Skip to content

Commit

Permalink
Updated FEB XML file handling, fixed minor bugs after running test an…
Browse files Browse the repository at this point in the history 
…d publish on all documentation
  • Loading branch information
@Kevin-Mattheus-Moerman
Kevin-Mattheus-Moerman committed Aug 18, 2017
1 parent 16a3138 commit dbe1946
Show file tree
Hide file tree
Showing 999 changed files with 8,610 additions and 4,492 deletions.
33 changes: 18 additions & 15 deletions docs/Contents.m
View file
Original file line number Diff line number Diff line change
Expand Up @@ -21,23 +21,26 @@

dY=ifft(fft_dY,[],dimDir,'symmetric');

%% <-- GIBBON footer text -->
%%
% _*GIBBON footer text*_
%
% GIBBON: The Geometry and Image-based Bioengineering add-On. A toolbox for
% image segmentation, image-based modeling, meshing, and finite element
% analysis.
% License: <https://github.com/gibbonCode/GIBBON/blob/master/LICENSE>
%
% Copyright (C) 2017 Kevin Mattheus Moerman
% 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.
% Copyright (C) 2017 Kevin Mattheus Moerman
%
% 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.
% 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.
%
% You should have received a copy of the GNU General Public License
% along with this program. If not, see <http://www.gnu.org/licenses/>.
% 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/>.
33 changes: 18 additions & 15 deletions docs/DEMO_AnyBody_force_analysys.m
View file
Original file line number Diff line number Diff line change
Expand Up @@ -448,23 +448,26 @@
%
% _Kevin Mattheus Moerman_, <[email protected]>

%% <-- GIBBON footer text -->
%%
% _*GIBBON footer text*_
%
% 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.
% GIBBON: The Geometry and Image-based Bioengineering add-On. A toolbox for
% image segmentation, image-based modeling, meshing, and finite element
% analysis.
%
% Copyright (C) 2017 Kevin Mattheus Moerman
% Copyright (C) 2017 Kevin Mattheus Moerman
%
% 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 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.
% 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/>.
% You should have received a copy of the GNU General Public License
% along with this program. If not, see <http://www.gnu.org/licenses/>.
96 changes: 96 additions & 0 deletions docs/DEMO_FEBio_XML_replacing_node_field.m
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,96 @@
%% DEMO_FEBio_XML_replacing_node_field
% Below is a demonstration for:
% 1) Creating basic XML data for a .feb file
% 2) Replacing field in the created XML data by first removing and
% recreating the field.

%%
clear; close all; clc;

%% Creating a feb structure with a geometry section and nodes

%Geometry section
FEB_struct.Geometry.Nodes=rand(8,3); %A set of 8 nodes

%% Using XML coding to build the FEB file

%Initialize docNode object
domNode = com.mathworks.xml.XMLUtils.createDocument('febio_spec');

%Add geometry level to XML file
domNode=addGeometryLevel_FEB(domNode,FEB_struct);

%View the XML data
% xmlView(domNode);
XML_str = gxmlwrite(domNode);
disp(XML_str);

%% Replacing the node field
% Remove the old node field
geometryNode = domNode.getElementsByTagName('Geometry').item(0); %Get parent node
nodesNode = geometryNode.getElementsByTagName('Nodes').item(0); %Get child node
geometryNode.removeChild(nodesNode); %Remove child node

%%
% Create some new nodes in the struct
FEB_struct.Geometry.Nodes=rand(12,3);

%%
% Add the new nodes to the XML description, see also |febStruct2febFile|

%Create new Nodes child
geometryNode = domNode.getElementsByTagName('Geometry').item(0); %Get parent node
parent_node = domNode.createElement('Nodes'); %Create node node
parent_node = geometryNode.appendChild(parent_node);

n_steps=size(FEB_struct.Geometry.Nodes,1);
for q_n=1:1:n_steps
node_node = domNode.createElement('node'); %create node entry
node_node = parent_node.appendChild(node_node); %add node entry
attr = domNode.createAttribute('id'); %Create id attribute
attr.setNodeValue(sprintf('%u',q_n)); %Set id text
node_node.setAttributeNode(attr); %Add id attribute
node_node.appendChild(domNode.createTextNode(sprintf('%6.7e, %6.7e, %6.7e',FEB_struct.Geometry.Nodes(q_n,:)))); %append data text child
end

%%
%View the new XML data
% xmlView(domNode);
XML_str = gxmlwrite(domNode);
disp(XML_str);

%% Writing the XML data to a .feb file
% Exporting the XML data to a .feb file can be done using |write_XML_no_extra_lines|

