rossant
commented
8 years ago can you try pip install docopt in a terminal?
Open salazarr opened 8 years ago
rossant
commented
8 years ago can you try pip install docopt in a terminal?
salazarr
commented
8 years ago Hi Cyrille,
I ran the command that you suggested and the problem persists:
salazarr@salazarr-Precision-WorkStation-T7500 ~ $ pip install docopt
Requirement already satisfied (use --upgrade to upgrade): docopt in ./miniconda3/lib/python3.5/site-packages
salazarr@salazarr-Precision-WorkStation-T7500 ~ $ source activate klusta
discarding /home/salazarr/miniconda3/bin from PATH
prepending /home/salazarr/miniconda3/envs/klusta/bin to PATH
(klusta)salazarr@salazarr-Precision-WorkStation-T7500 ~ $ klustaviewa
Traceback (most recent call last):
File "/home/salazarr/miniconda3/envs/klusta/bin/klustaviewa", line 7, in
Thanks for your help,
ROdrigo.
De : Cyrille Rossant notifications@github.com Envoyé : vendredi 8 avril 2016 19:28 À : kwikteam/klusta Cc : Rodrigo Salazar Toro Objet : Re: [kwikteam/klusta] error running klustaviewa on linux (#18)
can you try pip install docopt in a terminal?
You are receiving this because you authored the thread. Reply to this email directly or view it on GitHubhttps://github.com/kwikteam/klusta/issues/18#issuecomment-207526683
nippoo
commented
8 years ago @salazarr could you instead run it after running source activate klusta? This will install docopt into the correct virtual environment.
salazarr
commented
8 years ago Hi Max,
The problem remains and is similar on my windows, mac and linux machines...
Thanks,
Rodrigo.
De : Max Hunter notifications@github.com Envoyé : lundi 11 avril 2016 13:40 À : kwikteam/klusta Cc : Rodrigo Salazar Toro Objet : Re: [kwikteam/klusta] error running klustaviewa on linux (#18)
@salazarrhttps://github.com/salazarr could you instead run it after running source activate klusta? This will install docopt into the correct virtual environment.
You are receiving this because you were mentioned. Reply to this email directly or view it on GitHubhttps://github.com/kwikteam/klusta/issues/18#issuecomment-208301119
rossant
commented
8 years ago could you show us the terminal output? The command should look like this:
$ source activate klusta
(klusta)$ pip install docopt
(klusta)$ python -c "import klusta" the last line tests whether the "klusta" package works
salazarr
commented
8 years ago Here it is:
milodon-2:~ rsalazar$ source activate klusta discarding /Users/rsalazar/miniconda3/bin from PATH prepending /Users/rsalazar/miniconda3/envs/klusta/bin to PATH (klusta)milodon-2:~ rsalazar$ pip install docopt Requirement already satisfied (use --upgrade to upgrade): docopt in ./miniconda3/envs/klusta/lib/python2.7/site-packages (klusta)milodon-2:~ rsalazar$ python -c "import klusta" (klusta)milodon-2:~ rsalazar$
On Apr 11, 2016, at 2:01 PM, Cyrille Rossant notifications@github.com<mailto:notifications@github.com> wrote:
could you show us the terminal output? The command should look like this:
$ source activate klusta (klusta)$ pip install docopt (klusta)$ python -c "import klusta"
the last line tests whether the "klusta" package works
— You are receiving this because you were mentioned. Reply to this email directly or view it on GitHubhttps://github.com/kwikteam/klusta/issues/18#issuecomment-208309234
Rodrigo F. Salazar Toro, PhD
University of Geneva
Department of Basic Neuroscience
Rue Michel-Servet 1
CH-1211 Geneva 4
Switzerland
Phone #: +41 (0)22 379 54 69then do
(klusta)$ python -c "import klustaviewa"
(klusta)$ klustaviewaCyrille,
still teh same issue
salazarr@salazarr-Precision-WorkStation-T7500 ~/Downloads $ source activate klusta
discarding /home/salazarr/miniconda3/bin from PATH
prepending /home/salazarr/miniconda3/envs/klusta/bin to PATH
(klusta)salazarr@salazarr-Precision-WorkStation-T7500 ~/Downloads $ pip install docopt
Requirement already satisfied (use --upgrade to upgrade): docopt in /home/salazarr/miniconda3/envs/klusta/lib/python2.7/site-packages
(klusta)salazarr@salazarr-Precision-WorkStation-T7500 ~/Downloads $ python -c "import klusta"
(klusta)salazarr@salazarr-Precision-WorkStation-T7500 ~/Downloads $ python -c "import klustaviewa"
(klusta)salazarr@salazarr-Precision-WorkStation-T7500 ~/Downloads $ klustaviewa
/home/salazarr/miniconda3/envs/klusta/lib/python2.7/site-packages/IPython/qt.py:13: ShimWarning: The IPython.qt package has been deprecated. You should import from qtconsole instead.
