Set detector type of filter to photon counting if not found in the SV…

…O header

species/analysis/emission_line.py

@@ -209,9 +209,10 @@ def fit_gaussian(self,
             Minimum number of live points (see
             https://johannesbuchner.github.io/UltraNest/issues.html).
         bounds : dict(str, tuple(float, float)), None
-            The boundaries that are used for the uniform priors. Conservative prior boundaries will
-            be estimated from the spectrum if the argument is set to ``None`` or if any of the
-            required parameters is missing in the ``bounds`` dictionary.
+            The boundaries that are used for the uniform priors of the 3 Gaussian parameters
+            (``gauss_amplitude``, ``gauss_mean``, and ``gauss_sigma``). Conservative prior
+            boundaries will be estimated from the spectrum if the argument is set to ``None``
+            or if any of the required parameters is missing in the ``bounds`` dictionary.
         output : str
             Path that is used for the output files from ``UltraNest``.
         plot_filename : str

species/analysis/photometry.py

@@ -200,7 +200,7 @@ def spectrum_to_flux(self,
                         integrand1 = transmission[indices]*flux[indices]
                         integrand2 = transmission[indices]
 
-                    if self.det_type == 'photon':
+                    elif self.det_type == 'photon':
                         # Photon counting detector
                         integrand1 = wavelength[indices]*transmission[indices]*flux[indices]
                         integrand2 = wavelength[indices]*transmission[indices]

species/data/filters.py

@@ -3,14 +3,14 @@
 """
 
 import os
-import warnings
 import urllib.request
+import warnings
 
 from typing import Optional, Tuple
-from astropy.io.votable import parse_single_table
 
 import numpy as np
 
+from astropy.io.votable import parse_single_table
 from typeguard import typechecked
 
 
@@ -44,7 +44,7 @@ def download_filter(filter_id: str) -> Tuple[Optional[np.ndarray],
         wavelength, transmission, _, _ = np.loadtxt('VisAO_rp_filter_curve.dat', unpack=True)
 
         # Not sure if energy- or photon-counting detector
-        det_type = 'energy'
+        det_type = 'photon'
 
         os.remove('VisAO_rp_filter_curve.dat')
 
@@ -55,7 +55,7 @@ def download_filter(filter_id: str) -> Tuple[Optional[np.ndarray],
         wavelength, transmission, _, _ = np.loadtxt('VisAO_ip_filter_curve.dat', unpack=True)
 
         # Not sure if energy- or photon-counting detector
-        det_type = 'energy'
+        det_type = 'photon'
 
         os.remove('VisAO_ip_filter_curve.dat')
 
@@ -66,11 +66,11 @@ def download_filter(filter_id: str) -> Tuple[Optional[np.ndarray],
         wavelength, transmission, _, _ = np.loadtxt('VisAO_zp_filter_curve.dat', unpack=True)
 
         # Not sure if energy- or photon-counting detector
-        det_type = 'energy'
+        det_type = 'photon'
 
         os.remove('VisAO_zp_filter_curve.dat')
 
-    elif filter_id == 'LCO/VisAO.Ys' or filter_id == 'Magellan/VisAO.Ys':
+    elif filter_id  in ['LCO/VisAO.Ys', 'Magellan/VisAO.Ys']:
         url = 'https://xwcl.science/magao/visao/VisAO_Ys_filter_curve.dat'
         urllib.request.urlretrieve(url, 'VisAO_Ys_filter_curve.dat')
 
@@ -81,7 +81,7 @@ def download_filter(filter_id: str) -> Tuple[Optional[np.ndarray],
         transmission = transmission[:-7]
 
         # Not sure if energy- or photon-counting detector
-        det_type = 'energy'
+        det_type = 'photon'
 
         os.remove('VisAO_Ys_filter_curve.dat')
 
@@ -91,7 +91,7 @@ def download_filter(filter_id: str) -> Tuple[Optional[np.ndarray],
 
         wavelength, transmission = np.loadtxt('alma_band6.dat', unpack=True)
 
-        det_type = 'energy'
+        det_type = 'photon'
 
         os.remove('alma_band6.dat')
 
@@ -101,7 +101,7 @@ def download_filter(filter_id: str) -> Tuple[Optional[np.ndarray],
 
         wavelength, transmission = np.loadtxt('alma_band7.dat', unpack=True)
 
-        det_type = 'energy'
+        det_type = 'photon'
 
         os.remove('alma_band7.dat')
 
@@ -144,6 +144,12 @@ def download_filter(filter_id: str) -> Tuple[Optional[np.ndarray],
             elif int(det_type) == 1:
                 det_type = 'photon'
 
+            else:
+                det_type = 'photon'
+
+                warnings.warn(f'Detector type ({det_type}) not recognized. Setting detector type '
+                              f'to photon-counting detector.')
+
             wavelength *= 1e-4  # (um)
 
         os.remove('filter.xml')

species/read/read_model.py

@@ -62,7 +62,12 @@ def __init__(self,
 
         if self.filter_name is not None:
             transmission = read_filter.ReadFilter(self.filter_name)
+
             self.wavel_range = transmission.wavelength_range()
+            self.mean_wavelength = transmission.mean_wavelength()
+
+        else:
+            self.mean_wavelength = None
 
         config_file = os.path.join(os.getcwd(), 'species_config.ini')