def set_image_color_percentiles(image, plo, phi): # hackery... I = image.copy().ravel() I.sort() N = len(I) mn = I[max(0, int(round(plo * N / 100.)))] mx = I[min(N-1, int(round(phi * N / 100.)))] gci().set_clim(mn, mx) return (mn,mx)
def draw_inset_colorbar(self,
format=None,
label=None,
ticks=None,
fontsize=11,
**kwargs):
defaults = dict(width="25%",
height="5%",
loc=7,
bbox_to_anchor=(0., -0.04, 1, 1))
setdefaults(kwargs, defaults)
ax = plt.gca()
im = plt.gci()
cax = inset_axes(ax, bbox_transform=ax.transAxes, **kwargs)
cmin, cmax = im.get_clim()
if (ticks is None) and (cmin is not None) and (cmax is not None):
cmed = (cmax + cmin) / 2.
delta = (cmax - cmin) / 10.
ticks = np.array([cmin + delta, cmed, cmax - delta])
tmin = np.min(np.abs(ticks[0]))
tmax = np.max(np.abs(ticks[1]))
if format is None:
if (tmin < 1e-2) or (tmax > 1e3):
format = '$%.1e$'
elif (tmin > 0.1) and (tmax < 100):
format = '$%.1f$'
elif (tmax > 100):
format = '$%i$'
else:
format = '$%.2g$'
#format = '%.2f'
kwargs = dict(format=format, ticks=ticks, orientation='horizontal')
if format == 'custom':
ticks = np.array([cmin, 0.85 * cmax])
kwargs.update(format='$%.0e$', ticks=ticks)
cbar = plt.colorbar(cax=cax, **kwargs)
cax.xaxis.set_ticks_position('top')
cax.tick_params(axis='x', labelsize=fontsize)
if format == 'custom':
ticklabels = cax.get_xticklabels()
for i, l in enumerate(ticklabels):
val, exp = ticklabels[i].get_text().split('e')
ticklabels[i].set_text(r'$%s \times 10^{%i}$' %
(val, int(exp)))
cax.set_xticklabels(ticklabels)
if label is not None:
cbar.set_label(label, size=fontsize)
cax.xaxis.set_label_position('top')
plt.sca(ax)
return cbar, cax
def draw_inset_colorbar(self, format=None):
ax = plt.gca()
im = plt.gci()
cax = inset_axes(ax, width="25%", height="5%", loc=7)
cmin, cmax = im.get_clim()
cmed = (cmax + cmin) / 2.
delta = (cmax - cmin) / 10.
ticks = np.array([cmin + delta, cmed, cmax - delta])
tmin = np.min(np.abs(ticks[0]))
tmax = np.max(np.abs(ticks[1]))
if format is None:
if (tmin < 1e-2) or (tmax > 1e3):
format = '%.1e'
elif (tmin > 0.1) and (tmax < 100):
format = '%.1f'
elif (tmax > 100):
format = '%i'
else:
format = '%.2g'
cbar = plt.colorbar(cax=cax,
orientation='horizontal',
ticks=ticks,
format=format)
cax.xaxis.set_ticks_position('top')
cax.tick_params(axis='x', labelsize=10)
plt.sca(ax)
return cbar
def usecolormap(filename, name=None):
if name is None:
import os
name = os.path.splitext(filename)[0]
pass
mymap = makecolormap(filename, name)
import pylab
#pylab.rc( 'image', cmap = name )
gci = pylab.gci()
gci.set_cmap(mymap)
return
def usecolormap( filename, name = None ):
if name is None:
import os
name = os.path.splitext( filename )[0]
pass
mymap = makecolormap( filename, name )
import pylab
#pylab.rc( 'image', cmap = name )
gci = pylab.gci()
gci.set_cmap( mymap )
return
def X_axis_label_format(format):
"""
Define the X-axis label format
"""
this_axes = py.gca()
this_figure = py.gcf()
this_image = py.gci()
# Set a tick on every integer that is multiple of base in the view interval
# which is 1 in this case
majorLocator = py.MultipleLocator(1)
majorFormatter = py.FormatStrFormatter(format)
this_axes.xaxis.set_major_locator(majorLocator)
this_axes.xaxis.set_major_formatter(majorFormatter)
def __init__(self, im=None):
"""if figure.image is not passed as parameter,
use current image"""
from pylab import colorbar, gci
if im == None:
im = gci()
ax = im.axes
cb = colorbar(im, ax=ax)
self.colorbar_instance = cb
canvas = ax.figure.canvas
if not hasattr(canvas, '_colorbars'):
canvas._colorbars = {}
canvas._colorbars[cb.ax] = cb
canvas.mpl_connect('scroll_event', self.onWheel)
return
def __init__(self, im=None):
"""if figure.image is not passed as parameter,
use current image"""
from pylab import colorbar, gci
if im == None:
im = gci()
ax = im.axes
cb = colorbar(im, ax=ax)
self.colorbar_instance = cb
canvas = ax.figure.canvas
if not hasattr(canvas,'_colorbars'):
canvas._colorbars = {}
canvas._colorbars[cb.ax] = cb
canvas.mpl_connect('scroll_event', self.onWheel)
return
def new_ROI(im=None, shape='polygon'):
"""Set up an ROI picker and return it. This is the only way that the
ROI class should be involked. Requires an input image (the thing
returned by imshow), or can try the latest image in the current
axes."""
plt.ion()
im = plt.gci() if im is None else im
if im == None: raise ValueError('No image to pick on')
ax = im.axes
fig = ax.figure
if shape=='polygon' or shape=='p':
cursor = ROI(im, ax, fig)
elif shape=='circle' or shape=='c':
cursor = ROIcircle(im, ax, fig)
elif shape=='ellipse' or shape=='e':
cursor = ROIellipse(im, ax, fig)
elif shape=='rectangle' or shape=='r':
raise NotImplementedError("Rectangle ROI not yet created")
else:
raise ValueError("ROI shape must not understood")
return cursor
def data2roms(data,grd,sparams,**kargs):
'''
Interpolates data to roms 3D grid.
The dict data must contain the prognostic variables temp, salt, u,
v (3d) and ssh (zeta, 2d), as well as lon, lat (2d), depth (1d) and
time/date info: date (data date), date0 (reference date) and time
(difference between date and date0). The input data can be provided
by load_data.
Parameters
----------
data : dict with prognostic variables
grd : ROMS netcdf grid file
sparams : s-coordinates parameters, theta_s,theta_b, hc and NLevels
**kargs:
ij : axis for vertical interpolations (*i,j)
ij_ind : list of i or j index for vertical interpolation, all by
default (ij_ind=False)
horizAux : if True, the original data horizontally interpolated is
returned and can be used for next data2roms call with
this same karg
quiet : output messages flag (false by default)
'''
ij='j'
ij_ind=False
horizAux=False
quiet=False
if 'ij' in kargs.keys(): ij = kargs['ij']
if 'ij_ind' in kargs.keys(): ij_ind = kargs['ij_ind']
if 'horizAux' in kargs.keys(): horizAux = kargs['horizAux']
if 'quiet' in kargs.keys(): quiet = kargs['quiet']
if not quiet: print 'using grid %s' % grd
g=roms.Grid(grd)
xr,yr,hr,mr=g.vars('r')
xu,yu,hu,mu=g.vars('u')
xv,yv,hv,mv=g.vars('v')
ny,nx=hr.shape
nz=sparams[3]
NX=data['NX']
NY=data['NY']
NZ=data['NZ']
if not quiet: print 'calc s levels...'
sshr=calc.griddata(data['lon'],data['lat'],data['ssh'],xr,yr,extrap=True)
Zr = g.s_levels(sparams,sshr,hr,'r')
Zu = g.s_levels(sparams,sshr,hr,'u')
Zv = g.s_levels(sparams,sshr,hr,'v')
# interp horiz:
retHorizAux=horizAux is True
if horizAux in (True,False):
TEMP = np.ma.masked_all((NZ,ny,nx),data['temp'].dtype)
SALT = np.ma.masked_all((NZ,ny,nx),data['salt'].dtype)
U = np.ma.masked_all((NZ,ny,nx),data['u'].dtype)
V = np.ma.masked_all((NZ,ny,nx),data['v'].dtype)
if not quiet: print 'horizontal interpolation:'
for i in range(NZ):
if not quiet and i%10==0: print ' lev %d of %d' % (i,NZ)
#import pylab
#pylab.figure()
#pylab.pcolormesh(data['lon'],data['lat'],data['temp'][i,...])
