def generate_v_header(hdu, inhead, params):
"""
"""
today = datetime.datetime.today()
hdu.header = inhead.copy()
hdu.header.set('ORIGIN', 'rmsynthesis.py', 'Origin of the data set')
hdu.header.set('DATE', str(today), 'Date when the file was created')
hdu.header.set('NAXIS', 3, 'Number of axes in the data array, must be 3')
hdu.header.set('NAXIS3', params.nu.size, 'Length of the Frequency axis')
# In FITS, the first pixel is 1, not 0!!!
hdu.header.set('CRPIX3', 1, 'Reference pixel')
hdu.header.set('CRVAL3', params.nu[0])
hdu.header.set('CDELT3', params.dnu)
hdu.header.add_history('RMSYNTH: Stokes V cube generated by ' +
'rmsynthesis.py version ' + str(VERSION) + '.')
hdu.header.add_history(' WARNING! The frequency axis is not linear. ' +
'Look in the')
hdu.header.add_history(' accompanying _freqlist.txt file for ' +
'frequency axis information')
# Get the reference pixel for the new image
cpix_ra = (params.ra_lim[1] - params.ra_lim[0]) / 2. + 1.
cpix_dec = (params.dec_lim[1] - params.dec_lim[0]) / 2. + 1.
# Get the index of the new reference pixel in the old image
cpix_ra_old = params.ra_lim[0] + cpix_ra - 1
cpix_dec_old = params.dec_lim[1] - cpix_dec + 1
# Find its sky coordinate
wcs = WCS(inhead)
if inhead['NAXIS'] == 4:
crval_ra = wcs.wcs_pix2sky([[cpix_ra_old, cpix_dec_old, 0, 0]],
0)[0][0]
crval_dec = wcs.wcs_pix2sky([[cpix_ra_old, cpix_dec_old, 0, 0]],
0)[0][1]
if inhead['NAXIS'] == 3:
crval_ra = wcs.wcs_pix2sky([[cpix_ra_old, cpix_dec_old, 0]], 0)[0][0]
crval_dec = wcs.wcs_pix2sky([[cpix_ra_old, cpix_dec_old, 0]], 0)[0][1]
hdu.header.set('NAXIS1', params.ra_lim[1] - params.ra_lim[0])
hdu.header.set('CRVAL1', crval_ra)
hdu.header.set('CRPIX1', cpix_ra)
hdu.header.set('NAXIS2', params.dec_lim[1] - params.dec_lim[0])
hdu.header.set('CRVAL2', crval_dec)
hdu.header.set('CRPIX2', cpix_dec)
try:
hdu.header.__delitem__('NAXIS4')
hdu.header.__delitem__('CTYPE4')
hdu.header.__delitem__('CRVAL4')
hdu.header.__delitem__('CRPIX4')
hdu.header.__delitem__('CDELT4')
hdu.header.__delitem__('CUNIT4')
except:
pass
def generate_v_header(hdu, inhead, params):
"""
"""
today = datetime.datetime.today()
hdu.header = inhead.copy()
hdu.header.update('ORIGIN', 'rmsynthesis.py', 'Origin of the data set')
hdu.header.update('DATE', str(today), 'Date when the file was created')
hdu.header.update('NAXIS', 3,
'Number of axes in the data array, must be 3')
hdu.header.update('NAXIS3', params.nu.size, 'Length of the Frequency axis')
# In FITS, the first pixel is 1, not 0!!!
hdu.header.update('CRPIX3', 1, 'Reference pixel')
hdu.header.update('CRVAL3', params.nu[0])
hdu.header.update('CDELT3', params.dnu)
hdu.header.add_history('RMSYNTH: Stokes V cube generated by ' +
'rmsynthesis.py version ' +
str(VERSION) + '.')
hdu.header.add_history(' WARNING! The frequency axis is not linear. ' +
'Look in the')
hdu.header.add_history(' accompanying _freqlist.txt file for ' +
'frequency axis information')
# Get the reference pixel for the new image
cpix_ra = (params.ra_lim[1] - params.ra_lim[0]) / 2. + 1.
cpix_dec = (params.dec_lim[1] - params.dec_lim[0]) / 2. + 1.
