NumPy is the fundamental package for scientific computing with the programming language Python.
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Matplotlib: 2D color plot with irregular spaced data (mlab.griddata) [closed]
I want to create a colorplot of some irregularly sampled data. I've had some success with the interpolating using matplotlib.mlab.griddata. When I plot the interpolated data (using ...
1
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1answer
29 views
List of lists of arrays, zipping, modifying in place
I came back to some old code today and freaked out. I was like "How does this even work, and if it works it can't do what I intended." I ran a few quick tests and confirmed it did actually do what ...
3
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1answer
46 views
Averaging a list of intersecting rectangles
I have a list of rectangles as tuples (x, y, w, h). I need to find which ones intersect and if they do, average all the intersecting rectangles into a new rectangle. I also track the resultant ...
5
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1answer
58 views
Monte Carlo estimation of the Hypergeometric Function
I am trying to implement the algorithm described in the paper Statistical Test for the Comparison of Samples from Mutational Spectra (Adams & Skopek, 1986) DOI: 10.1016/0022-2836(87)90669-3:
$$p ...
2
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0answers
43 views
5
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1answer
97 views
Groupby in NumPy
To avoid the XY problem, here is an example of what I need. Given the sorted integer input array
[1 1 1 2 2 3], I would like to produce the following slices, ...
4
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1answer
38 views
Stable partition in Numpy
In essence, I need to do a stable partition: All elements of the 1D np.array a that are present in ...
3
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1answer
60 views
Where is the bottleneck in my Cython code?
The profile tells me it took ~15s to run, but without telling me more.
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1
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1answer
54 views
Neighbours from point connections
I am working with a mesh of triangles (in 3D, although I doubt it makes a difference). The mesh is given as list of lists, each list containing the indices of the three vertices of a triangle in said ...
3
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0answers
33 views
Parallelizing some model fitting code using multiprocessing
I'm trying to refactor some code for fitting parametric models that are defined symbolically using Theano. My goal is for all models to expose a common interface so that, as far as possible, they can ...
2
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1answer
49 views
How can I make this implementation of Euler's method more efficient?
I have an implementation of an Euler method for solving N-many 1st order coupled differential equations, but I feel that I did not write it as efficiently as I could, due to lack of programming ...
1
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0answers
17 views
Function that transforms input file based on a numpy poly1d function
I have written a function that gets a function as input (acquired from numpy.poly1d). The function has access to the GUI variables ...
3
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2answers
83 views
Optimization/speed up of reduction function
I'm working on an implementation of Rainbow tables as part of a project. I understand the main principles behind it had have a working solution. Unfortunately the reduction function portion of my ...
8
votes
1answer
137 views
Interpolate then maximize
I need to optimize
$$ \max_{a',\ m'} f(a, m, e, m', a') $$
I have approximated \$f\$ with a grid \$F\$ — it has shape \$(nA, nM, nE, nM, nA)\$. Now, I want to interpolate over the last two ...
3
votes
2answers
75 views
Calculating mesh centers runs very slowly
I have a piece of code that is used to calculate the cell centers in a rectangular mesh. The mesh size is pretty large (650 columns by 1150 rows). The code runs very slowly. I was wondering if I could ...
1
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1answer
46 views
Hints to make Sukoku solver more Pythonic (II)
I tried to implement as many changes suggested as possible as well as expanding the code base according to the suggested link. The original question can be found here. It does solve Sudokus gives ...
5
votes
1answer
387 views
Hints to make Sudoku solver more Pythonic
As you will see, I am not very familiar with Python and NumPy but want to learn it.
The following code is a very basic Sudoku solver which works fine for simple examples. Although it runs, I still ...
4
votes
1answer
82 views
Fixed point iteration and cobweb plot
I'm using Python to find fixed points of a given function and then draw a cobweb plot to visualize it. Thanks to this question, I have the core of the code written and can accomplish the task, but I ...
3
votes
2answers
95 views
Connect 4 game for AI agents
This Connect 4 game will be used for implementing game-playing AI. Sample players are supplied. One takes user input, and the other plays randomly. Right now it's set for a human player to play ...
4
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1answer
196 views
Efficient numpy cosine distance calculation
I want to calculate the nearest cosine neighbors of a vector using the rows of a matrix, and have been testing the performance of a few Python functions for doing this.
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4
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1answer
97 views
Flood fill algorithm
I am implementing a flood fill algorithm using Python and NumPy. I have written the following fill function which works fine:
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3
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1answer
95 views
Calculating the distance between one point, and many others
In my program, I have entities that I call "blobs", because they have a blobby shape. Blobs are polygons. If I have two blobs, then their information array would look like:
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3
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2answers
109 views
Calculating if a point is within a polygon, or outside of it
Here is the function (along with its support functions):
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5
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1answer
105 views
Calculating “element-wise” the angles between two lists of vectors
Let's say you have two lists of vectors:
v1s = [a, b, c]
v2s = [d, e, f]
I am interested in generating the following ...
