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KineSummaryCompact.py~
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import os
import re
from astropy.io import fits
import scipy
import scipy.signal
import matplotlib as mpl
# mpl.use('Agg')
import matplotlib.pyplot as plt
import numpy as np
from pylab import *
import matplotlib.colors as colors
from mpl_toolkits.axes_grid1 import make_axes_locatable
from scipy.signal import medfilt2d
include_path='/Users/simon/common/python/include/'
sys.path.append(include_path)
def addimage(iplotpos,label,atitle,filename_grey,filename_contours=False,VisibleXaxis=False,VisibleYaxis=False,DoBeamEllipse=False,DoGreyCont=False,DoCB=False,Clevs=False,Region=False,vsyst=0.,nplotsx=1,nplotsy=1,Region_Contours=False,SymmetricRange=False,UseScatter=False,cmap='ocean_r',filename_weights='',SubtractVsyst=False,ColorBarScale=1.,cblabel='km/s',Zoom=False,side=3.5,RegionOfInterest=False):
print("vsyst",vsyst)
print( "nplotsx ", nplotsx, iplotpos)
ax = plt.subplot(nplotsy, nplotsx, iplotpos)
# ax=axes[iplotpos]
plt.setp(ax.get_xticklabels(),visible=VisibleXaxis)
plt.setp(ax.get_yticklabels(),visible=VisibleYaxis)
ax.tick_params(axis='both',length = 5, width=1., color = 'grey',direction='in',left=True, right=True,bottom=True, top=True)
ax.spines['right'].set_color('grey')
ax.spines['left'].set_color('grey')
ax.spines['top'].set_color('grey')
ax.spines['bottom'].set_color('grey')
if ((iplotpos % nplotsx) == 1):
ax.set_ylabel(r'$\delta$ offset / arcsec')
if (iplotpos > (nplotsx*(nplotsy-1))):
ax.set_xlabel(r'$\alpha$ offset / arcsec')
print( "loading filename_grey",filename_grey)
flog.write("loading filename_grey "+filename_grey+"\n")
f = fits.open(filename_grey)
im_grey = f[0].data
hdr_grey= f[0].header
cdelt=3600.*hdr_grey['CDELT2']
side0=hdr_grey['NAXIS2']*cdelt
if Zoom:
if (side > side0):
sys.exit("side too large")
nx=np.rint(side/cdelt)
ny=np.rint(side/cdelt)
i_star = np.rint(( (0.)/ hdr_grey['CDELT1'] )+ (hdr_grey['CRPIX1']-1.))
j_star = np.rint(( (0.)/ hdr_grey['CDELT2'] )+ (hdr_grey['CRPIX2']-1.))
j0=int(j_star-(ny-1.)/2.+1)
j1=int(j_star+(ny-1.)/2.+1)
i0=int(i_star-(nx-1.)/2.+1)
i1=int(i_star+(nx-1.)/2.+1)
subim_grey = im_grey[j0:j1,i0:i1]
else:
side=side0
i0=0
i1=hdr_grey['NAXIS1']
j0=0
j1=hdr_grey['NAXIS2']
subim_grey=im_grey.copy()
a0 = side/2.
a1 = -side/2.
d0 = -side/2.
d1 = side/2.
