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Questions tagged [scientific-software]

Use this tag for questions relating to Scientific Software, i.e. software that is used for Scientific Computing.

is used in its general meaning, but, please remember that software recommendations are off-topic for Stack Overflow, thus scientific software recommendations are off-topic too.

For Software Recommendations use softwarerecs.

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Python subprocess: Giving stdin, reading stdout, then giving more stdin

I'm working with a piece of scientific software called Chimera. For some of the code downstream of this question, it requires that I use Python 2.7. I want to call a process, give that process some input, read its output, give it more input based on…
julianstanley
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Spyder: Keep variables in variable explorer after running a Python file

I am relatively new to Python and for the beginning I have chosen Spyder as an IDE. At the moment I am working on an optimization problem and want to keep the results for further postprocessing. If I run the code using F5 (or "Run>Run") the file is…
Cord Kaldemeyer
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Organizing Scientific Data and Code - Experiments, Models, Simulation, Implementation

I am working on a robotics research project, and would like to know: Does anyone have suggestions for best practices when organizing scientific data and code? Does anyone know of existing scientific libraries with source that I could examine? Here…
eacousineau
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Is there a way of batch sampling from Numpy's multivariate normal distribution in a vectorised fashion?

I'm presently trying to run a vectorised batch multivariate sampling operation via Numpy. I have k mean vectors of shape [N,] corresponding to k covariance matrices of dimensions [N, N], and I'm trying to return k draws of shape [N,] from the…
potpie
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Choosing starting point in GNU Scientific Library multiroot finder

I'm using an implementation of the GNU Scientific Library's multiroot finder to solve for the unknowns (x and y) in the following system of non-linear equations: I'm a bit confused, however, about the "starting point": Solve(const double *x, int…
10GeV
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Unit testing...should it be used here?

Duplicate: https://stackoverflow.com/questions/135651/learning-unit-testing I'm trying to develop some software for my research group to analyze and plot experimental data. I would like to make it where it's pretty error free. Would this be a…
Nope
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How to properly diagnose a cmake GLIBC version error?

Some background: I'm trying to use easybuild to build different versions of a rather complicated scientific software stack on the same HPC system. I am new to building software like this and could use some guidance on debugging. My current error…
lcleary
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Custom metadata from .nd2 files

I have a series of .nd2 files from NIS Elements AR, associated with Nikon microscopes. In Elements AR custom user defined metadata can be added to images/image series and is saved in the .nd2 format. When these files are saved and then reopened in…
j1ling67n
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Symbolic PDE solver alternative to SymPy for Python?

I like SymPy, but I have been running into issues with it when I solve partial differential equations. I've constructed a toy example: from sympy import Function, Eq from sympy.solvers import pdsolve from sympy.abc import x, y, t f =…
Galen
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Pycharm python-snowflake connector package works in all other projects except NOT FOUND in Scientific mode project

I need help getting Snowflake-Python connector package to work in a Pycharm Scientific mode project. When I previously setup the Snowflake-Python connector in a non-Scientific mode project I could simply picked it from the Project Intepreter …
CoolDocMan
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Multiply list of floats to retain maximum precision on a modern CPU

I have a list of many single-precision IEEE floating point numbers. How does one go through the list and multiply all numbers to ensure maximum precision, and no over/underflows? We assume there should be no over/underflows with arbitrary precision…
cheater
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How to align the center of a textwidget in pyqtgraph

I would like to use a textwidget to display a text over an image, and make sure that the text is centered in the image. (I actually want to make a movie where the text changes with every frame to indicate what was changed). I tried the following (in…
Dirklinux
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Division on Data.Scientific diverges with infinite decimal expansion

So, I recently started using the scientific package because it provides arbitrary precision numbers through Data.Scientific which I haven't seen anywhere else. One issue that I've run into is the divergence of division / (which is indeed warned…
m-renaud
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How can I edit a binary file under windows by scripting

I'm usually a reader but this time I don't find an answer. I've got some technical files produced by a scientific device. From time to time, recorded files get corrupted and we have to do some hexadecimal modification by hand. I'm wondering how I…
Benoit
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Sums on GNU Scientific Library (GSL)

I have used the 'mean' function on GSL which proved to be more accurate than my naive implementation. I haven't found a 'sum' function though, I'm using 'mean'*N instead, but I think it would be cleaner if I use a proper summing function. I'm…
Bunder
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