galpak3d_utils.py		galpak3d_utils.py
	import os		import os
	import configparser		import configparser
	from .spread_functions import *
	from .model_sersic3d import ModelSersic		from .model_sersic3d import ModelSersic
	from .instruments import *		DiskModel = DefaultModel = ModelSersic
	import logging		import logging
	logging.basicConfig(level=logging.INFO)		logging.basicConfig(level=logging.INFO)
	logger = logging.getLogger('GalPaK: Utils')		logger = logging.getLogger('GalPaK: Utils')
			#Python3 compatibility
			try:
			basestring
			except NameError:
			basestring = str
	def _save_to_file(filename, contents, clobber):		def _save_to_file(filename, contents, clobber):
	if not clobber and os.path.isfile(filename):		if not clobber and os.path.isfile(filename):
	raise IOError("The file {} already exists. Specify overwrite=True t o overwrite it.".format(filename))		raise IOError("The file {} already exists. Specify overwrite=True t o overwrite it.".format(filename))
	with open(filename, 'w') as f:		with open(filename, 'w') as f:
	f.write(contents)		f.write(contents)
	def _read_file(filename):		#def _read_file(filename):
	with open(filename, 'r') as f:		# with open(filename, 'r') as f:
	contents = f.read()		# contents = f.read()
	return contents		# return contents
	def _read_psf(file_config=None):
	"""
	set PSF from config file
	"""
	psf = None
	if file_config is not None:
	if os.path.isfile(file_config):
	config = configparser.RawConfigParser()
	config.read(file_config)
	else:
	raise ValueError("PSF Config file %s not present! " % (file_con
	fig))
	else:
	raise ValueError("PSF Config file not defined")
	config = config['PSF']
	psf_keys={}
	for k in ['type', 'r0', 'C', 'amp', 'fwhm', 'alpha', 'beta', 'ba', 'pa'
	, 'wvl_um', 'mode']:
	if k in config.keys():
	psf_keys[k] = k
	elif 'psf_'+k in config.keys():
	psf_keys[k] = 'psf_'+k
	if 'type' in psf_keys:
	psf_type = config[psf_keys['type']].lower()
	logger.info("CONFIG: PSF: type {%s} found " % (psf_type))
	else:
	logger.error("CONFIG: PSF: type not specified")
	if psf_type == 'moffat':
	psf = MoffatPointSpreadFunction
	elif psf_type == 'gaussian':
	psf = GaussianPointSpreadFunction
	elif psf_type == 'custom':
	psf = ImagePointSpreadFunction
	elif psf_type == 'maoppy':
	psf = MAOPPYPointSpreadFunction
	else:
	#@fixme add other options
	raise NotImplementedError("Currently only PSF type = `moffat` and `
	gaussian` supported")
	args = {}
	import inspect
	var_args = inspect.getargspec(psf).args
	for k in var_args[1:]:
	if k in list(config.keys()):
	try:
	args[k] = eval(config[k].split()[0])
	except:
	args[k] = config[k]
	return psf(**args)
	def _read_lsf(file_config=None):
	"""
	sets LSF from config LSF: lsf_fwhm
	:return:
	"""
	lsf = None
	if file_config is not None:
	if os.path.isfile(file_config):
	config =configparser.RawConfigParser()
	config.read(file_config)
	else:
	raise ValueError("LSF Config file %s not present! " % (file_con
	fig))
	else:
	raise ValueError("LSF Config file not defined")
	config = config['LSF']
	lsf_keys={}
	for k in ['type', 'fwhm']:
	if k in list(config.keys()):
	lsf_keys[k] = k
	elif 'lsf_'+k in config.keys():
	lsf_keys[k] = 'lsf_'+k
	if 'type' in lsf_keys:
	lsf_type = config[lsf_keys['type']].lower()
	else:
	lsf_type = None
	logger.warning("CONFIG: LSF: type not specified")
	if lsf_type == 'gaussian':
	lsf = GaussianLineSpreadFunction(
	fwhm=float(config[lsf_keys['fwhm']].split()[0])
	) # lsf_fwhm,
	elif lsf_type is None:
	lsf = None
	else:
	#@fixme
	raise NotImplementedError
	return lsf
	def _read_instrument(file_config):
	if file_config is not None:
	if os.path.isfile(file_config):
	config = configparser.RawConfigParser()
	config.read(file_config)
	else:
	raise ValueError("Instrument Config file %s not present! " % (f
	ile_config))
	else:
	raise ValueError("Instrument Config not defined")
	psf = _read_psf(file_config)
	try:
	lsf = _read_lsf(file_config)
	except:
	lsf = None
	logger.warning("CONFIG: LSF not found in config file")
	if 'INSTRUMENT' in config.sections():
	config = config['INSTRUMENT']
	myinstr = config['type'].lower()
	logger.info("CONFIG: INSTRUMENT: type {%s} found " % (myinstr))
