def main(input_str=None):
args_commd = parse_command_line(input_str)
if args_commd.path is None:
curloc = Path(__file__).resolve()
testpath = curloc.parent.parent/'Testdata'/'Barker'
else:
testpath = Path(args_commd.path)
origparamsdir = testpath/'Origparams'
testpath.mkdir(exist_ok=True,parents=True)
print("Making a path for testdata at {}".format(testpath))
origparamsdir.mkdir(exist_ok=True,parents=True)
print("Making a path for testdata at {}".format(origparamsdir))
makeconfigfilebarker(testpath)
if args_commd.makeorigdata:
Icont1 = MakeTestIonoclass(testv=True,testtemp=False,N_0=1e12,z_0=150.0,H_0=50.0)
makeinputh5(Icont1,str(testpath))
Icont1.saveh5(str(origparamsdir.joinpath('0 testiono.h5')))
funcnamelist = args_commd.funclist
failflag=runsim.main(funcnamelist,testpath,str(testpath.joinpath('barkertest.yml')),True)
if not failflag:
analysisdump(testpath,testpath.joinpath('barkertest.yml'))
def makehist(testpath, npulses):
"""
This functions are will create histogram from data made in the testpath.
Inputs
testpath - The path that the data is located.
npulses - The number of pulses in the sim.
"""
sns.set_style("whitegrid")
sns.set_context("notebook")
params = ['Ne', 'Te', 'Ti', 'Vi']
pvals = [1e11, 2.1e3, 1.1e3, 0.]
histlims = [[4e10, 2e11], [1200., 3000.], [300., 1900.], [-250., 250.]]
erlims = [[-2e11, 2e11], [-1000., 1000.], [-800., -800], [-250., 250.]]
erperlims = [[-100., 100.]] * 4
lims_list = [histlims, erlims, erperlims]
errdict = makehistdata(params, testpath)[:4]
ernames = ['Data', 'Error', 'Error Percent']
sig1 = sp.sqrt(1. / npulses)
# Two dimensiontal histograms
pcombos = [i for i in itertools.combinations(params, 2)]
c_rows = int(math.ceil(float(len(pcombos)) / 2.))
(figmplf, axmat) = plt.subplots(c_rows,
2,
figsize=(12, c_rows * 6),
facecolor='w')
axvec = axmat.flatten()
for icomn, icom in enumerate(pcombos):
curax = axvec[icomn]
str1, str2 = icom
_, _, _ = make2dhist(testpath, PARAMDICT[str1], PARAMDICT[str2],
figmplf, curax)
filetemplate = str(Path(testpath).joinpath('AnalysisPlots', 'TwoDDist'))
plt.tight_layout()
plt.subplots_adjust(top=0.95)
figmplf.suptitle('Pulses: {0}'.format(npulses), fontsize=20)
fname = filetemplate + '_{0:0>5}Pulses.png'.format(npulses)
plt.savefig(fname)
plt.close(figmplf)
# One dimensiontal histograms
for ierr, iername in enumerate(ernames):
filetemplate = str(Path(testpath).joinpath('AnalysisPlots', iername))
(figmplf, axmat) = plt.subplots(2, 2, figsize=(20, 15), facecolor='w')
axvec = axmat.flatten()
for ipn, iparam in enumerate(params):
plt.sca(axvec[ipn])
if sp.any(sp.isinf(errdict[ierr][iparam])):
continue
binlims = lims_list[ierr][ipn]
bins = sp.linspace(binlims[0], binlims[1], 100)
histhand = sns.distplot(errdict[ierr][iparam],
bins=bins,
kde=True,
rug=False)
axvec[ipn].set_title(iparam)
figmplf.suptitle(iername + ' Pulses: {0}'.format(npulses), fontsize=20)
fname = filetemplate + '_{0:0>5}Pulses.png'.format(npulses)
plt.savefig(fname)
plt.close(figmplf)
def saveh5(self,filename):
"""
This method will save the instance of the class to a structured h5 file.
Input:
filename - A string for the file name.
"""
filename=Path(filename)
if filename.is_file():
filename.unlink()
vardict = vars(self)
with tables.open_file(str(filename), mode = "w", title = "IonoContainer out.") as f:
try:
# XXX only allow 1 level of dictionaries, do not allow for dictionary of dictionaries.
# Make group for each dictionary
for cvar in vardict.keys():
#group = f.create_group(posixpath.sep, cvar,cvar +'dictionary')
if type(vardict[cvar]) ==dict: # Check if dictionary
dictkeys = vardict[cvar].keys()
group2 = f.create_group('/',cvar,cvar+' dictionary')
for ikeys in dictkeys:
f.create_array(group2,ikeys,vardict[cvar][ikeys],'Static array')
else:
if not(vardict[cvar] is None):
f.create_array('/',cvar,vardict[cvar],'Static array')
except Exception as inst:
print(type(inst))
print(inst.args)
print(inst)
raise NameError('Failed to write to h5 file.')
def makedata(testpath, tint):
""" This will make the input data for the test case. The data will have cases
where there will be enhancements in Ne, Ti and Te in one location. Each
case will have 3 integration periods. The first 3 integration periods will
be the default set of parameters Ne=Ne=1e11 and Te=Ti=2000.
Inputs
testpath - Directory that will hold the data.
tint - The integration time in seconds.
