Update CHIMERA documentation and version and remove unnecessary files

CosmoStatGW · Dec 11, 2023 · cc5f1b3 · cc5f1b3
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diff --git a/CHIMERA/Likelihood.py b/CHIMERA/Likelihood.py
@@ -451,36 +451,17 @@ def compute(self, lambda_cosmo, lambda_mass, lambda_rate, inspect=False):
         like_events = np.empty(self.nevents)
 
         # Compute overall rate normalization given lambda_rate (returns 1. if self.z_det_range is None)
-        p_z_norm = self.get_p_z_norm(lambda_cosmo, lambda_rate)
-        fR       = self.completeness.get_fR(lambda_cosmo, z_det_range=[0,0.12])
+        p_z_norm = self._get_p_z_norm(lambda_cosmo, lambda_rate)
 
-        # fR_ev = self.get_fR(lambda_cosmo)
+        fR_ev = self.get_fR(lambda_cosmo)
 
         # Compute like for each event
         for e in range(self.nevents):
             z_grid    = self.z_grids[e]
             p_cat     = self.p_cat_all[e]
 
-            idxs_mask = self.completeness.get_pix2mask(self.pix_conf[e], self.nside[e])
-            fR_ev     = fR[idxs_mask]
-            compl     = self.completeness.P_compl(z_grid, self.pix_conf[e], self.nside[e])
-
-            # compl     = self.P_compl(z_grid)
-
-            p_gal     = fR_ev * p_cat + ( (1.-compl)*np.array(self.model_cosmo.dV_dz(z_grid, lambda_cosmo)[:, np.newaxis] ))
-
-            # p_gal     = fR_ev * p_cat + ( (1.-compl)*np.array(self.model_cosmo.dV_dz(z_grid, lambda_cosmo)))[:, np.newaxis]
-
-            if 0:
-            # print(fR_ev * p_cat )
-                for pix in range(self.npix_event[e]):
-                    zz         = np.linspace(0, 10, 1000)
-                    compl      = self.P_compl(z_grid, self.pix_conf[e][pix], self.nside[e])
-                    # print(compl)
-                    fR         = np.trapz(self.P_compl(zz, self.pix_conf[e][pix], self.nside[e])*np.array(self.model_cosmo.dV_dz(zz, lambda_cosmo)), zz)
-                    p_gal[:,pix] = fR * p_cat[:,pix] + (1.-compl)*np.array(self.model_cosmo.dV_dz(z_grid, lambda_cosmo)) 
-
-
+            compl     = self.P_compl(z_grid)
+            p_gal     = fR_ev * p_cat + ( (1.-compl)*np.array(self.model_cosmo.dV_dz(z_grid, lambda_cosmo)))[:, np.newaxis]
             p_rate    = self.gw.model_rate(z_grid, lambda_rate)/(1.+z_grid)
             p_z       = (p_rate/p_z_norm)[:,np.newaxis] * p_gal
             p_gw      = self.gw.compute_event(e, z_grid, lambda_cosmo, lambda_mass)

diff --git a/CHIMERA/__version__.py b/CHIMERA/__version__.py
@@ -1 +1 @@
-__version__ = "0.1.dev58+ge14c507.d20231208"
+__version__ = "1.0.0"
diff --git a/CHIMERA/astro/spin.py b/CHIMERA/astro/spin.py
@@ -64,49 +64,3 @@ def logpdf_G(chi_eff, chi_p, lambda_s):
 
 
     return logpdf_eff + logpdf_p
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-class UniformSpinDistChiz(BBHDistFunction): 
-
-    '''
-    Uniform distribution in chi1z, chi2z, uncorrelated
-    '''
-
-    def __init__(self, ):
-        BBHDistFunction.__init__(self)
-        self.params = ['chiMin', 'chiMax', ] #'rho' ] # For the moment we ignore correlation
-
-        self.baseValues = {
-
-                           'chiMin': -0.75,
-                           'chiMax':0.75, 
-                           }
-
-        self.names = {
-                           'chiMin':r'$\chi_{ z, Min}$',
-                           'chiMax':r'$\chi_{ z, Max}$', }
-
-        self.n_params = len(self.params)
-
-        self.maxChi = 1
-        self.minChi = -1
-        self.nVars = 2
-
-
-
-        print('Uniform spin distribution in (chi1z, chi2z) base values: %s' %self.baseValues)
-
-
-
diff --git a/CHIMERA/utils/misc.py b/CHIMERA/utils/misc.py
@@ -136,7 +136,7 @@ def load_data_h5(fname):
 from scipy.optimize import fmin
 
