def printstuff(vals, vals_sum, file_count):
# create running sum of values
print file_count
print '----------------'
print 'sum', ma.sum(vals)
print 'total sum', ma.sum(vals_sum)
print '----------------'
print 'max', ma.amax(vals)
print 'min', ma.amin(vals)
print '\n----------------'
def printstuff(vals, vals_sum, file_count):
# create running sum of values
print file_count
print "----------------"
print "sum", ma.sum(vals)
print "total sum", ma.sum(vals_sum)
print "----------------"
print "max", ma.amax(vals)
print "min", ma.amin(vals)
print "\n----------------"
def printstuff(vals,vals_sum,file_count):
# create running sum of values
print file_count
print '----------------'
print 'sum', ma.sum(vals)
print 'total sum', ma.sum(vals_sum)
print '----------------'
print 'max', ma.amax(vals)
print 'min', ma.amin(vals)
print '\n----------------'
def printstuff(vals,vals_sum,file_count):
# create running sum of values
print file_count
print '----------------'
print 'sum', ma.sum(vals)
print 'total sum', ma.sum(vals_sum)
print 'perc masked:', ma.count_masked(vals_sum)/vals_sum.size*100.,'%'
print '----------------'
print 'max', ma.amax(vals)
print 'min', ma.amin(vals)
print '\n----------------'
def printstuff(vals, vals_sum, file_count):
# create running sum of values
print file_count
print '----------------'
print 'sum', ma.sum(vals)
print 'total sum', ma.sum(vals_sum)
print 'perc masked:', ma.count_masked(vals_sum) / vals_sum.size * 100., '%'
print '----------------'
print 'max', ma.amax(vals)
print 'min', ma.amin(vals)
print '\n----------------'
def normalizer(data_bank, special_input, data_bank_structure):
# TODO: do sth with special_input
# data_bank: dimensions are in 'Rows'
for row_index in range(size(data_bank, 0) - 1):
current_dimension = data_bank[row_index, :]
current_dimension = (current_dimension - mean(current_dimension)) / \
(amax(current_dimension) - amin(current_dimension))
data_bank[row_index, :] = current_dimension
return data_bank
def privImshow(img, noise, extent, ax=None, **kwargs):
args = {'cmap': colormap, 'sigma': 1}
args.update(kwargs)
ax = ax or plt.gca()
level0 = noise * args['sigma']
lev = []
for i in range(0, 10):
lev.append(level0 * 2**i)
col = ax.imshow(img,
cmap=args['cmap'],
norm=mpl.colors.SymLogNorm(linthresh=level0,
linscale=0.5,
vmin=lev[0],
vmax=0.5 * ma.amax(img)),
extent=extent)
divider = make_axes_locatable(ax)
cax = divider.append_axes('right', size='5%', pad='3%')
cbar = plt.colorbar(col, cax=cax)
cbar.set_label('Flux Density [Jy/beam]')
def plot_aligned_maps(maps,masked_shift=True, beam='max', fig_size='aanda*', **kwargs):
'''Derive shifts and plot images
All angles are in rad and converted if needed.
If the beam is given explicitly, please write it in terms of mas
'''
if 'sigma' in kwargs.keys():
sigma = kwargs.get('sigma',False)
else:
sigma=1
files = [eh.image.load_fits(m,aipscc=True) for m in maps]
fovx = np.array([m.fovx() for m in files])
fovy = np.array([m.fovy() for m in files])
header = [read_header(m) for m in maps]
freq1 = np.round(header[0]['CRVAL3']*1e-9,1)
freq2 = np.round(header[1]['CRVAL3']*1e-9,1)
maps_beam=[[h['BMAJ']*np.pi/180,h['BMIN']*np.pi/180,h['BPA']*np.pi/180] for h in header]
maps_ps = np.array([dm.psize for dm in files])
naxis1 = (fovx/maps_ps).astype(int)
naxis2 = (fovy/maps_ps).astype(int)
ppb=[PXPERBEAM(bp[0],bp[1],pxi) for bp,pxi in zip(maps_beam,maps_ps)]
noise1=header[0]['NOISE']
noise2=header[1]['NOISE']
r2m = 180/np.pi*3.6e6
if beam=='mean':
_maj = np.mean([maps_beam[0][0],maps_beam[1][0]])
_min = np.mean([maps_beam[0][1],maps_beam[1][1]])
_pos = np.mean([maps_beam[0][2],maps_beam[1][2]])
sys.stdout.write(' Will use mean beam.\n')
if beam=='max':
if np.logical_and(maps_beam[0][0] > maps_beam[1][0],maps_beam[0][1]>maps_beam[1][1]):
_maj = maps_beam[0][0]
_min = maps_beam[0][1]
_pos = maps_beam[0][2]
elif np.logical_and(maps_beam[0][0] < maps_beam[1][0],maps_beam[0][1]<maps_beam[1][1]):
_maj = maps_beam[1][0]
_min = maps_beam[1][1]
_pos = maps_beam[1][2]
else:
print('could not derive max beam.')
return
sys.stdout.write(' Will use max beam.\n')
if beam=='median':
_maj = np.median([maps_beam[0][0],maps_beam[1][0]])
_min = np.median([maps_beam[0][1],maps_beam[1][1]])
_pos = np.median([maps_beam[0][2],maps_beam[1][2]])
sys.stdout.write(' Will use median beam.\n')
if type(beam)==list:
_maj,_min,_pos = beam
_maj/=r2m
_min/=r2m
_pos = _pos*180/np.pi
common_beam = [_maj,_min,_pos]
sys.stdout.write('Will use beam of ({} , {} ) mas at PA {} degree.\n'.format(_maj*r2m,_min*r2m,_pos*180/np.pi))
#derive common parameter
common_ps = min(maps_ps)
common_fov = min([min(x,y) for x,y in zip(fovx,fovy)])
common_naxis= int(common_fov/common_ps)
common_ppb = PXPERBEAM(common_beam[0],common_beam[1],common_ps)
noise1_r = noise1/ppb[0]*common_ppb
noise2_r = noise2/ppb[1]*common_ppb
# regrid and blur the clean maps
#check for same fov and pixel size
if np.logical_and(maps_ps[0] != maps_ps[1], fovx[0]!=fovy[1]):
file1regrid = files[0].regrid_image(common_fov, common_naxis, interp='linear')
file1regridblur = file1regrid.blur_gauss(common_beam,frac=1)
file2regrid = files[1].regrid_image(common_fov, common_naxis, interp='linear')
file2regridblur = file2regrid.blur_gauss(common_beam, frac=1)
file1rb = file1regridblur.imarr(pol='I').copy()
file2rb = file2regridblur.imarr(pol='I').copy()
mask1=np.zeros_like(file1rb, dtype=np.bool)
mask2=np.zeros_like(file2rb, dtype=np.bool)
