Ctrl+K

utopya.eval package

Contents

utopya.eval package#

Implements a dantro-based simulation data evaluation pipeline.

Subpackages#

Submodules#

utopya.eval._plot_func_resolver module#

Implements a plot function resolver that takes model-specific information into account.

class utopya.eval._plot_func_resolver.PlotFuncResolver(*, _model_info_bundle: ModelInfoBundle, **kwargs)[source]#

Bases: PlotFuncResolver

A utopya-specific plot function resolver for PlotManager that takes information from the model info bundle into account.

BASE_PKG: str = 'utopya.eval.plots'#

Which package to use as base package for relative module imports

__init__(*, _model_info_bundle: ModelInfoBundle, **kwargs)[source]#

Initializes the plot function resolver and additionally stores the model info bundle.

_get_custom_module_paths() → Dict[str, str][source]#

Aggregates a dict of module paths from which imports are attempted.

Uses model- or project-specific information, if available:

  • A model’s py_plots_dir

  • A project’s py_plots_dir

  • A project’s additional py_modules

  • The framework’s additional py_modules

  • The framework’s py_plots_dir

_get_module_via_import(*, module: str, **kwargs) → module[source]#

Extends the parent method by making the custom modules available if the regular import failed.

utopya.eval.containers module#

Implements data container classes specialised on Utopia output data.

It is based on the dantro.base.BaseDataContainer classes, especially their numeric form, the NumpyDataContainer and the XrDataContainer.

class utopya.eval.containers.NumpyDC(*, name: str, data: ndarray, **dc_kwargs)[source]#

Bases: Hdf5ProxySupportMixin, NumpyDataContainer

This is the base class for numpy data containers used in Utopia.

It is based on the NumpyDataContainer provided by dantro and extends it with the Hdf5ProxySupportMixin, allowing to load the data from the Hdf5 file only once it becomes necessary.

_abc_impl = <_abc._abc_data object>#
class utopya.eval.containers.XarrayDC(*, name: str, data: Union[ndarray, xarray.DataArray], dims: Sequence[str] = None, coords: dict = None, extract_metadata: bool = True, apply_metadata: bool = True, **dc_kwargs)[source]#

Bases: Hdf5ProxySupportMixin, XrDataContainer

This is the base class for xarray data containers used in Utopia.

It is based on the XrDataContainer provided by dantro. As of now, it has no proxy support, but will gain it once available on dantro side.

PROXY_RESOLVE_ASTYPE = None#

Which type to resolve the proxy to. None defaults to numpy.ndarray.

PROXY_RETAIN = True#

Whether to retain a proxy after resolving it; allows reinstating proxy objects.

PROXY_REINSTATE_FAIL_ACTION = 'log_warning'#

Which action to take if reinstating a proxy was not possible

_XRC_DIMS_ATTR = 'dim_names'#

Define as class variable the name of the attribute that determines the dimensions of the xarray.DataArray.

_XRC_DIM_NAME_PREFIX = 'dim_name__'#

Attributes prefixed with this string can be used to set names for specific dimensions. The prefix should be followed by an integer-parsable string, e.g. dim_name__0 would be the dimension name for the 0th dim

_XRC_COORDS_ATTR_PREFIX = 'coords__'#

Attributes prefixed with this string determine the coordinate values for a specific dimension. The prefix should be followed by the _name_ of the dimension, e.g. coords__time. The values are interpreted according to the default coordinate mode or, if given, the coords_mode__* attribute

_XRC_COORDS_MODE_DEFAULT = 'values'#

The default mode by which coordinates are interpreted. See the base class, dantro.containers.xr.XrDataContainer for more information.

Available modes:

  • values: the explicit values (iterable) to use for coordinates

  • trivial: The trivial indices; ignores the coordinate argument

  • scalar: makes sure only a single coordinate is provided

  • range: python built-in range function arguments

  • arange: np.arange arguments

  • linspace: np.linspace arguments

  • logspace: np.logspace arguments

  • start_and_step: the start and step values of an integer range

    expression; the stop value is deduced by looking at the length of the corresponding dimension.

  • linked: Load the coordinates from a linked object within the

    tree, specified by a relative path from the current object.

