{"action":"closed","issue":{"url":"https://api.github.com/repos/cryoem-uoft/cryosparc-issues/issues/89","repository_url":"https://api.github.com/repos/cryoem-uoft/cryosparc-issues","labels_url":"https://api.github.com/repos/cryoem-uoft/cryosparc-issues/issues/89/labels{/name}","comments_url":"https://api.github.com/repos/cryoem-uoft/cryosparc-issues/issues/89/comments","events_url":"https://api.github.com/repos/cryoem-uoft/cryosparc-issues/issues/89/events","html_url":"https://github.com/cryoem-uoft/cryosparc-issues/issues/89","id":195167146,"number":89,"title":"Phase Plate Data","user":{"login":"tanyongzi","id":23065000,"avatar_url":"https://avatars.githubusercontent.com/u/23065000?v=3","gravatar_id":"","url":"https://api.github.com/users/tanyongzi","html_url":"https://github.com/tanyongzi","followers_url":"https://api.github.com/users/tanyongzi/followers","following_url":"https://api.github.com/users/tanyongzi/following{/other_user}","gists_url":"https://api.github.com/users/tanyongzi/gists{/gist_id}","starred_url":"https://api.github.com/users/tanyongzi/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/tanyongzi/subscriptions","organizations_url":"https://api.github.com/users/tanyongzi/orgs","repos_url":"https://api.github.com/users/tanyongzi/repos","events_url":"https://api.github.com/users/tanyongzi/events{/privacy}","received_events_url":"https://api.github.com/users/tanyongzi/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":5,"created_at":"2016-12-13T05:44:13Z","updated_at":"2016-12-17T08:40:49Z","closed_at":"2016-12-17T08:40:49Z","body":"I finally got around to testing the phase plate dataset on the latest CryoSPARC. However it seems to throw up an error during ab initio:\r\n\r\nTraceback (most recent call last):\r\n  File \"/mnt/fast_scratch/progs/cryosparc/cryosparc-compute/sparcjob.py\", line 218, in <module>\r\n    cuda_devs = exp_params['cuda_devs'])\r\n  File \"/mnt/fast_scratch/progs/cryosparc/cryosparc-compute/abinit.py\", line 338, in abinit\r\n    class_anneal_beta = class_anneal_beta)\r\n  File \"/mnt/fast_scratch/progs/cryosparc/cryosparc-compute/reconstruct.py\", line 281, in reconstruction_kernel\r\n    work(img)\r\n  File \"/mnt/fast_scratch/progs/cryosparc/cryosparc-compute/reconstruct.py\", line 229, in work\r\n    IW.compute_conditional_normalization_constant_and_logphis()\r\n  File \"/mnt/fast_scratch/progs/cryosparc/cryosparc-compute/objectives/cudaworker.py\", line 1462, in compute_conditional_normalization_constant_and_logphis\r\n    assert n.isfinite(self.conditional_logZ)\r\nAssertionError\r\n\r\nCould it be a problem with the amplitude contrast? Thank you."}}
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