def checkOptions(self):
"""
Makes sure that all the necessary options are present. If a non-essential option is
not present, used the default value. Raises warnings or error depending on the missing
value.
"""
_exitAtTheEnd = False
_errorOpts = ConfigParser.SafeConfigParser()
_errorOpts.optionxform = str
_errorOpts.read(self.mandatoryOptions)
_error = _errorOpts.get('Error', 'errorOpts').replace(' ', '').split(',')
_warning = _errorOpts.get('Warning', 'warningOpts').replace(' ', '').split(',')
if 'dusttype' not in self.options:
self.OptionsError('dusttype not defined', exit=False)
_exitAtTheEnd = True
else:
_error.append(_errorOpts.get('Dust',
self.options['dusttype']).replace(' ', '').split(','))
_fields = self.defaultOpts.keys()
for _field in sorted(_fields, key=str.lower):
if _field not in self.options.keys() and self.defaultOpts[_field] is not None \
and self.verbose is True:
self.options[_field] = self.defaultOpts[_field]
warnings.warn(cm.Fore.YELLOW + '[WARNING]: ' + cm.Style.RESET_ALL +
'Option %s not present. Using default value \'%s\'.' % (_field,
str(self.defaultOpts[_field])))
if self.options[_field] is None and _field in _error:
self.OptionsError('Option %s is mandatory' % _field, exit=False)
_exitAtTheEnd = True
elif self.options[_field] is None and _field in _warning and self.verbose is True:
# warnings.warn(cm.Fore.YELLOW + '[WARNING]: ' + cm.Style.RESET_ALL +
raiseWarning('Option %s is not defined. ' % _field +
'This won\'t stop the pipeline but may or may not be a problem.')
if _exitAtTheEnd is True:
self.OptionsError('Some mandatory parameters are missing. Exitting now.')
return
def createCatalog(image, mask, voTableCat, ds9RegsFile, logger,
peaksFile=None, ellipse=False, ellMode='linear', plot=False):
if voModule is False:
logger.write(cm.Fore.RED + 'No VO module found. A FITS table will be generated instead.' +
cm.Style.RESET_ALL, newLine=True)
# Reads the header, data and loads the astrometric solution
hduImage = pf.open(image)
hduMask = pf.open(mask)
try:
wcsMask = pw.WCS(hduMask[0].header)
except:
wcsMask = None
logger.write(cm.Fore.YELLOW + 'No WCS information. The VOTable file will not include those fields.' +
cm.Style.RESET_ALL)
logger.write('Gathering mask data ... ', newLine=True)
regions = RegionSet(hduMask[0].data, image=hduImage[0].data)
logger.write('Preparing data ... ')
centroids = np.array([regions.Regions[idReg].getCentroid()[0] for idReg in regions.idRegions])
radii = [regions.Regions[idReg].getCentroid()[1] for idReg in regions.idRegions]
sizes = [regions.Regions[idReg].where[0].size for idReg in regions.idRegions]
peaks = [regions.Regions[idReg].peak for idReg in regions.idRegions]
peaksPix = np.array([regions.Regions[idReg].peakWhere for idReg in regions.idRegions]) + 1
fluxes = [regions.Regions[idReg].getFlux() for idReg in regions.idRegions]
if wcsMask is not None:
skyCoordsCentroids = wcsMask.wcs_pix2sky(np.fliplr(centroids), 0)
skyCoordsPeak = wcsMask.wcs_pix2sky(np.fliplr(peaksPix), 0)
try:
scale = np.abs(hduImage[0].header['CD1_1']) * 3600.
except:
try:
scale = np.abs(hduImage[0].header['CDELT1']) * 3600.
