def setUp(self):
xidplus.__path__[0]
# Folder containing maps
imfolder = xidplus.__path__[0] + '/../test_files/'
pswfits = imfolder + 'cosmos_itermap_lacey_07012015_simulated_observation_w_noise_PSW_hipe.fits.gz' # SPIRE 250 map
pmwfits = imfolder + 'cosmos_itermap_lacey_07012015_simulated_observation_w_noise_PMW_hipe.fits.gz' # SPIRE 350 map
plwfits = imfolder + 'cosmos_itermap_lacey_07012015_simulated_observation_w_noise_PLW_hipe.fits.gz' # SPIRE 500 map
# Folder containing prior input catalogue
catfolder = xidplus.__path__[0] + '/../test_files/'
# prior catalogue
prior_cat = 'lacey_07012015_MillGas.ALLVOLS_cat_PSW_COSMOS_test.fits'
# output folder
output_folder = './'
# -----250-------------
hdulist = fits.open(pswfits)
im250phdu = hdulist[0].header
im250hdu = hdulist[1].header
im250 = hdulist[1].data * 1.0E3 # convert to mJy
nim250 = hdulist[2].data * 1.0E3 # convert to mJy
w_250 = wcs.WCS(hdulist[1].header)
pixsize250 = 3600.0 * w_250.wcs.cd[1, 1] # pixel size (in arcseconds)
hdulist.close()
# -----350-------------
hdulist = fits.open(pmwfits)
im350phdu = hdulist[0].header
im350hdu = hdulist[1].header
im350 = hdulist[1].data * 1.0E3 # convert to mJy
nim350 = hdulist[2].data * 1.0E3 # convert to mJy
w_350 = wcs.WCS(hdulist[1].header)
pixsize350 = 3600.0 * w_350.wcs.cd[1, 1] # pixel size (in arcseconds)
hdulist.close()
# -----500-------------
hdulist = fits.open(plwfits)
im500phdu = hdulist[0].header
im500hdu = hdulist[1].header
im500 = hdulist[1].data * 1.0E3 # convert to mJy
nim500 = hdulist[2].data * 1.0E3 # convert to mJy
w_500 = wcs.WCS(hdulist[1].header)
pixsize500 = 3600.0 * w_500.wcs.cd[1, 1] # pixel size (in arcseconds)
hdulist.close()
hdulist = fits.open(catfolder + prior_cat)
fcat = hdulist[1].data
hdulist.close()
inra = fcat['RA']
indec = fcat['DEC']
# select only sources with 100micron flux greater than 50 microJy
sgood = fcat['S100'] > 0.050
inra = inra[sgood]
indec = indec[sgood]
from astropy.coordinates import SkyCoord
from astropy import units as u
c = SkyCoord(ra=[150.74] * u.degree, dec=[2.03] * u.degree)
import pymoc
moc = pymoc.util.catalog.catalog_to_moc(c, 100, 15)
# ---prior250--------
prior250 = xidplus.prior(
im250, nim250, im250phdu, im250hdu, moc=moc
) # Initialise with map, uncertianty map, wcs info and primary header
prior250.prior_cat(inra, indec, prior_cat) # Set input catalogue
prior250.prior_bkg(
-5.0, 5
) # Set prior on background (assumes Gaussian pdf with mu and sigma)
# ---prior350--------
prior350 = xidplus.prior(im350, nim350, im350phdu, im350hdu, moc=moc)
prior350.prior_cat(inra, indec, prior_cat)
prior350.prior_bkg(-5.0, 5)
# ---prior500--------
prior500 = xidplus.prior(im500, nim500, im500phdu, im500hdu, moc=moc)
prior500.prior_cat(inra, indec, prior_cat)
prior500.prior_bkg(-5.0, 5)
self.priors = [prior250, prior350, prior500]
def fourier_combine(
highresfitsfile,
lowresfitsfile,
matching_scale=60 * u.arcsec,
scale=False,
return_hdu=False,
):
"""
Simple reimplementation of 'feather' for 2D images
"""
raise "Obsolete"
f1 = fits.open(highresfitsfile)
w1 = wcs.WCS(f1[0].header)
f2 = fits.open(lowresfitsfile)
w2 = wcs.WCS(f2[0].header)
nax1, nax2 = f1[0].header['NAXIS1'], f1[0].header['NAXIS2']
# We take care of zooming later...
#if not(nax1 == f2[0].header['NAXIS1'] and nax2 == f2[0].header['NAXIS2']):
# raise ValueError("Images are not in the same pixel space; reproject "
# "them to common pixel space first.")
pixscale1 = w1.wcs.get_cdelt()[1]
pixscale2 = w2.wcs.get_cdelt()[1]
center = w1.sub([wcs.WCSSUB_CELESTIAL]).wcs_pix2world([nax1 / 2.],
[nax2 / 2.], 1)
frame = 'icrs' if w1.celestial.wcs.ctype[0][:2] == 'RA' else 'galactic'
if w2.celestial.wcs.ctype[0][:2] == 'RA':
center = coordinates.SkyCoord(*(center * u.deg), frame=frame).fk5
cxy = center.ra.deg, center.dec.deg
elif w2.celestial.wcs.ctype[0][:4] == 'GLON':
center = coordinates.SkyCoord(*(center * u.deg), frame=frame).galactic
cxy = center.l.deg, center.b.deg
im1 = f1[0].data.squeeze()
im1[np.isnan(im1)] = 0
shape = im1.shape
im2raw = f2[0].data.squeeze()
im2raw[np.isnan(im2raw)] = 0
if len(shape) != im2raw.ndim:
raise ValueError("Different # of dimensions in the interferometer and "
"single-dish images")
if len(shape) == 3:
if shape[0] != im2raw.shape[0]:
raise ValueError("Spectral dimensions of cubes do not match.")
center_pixel = w2.sub([wcs.WCSSUB_CELESTIAL
]).wcs_world2pix(cxy[0], cxy[1], 0)[::-1]
zoomed = zoom_on_pixel(np.nan_to_num(im2raw),
center_pixel,
usfac=np.abs(pixscale2 / pixscale1),
outshape=shape)
im2 = zoomed
xax, psd1 = fft_psd_tools.PSD2(im1, oned=True)
xax, psd2 = fft_psd_tools.PSD2(im2, oned=True)
xax_as = (pixscale1 / xax * u.deg).to(u.arcsec)
if scale:
closest_point = np.argmin(np.abs(xax_as - matching_scale))
scale_2to1 = (psd1[closest_point] / psd2[closest_point])**0.5
else:
scale_2to1 = 1
fft1 = np.fft.fft2(im1)
fft2 = np.fft.fft2(im2) * scale_2to1
xgrid, ygrid = (np.indices(shape) -
np.array([(shape[0] - 1.) / 2,
(shape[1] - 1.) / 2.])[:, None, None])
sigma = np.abs(shape[0] / (
(matching_scale /
(pixscale1 * u.deg)).decompose().value)) / np.sqrt(8 * np.log(2))
kernel = np.fft.fftshift(np.exp(-(xgrid**2 + ygrid**2) / (2 * sigma**2)))
kernel /= kernel.max()
fftsum = kernel * fft2 + (1 - kernel) * fft1
combo = np.fft.ifft2(fftsum)
if not return_hdu:
return combo
elif return_hdu:
combo_hdu = fits.PrimaryHDU(data=np.abs(combo), header=w1.to_header())
return combo_hdu
def test_fits_transform():
hdr = fits.Header.fromfile(get_pkg_data_filename('data/simple_wcs2.hdr'))
gw1 = gwutils.make_fitswcs_transform(hdr)
w1 = fitswcs.WCS(hdr)
assert_allclose(gw1(1, 2), w1.wcs_pix2world(1, 2, 1), atol=10**-8)
def add_results(data, imagestretch='linear'):
"""
add results to website
"""
### create lightcurve plots for each target
data['lightcurveplots'] = {}
for target in data['targetnames']:
if sys.version_info < (3, 0):
target = str(target)
logging.info('create lightcurve plot for %s' % target)
plt.plot()
plt.title(target)
plt.xlabel('Observation Midtime (JD)')
plt.ylabel('Magnitude')
plt.errorbar([dat[9][0] for dat in data[target]],
[dat[7] for dat in data[target]],
yerr=[dat[8] for dat in data[target]],
linestyle='', color='black')
plt.ylim([plt.ylim()[1], plt.ylim()[0]])
plt.grid()
plt.savefig('.diagnostics/'
+ ('%s.png' % target.translate(_pp_conf.target2filename)),
format='png')
plt.close()
data['lightcurveplots'][target] = ('.diagnostics/' + '%s.png' %
target.translate(_pp_conf.target2filename))
##### create thumbnail images
data['thumbnailplots'] = {}
data['gifs'] = {}
boxsize = 300 # thumbnail boxsize
for target in data['targetnames']:
if sys.version_info < (3, 0):
target = str(target)
data['thumbnailplots'][target] = []
for dat in data[target]:
for fitsfilename in ['.fits', '.fit']:
fitsfilename = dat[10][:dat[10].find('.ldac')]+fitsfilename
if os.path.isfile(fitsfilename):
break
#= dat[10][:dat[10].find('.ldac')]+'.fits'
hdulist = fits.open(fitsfilename, ignore_missing_end=True)
logging.info('create thumbnail image for %s/%s' % (target,
fitsfilename))
# turn relevant header keywords into floats
# should be fixed in astropy.wcs
for key, val in list(hdulist[0].header.items()):
if 'CD1' in key or 'CD2' in key or \
'CRVAL' in key or 'CRPIX' in key or \
'EQUINOX' in key:
hdulist[0].header[key] = float(val)
# if 'PV1' in key or 'PV2' in key:
# del hdulist[0].header[key]
w = wcs.WCS(hdulist[0].header)
obj_x, obj_y = dat[11], dat[12]
image_coords = w.wcs_world2pix(numpy.array([[dat[1], dat[2]]]),
True)
exp_x, exp_y = image_coords[0][0], image_coords[0][1]
# create margin around image allowing for any cropping
composite = numpy.zeros((hdulist[0].data.shape[0]+2*boxsize,
hdulist[0].data.shape[1]+2*boxsize))
composite[boxsize:boxsize+hdulist[0].data.shape[0],
boxsize:boxsize+hdulist[0].data.shape[1]] = \
hdulist[0].data
# extract thumbnail data accordingly
thumbdata = composite[int(boxsize+obj_y-old_div(boxsize,2)):
int(boxsize+obj_y+old_div(boxsize,2)),
int(boxsize+obj_x-old_div(boxsize,2)):
int(boxsize+obj_x+old_div(boxsize,2))]
## run statistics over center of the frame around the target
if thumbdata.shape[0] > 0 and thumbdata.shape[1] > 0:
norm = ImageNormalize(thumbdata, interval=ZScaleInterval(),
stretch={'linear': LinearStretch(),
'log': LogStretch()}[imagestretch])
# extract aperture radius
if _pp_conf.photmode == 'APER':
aprad = float(hdulist[0].header['APRAD'])
# create plot
#plotsize = 7. # inches
fig = plt.figure()
img = plt.imshow(thumbdata, cmap='gray',
origin='lower', norm=norm)
# remove axes
plt.axis('off')
img.axes.get_xaxis().set_visible(False)
img.axes.get_yaxis().set_visible(False)
plt.annotate('%s\n%5.3f+-%5.3f mag' % (fitsfilename,
dat[7], dat[8]), (3,10),
color='white')
# place aperture
if _pp_conf.photmode == 'APER':
targetpos = plt.Circle((boxsize/2, boxsize/2),
aprad, ec='red', fc='none',
linewidth=1)
else:
targetpos = plt.Rectangle((boxsize/2-7, boxsize/2-7),
15, 15, ec='red', fc='none',
linewidth=1)
plt.gca().add_patch(targetpos)
# place expected position (if within thumbnail)
if (abs(exp_x-obj_x) <= old_div(boxsize,2.) and
abs(exp_y-obj_y) <= old_div(boxsize,2.)):
plt.scatter(exp_x-obj_x+old_div(boxsize,2.),
exp_y-obj_y+old_div(boxsize,2.),
marker='+', s=100, color='green')
thumbfilename = '.diagnostics/' + \
target.translate(_pp_conf.target2filename) + '_' + \
fitsfilename[:fitsfilename.find('.fit')] + \
'_thumb.png'
plt.savefig(thumbfilename, format='png',
bbox_inches='tight',
pad_inches=0)
plt.close()
hdulist.close()
data['thumbnailplots'][target].append((fitsfilename,
thumbfilename))
else:
logging.warning('cannot produce thumbnail image ' + \
'for %s in frame %s' % (target, dat[10]))
continue
## create gif animation
gif_filename = ('%s.gif' % target.translate(_pp_conf.target2filename))
logging.info('converting images to gif: %s' % gif_filename)
root = os.getcwd()
os.chdir(_pp_conf.diagroot)
try:
convert = subprocess.Popen(['convert', '-delay', '50',
('%s*thumb.png' %
(target.translate(_pp_conf.target2filename))),
'-loop', '0',
('%s' % gif_filename)])
convert.wait()
except:
logging.warning('could not produce gif animation for ' \
+ 'target %s' % target)
data['gifs'][target] = '.diagnostics/' + gif_filename
os.chdir(root)
### create results website for each target
data['resultswebsites'] = {}
for target in data['targetnames']:
if sys.version_info < (3, 0):
target = str(target)
html = "<H2>%s - Photometric Results</H2>\n" % target
html += "<P><IMG SRC=\"%s\">\n" % \
data['lightcurveplots'][target].split('.diagnostics/')[1]
html += "<IMG SRC=\"%s\">\n" % \
data['gifs'][target].split('.diagnostics/')[1]
# create summary table
html += "<TABLE BORDER=\"1\">\n<TR>\n"
html += "<TH>Filename</TH><TH>Julian Date</TH><TH>Target (mag)</TH>" \
+ "<TH>sigma (mag)</TH><TH>Target RA (deg)</TH>" \
+ "<TH>Target Dec (deg)</TH><TH>RA Offset (\")</TH>" \
+ "<TH>Dec Offset (\")</TH>\n</TR>\n"
for dat in data[target]:
html += ("<TR><TD><A HREF=\"#%s\">%s</A></TD>" \
+ "<TD>%15.7f</TD><TD>%7.4f</TD>" \
+ "<TD>%6.4f</TD><TD>%13.8f</TD>" \
+ "<TD>%+13.8f</TD><TD>%5.2f</TD><TD>%5.2f</TD>\n" \
+ "</TR>\n" )% \
(dat[10], dat[10], dat[9][0], dat[7], dat[8], dat[3], dat[4],
((dat[1]-dat[3])*3600.), ((dat[2]-dat[4])*3600.))
