Difference between revisions of "GPT tut interaction 20110530 on creating"

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[[Tutorial on the interaction function details|Tutorial on the interaction function details]]<br><br>
 
[[Tutorial on the interaction function details|Tutorial on the interaction function details]]<br><br>
<span style="color: CornflowerBlue">'''This file was output automatically on clicking Panel: Edit in the newly saved project called GPT tut interaction 20110530'''<br><br>
+
<span style="color: CornflowerBlue">'''This file was placed in the Matlab Editor automatically on clicking Panel: Edit in the newly saved project'''<br><br>
The code has been divided into Sections to help with the tutorial.<br><br>
+
  <span style="color: CornflowerBlue">Section 1</span>
  <span style="color: CornflowerBlue">Section 1 (automatic)</span>
+
function m = gpt_tut_fresh_interaction_function_20110530( m )
    function m = gpt_tut_interaction_20110530( m )
+
<span style="color: Green">%m = gpt_tut_fresh_interaction_function_20110530( m )</span>
        <span style="color: Green">%m = gpt_tut_interaction_20110530( m )</span>
+
<span style="color: Green">%  Morphogen interaction function.</span>
        <span style="color: Green">%  Morphogen interaction function.</span>
+
<span style="color: Green">%  Written at 2011-05-30 20:10:22.</span>
        <span style="color: Green">%  Written at 2011-05-30 09:42:07.</span>
+
<span style="color: Green">%  GFtbox revision 0, .</span>
        <span style="color: Green">%  GFtbox revision 0, .</span>
 
 
   
 
   
        <span style="color: Green">% The user may edit any part of this function between delimiters</span>
+
<span style="color: Green">% The user may edit any part of this function between delimiters</span>
        <span style="color: Green">% of the form "USER CODE..." and "END OF USER CODE...".  The</span>
+
<span style="color: Green">% of the form "USER CODE..." and "END OF USER CODE...".  The</span>
        <span style="color: Green">% delimiters themselves must not be moved, edited, deleted, or added.</span>
+
<span style="color: Green">% delimiters themselves must not be moved, edited, deleted, or added.</span>
 
   
 
   
        if isempty(m), return; end
+
    if isempty(m), return; end
 
   
 
   
        fprintf( 1, '<span style="color: Green">%s found in %s\n', mfilename(), which(mfilename()) );</span>
+
    fprintf( 1, '<span style="color: Green">%s found in %s\n', mfilename(), which(mfilename()) );</span>
 
   
 
   
        try
+
    try
            m = local_setproperties( m );
+
        m = local_setproperties( m );
        catch
+
    catch
        end
+
    end
 
   
 
   
        realtime = m.globalDynamicProps.currenttime;
+
    realtime = m.globalDynamicProps.currenttime;
 
        <span style="color: Green">%%% USER CODE: INITIALISATION</span>
 
 
   
 
   
 
  <span style="color: CornflowerBlue">Section 2</span>
 
  <span style="color: CornflowerBlue">Section 2</span>
        <span style="color: Green">% In this section you may modify the mesh in any way whatsoever.</span>
+
<span style="color: Green">%%% USER CODE: INITIALISATION</span>
        if (Steps(m)==0) && m.globalDynamicProps.doinit <span style="color: Green">% First iteration</span>
 
            <span style="color: Green">% Zero out a lot of stuff to create a blank slate.</span>
 
            <span style="color: Green">% If no morphogens are set in the GUI it may be useful to</span>
 
            <span style="color: Green">% zero some arrays by uncommenting the following.</span>
 
            <span style="color: Green">% m.morphogens(:) = 0;</span>
 
            <span style="color: Green">% m.morphogenclamp(:) = 0;</span>
 
            <span style="color: Green">% m.mgen_production(:) = 0;</span>
 
            <span style="color: Green">% m.mgen_absorption(:) = 0;</span>
 
            <span style="color: Green">% m.seams(:) = false;</span>
 
            <span style="color: Green">% m.mgen_dilution(:) = false;</span>
 
 
   
 
   
            <span style="color: Green">% Set up names for variant models.  Useful for running multiple models on a cluster.</span>
+
<span style="color: Green">% In this section you may modify the mesh in any way whatsoever.</span>
            m.userdata.ranges.modelname.range = { 'MODEL1', 'MODEL2' };  <span style="color: Green">% CLUSTER</span>
+
    if (Steps(m)==0) && m.globalDynamicProps.doinit <span style="color: Green">% First iteration</span>
            m.userdata.ranges.modelname.index = 1;                      <span style="color: Green">% CLUSTER</span>
+
        <span style="color: Green">% Zero out a lot of stuff to create a blank slate.  </span>
         end
+
        <span style="color: Green">% If no morphogens are set in the GUI it may be useful to</span>
         modelname = m.userdata.ranges.modelname.range{m.userdata.ranges.modelname.index}; <span style="color: Green">% CLUSTER</span>
+
         <span style="color: Green">% zero some arrays by uncommenting the following.</span>
         disp(sprintf('\nRunning <span style="color: Green">%s model %s\n',mfilename, modelname));</span>
+
         <span style="color: Green">% m.morphogens(:) = 0;</span>
         switch modelname
+
        <span style="color: Green">% m.morphogenclamp(:) = 0;</span>
            case 'MODEL1'
+
         <span style="color: Green">% m.mgen_production(:) = 0;</span>
                <span style="color: Green">% Set up the parameters (e.g. mutations) for this model here.</span>
+
         <span style="color: Green">% m.mgen_absorption(:) = 0;</span>
            case 'MODEL2'
+
        <span style="color: Green">% m.seams(:) = false;</span>
                <span style="color: Green">% Set up the parameters (e.g. mutations) for this model here.</span>
+
        <span style="color: Green">% m.mgen_dilution(:) = false;</span>
            otherwise
 
                <span style="color: Green">% If you reach here, you probably forgot a case.</span>
 
        end
 
 
   
 
   
         <span style="color: Green">% More examples of code for all iterations.</span>
+
         <span style="color: Green">% Set up names for variant models.  Useful for running multiple models on a cluster.</span>
 +
        m.userdata.ranges.modelname.range = { 'MODEL1', 'MODEL2' };  <span style="color: Green">% CLUSTER</span>
 +
        m.userdata.ranges.modelname.index = 1;                      <span style="color: Green">% CLUSTER</span>
 +
    end
 +
    modelname = m.userdata.ranges.modelname.range{m.userdata.ranges.modelname.index};  <span style="color: Green">% CLUSTER</span>
 +
    disp(sprintf('\nRunning <span style="color: Green">%s model %s\n',mfilename, modelname));</span>
 +
    switch modelname
 +
        case 'MODEL1'
 +
            <span style="color: Green">% Set up the parameters (e.g. mutations) for this model here.</span>
 +
        case 'MODEL2'
 +
            <span style="color: Green">% Set up the parameters (e.g. mutations) for this model here.</span>
 +
        otherwise
 +
            <span style="color: Green">% If you reach here, you probably forgot a case.</span>
 +
    end
 +
   
 +
    <span style="color: Green">% More examples of code for all iterations.</span>
 
   
 
   
        <span style="color: Green">% Set priorities for simultaneous plotting of multiple morphogens, if desired.</span>
+
    <span style="color: Green">% Set priorities for simultaneous plotting of multiple morphogens, if desired.</span>
        <span style="color: Green">% m = leaf_mgen_plotpriority( m, {'MGEN1', 'MGEN2'}, [1,2], [0.5,0.75] );</span>
+
    <span style="color: Green">% m = leaf_mgen_plotpriority( m, {'MGEN1', 'MGEN2'}, [1,2], [0.5,0.75] );</span>
 
   
 
   
        <span style="color: Green">% Set colour of polariser gradient arrows.</span>
+
    <span style="color: Green">% Set colour of polariser gradient arrows.</span>
        <span style="color: Green">% m = leaf_plotoptions(m,'highgradcolor',[0,0,0],'lowgradcolor',[1,0,0]);</span>
+
    <span style="color: Green">% m = leaf_plotoptions(m,'highgradcolor',[0,0,0],'lowgradcolor',[1,0,0]);</span>
 
   
 
   
        <span style="color: Green">% setup a multiplot of the following morphogens</span>
+
    <span style="color: Green">% setup a multiplot of the following morphogens</span>
        <span style="color: Green">% m = leaf_plotoptions( m, 'morphogen', {'V_PROFILE1','V_PROFILE2','KAPAR','S_LEFTRIGHT'});</span>
+
    <span style="color: Green">% m = leaf_plotoptions( m, 'morphogen', {'V_PROFILE1','V_PROFILE2','KAPAR','S_LEFTRIGHT'});</span>
 
   
 
   
        <span style="color: Green">% to plot polariser on the A side and resultant areal growth rate on the B side:</span>
+
    <span style="color: Green">% to plot polariser on the A side and resultant areal growth rate on the B side:</span>
        <span style="color: Green">% m = leaf_plotoptions( m, 'morphogenA', 'POLARISER', ...</span>
+
    <span style="color: Green">% m = leaf_plotoptions( m, 'morphogenA', 'POLARISER', ...</span>
        <span style="color: Green">%                      'outputquantityB', 'resultantgrowthrate', ...</span>
+
    <span style="color: Green">%                      'outputquantityB', 'resultantgrowthrate', ...</span>
        <span style="color: Green">%                      'outputaxesB', 'areal' );</span>
+
    <span style="color: Green">%                      'outputaxesB', 'areal' );</span>
 
   
 
   
        <span style="color: Green">% monitor properties of vertices must be done here - so that it reports newly equilibrated levels</span>
+
    <span style="color: Green">% monitor properties of vertices must be done here - so that it reports newly equilibrated levels</span>
        <span style="color: Green">% m=leaf_profile_monitor(m,... % essential</span>
+
    <span style="color: Green">% m=leaf_profile_monitor(m,... % essential</span>
        <span style="color: Green">%        'REGIONLABELS',{'V_PROFILE1','V_PROFILE2'},... % essential</span>
+
    <span style="color: Green">%        'REGIONLABELS',{'V_PROFILE1','V_PROFILE2'},... % essential</span>
        <span style="color: Green">%        'MORPHOGENS',{'S_LEFTRIGHT','S_CENTRE'},... % optional  (one element per REGIONLABEL)</span>
+
    <span style="color: Green">%        'MORPHOGENS',{'S_LEFTRIGHT','S_CENTRE'},... % optional  (one element per REGIONLABEL)</span>
        <span style="color: Green">%        'VERTLABELS',false,'FigNum',1,'EXCEL',true,'MODELNAME',modelname); % optional (file in snapshots directory')</span>
+
    <span style="color: Green">%        'VERTLABELS',false,'FigNum',1,'EXCEL',true,'MODELNAME',modelname); % optional (file in snapshots directory')</span>
 +
   
 
   
 
   
 +
<span style="color: Green">%%% END OF USER CODE: INITIALISATION</span>
 
   
 
   
  <span style="color: CornflowerBlue">Section 3 (automatic)</span>
+
  <span style="color: CornflowerBlue">Section 3</span>
        <span style="color: Green">%%% END OF USER CODE: INITIALISATION</span>
+
<span style="color: Green">%%% SECTION 1: ACCESSING MORPHOGENS AND TIME.</span>
 +
<span style="color: Green">%%% AUTOMATICALLY GENERATED CODE: DO NOT EDIT.</span>
 
   
 
   
        <span style="color: Green">%%% SECTION 1: ACCESSING MORPHOGENS AND TIME.</span>
+
    if isempty(m), return; end
        <span style="color: Green">%%% AUTOMATICALLY GENERATED CODE: DO NOT EDIT.</span>
 
 
   