5
votes
2answers
71 views
Taking wind data and simulating future wind profiles
I am new to programming, and am using Python to take wind data and simulate future wind profiles. The code as written takes a while to execute and I was hoping someone could suggest ways to make my ...
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0answers
45 views
Cythonized version of FDCT (fast discrete cosine transform) function, ported from Java
This is my Cython code for an FDCT function (invoked here):
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3
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1answer
90 views
Point in a polygon algorithm
I am implementing a Point in polygon algorithm.
Inputs:
M, N: size of the matrix
poly: a ...
3
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1answer
60 views
Fast loop to create an array of values
I have a code that creates a 3D array of values from a minimum to a maximum in X and Z with constant Y.
Right now I make it in normal Python, and then I transform it in a ...
2
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0answers
33 views
Plotting many images at once in matplotlib
I am using numpy and matplotlib to do a statistical simulation. The simulation itself is pretty fast thanks to numPy vectorizatio, however the plotting is slow since I still use a ...
8
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2answers
389 views
Possible optimizations for calculating squared euclidean distance
I need to do a few hundred million euclidean distance calculations every day in a Python project.
Here is what I started out with:
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4
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2answers
312 views
K-means clustering in Python
The following code uses scikit-learn to carry out K-means clustering where \$K = 4\$, on an example related to wine marketing from the book DataSmart. That book uses excel but I wanted to learn Python ...
2
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0answers
72 views
implementation of a new algorithm for sklearn
In the python library sklearn is implemented the algorithm for SparsePCA.
I have written the code for a another version of this algorithm that is much faster in some situations. I have not enough ...
5
votes
1answer
391 views
Sieve of Eratosthenes - Standard and Optimized implementation
I am a Java developer who is taking Python for the first time.
I'm sure this is not at all elegant since I am thinking more in C syntax.
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4
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1answer
50 views
Calculating minima values for each column of given data
Can anyone help make this perform faster?
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0answers
40 views
Optimizing visualization of waves
Any advice on making this code more optimal?
A_DATA_time_space.py
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0
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1answer
125 views
My Python code (for creation of MxM matrix) is much slower than my Matlab version
I have written the same code in Python (NumPy) and in Matlab, and I tried to use the same structure for both language and follow the same procedure. Now my problem is that when I run my code in Python ...
4
votes
1answer
63 views
Performing a special multiplication on two square matrices
I have a function called mult2 that takes in two square NumPy matrices and returns a matrix that is the result of a special multiplication:
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6
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1answer
63 views
Average of positive and negative part of numpy matrix
I’ve got a matrix of data and I want to take the average of the positive and negative parts of the values.
Is there a more Pythonic way of doing it?
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5
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1answer
51 views
Determining the least-accurately known physical constants
So, I thought I'd do this using scipy.constants:
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3
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1answer
53 views
Building a dict/list of lists
I have code which is matching features within regions. The first thing it does it matches features from one region to an entire database of region features.
I have a mapping from query feature index ...
12
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1answer
127 views
Temperature Interpolation
I want to interpolate temperature in correlation with height. I have temperature data from stations with coordinates and height in this format:
...
1
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1answer
253 views
Parse Bloomberg Excel/CSV with Pandas DataFrame
I retrieved Bloomberg data using the Excel API. In the typical fashion, the first row contains tickers in every fourth column, and the second row has the labels Date, PX_LAST, [Empty Column], Date, ...
6
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1answer
109 views
Calculating Euclidean norm for each vector in a sparse matrix
Below is a naive algorithm to find nearest neighbours for a point in some n-dimensional space.
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0answers
114 views
numpy array as quasi-hash table
Motivation: I have a large number of large read-only dicts with large string keys mapped to tuples of two floats. They are taking up a large amount of heap space.
Proposed solution: a 3xn numpy ...
4
votes
1answer
64 views
Pythonic way to manipulate arrays: a case study
I just spent almost one day to figure out the following code, which analyzes the output data from material science programs called VASP and Bader. As a Python beginner, I earnestly ask some aces to ...
5
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1answer
281 views
Optimizing very simple piece of “Game of Life” code by taking advantage of NumPy's functionality
Here is the code as it stands right now:
...
13
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1answer
185 views
Finding a zero crossing in a matrix
I am trying create an algorithm for finding the zero crossing (check that the signs of all the entries around the entry of interest are not the same) in a two dimensional matrix, as part of ...
4
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2answers
213 views
10
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2answers
244 views
Calculating the joint probability of n events from a sample sequence of occurrences
I'm writing an algorithm to take in a sample list of sequences of events, calculate 1-step transitional probabilities from the sequences, forward or in reverse, then calculate the joint probability of ...
4
votes
1answer
98 views
KMeans in the shortest and most readable format
I'm learning Python (coming from Java) so I decided to write KMeans as a practice for the language. However I want to see how could one improve the code and making it shorter and yet readable. I ...
