Merge 7b25755 into 56aff77

README.md

@@ -68,10 +68,10 @@ The methods that run empirical models can also be exported to any pysat instrume
 
 ```
 import pysat
-import pysatMissions.methods.pyglow as mm_glow
+import pysatMissions.methods.empirical as mm_emp
 
 ivm = pysat.Instrument(platform='cnofs', name='ivm')
-ivm.custom.add(mm_glow.add_iri_thermal_plasma, 'modify', glat_label='glat',
+ivm.custom.add(mm_emp.add_iri_thermal_plasma, 'modify', glat_label='glat',
                glong_label='glon', alt_label='altitude')
 ```
 Once the custom function is added, the model will automatically be run when the dataset is loaded.

docs/introduction.rst

@@ -8,8 +8,7 @@ Main Features
 -------------
 - Simulate satellite orbits from TLEs and add data from empirical models
 - Import ionosphere and thermosphere model values through pyglow
-- Import magnetic coordinates through apexpy
-- Import magnetic coordinates through aacgmv2
+- Import magnetic coordinates through apexpy and aacgmv2
 - Import geomagnetic basis vectors through pysatMagVect
 
 This document covers installation, a tutorial on pysatMissions including demonstration code, and an API reference.

docs/tutorial.rst

@@ -35,9 +35,9 @@ A number of methods are included to invoke several python wrappers for empirical
 .. code:: python
 
   import pysat
-  from pysatMissions.methods import pyglow as mm_glow
+  from pysatMissions.methods import empirical as mm_emp
 
   ivm = pysat.Instrument(platform='cnofs', name='ivm')
-  ivm.custom.add(mm_glow.add_iri_thermal_plasma, 'modify', 'end', glat_label='glat', glong_label='glon', alt_label='altitude')
+  ivm.custom.add(mm_emp.add_iri_thermal_plasma, 'modify', 'end', glat_label='glat', glong_label='glon', alt_label='altitude')
 
 Note that in this case, the latitude, longitude, and altitude variable names of the instrument must be specified since they are not identical to the default names in the function.

pysatMissions/instruments/pysat_ephem.py

@@ -18,9 +18,8 @@
 import pysatMagVect
 
 from pysatMissions.instruments import _core as mcore
-from pysatMissions.methods import aacgmv2 as mm_aacgm
-from pysatMissions.methods import apexpy as mm_apex
-from pysatMissions.methods import pyglow as mm_glow
+from pysatMissions.methods import magcoord as mm_magcoord
+from pysatMissions.methods import empirical as mm_emp
 from pysatMissions.methods import spacecraft as mm_sc
 
 # pysat required parameters
@@ -46,13 +45,13 @@ def init(self):
 
     """
 
-    self.custom.add(mm_apex.add_quasi_dipole_coordinates, 'modify')
-    self.custom.add(mm_aacgm.add_aacgm_coordinates, 'modify')
+    self.custom.add(mm_magcoord.add_quasi_dipole_coordinates, 'modify')
+    self.custom.add(mm_magcoord.add_aacgm_coordinates, 'modify')
     self.custom.add(mm_sc.calculate_ecef_velocity, 'modify')
     self.custom.add(mm_sc.add_sc_attitude_vectors, 'modify')
     # project simulated vectors onto s/c basis
     # IGRF
-    self.custom.add(mm_glow.add_igrf, 'modify')
+    self.custom.add(mm_emp.add_igrf, 'modify')
     # create metadata to be added along with vector projection
     in_meta = {'desc': 'IGRF geomagnetic field expressed in the s/c basis.',
                'units': 'nT'}
@@ -62,12 +61,12 @@ def init(self):
                     'B_sc_z', meta=[in_meta.copy(), in_meta.copy(),
                                     in_meta.copy()])
     # Thermal Ion Parameters
-    self.custom.add(mm_glow.add_iri_thermal_plasma, 'modify')
+    self.custom.add(mm_emp.add_iri_thermal_plasma, 'modify')
     # Thermal Neutral parameters
-    self.custom.add(mm_glow.add_msis, 'modify')
-    self.custom.add(mm_glow.add_hwm_winds_and_ecef_vectors, 'modify')
+    self.custom.add(mm_emp.add_msis, 'modify')
+    self.custom.add(mm_emp.add_hwm_winds_and_ecef_vectors, 'modify')
     # project total wind vector
-    self.custom.add(mm_glow.project_hwm_onto_sc, 'modify')
+    self.custom.add(mm_emp.project_hwm_onto_sc, 'modify')
 
 
 def load(fnames, tag=None, sat_id=None, obs_long=0., obs_lat=0., obs_alt=0.,

pysatMissions/methods/__init__.py

@@ -3,9 +3,8 @@
 the methods to interface with numerous empirical model packages
 """
 
-from pysatMissions.methods import aacgmv2
-from pysatMissions.methods import apexpy
-from pysatMissions.methods import pyglow
+from pysatMissions.methods import empirical
+from pysatMissions.methods import magcoord
 from pysatMissions.methods import spacecraft
 
-__all__ = ['aacgmv2', 'apexpy', 'pyglow', 'spacecraft']
+__all__ = ['empirical', 'magcoord', 'spacecraft']

pysatMissions/methods/apexpy.py → pysatMissions/methods/magcoord.py

@@ -1,11 +1,73 @@
-"""Provides default routines for projecting apexpy values onto locations
+"""Provides default routines for projecting aacgmv2 model values onto locations
 from pysat instruments.
 