# Get the index of the new reference pixel in the old image
cpix_ra_old = params.ra_lim[0] + cpix_ra - 1
cpix_dec_old = params.dec_lim[1] - cpix_dec + 1
# Find its sky coordinate
wcs = WCS(inhead)
if inhead['NAXIS'] == 4:
crval_ra = wcs.wcs_pix2sky([[cpix_ra_old, cpix_dec_old, 0, 0]], 0)[0][0]
crval_dec= wcs.wcs_pix2sky([[cpix_ra_old, cpix_dec_old, 0, 0]], 0)[0][1]
if inhead['NAXIS'] == 3:
crval_ra = wcs.wcs_pix2sky([[cpix_ra_old, cpix_dec_old, 0]], 0)[0][0]
crval_dec= wcs.wcs_pix2sky([[cpix_ra_old, cpix_dec_old, 0]], 0)[0][1]
hdu.header.update('NAXIS1', params.ra_lim[1] - params.ra_lim[0])
hdu.header.update('CRVAL1', crval_ra)
hdu.header.update('CRPIX1', cpix_ra)
hdu.header.update('NAXIS2', params.dec_lim[1] - params.dec_lim[0])
hdu.header.update('CRVAL2', crval_dec)
hdu.header.update('CRPIX2', cpix_dec)
try:
hdu.header.__delitem__('NAXIS4')
hdu.header.__delitem__('CTYPE4')
hdu.header.__delitem__('CRVAL4')
hdu.header.__delitem__('CRPIX4')
hdu.header.__delitem__('CDELT4')
hdu.header.__delitem__('CUNIT4')
except: pass
def main(srcMaps=None,
expCube=None,
binnedExpMap=None,
outname=None,
IRFs='CALDB',
index=2):
if srcMaps is None:
srcMaps = env['ccube']
expCube = env['lvtime']
binnedExpMap = env['bexpcube']
outname = env.get('mdlmap',
'modelcube.fits').replace('.fits', '_ps.fits')
IRFs = env.get('irfs', 'CALDB')
obs = BinnedObs(srcMaps=srcMaps,
expCube=expCube,
binnedExpMap=binnedExpMap,
irfs=IRFs)
with pyfits.open(srcMaps) as f:
w = WCS(f[0].header)
cpix = int(f[0].header['NAXIS1']) / 2
RA, DEC, e = w.wcs_pix2sky([[cpix, cpix, 0]], 0)[0]
xmlfile = outname.replace('.fits', '') + '.xml'
with open(xmlfile, 'w') as f:
f.write(content_xml % (index, RA, DEC))
like1 = BinnedAnalysis(obs, xmlfile, optimizer='')
os.remove(xmlfile)
print 'creating Model Map...'
like1.writeModelMap(outname)
print 'Done!'
def generate_header(hdu, inhead, params):
"""
"""
today = datetime.datetime.today()
hdu.header = inhead.copy()
hdu.header.set('ORIGIN', 'rmsynthesis.py', 'Origin of the data set')
hdu.header.set('DATE', str(today), 'Date when the file was created')
hdu.header.set('NAXIS', 3, 'Number of axes in the data array, must be 3')
hdu.header.set('NAXIS3', params.nphi, 'Length of the Faraday depth axis')
hdu.header.set('CTYPE3', 'Phi', 'Axis type')
hdu.header.set('CUNIT3', 'rad/m/m', 'Axis units')
# In FITS, the first pixel is 1, not 0!!!
hdu.header.set('CRPIX3', 1, 'Reference pixel')
hdu.header.set('CRVAL3', params.phi_min, 'Reference value')
hdu.header.set('CDELT3', params.dphi, 'Size of pixel bin')
# Get the reference pixel for the new image
cpix_ra = (params.ra_lim[1] - params.ra_lim[0]) / 2. + 1.
cpix_dec = (params.dec_lim[1] - params.dec_lim[0]) / 2. + 1.
