | utf_8 | ccbb3294b8723d824f8bfa35c4ea64dc | function vertex1 = compute_parameterization(vertex,face, options)
% compute_parameterization - compute a planar parameterization
%
% vertex1 = compute_parameterization(vertex,face, options);
%
% options.method can be:
% 'parameterization': solve classical parameterization, the boundary
% is... |
github | petteriTeikari/twoPhotonVessels-master | perform_dijkstra_propagation_old.m | .m | twoPhotonVessels-master/3rdParty/ToolboxGraph/perform_dijkstra_propagation_old.m | 5,116 | utf_8 | 28fc1b6f28ff90c69f6e7c7330aaa33f | function D = perform_dijkstra_propagation_old( G , S )
% dijkstra - Find shortest paths in graphs
%
% D = dijkstra_fast( G , S );
%
% use the full or sparse matrix G in which
% an entry (i,j) represents the arc length between nodes i and j in a
% graph. In a full matrix, the value INF represents the abse... |
github | petteriTeikari/twoPhotonVessels-master | compute_boundary.m | .m | twoPhotonVessels-master/3rdParty/ToolboxGraph/compute_boundary.m | 1,951 | utf_8 | a1d4f16ccb164b5d4d3dded2507bbee2 | function boundary=compute_boundary(face, options)
% compute_boundary - compute the vertices on the boundary of a 3D mesh
%
% boundary=compute_boundary(face);
%
% Copyright (c) 2007 Gabriel Peyre
options.null = 0;
verb = getoptions(options, 'verb', 1);
if size(face,1)<size(face,2)
face=face';
end... |
github | petteriTeikari/twoPhotonVessels-master | compute_geometric_laplacian.m | .m | twoPhotonVessels-master/3rdParty/ToolboxGraph/compute_geometric_laplacian.m | 5,760 | utf_8 | b6c0f7f8acdbb0c203c5f1a297957760 | function L = compute_geometric_laplacian(vertex,face,type)
% compute_geometric_laplacian - return a laplacian
% of a given triangulation (can be combinatorial or geometric).
%
% L = compute_geometric_laplacian(vertex,face,type);
%
% Type is either :
% - 'combinatorial' : combinatorial laplacian, d... |
github | petteriTeikari/twoPhotonVessels-master | check_face_vertex.m | .m | twoPhotonVessels-master/3rdParty/ToolboxGraph/check_face_vertex.m | 669 | utf_8 | c940a837f5afef7c3a7f7aed3aff9f7a | function [vertex,face] = check_face_vertex(vertex,face, options)
% check_face_vertex - check that vertices and faces have the correct size
%
% [vertex,face] = check_face_vertex(vertex,face);
%
% Copyright (c) 2007 Gabriel Peyre
vertex = check_size(vertex,2,4);
face = check_size(face,3,4);
%%%%%%%%%%%%%%%%%%%%%%%... |
github | petteriTeikari/twoPhotonVessels-master | plot_graph.m | .m | twoPhotonVessels-master/3rdParty/ToolboxGraph/plot_graph.m | 2,140 | utf_8 | 337033b66fe405903639bcac59c2b34d | function h = plot_graph(A,xy, options)
% plot_graph - display a 2D or 3D graph.
%
% plot_graph(A,xy, options);
%
% options.col set the display (e.g. 'k.-')
%
% Copyright (c) 2006 Gabriel Peyre
if size(xy,1)>size(xy,2)
xy = xy';
end
if nargin<3
options.null = 0;
end
if not(isstruct(options))
col = op... |
github | petteriTeikari/twoPhotonVessels-master | perform_delaunay_flipping.m | .m | twoPhotonVessels-master/3rdParty/ToolboxGraph/perform_delaunay_flipping.m | 2,420 | utf_8 | 7c5e250e94e9e69d99c556c805b4d2fe | function [face, flips, flipsinv] = perform_delaunay_flipping(vertex,face,options)
% perform_delaunay_flipping - compute Dalaunay triangulation via flipping
%
% [face1, flips, flipsinv] = perform_delaunay_flipping(vertex,face,options);
%
% Set options.display_flips = 1 for graphical display.
