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Vtools.py~
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Vtools.py~
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import sys
import numpy as np
import astropy
from astropy.io import fits
import matplotlib.pyplot as plt
import matplotlib.colors as colors
from matplotlib.widgets import RectangleSelector
from mpl_toolkits.axes_grid1 import make_axes_locatable
from pprint import pprint as pp
include_path='/Users/simon/common/python/include/'
sys.path.append(include_path)
import Resamp
icmap=0
cmaps=['Accent','Accent_r','Blues','Blues_r','BrBG','BrBG_r','BuGn','BuGn_r','BuPu','BuPu_r','CMRmap','CMRmap_r','Dark2','Dark2_r','GnBu','GnBu_r','Greens','Greens_r','Greys','Greys_r','OrRd','OrRd_r','Oranges','Oranges_r','PRGn','PRGn_r','Paired','Paired_r','Pastel1','Pastel1_r','Pastel2','Pastel2_r','PiYG','PiYG_r','PuBu','PuBuGn','PuBuGn_r','PuBu_r','PuOr','PuOr_r','PuRd','PuRd_r','Purples','Purples_r','RdBu','RdBu_r','RdGy','RdGy_r','RdPu','RdPu_r','RdYlBu','RdYlBu_r','RdYlGn','RdYlGn_r','Reds','Reds_r','Set1','Set1_r','Set2','Set2_r','Set3','Set3_r','Spectral','Spectral_r','Wistia','Wistia_r','YlGn','YlGnBu','YlGnBu_r','YlGn_r','YlOrBr','YlOrBr_r','YlOrRd','YlOrRd_r','afmhot','afmhot_r','autumn','autumn_r','binary','binary_r','bone','bone_r','brg','brg_r','bwr','bwr_r','cividis','cividis_r','cool','cool_r','coolwarm','coolwarm_r','copper','copper_r','cubehelix','cubehelix_r','flag','flag_r','gist_earth','gist_earth_r','gist_gray','gist_gray_r','gist_heat','gist_heat_r','gist_ncar','gist_ncar_r','gist_rainbow','gist_rainbow_r','gist_stern','gist_stern_r','gist_yarg','gist_yarg_r','gnuplot','gnuplot2','gnuplot2_r','gnuplot_r','gray','gray_r','hot','hot_r','hsv','hsv_r','inferno','inferno_r','jet','jet_r','magma','magma_r','nipy_spectral','nipy_spectral_r','ocean','ocean_r','pink','pink_r','plasma','plasma_r','prism','prism_r','rainbow','rainbow_r','seismic','seismic_r','spring','spring_r','summer','summer_r','tab10','tab10_r','tab20','tab20_r','tab20b','tab20b_r','tab20c','tab20c_r','terrain','terrain_r','twilight','twilight_r','twilight_shifted','twilight_shifted_r','viridis','viridis_r','winter','winter_r']
## WIDGET INBUILT KEY STROKES
# g: grid
# https://matplotlib.org/users/event_handling.html
# https://matplotlib.org/3.1.1/gallery/widgets/rectangle_selector.html
def pix2wcs_0CRVAL(j,i):
hdr=hdu.header
if ('pixel' in hdr['CTYPE1']):
pixscale=1.
else:
pixscale=3600.*hdr['CDELT2']
a=-pixscale*(i-(hdr['CRPIX1']-1.))
d=pixscale*(j-(hdr['CRPIX2']-1.))
return (d,a)
def wcs2pix_0CRVAL(d,a):
hdr=hdu.header
if ('pixel' in hdr['CTYPE1']):
pixscale=1.
else:
pixscale=3600.*hdr['CDELT2']
i = -a/pixscale+(hdr['CRPIX1']-1.)
j=d/pixscale+(hdr['CRPIX2']-1.)
return (j,i)
def line_select_callback(eclick, erelease):
'eclick and erelease are the press and release events'
x1, y1 = eclick.xdata, eclick.ydata
x2, y2 = erelease.xdata, erelease.ydata
diagdistance=np.sqrt( (y2-y1)**2 + (x2-x1)**2)
print("(%3.2f, %3.2f) --> (%3.2f, %3.2f): Diag %3.2f" % (x1, y1, x2, y2,diagdistance))
#print(" The buttons you used were: %s %s" % (eclick.button, erelease.button))
im=hdu.data
(j1,i1)=wcs2pix_0CRVAL(y1,x1)
(j2,i2)=wcs2pix_0CRVAL(y2,x2)
iis=[i1,i2]
(i1m,i2m) =map(lambda i: int(i), sorted(iis))
jjs=[j1,j2]
(j1m,j2m) =map(lambda j: int(j), sorted(jjs))
#print("i1m ",i1m," j1m ",j1m,"i2m ",i2m," j2m ",j2m)
subim=im[j1m:j2m,i1m:i2m]
#np.max(subim)/np.std(subim))
print("Flux: %.3e Rms: %.3e Min: %.3e Max: %.3e Median: %.3e" % (np.sum(subim),np.std(subim),np.min(subim),np.max(subim), np.median(subim)))
range2=np.max(subim[np.where(np.isfinite(subim))])
range1=np.min(subim[np.where(np.isfinite(subim))])
theimage.set_clim(vmin=range1, vmax=range2)
#zetransform=theimage.get_transform()
#invzetransform=zetransform.inverted()
##print("zetransform ",zetransform)
##help(zetransform)
#(i1,j1)=zetransform.transform_affine((x1,y1))
#(i2,j2)=zetransform.transform_affine((x2,y2))
#(j1,i1)=zetransform.transform_affine((y1,x1))
#(j2,i2)=zetransform.transform_affine((y2,x2))
#(invx1,invy1)=invzetransform.transform((i1,j1))
#(invx2,invy2)=invzetransform.transform((i2,j2))
if (eclick.dblclick):
# on double click clear and deactivate RectangleSelector
# had to place this here as a mouse event because it bugs in toggle_selector(event), where it gives a logx axis and an error.
