Merge pull request #114 from rkitano-1/develop

ENH: Issue #87

CHANGELOG.md

@@ -4,6 +4,11 @@ This project adheres to [Semantic Versioning](http://semver.org/).
 
 ## [next version] - 2020-07-27
 - Using numpy 1.16 as minimum test version in accordance with NEP 29
+- Removed the sami2py-1.00.namelist and version.txt files from run_name
+- Added ability to input custom ExB Drifts as a Fourier Series
+  - return_fourier function in utils.py 
+  - plot_exb function in _core_class.py
+  - Testing return_fourier function in test_utils.py
 
 ## [0.2.2] - 2020-07-17
 - Added simple port of core data to netcdf file

sami2py/_core_class.py

@@ -4,15 +4,12 @@
 # Full license can be found in License.md
 # -----------------------------------------------------------------------------
 """Wrapper for running sami2 model
-
 Classes
 -------------------------------------------------------------------------------
 Model
     Loads, reshapes, and holds SAMI2 output for a given model run
     specified by the user.
 -------------------------------------------------------------------------------
-
-
 Moduleauthor
 -------------------------------------------------------------------------------
 Jeff Klenzing (JK), 1 Dec 2017, Goddard Space Flight Center (GSFC)
@@ -21,7 +18,7 @@
 from os import path
 import numpy as np
 import xarray as xr
-from sami2py.utils import generate_path, get_unformatted_data
+from sami2py.utils import generate_path, get_unformatted_data, return_fourier
 
 
 class Model(object):
@@ -30,7 +27,6 @@ class Model(object):
     def __init__(self, tag, lon, year, day, outn=False, test=False):
         """ Loads a previously run sami2 model and sorts into
             appropriate array shapes
-
         Parameters
         ----------
         tag : (string)
@@ -47,25 +43,21 @@ def __init__(self, tag, lon, year, day, outn=False, test=False):
         test : (boolean)
             if true : use test model output
             if false : look for user made model output
-
         Returns
         -------
         self : model class object containing OCB file data
-
         Attributes
         ----------
         ut : (1D ndarray)
             Universal Time (hrs)
         slt : (1D ndarray)
             Solar Local Time (hr)
-
         glat : (2D ndarray)
             Geographic Latitude (deg)
         glon : (2D ndarray)
             Geographic Longitude (deg)
         zalt : (2D ndarray)
             Altitude (km)
-
         deni : (4D ndarray)
             Ion density by species (cm^-3)
         vsi : (4D ndarray)
@@ -74,12 +66,10 @@ def __init__(self, tag, lon, year, day, outn=False, test=False):
             Ion Temperature by species (K)
         te : (3D ndarray)
             Electron Temperature (K)
-
         Examples
         --------
         To load a previous model run:
             ModelRun = sami2py.Model(tag='run_name', lon=0, year=2012, day=210)
-
         """
 
         self.tag = tag
@@ -93,19 +83,16 @@ def __init__(self, tag, lon, year, day, outn=False, test=False):
 
     def __repr__(self):
         """Make a printable representation of a Model object
-
         Returns
         -------
         out : (string)
             string containing a printable representation of a Model object
-
         Examples
         --------
         Load the model
             ModelRun = sami2py.Model(tag='run_name', lon=0, year=2012, day=210)
         Check the model information
             ModelRun
-
         """
 
         out = ['']
@@ -149,7 +136,6 @@ def __repr__(self):
 
     def _calculate_slt(self):
         """Calculates Solar Local Time for reference point of model
-
         Returns
         -------
         self.slt : (float)
@@ -164,7 +150,6 @@ def _calculate_slt(self):
 
     def _load_model(self):
         """Loads model results
-
         Returns
         -------
         void
@@ -263,12 +248,10 @@ def _load_model(self):
 
