plot_utilities.py		plot_utilities.py
	skipping to change at line 180		skipping to change at line 180
	if (plot_likelihood):		if (plot_likelihood):
	ax.plot(np.exp(-chain['reduced_chi'] ))		ax.plot(np.exp(-chain['reduced_chi'] ))
	ax.set_ylim([0,1])		ax.set_ylim([0,1])
	ax.set_title(r'${\cal L}=\exp$[-$\chi^2$]')		ax.set_title(r'${\cal L}=\exp$[-$\chi^2$]')
	else:		else:
	ax.plot(np.log10(chain['reduced_chi'][idx] - np.min(cha in['reduced_chi'])))		ax.plot(np.log10(chain['reduced_chi'][idx] - np.min(cha in['reduced_chi'])))
	if method == 'MAP':		if method == 'MAP':
	ax.axvline(idx_map,lw=1)		ax.axvline(idx_map,lw=1)
	ax.set_title(r'$\log$ [$\chi^2 - \chi^2_{min}$]')		ax.set_title(r'$\log$ [$\chi^2 - \chi^2_{min}$]')
	if method is 'chi_sorted':		if method == 'chi_sorted':
	ax.set_xticks([])		ax.set_xticks([])
	else:		else:
	ax.set_xticks(np.arange(2.) / 2 * np.size(idx))		ax.set_xticks(np.arange(2.) / 2 * np.size(idx))
	fig.subplots_adjust(wspace=0.3)		fig.subplots_adjust(wspace=0.3)
	if filename is None:		if filename is None:
	plot.show()		plot.show()
	else:		else:
	plot.savefig(filename)		plot.savefig(filename)
	skipping to change at line 227		skipping to change at line 227
	if filepath is not None:		if filepath is not None:
	name, extension = os.path.splitext(filepath)		name, extension = os.path.splitext(filepath)
	supported_extensions = ['.png', '.pdf']		supported_extensions = ['.png', '.pdf']
	if not extension in supported_extensions:		if not extension in supported_extensions:
	raise ValueError("Extension '%s' is not supported, use %s." ,		raise ValueError("Extension '%s' is not supported, use %s." ,
	extension, ', '.join(supported_extensions) )		extension, ', '.join(supported_extensions) )
	chain = self.chain.copy()		chain = self.chain.copy()
	#plot geweke has no meaning with chi_sorted		#plot geweke has no meaning with chi_sorted
	if self.method is not 'chi_sorted':		if self.method != 'chi_sorted':
	if fontsize is None:		if fontsize is None:
	fontsize = plot.rcParams['font.size']		fontsize = plot.rcParams['font.size']
	fig = plot.figure(2, figsize=(16, 9))		fig = plot.figure(2, figsize=(16, 9))
	names = chain.dtype.names		names = chain.dtype.names
	short_dict = self.galaxy.short_dict()		short_dict = self.galaxy.short_dict()
	plot.clf() # clear current figure		plot.clf() # clear current figure
	plot.subplots_adjust(wspace=0.32, hspace=0.32,		plot.subplots_adjust(wspace=0.32, hspace=0.32,
	skipping to change at line 362		skipping to change at line 362
	for s in show[1:]:		for s in show[1:]:
	r.append((self.galaxy[s] - self.galaxy.stdev[s] * nsigm a, \		r.append((self.galaxy[s] - self.galaxy.stdev[s] * nsigm a, \
	self.galaxy[s] + self.galaxy.stdev[s] * nsigma))		self.galaxy[s] + self.galaxy.stdev[s] * nsigma))
	best.append(self.galaxy[s])		best.append(self.galaxy[s])
	ls.append(shorts_dict[s])		ls.append(shorts_dict[s])
	if fontsize is None:		if fontsize is None:
	fontsize = plot.rcParams['font.size']		fontsize = plot.rcParams['font.size']
	#@fixme how to make onto fig=plot.figure(3)		#@fixme how to make onto fig=plot.figure(3)