 
-def get_confidence_HDI(post, grid, kde=None, interval=0.683, ax=None, color="k", lab=None, median=False, ls='--'):
+def get_confidence_HDI(post, grid, kde=None, interval=0.683, ax=None, color="k", lab="auto", median=False, ls='--'):
 
     if kde is not None:
         N_samples = 10**6
@@ -177,10 +177,12 @@ def width(low):
         xmax = med
         xlow = lo
         xup  = hi 
-        
-
+
+    
     if ax is not None:
-        # lab = "$H_0={:.0f}^{{+{:.0f}}}_{{-{:.0f}}}$".format(xmax, xup-xmax, xmax-xlow)
+        if lab == "auto":
+            lab = r"$H_0={:.0f}^{{+{:.0f}}}_{{-{:.0f}}}$".format(xmax, xup-xmax, xmax-xlow)
+
         ax.fill_between(xx, 0, yy, where=(xx >= xlow) & (xx <= xup), color=color, alpha=0.2, linewidth=0.0)
         ax.plot([xmax,xmax], [0, float(post_int(xmax))/norm], color=color, linestyle=ls, label=lab)
         ax.plot(xx, yy, lw=1, color=color, ls="-")

diff --git a/CHIMERA/utils/plotting.py b/CHIMERA/utils/plotting.py
@@ -41,7 +41,7 @@ def plot_2Dcoring(like,
                   event         = 0,
                   do_boundaries = True,
                   do_KDE        = False,
-                  do_gal        = True,
+                  do_gal        = False,
                   do_p_gal      = True,
                   do_p_gw       = True,
                   do_p_z        = False,
@@ -51,7 +51,7 @@ def plot_2Dcoring(like,
                   KDE_levels    = [0.1,0.8,0.9, 0.99],
                   lw            = 1,
                   lab_p_gal     = "$p_{\mathrm{gal},k}(z)$",
-                  lab_p_gw      = "$p_{\mathrm{gw},k}(z)$",
+                  lab_p_gw      = "$p_{\mathrm{gw},k}(z|H_0)$",
                   lab_p_z       = "$p_{z,k}(z)$",
                   ax            = None, 
                   ):
@@ -75,7 +75,6 @@ def pdf(y):
     # Individual galaxies
     alpha = misc.remapMinMax(-zgal, a=.2, b=.7)
     ax[0].scatter(ragal, decgal, marker='x', c='darkred', s=30, label="Potential hosts", alpha=alpha)
-    # ax[0].scatter(ragal, decgal, marker='x', c='darkred', s=30, label="All galaxies", alpha=0.5)
 
     if do_boundaries: # Highlight Healpixels
         for jpix in pixels:
@@ -101,21 +100,19 @@ def pdf(y):
         [ax[1].plot(z_grid, pdf(like.p_gal_all[event][:,pix]), c="darkred", lw=lw, alpha=0.7, label=lab_p_gal if pix==0 else None) for pix in range(len(pixels))]
 
     if do_p_gw: # Plot p(z)_gw for each pixel
-        [ax[1].plot(z_grid, pdf(like.p_gw_all[iteration][event][:,pix]), c="darkblue", lw=lw, alpha=0.7, label=lab_p_gw if pix==0 else None) for pix in range(len(pixels))]
+        [ax[1].plot(z_grid, pdf(like.p_gw_all[iteration][:,pix]), c="darkblue", lw=lw, alpha=0.7, label=lab_p_gw if pix==0 else None) for pix in range(len(pixels))]
 
     if do_p_z: # Plot p(z) for each pixel
         [ax[1].plot(z_grid, pdf(like.p_z_all[iteration][event][:,pix]), c="teal", lw=lw, alpha=0.7, label=lab_p_z if pix==0 else None) for pix in range(len(pixels))]
 
     ax[0].set_xlabel("RA")
-    ax[0].set_ylabel("DEC")
+    ax[0].set_ylabel("Dec")
     ax[1].set_xlabel(r"$z$")
-    ax[1].set_ylabel(r"$p(z)~\textit{renormalized}$" if renorm_all else r"$p(z)$")
+    ax[1].set_ylabel(r"$p(z)$")
     ax[1].set_xlim(*z_lims)
     ax[0].legend()
     ax[1].legend()
 
-    return fig
-
 
 
 

diff --git a/README.md b/README.md
@@ -16,7 +16,7 @@ The code is designed to be accurate for different scenarios, encompassing bright
 
 ## Installation
 
-The code can be easily installed with pip:
+The code can be easily installed with pip (available soon):
 
     pip install chimera-gw
 
@@ -28,7 +28,7 @@ or by cloning the source repository hosted on GitHub
 
 ## Documentation
 
-Read the docs at [chimera-gw.readthedocs.io](https://chimera-gw.readthedocs.io)
+The full documentation is provided at [chimera-gw.readthedocs.io](https://chimera-gw.readthedocs.io)
 
 
 

diff --git a/docs/_static/CHIMERA_diagram.svg b/docs/_static/CHIMERA_diagram.svg
diff --git a/docs/api/GW.rst b/docs/api/GW.rst
@@ -12,5 +12,4 @@ GW
 
 .. autoclass:: CHIMERA.DataGW.DataLVK
    :members:
-   :inherited-members:
-   3
+   :inherited-members:
diff --git a/docs/api/Models.rst b/docs/api/Models.rst
@@ -24,7 +24,7 @@ fLCDM
 ^^^^^
 
