GPT tut interaction 20110530 on creating: Difference between revisions
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[[Tutorial on the interaction function details|Tutorial on the interaction function details]]<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> | |||
<span style="color: CornflowerBlue">Section 1</span> | |||
function m = gpt_tut_fresh_interaction_function_20110530( m ) | |||
<span style="color: Green">%m = gpt_tut_fresh_interaction_function_20110530( m )</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">% GFtbox revision 0, .</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">% delimiters themselves must not be moved, edited, deleted, or added.</span> | |||
if isempty(m), return; end | |||
fprintf( 1, '<span style="color: Green">%s found in %s\n', mfilename(), which(mfilename()) );</span> | |||
try | |||
m = local_setproperties( m ); | |||
catch | |||
end | |||
realtime = m.globalDynamicProps.currenttime; | |||
<span style="color: CornflowerBlue">Section 2</span> | |||
<span style="color: Green">%%% USER CODE: INITIALISATION</span> | |||
<span style="color: Green">% In this section you may modify the mesh in any way whatsoever.< | |||
Latest revision as of 20:12, 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 );