def calcParameters(root, configOpts, logger, sigmaSep=3.):
image = configOpts[root + 'Image']
sigma = configOpts[root + 'Sigma']
if configOpts[root + 'Background'] in [None, 'None', 'N', '', '-1', -1.]:
background = calcBackground(image, logger, verbose=configOpts['verbose'])
configOpts[root + 'Background'] = background
else:
background = configOpts[root + 'Background']
lLevel = background * sigma
configOpts[root + 'lLevel'] = lLevel
if configOpts[root + 'hLevel'] in [None, 'None', 'N', '', '-1', -1.]:
hLevel = np.nanmax(pf.getdata(image)) - background
configOpts[root + 'hLevel'] = hLevel
hLevel = configOpts[root + 'hLevel']
if configOpts[root + 'nLevels'] in [None, 'None', 'N', '', '-1', -1.]:
nLevels = np.floor((hLevel - lLevel)/(sigmaSep * background))
configOpts[root + 'nLevels'] = nLevels
configOpts[root + 'Levels'] = np.arange(lLevel, hLevel, sigmaSep * background)
else:
nLevels = configOpts[root + 'nLevels']
configOpts[root + 'Levels'] = np.arange(lLevel, hLevel, (hLevel-lLevel)/nLevels)
return
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