"""
testpath = Path(testpath).expanduser()
finalpath = testpath.joinpath('Origparams')
if not finalpath.is_dir():
finalpath.mkdir()
data = sp.array([[1e11, 1100.], [1e11, 2100.]])
z = (50. + sp.arange(50) * 10.)
nz = len(z)
params = sp.tile(data[sp.newaxis, sp.newaxis], (nz, 1, 1, 1))
epnt = range(20, 22)
p2 = sp.tile(params, (1, 4, 1, 1))
#enhancement in Ne
p2[epnt, 1, :, 0] = 5e11
#enhancement in Ti
p2[epnt, 2, 0, 1] = 2200.
#enhancement in Te
p2[epnt, 3, 1, 1] = 4200.
coords = sp.column_stack((sp.ones(nz), sp.ones(nz), z))
species = ['O+', 'e-']
times = sp.array([[0, 1e3]])
times2 = sp.column_stack((sp.arange(0, 4), sp.arange(1, 5))) * 3 * tint
vel = sp.zeros((nz, 1, 3))
vel2 = sp.zeros((nz, 4, 3))
Icontstart = IonoContainer(coordlist=coords,
paramlist=params,
times=times,
sensor_loc=sp.zeros(3),
ver=0,
coordvecs=['x', 'y', 'z'],
paramnames=None,
species=species,
velocity=vel)
Icont1 = IonoContainer(coordlist=coords,
paramlist=p2,
times=times2,
sensor_loc=sp.zeros(3),
ver=0,
coordvecs=['x', 'y', 'z'],
paramnames=None,
species=species,
velocity=vel2)
finalfile = finalpath.joinpath('0 stats.h5')
Icont1.saveh5(str(finalfile))
Icontstart.saveh5(str(testpath.joinpath('startfile.h5')))
def main(plist=None,
functlist=['spectrums', 'radardata', 'fitting', 'analysis', 'stats'],
datadir=None):
""" 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)
if datadir is None:
curloc = Path(__file__).resolve().parent
testpath = curloc.parent.joinpath('Testdata', 'StatsTest')
else:
datadir = Path(datadir)
testpath = datadir
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'
# 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, params=['Ne', 'Te', 'Ti', 'Vi'])
if 'stats' in functlist:
makehist(curfold, ip)
def main():
curloc = Path(__file__).resolve()
testpath = curloc.parent.parent / 'Testdata' / 'Barker'
origparamsdir = testpath / 'Origparams'
pdb.set_trace()
testpath.mkdir(exist_ok=True, parents=True)
print("Making a path for testdata at {}".format(testpath))
origparamsdir.mkdir(exist_ok=True, parents=True)
print("Making a path for testdata at {}".format(origparamsdir))
makeconfigfilebarker(testpath)
Icont1 = MakeTestIonoclass(testv=True,
testtemp=False,
N_0=1e12,
z_0=150.0,
H_0=50.0)
makeinputh5(Icont1, str(testpath))
Icont1.saveh5(str(origparamsdir.joinpath('0 testiono.h5')))
funcnamelist = ['spectrums', 'radardata', 'fitting']
failflag = runsim.main(funcnamelist, testpath,
str(testpath.joinpath('barkertest.ini')), True)
if not failflag:
analysisdump(testpath, testpath.joinpath('barkertest.ini'))
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 main():
"""This function will run the test simulation buy first making a simple set of
ionospheric parameters based off of a Chapman function. Then it will create configuration
and start files followed by running the simulation."""
curpath = Path(__file__).resolve().parent
testpath = curpath.parent/'Testdata'/'Long_Pulse'
origparamsdir = testpath/'Origparams'
if not testpath.is_dir():
testpath.mkdir(parents=True)
print("Making a path for testdata at {}".format(str(testpath)))
if not origparamsdir.is_dir():
origparamsdir.mkdir(parents=True)
print("Making a path for testdata at {}".format(origparamsdir))
# clear everything out
folderlist = ['Origparams','Spectrums','Radardata','ACF','Fitted']
for ifl in folderlist:
flist = (testpath/ifl).glob('*.h5')
for ifile in flist:
ifile.unlink()
# Now make stuff again
configsetup(testpath)
Icont1 = MakeTestIonoclass(testv=True,testtemp=True)
makeinputh5(MakeTestIonoclass(testv=True,testtemp=False),testpath)
Icont1.saveh5(origparamsdir/'0 testiono.h5')
funcnamelist=['spectrums','radardata','fitting']
failflag = runsim.main(funcnamelist,testpath, testpath/'PFISRExample.ini',True)
if not failflag:
analysisdump(testpath,str(testpath/'PFISRExample.ini'))
def makeinputh5(Iono, basedir):
basedir = Path(basedir).expanduser()
Param_List = Iono.Param_List
dataloc = Iono.Cart_Coords
times = Iono.Time_Vector
velocity = Iono.Velocity
zlist, idx = sp.unique(dataloc[:, 2], return_inverse=True)
siz = list(Param_List.shape[1:])
vsiz = list(velocity.shape[1:])
datalocsave = sp.column_stack(
(sp.zeros_like(zlist), sp.zeros_like(zlist), zlist))
outdata = sp.zeros([len(zlist)] + siz)
outvel = sp.zeros([len(zlist)] + vsiz)
for izn, iz in enumerate(zlist):
arr = sp.argwhere(idx == izn)
outdata[izn] = sp.mean(Param_List[arr], axis=0)
outvel[izn] = sp.mean(velocity[arr], axis=0)
Ionoout = IonoContainer(datalocsave,
outdata,
times,
Iono.Sensor_loc,
ver=0,
paramnames=Iono.Param_Names,
species=Iono.Species,
velocity=outvel)
ofn = basedir / 'startdata.h5'
print('writing {}'.format(ofn))
Ionoout.saveh5(str(ofn))
def makedatasets(maindir='~/DATA/Ion_Comp_Exp/',
nomult=sp.arange(1, 5, dtype=float),
baud_len=[7, 14, 21]):
"""
This will make all of the data sets.
