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github | vigente/gerardus-master | nlopt_minimize_constrained.m | .m | gerardus-master/matlab/ThirdPartyToolbox/OptiToolbox/Solvers/nlopt/distribution/nlopt_minimize_constrained.m | 5,213 | utf_8 | 8302b2f00438cf154ef1a9d032d1e983 | % Usage: [xopt, fmin, retcode] = nlopt_minimize_constrained
% (algorithm, f, f_data,
% fc, fc_data, lb, ub,
% xinit, stop)
%
% Minimizes a nonlinear multivariable function f(x, f_data{:}), subjec... |
github | vigente/gerardus-master | nlopt_minimize.m | .m | gerardus-master/matlab/ThirdPartyToolbox/OptiToolbox/Solvers/nlopt/distribution/nlopt_minimize.m | 3,978 | utf_8 | f71b68688b460e0440ff89bdf086d2a7 | % Usage: [xopt, fmin, retcode] = nlopt_minimize(algorithm, f, f_data, lb, ub,
% xinit, stop)
%
% Minimizes a nonlinear multivariable function f(x, f_data{:}), where
% x is a row vector, returning the optimal x found (xopt) along with
% the minimum function value (fmin = f(x... |
github | vigente/gerardus-master | opti_dsdp.m | .m | gerardus-master/matlab/ThirdPartyToolbox/OptiToolbox/Solvers/dsdp/opti_dsdp.m | 4,931 | utf_8 | c3e16b226bb3bf5ccd1e83f657819ca0 | function [x,fval,exitflag,info] = opti_dsdp(f,A,b,lb,ub,sdcone,x0,opts)
%OPTI_DSDP Solve a SDP using DSDP [Primal Form]
%
% min f'*x subject to: A*x <= b
% x lb <= x <= ub
% X = F1*x1 + F2*x2 + ... + Fn*xn - F0
% ... |
github | vigente/gerardus-master | dvec.m | .m | gerardus-master/matlab/ThirdPartyToolbox/OptiToolbox/Solvers/dsdp/distribution/matlab/dvec.m | 882 | utf_8 | b51147f3aed8da781d28a3148c97e048 | %%*******************************************************************
%% Convert a square symmetric matrix to a vector
%% representation used by DSDP
%%
%% [V] = dvec(A)
%%
%% Input: A = square symmetric matrix. Lower triangular entries
%% are ignored.
%%
%% Output: V = column vector representing ... |
github | vigente/gerardus-master | doptions.m | .m | gerardus-master/matlab/ThirdPartyToolbox/OptiToolbox/Solvers/dsdp/distribution/matlab/doptions.m | 3,602 | utf_8 | 6832767b637503d8750fe3a52517ec7b | %*****************************************************************************
% DSDP5: Dual-Scaling Algorithm for Positive Semidefinite Programming
% Copyright (c) 2005 by
% S. J. Benson, Y. Ye
% Last modified: 05 Feb 2005
%*****************************************************************************
% [OPTIONS] = do... |
github | vigente/gerardus-master | readsdpt3.m | .m | gerardus-master/matlab/ThirdPartyToolbox/OptiToolbox/Solvers/dsdp/distribution/matlab/readsdpt3.m | 997 | utf_8 | 8fff579c72c8aecfbcd8bc092ad6f433 | %%*******************************************************************
%% Convert problem from SDPT3 format to DSDP format
%%
%% [AC,b] = readsdpt3(blk,A,C,b)
%%
%% Input: blk, A, C, b = data in SDPT3 format.
%%
%%
%% DSDP: version 5.0
%% Copyright (c) 2004 by
%% S. Benson Y. Ye
%% Last modified: 2 Jan 04
%%********... |
github | vigente/gerardus-master | dadotx.m | .m | gerardus-master/matlab/ThirdPartyToolbox/OptiToolbox/Solvers/dsdp/distribution/matlab/dadotx.m | 995 | utf_8 | e5ad1ddb6729c0e99b8d11d2ac4999ac | %%*******************************************************************
%% Apply the operators A to the matrix X. Each column
%% of A and X is the vector representation of a square symmetric
%% matrix.
%%
%% [v] = dadotx(A,X)
%%
%% Input: A = square symmetric matrices in DSDP dvec form
%% Input: X = square sym... |
github | vigente/gerardus-master | dsdp2.m | .m | gerardus-master/matlab/ThirdPartyToolbox/OptiToolbox/Solvers/dsdp/distribution/matlab/dsdp2.m | 1,938 | utf_8 | 835398c7b6c011d61cba258222bcc56f | %*****************************************************************************
% DSDP5: Dual Scaling Algorithm for Positive Semidefinite Programming
% Copyright (c) 2002 by
% S. J. Benson, Y. Ye
% Last modified: 20 January 2004
%*****************************************************************************
%
% Converts... |
github | vigente/gerardus-master | derror.m | .m | gerardus-master/matlab/ThirdPartyToolbox/OptiToolbox/Solvers/dsdp/distribution/matlab/derror.m | 3,044 | utf_8 | beb671787c7f19613a70b6b6b2b534b8 | %%*************************************************************************
%% Verify solution of DSDP solver by computing objective values and errors
%%
%% [pobj,dobj,err] = derror(STAT,y,X,b,AC)
%%
%% Input: AC = DSDP Constraint data
%% b = DSDP objective
%% X = DSDP solution matrices
%%... |
github | vigente/gerardus-master | dsdp4.m | .m | gerardus-master/matlab/ThirdPartyToolbox/OptiToolbox/Solvers/dsdp/distribution/matlab/dsdp4.m | 2,026 | utf_8 | e777af33d073d67908925673c7b31ec3 | %*****************************************************************************
% DSDP5: Dual Scaling Algorithm for Positive Semidefinite Programming
% Copyright (c) 2002 by
% S. J. Benson, Y. Ye
% Last modified: 20 January 2004
%*****************************************************************************
%
% Converts... |
github | vigente/gerardus-master | dmat.m | .m | gerardus-master/matlab/ThirdPartyToolbox/OptiToolbox/Solvers/dsdp/distribution/matlab/dmat.m | 886 | utf_8 | de5d49e9b8a56c756d139aa8c1d2d526 | %%*******************************************************************
%% Convert a vector matrix used by DSDP to a square symmetric matrix.
%%
%% [A] = dmat(V)
%%
%% Input: V = column vector representing upper triangle of a symmetric matrix.
%%
%% Output: A = square symmetric matrix
%%
%% See also: DVEC (its inve... |
github | vigente/gerardus-master | dsparse.m | .m | gerardus-master/matlab/ThirdPartyToolbox/OptiToolbox/Solvers/dsdp/distribution/matlab/dsparse.m | 2,085 | utf_8 | e4ca1b09e61a51c206eaff7c36354dd0 | %%*******************************************************************
%% Create a column vector representing a symmetric matrix.
