[Numpy-discussion] Fortran order in recarray.
josef.pktd at gmail.com
josef.pktd at gmail.com
Wed Feb 22 12:39:38 EST 2017
On Wed, Feb 22, 2017 at 11:57 AM, Alex Rogozhnikov <
alex.rogozhnikov at yandex.ru> wrote:
> Hi Matthew,
> maybe it is not the best place to discuss problems of pandas, but to show
> that I am not missing something, let's consider a simple example.
>
> # simplest DataFrame
> x = pandas.DataFrame(dict(a=numpy.arange(10), b=numpy.arange(10, 20)))
> # simplest indexing. Can you predict results without looking at comments?
> x[:2] # returns two first rows, as expected
> x[[0, 1]] # returns copy of x, whole dataframe
> x[numpy.array(2)] # fails with IndexError: indices are out-of-bounds (can you guess why?)
> x[[0, 1], :] # unhashable type: list
>
>
> just in case - I know about .loc and .iloc, but when you write code with
> many subroutines, you concentrate on numpy inputs, and at some point you
> simply *forget* to convert some of the data you operated with to numpy
> and it *continues* to work, but it yields wrong results (while you tested
> everything, but you tested this for numpy). Checking all the inputs in each
> small subroutine is strange.
>
> Ok, a bit more:
>
> x[x['a'] > 5] # works as expected
> x[x['a'] > 5, :] # 'Series' objects are mutable, thus they cannot be hashed
> lookup = numpy.arange(10)
> x[lookup[x['a']] > 5] # works as expected
> x[lookup[x['a']] > 5, :] # TypeError: unhashable type: 'numpy.ndarray'
>
> x[lookup]['a'] # indexError
> x['a'][lookup] # works as expected
>
>
> Now let's go a bit further: train/test splitted the data for machine
> learning (again, the most frequent operation)
>
> from sklearn.model_selection import train_test_split
> x1, x2 = train_test_split(x, random_state=42)
> # compare next to operations with pandas.DataFrame
> col = x1['a']print col[:2] # first two elementsprint col[[0, 1]] # doesn't fail (while there in no row with index 0), fills it with NaNprint col[numpy.arange(2)] # same as previous
> print col[col > 4] # as expectedprint col[col.values > 4] # as expectedprint col.values[col > 4] # converts boolean to int, uses int indexing, but at least raises warning
>
>
> Mistakes done by such silent misoperating are not easy to detect (when
> your data pipeline consists of several steps), quite hard to locate the
> source of problem and almost impossible to be sure that you indeed avoided
> all such caveats. Code review turns into paranoidal process (if you care
> about the result, of course).
>
> Things are even worse, because I've demonstrated this for my installation,
> and probably if you run this with some other pandas installation, you get
> some other results (that were really basic operations). So things that
> worked ok in one version, may work different way in the other, this becomes
> completely intractable.
>
> Pandas may be nice, if you need a report, and you need get it done
> tomorrow. Then you'll throw away the code. When we initially used pandas as
> main data storage in yandex/rep, it looked like an good idea, but a year
> later it was obvious this was a wrong decision. In case when you build data
> pipeline / research that should be working several years later (using some
> other installation by someone else), usage of pandas shall be *minimal*.
>
> That's why I am looking for a reliable pandas substitute, which should be:
> - completely consistent with numpy and should fail when this wasn't
> implemented / impossible
> - fewer new abstractions, nobody wants to learn one-more-way-to-manipulate-the-data,
> specifically other researchers
> - it may be less convenient for interactive data mungling
> - in particular, less methods is ok
> - written code should be interpretable, and hardly can be misinterpreted.
> - not super slow, 1-10 gigabytes datasets are a normal situation
>
Just to the pandas part
statsmodels supported pandas almost from the very beginning (or maybe after
1.5 years) when the new pandas was still very young.
However, what I insisted on is that pandas is in the wrapper/interface
code, and internally only numpy arrays are used. Besides the confusing
"magic" indexing of early pandas, there were a lot of details that silently
produced different results, e.g. default iteration on axis=1, ddof in std
and var =1 instead of numpy =0.
Essentially, every interface corresponds to np.asarry, but we store the
DataFrame information, mainly the index and column names, wo we can return
the appropriate pandas object if a pandas object was used for the input.
This has worked pretty well. Users can have their dataframes, and we have
pure numpy algorithms.
Recently we have started to use pandas inside a few functions or classes
that are less tightly integrated into the overall setup. We also use pandas
for some things that are not convenient or not available in numpy. Our
internal use of pandas groupby and similar will most likely increase over
time.
(One of the main issues we had was date and time index because that was a
moving target in both numpy and pandas.)
One issue for computational efficiency that we do not control is whether
`asarray` creates a view or needs to make a copy because that depends on
whether the dtype and memory layout that the user has in the data frame
corresponds to what we need in the algorithms. If it matches, then no
copies should be made except where explicitly needed.
The intention is to extend this over time to other array structures like
xarray and likely dask arrays.
Josef
>
> Well, that's it.
> Sorry for large letter.
>
> Alex.
>
>
>
> 22 февр. 2017 г., в 18:38, Matthew Harrigan <harrigan.matthew at gmail.com>
> написал(а):
>
> Alex,
>
> Can you please post some code showing exactly what you are trying to do
> and any issues you are having, particularly the "irritating problems with
> its row indexing and some other problems" you quote above?
