GPT tut interaction 20110530 on creating

From BanghamLab
Jump to navigation Jump to search

Tutorial on the interaction function details

This file was output automatically on clicking Panel: Edit in the newly saved project called GPT tut interaction 20110530

The code has been divided into Sections to help with the tutorial.

Section 1 Automatic

   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

Section 2

   % 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 Automatic

   %%% 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.

Section 4

       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.
       % Code for specific models.
       switch modelname

Section 9

           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

Section 10

               % @@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 11 Automatic

   %%% 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

Section 12

   % 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

Section 13 Semi-automatic

   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

Section 14

   % 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 );