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github.com/SPOClab-ca/dn3
/ functions
Functions
482 in github.com/SPOClab-ca/dn3
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Functions
482
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Types & classes
87
↓ 1 callers
Method
_get_ds_data
(self)
dn3/configuratron/extensions.py:24
↓ 1 callers
Method
_get_person_name
(self, f: Path)
dn3/configuratron/config.py:388
↓ 1 callers
Method
_get_start_offset
(self, full_length)
dn3/transforms/instance.py:260
↓ 1 callers
Function
_handle_cropped
A straightforward helper that simply averages multiple crops if they are present. Parameters ---------- y_p: np.ndarray The
dn3/metrics/base.py:6
↓ 1 callers
Function
_heuristic_resolution
(old_type_dict: OrderedDict)
dn3/transforms/channels.py:134
↓ 1 callers
Method
_is_narrowly_excluded
(self, person_name, session_name)
dn3/configuratron/config.py:357
↓ 1 callers
Function
_likely_eeg_channel
(name)
dn3/transforms/channels.py:126
↓ 1 callers
Method
_load_raw
(self, path: Path)
dn3/configuratron/config.py:494
↓ 1 callers
Method
_optimize_dataloader_kwargs
(self, num_worker_cap=6, **loader_kwargs)
dn3/trainable/processes.py:137
↓ 1 callers
Method
_picks_as_types
(picks)
dn3/configuratron/config.py:309
↓ 1 callers
Method
_prepare_session
(raw, tlen, decimate, desired_sfreq, desired_samples, picks, exclude_channels, rename_channels,
dn3/configuratron/config.py:508
↓ 1 callers
Method
_raw_workaround
(self, raw)
dn3/data/dataset.py:314
↓ 1 callers
Method
add_custom_raw_loader
This is used to provide a custom implementation of taking a filename, and returning a :any:`mne.io.Raw()` instance. If properly const
dn3/configuratron/config.py:452
↓ 1 callers
Method
add_extension_handler
Provide callable code to create a raw instance from sessions with certain file extensions. This is useful for handling of custom file
dn3/configuratron/config.py:323
↓ 1 callers
Method
add_metrics
(self, metrics: dict, evaluation_only=False)
dn3/trainable/processes.py:132
↓ 1 callers
Method
add_progress_callbacks
Add callbacks to be invoked on successful loading of session and/or thinker. Optionally, these can modify the respective loaded insta
dn3/configuratron/config.py:476
↓ 1 callers
Method
add_transform
(self, transform, deep=False)
dn3/data/dataset.py:1122
↓ 1 callers
Method
auto_mapping
Generates a mapping of sessions and people of the dataset, assuming files are stored in the structure: `toplevel`/(*optional - <versi
dn3/configuratron/config.py:405
↓ 1 callers
Method
backward
(self, loss)
dn3/trainable/processes.py:261
↓ 1 callers
Function
balanced_oversampling
(dataset, replacement=True)
dn3/trainable/processes.py:784
↓ 1 callers
Function
balanced_undersampling
(dataset, replacement=False)
dn3/trainable/processes.py:778
↓ 1 callers
Method
build_network
This method is used to add trainable modules to the process. Rather than placing objects for training in the __init__ method, they sh
dn3/trainable/processes.py:178
↓ 1 callers
Method
collect_statistic
(self)
dn3/data/utils.py:218
↓ 1 callers
Function
create_ldam_loss
(training_dataset)
dn3/trainable/processes.py:827
↓ 1 callers
Method
deviation_threshold_rejection
(self, reject_iterations=10, num_deviations=4)
dn3/data/utils.py:246
↓ 1 callers
Function
download_test_dataset
()
tests/testConfig.py:17
↓ 1 callers
Method