%%
%% V = DSPARSE(i,j,s,m,n) uses the same arguments as SPARSE(i,j,s,m,n)
%%
%% However, this routine assumes the matrix will be symmetric, so
%% that n must equal m. The rows ... |
github | vigente/gerardus-master | nomadset.m | .m | gerardus-master/matlab/ThirdPartyToolbox/OptiToolbox/Solvers/nomad/nomadset.m | 17,749 | utf_8 | bef07073e563772eb31119455cc00d1f | function options = nomadset(varargin)
%NOMADSET Create or alter the options for Optimization with NOMAD
%
% options = nomadset('param1',value1,'param2',value2,...) creates an
% NOMAD options structure with the parameters 'param' set to their
% corresponding values in 'value'. Parameters not specified will be set to
... |
github | vigente/gerardus-master | opti_qsopt.m | .m | gerardus-master/matlab/ThirdPartyToolbox/OptiToolbox/Solvers/qsopt/opti_qsopt.m | 2,122 | utf_8 | d20f02d3ab501dd504a3275c02529c46 | function [x,fval,exitflag,info] = opti_qsopt(f,A,b,Aeq,beq,lb,ub,opts)
%OPTI_QSOPT Solve a LP using QSOPT
%
% [x,fval,exitflag,info] = opti_qsopt(f,A,b,Aeq,beq,lb,ub) solves the linear
% program min f'x where A,b are the inequality constraints, Aeq,beq are
% the equality constraints and lb,ub are the bounds.
%
% ... |
github | vigente/gerardus-master | nlp_HS.m | .m | gerardus-master/matlab/ThirdPartyToolbox/OptiToolbox/Test Problems/nlp_HS.m | 28,057 | utf_8 | c666d1feeb778a47af56997c10af7f9b | function [prob,sol,fmin] = nlp_HS(varargin)
%NLP_HS Return an OPTI NLP from the Hock-Schittkowski Collection
%
% prob = nlp_HS(no) return a pre-built optiprob of an HS problem no.
%
% [prob,sol,fmin] = nlp_HS(no) returns the optimum solution and function
% eval at the optimum
%
% no = nlp_HS() returns the numb... |
github | vigente/gerardus-master | nls_prob.m | .m | gerardus-master/matlab/ThirdPartyToolbox/OptiToolbox/Test Problems/nls_prob.m | 8,432 | utf_8 | ea46b85ceeda1a4dccc8962660aa4168 | function [prob,sol,fmin] = nls_prob(varargin)
%NLS_PROB Return an OPTI NLS
%
% prob = nls_prob(no) return a pre-built optiprob of a saved NLS.
%
% [prob,sol,fmin] = NLS_prob(no) returns the optimum solution and function
% eval at the optimum
%
% no = nls_prob() returns the number of problems available for tes... |
github | vigente/gerardus-master | qslim.m | .m | gerardus-master/matlab/ThirdPartyToolbox/GraphToolbox/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 | vigente/gerardus-master | perform_triangle_flipping.m | .m | gerardus-master/matlab/ThirdPartyToolbox/GraphToolbox/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 | vigente/gerardus-master | perform_point_picking.m | .m | gerardus-master/matlab/ThirdPartyToolbox/GraphToolbox/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 | vigente/gerardus-master | select3d.m | .m | gerardus-master/matlab/ThirdPartyToolbox/GraphToolbox/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 | vigente/gerardus-master | compute_parameterization.m | .m | gerardus-master/matlab/ThirdPartyToolbox/GraphToolbox/compute_parameterization.m | 7,662 | utf_8 | 1215e4168de2b431e1d81f0ea8df0af0 | 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 specifi... |
github | vigente/gerardus-master | perform_dijkstra_propagation_old.m | .m | gerardus-master/matlab/ThirdPartyToolbox/GraphToolbox/perform_dijkstra_propagation_old.m | 4,965 | utf_8 | ca5b091b67041559476ea2e63c92f254 | 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 absence of a... |
github | vigente/gerardus-master | compute_boundary.m | .m | gerardus-master/matlab/ThirdPartyToolbox/GraphToolbox/compute_boundary.m | 1,847 | utf_8 | 28c06ac30beb789fa90a2e484ba3f3a7 | 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
nvert=max(m... |
github | vigente/gerardus-master | compute_geometric_laplacian.m | .m | gerardus-master/matlab/ThirdPartyToolbox/GraphToolbox/compute_geometric_laplacian.m | 5,583 | utf_8 | 3d9b6480df20fdff10d38f34983646cb | 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, doesn't t... |
github | vigente/gerardus-master | check_face_vertex.m | .m | gerardus-master/matlab/ThirdPartyToolbox/GraphToolbox/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 | vigente/gerardus-master | plot_graph.m | .m | gerardus-master/matlab/ThirdPartyToolbox/GraphToolbox/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 | vigente/gerardus-master | perform_delaunay_flipping.m | .m | gerardus-master/matlab/ThirdPartyToolbox/GraphToolbox/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 | vigente/gerardus-master | check_incircle_edge.m | .m | gerardus-master/matlab/ThirdPartyToolbox/GraphToolbox/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 | vigente/gerardus-master | perform_faces_reorientation.m | .m | gerardus-master/matlab/ThirdPartyToolbox/GraphToolbox/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 | vigente/gerardus-master | plot_spherical_triangulation.m | .m | gerardus-master/matlab/ThirdPartyToolbox/GraphToolbox/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 | vigente/gerardus-master | compute_mesh_weight.m | .m | gerardus-master/matlab/ThirdPartyToolbox/GraphToolbox/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 | vigente/gerardus-master | perform_analysis_regularization.m | .m | gerardus-master/matlab/ThirdPartyToolbox/GraphToolbox/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 | vigente/gerardus-master | sssd.m | .m | gerardus-master/matlab/ThirdPartyToolbox/SphericalTrigToolbox/sssd.m | 673 | utf_8 | 182b4824dbffdca479ea93355a3f6a12 |
function [A1, B1, C1, A2, B2, C2] = sssd(a, b, c)
%SSS gives both solutions to the side-side-side problem, in degrees.
%
% SSSD(a, b, c) may result in a vector filled with NaNs if the existence
% condition |180 - a| - |180 - b| <= |180 - c| <= |180 - a| + |180 - b|
% is not met.
%
% See also SSS.
