Comments (5)
Older versions of scikits learn use scikits.learn namespace. We should import whichever the user has installed.
from spikesort.
I haven't found yet where the problem is originated, but I have two test fail now, namely:
======================================================================
ERROR: test gmm clustering algorithm
----------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/lib/python2.7/site-packages/nose/case.py", line 197, in runTest
self.test(*self.arg)
File "/home/dmytro/work/SpikeSort/tests/test_core.py", line 313, in test_gmm
cl = ss.cluster.cluster('gmm', self.features, self.K)
File "/home/dmytro/work/SpikeSort/src/spike_sort/core/cluster.py", line 166, in cluster
labels = cluster_func(data, *args, **kwargs)
File "/home/dmytro/work/SpikeSort/src/spike_sort/core/cluster.py", line 10, in foo
"scikits.learn must be installed to use %s" % method)
NotImplementedError: scikits.learn must be installed to use gmm
======================================================================
ERROR: test scikits k-means plus algorithm
----------------------------------------------------------------------
Traceback (most recent call last):
File "/usr/lib/python2.7/site-packages/nose/case.py", line 197, in runTest
self.test(*self.arg)
File "/home/dmytro/work/SpikeSort/tests/test_core.py", line 307, in test_k_means_plus
cl = ss.cluster.cluster('k_means_plus', self.features, self.K)
File "/home/dmytro/work/SpikeSort/src/spike_sort/core/cluster.py", line 166, in cluster
labels = cluster_func(data, *args, **kwargs)
File "/home/dmytro/work/SpikeSort/src/spike_sort/core/cluster.py", line 10, in foo
"scikits.learn must be installed to use %s" % method)
NotImplementedError: scikits.learn must be installed to use k_means_plus
----------------------------------------------------------------------
I have scikits.learn 0.8.1 installed.
from spikesort.
That is the problem with namespaces. Your scikits.learn probably uses the old scikits.learn namespace and not sklearn
from spikesort.
I reopened the issue but it's still has the "Closed" status :\
Anyway, I guess this code should have accounted for the old name, but apparently it doesn't work this way:
try:
import scikits.learn as sklearn
except ImportError:
pass
from sklearn import cluster as skcluster
from sklearn import mixture
from spikesort.
replaced with slightly uglier but working import
from spikesort.
Related Issues (20)
- allow for more than 4 electrodes in spikewave plot
- cluster labels disappear after manual sorting and some other actions
- SpikeBrowser is unbrowsable when changed 'show_cells' property HOT 1
- jerky motions of the legend plot when moused over
- deprecated matplotlib function warning when manual sorting HOT 1
- ClusterAnalyzer.delete_cells() fails, if called before self.labels is requested HOT 3
- making FilterStack even more general HOT 2
- add `use_features` property to PlotFeatures HOT 4
- convert `FeatureExtractor.feature_methods` from `list` to `dict` HOT 3
- add SpikeSort to PyPI HOT 1
- Integrate with Travis CI HOT 3
- SpikeSort Coding sprint
- Support for optional components HOT 1
- SpikeBrowser: single-electrode data goes out of range while rescaling HOT 2
- overlapping feature names in feature_plot
- possible matplotlib memory leaks
- type consistency in spike_features datastructure
- signature is not preserved for fet* functions
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- Tutorial file not available HOT 3
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from spikesort.