def plot_imag(fig,imag,mask,wcs,ftsize='xx-large',coor=None,title=None,beam=None,cmap='hot',colorbar=False,size=10):
ax = fig.add_subplot(1,1,1,projection=wcs)
# ------------------------
# Display the image
im = ax.imshow(imag,origin='lower',interpolation='nearest',cmap=colormap(cmap),\
aspect='equal',vmin=0.)
ax.contour(mask,linewidths=4,levels=[0.001],colors='blue')
# ------------------------
# coordinates
ra = ax.coords['ra']
de = ax.coords['dec']
ra.set_axislabel('R.A. (J2000)',minpad=0.5,size=ftsize)
de.set_axislabel('Dec. (J2000)',minpad=0.5,size=ftsize)
ra.set_separator(('$\mathrm{^h}$','$\mathrm{^m}$'))
ra.set_ticklabel(size=ftsize)
de.set_ticklabel(size=ftsize)
# ------------------------
if title is not None:
ax.set_title(title,fontsize=ftsize)
if coor is not None:
ax.set_xlim(coor[0]-size,coor[0]+size)
ax.set_ylim(coor[1]-size,coor[1]+size)
if colorbar:
cbar = ax.figure.colorbar(im)
cbar.ax.set_ylabel('mJy$\,$beam$^{-1}$ km$\,$s$^{-1}$',fontsize=ftsize)
if beam is not None:
bm = patches.Circle((5,5),radius=args.beam/2,edgecolor='k',facecolor='w',alpha=0.5) # pixel coordinates
ax.add_patch(bm)
return ax
def plot_imag(fig,
imag,
mask,
wcs,
ftsize='x-large',
coor=None,
title=None,
cmap='hot'):
ax = fig.add_subplot(1, 2, 2, projection=wcs)
# ------------------------
# Display the image
im = ax.imshow(imag,origin='lower',interpolation='nearest',cmap=colormap(cmap),\
aspect='equal',vmin=0.)#,norm=LogNorm()) #,vmin=0.0005,vmax=0.005
ax.contour(mask, linewidths=2, levels=[0.001], alpha=0.8, colors='grey')
# ------------------------
# coordinates
ra = ax.coords['ra']
de = ax.coords['dec']
ra.set_axislabel('R.A. (J2000)', minpad=0.5, size=ftsize)
de.set_axislabel('Dec. (J2000)', minpad=0.5, size=ftsize)
ra.set_separator(('$\mathrm{^h}$', '$\mathrm{^m}$'))
ra.set_ticklabel(size=ftsize)
de.set_ticklabel(size=ftsize)
# ------------------------
if title is not None:
ax.set_title(title, fontsize=ftsize)
if coor is not None:
ax.plot(coor[0], coor[1], marker='*')
cbar = ax.figure.colorbar(im)
cbar.ax.set_ylabel('mJy$\,$beam$^{-1}$ km$\,$s$^{-1}$', fontsize=ftsize)
return ax
def plot_image(file_in,
file_out=None,
file_contour=None,
file_reg=None,
resize=None,
contour=False,
levels=None,
contour_color='#d0d0d0',
plot=False,
oformat='png',
skycoor='equ',
vmin=None,
vmax=None,
pmin=0.25,
pmax=99.75,
stretch='linear',
vmid=None,
exponent=2,
cmap='hot',
beam=None,
colorbar=None,
dendro=None,
file_catalog=None,
addgal=True,
save=True,
smooth=None,
beamcolor='blue'):
if smooth == 0:
smooth = None
fig = aplpy.FITSFigure(file_in)
fig.show_colorscale(vmin=vmin,
vmax=vmax,
pmin=pmin,
pmax=pmax,
cmap=colormap(cmap),
aspect='equal',
smooth=smooth,
stretch=stretch,
vmid=vmid,
exponent=exponent)
# fig.hide_colorscale()
if resize is not None:
fig.recenter(resize[0], resize[1], width=resize[2], height=resize[3])
#-------------------------------------------------------------------
# ADD beam
if beam is not None:
fig.add_beam(major=beam / 60,
minor=beam / 60,
angle=0,
corner='bottom left')
fig.beam.set_alpha(0.5)
fig.beam.set_edgecolor(beamcolor)
fig.beam.set_facecolor('white')
fig.beam.set_linewidth(3)
#-------------------------------------------------------------------
# fig.show_circles([50.05,], [-0.85,], 0.028,color='white',linewidth=1)
# fig.add_label(50.05, -0.95,"FWHM 3.4'",color='white')
#-------------------------------------------------------------------
if addgal:
l = np.arange(30, 70, 0.05)
b0 = np.zeros(int((70 - 30) / 0.05))
bp = np.zeros(int((70 - 30) / 0.05)) + 0.5
bm = np.zeros(int((70 - 30) / 0.05)) - 0.5
gal_c0 = SkyCoord(l, b0, frame=Galactic, unit="deg")
gal_cp = SkyCoord(l, bp, frame=Galactic, unit="deg")
gal_cm = SkyCoord(l, bm, frame=Galactic, unit="deg")
ra0 = gal_c0.icrs.ra.value
rap = gal_cp.icrs.ra.value
ram = gal_cm.icrs.ra.value
dec0 = gal_c0.icrs.dec.value
decp = gal_cp.icrs.dec.value
decm = gal_cm.icrs.dec.value
fig.show_lines([np.array([ra0,dec0]),np.array([rap,decp]),np.array([ram,decm])], \