"You should import from qtconsole instead.", ShimWarning)
<klustaviewa.gui.mainwindow.MainWindow object at 0x7f4493da2c30>
And I cannot open any .kwik file once klustaviewa is opened.
Thanks again,
Rodrigo
De : Cyrille Rossant notifications@github.com Envoyé : lundi 11 avril 2016 19:57 À : kwikteam/klusta Cc : Rodrigo Salazar Toro Objet : Re: [kwikteam/klusta] error running klustaviewa on linux (#18)
then do
(klusta)$ python -c "import klustaviewa" (klusta)$ klustaviewa
You are receiving this because you were mentioned. Reply to this email directly or view it on GitHubhttps://github.com/kwikteam/klusta/issues/18#issuecomment-208475843
rossant
commented
8 years ago These warnings are all normal. What error message do you get when you try to open a kwik file in KlustaViewa? Have you tried to do klustaviewa yourfile.kwik to open directly the file when launching the application?
salazarr
commented
8 years ago I cannot open any file. The window browser cannot select any .kwik file.
If I try to run :
source activate klusta
discarding /Users/rsalazar/miniconda3/bin from PATH
prepending /Users/rsalazar/miniconda3/envs/klusta/bin to PATH
(klusta)milodon-2:example-master rsalazar$ klustaviewa hybrid_10sec.kwik
/Users/rsalazar/miniconda3/envs/klusta/lib/python2.7/site-packages/IPython/qt.py:13: ShimWarning: The IPython.qt package has been deprecated. You should import from qtconsole instead.
"You should import from qtconsole instead.", ShimWarning)
I get a window with the following errors:
An error occurred: Traceback (most recent call last):
File "/Users/rsalazar/miniconda3/envs/klusta/lib/python2.7/site-packages/klustaviewa/gui/threads.py", line 33, in open
loader.open(path)
File "/Users/rsalazar/miniconda3/envs/klusta/lib/python2.7/site-packages/kwiklib/dataio/kwikloader.py", line 120, in open
self.experiment = Experiment(basename, dir=dir, mode='a')
File "/Users/rsalazar/miniconda3/envs/klusta/lib/python2.7/site-packages/kwiklib/dataio/experiment.py", line 403, in init
self.channel_groups = self._gen_children('channel_groups', ChannelGroup)
File "/Users/rsalazar/miniconda3/envs/klusta/lib/python2.7/site-packages/kwiklib/dataio/experiment.py", line 165, in _gen_children
for child in container
File "/Users/rsalazar/miniconda3/envs/klusta/lib/python2.7/site-packages/kwiklib/dataio/experiment.py", line 440, in init
self.clusters = ClustersNode(self._files, self._node.clusters, root=self._root)
File "/Users/rsalazar/miniconda3/envs/klusta/lib/python2.7/site-packages/tables/group.py", line 813, in getattr
return self._f_get_child(name)
File "/Users/rsalazar/miniconda3/envs/klusta/lib/python2.7/site-packages/tables/group.py", line 683, in _f_get_child
self._g_check_has_child(childname)
File "/Users/rsalazar/miniconda3/envs/klusta/lib/python2.7/site-packages/tables/group.py", line 407, in _g_check_has_child
% (self._v_pathname, name))
NoSuchNodeError: group /channel_groups/0 does not have a child named clusters
AND NOTHING IS BEING DISPLAYED ON THE MAIN WINDOW OF KLUSTAVIEWA.
THANKS,
RODRIGO
On Apr 12, 2016, at 11:47 AM, Cyrille Rossant notifications@github.com<mailto:notifications@github.com> wrote:
These warnings are all normal. What error message do you get when you try to open a kwik file in KlustaViewa? Have you tried to do klustaviewa yourfile.kwik to open directly the file when launching the application?
— You are receiving this because you were mentioned. Reply to this email directly or view it on GitHubhttps://github.com/kwikteam/klusta/issues/18#issuecomment-208821668
Rodrigo F. Salazar Toro, PhD
University of Geneva
Department of Basic Neuroscience
Rue Michel-Servet 1
CH-1211 Geneva 4
Switzerland
Phone #: +41 (0)22 379 54 69can you send me your kwik and kwx files?
salazarr
commented
8 years ago Here are the files.
I am not sure about the klustakwik executable per_se as the kkwik is run with your klusta fct:
klusta *.prm
Correct? But I have attached the folder that might contain the klustakwik file and that is in my klusta environment.
