def test_pca_models_and_project_new():
from sklearn.decomposition import IncrementalPCA
if Path('toy_waveforms_1seg/principal_components').is_dir():
shutil.rmtree('toy_waveforms_1seg/principal_components')
we = WaveformExtractor.load_from_folder('toy_waveforms_1seg')
wfs0 = we.get_waveforms(unit_id=we.sorting.unit_ids[0])
n_samples = wfs0.shape[1]
n_channels = wfs0.shape[2]
n_components = 5
# local
pc_local = compute_principal_components(we, n_components=n_components,
load_if_exists=True, mode="by_channel_local")
all_pca = pc_local.get_pca_model()
assert len(all_pca) == we.recording.get_num_channels()
# project
new_waveforms = np.random.randn(100, n_samples, n_channels)
new_proj = pc_local.project_new(new_waveforms)
assert new_proj.shape == (100, n_components, n_channels)
# global
if Path('toy_waveforms_1seg/principal_components').is_dir():
shutil.rmtree('toy_waveforms_1seg/principal_components')
pc_global = compute_principal_components(we, n_components=n_components,
load_if_exists=True, mode="by_channel_global")
all_pca = pc_global.get_pca_model()
assert isinstance(all_pca, IncrementalPCA)
# project
new_waveforms = np.random.randn(100, n_samples, n_channels)
new_proj = pc_global.project_new(new_waveforms)
assert new_proj.shape == (100, n_components, n_channels)
# concatenated
if Path('toy_waveforms_1seg/principal_components').is_dir():
shutil.rmtree('toy_waveforms_1seg/principal_components')
pc_concatenated = compute_principal_components(we, n_components=n_components,
load_if_exists=True, mode="concatenated")
all_pca = pc_concatenated.get_pca_model()
assert isinstance(all_pca, IncrementalPCA)
# project
new_waveforms = np.random.randn(100, n_samples, n_channels)
new_proj = pc_concatenated.project_new(new_waveforms)
assert new_proj.shape == (100, n_components)
def test_select_units():
we = WaveformExtractor.load_from_folder('toy_waveforms_1seg')
pc = compute_principal_components(we, load_if_exists=True)
keep_units = we.sorting.get_unit_ids()[::2]
we_filt = we.select_units(keep_units, 'toy_waveforms_1seg_filt')
assert "principal_components" in we_filt.get_available_extension_names()
def test_compute_principal_components_for_all_spikes():
we = WaveformExtractor.load_from_folder('toy_waveforms_1seg')
pc = compute_principal_components(we, load_if_exists=True)
print(pc)
pc_file = 'all_pc.npy'
pc.run_for_all_spikes(pc_file, max_channels_per_template=7, chunk_size=10000, n_jobs=1)
all_pc = np.load(pc_file)
def test_compute_principal_components_for_all_spikes():
we = WaveformExtractor.load_from_folder('toy_waveforms_1seg')
pc = compute_principal_components(we, load_if_exists=True)
print(pc)
pc_file1 = 'all_pc1.npy'
pc.run_for_all_spikes(pc_file1, max_channels_per_template=7, chunk_size=10000, n_jobs=1)
all_pc1 = np.load(pc_file1)
pc_file2 = 'all_pc2.npy'
pc.run_for_all_spikes(pc_file2, max_channels_per_template=7, chunk_size=10000, n_jobs=2)
all_pc2 = np.load(pc_file2)
assert np.array_equal(all_pc1, all_pc2)
def test_compute_principal_components():
we = WaveformExtractor.load_from_folder('toy_waveforms')
pc = compute_principal_components(we, load_if_exists=True)
print(pc)