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Questions tagged [numpy]

NumPy is the fundamental package for scientific computing with Python.

5
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2answers
301 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
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1answer
54 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
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1answer
26 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
58 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
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1answer
33 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
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1answer
39 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
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1answer
700 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
26 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
617 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 ...
3
votes
2answers
161 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
54 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
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0answers
251 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
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0answers
83 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
58 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
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1answer
1k 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
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0answers
80 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
194 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
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0answers
137 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
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1answer
741 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
454 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
560 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
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1answer
402 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
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0answers
48 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,...
3
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2answers
2k 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
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1answer
2k 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
146 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
86 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
215 views

Speeding up a linear transform using Python

In an optical wavefront propagation problem, I need to do excessive Fourier-type computations: ...
0
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2answers
118 views

Trying to compute the error from comparing two arrays

Some context: I am working with the Black-Scholes model.. I have an explicit (Black-Scholes) formula which is the exact solution to my problem. I have written code which implements a finite-difference ...
2
votes
1answer
305 views

How to broadcast my matrix exponentiation

I'm trying -to no avail- to broadcast the following piece of code in Python: ...
1
vote
1answer
199 views

Power spectrum incorrectly yielding negative values

I have a real signal in time given by: And I am simply trying to compute its power spectrum, which is the Fourier transform of the autocorrelation of the signal, and is also a purely real and ...
1
vote
0answers
716 views

Wrong amplitude of convolution using numpy fft

I try to convolve a rectangle function in [-1/2, 1/2] with itself using fft. The convolution should be a tent shaped function, see figure below. The code is below. In the 3rd to last line I add /50 ...
4
votes
1answer
449 views

Chebyshev approximation by projection vs interpolation

Suppose we want to approximate a function $f: [a, b] \rightarrow \Re$ with a Chebyshev series: $$ f(x) \approx \sum_{k=0}^n c_k \, T_k\left( \frac{2x-b-a}{b-a} \right) $$ where $T_k(x) = \cos(k\, \...
3
votes
1answer
704 views

integral including a vector

I need to calculate the integral of this function def f(z): return ((1-2*z)*np.exp(-d/z))/(((1-z)**(2+d))*(z**(2-d))) Here d is a constant. I am using this ...
1
vote
1answer
60 views

nodal lines of wave-function $\psi(x,y) = \sin 12x \sin y + (1 + \epsilon) \sin x \sin 12y$

I am trying to reproduce this figure of nodal lines of a wavefunction from this work of Berry $$\psi = \sin 2r\,x \sin y + (1 + \epsilon) \sin x \sin 2r\,y$$ Here the image. The first is $\epsilon = ...
1
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0answers
873 views

Finding eigenvectors and eigenvalues of large matrices in Python's numpy

I am running a PCA analysis on a data set using Python's (v2.7.10) NumPy. I validated that my program works by running the PCA analysis on a smaller dataset and then confirming that I get similar ...
1
vote
1answer
89 views

Binary tensor operations in Nutils [closed]

How does one write general tensor contractions in the Python-based finite element package Nutils? For example, how does one write the contraction of a fourth-order elasticity tensor $\boldsymbol{C}$ ...
0
votes
2answers
153 views

Fast Python implementation of short-range interacting particles under Metroplis algorithm

Can anyone write a Python implementation of a set of particles interacting in 2D according to a short-range particle-particle force and evolving in time under a Metropolis algorithm, which randomly ...
2
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0answers
96 views

Is the numerical resolution of this huge sparse polynomial system tractable?

I'd like to find numerically a solution to a sparse system of 2000000 polynomial equations of degree 3 with 50000 variables and integer coefficients (or at least to decide whether or not a solution ...
1
vote
1answer
98 views

Vectorizing list of different functions for Gradient Descent

I am new to machine learning and statistical analysis and am having trouble figuring how I should go about a problem I have. I believe that I understand the gradient descent algorithm and how it ...
7
votes
3answers
4k views

What does Python offer for distributed/parallel/GPU computing?

Using the SciPy/NumPy libraries, Python is a pretty cool and performing platform for scientific computing. I just wonder: When I have to go parallel (multi-thread, multi-core, multi-node, gpu), what ...
3
votes
0answers
1k views

Efficiently creating an adjacency matrix from a lattice in numpy

I have an $n$ by $m$ numpy array representing a rectangular lattice $L$, where each site contains a one or a zero, representing two different materials. I'm modelling heat flow across this lattice. ...
2
votes
1answer
335 views

(numpy/scipy) Build a random vector given mean vector and covariance matrix

After running several calculations with numpy, I end with the mean vector and covariance matrix for a state vector. Is there a way with numpy or scipy to sample a random vector around this mean and ...
11
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2answers
5k views

Complexity of matrix inversion in numpy

I am solving differential equations that require to invert dense square matrices. This matrix inversion consumes the most of my computation time, so I was wondering if I am using the fastest algorithm ...
4
votes
1answer
4k views

Python Vectorizing a Function Returning an Array

I have the following function that has been vectorized so that for every element in input array t, an array is output: ...
4
votes
2answers
103 views

How to read the number of periods of this complicated graph?

I have two data sets that are quasi-periodic. They have the same period and can be seen clearly by eye. For example when $x\in(100,200)$, both of them have about 32 periods. Below is a zoom-in of the ...
1
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0answers
182 views

Inverse quadratic method only makes one iteration - python

I'm tryin' to implement this method with python3 but i don't solve the problem. This is my code: ...
4
votes
4answers
8k views

LCM builtin in Python / Numpy

I can write a function to find LCM (lowest common multiple) of an array of integers, but I thought it must have been implemented in numpy or scipy and was expecting something like ...
2
votes
3answers
3k views

Runge-Kutta Simulation For Projectile Motion With Drag

I am attempting to simulate projectile flight with drag. However, with a timestep of 0.1 seconds, I am consistently getting an error of ~0.1-1%. ...
5
votes
1answer
1k views

Alternatives to numpy.einsum

Given an $n_1 \times \cdots \times n_k \times g \times g$ tensor $A$ (i.e. a collection of $g \times g$ matrices) and an $n_1 \times \cdots \times n_k \times g$ tensor $b$ (i.e. a collection of ...