Merge pull request #439 from OceanParcels/updating_tools_dir

Updating tools dir

Author: delandmeterp

parcels/codegenerator.py

@@ -1,5 +1,5 @@
 from parcels.field import Field, VectorField, SummedField, SummedVectorField
-from parcels.loggers import logger
+from parcels.tools.loggers import logger
 import ast
 import cgen as c
 from collections import OrderedDict

parcels/field.py

@@ -1,145 +1,19 @@
-from parcels.loggers import logger
+from parcels.tools.loggers import logger
+from parcels.tools.converters import unitconverters_map, UnitConverter, Geographic, GeographicPolar
+from parcels.tools.error import FieldSamplingError, TimeExtrapolationError
 from collections import Iterable
 from py import path
 import numpy as np
 from ctypes import Structure, c_int, c_float, POINTER, pointer
 import xarray as xr
-from math import cos, pi
+from math import cos
 import datetime
 import math
 from .grid import (RectilinearZGrid, RectilinearSGrid, CurvilinearZGrid,
                    CurvilinearSGrid, CGrid, GridCode)
 
 
-__all__ = ['Field', 'VectorField', 'SummedField', 'SummedVectorField',
-           'Geographic', 'GeographicPolar', 'GeographicSquare', 'GeographicPolarSquare']
-
-
-class FieldSamplingError(RuntimeError):
-    """Utility error class to propagate erroneous field sampling"""
-
-    def __init__(self, x, y, z, field=None):
-        self.field = field
-        self.x = x
-        self.y = y
-        self.z = z
-        message = "%s sampled at (%f, %f, %f)" % (
-            field.name if field else "Field", self.x, self.y, self.z
-        )
-        super(FieldSamplingError, self).__init__(message)
-
-
-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 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)
-        message += " Try setting allow_time_extrapolation to True"
-        super(TimeExtrapolationError, self).__init__(message)
-
-
-class UnitConverter(object):
-    """ Interface class for spatial unit conversion during field sampling
-        that performs no conversion.
-    """
-    source_unit = None
-    target_unit = None
-
-    def to_target(self, value, x, y, z):
-        return value
-
-    def ccode_to_target(self, x, y, z):
-        return "1.0"
-
-    def to_source(self, value, x, y, z):
-        return value
-
-    def ccode_to_source(self, x, y, z):
-        return "1.0"
-
-
-class Geographic(UnitConverter):
-    """ Unit converter from geometric to geographic coordinates (m to degree) """
-    source_unit = 'm'
-    target_unit = 'degree'
-
-    def to_target(self, value, x, y, z):
-        return value / 1000. / 1.852 / 60.
-
-    def to_source(self, value, x, y, z):
-        return value * 1000. * 1.852 * 60.
-
-    def ccode_to_target(self, x, y, z):
-        return "(1.0 / (1000.0 * 1.852 * 60.0))"
-
-    def ccode_to_source(self, x, y, z):
-        return "(1000.0 * 1.852 * 60.0)"
-
-
-class GeographicPolar(UnitConverter):
-    """ Unit converter from geometric to geographic coordinates (m to degree)
-        with a correction to account for narrower grid cells closer to the poles.
-    """
-    source_unit = 'm'
-    target_unit = 'degree'
-
-    def to_target(self, value, x, y, z):
-        return value / 1000. / 1.852 / 60. / cos(y * pi / 180)
-
-    def to_source(self, value, x, y, z):
-        return value * 1000. * 1.852 * 60. * cos(y * pi / 180)
-
-    def ccode_to_target(self, x, y, z):
-        return "(1.0 / (1000. * 1.852 * 60. * cos(%s * M_PI / 180)))" % y
-
-    def ccode_to_source(self, x, y, z):
-        return "(1000. * 1.852 * 60. * cos(%s * M_PI / 180))" % y
-
-
-class GeographicSquare(UnitConverter):
-    """ Square distance converter from geometric to geographic coordinates (m2 to degree2) """
-    source_unit = 'm2'
-    target_unit = 'degree2'
-
-    def to_target(self, value, x, y, z):
-        return value / pow(1000. * 1.852 * 60., 2)
-
-    def to_source(self, value, x, y, z):
-        return value * pow(1000. * 1.852 * 60., 2)
-
-    def ccode_to_target(self, x, y, z):
-        return "pow(1.0 / (1000.0 * 1.852 * 60.0), 2)"
-
-    def ccode_to_source(self, x, y, z):
-        return "pow((1000.0 * 1.852 * 60.0), 2)"
-
-
-class GeographicPolarSquare(UnitConverter):
-    """ Square distance converter from geometric to geographic coordinates (m2 to degree2)
-        with a correction to account for narrower grid cells closer to the poles.
-    """
-    source_unit = 'm2'
-    target_unit = 'degree2'
-
-    def to_target(self, value, x, y, z):
-        return value / pow(1000. * 1.852 * 60. * cos(y * pi / 180), 2)
-
-    def to_source(self, value, x, y, z):
-        return value * pow(1000. * 1.852 * 60. * cos(y * pi / 180), 2)
-
-    def ccode_to_target(self, x, y, z):
-        return "pow(1.0 / (1000. * 1.852 * 60. * cos(%s * M_PI / 180)), 2)" % y
-
-    def ccode_to_source(self, x, y, z):
-        return "pow((1000. * 1.852 * 60. * cos(%s * M_PI / 180)), 2)" % y
-
-
-unitconverters = {'U': GeographicPolar(), 'V': Geographic(),
-                  'Kh_zonal': GeographicPolarSquare(),
-                  'Kh_meridional': GeographicSquare()}
+__all__ = ['Field', 'VectorField', 'SummedField', 'SummedVectorField']
 
