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296 lines
7.2 KiB
Python
Executable File
296 lines
7.2 KiB
Python
Executable File
# $Id$
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#
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# Copyright (C) 2001-2006 greg Landrum
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#
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# @@ All Rights Reserved @@
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#
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""" contains the Cluster class for representing hierarchical cluster trees
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"""
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from Numeric import *
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CMPTOL=1e-6
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class Cluster(object):
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"""a class for storing clusters/data
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**General Remarks**
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- It is assumed that the bottom of any cluster hierarchy tree is composed of
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the individual data points which were clustered.
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- Clusters objects store the following pieces of data, most are
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accessible via standard Setters/Getters:
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- Children: *Not Settable*, the list of children. You can add children
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with the _AddChild()_ and _AddChildren()_ methods.
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**Note** this can be of arbitrary length,
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but the current algorithms I have only produce trees with two children
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per cluster
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- Metric: the metric for this cluster (i.e. how far apart its children are)
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- Index: the order in which this cluster was generated
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- Points: *Not Settable*, the list of original points in this cluster
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(calculated recursively from the children)
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- PointsPositions: *Not Settable*, the list of positions of the original
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points in this cluster (calculated recursively from the children)
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- Position: the location of the cluster **Note** for a cluster this
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probably means the location of the average of all the Points which are
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its children.
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- Data: a data field. This is used with the original points to store their
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data value (i.e. the value we're using to classify)
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- Name: the name of this cluster
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"""
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def __init__(self,metric=0.0,children=None,position=None,index=-1,name=None,data=None):
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"""Constructor
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**Arguments**
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see the class documentation for the meanings of these arguments
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*my wrists are tired*
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"""
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if children is None:
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children = []
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if position is None:
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position = []
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self.metric = metric
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self.children = children
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self._UpdateLength()
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self.pos = position
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self.index = index
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self.name = name
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self._points = None
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self._pointsPositions = None
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self.data = data
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def SetMetric(self,metric):
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self.metric = metric
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def GetMetric(self):
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return self.metric
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def SetIndex(self,index):
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self.index = index
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def GetIndex(self):
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return self.index
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def SetPosition(self,pos):
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self.pos = pos
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def GetPosition(self):
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return self.pos
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def GetPointsPositions(self):
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if self._pointsPositions is not None:
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return self._pointsPositions
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else:
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self._GenPoints()
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return self._pointsPositions
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def GetPoints(self):
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if self._points is not None:
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return self._points
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else:
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self._GenPoints()
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return self._points
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def FindSubtree(self,index):
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""" finds and returns the subtree with a particular index
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"""
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res = None
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if index == self.index:
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res = self
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else:
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for child in self.children:
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res = child.FindSubtree(index)
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if res:
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break
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return res
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def _GenPoints(self):
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""" Generates the _Points_ and _PointsPositions_ lists
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*intended for internal use*
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"""
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if len(self) == 1:
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self._points = [self]
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self._pointsPositions = [self.GetPosition()]
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return self._points
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else:
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res = []
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children = self.GetChildren()
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children.sort(lambda x,y:cmp(len(y),len(x)))
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for child in children:
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res += child.GetPoints()
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self._points=res
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self._pointsPositions = map(lambda x:x.GetPosition(),res)
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def AddChild(self,child):
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"""Adds a child to our list
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**Arguments**
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- child: a Cluster
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"""
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self.children.append(child)
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self._GenPoints()
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self._UpdateLength()
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def AddChildren(self,children):
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"""Adds a bunch of children to our list
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**Arguments**
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- children: a list of Clusters
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"""
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self.children += children
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self._GenPoints()
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self._UpdateLength()
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def RemoveChild(self,child):
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"""Removes a child from our list
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**Arguments**
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- child: a Cluster
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"""
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self.children.remove(child)
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self._UpdateLength()
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def GetChildren(self):
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self.children.sort(lambda x,y:cmp(x.GetMetric(),y.GetMetric()))
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return self.children
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def SetData(self,data):
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self.data = data
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def GetData(self):
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return self.data
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def SetName(self,name):
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self.name = name
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def GetName(self):
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if self.name is None:
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return 'Cluster(%d)'%(self.GetIndex())
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else:
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return self.name
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def Print(self,level=0,showData=0,offset='\t'):
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if not showData or self.GetData() is None:
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print '%s%s%s Metric: %f'%(' '*level,self.GetName(),offset,self.GetMetric())
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else:
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print '%s%s%s Data: %f\t Metric: %f'%(' '*level,self.GetName(),offset,self.GetData(),self.GetMetric())
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for child in self.GetChildren():
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child.Print(level=level+1,showData=showData,offset=offset)
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def Compare(self,other,ignoreExtras=1):
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""" not as choosy as self==other
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"""
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if cmp(type(self),type(other)):
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return cmp(type(self),type(other))
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if cmp(len(self),len(other)):
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return cmp(len(self),len(other))
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if not ignoreExtras:
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m1,m2=self.GetMetric(),other.GetMetric()
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if abs(m1-m2)>CMPTOL:
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return cmp(m1,m2)
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if cmp(self.GetName(),other.GetName()):
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return cmp(self.GetName(),other.GetName())
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sP = self.GetPosition()
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oP = other.GetPosition()
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try:
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r = cmp(len(sP),len(oP))
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except:
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pass
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else:
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if r:
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return r
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try:
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r = cmp(sP,oP)
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except:
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r = sum(sP-oP)
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if r:
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return r
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c1,c2=self.GetChildren(),other.GetChildren()
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if cmp(len(c1),len(c2)):
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return cmp(len(c1),len(c2))
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for i in range(len(c1)):
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t = c1[i].Compare(c2[i],ignoreExtras=ignoreExtras)
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if t:
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return t
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return 0
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def _UpdateLength(self):
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""" updates our length
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*intended for internal use*
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"""
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self._len = reduce(lambda x,y: len(y)+x,self.children,1)
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def IsTerminal(self):
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return self._len<=1
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def __len__(self):
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""" allows _len(cluster)_ to work
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"""
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return self._len
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def __cmp__(self,other):
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""" allows _cluster1 == cluster2_ to work
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"""
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if cmp(type(self),type(other)):
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return cmp(type(self),type(other))
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m1,m2=self.GetMetric(),other.GetMetric()
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if abs(m1-m2)>CMPTOL:
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return cmp(m1,m2)
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if cmp(self.GetName(),other.GetName()):
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return cmp(self.GetName(),other.GetName())
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c1,c2=self.GetChildren(),other.GetChildren()
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return cmp(c1,c2)
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if __name__ == '__main__':
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from ML.Cluster import ClusterUtils
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root = Cluster(index=1,metric=1000)
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c1 = Cluster(index=10,metric=100)
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c1.AddChild(Cluster(index=30,metric=10))
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c1.AddChild(Cluster(index=31,metric=10))
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c1.AddChild(Cluster(index=32,metric=10))
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c2 = Cluster(index=11,metric=100)
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c2.AddChild(Cluster(index=40,metric=10))
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c2.AddChild(Cluster(index=41,metric=10))
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root.AddChild(c1)
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root.AddChild(c2)
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nodes = ClusterUtils.GetNodeList(root)
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indices = [x.GetIndex() for x in nodes]
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print 'XXX:',indices
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