custom survey notebook

EPOS/classes.py

@@ -325,7 +325,7 @@ def set_survey(self, xvar, yvar, eff_2D, Rstar=1.0, Mstar=1.0, vet_2D=None):
 					'\n: (nx,ny)={}, (nx,ny={})'.format(self.eff_2D.shape,
 								self.vetting.shape))
 
-			self.completeness_novet= self.completeness
+			self.completeness_novet= 1.*self.completeness
 			self.completeness*= self.vetting
 
 		self.DetectionEfficiency=True

EPOS/plot/occurrence.py

@@ -59,7 +59,7 @@ def all(epos, color=None, alpha_fac=None):
 	else:
 		print ('\nNo occurrence to plot, did you run EPOS.occurrence.all()? \n')
 
-def colored(epos, Bins=False, Poly=False):
+def colored(epos, Bins=False, Poly=False, NB=False):
 
 	f, (ax, axb) = plt.subplots(1,2, gridspec_kw = {'width_ratios':[20, 1]})
 	f.subplots_adjust(wspace=0)
@@ -69,7 +69,7 @@ def colored(epos, Bins=False, Poly=False):
 	ax.set_title(name)
 
 	helpers.set_axes(ax, epos, Trim=True)
-	#if epos.plot['']
+	#helpers.set_axes(ax, epos, Trim=hasattr(epos, 'xtrim'))
 
 	#ax.plot(epos.obs_xvar, epos.obs_yvar, ls='', marker='.', mew=0, ms=5.0, color='k')
 
@@ -117,7 +117,7 @@ def colored(epos, Bins=False, Poly=False):
 			ax.text(xbin[1]/xnudge,ybin[0]*ynudge,'n={}'.format(n), ha='right',
 				size=size)
 
-		helpers.save(plt, epos.plotdir+'occurrence/bins')
+		helpers.save(plt, epos.plotdir+'occurrence/bins', NB=NB)
 	elif Poly:
 		occpoly= epos.occurrence['poly']
 		for k, (xc, yc, coords, n, inbin, occ, err) in enumerate(
@@ -136,9 +136,9 @@ def colored(epos, Bins=False, Poly=False):
 			#ax.text(xbin[1]/xnudge,ybin[0]*ynudge,'n={}'.format(n), ha='right',
 			#	size=size)
 
-		helpers.save(plt, epos.plotdir+'occurrence/poly')
+		helpers.save(plt, epos.plotdir+'occurrence/poly', NB=NB)
 	else:
-		helpers.save(plt, epos.plotdir+'occurrence/colored')
+		helpers.save(plt, epos.plotdir+'occurrence/colored', NB=NB)
 
 def integrated(epos, MCMC=False, Planets=False, NB=False):
 

EPOS/plot/parametric.py

@@ -17,7 +17,7 @@ def oneD(epos, PlotZoom=False, MCMC=False, Occ=False):
 		# works with occ??
 		oneD_y(epos, PlotZoom=PlotZoom, MCMC=MCMC, PlotQ=True)
 
-def oneD_x(epos, PlotZoom=False, MCMC=False, Occ=False, Log=True, NB=False):	
+def oneD_x(epos, PlotZoom=False, MCMC=False, Occ=False, Log=True, Init=True, NB=False):	
 
 	if Occ:
 		fname= 'occurrence/posterior' if MCMC else 'occurrence/input'
@@ -33,7 +33,8 @@ def oneD_x(epos, PlotZoom=False, MCMC=False, Occ=False, Log=True, NB=False):
 		fname+= '.linear'
 
 	# initial guess
-	pps, _, pdf0_X, _= periodradius(epos, Init=True, ybin=ybin)
+	if Init:
+		pps, _, pdf0_X, _= periodradius(epos, Init=True, ybin=ybin)
 	if MCMC:
 		# best-fit parameters
 		pps, _, pdf_X, _= periodradius(epos, ybin=ybin)
@@ -69,7 +70,7 @@ def oneD_x(epos, PlotZoom=False, MCMC=False, Occ=False, Log=True, NB=False):
 					label='Starting Guess')
 		ax.plot(epos.MC_xvar, pdf_X, marker='',ls='-',color='k',
 					label='Best Fit')
-	else:
+	elif Init:
 		if 'P break' in epos.fitpars.keys2d:
 			ax.axvline(epos.fitpars.get('P break', Init=True), ls='-', color='gray')
 		ax.plot(epos.MC_xvar, pdf0_X, marker='',ls='-',color='k')
@@ -115,7 +116,7 @@ def oneD_x(epos, PlotZoom=False, MCMC=False, Occ=False, Log=True, NB=False):
 	helpers.save(plt, epos.plotdir+fname+'_x', NB=NB)
 	#print epos.plotdir+fname+'_x'
 
