Efficiently convert System.Single[,] to numpy array

Question

Using Python 3.6 and Python for dotNET/pythonnet I have manged to get hold of an image array. This is of type System.Single[,]

I'd like to convert that to a numpy array so that I can actually do something with it in Python. I've set up a function to step through that array and convert it elementwise - but is there something more sensible (and faster) that I could use?

def MeasurementArrayToNumpy(TwoDArray):
    hBound = TwoDArray.GetUpperBound(0)
    vBound = TwoDArray.GetUpperBound(1)

    resultArray = np.zeros([hBound, vBound])

    for c in range(TwoDArray.GetUpperBound(0)):            
            for r in range(TwoDArray.GetUpperBound(1)):
                resultArray[c,r] = TwoDArray[c,r]
    return resultArray

Answer 1

@denfromufa - that is a very useful link.

The suggestion there is to do a direct memory copy, either using Marshal.Copy or np.frombuffer. I couldn't manage to get the Marshal.Copy version working - some shenanigans are required to use a 2D array with Marshal and that changed the contents of of the array somehow - but the np.frombuffer version seems to work for me and reduced the time to complete by a factor of ~16000 for a 3296*2471 array (~25s -> ~1.50ms). This is good enough for my purposes

The method requires a couple more imports, so I've included those in the code snippet below

import ctypes
from System.Runtime.InteropServices import GCHandle, GCHandleType

def SingleToNumpyFromBuffer(TwoDArray):
    src_hndl = GCHandle.Alloc(TwoDArray, GCHandleType.Pinned)

    try:
        src_ptr = src_hndl.AddrOfPinnedObject().ToInt32()
        bufType = ctypes.c_float*len(TwoDArray)
        cbuf = bufType.from_address(src_ptr)
        resultArray = np.frombuffer(cbuf, dtype=cbuf._type_)
    finally:
        if src_hndl.IsAllocated: src_hndl.Free()
    return resultArray

Answer 2

Following denfromufa's link, I think Robert McLeod offers the best solution. He also points out a draw back of using np.frombuffer:

one can do a zero-copy with np.frombuffer but then you have a mess of memory manged both by Python's garbage collector and C#'s garbage collector.

Robert McLeod's snippet from the github issue:

import numpy as np
import ctypes
import clr, System
from System import Array, Int32
from System.Runtime.InteropServices import GCHandle, GCHandleType

_MAP_NP_NET = {
    np.dtype('float32'): System.Single,
    np.dtype('float64'): System.Double,
    np.dtype('int8')   : System.SByte,
    np.dtype('int16')  : System.Int16,
    np.dtype('int32')  : System.Int32,
    np.dtype('int64')  : System.Int64,
    np.dtype('uint8')  : System.Byte,
    np.dtype('uint16') : System.UInt16,
    np.dtype('uint32') : System.UInt32,
    np.dtype('uint64') : System.UInt64,
    np.dtype('bool')   : System.Boolean,
}
_MAP_NET_NP = {
    'Single' : np.dtype('float32'),
    'Double' : np.dtype('float64'),
    'SByte'  : np.dtype('int8'),
    'Int16'  : np.dtype('int16'), 
    'Int32'  : np.dtype('int32'),
    'Int64'  : np.dtype('int64'),
    'Byte'   : np.dtype('uint8'),
    'UInt16' : np.dtype('uint16'),
    'UInt32' : np.dtype('uint32'),
    'UInt64' : np.dtype('uint64'),
    'Boolean': np.dtype('bool'),
}

def asNumpyArray(netArray):
    '''
    Given a CLR `System.Array` returns a `numpy.ndarray`.  See _MAP_NET_NP for 
    the mapping of CLR types to Numpy dtypes.
    '''
    dims = np.empty(netArray.Rank, dtype=int)
    for I in range(netArray.Rank):
        dims[I] = netArray.GetLength(I)
    netType = netArray.GetType().GetElementType().Name

    try:
        npArray = np.empty(dims, order='C', dtype=_MAP_NET_NP[netType])
    except KeyError:
        raise NotImplementedError("asNumpyArray does not yet support System type {}".format(netType) )

    try: # Memmove 
        sourceHandle = GCHandle.Alloc(netArray, GCHandleType.Pinned)
        sourcePtr = sourceHandle.AddrOfPinnedObject().ToInt64()
        destPtr = npArray.__array_interface__['data'][0]
        ctypes.memmove(destPtr, sourcePtr, npArray.nbytes)
    finally:
        if sourceHandle.IsAllocated: sourceHandle.Free()
    return npArray

def asNetArray(npArray):
    '''
    Given a `numpy.ndarray` returns a CLR `System.Array`.  See _MAP_NP_NET for 
    the mapping of Numpy dtypes to CLR types.

