/usr/lib/python2.7/dist-packages/neo/io/rawbinarysignalio.py is in python-neo 0.3.3-2.
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"""
Class for reading/writing data in a raw binary interleaved compact file.
Sampling rate, units, number of channel and dtype must be externally known.
This generic format is quite widely used in old acquisition systems and is quite universal
for sharing data.
Supported : Read/Write
Author: sgarcia
"""
import os
import numpy as np
import quantities as pq
from neo.io.baseio import BaseIO
from neo.core import Segment, AnalogSignal
from neo.io.tools import create_many_to_one_relationship
class RawBinarySignalIO(BaseIO):
"""
Class for reading/writing data in a raw binary interleaved compact file.
Usage:
>>> from neo import io
>>> r = io.RawBinarySignalIO( filename = 'File_ascii_signal_2.txt')
>>> seg = r.read_segment(lazy = False, cascade = True,)
>>> print seg.analogsignals # doctest: +ELLIPSIS, +NORMALIZE_WHITESPACE
...
"""
is_readable = True
is_writable = True
supported_objects = [Segment , AnalogSignal]
readable_objects = [ Segment]
writeable_objects = [Segment]
has_header = False
is_streameable = False
read_params = { Segment : [
('sampling_rate' , { 'value' : 1000. } ) ,
('nbchannel' , { 'value' : 16 } ),
('bytesoffset' , { 'value' : 0 } ),
('t_start' , { 'value' : 0. } ),
('dtype' , { 'value' : 'float32' , 'possible' : ['float32' , 'float64',
'int16' , 'uint16', 'int32' , 'uint32', ] } ),
('rangemin' , { 'value' : -10 } ),
('rangemax' , { 'value' : 10 } ),
]
}
write_params = { Segment : [
('bytesoffset' , { 'value' : 0 } ),
('dtype' , { 'value' : 'float32' , 'possible' : ['float32' , 'float64',
'int16' , 'uint16', 'int32' , 'uint32', ] } ),
('rangemin' , { 'value' : -10 } ),
('rangemax' , { 'value' : 10 } ),
]
}
name = None
extensions = [ 'raw' ]
mode = 'file'
def __init__(self , filename = None) :
"""
This class read a binary file.
**Arguments**
filename : the filename to read
"""
BaseIO.__init__(self)
self.filename = filename
def read_segment(self,
cascade = True,
lazy = False,
sampling_rate = 1.*pq.Hz,
t_start = 0.*pq.s,
unit = pq.V,
nbchannel = 1,
bytesoffset = 0,
dtype = 'f4',
rangemin = -10,
rangemax = 10,
):
"""
Reading signal in a raw binary interleaved compact file.
Arguments:
sampling_rate : sample rate
t_start : time of the first sample sample of each channel
unit: unit of AnalogSignal can be a str or directly a Quantities
nbchannel : number of channel
bytesoffset : nb of bytes offset at the start of file
dtype : dtype of the data
rangemin , rangemax : if the dtype is integer, range can give in volt the min and the max of the range
"""
seg = Segment(file_origin = os.path.basename(self.filename))
if not cascade:
return seg
dtype = np.dtype(dtype)
if type(sampling_rate) == float or type(sampling_rate)==int:
# if not quantitities Hz by default
sampling_rate = sampling_rate*pq.Hz
if type(t_start) == float or type(t_start)==int:
# if not quantitities s by default
t_start = t_start*pq.s
unit = pq.Quantity(1, unit)
if not lazy:
sig = np.memmap(self.filename, dtype = dtype, mode = 'r', offset = bytesoffset)
if sig.size % nbchannel != 0 :
sig = sig[:- sig.size%nbchannel]
sig = sig.reshape((sig.size/nbchannel,nbchannel))
if dtype.kind == 'i' :
sig = sig.astype('f')
sig /= 2**(8*dtype.itemsize)
sig *= ( rangemax-rangemin )
sig += ( rangemax+rangemin )/2.
elif dtype.kind == 'u' :
sig = sig.astype('f')
sig /= 2**(8*dtype.itemsize)
sig *= ( rangemax-rangemin )
sig += rangemin
sig_with_units = pq.Quantity(sig, units=unit, copy = False)
for i in range(nbchannel) :
if lazy:
signal = [ ]*unit
else:
signal = sig_with_units[:,i]
anaSig = AnalogSignal(signal, sampling_rate=sampling_rate,
t_start=t_start, channel_index=i, copy = False)
if lazy:
# TODO
anaSig.lazy_shape = None
seg.analogsignals.append(anaSig)
create_many_to_one_relationship(seg)
return seg
def write_segment(self, segment, dtype='f4', rangemin=-10,
rangemax=10, bytesoffset=0):
"""
**Arguments**
segment : the segment to write. Only analog signals will be written.
dtype : dtype of the data
rangemin , rangemax : if the dtype is integer, range can give in volt the min and the max of the range
"""
if bytesoffset:
raise NotImplementedError('bytesoffset values other than 0 ' +
'not supported')
dtype = np.dtype(dtype)
# all AnaologSignal from Segment must have the same length
for anasig in segment.analogsignals[1:]:
assert anasig.size == segment.analogsignals[0].size
sigs = np.empty((segment.analogsignals[0].size, len(segment.analogsignals)))
for i, anasig in enumerate(segment.analogsignals):
sigs[:, i] = anasig.magnitude
if dtype.kind == 'i':
sigs -= ( rangemax+rangemin )/2.
sigs /= (rangemax - rangemin)
sigs *= 2 ** (8 * dtype.itemsize )
elif dtype.kind == 'u' :
sigs -= rangemin
sigs /= (rangemax - rangemin)
sigs *= 2 ** (8 * dtype.itemsize)
sigs = sigs.astype(dtype)
f = open(self.filename, 'wb')
f.write(sigs.tostring())
f.close()
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