%
% face is turned in... |
github | petteriTeikari/twoPhotonVessels-master | check_incircle_edge.m | .m | twoPhotonVessels-master/3rdParty/ToolboxGraph/check_incircle_edge.m | 1,633 | utf_8 | dca2fc799d9cf120df9156a15c47b5fa | function ic = check_incircle_edge(vertex, face, edge)
% check_incicle_edge - compute "empty circle" property for a set of edges
%
% ic = check_incicle_edge(vertex,face, edge);
%
% ic(i)==1 if edge(:,i) is delaunay valid (boundary or empty circles or non convex).
% It thus should be flipped if ic(i)==0.
%
% Cop... |
github | petteriTeikari/twoPhotonVessels-master | perform_faces_reorientation.m | .m | twoPhotonVessels-master/3rdParty/ToolboxGraph/perform_faces_reorientation.m | 2,816 | utf_8 | 2cf3d5c1ad6ea271b524352db5492c2c | function faces = perform_faces_reorientation(vertex,faces, options)
% perform_faces_reorientation - reorient the faces with respect to the center of the mesh
%
% faces = perform_faces_reorientation(vertex,faces, options);
%
% try to find a consistant reorientation for faces of a mesh.
%
% if options.method = 'fast... |
github | petteriTeikari/twoPhotonVessels-master | plot_spherical_triangulation.m | .m | twoPhotonVessels-master/3rdParty/ToolboxGraph/plot_spherical_triangulation.m | 1,397 | utf_8 | fde5d8ffb7898bb232257895ced3d53d | function plot_spherical_triangulation(svertex,face, options)
% plot_spherical_triangulation - display a nice spherical triangulation
%
% plot_spherical_triangulation(svertex,face,options);
%
% Copyright (c) 2008 Gabriel Peyre
options.null = 0;
hold on;
% draw a background sphere
[X,Y,Z] = sphere(30);
surf(X,Y... |
github | petteriTeikari/twoPhotonVessels-master | compute_mesh_weight.m | .m | twoPhotonVessels-master/3rdParty/ToolboxGraph/compute_mesh_weight.m | 2,783 | utf_8 | 435dabe64ab50ca5bf2c467bcbad6ab8 | function W = compute_mesh_weight(vertex,face,type,options)
% compute_mesh_weight - compute a weight matrix
%
% W = compute_mesh_weight(vertex,face,type,options);
%
% W is sparse weight matrix and W(i,j)=0 is vertex i and vertex j are not
% connected in the mesh.
%
% type is either
% 'combinatorial': W(i... |
github | petteriTeikari/twoPhotonVessels-master | perform_analysis_regularization.m | .m | twoPhotonVessels-master/3rdParty/ToolboxGraph/toolbox/perform_analysis_regularization.m | 2,585 | utf_8 | c15e65a8b4b77823cd42e992ac708563 | function [g,g_list,E] = perform_analysis_regularization(f, G, options)
% perform_analysis_regularization - perform a sparse regularization
%
% [g,g_list,E] = perform_analysis_regularization(f, A, options);
%
% Method solves, given f of length n, for
% min_g E(g) = 1/2*|f-g|^2 + lambda * |A*g|_1
% where A is a... |
github | petteriTeikari/twoPhotonVessels-master | meshresample.m | .m | twoPhotonVessels-master/3rdParty/iso2mesh/meshresample.m | 1,665 | utf_8 | a84fc4c4bfcb7894e079f34b8a9c6f9d | function [node,elem]=meshresample(v,f,keepratio)
%
% [node,elem]=meshresample(v,f,keepratio)
%
% resample mesh using CGAL mesh simplification utility
%
% author: Qianqian Fang (fangq<at> nmr.mgh.harvard.edu)
% date: 2007/11/12
%
% input:
% v: list of nodes
% f: list of surface elements (each row for each triangle... |
github | petteriTeikari/twoPhotonVessels-master | savejson.m | .m | twoPhotonVessels-master/3rdParty/iso2mesh/savejson.m | 14,350 | utf_8 | 9c4adfaa1058e68cbdad0f92b347d35a | function json=savejson(rootname,obj,varargin)
%
% json=savejson(rootname,obj,filename)
% or
% json=savejson(rootname,obj,opt)
% json=savejson(rootname,obj,'param1',value1,'param2',value2,...)
