def test_extraction_at_node_scale():
files = shared_data(openalea.strawberry).glob('*.mtg')
mtg_path = dict((name(f), f) for f in files)
gariguette = read_mtg_file(mtg_path['Gariguette'])
gariguette_extraction_at_node_scale = extract_at_node_scale(gariguette)
assert len(gariguette_extraction_at_node_scale) == 784
gariguette_axillary_prod = prob_axillary_production(gariguette, order=0)
assert len(gariguette_axillary_prod) == 19
def test4():
from openalea.core import alea
from openalea.mtg.io import read_mtg_file
fn = alea.run(('demo.mtg', 'agraf.mtg'), [])[0]
g = read_mtg_file(fn)
param = Quaking_Aspen()
param.order = 2
wp = Weber_MTG(param, g)
wp.run()
def __test_2D():
files = shared_data(openalea.strawberry).glob('*.mtg')
mtg_path = dict((name(f), f) for f in files)
gariguette = read_mtg_file(mtg_path['Gariguette'])
gariguette.properties()['order'] = orders(gariguette)
scene = visu2d.plot2d(gariguette,
gariguette.vertices(scale=1)[53:54],
dist=[3] * 3,
display=False)
PlantGL(scene)
def test_3D():
files = shared_data(openalea.strawberry).glob('*.mtg')
mtg_path = dict((name(f), f) for f in files)
gariguette = read_mtg_file(mtg_path['Gariguette'])
gariguette.properties()['order'] = orders(gariguette)
scene = visu3d.plot3d(gariguette,
by=["Sample_date"],
hide_leaves=False,
display=False)
assert scene.isValid() == True
p = PlantGL(scene, group_by_color=True)
assert len(p.object_ids) == 103
def test_extract_at_module_scale():
files = shared_data(openalea.strawberry).glob('*.mtg')
mtg_path = dict((name(f), f) for f in files)
gariguette = read_mtg_file(mtg_path['Gariguette'])
gariguette_extraction_at_module_scale = extract_at_module_scale(gariguette)
assert len(gariguette_extraction_at_module_scale) == 241
gariguette_frequency = occurence_module_order_along_time(data= gariguette_extraction_at_module_scale,frequency_type= "cdf")
assert len(gariguette_frequency) == 6
mean= gariguette_extraction_at_module_scale.groupby(["Genotype", "order"]).mean()
sd= gariguette_extraction_at_module_scale.groupby(["Genotype", "order"]).std()
assert len(mean) == 6
assert len(sd) == 6
def weber_penn_mtg(mtg_file, parameters, seed, position):
if not parameters or not mtg_file:
raise WeberPennError(
"Unable to run the Weber and Penn model without parameters.")
random.seed(seed)
if isinstance(mtg_file, str):
g = read_mtg_file(mtg_file)
else:
g = mtg_file
client = Weber_MTG(parameters, g)
client.run()
scene = client.plot()
return scene,
def on_change_get_files(widget, event, data):
# load mtgs
misc.all_mtg = MTG()
for file in data:
g = read_mtg_file(file_paths[file])
misc.all_mtg = union(misc.all_mtg, g)
# update table
if misc.all_mtg:
df = get_table_mtg(misc.all_mtg)
# TODO:
update_grid(df, tableMTG)
else:
update_grid(pd.DataFrame(), tableMTG)
# update genotype selections
update_selection_items()
# update file description
print_files_description()
def test_df2waffle():
files = shared_data(openalea.strawberry).glob('*.mtg')
mtg_path = dict((name(f), f) for f in files)
mtg = read_mtg_file(mtg_path['Capriss'])
df = extract_at_node_scale(mtg)
node_scale = df2waffle(df,
index='rank',
date='2015/03/02',
variable='branching_type')
assert node_scale.shape == (20, 9)
df = extract_at_module_scale(mtg)
module_scale = df2waffle(df,
index='order',
date='2015/03/02',
variable='crown_status',
aggfunc='median')
assert module_scale.shape == (3, 9)
def test_extract_at_plant_scale():
files = shared_data(openalea.strawberry).glob('*.mtg')
mtg_path = dict((name(f), f) for f in files)
mtg = MTG()
for k, genotype in enumerate(mtg_path):
if (genotype=="Sicile") or (genotype=="Nils") or (genotype=='origine_stolon_gariguetteDV_6novembre2018') \
or (genotype=='friendlyfruit_varieties'):
pass
else:
mtg = union(mtg, read_mtg_file(mtg_path[genotype]))
genotypes = mtg.property('Genotype')
for geno in set(genotypes.values()):
vids = [
vid for vid in mtg.vertices(scale=1) if genotypes.get(vid) == geno
]
df = extract_at_plant_scale(mtg, vids)
assert not df.empty
assert set(df['Genotype']) == {geno}
def MTG(filename):
"""
MTG constructor.
Builds a MTG from a coding file (text file) containing the description of one or several plants.
:Usage:
::
MTG(filename)
:Parameters:
- `filename` (str): name of the coding file describing the mtg
:Returns:
If the parsing process succeeds, returns an object of type :func:`MTG`.
Otherwise, an error is generated, and the formerly active `MTG` remains active.
:Side Effect:
If the :func:`MTG` is built, the new :func:`MTG` becomes the active :func:`MTG` (i.e. the :func:`MTG` implicitly
used by other functions such as :func:`Father()`, :func:`Sons()`, :func:`VtxList()`, ...).
:Details:
The parsing process is approximatively proportional to the number of components
defined in the coding file.
:Background:
MTG is an acronyme for Multiscale Tree Graph.
.. seealso:: :func:`Activate` and all :mod:`openalea.mtg.aml` functions.
"""
global _g
_g = read_mtg_file(filename)
return _g
def MTG(filename):
"""
MTG constructor.
Builds a MTG from a coding file (text file) containing the description of one or several plants.
:Usage:
::
MTG(filename)
:Parameters:
- `filename` (str): name of the coding file describing the mtg
:Returns:
If the parsing process succeeds, returns an object of type :func:`MTG`.
Otherwise, an error is generated, and the formerly active `MTG` remains active.
:Side Effect:
If the :func:`MTG` is built, the new :func:`MTG` becomes the active :func:`MTG` (i.e. the :func:`MTG` implicitly
used by other functions such as :func:`Father()`, :func:`Sons()`, :func:`VtxList()`, ...).
:Details:
The parsing process is approximatively proportional to the number of components
defined in the coding file.
:Background:
MTG is an acronyme for Multiscale Tree Graph.
.. seealso:: :func:`Activate` and all :mod:`openalea.mtg.aml` functions.
"""
global _g
_g = read_mtg_file(filename)
return _g
import openalea.mtg.io as io reload(io) #io.debug = 1 fn = r'data/agraf.mtg' fn2 = r'data/rapple.mtg' #fn = r'data/mtg5.mtg' """ f = open(fn) s = f.read() f.close() r = io.Reader(s) # skip the header r.header() # read the MTG header r._nb_feature=2 r._feature_head = ['nbEl', 'diam'] r._feature_slice=slice(5,7) #debug r.preprocess_code() print r._new_code """ g = io.read_mtg_file(fn)
def test_import_mtg():
files = shared_data(openalea.strawberry).glob('*.mtg')
mtg_path = dict((name(f), f) for f in files)
gariguette = read_mtg_file(mtg_path['Gariguette'])
straws = split(gariguette)
assert isinstance(straws[0], openalea.mtg.mtg.MTG)