Merge branch 'master' into version-from-archive

docs/index.rst

@@ -123,10 +123,10 @@ parcels.plotting module
     :members:
     :undoc-members:
 
-scripts.plotParticles module
-----------------------------
+scripts.plottrajectoriesfile module
+-----------------------------------
 
-.. automodule:: scripts.plotParticles
+.. automodule:: scripts.plottrajectoriesfile
     :members:
     :undoc-members:
 

parcels/field.py

@@ -32,7 +32,7 @@ class TimeExtrapolationError(RuntimeError):
     """Utility error class to propagate erroneous time extrapolation sampling"""
 
     def __init__(self, time, field=None):
-        if field is not None and field.grid.time_origin:
+        if field is not None and field.grid.time_origin and time is not None:
             time = field.grid.time_origin + np.timedelta64(int(time), 's')
         message = "%s sampled outside time domain at time %s." % (
             field.name if field else "Field", time)
@@ -349,7 +349,6 @@ def from_netcdf(cls, filenames, variable, dimensions, indices=None, grid=None,
                 ti += len(tslice)
         else:
             grid.defer_load = True
-            grid.time_full = grid.time
             grid.ti = -1
             data = None
 

parcels/grid.py

@@ -28,6 +28,7 @@ def __init__(self, lon, lat, time, time_origin, mesh):
         self.lon = lon
         self.lat = lat
         self.time = np.zeros(1, dtype=np.float64) if time is None else time
+        self.time_full = self.time  # needed for deferred_loaded Fields
         if not self.lon.dtype == np.float32:
             logger.warning_once("Casting lon data to np.float32")
             self.lon = self.lon.astype(np.float32)

parcels/kernel.py

@@ -51,6 +51,7 @@ def __init__(self, fieldset, ptype, pyfunc=None, funcname=None,
                  funccode=None, py_ast=None, funcvars=None, c_include=""):
         self.fieldset = fieldset
         self.ptype = ptype
+        self._lib = None
 
         # Derive meta information from pyfunc, if not given
         self.funcname = funcname or pyfunc.__name__
@@ -117,7 +118,6 @@ def __init__(self, fieldset, ptype, pyfunc=None, funcname=None,
             self.src_file = "%s.c" % basename
             self.lib_file = "%s.%s" % (basename, 'dll' if platform == 'win32' else 'so')
             self.log_file = "%s.log" % basename
-        self._lib = None
 
     def __del__(self):
         # Clean-up the in-memory dynamic linked libraries.

parcels/particleset.py

@@ -297,7 +297,7 @@ def execute(self, pyfunc=AdvectionRK4, endtime=None, runtime=None, dt=1.,
         # Set particle.time defaults based on sign of dt, if not set at ParticleSet construction
         for p in self:
             if np.isnan(p.time):
-                mintime, maxtime = self.fieldset.gridset.dimrange('time')
+                mintime, maxtime = self.fieldset.gridset.dimrange('time_full')
                 p.time = mintime if dt >= 0 else maxtime
 
         # Derive _starttime and endtime from arguments or fieldset defaults
@@ -309,7 +309,7 @@ def execute(self, pyfunc=AdvectionRK4, endtime=None, runtime=None, dt=1.,
         if runtime is not None:
             endtime = _starttime + runtime * np.sign(dt)
         elif endtime is None:
-            mintime, maxtime = self.fieldset.gridset.dimrange('time')
+            mintime, maxtime = self.fieldset.gridset.dimrange('time_full')
             endtime = maxtime if dt >= 0 else mintime
 
         if abs(endtime-_starttime) < 1e-5 or dt == 0 or runtime == 0:

parcels/plotting.py

@@ -33,7 +33,7 @@ def plotparticles(particles, with_particles=True, show_time=None, field=None, do
     if isinstance(show_time, delta):
         show_time = show_time.total_seconds()
     if np.isnan(show_time):
-        show_time, _ = particles.fieldset.gridset.dimrange('time')
+        show_time, _ = particles.fieldset.gridset.dimrange('time_full')
 
     if field is None:
         spherical = True if particles.fieldset.U.grid.mesh == 'spherical' else False