Formatting updates for releasing LC Fitting

exotic/api/colab.py

@@ -1,39 +1,78 @@
-
-# If the user presses enter to run the sample data, download sample data if needed and
-# put it into a sample-data directory at the top level of the user's Gdrive.  Count
-# the .fits files (images) and .json files (inits files) in the directory entered 
-# by the user (or in the sample-data directory if the user pressed enter).  If 
-# there are at least 20 .fits files, assume this is a directory of images and display
-# the first one in the series.  If there is exactly one inits file in the directory, 
-# show the specified target and comp coords so that the user can check these against
-# the displayed image.  Otherwise, prompt for target / comp coords and make an inits 
-# file based  on those (save this new inits file in the folder with the output files 
-# so that the student can consult it later).  Finally, run EXOTIC with the newly-made 
+# ########################################################################### #
+#    Copyright (c) 2019-2020, California Institute of Technology.
+#    All rights reserved.  Based on Government Sponsored Research under
+#    contracts NNN12AA01C, NAS7-1407 and/or NAS7-03001.
+#
+#    Redistribution and use in source and binary forms, with or without
+#    modification, are permitted provided that the following conditions
+#    are met:
+#      1. Redistributions of source code must retain the above copyright
+#         notice, this list of conditions and the following disclaimer.
+#      2. Redistributions in binary form must reproduce the above copyright
+#         notice, this list of conditions and the following disclaimer in
+#         the documentation and/or other materials provided with the
+#         distribution.
+#      3. Neither the name of the California Institute of
+#         Technology (Caltech), its operating division the Jet Propulsion
+#         Laboratory (JPL), the National Aeronautics and Space
+#         Administration (NASA), nor the names of its contributors may be
+#         used to endorse or promote products derived from this software
+#         without specific prior written permission.
+#
+#    THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+#    "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+#    LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+#    A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE CALIFORNIA
+#    INSTITUTE OF TECHNOLOGY BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+#    SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED
+#    TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
+#    PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
+#    LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
+#    NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+#    SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+#
+# ########################################################################### #
+#    EXOplanet Transit Interpretation Code (EXOTIC)
+#    # NOTE: See companion file version.py for version info.
+# ########################################################################### #
+# IMPORTANT RUNTIME INFORMATION ABOUT DATA ACCESS AND STORAGE
+#
+# If the user presses enter to run the sample data, download sample data if
+# needed and put it into a sample-data directory at the top level of the
+# user's Gdrive. Count the .fits files (images) and .json files (inits files)
+# in the directory entered by the user (or in the sample-data directory if the
+# user pressed enter).  If there are at least 20 .fits files, assume this is a
+# directory of images and display the first one in the series. If there is
+# exactly one inits file in the directory, show the specified target and comp
+# coords so that the user can check these against the displayed image.
+# Otherwise, prompt for target / comp coords and make an inits file based on
+# those (save this new inits file in the folder with the output files so that
+# the student can consult it later).  Finally, run EXOTIC with the newly-made
 # or pre-existing inits file, plus any other inits files in the directory.
-
+#
 #########################################################
-from IPython.display import display, HTML
+from astropy.io import fits
 from astropy.time import Time
 from barycorrpy import utc_tdb
-import numpy as np
-from io import BytesIO
-from astropy.io import fits
-from scipy.ndimage import label
-from bokeh.plotting import figure, output_file, show
+# import bokeh.io
+# from bokeh.io import output_notebook
 from bokeh.palettes import Viridis256
-from bokeh.models import ColorBar, LinearColorMapper, LogColorMapper, LogTicker
-from bokeh.models import BoxZoomTool,WheelZoomTool,ResetTool,HoverTool,PanTool,FreehandDrawTool
-#import bokeh.io
-#from bokeh.io import output_notebook
-from pprint import pprint
-#from IPython.display import Image
-#from ipywidgets import widgets, HBox
-from skimage.transform import rescale, resize, downscale_local_mean
-#import copy
+from bokeh.plotting import figure, output_file, show
+from bokeh.models import BoxZoomTool, ColorBar, FreehandDrawTool, HoverTool, LinearColorMapper, LogColorMapper, \
+  LogTicker, PanTool, ResetTool, WheelZoomTool
+# import copy
+from io import BytesIO
+from IPython.display import display, HTML
+# from IPython.display import Image
+# from ipywidgets import widgets, HBox
+import json
+import numpy as np
 import os
+from pprint import pprint
 import re
-import json
-#import subprocess
+from scipy.ndimage import label
+from skimage.transform import rescale, resize, downscale_local_mean
+# import subprocess
 import time
 
