Type checks added to analysis.photometry

docs/tutorials/synthetic_photometry.ipynb

@@ -56,19 +56,16 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Initiating species v0.1.4... [DONE]\n",
-      "Creating species_config.ini... [DONE]\n",
+      "Initiating species v0.2.2... [DONE]\n",
       "Database: /Users/tomasstolker/applications/species/docs/tutorials/species_database.hdf5\n",
       "Data folder: /Users/tomasstolker/applications/species/docs/tutorials/data\n",
-      "Working folder: /Users/tomasstolker/applications/species/docs/tutorials\n",
-      "Creating species_database.hdf5... [DONE]\n",
-      "Creating data folder... [DONE]\n"
+      "Working folder: /Users/tomasstolker/applications/species/docs/tutorials\n"
      ]
     },
     {
      "data": {
       "text/plain": [
-       "<species.core.setup.SpeciesInit at 0x12666a358>"
+       "<species.core.setup.SpeciesInit at 0x10a93e080>"
       ]
      },
      "execution_count": 2,
@@ -102,7 +99,7 @@
     {
      "data": {
       "text/plain": [
-       "('data/plnt_Jupiter.txt', <http.client.HTTPMessage at 0x1255d8d30>)"
+       "('data/plnt_Jupiter.txt', <http.client.HTTPMessage at 0x129989cc0>)"
       ]
      },
      "execution_count": 3,
@@ -168,7 +165,6 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Adding filter: JWST/NIRCam.F115W... [DONE]\n",
       "Plotting spectrum: spectrum.png... [DONE]\n"
      ]
     }
@@ -243,7 +239,7 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Flux [W m-2 micron-1] = 2.64e-09 +/- 1.00e-13\n"
+      "Flux [W m-2 micron-1] = 2.64e-09 +/- 9.89e-14\n"
      ]
     }
    ],
@@ -268,9 +264,7 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Downloading Vega spectrum (270 kB)... [DONE]\n",
-      "Adding Vega spectrum... [DONE]\n",
-      "Apparent magnitude [mag] = 0.49 +/- 4.05e-05\n"
+      "Apparent magnitude [mag] = 0.49 +/- 4.10e-05\n"
      ]
     }
    ],

species/analysis/photometry.py

@@ -7,9 +7,13 @@
 import warnings
 import configparser
 
+from typing import Optional, Union, Tuple, List
+
 import h5py
 import numpy as np
 
+from typeguard import typechecked
+
 from species.data import database
 from species.read import read_filter, read_calibration
 from species.util import phot_util
@@ -20,8 +24,9 @@ class SyntheticPhotometry:
     Class for calculating synthetic photometry from a spectrum.
     """
 
+    @typechecked
     def __init__(self,
-                 filter_name):
+                 filter_name: str) -> None:
         """
         Parameters
         ----------
@@ -48,7 +53,8 @@ def __init__(self,
 
         self.database = config['species']['database']
 
-    def zero_point(self):
+    @typechecked
+    def zero_point(self) -> np.float64:
         """
         Internal function for calculating the zero point of the provided ``filter_name``.
 
@@ -89,22 +95,25 @@ def zero_point(self):
 
         return self.spectrum_to_flux(wavelength_crop, flux_crop)[0]
 
+    @typechecked
     def spectrum_to_flux(self,
-                         wavelength,
-                         flux,
-                         error=None,
-                         threshold=0.05):
+                         wavelength: np.ndarray,
+                         flux: np.ndarray,
+                         error: Optional[np.ndarray] = None,
+                         threshold: Optional[float] = 0.05) -> Tuple[
+                             Union[np.float32, np.float64],
+                             Union[Optional[np.float32], Optional[np.float64]]]:
         """
         Function for calculating the average flux from a spectrum and a filter profile. The error
         is propagated by sampling 200 random values from the error distributions.
 
         Parameters
         ----------
-        wavelength : numpy.ndarray
+        wavelength : np.ndarray
             Wavelength points (um).
-        flux : numpy.ndarray
+        flux : np.ndarray
             Flux (W m-2 um-1).
-        error : numpy.ndarray
+        error : np.ndarray
             Uncertainty (W m-2 um-1). Not used if set to None.
         threshold : float, None
             Transmission threshold (value between 0 and 1). If the minimum transmission value is
@@ -208,24 +217,27 @@ def spectrum_to_flux(self,
 
         return syn_flux, error_flux
 
+    @typechecked
     def spectrum_to_magnitude(self,
-                              wavelength,
-                              flux,
-                              error=None,
-                              distance=None,
-                              threshold=0.05):
+                              wavelength: np.ndarray,
+                              flux: np.ndarray,
+                              error: Optional[Union[np.ndarray, List[np.ndarray]]] = None,
+                              distance: Optional[Tuple[float, Optional[float]]] = None,
+                              threshold: Optional[float] = 0.05) -> Tuple[
+                                  Tuple[float, Optional[float]],
+                                  Optional[Tuple[Optional[float], Optional[float]]]]:
         """
         Function for calculating the apparent and absolute magnitude from a spectrum and a
         filter profile. The error is propagated by sampling 200 random values from the error
         distributions.
 