subim_grey = im_grey[int(j0):int(j1),int(i0):int(i1)]
print( "i0 "+str(i0),"hdr_grey['CRPIX2']", hdr_grey['CRPIX2'])
if SubtractVsyst:
print( "subtracting vsyst=",vsyst)
subim_grey = subim_grey - vsyst
if (('_azim_av_drot' in filename_grey) and not ('diff' in filename_grey)):
print( "vsyst",vsyst)
subim_grey = subim_grey - vsyst
range2=subim_grey.max()
range1=np.amin(subim_grey)
#clevs = [np.amin(subim_grey),0.,np.amax(subim_grey)]
clevs = [np.amin(subim_grey),np.amax(subim_grey)]
#clabels=['%.0f' % (ColorBarScale*clevs[0]),'','%.0f' % (ColorBarScale*clevs[2])]
clabels=['%.2f' % (ColorBarScale*clevs[0]), '%.2f' % (ColorBarScale*clevs[1])]
if (isinstance(Clevs,tuple)):
print( "inherit Clevs")
clevs = Clevs[0]
range1=clevs[0]
range2=clevs[2]
#clabels=['%.0f' % (clevs[0]),'0.','%.0f' % (clevs[2])]
#clabels=['%.1f' % (clevs[0]-clevs[1]),'0.','%.1f' % (clevs[2]-clevs[1])]
clabels=Clevs[1]
if (isinstance(Region,str)):
file_region=Region
print( "loading ", file_region)
f = fits.open(file_region)
im_region = f[0].data
hdr_region= f[0].header
subim_region = im_region[int(j0):int(j1),int(i0):int(i1)]
dum=subim_region*subim_grey
print( "dum max:",np.max(dum))
print( "dum min:",np.min(dum))
subim_region[np.where(subim_region < 0.)] = 0.
subim_region[np.where(subim_region > 1.)] = 1.
subim_grey[np.where(subim_region < 0.5)] = 0.
print("vsyst",vsyst)
if (Clevs=='Region'): # and (not 'centered.fits' in filename_grey)):
subim_grey_filt=scipy.signal.medfilt(subim_grey,5)
range1=np.min(subim_grey_filt[np.where(subim_region > 0.99)])
range2=np.max(subim_grey_filt[np.where(subim_region > 0.99)])
scatter_subim_raw=np.std(subim_grey[np.where(subim_region > 0.9)])
mean_subim=np.median(subim_grey[np.where(subim_region > 0.9)])
scatter_subim=np.sqrt(np.median((subim_grey[np.where(subim_region > 0.9)] - mean_subim)**2))
print("Region: range1, range2",range1,range2)
if (os.path.exists(filename_weights)):
print( "loading ", filename_weights)
f = fits.open(filename_weights)
im_w = f[0].data
hdr_w= f[0].header
subim_w = im_w[int(j0):int(j1),int(i0):int(i1)]
medianval_w = np.median(subim_w)
print("medianval_w",medianval_w)
range1=np.min(subim_grey_filt[np.where( (subim_region > 0.99) & (subim_w > (medianval_w)))])
range2=np.max(subim_grey_filt[np.where( (subim_region > 0.99) & (subim_w > (medianval_w)))])
scatter_subim_raw=np.std(subim_grey[np.where( (subim_region > 0.9) & (subim_w > 1E-3))])
mean_subim=np.median(subim_grey[np.where( (subim_region > 0.9) & (subim_w > 1E-3))])
scatter_subim=np.sqrt(np.median((subim_grey[np.where( (subim_region > 0.9) & (subim_w > 1E-3))] - mean_subim)**2))
print("Region + weights: range1, range2",range1,range2)
print( "Region range: ",range1," ",range2, "soft scatter ",scatter_subim,"hard scatter ",scatter_subim_raw)
flog.write( "Region range: "+str(range1)+" "+str(range2)+" soft scatter "+str(scatter_subim)+" hard scatter "+str(scatter_subim_raw)+"\n")
av_range0=(range1+range2)/2.
if (SymmetricRange):
range0=max(np.fabs(range1),np.fabs(range2))
if (UseScatter):
print( "using scatter for ranges")
range0=5.*scatter_subim
range0= float('%.1f' % (range0))
range1=-range0
range2=range0
clevs = [range1,0.,range2]
clabels=['%.2f' % (clevs[0]),'0.','%.2f' % (clevs[2])]
else:
delta_range0=max(np.fabs(range1-av_range0),np.fabs(range2-av_range0))
if (UseScatter):
range1=-3.*scatter_subim+av_range0
range2=3.*scatter_subim+av_range0
clevs = [range1,range2]
clabels=['%.2f' % (ColorBarScale*clevs[0]),'%.2f' % (ColorBarScale*clevs[1])]
# norm=colors.PowerNorm(gamma=gamma)
print( "IMSHOW range1",range1,"range2",range2)
range1=clevs[0]
RegionOfInterestStats=True
if RegionOfInterest and RegionOfInterestStats:
(ny,nx) = subim_grey.shape
x=np.arange(1,nx+1)
y=np.arange(1,ny+1)
X, Y = np.meshgrid(x, y)
X0 = np.floor(nx/2)+1
Y0 = np.floor(ny/2)+1
dxxs = -cdelt *(X-X0)
dyys = cdelt *(Y-Y0)
[x_planet,y_planet] = RegionOfInterest
rrs = np.sqrt( (dxxs-x_planet)**2 + (dyys-y_planet)**2)
mask_planet = (rrs < 0.5)
print( "cdelt = ",cdelt,"\n")
#subim_grey[np.where(mask_planet)] = 0.