    Note: `complex64` and `complex128` arrays are converted to `float32` 
    and `float64` arrays respectively with shape [m,n,...] -> [m,n,...,2]
    '''
    dims = npArray.shape
    dtype = npArray.dtype
    # For complex arrays, we must make a view of the array as its corresponding 
    # float type.
    if dtype == np.complex64:
        dtype = np.dtype('float32')
        dims.append(2)
        npArray = npArray.view(np.float32).reshape(dims)
    elif dtype == np.complex128:
        dtype = np.dtype('float64')
        dims.append(2)
        npArray = npArray.view(np.float64).reshape(dims)

    netDims = Array.CreateInstance(Int32, npArray.ndim)
    for I in range(npArray.ndim):
        netDims[I] = Int32(dims[I])
    
    if not npArray.flags.c_contiguous:
        npArray = npArray.copy(order='C')
    assert npArray.flags.c_contiguous

    try:
        netArray = Array.CreateInstance(_MAP_NP_NET[dtype], netDims)
    except KeyError:
        raise NotImplementedError("asNetArray does not yet support dtype {}".format(dtype))

    try: # Memmove 
        destHandle = GCHandle.Alloc(netArray, GCHandleType.Pinned)
        sourcePtr = npArray.__array_interface__['data'][0]
        destPtr = destHandle.AddrOfPinnedObject().ToInt64()
        ctypes.memmove(destPtr, sourcePtr, npArray.nbytes)
    finally:
        if destHandle.IsAllocated: destHandle.Free()
    return netArray

if __name__ == '__main__':
    from time import perf_counter
    import matplotlib.pyplot as plt
    import psutil

    tries = 1000
    foo = np.full([1024,1024], 2.5, dtype='float32')


    netMem = np.zeros(tries)
    t_asNet = np.zeros(tries)
    netFoo = asNetArray( foo ) # Lazy loading makes the first iteration very slow
    for I in range(tries):
        t0 = perf_counter()
        netFoo = asNetArray( foo )
        t_asNet[I] = perf_counter() - t0
        netMem[I] = psutil.virtual_memory().free / 2.0**20

    t_asNumpy = np.zeros(tries)
    numpyMem = np.zeros(tries)
    unNetFoo = asNumpyArray( netFoo ) # Lazy loading makes the first iteration very slow
    for I in range(tries):
        t0 = perf_counter()
        unNetFoo = asNumpyArray( netFoo )
        t_asNumpy[I] = perf_counter() - t0
        numpyMem[I] = psutil.virtual_memory().free / 2.0**20

    # Convert times to milliseconds
    t_asNet *= 1000
    t_asNumpy *= 1000
    np.testing.assert_array_almost_equal( unNetFoo, foo )
    print( "Numpy to .NET converted {} bytes in {:.3f} +/- {:.3f} ms (mean: {:.1f} ns/ele)".format( \
        foo.nbytes, t_asNet.mean(), t_asNet.std(), t_asNet.mean()/foo.size*1e6 ) )
    print( ".NET to Numpy converted {} bytes in {:.3f} +/- {:.3f} ms (mean: {:.1f} ns/ele)".format( \
        foo.nbytes, t_asNumpy.mean(), t_asNumpy.std(), t_asNumpy.mean()/foo.size*1e6 ) )

    plt.figure()
    plt.plot(np.arange(tries), netMem, '-', label='asNetArray')
    plt.plot(np.arange(tries), numpyMem, '-', label='asNumpyArray')
    plt.legend(loc='best')
    plt.ylabel('Free memory (MB)')
    plt.xlabel('Iteration')
    plt.show(block=True)

---

It is also worth noting that pythonnet has a new experimental feature, which seems promising: Codecs. Only relevant if you build from source and manage to figure out the documentation:

• customizing interop
• Codecs: customizing object marshalling between .NET and Python