def extract_at_module_scale(g, vids=[], convert=convert):
if not vids:
vids = g.vertices(scale=1)
orders = algo.orders(g, scale=2)
module_variables = _module_variables(g)
visible_modules(g, vids=vids)
complete_module(g, vids=vids)
module_ids = [
v for v in g.property('visible')
if g.complex_at_scale(v, scale=1) in vids
]
module_df = OrderedDict()
module_df['Genotype'] = [genotype(mid, g) for mid in module_ids]
module_df['date'] = [date(mid, g) for mid in module_ids]
module_df['modality'] = [modality(mid, g) for mid in module_ids]
module_df['plant'] = [plant(mid, g) for mid in module_ids]
module_df['order'] = [orders[mid] for mid in module_ids]
visibles = property(g, 'visible')
for name in (module_variables):
f = module_variables[name]
module_df[name] = [f(mid, g) for mid in module_ids]
#plant_df['nb_ramifications'] = [sum(1 for v in g.components(pid) if (type_of_crown(v, g)==3 and v in visibles)) for pid in plant_ids]
module_df['vid'] = module_ids
module_df['plant_vid'] = [g.complex(v) for v in module_ids]
df = pd.DataFrame(module_df)
return df
def extract_at_plant_scale(g, vids=[], convert=convert):
"""Compute the properties at plant scale of a MTG.
:param g: The MTG
:type g: MTG
:param vids: list of vids that are included in the extraction at scale 1, defaults to []
:type vids: list, optional
:param convert: Dictionary of equivalence of data name from fr to eng , defaults to convert
:type convert: dict, optional
:return: A dataframe of computed properties at plant scale
:rtype: DataFrame
"""
#TODO: compute this only one. It would be nice if we can compute this in the init of a class Extractor.
orders = algo.orders(g, scale=2)
plant_variables = _plant_variables(g)
# plant_ids is a list of plants we wat to process.
if not vids:
plant_ids = g.vertices(scale=1)
else:
plant_ids = [pid for pid in g.vertices(scale=1) if pid in vids]
visible_modules(g, vids=plant_ids)
compute_leaf_area(g, vids=plant_ids)
plant_df = OrderedDict()
# for name in ('Genotype', 'date', 'plant'):
# plant_df[name] = [plant_variables[name](pid) for pid in plant_ids]
plant_df['Genotype'] = [genotype(pid, g) for pid in plant_ids]
plant_df['date'] = [date(pid, g) for pid in plant_ids]
plant_df['modality'] = [modality(pid, g) for pid in plant_ids]
plant_df['plant'] = [plant(pid, g) for pid in plant_ids]
visibles = property(g, 'visible')
for name in (plant_variables):
f = plant_variables[name]
plant_df[name] = [
sum(f(v, g) for v in g.components(pid) if v in visibles)
for pid in plant_ids
]
#plant_df['Total_leaf_area'] = [mean_leaf_area(pid, g) * (sum(nb_visible_leaves(v,g) for v in g.components(pid) if v in visibles) for pid in plant_ids]
plant_df['leaf_area'] = [mean_leaf_area(pid, g) for pid in plant_ids]
plant_df['order_max'] = [
max(orders[v] for v in g.components(pid) if v in visibles)
for pid in plant_ids
]
plant_df['nb_ramifications'] = [
sum(1 for v in g.components(pid)
if (type_of_crown(v, g) == 3 and v in visibles))
for pid in plant_ids
]
plant_df['vid'] = plant_ids
df = pd.DataFrame(plant_df)
return df
def extract_at_plant_scale(g, vids=[], convert=convert):
"""
Return computed properties at plant scale
Parameters
----------
- g: MTG
- vids : a subset of vertex ids at scale 1
Returns
-------
- a Dataframe
"""
#TODO: compute this only one. It would be nice if we can compute this in the init of a class Extractor.