 
   
        if isempty(m), return; end
+
    setGlobals();
 +
    global gNEW_KA_PAR gNEW_KA_PER gNEW_KB_PAR gNEW_KB_PER
 +
    global gNEW_K_NOR gNEW_POLARISER gNEW_STRAINRET gNEW_ARREST
 +
    dt = m.globalProps.timestep;
 +
    polariser_i = gNEW_POLARISER;
 +
    P = m.morphogens(:,polariser_i);
 +
    [kapar_i,kapar_p,kapar_a,kapar_l] = getMgenLevels( m, 'KAPAR' );
 +
    [kaper_i,kaper_p,kaper_a,kaper_l] = getMgenLevels( m, 'KAPER' );
 +
    [kbpar_i,kbpar_p,kbpar_a,kbpar_l] = getMgenLevels( m, 'KBPAR' );
 +
    [kbper_i,kbper_p,kbper_a,kbper_l] = getMgenLevels( m, 'KBPER' );
 +
    [knor_i,knor_p,knor_a,knor_l] = getMgenLevels( m, 'KNOR' );
 +
    [strainret_i,strainret_p,strainret_a,strainret_l] = getMgenLevels( m, 'STRAINRET' );
 +
    [arrest_i,arrest_p,arrest_a,arrest_l] = getMgenLevels( m, 'ARREST' );
 
   
 
   
        setGlobals();
+
<span style="color: Green">% Mesh type: circle</span>
         global gNEW_KA_PAR gNEW_KA_PER gNEW_KB_PAR gNEW_KB_PER
+
<span style="color: Green">%         centre: 0</span>
        global gNEW_K_NOR gNEW_POLARISER gNEW_STRAINRET gNEW_ARREST
+
<span style="color: Green">%      circumpts: 24</span>
        dt = m.globalProps.timestep;
+
<span style="color: Green">%      coneangle: 0</span>
        polariser_i = gNEW_POLARISER;
+
<span style="color: Green">%        dealign: 0</span>
        P = m.morphogens(:,polariser_i);
+
<span style="color: Green">%         height: 0</span>
        [kapar_i,kapar_p,kapar_a,kapar_l] = getMgenLevels( m, 'KAPAR' );
+
<span style="color: Green">%        innerpts: 0</span>
         [kaper_i,kaper_p,kaper_a,kaper_l] = getMgenLevels( m, 'KAPER' );
+
<span style="color: Green">%      randomness: 0.1</span>
        [kbpar_i,kbpar_p,kbpar_a,kbpar_l] = getMgenLevels( m, 'KBPAR' );
+
<span style="color: Green">%          rings: 4</span>
        [kbper_i,kbper_p,kbper_a,kbper_l] = getMgenLevels( m, 'KBPER' );
+
<span style="color: Green">%        version: 1</span>
        [knor_i,knor_p,knor_a,knor_l] = getMgenLevels( m, 'KNOR' );
+
<span style="color: Green">%         xwidth: 2</span>
        [strainret_i,strainret_p,strainret_a,strainret_l] = getMgenLevels( m, 'STRAINRET' );
+
<span style="color: Green">%         ywidth: 2</span>
        [arrest_i,arrest_p,arrest_a,arrest_l] = getMgenLevels( m, 'ARREST' );
 
         [id_plusorg_i,id_plusorg_p,id_plusorg_a,id_plusorg_l] = getMgenLevels( m, 'ID_PLUSORG' );
 
        [id_negorg_i,id_negorg_p,id_negorg_a,id_negorg_l] = getMgenLevels( m, 'ID_NEGORG' );
 
         [id_a_i,id_a_p,id_a_a,id_a_l] = getMgenLevels( m, 'ID_A' );
 
        [id_b_i,id_b_p,id_b_a,id_b_l] = getMgenLevels( m, 'ID_B' );
 
 
   
 
   
        <span style="color: Green">% Mesh type: circle</span>
+
<span style="color: Green">%           Morphogen  Diffusion  Decay  Dilution  Mutant</span>
        <span style="color: Green">%         centre: 0</span>
+
<span style="color: Green">%           -------------------------------------------------</span>
        <span style="color: Green">%      circumpts: 48</span>
+
<span style="color: Green">%               KAPAR        ----    ----       ----    ----</span>
        <span style="color: Green">%      coneangle: 0</span>
+
<span style="color: Green">%               KAPER        ----    ----       ----    ----</span>
        <span style="color: Green">%         dealign: 0</span>
+
<span style="color: Green">%               KBPAR        ----    ----      ----    ----</span>
        <span style="color: Green">%         height: 0</span>
+
<span style="color: Green">%               KBPER        ----    ----      ----    ----</span>
        <span style="color: Green">%        innerpts: 0</span>
+
<span style="color: Green">%                 KNOR       ----    ----      ----    ----</span>
        <span style="color: Green">%     randomness: 0.1</span>
+
<span style="color: Green">%           POLARISER        ----    ----      ----    ----</span>
        <span style="color: Green">%           rings: 6</span>
+
<span style="color: Green">%           STRAINRET        ----    ----      ----    ----</span>
        <span style="color: Green">%         version: 1</span>
+
<span style="color: Green">%               ARREST        ----    ----      ----    ----</span>
        <span style="color: Green">%          xwidth: 0.2</span>
 
        <span style="color: Green">%          ywidth: 0.2</span>
 
 
   
 
   
        <span style="color: Green">%            Morphogen  Diffusion  Decay  Dilution  Mutant</span>
 
        <span style="color: Green">%            -------------------------------------------------</span>
 
        <span style="color: Green">%                KAPAR        ----    ----      ----    ----</span>
 
        <span style="color: Green">%                KAPER        ----    ----      ----    ----</span>
 
        <span style="color: Green">%                KBPAR        ----    ----      ----    ----</span>
 
        <span style="color: Green">%                KBPER        ----    ----      ----    ----</span>
 
        <span style="color: Green">%                KNOR        ----    ----      ----    ----</span>
 
        <span style="color: Green">%            POLARISER        ----    ----      ----    ----</span>
 
        <span style="color: Green">%            STRAINRET        ----    ----      ----    ----</span>
 
        <span style="color: Green">%              ARREST        ----    ----      ----    ----</span>
 
        <span style="color: Green">%          ID_PLUSORG        ----    ----      ----    ----</span>
 
        <span style="color: Green">%            ID_NEGORG        ----    ----      ----    ----</span>
 
        <span style="color: Green">%                ID_A        ----    ----      ----    ----</span>
 
        <span style="color: Green">%                ID_B        ----    ----      ----    ----</span>
 
 
   
 
   
 +
<span style="color: Green">%%% USER CODE: MORPHOGEN INTERACTIONS</span>
 
   
 
   
        <span style="color: Green">%%% USER CODE: MORPHOGEN INTERACTIONS</span>
+
<span style="color: Green">% In this section you may modify the mesh in any way that does not</span>
 +
<span style="color: CornflowerBlue">Section 4</span>
 +
<span style="color: Green">% alter the set of nodes.</span>
 
   
 
   
         <span style="color: Green">% In this section you may modify the mesh in any way that does not</span>
+
    if (Steps(m)==0) && m.globalDynamicProps.doinit  <span style="color: Green">% Initialisation code.</span>
         <span style="color: Green">% alter the set of nodes.</span>
+
         <span style="color: Green">% Put any code here that should only be performed at the start of</span>
 +
        <span style="color: Green">% the simulation, for example, to set up initial morphogen values.</span>
 +
       
 +
         <span style="color: Green">% m.nodes is the set of vertex positions, an N by 3 array if there</span>
 +
        <span style="color: Green">% are N vertices.  Row number K contains the X, Y, and Z</span>
 +
        <span style="color: Green">% coordinates of the Kth vertex. To obtain a list of the X</span>
 +
        <span style="color: Green">% coordinates of every vertex, write m.nodes(:,1).  The Y</span>
 +
        <span style="color: Green">% coordinates are given by m.nodes(:,2) and the Z coordinates by</span>
 +
        <span style="color: Green">% m.nodes(:,3).</span>
 
   
 
   
         if (Steps(m)==0) && m.globalDynamicProps.doinit  <span style="color: Green">% Initialisation code.</span>
+
         <span style="color: Green">% Set up a morphogen promoter (_p suffix) region where x values are minimum</span>
            <span style="color: Green">% Put any code here that should only be performed at the start of</span>
+
        <span style="color: Green">% id_prox_p(m.nodes(:,1)==min(m.nodes(:,1)))=1;</span>
            <span style="color: Green">% the simulation, for example, to set up initial morphogen values.</span>
+
        <span style="color: Green">% if the morphogen level (_l suffix) is to be used in this iteration </span>
            <span style="color: Green">% m.nodes is the set of vertex positions, an N by 3 array if there</span>
+
        <span style="color: Green">% set the level using the morphogen activity (_a suffix).</span>
            <span style="color: Green">% are N vertices.  Row number K contains the X, Y, and Z</span>
+
        <span style="color: Green">% id_prox_l=id_prox_p * id_prox_a; % when a mutation is specified in the GUI </span>
            <span style="color: Green">% coordinates of the Kth vertex. To obtain a list of the X</span>
+
        <span style="color: Green">% the activity (_a) is set to zero</span>
            <span style="color: Green">% coordinates of every vertex, write m.nodes(:,1). The Y</span>
 
            <span style="color: Green">% coordinates are given by m.nodes(:,2) and the Z coordinates by</span>
 
            <span style="color: Green">% m.nodes(:,3).</span>
 
 
   
 
   
            <span style="color: Green">% Set up a morphogen promoter (_p suffix) region where x values are minimum</span>
+
        <span style="color: Green">% One way to set up a morphogen gradient is by ...</span>
            <span style="color: Green">% id_prox_p(m.nodes(:,1)==min(m.nodes(:,1)))=1;</span>
+
        <span style="color: Green">% Setting up a gradient by clamping the ends (execute only once)</span>
            <span style="color: Green">% if the morphogen level (_l suffix) is to be used in this iteration</span>
+
        <span style="color: Green">% P=id_prox_p;</span>
            <span style="color: Green">% set the level using the morphogen activity (_a suffix).</span>
+
        <span style="color: Green">% m.morphogenclamp( ((id_prox_p==1)|(id_dist_p==1)), polariser_i ) = 1;</span>
            <span style="color: Green">% id_prox_l=id_prox_p * id_prox_a; % when a mutation is specified in the GUI</span>
+
        <span style="color: Green">% m = leaf_mgen_conductivity( m, 'POLARISER', 0.01 ); %specifies the diffusion rate of polariser    </span>
            <span style="color: Green">% the activity (_a) is set to zero</span>
+
        <span style="color: Green">% m = leaf_mgen_absorption( m, 'POLARISER', 0.1 );    % specifies degradation rate of polariser</span>
 
   
 
   
            id_a_p(m.nodes(:,1)<-0.03)=1; <span style="color: Green">% setup region for A where identity factor A is represented by id_a_p</span>
+
        <span style="color: Green">% Fixing vertices, i.e. fix z for the base to prevent base from moving up or down</span>
            id_b_p(m.nodes(:,2)<-0.01)=1; <span style="color: Green">% setup region for B</span>
+
        <span style="color: Green">% m=leaf_fix_vertex(m,'vertex',find(id_prox_p==1),'dfs','z');</span>
 
   
 
   
            <span style="color: Green">% One way to set up a morphogen gradient is by ...</span>
+
        <span style="color: Green">% To cut the mesh, set a temporary morphogen to 1 in places to cut</span>
            <span style="color: Green">% Setting up a gradient by clamping the ends (execute only once)</span>
+
        <span style="color: Green">% seams=zeros(size(P));</span>
            <span style="color: Green">% P=id_prox_p;</span>
+
        <span style="color: Green">% seams(indexes to places to cut)=1;</span>
            <span style="color: Green">% m.morphogenclamp( ((id_prox_p==1)|(id_dist_p==1)), polariser_i ) = 1;</span>
+
        <span style="color: Green">% m=leaf_set_seams(m,seams);</span>
            <span style="color: Green">% m = leaf_mgen_conductivity( m, 'POLARISER', 0.01 );  %specifies the diffusion rate of polariser</span>
 
            <span style="color: Green">% m = leaf_mgen_absorption( m, 'POLARISER', 0.1 );    % specifies degradation rate of polariser</span>
 
 
            <span style="color: Green">% Fixing vertices, i.e. fix z for the base to prevent base from moving up or down</span>
 
            <span style="color: Green">% m=leaf_fix_vertex(m,'vertex',find(id_prox_p==1),'dfs','z');</span>
 
 
            <span style="color: Green">% To cut the mesh, set a temporary morphogen to 1 in places to cut</span>
 
            <span style="color: Green">% seams=zeros(size(P));</span>
 
            <span style="color: Green">% seams(indexes to places to cut)=1;</span>
 
            <span style="color: Green">% m=leaf_set_seams(m,seams);</span>
 
 
        end
 
 
   