# cut out inner, optically thick part of the image
if 'npix_x' in kwargs.keys():
npix_x = kwargs.get('npix_x',False)
npix_y = kwargs.get('npix_y',False)
px_min_x = int(common_naxis/2-npix_x)
px_max_x = int(common_naxis/2+npix_x)
px_min_y = int(common_naxis/2-npix_y)
px_max_y = int(common_naxis/2+npix_y)
px_range_x = np.arange(px_min_x,px_max_x+1,1)
px_range_y = np.arange(px_min_y,px_max_y+1,1)
index=np.meshgrid(px_range_y,px_range_x)
mask1[tuple(index)] = True
mask2[tuple(index)] = True
if 'cut_left' in kwargs.keys():
cut_left = kwargs.get('cut_left',False)
px_max = int(common_naxis/2.+cut_left)
px_range_x = np.arange(0,px_max,1)
mask1
mask1[:,px_range_x] = True
mask2[:,px_range_x] = True
if 'cut_right' in kwargs.keys():
cut_right = kwargs.get('cut_right',False)
px_max = int(common_naxis/2-cut_right)
px_range_x = np.arange(px_max,naxis,1)
mask1[:,px_range_x] = True
mask2[:,px_range_x] = True
if 'radius' in kwargs.keys():
radius = kwargs.get('radius',False)
rr,cc = circle(int(len(file1rb)/2),int(len(file1rb)/2),radius)
mask1[rr,cc] = True
mask2[rr,cc] = True
if 'e_maj' in kwargs.keys():
e_maj = kwargs.get('e_maj',False)
e_min = kwargs.get('e_min',False)
e_pa = kwargs.get('e_pa',False)
e_xoffset = kwargs.get('e_xoffset',False)
if e_xoffset!=False:
x,y = int(len(file1rb)/2)+e_xoffset,int(len(file1rb)/2)
else:
x,y = int(len(file1rb)/2),int(len(file1rb)/2)
if e_pa!=False:
e_pa = 90-e_pa
else:
e_pa = maps_beam[0][2]
rr,cc =ellipse(y,x,e_maj,e_min,rotation=e_pa*np.pi/180)
mask1[rr,cc] = True
mask2[rr,cc] = True
if 'flux_cut' in kwargs.keys():
flux_cut = kwargs.get('flux_cut',False)
mask1[file1>flux_cut*ma.amax(file1rb)] = True
mask2[file2>flux_cut*ma.amax(file2rb)] = True
file1rbm = file1rb.copy()
file2rbm = file2rb.copy()
file1rbm[mask1]=0
file2rbm[mask2]=0
#align image
# ps covnerted from radperpx to masperpx
if masked_shift:
sys.stdout.write('Will derive the shift using the mask during cross-correlation\n')
file2rb_shift = align(file1rb,file2rb,common_ps*180/np.pi*3.6e6,common_ps*180/np.pi*3.6e6,mask1=~mask1,mask2=~mask2)
else:
sys.stdout.write('Will derive the shift using already masked images\n')
file2rb_shift=align(file1rbm,file2rbm,common_ps*180/np.pi*3.6e6,common_ps*180/np.pi*3.6e6)
######################
#shift file2regridblur to found position
#file2regridblur_shift = apply_shift(np.flipud(file2regridblur.imarr(pol='I')),file2_shift['shift'])
# file2rb_shift = apply_shift(file2rb,file2_shift['shift'])
# file2rb_shift *= ppb_r
###########################
file1_plt = files[0].regrid_image(fovx[0],naxis1[0]).blur_gauss(maps_beam[0],frac=1).imarr(pol='I')
file2_plt = files[1].regrid_image(fovx[1],naxis1[1]).blur_gauss(maps_beam[1],frac=1).imarr(pol='I')
file1_plt = file1_plt*ppb[0]
file2_plt = file2_plt*ppb[1]
file1rb_plt = file1rb*common_ppb
file2rb_plt = file2rb*common_ppb
file1rbm_plt = file1rbm*common_ppb
file2rbm_plt = file2rbm*common_ppb
file2rb_shift_plt = apply_shift(file2rb,file2rb_shift['shift'])* common_ppb
ra=file2regridblur.fovx()/eh.RADPERUAS/1e3/2
dec=file2regridblur.fovy()/eh.RADPERUAS/1e3/3
ra_min=-ra
ra_max=ra
dec_min=-dec
dec_max=dec
scale1 = maps_ps[0]*180/np.pi*3.6e6
scale2 = maps_ps[1]*180/np.pi*3.6e6
x1=np.linspace(-naxis1[0]*0.5*scale1,(naxis1[0]*0.5-1)*scale1,naxis1[0])
y1=np.linspace(naxis2[0]*0.5*scale1,-(naxis2[0]*0.5-1)*scale1,naxis2[0])
x2=np.linspace(-naxis1[1]*0.5*scale2,(naxis1[1]*0.5-1)*scale2,naxis1[1])
y2=np.linspace(naxis2[1]*0.5*scale2,-(naxis2[1]*0.5-1)*scale2,naxis2[1])
extent1 = np.max(x1), np.min(x1), np.min(y1), np.max(y1)
extent2 = np.max(x2), np.min(x2), np.min(y2), np.max(y2)
f,ax = plt.subplots(2,2)
axe_ratio='scaled'
ax[0,0].set_title('{} GHz original'.format(freq1))
ax[0,1].set_title('{} GHz original'.format(freq2))
ax[1,0].set_title('{} GHz regrid $+$ blur'.format(freq1))
ax[1,1].set_title('{} GHz regrid $+$ blur'.format(freq2))
level0 = min([noise1,noise2,noise1_r,noise2_r])*sigma
lev=[]
for i in range(0,10):
lev.append(level0*2**i)
level1r = noise1_r*sigma
lev1_r=[]
for i in range(0,10):
lev1_r.append(level1r*2**i)
level2r = noise2_r*sigma
lev2_r=[]
for i in range(0,10):
lev2_r.append(level2r*2**i)
imax = max([ma.amax(ii) for ii in [file1_plt,file2_plt,file1rb_plt,file2rb_plt]])
norm = mpl.colors.SymLogNorm(linthresh=level0,linscale=0.5,vmin=level0,vmax=0.5*imax,base=10)
im1 = ax[0,0].imshow(file1_plt,cmap=colormap,norm=norm,extent=extent1)
im2 = ax[0,1].imshow(file2_plt,cmap=colormap,norm=norm,extent=extent2)
im3 = ax[1,0].imshow(file1rb_plt,cmap=colormap,norm=norm,extent=extent2)
im4 = ax[1,1].imshow(file2rb_plt,cmap=colormap,norm=norm,extent=extent2)
divider = make_axes_locatable(ax[0,1])
cax = divider.append_axes('right', size='5%', pad='3%')
#cbar = f.colorbar(im,ax=ax[:])
cbar = f.colorbar(im2,cax=cax)
cbar.set_label('Flux Density [Jy/beam]')
divider = make_axes_locatable(ax[1,1])
cax = divider.append_axes('right', size='5%', pad='3%')
#cbar = f.colorbar(im,ax=ax[:])
cbar = f.colorbar(im4,cax=cax)
cbar.set_label('Flux Density [Jy/beam]')
for aa in ax.flat:
aa.set(xlabel='RA [mas]', ylabel='Relative DEC [mas]')
aa.xaxis.set_minor_locator(AutoMinorLocator())
aa.yaxis.set_minor_locator(AutoMinorLocator())
aa.axis(axe_ratio)
aa.set_xlim(ra_max,ra_min)
aa.set_ylim(dec_min,dec_max)
figsize=set_size(fig_size,subplots=(2,2))
set_corrected_size(f,figsize)
plt.tight_layout(pad=0.4)
f.savefig(plotDir+'{:d}GHz_convolved_with_{:d}GHz.pdf'.format(int(freq2),int(freq1)))