         Parameters
         ----------
-        wavelength : numpy.ndarray
+        wavelength : np.ndarray
             Wavelength points (um).
-        flux : numpy.ndarray
+        flux : np.ndarray
             Flux (W m-2 um-1).
-        error : numpy.ndarray, list(numpy.ndarray), None
+        error : np.ndarray, list(np.ndarray), None
             Uncertainty (W m-2 um-1).
         distance : tuple(float, float), None
             Distance and uncertainty (pc). No absolute magnitude is calculated if set to None.
@@ -289,10 +301,11 @@ def spectrum_to_magnitude(self,
 
         return (app_mag, error_app_mag), (abs_mag, error_abs_mag)
 
+    @typechecked
     def magnitude_to_flux(self,
-                          magnitude,
-                          error=None,
-                          zp_flux=None):
+                          magnitude: float,
+                          error: Optional[float] = None,
+                          zp_flux: Optional[float] = None) -> Tuple[np.float64, np.float64]:
         """
         Function for converting a magnitude to a flux.
 
@@ -301,9 +314,9 @@ def magnitude_to_flux(self,
         magnitude : float
             Magnitude (mag).
         error : float, None
-            Error (mag). Not used if set to None.
-        zp_flux : float
-            Zero-point flux (W m-2 um-1). The value is calculated if set to None.
+            Error (mag). Not used if set to ``None``.
+        zp_flux : float, None
+            Zero-point flux (W m-2 um-1). The value is calculated if set to ``None``.
 
         Returns
         -------
@@ -328,30 +341,36 @@ def magnitude_to_flux(self,
 
         return flux, error_flux
 
+    @typechecked
     def flux_to_magnitude(self,
-                          flux,
-                          error=None,
-                          distance=None):
+                          flux: float,
+                          error: Optional[Union[float, np.ndarray]] = None,
+                          distance: Optional[Union[Tuple[float, Optional[float]],
+                                                   Tuple[np.ndarray, Optional[np.ndarray]]]] = None
+                          ) -> Tuple[Union[Tuple[float, Optional[float]],
+                                           Tuple[np.ndarray, Optional[np.ndarray]]],
+                                     Union[Tuple[float, Optional[float]],
+                                           Tuple[np.ndarray, Optional[np.ndarray]]]]:
         """
         Function for converting a flux into a magnitude.
 
         Parameters
         ----------
-        flux : float, numpy.ndarray
+        flux : float, np.ndarray
             Flux (W m-2 um-1).
-        error : float, numpy.ndarray, None
+        error : float, np.ndarray, None
             Uncertainty (W m-2 um-1). Not used if set to None.
-        distance : tuple(float, float), tuple(numpy.ndarray, numpy.ndarray)
+        distance : tuple(float, float), tuple(np.ndarray, np.ndarray)
             Distance and uncertainty (pc). The returned absolute magnitude is set to None in case
             ``distance`` is set to None. The error is not propagated into the error on the absolute
             magnitude in case the distance uncertainty is set to None, for example
             ``distance=(20., None)``
 
         Returns
         -------
-        tuple(float, float), tuple(numpy.ndarray, numpy.ndarray)
+        tuple(float, float), tuple(np.ndarray, np.ndarray)
             Apparent magnitude and uncertainty (mag).
-        tuple(float, float), tuple(numpy.ndarray, numpy.ndarray)
+        tuple(float, float), tuple(np.ndarray, np.ndarray)
             Absolute magnitude and uncertainty (mag).
         """
 

species/data/companions.py

@@ -2,8 +2,14 @@
 Module for extracting data of directly imaged planets and brown dwarfs.
 """
 
+from typing import Union, Dict, Tuple, List
 
-def get_data():
+from typeguard import typechecked
+
+
+@typechecked
+def get_data() -> Dict[str, Dict[str, Union[Tuple[float, float],
+                       Dict[str, Union[Tuple[float, float], List[Tuple[float, float]]]]]]]:
     """
     Function for extracting a dictionary with the distances (pc) and apparent magnitudes of
     directly imaged planets and brown dwarfs.

species/read/read_filter.py

@@ -5,7 +5,7 @@
 import os
 import configparser
 
-from typing import Tuple
+from typing import Union, Tuple
 
 import h5py
 import numpy as np
@@ -94,7 +94,8 @@ def interpolate_filter(self) -> interpolate.interp1d:
                         fill_value=float('nan'))
 
     @typechecked
-    def wavelength_range(self) -> Tuple[float, float]:
+    def wavelength_range(self) -> Tuple[Union[np.float32, np.float64],
+                                        Union[np.float32, np.float64]]:
         """
         Extract the wavelength range of the filter profile.
 
@@ -108,7 +109,7 @@ def wavelength_range(self) -> Tuple[float, float]:
 
         data = self.get_filter()
 
-        return np.amin(data[0, ]), np.amax(data[0, ])
+        return data[0, 0], data[0, -1]
 
     @typechecked
     def mean_wavelength(self) -> float: