Merge f3070b1 into 1c5e488

tomasstolker · Apr 30, 2020 · aa2a10e · aa2a10e
2 parents 1c5e488 + f3070b1
commit aa2a10e
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Showing 26 changed files with 423 additions and 306 deletions.
diff --git a/requirements.txt b/requirements.txt
@@ -10,4 +10,5 @@ pymultinest ~= 2.9
 scipy ~= 1.4
 spectres ~= 2.1
 tqdm ~= 4.45
+typeguard ~= 2.7
 xlrd ~= 1.2
diff --git a/species/analysis/fit_model.py b/species/analysis/fit_model.py
@@ -11,6 +11,7 @@
 import emcee
 import numpy as np
 
+# installation of MultiNest is not possible on readthedocs 
 try:
     import pymultinest
 except:

diff --git a/species/analysis/photometry.py b/species/analysis/photometry.py
@@ -131,19 +131,6 @@ def spectrum_to_flux(self,
             raise ValueError('Calculation of the mean flux is not possible because the '
                              'wavelength array is empty.')
 
-        indices = np.where((wavelength > self.wavel_range[0]) &
-                           (wavelength < self.wavel_range[1]))[0]
-
-        if indices.size == 1:
-            raise ValueError('Calculating synthetic photometry requires more than one '
-                             'wavelength point.')
-
-        wavelength = wavelength[indices]
-        flux = flux[indices]
-
-        if error is not None:
-            error = error[indices]
-
         indices = np.where((self.wavel_range[0] <= wavelength) &
                            (wavelength <= self.wavel_range[1]))[0]
 
@@ -160,7 +147,7 @@ def spectrum_to_flux(self,
 
                 warnings.warn(f'The filter profile of {self.filter_name} '
                               f'({self.wavel_range[0]:.4f}-{self.wavel_range[1]:.4f}) extends '
-                              f' beyond the wavelength range of the spectrum ({wavelength[0]:.4f} '
+                              f'beyond the wavelength range of the spectrum ({wavelength[0]:.4f} '
                               f'-{wavelength[-1]:.4f}). The flux is set to NaN. Setting the '
                               f'\'threshold\' parameter will loosen the wavelength constraints.')
 
@@ -202,21 +189,19 @@ def spectrum_to_flux(self,
                     syn_flux = integral1/integral2
 
         if error is not None and not np.any(np.isnan(error)):
-            error_flux = np.zeros(200)
+            phot_random = np.zeros(200)
 
             for i in range(200):
-                spec_random = flux+np.random.normal(loc=0.,
-                                                    scale=1.,
-                                                    size=wavelength.shape[0])*error
-
-                spec_tmp = self.spectrum_to_flux(wavelength,
-                                                 spec_random,
-                                                 error=None,
-                                                 threshold=threshold)[0]
+                spec_random = flux + np.random.normal(loc=0.,
+                                                      scale=1.,
+                                                      size=wavelength.shape[0])*error
 
-                error_flux[i] = spec_tmp
+                phot_random[i] = self.spectrum_to_flux(wavelength,
+                                                       spec_random,
+                                                       error=None,
+                                                       threshold=threshold)[0]
 
-            error_flux = np.std(error_flux)
+            error_flux = np.std(phot_random)
 
         else:
             error_flux = None
@@ -269,21 +254,21 @@ def spectrum_to_magnitude(self,
         app_mag = self.vega_mag - 2.5*math.log10(syn_flux[0]/zp_flux)
 
         if error is not None and not np.any(np.isnan(error)):
-            error_app_mag = np.zeros(200)
+            mag_random = np.zeros(200)
 
             for i in range(200):
-                spec_random = flux+np.random.normal(loc=0.,
-                                                    scale=1.,
-                                                    size=wavelength.shape[0])*error
+                spec_random = flux + np.random.normal(loc=0.,
+                                                      scale=1.,
+                                                      size=wavelength.shape[0])*error
 
                 flux_random = self.spectrum_to_flux(wavelength,
                                                     spec_random,
                                                     error=None,
                                                     threshold=threshold)
 
-                error_app_mag[i] = self.vega_mag - 2.5*np.log10(flux_random[0]/zp_flux)
+                mag_random[i] = self.vega_mag - 2.5*np.log10(flux_random[0]/zp_flux)
 
-            error_app_mag = np.std(error_app_mag)
+            error_app_mag = np.std(mag_random)
 
         else:
             error_app_mag = None

diff --git a/species/core/box.py b/species/core/box.py
@@ -60,13 +60,20 @@ def create_box(boxtype,
 
     elif boxtype == 'photometry':
         box = PhotometryBox()
-        box.name = kwargs['name']
-        box.sptype = kwargs['sptype']
-        box.wavelength = kwargs['wavelength']
-        box.flux = kwargs['flux']
-        box.app_mag = kwargs['app_mag']
-        box.abs_mag = kwargs['abs_mag']
-        box.filter_name = kwargs['filter_name']
+        if 'name' in kwargs:
+            box.name = kwargs['name']
+        if 'sptype' in kwargs:
+            box.sptype = kwargs['sptype']
+        if 'wavelength' in kwargs:
+            box.wavelength = kwargs['wavelength']
+        if 'flux' in kwargs:
+            box.flux = kwargs['flux']
+        if 'app_mag' in kwargs:
+            box.app_mag = kwargs['app_mag']
+        if 'abs_mag' in kwargs:
+            box.abs_mag = kwargs['abs_mag']
+        if 'filter_name' in kwargs:
+            box.filter_name = kwargs['filter_name']
 
