diff --git a/.travis.yml b/.travis.yml index 8bf1a29383..7ae0af3a30 100644 --- a/.travis.yml +++ b/.travis.yml @@ -112,11 +112,15 @@ install: - python setup.py --quiet install - # JUST FOR NOW : Install latest version of iris-grib. + # Install latest version of iris-grib. + # ONLY for Python 3, as Iris grib tests now require iris-grib >= v0.15. # TODO : remove when iris doesn't do an integration test requiring iris-grib. - - if [[ "${TEST_MINIMAL}" != true && ${PYTHON_VERSION} == 2* ]]; then - conda install --quiet -n ${ENV_NAME} python-ecmwf_grib; - pip install git+https://github.com/SciTools/iris-grib.git@v0.11.0; + # test against the latest version of python-eccodes. + # Conda-forge versioning is out of order (0.9.* is later than 2.12.*). + - > + if [[ "${TEST_MINIMAL}" != true && "${PYTHON_VERSION}" == 3* ]]; then + conda install --quiet -n ${ENV_NAME} python-eccodes">=0.9.1, <2"; + conda install --quiet -n ${ENV_NAME} --no-deps iris-grib; fi script: @@ -127,11 +131,11 @@ script: - > if [[ ${TEST_TARGET} == 'default' ]]; then export IRIS_REPO_DIR=${INSTALL_DIR}; - python -m iris.tests.runner --default-tests --system-tests --print-failed-images; + python -m iris.tests.runner --default-tests --system-tests; fi - if [[ ${TEST_TARGET} == 'example' ]]; then - python -m iris.tests.runner --example-tests --print-failed-images; + python -m iris.tests.runner --example-tests; fi # A call to check "whatsnew" contributions are valid, because the Iris test @@ -164,12 +168,18 @@ script: fi # Split the organisation out of the slug. See https://stackoverflow.com/a/5257398/741316 for description. - - ORG=(${TRAVIS_REPO_SLUG//\// }) + # NOTE: a *separate* "export" command appears to be necessary here : A command of the + # form "export ORG=.." failed to define ORG for the following command (?!) + - > + ORG=$(echo ${TRAVIS_REPO_SLUG} | cut -d/ -f1); + export ORG + + - echo "Travis job context ORG=${ORG}; TRAVIS_EVENT_TYPE=${TRAVIS_EVENT_TYPE}; PUSH_BUILT_DOCS=${PUSH_BUILT_DOCS}" # When we merge a change to SciTools/iris, we can push docs to github pages. # At present, only the Python 3.7 "doctest" job does this. # Results appear at https://scitools-docs.github.io/iris/<>/index.html - - if [[ ${ORG} == "SciTools" && ${TRAVIS_EVENT_TYPE} == 'push' && ${PUSH_BUILT_DOCS} == 'true' ]]; then + - if [[ "${ORG}" == 'SciTools' && "${TRAVIS_EVENT_TYPE}" == 'push' && "${PUSH_BUILT_DOCS}" == 'true' ]]; then cd ${INSTALL_DIR}; pip install doctr; doctr deploy --deploy-repo SciTools-docs/iris --built-docs docs/iris/build/html diff --git a/docs/iris/example_code/Meteorology/COP_maps.py b/docs/iris/example_code/Meteorology/COP_maps.py index aa5049feb9..a84f550004 100644 --- a/docs/iris/example_code/Meteorology/COP_maps.py +++ b/docs/iris/example_code/Meteorology/COP_maps.py @@ -103,7 +103,7 @@ def main(): # Add the first subplot showing the E1 scenario plt.subplot(121) - plt.title('HadGEM2 E1 Scenario', fontsize=10) + plt.title('HadGEM2 E1 Scenario', fontsize=10) iplt.contourf(delta_e1, levels, colors=colors, extend='both') plt.gca().coastlines() # get the current axes' subplot for use later on @@ -111,7 +111,7 @@ def main(): # Add the second subplot showing the A1B scenario plt.subplot(122) - plt.title('HadGEM2 A1B-Image Scenario', fontsize=10) + plt.title('HadGEM2 A1B-Image Scenario', fontsize=10) contour_result = iplt.contourf(delta_a1b, levels, colors=colors, extend='both') plt.gca().coastlines() @@ -131,8 +131,7 @@ def main(): width = left - first_plot_left + width # Add axes to the figure, to place the colour bar - colorbar_axes = fig.add_axes([first_plot_left, bottom + 0.07, - width, 0.03]) + colorbar_axes = fig.add_axes([first_plot_left, 0.18, width, 0.03]) # Add the colour bar cbar = plt.colorbar(contour_result, colorbar_axes, diff --git a/docs/iris/src/_templates/index.html b/docs/iris/src/_templates/index.html index e9f9b16111..391bce68d9 100644 --- a/docs/iris/src/_templates/index.html +++ b/docs/iris/src/_templates/index.html @@ -134,7 +134,7 @@ extra information on specific technical issues

  • -

    What's new in Iris 2.3?
    +

    What's new in Iris 2.4?
    recent changes in Iris's capabilities

    • diff --git a/docs/iris/src/_templates/layout.html b/docs/iris/src/_templates/layout.html index 22b91223d2..58e9fcf055 100644 --- a/docs/iris/src/_templates/layout.html +++ b/docs/iris/src/_templates/layout.html @@ -37,7 +37,7 @@

    - Iris v2.3 + Iris v2.4

    A powerful, format-agnostic, community-driven Python library for analysing and diff --git a/docs/iris/src/conf.py b/docs/iris/src/conf.py index 6cdfe634c4..d1cf00aa58 100644 --- a/docs/iris/src/conf.py +++ b/docs/iris/src/conf.py @@ -1,4 +1,4 @@ -# (C) British Crown Copyright 2010 - 2018, Met Office +# (C) British Crown Copyright 2010 - 2020, Met Office # # This file is part of Iris. # @@ -64,7 +64,6 @@ 'sphinx.ext.imgmath', 'sphinx.ext.intersphinx', 'matplotlib.sphinxext.mathmpl', - 'matplotlib.sphinxext.only_directives', 'matplotlib.sphinxext.plot_directive', # better class documentation diff --git a/docs/iris/src/userguide/cube_maths.rst b/docs/iris/src/userguide/cube_maths.rst index 6c6f846bc3..8fe6eb12d5 100644 --- a/docs/iris/src/userguide/cube_maths.rst +++ b/docs/iris/src/userguide/cube_maths.rst @@ -205,12 +205,12 @@ Finally, the cube we have created needs to be given a suitable name:: The result could now be plotted using the guidance provided in the :doc:`plotting_a_cube` section. -.. htmlonly:: +.. only:: html A very similar example to this can be found in :doc:`/examples/Meteorology/deriving_phenomena`. -.. latexonly:: +.. only:: latex A very similar example to this can be found in the examples section, with the title "Deriving Exner Pressure and Air Temperature". diff --git a/docs/iris/src/userguide/index.rst b/docs/iris/src/userguide/index.rst index 8c0b24bec3..4fb7b62155 100644 --- a/docs/iris/src/userguide/index.rst +++ b/docs/iris/src/userguide/index.rst @@ -13,7 +13,7 @@ fully before experimenting with your own data files. Much of the content has supplementary links to the reference documentation; you will not need to follow these links in order to understand the guide but they may serve as a useful reference for future exploration. -.. htmlonly:: +.. only:: html Since later pages depend on earlier ones, try reading this user guide sequentially using the ``next`` and ``previous`` links. diff --git a/docs/iris/src/userguide/loading_iris_cubes.rst b/docs/iris/src/userguide/loading_iris_cubes.rst index 2cb3b9b259..bf50acc614 100644 --- a/docs/iris/src/userguide/loading_iris_cubes.rst +++ b/docs/iris/src/userguide/loading_iris_cubes.rst @@ -166,18 +166,36 @@ As we have seen, loading the following file creates several Cubes:: cubes = iris.load(filename) Specifying a name as a constraint argument to :py:func:`iris.load` will mean -only cubes with a matching :meth:`name ` +only cubes with matching :meth:`name ` will be returned:: filename = iris.sample_data_path('uk_hires.pp') - cubes = iris.load(filename, 'specific_humidity') + cubes = iris.load(filename, 'surface_altitude') -To constrain the load to multiple distinct constraints, a list of constraints +Note that, the provided name will match against either the standard name, +long name, NetCDF variable name or STASH metadata of a cube. Therefore, the +previous example using the ``surface_altitude`` standard name constraint can +also be achieved using the STASH value of ``m01s00i033``:: + + filename = iris.sample_data_path('uk_hires.pp') + cubes = iris.load(filename, 'm01s00i033') + +If further specific name constraint control is required i.e., to constrain +against a combination of standard name, long name, NetCDF variable name and/or +STASH metadata, consider using the :class:`iris.NameConstraint`. For example, +to constrain against both a standard name of ``surface_altitude`` **and** a STASH +of ``m01s00i033``:: + + filename = iris.sample_data_path('uk_hires.pp') + constraint = iris.NameConstraint(standard_name='surface_altitude', STASH='m01s00i033') + cubes = iris.load(filename, constraint) + +To constrain the load to multiple distinct constraints, a list of constraints can be provided. This is equivalent to running load once for each constraint but is likely to be more efficient:: filename = iris.sample_data_path('uk_hires.pp') - cubes = iris.load(filename, ['air_potential_temperature', 'specific_humidity']) + cubes = iris.load(filename, ['air_potential_temperature', 'surface_altitude']) The :class:`iris.Constraint` class can be used to restrict coordinate values on load. For example, to constrain the load to match diff --git a/docs/iris/src/whatsnew/2.4.rst b/docs/iris/src/whatsnew/2.4.rst new file mode 100644 index 0000000000..d82cfd10fa --- /dev/null +++ b/docs/iris/src/whatsnew/2.4.rst @@ -0,0 +1,49 @@ +What's New in Iris 2.4.0 +************************ + +:Release: 2.4.0 +:Date: 2020-01-15 + +This document explains the new/changed features of Iris in version 2.4.0 +(:doc:`View all changes `.) + + +Iris 2.4.0 Features +=================== + +.. admonition:: Last python 2 version of Iris + + Iris 2.4 is a final extra release of Iris 2, which back-ports specific desired features from + Iris 3 (not yet released). + + The purpose of this is both to support early adoption of certain newer features, + and to provide a final release for Python 2. + + The next release of Iris will be version 3.0 : a major-version release which + introduces breaking API and behavioural changes, and only supports Python 3. + +* :class:`iris.coord_systems.Geostationary` can now accept creation arguments of + `false_easting=None` or `false_northing=None`, equivalent to values of 0. + Previously these kwargs could be omitted, but could not be set to `None`. + This also enables loading of netcdf data on a Geostationary grid, where either of these + keys is not present as a grid-mapping variable property : Previously, loading any + such data caused an exception. +* The area weights used when performing area weighted regridding with :class:`iris.analysis.AreaWeighted` + are now cached. + This allows a significant speedup when regridding multiple similar cubes, by repeatedly using + a `'regridder' object <../iris/iris/analysis.html?highlight=regridder#iris.analysis.AreaWeighted.regridder>`_ + which you created first. +* Name constraint matching against cubes during loading or extracting has been relaxed from strictly matching + against the :meth:`~iris.cube.Cube.name`, to matching against either the + ``standard_name``, ``long_name``, NetCDF ``var_name``, or ``STASH`` attributes metadata of a cube. +* Cubes and coordinates now have a new ``names`` property that contains a tuple of the + ``standard_name``, ``long_name``, NetCDF ``var_name``, and ``STASH`` attributes metadata. +* The :class:`~iris.NameConstraint` provides richer name constraint matching when loading or extracting + against cubes, by supporting a constraint against any combination of + ``standard_name``, ``long_name``, NetCDF ``var_name`` and ``STASH`` + from the attributes dictionary of a :class:`~iris.cube.Cube`. + + +Iris 2.4.0 Dependency Updates +============================= +* Iris is now able to use the latest version of matplotlib. diff --git a/docs/iris/src/whatsnew/index.rst b/docs/iris/src/whatsnew/index.rst index a4a472de53..fffcd406a1 100644 --- a/docs/iris/src/whatsnew/index.rst +++ b/docs/iris/src/whatsnew/index.rst @@ -9,6 +9,7 @@ Iris versions. .. toctree:: :maxdepth: 2 + 2.4.rst 2.3.rst 2.2.rst 2.1.rst diff --git a/lib/iris/__init__.py b/lib/iris/__init__.py index a07ab27d8b..30e1c66818 100644 --- a/lib/iris/__init__.py +++ b/lib/iris/__init__.py @@ -1,4 +1,4 @@ -# (C) British Crown Copyright 2010 - 2019, Met Office +# (C) British Crown Copyright 2010 - 2020, Met Office # # This file is part of Iris. # @@ -121,17 +121,29 @@ def callback(cube, field, filename): # Iris revision. -__version__ = '2.3.0' +__version__ = '2.4.0rc0' # Restrict the names imported when using "from iris import *" -__all__ = ['load', 'load_cube', 'load_cubes', 'load_raw', - 'save', 'Constraint', 'AttributeConstraint', 'sample_data_path', - 'site_configuration', 'Future', 'FUTURE', - 'IrisDeprecation'] +__all__ = [ + "load", + "load_cube", + "load_cubes", + "load_raw", + "save", + "Constraint", + "AttributeConstraint", + "NameConstraint", + "sample_data_path", + "site_configuration", + "Future", + "FUTURE", + "IrisDeprecation", +] Constraint = iris._constraints.Constraint AttributeConstraint = iris._constraints.AttributeConstraint +NameConstraint = iris._constraints.NameConstraint class Future(threading.local): diff --git a/lib/iris/_constraints.py b/lib/iris/_constraints.py index 18b7fb1f54..a757a80e21 100644 --- a/lib/iris/_constraints.py +++ b/lib/iris/_constraints.py @@ -1,4 +1,4 @@ -# (C) British Crown Copyright 2010 - 2019, Met Office +# (C) British Crown Copyright 2010 - 2020, Met Office # # This file is part of Iris. # @@ -52,7 +52,8 @@ def __init__(self, name=None, cube_func=None, coord_values=None, **kwargs): Args: * name: string or None - If a string, it is used as the name to match against Cube.name(). + If a string, it is used as the name to match against the + `~iris.cube.Cube.names` property. * cube_func: callable or None If a callable, it must accept a Cube as its first and only argument and return either True or False. @@ -140,7 +141,9 @@ def _coordless_match(self, cube): """ match = True if self._name: - match = self._name == cube.name() + # Require to also check against cube.name() for the fallback + # "unknown" default case, when there is no name metadata available. + match = self._name in cube.names or self._name == cube.name() if match and self._cube_func: match = self._cube_func(cube) return match @@ -477,4 +480,104 @@ def _cube_func(self, cube): return match def __repr__(self): - return 'AttributeConstraint(%r)' % self._attributes + return "AttributeConstraint(%r)" % self._attributes + + +class NameConstraint(Constraint): + """Provides a simple Cube name based :class:`Constraint`.""" + + def __init__( + self, + standard_name="none", + long_name="none", + var_name="none", + STASH="none", + ): + """ + Provides a simple Cube name based :class:`Constraint`, which matches + against each of the names provided, which may be either standard name, + long name, NetCDF variable name and/or the STASH from the attributes + dictionary. + + The name constraint will only succeed if *all* of the provided names + match. + + Kwargs: + * standard_name: + A string or callable representing the standard name to match + against. + * long_name: + A string or callable representing the long name to match against. + * var_name: + A string or callable representing the NetCDF variable name to match + against. + * STASH: + A string or callable representing the UM STASH code to match + against. + + .. note:: + The default value of each of the keyword arguments is the string + "none", rather than the singleton None, as None may be a legitimate + value to be matched against e.g., to constrain against all cubes + where the standard_name is not set, then use standard_name=None. + + Returns: + * Boolean + + Example usage:: + + iris.NameConstraint(long_name='air temp', var_name=None) + + iris.NameConstraint(long_name=lambda name: 'temp' in name) + + iris.NameConstraint(standard_name='air_temperature', + STASH=lambda stash: stash.item == 203) + + """ + self.standard_name = standard_name + self.long_name = long_name + self.var_name = var_name + self.STASH = STASH + self._names = ("standard_name", "long_name", "var_name", "STASH") + Constraint.