sigmavelo_planet = np.std(subim_grey[np.where(mask_planet)])
print( "sigmavelo_planet ",sigmavelo_planet)
rasterimage=ax.imshow(subim_grey, origin='lower', cmap=cmap, #norm=norm,
extent=[a0,a1,d0,d1], vmin=range1, vmax=range2,interpolation='nearest')
maxval=np.amax(subim_grey)
print( "a0",a0)
print( "d0",a0)
ax.text(a1*0.9,d0*0.9,label,weight='bold',fontsize=12,ha='right')
ax.text(a0*0.9,d0*0.9,atitle,weight='bold',fontsize=12)
#clevs = [float(np.amin(subim_grey)),maxval.astype('float')]
# clevs = [float(np.amin(subim_grey)),maxval]
# if (filename_grey == 'VLA_ABC_modout_nostar_noclump1_smooth.fits'):
plt.plot(0.,0.,marker='*',color='yellow',markersize=0.2,markeredgecolor='black')
plt.plot(0.,0.,marker='*',color='yellow',markersize=1.)
if RegionOfInterest:
from matplotlib.patches import Ellipse
[x_planet,y_planet] = RegionOfInterest
e = Ellipse(xy=[x_planet,y_planet], width=1.0, height=1.0, angle=0.,color='green',fill=False)
e.set_clip_box(ax.bbox)
e.set_facecolor('green')
e.set_alpha(0.5)
ax.add_artist(e)
if (DoCB):
#cmap1 = cmap
#norm = mpl.colors.Normalize(vmin=range1, vmax=range2)
#fig=plt.gcf()
#cbar_ax = fig.add_axes([0.92, 0.62, 0.01, 0.15])
#if (iplotpos > 2):
# cbar_ax = fig.add_axes([0.92, 0.22, 0.01, 0.15])
#cb = mpl.colorbar.ColorbarBase(cbar_ax, cmap=colors.Colormap(cmap1), norm=norm, orientation='vertical', ticks=clevs)
#cb.ax.set_yticklabels(clabels)
## cb.ax.set_ylabel('km/s', rotation=270)
#cb.ax.tick_params(labelsize=12)
#cmap1 = cmap
#norm = mpl.colors.Normalize(vmin=range1, vmax=range2)
#fig=plt.gcf()
#cbar_ax = fig.add_axes([0.92, 0.32, 0.01, 0.35])
#cb = mpl.colorbar.ColorbarBase(cbar_ax, cmap=colors.Colormap(cmap1), norm=norm, orientation='vertical', ticks=clevs)
#cb.ax.set_yticklabels(clabels)
#cb.ax.tick_params(labelsize=12)
from mpl_toolkits.axes_grid1 import make_axes_locatable
divider = make_axes_locatable(ax)
cax = divider.append_axes("right", size="3%", pad=0.2)
cax.yaxis.set_ticks_position('left')
cax.xaxis.set_ticks_position('top')
cax.xaxis.set_tick_params(labelsize=12, direction='in')
cax.yaxis.set_tick_params(labelsize=12, direction='in')
fmt='%.2f'
print("drawing colorbar")
print("clevs",clevs)
print("clabels",clabels)
#cb = plt.colorbar(rasterimage, cax=cax, format=fmt, ticks=clevs)
cb = plt.colorbar(rasterimage, cax=cax, ticks=clevs)
cb.ax.set_yticklabels(clabels)
cb.ax.set_ylabel(cblabel, rotation=270)
if (Region_Contours):
levels = np.array([0.1])
CS = ax.contour(subim_region, levels, origin='lower', linewidths=0.2,
