Reading corr_len and corr_amp parameters from bounds and use default …

…values otherwise, added effective_width method to ReadFilter, minor maintenance
tomasstolker · Jan 4, 2021 · 40bbe15 · 40bbe15
1 parent 6bafb97
commit 40bbe15
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Showing 8 changed files with 36 additions and 16 deletions.
diff --git a/LICENSE b/LICENSE
@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) 2018-2020 Tomas Stolker
+Copyright (c) 2018-2021 Tomas Stolker
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

diff --git a/Makefile b/Makefile
@@ -1,4 +1,4 @@
-.PHONY: help pypi ppypi-test docs coverage test clean
+.PHONY: help pypi pypi-test docs coverage test clean
 
 help:
 	@echo "pypi - submit package to the PyPI server"
@@ -29,7 +29,7 @@ docs:
 	$(MAKE) -C docs html
 
 coverage:
-	coverage run -m pytest
+	coverage run --source=species -m pytest
 	coverage report -m
 
 test:

diff --git a/docs/conf.py b/docs/conf.py
@@ -171,7 +171,7 @@
 #  dir menu entry, description, category)
 texinfo_documents = [
     (master_doc, 'species', 'species Documentation',
-     author, 'species', 'Toolkit for atmospheric characterization of exoplanets and brown dwarf',
+     author, 'species', 'Toolkit for atmospheric characterization of directly imaged exoplanets',
      'Miscellaneous'),
 ]
 
@@ -194,4 +194,4 @@
 epub_exclude_files = ['search.html']
 
 
-# -- Extension configuration -------------------------------------------------
+# -- Extension configuration -------------------------------------------------
diff --git a/docs/requirements.txt b/docs/requirements.txt
@@ -1,3 +1,3 @@
-nbsphinx ~= 0.7
-pandoc ~= 1.0
-jupyter ~= 1.0
+nbsphinx
+pandoc
+jupyter
diff --git a/docs/tutorials/spectral_library.ipynb b/docs/tutorials/spectral_library.ipynb
@@ -393,7 +393,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.6.10"
+   "version": "3.8.6"
   }
  },
  "nbformat": 4,

diff --git a/species/analysis/fit_model.py b/species/analysis/fit_model.py
@@ -726,8 +726,11 @@ def __init__(self,
                     self.modelpar.append(f'corr_len_{item}')
                     self.modelpar.append(f'corr_amp_{item}')
 
-                    self.bounds[f'corr_len_{item}'] = (-3., 0.)  # log10(corr_len) (um)
-                    self.bounds[f'corr_amp_{item}'] = (0., 1.)
+                    if f'corr_len_{item}' not in self.bounds:
+                        self.bounds[f'corr_len_{item}'] = (-3., 0.)  # log10(corr_len/um)
+
+                    if f'corr_amp_{item}' not in self.bounds:
+                        self.bounds[f'corr_amp_{item}'] = (0., 1.)
 
                     self.n_corr_par += 2
 
@@ -963,8 +966,8 @@ def run_mcmc(self,
 
         for item in self.spectrum:
             if item in self.fit_corr:
-                sigma[f'corr_len_{item}'] = 0.01  # (dex)
-                guess[f'corr_len_{item}'] = None  # (um)
+                sigma[f'corr_len_{item}'] = 0.01  # log10(corr_len/um)
+                guess[f'corr_len_{item}'] = None  # log10(corr_len/um)
 
                 sigma[f'corr_amp_{item}'] = 0.1
                 guess[f'corr_amp_{item}'] = None

diff --git a/species/read/read_filter.py b/species/read/read_filter.py
@@ -140,7 +140,7 @@ def filter_fwhm(self) -> float:
         Returns
         -------
         float
-            Filter full width at half maximum (um).
+            Full width at half maximum (um).
         """
 
         data = self.get_filter()
@@ -155,10 +155,27 @@ def filter_fwhm(self) -> float:
 
         return root2 - root1
 
+    @typechecked
+    def effective_width(self) -> np.float32:
+        """
+        Calculate the effective width of the filter profile. The effective width is equivalent to
+        the horizontal size of a rectangle with height equal to the maximum transmission and with
+        the same area as the one covered by the filter profile.
+
+        Returns
+        -------
+        float
+            Effective width (um).
+        """
+
+        data = self.get_filter()
+
+        return np.trapz(data[:, 1], data[:, 0]) / np.amax(data[:, 1])
+
     @typechecked
     def detector_type(self) -> str:
         """
-        Function for returning the detector type.
+        Return the detector type.
 
         Returns
         -------

diff --git a/test/test_read/test_calibration.py b/test/test_read/test_calibration.py
@@ -56,4 +56,4 @@ def test_get_magnitude(self):
         app_mag, abs_mag = read_calib.get_magnitude(model_param=self.model_param)
 
         assert app_mag[0] == 0.03
-        assert abs_mag[0] == None
+        assert abs_mag[0] is None