>
> On Wed, Feb 22, 2017 at 10:34 AM, Robert McLeod <robbmcleod at gmail.com>
> wrote:
>
>> Just as a note, Appveyor supports uploading modules to "public websites":
>>
>> https://packaging.python.org/appveyor/
>>
>> The main issue I would see from this, is the PyPi has my password stored
>> on my machine in a plain text file. I'm not sure whether there's a way to
>> provide Appveyor with a SSH key instead.
>>
>> On Wed, Feb 22, 2017 at 4:23 PM, Alex Rogozhnikov <
>> alex.rogozhnikov at yandex.ru> wrote:
>>
>>> Hi Francesc,
>>> thanks a lot for you reply and for your impressive job on bcolz!
>>>
>>> Bcolz seems to make stress on compression, which is not of much interest
>>> for me, but the *ctable*, and chunked operations look very appropriate
>>> to me now. (Of course, I'll need to test it much before I can say this for
>>> sure, that's current impression).
>>>
>>> The strongest concern with bcolz so far is that it seems to be
>>> completely non-trivial to install on windows systems, while pip provides
>>> binaries for most (or all?) OS for numpy.
>>> I didn't build pip binary wheels myself, but is it hard / impossible to
>>> cook pip-installabel binaries?
>>>
>>> You can change shapes of numpy arrays, but that usually involves copies
>>> of the whole container.
>>>
>>> sure, but this is ok for me, as I plan to organize column editing in
>>> 'batches', so this should require seldom copying.
>>> It would be nice to see an example to understand how deep I need to go
>>> inside numpy.
>>>
>>> Cheers,
>>> Alex.
>>>
>>>
>>>
>>>
>>> 22 февр. 2017 г., в 17:03, Francesc Alted <faltet at gmail.com> написал(а):
>>>
>>> Hi Alex,
>>>
>>> 2017-02-22 12:45 GMT+01:00 Alex Rogozhnikov <alex.rogozhnikov at yandex.ru>
>>> :
>>>
>>>> Hi Nathaniel,
>>>>
>>>>
>>>> pandas
>>>>
>>>>
>>>> yup, the idea was to have minimal pandas.DataFrame-like storage (which
>>>> I was using for a long time),
>>>> but without irritating problems with its row indexing and some other
>>>> problems like interaction with matplotlib.
>>>>
>>>> A dict of arrays?
>>>>
>>>>
>>>> that's what I've started from and implemented, but at some point I
>>>> decided that I'm reinventing the wheel and numpy has something already. In
>>>> principle, I can ignore this 'column-oriented' storage requirement, but
>>>> potentially it may turn out to be quite slow-ish if dtype's size is large.
>>>>
>>>> Suggestions are welcome.
>>>>
>>>
>>> You may want to try bcolz:
>>>
>>> https://github.com/Blosc/bcolz
>>>
>>> bcolz is a columnar storage, basically as you require, but data is
>>> compressed by default even when stored in-memory (although you can disable
>>> compression if you want to).
>>>
>>>
>>>
>>>>
>>>> Another strange question:
>>>> in general, it is considered that once numpy.array is created, it's
>>>> shape not changed.
>>>> But if i want to keep the same recarray and change it's dtype and/or
>>>> shape, is there a way to do this?
>>>>
>>>
>>> You can change shapes of numpy arrays, but that usually involves copies
>>> of the whole container. With bcolz you can change length and add/del
>>> columns without copies. If your containers are large, it is better to
>>> inform bcolz on its final estimated size. See:
>>>
>>> http://bcolz.blosc.org/en/latest/opt-tips.html
>>>
>>> Francesc
>>>
>>>
>>>>
>>>> Thanks,
>>>> Alex.
>>>>
>>>>
>>>>
>>>> 22 февр. 2017 г., в 3:53, Nathaniel Smith <njs at pobox.com> написал(а):
>>>>
>>>> On Feb 21, 2017 3:24 PM, "Alex Rogozhnikov" <alex.rogozhnikov at yandex.ru>
>>>> wrote:
>>>>
>>>> Ah, got it. Thanks, Chris!
>>>> I thought recarray can be only one-dimensional (like tables with named
>>>> columns).
>>>>
>>>> Maybe it's better to ask directly what I was looking for:
>>>> something that works like a table with named columns (but no labelling
>>>> for rows), and keeps data (of different dtypes) in a column-by-column way
>>>> (and this is numpy, not pandas).
>>>>
>>>> Is there such a magic thing?
>>>>
>>>>
>>>> Well, that's what pandas is for...
>>>>
>>>> A dict of arrays?
>>>>
>>>> -n
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>>>>
>>>>
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>>>>
>>>
>>>
>>> --
>>> Francesc Alted
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>>>
>>>
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>>>
>>
>>
>> --
>> Robert McLeod, Ph.D.
>> Center for Cellular Imaging and Nano Analytics (C-CINA)
>> Biozentrum der Universität Basel
>> Mattenstrasse 26, 4058 Basel
>> Work: +41.061.387.3225 <+41%2061%20387%2032%2025>
>> robert.mcleod at unibas.ch
>> robert.mcleod at bsse.ethz.ch <robert.mcleod at ethz.ch>
>> robbmcleod at gmail.com
>>
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