GPT tut interaction 20110530 on creating - Revision history

AndrewBangham at 19:12, 30 May 2011

2011-05-30T19:12:38Z

AndrewBangham at 19:06, 30 May 2011

2011-05-30T19:06:36Z

← Older revision		Revision as of 19:06, 30 May 2011
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	[[Tutorial on the interaction function details\|Tutorial on the interaction function details]]<br><br>		[[Tutorial on the interaction function details\|Tutorial on the interaction function details]]<br><br>
	<span style="color: CornflowerBlue">'''This file was ~~output~~ automatically on clicking Panel: Edit in the newly saved project called GPT tut interaction 20110530'''<br><br>		<span style="color: CornflowerBlue">'''This file was placed in the Matlab Editor automatically on clicking Panel: Edit in the newly saved project called GPT tut interaction 20110530'''<br><br>
	<span style="color: CornflowerBlue">Section 1</span>		<span style="color: CornflowerBlue">Section 1</span>
	function m = gpt_tut_interaction_20110530( m )		function m = gpt_tut_interaction_20110530( m )

AndrewBangham at 19:05, 30 May 2011

2011-05-30T19:05:33Z

Show changes

AndrewBangham at 18:45, 30 May 2011

2011-05-30T18:45:55Z

← Older revision		Revision as of 18:45, 30 May 2011
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	case 'MODEL1'		case 'MODEL1'
	<span style="color: Green">% Set up the parameters (e.g. mutations) for this model here.</span>		<span style="color: Green">% Set up the parameters (e.g. mutations) for this model here.</span>
	~~<span style="color: CornflowerBlue">Section 10</span>~~
	case 'MODEL2'		case 'MODEL2'
	<span style="color: Green">% Set up the parameters (e.g. mutations) for this model here.</span>		<span style="color: Green">% Set up the parameters (e.g. mutations) for this model here.</span>
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	<span style="color: Green">% Every equation to be formatted should end with an at-at Eqn N comment.</span>		<span style="color: Green">% Every equation to be formatted should end with an at-at Eqn N comment.</span>

			<span style="color: CornflowerBlue">Section 10</span>
	<span style="color: Green">% Code for specific models.</span>		<span style="color: Green">% Code for specific models.</span>
	switch modelname		switch modelname
Line 253:		Line 253:
	kbper_p(:) = kapar_p; <span style="color: Green">% same</span>		kbper_p(:) = kapar_p; <span style="color: Green">% same</span>
	knor_p(:) = 0; <span style="color: Green">% thickness not growing</span>		knor_p(:) = 0; <span style="color: Green">% thickness not growing</span>
	~~<span style="color: CornflowerBlue">Section 10</span>~~
	case 'MODEL2' <span style="color: Green">% @@model MODEL2</span>		case 'MODEL2' <span style="color: Green">% @@model MODEL2</span>
	<span style="color: Green">% @@PRN Polariser Regulatory Network</span>		<span style="color: Green">% @@PRN Polariser Regulatory Network</span>
Line 296:		Line 295:
	<span style="color: Green">%%% USER CODE: FINALISATION</span>		<span style="color: Green">%%% USER CODE: FINALISATION</span>

	~~<span style="color: CornflowerBlue">Section 2</span>~~
	<span style="color: Green">% In this section you may modify the mesh in any way whatsoever.</span>		<span style="color: Green">% In this section you may modify the mesh in any way whatsoever.</span>

