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Created with Raphaël 2.2.028Feb2019157653226Jan259822Dec21201914Nov1310763231Oct30272625222019181716141312111098529Sep2827262513127654131Aug302928242322Moved all of chaeo extension to trec-adaptive-feedback projectMerge branch 'chaeo_pipeline'Moved all of chaeo extension to trec-adaptive-feedback projectPorto script is running mostly problem-free, except for TSV export at endCorrected assertion error in relative bounding boxRenamed RoiSet export workflow in chaeo extension; optionally classify if an object classifier is part of models; loop_workflow now simply passes parameters through to workflowMerge branch 'chaeo_zmask_class' into chaeo_pipelineFolded remaining tests into baseFully merged PatchStack static functions into base.accessors; all tests passbase.accessors method to make patch mask from fileMoved PatchStack to base.accessorsTest coverage of patch stack object classificationRoughed in test coverage of ilastik classification by patch stackConsolidating RoiSet test data into base test configurationMove patch stack wrapper to ilastik extensionNow that RoiSet is in base, remove dependency on ilastik in its test; tests now open segmentation mask from fileAdded PCZYX getter mainly for ilastik useConsolidate usages of PatchStack in RoiSet classConverge to a single PatchStack accessor classMoved RoiSet method dependencies over to baseRemaining test addresses multiposition CZI caseMoved patch mask-specific processing method to baseBrought RoiSet package into baseRearranged methods, condensed into roiset packagecleanupCombined mono and multichannel patch export methodsRemoved zmask_meta referencesTest covering annotated multichannel z-stacks, tooSingle annotator method for annotated zstacksTests passRoiSet now iterable, i.e. traverse Rois over Pandas APISimplified tests, corrected errorsProgress on running workflow, still throwing errors but suspect these just require method signature updatesProgress on testing classify_by method; need to pass preference of channel to patch generator without disrupting existing options to export RGB / multichannel stacksSplit into two test classes to simplify things a bitRepaired all multichannel export casesMore test coverage of number of channels in multichannel exportMore test coverage of number of channels in multichannel exportDon't try to write PNG if > 3 channelsProgress on assembling RGB exports