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companion data
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Tomas Stolker committed Mar 6, 2019
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9 changes: 5 additions & 4 deletions docs/examples.rst
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Expand Up @@ -100,7 +100,8 @@ Here photometric data of 51 Eri b (Rajan et al. 2017) is added to the database.
database = species.Database()
database.add_companion(name=None)

object_cmd = ('51 Eri b', 'MKO/NSFCam.J', 'MKO/NSFCam.H', 'MKO/NSFCam.J')
object1 = ('beta Pic b', 'Paranal/NACO.J', 'Paranal/NACO.H', 'Paranal/NACO.J')
object2 = ('51 Eri b', 'MKO/NSFCam.J', 'MKO/NSFCam.H', 'MKO/NSFCam.J')

colormag = species.ReadColorMagnitude(library=('vlm-plx', ),
filters_color=('MKO/NSFCam.J', 'MKO/NSFCam.H'),
Expand All @@ -109,11 +110,11 @@ Here photometric data of 51 Eri b (Rajan et al. 2017) is added to the database.
colorbox = colormag.get_color_magnitude(object_type='field')

species.plot_color_magnitude(colorbox=colorbox,
objects=(object_cmd, ),
objects=(object1, object2),
label_x='J - H [mag]',
label_y='M$_\mathregular{J}$ [mag]',
output='color_mag.pdf')

output='color_mag.pdf',
legend='upper left')

.. image:: _images/color_mag.png
:width: 70%
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6 changes: 3 additions & 3 deletions docs/species.read.rst
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Expand Up @@ -4,10 +4,10 @@ species.read package
Submodules
----------

species.read.read\_colormag module
----------------------------------
species.read.read\_color module
-------------------------------

.. automodule:: species.read.read_colormag
.. automodule:: species.read.read_color
:members:
:undoc-members:
:show-inheritance:
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8 changes: 4 additions & 4 deletions species/analysis/fit.py
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Expand Up @@ -51,13 +51,13 @@ def lnprior(param,

if bounds[item][0] <= param[i] <= bounds[item][1]:

if prior[0] == 'mass':
if prior is None:
ln_prior = 0.

elif prior[0] == 'mass':
mass = read_model.get_mass(modeldict)
ln_prior = -0.5*(mass-prior[1])**2/prior[2]**2

else:
ln_prior = 0.

else:
ln_prior = -np.inf
break
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225 changes: 118 additions & 107 deletions species/data/companions.py
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Expand Up @@ -36,59 +36,70 @@ def get_data():
'Keck/NIRC2.Lp':(16.20, 0.11), # Rajan et al. 2017
'Keck/NIRC2.Ms':(16.1, 0.5)}}, # Rajan et al. 2017

