def get_cl2d(self, axis, prefix='cl2d_1', clfind_args=None):
density = self.get_fits_array('density', axis)
name_root = '%s/%s' % (self.fits_dir, prefix)
outname = "%s_Mask.fits" % name_root
if clfind_args is None:
clfind_args = {'levels': range(1, 12), 'log': True, 'nPixMin': 3}
if len(glob.glob(outname)) == 0:
clfind2d.clfind2d(self.fits_name, name_root, **clfind_args)
return pyfits.open(outname)[0].data
def calcBackground(image, logger, verbose=True):
import tempfile
print
print 'Automatic estimation of the background level'
imageData = pf.open(image)
tmpBackgroundLevel = calcBack(imageData[0].data)
print 'Step 1) Background level = %.4E' % tmpBackgroundLevel
sys.stdout.write('Step 2) Running CLFind to obtain mask ... ')
sys.stdout.flush()
if verbose is True:
print
tmpMask = tempfile.NamedTemporaryFile(dir='./', delete=False)
tmpLevels = np.linspace(10.0 * tmpBackgroundLevel, np.max(imageData[0].data), 20)
clfind2d(image, tmpMask.name, tmpLevels, log=False, nPixMin=20, verbose=verbose)
if verbose is False:
print 'done'
print 'Step 3) Calculating residuals'
dataMask = pf.getdata(tmpMask.name)
mask = np.where(dataMask > 0)
imageData[0].data[mask] = np.nan
backLevel = calcBack(imageData[0].data)
print 'Step 4) Background level of the residuals = %.4E' % backLevel
if os.path.exists(tmpMask.name):
os.remove(tmpMask.name)
del imageData, dataMask
return backLevel
def getRegions(configOpts, logger):
#####################################################################
########################## FUV processing ##########################
fuvImage = configOpts['fuvImage']
logger.write('FUV Image: %s' % fuvImage, newLine=True)
if not os.path.exists(fuvImage):
raiseError('FUV image does not exist.', logger)
if (configOpts['fuvMaskFile'].lower() == 'default') or (configOpts['fuvMaskFile'] is None):
configOpts['fuvMaskFile'] = configOpts['root'] + '_Mask.fits'
doCLFindFUV = True
if os.path.exists(configOpts['fuvMaskFile']):
if configOpts['overwrite'] is True:
doCLFindFUV = True
else:
doCLFindFUV = getYN('\nFound {0}. Rerun CLFind? [y/N] '.format(configOpts['fuvMaskFile']),
returnOpt=False)
if doCLFindFUV is False:
logger.write('FUV mask not created. Using previously generated mask %s.' % configOpts['fuvMaskFile'])
else:
if configOpts['fuvInteractive'] is False:
logger.write('FUV parameters loaded')
else:
logger.write('FUV: Running in interactive mode ... ', newLine=True)
data = pf.getdata(fuvImage)
logger.write('Image statistics', newLine=True, log=True)
logger.write('Max: %9.3e' % np.nanmax(data), log=True)
logger.write('Min: %9.3e' % np.nanmin(data), log=True)
logger.write('Mean: %9.3e' % np.mean(data), log=True)
logger.write('Median: %9.3e' % np.median(data), log=True)
configOpts['fuvBackground'] = calcBackground(fuvImage, logger, verbose=configOpts['verbose'])
logger.write('Background: %.5e' % configOpts['fuvBackground'],
newLine=True)
configOpts['fuvSigma'] = getFloat('Sigma [3]: ', 3)
configOpts['fuvhLevel'] = getFloat('Highest level [-1 for automatic]: ', -1)
configOpts['fuvnLevels'] = getFloat('Number of levels [-1 for automatic]: ', -1)
configOpts['fuvMinPixels'] = getFloat('Minimum number of pixels [20]: ', 20)
calcParameters('fuv', configOpts, logger)
printCLFindOptions('fuv', configOpts, logger)
resultCheck = checkCLFindOptions('fuv', configOpts)
if resultCheck is False:
raiseError('Some of the parameters are incorrect. Please, review the configuration file.',
logger)
clfind2d(fuvImage, configOpts['fuvMaskFile'], configOpts['fuvLevels'],
log=True, nPixMin=configOpts['fuvMinPixels'],
verbose=configOpts['verbose'])
logger.write('CLFind log can be found in %s.log' %
configOpts['fuvMaskFile'], newLine=True, doPrint=False)
#####################################################################
########################## FUV rejection ###########################
if configOpts['checkFUV']:
if (configOpts['fuvMaskFileRej'] is None) or (configOpts['fuvMaskFileRej'].lower() == 'default'):
configOpts['fuvMaskFileRej'] = os.path.splitext(configOpts['fuvImage'])[0] + '_RejMsk.fits'
doRejection = True
if os.path.exists(configOpts['fuvMaskFileRej']) and doCLFindFUV is False:
if configOpts['overwrite'] is False:
doRejection = getYN('\nFound %s. Redo FUV rejection? [y/N] ' %
configOpts['fuvMaskFileRej'], returnOpt=False)
if doRejection is True:
logger.write('FUV rejection', newLine=True)
checkFUV(configOpts, logger)
logger.write('New mask saved as %s' % configOpts['fuvMaskFileRej'],
newLine=True)
else:
logger.write('Not doing FUV rejection. Using image %s' %
configOpts['fuvMaskFileRej'])
#####################################################################
###################### FUV regions catalogue #######################
logger.write('Creating FUV catalogs ... ', newLine=True)
rejMask = configOpts['fuvMaskFileRej']
votRegsFile = os.path.splitext(rejMask)[0] + '.vot'
ds9RegsFile = os.path.splitext(rejMask)[0] + '.reg'
peaksFile = os.path.splitext(rejMask)[0] + '_Peaks.dat'
if False not in map(os.path.exists, [votRegsFile, ds9RegsFile, peaksFile]) and \
configOpts['overwrite'] is False:
logger.write('FUV catalogues already exist.', newLine=True)
if os.path.exists(votRegsFile):
logger.write('VOTable catalogue: %s' % votRegsFile)
logger.write('DS9 catalogue: %s' % ds9RegsFile)
logger.write('Peaks file: %s' % peaksFile)
else:
createCatalog(fuvImage, rejMask, votRegsFile, ds9RegsFile, logger,
peaksFile=peaksFile, ellipse=False, plot=configOpts['plotDS9'])
return
#####################################################################
########################## HI processing ###########################
# if configOpts['hiInteractive'] == False:
# areCLParamsOK = checkCLFindOptions('hi')
# if areCLParamsOK == False:
# fancyPrint('Some HI parameters in config file are wrong\n',
# newLine=True, log=True)
# sys.exit()
# fancyPrint('HI parameters loaded', newLine=True, log=True)
# else:
# fancyPrint('HI: Running in interactive mode ... ', newLine=True, log=True)
# data = pf.getdata(configOpts['hiImage'])
# fancyPrint('Image statistics', newLine=True, log=True)
# fancyPrint('Max: %9.3e' % np.nanmax(data), log=True)
# fancyPrint('Min: %9.3e' % np.nanmin(data), log=True)
# fancyPrint('Mean: %9.3e' % np.mean(data), log=True)
# fancyPrint('Median: %9.3e' % np.median(data), log=True)
# configOpts['hiBackground'] = \
# calcBackground(configOpts['hiImage'], fancyPrint)
# fancyPrint('Background: %.5e' % configOpts['hiBackground'],
# newLine=True, log=False)
# fancyPrint('')
# configOpts['hiSigma'] = getFloat('Sigma [3]: ', 3)
# configOpts['hihLevel'] = getFloat('Highest level [-1 for automatic]: ', -1)
# configOpts['hinLevels'] = getFloat('Number of levels [-1 for