{"action":"created","issue":{"url":"https://api.github.com/repos/cryoem-uoft/cryosparc-issues/issues/74","repository_url":"https://api.github.com/repos/cryoem-uoft/cryosparc-issues","labels_url":"https://api.github.com/repos/cryoem-uoft/cryosparc-issues/issues/74/labels{/name}","comments_url":"https://api.github.com/repos/cryoem-uoft/cryosparc-issues/issues/74/comments","events_url":"https://api.github.com/repos/cryoem-uoft/cryosparc-issues/issues/74/events","html_url":"https://github.com/cryoem-uoft/cryosparc-issues/issues/74","id":188669878,"number":74,"title":"New Dataset issue (IndexError: list index out of range)","user":{"login":"kylelmorris","id":19749872,"avatar_url":"https://avatars.githubusercontent.com/u/19749872?v=3","gravatar_id":"","url":"https://api.github.com/users/kylelmorris","html_url":"https://github.com/kylelmorris","followers_url":"https://api.github.com/users/kylelmorris/followers","following_url":"https://api.github.com/users/kylelmorris/following{/other_user}","gists_url":"https://api.github.com/users/kylelmorris/gists{/gist_id}","starred_url":"https://api.github.com/users/kylelmorris/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/kylelmorris/subscriptions","organizations_url":"https://api.github.com/users/kylelmorris/orgs","repos_url":"https://api.github.com/users/kylelmorris/repos","events_url":"https://api.github.com/users/kylelmorris/events{/privacy}","received_events_url":"https://api.github.com/users/kylelmorris/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":4,"created_at":"2016-11-11T02:22:36Z","updated_at":"2016-11-18T01:30:12Z","closed_at":null,"body":"I am consistently getting the following import error. Happens regardless of whether I point to the original location of the *.star and *.mrcs in the original relion directory structure or create a single new stack with associated star file. Not a python person, guessing this is an error in counting columns in the star file but could someone point me to where this error precisely arises from?\r\n\r\nThanks!\r\n\r\nLaunched job bvfWJP6DB7Q8ndAai\r\nLicense is valid.\r\nJob Type:  visualize_dataset  Job ID:  bvfWJP6DB7Q8ndAai\r\nAssigned Slots: RAM:  None  GPU:  None\r\nVisualizing Dataset ID fZx4etJcRK5Smg9bG\r\nLoading Dataset ... \r\n---- Loading File Set. Type: star Path: /home/kmorris/cryosparc/run/bulk/./sdd1/data/Qingtao/titan_K2_AP1_dataset/relion/autopick_all_bin4.star\r\nTraceback (most recent call last):\r\n  File \"/home/kmorris/cryosparc/cryosparc-compute/sparcjob.py\", line 78, in <module>\r\n    dataset = dataio.dataset_factory(dataset_params, do_cache=False, do_datasign_estimation=False)\r\n  File \"/home/kmorris/cryosparc/cryosparc-compute/dataio/__init__.py\", line 22, in dataset_factory\r\n    do_cache=do_cache)\r\n  File \"/home/kmorris/cryosparc/cryosparc-compute/dataio/load.py\", line 44, in fileset_into_dataset\r\n    images = extension_map[meta_type](dataset, meta_input)\r\n  File \"/home/kmorris/cryosparc/cryosparc-compute/dataio/load.py\", line 206, in star_into_dataset\r\n    data = n.loadtxt(fname, dtype=str, skiprows = numhdr, usecols=range(len(labels)))\r\n  File \"/home/kmorris/cryosparc/anaconda2/lib/python2.7/site-packages/numpy/lib/npyio.py\", line 806, in loadtxt\r\n    vals = [vals[i] for i in usecols]\r\nIndexError: list index out of range"},"comment":{"url":"https://api.github.com/repos/cryoem-uoft/cryosparc-issues/issues/comments/261423507","html_url":"https://github.com/cryoem-uoft/cryosparc-issues/issues/74#issuecomment-261423507","issue_url":"https://api.github.com/repos/cryoem-uoft/cryosparc-issues/issues/74","id":261423507,"user":{"login":"kylelmorris","id":19749872,"avatar_url":"https://avatars.githubusercontent.com/u/19749872?v=3","gravatar_id":"","url":"https://api.github.com/users/kylelmorris","html_url":"https://github.com/kylelmorris","followers_url":"https://api.github.com/users/kylelmorris/followers","following_url":"https://api.github.com/users/kylelmorris/following{/other_user}","gists_url":"https://api.github.com/users/kylelmorris/gists{/gist_id}","starred_url":"https://api.github.com/users/kylelmorris/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/kylelmorris/subscriptions","organizations_url":"https://api.github.com/users/kylelmorris/orgs","repos_url":"https://api.github.com/users/kylelmorris/repos","events_url":"https://api.github.com/users/kylelmorris/events{/privacy}","received_events_url":"https://api.github.com/users/kylelmorris/received_events","type":"User","site_admin":false},"created_at":"2016-11-18T01:30:12Z","updated_at":"2016-11-18T01:30:12Z","body":"I got relion to make the star file again by reextracting the particles and everything was fine. Sorry, in the process I lost the naughty star file.... If it happens again I'll send over, thanks for your help Ali!"}}
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