├── .gitignore ├── CFP_pyhpc.pdf ├── LICENSE ├── README.md ├── SC20_pyHPC_dask4volumes.pdf ├── code ├── 01_bead_segmentation.ipynb ├── 02_fibers_to_xarray_zarr.ipynb ├── 03_fiber_segmentation.ipynb ├── 04_distributed_processing_pipelines.ipynb ├── README.md └── extra │ ├── 01_b_bead_segmentation_distributed.ipynb │ ├── 01_readVolume.ipynb │ ├── 02_roi_mask.ipynb │ ├── 03_phasesML.ipynb │ ├── 04_FiberAnalysisExperimental.ipynb │ ├── 04_metricsML.ipynb │ ├── VoxelClustering.ipynb │ ├── evalSeg_SC20.ipynb │ ├── tempFiber.ipynb │ ├── tmpSlic.ipynb │ └── tmp_FiberAnalysisExperimental.ipynb ├── coiled ├── README.md └── create_software_environment.py ├── data ├── Results-slice1000-fiber_segm.textClipping ├── bead_pack.tif ├── cthead1.png ├── pyhpc_logo.png ├── segmented_bead_pack_GT.tif └── sliceWithClicks │ ├── Results-slice1000-ds3.csv │ ├── Results-slice1000-fiber_segmentation.csv │ └── rec_SFRR_2600_B0p2_01000_clicked.tif ├── environment.yml ├── img ├── fibers_3d_vesselness.png └── sc20_logo.png ├── nersc ├── .override-jupyter ├── README.md ├── install-kernel-spec.sh ├── install-override-jupyter.sh ├── kernel.json └── shifter │ ├── Dockerfile │ ├── README.md │ ├── build.sh │ └── requirements.txt ├── pyhpc_call.pdf └── refs ├── SC20 Workshop _ PyHPC 2020 Submission Form.pdf ├── hep_texas.pdf ├── nersc_jupyterhub.pdf └── zara.pdf /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dani-lbnl/SC20_pyHPC/HEAD/.gitignore -------------------------------------------------------------------------------- /CFP_pyhpc.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dani-lbnl/SC20_pyHPC/HEAD/CFP_pyhpc.pdf -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dani-lbnl/SC20_pyHPC/HEAD/LICENSE -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dani-lbnl/SC20_pyHPC/HEAD/README.md -------------------------------------------------------------------------------- /SC20_pyHPC_dask4volumes.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dani-lbnl/SC20_pyHPC/HEAD/SC20_pyHPC_dask4volumes.pdf -------------------------------------------------------------------------------- /code/01_bead_segmentation.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dani-lbnl/SC20_pyHPC/HEAD/code/01_bead_segmentation.ipynb -------------------------------------------------------------------------------- /code/02_fibers_to_xarray_zarr.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dani-lbnl/SC20_pyHPC/HEAD/code/02_fibers_to_xarray_zarr.ipynb -------------------------------------------------------------------------------- /code/03_fiber_segmentation.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dani-lbnl/SC20_pyHPC/HEAD/code/03_fiber_segmentation.ipynb -------------------------------------------------------------------------------- /code/04_distributed_processing_pipelines.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dani-lbnl/SC20_pyHPC/HEAD/code/04_distributed_processing_pipelines.ipynb -------------------------------------------------------------------------------- /code/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dani-lbnl/SC20_pyHPC/HEAD/code/README.md -------------------------------------------------------------------------------- /code/extra/01_b_bead_segmentation_distributed.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dani-lbnl/SC20_pyHPC/HEAD/code/extra/01_b_bead_segmentation_distributed.ipynb -------------------------------------------------------------------------------- /code/extra/01_readVolume.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dani-lbnl/SC20_pyHPC/HEAD/code/extra/01_readVolume.ipynb -------------------------------------------------------------------------------- /code/extra/02_roi_mask.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dani-lbnl/SC20_pyHPC/HEAD/code/extra/02_roi_mask.ipynb -------------------------------------------------------------------------------- /code/extra/03_phasesML.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dani-lbnl/SC20_pyHPC/HEAD/code/extra/03_phasesML.ipynb -------------------------------------------------------------------------------- /code/extra/04_FiberAnalysisExperimental.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dani-lbnl/SC20_pyHPC/HEAD/code/extra/04_FiberAnalysisExperimental.ipynb -------------------------------------------------------------------------------- /code/extra/04_metricsML.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dani-lbnl/SC20_pyHPC/HEAD/code/extra/04_metricsML.ipynb -------------------------------------------------------------------------------- /code/extra/VoxelClustering.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dani-lbnl/SC20_pyHPC/HEAD/code/extra/VoxelClustering.ipynb -------------------------------------------------------------------------------- /code/extra/evalSeg_SC20.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dani-lbnl/SC20_pyHPC/HEAD/code/extra/evalSeg_SC20.ipynb -------------------------------------------------------------------------------- /code/extra/tempFiber.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dani-lbnl/SC20_pyHPC/HEAD/code/extra/tempFiber.ipynb -------------------------------------------------------------------------------- /code/extra/tmpSlic.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dani-lbnl/SC20_pyHPC/HEAD/code/extra/tmpSlic.ipynb -------------------------------------------------------------------------------- /code/extra/tmp_FiberAnalysisExperimental.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dani-lbnl/SC20_pyHPC/HEAD/code/extra/tmp_FiberAnalysisExperimental.ipynb -------------------------------------------------------------------------------- /coiled/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dani-lbnl/SC20_pyHPC/HEAD/coiled/README.md -------------------------------------------------------------------------------- /coiled/create_software_environment.