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Created with Raphaël 2.2.028Nov272625222120191815141211109432131Oct3028272625222015141372130Sep2624232013126315Aug14131298752131Jul2624221817161585432124Jun2010765330May22876326Apr1917151211109543Applied 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 filesConfirm that multiposition object knows its length before lazy-loading dataCan create multiple accessors from single multiposition CZI over APISeparate out ndarray and Accessor functionsAdded function to route multiposition file importMerged in changes from remoteMerged in changes from remoteMerge remote-tracking branch 'origin/dev_batch_multiple_dirs' into dev_batch_multiple_dirsPropagated channel parameter change to FastAPI methods, tooRoiSet.run_exports and .get_export_product_accessors no longer take a channel directly, but rather pull these from parameters of individual patch productsMerge branch 'staging' into dev_batch_multiple_dirsMerge branch 'dev-cluster-build' into 'staging'Specified python version, needed to solve environment on clusterMerge remote-tracking branch 'origin/dev_batch_multiple_dirs' into dev_batch_multiple_dirsUpdated tests: smoothing is now more aggressive, lowered threshold of IOU for comparison; task endpoints updatedUpdated tests: smoothing is now more aggressive, lowered threshold of IOU for comparison; task endpoints updatedRepaired a couple tests failing because of changes to dtype propagation in .applyDefault smoothing to 0.5label_pixel_class returns bool againIntroduced post-smoothing threshold when rebinarizing floating-point gaussian smoothingWrite patches to subdirectories by their stack association