__init__(self, cube_func=self._cube_func) + + def _cube_func(self, cube): + def matcher(target, value): + if callable(value): + result = False + if target is not None: + # + # Don't pass None through into the callable. Users should + # use the "name=None" pattern instead. Otherwise, users + # will need to explicitly handle the None case, which is + # unnecessary and pretty darn ugly e.g., + # + # lambda name: name is not None and name.startswith('ick') + # + result = value(target) + else: + result = value == target + return result + + match = True + for name in self._names: + expected = getattr(self, name) + if expected != "none": + if name == "STASH": + actual = cube.attributes.get(name) + else: + actual = getattr(cube, name) + match = matcher(actual, expected) + # Make this is a short-circuit match. + if match is False: + break + + return match + + def __repr__(self): + names = [] + for name in self._names: + value = getattr(self, name) + if value != "none": + names.append("{}={!r}".format(name, value)) + return "{}({})".format(self.__class__.__name__, ", ".join(names)) diff --git a/lib/iris/_cube_coord_common.py b/lib/iris/_cube_coord_common.py index 6225b6f64c..9c75a815d2 100644 --- a/lib/iris/_cube_coord_common.py +++ b/lib/iris/_cube_coord_common.py @@ -1,4 +1,4 @@ -# (C) British Crown Copyright 2010 - 2019, Met Office +# (C) British Crown Copyright 2010 - 2020, Met Office # # This file is part of Iris. # @@ -19,6 +19,8 @@ from six.moves import (filter, input, map, range, zip) # noqa import six + +from collections import namedtuple import re import string @@ -31,6 +33,30 @@ _TOKEN_PARSE = re.compile(r'''^[a-zA-Z0-9][\w\.\+\-@]*$''') +class Names( + namedtuple("Names", ["standard_name", "long_name", "var_name", "STASH"]) +): + """ + Immutable container for name metadata. + + Args: + + * standard_name: + A string representing the CF Conventions and Metadata standard name, or + None. + * long_name: + A string representing the CF Conventions and Metadata long name, or + None + * var_name: + A string representing the associated NetCDF variable name, or None. + * STASH: + A string representing the `~iris.fileformats.pp.STASH` code, or None. + + """ + + __slots__ = () + + def get_valid_standard_name(name): # Standard names are optionally followed by a standard name # modifier, separated by one or more blank spaces @@ -177,6 +203,22 @@ def _check(item): return result + @property + def names(self): + """ + A tuple containing all of the metadata names. This includes the + standard name, long name, NetCDF variable name, and attributes + STASH name. + + """ + standard_name = self.standard_name + long_name = self.long_name + var_name = self.var_name + stash_name = self.attributes.get("STASH") + if stash_name is not None: + stash_name = str(stash_name) + return Names(standard_name, long_name, var_name, stash_name) + def rename(self, name): """ Changes the human-readable name. diff --git a/lib/iris/analysis/__init__.py b/lib/iris/analysis/__init__.py index 8c63ccb28d..34d8345fdd 100644 --- a/lib/iris/analysis/__init__.py +++ b/lib/iris/analysis/__init__.py @@ -1,4 +1,4 @@ -# (C) British Crown Copyright 2010 - 2019, Met Office +# (C) British Crown Copyright 2010 - 2020, Met Office # # This file is part of Iris. # @@ -1080,7 +1080,7 @@ def _percentile(data, axis, percent, fast_percentile_method=False, # Perform the percentile calculation. if fast_percentile_method: msg = 'Cannot use fast np.percentile method with masked array.' - if ma.isMaskedArray(data): + if ma.is_masked(data): raise TypeError(msg) result = np.percentile(data, percent, axis=-1) result = result.T @@ -1090,6 +1090,8 @@ def _percentile(data, axis, percent, fast_percentile_method=False, **kwargs) if not ma.isMaskedArray(data) and not ma.is_masked(result): result = np.asarray(result) + else: + result = ma.MaskedArray(result) # Ensure to unflatten any leading dimensions. if shape: diff --git a/lib/iris/analysis/_area_weighted.py b/lib/iris/analysis/_area_weighted.py index 2c484e4626..6e69b59b8e 100644 --- a/lib/iris/analysis/_area_weighted.py +++ b/lib/iris/analysis/_area_weighted.py @@ -1,4 +1,4 @@ -# (C) British Crown Copyright 2014 - 2016, Met Office +# (C) British Crown Copyright 2014 - 2020, Met Office # # This file is part of Iris. # @@ -55,36 +55,38 @@ def __init__(self, src_grid_cube, target_grid_cube, mdtol=1): .. Note:: - Both sourge and target cubes must have an XY grid defined by + Both source and target cubes must have an XY grid defined by separate X and Y dimensions with dimension coordinates. All of the XY dimension coordinates must also be bounded, and have the same cooordinate system. """ - # Snapshot the state of the cubes to ensure that the regridder is - # impervious to external changes to the original source cubes. + # Snapshot the state of the source cube to ensure that the regridder is + # impervious to external changes to the original cubes. self._src_grid = snapshot_grid(src_grid_cube) - self._target_grid = snapshot_grid(target_grid_cube) + # Missing data tolerance. if not (0 <= mdtol <= 1): msg = 'Value for mdtol must be in range 0 - 1, got {}.' raise ValueError(msg.format(mdtol)) self._mdtol = mdtol - # The need for an actual Cube is an implementation quirk caused by the - # current usage of the experimental regrid function. - self._target_grid_cube_cache = None - - @property - def _target_grid_cube(self): - if self._target_grid_cube_cache is None: - x, y = self._target_grid - data = np.empty((y.points.size, x.points.size)) - cube = iris.cube.Cube(data) - cube.add_dim_coord(y, 0) - cube.add_dim_coord(x, 1) - self._target_grid_cube_cache = cube - return self._target_grid_cube_cache + # Store regridding information + _regrid_info =\ + eregrid._regrid_area_weighted_rectilinear_src_and_grid__prepare( + src_grid_cube, target_grid_cube + ) + ( + src_x, + src_y, + src_x_dim, + src_y_dim, + self.grid_x, + self.grid_y, + self.meshgrid_x, + self.meshgrid_y, + self.weights_info, + ) = _regrid_info def __call__(self, cube): """ @@ -106,8 +108,25 @@ def __call__(self, cube): area-weighted regridding. """ - if get_xy_dim_coords(cube) != self._src_grid: - raise ValueError('The given cube is not defined on the same ' - 'source grid as this regridder.') - return eregrid.regrid_area_weighted_rectilinear_src_and_grid( - cube, self._target_grid_cube, mdtol=self._mdtol) + src_x, src_y = get_xy_dim_coords(cube) + if (src_x, src_y) != self._src_grid: + raise ValueError( + "The given cube is not defined on the same " + "source grid as this regridder." + ) + src_x_dim = cube.coord_dims(src_x)[0] + src_y_dim = cube.coord_dims(src_y)[0] + _regrid_info = ( + src_x, + src_y, + src_x_dim, + src_y_dim, + self.grid_x, + self.grid_y, + self.meshgrid_x, + self.meshgrid_y, + self.weights_info, + ) + return eregrid._regrid_area_weighted_rectilinear_src_and_grid__perform( + cube, _regrid_info, mdtol=self._mdtol + ) diff --git a/lib/iris/analysis/_regrid.py b/lib/iris/analysis/_regrid.py index f80d797642..44f91f9b82 100644 --- a/lib/iris/analysis/_regrid.py +++ b/lib/iris/analysis/_regrid.py @@ -1,4 +1,4 @@ -# (C) British Crown Copyright 2014 - 2019, Met Office +# (C) British Crown Copyright 2014 - 2020, Met Office # # This file is part of Iris. # @@ -829,9 +829,9 @@ def _create_cube(data, src, x_dim, y_dim, src_x_coord, src_y_coord, def copy_coords(src_coords, add_method): for coord in src_coords: dims = src.coord_dims(coord) - if coord is src_x_coord: + if coord == src_x_coord: coord = grid_x_coord - elif coord is src_y_coord: + elif coord == src_y_coord: coord = grid_y_coord elif x_dim in dims or y_dim in dims: continue diff --git a/lib/iris/coord_systems.py b/lib/iris/coord_systems.py index eab49e36de..90d1cd47ff 100644 --- a/lib/iris/coord_systems.py +++ b/lib/iris/coord_systems.py @@ -1,4 +1,4 @@ -# (C) British Crown Copyright 2010 - 2019, Met Office +# (C) British Crown Copyright 2010 - 2020, Met Office # # This file is part of Iris. # @@ -647,10 +647,16 @@ class Geostationary(CoordSystem): grid_mapping_name = 'geostationary' - def __init__(self, latitude_of_projection_origin, - longitude_of_projection_origin, - perspective_point_height, sweep_angle_axis, false_easting=0, - false_northing=0, ellipsoid=None): + def __init__( + self, + latitude_of_projection_origin, + longitude_of_projection_origin, + perspective_point_height, + sweep_angle_axis, + false_easting=None, + false_northing=None, + ellipsoid=None, + ): """ Constructs a Geostationary coord system. @@ -697,9 +703,13 @@ def __init__(self, latitude_of_projection_origin, self.perspective_point_height = float(perspective_point_height) #: X offset from planar origin in metres. + if false_easting is None: + false_easting = 0 self.false_easting = float(false_easting) #: Y offset from planar origin in metres. + if false_northing is None: + false_northing = 0 self.false_northing = float(false_northing) #: The axis along which the satellite instrument sweeps - 'x' or 'y'. diff --git a/lib/iris/experimental/regrid.py b/lib/iris/experimental/regrid.py index edcff3d3c4..d35501b313 100644 --- a/lib/iris/experimental/regrid.py +++ b/lib/iris/experimental/regrid.py @@ -1,4 +1,4 @@ -# (C) British Crown Copyright 2013 - 2019, Met Office +# (C) British Crown Copyright 2013 - 2020, Met Office # # This file is part of Iris. # @@ -22,7 +22,6 @@ from six.moves import (filter, input, map, range, zip) # noqa import six -from collections import namedtuple import copy import functools import warnings @@ -47,11 +46,6 @@ from iris.util import _meshgrid -_Version = namedtuple('Version', ('major', 'minor', 'micro')) -_NP_VERSION = _Version(*(int(val) for val in - np.version.version.split('.') if val.isdigit())) - - def _get_xy_coords(cube): """ Return the x and y coordinates from a cube. @@ -405,11 +399,7 @@ def _weighted_mean_with_mdtol(data, weights, axis=None, mdtol=0): return res -def _regrid_area_weighted_array(src_data, x_dim, y_dim, - src_x_bounds, src_y_bounds, - grid_x_bounds, grid_y_bounds, - grid_x_decreasing, grid_y_decreasing, - area_func, circular=False, mdtol=0): +def _regrid_area_weighted_array(src_data, x_dim, y_dim, weights_info, mdtol=0): """ Regrid the given data from its source grid to a new grid using an area weighted mean to determine the resulting data values. @@ -428,30 +418,12 @@ def _regrid_area_weighted_array(src_data, x_dim, y_dim, The X dimension within `src_data`. * y_dim: The Y dimension within `src_data`. - * src_x_bounds: - A NumPy array of bounds along the X axis defining the source grid. - * src_y_bounds: - A NumPy array of bounds along the Y axis defining the source grid. - * grid_x_bounds: - A NumPy array of bounds along the X axis defining the new grid. - * grid_y_bounds: - A NumPy array of bounds along the Y axis defining the new grid. - * grid_x_decreasing: - Boolean indicating whether the X coordinate of the new grid is - in descending order. - * grid_y_decreasing: - Boolean indicating whether the Y coordinate of the new grid is - in descending order. - * area_func: - A function that returns an (p, q) array of weights given an (p, 2) - shaped array of Y bounds and an (q, 2) shaped array of X bounds. + * weights_info: + The area weights information to be used for area-weighted + regridding. Kwargs: - * circular: - A boolean indicating whether the `src_x_bounds` are periodic. Default - is False. - * mdtol: Tolerance of missing data. The value returned in each element of the returned array will be masked if the fraction of missing data exceeds @@ -467,164 +439,149 @@ def _regrid_area_weighted_array(src_data, x_dim, y_dim, grid. """ - # Create empty data array to match the new grid. - # Note that dtype is not preserved and that the array is - # masked to allow for regions that do not overlap. + ( + cached_x_indices, + cached_y_indices, + max_x_indices, + max_y_indices, + cached_weights, + ) = weights_info + + # Ensure we have x_dim and y_dim. + x_dim_orig = x_dim + y_dim_orig = y_dim + if y_dim is None: + src_data = np.expand_dims(src_data, axis=src_data.ndim) + y_dim = src_data.ndim - 1 + if x_dim is None: + src_data = np.expand_dims(src_data, axis=src_data.ndim) + x_dim = src_data.ndim - 1 + # Move y_dim and x_dim to last dimensions + if not x_dim == src_data.ndim - 1: + src_data = np.moveaxis(src_data, x_dim, -1) + if not y_dim == src_data.ndim - 2: + if x_dim < y_dim: + # note: y_dim was shifted along by one position when + # x_dim was moved to the last dimension + src_data = np.moveaxis(src_data, y_dim - 1, -2) + elif x_dim > y_dim: + src_data = np.moveaxis(src_data, y_dim, -2) + x_dim = src_data.ndim - 1 + y_dim = src_data.ndim - 2 + + # Create empty "pre-averaging" data array that will enable the + # src_data data coresponding to a given target grid point, + # to be stacked per point. + # Note that dtype is not preserved and that the array mask + # allows for regions that do not overlap. new_shape = list(src_data.shape) - if x_dim is not None: - new_shape[x_dim] = grid_x_bounds.shape[0] - if y_dim is not None: - new_shape[y_dim] = grid_y_bounds.shape[0] - + new_shape[x_dim] = len(cached_x_indices) + new_shape[y_dim] = len(cached_y_indices) + num_target_pts = len(cached_y_indices) * len(cached_x_indices) + src_areas_shape = list(src_data.shape) + src_areas_shape[y_dim] = max_y_indices + src_areas_shape[x_dim] = max_x_indices + src_areas_shape += [num_target_pts] # Use input cube dtype or convert values to the smallest possible float # dtype when necessary. dtype = np.promote_types(src_data.dtype, np.float16) + # Create empty arrays to hold src_data per target point, and weights + src_area_datas = np.zeros(src_areas_shape, dtype=np.float64) + src_area_weights = np.zeros( + list((max_y_indices, max_x_indices, num_target_pts)) + ) # Flag to indicate whether the original data was a masked array. - src_masked = ma.isMaskedArray(src_data) + src_masked = src_data.mask.any() if ma.isMaskedArray(src_data) else False if src_masked: - new_data = ma.zeros(new_shape, fill_value=src_data.fill_value, - dtype=dtype) + src_area_masks = np.full(src_areas_shape, True, dtype=np.bool) else: - new_data = ma.zeros(new_shape, dtype=dtype) - # Assign to mask to explode it, allowing indexed assignment. - new_data.mask = False - - indices = [slice(None)] * new_data.ndim - - # Determine which grid bounds are within src extent. - y_within_bounds = _within_bounds(src_y_bounds, grid_y_bounds, - grid_y_decreasing) - x_within_bounds = _within_bounds(src_x_bounds, grid_x_bounds, - grid_x_decreasing) - - # Cache which src_bounds are within grid bounds - cached_x_bounds = [] - cached_x_indices = [] - for (x_0, x_1) in grid_x_bounds: - if grid_x_decreasing: - x_0, x_1 = x_1, x_0 - x_bounds, x_indices = _cropped_bounds(src_x_bounds, x_0, x_1) - cached_x_bounds.append(x_bounds) - cached_x_indices.append(x_indices) - - # Simple for loop approach. - for j, (y_0, y_1) in enumerate(grid_y_bounds): - # Reverse lower and upper if dest grid is decreasing. - if grid_y_decreasing: - y_0, y_1 = y_1, y_0 - y_bounds, y_indices = _cropped_bounds(src_y_bounds, y_0, y_1) - for i, (x_0, x_1) in enumerate(grid_x_bounds): - # Reverse lower and upper if dest grid is decreasing. - if grid_x_decreasing: - x_0, x_1 = x_1, x_0 - x_bounds = cached_x_bounds[i] - x_indices = cached_x_indices[i] - - # Determine whether to mask element i, j based on overlap with - # src. - # If x_0 > x_1 then we want [0]->x_1 and x_0->[0] + mod in the case - # of wrapped longitudes. However if the src grid is not global - # (i.e. circular) this new cell would include a region outside of - # the extent of the src grid and should therefore be masked. - outside_extent = x_0 > x_1 and not circular - if (outside_extent