Merge pull request handley-lab#327 from martinit18/nested_fit

compatibility with nested_fit output files

README.rst

@@ -2,7 +2,7 @@
 anesthetic: nested sampling post-processing
 ===========================================
 :Authors: Will Handley and Lukas Hergt
-:Version: 2.1.5
+:Version: 2.2.0
 :Homepage: https://github.com/handley-lab/anesthetic
 :Documentation: http://anesthetic.readthedocs.io/
 

anesthetic/_version.py

@@ -1 +1 @@
-__version__ = '2.1.5'
+__version__ = '2.2.0'

anesthetic/read/chain.py

@@ -4,6 +4,7 @@
 from anesthetic.read.cobaya import read_cobaya
 from anesthetic.read.multinest import read_multinest
 from anesthetic.read.ultranest import read_ultranest
+from anesthetic.read.nestedfit import read_nestedfit
 
 
 def read_chains(root, *args, **kwargs):
@@ -14,6 +15,7 @@ def read_chains(root, *args, **kwargs):
         * `PolyChord <https://github.com/PolyChord/PolyChordLite>`_,
         * `MultiNest <https://github.com/farhanferoz/MultiNest>`_,
         * `UltraNest <https://github.com/JohannesBuchner/UltraNest>`_,
+        * `Nested_fit <https://github.com/martinit18/Nested_Fit>`_,
         * `CosmoMC <https://github.com/cmbant/CosmoMC>`_,
         * `Cobaya <https://github.com/CobayaSampler/cobaya>`_,
         * or anything `GetDist <https://github.com/cmbant/getdist>`_
@@ -49,7 +51,7 @@ def read_chains(root, *args, **kwargs):
     errors = []
     readers = [
         read_polychord, read_multinest, read_cobaya,
-        read_ultranest, read_getdist
+        read_ultranest, read_nestedfit, read_getdist
     ]
     for read in readers:
         try:

anesthetic/read/nestedfit.py

@@ -0,0 +1,35 @@
+"""Read NestedSamples from Nested_Fit chains."""
+import os
+import numpy as np
+from anesthetic.read.getdist import read_paramnames
+from anesthetic.samples import NestedSamples
+
+
+def read_nestedfit(root, *args, **kwargs):
+    """Read Nested_Fit chain files.
+
+    Parameters
+    ----------
+    root : str
+        root specify the directory only, no specific roots,
+        The files read files are ``nf_output_points.txt``
+        and ``nf_output_diag.txt``.
+
+    """
+    dead_file = os.path.join(root, 'nf_output_points.txt')
+    birth_file = os.path.join(root, 'nf_output_diag.dat')
+    data_dead = np.loadtxt(dead_file)
+    data_birth = np.loadtxt(birth_file)
+    weight, logL, data = np.split(data_dead, [1, 2], axis=1)
+    logL_birth = data_birth[:, 0]
+    root_getdist = os.path.join(root, 'nf_output_points')
+    columns, labels = read_paramnames(root_getdist)
+    # No specific labeling is implemented in nested_fit
+    labels = columns
+    columns = kwargs.pop('columns', columns)
+    labels = kwargs.pop('labels', labels)
+    kwargs['label'] = kwargs.get('label', os.path.basename(root))
+
+    return NestedSamples(data=data, columns=columns,
+                         logL=logL, logL_birth=logL_birth,
+                         labels=labels, *args, **kwargs)

docs/source/reading_writing.rst

@@ -5,14 +5,15 @@ Reading and writing
 
 .. _reading chains:
 
-Reading chain files from PolyChord, MultiNest, UltraNest, CosmoMC, or Cobaya
-============================================================================
+Reading chain files from PolyChord, MultiNest, UltraNest, NestedFit, CosmoMC, or Cobaya
+=======================================================================================
 
 If you have finished nested sampling or MCMC runs from one of:
 
 * `PolyChord <https://polychord.io>`_: https://github.com/PolyChord/PolyChordLite
 * MultiNest: https://github.com/farhanferoz/MultiNest
 * `UltraNest <https://johannesbuchner.github.io/UltraNest/index.html>`_: https://github.com/JohannesBuchner/UltraNest
+* NestedFit: https://github.com/martinit18/nested_fit 
 * `CosmoMC <https://cosmologist.info/cosmomc/readme.html>`_: https://github.com/cmbant/CosmoMC
 * `Cobaya <https://cobaya.readthedocs.io>`_: https://github.com/CobayaSampler/cobaya
 
@@ -38,6 +39,14 @@ out the examples listed here.
       from anesthetic import read_chains
       samples = read_chains("anesthetic/tests/example_data/un")
 
+* NestedFit samples, which will be an instance of the
+  :class:`anesthetic.samples.NestedSamples` class:
+
+  ::
+      
+      from anesthetic import read_chains
+      samples = read_chains("anesthetic/tests/example_data/nf")
+
 * Cobaya samples, which will be an instance of the
   :class:`anesthetic.samples.MCMCSamples` class: