def main(testpath,npulse = 1400 ,functlist = ['spectrums','radardata','fitting','analysis']):
""" This function will call other functions to create the input data, config
file and run the radar data sim. The path for the simulation will be
created in the Testdata directory in the SimISR module. The new
folder will be called BasicTest. The simulation is a long pulse simulation
will the desired number of pulses from the user.
Inputs
npulse - Number of pulses for the integration period, default==100.
functlist - The list of functions for the SimISR to do.
"""
curloc = os.path.dirname(os.path.abspath(inspect.getfile(inspect.currentframe())))
if not os.path.isdir(testpath):
os.mkdir(testpath)
functlist_default = ['spectrums','radardata','fitting']
check_list = sp.array([i in functlist for i in functlist_default])
check_run =sp.any( check_list)
functlist_red = sp.array(functlist_default)[check_list].tolist()
configfilesetup(testpath,npulse)
config = os.path.join(testpath,'stats.ini')
(sensdict,simparams) = readconfigfile(config)
makedata(testpath,simparams['Tint'])
if check_run :
runsim(functlist_red,testpath,config,True)
if 'analysis' in functlist:
analysisdump(testpath,config)
def main(npulse=100, functlist=['spectrums', 'radardata', 'fitting', 'analysis'],radar='pfisr'):
""" This function will call other functions to create the input data, config
file and run the radar data sim. The path for the simulation will be
created in the Testdata directory in the SimISR module. The new
folder will be called BasicTest. The simulation is a long pulse simulation
will the desired number of pulses from the user.
Inputs
npulse - Number of pulses for the integration period, default==100.
functlist - The list of functions for the SimISR to do.
"""
curloc = Path(__file__).resolve()
testpath = curloc.parent.parent/'Testdata'/'BasicTest'
if not testpath.is_dir():
testpath.mkdir(parents=True)
functlist_default = ['spectrums', 'radardata', 'fitting']
check_list = sp.array([i in functlist for i in functlist_default])
check_run = sp.any(check_list)
functlist_red = sp.array(functlist_default)[check_list].tolist()
config = testpath.joinpath('stats.yml')
if not config.exists():
configfilesetup(str(testpath), npulse, radar)
(_, simparams) = readconfigfile(str(config))
makedata(testpath, simparams['Tint'])
if check_run:
runsim(functlist_red, str(testpath), config, True)
if 'analysis' in functlist:
analysisdump(str(testpath), config)
def main(npulse=100,
functlist=['spectrums', 'radardata', 'fitting', 'analysis']):
""" This function will call other functions to create the input data, config
file and run the radar data sim. The path for the simulation will be
created in the Testdata directory in the SimISR module. The new
folder will be called BasicTest. The simulation is a long pulse simulation
will the desired number of pulses from the user.
Inputs
npulse - Number of pulses for the integration period, default==100.
functlist - The list of functions for the SimISR to do.
"""
curloc = Path(__file__).resolve()
testpath = curloc.parent.parent / 'Testdata' / 'BasicTest'
if not testpath.is_dir():
testpath.mkdir(parents=True)
functlist_default = ['spectrums', 'radardata', 'fitting']
check_list = sp.array([i in functlist for i in functlist_default])
check_run = sp.any(check_list)
functlist_red = sp.array(functlist_default)[check_list].tolist()
configfilesetup(str(testpath), npulse)
config = testpath.joinpath('stats.ini')
(sensdict, simparams) = readconfigfile(str(config))
makedata(testpath, simparams['Tint'])
if check_run:
runsim(functlist_red, str(testpath), config, True)
if 'analysis' in functlist:
analysisdump(str(testpath), config)
def __init__(self,ionoin,configfile,timein=None,mattype='matrix'):
""" This will create the RadarSpaceTimeOperator object.
Inputs
ionoin - The input ionocontainer. This can be either an string that is a ionocontainer file,
a list of ionocontainer objects or a list a strings to ionocontainer files.
config - The ini file that used to set up the simulation.
timein - A Ntx2 numpy array of times.
RSTOPinv - The inverse operator object.
invmat - The inverse matrix to the original operator.
"""
mattype=mattype.lower()
accepttypes=['matrix','sim','real']
if not mattype in accepttypes:
raise ValueError('Matrix type can only be {0}'.format(', '.join(accepttypes)))
d2r = np.pi/180.0
(sensdict,simparams) = readconfigfile(configfile)
# determine if the input ionocontainer is a string, a list of strings or a list of ionocontainers.
ionoin=makeionocombined(ionoin)
#Input location
self.Cart_Coords_In = ionoin.Cart_Coords
self.Sphere_Coords_In = ionoin.Sphere_Coords
# Set the input times
if timein is None:
self.Time_In = ionoin.Time_Vector
else:
self.Time_In = timein
#Create an array of output location based off of the inputs
rng_vec2 = simparams['Rangegatesfinal']
nrgout = len(rng_vec2)
angles = simparams['angles']
nang =len(angles)
ang_data = np.array([[iout[0],iout[1]] for iout in angles])
rng_all = np.repeat(rng_vec2,(nang),axis=0)
ang_all = np.tile(ang_data,(nrgout,1))
self.Sphere_Coords_Out = np.column_stack((rng_all,ang_all))
(R_vec,Az_vec,El_vec) = (self.Sphere_Coords_Out[:,0],self.Sphere_Coords_Out[:,1],
self.Sphere_Coords_Out[:,2])
xvecmult = np.sin(Az_vec*d2r)*np.cos(El_vec*d2r)
yvecmult = np.cos(Az_vec*d2r)*np.cos(El_vec*d2r)
zvecmult = np.sin(El_vec*d2r)
X_vec = R_vec*xvecmult
Y_vec = R_vec*yvecmult
Z_vec = R_vec*zvecmult
self.Cart_Coords_Out = np.column_stack((X_vec,Y_vec,Z_vec))
self.Time_Out = np.column_stack((simparams['Timevec'],simparams['Timevec']+simparams['Tint']))+self.Time_In[0,0]
self.simparams=simparams
self.sensdict=sensdict
self.lagmat = self.simparams['amb_dict']['WttMatrix']
self.mattype=mattype
# create the matrix
(self.RSTMat,self.overlaps,self.blocklocs) = makematPA(ionoin.Sphere_Coords,ionoin.Cart_Coords,ionoin.Time_Vector,configfile,ionoin.Velocity,mattype)
def __init__(self, ionoacf, Ionosig=None, inifile='default.ini'):
""" The init function for the fitter take the inputs for the fitter programs.
Inputs:
ionoacf: The lags in ionocontainer format.
Ionosig:
sensdict: The dictionary that holds the sensor info.
simparams: The dictionary that hold the specific simulation params"""
(self.sensdict, self.simparams) = readconfigfile(inifile)
self.acf = ionoacf
self.sig = Ionosig
def loadfile(self):
"""Imports parameters from old files"""
fn = tkFileDialog.askopenfilename(title="Load File",filetypes=[('INI','.ini'),('PICKLE','.pickle')])
try:
sensdict,simparams = readconfigfile(fn)
rdrnames = {'PFISR':'PFISR','pfisr':'PFISR','risr':'RISR-N','RISR-N':'RISR-N','RISR':'RISR-N'}
currdr = rdrnames[sensdict['Name']]
fitnfound = True
for i in simparams:
try:
if i=='RangeLims':
self.paramdic[i][0].delete(0,Tk.END)
self.paramdic[i][1].delete(0,Tk.END)
self.paramdic[i][0].insert(0,str(simparams[i][0]))
self.paramdic[i][1].insert(0,str(simparams[i][1]))
elif i=='species':
self.paramdic[i].delete(0,Tk.END)
string=''
if isinstance(simparams[i],list):
for a in simparams[i]:
string+=a
string+=" "
else:
string = simparams[i]
self.paramdic[i].insert(0,string)
elif i=='Pulselength' or i=='t_s':
self.paramdic[i].delete(0,Tk.END)
num = float(simparams[i])*10**6
self.paramdic[i].insert(0,str(num))
elif i== 'FitType':
self.fittype = simparams[i]
fitnfound=False
else:
self.paramdic[i].delete(0,Tk.END)
self.paramdic[i].insert(0,str(simparams[i]))
except:
if simparams[i]==sp.complex128:
self.paramdic[i].set('complex128')
elif simparams[i]==sp.complex64:
self.paramdic[i].set('complex64')
elif i in self.paramdic:
self.paramdic[i].set(simparams[i])
if fitnfound:
self.fittype = 'Spectrum'
self.pickbeams.var.set(currdr)
self.pickbeams.Changefile()
self.pickbeams.addbeamlist(simparams['angles'])
except:
print "Failed to import file."
