Merge branch 'v2.0' of http://github.com/GeoscienceAustralia/tcrm int…

…o v2.0

.travis.yml

@@ -9,7 +9,6 @@ addons:
     packages: 
     - build-essential 
     - libgeos-c1
-    - lib-geos-dev
     - libhdf5-serial-dev
     - libatlas-base-dev
     - gfortran

PlotInterface/maps.py

@@ -175,7 +175,10 @@ def addGraticule(self, axes, mapobj):
         dd = max(dx, dy)
         gr_opts = np.array([30., 10., 5., 4., 2.])
         min_gr = 5
-        dl = gr_opts[np.where((dd/gr_opts) >= min_gr)[0][0]]
+        try:
+            dl = gr_opts[np.where((dd/gr_opts) >= min_gr)[0][0]]
+        except IndexError:
+            dl = 2.
 
         meridians = np.arange(dl*np.floor(xmin / dl),
                               dl*np.ceil(xmax / dl) + dl, dl)

TrackGenerator/trackSize.py

@@ -18,17 +18,16 @@
 
 LOG = logging.getLogger()
 
-def rmax(dp, lat, eps, coeffs=[4.4726049824584306, 
-                               -0.04057322103602546, 
-                               0.00031318220949448573, 
-                               0.00014553984831170656]):
+def rmax(dp, lat, eps, coeffs=[3.5843946536979779,-0.0045486143609339436,
+                               0.78621467400844858, 0.0024030344245284741,
+                               0.0015567629057007433]):
     """
     Calculate radius to maximum wind based on pressure deficit and
     latitude. This function allows for the random variate to be set
     when calling the function. Default coefficients for the functional
     form of ln(Rmw) are given, based on JTWC data for the southern hemisphere.
     
-    ln(Rmw) = a + b*dp + c*dp^2 + d*lat^2 + eps
+    ln(Rmw) = a + b*dp + c*exp(-d*dp^2) + f*lat^2 + eps
 
     eps is not included in the coefficients (though that may be considered
     by some to be more logical), so that it can remain constant for a single
@@ -47,17 +46,16 @@ def rmax(dp, lat, eps, coeffs=[4.4726049824584306,
     if len(coeffs) < 4:
         LOG.warn("Insufficient coefficients for rmw calculation!")
         LOG.warn("Using default values")
-        coeffs = [4.4726049824584306, 
-                  -0.04057322103602546, 
-                  0.00031318220949448573, 
-                  0.00014553984831170656]
+        coeffs = [3.5843946536979779,-0.0045486143609339436,
+                  0.78621467400844858, 0.0024030344245284741,
+                  0.0015567629057007433]
 
     if isinstance(dp, (np.ndarray, list)) and \
       isinstance(lat, (np.ndarray, list)):
         assert len(dp) == len(lat)
-    rm = np.exp(coeffs[0] + coeffs[1] * dp + coeffs[2] * dp * dp +
-                coeffs[3] * lat * lat + eps)
-      
+    yy = coeffs[0] + coeffs[1]*dp + coeffs[2] * np.exp(-coeffs[3] * dp * dp) +\
+         coeffs[4] * np.abs(lat) + eps
+    rm = np.exp(yy)
     return rm
 
 def fitRmax(rmw, dp, lat):

Utilities/track.py

@@ -26,6 +26,11 @@
 
 from netCDF4 import Dataset, date2num, num2date
 
+try:
+    from exceptions import WindowsError
+except:
+    class WindowsError(IOError): pass
+
 #if not getattr(__builtins__, "WindowsError", None):
 #    class WindowsError(IOError):
 #        pass
@@ -425,5 +430,5 @@ def loadTracksFromPath(path):
         msg = "Loading {0} track files in {1}".format(len(trackfiles), path)
         log.info(msg)
         return loadTracksFromFiles(sorted(trackfiles))
-    except (IOError, WindowsError):
+    except (IOError, OSError, WindowsError):
         raise IOError("Path {0} does not exist".format(path))

docs/install.rst

@@ -106,12 +106,14 @@ the ``$PATH`` for this to work.
 Compiling the extensions
 ------------------------
 
