{"action":"created","issue":{"url":"https://api.github.com/repos/nipy/dipy/issues/1018","repository_url":"https://api.github.com/repos/nipy/dipy","labels_url":"https://api.github.com/repos/nipy/dipy/issues/1018/labels{/name}","comments_url":"https://api.github.com/repos/nipy/dipy/issues/1018/comments","events_url":"https://api.github.com/repos/nipy/dipy/issues/1018/events","html_url":"https://github.com/nipy/dipy/pull/1018","id":143158791,"number":1018,"title":"Fix: denspeed.pyx to give correct output for nlmeans","user":{"login":"riddhishb","id":7941975,"avatar_url":"https://avatars.githubusercontent.com/u/7941975?v=3","gravatar_id":"","url":"https://api.github.com/users/riddhishb","html_url":"https://github.com/riddhishb","followers_url":"https://api.github.com/users/riddhishb/followers","following_url":"https://api.github.com/users/riddhishb/following{/other_user}","gists_url":"https://api.github.com/users/riddhishb/gists{/gist_id}","starred_url":"https://api.github.com/users/riddhishb/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/riddhishb/subscriptions","organizations_url":"https://api.github.com/users/riddhishb/orgs","repos_url":"https://api.github.com/users/riddhishb/repos","events_url":"https://api.github.com/users/riddhishb/events{/privacy}","received_events_url":"https://api.github.com/users/riddhishb/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":10,"created_at":"2016-03-24T05:41:21Z","updated_at":"2016-04-29T06:31:46Z","closed_at":null,"pull_request":{"url":"https://api.github.com/repos/nipy/dipy/pulls/1018","html_url":"https://github.com/nipy/dipy/pull/1018","diff_url":"https://github.com/nipy/dipy/pull/1018.diff","patch_url":"https://github.com/nipy/dipy/pull/1018.patch"},"body":"The bugfix in the implementation of denspeed in reference to #1011 \r\nNow we can use any patch_radius and block_radius for denoising purpose\r\n\r\n- The implementation follows the block weighing approach which is then averaged for each voxel.\r\n- Does not exactly follow the [coupe2008](http://www.ncbi.nlm.nih.gov/pubmed/18390341) block      averaging approach\r\n- To follow the [coupe2008] approach, the existing code by @omarocegueda [here](https://github.com/omarocegueda/denoise/blob/master/ornlm/ornlm.pyx) is accurate, but it needs to be optimized (I am working on that currently!)"},"comment":{"url":"https://api.github.com/repos/nipy/dipy/issues/comments/215637311","html_url":"https://github.com/nipy/dipy/pull/1018#issuecomment-215637311","issue_url":"https://api.github.com/repos/nipy/dipy/issues/1018","id":215637311,"user":{"login":"riddhishb","id":7941975,"avatar_url":"https://avatars.githubusercontent.com/u/7941975?v=3","gravatar_id":"","url":"https://api.github.com/users/riddhishb","html_url":"https://github.com/riddhishb","followers_url":"https://api.github.com/users/riddhishb/followers","following_url":"https://api.github.com/users/riddhishb/following{/other_user}","gists_url":"https://api.github.com/users/riddhishb/gists{/gist_id}","starred_url":"https://api.github.com/users/riddhishb/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/riddhishb/subscriptions","organizations_url":"https://api.github.com/users/riddhishb/orgs","repos_url":"https://api.github.com/users/riddhishb/repos","events_url":"https://api.github.com/users/riddhishb/events{/privacy}","received_events_url":"https://api.github.com/users/riddhishb/received_events","type":"User","site_admin":false},"created_at":"2016-04-29T06:31:46Z","updated_at":"2016-04-29T06:31:46Z","body":"@Garyfallidis I am trying to fix that bug, but for some reason I am not able to annotate the cython code for denspeed\r\n\r\nI do `cython -a denspeed.pyx`\r\n\r\nbut I get this \r\n\r\n\r\nError compiling Cython file\r\n\r\n> import numpy as np\r\n> cimport numpy as cnp\r\n> \r\n> cimport cython\r\n> cimport safe_openmp as openmp\r\n\r\ndenspeed.pyx:7:8: 'safe_openmp.pxd' not found\r\n\r\nError compiling Cython file\r\n\r\n> import numpy as np\r\n> cimport numpy as cnp\r\n> \r\n> cimport cython\r\n> cimport safe_openmp as openmp\r\n> from safe_openmp cimport have_openmp\r\n\r\ndenspeed.pyx:8:0: 'safe_openmp/have_openmp.pxd' not found\r\n\r\nI cannot figure out as to why os this happening, any ideas ?"}}