######################################################
# plt.cla()
f,ax = plt.subplots(2,2)
ax[0,0].set_title('{}GHz regrid $+$ blur'.format(freq1))
ax[0,1].set_title('{}GHz regrid $+$ blur'.format(freq2))
ax[1,0].set_title('{0}GHz/ {1}GHz not shifted'.format(freq1,freq2))
ax[1,1].set_title('{0}GHz/ {1}GHz shifted'.format(freq1,freq2))
imax = max([ma.amax(ii) for ii in [file1rbm_plt,file2rbm_plt]])
norm = mpl.colors.SymLogNorm(linthresh=level0,linscale=0.5,vmin=level0,vmax=0.5*imax,base=10)
im = ax[0,0].imshow(file1rbm_plt,cmap=colormap,norm=norm,extent=extent2)
im = ax[0,1].imshow(file2rbm_plt,cmap=colormap,norm=norm,extent=extent2)
divider = make_axes_locatable(ax[0,1])
cax = divider.append_axes('right', size='5%', pad=0.05)
#cbar = f.colorbar(col, use_gridspec=True,cax=cax)
cbar = f.colorbar(im,cax=cax)
cbar.set_label('Flux Density [Jy/beam]')
#
cntr1=ax[1,0].contour(np.flipud(file1rb_plt),linewidths=0.5,levels=lev1_r,colors='grey',extent=extent2,alpha=1)
cntr2=ax[1,0].contour(np.flipud(file2rb_plt),linewidths=0.5,levels=lev2_r,colors='darkblue',extent=extent2,alpha=0.6)
h1,_ = cntr1.legend_elements()
h2,_ = cntr2.legend_elements()
ax[1,0].legend([h1[0],h2[0]],['{}GHz'.format(freq1),'{}GHz'.format(freq2)],loc='upper right')
#
cntr1=ax[1,1].contour(np.flipud(file1rb_plt),linewidths=0.5,levels=lev1_r,colors='grey',extent=extent2)
cntr2=ax[1,1].contour(np.flipud(file2rb_shift_plt),linewidths=0.5,levels=lev2_r,colors='darkblue',extent=extent2,alpha=0.6)
h1,_ = cntr1.legend_elements()
h2,_ = cntr2.legend_elements()
ax[1,1].legend([h1[0],h2[0]],['{}GHz'.format(freq1),'{}GHz'.format(freq2)],loc='upper right')
for aa in ax.flat:
aa.set(xlabel='RA [mas]', ylabel='Relative Declination [mas]')
aa.axis(axe_ratio)
aa.xaxis.set_minor_locator(AutoMinorLocator())
aa.yaxis.set_minor_locator(AutoMinorLocator())
aa.set_xlim(ra_max,ra_min)
aa.set_ylim(dec_min,dec_max)
figsize=set_size(fig_size,subplots=(2,2))
set_corrected_size(f,figsize)
plt.tight_layout(pad=0.4)
f.savefig(plotDir+'shifted_maps_{:d}GHz_{:d}GHz.pdf'.format(int(freq1),int(freq2)))
#########
plt.cla()
shift_export=file2rb_shift['shift'].copy()
sys.stdout.write('final shift: {}'.format(shift_export))
shift_export[0]*=common_ps*180/np.pi*3.6e6
shift_export[1]*=common_ps*180/np.pi*3.6e6
if masked_shift:
sys.stdout.write('shift in mas: {}'.format(shift_export))
else:
error_export=file2rb_shift['error'].copy()
error_export*=common_ps*180/np.pi*3.6e6
sys.stdout.write('shift in mas: {}\pm{}'.format(shift_export,error_export))
#########################
# plot spix map
file1rb_plt = np.flipud(file1rb_plt)
file2rb_shift_plt = np.flipud(file2rb_shift_plt)
spix1 = file1rb_plt*(file1rb_plt > noise1*sigma) #replaces indices where condition is not met with 0
spix2 = file2rb_shift_plt*(file2rb_shift_plt > noise2*sigma)
spix1[spix1==0] = noise1*sigma
spix2[spix2==0] = noise2*sigma
a = np.log10(spix2/spix1)/np.log10(freq2/freq1)
spix_vmin,spix_vmax=-3,5
sys.stdout.write('\nSpectral index max(alpha)={} - min(alpha)={}\nCutoff {}<alpha<{}\n'.format(ma.amax(a),ma.amin(a),spix_vmin,spix_vmax))
a[a<spix_vmin] = spix_vmin
a[a>spix_vmax] = spix_vmax
a[spix2==noise2*sigma] =spix_vmin
level10 = noise1*sigma
lev1=[]
level20 = noise2*sigma
lev2=[]
for i in range(0,10):
lev1.append(level10*2**i)
lev2.append(level20*2**i)
f,ax = plt.subplots()
if fig_size=='aanda*':
fig_size='aanda'
cset = ax.contour(spix1,linewidths=[0.5],levels=lev1_r,colors=['grey'], extent=extent2,origin='lower',alpha=0.7)
im = ax.imshow(a,cmap='hot_r',origin='lower',extent= extent2,vmin=spix_vmin,vmax=spix_vmax)
divider = make_axes_locatable(ax)
cax = divider.append_axes('right', size='5%', pad=0.05)
cbar = f.colorbar(im, use_gridspec=True,cax=cax)
cbar.set_label(r'Spectral index $\alpha$')
h1,_ = cset.legend_elements()
ax.legend([h1[0]],['{}GHz'.format(freq1)],loc='upper right')
ax.axis('scaled')
ax.set_xlabel('RA [mas]')
ax.set_ylabel('Relative Dec [mas]')
ax.set_xlim(ra_max,ra_min)
ax.set_ylim(dec_min,dec_max)
ax.minorticks_on()
#ax.tick_params('both', length=8, width=2, which='major')
#f.tick_params(axis='both',which='both',direction='in', labelsize=13)
# cb = plt.colorbar(im,cax=cax,cmap='jet')
# cb.ax.tick_params(labelsize=13, width=2)
# cb.set_label(r'$\alpha$',fontsize=15)
figsize=set_size(fig_size)
set_corrected_size(f,figsize)
plt.savefig(plotDir+'spectral_index_between_{:d}_{:d}.pdf'.format(int(freq1),int(freq2)),bbox_inches='tight')
plt.close('all')
############################
if masked_shift:
return {'file1':file1regridblur,'file2':file2regridblur,'shift':shift_export,'increment_dec':common_ps*3.6e6,'increment_ra':common_ps*3.6e6}
else:
return {'file1':file1regridblur,'file2':file2regridblur,'shift':shift_export,'increment_dec':common_ps*3.6e6,'increment_ra':common_ps*3.6e6,'error':error_export,'diffphase':file2rb_shift['diffphase']}
def BHOSS2fits(filename,freq,source,date,history,user,plot=1,show=False):
##some definitions
DEGREE = 3.141592653589/180.0
HOUR = 15.0*DEGREE
RADPERAS = DEGREE/3600.0
RADPERUAS = RADPERAS*1.e-6
#get file name
filename_load=filename
tmp=filename.split('_')
#get source postion
loc=SkyCoord.from_name(source)
#get RA and DEC in degree
ra=loc.ra.deg
dec=loc.dec.deg
#convert date to mjd (modified julian date)
modjuldate=(aTime(date)).mjd
#get BHOSS GRRT file based on Z. Younsi script
#--> needs to be updated once the BHOSS header is modified!!!!