"""
basepath = Path(maindir).expanduser()
basepath.mkdir(exist_ok=True)
iono_orig = pyglowinput()
nion = len(iono_orig.Species) - 1
npulses = 1000
(sensdict, simparams) = getdefualtparams()
tint = simparams['IPP'] * npulses
ratio1 = tint / simparams['Tint']
simparams['RangeLims'] = [80., 750.]
simparams['Tint'] = ratio1 * simparams['Tint']
simparams['Fitinter'] = ratio1 * simparams['Fitinter']
simparams['TimeLim'] = 12 * tint
ts = simparams['t_s']
simparams['beamrate'] = 1
simparams['outangles'] = [[0]]
simparams['species'] = ['O+', 'NO+', 'O2+', 'H+', 'e-']
origtime = iono_orig.Time_Vector[0, 0]
for imult in nomult:
curiono = iono_orig.copy()
curiono.Param_List[:, :, 1, 0] *= imult
ratio = curiono.Param_List[:, :, -1, 0] / curiono.Param_List[:, :, :-1,
0].sum(-1)
ratio_ar = sp.repeat(ratio[:, :, sp.newaxis], nion, axis=-1)
curiono.Param_List[:, :, :-1, 0] *= ratio_ar
figout = plotiono(curiono)[0]
for ibaud in baud_len:
newpath = basepath.joinpath('NOMult{0:02d}baud{1:02d}'.format(
int(imult), int(ibaud)))
newpath.joinpath('Origparams').mkdir(exist_ok=True, parents=True)
figname = newpath.joinpath('InputParams.png')
figout.savefig(str(figname))
dataname = newpath.joinpath('Origparams',
'{0:d}Params.h5'.format(origtime))
curiono.saveh5(str(dataname))
simparams['Pulselength'] = ibaud * ts
sfile = str(newpath / 'startfile.h5')
iono_orig.saveh5(sfile)
simparams['startfile'] = sfile
makeconfigfile(str(newpath / 'chem_test.yml'), [23465.],
'millstone', simparams)
def main(input_str=None):
args_commd = parse_command_line(input_str)
if args_commd.path is None:
curloc = Path(__file__).resolve()
testpath = curloc.parent.parent / 'Testdata' / 'Barker'
else:
testpath = Path(args_commd.path)
origparamsdir = testpath / 'Origparams'
testpath.mkdir(exist_ok=True, parents=True)
print("Making a path for testdata at {}".format(testpath))
origparamsdir.mkdir(exist_ok=True, parents=True)
print("Making a path for testdata at {}".format(origparamsdir))
makeconfigfilebarker(testpath)
if args_commd.makeorigdata:
Icont1 = MakeTestIonoclass(testv=True,
testtemp=False,
N_0=1e12,
z_0=150.0,
H_0=50.0)
makeinputh5(Icont1, str(testpath))
Icont1.saveh5(str(origparamsdir.joinpath('0 testiono.h5')))
funcnamelist = args_commd.funclist
failflag = runsim.main(funcnamelist, testpath,
str(testpath.joinpath('barkertest.yml')), True)
if not failflag:
analysisdump(testpath, testpath.joinpath('barkertest.yml'))
def applymat(basedir, configfile, optinputs):
"""
This function apply the matrix version of the space time ambiugty function
to the ACFs and save the outcome in h5 files within the directory ACFMat.
Inputs:
basedir: A string for the directory that will hold all of the data for the simulation.
configfile: The configuration file for the simulation.
"""
dirio = ('Spectrums', 'Mat', 'ACFMat')
basedir = Path(basedir)
inputdir = basedir.joinpath(dirio[0])
outputdir2 = basedir.joinpath(dirio[2])
dirlist = [str(i) for i in inputdir.glob('*.h5')]
(listorder, timevector, _, _, _) = IonoContainer.gettimes(dirlist)
ionolist = [dirlist[ikey] for ikey in listorder]
rsto = RadarSpaceTimeOperator(ionolist, configfile, timevector, mattype='matrix')
ionoout = rsto.mult_iono(ionolist)
outfile = outputdir2.joinpath('00lags.h5')
ionoout.saveh5(str(outfile))
def makedata(testpath,tint):
""" This will make the input data for the test case. The data will have cases
where there will be enhancements in Ne, Ti and Te in one location. Each
case will have 3 integration periods. The first 3 integration periods will
be the default set of parameters Ne=Ne=1e11 and Te=Ti=2000.
Inputs
testpath - Directory that will hold the data.
tint - The integration time in seconds.
"""
testpath = Path(testpath).expanduser()
finalpath = testpath.joinpath('Origparams')
if not finalpath.is_dir():
finalpath.mkdir()
data = sp.array([[1e11,1100.], [1e11,2100.]])
z = (50.+sp.arange(50)*10.)
nz = len(z)
params = sp.tile(data[sp.newaxis, sp.newaxis],(nz, 1, 1, 1))
epnt = range(20,22)
p2 = sp.tile(params, (1, 4, 1, 1))
#enhancement in Ne
p2[epnt, 1, :, 0] = 5e11
#enhancement in Ti
p2[epnt,2,0,1] = 2200.
