Adding different sized/shaped displaced NumPy matrices
You just have to find the overlapping range, and then add the arrays using slicing.
b1 = np.zeros((4,5))
b2 = np.ones((4,3))
pos_v, pos_h = 2, 3 # offset
v_range1 = slice(max(0, pos_v), max(min(pos_v + b2.shape, b1.shape), 0))
h_range1 = slice(max(0, pos_h), max(min(pos_h + b2.shape, b1.shape), 0))
v_range2 = slice(max(0, -pos_v), min(-pos_v + b1.shape, b2.shape))
h_range2 = slice(max(0, -pos_h), min(-pos_h + b1.shape, b2.shape))
b1[v_range1, h_range1] += b2[v_range2, h_range2]
They're added in-place, but you could also create a new array. I might have missed some corner cases, though, but it seems to work fine.
Add submatrices at certain locations
The nice thing about array slicing in numpy is you don't need the for loops that you are using. Also the reason that it is only putting the center element is because you only put a single element there (c1[c1mid,c1mid] is a single number) here is what you could do:
z[7:12,7:12] = c1
z[7:12,27:32] = c2
z[26:33,6:14] = c3
z[25:34,25:33] = c4
Apply a function to two equally shaped numpy matrices
It seems your example is already in the docs, see the bottom of https://docs.scipy.org/doc/numpy-1.13.0/reference/generated/numpy.vectorize.html. So
pearsonr = np.vectorize(scipy.stats.pearsonr, signature='(n),(n)->(),()')
correlations = pearsonr(data["histograms"],regions_hist)
should work :)
Comparing matrices of different shapes
If I understand correctly, you are looking for the largest possible subarray that fits inside both
B. You could just compare each dimension of
B and take whichever is smallest:
def largest_subarray(A, B):
dims = np.minimum(A.shape, B.shape) # find smallest dimensions
idx = tuple(slice(None, dd) for dd in dims) # construct tuple of slice indices
return A[idx], B[idx] # index into A and B
For your example arrays it will return
A[:3, :2], B[:3, :2].
Aligning two binary matrices for maximum overlap
To find the maximum overlap you can use the
correlate2d function from scipy:
Or you can implement it from scratch using numpy (which is a little bit tricky):
import numpy as np
from numpy.lib.stride_tricks import as_strided
def max_overlap(a, b):
b_p = np.pad(b, ((a.shape-1, a.shape-1), (a.shape-1, a.shape-1)), 'constant', constant_values=0)
output_shape = (b_p.shape - a.shape + 1, b_p.shape - a.shape + 1)
b_w = as_strided(b_p, shape=output_shape + a.shape,
c = (b_w * a).sum(axis=(2,3))
Is there a Rust ndarray equivalent for numpy arithmetic on a slice?
That can be done with the same two steps as those performed in Python: slicing, then add-assigning to a broadcast right-handed array.
let mut a: Array2<f32> = Array2::zeros((100, 4));
let mut slice = a.slice_mut(s![20.., ..]);
slice += &ArrayView::from(&[1.0, 2.0, 3.0, 4.0]);
Slicing is done with
slice_mut and the
s! macro for defining the intended range.
The outcome of a slice is a mutable array view, and so, most operations seen in
ArrayBase are available, including arithmetic operations.
By broadcasting rules, a right-handed array of shape
 can be automatically broadcast to one of shape
[100, 4] for the
In case of other confusions in the transition from Python to Rust's
ndarray crate, the documentation contains a guide for Python users.