def make_rgb(
outname,
redline="H2CO303_202",
greenline="H2CO321_220",
blueline="H2CO322_221",
fntemplate=paths.dpath("merge/moments/W51_b6_7M_12M.{0}.image.pbcor_medsub_max.fits"),
suffix="_auto",
**kwargs
):
print(outname, suffix)
rgb_cube_fits = outname
if not os.path.exists(rgb_cube_fits):
# does not return anything
aplpy.make_rgb_cube(
[
fntemplate.format(redline) if "fits" not in redline else redline,
fntemplate.format(greenline) if "fits" not in greenline else greenline,
fntemplate.format(blueline) if "fits" not in blueline else blueline,
],
rgb_cube_fits,
)
rgb_cube_png = rgb_cube_fits[:-5] + suffix + ".png"
rgb_im = aplpy.make_rgb_image(data=rgb_cube_fits, output=rgb_cube_png, embed_avm_tags=True, **kwargs)
return rgb_im
def cut_rgb_image(tract, patch, ra, dec):
width = 10 / 3600.0 # in degree
img_r, img_g, img_b = download_image(tract, patch)
try:
cutoutimg(img_r,
ra,
dec,
xw=width,
yw=width,
units='wcs',
outfile='central_r.fits',
overwrite=True,
useMontage=False,
coordsys='celestial',
verbose=False,
centerunits=None)
cutoutimg(img_g,
ra,
dec,
xw=width,
yw=width,
units='wcs',
outfile='central_g.fits',
overwrite=True,
useMontage=False,
coordsys='celestial',
verbose=False,
centerunits=None)
cutoutimg(img_b,
ra,
dec,
xw=width,
yw=width,
units='wcs',
outfile='central_us.fits',
overwrite=True,
useMontage=False,
coordsys='celestial',
verbose=False,
centerunits=None)
except:
os.system('rm ' + img_r + ' ' + img_g + ' ' + img_b)
return 'no output img', False
output_img = 'rgb_image.png'
aplpy.make_rgb_cube(
['central_r.fits', 'central_g.fits', 'central_us.fits'], 'cube.fits')
aplpy.make_rgb_image('cube.fits',
output_img,
stretch_r='log',
stretch_g='log',
stretch_b='log',
vmin_r=0,
vmin_g=0,
vmin_b=0)
os.system('rm ' + img_r + ' ' + img_g + ' ' + img_b)
os.system('rm cube.fits')
return output_img, True
def show_contours_on_threecolor(self, color='c',clobber=False):
"""
Make a three-color image
"""
from extinction_distance.support import zscale
print("Making color-contour checkimage...")
if (not os.path.isfile(self.rgbcube)) or clobber:
aplpy.make_rgb_cube([self.kim,self.him,self.jim],self.rgbcube,north=True,system="GAL")
k = fits.getdata(self.kim)
r1,r2 = zscale.zscale(k)
h = fits.getdata(self.him)
g1,g2 = zscale.zscale(h)
j = fits.getdata(self.jim)
b1,b2 = zscale.zscale(j)
aplpy.make_rgb_image(self.rgbcube,self.rgbpng,
#G337 hand-coded
#vmin_r = 5671., vmax_r = 5952.,
#vmin_g = 8117., vmax_g = 8688.,
#vmin_b = 1462., vmax_b = 1606.)
vmin_r = r1, vmax_r = r2,
vmin_g = g1, vmax_g = g2,
vmin_b = b1, vmax_b = b2)
f = aplpy.FITSFigure(self.rgbcube2d)
f.show_rgb(self.rgbpng)
f.show_contour(self.continuum, colors='white', levels=[0.1,0.2,0.4,0.8,1.6,3.2],smooth=3,convention='calabretta')
f.show_markers([self.glon],[self.glat])
try:
f.show_polygons([self.contours],edgecolor='cyan',linewidth=2)
except:
pass
#f.show_contour(self.continuum,levels=[self.contour_level],convention='calabretta',colors='white')
f.save(self.contour_check)
def make_rgb(
outname,
redline='H2CO303_202',
greenline='H2CO321_220',
blueline='H2CO322_221',
fntemplate=paths.dpath(
'merge/moments/W51_b6_7M_12M.{0}.image.pbcor_medsub_max.fits'),
suffix="_auto",
**kwargs):
print(outname, suffix)
rgb_cube_fits = outname
if not os.path.exists(rgb_cube_fits):
# does not return anything
aplpy.make_rgb_cube([
fntemplate.format(redline) if 'fits' not in redline else redline,
fntemplate.format(greenline)
if 'fits' not in greenline else greenline,
fntemplate.format(blueline)
if 'fits' not in blueline else blueline,
], rgb_cube_fits)
rgb_cube_png = rgb_cube_fits[:-5] + suffix + ".png"
rgb_im = aplpy.make_rgb_image(data=rgb_cube_fits,
output=rgb_cube_png,
embed_avm_tags=True,
**kwargs)
return rgb_im
def do_cube(self,undone_cube):
"""Make a cube"""
version = 2
success = False
print("Making a cube for "+undone_cube)
print("Using files... "+str(self.cubes[undone_cube]))
aplpy.make_rgb_cube([self.filenames[self.cubes[undone_cube][0]],self.filenames[self.cubes[undone_cube][1]],
self.filenames[self.cubes[undone_cube][2]]],self.filenames[undone_cube],system="GAL")
print("Saving to: "+self.filenames[undone_cube])
success = True
if success:
self.report_success(undone_cube,version)
def makergbimage(rgbarray,iname,field,ra,dec):
os.system('rm -rf rgbcube.fits rgbcube2.fits rgbcube_2d.fits')
aplpy.make_rgb_cube(rgbarray, 'rgbcube.fits')
aplpy.make_rgb_image('rgbcube.fits', '%s_%s.png' % (field,iname), pmax_r=95., pmax_g=95., pmax_b=95.)
# # # Set a CTYPE
d = pyfits.open('rgbcube.fits')
hdr,data = d[0].header,d[0].data
hdr['CTYPE3'] = 'VELO-LSR'
pyfits.writeto('rgbcube2.fits',data,hdr)
f = aplpy.FITSFigure('rgbcube2.fits',dimensions=[0, 1], slices=[0])
f.show_rgb('%s_%s.png' % (field,iname))
f.show_circles(ra, dec, 30/3600.,facecolor='',edgecolor='w',alpha=0.5,linewidth=4)
#f.show_markers(ra,dec,marker='o',facecolor='',edgecolor='w',alpha=0.5,s=4000,linewidth=3)
savefig('results/%s_%s_rgb.png' % (field,iname),bbox_inches='tight',transparent=True,dpi=200)
os.system('rm -rf %s_%s.png' % (field,iname))
def show_contours_on_threecolor(self, color='c', clobber=False):
"""
Make a three-color image
"""
from extinction_distance.support import zscale
print("Making color-contour checkimage...")
if (not os.path.isfile(self.rgbcube)) or clobber:
aplpy.make_rgb_cube([self.kim, self.him, self.jim],
self.rgbcube,
north=True,
system="GAL")
k = fits.getdata(self.kim)
r1, r2 = zscale.zscale(k)
h = fits.getdata(self.him)
g1, g2 = zscale.zscale(h)
j = fits.getdata(self.jim)
b1, b2 = zscale.zscale(j)
aplpy.make_rgb_image(
self.rgbcube,
self.rgbpng,
#G337 hand-coded
#vmin_r = 5671., vmax_r = 5952.,
#vmin_g = 8117., vmax_g = 8688.,
#vmin_b = 1462., vmax_b = 1606.)