# 'HR 8799 b':{'distance':41.29,
# 'app_mag':{'':(),
# '':(),
# '':(),
# '':(),
# '':(),
# '':(),
# '':()}},

# 'HR 8799 c':{'distance':41.29,
# 'app_mag':{'':(),
# '':(),
# '':(),
# '':(),
# '':(),
# '':(),
# '':()}},

# 'HR 8799 d':{'distance':41.29,
# 'app_mag':{'':(),
# '':(),
# '':(),
# '':(),
# '':(),
# '':(),
# '':()}},

# 'HR 8799 e':{'distance':41.29,
# 'app_mag':{'':(),
# '':(),
# '':(),
# '':(),
# '':(),
# '':(),
# '':()}},

# 'HD 95086 b':{'distance':86.44,
# 'app_mag':{'':(),
# '':(),
# '':(),
# '':(),
# '':(),
# '':(),
# '':()}},

# '2M1207 B':{'distance':64.42,
# 'app_mag':{'':(),
# '':(),
# '':(),
# '':(),
# '':(),
# '':(),
# '':()}},
'HR 8799 b':{'distance':41.29,
'app_mag':{'Subaru/CIAO.z':(21.22, 0.29), # Currie et al. 2011
'Paranal/SPHERE.IRDIS_B_J':(19.78, 0.09), # Zurlo et al. 2016
'Keck/NIRC2.H':(18.05, 0.09), # Currie et al. 2012
'Paranal/SPHERE.IRDIS_D_H23_2':(18.08, 0.14), # Zurlo et al. 2016
'Paranal/SPHERE.IRDIS_D_H23_3':(17.78, 0.10), # Zurlo et al. 2016
'Keck/NIRC2.Ks':(17.03, 0.08), # Marois et al. 2010
'Paranal/SPHERE.IRDIS_D_K12_1':(17.15, 0.06), # Zurlo et al. 2016
'Paranal/SPHERE.IRDIS_D_K12_2':(16.97, 0.09), # Zurlo et al. 2016
'Keck/NIRC2.Lp':(15.58, 0.10), # Currie et al. 2014
'Keck/NIRC2.Ms':(16.05, 0.30)}}, # Galicher et al. 2011

'HR 8799 c':{'distance':41.29,
'app_mag':{'Paranal/SPHERE.IRDIS_B_J':(18.60, 0.13), # Zurlo et al. 2016
'Keck/NIRC2.H':(17.06, 0.13), # Currie et al. 2012
'Paranal/SPHERE.IRDIS_D_H23_2':(17.09, 0.12), # Zurlo et al. 2016
'Paranal/SPHERE.IRDIS_D_H23_3':(16.78, 0.10), # Zurlo et al. 2016
'Keck/NIRC2.Ks':(16.11, 0.08), # Marois et al. 2010
'Paranal/SPHERE.IRDIS_D_K12_1':(16.19, 0.05), # Zurlo et al. 2016
'Paranal/SPHERE.IRDIS_D_K12_2':(15.86, 0.07), # Zurlo et al. 2016
'Keck/NIRC2.Lp':(15.72, 0.08), # Currie et al. 2014
'Keck/NIRC2.Ms':(15.03, 0.14)}}, # Galicher et al. 2011

'HR 8799 d':{'distance':41.29,
'app_mag':{'Paranal/SPHERE.IRDIS_B_J':(18.59, 0.37), # Zurlo et al. 2016
'Keck/NIRC2.H':(16.71, 0.24), # Currie et al. 2012
'Paranal/SPHERE.IRDIS_D_H23_2':(17.02, 0.17), # Zurlo et al. 2016
'Paranal/SPHERE.IRDIS_D_H23_3':(16.68, 0.21), # Zurlo et al. 2016
'Keck/NIRC2.Ks':(16.09, 0.12), # Marois et al. 2010
'Paranal/SPHERE.IRDIS_D_K12_1':(16.20, 0.07), # Zurlo et al. 2016
'Paranal/SPHERE.IRDIS_D_K12_2':(15.84, 0.10), # Zurlo et al. 2016
'Keck/NIRC2.Lp':(14.56, 0.09), # Currie et al. 2014
'Keck/NIRC2.Ms':(14.65, 0.35)}}, # Galicher et al. 2011

'HR 8799 e':{'distance':41.29,
'app_mag':{'Paranal/SPHERE.IRDIS_B_J':(18.40, 0.21), # Zurlo et al. 2016
'Paranal/SPHERE.IRDIS_D_H23_2':(16.91, 0.20), # Zurlo et al. 2016
'Paranal/SPHERE.IRDIS_D_H23_3':(16.85, 0.16), # Zurlo et al. 2016
'Keck/NIRC2.Ks':(15.91, 0.22), # Marois et al. 2010
'Paranal/SPHERE.IRDIS_D_K12_1':(16.12, 0.10), # Zurlo et al. 2016
'Paranal/SPHERE.IRDIS_D_K12_2':(15.82, 0.11), # Zurlo et al. 2016
'Keck/NIRC2.Lp':(14.55, 0.12)}}, # Currie et al. 2014

'HD 95086 b':{'distance':86.44,
'app_mag':{'Gemini/GPI.H':(20.51, 0.25), # De Rosa et al. 2016
'Gemini/GPI.K1':(18.99, 0.20), # De Rosa et al. 2016
'Paranal/NACO.Lp':(16.27, 0.19)}}, # De Rosa et al. 2016