-Unix
-~~~~
 The model requires a number of C extensions to be compiled before
 execution. These can be built using Python's inbuilt :mod:`distutils`
-module. Copy the required files from the `installer` directory to the
-base directory and then execute the build process::
+module.
+
+
+Unix
+~~~~
+From the base directory, execute the build process::
 
     python intaller/setup.py build_ext -i
 
@@ -120,7 +122,12 @@ Windows
 ~~~~~~~
 
 For Windows users, the code includes the ``compile.cmd`` script in the
-main TCRM diretory that will build these extensions in place.
+main TCRM diretory that will build these extensions in place. By default, TCRM uses the MinGW suite (http://www.mingw.org) for compiling the extensions. Other Windows-based packages can also be used (e.g. Cygwin). See the Python documentation on writing configuration files for the :mod:`distutils` package for more details.
+
+Notes
+~~~~~
+
+It is recommended to use a stand-alone Python installation for compiling and running TCRM. Installations linked to other software such as ArcGIS have resulted in compilation errors, as the required :mod:`numpy` libraries are pre-compiled and packaged with such installations. 
 
 .. _testing:
 

tests/test_trackSize.py

@@ -21,49 +21,48 @@ def setUp(self):
         np.random.seed(10)
         self.dparray = np.arange(10, 51, 5)
         self.latarray = np.arange(-23, -5, 2)
-        self.rmaxout = np.array([104.08747056, 87.24373672, 74.36633603,
-                                 64.46512563, 56.83025497, 50.94959054,
-                                 46.45239542, 43.07069234, 40.61270477])
-        self.rmaxoutcoeffs = np.array([109.4918411, 90.31016614,
-                                       75.35799588, 63.61504735,
-                                       54.32855894, 46.93905396,
-                                       41.02780616, 36.27939815,
-                                       32.45485465])
+        self.rmaxout = np.array([66.21418972, 54.96078787, 45.7678418,
+                                 39.33639152, 35.22023191, 32.67958816,
+                                 31.07181726, 29.95463557, 29.06996118])
+
+        self.rmaxoutcoeffs = np.array([57.74931727, 49.76638251, 42.67145839,
+                                       37.24632781, 33.47199844, 30.98197273,
+                                       29.3570741, 28.25288743, 27.43217413])
 
 
     def test_rmaxDefaults(self):
         """Test rmax returns correct value based on defaults"""
         dp = 25
         lat = -15
-        eps = np.random.normal(0, scale=0.353)
+        eps = 0
         rmw = trackSize.rmax(dp, lat, eps)
-        self.assertEqual(rmw, 63.867449833342235)
+        self.assertAlmostEqual(rmw, 39.21410711, places=1)
 
     def test_rmaxWrongLengths(self):
         """rmax raises exception when inputs are different lengths"""
-        eps = np.random.normal(0, scale=0.353)
+        eps = 0
         latarray = np.arange(-23, 5, 2)
         self.assertRaises(Exception, trackSize.rmax, self.dparray, latarray, eps)
 
     def test_rmaxArrayInput(self):
         """Test rmax with array input"""
-        eps = np.random.normal(0, scale=0.353)
+        eps = 0
         rmw = trackSize.rmax(self.dparray, self.latarray, eps)
-        self.numpyAssertAlmostEqual(rmw, self.rmaxout)
+        self.numpyAssertAlmostEqual(rmw, self.rmaxout, prec=0.1)
 
     def test_rmaxWithCoeffs(self):
         """Test rmax with user-defined coefficients"""
-        eps = np.random.normal(0, scale=0.353)
-        coeffs = [4.5, -0.04, 0.0002, 0.0002]
+        eps = 0
+        coeffs = [3.5, -0.004, 0.7, 0.002, .001]
         rmw = trackSize.rmax(self.dparray, self.latarray, eps, coeffs)
         self.numpyAssertAlmostEqual(rmw, self.rmaxoutcoeffs)
 
     def test_rmaxWithIncompleteCoeffs(self):
         """Test rmax falls back to default coefficients if not enough given"""
         coeffs = [4.45, -0.05, 0.0002]
-        eps = np.random.normal(0, scale=0.353)
+        eps = 0
         rmw = trackSize.rmax(self.dparray, self.latarray, eps, coeffs=coeffs)
-        self.numpyAssertAlmostEqual(rmw, self.rmaxout)
+        self.numpyAssertAlmostEqual(rmw, self.rmaxout, prec=0.1)
 
 class TestFitRmax(NumpyTestCase.NumpyTestCase):
     """