def heights(g, scale=-1):
""" Compute the order of all vertices at scale `scale`.
If scale == -1, the compute the order for vertices at the finer scale.
"""
heights = {}
if scale <= 0:
for vid in traversal.iter_mtg2(g, g.root):
pid = g.parent(vid)
p_height = -1 if pid is None else heights[pid]
heights[vid] = p_height+1
else:
for rid in g.roots_iter(scale=scale):
for vid in traversal.pre_order2(g, rid):
pid = g.parent(vid)
p_height = -1 if pid is None else heights[pid]
heights[vid] = p_height+1
return heights
def orders(g, scale=-1):
""" Compute the order of all vertices at scale `scale`.
If scale == -1, the compute the order for vertices at the finer scale.
"""
orders = {}
if scale <= 0:
for vid in traversal.iter_mtg2(g, g.root):
pid = g.parent(vid)
p_order = 0 if pid is None else orders[pid]
orders[vid] = p_order+1 if g.edge_type(vid) == '+' else p_order
else:
for rid in g.roots_iter(scale=scale):
for vid in traversal.pre_order2(g, rid):
pid = g.parent(vid)
p_order = 0 if pid is None else orders[pid]
orders[vid] = p_order+1 if g.edge_type(vid) == '+' else p_order
return orders
def layout2d(g,
vid=None,
origin=(0, 0),
steps=(4, 8),
property_name='position'):
""" Compute 2d coordinates for each vertex.
This method compute a 2D layout of a tree or a MTG at a specific scale.
This will allow to plot tree in matplotlib for instance.
:Usage:
.. code-block:: python
>>> g.reindex()
>>> g1 = g.reindex(copy=True)
>>> mymap = dict(zip(list(traversal.iter_mtg2(g,g.root)), range(len(g))))
>>> g2 = g.reindex(mapping=mymap, copy=True)
:Optional Parameters:
- `origin` : a 2D point for the root of the tree.
- `property` (str) : Name of the property storing the 2D coordinates.
:Returns:
- a MTG
"""
if vid is None:
vid = g.root
if hasattr(g, 'max_scale'):
vid = g.component_roots_at_scale_iter(g.root, g.max_scale()).next()
# Algorithm
# 1. the y is defined by the Height of a node
# 2. The x is computed using non intersecting bounding box
x_step, y_step = steps
y = {}
vtxs = traversal.pre_order2(g, vid)
vtxs.next()
y[vid] = origin[1]
for v in vtxs:
y[v] = y[g.parent(v)] + y_step
bbox = {}
for v in traversal.post_order2(g, vid):
children = g.children(v)
if not children:
bbox[v] = 2 * x_step
else:
has_successor = [
cid for cid in children if g.edge_type(cid) == '<'
]
# 2 is for symmetry
bbox[v] = sum(bbox[cid] for cid in children)
if not has_successor:
bbox[v] += 2 * x_step
x = {}
vtxs = traversal.pre_order2(g, vid)
x[vid] = int(bbox[vid] / 2.)
for v in vtxs:
_width = bbox[v]
kids = g.children(v)
successor = [cid for cid in kids if g.edge_type(cid) == '<']
ramifs = [cid for cid in kids if g.edge_type(cid) == '+']
_min = x[v]
_max = x[v]
for cid in successor:
_x = x[cid] = x[v]
width = bbox[cid]
_min = _x - max(1, width / 2) - x_step
_max = _x + max(1, width / 2) + x_step
weights = [bbox[rid] for rid in ramifs]
def mean_ind(weights):
left = bool(random() < 0.5)
mid = sum(weights) / 2.
total = 0
n = 0
for w in weights:
if total + w <= mid:
total += w
else:
break
n += 1
if total - mid > 1 and left:
n += 1
if n == 0 and len(weights) > 1:
n += 1
return n
n = mean_ind(weights)
for rid in reversed(ramifs[:n]):
width = bbox[rid]
x[rid] = _min - max(1, width / 2)
_min -= width
for rid in ramifs[n:]:
width = bbox[rid]
x[rid] = _max + max(1, width / 2)
_max += width
# TODO: The tree s not well proportionned because we impose a constraint that the
# < is aligned to its parent
position = dict((k, (x[k], y[k])) for k in y)
g.properties()[property_name] = position
return g
def simple_layout(g,
vid=None,
origin=(0, 0),
steps=(4, 8),
property_name='position',
multiscale=True):
""" Compute 2d coordinates for each vertex.
