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SummaryDMoments.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)
import Resamp
import Cube2Im
#import Vtools
def colorbar(Mappable, Orientation='horizontal',cbfmt="%.1e"):
Ax = Mappable.axes
fig = Ax.figure
divider = make_axes_locatable(Ax)
Cax = divider.append_axes("top", size="5%", pad=0.55)
return fig.colorbar(
mappable=Mappable,
cax=Cax,
use_gridspec=True,
orientation=Orientation,
format=cbfmt
)
def addimage(iplotpos,label,atitle,filename_grey,filename_contours,filename_errormap=False, filename_fiterrormap=False,VisibleXaxis=False,VisibleYaxis=True,DoBeamEllipse=False,DoGreyCont=False,vsyst=0.,nplotsx=2,nplotsy=2,SymmetricRange=False,MedianvalRange=False,DoCB=True,cmap='RdBu_r',MedRms=True,Zoom=False,scaleim=1.,cbfmt="%.1e",cbunits='',Side=1.5):
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)
fin = fits.open(filename_grey)
fin = Cube2Im.slice0(fin)
im_grey = fin.data
hdr_grey= fin.header
cdelt=3600.*hdr_grey['CDELT2']
side0=hdr_grey['NAXIS2']*cdelt
if Zoom:
side=Side
if (side > side0):
print("side ",side,"vs",side0)
sys.exit("side too large")
nx=np.rint(side/cdelt)
ny=np.rint(side/cdelt)
Resample=True
if Resample:
hdrzoom=hdr_grey.copy()
hdrzoom['NAXIS1']=nx
hdrzoom['NAXIS2']=ny
hdrzoom['CRPIX1']=((nx-1.)/2.)+1.
hdrzoom['CRPIX2']=((ny-1.)/2.)+1.
hduzoom=Resamp.gridding(fin,hdrzoom,ReturnHDU=True)
subim_grey=hduzoom.data
hdr_grey=hduzoom.header
else:
i_star = hdr_grey['CRPIX1']-1.
j_star = hdr_grey['CRPIX2']-1.
i0=int(i_star-(nx-1.)/2.+0.5)
j0=int(j_star-(ny-1.)/2.+0.5)
i1=int(i_star+(nx-1.)/2.+0.5)
j1=int(j_star+(ny-1.)/2.+0.5)
subim_grey = im_grey[j0:j1,i0:i1]
#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)
else:
side=side0
i0=0
i1=hdr_grey['NAXIS1']-1
j0=0
j1=hdr_grey['NAXIS2']-1
subim_grey=im_grey.copy()
a0 = side/2.
a1 = -side/2.
d0 = -side/2.
d1 = side/2.
subim_grey *= scaleim
# if 'v' in filename_grey:
# subim_grey = subim_grey - vsyst
print( "loading filename_grey",filename_fiterrormap)
f = fits.open(filename_fiterrormap)
f = Cube2Im.slice0(f)
im_fiterrormap = f.data
hdr_fiterrormap= f.header
if Zoom:
Resample=True
if Resample:
hduzoom_fiterrmap=Resamp.gridding(f,hdrzoom,ReturnHDU=True)
subim_fiterrormap=hduzoom_fiterrmap.data
else:
subim_fiterrormap=im_fiterrormap[j0:j1,i0:i1]
else:
subim_fiterrormap=im_fiterrormap.copy()
# medsubim_fiterrormap=medfilt2d(subim_fiterrormap,kernel_size=11)
#Vtools.View(subim_fiterrormap)
#Vtools.View(medsubim_fiterrormap)
typicalerror=np.median(subim_fiterrormap)
#mask=np.where((subim_fiterrormap-medsubim_fiterrormap) > 3.* medsubim_fiterrormap)
mask=np.where(subim_fiterrormap<20.*typicalerror)
immask=np.zeros(subim_fiterrormap.shape)
immask[mask]=1
print("number of pixels masked:",np.sum(immask))
#print("viewing fiterrormap immask")
#Vtools.View(immask)
#plt.figure(2)
#plt.imshow(immask)
#plt.show()
#plt.figure(1)
if filename_errormap:
f = fits.open(filename_errormap)
im_errormap = f[0].data
hdr_errormap= f[0].header
if Zoom:
subim_errormap=im_errormap[j0:j1,i0:i1]
else:
subim_errormap=im_errormap.copy()
medsubim_errormap=medfilt2d(subim_errormap,kernel_size=5)
mask=np.where(mask and ( (subim_errormap-medsubim_errormap) > 3.* medsubim_errormap))
immask=np.zeros(subim_fiterrormap.shape)
immask[mask]=1.