html += "</TABLE>\n"
# plot individual thumbnails
html += "<H3>Thumbnails</H3>\n"
for idx, plts in enumerate(data['thumbnailplots'][target]):
html += "<P>%s<IMG ID=\"%s\" SRC=\"%s\">\n" % (plts[0],
data[target][idx][10],
plts[1].split('.diagnostics/')[1])
filename = '.diagnostics/' + \
target.translate(_pp_conf.target2filename) + \
'_' + 'results.html'
create_website(filename, html)
data['resultswebsites'][target] = filename
### update index.html
html = "<H2>Photometry Results</H2>\n"
html += "<P>photometric data obtained for %d object(s): \n" % \
len(data['targetnames'])
for target in data['targetnames']:
html += "<BR><A HREF=\"%s\">%s</A>\n" % \
(data['resultswebsites'][target], target)
for target in data['targetnames']:
html += "<P><IMG SRC=\"%s\">\n" % data['lightcurveplots'][target]
html += "<IMG SRC=\"%s\">\n" % data['gifs'][target]
append_website(_pp_conf.index_filename, html,
replace_below="<H2>Photometry Results</H2>\n")
return None
def hcongrid(image, header1, header2, **kwargs):
"""
Interpolate an image from one FITS header onto another
kwargs will be passed to `scipy.ndimage.map_coordinates`
Parameters
----------
image : ndarray
A two-dimensional image
header1 : `pyfits.Header` or `pywcs.WCS`
The header or WCS corresponding to the image
header2 : `pyfits.Header` or `pywcs.WCS`
The header or WCS to interpolate onto
Returns
-------
ndarray with shape defined by header2's naxis1/naxis2
Raises
------
TypeError if either is not a Header or WCS instance
Exception if image1's shape doesn't match header1's naxis1/naxis2
Examples
--------
(not written with >>> because test.fits/test2.fits do not exist)
fits1 = pyfits.open('test.fits')
target_header = pyfits.getheader('test2.fits')
new_image = hcongrid(fits1[0].data, fits1[0].header, target_header)
"""
if issubclass(pywcs.WCS, header1.__class__):
wcs1 = header1
else:
try:
wcs1 = pywcs.WCS(header1)
except:
raise TypeError(
"Header1 must either be a pyfits.Header or pywcs.WCS instance")
if not (wcs1.naxis1 == image.shape[1] and wcs1.naxis2 == image.shape[0]):
raise Exception("Image shape must match header shape.")
if issubclass(pywcs.WCS, header2.__class__):
wcs2 = header2
else:
try:
wcs2 = pywcs.WCS(header2)
except:
raise TypeError(
"Header2 must either be a pyfits.Header or pywcs.WCS instance")
if not all([w1 == w2 for w1, w2 in zip(wcs1.wcs.ctype, wcs2.wcs.ctype)]):
# do unit conversions
raise NotImplementedError(
"Unit conversions have not yet been implemented.")
# sigh... why does numpy use matrix convention? Makes everything so much harder...
outshape = [wcs2.naxis2, wcs2.naxis1]
yy2, xx2 = np.indices(outshape)
lon2, lat2 = wcs2.wcs_pix2sky(xx2, yy2, 0)
xx1, yy1 = wcs1.wcs_sky2pix(lon2, lat2, 0)
grid1 = np.array([yy1.reshape(outshape), xx1.reshape(outshape)])
newimage = scipy.ndimage.map_coordinates(np.nan_to_num(image), grid1,
**kwargs)
return newimage
def make_narrowband_image(
detectid=None,
coords=None,
shotid=None,
pixscale=0.25 * u.arcsec,
imsize=30.0 * u.arcsec,
wave_range=None,
convolve_image=True,
ffsky=True,
subcont=False,
dcont=50.,
):
"""
Function to make narrowband image from either a detectid or from a
coordinate/shotid combination.
Paramaters
----------
detectid: int
detectid from the continuum or lines catalog. Default is
None. Provide a coords/shotid combo if this isn't given
coords: SkyCoords object
coordinates to define the centre of the data cube
pixscale: astropy angle quantity
plate scale
imsize: astropy angle quantity
image size
wave_range: list or None
start and stop value for the wavelength range in Angstrom.
If not given, the detectid linewidth is used
convolve_image: bool
option to convolve image with shotid seeing
ffsky: bool
option to use full frame calibrated fibers. Default is
True.
subcont: bool
option to subtract continuum. Default is False. This
will measure the continuum 50AA below and above the
input wave_range
dcont
width in angstrom to measure the continuum. Default is to
measure 50 AA wide regions on either side of the line
Returns
-------
hdu: PrimaryHDU object
the 2D summed data array and associated 2d header
Units are '10^-17 erg cm-2 s-1'
Examples
--------
For a specific detectid:
>>> hdu = make_narrowband_image(detectid=2101046271)
For a SkyCoords object. You must provide shotid and
wavelength range
>>> coords = SkyCoord(188.79312, 50.855747, unit='deg')
>>> wave_obj = 4235.84 #in Angstrom
>>> hdu = make_narrowband_image(coords=coords,
shotid=20190524021,
wave_range=[wave_obj-10, wave_obj+10])
"""
global config, detecth5, surveyh5
if detectid is not None:
detectid_obj = detectid
det_info = detecth5.root.Detections.read_where("detectid == detectid_obj")[0]
shotid_obj = det_info["shotid"]
wave_obj = det_info["wave"]
linewidth = det_info["linewidth"]
wave_range = [wave_obj - 2.0 * linewidth,
wave_obj + 2.0 * linewidth]
coords = SkyCoord(det_info["ra"], det_info["dec"], unit="deg")
elif coords is not None:
if shotid is not None:
shotid_obj = shotid
else:
print("Provide a shotid")
if wave_range is None:
print(
"Provide a wavelength range to collapse. \
Example wave_range=[4500,4540]"
)
else:
print("Provide a detectid or both a coords and shotid")
fwhm = surveyh5.root.Survey.read_where("shotid == shotid_obj")["fwhm_virus"][0]
E = Extract()
E.load_shot(shotid_obj)
# get spatial dims:
ndim = int(imsize / pixscale)
center = int(ndim / 2)
rad = imsize
info_result = E.get_fiberinfo_for_coord(coords, radius=rad, ffsky=ffsky)
ifux, ifuy, xc, yc, ra, dec, data, error, mask = info_result
# get ifu center:
ifux_cen, ifuy_cen = E.convert_radec_to_ifux_ifuy(
ifux, ifuy, ra, dec, coords.ra.deg, coords.dec.deg
)
zarray = E.make_narrowband_image(
ifux_cen,
ifuy_cen,
ifux,
ifuy,
data,
mask,
seeing_fac=fwhm,
scale=pixscale.to(u.arcsec).value,
boxsize=imsize.to(u.arcsec).value,
wrange=wave_range,
convolve_image=convolve_image,
)
imslice = zarray[0]
if subcont:
zarray_blue = E.make_narrowband_image(
ifux_cen,
ifuy_cen,
ifux,
ifuy,
data,
mask,
seeing_fac=fwhm,
scale=pixscale.to(u.arcsec).value,
boxsize=imsize.to(u.arcsec).value,
wrange=[wave_range[0]-dcont, wave_range[0]],
convolve_image=convolve_image,
)
zarray_red = E.make_narrowband_image(
ifux_cen,
ifuy_cen,
ifux,
ifuy,
data,
mask,
seeing_fac=fwhm,
scale=pixscale.to(u.arcsec).value,
boxsize=imsize.to(u.arcsec).value,
wrange=[wave_range[1], wave_range[1]+dcont],
convolve_image=convolve_image,
)
dwave = wave_range[1]-wave_range[0]
im_cont = (zarray_blue[0] + zarray_red[0])/(2*dcont)
imslice = zarray[0] - dwave*im_cont
w = wcs.WCS(naxis=2)
imsize = imsize.to(u.arcsec).value
w.wcs.crval = [coords.ra.deg, coords.dec.deg]
w.wcs.crpix = [center, center]
w.wcs.ctype = ["RA---TAN", "DEC--TAN"]
w.wcs.cdelt = [-pixscale.to(u.deg).value, pixscale.to(u.deg).value]
hdu = fits.PrimaryHDU(imslice, header=w.to_header())
return hdu
def add_registration(data, extraction_data, imagestretch='linear'):
"""
add registration results to website
"""
obsparam = extraction_data[0]['parameters']['obsparam']
# create registration website
html = "<H2>Registration Results</H2>\n"
html += "<TABLE BORDER=\"1\">\n<TR>\n"
html += "<TH>Filename</TH><TH>AS_CONTRAST</TH><TH>XY_CONTRAST</TH>" \
+ "<TH>RA_sig (arcsec)</TH><TH>DEC_sig (arcsec)</TH>" \
+ "<TH>Chi2_Reference</TH><TH>Chi2_Internal</TH>\n</TR>\n"
for dat in data['fitresults']:
html += ("<TR><TD><A HREF=\"%s\">%s</A></TD>" \
+ "<TD>%4.1f</TD><TD>%4.1f</TD>" \
+ "<TD>%5.3f</TD><TD>%5.3f</TD>" \
+ "<TD>%e</TD><TD>%e</TD>\n</TR>\n" )% \
(dat[0] + '_astrometry.png',
dat[0], dat[1], dat[2], dat[3], dat[4], dat[5], dat[6])
html += "</TABLE>\n"
html += "<P>AS_CONTRAST: position angle/scale contrast " + \
"(>%.1f usually ok)\n" % _pp_conf.scamp_as_contrast_limit
html += "<BR>XY_CONTRAST: xy-shift contrast (>%.1f usually ok)\n" % \
_pp_conf.scamp_xy_contrast_limit
create_website(_pp_conf.reg_filename, content=html)
# load reference catalog
refcat = catalog(data['catalog'])
for filename in os.listdir('.'):
if data['catalog'] in filename and '.cat' in filename:
refcat.read_ldac(filename)
break
### create frame images
for dat in extraction_data:
framefilename = '.diagnostics/' + dat['fits_filename'] + \
'_astrometry.png'
imgdat = fits.open(dat['fits_filename'],
ignore_missing_end=True)[0].data
resize_factor = min(1., 1000./numpy.max(imgdat.shape))
# clip extreme values to prevent crash of imresize
imgdat = numpy.clip(imgdat, numpy.percentile(imgdat, 1),
numpy.percentile(imgdat, 99))
imgdat = imresize(imgdat, resize_factor, interp='nearest')
header = fits.open(dat['fits_filename'],
ignore_missing_end=True)[0].header
norm = ImageNormalize(imgdat, interval=ZScaleInterval(),
stretch={'linear': LinearStretch(),
'log': LogStretch()}[imagestretch])
# turn relevant header keys into floats
# astropy.io.fits bug
for key, val in list(header.items()):
if 'CD1_' in key or 'CD2_' in key or \
'CRVAL' in key or 'CRPIX' in key or \
'EQUINOX' in key:
header[key] = float(val)
plt.figure(figsize=(5, 5))
img = plt.imshow(imgdat, cmap='gray', norm=norm,
origin='lower')
# remove axes
plt.axis('off')
img.axes.get_xaxis().set_visible(False)
img.axes.get_yaxis().set_visible(False)
# plot reference sources
if refcat.shape[0] > 0:
try:
w = wcs.WCS(header)
world_coo = numpy.array(list(zip(refcat['ra.deg'],
refcat['dec.deg'])))
img_coo = w.wcs_world2pix(world_coo, True )
img_coo = [c for c
in img_coo if (c[0] > 0 and c[1] > 0 and
c[0] < header[obsparam['extent'][0]]
and
c[1] < header[obsparam['extent'][1]])]
plt.scatter([c[0]*resize_factor for c in img_coo],
[c[1]*resize_factor for c in img_coo],
s=5, marker='o', edgecolors='red', linewidth=0.1,
facecolor='none')
except astropy.wcs._wcs.InvalidTransformError:
logging.error('could not plot reference sources due to '
'astropy.wcs._wcs.InvalidTransformError; '
'most likely unknown distortion parameters.')
