GPT tut interaction 20110530 on creating

Tutorial on the interaction function details

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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 );