vmin_r=r1,
vmax_r=r2,
vmin_g=g1,
vmax_g=g2,
vmin_b=b1,
vmax_b=b2)
f = aplpy.FITSFigure(self.rgbcube2d)
f.show_rgb(self.rgbpng)
f.show_contour(self.continuum,
colors='white',
levels=[0.1, 0.2, 0.4, 0.8, 1.6, 3.2],
smooth=3,
convention='calabretta')
f.show_markers([self.glon], [self.glat])
try:
f.show_polygons([self.contours], edgecolor='cyan', linewidth=2)
except:
pass
#f.show_contour(self.continuum,levels=[self.contour_level],convention='calabretta',colors='white')
f.save(self.contour_check)
def do_cube(self, undone_cube):
"""Make a cube"""
version = 2
success = False
print("Making a cube for " + undone_cube)
print("Using files... " + str(self.cubes[undone_cube]))
aplpy.make_rgb_cube([
self.filenames[self.cubes[undone_cube][0]],
self.filenames[self.cubes[undone_cube][1]],
self.filenames[self.cubes[undone_cube][2]]
],
self.filenames[undone_cube],
system="GAL")
print("Saving to: " + self.filenames[undone_cube])
success = True
if success:
self.report_success(undone_cube, version)
def make_SDSS_FITSFigure(ra, dec, plate_num, width):
'''
aspect ratio is weird with this method, so trying something different
'''
ra, dec = str(ra), str(dec)
plate_num = str(plate_num)
aplpy.make_rgb_cube([plate_num + '_r.fits', plate_num +
'_g.fits', plate_num + '_u.fits'],
plate_num + '_cube.fits')
aplpy.make_rgb_image(plate_num + '_cube.fits',
plate_num + '_rgb.png')
plt.close('all')
f = aplpy.FITSFigure(plate_num + '_cube_2d.fits', figsize=(10, 10))
f.show_rgb(plate_num + '_rgb.png')
f.add_grid()
f.tick_labels.set_font(size='xx-small')
f.axis_labels.set_font(size='x-small')
f.axis_labels.set_xtext('Right Ascension (J2000)')
f.axis_labels.set_ytext('Declination (J2000)')
plt.tight_layout()
plt.show()
import numpy as np
import aplpy
fitslist = ['h_m51_h_s20_drz_sci.fits',
'h_m51_v_s20_drz_sci.fits',
'h_m51_b_s20_drz_sci.fits'
]
# Reproject the images to a common projection - this will also produce
# ``2mass_cube_2d.fits``
aplpy.make_rgb_cube(fitslist, 'm51_cube.fits')
# Make an RGB image
aplpy.make_rgb_image('m51_cube.fits', 'm51_rgb.png')
# Plot the RGB image using the 2d image to indicate the projection
f = aplpy.FITSFigure('m51_cube_2d.fits')
f.show_rgb('m51_rgb.png')
mean_SDOM_ZP_V = np.mean(SDOM_ZP_V)/np.sqrt(3)
#ZP in V filter is 21.68807 +/- 0.0058
##################################################################################
# +++RGB IMAGES+++ #
##################################################################################
#ordered R-V-B inside the data cube:
aplpy.make_rgb_cube([dir + '/mosaic_R/mosaic.fits', dir + '/mosaic_V/mosaic.fits', dir+ '/mosaic_B/mosaic.fits'], dir + '/rgb_cube.fits')
aplpy.make_rgb_image(dir + '/rgb_cube.fits', dir + '/cluster_rgb.png', embed_avm_tags=False)
fig = aplpy.FITSFigure(dir+'/rgb_cube_2d.fits')
fig.show_rgb(dir+'/cluster_rgb.png')
fig.add_grid()
fig.grid.set_linestyle('dotted')
##################################################################################
# +++HR DIAGRAM!+++ #
##################################################################################
def psocolor(source_name,keepfiles=False,allcolor='#FFFF00',rejcolor='b',tm_color='r',plot=False,savepdf=True,secondary='',skipdownloads=False,circle_radius=0.0015,size=2.0,override_directory=None,primarypos_label=None,title=None,filename=None,buffer=False):
# Set $FINDER_PATH in your bash_profile if you would like to control where the finder charts are output
# size: arcmin
# allwise: overplot AllWISE catalog positions
# rejallwise = overplot AllWISE reject positions
# tmass = overplot 2MASS psc positions
# keepfiles = keep fits, tbl, and xml files
# allcolor = color of allwise symbols
# rejcolor = color of allwise reject symbols
# tm_color = color of tmass symbols
# plot = show plot (otherwise, finder is just made)
# savepdf = save a pdf of the finder
circle_width = 2.5
circle_alpha = 0.8
fig_xsize = 11
fig_ysize = 8.5
#Convert sexagecimal
if source_name.find(' ') == -1:
symbol = '+'
if source_name.find('+') == -1:
symbol = '-'
radec = re.split('[\+ | -]',source_name)
ras = radec[0][0:2]+' '+radec[0][2:4]+' '+radec[0][4:]
decs = radec[1][0:2]+' '+radec[1][2:4]+' '+radec[1][4:]
ra = coord.Angle(ras, unit=u.hour)
dec = coord.Angle(symbol+decs,unit=u.degree)
source_name = str(ra.degree)+' '+str(dec.degree)
#Use buffer if needed
if buffer:
import matplotlib
matplotlib.use('Agg')
plot=False
import pylab,pyfits,aplpy
#Verify whether a working directory is set in the bash profile
main_dir = None
if override_directory:
main_dir = override_directory
else:
proc = subprocess.Popen(["echo $FINDER_PATH"], stdout=subprocess.PIPE,shell=True)
(out, err) = proc.communicate()
if out != '\n':
main_dir = out.split('\n')[0]
if main_dir:
initial_dir = os.getcwd()
if not os.path.exists(main_dir):
os.makedirs(main_dir)
os.chdir(main_dir)
#List of colors
color_blue = '#377eb8'#RGB=[55,126,184]
color_red = '#e41a1c'#RGB=[228,26,28]
color_purple = '#b27bba'#RGB=[178,123,186]
color_green = '#4daf4a'#RGB = [77,175,74]
t1 = datetime.now()
ra,de = simbad(source_name)
ra2 = None
de2 = None
if secondary:
ra2,de2 = simbad(secondary)
if filename is None:
filename = source_name
if skipdownloads is not True:
print("Downloading Pan-Starrs data")
#Remove previous data
os.system("rm *_PSO_TMP.fits*")
query_pso_fits(ra,de,size=size,output_file='PSO_TMP.fits')
#If no PSO data could be downloaded, return
if len(glob.glob('*_PSO_TMP.fits*')) == 0:
print("No PSO data !")
return
if plot:
pylab.ion()
fig = pylab.figure(figsize=(fig_xsize,fig_ysize))
pylab.rcParams['font.family'] = 'serif'
#Create and plot RGB PSO image
files = ['y_PSO_TMP.fits','i_PSO_TMP.fits','g_PSO_TMP.fits']
aplpy.make_rgb_cube(files,'PSO_rgb.fits')
impsoc = aplpy.FITSFigure('PSO_rgb_2d.fits',figure=fig)
impsoc.add_label(0.05,0.9,'PSO $y$/$i$/$g$',relative=True,size='medium',color='k',bbox=dict(facecolor='white', alpha=0.5),horizontalalignment='left')
meds = []
mads = []
devs = []
for filei in files:
datai = pyfits.getdata(filei)
medi = np.nanmedian(datai)
madi = np.nanmedian(abs(datai - np.nanmedian(datai)))
devi = np.nanpercentile(datai,95) - np.nanpercentile(datai,5)
meds.append(medi)
mads.append(madi)
devs.append(devi)
mins = []
maxs = []
for i in range(0,len(files)):
mini = (meds[i] - 2.0*mads[i])
#maxi = (meds[i] + 10.0*mads[i])
maxi = meds[i] + 2.0*devs[i]
mins.append(mini)
maxs.append(maxi)
aplpy.make_rgb_image('PSO_rgb.fits','PSO_rgb.png',vmin_r=mins[0],vmin_g=mins[1],vmin_b=mins[2],vmax_r=maxs[0],vmax_g=maxs[1],vmax_b=maxs[2])
impsoc.show_rgb('PSO_rgb.png')
impsoc.hide_tick_labels()
impsoc.ticks.hide()
impsoc.hide_xaxis_label()
impsoc.hide_yaxis_label()
impsoc.recenter(ra,de,width=(size/60.0),height=(size/60.0))
impsoc.show_circles(ra,de,edgecolor=color_red,linewidth=circle_width,facecolor='none',radius=circle_radius,alpha=circle_alpha)
if secondary:
impsoc.show_circles(ra2,de2,edgecolor=color_blue,linewidth=circle_width,facecolor='none', radius=circle_radius,alpha=circle_alpha)
# Remove files (or not)
if keepfiles:
pass
else:
print("Removing files...")
cmdrm1 = "rm PSO_rgb.png PSO_rgb*.fits"
os.system(cmdrm1)
if savepdf:
pylab.savefig(filename+'_pso_color.pdf')
#Return to initial directory
if main_dir:
os.chdir(initial_dir)
t2 = datetime.now()
tdiff = (t2 - t1)
print("PSO image creation took %s seconds" % (round(tdiff.total_seconds(),0)))
import sys,os
import aplpy
import random
from termcolor import colored
filelist = open('files_all','r').readlines()
random.shuffle(filelist)
for index in filelist[:1]:
index = index.rstrip()
print colored('RGB image gernerating :','green'), colored(' VCC'+index,'yellow')
image_r = index+'.i.fits'
image_g = index+'.g.fits'
image_b = index+'.u.fits'
cube_name = index+'_rgb.fits'
cube_name2 = index +'_rgb_2d.fits'
output_image_name =index+'.png'
if os.path.exists('./'+output_image_name)==False and index !=1347 and index !=0167:
aplpy.make_rgb_cube([image_r,image_g,image_b],cube_name)
aplpy.make_rgb_image(cube_name,output_image_name,
stretch_r='arcsinh',stretch_g='arcsinh',stretch_b='arcsinh',
#vmin_r=0, vmin_g=0,vmin_b=0,
embed_avm_tags = False)
os.system('rm '+cube_name+' '+cube_name2)
#os.system('shotwell '+output_image_name+'&')
cosmo = FlatLambdaCDM(H0=70, Om0=0.3)
fig = plt.figure(figsize=(20, 20))
for cont_gal, gal in enumerate(cataid):
print(gal)
create_sb_image(gal, images_gband_path, "g", zp, pix_scale)
create_sb_image(gal, images_rband_path, "r", zp, pix_scale)
create_sb_image(gal, images_iband_path, "i", zp, pix_scale)
#aplpy.make_rgb_cube([images_gband_path+str(gal)+'_kids_g.fits', images_rband_path+str(gal)+'_kids_r.fits', images_iband_path+str(gal)+'_kids_i.fits'], str(gal)+'_cube.fits')
aplpy.make_rgb_cube([
images_iband_path + str(gal) + '_kids_i_sb.fits',
images_rband_path + str(gal) + '_kids_r_sb.fits',
images_gband_path + str(gal) + '_kids_g_sb.fits'
],
str(gal) + '_cube.fits')
