patch2Im

Below is a demonstration of the features of the patch2Im function

Syntax
Description
Examples
EXAMPLE 1: CONVERTING PATCH DATA WITH A SINGLE BOUNDARY TO AN IMAGE
EXAMPLE 2: CONVERTING PATCH DATA WITH A SINGLE BOUNDARY TO AN IMAGE
EXAMPLE 3: CONVERTING PATCH DATA WITH A MULTIPLE BOUNDARIES AND PATCH TYPES TO AN IMAGE
EXAMPLE 4: Special treatment of boundary voxels

clear; close all; clc;

Syntax

[M,G,bwLabels]=patch2Im(F,V,C,voxelSize,imOrigin,imSiz);

Description

This function converts patch surface data to images. The input C can be used to set the label for each surface and corresponding image region. The regions are assigned in order according to the color label in C. See also triSurf2Im

Examples

Plot settings

fontSize=10;
faceAlpha1=1;
faceAlpha2=0.3;
cMap=[0.5 0.5 0.5; gjet(4)];

EXAMPLE 1: CONVERTING PATCH DATA WITH A SINGLE BOUNDARY TO AN IMAGE

Defining an example surface model

% Defining a deformed and rotated torus shape
r=1; %Sphere radius
rc=2; %Central radius
nr=16;
nc=30;
ptype='honey';
[F,V]=patchTorus(r,nr,rc,nc,ptype);
[THETA,RHO] = cart2pol(V(:,1),V(:,2));
V(:,3)=V(:,3)+sin(3*THETA);
[R,~]=euler2DCM([0.5*pi 0.5*pi 0.*pi]);
V=V*R;

% Using |patch2Im| function to convert patch data to image data
[M,G,~]=patch2Im(F,V);
voxelSize=G.voxelSize;
imOrigin=G.origin;

Plotting the results

L_plot=false(size(M));
L_plot(:,:,round(size(M,3)/2))=1;
L_plot(round(size(M,1)/2),:,:)=1;
L_plot(:,round(size(M,2)/2),:)=1;
L_plot=L_plot & ~isnan(M);
[Fm,Vm,Cm]=im2patch(M,L_plot,'v');
[Vm(:,1),Vm(:,2),Vm(:,3)]=im2cart(Vm(:,2),Vm(:,1),Vm(:,3),voxelSize*ones(1,3));
Vm=Vm+imOrigin(ones(size(Vm,1),1),:);

cFigure;
subplot(1,2,1); hold on;
title('Closed patch surface','FontSize',fontSize);

gpatch(F,V,'kw','k',faceAlpha1);

camlight('headlight');
axisGeom(gca,fontSize);

subplot(1,2,2); hold on;
title('Patch data derived image data (3 slices)','FontSize',fontSize);

gpatch(F,V,'kw','none',faceAlpha2);
gpatch(Fm,Vm,Cm,'k',faceAlpha1);

colormap(cMap); icolorbar;
camlight('headlight');
axisGeom(gca,fontSize);

drawnow;

EXAMPLE 2: CONVERTING PATCH DATA WITH A SINGLE BOUNDARY TO AN IMAGE

Defining an example surface model

[F,V]=graphicsModels(3);

% Defining the full set of possible control parameters
voxelSize=(max(V(:,1))-min(V(:,1)))/50; % The output image voxel size.
imOrigin=min(V,[],1)-voxelSize;
imMax=max(V,[],1)+voxelSize;
imSiz=round((imMax-imOrigin)/voxelSize);
imSiz=imSiz([2 1 3]); %Image size (x, y corresponds to j,i in image coordinates, hence the permutation)

% Using |patch2Im| function to convert patch data to image data
[M]=patch2Im(F,V,ones(size(F,1),1),voxelSize,imOrigin,imSiz);

Plotting the results

L_plot=false(size(M));
L_plot(:,:,round(size(M,3)/2))=1;
L_plot(round(size(M,1)/2),:,:)=1;
L_plot(:,round(size(M,2)/2),:)=1;
L_plot=L_plot & ~isnan(M);
[Fm,Vm,Cm]=im2patch(M,L_plot,'v');
[Vm(:,1),Vm(:,2),Vm(:,3)]=im2cart(Vm(:,2),Vm(:,1),Vm(:,3),voxelSize*ones(1,3));
Vm=Vm+imOrigin(ones(size(Vm,1),1),:);

cFigure;
subplot(1,2,1); hold on;
title('Closed patch surface','FontSize',fontSize);

gpatch(F,V,'kw','k',faceAlpha1);

camlight('headlight');
axisGeom(gca,fontSize);

subplot(1,2,2); hold on;
title('Patch data derived image data (3 slices)','FontSize',fontSize);

gpatch(F,V,'kw','none',faceAlpha2);
gpatch(Fm,Vm,Cm,'k',faceAlpha1);

colormap(cMap); icolorbar;
camlight('headlight');
axisGeom(gca,fontSize);

drawnow;

EXAMPLE 3: CONVERTING PATCH DATA WITH A MULTIPLE BOUNDARIES AND PATCH TYPES TO AN IMAGE

% Defining a multi boundary set

r=2; %Sphere radius
rc=3; %Central radius
nr=15;
nc=25;
ptype='quad';
[F1,V1]=patchTorus(r,nr,rc,nc,ptype);
[F2,V2]=quadSphere(2,r,2);
V2(:,2)=V2(:,2)-5;
[F3,V3]=quadSphere(2,r/2,2);
V3(:,2)=V3(:,2)-5;
[F4,V4]=quadSphere(3,r/2,2);
V4(:,1)=V4(:,1)+2;
V4(:,2)=V4(:,2)+2;

