updated docs

LICENSE

@@ -652,7 +652,7 @@ Also add information on how to contact you by electronic and paper mail.
   If the program does terminal interaction, make it output a short
 notice like this when it starts in an interactive mode:
 
-    SPECIES  Copyright (C) 2018  Tomas Stolker
+    species  Copyright (C) 2018  Tomas Stolker
     This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
     This is free software, and you are welcome to redistribute it
     under certain conditions; type `show c' for details.

README.rst

@@ -1,7 +1,7 @@
-SPECIES
+species
 =======
 
-**Spectral and Photometric Examination Code for Investigating Exoplanet and Substellar atmospheres**
+**spectral and photometric examination code for investigating exoplanet and substellar atmospheres**
 
 .. image:: https://badge.fury.io/py/species.svg
     :target: https://badge.fury.io/py/species
@@ -24,7 +24,7 @@ SPECIES
 .. image:: https://img.shields.io/badge/License-GPLv3-blue.svg
     :target: https://github.com/tomasstolker/species/blob/master/LICENSE
 
-SPECIES is a toolkit for analyzing spectral and photometric data of planetary and substellar objects.
+*species* is a toolkit for analyzing spectral and photometric data of planetary and substellar objects. It provides a coherent framework to characterize the atmospheres of directly imaged companions by combining data from various resources. A central database is used to store various data sets such as spectral and photometric libraries, atmospheric models, photometry of individual targets, filter transmission curves, and analysis results. There are tools available for creating color-magnitude diagrams, fitting atmospheric models and retrieving the posterior distributions, creating synthetic photometry, plotting spectra, etc. The package has been released on `PyPI <https://pypi.org/project/species/>`_ but is still under active development.
 
 Documentation
 -------------
@@ -34,11 +34,16 @@ Documentation can be found at `http://species.readthedocs.io <http://species.rea
 Attribution
 -----------
 
-Please cite Stolker et al. in prep. whenever results from SPECIES are used in a publication. Please also make sure to give credit the relevant papers regarding the use of the publicly available data that SPECIES is using, such as the photometric and spectral libraries, atmospheric models, filter transmission curves, and photometry of individual objects. More details will follow.
+Please cite Stolker et al. in prep. whenever results from *species* are used in a publication. Please also make sure to give credit to the relevant papers regarding the use of the publicly available data that *species* is profiting from. More details will follow.
+
+Contributing
+------------
+
+Contributions are very welcome, please consider forking the repository and creating a pull request. Bug reports can be provided by creating an `issue <https://github.com/tomasstolker/species/issues>`_ on the Github page.
 
 License
 -------
 
-Copyright 2018 Tomas Stolker
+Copyright 2019 Tomas Stolker
 
-SPECIES is distributed under the GNU General Public License v3. See the LICENSE file for the terms and conditions.
+*species* is distributed under the GNU General Public License v3. See the LICENSE file for the terms and conditions.

docs/about.rst

@@ -6,9 +6,9 @@ About
 Questions & feedback
 --------------------
 
-SPECIES is developed by Tomas Stolker (tomas.stolker@phys.ethz.ch). Feel free to send an email for questions, comments, or suggestions.
+*species* is developed by Tomas Stolker (tomas.stolker@phys.ethz.ch). Feel free to send an email for questions, comments, or suggestions.
 
 Attribution
 -----------
 
-Please cite Stolker et al. in prep. whenever results from SPECIES are used in a publication. Please also make sure to give credit the relevant papers regarding the use of the publicly available data that SPECIES is using, such as the photometric and spectral libraries, atmospheric models, filter transmission curves, and photometry of individual objects. More details will follow.
+Please cite Stolker et al. in prep. whenever results from *species* are used in a publication. Please also make sure to give credit the relevant papers regarding the use of the publicly available data that *species* is using, such as the photometric and spectral libraries, atmospheric models, filter transmission curves, and photometry of individual objects. More details will follow.

docs/examples.rst

@@ -47,7 +47,7 @@ Here photometric data of 51 Eri b (Rajan et al. 2017) is added to the database.
 
