I'm trying to get klustakwik/klustasuite working on my Ubuntu machine. Running klusta params.prm in the sample data causes the following error. I'd be happy to debug it: does anyone else have problems running it as instructed in linux, or another route for installing I should try?
~/Downloads/example-master$ klusta params.prm --overwrite
2015-03-24 15:36:58 __dir__ needs to be an attribute of /
2015-03-24 15:36:58 __members__ needs to be an attribute of /
2015-03-24 15:36:58 __methods__ needs to be an attribute of /
2015-03-24 15:36:58 __dir__ needs to be an attribute of 0
2015-03-24 15:36:58 __members__ needs to be an attribute of 0
2015-03-24 15:36:58 __methods__ needs to be an attribute of 0
2015-03-24 15:36:58 __dir__ needs to be an attribute of 0
2015-03-24 15:36:58 __members__ needs to be an attribute of 0
2015-03-24 15:36:58 __methods__ needs to be an attribute of 0
2015-03-24 15:36:58 __dir__ needs to be an attribute of cluster_groups
2015-03-24 15:36:58 __members__ needs to be an attribute of cluster_groups
2015-03-24 15:36:58 __methods__ needs to be an attribute of cluster_groups
2015-03-24 15:36:58 __dir__ needs to be an attribute of main
2015-03-24 15:36:58 __members__ needs to be an attribute of main
2015-03-24 15:36:58 __methods__ needs to be an attribute of main
2015-03-24 15:36:58 __dir__ needs to be an attribute of original
2015-03-24 15:36:58 __members__ needs to be an attribute of original
2015-03-24 15:36:58 __methods__ needs to be an attribute of original
2015-03-24 15:36:58 __dir__ needs to be an attribute of clusters
2015-03-24 15:36:58 __members__ needs to be an attribute of clusters
2015-03-24 15:36:58 __methods__ needs to be an attribute of clusters
2015-03-24 15:36:58 __dir__ needs to be an attribute of main
2015-03-24 15:36:58 __members__ needs to be an attribute of main
2015-03-24 15:36:58 __methods__ needs to be an attribute of main
2015-03-24 15:36:58 __dir__ needs to be an attribute of original
2015-03-24 15:36:58 __members__ needs to be an attribute of original
2015-03-24 15:36:58 __methods__ needs to be an attribute of original
2015-03-24 15:36:58 __dir__ needs to be an attribute of spikes
2015-03-24 15:36:58 __members__ needs to be an attribute of spikes
2015-03-24 15:36:58 __methods__ needs to be an attribute of spikes
2015-03-24 15:36:58 __dir__ needs to be an attribute of clusters
2015-03-24 15:36:58 __members__ needs to be an attribute of clusters
2015-03-24 15:36:58 __methods__ needs to be an attribute of clusters
2015-03-24 15:36:58 __dir__ needs to be an attribute of 0
2015-03-24 15:36:58 __members__ needs to be an attribute of 0
2015-03-24 15:36:58 __methods__ needs to be an attribute of 0
2015-03-24 15:36:58 Starting process on <ExperimentRawReader <Experiment 'test_hybrid_120sec'>
application_data
spikedetekt
canonical_pcs = None
chunk_overlap = 300
chunk_size = 20000
connected_component_join_size = 1
detect_spikes = negative
diagnostics_script_path = None
excerpt_size = 20000
experiment_name = test_hybrid_120sec
extract_s_after = 10
extract_s_before = 10
features_contiguous
filter_butter_order = 3
filter_high = 9500.0
filter_low = 500.0
nbits = 16
nchannels = 32
nexcerpts = 50
nfeatures_per_channel = 3
pca_nwaveforms_max = 10000
prb_file = 32chan1shankbuzsaki.prb
raw_data_files = test_hybrid_120sec.raw.kwd
sample_rate = 20000
save_high
save_low
save_raw
threshold_strong_std_factor = 4.5
threshold_weak_std_factor = 2.0
use_single_threshold
voltage_gain = 10.0
waveforms_nsamples = 20
weight_power = 2
channel_groups
0
application_data
channels
0
application_data
klustaviewa
spikedetekt
user_data
cluster_groups
main
add_group
color
iteritems
keys
name
remove_group
values
original
add_group
color
iteritems
keys
name
remove_group
values
clusters
main
add_cluster
color
group
iteritems
keys
remove_cluster
values
original
add_cluster
color
group
iteritems
keys
remove_cluster
values
spikes
add
channel_group_id = 0
clusters
copy
main [uint32 (0,)]
original [uint32 (0,)]
concatenated_time_samples
features
dtype
features_masks [float32 (0, 96, 2)]
init_cache
load_features_masks
load_features_masks_bg
load_waveforms
masks
dtype
nchannels = 32
nfeatures = 96
nsamples = 20
recording [uint16 (0,)]
time_fractional [uint8 (0,)]
time_samples [uint64 (0,)]
waveforms_filtered [int16 (0, 20, 32)]
waveforms_raw [int16 (0, 20, 32)]
user_data
close
dir =
gen_filename
name = test_hybrid_120sec
recordings
0
high [int16 (0, 32)]
low [int16 (0, 32)]
raw [int16 (0, 32)]
user_data
user_data>
2015-03-24 15:36:58 Traceback (most recent call last):
File "/home/me/Programming/miniconda/envs/klusta/bin/klusta", line 9, in <module>
load_entry_point('klustaviewa==0.3.0rc1', 'console_scripts', 'klusta')()
File "/home/me/Programming/miniconda/envs/klusta/lib/python2.7/site-packages/klustaviewa-0.3.0rc1-py2.7-linux-x86_64.egg/spikedetekt2/core/script.py", line 267, in main
runsd=runsd, runkk=runkk)
File "/home/me/Programming/miniconda/envs/klusta/lib/python2.7/site-packages/klustaviewa-0.3.0rc1-py2.7-linux-x86_64.egg/spikedetekt2/core/script.py", line 237, in run_all
run_spikedetekt(prm_filename, dir=dir, debug=debug)
File "/home/me/Programming/miniconda/envs/klusta/lib/python2.7/site-packages/klustaviewa-0.3.0rc1-py2.7-linux-x86_64.egg/spikedetekt2/core/script.py", line 115, in run_spikedetekt
_debug=debug)
File "/home/me/Programming/miniconda/envs/klusta/lib/python2.7/site-packages/klustaviewa-0.3.0rc1-py2.7-linux-x86_64.egg/spikedetekt2/core/main.py", line 182, in run
channels=probe.channels, **prm)
File "/home/me/Programming/miniconda/envs/klusta/lib/python2.7/site-packages/klustaviewa-0.3.0rc1-py2.7-linux-x86_64.egg/spikedetekt2/processing/threshold.py", line 46, in get_threshold
excerpt_size=excerpt_size))
File "/home/me/Programming/miniconda/envs/klusta/lib/python2.7/site-packages/numpy/core/shape_base.py", line 228, in vstack
return _nx.concatenate([atleast_2d(_m) for _m in tup], 0)
ValueError: need at least one array to concatenate
None
I'm trying to get klustakwik/klustasuite working on my Ubuntu machine. Running klusta params.prm in the sample data causes the following error. I'd be happy to debug it: does anyone else have problems running it as instructed in linux, or another route for installing I should try?
Thanks!