print("viewing errormap immask")
#Vtools.View(immask)
if SymmetricRange:
range2=vsyst+SymmetricRange
range1=vsyst-SymmetricRange
# subim_grey[np.where(subim_grey < range1)]=vsyst
# subim_grey[np.where(subim_grey > range2)]=vsyst
clevs = [range1,0.,range2]
clabels=['%.0f' % (clevs[0]),'','%.0f' % (clevs[2])]
elif MedianvalRange:
typicalvalue=np.median(subim_grey[mask])
rms=np.std(subim_grey[mask])
medrms=np.sqrt(np.median( (subim_grey[mask] - typicalvalue)**2))
print("typical value ",typicalvalue," rms ",rms,"medrms",medrms)
range1=np.min(subim_grey[mask])
if MedRms:
imagerms=medrms
else:
imagerms=rms
range2=typicalvalue+10.*imagerms
clevs = [range1,range2]
clabels=['%.1f' % (clevs[0]),'%.1f' % (clevs[1])]
else:
range2=np.max(subim_grey[mask])
range1=np.min(subim_grey[mask])
clevs = [range1,range2]
clabels=['%.1f' % (clevs[0]),'%.1f' % (clevs[1])]
if ('sigma' in filename_grey):
cmap='magma_r'
print("max:",np.max(subim_grey))
print("min:",np.min(subim_grey))
print("range1",range1,"range2",range2)
if (np.isnan(subim_grey).any()):
print("NaNs in subim_grey")
subim_grey=np.nan_to_num(subim_grey)
theimage=ax.imshow(subim_grey, origin='lower', cmap=cmap, #norm=norm,
extent=[a0,a1,d0,d1], vmin=range1, vmax=range2, interpolation='nearest') #'nearest' 'bicubic'
#plt.plot(0.,0.,marker='*',color='yellow',markersize=0.2,markeredgecolor='black')
plt.plot(0.,0.,marker='*',color='yellow',markersize=0.4)
ax.text(a1*0.9,d0*0.9,atitle,weight='bold',fontsize=12,ha='right',bbox=dict(facecolor='white', alpha=0.8))
ax.text(a0*0.9,d0*0.9,label,weight='bold',fontsize=12,bbox=dict(facecolor='white', alpha=0.8))
axcb=plt.gca()
if (DoCB):
cb=colorbar(theimage,cbfmt=cbfmt)
cb.ax.tick_params(labelsize='small')
print("CB label",cbunits)
cb.set_label(cbunits)
#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])
#
# print( "color bar clevs",clevs)
# print( "color bar clabels",clabels)
#
#
# 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)
# 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 = axcb.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 = axcb.contour(subim_grey,levels , origin='lower', linewidths=0.5,
# linestyles = 'solid',
# extent=[a0,a1,d0,d1], colors='green')
#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)]
