{"push_id":3152447275,"size":10,"distinct_size":0,"ref":"refs/heads/tonytung-labeled-indices-base","head":"3885ae4b66ff6913252a94b5bd18b1dbd72131a9","before":"e955cad00a479896559b80537a63a9e4b196dbbf","commits":[{"sha":"9f711118ac427e10de56293ba7c97210028878ca","author":{"name":"Tony Tung","email":"230d196ff2416c9232661c39ad7b0996916b1710@chanzuckerberg.com"},"message":"Extract the TileSet → ImageStack code into a separate module.\n\n1. `_get_dimension_size` gets moved to the new module as it is no longer needed in ImageStack.\n2. Rename `tile_metadata` to `tile_data` as it represents both the image data and the metadata now.\n\nDepends on #791\n\nThis is part of RFC #776\n\nTest plan: make -j run_notebooks","distinct":false,"url":"https://api.github.com/repos/spacetx/starfish/commits/9f711118ac427e10de56293ba7c97210028878ca"},{"sha":"0513251fc60faecdbd971c834e6f473d4588bb80","author":{"name":"Tony Tung","email":"230d196ff2416c9232661c39ad7b0996916b1710@chanzuckerberg.com"},"message":"Dynamically evaluate the tile shape and dtype as we decode.\n\nThere is an inefficiency in the code that has us decoding the image _twice_, once to find the common dtype of the data and once to constitute the 5D tensor.\n\n#802 exacerbates the inefficiency even more, by calling numpy_array multiple times, each time triggering a decode.\n\nThis PR changes the code so that we just decode the image once and storing it in a proxy object that looks a lot like a slicedimage Tile object.  Unlike a slicedimage Tile object, however, it retains the image for the lifetime of the object.  We tightly constrain the lifetime of these objects in the ImageStack constructor to avoid bloating memory requirements.\n\nThis PR also introduces an `_Expectations` class, which tracks the tile shapes and dtypes of the tiles seen during a decode of a TileSet.  If the shapes are not all identical, it will trigger a ValueError.  If the kind of dtypes are not all identical, it will trigger a TypeError.  Additionally, if the dtypes are all of the same kind, but not all of the same size, it will trigger a :py:class:`starfish.errors.DataFormatWarning`.\n\nDepends on #802\n\nThis is part of RFC #776\n\nTest plan: `make -j run_notebooks`","distinct":false,"url":"https://api.github.com/repos/spacetx/starfish/commits/0513251fc60faecdbd971c834e6f473d4588bb80"},{"sha":"5318fcb3e446ce51012764280aeb1587d86b10e4","author":{"name":"Tony Tung","email":"230d196ff2416c9232661c39ad7b0996916b1710@chanzuckerberg.com"},"message":"Add support for labeled indices in imagestack / experiment builders\n\nThe IDs for rounds/chs/zlayers for imagestack / experiment builders are now taken from a sequence rather than ranging from 0..(n-1).  At all existing call sites, we simply provide a range, so it's a functional noop.  However, this allows us to build tests for labeled indices.\n\nTest plan: `make -j test lint mypy`","distinct":false,"url":"https://api.github.com/repos/spacetx/starfish/commits/5318fcb3e446ce51012764280aeb1587d86b10e4"},{"sha":"a9fab5fc5df2f1702ec1232f6a1415caaaecd4d8","author":{"name":"Tony Tung","email":"230d196ff2416c9232661c39ad7b0996916b1710@chanzuckerberg.com"},"message":"Refactor ImageStack construction from numpy arrays.\n\nThis now uses the same abstractions from starfish.imagestack.parser to construct the ImageStack from numpy arrays.  This will allow us to propagate information about the labeled axes in a coherent way (in a future PR).\n\nTest plan: make -j fast\n\nDepends on #803","distinct":false,"url":"https://api.github.com/repos/spacetx/starfish/commits/a9fab5fc5df2f1702ec1232f6a1415caaaecd4d8"},{"sha":"ef9f9764b571b76f91d85a501325643cc1ad3b9c","author":{"name":"Tony Tung","email":"230d196ff2416c9232661c39ad7b0996916b1710@chanzuckerberg.com"},"message":"fake commit","distinct":false,"url":"https://api.github.com/repos/spacetx/starfish/commits/ef9f9764b571b76f91d85a501325643cc1ad3b9c"},{"sha":"79f4d1257231fd20c6e40f7ccb72e79aa782b74b","author":{"name":"Tony Tung","email":"230d196ff2416c9232661c39ad7b0996916b1710@chanzuckerberg.com"},"message":"merge","distinct":false,"url":"https://api.github.com/repos/spacetx/starfish/commits/79f4d1257231fd20c6e40f7ccb72e79aa782b74b"},{"sha":"a0c392f4454de5dcfd58731abc0f963502fa779e","author":{"name":"Tony Tung","email":"230d196ff2416c9232661c39ad7b0996916b1710@chanzuckerberg.com"},"message":"fake commit","distinct":false,"url":"https://api.github.com/repos/spacetx/starfish/commits/a0c392f4454de5dcfd58731abc0f963502fa779e"},{"sha":"26fc381bca69768bc7a0ea88675984404146ccfa","author":{"name":"Tony Tung","email":"230d196ff2416c9232661c39ad7b0996916b1710@chanzuckerberg.com"},"message":"merge","distinct":false,"url":"https://api.github.com/repos/spacetx/starfish/commits/26fc381bca69768bc7a0ea88675984404146ccfa"},{"sha":"1f64606ab486c5f6dfc53639f55f601140f68e11","author":{"name":"Tony Tung","email":"230d196ff2416c9232661c39ad7b0996916b1710@chanzuckerberg.com"},"message":"fake commit","distinct":false,"url":"https://api.github.com/repos/spacetx/starfish/commits/1f64606ab486c5f6dfc53639f55f601140f68e11"},{"sha":"3885ae4b66ff6913252a94b5bd18b1dbd72131a9","author":{"name":"Tony Tung","email":"230d196ff2416c9232661c39ad7b0996916b1710@chanzuckerberg.com"},"message":"merge","distinct":false,"url":"https://api.github.com/repos/spacetx/starfish/commits/3885ae4b66ff6913252a94b5bd18b1dbd72131a9"}]}
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