def plotparams(datapath,indch):
# read in the files
geofile = os.path.join(datapath,'Fitted','fitteddataGEOD.h5')
acffile = os.path.join(datapath,'ACF','00lags.h5')
geod = GeoData.read_h5(geofile)
acfIono = IonoContainer.readh5(acffile)
picklefile = os.path.join(datapath,'config.ini')
(sensdict,simparams) = readconfigfile(picklefile)
#determine the ind
dataloc = geod.dataloc
rngloc = 210
ind = sp.argmin(sp.absolute(dataloc[:,0]-rngloc))
#
Ne = geod.data['Ne'][ind]
Ti = geod.data['Ti'][ind]
Te = geod.data['Te'][ind]
#make a spectrum
npts = 128
datablock = sp.array([[Ne[indch],Ti[indch]],[Ne[indch],Te[indch]]])
specobj = ISRSpectrum(centerFrequency =sensdict['fc'],nspec = npts,sampfreq=sensdict['fs'])
(omeg,specexample,rcs) = specobj.getspecsep(datablock,simparams['species'],rcsflag=True)
specexample = rcs*npts*specexample/sp.absolute(specexample).sum()
acf = acfIono.Param_List[ind,indch]
origspec = scfft.fftshift(scfft.fft(acf,n=npts)).real
(figmplf, [[ax1,ax2],[ax3,ax4]]) = plt.subplots(2, 2,figsize=(16, 12), facecolor='w')
ax1.plot(sp.arange(len(Ne)),Ne)
ax1.set_title('$N_e$')
ax2.plot(sp.arange(len(Ti)),Ti)
ax2.set_title('$T_i$')
ax3.plot(sp.arange(len(Te)),Te)
ax3.set_title('$T_e$');
spec1 = ax4.plot(omeg*1e-3,origspec,label='Measured')
spec2 = ax4.plot(omeg*1e-3,specexample,label='Fitted')
ax4.set_title('Measured and Fitted Spectrums')
ax4.set_xlabel('Frequency KHz')
ax4.legend(loc = 1)
# Nevals = sp.linspace(5e10,5e11,10)
# Tivals = sp.linspace(1e3,2e5,10)
# Tevals = sp.linspace(1e3,2e5,10)
# xlist = [[1],Tivals,Nevals,Tevals,[0]]
# outsurf = makefitsurf(xlist,acf,sensdict,simparams)
return(figmplf)
def main(plist = None,functlist = ['spectrums','radardata','fitting','analysis','stats']):
""" This function will call other functions to create the input data, config
file and run the radar data sim. The path for the simulation will be
created in the Testdata directory in the SimISR module. The new
folder will be called BasicTest. The simulation is a long pulse simulation
will the desired number of pulses from the user.
Inputs
npulse - Number of pulses for the integration period, default==100.
functlist - The list of functions for the SimISR to do.
"""
if plist is None:
plist = sp.array([50,100,200,500,1000,2000,5000])
if isinstance(plist,list):
plist=sp.array(plist)
curloc = Path(__file__).resolve().parent
testpath=curloc.parent.joinpath('Testdata','StatsTest')
testpath.mkdir(exist_ok=True,parents=True)
functlist_default = ['spectrums','radardata','fitting']
check_list = sp.array([i in functlist for i in functlist_default])
check_run =sp.any( check_list)
functlist_red = sp.array(functlist_default)[check_list].tolist()
allfolds = []
# rsystools = []
for ip in plist:
foldname = 'Pulses_{:04d}'.format(ip)
curfold = testpath.joinpath(foldname)
allfolds.append(curfold)
curfold.mkdir(exist_ok=True,parents=True)
configfilesetup(curfold,ip)
makedata(curfold)
config = curfold/'stats.ini'
(sensdict,simparams) = readconfigfile(config)
# rtemp = RadarSys(sensdict,simparams['Rangegatesfinal'],ip)
# rsystools.append(rtemp.rms(sp.array([1e12]),sp.array([2.5e3]),sp.array([2.5e3])))
if check_run :
runsim(functlist_red,curfold,str(curfold.joinpath('stats.ini')),True)
if 'analysis' in functlist:
analysisdump(curfold,config)
if 'stats' in functlist:
makehist(curfold,ip)
def configfilesetup(testpath,npulses):
""" This will create the configureation file given the number of pulses for
the test. This will make it so that there will be 12 integration periods
for a given number of pulses.
Input
testpath - The location of the data.
npulses - The number of pulses.
"""
curloc = Path(__file__).resolve().parent
defcon = curloc.joinpath('statsbase.ini')
(sensdict, simparams) = readconfigfile(defcon)
tint = simparams['IPP']*npulses
ratio1 = tint/simparams['Tint']
simparams['Tint'] = ratio1 * simparams['Tint']
simparams['Fitinter'] = ratio1 * simparams['Fitinter']
simparams['TimeLim'] = ratio1 * simparams['TimeLim']
simparams['startfile'] = 'startfile.h5'
makeconfigfile(testpath.joinpath('stats.ini'),simparams['Beamlist'],sensdict['Name'],simparams)
def configfilesetup(testpath,npulses):
""" This will create the configureation file given the number of pulses for
the test. This will make it so that there will be 12 integration periods
for a given number of pulses.
Input
testpath - The location of the data.
npulses - The number of pulses.
"""
curloc = Path(__file__).resolve().parent
defcon = curloc.joinpath('statsbase.ini')
(sensdict,simparams) = readconfigfile(defcon)
tint = simparams['IPP']*npulses
ratio1 = tint/simparams['Tint']
simparams['Tint']=ratio1 * simparams['Tint']
simparams['Fitinter'] = ratio1 * simparams['Fitinter']
simparams['TimeLim'] = ratio1 * simparams['TimeLim']
simparams['startfile']='startfile.h5'
makeconfigfile(testpath.joinpath('stats.ini'),simparams['Beamlist'],sensdict['Name'],simparams)
def configfilesetup(testpath,npulses = 1400):
""" This will create the configureation file given the number of pulses for
the test. This will make it so that there will be 12 integration periods
for a given number of pulses.
Input
testpath - The location of the data.
npulses - The number of pulses.
"""
curloc = os.path.dirname(os.path.abspath(inspect.getfile(inspect.currentframe())))
defcon = os.path.join(curloc,'statsbase.ini')
(sensdict,simparams) = readconfigfile(defcon)
tint = simparams['IPP']*npulses
ratio1 = tint/simparams['Tint']
simparams['Tint']=ratio1 * simparams['Tint']
simparams['Fitinter'] = ratio1 * simparams['Fitinter']
simparams['TimeLim'] = 3*tint
simparams['startfile']='startfile.h5'
makeconfigfile(os.path.join(testpath,'stats.ini'),simparams['Beamlist'],sensdict['Name'],simparams)
def configfilesetup(testpath, npulses, radar='PFISR'):
""" This will create the configureation file given the number of pulses for
the test. This will make it so that there will be 12 integration periods
for a given number of pulses.
Input
testpath - The location of the data.
npulses - The number of pulses.
"""
testpath = Path(testpath).expanduser()
curloc = Path(__file__).resolve().parent
if radar.lower() == 'pfisr':
defcon = curloc / 'statsbase.ini'
elif radar.lower() == 'millstonez':
defcon = curloc / 'statsbasemhz.yml'
(sensdict, simparams) = readconfigfile(defcon)
tint = simparams['IPP'] * npulses
ratio1 = tint / simparams['Tint']
simparams['Tint'] = ratio1 * simparams['Tint']
simparams['Fitinter'] = ratio1 * simparams['Fitinter']
simparams['TimeLim'] = 2 * tint
simparams['fitmode'] = 1
simparams['startfile'] = 'startfile.h5'
makeconfigfile(str(testpath / 'stats.yml'), simparams['Beamlist'],
sensdict['Name'], simparams)
def makespectrums(basedir, configfile, printlines=True):
""" This will make all of the spectra for a set of data and save it in a
folder in basedir called Spectrums. It is assumed that the data in the Origparams
is time tagged in the title with a string seperated by a white space and the
rest of the file name. For example ~/DATA/Basedir/0 origdata.h5.
Inputs:
basedir: A string for the directory that will hold all of the data for the simulation.
configfile: The configuration file for the simulation.
"""
basedir = Path(basedir).expanduser()
dirio = ('Origparams', 'Spectrums')
inputdir = basedir/dirio[0]
outputdir = basedir/dirio[1]
# determine the list of h5 files in Origparams directory
dirlist = sorted(inputdir.glob('*.h5'))
# Make the lists of numbers and file names for the dictionary
(listorder, _, _, timebeg, _) = IonoContainer.gettimes(dirlist)
slist = [dirlist[ikey] for ikey in listorder]
(sensdict, simparams) = readconfigfile(configfile)
# Delete data
outfiles = outputdir.glob('*.h5')
for ifile in outfiles:
ifile.unlink()
for inum, curfile in zip(timebeg, slist):
outfile = outputdir / (str(inum)+' spectrum.h5')
update_progress(float(inum)/float(len(slist)),
'Processing file {} starting at {}'.format(curfile.name, datetime.now()))
curiono = IonoContainer.readh5(str(curfile))
curiono.makespectruminstanceopen(specfuncs.ISRSspecmake, sensdict,
int(simparams['numpoints']), float(inum),
float(len(slist)), printlines).saveh5(str(outfile))
update_progress(float(inum+1)/float(len(slist)),
'Finished file {} starting at {}'.format(curfile.name, datetime.now()))
def configfilesetup(testpath, npulses, radar='PFISR'):
""" This will create the configureation file given the number of pulses for
the test. This will make it so that there will be 12 integration periods
for a given number of pulses.
