Measuring using interaction function subroutines
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Measuring growth of a model
Download a project illustrating measurements GPT_MeasureGrowth_20121203
The GPT_MeasureGrowth_20121203 interaction function is shown at the bottom of this page.
There are several ways to measure growth on the model. For example, there are two auxiliary functions:
[out1, out2, out3, out4] = leaf_computeGrowthFromDisplacements( m, displacements, time, ... ) Compute the growth rate in each FE of m given the displacements of all the prism nodes and the time over which these displacements happened. This assumes that m is in the state after these displacements have happened. The results returned depend on the options and on how many output arguments are given. Note that unlike most leaf_* commands, m itself is not one of the output arguments, since this procedure does not need to modify m.
function m=leaf_profile_monitor(m,realtime,RegionLabels,Morphogens,start_figno)
monitor morphogen levels at a set of vertices
m, mesh
RegionLabels, vertices to be monitored as designated by cell array of strings, i.e. region labels
Morphogens, cell array of strings, i.e. uppercase morphogen names to
be monitored. There should be one RegionLabels string for each
Morphogens string
Vertlabels, if true then display vertex numbers in each region label on
the mesh default false
start_figno, default figure 1 (Must open a fig even if just monitoring to file)
MonData, optional output of data structure
- Measuring growth
(A) A single row of vertices (id_mid) labels a line along which measurements will be made. Here, it provides a source for s_mid.
(B) Kapar is promoted by s_a. Here, after 10 steps. We are going to view growth along id_mid.
(C) It has been through the interaction function 9 times. This shows the growth by the time it has reached the end of the 9th pass. Colour shows growth rate over the last time step and lines indicate the major axis.
(D) Spreadsheet showing distances along the line each time the system went through the interaction function. Line 3 shows the time. Column of numbers (lines 4 to 19) shows the distances of each vertex along i_mid. The spreadsheet is saved to the project snapshots directory.
(E) Left panel: distances between successive vertices along id_mid. Right panel: growth at each vertex along id_mid.
function m = gpt_measuregrowth_20121203( m ) %m = gpt_measuregrowth_20121203( m ) % Morphogen interaction function. % Written at 2012-12-04 15:01:27. % GFtbox revision 4418, . % 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 %%% 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_mid_i,id_mid_p,id_mid_a,id_mid_l] = getMgenLevels( m, 'ID_MID' ); [s_mid_i,s_mid_p,s_mid_a,s_mid_l] = getMgenLevels( m, 'S_MID' ); % Mesh type: rectangle % base: 0 % centre: 0 % randomness: 0.1 % version: 1 % xdivs: 16 % xwidth: 2 % ydivs: 16 % ywidth: 2 % Morphogen Diffusion Decay Dilution Mutant % -------------------------------------------------- % KAPAR ---- ---- ---- ---- % KAPER ---- ---- ---- ---- % KBPAR ---- ---- ---- ---- % KBPER ---- ---- ---- ---- % KNOR ---- ---- ---- ---- % POLARISER ---- ---- ---- ---- % STRAINRET ---- ---- ---- ---- % ARREST ---- ---- ---- ---- % ID_MID ---- ---- ---- ---- % S_MID 0.01 ---- ---- ---- %%% USER CODE: MORPHOGEN INTERACTIONS if (Steps(m)==0) && m.globalDynamicProps.doinit % Initialisation code. % assign a morphogen down the middle of the y axis id_mid_p((m.nodes(:,2)<0.1)&(m.nodes(:,2)>-0.1))=1; s_mid_p(:)=0; s_mid_p=id_mid_p; m.morphogenclamp( (id_mid_p==1), s_mid_i ) = 1; m = leaf_mgen_conductivity( m, 's_mid', 0.01 ); %specifies the diffusion rate of polariser m = leaf_mgen_absorption( m, 's_mid', 0.0 ); % specifies degradation rate of polariser end kapar_p=15 * pro(1,s_mid_p); kbpar_p=15 * pro(1,s_mid_p); kaper_p=10 * pro(1,s_mid_p); kbper_p=10 * pro(1,s_mid_p); knor_p =0; % calculate growth over dt interval if isfield(m.userdata,'oldpos') displacements = m.prismnodes - m.userdata.oldpos; [growth,gf] = leaf_computeGrowthFromDisplacements( m, displacements, ... realtime - m.userdata.starttime,'axisorder', 'maxminnor', ... 'anisotropythreshold', 0.05); % plot resultant areal growth rates over dt (i.e. one step). m = leaf_plotoptions( m, 'pervertex',perFEtoperVertex(m,sum(growth(:,1:2),2)) ,'perelementaxes', gf(:,1,:), 'drawtensoraxes', true ); % monitor properties of vertices must be done here - so that it reports newly equilibrated levels end m.userdata.oldpos = m.prismnodes; m.userdata.starttime = realtime; % monitor growth in a Figure and write excel file [m,MonData]=leaf_profile_monitor(m,... % essential 'REGIONLABELS',{'ID_MID'},... % essential 'VERTLABELS',false,'FigNum',1,'EXCEL',true); % optional (file in snapshots directory') % if sum(ismember(output,realtime)) && m.userdata.output ==1 % % Output - plot an image at high resolution % path = fileparts(which(m.globalProps.modelname)); % [m,ok] = leaf_snapshot( m,[path,filesep,'snapshots',filesep,modelname,'_',modeltype,'.png'], 'resolution',[]); % % % 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_mid_i) = id_mid_p; m.morphogens(:,s_mid_i) = s_mid_p; %%% USER CODE: FINALISATION %%% END OF USER CODE: FINALISATION end %%% USER CODE: SUBFUNCTIONS %%% 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', 0.200000 ); % 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', 10 ); % 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', 1.000000 ); % 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', 1.000000 ); % 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, 'colors', (6 values) ); % m = leaf_setproperty( m, 'colorvariation', 0.050000 ); % m = leaf_setproperty( m, 'colorparams', (12 values) ); % m = leaf_setproperty( m, 'biocolormode', 'auto' ); % m = leaf_setproperty( m, 'freezing', 0.999000 ); % m = leaf_setproperty( m, 'canceldrift', false ); % m = leaf_setproperty( m, 'mgen_interaction', (unknown type function_handle) ); % m = leaf_setproperty( m, 'mgen_interactionName', 'gpt_demosubdivision_20121114' ); % 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', 'max' ); % m = leaf_setproperty( m, 'diffusiontolerance', 0.000010 ); % m = leaf_setproperty( m, 'allowsparse', true ); % m = leaf_setproperty( m, 'maxIters', 3.000000 ); % m = leaf_setproperty( m, 'maxsolvetime', 1000.000000 ); % m = leaf_setproperty( m, 'cgiters', 0.000000 ); % 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', 0.000000 ); % 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, 'boingNeeded', false ); % m = leaf_setproperty( m, 'initialArea', 4.000000 ); % m = leaf_setproperty( m, 'bendunitlength', 2.000000 ); % 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\Growth models' ); % m = leaf_setproperty( m, 'modelname', 'GPT_DemoSubdivision_20121114' ); % m = leaf_setproperty( m, 'allowsave', 1.000000 ); % m = leaf_setproperty( m, 'addedToPath', true ); % 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', 4351.000000 ); % m = leaf_setproperty( m, 'coderevisiondate', ); % m = leaf_setproperty( m, 'modelrevision', 0.000000 ); % 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