Source code for dclab.rtdc_dataset.feat_anc_core.ancillary_feature

"""Computation of ancillary features

Ancillary features are computed on-the-fly in dclab if the
required data are available. The features are registered here
and are computed when `RTDCBase.__getitem__` is called with
the respective feature name. When `RTDCBase.__contains__` is
called with the feature name, then the feature is not yet
computed, but the prerequisites are evaluated:

.. ipython::

    In [1]: import dclab

    In [2]: ds = dclab.new_dataset("data/example.rtdc")

    In [4]: ds.config["calculation"]["emodulus lut"] = "LE-2D-FEM-19"

    In [3]: ds.config["calculation"]["emodulus medium"] = "CellCarrier"

    In [5]: ds.config["calculation"]["emodulus temperature"] = 23.0

    In [6]: ds.config["calculation"]["emodulus viscosity model"] = \

    In [7]: "emodulus" in ds  # nothing is computed yet

    In [8]: ds["emodulus"]  # now data are computed and cached

Once the data has been computed, `RTDCBase` caches it in
the `_ancillaries` property dict together with a hash
that is computed with `AncillaryFeature.hash`. The hash
is computed from the feature data `req_features` and the
configuration metadata `req_config`.

import hashlib
import warnings

import numpy as np

from ...util import obj2bytes
from ... import definitions as dfn

[docs] class BadFeatureSizeWarning(UserWarning): pass
[docs] class AncillaryFeature: #: All ancillary features registered features = [] #: All feature names registered feature_names = [] def __init__(self, feature_name, method, req_config=None, req_features=None, req_func=lambda x: True, priority=0, data=None, identifier=None): """A data feature that is computed from existing data Parameters ---------- feature_name: str The name of the ancillary feature, e.g. "emodulus". method: callable The method that computes the feature. This method takes an instance of `RTDCBase` as argument. req_config: list Required configuration parameters to compute the feature, e.g. ["calculation", ["emodulus lut", "emodulus viscosity"]] req_features: list Required existing features in the dataset, e.g. ["area_cvx", "deform"] req_func: callable A function that takes an instance of `RTDCBase` as an argument and checks whether any other necessary criteria are met. By default, this is a lambda function that returns True. The function should return False if the necessary criteria are not met. This function may also return a hashable object (via :func:`dclab.util.objstr`) instead of True, if the criteria are subject to change. In this case, the return value is used for identifying the cached ancillary feature. .. versionchanged:: 0.27.0 Support non-boolean return values for caching purposes. priority: int The priority of the feature; if there are multiple AncillaryFeature defined for the same feature_name, then the priority of the features defines which feature returns True in `self.is_available`. A higher value means a higher priority. data: object or BaseModel Any other data relevant for the feature (e.g. the ML model for computing 'ml_score_xxx' features) identifier: None or str A unique identifier (e.g. MD5 hash) of the ancillary feature. For PluginFeatures or ML features, this should be computed at least from the input file and the feature name. Notes ----- `req_config` and `req_features` are used to test whether the feature can be computed in `self.is_available`. """ if req_features is None: req_features = [] if req_config is None: req_config = [] self.feature_name = feature_name self.method = method self.req_config = req_config self.req_features = req_features self.req_func = req_func self.priority = priority = data self.identifier = identifier # register this feature AncillaryFeature.features.append(self) AncillaryFeature.feature_names.append(feature_name) def __repr__(self): repre = " ".join([ f"<{self.__class__.__name__}", f"'{self.feature_name}'", f"(id {self.identifier[:5]}...)" if self.identifier else "(no ID)", f"with priority {self.priority}", f"at {hex(id(self))}>", ]) return repre
[docs] @staticmethod def available_features(rtdc_ds): """Determine available features for an RT-DC dataset Parameters ---------- rtdc_ds: instance of RTDCBase The dataset to check availability for Returns ------- features: dict Dictionary with feature names as keys and instances of `AncillaryFeature` as values. """ cols = {} for inst in AncillaryFeature.features: if inst.is_available(rtdc_ds): cols[inst.feature_name] = inst return cols