#
# if MaskCont:
# subim_cont[np.where(subim_region < 0.5)] = 0.
#
#
#
# ######################################################################
# #Blue
# print( "full dvel range: ", np.min(subim_cont), " --> ",np.max(subim_cont))
# levels=np.array([0.6,])*np.fabs(np.min(subim_cont))
# #levels=np.array([0.7421825906386711,])
# alphas=np.ones(len(levels)) # 0.5+0.5*np.arange(len(levels))/(len(levels))
# linewidths=np.ones(len(levels)) # 1.0-((0.+np.arange(len(levels))-1.0)/(len(levels))) *0.5
#
# levels_list = levels.tolist()
# for ilevel in range(len(levels)):
# alpha_val = alphas[ilevel]
# alinew=linewidths[ilevel]
# alevel = -levels[ilevel]
# print( "blue level",alevel,"alpha_val",alpha_val,"lw",alinew)
# CS = axcb.contour(subim_cont, alevel, origin='lower', linewidths=alinew,
# linestyles = 'solid',
# extent=[a0,a1,d0,d1], colors='blue', alpha = alpha_val )
#
# ######################################################################
# #Red
# #levels=np.array([0.75,0.95])
#
#
# levels=np.array([0.6,])*np.fabs(np.max(subim_cont))
# #levels=np.array([0.6441364043826032,])
# levels_list = levels.tolist()
# for ilevel in range(len(levels)):
# alpha_val = alphas[ilevel]
# alinew=linewidths[ilevel]
# alevel = levels[ilevel]
# print( "red level",alevel,"alpha_val",alpha_val,"lw",alinew)
# CS = axcb.contour(subim_cont, alevel, origin='lower', linewidths=alinew,
# linestyles = 'solid',
# extent=[a0,a1,d0,d1], colors='red', alpha = alpha_val )
#
#
#
if DoBeamEllipse:
from matplotlib.patches import Ellipse
#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']
e = Ellipse(xy=[a1*0.8,d1*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)
axcb.add_artist(e)
return clevs, clabels
def exec_summary(workdir,fileout,vsyst=0.,vrange=10.,ngauss=2, Zoom=False, Side=1.5, WCont=True):
# global nplotsx
# global nplotsy
# global basename_log
print( "workdir:",workdir)
#matplotlib.rc('text', usetex=True)
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 (ngauss == 2):
figsize=(15., 15.)
nplotsx=3
nplotsy=3
elif (ngauss == 1):
figsize=(15., 10.)
nplotsx=3
nplotsy=2
# (fig0, axes) = plt.subplots(nrows=nplotsy,ncols=nplotsx,figsize=figsize)
plt.figure(figsize=figsize)
#axes=axes.flatten()
#print("axes",help(axes))
#print((axes.shape))
iplotpos=0
filename_fiterrormap=workdir+'fiterrormap.fits'
cmap='ocean_r'
atitle=r'$I_\mathrm{gauss}$'
label='a'
filename_contours=False
filename_grey=workdir+'im_gmom_0.fits'
filename_errormap=False
iplotpos += 1
#addimage(iplotpos,label,atitle,filename_grey,filename_contours,VisibleXaxis=False,VisibleYaxis=True,DoBeamEllipse=False,DoGreyCont=True,Clevs=[vsyst-vrange,vsyst,vsyst+vrange])
(clevs,clabels)=addimage(iplotpos,label,atitle,filename_grey,filename_contours=filename_contours,filename_errormap=filename_errormap, filename_fiterrormap=filename_fiterrormap,VisibleXaxis=False,VisibleYaxis=True,DoBeamEllipse=True,DoGreyCont=False,vsyst=vsyst,nplotsx=nplotsx,nplotsy=nplotsy,SymmetricRange=False,DoCB=True, cmap=cmap,scaleim=1E3,cbfmt='%.1f',cbunits=r'$\rm{mJy}\,\rm{beam}^{-1} \rm{km}\,\rm{s}^{-1}$',Zoom=Zoom, Side=Side)
atitle=r'$I_\mathrm{sum}$'
