Questions tagged [numpy]
NumPy is the fundamental package for scientific computing with Python.
115
questions
3
votes
1answer
46 views
Fast nonzero indices per row/column for (sparse) 2D numpy array
I am looking for the fastest way to obtain a list of the nonzero indices of a 2D array per row and per column. The following is a working piece of code:
...
0
votes
0answers
17 views
How to plot a function for multiple values of a parameter in the same set of axes in Python?
I'm currently trying to plot a graph wich describes a photoionization cross section as a function of incident photon energy for optical transition in a semiconductor for different values of the $\...
1
vote
1answer
87 views
Composite matrices in Numpy
Lets say I have four matrices A, B, C and D, and I want to combine them together into one new matrix for computation:
$$
\left( \begin{matrix}
A & B\\
C & D
\end{matrix}\right)
$$
How can I ...
0
votes
0answers
23 views
Can I visualize a numpy file in Paraview?
I've created a NPZ file from VTK data of an OpenFoam simulation.
The NPZ file is compressed an easy to manipulate, that's why I was wondering if it is possible to use it in order to visualized its ...
2
votes
1answer
35 views
Best way to convert a sparse (containing zeros) covariance matrix into a correlation matrix?
I have a $100$x$100$ covariance matrix that looks like this.
Some rows/cols are all-zero because those corresponding elements are not present in the sample from which covariance is calculated. I'm ...
1
vote
1answer
49 views
How do I find the portion of a cell/voxel lying within a defined surface?
We have a 3-dimensional grid of voxels (or cells), with individual voxels being of volume $dx\,dy\,dz$ where $dx=dy=dz=1$.
A cone-like surface is defined by some function, $z = f(x, y)$, which in ...
-1
votes
1answer
36 views
Numpys `tensordot` and what is happening mathematically
I've encountered a program where np.tensordot was used, so I tried looking it up but I can't really understand what this function is doing...
I feel rather ...
0
votes
0answers
40 views
Why am I not getting the flat phase when Fourier-transform a Fourier-limited Gaussian pulse?
I have been trying to obtain a spectrum and a spectral phase of a Gaussian pulse using the Fast Fourier Transform provided with numpy library in Python. Here are ...
4
votes
2answers
199 views
Fastest Way to Mutiply $10^4$ 2x2 Matrices
In a code that I work with (written in python, but also tagging as matlab because numpy is so close and I could use it if need be), we use a transfer matrix method to compute the properties of a ...
5
votes
1answer
79 views
How do I globally change the precision of a piece of code in Python to debug it?
I am solving a system of non-linear equations using the Newton-Raphson method in Python. This involves using the solve(Ax,b) function (...
2
votes
1answer
109 views
Numerical stability in the product of many matrices
I have to calculate in numpy the matrix-product of many matrices (~400). Are there common practices to increase numerical stability?
If this is relevant, the matrices are $300\times 300$ orthogonal ...
1
vote
0answers
70 views
Calculate integrals using numpy.fft
Good evening,
I would like to understand why I do not get the correct result:
I assume that I know my function on discrete data points and expand it as a discrete Fourier transform: $\text{sin}(x)=\...
6
votes
0answers
112 views
fastest way to compute many small dot products
I have two n-by-3 blocks contiguous in memory ("n vectors of length 3") and I'd like to compute the dot product between each of the rows as fast as possible. In numpy, using ...
3
votes
1answer
211 views
Numerical derivative in python
I am trying to take the numerical derivative of a dataset. My first attempt was to use the gradient function from numpy but in that case the graph of the derivative ...
0
votes
0answers
77 views
Smoothing FFT result
I am trying to calculate the spectrum of Bremmstrahlung, which involves calculating the Fourier transformed acceleration. I am solving a non-linear ODE to numerically calculate the acceleration in the ...
0
votes
0answers
150 views
What algorithm do BLAS and ATLAS use for matrix multiplication?
I have searched and what I understood was that they use the naive one with several memory and cache optimizations.
However, I wanted to know whether they are using the Strassen or the Coppersmith-...
4
votes
1answer
159 views
Diagonalize a unitary matrix with orthogonal matrices using numpy
An important component of the Cartan KAK decomposition for 2 qubit operations is to diagonalize a 4x4 unitary matrix using orthogonal (not unitary, purely real orthogonal) matrices. That is to say, ...
