def fit2geodata(inputfile):
Ionoin = IonoContainer.readh5(inputfile)
keep = ["Ne", "Te", "Ti"]
GD = GeoData(readIono, [Ionoin])
for ikey in GD.data.keys():
if ikey not in keep:
del GD.data[ikey]
indir, fnameall = os.path.split(inputfile)
fname = os.path.splitext(fnameall)[0]
GD.write_h5(os.path.join(indir, fname + "GEOD.h5"))
print("Saved " + os.path.join(indir, fname + ".h5"))
def main(allskydir,ionofdir,plotdir,latlim2,lonlim2,wl,tint,reinterp=False,timelim=[-sp.infty,sp.infty]):
""" This is the main function for plot data. This function will determine what is to be plotted
and call all of the spatial and time regestration programs from GeoData.
Inputs
allskydir - The directory that holds the FITS files for the allsky data.
If a None is passed then a the allsky is not plotted.
ionofdir - The directory that holds all of the ionofiles. If a None is
passed then a the allsky is not plotted.
plotdir - The directory where the plots are stored.
wl - The wavelength of the allsky light
tint - The number of minutes the GPS data is plotted over. Default is 5.
reinterp - A bool that determines if the GeoData files for the optical data
should be remade.
timelim - A list that shows the time boundaries in posix."""
wl = str(int(wl))
#%% Make map
fig,ax,m=setupmap(latlim2,lonlim2)
isallsky=False
isgps = False
TECtime = None
if ionofdir is not None:
isgps=True
TEClist = []
TECfiles = glob.glob(os.path.join(ionofdir,'*.iono'))
if not TECfiles:
raise IOError('found no TEC files in {}'.format(ionofdir))
print('found {} .iono files in {}'.format(len(TECfiles),ionofdir))
for i,ifile in enumerate(TECfiles):
print('processing {}/{} {} '.format(i+1,len(TECfiles),ifile))
TECGD = GeoData(readIonofiles,(ifile,))
if timelim is not None:
TECGD.timereduce(timelim)
if len(TECGD.times)==0:
continue
TEClist.append(TECGD)
if TECtime is not None:
TECtime[0] = min(TECGD.times[:,0].min(), TECtime[0])
TECtime[1] = max(TECGD.times[:,0].max(), TECtime[1])
else:
TECtime = [TECGD.times[:,0].min(), TECGD.times[:,0].max()]
if allskydir is not None:
isallsky=True
wlstr ='*_0'+wl+'_*.FITS'
interpsavedfile = os.path.join(allskydir,'interp'+wl+'.h5')
if reinterp or (not os.path.isfile(interpsavedfile)):
flist558 = glob.glob(os.path.join(allskydir,wlstr))
if not flist558:
raise IOError('no allsky files found in {}'.format(allskydir))
print(('{} allsky files found in {}'.format(len(flist558),allskydir)))
allsky_data = GeoData(readAllskyFITS,
(flist558,
('PKR_20111006_AZ_10deg.FITS','PKR_20111006_EL_10deg.FITS'),
150.))
if timelim is not None:
allsky_data.timereduce(timelim)
# reduce the size of the allskydata
allskytime = allsky_data.times[:,0]
allsky_data=allsky_data.timeslice(sp.where((allskytime>=TECtime[0]) & (allskytime<TECtime[1]))[0])
allskytime=allsky_data.times[:,0]
xcoords = allsky_data.__changecoords__('WGS84')
latlim=[xcoords[:,0].min(),xcoords[:,0].max()]
lonlim=[xcoords[:,1].min(),xcoords[:,1].max()]
nlat = 256
nlon = 256
latvec = sp.linspace(latlim[0],latlim[1],nlat)
lonvec = sp.linspace(lonlim[0],lonlim[1],nlon)
[LATM,LONM] = sp.meshgrid(latvec,lonvec)
newcoords = sp.column_stack((LATM.ravel(),LONM.ravel(),150.*sp.ones(LONM.size)))
allsky_data.interpolate(newcoords,'WGS84',method='linear',twodinterp=True)
print('writing {}'.format(interpsavedfile))
allsky_data.write_h5(interpsavedfile)
else:
allsky_data = GeoData.read_h5(interpsavedfile)
if timelim is not None:
allsky_data.timereduce(timelim)
allskytime=allsky_data.times[:,0]
#%% make lists for plotting
tectime = sp.arange(TECtime[0],TECtime[1],60.*tint)
nptimes= tectime.size
if isallsky and isgps:
allskylist = []
gpslist = []
tlistkeep = sp.zeros(nptimes-1,dtype=bool)
for itasn in range(nptimes-1):
techlist = []
tlistemp=True
itback=tectime[itasn]
itfor = tectime[itasn+1]
itas = sp.where((allskytime>=itback) & (allskytime<itfor))[0]
if len(itas)==0:
itas = sp.where(allskytime<=itback)[0]