#enhancement in Te
p2[epnt,3,1,1] = 4200.
coords = sp.column_stack((sp.zeros(nz), sp.zeros(nz), z))
species=['O+', 'e-']
times = sp.array([[0, 1e3]])
times2 = sp.column_stack((sp.arange(0, 4), sp.arange(1, 5)))*3*tint
vel = sp.zeros((nz, 1, 3))
vel2 = sp.zeros((nz, 4, 3))
Icontstart = IonoContainer(coordlist=coords, paramlist=params, times=times,
sensor_loc=sp.zeros(3), ver=0, coordvecs=['x', 'y', 'z'],
paramnames=None, species=species, velocity=vel)
Icont1 = IonoContainer(coordlist=coords, paramlist=p2, times=times2,
sensor_loc=sp.zeros(3), ver=0, coordvecs=['x', 'y', 'z'],
paramnames=None, species=species, velocity=vel2)
finalfile = finalpath.joinpath('0 stats.h5')
Icont1.saveh5(str(finalfile))
Icontstart.saveh5(str(testpath.joinpath('startfile.h5')))
def makeconfigfilebarker(testpath):
testpath = Path(testpath).expanduser()
beamlist = [
64094, 64091, 64088, 64085, 64082, 64238, 64286, 64070, 64061, 64058,
64055, 64052, 64049, 64046, 64043, 64067, 64040, 64037, 64034
]
radarname = 'pfisr'
Tint = 4.0 * 60.0
time_lim = 3.0 * Tint
pulse = GenBarker(7)
rng_lims = [75.0, 250.0]
IPP = .0087
NNs = 28
NNp = 100
t_s = 2e-5
Pulselength = len(pulse) * t_s
simparams = {
'IPP': IPP,
'TimeLim': time_lim,
'RangeLims': rng_lims,
'Pulse': pulse,
'Pulsetype': 'barker',
'Pulselength': Pulselength,
't_s': t_s,
'Tint': Tint,
'Fitinter': Tint,
'NNs': NNs,
'NNp': NNp,
'dtype': sp.complex128,
'ambupsamp': 30,
'species': ['O+', 'e-'],
'numpoints': 128,
'FitType': 'acf',
'startfile': str(testpath.joinpath('startdata.h5'))
}
fn = testpath / 'barkertest.yml'
makeconfigfile(fn, beamlist, radarname, simparams)
def makedatasets(maindir='~/DATA/Ion_Comp_Exp/', nomult=sp.arange(1, 5, dtype=float), baud_len=[7, 14, 21]):
"""
This will make all of the data sets.
"""
basepath = Path(maindir).expanduser()
basepath.mkdir(exist_ok=True)
iono_orig = pyglowinput()
nion = len(iono_orig.Species)-1
npulses = 1000
(sensdict, simparams) = getdefualtparams()
tint = simparams['IPP']*npulses
ratio1 = tint/simparams['Tint']
simparams['RangeLims'] = [80., 750.]
simparams['Tint'] = ratio1 * simparams['Tint']
simparams['Fitinter'] = ratio1 * simparams['Fitinter']
simparams['TimeLim'] = 12*tint
ts = simparams['t_s']
simparams['beamrate'] = 1
simparams['outangles'] = [[0]]
simparams['species'] = ['O+', 'NO+', 'O2+', 'H+', 'e-']
origtime = iono_orig.Time_Vector[0,0]
for imult in nomult:
curiono = iono_orig.copy()
curiono.Param_List[:, :, 1, 0] *= imult
ratio = curiono.Param_List[:, :, -1, 0]/curiono.Param_List[:, :, :-1, 0].sum(-1)
ratio_ar = sp.repeat(ratio[:, :, sp.newaxis], nion, axis=-1)
curiono.Param_List[:, :, :-1, 0] *= ratio_ar
figout = plotiono(curiono)[0]
for ibaud in baud_len:
newpath = basepath.joinpath('NOMult{0:02d}baud{1:02d}'.format(int(imult), int(ibaud)))
newpath.joinpath('Origparams').mkdir(exist_ok=True, parents=True)
figname = newpath.joinpath('InputParams.png')
figout.savefig(str(figname))
dataname = newpath.joinpath('Origparams', '{0:d}Params.h5'.format(origtime))
curiono.saveh5(str(dataname))
simparams['Pulselength'] = ibaud*ts
sfile = str(newpath/'startfile.h5')
iono_orig.saveh5(sfile)
simparams['startfile'] = sfile
makeconfigfile(str(newpath/'chem_test.yml'), [23465.], 'millstone', 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):
""" 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 makeconfigfilebarker(testpath):
testpath = Path(testpath).expanduser()
beamlist = [64094,64091,64088,64085,64082,64238,64286,64070,64061,64058,64055,64052,
64049,64046,64043,64067,64040,64037,64034]
radarname = 'pfisr'
Tint = 4.0*60.0
time_lim = 3.0*Tint
pulse = GenBarker(7)
rng_lims = [75.0,250.0]
IPP = .0087
NNs = 28
NNp = 100
t_s=2e-5
Pulselength=len(pulse)*t_s
simparams = {'IPP':IPP,
'TimeLim':time_lim,
'RangeLims':rng_lims,
'Pulse':pulse,
'Pulsetype':'barker',
'Pulselength':Pulselength,
't_s':t_s,
'Tint':Tint,
'Fitinter':Tint,
'NNs': NNs,
'NNp':NNp,
'dtype':sp.complex128,
'ambupsamp':30,
'species':['O+','e-'],
'numpoints':128,
'FitType':'acf',
'startfile':str(testpath.joinpath('startdata.h5'))}
fn = testpath/'barkertest.yml'
makeconfigfile(fn,beamlist,radarname,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 main(funcnamelist):
"""This function will run the test simulation buy first making a simple set of
ionospheric parameters based off of a Chapman function. Then it will create configuration
and start files followed by running the simulation."""