# Get the index of the new reference pixel in the old image
cpix_ra_old = params.ra_lim[0] + cpix_ra - 1
cpix_dec_old = params.dec_lim[1] - cpix_dec + 1
# Find its sky coordinate
wcs = WCS(inhead)
if inhead['NAXIS'] == 4:
crval_ra = wcs.wcs_pix2sky([[cpix_ra_old, cpix_dec_old, 0, 0]],
0)[0][0]
crval_dec = wcs.wcs_pix2sky([[cpix_ra_old, cpix_dec_old, 0, 0]],
0)[0][1]
if inhead['NAXIS'] == 3:
crval_ra = wcs.wcs_pix2sky([[cpix_ra_old, cpix_dec_old, 0]], 0)[0][0]
crval_dec = wcs.wcs_pix2sky([[cpix_ra_old, cpix_dec_old, 0]], 0)[0][1]
hdu.header.set('CRVAL1', crval_ra)
hdu.header.set('CRPIX1', cpix_ra)
hdu.header.set('NAXIS1', params.ra_lim[1] - params.ra_lim[0])
hdu.header.set('CRVAL2', crval_dec)
hdu.header.set('CRPIX2', cpix_dec)
hdu.header.set('NAXIS2', params.dec_lim[1] - params.dec_lim[0])
C2 = 8.98755179e16
nus = numpy.sort(params.nu)
dnu = params.dnu
delta_l2 = C2 * (nus[0]**(-2) - nus[len(nus) - 1]**(-2))
l2min = 0.5 * C2 * ((nus[len(nus) - 1] + dnu)**(-2) +
(nus[len(nus) - 1] - dnu)**(-2))
rmsf = 2. * math.sqrt(3) / delta_l2
maxscale = numpy.pi / l2min
hdu.header.set('TFFWHM', round(rmsf, 2),
'Theoretical FWHM of the RMSF ' + ', rad/m/m')
hdu.header.set('MAXSCL', round(maxscale, 2),
'Maximum scale in ' + 'Faraday depth rad/m/m')
hdu.header.add_history('RMSYNTH: RM Synthesis performed by ' +
'rmsynthesis.py version ' + str(VERSION) + '.')
if params.do_clean:
hdu.header.add_history(' RM Clean performed. niter=' +
str(params.niter) + ', gain=' +
str(params.gain) + ', cutoff=' +
str(params.cutoff))
else:
hdu.header.add_history(' No RM Clean performed.')
hdu.header.add_history(' See the accompanying _rmsf.txt for ' +
'RMSF information.')
try:
hdu.header.__delitem__('NAXIS4')
hdu.header.__delitem__('CTYPE4')
hdu.header.__delitem__('CRVAL4')
hdu.header.__delitem__('CRPIX4')
hdu.header.__delitem__('CDELT4')
hdu.header.__delitem__('CUNIT4')
except:
pass
def generate_header(hdu, inhead, params):
"""
"""
today = datetime.datetime.today()
hdu.header = inhead.copy()
hdu.header.set('ORIGIN', 'rmsynthesis.py', 'Origin of the data set')
hdu.header.set('DATE', str(today), 'Date when the file was created')
hdu.header.set('NAXIS', 3,
'Number of axes in the data array, must be 3')
hdu.header.set('NAXIS3', params.nphi,
'Length of the Faraday depth axis')
hdu.header.set('CTYPE3', 'Phi', 'Axis type')
hdu.header.set('CUNIT3', 'rad/m/m', 'Axis units')
# In FITS, the first pixel is 1, not 0!!!
hdu.header.set('CRPIX3', 1, 'Reference pixel')
hdu.header.set('CRVAL3', params.phi_min, 'Reference value')
hdu.header.set('CDELT3', params.dphi, 'Size of pixel bin')
# Get the reference pixel for the new image
cpix_ra = (params.ra_lim[1] - params.ra_lim[0]) / 2. + 1.
cpix_dec = (params.dec_lim[1] - params.dec_lim[0]) / 2. + 1.
