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Add version checking for dictionary calls #65

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146 changes: 115 additions & 31 deletions debacl/level_set_tree.py
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Original file line number Diff line number Diff line change
Expand Up @@ -8,6 +8,8 @@
from __future__ import print_function as _print_function
from __future__ import absolute_import as _absolute_import

from sys import version

import logging as _logging
import copy as _copy
import pickle as _pickle
Expand Down Expand Up @@ -271,7 +273,12 @@ def plot(self, form='mass', horizontal_spacing='uniform', color_nodes=[],
split_coords = {}

## Find the root connected components and corresponding plot intervals
ix_root = _np.array([k for k, v in self.nodes.iteritems()
if version[0] == '2':
nodes_items = self.nodes.iteritems()
if version[0] == '3':
nodes_items = self.nodes.items()

ix_root = _np.array([k for k, v in nodes_items
if v.parent is None])
n_root = len(ix_root)
census = _np.array([len(self.nodes[x].members) for x in ix_root],
Expand Down Expand Up @@ -322,7 +329,12 @@ def plot(self, form='mass', horizontal_spacing='uniform', color_nodes=[],
ax.yaxis.grid(color='gray')
ax.set_yticks(primary_ticks)
ax.set_yticklabels(primary_labels)


if version[0] == '2':
nodes_values = self.nodes.itervalues()
if version[0] == '3':
nodes_values = self.nodes.values()

## Form-specific details
if form == 'branch-mass':
yrange = max(primary_ticks)
Expand All @@ -331,23 +343,29 @@ def plot(self, form='mass', horizontal_spacing='uniform', color_nodes=[],

elif form == 'density':
ax.set_ylabel("density level")
ymin = min([v.start_level for v in self.nodes.itervalues()])
ymax = max([v.end_level for v in self.nodes.itervalues()])

ymin = min([v.start_level for v in nodes_values])
ymax = max([v.end_level for v in nodes_values])
yrange = ymax - ymin
ax.set_ylim(ymin - gap * yrange, ymax + 0.05 * yrange)

elif form == 'mass':
ax.set_ylabel("mass level")
ymin = min([v.start_mass for v in self.nodes.itervalues()])
ymax = max([v.end_mass for v in self.nodes.itervalues()])
ymin = min([v.start_mass for v in nodes_values])
ymax = max([v.end_mass for v in nodes_values])
yrange = ymax - ymin
ax.set_ylim(ymin - gap * yrange, ymax + 0.05 * yrange)

else:
raise ValueError('Plot form not understood')

## Color the line segments.
node_colors = {k: [0.0, 0.0, 0.0, 1.0] for k, v in self.nodes.items()}
if version[0] == '2':
nodes_items = self.nodes.iteritems()
if version[0] == '3':
nodes_items = self.nodes.items()

node_colors = {k: [0.0, 0.0, 0.0, 1.0] for k, v in nodes_items}
palette = _plt.get_cmap(colormap)
colorset = palette(_np.linspace(0, 1, len(color_nodes)))

Expand Down Expand Up @@ -604,16 +622,32 @@ def _merge_by_size(self, threshold):
tree.prune_threshold = threshold

## remove small root branches
small_roots = [k for k, v in tree.nodes.iteritems()
if version[0] == '2':
tree_nodes_items = tree.nodes.iteritems()
if version[0] == '3':
tree_nodes_items = tree.nodes.items()

small_roots = [k for k, v in tree_nodes_items
if v.parent is None and len(v.members) <= threshold]

for root in small_roots:
root_tree = tree._make_subtree(root)
for ix in root_tree.nodes.iterkeys():

if version[0] == '2':
root_tree_nodes_keys = root_tree.nodes.iterkeys()
if version[0] == '3':
root_tree_nodes_keys = root_tree.nodes.keys()

for ix in root_tree_nodes_keys:
del tree.nodes[ix]

## main pruning
parents = [k for k, v in tree.nodes.iteritems()
if version[0] == '2':
tree_nodes_items = tree.nodes.iteritems()
if version[0] == '3':
tree_nodes_items = tree.nodes.items()

parents = [k for k, v in tree_nodes_items
if len(v.children) >= 1]
parents = _np.sort(parents)[::-1]

Expand All @@ -622,9 +656,14 @@ def _merge_by_size(self, threshold):

# get size of each child
kid_size = {k: len(tree.nodes[k].members) for k in parent.children}

# print(_np.array([(key,val) for (key,val) in kid_size.items()]))

# count children larger than 'threshold'
n_bigkid = sum(_np.array(kid_size.values()) >= threshold)
# print(_np.array(kid_size.values()), threshold)
# n_bigkid = sum(_np.array(kid_size.values()) >= threshold)
# n_bigkid = 0
n_bigkid = sum([len(tree.nodes[k].members) for k in parent.children])
# n_bigkid = sum(_np.array([(key,val) for (key,val) in kid_size.items()]) >= threshold)

if n_bigkid == 0:
# update parent's end level and end mass
Expand All @@ -641,7 +680,12 @@ def _merge_by_size(self, threshold):
elif n_bigkid == 1:
pass
# identify the big kid
ix_bigkid = [k for k, v in kid_size.iteritems()
if version[0] == '2':
kid_size_items = kid_size.iteritems()
if version[0] == '3':
kid_size_items = kid_size.items()

ix_bigkid = [k for k, v in kid_size_items
if v >= threshold][0]
bigkid = tree.nodes[ix_bigkid]