#
# First header line: [image width, offset, resolution, # of observational frequencies]
header_1 = np.genfromtxt(filename, max_rows = 1)
# Second header line: [observational time, inclination, BH spin parameter, Luminosity F_nu correction to erg Hz, Jansky correction to Jy Hz ]
header_2 = np.genfromtxt(filename, skip_header = 1, max_rows = 1)
# Third header line: observational frequencies of interest
header_3 = np.genfromtxt(filename, skip_header = 2, max_rows = 1)
width = header_1[0]
offset = header_1[1]
M = int(header_1[2])
s1 = width + offset
s2 = 2*width/(M - 1)
N_obs_freqs = header_1[3]
time = header_2[0]
inclination = header_2[1]
phi = header_2[2]
spin = header_2[3]
L_corr = header_2[4]
Jansky_corr = header_2[5]
if source=='SgrA*':
Micro_Arcsecond_Corr = 5.04975 # New value based on Boehle et al. 2016
if source=='M 87':
Micro_Arcsecond_Corr = 3.622197344489511 # New value based from Yosuke for M87
width_scaled = Micro_Arcsecond_Corr*width # Scale from r_g to micro-arcseconds
#find select frequency within computed freqs
ind=np.where(header_3==freq)
if len(ind[0])<1:
sys.exit('EXIT:freq not in GRRT file. Available freqs are %s' %str((header_3)))
else:
freq_ID=ind[0][0]+3
print header_3
print header_3[freq_ID-3]
# Now read in all image data
ascii2 = np.loadtxt(filename_load, skiprows = 3, usecols = (0, 1, freq_ID))
data2=ascii2.reshape([M, M, 3])
# Convert from indices to (alpha,beta), in units of r_g, on the image plane
x = -s1 + s2*(data2[:,:,0] - 1)
y = -s1 + s2*(data2[:,:,1] - 1)
# Convert (alpha,beta) into micro-arcseconds
x = Micro_Arcsecond_Corr*x
y = Micro_Arcsecond_Corr*y
xmax = np.amax(x)
xmin = np.amin(x)
ymax = np.amax(y)
ymin = np.amin(y)
#flux in Jansky
jansky=(data2[:,:,2]*Jansky_corr)
#create pixel size
dxorg=(xmax-xmin)/x.shape[0]
dyorg=(ymax-ymin)/y.shape[0]
dim=x.shape[0]
print('image resolution %f' %(dxorg))
print('org res. total flux:', ma.sum(jansky), 'max flux:',ma.amax(jansky))
#create fits file
# Create header and fill in some values
header = fits.Header()
header['AUTHOR'] = user
header['OBJECT'] = source
header['CTYPE1'] = 'RA---SIN'
header['CTYPE2'] = 'DEC--SIN'
header['CDELT1'] = -dxorg*RADPERUAS/DEGREE
header['CDELT2'] = dxorg*RADPERUAS/DEGREE
header['OBSRA'] = ra
header['OBSDEC'] = dec
header['FREQ'] = freq
header['MJD'] = float(modjuldate)
header['TELESCOP'] = 'VLBI'
header['BUNIT'] = 'JY/PIXEL'
header['STOKES'] = 'I'
header['HISTORY'] = history
hdu = fits.PrimaryHDU(jansky, header=header)
hdulist = [hdu]
hdulist = fits.HDUList(hdulist)
# Save fits
tmp=filename.split('/')
outname=tmp[-1]
hdulist.writeto('FITS/%s_%i_%iGHz.fits' %(outname[:-4],dim,(freq/1e9)), overwrite=True)
if plot==1:
#create image (normalised)
fonts=12
cmap='cubehelix'
fig=plt.figure(figsize=(7,8))
plt.subplots_adjust(left=0.15, bottom=0.1, right=0.95, top=0.85, wspace=0.00001, hspace=0.00001)
ax=fig.add_subplot(111,frame_on='True',aspect='equal',axisbg='k')
#i1=ax.imshow(jansky/ma.amax(jansky),origin='lower', vmin=0,vmax=1,extent=[xmax, xmin, ymin, ymax], interpolation="bicubic",cmap=cmap )
i1=ax.imshow(ma.log10(jansky),origin='lower',vmin=-10,vmax=ma.log10(0.05),extent=[xmax, xmin, ymin, ymax], interpolation="bicubic",cmap=cmap )
ax.annotate(r'$\mathrm{%s}$' %(source), xy=(0.1, 0.91),xycoords='axes fraction', fontsize=18,
horizontalalignment='left', verticalalignment='bottom', color='w')
ax.annotate(r'$\mathrm{{\nu=%i\,GHz}}$' %(freq/1e9), xy=(0.1, 0.81),xycoords='axes fraction', fontsize=18,
horizontalalignment='left', verticalalignment='bottom', color='w')
#set axis
plt.xlabel('relative R.A [$\mu$as]', fontsize=fonts)
plt.ylabel('relative DEC [$\mu$as]', fontsize=fonts)
#set position of colorbar
p1=ax.get_position().get_points().flatten()
ax11 = fig.add_axes([p1[0], p1[3], p1[2]-p1[0], 0.02])
t1=plt.colorbar(i1,cax=ax11,orientation='horizontal',format='%1.1f')
#t1.set_label(r'$\rm{S/S}_{\rm{max}}$',fontsize=fonts+4,labelpad=-65)
t1.set_label(r'$\log_{10}(S)\,\mathrm{[Jy/pixel]}$',fontsize=fonts+4,labelpad=-65)
t1.ax.xaxis.set_ticks_position('top')
t1.ax.tick_params(labelsize=fonts)
#set xmax left and ticks
ax.set_xlim(xmax,xmin)
ax.set_ylim(ymin,ymax)
ax.yaxis.set_major_locator(plt.MultipleLocator(20))
ax.yaxis.set_minor_locator(plt.MultipleLocator(5))
ax.xaxis.set_major_locator(plt.MultipleLocator(20))
ax.xaxis.set_minor_locator(plt.MultipleLocator(5))
for spine in ax.spines.values():
spine.set_edgecolor('w')
#settings for axes and tickmarks
for label in ax.xaxis.get_ticklabels():
label.set_fontsize(fonts)
for label in ax.yaxis.get_ticklabels():
label.set_fontsize(fonts)
for tick in ax.xaxis.get_major_ticks():
tick.tick1line.set_color('w')
tick.tick2line.set_color('w')
tick.tick1line.set_markersize(14)
tick.tick2line.set_markersize(14)
for tick in ax.xaxis.get_minor_ticks():
tick.tick1line.set_color('w')
tick.tick2line.set_color('w')
tick.tick1line.set_markersize(10)
tick.tick2line.set_markersize(10)
for tick in ax.yaxis.get_major_ticks():
tick.tick1line.set_color('w')
tick.tick2line.set_color('w')
tick.tick1line.set_markersize(14)
tick.tick2line.set_markersize(14)
for tick in ax.yaxis.get_minor_ticks():
tick.tick1line.set_color('w')
tick.tick2line.set_color('w')
tick.tick1line.set_markersize(10)
tick.tick2line.set_markersize(10)
#save image
plt.savefig('IMAGE/%s_%i_%iGHz.pdf' %(source,dim,(freq/1e9)),dpi=150, bbox_inches='tight', pad_inches = 0.04)
if show==True:
plt.show()
return {'image':jansky,'dx':dxorg,'dy':dyorg}
def validationExterne():
""" Permet d'effectuer une validation externe entre l'image résultante de la réduction d'échelle et une image de
température de surface calculée à partir des bandes 10 et 11 de Landsat 8 (disponibles sur EarthData).