img_g = fits.open(images_gband_path + str(gal) + '_kids_g_sb.fits')
img_r = fits.open(images_rband_path + str(gal) + '_kids_r_sb.fits')
img_i = fits.open(images_iband_path + str(gal) + '_kids_i_sb.fits')
aplpy.make_rgb_image(str(gal) + '_cube.fits',
'./color_images/' + str(gal) + '_rgb.png',
stretch_r='linear',
stretch_g='linear',
stretch_b='linear',
vmin_r=min_i,
vmax_r=max_i,
vmin_g=min_r,
import aplpy
# Convert all images to common projection
aplpy.make_rgb_cube(['m1.fits', 'i3.fits', 'i2.fits'], 'rgb.fits')
# Make 3-color image
aplpy.make_rgb_image('rgb.fits',
'rgb.png',
vmin_r=20,
vmax_r=400,
vmin_g=0,
vmax_g=150,
vmin_b=-2,
vmax_b=50)
# Create a new figure
f = aplpy.FITSFigure('rgb_2d.fits')
# Show the RGB image
f.show_rgb('rgb.png')
# Add contours
f.show_contour('sc.fits', cmap='gist_heat', levels=[0.2, 0.4, 0.6, 0.8, 1.0])
# Overlay a grid
f.add_grid()
f.grid.set_alpha(0.5)
# Save image
f.save('plot.png')
import matplotlib.pyplot as plt
import numpy as np
import aplpy
# Convert all images to common projection
aplpy.make_rgb_cube([
'C:/Users/chaowang/r.fits', 'C:/Users/chaowang/g.fits',
'C:/Users/chaowang/u.fits'
], 'rgb.fits')
# Make 3-color image
aplpy.make_rgb_image('rgb.fits',
'rgb.png',
vmin_r=20,
vmax_r=400,
vmin_g=0,
vmax_g=150,
vmin_b=-2,
vmax_b=50)
# Create a new figure
fig = aplpy.FITSFigure('rgb.fits')
# Show the RGB image
fig.show_rgb('rgb.png')
# Add contours
fig.show_contour('sc.fits', cmap='gist_heat', levels=[0.2, 0.4, 0.6, 0.8, 1.0])
# Overlay a grid
fig.add_grid()
def sdss(input_file, output_dir, filters, output_format, pmin_r, pmax_r,
pmin_g, pmax_g, pmin_b, pmax_b):
"""
Generates RGB images using SDSS data and APLPY. Information for parameters can be found in inputHandler(). I separated them up to allow easier access from makeTable.py
"""
warnings.filterwarnings("ignore")
# get parameters and inputs into a suitable format
df = pd.read_csv(input_file, header=None)
output_format = output_format.lower()
filters = filters.split(',')
if len(filters) != 3:
raise Exception('Error. Please provide 3 filters separated by commas')
try:
os.mkdir(output_dir)
except:
typer.echo(
f'A dir with the name {typer.style(output_dir, bold=True, fg=typer.colors.RED)} already exists'
)
for i, line in df.iterrows():
try:
name = line[0]
ra = line[1]
dec = line[2]
styled_name = typer.style(name, fg=typer.colors.MAGENTA, bold=True)
typer.echo(f'Plotting: ' + styled_name)
pos = coords.SkyCoord(ra, dec, unit='deg')
# query SDSS for each target and get the images
try:
xid = Table(SDSS.query_region(pos, spectro=False)[0])
except:
raise Exception(f'No images found on SDSS for target {name}')
im = SDSS.get_images(matches=xid, band=filters)
# raise exception if no images are found
if len(im) == 0:
raise Exception(f'No images found on SDSS for target {name}')
# Obtain the PrimaryHDU from the HDUList for each band
r, g, b = im[0][0], im[1][0], im[2][0]
# save the fits files so they can be combined into a single rgb cube
r.writeto('r.fits', overwrite=True)
g.writeto('g.fits', overwrite=True)
b.writeto('b.fits', overwrite=True)
aplpy.make_rgb_cube(['r.fits', 'g.fits', 'b.fits'],
f'image.fits',
north=True)
aplpy.make_rgb_image(f'image.fits',
fr'{output_dir}/{name}.{output_format}',
pmin_r=pmin_r,
pmax_r=pmax_r,
pmin_g=pmin_g,
pmax_g=pmax_g,
pmin_b=pmin_b,
pmax_b=pmax_b)
image = aplpy.FITSFigure(fr'{output_dir}/{name}.{output_format}')
image.show_rgb()
# add labels for filters used
image.add_label(0.08,
0.15,
"FILTERS:",
relative=True,
color='white')
filter_wavelengths = {
'z': 913,
'i': 763,
'r': 623,
'g': 477,
'u': 354
}
bandColours = ['red', 'green', 'cyan']
for i in range(3):
w = filter_wavelengths[filters[i]]
c = bandColours[i]
image.add_label(0.08,
0.11 - 0.03 * i,
f"{filters[i]} ({w}nm)",
relative=True,
color=c)
# add arrows pointing to object
image.show_arrows(
x=[ra + 0.01, ra - 0.01, ra + 0.01, ra - 0.01],
y=[dec + 0.01, dec - 0.01, dec - 0.01, dec + 0.01],
dx=[-0.007, 0.007, -0.007, 0.007],
dy=[-0.007, 0.007, 0.007, -0.007],
color='red')
# add object name as label
image.add_label(ra, dec + 0.02, name, color='red')
# get redshift for scalebar
resTable = Ned.query_region(pos, radius=0.01 * u.deg)
resTable = resTable.to_pandas()
redshift = 0
for i, row in resTable.iterrows():
if row['Redshift'] > 0:
redshift = row['Redshift']
break
kpcArcmin = cosmo.kpc_proper_per_arcmin(float(redshift)).value
length = round(kpcArcmin * 2, 1)
# add scalebar
image.add_scalebar(1 / 30,
label=f'120" | {length}kpc | r = {redshift}',
color='red')
# save to output dir in the appropriate format
image.save(fr'{output_dir}/{name}.{output_format}')
typer.echo('Finished plotting: ' + styled_name)
except Exception as e:
typer.echo('Failed for: ' + styled_name)
print(e)
cleanup()
def zoomfigure(target=e2e, targetname='e2e', radius=7.5*u.arcsec, cutout='e2e8',
zoom_radius=3*u.arcsec, tick_spacing=1.8*u.arcsec):
fn = paths.dpath('merge/cutouts/W51_b6_7M_12M.HNCO10010-909.image.pbcor_{0}cutout.fits'.format(cutout))
m0hnco = get_mom0(fn, iterate=False)
cutout_cont = Cutout2D(cont_fits[0].data, target, radius, wcs=wcs.WCS(cont_fits[0].header))
cutout_ch3oh = Cutout2D(m0ch3oh.value, target, radius, wcs=wcs.WCS(m0ch3oh.header))
cutout_hnco = Cutout2D(m0hnco.value, target, radius, wcs=wcs.WCS(m0hnco.header))
cont_fits_cutout = fits.PrimaryHDU(data=cutout_cont.data, header=cutout_cont.wcs.to_header())
ch3oh_fits_cutout = fits.PrimaryHDU(data=cutout_ch3oh.data, header=cutout_ch3oh.wcs.to_header())
hnco_fits_cutout = fits.PrimaryHDU(data=cutout_hnco.data, header=cutout_hnco.wcs.to_header())
cont_fits_fn = "rgb/continuum_{0}_cutout.fits".format(targetname)
hnco_fits_fn = "rgb/hnco_{0}_cutout.fits".format(targetname)
ch3oh_fits_fn = "rgb/ch3oh_{0}_cutout.fits".format(targetname)
cont_fits_cutout.writeto(cont_fits_fn, clobber=True)
ch3oh_fits_cutout.writeto(ch3oh_fits_fn, clobber=True)
hnco_fits_cutout.writeto(hnco_fits_fn, clobber=True)
rgb_cube_fits = '{0}_ch3oh_hnco_cont.fits'.format(targetname)
if not os.path.exists(rgb_cube_fits):
# does not return anything
aplpy.make_rgb_cube([ch3oh_fits_fn, hnco_fits_fn, cont_fits_fn,], rgb_cube_fits)
rgb_cube_png = rgb_cube_fits[:-5]+"_auto.png"
rgb_im = aplpy.make_rgb_image(data=rgb_cube_fits, output=rgb_cube_png,
embed_avm_tags=True)
rgb_cube_png = rgb_cube_fits[:-5]+"_logcont.png"
rgb_im = aplpy.make_rgb_image(data=rgb_cube_fits, output=rgb_cube_png,
#vmin_b=0.005,
#vmax_b=0.15,
stretch_b='log', embed_avm_tags=True)
#rgb_cube_png = rgb_cube_fits[:-5]+"_asinhgreen.png"
#rgb_im = aplpy.make_rgb_image(data=rgb_cube_fits, output=rgb_cube_png,
# vmax_g=0.017,
# vmax_b=6.5,
# vmax_r=7.0,
# vmin_g=0.0001,
# stretch_g='arcsinh', embed_avm_tags=True)
#
#
pl.rcParams['font.size'] = 18
fig1 = pl.figure(1)
fig1.clf()
F = aplpy.FITSFigure(rgb_cube_png, figure=fig1)
F.show_rgb(rgb_cube_png)
#F.recenter(290.93315, 14.509584, radius=0.00075)
F.recenter(target.ra.deg, target.dec.deg, radius=zoom_radius.to(u.deg).value)
F.add_scalebar((0.025*u.pc / (5400*u.pc)).to(u.deg,u.dimensionless_angles()))
F.scalebar.set_label('5000 au / 0.025 pc')
F.scalebar.set_color('w')
F.set_tick_xspacing(tick_spacing.to(u.deg).value)
F.add_label(0.05, 0.95, "CH$_3$OH", relative=True, color='r', horizontalalignment='left')
F.add_label(0.05, 0.91, "HNCO", relative=True, color='g', horizontalalignment='left')
F.add_label(0.05, 0.87, "Continuum", relative=True, color='b', horizontalalignment='left')
F.save(paths.fpath("W51{0}_ch3oh_hnco_continuum_aplpy.png".format(targetname)))
F.save(paths.fpath("W51{0}_ch3oh_hnco_continuum_aplpy.pdf".format(targetname)))
F.show_contour(paths.vpath('data/W51Ku_BDarray_continuum_2048_both_uniform.hires.clean.image.fits'),
levels=np.array([0.0015,0.0045,0.0135,0.0270,0.054,0.108])*1.25,
colors=['w']*7, layer='evla_cont')
F.save(paths.fpath("W51{0}_ch3oh_hnco_continuum_aplpy_kucontours.png".format(targetname)))
F.save(paths.fpath("W51{0}_ch3oh_hnco_continuum_aplpy_kucontours.pdf".format(targetname)))
input_fits_image_band6='./input/G12v230_IRAC_Mosaic_45.fits'
band4_present=1 #=================================================================1:yes 0:no (I band)
band5_present=1 #=================================================================1:yes 0:no (3.6 band)
band6_present=1 #=================================================================1:yes 0:no (4.5 band)
#montage.mSubimage(input_fits_image_band5, './G12_3p6_trimmed.fits', ra=, dec=, xsize=0.0023)
aplpy.make_rgb_cube([input_fits_image_band1, input_fits_image_band2, input_fits_image_band4], 'G12_cube.fits') #R, G, B
#aplpy.make_rgb_image('G12_cube.fits','G12_cube.png')
aplpy.make_rgb_image('G12_cube.fits','G12_cube.png', vmin_b=500.0, vmax_b=3000.0, vmax_r=73.0, vmin_r=-20.0)
#aplpy.make_rgb_image('G12_JHK_cube.fits', 'G12_JHK_cube.png', pmin_r=0., pmax_r=80., pmin_g=0., pmax_g=80., pmin_b=0., pmax_b=80.)