# Get the index of the new reference pixel in the old image
cpix_ra_old = params.ra_lim[0] + cpix_ra - 1
cpix_dec_old = params.dec_lim[1] - cpix_dec + 1
# Find its sky coordinate
wcs = WCS(inhead)
if inhead['NAXIS'] == 4:
crval_ra = wcs.wcs_pix2sky([[cpix_ra_old, cpix_dec_old, 0, 0]], 0)[0][0]
crval_dec= wcs.wcs_pix2sky([[cpix_ra_old, cpix_dec_old, 0, 0]], 0)[0][1]
if inhead['NAXIS'] == 3:
crval_ra = wcs.wcs_pix2sky([[cpix_ra_old, cpix_dec_old, 0]], 0)[0][0]
crval_dec= wcs.wcs_pix2sky([[cpix_ra_old, cpix_dec_old, 0]], 0)[0][1]
hdu.header.set('CRVAL1', crval_ra)
hdu.header.set('CRPIX1', cpix_ra)
hdu.header.set('NAXIS1', params.ra_lim[1] - params.ra_lim[0])
hdu.header.set('CRVAL2', crval_dec)
hdu.header.set('CRPIX2', cpix_dec)
hdu.header.set('NAXIS2', params.dec_lim[1] - params.dec_lim[0])
C2 = 8.98755179e16
nus = numpy.sort(params.nu)
dnu = params.dnu
delta_l2 = C2 * (nus[0] ** (-2) - nus[len(nus) - 1] ** (-2))
l2min = 0.5 * C2 * ((nus[len(nus) - 1] + dnu) ** (-2)
+ (nus[len(nus) - 1] - dnu) ** (-2))
rmsf = 2. * math.sqrt(3) / delta_l2
maxscale = numpy.pi / l2min
hdu.header.set('TFFWHM', round(rmsf,2), 'Theoretical FWHM of the RMSF ' +
', rad/m/m')
hdu.header.set('MAXSCL', round(maxscale, 2), 'Maximum scale in ' +
'Faraday depth rad/m/m')
hdu.header.add_history('RMSYNTH: RM Synthesis performed by ' +
'rmsynthesis.py version ' + str(VERSION) + '.')
if params.do_clean:
hdu.header.add_history(' RM Clean performed. niter=' +
str(params.niter) +
', gain=' + str(params.gain) + ', cutoff=' +
str(params.cutoff))
else:
hdu.header.add_history(' No RM Clean performed.')
hdu.header.add_history(' See the accompanying _rmsf.txt for ' +
'RMSF information.')
try:
hdu.header.__delitem__('NAXIS4')
hdu.header.__delitem__('CTYPE4')
hdu.header.__delitem__('CRVAL4')
hdu.header.__delitem__('CRPIX4')
hdu.header.__delitem__('CDELT4')
hdu.header.__delitem__('CUNIT4')
except: pass
def dg_coords(self, hdr):
pw = WCS(header=hdr)
_x, _y = pw.wcs_pix2sky(self.xlist, self.ylist, 1)
return zip(list(_x), list(_y))
def dg_coords(self,hdr):
pw = WCS(header=hdr)
_x, _y = pw.wcs_pix2sky(self.xlist, self.ylist, 1)
return zip(list(_x), list(_y))
def main(options):
# Some filenames used within the script
maskedImFile = 'maskedFD.FITS'
validPixelFileName = 'validPixelList.txt'
maskedRMErrMap = 'maskedRMErrorMap.FITS'
plotValsFromC = 'plotPoints.txt'
# Remove all temp files from previous execution
print 'INFO: Cleaning up the workspace'
os.system('rm {} {} {} {}'.format(maskedImFile, validPixelFileName, maskedRMErrMap, plotValsFromC))
if options.fdImage == '':
raise Exception('Faraday Depth image was not specified.')
if options.rmError == '':
raise Exception('An RM Error map must be specified.')
if options.threshold == '' or options.polInt == '':
print 'INFO: A valid mask was not specified.'
print 'INFO: All pixels will be included for computing structure function.'
# Read in the Faraday depth image
try:
fdImage = pf.open(options.fdImage)
errImage= pf.open(options.rmError)
except: raise Exception('Unable to read the input image.')
