Numpy irregular array

If you find this content useful, please consider supporting the work by buying the book! Data manipulation in Python is nearly synonymous with NumPy array manipulation: even newer tools like Pandas Chapter 3 are built around the NumPy array. This section will present several examples of using NumPy array manipulation to access data and subarrays, and to split, reshape, and join the arrays.

While the types of operations shown here may seem a bit dry and pedantic, they comprise the building blocks of many other examples used throughout the book.

Get to know them well! First let's discuss some useful array attributes. We'll start by defining three random arrays, a one-dimensional, two-dimensional, and three-dimensional array. We'll use NumPy's random number generator, which we will seed with a set value in order to ensure that the same random arrays are generated each time this code is run:.

Each array has attributes ndim the number of dimensionsshape the size of each dimensionand size the total size of the array :. Another useful attribute is the dtypethe data type of the array which we discussed previously in Understanding Data Types in Python :. Other attributes include itemsizewhich lists the size in bytes of each array element, and nbyteswhich lists the total size in bytes of the array:.

In general, we expect that nbytes is equal to itemsize times size. If you are familiar with Python's standard list indexing, indexing in NumPy will feel quite familiar. Keep in mind that, unlike Python lists, NumPy arrays have a fixed type.

This means, for example, that if you attempt to insert a floating-point value to an integer array, the value will be silently truncated. Don't be caught unaware by this behavior! Just as we can use square brackets to access individual array elements, we can also use them to access subarrays with the slice notation, marked by the colon : character. The NumPy slicing syntax follows that of the standard Python list; to access a slice of an array xuse this:.

We'll take a look at accessing sub-arrays in one dimension and in multiple dimensions. A potentially confusing case is when the step value is negative. In this case, the defaults for start and stop are swapped. This becomes a convenient way to reverse an array:. Multi-dimensional slices work in the same way, with multiple slices separated by commas.

For example:.

NumPy - Iterating Over Array

One commonly needed routine is accessing of single rows or columns of an array. This can be done by combining indexing and slicing, using an empty slice marked by a single colon : :.

numpy irregular array

One important—and extremely useful—thing to know about array slices is that they return views rather than copies of the array data. This is one area in which NumPy array slicing differs from Python list slicing: in lists, slices will be copies.

Consider our two-dimensional array from before:. This default behavior is actually quite useful: it means that when we work with large datasets, we can access and process pieces of these datasets without the need to copy the underlying data buffer.

Despite the nice features of array views, it is sometimes useful to instead explicitly copy the data within an array or a subarray. This can be most easily done with the copy method:. Another useful type of operation is reshaping of arrays.By using our site, you acknowledge that you have read and understand our Cookie PolicyPrivacy Policyand our Terms of Service. The dark mode beta is finally here.

numpy irregular array

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I would like to create a two dimensional numpy array of arrays that has a different number of elements on each row. While Numpy knows about arrays of arbitrary objects, it's optimized for homogeneous arrays of numbers with fixed dimensions. If you really need arrays of arrays, better use a nested list. But depending on the intended use of your data, different data structures might be even better, e.

However this will create a one-dimensional array that stores references to lists, which means that you will lose most of the benefits of Numpy vector processing, locality, slicing, etc. An alternative to tom10's solution if you want to build your list of numpy arrays on the fly as new elements i.

This isn't well supported in Numpy by definition, almost everywhere, a "two dimensional array" has all rows of equal length. A Python list of Numpy arrays may be a good solution for you, as this way you'll get the advantages of Numpy where you can use them:. Another option would be to store your arrays as one contiguous array and also store their sizes or offsets. This takes a little more conceptual thought around how to operate on your arrays, but a surprisingly large number of operations can be made to work as if you had a two dimensional array with different sizes.

In the cases where they can't, then np. The easiest operations are ufuncs, because they require almost no modification. Here are some examples:. On the other hand.

Learn more. How to make a multidimension numpy array with a varying row size? Ask Question. Asked 9 years, 8 months ago. Active 1 year, 3 months ago. Viewed 63k times.

Active Oldest Votes. If you really want flexible Numpy arrays, use something like this: numpy. Philipp Philipp Abu Nafee Ibna Zahid 1 1 gold badge 5 5 silver badges 15 15 bronze badges. Problem is that you still can't use d.By using our site, you acknowledge that you have read and understand our Cookie PolicyPrivacy Policyand our Terms of Service.

The dark mode beta is finally here. Change your preferences any time. Stack Overflow for Teams is a private, secure spot for you and your coworkers to find and share information. If had a regular shape, then I could use np.

Because groups have different sizes, effectively, it is a list of lists of different lengths, of lists of the same length. I would like to avoid storing X as a list of lists of lists or a list of np. I know this sounds obvious, but, if you can afford the memory, I'd start just by checking the performance you get simply by padding the data to have a uniform size, that is, simply adding zeros and perform the operation.

