Squashed commit of the following:

commit 06d0499
Author: Michael Hirsch, Ph.D <scivision@users.noreply.github.com>
Date:   Fri Mar 30 03:28:53 2018 -0400

    lat profile working

commit 2720d13
Author: Michael Hirsch, Ph.D <scivision@users.noreply.github.com>
Date:   Fri Mar 30 02:54:27 2018 -0400

    fixed time profile too

commit 95082c2
Author: Michael Hirsch, Ph.D <scivision@users.noreply.github.com>
Date:   Fri Mar 30 02:43:56 2018 -0400

    needs thorough cleaning

commit 4b7eee9
Author: Michael Hirsch, Ph.D <scivision@users.noreply.github.com>
Date:   Fri Mar 30 02:40:27 2018 -0400

    altitude profile OK

commit 6c80575
Author: Michael Hirsch, Ph.D <scivision@users.noreply.github.com>
Date:   Tue Mar 6 23:27:05 2018 -0500

    template

commit 2ced97a
Author: Michael Hirsch, Ph.D <scivision@users.noreply.github.com>
Date:   Tue Mar 6 23:19:22 2018 -0500

    mpl2.2

commit 7fdac07
Author: Michael Hirsch, Ph.D <scivision@users.noreply.github.com>
Date:   Mon Mar 5 18:28:45 2018 -0500

    log

commit c994f87
Author: Michael Hirsch, Ph.D <scivision@users.noreply.github.com>
Date:   Mon Mar 5 18:12:32 2018 -0500

    alt plots OK

commit 5c76e42
Author: Michael Hirsch, Ph.D <scivision@users.noreply.github.com>
Date:   Mon Mar 5 18:07:46 2018 -0500

    uniform alt grid fixed

commit d2c48f3
Author: Michael Hirsch, Ph.D <scivision@users.noreply.github.com>
Date:   Mon Mar 5 17:42:23 2018 -0500

    ig

commit 8d1fb84
Author: Michael Hirsch, Ph.D <scivision@users.noreply.github.com>
Date:   Mon Mar 5 17:42:05 2018 -0500

    ig

commit 93e261a
Author: Michael Hirsch, Ph.D <scivision@users.noreply.github.com>
Date:   Mon Mar 5 17:41:35 2018 -0500

    INWORK: debug altitude all one height

commit e4dc4e3
Author: Michael Hirsch, Ph.D <scivision@users.noreply.github.com>
Date:   Mon Mar 5 17:29:58 2018 -0500

    first time density profile plot workign

commit adc1d9f
Author: Michael Hirsch, Ph.D <scivision@users.noreply.github.com>
Date:   Mon Mar 5 17:11:39 2018 -0500

    passing out data, fixing up plots

commit 60a814b
Author: Michael Hirsch, Ph.D <scivision@users.noreply.github.com>
Date:   Mon Mar 5 16:48:49 2018 -0500

    disable FIRI by default

commit 2a9218e
Author: Michael Hirsch, Ph.D <scivision@users.noreply.github.com>
Date:   Mon Mar 5 16:27:55 2018 -0500

    import syntax

commit 25e18df
Author: Michael Hirsch, Ph.D <scivision@users.noreply.github.com>
Date:   Mon Mar 5 16:20:28 2018 -0500

    OK repeated run

commit e195488
Author: Michael Hirsch, Ph.D <scivision@users.noreply.github.com>
Date:   Mon Mar 5 15:43:28 2018 -0500

    simplify

commit 803b41b
Author: Michael Hirsch, Ph.D <scivision@users.noreply.github.com>
Date:   Mon Mar 5 15:23:32 2018 -0500

    cleaning up

commit ac3483d
Author: Michael Hirsch, Ph.D <scivision@users.noreply.github.com>
Date:   Mon Mar 5 14:58:55 2018 -0500

    cleanup

commit 4cdbcd9
Author: Michael Hirsch, Ph.D <scivision@users.noreply.github.com>
Date:   Mon Mar 5 14:56:29 2018 -0500

    deblank

commit 95e7776
Author: Michael Hirsch, Ph.D <scivision@users.noreply.github.com>
Date:   Mon Mar 5 14:44:34 2018 -0500

    needed to read ig_rz.dat

commit dc14f41
Author: Michael Hirsch, Ph.D <scivision@users.noreply.github.com>
Date:   Mon Mar 5 14:27:21 2018 -0500

    pass data directory, error stop

commit 692d7b8
Author: Michael Hirsch, Ph.D <scivision@users.noreply.github.com>
Date:   Mon Mar 5 13:53:01 2018 -0500

    error stop

commit f7181af
Author: Michael Hirsch, Ph.D <scivision@users.noreply.github.com>
Date:   Mon Mar 5 13:42:52 2018 -0500

    init

commit f8ff215
Author: Michael Hirsch, Ph.D <scivision@users.noreply.github.com>
Date:   Mon Mar 5 13:42:44 2018 -0500

    large cleanup

.gitignore

@@ -1,3 +1,5 @@
+baseIRI2016
+testiri2016
 bin/
 
 # Byte-compiled / optimized / DLL files

.travis.yml

@@ -21,8 +21,11 @@ before_install:
     # temp for pip < 9.1
     - pip -q install numpy
 