Input
testpath - The location of the data.
npulses - The number of pulses.
"""
testpath = Path(testpath).expanduser()
curloc = Path(__file__).resolve().parent
if radar.lower() == 'pfisr':
defcon = curloc/'statsbase.ini'
elif radar.lower() == 'millstonez':
defcon = curloc/'statsbasemhz.yml'
(sensdict, simparams) = readconfigfile(defcon)
tint = simparams['IPP']*npulses
ratio1 = tint/simparams['Tint']
simparams['Tint'] = ratio1*simparams['Tint']
simparams['Fitinter'] = ratio1 * simparams['Fitinter']
simparams['TimeLim'] = 2*tint
simparams['fitmode'] = 1
simparams['startfile'] = 'startfile.h5'
makeconfigfile(str(testpath/'stats.yml'), simparams['Beamlist'],
sensdict['Name'], simparams)
def __init__(self, Ionodict, inifile, outdir, outfilelist=None):
"""
This function will create an instance of the RadarData class. It will
take in the values and create the class and make raw IQ data.
Inputs:
sensdict - A dictionary of sensor parameters
angles - A list of tuples which the first position is the az angle
and the second position is the el angle.
IPP - The interpulse period in seconds represented as a float.
Tint - The integration time in seconds as a float. This will be the
integration time of all of the beams.
time_lim - The length of time of the simulation the number of time points
will be calculated.
pulse - A numpy array that represents the pulse shape.
rng_lims - A numpy array of length 2 that holds the min and max range
that the radar will cover.
"""
(sensdict, simparams) = readconfigfile(inifile)
self.simparams = simparams
N_angles = len(self.simparams['angles'])
NNs = int(self.simparams['NNs'])
self.sensdict = sensdict
Npall = sp.floor(self.simparams['TimeLim'] / self.simparams['IPP'])
Npall = int(sp.floor(Npall / N_angles) * N_angles)
Np = Npall / N_angles
print("All spectrums created already")
filetimes = Ionodict.keys()
filetimes.sort()
ftimes = sp.array(filetimes)
simdtype = self.simparams['dtype']
pulsetimes = sp.arange(Npall) * self.simparams['IPP'] + ftimes.min()
pulsefile = sp.array(
[sp.where(itimes - ftimes >= 0)[0][-1] for itimes in pulsetimes])
# differentiate between phased arrays and dish antennas
if sensdict['Name'].lower() in ['risr', 'pfisr', 'risr-n']:
beams = sp.tile(sp.arange(N_angles), Npall / N_angles)
else:
# for dish arrays
brate = simparams['beamrate']
beams2 = sp.repeat(sp.arange(N_angles), brate)
beam3 = sp.concatenate((beams2, beams2[::-1]))
ntile = int(sp.ceil(Npall / len(beam3)))
leftover = int(Npall - ntile * len(beam3))
if ntile > 0:
beams = sp.tile(beam3, ntile)
beams = sp.concatenate((beams, beam3[:leftover]))
else:
beams = beam3[:leftover]
pulsen = sp.repeat(sp.arange(Np), N_angles)
pt_list = []
pb_list = []
pn_list = []
fname_list = []
self.datadir = outdir
self.maindir = outdir.parent
self.procdir = self.maindir / 'ACF'
Nf = len(filetimes)
progstr = 'Data from {:d} of {:d} being processed Name: {:s}.'
if outfilelist is None:
print('\nData Now being created.')
Noisepwr = v_Boltz * sensdict['Tsys'] * sensdict['BandWidth']
self.outfilelist = []
for ifn, ifilet in enumerate(filetimes):
outdict = {}
ifile = Ionodict[ifilet]
ifilename = Path(ifile).name
update_progress(
float(ifn) / Nf, progstr.format(ifn, Nf, ifilename))
curcontainer = IonoContainer.readh5(ifile)
if ifn == 0:
self.timeoffset = curcontainer.Time_Vector[0, 0]
pnts = pulsefile == ifn
pt = pulsetimes[pnts]
pb = beams[pnts]
pn = pulsen[pnts].astype(int)
rawdata = self.__makeTime__(pt, curcontainer.Time_Vector,
curcontainer.Sphere_Coords,
curcontainer.Param_List, pb)
d_shape = rawdata.shape
n_tempr = sp.random.randn(*d_shape).astype(simdtype)
n_tempi = 1j * sp.random.randn(*d_shape).astype(simdtype)
noise = sp.sqrt(Noisepwr / 2) * (n_tempr + n_tempi)
outdict['AddedNoise'] = noise
outdict['RawData'] = rawdata + noise
outdict['RawDatanonoise'] = rawdata
outdict['NoiseData'] = sp.sqrt(Noisepwr / 2) * (
sp.random.randn(len(pn), NNs).astype(simdtype) +
1j * sp.random.randn(len(pn), NNs).astype(simdtype))
outdict['Pulses'] = pn
outdict['Beams'] = pb
outdict['Time'] = pt
fname = '{0:d} RawData.h5'.format(ifn)
newfn = self.datadir / fname
self.outfilelist.append(str(newfn))
dict2h5(str(newfn), outdict)
#Listing info
pt_list.append(pt)
pb_list.append(pb)
pn_list.append(pn)
fname_list.append(fname)
infodict = {
'Files': fname_list,
'Time': pt_list,
'Beams': pb_list,
'Pulses': pn_list
}
dict2h5(str(outdir.joinpath('INFO.h5')), infodict)
else:
infodict = h52dict(str(outdir.joinpath('INFO.h5')))
alltime = sp.hstack(infodict['Time'])
self.timeoffset = alltime.min()
self.outfilelist = outfilelist
def makematPA(Sphere_Coords,Cart_Coords,timein,configfile,vel=None,mattype='matrix'):
"""Make a Ntimeout*Nbeam*Nrng x Ntime*Nloc sparse matrix for the space time operator.
The output space will have range repeated first, then beams then time.
The coordinates will be [t0,b0,r0],[t0,b0,r1],[t0,b0,r2],...
[t0,b1,r0],[t0,b1,r1], ... [t1,b0,r0],[t1,b0,r1],...[t1,b1,r0]...
Inputs
Sphere_Coords - A Nlocx3 array of the spherical coordinates of the input data.
timein - A Ntbegx2 numpy array with the start and stop times of the input data.
configfile - The ini file used for the simulation configuration.
vel - A NlocxNtx3 numpy array of velocity.
Outputs
outmat - A list of matricies or a single matrix that is the forward between physical space
to the discrete samples space of the radar.
blocks - A tuple that holds the number of block matricies in overall forward operator.
blocksize - A tuple that holds the shape of the outmatrix size.
blockloc - An Ntout x Ntbeg array that holds the corresponding spatial forward model.
"""
#
(sensdict,simparams) = readconfigfile(configfile)
timeout = simparams['Timevec']
Tint = simparams['Tint']
timeout = np.column_stack((timeout,timeout+Tint)) +timein[0,0]
rng_bin=sensdict['t_s']*v_C_0*1e-3/2.
angles = simparams['angles']
Nbeams = len(angles)
rng_vec2 = simparams['Rangegatesfinal']
nrgout = len(rng_vec2)
pulse=simparams['Pulse']
p_samps = pulse.shape[0]
rng_len=p_samps*rng_bin
Nlocbeg = Cart_Coords.shape[0]
Nlocout= Nbeams*nrgout
Ntbeg = len(timein)
Ntout = len(timeout)
if vel is None:
vel=np.zeros((Nlocbeg,Ntbeg,3))
# determine the overlaps
# change
blockloc_in = [[i*Nlocbeg,(i+1)*Nlocbeg] for i in range(Ntout)]
blockloc_out = [[i*Nlocout,(i+1)*Nlocout] for i in range(Ntout)]
blockloc = [blockloc_in,blockloc_out]
# set up blocks
blocksize = (Ntout*Nbeams*nrgout,Nlocbeg*Ntout)
# make the matrix
outmat = np.sparse.lil_matrix(blocksize,dtype =np.float64)
overlaps={}
if mattype.lower()=='real':
cor_ratio=.5
else:
cor_ratio=1.
