def single_cutout(ax,position,image,mask1=None,mask2=None,points=None,label=None,size=6*u.arcsec):
cutout_image = Cutout2D(image.data,position,size=size,wcs=image.wcs)
norm = simple_norm(cutout_image.data,clip=False,stretch='linear',percent=99.5)
ax.imshow(cutout_image.data,origin='lower',norm=norm,cmap=plt.cm.gray_r)
# plot the nebulae catalogue
cutout_mask, _ = reproject_interp(mask1,output_projection=cutout_image.wcs,shape_out=cutout_image.shape,order='nearest-neighbor')
region_ID = np.unique(cutout_mask[~np.isnan(cutout_mask)])
contours = []
for i in region_ID:
blank_mask = np.zeros_like(cutout_mask)
blank_mask[cutout_mask==i] = 1
contours += find_contours(blank_mask, 0.5)
for coords in contours:
ax.plot(coords[:,1],coords[:,0],color='tab:red',lw=1,label='HII-region')
mask = np.zeros((*cutout_mask.shape,4))
mask[~np.isnan(cutout_mask.data),:] = (0.84, 0.15, 0.16,0.1)
ax.imshow(mask,origin='lower')
# plot the association catalogue
if mask2:
cutout_mask, _ = reproject_interp(mask2,output_projection=cutout_image.wcs,shape_out=cutout_image.shape,order='nearest-neighbor')
region_ID = np.unique(cutout_mask[~np.isnan(cutout_mask)])
contours = []
for i in region_ID:
blank_mask = np.zeros_like(cutout_mask)
blank_mask[cutout_mask==i] = 1
contours += find_contours(blank_mask, 0.5)
for coords in contours:
ax.plot(coords[:,1],coords[:,0],color='tab:blue',lw=1,label='association')
mask = np.zeros((*cutout_mask.shape,4))
mask[~np.isnan(cutout_mask.data),:] = (0.12,0.47,0.71,0.1)
ax.imshow(mask,origin='lower')
# mark the position of the clusters within the cutout
if points:
region = RectangleSkyRegion(position,0.9*size,0.9*size)
in_frame = points[region.contains(points['SkyCoord'],cutout_image.wcs)]
for row in in_frame:
x,y = row['SkyCoord'].to_pixel(cutout_image.wcs)
if 5<x<cutout_image.data.shape[0]-5 and 5<y<cutout_image.data.shape[1]-5:
ax.scatter(x,y,marker='o',facecolors='none',s=20,lw=0.4,color='tab:blue',label='cluster')
if label:
t = ax.text(0.07,0.875,label, transform=ax.transAxes,color='black',fontsize=8)
t.set_bbox(dict(facecolor='white', alpha=1, ec='white'))
ax.set_xticks([])
ax.set_yticks([])
return ax
def getReference(image_in, header_in, reference_fits_file, useExactReproj=False):
"""Return the reference image aligned with the input image.
getReference accepts a numpy array (masked or not) and a header with WCS information and a master reference fits file and return
a reprojected reference image array for the same portion of the sky.
Return reference_image"""
from reproject import reproject_interp, reproject_exact
refHasWCS = _headerHasWCS(fits.getheader(reference_fits_file))
refhdulist = fits.open(reference_fits_file)
ref_mask = np.zeros(refhdulist[0].data.shape, dtype='bool')
for anhdu in refhdulist[1:]:
#Combine all the 'bad' and 'mask' masks into a single one, if any
if any(s in anhdu.name for s in ["bad", "mask"]):
ref_mask = ref_mask | anhdu.data
#Check if there is a header available
if (header_in is not None) and _headerHasWCS(header_in) and refHasWCS:
#reproject with reproject here...
if useExactReproj: ref_reproj_data, __ = reproject_exact(refhdulist[0], header_in)
else: ref_reproj_data, __ = reproject_interp(refhdulist[0], header_in)
ref_reproj_mask, __ = reproject_interp((ref_mask, refhdulist[0].header), header_in)
gold_master = np.ma.array(data=ref_reproj_data, mask=ref_reproj_mask)
else:
#Here do the no WCS method
gold_master = _no_wcs_available(image_in, np.ma.array(refhdulist[0].data, mask=ref_mask))
return gold_master
def example(self):
"""
This function ...
:return:
"""
# Read in the three images downloaded from here:
# g: http://dr13.sdss.org/sas/dr13/eboss/photoObj/frames/301/1737/5/frame-g-001737-5-0039.fits.bz2
# r: http://dr13.sdss.org/sas/dr13/eboss/photoObj/frames/301/1737/5/frame-r-001737-5-0039.fits.bz2
# i: http://dr13.sdss.org/sas/dr13/eboss/photoObj/frames/301/1737/5/frame-i-001737-5-0039.fits.bz2
g = fits.open('frame-g-001737-5-0039.fits.bz2')[0]
r = fits.open('frame-r-001737-5-0039.fits.bz2')[0]
i = fits.open('frame-i-001737-5-0039.fits.bz2')[0]
# remap r and i onto g
r_new, r_mask = reproject_interp(r, g.header)
i_new, i_mask = reproject_interp(i, g.header)
# zero out the unmapped values
i_new[np.logical_not(i_mask)] = 0
r_new[np.logical_not(r_mask)] = 0
# red=i, green=r, blue=g
# make a file with the default scaling
rgb_default = make_lupton_rgb(i_new,
r_new,
g.data,
filename="ngc6976-default.jpeg")
# this scaling is very similar to the one used in Lupton et al. (2004)
rgb = make_lupton_rgb(i_new,
r_new,
g.data,
Q=10,
stretch=0.5,
filename="ngc6976.jpeg")
def IQU_to_lic(fitsname, licfname):
I, Q, U = hp.read_map(fitsname, field=[0, 1, 2])
U = U * 2
psi = np.arctan2(-U, Q) * 0.5
I_car, psi_car = healpix_to_carteian(I, psi)
I_mol, footprint = reproject_interp((I_car, WCS(car_header)), mol_header)
psi_mol, footprint = reproject_interp((psi_car, WCS(car_header)),
mol_header)
licmap_mol = calc_lic(psi_mol)
licmap_car = calc_lic(psi_car)
hdul = fits.HDUList()
hdul.append(fits.PrimaryHDU())
hdul.append(
fits.ImageHDU(name='Imap', data=I_mol[:, ::-1], header=mol_header))
hdul.append(
fits.ImageHDU(name='LIC', data=licmap_mol[:, ::-1], header=mol_header))
hdul.append(
fits.ImageHDU(name='Imap', data=I_car[:, ::-1], header=car_header))
hdul.append(
fits.ImageHDU(name='LIC', data=licmap_car[:, ::-1], header=car_header))
hdul.writeto(licfname, overwrite=True)
def make_example_rgbs(self):
"""
This function ...
:return:
"""
# Read in the three images downloaded from here:
# g: http://dr13.sdss.org/sas/dr13/eboss/photoObj/frames/301/1737/5/frame-g-001737-5-0039.fits.bz2
# r: http://dr13.sdss.org/sas/dr13/eboss/photoObj/frames/301/1737/5/frame-r-001737-5-0039.fits.bz2
# i: http://dr13.sdss.org/sas/dr13/eboss/photoObj/frames/301/1737/5/frame-i-001737-5-0039.fits.bz2
g = fits.open('frame-g-001737-5-0039.fits.bz2')[0]
r = fits.open('frame-r-001737-5-0039.fits.bz2')[0]
i = fits.open('frame-i-001737-5-0039.fits.bz2')[0]
# remap r and i onto g
r_new, r_mask = reproject_interp(r, g.header)
i_new, i_mask = reproject_interp(i, g.header)
# zero out the unmapped values
i_new[np.logical_not(i_mask)] = 0
r_new[np.logical_not(r_mask)] = 0
# red=i, green=r, blue=g
# make a file with the default scaling
rgb_default = make_lupton_rgb(i_new, r_new, g.data, filename="ngc6976-default.jpeg")
# this scaling is very similar to the one used in Lupton et al. (2004)
rgb = make_lupton_rgb(i_new, r_new, g.data, Q=10, stretch=0.5, filename="ngc6976.jpeg")
def initDeflection_Image(imagefile, deflectionFileX, deflectionFileY, zlens,
zsource_in, zsource_out):
### Read in image file
### Read in deflection maps,
### reproject to image file coordinates
imhdu = fits.open(imagefile)
imdata = imhdu[0].data
hdudeflx = fits.open(deflectionFileX)
hdudefly = fits.open(deflectionFileY)
#reproject deflection fields to HST WCS pixels
deflxHST, footprint = reproject_interp(hdudeflx[0], imhdu[0].header)
deflyHST, footprint = reproject_interp(hdudefly[0], imhdu[0].header)
ax = deflxHST / 0.06 # arcsec -> pixels
ay = deflyHST / 0.06 # arcsec -> pixels
# convert back to Dds / Ds = 1
if zsource_in == 0:
Dds_Ds_out = Dds_Ds(zlens, zsource_out)
ax = ax * Dds_Ds_out
ay = ay * Dds_Ds_out
else:
Dds_Ds_in = Dds_Ds(zlens, zsource_in)
Dds_Ds_out = Dds_Ds(zlens, zsource_out)
ax = ax / Dds_Ds_in * Dds_Ds_out
ay = ay / Dds_Ds_in * Dds_Ds_out
return ax, ay, imdata
def reproject_dustmap(self, outheader):
"""
Reprojects dust map (and errors) on the desired WCS
:param outheader: `~astropy.io.fits.header.Header`
output map header
:return: outmap: `~numpy.ndarray`
output map
:return: errormap: `~numpy.ndarray`
erromap
"""
if self.hpx:
# load properties of healpix grid
coordsys = self.dustmap.header['COORDSYS']
if coordsys == 'C':
coordsys = 'ICRS'
elif coordsys == 'E':
coordsys = 'Ecliptic'
elif coordsys == 'G':
coordsys = 'Galactic'
else:
print('coordinate system of input dust map unknown:', coordsys)
nested = self.dustmap.header['ORDERING']
if nested == 'NESTED':
nested = True
elif nested == 'RING':
nested = False
else:
print('ordering of input dust map unknown:', nested)
# dust map
if self.dustmap.header['TFORM1'] == '1024E':
outmap, footprint = reproject_from_healpix(self.dustmap[1],outheader)
else:
outmap, footprint = reproject_from_healpix((self.dustmap[1].data[self.mapname], coordsys),
outheader, nested=nested)
# error map
if self.errorname == 'None':
errormap = np.ones(np.shape(outmap))
else:
errormap, footprint = reproject_from_healpix(
(self.dustmap[1].data[self.errorname], coordsys),
outheader, nested=nested)
else:
outmap, footprint = reproject_interp(self.dustmap[self.mapname], outheader)
if self.errorname == 'None':
errormap = np.ones(np.shape(outmap))
else:
errormap, footprint = reproject_interp(self.dustmap[self.errorname], outheader)
outmap *= self.scale
errormap *= self.scale
return outmap, errormap
def reproj_binning2(data, wcs_in, bin_num, centerCoord='', shape_out=''):
'''
centerCoord is the array of central coordinates in degree.