0
votes
1answer
187 views
Implementing structured grid boundary conditions using NumPy arrays?
I am making a toy code in Python to solve the advection equation $$u_t + cu_x = 0$$
with, for example, periodic boundary conditions.
Background information
The numerical grid is specified like this:
...
6
votes
2answers
912 views
Is there an efficient way to form this block matrix with numpy or scipy?
Is there an efficient way to form this block matrix with numpy or scipy?
$$
\left[
\begin{array}{cccc}
\mathbf{B} & \mathbf{0} & \cdots & \mathbf{0}\\
\mathbf{AB} & \mathbf{B} & \...
1
vote
1answer
74 views
Doing computations on a very large numpy array: streaming the calculation vs out-of-core memory
I am trying to perform a calculation in numpy that depends on several parameters, and involved the creation of many intermediate arrays. These intermediate steps involve integrals over more parameters....
2
votes
1answer
50 views
numpy.outer without flatten
$x$ is an $N \times M$ matrix.
$y$ is a $1 \times L$ vector.
I want to return "outer product" between $x$ and $y$, let's call it $z$.
z[n,m,l] = x[n,m] * y[l]
...
1
vote
2answers
228 views
Numpy FFT gives me a pulse shorter than it should be. Not sure what I am doing wrong
I've created a code (Python, numpy) that defines an ultrashort laser pulse in the frequency domain (pulse duration should be 4 fs), but when I perform the Fourier Transform using DFT, my pulse in the ...
5
votes
2answers
376 views
Python: vectorizing a structured linear system solve
Overview
I am looking for a way to solve a structured linear system in Python without using a for loop (preferably using vectorization, if possible).
Background
Consider the following linear system:...
2
votes
1answer
66 views
Problem of multiplication of big (sparse) matrix with numpy (python)
I wanted to multiply two simple (big and sparse) matrix with numpy. And I saw that the calculation fails when matrices are too big.
If i take $X$ a random vector (size $n$). With pandas, I ...
0
votes
1answer
52 views
Specifying mesh spacing for DFT in numpy
I was testing the .fft package of numpy 1.16.1 in Python 3.7.2. In particular I was trying to verify that the transform resembles the analytical one for: $$f(x) = \mathrm{exp}\left[-\left(\frac{x-5}{2}...
0
votes
1answer
81 views
Creating an Interpolation of a w = f(x,y,z) function
I am trying to finish a series of interpolation functions.
The problem is more related with organizing the data than how to do the interpolations.
Using the RegularGridInterpolator, I created this ...
0
votes
1answer
536 views
Problems with python's interp 2D
I am writing some functions to interpolate data. While using interp2D, somehow, a sample matrix works but when I change the size of the matrix, it returns an error.
...
1
vote
1answer
68 views
Minimizing the used memory in diffusion simulation using Python
I am recently dealing with a diffusion simulation project and I have come up with the following code:
...
0
votes
1answer
4k views
Python Finite Difference Schemes for 1D Heat Equation: How to express for loop using numpy expression
Hello all,
I've recently been introduced to Python and Numpy, and am still a beginner in applying it for numerical methods. I've been performing simple 1D diffusion computations. I suppose my ...
0
votes
1answer
88 views
Numpy: How to permute array into indices of larger array? [closed]
I have an array of length L with N zeros, and L-N non-zero values. I have another array of length N. I would like to put the values of the shorter array into the positions of the longer array which ...
0
votes
1answer
2k views
Applying neumann boundary conditions to diffusion equation solution in python [duplicate]
For the diffusion equation
$$
\frac{\partial u(x,t)}{\partial t} = D \frac{\partial ^2 u(x,t)}{\partial x^2} + Cu(x,t)
$$
with the boundary conditions $u(-\frac{L}{2},t)=u(\frac{L}{2},t)=0$ I've ...
4
votes
2answers
279 views
Moore-Penrose pseudoinverse of singular rank degenerate matrix
I am trying to attain the Moore-Penrose pseudoinverse of a very large, very sparse, rank-degenerate, singular, and square matrix. ($75000 \times 75000$, near rank). The matrix is a graph Laplacian and ...