plt.savefig(framefilename, format='png', bbox_inches='tight',
pad_inches=0, dpi=200)
plt.close()
# update index.html
html = '<H2>Registration</H2>\n'
html += '%d/%d files have been registered successfully based on %s; ' % \
(len(data['goodfits']), len(data['goodfits']+data['badfits']),
data['catalog'])
if len(data['badfits']) > 0:
html += '<B>%d files could not be registered</B>;' % \
len(data['badfits'])
html += 'see <A HREF=\"%s\">registration website</A> for details\n' % \
_pp_conf.reg_filename
append_website(_pp_conf.index_filename, html,
replace_below="<H2>Registration Results</H2>\n")
return None
def hdr_cood(filename):
hdulist = pf.open(filename)
w = wcs.WCS(hdulist[0].header)
hdulist.close()
return w
bad_ra, bad_dec, bad_z, bad_bcgx, bad_bcgy = [], [], [], [], []
norm_ra, norm_dec, norm_z, norm_bcgx, norm_bcgy = [], [], [], [], []
for kk in range(len(set_z)):
ra_g, dec_g, z_g = set_ra[kk], set_dec[kk], set_z[kk]
#file = home + 'wget_data/frame-%s-ra%.3f-dec%.3f-redshift%.3f.fits.bz2' % ('r', ra_g, dec_g, z_g)
file = home + 'redMap_random/rand_img-%s-ra%.3f-dec%.3f-redshift%.3f.fits.bz2' % (
'r', ra_g, dec_g, z_g)
data = fits.open(file)
img = data[0].data
head = data[0].header
wcs_lis = awc.WCS(head)
xn, yn = wcs_lis.all_world2pix(ra_g * U.deg, dec_g * U.deg, 1)
Da_g = Test_model.angular_diameter_distance(z_g).value
hdu = fits.PrimaryHDU()
hdu.data = img
hdu.header = head
hdu.writeto('test.fits', overwrite=True)
param_A = 'default_mask_A.sex'
out_cat = 'default_mask_A.param'
#out_load_A = load + 'source_find/mask_ra%.3f_dec%.3f_z%.3f_band-%s.cat' % (ra_g, dec_g, z_g, 'r')
#out_load_A = load + 'source_find/rand_mask_ra%.3f_dec%.3f_z%.3f_band-%s.cat' % (ra_g, dec_g, z_g, 'r')
# Set the WCS information manually by setting properties of the WCS # object. from __future__ import division, print_function import numpy from astropy import wcs from astropy.io import fits # Create a new WCS object. The number of axes must be set # from the start w = wcs.WCS(naxis=2) # Set up an "Airy's zenithal" projection # Vector properties may be set with Python lists, or Numpy arrays w.wcs.crpix = [-234.75, 8.3393] w.wcs.cdelt = numpy.array([-0.066667, 0.066667]) w.wcs.crval = [0, -90] w.wcs.ctype = ["RA---AIR", "DEC--AIR"] w.wcs.set_pv([(2, 1, 45.0)]) # Some pixel coordinates of interest. pixcrd = numpy.array([[0, 0], [24, 38], [45, 98]], numpy.float_) # Convert pixel coordinates to world coordinates world = w.wcs_pix2world(pixcrd, 1) print(world) # Convert the same coordinates back to pixel coordinates. pixcrd2 = w.wcs_world2pix(world, 1) print(pixcrd2)
from astropy import wcs
from astropy.io import fits
from astropy import units as u
from astropy import constants as const
from spectral_cube import SpectralCube
import spectral_cube
# _____________________________________
file = "./../Data/higal_data/column_properunits_conv36_source_only.fits"
hdu = fits.open(file)[0]
dend = astrodendro.Dendrogram.load_from("./../Dendrogram_files/clouds_only_dendrogram.fits")
leaves = dend.leaves[9:(len(dend.leaves)-3)]
colfile = file
header = fits.getheader(colfile)
mywcs = wcs.WCS(header)
molecules = ["C18O", "13CO", "H2CO_303_202"]
for mol in molecules:
if mol == "C18O":
cube_file = './APEX_data/APEX_C18O_2014_merge.fits'
if mol == "13CO":
cube_file = './APEX_data/APEX_13CO_2014_merge.fits'
if mol == "H2CO_303_202":
cube_file = './APEX_data/APEX_H2CO_303_202_bl.fits'
cube = SpectralCube.read(cube_file)
cube_header = cube.header.copy()
cube_header.update(mywcs.to_header())
cube_header['NAXIS1'] = header['NAXIS1']
def main(fits_model_root,
skymodel,
ref_freq='60e6',
fits_mask=None,
min_peak_flux_jy=0.001,
max_residual_jy=0.00,
interp='linear'):
"""
Make a makesourcedb sky model for input MS from WSClean fits model images
Parameters
----------
fits_model_root : str
Root name of WSClean fits model files (without the "-XXXX-model.fits" part)
skymodel : str
Filename of the output makesourcedb sky model
ref_freq : float, optional
Reference freq of the output catalogue in Hz
fits_mask : str, optional
Filename of fits mask
min_peak_flux_jy : float, optional
Minimum absolute value of flux in Jy of a source in lowest-frequency model image
to include in output model
max_residual_jy : float, optional
Maximum acceptible total residual absolute flux in Jy
interp : str, optional
Interpolation method. Can be any supported by scipy.interpolate.interp1d:
'linear', 'nearest', 'zero', 'slinear', 'quadratic', 'cubic'
"""
min_peak_flux_jy = float(min_peak_flux_jy)
max_residual_jy = float(max_residual_jy)
if type(fits_mask) is str:
if fits_mask.lower() == 'none':
fits_mask = None
# Find model images: look first for channel images and MFS image
fits_models = glob.glob(fits_model_root + '-*-model.fits')
if len(fits_models) > 0:
# Get the MFS image
mfs_model = fits_model_root + '-MFS-model.fits'
else:
# No channels images found, so look for non-MFS images
fits_models = glob.glob(fits_model_root + '-model.fits')
mfs_model = None
if len(fits_models) == 0:
print('ERROR: no model images found')
sys.exit(1)
# Read in model images
freqs = []
model_images = []
for f in fits_models:
# Get the frequency info
hdr = fits.getheader(f, 0, ignore_missing_end=True)
freqs.append(hdr['CRVAL3']) # Hz
model_images.append(fits.getdata(f, 0, ignore_missing_end=True))
w = wcs.WCS(hdr)
# Read in MFS image
if mfs_model is None:
mfs_model = fits_models[0]
mfs_image = fits.getdata(mfs_model, 0, ignore_missing_end=True)
# Sort by freq
sorted_ind = np.argsort(freqs)
freqs = np.array(freqs)[sorted_ind]
fits_models = np.array(fits_models)[sorted_ind]
model_images = np.array(model_images)[sorted_ind]
# Find pixels that meet the flux cut (and are in the mask, if given)
if fits_mask is not None:
if fits_mask.lower() == 'empty':
# Handle case in which no sources were found during masking
nonzero_ind = [[], []]
else:
mask = fits.getdata(fits_mask, 0, ignore_missing_end=True)
nonzero_ind = np.where((np.abs(mfs_image) > min_peak_flux_jy)
& (mask > 0))
else:
nonzero_ind = np.where(np.abs(mfs_image) > min_peak_flux_jy)
# Interpolate the fluxes to the frequency of the MS
nsources = len(nonzero_ind[0])
fluxes = []
names = []
ras = []
decs = []
for i in range(nsources):
index = [nonzero_ind[j][i] for j in range(4)]
index.reverse() # change to WCS coords
ras.append(
w.wcs_pix2world(np.array([index]), 0, ra_dec_order=True)[0][0])
decs.append(
w.wcs_pix2world(np.array([index]), 0, ra_dec_order=True)[0][1])
names.append('cc{}'.format(i))
index.reverse() # change back to image coords
flux_array = np.array([im[tuple(index)] for im in model_images])
# If MS frequency lies outside range, just use nearest freq
if ref_freq < freqs[0]:
flux = flux_array[0]
elif ref_freq > freqs[-1]:
flux = flux_array[-1]
else:
# Otherwise interpolate
flux = scipy.interpolate.interp1d(freqs, flux_array,
kind=interp)(ref_freq)
fluxes.append(flux)
# Remove sources until we reach the desired residual
if len(fluxes) > 0:
total_flux = np.sum(np.abs(fluxes))
keep_ind = np.where(np.abs(fluxes) > min_peak_flux_jy)
while (total_flux -
np.sum(np.abs(np.array(fluxes)[keep_ind]))) < max_residual_jy:
min_peak_flux_jy *= 1.1
keep_ind = np.where(np.abs(fluxes) > min_peak_flux_jy)
if len(keep_ind[0]) < 50:
# keep up to 50 sources regardless of the residual
break
fluxes = np.array(fluxes)[keep_ind]
ras = np.array(ras)[keep_ind]
decs = np.array(decs)[keep_ind]
names = np.array(names)[keep_ind]
# Write sky model
with open(skymodel, 'w') as outfile:
outfile.write(
'FORMAT = Name, Type, Ra, Dec, I, Q, U, V, ReferenceFrequency\n')
for name, ra, dec, flux in zip(names, ras, decs, fluxes):
ra_str, dec_str = convert_radec_str(ra, dec)
outfile.write(
'{0}, POINT, {1}, {2}, {3}, 0.0, 0.0, 0.0, {4}\n'.format(
name, ra_str, dec_str, flux, ref_freq))
imlist = [init,sc1,sc2,sc3,sc4,sc5,sc5tt,sc6tt]
residlist = [rinit,rsc1,rsc2,rsc3,rsc4,rsc5,rsc5tt,rsc6tt]
for name, ((ra1,dec1),(ra2,dec2)),(vmin,vmax) in [
('SgrB2M', ((ra1m,dec1m),(ra2m,dec2m)), [-0.001, 0.1]),
('SgrB2S', ((ra1s,dec1s),(ra2s,dec2s)), [-0.001, 0.05]),]:
fig = pl.figure(1, figsize=(20,6), dpi=75)
fig.clf()
for ii, (fh,rfh) in enumerate(zip(imlist,
residlist)
):
print(ii,fh,rfh)
mywcs = wcs.WCS(fh[0].header)
center = coordinates.SkyCoord((ra1+ra2)/2, (dec1+dec2)/2, frame='fk5',
unit=(u.deg, u.deg))
size = max([np.abs(ra2-center.ra.deg), np.abs(dec2-center.dec.deg)]) * 2.1 * u.deg
cutout_im = Cutout2D(fh[0].data, position=center, size=size, wcs=mywcs)
cutout_res = Cutout2D(rfh[0].data, position=center, size=size,
wcs=mywcs)
ax = fig.add_subplot(2,len(imlist),ii+1, projection=cutout_im.wcs)
im = ax.imshow(cutout_im.data*1e3, cmap='gray',
norm=astropy.visualization.simple_norm(fh[0].data,
stretch='asinh',
min_cut=vmin*1e3,
max_cut=vmax*1e3,
asinh_a=0.001),
transform=ax.get_transform(cutout_im.wcs),
def draw_rectangles(img,
catalog,
colnames=['x', 'y'],
header=None,
ax=None,
rectangle_size=[30, 30],
pixel_scale=0.168,
color='r',
**kwargs):
"""
Draw rectangles on an image according to a catalogue.
Parameters:
img (numpy 2-D array): Image itself.
catalog (``astropy.table.Table`` object): A catalog which contains positions.
colnames (list): List of string, indicating which columns correspond to positions.
It can also be "ra" and "dec", but then "header" is needed.
header: Header file of a FITS image containing WCS information, typically ``astropy.io.fits.header`` object.
ax (``matplotlib.pyplot.axes`` object): The user could provide axes on which the figure will be drawn.
rectangle_size (list of floats): Size of rectangles, in pixel.
pixel_scale (float): Pixel size, in arcsec/pixel. Needed for correct scale bar.
color (str): Color of rectangles.
**kwargs: other arguments of ``display_single``.
Returns:
ax: If the input ``ax`` is not ``None``.
"""
if ax is None:
fig = plt.figure(figsize=(12, 12))
fig.subplots_adjust(left=0.0,
right=1.0,
bottom=0.0,
top=1.0,
wspace=0.00,
hspace=0.00)
gs = gridspec.GridSpec(2, 2)
gs.update(wspace=0.0, hspace=0.00)
ax1 = fig.add_subplot(gs[0])
else:
ax1 = ax
# ax1.yaxis.set_major_formatter(NullFormatter())
# ax1.xaxis.set_major_formatter(NullFormatter())
# ax1.axis('off')
from matplotlib.patches import Rectangle
if np.any([item.lower() == 'ra' for item in colnames]):
if header is None:
raise ValueError(
'# Header containing WCS must be provided to convert sky coordinates into image coordinates.'
)
return
else:
w = wcs.WCS(header)
x, y = w.wcs_world2pix(
Table(catalog)[colnames[0]].data.data,
Table(catalog)[colnames[1]].data.data, 0)
else:
x, y = catalog[colnames[0]], catalog[colnames[1]]
display_single(img, ax=ax1, pixel_scale=pixel_scale, **kwargs)
for i in range(len(catalog)):
e = Rectangle(xy=(x[i] - rectangle_size[0] // 2,
y[i] - rectangle_size[1] // 2),
height=rectangle_size[0],
width=rectangle_size[1],
angle=0)
e.set_facecolor('none')
e.set_edgecolor(color)
e.set_alpha(0.7)
e.set_linewidth(1.3)
ax1.add_artist(e)
if ax is not None:
return ax
f.close()
print(ra, dec, field, ccd_num)
path = '/fred/oz100/pipes/DWF_PIPE/MARY_WORK/' + field + '_18060*_mrt1_*/ccd' + ccd_num + '/images_resampled/sci_*.resamp.fits'
print(path)
path_insidefield = []
fitsfileslist = glob.glob(path)
#print(fitsfileslist)
mydic = {}
for path in fitsfileslist:
hdulist = fits.open(path)
w = wcs.WCS(hdulist[0].header)
head = hdulist[0].header
print(head)
xlim = head['NAXIS1']
ylim = head['NAXIS2']
date = dt.datetime.strptime(head['DATE'], '%Y-%m-%dT%H:%M:%S')
pixcrd = np.array([[ra, dec]], np.float_)
print(pixcrd)
worldpix = w.wcs_world2pix(pixcrd, 1)
pixx, pixy = worldpix[0][0], worldpix[0][1]
print(pixx, pixy)
if pixy < ylim and pixy > 0 and pixx < xlim and pixx > 0:
path_insidefield.append(path)
def fits_XY(image_path,RA,DEC):
img, hdr = fits.getdata(image_path,header=True)
img = img.astype(np.float64)
w = wcs.WCS(hdr)
RA_px, DEC_px = w.all_world2pix(RA,DEC,0)
return RA_px, DEC_px, img, hdr
def __init__(self, image, ext, dq_bits=0, dqimage=None, dqext=None,
usermask=None, usermask_ext=None):
"""
Parameters
----------
image: ImageRef
An :py:class:`~stsci.skypac.utils.ImageRef` object that refers
to an open FITS file
ext: tuple, int, str
Extension specification in the `image` the `SkyLineMember`
object will be associated with.
An int `ext` specifies extension number. A tuple in the form
(str, int) specifies extension name and number. A string `ext`
specifies extension name and the extension version is assumed
to be 1. See documentation for `astropy.io.fits.getData`
for examples.
dq_bits: int, None (Default = 0)
Integer sum of all the DQ bit values from the
input `image`'s DQ array that should be considered "good"
when building masks for sky computations. For example,
if pixels in the DQ array can be combinations of 1, 2, 4,
and 8 flags and one wants to consider DQ "defects" having
flags 2 and 4 as being acceptable for sky computations,
then `dq_bits` should be set to 2+4=6. Then a DQ pixel
having values 2,4, or 6 will be considered a good pixel,
while a DQ pixel with a value, e.g., 1+2=3, 4+8=12, etc.
will be flagged as a "bad" pixel.
| Default value (0) will make *all* non-zero
pixels in the DQ mask to be considered "bad" pixels,
and the corresponding image pixels will not be used
for sky computations.
| Set `dq_bits` to `None` to turn off the use of
image's DQ array for sky computations.
.. note::
DQ masks (if used), *will be* combined with user masks
specified by the `usermask` parameter.
dqimage: ImageRef
An :py:class:`~stsci.skypac.utils.ImageRef` object that refers
to an open FITS file that has DQ data of the input `image`.
.. note::
When DQ data are located in the same FITS file as the
science image data (e.g., HST/ACS, HST/WFC3, etc.),
`dqimage` may point to the
same :py:class:`~stsci.skypac.utils.ImageRef` object.
In this case the reference count of the
:py:class:`~stsci.skypac.utils.ImageRef` object must be
increased adequately.
dqext: tuple, int, str
Extension specification of the `dqimage` that contains
`image`'s DQ information. See help for `ext` for more
details on acceptable formats for this parameter.
usermask: ImageRef
An :py:class:`~stsci.skypac.utils.ImageRef` object that refers
to an open FITS file that has user mask data that indicate
what pixels in the input `image` should be used for sky
computations (``1``) and which pixels should **not** be used
for sky computations (``0``).
usermask_ext: tuple, int, str
Extension specification of the `usermask` mask file that
contains user's mask data that should be associated with
the input `image` and `ext`. See help for `ext` for more
details on acceptable formats for this parameter.
