codes copied
This commit is contained in:
jeremias
57
codes/MATLAB/createU.m
Normal file
57
codes/MATLAB/createU.m
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@ -0,0 +1,57 @@
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clear all; close all
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folder_name = uigetdir([],'Load Folder...');
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data = load(strcat(folder_name,'/data.mat'));
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SEG = load(strcat(folder_name,'/SEG.mat'));
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data = data.data;
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SEG = SEG.SEG;
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VENC = data.VENC;
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VoxelSize = data.voxel_MR;
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vel_AP = data.MR_PCA_AP;
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vel_RL = data.MR_PCA_RL;
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vel_FH = data.MR_PCA_FH;
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SEG2 = permute(SEG,[2,3,1]);
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SEG2 = SEG2(:,:,:);
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vel_AP_seg = vel_AP.*SEG2(2:end-1,2:end-1,2:end-1);
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vel_RL_seg = vel_RL.*SEG2(2:end-1,2:end-1,2:end-1);
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vel_FH_seg = vel_FH.*SEG2(2:end-1,2:end-1,2:end-1);
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u_R1 = [] ;
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u_R1.x = vel_FH_seg;
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u_R1.y = vel_AP_seg;
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u_R1.z = vel_RL_seg;
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u_R1.VoxelSize = VoxelSize;
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save('/home/yeye/Desktop/u_R1.mat','u_R1');
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disp('data saved')
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%%
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%%%%%%%%%%%%%%%%%%%%%%%%%%%%
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% FIGURES
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%%%%%%%%%%%%%%%%%%%%%%%%%%%%
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figure
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size_vel = size(vel_FH);
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for n=1:size_vel(3)
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imshow(squeeze(vel_FH_seg(:,:,n,8)),[-100,100],'InitialMagnification',300);
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colormap(gca);
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pause(0.1)
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end
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%%
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size_seg2 = size(SEG2);
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for n=1:size_seg2(3)
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imshow(squeeze(SEG2(:,:,n)),'InitialMagnification',300);
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colormap(gca);
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pause(0.1)
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end
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14
codes/MATLAB/leo/CREATE_MESH.m
Executable file
14
codes/MATLAB/leo/CREATE_MESH.m
Executable file
@ -0,0 +1,14 @@
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% Program to create a structured mesh using the codes of Leo Sok
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clear all; close all
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nodes = load('LEO_files/nodes.txt');
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ux = load('LEO_files/ux.txt') ;
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uy = load('LEO_files/uy.txt') ;
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uz = load('LEO_files/uz.txt') ;
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u = sqrt(ux.^2 + uy.^2 + uz.^2);
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resol = load('LEO_files/resol.txt') ;
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dx = resol(1); dy = resol(2) ; dz = resol(3);
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nodes_masked = maskFEM(nodes,u);
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[N,tets,faces] = meshStructTess(nodes_masked,dx,dy,dz,0,0);
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writemesh('/home/yeye/Desktop/leomesh',N,tets,faces)
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19
codes/MATLAB/leo/maskFEM.m
Executable file
19
codes/MATLAB/leo/maskFEM.m
Executable file
@ -0,0 +1,19 @@
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function nodes2 = maskFEM(nodes,vel)
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a = [];
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b = [];
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c = [];
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ind = 1;
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for i=1:length(nodes)
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if vel(i)>0
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a(ind) = nodes(i,1);
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b(ind) = nodes(i,2);
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c(ind) = nodes(i,3);
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ind = ind +1;
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end
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end
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nodes2 = [a', b', c'];
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169
codes/MATLAB/leo/meshStructTess.m
Executable file
169
codes/MATLAB/leo/meshStructTess.m
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function [nodes, tets, faces, P] = meshStructTess(nodes, dx, dy, dz, check_mesh, plot_mesh)
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%% [nodes, tets, faces] = meshStructTess(nodes, dx, dy, dz, check_mesh, plot_mesh)
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% Generate a tessalation from a list of structured nodes.