or not y_within_bounds[j] or not - x_within_bounds[i]): - # Mask out element(s) in new_data - if x_dim is not None: - indices[x_dim] = i - if y_dim is not None: - indices[y_dim] = j - new_data[tuple(indices)] = ma.masked + new_data_mask = np.full(new_shape, False, dtype=np.bool) + + # Axes of data over which the weighted mean is calculated. + axis = (y_dim, x_dim) + + # Stack the src_area data and weights for each target point + target_pt_ji = -1 + for j, y_indices in enumerate(cached_y_indices): + for i, x_indices in enumerate(cached_x_indices): + target_pt_ji += 1 + # Determine whether to mask element i, j based on whether + # there are valid weights. + weights = cached_weights[j][i] + if isinstance(weights, bool) and not weights: + if not src_masked: + # Cheat! Fill the data with zeros and weights as one. + # The weighted average result will be the same, but + # we avoid dividing by zero. + src_area_weights[..., target_pt_ji] = 1 + new_data_mask[..., j, i] = True else: # Calculate weighted mean of data points. # Slice out relevant data (this may or may not be a view() # depending on x_indices being a slice or not). - if x_dim is not None: - indices[x_dim] = x_indices - if y_dim is not None: - indices[y_dim] = y_indices - if isinstance(x_indices, tuple) and \ - isinstance(y_indices, tuple): - raise RuntimeError('Cannot handle split bounds ' - 'in both x and y.') - data = src_data[tuple(indices)] - - # Calculate weights based on areas of cropped bounds. - weights = area_func(y_bounds, x_bounds) - - # Numpy 1.7 allows the axis keyword arg to be a tuple. - # If the version of NumPy is less than 1.7 manipulate the axes - # of the data so the x and y dimensions can be flattened. - if _NP_VERSION.minor < 7: - if y_dim is not None and x_dim is not None: - flattened_shape = list(data.shape) - if y_dim > x_dim: - data = np.rollaxis(data, y_dim, data.ndim) - data = np.rollaxis(data, x_dim, data.ndim) - del flattened_shape[y_dim] - del flattened_shape[x_dim] - else: - data = np.rollaxis(data, x_dim, data.ndim) - data = np.rollaxis(data, y_dim, data.ndim) - del flattened_shape[x_dim] - del flattened_shape[y_dim] - weights = weights.T - flattened_shape.append(-1) - data = data.reshape(*flattened_shape) - elif y_dim is not None: - flattened_shape = list(data.shape) - del flattened_shape[y_dim] - flattened_shape.append(-1) - data = data.swapaxes(y_dim, -1).reshape( - *flattened_shape) - elif x_dim is not None: - flattened_shape = list(data.shape) - del flattened_shape[x_dim] - flattened_shape.append(-1) - data = data.swapaxes(x_dim, -1).reshape( - *flattened_shape) - weights = weights.ravel() - axis = -1 - else: - # Transpose weights to match dim ordering in data. - weights_shape_y = weights.shape[0] - weights_shape_x = weights.shape[1] - if x_dim is not None and y_dim is not None and \ - x_dim < y_dim: - weights = weights.T - # Broadcast the weights array to allow numpy's ma.average - # to be called. - weights_padded_shape = [1] * data.ndim - axes = [] - if y_dim is not None: - weights_padded_shape[y_dim] = weights_shape_y - axes.append(y_dim) - if x_dim is not None: - weights_padded_shape[x_dim] = weights_shape_x - axes.append(x_dim) - # Assign new shape to raise error on copy. - weights.shape = weights_padded_shape - # Broadcast weights to match shape of data. - _, weights = np.broadcast_arrays(data, weights) - # Axes of data over which the weighted mean is calculated. - axis = tuple(axes) - - # Calculate weighted mean taking into account missing data. - new_data_pt = _weighted_mean_with_mdtol( - data, weights=weights, axis=axis, mdtol=mdtol) - - # Insert data (and mask) values into new array. - if x_dim is not None: - indices[x_dim] = i - if y_dim is not None: - indices[y_dim] = j - new_data[tuple(indices)] = new_data_pt - - # Remove new mask if original data was not masked - # and no values in the new array are masked. - if not src_masked and not new_data.mask.any(): - new_data = new_data.data + data = src_data[..., y_indices, x_indices] + len_x = data.shape[-1] + len_y = data.shape[-2] + src_area_datas[..., 0:len_y, 0:len_x, target_pt_ji] = data + src_area_weights[0:len_y, 0:len_x, target_pt_ji] = weights + if src_masked: + src_area_masks[ + ..., 0:len_y, 0:len_x, target_pt_ji + ] = data.mask + + # Broadcast the weights array to allow numpy's ma.average + # to be called. + # Assign new shape to raise error on copy. + src_area_weights.shape = src_area_datas.shape[-3:] + # Broadcast weights to match shape of data. + _, src_area_weights = np.broadcast_arrays(src_area_datas, src_area_weights) + + # Mask the data points + if src_masked: + src_area_datas = np.ma.array(src_area_datas, mask=src_area_masks) + + # Calculate weighted mean taking into account missing data. + new_data = _weighted_mean_with_mdtol( + src_area_datas, weights=src_area_weights, axis=axis, mdtol=mdtol + ) + new_data = new_data.reshape(new_shape) + if src_masked: + new_data_mask = new_data.mask + + # Mask the data if originally masked or if the result has masked points + if ma.isMaskedArray(src_data): + new_data = ma.array( + new_data, + mask=new_data_mask, + fill_value=src_data.fill_value, + dtype=dtype, + ) + elif new_data_mask.any(): + new_data = ma.array(new_data, mask=new_data_mask, dtype=dtype) + else: + new_data = new_data.astype(dtype) + + # Restore data to original form + if x_dim_orig is None and y_dim_orig is None: + new_data = np.squeeze(new_data, axis=x_dim) + new_data = np.squeeze(new_data, axis=y_dim) + elif y_dim_orig is None: + new_data = np.squeeze(new_data, axis=y_dim) + new_data = np.moveaxis(new_data, -1, x_dim_orig) + elif x_dim_orig is None: + new_data = np.squeeze(new_data, axis=x_dim) + new_data = np.moveaxis(new_data, -1, y_dim_orig) + elif x_dim_orig < y_dim_orig: + # move the x_dim back first, so that the y_dim will + # then be moved to its original position + new_data = np.moveaxis(new_data, -1, x_dim_orig) + new_data = np.moveaxis(new_data, -1, y_dim_orig) + else: + # move the y_dim back first, so that the x_dim will + # then be moved to its original position + new_data = np.moveaxis(new_data, -2, y_dim_orig) + new_data = np.moveaxis(new_data, -1, x_dim_orig) return new_data @@ -671,6 +628,25 @@ def regrid_area_weighted_rectilinear_src_and_grid(src_cube, grid_cube, Returns: A new :class:`iris.cube.Cube` instance. + """ + regrid_info = _regrid_area_weighted_rectilinear_src_and_grid__prepare( + src_cube, grid_cube + ) + result = _regrid_area_weighted_rectilinear_src_and_grid__perform( + src_cube, regrid_info, mdtol + ) + return result + + +def _regrid_area_weighted_rectilinear_src_and_grid__prepare( + src_cube, grid_cube +): + """ + First (setup) part of 'regrid_area_weighted_rectilinear_src_and_grid'. + + Check inputs and calculate related info. The 'regrid info' returned + can be re-used over many 2d slices. + """ # Get the 1d monotonic (or scalar) src and grid coordinates. src_x, src_y = _get_xy_coords(src_cube) @@ -727,6 +703,9 @@ def regrid_area_weighted_rectilinear_src_and_grid(src_cube, grid_cube, grid_x_bounds = _get_bounds_in_units(grid_x, x_units, dtype) grid_y_bounds = _get_bounds_in_units(grid_y, y_units, dtype) + # Create 2d meshgrids as required by _create_cube func. + meshgrid_x, meshgrid_y = _meshgrid(grid_x.points, grid_y.points) + # Determine whether target grid bounds are decreasing. This must # be determined prior to wrap_lons being called. grid_x_decreasing = grid_x_bounds[-1, 0] < grid_x_bounds[0, 0] @@ -753,17 +732,185 @@ def regrid_area_weighted_rectilinear_src_and_grid(src_cube, grid_cube, else: area_func = _cartesian_area + def _calculate_regrid_area_weighted_weights( + src_x_bounds, + src_y_bounds, + grid_x_bounds, + grid_y_bounds, + grid_x_decreasing, + grid_y_decreasing, + area_func, + circular=False, + ): + """ + Compute the area weights used for area-weighted regridding. + + Args: + + * src_x_bounds: + A NumPy array of bounds along the X axis defining the source grid. + * src_y_bounds: + A NumPy array of bounds along the Y axis defining the source grid. + * grid_x_bounds: + A NumPy array of bounds along the X axis defining the new grid. + * grid_y_bounds: + A NumPy array of bounds along the Y axis defining the new grid. + * grid_x_decreasing: + Boolean indicating whether the X coordinate of the new grid is + in descending order. + * grid_y_decreasing: + Boolean indicating whether the Y coordinate of the new grid is + in descending order. + * area_func: + A function that returns an (p, q) array of weights given an (p, 2) + shaped array of Y bounds and an (q, 2) shaped array of X bounds. + + Kwargs: + + * circular: + A boolean indicating whether the `src_x_bounds` are periodic. + Default is False. + + Returns: + The area weights to be used for area-weighted regridding. + + """ + # Determine which grid bounds are within src extent. + y_within_bounds = _within_bounds( + src_y_bounds, grid_y_bounds, grid_y_decreasing + ) + x_within_bounds = _within_bounds( + src_x_bounds, grid_x_bounds, grid_x_decreasing + ) + + # Cache which src_bounds are within grid bounds + cached_x_bounds = [] + cached_x_indices = [] + max_x_indices = 0 + for (x_0, x_1) in grid_x_bounds: + if grid_x_decreasing: + x_0, x_1 = x_1, x_0 + x_bounds, x_indices = _cropped_bounds(src_x_bounds, x_0, x_1) + cached_x_bounds.append(x_bounds) + cached_x_indices.append(x_indices) + # Keep record of the largest slice + if isinstance(x_indices, slice): + x_indices_size = np.sum(x_indices.stop - x_indices.start) + else: # is tuple of indices + x_indices_size = len(x_indices) + if x_indices_size > max_x_indices: + max_x_indices = x_indices_size + + # Cache which y src_bounds areas and weights are within grid bounds + cached_y_indices = [] + cached_weights = [] + max_y_indices = 0 + for j, (y_0, y_1) in enumerate(grid_y_bounds): + # Reverse lower and upper if dest grid is decreasing. + if grid_y_decreasing: + y_0, y_1 = y_1, y_0 + y_bounds, y_indices = _cropped_bounds(src_y_bounds, y_0, y_1) + cached_y_indices.append(y_indices) + # Keep record of the largest slice + if isinstance(y_indices, slice): + y_indices_size = np.sum(y_indices.stop - y_indices.start) + else: # is tuple of indices + y_indices_size = len(y_indices) + if y_indices_size > max_y_indices: + max_y_indices = y_indices_size + + weights_i = [] + for i, (x_0, x_1) in enumerate(grid_x_bounds): + # Reverse lower and upper if dest grid is decreasing. + if grid_x_decreasing: + x_0, x_1 = x_1, x_0 + x_bounds = cached_x_bounds[i] + x_indices = cached_x_indices[i] + + # Determine whether element i, j overlaps with src and hence + # an area weight should be computed. + # If x_0 > x_1 then we want [0]->x_1 and x_0->[0] + mod in + # the case of wrapped longitudes. However if the src grid is + # not global (i.e. circular) this new cell would include a + # region outside of the extent of the src grid and thus the + # weight is therefore invalid. + outside_extent = x_0 > x_1 and not circular + if ( + outside_extent or + not y_within_bounds[j] or + not x_within_bounds[i] + ): + weights = False + else: + # Calculate weights based on areas of cropped bounds. + if isinstance(x_indices, tuple) and isinstance( + y_indices, tuple + ): + raise RuntimeError( + "Cannot handle split bounds " "in both x and y." + ) + weights = area_func(y_bounds, x_bounds) + weights_i.append(weights) + cached_weights.append(weights_i) + return ( + tuple(cached_x_indices), + tuple(cached_y_indices), + max_x_indices, + max_y_indices, + tuple(cached_weights), + ) + + weights_info = _calculate_regrid_area_weighted_weights( + src_x_bounds, + src_y_bounds, + grid_x_bounds, + grid_y_bounds, + grid_x_decreasing, + grid_y_decreasing, + area_func, + circular, + ) + + return ( + src_x, + src_y, + src_x_dim, + src_y_dim, + grid_x, + grid_y, + meshgrid_x, + meshgrid_y, + weights_info, + ) + + +def _regrid_area_weighted_rectilinear_src_and_grid__perform( + src_cube, regrid_info, mdtol +): + """ + Second (regrid) part of 'regrid_area_weighted_rectilinear_src_and_grid'. + + Perform the prepared regrid calculation on a single 2d cube. + + """ + ( + src_x, + src_y, + src_x_dim, + src_y_dim, + grid_x, + grid_y, + meshgrid_x, + meshgrid_y, + weights_info, + ) = regrid_info + # Calculate new data array for regridded cube. - new_data = _regrid_area_weighted_array(src_cube.data, src_x_dim, src_y_dim, - src_x_bounds, src_y_bounds, - grid_x_bounds, grid_y_bounds, - grid_x_decreasing, - grid_y_decreasing, - area_func, circular, mdtol) + new_data = _regrid_area_weighted_array( + src_cube.data, src_x_dim, src_y_dim, weights_info, mdtol, + ) # Wrap up the data as a Cube. - # Create 2d meshgrids as required by _create_cube func. - meshgrid_x, meshgrid_y = _meshgrid(grid_x.points, grid_y.points) regrid_callback = RectilinearRegridder._regrid new_cube = RectilinearRegridder._create_cube(new_data, src_cube, src_x_dim, src_y_dim, diff --git a/lib/iris/tests/__init__.py b/lib/iris/tests/__init__.py index 0ce09b6ef1..dbb88b45d3 100644 --- a/lib/iris/tests/__init__.py +++ b/lib/iris/tests/__init__.py @@ -1,4 +1,4 @@ -# (C) British Crown Copyright 2010 - 2019, Met Office +# (C) British Crown Copyright 2010 - 2020, Met Office # # This file is part of Iris. # @@ -1210,9 +1210,10 @@ class MyPlotTests(test.GraphicsTest): 'which is not available.') -skip_sample_data = unittest.skipIf(not SAMPLE_DATA_AVAILABLE, - ('Test(s) require "iris-sample-data", ' - 'which is not available.')) +skip_sample_data = unittest.skipIf( + not SAMPLE_DATA_AVAILABLE, + ('Test(s) require "iris-sample-data", ' "which is not available."), +) skip_nc_time_axis = unittest.skipIf( diff --git a/lib/iris/tests/experimental/regrid/test_regrid_area_weighted_rectilinear_src_and_grid.py b/lib/iris/tests/experimental/regrid/test_regrid_area_weighted_rectilinear_src_and_grid.py index cce1c0e671..8c32029246 100644 --- a/lib/iris/tests/experimental/regrid/test_regrid_area_weighted_rectilinear_src_and_grid.py +++ b/lib/iris/tests/experimental/regrid/test_regrid_area_weighted_rectilinear_src_and_grid.py @@ -1,4 +1,4 @@ -# (C) British Crown Copyright 2013 - 2018, Met Office +# (C) British Crown Copyright 2013 - 2020, Met Office # # This file is part of Iris. # @@ -327,19 +327,36 @@ def test_regrid_latlon_reduced_res(self): res = regrid_area_weighted(src, dest) self.assertCMLApproxData(res, RESULT_DIR + ('latlonreduced.cml',)) - def test_regrid_transposed(self): - src = self.simple_cube.copy() - dest = _subsampled_grid(src, 2, 3) - # Transpose src so that the coords are not y, x ordered. - src.transpose() + def test_regrid_reorder_axis(self): + src = self.realistic_cube[0, :4, :3, :2] + z = src.coord("model_level_number") + lat = src.coord("grid_latitude") + lon = src.coord("grid_longitude") + dest = _resampled_grid(self.realistic_cube[0, 0, :3, :2], 3, 3) res = regrid_area_weighted(src, dest) - self.assertCMLApproxData(res, RESULT_DIR + ('trasposed.cml',)) - # Using original and transposing the result should give the - # same answer. - src = self.simple_cube.copy() + self.assertArrayShapeStats(src, (4, 3, 2), 288.08868, 0.008262919) + self.assertArrayShapeStats(res, (4, 9, 6), 288.08865, 0.00826281) + # Reshape src so that the coords are ordered [x, z, y], + # the mean and std statistics should be the same + data = np.moveaxis(src.data.copy(), 2, 0) + src = iris.cube.Cube(data) + src.add_dim_coord(lat, 2) + src.add_dim_coord(z, 1) + src.add_dim_coord(lon, 0) res = regrid_area_weighted(src, dest) - res.transpose() - self.assertCMLApproxData(res, RESULT_DIR + ('trasposed.cml',)) + self.assertArrayShapeStats(src, (2, 4, 3), 288.08868, 0.008262919) + self.assertArrayShapeStats(res, (6, 4, 9), 288.08865, 