%
% convert a MATLAB object (cell, struct or array) into a JSON (JavaScript
% Object Notation) string
%
% author: Qianqian Fa... |
github | petteriTeikari/twoPhotonVessels-master | loadjson.m | .m | twoPhotonVessels-master/3rdParty/iso2mesh/loadjson.m | 16,269 | ibm852 | 137087090c6ffe8c5d3afd55deed4a99 | function data = loadjson(fname,varargin)
%
% data=loadjson(fname,opt)
% or
% data=loadjson(fname,'param1',value1,'param2',value2,...)
%
% parse a JSON (JavaScript Object Notation) file or string
%
% authors:Qianqian Fang (fangq<at> nmr.mgh.harvard.edu)
% date: 2011/09/09
% Nedialko Krouchev: http:... |
github | petteriTeikari/twoPhotonVessels-master | surfaceclean.m | .m | twoPhotonVessels-master/3rdParty/iso2mesh/surfaceclean.m | 1,015 | utf_8 | 7e36bba6243ce6e4c9645e4599663dfe | function f=surfaceclean(f,v)
%
% f=surfaceclean(f,v)
%
% remove surface patches that are located inside
% the bounding box faces
%
% author: Qianqian Fang (fangq<at> nmr.mgh.harvard.edu)
% date: 2008/04/08
%
% input:
% v: surface node list, dimension (nn,3)
% f: surface face element list, dime... |
github | petteriTeikari/twoPhotonVessels-master | plotsurf.m | .m | twoPhotonVessels-master/3rdParty/iso2mesh/plotsurf.m | 3,890 | utf_8 | cb1cd7f508119c87ac12155d80e72f2d | function hm=plotsurf(node,face,varargin)
%
% hm=plotsurf(node,face,opt)
%
% plot 3D surface meshes
%
% author: Qianqian Fang <fangq at nmr.mgh.harvard.edu>
%
% input:
% node: node coordinates, dimension (nn,3); if node has a
% 4th column, it will be used to set the color at each node.
% face: tr... |
github | petteriTeikari/twoPhotonVessels-master | readoff.m | .m | twoPhotonVessels-master/3rdParty/iso2mesh/readoff.m | 1,446 | utf_8 | aece4a72343e6bece72b82ced7e8fbe6 | function [node,elem]=readoff(fname)
%
% [node,elem]=readoff(fname)
%
% read Geomview Object File Format (OFF)
%
% author: Qianqian Fang (fangq<at> nmr.mgh.harvard.edu)
% date: 2008/03/28
%
% input:
% fname: name of the OFF data file
%
% output:
% node: node coordinates of the mesh
% elem: list of elements of t... |
github | petteriTeikari/twoPhotonVessels-master | cp_apr.m | .m | twoPhotonVessels-master/3rdParty/tensor_toolbox/cp_apr.m | 61,623 | utf_8 | 2c608de3c714878f317a9beff7fca017 | function [M, Minit, output] = cp_apr(X, R, varargin)
%CP_APR Compute nonnegative CP with alternating Poisson regression.
%
% M = CP_APR(X, R) computes an estimate of the best rank-R CP model of a
% nonnegative tensor X using an alternating Poisson regression. This is
% most appropriate for sparse count data (i.e.... |
github | petteriTeikari/twoPhotonVessels-master | export_data.m | .m | twoPhotonVessels-master/3rdParty/tensor_toolbox/export_data.m | 3,457 | utf_8 | d3f06ab350afa3366c85edd195d6ef41 | function export_data(A, fname)
%EXPORT_DATA Export tensor-related data to a file.
%
% EXPORT(A,FNAME) exports object A to the file named FNAME in plain ASCII
% text. Export currently supports exporting the following data types:
%
% - tensor
% - sptensor
% - matrix
%
% In the case of a ... |
github | petteriTeikari/twoPhotonVessels-master | teneye.m | .m | twoPhotonVessels-master/3rdParty/tensor_toolbox/teneye.m | 14,333 | utf_8 | a4443de3ac394a33b8ee5e6efcc6c186 | function A = teneye(M,N)
%TENEYE Create identity tensor of specified size.
