Updated tutorial notebooks

tomasstolker · Jan 27, 2020 · 3943707 · 3943707
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Showing 8 changed files with 36 additions and 193 deletions.
diff --git a/docs/overview.rst b/docs/overview.rst
@@ -27,7 +27,6 @@ The following data are currently supported by *species* (support for other data
 - All isochrone data from the `Phoenix model grids <https://phoenix.ens-lyon.fr/Grids/>`_
 - Photometry from the `Database of Ultracool Parallaxes <http://www.as.utexas.edu/~tdupuy/plx/Database_of_Ultracool_Parallaxes.html>`_
 - Photometry from `Sandy Leggett <http://www.gemini.edu/staff/sleggett>`_
-- Photometry from `A Modern Mean Dwarf Stellar Color and Effective Temperature Sequence <http://www.pas.rochester.edu/~emamajek>`_
 - Photometry of directly imaged planets and brown dwarfs (see dictionary in :class:`~species.data.companions`)
 - Calibration spectrum of `Vega <http://ssb.stsci.edu/cdbs/calspec/>`_
 

diff --git a/docs/species.data.rst b/docs/species.data.rst
@@ -92,14 +92,6 @@ species.data.leggett module
     :undoc-members:
     :show-inheritance:
 
-species.data.mamajek module
----------------------------
-
-.. automodule:: species.data.mamajek
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
 species.data.petitcode module
 -----------------------------
 

diff --git a/docs/tutorials/fitting_photometry.ipynb b/docs/tutorials/fitting_photometry.ipynb
diff --git a/docs/tutorials/photometric_calibration.ipynb b/docs/tutorials/photometric_calibration.ipynb
diff --git a/species/data/database.py b/species/data/database.py
@@ -14,7 +14,7 @@
 from species.analysis import photometry
 from species.core import box
 from species.data import drift_phoenix, btnextgen, vega, irtf, spex, vlm_plx, leggett, \
-                         companions, filters, mamajek, btsettl, ames_dusty, ames_cond, \
+                         companions, filters, btsettl, ames_dusty, ames_cond, \
                          isochrones, petitcode
 from species.read import read_model, read_calibration, read_planck
 from species.util import data_util
@@ -391,7 +391,7 @@ def add_photometry(self,
         Parameters
         ----------
         phot_library : str
-            Photometric library ('vlm-plx', 'leggett' or 'mamajek').
+            Photometric library ('vlm-plx' or 'leggett').
 
         Returns
         -------
@@ -413,9 +413,6 @@ def add_photometry(self,
         elif phot_library[0:7] == 'leggett':
             leggett.add_leggett(self.input_path, h5_file)
 
-        elif phot_library[0:7] == 'mamajek':
-            mamajek.add_mamajek(self.input_path, h5_file)
-
         h5_file.close()
 
     def add_calibration(self,
@@ -746,8 +743,6 @@ def get_mcmc_spectra(self,
             Boxes with the randomly sampled spectra.
         """
 
-        print('Getting MCMC spectra...')
-
         h5_file = h5py.File(self.database, 'r')
         dset = h5_file[f'results/mcmc/{tag}/samples']
 
@@ -786,7 +781,7 @@ def get_mcmc_spectra(self,
 
         boxes = []
 
-        for i in tqdm.tqdm(range(samples.shape[0])):
+        for i in tqdm.tqdm(range(samples.shape[0]), desc='Getting MCMC spectra'):
             model_param = {}
             for j in range(samples.shape[1]):
                 model_param[param[j]] = samples[i, j]
@@ -831,8 +826,6 @@ def get_mcmc_photometry(self,
             Synthetic photometry (mag).
         """
 
-        print('Getting MCMC photometry...')
-
         h5_file = h5py.File(self.database, 'r')
         dset = h5_file[f'results/mcmc/{tag}/samples']
 
@@ -862,7 +855,7 @@ def get_mcmc_photometry(self,
 
         mcmc_phot = np.zeros((samples.shape[0], 1))
 
-        for i in tqdm.tqdm(range(samples.shape[0])):
+        for i in tqdm.tqdm(range(samples.shape[0]), desc='Getting MCMC photometry'):
             model_param = {}
             for j in range(nparam):
                 model_param[param[j]] = samples[i, j]

diff --git a/species/data/mamajek.py b/species/data/mamajek.py
diff --git a/species/data/queries.py b/species/data/queries.py
@@ -175,17 +175,17 @@ def get_distance(target):
             if not ma.is_masked(parallax):
                 break
 
-    if ma.is_masked(parallax):
-
-        if simbad is not None:
-            coord_ra = simbad['RA'][0]
-            coord_dec = simbad['DEC'][0]
-
-            coord = SkyCoord(ra=coord_ra, dec=coord_dec, unit=(u.hourangle, u.deg), frame='icrs')
-            result = Gaia.query_object(coordinate=coord, width=1.*u.arcsec, height=1.*u.arcsec)
-
-            if result:
-                parallax = result['parallax'][0]  # [mas]
+    # if ma.is_masked(parallax):
+    #
+    #     if simbad is not None:
+    #         coord_ra = simbad['RA'][0]
+    #         coord_dec = simbad['DEC'][0]
+    #
+    #         coord = SkyCoord(ra=coord_ra, dec=coord_dec, unit=(u.hourangle, u.deg), frame='icrs')
+    #         result = Gaia.query_object(coordinate=coord, width=1.*u.arcsec, height=1.*u.arcsec)
+    #
+    #         if result:
+    #             parallax = result['parallax'][0]  # [mas]
 
     if ma.is_masked(parallax) or parallax < 0.:
         distance = np.nan

diff --git a/species/data/spex.py b/species/data/spex.py
@@ -146,7 +146,9 @@ def add_spex(input_path, database):
 
             simbad_id, distance = queries.get_distance('2MASS '+twomass_id.decode('utf-8'))  # [pc]
 
-            if sptype[0] in ('M', 'L', 'T') and len(sptype) == 2:
+            print(twomass_id, simbad_id)
+
+            if sptype[0] in ['M', 'L', 'T'] and len(sptype) == 2:
                 sys.stdout.write('\rAdding SpeX Prism Spectral Library... '+'{:<40}'.format(name))
                 sys.stdout.flush()