def posang(l1, b1, l2, b2, system='galactic', units='degrees', **kwargs):
"""
Return the position angle between two points assuming a rectilinear
coordinate system (I think; at the very least I am making no corrections
for wcs).
INPUT:
longitude1, latitude1, longitude2, latitude2
Defaults to GALACTIC coordinates. **kwargs are passed to coords.Position
"""
pos1 = coords.Position([l1, b1], system=system, **kwargs)
ra1, dec1 = pos1.j2000()
pos2 = coords.Position([l2, b2], system=system, **kwargs)
ra2, dec2 = pos2.j2000()
radiff = (ra1 - ra2) / 180. * pi
angle = arctan2(
sin(radiff),
cos(dec1 * pi / 180.) * tan(dec2 * pi / 180.) -
sin(dec1 * pi / 180.) * cos(radiff))
if units == 'degrees':
return angle / pi * 180
elif units == 'radians':
return angle
else:
raise ValueError("Invalid units: %s" % units)
def coords_in_image(xc,yc,header,coordsys='celestial'):
"""
Determine whether the coordinates are within the boundaries of the image
"""
try:
wcs = pywcs.WCS(header)
except: # if the header isn't WCS compatible, we don't want it
return False
try:
if coordsys=='celestial' and wcs.wcs.lngtyp=='GLON':
xc,yc = coords.Position((xc,yc),system=coordsys).galactic()
elif coordsys=='galactic' and wcs.wcs.lngtyp=='RA':
xc,yc = coords.Position((xc,yc),system=coordsys).j2000()
xp,yp = wcs.wcs_sky2pix(xc,yc,0)
except:
return False
if xp > wcs.naxis1 or xp < 0:
return False
elif yp > wcs.naxis2 or yp < 0:
return False
else:
return True
def gal2cel(regfile):
"""
Converts a region file from galactic to celestial coordinates including
position angle reference from the center of the box (right now only works
on box regions)
Requires pyregion with the ShapeList.write() function implemented...
not clear if that exists in 1.0
"""
reg = pyregion.open(regfile)
for R in reg:
if R.name == 'box':
x, y, dx, dy, angle = R.coord_list
posn = coords.Position([x, y], system='galactic')
ra, dec = posn.j2000()
newang = posang.posang(x - dx, y, x + dx, y, system='galactic')
coord_list = [ra, dec, dx, dy, angle - newang - 90]
R.coord_format = 'fk5'
R.coord_list = coord_list
R.params = coord_list
reg.write(regfile[:-4] + "_fk5.reg")
def coords_in_image(fitsfile,lon,lat,system='galactic'):
"""
Determine whether the coordinates are inside the image
"""
if not isinstance(fitsfile,pyfits.HDUList):
fitsfile = pyfits.open(fitsfile)
wcs = pywcs.WCS(flatten_header(fitsfile[0].header))
if 'RA' in wcs.wcs.ctype[0]:
pos = coords.Position((lon,lat),system=system)
lon,lat = pos.j2000()
if 'GLON' in wcs.wcs.ctype[0]:
pos = coords.Position((lon,lat),system=system)
lon,lat = pos.galactic()
x,y = wcs.wcs_sky2pix(lon,lat,0)
#DEBUG print x,y,wcs.naxis1,wcs.naxis2
if (0 < x < wcs.naxis1) and (0 < y < wcs.naxis2):
return True
else:
return False
def output_tab_delineated_spreadsheet(spreadsheet, print_column_headers=False):
column_headers = [
key for key in match_table.columns.keys if 'index' not in key
]
primary_header = column_headers[0]
column_headers.insert(1, 'DEC')
column_headers.insert(1, 'RA')
row_strings = []
if print_column_headers:
row_strings.append('\t'.join(column_headers))
spreadsheet_matched = match_table.where(
np.in1d(match_table[primary_header],
spreadsheet[primary_header.lstrip('WUVARS_2014_')]))
RA_array = []
DEC_array = []
for (ra, dec) in zip(spreadsheet.RA, spreadsheet.DEC):
pp = coords.Position((ra, dec), units='rad')
ra_s, de_s = pp.hmsdms().split(' ')
RA_array.append(ra_s[:-1])
DEC_array.append(' ' + de_s[:-2])
for i in range(len(spreadsheet_matched)):
row_list = [str(spreadsheet_matched[primary_header][i])]
row_list.extend([str(RA_array[i]), str(DEC_array[i])])