_XRC_COORDS_MODE_ATTR_PREFIX = 'coords_mode__'#

Prefix for the coordinate mode if a custom mode is to be used. To, e.g., use mode start_and_step for time dimension, set the coords_mode__time attribute to value start_and_step

_XRC_INHERIT_CONTAINER_ATTRIBUTES = True#

Whether to inherit the other container attributes

_XRC_STRICT_ATTR_CHECKING = True#

Whether to use strict attribute checking; throws errors if there are container attributes available that match the prefix but don’t match a valid dimension name. Can be disabled for speed improvements.

_abc_impl = <_abc._abc_data object>#
class utopya.eval.containers.XarrayYamlDC(*, name: str, data: Union[ndarray, xarray.DataArray], dims: Sequence[str] = None, coords: dict = None, extract_metadata: bool = True, apply_metadata: bool = True, **dc_kwargs)[source]#

Bases: XarrayDC

An XarrayDC specialization that assumes that each array entry is a YAML string, which is subsequently loaded. This can be done alongside the metadata application of the XarrayDC.

_apply_metadata()[source]#

Whenever metadata is applied that is also a good point to resolve the YAML data…

_abc_impl = <_abc._abc_data object>#
class utopya.eval.containers.GridDC(*, name: str, data: Union[ndarray, DataArray], **dc_kwargs)[source]#

Bases: XarrayDC

This is the base class for all grid data used in Utopia.

It is based on the XarrayDC and reshapes the data to the grid shape. The last dimension is assumed to be the dimension that goes along the grid cell IDs.

_GDC_grid_shape_attr = 'grid_shape'#

The attribute to read the desired grid shape from

_GDC_space_extent_attr = 'space_extent'#

The attribute to read the space extent from

_GDC_index_order_attr = 'index_order'#

The attribute to read the index order from

_GDC_grid_structure_attr = 'grid_structure'#

The attribute to read the desired grid structure from

__init__(*, name: str, data: Union[ndarray, DataArray], **dc_kwargs)[source]#

Initialize a GridDC which represents grid-like data.

Given the container attribute (see _GDC_grid_shape_attr), this container takes care to reshape the underlying data such that it represents that grid, even if it is saved in another shape.

Note

Use this container if it is easier to store array data in a flat format (e.g. because there is no need to take care of slicing etc) but you still desire to work with it in its actual shape.

Parameters:

  • name (str) – The name of this container

  • data (Union[numpy.ndarray, xarray.DataArray]) – The not yet reshaped data. If this is 1D, it is assumed that there is no additional dimension. If it is 2D (or more), it is assumed to be (..., cell ids).

  • **kwargs – Further initialization kwargs, e.g. attrs …

_abc_impl = <_abc._abc_data object>#
_postprocess_proxy_resolution()[source]#

Invoked from Hdf5ProxySupportMixin after a proxy was resolved, this takes care to apply the reshaping operation onto the underlying data.

_parse_sizes_from_metadata() → Sequence[Tuple[str, int]][source]#

Invoked from _format_shape when no metadata was applied but the dimension names are available. Should return data in the same form as xr.DataArray.sizes.items() does.

property grid_shape: tuple#

The shape of the grid

property space_extent: tuple#

The space’s extent this grid is representing, read from attrs

property shape: tuple#

Returns shape, proxy-aware

This is an overload of the property in Hdf5ProxySupportMixin which takes care that not the actual underlying proxy data shape is returned but whatever the container’s shape is to be after reshaping.

property ndim: int#

Returns ndim, proxy-aware

This is an overload of the property in Hdf5ProxySupportMixin which takes care that not the actual underlying proxy data ndim is returned but whatever the container’s ndim is to be after reshaping.

_determine_shape()[source]#

Determine the new shape and store it as _new_shape attribute

_reshape_data() → DataArray[source]#

Looks at the current data shape and container attributes to reshape the data such that it represents a grid.

utopya.eval.data_ops module#

Custom data operations

utopya.eval.data_ops.update_attrs(d, attrs: dict)[source]#

Updates the data attributes in d with attrs.

Parameters:

  • d (xarray.DataArray) – The data array to write the attributes to.

  • attrs (dict) – The attributes to use for updating

Returns:

A new data array like d with updated attributes.

