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zolfa-nd2reader
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252 Commits (a2385164a1b9c136067a8d6212df894ff75f2027)

Author SHA1 Message Date
  Ruben Verweij 334817cead Fix bug 8 years ago
  Ruben Verweij bd10811aee Add unit tests for opening files and axis sizes 8 years ago
  Ruben Verweij fa0e0c9a86 Parse part of ND experiment metadata 8 years ago
  Ruben Verweij a56a7cc665 Fix dtype at np.float64 8 years ago
  Ruben Verweij a716471131 Small fixes 8 years ago
  Ruben Verweij 63a286d167 Hopefully fix Python 2 import error 8 years ago
  Ruben Verweij 685afb16ab Rename exceptions 8 years ago
  Ruben Verweij 7c779b3a40 Small refactor of common functions 8 years ago
  Ruben Verweij cb2c06f9a5 Complete refactor 8 years ago
  Ruben Verweij 6f151e8701 Reduce code complexity 8 years ago
  Ruben Verweij d19a9c305b Refactor, add metadata to Frame objects, support PIMS open function 8 years ago
  Ruben Verweij 7b7bf1ac25 Start porting to PIMS framework, cleanup unnecessary files 8 years ago
  Ruben Verweij 4ffc0bdf85 Correctly scale ROI sizes and position 8 years ago
  Ruben Verweij d0bb78f67a Add ROI type and shape 8 years ago
  Ruben Verweij 6f800c49f6 Added parsing for basic ROI metadata. 8 years ago
  jim 340d74fb8e deleted CameraSettings since it's no longer used 9 years ago
  Jim Rybarski b80ed8c75b possible fix for weird problem resulting from having many exposure times 9 years ago
  jim 4a48847630 resolves #152: images truly act like numpy arrays now and are also displayable 9 years ago
  jim 4194f073dd resolves #150, #149: removed camera settings entirely because they are buggy and terrible 9 years ago
  jim 19c45ed952 Version 2.1.1 9 years ago
  jim a1d73157b4 #147: this mostly resolves the issue and I'm going to close it out with this patch, however, I'm not satisfied with the solution (taken from http://stackoverflow.com/questions/16805987/python-numpy-ndarray-subclasses-and-zero-rank-arrays). While this allows most numpy operations to work, you still can't do basic things like adding two Image objects (even though np.sum([[n[0], n[1]]]) will work). Hopefully no one will care or notice 9 years ago
  Jim Rybarski 13139518b3 Bump version to 2.1.0, updated documentation, removed skips from some unit tests 9 years ago
  Jim Rybarski e992f743c7 resolves #132: The `select` method now allows you to specify a range of images to iterate over 9 years ago
  jim a7ddaadf39 bumped version to 2.0.2 9 years ago
  jim 7064e6f0ae #143 discovered that humans can ruin everything 9 years ago
  jim c3d7273dfa resolves #143: we can now programatically access the width of pixels in microns 9 years ago
  jim 4aa5a97e80 bumped version to 2.0.1 9 years ago
  jim 9bbbf7ba28 resolves #140 9 years ago
  Jim Rybarski 0289234391 Potential fix for #138. Makes select() work with ND2s that have a single frame by iterating over a range of integers instead of the frames. 9 years ago
  Jim Rybarski 25c4ce7f78 resolves #135. we're ready to publish version 2.0.0 9 years ago
  Jim Rybarski 343a39dd9d fixes #133. The index assigned to images produced by `select` was wrong. 9 years ago
  jim faa50235d3 moved public methods to the top of classes 9 years ago
  Jim Rybarski 47966b75dd resolves #129: renamed filter() to select() 9 years ago
  Jim Rybarski 7f359bacc1 updated docs, fixed typos 9 years ago
  Jim Rybarski aedfa921a5 resolves #117. The XML-formatted strings in a few raw_metadata are now parsed into OrderedDicts. This isn't exposed to the user but if we want to add any of the data it will be more convenient for contributors to examine the contents of the data 9 years ago
  Jim Rybarski f366f38009 resolves #114. added index to Images to help with testing. Increased test coverage for filter() 9 years ago
  Jim Rybarski e141b0504c #114: wrote fast filter that works, but we need way more testing for corner cases 9 years ago
  Jim Rybarski 1268b2768c #125: fixed bug by ordering channel names, which works but seems suspect. added py2 support to Dockerfile 9 years ago
  Jim Rybarski 1436068d4c #125: refactored to make adding more metadata easier 9 years ago
  jim 5196c7d2c7 #125 decoded much more metadata and also found pointers to XML data 9 years ago
  jim 4943a854f1 resolves #123: the label map and raw metadata are now accessible, so we can more easily compare what they contain to the information in the XML (which we're still not parsing) 9 years ago
  jim e9ff0915bf #123 switched to the new LabelMap object, added support for another metadata field 9 years ago
  jim 9548b92957 #123: created label map object, which parses the pointers to locations in the file where data is stored 9 years ago
  jim 09173fcb9e resolves #110: added comments and parameter types to every method with a few minor exceptions where it's super obvious and unimportant what's happening 9 years ago
  jim cc2a49ac6d #110 added many comments, fixed parameter names where frame_number was incorrectly used in place of index 9 years ago
  jim a102f6189b resolves #113: removed `.data` property from images now that they simply behave like numpy arrays 9 years ago
  jim 7c0c8be065 resolves #119: removed some commented-out code and an unused import 9 years ago
  jim fd3c67d65b resolves #112: removed ImageGroup object and image_sets method, as they were deprecated because of their general uselessness 9 years ago
  Jim Rybarski 90ae0907de resolves #106: implemented missing method and added tests 9 years ago
  Jim Rybarski 284f6775de resolves #103: ND2s with a single image could not be parsed properly as they do not contain any dimension data, so when absent we can assume a single frame exists 9 years ago