fdArray = np.squeeze(fdImage[0].data)
errArray= np.squeeze(errImage[0].data)
header = fdImage[0].header
fdImage.close()
# Loop over each pixel and get the sky coordinates
wcs = WCS(header)
decSize, raSize = fdArray.shape
tempRA = []; dec = []; RM = []; errRM = []
for j in range(raSize):
for i in range(decSize):
# Do not include blanked pixels. Pywcs reads them as nan
if str(fdArray[i,j]) == 'nan': continue
else:
tempRA.append(wcs.wcs_pix2sky([[j,i,0]], 0)[0][0])
dec.append (wcs.wcs_pix2sky([[j,i,0]], 0)[0][1])
RM.append (fdArray[i,j])
errRM.append (errArray[i,j])
nValidPixels = len(dec)
else:
# Use Pol Int image to select valid pixels
try:
fdImage = pf.open(options.fdImage)
iImage = pf.open(options.polInt)
errImage= pf.open(options.rmError)
except: raise Exception('Unable to read the input images')
fdArray = np.squeeze(fdImage[0].data)
iArray = np.squeeze(iImage[0].data)
errArray= np.squeeze(errImage[0].data)
header = fdImage[0].header
print fdArray.shape
#Initialize a new array which will be updated as per the mask
maskedIm= np.squeeze(fdImage[0].data)
maskerrRM = np.squeeze(errImage[0].data)
print maskedIm.shape
# Check if the input images have the same shape
if fdArray.shape != iArray.shape:
raise Exception('Input images have different shape')
wcs = WCS(header)
decSize, raSize = fdArray.shape
tempRA = []; dec = []; RM = []; errRM = []
nValidPixels = 0
for j in range(raSize):
for i in range(decSize):
if iArray[i,j] < float(options.threshold):
maskedIm[i,j] = np.nan
maskerrRM[i,j] = np.nan
elif str(fdArray[i,j]) == 'nan': continue
else:
tempRA.append(wcs.wcs_pix2sky([[j,i,0]], 0)[0][0])
dec.append (wcs.wcs_pix2sky([[j,i,0]], 0)[0][1])
RM.append (fdArray[i,j])
errRM.append (errArray[i,j])
nValidPixels += 1
print 'INFO: Selected {:} of {:} pixels'.format(nValidPixels, raSize*decSize)
# Write out the masked image to disk
print 'INFO: Writing out the masked to disk'
hdu = pf.PrimaryHDU(data=maskedIm, header=header)
hdu.writeto(maskedImFile)
hdu = pf.PrimaryHDU(data=maskerrRM, header=header)
hdu.writeto(maskedRMErrMap)
# If this data set is from WSRT, add 360 to RA
if options.isWSRT:
ra = [val+360. for val in tempRA]
else:
ra = tempRA
# Write (ra, dec, RM, eRM) to disk
tempFile = open(validPixelFileName, 'w')
for i in range(len(ra)):
tempFile.write('{:.5f} {:.5f} {:.5f} {:.5f}\n'.format(ra[i], dec[i], RM[i], errRM[i]))
tempFile.close()
# Get the resolution of the input images
bmaj = float(header['BMAJ'])*3600.
bmin = float(header['BMIN'])*3600.
print 'INFO: Resolution of the input image: {:.2f} arcsec by {:.2f} arcsec'.format(bmaj, bmin)
# Pass the pixel list and the number of entries to the C code
os.system('./computeStructureFunction {:} {:} {} {} {} {}'.format(\
validPixelFileName, nValidPixels, options.binStart, \
options.nBins, options.binSize, plotValsFromC))
# Read the plot points returned by C
xVal = []; diffVal = []; rmVal = []; eRMVal = []
for line in open(plotValsFromC, "r"):
xVal.append (float(line.split()[0]))
rmVal.append (float(line.split()[1]))
eRMVal.append (float(line.split()[2]))
xVal = np.asarray(xVal)
rmVal = np.asarray(rmVal)
eRMVal = np.asarray(eRMVal)
diffVal= np.absolute(np.subtract(rmVal, eRMVal))
# Plot
plt.plot(xVal, np.log10(diffVal), 'bo', label="My code")
plt.xlabel('Angular distance (deg)')
plt.ylabel('Structure function')
plt.savefig('output.png')
plt.show()
w.wcs.crpix = [(nxpix + 1) / 2., (nypix + 1) / 2.]
w.wcs.cdelt = np.array([-delta, delta])
w.wcs.crval = [ra, dec]
w.wcs.ctype = ['RA---%s' % proj, 'DEC--%s' % proj]
w.wcs.equinox = 2000.0
head = w.to_header()
x = np.array([Npix * (i + 0.5) - 0.5 for i in range(nxpix / Npix)])
y = np.array([Npix * (i + 0.5) - 0.5 for i in range(nypix / Npix)])
XX, YY = np.meshgrid(x, y)
NN = nxpix * nypix / Npix**2
RA, DEC = w.wcs_pix2sky(XX.reshape(NN), YY.reshape(NN), 0)
RA = RA.reshape((nxpix / Npix, nypix / Npix))
DEC = DEC.reshape((nxpix / Npix, nypix / Npix))
lockdir = 'tslock'
filedir = 'tsfile'
if not os.path.isdir(lockdir):
os.mkdir(lockdir)
if not os.path.isdir(filedir):
os.mkdir(filedir)
if env.get('SKIP') is None or env.get('SKIP') == '':
for i in range(nxpix / Npix):
for j in range(nypix / Npix):