try: TEMP[i,...] = calc.griddata(data['lon'],data['lat'],data['temp'][i,...],xr,yr,extrap=True)
except: pass
try: SALT[i,...] = calc.griddata(data['lon'],data['lat'],data['salt'][i,...],xr,yr,extrap=True)
except: pass
try: U[i,...] = calc.griddata(data['lon'],data['lat'],data['u'][i,...],xr,yr,extrap=True)
except: pass
try: V[i,...] = calc.griddata(data['lon'],data['lat'],data['v'][i,...],xr,yr,extrap=True)
except: pass
# rotate U,V:
if not quiet: print 'rotating U,V to grid angle'
angle=g.use('angle') # rad
U,V=calc.rot2d(U,V,angle)
U=rt.rho2uvp3d(U,'u')
V=rt.rho2uvp3d(V,'v')
horizAux={}
horizAux['TEMP'] = TEMP
horizAux['SALT'] = SALT
horizAux['U'] = U
horizAux['V'] = V
else:
TEMP = horizAux['TEMP']
SALT = horizAux['SALT']
U = horizAux['U']
V = horizAux['V']
# interp vert:
nxu=nx-1
nyv=ny-1
#> -----------------------------------------------------------------
useInd=not ij_ind is False
if ij_ind is False:
if ij=='j': ij_ind=range(ny)
elif ij=='i': ij_ind=range(nx)
else:
try: iter(ij_ind)
except: ij_ind=[ij_ind]
if ij=='j': ny=nyv=len(ij_ind)
elif ij=='i': nx=nxu=len(ij_ind)
# -----------------------------------------------------------------<
Temp = np.zeros((nz,ny ,nx ),data['temp'].dtype)
Salt = np.zeros((nz,ny ,nx ),data['salt'].dtype)
Uvel = np.zeros((nz,ny ,nxu),data['u'].dtype)
Vvel = np.zeros((nz,nyv,nx ),data['v'].dtype)
jslice=lambda x,ind: x[:,ind,:]
islice=lambda x,ind: x[:,:,ind]
ZZr = np.tile(data['depth'],(nx,ny,1)).T
ZZu = np.tile(data['depth'],(nxu,ny,1)).T
ZZv = np.tile(data['depth'],(nx,nyv,1)).T
if not useInd is False: #>------------------------------------------
if ij=='j':
slice=jslice
sshr=sshr[ij_ind,:]
hr =hr[ij_ind,:]
elif ij=='i':
slice=islice
sshr=sshr[:,ij_ind]
hr =hr[:,ij_ind]
Zr,Zu,Zv,TEMP,SALT,U,V=[slice(k,ij_ind) for k in [Zr,Zu,Zv,TEMP,SALT,U,V]]
# -----------------------------------------------------------------<
if useInd: # then store distances for a possible bry file
dtype=Temp.dtype
distr=np.zeros((nz,ny, nx ),dtype)
distu=np.zeros((nz,ny, nxu),dtype)
distv=np.zeros((nz,nyv,nx ),dtype)
if not quiet: print 'vertical interpolation:'
if ij=='j':
for j in range(ny):
if not quiet and (ny<10 or (ny>=10 and j%10==0)): print ' j=%3d of %3d' % (j,ny)
ind=ij_ind[j]
dr=np.tile(calc.distance(xr[ind,:],yr[ind,:]),(nz,1))
du=np.tile(calc.distance(xu[ind,:],yu[ind,:]),(nz,1))
Dr=np.tile(calc.distance(xr[ind,:],yr[ind,:]),(NZ,1))
Du=np.tile(calc.distance(xu[ind,:],yu[ind,:]),(NZ,1))
if useInd:
distr[:,j,:]=dr;
distu[:,j,:]=du;
Temp[:,j,:] = calc.griddata(Dr,ZZr[:,j,:],TEMP[:,j,:],dr,Zr[:,j,:],extrap=True)
Salt[:,j,:] = calc.griddata(Dr,ZZr[:,j,:],SALT[:,j,:],dr,Zr[:,j,:],extrap=True)
if 0 and j%10==0:
print Dr.shape, ZZr[:,j,:].shape
import pylab as pl
pl.figure(1)
pl.clf()
pl.pcolormesh(Dr,ZZr[:,j,:],SALT[:,j,:])
pl.colorbar()
clim=pl.gci().get_clim()
pl.figure(2)
pl.clf()
pl.pcolormesh(dr,Zr[:,j,:],Salt[:,j,:])
pl.clim(clim)
pl.colorbar()
raw_input()
Uvel[:,j,:] = calc.griddata(Du,ZZu[:,j,:],U[:,j,:], du,Zu[:,j,:],extrap=True)
if j<Vvel.shape[1]:
dv=np.tile(calc.distance(xv[ind,:],yv[ind,:]),(nz,1))
Dv=np.tile(calc.distance(xv[ind,:],yv[ind,:]),(NZ,1))
Vvel[:,j,:] = calc.griddata(Dv,ZZv[:,j,:],V[:,j,:], dv,Zv[:,j,:],extrap=True)
if useInd:
distv[:,j,:]=dv
if np.any(np.isnan(Temp[:,j,:])): print 'found nan in temp',j
if np.any(np.isnan(Salt[:,j,:])): print 'found nan in salt',j
if np.any(np.isnan(Uvel[:,j,:])): print 'found nan in u',j
if j<Vvel.shape[1] and np.any(np.isnan(Vvel[:,j,:])): print 'found nan in v',j
elif ij=='i':
for i in range(nx):
if not quiet and (nx<10 or (nx>=10 and i%10==0)): print ' i=%3d of %3d' % (i,nx)
ind=ij_ind[i]
dr=np.tile(calc.distance(xr[:,ind],yr[:,ind]),(nz,1))
dv=np.tile(calc.distance(xv[:,ind],yv[:,ind]),(nz,1))
Dr=np.tile(calc.distance(xr[:,ind],yr[:,ind]),(NZ,1))
Dv=np.tile(calc.distance(xv[:,ind],yv[:,ind]),(NZ,1))
if useInd:
distr[:,:,i]=dr;
distv[:,:,i]=dv;
Temp[:,:,i] = calc.griddata(Dr,ZZr[:,:,i],TEMP[:,:,i],dr,Zr[:,:,i],extrap=True)
Salt[:,:,i] = calc.griddata(Dr,ZZr[:,:,i],SALT[:,:,i],dr,Zr[:,:,i],extrap=True)
Vvel[:,:,i] = calc.griddata(Dv,ZZv[:,:,i],V[:,:,i], dv,Zv[:,:,i],extrap=True)
if i<Uvel.shape[2]:
du=np.tile(calc.distance(xu[:,ind],yu[:,ind]),(nz,1))
Du=np.tile(calc.distance(xu[:,ind],yu[:,ind]),(NZ,1))
Uvel[:,:,i] = calc.griddata(Du,ZZu[:,:,i],U[:,:,i], du,Zu[:,:,i],extrap=True)
if useInd:
distu[:,:,i]=du
# uv bar:
if not quiet: print 'calc uvbar'
if useInd is False:
ubar,vbar=rt.uvbar(Uvel,Vvel,sshr,hr,sparams)
else: #>------------------------------------------------------------
sshu=calc.griddata(data['lon'],data['lat'],data['ssh'],xu,yu,extrap=True)
sshv=calc.griddata(data['lon'],data['lat'],data['ssh'],xv,yv,extrap=True)
if ij=='j':
sshu=sshu[ij_ind,:]
sshv=sshv[ij_ind,:]
hu =hu[ij_ind,:]
hv =hv[ij_ind,:]
elif ij=='i':
sshu=sshu[:,ij_ind]
sshv=sshv[:,ij_ind]
hu =hu[:,ij_ind]
hv =hv[:,ij_ind]
ubar=rt.barotropic(Uvel,sshu,hu,sparams)
vbar=rt.barotropic(Vvel,sshv,hv,sparams)
# -----------------------------------------------------------------<
Vars=cb.odict()
Vars['temp'] = Temp
Vars['salt'] = Salt
Vars['u'] = Uvel
Vars['v'] = Vvel
Vars['zeta'] = sshr
Vars['ubar'] = ubar
Vars['vbar'] = vbar
Vars['date'] = data['date']
if not useInd is False: #>------------------------------------------
Vars['depth'] = Zr
Vars['depthu'] = Zu
Vars['depthv'] = Zv
Vars['dist'] = distr
Vars['distu'] = distu
Vars['distv'] = distv
# -----------------------------------------------------------------<
if retHorizAux: return Vars, horizAux
else: return Vars
def data2roms(data,grd,sparams,**kargs):
'''
Interpolates data to roms 3D grid.
The dict data must contain the prognostic variables temp, salt, u,
v (3d) and ssh (zeta, 2d), as well as lon, lat (2d), depth (1d) and
time/date info: date (data date), date0 (reference date) and time
(difference between date and date0). The input data can be provided
by load_data.
Parameters
----------
data : dict with prognostic variables
grd : ROMS netcdf grid file
sparams : s-coordinates parameters, theta_s,theta_b, hc and NLevels
**kargs:
ij : axis for vertical interpolations (*i,j)
ij_ind : list of i or j index for vertical interpolation, all by
default (ij_ind=False)
horizAux : if True, the original data horizontally interpolated is
returned and can be used for next data2roms call with
this same karg
quiet : output messages flag (false by default)
proj : projection - False, *auto* (use default grid projection) or basemap proj
if False, horizontal interpolations will use lonxlat instead of distances
interp_opts: options for griddata
rep_surf: repeat surface level (new upper level)
- If surface variables are present rep_surf must be True
and for each variable (ex temp) will be used the surface
variable (if present, ex ss_temp) instead of the upper layer.