orders = algo.orders(g, scale=2)
plant_variables = _plant_variables(g)
# plant_ids is a list of plants we wat to process.
if not vids:
plant_ids = g.vertices(scale=1)
else:
plant_ids = [pid for pid in g.vertices(scale=1) if pid in vids]
visible_modules(g, vids=plant_ids)
compute_leaf_area(g, vids=plant_ids)
plant_df = OrderedDict()
# for name in ('Genotype', 'date', 'plant'):
# plant_df[name] = [plant_variables[name](pid) for pid in plant_ids]
plant_df['Genotype'] = [genotype(pid, g) for pid in plant_ids]
plant_df['date'] = [date(pid, g) for pid in plant_ids]
plant_df['modality'] = [modality(pid, g) for pid in plant_ids]
plant_df['plant'] = [plant(pid, g) for pid in plant_ids]
visibles = property(g, 'visible')
for name in (plant_variables):
f = plant_variables[name]
plant_df[name] = [
sum(f(v, g) for v in g.components(pid) if v in visibles)
for pid in plant_ids
]
#plant_df['Total_leaf_area'] = [mean_leaf_area(pid, g) * (sum(nb_visible_leaves(v,g) for v in g.components(pid) if v in visibles) for pid in plant_ids]
plant_df['leaf_area'] = [mean_leaf_area(pid, g) for pid in plant_ids]
plant_df['order_max'] = [
max(orders[v] for v in g.components(pid) if v in visibles)
for pid in plant_ids
]
plant_df['nb_ramifications'] = [
sum(1 for v in g.components(pid)
if (type_of_crown(v, g) == 3 and v in visibles))
for pid in plant_ids
]
plant_df['vid'] = plant_ids
df = pd.DataFrame(plant_df)
return df
def print_2d_single_p(g, genotype, vid):
with plot2d_single_p:
plot2d_single_p.clear_output()
vids_selected = get_vid_of_genotype(g, genotypes=[genotype])
g.properties()['order'] = orders(g)
scene = visu2d.plot2d(g, [vids_selected[vid]],
dist=[3] * 3,
display=False)
display3d(scene)
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 print_2d_median(g, genotype):
with plot2d_most_central:
plot2d_most_central.clear_output()
vids_selected = get_vid_of_genotype(g, genotypes=[genotype])
g.properties()['order'] = orders(g)
df = extract_at_plant_scale(g, vids=vids_selected)
df_median = median_individuals(df, )
# selection of vid of median individuals
pids = list(df_median.vid)
n = len(pids)
scene = visu2d.plot2d(g, pids, dist=[6] * n, display=False)
display3d(scene)
def extract_at_node_scale(g, vids=[], convert=convert):
if not vids:
vids = g.vertices(scale=1)
node_df = OrderedDict()
visible_modules(g, vids=vids)
complete_module(g, vids=vids)
orders = algo.orders(g, scale=2)
# Define all the rows
props = [
'node_id', 'rank', 'branching_type', 'complete',
'nb_modules_branching', 'nb_branch_crown_branching',
'nb_extension_crown_branching', 'branching_length', 'Genotype',
'order', 'date', 'plant'
]
for prop in props:
node_df[prop] = []
roots = [
rid for pid in vids for rid in g.component_roots_at_scale(pid, scale=2)
]
trunks = [
list(
chain(*[(v for v in algo.axis(g, m, scale=3)
if g.label(v) in ('F', 'f'))
for m in apparent_axis(g, r)])) for r in roots
]
for trunk in trunks:
# Define your schema
for i, vid in enumerate(trunk):
node_df['node_id'].append(vid) #scale=3
node_df['rank'].append(i + 1) #scale=3
node_df['branching_type'].append(my_bt(vid, g)) #scale=2
node_df['complete'].append(my_complete(vid, g)) #scale=2