'PDS 70 b':{'distance':113.43,
'app_mag':{'Paranal/SPHERE.IRDIS_D_H23_2':(17.94, 0.24), # Keppler et al. 2018
'Paranal/SPHERE.IRDIS_D_H23_3':(17.95, 0.17), # Keppler et al. 2018
'Paranal/SPHERE.IRDIS_D_K12_1':(16.65, 0.06), # Müller et al. 2018
'Paranal/SPHERE.IRDIS_D_K12_2':(16.44, 0.05), # Müller et al. 2018
'Paranal/NACO.Lp':(14.75, 0.62)}}, # Keppler et al. 2018

'2M1207 b':{'distance':64.42,
'app_mag':{'HST/NICMOS1.F090M':(22.58, 0.35), # Song et al. 2006
'HST/NICMOS1.F145M':(19.05, 0.03), # Song et al. 2006
'HST/NICMOS1.F160W':(18.27, 0.02), # Song et al. 2006
'Paranal/NACO.J':(20.0, 0.20), # Mohanty et al. 200z
'Paranal/NACO.H':(18.09, 0.21), # Chauvin et al. 2004
'Paranal/NACO.Ks':(16.93, 0.11), # Chauvin et al. 2004
# 'Magellan/MagAO.3.3':(15.46, 0.10), # Skemer et al. 2014
'Paranal/NACO.Lp':(15.28, 0.14)}}, # Chauvin et al. 2004

'AB Pic B':{'distance':50.12,
'app_mag':{'Paranal/NACO.J':(16.18, 0.10), # Chauvin et al. 2005
Expand All @@ -99,20 +110,22 @@ def get_data():
'app_mag':{'Paranal/SPHERE.IRDIS_B_H':(16.79, 0.06), # Milli et al. 2016
'Paranal/SPHERE.IRDIS_D_K12_1':(15.2, 0.10), # Chauvin et al. 2017
'Paranal/SPHERE.IRDIS_D_K12_2':(14.88, 0.09), # Chauvin et al. 2017
'Paranal/NACO.Lp':(13.43, 0.16)}}, # Milli et al. 2016, error is +0.17, -0.15?
# 'Paranal/NACO.NB405':(), # Stolker et al. in prep.
# 'Paranal/NACO.Mp':(), # Stolker et al. in prep.

# 'GQ Lup B':{'distance':151.82,
# 'app_mag':{'':(),
# '':(),
# '':(),
# '':(),
# '':(),
# '':(),
# '':()}},
'Paranal/NACO.Lp':(13.43, 0.16)}}, # Milli et al. 2016, error is +0.17, -0.15

'GQ Lup B':{'distance':151.82,
'app_mag':{'HST/WFPC2.f606w':(19.19, 0.07), # Marois et al. 2006
'HST/WFPC2.f814w':(17.67, 0.05), # Marois et al. 2006
'HST/NICMOS2.F171M':(13.84, 0.13), # Marois et al. 2006
'HST/NICMOS2.F190N':(14.08, 0.20), # Marois et al. 2006
'HST/NICMOS2.F215N':(13.40, 0.15), # Marois et al. 2006
'Subaru/CIAO.CH4s':(13.76, 0.26), # Marois et al. 2006
'Subaru/CIAO.K':(13.37, 0.12), # Marois et al. 2006
'Subaru/CIAO.Lp':(12.44, 0.22)}}, # Marois et al. 2006

'PZ Tel B':{'distance':47.13,
'app_mag':{'Paranal/SPHERE.ZIMPOL_R_PRIM':(17.84, 0.3), # Maire et al. 2015, error is +0.22, −0.31?
'app_mag':{'Paranal/SPHERE.ZIMPOL_R_PRIM':(17.84, 0.3), # Maire et al. 2015, error is +0.22, −0.31
'Paranal/SPHERE.ZIMPOL_I_PRIM':(15.16, 0.12), # Maire et al. 2015
'Paranal/SPHERE.IRDIS_D_H23_2':(11.78, 0.19), # Maire et al. 2015
'Paranal/SPHERE.IRDIS_D_H23_3':(11.65, 0.19), # Maire et al. 2015
Expand All @@ -127,51 +140,49 @@ def get_data():
'Gemini/NICI.ED286':(11.68, 0.14), # Biller et al. 2010
'Gemini/NIRI.H2S1v2-1-G0220':(11.39, 0.14)}}, # Biller et al. 2010