If that doesn't work, then your best bet, as Tom Wyllie suggested, is probably a bucketing strategy. Assuming X is your list of lists of lists and alpha is an array, you can start by collecting the sizes of the second index maybe you already have this :.

Then you choose a number of buckets, which is the number of divisions of your work. You just need to divide the data so that more or less each piece is the same size:. Sorry I'm not giving a proper function, but I'm not sure how exactly is your input or expected output so I just put the pieces and you can use them as you see fit.

Learn more. Asked 2 years, 8 months ago. Active 2 years, 8 months ago. Viewed times. I would like to perform the operation If had a regular shape, then I could use np. Could you add a sample case? There are 82 groups. It was suggested to me I could make the structure regular by putting in zeros. Finding the optimum partitioning will be difficult though np-hard I think. Active Oldest Votes. Sign up or log in Sign up using Google. Sign up using Facebook. Sign up using Email and Password.

numpy tutorial - basic array operations

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numpy irregular array

The Overflow Blog. The Overflow How many jobs can be done at home? Featured on Meta. Community and Moderator guidelines for escalating issues via new response…. Feedback on Q2 Community Roadmap. Technical site integration observational experiment live on Stack Overflow. Dark Mode Beta - help us root out low-contrast and un-converted bits. Triage needs to be fixed urgently, and users need to be notified upon…. Related Hot Network Questions. Question feed.You already read in the introduction that NumPy arrays are a bit like Python lists, but still very much different at the same time.

As the name gives away, a NumPy array is a central data structure of the numpy library. In other words, NumPy is a Python library that is the core library for scientific computing in Python.

It contains a collection of tools and techniques that can be used to solve on a computer mathematical models of problems in Science and Engineering. One of these tools is a high-performance multidimensional array object that is a powerful data structure for efficient computation of arrays and matrices.

When you look at the print of a couple of arrays, you could see it as a grid that contains values of the same type:. You see that, in the example above, the data are integers.

The array holds and represents any regular data in a structured way. However, you should know that, on a structural level, an array is basically nothing but pointers.

Or, in other words, an array contains information about the raw data, how to locate an element and how to interpret an element. That also means that the array is stored in memory as 64 bytes as each integer takes up 8 bytes and you have an array of 8 integers. The strides of the array tell us that you have to skip 8 bytes one value to move to the next column, but 32 bytes 4 values to get to the same position in the next row.

As such, the strides for the array will be 32,8. Note that if you set the data type to int32the strides tuple that you get back will be 16, 4as you will still need to move one value to the next column and 4 values to get the same position. The only thing that will have changed is the fact that each integer will take up 4 bytes instead of 8. The array that you see above is, as its name already suggested, a 2-dimensional array: you have rows and columns.

Note that these axes are only valid for arrays that have at least 2 dimensions, as there is no point in having this for 1-D arrays. If you have the Python library already available, go ahead and skip this section :. If you still need to set up your environment, you must be aware that there are two major ways of installing NumPy on your pc: with the help of Python wheels or the Anaconda Python distribution. Make sure firstly that you have Python installed.

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You can go here if you still need to do this :. Note that recent versions of Python 3 come with pip, so double check if you have it and if you do, upgrade it before you install NumPy:. Next, you can go here or here to get your NumPy wheel. After you have downloaded it, navigate to the folder on your pc that stores it through the terminal and install it:.

The two last lines allow you to verify that you have installed NumPy and check the version of the package. To get NumPy, you could also download the Anaconda Python distribution. This is easy and will allow you to get started quickly!

numpy irregular array

Follow the instructions to install, and you're ready to start! But also for more seasoned data scientists, Anaconda is the way to go if you want to get started quickly on tackling data science problems. In short, consider downloading Anaconda to get started on working with numpy and other packages that are relevant to data science!

Admittedly, you have already tried out some stuff with arrays in the above DataCamp Light chunks. To make a numpy array, you can just use the np.

All you need to do is pass a list to it, and optionally, you can also specify the data type of the data. The data types are there when you need more control over how your data is stored in memory and on disk. The NumPy library follows an import convention: when you import this library, you have to make sure that you import it as np.

If you would like to know more about how to make lists, go here. You can initialize arrays with ones or zeros, but you can also create arrays that get filled up with evenly spaced values, constant or random values.

Python Numpy Array Tutorial

Remember that NumPy also allows you to create an identity array or matrix with np. An identity matrix is a square matrix of which all elements in the principal diagonal are ones, and all other elements are zeros. When you multiply a matrix with an identity matrix, the given matrix is left unchanged.NumPy package contains an iterator object numpy.

