/usr/share/pyshared/neo/io/winedrio.py is in python-neo 0.2.0-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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"""
Classe for reading data from WinEdr, a software tool written by
John Dempster.
WinEdr is free:
http://spider.science.strath.ac.uk/sipbs/software.htm
Depend on:
Supported : Read
Author: sgarcia
"""
from .baseio import BaseIO
from ..core import *
from .tools import create_many_to_one_relationship
import numpy as np
from numpy import dtype, zeros, fromstring, empty
import quantities as pq
import sys
import os
import struct
PY3K = (sys.version_info[0] == 3)
class WinEdrIO(BaseIO):
"""
Class for reading data from WinEDR.
Usage:
>>> from neo import io
>>> r = io.WinEdrIO(filename='File_WinEDR_1.EDR')
>>> seg = r.read_segment(lazy=False, cascade=True,)
>>> print seg.analogsignals
[<AnalogSignal(array([ 89.21203613, 88.83666992, 87.21008301, ..., 64.56298828,
67.94128418, 68.44177246], dtype=float32) * pA, [0.0 s, 101.5808 s], sampling rate: 10000.0 Hz)>]
"""
is_readable = True
is_writable = False
supported_objects = [ Segment , AnalogSignal ]
readable_objects = [Segment]
writeable_objects = []
has_header = False
is_streameable = False
read_params = { Segment : [ ], }
write_params = None
name = 'WinEDR'
extensions = [ 'EDR' ]
mode = 'file'
def __init__(self , filename = None) :
"""
This class read a WinEDR file.
Arguments:
filename : the filename
"""
BaseIO.__init__(self)
self.filename = filename
def read_segment(self , lazy = False, cascade = True):
seg = Segment(
file_origin = os.path.basename(self.filename),
)
if not cascade:
return seg
fid = open(self.filename , 'rb')
headertext = fid.read(2048)
if PY3K:
headertext = headertext.decode('ascii')
header = {}
for line in headertext.split('\r\n'):
if '=' not in line : continue
#print '#' , line , '#'
key,val = line.split('=')
if key in ['NC', 'NR','NBH','NBA','NBD','ADCMAX','NP','NZ','ADCMAX' ] :
val = int(val)
if key in ['AD', 'DT', ] :
val = val.replace(',','.')
val = float(val)
header[key] = val
if not lazy:
data = np.memmap(self.filename , dtype('i2') , 'r',
#shape = (header['NC'], header['NP']) ,
shape = (header['NP']/header['NC'],header['NC'], ) ,
offset = header['NBH'])
for c in range(header['NC']):
YCF = float(header['YCF%d'%c].replace(',','.'))
YAG = float(header['YAG%d'%c].replace(',','.'))
YZ = float(header['YZ%d'%c].replace(',','.'))
ADCMAX = header['ADCMAX']
AD = header['AD']
DT = header['DT']
if 'TU' in header:
if header['TU'] == 'ms':
DT *= .001
unit = header['YU%d'%c]
try :
unit = pq.Quantity(1., unit)
except:
unit = pq.Quantity(1., '')
if lazy:
signal = [ ] * unit
else:
signal = (data[:,header['YO%d'%c]].astype('f4')-YZ) *AD/( YCF*YAG*(ADCMAX+1)) * unit
ana = AnalogSignal( signal,
sampling_rate = pq.Hz/DT,
t_start = 0.*pq.s,
name = header['YN%d'%c],
)
ana.annotate(channel_index = c)
if lazy:
ana.lazy_shape = header['NP']/header['NC']
seg.analogsignals.append(ana)
create_many_to_one_relationship(seg)
return seg
AnalysisDescription = [
('RecordStatus','8s'),
('RecordType','4s'),
('GroupNumber','f'),
('TimeRecorded','f'),
('SamplingInterval','f'),
('VMax','8f'),
]
class HeaderReader():
def __init__(self,fid ,description ):
self.fid = fid
self.description = description
def read_f(self, offset =0):
self.fid.seek(offset)
d = { }
for key, format in self.description :
val = struct.unpack(format , self.fid.read(struct.calcsize(format)))
if len(val) == 1:
val = val[0]
else :
val = list(val)
d[key] = val
return d
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