	if 'pixscale' in list(config.keys()):
	scale = float(config['pixscale'].split()[0]) #
	else:
	scale = None
	if 'muse' == myinstr:
	instrument = MUSE(psf=psf, lsf=lsf)
	elif 'musewfm' == myinstr:
	instrument = MUSEWFM(psf=psf, lsf=lsf)
	elif 'musenfm' == myinstr:
	instrument = MUSENFM(psf=psf, lsf=lsf)
	elif 'alma' in myinstr:
	instrument = ALMA(psf=psf, lsf=lsf, pixscale=scale)
	elif 'sinfok250' in myinstr:
	instrument = SINFOK250(psf=psf, lsf=lsf)
	elif 'sinfok100' in myinstr:
	instrument = SINFOK100(psf=psf, lsf=lsf)
	elif 'sinfoj250' in myinstr:
	instrument = SINFOJ250(psf=psf, lsf=lsf)
	elif 'sinfoj100' in myinstr:
	instrument = SINFOJ100(psf=psf, lsf=lsf)
	elif 'harmoni' in myinstr:
	instrument = HARMONI(psf=psf, lsf=lsf, pixscale=scale)
	elif 'kmos' in myinstr:
	instrument = KMOS(psf=psf, lsf=lsf)
	elif 'osiris' in myinstr:
	instrument = OSIRIS(psf=psf, lsf=lsf)
	elif 'generic' in myinstr:
	instrument = Generic(psf=psf, lsf=lsf, default_spaxel_size=scal
	e)
	else:
	# @fixme:generalize
	raise NotImplementedError
	else:
	#default
	logger.info("CONFIG: INSTRUMENT not present. Will use MUSE as defau
	lt")
	instrument = MUSE(psf=psf, lsf=lsf)
	return instrument
	def _read_model(file_config):		def _read_model(file_config):
	"""		"""
	sets model from config MODEL		sets model from config MODEL
	:return:		:return:
	"""		"""
	model = None		model = None
	if file_config is not None:		if file_config is not None:
	if os.path.isfile(file_config):		if os.path.isfile(file_config):
	logger.info("Reading model {:s}".format(file_config))		logger.info("Reading model {:s}".format(file_config))
	config = configparser.RawConfigParser()		config = configparser.RawConfigParser()
	config.read(file_config)		config.read(file_config)
	else:		else:
	raise ValueError("Model Config file %s not present" % (file_con fig))		raise ValueError("Model Config file %s not present" % (file_con fig))
	else:		else:
	raise ValueErrror("Model Config file not defined")		raise ValueError("Model Config file not defined")
	if config.has_section('MODEL'):		if config.has_section('MODEL'):
	config = config['MODEL']		config = config['MODEL']
	else:		else:
	logger.warning("CONFIG file has no MODEL section")		logger.warning("CONFIG file has no MODEL section")
	if 'type' in list(config.keys()):		if 'type' in list(config.keys()):
	model_type = config['type'].lower()		model_type = config['type'].lower()
	else:		else:
	logger.error("CONFIG: Model: type not specified")		logger.error("CONFIG: Model: type not specified")
	skipping to change at line 215		skipping to change at line 65
	args={}		args={}
	#try:		#try:
	# redshift = float(config['redshift'])		# redshift = float(config['redshift'])
	#except:		#except:
	# redshift = None		# redshift = None
	#args['redshift']=redshift		#args['redshift']=redshift
	if 'default' in model_type:		if 'default' in model_type:
	model = DefaultModel		model = DefaultModel
	elif 'sersic2d' in model_type:
	model = ModelSersic2D
	elif 'sersic' in model_type:		elif 'sersic' in model_type:
	model = ModelSersic		model = ModelSersic
	if 'rotation_curve' in config.keys():		if 'rotation_curve' in config.keys():
	args['rotation_curve']=config['rotation_curve']		args['rotation_curve']=config['rotation_curve']
	elif 'decomp' in model_type:		elif 'disk' in model_type:
	model = ModelDecomp		model = DiskModel
	else:		else:
	raise ValueError("Model type invalid. Must be ModelSersic2D or Mode lSersic or ModelDecomp")		raise ValueError("Model type invalid. Must be DefaultModel or Model Sersic or DiskModel")
	#args parameters		#args parameters
	import inspect		import inspect
	var_args = inspect.getargspec(model).args		var_args = inspect.getfullargspec(model).args
	for k in var_args[1:]:		for k in var_args[1:]:
	if k.lower() in list(config.keys()):		if k.lower() in list(config.keys()):
	try:		try:
	args[k]=eval(config[k])		args[k]=eval(config[k])
	except:		except:
	args[k]=config[k]		args[k]=config[k]
	return model(**args)		return model(**args)
End of changes. 9 change blocks.
	175 lines changed or deleted		16 lines changed or added
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