'''
map_in_shape = np.shape(data)
nx_in, ny_in = map_in_shape
nx_out = math.trunc(nx_in / bin_num)
ny_out = math.trunc(ny_in / bin_num)
if shape_out == '':
shape_out = (nx_out, ny_out)
if centerCoord == '':
centerCoord = wcs_in.wcs.crval
wcs_out = WCS(naxis=2)
wcs_out.wcs.crval = centerCoord
wcs_out.wcs.crpix = [
math.trunc(shape_out[1] / 2),
math.trunc(shape_out[0] / 2)
]
wcs_out.wcs.cdelt = wcs_in.wcs.cdelt * bin_num
wcs_out.wcs.ctype = ['RA---SIN', 'DEC--SIN']
data_binned, footprint = reproject_interp((data, wcs_in),
wcs_out,
shape_out=shape_out)
return wcs_out, data_binned
def _reproject_to_wcs(self, geom, mode="interp", order=1):
from reproject import reproject_interp, reproject_exact
data = np.empty(geom.data_shape)
for img, idx in self.iter_by_image():
# TODO: Create WCS object for image plane if
# multi-resolution geom
shape_out = geom.get_image_shape(idx)[::-1]
if self.geom.projection == "CAR" and self.geom.is_allsky:
vals, footprint = reproject_car_to_wcs(
(img, self.geom.wcs), geom.wcs, shape_out=shape_out
)
elif mode == "interp":
vals, footprint = reproject_interp(
(img, self.geom.wcs), geom.wcs, shape_out=shape_out
)
elif mode == "exact":
vals, footprint = reproject_exact(
(img, self.geom.wcs), geom.wcs, shape_out=shape_out
)
else:
raise TypeError(
"mode must be 'interp' or 'exact'. Got: {!r}".format(mode)
)
data[idx] = vals
return self._init_copy(geom=geom, data=data)
def reprojection(table, outfolder_splus, outfolder_sdss):
for i in range(len(table)):
ra = table['RA'][i]
dec = table['DEC'][i]
id_1 = table['ID'][i]
#id_ = id_1[0:len(id_1) - 1]
name = '%s_%.6f_%.6f' % (id_1, ra, dec)
hdu_splus = fits.open(outfolder_splus + '/' + name + '-crop.fits')[0]
pasta = outfolder_sdss + '/' + name
try:
caminhos = [
os.path.join(pasta, nome) for nome in os.listdir(pasta)
]
except FileNotFoundError:
continue
arquivos = [arq for arq in caminhos if os.path.isfile(arq)]
sdss_files = [
arq for arq in arquivos if arq.lower().endswith(".fits.gz")
]
for i in range(len(sdss_files)):
filename_sdss = sdss_files[i]
hdu_sdss = fits.open(gzip.open(filename_sdss))[0]
array, footprint = reproject_interp(hdu_sdss, hdu_splus.header)
fits.writeto(outfolder_sdss + '/' + name + '/' + name + '-rep' +
str(i) + '.fits',
array,
hdu_sdss.header,
overwrite=True)
def build_image(id_,
set_,
bands=['EUC_VIS', 'EUC_H', 'EUC_J', 'EUC_Y'],
img_size=200,
scale=100,
clip=True):
tables = []
data = np.empty((img_size, img_size, len(bands)))
for i, band in enumerate(bands):
fname = get_image_filename_from_id(id_, band, set_)
try:
tables.append(fits.open(fname))
except FileNotFoundError as fe:
raise
if band != 'EUC_VIS':
band_data, data_footprint = reproject_interp(
tables[i][0], tables[0][0].header)
else:
band_data = tables[0][0].data
band_data[np.isnan(band_data)] = 0.
if clip:
interval = AsymmetricPercentileInterval(0.25,
99.75,
n_samples=100000)
vmin, vmax = interval.get_limits(band_data)
stretch = MinMaxInterval() + LogStretch()
data[:, :, i] = stretch(
((np.clip(band_data, -vmin * 0.7, vmax)) / (vmax)))
else:
stretch = LogStretch() + MinMaxInterval()
data[:, :, i] = stretch(band_data)
for t in tables:
t.close()
return data.astype(np.float32)
def merge_maps(maps, outmap, target_res, lmin, lmax, bmin, bmax):
# create output hdu
# determine map properties
nx = int((lmax - lmin) / target_res)
dx = (lmax - lmin) / nx
ny = int((bmax - bmin) / target_res)
dy = (bmax - bmin) / ny
crpix_y = -bmin / dy + 1
# wcs
w = wcs.WCS(naxis=2)
w.wcs.crpix = [1., crpix_y]
w.wcs.cdelt = np.array([-dx, dy])
w.wcs.crval = [lmax, 0.]
w.wcs.ctype = ["GLON-CAR", "GLAT-CAR"]
# header
header = w.to_header()
# empty map
map_data = np.zeros([ny, nx])
# hdu
hdu = fits.PrimaryHDU(map_data, header=header)
# reproject input maps onto output map
# and fill output map with input giving precedence to maps at the end of the list
for map in maps:
# reproject
array, footprint = reproject_interp(fits.open(map)[0], hdu.header)
hdu.data[footprint == 1] = array[footprint == 1]
# write new file
hdu.writeto(outmap)
def reproject_to(self, reference_cube, projection_type='bicubic'):
"""Spatially reprojects a `SkyCube` onto a reference cube.
Parameters
----------
reference_cube : `SkyCube`
Reference cube with the desired spatial projection.
projection_type : {'nearest-neighbor', 'bilinear',
'biquadratic', 'bicubic', 'flux-conserving'}
Specify method of reprojection. Default: 'bilinear'.
Returns
-------
reprojected_cube : `SkyCube`
Cube spatially reprojected to the reference cube.
"""
from reproject import reproject_interp
reference = reference_cube.data
shape_out = reference[0].shape
try:
wcs_in = self.wcs.dropaxis(2)
except:
wcs_in = self.wcs
try:
wcs_out = reference_cube.wcs.dropaxis(2)
except:
wcs_out = reference_cube.wcs
energy = self.energy
cube = self.data
new_cube = np.zeros((cube.shape[0], reference.shape[1],
reference.shape[2]))
energy_slices = np.arange(cube.shape[0])
# TODO: Re-implement to reproject cubes directly without needing
# to loop over energies here. Errors with reproject when doing this
# first need to be understood and fixed.
for i in energy_slices:
array = cube[i]
data_in = (array.value, wcs_in)
new_cube[i] = reproject_interp(data_in, wcs_out, shape_out, order=projection_type)[0]
new_cube = Quantity(new_cube, array.unit)
# Create new wcs
header_in = self.wcs.to_header()
header_out = reference_cube.wcs.to_header()
# Keep output energy info the same as input, but changes spatial information
# So need to restore energy parameters to input values here
try:
header_out['CRPIX3'] = header_in['CRPIX3']
header_out['CDELT3'] = header_in['CDELT3']
header_out['CTYPE3'] = header_in['CTYPE3']
header_out['CRVAL3'] = header_in['CRVAL3']
except:
pass
wcs_out = WCS(header_out).celestial
# TODO: how to fill 'meta' in better way?
meta = OrderedDict(header_out)
return SkyCube(data=new_cube, wcs=wcs_out, energy=energy, meta=meta)
def _reproject_to_wcs(self, geom, mode='interp', order=1):
from reproject import reproject_interp, reproject_exact
data = np.empty(geom.data_shape)
for img, idx in self.iter_by_image():
# TODO: Create WCS object for image plane if
# multi-resolution geom
shape_out = geom.get_image_shape(idx)[::-1]
if self.geom.projection == 'CAR' and self.geom.is_allsky:
vals, footprint = reproject_car_to_wcs((img, self.geom.wcs),
geom.wcs,
shape_out=shape_out)
elif mode == 'interp':
vals, footprint = reproject_interp((img, self.geom.wcs),
geom.wcs,
shape_out=shape_out)
elif mode == 'exact':
vals, footprint = reproject_exact((img, self.geom.wcs),
geom.wcs,
shape_out=shape_out)
else:
raise TypeError(
"Invalid reprojection mode, either choose 'interp' or 'exact'")
data[idx] = vals
return self._init_copy(geom=geom, data=data)
def heliographic(m):
shape_out = [720, 1440]
frame_out = SkyCoord(0,
0,
unit=u.deg,
frame="heliographic_stonyhurst",
obstime=m.date)
header = sunpy.map.make_fitswcs_header(
shape_out,
frame_out,
scale=[180 / shape_out[0], 360 / shape_out[1]] * u.deg / u.pix,
projection_code="CAR")
out_wcs = astropy.wcs.WCS(header)
array, footprint = reproject_interp(m, out_wcs, shape_out=shape_out)
outmap = sunpy.map.Map((array, header))
outmap.plot_settings = m.plot_settings
fig = plt.figure()
ax = plt.subplot(projection=outmap)
outmap.plot(ax)
ax.set_xlim(0, shape_out[1])
ax.set_ylim(0, shape_out[0])
plt.show()
def calc_stellar_mass(iracFile, MtoLFile, outFile):
'''
Calculate the stellar mass surface density for a given IRAC image
and MtoL image.
'''
# open IRAC data file
irac = fits.open(iracFile)
iracData = irac[0].data
iracHdr = irac[0].header
# open MtoL data file
MtoL = fits.open(MtoLFile)
MtoL_regrid = reproject_interp(MtoL,
output_projection=iracHdr,
hdu_in=0,
order='nearest-neighbor',
return_footprint=False)
irac.close()
MtoL.close()
# Equation 8 from Leroy+ 2019 (z0mgs paper)
mstarirac1 = 3.5e2 * (MtoL_regrid / 0.5) * (iracData)
# create output file
outHdr = iracHdr
outHdr['BUNIT'] = 'MSUN/PC^2'
outfits = fits.PrimaryHDU(data=mstarirac1, header=outHdr)
outfits.writeto(outFile, overwrite=True)
def rebin(self, reference_wcs, exact=True, parallel=True):
"""
This function ...
