def test_materials():
can = data_path('filterT.can')
cscene = read_can(can)
path = data_path('par.opt')
n, s, opts = read_opt(path)
materials = build_materials(cscene.keys(), opts, s)
assert len(materials) == len(cscene)
assert materials[materials.keys()[0]] == (0.1, 0.05)
return materials
def test_opt():
path = data_path('par.opt')
n, s, opts = read_opt(path)
assert n == 2
assert s == 0.15
assert opts[1] == (0.1, 0.1, 0.05, 0.1, 0.05)
return n, s, opts
def run_caribu(sources, scene, opticals='stem', optical_properties=None, output_by_triangle=False, domain=None,
zsoil=None):
"""
Calls Caribu for differents energy sources
:Parameters:
------------
- `sources` (int)
- `scene` : any scene format accepted by CaribuScene. This will be cast to a list of plantGL shapes
- opticals : a list of optical property labels ('leaf', 'soil', 'stem', 'ear' or 'awn') for all shapes in scene. If a shorter opticale list is provided, it will be recycled to match eength of shape list
- `optical_properties`: a filename (*.opt).
- `output_by_triangle` (bool)
Default 'False'. Return is done by id of geometry. If 'True', return is done by triangle.
:Returns:
---------
- 'out_moy' (dict)
A dict of intercepted variable (energy) per id
- 'out_tri' (dict) only if output_by_triangle = True, return a tuple (out_moy, out_tri)
A dict of intercepted variable (energy) per triangle
"""
raise DeprecationWarning('This function is deprecated, use CaribuScene / caribu_star instead')
from alinea.caribu.label import simple_canlabel
from alinea.caribu.file_adaptor import read_opt, build_materials
n, soil_reflectance, po = read_opt(optical_properties)
if not isinstance(opticals, list):
opticals = [opticals]
if len(opticals) < len(scene):
opticals = opticals * (len(scene) / len(opticals)) + [opticals[i] for i in range(len(scene) % len(opticals))]
labels = [simple_canlabel(opt) for opt in opticals]
materials = build_materials(labels, po, soil_reflectance)
band = CaribuScene.default_band
c_scene = CaribuScene(scene=scene, light=sources, pattern=domain, opt={band: materials},
soil_reflectance={band: soil_reflectance})
ifty = False
if domain is not None:
ifty = True
# if zsoil is not None:
# idmap_soil = c_scene.addSoil(zsoil=zsoil)
# idmap.update(idmap_soil)
raw, aggregated = c_scene.run(direct=True, infinite=ifty, simplify=True)
if output_by_triangle:
out = raw
else:
out = aggregated
return out
def __init__(self, scene=None, light=None, pattern=None, opt=None,
soil_reflectance=None, soil_mesh=None, z_soil=None,
scene_unit='m'):
""" Initialise a CaribuScene
Args:
scene (dict): a {primitive_id: [triangles,]} dict.A triangle is a
list of 3-tuples points coordinates
Alternatively, scene can be a *.can file or a mtg with
'geometry' property or a plantGL scene.
For the later case, shape.id are used as primitive_id.
light (list): a list of (Energy, (vx, vy, vz)) tuples defining light
sources
Alternatively, a *.light file
If None (default), a unit energy vertical light is used.
Energy unit should be given per square-meter (m-2)
pattern (tuple): 2D Coordinates of the domain bounding the scene for
its replication.
(xmin, ymin, xmax, ymax) scene is not bounded along z axis.
Alternatively a *.8 file.
if None (default), scene is not repeated
opt (dict): a {band_name: {primitive_id: material}} dict of dict
or a {band_name: material} dict of tuples.
In the second form the material is used for all primitives.
A material is a 1-, 2- or 4-tuple depending on its optical behavior.
A 1-tuple encode an opaque material characterised by its reflectance
A 2-tuple encode a symmetric translucent material defined
by a reflectance and a transmittance
A 4-tuple encode an asymmetric translucent material defined
the reflectance and transmittance
of the upper and lower side respectively
Alternatively, a list of band_name.opt files (require scene
to be given as a *.can file)
If None (default), all primitive are associated to the
default material of the class.
soil_reflectance (dict): a {band_name: reflectance} dict.
If None (default) class default soil reflectance is used for all bands
If *.opt files are provided, the values in opt files are used in priority
soil_mesh (int): a flag triggering for the creation of a soil mesh
in the scene during computations
If None (default) or -1, no soil is added
If an int (n), a soil is added to the scene, with n subdivisions
z_soil (float): the altitude of the soil.
If None (default), the soil is placed at the bottom of
the scene bounding box
scene_unit (str): the unit of length used for scene coordinate
and for pattern (should be one of class.units default)
By default, scene_unit is considered to be 'm' (meter).