node_df['nb_modules_branching'].append(nb_total_module_tree(
vid, g)) #scale=2
node_df['nb_branch_crown_branching'].append(
nb_branching_tree(vid, g)) #scale=2
node_df['nb_extension_crown_branching'].append(
nb_extension_tree(vid, g)) #scale=2
node_df['branching_length'].append(nb_visible_leaves_tree(vid, g))
node_df['Genotype'].append(genotype(vid, g)) #scale=1
node_df['order'].append(orders[g.complex(vid)]) #scale=2
node_df['plant'].append(plant(vid, g)) #scale=1
node_df['date'].append(date(vid, g)) #scale=1
df = pd.DataFrame(node_df)
return df
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 print_3d_floral_intensity(g, genotype):
if g:
with plot3d_floral_intensity:
plot3d_floral_intensity.clear_output()
print('3d floral_intensity ')
vids_selected = get_vid_of_genotype(g, genotypes=[genotype])
g.properties()['order'] = orders(g)
scene = visu3d.plot3d(g,
by=["Sample_date"],
hide_leaves=True,
display=False,
vids=vids_selected)
display3d(scene)
else:
with plot3d_floral_intensity:
plot3d_floral_intensity.clear_output()
print('Select a Genotype')
def print_3d_growth_developement(g, genotype):
if g:
with plot3d_growth_developement:
plot3d_growth_developement.clear_output()
print('3d growth developement')
vids_selected = get_vid_of_genotype(g, genotypes=[genotype])
g.properties()['order'] = orders(g)
scene = visu3d.plot3d(g,
by=["Sample_date"],
hide_leaves=False,
display=False,
vids=vids_selected)
display3d(scene)
else:
with plot3d_growth_developement:
plot3d_growth_developement.clear_output()
print('Select a Genotype')
def extract_at_module_scale(g, vids=[], convert=convert):
"""Compute the properties at module scale of a MTG.
:param g: The MTG
:type g: MTG
:param vids: list of vids that are included in the extraction at scale 1, defaults to []
:type vids: list, optional
:param convert: Dictionary of equivalence of data name from fr to eng , defaults to convert
:type convert: dict, optional
:return: A dataframe of computed properties at module scale
:rtype: DataFrame
"""
if not vids:
vids = g.vertices(scale=1)
orders = algo.orders(g, scale=2)
module_variables = _module_variables(g)
visible_modules(g, vids=vids)
complete_module(g, vids=vids)
module_ids = [
v for v in g.property('visible')
if g.complex_at_scale(v, scale=1) in vids
]
module_df = OrderedDict()
module_df['Genotype'] = [genotype(mid, g) for mid in module_ids]
module_df['date'] = [date(mid, g) for mid in module_ids]
module_df['modality'] = [modality(mid, g) for mid in module_ids]
module_df['plant'] = [plant(mid, g) for mid in module_ids]
module_df['order'] = [orders[mid] for mid in module_ids]
visibles = property(g, 'visible')
for name in (module_variables):
f = module_variables[name]
module_df[name] = [f(mid, g) for mid in module_ids]
#plant_df['nb_ramifications'] = [sum(1 for v in g.components(pid) if (type_of_crown(v, g)==3 and v in visibles)) for pid in plant_ids]
module_df['vid'] = module_ids
module_df['plant_vid'] = [g.complex(v) for v in module_ids]
df = pd.DataFrame(module_df)
return df
def to_dataframe(g, vertices=[], f=None):
"""Convert an MTG into a full dataframe.
