diff --git a/orbitize/example_data/reflected_light_example.csv b/orbitize/example_data/reflected_light_example.csv new file mode 100644 index 00000000..5a17cc4f --- /dev/null +++ b/orbitize/example_data/reflected_light_example.csv @@ -0,0 +1,10 @@ +epoch,object,raoff,decoff,raoff_err,decoff_err,brightness +57298,1,253.72,92.35,2.98,2.85,0.5 +57606,1,236.63,127.94,9.77,9.18,0.5 +57645,1,234.52,123.39,1.79,1.03,0.5 +57946,1,210.76,152.09,1.94,1.88,0.5 +58276,1,167.49,180.87,1.61,16.97,0.5 +58287,1,177.67,174.6,1.67,1.67,0.5 +58365,1,165.7,185.33,3.28,3.66,0.5 +58368,1,170.38,185.94,2.52,2.74,0.5 +58414,1,161.64,176.21,13.6,14.31, \ No newline at end of file diff --git a/orbitize/read_input.py b/orbitize/read_input.py index 69e2f0fe..9927c706 100644 --- a/orbitize/read_input.py +++ b/orbitize/read_input.py @@ -292,7 +292,7 @@ def read_file(filename): if have_brightness[index]: brightness = row["brightness"] else: - brightness = None + brightness = np.nan # check that "object" is an integer (instead of ABC/bcd) if not isinstance(row["object"], (int, np.int32, np.int64)): diff --git a/tests/test_brightness.py b/tests/test_brightness.py index e7b094ee..58fba946 100644 --- a/tests/test_brightness.py +++ b/tests/test_brightness.py @@ -40,9 +40,6 @@ def test_brightness_calculation(): ) ra, dec, vz, brightness = test_system.compute_all_orbits(params) - - - # TODO (farrah): make plot of brightness vs time plt.figure() plt.scatter(times, brightness) @@ -53,19 +50,20 @@ def test_brightness_calculation(): def test_read_input_with_brightness(): - # TODO (farrah): use code above as inspiration to read in a csv file with a brightness column num_secondary_bodies = 1 - # input_file = os.path.join(DATADIR, "GJ504.csv") - input_file = os.path.join(DATADIR, "betaPic.csv") + input_file = os.path.join(DATADIR, "reflected_light_example.csv") data_table = read_input.read_file(input_file) times = data_table["epoch"].value brightness_values = data_table["brightness"].value + print(data_table) - print("hello! :D ") + # TODO (Farrah): add a test that asserts the brightness column of the data table is + # what you expect (hint: check in the reflected_light_example.csv to see what + # the brightness values should be def test_compute_posteriors(): @@ -82,21 +80,29 @@ def test_compute_posteriors(): params_arr = np.array( [ - 10.0, - 0.1, - np.radians(89), - np.radians(21), - np.radians(31), - 0.0, # note: I didn't convert tau here, just picked random number - 51.5, - 1.75, + 10.0, # sma + 0.3, # ecc + np.radians(0), # inc + np.radians(45), # aop + np.radians(90), # pan + 0.0, # tau + 51.5, # plx + 1.75, # stellar maxx ] ) + epochs = np.linspace(0, 365*30, int(1e3)) + ra, dec, vz, brightness = test_system.compute_all_orbits(params_arr, epochs=epochs) + + fig, ax = plt.subplots(2, 1, figsize=(5,10)) - all_orbits = test_system.compute_all_orbits(params_arr) - print(all_orbits) - model = test_system.compute_model(params_arr) + ax[0].scatter(epochs, brightness, color=plt.cm.RdYlBu((epochs-epochs[0])/(epochs[-1] - epochs[0]))) + ax[1].scatter(ra[:,1,:], dec[:,1,:], color=plt.cm.RdYlBu((epochs-epochs[0])/(epochs[-1] - epochs[0]))) + + ax[1].axis('equal') + plt.savefig('visual4farrah.png') + + # model = test_system.compute_model(params_arr) # print(model) # test_mcmc = sampler.MCMC(test_system, 1, 50, num_threads=1) @@ -106,7 +112,5 @@ def test_compute_posteriors(): if __name__ == "__main__": # test_brightness_calculation() - # test_read_input_with_brightness() - test_compute_posteriors() - - # Test commit + test_read_input_with_brightness() + # test_compute_posteriors()