 
 class Field(object):
@@ -196,10 +70,10 @@ def __init__(self, name, data, lon=None, lat=None, depth=None, time=None, grid=N
         self.depth = self.grid.depth
         self.time = self.grid.time
         fieldtype = self.name if fieldtype is None else fieldtype
-        if self.grid.mesh == 'flat' or (fieldtype not in unitconverters.keys()):
+        if self.grid.mesh == 'flat' or (fieldtype not in unitconverters_map.keys()):
             self.units = UnitConverter()
         elif self.grid.mesh == 'spherical':
-            self.units = unitconverters[fieldtype]
+            self.units = unitconverters_map[fieldtype]
         else:
             raise ValueError("Unsupported mesh type. Choose either: 'spherical' or 'flat'")
         if type(interp_method) is dict:

parcels/fieldset.py

@@ -1,7 +1,7 @@
 from parcels.field import Field, VectorField, SummedField, SummedVectorField
 from parcels.gridset import GridSet
 from parcels.grid import RectilinearZGrid
-from parcels.loggers import logger
+from parcels.tools.loggers import logger
 import numpy as np
 from os import path
 from glob import glob

parcels/grid.py

@@ -1,4 +1,4 @@
-from parcels.loggers import logger
+from parcels.tools.loggers import logger
 import numpy as np
 from ctypes import Structure, c_int, c_float, c_double, POINTER, cast, c_void_p, pointer
 from enum import IntEnum

parcels/kernel.py

@@ -1,8 +1,8 @@
 from parcels.codegenerator import KernelGenerator, LoopGenerator
 from parcels.compiler import get_cache_dir
-from parcels.kernels.error import ErrorCode, recovery_map as recovery_base_map
+from parcels.tools.error import ErrorCode, recovery_map as recovery_base_map
 from parcels.field import FieldSamplingError
-from parcels.loggers import logger
+from parcels.tools.loggers import logger
 from parcels.kernels.advection import AdvectionRK4_3D
 from os import path, remove
 import numpy as np

parcels/kernels/__init__.py

@@ -1,3 +1,2 @@
 from .advection import *  # noqa
 from .diffusion import *  # noqa
-from .error import *  # noqa

parcels/kernels/advection.py

@@ -1,5 +1,5 @@
 """Collection of pre-built advection kernels"""
-from parcels.kernels.error import ErrorCode
+from parcels.tools.error import ErrorCode
 import math
 
 

parcels/particle.py

@@ -1,6 +1,6 @@
-from parcels.kernels.error import ErrorCode
+from parcels.tools.error import ErrorCode
 from parcels.field import Field
-from parcels.loggers import logger
+from parcels.tools.loggers import logger
 from operator import attrgetter
 import numpy as np
 from ctypes import c_void_p

parcels/particlefile.py

@@ -2,7 +2,7 @@
 import numpy as np
 import netCDF4
 from datetime import timedelta as delta
-from parcels.loggers import logger
+from parcels.tools.loggers import logger
 from os import path
 try:
     from parcels._version import version as parcels_version

parcels/particleset.py

@@ -3,7 +3,7 @@
 from parcels.compiler import GNUCompiler
 from parcels.kernels.advection import AdvectionRK4
 from parcels.particlefile import ParticleFile
-from parcels.loggers import logger
+from parcels.tools.loggers import logger
 from parcels.grid import GridCode
 import numpy as np
 import progressbar
@@ -257,7 +257,7 @@ def execute(self, pyfunc=AdvectionRK4, endtime=None, runtime=None, dt=1.,
                          It is either a timedelta object or a positive double.
                          None value means no animation.
         :param output_file: :mod:`parcels.particlefile.ParticleFile` object for particle output
-        :param recovery: Dictionary with additional `:mod:parcels.kernels.error`
+        :param recovery: Dictionary with additional `:mod:parcels.tools.error`
                          recovery kernels to allow custom recovery behaviour in case of
                          kernel errors.
         :param movie_background_field: field plotted as background in the movie if moviedt is set.