Mercurial > pylearn
view filetensor.py @ 347:3aa9e5a5802a
Automated merge with ssh://projects@lgcm.iro.umontreal.ca/hg/pylearn
author | Frederic Bastien <bastienf@iro.umontreal.ca> |
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date | Tue, 17 Jun 2008 14:46:15 -0400 |
parents | 82ba488b2c24 |
children | 040cb796f4e0 |
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""" Read and write the matrix file format described at U{http://www.cs.nyu.edu/~ylclab/data/norb-v1.0/index.html} The format is for dense tensors: - magic number indicating type and endianness - 4bytes - rank of tensor - int32 - dimensions - int32, int32, int32, ... - <data> The number of dimensions and rank is slightly tricky: - for scalar: rank=0, dimensions = [1, 1, 1] - for vector: rank=1, dimensions = [?, 1, 1] - for matrix: rank=2, dimensions = [?, ?, 1] For rank >= 3, the number of dimensions matches the rank exactly. @todo: add complex type support """ import sys import numpy def _prod(lst): p = 1 for l in lst: p *= l return p _magic_dtype = { 0x1E3D4C51 : ('float32', 4), #0x1E3D4C52 : ('packed matrix', 0), #what is a packed matrix? 0x1E3D4C53 : ('float64', 8), 0x1E3D4C54 : ('int32', 4), 0x1E3D4C55 : ('uint8', 1), 0x1E3D4C56 : ('int16', 2), } _dtype_magic = { 'float32': 0x1E3D4C51, #'packed matrix': 0x1E3D4C52, 'float64': 0x1E3D4C53, 'int32': 0x1E3D4C54, 'uint8': 0x1E3D4C55, 'int16': 0x1E3D4C56 } # # TODO: implement item selection: # e.g. load('some mat', subtensor=(:6, 2:5)) # # This function should be memory efficient by: # - allocating an output matrix at the beginning # - seeking through the file, reading subtensors from multiple places def read(f, subtensor=None, debug=False): """Load all or part of file 'f' into a numpy ndarray If f is a string, it will be treated as a filename, and opened in read mode. If subtensor is not None, it should be like the argument to numpy.ndarray.__getitem__. The following two expressions should return equivalent ndarray objects, but the one on the left may be faster and more memory efficient if the underlying file f is big. read(f, subtensor) <===> read(f)[*subtensor] Support for subtensors is currently spotty, so check the code to see if your particular type of subtensor is supported. """ def _read_int32(f): s = f.read(4) s_array = numpy.fromstring(s, dtype='int32') return s_array.item() if isinstance(f, str): if debug: print 'f', f f = file(f, 'r') #what is the data type of this matrix? #magic_s = f.read(4) #magic = numpy.fromstring(magic_s, dtype='int32') magic = _read_int32(f) magic_t, elsize = _magic_dtype[magic] if debug: print 'header magic', magic, magic_t, elsize if magic_t == 'packed matrix': raise NotImplementedError('packed matrix not supported') #what is the rank of the tensor? ndim = _read_int32(f) if debug: print 'header ndim', ndim #what are the dimensions of the tensor? dim = numpy.fromfile(f, dtype='int32', count=max(ndim,3))[:ndim] dim_size = _prod(dim) if debug: print 'header dim', dim, dim_size rval = None if subtensor is None: rval = numpy.fromfile(f, dtype=magic_t, count=_prod(dim)).reshape(dim) elif isinstance(subtensor, slice): if subtensor.step not in (None, 1): raise NotImplementedError('slice with step', subtensor.step) if subtensor.start not in (None, 0): bytes_per_row = _prod(dim[1:]) * elsize raise NotImplementedError('slice with start', subtensor.start) dim[0] = min(dim[0], subtensor.stop) rval = numpy.fromfile(f, dtype=magic_t, count=_prod(dim)).reshape(dim) else: raise NotImplementedError('subtensor access not written yet:', subtensor) return rval def write(f, mat): """Write a numpy.ndarray to file. If 'f' is a string, then it will be interpreted as a filename. This filename will be opened in 'w+' mode, and (automatically) closed at the end of the function. """ def _write_int32(f, i): i_array = numpy.asarray(i, dtype='int32') if 0: print 'writing int32', i, i_array i_array.tofile(f) if isinstance(f, str): f = file(f, 'w+') try: _write_int32(f, _dtype_magic[str(mat.dtype)]) except KeyError: raise TypeError('Invalid ndarray dtype for filetensor format', mat.dtype) _write_int32(f, len(mat.shape)) shape = mat.shape if len(shape) < 3: shape = list(shape) + [1] * (3 - len(shape)) if 0: print 'writing shape =', shape for sh in shape: _write_int32(f, sh) mat.tofile(f)