:param reference_wcs:
:param exact:
:param parallel:
:return:
"""
# Calculate rebinned data and footprint of the original image
if exact:
new_data, footprint = reproject_exact(
(self._data, self.wcs),
reference_wcs,
shape_out=reference_wcs.shape,
parallel=parallel)
else:
new_data, footprint = reproject_interp(
(self._data, self.wcs),
reference_wcs,
shape_out=reference_wcs.shape)
# Replace the data and WCS
self._data = new_data
self._wcs = reference_wcs
# Return the footprint
return Frame(footprint)
def _reproject_to_wcs(self, geom, mode="interp", order=1):
from reproject import reproject_interp, reproject_exact
data = np.empty(geom.data_shape)
for img, idx in self.iter_by_image():
# TODO: Create WCS object for image plane if
# multi-resolution geom
shape_out = geom.get_image_shape(idx)[::-1]
if self.geom.projection == "CAR" and self.geom.is_allsky:
vals, footprint = reproject_car_to_wcs(
(img, self.geom.wcs), geom.wcs, shape_out=shape_out
)
elif mode == "interp":
vals, footprint = reproject_interp(
(img, self.geom.wcs), geom.wcs, shape_out=shape_out
)
elif mode == "exact":
vals, footprint = reproject_exact(
(img, self.geom.wcs), geom.wcs, shape_out=shape_out
)
else:
raise TypeError(
"mode must be 'interp' or 'exact'. Got: {!r}".format(mode)
)
data[idx] = vals
return self._init_copy(geom=geom, data=data)
def err_func(pars,
inp,
data,
wcs_hires,
wcs_lowres,
pixscale=0.03,
bounds=np.array([[6, 20], [42, 57]])):
norm, fwhm, offset = pars
numseepix = fwhm / pixscale
nanpix_data = np.where(np.isnan(data))
data[nanpix_data] = 0
kern = Gaussian2DKernel(numseepix /
2.355) # FWHM = sigma * 2 sqrt(2.*ln(2))
if offset is None:
convdat = norm * convolve_fft(inp, kern, boundary='extend')
else:
convdat = norm * convolve_fft(inp, kern, boundary='extend') + offset
#convdat = norm * convolve(inp, kern, boundary='extend')
inpreproj, inpfootprint = \
reproject_interp((convdat, wcs_hires), wcs_lowres, order='nearest-neighbor',
shape_out=np.shape(data))
model = inpreproj
model[nanpix_data] = 0
nanpix_inp = np.where(np.isnan(model))
model[nanpix_inp] = 0
data[nanpix_inp] = 0
return np.sum(
(data[bounds[1, 0]:bounds[1, 1], bounds[0, 0]:bounds[0, 1]] -
model[bounds[1, 0]:bounds[1, 1], bounds[0, 0]:bounds[0, 1]])**2)
def comparison(source_name):
num_name = source_name[4:8]
hdu_MIPS24 = fits.open(direc + 'Bulles_Nicolas/MB' + str(num_name) +
'/MIPS24_MB' + str(num_name) + '.fits')
Source = np.load(str(source_name) + '.npy', allow_pickle=True).item()
#test=Source['NII_122_em']
test = Source['OH_119']
wcs_MIPS = WCS(hdu_MIPS24[0].header)
WCS_Source = test[2]
New_MIPS, footprint = reproject_interp(hdu_MIPS24,
WCS_Source,
shape_out=np.shape(test[0]))
fig = plt.figure(0)
fig.suptitle('Reprojection MIPS24 on Herschel')
gs = GridSpec(2, 2, hspace=0.3, wspace=0.3)
ax1 = plt.subplot(gs[0, 0], projection=wcs_MIPS)
ax2 = plt.subplot(gs[1, 0], projection=WCS_Source)
ax3 = plt.subplot(gs[0, 1], projection=WCS_Source)
ax4 = plt.subplot(gs[1, 1], projection=WCS_Source)
ax1.imshow(hdu_MIPS24[0].data)
ax1.set_title('MIPS24', fontsize=11)
ax1.coords[0].set_ticks(exclude_overlapping=True)
ax1.set_xlabel('RA (J2000)')
ax1.set_ylabel('DEC (J2000)')
ax1.grid()
ax2.imshow(test[0])
ax2.set_title('Herschel NII', fontsize=11)
ax2.coords[0].set_ticks(exclude_overlapping=True)
ax2.set_xlabel('RA (J2000)')
ax2.set_ylabel('DEC (J2000)')
ax2.contour(hdu_MIPS24[0].data,
transform=ax2.get_transform(wcs_MIPS),
colors='white',
linewidths=0.5)
ax2.set_xlim(0, len(test[0]) - 1)
ax2.set_ylim(0, len(test[0]) - 1)
#ax2.imshow(hdu_MIPS24[0].data, alpha=0.5)
ax2.grid()
ax3.imshow(New_MIPS)
ax3.set_title('MIPS24 on Herschel NII', fontsize=11)
ax3.coords[0].set_ticks(exclude_overlapping=True)
ax3.set_xlabel('RA (J2000)')
ax3.set_ylabel('DEC (J2000)')
ax4.imshow(test[0])
ax4.contour(New_MIPS, colors='white', linewidths=0.5)
ax4.coords[0].set_ticks(exclude_overlapping=True)
ax4.set_title('Overlap', fontsize=11)
ax4.set_xlabel('RA (J2000)')
ax4.set_ylabel('DEC (J2000)')
plt.show()
return hdu_MIPS24
def reproject(self, header, order='bilinear'):
"""
Reproject the image into a new header.
Parameters
----------
header : `astropy.io.fits.Header`
A header specifying a cube in valid WCS
order : int or str, optional
The order of the interpolation (if ``mode`` is set to
``'interpolation'``). This can be either one of the following
strings:
* 'nearest-neighbor'
* 'bilinear'
* 'biquadratic'
* 'bicubic'
or an integer. A value of ``0`` indicates nearest neighbor
interpolation.
"""
self._raise_wcs_no_celestial()
try:
from reproject.version import version
except ImportError:
raise ImportError("Requires the reproject package to be"
" installed.")
# Need version > 0.2 to work with cubes
from distutils.version import LooseVersion
if LooseVersion(version) < "0.3":
raise Warning("Requires version >=0.3 of reproject. The current "
"version is: {}".format(version))
from reproject import reproject_interp
# TODO: Find the minimal footprint that contains the header and only reproject that
# (see FITS_tools.regrid_cube for a guide on how to do this)
newwcs = wcs.WCS(header)
shape_out = [
header['NAXIS{0}'.format(i + 1)] for i in range(header['NAXIS'])
][::-1]
newproj, newproj_valid = reproject_interp((self.value, self.header),
newwcs,
shape_out=shape_out,
order=order)
self = Projection(newproj,
unit=self.unit,
wcs=newwcs,
meta=self.meta,
header=header,
read_beam=True)
return self
def get_cont(header):
contfn = paths.dpath('W51_te_continuum_best.fits')
beam = radio_beam.Beam.from_fits_header(contfn)
cont_Jy = reproject.reproject_interp(input_data=contfn,
output_projection=header)[0]*u.Jy
cont_K = cont_Jy.to(u.K, u.brightness_temperature(beam,
continuum_frequency))
return cont_K
def reproject_interp_rgb(input_data, *args, **kwargs):
data = input_data.data
wcs = WCS(input_data.header).celestial
return np.moveaxis(
np.stack([
reproject_interp((data[:, :, i], wcs), *args,
**kwargs)[0].astype(data.dtype) for i in range(3)
]), 0, -1)
def reproject(self, reference, mode='interp', *args, **kwargs):
"""
Reproject image to given reference.
Parameters
----------
reference : `~astropy.io.fits.Header`, or `~gammapy.image.SkyImage`
Reference image specification to reproject the data on.
mode : {'interp', 'exact'}
Interpolation mode.
*args : list
Arguments passed to `~reproject.reproject_interp` or
`~reproject.reproject_exact`.
**kwargs : dict
Keyword arguments passed to `~reproject.reproject_interp` or
`~reproject.reproject_exact`.
Returns
-------
image : `~gammapy.image.SkyImage`
Image reprojected onto ``reference``.
"""
from reproject import reproject_interp, reproject_exact
if isinstance(reference, SkyImage):
wcs_reference = reference.wcs
shape_out = reference.data.shape
elif isinstance(reference, fits.Header):
wcs_reference = WCS(reference)
shape_out = (reference['NAXIS2'], reference['NAXIS1'])
else:
raise TypeError("Invalid reference image. Must be either instance"
"of `Header`, `WCS` or `SkyImage`.")
if mode == 'interp':
out = reproject_interp((self.data, self.wcs),
wcs_reference,
shape_out=shape_out,
*args,
**kwargs)
elif mode == 'exact':
out = reproject_exact((self.data, self.wcs),
wcs_reference,
shape_out=shape_out,
*args,
**kwargs)
else:
raise TypeError(
"Invalid reprojection mode, either choose 'interp' or 'exact'")
return self.__class__(
name=self.name,
data=out[0],
wcs=wcs_reference,
unit=self.unit,
meta=self.meta,
)
def reproject_ref2sci(self, how: str = "swarp", **kwargs):
"""
:param how: 'swarp' or 'reproject'
:return:
"""
if how == "swarp":
nthreads = kwargs.get("nthreads", 4)
command, ref_reprojected, weight_name = prepare_swarp_align(
self, nthreads=nthreads)
_ = subprocess.run(command.split(),
capture_output=True,
check=True)
# load the result
with fits.open(ref_reprojected) as hdulist:
ref_projected = hdulist[0].data
# clean up
keep_tmp = kwargs.get("keep_tmp", False)
if not keep_tmp:
_, _, field, filt, ccd, _, quad = self.name.split("_")
path_ref_base = pathlib.Path(
os.path.join(self.path_base, "ref"))
path_ref = path_ref_base / pathlib.Path(
f"{field}/{ccd}/{quad}/{filt}/")
fs = list(
path_ref.glob(f"ref.{field}_{ccd}_{quad}_{filt}*remap*"))
if self.verbose:
print(fs)
for ff in fs:
try:
if self.verbose:
print(f"removing {str(ff)}")
os.remove(str(ff))
except OSError:
if self.verbose:
print(f"failed to remove {str(ff)}")
elif how == "reproject":
order = kwargs.get("order", "bicubic") # 'bilinear'
ref_projected = reproject_interp(
(self.ref, self.header_ref),
self.header_sci,
order=order,
return_footprint=False,
)
else:
raise ValueError("unknown reproject method")
return ref_projected
def spin_and_trim(imlist,
wcsrefimname,
trimfrac=0.4,
trimdir='DIA_TRIM',
verbose=False):
""" Rotate images to match the WCS of the WCS reference image (spin) and
then cut off a fraction of the outer region of the image (trim).
