fixing some keyword names

scripts/make_data.py

@@ -122,13 +122,13 @@ def write_data(data, ivars, xs, pipeline_rvs, pipeline_sigmas, dates, bervs, air
 
 if __name__ == "__main__":
 
-    if True: #51 Peg
+    if False: #51 Peg
         ccf_filelist = glob.glob('/Users/mbedell/python/wobble/data/51peg/HARPS*ccf_G2_A.fits')
         data, ivars, xs, pipeline_rvs, pipeline_sigmas, dates, bervs, airms, drifts = read_data_from_fits(ccf_filelist)
         hdffile = '../data/51peg_e2ds.hdf5'
         write_data(data, ivars, xs, pipeline_rvs, pipeline_sigmas, dates, bervs, airms, drifts, ccf_filelist, hdffile)
 
-    if True: #Barnard's Star
+    if False: #Barnard's Star
         ccf_filelist = glob.glob('/Users/mbedell/python/wobble/data/barnards/HARPS*ccf_M2_A.fits')
 
         if False: # check for missing wavelength files
@@ -140,7 +140,7 @@ def write_data(data, ivars, xs, pipeline_rvs, pipeline_sigmas, dates, bervs, air
         hdffile = '../data/barnards_e2ds.hdf5'
         write_data(data, ivars, xs, pipeline_rvs, pipeline_sigmas, dates, bervs, airms, drifts, ccf_filelist, hdffile)     
 
-    if True: # HD189733
+    if False: # HD189733
         ccf_filelist = glob.glob('/Users/mbedell/python/wobble/data/HD189733/HARPS*ccf_*_A.fits')
         if False: # check for missing wavelength files
             missing_files = missing_wavelength_files(ccf_filelist)
@@ -159,3 +159,13 @@ def write_data(data, ivars, xs, pipeline_rvs, pipeline_sigmas, dates, bervs, air
         data, ivars, xs, pipeline_rvs, pipeline_sigmas, dates, bervs, airms, drifts = read_data_from_fits(e2ds_filelist, e2ds=True)
         hdffile = '../data/telluric_e2ds.hdf5'
         write_data(data, ivars, xs, pipeline_rvs, pipeline_sigmas, dates, bervs, airms, drifts, e2ds_filelist, hdffile)
+
+    if True: # beta hyi
+        ccf_filelist = glob.glob('/mnt/ceph/users/mbedell/wobble/betahyi/HARPS*ccf_*_A.fits')
+        if True: # check for missing wavelength files
+            missing_files = missing_wavelength_files(ccf_filelist)
+            np.savetxt('missing_files.txt', missing_files, fmt='%s')
+            print('{0} missing wavelength files'.format(len(missing_files)))
+        data, ivars, xs, pipeline_rvs, pipeline_sigmas, dates, bervs, airms, drifts = read_data_from_fits(ccf_filelist)
+        hdffile = '/mnt/ceph/users/mbedell/wobble/betahyi_e2ds.hdf5'
+        write_data(data, ivars, xs, pipeline_rvs, pipeline_sigmas, dates, bervs, airms, drifts, ccf_filelist, hdffile)

scripts/regularization.py

@@ -38,7 +38,7 @@ def improve_order_regularization(r, o, star_filename, tellurics_filename,
     else:
         training_model.add_telluric('tellurics', rvs_fixed=True, variable_bases=K_t)
     training_model.setup()
-    training_model.optimize(niter=0, verbose=verbose, uncertainties=False)
+    training_model.optimize(niter=0, verbose=verbose, rv_uncertainties=False)
 
     if plot:
         n = 0 # epoch to plot
@@ -206,7 +206,7 @@ def test_regularization_value(par, val, training_model, validation_model, regula
     session = wobble.utils.get_session()
     session.run(tf.global_variables_initializer()) # reset both models
 
-    training_model.optimize(niter=training_niter, feed_dict=regularization_dict, verbose=verbose, uncertainties=False)
+    training_model.optimize(niter=training_niter, feed_dict=regularization_dict, verbose=verbose, rv_uncertainties=False)
     validation_dict = {**regularization_dict}
     for c in validation_model.components:
         validation_dict[getattr(c, 'template_xs')] = getattr(training_model.results, 

scripts/script_51peg.py

@@ -66,7 +66,7 @@
         if plots:
             wobble.optimize_order(model, niter=niter, save_history=True, 
                                   basename=plot_dir+'history', movies=movies,
-                                  rv_uncertainties=True) 
+                                  epochs_to_plot=epochs, rv_uncertainties=True) 
             fig, ax = plt.subplots(1, 1, figsize=(8,5))
             ax.plot(data.dates, results.star_rvs[r] + data.bervs - np.mean(results.star_rvs[r] + data.bervs), 
                     'k.', alpha=0.8)

scripts/script_HD189733.py

@@ -55,7 +55,7 @@
         print("--- ORDER {0} ---".format(o))
         if plots:
             wobble.optimize_order(model, niter=niter, save_history=True, 
-                                  basename=plot_dir+'history', movies=movies)
+                                  basename=plot_dir+'history', epochs_to_plot=epochs, movies=movies)
             fig, ax = plt.subplots(1, 1, figsize=(8,5))
             ax.plot(data.dates, results.star_rvs[r] + data.bervs - np.mean(results.star_rvs[r] + data.bervs), 
                     'k.', alpha=0.8)

scripts/script_barnards.py

@@ -52,7 +52,7 @@
         print("--- ORDER {0} ---".format(o))
         if plots:
             wobble.optimize_order(model, niter=niter, save_history=True, 
-                                  basename=plot_dir+'history', movies=movies) 
+                                  basename=plot_dir+'history', movies=movies, epochs_to_plot=epochs) 
             fig, ax = plt.subplots(1, 1, figsize=(8,5))
             ax.plot(data.dates, results.star_rvs[r] + data.bervs - np.mean(results.star_rvs[r] + data.bervs), 
                     'k.', alpha=0.8)

wobble/history.py

@@ -150,7 +150,7 @@ def plot_synth(self, e, nframes=None, ylims=None, ylims2=None, **kwargs):
         return ani  
 
 
-    def save_plots(self, basename, epochs=[0,50], movies=True):
+    def save_plots(self, basename, epochs_to_plot=[0,50], movies=True):
         plt.scatter(np.arange(len(self.nll_history)), self.nll_history)
         ax = plt.gca()
         ax.set_yscale('log')