0.00826281) + # Reshape src so that the coords are ordered [y, x, z], + # the mean and std statistics should be the same + data = np.moveaxis(src.data.copy(), 2, 0) + src = iris.cube.Cube(data) + src.add_dim_coord(z, 2) + src.add_dim_coord(lon, 1) + src.add_dim_coord(lat, 0) + dest = _resampled_grid(self.realistic_cube[0, 0, :3, :2], 3, 3) + res = regrid_area_weighted(src, dest) + self.assertArrayShapeStats(src, (3, 2, 4), 288.08868, 0.008262919) + self.assertArrayShapeStats(res, (9, 6, 4), 288.08865, 0.00826281) def test_regrid_lon_to_half_res(self): src = self.simple_cube @@ -370,13 +387,22 @@ def test_hybrid_height(self): def test_missing_data(self): src = self.simple_cube.copy() - src.data = ma.masked_array(src.data) + src.data = ma.masked_array(src.data, fill_value=999) src.data[1, 2] = ma.masked dest = _resampled_grid(self.simple_cube, 2.3, 2.4) res = regrid_area_weighted(src, dest) mask = np.zeros((7, 9), bool) mask[slice(2, 5), slice(4, 7)] = True self.assertArrayEqual(res.data.mask, mask) + self.assertArrayEqual(res.data.fill_value, 999) + + def test_masked_data_all_false(self): + src = self.simple_cube.copy() + src.data = ma.masked_array(src.data, mask=False, fill_value=999) + dest = _resampled_grid(self.simple_cube, 2.3, 2.4) + res = regrid_area_weighted(src, dest) + self.assertArrayEqual(res.data.mask, False) + self.assertArrayEqual(res.data.fill_value, 999) def test_no_x_overlap(self): src = self.simple_cube @@ -436,8 +462,19 @@ def test_cross_section(self): dest.add_dim_coord(lon, 1) dest.add_aux_coord(src.coord('grid_latitude').copy(), None) res = regrid_area_weighted(src, dest) - self.assertCMLApproxData(res, RESULT_DIR + - ('const_lat_cross_section.cml',)) + self.assertCMLApproxData( + res, RESULT_DIR + ("const_lat_cross_section.cml",) + ) + # Constant latitude, data order [x, z] + # Using original and transposing the result should give the + # same answer. + src.transpose() + dest.transpose() + res = regrid_area_weighted(src, dest) + res.transpose() + self.assertCMLApproxData( + res, RESULT_DIR + ("const_lat_cross_section.cml",) + ) # Constant longitude src = self.realistic_cube[0, :, :, 10] @@ -449,8 +486,19 @@ def test_cross_section(self): dest.add_dim_coord(lat, 1) dest.add_aux_coord(src.coord('grid_longitude').copy(), None) res = regrid_area_weighted(src, dest) - self.assertCMLApproxData(res, RESULT_DIR + - ('const_lon_cross_section.cml',)) + self.assertCMLApproxData( + res, RESULT_DIR + ("const_lon_cross_section.cml",) + ) + # Constant longitude, data order [y, z] + # Using original and transposing the result should give the + # same answer. + src.transpose() + dest.transpose() + res = regrid_area_weighted(src, dest) + res.transpose() + self.assertCMLApproxData( + res, RESULT_DIR + ("const_lon_cross_section.cml",) + ) def test_scalar_source_cube(self): src = self.simple_cube[1, 2] diff --git a/lib/iris/tests/integration/test_grib2.py b/lib/iris/tests/integration/test_grib2.py index 71e80147b9..5f0a8d5177 100644 --- a/lib/iris/tests/integration/test_grib2.py +++ b/lib/iris/tests/integration/test_grib2.py @@ -1,4 +1,4 @@ -# (C) British Crown Copyright 2014 - 2017, Met Office +# (C) British Crown Copyright 2014 - 2020, Met Office # # This file is part of Iris. # @@ -38,6 +38,10 @@ if tests.GRIB_AVAILABLE: from iris_grib import load_pairs_from_fields from iris_grib.message import GribMessage + try: + from iris_grib.grib_phenom_translation import GRIBCode + except ImportError: + GRIBCode = None @tests.skip_data @@ -146,7 +150,9 @@ def test_save_load(self): fpcoord = DimCoord(24, 'forecast_period', units=Unit('hours')) cube.add_aux_coord(tcoord) cube.add_aux_coord(fpcoord) - cube.attributes['WMO_constituent_type'] = 0 + cube.attributes["WMO_constituent_type"] = 0 + if GRIBCode is not None: + cube.attributes["GRIB_PARAM"] = GRIBCode("GRIB2:d000c014n000") with self.temp_filename('test_grib_pdt40.grib2') as temp_file_path: save(cube, temp_file_path) @@ -218,9 +224,14 @@ def test_save_load(self): self.assertEqual(test_cube.shape, (744, 744)) self.assertEqual(test_cube.cell_methods, ()) - # Check no cube attributes on the re-loaded cube. - # Note: this does *not* match the original, but is as expected. - self.assertEqual(cube_loaded_from_saved.attributes, {}) + if GRIBCode is not None: + # Python3 only --> iris-grib version >= 0.15 + # Check only the GRIB_PARAM attribute exists on the re-loaded cube. + # Note: this does *not* match the original, but is as expected. + self.assertEqual( + cube_loaded_from_saved.attributes, + {"GRIB_PARAM": GRIBCode("GRIB2:d000c003n001")}, + ) # Now remaining to check: coordinates + data... diff --git a/lib/iris/tests/integration/test_grib_load.py b/lib/iris/tests/integration/test_grib_load.py index 2cf18154fc..7e5aaf7234 100644 --- a/lib/iris/tests/integration/test_grib_load.py +++ b/lib/iris/tests/integration/test_grib_load.py @@ -1,4 +1,4 @@ -# (C) British Crown Copyright 2010 - 2017, Met Office +# (C) British Crown Copyright 2010 - 2020, Met Office # # This file is part of Iris. # diff --git a/lib/iris/tests/integration/test_netcdf.py b/lib/iris/tests/integration/test_netcdf.py index 4894de292c..2033cf76a6 100644 --- a/lib/iris/tests/integration/test_netcdf.py +++ b/lib/iris/tests/integration/test_netcdf.py @@ -1,4 +1,4 @@ -# (C) British Crown Copyright 2014 - 2019, Met Office +# (C) British Crown Copyright 2014 - 2020, Met Office # # This file is part of Iris. # @@ -27,7 +27,9 @@ from contextlib import contextmanager from itertools import repeat import os.path +from os.path import join as path_join import shutil +from subprocess import check_call import tempfile import warnings @@ -535,5 +537,79 @@ def test_standard_name_roundtrip(self): self.assertEqual(detection_limit_cube.standard_name, standard_name) +class TestLoadMinimalGeostationary(tests.IrisTest): + """ + Check we can load data with a geostationary grid-mapping, even when the + 'false-easting' and 'false_northing' properties are missing. + + """ + + _geostationary_problem_cdl = """ +netcdf geostationary_problem_case { +dimensions: + y = 2 ; + x = 3 ; +variables: + short radiance(y, x) ; + radiance:standard_name = "toa_outgoing_radiance_per_unit_wavelength" ; + radiance:units = "W m-2 sr-1 um-1" ; + radiance:coordinates = "y x" ; + radiance:grid_mapping = "imager_grid_mapping" ; + short y(y) ; + y:units = "rad" ; + y:axis = "Y" ; + y:long_name = "fixed grid projection y-coordinate" ; + y:standard_name = "projection_y_coordinate" ; + short x(x) ; + x:units = "rad" ; + x:axis = "X" ; + x:long_name = "fixed grid projection x-coordinate" ; + x:standard_name = "projection_x_coordinate" ; + int imager_grid_mapping ; + imager_grid_mapping:grid_mapping_name = "geostationary" ; + imager_grid_mapping:perspective_point_height = 35786023. ; + imager_grid_mapping:semi_major_axis = 6378137. ; + imager_grid_mapping:semi_minor_axis = 6356752.31414 ; + imager_grid_mapping:latitude_of_projection_origin = 0. ; + imager_grid_mapping:longitude_of_projection_origin = -75. ; + imager_grid_mapping:sweep_angle_axis = "x" ; + +data: + + // coord values, just so these can be dim-coords + y = 0, 1 ; + x = 0, 1, 2 ; + +} +""" + + @classmethod + def setUpClass(cls): + # Create a temp directory for transient test files. + cls.temp_dir = tempfile.mkdtemp() + cls.path_test_cdl = path_join(cls.temp_dir, "geos_problem.cdl") + cls.path_test_nc = path_join(cls.temp_dir, "geos_problem.nc") + # Create a reference file from the CDL text. + with open(cls.path_test_cdl, "w") as f_out: + f_out.write(cls._geostationary_problem_cdl) + # Call 'ncgen' to make an actual netCDF file from the CDL. + command = "ncgen -o {} {}".format(cls.path_test_nc, cls.path_test_cdl) + check_call(command, shell=True) + + @classmethod + def tearDownClass(cls): + # Destroy the temp directory. + shutil.rmtree(cls.temp_dir) + + def test_geostationary_no_false_offsets(self): + # Check we can load test data and coord system properties are correct. + cube = iris.load_cube(self.path_test_nc) + # Check the coord system properties has the correct default properties. + cs = cube.coord_system() + self.assertIsInstance(cs, iris.coord_systems.Geostationary) + self.assertEqual(cs.false_easting, 0.0) + self.assertEqual(cs.false_northing, 0.0) + + if __name__ == "__main__": tests.main() diff --git a/lib/iris/tests/integration/test_pickle.py b/lib/iris/tests/integration/test_pickle.py index a6506ea91e..2153457818 100644 --- a/lib/iris/tests/integration/test_pickle.py +++ b/lib/iris/tests/integration/test_pickle.py @@ -1,4 +1,4 @@ -# (C) British Crown Copyright 2014 - 2017, Met Office +# (C) British Crown Copyright 2014 - 2020, Met Office # # This file is part of Iris. # @@ -23,6 +23,7 @@ # importing anything else. import iris.tests as tests +import unittest import six.moves.cPickle as pickle import iris @@ -31,57 +32,82 @@ from iris_grib.message import GribMessage -@tests.skip_data -@tests.skip_grib -class TestGribMessage(tests.IrisTest): - def test(self): - # Check that a GribMessage pickles without errors. - path = tests.get_data_path(('GRIB', 'fp_units', 'hours.grib2')) - messages = GribMessage.messages_from_filename(path) - message = next(messages) +class Common(object): + def pickle_cube(self, protocol): + # Ensure that data proxies are pickleable. + cube = iris.load(self.path)[0] with self.temp_filename('.pkl') as filename: with open(filename, 'wb') as f: - pickle.dump(message, f) + pickle.dump(cube, f, protocol) + with open(filename, 'rb') as f: + ncube = pickle.load(f) + self.assertEqual(ncube, cube) - def test_data(self): - # Check that GribMessage.data pickles without errors. - path = tests.get_data_path(('GRIB', 'fp_units', 'hours.grib2')) - messages = GribMessage.messages_from_filename(path) - message = next(messages) - with self.temp_filename('.pkl') as filename: - with open(filename, 'wb') as f: - pickle.dump(message.data, f) + def test_protocol_0(self): + self.pickle_cube(0) + def test_protocol_1(self): + self.pickle_cube(1) -class Common(object): - # Ensure that data proxies are pickleable. - def pickle_cube(self, path): - cube = iris.load(path)[0] + def test_protocol_2(self): + self.pickle_cube(2) + + +@tests.skip_data +@tests.skip_grib +class TestGribMessage(Common, tests.IrisTest): + def setUp(self): + self.path = tests.get_data_path(('GRIB', 'fp_units', 'hours.grib2')) + + def pickle_obj(self, obj): with self.temp_filename('.pkl') as filename: with open(filename, 'wb') as f: - pickle.dump(cube, f) + pickle.dump(obj, f) + + # These probably "ought" to work, but currently fail. + # see https://github.com/SciTools/iris/pull/2608 + @unittest.expectedFailure + def test_protocol_0(self): + super(TestGribMessage, self).test_protocol_0() + + @unittest.expectedFailure + def test_protocol_1(self): + super(TestGribMessage, self).test_protocol_1() + + @unittest.expectedFailure + def test_protocol_2(self): + super(TestGribMessage, self).test_protocol_2() + + def test(self): + # Check that a GribMessage pickles without errors. + messages = GribMessage.messages_from_filename(self.path) + obj = next(messages) + self.pickle_obj(obj) + + def test_data(self): + # Check that GribMessage.data pickles without errors. + messages = GribMessage.messages_from_filename(self.path) + obj = next(messages).data + self.pickle_obj(obj) @tests.skip_data class test_netcdf(Common, tests.IrisTest): - def test(self): - path = tests.get_data_path(('NetCDF', 'global', 'xyt', - 'SMALL_hires_wind_u_for_ipcc4.nc')) - self.pickle_cube(path) + def setUp(self): + self.path = tests.get_data_path(('NetCDF', 'global', 'xyt', + 'SMALL_hires_wind_u_for_ipcc4.nc')) @tests.skip_data class test_pp(Common, tests.IrisTest): - def test(self): - path = tests.get_data_path(('PP', 'aPPglob1', 'global.pp')) - self.pickle_cube(path) + def setUp(self): + self.path = tests.get_data_path(('PP', 'aPPglob1', 'global.pp')) @tests.skip_data class test_ff(Common, tests.IrisTest): - def test(self): - path = tests.get_data_path(('FF', 'n48_multi_field')) - self.pickle_cube(path) + def setUp(self): + self.path = tests.get_data_path(('FF', 'n48_multi_field')) if __name__ == '__main__': diff --git a/lib/iris/tests/results/experimental/regrid/regrid_area_weighted_rectilinear_src_and_grid/trasposed.cml b/lib/iris/tests/results/experimental/regrid/regrid_area_weighted_rectilinear_src_and_grid/trasposed.cml deleted file mode 100644 index 9aecbfc388..0000000000 --- a/lib/iris/tests/results/experimental/regrid/regrid_area_weighted_rectilinear_src_and_grid/trasposed.cml +++ /dev/null @@ -1,20 +0,0 @@ - - - - - - - - - - - - - - - - - - - diff --git a/lib/iris/tests/results/experimental/regrid/regrid_area_weighted_rectilinear_src_and_grid/trasposed.data.0.json b/lib/iris/tests/results/experimental/regrid/regrid_area_weighted_rectilinear_src_and_grid/trasposed.data.0.json deleted file mode 100644 index 0525283f0a..0000000000 --- a/lib/iris/tests/results/experimental/regrid/regrid_area_weighted_rectilinear_src_and_grid/trasposed.data.0.json +++ /dev/null @@ -1 +0,0 @@ -{"std": 1.0, "min": 4.499593812507495, "max": 6.499593812507495, "shape": [2], "masked": false, "mean": 5.499593812507495} \ No newline at end of file diff --git a/lib/iris/tests/results/grib_load/3_layer.cml b/lib/iris/tests/results/grib_load/3_layer.cml index 24f24ed777..76cc41a04a 100644 --- a/lib/iris/tests/results/grib_load/3_layer.cml +++ b/lib/iris/tests/results/grib_load/3_layer.cml @@ -1,6 +1,9 @@ + + + @@ -31,6 +34,9 @@ + + + @@ -82,6 +88,9 @@ + + + diff --git a/lib/iris/tests/results/grib_load/earth_shape_0.cml b/lib/iris/tests/results/grib_load/earth_shape_0.cml index 1e1e491d58..bb51db3201 100644 --- a/lib/iris/tests/results/grib_load/earth_shape_0.cml +++ b/lib/iris/tests/results/grib_load/earth_shape_0.cml @@ -1,6 +1,9 @@ + + + diff --git a/lib/iris/tests/results/grib_load/earth_shape_1.cml b/lib/iris/tests/results/grib_load/earth_shape_1.cml index dd409ebb20..774e9921b5 100644 --- a/lib/iris/tests/results/grib_load/earth_shape_1.cml +++ b/lib/iris/tests/results/grib_load/earth_shape_1.cml @@ -1,6 +1,9 @@ + + + diff --git a/lib/iris/tests/results/grib_load/earth_shape_2.cml b/lib/iris/tests/results/grib_load/earth_shape_2.cml index 0e3a4a14ea..3ff9ccccb5 100644 --- a/lib/iris/tests/results/grib_load/earth_shape_2.cml +++ b/lib/iris/tests/results/grib_load/earth_shape_2.cml @@ -1,6 +1,9 @@ + + + diff --git a/lib/iris/tests/results/grib_load/earth_shape_3.cml b/lib/iris/tests/results/grib_load/earth_shape_3.cml index 0213c4a4a0..47d11467ee 100644 --- a/lib/iris/tests/results/grib_load/earth_shape_3.cml +++ b/lib/iris/tests/results/grib_load/earth_shape_3.cml @@ -1,6 +1,9 @@ + + + diff --git a/lib/iris/tests/results/grib_load/earth_shape_4.cml b/lib/iris/tests/results/grib_load/earth_shape_4.cml index 2573e867d1..e6aa14e45a 100644 --- a/lib/iris/tests/results/grib_load/earth_shape_4.cml +++ b/lib/iris/tests/results/grib_load/earth_shape_4.cml @@ -1,6 +1,9 @@ + + + diff --git a/lib/iris/tests/results/grib_load/earth_shape_5.cml b/lib/iris/tests/results/grib_load/earth_shape_5.cml index 56462c684b..1257c9c2ad 100644 --- a/lib/iris/tests/results/grib_load/earth_shape_5.cml +++ b/lib/iris/tests/results/grib_load/earth_shape_5.cml @@ -1,6 +1,9 @@ + + + diff --git a/lib/iris/tests/results/grib_load/earth_shape_6.cml b/lib/iris/tests/results/grib_load/earth_shape_6.cml index 1ad54d1f77..eb96657104 100644 --- a/lib/iris/tests/results/grib_load/earth_shape_6.cml +++ b/lib/iris/tests/results/grib_load/earth_shape_6.cml @@ -1,6 +1,9 @@ + + + diff --git a/lib/iris/tests/results/grib_load/earth_shape_7.cml b/lib/iris/tests/results/grib_load/earth_shape_7.cml index cea76b2739..d27ce04a4c 