'''
ij = kargs.get('ij','j')
ij_ind = kargs.get('ij_ind',False)
horizAux = kargs.get('horizAux',False)
quiet = kargs.get('quiet',False)
proj = kargs.get('proj','auto') # lonxlat to distance before
# horizontal interpolation
interp_opts = kargs.get('interp_opts',{})
rep_surf = kargs.get('rep_surf',True) # create a surface upper level
# before interpolation
if not quiet: print('using grid %s' % grd)
g=roms.Grid(grd)
xr,yr,hr,mr=g.vars('r')
xu,yu,hu,mu=g.vars('u')
xv,yv,hv,mv=g.vars('v')
ny,nx=hr.shape
ny0,nx0=hr.shape
nz=sparams[3]
if proj=='auto': proj=g.get_projection()
if proj:
print('projecting coordinates...')
xr,yr=proj(xr,yr)
xu,yu=proj(xu,yu)
xv,yv=proj(xv,yv)
dlon,dlat=proj(data['lon'],data['lat'])
Rdz=1/100. # distance to depth ratio (300km vs 3000m)
distance=lambda x,y: np.append(0.,np.sqrt(np.diff(x)**2+np.diff(y)**2).cumsum())
else:
dlon,dlat=data['lon'],data['lat']
Rdz=1.
distance=calc.distance
# needed for s_levels and for rep_surf!
sshr=calc.griddata(dlon,dlat,data['ssh'],xr,yr,extrap=True,**interp_opts)
# repeat surface:
any_ssvar=False
if rep_surf:
# copy data cos dont want to change the original dataset:
import copy
data=copy.deepcopy(data)
for vname in ['temp','salt','u','v','depth']:
if data[vname].ndim==1: # depth !
if np.ma.isMA(data[vname]): vstack=np.ma.hstack
else: vstack=np.hstack
else:
if np.ma.isMA(data[vname]): vstack=np.ma.vstack
else: vstack=np.vstack
ss_vname='ss_'+vname
if ss_vname in data and not quiet:
any_ssvar=True
print('- using surface variable %s'%ss_vname)
if data['depth'][0]>data['depth'][1]: # surf at ind 0
if ss_vname in data: data[vname]=vstack((data[ss_vname][np.newaxis],data[vname]))
else: data[vname]=vstack((data[vname][0][np.newaxis],data[vname]))
if vname=='depth': data[vname][0]=sshr.max()
surf_ind=0
else:
if ss_vname in data: data[vname]=vstack((data[vname],data[ss_vname][np.newaxis]))
else: data[vname]=vstack((data[vname],data[vname][-1][np.newaxis]))
if vname=='depth': data[vname][-1]=sshr.max()
surf_ind=-1
data['NZ']=data['NZ']+1
NX=data['NX']
NY=data['NY']
NZ=data['NZ']
if not quiet: print('calc s levels...')
Zr = g.s_levels(sparams,sshr,hr,'rr')
Zu = g.s_levels(sparams,sshr,hr,'ur')
Zv = g.s_levels(sparams,sshr,hr,'vr')
# interp horiz:
retHorizAux=horizAux is True
if horizAux in (True,False):
TEMP = np.ma.masked_all((NZ,ny,nx),data['temp'].dtype)
SALT = np.ma.masked_all((NZ,ny,nx),data['salt'].dtype)
U = np.ma.masked_all((NZ,ny,nx),data['u'].dtype)
V = np.ma.masked_all((NZ,ny,nx),data['v'].dtype)
if not quiet: print('horizontal interpolation:')
for i in range(NZ):
if not quiet and i%10==0: print(' lev %d of %d' % (i,NZ))
#import pylab
#pylab.figure()
#pylab.pcolormesh(data['lon'],data['lat'],data['temp'][i,...])
try: TEMP[i,...] = calc.griddata(dlon,dlat,data['temp'][i,...],xr,yr,extrap=True,**interp_opts)
except: pass
try: SALT[i,...] = calc.griddata(dlon,dlat,data['salt'][i,...],xr,yr,extrap=True,**interp_opts)
except: pass
try: U[i,...] = calc.griddata(dlon,dlat,data['u'][i,...],xr,yr,extrap=True,**interp_opts)
except: pass
try: V[i,...] = calc.griddata(dlon,dlat,data['v'][i,...],xr,yr,extrap=True,**interp_opts)
except: pass
# rotate U,V:
if not quiet: print('rotating U,V to grid angle')
U,V=calc.rot2d(U,V,g.angle) # g.angle in rad
U=rt.rho2uvp3d(U,'u')
V=rt.rho2uvp3d(V,'v')
horizAux={}
horizAux['TEMP'] = TEMP
horizAux['SALT'] = SALT
horizAux['U'] = U
horizAux['V'] = V
else:
TEMP = horizAux['TEMP']
SALT = horizAux['SALT']
U = horizAux['U']
V = horizAux['V']
# interp vert:
nxu=nx-1
nyv=ny-1
#> -----------------------------------------------------------------
useInd=not ij_ind is False
if ij_ind is False:
if ij=='j': ij_ind=range(ny)
elif ij=='i': ij_ind=range(nx)
else:
try: iter(ij_ind)
except: ij_ind=[ij_ind]
if ij=='j': ny=nyv=len(ij_ind)
elif ij=='i': nx=nxu=len(ij_ind)
# -----------------------------------------------------------------<
Temp = np.zeros((nz,ny ,nx ),data['temp'].dtype)
Salt = np.zeros((nz,ny ,nx ),data['salt'].dtype)
Uvel = np.zeros((nz,ny ,nxu),data['u'].dtype)
Vvel = np.zeros((nz,nyv,nx ),data['v'].dtype)
jslice=lambda x,ind: x[:,ind,:]
islice=lambda x,ind: x[:,:,ind]
if any_ssvar:
ZZr = np.tile(data['depth'],(nx0,ny0,1)).T
ZZu = np.tile(data['depth'],(nx0-1,ny0,1)).T
ZZv = np.tile(data['depth'],(nx0,ny0-1,1)).T
# replace 1st level by sea surface height!
# instead of sshr.max(). This is at least slightly more correct,
# and should be no problem for variables without surface counterpart.
ZZr[surf_ind]=sshr
ZZu[surf_ind]=(sshr[:,1:]+sshr[:,:-1])/2.
ZZv[surf_ind]=(sshr[1:]+sshr[:-1])/2.
else:
ZZr = np.tile(data['depth'],(nx,ny,1)).T
ZZu = np.tile(data['depth'],(nxu,ny,1)).T
ZZv = np.tile(data['depth'],(nx,nyv,1)).T
if not useInd is False: #>------------------------------------------
if ij=='j':
slice=jslice
sshr=sshr[ij_ind,:]
hr =hr[ij_ind,:]
elif ij=='i':
slice=islice
sshr=sshr[:,ij_ind]
hr =hr[:,ij_ind]
Zr,Zu,Zv,TEMP,SALT,U,V=[slice(k,ij_ind) for k in [Zr,Zu,Zv,TEMP,SALT,U,V]]
if any_ssvar:
ZZr,ZZu,ZZv=[slice(k,ij_ind) for k in [ZZr,ZZu,ZZv]]
# -----------------------------------------------------------------<
if useInd: # then store distances for a possible bry file
dtype=Temp.dtype
distr=np.zeros((nz,ny, nx ),dtype)
distu=np.zeros((nz,ny, nxu),dtype)
distv=np.zeros((nz,nyv,nx ),dtype)
if not quiet: print('vertical interpolation:')
if ij=='j':
for j in range(ny):
if not quiet and (ny<20 or (ny>=20 and j%20==0)): print(' j=%3d of %3d' % (j,ny))
ind=ij_ind[j]
dr=np.tile(distance(xr[ind,:],yr[ind,:]),(nz,1))
du=np.tile(distance(xu[ind,:],yu[ind,:]),(nz,1))
Dr=np.tile(distance(xr[ind,:],yr[ind,:]),(NZ,1))
Du=np.tile(distance(xu[ind,:],yu[ind,:]),(NZ,1))
if useInd:
distr[:,j,:]=dr;
distu[:,j,:]=du;
Temp[:,j,:] = calc.griddata(Rdz*Dr,ZZr[:,j,:],TEMP[:,j,:],Rdz*dr,Zr[:,j,:],extrap=True,**interp_opts)
Salt[:,j,:] = calc.griddata(Rdz*Dr,ZZr[:,j,:],SALT[:,j,:],Rdz*dr,Zr[:,j,:],extrap=True,**interp_opts)
if 0 and j%10==0:
print(Dr.shape, ZZr[:,j,:].shape)
import pylab as pl
pl.figure(1)
pl.clf()
pl.pcolormesh(Dr,ZZr[:,j,:],TEMP[:,j,:])
pl.colorbar()
clim=pl.gci().get_clim()
pl.figure(2)
pl.clf()
pl.pcolormesh(dr,Zr[:,j,:],Temp[:,j,:])
pl.clim(clim)
pl.colorbar()
try: raw_input()
except: input() # python 3
Uvel[:,j,:] = calc.griddata(Rdz*Du,ZZu[:,j,:],U[:,j,:], Rdz*du,Zu[:,j,:],extrap=True,**interp_opts)
if j<Vvel.shape[1]:
dv=np.tile(distance(xv[ind,:],yv[ind,:]),(nz,1))
Dv=np.tile(distance(xv[ind,:],yv[ind,:]),(NZ,1))
Vvel[:,j,:] = calc.griddata(Rdz*Dv,ZZv[:,j,:],V[:,j,:], Rdz*dv,Zv[:,j,:],extrap=True,**interp_opts)
if useInd:
distv[:,j,:]=dv
if np.any(np.isnan(Temp[:,j,:])): print('found nan in temp',j)
if np.any(np.isnan(Salt[:,j,:])): print('found nan in salt',j)
if np.any(np.isnan(Uvel[:,j,:])): print('found nan in u',j)
if j<Vvel.shape[1] and np.any(np.isnan(Vvel[:,j,:])): print('found nan in v',j)
elif ij=='i':
for i in range(nx):
if not quiet and (nx<20 or (nx>=20 and i%20==0)): print(' i=%3d of %3d' % (i,nx))
ind=ij_ind[i]
dr=np.tile(distance(xr[:,ind],yr[:,ind]),(nz,1))
dv=np.tile(distance(xv[:,ind],yv[:,ind]),(nz,1))
Dr=np.tile(distance(xr[:,ind],yr[:,ind]),(NZ,1))
Dv=np.tile(distance(xv[:,ind],yv[:,ind]),(NZ,1))
if useInd:
distr[:,:,i]=dr;
distv[:,:,i]=dv;
Temp[:,:,i] = calc.griddata(Rdz*Dr,ZZr[:,:,i],TEMP[:,:,i],Rdz*dr,Zr[:,:,i],extrap=True,**interp_opts)
Salt[:,:,i] = calc.griddata(Rdz*Dr,ZZr[:,:,i],SALT[:,:,i],Rdz*dr,Zr[:,:,i],extrap=True,**interp_opts)
Vvel[:,:,i] = calc.griddata(Rdz*Dv,ZZv[:,:,i],V[:,:,i], Rdz*dv,Zv[:,:,i],extrap=True,**interp_opts)
if i<Uvel.shape[2]:
du=np.tile(distance(xu[:,ind],yu[:,ind]),(nz,1))
Du=np.tile(distance(xu[:,ind],yu[:,ind]),(NZ,1))
Uvel[:,:,i] = calc.griddata(Rdz*Du,ZZu[:,:,i],U[:,:,i], Rdz*du,Zu[:,:,i],extrap=True,**interp_opts)
if useInd:
distu[:,:,i]=du
# uv bar:
if not quiet: print('calc uvbar')
if useInd is False:
ubar,vbar=rt.uvbar(Uvel,Vvel,sshr,hr,sparams)
else: #>------------------------------------------------------------
sshu=calc.griddata(dlon,dlat,data['ssh'],xu,yu,extrap=True,**interp_opts)
sshv=calc.griddata(dlon,dlat,data['ssh'],xv,yv,extrap=True,**interp_opts)
if ij=='j':
sshu=sshu[ij_ind,:]
sshv=sshv[ij_ind,:]
hu =hu[ij_ind,:]
hv =hv[ij_ind,:]
elif ij=='i':
sshu=sshu[:,ij_ind]
sshv=sshv[:,ij_ind]
hu =hu[:,ij_ind]
hv =hv[:,ij_ind]
ubar=rt.barotropic(Uvel,sshu,hu,sparams)
vbar=rt.barotropic(Vvel,sshv,hv,sparams)
# -----------------------------------------------------------------<
#Vars=cb.odict()
Vars=OrderedDict()
Vars['temp'] = Temp
Vars['salt'] = Salt
Vars['u'] = Uvel
Vars['v'] = Vvel
Vars['zeta'] = sshr
Vars['ubar'] = ubar
Vars['vbar'] = vbar
Vars['date'] = data['date']
if not useInd is False: #>------------------------------------------
Vars['depth'] = Zr
Vars['depthu'] = Zu
Vars['depthv'] = Zv
Vars['dist'] = distr
Vars['distu'] = distu
Vars['distv'] = distv
# -----------------------------------------------------------------<
if retHorizAux: return Vars, horizAux
else: return Vars
def data2roms(data, grd, sparams, **kargs):
'''
Interpolates data to roms 3D grid.
The dict data must contain the prognostic variables temp, salt, u,
v (3d) and ssh (zeta, 2d), as well as lon, lat (2d), depth (1d) and
time/date info: date (data date), date0 (reference date) and time
(difference between date and date0). The input data can be provided
by load_data.
Parameters
----------
data : dict with prognostic variables
grd : ROMS netcdf grid file
sparams : s-coordinates parameters, theta_s,theta_b, hc and NLevels
**kargs:
ij : axis for vertical interpolations (*i,j)
ij_ind : list of i or j index for vertical interpolation, all by
default (ij_ind=False)
horizAux : if True, the original data horizontally interpolated is
returned and can be used for next data2roms call with
this same karg
quiet : output messages flag (false by default)
proj : projection - False, name or basemap proj - lcc by default
if False, horizontal interpolations will use lonxlat instead of distances
interp_opts: options for griddata
rep_surf: repeat surface level (new upper level)
'''
ij = kargs.get('ij', 'j')
ij_ind = kargs.get('ij_ind', False)
horizAux = kargs.get('horizAux', False)
quiet = kargs.get('quiet', False)
proj = kargs.get('proj', 'lcc') # lonxlat to distance before
# horizontal interpolation
interp_opts = kargs.get('interp_opts', {})
rep_surf = kargs.get('rep_surf', True) # create a surface upper level
# before interpolation
if not quiet: print 'using grid %s' % grd
g = roms.Grid(grd)
xr, yr, hr, mr = g.vars('r')
xu, yu, hu, mu = g.vars('u')
xv, yv, hv, mv = g.vars('v')
ny, nx = hr.shape
nz = sparams[3]
if proj:
print 'projecting coordinates...'
if isinstance(proj, basestring):
lonc = (xr.max() + xr.min()) / 2.
latc = (yr.max() + yr.min()) / 2.
from mpl_toolkits.basemap import Basemap
proj = Basemap(projection=proj,
width=1,
height=1,
resolution=None,
lon_0=lonc,
lat_0=latc,
lat_1=latc)
xr, yr = proj(xr, yr)
xu, yu = proj(xu, yu)
xv, yv = proj(xv, yv)
dlon, dlat = proj(data['lon'], data['lat'])
Rdz = 1 / 100. # distance to depth ratio (300km vs 3000m)
distance = lambda x, y: np.append(
0.,
np.sqrt(np.diff(x)**2 + np.diff(y)**2).cumsum())
else:
dlon, dlat = data['lon'], data['lat']
distance = calc.distance
# needed for s_levels and for rep_surf!
sshr = calc.griddata(dlon,
dlat,
data['ssh'],
xr,
yr,
extrap=True,
**interp_opts)
# repeat surface:
if rep_surf:
# copy data cos dont want to change the original dataset:
import copy
data = copy.deepcopy(data)
for vname in ['temp', 'salt', 'u', 'v', 'depth']:
if data[vname].ndim == 1: # depth !
if np.ma.isMA(data[vname]): vstack = np.ma.hstack
else: vstack = np.hstack
else:
if np.ma.isMA(data[vname]): vstack = np.ma.vstack
else: vstack = np.vstack
if data['depth'][0] > data['depth'][1]: # surf at ind 0
data[vname] = vstack((data[vname][0][np.newaxis], data[vname]))
if vname == 'depth': data[vname][0] = sshr.max()
else:
data[vname] = vstack(
(data[vname], data[vname][-1][np.newaxis]))
if vname == 'depth': data[vname][-1] = sshr.max()
data['NZ'] = data['NZ'] + 1
NX = data['NX']
NY = data['NY']
NZ = data['NZ']
if not quiet: print 'calc s levels...'
Zr = g.s_levels(sparams, sshr, hr, 'r')
Zu = g.s_levels(sparams, sshr, hr, 'u')
Zv = g.s_levels(sparams, sshr, hr, 'v')
# interp horiz:
retHorizAux = horizAux is True
if horizAux in (True, False):
TEMP = np.ma.masked_all((NZ, ny, nx), data['temp'].dtype)
SALT = np.ma.masked_all((NZ, ny, nx), data['salt'].dtype)
U = np.ma.masked_all((NZ, ny, nx), data['u'].dtype)
V = np.ma.masked_all((NZ, ny, nx), data['v'].dtype)
if not quiet: print 'horizontal interpolation:'
for i in range(NZ):
if not quiet and i % 10 == 0: print ' lev %d of %d' % (i, NZ)
#import pylab
#pylab.figure()
#pylab.pcolormesh(data['lon'],data['lat'],data['temp'][i,...])