row_list.extend([
str(spreadsheet_matched[header][i]) for header in column_headers
if (header != primary_header) and (len(header) > 3)
])
row_strings.append('\t'.join(row_list))
return_string = '\n'.join(row_strings)
return return_string
def rotcrop_cube(x1, y1, x2, y2, cubename, outname, xwidth=25, ywidth=25,
in_system='galactic', out_system='equatorial', clobber=True,
newheader=None, xcen=None, ycen=None):
"""
Crop a data cube and then rotate it with montage
"""
cubefile = pyfits.open(cubename)
if xcen is None and ycen is None:
pos1 = coords.Position([x1,y1],system=in_system)
pos2 = coords.Position([x2,y2],system=in_system)
if cubefile[0].header.get('CTYPE1')[:2] == 'RA':
x1,y1 = pos1.j2000()
x2,y2 = pos2.j2000()
coord_system = 'celestial'
elif cubefile[0].header.get('CTYPE1')[:4] == 'GLON':
x1,y1 = pos1.galactic()
x2,y2 = pos2.galactic()
coord_system = 'galactic'
xcen = (x1+x2)/2.0
ycen = (y1+y2)/2.0
print xcen,ycen,xwidth,ywidth,coord_system
else:
coord_system = in_system
sc = subcube(cubefile[0].data, xcen, xwidth, ycen, ywidth,
widthunits='pixels', units="wcs", header=cubefile[0].header,
return_HDU=True)
# note: there should be no security risk here because pyfits' writeto
# will not overwrite by default
tempcube = tempfile.mktemp(suffix='.fits')
sc.writeto(tempcube)
pa = posang.posang(x1,y1,x2,y2,system=coord_system) - 90
if newheader is None:
newheader = sc.header.copy()
cd11 = newheader.get('CDELT1') if newheader.get('CDELT1') else newheader.get('CD1_1')
cd22 = newheader.get('CDELT2') if newheader.get('CDELT2') else newheader.get('CD2_2')
cd12 = newheader.get('CD1_2') if newheader.get('CD1_2') else 0.0
cd21 = newheader.get('CD2_1') if newheader.get('CD2_1') else 0.0
cdelt = numpy.sqrt(cd11**2+cd12**2)
tempheader = tempfile.mktemp(suffix='.hdr')
ycensign = "+" if numpy.sign(ycen) >= 0 else "-"
montage.mHdr("%s %1s%s" % (xcen, ycensign, numpy.abs(ycen)), xwidth*cdelt,
tempheader, system=out_system, height=ywidth*cdelt,
pix_size=cdelt*3600.0, rotation=pa)
os.system("sed -i bck '/END/d' %s" % (tempheader))
newheader2 = pyfits.Header()
newheader2.fromTxtFile(tempheader)
#newheader2.fromtextfile(tempheader)
for key in ('CRPIX3','CRVAL3','CDELT3','CD3_3','CUNIT3','WCSTYPE3','CTYPE3'):
if newheader.get(key):
newheader2.update(key,newheader.get(key))
if newheader.get('CD3_3') and newheader2.get('CDELT3') is None:
newheader2.update('CDELT3',newheader.get('CD3_3'))
newheader2.toTxtFile(tempheader,clobber=True)
#if newheader2.get('CDELT3') is None:
# raise Exception("No CD3_3 or CDELT3 in header.")
else:
if isinstance(newheader,str):
newheader2 = pyfits.Header()
newheader2.fromTxtFile(newheader)
tempheader = tempfile.mktemp(suffix='.hdr')
newheader2.toTxtFile(tempheader,clobber=True)
montage.wrappers.reproject_cube(tempcube,outname,header=tempheader,clobber=clobber)
#print "\n",outname
#os.system('imhead %s | grep CDELT' % outname)
# AWFUL hack because montage removes CDELT3
tempcube = pyfits.open(outname)
tempcube.header = newheader2
#if tempcube.header.get('CDELT3') is None:
# raise Exception("No CD3_3 or CDELT3 in header.")
#print tempcube.header.get('CDELT3')
tempcube.writeto(outname,clobber=True)
#print tempcube.get('CDELT3')
#print "\n",outname
#os.system('imhead %s | grep CDELT' % outname)
#print "\nnewheader2"
#print newheader2.ascard
#print
return
def aper_world2pix(ap,wcs,coordsys='galactic',wunit='arcsec'):
"""
Converts an elliptical aperture (x,y,width,height,PA) from
WCS to pixel coordinates given an input wcs (an instance
of the pywcs.WCS class). Must be a 2D WCS header.
