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Questions tagged [scipy]

SciPy is a Python-based ecosystem of open-source software for mathematics, science, and engineering.

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Poisson image blending artifacts

I am trying to implement Poisson image blending as in the paper Poisson Image Editing. This is the task of filling in a masked region of an image by minimizing $$\min_f\int_\Omega \left | \nabla f - \...
ShnitzelKiller's user avatar
2 votes
0 answers
99 views

ILUTP in sparse.linalg.spilu?

In Matlab, an ILU with threshold and pivoting (ILUTP) can be passed by default as: setup.type = 'ilutp'; [L, U] = ilu(A, setup); Looking for an equivalent in ...
arandoperson's user avatar
0 votes
0 answers
45 views

Time sampling changes solution

I'm currently trying to solve a problem using numerical methods. The set-up is rather long, so I apologize in advance... TL;DR: My solutions change depending on how big my steps are and I don't know ...
Sito's user avatar
  • 131
3 votes
4 answers
2k views

Numerical integration in Python with unknown constant

I’d like to solve the below equation for the unknown $T$: $$\int_0^\infty \frac{x^2}{\exp\left(\frac{x}{T}\right)-1}\kappa_x \mathrm{d}x = C,$$ where $C$ is a known constant and $\kappa_x$ is some ...
curious_cosmo's user avatar
0 votes
1 answer
788 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 ...
LM_O's user avatar
  • 77
0 votes
1 answer
4k 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. ...
LM_O's user avatar
  • 77
0 votes
1 answer
565 views

Solve multi-dimensional optimization problem using basinhopping

I am searching for an optimization solution, which is a 8d vector representing 4 complex elements, where each element is within the complex circle with maximal radius 1.2. The objective function is: ...
SuperKogito's user avatar
2 votes
1 answer
2k views

Memory and time requirements of the scipy sparse spsolve

I have a system of fairly large set of linear equations (approximately 30K equations). I am using scipy.sparse.spsolve to solve these equations. Initially, I tried ...
Shew's user avatar
  • 121
2 votes
0 answers
2k views

Solve system of polynomial equations with Python

I have 5 at most 4th order polynomials in 5 variables, $$p_i(x_1,x_2,x_3,x_4,x_5) \qquad i = 1, \ldots, 5$$ where all coefficients are either rational or floating point. I'd would like to get the ...
Fetchinson0234's user avatar
-1 votes
1 answer
3k views

Scipy Two-point Boundary value Problem

Nonlinear ODE Statement I would like to use scipy to solve the following: u'' + (u')^2 = sin(x) u(0)=0, u(1)=1 where u = u(x). Approach I am looking at the ...
georg's user avatar
  • 101
1 vote
1 answer
1k views

Minimize cost with Levenberg-Marquart method

I want to minimize a cost function of the form, $$ \min_{q,t}\left(q^T\left(\mathcal A + \mathcal B\right)q + t^T\mathcal C t+\delta t+\varepsilon Q(q)^TW(q)t+\lambda\left(1-q^Tq\right)^2\right) $$ ...
jpmuc's user avatar
  • 111
1 vote
1 answer
214 views

SciPy 3d plotting Integral of $\int x^y dx$ for $y$ in $[-4,4]$

Ideally, I would like to get the symbolic/algebraic integral of the function and plot the resulting surface in 3d. I am not sufficiently versed in SciPy to know if this is even really possible.
user20460's user avatar
2 votes
0 answers
762 views

finding null space to a complex matrix

I need to solve the following equation: $$ \begin{pmatrix} \frac{\omega^2}{c^2}\varepsilon_x-\mu_z^{-1}k_y^2-\mu_y^{-1}k_z^2 & \mu_z^{-1}k_xk_y & \mu_y^{-1}k_xk_z\\ \mu_z^{-1}k_xk_y &\...
Physicist's user avatar
  • 217
4 votes
2 answers
715 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 ...
feik's user avatar
  • 143
3 votes
2 answers
2k views

Which SciPy nonlinear solver when Jacobian is analytically known and sparse?

I have a nonlinear function fun with n inputs and n outputs. I also have a function jac which calculates the Jacobian, which is ...
user2357's user avatar
  • 169
3 votes
0 answers
462 views

Computing Small Eigenvalues with Sparse Symmetric Indefinite Mass Matrix

I want the eigenvalues of the following generalized eigenvalue problem: $$ Av = \lambda M v $$ where $A\in\mathbb{R}^{n\times n}$ is sparse, symmetric, and positive semi-definite $M\in\mathbb{R}^{n\...
user3658307's user avatar
2 votes
1 answer
3k views

Ways to solve $Ax=b$ for a sparse (banded) $A$ with updates

I want to solve the time-dependent Schrodinger Equation using the Crank-Nicolson scheme. I end up with the following matrix equation ...
Physicist's user avatar
  • 217
0 votes
2 answers
810 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 ...
Zac's user avatar
  • 127
5 votes
1 answer
2k views

