model_class.py		model_class.py
	# -*- coding: utf-8 -*-		# -*- coding: utf-8 -*-
	import numpy as np		import numpy as np
	from scipy.interpolate import interp1d		from scipy.interpolate import interp1d
	from scipy import ndimage		from scipy import ndimage
	from copy import deepcopy		from copy import deepcopy
	from distutils.version import LooseVersion, StrictVersion		try:
			from distutils.version import LooseVersion as Version
			except ImportError:
			# python3.13
			from packaging.version import Version
	try:		try:
	import bottleneck as bn		import bottleneck as bn
	except ImportError:		except ImportError:
	import numpy as bn		import numpy as bn
	from .hyperspectral_cube import HyperspectralCube as HyperCube		from .hyperspectral_cube import HyperspectralCube as HyperCube
	from .galaxy_parameters import GalaxyParameters		from .galaxy_parameters import GalaxyParameters
	# CONSTANTS		# CONSTANTS
	G = 6.67384e-11 # Gravitational Constant (m^3.kg^-1.s^-2)		G = 6.67384e-11 # Gravitational Constant (m^3.kg^-1.s^-2)
	SOL_MASS = 1.98e30 # Solar Mass (kg)		SOL_MASS = 1.9884e30 # Solar Mass (kg)
	PARSEC = 3e16 # Parsec (m)		PARSEC = 3.08567e16 # Parsec (m)
	# LOGGING CONFIGURATION		# LOGGING CONFIGURATION
	import logging		import logging
	logging.basicConfig(level=logging.INFO)
	logger = logging.getLogger('GalPaK: DiskModel ')
	#Python3 compatibility		#Python3 compatibility
	try:		try:
	basestring		basestring
	except NameError:		except NameError:
	basestring = str		basestring = str
	class Model:		class Model:
	"""		"""
	An **interface** for your simulation models.		An **interface** for your simulation models.
	The `runner` parameter is the instance of `galpak.Runner` using this mo del.		The `runner` parameter is the instance of `galpak.Runner` using this mo del.
	"""		"""
	logger = logger		logging.basicConfig(level=logging.INFO)
			logger = logging.getLogger('GalPaK: DiskModel ')
	flux_map_user = None		flux_map_user = None
	def set_cosmology(self, cosmo_string='planck15'):		def set_cosmology(self, cosmo_string='planck15'):
	try:		try:
	from colossus.cosmology import cosmology		from colossus.cosmology import cosmology
	from colossus import halo		from colossus import halo
	from colossus.halo import mass_defs, mass_adv, mass_so, concent ration		from colossus.halo import mass_defs, mass_adv, mass_so, concent ration
	self.logger.info("setting cosmology with colossus package")		self.logger.info("setting cosmology with colossus package")
	if cosmo_string in cosmology.cosmologies.keys():		if cosmo_string in cosmology.cosmologies.keys():
	cosmo=cosmology.setCosmology(cosmo_string)		cosmo=cosmology.setCosmology(cosmo_string)
	skipping to change at line 68		skipping to change at line 71
	self.h = cosmo.h		self.h = cosmo.h
	self.Ez = cosmo.Ez(self.redshift)		self.Ez = cosmo.Ez(self.redshift)
	DA = cosmo.angularDiameterDistance(self.redshift) / self.h ### #!!		DA = cosmo.angularDiameterDistance(self.redshift) / self.h ### #!!
	self.DeltaVir = halo.mass_so.deltaVir(self.redshift)		self.DeltaVir = halo.mass_so.deltaVir(self.redshift)
	self.halo = halo #Diemer Halo module for NFW halo models		self.halo = halo #Diemer Halo module for NFW halo models
	except ImportError:		except ImportError:
	try:		try:
	# using astropy		# using astropy
	import astropy		import astropy
	from astropy import cosmology		from astropy import cosmology
	if astropy.__version__ < LooseVersion('5.1'):		if astropy.__version__ < Version('5.1'):
	cosmo_available = cosmology.parameters.available		cosmo_available = cosmology.parameters.available
	cosmo_get = cosmology.default_cosmology.get_cosmology_f rom_string		cosmo_get = cosmology.default_cosmology.get_cosmology_f rom_string
	else:		else:
	cosmo_available = cosmology.available		cosmo_available = cosmology.available
	cosmo_get = cosmology.default_cosmology.get_cosmology_f rom_string		cosmo_get = lambda x: getattr(cosmology, x)
	if cosmo_string in cosmo_available:		if cosmo_string in cosmo_available:
	cosmo = cosmo_get(cosmo_string)		cosmo = cosmo_get(cosmo_string)
	else:		else:
	self.logger.info("Astropy: Parameter %s is not availabl e\n "		self.logger.info("Astropy: Parameter %s is not availabl e\n "
	"Please use one of %s \n"		"Please use one of %s \n"
	"Will be uing astropy.cosmology Planck 15 as default" \		"Will be uing astropy.cosmology Planck 15 as default" \
	% (cosmo_string, cosmo_available))		% (cosmo_string, cosmo_available))
	cosmo = cosmo_get('Planck15')		cosmo = cosmo_get('Planck15')
	cosmo_string = cosmo.name		cosmo_string = cosmo.name
	skipping to change at line 163		skipping to change at line 166
	# parameters.maximum_velocity *= -1		# parameters.maximum_velocity *= -1
	inc = parameters['inclination']		inc = parameters['inclination']
	if inc<0:		if inc<0:
	parameters.pa +=180		parameters.pa +=180
	parameters.pa = parameters.pa % 360. #to deal with circularity		parameters.pa = parameters.pa % 360. #to deal with circularity
	def sanitize_chain(self, chain):		def sanitize_chain(self, chain):
	"""		"""
	Mutates the `chain` with custom logic.		to force maxvelocity to be positive ; using circularity symmetry
	This is called at the end of the loop, before storing the chain.		This is called at the end of the loop, before storing the chain.