:param g: MTG graph
:type g: MTG
:param vertices: define the vertices you want to export, defaults to []
:type vertices: list, optional
:param f: v -> dict : function that returns a set of properties for any vertex, defaults to None
:type f: function, optional
:return: A dataframe that include all the MTG properties
:rtype: DataFrame
"""
# Recompute the properties for each vertices
if not vertices:
vertices = g.vertices()
if f is None:
f = lambda v: g[v]
d = dict()
for v in vertices:
props_v = f(v)
for k, value in props_v.items():
d.setdefault(k, {})[v] = value
parents = g._parent
complexes = {
vid: g.complex(vid)
for vid in g if g.complex(vid) is not None
}
scales = g._scale
_orders = orders(g)
d['parent'] = {v: parents.get(v) for v in vertices}
d['complex'] = {v: complexes.get(v) for v in vertices}
d['scale'] = {v: scales.get(v) for v in vertices}
d['order'] = {v: _orders.get(v) for v in vertices}
dataframe = pd.DataFrame.from_dict(d)
return dataframe
def to_dataframe(g, vertices=[], f=None):
""" Convert an MTG into a full dataframe.
Properties:
- vertices: define the vertices you want to export
- f : v -> dict : function that returns a set of properties for any vertex.
"""
# Recompute the properties for each vertices
if not vertices:
vertices = g.vertices()
if f is None:
f = lambda v: g[v]
d = dict()
for v in vertices:
props_v = f(v)
for k, value in props_v.iteritems():
d.setdefault(k, {})[v] = value
parents = g._parent
complexes = {
vid: g.complex(vid)
for vid in g if g.complex(vid) is not None
}
scales = g._scale
_orders = orders(g)
d['parent'] = {v: parents.get(v) for v in vertices}
d['complex'] = {v: complexes.get(v) for v in vertices}
d['scale'] = {v: scales.get(v) for v in vertices}
d['order'] = {v: _orders.get(v) for v in vertices}
dataframe = pd.DataFrame.from_dict(d)
return dataframe
def extract_at_node_scale(g, vids=[], convert=convert):
"""Compute the properties at node scale of a MTG.
:param g: The MTG
:type g: MTG
:param vids: list of vids that are included in the extraction at scale 1, defaults to []
:type vids: list, optional
:param convert: Dictionary of equivalence of data name from fr to eng , defaults to convert
:type convert: dict, optional
:return: A dataframe of computed properties at node scale
:rtype: DataFrame
"""
if not vids:
vids = g.vertices(scale=1)
node_df = OrderedDict()
visible_modules(g, vids=vids)
complete_module(g, vids=vids)
orders = algo.orders(g, scale=2)
# Define all the rows
props = [
'node_id', 'rank', 'branching_type', 'complete',
'nb_modules_branching', 'nb_branch_crown_branching',
'nb_extension_crown_branching', 'branching_length', 'stage',
'Genotype', 'order', 'date', 'plant'
]
for prop in props:
node_df[prop] = []
roots = [
rid for pid in vids for rid in g.component_roots_at_scale(pid, scale=2)
]
trunks = [
list(
chain(*[(v for v in algo.axis(g, m, scale=3)
if g.label(v) in ('F', 'f'))
for m in apparent_axis(g, r)])) for r in roots
]
for trunk in trunks:
# Define your schema
for i, vid in enumerate(trunk):
node_df['node_id'].append(vid) #scale=3
node_df['rank'].append(i + 1) #scale=3
node_df['branching_type'].append(my_bt(vid, g)) #scale=2
node_df['complete'].append(my_complete(vid, g)) #scale=2
node_df['nb_modules_branching'].append(nb_total_module_tree(
vid, g)) #scale=2
node_df['nb_branch_crown_branching'].append(
nb_branching_tree(vid, g)) #scale=2
node_df['nb_extension_crown_branching'].append(
nb_extension_tree(vid, g)) #scale=2
node_df['branching_length'].append(nb_visible_leaves_tree(vid, g))
node_df['Genotype'].append(genotype(vid, g)) #scale=1
node_df['order'].append(orders[g.complex(vid)]) #scale=2
node_df['plant'].append(plant(vid, g)) #scale=1
node_df['date'].append(date(vid, g)) #scale=1
node_df['stage'].append(stage(vid, g)) # scale=3
df = pd.DataFrame(node_df)
return df
def load_mtg(fn):
g = MTG(fn)
g = transform_date(g)
g.properties()['order'] = orders(g)
return g