linestyles = 'solid',
extent=[a0,a1,d0,d1], colors='green')
if (isinstance(DoGreyCont,str)):
filename_grey_cont=DoGreyCont
f_cont = fits.open(filename_grey_cont)
im_grey_cont = f_cont[0].data
hdr_grey_cont= f_cont[0].header
subim_grey_cont = im_grey_cont[int(j0):int(j1),int(i0):int(i1)]
print( "i0 "+str(i0),"hdr_grey['CRPIX2']", hdr_grey['CRPIX2'])
levels = [-1.65344452058093, -1.6129840879707 , -1.55158301988206, -1.51002707264227 ]
CS = ax.contour(subim_grey_cont,levels , origin='lower', linewidths=1.0,
linestyles = 'solid',
extent=[a0,a1,d0,d1], colors='red')
elif (DoGreyCont):
levels=np.array((vsyst))
CS = ax.contour(subim_grey,levels , origin='lower', linewidths=0.5,
linestyles = 'solid',
extent=[a0,a1,d0,d1], colors='green')
#ax.plot(0.,0.,marker='*',color='yellow',markersize=8)
if (filename_contours!=False):
######################################################################
# contours
print( "loading filename_contours",filename_contours)
f = fits.open(filename_contours)
im_cont = f[0].data
hdr_cont= f[0].header
subim_cont = im_cont[int(j0):int(j1),int(i0):int(i1)]
#subim_cont[np.where(subim_region < 0.5)] = 0.
if ('m2' in filename_contours):
levels = np.array([0.6,0.7,0.8]) * np.amax(subim_cont)
print( "m2 levels",levels)
if ('continuum' in filename_contours):
levels = np.array([0.2,0.4,0.6,0.8,0.9]) * np.amax(subim_cont)
levels = np.array([0.1]) * np.amax(subim_cont)
print( "continuum levels",levels)
print( "subim_cont.shape",subim_cont.shape)
#CS = axcb.contour(subim_cont,levels , origin='lower', linewidths=1.0,
# linestyles = 'solid',
# extent=[a0,a1,d0,d1], colors='white')
#CS = axcb.contour(subim_cont,levels , origin='lower', linewidths=1.0,
# linestyles = 'solid',
# extent=[a0,a1,d0,d1], colors='black', alpha = 0.5 )
#alphas=(1.+np.arange(len(levels)))/(len(levels)) * 0.6
#linewidths=1.0-((0.+np.arange(len(levels)))/(len(levels)-1)) *0.5
#print( "linewidths")
alphas=np.ones(len(levels))*0.5
linewidths=np.ones(len(levels))*0.5
levels_list = levels.tolist()
for ilevel in range(len(levels)):
alpha_val = alphas[ilevel]
alinew=linewidths[ilevel]
#print( "alpha_val",alpha_val,"lw",alinew)
alevel = levels[ilevel]
#print( "alevel ", alevel)
CS = ax.contour(subim_cont, [alevel,], origin='lower', linewidths=alinew,
linestyles = 'solid',
extent=[a0,a1,d0,d1], colors='black', alpha = alpha_val )
if DoBeamEllipse:
#Bmax/2 0.0579669470623286; Bmin/2 0.038567442164739;
#PA-51.682370436407deg (South of East);
bmaj = hdr_grey['BMAJ'] * 3600.
bmin = hdr_grey['BMIN'] * 3600.