-install: pip install -e .[tests]
+install: pip -q install -e .[tests]
 
-script: coverage run tests/test_all.py -v
+script:
+  - pytest -v
 
-after_success: coveralls
+after_success: 
+ - coverage run tests/test_all.py
+ - coveralls

AltitudeProfile.py

@@ -0,0 +1,38 @@
+#!/usr/bin/env python
+""" Height Profile Example """
+import pyiri2016
+#
+import numpy as np
+from matplotlib.pyplot import figure, show
+
+glat, glon = -11.95, -76.77
+
+alt_km = np.arange(80,1000,20.)
+
+iri = pyiri2016.IRI('2012-08-21T12', alt_km, glat, glon)
+
+fig = figure(figsize=(16,6))
+axs = fig.subplots(1,2)
+
+fig.suptitle(f'{str(iri.time[0].values)[:-13]}\n Glat, Glon: {iri.glat}, {iri.attrs["glon"]}')
+
+
+pn = axs[0]
+pn.plot(iri['ne'].squeeze(), iri.alt_km, label='N$_e$')
+#pn.set_title(iri2016Obj.title1)
+pn.set_xlabel('Density (m$^{-3}$)')
+pn.set_ylabel('Altitude (km)')
+pn.set_xscale('log')
+pn.legend(loc='best')
+pn.grid(True)
+
+pn = axs[1]
+pn.plot(iri['Ti'].squeeze(), iri.alt_km, label='T$_i$')
+pn.plot(iri['Te'].squeeze(), iri.alt_km, label='T$_e$')
+#pn.set_title(iri2016Obj.title2)
+pn.set_xlabel('Temperature (K)')
+pn.set_ylabel('Altitude (km)')
+pn.legend(loc='best')
+pn.grid(True)
+
+show()

LatitudeProfile.py

@@ -0,0 +1,45 @@
+#!/usr/bin/env python
+import pyiri2016
+from numpy import arange
+from matplotlib.pyplot import figure,  show
+
+""" Geog. Latitude Profile Example """
+
+latlim = [-60, 60]
+latstp = 2.
+sim = pyiri2016.geoprofile(altkm=600, latlim=latlim, dlat=latstp, \
+glon=-76.77,   time='2004-01-01T17')
+
+latbins = arange(latlim[0], latlim[1], latstp)
+
+
+fig = figure(figsize=(8,12))
+axs = fig.subplots(2,1, sharex=True)
+
+pn = axs[0]
+
+pn.plot(latbins, sim['NmF2'].squeeze(), label='N$_m$F$_2$')
+pn.plot(latbins, sim['NmF1'].squeeze(), label='N$_m$F$_1$')
+pn.plot(latbins, sim['NmE'].squeeze(), label='N$_m$E')
+pn.set_title(str(sim.time[0].values)[:-13] + '  latitude'+str(latlim))
+pn.set_xlim(latbins[[0, -1]])
+pn.set_xlabel('Geog. Lat. ($^\circ$)')
+pn.set_ylabel('(m$^{-3}$)')
+pn.set_yscale('log')
+
+
+pn = axs[1]
+pn.plot(latbins, sim['hmF2'].squeeze(), label='h$_m$F$_2$')
+pn.plot(latbins, sim['hmF1'].squeeze(), label='h$_m$F$_1$')
+pn.plot(latbins, sim['hmE'].squeeze(), label='h$_m$E')
+pn.set_xlim(latbins[[0, -1]])
+pn.set_title(str(sim.time[0].values)[:-13] + '  latitude'+str(latlim))
+pn.set_xlabel('Geog. Lat. ($^\circ$)')
+pn.set_ylabel('(km)')
+
+for a in axs:
+    a.legend(loc='best')
+    a.grid(True)
+
+
+show()

README.rst

@@ -31,20 +31,20 @@ Usage
 Height-profile
 ---------------
 
-`plot density and temperatures vs height <examples/iri1DExample01.py>`_
+`plot density and temperatures vs height <AltitudeProfile.py>`_
 