    import species
 
-   species.SpeciesInit("./", "./data")
+   species.SpeciesInit("./")
 
    magnitudes = {"MKO/NSFCam.J":19.04, "MKO/NSFCam.H":18.99, "MKO/NSFCam.K":18.67, "Keck/NIRC2.Lp":16.20, "Keck/NIRC2.Mp":16.1}
 

docs/index.rst

@@ -1,22 +1,6 @@
-.. Welcome to SPECIES' documentation!
-.. =================================
-..
-.. .. toctree::
-..    :maxdepth: 2
-..    :caption: Contents:
-..
-..
-..
-.. Indices and tables
-.. ==================
-..
-.. * :ref:`genindex`
-.. * :ref:`modindex`
-.. * :ref:`search`
-
 .. _index:
 
-Documentation for SPECIES
+Documentation for species
 =========================
 
 .. toctree::

docs/installation.rst

@@ -3,19 +3,19 @@
 Installation
 ============
 
-SPECIES can be installed from the |pypi| with the |pip|::
+*species* can be installed from the |pypi| with the |pip|::
 
     $ pip install species
 
 Alternatively, the repository can be cloned from |github|::
 
     $ git clone git@github.com:tomasstolker/species.git
 
-In that case, the dependencies can be installed from the SPECIES folder::
+In that case, the dependencies can be installed from the *species* folder::
 
     $ pip install -r requirements.txt
 
-The installation can be tested by starting Python in interactive mode and printing the SPECIES version::
+The installation can be tested by starting Python in interactive mode and printing the *species* version::
 
     >>> import species
     >>> print species.__version__

docs/species.data.rst

@@ -4,6 +4,22 @@ species.data package
 Submodules
 ----------
 
+species.data.btnextgen module
+-----------------------------
+
+.. automodule:: species.data.btnextgen
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+species.data.companions module
+------------------------------
+
+.. automodule:: species.data.companions
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
 species.data.database module
 ----------------------------
 
@@ -20,6 +36,14 @@ species.data.drift\_phoenix module
     :undoc-members:
     :show-inheritance:
 
+species.data.filters module
+---------------------------
+
+.. automodule:: species.data.filters
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
 species.data.irtf module
 ------------------------
 
@@ -28,6 +52,14 @@ species.data.irtf module
     :undoc-members:
     :show-inheritance:
 
+species.data.leggett module
+---------------------------
+
+.. automodule:: species.data.leggett
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
 species.data.queries module
 ---------------------------
 

docs/species.plot.rst

@@ -4,14 +4,6 @@ species.plot package
 Submodules
 ----------
 
-species.plot.plot\_chisquare module
------------------------------------
-
-.. automodule:: species.plot.plot_chisquare
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
 species.plot.plot\_mcmc module
 ------------------------------
 
@@ -36,6 +28,14 @@ species.plot.plot\_spectrum module
     :undoc-members:
     :show-inheritance:
 
+species.plot.util module
+------------------------
+
+.. automodule:: species.plot.util
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
 
 Module contents
 ---------------

species/__init__.py

@@ -28,7 +28,7 @@
 from species.plot.plot_mcmc import plot_posterior, \
                                    plot_walkers
 
-from species.plot.plot_photometry import plot_color_magnitude
+from species.plot.plot_color import plot_color_magnitude, plot_color_color
 
 from species.plot.plot_spectrum import plot_spectrum
 

species/analysis/fit.py

@@ -290,6 +290,8 @@ def store_samples(self,
         :type sampler: emcee.ensemble.EnsembleSampler
         :param model: Atmospheric model.
         :type model: str
+        :param tag: Database tag.
+        :type tag: str
         :param chisquare: Maximum likelihood solution. Tuple with the chi-square value and related
                           parameter values.
         :type chisquare: tuple(float, float)

species/core/box.py

@@ -2,8 +2,6 @@
 Box module.
 """
 
-import numpy as np
-
 
 def open_box(box):
     """
@@ -19,19 +17,24 @@ def create_box(boxtype, **kwargs):
     :return:
     """
 