Return type:

xarray.DataArray

utopya.eval.data_ops.update_with_attrs_from(t, s)[source]#

Updates the data attributes in t with those from s.

Parameters:
Returns:

A new data array for t with updated attributes from s.

Return type:

xarray.DataArray

utopya.eval.datamanager module#

Implements a class that manages data written out by Utopia models.

It is based on dantro’s DataManager class and the containers specialized for Utopia data.

utopya.eval.datamanager._condense_thresh_func(*, level: int, num_items: int, total_item_count: int) → int[source]#

Dynamically computes the condensation threshold for the current element in a DataManager tree.

class utopya.eval.datamanager.DataManager(data_dir: str, *, name: Optional[str] = None, load_cfg: Optional[Union[dict, str]] = None, out_dir: Union[str, bool] = '_output/{timestamp:}', out_dir_kwargs: Optional[dict] = None, create_groups: Optional[List[Union[str, dict]]] = None, condensed_tree_params: Optional[dict] = None, default_tree_cache_path: Optional[str] = None)[source]#

Bases: AllAvailableLoadersMixin, DataManager

This class manages the data that is written out by Utopia simulations.

It is based on the dantro DataManager class and adds the functionality for specific loader functions that are needed in Utopia: Hdf5 and Yaml. Furthermore, to enable file caching via the DAG framework, all available data loaders are included here.

_DATA_GROUP_CLASSES: Dict[str, type] = {'GraphGroup': <class 'utopya.eval.groups.GraphGroup'>, 'MultiverseGroup': <class 'utopya.eval.groups.MultiverseGroup'>}#

Known group types

_HDF5_DSET_DEFAULT_CLS#

Tells the HDF5 loader which container class to use

alias of XarrayDC

_HDF5_MAP_FROM_ATTR: str = 'content'#

The name of the attribute to read for the mapping

_HDF5_GROUP_MAP: Dict[str, type] = {'graph': <class 'utopya.eval.groups.GraphGroup'>, 'network': <class 'utopya.eval.groups.GraphGroup'>, 'time_series': <class 'utopya.eval.groups.TimeSeriesGroup'>, 'time_series_heterogeneous': <class 'utopya.eval.groups.HeterogeneousTimeSeriesGroup'>}#

The mapping of different content values to a data group type

_abc_impl = <_abc._abc_data object>#
_HDF5_DSET_MAP: Dict[str, type] = {'array_of_yaml_strings': <class 'utopya.eval.containers.XarrayYamlDC'>, 'grid': <class 'utopya.eval.containers.GridDC'>, 'labelled_data': <class 'utopya.eval.containers.XarrayDC'>, 'unlabelled_data': <class 'utopya.eval.containers.NumpyDC'>}#

The mapping of different content values to a data container types

_COND_TREE_MAX_LEVEL = 10#

Condensed tree representation maximum level

_COND_TREE_CONDENSE_THRESH(**kws)#

Condensed tree representation threshold parameter

_DEFAULT_TREE_CACHE_PATH = 'data/.tree_cache.d3'#

Where the tree cache file is to be stored; may be overwritten by a config entry

utopya.eval.groups module#

Implements specialized data group classes that are based on group types provided in dantro.groups. Here, they are configured using their class variables.

class utopya.eval.groups.UniverseGroup(*, name: str, containers: Optional[list] = None, attrs=None, parent: Optional[AbstractDataGroup] = None)[source]#

Bases: ParamSpaceStateGroup

This group represents the data of a single universe

_abc_impl = <_abc._abc_data object>#
class utopya.eval.groups.MultiverseGroup(*, name: str, pspace: Optional[ParamSpace] = None, containers: Optional[list] = None, **kwargs)[source]#

Bases: ParamSpaceGroup

This group is meant to manage the multiverse group of the loaded data, i.e. the group where output of the individual UniverseGroup objects is stored in.

Its main aim is to provide easy access to universes. By default, universes are only identified by their ID, which is a zero-padded string. This group adds the ability to access them via integer indices.

Furthermore, via dantro, an easy data selector method is available, see dantro.groups.psp.ParamSpaceGroup.select().