curpath = Path(__file__).resolve().parent
testpath = curpath / 'Testdata' / 'DishMode'
origparamsdir = testpath / 'Origparams'
testpath.mkdir(exist_ok=True, parents=True)
origparamsdir.mkdir(exist_ok=True, parents=True)
if 'configupdate' in funcnamelist:
configsetup(testpath)
funcnamelist.remove('configupdate')
# clear everything out
folddict = {
'origdata': ['Origparams'],
'spectrums': ['Spectrums'],
'radardata': ['ACF', 'Radardata'],
'fitting': ['Fitted']
}
folderlist = []
for i in funcnamelist:
folderlist = folderlist + folddict[i]
# folderlist = ['Origparams','Spectrums','Radardata','ACF','Fitted']
for ifl in folderlist:
flist = (testpath / ifl).glob('*.h5')
for ifile in flist:
ifile.unlink()
# Now make stuff again
if 'origdata' in funcnamelist:
Icont1 = MakeTestIonoclass(testv=True, testtemp=True)
makeinputh5(MakeTestIonoclass(testv=True, testtemp=False), testpath)
Icont1.saveh5(origparamsdir / '0 testiono.h5')
funcnamelist.remove('origdata')
# funcnamelist=['spectrums','radardata','fitting']
failflag = runsim.main(funcnamelist, testpath,
testpath / 'DishExample.ini', True)
if not failflag:
analysisdump(testpath, testpath / 'DishExample.ini')
def configsetup(testpath):
"""This function will make a pickle file used to configure the simulation.
Inputs
testpath - A string for the path that this file will be saved."""
testpath=Path(testpath)
beamlist = [64094,64091,64088,64085,64082,64238,64286,64070,64061,64058,64055,64052,
64049,64046,64043,64067,64040,64037,64034] # list of beams in
radarname = 'pfisr'# name of radar for parameters can either be pfisr or risr
Tint=60.0 # integration time in seconds
time_lim = 4.0*Tint # simulation length in seconds
fitter_int = 60.0 # time interval between fitted params
# pulse = sp.ones(14)# pulse
rng_lims = [150,500]# limits of the range gates
IPP = .0087 #interpulse period in seconds
NNs = 28 # number of noise samples per pulse
NNp = 100 # number of noise pulses
simparams = {'IPP':IPP, #interpulse period
'TimeLim':time_lim, # length of simulation
'RangeLims':rng_lims, # range swath limit
# 'Pulse':pulse, # pulse shape
'Pulselength':280e-6,
'FitType' :'acf',
't_s': 20e-6,
'Pulsetype':'long', # type of pulse can be long or barker,
'Tint':Tint, #Integration time for each fitting
'Fitinter':fitter_int, # time interval between fitted params
'NNs': NNs,# number of noise samples per pulse
'NNp':NNp, # number of noise pulses
'dtype':sp.complex128, #type of numbers used for simulation
'ambupsamp':1, # up sampling factor for ambiguity function
'species':['O+','e-'], # type of ion species used in simulation
'numpoints':128, # number of points for each spectrum
'startfile': str(testpath/'startdata.h5')} # file used for starting points
# 'SUMRULE': sp.array([[-2,-3,-3,-4,-4,-5,-5,-6,-6,-7,-7,-8,-8,-9]
# ,[1,1,2,2,3,3,4,4,5,5,6,6,7,7]])}
fname = testpath/'PFISRExample'
makeconfigfile(str(fname.with_suffix('.ini')),beamlist,radarname,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()))
Icont1.saveh5(origparamsdir / '0 testiono.h5')
funcnamelist.remove('origdata')
# funcnamelist=['spectrums','radardata','fitting']
failflag = runsim.main(funcnamelist, testpath,
testpath / 'DishExample.ini', True)
if not failflag:
analysisdump(testpath, testpath / 'DishExample.ini')
if __name__ == '__main__':
from argparse import ArgumentParser
p = ArgumentParser(
description=
'Planeproc.py -f <function: configupdate, origdata, spectrums, radardata, fitting or all>'
)
p.add_argument('-f', '--funcnamelist', nargs='+')
p.add_argument('-r', '--re', action='store_true')
p = p.parse_args()
curpath = Path(__file__).resolve().parent
remakealldata = p.re
if p.funcnamelist is None or 'all' in p.funcnamelist:
funcnamelist = [
'configupdate', 'origdata', 'spectrums', 'radardata', 'fitting'
]
main(funcnamelist)
fittersimple.py
This module will implement a simple fitter for ISR spectra.
@author: John Swoboda
"""
import scipy as sp
import scipy.optimize
from SimISR import Path
from SimISR.IonoContainer import IonoContainer, makeionocombined
from SimISR.utilFunctions import readconfigfile, update_progress,spect2acf
import SimISR.specfunctions as specfuncs
PVALS = [1e11, 2.1e3, 1.1e3, 0.]
SVALS = [1.1e3, 1e11, 2.1e3, 0.]
SIMVALUES = sp.array([[PVALS[0],PVALS[2]],[PVALS[0],PVALS[1]]])
curloc = Path(__file__).resolve().parent
defcon = curloc/'statsbase.ini'
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))
def makehistdata(params, maindir):
""" This will make the histogram data for the statistics.
Inputs
params - A list of parameters that will have statistics created
maindir - The directory that the simulation data is held.