rgb_image = aplpy.FITSFigure('./G12_cube_2d.fits')
rgb_image.show_rgb('G12_cube.png')
#rgb_image.show_contour(input_fits_image_band5, levels=3, colors='red', linewidths=0.5)
#rgb_image.recenter(176.65903,-0.19764512, radius=0.036)
rgb_image.recenter(176.65903,-0.19764512, width=0.066, height=0.07)
rgb_image.add_scalebar(1.0/60.0)
def plot_RGB(
figname,
filename,
title,
subplot=None,
rgb = [10,99.75],rgb_stretch=['linear'], # can put lists here
show_circles = False,show_grid=False,show_xaxis=True,show_yaxis=True,show_contours=True,
show_scalebar=True,show=True,show_fields=True,show_labels=False,show_focus=False,
focus = [], #ra,dec,size
labels=[],
fields=[['20h07m07.178s','+27d28m23.79s',-15,180],['20h07m02.561s','+27d30m25.90s',25,180]],
scale_bar=20, #arcsec
dist = 700., # pc
name='IRAS20050', contours=None,
contours_levels=[],
radius_source = 2.4, # arcsec
ra='20:07:06.70',dec='27:28:54.5',
radius = 200.): # of snapshot, arcsec
'''
this function displays the file in filename in all a uniform format
all defaults to IRAS20050
dist in pc
radius in asec
radius_source in asec
'''
aplpy.make_rgb_cube([filename[0],filename[1],filename[2]],title+'_rgb_cube.fits')
if len(rgb_stretch)==1:
stretch_r= stretch_g= stretch_b = rgb_stretch[0]
else:
[stretch_r, stretch_g, stretch_b] = rgb_stretch
if len(rgb)==2:
pmin_r=pmin_g=pmin_b=rgb[0]; pmax_r=pmax_g=pmax_b=rgb[1]
else:
[pmin_r,pmin_g,pmin_b,pmax_r,pmax_g,pmax_b] = rgb
aplpy.make_rgb_image(title+'_rgb_cube.fits', title+'_rgb_cube.png',pmin_r=pmin_r,pmin_g=pmin_g,pmin_b=pmin_b,
pmax_r=pmax_r,pmax_g=pmax_g,pmax_b=pmax_b,stretch_r=stretch_r, stretch_g=stretch_g, stretch_b=stretch_b)
if subplot==None:
fig = aplpy.FITSFigure(title+'_rgb_cube_2d.fits',figure=figname)
else:
fig = aplpy.FITSFigure(title+'_rgb_cube_2d.fits',figure=figname,subplot=subplot)
fig.show_rgb(title+'_rgb_cube.png')
# coordinates of the center of the image
c = SkyCoord(ra=ra,dec=dec,frame='fk5',unit=(u.hour,u.deg))
# recenter image
fig.recenter(c.ra.deg,c.dec.deg,radius=radius/3600.)
# put axes on top
fig.tick_labels.set_xposition('top')
fig.axis_labels.set_xposition('top')
fig.tick_labels.set_font(size='small')
fig.tick_labels.set_xformat('hh:mm:ss')
fig.tick_labels.set_yformat('dd:mm:ss')
#fig.ticks.set_xspacing(10./3600.)
# turn grid on
if show_grid:
fig.add_grid()
# show/hide axes
if not show_xaxis:
fig.axis_labels.hide_x()
fig.tick_labels.hide_x()
if not show_yaxis:
fig.axis_labels.hide_y()
fig.tick_labels.hide_y()
if show_labels:
c = SkyCoord(ra='20h07m06.782s',dec='27d28m43.00s',frame='fk5',unit=(u.hour,u.deg))
fig.add_label(c.ra.deg,c.dec.deg,'SOF1',color='red',weight='bold',size=20)
c = SkyCoord(ra='20h07m06.798s',dec='27d28m56.48s',frame='fk5',unit=(u.hour,u.deg))
fig.add_label(c.ra.deg,c.dec.deg,'SOF2',color='red',weight='bold',size=20)
c = SkyCoord(ra='20h07m06.458s',dec='27d29m00.78s',frame='fk5',unit=(u.hour,u.deg))
fig.add_label(c.ra.deg,c.dec.deg,'SOF3',color='red',weight='bold',size=20)
c = SkyCoord(ra='20h07m05.592s',dec='27d29m03.0s',frame='fk5',unit=(u.hour,u.deg))
fig.add_label(c.ra.deg,c.dec.deg,'SOF4',color='red',weight='bold',size=20)
c = SkyCoord(ra='20h07m05.795s',dec='27d28m46.82s',frame='fk5',unit=(u.hour,u.deg))
fig.add_label(c.ra.deg,c.dec.deg,'SOF5',color='red',weight='bold',size=20)
# add title
fig.add_label(0.2,0.9,title,relative=True,color='red',weight='bold')
#fig.set_title(title)
# load source list
sources = pickle.load(open(folder_export+"totsourcetable_fits.data","r"))
# extract only the RA, DEC column for name
if show_circles:
for i in range(len(sources)):
if name in sources['SOFIA_name'][i] and "Total_Cluster" not in sources['Property'][i]:
s = "%d" % (i)
fig.show_circles(sources['RA'][i],sources['DEC'][i],radius_source/3600.,edgecolor='red',facecolor='none',alpha=0.8,lw=2,label=s)
# add scalebar
if show_scalebar:
scale_pc = 1./dist*scale_bar
fig.add_scalebar(scale_bar/3600.)
#fig.scalebar.set_frame(True)
fig.scalebar.set_alpha(0.7)
fig.scalebar.set_color('red')
fig.scalebar.set_label('%d" = %.3f pc' % (scale_bar,scale_pc))
fig.scalebar.set_linewidth(3)
fig.scalebar.set_font(weight='bold')
# add another dashed rectangle showing the region of interest
if show_focus:
rafoc,decfoc,sizefoc=focus
foc = SkyCoord(ra=rafoc,dec=decfoc,frame='fk5',unit=(u.hour,u.deg))
fig.show_rectangles(foc.ra.deg,foc.dec.deg,sizefoc/3600.,decfoc/3600.,edgecolor='red',facecolor='none',alpha=0.8,lw=2,linestyle='dashed')
# show the SOFIA fields
if show_fields:
patches = []
for field in fields:
raf,decf,ang,width = field
c = SkyCoord(ra=raf,dec=decf,frame='fk5',unit=(u.hour,u.deg))
xp, yp = wcs_util.world2pix(fig._wcs, c.ra, c.dec)
wp = hp = width/3600. / wcs_util.celestial_pixel_scale(fig._wcs)
rect = Rectangle((-wp/2., -hp/2), width=wp, height=hp)
t1 = mpl.transforms.Affine2D().rotate_deg(ang).translate(xp, yp)
rect.set_transform(t1)
patches.append(rect)
# add all patches to the collection
p = PatchCollection(patches, edgecolor='white',facecolor='none',alpha=0.8,lw=2)
# add collection to figure
t = fig._ax1.add_collection(p)
# display contours
if contours != None:
fig.show_contour(contours,colors='white',returnlevels=True,levels=contours_levels)
if show:
plt.show()
def make_cube(process=True):
'''
Turn all the UV data into a cube!
'''
cr_img_exists = glob.glob(
'*cr.fits'
) #makes a list of count rate images that exist in the current directory, checks if uvot_deep done
filter_list = ['w2', 'm2', 'w1']
if len(cr_img_exists) == 0:
id_list = glob.glob('000*')
try:
uvot_deep.uvot_deep(id_list, gal + '_',
filter_list) #tool adapted by Lea Hagen
except FileNotFoundError:
print('* Required files not made out of uvot_deep for ' + gal +
', moving on...')
unprocessed_gals.write(gal + '\n')
why_bypass.write(gal +
': required files not made out of uvot_deep' +
'\n')
process = False
except OSError:
print(
'Too many open files error thrown, whatever that means. Moving on...'
) #sass maybe not good, maybe chill
unprocessed_gals.write(gal + '\n')
why_bypass.write(gal + ': too many open files error' + '\n')
process = False #does this work here?
else:
print("* uvot_deep already completed successfully, moving on!")
