4.2.3. Analysis results and their aggregation — MDAnalysis.analysis.results

Module introduces two classes, Results and ResultsGroup, used for storing and aggregating data in MDAnalysis.analysis.base.AnalysisBase.run(), respectively.

4.2.3.1. Classes

The Results class is an extension of a built-in dictionary type, that holds all assigned attributes in self.data and allows for access either via dict-like syntax, or via class-like syntax:

from MDAnalysis.analysis.results import Results
r = Results()
r.array = [1, 2, 3, 4]
assert r['array'] == r.array == [1, 2, 3, 4]

The ResultsGroup can merge multiple Results objects. It is mainly used by MDAnalysis.analysis.base.AnalysisBase class, that uses ResultsGroup.merge() method to aggregate results from multiple workers, initialized during a parallel run:

from MDAnalysis.analysis.results import Results, ResultsGroup
import numpy as np

r1, r2 = Results(), Results()
r1.masses = [1, 2, 3, 4, 5]
r2.masses = [0, 0, 0, 0]
r1.vectors = np.arange(10).reshape(5, 2)
r2.vectors = np.arange(8).reshape(4, 2)

group = ResultsGroup(
    lookup = {
        'masses': ResultsGroup.flatten_sequence,
        'vectors': ResultsGroup.ndarray_vstack
        }
    )

r = group.merge([r1, r2])
assert r.masses == list((*r1.masses, *r2.masses))
assert (r.vectors == np.vstack([r1.vectors, r2.vectors])).all()

class MDAnalysis.analysis.results.Results(*args, **kwargs)

Container object for storing results.

Results are dictionaries that provide two ways by which values can be accessed: by dictionary key results["value_key"] or by object attribute, results.value_key. Results stores all results obtained from an analysis after calling run().

The implementation is similar to the sklearn.utils.Bunch class in scikit-learn.

Raises:

• AttributeError – If an assigned attribute has the same name as a default attribute.

• ValueError – If a key is not of type str and therefore is not able to be accessed by attribute.

Examples

>>> from MDAnalysis.analysis.base import Results
>>> results = Results(a=1, b=2)
>>> results['b']
2
>>> results.b
2
>>> results.a = 3
>>> results['a']
3
>>> results.c = [1, 2, 3, 4]
>>> results['c']
[1, 2, 3, 4]

New in version 2.0.0.

Changed in version 2.8.0: Moved Results to MDAnalysis.analysis.results

class MDAnalysis.analysis.results.ResultsGroup(lookup: dict[str, Callable] = None)

Management and aggregation of results stored in Results instances.

A ResultsGroup is an optional description for Result “dictionaries” that are used in analysis classes based on AnalysisBase. For each key in a Result it describes how multiple pieces of the data held under the key are to be aggregated. This approach is necessary when parts of a trajectory are analyzed independently (e.g., in parallel) and then need to me merged (with merge()) to obtain a complete data set.

Parameters:

lookup (dict[str, Callable], optional) – aggregation functions lookup dict, by default None

Examples

from MDAnalysis.analysis.results import ResultsGroup, Results
group = ResultsGroup(lookup={'mass': ResultsGroup.float_mean})
obj1 = Results(mass=1)
obj2 = Results(mass=3)
assert {'mass': 2.0} == group.merge([obj1, obj2])

# you can also set `None` for those attributes that you want to skip
lookup = {'mass': ResultsGroup.float_mean, 'trajectory': None}
group = ResultsGroup(lookup)
objects = [Results(mass=1, skip=None), Results(mass=3, skip=object)]
assert group.merge(objects, require_all_aggregators=False) == {'mass': 2.0}

New in version 2.8.0.

static flatten_sequence(arrs: list[list])

Flatten a list of lists into a list

Parameters:

arrs (list[list]) – list of lists

Returns:

flattened list

Return type:

list

static float_mean(floats: list[float])

calculates mean of input float values

Parameters:

floats (list[float]) – list of float values

Returns:

mean value

Return type:

float

merge(objects: Sequence[Results], require_all_aggregators: bool = True) → Results

Merge multiple Results into a single Results instance.

Merge multiple Results instances into a single one, using the lookup dictionary to determine the appropriate aggregator functions for each named results attribute. If the resulting object only contains a single element, it just returns it without using any aggregators.

Parameters:

• objects (Sequence[Results]) – Multiple Results instances with the same data attributes.

• require_all_aggregators (bool, optional) – if True, raise an exception when no aggregation function for a particular argument is found. Allows to skip aggregation for the parameters that aren’t needed in the final object – see ResultsGroup.

Returns:

merged Results

Return type:

Results

Raises:

ValueError – if no aggregation function for a key is found and require_all_aggregators=True

static ndarray_hstack(arrs: list[numpy.ndarray])

Performs horizontal stack of input arrays

Parameters:

arrs (list[np.ndarray]) – input numpy arrays

Returns:

result of stacking

Return type:

np.ndarray

static ndarray_mean(arrs: list[numpy.ndarray])

calculates mean of input ndarrays along axis=0

Parameters:

arrs (list[np.ndarray]) – list of input arrays. Must have the same shape.

Returns:

mean of input arrays

Return type:

np.ndarray

static ndarray_sum(arrs: list[numpy.ndarray])

sums an ndarray along axis=0

Parameters:

arrs (list[np.ndarray]) – list of input arrays. Must have the same shape.

Returns:

sum of input arrays

Return type:

np.ndarray

static ndarray_vstack(arrs: list[numpy.ndarray])

Performs vertical stack of input arrays

Parameters:

arrs (list[np.ndarray]) – input numpy arrays

Returns:

result of stacking

Return type:

np.ndarray