def __setitem__(self, wavelength, intensity):
index, = pylab.where(self.wavelengths == wavelength)
if pylab.any(index.shape):
self.intensities[index] = intensity
else:
index, = pylab.where(self.wavelengths < wavelength)
if pylab.any(index.shape):
self.wavelengths = pylab.insert(self.wavelengths, index[-1] + 1,
wavelength)
self.intensities = pylab.insert(self.intensities, index[-1] + 1,
intensity)
else:
self.wavelengths = pylab.insert(self.wavelengths, 0, wavelength)
self.intensities = pylab.insert(self.intensities, 0, intensity)
def read_csc(fin, assume_same_fs=True):
"""Read a continuous record file. We return the raw packets but, in addition, if we set assume_same_fs as true we
return a trace with all the data concatenated together, assuming that a constant sampling frequency was maintained
through out. Gaps in the record are padded with zeros.
Input:
fin - file handle
assume_same_fs - if True, concatenate any segments together, fill time gaps with zeros and return average Fs
Ouput:
Dictionary with fields
'header' - the file header
'packets' - the actual packets as read. This is a new pylab dtype with fields:
'timestamp' - timestamp (us)
'chan' - channel
'Fs' - the sampling frequency
'Ns' - the number of valid samples in the packet
'samp' - the samples in the packet.
e.g. x['packets']['samp'] will return a 2D array, number of packets long and 512 wide (since each packet carries 512 wave points)
similarly x['packets']['timestamp'] will return an array number of packets long
'Fs': the average frequency computed from the timestamps (can differ from the nominal frequency the device reports)
'trace': the concatenated data from all the packets
't0': the timestamp of the first packet.
NOTE: while 'packets' returns the exact packets read, 'Fs' and 'trace' assume that the record has no gaps and that the
sampling frequency has not changed during the recording
"""
hdr = read_header(fin)
csc_packet = pylab.dtype([
('timestamp', 'Q'),
('chan', 'I'),
('Fs', 'I'),
('Ns', 'I'),
('samp', '512h')
])
data = pylab.fromfile(fin, dtype=csc_packet, count=-1)
Fs = None
trace = None
if assume_same_fs:
if data['Fs'].std() > 1e-6: #
logger.warning('Fs is not fixed across trace, not packing packets together')
assume_same_fs = False
if not assume_same_fs: return {'header': hdr, 'packets': data}
packet_duration_us = 512*(1./data['Fs'][0])*1e6
#For the version we are dealing with, Neuralynx packets are always 512
#This is actually a very poor estimate if the sampling freq is low, since it rounds to nearest Hz
#So we'll not rely on this but come up with our own estimate
samp = data['samp']
ts_us = data['timestamp']
dt_us = pylab.diff(ts_us).astype('f')
idx = pylab.find(dt_us > packet_duration_us) #This will find any instances where we paused the recording
if idx.size == 0:#No padding needed
trace = samp.ravel()
Fs = (data['Ns'][:-1]/(dt_us*1e-6)).mean()
else: #We have some padding to do.