% Rody P.... |
github | vigente/gerardus-master | ssa.m | .m | gerardus-master/matlab/ThirdPartyToolbox/SphericalTrigToolbox/ssa.m | 2,183 | utf_8 | 1a87fb9d864c04c4636467fa85b4ad45 | function [B1, C1, c1, B2, C2, c2] = ssa(a, b, A)
%SSA gives both solutions to the side-side-angle problem, in radians.
%
% SSA(a, b, A) will result in NaNs if the existence condition
% |sin b * sin A| <= | sin a | is not met.
%
% See also SSAD, MAL, MSL.
% Rody P.S. Oldenhuis
% Delft University of Technolog... |
github | vigente/gerardus-master | aas.m | .m | gerardus-master/matlab/ThirdPartyToolbox/SphericalTrigToolbox/aas.m | 2,328 | utf_8 | e63f80179ae5c421e321aa454fd24637 | function [b1, c1, C1, b2, c2, C2] = aas(A, B, a)
%AAS gives both solutions to the angle-angle-side problem, in radians.
%
% AAS(A, B, a) may result in a vector filled with NaNs if the existence
% condition |sin(B)sin(a)| <= |sin(A)| is not met. This function uses the
% Middle Side Law function MSL.m and Middle ... |
github | vigente/gerardus-master | ParticleSampleSphere.m | .m | gerardus-master/matlab/ThirdPartyToolbox/SphereUniformSamplingToolbox/ParticleSampleSphere.m | 11,169 | utf_8 | 2ae27936ac108ce541d0bad2875a2a6f | function [V,Tri,Ue_i,Ue]=ParticleSampleSphere(varargin)
% Create an approximately uniform triangular tessellation of the unit
% sphere by minimizing generalized electrostatic potential energy
% (aka Reisz s-energy) of the system of charged particles. Effectively,
% this function produces a locally optimal solution t... |
github | vigente/gerardus-master | load_nii_ext.m | .m | gerardus-master/matlab/ThirdPartyToolbox/niftiToolbox/load_nii_ext.m | 5,337 | utf_8 | fa0e831b0a596c3208b21bddc1c6d812 | % Load NIFTI header extension after its header is loaded using load_nii_hdr.
%
% Usage: ext = load_nii_ext(filename)
%
% filename - NIFTI file name.
%
% Returned values:
%
% ext - Structure of NIFTI header extension, which includes num_ext,
% and all the extended header sections in the header extension.
% ... |
github | vigente/gerardus-master | rri_orient.m | .m | gerardus-master/matlab/ThirdPartyToolbox/niftiToolbox/rri_orient.m | 1,986 | utf_8 | d900d68efd72ce15b9cf672e400aefc7 | % Convert image of different orientations to standard Analyze orientation
%
% Usage: nii = rri_orient(nii);
% Jimmy Shen (jimmy@rotman-baycrest.on.ca), 26-APR-04
%___________________________________________________________________
function [nii, orient, pattern] = rri_orient(nii, varargin)
if nargin > 1
... |
github | vigente/gerardus-master | save_untouch0_nii_hdr.m | .m | gerardus-master/matlab/ThirdPartyToolbox/niftiToolbox/save_untouch0_nii_hdr.m | 8,594 | utf_8 | 7e8b1b327e1924837820f75780d52d01 | % internal function
% - Jimmy Shen (jimmy@rotman-baycrest.on.ca)
function save_nii_hdr(hdr, fid)
if ~isequal(hdr.hk.sizeof_hdr,348),
error('hdr.hk.sizeof_hdr must be 348.');
end
write_header(hdr, fid);
return; % save_nii_hdr
%---------------------------------------------------------------... |
github | vigente/gerardus-master | rri_zoom_menu.m | .m | gerardus-master/matlab/ThirdPartyToolbox/niftiToolbox/rri_zoom_menu.m | 737 | utf_8 | d8151523470b0fba970eb1d98ba56030 | % Imbed a zoom menu to any figure.
%
% Usage: rri_zoom_menu(fig);
%
% - Jimmy Shen (jimmy@rotman-baycrest.on.ca)
%
%--------------------------------------------------------------------
function menu_hdl = rri_zoom_menu(fig)
if isnumeric(fig)
menu_hdl = uimenu('Parent',fig, ...
'Label','Zoom on', ..... |
github | vigente/gerardus-master | rri_select_file.m | .m | gerardus-master/matlab/ThirdPartyToolbox/niftiToolbox/rri_select_file.m | 16,599 | utf_8 | e349954ca803370f62ceeabdbab5912e | function [selected_file, selected_path] = rri_select_file(varargin)
%
% USAGE: [selected_file, selected_path] = ...
% rri_select_file(dir_name, fig_title)
%
% Allow user to select a file from a list of Matlab competible
% file format
%
% Example:
%
% [selected_file, selected_path] = ...
% rri_select_... |
github | vigente/gerardus-master | clip_nii.m | .m | gerardus-master/matlab/ThirdPartyToolbox/niftiToolbox/clip_nii.m | 3,306 | utf_8 | a70bdbed5a0813312d4c83f94b99a710 | % CLIP_NII: Clip the NIfTI volume from any of the 6 sides
%
% Usage: nii = clip_nii(nii, [option])
%
% Inputs:
%
% nii - NIfTI volume.
%
% option - struct instructing how many voxel to be cut from which side.
%
% option.cut_from_L = ( number of voxel )
% option.cut_from_R = ( number of voxel )
% option.cut_from_P ... |
github | vigente/gerardus-master | affine.m | .m | gerardus-master/matlab/ThirdPartyToolbox/niftiToolbox/affine.m | 16,110 | utf_8 | 768d2303e551a9584685bdb01abf6f8b | % Using 2D or 3D affine matrix to rotate, translate, scale, reflect and
% shear a 2D image or 3D volume. 2D image is represented by a 2D matrix,
% 3D volume is represented by a 3D matrix, and data type can be real
% integer or floating-point.
%
% You may notice that MATLAB has a function called 'imtransform.m' fo... |
github | vigente/gerardus-master | load_untouch_nii_img.m | .m | gerardus-master/matlab/ThirdPartyToolbox/niftiToolbox/load_untouch_nii_img.m | 14,756 | utf_8 | 688b2a42f8071c6402a037c7ca923689 | % internal function
% - Jimmy Shen (jimmy@rotman-baycrest.on.ca)
function [img,hdr] = load_untouch_nii_img(hdr,filetype,fileprefix,machine,img_idx,dim5_idx,dim6_idx,dim7_idx,old_RGB,slice_idx)
if ~exist('hdr','var') | ~exist('filetype','var') | ~exist('fileprefix','var') | ~exist('machine','var')
error('U... |
github | vigente/gerardus-master | load_untouch_nii.m | .m | gerardus-master/matlab/ThirdPartyToolbox/niftiToolbox/load_untouch_nii.m | 6,182 | utf_8 | 93108a725d2e357d773c8aa0acf71328 | % Load NIFTI or ANALYZE dataset, but not applying any appropriate affine
% geometric transform or voxel intensity scaling.