Also:
The first time that I installed klusta, both klustakwik and klustaviewa for windows worked and I produced a .kwik file (20150401.kwik with
2015060401earlier.kwik.zip 2015060401later.kwik.zip
subfolder ‘_klustakwik') that is readable by klustaviewa. Unfortunately, I don’t remember the version #. I can only tell you that it involved many steps and dependencies that needed to be satisfied. The version got compromised because we tried to make it usable by several users of the same machine. Anyway, since I reinstalled the klusta environment using your simplified installation (https://github.com/kwikteam/klusta/#quick-install-guide), I cannot open any .kwik file (and subfolder named '.klustakwik2') that has been produced since.
Thanks,
Rodrigo.
salazarr
commented
8 years ago Sorry I have just realized that I forgot the kwik folder containing the executable. klustakwik2-0.2.4-nppy27_0.zip
rossant
commented
8 years ago I cannot reproduce the problem on the earlier dataset. Regarding the later dataset, it looks like KlustaKwik has not run on it? So KlustaViewa cannot open it.
I would suggest to try running klusta and KlustaViewa on the test dataset as explained in the instructions.
Something else you can do: install phy and use phy kwik-gui yourfile.kwik to open the newer GUI instead of KlustaViewa on your file.
salazarr
commented
8 years ago Cyrille,
The first one has always worked for me thus you should not have any problem with this one. About the second one, thanks a lot for the info. Kkwik did run on it and did not display any particular error message. I dig into running Kkwik on a Buzsaki64-A64 probe and it seems to me that your Buzsaki64.prb are not correct about the graph neighbors. I ran klusta again with one .prm file per shank (inspired from your 1x32_buzsaki.prb) and Kkwik produced a .kwik file that is readable by klustaviewa.
Anyway, for now, I can use your code on our dataset (separately for each shank but that’s OK) and it works very nicely. Good job by the way! It is very nice to have simplified the procedures to this level.
Thanks again for your help and support,
Rodrigo.
On Apr 13, 2016, at 6:27 PM, Cyrille Rossant notifications@github.com<mailto:notifications@github.com> wrote:
I cannot reproduce the problem on the earlier dataset. Regarding the later dataset, it looks like KlustaKwik has not run on it? So KlustaViewa cannot open it.
I would suggest to try running klusta and KlustaViewa on the test datasethttp://klusta.readthedocs.org/en/latest/ as explained in the instructions.
Something else you can do: install phyhttps://github.com/kwikteam/phy#installation and use phy kwik-gui yourfile.kwik to open the newer GUI instead of KlustaViewa on your file.
— You are receiving this because you were mentioned. Reply to this email directly or view it on GitHubhttps://github.com/kwikteam/klusta/issues/18#issuecomment-209531849
Rodrigo F. Salazar Toro, PhD
University of Geneva
Department of Basic Neuroscience
Rue Michel-Servet 1
CH-1211 Geneva 4
Switzerland
Phone #: +41 (0)22 379 54 69
Hi
I have installed klusta from the web page :
https://github.com/kwikteam/klusta/#quick-install-guide
and tried to open klustaviewa but I get the following error message:
klustaviewa Traceback (most recent call last): File "/home/mint/miniconda3/envs/klusta/bin/klustaviewa", line 7, in
from klustaviewa.scripts.runklustaviewa import main
File "/home/mint/miniconda3/envs/klusta/lib/python2.7/site-packages/klustaviewa/init.py", line 44, in
from kwiklib.utils import logger as log
File "/home/mint/miniconda3/envs/klusta/lib/python2.7/site-packages/kwiklib/init.py", line 9, in
import dataio
File "/home/mint/miniconda3/envs/klusta/lib/python2.7/site-packages/kwiklib/dataio/init.py", line 4, in
from kwikloader import *
File "/home/mint/miniconda3/envs/klusta/lib/python2.7/site-packages/kwiklib/dataio/kwikloader.py", line 31, in
from .experiment import Experiment
File "/home/mint/miniconda3/envs/klusta/lib/python2.7/site-packages/kwiklib/dataio/experiment.py", line 16, in
from klusta.traces.waveform import WaveformLoader, SpikeLoader
File "/home/mint/miniconda3/envs/klusta/lib/python2.7/site-packages/klusta/traces/init.py", line 9, in
from .spikedetekt import SpikeDetekt
File "/home/mint/miniconda3/envs/klusta/lib/python2.7/site-packages/klusta/traces/spikedetekt.py", line 13, in
from tqdm import tqdm
File "/home/mint/miniconda3/envs/klusta/lib/python2.7/site-packages/tqdm/init.py", line 6, in
from ._main import main
File "/home/mint/miniconda3/envs/klusta/lib/python2.7/site-packages/tqdm/_main.py", line 3, in
from docopt import docopt
ImportError: No module named docopt
Any idea?
Thanks,
Rodrigo.