{"action":"created","issue":{"url":"https://api.github.com/repos/NeuralEnsemble/python-neo/issues/211","labels_url":"https://api.github.com/repos/NeuralEnsemble/python-neo/issues/211/labels{/name}","comments_url":"https://api.github.com/repos/NeuralEnsemble/python-neo/issues/211/comments","events_url":"https://api.github.com/repos/NeuralEnsemble/python-neo/issues/211/events","html_url":"https://github.com/NeuralEnsemble/python-neo/issues/211","id":106833940,"number":211,"title":"non-integer indexing in Plexon.IO","user":{"login":"Palaeocortex","id":14318158,"avatar_url":"https://avatars.githubusercontent.com/u/14318158?v=3","gravatar_id":"","url":"https://api.github.com/users/Palaeocortex","html_url":"https://github.com/Palaeocortex","followers_url":"https://api.github.com/users/Palaeocortex/followers","following_url":"https://api.github.com/users/Palaeocortex/following{/other_user}","gists_url":"https://api.github.com/users/Palaeocortex/gists{/gist_id}","starred_url":"https://api.github.com/users/Palaeocortex/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/Palaeocortex/subscriptions","organizations_url":"https://api.github.com/users/Palaeocortex/orgs","repos_url":"https://api.github.com/users/Palaeocortex/repos","events_url":"https://api.github.com/users/Palaeocortex/events{/privacy}","received_events_url":"https://api.github.com/users/Palaeocortex/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":5,"created_at":"2015-09-16T18:31:41Z","updated_at":"2015-09-16T20:56:59Z","closed_at":null,"body":"Hi group!\r\n\r\nI am trying to import Plexon files and I keep getting this message in the terminal, without anything being loaded into the db:\r\n\r\n  sigarrays[chan][sample_positions[chan] : sample_positions[chan]+data.size] = data\r\n/usr/local/lib/python2.7/dist-packages/neo/io/plexonio.py:233: DeprecationWarning: using a non-integer number instead of an integer will result in an error in the future\r\n\r\nThis message keeps appearing continuously. After 30 min I end OpenElectrophy and nothing is in the db. My files contain 1-2h long recordings and have 100 - 200 MB (low sampling rate LFP signals).\r\n\r\nIt looks like the non-integer indexing in scikit-learn will be removed in future versions, so plexon.io needs an update:\r\n\r\nhttps://github.com/numpy/numpy/pull/3243\r\nhttp://stackoverflow.com/questions/20084218/deprecation-warning-in-scikit-learn-svmlight-format-loader\r\n\r\nThe continuous terminal output makes loading impossible. One can start openElectrophy with the &>  /dev/null command, which works well but no error messages appears making trouble shooting impossible. \r\n\r\nBasically it is not possible to load .plx data with neo.io."},"comment":{"url":"https://api.github.com/repos/NeuralEnsemble/python-neo/issues/comments/140892232","html_url":"https://github.com/NeuralEnsemble/python-neo/issues/211#issuecomment-140892232","issue_url":"https://api.github.com/repos/NeuralEnsemble/python-neo/issues/211","id":140892232,"user":{"login":"pmeier82","id":300202,"avatar_url":"https://avatars.githubusercontent.com/u/300202?v=3","gravatar_id":"","url":"https://api.github.com/users/pmeier82","html_url":"https://github.com/pmeier82","followers_url":"https://api.github.com/users/pmeier82/followers","following_url":"https://api.github.com/users/pmeier82/following{/other_user}","gists_url":"https://api.github.com/users/pmeier82/gists{/gist_id}","starred_url":"https://api.github.com/users/pmeier82/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/pmeier82/subscriptions","organizations_url":"https://api.github.com/users/pmeier82/orgs","repos_url":"https://api.github.com/users/pmeier82/repos","events_url":"https://api.github.com/users/pmeier82/events{/privacy}","received_events_url":"https://api.github.com/users/pmeier82/received_events","type":"User","site_admin":false},"created_at":"2015-09-16T20:56:59Z","updated_at":"2015-09-16T20:56:59Z","body":"Just discovered that there are updated versions PlexonIO and BlackrockIO\n(and several others) on the master branch. I have to check in detail when I\nfind the time, but I think they already cover what I could contribute.\n\n@Palaeocortex\n​Not sure what version of neo you are using, if you got it by\npip/easyinstall or the like it should be the 0.3.3 release with the old io\nclasses. In that case switching to the master branch might already solve\nyour problem.\n\n\n--\nφιλ\n\nOn 16 September 2015 at 22:31, Philipp Meier <pmeier82@gmail.com> wrote:\n\n> Aye, that is a quite common warning (DeprecationWarning) and not an\n> error. The only practical impact should be the flooding of the console.\n> You can ignore warnings like so:\n> http://stackoverflow.com/questions/14463277/how-to-disable-python-warnings\n> .\n>\n> I guess this has to be addressed on the neo.io level, perhaps by\n> refactoring the indexing on the base class level. Seems to be stem from the\n> use of quantities and their conversion to array indices.\n>\n>\n> ​Still, this might not be your actual problem. I had problems reading .plx\n> file with versions >1.04 with the 0.3x branch.\n>\n> --\n> φιλ\n>\n> On 16 September 2015 at 21:33, Palaeocortex <notifications@github.com>\n> wrote:\n>\n>> I think it is rather related to the indexing of arrays than the channel\n>> counts. The index var has to be int not float. At least that is what I\n>> understand from the error message and from the links I posted.\n>>\n>> PlexUtil shows Version 106 and Acquiring software OmniPlex 1.4.3.\n>>\n>> —\n>> Reply to this email directly or view it on GitHub\n>> <https://github.com/NeuralEnsemble/python-neo/issues/211#issuecomment-140860645>\n>> .\n>>\n>\n>\n"}}