Returns a list of the trimmed images.
"""
if verbose:
print('Spinning Input Images: ' + str(imlist))
print("to match WCS Ref image: " + wcsrefimname)
print("and trimming by : %i pct" % (trimfrac * 100))
if not os.path.exists(trimdir):
os.makedirs(trimdir)
trimmed_image_list = []
hdr_imref = fits.getheader(wcsrefimname)
wcs_imref = WCS(hdr_imref)
for imname in list(imlist) + [wcsrefimname]:
imname_trimmed = os.path.join(
trimdir,
os.path.basename(imname).replace('.fits', '_trim.fits'))
if os.path.isfile(imname_trimmed):
print("%s exists. Skipping trimming." % imname_trimmed,
file=sys.stderr)
continue
if verbose:
print("Reprojecting %s to x,y frame of %s " %
(imname, wcsrefimname),
file=sys.stderr)
im = fits.open(imname)
if imname != wcsrefimname:
array, footprint = reproject_interp(im[0], hdr_imref)
else:
# WCS Ref image does not need reprojection
array = im[0].data
# Trim off the outer trimfrac to reduce chances of NaN errors due to
# empty array segments after rotation (also speeds up DIA processing)
arraysize = array.shape
cutout = Cutout2D(array,
position=[arraysize[1] / 2., arraysize[0] / 2.],
size=[
round(arraysize[1] * (1 - trimfrac)),
round(arraysize[0] * (1 - trimfrac))
],
wcs=wcs_imref)
# save reprojected-and-trimmed image:
im[0].data = cutout.data
im[0].header.update(cutout.wcs.to_header())
im.writeto(imname_trimmed, output_verify='fix+warn')
im.close()
trimmed_image_list.append(imname_trimmed)
return (trimmed_image_list)
def align_image(self, img, header, ref_img_header):
"""
Takes an ImageHDU object as img, the header of that image for header
and a astropy header object from the reference image for ref_img
"""
aligned_img, footprint = reproject_interp((img, header),
ref_img_header)
return aligned_img
def FitsCutout(pathname, ra, dec, rad_arcsec, pix_width_arcsec=None, exten=0, reproj=False, variable=False, outfile=False, parallel=True, fast=True):
# Open input fits and extract data
if isinstance(pathname,basestring):
in_fitsdata = astropy.io.fits.open(pathname)
elif isinstance(pathname,astropy.io.fits.HDUList):
in_fitsdata = pathname
in_map = in_fitsdata[exten].data
in_header = in_fitsdata[exten].header
in_wcs = astropy.wcs.WCS(in_header)
# If reprojection not requesed, pass input parameters to astropy cutout function
if reproj==False:
pos = astropy.coordinates.SkyCoord(ra, dec, unit='deg')
size = astropy.units.Quantity(2.0*rad_arcsec, astropy.units.arcsec)
cutout_obj = astropy.nddata.utils.Cutout2D(in_map, pos, size, wcs=in_wcs, mode='partial', fill_value=np.NaN)
# Extract outputs of interest
out_map = cutout_obj.data
out_wcs = cutout_obj.wcs
out_header = out_wcs.to_header()
# If reporjection requested, pass input parameters to reprojection function (fast or thorough, as specified)
if reproj==True:
import reproject
width_deg = ( 2.0 * float(rad_arcsec) ) / 3600.0
if pix_width_arcsec == None:
pix_width_arcsec = 3600.0*np.mean(np.abs(np.diagonal(in_wcs.pixel_scale_matrix)))
cutout_header = FitsHeader(ra, dec, width_deg, pix_width_arcsec)
cutout_shape = ( cutout_header['NAXIS1'], cutout_header['NAXIS1'] )
try:
if fast==False:
cutout_tuple = reproject.reproject_exact(in_fitsdata, cutout_header, shape_out=cutout_shape, hdu_in=exten, parallel=parallel)
elif fast==True:
cutout_tuple = reproject.reproject_interp(in_fitsdata, cutout_header, shape_out=cutout_shape, hdu_in=exten)
except Exception as exception:
print(exception.message)
# Extract outputs of interest
try:
out_map = cutout_tuple[0]
except:
pdb.set_trace()
out_wcs = astropy.wcs.WCS(cutout_header)
out_header = cutout_header
# Save, tidy, and return; all to taste
if outfile!=False:
out_hdu = astropy.io.fits.PrimaryHDU(data=out_map, header=out_header)
out_hdulist = astropy.io.fits.HDUList([out_hdu])
out_hdulist.writeto(outfile, overwrite=True)
if isinstance(pathname,basestring):
in_fitsdata.close()
if variable==True:
out_hdu = astropy.io.fits.PrimaryHDU(data=out_map, header=out_header)
out_hdulist = astropy.io.fits.HDUList([out_hdu])
return out_hdulist
def convolve_reproj(inp,
norm,
fwhm,
data,
wcs_hires,
wcs_lowres,
offset=None,
pixscale=0.03,
bounds=np.array([[10, 23], [37, 52]]),
inneroffset=None,
angle=None):
if isinstance(fwhm, float):
numseepix = fwhm / pixscale
kern = Gaussian2DKernel(numseepix /
2.355) # FWHM = sigma * 2 sqrt(2.*ln(2))
else:
try:
fwhmx, fwhmy = fwhm
except:
import pdb
pdb.set_trace()
numseepix_x = fwhmx / pixscale
numseepix_y = fwhmy / pixscale
if angle is None:
angle = 0
try:
kern = Gaussian2DKernel(numseepix_x / 2.355,
numseepix_y / 2.355,
theta=angle)
except:
import pdb
pdb.set_trace()
if (offset is None) & (inneroffset is None):
convdat = norm * convolve_fft(inp, kern, boundary='wrap')
elif (inneroffset is None):
convdat = norm * convolve_fft(inp, kern, boundary='wrap') + offset
elif (offset is None):
convdat = norm * convolve_fft(inp + inneroffset, kern, boundary='wrap')
else:
convdat = norm * convolve_fft(inp + inneroffset, kern,
boundary='wrap') + offset
#convdat = norm * convolve(inp, kern, boundary='extend')
try:
inpreproj, inpfootprint = \
reproject_interp((convdat, wcs_hires), wcs_lowres,
order='nearest-neighbor',
shape_out=np.shape(data))
except:
import pdb
pdb.set_trace()
if offset is not None:
inpreproj += offset
if bounds is not None:
return inpreproj[bounds[1, 0]:bounds[1, 1], bounds[0, 0]:bounds[0, 1]]
else:
return inpreproj
def reproject(self, header, order='bilinear'):
"""
Reproject the image into a new header.
Parameters
----------
header : `astropy.io.fits.Header`
A header specifying a cube in valid WCS
order : int or str, optional
The order of the interpolation (if ``mode`` is set to
``'interpolation'``). This can be either one of the following
strings:
* 'nearest-neighbor'
* 'bilinear'
* 'biquadratic'
* 'bicubic'
or an integer. A value of ``0`` indicates nearest neighbor
interpolation.
"""
self._raise_wcs_no_celestial()
try:
from reproject.version import version
except ImportError:
raise ImportError("Requires the reproject package to be"
" installed.")
# Need version > 0.2 to work with cubes
from distutils.version import LooseVersion
if LooseVersion(version) < "0.3":
raise Warning("Requires version >=0.3 of reproject. The current "
"version is: {}".format(version))
from reproject import reproject_interp
# TODO: Find the minimal footprint that contains the header and only reproject that
# (see FITS_tools.regrid_cube for a guide on how to do this)
newwcs = wcs.WCS(header)
shape_out = [header['NAXIS{0}'.format(i + 1)] for i in range(header['NAXIS'])][::-1]
newproj, newproj_valid = reproject_interp((self.value,
self.header),
newwcs,
shape_out=shape_out,
order=order)
self = Projection(newproj, unit=self.unit, wcs=newwcs,
meta=self.meta, header=header,
read_beam=True)
return self
def align_objects(self, object_list, output_dir, method):
"""Align a series of frames to a reference frame via ASTROALIGN or WCS REPROJECTION"""
if len(object_list) == 0 or len(object_list) == 1:
print("Insufficient number of images for alignment")
else:
print("Opening reference frame", object_list[0])
reference_frame = fits.open(object_list[0])
reference_data = reference_frame[0].data
reference_header = reference_frame[0].header
print("Converting reference data to FITS")
reference_hdu = fits.PrimaryHDU(reference_data, header=reference_header)
print("Writing reference frame to output directory")
reference_hdu.writeto(output_dir + "/a-" + str(object_list[0]), overwrite=True)
for i in range(1, len(object_list)):
if os.path.isfile("a-" + object_list[i]):
print("Skipping align on", object_list[i])
else:
print("Opening target frame", object_list[i])
target_frame = fits.open(object_list[i])
target_data = target_frame[0].data
target_header = target_frame[0].header
if method == "astroalign":
print("Aligning target frame with reference frame via ASTROALIGN")
array = aa.register(target_data, reference_data)
elif method == "reproject":
print("Converting target data to FITS")
target_hdu = fits.PrimaryHDU(target_data, header=target_header)
print("Aligning target frame with reference frame via WCS")
array, footprint = reproject_interp(target_hdu, reference_header)
print("Converting aligned target data to FITS")
target_hdu = fits.PrimaryHDU(array, header=target_header)
print("Writing aligned frame to output directory")
target_hdu.writeto(output_dir + "/a-" + str(object_list[i]), overwrite=True)
return
def project_data_into_region():
to_region_fn = "/Volumes/DataDavy/GALFA/SC_241/LAB_corrected_coldens.fits"
to_region_hdr = fits.getheader(to_region_fn)
allsky_fn = "/Volumes/DataDavy/GALFA/DR2/FullSkyNarrow/GALFA_HI_W_S1011_V-009.2kms.fits"
allsky_hdr = fits.getheader(allsky_fn)
allsky_data = fits.getdata(allsky_fn)
new_image, footprint = reproject_interp((allsky_data, allsky_hdr), to_region_hdr)
return new_image
def project_data_into_region(from_data_fn, to_region = "SC_241"):
if to_region == "SC_241":
to_region_fn = "/Volumes/DataDavy/GALFA/SC_241/LAB_corrected_coldens.fits"
to_region_hdr = fits.getheader(to_region_fn)
from_data_hdr = fits.getheader(from_data_fn)
from_data_data = fits.getdata(from_data_fn)
new_image, footprint = reproject_interp((from_data_data, from_data_hdr), to_region_hdr)
return new_image
def inject_model_into_precal_single(precal_name, model_name):
# Lets reproject the simulation file to the exposure CCDs planes
target_projection = fits.open(precal_name, mode="update")
simulated_frame = fits.open(model_name)
array, footprint = reproject_interp(simulated_frame[0],
target_projection[1].header)
array[np.isnan(array)] = 0
array = array / target_projection[1].header['FLXSCALE']
target_projection[1].data = target_projection[1].data + array
target_projection.flush()
target_projection.close()
return (precal_name)
def getReference(image_in,
header_in,
reference_fits_file,
useExactReproj=False):
"""Return the reference image aligned with the input image.
getReference accepts a numpy array (masked or not) and a header with WCS information and a master reference fits file and return
a reprojected reference image array for the same portion of the sky.