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% input: nodes: n times 3 matrix with on the rows the coordinates of
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% the n points in the mesh
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% dx, dy, dz: the mesh-size in the directions x, y and z
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% check_mesh: if true, then it solves a Poisson problem
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% plot_mesh: if true, then it plots the mesh
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% output: nodes: m times 3 matrix with on the rows the coordinates of
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% the m <= n points in the triangulationedi
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% tets: l times 4 matrix with on the rows the tetrahedra
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% faces: k times 3 matrix with on the rows the triangles of the
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% boundary of the mesh
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% P: Transformation matrix from input nodes to output nodes.
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% Useful also for transforming node-valued functions on
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% the input nodes to node-valued functions on the output
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% nodes
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%
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% The triangulation can be plotted using tetramesh(tets,nodes)
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% compute the minimum and number of points in each direction
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if size(nodes,1) < 4
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error('Triangulation needs at least 4 points')
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end
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mn = min(nodes);
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xmin = mn(1);
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ymin = mn(2);
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zmin = mn(3);
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mn = max(nodes);
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xmax = mn(1);
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ymax = mn(2);
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zmax = mn(3);
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nx = round((xmax-xmin)/dx +1);
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ny = round((ymax-ymin)/dy +1);
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nz = round((zmax-zmin)/dz +1);
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Nnodes = size(nodes,1);
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% Define tensor which consist of nodes indices, used for the creation of
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% the tetrahedra
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nodes3d = zeros(nx,ny,nz); % preallocate
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for i=1:Nnodes
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nodes3d(round((nodes(i,1)-xmin)/dx)+1,round((nodes(i,2)-ymin)/dy)+1,round((nodes(i,3)-zmin)/dz)+1)=i;
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end
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disp('Creating Tetrahedra')
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% create tetrahedral mesh in cube, which we will reuse.
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ii = 1;
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X = zeros(8,3);
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for i=0:1
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for j=0:1
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for k=0:1
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X(ii,:) = [i,j,k];
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ii = ii+1;
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end
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end
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end
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cubetet = delaunay(X);
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% Run through the mesh
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el = 1;
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Tetrahedra = zeros(6*(nnz(nodes3d)),4); % preallocate
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for i=1:nx-1
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for j=1:ny-1
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for k=1:nz-1
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% take [i:i+1,j:j+1,k:k+1] as cube
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nod = zeros(1,8); % perallocate
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for l = 1:8
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% nod is vector with node indices of cube
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nod(l) = nodes3d(i + X(l,1), j + X(l,2), k + X(l,3));
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end
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if nnz(nod) == 8 % then the cube is inside the mesh
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tet = nod(cubetet);
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else % then there is at least one point of the cube outside the mesh
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Xs = X(logical(nod),:); % take only nodes inside the mesh
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nodx = nod(logical(nod));
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if nnz(nod) == 4 % 4 nodes, check if points are coplanar
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C = cross(Xs(2,:)-Xs(1,:), Xs(3,:)-Xs(1,:));
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cop = logical(dot(C,Xs(4,:)-Xs(1,:)));
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% if cop = 0, then points are coplanar end thus no
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% tetrahedra exists.
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end
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if (nnz(nod)>4) || (nnz(nod) == 4 && cop)
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% create tetrahedra
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tet1 = delaunay(Xs);
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tet = nodx(tet1);
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else % no tetrahedra exists
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tet = [];
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end
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end
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% add new tetrahedra to list
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Tetrahedra(el:el+size(tet,1)-1,:) = tet;
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el = el+size(tet,1);
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end
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end
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end
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tets = Tetrahedra(1:el-1,:); % Delete extra preallocated rows.
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clear Tetrahedra
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disp([num2str(size(tets,1)), ' tetrahedra created'])
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% Delete nodes which are not in any tetrahedra.
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disp('Update mesh')
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contr = zeros(size(nodes,1),1);
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for i=1:size(tets,1)
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for j=1:4
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contr(tets(i,j))=1;
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end
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end
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nodes = nodes(logical(contr),:);
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% compute P
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P = speye(Nnodes);
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P = P(logical(contr),:);
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disp([num2str(nnz(~contr)), ' unused nodes in triangulation deleted.'])