%
% We say E is the "identity tensor" if TTSV(E,X,-1) = X for all X such
% that NORM(X) = 1.
%
% TENEYE(M,N) returns a (dense) identity tensor of order M and size N.
% The identity tensor only exists when M is even and returns an ... |
github | petteriTeikari/twoPhotonVessels-master | eig_sshopm.m | .m | twoPhotonVessels-master/3rdParty/tensor_toolbox/eig_sshopm.m | 6,061 | utf_8 | 1a26fcde8a04addcb33888337d3544b6 | function [lambda,x,flag,its,x0] = eig_sshopm(A,varargin)
%EIG_SSHOPM Shifted power method for finding real eigenpair of real tensor.
%
% [LAMBDA,X]=EIG_SSHOPM(A) finds an eigenvalue (LAMBDA) and eigenvector
% (X) for the real tensor A such that Ax^{m-1} = lambda*x.
%
% [LAMBDA,X]=EIG_SSHOPM(A,parameter,valu... |
github | petteriTeikari/twoPhotonVessels-master | cp_nmu.m | .m | twoPhotonVessels-master/3rdParty/tensor_toolbox/cp_nmu.m | 4,976 | utf_8 | 94d539037219c5c137f98b759143ad81 | function [P,Uinit] = cp_nmu(X,R,opts)
%CP_NMU Compute nonnegative CP with multiplicative updates.
%
% P = CP_NMU(X,R) computes an estimate of the best rank-R PARAFAC
% model of a tensor X with nonnegative constraints on the factors.
% This version uses the Lee & Seung multiplicative updates from
% their NMF alg... |
github | petteriTeikari/twoPhotonVessels-master | eig_geap.m | .m | twoPhotonVessels-master/3rdParty/tensor_toolbox/eig_geap.m | 10,591 | utf_8 | 83ee5c38064ef55a82be4fac969c7010 | function [varargout] = eig_geap(A,B,varargin)
%EIG_GEAP Shifted power method for generalized tensor eigenproblem.
%
% [LAMBDA,X] = EIG_GEAP(A,B) finds an eigenvalue (LAMBDA) and eigenvector
% (X) for the real tensor A and the positive definite tensor B such that
% Ax^{m-1} = lambda * Bx^{m-1}.
%
% [LAMB... |
github | petteriTeikari/twoPhotonVessels-master | import_data.m | .m | twoPhotonVessels-master/3rdParty/tensor_toolbox/import_data.m | 3,172 | utf_8 | 4eb0c41bdec17ef5ac822ae082a262c5 | function A = import_data(fname)
%IMPORT_DATA Import tensor-related data to a file.
%
% A = IMPORT_DATA(FNAME) imports an object A from the file named FNAME.
% The supported data types and formatting of the file are explained in
% EXPORT_DATA.
%
% See also TENSOR, EXPORT_DATA
%
%MATLAB Tensor Toolbox.
... |
github | petteriTeikari/twoPhotonVessels-master | create_problem.m | .m | twoPhotonVessels-master/3rdParty/tensor_toolbox/create_problem.m | 15,796 | utf_8 | 789412e9f6787bcf6819eec15d3c2103 | function [info,params] = create_problem(varargin)
%CREATE_PROBLEM Create test problems for tensor factorizations.
%
% INFO = CREATE_PROBLEM('Param',value,...) creates a tensor factorization
% test problem. It generates a solution corresponding to a ktensor or a
% ttensor, and then it generates an example dat... |
github | petteriTeikari/twoPhotonVessels-master | subsasgn.m | .m | twoPhotonVessels-master/3rdParty/tensor_toolbox/@sptensor/subsasgn.m | 12,129 | utf_8 | 359895987eff5a90ca8d4121acfd37ea | function t = subsasgn(t,s,rhs)
%SUBSASGN Subscripted assignment for sparse tensor.
%
% We can assign elements to a sptensor in three ways.
