]
cubes = [
hpath(x) for x in (
"H2CO_321220_to_303202_cube_bl.fits",
"H2CO_321220_to_303202_cube_smooth_bl.fits",
"APEX_H2CO_303_202_bl.fits",
"APEX_H2CO_321_220_bl.fits",
"APEX_H2CO_322_221_bl.fits",
)
] + [
mpath(x) for x in (
"APEX_13CO_2014_merge.fits",
"APEX_C18O_2014_merge.fits",
"APEX_H2CO_merge_high_plait_all.fits",
)
] + [molpath(x) for x in ("APEX_SiO_54_bl.fits", )]
dendrograms = [hpath(x) for x in ("DendroMask_H2CO303202.hdf5", )] + [
tpath(x) for x in (
"fitted_line_parameters_Chi2Constraints.ipac",
"PPV_H2CO_Temperature.ipac",
)
]
if not os.path.isdir('cds'):
os.mkdir('cds')
if not os.path.isdir('cds/integrated'):
os.mkdir('cds/integrated')
if not os.path.isdir('cds/cubes'):
os.mkdir('cds/cubes')
if not os.path.isdir('cds/catalogs'):
blue = pl.mpl.colors.LinearSegmentedColormap(
'blue', {
'red': [(0, 0, 0), (1, 1, 1)],
'green': [(0, 0, 0), (1, 1, 1)],
'blue': [(0, 1, 1), (1, 1, 1)]
})
if 'yt13co' not in locals():
cube13co = spectral_cube.SpectralCube.read(
paths.mpath('APEX_13CO_2014_merge.fits'))
yt13co = cube13co.with_mask(cube13co > 0.1).to_yt()
mask = cube13co > 0.2
if 'cube_h2co303' not in locals():
cube_sio = SpectralCube.read(paths.molpath('APEX_SiO_54_bl.fits'))
# HACK:
mask._wcs = cube_sio.wcs
ytsio = cube_sio.with_mask(mask).to_yt()
cube_h2co303 = SpectralCube.read(
paths.molpath('APEX_H2CO_303_202_bl.fits'))
mask._wcs = cube_h2co303.wcs
yth2co303 = cube_h2co303.with_mask(mask).to_yt()
cube_h2co321 = SpectralCube.read(
paths.molpath('APEX_H2CO_321_220_bl.fits'))
mask._wcs = cube_h2co321.wcs
yth2co321 = cube_h2co321.with_mask(mask).to_yt()
#temcube = SpectralCube.read(paths.dpath('H2CO_321220_to_303202_cube_bl_temperature.fits'))
#mask._wcs = temcube.wcs
#yttem = temcube.with_mask(mask).to_yt()
coords = coordinates.SkyCoord(glon * u.deg, glat * u.deg, frame='galactic')
P = pvextractor.Path(coords, width=300 * u.arcsec)
vlos = glon * 0 # TODO: replace this
dl = (glon[1:] - glon[:-1])
db = (glat[1:] - glat[:-1])
dist = (dl**2 + db**2)**0.5
cdist = np.zeros(dist.size + 1)
cdist[1:] = dist.cumsum()
molecules = ('13CO_2014_merge', 'C18O_2014_merge', 'H2CO_303_202_bl',
'SiO_54_bl')
filenames = [
molpath('APEX_{0}.fits'.format(molecule)) for molecule in molecules
]
molecules = molecules + (
'H2CO_TemperatureFromRatio',
'H2CO_TemperatureFromRatio_smooth',
'H2CO_Ratio',
'H2CO_Ratio_smooth',
#'H2CO_DendrogramTemperature',
#'H2CO_DendrogramTemperature_smooth',
#'H2CO_DendrogramTemperature_Leaves',
#'H2CO_DendrogramTemperature_Leaves_smooth',
)
filenames.append(hpath('TemperatureCube_PiecewiseFromRatio.fits'))
filenames.append(hpath('TemperatureCube_smooth_PiecewiseFromRatio.fits'))
filenames.append(hpath('H2CO_321220_to_303202_cube_bl.fits'))
import numpy as np
from astropy import units as u
from astropy import coordinates
from astropy import wcs
from astropy.io import ascii
from paths import mpath,apath,fpath,molpath,hpath