100644 --- a/lib/iris/tests/results/grib_load/earth_shape_7.cml +++ b/lib/iris/tests/results/grib_load/earth_shape_7.cml @@ -1,6 +1,9 @@ + + + diff --git a/lib/iris/tests/results/grib_load/ineg_jneg.cml b/lib/iris/tests/results/grib_load/ineg_jneg.cml index 344fbbacf2..a7d7741092 100644 --- a/lib/iris/tests/results/grib_load/ineg_jneg.cml +++ b/lib/iris/tests/results/grib_load/ineg_jneg.cml @@ -1,6 +1,9 @@ + + + diff --git a/lib/iris/tests/results/grib_load/ineg_jpos.cml b/lib/iris/tests/results/grib_load/ineg_jpos.cml index 14967e6a88..f578fceadb 100644 --- a/lib/iris/tests/results/grib_load/ineg_jpos.cml +++ b/lib/iris/tests/results/grib_load/ineg_jpos.cml @@ -1,6 +1,9 @@ + + + diff --git a/lib/iris/tests/results/grib_load/ipos_jneg.cml b/lib/iris/tests/results/grib_load/ipos_jneg.cml index 1e1e491d58..bb51db3201 100644 --- a/lib/iris/tests/results/grib_load/ipos_jneg.cml +++ b/lib/iris/tests/results/grib_load/ipos_jneg.cml @@ -1,6 +1,9 @@ + + + diff --git a/lib/iris/tests/results/grib_load/ipos_jpos.cml b/lib/iris/tests/results/grib_load/ipos_jpos.cml index 373d8fc475..4dc6d7f980 100644 --- a/lib/iris/tests/results/grib_load/ipos_jpos.cml +++ b/lib/iris/tests/results/grib_load/ipos_jpos.cml @@ -1,6 +1,9 @@ + + + diff --git a/lib/iris/tests/results/grib_load/lambert_grib2.cml b/lib/iris/tests/results/grib_load/lambert_grib2.cml index e8b3f1c4c6..dc938f0aca 100644 --- a/lib/iris/tests/results/grib_load/lambert_grib2.cml +++ b/lib/iris/tests/results/grib_load/lambert_grib2.cml @@ -1,6 +1,9 @@ + + + diff --git a/lib/iris/tests/results/grib_load/missing_values_grib2.cml b/lib/iris/tests/results/grib_load/missing_values_grib2.cml index b090d56a92..c4c0d81915 100644 --- a/lib/iris/tests/results/grib_load/missing_values_grib2.cml +++ b/lib/iris/tests/results/grib_load/missing_values_grib2.cml @@ -1,6 +1,9 @@ + + + diff --git a/lib/iris/tests/results/grib_load/reduced_gg_grib2.cml b/lib/iris/tests/results/grib_load/reduced_gg_grib2.cml index f34938ce3f..fa3ba45e3d 100644 --- a/lib/iris/tests/results/grib_load/reduced_gg_grib2.cml +++ b/lib/iris/tests/results/grib_load/reduced_gg_grib2.cml @@ -2,6 +2,7 @@ + diff --git a/lib/iris/tests/results/grib_load/regular_gg_grib2.cml b/lib/iris/tests/results/grib_load/regular_gg_grib2.cml index 20230aee0f..14213c1602 100644 --- a/lib/iris/tests/results/grib_load/regular_gg_grib2.cml +++ b/lib/iris/tests/results/grib_load/regular_gg_grib2.cml @@ -1,6 +1,9 @@ + + + diff --git a/lib/iris/tests/results/grib_load/time_bound_grib2.cml b/lib/iris/tests/results/grib_load/time_bound_grib2.cml index 1e1e491d58..bb51db3201 100644 --- a/lib/iris/tests/results/grib_load/time_bound_grib2.cml +++ b/lib/iris/tests/results/grib_load/time_bound_grib2.cml @@ -1,6 +1,9 @@ + + + diff --git a/lib/iris/tests/results/imagerepo.json b/lib/iris/tests/results/imagerepo.json index 3a5f0ab17d..e22b147de6 100644 --- a/lib/iris/tests/results/imagerepo.json +++ b/lib/iris/tests/results/imagerepo.json @@ -5,12 +5,14 @@ ], "example_tests.test_COP_maps.TestCOPMaps.test_cop_maps.0": [ 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"https://scitools.github.io/test-iris-imagehash/images/v4/cee8953a7a15856978579696d03d672cc49a6e5a842d3d2cc0b66bd1c2ea39f1.png", - "https://scitools.github.io/test-iris-imagehash/images/v4/aee1f93a63168569b852d697913d632485ca2e43952d3bbcc2b66bd1426b3c71.png" + "https://scitools.github.io/test-iris-imagehash/images/v4/aee1f93a63168569b852d697913d632485ca2e43952d3bbcc2b66bd1426b3c71.png", + "https://scitools.github.io/test-iris-imagehash/images/v4/aee1793a6b168569b852d697913c622cc5ca2e4b952d3bb4c2b66bd1426b3c71.png" ], "iris.tests.test_plot.TestPlotCoordinatesGiven.test_zx.4": [ "https://scitools.github.io/test-iris-imagehash/images/v4/ee953f0591ea3f07914a95fa7e07d1fa68156a15d07c6a3dd038c0fef000d0fa.png", @@ -794,7 +814,8 @@ "https://scitools.github.io/test-iris-imagehash/images/v4/a3ffd5ae7f51efb6200378d7d4082c17d7280906d6e58962db31d800da6cdd26.png", "https://scitools.github.io/test-iris-imagehash/images/v4/a3ffd4ae7f55efbe200178d7d4082c17d7280906d6e58962df319800da6cdd26.png", "https://scitools.github.io/test-iris-imagehash/images/v4/a3ffd4827f51ef94200078d7c4082c57d739095ed6ed8962db759808da6cdd26.png", - "https://scitools.github.io/test-iris-imagehash/images/v4/82fd958a7e006f9ba0077bc5c9462c759873dd3c8d8f826699a187b358c82f67.png" + "https://scitools.github.io/test-iris-imagehash/images/v4/82fd958a7e006f9ba0077bc5c9462c759873dd3c8d8f826699a187b358c82f67.png", + "https://scitools.github.io/test-iris-imagehash/images/v4/82fe958b7e046f89a0033bd4d9632c74d8799d3e8d8d826789e487b348dc2f69.png" ], "iris.tests.test_plot.TestQuickplotPlot.test_x.0": [ "https://scitools.github.io/test-iris-imagehash/images/v4/83ffb5097e84c54a621799d8601d9966d213cd67c039d876d078d866d869d8f7.png", @@ -831,7 +852,8 @@ "iris.tests.test_quickplot.TestLabels.test_contour.0": [ "https://scitools.github.io/test-iris-imagehash/images/v4/a3fd956a7a01a5ee321fc96666919b6ec15fdca593600d2586785a259dfa5a01.png", "https://scitools.github.io/test-iris-imagehash/images/v4/a3fd956a7a01a5ee3217c9e66691996ec15fdca593680d2586785a259dfa5a01.png", - "https://scitools.github.io/test-iris-imagehash/images/v4/a7fd95da7a01654a3217c962e4819a56c96f3c8593624da584da3b658db662db.png" + "https://scitools.github.io/test-iris-imagehash/images/v4/a7fd95da7a01654a3217c962e4819a56c96f3c8593624da584da3b658db662db.png", + "https://scitools.github.io/test-iris-imagehash/images/v4/a7fd955a7a016d1a3217c962e4819a56c96f3c859b624d2584de3a6999b662db.png" ], "iris.tests.test_quickplot.TestLabels.test_contour.1": [ "https://scitools.github.io/test-iris-imagehash/images/v4/faa12bc1954ef43fc0bf9f02854a4ee48548c17a5ab5c17e7a0d7875a17e3a81.png", @@ -855,11 +877,13 @@ ], "iris.tests.test_quickplot.TestLabels.test_map.0": [ "https://scitools.github.io/test-iris-imagehash/images/v4/ea5e618434ac36e5c1c9369b95b39c38c3a39a4fcee19a6e9b64cb609925cd25.png", - 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"iris.tests.test_quickplot.TestQuickplotCoordinatesGiven.test_x.0": [ "https://scitools.github.io/test-iris-imagehash/images/v4/a6ffb5097e84cde2224598d1649f8d6cd2388c76d0799867d009da76c9f8d866.png", "https://scitools.github.io/test-iris-imagehash/images/v4/a6bfb5097f84cde2224599d1649f8d6cd2388c76d0799867d009da76c1f8d866.png", - "https://scitools.github.io/test-iris-imagehash/images/v4/a6fbb50cfbd0c036203598dce4c88d26d32f8cf3886e1df3dc047b4289ec6e72.png" + "https://scitools.github.io/test-iris-imagehash/images/v4/a6fbb50cfbd0c036203598dce4c88d26d32f8cf3886e1df3dc047b4289ec6e72.png", + "https://scitools.github.io/test-iris-imagehash/images/v4/a6fb958dfb50c03e203598dca4c9cd26933f9cb3886e1df1dc047b4289ec2e72.png" ], "iris.tests.test_quickplot.TestQuickplotCoordinatesGiven.test_y.0": [ "https://scitools.github.io/test-iris-imagehash/images/v4/a7ff978b7f00c9c830d7992166179e969509d866c478d964d079c876d869da26.png", @@ -923,11 +950,13 @@ "iris.tests.test_quickplot.TestQuickplotCoordinatesGiven.test_yx.2": [ "https://scitools.github.io/test-iris-imagehash/images/v4/afffe6d67700958636179d92e019992dd039daf5817d987a807a48e499684a6d.png", "https://scitools.github.io/test-iris-imagehash/images/v4/aeffe6d67780958636179d92e019892dd139daf5815d987a807a48e699684a6d.png", - "https://scitools.github.io/test-iris-imagehash/images/v4/eaff6ad4f74ab16490109c9b942999add1b74bb785a41d4acd526a254acc6365.png" + "https://scitools.github.io/test-iris-imagehash/images/v4/eaff6ad4f74ab16490109c9b942999add1b74bb785a41d4acd526a254acc6365.png", + "https://scitools.github.io/test-iris-imagehash/images/v4/aaffead4f7cab16490109c9b946d99add1b34bb385a41c4acd526a254acc6365.png" ], "iris.tests.test_quickplot.TestQuickplotCoordinatesGiven.test_yx.3": [ "https://scitools.github.io/test-iris-imagehash/images/v4/ea5e618434ac36e5c1c9369b95b39c38c3a39a4fcee19a6e9b64cb609925cd25.png", - "https://scitools.github.io/test-iris-imagehash/images/v4/e85a636c86a597a593c9b49b94b79969c396c95bccc69a64db30d9b039a52c26.png" + "https://scitools.github.io/test-iris-imagehash/images/v4/e85a636c86a597a593c9b49b94b79969c396c95bccc69a64db30d9b039a52c26.png", + "https://scitools.github.io/test-iris-imagehash/images/v4/e85a636c86a597a791c9349b94b79969c396c95bccc69a64db38c9b039a58ca6.png" ], "iris.tests.test_quickplot.TestQuickplotCoordinatesGiven.test_yx.4": [ "https://scitools.github.io/test-iris-imagehash/images/v4/ad2f6d2fd2d09295c2d1c3d33c1bc2d67d2c696ce0653c3ac2b1d976da05c2c4.png", @@ -952,12 +981,14 @@ "https://scitools.github.io/test-iris-imagehash/images/v4/87ed2f867f008d8220179852f01fd9bed1789a6c847cc877c46ac972987ec8fd.png", "https://scitools.github.io/test-iris-imagehash/images/v4/87ed2f067f008d8220179852f01fd9bed1789a6c847cc877c468c9f6987ec8fd.png", "https://scitools.github.io/test-iris-imagehash/images/v4/87ed2f067f008d8220179c52f01fd9bed1789a6c847cc877c560c976987ec8fd.png", - "https://scitools.github.io/test-iris-imagehash/images/v4/a3eded05fe11a492b000985af07fdbb4d1e3366d8c644da79fa68993180f6ec1.png" + "https://scitools.github.io/test-iris-imagehash/images/v4/a3eded05fe11a492b000985af07fdbb4d1e3366d8c644da79fa68993180f6ec1.png", + "https://scitools.github.io/test-iris-imagehash/images/v4/a3eded04ff11a492b000985af07fdbb4d1eb366d8c644da79fa68993180f6e81.png" ], "iris.tests.test_quickplot.TestQuickplotCoordinatesGiven.test_zx.3": [ "https://scitools.github.io/test-iris-imagehash/images/v4/a2f9b5ba7600a56962df9e96f01dc926c498cc46847f9d6cd0244bf19a6b19f1.png", "https://scitools.github.io/test-iris-imagehash/images/v4/a2f9b5ba7600856962df9e96f01dcd26c498cc46847f9d6cd0244bf19a6b1975.png", - "https://scitools.github.io/test-iris-imagehash/images/v4/aef9f93a770085e9205fd696d13c4b2485ca1a43952f1934daa66bd1ca6b3c71.png" + "https://scitools.github.io/test-iris-imagehash/images/v4/aef9f93a770085e9205fd696d13c4b2485ca1a43952f1934daa66bd1ca6b3c71.png", + "https://scitools.github.io/test-iris-imagehash/images/v4/aef9793a770085e9205fd696d03ccb2485ca1e43952f1934daa66bd1ca6b3c71.png" ], "iris.tests.test_quickplot.TestQuickplotCoordinatesGiven.test_zx.4": [ "https://scitools.github.io/test-iris-imagehash/images/v4/ae953f87d5e82d86801f91ee6e1591fe7e117876c07d6877d068d878d800d07a.png", diff --git a/lib/iris/tests/results/integration/grib2/TestDRT3/grid_complex_spatial_differencing.cml b/lib/iris/tests/results/integration/grib2/TestDRT3/grid_complex_spatial_differencing.cml index b15c6a4308..2cfe06f8f6 100644 --- a/lib/iris/tests/results/integration/grib2/TestDRT3/grid_complex_spatial_differencing.cml +++ b/lib/iris/tests/results/integration/grib2/TestDRT3/grid_complex_spatial_differencing.cml @@ -1,6 +1,9 @@ + + + diff --git a/lib/iris/tests/results/integration/grib2/TestGDT30/lambert.cml b/lib/iris/tests/results/integration/grib2/TestGDT30/lambert.cml index a33d0b04ba..215a0de88d 100644 --- a/lib/iris/tests/results/integration/grib2/TestGDT30/lambert.cml +++ b/lib/iris/tests/results/integration/grib2/TestGDT30/lambert.cml @@ -1,6 +1,9 @@ + + + diff --git a/lib/iris/tests/results/integration/grib2/TestGDT40/reduced.cml b/lib/iris/tests/results/integration/grib2/TestGDT40/reduced.cml index f2ca666998..3a963b3203 100644 --- a/lib/iris/tests/results/integration/grib2/TestGDT40/reduced.cml +++ b/lib/iris/tests/results/integration/grib2/TestGDT40/reduced.cml @@ -2,6 +2,7 @@ + diff --git a/lib/iris/tests/results/integration/grib2/TestGDT40/regular.cml b/lib/iris/tests/results/integration/grib2/TestGDT40/regular.cml index fb6445b8b1..e5eea0fc7c 100644 --- a/lib/iris/tests/results/integration/grib2/TestGDT40/regular.cml +++ b/lib/iris/tests/results/integration/grib2/TestGDT40/regular.cml @@ -1,6 +1,9 @@ + + + diff --git a/lib/iris/tests/results/integration/grib2/TestImport/gdt1.cml b/lib/iris/tests/results/integration/grib2/TestImport/gdt1.cml index d3cc6b4732..d304d8a843 100644 --- a/lib/iris/tests/results/integration/grib2/TestImport/gdt1.cml +++ b/lib/iris/tests/results/integration/grib2/TestImport/gdt1.cml @@ -1,6 +1,9 @@ + + + diff --git a/lib/iris/tests/results/integration/grib2/TestImport/gdt90_with_bitmap.cml b/lib/iris/tests/results/integration/grib2/TestImport/gdt90_with_bitmap.cml index 9f950b5e1f..3118f86823 100644 --- a/lib/iris/tests/results/integration/grib2/TestImport/gdt90_with_bitmap.cml +++ b/lib/iris/tests/results/integration/grib2/TestImport/gdt90_with_bitmap.cml @@ -1,6 +1,9 @@ + + + diff --git a/lib/iris/tests/results/integration/name_grib/NAMEII/0_TRACER_AIR_CONCENTRATION.cml b/lib/iris/tests/results/integration/name_grib/NAMEII/0_TRACER_AIR_CONCENTRATION.cml index 4d0fddbba5..b0daf50907 100644 --- a/lib/iris/tests/results/integration/name_grib/NAMEII/0_TRACER_AIR_CONCENTRATION.cml +++ b/lib/iris/tests/results/integration/name_grib/NAMEII/0_TRACER_AIR_CONCENTRATION.cml @@ -1,6 +1,9 @@ + + + diff --git a/lib/iris/tests/results/integration/name_grib/NAMEII/1_TRACER_DOSAGE.cml b/lib/iris/tests/results/integration/name_grib/NAMEII/1_TRACER_DOSAGE.cml index fd61a67eb6..aef4988ce6 100644 --- a/lib/iris/tests/results/integration/name_grib/NAMEII/1_TRACER_DOSAGE.cml +++ b/lib/iris/tests/results/integration/name_grib/NAMEII/1_TRACER_DOSAGE.cml @@ -1,6 +1,9 @@ + + + diff --git a/lib/iris/tests/results/integration/name_grib/NAMEII/2_TRACER_WET_DEPOSITION.cml b/lib/iris/tests/results/integration/name_grib/NAMEII/2_TRACER_WET_DEPOSITION.cml deleted file mode 100644 index 029aa022ea..0000000000 --- a/lib/iris/tests/results/integration/name_grib/NAMEII/2_TRACER_WET_DEPOSITION.cml +++ /dev/null @@ -1,31 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff --git a/lib/iris/tests/results/integration/name_grib/NAMEII/3_TRACER_DRY_DEPOSITION.cml b/lib/iris/tests/results/integration/name_grib/NAMEII/3_TRACER_DRY_DEPOSITION.cml index 429d9db2ff..5787c19643 100644 --- a/lib/iris/tests/results/integration/name_grib/NAMEII/3_TRACER_DRY_DEPOSITION.cml +++ b/lib/iris/tests/results/integration/name_grib/NAMEII/3_TRACER_DRY_DEPOSITION.cml @@ -1,6 +1,9 @@ + + + diff --git a/lib/iris/tests/results/integration/name_grib/NAMEII/4_TRACER_TOTAL_DEPOSITION.cml b/lib/iris/tests/results/integration/name_grib/NAMEII/4_TRACER_TOTAL_DEPOSITION.cml index 429d9db2ff..5787c19643 100644 --- a/lib/iris/tests/results/integration/name_grib/NAMEII/4_TRACER_TOTAL_DEPOSITION.cml +++ b/lib/iris/tests/results/integration/name_grib/NAMEII/4_TRACER_TOTAL_DEPOSITION.cml @@ -1,6 +1,9 @@ + + + diff --git a/lib/iris/tests/results/integration/name_grib/NAMEIII/0_TRACER_AIR_CONCENTRATION.cml b/lib/iris/tests/results/integration/name_grib/NAMEIII/0_TRACER_AIR_CONCENTRATION.cml index 8412a4f814..1a31427de0 100644 --- a/lib/iris/tests/results/integration/name_grib/NAMEIII/0_TRACER_AIR_CONCENTRATION.cml +++ b/lib/iris/tests/results/integration/name_grib/NAMEIII/0_TRACER_AIR_CONCENTRATION.cml @@ -1,6 +1,9 @@ + + + diff --git a/lib/iris/tests/results/integration/name_grib/NAMEIII/1_TRACER_AIR_CONCENTRATION.cml b/lib/iris/tests/results/integration/name_grib/NAMEIII/1_TRACER_AIR_CONCENTRATION.cml index 590e8ef463..7007836e62 100644 --- a/lib/iris/tests/results/integration/name_grib/NAMEIII/1_TRACER_AIR_CONCENTRATION.cml +++ b/lib/iris/tests/results/integration/name_grib/NAMEIII/1_TRACER_AIR_CONCENTRATION.cml @@ -1,6 +1,9 @@ + + + diff --git a/lib/iris/tests/results/integration/name_grib/NAMEIII/2_TRACER_DRY_DEPOSITION.cml b/lib/iris/tests/results/integration/name_grib/NAMEIII/2_TRACER_DRY_DEPOSITION.cml index d3edb03a56..850ef89ed2 100644 --- a/lib/iris/tests/results/integration/name_grib/NAMEIII/2_TRACER_DRY_DEPOSITION.cml +++ b/lib/iris/tests/results/integration/name_grib/NAMEIII/2_TRACER_DRY_DEPOSITION.cml @@ -1,6 +1,9 @@ + + + diff --git