scipy / scipy-cookbook

Scipy Cookbook

SciPy (pronounced "Sigh Pie") is an open-source software for mathematics, science, and engineering. It includes modules for statistics, optimization, integration, linear algebra, Fourier transforms, signal and image processing, ODE solvers, and more.

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SciPy is built to work with NumPy arrays, and provides many user-friendly and efficient numerical routines, such as routines for numerical integration and optimization. Together, they run on all popular operating systems, are quick to install, and are free of charge. NumPy and SciPy are easy to use, but powerful enough to be depended upon by some of the world's leading scientists and engineers. If you need to manipulate numbers on a computer and display or publish the results, give SciPy a try!

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scipy-cookbook's Issues

Small but important correction

In the section titled "Parallel Programming with numpy and scipy" in ParallelProgramming.ipynb, there's statement that while true in most cases, is not universally valid: "Using a multicore machine will provide at best a speedup by a factor of the number of cores available."

For things like searching a tree, depending on where the sought-after node is, it is possible to observe speedups of factors far greater than the number of cores available.

Value, Point methods not available in matplotlib.transforms

Hi,

I am trying to reproduce the multiline transforms code, but it seems that some methods (Value, Point) from the .transforms module haven't been included in it since a decade already. What can I use instead of these methods?

Best,
Izabel

Missing words in scipy-cookbook/ipython/ViewsVsCopies.ipynb

"For example, fancy indexing for could have been expressed by , but it is not possible to do the same for by means of a slice. So, this is why an object with a copy of the original data is returned instead."

"i.e. a new object with a copy (remember, fancy indexing does not return views) of some elements of is created and returned prior to call <is there missing information here? which call?>."

''Hint: think in terms of the sequence of {{{getitem()}}} and {{{setitem()}}} calls and what they do on each example.'' Not sure if something else is meant with the triple braces.

Sorry I would put up a PR if I knew what info to fill in, but i'm learning now!

Unclear variable names in Bundle adjustment notebook

Very unclear names,
https://github.com/scipy/scipy-cookbook/blob/master/ipython/bundle_adjustment.ipynb

i don't understand the variable used in this code at all? for example:

points_2d with shape (n_observations, 2) contains measured 2-D coordinates of points projected on images in each observations.

in what image exactly are the coordinates given, assuming i see the point in multiple images, what coordinate do i enter exactly?

Trivial misspelling, "completly"

"completly" is trivially misspelled

Incorrect variable used in RadialBasisFunctions.ipynb

In the 1D example, when plotting the two curves, it plots the same curve twice.

On line 58:
plt.plot(xi, yi, 'g')
Should be:
plt.plot(xi, fi, 'g')

I would do a pull request but this would require updating the image as well, and I'm not able to produce the image without the title of the RBF curve overlapping with the xticks of the first curve.

Alternative / Suggestion for Incorperation

https://github.com/ml31415/numpy-groupies is similar to the matlab accumarray in some ways - and its fast.

As an Alternative to accum refrenced in AccumarrayLike.ipynb

a

License?

I cannot find license information in this repo. What is the license for this material?

Is there appetite for trying to revitalize the cookbook?

The scipy-cookbook has been a great resource in the past, but (as noted in the book itself) it is not really curated/had a high volume of attention paid to it. Is there any interest among maintainers to try to kick-start the cookbook and perhaps make it a more easy/visible place for users to contribute scipy tutorial content?

Specifically, I'd think of starting with updating the infrastructure - moving away from the custom build/cookbookrebuild.py workflow to a pure sphinx-based workflow using some of the excellent tools of the executablebooks project. I've had some experience working on similar projects for NumPy (numpy-tutorials) and NetworkX (nx-guides) and have found that the tools of the executablebooks project work very well and offer some great benefits like including (but not limited to):

• The possibility for a fully sphinx-based workflow (doesn't require any custom building/rendering scripts - notebook execution and execution caching via sphinx extensions)
• Support for jupyter notebooks out of the box (a major advantage here, since the content is already in notebooks)
• Support for a markdown-based text format for Jupyter notebooks that makes diffing/reviewing notebooks much more straightforward

I realize that this is just the tip of the iceberg - the real challenge would be evaluating/updating the content of the cookbook - but I think modernizing the workflow might make subsequent steps/improvements easier.

I'd be happy to work on this, but I want to make sure that this is something that others/maintainers would be interested in!

line 136, in accum vals[indx].append(val) AttributeError: 'numpy.ndarray' object has no attribute 'append'

Hi,
I'm trying to run your function on Pyhton3.4, but getting the following error:

File "./demo_non_local_dehazing.py", line 136, in accum
vals[indx].append(val)
AttributeError: 'numpy.ndarray' object has no attribute 'append'

How can I solve this issue?

Thank you in advance!
Evgeny

Trivial typographical error

Trivial typo: "convinient" should be spelled "convenient"

slice in https://github.com/scipy/scipy-cookbook/blob/master/ipython/SignalSmooth.ipynb

Sorry not sending pull request as I am not sure I am correct. But I tried returning the slice suggested and had different output length. I am not sure of the math and how numpy.convolve works but my correction seems to pull the "middle" slice. E.g,. for window_len = 5 my suggested slice omits first two and last two elements.

NOTE: length(output) != length(input), to correct this: return y[(window_len/2-1):-(window_len/2)] instead of just y.

be

NOTE: length(output) != length(input), to correct this: return y[(window_len/2):-(window_len/2)] instead of just y.

Discussion

Thank you for this work. It’s pretty amazing.

Please open a discussion.

Miss-assigned errors in power-law fit?

The current error assignment in the power-law fit is:
indexErr = np.sqrt( covar[0][0] )
ampErr = np.sqrt( covar[1][1] ) * amp

But since index is the first component and amp is the zeroth component:
index = pfinal[1]
amp = 10.0**pfinal[0]
Shouldn't the error assignment be:
indexErr = np.sqrt( covar[1][1] )
ampErr = np.sqrt( covar[0][0] ) * amp
? Am I missing something obvious? Thanks!

Notebook formats

If I want to submit a PR with an updated notebook, the notebook format will be updated to the current one (v4 i think?). Is that okay? It will mean that the notebook formats are mixed in the repo, because i won't update all of them?

Output text without formatting

Hi!

I noticed that all text in output cells is displayed with all formatting ignored. For example the first "out" here.

Maybe you can fix it?

Broken links in "Coupled spring-mass system"

The links to the other examples in "Coupled spring-mass system" are broken. For example, the link to the KdV example should be https://scipy-cookbook.readthedocs.io/items/KdV.html, but currently it is https://scipy-cookbook.readthedocs.io/items/KdV_example.