 .. image:: figures/iri1DExample01.png
 
 Latitudinal profile
 -------------------
 
-`plot densities and height at the peak of F2, F2, and E regions vs geographic latitude <examples/iri1DExample02.py>`_
+`plot densities and height at the peak of F2, F2, and E regions vs geographic latitude <LatitudeProfile.py>`_
 
 .. image:: figures/iri1DExample02.png
 
 GMT profile
 -----------
-`plot densities and height at the peak of F2, F2, and E regions vs universal time <examples/iri_timeprofile.py>`_
+`plot densities and height at the peak of F2, F2, and E regions vs universal time <TimeProfile.py>`_
 
 .. image:: figures/iri1DExample08.png
 
@@ -74,7 +74,7 @@ Fortran compile
 
     make
 
-    ./testiri2016
+    make test
 
 
 f2py compile

TimeProfile.py

@@ -0,0 +1,104 @@
+#!/usr/bin/env python
+""" Time Profile: IRI2016 """
+import numpy as np
+from datetime import timedelta
+from matplotlib.pyplot import figure, show
+try:
+    import ephem
+except ImportError:
+    ephem = None
+#
+import pyiri2016
+
+
+# %% user parameters
+#lat = -11.95; lon = -76.77
+#glat, glon = 0,0
+glat,glon = 65,-148
+alt_km = np.arange(120, 180, 20)
+# %% ru
+sim = pyiri2016.timeprofile(('2012-08-21','2012-08-22'),timedelta(hours=0.25),
+                            alt_km,glat,glon)
+
+# %% Plots
+Nplot=3
+
+if Nplot>2:
+    fig = figure(figsize=(16,12))
+    axs = fig.subplots(3,1, sharex=True).ravel()
+else:
+    fig = figure(figsize=(16,6))
+    axs = fig.subplots(1,2).ravel()
+
+fig.suptitle(f'{str(sim.time[0].values)[:-13]} to {str(sim.time[-1].values)[:-13]}\n Glat, Glon: {sim.glat}, {sim.glon}')
+
+ax = axs[0]
+#NmF1 = pyiri2016.IRI2016()._RmNeg(sim.b[2, :])
+#NmE = sim.loc[4, :]
+ax.plot(sim.time, sim['NmF2'].squeeze(), label='N$_m$F$_2$')
+#ax.plot(sim.time, NmF1, label='N$_m$F$_1$')
+#ax.plot(sim.time, NmE, label='N$_m$E')
+ax.set_title('Maximum number densities vs. ionospheric layer')
+ax.set_xlabel('Hour (UT)')
+ax.set_ylabel('(m$^{-3}$)')
+ax.set_yscale('log')
+ax.legend(loc='best')
+
+ax = axs[1]
+#hmF1 = pyiri2016.IRI2016()._RmNeg(sim.b[3, :])
+#hmE = sim.b[5, :]
+ax.plot(sim.time, sim['hmF2'].squeeze(), label='h$_m$F$_2$')
+#ax.plot(sim.time, hmF1, label='h$_m$F$_1$')
+#ax.plot(sim.time, hmE, label='h$_m$E')
+ax.set_title('Height of maximum density vs. ionospheric layer')
+ax.set_xlabel('Hour (UT)')
+ax.set_ylabel('(km)')
+ax.legend(loc='best')
+# %%
+if Nplot > 2:
+    ax = axs[2]
+
+    for a in sim.alt_km:
+        ax.plot(sim.time, sim['ne'].squeeze(), marker='.', label=f'{a.item()} km')
+    ax.set_xlabel('time UTC (hours)')
+    ax.set_ylabel('[m$^{-3}$]')
+    ax.set_title(f'$N_e$ vs. altitude and time')
+    ax.set_yscale('log')
+    ax.legend(loc='best')
+# %%
+if Nplot > 4:
+    ax = axs[4]
+    tec = sim.b[36, :]
+    ax.plot(sim.time, tec, label=r'TEC')
+    ax.set_xlabel('Hour (UT)')
+    ax.set_ylabel('(m$^{-2}$)')
+    #ax.set_yscale('log')
+    ax.legend(loc='best')
+
+    ax = axs[5]
+    vy = sim.b[43, :]
+    ax.plot(sim.time, vy, label=r'V$_y$')
+    ax.set_xlabel('Hour (UT)')
+    ax.set_ylabel('(m/s)')
+    ax.legend(loc='best')
+
+for a in axs.ravel():
+    a.grid(True)
+
+
+if __name__ == '__main__':
+    from argparse import ArgumentParser
+    p = ArgumentParser(description='IRI2016 time profile plot')
+    p.add_argument('-t','--trange',help='START STOP STEP (hours) time [UTC]',nargs=3,
+                   default=('2012-08-21','2012-08-22',0.25))
+    p.add_argument('--alt',help='START STOP STEP altitude [km]',type=float, nargs=3,default=(120,180,20))
+    p.add_argument('-c','--latlon',help='geodetic coordinates of simulation',
+                   type=float,default=(65,-147.5))
+    p.add_argument('--f107',type=float,default=200.)
+    p.add_argument('--f107a', type=float,default=200.)
+    p.add_argument('--ap', type=int, default=4)
+    p.add_argument('--species',help='species to plot',nargs='+',default=('ne'))
+    p = p.parse_args()
+
+
+show()