label='b'
filename_contours=False
filename_grey=workdir+'Smom_0.fits'
filename_errormap=False
iplotpos += 1
#addimage(iplotpos,label,atitle,filename_grey,filename_contours,VisibleXaxis=False,VisibleYaxis=False,DoBeamEllipse=False,DoGreyCont=True,Clevs=[vsyst-vrange,vsyst,vsyst+vrange])
(clevs,clabels)=addimage(iplotpos,label,atitle,filename_grey,filename_contours=filename_contours,filename_errormap=filename_errormap, filename_fiterrormap=filename_fiterrormap,VisibleXaxis=False,VisibleYaxis=False,DoBeamEllipse=True,DoGreyCont=False,vsyst=vsyst,nplotsx=nplotsx,nplotsy=nplotsy,SymmetricRange=False,DoCB=True, cmap=cmap,scaleim=1E3,cbfmt='%.1f',cbunits=r'$\rm{mJy}\,\rm{beam}^{-1} / \rm{km}\,\rm{s}^{-1}$',Zoom=Zoom, Side=Side)
if (ngauss > 1):
atitle=r'$v^\mathrm{peak}_\mathrm{gauss}$'
label='c'
filename_contours=False
filename_grey=workdir+'im_gmom_8.fits'
filename_errormap=False
iplotpos += 1
#addimage(iplotpos,label,atitle,filename_grey,filename_contours,VisibleXaxis=False,VisibleYaxis=False,DoBeamEllipse=False,DoGreyCont=True,Clevs=[vsyst-vrange,vsyst,vsyst+vrange])
(clevs,clabels)=addimage(iplotpos,label,atitle,filename_grey,filename_contours=filename_contours,filename_errormap=filename_errormap, filename_fiterrormap=filename_fiterrormap,VisibleXaxis=False,VisibleYaxis=False,DoBeamEllipse=False,DoGreyCont=False,vsyst=vsyst,nplotsx=nplotsx,nplotsy=nplotsy,SymmetricRange=5.,DoCB=True, cmap='RdBu_r',Zoom=Zoom, Side=Side)
atitle=r'$v^\circ$'
label='c'
filename_contours=False
filename_grey=workdir+'im_g_v0.fits'
filename_errormap=False
iplotpos += 1
#addimage(iplotpos,label,atitle,filename_grey,filename_contours,VisibleXaxis=False,VisibleYaxis=False,DoBeamEllipse=False,DoGreyCont=True,Clevs=[vsyst-vrange,vsyst,vsyst+vrange])
(clevs,clabels)=addimage(iplotpos,label,atitle,filename_grey,filename_contours=filename_contours,filename_errormap=filename_errormap, filename_fiterrormap=filename_fiterrormap,VisibleXaxis=False,VisibleYaxis=False,DoBeamEllipse=True,DoGreyCont=False,vsyst=vsyst,nplotsx=nplotsx,nplotsy=nplotsy,SymmetricRange=2.,DoCB=True, cmap='RdBu_r',scaleim=1.,cbfmt='%.1f',cbunits=r'$\rm{km}\,\rm{s}^{-1}$',Zoom=Zoom, Side=Side)
atitle=r'$I^\mathrm{A}$'
label='d'
filename_contours=False
filename_grey=workdir+'im_g_a.fits'
filename_errormap=False
iplotpos += 1
(clevs,clabels)=addimage(iplotpos,label,atitle,filename_grey,filename_contours=filename_contours,filename_errormap=filename_errormap, filename_fiterrormap=filename_fiterrormap,VisibleXaxis=True,VisibleYaxis=True,DoBeamEllipse=True,DoGreyCont=False,vsyst=vsyst,nplotsx=nplotsx,nplotsy=nplotsy,SymmetricRange=False,MedianvalRange=True,DoCB=True, cmap=cmap,scaleim=1E3,cbfmt='%.1f',cbunits=r'$\rm{mJy}\,\rm{beam}^{-1}$',Zoom=Zoom, Side=Side)
atitle=r'$\sigma$'
label='e'
filename_contours=False
filename_grey=workdir+'im_g_sigma.fits'
filename_errormap=False
iplotpos += 1
#addimage(iplotpos,label,atitle,filename_grey,filename_contours,VisibleXaxis=False,VisibleYaxis=False,DoBeamEllipse=False,DoGreyCont=True,Clevs=[vsyst-vrange,vsyst,vsyst+vrange])