 
   
 +
    end
 +
   
 
  <span style="color: CornflowerBlue">Section 5</span>
 
  <span style="color: CornflowerBlue">Section 5</span>
        <span style="color: Green">% Second way to generate a gradient</span>
+
    <span style="color: Green">% Second way to generate a gradient</span>
        <span style="color: Green">% generating (+) and sinking (-) a diffusing signal (in this case polariser)</span>
+
    <span style="color: Green">% generating (+) and sinking (-) a diffusing signal (in this case polariser)</span>
        <span style="color: Green">% m.mgen_production( :, polariser_i ) = + 5*s_spur_p - P .* id_dist_p;</span>
+
    <span style="color: Green">% m.mgen_production( :, polariser_i ) = + 5*s_spur_p - P .* id_dist_p;</span>
 
   
 
   
        <span style="color: Green">% Monitor growth by scattering discs that deform over time (c.f. inducing biological clones)</span>
+
    <span style="color: Green">% Monitor growth by scattering discs that deform over time (c.f. inducing biological clones)</span>
        <span style="color: Green">% (CARE - if the canvas is flat ensure that Plot:Hide Thickness is true,</span>
+
    <span style="color: Green">% (CARE - if the canvas is flat ensure that Plot:Hide Thickness is true, </span>
        <span style="color: Green">% because a quirk of the Matlab z-buffer means that they can get hidden by mistake)</span>
+
    <span style="color: Green">% because a quirk of the Matlab z-buffer means that they can get hidden by mistake)</span>
        <span style="color: Green">%    if (340>realtime-dt) && (340<realtime+dt) % discs to be added at realtime==340</span>
+
    <span style="color: Green">%    if (340>realtime-dt) && (340<realtime+dt) % discs to be added at realtime==340</span>
        <span style="color: Green">%        m = leaf_makesecondlayer( m, ...  % This function adds discs that represent transformed cells.</span>
+
    <span style="color: Green">%        m = leaf_makesecondlayer( m, ...  % This function adds discs that represent transformed cells.</span>
        <span style="color: Green">%            'mode', 'each', ...  % Make discs randomly scattered over the canvas.</span>
+
    <span style="color: Green">%            'mode', 'each', ...  % Make discs randomly scattered over the canvas.</span>
        <span style="color: Green">%            'relarea', 1/16000, ...  % Each discs has area was 1/16000 of the initial area of the canvas.</span>
+
    <span style="color: Green">%            'relarea', 1/16000, ...  % Each discs has area was 1/16000 of the initial area of the canvas.</span>
        <span style="color: Green">%            'probpervx', 'V_FLOWER', ... % induce discs over whole canvas (V_FLOWER is 1 over whole canvas)</span>
+
    <span style="color: Green">%            'probpervx', 'V_FLOWER', ... % induce discs over whole canvas (V_FLOWER is 1 over whole canvas)</span>
        <span style="color: Green">%            'numcells',4500,...%number of discs (that will become ellipses)</span>
+
    <span style="color: Green">%            'numcells',4500,...%number of discs (that will become ellipses)</span>
        <span style="color: Green">%            'sides', 6, ...  % Each discs is approximated as a 6-sided regular polygon.</span>
+
    <span style="color: Green">%            'sides', 6, ...  % Each discs is approximated as a 6-sided regular polygon.</span>
        <span style="color: Green">%            'colors', [0.5 0.5 0.5], ...  % Default colour is gray but</span>
+
    <span style="color: Green">%            'colors', [0.5 0.5 0.5], ...  % Default colour is gray but</span>
        <span style="color: Green">%            'colorvariation',1,... % Each disc is a random colour</span>
+
    <span style="color: Green">%            'colorvariation',1,... % Each disc is a random colour</span>
        <span style="color: Green">%            'add', true );  % These discs are added to any discs existing already</span>
+
    <span style="color: Green">%            'add', true );  % These discs are added to any discs existing already</span>
        <span style="color: Green">%    end</span>
+
    <span style="color: Green">%    end</span>
 +
   
 +
<span style="color: CornflowerBlue">Section 6</span>
 +
    <span style="color: Green">% Directives for creating latex representation directly from Matlab code</span>
 +
    <span style="color: Green">% not fully implemented yet but will use @@ directives</span>
 +
    <span style="color: Green">% @@at t</span>
 +
    <span style="color: Green">% @@before t</span>
 +
    <span style="color: Green">% @@after t</span>
 +
    <span style="color: Green">% @@between t1 t2</span>
 
   
 
   
 
  <span style="color: CornflowerBlue">Section 7</span>
 
  <span style="color: CornflowerBlue">Section 7</span>
        <span style="color: Green">% Directives for creating latex representation directly from Matlab code</span>
+
<span style="color: Green">%     % If you want to define different phases according to the absolute</span>
        <span style="color: Green">% not fully implemented yet but will use @@ directives</span>
+
<span style="color: Green">%    % time, create a morphogen for each phase and modulate </span>
        <span style="color: Green">% @@at t</span>
+
<span style="color: Green">%    % expressions using the morphogen</span>
        <span style="color: Green">% @@before t</span>
+
<span style="color: Green">%    % like.  For example:</span>
        <span style="color: Green">% @@after t</span>
+
<span style="color: Green">%    if (realtime < 10)  % first growth phase</span>
        <span style="color: Green">% @@between t1 t2</span>
+
<span style="color: Green">%        f_firstgrowth_p = 1;</span>
 +
<span style="color: Green">%    else</span>
 +
<span style="color: Green">%        f_firstgrowth_p = 0;</span>
 +
<span style="color: Green">%    end</span>
 +
<span style="color: Green">%    if (realtime >= 10) % second growth phase</span>
 +
<span style="color: Green">%        f_secondgrowth_p = 1;</span>
 +
<span style="color: Green">%    else</span>
 +
<span style="color: Green">%        f_secondgrowth_p = 0;</span>
 +
<span style="color: Green">%    end</span>
 +
<span style="color: Green">%</span>
 +
<span style="color: Green">%     % If you want one morphogen to affect others only during a certain</span>
 +
<span style="color: Green">%     % phase, write something like:</span>
 +
<span style="color: Green">%</span>
 +
<span style="color: Green">%     mgen_a_p = f_firstgrowth_p .* (various terms); % will zero except in firstgrowth</span>
 
   
 
   
 
  <span style="color: CornflowerBlue">Section 8</span>
 
  <span style="color: CornflowerBlue">Section 8</span>
        <span style="color: Green">%    % If you want to define different phases according to the absolute</span>
+
    <span style="color: Green">% Code common to all models.</span>
        <span style="color: Green">%    % time, create a morphogen for each phase and modulate</span>
+
    <span style="color: Green">% @@PRN Polariser Regulatory Network</span>
        <span style="color: Green">%    % expressions using the morphogen</span>
 
        <span style="color: Green">%    % like.  For example:</span>
 
        <span style="color: Green">%    if (realtime < 10)  % first growth phase</span>
 
        <span style="color: Green">%        f_firstgrowth_p = 1;</span>
 
        <span style="color: Green">%    else</span>
 
        <span style="color: Green">%        f_firstgrowth_p = 0;</span>
 
        <span style="color: Green">%    end</span>
 
        <span style="color: Green">%    if (realtime >= 10) % second growth phase</span>
 
        <span style="color: Green">%        f_secondgrowth_p = 1;</span>
 
        <span style="color: Green">%    else</span>
 
        <span style="color: Green">%        f_secondgrowth_p = 0;</span>
 
        <span style="color: Green">%    end</span>
 
        <span style="color: Green">%</span>
 
        <span style="color: Green">%    % If you want one morphogen to affect others only during a certain</span>
 
        <span style="color: Green">%    % phase, write something like:</span>
 
        <span style="color: Green">%</span>
 
        <span style="color: Green">%    mgen_a_p = f_firstgrowth_p .* (various terms); % will zero except in firstgrowth</span>
 
 
<span style="color: CornflowerBlue">Section 9</span>
 
        <span style="color: Green">% Code common to all models.</span>
 
        <span style="color: Green">% @@PRN Polariser Regulatory Network</span>
 
 
         <span style="color: Green">% Every equation to be formatted should end with an at-at Eqn N comment.</span>
 
         <span style="color: Green">% Every equation to be formatted should end with an at-at Eqn N comment.</span>
        <span style="color: Green">% @@GRN Gene Regulatory Network</span>
+
    <span style="color: Green">% @@GRN Gene Regulatory Network</span>
 
         <span style="color: Green">% Every equation to be formatted should end with an at-at Eqn N comment.</span>
 
         <span style="color: Green">% Every equation to be formatted should end with an at-at Eqn N comment.</span>
        <span style="color: Green">% @@KRN Growth Regulatory Network</span>
+
    <span style="color: Green">% @@KRN Growth Regulatory Network</span>
 
         <span style="color: Green">% Every equation to be formatted should end with an at-at Eqn N comment.</span>
 
         <span style="color: Green">% Every equation to be formatted should end with an at-at Eqn N comment.</span>
 
   
 
   
 +
<span style="color: CornflowerBlue">Section 9</span>
 +
    <span style="color: Green">% Code for specific models.</span>
 +
    switch modelname
 
  <span style="color: CornflowerBlue">Section 10</span>
 
  <span style="color: CornflowerBlue">Section 10</span>
         <span style="color: Green">% Code for specific models.</span>
+
         case 'MODEL1'  <span style="color: Green">% @@model MODEL1</span>
        switch modelname
+
            <span style="color: Green">% @@PRN Polariser Regulatory Network</span>
            case 'MODEL1'  <span style="color: Green">% @@model MODEL1</span>
 
                <span style="color: Green">% @@PRN Polariser Regulatory Network</span>
 
 
                 <span style="color: Green">% Every equation to be formatted should end with an at-at Eqn N comment.</span>
 
                 <span style="color: Green">% Every equation to be formatted should end with an at-at Eqn N comment.</span>
 
                 <span style="color: Green">% P(:) = ...  % @@ Eqn xx</span>
 
                 <span style="color: Green">% P(:) = ...  % @@ Eqn xx</span>
                <span style="color: Green">% @@GRN Gene Regulatory Network</span>
+
            <span style="color: Green">% @@GRN Gene Regulatory Network</span>
 
                 <span style="color: Green">% Every equation to be formatted should end with an at-at Eqn N comment.</span>
 
                 <span style="color: Green">% Every equation to be formatted should end with an at-at Eqn N comment.</span>
                <span style="color: Green">% @@KRN Growth Regulatory Network</span>
+
            <span style="color: Green">% @@KRN Growth Regulatory Network</span>
 
                 <span style="color: Green">% Every equation to be formatted should end with an at-at Eqn N comment.</span>
 
                 <span style="color: Green">% Every equation to be formatted should end with an at-at Eqn N comment.</span>
 
                 <span style="color: Green">% kapar_p(:) = 0;  % @@ Eqn xx</span>
 
                 <span style="color: Green">% kapar_p(:) = 0;  % @@ Eqn xx</span>
Line 248: Line 239:
 
                 <span style="color: Green">% kbper_p(:) = 0;  % @@ Eqn xx</span>
 
                 <span style="color: Green">% kbper_p(:) = 0;  % @@ Eqn xx</span>
 
                 <span style="color: Green">% knor_p(:)  = 0;  % @@ Eqn xx</span>
 
                 <span style="color: Green">% knor_p(:)  = 0;  % @@ Eqn xx</span>
                kapar_p(:) = id_a_l .* inh(1,id_b_l); <span style="color: Green">% growth rate</span>
+
  <span style="color: CornflowerBlue">Section 11</span>
                kaper_p(:) = kapar_p; <span style="color: Green">% isotropic growth</span>
+
        case 'MODEL2'  <span style="color: Green">% @@model MODEL2</span>
                kbpar_p(:) = kapar_p; <span style="color: Green">% same on both sides of the sheet</span>
+
            <span style="color: Green">% @@PRN Polariser Regulatory Network</span>
                kbper_p(:) = kapar_p; <span style="color: Green">% same</span>
 
                knor_p(:) = 0;      <span style="color: Green">% thickness not growing</span>
 
            case 'MODEL2'  <span style="color: Green">% @@model MODEL2</span>
 
                <span style="color: Green">% @@PRN Polariser Regulatory Network</span>
 
 
                 <span style="color: Green">% Every equation to be formatted should end with an at-at Eqn N comment.</span>
 