"""
assert(hasattr(self.__class__, '_initialized') and
self.__class__._initialized)
self._reset()
# check that input images and extensions are valid --
# either integers or tuples of strings and integers, e.g., ('sci',1):
_check_valid_imgext(image, 'image', ext, 'ext', can_img_be_None=False)
if dq_bits is not None:
if dqimage is None:
dq_bits = 0
else:
_check_valid_imgext(dqimage, 'dqimage', dqext, 'dqext')
_check_valid_imgext(usermask, 'usermask', usermask_ext, 'usermask_ext')
# get telescope, instrument, and detector info:
self.telescope, self.instrument, self.detector = get_instrument_info(
image, ext)
# check dq_bits:
if dq_bits is not None and not isinstance(dq_bits, int):
if image:
dqimage.release()
if usermask:
usermask.release()
if dqimage:
dqimage.release()
raise TypeError(
"Argument 'dq_bits' must be either an integer or None."
)
# buld mask:
self._buildMask(image.original_fname, ext, dq_bits,
dqimage, dqext, usermask, usermask_ext)
if dqimage:
dqimage.release()
if usermask:
usermask.release()
# save file, user mask, and DQ extension info:
self._fname = image.original_fname
self._basefname = basename(self._fname)
self._image = image
self._ext = ext
self._can_free_image = (image.can_reload_data and
self.optimize != 'speed')
# check extension and create a string representation:
try:
extstr = ext2str(ext)
except ValueError:
raise ValueError("Unexpected extension type '{}' for file {}.".
format(ext, self._basefname))
self._id = "{:s}[{:s}]".format(self._basefname, extstr)
# extract WCS for bounding-box computation
try:
if hasattr(image.hdu[ext], 'wcs'):
self._wcs = image.hdu[ext].wcs
else:
if self.telescope in supported_telescopes:
self._wcs = wcsutil.HSTWCS(image.hdu, ext)
else:
self._wcs = pywcs.WCS(image.hdu[ext].header, image.hdu)
if self._wcs is None:
raise Exception("Invalid WCS.")
except Exception as e:
msg = "Unable to obtain WCS information for the file {:s}." \
.format(self._id)
self._ml.error(msg)
self._ml.flush()
self._release_all()
raise e
# determine pixel scale:
self._get_pixel_scale()
# see if image data are in counts or count-rate
# and compute count(-rate) to flux (per arcsec^2) conversion factor:
self._brightness_conv_from_hdu(image.hdu, self._idcscale)
# process Sky user's keyword and its value:
self._init_skyuser(image.hdu[ext].header)
# Set polygon to be the bounding box of the chip:
self._polygon = SphericalPolygon.from_wcs(self.wcs, steps=1)
def main(input_image_file,
vertices_file,
output_image_file,
blank_value='zero',
image_is_wsclean_model=False):
"""
Blank a region in an image
Parameters
----------
input_image_file : str
Filename of input image to blank
vertices_file : str, optional
Filename of file with vertices (must be a pickle file containing
a dictionary with the vertices in the 'vertices' entry)
output_image_file : str
Filename of output image
blank_value : str, optional
Value for blanks (one of 'zero' or 'nan')
image_is_wsclean_model : bool, optional
If True, the input and output image files are treated as the root name
of a WSClean model image (or images)
"""
if type(image_is_wsclean_model) is str:
if image_is_wsclean_model.lower() == 'true':
image_is_wsclean_model = True
else:
image_is_wsclean_model = False
if image_is_wsclean_model:
input_image_files = glob.glob(input_image_file + '*-model.fits')
output_image_files = [
f.replace(input_image_file, output_image_file)
for f in input_image_files
]
else:
input_image_files = [input_image_file]
output_image_files = [output_image_file]
if blank_value == 'zero':
blank_val = 0.0
elif blank_value == 'nan':
blank_val = np.nan
else:
print('Blank value type "{}" not understood.'.format(blank_with))
sys.exit(1)
# Construct polygon of facet region
header = pyfits.getheader(input_image_files[0], 0)
w = wcs.WCS(header)
RAind = w.axis_type_names.index('RA')
Decind = w.axis_type_names.index('DEC')
vertices = read_vertices(vertices_file)
RAverts = vertices[0]
Decverts = vertices[1]
xvert = []
yvert = []
for RAvert, Decvert in zip(RAverts, Decverts):
ra_dec = np.array([[0.0, 0.0, 0.0, 0.0]])
ra_dec[0][RAind] = RAvert
ra_dec[0][Decind] = Decvert
xvert.append(w.wcs_world2pix(ra_dec, 0)[0][Decind])
yvert.append(w.wcs_world2pix(ra_dec, 0)[0][RAind])
poly = Polygon(xvert, yvert)
for input_image, output_image in zip(input_image_files,
output_image_files):
hdu = pyfits.open(input_image, memmap=False)
data = hdu[0].data
# Find limits of facet poly and blank pixels outside them
xmin = max(int(np.min(xvert)) - 2, 0)
xmax = min(int(np.max(xvert)) + 2, data.shape[2])
ymin = max(int(np.min(yvert)) - 2, 0)
ymax = min(int(np.max(yvert)) + 2, data.shape[3])
data[0, 0, :, :ymin] = blank_val
data[0, 0, :, ymax:] = blank_val
data[0, 0, :xmin, :] = blank_val
data[0, 0, xmax:, :] = blank_val
# Find distance to nearest poly edge and blank those that
# are outside the facet (dist < 0)
pix_ind = np.indices((xmax - xmin, ymax - ymin))
pix_ind[0] += xmin
pix_ind[1] += ymin
dist = poly.is_inside(pix_ind[0], pix_ind[1])
outside_ind = np.where(dist < 0.0)
if len(outside_ind[0]) > 0:
data[0, 0, pix_ind[0][outside_ind],
pix_ind[1][outside_ind]] = blank_val
hdu[0].data = data
hdu.writeto(output_image, clobber=True)
def make_data_cube(
detectid=None,
coords=None,
shotid=None,
pixscale=0.25 * u.arcsec,
imsize=30.0 * u.arcsec,
wave_range=[3470, 5540],
dwave=2.0,
dcont=50.0,
convolve_image=True,
ffsky=True,
subcont=False,
):
"""
Function to make a datacube from either a detectid or from a
coordinate/shotid combination.
Paramaters
----------
detectid: int
detectid from the continuum or lines catalog. Default is
None. Provide a coords/shotid combo if this isn't given
coords: SkyCoords object
coordinates to define the centre of the data cube
pixscale: astropy angle quantity
plate scale
imsize: astropy angle quantity
spatial length of cube (equal dims is only option)
wave_range: list
start and stop value for the wavelength range in Angstrom
dwave
step in wavelength range in Angstrom
convolve_image: bool
option to convolve image with shotid seeing
ffsky: bool
option to use full frame calibrated fibers. Default is
True.
subcont: bool
option to subtract continuum. Default is False. This
will measure the continuum 50AA below and above the
input wave_range
dcont
width in angstrom to measure the continuum. Default is to
measure 50 AA wide regions on either side of the line
Returns
-------
hdu: PrimaryHDU object
the data cube 3D array and associated 3d header
Units are '10^-17 erg cm-2 s-1 per spaxel'
Examples
--------
Can either pass in a detectid:
>>> detectid_obj=2101602788
>>> hdu = make_data_cube( detectid=detectid_obj)
>>> hdu.writeto( str(detectid_obj) + '.fits', overwrite=True)
or can put in an SkyCoord object:
>>> star_coords = SkyCoord(9.625181, -0.043587, unit='deg')
>>> hdu = make_data_cube( coords=star_coords[0], shotid=20171016108, dwave=2.0)
>>> hdu.writeto( 'star.fits', overwrite=True)
"""
global config, detecth5, surveyh5
if detectid is not None:
detectid_obj = detectid
det_info = detecth5.root.Detections.read_where("detectid == detectid_obj")[0]
shotid = det_info["shotid"]
coords = SkyCoord(det_info["ra"], det_info["dec"], unit="deg")
if coords is None or shotid is None:
print("Provide a detectid or both a coords and shotid")
E = Extract()
E.load_shot(shotid)
# get spatial dims:
ndim = int(imsize / pixscale)
center = int(ndim / 2)
# get wave dims:
nwave = int((wave_range[1] - wave_range[0]) / dwave + 1)
w = wcs.WCS(naxis=3)
w.wcs.crval = [coords.ra.deg, coords.dec.deg, wave_range[0]]
w.wcs.crpix = [center, center, 1]
w.wcs.ctype = ["RA---TAN", "DEC--TAN", "WAVE"]
w.wcs.cdelt = [-pixscale.to(u.deg).value, pixscale.to(u.deg).value, dwave]
rad = imsize
info_result = E.get_fiberinfo_for_coord(coords, radius=rad, ffsky=False)
ifux, ifuy, xc, yc, ra, dec, data, error, mask = info_result
# get ifu center:
ifux_cen, ifuy_cen = E.convert_radec_to_ifux_ifuy(
ifux, ifuy, ra, dec, coords.ra.deg, coords.dec.deg
)
if convolve_image:
surveyh5 = tb.open_file(config.surveyh5, "r")
shotid_obj = shotid
fwhm = surveyh5.root.Survey.read_where("shotid == shotid_obj")["fwhm_virus"][0]
surveyh5.close()
else:
fwhm = 1.8 # just a dummy variable as convolve_image=False
im_cube = np.zeros((nwave, ndim, ndim))
wave_i = wave_range[0]
i = 0
while wave_i <= wave_range[1]:
try:
im_src = E.make_narrowband_image(
ifux_cen,
ifuy_cen,
ifux,
ifuy,
data,
mask,
scale=pixscale.to(u.arcsec).value,
wrange=[wave_i, wave_i + dwave],
nchunks=1,
seeing_fac=fwhm,
convolve_image=convolve_image,
boxsize=imsize.to(u.arcsec).value,
)
im_slice = im_src[0]
if subcont:
zarray_blue = E.make_narrowband_image(
ifux_cen,
ifuy_cen,
ifux,
ifuy,
data,
mask,
seeing_fac=fwhm,
scale=pixscale.to(u.arcsec).value,
boxsize=imsize.to(u.arcsec).value,
nchunks=2,
wrange=[wave_i-dcont, wave_i],
convolve_image=convolve_image,
)
zarray_red = E.make_narrowband_image(
ifux_cen,
ifuy_cen,
ifux,
ifuy,
data,
mask,
seeing_fac=fwhm,
nchunks=2,
scale=pixscale.to(u.arcsec).value,
boxsize=imsize.to(u.arcsec).value,
wrange=[wave_i + dwave, wave_i + dwave + dcont],
convolve_image=convolve_image,
)
im_cont = (zarray_blue[0] + zarray_red[0])/(2*dcont)
im_slice = im_src[0] - dwave*im_cont
im_cube[i, :, :] = im_slice
except Exception:
im_cube[i, :, :] = np.zeros((ndim, ndim))
wave_i += dwave
i += 1
hdu = fits.PrimaryHDU(im_cube, header=w.to_header())
E.close()
return hdu
def statmorphWrapper(index_pairs):
crash = ['NGVSJ12:29:48.87+13:25:46.0', 'NGVSJ12:30:49.42+12:23:28.0']
df = pd.read_csv('NGVSgalaxies.csv')
# Iterate through rows in csv file containing measurements for each galaxy
for row in df.iloc[index_pairs[0]:index_pairs[1]].itertuples(index=True, name='Pandas'):
galaxy = row.Official_name
base = 'https://www.cadc-ccda.hia-iha.nrc-cnrc.gc.ca/files/vault/ngvs/data/NGVS/galaxies/'
galaxyPath = f'{galaxy}/{galaxy}_G'
if galaxy in crash :
continue
startcopy = time.time()
# Try to copy galaxy files
os.system(f'vcp vos:ngvs/data/NGVS/galaxies/{galaxy}/{galaxy}_G.fits /mnt/scratch/temp_galaxy_storage')
os.system(f'vcp vos:ngvs/data/NGVS/galaxies/{galaxyPath}_iso_model.fits /mnt/scratch/temp_galaxy_storage')
os.system(f'vcp vos:ngvs/data/NGVS/galaxies/{galaxyPath}_galfit_model.fits /mnt/scratch/temp_galaxy_storage')
os.system(f'vcp vos:ngvs/data/NGVS/galaxies/{galaxyPath}_mask.fits /mnt/scratch/temp_galaxy_storage')
os.system(f'vcp vos:ngvs/data/NGVS/galaxies/{galaxyPath}_psf.fits /mnt/scratch/temp_galaxy_storage')
os.system(f'vcp vos:ngvs/data/NGVS/galaxies/{galaxyPath}_sig.fits /mnt/scratch/temp_galaxy_storage')
os.system(f'vcp vos:ngvs/data/NGVS/galaxies/{galaxyPath}_iso_residual.fits /mnt/scratch/temp_galaxy_storage')
os.system(f'vcp vos:ngvs/data/NGVS/galaxies/{galaxyPath}_galfit_residual.fits /mnt/scratch/temp_galaxy_storage')
endcopy = time.time() - startcopy
# If one of the required files is missing, continue to next galaxy
if(not path.isfile(f'/mnt/scratch/temp_galaxy_storage/{galaxy}_G.fits') or (not path.isfile(f'/mnt/scratch/temp_galaxy_storage/{galaxy}_G_iso_model.fits') and not \
path.isfile(f'/mnt/scratch/temp_galaxy_storage/{galaxy}_G_galfit_model.fits')) or not path.isfile(f'/mnt/scratch/temp_galaxy_storage/{galaxy}_G_mask.fits') or not \
path.isfile(f'/mnt/scratch/temp_galaxy_storage/{galaxy}_G_psf.fits') or not path.isfile(f'/mnt/scratch/temp_galaxy_storage/{galaxy}_G_sig.fits') or (not \
path.isfile(f'/mnt/scratch/temp_galaxy_storage/{galaxy}_G_iso_residual.fits') and not path.isfile(f'/mnt/scratch/temp_galaxy_storage/{galaxy}_G_galfit_residual.fits'))):
print(f'missing {galaxy}')
writeFile = open(f'/mnt/scratch/missing/{galaxy}.txt', 'w')
writeFile.write(f'{galaxy}\n')
if(not path.isfile(f'/mnt/scratch/temp_galaxy_storage/{galaxy}_G.fits')):
writeFile.write('missing original\n')
if(not path.isfile(f'/mnt/scratch/temp_galaxy_storage/{galaxy}_G_iso_model.fits')):
writeFile.write('missing iso model\n')
if(not path.isfile(f'/mnt/scratch/temp_galaxy_storage/{galaxy}_G_galfit_model.fits')):
writeFile.write('missing galfit model\n')
if(not path.isfile(f'/mnt/scratch/temp_galaxy_storage/{galaxy}_G_mask.fits')):
writeFile.write('missing mask\n')
if(not path.isfile(f'/mnt/scratch/temp_galaxy_storage/{galaxy}_G_psf.fits')):
writeFile.write('missing psf\n')
if(not path.isfile(f'/mnt/scratch/temp_galaxy_storage/{galaxy}_G_sig.fits')):
writeFile.write('missing sig\n')
if(not path.isfile(f'/mnt/scratch/temp_galaxy_storage/{galaxy}_G_iso_residual.fits')):
writeFile.write('missing iso residual\n')
if(not path.isfile(f'/mnt/scratch/temp_galaxy_storage/{galaxy}_G_galfit_residual.fits')):
writeFile.write('missing galfit residual\n')
writeFile.close()
clearTempFiles(galaxy)
continue
# ONLY PROCESS LARGE FILE
#---------------------------------------------------------------------------------------
if(os.path.getsize(f'/mnt/scratch/temp_galaxy_storage/{galaxy}_G.fits') < 300000000):
clearTempFiles(galaxy)
continue
#---------------------------------------------------------------------------------------
# Create check file for current galaxy
print(f'checking {galaxy}')
writeFile = open(f'/mnt/scratch/check/{galaxy}.txt', 'w')
writeFile.write('checking')
writeFile.close()
# If any of the galaxy files are empty then create galaxy corrupt file and continue to next galaxy
if(checkCorrupt(galaxy)):
writeFile = open(f'/mnt/scratch/corrupt/{galaxy}.txt', 'w')
writeFile.write(f'corrupt\n')
writeFile.close()
clearTempFiles(galaxy)
continue
# Beginning of segmentation map creation
startseg = time.time()
hdu = fits.open(f'/mnt/scratch/temp_galaxy_storage/{galaxy}_G.fits')
im_header = hdu[0].header
im_data = hdu[0].data
# Sky subtraction from original image
sky_data = np.zeros(np.shape(im_data))
sky_data += row.SKY
im_sky_subtracted = im_data - sky_data
# Calculate nucleus center
ra = row.NGVS_ra
dec = row.NGVS_dec
mywcs = wcs.WCS(im_header)
xCenter, yCenter = mywcs.all_world2pix([[ra, dec]], 0)[0]
mask_data = fits.getdata(f'/mnt/scratch/temp_galaxy_storage/{galaxy}_G_mask.fits')
# If a iso model exists then use that file for the original model data, otherwise use galfit
if path.isfile(f'/mnt/scratch/temp_galaxy_storage/{galaxy}_G_iso_model.fits'):
original_model_data = fits.getdata(f'/mnt/scratch/temp_galaxy_storage/{galaxy}_G_iso_model.fits')
else:
original_model_data = fits.getdata(f'/mnt/scratch/temp_galaxy_storage/{galaxy}_G_galfit_model.fits')
# If nucleus exists then mask nucleus
if(row.Nuc_Flag == 1):
for i in range(len(mask_data)):
for j in range(len(mask_data)):
# TODO: Change radius of nucleus mask
if(((i-xCenter)**2) + ((j-yCenter)**2) <= (5**2)):
mask_data[i][j] = 100
ellipse_data = np.zeros(np.shape(original_model_data))
# Calculate median of original model values within 10 pixel radius from nucleus center
pixelList = []
for i in range(len(original_model_data)):
for j in range(len(original_model_data)):
if(((i-xCenter)**2) + ((j-yCenter)**2) <= (10**2) and mask_data[i][j] != 100):
pixelList.append(original_model_data[i][j])
median = statistics.median(pixelList)
# Create Segmentation Map
seg_data = np.zeros(np.shape(original_model_data))
ellipse_data = np.zeros(np.shape(original_model_data))
# isEmpty flag is used for checking if a segmentation map is valid for processing. If segmentation map 2D list is all 0's then script crashes.