bpa = hdr_grey['BPA']
print( "bpa ", bpa,"\n")
print( "bmaj ", bmaj,"\n")
print( "bmin ", bmin,"\n")
e = Ellipse(xy=[a1*0.8,d0*0.8], width=bmin, height=bmaj, angle=-bpa,color='blue')
e.set_clip_box(axcb.bbox)
e.set_facecolor('yellow')
e.set_alpha(0.5)
ax.add_artist(e)
return clevs, clabels
def exec_summary_allrads(workdir,filename_source,vsyst=0.,basename_errormap=False,file_m0=False,file_m2=False,file_continuum=False,Zoom=False,RegionOfInterest=False):
if (not re.search(r"\/$",workdir)):
workdir+='/'
print("added trailing back slach to workdir")
inbasename=os.path.basename(filename_source)
inbasename=re.sub('\.fits','',inbasename)
print("inbasename",inbasename)
global flog
flog=open(workdir+inbasename+"_region_scatter_diff.txt","w+")
fileout = workdir+'fig_'+inbasename+'_report_allrads_diff.pdf'
#file_continuum='/Users/simon/common/ppdisks/HD97048/data/b7_2016/continuum/mod_out.fits'
print( "inbasename:",inbasename)
matplotlib.rc('font', family='sans-serif')
#matplotlib.rcParams.update({'font.size': 16})
font = {'family' : 'Arial',
'weight' : 'normal',
'size' : 12}
matplotlib.rc('font', **font)
size_marker=10
#cmaps = ['magma', 'inferno', 'plasma', 'viridis', 'bone', 'afmhot', 'gist_heat', 'CMRmap', 'gnuplot', 'Blues_r', 'Purples_r', 'ocean', 'hot', 'seismic_r']
gamma=1.0
if file_continuum:
figsize=(20., 5)
nplotsx=3
nplotsy=1
else:
figsize=(13, 5)
nplotsx=2
nplotsy=1
plt.figure(figsize=figsize)
iplotpos=0
#inbasename='work_optim_DConeF_vsyst0/mom_1'
#inbasename='work_optim_DConeT_vsyst0/mom_1'
vrange=3.0
#inc=''
#label=r'$v_\circ - v^m_\circ$ '
#atitle='c'
#filename_contours=False
##filename_grey='/Users/simon/common/ppdisks/MWC758/VLA-2016/C-array/MWC758_C-array_clean.fits'
##filename_grey='/Users/simon/common/ppdisks/MWC758/VLA-2016/reproc/C-array/clean_MWC758_C-array.16chan.ms.fits'
#filename_grey=workdir+inbasename+'_allrads_azim_av_drot_diff.fits'
#filename_region=workdir+inbasename+'_imregions.fits'
#iplotpos += 1
#(clevs, clabels)=addimage(iplotpos,label,atitle,filename_grey,filename_contours,VisibleXaxis=True,VisibleYaxis=False,DoBeamEllipse=False,Clevs='Region',Region=filename_region,nplotsx=nplotsx,nplotsy=nplotsy,Region_Contours=False,SymmetricRange=True)
#inc=''
#label=r'cont.'
