Add brigtness calc to comp all orbits

HDF5_Test.py

@@ -0,0 +1,19 @@
+from orbitize import results
+import matplotlib.pyplot as plt
+hdf5_filename = "my_posterior_brightness.hdf5"
+
+
+loaded_results = results.Results()  # Create blank results object for loading
+loaded_results.load_results(hdf5_filename)
+
+print(loaded_results.post)
+
+orbit_plot_fig = loaded_results.plot_orbits(
+    object_to_plot=1,
+    num_orbits_to_plot=100,
+    start_mjd=0,   
+    sep_pa_end_year=1861  
+)
+# Save or show the figure
+orbit_plot_fig.savefig("reloaded_short_bright_orbit_plot.png")
+plt.show()

HDF5_shortpos.py

@@ -0,0 +1,20 @@
+from orbitize import results
+import matplotlib.pyplot as plt
+hdf5_filename = "/home/fmolina/orbitize/tests/my_posterior_shortpos.hdf5"
+
+
+loaded_results = results.Results()  # Create blank results object for loading
+loaded_results.load_results(hdf5_filename)
+
+print(loaded_results.labels)
+
+
+orbit_plot_fig = loaded_results.plot_orbits(
+    object_to_plot=1,
+    num_orbits_to_plot=100,
+    start_mjd=0,   
+    sep_pa_end_year=1859  
+)
+# save fig
+orbit_plot_fig.savefig("/home/fmolina/orbitize/reloaded_shortpos_plot.png")
+plt.show()

mcmc_test.py

@@ -0,0 +1,82 @@
+import numpy as np
+
+import orbitize
+from orbitize import driver
+import multiprocessing as mp
+
+filename = "{}/simulated_ra_dec_data.csv".format(orbitize.DATADIR)
+
+# system parameters
+num_secondary_bodies = 1
+total_mass = 1.75  # [Msol]
+plx = 30  # [mas]
+mass_err = 0.05  # [Msol]
+plx_err = 0.12  # [mas]
+
+# MCMC parameters
+num_temps = 20
+num_walkers = 1000
+num_threads = 20  # or a different number if you prefer, mp.cpu_count() for example
+
+
+my_driver = driver.Driver(
+    filename,
+    "MCMC",
+    num_secondary_bodies,
+    total_mass,
+    plx,
+    mass_err=mass_err,
+    plx_err=plx_err,
+    mcmc_kwargs={
+        "num_temps": num_temps,
+        "num_walkers": num_walkers,
+        "num_threads": num_threads,
+    }, system_kwargs={"restrict_angle_ranges": True},
+)
+
+
+if __name__ == '__main__':
+
+    total_orbits = 50000000  # number of steps x number of walkers (at lowest temperature)
+    burn_steps = 500000  # steps to burn in per walker
+    thin = 10  # only save every 2nd step
+
+    my_driver.sampler.run_sampler(total_orbits, burn_steps=burn_steps, thin=thin)
+
+    corner_plot_fig = (
+    my_driver.sampler.results.plot_corner()
+    )  # Creates a corner plot and returns Figure object
+    corner_plot_fig.savefig(
+    "my_corner_plot.png"
+   )     # This is matplotlib.figure.Figure.savefig()
+
+    epochs = my_driver.system.data_table["epoch"]
+
+    orbit_plot_fig = my_driver.sampler.results.plot_orbits(
+    object_to_plot=1,  # Plot orbits for the first (and only, in this case) companion
+    num_orbits_to_plot=100,  # Will plot 100 randomly selected orbits of this companion
+    start_mjd=epochs[0],  # Minimum MJD for colorbar (here we choose first data epoch)
+    sep_pa_end_year=1870.0
+    )
+    orbit_plot_fig.savefig(
+    "my_orbit_plot.png"
+    )  # This is matplotlib.figure.Figure.savefig()
+
+    sma_chains, ecc_chains = my_driver.sampler.examine_chains(
+    param_list=["sma1", "ecc1"], n_walkers=5
+    )
+
+    from orbitize import results
+
+
+    hdf5_filename = "my_posterior.hdf5"
+    import os
+
+# To avoid weird behaviours, delete saved file if it already exists from a previous run of this notebook
+    if os.path.isfile(hdf5_filename):
+        os.remove(hdf5_filename)
+
+    my_driver.sampler.results.save_results(hdf5_filename)
+    loaded_results = results.Results()  # Create blank results object for loading
+    loaded_results.load_results(hdf5_filename)
+

orbitize/example_data/orbital_data_with_id.csv

@@ -0,0 +1,51 @@
+epoch,object,raoff,decoff,raoff_err,decoff_err,brightness,brightness_err
+0.0,1,0.811231477773281,0.7594337387611091,0.01,0.01,0.09358490399640425,0.01
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orbitize/example_data/reflected_light_example.csv

@@ -0,0 +1,10 @@
+epoch,object,raoff,decoff,raoff_err,decoff_err,brightness,brightness_err
+57298,1,253.72,92.35,2.98,2.85,0.5,0.1
+57606,1,236.63,127.94,9.77,9.18,0.5,0.1
+57645,1,234.52,123.39,1.79,1.03,0.5,0.1
+57946,1,210.76,152.09,1.94,1.88,0.5,0.1
+58276,1,167.49,180.87,1.61,16.97,,
+58287,1,177.67,174.6,1.67,1.67,0.5,0.1
+58365,1,165.7,185.33,3.28,3.66,0.5,0.1
+58368,1,170.38,185.94,2.52,2.74,0.5,0.1
+58414,1,161.64,176.21,13.6,14.31,,

orbitize/example_data/simulated_ra_dec_data.csv

@@ -0,0 +1,51 @@
+epoch,object,raoff,decoff,raoff_err,decoff_err
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