logger.debug('Gaps in record, padding')
#Our first task is to find all the contiguous sections of data
idx += 1 #Shifting indexes to point at the packets that come after a gap
idx = pylab.insert(idx, 0, 0) #Now idx contains the indexes of every packet that starts a contiguous section
idx = pylab.append(idx,ts_us.size) #And the index of the last packet
Ns = data['Ns']
estimFs_sum = 0
N_samps = 0
sections = []
for n in xrange(idx.size-1): #collect all the sections
n0 = idx[n]; n1=idx[n+1]
sections.append(samp[n0:n1].ravel())
if n1-n0 > 1:#We need more than one packet in a section to get an estimate
estimFs_sum += (Ns[n0:n1-1]/(dt_us[n0:n1-1]*1e-6)).sum()
N_samps += n1-1-n0
Fs = estimFs_sum / float(N_samps)
#Now pad the data appropriately
padded = [sections[0]]
cum_N = sections[0].size
for n in xrange(1,len(sections)):
#Now figure out how many zeros we have to pad to get the right length
Npad = int((ts_us[idx[n]] - ts_us[0])*1e-6*Fs - cum_N)
padded.append(pylab.zeros(Npad))
padded.append(sections[n])
cum_N += Npad + sections[n].size
trace = pylab.concatenate(padded) #From this packet to the packet before the gap
return {'header': hdr, 'packets': data, 'Fs': Fs, 'trace': trace, 't0': ts_us[0]}
print(len(rho), len(beta), len(d))
N = np.ones_like(rho) * 2
mif.create_layers(N, d, rho, beta)
N = len(rho)
print(N)
mif.evolve(qmax=qmax,
iplot=10,
iprint=3,
deltam=0.001,
avg=3,
saveFig=True,
dir=dir + 'Images/')
x = mif.x
y = mif.y
yerr = mif.y_err
#z=mif.z
q = np.arange(data[0, 0], data[-1, 0], 0.001)
fit = mif.func(q)
rho = mif.rhol
z = mif.z
print(len(rho), len(z))
#fit_fname=fname.split('.')[0]+'_fit1.txt'
fit_fname = fname + '_fit1.txt'
#rho_fname=fname.split('.')[0]+'_edp1.txt'
rho_fname = fname + '_edp1.txt'
edp = np.vstack((z, rho)).transpose()
edp = pl.insert(edp, 0, [z[0] - 20, rho[0]], axis=0)
edp[-1, 0] = z[-1] + 20
np.savetxt(dir + fit_fname, np.vstack((q, fit)).transpose())
np.savetxt(dir + rho_fname, edp)
def read_csc(fin, assume_same_fs=True):
"""Read a continuous record file. We return the raw packets but, in addition, if we set assume_same_fs as true we
return a trace with all the data concatenated together, assuming that a constant sampling frequency was maintained
through out. Gaps in the record are padded with zeros.
Input:
fin - file handle
assume_same_fs - if True, concatenate any segments together, fill time gaps with zeros and return average Fs
Ouput:
Dictionary with fields
'header' - the file header
'packets' - the actual packets as read. This is a new pylab dtype with fields:
'timestamp' - timestamp (us)
'chan' - channel
'Fs' - the sampling frequency
'Ns' - the number of valid samples in the packet
'samp' - the samples in the packet.
e.g. x['packets']['samp'] will return a 2D array, number of packets long and 512 wide (since each packet carries 512 wave points)
similarly x['packets']['timestamp'] will return an array number of packets long
'Fs': the average frequency computed from the timestamps (can differ from the nominal frequency the device reports)
'trace': the concatenated data from all the packets
't0': the timestamp of the first packet.
NOTE: while 'packets' returns the exact packets read, 'Fs' and 'trace' assume that the record has no gaps and that the
sampling frequency has not changed during the recording
"""
hdr = read_header(fin)
csc_packet = pylab.dtype([('timestamp', 'Q'), ('chan', 'I'), ('Fs', 'I'),
('Ns', 'I'), ('samp', '512h')])
data = pylab.fromfile(fin, dtype=csc_packet, count=-1)
Fs = None
trace = None
if assume_same_fs:
if data['Fs'].std() > 1e-6: #
logger.warning(
'Fs is not fixed across trace, not packing packets together')
assume_same_fs = False
if not assume_same_fs: return {'header': hdr, 'packets': data}
packet_duration_us = 512 * (1. / data['Fs'][0]) * 1e6
#For the version we are dealing with, Neuralynx packets are always 512
#This is actually a very poor estimate if the sampling freq is low, since it rounds to nearest Hz
#So we'll not rely on this but come up with our own estimate
samp = data['samp']
ts_us = data['timestamp']
dt_us = pylab.diff(ts_us).astype('f')
idx = pylab.find(
dt_us > packet_duration_us
) #This will find any instances where we paused the recording
if idx.size == 0: #No padding needed
trace = samp.ravel()
Fs = (data['Ns'][:-1] / (dt_us * 1e-6)).mean()
else: #We have some padding to do.