	corner.corner(self.sub_chain[show].as_array().tolist(),\		corner.corner(self.sub_chain[show].to_pandas(),\
	labels=ls, truths=best, range=r, \		labels=ls, truths=best, range=r, \
	smooth=smooth, label_kwargs={'fontname':'sans -serif', 'fontsize': fontsize})		smooth=smooth, label_kwargs={'fontname':'sans -serif', 'fontsize': fontsize})
	if filepath is None:		if filepath is None:
	plot.show()		plot.show()
	else:		else:
	plot.savefig(filepath)		plot.savefig(filepath)
	plot.close()		plot.close()
	else:		else:
	skipping to change at line 535		skipping to change at line 535
	if filepath is None:		if filepath is None:
	fig.show()		fig.show()
	else:		else:
	fig.savefig(filepath)		fig.savefig(filepath)
	plot.close()		plot.close()
	rotation_curve = [pixscale * xx[good], xx[good]/self.galaxy.rad ius, slice_f[good], slice_v[good], slice_s[good]]		rotation_curve = [pixscale * xx[good], xx[good]/self.galaxy.rad ius, slice_f[good], slice_v[good], slice_s[good]]
	rotation_name=re.sub('true_maps','true_Vrot',filepath[:-4])+'.d at'		rotation_name=re.sub('true_maps','true_Vrot',filepath[:-4])+'.d at'
	asciitable.write(rotation_curve, \		asciitable.write(rotation_curve, \
	output=rotation_name,Writer=asciitable.FixedWi dth, \		output=rotation_name,format='fixed_width', \
	names=['dx_arcsec', 'rad_Re', 'flux_slit', 'v_ kms', 'sig_kms'], overwrite=True)		names=['dx_arcsec', 'rad_Re', 'flux_slit', 'v_ kms', 'sig_kms'], overwrite=True)
	def plot_obs_vfield(self, filepath=None, mask=None, contours=None,		def plot_obs_vfield(self, filepath=None, mask=None, contours=None,
	fontsize=10, slitwidth=3):		fontsize=10, slitwidth=3):
	"""		"""
	plot the observed 2d maps and the 1d along the major axis		plot the observed 2d maps and the 1d along the major axis
	mask: [optional] 2d nd-array		mask: [optional] 2d nd-array
	mask for display purposes		mask for display purposes
	None: [default] default mask is flux>max(flux)/20.		None: [default] default mask is flux>max(flux)/20.
	skipping to change at line 919		skipping to change at line 919
	xaxis = np.where(b!=0, bn.nansum(dist_rot, axis=(0)) / b, 0.)		xaxis = np.where(b!=0, bn.nansum(dist_rot, axis=(0)) / b, 0.)
	return xaxis, profile		return xaxis, profile
	def _make_maps_Epinat(self, cube=None, mask=False, cut_level=50, use_co nv='other'):		def _make_maps_Epinat(self, cube=None, mask=False, cut_level=50, use_co nv='other'):
	"""		"""
	make observed maps from true maps using formulas in Epinat 2010		make observed maps from true maps using formulas in Epinat 2010
	:param cube: input cube for computing masking		:param cube: input cube for computing masking
	:param mask: boolean [default: None] to apply masking		:param mask: boolean [default: None] to apply masking
	:param use_conv: astropy [default] | scipy		:param use_conv: other [default] | scipy | astropy
	:param cut_level: 50 [default] cut used if mask=True		:param cut_level: 50 [default] cut used if mask=True
	:return:		:return:
	"""		"""
	if (cube is None):		if (cube is None):
	cube = self.convolved_cube		cube = self.convolved_cube
	if mask is True:		if mask is True:
	# default mask is flux>max(flux)/30.		# default mask is flux>max(flux)/30.
	mask = (bn.nansum(cube.data,0) > bn.nanmax(cube.data.sum(0)) / cut_level )		mask = (bn.nansum(cube.data,0) > bn.nanmax(cube.data.sum(0)) / cut_level )
	else:		else:
	mask = np.ones_like(cube.data[1,:,:])		mask = np.ones_like(cube.data[1,:,:])
	#Eq A15 Epinat		#Eq A15 Epinat
	psf2d = self.instrument.psf3d.sum(axis=0)		psf2d = self.instrument.psf3d.sum(axis=0)
	if use_conv is 'scipy' :		if use_conv == 'scipy' :
	logger.debug("Using scipy %s for convolution" % (scipy.__versio n__))		logger.debug("Using scipy %s for convolution" % (scipy.__versio n__))
	Fmap = conv2d_scipy(self.true_flux_map.data, psf2d, mode='same' )		Fmap = conv2d_scipy(self.true_flux_map.data, psf2d, mode='same' )
	elif use_conv is 'astropy':		elif use_conv == 'astropy':
	logger.debug("Using astropy %s for convolution" % (astropy.__ve rsion__))		logger.debug("Using astropy %s for convolution" % (astropy.__ve rsion__))
	Fmap = conv2d_astro(self.true_flux_map.data, psf2d)		Fmap = conv2d_astro(self.true_flux_map.data, psf2d)
	else:		else:
	Fmap, psf2d_fft = conv2d_intern(self.true_flux_map.data, psf2d, compute_fourier=True)		Fmap, psf2d_fft = conv2d_intern(self.true_flux_map.data, psf2d, compute_fourier=True)
	#Eq A16 Epinat		#Eq A16 Epinat
	V1 = self.true_velocity_map.data * self.true_flux_map.data # V.M		V1 = self.true_velocity_map.data * self.true_flux_map.data # V.M
	if use_conv is 'scipy':		if use_conv == 'scipy':
	Vtemp = conv2d_scipy(V1, psf2d, mode='same')		Vtemp = conv2d_scipy(V1, psf2d, mode='same')
	elif use_conv is 'astropy':		elif use_conv == 'astropy':
	Vtemp = conv2d_astro(V1, psf2d)		Vtemp = conv2d_astro(V1, psf2d)
	else:		else:
	Vtemp, psf2d_fft = conv2d_intern(V1, psf2d, compute_fourier=Tru e)		Vtemp, psf2d_fft = conv2d_intern(V1, psf2d, compute_fourier=Tru e)
	Vmap = Vtemp / Fmap		Vmap = Vtemp / Fmap
	#Eq A17 Epinat		#Eq A17 Epinat
	S1 = self.true_disp_map.data**2 * self.true_flux_map.data		S1 = self.true_disp_map.data**2 * self.true_flux_map.data
	if use_conv is 'scipy':		if use_conv == 'scipy':
	Stemp = conv2d_scipy(S1, psf2d, mode='same')		Stemp = conv2d_scipy(S1, psf2d, mode='same')
	elif use_conv is 'astropy':		elif use_conv == 'astropy':
	Stemp = conv2d_astro(S1, psf2d)		Stemp = conv2d_astro(S1, psf2d)
	else:		else:
	Stemp, psf2d_fft = conv2d_intern(S1, psf2d, compute_fourier=Tru e)		Stemp, psf2d_fft = conv2d_intern(S1, psf2d, compute_fourier=Tru e)
	V2 = self.true_velocity_map.data**2 * self.true_flux_map.data		V2 = self.true_velocity_map.data**2 * self.true_flux_map.data
	if use_conv is 'scipy':		if use_conv == 'scipy':
	Vtemp = conv2d_scipy(V2, psf2d, mode='same')		Vtemp = conv2d_scipy(V2, psf2d, mode='same')
	elif use_conv is 'astropy':		elif use_conv == 'astropy':
	Vtemp = conv2d_astro(V2, psf2d)		Vtemp = conv2d_astro(V2, psf2d)
	else:		else:
	Vtemp, psf2d_fft = conv2d_intern(V2, psf2d, compute_fourier=Tru e)		Vtemp, psf2d_fft = conv2d_intern(V2, psf2d, compute_fourier=Tru e)
	Smap_sq = Stemp / Fmap + Vtemp / Fmap - Vmap**2		Smap_sq = Stemp / Fmap + Vtemp / Fmap - Vmap**2
	Smap = np.sqrt(Smap_sq)		Smap = np.sqrt(Smap_sq)
	self.obs_flux_map = HyperCube(Fmap * mask)		self.obs_flux_map = HyperCube(Fmap * mask)
	self.obs_velocity_map = HyperCube(Vmap * mask)		self.obs_velocity_map = HyperCube(Vmap * mask)
	self.obs_disp_map = HyperCube(Smap * mask)		self.obs_disp_map = HyperCube(Smap * mask)
End of changes. 13 change blocks.
	13 lines changed or deleted		13 lines changed or added
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