for iton,ito in enumerate(timeout):
overlaps[iton]=[]
firstone=True
for ix, x in enumerate(timein):
if ( x[0]+1<ito[1] or ix==(Ntbeg-1)) and x[1]-1>ito[0]:
# find the end of the data
if ix ==Ntbeg-1:
enp=ito[1]
else:
enp = np.minimum(ito[1],x[1])
stp = np.maximum(x[0],ito[0])
curvel=vel[:,0]*1e-3
# XXX This is just a quick fix
curvel[:,-1]=0
if firstone:
firstone=False
t_0 = stp.copy()
curdiff=np.zeros_like(vel[:,ix])
curdiff2=curdiff+float(enp-stp)*curvel
else:
# T_1=float(x[0]-t_0)
t_0=stp.copy()
curdiff= curdiff2
curdiff2=curdiff+float(enp-stp)*curvel
#find amount of time for overlap
ratio = float(enp-stp)/Tint
# set up new coordinate system
# The thee types of coordinates are as follows
# The matrix type assumes that the matrix will be applied to the data.
# The sim type
if mattype.lower()=='matrix':
newcoorsds1 = cart2sphere(Cart_Coords)
newcoorsds2 = cart2sphere(Cart_Coords)
elif mattype.lower=='real':
newcoorsds1 = cart2sphere(Cart_Coords+curdiff)
newcoorsds2 = cart2sphere(Cart_Coords+curdiff2)
else:
newcoorsds1 = cart2sphere(Cart_Coords+curdiff)
newcoorsds2 = cart2sphere(Cart_Coords+curdiff)
overlaps[iton].append([ix,ratio,newcoorsds1,newcoorsds2])
# make the matrix
for iton,ito in enumerate(timeout):
cur_over = overlaps[iton]
# if mattype=='matrix':
# cur_over=[cur_over[0]]
# cur_over[0][1]=1.
beamnorm=np.ones(Nbeams*nrgout)
for it_in,it_info in enumerate(cur_over):
print('\t Making Input time {0:d} of {1:d}'.format(it_in,len(cur_over)))
cur_it,cur_ratio,Sp1,Sp2 = it_info
# if mattype.lower()=='sim':
# cur_ratio=1.
rho1 = Sp1[:,0]
Az1 = Sp1[:,1]
El1 = Sp1[:,2]
rho2 = Sp2[:,0]
Az2 = Sp2[:,1]
El2 = Sp2[:,2]
# get the weights
weights1 = {ibn:sensdict['ArrayFunc'](Az1,El1,ib[0],ib[1],sensdict['Angleoffset']) for ibn, ib in enumerate(angles)}
weights2 = {ibn:sensdict['ArrayFunc'](Az2,El2,ib[0],ib[1],sensdict['Angleoffset']) for ibn, ib in enumerate(angles)}
for ibn in range(Nbeams):
print('\t\t Making Beam {0:d} of {1:d}'.format(ibn,Nbeams))
weight1 = weights1[ibn]
weight2 = weights2[ibn]
for isamp in range(nrgout):
# make the row
irow = ibn + isamp*Nbeams + Nbeams*nrgout*iton
range_g = rng_vec2[isamp]
rnglims = [range_g-rng_len/2.,range_g+rng_len/2.]
# assume centered lag product.
rangelog = ((rho1>=rnglims[0])&(rho1<rnglims[1]))
# This is a nearest neighbors interpolation for the spectrums in the range domain
if np.sum(rangelog)==0:
minrng = np.argmin(np.absolute(range_g-rho1))
rangelog[minrng] = True
#create the weights and weight location based on the beams pattern.
weight_cur = weight1[rangelog]
# fix averaging problems
if it_in==0:
beamnorm[ibn + isamp*Nbeams]=weight_cur.sum()
weight_cur = weight_cur/beamnorm[ibn + isamp*Nbeams]
icols = np.where(rangelog)[0] + Nlocbeg*iton
# icols = np.where(rangelog)[0] + Nlocbeg*cur_it
weights_final = weight_cur*range_g**2/rho1[rangelog]**2
outmat[irow,icols] = weights_final*cur_ratio*cor_ratio+outmat[irow,icols]
if mattype.lower()=='real':
# assume centered lag product.
rangelog = ((rho2>=rnglims[0])&(rho2<rnglims[1]))
# This is a nearest neighbors interpolation for the spectrums in the range domain
if np.sum(rangelog)==0:
minrng = np.argmin(np.absolute(range_g-rho2))
rangelog[minrng] = True
#create the weights and weight location based on the beams pattern.
weight_cur =weight2[rangelog]
weight_cur = weight_cur//beamnorm[ibn + isamp*Nbeams]
# icols = np.where(rangelog)[0]+ Nlocbeg*cur_it
icols = np.where(rangelog)[0]+ Nlocbeg*iton
weights_final = weight_cur*range_g**2/rho2[rangelog]**2
outmat[irow,icols] = weights_final*cur_ratio*cor_ratio+outmat[irow,icols]
return(outmat,overlaps,blockloc)
def makematPA(Sphere_Coords,
Cart_Coords,
timein,
configfile,
vel=None,
mattype='matrix'):
"""Make a Ntimeout*Nbeam*Nrng x Ntime*Nloc sparse matrix for the space time operator.
The output space will have range repeated first, then beams then time.
The coordinates will be [t0,b0,r0],[t0,b0,r1],[t0,b0,r2],...
[t0,b1,r0],[t0,b1,r1], ... [t1,b0,r0],[t1,b0,r1],...[t1,b1,r0]...
Inputs
Sphere_Coords - A Nlocx3 array of the spherical coordinates of the input data.
timein - A Ntbegx2 numpy array with the start and stop times of the input data.
configfile - The ini file used for the simulation configuration.
vel - A NlocxNtx3 numpy array of velocity.
Outputs
outmat - A list of matricies or a single matrix that is the forward between physical space
to the discrete samples space of the radar.
blocks - A tuple that holds the number of block matricies in overall forward operator.
blocksize - A tuple that holds the shape of the outmatrix size.
blockloc - An Ntout x Ntbeg array that holds the corresponding spatial forward model.
"""
#
(sensdict, simparams) = readconfigfile(configfile)
timeout = simparams['Timevec']
Tint = simparams['Tint']
timeout = np.column_stack((timeout, timeout + Tint)) + timein[0, 0]
rng_bin = sensdict['t_s'] * v_C_0 * 1e-3 / 2.
angles = simparams['angles']
Nbeams = len(angles)
rng_vec2 = simparams['Rangegatesfinal']
nrgout = len(rng_vec2)
pulse = simparams['Pulse']
p_samps = pulse.shape[0]
rng_len = p_samps * rng_bin
Nlocbeg = Cart_Coords.shape[0]
Nlocout = Nbeams * nrgout
Ntbeg = len(timein)
Ntout = len(timeout)
if vel is None:
vel = np.zeros((Nlocbeg, Ntbeg, 3))
# determine the overlaps
# change
blockloc_in = [[i * Nlocbeg, (i + 1) * Nlocbeg] for i in range(Ntout)]
blockloc_out = [[i * Nlocout, (i + 1) * Nlocout] for i in range(Ntout)]
blockloc = [blockloc_in, blockloc_out]
# set up blocks
blocksize = (Ntout * Nbeams * nrgout, Nlocbeg * Ntout)
# make the matrix
outmat = np.sparse.lil_matrix(blocksize, dtype=np.float64)
overlaps = {}
if mattype.lower() == 'real':
cor_ratio = .5
else:
cor_ratio = 1.
for iton, ito in enumerate(timeout):
overlaps[iton] = []
firstone = True
for ix, x in enumerate(timein):
if (x[0] + 1 < ito[1] or ix == (Ntbeg - 1)) and x[1] - 1 > ito[0]:
# find the end of the data
if ix == Ntbeg - 1:
enp = ito[1]
else:
enp = np.minimum(ito[1], x[1])
stp = np.maximum(x[0], ito[0])
curvel = vel[:, 0] * 1e-3
# XXX This is just a quick fix
curvel[:, -1] = 0
if firstone:
firstone = False
t_0 = stp.copy()
curdiff = np.zeros_like(vel[:, ix])
curdiff2 = curdiff + float(enp - stp) * curvel
else:
# T_1=float(x[0]-t_0)
t_0 = stp.copy()