                 <span style="color: Green">% Every equation to be formatted should end with an at-at Eqn N comment.</span>
 
                 <span style="color: Green">% P(:) = ...  % @@ Eqn xx</span>
 
                 <span style="color: Green">% P(:) = ...  % @@ Eqn xx</span>
                <span style="color: Green">% @@GRN Gene Regulatory Network</span>
+
            <span style="color: Green">% @@GRN Gene Regulatory Network</span>
 
                 <span style="color: Green">% Every equation to be formatted should end with an at-at Eqn N comment.</span>
 
                 <span style="color: Green">% Every equation to be formatted should end with an at-at Eqn N comment.</span>
                <span style="color: Green">% @@KRN Growth Regulatory Network</span>
+
            <span style="color: Green">% @@KRN Growth Regulatory Network</span>
 
                 <span style="color: Green">% Every equation to be formatted should end with an at-at Eqn N comment.</span>
 
                 <span style="color: Green">% Every equation to be formatted should end with an at-at Eqn N comment.</span>
 
                 <span style="color: Green">% kapar_p(:) = 0;  % @@ Eqn xx</span>
 
                 <span style="color: Green">% kapar_p(:) = 0;  % @@ Eqn xx</span>
Line 266: Line 253:
 
                 <span style="color: Green">% kbper_p(:) = 0;  % @@ Eqn xx</span>
 
                 <span style="color: Green">% kbper_p(:) = 0;  % @@ Eqn xx</span>
 
                 <span style="color: Green">% knor_p(:)  = 0;  % @@ Eqn xx</span>
 
                 <span style="color: Green">% knor_p(:)  = 0;  % @@ Eqn xx</span>
                kapar_p(:) = id_a_l .* inh(1,id_b_l); <span style="color: Green">% growth rate</span>
+
        otherwise
                kaper_p(:) = kapar_p; <span style="color: Green">% isotropic growth</span>
+
             <span style="color: Green">% If this happens, maybe you forgot a model.</span>
                kbpar_p(:) = kapar_p; <span style="color: Green">% same on both sides of the sheet</span>
+
    end
                kbper_p(:) = kapar_p; <span style="color: Green">% same</span>
 
                knor_p(:)  = 0;      <span style="color: Green">% thickness not growing</span>
 
             otherwise
 
                <span style="color: Green">% If this happens, maybe you forgot a model.</span>
 
        end
 
 
   
 
   
  <span style="color: CornflowerBlue">Section 11 (automatic)</span>
+
  <span style="color: CornflowerBlue">Section 12</span>
        <span style="color: Green">%%% END OF USER CODE: MORPHOGEN INTERACTIONS</span>
+
<span style="color: Green">%%% END OF USER CODE: MORPHOGEN INTERACTIONS</span>
 
   
 
   
        <span style="color: Green">%%% SECTION 3: INSTALLING MODIFIED VALUES BACK INTO MESH STRUCTURE</span>
+
<span style="color: Green">%%% SECTION 3: INSTALLING MODIFIED VALUES BACK INTO MESH STRUCTURE</span>
        <span style="color: Green">%%% AUTOMATICALLY GENERATED CODE: DO NOT EDIT.</span>
+
<span style="color: Green">%%% AUTOMATICALLY GENERATED CODE: DO NOT EDIT.</span>
        m.morphogens(:,polariser_i) = P;
+
    m.morphogens(:,polariser_i) = P;
        m.morphogens(:,kapar_i) = kapar_p;
+
    m.morphogens(:,kapar_i) = kapar_p;
        m.morphogens(:,kaper_i) = kaper_p;
+
    m.morphogens(:,kaper_i) = kaper_p;
        m.morphogens(:,kbpar_i) = kbpar_p;
+
    m.morphogens(:,kbpar_i) = kbpar_p;
        m.morphogens(:,kbper_i) = kbper_p;
+
    m.morphogens(:,kbper_i) = kbper_p;
        m.morphogens(:,knor_i) = knor_p;
+
    m.morphogens(:,knor_i) = knor_p;
        m.morphogens(:,strainret_i) = strainret_p;
+
    m.morphogens(:,strainret_i) = strainret_p;
        m.morphogens(:,arrest_i) = arrest_p;
+
    m.morphogens(:,arrest_i) = arrest_p;
        m.morphogens(:,id_plusorg_i) = id_plusorg_p;
 
        m.morphogens(:,id_negorg_i) = id_negorg_p;
 
        m.morphogens(:,id_a_i) = id_a_p;
 
        m.morphogens(:,id_b_i) = id_b_p;
 
 
   
 
   
        <span style="color: Green">%%% USER CODE: FINALISATION</span>
+
<span style="color: Green">%%% USER CODE: FINALISATION</span>
 
   
 
   
        <span style="color: Green">% In this section you may modify the mesh in any way whatsoever.</span>
+
<span style="color: Green">% In this section you may modify the mesh in any way whatsoever.</span>
 
   
 
   
  <span style="color: CornflowerBlue">Section 12</span>
+
  <span style="color: CornflowerBlue">Section 13</span>
        <span style="color: Green">% If needed force FE to subdivide (increase number FE's) here</span>
+
    <span style="color: Green">% If needed force FE to subdivide (increase number FE's) here</span>
        <span style="color: Green">% if realtime==280+dt</span>
+
    <span style="color: Green">% if realtime==280+dt</span>
        <span style="color: Green">% m = leaf_subdivide( m, 'morphogen','id_vent',...</span>
+
          <span style="color: Green">% m = leaf_subdivide( m, 'morphogen','id_vent',...</span>
        <span style="color: Green">%      'min',0.5,'max',1,...</span>
+
          <span style="color: Green">%      'min',0.5,'max',1,...</span>
        <span style="color: Green">%      'mode','mid','levels','all');</span>
+
          <span style="color: Green">%      'mode','mid','levels','all');</span>
        <span style="color: Green">% end</span>
+
    <span style="color: Green">% end</span>
        <span style="color: Green">% Cut the mesh along the seams (see above)</span>
+
<span style="color: Green">% Cut the mesh along the seams (see above)</span>
        <span style="color: Green">% if m.userdata.CutOpen==1</span>
+
    <span style="color: Green">% if m.userdata.CutOpen==1</span>
        <span style="color: Green">%    m=leaf_dissect(m);</span>
+
    <span style="color: Green">%    m=leaf_dissect(m);</span>
        <span style="color: Green">%    m.userdata.CutOpen=2;</span>
+
    <span style="color: Green">%    m.userdata.CutOpen=2;       </span>
        <span style="color: Green">%    Relax accumulated stresses slowly i.e. 0.95 to 0.999</span>
+
    <span style="color: Green">%    Relax accumulated stresses slowly i.e. 0.95 to 0.999</span>
        <span style="color: Green">%    m = leaf_setproperty( m, 'freezing', 0.999 );</span>
+
    <span style="color: Green">%    m = leaf_setproperty( m, 'freezing', 0.999 );</span>
        <span style="color: Green">% end</span>
+
    <span style="color: Green">% end</span>
 
   
 
   
        <span style="color: Green">%%% END OF USER CODE: FINALISATION</span>
+
<span style="color: Green">%%% END OF USER CODE: FINALISATION</span>
 
   
 
   
    end
+
end
 
   
 
   
 
   
 
   
    <span style="color: Green">%%% USER CODE: SUBFUNCTIONS</span>
+
<span style="color: Green">%%% USER CODE: SUBFUNCTIONS</span>
 
   
 
   
  <span style="color: CornflowerBlue">Section 1 (automatic)</span>
+
  <span style="color: CornflowerBlue">Section 14</span>
    function m = local_setproperties( m )
+
function m = local_setproperties( m )
        <span style="color: Green">% This function is called at time zero in the INITIALISATION section of the</span>
+
<span style="color: Green">% This function is called at time zero in the INITIALISATION section of the</span>
        <span style="color: Green">% interaction function.  It provides commands to set each of the properties</span>
+
<span style="color: Green">% interaction function.  It provides commands to set each of the properties</span>
        <span style="color: Green">% that are contained in m.globalProps.  Uncomment whichever ones you would</span>
+
<span style="color: Green">% that are contained in m.globalProps.  Uncomment whichever ones you would</span>
        <span style="color: Green">% like to set yourself, and put in whatever value you want.</span>
+
<span style="color: Green">% like to set yourself, and put in whatever value you want.</span>
        <span style="color: Green">%</span>
+
<span style="color: Green">%</span>
        <span style="color: Green">% Some of these properties are for internal use only and should never be</span>
+
<span style="color: Green">% Some of these properties are for internal use only and should never be</span>
        <span style="color: Green">% set by the user.  At some point these will be moved into a different</span>
+
<span style="color: Green">% set by the user.  At some point these will be moved into a different</span>
        <span style="color: Green">% component of m, but for the present, just don't change anything unless</span>
+
<span style="color: Green">% component of m, but for the present, just don't change anything unless</span>
        <span style="color: Green">% you know what it is you're changing.</span>
+
<span style="color: Green">% you know what it is you're changing.</span>
 
   
 