try:
TEMP[i, ...] = calc.griddata(dlon,
dlat,
data['temp'][i, ...],
xr,
yr,
extrap=True,
**interp_opts)
except:
pass
try:
SALT[i, ...] = calc.griddata(dlon,
dlat,
data['salt'][i, ...],
xr,
yr,
extrap=True,
**interp_opts)
except:
pass
try:
U[i, ...] = calc.griddata(dlon,
dlat,
data['u'][i, ...],
xr,
yr,
extrap=True,
**interp_opts)
except:
pass
try:
V[i, ...] = calc.griddata(dlon,
dlat,
data['v'][i, ...],
xr,
yr,
extrap=True,
**interp_opts)
except:
pass
# rotate U,V:
if not quiet: print 'rotating U,V to grid angle'
angle = g.use('angle') # rad
U, V = calc.rot2d(U, V, angle)
U = rt.rho2uvp3d(U, 'u')
V = rt.rho2uvp3d(V, 'v')
horizAux = {}
horizAux['TEMP'] = TEMP
horizAux['SALT'] = SALT
horizAux['U'] = U
horizAux['V'] = V
else:
TEMP = horizAux['TEMP']
SALT = horizAux['SALT']
U = horizAux['U']
V = horizAux['V']
# interp vert:
nxu = nx - 1
nyv = ny - 1
#> -----------------------------------------------------------------
useInd = not ij_ind is False
if ij_ind is False:
if ij == 'j': ij_ind = range(ny)
elif ij == 'i': ij_ind = range(nx)
else:
try:
iter(ij_ind)
except:
ij_ind = [ij_ind]
if ij == 'j': ny = nyv = len(ij_ind)
elif ij == 'i': nx = nxu = len(ij_ind)
# -----------------------------------------------------------------<
Temp = np.zeros((nz, ny, nx), data['temp'].dtype)
Salt = np.zeros((nz, ny, nx), data['salt'].dtype)
Uvel = np.zeros((nz, ny, nxu), data['u'].dtype)
Vvel = np.zeros((nz, nyv, nx), data['v'].dtype)
jslice = lambda x, ind: x[:, ind, :]
islice = lambda x, ind: x[:, :, ind]
ZZr = np.tile(data['depth'], (nx, ny, 1)).T
ZZu = np.tile(data['depth'], (nxu, ny, 1)).T
ZZv = np.tile(data['depth'], (nx, nyv, 1)).T
if not useInd is False: #>------------------------------------------
if ij == 'j':
slice = jslice
sshr = sshr[ij_ind, :]
hr = hr[ij_ind, :]
elif ij == 'i':
slice = islice
sshr = sshr[:, ij_ind]
hr = hr[:, ij_ind]
Zr, Zu, Zv, TEMP, SALT, U, V = [
slice(k, ij_ind) for k in [Zr, Zu, Zv, TEMP, SALT, U, V]
]
# -----------------------------------------------------------------<
if useInd: # then store distances for a possible bry file
dtype = Temp.dtype
distr = np.zeros((nz, ny, nx), dtype)
distu = np.zeros((nz, ny, nxu), dtype)
distv = np.zeros((nz, nyv, nx), dtype)
if not quiet: print 'vertical interpolation:'
if ij == 'j':
for j in range(ny):
if not quiet and (ny < 10 or (ny >= 10 and j % 10 == 0)):
print ' j=%3d of %3d' % (j, ny)
ind = ij_ind[j]
dr = np.tile(distance(xr[ind, :], yr[ind, :]), (nz, 1))
du = np.tile(distance(xu[ind, :], yu[ind, :]), (nz, 1))
Dr = np.tile(distance(xr[ind, :], yr[ind, :]), (NZ, 1))
Du = np.tile(distance(xu[ind, :], yu[ind, :]), (NZ, 1))
if useInd:
distr[:, j, :] = dr
distu[:, j, :] = du
Temp[:, j, :] = calc.griddata(Rdz * Dr,
ZZr[:, j, :],
TEMP[:, j, :],
Rdz * dr,
Zr[:, j, :],
extrap=True,
**interp_opts)
Salt[:, j, :] = calc.griddata(Rdz * Dr,
ZZr[:, j, :],
SALT[:, j, :],
Rdz * dr,
Zr[:, j, :],
extrap=True,
**interp_opts)
if 0 and j % 10 == 0:
print Dr.shape, ZZr[:, j, :].shape
import pylab as pl
pl.figure(1)
pl.clf()
pl.pcolormesh(Dr, ZZr[:, j, :], SALT[:, j, :])
pl.colorbar()
clim = pl.gci().get_clim()
pl.figure(2)
pl.clf()
pl.pcolormesh(dr, Zr[:, j, :], Salt[:, j, :])
pl.clim(clim)
pl.colorbar()
raw_input()
Uvel[:, j, :] = calc.griddata(Rdz * Du,
ZZu[:, j, :],
U[:, j, :],
Rdz * du,
Zu[:, j, :],
extrap=True,
**interp_opts)
if j < Vvel.shape[1]:
dv = np.tile(distance(xv[ind, :], yv[ind, :]), (nz, 1))
Dv = np.tile(distance(xv[ind, :], yv[ind, :]), (NZ, 1))
Vvel[:, j, :] = calc.griddata(Rdz * Dv,
ZZv[:, j, :],
V[:, j, :],
Rdz * dv,
Zv[:, j, :],
extrap=True,
**interp_opts)
if useInd:
distv[:, j, :] = dv
if np.any(np.isnan(Temp[:, j, :])): print 'found nan in temp', j
if np.any(np.isnan(Salt[:, j, :])): print 'found nan in salt', j
if np.any(np.isnan(Uvel[:, j, :])): print 'found nan in u', j
if j < Vvel.shape[1] and np.any(np.isnan(Vvel[:, j, :])):
print 'found nan in v', j
elif ij == 'i':
for i in range(nx):
if not quiet and (nx < 10 or (nx >= 10 and i % 10 == 0)):
print ' i=%3d of %3d' % (i, nx)
ind = ij_ind[i]
dr = np.tile(distance(xr[:, ind], yr[:, ind]), (nz, 1))
dv = np.tile(distance(xv[:, ind], yv[:, ind]), (nz, 1))
Dr = np.tile(distance(xr[:, ind], yr[:, ind]), (NZ, 1))
Dv = np.tile(distance(xv[:, ind], yv[:, ind]), (NZ, 1))
if useInd:
distr[:, :, i] = dr
distv[:, :, i] = dv
Temp[:, :, i] = calc.griddata(Rdz * Dr,
ZZr[:, :, i],
TEMP[:, :, i],
Rdz * dr,
Zr[:, :, i],
extrap=True,
**interp_opts)
Salt[:, :, i] = calc.griddata(Rdz * Dr,
ZZr[:, :, i],
SALT[:, :, i],
Rdz * dr,
Zr[:, :, i],
extrap=True,
**interp_opts)
Vvel[:, :, i] = calc.griddata(Rdz * Dv,
ZZv[:, :, i],
V[:, :, i],
Rdz * dv,
Zv[:, :, i],
extrap=True,
**interp_opts)
if i < Uvel.shape[2]:
du = np.tile(distance(xu[:, ind], yu[:, ind]), (nz, 1))
Du = np.tile(distance(xu[:, ind], yu[:, ind]), (NZ, 1))
Uvel[:, :, i] = calc.griddata(Rdz * Du,
ZZu[:, :, i],
U[:, :, i],
Rdz * du,
Zu[:, :, i],
extrap=True,
**interp_opts)
if useInd:
distu[:, :, i] = du
# uv bar:
if not quiet: print 'calc uvbar'
if useInd is False:
ubar, vbar = rt.uvbar(Uvel, Vvel, sshr, hr, sparams)
else: #>------------------------------------------------------------
sshu = calc.griddata(dlon,
dlat,
data['ssh'],
xu,
yu,
extrap=True,
**interp_opts)
sshv = calc.griddata(dlon,
dlat,
data['ssh'],
xv,
yv,
extrap=True,
**interp_opts)
if ij == 'j':
sshu = sshu[ij_ind, :]
sshv = sshv[ij_ind, :]
hu = hu[ij_ind, :]
hv = hv[ij_ind, :]
elif ij == 'i':
sshu = sshu[:, ij_ind]
sshv = sshv[:, ij_ind]
hu = hu[:, ij_ind]
hv = hv[:, ij_ind]
ubar = rt.barotropic(Uvel, sshu, hu, sparams)
vbar = rt.barotropic(Vvel, sshv, hv, sparams)
# -----------------------------------------------------------------<
Vars = cb.odict()
Vars['temp'] = Temp
Vars['salt'] = Salt
Vars['u'] = Uvel
Vars['v'] = Vvel
Vars['zeta'] = sshr
Vars['ubar'] = ubar
Vars['vbar'] = vbar
Vars['date'] = data['date']
if not useInd is False: #>------------------------------------------
Vars['depth'] = Zr
Vars['depthu'] = Zu
Vars['depthv'] = Zv
Vars['dist'] = distr
Vars['distu'] = distu
Vars['distv'] = distv
# -----------------------------------------------------------------<
if retHorizAux: return Vars, horizAux
else: return Vars
def getCorr(order=5,i0=None,Imat=None,i0_wp=1e6,fraclims_dc=[.9,1.1]):
""" Getting nonlinear correction factors form a calibration dataset consiting of:
i0 array of intensities the calibration has been made for
Imat 2D array of the corresponding reference patterns, in each row
there is one ravelled array of each intensity bin in i0.
i0_wp a working point around which a correction polynomial will be
developed for each pixel.
order the polynomial order up to which will be deveoped.
fraclims_dc relative factor for the i0,Imat data limits which are used to
determine the working point location.
