Xarray and other upgrades

.travis.yml

@@ -20,7 +20,6 @@ before_install:
 install:
   - source activate test-environment
   - python setup.py install
-  - make -C sami2py/fortran compile
 script:
   - nosetests -vs --with-coverage --cover-package=sami2py
 

README.md

@@ -33,14 +33,12 @@ a local install use the "--user" flag after "install".
   python setup.py install
 ```
 
-Additionally, you must make and install the fortran executables.
+If something has gone wrong, you may be prompted to manually install the fortran executables.
 
 ```
   make -C sami2py/fortran compile
 ```
 
-Now you can run the sami2 executable (sami2py.x) from anywhere.
-
 
 # Example
 

docs/installation.rst

@@ -15,10 +15,8 @@ a local install use the "--user" flag after "install".
   cd sami2py/
   python setup.py install
 
-Additionally, you must make and install the fortran executables.
+If something has gone wrong, you may be prompted to manually install the fortran executables.
 
 ::
 
   make -C sami2py/fortran compile
-
-Now you can run the sami2 executable (sami2py.x) from anywhere.

docs/sample_workflow.rst

@@ -27,4 +27,37 @@ Now load the resultant data:
 
   ModelRun = sami2py.Model(tag='run_name', lon=0, year=2012, day=210)
 
+The data is stored as `ModelRun.data`, which is an `xarray.Dataset`.  Information about the run is stored as 'ModelRun.MetaData', which is a human-readable dictionary of the namelist.
+
+The MetaData can be accessed directly via the dictionary, or through the __repr__.  Typing
+
+.. code:: python
+
+  ModelRun
+
+yields
+
+.. code:: python
+
+  Model Run Name = test
+  Day 256, 1999
+  Longitude = 256 deg
+  2 time steps from  0.1 to  0.1 UT
+  Ions Used: H+, O+, NO+, O2+, He+, N2+
+
+  Solar Activity
+  --------------
+  F10.7: 120.0 sfu
+  F10.7A: 120.0 sfu
+  ap: 0
+
+  Component Models Used
+  ---------------------
+  Neutral Atmosphere: NRLMSISe-2000
+  Winds: HWM-14
+  Photoproduction: EUVAC
+  ExB Drifts: Fejer-Scherliess
+
+  No modifications to empirical models
+
 Full description coming soon

sami2py/__init__.py

@@ -4,33 +4,16 @@
 # Full license can be found in License.md
 # -----------------------------------------------------------------------------
 """
-sami2py
------------
+sami2py - sami2py is another model of the ionosphere python style
+=================================================================
 
-Functions
----------------------------------------------------------------------------
-run_model(year, day, lat=0, lon=0, alt=300,
-          f107=120, f107a=120, ap=0,
-          rmin=100, rmax=2000, gams=3, gamp=3, altmin=85.,
-          dthr=0.25, hrinit=0., hrpr=24., hrmax=48.,
-          dt0=30., maxstep=100000000, denmin=1.e-6,
-          nion1=1, nion2=7, mmass=48, h_scale=1, o_scale=1,
-          no_scale=1, o2_scale=1, he_scale=1, n2_scale=1, n_scale=1,
-          Tinf_scale=1, Tn_scale=1., euv_scale=1,
-          wind_scale=1, hwm_model=14,
-          fejer=True, ExB_drifts=np.zeros((10,2)), ve01=0., exb_scale=1,
-          alt_crit=150., cqe=7.e-14,
-          tag='test', clean=False, test=False)
+Sami2py is a python module that runs the SAMI2 model, as well as archives,
+loads and plots the resulting modeled values. SAMI2 is a model developed
+by the Naval Research Laboratory to simulate the motions of plasma in a
+2D ionospheric environment along a dipole magnetic field [Huba et al, 2000].
+SAMI2 solves for the chemical and dynamical evolution of seven ion species
+in this environment (H+, He+, N+, O+, N2+, NO+, and O2+).
 
-    Initializes a run of the SAMI2 model and archives the data.
----------------------------------------------------------------------------
-
-Classes
----------------------------------------------------------------------------
-model
-    Loads, reshapes, and holds SAMI2 output for a given model run
-    specified by the user.
