{"action":"created","issue":{"url":"https://api.github.com/repos/BodenmillerGroup/imctools/issues/27","repository_url":"https://api.github.com/repos/BodenmillerGroup/imctools","labels_url":"https://api.github.com/repos/BodenmillerGroup/imctools/issues/27/labels{/name}","comments_url":"https://api.github.com/repos/BodenmillerGroup/imctools/issues/27/comments","events_url":"https://api.github.com/repos/BodenmillerGroup/imctools/issues/27/events","html_url":"https://github.com/BodenmillerGroup/imctools/issues/27","id":346737421,"node_id":"MDU6SXNzdWUzNDY3Mzc0MjE=","number":27,"title":"ome2singletiff error on windows, histocat conversion errors.","user":{"login":"arcolombo","id":5473099,"node_id":"MDQ6VXNlcjU0NzMwOTk=","avatar_url":"https://avatars0.githubusercontent.com/u/5473099?v=4","gravatar_id":"","url":"https://api.github.com/users/arcolombo","html_url":"https://github.com/arcolombo","followers_url":"https://api.github.com/users/arcolombo/followers","following_url":"https://api.github.com/users/arcolombo/following{/other_user}","gists_url":"https://api.github.com/users/arcolombo/gists{/gist_id}","starred_url":"https://api.github.com/users/arcolombo/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/arcolombo/subscriptions","organizations_url":"https://api.github.com/users/arcolombo/orgs","repos_url":"https://api.github.com/users/arcolombo/repos","events_url":"https://api.github.com/users/arcolombo/events{/privacy}","received_events_url":"https://api.github.com/users/arcolombo/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":2,"created_at":"2018-08-01T19:31:35Z","updated_at":"2018-08-02T07:01:36Z","closed_at":null,"author_association":"NONE","body":"Hello. I am working on the IMCpipeline and the imc2tiff conversion successfully completed! \r\n\r\nNow, I am working off the IMCpipeline in particular this section\r\n if do_histocat:\r\n    if not(os.path.exists(folder_histocat)):\r\n        os.makedirs(folder_histocat)\r\n    ome2micat.omefolder2micatfolder(folder_ome, folder_histocat, dtype='uint16')\r\n\r\n\r\nI do have the imctools with this script successfully installed. \r\npython -m imctools.scripts.ome2micat -h\r\nusage: ome2micat [-h] [--mask_folder MASK_FOLDER] [--mask_suffix MASK_SUFFIX]\r\n                 [--imagetype {None,uint16,int16,float}]\r\n                 ome_folder out_folder\r\n\r\nConvertes an ome folder (or file) to a micat folder\r\n\r\npositional arguments:\r\n  ome_folder            A folder with ome images or a single ome file\r\n  out_folder            Folder to output the micat folders\r\n\r\noptional arguments:\r\n  -h, --help            show this help message and exit\r\n  --mask_folder MASK_FOLDER\r\n                        Folder containing the masks, or single mask file.\r\n  --mask_suffix MASK_SUFFIX\r\n                        suffix of the mask tiffs\r\n  --imagetype {None,uint16,int16,float}\r\n                        The output image type\r\n\r\n\r\nHowever when I issue the command to convert the ome.tiffs to HistoCAT compatible files, there is an error.\r\n\r\n>>> folder_ome\r\n'C:/Users/Mohan/Desktop/testing/OUTPUT\\\\ometiff'\r\n>>> folder_histocat\r\n'C:/Users/Mohan/Desktop/testing/OUTPUT\\\\histocat'\r\n>>> ome2micat.omefolder2micatfolder(folder_ome, folder_histocat, dtype='uint16')\r\nTraceback (most recent call last):\r\n  File \"<stdin>\", line 1, in <module>\r\n  File \"C:\\Users\\Mohan\\Anaconda3\\lib\\site-packages\\imctools\\scripts\\ome2micat.py\", line 72, in omefolder2micatfolder\r\n    ome2micatfolder(path_ome, outfolder, path_mask=path_mask, dtype=dtype)\r\n  File \"C:\\Users\\Mohan\\Anaconda3\\lib\\site-packages\\imctools\\scripts\\ome2micat.py\", line 39, in ome2micatfolder\r\n    ome2singletiff(path_ome, outfolder,basename='', dtype=dtype)\r\n  File \"C:\\Users\\Mohan\\Anaconda3\\lib\\site-packages\\imctools\\scripts\\ome2micat.py\", line 15, in ome2singletiff\r\n    ome = ometiffparser.OmetiffParser(path_ome)\r\n  File \"C:\\Users\\Mohan\\Anaconda3\\lib\\site-packages\\imctools\\io\\ometiffparser.py\", line 22, in __init__\r\n    self.read_image(original_file)\r\n  File \"C:\\Users\\Mohan\\Anaconda3\\lib\\site-packages\\imctools\\io\\ometiffparser.py\", line 46, in read_image\r\n    self.ome = tif.pages[0].tags['image_description'].value\r\nKeyError: 'image_description'\r\n>>>\r\n\r\n####\r\nI have tifffile installed \r\ntifffile                  0.15.1                   py36_1    conda-forge\r\n>python -V\r\nPython 3.6.4 :: Anaconda, Inc.\r\n\r\n\r\n\r\nI have CellProfiler Desktop app installed version 2.2.0.    \r\nMy question is that the error is related to ometiffparser, how can I debug this?  is this related to my tifffile version?  What should be the dtype parameter for a windows OS?  \r\n\r\nThank you very much,\r\n\r\nSIncerely,\r\nAC\r\n"},"comment":{"url":"https://api.github.com/repos/BodenmillerGroup/imctools/issues/comments/409827107","html_url":"https://github.com/BodenmillerGroup/imctools/issues/27#issuecomment-409827107","issue_url":"https://api.github.com/repos/BodenmillerGroup/imctools/issues/27","id":409827107,"node_id":"MDEyOklzc3VlQ29tbWVudDQwOTgyNzEwNw==","user":{"login":"votti","id":3743016,"node_id":"MDQ6VXNlcjM3NDMwMTY=","avatar_url":"https://avatars1.githubusercontent.com/u/3743016?v=4","gravatar_id":"","url":"https://api.github.com/users/votti","html_url":"https://github.com/votti","followers_url":"https://api.github.com/users/votti/followers","following_url":"https://api.github.com/users/votti/following{/other_user}","gists_url":"https://api.github.com/users/votti/gists{/gist_id}","starred_url":"https://api.github.com/users/votti/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/votti/subscriptions","organizations_url":"https://api.github.com/users/votti/orgs","repos_url":"https://api.github.com/users/votti/repos","events_url":"https://api.github.com/users/votti/events{/privacy}","received_events_url":"https://api.github.com/users/votti/received_events","type":"User","site_admin":false},"created_at":"2018-08-02T07:01:36Z","updated_at":"2018-08-02T07:01:36Z","author_association":"CONTRIBUTOR","body":"Hey arcolombo,\r\n\r\nThanks for reporting the issue!\r\nThis is a duplicate of issue #22 - it originates from a change in the `tifffile` library.\r\n\r\nThis is already fixed in the development branch of `imctools`\r\nCould you try to install the development branch:\r\n`pip install git+https://github.com/BodenmillerGroup/imctools.git@development`\r\nand report back if this fixes the issue?\r\n"}}
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