GPT tut interaction 20110530 on creating

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function m = gpt_tut_interaction_20110530( m ) %m = gpt_tut_interaction_20110530( m ) % Morphogen interaction function. % Written at 2011-05-30 09:42:07. % 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;

%%% 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 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' );
   [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' );

% Mesh type: circle % centre: 0 % circumpts: 48 % coneangle: 0 % dealign: 0 % height: 0 % innerpts: 0 % randomness: 0.1 % rings: 6 % version: 1 % xwidth: 0.2 % ywidth: 0.2

% Morphogen Diffusion Decay Dilution Mutant % ------------------------------------------------- % KAPAR ---- ---- ---- ---- % KAPER ---- ---- ---- ---- % KBPAR ---- ---- ---- ---- % KBPER ---- ---- ---- ---- % KNOR ---- ---- ---- ---- % POLARISER ---- ---- ---- ---- % STRAINRET ---- ---- ---- ---- % ARREST ---- ---- ---- ---- % ID_PLUSORG ---- ---- ---- ---- % ID_NEGORG ---- ---- ---- ---- % ID_A ---- ---- ---- ---- % ID_B ---- ---- ---- ----


%%% USER CODE: MORPHOGEN INTERACTIONS

% In this section you may modify the mesh in any way that does not % 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
   
   % 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
   
   % 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

% % 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

   % 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.
   % Code for specific models.
   switch modelname
       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
       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

%%% 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;
   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;

%%% USER CODE: FINALISATION

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

   % 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

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', 0.020000 ); % 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', 0.000841 ); % 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_interaction_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', 0.031326 ); % m = leaf_setproperty( m, 'bendunitlength', 0.176992 ); % 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_interaction_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', 0.200000 ); end

% 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:

% 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 );