%
% Although according to NIFTI website, all those header information are
% supposed to be applied to the loaded NIFTI image, there are some
% situations that people do want to leave the origi... |
github | vigente/gerardus-master | collapse_nii_scan.m | .m | gerardus-master/matlab/ThirdPartyToolbox/niftiToolbox/collapse_nii_scan.m | 6,778 | utf_8 | 64b1cb0f7cd9e095d3c11ca66453df69 | % Collapse multiple single-scan NIFTI files into a multiple-scan NIFTI file
%
% Usage: collapse_nii_scan(scan_file_pattern, [collapsed_fileprefix], [scan_file_folder])
%
% Here, scan_file_pattern should look like: 'myscan_0*.img'
% If collapsed_fileprefix is omit, 'multi_scan' will be used
% If scan_file_folder is... |
github | vigente/gerardus-master | rri_orient_ui.m | .m | gerardus-master/matlab/ThirdPartyToolbox/niftiToolbox/rri_orient_ui.m | 5,384 | utf_8 | e1196b81940d9f93fbdb43c33799e587 | % Return orientation of the current image:
% orient is orientation 1x3 matrix, in that:
% Three elements represent: [x y z]
% Element value: 1 - Left to Right; 2 - Posterior to Anterior;
% 3 - Inferior to Superior; 4 - Right to Left;
% 5 - Anterior to Posterior; 6 - Superior to Inferior;
% e.g.:
% Standard RAS Or... |
github | vigente/gerardus-master | load_untouch0_nii_hdr.m | .m | gerardus-master/matlab/ThirdPartyToolbox/niftiToolbox/load_untouch0_nii_hdr.m | 8,093 | utf_8 | 3de9ff6a1da47b56ae680e7660eaa041 | % internal function
% - Jimmy Shen (jimmy@rotman-baycrest.on.ca)
function hdr = load_nii_hdr(fileprefix, machine)
fn = sprintf('%s.hdr',fileprefix);
fid = fopen(fn,'r',machine);
if fid < 0,
msg = sprintf('Cannot open file %s.',fn);
error(msg);
else
fseek(fid,0,'bof');
hdr =... |
github | vigente/gerardus-master | load_nii.m | .m | gerardus-master/matlab/ThirdPartyToolbox/niftiToolbox/load_nii.m | 6,808 | utf_8 | d098a5dbea3cd4ad76cea624ffbef9db | % Load NIFTI or ANALYZE dataset. Support both *.nii and *.hdr/*.img
% file extension. If file extension is not provided, *.hdr/*.img will
% be used as default.
%
% A subset of NIFTI transform is included. For non-orthogonal rotation,
% shearing etc., please use 'reslice_nii.m' to reslice the NIFTI file.
% It will... |
github | vigente/gerardus-master | unxform_nii.m | .m | gerardus-master/matlab/ThirdPartyToolbox/niftiToolbox/unxform_nii.m | 1,181 | utf_8 | a77d113be34b09d588b2eb326a3c65c8 | % Undo the flipping and rotations performed by xform_nii; spit back only
% the raw img data block. Initial cut will only deal with 3D volumes
% strongly assume we have called xform_nii to write down the steps used
% in xform_nii.
%
% Usage: a = load_nii('original_name');
% manipulate a.img to make array... |
github | vigente/gerardus-master | load_untouch_nii_hdr.m | .m | gerardus-master/matlab/ThirdPartyToolbox/niftiToolbox/load_untouch_nii_hdr.m | 8,522 | utf_8 | 2d4bc8c8ffb83b37daf1e8dd87c108e6 | % internal function
% - Jimmy Shen (jimmy@rotman-baycrest.on.ca)
function hdr = load_nii_hdr(fileprefix, machine, filetype)
if filetype == 2
fn = sprintf('%s.nii',fileprefix);
if ~exist(fn)
msg = sprintf('Cannot find file "%s.nii".', fileprefix);
error(msg);
end
else
... |
github | vigente/gerardus-master | save_nii_ext.m | .m | gerardus-master/matlab/ThirdPartyToolbox/niftiToolbox/save_nii_ext.m | 977 | utf_8 | b60a98ab7537a883dc3ffef3175f19ae | % Save NIFTI header extension.
%
% Usage: save_nii_ext(ext, fid)
%
% ext - struct with NIFTI header extension fields.
%
% NIFTI data format can be found on: http://nifti.nimh.nih.gov
%
% - Jimmy Shen (jimmy@rotman-baycrest.on.ca)
%
function save_nii_ext(ext, fid)
if ~exist('ext','var') | ~exist('fid','var')
... |
github | vigente/gerardus-master | view_nii_menu.m | .m | gerardus-master/matlab/ThirdPartyToolbox/niftiToolbox/view_nii_menu.m | 14,415 | utf_8 | 32dd591fa1070721f0255f47f6e02510 | % Imbed Zoom, Interp, and Info menu to view_nii window.
%
% Usage: view_nii_menu(fig);
%
% - Jimmy Shen (jimmy@rotman-baycrest.on.ca)
%
%--------------------------------------------------------------------
function menu_hdl = view_nii_menu(fig, varargin)
if isnumeric(fig)
menu_hdl = init(fig);
retur... |
github | vigente/gerardus-master | load_nii_hdr.m | .m | gerardus-master/matlab/ThirdPartyToolbox/niftiToolbox/load_nii_hdr.m | 10,031 | utf_8 | e95839e314863f7ee463cc2626dd447c | % internal function
% - Jimmy Shen (jimmy@rotman-baycrest.on.ca)
function [hdr, filetype, fileprefix, machine] = load_nii_hdr(fileprefix)
if ~exist('fileprefix','var'),
error('Usage: [hdr, filetype, fileprefix, machine] = load_nii_hdr(filename)');
end
machine = 'ieee-le';
new_ext = 0;
if fin... |
github | vigente/gerardus-master | save_untouch_slice.m | .m | gerardus-master/matlab/ThirdPartyToolbox/niftiToolbox/save_untouch_slice.m | 19,683 | utf_8 | 364468e5dbd3790c1aadf9a768534f1f | % Save back to the original image with a portion of slices that was
% loaded by "load_untouch_nii". You can process those slices matrix
% in any way, as long as their dimension is not altered.
%
% Usage: save_untouch_slice(slice, filename, ...