except:
wcsMask = None
logger.write(cm.Fore.YELLOW + 'No WCS information. The VOTable file will ' +
'not include those fields.' + cm.Style.RESET_ALL)
radiiSky = radii * scale
# Calculates an ellipse fit for the pixels in the region
if ellipse:
logger.write('Fitting ellipse parameters ... ')
def getEllParams(data, id):
try:
return list(fitellipse(data, ellMode)) + [0]
except RuntimeError:
return [regions.Regions[id].getCentroid()[0][0], regions.Regions[id].getCentroid()[0][1],
regions.Regions[idReg].getCentroid()[1], regions.Regions[idReg].getCentroid()[1],
0.0, 1]
ellipseFit = np.array([getEllParams(regions.Regions[idReg].pixels, idReg) for idReg in regions.idRegions])
ellipseCentroidWCS = np.array(wcsMask.wcs_pix2sky(ellipseFit[:, [1, 0]], 0))
ellipseAxisWCS = np.array(ellipseFit[:, [2, 3]] * scale)
ellipseAngle = np.array(-ellipseFit[:, 4] * 180. / np.pi + 90.)
if voModule is True:
# Creates a VOTable with the data
logger.write('Creating VOTable ... ')
if os.path.exists(voTableCat):
os.remove(voTableCat)
# from vo.tree import VOTableFile, Resource, Table, Field
votable = VOTableFile()
resource = Resource()
votable.resources.append(resource)
table = Table(votable)
resource.tables.append(table)
# Define fields
fieldsVO = [Field(votable, name='ID', datatype='int'),
Field(votable, name='X_CENTROID', datatype='float', unit='pix'),
Field(votable, name='Y_CENTROID', datatype='float', unit='pix'),
Field(votable, name='RADIUS_PIX', datatype='float', unit='pix'),
Field(votable, name='SIZE', datatype='float', unit='pix')]
if wcsMask is not None:
fieldsVO += [Field(votable, name='RA_CENTROID', datatype='double', unit='deg'),
Field(votable, name='DEC_CENTROID', datatype='double', unit='deg'),
Field(votable, name='RADIUS_SKY', datatype='float', unit='arcsec')]
fieldsVO += [Field(votable, name='PEAK', datatype='float', unit='CPS'),
Field(votable, name='X_PEAK', datatype='float', unit='pix'),
Field(votable, name='Y_PEAK', datatype='float', unit='pix')]
if wcsMask is not None:
fieldsVO += [Field(votable, name='RA_PEAK', datatype='double', unit='deg'),
Field(votable, name='DEC_PEAK', datatype='double', unit='deg')]
fieldsVO += [Field(votable, name='FLUX', datatype='float', unit='CPS')]
if ellipse is True:
fieldsVO += [Field(votable, name='X_ELLIPSE', datatype='float', unit='pix'),
Field(votable, name='Y_ELLIPSE', datatype='float', unit='pix'),
Field(votable, name='SEMIAX1_PIX', datatype='float', unit='pix'),
Field(votable, name='SEMIAX2_PIX', datatype='float', unit='pix'),
Field(votable, name='ELL_ANGLE', datatype='float', unit='deg'),
Field(votable, name='ELL_ERROR', datatype='double')]
if wcsMask is not None:
fieldsVO += [Field(votable, name='RA_ELLIPSE', datatype='double', unit='deg'),
Field(votable, name='DEC_ELLIPSE', datatype='double', unit='deg'),
Field(votable, name='SEMIAX1_SKY', datatype='float', unit='arcsec'),
Field(votable, name='SEMIAX2_SKY', datatype='float', unit='arcsec')]
table.fields.extend(fieldsVO)
table.create_arrays(len(regions.idRegions))
for nReg in range(len(regions.idRegions)):
row = [regions.idRegions[nReg],
centroids[nReg, 1]+1, centroids[nReg, 0]+1, radii[nReg], sizes[nReg]]
if wcsMask is not None:
row += [skyCoordsCentroids[nReg, 0], skyCoordsCentroids[nReg, 1], radiiSky[nReg]]
row += [peaks[nReg], peaksPix[nReg, 1]+1, peaksPix[nReg, 0]+1]
if wcsMask is not None:
row += [skyCoordsPeak[nReg, 0], skyCoordsPeak[nReg, 1]]
row.append(fluxes[nReg])
if ellipse is True:
row += [ellipseFit[nReg, 1]+1, ellipseFit[nReg, 0]+1, ellipseFit[nReg, 2], ellipseFit[nReg, 3],
ellipseAngle[nReg], ellipseFit[nReg, 4]]
if wcsMask is not None:
row += [ellipseCentroidWCS[nReg, 0], ellipseCentroidWCS[nReg, 1], ellipseAxisWCS[nReg, 0],
ellipseAxisWCS[nReg, 1]]
table.array[nReg] = tuple(row)
votable.to_xml(voTableCat)
logger.write('VOTable catalogue: %s' % voTableCat)
else:
# If the vo module is not available, uses PyFits to create a Fits table
logger.write('Creating FITS table ... ', newLine=True)
fields = [pf.Column(name='ID', format='J', array=regions.idRegions),
pf.Column(name='X_CENTROID', format='E', unit='pix', array=centroids[:, 1]+1),
pf.Column(name='Y_CENTROID', format='E', unit='pix', array=centroids[:, 0]+1),
pf.Column(name='RADIUS_PIX', format='E', unit='pix', array=radii),
pf.Column(name='SIZE', format='E', unit='pix', array=sizes)]
if wcsMask is not None:
fields += [pf.Column(name='RA_CENTROID', format='D', unit='deg',
array=skyCoordsCentroids[:, 0]),
pf.Column(name='DEC_CENTROID', format='D', unit='deg',
array=skyCoordsCentroids[:, 1]),
pf.Column(name='RADIUS_SKY', format='D', unit='arcsec',
array=radiiSky)]
fields += [pf.Column(name='PEAK', format='E', unit='CPS', array=peaks),
pf.Column(name='X_PEAK', format='E', unit='pix', array=peaksPix[:, 1]+1),
pf.Column(name='Y_PEAK', format='E', unit='pix', array=peaksPix[:, 0]+1)]
if wcsMask is not None:
fields += [pf.Column(name='RA_PEAK', format='D', unit='deg',
array=skyCoordsPeak[:, 0]),
pf.Column(name='DEC_PEAK', format='D', unit='deg',
array=skyCoordsPeak[:, 1])]
fields += [pf.Column(name='FLUX', format='E', unit='CPS', array=fluxes)]
if ellipse is True:
fields += [pf.Column(name='X_ELLIPSE', format='E', unit='pix',
array=ellipseFit[:, 1]+1),
pf.Column(name='Y_ELLIPSE', format='E', unit='pix',
array=ellipseFit[:, 0]+1),
pf.Column(name='SEMIAX1_PIX', format='E', unit='pix',
array=ellipseFit[:, 2]),
pf.Column(name='SEMIAX2_PIX', format='E', unit='pix',
array=ellipseFit[:, 3]),
pf.Column(name='ELL_ANGLE', format='E', unit='deg',
array=ellipseAngle),
pf.Column(name='ELL_ERROR', format='L', array=ellipseFit[:, 4])]
if wcsMask is not None:
fields += [pf.Column(name='RA_ELLIPSE', format='D', unit='deg',
array=ellipseCentroidWCS[:, 0]),
pf.Column(name='DEC_ELLIPSE', format='D', unit='deg',
array=ellipseCentroidWCS[:, 1]),
pf.Column(name='SEMIAX1_SKY', format='E', unit='arcsec',
array=ellipseAxisWCS[:, 0]),
pf.Column(name='SEMIAX2_SKY', format='E', unit='arcsec',
array=ellipseAxisWCS[:, 1])]
tbhdu = pf.new_table(fields)
hdu = pf.PrimaryHDU()
thdulist = pf.HDUList([hdu, tbhdu])
fitsTableCat = os.path.splitext(voTableCat)[0] + '_Cat.fits'
if os.path.exists(fitsTableCat): os.remove(fitsTableCat)
thdulist.writeto(fitsTableCat)
logger.write('FITS catalogue: %s' % fitsTableCat)
# Creates the DS9 regions file using the centroid and radius information for each region.
logger.write('Creating DS9 regions files ... ', newLine=True)
