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Created with Raphaël 2.2.03Apr229Mar2825222176429Feb282019157653226Jan259822Dec21201913Nov10763231Oct30272625222019181716141312111098529Sep2827262513127654131Aug302928242322Merge branch 'revert-1851ba66' into 'master'Revert "Merge branch 'issue0027-serialize-roiset' into 'master'"Merge branch 'issue0027-serialize-roiset' into 'master'Fixed a few parameters in tests, confirmed all export products look the way they shouldFixed a few parameters in tests, confirmed all export products look the way they shouldPatch masks are the same after deserializationSerialization/deserialization tests passStill not showing equivalency between test and reference RoiSetsSerialization/deserialization leads to identical z-masksMove DataFrame and patch mask exports to .serialize()Exporting patch masks does not automatically make a PatchStack, which forces them to all be the same sizeAdded height, width fields for convenienceTest on expanded, padded patchesCorrectly export 3D patchesCorrectly export 3D patchesBy default, return non-expanded patches and masks; allow contour and mask overlays in non-expanded patchesStandardize patch (mask) getters return ad-hoc DataFrames, and _acc methods wrap these in PatchStack accessors (which automatically become shape of largest patch)Option to export non-expanded patchesReturn simple list of path objects instead of dictionariesslice object is now tight bounding box, expanded_slice is post-expansionForce export of dataset and patches; just need to override bounding box expansionNo longer export slice, relative_slice, and mask (all non-serialized) to CSV exportRolled back changes to how masks and slices are handled, but kept updated testsRoiSet init can now access both 2d and 3d segmentationsBroadcasting is work except in some cases that appear to coincide with truncation of ROI in patch boundsNow just running into broadcast errors, presumably on patch mask boundariesCan deal with 3d object ID maps straight in __init__ nowRemoved solidity from features, this was no longer being used and was triggering convex hull warningsPasses, long warnings that convex hull calcs don't workImplementing alternative dataframe generation where z-positions are in object map, i.e. do not need to be de-projected from rawImplemented and tested object identity labeling in 3D with and without connectivity between z-framesTest coverage with 3D object identities mapBypass init with factory method that takes 2d object identities mapMerge branch 'roiset_api' into 'staging'Revert "Temporary error-handling for debug..."Temporary error-handling for debug...Stopped assuming that object is identified in patchParameterize reload to command line optionParameterize reload to command line optionReload False by default, just to be conservative