[Python.NET] Efficient copy of .NET Array to ctypes or numpy array

Jeffrey Bush jeff at coderforlife.com
Wed Nov 5 23:32:45 CET 2014 

To copy from a list or tuple you need to use the Python buffer() function.
You can use that on numpy arrays as well. In buffer form, the len() is the
byte length so then you don't need to know the data type or size. However,
some additional work would be required if you wanted to make sure the C#
array was of the proper type and length.

Jeff

On Wed, Nov 5, 2014 at 11:28 AM, Denis Akhiyarov <denis.akhiyarov at gmail.com>
wrote:

> Finally decided to generate the managed object on Python side and return
> it to C# with no conversion necessary in C#. This way I can even wrap
> regular function with Python with @decorator to handle the conversion.  I
> suppose the dynamic version of pythonnet may have auto conversion for
> Python 3, but I have not tried. I'm on Python 2.7.
>
> On Wed, Nov 5, 2014 at 9:31 AM, Denis Akhiyarov <denis.akhiyarov at gmail.com
> > wrote:
>
>> And more important question - is it possible to generalize the copying of
>> python array object to managed C# array object without knowing the data
>> type/size/length?
>>
>> On Wed, Nov 5, 2014 at 8:58 AM, Denis Akhiyarov <
>> denis.akhiyarov at gmail.com> wrote:
>>
>>> How to copy unmanaged array (python list/tuple or numpy array) into
>>> managed C# array? I guess using Marshal.Copy, but can anyone point to
>>> example?
>>>
>>> Thanks,
>>> Denis
>>>
>>> On Thu, Oct 30, 2014 at 12:19 PM, Nikhil Garg <nikhilgarg.gju at gmail.com>
>>> wrote:
>>>
>>>> Thanks Brad and Jeff for the detailed info. For now, fromiter is
>>>> serving me well and has reduced my processing time considerably, so I am
>>>> just going to stick with it.
>>>>
>>>>
>>>> On 29 October 2014 11:04, Jeffrey Bush <jeff at coderforlife.com> wrote:
>>>>
>>>>> I finally have a chance to chime in, and Bradley is exactly right.
>>>>> Marshall.Copy copies the raw data, and apparently your file library does
>>>>> not store that data in a nice, contiguous, manner. While it is highly
>>>>> likely that copying all the data to an array in C# will be faster than the
>>>>> fromiter in Python, I am unsure if copying all the data to an array in C#
>>>>> then copying all the data again to a numpy array will be faster than
>>>>> fromiter (cause you have to copy it twice). The exception is if the file
>>>>> library has a function like ToArray that is optimized to copy the data to a
>>>>> linear chunk of data. So, what type is "Data"?
>>>>>
>>>>> Another factor is how long the chunk of data you are copying is. You
>>>>> say the last axis is only 400 elements long. Check out my code and you will
>>>>> see that at 400 elements long, fromiter is actually the fastest (at least
>>>>> when I tried). An example run:
>>>>>
>>>>> Copy using for loop in 0.000884 sec
>>>>> Copy using fromiter in 0.000144 sec # fastest
>>>>> Copy using fromstring in 0.001460 sec # fairly slow, 10.3x slower than
>>>>> fromiter
>>>>> Copy using Marshal.Copy in 0.001680 sec # slowest, 11.7x slower than
>>>>> fromiter
>>>>>
>>>>> I start to do better with Marshal.Copy then fromiter around 5000
>>>>> elements copied. This is because the overhead of the mass copies is high
>>>>> but adding each element doesn't take much time. fromstring has a lower
>>>>> overhead but slightly longer per-element time (fromstring is better than
>>>>> Marshal.Copy until ~200,000 elements).
>>>>>
>>>>> So you might be doing as good as you can possibly do. If I knew more
>>>>> about your file format library I might be able to provide more insight.
>>>>>
>>>>> Jeff
>>>>>
>>>>> On Tue, Oct 28, 2014 at 2:45 PM, Bradley Friedman <brad at fie.us> wrote:
>>>>>
>>>>>> Well it makes sense to me that doing it via an iterator, and element
>>>>>> at a time, would be slow.  There’s a lot of call overhead associated with
>>>>>> each iteration step.  Whether it’s done in .net, or in python, or a call
>>>>>> from one to the other, it will be slow.  It’s still a call where you’d be
>>>>>> better off copying whole buffers.
>>>>>>
>>>>>> Ideally you’d pull the data into as simple and raw a data structure
>>>>>> as you can on the dotnet side, in a buffered manner.  Then you’d execute a
>>>>>> movement of the data across, a reasonably sized chunk of buffer at a time.
>>>>>> This will reduce call overhead and also allow read-ahead caching to do its
>>>>>> thing on the file-access side of things.
>>>>>>
>>>>>> Your suggestion of loading into a .net array and then moving that
>>>>>> array over, makes sense.  But I think it comes down to what you can do with
>>>>>> the third party file-format library. If its not going to provide you with
>>>>>> the data as some kind of buffer with a cohesive and known format in memory,
>>>>>> you’re not really going to be able to move it over without iterating over
>>>>>> it and reformatting it at some point.
>>>>>>
>>>>>> Specifically, I’d point to Jeffery’s original caveat:
>>>>>>
>>>>>> "but does involve a number of assumptions (for example that the data
>>>>>> in the two arrays are laid out in the same way)."
>>>>>>
>>>>>> The question is:  is there a way to get the data off of disk and in
>>>>>> memory from dotnet library, where its layout in memory is known, and
>>>>>> something you want exactly as it is, but in python?  If so, you should be
>>>>>> able to use the methods from the afore linked thread.  If not, you’re
>>>>>> probably stuck iterating somewhere to reformat it, no matter what.  Which
>>>>>> is probably why you got garbage back.  I’m guessing the object returned
>>>>>> from the dotnet file-format-library isn’t laid out right, as suggested in
>>>>>> the afore referenced caveat.
>>>>>>
>>>>>>
>>>>>> > On Oct 28, 2014, at 9:55 AM, Nikhil <nikhilgarg.gju at gmail.com>
>>>>>> wrote:
>>>>>> >
>>>>>> > Hello,
>>>>>> > Yeah, I read data from a file say at each node and each time step,
>>>>>> but when i try to use Marshal approach i get gibberish but when i use
>>>>>> simple iter i get correct values. i have been trying the approach used in
>>>>>> example in the previous post and that example makes sense but it doesnt
>>>>>> make sense when i use it in my case. I am right now assigning it to a
>>>>>> variable, i am now thinking of exploring the possibility of saving data to
>>>>>> a dot net array maybe using System.Array and saving data to it but not sure
>>>>>> if that even make sense.
>>>>>> >
>>>>>> > Sent from my iPhone
>>>>>>
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>>>>>>
>>>>>
>>>>>
>>>>> _________________________________________________
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>>>>
>>>>
>>>>
>>>> --
>>>> Regards
>>>>
>>>> Nikhil
>>>>
>>>> -------------------------------------------------------------------
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>>>> And so on to viscosity
>>>> (Richardson, 1922)
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>>
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