[F,V,C]=joinElementSets({F1,F2,F3,F4},{V1,V2,V3,V4});

% Defining the full set of possible control parameters
voxelSize=r/8; % The output image voxel size.
imOrigin=min(V,[],1)-voxelSize;
imMax=max(V,[],1)+voxelSize;
imSiz=round((imMax-imOrigin)/voxelSize);
imSiz=imSiz([2 1 3]); %Image size (x, y corresponds to j,i in image coordinates, hence the permutation)

% Using |patch2Im| function to convert patch data to image data
[M]=patch2Im(F,V,C,voxelSize,imOrigin,imSiz);

Plotting the results

L_plot=false(size(M));
L_plot(:,:,round(size(M,3)/2))=1;
L_plot(round(size(M,1)/2),:,:)=1;
L_plot(:,round(size(M,2)/2),:)=1;
L_plot=L_plot & ~isnan(M);
[Fm,Vm,Cm]=im2patch(M,L_plot,'v');
[Vm(:,1),Vm(:,2),Vm(:,3)]=im2cart(Vm(:,2),Vm(:,1),Vm(:,3),voxelSize*ones(1,3));
Vm=Vm+imOrigin(ones(size(Vm,1),1),:);

cFigure;
subplot(1,2,1); hold on;
title('Closed patch surface','FontSize',fontSize);

gpatch(F,V,C,'none',faceAlpha2);

camlight('headlight');
axisGeom(gca,fontSize);
colormap(gca,cMap); icolorbar([0 4]);

subplot(1,2,2); hold on;
title('Patch data derived image data (3 slices)','FontSize',fontSize);

gpatch(F,V,'kw','none',faceAlpha2);
gpatch(Fm,Vm,Cm,'k',faceAlpha1);

camlight('headlight');
axisGeom(gca,fontSize);
colormap(gca,cMap); icolorbar([0 4]);
drawnow;

EXAMPLE 4: Special treatment of boundary voxels

% Defining a multi boundary set

r=2; %Sphere radius
rc=3; %Central radius
nr=15;
nc=25;
ptype='quad';
[F1,V1]=patchTorus(r,nr,rc,nc,ptype);
[F2,V2]=quadSphere(2,r,2);
V2(:,2)=V2(:,2)-5;
[F3,V3]=quadSphere(2,r/2,2);
V3(:,2)=V3(:,2)-5;
[F4,V4]=quadSphere(3,r/2,2);
V4(:,1)=V4(:,1)+2;
V4(:,2)=V4(:,2)+2;

[F,V,C]=joinElementSets({F1,F2,F3,F4},{V1,V2,V3,V4});

% Defining the full set of possible control parameters
voxelSize=r/8; % The output image voxel size.
imOrigin=min(V,[],1)-voxelSize;
imMax=max(V,[],1)+voxelSize;
imSiz=round((imMax-imOrigin)/voxelSize);
imSiz=imSiz([2 1 3]); %Image size (x, y corresponds to j,i in image coordinates, hence the permutation)

Plotting the results

cFigure;
subplot(2,2,1); hold on;
title('Closed patch surface','FontSize',fontSize);

gpatch(F,V,C,'none',faceAlpha2);

camlight('headlight');
axisGeom(gca,fontSize);
colormap(gca,cMap); icolorbar([0 4]);

boundaryTypes=[-1 0 1];
titleString={'Exclusive','Default','Inclusive'};

for q=1:numel(boundaryTypes)
    % Using |patch2Im| function to convert patch data to image data
    [M]=patch2Im(F,V,C,voxelSize,imOrigin,imSiz,boundaryTypes(q));

    L_plot=false(size(M));
    L_plot(:,:,round(size(M,3)/2))=1;
    L_plot(round(size(M,1)/2),:,:)=1;
    L_plot(:,round(size(M,2)/2),:)=1;
    L_plot=L_plot & ~isnan(M);
    [Fm,Vm,Cm]=im2patch(M,L_plot,'v');
    [Vm(:,1),Vm(:,2),Vm(:,3)]=im2cart(Vm(:,2),Vm(:,1),Vm(:,3),voxelSize*ones(1,3));
    Vm=Vm+imOrigin(ones(size(Vm,1),1),:);

    subplot(2,2,q+1); hold on;
    title(titleString{q},'FontSize',fontSize);

    gpatch(F,V,'kw','none',faceAlpha2);
    gpatch(Fm,Vm,Cm,'k',faceAlpha1);

    camlight('headlight');
    axisGeom(gca,fontSize);
    colormap(gca,cMap); icolorbar([0 4]);
end
drawnow;

GIBBON www.gibboncode.org

Kevin Mattheus Moerman, [email protected]

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License: https://github.com/gibbonCode/GIBBON/blob/master/LICENSE

GIBBON: The Geometry and Image-based Bioengineering add-On. A toolbox for image segmentation, image-based modeling, meshing, and finite element analysis.

This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/.

patch2Im

Contents

Syntax

Description

Examples

EXAMPLE 1: CONVERTING PATCH DATA WITH A SINGLE BOUNDARY TO AN IMAGE

EXAMPLE 2: CONVERTING PATCH DATA WITH A SINGLE BOUNDARY TO AN IMAGE

EXAMPLE 3: CONVERTING PATCH DATA WITH A MULTIPLE BOUNDARIES AND PATCH TYPES TO AN IMAGE

EXAMPLE 4: Special treatment of boundary voxels