{"action":"created","issue":{"url":"https://api.github.com/repos/scikit-image/scikit-image/issues/1362","labels_url":"https://api.github.com/repos/scikit-image/scikit-image/issues/1362/labels{/name}","comments_url":"https://api.github.com/repos/scikit-image/scikit-image/issues/1362/comments","events_url":"https://api.github.com/repos/scikit-image/scikit-image/issues/1362/events","html_url":"https://github.com/scikit-image/scikit-image/issues/1362","id":56147827,"number":1362,"title":"Remove umfpack dependency from random walker segmentation.","user":{"login":"r3vl1s","id":8863799,"avatar_url":"https://avatars.githubusercontent.com/u/8863799?v=3","gravatar_id":"","url":"https://api.github.com/users/r3vl1s","html_url":"https://github.com/r3vl1s","followers_url":"https://api.github.com/users/r3vl1s/followers","following_url":"https://api.github.com/users/r3vl1s/following{/other_user}","gists_url":"https://api.github.com/users/r3vl1s/gists{/gist_id}","starred_url":"https://api.github.com/users/r3vl1s/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/r3vl1s/subscriptions","organizations_url":"https://api.github.com/users/r3vl1s/orgs","repos_url":"https://api.github.com/users/r3vl1s/repos","events_url":"https://api.github.com/users/r3vl1s/events{/privacy}","received_events_url":"https://api.github.com/users/r3vl1s/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":5,"created_at":"2015-02-01T01:40:58Z","updated_at":"2015-02-05T07:21:10Z","closed_at":null,"body":"This is a low priority issue as it doesn't affect random walker functionality, but as of scipy 0.14 umfpack is deprecated (see http://docs.scipy.org/doc/scipy-dev/reference/release.0.14.0.html#scipy-sparse-linalg).\r\n\r\nIt's used to speed up some cases in random_walker_segmentation.py from skimage.segmentation.\r\nThere seems to be an unmaintained scikit (https://github.com/rc/scikit-umfpack). \r\n\r\nI think removing it from random_walker_segmentation.py is a good idea. "},"comment":{"url":"https://api.github.com/repos/scikit-image/scikit-image/issues/comments/73004703","html_url":"https://github.com/scikit-image/scikit-image/issues/1362#issuecomment-73004703","issue_url":"https://api.github.com/repos/scikit-image/scikit-image/issues/1362","id":73004703,"user":{"login":"emmanuelle","id":263366,"avatar_url":"https://avatars.githubusercontent.com/u/263366?v=3","gravatar_id":"","url":"https://api.github.com/users/emmanuelle","html_url":"https://github.com/emmanuelle","followers_url":"https://api.github.com/users/emmanuelle/followers","following_url":"https://api.github.com/users/emmanuelle/following{/other_user}","gists_url":"https://api.github.com/users/emmanuelle/gists{/gist_id}","starred_url":"https://api.github.com/users/emmanuelle/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/emmanuelle/subscriptions","organizations_url":"https://api.github.com/users/emmanuelle/orgs","repos_url":"https://api.github.com/users/emmanuelle/repos","events_url":"https://api.github.com/users/emmanuelle/events{/privacy}","received_events_url":"https://api.github.com/users/emmanuelle/received_events","type":"User","site_admin":false},"created_at":"2015-02-05T07:21:10Z","updated_at":"2015-02-05T07:21:10Z","body":"Yes, it's easy to replace the linear system inversion by a fixed-point equation that is a set of local updates. The issue is that when doing so, one loses the multigrid acceleration. of pyamg For example, if there are only a few markers in a large image, it will take a large number of iterations to broadcast the information of the markers to the other pixels. I think pyamg uses coarser aggregated versions of the graph of pixels, resulting in a faster convergence.\r\n\r\nI could open a pull request with the code that I already have (using the local fixed-point equations) so that we can discuss such matters."}}