[c36663]: / test / unit_tests / samplers / test_samplers.py

Download this file

363 lines (298 with data), 12.7 kB

  1
  2
  3
  4
  5
  6
  7
  8
  9
 10
 11
 12
 13
 14
 15
 16
 17
 18
 19
 20
 21
 22
 23
 24
 25
 26
 27
 28
 29
 30
 31
 32
 33
 34
 35
 36
 37
 38
 39
 40
 41
 42
 43
 44
 45
 46
 47
 48
 49
 50
 51
 52
 53
 54
 55
 56
 57
 58
 59
 60
 61
 62
 63
 64
 65
 66
 67
 68
 69
 70
 71
 72
 73
 74
 75
 76
 77
 78
 79
 80
 81
 82
 83
 84
 85
 86
 87
 88
 89
 90
 91
 92
 93
 94
 95
 96
 97
 98
 99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
"""
Test for samplers.
"""
# Authors: Hubert Banville <hubert.jbanville@gmail.com>
# Young Truong <dt.young112@gmail.com>
#
# License: BSD (3-clause)
import bisect
import platform
import pytest
import numpy as np
import pandas as pd
from braindecode.samplers import (
RecordingSampler,
DistributedRecordingSampler,
SequenceSampler,
BalancedSequenceSampler,
)
from braindecode.samplers.ssl import RelativePositioningSampler, DistributedRelativePositioningSampler
from braindecode.datasets import BaseDataset, BaseConcatDataset
from braindecode.datasets.moabb import fetch_data_with_moabb
from braindecode.preprocessing.windowers import (
create_fixed_length_windows,
create_windows_from_events,
)
import torch.distributed as dist
import torch.multiprocessing as mp
@pytest.fixture(scope="module")
def windows_ds():
raws, description = fetch_data_with_moabb(dataset_name="BNCI2014001", subject_ids=4)
ds = [BaseDataset(raws[i], description.iloc[i]) for i in range(3)]
concat_ds = BaseConcatDataset(ds)
windows_ds = create_fixed_length_windows(
concat_ds=concat_ds,
start_offset_samples=0,
stop_offset_samples=None,
window_size_samples=500,
window_stride_samples=500,
drop_last_window=False,
preload=False,
)
return windows_ds
@pytest.fixture(scope="module")
def target_windows_ds():
raws, description = fetch_data_with_moabb(dataset_name="BNCI2014001", subject_ids=4)
ds = [BaseDataset(raws[i], description.iloc[i]) for i in range(3)]
concat_ds = BaseConcatDataset(ds)
windows_ds = create_windows_from_events(
concat_ds,
trial_start_offset_samples=0,
trial_stop_offset_samples=0,
window_size_samples=None,
window_stride_samples=None,
drop_last_window=False,
)
return windows_ds
def find_dataset_ind(windows_ds, win_ind):
"""Taken from torch.utils.data.dataset.ConcatDataset."""
return bisect.bisect_right(windows_ds.cumulative_sizes, win_ind)
def test_recording_sampler(windows_ds):
sampler = RecordingSampler(windows_ds.get_metadata(), random_state=87)
assert sampler.n_recordings == windows_ds.description.shape[0]
# Test info attribute
assert isinstance(sampler.info, pd.DataFrame)
assert isinstance(sampler.info.index, pd.MultiIndex)
inds = np.concatenate(sampler.info["index"].values)
assert len(inds) == len(windows_ds)
assert len(inds) == len(set(inds))
# Test methods
for _ in range(100):
rec_ind = sampler.sample_recording()
assert rec_ind in range(windows_ds.description.shape[0])
win_ind, rec_ind2 = sampler.sample_window(rec_ind=rec_ind)
dataset_ind = find_dataset_ind(windows_ds, win_ind)
assert rec_ind2 == rec_ind == dataset_ind
X, y, z = windows_ds[win_ind]
win_ind, rec_ind = sampler.sample_window(rec_ind=None)
assert rec_ind in range(windows_ds.description.shape[0])
def dist_sampler_init_process(rank, world_size, windows_ds):
"""Initialize the process group for multi-CPU training."""
