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  • chaeo_pipeline
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Created with Raphaël 2.2.022Dec21201914Nov1310763231Oct30272625222019181716141312111098529Sep2827262513127654131Aug302928242322Added installation instructions in README.mdpip_buildpip_buildMerge branch 'master' of git.embl.de:rhodes/model_serverAdded Windows shortcutsIgnore PyCharm filesIgnore PyCharm filesIgnore build artifactsTests pass in this project structureMinimal docs for pip build to useExport DataFrame from workflowFilters propagate from parameters dictDummy object classification exports mapCan make patch stack from itselfConsolidated more parameters into pydantic modelsConsolidated more parameters into pydantic modelsRemoved direct pixel map access from workflow functionPropagate filename to export productsCombined all export products into a single call, which routes individual products' export methods and parametersPass params model straight to product exporters, so less code dedicated to matching parametersFixed bug where error was raised generating 3D patches where expanded 3D stack encountered min/max of rangeProducts export successfully from workflowIroning out issues with parameterized patch product exportTest covering unified zmask workflow passesTest covers instance segmentation base classImplemented but did not yet test adding object classification result to RoiSet dataframeAdapted base segmentation worklow and API endpoint for generic semantic segmentation model; made dummy model this type tooTest and example notebook that covers object classification from binary segmentationRetained object classification from pixel probabilitieUpdated ilastik tests to cover semantic and instance segmentation methodsAdded superclass for instance segmentation models and modified ilastik object classification to inherit from itAdded superclass for semantic segmentation models and modified ilastik pixel classification to inherit from itAdded superclass for semantic segmentation models and modified ilastik pixel classification to inherit from itRenamed ZMask to RoiSet, prototyped object classification methods that add classification result as a dataframe columnTrying to test with batch operation but currently these do not involve object classificationDelegated export of patch products to ZMaskObjectTable class; consolidated both batch runner and API-facing workflows into infer_object_map_from_zstack(); consolidated parameterization of export products into pydantic modelSegmentation with broken aggregates is passed to object classifierdev_watersheddev_watershedCombine non-aggregates and watershed-separated aggregates into a final segmentation map with label IDsSuccessfully breaking up aggregates based on solidity priorDemo using watershed to break up suspected aggregatesCombine mask in color stackMerge branch 'chaeo_pipeline' into dev_watershed