ECOPHYS visualization project: File Formats

Graphical Visualization of a Tree Growth Process Model

The Visualization Program: File Formats

There are three main sections of the tree: the branch system, leaves, and the root system. The ECOPHYS model outputs the data defining these sections into data files that are read in by the visualization program (see File Formats below).

Description of the Tree Data

Each tree branch consists of a series of segments, or internodes. Internodes are cylindrical objects, and are defined by two, three-dimensional coordinates of the cylinder's endpoints, and its radius (figure 1). If an internode has a branch that forks from it, that branch is a sub-branch of the internode. Each internode has a pointer to its sub-branch, which is NULL if no sub-branch exists.

Each branch in a branch system is a linked-list of internodes. If any internodes within a branch have a sub-branch, then the sub-branch pointer points to the linked list for that sub-branch. Those internodes may have sub-branches, and so on. To traverse the entire branch system, a recursive algorithm is used:


	while internode_pointer is not NULL {
	   process internode
		.
		.
	   if sub-branch_pointer is not NULL {
	      recurse with sub-branch
	   }
	   move internode_pointer to next internode in list
	}

When none of the internodes that make up a branch have a sub-branch, that branch has the potential to contain a leaf. The ECOPHYS model represents leaves as diamond-shaped quadrilaterals. The leaf is defined by the four three-dimensional coordinates of the vertices of the quadrilateral (see figure to right).

File Formats

Tree files loaded by the user are of the form *.eco. Files of this format contain pointers to three other files: a branches file, a leaves file, and a roots file. The structure of the *.eco file is as follows:


	*.brch

	*.lvs

	*.rts

	sunVec_x sunVec_y sunVec_z

The three "sunVec" values are floating point numbers defining the coordinates of a sun vector. These coordinates are calculated in the ECOPHYS model and printed out to the file. **Note: the calculation of this vector is unknown at this time. It has not been implemented due to time contraints.

It is typical to for the *.eco, *.brch, *.lvs, and *.rts files to have the same name, but is not necessary.

Branch Files

Each line of the branches file (*.brch) contains the geometric information of one inode in the tree. The inode is a cylinder defined by the three-dimensional coordinates for the endpoints of the cylinder, plus the radius. The format of the file is as follows:


	x11 y11 z11 x21 y21 z11 radius1
	x12 y12 z12 x22 y22 z22 radius2
	 .   .   .   .   .   .	   .
 	 .   .   .   .   .   .     .
	x1N y1N z1N x2N y2N z2N radiusN

N is the number of inodes contained in the tree. The file tree260-7.brch is an example of a branch data file.

Leaf Files

The leaves file contains, on each line, the information for one leaf on the tree. Each leaf has a diamond shape and is defined by the four three-dimensional coordinates of the diamond. The visualization program has a feature that, during the display of the leaves, colors each leaf according to the value of certain attributes. The current version of the program has five attributes: gross photosynthate (psyn), percent of the leaf that is shaded, LPI, ppfd-sun, and ppfd-shade. Each line of the data file also contains the values a leaf has for each attribute. These values are listed first on the line, followed by the leaf coordinates, since the attribute information is accessed more frequently. The format for the file is as follows: psyn1 %shaded1 LPI1 ppfd-sun1 ppfd-shade1 x11 y11 z11 x21 y21 z21 x31 y31 z31 x41 y41 z41
psyn2 %shaded2 LPI2 ppfd-sun2 ppfd-shade2 x12 y12 z12 x22 y22 z22 x32 y32 z32 x42 y42 z42
. . . . . . . . . . . . . . . . .
. . . . . . . . . . . . . . . . .
psynN %shadedN LPIN ppfd-sunN ppfd-shadeN x1N y1N z1N x2N y2N z2N x3N y3N z3N x4N y4N z4N
N is the number of leaves contained in the tree.

The file tree260-7.lvs is an example of a leaves data file.

Root Files

The roots file has a similar format as the branches file. The root system is made up of numerous cylindrical root sections, defined exactly as the branch inodes. The only difference between the two file formats is the attribute data included in root files. The attribute data is found in the first two columns of the roots file. The rest of the file is exactly as the branches file:


	rho1 order1 x11 y11 z11 x21 y21 z21 radius1
	rho2 order2 x12 y12 z12 x22 y22 z22 radius2
	 .     .     .   .   .   .   .   .     .
	 .     .     .   .   .   .   .   .     .
	rhoN orderN x1N y1N z1N x2N y2N z2N radiusN

Here, rho* is the rho angle of the leaf, order* is the order of the leaf, and N is the number of root segments contained in the root system.

The file tree260-7.rts is an example of a roots data file.

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