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Created with Raphaël 2.2.07Dec6530Nov2928272625222120191815141211109432131Oct3028272625222015141372130Sep2624232013126315Aug14131298752131Jul2624221817161585432124Jun2010765330May22876326Apr191715121110954Getting a patch mask can optionally update patch focusexport_patch_masks now return pd.SeriesCan export both 2d and 3d patch masksCan export both 2d and 3d patch masksMerge branch 'issue_resume_batch' into 'staging'Implemented option to resume a batch job from previous filelistMerge branch 'dev_3dseg_bug' into 'staging'Corrected bug where 3d patch was modified in-place during rescalingRemoved min_sobel, which was there for debuggingFixed error with zero-length dataframe in 3d seg caseMerge branch 'dev_batch_seg' into 'staging'Rescale channels separately unless making an RGB imageCopy config.json and filelist.csv to output folderPropagate force_tif from run_exportsSplit out local and remot path roots, but successfully completed a test run on remoteMerge branch 'dev_batch_multiple_dirs' into 'staging'Deserialization does not solve deprojection a second time; a deprojected RoiSet is serialized as 3D. Tight patch mask format depends on dimensions of ROIs themselves, so 2d PNGs are possible in a 3D set if no ROI is thicker than 1Tests pass, caught bug where a deserialized RoiSet would become 3dNo longer copy and pass around dataframes when running patch exportsPatch exports are passed to a single parameter now, but still working out bugsApplied same optimization to binary mask computation, but this still his memory issue on large datasetSmall optimization for making RoiSets from 3d labels3d RoiSet can be serialized/deserializedLabel overlays on 3d exports are correctTest confirms that 3d patches are writtenSlices are 3dPatch masks become TIFs when they are 3dAll pre-existing tests passGradually handling three different cases of RoiStack: pure 2d, pure 3d, mixed (3d stack, 2d deprojected object IDs)Added convenience method for cropping in three dimensionsMade (failing) tests of 3d product exports and TODOs needed to correct themCreated overridable method that makes accessor from np.ndarrayAdded alternate constructor for RoiSet from either YX or YXZ monochromatic dataFine-tuned formatting and references to patch export productsParameterized option to create unique subdirectory for each RoiSet, but this still isn't propagating to dataframe called in .serializeAccessor convenience property for either data_yx or data_yxz depending on dimensionalityPatches are exported to subdirectory named by prefix argumentFilelist is reindexed after resolving multiposition filesBatch runner outputs position index for multiposition filesBatch runner successfully reads multiposition input files