 

exotic/api/elca.py

@@ -35,35 +35,32 @@
 #    EXOplanet Transit Interpretation Code (EXOTIC)
 #    # NOTE: See companion file version.py for version info.
 # ########################################################################### #
-# ########################################################################### #
 # Exoplanet light curve analysis
 #
 # Fit an exoplanet transit model to time series data.
 # ########################################################################### #
-
 from astropy.time import Time
 import copy
 from itertools import cycle
 import matplotlib.pyplot as plt
 import numpy as np
+from pylightcurve.models.exoplanet_lc import transit as pytransit
 from scipy import spatial
 from scipy.optimize import least_squares
 from scipy.signal import savgol_filter
-
 try:
     from ultranest import ReactiveNestedSampler
 except ImportError:
     import dynesty
     import dynesty.plotting
     from dynesty.utils import resample_equal
     from scipy.stats import gaussian_kde
+
 try:
     from plotting import corner
-except:
+except ImportError:
     from .plotting import corner
 
-from pylightcurve.models.exoplanet_lc import transit as pytransit
-
 
 def weightedflux(flux, gw, nearest):
     return np.sum(flux[nearest] * gw, axis=-1)

exotic/api/ephemeris.py

@@ -41,16 +41,31 @@
 # a periodogram analysis.
 # 
 # ########################################################################### #
-
-import numpy as np
-from itertools import cycle
-import statsmodels.api as sm
-import matplotlib.pyplot as plt
-from exotic.api.plotting import corner
-from ultranest import ReactiveNestedSampler
 from astropy.timeseries import LombScargle
 from astropy import units as u
 import copy
+from itertools import cycle
+import matplotlib.pyplot as plt
+import numpy as np
+import rebound
+import statsmodels.api as sm
+try:
+    from ultranest import ReactiveNestedSampler
+except ImportError:
+    import dynesty
+    import dynesty.plotting
+    from dynesty.utils import resample_equal
+    from scipy.stats import gaussian_kde
+
+try:
+    from nested_linear_fitter import linear_fitter, non_linear_fitter
+except ImportError:
+    from .nested_linear_fitter import linear_fitter, non_linear_fitter
+try:
+    from plotting import corner
+except ImportError:
+    from .plotting import corner
+
 
 class ephemeris_fitter(object):
 
@@ -1369,6 +1384,7 @@ def prior_transform(upars):
 
     # TODO extend plot, BIC Values
 
+    # should this be here?
     dude()
     # mearth = u.M_earth.to(u.kg).value
     msun = u.M_sun.to(u.kg)

exotic/api/ew.py

@@ -1,10 +1,48 @@
-import os
+# ########################################################################### #
+#    Copyright (c) 2019-2020, California Institute of Technology.
+#    All rights reserved.  Based on Government Sponsored Research under
+#    contracts NNN12AA01C, NAS7-1407 and/or NAS7-03001.
+#
+#    Redistribution and use in source and binary forms, with or without
+#    modification, are permitted provided that the following conditions
+#    are met:
+#      1. Redistributions of source code must retain the above copyright
+#         notice, this list of conditions and the following disclaimer.
+#      2. Redistributions in binary form must reproduce the above copyright
+#         notice, this list of conditions and the following disclaimer in
+#         the documentation and/or other materials provided with the
+#         distribution.
+#      3. Neither the name of the California Institute of
+#         Technology (Caltech), its operating division the Jet Propulsion
+#         Laboratory (JPL), the National Aeronautics and Space
+#         Administration (NASA), nor the names of its contributors may be
+#         used to endorse or promote products derived from this software
+#         without specific prior written permission.
+#
+#    THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+#    "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+#    LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+#    A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE CALIFORNIA
+#    INSTITUTE OF TECHNOLOGY BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+#    SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED
+#    TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
+#    PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
+#    LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
+#    NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+#    SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+#
+# ########################################################################### #
+#    EXOplanet Transit Interpretation Code (EXOTIC)
+#    # NOTE: See companion file version.py for version info.
+# ########################################################################### #
 import json
-import urllib
 import numpy as np
+import os
+import urllib
 
 base_uri = "https://exoplanets.nasa.gov/watch_results/"
 