Solving for a set of coupled ODEs to get correct variable values

My question is about how I can solve a coupled system of ODE's, and print out the variables in a plot. I am solving for an q value and an e value, seen in this set of coupled ODE's below: $$ \begin{...
Nicole I.'s user avatar
5 votes
3 answers
5k views

Integration of the Fermi distribution using Python

I want to calculate the carrier concentration of my semiconductor using this equation: $$ n(x) = \frac{m^*}{\pi\hbar^2}\int_{E_k}^{\infty}\frac{1}{1+\exp\left(\frac{E-E_f}{k_BT}\right)} \mathrm{d}E $$...
ju.'s user avatar
  • 153
3 votes
0 answers
104 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) $...
bela83's user avatar
  • 443
1 vote
1 answer
338 views

Scipy odeint Unexpected Results

I am attempting to numerically integrate the equation $$\frac{\mathrm{dP} }{\mathrm{d} r}=-\left ( P+\rho\left ( r \right ) \right )\frac{m\left ( r \right )+4\pi r^{3}P}{r\left [ r-2m\left ( r \...
Java Newbie's user avatar
2 votes
1 answer
4k views

Three dimensional irregular grid data interpolation to regular grid

I have three-dimensional radar reflectivity data obtained as voxels (scans, rays, altitudes). The data has been sampled at irregular spacings and I want to convert this into a regular grid. In ...
user avatar
1 vote
1 answer
5k views

How to Solve Optimisation Problems using Penalty Functions in Python

I am working on a implementing a simple quadratic optimisation problem: $$\min _x \; {\underline{x}}^T Q {\underline{x}}$$ $$s.t. \,\quad {\underline{\mu}}^T{\underline{x}} = R^*$$ $$ \quad \quad \...
Zac's user avatar
  • 127
3 votes
0 answers
389 views

Left eigenvectors using ARPACK

I'm trying to find both the dominant $k$ left and right eigenvectors, that is, $$V_L\mathcal{A} = \Lambda V_L\\ \mathcal{A}V_R = V_R\Lambda\\ V_LV_R = I_{k\times k}$$ $V_L$ being the $k\times N$ ...
Nikko's user avatar
  • 31
0 votes
1 answer
3k views

How to define the derivative for Scipy.Optimize.Minimize

I am trying to use scipy.optimize.minimize to minimise a quadratic objective function: $f(x) =x^\top Q x$. As a start, I have successfully implemented this using the built-in Nelder-Mead Simplex ...
Zac's user avatar
  • 127
2 votes
1 answer
4k views

Solving a system of quadratic equations in Python

I'd like to solve numerically a system of quadratic equations: $A_{11}x_1+A_{12}x_2+A_{13}x_3+B_{12}x_1x_2+B_{13}x_1x_3=C_1$ $A_{21}x_1+A_{22}x_2+A_{23}x_3+B_{21}x_2x_1+B_{23}x_2x_3=C_2$ $A_{31}x_1+...
JaneFlo's user avatar
  • 21
1 vote
0 answers
382 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: ...
user88484's user avatar
  • 121
0 votes
1 answer
65 views

Inverting a transition matrix with small grid size

Time is continuous time. I have a 3D state space, and transition rates across all of these. Using the transition rates, I can compute a generator matrix A ...
FooBar's user avatar
  • 119
2 votes
1 answer
634 views

Computation time of eigenvalues with ARPACK depends on what?

My goal is to compute the k smallest eigenvalues of large symmetric sparse matrices. For this purpose I use python scipy's eigsh method in shift-invert mode which uses ARPACK. The matrices usually ...
Rena's user avatar
  • 21
0 votes
1 answer
551 views

``scipy.odeint`` giving different answer than analytical

I was using scipy.integrate.odeint function , the ode is $$\frac{y\ dx - x\ dy}{(x+y)^2} + dy = dx$$ with solution $$y^2 - x^2 - y = c (x + y)\ .$$ Solving it ...
Fenil's user avatar
  • 111
1 vote
1 answer
7k views

How to simulate 3D diffusion in python?

I want to simulate a simple 3D diffusion (e.g., an ink released from one side of a vessel) using SciPy. There are some tutorials for one-dimensional diffusion. ...
Kama's user avatar
  • 23
1 vote
0 answers
60 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,...
neo4k's user avatar
  • 11
4 votes
2 answers
553 views

Leveraging scipy for matrix free finite elements

This will be a very general question. I have a 3D finite element code in Python which I would like to extend to handle "large" problems (~10^8 unknowns in the global system). Right now I am using the ...
user3482876's user avatar
2 votes
2 answers
2k views

Correct use of scipy's sparse.linalg.spilu

I'm attempting to use scipy's spilu routine as a preconditioner and I'm finding bad performance for my application (solving a global linear system arising from a DG ...
user3482876's user avatar
-1 votes
1 answer
6k views

