Section author: Dougal Cowan
FieldML models in the Auckland Physiome Repository are presented through exposures. A FieldML exposure has some similarities to a CellML exposure - usually consisting of a main documentation page with some information about the model, accompanied by a range of different views of the model data and or metadata. FieldML exposures also allow the real-time three-dimensional display of model meshes within the browser through the use of the Zinc plugin.
The example screenshots below show the main documentation page view and the 3D visualization provided by the Zinc viewer.
To create a FieldML exposure, the following files will need to be stored in a workspace in the repository:
The following example RDF file from comes from the Laminar Structure of the Heart workspace in the repository:
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 | <?xml version="1.0" encoding="utf-8"?>
<rdf:RDF
xmlns="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
xmlns:dc="http://purl.org/dc/elements/1.1/"
xmlns:dcterms="http://purl.org/dc/terms/"
xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#"
xmlns:pmr2="http://namespace.physiomeproject.org/pmr2#">
<rdf:Description rdf:about="">
<dc:title>
Laminar structure of the Heart: A mathematical model.
</dc:title>
<dc:creator>
<rdf:Seq>
<rdf:li>LeGrice, I.J.</rdf:li>
<rdf:li>Hunter, P.J.</rdf:li>
<rdf:li>Smaill, B.H.</rdf:li>
</rdf:Seq>
</dc:creator>
<dcterms:bibliographicCitation>
American Journal of Physiology 272: H2466-H2476, 1997.
</dcterms:bibliographicCitation>
<dcterms:isPartOf rdf:resource="info:pmid/9176318"/>
<pmr2:annotation rdf:parseType="Resource">
<pmr2:type
rdf:resource="http://namespace.physiomeproject.org/pmr2/note#json_zinc_viewer"/>
<pmr2:fields>
<rdf:Bag>
<rdf:li rdf:parseType="Resource">
<pmr2:field rdf:parseType="Resource">
<pmr2:key>json</pmr2:key>
<pmr2:value>heart.json</pmr2:value>
</pmr2:field>
</rdf:li>
</rdf:Bag>
</pmr2:fields>
</pmr2:annotation>
</rdf:Description>
</rdf:RDF>
|
This file provides citation metadata and a reference to the resource that specifies the Zinc viewer JSON file which will be used to describe the 3D visualisation of the FieldML model. The file breaks down into three main sections:
Example of the JSON file from the same (Laminar Structure of the Heart) workspace:
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 | {
"View" : [
{
"camera" : [9.70448, -288.334, -4.43035],
"target" : [9.70448, 6.40667, -4.43035],
"up" : [-1, 0, 0],
"angle" : 40
}
],
"Models": [
{
"files": [
"heart.xml"
],
"externalresources": [
"heart_mesh.connectivity",
"heart_mesh.node.coordinates"
],
"graphics": [
{
"type": "surfaces",
"ambient" : [0.4, 0, 0.9],
"diffuse" : [0.4, 0,0.9],
"alpha" : 0.3,
"xiFace" : "xi3_1",
"coordinatesField": "heart.coordinates"
},
{
"type": "surfaces",
"ambient" : [0.3, 0, 0.3],
"diffuse" : [1, 0, 0],
"specular" : [0.5, 0.5, 0.5],
"shininess" : 0.5,
"xiFace" : "xi3_0",
"coordinatesField" : "heart.coordinates"
},
{
"type": "lines",
"coordinatesField" : "heart.coordinates"
}
],
"elementDiscretization" : 8,
"region_name" : "heart",
"group": "Structures",
"label": "heart",
"load": true
}
]
}
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For more information on these settings, please see the cmgui documentation.
Note
The specifics of these RDF and JSON files are a work in progress, and may change with each new version of the Zinc viewer plugin or PMR2.
First you will need to create a workspace to put your model in, following the process outlined in the document on working with workspaces.
View generator as per CellML; select HTML annotator and HTML doc file
New exposure file entry: select .rdf file and select FieldML (JSON) type. Click Add.
Click Update.
Click Build.
To see the 3D visualisation, you will need to have the latest Zinc plugin installed.