curdiff = curdiff2
curdiff2 = curdiff + float(enp - stp) * curvel
#find amount of time for overlap
ratio = float(enp - stp) / Tint
# set up new coordinate system
# The thee types of coordinates are as follows
# The matrix type assumes that the matrix will be applied to the data.
# The sim type
if mattype.lower() == 'matrix':
newcoorsds1 = cart2sphere(Cart_Coords)
newcoorsds2 = cart2sphere(Cart_Coords)
elif mattype.lower == 'real':
newcoorsds1 = cart2sphere(Cart_Coords + curdiff)
newcoorsds2 = cart2sphere(Cart_Coords + curdiff2)
else:
newcoorsds1 = cart2sphere(Cart_Coords + curdiff)
newcoorsds2 = cart2sphere(Cart_Coords + curdiff)
overlaps[iton].append([ix, ratio, newcoorsds1, newcoorsds2])
# make the matrix
for iton, ito in enumerate(timeout):
cur_over = overlaps[iton]
# if mattype=='matrix':
# cur_over=[cur_over[0]]
# cur_over[0][1]=1.
beamnorm = np.ones(Nbeams * nrgout)
for it_in, it_info in enumerate(cur_over):
print('\t Making Input time {0:d} of {1:d}'.format(
it_in, len(cur_over)))
cur_it, cur_ratio, Sp1, Sp2 = it_info
# if mattype.lower()=='sim':
# cur_ratio=1.
rho1 = Sp1[:, 0]
Az1 = Sp1[:, 1]
El1 = Sp1[:, 2]
rho2 = Sp2[:, 0]
Az2 = Sp2[:, 1]
El2 = Sp2[:, 2]
# get the weights
weights1 = {
ibn: sensdict['ArrayFunc'](Az1, El1, ib[0], ib[1],
sensdict['Angleoffset'])
for ibn, ib in enumerate(angles)
}
weights2 = {
ibn: sensdict['ArrayFunc'](Az2, El2, ib[0], ib[1],
sensdict['Angleoffset'])
for ibn, ib in enumerate(angles)
}
for ibn in range(Nbeams):
print('\t\t Making Beam {0:d} of {1:d}'.format(ibn, Nbeams))
weight1 = weights1[ibn]
weight2 = weights2[ibn]
for isamp in range(nrgout):
# make the row
irow = ibn + isamp * Nbeams + Nbeams * nrgout * iton
range_g = rng_vec2[isamp]
rnglims = [range_g - rng_len / 2., range_g + rng_len / 2.]
# assume centered lag product.
rangelog = ((rho1 >= rnglims[0]) & (rho1 < rnglims[1]))
# This is a nearest neighbors interpolation for the spectrums in the range domain
if np.sum(rangelog) == 0:
minrng = np.argmin(np.absolute(range_g - rho1))
rangelog[minrng] = True
#create the weights and weight location based on the beams pattern.
weight_cur = weight1[rangelog]
# fix averaging problems
if it_in == 0:
beamnorm[ibn + isamp * Nbeams] = weight_cur.sum()
weight_cur = weight_cur / beamnorm[ibn + isamp * Nbeams]
icols = np.where(rangelog)[0] + Nlocbeg * iton
# icols = np.where(rangelog)[0] + Nlocbeg*cur_it
weights_final = weight_cur * range_g**2 / rho1[rangelog]**2
outmat[
irow,
icols] = weights_final * cur_ratio * cor_ratio + outmat[
irow, icols]
if mattype.lower() == 'real':
# assume centered lag product.
rangelog = ((rho2 >= rnglims[0]) & (rho2 < rnglims[1]))
# This is a nearest neighbors interpolation for the spectrums in the range domain
if np.sum(rangelog) == 0:
minrng = np.argmin(np.absolute(range_g - rho2))
rangelog[minrng] = True
#create the weights and weight location based on the beams pattern.
weight_cur = weight2[rangelog]
weight_cur = weight_cur // beamnorm[ibn +
isamp * Nbeams]
# icols = np.where(rangelog)[0]+ Nlocbeg*cur_it
icols = np.where(rangelog)[0] + Nlocbeg * iton
weights_final = weight_cur * range_g**2 / rho2[
rangelog]**2
outmat[
irow,
icols] = weights_final * cur_ratio * cor_ratio + outmat[
irow, icols]
return (outmat, overlaps, blockloc)
def runfitter(paramdict, SNR, n_pulses, n_runs, Niratio, x_0=SVALS):
"""
paramdict
"""
data = SIMVALUES
z = sp.linspace(50., 1e3, 50)
nz = len(z)
params = sp.tile(data[sp.newaxis, sp.newaxis, :, :], (nz, 1, 1, 1))
coords = sp.column_stack((sp.ones(nz), sp.ones(nz), z))
species = ['O+', 'e-']
times = sp.array([[0, 1e9]])
vel = sp.zeros((nz, 1, 3))
(sensdict, simparams) = readconfigfile(defcon)
species = paramdict['species']
nspecies = len(species)
ni = nspecies-1
Icont1 = IonoContainer(coordlist=coords, paramlist=params, times=times,
sensor_loc=sp.zeros(3), ver=0, coordvecs=['x', 'y', 'z'],
paramnames=None, species=species, velocity=vel)
omeg, outspecs = specfuncs.ISRSspecmake(Icont1, sensdict, int(simparams['numpoints']))
tau, acf = spect2acf(omeg, outspecs)
t_log = sp.logical_and(tau<simparams['Pulselength'],tau>=0)
plen = t_log.sum()
amb_dict = simparams['amb_dict']
amb_mat_flat = sp.zeros_like(amb_dict['WttMatrix'])
eyemat = sp.eye(plen)
amb_mat_flat[:plen, t_log] = eyemat
fitmode = simparams['fitmode']
simparams['amb_dict']['WttMatrix'] = amb_mat_flat
Nloc, Nt = acf.shape[:2]
# output Files
fittedarray = sp.zeros((Nloc, Nt, nparams+1))*sp.nan
fittederror = sp.zeros((Nloc, Nt, nparams+1))*sp.nan
fittedcov = sp.zeros((Nloc, Nt, 4, 4))*sp.nan
funcevals = sp.zeros((Nloc, Nt))
for iloc, ilocvec in acf:
for itn, iacf in ilocvec:
curlag = sp.dot(amb_mat_flat, iacf)
std_lag = sp.absolute(curlag)(1.+1./SNR)/sp.sqrt(n_pulses)
covar_lag = sp.diag(sp.power(std_lag,2.))
curlag = curlag + std_lag*sp.random.randn(curlag.shape)
d_func = (curlag, sensdict, simparams, Niratio)
# Only fit Ti, Te, Ne and Vi
# change variables because of new fit mode
# Perform the fitting
optresults = scipy.optimize.least_squares(fun=specfuncs.ISRSfitfunction, x0=x_0,
method='lm', verbose=0, args=d_func)
x_res = optresults.x.real
# Derive data for the ions using output from the fitter and ion
# species ratios which are assumed to be given.
ionstuff = sp.zeros(ni*2-1)
ionstuff[:2*ni:2] = x_res[1]*Niratio
ionstuff[1:2*ni-1:2] = x_res[0]
# change variables because of new fit mode
if fitmode == 1:
x_res[2] = x_res[2]*x_res[0]
fittedarray[iloc, itn] = sp.append(ionstuff,
sp.append(x_res, Ne_start[iloc, itime]))
funcevals[iloc, itn] = optresults.nfev
# fittedarray[iloc,itime] = sp.append(optresults.x,Ne_start[iloc,itime])
resid = optresults.cost
jac = optresults.jac
# combine the rows because of the complex conjugates
jacc = jac[0::2]+jac[1::2]
try:
# Derive covariances for the ions using output from the fitter and ion species ratios which are assumed to be given.
#covf = sp.linalg.inv(sp.dot(jac.transpose(),jac))*resid/dof
covf = sp.linalg.inv(sp.dot(sp.dot(jacc.transpose(),
sp.linalg.inv(covar_lag)), jacc))
# change variables because of new fit mode
if fitmode == 1:
# is this right?
covf[2] = covf[2]*x_res[0]
covf[:,2] = covf[:,2]*x_res[0]
vars_vec = sp.diag(covf).real
ionstuff = sp.zeros(ni*2-1)
ionstuff[:2*ni:2] = vars_vec[1]*Niratio
ionstuff[1:2*ni-1:2] = vars_vec[0]
vars_vec = sp.append(ionstuff, vars_vec)
fittedcov[iloc, itn] = covf
except:#sp.linalg.LinAlgError('singular matrix'):
vars_vec = sp.ones(nparams)*float('nan')
# if len(vars_vec)<fittederror.shape[-1]-1:
# pdb.set_trace()
fittederror[iloc, itn, :-1] = vars_vec
return(fittedarray, fittederror, funcevals, fittedcov)
if basedir.lower() == 'all':
basedirlist = glob.glob(os.path.join(curpath,'exp_width_*'))
else:
basedirlist = basedir.split()
if 'paramsweep' in funcnamelist:
parametersweep(basedir,configfile,acfdir=acffolder,invtype=invtype)
funcnamelist.remove('paramsweep')
if 'invertdata' in funcnamelist:
runinversion(basedir,configfile,acfdir=acffolder,invtype=invtype)
funcnamelist.remove('invertdata')
if 'origdata' in funcnamelist:
funcnamelist.remove('origdata')
makedirs = True
(sensdict,simparams) = readconfigfile(configfile)
azangles = [iang[0] for iang in simparams['angles']]
meanaz = sp.mean(azangles)
for ibase in basedirlist:
makeline(ibase,meanaz,linewidth=lw,multval = mult)
if 'all' in funcnamelist:
funcnamelist=['spectrums','applymat','fittingmat','plotting']
plotboolin = False
plotboolout= False
ploterror=False
plotmat=False
def plotpercenterror(testdir,imgdir,config,wtimes=False,fitpath='Fitted',fitfile='fitteddata.h5'):
"""
This will plot all of the fitted data with each time step as a pcolor images of
electron density and electron density from power mesurements.