-def oneD_y(epos, PlotZoom=False, MCMC=False, PlotQ=False, Occ=False, Convert=False, NB=False):
+def oneD_y(epos, PlotZoom=False, MCMC=False, PlotQ=False, Occ=False, Convert=False, NB=False, Init=True):
 	if Occ:
 		fname= 'occurrence/posterior' if MCMC else 'occurrence/input'
 		xbin= epos.xzoom
@@ -127,7 +128,8 @@ def oneD_y(epos, PlotZoom=False, MCMC=False, PlotQ=False, Occ=False, Convert=Fal
 		title= 'Marginalized Distribution ({:.2g}-{:.0f} days)'.format(*epos.xtrim)
 
 	# initial guess
-	pps, _, _, pdf0_Y= periodradius(epos, Init=True, xbin=xbin, Convert=Convert)
+	if Init:
+		pps, _, _, pdf0_Y= periodradius(epos, Init=True, xbin=xbin, Convert=Convert)
 	if MCMC:
 		# best-fit parameters
 		pps, _, _, pdf_Y= periodradius(epos, xbin=xbin, Convert=Convert)
@@ -182,7 +184,7 @@ def oneD_y(epos, PlotZoom=False, MCMC=False, PlotQ=False, Occ=False, Convert=Fal
 			ax.plot(yvar, ypdf*yscale, color='b', alpha=0.1)
 		ax.plot(yvar, pdf0_Y*yscale, marker='',ls=':',color='k', label='starting guess')
 		ax.plot(yvar, pdf_Y*yscale, marker='',ls='-',color='k', label='best-fit')
-	else:
+	elif Init:
 		if 'R break' in epos.fitpars.keys2d:
 			ax.axvline(epos.fitpars.get('R break', Init=True), ls='-', color='gray')
 

EPOS/run.py

@@ -278,12 +278,18 @@ def prep_obs(epos):
 
 	x= epos.obs_xvar[ix&iy]
 	y= epos.obs_yvar[ix&iy]
-	t= epos.obs_tdur[ix&iy]
-
-	for key, var in zip(['x','y','t'], [x,y,t]):
+	for key, var in zip(['x','y'], [x,y]):
 		z[key]= np.sort(var) # add (x0,0) and (x1,1)?
 		z[key+' cum']= np.arange(z[key].size,dtype=float)
 		z[key+' cdf']= z[key+' cum']/z[key+' cum'][-1]
+
+	if hasattr(epos, 'obs_tdur') and not epos.RV:
+		t= epos.obs_tdur[ix&iy]
+
+		for key, var in zip(['t'], [t]):
+			z[key]= np.sort(var) # add (x0,0) and (x1,1)?
+			z[key+' cum']= np.arange(z[key].size,dtype=float)
+			z[key+' cdf']= z[key+' cum']/z[key+' cum'][-1]
 
 	# multis
 	z['multi']={}

docs/index.rst

@@ -52,6 +52,7 @@ Familiarize yourself with the code is to take a look at the :doc:`notebooks`
    tutorials/parameteric_mode.ipynb
    tutorials/multiplanet_mode.ipynb
    tutorials/radial_velocity.ipynb
+   tutorials/custom_survey.ipynb
 
 .. toctree::
    :maxdepth: 2
@@ -98,10 +99,11 @@ Version Notes:
 
 :1.0.1: first public release
 :1.0.2: pip installable version
-:1.1.0: radial velocity without Monte Carlo |ImageLink|_
+:1.1.0: radial velocity without Monte Carlo
+:2.0.2: planet formation models |ImageLink|_
 
-.. |ImageLink| image:: https://zenodo.org/badge/132065382.svg
-.. _ImageLink: https://zenodo.org/badge/latestdoi/132065382
+.. |ImageLink| image:: https://zenodo.org/DOI/10.5281/zenodo.3515380.svg
+.. _ImageLink: https://doi.org/10.5281/zenodo.3515380
 
 Indices and tables
 ------------------

docs/notebooks.rst

@@ -6,7 +6,8 @@ Examples
 
 * :ref:`/tutorials/parameteric_mode.ipynb`  (:download:`save to disk </tutorials/parameteric_mode.ipynb>`)
 * :ref:`/tutorials/multiplanet_mode.ipynb`  (:download:`save to disk </tutorials/multiplanet_mode.ipynb>`)
-*
+* :ref:`/tutorials/custom_survey.ipynb`  (:download:`save to disk </tutorials/custom_survey.ipynb.ipynb>`)
+
 
 The notebooks are also viewable on `github  <https://github.com/GijsMulders/epos/docs/tutorials>`_
 

docs/tutorials/parameteric_mode.ipynb

@@ -756,7 +756,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.4"
+   "version": "3.7.5"
   }
  },
  "nbformat": 4,