"""
convopt = {'arcsec':3600,'arcmin':60,'degree':1}
try:
conv = convopt[wunit]
except:
raise Exception("Must specify wunit='arcsec','arcmin', or 'degree'")
if len(wcs.wcs.cdelt) != 2:
raise Exception("WCS header is not strictly 2-dimensional. Look for 3D keywords.")
if '' in wcs.wcs.ctype:
raise Exception("WCS header has no CTYPE.")
pos = coords.Position((ap[0],ap[1]),system=coordsys)
if wcs.wcs.ctype[0][:2] == 'RA':
ra,dec = pos.j2000()
corrfactor = cos(dec*dtor)
elif wcs.wcs.ctype[0][:4] == 'GLON':
ra,dec = pos.galactic()
corrfactor=1
else:
raise Exception("WCS CTYPE has no match.")
# workaround for a broken wcs.wcs_sky2pix
try:
radif = (wcs.wcs.crval[0]-ra)*dtor
gamma = acos(cos(dec*dtor)*cos(wcs.wcs.crval[1]*dtor)*cos(radif)+sin(dec*dtor)*sin(wcs.wcs.crval[1]*dtor)) / dtor
theta = atan2( sin(radif) , ( tan(dec*dtor)*cos(wcs.wcs.crval[1]*dtor)-sin(wcs.wcs.crval[1]*dtor)*cos(radif) ) )
x = -gamma * sin(theta) / wcs.wcs.cd[0,0] + wcs.wcs.crpix[0]
y = gamma * cos(theta) / wcs.wcs.cd[1,1] + wcs.wcs.crpix[1]
except:
radif = (wcs.wcs.crval[0]-ra)*dtor
gamma = acos(cos(dec*dtor)*cos(wcs.wcs.crval[1]*dtor)*cos(radif)+sin(dec*dtor)*sin(wcs.wcs.crval[1]*dtor)) / dtor
theta = atan2( sin(radif) , ( tan(dec*dtor)*cos(wcs.wcs.crval[1]*dtor)-sin(wcs.wcs.crval[1]*dtor)*cos(radif) ) )
x = -gamma * sin(theta) / wcs.wcs.cdelt[0] + wcs.wcs.crpix[0]
y = gamma * cos(theta) / wcs.wcs.cdelt[1] + wcs.wcs.crpix[1]
#print "DEBUG: x,y from math (vectors): ",x,y
#x,y = wcs.wcs_sky2pix(ra,dec,0) # convert WCS coordinate to pixel coordinate (0 is origin, do not use fits convention)
#print "DEBUG: x,y from wcs: ",x,y
try:
x=x[0] - 1 # change from FITS to python convention
y=y[0] - 1 # change from FITS to python convention
#print "DEBUG: x,y from math: ",x,y
except:
pass
# cd is default, cdelt is backup
if len(ap) > 3:
try:
width = ap[2] / conv / abs(wcs.wcs.cd[0,0]) # first is width, second is height in DS9 PA convention
height = ap[3] / conv / abs(wcs.wcs.cd[0,0])
except:
width = ap[2] / conv / abs(wcs.wcs.cdelt[0]) # first is width, second is height in DS9 PA convention
height = ap[3] / conv / abs(wcs.wcs.cdelt[0])
apold = copy.copy(ap)
if len(ap) == 5:
PA = ap[4]
ap = [x,y,width,height,PA]
else:
ap = [x,y,width,height]
elif len(ap) == 3:
try:
width = ap[2] / conv / abs(wcs.wcs.cd[0,0]) # first is width, second is height in DS9 PA convention
except:
width = ap[2] / conv / abs(wcs.wcs.cdelt[0]) # first is width, second is height in DS9 PA convention
apold = copy.copy(ap)
ap = [x,y,width]
return ap
pcd_ra = pc['m0']['value'] * 180 / np.pi
if pcd_ra < 0:
pcd_ra += 360
ms.done()
pcd = [pcd_ra, pcd_dec]
return pcd
if __name__ == '__main__':
import astrolib.coords as coords
import pyfits
# lens positions for RXJ0911, presumably we want to this to be the phase center of the data/input visibilities for Ripples!!!!
p_list = [
coords.Position("09:11:27.56447 05:50:54.302").j2000(),
coords.Position("09:11:27.51420 05:50:54.967").j2000()
]
fits_cube = pyfits.open('calibrated.LSRK_cont_R05.image.fits')
header = fits_cube[0].header
ra_px, dec_px = coord2pix(p_list, header)
print "RA, Dec: "
print zip(ra_px, dec_px)
x_cen, y_cen = offset_from_phs(header, ra_px[0], dec_px[0])
print("X, Y offset in px from ideal phase center: {:.2f}, {:.2f}").format(
x_cen, y_cen)
# for Ripples input
get_PB_arcsec(header)
def cutout(filename, xc, yc, xw=25, yw=25, units='pixels', outfile=None,
clobber=True, useMontage=False, coordsys='celestial', verbose=False):
"""
Inputs:
file - .fits filename or pyfits HDUList (must be 2D)
xc,yc - x and y coordinates in the fits files' coordinate system (CTYPE)
xw,yw - x and y width (pixels or wcs)
units - specify units to use: either pixels or wcs
outfile - optional output file
"""
if isinstance(filename,str):
file = pyfits.open(filename)
opened=True
elif isinstance(filename,pyfits.HDUList):
file = filename
opened=False
else:
raise Exception("cutout: Input file is wrong type (string or HDUList are acceptable).")