Returns
"""
#i0,Imat = getData()
msk = tools.filtvec(i0,i0_wp*np.asarray(fraclims_dc))
p0 = tools.polyFit(i0[msk],Imat[msk,:],2)
dc = tools.polyVal(p0,i0_wp)
comps = tools.polyFit(i0-i0_wp,Imat-dc,order,removeOrders=[0])
compsder = tools.polyDer(comps)
c = lambda(i): tools.polyVal(comps,i-np.asarray(tools.iterfy(i0_wp)))+dc
c_prime = lambda(i): tools.polyVal(compsder,i-np.asarray(tools.iterfy(i0_wp)))
t = lambda(i): (c_prime(i0_wp).T * (i-i0_wp)).T + dc
cprimeic = c_prime(i0_wp)
dcorr_const = -cprimeic*i0_wp + c(i0_wp) - t(0)
def dcorr(i,D):
return (i*cprimeic.T + dcorr_const.T + ((D-c(i))*cprimeic/c_prime(i)).T).T
#return (i*cprimeic.T + dcorr_const.T ).T
return dcorr,comps,t
tools.nfigure('testplot')
plt.clf()
plt.subplot(1,2,1)
Imean = (Imat.T/i0).T
tools.imagesc(np.asarray([ti / np.mean(Imean[-10:,:],0) for ti in Imean]))
tools.clim_std(6)
cl = plt.gci().get_clim()
plt.colorbar()
plt.set_cmap(plt.cm.RdBu_r)
plt.subplot(1,2,2)
cmps = copy.copy(comps)
cmps[-2,:] = 0
cc = lambda(i): tools.polyVal(cmps,i-np.asarray(tools.iterfy(i0_wp)))
Ir = Imat-c(i0)+t(i0)-t(0)
Ir = dcorr(i0,Imat)
#Ir = ((Imat-cc(i0)).T/i0).T
#tools.imagesc(Ir)
Ir = (Ir.T/i0).T
tools.imagesc(np.asarray([ti / np.mean(Ir[-10:,:],0) for ti in Ir]))
plt.clim(cl)
plt.colorbar()
plt.set_cmap(plt.cm.RdBu_r)
plt.draw()
tools.nfigure('testplot_components')
plt.clf()
ah = None
for n,comp in enumerate(comps):
if ah is None:
ah = plt.subplot(len(comps),1,n+1)
else:
plt.subplot(len(comps),1,n+1,sharex=ah)
plt.plot(comp)
lims = np.percentile(comp,[1,99])
plt.ylim(lims)
return c,c_prime
def plot2D(array,
marker='',
colour='',
vmin=0,
vmax=200,
cbar=3,
fig=1,
figsize=None,
aspect="equal",
name="",
fname="Cmax",
dir=this_dir,
axes=['on', 'off']):
""" Plots a surface represented explicitly by a 2D array XY or implicitly by a set of 3D points XYZ """
cmap = "Greys_r"
norm = plt.Normalize(vmin=vmin, vmax=vmax)
if dir != "":
fname = '%s/%s' % (dir, fname)
ext = ".png"
if fig != 0:
plt.figure(fig, figsize=figsize)
plt.title("%s gamut" % name)
plt.xlabel("H")
plt.ylabel("L", rotation='horizontal')
plt.xlim([0, 360])
plt.ylim([0, 100])
if array.shape[1] == 3:
# array is the 3D surface of a 2D function
L = array[:, 0]
C = array[:, 1]
H = array[:, 2]
plt.tricontourf(H, L, C, cmap=cmap, norm=norm)
if marker != '':
ax = plt.gca()
if len(colour) > 0:
ax.plot(H, L, marker, c=colour)
else:
#ax.plot(H,L,marker,color=convert.clip3(convert.LCH2RGB(L,C,H)).tolist())
for h, l, c in zip(H, L, array):
ax.plot(h,
l,
marker,
color=convert.clip3(
convert.LCH2RGB(c[0], c[1], c[2])))
plt.gca().set_aspect(aspect)
else:
# array is a 2D map
plt.imshow(array,
origin='lower',
extent=[H_min, H_max, L_min, L_max],
aspect=aspect,
interpolation='nearest',
cmap=cmap,
norm=norm)
locator = ticker.MultipleLocator(60)
plt.gca().xaxis.set_major_locator(locator)
if cbar > 0:
cax = make_axes_locatable(plt.gca()).append_axes("right",
size="%.f%%" %
cbar,
pad=0.10)
cb = plt.colorbar(plt.gci(), cax=cax)
cb.locator = ticker.MultipleLocator(50)
cb.update_ticks()
cb.set_label("Cmax")
if dir != "" and 'on' in axes:
print("writing %s" % (fname + "_axon" + ext))
plt.savefig(fname + "_axon" + ext, dpi=None, bbox_inches='tight')
if dir != "" and 'off' in axes and array.shape[1] > 3:
print("writing %s" % (fname + "_axoff" + ext))
plt.imsave(arr=array,
origin='lower',
cmap=cmap,
vmin=vmin,
vmax=vmax,
fname=fname + "_axoff" + ext)
def ridge_detection(y, sampling_frequency, framesz, hop,sigma,prct_thr=98, cf_cutoff=5000, prune=True, plot=True):
BWallangles = [[0 for x in range(8)] for x1 in range(len(sigma))]
nsamples = len(y)
T = 1.0*nsamples/sampling_frequency
gabor_orig_allsigma = []
for sigma_i in range(len(sigma)):
gabor_orig, gabor_orig_dw, gabor_orig_dt, freq = stft(y, sampling_frequency, framesz, hop, sigma=sigma[sigma_i])
gabor_orig_allsigma.append(gabor_orig)
if plot:
pl.figure()
pl.imshow(db(np.square(scipy.absolute(gabor_orig))).T,origin='lower',aspect='auto',
extent=[0, T, 0, sampling_frequency], interpolation='nearest')
pl.ylim((0,sampling_frequency/2))
pl.xlabel('Time')
pl.ylabel('Frequency')
vmin, vmax = pl.gci().get_clim()
pl.figure()
pl.imshow(db(np.square(scipy.absolute(gabor_orig_dw))).T,origin='lower',aspect='auto',
extent=[0, T, 0, sampling_frequency], interpolation='nearest')
pl.ylim((0,sampling_frequency/2))
pl.xlabel('Time')
pl.ylabel('Frequency')
lowpass_gabor_orig_dw = gabor_orig_dw[:,freq<=cf_cutoff]
# pruning using mixed partial derivative dtdw
if prune:
lowfreq = freq[freq<=cf_cutoff]
freq_orig = np.repeat(lowfreq[:,None], lowpass_gabor_orig_dw.shape[0], axis=1).T
freq_shift = np.imag(lowpass_gabor_orig_dw)
freq_new = freq_orig - freq_shift
[gx,gy] = np.gradient(freq_new)
prune_mask = np.abs(gy/freq[1]) < 0.6
else:
prune_mask = np.ones(lowpass_gabor_orig_dw.shape).astype(bool)
n_angle = 1
if plot:
fig = pl.figure()
for angle_i in range(n_angle):
theta = np.pi/8*angle_i
s = (-1)*(np.imag(lowpass_gabor_orig_dw*np.exp(1j*theta))<0)+(np.imag(lowpass_gabor_orig_dw*np.exp(1j*theta))>0)
[gx,gy]=np.gradient(s)
BW=((-gx*np.cos(theta+np.pi/2)+gy*np.sin(theta+np.pi/2))>.1)
BW = BW & prune_mask
CC = measure.regionprops(measure.label(BW))
weightv = np.zeros((len(CC),))
powerv = np.zeros((len(CC),))
for i in range(len(CC)):
weightv[i] = CC[i].area
inds = CC[i].coords
powerv[i] = np.mean(np.abs(gabor_orig[inds[:,0], inds[:,1]]))
a = np.logical_and(weightv>=np.percentile(weightv, prct_thr),powerv>=np.percentile(powerv, 10))
tempv = np.zeros_like(BW)
for index in np.nonzero(a)[0]:
ind = CC[index].coords
tempv[ind[:,0], ind[:,1]] = 1
BWallangles[sigma_i][angle_i]=tempv.astype(int)
if plot:
ax = fig.add_subplot(2,4,angle_i+1)
ax.imshow(tempv.T,origin='lower',aspect='auto', extent=[0, T, 0, cf_cutoff], cmap='binary',interpolation='nearest')
ax.set_xlabel('Time')
ax.set_ylabel('Frequency')
consensus_allsigma = []
for sigma_i in range(len(sigma)):
consensus = np.zeros(BW.shape)
if sigma_i == len(sigma)-1:
neighboor_sigma = sigma_i-1
else:
neighboor_sigma = sigma_i+1
for angle_i in range(n_angle):
# if angle_i==0:
# cv= BWallangles[sigma_i][0]+BWallangles[sigma_i][1]+BWallangles[sigma_i][7] \
# + BWallangles[neighboor_sigma][0]
# consensus=consensus+(cv>1).astype(int)
# elif angle_i==7:
# cv= BWallangles[sigma_i][0]+BWallangles[sigma_i][6]+BWallangles[sigma_i][7] \
# + BWallangles[neighboor_sigma][7]
# consensus=consensus+(cv>1).astype(int)
# else:
# cv= BWallangles[sigma_i][angle_i] + BWallangles[sigma_i][angle_i-1]+BWallangles[sigma_i][angle_i+1] \
# + BWallangles[neighboor_sigma][angle_i]
cv= BWallangles[sigma_i][angle_i]
consensus=consensus+(cv>0).astype(int)
consensus_allsigma.append(consensus>0)
if plot:
pl.figure()
for i in range(len(sigma)):
pl.subplot(2,2,i+1)
pl.imshow(consensus_allsigma[i].T,origin='lower',aspect='auto', extent=[0, T, 0, cf_cutoff], cmap='binary',interpolation='nearest')
pl.xlabel('Time')
pl.ylabel('Frequency')
pl.clim((0,1))
return gabor_orig_allsigma, consensus_allsigma
def data2roms(data, grd, sparams, **kargs):
'''
Interpolates data to roms 3D grid.