Using scipy.odeint to solve coupled equations [closed]

I have a set of three coupled autonomous equations: ${y_{1}}\prime = y_{1}(\frac{\Omega_{m}}{y_{1}^3} + \frac{y_{3}^2}{6.0} + \frac{V(y_{2})}{2.H_{0}^2})$ $y_{2}\prime = y_{3}$ $y_{3}\prime = -3\frac{...
anon_particle's user avatar
1 vote
0 answers
468 views

Numerical integral of oscillating function with known zeros

I have a function that I need to numerically integrate from $0$ to $+\infty$, given by: $$I = \int_0^{+\infty} \mathrm{d}x\,x\,T^2(x)f(x)$$ where $T^2$ is an interpolated function that goes to $1$ ...
HR_8938's user avatar
  • 111
1 vote
1 answer
844 views

Confusion about determining the jacobian in a rootfinding algorithm

I have written some Python code to determine the numerical roots of the following non-linear equation: $$f_m=\tan\lambda_m - \frac{\lambda_m}{1+a}$$ where $\lambda_m\gt0$ and $a\geq0$. The code is: <...
nluigi's user avatar
  • 277
3 votes
5 answers
13k views

Fast c++ library to solve very big sparse systems

I am working on a project with electrical circuits, where I am trying to compute the voltages at all the nodes of an electrical circuit. I know that the electrical circuit is a perfect grid, so each ...
excalibur1491's user avatar
1 vote
0 answers
113 views

solving numerically a 2D integral by using simps and quad combined

I have the following function $$f(x,y) =\left(\frac{1}{\exp(x-E_f)+1}-\frac{1}{\exp(x-y-E_f)+1} \right)\frac{1}{\sqrt{4-xy}}$$ I want to integrate it using Python 3. The domain of the $y$ variable ...
Small Pole's user avatar
2 votes
2 answers
3k views

Plotting Voigt Function in Python

I've been trying to plot the following function in Python: $H(a,u) = \frac{a}{\pi} \int_{-\infty}^{\infty}\frac{exp(-y^2)}{a^2 + (u - y)^2}dy $ But I keep receiving the following error: ...
Daniel's user avatar
  • 33
3 votes
2 answers
4k views

Small errors accumulate while solving ODE of motion

I'm trying to solve the ODE of motion: $$ \begin{align} x''=&\ -myu \frac{x}{r^3} \left(1+\frac{3}{2} {J_2} \left(\frac{{r_{\text{eq}}}}{r}\right)^2 \left(1-\frac{5z^2}{r^2}\right)\right) \\ ...
Sonya Seyrios's user avatar
0 votes
0 answers
1k views

Tridiagonal Solver in Python

I have a code I'm working on that involves solving a 1D Schrodinger equation using a Crank-Nicolson time step. The code is written in NumPy/SciPy, and I was doing a bit of profiling and discovered ...
user2379888's user avatar
2 votes
0 answers
754 views

How to use "fill_factor" in spilu (scipy) [closed]

I am using spilu (incomplete LU decomposition for sparse matrix) in scipy: https://docs.scipy.org/doc/scipy-0.14.0/reference/generated/scipy.sparse.linalg.spilu.html However there is an option call "...
HappyMan's user avatar
2 votes
1 answer
447 views

How to broadcast my matrix exponentiation

I'm trying -to no avail- to broadcast the following piece of code in Python: ...
bela83's user avatar
  • 443
1 vote
1 answer
5k views

scipy optimize fsolve or root

I have a function: delt=1 #trial def f(z): return ((1-2*z)*np.exp(-delt/z))/(((1-z)**(2+delt))*(z**(2-delt))) I also have a variable: ...
dayum's user avatar
  • 163
1 vote
1 answer
467 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 ...
Mathews24's user avatar
  • 568
5 votes
0 answers
540 views

Optimisation of matrix exponential

I have a 7000x7000 sparse matrix (scipy), which I want to exponentiate. I've tried using scipy.sparse.linalg.expm, which works quite well for smaller matrices (takes a few seconds for a 1000x1000 ...
ferros's user avatar
  • 51
1 vote
0 answers
871 views

Numerical Double integration with endpoint singularity in scipy Python gives incorrect answer

I am trying to integrate the following function in Python, $\int_{0}^{\infty}\int_{0}^{\infty} \dfrac{e^{-x-y}}{B(x,y)}dx dy$, where $B(x,y)$ is the beta function - $B(x,y) = \int_0^{1}a^{x-1}(1-a)^{...
Siddhartha Satpathi's user avatar
2 votes
3 answers
3k views

stop condition in scipy.integrate.ode for stiff system

I'm using Python scipy.integrate.ode, and I want to stop my integration at a certain condition. So I use the integrator "dopri5" and use the method "set_solout" to specify a function for my stop ...
Peter B's user avatar
  • 121