Question

I can’t get simple matrix operations to work on data, for the life of me I haven’t been able to figure out what I’m doing incorrectly:

data = np.genfromtxt(dataset1, names=True, delimiter=",", dtype=float)

X = np.matrix(data)
print(X.T*X)

Traceback (most recent call last):
  File "genfromtxt.py", line 11, in <module>
    print(X.T*X)
  File "/usr/lib/pymodules/python2.6/numpy/matrixlib/defmatrix.py", line 319, in __mul__
    return N.dot(self, asmatrix(other))
TypeError: can't multiply sequence by non-int of type 'tuple'

print(data) gives:

[ (3.0, 32.0, 0.0, 0.0, 1.0, 0.0, 1.0, 0.0, 0.0, 9.0, 0.0, 5.5606799999999996, 9.0)
 (4.0, 43.0, 0.0, 0.0, 1.0, 0.0, 1.0, 0.0, 0.0, 9.0, 0.0, 5.7203099999999996, 16.0)
 (5.0, 40.0, 0.0, 0.0, 1.0, 0.0, 1.0, 0.0, 0.0, 9.0, 0.0, 5.9964500000000003, 25.0)
 ...,
 (5.0, 50.0, 0.0, 0.0, 0.0, 1.0, 0.0, 1.0, 0.0, 12.0, 0.0, 6.2146100000000004, 25.0)
 (6.0, 50.0, 0.0, 0.0, 0.0, 1.0, 0.0, 1.0, 0.0, 12.0, 0.0, 6.2915700000000001, 36.0)
 (7.0, 50.0, 0.0, 0.0, 0.0, 1.0, 0.0, 1.0, 0.0, 12.0, 0.0, 6.3716100000000004, 49.0)]

EDIT:

Further, this code

reader = csv.reader(open(dataset1, 'r'))
header = reader.next()
X = np.array([[float(col) for col in row] for row in reader])

print(X.shape)
print(X.T.shape)
print(X * X.T)

gives this output:

(4165, 13)
(13, 4165)
Traceback (most recent call last):
  File "genfromtxt.py", line 17, in <module>
    print(X * X.T)
ValueError: shape mismatch: objects cannot be broadcast to a single shape
>>> 

Answer 1

The problem with the second example seems to be that the operator * performs element-wise multilpication for NumPy arrays. Presumably you would like to perform a matrix multiplication. There are two options to do this:

1. Use numpy.matrix instead of numpy.array — then multiplication will be matrix multiplication and powers by integer exponents will work as expected.

2. Use numpy.dot(A, B) instead of A*B — this will perform matrix multiplication for both arrays and matrices.