Returns:
A CaribuScene instance
Note:
File format specifications (*.can, *.light, *.8, *.opt) can be found in data/CanestraDoc.pdf
"""
if scene_unit not in self.units:
raise ValueError('unrecognised scene unit: ' + scene_unit)
self.conv_unit = self.units[scene_unit]
self.scene = None
if scene is not None:
if isinstance(scene, dict):
elt = scene[scene.keys()[0]]
try:
assert isinstance(elt, list)
assert isinstance(elt[0], list)
assert isinstance(elt[0][0], tuple)
except:
raise ValueError('Unrecognised scene format')
self.scene = scene
elif isinstance(scene, str):
self.scene = read_can(scene)
elif isinstance(scene, MTG):
self.scene = mtg_to_cscene(scene)
elif isinstance(scene, pglScene):
self.scene = scene_to_cscene(scene)
else:
raise ValueError('Unrecognised scene format')
self.light = [self.default_light]
if light is not None:
if isinstance(light, list):
elt = light[0]
try:
assert isinstance(elt, tuple)
assert isinstance(elt[1], tuple)
except:
raise ValueError('Unrecognised light format')
self.light = light
elif isinstance(light, str):
self.light = read_light(light)
else:
raise ValueError('Unrecognised light format')
self.pattern = None
if pattern is not None:
if isinstance(pattern, tuple):
if len(pattern) == 2:
pattern = sum(pattern, ())
if len(pattern) != 4:
raise ValueError('Unrecognised pattern format')
self.pattern = pattern
elif isinstance(pattern, str):
self.pattern = read_pattern(pattern)
else:
raise ValueError('Unrecognised pattern format')
self.material = None
if opt is None:
if soil_reflectance is None:
self.soil_reflectance = {
self.default_band: self.default_soil_reflectance}
bands = [self.default_band]
else:
self.soil_reflectance = soil_reflectance
bands = soil_reflectance.keys()
if self.scene is not None:
self.material = {}
for band in bands:
self.material[band] = {pid: self.default_material for pid in
self.scene}
else:
if isinstance(opt, list):
if not isinstance(opt[0], str):
raise ValueError('Unrecognised opt format')
if not isinstance(scene, str):
raise ValueError(
'un-compatible inputs types: opt file and scene not a can file')
if self.scene is not None:
self.material = {}
self.soil_reflectance = {}
for path in opt:
band = os.path.basename(path).split('.')[0]
n, ro_soil, po = read_opt(path)
self.material[band] = build_materials(self.scene.keys(),
po, ro_soil)
self.soil_reflectance[band] = ro_soil
elif isinstance(opt, dict):
elt = opt[opt.keys()[0]]
if not isinstance(elt, dict):
if isinstance(elt, tuple):
self.material = {}
if self.scene is not None:
for band in opt:
self.material[band] = {pid: opt[band] for pid in
self.scene}
else:
raise ValueError('Unrecognised opt format')
else:
self.material = opt
if soil_reflectance is None:
self.soil_reflectance = {band: self.default_soil_reflectance
for band in self.material}
else:
if isinstance(soil_reflectance, dict):
if not len(soil_reflectance) == len(opt):
raise ValueError(
'the number of bands for optical properties and soil reflectance should match')
self.soil_reflectance = soil_reflectance
else:
raise ValueError('Unrecognised soil_reflectance format')
else:
raise ValueError('Unrecognised opt format')
self.soil = None
if soil_mesh is not None:
if soil_mesh != -1:
if self.pattern is None:
raise ValueError(
'Adding a soil needs the scene domain to be defined')
if z_soil is None:
if self.scene is None:
z_soil = 0
else:
triangles = reduce(lambda x, y: x + y,
self.scene.values())
z = (pt[2] for tri in triangles for pt in tri)
z_soil = min(z)
self.soil = domain_mesh(self.pattern, z_soil, soil_mesh)
def __init__(self,
scene=None,
light=None,
pattern=None,
opt=None,
soil_reflectance=None,
soil_mesh=None,
z_soil=None,
scene_unit='m',
debug=False,
filecache=True):
""" Initialise a CaribuScene
Args:
scene (dict): a {primitive_id: [triangles,]} dict.A triangle is a
list of 3-tuples points coordinates
Alternatively, scene can be a *.can file or a mtg with
'geometry' property or a plantGL scene.
For the later case, shape.id are used as primitive_id.
light (list): a list of (Energy, (vx, vy, vz)) tuples defining light
sources
Alternatively, a *.light file
If None (default), a unit energy vertical light is used.
Energy unit should be given per square-meter (m-2)
pattern (tuple): 2D Coordinates of the domain bounding the scene for
its replication.
(xmin, ymin, xmax, ymax) scene is not bounded along z axis.
Alternatively a *.8 file.
if None (default), scene is not repeated
opt (dict): a {band_name: {primitive_id: material}} dict of dict
or a {band_name: material} dict of tuples.
In the second form the material is used for all primitives.
A material is a 1-, 2- or 4-tuple depending on its optical behavior.
