IPKM/python-damaris
3
0
Fork 0
Code Issues 6 Pull Requests Actions Packages Activity

modifications to write_to_tecmag, allow 2D experiments (by Oleg Petrov)

Browse Source
This commit is contained in:
Markus Rosenstihl 2016-02-15 12:42:45 +00:00
parent eed1d10f63
commit 6dc67edaaf
1 changed files with 50 additions and 45 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

77
src/data/Accumulation.py
View File

@ -279,40 +279,55 @@ class Accumulation(Errorable, Drawable, DamarisFFT, Signalpath):
# ------------- added by Oleg Petrov, 10 Sep 2013 ----------------------- # ------------- added by Oleg Petrov, 10 Sep 2013 -----------------------
def write_to_tecmag(self, destination=sys.stdout, nrecords=1,\ def write_to_tecmag(self, destination=sys.stdout, nrecords=1,\
frequency=100e6,\ frequency=100.,\
last_delay = 1.,\ last_delay = 1.,\
receiver_phase=0.,\ receiver_phase=0.,\
nucleus='1H'): nucleus='1H'):
""" """
writes the data to a binary file in TecMag format; writes the data to a binary file in TecMag format;
destination can be a file object or a filename; destination can be a file object or a filename;
nrecords determines the 2nd dimension of data; nrecords determines an indirect dimension in 2D experiments;
""" """
if self.job_id == None or self.n == 0: if self.job_id == None or self.n == 0:
raise ValueError("write_to_tecmag: cannot get a record number") raise ValueError("write_to_tecmag: cannot get a record number")
else: else:
record = self.job_id/self.n + 1 record = (self.job_id/self.n)%nrecords + 1
the_destination=destination the_destination=destination
if type(destination) in types.StringTypes: if type(destination) in types.StringTypes:
if record == 1 and os.path.exists(destination): if record == 1 and os.path.exists(destination):
os.rename(destination, os.path.dirname(destination)+'/~'+os.path.basename(destination)) os.rename(destination, os.path.dirname(destination)+'/~'+os.path.basename(destination))
the_destination=file(destination, "ab")
self.lock.acquire() self.lock.acquire()
try: try:
npts = [len(self), nrecords, 1, 1] npts = [len(self), nrecords, 1, 1]
data_offset = 2*4*npts[0]*npts[1]*npts[2]*npts[3] # length of data section
dwell = 1./self.get_sampling_rate() dwell = 1./self.get_sampling_rate()
sw = 0.5/dwell sw = 0.5/dwell
base_freq = [frequency, 100., 0., 0.] base_freq = [frequency, frequency, 0., 0.]
offset_freq = [0., 0., 0., 0.] offset_freq = [0., 0., 0., 0.]
ob_freq = [sum(x) for x in zip(base_freq, offset_freq)] ob_freq = [sum(x) for x in zip(base_freq, offset_freq)]
date = self.time_period[0].strftime("%Y/%m/%d %H:%M:%S") date = self.time_period[0].strftime("%Y/%m/%d %H:%M:%S")
# data handling:
ch_no=self.get_number_of_channels()
ydata = map(self.get_ydata, xrange(ch_no))
if ch_no == 1:
ydata = [ydata, numpy.zeros(len(ydata))]
# data is arranged in RIRIRIRI blocks in linear order:
data = numpy.append([ydata[0]], [ydata[1]], axis=0)
data = data.T
data = data.flatten()
if record == 1: if record == 1:
buff = ctypes.create_string_buffer(1056) the_destination=file(destination, "wb")
# allocate space for all records in advance:
buff = ctypes.create_string_buffer(1056+data_offset+2068)
struct.pack_into('8s', buff, 0, 'TNT1.005') # 'TNT1.000' version ID struct.pack_into('8s', buff, 0, 'TNT1.005') # 'TNT1.000' version ID
struct.pack_into('4s', buff, 8, 'TMAG') # 'TMAG' tag struct.pack_into('4s', buff, 8, 'TMAG') # 'TMAG' tag
@ -335,8 +350,8 @@ class Accumulation(Errorable, Drawable, DamarisFFT, Signalpath):
struct.pack_into('h', buff, 216, 1) # obs_channel struct.pack_into('h', buff, 216, 1) # obs_channel
struct.pack_into('42s', buff, 218, 42*'2') # space2[42] struct.pack_into('42s', buff, 218, 42*'2') # space2[42]
struct.pack_into('4d', buff, 260, sw, 0., 0., 0.) # sw[4], sw = 0.5/dwell struct.pack_into('4d', buff, 260, sw, sw, 0., 0.) # sw[4], sw = 0.5/dwell
struct.pack_into('4d', buff, 292, dwell, 0., 0., 0.) # dwell[4] struct.pack_into('4d', buff, 292, dwell, dwell, 0., 0.) # dwell[4]
struct.pack_into('d', buff, 324, sw) # filter, = 0.5/dwell struct.pack_into('d', buff, 324, sw) # filter, = 0.5/dwell
struct.pack_into('d', buff, 340, (npts[0]*dwell)) # acq_time struct.pack_into('d', buff, 340, (npts[0]*dwell)) # acq_time
struct.pack_into('d', buff, 348, 1.) # last_delay (5*T1 minus sequence length) struct.pack_into('d', buff, 348, 1.) # last_delay (5*T1 minus sequence length)
@ -354,42 +369,32 @@ class Accumulation(Errorable, Drawable, DamarisFFT, Signalpath):
struct.pack_into('4s', buff, 1044, 'DATA') # 'DATA' tag struct.pack_into('4s', buff, 1044, 'DATA') # 'DATA' tag
struct.pack_into('?', buff, 1048, True) # BOOLean struct.pack_into('?', buff, 1048, True) # BOOLean
struct.pack_into('i', buff, 1052, 2*4*npts[0]*npts[1]) # length of data (2 = [Re, Im]; 4 = len(c_float)) struct.pack_into('i', buff, 1052, data_offset) # length of data
the_destination.write(buff) struct.pack_into('%sf' % (2*npts[0]), buff, 1056, *data) # actual data (one record)
# append data to the file as they appear in an experiment (RIRIRIRI blocks in linear order): struct.pack_into('4s', buff, 1056+data_offset, 'TMG2') # 'TMG2' tag
ch_no=self.get_number_of_channels() struct.pack_into('?', buff, 1056+data_offset+4, True) # BOOLean
struct.pack_into('i', buff, 1056+data_offset+8, 2048) # length of Tecmag2 struct
ydata = map(self.get_ydata, xrange(ch_no))
if ch_no == 1:
ydata = [ydata, numpy.zeros(len(ydata))]
data = numpy.append([ydata[0]], [ydata[1]], axis=0)
data = data.T
data = data.flatten()
buff = ctypes.create_string_buffer(4*len(data))
struct.pack_into('%sf' % len(data), buff, 0, *data)
the_destination.write(buff)
if record == nrecords:
buff = ctypes.create_string_buffer(2068)
struct.pack_into('4s', buff, 0, 'TMG2') # 'TMG2' tag
struct.pack_into('?', buff, 4, True) # BOOLean
struct.pack_into('i', buff, 8, 2048) # length of Tecmag2 struct
# Leave TECMAG2 structure empty: # Leave TECMAG2 structure empty:
struct.pack_into('52s', buff, 372, 52*'2') # space[52] struct.pack_into('52s', buff, 1056+data_offset+372, 52*'2') # space[52]
struct.pack_into('866s', buff, 1194, 866*'2') # space[610]+names+strings struct.pack_into('866s', buff, 1056+data_offset+1194, 866*'2') # space[610]+names+strings
# TECMAG2 Structure total => 2048 # TECMAG2 Structure total => 2048
struct.pack_into('4s', buff, 2060, 'PSEQ') # 'PSEQ' tag 658476 struct.pack_into('4s', buff, 1056+data_offset+2060, 'PSEQ') # 'PSEQ' tag 658476
struct.pack_into('?', buff, 2064, False) # BOOLean 658480 struct.pack_into('?', buff, 1056+data_offset+2064, False) # BOOLean 658480
the_destination.write(buff) the_destination.write(buff)
else:
the_destination=file(destination, "rb+")
buff = ctypes.create_string_buffer(4*2*npts[0])
struct.pack_into('%sf' % (2*npts[0]), buff, 0, *data)
the_destination.seek(1056+4*2*npts[0]*(record-1))
the_destination.write(buff)
the_destination = None the_destination = None
ydata=None ydata=None
@ -560,7 +565,7 @@ class Accumulation(Errorable, Drawable, DamarisFFT, Signalpath):
r = Accumulation(x = numpy.array(self.x, dtype="Float64"), y = tmp_y, y_2 = tmp_ysquare, n = self.n, index = self.index, sampl_freq = self.sampling_rate, error = self.use_error) r = Accumulation(x = numpy.array(self.x, dtype="Float64"), y = tmp_y, y_2 = tmp_ysquare, n = self.n, index = self.index, sampl_freq = self.sampling_rate, error = self.use_error)
else: else:
r = Accumulation(x = numpy.array(self.x, dtype="Float64"), y = tmp_y, n = self.n, index = self.index, sampl_freq = self.sampling_rate, error = self.use_error) r = Accumulation(x = numpy.array(self.x, dtype="Float64"), y = tmp_y, n = self.n, index = self.index, sampl_freq = self.sampling_rate, error = self.use_error)
r.job_id = self.job_id # added by Oleg Petrov
self.lock.release() self.lock.release()
return r return r