The dict data must contain the prognostic variables temp, salt, u,
v (3d) and ssh (zeta, 2d), as well as lon, lat (2d), depth (1d) and
time/date info: date (data date), date0 (reference date) and time
(difference between date and date0). The input data can be provided
by load_data.
Parameters
----------
data : dict with prognostic variables
grd : ROMS netcdf grid file
sparams : s-coordinates parameters, theta_s,theta_b, hc and NLevels
**kargs:
ij : axis for vertical interpolations (*i,j)
ij_ind : list of i or j index for vertical interpolation, all by
default (ij_ind=False)
horizAux : if True, the original data horizontally interpolated is
returned and can be used for next data2roms call with
this same karg
quiet : output messages flag (false by default)
'''
ij = 'j'
ij_ind = False
horizAux = False
quiet = False
if 'ij' in kargs.keys(): ij = kargs['ij']
if 'ij_ind' in kargs.keys(): ij_ind = kargs['ij_ind']
if 'horizAux' in kargs.keys(): horizAux = kargs['horizAux']
if 'quiet' in kargs.keys(): quiet = kargs['quiet']
if not quiet: print 'using grid %s' % grd
g = roms.Grid(grd)
xr, yr, hr, mr = g.vars('r')
xu, yu, hu, mu = g.vars('u')
xv, yv, hv, mv = g.vars('v')
ny, nx = hr.shape
nz = sparams[3]
NX = data['NX']
NY = data['NY']
NZ = data['NZ']
if not quiet: print 'calc s levels...'
sshr = calc.griddata(data['lon'],
data['lat'],
data['ssh'],
xr,
yr,
extrap=True)
Zr = g.s_levels(sparams, sshr, hr, 'r')
Zu = g.s_levels(sparams, sshr, hr, 'u')
Zv = g.s_levels(sparams, sshr, hr, 'v')
# interp horiz:
retHorizAux = horizAux is True
if horizAux in (True, False):
TEMP = np.ma.masked_all((NZ, ny, nx), data['temp'].dtype)
SALT = np.ma.masked_all((NZ, ny, nx), data['salt'].dtype)
U = np.ma.masked_all((NZ, ny, nx), data['u'].dtype)
V = np.ma.masked_all((NZ, ny, nx), data['v'].dtype)
if not quiet: print 'horizontal interpolation:'
for i in range(NZ):
if not quiet and i % 10 == 0: print ' lev %d of %d' % (i, NZ)
#import pylab
#pylab.figure()
#pylab.pcolormesh(data['lon'],data['lat'],data['temp'][i,...])
try:
TEMP[i, ...] = calc.griddata(data['lon'],
data['lat'],
data['temp'][i, ...],
xr,
yr,
extrap=True)
except:
pass
try:
SALT[i, ...] = calc.griddata(data['lon'],
data['lat'],
data['salt'][i, ...],
xr,
yr,
extrap=True)
except:
pass
try:
U[i, ...] = calc.griddata(data['lon'],
data['lat'],
data['u'][i, ...],
xr,
yr,
extrap=True)
except:
pass
try:
V[i, ...] = calc.griddata(data['lon'],
data['lat'],
data['v'][i, ...],
xr,
yr,
extrap=True)
except:
pass
# rotate U,V:
if not quiet: print 'rotating U,V to grid angle'
angle = g.use('angle') # rad
U, V = calc.rot2d(U, V, angle)
U = rt.rho2uvp3d(U, 'u')
V = rt.rho2uvp3d(V, 'v')
horizAux = {}
horizAux['TEMP'] = TEMP
horizAux['SALT'] = SALT
horizAux['U'] = U
horizAux['V'] = V
else:
TEMP = horizAux['TEMP']
SALT = horizAux['SALT']
U = horizAux['U']
V = horizAux['V']
# interp vert:
nxu = nx - 1
nyv = ny - 1
#> -----------------------------------------------------------------
useInd = not ij_ind is False
if ij_ind is False:
if ij == 'j': ij_ind = range(ny)
elif ij == 'i': ij_ind = range(nx)
else:
try:
iter(ij_ind)
except:
ij_ind = [ij_ind]
if ij == 'j': ny = nyv = len(ij_ind)
elif ij == 'i': nx = nxu = len(ij_ind)
# -----------------------------------------------------------------<
Temp = np.zeros((nz, ny, nx), data['temp'].dtype)
Salt = np.zeros((nz, ny, nx), data['salt'].dtype)
Uvel = np.zeros((nz, ny, nxu), data['u'].dtype)
Vvel = np.zeros((nz, nyv, nx), data['v'].dtype)
jslice = lambda x, ind: x[:, ind, :]
islice = lambda x, ind: x[:, :, ind]
ZZr = np.tile(data['depth'], (nx, ny, 1)).T
ZZu = np.tile(data['depth'], (nxu, ny, 1)).T
ZZv = np.tile(data['depth'], (nx, nyv, 1)).T
if not useInd is False: #>------------------------------------------
if ij == 'j':
slice = jslice
sshr = sshr[ij_ind, :]
hr = hr[ij_ind, :]
elif ij == 'i':
slice = islice
sshr = sshr[:, ij_ind]
hr = hr[:, ij_ind]
Zr, Zu, Zv, TEMP, SALT, U, V = [
slice(k, ij_ind) for k in [Zr, Zu, Zv, TEMP, SALT, U, V]
]
# -----------------------------------------------------------------<
if useInd: # then store distances for a possible bry file
dtype = Temp.dtype
distr = np.zeros((nz, ny, nx), dtype)
distu = np.zeros((nz, ny, nxu), dtype)
distv = np.zeros((nz, nyv, nx), dtype)
if not quiet: print 'vertical interpolation:'
if ij == 'j':
for j in range(ny):
if not quiet and (ny < 10 or (ny >= 10 and j % 10 == 0)):
print ' j=%3d of %3d' % (j, ny)
ind = ij_ind[j]
dr = np.tile(calc.distance(xr[ind, :], yr[ind, :]), (nz, 1))
du = np.tile(calc.distance(xu[ind, :], yu[ind, :]), (nz, 1))
Dr = np.tile(calc.distance(xr[ind, :], yr[ind, :]), (NZ, 1))
Du = np.tile(calc.distance(xu[ind, :], yu[ind, :]), (NZ, 1))
if useInd:
distr[:, j, :] = dr
distu[:, j, :] = du
Temp[:, j, :] = calc.griddata(Dr,
ZZr[:, j, :],
TEMP[:, j, :],
dr,
Zr[:, j, :],
extrap=True)
Salt[:, j, :] = calc.griddata(Dr,
ZZr[:, j, :],
SALT[:, j, :],
dr,
Zr[:, j, :],
extrap=True)
if 0 and j % 10 == 0:
print Dr.shape, ZZr[:, j, :].shape
import pylab as pl
pl.figure(1)
pl.clf()
pl.pcolormesh(Dr, ZZr[:, j, :], SALT[:, j, :])
pl.colorbar()
clim = pl.gci().get_clim()
pl.figure(2)
pl.clf()
pl.pcolormesh(dr, Zr[:, j, :], Salt[:, j, :])
pl.clim(clim)
pl.colorbar()
raw_input()
Uvel[:, j, :] = calc.griddata(Du,
ZZu[:, j, :],
U[:, j, :],
du,
Zu[:, j, :],
extrap=True)
if j < Vvel.shape[1]:
dv = np.tile(calc.distance(xv[ind, :], yv[ind, :]), (nz, 1))
Dv = np.tile(calc.distance(xv[ind, :], yv[ind, :]), (NZ, 1))
Vvel[:, j, :] = calc.griddata(Dv,
ZZv[:, j, :],
V[:, j, :],
dv,
Zv[:, j, :],
extrap=True)
if useInd:
distv[:, j, :] = dv
if np.any(np.isnan(Temp[:, j, :])): print 'found nan in temp', j
if np.any(np.isnan(Salt[:, j, :])): print 'found nan in salt', j
if np.any(np.isnan(Uvel[:, j, :])): print 'found nan in u', j
if j < Vvel.shape[1] and np.any(np.isnan(Vvel[:, j, :])):
print 'found nan in v', j
elif ij == 'i':
for i in range(nx):
if not quiet and (nx < 10 or (nx >= 10 and i % 10 == 0)):
print ' i=%3d of %3d' % (i, nx)
ind = ij_ind[i]
dr = np.tile(calc.distance(xr[:, ind], yr[:, ind]), (nz, 1))
dv = np.tile(calc.distance(xv[:, ind], yv[:, ind]), (nz, 1))
Dr = np.tile(calc.distance(xr[:, ind], yr[:, ind]), (NZ, 1))
Dv = np.tile(calc.distance(xv[:, ind], yv[:, ind]), (NZ, 1))
if useInd:
distr[:, :, i] = dr
distv[:, :, i] = dv
Temp[:, :, i] = calc.griddata(Dr,
ZZr[:, :, i],
TEMP[:, :, i],
dr,
Zr[:, :, i],
extrap=True)
Salt[:, :, i] = calc.griddata(Dr,
ZZr[:, :, i],
SALT[:, :, i],
dr,
Zr[:, :, i],
extrap=True)
Vvel[:, :, i] = calc.griddata(Dv,