dump_dataset
Dumps the dataset to the directory specified by toplevel, with a single file per index. Parameters ---------- toplev
dn3/data/dataset.py:1156
↓ 1 callers
Method
features_forward
(self, x)
dn3/trainable/models.py:165
↓ 1 callers
Method
features_forward
(self, x)
dn3/trainable/experimental.py:76
↓ 1 callers
Method
fit
sklearn/keras-like convenience method to simply proceed with training across multiple epochs of the provided dataset Paramet
dn3/trainable/processes.py:427
↓ 1 callers
Method
forward
(self, x, target)
dn3/trainable/processes.py:813
↓ 1 callers
Method
from_dataset
Create a classifier from a dataset. Parameters ---------- dataset modelargs: dict Options
dn3/trainable/models.py:73
↓ 1 callers
Method
get_configuratron_exclusions
Creates exclusions to be used by configuratron on next dataset loading. Parameters ---------- save_to_file : str (pa
dn3/data/utils.py:314
↓ 1 callers
Method
get_pseudo_mapping
(self, exclusion_cb)
dn3/configuratron/extensions.py:29
↓ 1 callers
Method
get_sessions
Accumulates all the sessions from each thinker in the dataset in a nested dictionary. Returns ------- session_dict:
dn3/data/dataset.py:960
↓ 1 callers
Method
is_excluded
(self, f: Path, person_name, session_name)
dn3/configuratron/config.py:367
↓ 1 callers
Method
load
(self, filename, include_classifier=False, freeze_features=True)
dn3/trainable/experimental.py:57
↓ 1 callers
Method
load_best
Load the parameters as saved by :py:meth:`save_best()`. Parameters ---------- best: Any
dn3/trainable/processes.py:380
↓ 1 callers
Function
make_epochs_from_raw
(raw: mne.io.Raw, tmin, tlen, event_ids=None, baseline=None, decim=1, filter_bp=None,
dn3/utils.py:91
↓ 1 callers
Method
make_new_classification_layer
This allows for a distinction between the classification layer(s) and the rest of the network. Using a basic formulation of a network
dn3/trainable/models.py:120
↓ 1 callers
Function
map_dataset_channels_deep_1010
Maps channels as stored by a :any:`DN3ataset` to the Deep1010 format, will automatically map EOG and extra channels by type. Parameters
dn3/transforms/channels.py:224
↓ 1 callers
Function
match_old_new_idx
(old_idx, new_idx_set: list)
dn3/transforms/channels.py:296
↓ 1 callers
Function
namespaceify
(v)
dn3/configuratron/config.py:69
↓ 1 callers
Method
parameters
(self)
dn3/trainable/experimental.py:121
↓ 1 callers
Method
predict
Determine the outputs for all loaded data from the dataset Parameters ---------- dataset: DN3ataset, DataLoader
dn3/trainable/processes.py:308
↓ 1 callers
Method
save
(self, filename)
dn3/trainable/layers.py:262
↓ 1 callers
Method
scan_toplevel
Scan the provided toplevel for all files that may belong to the dataset. Returns ------- files: list
dn3/configuratron/config.py:339
↓ 1 callers
Function
simple_zscoring
(data: torch.Tensor)
tests/testTransforms.py:13
↓ 1 callers
Function
skip_inds_from_bad_spans
(epochs: mne.Epochs, bad_spans: list)
dn3/utils.py:114
↓ 1 callers
Method
to_numpy
Commits the dataset to numpy-formatted arrays. Useful for saving dataset to disk, or preparing for tools that expect numpy-formatted
dn3/data/dataset.py:137
↓ 1 callers
Method
train_step
(self, *inputs)
dn3/trainable/processes.py:270
Method
__call__
Preprocess a particular recording. This is allowed to modify aspects of the recording in-place, but is not strictly advised.
