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arfread.py
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arfread.py
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import struct
import numpy as np
def arfread(PATH, PLOT=False, RP=False):
def get_str(byte_str):
null_char_idx = byte_str.find(b'\x00')
if null_char_idx > 0:
return byte_str[:null_char_idx].decode('utf-8')
return byte_str.decode('utf-8')
isRZ = not RP
data = {
'RecHead': {},
'groups': []
}
with open(PATH, 'rb') as file:
data['RecHead']['ftype'] = struct.unpack('h', file.read(2))[0]
data['RecHead']['ngrps'] = struct.unpack('h', file.read(2))[0]
data['RecHead']['nrecs'] = struct.unpack('h', file.read(2))[0]
data['RecHead']['grpseek'] = struct.unpack('200i', file.read(800))
data['RecHead']['recseek'] = struct.unpack('2000i', file.read(8000))
data['RecHead']['file_ptr'] = struct.unpack('i', file.read(4))[0]
bFirstPass = True
for x in range(data['RecHead']['ngrps']):
file.seek(data['RecHead']['grpseek'][x], 0)
group = {
'grpn': struct.unpack('h', file.read(2))[0],
'frecn': struct.unpack('h', file.read(2))[0],
'nrecs': struct.unpack('h', file.read(2))[0],
'ID': get_str(file.read(16)),
'ref1': get_str(file.read(16)),
'ref2': get_str(file.read(16)),
'memo': get_str(file.read(50))
}
if bFirstPass:
if isRZ:
ttt = struct.unpack('q', file.read(8))[0]
file.seek(-8, 1)
data['fileType'] = 'BioSigRZ'
else:
ttt = struct.unpack('I', file.read(4))[0]
file.seek(-4, 1)
data['fileType'] = 'BioSigRP'
data['fileTime'] = str(np.datetime64('1970-01-01') + np.timedelta64(ttt, 's'))
bFirstPass = False
if isRZ:
group['beg_t'] = struct.unpack('q', file.read(8))[0]
group['end_t'] = struct.unpack('q', file.read(8))[0]
else:
group['beg_t'] = struct.unpack('i', file.read(4))[0]
group['end_t'] = struct.unpack('i', file.read(4))[0]
group['sgfname1'] = get_str(file.read(100))
group['sgfname2'] = get_str(file.read(100))
group['VarName1'] = get_str(file.read(15))
group['VarName2'] = get_str(file.read(15))
group['VarName3'] = get_str(file.read(15))
group['VarName4'] = get_str(file.read(15))
group['VarName5'] = get_str(file.read(15))
group['VarName6'] = get_str(file.read(15))
group['VarName7'] = get_str(file.read(15))
group['VarName8'] = get_str(file.read(15))
group['VarName9'] = get_str(file.read(15))
group['VarName10'] = get_str(file.read(15))
group['VarUnit1'] = get_str(file.read(5))
group['VarUnit2'] = get_str(file.read(5))
group['VarUnit3'] = get_str(file.read(5))
group['VarUnit4'] = get_str(file.read(5))
group['VarUnit5'] = get_str(file.read(5))
group['VarUnit6'] = get_str(file.read(5))
group['VarUnit7'] = get_str(file.read(5))
group['VarUnit8'] = get_str(file.read(5))
group['VarUnit9'] = get_str(file.read(5))
group['VarUnit10'] = get_str(file.read(5))
group['SampPer_us'] = struct.unpack('f', file.read(4))[0]
group['cc_t'] = struct.unpack('i', file.read(4))[0]
group['version'] = struct.unpack('h', file.read(2))[0]
group['postproc'] = struct.unpack('i', file.read(4))[0]
group['dump'] = get_str(file.read(92))
group['recs'] = []
for i in range(group['nrecs']):
rec = {
'recn': struct.unpack('h', file.read(2))[0],
'grpid': struct.unpack('h', file.read(2))[0]
}
if isRZ:
rec['grp_t'] = struct.unpack('q', file.read(8))[0]
else:
rec['grp_t'] = struct.unpack('i', file.read(4))[0]
rec['grp_d'] = str(np.datetime64('1970-01-01') + np.timedelta64(rec['grp_t'], 's'))
rec['newgrp'] = struct.unpack('h', file.read(2))[0]
rec['sgi'] = struct.unpack('h', file.read(2))[0]
rec['chan'] = struct.unpack('B', file.read(1))[0]
rec['rtype'] = get_str(file.read(1))
if isRZ:
rec['npts'] = struct.unpack('H', file.read(2))[0]
else:
rec['npts'] = struct.unpack('h', file.read(2))[0]
rec['osdel'] = struct.unpack('f', file.read(4))[0]
rec['dur_ms'] = struct.unpack('f', file.read(4))[0]
rec['SampPer_us'] = struct.unpack('f', file.read(4))[0]
rec['artthresh'] = struct.unpack('f', file.read(4))[0]
rec['gain'] = struct.unpack('f', file.read(4))[0]
rec['accouple'] = struct.unpack('h', file.read(2))[0]
rec['navgs'] = struct.unpack('h', file.read(2))[0]
rec['narts'] = struct.unpack('h', file.read(2))[0]
if isRZ:
rec['beg_t'] = struct.unpack('q', file.read(8))[0]
rec['end_t'] = struct.unpack('q', file.read(8))[0]
else:
rec['beg_t'] = struct.unpack('i', file.read(4))[0]
rec['end_t'] = struct.unpack('i', file.read(4))[0]
rec['Var1'] = struct.unpack('f', file.read(4))[0]
rec['Var2'] = struct.unpack('f', file.read(4))[0]
rec['Var3'] = struct.unpack('f', file.read(4))[0]
rec['Var4'] = struct.unpack('f', file.read(4))[0]
rec['Var5'] = struct.unpack('f', file.read(4))[0]
rec['Var6'] = struct.unpack('f', file.read(4))[0]
rec['Var7'] = struct.unpack('f', file.read(4))[0]
rec['Var8'] = struct.unpack('f', file.read(4))[0]
rec['Var9'] = struct.unpack('f', file.read(4))[0]
rec['Var10'] = struct.unpack('f', file.read(4))[0]
# skip all 10 cursors placeholders
file.seek(36 * 10, 1)
rec_data = struct.unpack(f'{rec["npts"]}f', file.read(4 * rec['npts']))
rec['data'] = list(rec_data)
group['recs'].append(rec)
data['groups'].append(group)
if PLOT:
import matplotlib.pyplot as plt
for group in data['groups']:
plt.figure()
plot_offset = max([max(np.abs(rec['data'])) for rec in group['recs']]) * 1.2
for rec in group['recs']:
plt.plot(np.array(rec['data']) - plot_offset * group['recs'].index(rec))
plt.title(f'Group {group["grpn"]}')
plt.axis('off')
return data