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disp('Update tetrahedra')
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% make tetrahedra compatible with new node indices
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cumcon = cumsum(~contr)';
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tets = tets - cumcon(tets);
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% create triangles
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if size(tets,1) == 0
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warning('No tetrahedra created')
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faces = zeros(0,3);
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else
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disp('Create Triangles')
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faces = freeBoundary(triangulation(tets,nodes));
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disp([num2str(size(faces,1)), ' triangles created'])
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end
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% checking the mesh by solving a Poisson problem
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if check_mesh
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% Builds the P1 stiffness matrix from tets and nodes
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[A,volumes]=stifness_matrixP1_3D(tets,nodes);
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% Check if element volumes may be negative
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if any(volumes<=0)
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warning('Some elements have zero or negative volume')
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end
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% solve the Poisson problem with Dirichlet BC
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A(2:end,2:end)\ones(size(A(2:end,2:end),1),1);
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disp('If there are no warnings, it probably means that the mesh is fine')
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end
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% Plots mesh
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if plot_mesh
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tetramesh(tets,nodes)
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xlabel('x')
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ylabel('y')
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zlabel('z')
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end
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end
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97
codes/MATLAB/leo/writemesh.m
Executable file
97
codes/MATLAB/leo/writemesh.m
Executable file
@ -0,0 +1,97 @@
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function writemesh(varargin)
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%% writemesh(path, mesh)
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% Save triangulation as path.xml and path.msh
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% mesh is a struct with fields Pts, Tet, Tri
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% alernatively one can use writemesh(path, Pts, Tet, Tri)
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% Pts should by a n times 3 matrix consisting points of the mesh
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% Tet is the m times 4 matrix consisting the tetrahedra
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% Tri is the l times 3 matrix consisting the triangles at the boundary
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if nargin > 3
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mesh.Pts=varargin{2};
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mesh.Tet=varargin{3};
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mesh.Tri=varargin{4};
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writemesh(varargin{1},mesh,varargin(nargin));
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elseif isstruct(varargin{2})
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rootMeshFile = varargin{1};
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% NEW FILE
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obj = [rootMeshFile,'.msh'];
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meshfile = fopen(obj,'w');
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obj2 = [rootMeshFile,'.xml'];
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xmlfile = fopen(obj2,'w');
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% MESH
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fprintf(meshfile,['$MeshFormat','\n']);
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fprintf(meshfile,['2.2 0 8','\n']);
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fprintf(meshfile,['$EndMeshFormat','\n']);
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fprintf(xmlfile,['<?xml version="1.0" encoding="UTF-8"?>','\n']);
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fprintf(xmlfile,'\n');
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fprintf(xmlfile,['<dolfin xmlns:dolfin="http://www.fenicsproject.org">','\n']);
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mesh = varargin{2};
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Nodes = mesh.('Pts');
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mesh = rmfield(mesh,'Pts');
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Nodes = [(1:size(Nodes,1))' Nodes(:,1:3)];
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% POINTS
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if ~strcmp(varargin{nargin},'mute')
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disp('Write Points')
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end
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fprintf(meshfile,['$Nodes','\n']);
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fprintf(meshfile,['%i','\n'],size(Nodes,1));
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fprintf(xmlfile,[' <mesh celltype="tetrahedron" dim="3">','\n']);
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fprintf(xmlfile,[' <vertices size="%i">','\n'],size(Nodes,1));
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fprintf(meshfile,'%i %13.6f %13.6f %13.6f\n',Nodes');