color='darkgrey', linewidths=2, linestyle=['-','--','--'])
fig.add_label(283.95,
2.18,
r"b=$0^{\circ}$",
color='black',
fontsize=14)
fig.add_label(283.38,
2.18,
r"b=$0.5^{\circ}$",
color='black',
fontsize=14)
fig.add_label(284.42,
1.8,
r"b=$-0.5^{\circ}$",
color='black',
fontsize=14)
if skycoor == 'gal':
fig.axis_labels.set_xtext('Galactic Longitude')
fig.axis_labels.set_ytext('Galactic Latitude')
fig.tick_labels.set_xformat('dd.d')
fig.tick_labels.set_yformat('dd.d')
fig.ticks.set_xspacing(0.5)
fig.ticks.set_yspacing(0.5)
#fig.ticks.set_minor_frequency(5)
else:
z = 0
fig.axis_labels.set_font(size='xx-large')
fig.tick_labels.set_font(size='xx-large')
fig.ticks.show_x()
fig.ticks.show_y()
fig.ticks.set_linewidth(1)
fig.ticks.set_length(2)
fig.ticks.set_color('black')
fig.ticks.show()
fig.set_nan_color('white')
if colorbar is not None:
fig.add_colorbar()
fig.colorbar.show()
fig.colorbar.set_axis_label_text(colorbar)
fig.colorbar.set_axis_label_font(size='xx-large')
fig.colorbar.set_font(size='xx-large')
#-------------------------------------------
# DS9 regions
if file_reg is not None:
fig.show_regions(file_reg)
#-------------------------------------------
# add contour
#-------------------------------------------
if contour:
if levels is not None:
if file_contour is None:
file_contour = file_in
fig.show_contour(file_contour,
levels=levels,
smooth=1,
colors=contour_color,
linewidths=1)
else:
print("contour levels is not set")
#------------------------
# Plot all leaves and branches on full frame of Moment0 map.
#------------------------
# add sources in catalog
# add_source(ax0,catalog,wcs)
# ------------------------
# leaf label
list_idx = [] # raw index
list_idv = [] # sorted index
list_peak = [] # raw peaks
for i, struc in enumerate(dendro.leaves):
peak = struc.get_peak()[1]
list_peak.append(peak)
list_idx.append(struc.idx)
peak_ind = np.argsort(np.array(list_peak))[::-1]
leaves_idx_arr = np.array(list_idx)[peak_ind]
# ------------------------
colors = ['blue', 'red', 'green']
c = 1
for i, struc in enumerate(dendro.trunk):
if struc.is_leaf:
leaf_label = add_leaf_label(fig, leaves_idx_arr, struc)
color = colors[0]
subtree = []
line = 'solid'
elif struc.is_branch: # branch
color = colors[c]
c = c + 1
subtree = struc.descendants
line = 'dashed'
mask = struc.get_mask().mean(axis=0)
fig.show_contour(mask,
linewidths=1.5,
levels=[0.001],
alpha=0.8,
colors=[color],
linestyles=line) #,smooth=1)
fig.add_label(283.95,
2.18,
r"b=$0^{\circ}$",
color='black',
fontsize=14)
print(color)
for j, sub_struc in enumerate(subtree):
if sub_struc.is_leaf:
leaf_label = add_leaf_label(fig, leaves_idx_arr, sub_struc)
mask = sub_struc.get_mask().mean(axis=0)
fig.show_contour(mask,
linewidths=1.5,
levels=[0.001],
alpha=0.8,
colors=[color]) #,smooth=1)
if file_catalog is not None:
add_source(fig, file_catalog)
if save:
if file_out is None:
file_out = 'm0-clumps_{}.png'.format(cmap)
fig.save(file_out, dpi=300, format=oformat, adjust_bbox=True)
if plot:
plt.show()
fig.close()
return 0
def main(args):
# #------------------------
# # Load DataCube
# #------------------------
# print('Load DataCube')
# hdu = fits.open(args.file_cube)[0]
# hdr = hdu.header
# wcs = WCS(header=hdr).celestial
# data = hdu.data
# nchan = data.shape[0]
# velo = (np.arange(nchan) - hdr['CRPIX3'] + 1) * hdr['CDELT3'] + hdr['CRVAL3']
# ny = data.shape[1]
# nx = data.shape[2]
#
# # unit convert: Jy/beam -> mJy/pix
# beam = 4.7 # arcmin
# pix = 1.0 # arcmin
# pix_over_beam = pix**2/((beam/2)**2*np.pi)
# data = data * 1000 * pix_over_beam # x Jy/beam = (x * pix/beam) Jy/pix
# imag0 = data[args.chan_0:args.chan_1,:,:].mean(axis=0)
# print(imag0.shape)
#------------------------
# Load Moment 0 map
#------------------------
hdu = fits.open(args.file_map)[0]
hdr = hdu.header
wcs = WCS(header=hdr).celestial
imag0 = hdu.data
print(imag0.shape)
#------------------------
# Load dendrogram
#------------------------
print('Load Dendrogram')
d = Dendrogram.load_from(args.file_d + '.hdf5')
