{"action":"created","issue":{"url":"https://api.github.com/repos/NeurodataWithoutBorders/pynwb/issues/447","repository_url":"https://api.github.com/repos/NeurodataWithoutBorders/pynwb","labels_url":"https://api.github.com/repos/NeurodataWithoutBorders/pynwb/issues/447/labels{/name}","comments_url":"https://api.github.com/repos/NeurodataWithoutBorders/pynwb/issues/447/comments","events_url":"https://api.github.com/repos/NeurodataWithoutBorders/pynwb/issues/447/events","html_url":"https://github.com/NeurodataWithoutBorders/pynwb/issues/447","id":312168163,"number":447,"title":"tool for creating partial nwb files","user":{"login":"bendichter","id":844306,"avatar_url":"https://avatars0.githubusercontent.com/u/844306?v=4","gravatar_id":"","url":"https://api.github.com/users/bendichter","html_url":"https://github.com/bendichter","followers_url":"https://api.github.com/users/bendichter/followers","following_url":"https://api.github.com/users/bendichter/following{/other_user}","gists_url":"https://api.github.com/users/bendichter/gists{/gist_id}","starred_url":"https://api.github.com/users/bendichter/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/bendichter/subscriptions","organizations_url":"https://api.github.com/users/bendichter/orgs","repos_url":"https://api.github.com/users/bendichter/repos","events_url":"https://api.github.com/users/bendichter/events{/privacy}","received_events_url":"https://api.github.com/users/bendichter/received_events","type":"User","site_admin":false},"labels":[{"id":661411412,"url":"https://api.github.com/repos/NeurodataWithoutBorders/pynwb/labels/enhancement","name":"enhancement","color":"84b6eb","default":true},{"id":661458004,"url":"https://api.github.com/repos/NeurodataWithoutBorders/pynwb/labels/proposal","name":"proposal","color":"ededed","default":false}],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":0,"created_at":"2018-04-07T04:02:56Z","updated_at":"2018-04-09T03:53:38Z","closed_at":null,"author_association":"CONTRIBUTOR","body":"## Feature Request\r\n\r\n### Problem/Use Case\r\nI have heard from several groups that they have the desire to store stimulus data in an external file and link to the file. This is important for them because they often play the exact same stimulus and do not want to duplicate the data for every NWB file. Sometimes the stimulus file is big (e.g. videos) and even when it is not that big it's a bad idea to duplicate data. This is a critical issue for many labs. (@the-moliver)\r\n\r\nAnother application for externally linking files is for subject data. For instance, brain imaging data that is constant for a subject could be stored externally and linked to. I have this issue with the Chang Lab, where I would really like to not store the cortical surface mesh of each subject every time I record an experimental block (there are often >100 per subject).\r\n\r\nWe support this! (#408) However it's not easy to create the file that is to be linked to and there isn't really a convention for doing this. I would like a tool that writes a file containing a single dataset or a small set of datasets. This file is not strictly nwb-compliant because it does not contain all the necessary parts (processing, acquisition, etc.) but the dataset(s) created are compliant and fit perfectly in to an nwb file when linked to. I propose that these files be designated by .nwbaux and we should have a tool to create them:\r\n\r\n```python\r\nwith NWBHDF5IO('subject_001.nwbaux', mode='w') as io:\r\n    io.write_aux_file(container_or_list_of_containers)\r\n```\r\n\r\nI'd like to open the discussion here. Is this a good idea? Do others think this would be useful? Any suggestions for a better naming convention (I'd prefer .nwb-aux but is a dash in the file suffix a bad idea?)"},"comment":{"url":"https://api.github.com/repos/NeurodataWithoutBorders/pynwb/issues/comments/379622697","html_url":"https://github.com/NeurodataWithoutBorders/pynwb/issues/447#issuecomment-379622697","issue_url":"https://api.github.com/repos/NeurodataWithoutBorders/pynwb/issues/447","id":379622697,"user":{"login":"neuromusic","id":1245615,"avatar_url":"https://avatars1.githubusercontent.com/u/1245615?v=4","gravatar_id":"","url":"https://api.github.com/users/neuromusic","html_url":"https://github.com/neuromusic","followers_url":"https://api.github.com/users/neuromusic/followers","following_url":"https://api.github.com/users/neuromusic/following{/other_user}","gists_url":"https://api.github.com/users/neuromusic/gists{/gist_id}","starred_url":"https://api.github.com/users/neuromusic/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/neuromusic/subscriptions","organizations_url":"https://api.github.com/users/neuromusic/orgs","repos_url":"https://api.github.com/users/neuromusic/repos","events_url":"https://api.github.com/users/neuromusic/events{/privacy}","received_events_url":"https://api.github.com/users/neuromusic/received_events","type":"User","site_admin":false},"created_at":"2018-04-09T03:53:38Z","updated_at":"2018-04-09T03:53:38Z","author_association":"CONTRIBUTOR","body":"I think this is a common need. Another need is to maintain LFP or raw calcium movies in a separate file. Establishing some conventions around this & providing utilities to support such a workflow would be very beneficial, I think.\r\n\r\n> This file is not strictly nwb-compliant because it does not contain all the necessary parts (processing, acquisition, etc.) but the dataset(s) created are compliant and fit perfectly in to an nwb file when linked to.\r\n\r\nIs there a reason that the \"auxilliary\" file cannot be NWB compliant? For example, our ophys files don't have \"acquisition\". Otherwise, we are talking about developing yet another schema.\r\n"}}
{"actor":{"display_login":"neuromusic"}}