toggle_selector.RS.set_visible(False)
toggle_selector.RS.set_active(False)
fig1.canvas.draw()
def toggle_selector(event):
#print(' Key pressed.',event.key)
# return
if event.key in ['C', 'c']:
print("COLOR MAPS: Accent, Accent_r, Blues, Blues_r, BrBG, BrBG_r, BuGn, BuGn_r, BuPu, BuPu_r, CMRmap, CMRmap_r, Dark2, Dark2_r, GnBu, GnBu_r, Greens, Greens_r, Greys, Greys_r, OrRd, OrRd_r, Oranges, Oranges_r, PRGn, PRGn_r, Paired, Paired_r, Pastel1, Pastel1_r, Pastel2, Pastel2_r, PiYG, PiYG_r, PuBu, PuBuGn, PuBuGn_r, PuBu_r, PuOr, PuOr_r, PuRd, PuRd_r, Purples, Purples_r, RdBu, RdBu_r, RdGy, RdGy_r, RdPu, RdPu_r, RdYlBu, RdYlBu_r, RdYlGn, RdYlGn_r, Reds, Reds_r, Set1, Set1_r, Set2, Set2_r, Set3, Set3_r, Spectral, Spectral_r, Wistia, Wistia_r, YlGn, YlGnBu, YlGnBu_r, YlGn_r, YlOrBr, YlOrBr_r, YlOrRd, YlOrRd_r, afmhot, afmhot_r, autumn, autumn_r, binary, binary_r, bone, bone_r, brg, brg_r, bwr, bwr_r, cividis, cividis_r, cool, cool_r, coolwarm, coolwarm_r, copper, copper_r, cubehelix, cubehelix_r, flag, flag_r, gist_earth, gist_earth_r, gist_gray, gist_gray_r, gist_heat, gist_heat_r, gist_ncar, gist_ncar_r, gist_rainbow, gist_rainbow_r, gist_stern, gist_stern_r, gist_yarg, gist_yarg_r, gnuplot, gnuplot2, gnuplot2_r, gnuplot_r, gray, gray_r, hot, hot_r, hsv, hsv_r, inferno, inferno_r, jet, jet_r, magma, magma_r, nipy_spectral, nipy_spectral_r, ocean, ocean_r, pink, pink_r, plasma, plasma_r, prism, prism_r, rainbow, rainbow_r, seismic, seismic_r, spring, spring_r, summer, summer_r, tab10, tab10_r, tab20, tab20_r, tab20b, tab20b_r, tab20c, tab20c_r, terrain, terrain_r, twilight, twilight_r, twilight_shifted, twilight_shifted_r, viridis, viridis_r, winter, winter_r")
cmap=input('Enter new color map> ')
theimage.set_cmap(cmap)
print('Switch to ',cmap)
fig1.canvas.draw()
return
if event.key in ['L', 'l']:
print("looping over all available color maps")
global cmaps
global icmap
print(cmaps)
print("icmap = ",icmap)
acmap=cmaps[icmap]
icmap += 1
print("trying ",acmap)
theimage.set_cmap(acmap)
print('Switch to ',acmap)
fig1.canvas.draw()
return
if event.key in ['A', 'a'] and not toggle_selector.RS.active:
print('RectangleSelector activated.')
toggle_selector.RS.set_active(True)
toggle_selector.RS.set_visible(True)
return
if event.key in ['H', 'h']:
print('key a: activate RectangleSelector (dbleclick deactivates)')
print('key c: change colormap')
return
def colorbar(Mappable, Orientation='vertical'):
Ax = Mappable.axes
fig = Ax.figure
divider = make_axes_locatable(Ax)
Cax = divider.append_axes("right", size="5%", pad=0.08)
return fig.colorbar(
mappable=Mappable,
cax=Cax,
use_gridspec=True,
orientation=Orientation,
format="%.1e"
)
def View(indata,cmap='RdBu_r',AllContours=False):
#help(indata)
#indatatype=type(indata)
global hdu
AddContours=False
if isinstance(indata,list): # astropy.io.fits.hdu.hdulist.HDUList):
#print("This is an HDU List")
hdu=indata[0]
if isinstance(hdu,astropy.io.fits.hdu.hdulist.HDUList):
hdu=hdu[0]
elif isinstance(indata,np.ndarray):
hdu = fits.PrimaryHDU()
hdu.data = indata
hdr=hdu.header
hdr['CDELT1']=1.
hdr['CDELT2']=1.