+
 class ExoplanetWatch():
     url = 'https://exoplanets.nasa.gov/api/v1/exoplanet_watch_results/?per_page=-1&order=planet_name+asc'
     def __init__(self) -> None:
@@ -50,6 +88,7 @@ def get(self, target):
             print(f"{target} not in list")
             return {}
 
+
 class ExoplanetWatchTarget():
     def __init__(self,result) -> None:
         self.raw_result = result
@@ -92,6 +131,7 @@ def check4floats(dictionary):
             pass
     return dictionary
 
+
 class ExoplanetWatchObservation():
     def __init__(self, name, observation) -> None:
         self.raw_observation = observation
@@ -130,6 +170,7 @@ def get_data(self):
         jdata = json.loads(r.read().decode(r.info().get_param('charset') or 'utf-8'))
         return np.array(jdata[1:],dtype=float).T
 
+
 def translate_keys(rdict):
     """ Translates the keys to a compatible format for EXOTIC/ELCA
 
@@ -165,11 +206,11 @@ def translate_keys(rdict):
             lc_pars[k] = np.nan
     return lc_pars
 
-if __name__ == "__main__":
 
+if __name__ == "__main__":
     EW = ExoplanetWatch()
     print(EW.target_list)
     result = EW.get('WASP-33 b')
     print(result)
     time, flux, fluxerr, airmass, airmasscorr = result.observations[0].get_data()
-    print(result.observations[0].parameters)
+    print(result.observations[0].parameters)

exotic/api/gael_ld.py

@@ -35,14 +35,12 @@
 #    EXOplanet Transit Interpretation Code (EXOTIC)
 #    # NOTE: See companion file version.py for version info.
 # ########################################################################### #
-
-import logging
-import numpy as np
-import lmfit as lm
-import matplotlib.pyplot as plt
 import ldtk
-from ldtk import LDPSetCreator, BoxcarFilter
 from ldtk.ldmodel import LinearModel, QuadraticModel, NonlinearModel
+import lmfit as lm
+import logging
+import matplotlib.pyplot as plt
+import numpy as np
 
 log = logging.getLogger(__name__)
 
@@ -92,9 +90,9 @@ def createldgrid(minmu, maxmu, orbp,
         munm = 1e3*np.array(avmu[loweri:upperi])
         munmmin = 1e3*np.array(minmu[loweri:upperi])
         munmmax = 1e3*np.array(maxmu[loweri:upperi])
-        filters = [BoxcarFilter(str(mue), mun, mux)
+        filters = [ldtk.BoxcarFilter(str(mue), mun, mux)
                    for mue, mun, mux in zip(munm, munmmin, munmmax)]
-        sc = LDPSetCreator(teff=(tstar, terr), logg=(loggstar, loggerr),
+        sc = ldtk.LDPSetCreator(teff=(tstar, terr), logg=(loggstar, loggerr),
                            z=(fehstar, feherr), filters=filters)
         ps = sc.create_profiles(nsamples=int(1e4))
         itpfail = False
@@ -105,7 +103,7 @@ def createldgrid(minmu, maxmu, orbp,
         nfail = 1e0
         while itpfail:
             nfail *= 2
-            sc = LDPSetCreator(teff=(tstar, nfail*terr), logg=(loggstar, loggerr),
+            sc = ldtk.LDPSetCreator(teff=(tstar, nfail*terr), logg=(loggstar, loggerr),
                                z=(fehstar, feherr), filters=filters)
             ps = sc.create_profiles(nsamples=int(1e4))
             itpfail = False
@@ -254,4 +252,3 @@ def nl_ldx(params, x, data=None, weights=None):
     if weights is None:
         return data - model
     return (data - model)/weights
-