#input()
#offset_mosaic running over and over again, need to skip over this right now
#if images have been created already, don't run it again
#later will have to take into consideration whether or not there is new data that requires a rerun of uvot_deep
offset_done = glob.glob(gal + '_offset_*')
if len(offset_done) == 0:
try: #make sure this does run again
if True:
print('* running offset_mosaic')
offset_mosaic.offset_mosaic(gal + '_',
gal + '_offset_',
filter_list,
min_exp_w2=150,
min_exp_m2=150,
min_exp_w1=150,
restack_id=True)
except IndexError:
print("* index 0 is out of bounds for axis 0 with size zero")
unprocessed_gals.write(gal + '\n')
why_bypass.write(
gal +
': offset mosaic problem, index 0 is out of bounds for axis 0 with size zero'
+ '\n')
#continue #fix continue
process = False
else:
print('* offset_mosaic has been run already, moving on!')
#list of uv filters, can be changed if someone needs optical filter images as well.
#filter_list = ['w1', 'm2', 'w2']
idl = pidly.IDL('/bulk/pkg/local/bin/idl')
for filt in filter_list:
#taken from Lea's code stack_uvot
with fits.open(gal + "_" + filt +
'_cr.fits') as hdu_cr: #cr = count rate
pix_clip = sigma_clip(hdu_cr[0].data, sigma=2.5, maxiters=3)
cr_mode = biweight_location(pix_clip.data[~pix_clip.mask])
#print('cr_mode: ', cr_mode)
hdu_cr[0].data -= cr_mode
hdu_cr.writeto(gal + '_offset_' + filt + '_cr_bgsub.fits',
overwrite=True)
idl.pro('image_shift',
gal) #idl procedure that aligns all the image_shift
idl.close()
#replaces mkcolor idl script (credits to Lea)
# make RGB image
cube_done = glob.glob(gal + '_rgb_cube*')
if len(cube_done) == 0:
#if no data for the filter, gotta skip over the image that would be created
im_r = gal + '_offset_w1_cr_bgsub.fits'
im_g = gal + '_offset_m2_cr_bgsub.fits'
im_b = gal + '_offset_w2_cr_bgsub.fits'
vmid_list = 0.001
vmin_list = []
for i, im in enumerate([im_r, im_g, im_b]):
hdu_list = fits.open(im)
filt = sigma_clip(hdu_list[0].data, sigma=2, maxiters=5)
vmin_list.append(
np.mean(filt.data[~filt.mask]) +
1.5 * np.std(filt.data[~filt.mask]))
hdu_list.close()
# - create fits images in same projection
print('* creating rgb fits cube for ' + gal)
aplpy.make_rgb_cube([im_r, im_g, im_b],
gal + '_rgb_cube.fits',
north=True)
# - make the rgb image
print('* creating rgb png image of ' + gal)
aplpy.make_rgb_image(gal + '_rgb_cube.fits',
gal + '_image' + '.png',
stretch_r='log',
stretch_g='log',
stretch_b='log',
vmin_r=vmin_list[0],
vmin_g=vmin_list[1],
vmin_b=vmin_list[2],
vmid_r=vmid_list,
vmid_g=vmid_list,
vmid_b=vmid_list,
pmax_r=99.95,
pmax_g=99.9,
pmax_b=99.9,
make_nans_transparent=True)
else:
print(
'rgb_cube FITS file already exists, moving on to .png creation and photometry!'
)
return process
make_rgb(
"ku_so_c18o_rgb.fits",
greenline="SO65-54",
redline=fnku,
blueline="C18O2-1",
pmax_g=99.99,
pmax_r=99.95,
pmax_b=99.99,
)
rgb_cube_fits = "full_h2co_rgb.fits"
if not os.path.exists(rgb_cube_fits):
# does not return anything
aplpy.make_rgb_cube([fn303, fn321, fn322], rgb_cube_fits)
rgb_cube_png = rgb_cube_fits[:-5] + "_auto.png"
rgb_im = aplpy.make_rgb_image(data=rgb_cube_fits, output=rgb_cube_png, embed_avm_tags=True)
rgb_cube_png = rgb_cube_fits[:-5] + "_setlevels.png"
rgb_im = aplpy.make_rgb_image(
data=rgb_cube_fits,
output=rgb_cube_png,
vmin_b=-0.005,
vmax_b=0.4,
vmin_g=-0.005,
vmax_g=0.4,
vmin_r=-0.005,
vmax_r=0.4,
embed_avm_tags=True,
import paths
for species, blue_fits, red_fits in (('co',
paths.dpath('moments/w51_12co2-1_blue0to45_masked.fits'),
paths.dpath('moments/w51_12co2-1_red73to130_masked.fits')),
('so',
paths.dpath('moments/w51_so_65-54_blue0to45.fits'),
paths.dpath('moments/w51_so_65-54_red65to130.fits'))
):
green_fits = '/Users/adam/work/w51/paper_w51_evla/data/W51Ku_BDarray_continuum_2048_both_uniform.hires.clean.image.fits'
rgb_cube_fits = 'outflow_co_redblue_kucont_green.fits'
if not os.path.exists(rgb_cube_fits):
# does not return anything
aplpy.make_rgb_cube([red_fits, green_fits, blue_fits], rgb_cube_fits)
rgb_cube_png = rgb_cube_fits[:-5]+"_auto.png"
rgb_im = aplpy.make_rgb_image(data=rgb_cube_fits, output=rgb_cube_png,
embed_avm_tags=True)
rgb_cube_png = rgb_cube_fits[:-5]+"_loggreen.png"
rgb_im = aplpy.make_rgb_image(data=rgb_cube_fits, output=rgb_cube_png,
stretch_g='log', embed_avm_tags=True)
rgb_cube_png = rgb_cube_fits[:-5]+"_loggreen_max.png"
rgb_im = aplpy.make_rgb_image(data=rgb_cube_fits, output=rgb_cube_png,
pmax_g=99.99,
stretch_g='log', embed_avm_tags=True)
rgb_cube_png = rgb_cube_fits[:-5]+"_asinhgreen.png"
##############
# ASTROPY WAY
##############
#the SPT0348 fits files: bands 3, 6, 7
#b3 = dir+'spt0348_b3ctm_dirty_briggs_robust05_15klambda_uvtaperbeam_2.fits' #red: 3.6mm to 2.6mm
#b6 = dir+'spt0348_b6ctm_dirty_briggs_robust05_15klambda_uvtaperbeam_2.fits' #green: 1.4mm to 1.1mm
#b7 = dir+'spt0348_b7ctm_dirty_briggs_robust05_15klambda_uvtaperbeam_2.fits' #blue: 1.1mm to 0.8mm
b3 = 'best/spt0348_band3_clean1000_cont.fits'
b6 = 'best/spt0348_band6_clean1000_cont.fits'
b7 = 'best/spt0348_band7_clean1000_cont.fits'
#making a 3D cube from the bands
ap.make_rgb_cube([b3, b6, b7], 'spt0348_cube.fits')
ap.make_rgb_cube([b3, b6, b7], 'spt0348_cube')
##making an image from the cubes
ap.make_rgb_image(data='spt0348_cube.fits',
output='spt0348_rgb_astropy.png',
vmax_r=0.4 * 0.000553248,
vmax_g=0.3 * 0.00875461,
vmax_b=0.3 * 0.016697,
vmin_r=1.2 * -7.19859e-05,
vmin_g=1.2 * -0.000468956,
vmin_b=1.2 * -0.000726759)
###show the rgb image of SPT0348
#rgb = ap.FITSFigure('spt0348_cube_2d.fits')
##rgb.recenter(co.convDMS('3:48:42.312'), co.convHMS('-62:20:50.63'),width = 10.0/3600, height= 10.0/3600)
cmd_args = parser.parse_args()
image_r = cmd_args.image_r + ".fits"
image_g = cmd_args.image_g + ".fits"
image_b = cmd_args.image_b + ".fits"
hdul_r = fits.open(image_r)
instrument_r = hdul_r[0].header['FILTER']
hdul_g = fits.open(image_g)
instrument_g = hdul_g[0].header['FILTER']
hdul_b = fits.open(image_b)
instrument_b = hdul_b[0].header['FILTER']
#aplpy.make_rgb_cube(['1000001-JPLUS-01485-v2_iSDSS_swp-crop.fits', '1000001-JPLUS-01485-v2_rSDSS_swp-crop.fits',
#'1000001-JPLUS-01485-v2_gSDSS_swp-crop.fits'], 'JPLUS_cube.fits')
aplpy.make_rgb_cube([image_r, image_g, image_b], image_r.replace('.fits', '_cube.fits'))
aplpy.make_rgb_image(image_r.replace('.fits', '_cube.fits'),
image_r.replace('.fits', '_rgb.png'),
vmin_r=cmd_args.vmin_r, vmax_r=cmd_args.vmax_r, vmin_g=cmd_args.vmin_g,
vmax_g=cmd_args.vmax_g, vmin_b=cmd_args.vmin_b, vmax_b=cmd_args.vmax_b)
#aplpy.make_rgb_image('JPLUS_cube.fits','JPLUS_linear.png')
#hdul = fits.open('JPLUS_cube_2d.fits')
# aplpy.make_rgb_image('JPLUS_cube.fits','JPLUS_rgb.png',
# stretch_r='arcsinh', stretch_g='arcsinh',
# stretch_b='arcsinh')
# With the mask regions, the file may not exist
position = cmd_args.position + ".reg"
red_fits_cutoute2e_fn = '/Users/adam/work/w51/alma/FITS/moments/w51_12co2-1_red73to130_masked_cutoute2e.fits'
redhead.update(cutout_red.wcs.to_header())
red_fits_co = fits.PrimaryHDU(data=cutout_red.data, header=redhead)
red_fits_co.writeto(red_fits_cutoute2e_fn, clobber=True)
blue_fits_cutoute2e_fn = '/Users/adam/work/w51/alma/FITS/moments/w51_12co2-1_blue0to45_masked_cutoute2e.fits'