%%
%
% <<gibbVerySmall.gif>>
%
% _*GIBBON*_
% <www.gibboncode.org>
%
% _Kevin Mattheus Moerman_, <[email protected]>

%%
% _*GIBBON footer text*_
%
% 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.
%
% Copyright (C) 2017 Kevin Mattheus Moerman
%
% 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/>.
33 changes: 18 additions & 15 deletions docs/DEMO_FEBio_active_contraction_01.m
View file
Original file line number Diff line number Diff line change
Expand Up @@ -301,23 +301,26 @@
%
% _Kevin Mattheus Moerman_, <[email protected]>

%% <-- GIBBON footer text -->
%%
% _*GIBBON footer text*_
%
% 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.
% GIBBON: The Geometry and Image-based Bioengineering add-On. A toolbox for
% image segmentation, image-based modeling, meshing, and finite element
% analysis.
%
% Copyright (C) 2017 Kevin Mattheus Moerman
% Copyright (C) 2017 Kevin Mattheus Moerman
%
% 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 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.
% 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/>.
% You should have received a copy of the GNU General Public License
% along with this program. If not, see <http://www.gnu.org/licenses/>.
33 changes: 18 additions & 15 deletions docs/DEMO_FEBio_active_responsive_interface.m
View file
Original file line number Diff line number Diff line change
Expand Up @@ -598,23 +598,26 @@
%
% _Kevin Mattheus Moerman_, <[email protected]>

%% <-- GIBBON footer text -->
%%
% _*GIBBON footer text*_
%
% 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.
% GIBBON: The Geometry and Image-based Bioengineering add-On. A toolbox for
% image segmentation, image-based modeling, meshing, and finite element
% analysis.
%
% Copyright (C) 2017 Kevin Mattheus Moerman
% Copyright (C) 2017 Kevin Mattheus Moerman
%
% 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 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.
% 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/>.
% You should have received a copy of the GNU General Public License
% along with this program. If not, see <http://www.gnu.org/licenses/>.
33 changes: 18 additions & 15 deletions docs/DEMO_FEBio_bar_force.m
View file
Original file line number Diff line number Diff line change
Expand Up @@ -268,23 +268,26 @@
%
% _Kevin Mattheus Moerman_, <[email protected]>

%% <-- GIBBON footer text -->
%%
% _*GIBBON footer text*_
%
% 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.
% GIBBON: The Geometry and Image-based Bioengineering add-On. A toolbox for
% image segmentation, image-based modeling, meshing, and finite element
% analysis.
%
% Copyright (C) 2017 Kevin Mattheus Moerman
% Copyright (C) 2017 Kevin Mattheus Moerman
%
% 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 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.
% 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/>.
% You should have received a copy of the GNU General Public License
% along with this program. If not, see <http://www.gnu.org/licenses/>.
33 changes: 18 additions & 15 deletions docs/DEMO_FEBio_bar_soft_sphere_indentation.m
View file
Original file line number Diff line number Diff line change
Expand Up @@ -361,23 +361,26 @@
%
% _Kevin Mattheus Moerman_, <[email protected]>

%% <-- GIBBON footer text -->
%%
% _*GIBBON footer text*_
%
% 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.
% GIBBON: The Geometry and Image-based Bioengineering add-On. A toolbox for
% image segmentation, image-based modeling, meshing, and finite element
% analysis.
%
% Copyright (C) 2017 Kevin Mattheus Moerman
% Copyright (C) 2017 Kevin Mattheus Moerman
%
% 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 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.
% 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/>.
% You should have received a copy of the GNU General Public License
% along with this program. If not, see <http://www.gnu.org/licenses/>.
33 changes: 18 additions & 15 deletions docs/DEMO_FEBio_bar_sphere_indentation.m
View file
Original file line number Diff line number Diff line change
Expand Up @@ -331,23 +331,26 @@
%
% _Kevin Mattheus Moerman_, <[email protected]>

%% <-- GIBBON footer text -->
%%
% _*GIBBON footer text*_
%
% 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.
% GIBBON: The Geometry and Image-based Bioengineering add-On. A toolbox for
% image segmentation, image-based modeling, meshing, and finite element
% analysis.
%
% Copyright (C) 2017 Kevin Mattheus Moerman
% Copyright (C) 2017 Kevin Mattheus Moerman
%
% 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 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.
% 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/>.
% You should have received a copy of the GNU General Public License
% along with this program. If not, see <http://www.gnu.org/licenses/>.
Loading

0 comments on commit dbe1946

Please sign in to comment.