ZZv[:, :, i],
V[:, :, i],
dv,
Zv[:, :, i],
extrap=True)
if i < Uvel.shape[2]:
du = np.tile(calc.distance(xu[:, ind], yu[:, ind]), (nz, 1))
Du = np.tile(calc.distance(xu[:, ind], yu[:, ind]), (NZ, 1))
Uvel[:, :, i] = calc.griddata(Du,
ZZu[:, :, i],
U[:, :, i],
du,
Zu[:, :, i],
extrap=True)
if useInd:
distu[:, :, i] = du
# uv bar:
if not quiet: print 'calc uvbar'
if useInd is False:
ubar, vbar = rt.uvbar(Uvel, Vvel, sshr, hr, sparams)
else: #>------------------------------------------------------------
sshu = calc.griddata(data['lon'],
data['lat'],
data['ssh'],
xu,
yu,
extrap=True)
sshv = calc.griddata(data['lon'],
data['lat'],
data['ssh'],
xv,
yv,
extrap=True)
if ij == 'j':
sshu = sshu[ij_ind, :]
sshv = sshv[ij_ind, :]
hu = hu[ij_ind, :]
hv = hv[ij_ind, :]
elif ij == 'i':
sshu = sshu[:, ij_ind]
sshv = sshv[:, ij_ind]
hu = hu[:, ij_ind]
hv = hv[:, ij_ind]
ubar = rt.barotropic(Uvel, sshu, hu, sparams)
vbar = rt.barotropic(Vvel, sshv, hv, sparams)
# -----------------------------------------------------------------<
Vars = cb.odict()
Vars['temp'] = Temp
Vars['salt'] = Salt
Vars['u'] = Uvel
Vars['v'] = Vvel
Vars['zeta'] = sshr
Vars['ubar'] = ubar
Vars['vbar'] = vbar
Vars['date'] = data['date']
if not useInd is False: #>------------------------------------------
Vars['depth'] = Zr
Vars['depthu'] = Zu
Vars['depthv'] = Zv
Vars['dist'] = distr
Vars['distu'] = distu
Vars['distv'] = distv
# -----------------------------------------------------------------<
if retHorizAux: return Vars, horizAux
else: return Vars
def plot(self, z, cmap=meg_cmap, zrange="zero", label=False, showsens=False):
"""The array z of values to be plotted must be in the same
order as the array returned by get_names(). zrange can be
'auto', 'zero' which is auto but symmetric around 0, or
a pair of min, max."""
make_spline(self.x, self.y, array(z, "d"))
r = range(self.M)
for i in r:
xx = self.X[i]
for j in r:
yy = self.Y[j]
if not self.mask[j, i]:
self.Z[j, i] = interpolate(xx, yy, self.x, self.y)
Z = ma.array(self.Z, mask=self.mask)
if zrange == "auto" or zrange == "zero":
zmin = ma.minimum.reduce(Z)
zmax = ma.maximum.reduce(Z)
if zrange == "zero":
# If it crosses zero make it symmetrical.
if (zmin < 0) and (0 < zmax):
maxmax = max(-zmin, zmax)
zmin = -maxmax
zmax = maxmax
else:
zmin = zrange[0]
zmax = zrange[1]
# First make nice tics for this range.
# Then switch to the new limits given by the tics
# so the contour plot will use the whole range.
ticks, mticks = scale1(zmin, zmax)
zmin, zmax = ticks[0], ticks[-1]
nlevels = 100
levels = linspace(zmin, zmax, nlevels)
# plot the boundary and maybe the sensors
plot(self.boundx, self.boundy, color="black", zorder=1, linewidth=3)
if showsens:
scatter(self.x, self.y, s=15, c=(0, 1, 0), zorder=2, marker="o", linewidth=0.5)
# contourf(self.X, self.Y, Z, levels, cmap = cmap)
# contourf(self.X, self.Y, Z, levels, cmap = matplotlib.cm.hot)
contourf(self.X, self.Y, Z, levels)
im = gci() # save the ContourSet to return
contour(self.X, self.Y, Z, 10, colors="black")
if label:
for name in self.sensors:
s = self.topo[name]
text(s.x, s.y, name)
l = 1.02
x = -0.01
y = -0.04
axis([x, x + l, y, y + l])
axis("off")
axis("scaled")
return im, ticks
def make_panels(fig,datafiles, width=4, height = 3,
prefix='tmprot_',**kwargs):
"""
Makes png pictures of the given plot, with different angles.
Args:
ax (3D axis): te ax
angles (list): the list of angles (in degree) under which to
take the picture.
width,height (float): size, in inches, of the output images.
prefix (str): prefix for the files created.
Returns: the list of files created (for later removal)
"""
files = []
for i,df in enumerate(datafiles):
pl.clf()
fig.set_size_inches(width,height)
ticks = pub_plots(xmaj = 1000, xmin = 50, xstr = '%d', ymaj = 1000, ymin = 50, ystr = '%d')
MatPlotParams = {'xtick.major.size': 4, 'ytick.major.size' : 4,
'xtick.minor.size': 4, 'ytick.minor.size': 4,
'axes.labelsize': 6, 'xtick.labelsize': 10,
'ytick.labelsize': 8}
rcParams.update(MatPlotParams)
pl.subplots_adjust(wspace = 0.35,hspace = 0.35)
pl.figtext(.5,.95, 'Iteration:%d' %i, ha='center')
indat = pf.open(df)
data = indat[1].data
model = indat[2].data
residual = indat[3].data
header = indat[2].header
indat.close()
zoom_min = data.shape[0]/2 - 100
zoom_max = data.shape[0]/2 + 100
fig.add_subplot(2,2,1)
pl.title('data')
pl.imshow(-2.5*np.log10(data[zoom_min:zoom_max,zoom_min:zoom_max])+25.256, cmap = cm.jet_r)
pl.colorbar()
ticks.set_plot(pl.gca())
pl.gca().axes.get_xaxis().set_ticks([])
pl.gca().axes.get_yaxis().set_ticks([])
vmin, vmax = pl.gci().get_clim()
fig.add_subplot(2,2,2)
pl.title('model')
pl.imshow(-2.5*np.log10(model[zoom_min:zoom_max,zoom_min:zoom_max])+25.256, cmap = cm.jet_r, vmin=vmin, vmax=vmax)
ticks.set_plot(pl.gca())
pl.text(0.1, 0.95,'$m_{total}$: %4.2f, $r_e$: %4.1f' %(float(header['1_MAG'].split()[0]),float(header['1_RE'].split()[0])),
horizontalalignment='left',
verticalalignment='center',
fontsize=6, color = 'white',
transform = pl.gca().transAxes)
if i==17:
pl.text(0.1, 0.05,'$n$: %3.2f, $\chi^2_{DOF}$: %.2f' %(float(header['1_N'].split()[0]),header['CHI2NU']),
horizontalalignment='left',
verticalalignment='center',
fontsize=6, color = 'white',
transform = pl.gca().transAxes)
else:
pl.text(0.1, 0.05,'$n$: %3.2f' %(float(header['1_N'].split()[0])),
horizontalalignment='left',
verticalalignment='center',
fontsize=6, color = 'white',
transform = pl.gca().transAxes)
pl.gca().axes.get_xaxis().set_ticks([])
pl.gca().axes.get_yaxis().set_ticks([])
pl.colorbar()
zoom_resid = -2.5*np.log10(data[zoom_min:zoom_max,zoom_min:zoom_max])+2.5*np.log10(model[zoom_min:zoom_max,zoom_min:zoom_max])
fig.add_subplot(2,2,4)
pl.title('residual')
pl.imshow(zoom_resid, cmap = cm.jet)
#pl.text(0.5, 0.9,'$\chi^2_{DOF}$: %.2f' %header['CHI2NU'],
# horizontalalignment='center',
# verticalalignment='center',
# fontsize=10, color = 'black',
# transform = pl.gca().transAxes)
pl.colorbar()
vmin, vmax = pl.gci().get_clim()
ticks.set_plot(pl.gca())
pl.gca().axes.get_xaxis().set_ticks([])
pl.gca().axes.get_yaxis().set_ticks([])
fig.add_subplot(2,2,3)
pl.title('full frame')
pl.imshow(-2.5*np.log10(data)+2.5*np.log10(model), cmap = cm.jet, vmin = vmin, vmax = vmax)
cbar = pl.colorbar()
ticks.set_plot(pl.gca())
pl.gca().axes.get_xaxis().set_ticks([])
pl.gca().axes.get_yaxis().set_ticks([])
fname = '%s%03d.png'%(prefix,i)
pl.savefig(fname)
pl.savefig('%s_%d.eps'%('my_epsfiles',i))
files.append(fname)
return files