Return reference_image"""
from reproject import reproject_interp, reproject_exact
refHasWCS = _headerHasWCS(fits.getheader(reference_fits_file))
refhdulist = fits.open(reference_fits_file)
ref_mask = np.zeros(refhdulist[0].data.shape, dtype='bool')
for anhdu in refhdulist[1:]:
#Combine all the 'bad' and 'mask' masks into a single one, if any
if any(s in anhdu.name for s in ["bad", "mask"]):
ref_mask = ref_mask | anhdu.data
#Check if there is a header available
if (header_in is not None) and _headerHasWCS(header_in) and refHasWCS:
#reproject with reproject here...
if useExactReproj:
ref_reproj_data, __ = reproject_exact(refhdulist[0], header_in)
else:
ref_reproj_data, __ = reproject_interp(refhdulist[0], header_in)
ref_reproj_mask, __ = reproject_interp(
(ref_mask, refhdulist[0].header), header_in)
gold_master = np.ma.array(data=ref_reproj_data, mask=ref_reproj_mask)
else:
#Here do the no WCS method
gold_master = _no_wcs_available(
image_in, np.ma.array(refhdulist[0].data, mask=ref_mask))
return gold_master
def assemble_reference(refdatas, wcs, shape):
"""Reproject and stack the reference images to match the science image"""
refdatas_reprojected = []
refdata_foot = np.zeros(shape, float)
for data in refdatas:
reprojected, foot = reproject_interp((data.data, data.wcs), wcs, shape)
refdatas_reprojected.append(reprojected)
refdata_foot += foot
refdata_reproj = np.nanmean(refdatas_reprojected, axis=0)
refdata_reproj[np.isnan(refdata_reproj)] = 0.
refdata = CCDData(refdata_reproj, wcs=wcs, mask=refdata_foot == 0., unit='adu')
return refdata
def image_reproject_wcs_to_file(source_image_hdu, target_image_hdu_header, filepath=None):
"""reproject one wcs image to the wcs of another image
:param source_image_hdu: the HDU object of source image
:param target_image_hdu_header: the header object of target image
:param filepath: the output file path
:return:
"""
array, footprint = reproject_interp(source_image_hdu, target_image_hdu_header)
if filepath is not None:
# write file
fits.writeto(filepath, array, target_image_hdu_header, clobber=True) # clobber=OVERWRITE
else:
# return array & footprint
return array, footprint
def reproject(self, reference, mode='interp', *args, **kwargs):
"""
Reproject image to given reference.
Parameters
----------
reference : `~astropy.io.fits.Header`, or `~gammapy.image.SkyImage`
Reference image specification to reproject the data on.
mode : {'interp', 'exact'}
Interpolation mode.
*args : list
Arguments passed to `~reproject.reproject_interp` or
`~reproject.reproject_exact`.
**kwargs : dict
Keyword arguments passed to `~reproject.reproject_interp` or
`~reproject.reproject_exact`.
Returns
-------
image : `~gammapy.image.SkyImage`
Image reprojected onto ``reference``.
"""
from reproject import reproject_interp, reproject_exact
if isinstance(reference, SkyImage):
wcs_reference = reference.wcs
shape_out = reference.data.shape
elif isinstance(reference, fits.Header):
wcs_reference = WCS(reference)
shape_out = (reference['NAXIS2'], reference['NAXIS1'])
else:
raise TypeError("Invalid reference image. Must be either instance"
"of `Header`, `WCS` or `SkyImage`.")
if mode == 'interp':
out = reproject_interp((self.data, self.wcs), wcs_reference,
shape_out=shape_out, *args, **kwargs)
elif mode == 'exact':
out = reproject_exact((self.data, self.wcs), wcs_reference,
shape_out=shape_out, *args, **kwargs)
else:
raise TypeError("Invalid reprojection mode, either choose 'interp' or 'exact'")
return self.__class__(
name=self.name, data=out[0], wcs=wcs_reference,
unit=self.unit, meta=self.meta,
)
def rebin(self, reference_wcs, exact=False, parallel=True, threshold=0.5, dilate=False, rank=2, connectivity=1,
iterations=2):
"""
This function ...
:param reference_wcs:
:param exact:
:param parallel:
:param threshold:
:param dilate:
:param rank:
:param connectivity:
:param iterations:
:return:
"""
from .frame import Frame
# Check whether the frame has a WCS
if not self.has_wcs: raise RuntimeError("Cannot rebin a mask without coordinate system")
# Check whether the WCS is the same
if self.wcs == reference_wcs: return Frame.ones_like(self)
#from ..tools import plotting
#print(self._data.shape)
#plotting.plot_box(self._data.astype(int), title="before")
# Calculate rebinned data and footprint of the original image
if exact: new_data, footprint = reproject_exact((self._data.astype(int), self.wcs), reference_wcs, shape_out=reference_wcs.shape, parallel=parallel)
else: new_data, footprint = reproject_interp((self._data.astype(int), self.wcs), reference_wcs, shape_out=reference_wcs.shape)
#from ..tools import plotting
#print(new_data.shape)
#plotting.plot_box(new_data, title="after")
# Get binary mask data
mask_data = np.logical_or(new_data > threshold, np.isnan(new_data))
# Replace the data and WCS
self._data = mask_data
self._wcs = reference_wcs.copy()
# Dilate?
if dilate: self.dilate_rc(rank, connectivity=connectivity, iterations=iterations) # 1 also worked in test
# Return the footprint
return Frame(footprint, wcs=reference_wcs.copy())
def extract_mapcube_region(infile, skydir, outfile, maphdu=0):
"""Extract a region out of an all-sky mapcube file.
Parameters
----------
infile : str
Path to mapcube file.
skydir : `~astropy.coordinates.SkyCoord`
"""
h = fits.open(os.path.expandvars(infile))
npix = 200
shape = list(h[maphdu].data.shape)
shape[1] = 200
shape[2] = 200
wcs = WCS(h[maphdu].header)
skywcs = WCS(h[maphdu].header, naxis=[1, 2])
coordsys = get_coordsys(skywcs)
region_wcs = wcs.deepcopy()
if coordsys == 'CEL':
region_wcs.wcs.crval[0] = skydir.ra.deg
region_wcs.wcs.crval[1] = skydir.dec.deg
elif coordsys == 'GAL':
region_wcs.wcs.crval[0] = skydir.galactic.l.deg
region_wcs.wcs.crval[1] = skydir.galactic.b.deg
else:
raise Exception('Unrecognized coordinate system.')
region_wcs.wcs.crpix[0] = npix // 2 + 0.5
region_wcs.wcs.crpix[1] = npix // 2 + 0.5
from reproject import reproject_interp
data, footprint = reproject_interp(h, region_wcs.to_header(),
hdu_in=maphdu,
shape_out=shape)
hdu_image = fits.PrimaryHDU(data, header=region_wcs.to_header())
hdulist = fits.HDUList([hdu_image, h['ENERGIES']])
hdulist.writeto(outfile, clobber=True)
def _reproject_wcs(self, geom, mode='interp', order=1):
from reproject import reproject_interp, reproject_exact
map_out = WcsNDMap(geom)
axes_eq = np.all([ax0 == ax1 for ax0, ax1 in
zip(geom.axes, self.geom.axes)])
for vals, idx in map_out.iter_by_image():
if self.geom.ndim == 2 or axes_eq:
img = self.data[idx[::-1]]
else:
coords = axes_pix_to_coord(geom.axes, idx)
img = self.interp_image(coords, order=order).data
# FIXME: This is a temporary solution for handling maps
# with undefined pixels
if np.any(~np.isfinite(img)):
img = img.copy()
img[~np.isfinite(img)] = 0.0
# TODO: Create WCS object for image plane if
# multi-resolution geom
shape_out = geom.get_image_shape(idx)[::-1]
if self.geom.projection == 'CAR' and self.geom.is_allsky:
data, footprint = reproject_car_to_wcs((img, self.geom.wcs),
geom.wcs,
shape_out=shape_out)
elif mode == 'interp':
data, footprint = reproject_interp((img, self.geom.wcs),
geom.wcs,
shape_out=shape_out)
elif mode == 'exact':
data, footprint = reproject_exact((img, self.geom.wcs),
geom.wcs,
shape_out=shape_out)
else:
raise TypeError(
"Invalid reprojection mode, either choose 'interp' or 'exact'")
vals[...] = data
return map_out
def rebin(self, reference_wcs, exact=True, parallel=True):
"""
This function ...