#atitle='a'
#filename_contours=False
## filename_region=False
#import Resamp
#file_im_continuum=workdir+inbasename+'_fullimcont.fits'
#Resamp.cube2im(file_continuum,file_im_continuum)
#Resamp.gridding(file_im_continuum,workdir+inbasename+'_centered.fits',fileout=workdir+inbasename+'_subimcont.fits')
#filename_grey=workdir+inbasename+'_subimcont.fits'
#iplotpos += 1
#addimage(iplotpos,label,atitle,filename_grey,filename_contours,VisibleXaxis=True,VisibleYaxis=True,DoBeamEllipse=False,Clevs=False,Region=False,nplotsx=nplotsx,nplotsy=nplotsy,cmap='ocean_r')
#cmap='magma_r'
inc=''
label=r'$v_\circ$'
atitle=''
import Resamp
import Cube2Im
filename_contours=False
if (file_continuum):
file_im_continuum=workdir+inbasename+'_fullim_continuum.fits'
Cube2Im.slice0(file_continuum,file_im_continuum)
Resamp.gridding(file_im_continuum,workdir+inbasename+'_centered.fits',fileout=workdir+inbasename+'_subim_continuum.fits')
filename_contours=workdir+inbasename+'_subim_continuum.fits'
#filename_contours=False
label=r'$v_\circ - v^m_\circ$'
filename_grey=workdir+inbasename+'_centered.fits'
filename_region=workdir+inbasename+'_imregions.fits'
#filename_weights=workdir+inbasename+'_e_wcentered.fits'
iplotpos += 1
print("iplotpos",iplotpos)
(clevs, clabels)=addimage(iplotpos,label,atitle,filename_grey,filename_contours,VisibleXaxis=True,VisibleYaxis=True,DoBeamEllipse=False,Clevs='Region',Region=filename_region,nplotsx=nplotsx,nplotsy=nplotsy,Region_Contours=False,SymmetricRange=False,cmap='RdBu_r',UseScatter=False,DoCB=True, SubtractVsyst=True,vsyst=vsyst, Zoom=Zoom,RegionOfInterest=RegionOfInterest)
filename_grey=workdir+inbasename+'_allrads_azim_av_drot_diff.fits'
filename_region=workdir+inbasename+'_imregions.fits'
filename_weights=workdir+inbasename+'_e_wcentered.fits'
iplotpos += 1
print("iplotpos",iplotpos)
(clevs, clabels)=addimage(iplotpos,label,atitle,filename_grey,filename_contours,VisibleXaxis=True,VisibleYaxis=True,DoBeamEllipse=False,Clevs='Region',Region=filename_region,nplotsx=nplotsx,nplotsy=nplotsy,Region_Contours=False,SymmetricRange=True,cmap='RdBu_r',filename_weights=filename_weights,UseScatter=True,DoCB=True,vsyst=vsyst, Zoom=Zoom,RegionOfInterest=RegionOfInterest)
if file_continuum:
label=r'continuum'
filename_grey=workdir+inbasename+'_subim_continuum.fits'
filename_contours=False
iplotpos += 1
print("iplotpos",iplotpos)
addimage(iplotpos,label,atitle,filename_grey,filename_contours,VisibleXaxis=True,VisibleYaxis=False,DoBeamEllipse=False,nplotsx=nplotsx,nplotsy=nplotsy,Region_Contours=False,SymmetricRange=False,cmap='ocean_r',DoCB=True,ColorBarScale=1E6,cblabel=r'$\mu$Jy/pix',vsyst=vsyst, Zoom=Zoom,RegionOfInterest=RegionOfInterest)
#
#
#
#inc=''
#atitle='e'
#import Resamp
#file_im_m2=workdir+inbasename+'_fullim_m2.fits'
#label=r'$v_\circ - v^m_\circ + \sigma$'
#Resamp.cube2im(file_m2,file_im_m2)
#Resamp.gridding(file_im_m2,workdir+inbasename+'_centered.fits',fileout=workdir+inbasename+'_subim_m2.fits')
#filename_grey=workdir+inbasename+'_allrads_azim_av_drot_diff.fits'
#filename_region=workdir+inbasename+'_imregions.fits'
#filename_contours=workdir+inbasename+'_subim_m2.fits'
#iplotpos += 1
#addimage(iplotpos,label,atitle,filename_grey,filename_contours,VisibleXaxis=True,VisibleYaxis=False,DoBeamEllipse=False,Clevs='Region',Region=filename_region,nplotsx=nplotsx,nplotsy=nplotsy,Region_Contours=False,SymmetricRange=True)
plt.subplots_adjust(hspace=0.15)
plt.subplots_adjust(wspace=0.)
