{"action":"created","issue":{"url":"https://api.github.com/repos/metabolite-atlas/metatlas/issues/4","labels_url":"https://api.github.com/repos/metabolite-atlas/metatlas/issues/4/labels{/name}","comments_url":"https://api.github.com/repos/metabolite-atlas/metatlas/issues/4/comments","events_url":"https://api.github.com/repos/metabolite-atlas/metatlas/issues/4/events","html_url":"https://github.com/metabolite-atlas/metatlas/issues/4","id":68111745,"number":4,"title":"speed up mzML to HDF5 conversion","user":{"login":"benbowen","id":810953,"avatar_url":"https://avatars.githubusercontent.com/u/810953?v=3","gravatar_id":"","url":"https://api.github.com/users/benbowen","html_url":"https://github.com/benbowen","followers_url":"https://api.github.com/users/benbowen/followers","following_url":"https://api.github.com/users/benbowen/following{/other_user}","gists_url":"https://api.github.com/users/benbowen/gists{/gist_id}","starred_url":"https://api.github.com/users/benbowen/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/benbowen/subscriptions","organizations_url":"https://api.github.com/users/benbowen/orgs","repos_url":"https://api.github.com/users/benbowen/repos","events_url":"https://api.github.com/users/benbowen/events{/privacy}","received_events_url":"https://api.github.com/users/benbowen/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":{"login":"blink1073","id":2096628,"avatar_url":"https://avatars.githubusercontent.com/u/2096628?v=3","gravatar_id":"","url":"https://api.github.com/users/blink1073","html_url":"https://github.com/blink1073","followers_url":"https://api.github.com/users/blink1073/followers","following_url":"https://api.github.com/users/blink1073/following{/other_user}","gists_url":"https://api.github.com/users/blink1073/gists{/gist_id}","starred_url":"https://api.github.com/users/blink1073/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/blink1073/subscriptions","organizations_url":"https://api.github.com/users/blink1073/orgs","repos_url":"https://api.github.com/users/blink1073/repos","events_url":"https://api.github.com/users/blink1073/events{/privacy}","received_events_url":"https://api.github.com/users/blink1073/received_events","type":"User","site_admin":false},"milestone":null,"comments":9,"created_at":"2015-04-13T14:26:15Z","updated_at":"2015-04-14T13:48:31Z","closed_at":null,"body":"It is slow because it is looking at each [mz, intensity] value in each scan.  Instead it should make arrays for the following (using fill values) for scan_time, polarity, mz_level, precursor_MZ, precursor_intensity, and collision_energy and write it once to the hdf5 file as arrays instead of values.  Maybe as a 2d array."},"comment":{"url":"https://api.github.com/repos/metabolite-atlas/metatlas/issues/comments/92854681","html_url":"https://github.com/metabolite-atlas/metatlas/issues/4#issuecomment-92854681","issue_url":"https://api.github.com/repos/metabolite-atlas/metatlas/issues/4","id":92854681,"user":{"login":"benbowen","id":810953,"avatar_url":"https://avatars.githubusercontent.com/u/810953?v=3","gravatar_id":"","url":"https://api.github.com/users/benbowen","html_url":"https://github.com/benbowen","followers_url":"https://api.github.com/users/benbowen/followers","following_url":"https://api.github.com/users/benbowen/following{/other_user}","gists_url":"https://api.github.com/users/benbowen/gists{/gist_id}","starred_url":"https://api.github.com/users/benbowen/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/benbowen/subscriptions","organizations_url":"https://api.github.com/users/benbowen/orgs","repos_url":"https://api.github.com/users/benbowen/repos","events_url":"https://api.github.com/users/benbowen/events{/privacy}","received_events_url":"https://api.github.com/users/benbowen/received_events","type":"User","site_admin":false},"created_at":"2015-04-14T13:48:31Z","updated_at":"2015-04-14T13:48:31Z","body":"I just did a file conversion and everything is much faster!  I converted a 1.8GB file in less than a minute to a 0.35 GB hdf5 file.  Checked a few values manually and everything seems in order."}}