%
% Case 1: X(R1,R2,...,RN) = Y, in which case we replace the
% rectangular subtensor (or single element) specified by the ranges
% R1,...,RN with Y. The right-hand-side can... |
github | petteriTeikari/twoPhotonVessels-master | sptensor.m | .m | twoPhotonVessels-master/3rdParty/tensor_toolbox/@sptensor/sptensor.m | 10,151 | utf_8 | 562cc6d528208a2aa012b6ca2b4ca664 | %SPTENSOR Class for sparse tensors.
%
%SPTENSOR Methods:
% and - Logical AND (&) for sptensors.
% collapse - Collapse sparse tensor along specified dimensions.
% contract - Contract sparse tensor along two dimensions (array trace).
% ctranspose - is not defined for sparse tensors.
% disp - Co... |
github | petteriTeikari/twoPhotonVessels-master | renumber.m | .m | twoPhotonVessels-master/3rdParty/tensor_toolbox/@sptensor/private/renumber.m | 1,606 | utf_8 | e874a514c74cccd20e6921485ca60ac5 | function [newsubs, newsz] = renumber(subs, sz, range)
%RENUMBER indices for sptensor subsref
%
% [NEWSUBS,NEWSZ] = RENUMBER(SUBS,SZ,RANGE) takes a set of
% original subscripts SUBS with entries from a tensor of size
% SZ. All the entries in SUBS are assumed to be within the
% specified RANGE. These subscripts are t... |
github | petteriTeikari/twoPhotonVessels-master | sptenmat.m | .m | twoPhotonVessels-master/3rdParty/tensor_toolbox/@sptenmat/sptenmat.m | 7,570 | utf_8 | 9fb606d8b0ae7a72a31162915f1a94fa | %SPTENMAT
%
%SPTENMAT Methods:
% aatx - Implicitly compute A * A' * x for sptenmat.
% disp - Command window display of a sptenmat.
% display - Command window display of a sptenmat.
% double - Convert a sptenmat to a sparse matrix.
% end - Last index of indexing expression for sptenmat.
% ful... |
github | petteriTeikari/twoPhotonVessels-master | ttensor.m | .m | twoPhotonVessels-master/3rdParty/tensor_toolbox/@ttensor/ttensor.m | 3,672 | utf_8 | 6053cf08055f763b2c54443e0e33d92b | %TTENSOR Class for Tucker tensors (decomposed).
%
%TTENSOR Methods:
% disp - Command window display of a ttensor.
% display - Command window display of a ttensor.
% double - Convert ttensor to double array.
% end - Last index of indexing expression for ttensor.
% full - Convert a ttensor ... |
github | petteriTeikari/twoPhotonVessels-master | tensor.m | .m | twoPhotonVessels-master/3rdParty/tensor_toolbox/@tensor/tensor.m | 6,418 | utf_8 | bb53a4e476272c2db71d813e27bc6831 | %TENSOR Class for dense tensors.
%
%TENSOR Methods:
% and - Logical AND (&) for tensors.
% collapse - Collapse tensor along specified dimensions.
% contract - Contract tensor along two dimensions (array trace).
% ctranspose - is not defined for tensors.
% disp - Command window display of... |
github | petteriTeikari/twoPhotonVessels-master | tenmat.m | .m | twoPhotonVessels-master/3rdParty/tensor_toolbox/@tenmat/tenmat.m | 6,383 | utf_8 | eb8b4b1a34374db09851406a99970cad | %TENMAT Store tensor as a matrix.
%
%TENMAT Methods:
% ctranspose - Complex conjugate transpose for tenmat.
% disp - Command window display of a matricized tensor (tenmat).
% display - Command window display of a tenmat.
% double - Convert tenmat to double array.
% end - Last index of inde... |
github | petteriTeikari/twoPhotonVessels-master | tucker_me.m | .m | twoPhotonVessels-master/3rdParty/tensor_toolbox/met/tucker_me.m | 4,560 | utf_8 | 3216bec3b59aecd3b4a11c8e4c559039 | function [T, max_mem, Uinit] = tucker_me(X, R, esz, opts)
%TUCKER_ME Memory-efficient Tucker higher-order orthogonal iteration.