print( fileout)
#plt.tight_layout()
print( "USED VSYST=",vsyst)
plt.savefig(fileout, bbox_inches='tight', dpi=600)
#plt.savefig(fileout, bbox_inches='tight')
#plt.savefig(fileout)
flog.close()
return
def exec_summary_faceon(workdir,filename_source,vsyst=0.,basename_errormap=False,file_m0=False,file_m2=False,file_continuum=False, Zoom=False,RegionOfInterest=False):
if (not re.search(r"\/$",workdir)):
workdir+='/'
print("added trailing back slach to workdir")
inbasename=os.path.basename(filename_source)
inbasename=re.sub('\.fits','',inbasename)
print("inbasename",inbasename)
global flog
flog=open(workdir+inbasename+"_region_scatter_diff.txt","w+")
if Zoom:
fileout = workdir+'fig_'+inbasename+'_report_allrads_faceon_zoom.pdf'
else:
fileout = workdir+'fig_'+inbasename+'_report_allrads_faceon.pdf'
#file_continuum='/Users/simon/common/ppdisks/HD97048/data/b7_2016/continuum/mod_out.fits'
print( "inbasename:",inbasename)
matplotlib.rc('font', family='sans-serif')
#matplotlib.rcParams.update({'font.size': 16})
font = {'family' : 'Arial',
'weight' : 'normal',
'size' : 12}
matplotlib.rc('font', **font)
size_marker=10
#cmaps = ['magma', 'inferno', 'plasma', 'viridis', 'bone', 'afmhot', 'gist_heat', 'CMRmap', 'gnuplot', 'Blues_r', 'Purples_r', 'ocean', 'hot', 'seismic_r']
gamma=1.0
if file_continuum:
figsize=(20., 5)
nplotsx=3
nplotsy=1
else:
figsize=(13, 5)
nplotsx=2
nplotsy=1
plt.figure(figsize=figsize)
iplotpos=0
#inbasename='work_optim_DConeF_vsyst0/mom_1'
#inbasename='work_optim_DConeT_vsyst0/mom_1'
vrange=3.0
#inc=''
#label=r'$v_\circ - v^m_\circ$ '
#atitle='c'
#filename_contours=False
##filename_grey='/Users/simon/common/ppdisks/MWC758/VLA-2016/C-array/MWC758_C-array_clean.fits'
##filename_grey='/Users/simon/common/ppdisks/MWC758/VLA-2016/reproc/C-array/clean_MWC758_C-array.16chan.ms.fits'
#filename_grey=workdir+inbasename+'_allrads_azim_av_drot_diff.fits'
#filename_region=workdir+inbasename+'_imregions.fits'
#iplotpos += 1
#(clevs, clabels)=addimage(iplotpos,label,atitle,filename_grey,filename_contours,VisibleXaxis=True,VisibleYaxis=False,DoBeamEllipse=False,Clevs='Region',Region=filename_region,nplotsx=nplotsx,nplotsy=nplotsy,Region_Contours=False,SymmetricRange=True)
#inc=''
#label=r'cont.'
#atitle='a'
#filename_contours=False
## filename_region=False
#import Resamp
#file_im_continuum=workdir+inbasename+'_fullimcont.fits'
#Resamp.cube2im(file_continuum,file_im_continuum)
#Resamp.gridding(file_im_continuum,workdir+inbasename+'_centered.fits',fileout=workdir+inbasename+'_subimcont.fits')
#filename_grey=workdir+inbasename+'_subimcont.fits'
#iplotpos += 1
#addimage(iplotpos,label,atitle,filename_grey,filename_contours,VisibleXaxis=True,VisibleYaxis=True,DoBeamEllipse=False,Clevs=False,Region=False,nplotsx=nplotsx,nplotsy=nplotsy,cmap='ocean_r')
#cmap='magma_r'
inc=''
label=r'$v_\circ$'
atitle=''
import Resamp
import Cube2Im
filename_contours=False
if (file_continuum):
file_im_continuum=workdir+inbasename+'_fullim_continuum.fits'
Cube2Im.slice0(file_continuum,file_im_continuum)
Resamp.gridding(file_im_continuum,workdir+inbasename+'_allrads_resamp_faceon.fits',fileout=workdir+inbasename+'_subim_continuum_faceon.fits')
