Begin testing TFR likelihood

notebooks/Analyse_chain.ipynb

@@ -1,11 +1,9 @@
 {
  "cells": [
   {
-   "cell_type": "code",
-   "execution_count": 1,
-   "id": "40ad2d23-227d-4101-a195-f3b70fe0e33b",
+   "cell_type": "raw",
+   "id": "274fbd8b-2272-443c-b71d-4fcbc8946167",
    "metadata": {},
-   "outputs": [],
    "source": [
     "import numpy as np\n",
     "import matplotlib.pyplot as plt\n",

notebooks/analysis.py

@@ -327,17 +327,18 @@ def crop_velmass_to_borg(ini_file, field_type):
     return true_field
 
 
-def get_spectra(ini_name, dirname, nframe, iter_max, iter_min, which_field='delta', cut_field=True, mock_type='borg'):
+def get_spectra(ini_name, dirname, nframe, iter_max, iter_min, which_field='delta', cut_field=True, mock_type='borg', MAS=''):
     
     # Which steps to use
     all_mcmc = get_mcmc_steps(dirname, nframe, iter_max, iter_min=iter_min)
     
-    if which_field == 'delta':
-        MAS = "CIC"
-    elif which_field == 'ics':
-        MAS = None
-    else:
-        raise NotImplementedError
+    if MAS == '':
+        if which_field == 'delta':
+            MAS = "CIC"
+        elif which_field == 'ics':
+            MAS = None
+        else:
+            raise NotImplementedError
     
     # Compute original power spectrum
     if mock_type == 'borg':
@@ -350,6 +351,11 @@ def get_spectra(ini_name, dirname, nframe, iter_max, iter_min, which_field='delt
             boxsize = get_borg_Lbox(ini_name)
     else:
         raise NotImplementedError
+        
+    # Turn to overdensity
+    if which_field == 'delta':
+        delta1 = (1. + delta1) / (1. + delta1).mean() - 1.
+        
     print("BOXSIZE", boxsize)
     Pk = PKL.Pk(delta1.astype(np.float32), boxsize, axis=0, MAS=MAS, threads=1, verbose=True)
     k      = Pk.k3D