head = file[0].header.copy()
if head['NAXIS'] > 2:
raise DimensionError("Too many (%i) dimensions!" % head['NAXIS'])
cd1 = head.get('CDELT1') if head.get('CDELT1') else head.get('CD1_1')
cd2 = head.get('CDELT2') if head.get('CDELT2') else head.get('CD2_2')
if cd1 is None or cd2 is None:
raise Exception("Missing CD or CDELT keywords in header")
wcs = pywcs.WCS(head)
if units == 'wcs':
if coordsys=='celestial' and wcs.wcs.lngtyp=='GLON':
xc,yc = coords.Position((xc,yc),system=coordsys).galactic()
elif coordsys=='galactic' and wcs.wcs.lngtyp=='RA':
xc,yc = coords.Position((xc,yc),system=coordsys).j2000()
if useMontage and CanUseMontage:
head['CRVAL1'] = xc
head['CRVAL2'] = yc
if units == 'pixels':
head['CRPIX1'] = xw
head['CRPIX2'] = yw
head['NAXIS1'] = int(xw*2)
head['NAXIS2'] = int(yw*2)
elif units == 'wcs':
cdelt = numpy.sqrt(cd1**2+cd2**2)
head['CRPIX1'] = xw / cdelt
head['CRPIX2'] = yw / cdelt
head['NAXIS1'] = int(xw*2 / cdelt)
head['NAXIS2'] = int(yw*2 / cdelt)
head.toTxtFile('temp_montage.hdr',clobber=True)
newfile = montage.wrappers.reproject_hdu(file[0],header='temp_montage.hdr',exact_size=True)
os.remove('temp_montage.hdr')
else:
xx,yy = wcs.wcs_sky2pix(xc,yc,0)
if units=='pixels':
xmin,xmax = numpy.max([0,xx-xw]),numpy.min([head['NAXIS1'],xx+xw])
ymin,ymax = numpy.max([0,yy-yw]),numpy.min([head['NAXIS2'],yy+yw])
elif units=='wcs':
xmin,xmax = numpy.max([0,xx-xw/numpy.abs(cd1)]),numpy.min([head['NAXIS1'],xx+xw/numpy.abs(cd1)])
ymin,ymax = numpy.max([0,yy-yw/numpy.abs(cd2)]),numpy.min([head['NAXIS2'],yy+yw/numpy.abs(cd2)])
else:
raise Exception("Can't use units %s." % units)
if xmax < 0 or ymax < 0:
raise ValueError("Max Coordinate is outside of map: %f,%f." % (xmax,ymax))
if ymin >= head.get('NAXIS2') or xmin >= head.get('NAXIS1'):
raise ValueError("Min Coordinate is outside of map: %f,%f." % (xmin,ymin))
head['CRPIX1']-=xmin
head['CRPIX2']-=ymin
head['NAXIS1']=int(xmax-xmin)
head['NAXIS2']=int(ymax-ymin)
if head.get('NAXIS1') == 0 or head.get('NAXIS2') == 0:
raise ValueError("Map has a 0 dimension: %i,%i." % (head.get('NAXIS1'),head.get('NAXIS2')))
img = file[0].data[ymin:ymax,xmin:xmax]
newfile = pyfits.PrimaryHDU(data=img,header=head)
if verbose: print "Cut image %s with dims %s to %s. xrange: %f:%f, yrange: %f:%f" % (filename, file[0].data.shape,img.shape,xmin,xmax,ymin,ymax)
if isinstance(outfile,str):
newfile.writeto(outfile,clobber=clobber)
if opened:
file.close()
return newfile
def kdist(l, b, vin, near=True,r0=8.4e3,v0=2.54e2,dynamical=False,
kinematic=True,regular=False,rrgal=False,verbose=False,
inverse=False,silent=False, returnvtan=False):
"""
NAME:
KINDIST
PURPOSE:
To return the distance to an object given l,b,v
CALLING SEQUENCE:
dist = KDIST (L, B, V)
INPUTS:
L, B -- Galactic Longitude and Latitude (decimal degrees)
V - Velocity w.r.t. LSR in km/s
KEYWORD PARAMETERS:
/NEAR, /FAR -- Report the near/far kinematic distances for Q1 and
Q4 data.