     def _generate_metadata(self, namelist):
         """Reads the namelist and generates MetaData based on Parameters
-
         Parameters
         -----------
         namelist : (list)
             variable namelist from SAMI2 model
-
         Returns
         -------
         void
@@ -345,26 +328,22 @@ def find_int(name, ind):
 
     def check_standard_model(self, model_type="all"):
         """Checks for standard atmospheric inputs
-
         Parameters
         ----------
         model_type : (str)
             Limit check to certain models (default='all')
             Not currently implemented
-
         Returns
         -------
         mod_keys : (list)
             List of modified keyword for self.MetaData, empty
             if no modifications were made
-
         Examples
         --------
         Load the model
             ModelRun = sami2py.Model(tag='run_name', lon=0, year=2012, day=210)
         Check the model information for changes to the standard inputs
             ModelRun.check_standard_model()
-
         """
         mod_keys = list()
         meta_keys = list(self.MetaData.keys())
@@ -391,15 +370,13 @@ def to_netcdf(self, path=''):
 
     def plot_lat_alt(self, time_step=0, species=1):
         """Plots input parameter as a function of latitude and altitude
-
         Parameters
         ----------
         time_step : (int)
             time index for SAMI2 model results
         species : (int)
             ion species index :
             0: H+, 1: O+, 2: NO+, 3: O2+, 4: He+, 5: N2+, 6: N+
-
         Examples
         --------
         Load the model
@@ -408,7 +385,6 @@ def plot_lat_alt(self, time_step=0, species=1):
             ModelRun.plot_lat_alt()
         Plot the H+ density at the 100th time step (initial step is 0)
             ModelRun.plot_lat_alt(time_step=99, species=0)
-
         """
         import matplotlib.pyplot as plt
         import warnings
@@ -425,3 +401,27 @@ def plot_lat_alt(self, time_step=0, species=1):
         plt.ylabel('Altitude (km)')
 
         return fig
+
+    def plot_exb(self):
+        """Plots ExB drifts from the return_fourier function
+
+        Examples
+        --------
+        Load the model
+            ModelRun = sami2py.Model(tag='exb', lon=0, year=2012, day=210)
+        Plot ExB drifts
+            ModelRun.plot_exb()
+        """
+        import matplotlib.pyplot as plt
+        import warnings
+
+        warnings.warn(' '.join(["Model.plot_exb is deprecated and will be",
+                                "removed in a future version. ",
+                                "Use sami2py_vis instead"]),
+                      DeprecationWarning)
+
+        plt.xlabel('Time (hrs)')
+        plt.ylabel('ExB Drifts')
+        plt.plot(return_fourier(self.slt, self.MetaData['Fourier Coeffs']))
+
+        return plt