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dani-lbnl/SC20_pyHPC/HEAD/coiled/create_software_environment.py -------------------------------------------------------------------------------- /data/Results-slice1000-fiber_segm.textClipping: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dani-lbnl/SC20_pyHPC/HEAD/data/Results-slice1000-fiber_segm.textClipping -------------------------------------------------------------------------------- /data/bead_pack.tif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dani-lbnl/SC20_pyHPC/HEAD/data/bead_pack.tif -------------------------------------------------------------------------------- /data/cthead1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dani-lbnl/SC20_pyHPC/HEAD/data/cthead1.png -------------------------------------------------------------------------------- /data/pyhpc_logo.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dani-lbnl/SC20_pyHPC/HEAD/data/pyhpc_logo.png -------------------------------------------------------------------------------- /data/segmented_bead_pack_GT.tif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dani-lbnl/SC20_pyHPC/HEAD/data/segmented_bead_pack_GT.tif -------------------------------------------------------------------------------- /data/sliceWithClicks/Results-slice1000-ds3.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dani-lbnl/SC20_pyHPC/HEAD/data/sliceWithClicks/Results-slice1000-ds3.csv -------------------------------------------------------------------------------- /data/sliceWithClicks/Results-slice1000-fiber_segmentation.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dani-lbnl/SC20_pyHPC/HEAD/data/sliceWithClicks/Results-slice1000-fiber_segmentation.csv -------------------------------------------------------------------------------- /data/sliceWithClicks/rec_SFRR_2600_B0p2_01000_clicked.tif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dani-lbnl/SC20_pyHPC/HEAD/data/sliceWithClicks/rec_SFRR_2600_B0p2_01000_clicked.tif -------------------------------------------------------------------------------- /environment.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dani-lbnl/SC20_pyHPC/HEAD/environment.yml -------------------------------------------------------------------------------- /img/fibers_3d_vesselness.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dani-lbnl/SC20_pyHPC/HEAD/img/fibers_3d_vesselness.png -------------------------------------------------------------------------------- /img/sc20_logo.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dani-lbnl/SC20_pyHPC/HEAD/img/sc20_logo.png -------------------------------------------------------------------------------- /nersc/.override-jupyter: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dani-lbnl/SC20_pyHPC/HEAD/nersc/.override-jupyter -------------------------------------------------------------------------------- /nersc/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dani-lbnl/SC20_pyHPC/HEAD/nersc/README.md -------------------------------------------------------------------------------- /nersc/install-kernel-spec.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dani-lbnl/SC20_pyHPC/HEAD/nersc/install-kernel-spec.sh -------------------------------------------------------------------------------- /nersc/install-override-jupyter.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dani-lbnl/SC20_pyHPC/HEAD/nersc/install-override-jupyter.sh -------------------------------------------------------------------------------- /nersc/kernel.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dani-lbnl/SC20_pyHPC/HEAD/nersc/kernel.json -------------------------------------------------------------------------------- /nersc/shifter/Dockerfile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dani-lbnl/SC20_pyHPC/HEAD/nersc/shifter/Dockerfile -------------------------------------------------------------------------------- /nersc/shifter/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dani-lbnl/SC20_pyHPC/HEAD/nersc/shifter/README.md -------------------------------------------------------------------------------- /nersc/shifter/build.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dani-lbnl/SC20_pyHPC/HEAD/nersc/shifter/build.sh -------------------------------------------------------------------------------- /nersc/shifter/requirements.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dani-lbnl/SC20_pyHPC/HEAD/nersc/shifter/requirements.txt -------------------------------------------------------------------------------- /pyhpc_call.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dani-lbnl/SC20_pyHPC/HEAD/pyhpc_call.pdf -------------------------------------------------------------------------------- /refs/SC20 Workshop _ PyHPC 2020 Submission Form.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dani-lbnl/SC20_pyHPC/HEAD/refs/SC20 Workshop _ PyHPC 2020 Submission Form.pdf -------------------------------------------------------------------------------- /refs/hep_texas.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dani-lbnl/SC20_pyHPC/HEAD/refs/hep_texas.pdf -------------------------------------------------------------------------------- /refs/nersc_jupyterhub.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dani-lbnl/SC20_pyHPC/HEAD/refs/nersc_jupyterhub.pdf -------------------------------------------------------------------------------- /refs/zara.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dani-lbnl/SC20_pyHPC/HEAD/refs/zara.pdf --------------------------------------------------------------------------------