     elif boxtype == 'residuals':
         box = ResidualsBox()

diff --git a/species/data/ames_cond.py b/species/data/ames_cond.py
@@ -3,6 +3,7 @@
 """
 
 import os
+import math
 import gzip
 import tarfile
 import warnings
@@ -11,7 +12,7 @@
 import spectres
 import numpy as np
 
-from species.util import data_util
+from species.util import data_util, read_util
 
 
 def add_ames_cond(input_path,
@@ -73,12 +74,7 @@ def add_ames_cond(input_path,
     logg = []
     flux = []
 
-    wavelength = [wavel_range[0]]
-
-    while wavelength[-1] <= wavel_range[1]:
-        wavelength.append(wavelength[-1] + wavelength[-1]/(2.*spec_res))
-
-    wavelength = np.asarray(wavelength[:-1])
+    wavelength = read_util.create_wavelengths(wavel_range, spec_res)
 
     for _, _, file_list in os.walk(data_folder):
         for filename in sorted(file_list):
@@ -168,12 +164,7 @@ def add_ames_cond(input_path,
                 logg.append(logg_val)
 
                 try:
-                    flux.append(spectres.spectres(wavelength,
-                                                  data[:, 0],
-                                                  data[:, 1],
-                                                  fill=0.,
-                                                  verbose=False))
-
+                    flux.append(spectres.spectres(wavelength, data[:, 0], data[:, 1]))
                 except ValueError:
                     flux.append(np.zeros(wavelength.shape[0]))
 

diff --git a/species/data/ames_dusty.py b/species/data/ames_dusty.py
@@ -11,7 +11,7 @@
 import spectres
 import numpy as np
 
-from species.util import data_util
+from species.util import data_util, read_util
 
 
 def add_ames_dusty(input_path,
@@ -73,12 +73,7 @@ def add_ames_dusty(input_path,
     logg = []
     flux = []
 
-    wavelength = [wavel_range[0]]
-
-    while wavelength[-1] <= wavel_range[1]:
-        wavelength.append(wavelength[-1] + wavelength[-1]/(2.*spec_res))
-
-    wavelength = np.asarray(wavelength[:-1])
+    wavelength = read_util.create_wavelengths(wavel_range, spec_res)
 
     for _, _, file_list in os.walk(data_folder):
         for filename in sorted(file_list):

diff --git a/species/data/btnextgen.py b/species/data/btnextgen.py
@@ -11,7 +11,7 @@
 import numpy as np
 import pandas as pd
 
-from species.util import data_util
+from species.util import data_util, read_util
 
 
 def add_btnextgen(input_path,
@@ -77,12 +77,7 @@ def add_btnextgen(input_path,
     feh = []
     flux = []
 
-    wavelength = [wavel_range[0]]
-
-    while wavelength[-1] <= wavel_range[1]:
-        wavelength.append(wavelength[-1] + wavelength[-1]/(2.*spec_res))
-
-    wavelength = np.asarray(wavelength[:-1])
+    wavelength = read_util.create_wavelengths(wavel_range, spec_res)
 
     for _, _, file_list in os.walk(data_folder):
         for filename in sorted(file_list):

diff --git a/species/data/btsettl.py b/species/data/btsettl.py
@@ -16,7 +16,7 @@
 import spectres
 import numpy as np
 
-from species.util import data_util
+from species.util import data_util, read_util
 
 
 def add_btsettl(input_path,
@@ -76,12 +76,7 @@ def add_btsettl(input_path,
     logg = []
     flux = []
 
-    wavelength = [wavel_range[0]]
-
-    while wavelength[-1] <= wavel_range[1]:
-        wavelength.append(wavelength[-1] + wavelength[-1]/(2.*spec_res))
-
-    wavelength = np.asarray(wavelength[:-1])
+    wavelength = read_util.create_wavelengths(wavel_range, spec_res)
 
     for _, _, file_list in os.walk(data_folder):
         for filename in sorted(file_list):

diff --git a/species/data/companions.py b/species/data/companions.py
@@ -102,8 +102,8 @@ def get_data():
             'PDS 70 b': {'distance': (113.43, 0.52),
                          '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': (16.78, 0.31),  # Stolker et al. in prep.
-                                     'Paranal/SPHERE.IRDIS_D_K12_2': (16.23, 0.32),  # Stolker et al. in prep.
+                                     'Paranal/SPHERE.IRDIS_D_K12_1': [(16.78, 0.31), (16.68, 0.04)],  # Stolker et al. in prep.
+                                     'Paranal/SPHERE.IRDIS_D_K12_2': [(16.23, 0.32), (16.35, 0.07)], # Stolker et al. in prep.
                                      '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.