sami2py/tests/test_utils.py

@@ -60,7 +60,6 @@ class TestArchiveDir():
     """Test basic functionality of the set_archive_dir function"""
     def test_set_archive_dir(self):
         """Test that set_archive_dir has set and stored the archive directory
-
            To leave the archive directory unchanged it must be gathered and
            reset after the test is complete
         """
@@ -127,3 +126,49 @@ def file_open_error(self):
         """File open should raise an error if invalid file path provided"""
         with pytest.raises(IOError):
             sami2py.utils.get_unformatted_data(self.model_pathU, 'glat')
+
+
+class TestFourierFunction():
+    """Test basic functionality of the return_fourier function"""
+    def setup(self):
+        """Setup the x and coefficient variables with general x values and
+        coefficients"""
+        self.x = np.array([0.11, 0.36, 0.61, 0.86, 1.12, 1.37, 1.62, 1.88,
+                           2.13, 2.38, 2.64, 2.89, 3.14, 3.4, 3.65, 3.9,
+                           4.16, 4.41, 4.66, 4.92, 5.17, 5.42, 5.68, 5.93,
+                           6.18, 6.44, 6.69, 6.94, 7.2, 7.45, 7.7, 7.95,
+                           8.2, 8.46, 8.71, 8.96, 9.21, 9.46, 9.72, 9.97,
+                          10.23, 10.49, 10.74, 10.99, 11.24, 11.49, 11.74,
+                          11.99, 12.24, 12.49, 12.74, 13., 13.26, 13.51, 13.76,
+                          14.02, 14.27, 14.53, 14.79, 15.04, 15.29, 15.54,
+                          15.79, 16.04, 16.29, 16.54, 16.79, 17.04, 17.29,
+                          17.54, 17.8, 18.05, 18.31, 18.56, 18.81, 19.07,
+                          19.32, 19.57, 19.83, 20.08, 20.33, 20.59, 20.84,
+                          21.09, 21.35, 21.6, 21.85, 22.11, 22.36, 22.61,
+                          22.86, 23.12, 23.37, 23.624, 23.87])
+
+        self.coeffs = np.zeros((10, 2))
+
+    def teardown(self):
+        """Resets both parameters"""
+        del self.x, self.coeffs
+
+    def test_cos(self):
+        """Test the cos function when coeffs are all 0s except for one with 1
+        value
+        """
+        self.coeffs[0, 0] = 1.0
+
+        y = sami2py.utils.return_fourier(self.x, self.coeffs)
+        target = np.cos(np.pi * self.x / 12.)
+        assert (y == target).all()
+
+    def test_sin(self):
+        """Test the sine function when coeffs are all 0s except for one with 1
+        value
+        """
+        self.coeffs[0, 1] = 1.0
+
+        y = sami2py.utils.return_fourier(self.x, self.coeffs)
+        target = np.sin(np.pi * self.x / 12.)
+        assert (y == target).all()

sami2py/utils.py

@@ -13,6 +13,9 @@
 set_archive_dir(path=None, store=None)
     Allows user to specify the location where the model outputs will be stored
 
+return_fourier(x, coeffs)
+    Returns Fourier Series up to NumF Coefficients
+
 get_unformatted_data(dat_dir, var_name, nz, nf, ni, nt, reshape=False)
     routine to interpret unformatted binary files created by the SAMI2 model
 -------------------------------------------------------------------------------
@@ -24,6 +27,7 @@
 """
 
 import os
+import numpy as np
 
 
 def generate_path(tag, lon, year, day, test=False):
@@ -113,6 +117,39 @@ def set_archive_dir(path=None, store=True):
         raise ValueError('Path does not lead to a valid directory.')
 
 
+def return_fourier(x, coeffs):
+    """
+    Returns a Fourier series up to NumF coefficients
+
+    Parameters
+    ----------
+    x : (1d ndarray)
+        solar local time in hours (slt)
+    coeffs : (array)
+        10x2 array of fourier coefficients
+
+    Returns
+    --------
+    y : (array)
+        result of the fourier series
+    """
+    def cos_a(x, n):
+        """simple cosine"""
+        return np.cos(n * np.pi * x / 12.0)
+
+    def sin_a(x, n):
+        """simple sine"""
+        return np.sin(n * np.pi * x / 12.0)
+
+    NumF = coeffs.shape
+
+    y = 0.0 * x
+    for i in range(0, NumF[0]):
+        y += coeffs[i, 0] * cos_a(x, i + 1) + coeffs[i, 1] * sin_a(x, i + 1)
+
+    return y
+
+
 def get_unformatted_data(dat_dir, var_name, reshape=False, dim=(0, 0)):
     """Routine to interpret unformatted binary files created by the SAMI2 model
 
@@ -139,7 +176,6 @@ def get_unformatted_data(dat_dir, var_name, reshape=False, dim=(0, 0)):
     float_data : (numpy.ndarray)
         unformatted data organized into a numpy array for handling in python
     """
-    import numpy as np
 
     binary_file = open(os.path.join(dat_dir, var_name + 'u.dat'), 'rb')
     float_data = np.fromfile(binary_file, dtype='float32')