som_topol_struct

class som_topol_struct:
        def __init__(self, dlen=[], data=[], munits=[], msize=mat(""),lattice="",mapshape="", topol=[]):
		self.type="som_topol"
		self.msize=msize #needs to be a 2x1 matrix 
		self.lattice=lattice
		self.mapshape=mapshape
		if data==[]: 
			D=mat("") 		
			dim=2
		else:
			D=data.data #elements must be formatted as float, or this won't work right
			dlen=D.shape[0]
			dim=D.shape[1]


		if lattice=="":
			self.lattice="hexa"

		
		if mapshape=="":
			self.mapshape="sheet"
		

		#if necessary determine the number of map units
		if munits==[]:
			if dlen!=[]:
				munits=ceil(5 * sqrt(dlen) )
			else:
				munits=100.0
		
		
		#then determine the map size
		if msize.shape[1]==0: 
			self.msize=mat("0 0")	
			if dim==1: #one dimensional data
				self.msize[0,0]=1
				self.msize[0,1]=ceil(munits)
			elif D.shape[0] < 2: #no data provided, determine msize using munits
				self.msize[0,0]=round(sqrt(munits))
				self.msize[0,1]=round(munits/self.msize[0,0])
			else:	#determine a map size based on eigenvalues. 
				#initialize xdim/ydim ratio using principal components of the input space; 
				#the ratio is the square root of two largest eigenvalues	
				A=zeros((dim,dim))+Inf #autocorrelation matrix
				for i in range(0,dim):
					mean= D[:,i].sum(0)/D[:,i].shape[0]
					D[:,i]=D[:,i]-mean
	
		
				for i in range(0,dim):
					for j in range(i,dim):
						c=multiply(D[:,i],D[:,j] )
						A[i,j]=float(sum(c))/c.shape[0] 
						A[j,i]=A[i,j]			
			
				S,V=linalg.eig(A)
				I=argsort(S)
				eigval=S[I,:]
				
				if eigval[-1]==0 or eigval[-2]*munits<eigval[-1]:
					ratio=1.0
				else:
					ratio = sqrt(eigval[-1]/eigval[-2]) #ratio between xdim and ydim
				
	
				if self.lattice=="hexa":
					self.msize[0,1]=min(munits, round( sqrt(munits/ratio * sqrt(0.75))) )
				else:
					self.msize[0,1]=min(munits, round(sqrt(munits/ratio)))
	
				self.msize[0,0]=round(munits/self.msize[0,1])
	
				if min(self.msize)==1:
					self.msize[0,0]=1
					self.msize[0,1]=max(self.msize)
	
				if self.lattice=="hexa" and self.mapshape=="toroid":
					if self.msize[0,0]%2 ==1:
						self.msize[0,0]=self.msize[0,0]+1