This page illustrates the usage of all the functionalities available in openalea.mtg.aml module. All the examples uses the MTG file code_file2.mtg. If you are interested in the syntax, we stronly recommend you to look at Section newmtg_intro.
First, let us read the MTG file with the function MTG. Note that only one MTG object can be manipulated at a time. This MTG object is the active MTG.
>>> from openalea.mtg.aml import * >>> g = MTG('user/code_file2.mtg') >>> Active() == g True
The Active function checks that g is currently the active MTG.
If a new MTG file is read, it becomes the new active MTG object. However, the function Activate can be use to switch between MTG objects as follows:
>>> h = MTG('user/agraf.mtg') >>> Active() == h True >>> Activate(g)
>>> MTGRoot() 0
Order (AlgOrder) look at the number of + sign that need to be crossed before reaching the vertex considered
>>> Order(3) 0 >>> Order(14) 1 >>> AlgOrder(3,14) 1
Height (AlgHeight) look at the number of components between the root of the vertex's branch and the vertex's position.
>>> Height(3) 0 >>> Height(14) 10 >>> AlgHeight(3, 14) 10
Rank (AlgRank) returns the number < sign that need to be crosssed before reaching the vertex considered.
>>> Rank(3) 0 >>> Rank(14) 4 >>> AlgRank(3, 14) 5
Class gives the type of vertex usually defined by a letter
>>> Class(3) 'I'
and Index gives the other part of the label
>>> Index(3) 1
When speaking about multiscale tree graph, we also want to access the Scale:
>>> Scale(3) 3
A new function called Label combines the Class and `Index`:
>>> Label(3) 'I1'
Finally, Feature returns value of a given feature coded in the MTG file.
>>> Feature(2, "Len") 10.0
ClassScale returns the Scale at which appears a given class of vertex:
>>> ClassScale('U') 3
EdgeType returns the type of connection between two vertices (e.g., +, <)
>>> i=8; Class(i), Index(i) ('I', 6) >>> i=9; Class(i), Index(i) ('U', 1) >>> EdgeType(8,9) '+'
Defined tests whether a vertex's id is present in the active MTG
>>> Defined(1) True >>> Defined(100000) False
The following function requires MTG files to contain Date information.
not yet implemented
| Function | |
|---|---|
DateSample(e1) FirstDefinedFeature(e1, e2) LastDefinedFeature(e1, e2) NextDate(e1) PreviousDate(e1) |
Trunk returns the list of vertices constituting the bearing botanical axis of a branching system
>>> Trunk(2) # vertex 2 is U1 therefore the Trunk should return index related to U1, U2, U3 [2, 24, 31] >>> Class(24), Index(24) ('U', 2)
>>> Trunk(3) # vertex 3 is an internode, so we get all internode of the axis containing vertex 3 [3, 4, 5, 6, 7, 8, 21, 22, 23, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35] >>> Class(35), Index(35) ('I', 19)
Topological father of a given vertex.
>>> Label(8) 'I6' >>> Father(8) 7 >>> Label(9) # Let us look at vertex 9 (with the U1 label) 'U1' >>> Father(9) # and look for its father's index 2 >>> Label(2) # and its father's label that appear to also be equal to 1 'U1'
Axis returns the vertices of the axis to which belongs a given vertex.
>>> [Label(x) for x in Axis(9)] ['U1', 'U2']
The scale may be specified
>>> [Label(x) for x in Axis(9, Scale=3)] ['I20', 'I21', 'I22', 'I23', 'I24', 'I25', 'I26', 'I27', 'I28', 'I29']
Ancestors returns a list of ancestors of a given vertex
>>> Ancestors(20) # of I29 [20, 19, 18, 17, 16, 14, 13, 12, 11, 10, 8, 7, 6, 5, 4, 3] >>> [Class(x)+str(Index(x)) for x in Ancestors(20)] ['I29', 'I28', 'I27', 'I26', 'I25', 'I24', 'I23', 'I22', 'I21', 'I20', 'I6', 'I5', 'I4', 'I3', 'I2', 'I1']
The Path returns a list of vertices defining the path between two vertices
>>> [Class(x)+str(Index(x)) for x in Path(8, 20)] ['I20', 'I21', 'I22', 'I23', 'I24', 'I25', 'I26', 'I27', 'I28', 'I29']
In order to illustrate the Sons function, let us consider the vertex 8
>>> Class(8), Index(8) ('I', 6) >>> [Class(x)+str(Index(x)) for x in Sons(8)] ['I20', 'I7']
Descendants an array with all the vertices, at the same scale as v, that belong to the branching system starting at v:
>>> [Class(x)+str(Index(x)) for x in Descendants(8)]Ancestors contains the vertices on the path from v back to the root (in this order) and finishes by the tree root.:
>>> [Class(x)+str(Index(x)) for x in Ancestors(8)]Predecessor returns the Father of a vertex connected to it by a ‘<’ edge, and is therefore equivalent to:
Father(v, EdgeType-> ‘<’). Similarly, Successor is equivalent to :
Sons(v, EdgeType=’<’)[0]Root returns root of the branching systenme containing a given vertex and therefore is equivalent to:
Ancestors(v, EdgeType=’<’)[-1]
>>> [Class(x)+str(Index(x)) for x in Ancestors(8)]
['I6', 'I5', 'I4', 'I3', 'I2', 'I1']
>>> Root(8)
3
>>> Class(3)+str(Index(3))
'I1'Complex returns Scale(v)-1 why what is it for?
>>> Complex(8) 2
Returns a list of vertices that are included in the upper scale of the vertex's id considered. The array is empty if the vertex has no components.
>>> Components(1, Scale=2) [2, 9, 15, 24, 31] >>> Components(1, Scale=3) [3, 4, 5, 6, 7, 8, 21, 22, 23, 10, 11, 12, 13, 14, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35]
to be done. find example
Vertex defining the father of a vertex with maximum scale.
>>> Label(9) # starting from a Component U1 at vertex's id 9 'U1' >>> Father(9) # what is its Father ? 2 >>> Label(Father(9)) # answer: another U1 of vertex's id 2 'U1' >>> Location(9) # what is the location of vertex 9 8 >>> Label(Location(9)) # the internode I6 'I6'
>>> Label(8) 'I6' >>> Label(Extremities(8)) ['I29', 'I19']
Most of the following functions are not yet implemented. See newmtg_quick_start to see the usage of PlantFrame with dressing data.
You may also use the former AML code using openalea.aml package
One can use openalea.aml for now:
>>> import openalea.aml as aml >>> aml.MTG('code_file2.txt') >>> pf = aml.PlantFrame(2) >>> aml.Plot()
Shows the MTG file at scale 2. This is possible because Diameter and Lenmgth features are provided at that scale.
========================= |
not yet implemented
TreeMatching(e1) MatchingExtract(e1)
documentation status:
Thomas Cokelaer <Thomas.Cokelaer@inria.fr>, Dec 2009
Documentation adapted from the AMAPmod user manual version 1.8 Dec 2009.
Documentation to be revised