logger.debug('Gaps in record, padding')
#Our first task is to find all the contiguous sections of data
idx += 1 #Shifting indexes to point at the packets that come after a gap
idx = pylab.insert(
idx, 0, 0
) #Now idx contains the indexes of every packet that starts a contiguous section
idx = pylab.append(idx, ts_us.size) #And the index of the last packet
Ns = data['Ns']
estimFs_sum = 0
N_samps = 0
sections = []
for n in xrange(idx.size - 1): #collect all the sections
n0 = idx[n]
n1 = idx[n + 1]
sections.append(samp[n0:n1].ravel())
if n1 - n0 > 1: #We need more than one packet in a section to get an estimate
estimFs_sum += (Ns[n0:n1 - 1] /
(dt_us[n0:n1 - 1] * 1e-6)).sum()
N_samps += n1 - 1 - n0
Fs = estimFs_sum / float(N_samps)
#Now pad the data appropriately
padded = [sections[0]]
cum_N = sections[0].size
for n in xrange(1, len(sections)):
#Now figure out how many zeros we have to pad to get the right length
Npad = int((ts_us[idx[n]] - ts_us[0]) * 1e-6 * Fs - cum_N)
padded.append(pylab.zeros(Npad))
padded.append(sections[n])
cum_N += Npad + sections[n].size
trace = pylab.concatenate(
padded) #From this packet to the packet before the gap
return {
'header': hdr,
'packets': data,
'Fs': Fs,
'trace': trace,
't0': ts_us[0]
}
def read_bunch_data(file_list, format='ascii'):
A, R = [], []
if format == 'ascii':
data_list = [f.replace('.cfg', '_prt.dat') for f in file_list]
for i, d in enumerate(data_list):
try:
A.append(plt.loadtxt(d).T)
except IOError:
print '*** WARNING: no file ', d
# R.append((i, file_list[i]))
A.append(A[-1])
except ValueError:
print i, d
raise ValueError
elif format == 'hdf5':
data_list = [f.replace('.cfg', '.prt.h5') for f in file_list]
for i, d in enumerate(data_list):
try:
hf = h5py.File(d, 'r')
A.append(
plt.insert(hf['Fields']['Data'], 0, hf['Time']['time'], axis=1).T)
except IOError:
print '*** WARNING: no file ', d
R.append((i, file_list[i]))
elif format == 'h5':
data_list = file_list
A = None
for i, d in enumerate(data_list):
try:
hf = h5py.File(d, 'r')['Bunch']
if A == None:
keys = hf.keys()
a = hf[keys[0]]
A = plt.zeros((len(data_list), len(keys) + 1, len(a)))
A[i, 0, :] = plt.arange(len(hf['mean_x']))
A[i, 1, :] = hf['mean_x']
A[i, 2, :] = hf['mean_xp']
A[i, 3, :] = hf['mean_y']
A[i, 4, :] = hf['mean_yp']
A[i, 5, :] = hf['mean_z']
A[i, 6, :] = hf['mean_dp']
A[i, 7, :] = hf['sigma_x']
A[i, 8, :] = hf['sigma_y']
A[i, 9, :] = hf['sigma_z']
A[i, 10, :] = hf['sigma_dp']
A[i, 11, :] = hf['epsn_x']
A[i, 12, :] = hf['epsn_y']
A[i, 13, :] = hf['epsn_z']
A[i, 14, :] = hf['n_macroparticles']
# A.append(plt.array(
# [,
# hf['mean_x'], hf['mean_xp'], hf['mean_y'], hf['mean_yp'], hf['mean_dz'], hf['mean_dp'],
# hf['sigma_x'], hf['sigma_y'], hf['sigma_dz'], hf['sigma_dp'],
# hf['epsn_x'], hf['epsn_y'], hf['epsn_z'], hf['n_macroparticles']]).T)
except IOError:
print '*** WARNING: no file ', d
R.append((i, file_list[i]))
except KeyError:
print '*** WARNING: damaged file ', d
R.append((i, file_list[i]))
else:
raise(ValueError('*** Unknown format: ', format))
for r in R:
file_list.remove(r[1])
delete_from_data_array = [r[0] for r in R]
A = plt.delete(A, delete_from_data_array, axis=0)
A = plt.array(A)
A = plt.rollaxis(A, 0, 3)
# [n_cols, n_turns, n_files] = A.shape
return A, file_list