{"action":"created","comment":{"url":"https://api.github.com/repos/jni/cellom2tif/pulls/comments/25754057","id":25754057,"diff_hunk":"@@ -1,3 +1,32 @@\n+import os\n+\n+\n+def fn_has_ext(fn, ext, case_sensitive=False):","path":"cellom2tif/filetypes.py","position":4,"original_position":4,"commit_id":"15b4420b1fee11aca1f57063aa8f27d28006012d","original_commit_id":"15b4420b1fee11aca1f57063aa8f27d28006012d","user":{"login":"starcalibre","id":7637964,"avatar_url":"https://avatars.githubusercontent.com/u/7637964?v=3","gravatar_id":"","url":"https://api.github.com/users/starcalibre","html_url":"https://github.com/starcalibre","followers_url":"https://api.github.com/users/starcalibre/followers","following_url":"https://api.github.com/users/starcalibre/following{/other_user}","gists_url":"https://api.github.com/users/starcalibre/gists{/gist_id}","starred_url":"https://api.github.com/users/starcalibre/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/starcalibre/subscriptions","organizations_url":"https://api.github.com/users/starcalibre/orgs","repos_url":"https://api.github.com/users/starcalibre/repos","events_url":"https://api.github.com/users/starcalibre/events{/privacy}","received_events_url":"https://api.github.com/users/starcalibre/received_events","type":"User","site_admin":false},"body":"That looks good to me.\r\n\r\nI'm also reconsidering the need for the ``case_sensitive`` parameter, I can't think of a use case where someone would want ``DIB`` files and not ``dib`` files. Any objections to removing it?","created_at":"2015-03-04T06:06:02Z","updated_at":"2015-03-04T06:06:02Z","html_url":"https://github.com/jni/cellom2tif/pull/2#discussion_r25754057","pull_request_url":"https://api.github.com/repos/jni/cellom2tif/pulls/2","_links":{"self":{"href":"https://api.github.com/repos/jni/cellom2tif/pulls/comments/25754057"},"html":{"href":"https://github.com/jni/cellom2tif/pull/2#discussion_r25754057"},"pull_request":{"href":"https://api.github.com/repos/jni/cellom2tif/pulls/2"}}},"pull_request":{"url":"https://api.github.com/repos/jni/cellom2tif/pulls/2","id":30034736,"html_url":"https://github.com/jni/cellom2tif/pull/2","diff_url":"https://github.com/jni/cellom2tif/pull/2.diff","patch_url":"https://github.com/jni/cellom2tif/pull/2.patch","issue_url":"https://api.github.com/repos/jni/cellom2tif/issues/2","number":2,"state":"open","locked":false,"title":"Add support for DIB files and large data sets -- WIP","user":{"login":"starcalibre","id":7637964,"avatar_url":"https://avatars.githubusercontent.com/u/7637964?v=3","gravatar_id":"","url":"https://api.github.com/users/starcalibre","html_url":"https://github.com/starcalibre","followers_url":"https://api.github.com/users/starcalibre/followers","following_url":"https://api.github.com/users/starcalibre/following{/other_user}","gists_url":"https://api.github.com/users/starcalibre/gists{/gist_id}","starred_url":"https://api.github.com/users/starcalibre/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/starcalibre/subscriptions","organizations_url":"https://api.github.com/users/starcalibre/orgs","repos_url":"https://api.github.com/users/starcalibre/repos","events_url":"https://api.github.com/users/starcalibre/events{/privacy}","received_events_url":"https://api.github.com/users/starcalibre/received_events","type":"User","site_admin":false},"body":"* DIB files are added to the list of files converted to TIF.\r\n* Assuming masks in the DIB format also have the o1 suffix in their filename, these can be included or ignored too.\r\n* After converting ~2000 files, I was getting a 'Too many open files' error. See below:\r\n\r\n``\r\nJavaException: /media/starcalibre/New Volume/HT29/NIRHTa-001/AS_09125_050116110001_E16f01d0.DIB (Too many open files)\r\n``\r\n\r\nThis was because the Bioformats reader was not being closed after a file was read. This is now fixed! However I think it might be worth doing the file reading in batches. The size of the batches could be dependent upon the amount of memory allocated to the JVM, or just be a user defined parameter. This would reduce the extra overhead of having to load and close the reader each time a file is read. Any thoughts?\r\n\r\nStill outstanding:\r\nUpdated tests comprising test DIB files.\r\nUpdated 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