:param reference_wcs:
:param exact:
:param parallel:
:return:
"""
# Calculate rebinned data and footprint of the original image
if exact: new_data, footprint = reproject_exact((self._data, self.wcs), reference_wcs, shape_out=reference_wcs.shape, parallel=parallel)
else: new_data, footprint = reproject_interp((self._data, self.wcs), reference_wcs, shape_out=reference_wcs.shape)
# Replace the data and WCS
self._data = new_data
self._wcs = reference_wcs
# Return the footprint
return Frame(footprint)
def project_to_header(fitsfile, header, **kwargs):
"""
Reproject an image to a header. Simple wrapper of
reproject.reproject_interp
Parameters
----------
fitsfile : string
a FITS file name
header : pyfits.Header
A pyfits Header instance with valid WCS to project to
quiet : bool
Silence Montage's output
Returns
-------
np.ndarray image projected to header's coordinates
"""
import reproject
return reproject.reproject_interp(fitsfile, header, **kwargs)[0]
def regrid(hdu, output_header, order='bilinear'):
outh = output_header['N2HASH']
logger.info('(regrid) output_header={outh}, order={order}'.format(**locals()))
logger.info('(regrid) start calculation'.format(**locals()))
regrided, footprint = reproject.reproject_interp(hdu, output_header, order=order)
logger.info('(regrid) done'.format(**locals()))
new_hdu = astropy.io.fits.PrimaryHDU(regrided, output_header)
hist1 = hdu.header['HISTORY']
hist2 = new_hdu.header['HISTORY']
hist1n2 = '\n'.join([_ for _ in str(hist1).split('\n')
if _.startswith('n2:')])
hist2other = '\n'.join([_ for _ in str(hist1).split('\n')
if not _.startswith('n2:')])
new_hist = hist2other + '\n' + hist1n2
try:
new_hdu.header.pop('HISTORY')
except KeyError:
pass
[new_hdu.header.add_history(_) for _ in new_hist.split('\n')]
if 'BUNIT' in hdu.header: new_hdu.header['BUNIT'] = hdu.header['BUNIT']
if 'BSCALE' in hdu.header: new_hdu.header['BSCALE'] = hdu.header['BSCALE']
if 'BZERO' in hdu.header: new_hdu.header['BZERO'] = hdu.header['BZERO']
if 'BMAJ' in hdu.header: new_hdu.header['BMAJ'] = hdu.header['BMAJ']
if 'BMIN' in hdu.header: new_hdu.header['BMIN'] = hdu.header['BMIN']
if 'BTYPE' in hdu.header: new_hdu.header['BTYPE'] = hdu.header['BTYPE']
if 'BUNIT' in hdu.header: new_hdu.header['BUNIT'] = hdu.header['BUNIT']
if 'OBJECT' in hdu.header: new_hdu.header['OBJECT'] = hdu.header['OBJECT']
if 'MAPID' in hdu.header: new_hdu.header['MAPID'] = hdu.header['MAPID']
if 'MAPVER' in hdu.header: new_hdu.header['MAPVER'] = hdu.header['MAPVER']
if 'RESTFRQ' in hdu.header: new_hdu.header['RESTFRQ'] = hdu.header['RESTFRQ']
if 'SPECSYS' in hdu.header: new_hdu.header['SPECSYS'] = hdu.header['SPECSYS']
if 'LINE' in hdu.header: new_hdu.header['LINE'] = hdu.header['LINE']
if 'TELESCOP' in hdu.header: new_hdu.header['TELESCOP'] = hdu.header['TELESCOP']
if 'INSTRUME' in hdu.header: new_hdu.header['INSTRUME'] = hdu.header['INSTRUME']
return new_hdu
CRVAL2=-2.839256111111E+01,
CDELT2=0.0002777777777777778,
CRPIX2=225.0,
CUNIT2='deg ',)
)
tbl = table.Table.read(paths.tpath("continuum_photometry.ipac"), format='ascii.ipac',)
for imname in files:
tbl.add_column(table.Column(name=imname, data=np.zeros(len(tbl),
dtype='float'),
unit=files[imname]['bunit']))
ffile = fits.open(os.path.join(datapath, files[imname]['filename']))
new_data,_ = reproject.reproject_interp(ffile, alma_hdr)
new_hdu = fits.PrimaryHDU(data=new_data, header=alma_hdr)
files[imname]['file'] = new_hdu
ww = wcs.WCS(files[imname]['file'].header)
files[imname]['wcs'] = ww
assert ww.naxis == 2
# Fix column around Sgr B2
col = files['Column']['file'].data
col_conv = convolve_fft(col, Gaussian2DKernel(5), interpolate_nan=True,
normalize_kernel=True)
files['Column']['file'].data[np.isnan(col)] = col_conv[np.isnan(col)]
files['Column']['file'].data *= 1e21
#!/usr/bin/env python
import numpy as np
from astropy.io import fits
from astropy.wcs import WCS
import glob
# an astropy module to reproject images
from reproject import reproject_interp
import argparse
parser = argparse.ArgumentParser(description ='group objects by filter and target for combining with swarp')
parser.add_argument('--image1', dest = 'image1', default = 'test-ha.fits', help = 'Image to serve as reference')
parser.add_argument('--image2', dest = 'image2', default = 'test-r.fits', help = 'Image to align to reference')
args = parser.parse_args()
hdu1 = fits.open(args.image1)[0]
hdu2 = fits.open(args.image2)[0]
im2new, im2footprint = reproject_interp(hdu2, hdu1.header)
fits.writeto(args.image2.split('.fits')[0]+'-shifted.fits', im2new, hdu1.header, overwrite=True)
#hdu1.close()
#hdu2.close()
def make_cutouts(catalogname, imagename, image_label, apply_rotation=False,
table_format='ascii.ecsv', image_ext=0, clobber=False,
verbose=True):
"""Make cutouts from a 2D image and write them to FITS files.
Catalog must have the following columns with unit info, where applicable:
* ``'id'`` - ID string; no unit necessary.
* ``'ra'`` - RA (e.g., in degrees).
* ``'dec'`` - DEC (e.g., in degrees).
* ``'cutout_x_size'`` - Cutout width (e.g., in arcsec).
* ``'cutout_y_size'`` - Cutout height (e.g., in arcsec).
* ``'cutout_pa'`` - Cutout angle (e.g., in degrees). This is only
use if user chooses to rotate the cutouts. Positive value
will result in a clockwise rotation.
* ``'spatial_pixel_scale'`` - Pixel scale (e.g., in arcsec/pix).
The following are no longer used, so they are now optional:
* ``'slit_pa'`` - Slit angle (e.g., in degrees).
* ``'slit_width'`` - Slit width (e.g., in arcsec).
* ``'slit_length'`` - Slit length (e.g., in arcsec).
Cutouts are organized as follows::
working_dir/
<image_label>_cutouts/
<id>_<image_label>_cutout.fits
Each cutout image is a simple single-extension FITS with updated WCS.
Its header has the following special keywords:
* ``OBJ_RA`` - RA of the cutout object in degrees.
* ``OBJ_DEC`` - DEC of the cutout object in degrees.
* ``OBJ_ROT`` - Rotation of cutout object in degrees.
Parameters
----------
catalogname : str
Catalog table defining the sources to cut out.
imagename : str
Image to cut.
image_label : str
Label to name the cutout sub-directory and filenames.
apply_rotation : bool
Cutout will be rotated to a given angle. Default is `False`.
table_format : str, optional
Format as accepted by `~astropy.table.QTable`. Default is ECSV.
image_ext : int, optional
Image extension to extract header and data. Default is 0.
clobber : bool, optional
Overwrite existing files. Default is `False`.
verbose : bool, optional
Print extra info. Default is `True`.
"""
# Optional dependencies...
from reproject import reproject_interp
table = QTable.read(catalogname, format=table_format)
with fits.open(imagename) as pf:
data = pf[image_ext].data
wcs = WCS(pf[image_ext].header)
# It is more efficient to operate on an entire column at once.
c = SkyCoord(table['ra'], table['dec'])
x = (table['cutout_x_size'] / table['spatial_pixel_scale']).value # pix
y = (table['cutout_y_size'] / table['spatial_pixel_scale']).value # pix
pscl = table['spatial_pixel_scale'].to(u.deg / u.pix)
# Do not rotate if column is missing.
if 'cutout_pa' not in table.colnames:
apply_rotation = False
# Sub-directory, relative to working directory.
path = '{0}_cutouts'.format(image_label)
if not os.path.exists(path):
os.mkdir(path)
cutcls = partial(Cutout2D, data, wcs=wcs, mode='partial')
for position, x_pix, y_pix, pix_scl, row in zip(c, x, y, pscl, table):
if apply_rotation:
pix_rot = row['cutout_pa'].to(u.degree).value
cutout_wcs = WCS(naxis=2)
cutout_wcs.wcs.ctype = ['RA---TAN', 'DEC--TAN']
cutout_wcs.wcs.crval = [position.ra.deg, position.dec.deg]
cutout_wcs.wcs.crpix = [(x_pix - 1) * 0.5, (y_pix - 1) * 0.5]
try:
cutout_wcs.wcs.cd = wcs.wcs.cd
cutout_wcs.rotateCD(-pix_rot)
except AttributeError:
cutout_wcs.wcs.cdelt = wcs.wcs.cdelt
cutout_wcs.wcs.crota = [0, -pix_rot]
cutout_hdr = cutout_wcs.to_header()
try:
cutout_arr = reproject_interp(
(data, wcs), cutout_hdr,
shape_out=(math.floor(y_pix + math.copysign(0.5, y_pix)),
math.floor(x_pix + math.copysign(0.5, x_pix))),
order=2)
except Exception:
if verbose:
log.info('reproject failed: '
'Skipping {0}'.format(row['id']))
continue
cutout_arr = cutout_arr[0] # Ignore footprint
cutout_hdr['OBJ_ROT'] = (pix_rot, 'Cutout rotation in degrees')
else:
try:
cutout = cutcls(position, size=(y_pix, x_pix))
except NoConvergence:
if verbose:
log.info('WCS solution did not converge: '
'Skipping {0}'.format(row['id']))
continue
except NoOverlapError:
if verbose:
log.info('Cutout is not on image: '
'Skipping {0}'.format(row['id']))
continue
else:
cutout_hdr = cutout.wcs.to_header()
cutout_arr = cutout.data
if np.array_equiv(cutout_arr, 0):
if verbose:
log.info('No data in cutout: Skipping {0}'.format(row['id']))
continue
fname = os.path.join(
path, '{0}_{1}_cutout.fits'.format(row['id'], image_label))
# Construct FITS HDU.
hdu = fits.PrimaryHDU(cutout_arr)
hdu.header.update(cutout_hdr)
hdu.header['OBJ_RA'] = (position.ra.deg, 'Cutout object RA in deg')
hdu.header['OBJ_DEC'] = (position.dec.deg, 'Cutout object DEC in deg')
hdu.writeto(fname, clobber=clobber)
if verbose:
log.info('Wrote {0}'.format(fname))
def make_rgb_cube(files, output, north=True):
"""
Make an RGB data cube from a list of three FITS images.
This method can read in three FITS files with different
projections/sizes/resolutions and uses the `reproject
<https://reproject.readthedocs.io/en/stable/>`_ package to reproject them all
to the same projection.
Two files are produced by this function. The first is a three-dimensional
FITS cube with a filename give by ``output``, where the third dimension
contains the different channels. The second is a two-dimensional FITS
image with a filename given by ``output`` with a `_2d` suffix. This file
contains the mean of the different channels, and is required as input to
FITSFigure if show_rgb is subsequently used to show a color image
generated from the FITS cube (to provide the correct WCS information to
FITSFigure).
Parameters
----------
files : tuple or list
A list of the filenames of three FITS filename to reproject.
The order is red, green, blue.
output : str
The filename of the output RGB FITS cube.
north : bool, optional
Whether to rotate the image so that north is up. By default, this is
assumed to be 'north' in the ICRS frame, but you can also pass any
astropy :class:`~astropy.coordinates.BaseCoordinateFrame` to indicate
to use the north of that frame.