a/lib/iris/tests/results/integration/name_grib/NAMEIII/3_TRACER_WET_DEPOSITION.cml b/lib/iris/tests/results/integration/name_grib/NAMEIII/3_TRACER_WET_DEPOSITION.cml index 3e8d62ef3d..ade4cea92d 100644 --- a/lib/iris/tests/results/integration/name_grib/NAMEIII/3_TRACER_WET_DEPOSITION.cml +++ b/lib/iris/tests/results/integration/name_grib/NAMEIII/3_TRACER_WET_DEPOSITION.cml @@ -1,6 +1,9 @@ + + + diff --git a/lib/iris/tests/results/integration/name_grib/NAMEIII/4_TRACER_DEPOSITION.cml b/lib/iris/tests/results/integration/name_grib/NAMEIII/4_TRACER_DEPOSITION.cml index 586aaa6b56..088b622c46 100644 --- a/lib/iris/tests/results/integration/name_grib/NAMEIII/4_TRACER_DEPOSITION.cml +++ b/lib/iris/tests/results/integration/name_grib/NAMEIII/4_TRACER_DEPOSITION.cml @@ -1,6 +1,9 @@ + + + diff --git a/lib/iris/tests/results/system/supported_filetype_.grib2.cml b/lib/iris/tests/results/system/supported_filetype_.grib2.cml index c230684fbd..f334b13863 100644 --- a/lib/iris/tests/results/system/supported_filetype_.grib2.cml +++ b/lib/iris/tests/results/system/supported_filetype_.grib2.cml @@ -1,6 +1,9 @@ + + + diff --git a/lib/iris/tests/results/uri_callback/grib_global.cml b/lib/iris/tests/results/uri_callback/grib_global.cml index a7a23e7235..aef0310a96 100644 --- a/lib/iris/tests/results/uri_callback/grib_global.cml +++ b/lib/iris/tests/results/uri_callback/grib_global.cml @@ -1,6 +1,9 @@ + + + diff --git a/lib/iris/tests/runner/_runner.py b/lib/iris/tests/runner/_runner.py index 340923f370..ac5749a65b 100644 --- a/lib/iris/tests/runner/_runner.py +++ b/lib/iris/tests/runner/_runner.py @@ -1,4 +1,4 @@ -# (C) British Crown Copyright 2010 - 2017, Met Office +# (C) British Crown Copyright 2010 - 2020, Met Office # # This file is part of Iris. # @@ -29,41 +29,6 @@ import sys -def failed_images_html(): - """ - Generates HTML which shows the image failures side-by-side - when viewed in a web browser. - """ - from iris.tests.idiff import step_over_diffs - - data_uri_template = '{alt}' - - def image_as_base64(fname): - with open(fname, "rb") as fh: - return fh.read().encode("base64").replace("\n", "") - - html = ['', '', ''] - rdir = os.path.join(os.path.dirname(__file__), os.path.pardir, - 'result_image_comparison') - if not os.access(rdir, os.W_OK): - rdir = os.path.join(os.getcwd(), 'iris_image_test_output') - - for expected, actual, diff in step_over_diffs(rdir, 'similar', False): - expected_html = data_uri_template.format( - alt='expected', img=image_as_base64(expected)) - actual_html = data_uri_template.format( - alt='actual', img=image_as_base64(actual)) - diff_html = data_uri_template.format( - alt='diff', img=image_as_base64(diff)) - - html.extend([expected, '
    ', - expected_html, actual_html, diff_html, - '

    ']) - - html.extend(['', '']) - return '\n'.join(html) - - # NOTE: Do not inherit from object as distutils does not like it. class TestRunner(): """Run the Iris tests under nose and multiprocessor for performance""" @@ -84,12 +49,9 @@ class TestRunner(): ('num-processors=', 'p', 'The number of processors used for running ' 'the tests.'), ('create-missing', 'm', 'Create missing test result files.'), - ('print-failed-images', 'f', 'Print HTML encoded version of failed ' - 'images.'), ] boolean_options = ['no-data', 'system-tests', 'stop', 'example-tests', - 'default-tests', 'coding-tests', 'create-missing', - 'print-failed-images'] + 'default-tests', 'coding-tests', 'create-missing'] def initialize_options(self): self.no_data = False @@ -100,7 +62,6 @@ def initialize_options(self): self.coding_tests = False self.num_processors = None self.create_missing = False - self.print_failed_images = False def finalize_options(self): # These enviroment variables will be propagated to all the @@ -185,6 +146,4 @@ def run(self): # word Mixin. result &= nose.run(argv=args) if result is False: - if self.print_failed_images: - print(failed_images_html()) exit(1) diff --git a/lib/iris/tests/test_analysis.py b/lib/iris/tests/test_analysis.py index e07848a3d8..56f5737862 100644 --- a/lib/iris/tests/test_analysis.py +++ b/lib/iris/tests/test_analysis.py @@ -1,4 +1,4 @@ -# (C) British Crown Copyright 2010 - 2018, Met Office +# (C) British Crown Copyright 2010 - 2020, Met Office # # This file is part of Iris. # @@ -411,10 +411,12 @@ class TestAggregators(tests.IrisTest): def _check_collapsed_percentile(self, cube, percents, collapse_coord, expected_result, CML_filename=None, **kwargs): + cube_data_type = type(cube.data) expected_result = np.array(expected_result, dtype=np.float32) result = cube.collapsed(collapse_coord, iris.analysis.PERCENTILE, percent=percents, **kwargs) np.testing.assert_array_almost_equal(result.data, expected_result) + self.assertEqual(type(result.data), cube_data_type) if CML_filename is not None: self.assertCML(result, ('analysis', CML_filename), checksum=False) @@ -422,6 +424,7 @@ def _check_percentile(self, data, axis, percents, expected_result, **kwargs): result = iris.analysis._percentile(data, axis, percents, **kwargs) np.testing.assert_array_almost_equal(result, expected_result) + self.assertEqual(type(result), type(expected_result)) def test_percentile_1d_25_percent(self): cube = tests.stock.simple_1d() @@ -445,6 +448,13 @@ def test_fast_percentile_1d_75_percent(self): cube, 75, 'foo', 7.5, fast_percentile_method=True, CML_filename='third_quartile_foo_1d_fast_percentile.cml') + def test_fast_percentile_1d_75_percent_masked_type_no_mask(self): + cube = tests.stock.simple_1d() + cube.data = ma.MaskedArray(cube.data) + self._check_collapsed_percentile( + cube, 75, 'foo', 7.5, fast_percentile_method=True, + CML_filename='third_quartile_foo_1d_fast_percentile.cml') + def test_percentile_2d_single_coord(self): cube = tests.stock.simple_2d() self._check_collapsed_percentile( @@ -469,6 +479,20 @@ def test_fast_percentile_2d_two_coords(self): cube, 25, ['foo', 'bar'], [2.75], fast_percentile_method=True, CML_filename='first_quartile_foo_bar_2d_fast_percentile.cml') + def test_fast_percentile_2d_single_coord_masked_type_no_mask(self): + cube = tests.stock.simple_2d() + cube.data = ma.MaskedArray(cube.data) + self._check_collapsed_percentile( + cube, 25, 'foo', [0.75, 4.75, 8.75], fast_percentile_method=True, + CML_filename='first_quartile_foo_2d_fast_percentile.cml') + + def test_fast_percentile_2d_two_coords_masked_type_no_mask(self): + cube = tests.stock.simple_2d() + cube.data = ma.MaskedArray(cube.data) + self._check_collapsed_percentile( + cube, 25, ['foo', 'bar'], [2.75], fast_percentile_method=True, + CML_filename='first_quartile_foo_bar_2d_fast_percentile.cml') + def test_percentile_3d(self): array_3d = np.arange(24, dtype=np.int32).reshape((2, 3, 4)) expected_result = np.array([[6., 7., 8., 9.], @@ -503,6 +527,16 @@ def test_fast_percentile_3d_axis_one(self): self._check_percentile(array_3d, 1, 50, expected_result, fast_percentile_method=True) + def test_fast_percentile_3d_axis_one_masked_type_no_mask(self): + array_3d = np.arange(24, dtype=np.int32).reshape((2, 3, 4)) + array_3d = np.ma.MaskedArray(array_3d) + expected_result = ma.MaskedArray([[4., 5., 6., 7.], + [16., 17., 18., 19.]], + dtype=np.float32) + + self._check_percentile(array_3d, 1, 50, expected_result, + fast_percentile_method=True) + def test_percentile_3d_axis_two(self): array_3d = np.arange(24, dtype=np.int32).reshape((2, 3, 4)) expected_result = np.array([[1.5, 5.5, 9.5], @@ -520,6 +554,16 @@ def test_fast_percentile_3d_axis_two(self): self._check_percentile(array_3d, 2, 50, expected_result, fast_percentile_method=True) + def test_fast_percentile_3d_axis_two_masked_type_no_mask(self): + array_3d = np.arange(24, dtype=np.int32).reshape((2, 3, 4)) + array_3d = ma.MaskedArray(array_3d) + expected_result = ma.MaskedArray([[1.5, 5.5, 9.5], + [13.5, 17.5, 21.5]], + dtype=np.float32) + + self._check_percentile(array_3d, 2, 50, expected_result, + fast_percentile_method=True) + def test_percentile_3d_masked(self): cube = tests.stock.simple_3d_mask() expected_result = [[12., 13., 14., 15.], @@ -530,7 +574,7 @@ def test_percentile_3d_masked(self): cube, 75, 'wibble', expected_result, CML_filename='last_quartile_foo_3d_masked.cml') - def test_fast_percentile_3d_masked(self): + def test_fast_percentile_3d_masked_type_masked(self): cube = tests.stock.simple_3d_mask() msg = 'Cannot use fast np.percentile method with masked array.' diff --git a/lib/iris/tests/test_constraints.py b/lib/iris/tests/test_constraints.py index fd74bf8e53..deb3c86622 100644 --- a/lib/iris/tests/test_constraints.py +++ b/lib/iris/tests/test_constraints.py @@ -1,4 +1,4 @@ -# (C) British Crown Copyright 2010 - 2017, Met Office +# (C) British Crown Copyright 2010 - 2020, Met Office # # This file is part of Iris. # @@ -29,6 +29,7 @@ import datetime import iris +from iris import AttributeConstraint, NameConstraint import iris.tests.stock as stock @@ -282,6 +283,289 @@ def load_match(self, files, constraints): return cubes +@tests.skip_data +class TestCubeExtract__names(TestMixin, tests.IrisTest): + def setUp(self): + fname = iris.sample_data_path("atlantic_profiles.nc") + self.cubes = iris.load(fname) + TestMixin.setUp(self) + cube = iris.load_cube(self.theta_path) + # Expected names... + self.standard_name = "air_potential_temperature" + self.long_name = "AIR POTENTIAL TEMPERATURE" + self.var_name = "apt" + self.stash = "m01s00i004" + # Configure missing names... + cube.long_name = self.long_name + cube.var_name = self.var_name + # Add this cube to the mix... + self.cubes.append(cube) + self.index = len(self.cubes) - 1 + + def test_standard_name(self): + constraint = iris.Constraint(self.standard_name) + result = self.cubes.extract(constraint, strict=True) + self.assertIsNotNone(result) + self.assertEqual(result.standard_name, self.standard_name) + + def test_long_name(self): + constraint = iris.Constraint(self.long_name) + result = self.cubes.extract(constraint, strict=True) + self.assertIsNotNone(result) + self.assertEqual(result.long_name, self.long_name) + + def test_var_name(self): + constraint = iris.Constraint(self.var_name) + result = self.cubes.extract(constraint, strict=True) + self.assertIsNotNone(result) + self.assertEqual(result.var_name, self.var_name) + + def test_stash(self): + constraint = iris.Constraint(self.stash) + result = self.cubes.extract(constraint, strict=True) + self.assertIsNotNone(result) + self.assertEqual(str(result.attributes["STASH"]), self.stash) + + def test_unknown(self): + cube = self.cubes[self.index] + # Clear the cube metadata. + cube.standard_name = None + cube.long_name = None + cube.var_name = None + cube.attributes = None + # Extract the unknown cube. + constraint = iris.Constraint("unknown") + result = self.cubes.extract(constraint, strict=True) + self.assertIsNotNone(result) + self.assertEqual(result.name(), "unknown") + + +@tests.skip_data +class TestCubeExtract__name_constraint(TestMixin, tests.IrisTest): + def setUp(self): + fname = iris.sample_data_path("atlantic_profiles.nc") + self.cubes = iris.load(fname) + TestMixin.setUp(self) + cube = iris.load_cube(self.theta_path) + # Expected names... + self.standard_name = "air_potential_temperature" + self.long_name = "air potential temperature" + self.var_name = "apt" + self.stash = "m01s00i004" + # Configure missing names... + cube.long_name = self.long_name + cube.var_name = self.var_name + # Add this cube to the mix... + self.cubes.append(cube) + self.index = len(self.cubes) - 1 + + def test_standard_name(self): + # No match. + constraint = NameConstraint(standard_name="wibble") + result = self.cubes.extract(constraint) + self.assertFalse(result) + + # Match. + constraint = NameConstraint(standard_name=self.standard_name) + result = self.cubes.extract(constraint, strict=True) + self.assertIsNotNone(result) + self.assertEqual(result.standard_name, self.standard_name) + + # Match - callable. + kwargs = dict(standard_name=lambda item: item.startswith("air_pot")) + constraint = NameConstraint(**kwargs) + result = self.cubes.extract(constraint, strict=True) + self.assertIsNotNone(result) + self.assertEqual(result.standard_name, self.standard_name) + + def test_standard_name__None(self): + cube = self.cubes[self.index] + cube.standard_name = None + constraint = NameConstraint( + standard_name=None, long_name=self.long_name + ) + result = self.cubes.extract(constraint, strict=True) + self.assertIsNotNone(result) + self.assertIsNone(result.standard_name) + self.assertEqual(result.long_name, self.long_name) + + def test_long_name(self): + # No match. + constraint = NameConstraint(long_name="wibble") + result = self.cubes.extract(constraint) + self.assertFalse(result) + + # Match. + constraint = NameConstraint(long_name=self.long_name) + result = self.cubes.extract(constraint, strict=True) + self.assertIsNotNone(result) + self.assertEqual(result.long_name, self.long_name) + + # Match - callable. + kwargs = dict( + long_name=lambda item: item is not None + and item.startswith("air pot") + ) + constraint = NameConstraint(**kwargs) + result = self.cubes.extract(constraint, strict=True) + self.assertIsNotNone(result) + self.assertEqual(result.long_name, self.long_name) + + def test_long_name__None(self): + cube = self.cubes[self.index] + cube.long_name = None + constraint = NameConstraint( + standard_name=self.standard_name, long_name=None + ) + result = self.cubes.extract(constraint, strict=True) + self.assertIsNotNone(result) + self.assertEqual(result.standard_name, self.standard_name) + self.assertIsNone(result.long_name) + + def test_var_name(self): + # No match. + constraint = NameConstraint(var_name="wibble") + result = self.cubes.extract(constraint) + self.assertFalse(result) + + # Match. + constraint = NameConstraint(var_name=self.var_name) + result = self.cubes.extract(constraint, strict=True) + self.assertIsNotNone(result) + self.assertEqual(result.var_name, self.var_name) + + # Match - callable. + kwargs = dict(var_name=lambda item: item.startswith("ap")) + constraint = NameConstraint(**kwargs) + result = self.cubes.extract(constraint, strict=True) + self.assertIsNotNone(result) + self.assertEqual(result.var_name, self.var_name) + + def test_var_name__None(self): + cube = self.cubes[self.index] + cube.var_name = None + constraint = NameConstraint( + standard_name=self.standard_name, var_name=None + ) + result = self.cubes.extract(constraint, strict=True) + self.assertIsNotNone(result) + self.assertEqual(result.standard_name, self.standard_name) + self.assertIsNone(result.var_name) + + def test_stash(self): + # No match. + constraint = NameConstraint(STASH="m01s00i444") + result = self.cubes.extract(constraint) + self.assertFalse(result) + + # Match. + constraint = NameConstraint(STASH=self.stash) + result = self.cubes.extract(constraint, strict=True) + self.assertIsNotNone(result) + self.assertEqual(str(result.attributes["STASH"]), self.stash) + + # Match - callable. + kwargs = dict(STASH=lambda stash: stash.item == 4) + constraint = NameConstraint(**kwargs) + result = self.cubes.extract(constraint, strict=True) + self.assertIsNotNone(result) + + def test_stash__None(self): + cube = self.cubes[self.index] + del cube.attributes["STASH"] + constraint = NameConstraint( + standard_name=self.standard_name, STASH=None + ) + result = self.cubes.extract(constraint, strict=True) + self.assertIsNotNone(result) + self.assertEqual(result.standard_name, self.standard_name) + self.assertIsNone(result.attributes.get("STASH")) + + def test_compound(self): + # Match. + constraint = NameConstraint( + standard_name=self.standard_name, long_name=self.long_name + ) + result = self.cubes.extract(constraint, strict=True) + self.assertIsNotNone(result) + self.assertEqual(result.standard_name, self.standard_name) + + # No match - var_name. + constraint = NameConstraint( + standard_name=self.standard_name, + long_name=self.long_name, + var_name="wibble", + ) + result = self.cubes.extract(constraint) + self.assertFalse(result) + + # Match. + constraint = NameConstraint( + standard_name=self.standard_name, + long_name=self.long_name, + var_name=self.var_name, + ) + result = self.cubes.extract(constraint, strict=True) + self.assertIsNotNone(result) + self.assertEqual(result.standard_name, self.standard_name) + self.assertEqual(result.long_name, self.long_name) + self.assertEqual(result.var_name, self.var_name) + + # No match - STASH. + constraint = NameConstraint( + standard_name=self.standard_name, + long_name=self.long_name, + var_name=self.var_name, + STASH="m01s00i444", + ) + result = self.cubes.extract(constraint) + self.assertFalse(result) + + # Match. + constraint = NameConstraint( + standard_name=self.standard_name, + long_name=self.long_name, + var_name=self.var_name, + STASH=self.stash, + ) + result = self.cubes.extract(constraint, strict=True) + self.assertIsNotNone(result) + self.assertEqual(result.standard_name, self.standard_name) + self.assertEqual(result.long_name, self.long_name) + self.assertEqual(result.var_name, self.var_name) + self.assertEqual(result.var_name, self.var_name) + + # No match - standard_name. + constraint = NameConstraint( + standard_name="wibble", + long_name=self.long_name, + var_name=self.var_name, + STASH=self.stash, + ) + result = self.cubes.extract(constraint) + self.assertFalse(result) + + def test_unknown(self): + # No match. + constraint = NameConstraint(None, None, None, None) + result = self.cubes.extract(constraint) + self.assertFalse(result) + + # Match. + cube = self.cubes[self.index] + cube.standard_name = None + cube.long_name = None + cube.var_name = None + cube.attributes = None + constraint = NameConstraint(None, None, None, None) + result = self.cubes.extract(constraint, strict=True) + self.assertIsNotNone(result) + self.assertIsNone(result.standard_name) + self.assertIsNone(result.long_name) + self.assertIsNone(result.var_name) + self.assertIsNone(result.attributes.get("STASH")) + + @tests.skip_data class TestCubeExtract(TestMixin, tests.IrisTest): def setUp(self): @@ -289,27 +573,36 @@ def setUp(self): self.cube = iris.load_cube(self.theta_path) def test_attribute_constraint(self): - # there is no my_attribute attribute on the cube, so ensure it returns None - cube = self.cube.extract(iris.AttributeConstraint(my_attribute='foobar')) + # There is no my_attribute on the cube, so ensure it returns None. + constraint = AttributeConstraint(my_attribute="foobar") + cube = self.cube.extract(constraint) self.assertIsNone(cube) orig_cube = self.cube # add an attribute to the cubes orig_cube.attributes['my_attribute'] = 'foobar' - cube = orig_cube.extract(iris.AttributeConstraint(my_attribute='foobar')) - self.assertCML(cube, ('constrained_load', 'attribute_constraint.cml')) + constraint = AttributeConstraint(my_attribute="foobar") + cube = orig_cube.extract(constraint) + self.assertCML(cube, ("constrained_load", "attribute_constraint.cml")) - cube = orig_cube.extract(iris.AttributeConstraint(my_attribute='not me')) + constraint = AttributeConstraint(my_attribute="not me") + cube = orig_cube.extract(constraint) self.assertIsNone(cube) - cube = orig_cube.extract(iris.AttributeConstraint(my_attribute=lambda val: val.startswith('foo'))) - self.assertCML(cube, ('constrained_load', 'attribute_constraint.cml')) + kwargs = dict(my_attribute=lambda val: val.startswith("foo")) + constraint = AttributeConstraint(**kwargs) + cube = orig_cube.extract(constraint) + self.assertCML(cube, ("constrained_load", "attribute_constraint.cml")) - cube = orig_cube.extract(iris.AttributeConstraint(my_attribute=lambda val: not val.startswith('foo'))) + kwargs = dict(my_attribute=lambda val: not val.startswith("foo")) + constraint = AttributeConstraint(**kwargs) + cube = orig_cube.extract(constraint) self.assertIsNone(cube) - cube = orig_cube.extract(iris.AttributeConstraint(my_non_existant_attribute='hello world')) + kwargs = dict(my_non_existant_attribute="hello world") + constraint = AttributeConstraint(**kwargs) + cube = orig_cube.extract(constraint) self.assertIsNone(cube) def test_standard_name(self): @@ -329,7 +622,7 @@ def test_empty_data(self): cube = self.cube.extract(self.level_10).extract(self.level_10) self.assertTrue(cube.has_lazy_data()) - def test_non_existant_coordinate(self): + def test_non_existent_coordinate(self): # Check the behaviour when a constraint is given for a coordinate which does not exist/span a dimension self.assertEqual(self.cube[0, :, :].extract(self.level_10), None) diff --git a/lib/iris/tests/test_grib_load_translations.py b/lib/iris/tests/test_grib_load_translations.py index dbb6bc8e1f..411ea5b352 100644 --- a/lib/iris/tests/test_grib_load_translations.py +++ b/lib/iris/tests/test_grib_load_translations.py @@ -1,4 +1,4 @@ -# (C) British Crown Copyright 2010 - 2017, Met Office +# (C) British Crown Copyright 2010 - 2020, Met Office # # This file is part of Iris. # @@ -60,7 +60,7 @@ def _mock_gribapi_fetch(message, key): if key in message: return message[key] else: - raise _mock_gribapi.GribInternalError + raise _mock_gribapi.errors.GribInternalError def _mock_gribapi__grib_is_missing(grib_message, keyname): @@ -83,13 +83,13 @@ def _mock_gribapi__grib_get_native_type(grib_message, keyname): """ if keyname in grib_message: return type(grib_message[keyname]) - raise _mock_gribapi.GribInternalError(keyname) + raise _mock_gribapi.errors.GribInternalError(keyname) if tests.GRIB_AVAILABLE: # Construct a mock object to mimic the gribapi for GribWrapper testing. _mock_gribapi = mock.Mock(spec=gribapi) - _mock_gribapi.GribInternalError = Exception + _mock_gribapi.errors.GribInternalError = Exception _mock_gribapi.grib_get_long = mock.Mock(side_effect=_mock_gribapi_fetch) _mock_gribapi.grib_get_string = mock.Mock(side_effect=_mock_gribapi_fetch) diff --git a/lib/iris/tests/test_grib_save.py b/lib/iris/tests/test_grib_save.py index 0befc8d56a..0367902290 100644 --- a/lib/iris/tests/test_grib_save.py +++ b/lib/iris/tests/test_grib_save.py @@ -1,4 +1,4 @@ -# (C) British Crown Copyright 2010 - 2017, Met Office +# (C) British Crown Copyright 2010 - 2020, Met Office # # This file is part of Iris. # @@ -56,6 +56,10 @@ def test_latlon_forecast_plev(self): 'shapeOfTheEarth': (0, 1), 'scaledValueOfRadiusOfSphericalEarth': (MDI, 6367470), + 'scaledValueOfEarthMajorAxis': (MDI, 0), + 'scaleFactorOfEarthMajorAxis': (MDI, 0), + 'scaledValueOfEarthMinorAxis': (MDI, 0), + 'scaleFactorOfEarthMinorAxis': (MDI, 0), 'typeOfGeneratingProcess': (0, 255), 'generatingProcessIdentifier': (128, 255), } @@ -76,6 +80,10 @@ def test_rotated_latlon(self): 'shapeOfTheEarth': (0, 1), 'scaledValueOfRadiusOfSphericalEarth': (MDI, 6367470), + 'scaledValueOfEarthMajorAxis': (MDI, 0), + 'scaleFactorOfEarthMajorAxis': (MDI, 0), + 'scaledValueOfEarthMinorAxis': (MDI, 0), + 'scaleFactorOfEarthMinorAxis': (MDI, 0), 'longitudeOfLastGridPoint': (392109982, 32106370), 'latitudeOfLastGridPoint': (19419996, 19419285), 'typeOfGeneratingProcess': (0, 255), @@ -97,6 +105,10 @@ def test_time_mean(self): 'shapeOfTheEarth': (0, 1), 'scaledValueOfRadiusOfSphericalEarth': (MDI, 6367470), + 'scaledValueOfEarthMajorAxis': (MDI, 0), + 'scaleFactorOfEarthMajorAxis': (MDI, 0), + 'scaledValueOfEarthMinorAxis': (MDI, 0), + 'scaleFactorOfEarthMinorAxis': (MDI, 0), 'longitudeOfLastGridPoint': (356249908, 356249809), 'latitudeOfLastGridPoint': (-89999938, -89999944), 'typeOfGeneratingProcess': (0, 255), diff --git a/lib/iris/tests/unit/analysis/area_weighted/test_AreaWeightedRegridder.py b/lib/iris/tests/unit/analysis/area_weighted/test_AreaWeightedRegridder.py index 3c28ca6134..f6d4332623 100644 --- a/lib/iris/tests/unit/analysis/area_weighted/test_AreaWeightedRegridder.py +++ b/lib/iris/tests/unit/analysis/area_weighted/test_AreaWeightedRegridder.py @@ -1,4 +1,4 @@ -# (C) British Crown Copyright 2014 - 2015, Met Office +# (C) British Crown Copyright 2014 - 2020, Met Office # # This file is part of Iris. # @@ -25,6 +25,7 @@ # Import iris.tests first so that some things can be initialised before # importing anything else. import iris.tests as tests +import iris.experimental.regrid as eregrid import numpy as np @@ -43,11 +44,13 @@ def cube(self, x, y): lon = DimCoord(x, 'longitude', units='degrees') cube.add_dim_coord(lat, 0) cube.add_dim_coord(lon, 1) + cube.coord("latitude").guess_bounds() + cube.coord("longitude").guess_bounds() return cube def grids(self): src = self.cube(np.linspace(20, 30, 3), np.linspace(10, 25, 4)) - target = self.cube(np.linspace(6, 18, 8), np.linspace(11, 22, 9)) + target = self.cube(np.linspace(22, 28, 8), np.linspace(11, 22, 9)) return src, target def extract_grid(self, cube): @@ -55,31 +58,53 @@ def extract_grid(self, cube): def check_mdtol(self, mdtol=None): src_grid, target_grid = self.grids() - if mdtol is None: - regridder = AreaWeightedRegridder(src_grid, target_grid) - mdtol = 1 - else: - regridder = AreaWeightedRegridder(src_grid, target_grid, - mdtol=mdtol) - - # Make a new cube to regrid with different data so we can - # distinguish between regridding the original src grid - # definition cube and the cube passed to the regridder. - src = src_grid.copy() - src.data += 10 - - with mock.patch('iris.experimental.regrid.' - 'regrid_area_weighted_rectilinear_src_and_grid', - return_value=mock.sentinel.result) as regrid: - result = regridder(src) - - self.assertEqual(regrid.call_count, 1) - _, args, kwargs = regrid.mock_calls[0] + # Get _regrid_info result + _regrid_info =\ + eregrid._regrid_area_weighted_rectilinear_src_and_grid__prepare( + src_grid, target_grid + ) + self.assertEqual(len(_regrid_info), 9) + with mock.patch( + "iris.experimental.regrid." + "_regrid_area_weighted_rectilinear_src_and_grid__prepare", + return_value=_regrid_info, + ) as prepare: + with mock.patch( + "iris.experimental.regrid." + "_regrid_area_weighted_rectilinear_src_and_grid__perform", + return_value=mock.sentinel.result, + ) as perform: + # Setup the regridder + if mdtol is None: + regridder = AreaWeightedRegridder(src_grid, target_grid) + mdtol = 1 + else: + regridder = AreaWeightedRegridder( + src_grid, target_grid, mdtol=mdtol + ) + # Now regrid the source cube + src = src_grid + result = regridder(src) + # Make a new cube to regrid with different data so we can + # distinguish between regridding the original src grid + # definition cube and the cube passed to the regridder. + src = src_grid.copy() + src.data += 10 + result = regridder(src) + + # Prepare: + self.assertEqual(prepare.call_count, 1) + _, args, kwargs = prepare.mock_calls[0] + self.assertEqual( + self.extract_grid(args[1]), self.extract_grid(target_grid) + ) + + # Perform: + self.assertEqual(perform.call_count, 2) + _, args, kwargs = perform.mock_calls[1] self.assertEqual(args[0], src) - self.assertEqual(self.extract_grid(args[1]), - self.extract_grid(target_grid)) - self.assertEqual(kwargs, {'mdtol': mdtol}) + self.assertEqual(kwargs, {"mdtol": mdtol}) self.assertIs(result, mock.sentinel.result) def test_default(self): @@ -111,6 +136,129 @@ def test_mismatched_src_coord_systems(self): with self.assertRaises(ValueError): AreaWeightedRegridder(src, target) + def test_src_and_target_are_the_same(self): + src = self.cube(np.linspace(20, 30, 3), np.linspace(10, 25, 4)) + target = self.cube(np.linspace(20, 30, 3), np.linspace(10, 25, 4)) + regridder = AreaWeightedRegridder(src, target) + result = regridder(src) + self.assertArrayAllClose(result.data, target.data) + + def test_multiple_src_on_same_grid(self): + coord_names = ["latitude", "longitude"] + src1 = self.cube(np.linspace(20, 32, 4), np.linspace(10, 22, 4)) + src2 = self.cube(np.linspace(20, 32, 4), np.linspace(10, 22, 4)) + src2.data *= 4 + self.assertArrayEqual(src1.data * 4, src2.data) + for name in coord_names: + # Remove coords system and units so it is no longer spherical. + src1.coord(name).coord_system = None + src1.coord(name).units = None + src2.coord(name).coord_system = None + src2.coord(name).units = None + + target = self.cube(np.linspace(20, 32, 2), np.linspace(10, 22, 2)) + # Ensure the bounds of the target cover the same range as the + # source. + target_lat_bounds = np.column_stack( + ( + src1.coord("latitude").bounds[[0, 1], [0, 1]], + src1.coord("latitude").bounds[[2, 3], [0, 1]], + ) + ) + target.coord("latitude").bounds = target_lat_bounds + target_lon_bounds = np.column_stack( + ( + src1.coord("longitude").bounds[[0, 1], [0, 1]], + src1.coord("longitude").bounds[[2, 3], [0, 1]], + ) + ) + target.coord("longitude").bounds = target_lon_bounds + for name in coord_names: + # Remove coords system and units so it is no longer spherical. + target.coord(name).coord_system = None + target.coord(name).units = None + + regridder = AreaWeightedRegridder(src1, target) + result1 = regridder(src1) + result2 = regridder(src2) + + reference1 = self.cube(np.linspace(20, 32, 2), np.linspace(10, 22, 2)) + reference1.data = np.array( + [ + [np.mean(src1.data[0:2, 0:2]), np.mean(src1.data[0:2, 2:4])], + [np.mean(src1.data[2:4, 0:2]), np.mean(src1.data[2:4, 2:4])], + ] + ) + reference1.coord("latitude").bounds = target_lat_bounds + reference1.coord("longitude").bounds = target_lon_bounds + + reference2 = self.cube(np.linspace(20, 32, 2), np.linspace(10, 22, 2)) + reference2.data = np.array( + [ + [np.mean(src2.data[0:2, 0:2]), np.mean(src2.data[0:2, 2:4])], + [np.mean(src2.data[2:4, 0:2]), np.mean(src2.data[2:4, 2:4])], + ] + ) + reference2.coord("latitude").bounds = target_lat_bounds + reference2.coord("longitude").bounds = target_lon_bounds + + for name in coord_names: + # Remove coords system and units so it is no longer spherical. + reference1.coord(name).coord_system = None + reference1.coord(name).units = None + reference2.coord(name).coord_system = None + reference2.coord(name).units = None + + # Compare the cubes rather than just the data. + self.assertEqual(result1, reference1) + self.assertEqual(result2, reference2) + + def test_src_data_different_dims(self): + src, target = self.grids() + regridder = AreaWeightedRegridder(src, target) + result = regridder(src) + expected_mean, expected_std = 4.772097735195653, 2.211698479817678 + self.assertArrayShapeStats(result, (9, 8), expected_mean, expected_std) + # New source cube with additional "levels" dimension + # Each level has identical x-y data so the mean and std stats remain + # identical when x, y and z dims are reordered + levels = DimCoord(np.arange(5), "model_level_number") + lat = src.coord("latitude") + lon = src.coord("longitude") + data = np.repeat(src.data[np.newaxis, ...], 5, axis=0) + src = Cube(data) + src.add_dim_coord(levels, 0) + src.add_dim_coord(lat, 1) + src.add_dim_coord(lon, 2) + result = regridder(src) + self.assertArrayShapeStats( + result, (5, 9, 8), expected_mean, expected_std + ) + # Check data with dims in different order + # Reshape src so that the coords are ordered [x, z, y], + # the mean and std statistics should be the same + data = np.moveaxis(src.data.copy(), 2, 0) + src = Cube(data) + src.add_dim_coord(lon, 0) + src.add_dim_coord(levels, 1) + src.add_dim_coord(lat, 2) + result = regridder(src) + self.assertArrayShapeStats( + result, (8, 5, 9), expected_mean, expected_std + ) + # Check data with dims in different order + # Reshape src so that the coords are ordered [y, x, z], + # the mean and std statistics should be the same + data = np.moveaxis(src.data.copy(), 2, 0) + src = Cube(data) + src.add_dim_coord(lat, 0) + src.add_dim_coord(lon, 1) + src.add_dim_coord(levels, 2) + result = regridder(src) + self.assertArrayShapeStats( + result, (9, 8, 5), expected_mean, expected_std + ) + if __name__ == '__main__': tests.main() diff --git a/lib/iris/tests/unit/constraints/__init__.py b/lib/iris/tests/unit/constraints/__init__.py new file mode 100644 index 0000000000..e325fde367 --- /dev/null +++ b/lib/iris/tests/unit/constraints/__init__.py @@ -0,0 +1,20 @@ +# (C) British Crown Copyright 2020, Met Office +# +# This file is part of Iris. +# +# Iris is free software: you can redistribute it and/or modify it under +# the terms of the GNU Lesser General Public License as published by the +# Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# Iris is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public License +# along with Iris. If not, see . +"""Unit tests for the :mod:`iris._constraints` module.""" + +from __future__ import (absolute_import, division, print_function) +from six.moves import (filter, input, map, range, zip) # noqa diff --git a/lib/iris/tests/unit/constraints/test_NameConstraint.py b/lib/iris/tests/unit/constraints/test_NameConstraint.py new file mode 100644 index 0000000000..9160605a2a --- /dev/null +++ b/lib/iris/tests/unit/constraints/test_NameConstraint.py @@ -0,0 +1,243 @@ +# (C) British Crown Copyright 2020, Met Office +# +# This file is part of Iris. +# +# Iris is free software: you can redistribute it and/or modify it under +# the terms of the GNU Lesser General Public License as published by the +# Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# Iris is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public License +# along with Iris. If not, see . +"""Unit tests for the `iris._constraints.NameConstraint` class.""" + +from __future__ import (absolute_import, division, print_function) +from six.moves import (filter, input, map, range, zip) # noqa + +# Import iris.tests first so that some things can be initialised before +# importing anything else. +import iris.tests as tests + +from iris.tests import mock + +from iris._constraints import NameConstraint + + +class Test___init__(tests.IrisTest): + def setUp(self): + self.default = "none" + + def test_default(self): + constraint = NameConstraint() + self.assertEqual(constraint.standard_name, self.default) + self.assertEqual(constraint.long_name, self.default) + self.assertEqual(constraint.var_name, self.default) + self.assertEqual(constraint.STASH, self.default) + + def test_standard_name(self): + standard_name = mock.sentinel.standard_name + constraint = NameConstraint(standard_name=standard_name) + self.assertEqual(constraint.standard_name, standard_name) + constraint = NameConstraint(standard_name=standard_name) + self.assertEqual(constraint.standard_name, standard_name) + + def test_long_name(self): + long_name = mock.sentinel.long_name + constraint = NameConstraint(long_name=long_name) + self.assertEqual(constraint.standard_name, self.default) + self.assertEqual(constraint.long_name, long_name) + constraint = NameConstraint(standard_name=None, long_name=long_name) + self.assertIsNone(constraint.standard_name) + self.assertEqual(constraint.long_name, long_name) + + def test_var_name(self): + var_name = mock.sentinel.var_name + constraint = NameConstraint(var_name=var_name) + self.assertEqual(constraint.standard_name, self.default) + self.assertEqual(constraint.long_name, self.default) + self.assertEqual(constraint.var_name, var_name) + constraint = NameConstraint( + standard_name=None, long_name=None, var_name=var_name + ) + self.assertIsNone(constraint.standard_name) + self.assertIsNone(constraint.long_name) + self.assertEqual(constraint.var_name, var_name) + + def test_STASH(self): + STASH = mock.sentinel.STASH + constraint = NameConstraint(STASH=STASH) + self.assertEqual(constraint.standard_name, self.default) + self.assertEqual(constraint.long_name, self.default) + self.assertEqual(constraint.var_name, self.default) + self.assertEqual(constraint.STASH, STASH) + constraint = NameConstraint( + standard_name=None, long_name=None, var_name=None, STASH=STASH + ) + self.assertIsNone(constraint.standard_name) + self.assertIsNone(constraint.long_name) + self.assertIsNone(constraint.var_name) + self.assertEqual(constraint.STASH, STASH) + + +class Test__cube_func(tests.IrisTest): + def setUp(self): + self.standard_name = mock.sentinel.standard_name + self.long_name = mock.sentinel.long_name + self.var_name = mock.sentinel.var_name + self.STASH = mock.sentinel.STASH + self.cube = mock.Mock( + standard_name=self.standard_name, + long_name=self.long_name, + var_name=self.var_name, + attributes=dict(STASH=self.STASH), + ) + + def test_standard_name(self): + # Match. + constraint = NameConstraint(standard_name=self.standard_name) + self.assertTrue(constraint._cube_func(self.cube)) + # Match. + constraint = NameConstraint(standard_name=self.standard_name) + self.assertTrue(constraint._cube_func(self.cube)) + # No match. + constraint = NameConstraint(standard_name="wibble") + self.assertFalse(constraint._cube_func(self.cube)) + # No match. + constraint = NameConstraint(standard_name="wibble") + self.assertFalse(constraint._cube_func(self.cube)) + + def test_long_name(self): + # Match. + constraint = NameConstraint(long_name=self.long_name) + self.assertTrue(constraint._cube_func(self.cube)) + # Match. + constraint = NameConstraint( + standard_name=self.standard_name, long_name=self.long_name + ) + self.assertTrue(constraint._cube_func(self.cube)) + # No match. + constraint = NameConstraint(long_name=None) + self.assertFalse(constraint._cube_func(self.cube)) + # No match. + constraint = NameConstraint( + standard_name=None, long_name=self.long_name + ) + self.assertFalse(constraint._cube_func(self.cube)) + + def test_var_name(self): + # Match. + constraint = NameConstraint(var_name=self.var_name) + self.assertTrue(constraint._cube_func(self.cube)) + # Match. + constraint = NameConstraint( + standard_name=self.standard_name, + long_name=self.long_name, + var_name=self.var_name, + ) + self.assertTrue(constraint._cube_func(self.cube)) + # No match. + constraint = NameConstraint(var_name=None) + self.assertFalse(constraint._cube_func(self.cube)) + # No match. + constraint = NameConstraint( + standard_name=None, long_name=None, var_name=self.var_name + ) + self.assertFalse(constraint._cube_func(self.cube)) + + def test_STASH(self): + # Match. + constraint = NameConstraint(STASH=self.STASH) + self.assertTrue(constraint._cube_func(self.cube)) + # Match. + constraint = NameConstraint( + standard_name=self.standard_name, + long_name=self.long_name, + var_name=self.var_name, + STASH=self.STASH, + ) + self.assertTrue(constraint._cube_func(self.cube)) + # No match. + constraint = NameConstraint(STASH=None) + self.assertFalse(constraint._cube_func(self.cube)) + # No match. + constraint = NameConstraint( + standard_name=None, long_name=None, var_name=None, STASH=self.STASH + ) + self.assertFalse(constraint._cube_func(self.cube)) + + +class Test___repr__(tests.IrisTest): + def setUp(self): + self.standard_name = mock.sentinel.standard_name + self.long_name = mock.sentinel.long_name + self.var_name = mock.sentinel.var_name + self.STASH = mock.sentinel.STASH + self.msg = "NameConstraint({})" + self.f_standard_name = "standard_name={!r}".format(self.standard_name) + self.f_long_name = "long_name={!r}".format(self.long_name) + self.f_var_name = "var_name={!r}".format(self.var_name) + self.f_STASH = "STASH={!r}".format(self.STASH) + + def test(self): + constraint = NameConstraint() + expected = self.msg.format("") + self.assertEqual(repr(constraint), expected) + + def test_standard_name(self): + constraint = NameConstraint(standard_name=self.standard_name) + expected = self.msg.format(self.f_standard_name) + self.assertEqual(repr(constraint), expected) + + def test_long_name(self): + constraint = NameConstraint(long_name=self.long_name) + expected = self.msg.format(self.f_long_name) + self.assertEqual(repr(constraint), expected) + constraint = NameConstraint( + standard_name=self.standard_name, long_name=self.long_name + ) + args = "{}, {}".format(self.f_standard_name, self.f_long_name) + expected = self.msg.format(args) + self.assertEqual(repr(constraint), expected) + + def test_var_name(self): + constraint = NameConstraint(var_name=self.var_name) + expected = self.msg.format(self.f_var_name) + self.assertEqual(repr(constraint), expected) + constraint = NameConstraint( + standard_name=self.standard_name, + long_name=self.long_name, + var_name=self.var_name, + ) + args = "{}, {}, {}".format( + self.f_standard_name, self.f_long_name, self.f_var_name + ) + expected = self.msg.format(args) + self.assertEqual(repr(constraint), expected) + + def test_STASH(self): + constraint = NameConstraint(STASH=self.STASH) + expected = self.msg.format(self.f_STASH) + self.assertEqual(repr(constraint), expected) + constraint = NameConstraint( + standard_name=self.standard_name, + long_name=self.long_name, + var_name=self.var_name, + STASH=self.STASH, + ) + args = "{}, {}, {}, {}".format( + self.f_standard_name, + self.f_long_name, + self.f_var_name, + self.f_STASH, + ) + expected = self.msg.format(args) + self.assertEqual(repr(constraint), expected) + + +if __name__ == "__main__": + tests.main() diff --git a/lib/iris/tests/unit/cube_coord_common/test_CFVariableMixin.py b/lib/iris/tests/unit/cube_coord_common/test_CFVariableMixin.py index 9366bb848a..ddbe537122 100644 --- a/lib/iris/tests/unit/cube_coord_common/test_CFVariableMixin.py +++ b/lib/iris/tests/unit/cube_coord_common/test_CFVariableMixin.py @@ -1,4 +1,4 @@ -# (C) British Crown Copyright 2019, Met Office +# (C) British Crown Copyright 2020, Met Office # # This file is part of Iris. # @@ -145,6 +145,52 @@ def test_fail_token_default(self): self.cf_var.name(default='_nope', token=True) +class Test_names(tests.IrisTest): + def setUp(self): + self.cf_var = CFVariableMixin() + self.cf_var.standard_name = None + self.cf_var.long_name = None + self.cf_var.var_name = None + self.cf_var.attributes = dict() + + def test_standard_name(self): + standard_name = "air_temperature" + self.cf_var.standard_name = standard_name + expected = (standard_name, None, None, None) + result = self.cf_var.names + self.assertEqual(expected, result) + self.assertEqual(result.standard_name, standard_name) + + def test_long_name(self): + long_name = "air temperature" + self.cf_var.long_name = long_name + expected = (None, long_name, None, None) + result = self.cf_var.names + self.assertEqual(expected, result) + self.assertEqual(result.long_name, long_name) + + def test_var_name(self): + var_name = "atemp" + self.cf_var.var_name = var_name + expected = (None, None, var_name, None) + result = self.cf_var.names + self.assertEqual(expected, result) + self.assertEqual(result.var_name, var_name) + + def test_STASH(self): + stash = "m01s16i203" + self.cf_var.attributes = dict(STASH=stash) + expected = (None, None, None, stash) + result = self.cf_var.names + self.assertEqual(expected, result) + self.assertEqual(result.STASH, stash) + + def test_None(self): + expected = (None, None, None, None) + result = self.cf_var.names + self.assertEqual(expected, result) + + class Test_standard_name__setter(tests.IrisTest): def test_valid_standard_name(self): cf_var = CFVariableMixin() diff --git a/lib/iris/tests/unit/fileformats/pyke_rules/compiled_krb/fc_rules_cf_fc/test_build_geostationary_coordinate_system.py b/lib/iris/tests/unit/fileformats/pyke_rules/compiled_krb/fc_rules_cf_fc/test_build_geostationary_coordinate_system.py index c530538b90..67145fe4b0 100644 --- a/lib/iris/tests/unit/fileformats/pyke_rules/compiled_krb/fc_rules_cf_fc/test_build_geostationary_coordinate_system.py +++ b/lib/iris/tests/unit/fileformats/pyke_rules/compiled_krb/fc_rules_cf_fc/test_build_geostationary_coordinate_system.py @@ -1,4 +1,4 @@ -# (C) British Crown Copyright 2019, Met Office +# (C) British Crown Copyright 2020, Met Office # # This file is part of Iris. # @@ -35,43 +35,44 @@ class TestBuildGeostationaryCoordinateSystem(tests.IrisTest): - def _test(self, inverse_flattening=False): + def _test(self, inverse_flattening=False, replace_props=None, + remove_props=None): """ Generic test that can check vertical perspective validity with or without inverse flattening. """ - cf_grid_var_kwargs = { - 'spec': [], + # Make a dictionary of the non-ellipsoid properties to be added to + # both a test coord-system, and a test grid-mapping cf_var. + non_ellipsoid_kwargs = { 'latitude_of_projection_origin': 0.0, 'longitude_of_projection_origin': 2.0, 'perspective_point_height': 2000000.0, 'sweep_angle_axis': 'x', 'false_easting': 100.0, - 'false_northing': 200.0, - 'semi_major_axis': 6377563.396} + 'false_northing': 200.0} + # Make specified adjustments to the non-ellipsoid properties. + if remove_props: + for key in remove_props: + non_ellipsoid_kwargs.pop(key, None) + if replace_props: + for key, value in replace_props.items(): + non_ellipsoid_kwargs[key] = value + + # Make a dictionary of ellipsoid properties, to be added to both a test + # ellipsoid and the grid-mapping cf_var. ellipsoid_kwargs = {'semi_major_axis': 6377563.396} if inverse_flattening: ellipsoid_kwargs['inverse_flattening'] = 299.3249646 else: ellipsoid_kwargs['semi_minor_axis'] = 6356256.909 - cf_grid_var_kwargs.update(ellipsoid_kwargs) - - cf_grid_var = mock.Mock(**cf_grid_var_kwargs) - ellipsoid = iris.coord_systems.GeogCS(**ellipsoid_kwargs) + cf_grid_var_kwargs = non_ellipsoid_kwargs.copy() + cf_grid_var_kwargs.update(ellipsoid_kwargs) + cf_grid_var = mock.Mock(spec=[], **cf_grid_var_kwargs) cs = build_geostationary_coordinate_system(None, cf_grid_var) - expected = Geostationary( - latitude_of_projection_origin=cf_grid_var. - latitude_of_projection_origin, - longitude_of_projection_origin=cf_grid_var. - longitude_of_projection_origin, - perspective_point_height=cf_grid_var.perspective_point_height, - sweep_angle_axis=cf_grid_var.sweep_angle_axis, - false_easting=cf_grid_var.false_easting, - false_northing=cf_grid_var.false_northing, - ellipsoid=ellipsoid) - + ellipsoid = iris.coord_systems.GeogCS(**ellipsoid_kwargs) + expected = Geostationary(ellipsoid=ellipsoid, **non_ellipsoid_kwargs) self.assertEqual(cs, expected) def test_valid(self): @@ -79,3 +80,14 @@ def test_valid(self): def test_inverse_flattening(self): self._test(inverse_flattening=True) + + def test_false_offsets_missing(self): + self._test(remove_props=['false_easting', 'false_northing']) + + def test_false_offsets_none(self): + self._test(replace_props={'false_easting': None, + 'false_northing': None}) + + +if __name__ == "__main__": + tests.main() diff --git a/requirements/core.txt b/requirements/core.txt index 48ee3f1dfd..64453dcb27 100644 --- a/requirements/core.txt +++ b/requirements/core.txt @@ -8,7 +8,7 @@ cartopy cf-units>=2 cftime dask[array]>=1.2.0 #conda: dask>=1.2.0 -matplotlib>=2,<3 +matplotlib netcdf4 numpy>=1.14 scipy diff --git a/requirements/extensions.txt b/requirements/extensions.txt index 0f3d0e0379..8e8e847f88 100644 --- a/requirements/extensions.txt +++ b/requirements/extensions.txt @@ -5,5 +5,5 @@ # struggle. To install these extensions, ensure iris[core] has been installed # first. -iris_grib;python_version<"3" #conda: +iris-grib #conda: gdal diff --git a/requirements/test.txt b/requirements/test.txt index 38d7410a9b..34719a2d04 100644 --- a/requirements/test.txt +++ b/requirements/test.txt @@ -5,5 +5,6 @@ mock nose pep8 filelock +pillow<7 imagehash>=4.0 requests