automatic]: ', -1)
# configOpts['hiMinPixels'] = getFloat('Minimum number of pixels [20]: ', 20)
# fancyPrint('')
# hiLevels = calcParameters('hi')
# if (configOpts['hiMaskFile'].lower() == 'default') or (configOpts['hiMaskFile'] == None):
# configOpts['hiMaskFile'] = os.path.splitext(configOpts['hiImage'])[0] + '_Msk.fits'
# doIDL = True
# if os.path.exists(configOpts['hiMaskFile']):
# doIDL = getYN('\nFound {0}. Rerun CLFind? [y/N] '.format(configOpts['hiMaskFile']),
# returnOpt=False)
# if doIDL:
# status, maskFile, idlLogFile = clfind2dIDL(configOpts['hiImage'], hiLevels,
# log=configOpts['log'], nPixMin=configOpts['hiMinPixels'],
# verbose=configOpts['verbose'])
# if not status:
# fancyPrint('Problem found running IDL', newLine=True, log=True)
# fancyPrint('Kill IDL, check {0} and try again\n'.format(idlLogFile), log=True)
# sys.exit()
# sh.move(maskFile, configOpts['hiMaskFile'])
# logData = open(idlLogFile, 'r').read().splitlines()
# sh.move(idlLogFile, 'clfind2dHI.log')
# else:
# logData = open('clfind2dHI.log', 'r').read().splitlines()
# for line in logData:
# fancyPrint(line, log=True, noPrint=True)
# if 'clumps found (' in line:
# m = re.match(r'(\d+)(.+)(\(+)(\d+)', line.replace(' ',''))
# nClumpsHI = int(m.groups(0)[0])
# nClumpsRejHI = nClumps = int(m.groups(0)[-1])
# fancyPrint('HI mask file: {0}'.format(configOpts['hiMaskFile']), newLine=True, log=True)
# fancyPrint('Number of clumps: {0}'.format(nClumpsHI), log=True)
# fancyPrint('Number of clumps rejected: {0}'.format(nClumpsRejHI), log=True)
# # #####################################################################
# # ########################## HI rejection ###########################
# #
# # if configOpts['checkHI']:
# # if (configOpts['fuvMaskFileRej'] == None) or (configOpts['fuvMaskFileRej'].lower() == 'default'):
# # configOpts['fuvMaskFileRej'] = os.path.splitext(configOpts['fuvImage'])[0] + '_RejMsk.fits'
# #
# # doRejection = True
# # if os.path.exists(configOpts['fuvMaskFileRej']) and doIDL == False:
# # doRejection = getYN('\nFound {0}. Redo FUV rejection? [y/N] '.format(configOpts['fuvMaskFileRej']),
# # returnOpt=False)
# #
# # if doRejection == True:
# # try:
# # checkFUV(configOpts, fancyPrint)
# # except Exception as detail:
# # raise detail
# # else:
# # fancyPrint('Not doing FUV rejection. Using image {0}'.format(configOpts['fuvMaskFileRej']),
# # log=True, noPrint=True, newLine=True)
# #
# #
# # #####################################################################
# fancyPrint('')
return configOpts
if 0:
field = 'Density'
fits_name = 'p14b_atest.fits'
hdu = pyfits.PrimaryHDU(frb[field])
hdulist = pyfits.HDUList([hdu])
hdulist.writeto(fits_name)
clump_fname = 'p14_atest1_Mask.fits'
if 0:
import clfind2d
import pyfits
if os.path.exists(clump_fname):
os.remove(clump_fname)
clfind_args = {'levels': [3], 'log': True, 'nPixMin': 3}
clfind2d.clfind2d(fits_name, 'p14_atest1', **clfind_args)
if 0:
#twod_clump = np.transpose(pyfits.open(clump_fname)[0].data)
twod_clump = pyfits.open(clump_fname)[0].data
flat_clump = twod_clump.flatten()
clump_axis = 0
plt.clf()
plt.imshow(twod_clump)
plt.savefig('p14_atest_clump.png')
if 0:
clump_axis = 0
twod_clump = np.transpose(pyfits.open(clump_fname)[0].data)
flat_clump = twod_clump.flatten()
clump_stuff_tuple = (flat_clump, 'xyz'[clump_axis], twod_clump)