   
        <span style="color: Green">%    m = leaf_setproperty( m, 'trinodesvalid', true );</span>
+
<span style="color: Green">%    m = leaf_setproperty( m, 'trinodesvalid', true );</span>
        <span style="color: Green">%    m = leaf_setproperty( m, 'prismnodesvalid', true );</span>
+
<span style="color: Green">%    m = leaf_setproperty( m, 'prismnodesvalid', true );</span>
        <span style="color: Green">%    m = leaf_setproperty( m, 'thicknessRelative', 0.020000 );</span>
+
<span style="color: Green">%    m = leaf_setproperty( m, 'thicknessRelative', 0.200000 );</span>
        <span style="color: Green">%    m = leaf_setproperty( m, 'thicknessArea', 0.000000 );</span>
+
<span style="color: Green">%    m = leaf_setproperty( m, 'thicknessArea', 0.000000 );</span>
        <span style="color: Green">%    m = leaf_setproperty( m, 'thicknessMode', 'physical' );</span>
+
<span style="color: Green">%    m = leaf_setproperty( m, 'thicknessMode', 'physical' );</span>
        <span style="color: Green">%    m = leaf_setproperty( m, 'activeGrowth', 1.000000 );</span>
+
<span style="color: Green">%    m = leaf_setproperty( m, 'activeGrowth', 1.000000 );</span>
        <span style="color: Green">%    m = leaf_setproperty( m, 'displayedGrowth', 1.000000 );</span>
+
<span style="color: Green">%    m = leaf_setproperty( m, 'displayedGrowth', 1.000000 );</span>
        <span style="color: Green">%    m = leaf_setproperty( m, 'displayedMulti', [] );</span>
+
<span style="color: Green">%    m = leaf_setproperty( m, 'displayedMulti', [] );</span>
        <span style="color: Green">%    m = leaf_setproperty( m, 'allowNegativeGrowth', true );</span>
+
<span style="color: Green">%    m = leaf_setproperty( m, 'allowNegativeGrowth', true );</span>
        <span style="color: Green">%    m = leaf_setproperty( m, 'usePrevDispAsEstimate', true );</span>
+
<span style="color: Green">%    m = leaf_setproperty( m, 'usePrevDispAsEstimate', true );</span>
        <span style="color: Green">%    m = leaf_setproperty( m, 'perturbInitGrowthEstimate', 0.000010 );</span>
+
<span style="color: Green">%    m = leaf_setproperty( m, 'perturbInitGrowthEstimate', 0.000010 );</span>
        <span style="color: Green">%    m = leaf_setproperty( m, 'perturbRelGrowthEstimate', 0.010000 );</span>
+
<span style="color: Green">%    m = leaf_setproperty( m, 'perturbRelGrowthEstimate', 0.010000 );</span>
        <span style="color: Green">%    m = leaf_setproperty( m, 'perturbDiffusionEstimate', 0.000100 );</span>
+
<span style="color: Green">%    m = leaf_setproperty( m, 'perturbDiffusionEstimate', 0.000100 );</span>
        <span style="color: Green">%    m = leaf_setproperty( m, 'resetRand', false );</span>
+
<span style="color: Green">%    m = leaf_setproperty( m, 'resetRand', false );</span>
        <span style="color: Green">%    m = leaf_setproperty( m, 'mingradient', 0.000000 );</span>
+
<span style="color: Green">%    m = leaf_setproperty( m, 'mingradient', 0.000000 );</span>
        <span style="color: Green">%    m = leaf_setproperty( m, 'relativepolgrad', false );</span>
+
<span style="color: Green">%    m = leaf_setproperty( m, 'relativepolgrad', false );</span>
        <span style="color: Green">%    m = leaf_setproperty( m, 'usefrozengradient', true );</span>
+
<span style="color: Green">%    m = leaf_setproperty( m, 'usefrozengradient', true );</span>
        <span style="color: Green">%    m = leaf_setproperty( m, 'userpolarisation', false );</span>
+
<span style="color: Green">%    m = leaf_setproperty( m, 'userpolarisation', false );</span>
        <span style="color: Green">%    m = leaf_setproperty( m, 'thresholdsq', 0.000841 );</span>
+
<span style="color: Green">%    m = leaf_setproperty( m, 'thresholdsq', 0.227223 );</span>
        <span style="color: Green">%    m = leaf_setproperty( m, 'splitmargin', 1.400000 );</span>
+
<span style="color: Green">%    m = leaf_setproperty( m, 'splitmargin', 1.400000 );</span>
        <span style="color: Green">%    m = leaf_setproperty( m, 'splitmorphogen', '' );</span>
+
<span style="color: Green">%    m = leaf_setproperty( m, 'splitmorphogen', '' );</span>
        <span style="color: Green">%    m = leaf_setproperty( m, 'thresholdmgen', 0.500000 );</span>
+
<span style="color: Green">%    m = leaf_setproperty( m, 'thresholdmgen', 0.500000 );</span>
        <span style="color: Green">%    m = leaf_setproperty( m, 'bulkmodulus', 1.000000 );</span>
+
<span style="color: Green">%    m = leaf_setproperty( m, 'bulkmodulus', 1.000000 );</span>
        <span style="color: Green">%    m = leaf_setproperty( m, 'unitbulkmodulus', true );</span>
+
<span style="color: Green">%    m = leaf_setproperty( m, 'unitbulkmodulus', true );</span>
        <span style="color: Green">%    m = leaf_setproperty( m, 'poissonsRatio', 0.300000 );</span>
+
<span style="color: Green">%    m = leaf_setproperty( m, 'poissonsRatio', 0.300000 );</span>
        <span style="color: Green">%    m = leaf_setproperty( m, 'starttime', 0.000000 );</span>
+
<span style="color: Green">%    m = leaf_setproperty( m, 'starttime', 0.000000 );</span>
        <span style="color: Green">%    m = leaf_setproperty( m, 'timestep', 0.010000 );</span>
+
<span style="color: Green">%    m = leaf_setproperty( m, 'timestep', 0.010000 );</span>
        <span style="color: Green">%    m = leaf_setproperty( m, 'timeunitname', '' );</span>
+
<span style="color: Green">%    m = leaf_setproperty( m, 'timeunitname', '' );</span>
        <span style="color: Green">%    m = leaf_setproperty( m, 'distunitname', 'mm' );</span>
+
<span style="color: Green">%    m = leaf_setproperty( m, 'distunitname', 'mm' );</span>
        <span style="color: Green">%    m = leaf_setproperty( m, 'scalebarvalue', 0.000000 );</span>
+
<span style="color: Green">%    m = leaf_setproperty( m, 'scalebarvalue', 0.000000 );</span>
        <span style="color: Green">%    m = leaf_setproperty( m, 'validateMesh', true );</span>
+
<span style="color: Green">%    m = leaf_setproperty( m, 'validateMesh', true );</span>
        <span style="color: Green">%    m = leaf_setproperty( m, 'rectifyverticals', false );</span>
+
<span style="color: Green">%    m = leaf_setproperty( m, 'rectifyverticals', false );</span>
        <span style="color: Green">%    m = leaf_setproperty( m, 'allowSplitLongFEM', true );</span>
+
<span style="color: Green">%    m = leaf_setproperty( m, 'allowSplitLongFEM', true );</span>
        <span style="color: Green">%    m = leaf_setproperty( m, 'longSplitThresholdPower', 0.000000 );</span>
+
<span style="color: Green">%    m = leaf_setproperty( m, 'longSplitThresholdPower', 0.000000 );</span>
        <span style="color: Green">%    m = leaf_setproperty( m, 'allowSplitBentFEM', false );</span>
+
<span style="color: Green">%    m = leaf_setproperty( m, 'allowSplitBentFEM', false );</span>
        <span style="color: Green">%    m = leaf_setproperty( m, 'allowSplitBio', true );</span>
+
<span style="color: Green">%    m = leaf_setproperty( m, 'allowSplitBio', true );</span>
        <span style="color: Green">%    m = leaf_setproperty( m, 'allowFlipEdges', false );</span>
+
<span style="color: Green">%    m = leaf_setproperty( m, 'allowFlipEdges', false );</span>
        <span style="color: Green">%    m = leaf_setproperty( m, 'allowElideEdges', true );</span>
+
<span style="color: Green">%    m = leaf_setproperty( m, 'allowElideEdges', true );</span>
        <span style="color: Green">%    m = leaf_setproperty( m, 'mincellangle', 0.200000 );</span>
+
<span style="color: Green">%    m = leaf_setproperty( m, 'mincellangle', 0.200000 );</span>
        <span style="color: Green">%    m = leaf_setproperty( m, 'alwaysFlat', 0.000000 );</span>
+
<span style="color: Green">%    m = leaf_setproperty( m, 'alwaysFlat', 0.000000 );</span>
        <span style="color: Green">%    m = leaf_setproperty( m, 'flattenforceconvex', true );</span>
+
<span style="color: Green">%    m = leaf_setproperty( m, 'flattenforceconvex', true );</span>
        <span style="color: Green">%    m = leaf_setproperty( m, 'flatten', false );</span>
+
<span style="color: Green">%    m = leaf_setproperty( m, 'flatten', false );</span>
        <span style="color: Green">%    m = leaf_setproperty( m, 'flattenratio', 1.000000 );</span>
+
<span style="color: Green">%    m = leaf_setproperty( m, 'flattenratio', 1.000000 );</span>
        <span style="color: Green">%    m = leaf_setproperty( m, 'useGrowthTensors', false );</span>
+
<span style="color: Green">%    m = leaf_setproperty( m, 'useGrowthTensors', false );</span>
        <span style="color: Green">%    m = leaf_setproperty( m, 'plasticGrowth', false );</span>
+
<span style="color: Green">%    m = leaf_setproperty( m, 'plasticGrowth', false );</span>
        <span style="color: Green">%    m = leaf_setproperty( m, 'totalinternalrotation', 0.000000 );</span>
+
<span style="color: Green">%    m = leaf_setproperty( m, 'totalinternalrotation', 0.000000 );</span>
        <span style="color: Green">%    m = leaf_setproperty( m, 'stepinternalrotation', 2.000000 );</span>
+
<span style="color: Green">%    m = leaf_setproperty( m, 'stepinternalrotation', 2.000000 );</span>
        <span style="color: Green">%    m = leaf_setproperty( m, 'showinternalrotation', false );</span>
+
<span style="color: Green">%    m = leaf_setproperty( m, 'showinternalrotation', false );</span>
        <span style="color: Green">%    m = leaf_setproperty( m, 'performinternalrotation', false );</span>
+
<span style="color: Green">%    m = leaf_setproperty( m, 'performinternalrotation', false );</span>
        <span style="color: Green">%    m = leaf_setproperty( m, 'internallyrotated', false );</span>
+
<span style="color: Green">%    m = leaf_setproperty( m, 'internallyrotated', false );</span>
        <span style="color: Green">%    m = leaf_setproperty( m, 'maxFEcells', 0 );</span>
+
<span style="color: Green">%    m = leaf_setproperty( m, 'maxFEcells', 0 );</span>
        <span style="color: Green">%    m = leaf_setproperty( m, 'inittotalcells', 0 );</span>
+
<span style="color: Green">%    m = leaf_setproperty( m, 'inittotalcells', 0 );</span>
        <span style="color: Green">%    m = leaf_setproperty( m, 'bioApresplitproc', '' );</span>
+
<span style="color: Green">%    m = leaf_setproperty( m, 'bioApresplitproc', '' );</span>
        <span style="color: Green">%    m = leaf_setproperty( m, 'bioApostsplitproc', '' );</span>
+
<span style="color: Green">%    m = leaf_setproperty( m, 'bioApostsplitproc', '' );</span>
        <span style="color: Green">%    m = leaf_setproperty( m, 'maxBioAcells', 0 );</span>
+
<span style="color: Green">%    m = leaf_setproperty( m, 'maxBioAcells', 0 );</span>
        <span style="color: Green">%    m = leaf_setproperty( m, 'maxBioBcells', 0 );</span>
+
<span style="color: Green">%    m = leaf_setproperty( m, 'maxBioBcells', 0 );</span>
        <span style="color: Green">%    m = leaf_setproperty( m, 'colors', (6 values) );</span>
+
<span style="color: Green">%    m = leaf_setproperty( m, 'colors', (6 values) );</span>
        <span style="color: Green">%    m = leaf_setproperty( m, 'colorvariation', 0.050000 );</span>
+
<span style="color: Green">%    m = leaf_setproperty( m, 'colorvariation', 0.050000 );</span>
        <span style="color: Green">%    m = leaf_setproperty( m, 'colorparams', (12 values) );</span>
+
<span style="color: Green">%    m = leaf_setproperty( m, 'colorparams', (12 values) );</span>
        <span style="color: Green">%    m = leaf_setproperty( m, 'freezing', 0.000000 );</span>
+
<span style="color: Green">%    m = leaf_setproperty( m, 'freezing', 0.000000 );</span>
        <span style="color: Green">%    m = leaf_setproperty( m, 'canceldrift', false );</span>
+
<span style="color: Green">%    m = leaf_setproperty( m, 'canceldrift', false );</span>
        <span style="color: Green">%    m = leaf_setproperty( m, 'mgen_interaction', '' );</span>
+
<span style="color: Green">%    m = leaf_setproperty( m, 'mgen_interaction', '' );</span>
        <span style="color: Green">%    m = leaf_setproperty( m, 'mgen_interactionName', 'gpt_tut_interaction_20110530' );</span>
+
<span style="color: Green">%    m = leaf_setproperty( m, 'mgen_interactionName', 'gpt_tut_fresh_interaction_function_20110530' );</span>
        <span style="color: Green">%    m = leaf_setproperty( m, 'allowInteraction', true );</span>
+
<span style="color: Green">%    m = leaf_setproperty( m, 'allowInteraction', true );</span>
        <span style="color: Green">%    m = leaf_setproperty( m, 'interactionValid', true );</span>
+
<span style="color: Green">%    m = leaf_setproperty( m, 'interactionValid', true );</span>
        <span style="color: Green">%    m = leaf_setproperty( m, 'gaussInfo', (unknown type ''struct'') );</span>
+
<span style="color: Green">%    m = leaf_setproperty( m, 'gaussInfo', (unknown type ''struct'') );</span>
        <span style="color: Green">%    m = leaf_setproperty( m, 'stitchDFs', [] );</span>
+
<span style="color: Green">%    m = leaf_setproperty( m, 'stitchDFs', [] );</span>
        <span style="color: Green">%    m = leaf_setproperty( m, 'D', (36 values) );</span>
+
<span style="color: Green">%    m = leaf_setproperty( m, 'D', (36 values) );</span>
        <span style="color: Green">%    m = leaf_setproperty( m, 'C', (36 values) );</span>
+
<span style="color: Green">%    m = leaf_setproperty( m, 'C', (36 values) );</span>
        <span style="color: Green">%    m = leaf_setproperty( m, 'G', (6 values) );</span>
+
<span style="color: Green">%    m = leaf_setproperty( m, 'G', (6 values) );</span>
        <span style="color: Green">%    m = leaf_setproperty( m, 'solver', 'cgs' );</span>
+
<span style="color: Green">%    m = leaf_setproperty( m, 'solver', 'cgs' );</span>
        <span style="color: Green">%    m = leaf_setproperty( m, 'solverprecision', 'double' );</span>
+
<span style="color: Green">%    m = leaf_setproperty( m, 'solverprecision', 'double' );</span>
        <span style="color: Green">%    m = leaf_setproperty( m, 'solvertolerance', 0.001000 );</span>
+
<span style="color: Green">%    m = leaf_setproperty( m, 'solvertolerance', 0.001000 );</span>
        <span style="color: Green">%    m = leaf_setproperty( m, 'solvertolerancemethod', 'norm' );</span>
+
<span style="color: Green">%    m = leaf_setproperty( m, 'solvertolerancemethod', 'norm' );</span>
        <span style="color: Green">%    m = leaf_setproperty( m, 'diffusiontolerance', 0.000010 );</span>
+
<span style="color: Green">%    m = leaf_setproperty( m, 'diffusiontolerance', 0.000010 );</span>
        <span style="color: Green">%    m = leaf_setproperty( m, 'allowsparse', true );</span>
+
<span style="color: Green">%    m = leaf_setproperty( m, 'allowsparse', true );</span>
        <span style="color: Green">%    m = leaf_setproperty( m, 'maxIters', 0 );</span>
+
<span style="color: Green">%    m = leaf_setproperty( m, 'maxIters', 0 );</span>
        <span style="color: Green">%    m = leaf_setproperty( m, 'maxsolvetime', 1000.000000 );</span>
+
<span style="color: Green">%    m = leaf_setproperty( m, 'maxsolvetime', 1000.000000 );</span>
        <span style="color: Green">%    m = leaf_setproperty( m, 'cgiters', 0 );</span>
+
<span style="color: Green">%    m = leaf_setproperty( m, 'cgiters', 0 );</span>
        <span style="color: Green">%    m = leaf_setproperty( m, 'simsteps', 0 );</span>
+
<span style="color: Green">%    m = leaf_setproperty( m, 'simsteps', 0 );</span>
        <span style="color: Green">%    m = leaf_setproperty( m, 'stepsperrender', 0 );</span>
+
<span style="color: Green">%    m = leaf_setproperty( m, 'stepsperrender', 0 );</span>
        <span style="color: Green">%    m = leaf_setproperty( m, 'growthEnabled', true );</span>
+
<span style="color: Green">%    m = leaf_setproperty( m, 'growthEnabled', true );</span>
        <span style="color: Green">%    m = leaf_setproperty( m, 'diffusionEnabled', true );</span>
+
<span style="color: Green">%    m = leaf_setproperty( m, 'diffusionEnabled', true );</span>
        <span style="color: Green">%    m = leaf_setproperty( m, 'flashmovie', false );</span>
+
<span style="color: Green">%    m = leaf_setproperty( m, 'flashmovie', false );</span>
        <span style="color: Green">%    m = leaf_setproperty( m, 'makemovie', false );</span>
+
<span style="color: Green">%    m = leaf_setproperty( m, 'makemovie', false );</span>
        <span style="color: Green">%    m = leaf_setproperty( m, 'moviefile', '' );</span>
+
<span style="color: Green">%    m = leaf_setproperty( m, 'moviefile', '' );</span>
        <span style="color: Green">%    m = leaf_setproperty( m, 'codec', 'None' );</span>
+
<span style="color: Green">%    m = leaf_setproperty( m, 'codec', 'None' );</span>
        <span style="color: Green">%    m = leaf_setproperty( m, 'autonamemovie', true );</span>
+
<span style="color: Green">%    m = leaf_setproperty( m, 'autonamemovie', true );</span>
        <span style="color: Green">%    m = leaf_setproperty( m, 'overwritemovie', false );</span>
+
<span style="color: Green">%    m = leaf_setproperty( m, 'overwritemovie', false );</span>
        <span style="color: Green">%    m = leaf_setproperty( m, 'framesize', [] );</span>
+
<span style="color: Green">%    m = leaf_setproperty( m, 'framesize', [] );</span>
        <span style="color: Green">%    m = leaf_setproperty( m, 'mov', [] );</span>
+
<span style="color: Green">%    m = leaf_setproperty( m, 'mov', [] );</span>
        <span style="color: Green">%    m = leaf_setproperty( m, 'jiggleProportion', 1.000000 );</span>
+
<span style="color: Green">%    m = leaf_setproperty( m, 'jiggleProportion', 1.000000 );</span>
        <span style="color: Green">%    m = leaf_setproperty( m, 'cvtperiter', 0.200000 );</span>
+
<span style="color: Green">%    m = leaf_setproperty( m, 'cvtperiter', 0.200000 );</span>
        <span style="color: Green">%    m = leaf_setproperty( m, 'boingNeeded', false );</span>
+
<span style="color: Green">%    m = leaf_setproperty( m, 'boingNeeded', false );</span>
        <span style="color: Green">%    m = leaf_setproperty( m, 'initialArea', 0.031326 );</span>
+
<span style="color: Green">%    m = leaf_setproperty( m, 'initialArea', 3.105828 );</span>
        <span style="color: Green">%    m = leaf_setproperty( m, 'bendunitlength', 0.176992 );</span>
+
<span style="color: Green">%    m = leaf_setproperty( m, 'bendunitlength', 1.762336 );</span>
        <span style="color: Green">%    m = leaf_setproperty( m, 'targetRelArea', 1.000000 );</span>
+
<span style="color: Green">%    m = leaf_setproperty( m, 'targetRelArea', 1.000000 );</span>
        <span style="color: Green">%    m = leaf_setproperty( m, 'defaultinterp', 'min' );</span>
+
<span style="color: Green">%    m = leaf_setproperty( m, 'defaultinterp', 'min' );</span>
        <span style="color: Green">%    m = leaf_setproperty( m, 'readonly', false );</span>
+
<span style="color: Green">%    m = leaf_setproperty( m, 'readonly', false );</span>
        <span style="color: Green">%    m = leaf_setproperty( m, 'projectdir', 'D:\ab\Matlab stuff' );</span>
+
<span style="color: Green">%    m = leaf_setproperty( m, 'projectdir', 'D:\ab\Matlab stuff' );</span>
        <span style="color: Green">%    m = leaf_setproperty( m, 'modelname', 'GPT_tut_interaction_20110530' );</span>
+
<span style="color: Green">%    m = leaf_setproperty( m, 'modelname', 'GPT_tut_fresh_interaction_function_20110530' );</span>
        <span style="color: Green">%    m = leaf_setproperty( m, 'allowsave', true );</span>
+
<span style="color: Green">%    m = leaf_setproperty( m, 'allowsave', true );</span>
        <span style="color: Green">%    m = leaf_setproperty( m, 'addedToPath', false );</span>
+
<span style="color: Green">%    m = leaf_setproperty( m, 'addedToPath', false );</span>
        <span style="color: Green">%    m = leaf_setproperty( m, 'bendsplit', 0.300000 );</span>
+
<span style="color: Green">%    m = leaf_setproperty( m, 'bendsplit', 0.300000 );</span>
        <span style="color: Green">%    m = leaf_setproperty( m, 'usepolfreezebc', false );</span>
+
<span style="color: Green">%    m = leaf_setproperty( m, 'usepolfreezebc', false );</span>
        <span style="color: Green">%    m = leaf_setproperty( m, 'dorsaltop', true );</span>
+
<span style="color: Green">%    m = leaf_setproperty( m, 'dorsaltop', true );</span>
        <span style="color: Green">%    m = leaf_setproperty( m, 'defaultazimuth', -45.000000 );</span>
+
<span style="color: Green">%    m = leaf_setproperty( m, 'defaultazimuth', -45.000000 );</span>
        <span style="color: Green">%    m = leaf_setproperty( m, 'defaultelevation', 33.750000 );</span>
+
<span style="color: Green">%    m = leaf_setproperty( m, 'defaultelevation', 33.750000 );</span>
        <span style="color: Green">%    m = leaf_setproperty( m, 'defaultroll', 0.000000 );</span>
+
<span style="color: Green">%    m = leaf_setproperty( m, 'defaultroll', 0.000000 );</span>
        <span style="color: Green">%    m = leaf_setproperty( m, 'defaultViewParams', (unknown type ''struct'') );</span>
+
<span style="color: Green">%    m = leaf_setproperty( m, 'defaultViewParams', (unknown type ''struct'') );</span>
        <span style="color: Green">%    m = leaf_setproperty( m, 'comment', '' );</span>
+
<span style="color: Green">%    m = leaf_setproperty( m, 'comment', '' );</span>
        <span style="color: Green">%    m = leaf_setproperty( m, 'legendTemplate', '%T: %q\n%m' );</span>
+
<span style="color: Green">%    m = leaf_setproperty( m, 'legendTemplate', '%T: %q\n%m' );</span>
        <span style="color: Green">%    m = leaf_setproperty( m, 'bioAsplitcells', true );</span>
+
<span style="color: Green">%    m = leaf_setproperty( m, 'bioAsplitcells', true );</span>
        <span style="color: Green">%    m = leaf_setproperty( m, 'bioApullin', 0.142857 );</span>
+
<span style="color: Green">%    m = leaf_setproperty( m, 'bioApullin', 0.142857 );</span>
        <span style="color: Green">%    m = leaf_setproperty( m, 'bioAfakepull', 0.202073 );</span>
+
<span style="color: Green">%    m = leaf_setproperty( m, 'bioAfakepull', 0.202073 );</span>
        <span style="color: Green">%    m = leaf_setproperty( m, 'interactive', false );</span>
+
<span style="color: Green">%    m = leaf_setproperty( m, 'interactive', false );</span>
        <span style="color: Green">%    m = leaf_setproperty( m, 'coderevision', 0 );</span>
+
<span style="color: Green">%    m = leaf_setproperty( m, 'coderevision', 0 );</span>
        <span style="color: Green">%    m = leaf_setproperty( m, 'coderevisiondate', '' );</span>
+
<span style="color: Green">%    m = leaf_setproperty( m, 'coderevisiondate', '' );</span>
        <span style="color: Green">%    m = leaf_setproperty( m, 'modelrevision', 0 );</span>
+
<span style="color: Green">%    m = leaf_setproperty( m, 'modelrevision', 0 );</span>
        <span style="color: Green">%    m = leaf_setproperty( m, 'modelrevisiondate', '' );</span>
+
<span style="color: Green">%    m = leaf_setproperty( m, 'modelrevisiondate', '' );</span>
        <span style="color: Green">%    m = leaf_setproperty( m, 'savedrunname', '' );</span>
+
<span style="color: Green">%    m = leaf_setproperty( m, 'savedrunname', '' );</span>
        <span style="color: Green">%    m = leaf_setproperty( m, 'savedrundesc', '' );</span>
+
<span style="color: Green">%    m = leaf_setproperty( m, 'savedrundesc', '' );</span>
        <span style="color: Green">%    m = leaf_setproperty( m, 'vxgrad', (108 values) );</span>
+
<span style="color: Green">%    m = leaf_setproperty( m, 'vxgrad', (108 values) );</span>
        <span style="color: Green">%    m = leaf_setproperty( m, 'lengthscale', 0.200000 );</span>
+
<span style="color: Green">%    m = leaf_setproperty( m, 'lengthscale', 2.000000 );</span>
    end
+
end
 