(nx,ny)=indata.shape
hdr['CRPIX1']=int(nx/2.)
hdr['CRPIX2']=int(ny/2.)
hdr['CTYPE1']='pixel'
hdr['CTYPE2']='pixel'
if (len(indata) > 1):
hducontours=indata[1]
AddContours=True
if isinstance(hducontours,astropy.io.fits.hdu.hdulist.HDUList):
hducontours=hducontours[0]
elif isinstance(hducontours,np.ndarray):
imcont=indata[1]
hducontours = fits.PrimaryHDU()
hducontours.data = imcont
hdr=hducontours.header
hdrcontours['CDELT1']=1.
hdrcontours['CDELT2']=1.
(nx,ny)=imcont.shape
hdrcontours['CRPIX1']=int(nx/2.)
hdrcontours['CRPIX2']=int(ny/2.)
hdrcontours['CTYPE1']='pixel'
hdrcontours['CTYPE2']='pixel'
else: # isinstance(indata,astropy.io.fits.hdu.hdulist):
#print("This is an HDU")
hdu=indata
if isinstance(hdu,astropy.io.fits.hdu.hdulist.HDUList):
hdu=hdu[0]
elif isinstance(indata,np.ndarray):
hdu = fits.PrimaryHDU()
hdu.data = indata
hdr=hdu.header
hdr['CDELT1']=1.
hdr['CDELT2']=1.
(nx,ny)=indata.shape
hdr['CRPIX1']=int(nx/2.)
hdr['CRPIX2']=int(ny/2.)
hdr['CTYPE1']='pixel'
hdr['CTYPE2']='pixel'
im=hdu.data
hdr=hdu.header
if (not 'CTYPE1' in hdr.keys()):
hdr['CTYPE1']='pixel'
hdr['CTYPE2']='pixel'
(nx,ny)=im.shape
hdr['CRPIX1']=int(nx/2.)
hdr['CRPIX2']=int(ny/2.)
# mpl.use('TkAgg')
global fig1
global ax1
fig1,ax1=plt.subplots()
(d0,a0)=pix2wcs_0CRVAL(0.,0.)
(d1,a1)=pix2wcs_0CRVAL(hdr['NAXIS2']-1,hdr['NAXIS1']-1)
#(j0,i0)=wcs2pix_0CRVAL(d0,a0)
#(j1,i1)=wcs2pix_0CRVAL(d1,a1)
#print("a0 d0 a1 d1", a0,d0,a1,d1)
#print("i0 j0 i1 j1", i0,j0,i1,j1)
range2=np.max(im[np.where(np.isfinite(im))])
range1=np.min(im[np.where(np.isfinite(im))])
MedianvalRange=False
if MedianvalRange:
typicalvalue=np.median(im)
medrms=np.sqrt(np.median( (im - typicalvalue)**2))
print("typical value ",typicalvalue," rms ",rms,"medrms",medrms)
range1=typicalvalue-3.*medrms
range2=typicalvalue+3.*medrms
global theimage
theimage=ax1.imshow(im, origin='lower', cmap=cmap, #norm=norm,
extent=[a0,a1,d0,d1], vmin=range1, vmax=range2, interpolation='nearest') #'nearest' 'bicubic'
colorbar(theimage)
if AllContours:
levels=np.array([0.2,0.4,0.6,0.8])*np.max(im)
#ax1.contour(im, origin='lower', extent=[a0,a1,d0,d1], levels=levels,colors='green',linewidths=2.0,alpha=0.5)
ax1.contour(im, origin='lower', extent=[a0,a1,d0,d1], levels=levels, cmap=cmap)
if AddContours:
hducontours_matched=Resamp.gridding(hducontours,hdr,ReturnHDU=True)
imcontours=hducontours_matched.data
levels=np.array([0.2,0.4,0.6,0.8])*np.max(imcontours)
if AllContours:
ax1.contour(imcontours,origin='lower', colors='green', extent=[a0,a1,d0,d1], levels=levels,linewidths=2.0,alpha=0.5)
else:
ax1.contour(imcontours,origin='lower', cmap=cmap, extent=[a0,a1,d0,d1], levels=levels)
#help(theimage)
global ClearAll
ClearAll=False
toggle_selector.RS = RectangleSelector(ax1, line_select_callback,
drawtype='box', useblit=True,
button=[1, 3], # don't use middle button
minspanx=5, minspany=5,
spancoords='pixels', interactive=True)
#help(toggle_selector.RS)
#print("Pretty printing togle_selector")
#pp(toggle_selector.RS)
toggle_selector.RS.set_active(False)
plt.connect('key_press_event', toggle_selector)
plt.show()
def Spec(indata):
if not isinstance(indata,list): #
indata=[indata,]
global fig1
global ax1
fig1,ax1=plt.subplots()
for ispec,aspec in enumerate(indata):
theplot=ax1.plot(aspec[:,0],aspec[:,1],label=str(ispec))
plt.legend()
plt.show()