----------------------------------------------------------------------------
 """
 import logging
 import sys

sami2py/_core.py

@@ -32,7 +32,7 @@
 import os
 import subprocess
 import numpy as np
-from sami2py import fortran_dir
+from sami2py import fortran_dir, __version__
 from .utils import generate_path
 
 
@@ -252,8 +252,8 @@ def run_model(tag='model_run', lat=0, lon=0, alt=300, year=2018, day=1,
             'wind_scale': wind_scale, 'hwm_model': hwm_model}
 
     info['fejer'] = _generate_drift_info(fejer, ExB_drifts)
-    info['fmtout'] = _generate_format_info(fmtout)
-    info['outn'] = _generate_neutral_info(outn)
+    info['fmtout'] = _generate_fortran_bool(fmtout)
+    info['outn'] = _generate_fortran_bool(outn)
     _generate_namelist(info)
     archive_path = generate_path(tag, lon, year, day, test)
     if not test:
@@ -268,36 +268,22 @@ def _generate_drift_info(fejer, ExB_drifts=None):
     """Generates the information regarding the ExB drifts used by the model.
     This information is later stored in the namelist file for SAMI2
     """
-    if fejer:
-        drift_info = '.true.'
-    else:
+    drift_info = _generate_fortran_bool(fejer)
+    if not fejer:
         if ExB_drifts.shape != (10, 2):
             raise Exception('Invalid ExB drift shape!  Must be 10x2 ndarray.')
-        drift_info = '.false.'
         np.savetxt('exb.inp', ExB_drifts)
     return drift_info
 
 
-def _generate_format_info(fmtout):
-    """Generates the namelist information needed to tell the SAMI2 model to
-    output the model results in formatted or unformatted data files
-    """
-    if fmtout:
-        format_info = '.true.'
-    else:
-        format_info = '.false.'
-    return format_info
-
-
-def _generate_neutral_info(outn):
-    """Generates the namelist information needed to tell the SAMI2 model to
-    output the model results of neutral species and wind
+def _generate_fortran_bool(pybool):
+    """Generates a fortran bool as a string for the namelist generator
     """
-    if outn:
-        neutral_info = '.true.'
+    if pybool:
+        fbool = '.true.'
     else:
-        neutral_info = '.false.'
-    return neutral_info
+        fbool = '.false.'
+    return fbool
 
 
 def _generate_namelist(info):
@@ -380,6 +366,7 @@ def _archive_model(path, clean, fejer, fmtout, outn):
         If False, then 'exb.inp' is also archived
     """
     import shutil
+    import subprocess
 
     if fmtout:
         filelist = ['glonf.dat', 'glatf.dat', 'zaltf.dat',
@@ -392,19 +379,27 @@ def _archive_model(path, clean, fejer, fmtout, outn):
         filelist = ['glonu.dat', 'glatu.dat', 'zaltu.dat',
                     'deniu.dat', 'vsiu.dat', 'tiu.dat', 'teu.dat',
                     'time.dat', 'sami2py-1.00.namelist']
+        if outn:
+            filelist.append('dennu.dat')
+            filelist.append('u4u.dat')
 
     if os.path.isfile(filelist[0]):
         try:
             os.stat(path)
         except FileNotFoundError:
             os.makedirs(path)
 
+        hash = subprocess.check_output(['git', 'rev-parse', '--short', 'HEAD'])
+        with open(os.path.join(path, 'version.txt'), 'w+') as f:
+            f.write('sami2py v' + __version__ + '\n')
+            f.write('short hash ' + hash.decode("utf-8"))
+
         for list_file in filelist:
-            shutil.copyfile(list_file, path + list_file)
+            shutil.copyfile(list_file, os.path.join(path, list_file))
         if clean:
             for list_file in filelist[:-1]:
                 os.remove(list_file)
         if not fejer:
-            shutil.copyfile('exb.inp', path + 'exb.inp')
+            shutil.copyfile('exb.inp', os.path.join(path, 'exb.inp'))
     else:
         print('No files to move!')

sami2py/_core_class.py

@@ -20,6 +20,7 @@
 """
 from os import path
 import numpy as np
+import xarray as xr
 from .utils import generate_path, get_unformatted_data
 
 
@@ -210,18 +211,27 @@ def _load_model(self):
             te = get_unformatted_data(model_path, 'te',
                                       dim0=dim0, dim1=dim1, reshape=True)
 
-        self.glat = np.reshape(glat, (nz, nf), order="F")
-        self.glon = np.reshape(glon, (nz, nf), order="F")
-        self.zalt = np.reshape(zalt, (nz, nf), order="F")
-        self.deni = np.reshape(deni, (nz, nf, ni, nt), order="F")
-        self.vsi = np.reshape(vsi, (nz, nf, ni, nt), order="F")
-        self.ti = np.reshape(ti, (nz, nf, ni, nt), order="F")
-        self.te = np.reshape(te, (nz, nf, nt), order="F")
+        glat = np.reshape(glat, (nz, nf), order="F")
+        glon = np.reshape(glon, (nz, nf), order="F")
+        zalt = np.reshape(zalt, (nz, nf), order="F")
+        deni = np.reshape(deni, (nz, nf, ni, nt), order="F")
+        vsi = np.reshape(vsi, (nz, nf, ni, nt), order="F")
+        ti = np.reshape(ti, (nz, nf, ni, nt), order="F")
+        te = np.reshape(te, (nz, nf, nt), order="F")
+        self.data = xr.Dataset({'deni': (['z', 'f', 'ion', 'ut'], deni),
+                                'vsi': (['z', 'f', 'ion', 'ut'], vsi),
+                                'ti': (['z', 'f', 'ion', 'ut'], ti),
+                                'te': (['z', 'f', 'ut'], te),
+                                'slt': (['ut'], self.slt)},
+                               coords={'glat': (['z', 'f'], glat),
+                                       'glon': (['z', 'f'], glon),
+                                       'zalt': (['z', 'f'], zalt),
+                                       'ut': self.ut})
         if self.outn:
-            self.denn = np.reshape(denn, (nz, nf, 7, nt), order="F")
-            self.u = np.reshape(u, (nz, nf, nt), order="F")
-            del denn, u
-        del glat, glon, zalt, deni, vsi, ti, te
+            denn = np.reshape(denn, (nz, nf, 7, nt), order="F")
+            self.data['denn'] = denn
+            u = np.reshape(u, (nz, nf, nt), order="F")
+            self.data['u'] = u
 
     def _generate_metadata(self, namelist):
         """Reads the namelist and generates MetaData based on Parameters
@@ -345,7 +355,8 @@ def plot_lat_alt(self, time_step=0, species=1):
         """
         import matplotlib.pyplot as plt
 
-        plt.pcolor(self.glat, self.zalt, self.deni[:, :, species, time_step])
+        plt.pcolor(self.data['glat'], self.data['zalt'],
+                   self.data['deni'][:, :, species, time_step])
         plt.xlabel('Geo Lat (deg)')
         plt.ylabel('Altitude (km)')
         plt.show()

sami2py/fortran/exb.inp

@@ -1,10 +1,10 @@
--2.256592115245508268e+01 -1.700658929016086063e+01
-6.970157155494434598e+00 -1.785773092653965932e+01
-7.715990594846469097e-01 -1.457794556537672204e+00
-1.133009384321719537e+01 6.217447257350539047e+00
-5.315180719049175551e+00 6.543500525980066485e+00
--4.754135936133724094e+00 7.493698025175492994e+00
--3.036451049580922046e+00 -1.789034697779917638e+00
--3.791099765373269648e+00 -8.665409647917849956e-01
-2.083139968647748308e+00 -3.636326810220660732e+00
-2.205828847907577828e+00 0.000000000000000000e+00
+0.000000000000000000e+00 0.000000000000000000e+00
+0.000000000000000000e+00 0.000000000000000000e+00
+0.000000000000000000e+00 0.000000000000000000e+00
+0.000000000000000000e+00 0.000000000000000000e+00
+0.000000000000000000e+00 0.000000000000000000e+00
+0.000000000000000000e+00 0.000000000000000000e+00
+0.000000000000000000e+00 0.000000000000000000e+00
+0.000000000000000000e+00 0.000000000000000000e+00
+0.000000000000000000e+00 0.000000000000000000e+00
+0.000000000000000000e+00 0.000000000000000000e+00

sami2py/fortran/sami2py-1.00.f

@@ -2914,6 +2914,8 @@ subroutine sf1216 ( f,line,nfl )
 
       subroutine open_u
 
+      include 'param-1.00.inc'
+      include 'com-1.00.inc'
 !     open output files (unformatted, except time.dat)
 
       open ( unit=70, file='time.dat'      ,form='formatted'   )
@@ -2924,7 +2926,9 @@ subroutine open_u
 !      open ( unit=78, file='vnu.dat'       ,form='unformatted' )
 !      open ( unit=90, file='vtu.dat'       ,form='unformatted' )
 !      open ( unit=91, file='vru.dat'       ,form='unformatted' )
-!      open ( unit=92, file='dennu.dat'     ,form='unformatted' )
+      if (outn) then
+          open ( unit=92, file='dennu.dat'     ,form='unformatted' )
+      endif
 !      open ( unit=93, file='vexbu.dat'     ,form='unformatted' )
 
 !     diagnostic files (unformatted)
@@ -2935,7 +2939,9 @@ subroutine open_u
 !      open ( unit=84, file='u1u.dat'  ,form='unformatted' )
 !      open ( unit=85, file='u2u.dat'  ,form='unformatted' )
 !      open ( unit=86, file='u3u.dat'  ,form='unformatted' )
-!      open ( unit=87, file='u4u.dat'  ,form='unformatted' )
+      if (outn) then
+          open ( unit=87, file='u4u.dat'  ,form='unformatted' )
+      endif
 !      open ( unit=88, file='u5u.dat'  ,form='unformatted' )
 
       return

sami2py/fortran/sami2py-1.00.namelist

@@ -1,22 +1,22 @@
 &go
   fmtout   = .true.,
   maxstep  =  100000000,
-  hrmax    =  48.000000,
+  hrmax    =  0.110000,
   dt0      =  30.000000,
-  dthr     =  0.250000,
-  hrpr     =  24.000000,
+  dthr     =  0.050000,
+  hrpr     =  0.000000,
   grad_in  =  300.000000,
   glat_in  =  0.000000,
-  glon_in  =  0.000000,
+  glon_in  =  256.000000,
   fejer    =  .true.,
   rmin     =  100.000000,
   rmax     =  2000.000000,
   altmin   =  85.000000,
   fbar     =  120.000000,
   f10p7    =  120.000000,
   ap       =  0,
-  year     =  2012,
-  day      =  211,
+  year     =  1958,
+  day      =  30,
   mmass    =  48,
   nion1    =  1,
   nion2    =  7,

sami2py/tests/test_core.py

@@ -23,7 +23,8 @@ def setup(self):
         if not os.path.exists(self.model_path):
             os.makedirs(self.model_path)
         self.filelist = ['glonf.dat', 'glatf.dat', 'zaltf.dat', 'denif.dat',
-                         'vsif.dat', 'tif.dat', 'tef.dat', 'time.dat']
+                         'dennf.dat', 'u4f.dat', 'vsif.dat', 'tif.dat',
+                         'tef.dat', 'time.dat']
         for filename in self.filelist:
             open(os.path.join(fortran_dir, filename), 'w').close()
 
@@ -42,7 +43,7 @@ def teardown(self):
     def test_run_model_namelist(self):
         """The test to ensure that the namelist file is generated properly
         """
-        sami2py.run_model(tag='test', year=2012, day=211, test=True,
+        sami2py.run_model(tag='test', lon=0, year=2012, day=211, test=True,
                           fmtout=self.format)
         namelist_file = self.model_path + 'sami2py-1.00.namelist'
         ref_namelist = os.path.join(test_data_dir, self.ref_file)
@@ -61,7 +62,7 @@ def test_run_model_dat_files(self):
         """Test to ensure that the dat files are copied properly
         """
         sami2py.run_model(tag='test', lon=0, year=2012, day=211, test=True,
-                          fmtout=self.format)
+                          fmtout=self.format, outn=True)
         if self.format:
             fname = 'glonf.dat'
         else:
@@ -123,7 +124,8 @@ def setup(self):
         if not os.path.exists(self.model_path):
             os.makedirs(self.model_path)
         self.filelist = ['glonu.dat', 'glatu.dat', 'zaltu.dat', 'deniu.dat',
-                         'vsiu.dat', 'tiu.dat', 'teu.dat', 'time.dat']
+                         'dennu.dat', 'u4u.dat', 'vsiu.dat', 'tiu.dat',
+                         'teu.dat', 'time.dat']
         for filename in self.filelist:
             open(os.path.join(fortran_dir, filename), 'w').close()