data/index/ig_rz.dat

@@ -1,4 +1,4 @@
-10,17,2016,
+11,2,2017,
 
 1,1958,12,2018,
 
@@ -61,10 +61,10 @@
  75.5, 75.8, 75.1, 74.5, 75.4, 78.0, 79.4, 81.6, 86.6, 90.8, 92.1, 91.8,
  92.1, 92.5, 93.2, 94.8, 95.6, 96.0, 96.8, 96.8, 94.4, 92.0, 91.4, 91.2,
  90.1, 88.1, 85.0, 81.0, 76.4, 71.3, 66.5, 62.0, 58.5, 55.5, 53.0, 50.1,
- 41.0, 38.5, 37.0, 35.7, 35.3, 35.3, 34.1, 33.5, 33.2, 33.9, 34.4, 33.0,
- 35.6, 30.3, 31.0, 29.6, 30.7, 28.9, 27.0, 23.6, 22.2, 15.7, 17.4, 11.8,
-  9.0,  8.3,  6.9,  3.0,  4.1,  8.8,  6.2,  8.5, 11.5, 13.5, 15.2, 14.3,
- 18.3,
+ 41.0, 38.5, 37.0, 35.2, 32.3, 28.6, 24.7, 21.2, 18.2, 15.9, 14.2, 12.6,
+ 11.0,  9.2,  8.0,  8.3,  8.7,  9.3,  9.8,  8.6,  9.8,  9.7,  9.7,  9.5,
+  8.1,  9.5,  8.0,  9.6,  8.8, 10.0,  7.7,  5.9,  6.6,  5.7,  7.2,  5.2,
+  2.5,
 
 200.1,
 199.0,200.9,201.3,196.8,191.4,186.8,185.2,184.9,183.8,182.2,180.7,180.5,
@@ -124,9 +124,10 @@
  65.5, 66.9, 66.8, 64.6, 61.7, 58.9, 57.8, 58.2, 58.1, 58.6, 59.7, 59.6, 
  58.7, 58.4, 57.5, 57.8, 59.8, 62.6, 65.4, 68.9, 73.1, 75.0, 75.4, 76.0,
 109.3,110.5,114.3,116.4,115.0,114.1,112.6,108.3,101.9, 97.3, 94.7, 92.2,
- 89.3, 86.1, 82.2, 78.9, 76.1, 72.1, 68.3, 66.4, 65.9, 64.3, 61.3  57.8, 
- 54.5, 52.6, 50.6, 48.2, 46.3, 44.5, 42.7, 40.9, 39.2, 38.2, 37.1, 36.7,
- 37.0, 35.9, 34.3, 33.2, 32.0, 30.7, 29.4, 28.3, 27.4, 26.7, 26.1, 25.3, 
- 24.5, 23.6, 22.6, 21.8, 21.2, 20.3, 19.5, 18.6, 17.4, 16.5, 15.9, 15.5,
- 15.3,
+ 89.3, 86.1, 82.2, 78.9, 76.1, 72.1, 68.3, 66.4, 65.9, 64.3, 61.2, 57.8, 
+ 54.4, 52.5, 50.4, 47.8, 44.8, 41.5, 38.5, 36.0, 33.2, 31.5, 29.9, 28.5,
+ 27.8, 26.5, 25.8, 24.9, 24.1, 24.1, 23.9, 23.4, 23.2, 22.6, 21.9, 21.7,
+ 21.5, 20.6, 18.6, 17.4, 17.0, 16.1, 15.4, 14.8, 14.3, 14.0, 13.7, 13.2,
+ 12.7
 
+

examples/example01.py

@@ -1,9 +1,8 @@
 #!/usr/bin/env python
-from pyiri2016 import IRI2016
+from pyiri2016 import IRI
 
 
-sim = IRI2016()
-IRIData, IRIDATAAdd = sim.IRI()
+IRIData, IRIDATAAdd = IRI()
 print('Ne {:.3e}'.format(IRIData['ne']))
 print('NmF2 {:.3e}'.format(IRIDATAAdd['NmF2']))
 print('hmF2 {:.3e}'.format(IRIDATAAdd['hmF2']))