Outputs
datadict - A dictionary with the data values in numpy arrays. The keys are param names.
errordict - A dictionary with the data values in numpy arrays. The keys are param names.
errdictrel - A dictionary with the error values in numpy arrays, normalized by the correct value. The keys are param names.
"""
maindir = Path(maindir)
ffit = maindir.joinpath('Fitted', 'fitteddata.h5')
inputfiledir = maindir.joinpath('Origparams')
paramslower = [ip.lower() for ip in params]
eparamslower = ['n' + ip.lower() for ip in params]
# set up data dictionary
errordict = {ip: [] for ip in params}
errordictrel = {ip: [] for ip in params}
#Read in fitted data
Ionofit = IonoContainer.readh5(str(ffit))
times = Ionofit.Time_Vector
dataloc = Ionofit.Sphere_Coords
rng = dataloc[:, 0]
rng_log = sp.logical_and(rng > 200., rng < 400)
dataloc_out = dataloc[rng_log]
pnames = Ionofit.Param_Names
pnameslower = sp.array([ip.lower() for ip in pnames.flatten()])
p2fit = [
sp.argwhere(ip == pnameslower)[0][0] if ip in pnameslower else None
for ip in paramslower
]
datadict = {
ip: Ionofit.Param_List[rng_log, :, p2fit[ipn]].flatten()
for ipn, ip in enumerate(params)
}
ep2fit = [
sp.argwhere(ip == pnameslower)[0][0] if ip in pnameslower else None
for ip in eparamslower
]
edatadict = {
ip: Ionofit.Param_List[rng_log, :, ep2fit[ipn]].flatten()
for ipn, ip in enumerate(params)
}
# Determine which input files are to be used.
dirlist = [str(i) for i in inputfiledir.glob('*.h5')]
_, outime, filelisting, _, _ = IonoContainer.gettimes(dirlist)
time2files = []
for itn, itime in enumerate(times):
log1 = (outime[:, 0] >= itime[0]) & (outime[:, 0] < itime[1])
log2 = (outime[:, 1] > itime[0]) & (outime[:, 1] <= itime[1])
log3 = (outime[:, 0] <= itime[0]) & (outime[:, 1] > itime[1])
tempindx = sp.where(log1 | log2 | log3)[0]
time2files.append(filelisting[tempindx])
curfilenum = -1
for iparam, pname in enumerate(params):
curparm = paramslower[iparam]
# Use Ne from input to compare the ne derived from the power.
if curparm == 'nepow':
curparm = 'ne'
datalist = []
for itn, itime in enumerate(times):
for filenum in time2files[itn]:
filenum = int(filenum)
if curfilenum != filenum:
curfilenum = filenum
datafilename = dirlist[filenum]
Ionoin = IonoContainer.readh5(datafilename)
if ('ti' in paramslower) or ('vi' in paramslower):
Ionoin = maketi(Ionoin)
pnames = Ionoin.Param_Names
pnameslowerin = sp.array(
[ip.lower() for ip in pnames.flatten()])
prmloc = sp.argwhere(curparm == pnameslowerin)
if prmloc.size != 0:
curprm = prmloc[0][0]
# build up parameter vector bs the range values by finding the closest point in space in the input
curdata = sp.zeros(len(dataloc_out))
for irngn, curcoord in enumerate(dataloc_out):
tempin = Ionoin.getclosestsphere(curcoord, [itime])[0]
Ntloc = tempin.shape[0]
tempin = sp.reshape(tempin, (Ntloc, len(pnameslowerin)))
curdata[irngn] = tempin[0, curprm]
datalist.append(curdata)
errordict[pname] = datadict[pname] - sp.hstack(datalist)
errordictrel[pname] = 100. * errordict[pname] / sp.absolute(
sp.hstack(datalist))
return datadict, errordict, errordictrel, edatadict
def main():
curpath = Path(__file__).resolve().parents[1]
print(curpath)
testpath = curpath / 'Testdata' / 'MatrixTest'
origparamsdir = testpath / 'Origparams'
testpath.mkdir(exist_ok=True, parents=True)
origparamsdir.mkdir(exist_ok=True, parents=True)
# clear everything out
folderlist = ['Origparams', 'Spectrums', 'Radardata', 'ACF', 'Fitted']
for ifl in folderlist:
flist = (testpath / ifl).glob('*.h5')
for ifile in flist:
ifile.unlink()
# Make Config file
configname = testpath / 'config.ini'
if not configname.is_file():
srcfile = curpath / 'SimISR' / 'default.ini'
shutil.copy(str(srcfile), str(configname))
# make the coordinates
xvec = sp.zeros((1))
yvec = sp.zeros((1))
zvec = sp.arange(50.0, 900.0, 2.0)
# Mesh grid is set up in this way to allow for use in MATLAB with a simple reshape command
xx, zz, yy = sp.meshgrid(xvec, zvec, yvec)
coords = sp.zeros((xx.size, 3))
coords[:, 0] = xx.flatten()
coords[:, 1] = yy.flatten()
coords[:, 2] = zz.flatten()
Z_0 = 250.
H_0 = 30.
N_0 = 6.5e11
Icont1 = MakeTestIonoclass(testv=True,
testtemp=True,
N_0=N_0,
z_0=Z_0,
H_0=H_0,
coords=coords)
Icont1.saveh5(origparamsdir / '0 testiono.h5')
Icont1.saveh5(testpath / 'startdata.h5')
funcnamelist = ['spectrums', 'applymat', 'fittingmat']
runsim.main(funcnamelist, testpath, configname, True)
plotdir = testpath / 'AnalysisPlots'
plotdir.mkdir(exist_ok=True, parents=True)
f_templ = str(plotdir / 'params')
plotbeamparametersv2([0.],
str(configname),
str(testpath),
fitdir='FittedMat',
params=['Ne', 'Ti', 'Te'],
filetemplate=f_templ,
suptitle='With Mat',
werrors=False,
nelog=False)
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 makehistdata(params,maindir):
""" This will make the histogram data for the statistics.
