def make_pca_features_from_spk(SpkFileName):
"""
Make pca features from a .spk file and save them to features.txt
"""
SpkDir = os.path.dirname(SpkFileName)
n_ch,sample_rate,s_before,s_after = get_pars_from_xml2(find_file_with_ext(SpkDir,"xml",True))
X_ns = np.fromfile(SpkFileName,dtype=np.int16).reshape(-1,s_before+s_after,n_ch)[:,:,0]
Feats_ss = compute_pcs(X_ns)
save_feature_info(Feats_ss,s_before,s_after,sample_rate)
def make_pca_features_from_spk(SpkFileName):
"""
Make pca features from a .spk file and save them to features.txt
"""
SpkDir = os.path.dirname(SpkFileName)
n_ch, sample_rate, s_before, s_after = get_pars_from_xml2(
find_file_with_ext(SpkDir, "xml", True))
X_ns = np.fromfile(SpkFileName,
dtype=np.int16).reshape(-1, s_before + s_after,
n_ch)[:, :, 0]
Feats_ss = compute_pcs(X_ns)
save_feature_info(Feats_ss, s_before, s_after, sample_rate)
def combine_h5s(*dirs):
"combine the data from a bunch of h5 files. Also make klusters files"
outdirname = common_start(dirs) + "COMBINED"
print dirs
print os.path.abspath(os.curdir)
h5files = [
tables.openFile(find_file_with_ext(dir, ".h5"), mode="r")
for dir in dirs
]
spike_tables = [h5file.root.SpikeTable for h5file in h5files]
with indir(outdirname):
global N_CH, S_TOTAL, FPC, SAMPLE_RATE
num_ch = [table.cols.st.shape[1] for table in spike_tables]
N_CH = max(num_ch)
S_TOTAL = table.cols.wave.shape[1]
FPC = table.cols.fet.shape[2]
new_file = tables.openFile(outdirname + ".h5", mode="w")
new_table = new_file.createTable("/", "SpikeTable", spike_dtype())
clu_start = np.arange(0, 5000, 100)
SAMPLE_RATE = 25000. # Doesn't actually matter for this script, but write_xml wants it
# files in same order as tables
clu2DatChannels = {}
for (i_file, h5file) in enumerate(h5files):
for clu in xrange(clu_start[i_file], clu_start[i_file + 1]):
clu2DatChannels[clu] = list(h5file.root.DatChannels)
dump("clu2DatChannels.pickle", clu2DatChannels)
triples = [(row["time"], i_spike, i_table)
for (i_table, table) in enumerate(spike_tables)
for (i_spike, row) in enumerate(table)]
for time, i_spike, i_table in sorted(triples, key=lambda tup: tup[0]):
oldrow = spike_tables[i_table][i_spike]
new_table.row["time"] = time
new_table.row["fet"] = zero_pad(oldrow["fet"], N_CH)
new_table.row["st"] = zero_pad(oldrow["st"], N_CH)
new_table.row["wave"] = zero_pad(oldrow["wave"], N_CH)
new_table.row["clu"] = oldrow["clu"] + clu_start[i_table]
new_table.row.append()
new_table.flush()
klusters_files(new_table, outdirname)
new_file.close()
def combine_h5s(*dirs):
"combine the data from a bunch of h5 files. Also make klusters files"
outdirname = common_start(dirs) + "COMBINED"
print dirs
print os.path.abspath(os.curdir)
h5files = [tables.openFile(find_file_with_ext(dir,".h5"),mode="r") for dir in dirs]
spike_tables = [h5file.root.SpikeTable for h5file in h5files]
with indir(outdirname):
global N_CH,S_TOTAL,FPC,SAMPLE_RATE
num_ch =[table.cols.st.shape[1] for table in spike_tables]
N_CH = max(num_ch)
S_TOTAL = table.cols.wave.shape[1]
FPC = table.cols.fet.shape[2]
new_file = tables.openFile(outdirname+".h5",mode="w")
new_table = new_file.createTable("/","SpikeTable",spike_dtype())
clu_start = np.arange(0,5000,100)
SAMPLE_RATE = 25000. # Doesn't actually matter for this script, but write_xml wants it
# files in same order as tables
clu2DatChannels = {}
for (i_file,h5file) in enumerate(h5files):
for clu in xrange(clu_start[i_file],clu_start[i_file+1]):
clu2DatChannels[clu] = list(h5file.root.DatChannels)
dump("clu2DatChannels.pickle",clu2DatChannels)
triples = [(row["time"],i_spike,i_table) for (i_table,table) in enumerate(spike_tables) for (i_spike,row) in enumerate(table)]
for time,i_spike,i_table in sorted(triples, key = lambda tup: tup[0]):
oldrow = spike_tables[i_table][i_spike]
new_table.row["time"] = time
new_table.row["fet"]= zero_pad(oldrow["fet"],N_CH)
new_table.row["st"] = zero_pad(oldrow["st"],N_CH)
new_table.row["wave"] = zero_pad(oldrow["wave"],N_CH)
new_table.row["clu"] = oldrow["clu"]+clu_start[i_table]
new_table.row.append()
new_table.flush()
klusters_files(new_table,outdirname)
new_file.close()
