AmSC Genesis#127
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…e probe modes for ptychopinn-torch
- Refactor FluorescenceEnhancingAlgorithm into an iterator-based FluorescenceEnhancer (Input/Output dataclasses, progress goal) and add FluorescenceAPI + FluorescenceTaskMonitor mirroring processing. - Extract shared TaskProgressMonitor/TaskLogHandler into model/task_monitor.py; drop model/processing/context.py in favor of model/processing/monitor.py. - Add WorkflowProductAPI.enhance_fluorescence_local for batch/remote runs. - Expand api/metrics.py with ObjectComparison (alignment + ambiguity standardization) and SSIM/PSNR helpers; add tests/test_metrics.py. - Wire the new fluorescence task monitor through the probe/object/product controllers and view; update api.rst.
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ptychodus-iri-tokensandptychodus-transfer-tokenssrc/ptychodus/scripts/genesis/{alcf,nersc,olcf}/ptychodus-bdp: load bad-pixel masks from fileReconstructionAmbiguitiesestimator (global complex scale, linear phase ramp, sub-pixel shift) so quality metrics compare reconstructions on equal footingTaskMonitor) withenhance_fluorescence_localworkflow APIDockerfileinto per-accelerator variants:Dockerfile.cpu,Dockerfile.cuda,Dockerfile.rocm,Dockerfile.xpu, each with build-arg knobs (CUDA / ROCm / PyTorch versions, XPU base tag)podmanwrapper script (src/ptychodus/scripts/podman/ptychodus) that builds, runs, and mounts the container with the right GPU / display / volume flagsptychodus-system-checkCLI for smoke-checking the installed environment