instruments.py		instruments.py
	# -*- coding: utf-8 -*-		# -*- coding: utf-8 -*-
	import logging		import logging, os
			import configparser
	logging.basicConfig(level=logging.INFO)		logging.basicConfig(level=logging.INFO)
	logger = logging.getLogger('GalPaK: Instrument: ')		import numpy as np
	from .spread_functions import *		from .spread_functions import PointSpreadFunction, LineSpreadFunction, Gaus sianLineSpreadFunction, GaussianPointSpreadFunction, MoffatPointSpreadFunct ion
	from . import convolution		from . import convolution
			#Python3 compatibility
			try:
			basestring
			except NameError:
			basestring = str
			logger = logging.getLogger('GalPaK: Instrument ')
			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.getfullargspec(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
	class Instrument(object):		class Instrument(object):
	"""		"""
	This is a generic instrument class to use or extend.		This is a generic instrument class to use or extend.
	psf: None|PointSpreadFunction		psf: None|PointSpreadFunction
	The 2D Point Spread Function instance to use in the convolution, or None (the default).		The 2D Point Spread Function instance to use in the convolution, or None (the default).
	When this parameter is None, the instrument's PSF will not be appli ed to the cube.		When this parameter is None, the instrument's PSF will not be appli ed to the cube.
	lsf: None|LineSpreadFunction		lsf: None|LineSpreadFunction
	The 1D Line Spread Function instance to use in the convolution, or None (the default).		The 1D Line Spread Function instance to use in the convolution, or None (the default).
	Will be used in the convolution to spread the PSF 2D image through a third axis, z.		Will be used in the convolution to spread the PSF 2D image through a third axis, z.
	skipping to change at line 55		skipping to change at line 219
	if (self.xy_step is None) and (self.cube_default_xy_step is not Non e):		if (self.xy_step is None) and (self.cube_default_xy_step is not Non e):
	self.xy_step = self.cube_default_xy_step		self.xy_step = self.cube_default_xy_step
	if (self.z_step is not None) and (self.z_central is not None):		if (self.z_step is not None) and (self.z_central is not None):
	self.z_step_kms = 3e5 * self.z_step / self.z_central		self.z_step_kms = 3e5 * self.z_step / self.z_central
	else:		else:
	self.z_step_kms = None		self.z_step_kms = None
	if psf:		if psf:
	if not isinstance(psf, PointSpreadFunction):		if isinstance(psf, basestring):
	raise ValueError("PSF should be an instance of galpak.Point		psf = _read_psf(psf)
	SpreadFunction")		elif not isinstance(psf, PointSpreadFunction):
			raise ValueError("PSF should be an instance of galpak.Point
			SpreadFunction or a string")
	self.psf = psf		self.psf = psf
	if lsf:		if lsf:
	if not isinstance(lsf, LineSpreadFunction):		if not isinstance(lsf, LineSpreadFunction):
	raise ValueError("LSF should be an instance of galpak.LineS preadFunction")		raise ValueError("LSF should be an instance of galpak.LineS preadFunction")
	self.lsf = lsf		self.lsf = lsf
	self.lsf.z_cunit = self.z_cunit		self.lsf.z_cunit = self.z_cunit
	def use_pixelsize_from_cube(self, cube):		def use_pixelsize_from_cube(self, cube):
	"""		"""
End of changes. 5 change blocks.
	6 lines changed or deleted		179 lines changed or added
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