dist.init_process_group(
backend="gloo",
init_method="tcp://127.0.0.1:29500", # Localhost for single machine
rank=rank,
world_size=world_size
)
print(f"Process {rank} initialized")
sampler = DistributedRecordingSampler(windows_ds.get_metadata(), random_state=87)
if world_size == 1:
sampler_single = RecordingSampler(windows_ds.get_metadata(), random_state=87)
assert sampler.n_recordings == windows_ds.description.shape[0] == sampler_single.n_recordings
assert len(sampler.dataset) == windows_ds.description.shape[0]
assert sampler.n_recordings <= windows_ds.description.shape[0] // world_size
print(f"Rank {rank} has {sampler.n_recordings} datasets after splitting")
# Test info attribute
assert isinstance(sampler.info, pd.DataFrame)
assert isinstance(sampler.info.index, pd.MultiIndex)
inds = np.concatenate(sampler.info["index"].values)
assert len(inds) == len(windows_ds)
assert len(inds) == len(set(inds))
# Test methods
for _ in range(100):
rec_ind = sampler.sample_recording()
assert rec_ind in range(windows_ds.description.shape[0])
win_ind, rec_ind2 = sampler.sample_window(rec_ind=rec_ind)
dataset_ind = find_dataset_ind(windows_ds, win_ind)
assert rec_ind2 == rec_ind == dataset_ind
X, y, z = windows_ds[win_ind]
win_ind, rec_ind = sampler.sample_window(rec_ind=None)
assert rec_ind in range(windows_ds.description.shape[0])
# Cleanup
dist.destroy_process_group()
@pytest.mark.skipif(platform.system() == 'Windows',
reason="Not supported on Windows because of use_libuv compatibility")
def test_distributed_recording_sampler(windows_ds):
world_size = 1 # Test single process - no dataset splitting
mp.spawn(dist_sampler_init_process, args=(world_size,windows_ds), nprocs=world_size, join=True)
world_size = 3 # Test multiple processes - dataset splitting
mp.spawn(dist_sampler_init_process, args=(world_size,windows_ds), nprocs=world_size, join=True)
@pytest.mark.parametrize("same_rec_neg", [True, False])
def test_relative_positioning_sampler(windows_ds, same_rec_neg):
tau_pos, tau_neg = 2000, 3000
n_examples = 100
sampler = RelativePositioningSampler(
windows_ds.get_metadata(),
tau_pos=tau_pos,
tau_neg=tau_neg,
n_examples=n_examples,
tau_max=None,
same_rec_neg=same_rec_neg,
random_state=33,
)
pairs = [pair for pair in sampler]
pairs_df = pd.DataFrame(pairs, columns=["win_ind1", "win_ind2", "y"])
pairs_df["diff"] = pairs_df.apply(
lambda x: abs(
windows_ds[int(x["win_ind1"])][2][1] - windows_ds[int(x["win_ind2"])][2][1]
),
axis=1,
)
pairs_df["same_rec"] = pairs_df.apply(
lambda x: (
find_dataset_ind(windows_ds, int(x["win_ind1"]))
== find_dataset_ind(windows_ds, int(x["win_ind2"]))
),
axis=1,
)
assert len(pairs) == n_examples == len(sampler)
assert all(pairs_df.loc[pairs_df["y"] == 1, "diff"] <= tau_pos)
if same_rec_neg:
assert all(pairs_df.loc[pairs_df["y"] == 0, "diff"] >= tau_neg)
assert all(pairs_df["same_rec"] == same_rec_neg)
else:
assert all(pairs_df.loc[pairs_df["y"] == 0, "same_rec"] == False) # noqa: E712
assert all(pairs_df.loc[pairs_df["y"] == 1, "same_rec"] == True) # noqa: E712
assert abs(np.diff(pairs_df["y"].value_counts())) < 20
def test_relative_positioning_sampler_presample(windows_ds):
tau_pos, tau_neg = 2000, 3000
n_examples = 100
sampler = RelativePositioningSampler(
windows_ds.get_metadata(),
tau_pos=tau_pos,
tau_neg=tau_neg,
n_examples=n_examples,
tau_max=None,
same_rec_neg=True,
random_state=33,
)
sampler.presample()
assert hasattr(sampler, "examples")
assert len(sampler.examples) == n_examples
pairs = [pair for pair in sampler]
pairs2 = [pair for pair in sampler]
assert np.array_equal(sampler.examples, pairs)
assert np.array_equal(sampler.examples, pairs2)
def distributed_relative_positioning_sampler_init_process(rank, world_size, windows_ds, same_rec_neg):
dist.init_process_group(
backend="gloo",
init_method="tcp://127.0.0.1:29500", # Localhost for single machine
rank=rank,
world_size=world_size
)
print(f"Process {rank} initialized")
tau_pos, tau_neg = 2000, 3000
n_examples = 100
sampler = DistributedRelativePositioningSampler(
windows_ds.get_metadata(),
tau_pos=tau_pos,
tau_neg=tau_neg,
n_examples=n_examples,
tau_max=None,
same_rec_neg=same_rec_neg,
random_state=33,
)