Inputs
params - A list of parameters that will have statistics created
maindir - The directory that the simulation data is held.
Outputs
datadict - A dictionary with the data values in numpy arrays. The keys are param names.
errordict - A dictionary with the data values in numpy arrays. The keys are param names.
errdictrel - A dictionary with the error values in numpy arrays, normalized by the correct value. The keys are param names.
"""
maindir=Path(maindir)
ffit = maindir.joinpath('Fitted','fitteddata.h5')
inputfiledir = maindir.joinpath('Origparams')
paramslower = [ip.lower() for ip in params]
eparamslower = ['n'+ip.lower() for ip in params]
# set up data dictionary
errordict = {ip:[] for ip in params}
errordictrel = {ip:[] for ip in params}
#Read in fitted data
Ionofit = IonoContainer.readh5(ffit)
times=Ionofit.Time_Vector
dataloc = Ionofit.Sphere_Coords
pnames = Ionofit.Param_Names
pnameslower = sp.array([ip.lower() for ip in pnames.flatten()])
p2fit = [sp.argwhere(ip==pnameslower)[0][0] if ip in pnameslower else None for ip in paramslower]
datadict = {ip:Ionofit.Param_List[:,:,p2fit[ipn]].flatten() for ipn, ip in enumerate(params)}
ep2fit = [sp.argwhere(ip==pnameslower)[0][0] if ip in pnameslower else None for ip in eparamslower]
edatadict = {ip:Ionofit.Param_List[:,:,ep2fit[ipn]].flatten() for ipn, ip in enumerate(params)}
# Determine which input files are to be used.
dirlist = [str(i) for i in inputfiledir.glob('*.h5')]
sortlist,outime,filelisting,timebeg,timelist_s = IonoContainer.gettimes(dirlist)
time2files = []
for itn,itime in enumerate(times):
log1 = (outime[:,0]>=itime[0]) & (outime[:,0]<itime[1])
log2 = (outime[:,1]>itime[0]) & (outime[:,1]<=itime[1])
log3 = (outime[:,0]<=itime[0]) & (outime[:,1]>itime[1])
tempindx = sp.where(log1|log2|log3)[0]
time2files.append(filelisting[tempindx])
curfilenum=-1
for iparam,pname in enumerate(params):
curparm = paramslower[iparam]
# Use Ne from input to compare the ne derived from the power.
if curparm == 'nepow':
curparm = 'ne'
datalist = []
for itn,itime in enumerate(times):
for iplot,filenum in enumerate(time2files[itn]):
filenum = int(filenum)
if curfilenum!=filenum:
curfilenum=filenum
datafilename = dirlist[filenum]
Ionoin = IonoContainer.readh5(datafilename)
if ('ti' in paramslower) or ('vi' in paramslower):
Ionoin = maketi(Ionoin)
pnames = Ionoin.Param_Names
pnameslowerin = sp.array([ip.lower() for ip in pnames.flatten()])
prmloc = sp.argwhere(curparm==pnameslowerin)
if prmloc.size !=0:
curprm = prmloc[0][0]
# build up parameter vector bs the range values by finding the closest point in space in the input
curdata = sp.zeros(len(dataloc))
for irngn, curcoord in enumerate(dataloc):
tempin = Ionoin.getclosestsphere(curcoord,[itime])[0]
Ntloc = tempin.shape[0]
tempin = sp.reshape(tempin,(Ntloc,len(pnameslowerin)))
curdata[irngn] = tempin[0,curprm]
datalist.append(curdata)
errordict[pname] = datadict[pname]-sp.hstack(datalist)
errordictrel[pname] = 100.*errordict[pname]/sp.absolute(sp.hstack(datalist))
return datadict,errordict,errordictrel,edatadict
the full simulation. The user can also start with a directory
from a later stage of the simulation instead though.
-c The configuration used for the simulation. Can be an ini file or
a pickle file.
Optional arguments
-r If a y follows this then the raw radar data will be remade. If
this is not used the radar data will only be made if it does
not exist in the file first.
Example:
python runsim.py -f radardata -f fitting -i ~/DATA/ExampleLongPulse -c ~/DATA/Example -r y'''
args_commd = parse_command_line()
if args_commd.path is None:
print("Please provide an input source with the -p option!")
sys.exit(1)
basedir = str(Path(args_commd.path).expanduser())
configfile = str(Path(args_commd.config).expanduser())
funcname = args_commd.funclist
remakealldata = args_commd.remake
if funcname.lower() == 'all':
funcnamelist = ['spectrums', 'radardata', 'fitting']
else:
funcnamelist = funcname.split()
failflag = main(funcnamelist, basedir, configfile, remakealldata)
axmat[0].set_xlim([maxden*1e-5, maxden])
axmat[0].set_xlabel(r'Densities in m$^{-3}$')
axmat[0].set_ylabel('Alt in km')
axmat[0].legend()
axmat[1].set_title('Temperture')
axmat[1].set_xlim([100., 2500.])
