From cd0c00a5386e9c7ca5ab0fc9ca2b8aa922f8480d Mon Sep 17 00:00:00 2001
From: Sarah Blunt <sarah.blunt.3@gmail.com>
Date: Tue, 8 Oct 2024 16:13:07 -0700
Subject: [PATCH] mcmc running

---
 orbitize/system.py       |  7 +++++++
 tests/test_brightness.py | 11 +++++------
 2 files changed, 12 insertions(+), 6 deletions(-)

diff --git a/orbitize/system.py b/orbitize/system.py
index c016b4ba..d2ed093c 100644
--- a/orbitize/system.py
+++ b/orbitize/system.py
@@ -98,10 +98,15 @@ def __init__(
         # List of index arrays corresponding to each rv for each body
         self.rv = []
 
+        # index arrays corresponding to brightness for each body
+        self.brightness = []
+
         self.fit_astrometry = True
         radec_indices = np.where(self.data_table["quant_type"] == "radec")
         seppa_indices = np.where(self.data_table["quant_type"] == "seppa")
 
+        brightness_indices = np.where(~np.isnan(self.data_table["brightness"]))
+
         if len(radec_indices[0]) == 0 and len(seppa_indices[0]) == 0:
             self.fit_astrometry = False
         rv_indices = np.where(self.data_table["quant_type"] == "rv")
@@ -140,6 +145,7 @@ def __init__(
                 np.intersect1d(self.body_indices[body_num], seppa_indices)
             )
             self.rv.append(np.intersect1d(self.body_indices[body_num], rv_indices))
+            self.brightness.append(np.intersect1d(self.body_indices[body_num], brightness_indices))
 
         # we should track the influence of the planet(s) on each other/the star if:
         # we are not fitting massless planets and
@@ -302,6 +308,7 @@ def __init__(
 
         self.param_idx = self.basis.param_idx
 
+
     def save(self, hf):
         """
         Saves the current object to an hdf5 file
diff --git a/tests/test_brightness.py b/tests/test_brightness.py
index 36afe73e..7f938bdf 100644
--- a/tests/test_brightness.py
+++ b/tests/test_brightness.py
@@ -120,16 +120,15 @@ def test_compute_posteriors():
     ax[1].axis('equal')
     plt.savefig('visual4farrah.png')
 
-    # model = test_system.compute_model(params_arr)
+    model = test_system.compute_model(params_arr)
     # print(model)
 
-    # test_mcmc = sampler.MCMC(test_system, 1, 50, num_threads=1)
-
-    # test_mcmc.run_sampler(10)
+    test_mcmc = sampler.MCMC(test_system, 1, 50, num_threads=1)
 
+    test_mcmc.run_sampler(10)
 
 if __name__ == "__main__":
     # test_brightness_calculation()
     #test_read_input_with_brightness()
-    test_assert_brightness()
-    # test_compute_posteriors()
+    # test_assert_brightness()
+    test_compute_posteriors()