Legend **kwargs in plot_spectrum

tomasstolker · Mar 13, 2020 · bc49711 · bc49711
1 parent ab63e03
commit bc49711
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Showing 6 changed files with 29 additions and 25 deletions.
diff --git a/species/analysis/fit_planck.py b/species/analysis/fit_planck.py
@@ -55,7 +55,7 @@ def lnlike(param,
            distance,
            spectrum):
     """
-    Internal function for the likelihood probability.
+    Internal function for the likelihood function.
 
     Parameters
     ----------
@@ -177,7 +177,7 @@ def lnprob(param,
 
 class FitPlanck:
     """
-    Class for fitting Planck spectra to spectral and photometric data.
+    Class for fitting Planck spectra to photometric and/or spectroscopic data.
     """
 
     def __init__(self,
@@ -192,16 +192,16 @@ def __init__(self,
         object_name : str
             Object name in the database.
         filters : tuple(str, )
-            Filter names for which the photometry is selected. All available photometry of the
-            object are used if set to None.
+            Filter names for which the photometry is selected. All available photometric data of
+            the object are used if set to None.
         bounds : dict
             Parameter boundaries for 'teff' and 'radius'. The values should be provided either as
             float or as list of floats such that multiple Planck functions can be combined,
             e.g. ``{'teff': [(1000., 2000.), (500., 1500.)], 'radius': [(0.5, 1.5), (1.5, 2.0)]}``.
         inc_phot : bool
-            Include photometry data with the fit.
+            Include photometric data with the fit.
         inc_spec : bool
-            Include spectral data with the fit.
+            Include spectroscopic data with the fit.
 
         Returns
         -------
@@ -210,7 +210,7 @@ def __init__(self,
         """
 
         if not inc_phot and not inc_spec:
-            raise ValueError('No photometric or spectral data has been selected.')
+            raise ValueError('No photometric or spectroscopic data has been selected.')
 
         if 'teff' not in bounds or 'radius' not in bounds:
             raise ValueError('The \'bounds\' dictionary should contain \'teff\' and \'radius\'.')

diff --git a/species/data/companions.py b/species/data/companions.py
@@ -101,7 +101,10 @@ def get_data():
                          'app_mag': {'Paranal/SPHERE.IRDIS_D_H23_2': (17.94, 0.24),  # Keppler et al. 2018
                                      'Paranal/SPHERE.IRDIS_D_H23_3': (17.95, 0.17),  # Keppler et al. 2018
                                      'Paranal/SPHERE.IRDIS_D_K12_1': (16.65, 0.06),  # Müller et al. 2018
-                                     'Paranal/SPHERE.IRDIS_D_K12_2': (16.44, 0.05)}},  # Müller et al. 2018
+                                     'Paranal/SPHERE.IRDIS_D_K12_2': (16.44, 0.05),  # Müller et al. 2018
+                                     'Paranal/NACO.Lp': (14.08, 0.33),  # Stolker et al. in prep.
+                                     'Paranal/NACO.NB405': (13.91, 0.34),  # Stolker et al. in prep.
+                                     'Paranal/NACO.Mp': (13.64, 0.22)}},  # Stolker et al. in prep.
 
             'PDS 70 c': {'distance': (113.43, 0.52),
                          'app_mag': {'Paranal/NACO.NB405': (15.05, 0.59)}},  # Stolker et al. in prep.

diff --git a/species/plot/plot_color.py b/species/plot/plot_color.py
@@ -92,7 +92,7 @@ def plot_color_magnitude(boxes,
 
     """
 
-    print(f'Plotting color-magnitude diagram: {output}... ', end='', flush=True)
+    print(f'Plotting color-magnitude diagram: {output}...', end='', flush=True)
 
     model_color = ('#234398', '#f6a432', 'black')
     model_linestyle = ('-', '--', ':', '-.')
@@ -389,7 +389,7 @@ def plot_color_magnitude(boxes,
     plt.clf()
     plt.close()
 
-    print('[DONE]')
+    print(' [DONE]')
 
 
 def plot_color_color(boxes,
@@ -454,7 +454,7 @@ def plot_color_color(boxes,
         None
     """
 
-    print(f'Plotting color-color diagram: {output}... ', end='', flush=True)
+    print(f'Plotting color-color diagram: {output}...', end='', flush=True)
 
     model_color = ('#234398', '#f6a432')
     model_linestyle = ('-', '--', ':', '-.')
@@ -687,4 +687,4 @@ def plot_color_color(boxes,
     plt.clf()
     plt.close()
 
-    print('[DONE]')
+    print(' [DONE]')
diff --git a/species/plot/plot_spectrum.py b/species/plot/plot_spectrum.py
@@ -32,7 +32,7 @@ def plot_spectrum(boxes,
                   scale=('linear', 'linear'),
                   title=None,
                   offset=None,
-                  legend='upper left',
+                  legend=None,
                   figsize=(7., 5.),
                   object_type='planet',
                   quantity='flux',
@@ -63,8 +63,9 @@ def plot_spectrum(boxes,
         Title.
     offset : tuple(float, float)
         Offset for the label of the x- and y-axis.
-    legend : str, None
-        Location of the legend.
+    legend : str, tuple, dict, None
+        Location of the legend (str, tuple) or a dictionary with the ``**kwargs`` of
+        ``matplotlib.pyplot.legend``, e.g. ``{'loc': 'upper left', 'fontsize: 12.}``.
     figsize : tuple(float, float)
         Figure size.
     object_type : str
@@ -465,8 +466,11 @@ def plot_spectrum(boxes,
 
     handles, _ = ax1.get_legend_handles_labels()
 
-    if handles and legend:
-        ax1.legend(loc=legend, fontsize=10, frameon=False)
+    if handles and legend is not None:
+        if isinstance(legend, (str, tuple)):
+            ax1.legend(loc=legend, fontsize=8, frameon=False)
+        else:
+            ax1.legend(**legend)
 
     plt.savefig(os.getcwd()+'/'+output, bbox_inches='tight')
     plt.clf()

diff --git a/species/util/phot_util.py b/species/util/phot_util.py
@@ -205,8 +205,13 @@ def get_residuals(datatype,
 
             if spectrum == 'planck':
                 readmodel = read_planck.ReadPlanck(wavel_range=wavel_range)
+
                 model = readmodel.get_spectrum(model_param=parameters, spec_res=1000.)
 
+                flux_new = spectres.spectres(new_spec_wavs=wl_new,
+                                             old_spec_wavs=model.wavelength,
+                                             spec_fluxes=model.flux)
+
             else:
                 if spectrum == 'petitradtrans':
                     # TODO change back

diff --git a/species/util/plot_util.py b/species/util/plot_util.py
@@ -137,14 +137,6 @@ def update_labels(param):
         index = param.index('radius')
         param[index] = r'$R$ ($\mathregular{R_{Jup}}$)'
 
-    if 'scaling' in param:
-        index = param.index('scaling')
-        param[index] = 'Scaling'
-
-    if 'offset' in param:
-        index = param.index('offset')
-        param[index] = 'Offset'
-
     if 'teff' in param:
         index = param.index('teff')
         param[index] = r'$T_\mathregular{eff}$ (K)'