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Nodes(:,1) = Nodes(:,1) - 1;
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fprintf(xmlfile,' <vertex index="%i" x="%0.16e" y="%0.16e" z="%0.16e"/>\n',Nodes');
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fprintf(meshfile,['$EndNodes','\n']);
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fprintf(meshfile,['$Elements','\n']);
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fprintf(meshfile,['%i','\n'],size(mesh.Tet,1)+size(mesh.Tri,1));
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fprintf(xmlfile,[' </vertices>','\n']);
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fprintf(xmlfile,[' <cells size="%i">','\n'],size(mesh.Tet,1));
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% Triangles
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if ~strcmp(varargin{nargin},'mute')
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disp('Write Triangles')
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end
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tri = mesh.('Tri');
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tri = [(1:size(tri,1))' 2*ones(size(tri,1),1) 2*ones(size(tri,1),1) zeros(size(tri,1),1) 2*ones(size(tri,1),1) tri(:,1:3)];
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fprintf(meshfile,'%i %i %i %i %i %i %i %i\n',tri');
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% Tetrahedra
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if ~strcmp(varargin{nargin},'mute')
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disp('Write Tetrahedra')
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end
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tet = mesh.('Tet');
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tet = [(size(tri,1)+1:size(tri,1)+size(tet,1))' 4*ones(size(tet,1),1) 2*ones(size(tet,1),1) zeros(size(tet,1),1) ones(size(tet,1),1) tet(:,1:4)];
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fprintf(meshfile,'%i %i %i %i %i %i %i %i %i\n',tet');
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tet = mesh.('Tet');
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tet = [(0:size(tet,1)-1)' (tet(:,1:4)-1)];
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fprintf(xmlfile,' <tetrahedron index="%i" v0="%i" v1="%i" v2="%i" v3="%i"/>\n',tet');
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fprintf(meshfile,['$EndElements','\n']);
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fprintf(xmlfile,' </cells>\n </mesh>\n</dolfin>\n');
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fclose('all');
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end
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126
codes/MATLAB/load_dicom.m
Normal file
126
codes/MATLAB/load_dicom.m
Normal file
@ -0,0 +1,126 @@
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clear all ; close all
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% Load dicom
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name = 'Ronald' ;
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if strcmp(name, 'Ronald')
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path_all = [
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'/home/yeye/Desktop/PhD/MEDICAL_DATA/DatosSEPT2019/20190909_Ronald/FH/DICOM/IM_0001',
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'/home/yeye/Desktop/PhD/MEDICAL_DATA/DatosSEPT2019/20190909_Ronald/AP/DICOM/IM_0001',
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'/home/yeye/Desktop/PhD/MEDICAL_DATA/DatosSEPT2019/20190909_Ronald/RL/DICOM/IM_0001'
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] ;
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end
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if strcmp(name, 'Jeremias')
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path_all = [
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'/home/yeye/Desktop/PhD/MEDICAL_DATA/DatosSEPT2019/20190909_Jeremias/FH/DICOM/IM_0001',
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'/home/yeye/Desktop/PhD/MEDICAL_DATA/DatosSEPT2019/20190909_Jeremias/AP/DICOM/IM_0001',
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'/home/yeye/Desktop/PhD/MEDICAL_DATA/DatosSEPT2019/20190909_Jeremias/RL/DICOM/IM_0001'
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] ;
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end
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if strcmp(name, 'Hugo')
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path_all = [
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'/home/yeye/Desktop/PhD/MEDICAL_DATA/DatosSEPT2019/20190924_Hugo/Dicom/DICOM/IM_0013',
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'/home/yeye/Desktop/PhD/MEDICAL_DATA/DatosSEPT2019/20190924_Hugo/Dicom/DICOM/IM_0009',
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'/home/yeye/Desktop/PhD/MEDICAL_DATA/DatosSEPT2019/20190924_Hugo/Dicom/DICOM/IM_0005'
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] ;
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end
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for i=1:3
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if i==1
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%path = '/home/yeye/Desktop/PhD/MEDICAL_DATA/DatosSEPT2019/20190924_Paloma/Dicom/DICOM/IM_0013'
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disp('Reading the FH component from ...')
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path = path_all(1,:)
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end
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if i==2
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%path = '/home/yeye/Desktop/PhD/MEDICAL_DATA/DatosSEPT2019/20190924_Paloma/Dicom/DICOM/IM_0009' ;
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disp('Reading the AP component from ...')
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path = path_all(2,:)
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end
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if i==3
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%path = '/home/yeye/Desktop/PhD/MEDICAL_DATA/DatosSEPT2019/20190924_Paloma/Dicom/DICOM/IM_0005' ;
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disp('Reading the RL component from ...')
