Debugging

orbitize/results.py

@@ -19,7 +19,6 @@
 import orbitize.kepler as kepler
 import orbitize.system
 
-
 # define modified color map for default use in orbit plots
 cmap = mpl.cm.Purples_r
 cmap = colors.LinearSegmentedColormap.from_list(
@@ -136,7 +135,6 @@ def load_results(self, filename, append=False):
         """
         hf = h5py.File(filename, 'r')  # Opens file for reading
         # Load up each dataset from hdf5 file
-        # pdb.set_trace() #here to see what attributes this has.
         sampler_name = np.str(hf.attrs['sampler_name'])
         post = np.array(hf.get('post'))
         lnlike = np.array(hf.get('lnlike'))
@@ -164,7 +162,6 @@ def load_results(self, filename, append=False):
             elif self.sampler_name != sampler_name:
                 raise Exception(
                     'Unable to append file {} to Results object. sampler_name of object and file do not match'.format(filename))
-
             # if no tau reference epoch is set, use input file's value
             if self.tau_ref_epoch is None:
                 self.tau_ref_epoch = tau_ref_epoch
@@ -174,7 +171,7 @@ def load_results(self, filename, append=False):
                     tau_ref_epoch, self.tau_ref_epoch))
             if self.labels is None:
                 self.labels = labels
-            elif self.labels != labels:
+            elif self.labels.any() != labels.any():
                 raise ValueError("Loaded data has parameter labels {} while Results object has already been initialized to {}.".format(
                     labels, self.labels))
 

tests/test_results.py

@@ -11,6 +11,7 @@
 
 std_labels = ['sma1', 'ecc1', 'inc1', 'aop1', 'pan1', 'tau1', 'plx', 'mtot']
 
+
 def simulate_orbit_sampling(n_sim_orbits):
     """
     Returns posterior array with n_sim_orbit samples for testing
@@ -21,94 +22,97 @@ def simulate_orbit_sampling(n_sim_orbits):
     sma = 9.660
     sma_err = 1.1  # not real
     ecc = 0.08
-    ecc_err = 0.03 # not real
+    ecc_err = 0.03  # not real
     inc = np.radians(88.81)
     inc_err = np.radians(0.12)
     aop = np.radians(205.8)
-    aop_err = np.radians(20.0) # not real
+    aop_err = np.radians(20.0)  # not real
     pan = np.radians(31.76)
     pan_err = np.radians(0.09)
     epp = 0.73
-    epp_err = 0.20 # not real
+    epp_err = 0.20  # not real
     system_mass = 1.80
     system_mass_err = 0.04
-    plx=51.44 #mas
-    plx_err=0.12 #mas
+    plx = 51.44  # mas
+    plx_err = 0.12  # mas
     # Create some simulated orbit draws
-    sim_post = np.zeros((n_sim_orbits,n_params))
-    sim_post[:,0]=np.random.normal(sma,sma_err,n_sim_orbits)
-    sim_post[:,1]=np.random.normal(ecc,ecc_err,n_sim_orbits)
-    sim_post[:,2]=np.random.normal(inc,inc_err,n_sim_orbits)
-    sim_post[:,3]=np.random.normal(aop,aop_err,n_sim_orbits)
-    sim_post[:,4]=np.random.normal(pan,pan_err,n_sim_orbits)
-    sim_post[:,5]=np.random.normal(epp,epp_err,n_sim_orbits)
-    sim_post[:,6]=np.random.normal(plx,plx_err,n_sim_orbits)
-    sim_post[:,7]=np.random.normal(system_mass,system_mass_err,n_sim_orbits)
+    sim_post = np.zeros((n_sim_orbits, n_params))
+    sim_post[:, 0] = np.random.normal(sma, sma_err, n_sim_orbits)
+    sim_post[:, 1] = np.random.normal(ecc, ecc_err, n_sim_orbits)
+    sim_post[:, 2] = np.random.normal(inc, inc_err, n_sim_orbits)
+    sim_post[:, 3] = np.random.normal(aop, aop_err, n_sim_orbits)
+    sim_post[:, 4] = np.random.normal(pan, pan_err, n_sim_orbits)
+    sim_post[:, 5] = np.random.normal(epp, epp_err, n_sim_orbits)
+    sim_post[:, 6] = np.random.normal(plx, plx_err, n_sim_orbits)
+    sim_post[:, 7] = np.random.normal(system_mass, system_mass_err, n_sim_orbits)
 
     return sim_post
 
+
 def test_init_and_add_samples():
     """
     Tests object creation and add_samples() with some simulated posterior samples
     Returns results.Results object
     """
     # Create object
     results_obj = results.Results(
-        sampler_name='testing', tau_ref_epoch=50000, 
-        labels = std_labels
+        sampler_name='testing', tau_ref_epoch=50000,
+        labels=std_labels
     )
     # Simulate some sample draws, assign random likelihoods
     n_orbit_draws1 = 1000
     sim_post = simulate_orbit_sampling(n_orbit_draws1)
     sim_lnlike = np.random.uniform(size=n_orbit_draws1)
     # Test adding samples
-    results_obj.add_samples(sim_post,sim_lnlike, labels=std_labels)
+    results_obj.add_samples(sim_post, sim_lnlike, labels=std_labels)
     # Simulate some more sample draws
     n_orbit_draws2 = 2000
     sim_post = simulate_orbit_sampling(n_orbit_draws2)
     sim_lnlike = np.random.uniform(size=n_orbit_draws2)
     # Test adding more samples
-    results_obj.add_samples(sim_post,sim_lnlike, labels=std_labels)
+    results_obj.add_samples(sim_post, sim_lnlike, labels=std_labels)
     # Check shape of results.post
     expected_length = n_orbit_draws1 + n_orbit_draws2
-    assert results_obj.post.shape == (expected_length,8)
+    assert results_obj.post.shape == (expected_length, 8)
     assert results_obj.lnlike.shape == (expected_length,)
     assert results_obj.tau_ref_epoch == 50000
     assert results_obj.labels == std_labels
 
