def parse(self):
self.sLC = {key:list() for key in self.keys()}
self.mdb_shape = {key:list() for key in self.keys()}
for mdb in self.mdb_list:
if mdb.is_flag_set('ACQEND') or mdb.is_flag_set('SYNCDATA'):
continue
for cat in list(self.keys())[:-1]:
if mdb.is_flag_set(cat):
self.get(cat).append(mdb)
self.sLC[cat].append(mdb.mdh['sLC'])
self.mdb_shape[cat].append([mdb.mdh['ushUsedChannels'], mdb.mdh['ushSamplesInScan']])
if mdb.is_image_scan():
self['IMASCAN'].append(mdb)
self.sLC['IMASCAN'].append(mdb.mdh['sLC'])
self.mdb_shape['IMASCAN'].append([mdb.mdh['ushUsedChannels'], mdb.mdh['ushSamplesInScan']])
for cat in list(self.keys()):
if len(self.get(cat))==0:
# remove empty categories
del(self[cat])
del(self.sLC[cat])
del(self.mdb_shape[cat])
else:
# add category to self
pass
def read_twix(infile, read_prot=True, keep_syncdata_and_acqend=True, include_scans=None):
"""Function for reading siemens twix raw data files."""
if isinstance(infile, str):
# assume that complete path is given
if infile[-4:].lower() != '.dat':
infile += '.dat' # adds filetype ending to file
else:
# filename not a string, so assume that it is the MeasID
measID = infile
infile = [f for f in os.listdir('.') if re.search(
r'^meas_MID0*' + str(measID) + '.*\.dat$', f)]
if len(infile) == 0:
print('error: .dat file with measID', measID, 'not found')
raise ValueError
elif len(infile) > 1:
print('multiple files with measID', measID,
'found, choosing first occurence')
infile = infile[0]
infile = os.path.realpath(infile)
fid = open(infile, 'rb')
fid.seek(0, os.SEEK_END)
fileSize = np.uint64(fid.tell())
version_is_ve, NScans = helpers.idea_version_check(fid)
out = list()
# lazy software version check (VB or VD?)
if version_is_ve:
print('Software version: VD/VE (!?)')
fid.seek(0, os.SEEK_SET) # move pos to 9th byte in file
raidfile_hdr = np.fromfile(fid, dtype=hdr_def.MultiRaidFileHeader, count=1)[0]
out.append(raidfile_hdr)
NScans = raidfile_hdr["hdr"]["count_"]
measOffset = list()
measLength = list()
for k in range(NScans):
measOffset.append(raidfile_hdr['entry'][k]['off_'])
measLength.append(raidfile_hdr['entry'][k]['len_'])
else:
# in VB versions, the first 4 bytes indicate the beginning of the
# raw data part of the file
print('Software : VB (!?)')
# VB does not support multiple scans in one file:
measOffset = [np.uint64(0)]
measLength = [fileSize]
print('')
for s in range(NScans):
if include_scans is not None and s not in include_scans:
# skip scan if it is not requested
continue
scanStart = measOffset[s]
scanEnd = scanStart + measLength[s]
pos = measOffset[s]
fid.seek(pos, os.SEEK_SET)
meas_init = np.fromfile(fid, dtype=hdr_def.SingleMeasInit, count=1)[0]
hdr_len = meas_init["hdr_len"]
out.append(dict())
if read_prot:
fid.seek(pos, os.SEEK_SET)
hdr = twixprot.parse_twix_hdr(fid)
out[-1]['init'] = meas_init
out[-1]['hdr'] = hdr
fid.seek(pos, os.SEEK_SET)
out[-1]['hdr_str'] = np.fromfile(fid, dtype="<S1", count=hdr_len)
# prot = twixprot(fid, hdr_len, version_is_ve)
# out[-1]['prot'] = prot
out[-1]['mdb'] = list()
pos = measOffset[s] + np.uint64(hdr_len)
scanStart = pos
print('Scan ', s)
helpers.update_progress(pos - scanStart, scanEnd - scanStart, True)
while pos + 128 < scanEnd: # fail-safe not to miss ACQEND
helpers.update_progress(pos - scanStart, scanEnd - scanStart, False)
fid.seek(pos, os.SEEK_SET)
mdb = twixtools.mdb.Mdb(fid, version_is_ve)
# jump to mdh of next scan
pos += mdb.dma_len
if not keep_syncdata_and_acqend:
if mdb.is_flag_set('SYNCDATA'):
continue
elif mdb.is_flag_set('ACQEND'):
break
out[-1]['mdb'].append(mdb)
if mdb.is_flag_set('ACQEND'):
break
print('')
fid.close()
return out
def write_twix(scanlist, outfile, version_is_ve=True):
def write_sync_bytes(fid):
syncbytes = (512-(fid.tell())%512)%512
fid.write(b'\x00' * syncbytes)
if isinstance(scanlist, dict):
scanlist = [scanlist]
with open(outfile, 'xb') as fid:
if version_is_ve:
# allocate space for multi-header
fid.write(b'\x00' * 10240)
scan_pos = list()
scan_len = list()
for key, scan in enumerate(scanlist):
if not isinstance(scan, dict):
continue
# keep track of byte pos
scan_pos.append(fid.tell())
# write header
scan['hdr_str'].tofile(fid)
# make sure that scan counters are consecutive integers
fix_scancounters(scan['mdb'])
# write mdbs
for mdb in scan['mdb']:
# write mdh
mdb.mdh.tofile(fid)
data = np.atleast_2d(mdb.data)
if version_is_ve:
if mdb.is_flag_set('SYNCDATA') or mdb.is_flag_set('ACQEND'):
data.tofile(fid)
else:
for c in range(data.shape[0]):
#write channel header
mdb.channel_hdr[c].tofile(fid)
# write data
data[c].tofile(fid)
else: # WIP: VB version
mdb.mdh.tofile(fid)
# write data
data[c].tofile(fid)
# update scan_len
scan_len.append(fid.tell() - scan_pos[-1])
# add sync bytes between scans
write_sync_bytes(fid)
# now write preallocated MultiRaidFileHeader
if version_is_ve:
n_scans = len(scan_pos)
if isinstance(scanlist[0], np.void):
# we have a template
multi_header = scanlist[0].copy()
else:
# start from scratch
multi_header = np.zeros(1, dtype=hdr_def.MultiRaidFileHeader)[0]
for _ in range(n_scans):
multi_header['entry']['patName_'] = b'x'*45
multi_header['entry']['protName_'] = b'noname'
# write NScans
multi_header['hdr']['count_'] = n_scans
# write scan_pos & scan_len for each scan
for i, (pos_, len_) in enumerate(zip(scan_pos, scan_len)):
multi_header['entry'][i]['len_'] = len_
multi_header['entry'][i]['off_'] = pos_
# write MultiRaidFileHeader
fid.seek(0)
multi_header.tofile(fid)