isEmpty = True
# if median is greater than 2*sky value then create segmentation map from original model values greater than 1.4*sky value within ellipse area
if(median > 2*row.SKY):
for i in range(len(original_model_data)):
for j in range(len(original_model_data)):
if(inEllipse(i,j,xCenter,yCenter,row.Size,row.AxisRatio,row.PA)):
ellipse_data[i][j] = 100
if(original_model_data[i][j] > (1.4*row.SKY)):
seg_data[i][j] = 100
isEmpty = False
# If median is less than 2*sky value then create segmentation map from original model values greater than 1.1*sky value within ellipse area
else:
for i in range(len(original_model_data)):
for j in range(len(original_model_data)):
if(inEllipse(i,j,xCenter,yCenter,row.Size,row.AxisRatio,row.PA)):
ellipse_data[i][j] = 100
if(original_model_data[i][j] > (1.1*row.SKY)):
seg_data[i][j] = 100
isEmpty = False
psf = fits.getdata(f'/mnt/scratch/temp_galaxy_storage/{galaxy}_G_psf.fits')
weightmap = fits.getdata(f'/mnt/scratch/temp_galaxy_storage/{galaxy}_G_sig.fits')
mask_data = np.array(mask_data, dtype=bool)
endseg = time.time() - startseg
# End of segmentation map creation
# If the galaxy's segmentation map is empty with no area of interest, then create empty galaxy file and continue to next galaxy
if(isEmpty):
writeFile = open(f'/mnt/scratch/emptyseg/{galaxy}.txt', 'w')
writeFile.write('empty')
writeFile.close()
clearTempFiles(galaxy)
continue
start_time = time.time()
# run statmorph on current galaxy
source_morphs = statmorph.source_morphology(im_sky_subtracted, seg_data, mask=mask_data, weightmap=weightmap, psf=psf)
end_time = time.time() - start_time
morph = source_morphs[0]
startmodelcreate = time.time()
# create model from statmorph results
ny, nx = im_sky_subtracted.shape
y, x = np.mgrid[0:ny, 0:nx]
fitted_model = statmorph.ConvolvedSersic2D(
amplitude=morph.sersic_amplitude,
r_eff=morph.sersic_rhalf,
n=morph.sersic_n,
x_0=morph.sersic_xc,
y_0=morph.sersic_yc,
ellip=morph.sersic_ellip,
theta=morph.sersic_theta)
fitted_model.set_psf(psf)
output_model_data = fitted_model(x, y)
endmodelcreate = time.time() - startmodelcreate
if path.isfile(f'/mnt/scratch/temp_galaxy_storage/{galaxy}_G_iso_residual.fits'):
original_res_data = fits.getdata(f'/mnt/scratch/temp_galaxy_storage/{galaxy}_G_iso_residual.fits')
else:
original_res_data = fits.getdata(f'/mnt/scratch/temp_galaxy_storage/{galaxy}_G_galfit_residual.fits')
startfig = time.time()
# normalize images, models, segmentation map
output_res_data = im_sky_subtracted - output_model_data
p1 = 10. ; p2 = 90.
im_p1 = np.percentile(im_sky_subtracted.ravel(), p1)
im_p2 = np.percentile(im_sky_subtracted.ravel(), p2)
normSky = ImageNormalize(im_sky_subtracted, vmin=im_p1, vmax=im_p2)
im_p1 = np.percentile(output_model_data.ravel(), p1)
im_p2 = np.percentile(output_model_data.ravel(), p2)
normOutputMod = ImageNormalize(output_model_data, vmin=im_p1, vmax=im_p2)
im_p1 = np.percentile(original_model_data.ravel(), p1)
im_p2 = np.percentile(original_model_data.ravel(), p2)
normOriginalMod = ImageNormalize(original_model_data, vmin=im_p1, vmax=im_p2)
im_p1 = np.percentile(output_res_data.ravel(), p1)
im_p2 = np.percentile(output_res_data.ravel(), p2)
normOutputRes = ImageNormalize(output_res_data, vmin=im_p1, vmax=im_p2)
im_p1 = np.percentile(original_res_data.ravel(), p1)
im_p2 = np.percentile(original_res_data.ravel(), p2)
normOriginalRes = ImageNormalize(original_res_data, vmin=im_p1, vmax=im_p2)
# create figures for images, models, segmentation map
gs = gridspec.GridSpec(2, 4, width_ratios=[1, 1, 1, 1],
wspace=0.2, hspace=0, top=0.7, bottom=0.05, left=0.1, right=0.5)
fig = plt.figure(figsize=(30,10))
ax= plt.subplot(gs[0,0])
ax.imshow(im_sky_subtracted, norm=normSky, cmap='gray', origin='lower')
ax.set_title('Sky Subtracted Image', fontsize=15)
ax= plt.subplot(gs[0,1])
ax.imshow(original_model_data, norm=normOriginalMod, cmap='gray', origin='lower')
ax.set_title('Original Model', fontsize=15)
ax= plt.subplot(gs[0,2])
ax.imshow(output_model_data, norm=normOutputMod, cmap='gray', origin='lower')
ax.set_title('Output Model', fontsize=15)
ax= plt.subplot(gs[0,3])
ax.imshow(mask_data, cmap='gray', origin='lower')
ax.set_title('Mask', fontsize=15)
ax= plt.subplot(gs[1,0])
ax.imshow(seg_data, cmap='gray', origin='lower')
ax.set_title('Segmap', fontsize=15)
ax= plt.subplot(gs[1,1])
ax.imshow(ellipse_data, cmap='gray', origin='lower')
ax.set_title('Ellipse Area', fontsize=15)
ax= plt.subplot(gs[1,2])
ax.imshow(original_res_data, norm=normOriginalRes, cmap='gray', origin='lower')
ax.set_title('Original Residual', fontsize=15)
ax= plt.subplot(gs[1,3])
ax.imshow(output_res_data, norm=normOutputRes, cmap='gray', origin='lower')
ax.set_title('Output Residual', fontsize=15)
endfig = time.time() - startfig
# save figures as PNG image to output directory
fig.savefig(f'/mnt/scratch/output/{galaxy}_sourcemorph:{round(end_time, 2)}_seg={round(endseg, 2)}_RE={round(row.Size, 3)}_mag={round(row.principleg_mag_cg, 3)}.png', facecolor='w', edgecolor='w', transparent=False, bbox_inches='tight')
plt.close(fig)
# UNCOMMENT TO SAVE AS MULTI EXTENSION FITS FILE INSTEAD OF PNG
#------------------------------------------------------------------------------------------------------------------------
# primary_hdu = fits.PrimaryHDU(im_sky_subtracted, header=im_header)
# image_hdu = fits.ImageHDU(output_model_data)
# image_hdu2 = fits.ImageHDU(output_res_data)
# hdul = fits.HDUList([primary_hdu, image_hdu, image_hdu2])
# upload fits file to VOSpace
# hdul.writeto(f'/mnt/scratch/output/{galaxy}_output.fits', overwrite=True)
# os.system(f'vcp /mnt/scratch/output/{galaxy}_output.fits vos:ngvs/data/STATMORPH/FITS_output/{galaxy}_output.fits')
# if path.isfile(f'/mnt/scratch/output/{galaxy}_output.fits'):
# os.system(f'rm /mnt/scratch/output/{galaxy}_output.fits')
#------------------------------------------------------------------------------------------------------------------------
# UPLOAD PNG FILE WITH FLAGS
# os.system(f'vcp /mnt/scratch/output/{galaxy}_time:{round(end_time, 2)}_Flag={morph.flag}_SersicFlag={morph.flag_sersic}.png \
# vos:ngvs/data/STATMORPH/filesize_bug/{galaxy}_time:{round(end_time, 2)}_Flag={morph.flag}_SersicFlag={morph.flag_sersic}.png')
# if path.isfile(f'/mnt/scratch/output/{galaxy}_time:{round(end_time, 2)}_Flag={morph.flag}_SersicFlag={morph.flag_sersic}.png'):
# os.system(f'rm /mnt/scratch/output/{galaxy}_time:{round(end_time, 2)}_Flag={morph.flag}_SersicFlag={morph.flag_sersic}.png')
# UPLOAD PNG FILE WITH MEDIAN & SKY VALUES
# os.system(f'vcp /mnt/scratch/output/{galaxy}_time:{round(end_time, 2)}_size={row.Size}_median={median}_2*sky={2*row.SKY}sky={row.SKY}.png \
# vos:ngvs/data/STATMORPH/memory_bug/{galaxy}_time:{round(end_time, 2)}_size={row.Size}_median={median}_2*sky={2*row.SKY}sky={row.SKY}.png')
# if path.isfile(f'/mnt/scratch/output/{galaxy}_time:{round(end_time, 2)}_size={row.Size}_median={median}_2*sky={2*row.SKY}sky={row.SKY}.png'):
# os.system(f'rm /mnt/scratch/output/{galaxy}_time:{round(end_time, 2)}_size={row.Size}_median={median}_2*sky={2*row.SKY}sky={row.SKY}.png')
# UPLOAD PNG FILE WITH RUNNING TIMES & RE FACTOR & MAGNITUDE
os.system(f'vcp /mnt/scratch/output/{galaxy}_sourcemorph:{round(end_time, 2)}_seg={round(endseg, 2)}_RE={round(row.Size, 3)}_mag={round(row.principleg_mag_cg, 3)}.png \
vos:ngvs/data/STATMORPH/memory_fix/{galaxy}_sourcemorph:{round(end_time, 2)}_seg={round(endseg, 2)}_RE={round(row.Size, 3)}_mag={round(row.principleg_mag_cg, 3)}.png')
if path.isfile(f'/mnt/scratch/output/{galaxy}_sourcemorph:{round(end_time, 2)}_seg={round(endseg, 2)}_RE={round(row.Size, 3)}_mag={round(row.principleg_mag_cg, 3)}.png'):
os.system(f'rm /mnt/scratch/output/{galaxy}_sourcemorph:{round(end_time, 2)}_seg={round(endseg, 2)}_RE={round(row.Size, 3)}_mag={round(row.principleg_mag_cg, 3)}.png')
hdu.close()
clearTempFiles(galaxy)
print(f'complete {galaxy}')
def add_calibration(data, imagestretch='linear'):
"""
add calibration results to website
"""
### produce calibration plot for each frame
for idx, cat in enumerate(data['catalogs']):
if not data['zeropoints'][idx]['success']:
continue
ax1 = plt.subplot(211)
ax1.set_title('%s: %s-band from %s' %
(cat.catalogname, data['filtername'],
data['ref_cat'].catalogname))
ax1.set_xlabel('Number of Reference Stars')
ax1.set_ylabel('Magnitude Zeropoint', fontdict={'color':'red'})
#ax1.ticklabel_format(style='sci', axis='y', scilimits=(-5,5))
zp_idx = data['zeropoints'][idx]['zp_idx']
clipping_steps = data['zeropoints'][idx]['clipping_steps']
x = [len(clipping_steps[i][3]) for i in range(len(clipping_steps))]
ax1.errorbar(x, [clipping_steps[i][0] for i
in range(len(clipping_steps))],
yerr=[clipping_steps[i][1] for i
in range(len(clipping_steps))], color='red')
ax1.set_ylim(ax1.get_ylim()[::-1]) # reverse y axis
ax1.plot([len(clipping_steps[zp_idx][3]),
len(clipping_steps[zp_idx][3])],
ax1.get_ylim(), color='black')
ax2 = ax1.twinx()
ax2.plot(x, [clipping_steps[i][2] for i
in range(len(clipping_steps))],
color='blue')
ax2.set_ylabel(r'reduced $\chi^2$', fontdict={'color':'blue'})
ax2.set_yscale('log')
# residual plot
ax3 = plt.subplot(212)
ax3.set_xlabel('Reference Star Magnitude')
ax3.set_ylabel('Calibration-Reference (mag)')
match = data['zeropoints'][idx]['match']
x = match[0][0][clipping_steps[zp_idx][3]]
residuals = match[1][0][clipping_steps[zp_idx][3]] \
+ clipping_steps[zp_idx][0] \
- match[0][0][clipping_steps[zp_idx][3]]
residuals_sig = numpy.sqrt(match[1][1][clipping_steps[zp_idx][3]]**2\
+ clipping_steps[zp_idx][1]**2)
ax3.errorbar(x, residuals, yerr=residuals_sig, color='black',
