raw_data_ivm = ephys.load_raw_data(raw_data_filename, numchannels=num_ivm_channels, dtype=amp_dtype).dataMatrix
data_cube_filename = join(base_dir, data_cube_dir, 'baselined_data_cube.npy')
autocor_bin_number = 100
cluster_info_filename = join(base_dir, tsne_dir, 'cluster_info.pkl')
prb_file = r'D:\Data\George\Projects\SpikeSorting\Joana_Paired_128ch\2015-09-03\Analysis\klustakwik\128ch_passive_imec.prb'
tsne_cluster.gui_manual_cluster_tsne_spikes(tsne_array_or_filename=tsne_filename,
spike_times_list_or_filename=kwik_filename,
time_samples_h5_dir=time_samples_h5_dir,
raw_extracellular_data=None,
num_of_points_for_baseline=num_of_points_for_baseline,
cut_extracellular_data_or_filename=data_cube_filename,
shape_of_cut_extracellular_data=shape_of_cut_extracellular_data,
cube_type=cube_type,
sampling_freq=sampling_freq,
autocor_bin_number=autocor_bin_number,
cluster_info_file=cluster_info_filename,
use_existing_cluster=True,
spike_indices_to_use=spike_indices_to_use,
prb_file=prb_file,
k4=True,
verbose=True)
# Make video from interim data
label_path = r'D:\Data\George\Projects\SpikeSorting\Joana_Paired_128ch\2015-09-03\Analysis\klustakwik\threshold_6_5std\cluster_info.pkl'
pkl_file = open(label_path, 'rb')
labels = pickle.load(pkl_file)
pkl_file.close()
spike_indices_to_use = None
num_of_spikes = len(spikes_used)
shape_of_cut_extracellular_data = (num_ivm_channels, num_of_points_in_spike_trig, num_of_spikes)
raw_data_filename = os.path.join(base_dir, data_dir, 'amplifier2015-09-03T21_18_47.bin')
raw_data_ivm = ephys.load_raw_data(raw_data_filename, numchannels=num_ivm_channels, dtype=amp_dtype).dataMatrix
tsne_cluster.gui_manual_cluster_tsne_spikes(tsne_array_or_filename=template_features_tsne,
spike_times_list_or_filename=np.reshape(spike_times_kilosort,
(len(spike_times_kilosort))),
raw_extracellular_data=None,
num_of_points_for_baseline=num_of_points_for_baseline,
cut_extracellular_data_or_filename=data_cube_filename,
shape_of_cut_extracellular_data=shape_of_cut_extracellular_data,
cube_type=cube_type,
sampling_freq=sampling_freq,
autocor_bin_number=autocor_bin_number,
cluster_info_file=cluster_info_filename,
use_existing_cluster=True,
spike_indices_to_use=spike_indices_to_use,
prb_file=prb_file,
k4=True,
verbose=True)
# ======================================================================================================================
# Test code to sort out the SHIFT bug in Bokeh
from bokeh.client import push_session
from bokeh.layouts import column
if spike_indices_to_use is not None:
num_of_spikes = len(spike_indices_to_use)
shape_of_cut_extracellular_data = (num_ivm_channels, num_of_points_in_spike_trig, num_of_spikes)
raw_data_filename = os.path.join(base_dir, data_dir, 'amplifier2015-09-03T21_18_47.bin')
raw_data_ivm = ephys.load_raw_data(raw_data_filename, numchannels=num_ivm_channels, dtype=amp_dtype).dataMatrix
tsne_cluster.gui_manual_cluster_tsne_spikes(tsne_array_or_filename=np.transpose(template_features_tsne)[:, indices_of_common_spikes_in_kilosort.tolist()],
spike_times_list_or_filename=common_spikes,
raw_extracellular_data=raw_data_ivm,
num_of_points_for_baseline=num_of_points_for_baseline,
cut_extracellular_data_or_filename=data_cube_filename,
shape_of_cut_extracellular_data=shape_of_cut_extracellular_data,
cube_type=cube_type,
sampling_freq=sampling_freq,
autocor_bin_number=autocor_bin_number,
cluster_info_file=cluster_info_filename,
use_existing_cluster=False,
spike_indices_to_use=spike_indices_to_use,
prb_file=prb_file,
k4=True,
verbose=True)
# manual clustering all of the kilosort template_feature_tsne data
cluster_info_filename = os.path.join(kilosort_path, 'tsne\\cluster_info_full.pkl')
spike_indices_to_use = None
num_of_spikes = np.shape(template_features_tsne)[0]
shape_of_cut_extracellular_data = (num_ivm_channels, num_of_points_in_spike_trig, num_of_spikes)