# 'kappa And B':{'distance':50.06,
# 'app_mag':{'':(),
# '':(),
# '':(),
# '':(),
# '':(),
# '':(),
# '':()}},
'kappa And b':{'distance':50.06,
'app_mag':{'Subaru/CIAO.J':(15.86, 0.21), # Bonnefoy et al. 2014
'Subaru/CIAO.H':(14.95, 0.13), # Bonnefoy et al. 2014
'Subaru/CIAO.Ks':(14.32, 0.09), # Bonnefoy et al. 2014
'Keck/NIRC2.Lp':(13.12, 0.1), # Bonnefoy et al. 2014
# 'Keck/NIRC2.NB_4.05':(13.0, 0.2), # Bonnefoy et al. 2014
'LBT/LMIRCam.M_77K':(13.3, 0.3)}}, # Bonnefoy et al. 2014

'GJ 504 b':{'distance':17.54,
'app_mag':{'Paranal/SPHERE.IRDIS_D_Y23_2':(20.98, 0.20),
'Paranal/SPHERE.IRDIS_D_Y23_3':(20.14, 0.09),
# 'Paranal/SPHERE.IRDIS_D_J23_2':(>21.28, ),
'Paranal/SPHERE.IRDIS_D_J23_3':(19.01, 0.17),
'Paranal/SPHERE.IRDIS_D_H23_2':(18.95, 0.30),
'Paranal/SPHERE.IRDIS_D_H23_3':(21.81, 0.35),
'Paranal/SPHERE.IRDIS_D_K12_1':(18.77, 0.20),
# 'Paranal/SPHERE.IRDIS_D_K12_2':(>19.96, ),
'Subaru/CIAO.J':(19.78, 0.10),
'Subaru/CIAO.H':(20.01, 0.14),
'Subaru/CIAO.Ks':(19.38, 0.11),
'Subaru/CIAO.CH4s':(19.58, 0.13),
# 'Subaru/CIAO.CH4l':(>20.63, ),
# 'LBTI/LMIRcam.L_NB6':(17.59, 0.17),
# 'LBTI/LMIRcam.L_NB7':(16.47, 0.19),
# 'LBTI/LMIRcam.L_NB8':(15.85, 0.17),
'Subaru/IRCS.Lp':(16.70, 0.17)}},

# 'GU Psc B':{'distance':47.61,
# 'app_mag':{'':(),
# '':(),
# '':(),
# '':(),
# '':(),
# '':(),
# '':()}},

# '1RXS 1609 B':{'distance':139.67,
# 'app_mag':{'':(),
# '':(),
# '':(),
# '':(),
# '':(),
# '':(),
# '':()}},
'app_mag':{'Paranal/SPHERE.IRDIS_D_Y23_2':(20.98, 0.20), # Bonnefoy et al. 2018
'Paranal/SPHERE.IRDIS_D_Y23_3':(20.14, 0.09), # Bonnefoy et al. 2018
# 'Paranal/SPHERE.IRDIS_D_J23_2':(>21.28, ), # Bonnefoy et al. 2018
'Paranal/SPHERE.IRDIS_D_J23_3':(19.01, 0.17), # Bonnefoy et al. 2018
'Paranal/SPHERE.IRDIS_D_H23_2':(18.95, 0.30), # Bonnefoy et al. 2018
'Paranal/SPHERE.IRDIS_D_H23_3':(21.81, 0.35), # Bonnefoy et al. 2018
'Paranal/SPHERE.IRDIS_D_K12_1':(18.77, 0.20), # Bonnefoy et al. 2018
# 'Paranal/SPHERE.IRDIS_D_K12_2':(>19.96, ), # Bonnefoy et al. 2018
'Subaru/CIAO.J':(19.78, 0.10), # Janson et al. 2013
'Subaru/CIAO.H':(20.01, 0.14), # Janson et al. 2013
'Subaru/CIAO.Ks':(19.38, 0.11), # Janson et al. 2013
'Subaru/CIAO.CH4s':(19.58, 0.13), # Janson et al. 2013
# 'Subaru/CIAO.CH4l':(>20.63, ), # Janson et al. 2013
# 'LBTI/LMIRcam.L_NB6':(17.59, 0.17), # Skemer et al. 2016
# 'LBTI/LMIRcam.L_NB7':(16.47, 0.19), # Skemer et al. 2016
# 'LBTI/LMIRcam.L_NB8':(15.85, 0.17), # Skemer et al. 2016
'Subaru/IRCS.Lp':(16.70, 0.17)}}, # Kuzuhara et al. 2013

