From 74800fa19947cd65367d0754df5dab21ab769895 Mon Sep 17 00:00:00 2001
From: calumgordon <calumrossgordon@hotmail.com>
Date: Thu, 11 Apr 2024 23:59:07 +0200
Subject: [PATCH] fixes to gamma gamma

---
 lya_2pt/correlation.py | 26 +++++++++++++++++---------
 lya_2pt/interface.py   |  5 +++--
 2 files changed, 20 insertions(+), 11 deletions(-)

diff --git a/lya_2pt/correlation.py b/lya_2pt/correlation.py
index 0578082..8a38047 100644
--- a/lya_2pt/correlation.py
+++ b/lya_2pt/correlation.py
@@ -56,6 +56,8 @@ def compute_xi(healpix_id):
     num_pairs_grid = np.zeros(total_size, dtype=np.int32)
     gamma_grid = np.zeros(total_size)
 
+    sigma_v = globals.gamma_z_error
+
     for tracer1 in globals.tracers1[healpix_id]:
         with globals.lock:
             xicounter = round(globals.counter.value * 100. / globals.num_tracers, 2)
@@ -72,7 +74,16 @@ def compute_xi(healpix_id):
             globals.rp_max, globals.rt_max
             )
 
+        #calculate rest frame waves and gamma function of tracer 1
+        lambda_rest_1 = 1215.67 * (1 + tracer1.z) / (1 + tracer1.z_qso)
+        gamma_1 = gen_gamma(lambda_rest_1,sigma_v)
+
         for tracer2 in neighbours:
+
+            #calculate rest frame waves and gamma function of tracer 2
+            lambda_rest_2 = 1215.67 * (1 + tracer2.z) / (1 + tracer2.z_qso)
+            gamma_2 = gen_gamma(lambda_rest_2,sigma_v)
+
             angle = get_angle(
                 tracer1.x_cart, tracer1.y_cart, tracer1.z_cart, tracer1.ra, tracer1.dec,
                 tracer2.x_cart, tracer2.y_cart, tracer2.z_cart, tracer2.ra, tracer2.dec
@@ -81,8 +92,8 @@ def compute_xi(healpix_id):
             compute_xi_pair(
                 tracer1.deltas, tracer1.weights, tracer1.z, tracer1.dist_c, tracer1.dist_m,
                 tracer2.deltas, tracer2.weights, tracer2.z, tracer2.dist_c, tracer2.dist_m,
-                angle, xi_grid, weights_grid, rp_grid, rt_grid, z_grid, num_pairs_grid, 
-                tracer1.z_qso, tracer2.z_qso 
+                angle, xi_grid, weights_grid, rp_grid, rt_grid, z_grid, num_pairs_grid, gamma_grid,
+                gamma_1, gamma_2
                 )
 
     # Normalize correlation and average coordinate grids
@@ -100,8 +111,8 @@ def compute_xi(healpix_id):
 def compute_xi_pair(
         deltas1, weights1, z1, dist_c1, dist_m1,
         deltas2, weights2, z2, dist_c2, dist_m2, angle,
-        xi_grid, weights_grid, rp_grid, rt_grid, z_grid, num_pairs_grid,
-        z_qso1,z_qso2
+        xi_grid, weights_grid, rp_grid, rt_grid, z_grid, num_pairs_grid, gamma_grid,
+        gamma_1,gamma_2
 ):
     sin_angle = np.sin(angle / 2)
     cos_angle = np.cos(angle / 2)
@@ -138,8 +149,5 @@ def compute_xi_pair(
             z_grid[bins] += (z1[i] + z2[j]) / 2 * weight12
             num_pairs_grid[bins] += 1
 
-            #GAMMA FUNCTION
-            sigma_v = globals.gamma_z_error
-            lambda_rest_i = 1215.67 * (1 + z1) / (1 + z_qso1)
-            lambda_rest_j = 1215.67 * (1 + z2)/ (1 + z_qso2)
-            gamma_grid[bins] += gen_gamma(lambda_rest_i,sigma_v) * gen_gamma(lambda_rest_j,sigma_v) * weight12
\ No newline at end of file
+            #<gamma gamma>
+            gamma_grid[bins] += gamma_1[i] * gamma_2[j] * weight12
\ No newline at end of file
diff --git a/lya_2pt/interface.py b/lya_2pt/interface.py
index c1e8c92..c0b6082 100644
--- a/lya_2pt/interface.py
+++ b/lya_2pt/interface.py
@@ -16,7 +16,7 @@
 accepted_options = [
     "nside", "num-cpu", "z_min", "z_max", "rp_min", "rp_max", "rt_max",
     "num_bins_rp", "num_bins_rt", "num_bins_rp_model", "num_bins_rt_model",
-    "rejection_fraction", "get-old-distortion"
+    "rejection_fraction", "get-old-distortion",'gamma_z_error'
 ]
 
 defaults = {
@@ -32,7 +32,8 @@
     "num_bins_rp_model": 50,
     "num_bins_rt_model": 50,
     "rejection_fraction": 0.99,
-    "get-old-distortion": True
+    "get-old-distortion": True,
+    "gamma_z_error": 0
 }