-    if boxtype == 'model':
+    if boxtype == 'colormag':
+        box = ColorMagBox()
+        box.library = kwargs['library']
+        box.object_type = kwargs['object_type']
+        box.filters_color = kwargs['filters_color']
+        box.filter_mag = kwargs['filter_mag']
+        box.color = kwargs['color']
+        box.magnitude = kwargs['magnitude']
+        box.sptype = kwargs['sptype']
+
+    elif boxtype == 'model':
         box = ModelBox()
         box.model = kwargs['model']
+        box.type = kwargs['type']
         box.wavelength = kwargs['wavelength']
         box.flux = kwargs['flux']
         box.parameters = kwargs['parameters']
 
-    elif boxtype == 'photometry':
-        box = PhotometryBox()
-        box.name = kwargs['name']
-        box.wavelength = kwargs['wavelength']
-        box.flux = kwargs['flux']
-
     elif boxtype == 'object':
         box = ObjectBox()
         box.name = kwargs['name']
@@ -40,6 +43,12 @@ def create_box(boxtype, **kwargs):
         box.flux = kwargs['flux']
         box.distance = kwargs['distance']
 
+    elif boxtype == 'photometry':
+        box = PhotometryBox()
+        box.name = kwargs['name']
+        box.wavelength = kwargs['wavelength']
+        box.flux = kwargs['flux']
+
     elif boxtype == 'samples':
         box = SamplesBox()
         box.model = kwargs['model']
@@ -49,9 +58,10 @@ def create_box(boxtype, **kwargs):
 
     elif boxtype == 'spectrum':
         box = SpectrumBox()
+        box.spectrum = kwargs['spectrum']
+        box.wavelength = kwargs['wavelength']
+        box.flux = kwargs['flux']
         box.name = kwargs['name']
-        box.wavelength = np.asarray([kwargs['wavelength']])
-        box.flux = np.asarray([kwargs['flux']])
 
     elif boxtype == 'synphot':
         box = SynphotBox()
@@ -61,7 +71,7 @@ def create_box(boxtype, **kwargs):
     return box
 
 
-class SpectrumBox:
+class ColorMagBox:
     """
     Text
     """
@@ -71,13 +81,13 @@ def __init__(self):
         :return:
         """
 
-        self.spectrum = None
-        self.wavelength = None
-        self.flux = None
-        self.name = None
-        self.simbad = None
+        self.library = None
+        self.object_type = None
+        self.filters_color = None
+        self.filter_mag = None
+        self.color = None
+        self.magnitude = None
         self.sptype = None
-        self.distance = None
 
 
 class ModelBox:
@@ -97,6 +107,23 @@ def __init__(self):
         self.parameters = None
 
 
+class ObjectBox:
+    """
+    Text
+    """
+
+    def __init__(self):
+        """
+        :return:
+        """
+
+        self.name = None
+        self.filter = None
+        self.magnitude = None
+        self.flux = None
+        self.distance = None
+
+
 class PhotometryBox:
     """
     Text
@@ -127,7 +154,8 @@ def __init__(self):
         self.samples = None
         self.chisquare = None
 
-class ObjectBox:
+
+class SpectrumBox:
     """
     Text
     """
@@ -137,12 +165,15 @@ def __init__(self):
         :return:
         """
 
-        self.name = None
-        self.filter = None
-        self.magnitude = None
+        self.spectrum = None
+        self.wavelength = None
         self.flux = None
+        self.name = None
+        self.simbad = None
+        self.sptype = None
         self.distance = None
 
+
 class SynphotBox:
     """
     Text

species/data/companions.py

@@ -64,7 +64,7 @@ def get_data():
                                     'Paranal/SPHERE.IRDIS_D_H23_2':(18.41, 0.26), # Samland et al. 2017
                                     'Paranal/SPHERE.IRDIS_D_K12_1':(17.55, 0.14), # Samland et al. 2017
                                     'Keck/NIRC2.Lp':(16.20, 0.11), # Rajan et al. 2017
-                                    'Keck/NIRC2.Mp':(16.1, 0.5)}}, # Rajan et al. 2017
+                                    'Keck/NIRC2.Ms':(16.1, 0.5)}}, # Rajan et al. 2017
 
              'GSC 06214 B':{'distance':108.84,
                             'app_mag':{'MKO/NSFCam.J':(16.24, 0.04), # Ireland et al. 2011