def info(self):
d = super(ThermoDXF, self).info
#try: #TODO: this crashes in python 3; not clear why?
#except:
# pass
#info['file name'] = os.path.basename(self.filename)
d['name'] = os.path.splitext(os.path.basename(self.filename))[0]
with open(self.filename, 'rb') as f:
foff_o = find_offset(f, 'd 18O/16O'.encode('utf_16_le'))
foff_c = find_offset(f, 'd 13C/12C'.encode('utf_16_le'))
if foff_o is not None:
f.seek(foff_o + 68)
d['d18o_std'] = str(struct.unpack('<d', f.read(8))[0])
if foff_c is not None:
f.seek(foff_c + 68)
d['d13c_std'] = str(struct.unpack('<d', f.read(8))[0])
return d
def data(self):
f = open(self.filename, 'rb')
#TODO: use find_offset to find this?
#f.seek(11)
#while True:
# f.seek(f.tell() - 11)
# if f.read(11) == b'CEvalGCData':
# break
# if f.read(1) == b'':
# f.close()
# return
f.seek(find_offset(f, b'CRawData') + 9)
strlen = 2 * struct.unpack('<B', f.read(1))[0]
tname = f.read(strlen).decode('utf_16_le')
if tname == 'CO2':
ions = [44, 45, 46]
elif tname == 'CO':
ions = [28, 29, 30]
elif tname == 'SO2,SO-SO2 Ext,SO':
#TODO: check this is in the right order
ions = [48, 49, 50, 64, 65, 66]
else:
#TODO: should save the tname somewhere for future reference
ions = [1, 2, 3]
f.seek(find_offset(f, b'CEvalGCData') + 4)
#bytes until the end converted to # of records
nscans = int(struct.unpack('<I', f.read(4))[0] / \
(4.0 + len(ions) * 8.0))
dtype = np.dtype([('index', '<f4'), ('values', '<f8', len(ions))])
data = np.fromfile(f, dtype=dtype, count=nscans)
# convert time to minutes
data['index'] /= 60.
f.close()
return AstonFrame(data['values'], data['index'], ions)
def data(self):
#TODO: handle skip mass ranges
with open(self.filename, 'rb') as f:
# read in the time segments/mz ranges for the run
# read in the data itself
doff = find_offset(f, 4 * b'\xff' + 'HapsScan'.encode('ascii'))
if doff is None:
return
f.seek(doff - 20)
data_end = doff + struct.unpack('<I', f.read(4))[0] + 55
f.seek(doff + 56)
times, abns, mzs = [], [], []
cur_seg = None
mz_reader = self._ions(f)
while f.tell() <= data_end:
# record info looks like a standard format
n, t, _, recs, _, seg = struct.unpack('<IiHHHH', f.read(16))
if cur_seg != seg:
# if we've switched segments, update the list of mzs
try:
cur_mzs = next(mz_reader)
except StopIteration:
break
mzs += set(cur_mzs).difference(mzs)
mz_idx = [mzs.index(i) for i in cur_mzs]
cur_seg = seg
# just add the new time in
times.append(t)
# read the list of abundances
cur_abns = struct.unpack('<' + 'f' * recs, f.read(4 * recs))
# convert this list into an array that matches up with
# whatever mzs we currently have
empty_row = np.zeros(len(mzs))
empty_row[mz_idx] = cur_abns
# add that row into the list
abns.append(empty_row)
# convert the time from milliseconds to minutes
times = np.array(times, dtype=float) / 60000
# create the data array and populate it
data = np.zeros((len(times), len(mzs)))
for i, r in enumerate(abns):
data[i, 0:len(r)] = r
return AstonFrame(data, times, mzs)
def _ions(self, f):
"""
This is a generator that returns the mzs being measured during
each time segment, one segment at a time.
"""
outside_pos = f.tell()
doff = find_offset(f, 4 * b'\xff' + 'HapsSearch'.encode('ascii'))
# actual end of prev section is 34 bytes before, but assume 1 rec
f.seek(doff - 62)
# seek backwards to find the FFFFFFFF header
while True:
f.seek(f.tell() - 8)
if f.read(4) == 4 * b'\xff':
break
f.seek(f.tell() + 64)
nsegments = struct.unpack('<I', f.read(4))[0]
for _ in range(nsegments):
# first 32 bytes are segment name, rest are something else?
f.seek(f.tell() + 96)
nions = struct.unpack('<I', f.read(4))[0]
ions = []
for _ in range(nions):
#TODO: check that itype is actually a SIM/full scan switch
i1, i2, _, _, _, _, itype, _ = \
struct.unpack('<' + 8 * 'I', f.read(32))
if itype == 0: # SIM
ions.append(i1 / 100.)
else: # full scan
#TODO: this might be a little hacky?
# ideally we would need to know n for this, e.g.:
#ions += np.linspace(i1 / 100, i2 / 100, n).tolist()
ions += np.arange(i1 / 100., i2 / 100. + 1, 1).tolist()
# save the file position and load the position
# that we were at before we started this code
inside_pos = f.tell()
f.seek(outside_pos)
yield ions
outside_pos = f.tell()
f.seek(inside_pos)
f.seek(outside_pos)