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path = path_all(3,:)
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end
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I_info = dicominfo(path);
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I = double(dicomread(path));
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VENC = eval(['I_info.PerFrameFunctionalGroupsSequence.Item_1.MRVelocityEncodingSequence.Item_1.VelocityEncodingMaximumValue']) ;
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heart_rate = eval(['I_info.PerFrameFunctionalGroupsSequence.Item_1.Private_2005_140f.Item_1.HeartRate']);
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MAG = zeros(size(I,1),size(I,2),I_info.Private_2001_1018,I_info.Private_2001_1017);
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PHASE = zeros(size(I,1),size(I,2),I_info.Private_2001_1018,I_info.Private_2001_1017);
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for n=1:size(I,4)
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RI = eval(['I_info.PerFrameFunctionalGroupsSequence.Item_',num2str(n),'.Private_2005_140f.Item_1.RescaleIntercept']); % intercept
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RS = eval(['I_info.PerFrameFunctionalGroupsSequence.Item_',num2str(n),'.Private_2005_140f.Item_1.RescaleSlope']); % slope
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cp = eval(['I_info.PerFrameFunctionalGroupsSequence.Item_',num2str(n),'.Private_2005_140f.Item_1.Private_2001_1008']); %cp
|
||||
slc = eval(['I_info.PerFrameFunctionalGroupsSequence.Item_',num2str(n),'.Private_2005_140f.Item_1.Private_2001_100a']); %scl
|
||||
id = eval(['I_info.PerFrameFunctionalGroupsSequence.Item_',num2str(n),'.Private_2005_140f.Item_1.Private_2005_106e']); % PCA o FFE
|
||||
|
||||
if strcmp(id,'FFE')==1
|
||||
MAG(:,:,slc,cp) = I(:,:,1,n)*RS + RI;
|
||||
else
|
||||
PHASE(:,:,slc,cp) = I(:,:,1,n)*RS + RI;
|
||||
end
|
||||
|
||||
end
|
||||
|
||||
|
||||
MASK = double(abs((PHASE==PHASE(1,1,1,1))-1));
|
||||
PHASE = PHASE.*MASK;
|
||||
|
||||
|
||||
if i==1
|
||||
MR_FFE_FH = MAG;
|
||||
MR_PCA_FH = VENC*PHASE/pi/100;
|
||||
end
|
||||
|
||||
if i==2
|
||||
MR_FFE_AP = MAG;
|
||||
MR_PCA_AP = VENC*PHASE/pi/100;
|
||||
end
|
||||
if i==3
|
||||
MR_FFE_RL = MAG;
|
||||
MR_PCA_RL = VENC*PHASE/pi/100;
|
||||
end
|
||||
|
||||
|
||||
end
|
||||
|
||||
|
||||
disp('Saving the data ...')
|
||||
|
||||
spaceslices = eval(['I_info.PerFrameFunctionalGroupsSequence.Item_1.PixelMeasuresSequence.Item_1.SpacingBetweenSlices']);
|
||||
pixelspacing = eval(['I_info.PerFrameFunctionalGroupsSequence.Item_1.PixelMeasuresSequence.Item_1.PixelSpacing']);
|
||||
|
||||
disp('voxel-size recognized:')
|
||||
voxel_MR = [pixelspacing(1),pixelspacing(1),spaceslices]
|
||||
|
||||
|
||||
data = [];
|
||||
data.MR_FFE_AP = MR_FFE_AP;
|
||||
data.MR_FFE_RL = MR_FFE_RL;
|
||||
data.MR_FFE_FH = MR_FFE_FH;
|
||||
data.MR_PCA_AP = MR_PCA_AP;
|
||||
data.MR_PCA_RL = MR_PCA_RL;
|
||||
data.MR_PCA_FH = MR_PCA_FH;
|
||||
data.type = 'DAT';
|
||||
data.VENC = VENC ;
|
||||
data.voxel_MR = voxel_MR;
|
||||
data.heart_rate = heart_rate;
|
||||
|
||||
save('/home/yeye/Desktop/data.mat','data','-v7.3');
|
||||
disp('data saved')
|
||||
|
||||
|
||||
|
||||
|
||||
Reference in New Issue
Block a user