%
% T = TUCKER_ME(X,R,ESZ) computes the best rank(R1,R2,..,Rn)
% approximation of tensor X, according to the specified dimensions
% in vector R. ESZ specifies the number of dimensions th... |
github | petteriTeikari/twoPhotonVessels-master | tucker_me_test.m | .m | twoPhotonVessels-master/3rdParty/tensor_toolbox/met/tucker_me_test.m | 3,079 | utf_8 | 7cd5d5bf56ea1d8a82ef189d3c71d564 | function tucker_me_test
%TUCKER_ME_TEST Very simple tests of tucker_me.
% Code by Tamara Kolda and Jimeng Sun, 2008.
%
% Based on the paper:
% T. G. Kolda and J. Sun. Scalable Tensor Decompositions for Multi-aspect
% Data Mining. In: ICDM 2008: Proceedings of the 8th IEEE International
% Conference on Data M... |
github | petteriTeikari/twoPhotonVessels-master | ttm_me.m | .m | twoPhotonVessels-master/3rdParty/tensor_toolbox/met/ttm_me.m | 4,085 | utf_8 | 241d426fee6a1d228fd2ca6c01db66b1 | function Y = ttm_me(X, U, edims, sdims, tflag)
%TTM_ME Memory-efficient sptensor times matrix.
%
% Y = TTM_ME(X, U, EDIMS, SDIMS, TFLAG) handles some dimensions
% elementwise and others in the standard way. Here, X is a sparse tensor
% (sptensor), U is a cell array of matrices of length ndims(X),
% EDIMS speci... |
github | petteriTeikari/twoPhotonVessels-master | ktensor.m | .m | twoPhotonVessels-master/3rdParty/tensor_toolbox/@ktensor/ktensor.m | 4,722 | utf_8 | d4bd992e21b3b4ffc16eaa7cf3e2741e | %KTENSOR Class for Kruskal tensors (decomposed).
%
%KTENSOR Methods:
% arrange - Arranges the rank-1 components of a ktensor.
% datadisp - Special display of a ktensor.
% disp - Command window display for a ktensor.
% display - Command window display for a ktensor.
% double - Conve... |
github | petteriTeikari/twoPhotonVessels-master | fixsigns.m | .m | twoPhotonVessels-master/3rdParty/tensor_toolbox/@ktensor/fixsigns.m | 3,162 | utf_8 | 179e4f84ad6028d62e3405c690654221 | function K = fixsigns(K,K0)
%FIXSIGNS Fix sign ambiguity of a ktensor.
%
% K = FIXSIGNS(K) makes it so that the largest magnitude entries for
% each vector in each factor of K are positive, provided that the
% sign on *pairs* of vectors in a rank-1 component can be flipped.
%
% K = FIXSIGNS(K,K0) returns a vers... |
github | petteriTeikari/twoPhotonVessels-master | datadisp.m | .m | twoPhotonVessels-master/3rdParty/tensor_toolbox/@ktensor/datadisp.m | 3,162 | utf_8 | f45b3fed42e7efb5d8211adc5c34a980 | function datadisp(T, dimlabels, opts)
%DATADISP Special display of a ktensor.
%
% DATADISP(T,LABELS) displays the largest positive entries of each rank-1
% factor of T using the corresponding labels. LABELS is a cell array of
% size ndims(T) such that LABELS{n} is a string cell array of length
% size(T,n).
%
%... |
github | petteriTeikari/twoPhotonVessels-master | bfCheckJavaPath.m | .m | twoPhotonVessels-master/3rdParty/bfmatlab/bfCheckJavaPath.m | 3,238 | utf_8 | df2438a6172c5e934df6ce23d46fd2c8 | 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 | petteriTeikari/twoPhotonVessels-master | createMinimalOMEXMLMetadata.m | .m | twoPhotonVessels-master/3rdParty/bfmatlab/createMinimalOMEXMLMetadata.m | 3,882 | utf_8 | 79ebcee15e7bbba35640e503048ac290 | 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 | petteriTeikari/twoPhotonVessels-master | bfsave.m | .m | twoPhotonVessels-master/3rdParty/bfmatlab/bfsave.m | 4,874 | utf_8 | de4d1742bd03d4e2ba2c0dacd0e4ff19 | 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 | petteriTeikari/twoPhotonVessels-master | helper.m | .m | twoPhotonVessels-master/3rdParty/BM4D/helper.m | 19,783 | utf_8 | e925f278ffb9fd59a36f47a81a54555e | classdef helper
methods (Static)
function [ map ] = getNoiseMap( y, noise_factor)
% noise modulation field
map = ones(3,3,3);
map(2,2,2) = noise_factor;
s = size(y);
[x1,y1,z1] = meshgrid(1:3,1:3,1:3);
[x2,y2,z2] = meshgrid(1:2... |
github | petteriTeikari/twoPhotonVessels-master | ssim_index3d.m | .m | twoPhotonVessels-master/3rdParty/BM4D/ssim_index3d.m | 6,644 | utf_8 | cc85d5bfd739bdec0e7908be53b14520 | function [mssim, ssim_map] = ssim_index3d(img1, img2, sw, ind)
%========================================================================
%SSIM Index, Version 1.0
%Copyright(c) 2003 Zhou Wang
%All Rights Reserved.