 """
 
+import aacgmv2
 import apexpy
 
 
+def add_aacgm_coordinates(inst, glat_label='glat', glong_label='glong',
+                          alt_label='alt'):
+    """
+    Uses AACGMV2 package to add AACGM coordinates to instrument object.
+
+    The Altitude Adjusted Corrected Geomagnetic Coordinates library is used
+    to calculate the latitude, longitude, and local time
+    of the spacecraft with respect to the geomagnetic field.
+
+    Parameters
+    ----------
+    inst : pysat.Instrument
+        instrument object including lat, lon, and alt as timeseries
+    glat_label : string
+        label used in inst to identify WGS84 geodetic latitude (degrees N)
+    glong_label : string
+        label used in inst to identify WGS84 geodetic longitude (degrees E)
+    alt_label : string
+        label used in inst to identify WGS84 geodetic altitude (km, height
+        above surface)
+
+    Returns
+    -------
+    inst
+        Input pysat.Instrument object modified to include quasi-dipole
+        coordinates, 'aacgm_lat' for magnetic latitude, 'aacgm_long' for
+        longitude, and 'aacgm_mlt' for magnetic local time.
+
+    Example
+    -------
+        # function added velow modifies the inst object upon every inst.load
+        call inst.custom.add(add_quasi_dipole_coordinates, 'modify',
+        glat_label='custom_label')
+
+    """
+
+    aalat = []
+    aalon = []
+    mlt = []
+    for lat, lon, alt, time in zip(inst[glat_label], inst[glong_label],
+                                   inst[alt_label], inst.data.index):
+        # aacgmv2 latitude and longitude from geodetic coords
+        tlat, tlon, tmlt = aacgmv2.get_aacgm_coord(lat, lon, alt, time)
+        aalat.append(tlat)
+        aalon.append(tlon)
+        mlt.append(tmlt)
+
+    inst['aacgm_lat'] = aalat
+    inst['aacgm_long'] = aalon
+    inst['aacgm_mlt'] = mlt
+
+    inst.meta['aacgm_lat'] = {'units': 'degrees',
+                              'long_name': 'AACGM latitude'}
+    inst.meta['aacgm_long'] = {'units': 'degrees',
+                               'long_name': 'AACGM longitude'}
+    inst.meta['aacgm_mlt'] = {'units': 'hrs',
+                              'long_name': 'AACGM Magnetic local time'}
+
+    return
+
+
 def add_quasi_dipole_coordinates(inst, glat_label='glat', glong_label='glong',
                                  alt_label='alt'):
     """

pysatMissions/tests/test_methods_pyglow.py → pysatMissions/tests/test_methods_empirical.py

@@ -3,7 +3,7 @@
 
 import numpy as np
 import pysat
-from pysatMissions.methods import pyglow as mm_glow
+from pysatMissions.methods import empirical as mm_emp
 
 
 def add_altitude(inst, altitude=400.0):
@@ -25,7 +25,7 @@ def teardown(self):
 
     def test_add_iri_thermal_plasma(self):
         """Test adding thermal plasma data to test inst"""
-        self.testInst.custom.add(mm_glow.add_iri_thermal_plasma, 'modify',
+        self.testInst.custom.add(mm_emp.add_iri_thermal_plasma, 'modify',
                                  glat_label='latitude',
                                  glong_label='longitude',
                                  alt_label='altitude')
@@ -41,7 +41,7 @@ def test_add_iri_thermal_plasma(self):
 
     def test_add_igrf(self):
         """Test adding igrf model to test inst"""
-        self.testInst.custom.add(mm_glow.add_igrf, 'modify',
+        self.testInst.custom.add(mm_emp.add_igrf, 'modify',
                                  glat_label='latitude',
                                  glong_label='longitude',
                                  alt_label='altitude')
@@ -57,7 +57,7 @@ def test_add_igrf(self):
 
     def test_add_msis(self):
         """Test adding msis model to test inst"""
-        self.testInst.custom.add(mm_glow.add_msis, 'modify',
+        self.testInst.custom.add(mm_emp.add_msis, 'modify',
                                  glat_label='latitude',
                                  glong_label='longitude',
                                  alt_label='altitude')

pysatMissions/tests/test_methods_aacgmv2.py → pysatMissions/tests/test_methods_magcoord.py

@@ -3,7 +3,7 @@
 
 import numpy as np
 import pysat
-import pysatMissions.methods.aacgmv2 as mm_aacgm
+import pysatMissions.methods.magcoord as mm_magcoord
 
 
 def add_altitude(inst, altitude=400.0):
@@ -25,7 +25,8 @@ def teardown(self):
 
     def test_add_aacgm_coordinates(self):
         """Test adding thermal plasma data to test inst"""
-        self.testInst.custom.add(mm_aacgm.add_aacgm_coordinates, 'modify',
+        self.testInst.custom.add(mm_magcoord.add_aacgm_coordinates,
+                                 'modify',
                                  glat_label='latitude',
                                  glong_label='longitude',
                                  alt_label='altitude')
@@ -37,3 +38,19 @@ def test_add_aacgm_coordinates(self):
             assert not np.isnan(self.testInst[target]).any()
             # Check if metadata is added
             assert target in self.testInst.meta.data.index
+
+    def test_add_quasi_dipole_coordinates(self):
+        """Test adding thermal plasma data to test inst"""
+        self.testInst.custom.add(mm_magcoord.add_quasi_dipole_coordinates,
+                                 'modify',
+                                 glat_label='latitude',
+                                 glong_label='longitude',
+                                 alt_label='altitude')
+        self.testInst.load(date=pysat.datetime(2009, 1, 1))
+        targets = ['qd_lat', 'qd_long', 'mlt']
+        for target in targets:
+            # Check if data is added
+            assert target in self.testInst.data.keys()
+            assert not np.isnan(self.testInst[target]).any()
+            # Check if metadata is added
+            assert target in self.testInst.meta.data.index