'GU Psc b':{'distance':47.61,
'app_mag':{'Gemini/GMOS-S.z':(21.75, 0.07), # Naud et al. 2014
'CFHT/Wircam.Y':(19.4, 0.05), # Naud et al. 2014
'CFHT/Wircam.J':(18.12, 0.03), # Naud et al. 2014
'CFHT/Wircam.H':(17.70, 0.03), # Naud et al. 2014
'CFHT/Wircam.Ks':(17.40, 0.03), # Naud et al. 2014
'WISE/WISE.W1':(17.17, 0.33), # Naud et al. 2014
'WISE/WISE.W2':(15.41, 0.22)}}, # Naud et al. 2014

'1RXS 1609 B':{'distance':139.67,
'app_mag':{'Gemini/NIRI.J-G0202w':(17.90, 0.12), # Lafreniere et al. 2008
'Gemini/NIRI.H-G0203w':(16.87, 0.07), # Lafreniere et al. 2008
'Gemini/NIRI.K-G0204w':(16.17, 0.18), # Lafreniere et al. 2008
# 'MMT/Clio.3.1':(15.65, 0.21), # Bailey et al. 2013
# 'MMT/Clio.3.3':(15.2, 0.16), # Bailey et al. 2013
'Gemini/NIRI.Lprime-G0207w':(14.8, 0.3)}}, # Lafreniere et al. 2010

'GSC 06214 B':{'distance':108.84,
'app_mag':{'MKO/NSFCam.J':(16.24, 0.04), # Ireland et al. 2011
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5 changes: 1 addition & 4 deletions species/plot/plot_color.py
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Expand Up @@ -22,6 +22,7 @@

plt.rc('axes', edgecolor='black', linewidth=2)

marker = itertools.cycle(('o', 's', 'p', '<', '>', 'p', 'v', '^', '*', 'd', 'x', '+', '1', '2', '3', '4'))

def plot_color_magnitude(colorbox,
objects,
Expand Down Expand Up @@ -58,8 +59,6 @@ def plot_color_magnitude(colorbox,
sys.stdout.write('Plotting color-magnitude diagram: '+output+'... ')
sys.stdout.flush()

marker = itertools.cycle(('o', 's', 'p', '<', '>', 'P', 'v', '^', '*'))

plt.figure(1, figsize=(4, 4.8))
gridsp = mpl.gridspec.GridSpec(3, 1, height_ratios=[0.2, 0.1, 4.5])
gridsp.update(wspace=0., hspace=0., left=0, right=1, bottom=0, top=1)
Expand Down Expand Up @@ -192,8 +191,6 @@ def plot_color_color(colorbox,
sys.stdout.write('Plotting color-color diagram: '+output+'... ')
sys.stdout.flush()

marker = itertools.cycle(('o', 's', 'p', '<', '>', 'P', 'v', '^', '*'))

plt.figure(1, figsize=(4, 4.3))
gridsp = mpl.gridspec.GridSpec(3, 1, height_ratios=[0.2, 0.1, 4.])
gridsp.update(wspace=0., hspace=0., left=0, right=1, bottom=0, top=1)
Expand Down

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