   
 
   
  <span style="color: CornflowerBlue">Section 14</span>
+
  <span style="color: CornflowerBlue">Section 15</span>
    <span style="color: Green">% Here you may write any functions of your own, that you want to call from</span>
+
<span style="color: Green">% Here you may write any functions of your own, that you want to call from</span>
    <span style="color: Green">% the interaction function, but never need to call from outside it.</span>
+
<span style="color: Green">% the interaction function, but never need to call from outside it.</span>
    <span style="color: Green">% Remember that they do not have access to any variables except those</span>
+
<span style="color: Green">% Remember that they do not have access to any variables except those</span>
    <span style="color: Green">% that you pass as parameters, and cannot change anything except by</span>
+
<span style="color: Green">% that you pass as parameters, and cannot change anything except by</span>
    <span style="color: Green">% returning new values as results.</span>
+
<span style="color: Green">% returning new values as results.</span>
    <span style="color: Green">% Whichever section they are called from, they must respect the same</span>
+
<span style="color: Green">% Whichever section they are called from, they must respect the same</span>
    <span style="color: Green">% restrictions on what modifications they are allowed to make to the mesh.</span>
+
<span style="color: Green">% restrictions on what modifications they are allowed to make to the mesh.</span>
 
   
 
   
    <span style="color: Green">% For example:</span>
+
<span style="color: Green">% For example:</span>
 
   
 
   
  <span style="color: CornflowerBlue">Section 1 (automatic)</span>
+
  <span style="color: CornflowerBlue">Section 16</span>
    <span style="color: Green">% function m = do_something( m )</span>
+
<span style="color: Green">% function m = do_something( m )</span>
    <span style="color: Green">%  % Change m in some way.</span>
+
<span style="color: Green">%  % Change m in some way.</span>
    <span style="color: Green">% end</span>
+
<span style="color: Green">% end</span>
 
   
 
   
    <span style="color: Green">% Call it from the main body of the interaction function like this:</span>
+
<span style="color: Green">% Call it from the main body of the interaction function like this:</span>
    <span style="color: Green">%      m = do_something( m );</span>
+
<span style="color: Green">%      m = do_something( m );</span>

Latest revision as of 19:12, 30 May 2011

Tutorial on the interaction function details

This file was placed in the Matlab Editor automatically on clicking Panel: Edit in the newly saved project

Section 1
function m = gpt_tut_fresh_interaction_function_20110530( m )
%m = gpt_tut_fresh_interaction_function_20110530( m )
%   Morphogen interaction function.
%   Written at 2011-05-30 20:10:22.
%   GFtbox revision 0, .

% The user may edit any part of this function between delimiters
% of the form "USER CODE..." and "END OF USER CODE...".  The
% delimiters themselves must not be moved, edited, deleted, or added.

    if isempty(m), return; end

    fprintf( 1, '%s found in %s\n', mfilename(), which(mfilename()) );

    try
        m = local_setproperties( m );
    catch
    end

    realtime = m.globalDynamicProps.currenttime;

Section 2
%%% USER CODE: INITIALISATION

% In this section you may modify the mesh in any way whatsoever.
    if (Steps(m)==0) && m.globalDynamicProps.doinit % First iteration
        % Zero out a lot of stuff to create a blank slate.  
        % If no morphogens are set in the GUI it may be useful to
        % zero some arrays by uncommenting the following.
        % m.morphogens(:) = 0;
        % m.morphogenclamp(:) = 0;
        % m.mgen_production(:) = 0;
        % m.mgen_absorption(:) = 0;
        % m.seams(:) = false;
        % m.mgen_dilution(:) = false;

        % Set up names for variant models.  Useful for running multiple models on a cluster.
        m.userdata.ranges.modelname.range = { 'MODEL1', 'MODEL2' };  % CLUSTER
        m.userdata.ranges.modelname.index = 1;                       % CLUSTER
    end
    modelname = m.userdata.ranges.modelname.range{m.userdata.ranges.modelname.index};  % CLUSTER
    disp(sprintf('\nRunning %s model %s\n',mfilename, modelname));
    switch modelname
        case 'MODEL1'
            % Set up the parameters (e.g. mutations) for this model here.
        case 'MODEL2'
            % Set up the parameters (e.g. mutations) for this model here.
        otherwise
            % If you reach here, you probably forgot a case.
    end
    	
    % More examples of code for all iterations.

    % Set priorities for simultaneous plotting of multiple morphogens, if desired.
    % m = leaf_mgen_plotpriority( m, {'MGEN1', 'MGEN2'}, [1,2], [0.5,0.75] );

    % Set colour of polariser gradient arrows.
    % m = leaf_plotoptions(m,'highgradcolor',[0,0,0],'lowgradcolor',[1,0,0]);

    % setup a multiplot of the following morphogens
    % m = leaf_plotoptions( m, 'morphogen', {'V_PROFILE1','V_PROFILE2','KAPAR','S_LEFTRIGHT'});

    % to plot polariser on the A side and resultant areal growth rate on the B side:
    % m = leaf_plotoptions( m, 'morphogenA', 'POLARISER', ...
    %                      'outputquantityB', 'resultantgrowthrate', ...
    %                      'outputaxesB', 'areal' );

    % monitor properties of vertices must be done here - so that it reports newly equilibrated levels
    % m=leaf_profile_monitor(m,... % essential
    %         'REGIONLABELS',{'V_PROFILE1','V_PROFILE2'},... % essential
    %         'MORPHOGENS',{'S_LEFTRIGHT','S_CENTRE'},... % optional  (one element per REGIONLABEL)
    %         'VERTLABELS',false,'FigNum',1,'EXCEL',true,'MODELNAME',modelname); % optional (file in snapshots directory')
    

%%% END OF USER CODE: INITIALISATION

Section 3
%%% SECTION 1: ACCESSING MORPHOGENS AND TIME.
%%% AUTOMATICALLY GENERATED CODE: DO NOT EDIT.

    if isempty(m), return; end

    setGlobals();
    global gNEW_KA_PAR gNEW_KA_PER gNEW_KB_PAR gNEW_KB_PER
    global gNEW_K_NOR gNEW_POLARISER gNEW_STRAINRET gNEW_ARREST
    dt = m.globalProps.timestep;
    polariser_i = gNEW_POLARISER;
    P = m.morphogens(:,polariser_i);
    [kapar_i,kapar_p,kapar_a,kapar_l] = getMgenLevels( m, 'KAPAR' );
    [kaper_i,kaper_p,kaper_a,kaper_l] = getMgenLevels( m, 'KAPER' );
    [kbpar_i,kbpar_p,kbpar_a,kbpar_l] = getMgenLevels( m, 'KBPAR' );
    [kbper_i,kbper_p,kbper_a,kbper_l] = getMgenLevels( m, 'KBPER' );
    [knor_i,knor_p,knor_a,knor_l] = getMgenLevels( m, 'KNOR' );
    [strainret_i,strainret_p,strainret_a,strainret_l] = getMgenLevels( m, 'STRAINRET' );
    [arrest_i,arrest_p,arrest_a,arrest_l] = getMgenLevels( m, 'ARREST' );

% Mesh type: circle
%          centre: 0
%       circumpts: 24
%       coneangle: 0
%         dealign: 0
%          height: 0
%        innerpts: 0
%      randomness: 0.1
%           rings: 4
%         version: 1
%          xwidth: 2
%          ywidth: 2

%            Morphogen   Diffusion   Decay   Dilution   Mutant
%            -------------------------------------------------
%                KAPAR        ----    ----       ----     ----
%                KAPER        ----    ----       ----     ----
%                KBPAR        ----    ----       ----     ----
%                KBPER        ----    ----       ----     ----
%                 KNOR        ----    ----       ----     ----
%            POLARISER        ----    ----       ----     ----
%            STRAINRET        ----    ----       ----     ----
%               ARREST        ----    ----       ----     ----


%%% USER CODE: MORPHOGEN INTERACTIONS

% In this section you may modify the mesh in any way that does not
Section 4
% alter the set of nodes.

    if (Steps(m)==0) && m.globalDynamicProps.doinit  % Initialisation code.
        % Put any code here that should only be performed at the start of
        % the simulation, for example, to set up initial morphogen values.
        
        % m.nodes is the set of vertex positions, an N by 3 array if there
        % are N vertices.  Row number K contains the X, Y, and Z
        % coordinates of the Kth vertex. To obtain a list of the X
        % coordinates of every vertex, write m.nodes(:,1).  The Y
        % coordinates are given by m.nodes(:,2) and the Z coordinates by
        % m.nodes(:,3).

        % Set up a morphogen promoter (_p suffix) region where x values are minimum
        % id_prox_p(m.nodes(:,1)==min(m.nodes(:,1)))=1;
        % if the morphogen level (_l suffix) is to be used in this iteration 
        % set the level using the morphogen activity (_a suffix).
        % id_prox_l=id_prox_p * id_prox_a; % when a mutation is specified in the GUI 
        % the activity (_a) is set to zero

        % One way to set up a morphogen gradient is by ...
        % Setting up a gradient by clamping the ends (execute only once)
        % P=id_prox_p;
        % m.morphogenclamp( ((id_prox_p==1)|(id_dist_p==1)), polariser_i ) = 1;
        % m = leaf_mgen_conductivity( m, 'POLARISER', 0.01 );  %specifies the diffusion rate of polariser    
        % m = leaf_mgen_absorption( m, 'POLARISER', 0.1 );     % specifies degradation rate of polariser

        % Fixing vertices, i.e. fix z for the base to prevent base from moving up or down
        % m=leaf_fix_vertex(m,'vertex',find(id_prox_p==1),'dfs','z');

        % To cut the mesh, set a temporary morphogen to 1 in places to cut
        % seams=zeros(size(P));
        % seams(indexes to places to cut)=1;
        % m=leaf_set_seams(m,seams);

    end
    
Section 5
    % Second way to generate a gradient
    % generating (+) and sinking (-) a diffusing signal (in this case polariser)
    % m.mgen_production( :, polariser_i ) = + 5*s_spur_p - P .* id_dist_p;

    % Monitor growth by scattering discs that deform over time (c.f. inducing biological clones)
    % (CARE - if the canvas is flat ensure that Plot:Hide Thickness is true, 
    % because a quirk of the Matlab z-buffer means that they can get hidden by mistake)
    %    if (340>realtime-dt) && (340<realtime+dt) % discs to be added at realtime==340
    %        m = leaf_makesecondlayer( m, ...  % This function adds discs that represent transformed cells.
    %            'mode', 'each', ...  % Make discs randomly scattered over the canvas.
    %            'relarea', 1/16000, ...   % Each discs has area was 1/16000 of the initial area of the canvas.
    %            'probpervx', 'V_FLOWER', ... % induce discs over whole canvas (V_FLOWER is 1 over whole canvas)
    %            'numcells',4500,...%number of discs (that will become ellipses)
    %            'sides', 6, ...  % Each discs is approximated as a 6-sided regular polygon.
    %            'colors', [0.5 0.5 0.5], ...  % Default colour is gray but
    %            'colorvariation',1,... % Each disc is a random colour
    %            'add', true );  % These discs are added to any discs existing already
    %    end
    
Section 6
    % Directives for creating latex representation directly from Matlab code
    % not fully implemented yet but will use @@ directives
    % @@at t
    % @@before t
    % @@after t
    % @@between t1 t2

Section 7
%     % If you want to define different phases according to the absolute
%     % time, create a morphogen for each phase and modulate 
%     % expressions using the morphogen
%     % like.  For example:
%     if (realtime < 10)  % first growth phase
%         f_firstgrowth_p = 1;
%     else
%         f_firstgrowth_p = 0;
%     end
%     if (realtime >= 10) % second growth phase
%         f_secondgrowth_p = 1;
%     else
%         f_secondgrowth_p = 0;
%     end
%
%     % If you want one morphogen to affect others only during a certain
%     % phase, write something like:
%
%     mgen_a_p = f_firstgrowth_p .* (various terms); % will zero except in firstgrowth

Section 8
    % Code common to all models.
    % @@PRN Polariser Regulatory Network
        % Every equation to be formatted should end with an at-at Eqn N comment.
    % @@GRN Gene Regulatory Network
        % Every equation to be formatted should end with an at-at Eqn N comment.
    % @@KRN Growth Regulatory Network
        % Every equation to be formatted should end with an at-at Eqn N comment.