Les résultats de la validation externe sont des métriques de qualité en comparant les résultats de la réduction
d'échelle à la température de surface calculée à 100m. Ces résultats sont présentés dans la console par des
'print' (lignes 129 à 144).
"""
# Match prediction result extent
landsat_b10 = Image(
r'data/LC08_L1TP_014028_20200706_20200721_01_T1_B10.TIF')
landsat_b10.reprojectMatch(
r'data/MOD11_L2.clipped_test2.tif'.split(".")[0] +
'_subdivided_100m.tif', False)
landsat_b10.setNewFile(
landsat_b10.filename.replace(".TIF", "_reproject.tif"))
# Get TOA radiance
b10_array = landsat_b10.getArray(masked=True,
lower_valid_range=1,
upper_valid_range=65535)
b10_array_radiance = ma.add(ma.multiply(b10_array, 0.00033420), 0.10000)
# Get Brightness Temperature
b10_array_brightness_temp = (1321.0789 / (ma.log(
(774.8853 / b10_array_radiance) + 1))) - 273.15
# Get NDVI
landsat_b4 = Image(
r'data/LC08_L1TP_014028_20200706_20200721_01_T1_B4_reproject.tif')
b4_DN = landsat_b4.getArray(masked=True,
lower_valid_range=1,
upper_valid_range=65535)
b4 = np.add(np.multiply(b4_DN, float(0.00002)), float(-0.10))
landsat_b5 = Image(
r'data/LC08_L1TP_014028_20200706_20200721_01_T1_B5_reproject.tif')
b5_DN = landsat_b5.getArray(masked=True,
lower_valid_range=1,
upper_valid_range=65535)
b5 = np.add(np.multiply(b5_DN, float(0.00002)), float(-0.10))
ndvi = np.divide(np.subtract(b5, b4),
np.add(b5, b4),
where=((np.add(b5, b4)) != 0))
# Get proportion of vegetation
min_ndvi = ma.amin(ndvi)
max_ndvi = ma.amax(ndvi)
pv = ma.power(
ma.divide(ma.subtract(ndvi, min_ndvi),
(ma.subtract(max_ndvi, min_ndvi)),
where=(ma.subtract(max_ndvi, min_ndvi)) != 0), 2)
# Get emissivity
emissivity = 0.004 * pv + 0.986
# Get Landsat 8 LST
landsat_lst = b10_array_brightness_temp / (
1 +
(0.00115 * b10_array_brightness_temp / 1.4388) * ma.log(emissivity))
# Save LST image for visualization
landsat_b10.save_band(landsat_lst, r'data/landsat_lst.tif')
# Validation between both arrays
predicted_lst = ma.masked_invalid(
Image(r'data/MODIS_predit_100m.tif').getArray())
predicted_lst_with_residuals = ma.masked_invalid(
Image(r'data/MODIS_predit_100m_avec_residus.tif').getArray())
predicted_lst = ma.filled(predicted_lst, 0)
predicted_lst_with_residuals = ma.filled(predicted_lst_with_residuals, 0)
# Without residuals
print('Without residual correction')
print('Mean Absolute Error (MAE):',
metrics.mean_absolute_error(predicted_lst, landsat_lst))
print('Mean Squared Error:',
metrics.mean_squared_error(predicted_lst, landsat_lst))
print('Root Mean Squared Error:',
np.sqrt(metrics.mean_squared_error(predicted_lst, landsat_lst)),
"°C")
print(
'Accuracy:', 100 -
np.mean(100 * ((abs(predicted_lst - landsat_lst)) / landsat_lst)), "%")
print('Explained variance score (EVS):',
metrics.explained_variance_score(predicted_lst, landsat_lst))
# With residuals
print("\n")
print('With residual correction')
print(
'Mean Absolute Error (MAE):',
metrics.mean_absolute_error(predicted_lst_with_residuals, landsat_lst))
print(
'Mean Squared Error:',
metrics.mean_squared_error(predicted_lst_with_residuals, landsat_lst))
print(
'Root Mean Squared Error:',
np.sqrt(
metrics.mean_squared_error(predicted_lst_with_residuals,
landsat_lst)), "°C")
print(
'Accuracy:', 100 - np.mean(100 * (
(abs(predicted_lst_with_residuals - landsat_lst)) / landsat_lst)),
"%")
print(
'Explained variance score (EVS):',
metrics.explained_variance_score(predicted_lst_with_residuals,
landsat_lst))
if i >= BATS_lon_min and i <= BATS_lon_max:
lon_index.add(index2) # Must do .add in order to add for a set
index2 += 1
print(lon_index)
lat_index_min = min(lat_index)
lat_index_max = max(lat_index)
lon_index_min = min(lon_index)
lon_index_max = max(lon_index)
BATSadt = adt[:, lat_index_min:lat_index_max, lon_index_min:lon_index_max]
# creating colorbar scale:
high = ma.amax(adt)
low = ma.amin(adt)
colorbar_scale = ["%.2E" % low]
i = 0.16
while i < 1:
value = (high - low) * i
colorbar_scale.append("%.2E" % value)
i += 0.16
## ^^ ignore this but when you make your colorbar you can add the
## scale by: cbar.ax.set_yticklabels(colorbar_scale)
# write code for global ocean here:
# write code for BATS part here:
print(BATSadt.shape)
def make_closea_masks(config=None,domcfg_file=None,mask=None):
#=========================
# 1. Read in domcfg file
#=========================
if config is None:
raise Exception('configuration must be specified')
if domcfg_file is None:
raise Exception('domain_cfg file must be specified')
if mask is None:
mask=False
domcfg = nc.Dataset(domcfg_file,'r+')
lon = domcfg.variables['nav_lon'][:]
lat = domcfg.variables['nav_lat'][:]
top_level = domcfg.variables['top_level'][0][:]
nx = top_level.shape[1]
ny = top_level.shape[0]
# Generate 2D "i" and "j" fields for use in "where" statements.
# These are the Fortran indices, counting from 1, so we have to
# add 1 to np.arange because python counts from 0.
ones_2d = np.ones((ny,nx))
ii1d = np.arange(nx)+1
jj1d = np.arange(ny)+1
ii2d = ii1d * ones_2d
jj2d = np.transpose(jj1d*np.transpose(ones_2d))
