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"""
A plot to visualize trees
"""
from __future__ import absolute_import, division, print_function
import numpy as np
from glue.core.edit_subset_mode import EditSubsetMode
from glue.core.state import lookup_class_with_patches
from glue.core.subset import CategorySubsetState
from glue.core.roi import PointROI
from glue.core.callback_property import CallbackProperty, add_callback, delay_callback
from glue.core.data import IncompatibleAttribute, Data
from glue.viewers.common.viz_client import GenericMplClient
from glue.plugins.dendro_viewer.layer_artist import DendroLayerArtist
from glue.utils import nonpartial
class DendroClient(GenericMplClient):
height_attr = CallbackProperty()
parent_attr = CallbackProperty()
order_attr = CallbackProperty()
ylog = CallbackProperty(False)
display_data = CallbackProperty(None)
select_substruct = CallbackProperty(True)
def __init__(self, *args, **kwargs):
super(DendroClient, self).__init__(*args, **kwargs)
self._layout = None
self.axes.set_xticks([])
self.axes.spines['top'].set_visible(False)
self.axes.spines['bottom'].set_visible(False)
def _connect(self):
add_callback(self, 'ylog', self._set_ylog)
add_callback(self, 'height_attr', nonpartial(self._relayout))
add_callback(self, 'order_attr', nonpartial(self._relayout))
add_callback(self, 'parent_attr', nonpartial(self._relayout))
def _default_attributes(self):
assert self.display_data is not None
fallback = self.display_data.components[0]
with delay_callback(self, 'height_attr', 'parent_attr',
'order_attr'):
if self.height_attr is None:
comp = self.display_data.find_component_id('height') or fallback
self.height_attr = comp
if self.parent_attr is None:
comp = self.display_data.find_component_id('parent') or fallback
self.parent_attr = comp
if self.order_attr is None:
self.order_attr = self.height_attr
def new_layer_artist(self, layer):
return DendroLayerArtist(layer, self.axes)
def _set_ylog(self, log):
self.axes.set_yscale('log' if log else 'linear')
self._redraw()
def _relayout(self):
if self.display_data is None:
return
if self.height_attr is None:
return
if self.parent_attr is None:
return
if self.order_attr is None:
return
try:
parent = np.asarray(self.display_data[self.parent_attr],
dtype=np.int).ravel()
y = self.display_data[self.height_attr].ravel()
key = self.display_data[self.order_attr].ravel()
except IncompatibleAttribute:
return
children = self._children
pos = np.zeros(key.size) - 1
cur_pos = 0
for struct in _iter_sorted(children, parent, key):
if children[struct].size == 0: # leaf
pos[struct] = cur_pos
cur_pos += 1
else: # branch
assert pos[children[struct]].mean() >= 0
pos[struct] = pos[children[struct]].mean()
layout = np.zeros((2, 3 * y.size))
layout[0, ::3] = pos
layout[0, 1::3] = pos
layout[0, 2::3] = np.where(parent >= 0, pos[parent], np.nan)
layout[1, ::3] = y
layout[1, 1::3] = np.where(parent >= 0, y[parent], y.min())
layout[1, 2::3] = layout[1, 1::3]
self._layout = layout
self._snap_limits()
self._update_all()
def _snap_limits(self):
if self._layout is None:
return
x, y = self._layout[:, ::3]
xlim = np.array([x.min(), x.max()])
xpad = .05 * xlim.ptp()
xlim[0] -= xpad
xlim[1] += xpad
ylim = np.array([y.min(), y.max()])
if self.ylog:
ylim = np.maximum(ylim, 1e-5)
pad = 1.05 * ylim[1] / ylim[0]
ylim[0] /= pad
ylim[1] *= pad
else:
pad = .05 * ylim.ptp()
ylim[0] -= pad
ylim[1] += pad
self.axes.set_xlim(*xlim)
self.axes.set_ylim(*ylim)
def add_layer(self, layer):
if layer.data.ndim != 1:
return
if layer.data not in self.data:
raise TypeError("Layer not in data collection")
if layer in self.artists:
return self.artists[layer][0]
self.display_data = self.display_data or layer.data
result = DendroLayerArtist(layer, self.axes)
self.artists.append(result)
self._update_layer(layer)
self._ensure_subsets_added(layer)
self._default_attributes()
return result
def _ensure_subsets_added(self, layer):
if not isinstance(layer, Data):
return
for subset in layer.subsets:
self.add_layer(subset)
def _update_layer(self, layer):
for artist in self.artists[layer]:
if not isinstance(artist, DendroLayerArtist):
continue
artist.layout = self._layout
artist.update()
self._redraw()
def remove_layer(self, layer):
super(DendroClient, self).remove_layer(layer)
if layer is self.display_data:
self.display_data = None
@property
def _parents(self):
return np.asarray(self.display_data[self.parent_attr],
dtype=np.int).ravel()
@property
def _children(self):
children = _dendro_children(self._parents)
return children
def _substructures(self, idx):
"""
Return an array of all substructure indices of a given index.
The input is included in the output.
Parameters
----------
idx : int
The structure to extract.
Returns
-------
array
"""
children = self._children
result = []
todo = [idx]
while todo:
result.append(todo.pop())
todo.extend(children[result[-1]])
return np.array(result, dtype=np.int)
def apply_roi(self, roi):
if not isinstance(roi, PointROI):
raise NotImplementedError("Only PointROI supported")
if self._layout is None or self.display_data is None:
return
x, y = roi.x, roi.y
if not roi.defined():
return
xs, ys = self._layout[:, ::3]
parent_ys = self._layout[1, 1::3]
delt = np.abs(x - xs)
delt[y > ys] = np.nan
delt[y < parent_ys] = np.nan
if np.isfinite(delt).any():
select = np.nanargmin(delt)
if self.select_substruct:
select = self._substructures(select)
select = np.asarray(select, dtype=np.int)
else:
select = np.array([], dtype=np.int)
state = CategorySubsetState(self.display_data.pixel_component_ids[0],
select)
EditSubsetMode().update(self.collect, state,
focus_data=self.display_data)
def restore_layers(self, layers, context):
"""
Re-generate a list of plot layers from a glue-serialized list
"""
for l in layers:
cls = lookup_class_with_patches(l.pop('_type'))
if cls != DendroLayerArtist:
raise ValueError("Dendrogram client cannot restore layer of type "
"%s" % cls)
props = dict((k, context.object(v)) for k, v in l.items())
layer = self.add_layer(props['layer'])
layer.properties = props
def _dendro_children(parent):
children = [[] for _ in range(parent.size)]
for i, p in enumerate(parent):
if p < 0:
continue
children[p].append(i)
return list(map(np.asarray, children))
def _iter_sorted(children, parent, key):
# must yield both children before parent
yielded = set()
trunks = np.array([i for i, p in enumerate(parent) if p < 0], dtype=np.int)
for idx in np.argsort(key[trunks]):
idx = trunks[idx]
for item in _postfix_iter(idx, children, parent, yielded, key):
yield item
def _postfix_iter(node, children, parent, yielded, key):
"""
Iterate over a node and its children, in the following fashion:
parents are yielded after children
children are yielded in order of ascending key value
"""
todo = [node]
expanded = set()
while todo:
node = todo[-1]
if node in yielded:
todo.pop()
continue
if children[node].size == 0 or node in expanded:
yield todo.pop()
yielded.add(node)
continue
c = children[node]
ind = np.argsort(key[c])[::-1]
todo.extend(c[ind])
expanded.add(node)
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