axmat[1].set_xlabel(r'Temp in $^{\circ}$ K')
axmat[1].set_ylabel('Alt in km')
axmat[1].legend()
plt.tight_layout()
return figmplf,axmat
if __name__ == '__main__':
exppath = Path('~/DATA/Ion_Comp_Exp').expanduser()
drpath = Path('~/Dropbox (MIT)/').expanduser()
funclist = ['spectrums', 'radardata','fitting']
list1 = [i for i in exppath.glob('NO*')]
configlist = [i.joinpath('chem_test.yml') for i in exppath.glob('NO*')]
for idata,icon in zip(list1,configlist):
runsimisr(funclist,str(idata),str(icon),True)
for idata,icon in zip(list1,configlist):
analysisdump(str(idata),str(icon),params = ['Ne','Nepow','Te','Ti'])
for ipath in list1:
idir=ipath.joinpath('AnalysisPlots')
idest = drpath.joinpath(*ipath.parts[-2:])
shutil.copytree(str(idir),str(idest))
def main(funcnamelist,basedir,configfile,remakealldata,fitlist=None,invtype='',printlines=True):
""" Main function for this module. The function will set up the directory
structure, create or update a diary file and run the simulation depending
on the user input.
Inputs
funcnamelist: A list of strings that coorespond to specific functions.
The stirng and function they correspond to, that will be shown.
spectrums: makespectrums, This will create the ISR spectrums
radardata :makeradardata, This will make the radar data and
form the ACF estimates. If the raw radar data exists then
the user must use the -r option on the command line and set
it to y.
fitting :fitdata, This will apply the fitter to the data in
the ACF folder of the base directory.
fittingmat :fitdata,This will apply the fitter to the data in
the ACFMat folder of the base directory.
fittinginv :fitdata,This will apply the fitter to the data in
the ACFInv folder of the base directory.
applymat :applymat, This wil create and apply a matrix
formulation of thespace-time ambiguity function to ISR spectrums.
basedir: The base directory that will contain all of the data. This directory
must contain a directory called Origparams with h5 files to run
the full simulation. The user can also start with a directory
from a later stage of the simulation instead though.
configfile: The configuration used for the simulation. Can be an ini file or
a pickle file.
remakealldata: A bool to determine if the raw radar data will be remade. If
this is False the radar data will only be made if it does
not exist in the file first.
fitlist: A list of time entries that will be fit.
invtype
"""
inputsep = '***************************************************************\n'
funcdict = {'spectrums':makespectrums, 'radardata':makeradardata, 'fitting':fitdata,'fittingmat':fitdata,
'fittinginv':fitdata,'applymat':applymat,'fittingmatinv':fitdata}
#inout = {'spectrums':('Origparams','Spectrums'),'radardata':('Spectrums','Radardata'),'fitting':('ACF','Fitted')}
#pdb.set_trace()
# check for the directories
dirnames = ['Origparams','Spectrums','Radardata','ACF','Fitted','ACFOrig','ACFMat','ACFInv','FittedMat','FittedInv','ACFMatInv','FittedMatInv']
basedir=Path(basedir).expanduser()
for idir in dirnames:
curdir = basedir/idir
curdir.mkdir(exist_ok=True,parents=True)
if len(funcnamelist)==3:
funcname='all'
else:
funcname=''.join(funcnamelist)
dfilename = 'diary'+funcname+'.txt'
dfullfilestr = basedir/dfilename
with open(str(dfullfilestr),'a') as f:
failure=False
for curfuncn in funcnamelist:
curfunc = funcdict[curfuncn]
f.write(inputsep)
f.write(curfunc.__name__+'\n')
f.write(time.asctime()+'\n')
if curfunc.__name__=='fitdata':
ex_inputs=[curfuncn,fitlist,invtype,printlines]
elif curfunc.__name__=='makeradardata':
ex_inputs = remakealldata
else:
ex_inputs=printlines
try:
stime = datetime.now()
curfunc(basedir,configfile,ex_inputs)
ftime = datetime.now()
ptime = ftime-stime
f.write('Success!\n')
f.write('Duration: {}\n'.format(ptime))
f.write('Base directory: {}\n'.format(basedir))
except Exception as e:
f.write('Failed!\n')
ftime = datetime.now()
ptime = ftime-stime
f.write('Duration: {}\n'.format(ptime))
f.write('Base directory: {}\n'.format(basedir))
traceback.print_exc(file=sys.stdout)
traceback.print_exc(file=f)
failure = True
break
f.write(inputsep)
return failure
axmat[0].set_xlim([maxden * 1e-5, maxden])
axmat[0].set_xlabel(r'Densities in m$^{-3}$')
axmat[0].set_ylabel('Alt in km')
axmat[0].legend()
axmat[1].set_title('Temperture')
axmat[1].set_xlim([100., 2500.])
axmat[1].set_xlabel(r'Temp in $^{\circ}$ K')
axmat[1].set_ylabel('Alt in km')
axmat[1].legend()
plt.tight_layout()
return figmplf, axmat
if __name__ == '__main__':
exppath = Path('~/DATA/Ion_Comp_Exp').expanduser()
drpath = Path('~/Dropbox (MIT)/').expanduser()
funclist = ['spectrums', 'radardata', 'fitting']
list1 = [i for i in exppath.glob('NO*')]
configlist = [i.joinpath('chem_test.yml') for i in exppath.glob('NO*')]
for idata, icon in zip(list1, configlist):
runsimisr(funclist, str(idata), str(icon), True)
for idata, icon in zip(list1, configlist):
analysisdump(str(idata), str(icon), params=['Ne', 'Nepow', 'Te', 'Ti'])
for ipath in list1:
idir = ipath.joinpath('AnalysisPlots')
idest = drpath.joinpath(*ipath.parts[-2:])
shutil.copytree(str(idir), str(idest))
