Region tagging

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\nAuthor: Edward Vigmond edward.vigmond@u-bordeaux.fr\n\ <div id=\"region-tagging-tutorial\">\n

In CARPentry regions are used to manage\ \ the assignment of heterogeneous tissue properties. This tutorial explains the\ \ different approches of how regions can be defined.

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Regions\n
Regions are a general concept in CARPentry for volumes which share\ \ common properties, be they ionic, mechanical or conductivity. For a general introduction\ \ of this concept see the region section of the manual. In the mesh files, elements\ \ may be given a region tag as an optional field in the .elem file.
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Note
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If no region\ \ tag is specified, the element is assigned a region tag of 0.
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A\ \ region tag is a simply an integer associated with an element. CARPentry regions\ \ are then conglomerations of element region tags. The following is an example of\ \ how to assign some region tags to IMP and conductivity regions:
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imp_region[1].num_IDS\
\ = 2\nimp_region[1].ID[0] = 1000 \nimp_region[1].ID[1] = 1100\n\ngregion[3].num_IDS\
\ = 5\ngregion[3].ID = 100 200 201 1000 2000 
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Two slightly different\ \ syntaxes are shown for specifying the region tags.
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Note
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If a region tag is not explicitly\ \ included in any region, it will be assigned to region 0.
\n\n<h2 id=\"\ dynamic-retagging\">Dynamic Retagging\n
Each element in a mesh is designated\ \ as being in a region, and properties, be they electrical or mechanical, are assigned\ \ based on region. It may be desired to change properties in a small volume which\ \ is not defined in the original mesh. To avoid touching the mesh files, dynamic\ \ tagging was introduced.
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Essentially, a geometrical volume is defined,\ \ and all elements wthin the volume are given a new tag. Overlaps are governed by\ \ a simple rule: the highest region tag wins. This also implies\ \ that your reassigned tags have to be higher than the original model tags. The\ \ case where some but not all of an element's nodes are contained with the tagging\ \ volume must be handled. By default, elements with at least one node in the tagging\ \ volume are included, but ensuring that only elements with all nodes contained\ \ can be enabled by setting an option below.(no_split_elem)
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Tag\ \ volumes can also be created by simply specifying a list of elements within the\ \ volume.
\n<h2 id=\"region-definitions\">Region Definitions\n
The number\ \ of new tag regions is specified by numtagreg. For each region defined\ \ by tagreg[*], the table below lists the available fields to set.\ \ Bolded fields need to be specified and depending on the value of type,\ \ different fields define the geometrical volume. Note that the units are micrometers.\ \ See the figure below:
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Field Meaning

03_study_prep_APD 05A_Regions_vs_Gradients