import pvextractor
catalog = astropy_tabular_data(apath('fitted_line_parameters_Chi2Constraints.ipac'),
format='ascii.ipac')
catalog.label='FittedLineParameters'
catalog.style.color = 'green'
catalog.style.marker = 'o'
cube = load_data(hpath('APEX_H2CO_303_202_bl.fits'))
cube.label='H2CO 303/202'
cube2 = load_data(molpath('APEX_SiO_54.fits'))
cube2.label='SiO'
cube3 = load_data(hpath('APEX_13CO_matched_H2CO.fits'))
cube3.label='13CO'
higaltem = load_data('/Users/adam/work/gc/gcmosaic_temp_conv36.fits')
dc = DataCollection([cube, catalog, cube2, cube3, higaltem])
dc.merge(cube,cube2,cube3)
dc.add_link(LinkSame(cube.id['Galactic Longitude'], catalog.id['GLON']))
dc.add_link(LinkSame(cube.id['Galactic Latitude'], catalog.id['GLAT']))
def ms_to_kms(x): return x/1e3
def kms_to_ms(x): return x*1e3
dc.add_link(LinkTwoWay(cube.id['Vrad'], catalog.id['center'], ms_to_kms, kms_to_ms))
import numpy as np
from astropy import units as u
from astropy import coordinates
from astropy import wcs
from astropy.io import ascii
from paths import mpath, apath, fpath, molpath, hpath
import pvextractor
catalog = astropy_tabular_data(
apath('fitted_line_parameters_Chi2Constraints.ipac'), format='ascii.ipac')
catalog.label = 'FittedLineParameters'
catalog.style.color = 'green'
catalog.style.marker = 'o'
cube = load_data(hpath('APEX_H2CO_303_202_bl.fits'))
cube.label = 'H2CO 303/202'
cube2 = load_data(molpath('APEX_SiO_54.fits'))
cube2.label = 'SiO'
cube3 = load_data(hpath('APEX_13CO_matched_H2CO.fits'))
cube3.label = '13CO'
higaltem = load_data('/Users/adam/work/gc/gcmosaic_temp_conv36.fits')
dc = DataCollection([cube, catalog, cube2, cube3, higaltem])
dc.merge(cube, cube2, cube3)
dc.add_link(LinkSame(cube.id['Galactic Longitude'], catalog.id['GLON']))
dc.add_link(LinkSame(cube.id['Galactic Latitude'], catalog.id['GLAT']))
def ms_to_kms(x):
return x / 1e3
F = aplpy.FITSFigure(
'/Users/adam/Dropbox/SMA_CMZ_FITS_files/gcmosaic_column_conv25.fits',
convention='calabretta')
F.show_colorscale(cmap=cm.hot_r, vmax=100, vmin=0, vmid=-2.5, stretch='log')
F.recenter(0.6, -0.1, height=0.5, width=2.6)
F.show_contour(paths.mpath('coverage_bool.fits'),
levels=[0.5],
colors=['b'],
convention='calabretta')
F.set_tick_labels_xformat('d.dd')
F.set_tick_labels_yformat('d.dd')
F.save(paths.fpath('coverage_on_herschel.png'), dpi=150)
F.save(paths.fpath('coverage_on_herschel.pdf'), dpi=150)
F.remove_layer('contour_set_1')
F.show_contour(paths.molpath('APEX_H2CO_303_202_smooth_bl_mask_integ.fits'),
levels=[5, 10, 20, 50],
colors=['b'],
convention='calabretta')
F.save(paths.fpath('H2CO_on_herschel.png'), dpi=150)
F.save(paths.fpath('H2CO_on_herschel.pdf'), dpi=150)
F.remove_layer('contour_set_2')
F.show_contour(paths.molpath('APEX_SiO_54_smooth_mask_integ.fits'),
levels=[2, 5, 10],
colors=['g'],
convention='calabretta')
F.save(paths.fpath('SiO_on_herschel.png'), dpi=150)