linestyle='')
ax3.plot(ax3.get_xlim(), [0,0], color='black', linestyle='--')
ax3.set_ylim(ax3.get_ylim()[::-1]) # reverse y axis
plt.grid()
plt.savefig(('.diagnostics/%s_photcal.png') % cat.catalogname,
format='png')
data['zeropoints'][idx]['plotfilename'] = \
('.diagnostics/%s_photcal.png') % \
cat.catalogname
plt.close()
### create zeropoint overview plot
times = [dat['obstime'][0] for dat in data['zeropoints']]
zp = [dat['zp'] for dat in data['zeropoints']]
zperr = [dat['zp_sig'] for dat in data['zeropoints']]
plt.subplot()
plt.errorbar(times, zp, yerr=zperr, linestyle='')
plt.xlabel('Observation Midtime (JD)')
plt.ylabel('Magnitude Zeropoints (mag)')
plt.show()
plt.ylim([plt.ylim()[1], plt.ylim()[0]])
plt.grid()
plt.savefig('.diagnostics/zeropoints.png', format='png')
plt.close()
data['zpplot'] = 'zeropoints.png'
### create calibration website
html = "<H2>Calibration Results</H2>\n"
html += ("<P>Calibration input: minimum number/fraction of reference " \
+ "stars %.2f, reference catalog: %s, filter name: %s\n") % \
(data['minstars'], data['ref_cat'].catalogname, data['filtername'])
html += "<TABLE BORDER=\"1\">\n<TR>\n"
html += "<TH>Filename</TH><TH>Zeropoint (mag)</TH><TH>ZP_sigma (mag)</TH>" \
+ "<TH>N_stars</TH><TH>N_matched</TH>\n</TR>\n"
for dat in data['zeropoints']:
if 'plotfilename' in list(dat.keys()):
html += ("<TR><TD><A HREF=\"#%s\">%s</A></TD>" \
+ "<TD>%7.4f</TD><TD>%7.4f</TD><TD>%d</TD>" \
+ "<TD>%d</TD>\n</TR>" ) % \
(dat['plotfilename'].split('.diagnostics/')[1],
dat['filename'], dat['zp'],
dat['zp_sig'], dat['zp_nstars'],
len(dat['match'][0][0]))
html += "</TABLE>\n"
html += "<P><IMG SRC=\"%s\">" % data['zpplot']
for dat in data['zeropoints']:
if not dat['success']:
continue
catframe = '.diagnostics/'+ \
dat['filename'][:dat['filename'].find('.ldac')] + \
'.fits_reference_stars.png'
html += ("<H3>%s</H3>" \
+ "<TABLE BORDER=\"0\">\n" \
+ "<TR><TD><A HREF=\"%s\">" \
+ "<IMG ID=\"%s\" SRC=\"%s\" HEIGHT=300 WIDTH=400>" \
+ "</A></TD><TD><A HREF=\"%s\">" \
+ "<IMG ID=\"%s\" SRC=\"%s\" HEIGHT=400 WIDTH=400>" \
+ "</A></TD>\n") % \
(dat['filename'],
dat['plotfilename'].split('.diagnostics/')[1],
dat['plotfilename'].split('.diagnostics/')[1],
dat['plotfilename'].split('.diagnostics/')[1],
catframe.split('.diagnostics/')[1],
catframe.split('.diagnostics/')[1],
catframe.split('.diagnostics/')[1])
html += "<TD><TABLE BORDER=\"1\">\n<TR>\n"
html += "<TH>Idx</TH><TH>Name</TH><TH>RA</TH><TH>Dec</TH>" \
+ "<TH>Catalog (mag)</TH>" \
+ "<TH>Instrumental (mag)</TH><TH>Calibrated (mag)</TH>" \
+ "<TH>Residual (mag</TH>\n</TR>\n"
for i, idx in enumerate(dat['zp_usedstars']):
name = dat['match'][0][2][idx]
if isinstance(name, bytes):
name = name.decode('utf8')
html += ("<TR><TD>%d</TD><TD>%s</TD><TD>%12.8f</TD>" \
+ "<TD>%12.8f</TD><TD>%.3f+-%.3f</TD>" \
+ "<TD>%.3f+-%.3f</TD>" \
+ "<TD>%.3f+-%.3f</TD><TD>%.3f</TD></TR>") % \
(i+1, name,
dat['match'][0][3][idx],
dat['match'][0][4][idx], dat['match'][0][0][idx],
dat['match'][0][1][idx],
dat['match'][1][0][idx], dat['match'][1][1][idx],
dat['zp']+dat['match'][1][0][idx],
numpy.sqrt(dat['zp_sig']**2 + dat['match'][1][1][idx]**2),
(dat['zp']+dat['match'][1][0][idx])-dat['match'][0][0][idx])
html += "</TABLE><P>derived zeropoint: %7.4f+-%6.4f mag\n" % \
(dat['zp'], dat['zp_sig'])
html += "</TR></TD></TR></TABLE>\n"
### create catalog frame
fits_filename = dat['filename'][:dat['filename'].find('.ldac')] + \
'.fits'
imgdat = fits.open(fits_filename, ignore_missing_end=True)[0].data
resize_factor = min(1., 1000./numpy.max(imgdat.shape))
# clip extreme values to prevent crash of imresize
imgdat = numpy.clip(imgdat, numpy.percentile(imgdat, 1),
numpy.percentile(imgdat, 99))
imgdat = imresize(imgdat, resize_factor, interp='nearest')
header = fits.open(fits_filename, ignore_missing_end=True)[0].header
norm = ImageNormalize(imgdat, interval=ZScaleInterval(),
stretch={'linear': LinearStretch(),
'log': LogStretch()}[imagestretch])
# turn relevant header keys into floats
# astropy.io.fits bug
for key, val in list(header.items()):
if 'CD1_' in key or 'CD2_' in key or \
'CRVAL' in key or 'CRPIX' in key or \
'EQUINOX' in key:
header[key] = float(val)
plt.figure(figsize=(5, 5))
img = plt.imshow(imgdat, cmap='gray', norm=norm,
origin='lower')
# remove axes
plt.axis('off')
img.axes.get_xaxis().set_visible(False)
img.axes.get_yaxis().set_visible(False)
# plot reference sources
if len(dat['match'][0][3]) > 0 and len(dat['match'][0][4]) > 0:
try:
w = wcs.WCS(header)
world_coo = [[dat['match'][0][3][idx],
dat['match'][0][4][idx]] \
for idx in dat['zp_usedstars']]
img_coo = w.wcs_world2pix(world_coo, True )
plt.scatter([c[0]*resize_factor for c in img_coo],
[c[1]*resize_factor for c in img_coo],
s=10, marker='o', edgecolors='red', linewidth=0.1,
facecolor='none')
for i in range(len(dat['zp_usedstars'])):
plt.annotate(str(i+1), xy=((img_coo[i][0]*resize_factor)+15,
img_coo[i][1]*resize_factor),
color='red', horizontalalignment='left',
verticalalignment='center')
except astropy.wcs._wcs.InvalidTransformError:
logging.error('could not plot reference sources due to '
'astropy.wcs._wcs.InvalidTransformError; '
'most likely unknown distortion parameters.')
plt.savefig(catframe, format='png', bbox_inches='tight',
pad_inches=0, dpi=200)
plt.close()
create_website(_pp_conf.cal_filename, content=html)
### update index.html
html = "<H2>Photometric Calibration - Zeropoints</H2>\n"
html += "match image data with %s (%s);\n" % \
(data['ref_cat'].catalogname, data['ref_cat'].history)
html += "see <A HREF=\"%s\">calibration</A> website for details\n" % \
_pp_conf.cal_filename
html += "<P><IMG SRC=\"%s\">\n" % ('.diagnostics/' + data['zpplot'])
append_website(_pp_conf.index_filename, html,
replace_below=("<H2>Photometric Calibration "
"- Zeropoints</H2>\n"))
return None
import os
from astropy.io import fits
from astropy import wcs
from astropy import units as u
import regions
import numpy as np
import pylab as pl
if not os.path.exists('W51e2w_ALMAB3_cutout.fits'):
fh = fits.open(
'/Users/adam/work/w51/alma/FITS/longbaseline/w51e2_sci.spw0_1_2_3_4_5_6_7_8_9_10_11_12_13_14_15_16_17_18_19.mfs.I.manual.image.tt0.pbcor.fits'
)
ww = wcs.WCS(fh[0].header).celestial
pr0 = regions.read_ds9(
'/Users/adam/work/w51/vla_q/regions/e2w_ellipse.reg')[0].to_pixel(ww)
pr0.width *= 2.5
pr0.height *= 2.5
msk = pr0.to_mask()
img_95ghz = msk.multiply(fh[0].data.squeeze())
header = fh[0].header
ww_cutout = ww[msk.bbox.slices]
header.update(ww_cutout.to_header())
fits.PrimaryHDU(data=img_95ghz,
header=header).writeto('W51e2w_ALMAB3_cutout.fits',
overwrite=True)
else:
img_95ghz = fits.getdata('W51e2w_ALMAB3_cutout.fits')
if not os.path.exists('W51e2w_VLA_Q_cutout.fits'):
fh = fits.open(
def radprof2map(pos, energy, profile, nametag):
# read energies and angular profiles
energies = np.array(pd.read_hdf(energy))[:, 0]
fluxes = np.array(pd.read_hdf(profile))
angles = np.array(pd.read_hdf(profile).keys())
# determine number of pixels to cover the entire profile
# reduce resolution by factor of 2
# + 1 makes the final map centered on the pulsar
npix = len(angles) + 1
# create wcs for output map
# output binning will cover the whole model with npix pixels
out_res = 2 * angles[-1] / (npix - 1)
out_wcs = wcs.WCS(naxis=3)
out_wcs.wcs.crpix = [(npix - 1.) / 2 + 1., (npix - 1) / 2 + 1., 1]
out_wcs.wcs.cdelt = [-out_res, out_res, np.ediff1d(np.log10(energies))[0]]
out_wcs.wcs.crval = [
pos.ra.deg[0],
pos.dec.deg[0], # centered on pulsar
np.log10(energies[0])
]
out_wcs.wcs.ctype = ["RA---TAN", "DEC--TAN", "Log10(Energy/1 MeV)"]
# create output map
out_map = np.zeros([len(energies), npix, npix])
# create pixel arrays
ii = np.linspace(1, npix, npix)
xv, yv = np.meshgrid(ii, ii)
xx = xv.flatten()
yy = yv.flatten()
# fake array for energy
zz = np.zeros(np.shape(xx))
# world position array
world = out_wcs.wcs_pix2world(np.array([xx, yy, zz]).T, 1)
# sky coordinate array
sc = SkyCoord(world[:, 0] * u.deg, world[:, 1] * u.deg, frame='icrs')
# angular distance array in deg
sep = sc.separation(pos).base.base
for k in range(len(energies)):
# get flux interpolating over angular bins
flux = np.interp(sep, angles, fluxes[k])
# set flux to 0 beyond range covered by model
flux[sep > angles[-1]] = 0.
# reshape array and fill map
out_map[k] = flux.reshape(npix, npix)
# create the main hdu
hdu = fits.PrimaryHDU(out_map)
hdu.header = out_wcs.to_header()
hdu.header.set('BUNIT',
'photon/cm2/s/MeV/sr',
'Photon flux',
after='CRVAL3')
hdu.verify('fix')
# create the energy table
ecol = fits.Column(name='Energy', format='D', unit='MeV', array=energies)
tbhdu = fits.BinTableHDU.from_columns([ecol], name='ENERGIES')
tbhdu.verify('fix')
# write file
hdulist = fits.HDUList([hdu, tbhdu])
hdulist.writeto(nametag + '_map.fits', overwrite=True)
def get_cubeinfo(header, returnHeader=False, origin=1):
'''
A function created to parse the RA, DEC, (and velocity) information from the 2D (3D) header
- This function has been tested with GALFA-HI/EBHIS cubes, and GALFA-HI 2D images.
- also been tested with LAB cubes/images that are in (glon, glat) coordinates.
- The input header can be 2D: NAXIS=2. NAXIS1 is RA (glon), 2 is DEC (glat)
- or 3D: NAXIS=3. NAXIS1 is RA (glon), 2 is DEC (glat), 3 is Velocity
- Return: if GALFA-HI or EBHIS:
ra and dec in 2D, with shape of (dec.size, ra.size) or (NAXIS2, NAXIS1)
- velocity in 1D.
or (ra, dec, vlsr, header array)
- if LAB:
glon, glat in 2D, with shape of (glat.size, glon.size) or (NAXIS2, NAXIS1)
- velocity in 1D.
or (gl, gb, vlsr, header array)
- History: updated as of 2016.10.03. Yong Zheng @ Columbia Astro.