"""
# Check that input files exist
for f in files:
if not os.path.exists(f):
raise Exception("File does not exist : " + f)
if north is not False:
frame = ICRS() if north is True else north
auto_rotate = False
else:
frame = None
auto_rotate = True
# Find optimal WCS and shape based on input images
wcs, shape = find_optimal_celestial_wcs(files, frame=frame, auto_rotate=auto_rotate)
header = wcs.to_header()
# Generate empty datacube
image_cube = np.zeros((len(files),) + shape, dtype=np.float32)
# Loop through files and reproject
for i, filename in enumerate(files):
image_cube[i, :, :] = reproject_interp(filename, wcs, shape_out=shape)[0]
# Write out final cube
fits.writeto(output, image_cube, header, overwrite=True)
# Write out collapsed version of cube
fits.writeto(output.replace('.fits', '_2d.fits'),
np.mean(image_cube, axis=0), header, overwrite=True)
model = model[::-1, ::-1]
sd_beam = Beam.from_fits_header(append_path("M33_14B-088_HI_model_channel_330.fits"))
fft_sd = np.fft.fftshift(np.fft.fft2(np.nan_to_num(model)))
# Also load in the original Arecibo channel that has not been regridded.
low_hdu_orig = \
fits.open(append_path("M33_14B-088_HI_model_original_arecibo.fits"))[0]
# The commented out sections were for ensuring that the model matched
# regridded versions using FITS_tools and reproject. On the large scales that
# matter, the answer is yes they do match.
# regrid_model, footprint = reproject_interp(low_hdu_orig, low_hdu.header)
# regrid_model_fitstools = hcongrid(low_hdu_orig.data, low_hdu_orig.header,
# low_hdu.header)
regrid_mask = reproject_interp(mask_hdu, low_hdu_orig.header)[0]
regrid_mask[np.isnan(regrid_mask)] = 0.0
regrid_mask = regrid_mask == 1.0
regrid_mask = nd.binary_fill_holes(regrid_mask)
low_hdu_orig.data[~regrid_mask] = np.NaN
# regrid_model[~mask[::-1, ::-1]] = np.NaN
fft_sd_arecibo = np.fft.fftshift(np.fft.fft2(np.nan_to_num(low_hdu_orig.data)))
pixscale_arecibo = \
wcs.utils.proj_plane_pixel_area(wcs.WCS(low_hdu_orig))**0.5 * \
u.deg
# SD Azimuthal average
def cleaning(filename_cube='paws-pdbi+30m-12co10-1as.cube.fixed', filename_rotmap='paws_rotmod'): """ Argument format: "(filename_cube='paws-pdbi+30m-12co10-1as.cube.fixed', filename_rotmap='paws_rotmod')". Be sure to leave out the ".fits" extension when inputting a file name. filename_cube - the filename of the .fits file containing the uncorrected spectral data that we want to work with. filename_rotmap - the filename of the above file's corresponding rotational velocity map. NOTE: Currently only supports 'paws-pdbi+30m-12co10-1as.cube.fixed' (M51) and 'm33.co21_iram' (M33), along with their respective velocity maps. """ cube = SpectralCube.read(filename_cube+".fits") # This is the cube of the raw, uncorrected data. rot = fits.open(filename_rotmap+'.fits')[0] # Checks if 'reprojection' is necessary. If so, then it reprojects the rotational velocity map to match # the cube's dimensions. data = cube.filled_data[:] # Pulls "cube"'s information (position, spectral info (?)) into a 3D Numpy array. data0 = data.value if (cube.shape[1] == rot.shape[0]) and (cube.shape[2] == rot.shape[1]): # The spatial dimensions of the cube and its rotation map match. Reprojection is not necessary. if filename_cube =='m33.co21_iram': # Checks if we're using the M33 data, which is in m/s for some reason. array = rot.data/1000.0 # If so, converts M33's data from m/s to km/s. else: array = rot.data else: # The spatial dimensions of the cube and its rotation map DO NOT match. Reprojection is necessary, # and the cube information must appear in a moment map for it to work. moment0 = cube.moment(axis=0,order=0) if os.path.isfile(filename_cube+'.mom0.fits') == False: moment0.write(filename_cube+'.mom0.fits') else: print "WARNING: "+filename_cube+".mom0.fits' already exists. Please delete the file and try again." array, footprint = reproject_interp(rot, moment0.header) if filename_cube =='m33.co21_iram': array = array/1000. # Converts M33's data from m/s to km/s. # (!!!) INCOMPLETE (!!!) # This "spec_peak" is not the central velocity of "array". But it should be. if filename_cube =='m33.co21_iram': # Checks if we're dealing with M33 or M51. spec_peak = cube.spectral_axis[data0.shape[0]/2].value / 1000. # M33's data's velocity axis is NOT centered at # zero. Will be accounted for later. else: spec_peak = 0 # (!!!) PICK ONE. At the moment, 'spec_peak' is not the correct value to use. # Neither is np.mean(array), but it's much closer. # array = array - spec_peak # Creates a ROTATIONAL velocity map, centered at zero km/s. array = array - np.mean(array) # Creates a ROTATIONAL velocity map, centered at zero km/s. velocityres = cube.header['CDELT3'] velocityres = velocityres / 1000. # This is the velocity resolution of the raw data file in km/s. # f(x) = magnitude of each entry in 3D cube, where "x" refers to the velocity we're receiving at. There's a different # f(x) for each "position" on the cube. # # For each pixel on the *601x935* velocity distribution plot (which has its own *f(x)*): # 1. Find its *F(s)*, multiply it by *e<sup>$-i2\pi as$</sup>*, where "a" is the rotational velocity at that pixel. # Note: The "s" refers to the corresponding frequencies to the Fourier Transform of f(x). This "s" # should be a vector with the same length as *F(s)*, which in turn has the same length as f(x). # 2. Use that e<sup>$-i2\pi as$</sup> *F(s)* to find *f(x-a)*, and populate an empty matrix with the cube's dimensions with it. # When all *f(x-a)* values are found, the result SHOULD BE a 3D matrix like"cube", but corrected for rotational velocity. vmax,ymax,xmax = data0.shape cleancube = np.zeros(vmax*ymax*xmax).reshape(vmax,ymax,xmax) # This is the final rotation-corrected cube that we'll use. if os.path.isfile(filename_cube+'_CLEANED.fits') == False: for i in range (0,xmax): for j in range (0,ymax): fx = data0[:,j,i] # This is the f(x) mentioned above. fx_bad = np.array(np.isnan(fx), dtype=np.float) # This is an array of all the values in "fx" that are NaN. fx_temp = np.nan_to_num(fx) # Copy of fx, but all NaN values are now zeroes. Fs = np.fft.fft(fx_temp) # This is the F(s) of f(x), including all the NaN values which were # (inaccurately) turned into zeroes. Fs_bad = np.fft.fft(fx_bad) # This is the F_bad(s) of fx_bad. Will be turned into F_bad(x-a) to deal with the # final result. s = np.fft.fftfreq(len(fx_temp)) # These are the frequencies corresponding to each F(s) value. shift = (array[j,i]) / velocityres phase = np.exp(2*np.pi*s*1j * shift) # This "j" is not to be confused with the parameter used in the For loop. fxa = np.fft.ifft(Fs*phase) # This is f(x-a). We just need to turn all those near-zero values back to NaN. fxa_bad = np.fft.ifft(Fs_bad*phase) fxa[fxa_bad>0.001]=np.nan cleancube[:,j,i] = fxa # Populates each "position" with the corrected velocity spectrum. hdu = fits.PrimaryHDU(cleancube,header=cube.header) hdulist = fits.HDUList([hdu]) hdulist.writeto(filename_cube+'_CLEANED.fits') else: print "\n ERROR: "+filename_cube+"_CLEANED.fits' already exists. Please delete the file and try again."
slices = (slice(330, 680), slice(250, 820))
ordering = ["HI", "CO(2-1)", r"H$\alpha$", "24 $\mu$m", "250 $\mu$m", "UV"]
for ii, key in enumerate(ordering):
if key != "HI":
# Why so many redundant axes!!
if key == "CO(2-1)":
arr = data[key].data.squeeze()
mywcs = wcs.WCS(data[key].header).dropaxis(2)
input_data = (arr, mywcs)
else:
input_data = data[key]
# Regrid to the HERACLES data
arr = reproject_interp(input_data, hi_wcs_corr,
shape_out=data["HI"].data.squeeze().shape)[0]
else:
arr = data[key].data.squeeze()
y, x = np.unravel_index(ii, (Nrows, Ncols))
# if key == r"H$\alpha$":
# vmin = 0
# vmax = 10
# else:
vmin = None
vmax = None
im = ax[y, x].imshow(np.arctan(arr[slices] / np.nanpercentile(arr[slices], 85)),
origin='lower', cmap=p.cm.gray_r,
vmin=vmin, vmax=vmax)
ax[y, x].annotate(key, (0.7, 0.9),
vcube7m = cube7m.with_spectral_unit(u.km/u.s, velocity_convention='radio') vcube12m = cube12m.with_spectral_unit(u.km/u.s, velocity_convention='radio') bg7m = vcube7m.spectral_slab(-150*u.km/u.s, -5*u.km/u.s).median(axis=0) bg12m = vcube12m.spectral_slab(-150*u.km/u.s, -5*u.km/u.s).median(axis=0) bg7m12m = vcube7m12m.spectral_slab(-150*u.km/u.s, -5*u.km/u.s).median(axis=0) ch_65kms_7m = vcube7m.closest_spectral_channel(65*u.km/u.s) ch_65kms_12m = vcube12m.closest_spectral_channel(65*u.km/u.s) ch_65kms_7m12m = vcube7m12m.closest_spectral_channel(65*u.km/u.s) slc7m = cube7m[ch_65kms_7m] - bg7m slc12m = cube12m[ch_65kms_12m] - bg12m slc7m12m = vcube7m12m[ch_65kms_12m] - bg7m12m slcTP = reproject_interp(fits.open(tp_fn), slc12m.header)[0] pixscale7m = wcs.utils.proj_plane_pixel_area(cube7m.wcs.celestial)**0.5 * u.deg pixscale12m = wcs.utils.proj_plane_pixel_area(cube12m.wcs.celestial)**0.5 * u.deg pixscaleTP = pixscale12m #old pixscaletp = wcs.utils.proj_plane_pixel_area(wcs.WCS(fits.getheader(tp_fn)))**0.5 * u.deg convbeam_12mto7m = cube7m.beams[ch_65kms_7m].deconvolve(cube12m.beams[ch_65kms_12m]) kernel = convbeam_12mto7m.as_kernel(pixscale12m) slc12m_conv_to_7m = convolve_fft(slc12m.value, kernel) frq7m,pow7m = fft_psd_tools.psds.pspec(fft_psd_tools.psds.PSD2(slc7m.value*jtok_7m[ch_65kms_7m]), view=False) frq12m,pow12m = fft_psd_tools.psds.pspec(fft_psd_tools.psds.PSD2(slc12m.value*jtok_12m[ch_65kms_12m]), view=False) frq12m_conv,pow12m_conv = fft_psd_tools.psds.pspec(fft_psd_tools.psds.PSD2(slc12m_conv_to_7m*jtok_12m[ch_65kms_12m]), view=False) frqTP,powTP = fft_psd_tools.psds.pspec(fft_psd_tools.psds.PSD2(slcTP), view=False) frq7m12m,pow7m12m = fft_psd_tools.psds.pspec(fft_psd_tools.psds.PSD2(slc7m12m.value*jtok_7m12m[ch_65kms_7m12m]), view=False)
def wcs_project(ccd, target_wcs, target_shape=None, order='bilinear'):
"""
Given a CCDData image with WCS, project it onto a target WCS and
return the reprojected data as a new CCDData image.