bluehead.update(cutout_blue.wcs.to_header())
blue_fits_co = fits.PrimaryHDU(data=cutout_blue.data, header=bluehead)
blue_fits_co.writeto(blue_fits_cutoute2e_fn, clobber=True)
rgb_cube_fits = 'e2e_outflow_co_redblue_cycle3green.fits'
if not os.path.exists(rgb_cube_fits):
# does not return anything
aplpy.make_rgb_cube([red_fits_cutoute2e_fn, e2_green_fits, blue_fits_cutoute2e_fn], rgb_cube_fits)
rgb_cube_png = rgb_cube_fits[:-5]+"_auto.png"
rgb_im = aplpy.make_rgb_image(data=rgb_cube_fits, output=rgb_cube_png,
vmax_g=0.017,
vmax_b=6.5,
vmax_r=7.0,
vmin_g=0.0001,
embed_avm_tags=True)
rgb_cube_png = rgb_cube_fits[:-5]+"_loggreen.png"
rgb_im = aplpy.make_rgb_image(data=rgb_cube_fits, output=rgb_cube_png,
vmax_g=0.017,
vmax_b=6.5,
vmax_r=7.0,
vmin_g=0.0001,
gc = aplpy.FITSFigure('j9cv49010_drz.fits',north=True)
gc.show_grayscale(invert=False)
gc.add_scalebar(0.000562,color='white')
gc.scalebar.set_corner('top left')
gc.scalebar.set_label('1kpc')
gc.show_contour(contour,levels=levels,colors=['white','green','yellow','orange','red'])
gc.show_contour(contour1,levels=levels,colors=['white','green','yellow','orange','red'])
gc.axis_labels.hide()
gc.tick_labels.hide()
gc.save('test.png')
'''
# files1=['icom15030_drz.fits','j9cv49020_drz.fits','j9cv49010_drz.fits']
# aplpy.make_rgb_cube(files1,'hst_combine.fits')
# aplpy.make_rgb_image('test2_cube.fits','test_cube.png')
'''
files1=['icom15030_drz.fits','j9cv49020_drz.fits','j9cv49010_drz.fits']
files=['j9cv49020_drz.fits','j9cv49010_drz.fits','u6dw6201r_drz.fits']
def isolate_image_extension(fits_file, extension):
header = fits.getheader(fits_file, extension)
data = fits.getdata(fits_file, extension)
fits.writeto('%s_image.fits' % fits_file.rstrip('.fits'), data, header)
for i in range(len(files)):
files[i]=files[i].replace('.fits','_image.fits')
aplpy.make_rgb_cube(files,output='test_uv'+'_cube.fits',north=True)
aplpy.make_rgb_image('test_uv'+'_cube.fits','test_uv_cube.png')
input_fits_image_band1 = './input/bootes1_ks_2h_20160228_astro_2MASS_0p248rms.fits'
input_fits_image_band2 = './input/bootes1_j_1h12min_20160226_astro_2MASS_0p182rms.fits'
input_fits_image_band3 = './input/bootes1_h_42min_20160226_astro_2MASS_0p220rms.fits'
input_fits_image_band4 = './input/Bootes1_cutout_herschel_250.fits'
#input_fits_image_band5='./input/G12v230_IRAC_Mosaic_36.fits'
#input_fits_image_band6='./input/G12v230_IRAC_Mosaic_45.fits'
band4_present = 1 #=================================================================1:yes 0:no (I band)
band5_present = 1 #=================================================================1:yes 0:no (3.6 band)
band6_present = 1 #=================================================================1:yes 0:no (4.5 band)
#montage.mSubimage(input_fits_image_band5, './G12_3p6_trimmed.fits', ra=, dec=, xsize=0.0023)
aplpy.make_rgb_cube(
[input_fits_image_band1, input_fits_image_band3, input_fits_image_band2],
'Bootes1_cube.fits') #R, G, B
aplpy.make_rgb_image('Bootes1_cube.fits',
'Bootes1_cube.png',
vmin_g=-20.0,
vmin_r=-10.0,
vmin_b=-10.0)
#aplpy.make_rgb_image('NGP7_cube.fits','NGP7_cube.png', vmin_b=-30.0, vmax_b=3000.0, vmax_r=73.0)
#aplpy.make_rgb_image('G12_JHK_cube.fits', 'G12_JHK_cube.png', pmin_r=0., pmax_r=80., pmin_g=0., pmax_g=80., pmin_b=0., pmax_b=80.)
rgb_image = aplpy.FITSFigure('./Bootes1_cube_2d.fits')
rgb_image.show_rgb('Bootes1_cube.png')
rgb_image.show_contour(input_fits_image_band4,
levels=5,
colors='white',
linewidths=0.5)
red_fits_cutoute2e_fn = '/Users/adam/work/w51/alma/FITS/moments/w51_12co2-1_red73to130_masked_cutoute2e.fits'
redhead.update(cutout_red.wcs.to_header())
red_fits_co = fits.PrimaryHDU(data=cutout_red.data, header=redhead)
red_fits_co.writeto(red_fits_cutoute2e_fn, clobber=True)
blue_fits_cutoute2e_fn = '/Users/adam/work/w51/alma/FITS/moments/w51_12co2-1_blue0to45_masked_cutoute2e.fits'
bluehead.update(cutout_blue.wcs.to_header())
blue_fits_co = fits.PrimaryHDU(data=cutout_blue.data, header=bluehead)
blue_fits_co.writeto(blue_fits_cutoute2e_fn, clobber=True)
rgb_cube_fits = 'e2e_outflow_co_redblue_cycle3green.fits'
if not os.path.exists(rgb_cube_fits):
# does not return anything
aplpy.make_rgb_cube(
[red_fits_cutoute2e_fn, e2_green_fits, blue_fits_cutoute2e_fn],
rgb_cube_fits)
rgb_cube_png = rgb_cube_fits[:-5] + "_auto.png"
rgb_im = aplpy.make_rgb_image(data=rgb_cube_fits,
output=rgb_cube_png,
vmax_g=0.017,
vmax_b=6.5,
vmax_r=7.0,
vmin_g=0.0001,
embed_avm_tags=True)
rgb_cube_png = rgb_cube_fits[:-5] + "_loggreen.png"
rgb_im = aplpy.make_rgb_image(data=rgb_cube_fits,
output=rgb_cube_png,
vmax_g=0.017,
import aplpy
# Convert all images to common projection
aplpy.make_rgb_cube(['m1.fits', 'i3.fits', 'i2.fits'], 'rgb.fits')
# Make 3-color image
aplpy.make_rgb_image('rgb.fits', 'rgb.png', vmin_r=20, vmax_r=400,
vmin_g=0, vmax_g=150, vmin_b=-2,vmax_b=50)
# Create a new figure
f = aplpy.FITSFigure('rgb_2d.fits')
# Show the RGB image
f.show_rgb('rgb.png')
# Add contours
f.show_contour('sc.fits', cmap='gist_heat', levels=[0.2,0.4,0.6,0.8,1.0])
# Overlay a grid
f.add_grid()
f.grid.set_alpha(0.5)
# Save image
f.save('plot.png')
default=None,
help="""Set maximum brightness directly - overrides maxfactor - b""")
parser.add_argument("--debug",
action="store_true",
help="Print out verbose debugging info")
cmd_args = parser.parse_args()
image_r = cmd_args.image_r + ".fits"
image_g = cmd_args.image_g + ".fits"
image_b = cmd_args.image_b + ".fits"
#aplpy.make_rgb_cube(['1000001-JPLUS-01485-v2_iSDSS_swp-crop.fits', '1000001-JPLUS-01485-v2_rSDSS_swp-crop.fits',
#'1000001-JPLUS-01485-v2_gSDSS_swp-crop.fits'], 'JPLUS_cube.fits')
aplpy.make_rgb_cube([image_r, image_g, image_b], 'JPLUS_cube.fits')
aplpy.make_rgb_image('JPLUS_cube.fits',
'JPLUS_rgb.png',
vmin_r=cmd_args.vmin_r,
vmax_r=cmd_args.vmax_r,
vmin_g=cmd_args.vmin_g,
vmax_g=cmd_args.vmax_g,
vmin_b=cmd_args.vmin_b,
vmax_b=cmd_args.vmax_b)
#aplpy.make_rgb_image('JPLUS_cube.fits','JPLUS_linear.png')
#hdul = fits.open('JPLUS_cube_2d.fits')
# aplpy.make_rgb_image('JPLUS_cube.fits','JPLUS_rgb.png',
# stretch_r='arcsinh', stretch_g='arcsinh',
# stretch_b='arcsinh')
dec_0 = sourList['dec'][isour]
coor = coords.SkyCoord(ra_0, dec_0, frame='icrs', unit=(u.deg, u.deg))
ra_0 = coor.fk5.ra.deg
dec_0 = coor.fk5.dec.deg
c1 = coords.SkyCoord(ra_0, dec_0, frame='fk5', unit=(u.deg, u.deg))
c2 = coords.SkyCoord(ra_0, dec_0 + 0.01, frame='fk5', unit=(u.deg, u.deg))
c1G = c1.galactic
ang = c1G.position_angle(c2.galactic).deg
pa = paG + 90 - ang
#radi = sourList['amaj'][isour] / 3600.0 / 2
ap.make_rgb_cube([
iracDir + sour_name + '/' + sour_name + '_I4.fits',
iracDir + sour_name + '/' + sour_name + '_I2.fits',
iracDir + sour_name + '/' + sour_name + '_I1.fits'
],
iracDir + sour_name + '/' + sour_name +
'Spitzer_cube.fits',
system='EQUJ',
north='Ture')
ap.make_rgb_image(
iracDir + sour_name + '/' + sour_name + 'Spitzer_cube.fits',
iracDir + sour_name + '/' + sour_name + '_Spitzer_rgb.png',
pmin_r=0.5,
pmax_r=99.6,
pmin_g=0.5,
pmax_g=99.6,
pmin_b=0.5,
pmax_b=99.6,
stretch_r='log',
def make_RGBplot(fns, ofn, stretch = 'linear',
plims = [None, None, None, None, None, None],
vlims = [None, None, None, None, None, None],
title = None,
scalebar = None,
):
'''Creates an RGB image from three fits files.