% slice_idx, [img_idx], [dim5_idx], [dim6_idx], [dim7_idx])
%
% slice ... |
github | vigente/gerardus-master | load_nii_img.m | .m | gerardus-master/matlab/ThirdPartyToolbox/niftiToolbox/load_nii_img.m | 12,328 | utf_8 | b1b9dd2838a8f217b10fefdc8a931d5e | % internal function
% - Jimmy Shen (jimmy@rotman-baycrest.on.ca)
function [img,hdr] = load_nii_img(hdr,filetype,fileprefix,machine,img_idx,dim5_idx,dim6_idx,dim7_idx,old_RGB)
if ~exist('hdr','var') | ~exist('filetype','var') | ~exist('fileprefix','var') | ~exist('machine','var')
error('Usage: [img,hdr] = ... |
github | vigente/gerardus-master | bresenham_line3d.m | .m | gerardus-master/matlab/ThirdPartyToolbox/niftiToolbox/bresenham_line3d.m | 4,493 | utf_8 | c19f06df423676afeb59762ac55c0c2f | % Generate X Y Z coordinates of a 3D Bresenham's line between
% two given points.
%
% A very useful application of this algorithm can be found in the
% implementation of Fischer's Bresenham interpolation method in my
% another program that can rotate three dimensional image volume
% with an affine matrix:
% http... |
github | vigente/gerardus-master | make_nii.m | .m | gerardus-master/matlab/ThirdPartyToolbox/niftiToolbox/make_nii.m | 6,849 | utf_8 | 3c7c8b81655c111a9ce4b82086bde4f5 | % Make NIfTI structure specified by an N-D matrix. Usually, N is 3 for
% 3D matrix [x y z], or 4 for 4D matrix with time series [x y z t].
% Optional parameters can also be included, such as: voxel_size,
% origin, datatype, and description.
%
% Once the NIfTI structure is made, it can be saved into NIfTI fil... |
github | vigente/gerardus-master | verify_nii_ext.m | .m | gerardus-master/matlab/ThirdPartyToolbox/niftiToolbox/verify_nii_ext.m | 1,676 | utf_8 | db3d32ecba688905185f5ed01b409fd1 | % Verify NIFTI header extension to make sure that each extension section
% must be an integer multiple of 16 byte long that includes the first 8
% bytes of esize and ecode. If the length of extension section is not the
% above mentioned case, edata should be padded with all 0.
%
% Usage: [ext, esize_total] = verif... |
github | vigente/gerardus-master | get_nii_frame.m | .m | gerardus-master/matlab/ThirdPartyToolbox/niftiToolbox/get_nii_frame.m | 4,333 | utf_8 | 8b0cba9d07733a6f82753b0c40b51107 | % Return time frame of a NIFTI dataset. Support both *.nii and
% *.hdr/*.img file extension. If file extension is not provided,
% *.hdr/*.img will be used as default.
%
% It is a lightweighted "load_nii_hdr", and is equivalent to
% hdr.dime.dim(5)
%
% Usage: [ total_scan ] = get_nii_frame(filename)
%
% filen... |
github | vigente/gerardus-master | flip_lr.m | .m | gerardus-master/matlab/ThirdPartyToolbox/niftiToolbox/flip_lr.m | 3,484 | utf_8 | a0b2d0189d90339a841863efeb60681a | % When you load any ANALYZE or NIfTI file with 'load_nii.m', and view
% it with 'view_nii.m', you may find that the image is L-R flipped.
% This is because of the confusion of radiological and neurological
% convention in the medical image before NIfTI format is adopted. You
% can find more details from:
%
% http... |
github | vigente/gerardus-master | save_nii.m | .m | gerardus-master/matlab/ThirdPartyToolbox/niftiToolbox/save_nii.m | 9,404 | utf_8 | 88aa93174482539fe993ac335fb01541 | % Save NIFTI dataset. Support both *.nii and *.hdr/*.img file extension.
% If file extension is not provided, *.hdr/*.img will be used as default.
%
% Usage: save_nii(nii, filename, [old_RGB])
%
% nii.hdr - struct with NIFTI header fields (from load_nii.m or make_nii.m)
%
% nii.img - 3D (or 4D) matrix of NIFTI... |
github | vigente/gerardus-master | rri_file_menu.m | .m | gerardus-master/matlab/ThirdPartyToolbox/niftiToolbox/rri_file_menu.m | 3,974 | utf_8 | 1ec91620ceb4108dde9a63945380028f | % Imbed a file menu to any figure. If file menu exist, it will append
% to the existing file menu. This file menu includes: Copy to clipboard,
% print, save, close etc.
%
% Usage: rri_file_menu(fig);
%
% rri_file_menu(fig,0) means no 'Close' menu.
%
% - Jimmy Shen (jimmy@rotman-baycrest.on.ca)
%
%---------... |
github | vigente/gerardus-master | reslice_nii.m | .m | gerardus-master/matlab/ThirdPartyToolbox/niftiToolbox/reslice_nii.m | 9,825 | utf_8 | 79013b03e55231e8bb52036f14c83d2e | % The basic application of the 'reslice_nii.m' program is to perform
% any 3D affine transform defined by a NIfTI format image.
%
% In addition, the 'reslice_nii.m' program can also be applied to
% generate an isotropic image from either a NIfTI format image or
% an ANALYZE format image.
%
% The resliced NIfTI fi... |
github | vigente/gerardus-master | save_untouch_nii.m | .m | gerardus-master/matlab/ThirdPartyToolbox/niftiToolbox/save_untouch_nii.m | 6,494 | utf_8 | 50fa95cbb847654356241a853328f912 | % Save NIFTI or ANALYZE dataset that is loaded by "load_untouch_nii.m".
% The output image format and file extension will be the same as the
% input one (NIFTI.nii, NIFTI.img or ANALYZE.img). Therefore, any file
% extension that you specified will be ignored.
%
% Usage: save_untouch_nii(nii, filename)
%
% nii -... |
github | vigente/gerardus-master | view_nii.m | .m | gerardus-master/matlab/ThirdPartyToolbox/niftiToolbox/view_nii.m | 141,432 | utf_8 | d45267cd469c72c8b9679efd9ddd0fce | % VIEW_NII: Create or update a 3-View (Front, Top, Side) of the
% brain data that is specified by nii structure
%
% Usage: status = view_nii([h], nii, [option]) or
% status = view_nii(h, [option])
%
% Where, h is the figure on which the 3-View will be plotted;
% nii is the brain data in NIFTI format;
% option is... |
github | vigente/gerardus-master | mat_into_hdr.m | .m | gerardus-master/matlab/ThirdPartyToolbox/niftiToolbox/mat_into_hdr.m | 2,608 | utf_8 | d53006b93ff90a4a5561d16ff2f4e9a6 | %MAT_INTO_HDR The old versions of SPM (any version before SPM5) store
% an affine matrix of the SPM Reoriented image into a matlab file
% (.mat extension). The file name of this SPM matlab file is the
% same as the SPM Reoriented image file (.img/.hdr extension).