[docs] @staticmethod def get_instances(feature_name): """Return all instances that compute `feature_name`""" feats = [] for ft in AncillaryFeature.features: if ft.feature_name == feature_name: feats.append(ft) return feats
[docs] @staticmethod def check_data_size(rtdc_ds, data_dict): """Check the feature data is the correct size. If it isn't, resize it. Parameters ---------- rtdc_ds: instance of RTDCBase The dataset from which the features are computed data_dict: dict Dictionary with `AncillaryFeature.feature_name` as keys and the computed data features (to be resized) as values. Returns ------- data_dict: dict Dictionary with `feature_name` as keys and the correctly resized data features as values. """ for key in data_dict: dsize = len(rtdc_ds) - len(data_dict[key]) if dsize > 0: msg = "Growing feature {} in {} by {} to match event number!" warnings.warn(msg.format(key, rtdc_ds, abs(dsize)), BadFeatureSizeWarning) data_dict[key] = np.array(data_dict[key], dtype=float) data_dict[key].resize(len(rtdc_ds), refcheck=False) data_dict[key][-dsize:] = np.nan elif dsize < 0: msg = "Shrinking feature {} in {} by {} to match event number!" warnings.warn(msg.format(key, rtdc_ds, abs(dsize)), BadFeatureSizeWarning) data_dict[key].resize(len(rtdc_ds), refcheck=False) if isinstance(data_dict[key], np.ndarray): data_dict[key].setflags(write=False) elif isinstance(data_dict[key], list): for item in data_dict[key]: if isinstance(item, np.ndarray): item.setflags(write=False) return data_dict
[docs] def compute(self, rtdc_ds): """Compute the feature with self.method. All ancillary features that share the same method will also be populated automatically. Parameters ---------- rtdc_ds: instance of RTDCBase The dataset to compute the feature for Returns ------- data_dict: dict Dictionary with `AncillaryFeature.feature_name` as keys and the computed data features (read-only) as values. """ data_dict = self.method(rtdc_ds) if not isinstance(data_dict, dict): data_dict = {self.feature_name: data_dict} data_dict = AncillaryFeature.check_data_size(rtdc_ds, data_dict) if self.feature_name not in data_dict: raise KeyError( f"I expected the feature '{self.feature_name}' to be a key " + f"in the dictionary returned by {self}. But I found only " + f"the following: {sorted(data_dict.keys())}") for key in data_dict: dfn.check_feature_shape(key, data_dict[key]) return data_dict
[docs] def hash(self, rtdc_ds): """Used for identifying an ancillary computation The required features, the used configuration keys/values, and the return value of the requirement function are hashed. """ hasher = hashlib.md5() # data columns for col in self.req_features: hasher.update(obj2bytes(rtdc_ds[col])) # config keys for sec, keys in self.req_config: for key in keys: val = rtdc_ds.config[sec][key] data = "{}:{}={}".format(sec, key, val) hasher.update(obj2bytes(data)) # custom requirement function hash reqret = self.req_func(rtdc_ds) if not isinstance(reqret, bool): # add to hash if not a boolean hasher.update(obj2bytes(reqret)) return hasher.hexdigest()
[docs] def is_available(self, rtdc_ds, verbose=False): """Check whether the feature is available Parameters ---------- rtdc_ds: instance of RTDCBase The dataset to check availability for Returns ------- available: bool `True`, if feature can be computed with `compute` Notes ----- This method returns `False` for a feature if there is a feature defined with the same name but with higher priority (even if the feature would be available otherwise). """ # Check config keys for item in self.req_config: section, keys = item if section not in rtdc_ds.config: if verbose: print("{} not in config".format(section)) return False else: for key in keys: if key not in rtdc_ds.config[section]: if verbose: print("{} not in config['{}']".format(key, section)) return False # Check features for col in self.req_features: if col not in rtdc_ds: return False # Check priorities of other features for of in AncillaryFeature.features: if of == self: # nothing to compare continue elif of.feature_name == self.feature_name: # same feature name if of.priority <= self.priority: # lower priority, ignore continue else: # higher priority if of.is_available(rtdc_ds): # higher priority is available, thus # this feature is not available return False else: # higher priority not available continue else: # other feature continue # Check user-defined function if not self.req_func(rtdc_ds): return False return True