def klusters_files(table,basename):
CluFileName,FetFileName,ResFileName,SpkFileName,XMLFileName = (basename + ext for ext in [".clu.1",".fet.1",".res.1",".spk.1",".xml"])
output.write_clu(table.cols.clu[:],CluFileName)
output.write_fet(to2d(table.cols.fet[:]),FetFileName,samples=table.cols.time[:])
output.write_res(table.cols.time[:],ResFileName)
output.write_spk(table.cols.wave[:],SpkFileName)
output.write_xml(n_ch=N_CH,n_samp=S_TOTAL,n_feat=N_CH*FPC,sample_rate=SAMPLE_RATE,filepath=XMLFileName)
def klustakwik_cluster(Fet_nc3):
kk_path = "KlustaKwik"
tempdir = tempfile.mkdtemp()
kk_input_filepath = join(tempdir,'k_input.fet.1')
kk_output_filepath = join(tempdir,'k_input.clu.1')
Fet_nf = Fet_nc3.reshape(len(Fet_nc3),-1)
write_fet(Fet_nf,kk_input_filepath)
n_fet = Fet_nf.shape[1]
os.system( ' '.join([kk_path, kk_input_filepath[:-6], '1', '-UseFeatures', '1'*n_fet,'-MinClusters',str(MINCLUSTERS),'-MaxClusters',str(MAXCLUSTERS),'-Screen','0']) )
return read_clu(kk_output_filepath)
def klustakwik_cluster(Fet_nc3, clusterdir):
kk_path = "KlustaKwik"
if not (os.path.exists(clusterdir)):
os.makedirs(clusterdir)
kk_input_filepath = join(clusterdir,'k_input.fet.1')
kk_output_filepath = join(clusterdir,'k_input.clu.1')
Fet_nf = Fet_nc3.reshape(len(Fet_nc3),-1)
write_fet(Fet_nf,kk_input_filepath)
n_fet = Fet_nf.shape[1]
os.system( ' '.join([kk_path, kk_input_filepath[:-6], '1', '-UseFeatures', '1'*n_fet,'-MinClusters',str(MINCLUSTERS),'-MaxClusters',str(MAXCLUSTERS),'-Screen','0']) )
return read_clu(kk_output_filepath)
def write_files(basename,CluList,TmList,FetList,ChannelGraph=None,STArr=None):
"""Writes files that result from a clustering job."""
CluFileName = basename+'.clu.1'
FetFileName = basename+'.fet.1'
ResFileName = basename+'.res.1'
XMLFileName = basename+'.xml'
if CluList is not None: output.write_clu(np.array(CluList),CluFileName)
output.write_res(np.array(TmList),ResFileName)
output.write_fet(np.array(FetList),FetFileName,samples=np.array(TmList))
output.write_xml(n_ch=N_CH,n_samp=S_TOTAL,n_feat=N_CH*FPC,sample_rate=SAMPLE_RATE,filepath=XMLFileName)
if STArr is not None:
np.save("ST.npy",STArr)
def klusters_files(table, basename):
CluFileName, FetFileName, ResFileName, SpkFileName, XMLFileName = (
basename + ext
for ext in [".clu.1", ".fet.1", ".res.1", ".spk.1", ".xml"])
output.write_clu(table.cols.clu[:], CluFileName)
output.write_fet(to2d(table.cols.fet[:]),
FetFileName,
samples=table.cols.time[:])
output.write_res(table.cols.time[:], ResFileName)
output.write_spk(table.cols.wave[:], SpkFileName)
output.write_xml(n_ch=N_CH,
n_samp=S_TOTAL,
n_feat=N_CH * FPC,
sample_rate=SAMPLE_RATE,
filepath=XMLFileName)
def klustakwik_cluster(Fet_nc3):
kk_path = "KlustaKwik"
tempdir = tempfile.mkdtemp()
kk_input_filepath = join(tempdir, 'k_input.fet.1')
kk_output_filepath = join(tempdir, 'k_input.clu.1')
Fet_nf = Fet_nc3.reshape(len(Fet_nc3), -1)
write_fet(Fet_nf, kk_input_filepath)
n_fet = Fet_nf.shape[1]
os.system(' '.join([
kk_path, kk_input_filepath[:-6], '1', '-UseFeatures', '1' * n_fet,
'-MinClusters',
str(MINCLUSTERS), '-MaxClusters',
str(MAXCLUSTERS), '-Screen', '0'
]))
return read_clu(kk_output_filepath)
def write_files(basename,
CluList,
TmList,
FetList,
ChannelGraph=None,
STArr=None):
"""Writes files that result from a clustering job."""
CluFileName = basename + '.clu.1'
FetFileName = basename + '.fet.1'
ResFileName = basename + '.res.1'
XMLFileName = basename + '.xml'
if CluList is not None: output.write_clu(np.array(CluList), CluFileName)
output.write_res(np.array(TmList), ResFileName)
output.write_fet(np.array(FetList), FetFileName, samples=np.array(TmList))
output.write_xml(n_ch=N_CH,
n_samp=S_TOTAL,
n_feat=N_CH * FPC,
sample_rate=SAMPLE_RATE,
filepath=XMLFileName)
if STArr is not None:
np.save("ST.npy", STArr)
