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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!
~/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
This isn't really a bug, but the example code won't complete in its current form with the existing params.prm file. It finishes spikedetekt, but spits out the following error when it is time to run klustakwik.
ERROR: All PRM KlustaKwik parameters must now be prefixed by KK_ or they will be ignored.
See https://github.com/klusta-team/example/blob/master/params.prm for an example.
Please update or comment out the parameters to use the defaults, then re-run with klusta --cluster-only.
It's an easy fix to replace the text in params.prm, but I wonder if you guys want to just update the file in the google drive?
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