Section 9
    % Code for specific models.
    switch modelname
Section 10
        case 'MODEL1'  % @@model MODEL1
            % @@PRN Polariser Regulatory Network
                % Every equation to be formatted should end with an at-at Eqn N comment.
                % P(:) = ...  % @@ Eqn xx
            % @@GRN Gene Regulatory Network
                % Every equation to be formatted should end with an at-at Eqn N comment.
            % @@KRN Growth Regulatory Network
                % Every equation to be formatted should end with an at-at Eqn N comment.
                % kapar_p(:) = 0;  % @@ Eqn xx
                % kaper_p(:) = 0;  % @@ Eqn xx
                % kbpar_p(:) = 0;  % @@ Eqn xx
                % kbper_p(:) = 0;  % @@ Eqn xx
                % knor_p(:)  = 0;  % @@ Eqn xx
Section 11
        case 'MODEL2'  % @@model MODEL2
            % @@PRN Polariser Regulatory Network
                % Every equation to be formatted should end with an at-at Eqn N comment.
                % P(:) = ...  % @@ Eqn xx
            % @@GRN Gene Regulatory Network
                % Every equation to be formatted should end with an at-at Eqn N comment.
            % @@KRN Growth Regulatory Network
                % Every equation to be formatted should end with an at-at Eqn N comment.
                % kapar_p(:) = 0;  % @@ Eqn xx
                % kaper_p(:) = 0;  % @@ Eqn xx
                % kbpar_p(:) = 0;  % @@ Eqn xx
                % kbper_p(:) = 0;  % @@ Eqn xx
                % knor_p(:)  = 0;  % @@ Eqn xx
        otherwise
            % If this happens, maybe you forgot a model.
    end

Section 12
%%% END OF USER CODE: MORPHOGEN INTERACTIONS

%%% SECTION 3: INSTALLING MODIFIED VALUES BACK INTO MESH STRUCTURE
%%% AUTOMATICALLY GENERATED CODE: DO NOT EDIT.
    m.morphogens(:,polariser_i) = P;
    m.morphogens(:,kapar_i) = kapar_p;
    m.morphogens(:,kaper_i) = kaper_p;
    m.morphogens(:,kbpar_i) = kbpar_p;
    m.morphogens(:,kbper_i) = kbper_p;
    m.morphogens(:,knor_i) = knor_p;
    m.morphogens(:,strainret_i) = strainret_p;
    m.morphogens(:,arrest_i) = arrest_p;

%%% USER CODE: FINALISATION

% In this section you may modify the mesh in any way whatsoever.

Section 13
    % If needed force FE to subdivide (increase number FE's) here
    % if realtime==280+dt
         % m = leaf_subdivide( m, 'morphogen','id_vent',...
         %       'min',0.5,'max',1,...
         %       'mode','mid','levels','all');
    % end
% Cut the mesh along the seams (see above)
    % if m.userdata.CutOpen==1
    %    m=leaf_dissect(m);
    %    m.userdata.CutOpen=2;        
    %    Relax accumulated stresses slowly i.e. 0.95 to 0.999
    %    m = leaf_setproperty( m, 'freezing', 0.999 );
    % end

%%% END OF USER CODE: FINALISATION

end


%%% USER CODE: SUBFUNCTIONS

Section 14
function m = local_setproperties( m )
% This function is called at time zero in the INITIALISATION section of the
% interaction function.  It provides commands to set each of the properties
% that are contained in m.globalProps.  Uncomment whichever ones you would
% like to set yourself, and put in whatever value you want.
%
% Some of these properties are for internal use only and should never be
% set by the user.  At some point these will be moved into a different
% component of m, but for the present, just don't change anything unless
% you know what it is you're changing.

%    m = leaf_setproperty( m, 'trinodesvalid', true );
%    m = leaf_setproperty( m, 'prismnodesvalid', true );
%    m = leaf_setproperty( m, 'thicknessRelative', 0.200000 );
%    m = leaf_setproperty( m, 'thicknessArea', 0.000000 );
%    m = leaf_setproperty( m, 'thicknessMode', 'physical' );
%    m = leaf_setproperty( m, 'activeGrowth', 1.000000 );
%    m = leaf_setproperty( m, 'displayedGrowth', 1.000000 );
%    m = leaf_setproperty( m, 'displayedMulti', [] );
%    m = leaf_setproperty( m, 'allowNegativeGrowth', true );
%    m = leaf_setproperty( m, 'usePrevDispAsEstimate', true );
%    m = leaf_setproperty( m, 'perturbInitGrowthEstimate', 0.000010 );
%    m = leaf_setproperty( m, 'perturbRelGrowthEstimate', 0.010000 );
%    m = leaf_setproperty( m, 'perturbDiffusionEstimate', 0.000100 );
%    m = leaf_setproperty( m, 'resetRand', false );
%    m = leaf_setproperty( m, 'mingradient', 0.000000 );
%    m = leaf_setproperty( m, 'relativepolgrad', false );
%    m = leaf_setproperty( m, 'usefrozengradient', true );
%    m = leaf_setproperty( m, 'userpolarisation', false );
%    m = leaf_setproperty( m, 'thresholdsq', 0.227223 );
%    m = leaf_setproperty( m, 'splitmargin', 1.400000 );
%    m = leaf_setproperty( m, 'splitmorphogen',  );
%    m = leaf_setproperty( m, 'thresholdmgen', 0.500000 );
%    m = leaf_setproperty( m, 'bulkmodulus', 1.000000 );
%    m = leaf_setproperty( m, 'unitbulkmodulus', true );
%    m = leaf_setproperty( m, 'poissonsRatio', 0.300000 );
%    m = leaf_setproperty( m, 'starttime', 0.000000 );
%    m = leaf_setproperty( m, 'timestep', 0.010000 );
%    m = leaf_setproperty( m, 'timeunitname',  );
%    m = leaf_setproperty( m, 'distunitname', 'mm' );
%    m = leaf_setproperty( m, 'scalebarvalue', 0.000000 );
%    m = leaf_setproperty( m, 'validateMesh', true );
%    m = leaf_setproperty( m, 'rectifyverticals', false );
%    m = leaf_setproperty( m, 'allowSplitLongFEM', true );
%    m = leaf_setproperty( m, 'longSplitThresholdPower', 0.000000 );
%    m = leaf_setproperty( m, 'allowSplitBentFEM', false );
%    m = leaf_setproperty( m, 'allowSplitBio', true );
%    m = leaf_setproperty( m, 'allowFlipEdges', false );
%    m = leaf_setproperty( m, 'allowElideEdges', true );
%    m = leaf_setproperty( m, 'mincellangle', 0.200000 );
%    m = leaf_setproperty( m, 'alwaysFlat', 0.000000 );
%    m = leaf_setproperty( m, 'flattenforceconvex', true );
%    m = leaf_setproperty( m, 'flatten', false );
%    m = leaf_setproperty( m, 'flattenratio', 1.000000 );
%    m = leaf_setproperty( m, 'useGrowthTensors', false );
%    m = leaf_setproperty( m, 'plasticGrowth', false );
%    m = leaf_setproperty( m, 'totalinternalrotation', 0.000000 );
%    m = leaf_setproperty( m, 'stepinternalrotation', 2.000000 );
%    m = leaf_setproperty( m, 'showinternalrotation', false );
%    m = leaf_setproperty( m, 'performinternalrotation', false );
%    m = leaf_setproperty( m, 'internallyrotated', false );
%    m = leaf_setproperty( m, 'maxFEcells', 0 );
%    m = leaf_setproperty( m, 'inittotalcells', 0 );
%    m = leaf_setproperty( m, 'bioApresplitproc',  );
%    m = leaf_setproperty( m, 'bioApostsplitproc',  );
%    m = leaf_setproperty( m, 'maxBioAcells', 0 );
%    m = leaf_setproperty( m, 'maxBioBcells', 0 );
%    m = leaf_setproperty( m, 'colors', (6 values) );
%    m = leaf_setproperty( m, 'colorvariation', 0.050000 );
%    m = leaf_setproperty( m, 'colorparams', (12 values) );
%    m = leaf_setproperty( m, 'freezing', 0.000000 );
%    m = leaf_setproperty( m, 'canceldrift', false );
%    m = leaf_setproperty( m, 'mgen_interaction',  );
%    m = leaf_setproperty( m, 'mgen_interactionName', 'gpt_tut_fresh_interaction_function_20110530' );
%    m = leaf_setproperty( m, 'allowInteraction', true );
%    m = leaf_setproperty( m, 'interactionValid', true );
%    m = leaf_setproperty( m, 'gaussInfo', (unknown type struct) );
%    m = leaf_setproperty( m, 'stitchDFs', [] );
%    m = leaf_setproperty( m, 'D', (36 values) );
%    m = leaf_setproperty( m, 'C', (36 values) );
%    m = leaf_setproperty( m, 'G', (6 values) );
%    m = leaf_setproperty( m, 'solver', 'cgs' );
%    m = leaf_setproperty( m, 'solverprecision', 'double' );
%    m = leaf_setproperty( m, 'solvertolerance', 0.001000 );
%    m = leaf_setproperty( m, 'solvertolerancemethod', 'norm' );
%    m = leaf_setproperty( m, 'diffusiontolerance', 0.000010 );
%    m = leaf_setproperty( m, 'allowsparse', true );
%    m = leaf_setproperty( m, 'maxIters', 0 );
%    m = leaf_setproperty( m, 'maxsolvetime', 1000.000000 );
%    m = leaf_setproperty( m, 'cgiters', 0 );
%    m = leaf_setproperty( m, 'simsteps', 0 );
%    m = leaf_setproperty( m, 'stepsperrender', 0 );
%    m = leaf_setproperty( m, 'growthEnabled', true );
%    m = leaf_setproperty( m, 'diffusionEnabled', true );
%    m = leaf_setproperty( m, 'flashmovie', false );
%    m = leaf_setproperty( m, 'makemovie', false );
%    m = leaf_setproperty( m, 'moviefile',  );
%    m = leaf_setproperty( m, 'codec', 'None' );
%    m = leaf_setproperty( m, 'autonamemovie', true );
%    m = leaf_setproperty( m, 'overwritemovie', false );
%    m = leaf_setproperty( m, 'framesize', [] );
%    m = leaf_setproperty( m, 'mov', [] );
%    m = leaf_setproperty( m, 'jiggleProportion', 1.000000 );
%    m = leaf_setproperty( m, 'cvtperiter', 0.200000 );
%    m = leaf_setproperty( m, 'boingNeeded', false );
%    m = leaf_setproperty( m, 'initialArea', 3.105828 );
%    m = leaf_setproperty( m, 'bendunitlength', 1.762336 );
%    m = leaf_setproperty( m, 'targetRelArea', 1.000000 );
%    m = leaf_setproperty( m, 'defaultinterp', 'min' );
%    m = leaf_setproperty( m, 'readonly', false );
%    m = leaf_setproperty( m, 'projectdir', 'D:\ab\Matlab stuff' );
%    m = leaf_setproperty( m, 'modelname', 'GPT_tut_fresh_interaction_function_20110530' );
%    m = leaf_setproperty( m, 'allowsave', true );
%    m = leaf_setproperty( m, 'addedToPath', false );
%    m = leaf_setproperty( m, 'bendsplit', 0.300000 );
%    m = leaf_setproperty( m, 'usepolfreezebc', false );
%    m = leaf_setproperty( m, 'dorsaltop', true );
%    m = leaf_setproperty( m, 'defaultazimuth', -45.000000 );
%    m = leaf_setproperty( m, 'defaultelevation', 33.750000 );
%    m = leaf_setproperty( m, 'defaultroll', 0.000000 );
%    m = leaf_setproperty( m, 'defaultViewParams', (unknown type struct) );
%    m = leaf_setproperty( m, 'comment',  );
%    m = leaf_setproperty( m, 'legendTemplate', '%T: %q\n%m' );
%    m = leaf_setproperty( m, 'bioAsplitcells', true );
%    m = leaf_setproperty( m, 'bioApullin', 0.142857 );
%    m = leaf_setproperty( m, 'bioAfakepull', 0.202073 );
%    m = leaf_setproperty( m, 'interactive', false );
%    m = leaf_setproperty( m, 'coderevision', 0 );
%    m = leaf_setproperty( m, 'coderevisiondate',  );
%    m = leaf_setproperty( m, 'modelrevision', 0 );
%    m = leaf_setproperty( m, 'modelrevisiondate',  );
%    m = leaf_setproperty( m, 'savedrunname',  );
%    m = leaf_setproperty( m, 'savedrundesc',  );
%    m = leaf_setproperty( m, 'vxgrad', (108 values) );
%    m = leaf_setproperty( m, 'lengthscale', 2.000000 );
end

Section 15
% Here you may write any functions of your own, that you want to call from
% the interaction function, but never need to call from outside it.
% Remember that they do not have access to any variables except those
% that you pass as parameters, and cannot change anything except by
% returning new values as results.
% Whichever section they are called from, they must respect the same
% restrictions on what modifications they are allowed to make to the mesh.

% For example:

Section 16
% function m = do_something( m )
%   % Change m in some way.
% end

% Call it from the main body of the interaction function like this:
%       m = do_something( m );