This method compute a 2D layout of a tree or a MTG at a specific scale.
This will allow to plot tree in matplotlib for instance.
:Usage:
.. code-block:: python
>>> g = simple_layout(g)
:Optional Parameters:
- `origin` : a 2D point for the root of the tree.
- `property` (str) : Name of the property storing the 2D coordinates.
:Returns:
- a MTG
"""
def shuffle_post_order(tree, vtx_id):
'''
Traverse a tree in a postfix way.
(from leaves to root)
Same algorithm than post_order.
The goal is to replace the post_order implementation.
'''
edge_type = tree.property('edge_type')
def shuffle_children(vid):
''' Internal function to retrieve the children in a correct order:
- Branch before successor.
'''
kids = tree.children(vid)
plus = []
successor = []
for v in kids:
if edge_type.get(v) == '<':
successor.append(v)
else:
plus.append(v)
n = len(plus)
i = n / 2
if n % 2 != 0:
left = int(random() < 0.5)
i += left
child = plus[:i] + successor + plus[i:]
return child
visited = set([])
queue = [vtx_id]
# 1. select first '+' edges
while queue:
vtx_id = queue[-1]
for vid in shuffle_children(vtx_id):
if vid not in visited:
queue.append(vid)
break
else: # no child or all have been visited
yield vtx_id
visited.add(vtx_id)
queue.pop()
if vid is None:
vid = g.root
if hasattr(g, 'max_scale'):
vid = g.component_roots_at_scale_iter(g.root, g.max_scale()).next()
# Algorithm
# 1. the y is defined by the Height of a node
# 2. The x is computed using non intersecting bounding box
x_step, y_step = steps
y = {}
vtxs = traversal.pre_order2(g, vid)
vtxs.next()
y[vid] = origin[1]
for v in vtxs:
y[v] = y[g.parent(v)] + y_step
def leaves(g, vid):
for v in shuffle_post_order(g, vid):
if g.is_leaf(v):
yield v
def successor(g, vid):
for cid in g.children(vid):
if g.edge_type(cid) == '<':
return cid
return
x = {}
x_pos = origin[0]
for v in leaves(g, vid):
x[v] = x_pos
x_pos += x_step * 10
for v in shuffle_post_order(g, vid):
if v in x:
continue
son_id = successor(g, v)
if son_id:
x[v] = x[son_id]
else:
children = g.children(v)
x[v] = int(
float(sum(x[cid] for cid in children)) / (len(children)))
position = dict((k, (x[k], y[k])) for k in y)
if multiscale:
# get the position at the lower scales
max_scale = g.scale(vid)
for s in range(max_scale - 1, 0, -1):
v_root = g.complex_at_scale(vid, scale=s)
vtxs = traversal.pre_order2(g, v_root)
for v in vtxs:
comp_id = g.component_roots_at_scale_iter(
v, scale=max_scale).next()
position[v] = position[comp_id]
g.properties()[property_name] = position
return g
def layout2d(g, vid=None, origin=(0,0), steps=(4,8), property_name='position'):
""" Compute 2d coordinates for each vertex.
This method compute a 2D layout of a tree or a MTG at a specific scale.
This will allow to plot tree in matplotlib for instance.
:Usage:
.. code-block:: python
>>> g.reindex()
>>> g1 = g.reindex(copy=True)
>>> mymap = dict(zip(list(traversal.iter_mtg2(g,g.root)), range(len(g))))
>>> g2 = g.reindex(mapping=mymap, copy=True)
:Optional Parameters:
- `origin` : a 2D point for the root of the tree.
- `property` (str) : Name of the property storing the 2D coordinates.
:Returns:
- a MTG
"""
if vid is None:
vid = g.root
if hasattr(g, 'max_scale'):
vid = g.component_roots_at_scale_iter(g.root, g.max_scale()).next()
# Algorithm
# 1. the y is defined by the Height of a node
# 2. The x is computed using non intersecting bounding box
x_step, y_step = steps
y= {}
vtxs = traversal.pre_order2(g,vid)
vtxs.next()
y[vid] = origin[1]
for v in vtxs:
y[v] = y[g.parent(v)]+y_step
bbox = {}
for v in traversal.post_order2(g,vid):
children = g.children(v)
if not children:
bbox[v] = 2*x_step
else:
has_successor = [cid for cid in children if g.edge_type(cid)=='<']
# 2 is for symmetry
bbox[v] = sum(bbox[cid] for cid in children)
if not has_successor:
bbox[v]+=2*x_step
x ={}
vtxs = traversal.pre_order2(g,vid)
x[vid] = int(bbox[vid]/2.)
