Difference between revisions of "Tutorial on mapping results into shape space"

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           'VERTLABELS',false,'FigNum',1,'EXCEL',true,'MODELNAME',modelname); % optional (file in snapshots directory')
 
           'VERTLABELS',false,'FigNum',1,'EXCEL',true,'MODELNAME',modelname); % optional (file in snapshots directory')
  
This function is called from the Gftbox interaction function and writes a .mat file to xxxxLocation after each model step has been computed.
+
leaf_profile_monitor is called from the Gftbox interaction function. It writes a DataXXX.mat file, where XXX corresponds to the model step time stamp, to the project directory in ./snapshots.
 +
 
 +
We now need to convert these DataXXX.mat files into the format read by the AAMToolbox. The function that converts our growing leaf shapes is
 +
 
 +
kparKperModel
 +
 
 +
which like leaf_profile_monitor is tailored to the Arabidopsis leaf and the AAMToolbox Arabidopsis leaf template but could be adapted to other shapes.
 +
 
 +
[tempprojectpath, aamModelType] = fileparts(Cwd);
 +
projectname='GPT_leafFromBullet_20121017';
 +
%projectpath='D:\ab\Matlab stuff';
 +
projectpath='K:\Paul\Karen\growthModels';
 +
[FileName,PathNameA] = uigetfile(fullfile('..','*.m'),...
 +
  'Select GFtbox project interaction function m file',fullfile(projectpath,projectname,[lower(projectname),'.m'])) ;
 +
 
 +
kparKperModel requires three inputs, 1) The Gftbox project name, 2) The AAMToolbox project location and 3) the location of the Gftbox interaction function. This function should write xxx_pm.mat files into the ./pointmodels directory in the AAMToolbox project. These xxx_pm.mat files can be added to an exisiting AAMToolbox project or used to create a new project.  
  
 
==Example==
 
==Example==
 
Based on the GFtbox project  ''GPT_ArLeaf_110323A'' that computes leaf growth corresponding to experimental observations analysed in ''PRJ_???''
 
Based on the GFtbox project  ''GPT_ArLeaf_110323A'' that computes leaf growth corresponding to experimental observations analysed in ''PRJ_???''

Latest revision as of 12:26, 14 January 2013

Return to GFtbox Tutorial pages

Shape space for a growing leaf is computed from a set of labelled leaf outlines - see AAMToolbox. Each outline is captured by a set of landmarks placed around the leaf. To project the output from the GFtbox into a shape space requires landmarks to be placed around the model leaf at corresponding position. In the case of leaves there is a GFtbox function

leaf_profile_monitor

which is tailored to the Arabidopsis leaf. It could be adapted to suit other shapes.

>> help leaf_profile_monitor
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 regionlabel on
         the mesh default false
start_figno, default figure 1 (Must open a fig even if just monitoring to file)

e.g.
 monitor properties of vertices
     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')

leaf_profile_monitor is called from the Gftbox interaction function. It writes a DataXXX.mat file, where XXX corresponds to the model step time stamp, to the project directory in ./snapshots.

We now need to convert these DataXXX.mat files into the format read by the AAMToolbox. The function that converts our growing leaf shapes is

kparKperModel

which like leaf_profile_monitor is tailored to the Arabidopsis leaf and the AAMToolbox Arabidopsis leaf template but could be adapted to other shapes.

[tempprojectpath, aamModelType] = fileparts(Cwd);
projectname='GPT_leafFromBullet_20121017';
%projectpath='D:\ab\Matlab stuff';
projectpath='K:\Paul\Karen\growthModels';
[FileName,PathNameA] = uigetfile(fullfile('..','*.m'),...
 'Select GFtbox project interaction function m file',fullfile(projectpath,projectname,[lower(projectname),'.m'])) ;

kparKperModel requires three inputs, 1) The Gftbox project name, 2) The AAMToolbox project location and 3) the location of the Gftbox interaction function. This function should write xxx_pm.mat files into the ./pointmodels directory in the AAMToolbox project. These xxx_pm.mat files can be added to an exisiting AAMToolbox project or used to create a new project.

Example

Based on the GFtbox project GPT_ArLeaf_110323A that computes leaf growth corresponding to experimental observations analysed in PRJ_???