{"action":"created","issue":{"url":"https://api.github.com/repos/tlambert03/tifffolder/issues/2","repository_url":"https://api.github.com/repos/tlambert03/tifffolder","labels_url":"https://api.github.com/repos/tlambert03/tifffolder/issues/2/labels{/name}","comments_url":"https://api.github.com/repos/tlambert03/tifffolder/issues/2/comments","events_url":"https://api.github.com/repos/tlambert03/tifffolder/issues/2/events","html_url":"https://github.com/tlambert03/tifffolder/issues/2","id":363038099,"node_id":"MDU6SXNzdWUzNjMwMzgwOTk=","number":2,"title":"Folder of 2D tifs","user":{"login":"VolkerH","id":2210044,"node_id":"MDQ6VXNlcjIyMTAwNDQ=","avatar_url":"https://avatars2.githubusercontent.com/u/2210044?v=4","gravatar_id":"","url":"https://api.github.com/users/VolkerH","html_url":"https://github.com/VolkerH","followers_url":"https://api.github.com/users/VolkerH/followers","following_url":"https://api.github.com/users/VolkerH/following{/other_user}","gists_url":"https://api.github.com/users/VolkerH/gists{/gist_id}","starred_url":"https://api.github.com/users/VolkerH/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/VolkerH/subscriptions","organizations_url":"https://api.github.com/users/VolkerH/orgs","repos_url":"https://api.github.com/users/VolkerH/repos","events_url":"https://api.github.com/users/VolkerH/events{/privacy}","received_events_url":"https://api.github.com/users/VolkerH/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":0,"created_at":"2018-09-24T07:31:22Z","updated_at":"2018-09-24T13:29:17Z","closed_at":null,"author_association":"NONE","body":"I'm trying to use this on a folder full of 2D tiff slices. All in all, I have 6 dimensions:\r\n\r\n1. illumination direction\r\n2. tile postion u\r\n3. tile position v\r\n4. z-slice\r\n5. x\r\n6. y\r\n\r\nonly `x` and `y` dimensions are contained in the individual tiff files  in the folder.\r\nThe code bombs out with a `ShapeError`. This should not be quite unexpected as during debugging I noticed that this happens in a section of code with a `# FIX ME: ASSUMING THAT FILES ARE Z STACKS FOR NOW` tag.\r\n\r\nIs this something that is a fairly quick fix? I started looking into the code, but haven't quite gotten my head around how you pass around indexing and slicing objects.  \r\n\r\nThis is the code snippet that produces the error:\r\n\r\n```\r\npattern = {'u':'{d} x', 'w':'x {d}', 'd': 'C{d2}', 's': ' Z{d}'}\r\nf = tifffolder.TiffFolder('C:/Users/Volker/Data/180903_UM_Test/tmp', pattern, axes ='uwds' )\r\nprint(\"excluded\" , f.list_excluded())\r\nprint(\"files\", f.files)\r\nprint(\"shape\", f.shape)\r\nprint(\"pixel\", f[0,0,0,0,0,0])\r\n```\r\nand here is what happens when trying to get to that first voxel:\r\n\r\n![image](https://user-images.githubusercontent.com/2210044/45940910-16923580-c01f-11e8-8bfe-b7e4ecf0f6d3.png)\r\n\r\nBTW: I came across your `tifffolder` and `imarispy` repos while looking at LLSpy. As I'm trying to create some sort of streamlined workflow to collect files from a LaVision Biotech Ultramicroscope and convert them to Big Data Viewer format for stitching with Big Data Viewer both these projects seem to offer an elegant solution (without using Java). So thanks for making these public. "},"comment":{"url":"https://api.github.com/repos/tlambert03/tifffolder/issues/comments/423974511","html_url":"https://github.com/tlambert03/tifffolder/issues/2#issuecomment-423974511","issue_url":"https://api.github.com/repos/tlambert03/tifffolder/issues/2","id":423974511,"node_id":"MDEyOklzc3VlQ29tbWVudDQyMzk3NDUxMQ==","user":{"login":"tlambert03","id":1609449,"node_id":"MDQ6VXNlcjE2MDk0NDk=","avatar_url":"https://avatars3.githubusercontent.com/u/1609449?v=4","gravatar_id":"","url":"https://api.github.com/users/tlambert03","html_url":"https://github.com/tlambert03","followers_url":"https://api.github.com/users/tlambert03/followers","following_url":"https://api.github.com/users/tlambert03/following{/other_user}","gists_url":"https://api.github.com/users/tlambert03/gists{/gist_id}","starred_url":"https://api.github.com/users/tlambert03/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/tlambert03/subscriptions","organizations_url":"https://api.github.com/users/tlambert03/orgs","repos_url":"https://api.github.com/users/tlambert03/repos","events_url":"https://api.github.com/users/tlambert03/events{/privacy}","received_events_url":"https://api.github.com/users/tlambert03/received_events","type":"User","site_admin":false},"created_at":"2018-09-24T13:29:17Z","updated_at":"2018-09-24T13:29:17Z","author_association":"OWNER","body":"Hey, thanks for having a look.\r\n\r\nglad you're playing around with it and hope that it can be useful for you!  I'm not sure anyone else has really tried to use this besides me, so there will likely be some issues like this that need addressing... but i'm happy to try to modify the code (or accept PRs) to get it working for you if you think it's going to be a good match for your needs.  The `imarispy` repo should also be \"close\" to working (particularly for BDV... less so for imaris without a modified h5py library).\r\n\r\nfor this problem of 2D images, it will be easiest to help if I can get a sample dataset to play with.  Can you email me a dropbox link (or post here or use whatever method you prefer for sharing larger data)?  It doesn't need to have all the data, but at least a few images across each dimension.  I think it shouldn't be too hard, and it would obviously improve the library to handle this scenario."}}
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