It is an efficient multidimensional iterator object using which it is possible to iterate over an array. The order of iteration is chosen to match the memory layout of an array, without considering a particular ordering. This can be seen by iterating over the transpose of the above array. If the same elements are stored using F-style order, the iterator chooses the more efficient way of iterating over an array.

It is possible to force nditer object to use a specific order by explicitly mentioning it. Its default value is read-only, but can be set to read-write or write-only mode. This will enable modifying array elements using this iterator. Causes values given to be one-dimensional arrays with multiple values instead of zero-dimensional array. In the following example, one-dimensional arrays corresponding to each column is traversed by the iterator.

If two arrays are broadcastablea combined nditer object is able to iterate upon them concurrently. Assuming that an array a has dimension 3X4, and there is another array b of dimension 1X4, the iterator of following type is used array b is broadcast to size of a. Previous Page. Next Page. Live Demo. Previous Page Print Page.A commonly asked question on the matplotlib mailing lists is "how do I make a contour plot of my irregularly spaced data? The answer is, first you interpolate it to a regular grid.

As of version 0. It performs "natural neighbor interpolation" of irregularly spaced data a regular grid, which you can then plot with contour, imshow or pcolor. By default, griddata uses the scikits delaunay package included in matplotlib to do the natural neighbor interpolation.

Unfortunately, the delaunay package is known to fail for some nearly pathological cases. If you run into one of those cases, you can install the matplotlib natgrid toolkit.

Once that is installed, the griddata function will use it instead of delaunay to do the interpolation. The natgrid algorithm is a bit more robust, but cannot be included in matplotlib proper because of licensing issues. A less robust but perhaps more intuitive method is presented in the code below. This function takes three 1D arrays, namely two independent data arrays and one dependent data array and bins them into a 2D grid. On top of that, the code also returns two other grids, one where each binned value represents the number of points in that bin and another in which each bin contains the indices of the original dependent array which are contained in that bin.

These can be further used for interpolation between bins if necessary. The is essentially an Occam's Razor approach to the matplotlib. SciPy Cookbook latest. Parameters x : ndarray 1D The idependent data x-axis of the grid.

If each bin is a cube, then this is the x and y dimension. This is the step in both directions, x and y. Defaults to 0. Defaults to True. Returns grid : ndarray 2D The evenly gridded data.GitHub is home to over 40 million developers working together to host and review code, manage projects, and build software together. Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Already on GitHub? Sign in to your account. Someone using my code reported this error message, and I would have been able to track down the problem more quickly if the message had been more informative, maybe like ValueError: setting an irregularly shaped array with a non-object dtype instead of ValueError: setting an array element with a sequence. Wtf we seriously autodetect that as being an object array? I feel like the real fix is that asarray should unconditionally treat list objects as defining slices of the output array, and if they're irregular than just throw an error, don't try to back up and make an object array.

I don't know if we can get away with such a change though. But the current behaviour is both surprising and dangerous what if one day your lists just happen to have the same number of elements? On 20 Nov"argriffing" notifications github. I agree this "feature" is awful but I doubt we can change this, its most likely baked into lots of existing code that may happen to even work alright just slower than the user probably anticipated.

The generation of object arrays is kind of screwed up anyway, probably they should only be produced with an explicit object dtype, and a maxdepth keyword would also be helpful. I don't know how much use of this feature is in the wild, usually we recommend producing and empty array of object type and initializing it in a separate operation. Might try making this change with a deprecation and see what breaks. It's not clear to me how much use object arrays even get in the wild -- I'm pretty confident that all the big projects like scikit-learn etc.

The main users are probably people who are somewhat confused and maybe even using them by accident Or maybe I'm underestimating our users, I dunno. Too bad we can't reasonably ship an instrumented version of numpy that phones home and tells us what features people actually use :- For Science!

Nathaniel J. I think object arrays are especially common in pandas space. Object arrays can be useful, for instance if the elements are polynomials, Decimals, matrices. Yeah, pandas uses object arrays for strings, because numpy's fixed-length string types are pretty None of the mentioned use cases would ever involve passing mismatched lists to asarray and expecting it to turn them into array entries, though.

On 21 Nov"Julian Taylor" notifications github. I don't know, but it sounds to me like a painful and long deprecation. Less because larger packages do that, but more because of loads of scripts just doing it for not very good reasons. If it's logistically impractical to backwards-incompatibly change the details of object array creation, would it make sense to instead add some backwards-compatible code for the purpose of giving nicer error messages?

We do actually, in a few places that handle arrays of variable-length strings. We don't use them a lot, but there are a few yet-to-be-implemented features that could use them esp. There are a couple uses of object arrays in scipy. A situation similar to this unexpected behavior caused by numpy's magic regarding conformability vs. So to summarize, we've found a bunch of cases where well-written code uses object arrays but none that rely on the "clever" handling of non-conformable lists.

I think we ought to move via deprecation etc.

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