RO, VO -- Force values for galactocentric distance for sun and
velocity of the LSR around the GC. Default to 8.4 kpc
and 254 km/s (Reid et al., 2009)
RGAL -- Named keyword containing galactocentric radius of sources.
rrgal - return galactocentric distance in addition to distance from us
/DYNAMICAL -- Use the dynamical definition of the LSR
/KINEMATIC -- Use the kinematic definition of the LSR (default)
/REGULAR -- Do not apply the rotation correction for High mass
star forming regions.
INVERSE -- If set, pass DISTANCE instead of velocity, and output is
velocity
returnvtan - if set, return the tanent velocity and ignore the input
velocity
OUTPUTS:
DIST -- the kinematic distance in units of R0 (defaults to pc).
MODIFICATION HISTORY:
Fri Feb 27 00:47:18 2009, Erik <*****@*****.**>
Adapted from kindist.pro
Translated from IDL to Python by Adam Ginsburg ([email protected])
"""
dtor = pi/180.
if regular: vs = 0.0
else: vs=15.0
if kinematic or not(dynamical):
solarmotion_ra = ((18+03/6e1+50.29/3.6e3)*15)
solarmotion_dec = (30+0/6e1+16.8/3.6e3)
solarmotion_mag = 20.0
else:
solarmotion_ra = ((17+49/6e1+58.667/3.6e3)*15)
solarmotion_dec = (28+7/6e1+3.96/3.6e3)
solarmotion_mag = 16.55294
cg = coords.Position((l,b),system='galactic')
solarmotion = coords.Position((solarmotion_ra,solarmotion_dec))
# ra,dec = cg.j2000()
# gcirc, 2, solarmotion_ra, solarmotion_dec, ra, dec, theta
theta = cg.angsep(solarmotion).arcsec()
vhelio = vin-solarmotion_mag*cos(theta/206265.)
# UVW from Dehnen and Binney
bigu = 10.0
bigv = 5.23
bigw = 7.17
v = vhelio+(bigu*cos(l*dtor)+bigv*sin(l*dtor))*cos(b*dtor)+bigw*sin(b*dtor)
# Compute tangent distance and velocity
rtan = r0*(cos(l*dtor))/(cos(b*dtor))
vTEMP = (1/sin(l*dtor) - v0/(v0-vs)) * ((v0-vs)*sin(l*dtor)*cos(b*dtor))
vhelioTEMP = vTEMP - ((bigu*cos(l*dtor)+bigv*sin(l*dtor))*cos(b*dtor)+bigw*sin(b*dtor))
vtan = vhelioTEMP+solarmotion_mag*cos(theta/206265.)
if returnvtan:
return vtan
# This is r/r0
null = (v0/(v0-vs)+v/((v0-vs)*sin(l*dtor)*cos(b*dtor)))**(-1)
if inverse:
radical = cos(l*dtor) - cos(b*dtor) * vin / r0
null = sqrt(1 - cos(l*dtor)**2 + radical**2)
v = (1/null - v0/(v0-vs)) * ((v0-vs)*sin(l*dtor)*cos(b*dtor))
vhelio = v - ((bigu*cos(l*dtor)+bigv*sin(l*dtor))*cos(b*dtor)+bigw*sin(b*dtor))
vlsr = vhelio+solarmotion_mag*cos(theta/206265.)
return vlsr
else:
if vin > vtan:
if not silent:
print "Velocity is greater than tangent velocity v=%f. Returning tangent distance." % vtan
if rrgal: return rtan,null*r0
return rtan
# The > 0 traps things near the tangent point and sets them to the
# tangent distance. So quietly. Perhaps this should pitch a flag?
radical = max(sqrt(((cos(l*dtor))**2-(1-null**2)) ),0)
fardist = r0*(cos(l*dtor)+radical)/(cos(b*dtor))
neardist = r0*(cos(l*dtor)-radical)/(cos(b*dtor))
rgal = null*r0
ind = (abs(l-180) < 90)
if ind.sum() > 1: neardist[ind] = fardist[ind]
elif ind==True: neardist = fardist
if not(near): dist = fardist
else: dist = neardist
if verbose:
print "radical: %f null: %f vin: %f v: %f vhelio: %f rgal: %f neardist: %f fardist: %f" % (radical,null,vin,v,vhelio,rgal,neardist,fardist)
if rrgal: return abs(dist),abs(rgal)
return abs(dist)
