{"action":"created","issue":{"url":"https://api.github.com/repos/OpenChemistry/tomviz/issues/752","repository_url":"https://api.github.com/repos/OpenChemistry/tomviz","labels_url":"https://api.github.com/repos/OpenChemistry/tomviz/issues/752/labels{/name}","comments_url":"https://api.github.com/repos/OpenChemistry/tomviz/issues/752/comments","events_url":"https://api.github.com/repos/OpenChemistry/tomviz/issues/752/events","html_url":"https://github.com/OpenChemistry/tomviz/pull/752","id":188364003,"number":752,"title":"Improve automatic tilt image alignment","user":{"login":"yijiang1","id":13088588,"avatar_url":"https://avatars.githubusercontent.com/u/13088588?v=3","gravatar_id":"","url":"https://api.github.com/users/yijiang1","html_url":"https://github.com/yijiang1","followers_url":"https://api.github.com/users/yijiang1/followers","following_url":"https://api.github.com/users/yijiang1/following{/other_user}","gists_url":"https://api.github.com/users/yijiang1/gists{/gist_id}","starred_url":"https://api.github.com/users/yijiang1/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/yijiang1/subscriptions","organizations_url":"https://api.github.com/users/yijiang1/orgs","repos_url":"https://api.github.com/users/yijiang1/repos","events_url":"https://api.github.com/users/yijiang1/events{/privacy}","received_events_url":"https://api.github.com/users/yijiang1/received_events","type":"User","site_admin":false},"labels":[{"id":287923090,"url":"https://api.github.com/repos/OpenChemistry/tomviz/labels/ready","name":"ready","color":"ededed","default":false}],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":1,"created_at":"2016-11-09T22:02:47Z","updated_at":"2016-11-10T19:51:07Z","closed_at":null,"pull_request":{"url":"https://api.github.com/repos/OpenChemistry/tomviz/pulls/752","html_url":"https://github.com/OpenChemistry/tomviz/pull/752","diff_url":"https://github.com/OpenChemistry/tomviz/pull/752.diff","patch_url":"https://github.com/OpenChemistry/tomviz/pull/752.patch"},"body":"Made a couple of changes related to automatic tilt image alignment.\r\n1. Added a new section \"simulation\" to  tomography menu:\r\n<img width=\"200\" alt=\"screen shot 2016-11-09 at 5 04 52 pm\" src=\"https://cloud.githubusercontent.com/assets/13088588/20156547/b8198896-a69e-11e6-8b67-44eb045437a5.png\">\r\n<img width=\"200\" alt=\"screen shot 2016-11-09 at 5 05 04 pm\" src=\"https://cloud.githubusercontent.com/assets/13088588/20156551/c05f82f8-a69e-11e6-9c92-5bd010f7ccda.png\">\r\n\r\n2. Added a python function that applies random integer shifts to tilt images. This is useful when testing various alignment methods.\r\n![tomviz_test_tilt_series128_random_shifted](https://cloud.githubusercontent.com/assets/13088588/20156841/176e10fe-a6a0-11e6-8f81-292aa17c47a2.gif)\r\n\r\n3. Added real space and Fourier space to the old cross correlation alignment method. Also the reference image is now the zero-degree tilt image instead of the first tilt image.\r\n![tomviz_test_tilt_series256_random_shifted_cc_align](https://cloud.githubusercontent.com/assets/13088588/20157246/fa09702e-a6a1-11e6-865f-e4ecadc62084.gif)\r\n\r\n4. Added a simple center of mass alignment method, which shifts the center of mass of each tilt image to origin (center of matrix). This works best after background subtraction.\r\n![tomviz_test_tilt_series256_random_shifted_com_align](https://cloud.githubusercontent.com/assets/13088588/20157119/616e049c-a6a1-11e6-9ead-b87d1e063584.gif)\r\n"},"comment":{"url":"https://api.github.com/repos/OpenChemistry/tomviz/issues/comments/259789558","html_url":"https://github.com/OpenChemistry/tomviz/pull/752#issuecomment-259789558","issue_url":"https://api.github.com/repos/OpenChemistry/tomviz/issues/752","id":259789558,"user":{"login":"yijiang1","id":13088588,"avatar_url":"https://avatars.githubusercontent.com/u/13088588?v=3","gravatar_id":"","url":"https://api.github.com/users/yijiang1","html_url":"https://github.com/yijiang1","followers_url":"https://api.github.com/users/yijiang1/followers","following_url":"https://api.github.com/users/yijiang1/following{/other_user}","gists_url":"https://api.github.com/users/yijiang1/gists{/gist_id}","starred_url":"https://api.github.com/users/yijiang1/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/yijiang1/subscriptions","organizations_url":"https://api.github.com/users/yijiang1/orgs","repos_url":"https://api.github.com/users/yijiang1/repos","events_url":"https://api.github.com/users/yijiang1/events{/privacy}","received_events_url":"https://api.github.com/users/yijiang1/received_events","type":"User","site_admin":false},"created_at":"2016-11-10T19:51:07Z","updated_at":"2016-11-10T19:51:07Z","body":"I changed the label in ShiftTiltSeriesRandomly dialog and tweak the tomography menu based on @ElliotPadgett 's feedback.\r\n<img width=\"200\" alt=\"screen shot 2016-11-10 at 2 44 27 pm\" src=\"https://cloud.githubusercontent.com/assets/13088588/20191772/fc1243d8-a754-11e6-854c-c6919d6805e9.png\"><img width=\"200\" alt=\"screen shot 2016-11-10 at 2 45 15 pm\" src=\"https://cloud.githubusercontent.com/assets/13088588/20191785/06c1d03c-a755-11e6-8c41-d42ef62e4a2d.png\">\r\n\r\n"}}
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