%
% This program will convert the ANALYZE 7.5 SPM Reor... |
github | vigente/gerardus-master | xform_nii.m | .m | gerardus-master/matlab/ThirdPartyToolbox/niftiToolbox/xform_nii.m | 18,107 | utf_8 | 29a1cff91c944d6a93e5101946a5da4d | % internal function
% 'xform_nii.m' is an internal function called by "load_nii.m", so
% you do not need run this program by yourself. It does simplified
% NIfTI sform/qform affine transform, and supports some of the
% affine transforms, including translation, reflection, and
% orthogonal rotation (N*90 degree... |
github | vigente/gerardus-master | make_ana.m | .m | gerardus-master/matlab/ThirdPartyToolbox/niftiToolbox/make_ana.m | 5,455 | utf_8 | 2f62999cbcad72129c892135ff492a1e | % Make ANALYZE 7.5 data structure specified by a 3D or 4D matrix.
% Optional parameters can also be included, such as: voxel_size,
% origin, datatype, and description.
%
% Once the ANALYZE structure is made, it can be saved into ANALYZE 7.5
% format data file using "save_untouch_nii" command (for more detail,... |
github | vigente/gerardus-master | extra_nii_hdr.m | .m | gerardus-master/matlab/ThirdPartyToolbox/niftiToolbox/extra_nii_hdr.m | 7,830 | utf_8 | 853f39f00cbf133e90d0f2cf08d79488 | % Decode extra NIFTI header information into hdr.extra
%
% Usage: hdr = extra_nii_hdr(hdr)
%
% hdr can be obtained from load_nii_hdr
%
% NIFTI data format can be found on: http://nifti.nimh.nih.gov
%
% - Jimmy Shen (jimmy@rotman-baycrest.on.ca)
%
function hdr = extra_nii_hdr(hdr)
switch hdr.dime.datatype
ca... |
github | vigente/gerardus-master | rri_xhair.m | .m | gerardus-master/matlab/ThirdPartyToolbox/niftiToolbox/rri_xhair.m | 2,208 | utf_8 | b3ae9df90d43e5d9538b6b135fa8af20 | % rri_xhair: create a pair of full_cross_hair at point [x y] in
% axes h_ax, and return xhair struct
%
% Usage: xhair = rri_xhair([x y], xhair, h_ax);
%
% If omit xhair, rri_xhair will create a pair of xhair; otherwise,
% rri_xhair will update the xhair. If omit h_ax, current axes will
% be used.... |
github | vigente/gerardus-master | save_untouch_nii_hdr.m | .m | gerardus-master/matlab/ThirdPartyToolbox/niftiToolbox/save_untouch_nii_hdr.m | 8,514 | utf_8 | 582f82c471a9a8826eda59354f61dd1a | % internal function
% - Jimmy Shen (jimmy@rotman-baycrest.on.ca)
function save_nii_hdr(hdr, fid)
if ~isequal(hdr.hk.sizeof_hdr,348),
error('hdr.hk.sizeof_hdr must be 348.');
end
write_header(hdr, fid);
return; % save_nii_hdr
%---------------------------------------------------------------... |
github | vigente/gerardus-master | expand_nii_scan.m | .m | gerardus-master/matlab/ThirdPartyToolbox/niftiToolbox/expand_nii_scan.m | 1,333 | utf_8 | 748da05d09c1a005401c67270c4b94ab | % Expand a multiple-scan NIFTI file into multiple single-scan NIFTI files
%
% Usage: expand_nii_scan(multi_scan_filename, [img_idx], [path_to_save])
%
% NIFTI data format can be found on: http://nifti.nimh.nih.gov
%
% - Jimmy Shen (jimmy@rotman-baycrest.on.ca)
%
function expand_nii_scan(filename, img_idx, newpath)
... |
github | vigente/gerardus-master | load_untouch_header_only.m | .m | gerardus-master/matlab/ThirdPartyToolbox/niftiToolbox/load_untouch_header_only.m | 7,068 | utf_8 | 8996c72db42b01029c92a4ecd88f4b21 | % Load NIfTI / Analyze header without applying any appropriate affine
% geometric transform or voxel intensity scaling. It is equivalent to
% hdr field when using load_untouch_nii to load dataset. Support both
% *.nii and *.hdr file extension. If file extension is not provided,
% *.hdr will be used as default.
% ... |
github | vigente/gerardus-master | bipolar.m | .m | gerardus-master/matlab/ThirdPartyToolbox/niftiToolbox/bipolar.m | 2,145 | utf_8 | 295f87ece96ca4c5dff8dce4cd912a34 | %BIPOLAR returns an M-by-3 matrix containing a blue-red colormap, in
% in which red stands for positive, blue stands for negative,
% and white stands for 0.
%
% Usage: cmap = bipolar(M, lo, hi, contrast); or cmap = bipolar;
%
% cmap: output M-by-3 matrix for BIPOLAR colormap.
% M: number of shades in the color... |
github | vigente/gerardus-master | save_nii_hdr.m | .m | gerardus-master/matlab/ThirdPartyToolbox/niftiToolbox/save_nii_hdr.m | 9,270 | utf_8 | f97c194f5bfc667eb4f96edf12be02a7 | % internal function
% - Jimmy Shen (jimmy@rotman-baycrest.on.ca)
function save_nii_hdr(hdr, fid)
if ~exist('hdr','var') | ~exist('fid','var')
error('Usage: save_nii_hdr(hdr, fid)');
end
if ~isequal(hdr.hk.sizeof_hdr,348),
error('hdr.hk.sizeof_hdr must be 348.');
end
if hdr.h... |
github | vigente/gerardus-master | histology_preprocessing.m | .m | gerardus-master/matlab/CardiacToolbox/histology_preprocessing.m | 13,111 | utf_8 | e86ea254304be213671840f5503fd7c8 | function [imref, im, mask] = histology_preprocessing(imref, im, opts)
% HISTOLOGY_PREPROCESSING Prepare slices for intra-histology registration.
%
% HISTOLOGY_PREPROCESSING converts a list of histology images to grayscale,
% inverts and thresholds them (so that the background is black instead of
% white), extends the ... |
github | vigente/gerardus-master | histology_intraframe_reg.m | .m | gerardus-master/matlab/CardiacToolbox/histology_intraframe_reg.m | 15,683 | utf_8 | 7435ca7ab5d4e2445ca7447b8f7e31fc | function [tParam, regParam] = histology_intraframe_reg(pathstr, files, opts)
% histology_intraframe_reg Registration diffusion of histology slices.