Inputs
testdir - The directory with the input data in h5 files formated for the ionocontainer structure.
imgdir - The directory that holds the images.
"""
(sensdict,simparams)=readconfigfile(config)
tvec = simparams['Timevec']
filetemplate = 'fitteddataerrorpercent'
if os.path.exists(imgdir):
imgfiles = glob.glob(os.path.join(imgdir,'*'+filetemplate+'.png'))
for imgf in imgfiles:
os.remove(imgf)
else:
os.mkdir(imgdir)
filename = os.path.join(testdir,fitpath,fitfile)
iono = IonoContainer.readh5(filename)
Iono1 = GeoData(readIono,[iono])
rngrdr =Iono1.dataloc[:,0].astype('float32')
sign1 = sp.sign(Iono1.dataloc[:,1])
el = Iono1.dataloc[:,2].astype('float32')
elvec,elinv = sp.unique(el,return_inverse=True)
nbeams = len(elvec)
nrg = len(rngrdr)/nbeams
nt = Iono1.times.shape[0]
Rngrdrmat = sp.reshape(rngrdr,(nrg,nbeams))
Signmat = sp.reshape(sign1,(nrg,nbeams))
Elmat = sp.reshape(el,(nrg,nbeams))
permin,permax=[0.,100.]
Xmat = Rngrdrmat*Signmat*sp.cos(Elmat*sp.pi/180.)
Zmat = Rngrdrmat*sp.sin(Elmat*sp.pi/180.)
Ne = Iono1.data['Ne'].reshape(nrg,nbeams,nt)
Ti = Iono1.data['Ti'].reshape(nrg,nbeams,nt)
Te = Iono1.data['Te'].reshape(nrg,nbeams,nt)
nNe = 100.*Iono1.data['nNe'].reshape(nrg,nbeams,nt)/Ne
nTe = 100.*Iono1.data['nTe'].reshape(nrg,nbeams,nt)/Te
nTi = 100.*Iono1.data['nTi'].reshape(nrg,nbeams,nt)/Ti
imcount=0
dsetname = os.path.split(os.path.dirname(testdir))[-1]
print "Plotting Output error data for "+dsetname
if 'perryplane' in testdir.lower():
xlim = [-200.,360.]
xticks = [-150.,0.,150.,300.]
allparams=True
ncols=3
figsize = (15,7)
else:
xlim = [0.,400.]
xticks = [0.,150.,300]
allparams = False
ncols=1
figsize = (5,7)
ylim = [100.,500]
for itimen,itime in enumerate(Iono1.times):
print "{0} Output for {1} of {2}".format(dsetname,itimen,len(Iono1.times))
Nemat = nNe[:,:,itimen]
Timat = nTi[:,:,itimen]
Temat = nTe[:,:,itimen]
fig ,axmat= plt.subplots(nrows=1,ncols=ncols,facecolor='w',figsize=figsize,sharey=True)
if allparams:
avec=axmat.flatten()
else:
avec=[axmat]
plt.sca(avec[0])
avec[0].set_xlabel('X Plane in km',fontsize=fs)
avec[0].set_ylabel('Alt in km',fontsize=fs)
pc1 = avec[0].pcolor(Xmat,Zmat,Nemat,cmap = defmap,vmin=permin,vmax=permax)
plt.tick_params(labelsize=16)
plt.xticks(xticks)
avec[0].set_xlim(xlim)
avec[0].set_ylim(ylim)
avec[0].set_title('Electron Density % Error',fontsize=fs)
tick_locator = ticker.MaxNLocator(nbins=5)
cb1 = plt.colorbar(pc1, ax=avec[0])
cb1.ax.xaxis.set_label_position('top')
cb1.ax.set_xlabel(ercbarstr,fontsize=fscb)
cb1.locator = tick_locator
cb1.update_ticks()
if allparams:
plt.sca(avec[1])
plt.tick_params(labelsize=16)
plt.xticks(xticks)
avec[1].set_xlabel('X Plane in km',fontsize=fs)
pc2 = avec[1].pcolor(Xmat,Zmat,Temat,cmap = defmap,vmin=permin,vmax=permax)
avec[1].set_xlim(xlim)
avec[1].set_ylim(ylim)
avec[1].set_title('Electron Temperature % Error',fontsize=fs)
cb2 = plt.colorbar(pc2, ax=avec[1])
cb2.ax.xaxis.set_label_position('top')
cb2.ax.set_xlabel(ercbarstr,fontsize=fscb)
cb2.locator = tick_locator
cb2.update_ticks()
plt.sca(avec[2])
plt.xticks(xticks)
plt.tick_params(labelsize=16)
avec[2].set_xlabel('X Plane in km',fontsize=fs)
pc3 = avec[2].pcolor(Xmat,Zmat,Timat,cmap = defmap,vmin=permin,vmax=permax)
avec[2].set_xlim(xlim)
avec[2].set_ylim(ylim)
avec[2].set_title('Ion Temperature % Error',fontsize=fs)
cb3 = plt.colorbar(pc3, ax=avec[2])
cb3.ax.xaxis.set_label_position('top')
cb3.ax.set_xlabel(ercbarstr,fontsize=fscb)
cb3.locator = tick_locator
cb3.update_ticks()
plt.tight_layout()
if wtimes:
plt.subplots_adjust(top=0.9)
spti = fig.suptitle('Percent Error at {0} seconds'.format(int(tvec[itimen])),fontsize=24)
fname= '{0:0>3}_'.format(imcount)+filetemplate+'.png'
plt.savefig(os.path.join(imgdir,fname),dpi=300)
imcount=imcount+1
plt.close(fig)
def fitcheck(repall=[100]):
x_0=sp.array([[[ 1.00000000e+11, 2.00000000e+03],
[ 1.00000000e+11, 2.00000000e+03]],
[[ 5.00000000e+11, 2.00000000e+03],
[ 5.00000000e+11, 2.00000000e+03]],
[[ 1.00000000e+11, 3.00000000e+03],
[ 1.00000000e+11, 2.00000000e+03]],
[[ 1.00000000e+11, 2.00000000e+03],
[ 1.00000000e+11, 3.00000000e+03]]])
sns.set_style("whitegrid")
sns.set_context("notebook")
x_0_red = x_0[0].flatten()
x_0_red[-2]=x_0_red[-1]
x_0_red[-1]=0.
