Difference between revisions of "Tutorial on mapping results into shape space"
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− | [[GFtbox Tutorial pages#Comparing resultant shapes with observed organ shapes|GFtbox Tutorial pages]] | + | [[GFtbox Tutorial pages#4 Comparing resultant shapes with observed organ shapes|Return to GFtbox Tutorial pages]]<br><br> |
+ | |||
+ | 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') | ||
+ | |||
+ | ==Example== | ||
+ | Based on the GFtbox project ''GPT_ArLeaf_110323A'' that computes leaf growth corresponding to experimental observations analysed in ''PRJ_???'' |
Revision as of 16:32, 13 May 2012
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')
Example
Based on the GFtbox project GPT_ArLeaf_110323A that computes leaf growth corresponding to experimental observations analysed in PRJ_???