# For testing purposes we write a file in X, Y.
ds9XYFile = os.path.splitext(ds9RegsFile)[0] + '_XY.reg'
unitRegCentroid = open(ds9XYFile, 'w')
print >>unitRegCentroid, 'global color = green'
ii = 0
for yy, xx in centroids:
regID = regions.idRegions[ii]
rad = radii[ii]
if rad > 0.0:
print >>unitRegCentroid, 'image; circle ' + str(xx+1) + ' ' + str(yy+1) + ' ' + \
str(rad) + '# text = {%d}' % regID
# print >>unitRegCentroid, 'image; x point ' + str(xx+1) + ' ' + str(yy+1) + ' # color=green'
ii += 1
unitRegCentroid.close()
# Write RA, Dec instead:
if wcsMask is not None:
ds9WCSFile = os.path.splitext(ds9RegsFile)[0] + '_WCS.reg'
unitRegCentroid = open(ds9WCSFile, 'w')
print >>unitRegCentroid, 'global color = blue'
print >>unitRegCentroid, 'fk5'
ii = 0
for ra, dec in skyCoordsCentroids:
regID = regions.idRegions[ii]
rad = radii[ii]
if rad > 0.0:
print >> unitRegCentroid, 'circle(' + str(ra) + ',' + str(dec) + ',' + str(rad) + '")' + \
' # text = {%d}' % regID
ii += 1
unitRegCentroid.close()
if ellipse:
ds9EllFile = os.path.splitext(ds9RegsFile)[0] + '_Ell.reg'
unitRegEllipse = open(ds9EllFile, 'w')
print >>unitRegEllipse, 'global color = red'
for ii in range(regions.nRegs):
regID = regions.idRegions[ii]
print >>unitRegEllipse, 'image; ellipse ' + str(ellipseFit[ii, 1]+1) + ' ' + \
str(ellipseFit[ii, 0]+1) + ' ' + str(ellipseFit[ii, 2]) + ' ' + str(ellipseFit[ii, 3]) + \
' ' + str(ellipseAngle[ii]) + '# text = {%d}' % regID
# print >>unitRegEllipse, 'image; x point ' + str(xx+1) + ' ' + str(yy+1) + ' # color=green'
ii += 1
unitRegEllipse.close()
# Writes a file with the peak positions
if peaksFile is not None:
if wcsMask is None:
raiseError('No WCS information. Cannot continue.')
def dec2dms(dd):
sign = -1. if dd < 0 else 1. # Remember to deal with negative DEC
mnt, sec = divmod(abs(dd) * 3600, 60)
deg, mnt = divmod(mnt, 60)
return deg * sign, mnt, sec
logger.write('Saving peak positions ... ', newLine=True)
peaksUnit = open(peaksFile, 'w')
print >>peaksUnit, '# PDRID, XPIXEL, YPIXEL, RA, DEC'
nn = 0
for yy, xx in peaksPix:
ra = skyCoordsPeak[nn, 0]
dec = skyCoordsPeak[nn, 1]
raHH, raMM, raSS = dec2dms(ra/15.)
decDD, decMM, decSS = dec2dms(dec)
row = '%d, %.2f, %.2f, %02d %02d %05.2f, %+02d %02d %05.2f' % \
(nn, xx, yy, raHH, raMM, raSS, decDD, decMM, decSS)
print >>peaksUnit, row
nn += 1
peaksUnit.close()
if plot:
logger.write('Plotting regions ... ', newLine=True)
try:
from plotDS9 import plotDS9
import ds9
except:
raiseWarning('No pyDS9 module find. Skipping plot.')
return
d = ds9.ds9()
d.set('frame delete all')
plotDS9(image, frame=1)
d.set('scale mode minmax')
d.set('regions load ' + os.path.realpath(ds9XYFile))
plotDS9(mask, frame=2)
d.set('scale log')
d.set('scale mode minmax')
d.set('regions load ' + os.path.realpath(ds9XYFile))
if ellipse:
plotDS9(image, frame=3)
d.set('scale mode minmax')
d.set('regions load ' + os.path.realpath(ds9EllFile))
plotDS9(mask, frame=4)
d.set('scale log')
d.set('scale mode minmax')
d.set('regions load ' + os.path.realpath(ds9EllFile))
return