configfile = 'statsbase.ini'
(sensdict,simparams) = readconfigfile(configfile)
ambdict = simparams['amb_dict']
pulse = simparams['Pulse']
l_p = len(pulse)
Nlags = l_p
lagv = sp.arange(l_p)
ntypes = x_0.shape[0]
nspec = 128
nrg = 64
des_pnt = 16
ISpec = ISRSpectrum(nspec=nspec,sampfreq=50e3)
species = ['O+','e-']
spvtime=sp.zeros((ntypes,nspec))
lablist =['Normal','E-Ne','E-Ti','E-Te']
v_i = 0
fitfunc=ISRSfitfunction
sumrule = simparams['SUMRULE']
Nrg1 = nrg+1-l_p
minrg = -sumrule[0].min()
maxrg = Nrg1-sumrule[1].max()
Nrg2 = maxrg-minrg
for i in range(ntypes):
f,curspec,rcs = ISpec.getspecsep(x_0[i],species,v_i,rcsflag=True)
specsum = sp.absolute(curspec).sum()
spvtime[i] = rcs*curspec*nspec**2/specsum
acforig = scfft.ifft(scfft.ifftshift(spvtime,axes=1),axis=1)/nspec
acfamb = sp.dot(ambdict['WttMatrix'],scfft.fftshift(acforig,axes=1).transpose()).transpose()
specamb = scfft.fftshift(scfft.fft(acfamb,n=nspec,axis=1),axes=1)
fig, axmat = plt.subplots(2,2)
axvec=axmat.flatten()
figs,axmats = plt.subplots(2,2)
axvecs = axmats.flatten()
for i in range(ntypes):
ax=axvec[i]
ax.plot(lagv,acfamb[i].real,label='Input')
ax.set_title(lablist[i])
axs=axvecs[i]
axs.plot(f*1e-3,specamb[i].real,label='Input',linewidth=4)
axs.set_title(lablist[i])
for irep, rep1 in enumerate(repall):
rawdata = sp.zeros((ntypes,rep1,nrg),dtype=sp.complex128)
acfest = sp.zeros((ntypes,Nrg1,l_p),dtype=rawdata.dtype)
acfestsr = sp.zeros((ntypes,Nrg2,l_p),dtype=rawdata.dtype)
specest = sp.zeros((ntypes,nspec),dtype=rawdata.dtype)
for i in range(ntypes):
for j in range(nrg-(l_p-1)):
rawdata[i,:,j:j+l_p] = MakePulseDataRepLPC(pulse,spvtime[i],20,rep1)+rawdata[i,:,j:j+l_p]
acfest[i]=CenteredLagProduct(rawdata[i],pulse=pulse)/(rep1)
for irngnew,irng in enumerate(sp.arange(minrg,maxrg)):
for ilag in range(Nlags):
acfestsr[i][irngnew,ilag] = acfest[i][irng+sumrule[0,ilag]:irng+sumrule[1,ilag]+1,ilag].mean(axis=0)
ax=axvec[i]
ax.plot(lagv,acfestsr[i,des_pnt].real/l_p,label='Np = {0}'.format(rep1))
if irep==len(repall)-1:
ax.legend()
specest[i] = scfft.fftshift(scfft.fft(acfestsr[i,des_pnt],n=nspec))
axs=axvecs[i]
axs.plot(f*1e-3,specest[i].real/l_p,label='Np = {0}'.format(rep1),linewidth=4)
if irep==len(repall)-1:
axs.legend()
print('Parameters fitted after {0} pulses'.format(rep1))
print('Ni Ti Te Vi')
for i in range(ntypes):
d_func = (acfestsr[i,des_pnt]/l_p,sensdict,simparams)
(x,cov_x,infodict,mesg,ier) = scipy.optimize.leastsq(func=fitfunc,
x0=x_0_red,args=d_func,full_output=True)
print(x)
print(' ')
fig.suptitle('ACF with Sum Rule')
fig.savefig('pulsetestacf.png',dpi=400)
plt.close(fig)
figs.suptitle('Spectrum Full Array')
figs.savefig('pulsetestspec.png',dpi=400)
plt.close(figs)
def fitcheck(repall=[100]):
x_0 = sp.array([[[1.00000000e+11, 2.00000000e+03],
[1.00000000e+11, 2.00000000e+03]],
[[5.00000000e+11, 2.00000000e+03],
[5.00000000e+11, 2.00000000e+03]],
[[1.00000000e+11, 3.00000000e+03],
[1.00000000e+11, 2.00000000e+03]],
[[1.00000000e+11, 2.00000000e+03],
[1.00000000e+11, 3.00000000e+03]]])
sns.set_style("whitegrid")
sns.set_context("notebook")
x_0_red = x_0[0].flatten()
x_0_red[-2] = x_0_red[-1]
x_0_red[-1] = 0.
configfile = 'statsbase.ini'
(sensdict, simparams) = readconfigfile(configfile)
ambdict = simparams['amb_dict']
pulse = simparams['Pulse']
l_p = len(pulse)
Nlags = l_p
lagv = sp.arange(l_p)
ntypes = x_0.shape[0]
nspec = 128
nrg = 64
des_pnt = 16
ISpec = ISRSpectrum(nspec=nspec, sampfreq=50e3)
species = ['O+', 'e-']
spvtime = sp.zeros((ntypes, nspec))
lablist = ['Normal', 'E-Ne', 'E-Ti', 'E-Te']
v_i = 0
fitfunc = ISRSfitfunction
sumrule = simparams['SUMRULE']
Nrg1 = nrg + 1 - l_p
minrg = -sumrule[0].min()
maxrg = Nrg1 - sumrule[1].max()
Nrg2 = maxrg - minrg
for i in range(ntypes):
f, curspec, rcs = ISpec.getspecsep(x_0[i], species, v_i, rcsflag=True)
specsum = sp.absolute(curspec).sum()
spvtime[i] = rcs * curspec * nspec**2 / specsum
acforig = scfft.ifft(scfft.ifftshift(spvtime, axes=1), axis=1) / nspec
acfamb = sp.dot(ambdict['WttMatrix'],
scfft.fftshift(acforig, axes=1).transpose()).transpose()
specamb = scfft.fftshift(scfft.fft(acfamb, n=nspec, axis=1), axes=1)
fig, axmat = plt.subplots(2, 2)
axvec = axmat.flatten()
figs, axmats = plt.subplots(2, 2)
axvecs = axmats.flatten()
for i in range(ntypes):
ax = axvec[i]
ax.plot(lagv, acfamb[i].real, label='Input')
ax.set_title(lablist[i])
axs = axvecs[i]
axs.plot(f * 1e-3, specamb[i].real, label='Input', linewidth=4)
axs.set_title(lablist[i])
for irep, rep1 in enumerate(repall):
rawdata = sp.zeros((ntypes, rep1, nrg), dtype=sp.complex128)
acfest = sp.zeros((ntypes, Nrg1, l_p), dtype=rawdata.dtype)
acfestsr = sp.zeros((ntypes, Nrg2, l_p), dtype=rawdata.dtype)
specest = sp.zeros((ntypes, nspec), dtype=rawdata.dtype)
for i in range(ntypes):
for j in range(nrg - (l_p - 1)):
rawdata[i, :, j:j + l_p] = MakePulseDataRepLPC(
pulse, spvtime[i], 20, rep1) + rawdata[i, :, j:j + l_p]
acfest[i] = CenteredLagProduct(rawdata[i], pulse=pulse) / (rep1)
for irngnew, irng in enumerate(sp.arange(minrg, maxrg)):
for ilag in range(Nlags):
acfestsr[i][irngnew,
ilag] = acfest[i][irng +
sumrule[0, ilag]:irng +
sumrule[1, ilag] + 1,
ilag].mean(axis=0)
ax = axvec[i]
ax.plot(lagv,
acfestsr[i, des_pnt].real / l_p,
label='Np = {0}'.format(rep1))
if irep == len(repall) - 1:
ax.legend()
specest[i] = scfft.fftshift(
scfft.fft(acfestsr[i, des_pnt], n=nspec))
axs = axvecs[i]
axs.plot(f * 1e-3,
specest[i].real / l_p,
label='Np = {0}'.format(rep1),
linewidth=4)
if irep == len(repall) - 1:
axs.legend()
print('Parameters fitted after {0} pulses'.format(rep1))
print('Ni Ti Te Vi')
for i in range(ntypes):
d_func = (acfestsr[i, des_pnt] / l_p, sensdict, simparams)
(x, cov_x, infodict, mesg,
ier) = scipy.optimize.leastsq(func=fitfunc,
x0=x_0_red,
args=d_func,
full_output=True)
print(x)
print(' ')
fig.suptitle('ACF with Sum Rule')
fig.savefig('pulsetestacf.png', dpi=400)
plt.close(fig)
figs.suptitle('Spectrum Full Array')
figs.savefig('pulsetestspec.png', dpi=400)
plt.close(figs)
def __init__(self, ionoin, configfile, timein=None, mattype='matrix'):
""" This will create the RadarSpaceTimeOperator object.
Inputs
ionoin - The input ionocontainer. This can be either an string that is a ionocontainer file,
a list of ionocontainer objects or a list a strings to ionocontainer files.
config - The ini file that used to set up the simulation.
timein - A Ntx2 numpy array of times.
RSTOPinv - The inverse operator object.
invmat - The inverse matrix to the original operator.
"""
mattype = mattype.lower()
accepttypes = ['matrix', 'sim', 'real']
if not mattype in accepttypes:
raise ValueError('Matrix type can only be {0}'.format(
', '.join(accepttypes)))
d2r = np.pi / 180.0
(sensdict, simparams) = readconfigfile(configfile)
# determine if the input ionocontainer is a string, a list of strings or a list of ionocontainers.
ionoin = makeionocombined(ionoin)
#Input location
self.Cart_Coords_In = ionoin.Cart_Coords
self.Sphere_Coords_In = ionoin.Sphere_Coords
# Set the input times
if timein is None:
self.Time_In = ionoin.Time_Vector
else:
self.Time_In = timein
#Create an array of output location based off of the inputs
rng_vec2 = simparams['Rangegatesfinal']
nrgout = len(rng_vec2)
angles = simparams['angles']
nang = len(angles)
ang_data = np.array([[iout[0], iout[1]] for iout in angles])
rng_all = np.repeat(rng_vec2, (nang), axis=0)
ang_all = np.tile(ang_data, (nrgout, 1))
self.Sphere_Coords_Out = np.column_stack((rng_all, ang_all))
(R_vec, Az_vec,
El_vec) = (self.Sphere_Coords_Out[:, 0], self.Sphere_Coords_Out[:, 1],
self.Sphere_Coords_Out[:, 2])
xvecmult = np.sin(Az_vec * d2r) * np.cos(El_vec * d2r)
yvecmult = np.cos(Az_vec * d2r) * np.cos(El_vec * d2r)
zvecmult = np.sin(El_vec * d2r)
X_vec = R_vec * xvecmult
Y_vec = R_vec * yvecmult
Z_vec = R_vec * zvecmult
self.Cart_Coords_Out = np.column_stack((X_vec, Y_vec, Z_vec))
self.Time_Out = np.column_stack(
(simparams['Timevec'],
simparams['Timevec'] + simparams['Tint'])) + self.Time_In[0, 0]
self.simparams = simparams
self.sensdict = sensdict
self.lagmat = self.simparams['amb_dict']['WttMatrix']
self.mattype = mattype
# create the matrix
(self.RSTMat, self.overlaps,
self.blocklocs) = makematPA(ionoin.Sphere_Coords, ionoin.Cart_Coords,
ionoin.Time_Vector, configfile,
ionoin.Velocity, mattype)
def __init__(self, Ionodict, inifile, outdir, outfilelist=None):
"""
This function will create an instance of the RadarData class. It will
take in the values and create the class and make raw IQ data.