#=====================================
# 2. Closea definitions (old style)
#=====================================
# NB. The model i and j indices defined here are Fortran indices,
# ie. counting from 1 as in the NEMO code. Also the indices
# of the arrays (ncsi1 etc) count from 1 in order to match
# the Fortran code.
# This means that you can cut and paste the definitions from
# the NEMO code and change round brackets to square brackets.
# But BEWARE: Fortran array(a:b) == Python array[a:b+1] !!!
#
# If use_runoff_box = True then specify runoff area as all sea points within
# a rectangular area. If use_runoff_box = False then specify a list of points
# as in the old NEMO code. Default to false.
use_runoff_box = False
#================================================================
if config == 'ORCA2':
num_closea = 4
max_runoff_points = 4
ncsnr = np.zeros(num_closea+1,dtype=np.int) ; ncstt = np.zeros(num_closea+1,dtype=np.int)
ncsi1 = np.zeros(num_closea+1,dtype=np.int) ; ncsj1 = np.zeros(num_closea+1,dtype=np.int)
ncsi2 = np.zeros(num_closea+1,dtype=np.int) ; ncsj2 = np.zeros(num_closea+1,dtype=np.int)
ncsir = np.zeros((num_closea+1,max_runoff_points+1),dtype=np.int) ; ncsjr = np.zeros((num_closea+1,max_runoff_points+1),dtype=np.int)
# Caspian Sea (spread over globe)
ncsnr[1] = 1 ; ncstt[1] = 0
ncsi1[1] = 11 ; ncsj1[1] = 103
ncsi2[1] = 17 ; ncsj2[1] = 112
# Great Lakes - North America - put at St Laurent mouth
ncsnr[2] = 1 ; ncstt[2] = 2
ncsi1[2] = 97 ; ncsj1[2] = 107
ncsi2[2] = 103 ; ncsj2[2] = 111
ncsir[2,1] = 110 ; ncsjr[2,1] = 111
# Black Sea (crossed by the cyclic boundary condition)
# put in Med Sea (north of Aegean Sea)
ncsnr[3:5] = 4 ; ncstt[3:5] = 2
ncsir[3:5,1] = 171; ncsjr[3:5,1] = 106
ncsir[3:5,2] = 170; ncsjr[3:5,2] = 106
ncsir[3:5,3] = 171; ncsjr[3:5,3] = 105
ncsir[3:5,4] = 170; ncsjr[3:5,4] = 105
# west part of the Black Sea
ncsi1[3] = 174 ; ncsj1[3] = 107
ncsi2[3] = 181 ; ncsj2[3] = 112
# east part of the Black Sea
ncsi1[4] = 2 ; ncsj1[4] = 107
ncsi2[4] = 6 ; ncsj2[4] = 112
#================================================================
elif config == 'eORCA1':
num_closea = 1
max_runoff_points = 1
ncsnr = np.zeros(num_closea+1,dtype=np.int) ; ncstt = np.zeros(num_closea+1,dtype=np.int)
ncsi1 = np.zeros(num_closea+1,dtype=np.int) ; ncsj1 = np.zeros(num_closea+1,dtype=np.int)
ncsi2 = np.zeros(num_closea+1,dtype=np.int) ; ncsj2 = np.zeros(num_closea+1,dtype=np.int)
ncsir = np.zeros((num_closea+1,max_runoff_points+1),dtype=np.int) ; ncsjr = np.zeros((num_closea+1,max_runoff_points+1),dtype=np.int)
# Caspian Sea (spread over the globe)
ncsnr[1] = 1 ; ncstt[1] = 0
ncsi1[1] = 332 ; ncsj1[1] = 243
ncsi2[1] = 344 ; ncsj2[1] = 275
#================================================================
elif config == 'eORCA025_UK':
num_closea = 10
max_runoff_points = 1
ncsnr = np.zeros(num_closea+1,dtype=np.int) ; ncstt = np.zeros(num_closea+1,dtype=np.int)
ncsi1 = np.zeros(num_closea+1,dtype=np.int) ; ncsj1 = np.zeros(num_closea+1,dtype=np.int)
ncsi2 = np.zeros(num_closea+1,dtype=np.int) ; ncsj2 = np.zeros(num_closea+1,dtype=np.int)
ncsir = np.zeros((num_closea+1,max_runoff_points+1),dtype=np.int) ; ncsjr = np.zeros((num_closea+1,max_runoff_points+1),dtype=np.int)
# Caspian Sea
ncsnr[1] = 1 ; ncstt[1] = 0
ncsi1[1] = 1330 ; ncsj1[1] = 831
ncsi2[1] = 1375 ; ncsj2[1] = 981
# Aral Sea
ncsnr[2] = 1 ; ncstt[2] = 0
ncsi1[2] = 1376 ; ncsj1[2] = 900
ncsi2[2] = 1400 ; ncsj2[2] = 981
# Azov Sea
ncsnr[3] = 1 ; ncstt[3] = 0
ncsi1[3] = 1284 ; ncsj1[3] = 908
ncsi2[3] = 1304 ; ncsj2[3] = 933
# Lake Superior
ncsnr[4] = 1 ; ncstt[4] = 0
ncsi1[4] = 781 ; ncsj1[4] = 905
ncsi2[4] = 815 ; ncsj2[4] = 926
# Lake Michigan
ncsnr[5] = 1 ; ncstt[5] = 0
ncsi1[5] = 795 ; ncsj1[5] = 871
ncsi2[5] = 813 ; ncsj2[5] = 905
# Lake Huron part 1
ncsnr[6] = 1 ; ncstt[6] = 0
ncsi1[6] = 814 ; ncsj1[6] = 882
ncsi2[6] = 825 ; ncsj2[6] = 905
# Lake Huron part 2
ncsnr[7] = 1 ; ncstt[7] = 0
ncsi1[7] = 826 ; ncsj1[7] = 889
ncsi2[7] = 833 ; ncsj2[7] = 905
# Lake Erie
ncsnr[8] = 1 ; ncstt[8] = 0
ncsi1[8] = 816 ; ncsj1[8] = 871
ncsi2[8] = 837 ; ncsj2[8] = 881
# Lake Ontario
ncsnr[9] = 1 ; ncstt[9] = 0
ncsi1[9] = 831 ; ncsj1[9] = 882
ncsi2[9] = 847 ; ncsj2[9] = 889
# Lake Victoria
ncsnr[10] = 1 ; ncstt[10] = 0
ncsi1[10] = 1274 ; ncsj1[10] = 672
ncsi2[10] = 1289 ; ncsj2[10] = 687
#================================================================
elif config == 'eORCA025_UK_rnf':
num_closea = 10
max_runoff_points = 1
use_runoff_box = True
ncsnr = np.zeros(num_closea+1,dtype=np.int) ; ncstt = np.zeros(num_closea+1,dtype=np.int)
ncsi1 = np.zeros(num_closea+1,dtype=np.int) ; ncsj1 = np.zeros(num_closea+1,dtype=np.int)
ncsi2 = np.zeros(num_closea+1,dtype=np.int) ; ncsj2 = np.zeros(num_closea+1,dtype=np.int)
ncsir1 = np.zeros(num_closea+1,dtype=np.int) ; ncsjr1 = np.zeros(num_closea+1,dtype=np.int)
