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Switch to numpy (scipy_version>1.0) changes

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Arnar Flatberg
2006-08-31 10:04:19 +00:00
parent a0786d521a
commit 0b58c5ea28
3 changed files with 22 additions and 27 deletions
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21
system/dataset.py
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@@ -1,4 +1,4 @@
from scipy import atleast_2d,asarray,ArrayType,shape,nonzero,io,transpose
from scipy import ndarray,atleast_2d,asarray
from scipy import sort as array_sort
from itertools import izip
import shelve
@@ -40,11 +40,11 @@ class Dataset:
self._name = name
self._identifiers = identifiers
self._type = 'n'
if isinstance(array,ArrayType):
if isinstance(array,ndarray):
array = atleast_2d(asarray(array))
# vectors are column vectors
if array.shape[0]==1:
array = transpose(array)
array = array.T
self.shape = array.shape
if identifiers!=None:
self._set_identifiers(identifiers,self._all_dims)
@@ -55,10 +55,7 @@ class Dataset:
self._array = array
else:
raise ValueError, "Array input must be of ArrayType"
#def __str__(self):
# return self._name + ":\n" + "Dim names: " + self._dims.__str__()
raise ValueError, "Array input must be of type ndarray"
def __iter__(self):
"""Returns an iterator over dimensions of dataset."""
@@ -177,7 +174,9 @@ class Dataset:
Identifiers are the unique names (strings) for a variable in a given dim.
Index (Indices) are the Identifiers position in a matrix in a given dim."""
Index (Indices) are the Identifiers position in a matrix in a given dim.
If none of the input identifiers are found an empty index is returned
"""
if idents==None:
index = array_sort(self._map[dim].values())
else:
@@ -217,7 +216,7 @@ class CategoryDataset(Dataset):
"""
data={}
for name,ind in self._map[self.get_dim_name(0)].items():
data[name] = self.get_identifiers(self.get_dim_name(1),list(nonzero(self._array[ind,:])))
data[name] = self.get_identifiers(self.get_dim_name(1),list(self._array[ind,:].nonzero()))
self._dictlists = data
self.has_dictlists = True
return data
@@ -227,7 +226,7 @@ class CategoryDataset(Dataset):
"""
ret_list = []
for cat_name,ind in self._map[self.get_dim_name(1)].items():
ids = self.get_identifiers(self.get_dim_name(0),nonzero(self._array[:,ind]))
ids = self.get_identifiers(self.get_dim_name(0),self._array[:,ind].nonzero())
selection = Selection(cat_name)
selection.select(cat_name,ids)
ret_list.append(selection)
@@ -263,7 +262,7 @@ class GraphDataset(Dataset):
"""
import networkx as nx
m,n = shape(A)# adjacency matrix must be of type that evals to true/false for neigbours
m,n = A.shape# adjacency matrix must be of type that evals to true/false for neigbours
if m!=n:
raise IOError, "Adjacency matrix must be square"
if nx_type=='graph':