def make_image(self,
image_name="output.fits",
npix=600,
phi=0.0,
convolve=False):
inclination = self.parameters["inclination"]
posang = self.parameters["posang"]
wavelength = self.parameters["wavelength"]
print(self.domain_size())
image.makeImage(npix=npix,
incl=inclination,
posang=posang,
phi=phi,
wav=wavelength,
binary=True,
sizeau=self.domain_size()) # This calls radmc3d
im = image.readImage(binary=True)
self.parameters["sizepix_x"] = im.sizepix_x
self.parameters["sizepix_y"] = im.sizepix_y
if len(im.x) == 0:
raise RuntimeError("Image creation failed, image is empty")
if convolve:
im = im.imConv(fwhm=1e-3 * np.array(self.parameters["beam_fwhm"]),
pa=1e-3 * self.parameters["beam_posang"],
dpc=self.parameters["distance"])
im.raw_input = lambda s: "y"
image.plotImage(im, log=True, maxlog=2, dpc=101.0, cmap='inferno')
import radmc3dPy.image as image
import matplotlib.pyplot as plt
import numpy as np
i = 7
dist = 5410.
#lambdas = np.array([ 37500., 20000., 13043.47826087, 9375., 7142.85714286,
# 5454.54545455, 4285.71428571, 3529.41176471])
#en GHz: np.array([8,15,23,32,42,55,70,85])*1. GHz.
im = image.readImage()
#image.plotImage(im, au=True, log=True, maxlog=10, saturate=1e-5, cmap=plt.cm.gist_heat)
"""
image.plotImage(im, dpc=140, arcsec=True, log=True, maxlog=10, saturate=1e-5, cmap=plt.cm.gist_heat)
image.plotImage(im, dpc=dist, arcsec=True, log=True, maxlog=10, saturate=1e-5, cmap=plt.cm.gist_heat)
cim = im.imConv(fwhm=[1.0, 0.6], pa=120., dpc=dist)
image.plotImage(cim, arcsec=True, dpc=dist, log=True, maxlog=10, bunit='snu', cmap=plt.cm.gist_heat)
"""
im.writeFits('img_shell.fits', dpc=5410.) #, coord='03h10m05s -10d05m30s')
#Mirar lo de inputs desde terminal
def getOutput_im(ifreq, dis, im, optim, tauim, polunitlen, fkabs, fksca,pngname,
polmax=None, imUnits='Tb', imlim=None,
xlim=None, ylim=None, axisUnits='au',
opltr=None, inc=None):
""" calculates image
xlim : tuple
ylim : tuple
axisUnits = 'cm', 'arcsec', 'AU'
"""
# determine if there is stokes data
dostokes = False
if im.stokes:
if im.image[:,:,1,ifreq].max() == 0 and im.image[:,:,2,ifreq].max() ==0:
dostokes = False
else:
dostokes = True
# image, polarized intensity, pol frac, tau, optical depth, pol vectors
nsub = 1 #image
if dostokes: # polarized intensity
nsub = nsub + 1
if dostokes: # polarization fraction
nsub = nsub + 1
if optim is not None:
nsub = nsub + 1
if tauim is not None:
nsub = nsub + 1
if dostokes: #vectors
nsub = nsub + 1
# axis units
if axisUnits.lower() == 'cm':
axis_au = False
axis_arcsec = False
elif axisUnits.lower() == 'arcsec':
axis_au = False
axis_arcsec = True
elif axisUnits.lower() == 'au':
axis_au = True
axis_arcsec = False
else:
raise ValueError('axisUnits not understood')
nrow = np.floor(np.sqrt(nsub))
ncol = np.ceil(nsub / nrow)
nrow, ncol = int(nrow), int(ncol)
fig, axgrid = plt.subplots(nrows=nrow, ncols=ncol, figsize=(4*ncol, 3*nrow),
sharex=True, sharey=True, squeeze=False)
axes = axgrid.flatten()
isubplot = 0
# image
if imlim is not None:
imvmin, imvmax = imlim[0], imlim[1]
else:
imvmin, imvmax = 0, None
ax = axes[isubplot]
image.plotImage(image=im, cmap=plt.cm.jet, interpolation='bilinear',
arcsec=axis_arcsec, au=axis_au, dpc=dis, oplotbeam='w',
stokes='I', bunit=imUnits,ifreq=ifreq, saturate='90percent',
clevs=[1, 20, 40, 60, 80, 100, 120, 140, 160, 180, 200], clcol='w',
vmin=imvmin, vmax=imvmax, ax=ax)
if im.stokes is True:
image.plotPolDir(image=im, arcsec=False, au=True, dpc=dis, color='w',
nx=16, ny=16, polunitlen=polunitlen, ifreq=ifreq, ax=ax)
isubplot = isubplot + 1
#
# polarized intensity
if dostokes:
#ax = fig.add_subplot(nrow,ncol,isubplot)
ax = axes[isubplot]
image.plotImage(image=im, cmap=plt.cm.jet, interpolation='bilinear',
