This is a standard format to describe plant architecture. 10.1.2011 - JF. Barczi , S. Griffon
Xplo handles plant architecture data with ArchiTree data structure. ArchiTree is an improved Java implementation of the MTG formalism. It is a Multiscale Tree Graph ready to represents plant topology AND geometry attached to it.
Each graph node is a topology element and may carry any attribute(length, diameter, weight, notes …) and geometry (mesh, transform matrix, material).
ArchiTree can be stored in standardized XML file with an extension _.opf_.
A simple .opf file example (only topology) :
<?xml version="1.0" encoding="UTF-8" ?> <opf version="2.0" editable="true"> <topology class="Individual" scale="1"> <decomp class="Axis" scale="2"> <Name>Trunk</Name> <decomp class="Internode" scale="6"> <Length>5.0</Length> </decomp> <follow class="Internode" scale="6"> <Length>4.0</Length> </follow> <follow class="Internode" scale="6"> <Length>2.0</Length> <branch class="Axis" scale="2"> <Length>3.0</Length> <decomp class="Internode" scale="6"> </decomp> </branch> </follow> <follow class="Internode" scale="6"> <Length>1.0</Length> </follow> </decomp> </topology> </opf>
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3D View (with default geometry rules reconstruction) + browser view !https://amap-dev.cirad.fr/attachments/624/opfTopology.jpg! !https://amap-dev.cirad.fr/attachments/623/opfTopologyBrowser.jpg!
An OPF contains one main node : TOPOLOGY. The TOPOLOGY node contains all the tree graph topology relations. Attributes for the OPF tag are :
* version : version number (actually 2.0).
* editable (optional): If true, this opf will be editable in Xplo.
The TOPOLOGY node contains all the tree graph topology relations. It contains three main nodes : DECOMP, FOLLOW and BRANCH. DECOMP tag defines decomposition link to the previous node. FOLLOW tag defines succession link to the previous node. BRANCH tag defines ramification link to the previous node.
Inside the TOPOLOGY, DECOMP, FOLLOW and BRANCH you can insert attribute nodes. (see 2.5. _ATTRIBUTE_ TAGS)
Attributes for the TOPOLOGY, DECOMP, FOLLOW and BRANCH tags are :
* class : a class or type name for the current node.
* scale (optional) : a specific decomposition level (scale) for the current node.
TOPOLOGY, DECOMP, FOLLOW and BRANCH can have unlimited attribute tags. Xplo known attributes (such as LENGTH tag in above example) are listed in ArchiTree documentation. However, custom attribute can have any name and their values can be integer, float or string.
An OPF file example with geometry looks like :
<?xml version="1.0" encoding="UTF-8" ?> <opf version="2.0" editable="true"> <meshBDD> <mesh name="" shape="" id="0"> <points> 0.0 0.9511 0.309 0.0 0.0 1.0 1.0 0.0 1.0 1.0 0.9511 0.309 0.0 -0.9511 0.309 1.0 -0.9511 0.309 0.0 -0.5878 -0.809 1.0 -0.5878 -0.809 0.0 0.5878 -0.809 1.0 0.5878 -0.809 0.0 0.9511 0.309 1.0 0.9511 0.309 </points> <normals> 0.0 0.9511 0.309 0.0 0.0 1.0 0.0 0.0 1.0 0.0 0.9511 0.309 0.0 -0.9511 0.309 0.0 -0.9511 0.309 -0.0 -0.5878 -0.809 -0.0 -0.5878 -0.809 0.0 0.5878 -0.809 0.0 0.5878 -0.809 0.0 0.9511 0.309 0.0 0.9511 0.309 </normals> <textureCoords> 1.0 0.0 0.5 0.0 0.5 1.0 1.0 1.0 0.0 0.0 0.0 1.0 0.19098936 0.0 0.19098936 1.0 0.8090106 0.0 0.8090106 1.0 1.0 0.0 1.0 1.0 </textureCoords> <faces> <face Id="0"> 0 1 2 </face> <face Id="1"> 2 3 0 </face> <face Id="2"> 1 4 5 </face> <face Id="3"> 5 2 1 </face> <face Id="4"> 4 6 7 </face> <face Id="5"> 7 5 4 </face> <face Id="6"> 6 8 9 </face> <face Id="7"> 9 7 6 </face> <face Id="8"> 8 10 11 </face> <face Id="9"> 11 9 8 </face> </faces> </mesh> </meshBDD> <materialBDD> <material Id="1"> <emission>0.0 0.0 0.0 0.0 </emission> <ambient>0.5019608 0.3019608 0.7019608 1.0 </ambient> <diffuse>0.5019608 0.3019608 0.7019608 1.0 </diffuse> <specular>0.5019608 0.3019608 0.7019608 1.0 </specular> <shininess>64.0 </shininess> </material> </materialBDD> <shapeBDD> <shape Id="0"> <name> Mesh0</name> <meshIndex>0</meshIndex> <materialIndex>0</materialIndex> </shape> </shapeBDD> <topology class="Individual" scale="1"> <geometry class="Mesh"> <mat> -4.371139E-8 0.0 -1.0 0.0 0.0 1.0 0.0 0.0 1.0 0.0 -4.371139E-8 0.0 </mat> <dUp>1.0</dUp> <dDwn>1.0</dDwn> </geometry> <decomp class="Axis" scale="2"> <Notes>Trunk</Notes> <geometry class="Mesh"> <mat> -4.371139E-8 0.0 -1.0 0.0 0.0 1.0 0.0 0.0 1.0 0.0 -4.371139E-8 0.0 </mat> <dUp>1.0</dUp> <dDwn>1.0</dDwn> </geometry> <decomp class="Internode" scale="6"> <Length>5.0</Length> <geometry class="Mesh"> <shapeIndex>0</shapeIndex> <mat> -2.1855695E-7 0.0 -1.0 0.0 0.0 1.0 0.0 0.0 5.0 0.0 -4.371139E-8 0.0 </mat> <dUp>1.0</dUp> <dDwn>1.0</dDwn> </geometry> </decomp> <follow class="Internode" scale="6"> <Length>4.0</Length> <geometry class="Mesh"> <shapeIndex>0</shapeIndex> <mat> -1.7484555E-7 0.0 -1.0 -2.1855695E-7 0.0 1.0 0.0 0.0 4.0 0.0 -4.371139E-8 5.0 </mat> <dUp>1.0</dUp> <dDwn>1.0</dDwn> </geometry> </follow> <follow class="Internode" scale="6"> <Length>2.0</Length> <geometry class="Mesh"> <shapeIndex>0</shapeIndex> <mat> -8.742278E-8 0.0 -1.0 -3.934025E-7 0.0 1.0 0.0 0.0 2.0 0.0 -4.371139E-8 9.0 </mat> <dUp>1.0</dUp> <dDwn>1.0</dDwn> </geometry> <branch class="Axis" scale="2"> <Length>3.0</Length> <geometry class="Mesh"> <mat> 2.5980763 0.0 -0.5 0.49999952 0.0 1.0 0.0 0.0 1.5 0.0 0.86602545 11.0 </mat> <dUp>1.0</dUp> <dDwn>1.0</dDwn> </geometry> <decomp class="Internode" scale="6"> <geometry class="Mesh"> <shapeIndex>0</shapeIndex> <mat> 2.5980763 0.0 -0.5 0.49999952 0.0 1.0 0.0 0.0 1.5 0.0 0.86602545 11.0 </mat> <dUp>1.0</dUp> <dDwn>1.0</dDwn> </geometry> </decomp> </branch> </follow> <follow class="Internode" scale="6"> <Length>1.0</Length> <geometry class="Mesh"> <shapeIndex>0</shapeIndex> <mat> -4.371139E-8 0.0 -1.0 -4.808253E-7 0.0 1.0 0.0 0.0 1.0 0.0 -4.371139E-8 11.0 </mat> <dUp>1.0</dUp> <dDwn>1.0</dDwn> </geometry> </follow> </decomp> </topology> </opf>
This file loaded in Xplo:
3D View
The MESHBDD node contains all the mesh collection used in the plant geometry. A mesh is reprensted by a *MESH* node.
It contains four main nodes : POINTS, NORMALS, TEXTURECOORDS and FACES Attributes for the MESH tag :
* name : a string to identify mesh.
* id : an integer to identify mesh.
The POINTS node contains all the xyz mesh point coordinates. Coordinates are written in raw : <pre> xp1 yp1 zp1 xp2 yp2 zp2 xp3 yp3 zp3 …. </pre>
The NORMALS node contains all the xyz mesh normal coordinates (linked to each point mesh ⇒ must be described in the same order than points). Coordinates are written in raw : <pre> xn1 yn1 zn1 xn2 yn2 zn2 xn3 yn3 zn3 …. </pre>
The TEXTURECOORDS node contains all the uv mesh texture coordinates (linked to each point mesh ⇒ must be described in the same order than points). Coordinates are written in raw : <pre> u1 v1 u2 v2 u3 v3 …. </pre>
The FACES node contains all the mesh faces. A FACE node references all the points to build a face. The point reference is an index into the point list (described by POINTS). Point index are written in raw : (here a face composed by 4 points) <pre> i1 i2 i3 i4 </pre>
The MATERIALBDD node contains all the material collection used by the meshes. A material is reprensted by a MATERIAL node.
The MATERIAL node contains four main nodes : EMISSION, AMBIENT, DIFFUSE, SPECULAR and SHININESS. EMISSION, AMBIENT, DIFFUSE and SPECULAR color are written in raw (float value between 0.0 and 1.0): <pre> r g b a </pre> SHININESS is a single float value.
Attributes for the MATERIAL tag :
* id : an integer to identify material
The SHAPEBDD node contains a list of shape. A shape is referencing a mesh and a material. A SHAPE node has one attribute (id : an integer to identify the shape) and is componed by 3 nodes : NAME, MESHINDEX and MATERIALINDEX. MESHINDEX and MATERIALINDEX node refers respectively to the MESH id and the MATERIAL id.
The GEOMETRY node is always linked to a topology element (like an attribute tag).
A geometry contains at least a MAT node. This is a 4×4 transformation matrix written in raw : <pre> x1 y1 z1 t1 x2 y2 z2 t2 x3 y3 z3 t3 x4 y4 z4 t4 </pre>
Attributes for the GEOMETRY tag :
* class : a string to define the type of geometry (mesh, bezier, spline…).
If geometry class is _Mesh_, then Mesh can be componed by : shapeIndex : the shape index (defined in shapeBDD). dDwn : the bottom diameter of the mesh dUp : the top diameter of the mesh