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Functions482 in github.com/SPOClab-ca/dn3

↓ 45 callersMethodkeys
(self)
dn3/configuratron/config.py:58
↓ 37 callersMethodget_thinkers
Accumulates a consistently ordered list of all the thinkers in the dataset. It is this order that any automatic segmenting through :p
dn3/data/dataset.py:949
↓ 20 callersMethodadd_transform
(self, transform, deep=False)
dn3/data/dataset.py:659
↓ 15 callersMethod__init__
(self, mean=None, std=None)
dn3/transforms/instance.py:117
↓ 12 callersMethod__init__
(self)
dn3/trainable/layers.py:387
↓ 9 callersMethodauto_construct_dataset
This creates a dataset using the config values. If tlen and tmin are specified in the config, creates epoched dataset, otherwise Raw.
dn3/configuratron/config.py:686
↓ 8 callersMethodtrain
(self, mode=True)
dn3/trainable/processes.py:265
↓ 7 callersMethod__init__
Collects multiple recordings of the same person, intended to be of the same task, at different times or conditions. Paramete
dn3/data/dataset.py:442
↓ 7 callersFunctioncreate_dummy_dataset
(epoched=True, sessions_per_thinker=2, num_thinkers=THINKERS_IN_DATASETS, sess_args=d
tests/dummy_data.py:63
↓ 6 callersMethod__init__
(self, targets, samples, channels, s_growth=24, t_filters=32, do=0.4, pooling=20, activation=
dn3/trainable/models.py:231
↓ 6 callersMethod_execute_transforms
(self, *x)
dn3/data/dataset.py:91
↓ 6 callersMethodget_targets
Collect all the targets (i.e. labels) that this Thinker's data is annotated with. Returns ------- targets: np.ndarra
dn3/data/dataset.py:666
↓ 6 callersMethodmake_raw_recording
(self, **kwargs)
tests/testDataset.py:25
↓ 6 callersMethodparameters
All the trainable parameters in the Trainable. This includes any architecture parameters and meta-parameters. Returns ------
dn3/trainable/processes.py:187
↓ 6 callersMethodupdate_id_returns
Updates which ids are to be returned by the dataset. If any argument is `None` it preserves the previous value. Parameters -
dn3/data/dataset.py:774
↓ 5 callersFunction_make_mask
(shape, p, total, span, allow_no_inds=False)
dn3/trainable/utils.py:16
↓ 5 callersFunctioncheck_raw_against_data
(retrieved, index, normalizer=lambda x: x, decimate=1)
tests/dummy_data.py:75
↓ 4 callersMethod_generate_splits
(self, validation, testing)
dn3/data/dataset.py:991
↓ 4 callersMethod_reset_dataset
(self)
dn3/data/dataset.py:801
↓ 4 callersMethodcalculate_loss
Given the inputs to and outputs from underlying modules, calculate the loss. Returns ------- Loss : Sin
dn3/trainable/processes.py:216
↓ 4 callersFunctioncheck_epoch_against_data
(retrieved, event_index, normalizer=lambda x: x)
tests/dummy_data.py:89
↓ 4 callersFunctioncreate_basic_data
()
tests/dummy_data.py:22
↓ 4 callersFunctioncreate_dummy_raw
Creates a Raw instance from `create_basic_data` Returns: ------- raw : mne.io.Raw
tests/dummy_data.py:31
↓ 4 callersFunctioncreate_dummy_session
(epoched=True, raw=None, **kwargs)
tests/dummy_data.py:48
↓ 4 callersMethodload
(self, filename, include_classifier=False, freeze_features=True)
dn3/trainable/models.py:168
↓ 4 callersMethodloso
This *generates* a "Leave-one-subject-out" (LOSO) split. Tests each person one-by-one, and validates on the previous (the first is va
dn3/data/dataset.py:1016
↓ 4 callersMethodnew_channels
(self, old_channels)
dn3/transforms/instance.py:425
↓ 4 callersMethodnew_sequence_length
(self, old_sequence_length)
dn3/transforms/instance.py:276
↓ 4 callersMethodnew_sfreq
This is an optional method that indicates the transformation modifies the sampling frequency of the underlying time-series.