filename_contours=workdir+inbasename+'_subim_continuum_faceon.fits'
#filename_contours=False
#work_dgaussmoments_LOSNoise_tclean_briggs0.5_pix2_Merid_fixPAinc/im_g_v0_allrads_diff_faceon.fits
#work_dgaussmoments_LOSNoise_tclean_briggs0.5_pix2_Merid_fixPAinc/im_g_v0_imregions_faceon.fits
#work_dgaussmoments_LOSNoise_tclean_briggs0.5_pix2_Merid_fixPAinc/im_g_v0_allrads_resamp_faceon.fits
filename_grey=workdir+inbasename+'_allrads_resamp_faceon.fits'
filename_region=workdir+inbasename+'_imregions_faceon.fits'
#filename_weights=workdir+inbasename+'_e_wcentered.fits'
iplotpos += 1
print("iplotpos",iplotpos)
(clevs, clabels)=addimage(iplotpos,label,atitle,filename_grey,filename_contours,VisibleXaxis=True,VisibleYaxis=True,DoBeamEllipse=False,Clevs='Region',Region=filename_region,nplotsx=nplotsx,nplotsy=nplotsy,Region_Contours=False,SymmetricRange=False,cmap='RdBu_r',UseScatter=False,DoCB=True, SubtractVsyst=True,vsyst=vsyst,Zoom=Zoom,RegionOfInterest=RegionOfInterest)
label=r'$v_\circ - v^m_\circ$'
filename_grey=workdir+inbasename+'_allrads_diff_faceon.fits'
filename_region=workdir+inbasename+'_imregions_faceon.fits'
#filename_weights=workdir+inbasename+'_e_wcentered.fits'
iplotpos += 1
print("iplotpos",iplotpos)
(clevs, clabels)=addimage(iplotpos,label,atitle,filename_grey,filename_contours,VisibleXaxis=True,VisibleYaxis=True,DoBeamEllipse=False,Clevs='Region',Region=filename_region,nplotsx=nplotsx,nplotsy=nplotsy,Region_Contours=False,SymmetricRange=True,cmap='RdBu_r',UseScatter=True,DoCB=True,Zoom=Zoom,RegionOfInterest=RegionOfInterest) # ,vsyst=vsyst)
if file_continuum:
label=r'continuum'
filename_grey=workdir+inbasename+'_subim_continuum_faceon.fits'
filename_contours=False
iplotpos += 1
print("iplotpos",iplotpos)
addimage(iplotpos,label,atitle,filename_grey,filename_contours,VisibleXaxis=True,VisibleYaxis=False,DoBeamEllipse=False,nplotsx=nplotsx,nplotsy=nplotsy,Region_Contours=False,SymmetricRange=False,cmap='ocean_r',DoCB=True,ColorBarScale=1E6,cblabel=r'$\mu$Jy/pix',Zoom=Zoom,RegionOfInterest=RegionOfInterest) #,vsyst=vsyst)
#
#
#
#inc=''
#atitle='e'
#import Resamp
#file_im_m2=workdir+inbasename+'_fullim_m2.fits'
#label=r'$v_\circ - v^m_\circ + \sigma$'
#Resamp.cube2im(file_m2,file_im_m2)
#Resamp.gridding(file_im_m2,workdir+inbasename+'_centered.fits',fileout=workdir+inbasename+'_subim_m2.fits')
#filename_grey=workdir+inbasename+'_allrads_azim_av_drot_diff.fits'
#filename_region=workdir+inbasename+'_imregions.fits'
#filename_contours=workdir+inbasename+'_subim_m2.fits'
#iplotpos += 1
#addimage(iplotpos,label,atitle,filename_grey,filename_contours,VisibleXaxis=True,VisibleYaxis=False,DoBeamEllipse=False,Clevs='Region',Region=filename_region,nplotsx=nplotsx,nplotsy=nplotsy,Region_Contours=False,SymmetricRange=True)
plt.subplots_adjust(hspace=0.15)
plt.subplots_adjust(wspace=0.)
print( fileout)
#plt.tight_layout()
print( "USED VSYST=",vsyst)
plt.savefig(fileout, bbox_inches='tight', dpi=600)
#plt.savefig(fileout, bbox_inches='tight')
#plt.savefig(fileout)
flog.close()
return