openalea.plantconvert#

Generic interface to handle a plant object#

class openalea.plantconvert.plant.Plant(file: str = 'None', ignored_attrs=[], verbose=False)[source]#

Bases: object

General interface for plantconvert.

This class allows to read from different file types and to export other file types.

The supported types are :

.mtg .opf .vtk .gltf

Parameters:

  • file (str, optional) – name of the file to read using the read method. Defaults to None.

  • ignored_attrs (list of string, optional) – a list of attributes that will not appear in the final exported file in addition to attributes from RESERVED_NAMES. Defaults set to empty list.

  • verbose (bool, optional) – verbose mode, more information will be printed on the screen if you activate it. Defaults to False.

read()[source]#

Analyse file type from extension and reads it.

This method also prepare the self.mtg object so that it can be written again in any other file format.

write(filename)[source]#

Write the Plant object to file.

Parameters:

filename (string) – output file. Extension will determine which format will be used

openalea.plantconvert.plant.plant_from_mtg(g: MTG) → Plant[source]#

Generate a plant object from an mtg.MTG object.

Note: This can be usefull if we couple this package to another openalea package and want to save to another format.

Parameters:

g (mtg.MTG) – mtg object of the plant we later want to write

Returns:

Plant object that embeds the mtg.MTG objects.

Return type:

plantconvert.Plant

Internal functions for binary format#

openalea.plantconvert.binary_tools.pack_vec_array(vec_array, dtype)[source]#

Transform the input array of vectors into a binary string.

Parameters:

  • vec_array (array) – list of vectors

  • dtype (str) – data type

Returns:

binary string that store the data in compact way, and always pack bytes

in litte endian order. You can write the binary string into a file when you open it by ‘wb’. :rtype: bytes

Geometry related functions#

openalea.plantconvert.geometry.get_scene(g: MTG, filter=None)[source]#

Generate a plantGL Scene object from mtg geometry properties.

This method traverses the mtg g and reads the geometry property of the nodes that are allowed by the filter. It creates a plantgl Scene object of all geometric objects combined.

Parameters:

  • g (mtg.MTG) – mtg object that contains the plant

  • filter (function, optional) – takes 2 inputs: mtg.MTG and node ID and returns a bool. Defaults to None, i.e. all nodes are taken into account.

Returns:

plantGL Scene object containing all geometric objects

Return type:

plantGL.Scene

openalea.plantconvert.geometry.mat_from_transformed(geo)[source]#

Extract the global transformation matrix from a transformed geometry.

Parameters:

geo (plantgl.Geometry) – a geometry object from PlantGL

Raises:

TypeError – if the transformation is not recognized (i.e. not a plantGL instance)

Returns:

transformation matrix used to obtain the transformed geometry

Return type:

plantGL.Matrix4

class openalea.plantconvert.geometry.taper_along_x(ref_meshes=None)[source]#

Bases: object

Class with information to perform tapering along x axis.

To initialize this class with a list of reference meshes (represented by TriangleSet) If the given mesh is not in the list then it will be added.

Parameters:

ref_meshes (list) – list of reference meshes

openalea.plantconvert.geometry.tapering_radius_from_transformed(geo)[source]#

Extract the tapering radii from the input geometry.

Parameters:

geo (either a plantGL.TriangleSet, a plantGL.Tapered or a plantGL shape) – a geometry object from PlantGL

Returns:

top and base radii of the tapering geometry

Return type:

tuple

openalea.plantconvert.geometry.transformed_from_mat(A, geo, is_mesh=False)[source]#

Apply the transformation A (a 3 by 4 matrix) on the geometry.

Qr transformation of matrix A is done so that A = Q*r where:

Q is a unity matrix and r is upper-triangular. To use the oriented object of plantgl, Q should have positive determinant. r is in our case diagonal since A is a composition of rotations and scaling.

Parameters:

  • A (numpy.ndarray) – a 3 by 4 array that describes the transformation in the reference of the scene. This matrix is supposed to be TRS decomposible

  • geo (plantgl.Geometry) – a geometry object from PlantGL

  • is_mesh (bool) – if true a new mesh (TriangleSet) will be created. Otherwise we only create a geometry object (no duplication of mesh in the memory). Defaults to False.

Returns:

Transformed geometry. if is_mesh then we get a new mesh otherwise we only create a geometry object

Return type:

plantgl.Geometry

Plant material related functions#

openalea.plantconvert.material.to_gltf(material_data)[source]#

Create the material information accepted by GLTF, not implemented yet.

openalea.plantconvert.material.to_plantgl(material_data)[source]#

Create a plantgl object to represent a material from the input material_data.

Parameters:

material_data (dict) – dictionary that contains exactly : An Id 4 colors in RGBA : emission, ambient, diffuse and specular. shininess value.

Returns:

plantgl.Material object. Note that some information might be lost. For example, the alpha value in .opf is defined for each color (emission, etc. ) while in plantgl there is only a global alpha value : transparency = 1 - alpha

Return type:

plantgl.Material

Transformation-Matrix related functions#

exception openalea.plantconvert.matrix.TRSError[source]#

Bases: Exception

openalea.plantconvert.matrix.TRS_from_matrix4(A: ndarray)[source]#

Return the TRS components of a TRS matrix.

Parameters:

A (numpy.ndarray) – a 4x4 TRS matrix

Returns:

t, Q, s: the TRS components of the input matrix.

Return type:

tuple of numpy.ndarray vector of length 3, 3x3 matrix, vector of length 3

openalea.plantconvert.matrix.global_to_local_matrix(mat_c, mat_p=None)[source]#

Return the local matrix of mat_c in the reference of mat_p.

Parameters:

  • mat_c (numpy.ndarray) – a 4x4 matrix

  • mat_p (numpy.ndarray) – a 4x4 matrix

Returns:

the local matrix of mat_c in the reference of mat_p.

Return type:

numpy.ndarray

openalea.plantconvert.matrix.inv_TRS(A: ndarray)[source]#

Return the inverse of a TRS matrix.

Parameters:

A (numpy.ndarray) – a 4x4 TRS matrix

Returns:

inverted matrix of A of size 4x4

Return type:

numpy.ndarray

openalea.plantconvert.matrix.is_TRS(A: ndarray)[source]#

Test if the input matrix A is a 4D TRS matrix.

This requires to test if A’s linear part is the composition of a rotation and a scaling. If this is the case, the first three columns should be orthogonal.

Parameters:

A (numpy.ndarray) – a 4x4 matrix

Returns:

True if A is a TRS matrix, False otherwise

Return type:

bool

openalea.plantconvert.matrix.mat4_to_numpy(A)[source]#

Convert the pgl.Matrix4 object to a 2d array.

Parameters:

A (pgl.Matrix4) – a pgl.Matrix4 object.

Returns:

the corresponding 2d numpy array.

Return type:

numpy.ndarray

openalea.plantconvert.matrix.numpy_to_mat4(A)[source]#

Convert the 2d array A to pgl.Matrix4 object.

Parameters:

A (numpy.ndarray) – a 2d numpy array. Accepted shape = 3*4, 4*4, 3*3

Returns:

the corresponding Matrix4 object.

Return type:

pgl.Matrix4

openalea.plantconvert.matrix.random_matrix4()[source]#

Return a random TRS matrix.

Implemented for test only.