ncsir2 = np.zeros(num_closea+1,dtype=np.int) ; ncsjr2 = np.zeros(num_closea+1,dtype=np.int)
ncsir = np.zeros((num_closea+1,max_runoff_points+1),dtype=np.int) ; ncsjr = np.zeros((num_closea+1,max_runoff_points+1),dtype=np.int)
# Caspian Sea
ncsnr[1] = 1 ; ncstt[1] = 0
ncsi1[1] = 1330 ; ncsj1[1] = 831
ncsi2[1] = 1375 ; ncsj2[1] = 981
# Aral Sea
ncsnr[2] = 1 ; ncstt[2] = 0
ncsi1[2] = 1376 ; ncsj1[2] = 900
ncsi2[2] = 1400 ; ncsj2[2] = 981
# Azov Sea
ncsnr[3] = 1 ; ncstt[3] = 0
ncsi1[3] = 1284 ; ncsj1[3] = 908
ncsi2[3] = 1304 ; ncsj2[3] = 933
# Lake Superior
ncsnr[4] = 1 ; ncstt[4] = 1
ncsi1[4] = 781 ; ncsj1[4] = 905
ncsi2[4] = 815 ; ncsj2[4] = 926
# runff points the St Laurence Seaway for all Great Lakes
ncsir1[4:10] = 873 ; ncsjr1[4:10] = 909
ncsir2[4:10] = 884 ; ncsjr2[4:10] = 920
# Lake Michigan
ncsnr[5] = 1 ; ncstt[5] = 1
ncsi1[5] = 795 ; ncsj1[5] = 871
ncsi2[5] = 813 ; ncsj2[5] = 905
# Lake Huron part 1
ncsnr[6] = 1 ; ncstt[6] = 1
ncsi1[6] = 814 ; ncsj1[6] = 882
ncsi2[6] = 825 ; ncsj2[6] = 905
# Lake Huron part 2
ncsnr[7] = 1 ; ncstt[7] = 1
ncsi1[7] = 826 ; ncsj1[7] = 889
ncsi2[7] = 833 ; ncsj2[7] = 905
# Lake Erie
ncsnr[8] = 1 ; ncstt[8] = 1
ncsi1[8] = 816 ; ncsj1[8] = 871
ncsi2[8] = 837 ; ncsj2[8] = 881
# Lake Ontario
ncsnr[9] = 1 ; ncstt[9] = 1
ncsi1[9] = 831 ; ncsj1[9] = 882
ncsi2[9] = 847 ; ncsj2[9] = 889
# Lake Victoria
ncsnr[10] = 1 ; ncstt[10] = 0
ncsi1[10] = 1274 ; ncsj1[10] = 672
ncsi2[10] = 1289 ; ncsj2[10] = 687
#================================================================
elif config == 'eORCA025_UK_empmr':
num_closea = 10
max_runoff_points = 1
use_runoff_box = True
ncsnr = np.zeros(num_closea+1,dtype=np.int) ; ncstt = np.zeros(num_closea+1,dtype=np.int)
ncsi1 = np.zeros(num_closea+1,dtype=np.int) ; ncsj1 = np.zeros(num_closea+1,dtype=np.int)
ncsi2 = np.zeros(num_closea+1,dtype=np.int) ; ncsj2 = np.zeros(num_closea+1,dtype=np.int)
ncsir1 = np.zeros(num_closea+1,dtype=np.int) ; ncsjr1 = np.zeros(num_closea+1,dtype=np.int)
ncsir2 = np.zeros(num_closea+1,dtype=np.int) ; ncsjr2 = np.zeros(num_closea+1,dtype=np.int)
ncsir = np.zeros((num_closea+1,max_runoff_points+1),dtype=np.int) ; ncsjr = np.zeros((num_closea+1,max_runoff_points+1),dtype=np.int)
# Caspian Sea
ncsnr[1] = 1 ; ncstt[1] = 0
ncsi1[1] = 1330 ; ncsj1[1] = 831
ncsi2[1] = 1375 ; ncsj2[1] = 981
# Aral Sea
ncsnr[2] = 1 ; ncstt[2] = 0
ncsi1[2] = 1376 ; ncsj1[2] = 900
ncsi2[2] = 1400 ; ncsj2[2] = 981
# Azov Sea
ncsnr[3] = 1 ; ncstt[3] = 0
ncsi1[3] = 1284 ; ncsj1[3] = 908
ncsi2[3] = 1304 ; ncsj2[3] = 933
# Lake Superior
ncsnr[4] = 1 ; ncstt[4] = 2
ncsi1[4] = 781 ; ncsj1[4] = 905
ncsi2[4] = 815 ; ncsj2[4] = 926
# runff points the St Laurence Seaway for all Great Lakes
ncsir1[4:10] = 873 ; ncsjr1[4:10] = 909
ncsir2[4:10] = 884 ; ncsjr2[4:10] = 920
# Lake Michigan
ncsnr[5] = 1 ; ncstt[5] = 2
ncsi1[5] = 795 ; ncsj1[5] = 871
ncsi2[5] = 813 ; ncsj2[5] = 905
# Lake Huron part 1
ncsnr[6] = 1 ; ncstt[6] = 2
ncsi1[6] = 814 ; ncsj1[6] = 882
ncsi2[6] = 825 ; ncsj2[6] = 905
# Lake Huron part 2
ncsnr[7] = 1 ; ncstt[7] = 2
ncsi1[7] = 826 ; ncsj1[7] = 889
ncsi2[7] = 833 ; ncsj2[7] = 905
# Lake Erie
ncsnr[8] = 1 ; ncstt[8] = 2
ncsi1[8] = 816 ; ncsj1[8] = 871
ncsi2[8] = 837 ; ncsj2[8] = 881
# Lake Ontario
ncsnr[9] = 1 ; ncstt[9] = 2
ncsi1[9] = 831 ; ncsj1[9] = 882
ncsi2[9] = 847 ; ncsj2[9] = 889
# Lake Victoria
ncsnr[10] = 1 ; ncstt[10] = 0
ncsi1[10] = 1274 ; ncsj1[10] = 672
ncsi2[10] = 1289 ; ncsj2[10] = 687
#=====================================
# 3. Generate mask fields
#=====================================
rnf_count = 0
empmr_count = 0
closea_mask = ma.zeros(top_level.shape,dtype=np.int)
temp_mask_rnf = ma.zeros(top_level.shape,dtype=np.int)
temp_mask_empmr = ma.zeros(top_level.shape,dtype=np.int)
closea_mask_rnf = ma.zeros(top_level.shape,dtype=np.int)
closea_mask_empmr = ma.zeros(top_level.shape,dtype=np.int)
for ics in range(num_closea):
closea_mask = ma.where( ( ii2d[:] >= ncsi1[ics+1] ) & ( ii2d[:] <= ncsi2[ics+1] ) &
( jj2d[:] >= ncsj1[ics+1] ) & ( jj2d[:] <= ncsj2[ics+1] ) &
( top_level == 1 ), ics+1, closea_mask)
if ncstt[ics+1] == 1:
rnf_count = rnf_count + 1
temp_mask_rnf[:] = 0
if use_runoff_box:
temp_mask_rnf = ma.where( ( ii2d[:] >= ncsir1[ics+1] ) & ( ii2d[:] <= ncsir2[ics+1] ) &
( jj2d[:] >= ncsjr1[ics+1] ) & ( jj2d[:] <= ncsjr2[ics+1] ) &
( top_level == 1 ), rnf_count, 0)
else:
for ir in range(ncsnr[ics+1]):
temp_mask_rnf[ncsjr[ics+1],ncsjr[ics+1]] = rnf_count
temp_mask_rnf = ma.where( closea_mask_rnf > 0, ma.minimum(temp_mask_rnf,closea_mask_rnf), temp_mask_rnf)
min_rnf = ma.amin(temp_mask_rnf[ma.where(temp_mask_rnf > 0)])
max_rnf = ma.amax(temp_mask_rnf[ma.where(temp_mask_rnf > 0)])
if min_rnf != max_rnf:
print 'min_rnf, max_rnf : ',min_rnf,max_rnf
raise Exception('Partially overlapping target rnf areas for two closed seas.')