:Args:
fn: list strings
The filename (+path!) fo the 3 fits file to display (in R, G and B orders).
ofn: string
The filneame (+path) of the output file.
stretch: string [default: 'log']
The stretch to apply to the data, e.g. 'linear', 'log', 'arcsinh'.
plims: list of floats [default: [None, None, None, None, None, None]]
The limiting percentiles for the plot, as
[pmin_r, pmax_r, pmin_g, pmax_g, pmin_b, pmax_b]
vlims: list of floats [default: [None, None, None, None, None, None]]
The limtiing values for the plot (superseeds plims), as
[vmin_r, vmax_r, vmin_g, vmax_g, vmin_b, vmax_b]
scalebar: list [default: None]
If set, adds a scale bar to the plot. Format: [lenght arcsec, length kpc, loc]
:Returns:
out: True
Always.
:Notes:
This function absolutely requires WCS coordinates, and a 2-D array.
'''
# First, make an RGB cube
fn_RGB = os.path.join('.','RGB_tmp_cube.fits')
aplpy.make_rgb_cube(fns, fn_RGB)
# And an RGB image
fn_RGB_im = os.path.join('.','RGB_tmp_im.png')
aplpy.make_rgb_image(fn_RGB, fn_RGB_im,
stretch_r=stretch,
stretch_g=stretch,
stretch_b=stretch,
vmin_r = vlims[0],
vmin_g = vlims[2],
vmin_b = vlims[4],
vmax_r = vlims[1],
vmax_g = vlims[3],
vmax_b = vlims[5],
pmin_r = plims[0],
pmax_r = plims[1],
pmin_g = plims[2],
pmax_g = plims[3],
pmin_b = plims[4],
pmax_b = plims[5],
embed_avm_tags = False, make_nans_transparent=True)
# Plot the RGB image using the 2d image to indicate the projection
plt.close(1)
fig1 = plt.figure(1, figsize=(10,9))
fn_RGB_2d = os.path.join('.','RGB_tmp_cube_2d.fits')
ax1 = aplpy.FITSFigure(fn_RGB_2d, figure=fig1)
ax1.show_rgb(fn_RGB_im, interpolation='nearest')
ax1.set_tick_color('k')
if not(title is None):
ax1.set_title(title, y=1.025)
ax1.add_grid()
# Make it look pretty
ax1.grid.set_color('k')
ax1.grid.set_linestyle('dotted')
ax1.set_nan_color((0.5,0.5,0.5))
ax1._ax1.set_axis_bgcolor((0.5, 0.5, 0.5))
# Do I want to add a scalebar ?
if not(scalebar is None):
show_scale(ax1, scale_length = scalebar[:2], scale_loc = scalebar[2])
# Make it look pretty
ax1.set_axis_labels(ylabel='Dec. (J2000)')
ax1.set_axis_labels(xlabel='R.A. (J2000)')
ax1.tick_labels.set_xformat('hh:mm:ss')
ax1.tick_labels.set_yformat('dd:mm:ss')
# Save it
fig1.savefig(ofn, bbox_inches='tight')
# And remember to delete all the temporary files
for f in [fn_RGB_im, fn_RGB_2d, fn_RGB]:
os.remove(f)
return True
from astropy import units as u
import pylab as pl
from spectral_cube import SpectralCube
import aplpy
import os
import paths
green_fits = '/Users/adam/work/w51/paper_w51_evla/data/W51Ku_BDarray_continuum_2048_both_uniform.hires.clean.image.fits'
blue_fits = '/Users/adam/work/w51/alma/FITS/moments/w51_12co2-1_blue0to45_masked.fits'
red_fits = '/Users/adam/work/w51/alma/FITS/moments/w51_12co2-1_red73to130_masked.fits'
rgb_cube_fits = 'outflow_co_redblue_kucont_green.fits'
if not os.path.exists(rgb_cube_fits):
# does not return anything
aplpy.make_rgb_cube([red_fits, green_fits, blue_fits], rgb_cube_fits)
rgb_cube_png = rgb_cube_fits[:-5] + "_auto.png"
rgb_im = aplpy.make_rgb_image(data=rgb_cube_fits,
output=rgb_cube_png,
embed_avm_tags=True)
rgb_cube_png = rgb_cube_fits[:-5] + "_loggreen.png"
rgb_im = aplpy.make_rgb_image(data=rgb_cube_fits,
output=rgb_cube_png,
stretch_g='log',
embed_avm_tags=True)
rgb_cube_png = rgb_cube_fits[:-5] + "_asinhgreen.png"
rgb_im = aplpy.make_rgb_image(data=rgb_cube_fits,
output=rgb_cube_png,
stretch_g='arcsinh',
red_fits_cutoute2e_fn = '/Users/adam/work/w51/alma/FITS/moments/w51_LB_SiO_red74to118_masked_cutoute2e.fits'
redhead.update(cutout_red.wcs.to_header())
red_fits_co = fits.PrimaryHDU(data=cutout_red.data, header=redhead)
red_fits_co.writeto(red_fits_cutoute2e_fn, clobber=True)
blue_fits_cutoute2e_fn = '/Users/adam/work/w51/alma/FITS/moments/w51_LB_SiO_bluem32to55_masked_cutoute2e.fits'
bluehead.update(cutout_blue.wcs.to_header())
blue_fits_co = fits.PrimaryHDU(data=cutout_blue.data, header=bluehead)
blue_fits_co.writeto(blue_fits_cutoute2e_fn, clobber=True)
e2_rgb_cube_fits = 'e2e_outflow_SiO_redblue_cycle3green.fits'
if not os.path.exists(e2_rgb_cube_fits):
# does not return anything
aplpy.make_rgb_cube([red_fits_cutoute2e_fn, e2_green_fits, blue_fits_cutoute2e_fn], e2_rgb_cube_fits)
rgb_cube_png = e2_rgb_cube_fits[:-5]+"_auto.png"
rgb_im = aplpy.make_rgb_image(data=e2_rgb_cube_fits, output=rgb_cube_png,
vmax_g=0.017,
vmax_b=0.3,
vmax_r=0.6,
vmin_g=0.0001,
embed_avm_tags=True)
rgb_cube_png = e2_rgb_cube_fits[:-5]+"_loggreen.png"
rgb_im = aplpy.make_rgb_image(data=e2_rgb_cube_fits, output=rgb_cube_png,
vmax_g=0.017,
vmax_b=0.3,
vmax_r=0.6,
vmin_g=0.0001,
SDOM_ZP_V = np.std(ZP_V, axis=0) / np.sqrt(5)
mean_SDOM_ZP_V = np.mean(SDOM_ZP_V) / np.sqrt(3)
#ZP in V filter is 21.68807 +/- 0.0058
#################
#################
################## RBG IMAGING ########################
#################
aplpy.make_rgb_cube([
dir + '/Data_r/mosaic_r/mosaic.fits', dir + '/Data_v/mosaic_v/mosaic.fits',
dir + '/Data_b/mosaic_b/mosaic.fits'
], dir + '/rgb_cube.fits')
aplpy.make_rgb_image(dir + '/rgb_cube.fits',
dir + '/cluster_rgb.png',
embed_avm_tags=False)
fig = aplpy.FITSFigure(dir + '/rgb_cube_2d.fits')
fig.show_rgb(dir + '/cluster_rgb.png')
fig.add_grid()
fig.grid.set_linestyle('dotted')
############# HR Diagram ################
mosaic_area_b = fits.getdata(dir + '/Data_b/mosaic_b/mosaic_area.fits')
def zoomfigure(
target=e2e,
targetname="e2e",
radius=7.5 * u.arcsec,
cutout="e2e8",
zoom_radius=3 * u.arcsec,
tick_spacing=1.8 * u.arcsec,
):
fn = paths.dpath("merge/cutouts/W51_b6_7M_12M.HNCO10010-909.image.pbcor_{0}cutout.fits".format(cutout))
m0hnco = get_mom0(fn, iterate=False)
cutout_cont = Cutout2D(cont_fits[0].data, target, radius, wcs=wcs.WCS(cont_fits[0].header))
cutout_ch3oh = Cutout2D(m0ch3oh.value, target, radius, wcs=wcs.WCS(m0ch3oh.header))
cutout_hnco = Cutout2D(m0hnco.value, target, radius, wcs=wcs.WCS(m0hnco.header))
cont_fits_cutout = fits.PrimaryHDU(data=cutout_cont.data, header=cutout_cont.wcs.to_header())
ch3oh_fits_cutout = fits.PrimaryHDU(data=cutout_ch3oh.data, header=cutout_ch3oh.wcs.to_header())
hnco_fits_cutout = fits.PrimaryHDU(data=cutout_hnco.data, header=cutout_hnco.wcs.to_header())
cont_fits_fn = "rgb/continuum_{0}_cutout.fits".format(targetname)
hnco_fits_fn = "rgb/hnco_{0}_cutout.fits".format(targetname)
ch3oh_fits_fn = "rgb/ch3oh_{0}_cutout.fits".format(targetname)
cont_fits_cutout.writeto(cont_fits_fn, clobber=True)
ch3oh_fits_cutout.writeto(ch3oh_fits_fn, clobber=True)
hnco_fits_cutout.writeto(hnco_fits_fn, clobber=True)
rgb_cube_fits = "{0}_ch3oh_hnco_cont.fits".format(targetname)
if not os.path.exists(rgb_cube_fits):