Inputs:
sensdict - A dictionary of sensor parameters
angles - A list of tuples which the first position is the az angle
and the second position is the el angle.
IPP - The interpulse period in seconds represented as a float.
Tint - The integration time in seconds as a float. This will be the
integration time of all of the beams.
time_lim - The length of time of the simulation the number of time points
will be calculated.
pulse - A numpy array that represents the pulse shape.
rng_lims - A numpy array of length 2 that holds the min and max range
that the radar will cover.
"""
(sensdict, simparams) = readconfigfile(inifile)
self.simparams = simparams
N_angles = len(self.simparams['angles'])
NNs = int(self.simparams['NNs'])
self.sensdict = sensdict
Npall = sp.floor(self.simparams['TimeLim']/self.simparams['IPP'])
Npall = int(sp.floor(Npall/N_angles)*N_angles)
Np = Npall/N_angles
print("All spectrums created already")
filetimes = Ionodict.keys()
filetimes.sort()
ftimes = sp.array(filetimes)
simdtype = self.simparams['dtype']
pulsetimes = sp.arange(Npall)*self.simparams['IPP'] +ftimes.min()
pulsefile = sp.array([sp.where(itimes-ftimes >= 0)[0][-1] for itimes in pulsetimes])
# differentiate between phased arrays and dish antennas
if sensdict['Name'].lower() in ['risr', 'pfisr', 'risr-n']:
beams = sp.tile(sp.arange(N_angles), Npall/N_angles)
else:
# for dish arrays
brate = simparams['beamrate']
beams2 = sp.repeat(sp.arange(N_angles), brate)
beam3 = sp.concatenate((beams2, beams2[::-1]))
ntile = int(sp.ceil(Npall/len(beam3)))
leftover = int(Npall-ntile*len(beam3))
if ntile > 0:
beams = sp.tile(beam3, ntile)
beams = sp.concatenate((beams, beam3[:leftover]))
else:
beams = beam3[:leftover]
pulsen = sp.repeat(sp.arange(Np), N_angles)
pt_list = []
pb_list = []
pn_list = []
fname_list = []
self.datadir = outdir
self.maindir = outdir.parent
self.procdir = self.maindir/'ACF'
Nf = len(filetimes)
progstr = 'Data from {:d} of {:d} being processed Name: {:s}.'
if outfilelist is None:
print('\nData Now being created.')
Noisepwr = v_Boltz*sensdict['Tsys']*sensdict['BandWidth']
self.outfilelist = []
for ifn, ifilet in enumerate(filetimes):
outdict = {}
ifile = Ionodict[ifilet]
ifilename = Path(ifile).name
update_progress(float(ifn)/Nf, progstr.format(ifn, Nf, ifilename))
curcontainer = IonoContainer.readh5(ifile)
if ifn == 0:
self.timeoffset = curcontainer.Time_Vector[0, 0]
pnts = pulsefile == ifn
pt = pulsetimes[pnts]
pb = beams[pnts]
pn = pulsen[pnts].astype(int)
rawdata = self.__makeTime__(pt, curcontainer.Time_Vector,
curcontainer.Sphere_Coords,
curcontainer.Param_List, pb)
d_shape = rawdata.shape
n_tempr = sp.random.randn(*d_shape).astype(simdtype)
n_tempi = 1j*sp.random.randn(*d_shape).astype(simdtype)
noise = sp.sqrt(Noisepwr/2)*(n_tempr+n_tempi)
outdict['AddedNoise'] = noise
outdict['RawData'] = rawdata+noise
outdict['RawDatanonoise'] = rawdata
outdict['NoiseData'] = sp.sqrt(Noisepwr/2)*(sp.random.randn(len(pn), NNs).astype(simdtype)+
1j*sp.random.randn(len(pn), NNs).astype(simdtype))
outdict['Pulses'] = pn
outdict['Beams'] = pb
outdict['Time'] = pt
fname = '{0:d} RawData.h5'.format(ifn)
newfn = self.datadir/fname
self.outfilelist.append(str(newfn))
dict2h5(str(newfn), outdict)
#Listing info
pt_list.append(pt)
pb_list.append(pb)
pn_list.append(pn)
fname_list.append(fname)
infodict = {'Files':fname_list, 'Time':pt_list, 'Beams':pb_list, 'Pulses':pn_list}
dict2h5(str(outdir.joinpath('INFO.h5')), infodict)
else:
infodict = h52dict(str(outdir.joinpath('INFO.h5')))
alltime = sp.hstack(infodict['Time'])
self.timeoffset = alltime.min()
self.outfilelist = outfilelist
def main():
(sensdict,simparams) = readconfigfile(inifile)
simdtype = simparams['dtype']
sumrule = simparams['SUMRULE']
npts = simparams['numpoints']
amb_dict = simparams['amb_dict']
# for spectrum
ISS2 = ISRSpectrum(centerFrequency = 440.2*1e6, bMag = 0.4e-4, nspec=npts, sampfreq=sensdict['fs'],dFlag=True)
ti = 2e3
te = 2e3
Ne = 1e11
Ni = 1e11
datablock90 = sp.array([[Ni,ti],[Ne,te]])
species = simparams['species']
(omega,specorig,rcs) = ISS2.getspecsep(datablock90, species,rcsflag = True)
cur_filt = sp.sqrt(scfft.ifftshift(specorig*npts*npts*rcs/specorig.sum()))
#for data
Nrep = 10000
pulse = sp.ones(14)
lp_pnts = len(pulse)
N_samps = 100
minrg = -sumrule[0].min()
maxrg = N_samps+lp_pnts-sumrule[1].max()
Nrng2 = maxrg-minrg;
out_data = sp.zeros((Nrep,N_samps+lp_pnts),dtype=simdtype)
samp_num = sp.arange(lp_pnts)
for isamp in range(N_samps):
cur_pnts = samp_num+isamp
cur_pulse_data = MakePulseDataRep(pulse,cur_filt,rep=Nrep)
out_data[:,cur_pnts] = cur_pulse_data+out_data[:,cur_pnts]
lagsData = CenteredLagProduct(out_data,numtype=simdtype,pulse =pulse)
lagsData=lagsData/Nrep # divide out the number of pulses summed
Nlags = lagsData.shape[-1]
lagsDatasum = sp.zeros((Nrng2,Nlags),dtype=lagsData.dtype)
for irngnew,irng in enumerate(sp.arange(minrg,maxrg)):
for ilag in range(Nlags):
lagsDatasum[irngnew,ilag] = lagsData[irng+sumrule[0,ilag]:irng+sumrule[1,ilag]+1,ilag].mean(axis=0)
lagsDatasum=lagsDatasum/lp_pnts # divide out the pulse length
(tau,acf) = spect2acf(omega,specorig)
# apply ambiguity function
tauint = amb_dict['Delay']
acfinterp = sp.zeros(len(tauint),dtype=simdtype)
acfinterp.real =spinterp.interp1d(tau,acf.real,bounds_error=0)(tauint)
acfinterp.imag =spinterp.interp1d(tau,acf.imag,bounds_error=0)(tauint)
# Apply the lag ambiguity function to the data
guess_acf = sp.zeros(amb_dict['Wlag'].shape[0],dtype=sp.complex128)
for i in range(amb_dict['Wlag'].shape[0]):
guess_acf[i] = sp.sum(acfinterp*amb_dict['Wlag'][i])
# pdb.set_trace()
guess_acf = guess_acf*rcs/guess_acf[0].real
# fit to spectrums
spec_interm = scfft.fftshift(scfft.fft(guess_acf,n=npts))
spec_final = spec_interm.real
allspecs = scfft.fftshift(scfft.fft(lagsDatasum,n=len(spec_final),axis=-1),axes=-1)
# allspecs = scfft.fftshift(scfft.fft(lagsDatasum,n=npts,axis=-1),axes=-1)
fig = plt.figure()
plt.plot(omega,spec_final.real,label='In',linewidth=5)
plt.hold(True)
plt.plot(omega,allspecs[40].real,label='Out',linewidth=5)
plt.axis((omega.min(),omega.max(),0.0,2e11))
plt.show(False)