(clevs,clabels)=addimage(iplotpos,label,atitle,filename_grey,filename_contours=filename_contours,filename_errormap=filename_errormap, filename_fiterrormap=filename_fiterrormap,VisibleXaxis=True,VisibleYaxis=False,DoBeamEllipse=True,DoGreyCont=False,vsyst=vsyst,nplotsx=nplotsx,nplotsy=nplotsy,SymmetricRange=False,MedianvalRange=True,MedRms=True,DoCB=True, cmap='RdBu_r',scaleim=1.,cbfmt='%.2f',cbunits=r'$\rm{km}\,\rm{s}^{-1}$',Zoom=Zoom, Side=Side)
atitle=r'$I^\mathrm{peak}$'
label='f'
filename_contours=False
filename_grey=workdir+'im_Ipeak.fits'
filename_errormap=False
iplotpos += 1
(clevs,clabels)=addimage(iplotpos,label,atitle,filename_grey,filename_contours=filename_contours,filename_errormap=filename_errormap, filename_fiterrormap=filename_fiterrormap,VisibleXaxis=True,VisibleYaxis=False,DoBeamEllipse=True,DoGreyCont=False,vsyst=vsyst,nplotsx=nplotsx,nplotsy=nplotsy,SymmetricRange=False,MedianvalRange=False,DoCB=True, cmap=cmap,scaleim=1E3,cbfmt='%.1f',cbunits=r'$\rm{mJy}\,\rm{beam}^{-1}$',Zoom=Zoom, Side=Side)
if (ngauss > 1):
atitle=r'$I^\mathrm{A}_2$'
label='g'
filename_contours=False
filename_grey=workdir+'im_g2_a.fits'
filename_errormap=False
iplotpos += 1
(clevs,clabels)=addimage(iplotpos,label,atitle,filename_grey,filename_contours=filename_contours,filename_errormap=filename_errormap, filename_fiterrormap=filename_fiterrormap,VisibleXaxis=False,VisibleYaxis=False,DoBeamEllipse=False,DoGreyCont=False,vsyst=vsyst,nplotsx=nplotsx,nplotsy=nplotsy,SymmetricRange=False,MedianvalRange=False,DoCB=True, cmap=cmap,Zoom=Zoom, Side=Side)
atitle=r'$v^\circ_2$'
label='m'
filename_contours=False
filename_grey=workdir+'im_g2_v0.fits'
filename_errormap=False
iplotpos += 1
#addimage(iplotpos,label,atitle,filename_grey,filename_contours,VisibleXaxis=False,VisibleYaxis=False,DoBeamEllipse=False,DoGreyCont=True,Clevs=[vsyst-vrange,vsyst,vsyst+vrange])
(clevs,clabels)=addimage(iplotpos,label,atitle,filename_grey,filename_contours=filename_contours,filename_errormap=filename_errormap, filename_fiterrormap=filename_fiterrormap,VisibleXaxis=False,VisibleYaxis=False,DoBeamEllipse=False,DoGreyCont=False,vsyst=vsyst,nplotsx=nplotsx,nplotsy=nplotsy,SymmetricRange=5.,DoCB=True, cmap='RdBu_r',Zoom=Zoom, Side=Side)
atitle=r'$\sigma_2$'
label='o'
filename_contours=False
filename_grey=workdir+'im_g2_sigma.fits'
filename_errormap=False
iplotpos += 1
#addimage(iplotpos,label,atitle,filename_grey,filename_contours,VisibleXaxis=False,VisibleYaxis=False,DoBeamEllipse=False,DoGreyCont=True,Clevs=[vsyst-vrange,vsyst,vsyst+vrange])
(clevs,clabels)=addimage(iplotpos,label,atitle,filename_grey,filename_contours=filename_contours,filename_errormap=filename_errormap, filename_fiterrormap=filename_fiterrormap,VisibleXaxis=False,VisibleYaxis=False,DoBeamEllipse=False,DoGreyCont=False,vsyst=vsyst,nplotsx=nplotsx,nplotsy=nplotsy,SymmetricRange=False,MedianvalRange=True,MedRms=True,DoCB=True, cmap='RdBu_r',Zoom=Zoom, Side=Side)
plt.subplots_adjust(hspace=0.1)
plt.subplots_adjust(wspace=0.)
print( fileout)
#plt.tight_layout()
print( "USED VSYST=",vsyst)
plt.savefig(fileout, bbox_inches='tight', dpi=500)
#plt.savefig(fileout)
return