F.save(paths.fpath('SiO_on_herschel.pdf'), dpi=150)
F.remove_layer('contour_set_3')
F.show_contour(paths.molpath('APEX_13CO_smooth_mask_integ.fits'),
green = pl.mpl.colors.LinearSegmentedColormap('green',
{'red':[(0,0,0),(1,1,1)],
'green':[(0,1,1),(1,1,1)],
'blue':[(0,0,0),(1,1,1)]})
blue = pl.mpl.colors.LinearSegmentedColormap('blue', {'red':[(0,0,0),(1,1,1)],
'green':[(0,0,0),(1,1,1)],
'blue':[(0,1,1),(1,1,1)]})
if 'yt13co' not in locals():
cube13co = spectral_cube.SpectralCube.read(paths.mpath('APEX_13CO_2014_merge.fits'))
yt13co = cube13co.with_mask(cube13co>0.1).to_yt()
mask = cube13co>0.2
if 'cube_h2co303' not in locals():
cube_sio = SpectralCube.read(paths.molpath('APEX_SiO_54_bl.fits'))
# HACK:
mask._wcs = cube_sio.wcs
ytsio = cube_sio.with_mask(mask).to_yt()
cube_h2co303 = SpectralCube.read(paths.molpath('APEX_H2CO_303_202_bl.fits'))
mask._wcs = cube_h2co303.wcs
yth2co303 = cube_h2co303.with_mask(mask).to_yt()
cube_h2co321 = SpectralCube.read(paths.molpath('APEX_H2CO_321_220_bl.fits'))
mask._wcs = cube_h2co321.wcs
yth2co321 = cube_h2co321.with_mask(mask).to_yt()
#temcube = SpectralCube.read(paths.dpath('H2CO_321220_to_303202_cube_bl_temperature.fits'))
#mask._wcs = temcube.wcs
#yttem = temcube.with_mask(mask).to_yt()
def isosurfaces(yt13co):
vmin,vmax=10,200
def offset_to_point(glon, glat):
"""
Determine the offset along the orbit to the nearest point on an orbit to
the specified point
"""
import shapely.geometry as geom
line = geom.LineString(table['l','b'])
point = geom.Point(glon, glat)
return line.project(point)
molecules = ('13CO_2014_merge', 'C18O_2014_merge', 'H2CO_303_202_bl', 'SiO_54_bl')
filenames = [molpath('APEX_{0}.fits'.format(molecule))
for molecule in molecules]
molecules = molecules + (
'H2CO_Ratio',
#'H2CO_Ratio_smooth',
'H2CO_TemperatureFromRatio',
#'H2CO_TemperatureFromRatio_smooth',
#'H2CO_DendrogramTemperature',
#'H2CO_DendrogramTemperature_smooth',
#'H2CO_DendrogramTemperature_Leaves',
#'H2CO_DendrogramTemperature_Leaves_smooth'
)
# make_piecewise_temcube:
#filenames.append(hpath('TemperatureCube_PiecewiseFromRatio.fits'))
#filenames.append(hpath('TemperatureCube_smooth_PiecewiseFromRatio.fits'))
import pylab as pl
import glob
from astropy.io import fits
import aplpy
import paths
import os
if not os.path.isdir(paths.molpath('integ_imgs')):
os.mkdir(paths.molpath('integ_imgs'))
fig1 = pl.figure(1)
for fn in glob.glob(paths.molpath("*integ.fits")):
hdr = fits.getheader(fn)
if hdr['CRVAL2'] == 0:
fig1.clf()
F = aplpy.FITSFigure(fn, convention='calabretta', figure=fig1)
F.show_colorscale(cmap=pl.cm.hot)
F.save(paths.molpath('integ_imgs/{0}.pdf').format(os.path.basename(fn[:-5])))
vmin,vmax=10,200
def offset_to_point(glon, glat):
"""
Determine the offset along the orbit to the nearest point on an orbit to
the specified point
"""
import shapely.geometry as geom
line = geom.LineString(table['l','b'])