#------------------------
# Plot all leaves and branches on full frame of Moment0 map.
#------------------------
norm = simple_norm(imag0,
stretch='asinh',
asinh_a=0.18,
min_percent=5,
max_percent=100)
fig0 = plt.figure(figsize=(8, 8))
ax0 = fig0.add_subplot(1, 1, 1, projection=wcs)
im0 = ax0.imshow(imag0,origin='lower',interpolation='nearest',cmap=colormap(args.cmap),\
aspect='equal')#,norm=norm)
# coordinates
if args.proj == 'equ':
ra0 = ax0.coords['ra']
de0 = ax0.coords['dec']
ra0.set_axislabel('R.A. (J2000)', minpad=0.5, size="xx-large")
de0.set_axislabel('Dec. (J2000)', minpad=0.5, size="xx-large")
ra0.set_separator(('$\mathrm{^h}$', '$\mathrm{^m}$'))
ra0.set_ticklabel(size="xx-large")
de0.set_ticklabel(size="xx-large")
elif args.proj == 'gal':
l0 = ax0.coords['glon']
b0 = ax0.coords['glat']
l0.set_axislabel('l deg', minpad=0.5, size="xx-large")
b0.set_axislabel('b deg', minpad=0.5, size="xx-large")
l0.set_ticklabel(size="xx-large")
b0.set_ticklabel(size="xx-large")
# beam
if args.beam is not None:
beam = patches.Circle((5, 5),
radius=args.beam / 2,
edgecolor='k',
facecolor='w',
alpha=0.5) # pixel coordinates
ax0.add_patch(beam)
# ------------------------
# add sources in catalog
if args.file_c is not None:
add_source(ax0, args.file_c, wcs)
# ------------------------
# leaf label
list_idx = [] # raw index
list_idv = [] # sorted index
list_peak = [] # raw peaks
for i, struc in enumerate(d.leaves):
peak = struc.get_peak()[1]
list_peak.append(peak)
list_idx.append(struc.idx)
peak_ind = np.argsort(np.array(list_peak))[::-1]
leaves_idx_arr = np.array(list_idx)[peak_ind]
# ------------------------
colors = ['blue', 'red', 'green']
c = 1
for i, struc in enumerate(d.trunk):
if struc.is_leaf:
leaf_label = add_leaf_label(ax0, leaves_idx_arr, struc)
file_out = 'leaf_{:d}_{}.png'.format(leaf_label, args.cmap)
color = colors[0]
subtree = []
line = 'solid'
elif struc.is_branch: # branch
file_out = 'branch_{:d}_{}.png'.format(struc.idx, args.cmap)
color = colors[c]
c = c + 1
subtree = struc.descendants
line = 'dashed'
mask = struc.get_mask().mean(axis=0)
ax0.contour(mask,
linewidths=1.5,
levels=[0.001],
alpha=0.8,
colors=[color],
linestyles=line)
for j, sub_struc in enumerate(subtree):
if sub_struc.is_leaf:
leaf_label = add_leaf_label(ax0, leaves_idx_arr, sub_struc)
file_out = 'leaf_{:d}_{}.png'.format(leaf_label, args.cmap)
mask = sub_struc.get_mask().mean(axis=0)
print(mask.shape)
ax0.contour(mask,
linewidths=1.5,
levels=[0.001],
alpha=0.8,
colors=[color])
fig0.savefig('m0-clumps_{}.png'.format(args.cmap),
dpi=300,
format='png',
bbox_inches='tight')
return 0