%
%The author was with Howard Hughes Medical Institute, and Laboratory
%for Computational Vision a... |
github | petteriTeikari/twoPhotonVessels-master | bm4d.m | .m | twoPhotonVessels-master/3rdParty/BM4D/bm4d.m | 13,407 | utf_8 | 9c882e6d77bf576d81da0a1600779452 | function [y_est, sigma_est] = bm4d(z, distribution, sigma, profile, do_wiener, verbose)
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% BM4D is an algorithm for attenuation of Gaussian or Rician noise in
% volumetric data. This algorithm reproduces the results from the articles:
%
% ... |
github | petteriTeikari/twoPhotonVessels-master | MarchingCubes.m | .m | twoPhotonVessels-master/3rdParty/marchingCubes/MarchingCubes.m | 23,430 | utf_8 | 6a388ccbe7dabcadeef466354d81d25d | function [F,V,col] = MarchingCubes(x,y,z,c,iso,colors)
% [F,V] = MarchingCubes(X,Y,Z,C,ISO)
% [F,V,COL] = MarchingCubes(X,Y,Z,C,ISO,COLORS)
%
% Use marching cubes algorithm to compute a triangulated mesh of the
% isosurface within the 3D matrix of scalar values C at isosurface value
% ISO. The 3D matrices (X,Y,Z) re... |
github | petteriTeikari/twoPhotonVessels-master | oofofa2.m | .m | twoPhotonVessels-master/3rdParty/OOF/oofofa2.m | 8,016 | UNKNOWN | 2517a933b16ccd26d058488afd65e2ca | % 2D Implementation of the OOF (Optimally Oriented Flux) - OFA (oriented flux antisymmetry)
% vesselness operator for enhancement of tubular (i.e. vessels) structures
% proposed by Max K. Law and ACS Chung (http://www.cse.ust.hk/~maxlawwk)
% Law MWK, Chung ACS. 2008.
% Three Dimensional Curvilinear Structure De... |
github | petteriTeikari/twoPhotonVessels-master | eigenvaluefield33.m | .m | twoPhotonVessels-master/3rdParty/OOF/eigenvaluefield33.m | 3,458 | utf_8 | 2582f897ae36dfcee65769ab18b761e5 | % Calculate the eigenvalues of massive 3x3 real symmetric matrices.
% Computation is based on matrix operation and GPU computation is
% supported.
% Syntax:
% [eigenvalue1,eigenvalue2,eigenvalue3] = eigenvaluefield33( a11, a12, a13, a22, a23, a33)
% a11, a12, a13, a22, a23 and a33 specify the symmetric 3x3 real s... |
github | petteriTeikari/twoPhotonVessels-master | oof3response.m | .m | twoPhotonVessels-master/3rdParty/OOF/oof3response.m | 16,392 | utf_8 | cf98c023a1dfa262de0c8b0dcf588641 | % Compute the analytical 3D multi-radii optimally oriented flux responses
% for curvilinear structure analysis. Implementation based on,
% [1] M.W.K. Law and A.C.S. Chung, ``Three Dimensional Curvilinear
% Structure Detection using Optimally Oriented Flux'', ECCV 2008, pp.
% 368--382.