point = geom.Point(glon, glat)
return line.project(point)
molecules = ('13CO_2014_merge', 'C18O_2014_merge', 'H2CO_303_202_bl', 'SiO_54_bl')
filenames = [molpath('APEX_{0}.fits'.format(molecule))
for molecule in molecules]
molecules = molecules + (
'H2CO_Ratio',
#'H2CO_Ratio_smooth',
'H2CO_TemperatureFromRatio',
#'H2CO_TemperatureFromRatio_smooth',
#'H2CO_DendrogramTemperature',
#'H2CO_DendrogramTemperature_smooth',
#'H2CO_DendrogramTemperature_Leaves',
#'H2CO_DendrogramTemperature_Leaves_smooth'
)
# make_piecewise_temcube:
#filenames.append(hpath('TemperatureCube_PiecewiseFromRatio.fits'))
#filenames.append(hpath('TemperatureCube_smooth_PiecewiseFromRatio.fits'))
"pv_H2CO_321220_to_303202_bl_integ_weighted_temperature_dens3e4.fits",
)
]
cubes = [hpath(x)
for x in ("H2CO_321220_to_303202_cube_bl.fits",
"H2CO_321220_to_303202_cube_smooth_bl.fits",
"APEX_H2CO_303_202_bl.fits",
"APEX_H2CO_321_220_bl.fits",
"APEX_H2CO_322_221_bl.fits",
)
] + [mpath(x)
for x in ("APEX_13CO_2014_merge.fits",
"APEX_C18O_2014_merge.fits",
"APEX_H2CO_merge_high_plait_all.fits",
)
] + [molpath(x)
for x in
("APEX_SiO_54_bl.fits",)
]
dendrograms = [hpath(x) for x in
("DendroMask_H2CO303202.hdf5",)
] + [tpath(x) for x in
("fitted_line_parameters_Chi2Constraints.ipac",
"PPV_H2CO_Temperature.ipac",
)
]
if not os.path.isdir('cds'):
os.mkdir('cds')
# create "coverage" mask map
covgf = fits.open(paths.mpath('APEX_H2CO_merge_high_nhits.fits'))
covgf[0].data = (covgf[0].data > 0.05).astype('int')
covgf.writeto(paths.mpath('coverage_bool.fits'),clobber=True)
F = aplpy.FITSFigure('/Users/adam/Dropbox/SMA_CMZ_FITS_files/gcmosaic_column_conv25.fits',convention='calabretta')
F.show_colorscale(cmap=cm.hot_r,vmax=100,vmin=0, vmid=-2.5, stretch='log')
F.recenter(0.6,-0.1,height=0.5,width=2.6)
F.show_contour(paths.mpath('coverage_bool.fits'),levels=[0.5], colors=['b'], convention='calabretta')
F.set_tick_labels_xformat('d.dd')
F.set_tick_labels_yformat('d.dd')
F.save(paths.fpath('coverage_on_herschel.png'),dpi=150)
F.save(paths.fpath('coverage_on_herschel.pdf'),dpi=150)
F.remove_layer('contour_set_1')
F.show_contour(paths.molpath('APEX_H2CO_303_202_smooth_bl_mask_integ.fits'),
levels=[5,10,20,50], colors=['b'], convention='calabretta')
F.save(paths.fpath('H2CO_on_herschel.png'),dpi=150)
F.save(paths.fpath('H2CO_on_herschel.pdf'),dpi=150)
F.remove_layer('contour_set_2')
F.show_contour(paths.molpath('APEX_SiO_54_smooth_mask_integ.fits'),
levels=[2,5,10], colors=['g'], convention='calabretta')
F.save(paths.fpath('SiO_on_herschel.png'),dpi=150)
F.save(paths.fpath('SiO_on_herschel.pdf'),dpi=150)
F.remove_layer('contour_set_3')
F.show_contour(paths.molpath('APEX_13CO_smooth_mask_integ.fits'),
levels=[10,50,100,200], colors=['c'], convention='calabretta')
F.save(paths.fpath('13CO_on_herschel.png'),dpi=150)
F.save(paths.fpath('13CO_on_herschel.pdf'),dpi=150)