	"""		"""
	pa = chain['pa']		pa = chain['pa']
	pa_corr = pa % 360		pa_corr = pa % 360
	chain['pa'] = pa_corr		chain['pa'] = pa_corr
	def setup_random_amplitude(self, amplitude):		def setup_random_amplitude(self, amplitude):
	"""		"""
	Mutates the random `amplitude` of the parameter jump with custom lo gic.		Mutates the random `amplitude` of the parameter jump with custom lo gic.
	This is called during the setup of the MCMC runner.		This is called during the setup of the MCMC runner.
	skipping to change at line 458		skipping to change at line 461
	radius_cube = np.hypot(nx,ny) #np.sqrt(nx**2. + ny**2.)		radius_cube = np.hypot(nx,ny) #np.sqrt(nx**2. + ny**2.)
	flux_cube = self.set_flux_profile(parameters, radius_cube)		flux_cube = self.set_flux_profile(parameters, radius_cube)
	# Adjust disk thickness		# Adjust disk thickness
	flux_cube = self.set_thickness_profile(nz, hz, flux_cube)		flux_cube = self.set_thickness_profile(nz, hz, flux_cube)
	# Normalize by flux		# Normalize by flux
	total = bn.nansum(flux_cube) #should always be >0		total = bn.nansum(flux_cube) #should always be >0
	if total>0:		if total>0:
	flux_cube = flux_cube / total		flux_cube = flux_cube / total
	else:		else:
	raise ValueError("Something is wrong. Total flux is zero")		raise ValueError("Something is wrong. Total flux is zero")
	# Flux weighted		# Flux weighted
	flux_map = bn.nansum(flux_cube, 0)		flux_map = bn.nansum(flux_cube, 0)
	bad = (flux_map**2 == 0)		bad = (flux_map**2 == 0)
	vz_map = bn.nansum(vz_cube * flux_cube / flux_map, 0)		vz_map = bn.nansum(vz_cube * flux_cube / flux_map, 0)
	vz_map[bad] = np.nan #force outer to 0		vz_map[bad] = np.nan #force outer to 0
	skipping to change at line 490		skipping to change at line 493
	# c) Normalized with flux squared		# c) Normalized with flux squared
	norm = bn.nansum(flux_cube * flux_cube, 0)		norm = bn.nansum(flux_cube * flux_cube, 0)
	sigz_map_ale = np.sqrt(bn.nansum(sig_ale_disk ** 2 * flux_cube ** 2 , 0) / norm)		sigz_map_ale = np.sqrt(bn.nansum(sig_ale_disk ** 2 * flux_cube ** 2 , 0) / norm)
	# Intrinsic Dispersionmodel		# Intrinsic Dispersionmodel
	if 'velocity_dispersion' in parameters.names:		if 'velocity_dispersion' in parameters.names:
	sig_intr = np.ones_like(sigz_map_ale) * parameters.velocity_dis persion		sig_intr = np.ones_like(sigz_map_ale) * parameters.velocity_dis persion
	else:		else:
	sig_intr = np.ones_like(sigz_map_ale)		sig_intr = np.ones_like(sigz_map_ale)
	#correct outer regions
	#sigz_map_ale = np.where(bad, sig_intr, sigz_map_ale)
	# Total S-map		# Total S-map
	s_map = np.sqrt(sig_map_disk ** 2 + sigz_map_ale ** 2 + sig_intr ** 2)		s_map = np.sqrt(sig_map_disk ** 2 + sigz_map_ale ** 2 + sig_intr ** 2)
	s_map[bad]=np.nan		s_map[bad]=np.nan
	return flux_cube, vz_cube, vz_map, s_map, \		return flux_cube, vz_cube, vz_map, s_map, \
	sig_map_disk, sigz_map_ale, sig_intr		sig_map_disk, sigz_map_ale, sig_intr
	def _map_indices(self, xx, yy, zz, parameters):		def _map_indices(self, xx, yy, zz, parameters):
	"""		"""
	Takes arrays of indices, galaxy parameters, and rotates accordingly .		Takes arrays of indices, galaxy parameters, and rotates accordingly .
End of changes. 9 change blocks.
	13 lines changed or deleted		13 lines changed or added
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