dn3/transforms/preprocessors.py:15
Method
__call__
(self, session, session_id=0, thinker_id=0)
dn3/transforms/preprocessors.py:55
Method
__call__
Modifies a batch of tensors. Parameters ---------- x : torch.Tensor, tuple A batch of trial instance ten
dn3/transforms/batch.py:18
Method
__call__
(self, x, training=False)
dn3/transforms/batch.py:55
Method
__call__
(self, x, training=False)
dn3/transforms/batch.py:86
Method
__call__
Modifies a batch of tensors. Parameters ---------- x : torch.Tensor, tuple The trial tensor, not includin
dn3/transforms/instance.py:39
Method
__call__
(self, *x)
dn3/transforms/instance.py:109
Method
__call__
(self, x)
dn3/transforms/instance.py:137
Method
__call__
(self, x)
dn3/transforms/instance.py:164
Method
__call__
(self, x)
dn3/transforms/instance.py:202
Method
__call__
(self, x)
dn3/transforms/instance.py:228
Method
__call__
(self, x)
dn3/transforms/instance.py:272
Method
__call__
(self, x)
dn3/transforms/instance.py:302
Method
__call__
(self, x)
dn3/transforms/instance.py:354
Method
__call__
(self, *x)
dn3/transforms/instance.py:394
Method
__call__
(self, *x)
dn3/transforms/instance.py:428
Method
__call__
(self, x)
dn3/transforms/instance.py:445
Method
__call__
(self, *x)
dn3/transforms/instance.py:463
Method
__call__
(self, x)
dn3/transforms/instance.py:483
Method
__call__
(self, *x)
dn3/transforms/instance.py:525
Method
__call__
(self, *x)
dn3/transforms/instance.py:560
Method
__call__
(self, x)
dn3/trainable/experimental.py:149
Method
__call__
(self, x)
tests/testDataset.py:12
Method
__getitem__
(self, item)
dn3/configuratron/config.py:61
Method
__getitem__
(self, item)
dn3/data/utils.py:52
Method
__getitem__
(self, item)
dn3/data/dataset.py:31
Method
__getitem__
(self, index)
dn3/data/dataset.py:317
Method
__getitem__
(self, index)
dn3/data/dataset.py:389
Method
__getitem__
(self, item)
dn3/data/dataset.py:845
Method
__getitem__
(self, index)
dn3/data/dataset.py:1246
Method
__init__
(self, n_classes, smoothing=0.0, dim=-1)
dn3/utils.py:136
Method
__init__
(self, d: dict)
dn3/configuratron/config.py:49
Method
__init__
Parses DN3 configuration files. Checking the DN3 token for listed datasets. Parameters ---------- config_filename :
dn3/configuratron/config.py:84
Method
__init__
This provides a workaround for the normal raw recording pipeline so that files are not loaded in any way until they are needed. MNE's
dn3/configuratron/config.py:767
Method
__init__
(self, ds_name, data_location, **kwargs)
dn3/configuratron/extensions.py:15
Method
__init__
This integrates the loading of multiple datasets, and facilitates over-sampling smaller ones to prevent larger datasets from crowding
dn3/data/utils.py:8
Method
__init__
With larger datasets, it may be prudent to triage the data based on global statistics. Here spans of time are rejected based on a pro
dn3/data/utils.py:148
Method
__init__
Base class for that specifies the interface for DN3 datasets.
dn3/data/dataset.py:22
Method
__init__
(self, info, session_id, person_id, tlen, ch_ind_picks=None)
dn3/data/dataset.py:189
Method
__init__
Interface for bridging mne Raw instances as PyTorch compatible "Dataset". Parameters ---------- raw : mne.io.Raw
dn3/data/dataset.py:246
Method
__init__
Wraps :any:`mne.Epochs` instances so that they conform to the :any:`Recording` API. Parameters ---------- epochs
dn3/data/dataset.py:352
Method
__init__
(self, dataset_name, data_max=None, data_min=None, excluded_people=None, targets=None)
dn3/data/dataset.py:690
Method
__init__
Collects recordings from multiple people, intended to be of the same task, at different times or conditions. Optionally, can
dn3/data/dataset.py:708
Method
__init__
(self, toplevel, cache_all=False, summary_file='dataset-dump.npz', info=None, cache_chunk_factor=0.1)
dn3/data/dataset.py:1201
Method
__init__
(self, inds=None, complex_tolerance=1e-4)
dn3/transforms/preprocessors.py:49
Method
__init__
Uniformly crops the time-dimensions of a batch. Parameters ---------- max_crop_frac: float Th
dn3/transforms/batch.py:41
Method
__init__
Crops the time dimension of an entire batch. Parameters ---------- end_crop_frac: float If th
dn3/transforms/batch.py:68
Method
__init__
Trial transforms are, for the most part, simply operations that are performed on the loaded tensors when they are fetched via the :me
dn3/transforms/instance.py:28
Method
__init__
(self)
dn3/transforms/instance.py:106
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