AndrewBangham at 17:56, 30 May 2011

2011-05-30T17:56:59Z

← Older revision		Revision as of 17:56, 30 May 2011
Line 2:		Line 2:
	<span style="color: CornflowerBlue">'''This file was output automatically on clicking Panel: Edit in the newly saved project called GPT tut interaction 20110530'''<br><br>		<span style="color: CornflowerBlue">'''This file was output automatically on clicking Panel: Edit in the newly saved project called GPT tut interaction 20110530'''<br><br>
	The code has been divided into Sections to help with the tutorial.<br><br>		The code has been divided into Sections to help with the tutorial.<br><br>
	~~'''Section 1 Automatic'''</span>~~		<span style="color: CornflowerBlue">Section 1 (automatic)</span>
	~~function m = gpt_tut_interaction_20110530( m )~~		function m = gpt_tut_interaction_20110530( m )
	~~%m = gpt_tut_interaction_20110530( m )~~		<span style="color: Green">%m = gpt_tut_interaction_20110530( m )</span>
	~~% Morphogen interaction function.~~		<span style="color: Green">% Morphogen interaction function.</span>
	~~% Written at 2011-05-30 09:42:07.~~		<span style="color: Green">% Written at 2011-05-30 09:42:07.</span>
	~~% GFtbox revision 0, .~~		<span style="color: Green">% GFtbox revision 0, .</span>
	~~% The user may edit any part of this function between delimiters~~
	~~% of the form "USER CODE..." and "END OF USER CODE...". The~~		<span style="color: Green">% The user may edit any part of this function between delimiters</span>
	~~% delimiters themselves must not be moved, edited, deleted, or added.~~		<span style="color: Green">% of the form "USER CODE..." and "END OF USER CODE...". The</span>
	~~if isempty(m), return; end~~		<span style="color: Green">% delimiters themselves must not be moved, edited, deleted, or added.</span>
	~~fprintf( 1, '%s found in %s\n', mfilename(), which(mfilename()) );~~
	~~try~~		if isempty(m), return; end
	~~m = local_setproperties( m );~~
	~~catch~~		fprintf( 1, '<span style="color: Green">%s found in %s\n', mfilename(), which(mfilename()) );</span>
	~~end~~
	~~realtime = m.globalDynamicProps.currenttime;~~		try
	~~%%% USER CODE: INITIALISATION~~		m = local_setproperties( m );
	~~<span style="color: CornflowerBlue">'''Section 2'''</span>~~		catch
			end
	~~% In this section you may modify the mesh in any way whatsoever.~~
	~~if (Steps(m)==0) && m.globalDynamicProps.doinit % First iteration~~		realtime = m.globalDynamicProps.currenttime;
	~~% Zero out a lot of stuff to create a blank slate.~~
	~~% If no morphogens are set in the GUI it may be useful to~~		<span style="color: Green">%%% USER CODE: INITIALISATION</span>
	~~% zero some arrays by uncommenting the following.~~
	~~% m.morphogens(:) = 0;~~		<span style="color: CornflowerBlue">Section 2</span>
	~~% m.morphogenclamp(:) = 0;~~		<span style="color: Green">% In this section you may modify the mesh in any way whatsoever.</span>
	~~% m.mgen_production(:) = 0;~~		if (Steps(m)==0) && m.globalDynamicProps.doinit <span style="color: Green">% First iteration</span>
	~~% m.mgen_absorption(:) = 0;~~		<span style="color: Green">% Zero out a lot of stuff to create a blank slate.</span>
	~~% m.seams(:) = false;~~		<span style="color: Green">% If no morphogens
	~~% 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~~

AndrewBangham at 10:34, 30 May 2011

2011-05-30T10:34:18Z

← Older revision		Revision as of 10:34, 30 May 2011
Line 1:		Line 1:
			[[Tutorial on the interaction function details\|Tutorial on the interaction function details]]<br><br>
	<span style="color: CornflowerBlue">'''This file was output automatically on clicking Panel: Edit in the newly saved project called GPT tut interaction 20110530'''<br><br>		<span style="color: CornflowerBlue">'''This file was output automatically on clicking Panel: Edit in the newly saved project called GPT tut interaction 20110530'''<br><br>
	The code has been divided into Sections to help with the tutorial.<br><br>		The code has been divided into Sections to help with the tutorial.<br><br>

AndrewBangham at 10:32, 30 May 2011

2011-05-30T10:32:46Z

← Older revision		Revision as of 10:32, 30 May 2011
Line 1:		Line 1:
	<span style="color: CornflowerBlue">'''This file is output automatically on clicking Panel: Edit in a newly saved project. '''~~<br>~~		<span style="color: CornflowerBlue">'''This file was output automatically on clicking Panel: Edit in the newly saved project called GPT tut interaction 20110530'''<br><br>
	Once the file has been edited save it in the usual way from the Matlab editor. The project as whole can be saved under a different name using Panel: Save as. This will automatically create a new copy of the current interaction function, but with the new name and in the new project directory.<br><br>
	The code has been divided into Sections to help with the tutorial.<br><br>		The code has been divided into Sections to help with the tutorial.<br><br>
	'''Section 1 Automatic'''</span>		'''Section 1 Automatic'''</span>

AndrewBangham at 10:31, 30 May 2011

2011-05-30T10:31:24Z

Show changes

AndrewBangham: Created page with '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 …'

2011-05-30T10:23:45Z

Created page with '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 …'

New page

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 );