{"action":"created","issue":{"url":"https://api.github.com/repos/openmicroscopy/openmicroscopy/issues/5722","repository_url":"https://api.github.com/repos/openmicroscopy/openmicroscopy","labels_url":"https://api.github.com/repos/openmicroscopy/openmicroscopy/issues/5722/labels{/name}","comments_url":"https://api.github.com/repos/openmicroscopy/openmicroscopy/issues/5722/comments","events_url":"https://api.github.com/repos/openmicroscopy/openmicroscopy/issues/5722/events","html_url":"https://github.com/openmicroscopy/openmicroscopy/pull/5722","id":312059091,"number":5722,"title":"OmeroReader: use RawPixelsStore.getTile to retrieve tiles","user":{"login":"melissalinkert","id":109998,"avatar_url":"https://avatars0.githubusercontent.com/u/109998?v=4","gravatar_id":"","url":"https://api.github.com/users/melissalinkert","html_url":"https://github.com/melissalinkert","followers_url":"https://api.github.com/users/melissalinkert/followers","following_url":"https://api.github.com/users/melissalinkert/following{/other_user}","gists_url":"https://api.github.com/users/melissalinkert/gists{/gist_id}","starred_url":"https://api.github.com/users/melissalinkert/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/melissalinkert/subscriptions","organizations_url":"https://api.github.com/users/melissalinkert/orgs","repos_url":"https://api.github.com/users/melissalinkert/repos","events_url":"https://api.github.com/users/melissalinkert/events{/privacy}","received_events_url":"https://api.github.com/users/melissalinkert/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":0,"created_at":"2018-04-06T17:39:36Z","updated_at":"2018-04-09T09:13:28Z","closed_at":null,"author_association":"OWNER","pull_request":{"url":"https://api.github.com/repos/openmicroscopy/openmicroscopy/pulls/5722","html_url":"https://github.com/openmicroscopy/openmicroscopy/pull/5722","diff_url":"https://github.com/openmicroscopy/openmicroscopy/pull/5722.diff","patch_url":"https://github.com/openmicroscopy/openmicroscopy/pull/5722.patch"},"body":"# What this PR does\r\n\r\nInstead of calling ```getPlane``` on ```RawPixelsStore``` and then cropping, this\r\nupdates the reader to pass the tile parameters in ```openBytes``` through to\r\n```RawPixelsStore.getTile(...)```.  This allows ```OmeroReader``` (and thus OMERO.insight-ij) to support big images.\r\n\r\n# Testing this PR\r\n\r\nFirst import a big image with more than 2GB of pixels per plane into an OMERO server without this PR.  I was using ```data_repo/curated/svs/public/77917.svs``` and a local server built from current develop (https://github.com/openmicroscopy/openmicroscopy/commit/0f0bf5c99543ff2bd5e29427ccbec4f89387f1ea).  If using a big image that requires pyramid generation, wait for the pyramid generation to complete.\r\n\r\nTo observe the original problem:\r\n\r\n1. Install Bio-Formats 5.8.2-SNAPSHOT and OMERO.insight-ij built without this PR into ImageJ.\r\n2. Start ImageJ and select ```OMERO > Connect to OMERO```.\r\n3. Log in to the server used for import and navigate to the imported big image (```77917.svs [Series 1]``` if using the noted test file).\r\n4. Double-click on the image; the ```Bio-Formats Import Options``` window should appear.\r\n5. Check the ```Autoscale``` and ```Crop on import``` options, leaving all others unchecked, and click ```OK```.\r\n6. In the crop options window, enter parameters for a small tile (e.g. ```0```, ```0```, ```512```, and ```512```) and click ```OK```.\r\n7. An error message should be shown, with an ```ApiUsageException``` in the ImageJ log window.  The stack trace should be consistent with attempting to read more than 2GB of data into a single byte array.\r\n\r\nTo verify the fix:\r\n\r\n1. Install OMERO.insight-ij built with this PR into ImageJ (overwriting the previous installation).\r\n2. Repeat steps 2-6 above\r\n3. An image with the specified tile dimensions should appear with no error message or logged exception.\r\n4. Check that the image is correct by opening the file from disk using ```Plugins > Bio-Formats > Bio-Formats Importer``` and the same options described in steps 5-6 above.\r\n\r\nI would not expect the server itself to need rebuilding, redeploying or restarting with this PR included.  Only the OMERO.insight-ij client needs to be rebuilt and reinstalled to test.\r\n\r\n# Related reading\r\n\r\nSee https://trello.com/c/2GKksxIS/59-omero-imagej-plugin-cannot-open-big-images\r\n\r\nThis isn't urgent from my perspective, so feel free to defer until a later release as needed."},"comment":{"url":"https://api.github.com/repos/openmicroscopy/openmicroscopy/issues/comments/379687171","html_url":"https://github.com/openmicroscopy/openmicroscopy/pull/5722#issuecomment-379687171","issue_url":"https://api.github.com/repos/openmicroscopy/openmicroscopy/issues/5722","id":379687171,"user":{"login":"jburel","id":1022396,"avatar_url":"https://avatars1.githubusercontent.com/u/1022396?v=4","gravatar_id":"","url":"https://api.github.com/users/jburel","html_url":"https://github.com/jburel","followers_url":"https://api.github.com/users/jburel/followers","following_url":"https://api.github.com/users/jburel/following{/other_user}","gists_url":"https://api.github.com/users/jburel/gists{/gist_id}","starred_url":"https://api.github.com/users/jburel/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jburel/subscriptions","organizations_url":"https://api.github.com/users/jburel/orgs","repos_url":"https://api.github.com/users/jburel/repos","events_url":"https://api.github.com/users/jburel/events{/privacy}","received_events_url":"https://api.github.com/users/jburel/received_events","type":"User","site_admin":false},"created_at":"2018-04-09T09:13:28Z","updated_at":"2018-04-09T09:13:28Z","author_association":"OWNER","body":"Without this PR, it is not possible to read the image data.\r\nWith the PR, it is possible to view the image using the crop options (without it will not work, that's expected)\r\nI have tried various tile size (521, 512), (1000, 1000) (4000, 4000)\r\nEverything works as expected. \r\nThanks for fixing the issue"}}
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