_NEW_GROUP_CLS#

alias of UniverseGroup

_abc_impl = <_abc._abc_data object>#
class utopya.eval.groups.TimeSeriesGroup(*args, dims: Optional[Tuple[str]] = None, mode: Optional[str] = None, allow_deep_selection: Optional[bool] = None, **kwargs)[source]#

Bases: TimeSeriesGroup

This group is meant to manage time series data, with the container names being interpreted as the time coordinate.

_NEW_CONTAINER_CLS#

alias of XarrayDC

_abc_impl = <_abc._abc_data object>#
class utopya.eval.groups.HeterogeneousTimeSeriesGroup(*args, dims: Optional[Tuple[str]] = None, mode: Optional[str] = None, allow_deep_selection: Optional[bool] = None, **kwargs)[source]#

Bases: HeterogeneousTimeSeriesGroup

This group is meant to manage time series data, with the container names being interpreted as the time coordinate.

_NEW_CONTAINER_CLS#

alias of XarrayDC

_abc_impl = <_abc._abc_data object>#
class utopya.eval.groups.GraphGroup(*args, **kwargs)[source]#

Bases: GraphGroup

This group is meant to manage graph data and create a NetworkX graph from it.

_NEW_GROUP_CLS#

alias of TimeSeriesGroup

_ALLOWED_CONT_TYPES: Optional[tuple] = (<class 'utopya.eval.groups.TimeSeriesGroup'>, <class 'utopya.eval.containers.XarrayDC'>)#

The types that are allowed to be stored in this group. If None, all types derived from the dantro base classes are allowed. This applies to both containers and groups that are added to this group.

Hint

To add the type of the current object, add a string entry self to the tuple. This will be resolved to type(self) at invocation.

_GG_node_container = '_vertices'#
_GG_edge_container = '_edges'#
_GG_attr_directed = 'is_directed'#
_GG_attr_parallel = 'allows_parallel'#
_GG_attr_edge_container_is_transposed = 'edge_container_is_transposed'#
_GG_attr_keep_dim = 'keep_dim'#
_GG_WARN_UPON_BAD_ALIGN = True#
_abc_impl = <_abc._abc_data object>#

utopya.eval.plotcreators module#

Implements utopya-specializations of dantro.plot.creators

class utopya.eval.plotcreators.PyPlotCreator(name: str, *, style: Optional[dict] = None, **parent_kwargs)[source]#

Bases: PyPlotCreator

This is the Utopia-specific version of dantro’s PyPlotCreator.

Its main purpose is to define common settings for plotting. By adding this extra layer, it allows for future extensibility as well.

EXTENSIONS: Union[Tuple[str], str] = 'all'#

Which file extensions to support. A value of all leads to no checks being performed on the extension.

DEFAULT_EXT = 'pdf'#

Default plot file extension

PLOT_HELPER_CLS#

The PlotHelper class to use; here, the utopya-specific one

alias of PlotHelper

_abc_impl = <_abc._abc_data object>#
class utopya.eval.plotcreators.UniversePlotCreator(*args, psgrp_path: Optional[str] = None, **kwargs)[source]#

Bases: UniversePlotCreator, PyPlotCreator

Makes plotting with data from a single universe more convenient

_abc_impl = <_abc._abc_data object>#
PSGRP_PATH: str = 'multiverse'#

The path within the data tree to arrive at the MultiverseGroup that this plot creator expects universes to be located in.

class utopya.eval.plotcreators.MultiversePlotCreator(*args, psgrp_path: Optional[str] = None, **kwargs)[source]#

Bases: MultiversePlotCreator, PyPlotCreator

Makes plotting with data from all universes more convenient

_abc_impl = <_abc._abc_data object>#
PSGRP_PATH: str = 'multiverse'#

The path within the data tree to arrive at the MultiverseGroup.

utopya.eval.plothelper module#

Implements utopya’s PlotHelper specialization

class utopya.eval.plothelper.PlotHelper(*, out_path: str, helper_defaults: Optional[dict] = None, update_helper_cfg: Optional[dict] = None, raise_on_error: bool = True, animation_enabled: bool = False)[source]#

Bases: PlotHelper

A specialization of dantro’s PlotHelper which is used for creating matplotlib.pyplot-based plots using PyPlotCreator.

This can be used to add additional helpers for use in utopya without requiring changes to dantro.