 .. autofunction:: CHIMERA.cosmo.fLCDM.dC
-.. autofunction:: CHIMERA.cosmo.fLCDM.d_L
+.. autofunction:: CHIMERA.cosmo.fLCDM.dL
 .. autofunction:: CHIMERA.cosmo.fLCDM.ddL_dz
 .. autofunction:: CHIMERA.cosmo.fLCDM.V
 .. autofunction:: CHIMERA.cosmo.fLCDM.dV_dz

diff --git a/docs/index.rst b/docs/index.rst
@@ -11,32 +11,29 @@
 
     <div style="min-height:0.1em;"></div>
 
+
 *******
 CHIMERA
 *******
 
-.. .. raw:: html
-
-..    <img src="_static/CHIMERA_logoNB2.svg";" style="width:350px; margin:5px;"/>
-   
-..    <br/>
-
-
 **CHIMERA** (Combined Hierarchical Inference Model for Electromagnetic and gRavitational-wave Analysis), is a flexible Python code to analyze standard sirens with galaxy catalogs, allowing for a joint fitting of the cosmological and astrophysical population parameters within a Hierarchical Bayesian Inference framework. 
 
-.. The code is designed to be accurate for different scenarios, encompassing bright, dark, and spectral sirens methods, and computationally efficient in view of next-generation GW observatories and galaxy surveys. It uses the LAX-backend implementation and Just In Time (JIT) computation capabilities of JAX. 
-
 
 .. image:: https://img.shields.io/badge/GitHub-CHIMERA-9e8ed7
     :target: https://github.com/CosmoStatGW/CHIMERA/
+    :alt: GitHub
 .. image:: https://img.shields.io/badge/arXiv-2106.14894-28bceb
     :target: https://arxiv.org/abs/2106.14894
+    :alt: arXiv
 .. image:: https://readthedocs.org/projects/chimera-gw/badge/?version=latest
-    :target: https://chimera-gw.readthedocs.io/en/latest/?badge=latest
+    :target: https://chimera-gw.readthedocs.io/latest/?badge=latest
+    :alt: Documentation Status
 .. image:: https://img.shields.io/badge/license-MIT-fb7e21
     :target: https://github.com/CosmoStatGW/CHIMERA/blob/main/LICENSE
+    :alt: License
 .. image:: https://img.shields.io/gitlab/v/release/14528131
     :target: https://gitlab.com/mmoresco/CHIMERA/-/tags
+    :alt: Release
 
 .. raw:: html
 
@@ -53,7 +50,6 @@ Installation
    pip install chimera-gw
 
 
-
 License & Attribution
 ---------------------
 
@@ -77,44 +73,46 @@ If you find this code useful in your research, please cite the following paper (
     }
 
 
-
 The team
 --------
 
-Main developers:
+**Core team**
 
-- `Nicola Borghi (nicola.borghi6@unibo.it) <https://orcid.org/0000-0002-2889-8997>`_
-- `Michele Mancarella (michele.mancarella@unimib.it) <https://orcid.org/0000-0002-0675-508X>`_
+- `Nicola Borghi <https://orcid.org/0000-0002-2889-8997>`_ (**main developer**, nicola.borghi6@unibo.it)
+- `Michele Mancarella <https://orcid.org/0000-0002-0675-508X>`_ (michele.mancarella@unimib.it) 
+- `Michele Moresco <https://orcid.org/0000-0002-7616-7136>`_ (michele.moresco@unibo.it) 
 
+**Contributors**
 
-Contributors:
-
-- `Michele Moresco (michele.moresco@unibo.it) <https://orcid.org/0000-0002-7616-7136>`_
 - `Matteo Tagliazucchi <https://orcid.org/0000-0002-2889-8997>`_
-- `Francesco Iacovelli <https://orcid.org/0000-0002-4875-5862>`_
 - Niccolò Passaleva
-
+- `Francesco Iacovelli <https://orcid.org/0000-0002-4875-5862>`_
 
 The code was developed starting from https://github.com/CosmoStatGW/DarkSirensStat (`Finke et al. 2019 <https://orcid.org/0000-0002-2889-8997>`_) and https://github.com/CosmoStatGW/MGCosmoPop (`Mancarella et al. 2021 <https://orcid.org/0000-0002-2889-8997>`_).
 
 
-
 Documentation
 -------------
 
 .. toctree::
-    :maxdepth: 2
+    :maxdepth: 1
     :caption: User Guide
 
     user_guide/installation
     user_guide/introduction
     user_guide/getting_started
     user_guide/framework
+    user_guide/changelog
     user_guide/citing
 
+.. toctree::
+   :maxdepth: 1
+   :caption: Tutorials
+
+   tutorials/GW170817
 
 .. toctree::
-    :maxdepth: 2
+    :maxdepth: 1
     :caption: Python APIs
 
     api/MCMC
@@ -125,11 +123,7 @@ Documentation
     api/Models
 
 
-.. .. toctree::
-..    :maxdepth: 1
-..    :caption: Tutorials
 
-..    tutorials/quickstart
 
 
 .. Changelog