for v in vtxs:
_width = bbox[v]
kids = g.children(v)
successor = [cid for cid in kids if g.edge_type(cid)=='<']
ramifs = [cid for cid in kids if g.edge_type(cid)=='+']
_min = x[v]; _max = x[v]
for cid in successor:
_x = x[cid] = x[v]
width = bbox[cid]
_min = _x-max(1,width/2)-x_step
_max = _x+max(1,width/2)+x_step
weights = [bbox[rid] for rid in ramifs]
def mean_ind(weights):
left = bool(random()<0.5)
mid= sum(weights)/2.
total = 0
n = 0
for w in weights:
if total+w <= mid:
total+= w
else:
break
n+=1
if total-mid > 1 and left:
n+=1
if n == 0 and len(weights)>1:
n+=1
return n
n = mean_ind(weights)
for rid in reversed(ramifs[:n]):
width = bbox[rid]
x[rid] = _min - max(1,width/2)
_min -= width
for rid in ramifs[n:]:
width = bbox[rid]
x[rid] = _max + max(1,width/2)
_max += width
# TODO: The tree s not well proportionned because we impose a constraint that the
# < is aligned to its parent
position = dict((k, (x[k],y[k])) for k in y)
g.properties()[property_name] = position
return g
def simple_layout(g, vid=None, origin=(0,0), steps=(4,8), property_name='position', multiscale=True):
""" Compute 2d coordinates for each vertex.
This method compute a 2D layout of a tree or a MTG at a specific scale.
This will allow to plot tree in matplotlib for instance.
:Usage:
.. code-block:: python
>>> g = simple_layout(g)
:Optional Parameters:
- `origin` : a 2D point for the root of the tree.
- `property` (str) : Name of the property storing the 2D coordinates.
:Returns:
- a MTG
"""
def shuffle_post_order(tree, vtx_id):
'''
Traverse a tree in a postfix way.
(from leaves to root)
Same algorithm than post_order.
The goal is to replace the post_order implementation.
'''
edge_type = tree.property('edge_type')
def shuffle_children(vid):
''' Internal function to retrieve the children in a correct order:
- Branch before successor.
'''
kids = tree.children(vid)
plus = []
successor = []
for v in kids:
if edge_type.get(v) == '<':
successor.append(v)
else:
plus.append(v)
n = len(plus)
i = n/2
if n%2!=0:
left = int(random()<0.5)
i += left
child = plus[:i]+successor+plus[i:]
return child
visited = set([])
queue = [vtx_id]
# 1. select first '+' edges
while queue:
vtx_id = queue[-1]
for vid in shuffle_children(vtx_id):
if vid not in visited:
queue.append(vid)
break
else: # no child or all have been visited
yield vtx_id
visited.add(vtx_id)
queue.pop()
if vid is None:
vid = g.root
if hasattr(g, 'max_scale'):
vid = g.component_roots_at_scale_iter(g.root, g.max_scale()).next()
# Algorithm
# 1. the y is defined by the Height of a node
# 2. The x is computed using non intersecting bounding box
x_step, y_step = steps
y= {}
vtxs = traversal.pre_order2(g,vid)
vtxs.next()
y[vid] = origin[1]
for v in vtxs:
y[v] = y[g.parent(v)]+y_step
def leaves(g, vid):
for v in shuffle_post_order(g,vid):
if g.is_leaf(v):
yield v
def successor(g, vid):
for cid in g.children(vid):
if g.edge_type(cid)=='<':
return cid
return
x = {}
x_pos = origin[0]
for v in leaves(g,vid):
x[v] = x_pos
x_pos += x_step*10
for v in shuffle_post_order(g,vid):
if v in x:
continue
son_id = successor(g,v)
if son_id:
x[v] = x[son_id]
else:
children = g.children(v)
x[v] = int(float(sum(x[cid] for cid in children)) / (len(children)))
position = dict((k, (x[k],y[k])) for k in y)
if multiscale:
# get the position at the lower scales
max_scale = g.scale(vid)
for s in range(max_scale-1,0,-1):
v_root = g.complex_at_scale(vid, scale=s)
vtxs = traversal.pre_order2(g, v_root)
for v in vtxs:
comp_id = g.component_roots_at_scale_iter(v, scale=max_scale).next()
position[v] = position[comp_id]
g.properties()[property_name] = position
return g