%
% histology_intraframe_reg computes the registration of each slices to the
% two adjacent slices. The two resulting transforms are combined to
% produce a compromise tra... |
github | vigente/gerardus-master | crest_envelope.m | .m | gerardus-master/matlab/CardiacToolbox/crest_envelope.m | 4,913 | utf_8 | 60c44182567ca2d0ba9a2118750cffc6 | function y = crest_envelope(x, c, ITER, P)
% CREST_ENVELOPE Compute the envelope for the Right Ventricle's crest
%
% Y = CREST_ENVELOPE(X, C)
%
% X is a 3-column matrix with the coordinates of the Right Ventricle's
% crest points.
%
% C is a 3-column matrix with the coordinates of the Left Ventricle's
% centro... |
github | vigente/gerardus-master | blockface_intraframe_reg.m | .m | gerardus-master/matlab/CardiacToolbox/blockface_intraframe_reg.m | 8,446 | utf_8 | da7bf091a110687bc1ee2043398d480d | function [t, tParam, iterInfo, regParam] = blockface_intraframe_reg(pathstr, files, idx)
% BLOCKFACE_INTRAFRAME_REG Register consecutive frames in a list of
% blockface images.
%
% BLOCKFACE_INTRAFRAME_REG takes a list of files with blockface images, and
% registers each file(I) to file(I-1), using a similarity transf... |
github | vigente/gerardus-master | histology_blockface_manual_correction.m | .m | gerardus-master/matlab/CardiacToolbox/histology_blockface_manual_correction.m | 7,100 | utf_8 | 4305e51d19b5439feb1745fbdaefb607 | function [tParam, ptsh, ptsbf] = histology_blockface_manual_correction(pathstrh, fileh, pathstrbf, filebf, idx, opts)
% HISTOLOGY_BLOCKFACE_MANUAL_CORRECTION Manual landmark correction of
% 3D histology volume to match blockface volume.
%
% HISTOLOGY_BLOCKFACE_MANUAL_CORRECTION is used after
% histology_intraframe_reg... |
github | vigente/gerardus-master | blockface_correct_frame_shifts.m | .m | gerardus-master/matlab/CardiacToolbox/blockface_correct_frame_shifts.m | 6,585 | utf_8 | 1b9425dbd918671fc054e7804f056d13 | function blockface_correct_frame_shifts(indir, files, t, idxnoprop, outdir)
% blockface_correct_frame_shifts Correct shift between blockface image
% frames.
%
% When the wax block is sliced with a microtome, and photographs taken of
% the blockface, artifacts invariable happen. Artifacts are typically
% caused by the ... |
github | vigente/gerardus-master | vmu2png.m | .m | gerardus-master/matlab/FileFormatToolbox/vmu2png.m | 10,427 | utf_8 | 5234d592d7ce2f9bc53107d2f20a63fd | function vmu2png(file, outfile)
% VMU2PNG Convert a microscope image file from .vmu to .png format.
%
% vmu2png(FILE)
%
% FILE is a string with the path and name of a .vmu (Uncompressed Virtual
% Microscope Specimen) Hamamatsu file. It is expected that the .vmu file
% contains only the header information, and a ... |
github | vigente/gerardus-master | scimat_load.m | .m | gerardus-master/matlab/FileFormatToolbox/scimat_load.m | 22,868 | utf_8 | a84ffc2ca85352cdc00abb9a81192d72 | function scimat = scimat_load(file, varargin)
% SCIMAT_LOAD Load an image into a SCIMAT struct from a Matlab, MetaImage,
% Carl Zeiss LSM, Hamamatsu VMU or regular graphics file (PNG, TIFF, etc).
%
% SCIMAT = SCIMAT_LOAD(FILE)
%
% This function loads the image and metainformation into a scimat struct.
% If necessa... |
github | vigente/gerardus-master | scimat_varian2scimat.m | .m | gerardus-master/matlab/FileFormatToolbox/scimat_varian2scimat.m | 10,891 | utf_8 | 5dd2e9b127802893153d15018787c6a2 | function scimat = scimat_varian2scimat(file_path)
% SCIMAT_VARIAN2SCIMAT Create SCIMAT struct from data obtained from Varian MR system.
%
% This function creates a struct with the scimat format (see "help scimat"
% for details) for data from Varian MR scanners. The output is a vector of scimat structures,
% one per 2D ... |
github | vigente/gerardus-master | elastix_affine_matrix2struct.m | .m | gerardus-master/matlab/ElastixToolbox/elastix_affine_matrix2struct.m | 4,494 | utf_8 | 59c13e07b447a357c174c2cafa784d61 | function tf = elastix_affine_matrix2struct(a, tf)
% ELASTIX_AFFINE_MATRIX2STRUCT Convert homogeneous coordinates matrix
% format to elastix struct format.
%
% TF2 = ELASTIX_AFFINE_MATRIX2STRUCT(A, TF)
%
% A is an affine transform matrix in homegeneous coordinates, referred to
% the centre of coordinates = 0. The t... |
github | vigente/gerardus-master | elastix_write_param2file.m | .m | gerardus-master/matlab/ElastixToolbox/elastix_write_param2file.m | 5,621 | utf_8 | b9a4055f09b73de1b8d72949e547330d | function filename = elastix_write_param2file(filename, param)
% elastix_write_param2file Write struct with elastix parameters to file.
% It accepts nested transform parameters.
%
% FILENAME = elastix_write_param2file([], PARAM)
% FILENAME = elastix_write_param2file('', PARAM)
%
% PARAM is a struct with parameters fo... |
github | vigente/gerardus-master | elastix_cat.m | .m | gerardus-master/matlab/ElastixToolbox/elastix_cat.m | 5,439 | utf_8 | 899b7f641fa081ea01eb189cf3bd628c | function tfout = elastix_cat(varargin)
% ELASTIX_CAT Concatenation of elastix transforms.
%
% ELASTIX_CAT allows to concatenate a list of elastix transforms, each of
% which can be a simple transform or a list of transforms.
%
% Elastix allows for a list of transforms to be applied to an image. For
% example, if we wa... |
github | vigente/gerardus-master | elastix_read_file2param.m | .m | gerardus-master/matlab/ElastixToolbox/elastix_read_file2param.m | 5,749 | utf_8 | 31917895189be574d860342e51d06616 | function param = elastix_read_file2param(filename)
% ELASTIX_READ_FILE2PARAM Read file with elastix parameters into struct.
% It accepts nested transform files.