A 1-tuple encode an opaque material characterised by its reflectance
A 2-tuple encode a symmetric translucent material defined
by a reflectance and a transmittance
A 4-tuple encode an asymmetric translucent material defined
the reflectance and transmittance
of the upper and lower side respectively
Alternatively, a list of band_name.opt files (require scene
to be given as a *.can file)
If None (default), all primitive are associated to the
default material of the class.
soil_reflectance (dict): a {band_name: reflectance} dict.
If None (default) class default soil reflectance is used for all bands
If *.opt files are provided, the values in opt files are used in priority
soil_mesh (int): a flag triggering for the creation of a soil mesh
in the scene during computations
If None (default) or -1, no soil is added
If an int (n), a soil is added to the scene, with n subdivisions
z_soil (float): the altitude of the soil.
If None (default), the soil is placed at the bottom of
the scene bounding box
scene_unit (str): the unit of length used for scene coordinate
and for pattern (should be one of class.units default)
By default, scene_unit is considered to be 'm' (meter).
Returns:
A CaribuScene instance
Note:
File format specifications (*.can, *.light, *.8, *.opt) can be found in data/CanestraDoc.pdf
"""
self.debug = debug
if scene_unit not in self.units:
raise ValueError('unrecognised scene unit: ' + scene_unit)
self.conv_unit = self.units[scene_unit]
self.scene = None
if scene is not None:
if isinstance(scene, dict):
elt = scene[list(scene.keys())[0]]
try:
assert isinstance(elt, list)
assert isinstance(elt[0], list)
assert isinstance(elt[0][0], tuple)
except:
raise ValueError('Unrecognised scene format')
self.scene = CaribuTriangleSet(scene)
elif isinstance(scene, str):
self.scene = CaribuTriangleSet(read_can(scene))
elif isinstance(scene, MTG):
self.scene = CaribuTriangleSet(mtg_to_cscene(scene))
elif isinstance(scene, pglScene):
self.scene = CaribuTriangleSet(scene_to_cscene(scene))
elif isinstance(scene, AbstractCaribuTriangleSet):
self.scene = scene
else:
raise ValueError('Unrecognised scene format')
self.light = [self.default_light]
if light is not None:
self.setLight(light)
self.pattern = None
if pattern is not None:
if isinstance(pattern, tuple):
if len(pattern) == 2:
pattern = sum(pattern, ())
if len(pattern) != 4:
raise ValueError('Unrecognised pattern format')
self.pattern = pattern
elif isinstance(pattern, str):
self.pattern = read_pattern(pattern)
else:
raise ValueError('Unrecognised pattern format')
self.material = None
if opt is None:
if soil_reflectance is None:
self.soil_reflectance = {
self.default_band: self.default_soil_reflectance
}
bands = [self.default_band]
else:
self.soil_reflectance = soil_reflectance
bands = list(soil_reflectance.keys())
if self.scene is not None:
self.material = {}
for band in bands:
self.material[band] = {
pid: self.default_material
for pid in self.scene.keys()
}
else:
if isinstance(opt, list):
if not isinstance(opt[0], str):
raise ValueError('Unrecognised opt format')
if not isinstance(scene, str):
raise ValueError(
'un-compatible inputs types: opt file and scene not a can file'
)
if self.scene is not None:
self.material = {}
self.soil_reflectance = {}
for path in opt:
band = os.path.basename(path).split('.')[0]
n, ro_soil, po = read_opt(path)
self.material[band] = build_materials(
list(self.scene.keys()), po, ro_soil)
self.soil_reflectance[band] = ro_soil
elif isinstance(opt, dict):
elt = opt[list(opt.keys())[0]]
if not isinstance(elt, dict):
if isinstance(elt, tuple):
self.material = {}
if self.scene is not None:
for band in opt:
self.material[band] = {
pid: opt[band]
for pid in self.scene.keys()
}
else:
raise ValueError('Unrecognised opt format')
else:
self.material = opt
if soil_reflectance is None:
self.soil_reflectance = {
band: self.default_soil_reflectance
for band in self.material
}
else:
if isinstance(soil_reflectance, dict):
if not len(soil_reflectance) == len(opt):
raise ValueError(
'the number of bands for optical properties and soil reflectance should match'
)
self.soil_reflectance = soil_reflectance
else:
raise ValueError(
'Unrecognised soil_reflectance format')
else:
raise ValueError('Unrecognised opt format')
self.soil = None
if soil_mesh is not None:
if soil_mesh != -1:
if self.pattern is None:
raise ValueError(
'Adding a soil needs the scene domain to be defined')
if z_soil is None:
if self.scene is None:
z_soil = 0
else:
z_soil = self.scene.getZmin()
self.soil = domain_mesh(self.pattern, z_soil, soil_mesh)
self.tempdir = None
if filecache:
self.tempdir = tempfile.mkdtemp(
) if not debug else './caribuscene_' + str(id(self))
self.canfile = None
self.optfile = None