Any flags, weight, or uncertainty are ignored in doing the
reprojection.
Parameters
----------
ccd : `~ccdproc.CCDData`
Data to be projected.
target_wcs : `~astropy.wcs.WCS` object
WCS onto which all images should be projected.
target_shape : two element list-like or None, optional
Shape of the output image. If omitted, defaults to the shape of the
input image.
Default is ``None``.
order : str, optional
Interpolation order for re-projection. Must be one of:
+ 'nearest-neighbor'
+ 'bilinear'
+ 'biquadratic'
+ 'bicubic'
Default is ``'bilinear'``.
{log}
Returns
-------
ccd : `~ccdproc.CCDData`
A transformed CCDData object.
"""
from reproject import reproject_interp
if not (ccd.wcs.is_celestial and target_wcs.is_celestial):
raise ValueError('one or both WCS is not celestial.')
if target_shape is None:
target_shape = ccd.shape
projected_image_raw, _ = reproject_interp((ccd.data, ccd.wcs),
target_wcs,
shape_out=target_shape,
order=order)
reprojected_mask = None
if ccd.mask is not None:
reprojected_mask, _ = reproject_interp((ccd.mask, ccd.wcs),
target_wcs,
shape_out=target_shape,
order=order)
# Make the mask 1 if the reprojected mask pixel value is non-zero.
# A small threshold is included to allow for some rounding in
# reproject_interp.
reprojected_mask = reprojected_mask > 1e-8
# The reprojection will contain nan for any pixels for which the source
# was outside the original image. Those should be masked also.
output_mask = np.isnan(projected_image_raw)
if reprojected_mask is not None:
output_mask = output_mask | reprojected_mask
# Need to scale counts by ratio of pixel areas
area_ratio = (proj_plane_pixel_area(target_wcs) /
proj_plane_pixel_area(ccd.wcs))
# If nothing ended up masked, don't create a mask.
if not output_mask.any():
output_mask = None
nccd = CCDData(area_ratio * projected_image_raw, wcs=target_wcs,
mask=output_mask,
header=ccd.header, unit=ccd.unit)
return nccd
# the License. You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
#
import numpy as np
import sep
import sys
from astropy.io import fits
from astropy.wcs import WCS
import reproject
from reproject import reproject_interp
from pyspark import SparkContext
if __name__ == "__main__":
sc = SparkContext(appName="Reproject")
rdd = sc.fitsFiles("/Users/zhaozhang/projects/SDSS/data")
header = rdd.take(1).pop().pop().header
rprordd = rdd.map(lambda x: reproject_interp(x.pop(), header))
nrdd = rprordd.zipWithIndex()
nrdd.foreach(lambda ((array, footprint), index): fits.writeto(str(index)+".fits", array, header))
sc.stop()
hi_beam = average_beams(hi_cube.beams)
# Estimate the noise level in an equivalent slab
hi_mom0 = hi_cube.spectral_slab(-180 * u.km / u.s, -183 * u.km / u.s).moment0()
sigma = sig_clip(hi_mom0.value, nsig=10) * \
hi_beam.jtok(hi_freq).value
for i, (end, start) in enumerate(ProgressBar(zip(vels[1:], vels[:-1]))):
hi_slab = hi_cube.spectral_slab(start, end)
hi_mom0 = hi_slab.moment0() * hi_beam.jtok(hi_freq) / u.Jy
# Make the CO slab, then reproject onto the HI grid
co_mom0 = co_cube.spectral_slab(start, end).moment0()
co_mom0_reproj = reproject_interp(co_mom0.hdu, hi_mom0.header)[0]
co_mom0 = Projection(co_mom0_reproj, wcs=hi_mom0.wcs)
# Need a mask from the HI
# Adjust the sigma in a single channel to the moment0 in the slab
# sigma = 0.00152659 * hi_slab.shape[0] * \
# np.abs((hi_slab.spectral_axis[1] - hi_slab.spectral_axis[0]).value)
bub = BubbleFinder2D(hi_mom0, auto_cut=False, sigma=sigma)
bub.create_mask(bkg_nsig=30, region_min_nsig=60, mask_clear_border=False)
# skeleton = medial_axis(~bub.mask)
# skeletons.append(skeleton)
edge_mask = find_boundaries(bub.mask, connectivity=2, mode='outer')
hole_mask = bub.mask.copy()
colors=['r']*11,
levels=[0.015, 0.0256944, 0.0577778, 0.11125, 0.186111,
0.282361, 0.4, ])
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('k')
F.save(paths.fpath("chemistry/{0}_continuum_contours_on_ch3oh_temperature.png".format(source)))
# compare CH3OH LTE column to dust emission
ch3ohN_hdul = fits.open(paths.dpath('12m/moments/CH3OH_{0}_cutout_columnmap.fits'.format(source)))
ch3ohT_hdul = fits.open(paths.dpath('12m/moments/CH3OH_{0}_cutout_temperaturemap.fits'.format(source)))
dust_brightness,wts = reproject.reproject_interp(fits.open(paths.dpath('W51_te_continuum_best.fits')),
ch3ohN_hdul[0].header)
w = wcs.WCS(ch3ohT_hdul[0].header)
pixscale = (w.pixel_scale_matrix.diagonal()**2).sum()**0.5 * u.deg
pl.figure(5).clf()
ch3ohN = ch3ohN_hdul[0].data
ch3ohT = ch3ohT_hdul[0].data
pl.scatter(dust_brightness, ch3ohN, c=ch3ohT, vmax=600, vmin=50,
edgecolor='none', alpha=0.9)
pl.axis((1e-3, 0.2, 1e17, 1e19))
pl.loglog()
pl.xlabel("Dust Brightness (Jy/beam)")
pl.ylabel("N(CH$_3$OH) [cm$^{-2}$]")
cb = pl.colorbar()
cb.set_label('CH$_3$OH-derived Temperature')
#hdu_todata.data = galfa_cube_data[0, :, :]
#new_header = fits.getheader(hdu_todata)#copy.copy(hdu_todata.header)
for thet_i in xrange(nthets):
allsky_fn = path_to_rht_thetaslices + "GALFA_HI_allsky_-10_10_w75_s15_t70_thetabin_"+str(thet_i)+".fits"
allsky_thetaslice_data = fits.getdata(allsky_fn)
allsky_thetaslice_hdr = fits.getheader(allsky_fn)
# try reprojecting allsky thetaslice first
allsky_thetaslice_hdr_new = copy.copy(allsky_thetaslice_hdr)
allsky_thetaslice_hdr_new['CTYPE1'] = 'RA '
allsky_thetaslice_hdr_new['CTYPE2'] = 'DEC '
output0, footprint0 = reproject_interp((allsky_thetaslice_data, allsky_thetaslice_hdr), allsky_thetaslice_hdr_new)
print('theta_i', thet_i)
# Reproject each theta slice into appropriate theta bin in cube
output, footprint = reproject_interp((allsky_thetaslice_data, allsky_thetaslice_hdr), new_header)
rht_data_cube[thet_i, :, :] = output
new_hdr = copy.copy(galfa_cube_hdr)
new_hdr['NAXIS3'] = nthets
new_hdr['CTYPE3'] = 'THETARHT'
new_hdr['CRVAL3'] = 0.000000
new_hdr['CRPIX3'] = 0.000000
new_hdr['CDELT3'] = np.pi/nthets
out_fn = path_to_galfa_cubes + galfa_cube_name + "_RHT.fits"
result = Observations.query_object('M83')
selected_bands = result[(result['obs_collection'] == 'HST') &
(result['instrument_name'] == 'WFC3/UVIS') &
((result['filters'] == 'F657N') |
(result['filters'] == 'F487N') |
(result['filters'] == 'F336W')) &
(result['target_name'] == 'MESSIER-083')]
prodlist = Observations.get_product_list(selected_bands)
filtered_prodlist = Observations.filter_products(prodlist)
downloaded = Observations.download_products(filtered_prodlist)
blue = fits.open(downloaded['Local Path'][2])
red = fits.open(downloaded['Local Path'][5])
green = fits.open(downloaded['Local Path'][8])
target_header = red['SCI'].header
green_repr, _ = reproject.reproject_interp(green['SCI'], target_header)
blue_repr, _ = reproject.reproject_interp(blue['SCI'], target_header)
rgb_img = make_lupton_rgb(ImageNormalize(vmin=0, vmax=1)(red['SCI'].data),
ImageNormalize(vmin=0, vmax=0.3)(green_repr),
ImageNormalize(vmin=0, vmax=1)(blue_repr),
stretch=0.1,
minimum=0,
)
plt.imshow(rgb_img, origin='lower', interpolation='none')
'''
Reproject the CO to match the HI.
Not taking the beam difference into account here since they are quite close.
Once this is merged https://github.com/astrofrog/reproject/pull/115/files,
make a full regrid of the whole cube.
'''
hi_header = fits.getheader(fourteenB_HI_data_path(moment0_name))
co_ico = fits.open(iram_co21_data_path("m33.ico.fits"))[0]
proj = Projection(co_ico.data.squeeze(),
wcs=WCS(co_ico.header).dropaxis(3).dropaxis(2))
rep_array, footprint = reproject_interp(proj.hdu, hi_header)
new_header = hi_header.copy()
# Need to change some of the properties before saving
keys = ["BMAJ", "BMIN", "BPA", "BUNIT"]
for key in keys:
new_header[key] = co_ico.header[key]
new_hdu = fits.PrimaryHDU(rep_array, header=new_header)
new_hdu.writeto(iram_co21_data_path("m33.ico.hireprojection.fits",
no_check=True), clobber=True)