arcsec=axis_arcsec, au=axis_au, dpc=dis, oplotbeam='w',
stokes='PI', bunit=imUnits,ifreq=ifreq, saturate='90percent',
clevs=[0, 1.0, 10., 100., 200., 500.], clcol='w',
ax=ax)
isubplot = isubplot + 1
# polarized degree
if dostokes:
#ax = fig.add_subplot(nrow,ncol,isubplot)
ax = axes[isubplot]
image.plotImage(image=im, cmap=plt.cm.jet, interpolation='bilinear',
arcsec=axis_arcsec, au=axis_au, dpc=dis, ifreq=ifreq,
saturate='100percent', stokes='P',bunit='percent' , vmin=0, vmax=polmax,
clevs=[1., 5.0, 10., 20.], clcol='k', ax=ax)
isubplot = isubplot + 1
# optical depth
if optim is not None:
ax = axes[isubplot]
kext = fkabs(im.wav[ifreq]) + fksca(im.wav[ifreq])
image.plotImage(image=optim, cmap=plt.cm.jet, interpolation='bilinear',
arcsec=axis_arcsec, au=axis_au, dpc=dis, ifreq=ifreq,
saturate='100percent', stokes='I', bunit='optdepth',
clevs=[0.1,1.,5., 10.,100.], clcol='w', ax=ax
)
isubplot = isubplot + 1
# tau image
if tauim is not None:
ax = axes[isubplot]
reg = tauim.image[:,tauim.ny/2,0,ifreq] > tauim.image.min()
if True in reg:
xmax = tauim.x[reg].max()/natconst.au
vmax = tauim.image[:,:,0,ifreq].max()/natconst.au
else:
xmax = tauim.x.max()/natconst.au
vmax = tauim.image[:,:,0,:].max()/natconst.au
# tausurface
image.plotImage(image=tauim, cmap=plt.cm.jet, interpolation='bilinear',
arcsec=axis_arcsec, au=axis_au, dpc=dis,
stokes='I', bunit='length', ifreq=ifreq,
vmin=-vmax,
vmax=vmax, ax=ax)
nx = int(2.*tauim.x.max()/natconst.au / (xmax / 8))
if (nx % 2) == 1:
nx = nx + 1
if nx > 50: nx = 50
ny = nx
# polarization vectors
image.plotPolDir(image=im, arcsec=axis_arcsec, au=axis_au, dpc=dis, color='k',
nx=nx, ny=ny, polunitlen=polunitlen, ifreq=ifreq, ax=ax)
ax.set_xlim(-xmax, xmax)
ax.set_ylim(-xmax, xmax)
isubplot = isubplot + 1
# only polarized vectors that varies with polarized fraction, no image
if dostokes:
ax = axes[isubplot]
image.plotPolDir(image=im, arcsec=axis_arcsec, au=axis_au, dpc=dis, color='k',
nx=16, ny=16, polunitlen=-1, ifreq=ifreq, ax=ax)
ax.set_title('Polarization E Vectors')
# xlim and ylim
if xlim is not None:
for ii in range(len(axes)):
axes[ii].set_xlim(xlim)
if ylim is not None:
for ii in range(len(axes)):
axes[ii].set_ylim(ylim)
# set aspect radtio
for ii in range(len(axes)):
axes[ii].set_aspect('equal')
# over plot ellipses
if (opltr is not None) and (inc is not None):
for axii in axes:
for ir in opltr:
ells = Ellipse(xy=(0,0), width=2*ir, height=np.cos(inc*natconst.rad)*2*ir, angle=0,
fill=False, color='k', linestyle='-', linewidth=1)
axii.axes.add_patch(ells)
fig.tight_layout()
fig.savefig(pngname)
plt.close()
def getOutput_wavim(im, dis, pngname, imTblim=None, imxlim=None, imylim=None, opltr=None, inc=None,
anglim=None, angcmap='hsv'):
"""
plots all the images across wavelength: stokes I, polarization fraction, angles
Parameters
----------
im : radmc3dImage
dis : float
distance in pc
pngname : str
name for png file output
opltr : list of floats
radius to overplot in au
inc : float
inclination in degrees
angcmap : str
name of colormap to use for angle plot. Default is 'hsv'
"""
if imTblim is None:
vlim = [0, None]
else:
vlim = imTblim
if imxlim is None:
imxlim = (im.x.min()/natconst.au, im.x.max()/natconst.au)
if imylim is None:
imylim = (im.y.min()/natconst.au, im.y.max()/natconst.au)
if anglim is None:
anglim = [None, None]
nwav = len(im.wav)
if im.stokes:
nrow = nwav
ncol = 4
else:
nrow = np.floor(np.sqrt(nwav))
ncol = np.ceil(nwav / nrow)
nrow, ncol = int(nrow), int(ncol)
fig, axgrid = plt.subplots(nrows=nrow, ncols=ncol, figsize=(ncol*3, nrow*3),
squeeze=False, sharex=True, sharey=True)
axes = axgrid.flatten()
for ii in range(nwav):