%
% PARAM = ELASTIX_READ_FILE2PARAM(FILENAME)
%
% FILENAME is a string with the path and filename of a parameter file
% created by elastix (e.g. parameter... |
github | vigente/gerardus-master | transformix.m | .m | gerardus-master/matlab/ElastixToolbox/transformix.m | 8,361 | utf_8 | 8d6dc84a88b8d77f7908c85771c2d054 | function sciout = transformix(t, scimat, opts)
% TRANSFORMIX Matlab interface to the image warping program "transformix".
%
% TRANSFORMIX is a simple interface to the command line program
% "transformix"
%
% http://elastix.isi.uu.nl/
%
% FILENAMEOUT = TRANSFORMIX(T, FILENAMEIN)
% IMOUT = TRANSFORMIX(T, IMIN)
% SCIOU... |
github | vigente/gerardus-master | elastix.m | .m | gerardus-master/matlab/ElastixToolbox/elastix.m | 19,736 | utf_8 | 69b459d47cf10554d3ab9e6943fefddc | function [t, movingReg, iterInfo] = elastix(regParam, fixed, moving, opts)
% ELASTIX Matlab interface to the image registration program "elastix".
%
% ELASTIX is a simple interface to the command line program "elastix"
%
% http://elastix.isi.uu.nl/
%
% Command-line "elastix" is a powerful image registration program,... |
github | vigente/gerardus-master | elastix_affine_struct2matrix.m | .m | gerardus-master/matlab/ElastixToolbox/elastix_affine_struct2matrix.m | 4,642 | utf_8 | 39d309e802cc69fd1279d0748baf6a03 | function a = elastix_affine_struct2matrix(tf)
% ELASTIX_AFFINE_STRUCT2MATRIX Convert any type of affine transform from
% elastix struct format to homogeneous coordinates matrix format.
%
% A = ELASTIX_AFFINE_STRUCT2MATRIX(TF)
%
% TF is a struct in elastix format of a 2D transform. The transform may
% be of any aff... |
github | vigente/gerardus-master | view_tensors.m | .m | gerardus-master/matlab/DiffusionMRIToolbox/view_tensors.m | 4,639 | utf_8 | f14a55e94233da6e4be19d85c9ff88fc | function view_tensors(D, HA, delta, dim_order)
% VIEW_TENSORS Renders diffusion tensors in 3D, colour coded by HA
%
%
% Inputs:
%
% D is the diffusion tensor from fit_DT in 2 dimensions only (i.e. a 3D
% volume with [x, y, DT])
%
% HA is the helix angle (in 2D). HA values of NaN are coloured grey.
%
% delta... |
github | vigente/gerardus-master | fit_stretched_exponential_tensor.m | .m | gerardus-master/matlab/DiffusionMRIToolbox/fit_stretched_exponential_tensor.m | 4,397 | utf_8 | 4fa736b451d88185517cda0c72e334a4 | function [ DT, I_fit] = fit_stretched_exponential_tensor( im, b, thresh_val)
% Author: Darryl McClymont <darryl.mcclymont@gmail.com>
% Copyright © 2014-2015 University of Oxford
% Version: 0.1.8
%
% University of Oxford means the Chancellor, Masters and Scholars of
% the University of Oxford, having an administr... |
github | vigente/gerardus-master | fit_DT.m | .m | gerardus-master/matlab/DiffusionMRIToolbox/fit_DT.m | 9,975 | utf_8 | bb57bf4da04e156bf6106aa987924f26 | function [ DT, FA, ADC, VectorField, EigVals] = fit_DT( im, b, thresh_val, method)
% FIT_DT Fits the diffusion tensor model voxelwise to an image
% S = S0 exp(-bD)
%
%
% Inputs:
%
% IM is the input image, of any dimensionality, with the diffusion
% scans in the last dimension
%
% B is the b-mat... |
github | vigente/gerardus-master | fit_DKI_model.m | .m | gerardus-master/matlab/DiffusionMRIToolbox/fit_DKI_model.m | 14,727 | utf_8 | 77e9aa34e95532bb6b708dd428ae1ae3 | function [ DKI, K_ADC, K_AKC, Kv1, Kv2, Kv3, I_DKI ] = fit_DKI_model( im, B_mat, thresh_val, method)
% FIT_DT Fits the diffusion kurtosis model voxelwise to an image
% S = S0 exp(-(bD + 1/6 b^2 * K))
%
%
% Inputs:
%
% IM is the input image, of any dimensionality, with the diffusion
% scans in the last... |
github | vigente/gerardus-master | tri_ccqp_smacof_nofold_sph_pip.m | .m | gerardus-master/matlab/ManifoldToolbox/tri_ccqp_smacof_nofold_sph_pip.m | 20,815 | utf_8 | b1b2eb9795aa34ac0ed3b1247b7d573f | function [con, bnd] = tri_ccqp_smacof_nofold_sph_pip(tri, R, vmin, vmax, lmax, isFree, y, feastol)
% TRI_CCQP_SMACOF_NOFOLD_SPH_PIP Constraints in PIP format for CCQP-SMACOF
% to ensure that 2D triangules on the sphere preserve positive orientation.
%
% This function generates the linear, quadratic and cubic constrain... |
github | vigente/gerardus-master | scimat_surface2seg.m | .m | gerardus-master/matlab/ManifoldToolbox/scimat_surface2seg.m | 4,222 | utf_8 | bc98ceb2e06b5ac103a5506f1a196468 | function scimat = scimat_surface2seg(scimat, tri, x)
% scimat_surface2seg Convert triangular mesh into segmentation.
%
% scimat_surface2seg sets to "1" those voxels in a segmentation volume
% that contain or are intersected by the triangles in a triangular mesh.
% The method works by sampling each triangle in th... |
github | vigente/gerardus-master | vertex_untangle.m | .m | gerardus-master/matlab/ManifoldToolbox/vertex_untangle.m | 9,754 | utf_8 | 7b564ca8b24f0928f40315afe5a12f0d | function [x0, exitflag] = vertex_untangle(tri, x, idx0)
% VERTEX_UNTANGLE Find 2D coordinates for a free vertex surrounded
% by a polygon of fixed counter-clockwise sorted vertices such that the
% free vertex is untangled.
%
% This function is an enhanced implementation of the 2D case (i.e. each
% simplex is a triangl... |
github | vigente/gerardus-master | smdscale.m | .m | gerardus-master/matlab/ManifoldToolbox/smdscale.m | 18,290 | utf_8 | 517267a9cfe03150e6bcdec8f87b412d | function [lat, lon, stopCondition, err, dout, sphrad] = smdscale(d, sphrad, lat, lon, opt)
% SMDSCALE Local neighbourhood Multidimensional scaling on a sphere
%
% This function solves a Multidimensional Scaling problem by finding a way
% to distribute (embed) a set of points on a sphere so that the matrix
% formed fro... |
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