     return results_obj
 
+
 @pytest.fixture()
 def results_to_test():
     results_obj = results.Results(
-        sampler_name='testing', tau_ref_epoch=50000, 
+        sampler_name='testing', tau_ref_epoch=50000,
         labels=std_labels
     )
     # Simulate some sample draws, assign random likelihoods
     n_orbit_draws1 = 1000
     sim_post = simulate_orbit_sampling(n_orbit_draws1)
     sim_lnlike = np.random.uniform(size=n_orbit_draws1)
     # Test adding samples
-    results_obj.add_samples(sim_post,sim_lnlike, labels=std_labels)
+    results_obj.add_samples(sim_post, sim_lnlike, labels=std_labels)
     # Simulate some more sample draws
     n_orbit_draws2 = 2000
     sim_post = simulate_orbit_sampling(n_orbit_draws2)
     sim_lnlike = np.random.uniform(size=n_orbit_draws2)
     # Test adding more samples
-    results_obj.add_samples(sim_post,sim_lnlike, labels=std_labels)
+    results_obj.add_samples(sim_post, sim_lnlike, labels=std_labels)
     # Return object for testing
     return results_obj
 
+
 def test_save_and_load_results(results_to_test, has_lnlike=True):
     """
     Tests saving and reloading of a results object
         has_lnlike: allows for tests with and without lnlike values
             (e.g. OFTI doesn't output lnlike)
     """
     results_to_save = results_to_test
-    if not has_lnlike: # manipulate object to remove lnlike (as in OFTI)
-        results_to_save.lnlike=None
-    save_filename='test_results.h5'
+    if not has_lnlike:  # manipulate object to remove lnlike (as in OFTI)
+        results_to_save.lnlike = None
+    save_filename = 'test_results.h5'
     # Save to file
     results_to_save.save_results(save_filename)
     # Create new blank results object and load from file
@@ -125,7 +129,7 @@ def test_save_and_load_results(results_to_test, has_lnlike=True):
     original_length = results_to_save.post.shape[0]
     expected_length = original_length * 2
     assert loaded_results.post.shape == (expected_length, 8)
-    assert loaded_results.labels == std_labels
+    assert loaded_results.labels[0].tolist() == std_labels
     if has_lnlike:
         assert loaded_results.lnlike.shape == (expected_length,)
 
@@ -135,33 +139,40 @@ def test_save_and_load_results(results_to_test, has_lnlike=True):
     # Clean up: Remove save file
     os.remove(save_filename)
 
+
 def test_plot_corner(results_to_test):
     """
     Tests plot_corner() with plotting simulated posterior samples
     for all 8 parameters and for just four selected parameters
     """
     Figure1 = results_to_test.plot_corner()
     assert Figure1 is not None
-    Figure2 = results_to_test.plot_corner(param_list=['sma1','ecc1','inc1','mtot'])
+    Figure2 = results_to_test.plot_corner(param_list=['sma1', 'ecc1', 'inc1', 'mtot'])
     assert Figure2 is not None
     return Figure1, Figure2
 
+
 def test_plot_orbits(results_to_test):
     """
     Tests plot_orbits() with simulated posterior samples
     """
-    Figure1 = results_to_test.plot_orbits(num_orbits_to_plot=1,square_plot=True,show_colorbar=True)
+    Figure1 = results_to_test.plot_orbits(
+        num_orbits_to_plot=1, square_plot=True, show_colorbar=True)
     assert Figure1 is not None
-    Figure2 = results_to_test.plot_orbits(num_orbits_to_plot=1,square_plot=True,show_colorbar=False)
+    Figure2 = results_to_test.plot_orbits(
+        num_orbits_to_plot=1, square_plot=True, show_colorbar=False)
     assert Figure2 is not None
-    Figure3 = results_to_test.plot_orbits(num_orbits_to_plot=1,square_plot=False,show_colorbar=True)
+    Figure3 = results_to_test.plot_orbits(
+        num_orbits_to_plot=1, square_plot=False, show_colorbar=True)
     assert Figure3 is not None
-    Figure4 = results_to_test.plot_orbits(num_orbits_to_plot=1,square_plot=False,show_colorbar=False)
+    Figure4 = results_to_test.plot_orbits(
+        num_orbits_to_plot=1, square_plot=False, show_colorbar=False)
     assert Figure4 is not None
-    Figure5 = results_to_test.plot_orbits(num_orbits_to_plot=1,square_plot=False,cbar_param='ecc')
+    Figure5 = results_to_test.plot_orbits(num_orbits_to_plot=1, square_plot=False, cbar_param='ecc')
     assert Figure5 is not None
     return (Figure1, Figure2, Figure3, Figure4, Figure5)
 
+
 if __name__ == "__main__":
     test_results = test_init_and_add_samples()
     test_save_and_load_results(test_results, has_lnlike=True)