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PEP8 compliance #16

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PEP8 compliance #16

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93 changes: 48 additions & 45 deletions EDF.py
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Original file line number Diff line number Diff line change
Expand Up @@ -8,15 +8,17 @@
import re
import warnings


def padtrim(buf, num):
num -= len(buf)
if num>=0:
if num >= 0:
# pad the input to the specified length
return str(buf) + ' ' * num
else:
# trim the input to the specified length
return buf[0:num]


####################################################################################################
# the EDF header is represented as a tuple of (meas_info, chan_info)
# meas_info should have ['record_length', 'magic', 'hour', 'subject_id', 'recording_id', 'n_records', 'month', 'subtype', 'second', 'nchan', 'data_size', 'data_offset', 'lowpass', 'year', 'highpass', 'day', 'minute']
Expand Down Expand Up @@ -65,7 +67,6 @@ def close(self):
self.calibrate = None
self.offset = None
self.n_records = 0
return

def writeHeader(self, header):
meas_info = header[0]
Expand All @@ -76,18 +77,18 @@ def writeHeader(self, header):
assert(fid.tell() == 0)

# fill in the missing or incomplete information
if not 'subject_id' in meas_info:
if 'subject_id' not in meas_info:
meas_info['subject_id'] = ''
if not 'recording_id' in meas_info:
if 'recording_id' not in meas_info:
meas_info['recording_id'] = ''
if not 'subtype' in meas_info:
if 'subtype' not in meas_info:
meas_info['subtype'] = 'edf'
nchan = meas_info['nchan']
if not 'ch_names' in chan_info or len(chan_info['ch_names'])<nchan:
if 'ch_names' not in chan_info or len(chan_info['ch_names']) < nchan:
chan_info['ch_names'] = [str(i) for i in range(nchan)]
if not 'transducers' in chan_info or len(chan_info['transducers'])<nchan:
if 'transducers' not in chan_info or len(chan_info['transducers']) < nchan:
chan_info['transducers'] = ['' for i in range(nchan)]
if not 'units' in chan_info or len(chan_info['units'])<nchan:
if 'units' not in chan_info or len(chan_info['units']) < nchan:
chan_info['units'] = ['' for i in range(nchan)]

if meas_info['subtype'] in ('24BIT', 'bdf'):
Expand All @@ -111,11 +112,11 @@ def writeHeader(self, header):
chan_info[key] = np.asarray(chan_info[key])

for i in range(meas_info['nchan']):
fid.write(padtrim( chan_info['ch_names'][i], 16))
fid.write(padtrim(chan_info['ch_names'][i], 16))
for i in range(meas_info['nchan']):
fid.write(padtrim( chan_info['transducers'][i], 80))
fid.write(padtrim(chan_info['transducers'][i], 80))
for i in range(meas_info['nchan']):
fid.write(padtrim( chan_info['units'][i], 8))
fid.write(padtrim(chan_info['units'][i], 8))
for i in range(meas_info['nchan']):
fid.write(padtrim(str(chan_info['physical_min'][i]), 8))
for i in range(meas_info['nchan']):
Expand All @@ -125,22 +126,22 @@ def writeHeader(self, header):
for i in range(meas_info['nchan']):
fid.write(padtrim(str(chan_info['digital_max'][i]), 8))
for i in range(meas_info['nchan']):
fid.write(' ' * 80) # prefiltering
fid.write(' ' * 80) # prefiltering
for i in range(meas_info['nchan']):
fid.write(padtrim(str(chan_info['n_samps'][i]), 8))
for i in range(meas_info['nchan']):
fid.write(' ' * 32) # reserved
fid.write(' ' * 32) # reserved
meas_info['data_offset'] = fid.tell()

self.meas_info = meas_info
self.chan_info = chan_info
self.calibrate = (chan_info['physical_max'] - chan_info['physical_min'])/(chan_info['digital_max'] - chan_info['digital_min']);
self.offset = chan_info['physical_min'] - self.calibrate * chan_info['digital_min'];
self.calibrate = (chan_info['physical_max'] - chan_info['physical_min']) / (chan_info['digital_max'] - chan_info['digital_min'])
self.offset = chan_info['physical_min'] - self.calibrate * chan_info['digital_min']
channels = list(range(meas_info['nchan']))
for ch in channels:
if self.calibrate[ch]<0:
self.calibrate[ch] = 1;
self.offset[ch] = 0;
if self.calibrate[ch] < 0:
self.calibrate[ch] = 1
self.offset[ch] = 0

def writeBlock(self, data):
meas_info = self.meas_info
Expand All @@ -150,11 +151,11 @@ def writeBlock(self, data):
for i in range(meas_info['nchan']):
raw = deepcopy(data[i])

assert(len(raw)==chan_info['n_samps'][i])
if min(raw)<chan_info['physical_min'][i]:
warnings.warn('Value exceeds physical_min: ' + str(min(raw)) );
if max(raw)>chan_info['physical_max'][i]:
warnings.warn('Value exceeds physical_max: '+ str(max(raw)));
assert(len(raw) == chan_info['n_samps'][i])
if min(raw) < chan_info['physical_min'][i]:
warnings.warn('Value exceeds physical_min: ' + str(min(raw)))
if max(raw) > chan_info['physical_max'][i]:
warnings.warn('Value exceeds physical_max: ' + str(max(raw)))

raw -= self.offset[i] # FIXME I am not sure about the order of calibrate and offset
raw /= self.calibrate[i]
Expand All @@ -167,6 +168,7 @@ def writeBlock(self, data):

####################################################################################################


class EDFReader():
def __init__(self, fname=None):
self.fname = None
Expand Down Expand Up @@ -203,8 +205,8 @@ def readHeader(self):
meas_info['subject_id'] = fid.read(80).strip().decode() # subject id
meas_info['recording_id'] = fid.read(80).strip().decode() # recording id

day, month, year = [int(x) for x in re.findall('(\d+)', fid.read(8).decode())]
hour, minute, second = [int(x) for x in re.findall('(\d+)', fid.read(8).decode())]
day, month, year = [int(x) for x in re.findall(r'(\d+)', fid.read(8).decode())]
hour, minute, second = [int(x) for x in re.findall(r'(\d+)', fid.read(8).decode())]
meas_info['day'] = day
meas_info['month'] = month
meas_info['year'] = year
Expand Down Expand Up @@ -249,14 +251,14 @@ def readHeader(self):
chan_info['digital_max'] = digital_max = np.array([float(fid.read(8).decode()) for ch in channels])

prefiltering = [fid.read(80).strip().decode() for ch in channels][:-1]
highpass = np.ravel([re.findall('HP:\s+(\w+)', filt) for filt in prefiltering])
lowpass = np.ravel([re.findall('LP:\s+(\w+)', filt) for filt in prefiltering])
high_pass_default = 0.
highpass = np.ravel([re.findall(r'HP:\s+(\w+)', filt) for filt in prefiltering])
lowpass = np.ravel([re.findall(r'LP:\s+(\w+)', filt) for filt in prefiltering])
highpass_default = 0.
if highpass.size == 0:
meas_info['highpass'] = high_pass_default
meas_info['highpass'] = highpass_default
elif all(highpass):
if highpass[0] == 'NaN':
meas_info['highpass'] = high_pass_default
meas_info['highpass'] = highpass_default
elif highpass[0] == 'DC':
meas_info['highpass'] = 0.
else:
Expand All @@ -280,27 +282,27 @@ def readHeader(self):
# number of samples per record
chan_info['n_samps'] = n_samps = np.array([int(fid.read(8).decode()) for ch in channels])

fid.read(32 *meas_info['nchan']).decode() # reserved
fid.read(32 * meas_info['nchan']).decode() # reserved
assert fid.tell() == header_nbytes

if meas_info['n_records']==-1:
if meas_info['n_records'] == -1:
# this happens if the n_records is not updated at the end of recording
tot_samps = (os.path.getsize(self.fname)-meas_info['data_offset'])/meas_info['data_size']
meas_info['n_records'] = tot_samps/sum(n_samps)
tot_samps = (os.path.getsize(self.fname) - meas_info['data_offset']) / meas_info['data_size']
meas_info['n_records'] = tot_samps / sum(n_samps)

self.calibrate = (chan_info['physical_max'] - chan_info['physical_min'])/(chan_info['digital_max'] - chan_info['digital_min']);
self.offset = chan_info['physical_min'] - self.calibrate * chan_info['digital_min'];
self.calibrate = (chan_info['physical_max'] - chan_info['physical_min']) / (chan_info['digital_max'] - chan_info['digital_min'])
self.offset = chan_info['physical_min'] - self.calibrate * chan_info['digital_min']
for ch in channels:
if self.calibrate[ch]<0:
self.calibrate[ch] = 1;
self.offset[ch] = 0;
if self.calibrate[ch] < 0:
self.calibrate[ch] = 1
self.offset[ch] = 0

self.meas_info = meas_info
self.chan_info = chan_info
return (meas_info, chan_info)

def readBlock(self, block):
assert(block>=0)
assert(block >= 0)
meas_info = self.meas_info
chan_info = self.chan_info
data = []
Expand All @@ -309,7 +311,7 @@ def readBlock(self, block):
blocksize = np.sum(chan_info['n_samps']) * meas_info['data_size']
fid.seek(meas_info['data_offset'] + block * blocksize)
for i in range(meas_info['nchan']):
buf = fid.read(chan_info['n_samps'][i]*meas_info['data_size'])
buf = fid.read(chan_info['n_samps'][i] * meas_info['data_size'])
raw = np.asarray(unpack('<{}h'.format(chan_info['n_samps'][i]), buf), dtype=np.float32)
raw *= self.calibrate[i]
raw += self.offset[i] # FIXME I am not sure about the order of calibrate and offset
Expand All @@ -325,8 +327,8 @@ def readSamples(self, channel, begsample, endsample):
data = self.readBlock(begblock)[channel]
for block in range(begblock+1, endblock+1):
data = np.append(data, self.readBlock(block)[channel])
begsample -= begblock*n_samps
endsample -= begblock*n_samps
begsample -= begblock * n_samps
endsample -= begblock * n_samps
return data[begsample:(endsample+1)]

####################################################################################################
Expand All @@ -348,12 +350,13 @@ def getNSamples(self):
return self.chan_info['n_samps'] * self.meas_info['n_records']

def readSignal(self, chanindx):
begsample = 0;
endsample = self.chan_info['n_samps'][chanindx] * self.meas_info['n_records'] - 1;
begsample = 0
endsample = self.chan_info['n_samps'][chanindx] * self.meas_info['n_records'] - 1
return self.readSamples(chanindx, begsample, endsample)

####################################################################################################


if False:
file_in = EDFReader()
file_in.open('/Users/roboos/day 01[10.03].edf')
Expand Down