dn3/transforms/instance.py:73
↓ 4 callersMethodstandard_logging
(cls, metrics: dict, start_message="End of Epoch")
dn3/trainable/processes.py:357
↓ 4 callersFunctionunfurl
(_set: set)
dn3/utils.py:59
↓ 3 callersMethod__call__
(self, x)
dn3/transforms/instance.py:122
↓ 3 callersMethod__init__
(self, cls_num_list, max_m=0.5, weight=None, s=30)
dn3/trainable/processes.py:794
↓ 3 callersMethod_add_bad_span
(self, tid, sid, start, end)
dn3/data/utils.py:304
↓ 3 callersMethod_get_session_name
(self, f: Path)
dn3/configuratron/config.py:398
↓ 3 callersMethod_make_like_me
(self, people: list)
dn3/data/dataset.py:976
↓ 3 callersMethod_reset_dataset
(self)
dn3/data/dataset.py:483
↓ 3 callersMethodclone
A copy of this object to allow the repetition of recordings, thinkers, etc. that load data from the same memory/files but have their
dn3/data/dataset.py:67
↓ 3 callersMethodclone
This provides a standard way to copy models, weights and all.
dn3/trainable/models.py:39
↓ 3 callersFunctionget_label_balance
Given a dataset, return the proportion of each target class and the counts of each class type Parameters ---------- dataset Ret
dn3/trainable/processes.py:753
↓ 3 callersMethodget_transform
Generate and return any transform associated with this preprocessor. Should be used after applying this to a dataset, i.e. through :m
dn3/transforms/preprocessors.py:29
↓ 3 callersMethodlmso
This *generates* a "Leave-multiple-subject-out" (LMSO) split. In other words X-fold cross-validation, with boundaries enforced at thi
dn3/data/dataset.py:1067
↓ 3 callersMethodmake_epoch_recording
(self, **kwargs)
tests/testDataset.py:28
↓ 3 callersMethodpreprocess
Applies a preprocessor to the dataset Parameters ---------- preprocessor : Preprocessor A pre
dn3/data/dataset.py:628
↓ 3 callersFunctionsame_channel_sets
Validate that all the channel sets are consistent, return false if not
dn3/transforms/instance.py:16
↓ 3 callersMethodset_scheduler
This allow the addition of a learning rate schedule to the process. By default, a linear warmup with cosine decay will be used. Any s
dn3/trainable/processes.py:106
↓ 3 callersMethodsplit
Split the thinker's data into training, validation and testing sets. Parameters ---------- test_frac : float
dn3/data/dataset.py:568
↓ 2 callersMethod__init__
Batch transforms are operations that are performed on trial tensors after being accumulated into batches via the :meth:`__call__` met
dn3/transforms/batch.py:7
↓ 2 callersMethod__init__
(self, num_target_people=None, channels=len(DEEP_1010_CHS_LISTING), hidden_size=384, dropout=0.1,
dn3/trainable/experimental.py:12
↓ 2 callersMethod_add_deep1010
(self, ch_names: list, deep1010map: np.ndarray, unused)
dn3/configuratron/config.py:445
↓ 2 callersFunction_adopt_auxiliaries
(obj, remaining)
dn3/configuratron/config.py:68
↓ 2 callersMethod_check_fully_specified_requirements
(self, dataset)
tests/testConfig.py:131
↓ 2 callersFunction_check_zscored_trial
(event_id)
tests/testTransforms.py:17
↓ 2 callersFunction_clear_include_files
()
tests/testConfig.py:35
↓ 2 callersMethod_dataloader_args
(dataset, training=False, **loader_kwargs)
dn3/trainable/processes.py:413
↓ 2 callersFunction_generate_include_files
()
tests/testConfig.py:42
↓ 2 callersMethod_get_batch
(self, iterator)
dn3/trainable/processes.py:159
↓ 2 callersFunction_get_prediction
Checks if multiple outputs were provided, and selects
dn3/metrics/base.py:36
↓ 2 callersMethod_make_dataloader
Any args that make more sense as a convenience function to be set
dn3/trainable/processes.py:420
↓ 2 callersMethod_make_ff_layer
(self, in_ch, out_ch)
dn3/trainable/experimental.py:40
↓ 2 callersMethod_make_like_me
(self, sessions: Iterable)
dn3/data/dataset.py:560
↓ 2 callersMethod_make_numpy_convenience
(self)
dn3/data/utils.py:239
↓ 2 callersFunction_make_span_from_seeds
(seeds, span, total=None)
dn3/trainable/utils.py:5
↓ 2 callersMethod_retain_best
(self, old_checkpoint, metrics_to_check: dict, retain_string: str)
dn3/trainable/processes.py:391
↓ 2 callersMethod_simple_accuracy