% [2] Max W. K. Law et al.,... |
github | petteriTeikari/twoPhotonVessels-master | coormatrix.m | .m | twoPhotonVessels-master/3rdParty/OOF/coormatrix.m | 768 | utf_8 | 95ede39d5f85c131dac3d74d6f85fde1 | % varargout=coorMatrix(dimension)
% The dimension is a vector to specify the size of the returned coordinate
% matrices. The number of output argument is equals to the dimensionality
% of the vector "dimension". All the dimension is starting from "1"
function varargout=coormatrix(dimension)
dim=length(dimension);... |
github | petteriTeikari/twoPhotonVessels-master | buildVigraExtensions.m | .m | twoPhotonVessels-master/3rdParty/vigraMatlab/buildVigraExtensions.m | 8,950 | utf_8 | 2698ec33bd2ff02d45b9b3b51aa98ce1 | % buildVigraExtensions(OUTDIR, TARGET, options)
%
% Makefile that compiles the VIGRA MEX functions and installs them into the specified
% OUTDIR, along with corresponding documentation.
% Afterward installation, you may call
%
% help vigraIndex
%
% to get a list of the installed functions.
%
% Arguments
% - OUT... |
github | petteriTeikari/twoPhotonVessels-master | testVigraExtensions.m | .m | twoPhotonVessels-master/3rdParty/vigraMatlab/testVigraExtensions.m | 20,681 | utf_8 | 8e43115eb2eee841aac4ed24015ded3b | function testVigraExtensions()
% unit tests for the VIGRA-MATLAB gateway ($VIGRA/include/vigra/matlab.hxx)
%
% call testVigraExtensions() in the source directory to compile and run tests
%
disp('Compiling VIGRA test programms...');
buildVigraExtensions('test-routines', 'test')
disp('Done. Running tests... |
github | petteriTeikari/twoPhotonVessels-master | stlwrite.m | .m | twoPhotonVessels-master/3rdParty/stlwrite/stlwrite.m | 10,284 | utf_8 | 53dc2b4162d4f781879a976dc5c2e72c | function stlwrite(filename, varargin)
%STLWRITE Write STL file from patch or surface data.
%
% STLWRITE(FILE, FV) writes a stereolithography (STL) file to FILE for a
% triangulated patch defined by FV (a structure with fields 'vertices'
% and 'faces').
%
% STLWRITE(FILE, FACES, VERTICES) takes faces an... |
github | F-Dominguez/Diffusion-Matlab-Code-master | Init_Pop.m | .m | Diffusion-Matlab-Code-master/Init_Pop.m | 3,620 | utf_8 | 7c14180c63ca98033547c08284248e73 | %************************************************************
%* Init_Pop
%*
%* Generation of General Adjacency Matrix and Population Vector.
%* By Francisco Dominguez ... |
github | F-Dominguez/Diffusion-Matlab-Code-master | Variation_MP.m | .m | Diffusion-Matlab-Code-master/Variation_MP.m | 5,022 | utf_8 | 9b46e191d587ad940943c922a399b87a | %*****************************************************
%* Variation_MP *
%* Nested 'for' loop for every combination of values *
%* This is fed to Init_Pop which creates the Nvect *
%* and Adjacency Matrix, and to Evolve_MPopulation *
%* which carries out the evolution. ... |
github | F-Dominguez/Diffusion-Matlab-Code-master | Variation_Perm.m | .m | Diffusion-Matlab-Code-master/Variation_Perm.m | 2,172 | utf_8 | 7bbc9663114274920ef2615f5def0bfe | %*************************************************
%* Variation_Perm *
%* *
%* Calculation and reformatting of all possible *
%* permutations asked in the program. *
%* By Francisco Dominguez *
%*************... |
github | F-Dominguez/Diffusion-Matlab-Code-master | Find_Perm_Data.m | .m | Diffusion-Matlab-Code-master/Find_Perm_Data.m | 2,252 | utf_8 | de9bfe45989487ffae83a2fe0cdf53c6 | %*****************************************************
%* Find_Perm_Data *
%* Data Ordering and formatting for plot generation. *
%* By Francisco Dominguez *
%*****************************************************
%In order to easily access any values of the... |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.