pairs = [pair for pair in sampler]
pairs_df = pd.DataFrame(pairs, columns=["win_ind1", "win_ind2", "y"])
pairs_df["diff"] = pairs_df.apply(
lambda x: abs(
windows_ds[int(x["win_ind1"])][2][1] - windows_ds[int(x["win_ind2"])][2][1]
),
axis=1,
)
pairs_df["same_rec"] = pairs_df.apply(
lambda x: (
find_dataset_ind(windows_ds, int(x["win_ind1"]))
== find_dataset_ind(windows_ds, int(x["win_ind2"]))
),
axis=1,
)
assert len(pairs) == len(sampler) <= n_examples // world_size
assert all(pairs_df.loc[pairs_df["y"] == 1, "diff"] <= tau_pos)
if same_rec_neg:
assert all(pairs_df.loc[pairs_df["y"] == 0, "diff"] >= tau_neg)
assert all(pairs_df["same_rec"] == same_rec_neg)
else:
assert all(pairs_df.loc[pairs_df["y"] == 0, "same_rec"] == False) # noqa: E712
assert all(pairs_df.loc[pairs_df["y"] == 1, "same_rec"] == True) # noqa: E712
assert abs(np.diff(pairs_df["y"].value_counts())) < 20
@pytest.mark.skipif(platform.system() == 'Windows',
reason="Not supported on Windows because of use_libuv compatibility")
@pytest.mark.parametrize("same_rec_neg", [True, False])
def test_distributed_relative_positioning_sampler(windows_ds, same_rec_neg):
world_size = 1
mp.spawn(distributed_relative_positioning_sampler_init_process, args=(world_size, windows_ds, same_rec_neg), nprocs=world_size, join=True)
@pytest.mark.parametrize("n_windows,n_windows_stride", [[10, 5], [10, 100], [1, 1]])
def test_sequence_sampler(windows_ds, n_windows, n_windows_stride):
sampler = SequenceSampler(
windows_ds.get_metadata(), n_windows, n_windows_stride, random_state=31
)
seqs = [seq for seq in sampler]
seq_lens = [
(len(ds) - n_windows) // n_windows_stride + 1 for ds in windows_ds.datasets
]
file_ids = np.concatenate([[i] * length for i, length in enumerate(seq_lens)])
n_seqs = sum(seq_lens)
assert len(seqs) == n_seqs
assert all([len(s) == n_windows for s in seqs])
for i in range(seq_lens[0] - 1):
np.testing.assert_array_equal(
seqs[i][n_windows_stride:], seqs[i + 1][:-n_windows_stride]
)
assert (sampler.file_ids == file_ids).all()
# for randomized sampler
sampler = SequenceSampler(
windows_ds.get_metadata(),
n_windows,
n_windows_stride,
randomize=True,
random_state=31,
)
seqs = [seq for seq in sampler]
seq_lens = [
(len(ds) - n_windows) // n_windows_stride + 1 for ds in windows_ds.datasets
]
file_ids = np.concatenate([[i] * length for i, length in enumerate(seq_lens)])
n_seqs = sum(seq_lens)
assert len(seqs) == n_seqs
assert all([len(s) == n_windows for s in seqs])
@pytest.mark.parametrize("n_sequences,n_windows", [[10, 2], [2, 40], [99, 1]])
def test_balanced_sequence_sampler(target_windows_ds, n_sequences, n_windows):
md = target_windows_ds.get_metadata()
sampler = BalancedSequenceSampler(
md, n_windows, n_sequences=n_sequences, random_state=87
)
seqs = [seq for seq in sampler]
assert len(seqs) == n_sequences
assert all([len(s) == n_windows for s in seqs])
# Make sure the sequences are valid
for seq in seqs:
assert all(np.diff(seq) == 1) # windows must be consecutive
seq_md = md.iloc[seq[0] : seq[-1] + 1]
for c in ["subject", "session", "run"]:
assert len(seq_md[c].unique()) == 1
# Make sure the target is always in the sequence
for _ in range(100):
start_ind, rec_ind, class_ind = sampler._sample_seq_start_ind()
seq_targets = md.iloc[start_ind : start_ind + n_windows + 1]["target"]
assert class_ind in seq_targets.values
rec_info = sampler.info.iloc[rec_ind].name
rec_info_md = md.iloc[start_ind][["subject", "session", "run"]]
assert rec_info == tuple(rec_info_md.tolist())
def test_balanced_sequence_sampler_single_category(target_windows_ds):
"""Test the case where there's only one category in the metadata, e.g.
'subject'.
"""
n_windows = 3
n_sequences = 10
md = target_windows_ds.get_metadata().drop(columns=["session", "run"])
sampler = BalancedSequenceSampler(
md, n_windows, n_sequences=n_sequences, random_state=87
)
seqs = [seq for seq in sampler]
assert len(seqs) == n_sequences
assert all([len(s) == n_windows for s in seqs])
def test_balanced_sequence_sampler_no_targets(windows_ds):
md = windows_ds.get_metadata().drop(columns="target")
with pytest.raises(ValueError):
BalancedSequenceSampler(md, 10, n_sequences=5, random_state=87)