else:
# source area:
closea_mask_rnf[ma.where(closea_mask==ics+1)] = min_rnf
# target area:
closea_mask_rnf[ma.where(temp_mask_rnf>0)] = min_rnf
# reset rnf_count:
rnf_count = min_rnf
if ncstt[ics+1] == 2:
empmr_count = empmr_count + 1
temp_mask_empmr[:] = 0
if use_runoff_box:
temp_mask_empmr = ma.where( ( ii2d[:] >= ncsir1[ics+1] ) & ( ii2d[:] <= ncsir2[ics+1] ) &
( jj2d[:] >= ncsjr1[ics+1] ) & ( jj2d[:] <= ncsjr2[ics+1] ) &
( top_level == 1 ), empmr_count, 0)
else:
for ir in range(ncsnr[ics+1]):
temp_mask_empmr[ncsjr[ics+1],ncsjr[ics+1]] = empmr_count
temp_mask_empmr = ma.where( closea_mask_empmr > 0, ma.minimum(temp_mask_empmr,closea_mask_empmr), temp_mask_empmr)
min_empmr = ma.amin(temp_mask_empmr[ma.where(temp_mask_empmr > 0)])
max_empmr = ma.amax(temp_mask_empmr[ma.where(temp_mask_empmr > 0)])
if min_empmr != max_empmr:
raise Exception('Partially overlapping target empmr areas for two closed seas.')
else:
# source area:
closea_mask_empmr[ma.where(closea_mask==ics+1)] = min_empmr
# target area:
closea_mask_empmr[ma.where(temp_mask_empmr>0)] = min_empmr
# reset empmr_count:
empmr_count = min_empmr
if mask:
# apply land-sea mask if required
closea_mask.mask = np.where(top_level==0,True,False)
closea_mask_rnf.mask = np.where(top_level==0,True,False)
closea_mask_empmr.mask = np.where(top_level==0,True,False)
#=====================================
# 4. Append masks to domain_cfg file.
#=====================================
domcfg.createVariable('closea_mask',datatype='i',dimensions=('y','x'),fill_value=closea_mask.fill_value,chunksizes=(1000,1000))
domcfg.variables['closea_mask'][:]=closea_mask
if rnf_count > 0:
domcfg.createVariable('closea_mask_rnf',datatype='i',dimensions=('y','x'),fill_value=closea_mask_rnf.fill_value,chunksizes=(1000,1000))
domcfg.variables['closea_mask_rnf'][:]=closea_mask_rnf
if empmr_count > 0:
domcfg.createVariable('closea_mask_empmr',datatype='i',dimensions=('y','x'),fill_value=closea_mask_empmr.fill_value,chunksizes=(1000,1000))
domcfg.variables['closea_mask_empmr'][:]=closea_mask_empmr
domcfg.close()
def __init__(self,imgFiles,shiftFile=None):
self.header = [read_header(m) for m in imgFiles]
self.shift_ra = None
self.shift_dec = None
self.shift_date = None
if shiftFile is not None:
shift_ra,shift_dec,shift_date = read_shift(shiftFile)
self.date_im = np.array([parse(h['DATE-OBS']) for h in self.header])
date_shift = np.array([parse(d) for d in shift_date])
intersecS = np.in1d(date_shift,self.date_im)
intersecI = np.in1d(self.date_im,date_shift)
#self.date_im= [np.round(Time(h['DATE-OBS']).to_value('decimalyear'),4) for h in self.header] #previous way of doing it
#date_shift = [np.round(Time(d, format='decimalyear').value,4) for d in shift_date]
#date_intersection = list(set(self.date_im).intersection(date_shift))
if np.array_equal(intersecI,intersecS):
sys.stdout.write('Shifts for all epochs are there. Will continue\n')
self.shift_ra = np.array(shift_ra)
self.shift_dec = np.array(shift_dec)
self.shift_date= np.array(shift_date)
else:
sys.stdout.write('Dates/Number of shifts are not equal to the given image observing dates.\n')
input('Do you want to continute by only using the images for which shifts are there?\n Press Enter to continue...')
self.shift_ra = np.array(shift_ra)[intersecS]
self.shift_dec = np.array(shift_dec)[intersecS]
self.shift_date= np.array(date_shift)[intersecS]
imgFiles = np.array(imgFiles)[intersecI]
self.header = [read_header(m) for m in imgFiles]
self.ehtFiles = [eh.image.load_fits(m, aipscc=True) for m in imgFiles]
self.beam = [[h['BMAJ']*np.pi/180,h['BMIN']*np.pi/180,h['BPA']*np.pi/180] for h in self.header]
self.fovx = np.array([m.fovx() for m in self.ehtFiles])
self.fovy = np.array([m.fovy() for m in self.ehtFiles])
self.naxis1 = np.array([h['NAXIS1'] for h in self.header])
self.naxis2 = np.array([h['NAXIS2'] for h in self.header])
self.px_inc = np.array([h['cdelt2'] for h in self.header])
self.noise_difmap = np.array([h['noise'] for h in self.header])
self.ppb = [PXPERBEAM(b[0],b[1],pxi*np.pi/180) for b,pxi in zip(self.beam,self.px_inc)]
self.median_beam= np.array([np.sqrt(b[0]*b[1]) for b in self.beam])
self.stacked_beam = np.median(self.median_beam)
self.stacked_naxis= ma.amax([self.naxis1,self.naxis2])
self.stacked_fov = ma.amax([self.fovx,self.fovy])
self.stacked_px_inc = self.stacked_fov/self.stacked_naxis*180/np.pi
self.stacked_ppb = PXPERBEAM(self.stacked_beam,self.stacked_beam,self.stacked_px_inc*np.pi/180)
self.date_im = None
self.stackedImg = None
self.blurImg = None
self.stacked_noise_diff = None
#check whether all images have the same field of view. If not, regrid them to the smalles fov.
if len(np.unique(np.concatenate([self.fovx,self.fovy])))>1:
sys.stdout.write('Regrid images as they do not have the same FOV.\n')
maxfov = [max(x,y) for x,y in zip(self.fovx,self.fovy)]
self.ehtFiles = [f.pad(mf,mf) for f,mf in zip(self.ehtFiles,maxfov)]
self.ehtFiles = [f.regrid_image(self.stacked_fov,self.stacked_naxis,interp='linear') for f in self.ehtFiles]
# blur with a circular gauss
blurFiles = [im.blur_circ(self.stacked_beam) for im in self.ehtFiles]
self.blurImg= np.array([im.imarr(pol='I') for im in blurFiles])
######################
if shiftFile is not None:
print(self.shift_ra)
self.shift_ra = self.shift_ra/self.stacked_px_inc/3.6e6
self.shift_dec= self.shift_dec/self.stacked_px_inc/3.6e6
print(self.shift_ra)
self.blurImg = np.array([apply_shift(f,[sd,sr]) for f,sd,sr in zip(self.blurImg,self.shift_dec,self.shift_ra)])
self.stackedImg = self.blurImg.sum(axis=0)/len(self.blurImg)*self.stacked_ppb
print(np.sum(self.noise_difmap)/len(self.noise_difmap))