Note

The helpers implemented here should try to adhere to the interface exemplified by the dantro PlotHelper, with the aim that they can then be migrated into dantro in the long run.

utopya.eval.plotmanager module#

Implements a plotting framework based on dantro

In order to make the plotting framework specific to Utopia, this module derives both from the dantro PlotManager and some PlotCreator classes.

class utopya.eval.plotmanager.PlotManager(*args, _model_info_bundle: Optional[ModelInfoBundle] = None, **kwargs)[source]#

Bases: PlotManager

This is the Utopia-specific version of the dantro PlotManager.

It registers the Utopia-specific plot creators and allows for custom interface specifications, e.g. by preloading custom modules.

CREATORS: Dict[str, type] = {'base': <class 'dantro.plot.creators.base.BasePlotCreator'>, 'external': <class 'utopya.eval.plotcreators.PyPlotCreator'>, 'multiverse': <class 'utopya.eval.plotcreators.MultiversePlotCreator'>, 'pyplot': <class 'utopya.eval.plotcreators.PyPlotCreator'>, 'universe': <class 'utopya.eval.plotcreators.UniversePlotCreator'>}#

Supported plot creator classes

MODEL_PLOTS_MODULE_NAME = 'model_plots'#

Name under which the model-specific plots are made importable

PLOT_FUNC_RESOLVER#

The custom plot function resolver type to use.

alias of PlotFuncResolver

__init__(*args, _model_info_bundle: Optional[ModelInfoBundle] = None, **kwargs)[source]#

Sets up a PlotManager.

This specialization of the dantro.plot_mngr.PlotManager additionally stores some utopya-specific metadata in form of a ModelInfoBundle that describes the model this PlotManager is used with. That information is then used to load some additional model-specific information once a creator is invoked.

Furthermore, the _preload_modules() method takes care to make model-, project-, or framework-specific plot functions available.

Parameters:

  • *args – Positional arguments passed to PlotManager.

  • _model_info_bundle (ModelInfoBundle, optional) – The internally-used argument to pass model information to the plot manager.

  • **kwargs – Keyword arguments passed on to PlotManager.

property common_out_dir: str#

The common output directory of all plots that were created with this plot manager instance. This uses the plot output paths stored in the plot information dict, specifically the target_dir entry.

If there was no plot information yet, the return value will be empty.

plot_from_cfg(*args, plots_cfg: Optional[Union[dict, str]] = None, **kwargs)[source]#

Thin wrapper around parent method that shows which plot configuration file will be used.

_get_plot_func_resolver(**init_kwargs) → PlotFuncResolver[source]#

Instantiates the plot function resolver object.

Additionally attaches the model info bundle to the resolver, such that it can use that information for plot function lookup.

_get_plot_creator(*args, **kwargs) → BasePlotCreator[source]#

Sets up the BasePlotCreator and attaches a model information bundle to it such that this information is available downstream.

_preload_modules()[source]#

Pre-loads the model-, project-, and framework-specific plot function modules. This allows to execute code (like registering model-specific dantro data operations) and have them available prior to the invocation of the creator and independently from the module that contains the plot function (which may be part of dantro, for instance).

Uses dantro._import_tools.import_module_from_path()

utopya.eval.transform module#

Overloads and additions for dantro’s data transformation framework.

utopya.eval.transform.register_operation(*args, skip_existing: bool = True, **kws) → None[source]#

Register an operation with the dantro data operations database.

This invokes register_operation(), but has skip_existing == True as default in order to reduce number of arguments that need to be specified in utopya model plots, where duplicate module imports frequently cause existing entries.

Parameters:
utopya.eval.transform.is_operation(arg: Optional[Union[Callable, str]] = None, /, **kws)[source]#

Overload of dantro’s is_operation decorator, using utopya’s own registration function.

Usage example:

from utopya.eval import is_operation

@is_operation
def my_operation(data, *args):
    pass

@is_operation("op_with_custom_name")
def my_other_operation(data, *args):
    pass

@is_operation("my_operation", overwrite_existing=True)
def yet_some_other_operation(data, *args):
    pass
Parameters:

  • arg (Union[str, Callable], optional) – The name that should be used in the operation registry. If not given, will use the name of the decorated function instead. If a callable, this refers to the @is_operation call syntax and will use that as a function.

  • **kws – Passed to register_operation().

Contents