{"action":"created","issue":{"url":"https://api.github.com/repos/BlueBrain/NeuroM/issues/324","repository_url":"https://api.github.com/repos/BlueBrain/NeuroM","labels_url":"https://api.github.com/repos/BlueBrain/NeuroM/issues/324/labels{/name}","comments_url":"https://api.github.com/repos/BlueBrain/NeuroM/issues/324/comments","events_url":"https://api.github.com/repos/BlueBrain/NeuroM/issues/324/events","html_url":"https://github.com/BlueBrain/NeuroM/issues/324","id":152943191,"number":324,"title":"Discrepancy between h5 and neurolicuda ASCII data","user":{"login":"juanchopanza","id":675013,"avatar_url":"https://avatars.githubusercontent.com/u/675013?v=3","gravatar_id":"","url":"https://api.github.com/users/juanchopanza","html_url":"https://github.com/juanchopanza","followers_url":"https://api.github.com/users/juanchopanza/followers","following_url":"https://api.github.com/users/juanchopanza/following{/other_user}","gists_url":"https://api.github.com/users/juanchopanza/gists{/gist_id}","starred_url":"https://api.github.com/users/juanchopanza/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/juanchopanza/subscriptions","organizations_url":"https://api.github.com/users/juanchopanza/orgs","repos_url":"https://api.github.com/users/juanchopanza/repos","events_url":"https://api.github.com/users/juanchopanza/events{/privacy}","received_events_url":"https://api.github.com/users/juanchopanza/received_events","type":"User","site_admin":false},"labels":[{"id":206458630,"url":"https://api.github.com/repos/BlueBrain/NeuroM/labels/bug","name":"bug","color":"fc2929","default":true}],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":18,"created_at":"2016-05-04T07:07:46Z","updated_at":"2016-11-07T06:21:27Z","closed_at":null,"body":"Related to #322. \n\nTwo files supposedly representing the same neurons in different formats show small differences in some of the morphometrics obtained with `neurom`.\n\nIt is not clear whether this is a problem with the data or an artifact of `neurom`'s data readers, so it might require some detailed investigation of the data itself, and / or the production of `h5` and `neurolucida` samples that we can be completely sure are equivalent. \n\nThis is an example highlighting the issue:\n\n``` python\nh5 number of sections: 562.0\nnl number of sections: 563.0\n\nh5 number of segments: 5659.0\nnl number of segments: 6216.0\n\nh5 total neurite surface area: 22321.4425649\nnl total neurite surface area: 22186.5760705\n\nh5 total neurite volume: 2533.15174575\nnl total neurite volume: 2423.22948318\n\nh5 total neurite length: 21075.2318211\nnl total neurite length: 21077.0057435\n```\n\nThis is the code I used:\n\n``` python\nimport numpy as np\nfrom neurom import ezy\n\nnrn_h5 = ezy.load_neuron('C050600B1.h5')\nnrn_asc = ezy.load_neuron('C050600B1.asc')\n\nprint 'h5 number of sections: %s' % ezy.get('number_of_sections', nrn_h5)[0]\nprint 'nl number of sections: %s\\n' % ezy.get('number_of_sections', nrn_asc)[0]\nprint 'h5 number of segments: %s' % ezy.get('number_of_segments', nrn_h5)[0]\nprint 'nl number of segments: %s\\n' % ezy.get('number_of_segments', nrn_asc)[0]\nprint 'h5 total neurite surface area: %s' % np.sum(ezy.get('section_areas', nrn_h5))\nprint 'nl total neurite surface area: %s\\n' % np.sum(ezy.get('section_areas', nrn_asc))\nprint 'h5 total neurite volume: %s' % np.sum(ezy.get('section_volumes', nrn_h5))\nprint 'nl total neurite volume: %s\\n' % np.sum(ezy.get('section_volumes', nrn_asc))\nprint 'h5 total neurite length: %s' % np.sum(ezy.get('section_lengths', nrn_h5))\nprint 'nl total neurite length: %s\\n' % np.sum(ezy.get('section_lengths', nrn_asc))\n```\n\nThe sample files can be found [here](https://github.com/BlueBrain/NeuroM/files/248269/Morphs.zip)\n"},"comment":{"url":"https://api.github.com/repos/BlueBrain/NeuroM/issues/comments/258756032","html_url":"https://github.com/BlueBrain/NeuroM/issues/324#issuecomment-258756032","issue_url":"https://api.github.com/repos/BlueBrain/NeuroM/issues/324","id":258756032,"user":{"login":"juanchopanza","id":675013,"avatar_url":"https://avatars.githubusercontent.com/u/675013?v=3","gravatar_id":"","url":"https://api.github.com/users/juanchopanza","html_url":"https://github.com/juanchopanza","followers_url":"https://api.github.com/users/juanchopanza/followers","following_url":"https://api.github.com/users/juanchopanza/following{/other_user}","gists_url":"https://api.github.com/users/juanchopanza/gists{/gist_id}","starred_url":"https://api.github.com/users/juanchopanza/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/juanchopanza/subscriptions","organizations_url":"https://api.github.com/users/juanchopanza/orgs","repos_url":"https://api.github.com/users/juanchopanza/repos","events_url":"https://api.github.com/users/juanchopanza/events{/privacy}","received_events_url":"https://api.github.com/users/juanchopanza/received_events","type":"User","site_admin":false},"created_at":"2016-11-07T06:21:26Z","updated_at":"2016-11-07T06:21:26Z","body":"@mgeplf Wait, it isn't clear at all that SWC files come with the duplicate point at the beginning of (non-trunk) sections. We used to think yes, then we looked at files from neuromorpho.org and the conclusion was no. BBP files coming from out tool chains may have these. But these are an internal subset of NL .asc files."}}
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