(inputs, outputs)
dn3/trainable/processes.py:637
↓ 2 callersFunction_valid_character_heuristics
(name, informative_characters)
dn3/transforms/channels.py:78
↓ 2 callersMethodcalculate_metrics
Given the inputs to and outputs from the underlying module. Return tracked metrics. Parameters ---------- inputs :
dn3/trainable/processes.py:234
↓ 2 callersMethodchannel_listing
()
dn3/transforms/instance.py:351
↓ 2 callersMethodclassifier_forward
(self, features)
dn3/trainable/models.py:162
↓ 2 callersMethodclear_transforms
(self, deep_clear=False)
dn3/data/dataset.py:653
↓ 2 callersFunctioncreate_dummy_thinker
(epoched=True, sessions_per_thinker=2, sess_args=dict(), **kwargs)
tests/dummy_data.py:57
↓ 2 callersMethodevaluate
Calculate and return metrics for a dataset Parameters ---------- dataset: DN3ataset, DataLoader The
dn3/trainable/processes.py:285
↓ 2 callersMethodfit
sklearn/keras-like convenience method to simply proceed with training across multiple epochs of the provided dataset Paramet
dn3/trainable/processes.py:664
↓ 2 callersMethodforward
Given a batch of inputs, return the outputs produced by the trainable module. Parameters ---------- inputs :
dn3/trainable/processes.py:199
↓ 2 callersMethodfreeze_features
In many cases, the features learned by a model in one domain can be applied to another case. This method freezes (or un-freezes) all
dn3/trainable/models.py:137
↓ 2 callersMethodget_transform
(self)
dn3/transforms/preprocessors.py:97
↓ 2 callersMethodload
(self, filename, strict=True)
dn3/trainable/layers.py:258
↓ 2 callersFunctionmap_named_channels_deep_1010
Maps channel names to the Deep1010 format, will automatically map EOG and extra channels if they have been named according to standard conven
dn3/transforms/channels.py:159
↓ 2 callersFunctionmin_max_normalize
(x: torch.Tensor, low=-1, high=1)
dn3/utils.py:67
↓ 2 callersFunctionrand_split
(dataset, frac=0.75)
dn3/utils.py:52
↓ 2 callersMethodreset
(self, rejections_only=False)
dn3/data/utils.py:178
↓ 2 callersFunctionretrieve_underlying_dummy_data
(event_index)
tests/dummy_data.py:82
↓ 2 callersMethodsave
(self, filename, ignore_classifier=False)
dn3/trainable/models.py:177
↓ 2 callersMethodsave_best
Create a snapshot of what is being currently trained for re-laoding with the :py:meth:`load_best()` method. Returns -------
dn3/trainable/processes.py:369
↓ 2 callersFunctionstringify_channel_mapping
(original_names: list, mapping: np.ndarray)
dn3/transforms/channels.py:292
↓ 2 callersMethodtrunc_norm
(mean, std, max_diff)
dn3/transforms/instance.py:293
↓ 1 callersMethod__add__
(self, sessions)
dn3/data/dataset.py:523
↓ 1 callersMethod__add__
(self, thinker, person_id=None, return_session_id=None, return_trial_id=None)
dn3/data/dataset.py:819
↓ 1 callersMethod__getitem__
(self, item, return_id=False)
dn3/data/dataset.py:546
↓ 1 callersMethod__init__
Parses dataset entries in DN3 config Parameters ---------- name : str The name of the dataset specifi
dn3/configuratron/config.py:151
↓ 1 callersMethod_apply
(self, lam_fn)
dn3/data/dataset.py:809
↓ 1 callersFunction_binarize_two_class
(y_p)
dn3/metrics/base.py:28
↓ 1 callersMethod_calculate_similarity
(self, z, c, negatives)
dn3/trainable/processes.py:898
↓ 1 callersFunction_check_num_and_get_types
(type_dict: OrderedDict)
dn3/transforms/channels.py:86
↓ 1 callersMethod_construct_session_from_config
(self, session, sess_id, thinker_id)
dn3/configuratron/config.py:554
↓ 1 callersMethod_construct_thinker_from_config
(self, thinker: list, thinker_id)
dn3/configuratron/config.py:641
↓ 1 callersFunction_deep_1010
(map, names, eog, ear_ref, extra)
dn3/transforms/channels.py:61
↓ 1 callersMethod_determine_drw_weights
(self, beta=0.9999)
dn3/trainable/processes.py:805
↓ 1 callersMethod_determine_path
(toplevel, relative_directory=None)
dn3/configuratron/config.py:318
↓ 1 callersMethod_generate_negatives
Generate negative samples to compare each sequence location against
dn3/trainable/processes.py:882
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