# stokes I
if im.stokes:
axii = axgrid[ii, 0]
else:
axii = axes[ii]
dum = image.plotImage(ax=axii, image=im, au=True, cmap=plt.cm.jet,
stokes='I', bunit='Tb', dpc=dis, vmin=vlim[0], vmax=vlim[1],
ifreq=ii, clevs=[20,40,60,80, 100], clcol='k',
oplotbeam='w', beamxy=[imxlim[0]*0.75, imylim[0]*0.75],
titleplt='I')
axii.set_xlim(imxlim)
axii.set_ylim(imylim)
# polarized intensity
if im.stokes:
axii = axgrid[ii,1]
dum = image.plotImage(ax=axii, image=im, au=True, cmap=plt.cm.jet,
stokes='PI', bunit='Tb', dpc=dis,
ifreq=ii,
oplotbeam='w', beamxy=[imxlim[0]*0.75, imylim[0]*0.75],
titleplt='PI')
axii.set_xlim(imxlim)
axii.set_ylim(imylim)
# polarization fraction
if im.stokes:
axii = axgrid[ii,2]
dum = image.plotImage(ax=axii, image=im, au=True, cmap=plt.cm.jet,
stokes='P', bunit='percent', dpc=dis,
ifreq=ii,
oplotbeam='w', beamxy=[imxlim[0]*0.75, imylim[0]*0.75],
titleplt='PFrac')
axii.set_xlim(imxlim)
axii.set_ylim(imylim)
# polarization angle
if im.stokes:
axii = axgrid[ii,3]
dum = image.plotImage(ax=axii, image=im, au=True,
cmap=plt.cm.bwr, #plt.get_cmap(angcmap),
stokes='ang', bunit='deg', dpc=dis,
ifreq=ii,
oplotbeam='w', beamxy=[imxlim[0]*0.75, imylim[0]*0.75],
titleplt='PA',
vmin=anglim[0], vmax=anglim[1])
axii.set_xlim(imxlim)
axii.set_ylim(imylim)
image.plotPolDir(image=im, au=True, ax=axii, ifreq=ii, polunitlen=-2,
nx=16, ny=16, color='k')
if (opltr is not None) and (inc is not None):
for axii in axes:
for ir in opltr:
ells = Ellipse(xy=(0,0), width=2*ir, height=np.cos(inc*natconst.rad)*2*ir, angle=0,
fill=False, color='k', linestyle=':', linewidth=1)
axii.axes.add_patch(ells)
fig.tight_layout()
fig.savefig(pngname)
plt.close()
def getOutput_stokes(ifreq, dis, im, pngname, polmax=None):
# plot stokes values: I, Q, U, V, Polarized Linear Intensity, fraction
plt.figure(num=ifreq, figsize=(14,8))
# image
plt.subplot(2,3,1)
image.plotImage(image=im, cmap=plt.cm.jet, interpolation='bilinear',
arcsec=False, au=True, dpc=dis, oplotbeam='w',
stokes='I', bunit='inu',ifreq=ifreq,saturate='90percent')
plt.subplot(2,3,2)
image.plotImage(image=im, cmap=plt.cm.bwr, interpolation='bilinear',
arcsec=False, au=True, dpc=dis, textcolor='k',
stokes='Q', bunit='norm',ifreq=ifreq, vmin=-1, vmax=1)
plt.subplot(2,3,3)
image.plotImage(image=im, cmap=plt.cm.bwr, interpolation='bilinear',
arcsec=False, au=True, dpc=dis, textcolor='k',
stokes='U', bunit='norm',ifreq=ifreq, vmin=-1,vmax=1)
plt.subplot(2,3,4)
image.plotImage(image=im, cmap=plt.cm.bwr, interpolation='bilinear',
arcsec=False, au=True, dpc=dis, textcolor='k',
stokes='V', bunit='norm',ifreq=ifreq, vmin=-1, vmax=1)
plt.subplot(2,3,5)
image.plotImage(image=im, cmap=plt.cm.jet, interpolation='bilinear',
arcsec=False, au=True, dpc=dis,
stokes='PI', bunit='inu',ifreq=ifreq,saturate='90percent')
image.plotPolDir(image=im, arcsec=False, au=True, dpc=dis, color='w',
nx=16, ny=22, polunitlen=-2, ifreq=ifreq)
plt.subplot(2,3,6)
image.plotImage(image=im, cmap=plt.cm.jet, interpolation='bilinear',
arcsec=False, au=True, dpc=dis, ifreq=ifreq,
saturate='100percent', stokes='P',bunit='percent' , vmin=0,vmax=polmax,
clevs=[5.0, 10., 20.], clcol='k')
image.plotPolDir(image=im, arcsec=False, au=True, dpc=dis, color='w',
nx=16, ny=22, polunitlen=-2, ifreq=ifreq)
plt.tight_layout()
plt.savefig(pngname)
plt.close()
import radmc3dPy.image as image
import subprocess
output = 'img_rl_powerlaw.fits'
subprocess.call(['rm', output])
dist = 2000.
im = image.readImage()
data = im.image #Image data, channels lie on axis 2.
image.plotImage(im,
dpc=dist,
au=True,
bunit='jy/pixel',
ifreq=29,
cmap='gnuplot') #plotting channel 29
im.writeFits(fname=output, dpc=dist,
coord='03h10m05s -10d05m30s') #writting 3d fits cube