fix for --plot_traj: - saving `q_pos_traj_0` and not `q_pos_0` - saving under `qpos_traj.dat`

Codes/main.py

@@ -554,7 +554,7 @@ if __name__ == '__main__':
         sampler.dict_of_trajectories = dict(
             H_p_logL_logP=[],
             pmom_trajs=[],
-            qpos=[],
+            qpos_traj=[],
             dlogL=[],
             dlogTrajPi_traj=[],
             lengths=[]
@@ -650,10 +650,10 @@ if __name__ == '__main__':
         if RUN_CONST.plot_traj:
             np.savetxt(sampler.plot_traj_dir + 'H_p_logL_logP.dat', sampler.dict_of_trajectories['H_p_logL_logP'])
             np.savetxt(sampler.plot_traj_dir + 'pmom_trajs.dat', sampler.dict_of_trajectories['pmom_trajs'])
-            np.savetxt(sampler.plot_traj_dir + 'qpos.dat', sampler.dict_of_trajectories['qpos'])
+            np.savetxt(sampler.plot_traj_dir + 'qpos_traj.dat', sampler.dict_of_trajectories['qpos_traj'])
             np.savetxt(sampler.plot_traj_dir + 'dlogL.dat', sampler.dict_of_trajectories['dlogL'])
             np.savetxt(sampler.plot_traj_dir + 'dlogTrajPi_traj.dat', sampler.dict_of_trajectories['dlogTrajPi_traj'])
-            np.savetxt(sampler.plot_traj_dir + 'lengths.dat', sampler.dict_of_trajectories['lengths'])
+            np.savetxt(sampler.plot_traj_dir + 'lengths.dat', sampler.dict_of_trajectories['lengths'], fmt='%.0f')
 
         # Make a walker and corner plots of the chain in phase1
         sampler.plot_corner(sis=False, reweighted=False, priors=True, save=True, outdir=outdir + 'plots/phase1/', in_comp_mass=False)
@@ -1448,10 +1448,10 @@ if __name__ == '__main__':
         if RUN_CONST.plot_traj:
             np.savetxt(sampler.plot_traj_dir + 'H_p_logL_logP.dat', sampler.dict_of_trajectories['H_p_logL_logP'])
             np.savetxt(sampler.plot_traj_dir + 'pmom_trajs.dat', sampler.dict_of_trajectories['pmom_trajs'])
-            np.savetxt(sampler.plot_traj_dir + 'qpos.dat', sampler.dict_of_trajectories['qpos'])
+            np.savetxt(sampler.plot_traj_dir + 'qpos_traj.dat', sampler.dict_of_trajectories['qpos_traj'])
             np.savetxt(sampler.plot_traj_dir + 'dlogL.dat', sampler.dict_of_trajectories['dlogL'])
             np.savetxt(sampler.plot_traj_dir + 'dlogTrajPi_traj.dat', sampler.dict_of_trajectories['dlogTrajPi_traj'])
-            np.savetxt(sampler.plot_traj_dir + 'lengths.dat', sampler.dict_of_trajectories['lengths'])
+            np.savetxt(sampler.plot_traj_dir + 'lengths.dat', sampler.dict_of_trajectories['lengths'], fmt='%.0f')
 
         sampler.plot_all_corners()
         sampler.plot_autocorrelations_of_parameters()

Library/BNS_HMC_Tools.py

@@ -48,7 +48,8 @@ def NumericalGradientLeapfrog_ThreeDetectors(q_pos_0, logL_0, dlogL_0, randGen,
 			H_p_logL_logP_0 = [H_0, 0.5 * (p_mom_0**2).sum(), logL_0, logTrajPi_0]
 			sampler.dict_of_trajectories['H_p_logL_logP'].append(H_p_logL_logP_0)
 			sampler.dict_of_trajectories['pmom_trajs'].append(p_mom_0.tolist())
-			sampler.dict_of_trajectories['qpos'].append(q_pos_0.tolist())
+			q_pos_traj_0 = sampler.q_pos_to_q_pos_traj(q_pos_0)
+			sampler.dict_of_trajectories['qpos_traj'].append(q_pos_traj_0.tolist())
 			sampler.dict_of_trajectories['dlogL'].append(dlogL_0)
 			dlogTrajPi_0 = sampler.traj_prior_gradients.calculate_dlogPi_np(qpos_dict_0)
 			sampler.dict_of_trajectories['dlogTrajPi_traj'].append(dlogTrajPi_0.tolist())
@@ -90,13 +91,13 @@ def NumericalGradientLeapfrog_ThreeDetectors(q_pos_0, logL_0, dlogL_0, randGen,
 			H_p_logL_logP_0 = [0, 0, 0, 0]
 			sampler.dict_of_trajectories['H_p_logL_logP'].append(0)
 			sampler.dict_of_trajectories['pmom_trajs'].append([0]*sampler.n_dim)
-			sampler.dict_of_trajectories['qpos'].append([0]*sampler.n_dim)
+			sampler.dict_of_trajectories['qpos_traj'].append([0]*sampler.n_dim)
 			sampler.dict_of_trajectories['dlogL'].append(0)
 			sampler.dict_of_trajectories['dlogTrajPi_traj'].append([0]*sampler.n_dim)
 		for i in range(len(pt_fit_traj)):
 			sampler.dict_of_trajectories['H_p_logL_logP'].append(H_p_logL_logP_traj[i])
 			sampler.dict_of_trajectories['pmom_trajs'].append(pmom_traj[i])
-			sampler.dict_of_trajectories['qpos'].append(pt_fit_traj[i])
+			sampler.dict_of_trajectories['qpos_traj'].append(pt_fit_traj[i])
 			sampler.dict_of_trajectories['dlogL'].append(dlogL_fit_traj[i])
 			sampler.dict_of_trajectories['dlogTrajPi_traj'].append(dlogTrajPi_traj[i])
 		sampler.dict_of_trajectories['lengths'].append(lengthT)

Tests/plot_trajectory.py

@@ -79,8 +79,11 @@ search_trajectory_inv_functions = get_trajectory_inverse_functions(search_trajec
 # dict_trajectory_parameters_keys = get_dict_trajectory_parameters_keys(search_parameter_keys, sampler_dict['trajectory_parameters_keys'])
 dict_parameters_offsets = sampler_dict['parameters_offsets']
 
-
-pt_fit_traj_file = outdir_plot_traj + 'qpos.dat'
+# For a long time I used to save the positions of the trajectories under `qpos.dat` and then renamed for `qpos_traj.dat` because I am actually saving the "trajectory" parameters values.
+if os.path.isfile(outdir_plot_traj + 'qpos.dat'):
+    pt_fit_traj_file = outdir_plot_traj + 'qpos.dat'
+else:
+    pt_fit_traj_file = outdir_plot_traj + 'qpos_traj.dat'
 dlogL_file = outdir_plot_traj + 'dlogL.dat'
 H_p_logL_logP_file = outdir_plot_traj + 'H_p_logL_logP.dat'
 pmom_trajs_file = outdir_plot_traj + 'pmom_trajs.dat'