{"action":"created","issue":{"url":"https://api.github.com/repos/ChristophKirst/ClearMap/issues/4","repository_url":"https://api.github.com/repos/ChristophKirst/ClearMap","labels_url":"https://api.github.com/repos/ChristophKirst/ClearMap/issues/4/labels{/name}","comments_url":"https://api.github.com/repos/ChristophKirst/ClearMap/issues/4/comments","events_url":"https://api.github.com/repos/ChristophKirst/ClearMap/issues/4/events","html_url":"https://github.com/ChristophKirst/ClearMap/issues/4","id":165424641,"number":4,"title":"IndexError: tuple index out of range in ClearMap.Anlysis.Voxelization.voxelizeSphere()","user":{"login":"pforai","id":32458,"avatar_url":"https://avatars.githubusercontent.com/u/32458?v=3","gravatar_id":"","url":"https://api.github.com/users/pforai","html_url":"https://github.com/pforai","followers_url":"https://api.github.com/users/pforai/followers","following_url":"https://api.github.com/users/pforai/following{/other_user}","gists_url":"https://api.github.com/users/pforai/gists{/gist_id}","starred_url":"https://api.github.com/users/pforai/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/pforai/subscriptions","organizations_url":"https://api.github.com/users/pforai/orgs","repos_url":"https://api.github.com/users/pforai/repos","events_url":"https://api.github.com/users/pforai/events{/privacy}","received_events_url":"https://api.github.com/users/pforai/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":4,"created_at":"2016-07-13T21:22:21Z","updated_at":"2016-07-14T15:43:48Z","closed_at":null,"body":"Hi Christoph,\r\n\r\nNext hiccup on our end can be seen here: \r\n\r\n```bash \r\n[...]\r\nTransformix has finished at Wed Jul 13 23:13:36 2016.\r\nElapsed time: 4 Seconds.\r\n\r\nTraceback (most recent call last):\r\n  File \"process_template_1.py\", line 76, in <module>\r\n    vox = voxelize(points, AtlasFile, **voxelizeParameter);\r\n  File \"/groups/keays/software/clearmap/lib/python2.7/site-packages/ClearMap-0.9.2-py2.7.egg/ClearMap/Analysis/Voxelization.py\", line 45, in voxelize\r\n    data = vox.voxelizeSphere(points.astype('float'), dataSize[0], dataSize[1], dataSize[2], size[0], size[1], size[2]);\r\nIndexError: tuple index out of range\r\n```\r\n\r\nAny idea what to try to debug this?\r\n\r\nThe voxelization params are \r\n\r\n```Python\r\n\r\nvoxelizeParameter = {\r\n     \"method\" : 'Spherical',\r\n     \"size\" : (15,15,15),\r\n     \"weights\" : None,\r\n}\r\n```"},"comment":{"url":"https://api.github.com/repos/ChristophKirst/ClearMap/issues/comments/232704417","html_url":"https://github.com/ChristophKirst/ClearMap/issues/4#issuecomment-232704417","issue_url":"https://api.github.com/repos/ChristophKirst/ClearMap/issues/4","id":232704417,"user":{"login":"lukasla","id":20461620,"avatar_url":"https://avatars.githubusercontent.com/u/20461620?v=3","gravatar_id":"","url":"https://api.github.com/users/lukasla","html_url":"https://github.com/lukasla","followers_url":"https://api.github.com/users/lukasla/followers","following_url":"https://api.github.com/users/lukasla/following{/other_user}","gists_url":"https://api.github.com/users/lukasla/gists{/gist_id}","starred_url":"https://api.github.com/users/lukasla/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/lukasla/subscriptions","organizations_url":"https://api.github.com/users/lukasla/orgs","repos_url":"https://api.github.com/users/lukasla/repos","events_url":"https://api.github.com/users/lukasla/events{/privacy}","received_events_url":"https://api.github.com/users/lukasla/received_events","type":"User","site_admin":false},"created_at":"2016-07-14T15:43:48Z","updated_at":"2016-07-14T15:43:48Z","body":"Following is the info from Fiji the template_25.tif file we used.\r\n```Bash\r\nNRRD0004\r\n# Complete NRRD file format specification at:\r\n# http://teem.sourceforge.net/nrrd/format.html\r\ntype: unsigned short\r\ndimension: 3\r\nspace: left-posterior-superior\r\nsizes: 528 320 456\r\nspace directions: (25,0,0) (0,25,0) (0,0,25)\r\nkinds: domain domain domain\r\nendian: little\r\nencoding: gzip\r\nspace origin: (0,0,0)\r\n\r\n------------------------------------------------------\r\n(Fiji Is Just) ImageJ 2.0.0-rc-43/1.50e; Java 1.6.0_65 [64-bit]; Mac OS X 10.10.5; 365MB of 5205MB (7%)\r\n \r\nTitle: template_25-1.tif\r\nWidth:  8000 microns (320)\r\nHeight:  13200 microns (528)\r\nDepth:  11400 microns (456)\r\nSize:  147MB\r\nResolution:  0.04 pixels per micron\r\nVoxel size: 25x25x25 micron^3\r\nID: -4\r\nBits per pixel: 16 (unsigned)\r\nDisplay range: 0 - 516\r\nImage: 210/456\r\nNo threshold\r\nUncalibrated\r\nPath: /Volumes/groups-2/keays/Clearedbrains/MRIBrainsI/ClearMap_ressources/25umAutofluoReference/template_25.tif\r\nScreen location: 820,99 (1280x800)\r\nCoordinate origin:  0,0,0\r\nNo overlay\r\nNo selection\r\n\r\n````\r\n\r\nRunning your python code gives us \r\n\r\n```Python\r\n>>> import ClearMap.IO as io\r\n>>> fn = 'template_25.tif'\r\n>>> fn = '/groups/keays/Clearedbrains/MRIBrainsI/ClearMap_ressources/template_25.tif' \r\n>>> io.dataSize(fn)\r\n(528, 456)\r\n>>> \r\n```\r\n\r\nAre 3D TIFFs some extension that libtiff or Python tifffile doesnt support?"}}
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