'''
#import sys
#import astropy.wcs as wcs
#import numpy as np
hdrarrs = []
if header['NAXIS'] == 2:
hdr2d = header.copy()
hdrarrs.append(hdr2d)
elif header['NAXIS'] == 3:
# create a 2D header (RA/DEC) to speed up the RA/DEC calculation using astropy.wcs
hdr2d = header.copy()
# we don't need the velocity (3) information in the header
delkey = []
for key in hdr2d.keys():
if len(key) != 0 and key[-1] == '3': delkey.append(key)
for i in delkey: del hdr2d[i]
hdr2d['NAXIS'] = 2
if 'WCSAXES' in hdr2d.keys(): hdr2d['WCSAXES']=2
# create a 1D header (vel) to parse the velocity using astropy.wcs
hdr1d = header.copy()
# we don't need the RA/DEC keywords info in the header now.
delkey = []
for keya in hdr1d.keys():
if len(keya) != 0 and keya[-1] in ['1', '2']: delkey.append(keya)
for i in delkey: del hdr1d[i]
delkey = []
for keyb in hdr1d.keys():
if len(keyb) != 0 and keyb[-1] == '3':
hdr1d.append('%s1'%(keyb[:-1]))
hdr1d['%s1'%(keyb[:-1])] = hdr1d[keyb]
delkey.append(keyb)
for i in delkey: del hdr1d[i]
hdr1d['NAXIS'] = 1
if 'WCSAXES' in hdr1d.keys(): hdr1d['WCSAXES']=1
# save header arrays
hdrarrs.append(hdr2d)
hdrarrs.append(hdr1d)
else:
print("This code can only handle 2D or 3D data")
sys.exit(1)
return_arrays = []
# calculate RA, DEC
gwcsa = wcs.WCS(hdr2d)
n1, n2 = hdr2d['NAXIS1'], hdr2d['NAXIS2']
ax = np.reshape(np.mgrid[0:n1:1]+1, (1, n1)) # For FITS standard, origin = 1
ay = np.reshape(np.mgrid[0:n2:1]+1, (n2, 1)) # then for numpy standard, origin = 0
coor1, coor2 = gwcsa.all_pix2world(ax, ay, origin) # coor1 = ra or glon
return_arrays.append(coor1) # coor2 = dec or glat
return_arrays.append(coor2)
## calculate VLSR
if header['NAXIS'] == 3:
gwcsb = wcs.WCS(hdr1d)
n1 = hdr1d['NAXIS1']
ax = np.mgrid[0:n1:1]+1
# ax = np.linspace(0, n1, n1) # nope, wrong
vel = gwcsb.all_pix2world(ax, origin)[0]
if 'CUNIT1' in hdr1d.keys():
if hdr1d['CUNIT1'] in ['m/s', 'M/S', 'M/s', 'm/S']:
vel = vel/1e3
else: vel = vel/1e3 # default is usually in m/s
return_arrays.append(vel)
if returnHeader == True: return_arrays.append(hdrarrs)
return return_arrays
imagein = 'mask_han1_mask_imfit_13co_pix_2_Tmb.fits'
hdulist = fits.open(imagein)
print hdulist[0].data.shape
#sys.exit()
data = hdulist[0].data[0, :, :, :]
datarms = 0.64 # K from data paper table 2
header = hdulist[0].header
crpix3 = header['CRPIX3']
cdelt3 = header['CDELT3']
crval3 = header['CRVAL3']
bmaj = 8. # header['BMAJ']*3600. # in arcsec
bmin = 8. # header['BMIN']*3600. # in arcsec
bpa = 0. # header['BPA']
cellsize = 2. # abs(header['CDELT1']*3600.) # in arcsec
n1, n2, n3 = data.shape
w = wcs.WCS(header)
hdulist.close()
def beampixel(
bmaj,
bmin,
bpa,
corecenter,
cellsize,
beamfraction=1.
): # bmaj, bmin, cellsize in arcsec, corecenter = [pixelx, pixely], input bpa in degree
pixellist = []
rotation = float(bpa) / 180. * np.pi
cosa = np.cos(rotation)
sina = np.sin(rotation)
def detect_with_sep(
event,
detect_thresh=2.,
npixels=8,
grow_seg=5,
gauss_fwhm=2.,
gsize=3,
im_wcs=None,
):
""" Run SExtractor on a FITS file contained in the Lambda event
This function will generate a catalog and a PNG for the FITS file stored in
the Lambda event. The catalog and PNG will be stored in the s3 output
bucket specified by the Lambda event.
Parameters
----------
event : dict
dict containing the data passed to the Lambda function
detect_thresh: int,
detection threshold to use for sextractor
npixels: int,
minimum number of pixels comprising an object
grow_seg: int,
gauss_fwhm: float,
FWHM of the kernel to use for filtering prior to source finding
gsize: float
im_wcs: astropy.wcs.WCS
WCS object defining the coordinate system of the observation
Returns
-------
"""
drz_file = event['fits_s3_key']
drz_file_bucket = event['fits_s3_bucket']
fname = drz_file.split('/')[-1]
s3 = boto3.resource('s3')
bkt = s3.Bucket(drz_file_bucket)
bkt.download_file(drz_file,
f"/tmp/{fname}",
ExtraArgs={"RequestPayer": "requester"})
im = fits.open(f"/tmp/{fname}")
if im_wcs is None:
im_wcs = wcs.WCS(im[1].header, relax=True)
data = im[1].data.byteswap().newbyteorder()
wht_data = im[2].data.byteswap().newbyteorder()
data_mask = np.cast[data.dtype](data == 0)
## Get AB zeropoint
try:
photfnu = im[0].header['PHOTFNU']
except KeyError as e:
LOG.warning(e)
ZP = None
else:
ZP = -2.5 * np.log10(photfnu) + 8.90
try:
photflam = im[0].header['PHOTFLAM']
except KeyError as e:
LOG.warning(e)
ZP = None
else:
ZP = -2.5*np.log10(photflam) - 21.10 - \
5*np.log10(im[0].header['PHOTPLAM']) + 18.6921
if ZP is None:
msg = ("Whoops! No zeropoint information found in primary header, "
f"skipping file {fname}")
LOG.warning(msg)
# Scale fluxes to mico-Jy
uJy_to_dn = 1 / (3631 * 1e6 * 10**(-0.4 * ZP))
# set up the error array
err = 1 / np.sqrt(wht_data)
err[~np.isfinite(err)] = 0
mask = (err == 0)
# get the background
bkg = sep.Background(data, mask=mask, bw=32, bh=32, fw=3, fh=3)
bkg_data = bkg.back()
ratio = bkg.rms() / err
err_scale = np.median(ratio[(~mask) & np.isfinite(ratio)])
err *= err_scale
# Generate a kernel to use for filtering
gaussian_kernel = kernels.Gaussian2DKernel(
x_stddev=gauss_fwhm / gaussian_sigma_to_fwhm,
y_stddev=gauss_fwhm / gaussian_sigma_to_fwhm,
x_size=7,
y_size=7)
# Normalize the kernel
gaussian_kernel.normalize()
# Package the inputs for sextractor
inputs = {
'err': err,
'mask': mask,
'filter_kernel': gaussian_kernel.array,
'filter_type': 'conv',
'minarea': npixels,
'deblend_nthresh': 32,
'deblend_cont': 0.005,
'clean': True,
'clean_param': 1,
'segmentation_map': False
}
objects = sep.extract(data - bkg_data, detect_thresh, **inputs)
catalog = Table(objects)
# add things to catalog
autoparams = [2.5, 3.5]
catalog['number'] = np.arange(len(catalog), dtype=np.int32) + 1
catalog['theta'] = np.clip(catalog['theta'], -np.pi / 2, np.pi / 2)
# filter out any NaNs
for c in ['a', 'b', 'x', 'y', 'theta']:
catalog = catalog[np.isfinite(catalog[c])]
catalog['ra'], catalog['dec'] = im_wcs.all_pix2world(
catalog['x'], catalog['y'], 1)
catalog['ra'].unit = u.deg
catalog['dec'].unit = u.deg
catalog['x_world'], catalog['y_world'] = catalog['ra'], catalog['dec']
kronrad, krflag = sep.kron_radius(data - bkg_data, catalog['x'],
catalog['y'], catalog['a'], catalog['b'],
catalog['theta'], 6.0)
kronrad *= autoparams[0]
kronrad[~np.isfinite(kronrad)] = autoparams[1]
kronrad = np.maximum(kronrad, autoparams[1])
kron_out = sep.sum_ellipse(data - bkg_data,
catalog['x'],
catalog['y'],
catalog['a'],
catalog['b'],
catalog['theta'],
kronrad,
subpix=5,
err=err)
kron_flux, kron_fluxerr, kron_flag = kron_out
kron_flux_flag = kron_flag
catalog['mag_auto_raw'] = ZP - 2.5 * np.log10(kron_flux)
catalog['magerr_auto_raw'] = 2.5 / np.log(10) * kron_fluxerr / kron_flux
catalog['mag_auto'] = catalog['mag_auto_raw'] * 1.
catalog['magerr_auto'] = catalog['magerr_auto_raw'] * 1.
catalog['kron_radius'] = kronrad * u.pixel
catalog['kron_flag'] = krflag
catalog['kron_flux_flag'] = kron_flux_flag
# Make a plot
im_data = im[1].data
im_shape = im_data.shape
im_data[np.isnan(im_data)] = 0.0
# Trim the top and bottom 1 percent of pixel values
top = np.percentile(im_data, 99)
im_data[im_data > top] = top
bottom = np.percentile(im_data, 1)
im_data[im_data < bottom] = bottom
# Scale the data.
im_data = im_data - im_data.min()
im_data = (im_data / im_data.max()) * 255.
im_data = np.uint8(im_data)
f, (ax) = plt.subplots(1, 1, sharex=True)
f.set_figheight(12)
f.set_figwidth(12)
ax.imshow(im_data, cmap="Greys", clim=(0, 255), origin='lower')
ax.plot(catalog['x'],
catalog['y'],
'o',
markeredgewidth=1,
markeredgecolor='red',
markerfacecolor='None')
ax.set_xlim([-0.05 * im_shape[1], 1.05 * im_shape[1]])
ax.set_ylim([-0.05 * im_shape[0], 1.05 * im_shape[0]])
basename = fname.split('_')[0]
f.savefig(f"/tmp/{basename}.png")
# Write the catalog to local disk
catalog.write(f"/tmp/{basename}.catalog.fits", format='fits')
# Write out to S3
s3 = boto3.resource('s3')
s3.meta.client.upload_file(f"/tmp/{basename}.catalog.fits",
event['s3_output_bucket'],
f"{basename}/{basename}.catalog.fits")
s3.meta.client.upload_file(f"/tmp/{basename}.png",
event['s3_output_bucket'],
f"{basename}/{basename}.png")
def fourier_combine_cubes(
cube1,
cube2,
highresextnum=0,
highresscalefactor=1.0,
lowresscalefactor=1.0,
lowresfwhm=1 * u.arcmin,
return_regridded_cube2=False,
return_hdu=False,
):
"""
Fourier combine two data cubes
Parameters
----------
cube1 : SpectralCube
highresfitsfile : str
The high-resolution FITS file
cube2 : SpectralCube
lowresfitsfile : str
The low-resolution (single-dish) FITS file
highresextnum : int
The extension number to use from the high-res FITS file
highresscalefactor : float
lowresscalefactor : float
A factor to multiply the high- or low-resolution data by to match the
low- or high-resolution data
lowresfwhm : `astropy.units.Quantity`
The full-width-half-max of the single-dish (low-resolution) beam;
or the scale at which you want to try to match the low/high resolution
data
return_hdu : bool
Return an HDU instead of just a cube. It will contain two image
planes, one for the real and one for the imaginary data.
return_regridded_cube2 : bool
Return the 2nd cube regridded into the pixel space of the first?
"""
if isinstance(cube1, str):
cube1 = SpectralCube.read(cube1)
if isinstance(cube2, str):
cube2 = SpectralCube.read(cube2)
#cube1 = spectral_cube.io.fits.load_fits_cube(highresfitsfile,
# hdu=highresextnum)
im1 = cube1._data # want the raw data for this
hd1 = cube1.header
assert hd1['NAXIS'] == im1.ndim == 3
w1 = cube1.wcs
pixscale = np.abs(w1.wcs.get_cdelt()[0]) # REPLACE EVENTUALLY...
cube2 = cube2.to(cube1.unit)
assert cube1.unit == cube2.unit, 'Cubes must have same or equivalent unit'
assert cube1.unit.is_equivalent(u.Jy / u.beam) or cube1.unit.is_equivalent(
u.K), "Cubes must have brightness units."
#f2 = regrid_fits_cube(lowresfitsfile, hd1)
f2 = regrid_cube_hdu(cube2.hdu, hd1)
w2 = wcs.WCS(f2.header)
nax1, nax2, nax3 = (hd1['NAXIS1'], hd1['NAXIS2'], hd1['NAXIS3'])
dcube1 = im1 * highresscalefactor
dcube2 = f2.data * lowresscalefactor
outcube = np.empty_like(dcube1)
xgrid, ygrid = (np.indices([nax2, nax1]) -
np.array([(nax2 - 1.) / 2,
(nax1 - 1.) / 2.])[:, None, None])
fwhm = np.sqrt(8 * np.log(2))
# sigma in pixels
sigma = ((lowresfwhm / fwhm / (pixscale * u.deg)).decompose().value)
#sigma_fftspace = (1/(4*np.pi**2*sigma**2))**0.5
sigma_fftspace = (2 * np.pi * sigma)**-1
log.debug('sigma = {0}, sigma_fftspace={1}'.format(sigma, sigma_fftspace))
kernel = np.fft.fftshift(np.exp(-(xgrid**2 + ygrid**2) / (2 * sigma**2)))
# convert the kernel, which is just a gaussian in image space,
# to its corresponding kernel in fourier space
kfft = np.abs(np.fft.fft2(kernel)) # should be mostly real
# normalize the kernel
kfft /= kfft.max()
ikfft = 1 - kfft
pb = ProgressBar(dcube1.shape[0])
for ii, (im1, im2) in enumerate(zip(dcube1, dcube2)):
fft1 = np.fft.fft2(np.nan_to_num(im1))
fft2 = np.fft.fft2(np.nan_to_num(im2))
fftsum = kfft * fft2 + ikfft * fft1
combo = np.fft.ifft2(fftsum)
outcube[ii, :, :] = combo.real
pb.update(ii + 1)
if return_regridded_cube2:
return outcube, f2
elif return_hdu:
return fits.PrimaryHDU(data=outcube, header=w1.to_header())
else:
return outcube
def buildmasks(filename, nChan=2000, width=2e9, outdir=None):
"""Builds masks for use in DEGAS imaging pipeline.