Expand Down Expand Up @@ -786,8 +830,13 @@ def _upper_set_cluster(self, threshold, form='mass'):
form='density')

else:
if version[0] == '2':
nodes_items = self.nodes.iteritems()
if version[0] == '3':
nodes_items = self.nodes.items()

upper_level_set = _np.where(_np.array(self.density) > threshold)[0]
active_nodes = [k for k, v in self.nodes.iteritems()
active_nodes = [k for k, v in nodes_items
if (v.start_level <= threshold and
v.end_level > threshold)]

Expand Down Expand Up @@ -835,7 +884,7 @@ def _first_K_level_cluster(self, k):
"""

cut = self._find_K_cut(k)
nodes = [e for e, v in self.nodes.iteritems()
nodes = [e for e, v in self.nodesiteritems()
if v.start_level <= cut and v.end_level > cut]

points = []
Expand Down Expand Up @@ -896,25 +945,39 @@ def _find_K_cut(self, k):
"""

## Find the lowest level to cut at that has k or more clusters
starts = [v.start_level for v in self.nodes.itervalues()]
ends = [v.end_level for v in self.nodes.itervalues()]
if version[0] == '2':
nodes_values = self.nodes.itervalues()
nodes_items = self.nodes.iteritems()
if version[0] == '3':
nodes_values = self.nodes.values()
nodes_values = self.nodes.items()

starts = [v.start_level for v in nodes_values]
ends = [v.end_level for v in nodes_values]
crits = _np.unique(starts + ends)
nclust = {}

for c in crits:
nclust[c] = len([e for e, v in self.nodes.iteritems()
nclust[c] = len([e for e, v in nodes_items
if v.start_level <= c and v.end_level > c])

width = _np.max(nclust.values())


if version[0] == '2':
nclust_items = nclust.iteritems()
nclust_values = nclust.itervalues()
if version[0] == '3':
nclust_items = nclust.items()
nclust_values = nclust.values()

if k in nclust.values():
cut = _np.min([e for e, v in nclust.iteritems() if v == k])
cut = _np.min([e for e, v in nclust_items if v == k])
else:
if width < k:
cut = _np.min([e for e, v in nclust.iteritems() if v == width])
cut = _np.min([e for e, v in nclust_items if v == width])
else:
ktemp = _np.min([v for v in nclust.itervalues() if v > k])
cut = _np.min([e for e, v in nclust.iteritems() if v == ktemp])
ktemp = _np.min([v for v in nclust_values if v > k])
cut = _np.min([e for e, v in nclust_items if v == ktemp])

return cut

Expand Down Expand Up @@ -1039,8 +1102,13 @@ def _construct_branch_map(self, ix, interval, form, horizontal_spacing,

segmap += branch_segmap
splitmap += branch_splitmap
splits = dict(splits.items() + branch_splits.items())
segments = dict(segments.items() + branch_segs.items())
# d = dict1.copy()
# d.update(dict2)
#splits = dict(splits.items() + branch_splits.items())
splits.update(branch_splits.items())

segments.update(branch_segs.items())
# segments = dict(segments.items() + branch_segs.items())

## find the middle of the children's x-position and make vertical
# segment ix
Expand Down Expand Up @@ -1183,8 +1251,13 @@ def _construct_mass_map(self, ix, start_pile, interval,

segmap += branch_segmap
splitmap += branch_splitmap
splits = dict(splits.items() + branch_splits.items())
segments = dict(segments.items() + branch_segs.items())
# d = dict1.copy()
# d.update(dict2)
# splits = dict(splits.items() + branch_splits.items())
splits.update(branch_splits.items())

segments.update(branch_segs.items())
# segments = dict(segments.items() + branch_segs.items())

## find the middle of the children's x-position and make vertical
## segment ix
Expand Down Expand Up @@ -1379,15 +1452,26 @@ def construct_tree_from_graph(adjacency_list, density, prune_threshold=None,
previous_level = level

## compute the mass after the current bg set is removed
if version[0] == '2':
T_subGraph_values = T._subgraphs.itervalues()
if version[0] == '3':
T_subGraph_values = T._subgraphs.values()

old_vcount = sum([x.number_of_nodes()
for x in T._subgraphs.itervalues()])
for x in T_subGraph_values])

current_mass = 1. - ((old_vcount - len(bg)) / n)

# loop through active components, i.e. subgraphs
deactivate_keys = [] # subgraphs to deactivate at the iter end
activate_subgraphs = {} # new subgraphs to add at the end of the iter

for (k, H) in T._subgraphs.iteritems():

if version[0] == '2':
T_subGraph_items = T._subgraphs.iteritems()
if version[0] == '3':
T_subGraph_items = T._subgraphs.items()

for (k, H) in T_subGraph_items:

## remove nodes at the current level
H.remove_nodes_from(bg)
Expand Down