# does not return anything
aplpy.make_rgb_cube([ch3oh_fits_fn, hnco_fits_fn, cont_fits_fn], rgb_cube_fits)
rgb_cube_png = rgb_cube_fits[:-5] + "_auto.png"
rgb_im = aplpy.make_rgb_image(data=rgb_cube_fits, output=rgb_cube_png, embed_avm_tags=True)
rgb_cube_png = rgb_cube_fits[:-5] + "_logcont.png"
rgb_im = aplpy.make_rgb_image(
data=rgb_cube_fits,
output=rgb_cube_png,
# vmin_b=0.005,
# vmax_b=0.15,
stretch_b="log",
embed_avm_tags=True,
)
# rgb_cube_png = rgb_cube_fits[:-5]+"_asinhgreen.png"
# rgb_im = aplpy.make_rgb_image(data=rgb_cube_fits, output=rgb_cube_png,
# vmax_g=0.017,
# vmax_b=6.5,
# vmax_r=7.0,
# vmin_g=0.0001,
# stretch_g='arcsinh', embed_avm_tags=True)
#
#
pl.rcParams["font.size"] = 18
fig1 = pl.figure(1)
fig1.clf()
F = aplpy.FITSFigure(rgb_cube_png, figure=fig1)
F.show_rgb(rgb_cube_png)
# F.recenter(290.93315, 14.509584, radius=0.00075)
F.recenter(target.ra.deg, target.dec.deg, radius=zoom_radius.to(u.deg).value)
F.add_scalebar((0.025 * u.pc / (5400 * u.pc)).to(u.deg, u.dimensionless_angles()))
F.scalebar.set_label("5000 au / 0.025 pc")
F.scalebar.set_color("w")
F.set_tick_xspacing(tick_spacing.to(u.deg).value)
F.add_label(0.05, 0.95, "CH$_3$OH", relative=True, color="r", horizontalalignment="left")
F.add_label(0.05, 0.91, "HNCO", relative=True, color="g", horizontalalignment="left")
F.add_label(0.05, 0.87, "Continuum", relative=True, color="b", horizontalalignment="left")
F.save(paths.fpath("rgb_zooms/W51{0}_ch3oh_hnco_continuum_aplpy.png".format(targetname)))
F.save(paths.fpath("rgb_zooms/W51{0}_ch3oh_hnco_continuum_aplpy.pdf".format(targetname)))
F.show_contour(
paths.vpath("data/W51Ku_BDarray_continuum_2048_both_uniform.hires.clean.image.fits"),
levels=np.array([0.0015, 0.0045, 0.0135, 0.0270, 0.054, 0.108]) * 1.25,
colors=["w"] * 7,
layer="evla_cont",
)
F.save(paths.fpath("rgb_zooms/W51{0}_ch3oh_hnco_continuum_aplpy_kucontours.png".format(targetname)))
F.save(paths.fpath("rgb_zooms/W51{0}_ch3oh_hnco_continuum_aplpy_kucontours.pdf".format(targetname)))
import aplpy
# Reproject all images to same projection (requires Montage and
# python-montage)
aplpy.make_rgb_cube(["data/2MASS_k.fits.gz", "data/2MASS_h.fits.gz", "data/2MASS_j.fits.gz"], "2MASS_cube.fits")
# Make an RGB image with embedded AVM metadata containing the WCS information
# (requires PyAVM). This function takes many arguments to control levels and
# stretch functions. See the full documentation for more details
aplpy.make_rgb_image("2MASS_cube.fits", "2MASS_rgb.png", embed_avm_tags=True)
# Make the plot using the RGB image directly
f = aplpy.FITSFigure("2MASS_rgb.png")
f.show_rgb()
f.save("make_rgb.png")
pmax_b=99.9,
pmax_g=99.9999,
redline=fnku,
blueline='HC3N24-23',
greenline='CH3OH422-312')
make_rgb('hc3n_ch3oh_ocs_rgb.fits',
greenline='OCS18-17',
redline='HC3N24-23',
blueline='CH3OH422-312')
rgb_cube_fits = 'full_h2co_rgb.fits'
if not os.path.exists(rgb_cube_fits):
# does not return anything
aplpy.make_rgb_cube([
fn303,
fn321,
fn322,
], rgb_cube_fits)
rgb_cube_png = rgb_cube_fits[:-5] + "_auto.png"
rgb_im = aplpy.make_rgb_image(data=rgb_cube_fits,
output=rgb_cube_png,
embed_avm_tags=True)
rgb_cube_png = rgb_cube_fits[:-5] + "_setlevels.png"
rgb_im = aplpy.make_rgb_image(data=rgb_cube_fits,
output=rgb_cube_png,
vmin_b=-0.005,
vmax_b=0.4,
vmin_g=-0.005,
vmax_g=0.4,
"""
import aplpy
from pathlib import Path
import os
"""
SiO first ...
"""
os.chdir(
'/Users/danielwalker/Dropbox/Papers_DB/Brick_core/SiO_13CO_figs/Moments_SiO/'
)
if Path('./rgb_cubes/SiO_29_42__43_56.fits').exists() == False:
aplpy.make_rgb_cube([
'SiO_mom0_43_to_56.fits', 'SiO_mom0_29_to_42.fits',
'SiO_mom0_29_to_42.fits'
], './rgb_cubes/SiO_29_42__43_56.fits')
aplpy.make_rgb_image('./rgb_cubes/SiO_29_42__43_56.fits',
'./rgb_pngs/SiO_29_42__43_56.png',
pmin_r=45,
pmax_r=100,
pmin_g=80,
pmax_g=100,
pmin_b=16,
pmax_b=99.9)
if Path('./rgb_cubes/SiO_29_36__23_29__16_22.fits').exists() == False:
aplpy.make_rgb_cube([
'SiO_mom0_29_to_36.fits', 'SiO_mom0_23_to_29.fits',
'SiO_mom0_16_to_22.fits'
], './rgb_cubes/SiO_29_36__23_29__16_22.fits')
def make_RGBplot(
fns,
ofn,
stretch='linear',
plims=[None, None, None, None, None, None],
vlims=[None, None, None, None, None, None],
title=None,
scalebar=None,
):
'''Creates an RGB image from three fits files.
:Args:
fn: list strings
The filename (+path!) fo the 3 fits file to display (in R, G and B orders).
ofn: string
The filneame (+path) of the output file.
stretch: string [default: 'log']
The stretch to apply to the data, e.g. 'linear', 'log', 'arcsinh'.
plims: list of floats [default: [None, None, None, None, None, None]]
The limiting percentiles for the plot, as
[pmin_r, pmax_r, pmin_g, pmax_g, pmin_b, pmax_b]
vlims: list of floats [default: [None, None, None, None, None, None]]
The limtiing values for the plot (superseeds plims), as
[vmin_r, vmax_r, vmin_g, vmax_g, vmin_b, vmax_b]
scalebar: list [default: None]
If set, adds a scale bar to the plot. Format: [lenght arcsec, length kpc, loc]
:Returns:
out: True
Always.
:Notes:
This function absolutely requires WCS coordinates, and a 2-D array.
'''
# First, make an RGB cube
fn_RGB = os.path.join('.', 'RGB_tmp_cube.fits')
aplpy.make_rgb_cube(fns, fn_RGB)
# And an RGB image
fn_RGB_im = os.path.join('.', 'RGB_tmp_im.png')
aplpy.make_rgb_image(fn_RGB,
fn_RGB_im,
stretch_r=stretch,
stretch_g=stretch,
stretch_b=stretch,
vmin_r=vlims[0],
vmin_g=vlims[2],
vmin_b=vlims[4],
vmax_r=vlims[1],
vmax_g=vlims[3],
vmax_b=vlims[5],
pmin_r=plims[0],
pmax_r=plims[1],
pmin_g=plims[2],
pmax_g=plims[3],
pmin_b=plims[4],
pmax_b=plims[5],
embed_avm_tags=False,
make_nans_transparent=True)
# Plot the RGB image using the 2d image to indicate the projection
plt.close(1)
fig1 = plt.figure(1, figsize=(10, 9))
fn_RGB_2d = os.path.join('.', 'RGB_tmp_cube_2d.fits')
ax1 = aplpy.FITSFigure(fn_RGB_2d, figure=fig1)
ax1.show_rgb(fn_RGB_im, interpolation='nearest')
ax1.set_tick_color('k')
if not (title is None):
ax1.set_title(title, y=1.025)
ax1.add_grid()
# Make it look pretty
ax1.grid.set_color('k')
ax1.grid.set_linestyle('dotted')
ax1.set_nan_color((0.5, 0.5, 0.5))
ax1._ax1.set_axis_bgcolor((0.5, 0.5, 0.5))
# Do I want to add a scalebar ?
if not (scalebar is None):
show_scale(ax1, scale_length=scalebar[:2], scale_loc=scalebar[2])
# Make it look pretty
ax1.set_axis_labels(ylabel='Dec. (J2000)')
ax1.set_axis_labels(xlabel='R.A. (J2000)')
ax1.tick_labels.set_xformat('hh:mm:ss')
ax1.tick_labels.set_yformat('dd:mm:ss')
# Save it
fig1.savefig(ofn, bbox_inches='tight')
# And remember to delete all the temporary files
for f in [fn_RGB_im, fn_RGB_2d, fn_RGB]:
os.remove(f)
return True