Parameters
----------
filename : str
FITS filename of spectral cube mask. The file should be a
binary mask with True / 1 indicating emission and False / 0
otherwise. This assumes the cube has a spectral axis in
velocity and that the cube or has the metadata required to
convert to velocity. Note there is no checking of the
spectral frame (LSRK, LSRD, BARY) and the conversion assumes
radio Doppler convention.
nChan : int
Number of channels in output mask. This should be larger than
the number of channels in the DEGAS bandpass (1024)
width : float
Spectral width in Hz of the resulting mask. This should be
larger than the GBT bandwidth used (usually 1.5 GHz for DEGAS)
outdir : str
Directory for output masks to be stored in
"""
if outdir is None:
outdir = os.environ['DEGASDIR'] + 'masks/'
if not os.access(outdir,os.W_OK):
try:
os.mkdir(outdir)
print('Made directory {0}'.format(outdir))
except OSError:
try:
os.mkdir('/'.join((outdir.split('/'))[0:-1])) # there may be a safer what to do this with os.path.split
os.mkdir(outdir)
print('Made directory {0}'.format(outdir))
except:
warnings.warn('Unable to make output directory '+outdir)
raise
except:
warnings.warn('Unable to make output directory '+outdir)
raise
# Read in original cube, ensure in velocity space
s = SpectralCube.read(filename)
s = s.with_spectral_unit(u.km / u.s, velocity_convention='radio')
vmid = s.spectral_axis[len(s.spectral_axis)//2].value
c = 299792.458
# HCN_HCO+
# Build a mask with a spectral width of 2 GHz and the same spatial
# dimensions as the original mask
s_hcn = s.with_spectral_unit(u.Hz, rest_value=88.631847 * u.GHz)
s_hcop = s.with_spectral_unit(u.Hz, rest_value=89.188518 * u.GHz)
mask = np.zeros((nChan, s.shape[1], s.shape[2]), dtype=np.byte)
hdr = s_hcn.wcs.to_header()
hdr['CRPIX3'] = 1000
hdr['CDELT3'] = width / nChan
hdr['CRVAL3'] = (89.188518 + 88.631847) / 2 * 1e9 * (1 - vmid / c)
hdr['NAXIS'] = 3
hdr['NAXIS1'] = mask.shape[0]
hdr['NAXIS2'] = mask.shape[1]
hdr['NAXIS3'] = mask.shape[2]
hdr['SIMPLE'] = 'T'
hdr['BITPIX'] = 8
hdr['EXTEND'] = 'T'
hdr = deduplicate_keywords(hdr)
w = wcs.WCS(hdr)
maskcube = SpectralCube(mask, w, header=hdr)
for zz in range(nChan):
nu = maskcube.spectral_axis[zz]
_, _, zz_hcn = s_hcn.wcs.wcs_world2pix(hdr['CRVAL1'],
hdr['CRVAL2'],
nu, 0)
zz_hcn = int(zz_hcn)
_, _, zz_hcop = s_hcop.wcs.wcs_world2pix(hdr['CRVAL1'],
hdr['CRVAL2'],
nu, 0)
zz_hcop = int(zz_hcop)
if 0 <= zz_hcn < s_hcn.shape[0]:
mask[zz, :, :] = np.array(s_hcn.filled_data[zz_hcn, :, :],
dtype=np.bool)
if 0 <= zz_hcop < s_hcop.shape[0]:
mask[zz, :, :] = np.array(s_hcop.filled_data[zz_hcop, :, :],
dtype=np.bool)
maskcube = SpectralCube(mask, w, header=hdr)
galname = os.path.split(filename)[1].split('_')[0]
maskcube.write(outdir + galname+'.hcn_hcop.mask.fits',
overwrite=True)
# C18O/13CO
# Build a mask with a spectral width of 2 GHz and the same spatial
# dimensions as the original mask
s_13co = s.with_spectral_unit(u.Hz, rest_value=110.20135 * u.GHz)
s_c18o = s.with_spectral_unit(u.Hz, rest_value=109.78217 * u.GHz)
mask = np.zeros((nChan, s.shape[1], s.shape[2]), dtype=np.byte)
hdr = s_13co.wcs.to_header()
hdr['CRPIX3'] = 1000
hdr['CDELT3'] = width / nChan
hdr['CRVAL3'] = (110.20135 + 109.78217) / 2 * 1e9 * (1 - vmid / c)
hdr['NAXIS'] = 3
hdr['NAXIS1'] = mask.shape[0]
hdr['NAXIS2'] = mask.shape[1]
hdr['NAXIS3'] = mask.shape[2]
hdr['SIMPLE'] = 'T'
hdr['BITPIX'] = 8
hdr['EXTEND'] = 'T'
w = wcs.WCS(hdr)
hdr = deduplicate_keywords(hdr)
maskcube = SpectralCube(mask, w, header=hdr)
for zz in range(nChan):
nu = maskcube.spectral_axis[zz]
_, _, zz_13co = s_13co.wcs.wcs_world2pix(hdr['CRVAL1'],
hdr['CRVAL2'],
nu, 0)
zz_13co = int(zz_13co)
_, _, zz_c18o = s_c18o.wcs.wcs_world2pix(hdr['CRVAL1'],
hdr['CRVAL2'],
nu, 0)
zz_c18o = int(zz_c18o)
if 0 <= zz_13co < s_13co.shape[0]:
mask[zz, :, :] = np.array(s_13co.filled_data[zz_13co, :, :],
dtype=np.bool)
if 0 <= zz_c18o < s_c18o.shape[0]:
mask[zz, :, :] = np.array(s_c18o.filled_data[zz_c18o, :, :],
dtype=np.bool)
maskcube = SpectralCube(mask, w, header=hdr)
maskcube.write(outdir + galname + '.13co_c18o.mask.fits',
overwrite=True)
# 12CO
# Build a mask with a spectral width of 2 GHz and the same spatial
# dimensions as the original mask
s_12co = s.with_spectral_unit(u.Hz, rest_value=115.271204 * u.GHz)
mask = np.zeros((nChan, s.shape[1], s.shape[2]), dtype=np.byte)
hdr = s_12co.wcs.to_header()
hdr['CRPIX3'] = 1000
hdr['CDELT3'] = width / nChan
hdr['CRVAL3'] = (115.271204) * 1e9
hdr['NAXIS'] = 3
hdr['NAXIS1'] = mask.shape[0]
hdr['NAXIS2'] = mask.shape[1]
hdr['NAXIS3'] = mask.shape[2]
hdr['SIMPLE'] = 'T'
hdr['BITPIX'] = 8
hdr['EXTEND'] = 'T'
w = wcs.WCS(hdr)
hdr = deduplicate_keywords(hdr)
maskcube = SpectralCube(mask, w, header=hdr)
for zz in range(nChan):
nu = maskcube.spectral_axis[zz]
_, _, zz_12co = s_12co.wcs.wcs_world2pix(hdr['CRVAL1'],
hdr['CRVAL2'],
nu, 0)
zz_12co = int(zz_12co)
if 0 <= zz_12co < s_12co.shape[0]:
mask[zz, :, :] = np.array(s_12co.filled_data[zz_12co, :, :],
dtype=np.bool)
maskcube = SpectralCube(mask, w, header=hdr)
maskcube.write(outdir + galname+'.12co.mask.fits', overwrite=True)
def main1():
m31 = fits.open('fitsfiles/m31cm6i_full_3min_large.fits')
hdr = m31[0].header
hdr['NAXIS'] = 2
m31_w = wcs.WCS(naxis=2) #[0,:,:]#.slice((0,slice(0,None),slice(0,None)))
m31_w.wcs.crpix = [hdr['CRPIX1'], hdr['CRPIX2']]
m31_w.wcs.cdelt = [hdr['CDELT1'], hdr['CDELT2']]
m31_w.wcs.crval = [hdr['CRVAL1'], hdr['CRVAL2']]
m31_w.wcs.ctype = [hdr['CTYPE1'], hdr['CTYPE2']]
m31_w.wcs.crota = [hdr['CROTA1'], hdr['CROTA2']]
m31_w.wcs.equinox = hdr['EPOCH']
for k, v in hdr.items():
print(k, v)
#stop
m31_img = m31[0].data[0, :, :]
#img_flat[select] = 1000
#img = np.reshape(img_flat, img.shape)
#img1, w = read_image('fitsfiles/fg4_feeds15.0-17.0-18.0_offset50.0_band1.0_freq0.0.fits')#sys.argv[1])
#img2, w = read_image('fitsfiles/fg4_feeds15.0-17.0-18.0_offset50.0_band0.0_freq0.0.fits')#sys.argv[1])
#img = img1-img2
img, w = read_image(sys.argv[1])
cmap = pyplot.get_cmap('RdBu_r')
pyplot.figure(figsize=(12, 8))
ax = pyplot.subplot(projection=w)
sources = [SkyCoord('00h38m24.84s', '+41d37m06.00s', frame='icrs')]
#SkyCoord('00h46m48.1s' ,'+41d41m07.00s',frame='icrs'),
#SkyCoord('00h42m44.33s','+41d16m07.50s',frame='icrs')]
mimg = img * 1
mimg[np.isnan(img)] = 0
mimg = gaussian_filter(mimg, sigma=2)
img[img == 0] = np.nan
mimg[mimg == 0] = np.nan
zimg = ax.imshow(img, cmap=cmap, origin='lower', aspect='auto')
cbar = pyplot.colorbar(zimg)
cbar.set_label('K', size=20)
for source in sources:
ax.scatter(source.ra,
source.dec,
transform=ax.get_transform('icrs'),
s=300,
edgecolor='k',
facecolor='none')
#print(m31_w)
#print(w)
# ax.contour(m31_img, transform=ax.get_transform(m31_w),
# origin='lower',
# cmap=pyplot.get_cmap('Greys'),
# linewidths=3,
# alpha=0.85,
# levels=[-0.005,0.005,0.010,0.015])
##pyplot.contour(mimg, cmap = pyplot.get_cmap('Greys_r'),
# levels=[-0.02,-0.015,-0.01,-0.005,0,0.01,0.02,0.045,0.07,0.08,0.09,0.135,0.3,0.4])
fname = sys.argv[1].split('/')[-1].split('.fit')[0]
pyplot.gca().invert_xaxis()
pyplot.grid()
pyplot.xlabel(r'$\alpha$', size=20)
pyplot.ylabel(r'$\delta$', size=20)
pyplot.gca().set_xlim(0.9 * img.shape[1], 0.1 * img.shape[1])
pyplot.gca().set_ylim(0.1 * img.shape[0], 0.9 * img.shape[0])
#xpyplot.gca().add_patch(circle)
pyplot.title(sys.argv[1], size=5)
#pyplot.savefig('jackknife.png')#.format(fname))
pyplot.savefig('nooverlay_{}.png'.format(fname))
pyplot.show()
def create_image_from_visibility(vis, **kwargs) -> Image:
"""Make an empty image from params and Visibility
This makes an empty, template image consistent with the visibility, allowing optional overriding of select
parameters. This is a convenience function and does not transform the visibilities.
:param vis:
:param phasecentre: Phasecentre (Skycoord)
:param channel_bandwidth: Channel width (Hz)
:param cellsize: Cellsize (radians)
:param npixel: Number of pixels on each axis (512)
:param frame: Coordinate frame for WCS (ICRS)
:param equinox: Equinox for WCS (2000.0)
:param nchan: Number of image channels (Default is 1 -> MFS)
:return: image
"""
assert isinstance(vis, Visibility) or isinstance(vis, BlockVisibility), \
"vis is not a Visibility or a BlockVisibility: %r" % (vis)
log.info("create_image_from_visibility: Parsing parameters to get definition of WCS")
imagecentre = get_parameter(kwargs, "imagecentre", vis.phasecentre)
phasecentre = get_parameter(kwargs, "phasecentre", vis.phasecentre)
# Spectral processing options
ufrequency = numpy.unique(vis.frequency)
vnchan = len(ufrequency)
frequency = get_parameter(kwargs, "frequency", vis.frequency)
inchan = get_parameter(kwargs, "nchan", vnchan)
reffrequency = frequency[0] * units.Hz
channel_bandwidth = get_parameter(kwargs, "channel_bandwidth", 0.99999999999 * vis.channel_bandwidth[0]) * units.Hz
if (inchan == vnchan) and vnchan > 1:
log.info(
"create_image_from_visibility: Defining %d channel Image at %s, starting frequency %s, and bandwidth %s"
% (inchan, imagecentre, reffrequency, channel_bandwidth))
elif (inchan == 1) and vnchan > 1:
assert numpy.abs(channel_bandwidth.value) > 0.0, "Channel width must be non-zero for mfs mode"
log.info("create_image_from_visibility: Defining single channel MFS Image at %s, starting frequency %s, "
"and bandwidth %s"
% (imagecentre, reffrequency, channel_bandwidth))
elif inchan > 1 and vnchan > 1:
assert numpy.abs(channel_bandwidth.value) > 0.0, "Channel width must be non-zero for mfs mode"
log.info("create_image_from_visibility: Defining multi-channel MFS Image at %s, starting frequency %s, "
"and bandwidth %s"
% (imagecentre, reffrequency, channel_bandwidth))
elif (inchan == 1) and (vnchan == 1):
assert numpy.abs(channel_bandwidth.value) > 0.0, "Channel width must be non-zero for mfs mode"
log.info("create_image_from_visibility: Defining single channel Image at %s, starting frequency %s, "
"and bandwidth %s"
% (imagecentre, reffrequency, channel_bandwidth))
else:
raise ValueError("create_image_from_visibility: unknown spectral mode ")
# Image sampling options
npixel = get_parameter(kwargs, "npixel", 512)
uvmax = numpy.max((numpy.abs(vis.data['uvw'][:, 0:1])))
if isinstance(vis, BlockVisibility):
uvmax *= numpy.max(frequency) / constants.c.to('m s^-1').value
log.info("create_image_from_visibility: uvmax = %f wavelengths" % uvmax)
criticalcellsize = 1.0 / (uvmax * 2.0)
log.info("create_image_from_visibility: Critical cellsize = %f radians, %f degrees" % (
criticalcellsize, criticalcellsize * 180.0 / numpy.pi))
cellsize = get_parameter(kwargs, "cellsize", 0.5 * criticalcellsize)
log.info("create_image_from_visibility: Cellsize = %f radians, %f degrees" % (cellsize,
cellsize * 180.0 / numpy.pi))
override_cellsize = get_parameter(kwargs, "override_cellsize", True)
if override_cellsize and cellsize > criticalcellsize:
log.info("create_image_from_visibility: Resetting cellsize %f radians to criticalcellsize %f radians" % (
cellsize, criticalcellsize))
cellsize = criticalcellsize
pol_frame = get_parameter(kwargs, "polarisation_frame", PolarisationFrame("stokesI"))
inpol = pol_frame.npol
# Now we can define the WCS, which is a convenient place to hold the info above
# Beware of python indexing order! wcs and the array have opposite ordering
shape = [inchan, inpol, npixel, npixel]
w = wcs.WCS(naxis=4)
# The negation in the longitude is needed by definition of RA, DEC
w.wcs.cdelt = [-cellsize * 180.0 / numpy.pi, cellsize * 180.0 / numpy.pi, 1.0, channel_bandwidth.to(units.Hz).value]
# The numpy definition of the phase centre of an FFT is n // 2 (0 - rel) so that's what we use for
# the reference pixel. We have to use 0 rel everywhere.
w.wcs.crpix = [npixel // 2 + 1, npixel // 2 + 1, 1.0, 1.0]
w.wcs.ctype = ["RA---SIN", "DEC--SIN", 'STOKES', 'FREQ']
w.wcs.crval = [phasecentre.ra.deg, phasecentre.dec.deg, 1.0, reffrequency.to(units.Hz).value]
w.naxis = 4
direction_centre = pixel_to_skycoord(npixel // 2 + 1, npixel // 2 + 1, wcs=w, origin=1)
assert direction_centre.separation(imagecentre).value < 1e-7, \
"Image phase centre [npixel//2, npixel//2] should be %s, actually is %s" % \
(str(imagecentre), str(direction_centre))
w.wcs.radesys = get_parameter(kwargs, 'frame', 'ICRS')
w.wcs.equinox = get_parameter(kwargs, 'equinox', 2000.0)
return create_image_from_array(numpy.zeros(shape), wcs=w, polarisation_frame=pol_frame)