if len(itas)==0:
continue
itas = [itas[-1]]
for k in range(len(TEClist)):
Geoone=TEClist[k];
timevec = Geoone.times[:,0];
itgps = sp.where((timevec>=itback) & (timevec<itfor))[0]
if len(itgps)>0:
tlistemp=False
techlist.append(itgps)
if tlistemp:
continue
allskylist.append(itas)
gpslist.append(techlist)
tlistkeep[itasn]=True
plotgpswoptics(allsky_data,TEClist,allskylist,gpslist,plotdir,m,ax,fig,latlim2,lonlim2)
elif isgps:
gpslist = []
tlistkeep = sp.zeros(nptimes-1,dtype=bool)
for itasn in range(nptimes-1):
techlist = []
tlistemp=True
itback=tectime[itasn]
itfor = tectime[itasn+1]
for k in range(len(TEClist)):
Geoone=TEClist[k];
timevec = Geoone.times[:,0];
itgps = sp.where((timevec>=itback)& (timevec<itfor))[0]
if len(itgps)>0:
tlistemp=False
techlist.append(itgps)
if tlistemp:
continue
gpslist.append(techlist)
tlistkeep[itasn]=True
plotgpsonly(TEClist,gpslist,plotdir,m,ax,fig,latlim2,lonlim2)
elif isallsky:
plotopticsonly(allsky_data,plotdir,m,ax,fig,latlim2,lonlim2)
plt.close(fig)
from GeoData.GeoData import GeoData
from GeoData.utilityfuncs import readIono
if __name__ == "__main__":
inputdir = "/Users/Bodangles/Documents/Python/PhantomProc/Origparams"
outdir = "/Users/Bodangles/Documents/MATLAB/phantoms/Origparams"
dirlist = glob.glob(os.path.join(inputdir, "*.mat"))
keep = ["Ne", "Te", "Ti"]
for ifile in dirlist:
Ionoin = IonoContainer.readmat(ifile)
GD = GeoData(readIono, [Ionoin])
for ikey in GD.data.keys():
if ikey not in keep:
del GD.data[ikey]
fname = os.path.splitext(os.path.split(ifile)[1])[0]
GD.write_h5(os.path.join(outdir, fname + ".h5"))
print("Saved " + os.path.join(outdir, fname + ".h5"))
def fit2geodata(inputfile):
Ionoin = IonoContainer.readh5(inputfile)
keep = ["Ne", "Te", "Ti"]
GD = GeoData(readIono, [Ionoin])
for ikey in GD.data.keys():
if ikey not in keep:
del GD.data[ikey]
indir, fnameall = os.path.split(inputfile)
fname = os.path.splitext(fnameall)[0]
GD.write_h5(os.path.join(indir, fname + "GEOD.h5"))
print("Saved " + os.path.join(indir, fname + ".h5"))
def ASRead(self,ASloc):
""" This function will read in the All sky data from FITS files or structured
h5 files for GeoData.
Input
ASloc - This can be either a directory holding the FITS files or a
h5 file thats been pre interpolated. It will assign the class variable GDAS to the
resultant GeoData object."""
if ASloc is None:
return
ASloc = Path(ASloc).expanduser()
if not ASloc.is_dir() and not ASloc.is_file():
print('All Sky Data cannot be read')
return
self.numGD+=1
print('Reading in All sky data')
wl = str(int(self.params['wl']))
wlstr ='*_0'+wl+'_*.FITS'
interpsavedfile = ASloc/('interp'+wl+'.h5')
reinterp=self.params['reinterp']
timelim=self.params['timebounds']
if self.nointerp:
flist558 = sorted(ASloc.glob(wlstr))
self.GDAS = GeoData(readAllskyFITS,(flist558,
('PKR_DASC_20110112_AZ_10deg.FITS',
'PKR_DASC_20110112_EL_10deg.FITS'),
150.,timelim))
return
if reinterp or not ASloc.is_file():
# pfalla = sp.array([65.136667,-147.447222,689.])
flist558 = sorted(ASloc.glob(wlstr))
if not flist558:
return
allsky_data = GeoData(readAllskyFITS,(flist558,('PKR_DASC_20110112_AZ_10deg.FITS','PKR_DASC_20110112_EL_10deg.FITS'),150.,timelim))
if timelim is not None:
allsky_data.timereduce(timelim)
xcoords = allsky_data.__changecoords__('WGS84')
latlim=[xcoords[:,0].min(),xcoords[:,0].max()]
lonlim=[xcoords[:,1].min(),xcoords[:,1].max()]
nlat = 256
nlon = 256
latvec = sp.linspace(latlim[0],latlim[1],nlat)
lonvec = sp.linspace(lonlim[0],lonlim[1],nlon)
[LATM,LONM] = sp.meshgrid(latvec,lonvec)
newcoords = sp.column_stack((LATM.flatten(),LONM.flatten(),150.*sp.ones(LONM.size)))
allsky_data.interpolate(newcoords,'WGS84',method='linear',twodinterp=True)
allsky_data.write_h5(interpsavedfile)
else:
allsky_data = GeoData.read_h5(ASloc)
if timelim is not None:
allsky_data.timereduce(timelim)
self.GDAS = allsky_data
print('Finished Reading in Allsky Data')