0
votes
1answer
79 views
Is it possible to partition 2D data into bins such that each bin contains the same number of samples?
I am trying to sort data following a bivariate distribution into a numpy histogramdd, where each bin should contain the same number of data points (to the nearest whole sample).
I expect that some ...
8
votes
0answers
460 views
Fast Automatic Differentiation for numpy?
I would like to use automatic differentiation to calculate gradients to function written in numpy.
I've come across a number of packages, including
autograd
tangent
chainer
But none of them seem ...
3
votes
0answers
86 views
Inconsistency in optimize.minimize
I am trying to fit a time-dependent curve at each time step. I do so in minimizing along $x_c$ the quadratic error between the curve and a reference solution $ 1/(1 + \exp\left(\sqrt{S}(x-x_c)\right) $...
3
votes
1answer
59 views
why am I not getting a staircase for the rotation number?
I'm trying to understand the staircase map. Look at this map from the circle to itself:
$$ x \stackrel{F}{\mapsto} \big[\omega + x + \tfrac{\epsilon}{2\pi} \sin (2\pi x) \big] \pmod 1 $$
Such a map ...
1
vote
1answer
2k views
Why `import numpy as np` for scientific computing? [closed]
Why do scientists bother with the np for numpy?
(Note this is more a "philosophical"/reasoning question - let us assume that ...
1
vote
0answers
102 views
computing dual matrix trace norm and tensor gradient in python
I'm trying to write the following function in python:
$$
f_\mu(\mathcal X) = f_0(\mathcal X) + \sum_{i = 1}^n \max_{||\mathcal Y_{i(i)}|| \leq1} \alpha_i\langle \mathcal X_{(i)},\mathcal Y_{i(i)} \...
1
vote
1answer
298 views
Performing a random walk on a lattice that traps the particles
I am trying to solve this problem where we have a 1D-lattice of size 100 and the particle can start from any position in the lattice and moves randomly on it(with equal probability of moving to either ...
1
vote
0answers
214 views
Rank filter on an nXm array using python
I would like to apply a rank filter on an nXm numpy array. Let's say I have this array:
...
0
votes
1answer
1k views
Numpy.polyfit with regularization
I am trying to use the numpy polyfit method to add regularization to my solution.
My non-regularized solution is
...
0
votes
1answer
709 views
Numpy attributes not recognized in Numba [closed]
Numba offers JIT for Python. In its documentation it says "One objective of Numba is having a seamless integration with NumPy."
So why including some of the simplest features from numpy isn't ...
1
vote
1answer
1k views
Why doesn't multiplying two matrices with NumPy work sometimes? [closed]
Using NumPy and attempting to multiply matrices together sometimes doesn't work. For example
...
4
votes
1answer
575 views
Poor SVD reconstruction of singular matrix
I am trying to calculate the singular value decomposition of this matrix using numpy.linalg.svd .
However, reconstructing the matrix from the SVD gives a poor ...
1
vote
0answers
49 views
Update model parameter with new data, discarding old data
I have this dataset, and I am using y = (a * x^n) / (b + x^n) Hill function as the model, where a is the limit of the Hill curve,...
5
votes
3answers
3k views
Calculating partial trace of array in NumPy
A simulation I'm doing requires me to calculate the partial trace of a large density matrix. I am trying to calculate it using tools from numpy, but my code seems to be having some problems. For ...
1
vote
1answer
4k views
Python: Comparing 2D arrays and Returning independent values from those arrays [closed]
I'm sure this would be a common question, however yet to find an answer for.
Suppose I have two, 2D vectors in Python
...
2
votes
0answers
178 views
Optimizing for loops by using Einstein summations instead
I have some Python code containing a couple of for loops, which I would like to optimize by using low-level functions. My first approach is to use ...
1
vote
1answer
108 views
Fast table interpolation on regular time data for ODE
I am using scipy.integrate.odeint to simulate the reaction of a system with known input signals via integration. The simplified code below illustrates what I'm ...
5
votes
2answers
282 views
Speeding up a linear transform using Python
In an optical wavefront propagation problem, I need to do excessive Fourier-type computations:
...
