JIT compiled gaussian mixture model (GMM)#1802

Merged

wyli merged 101 commits into

Project-MONAI:devfrom

charliebudd:gmm-implementation

Jun 20, 2021

Commits on Feb 15, 2021

initial gmm commit
charliebudd
committed

Commits on Feb 16, 2021

connecting up to python (not working)
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fixed pitch issue
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Commits on Feb 17, 2021

initialising alpha with trimap
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Commits on Feb 18, 2021

changing output to normalised properbilities per mixture
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removing pitched allocation, performance increased
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some code cleaning
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fixing class labeling
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Commits on Feb 19, 2021

clearing up
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reorg
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moving to reading directly from input tensor
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swapping to int for alpha
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using output tensor as scratch memory
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cleaning
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adding pytorch interpretation layer
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Commits on Feb 22, 2021

moving to 1D indexing for dataterm kernel
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1D indexing for DoSplit kernel
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Commits on Feb 24, 2021

standardising thread indexing
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1D blocks for reduction
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naming scratch memory sections
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sequential warps in reduction kernel
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fully 1 dimensional reduction
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code cleaning
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Commits on Feb 25, 2021

renaming gmm_pitch to component_count
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Commits on Feb 26, 2021

starting to generalise of mixture count
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Commits on Mar 3, 2021

storing mixture in 4 bits not 1
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fixing gmm_index calculation
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Commits on Mar 4, 2021

adding channel count to reduction dispatch
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removing active block check
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Commits on Mar 9, 2021

partial change to new reduction kernels
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removing uneeded thread id checks
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Commits on Mar 11, 2021

new reduction scheme
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Commits on Mar 12, 2021

simplifying GMcommonTerm kernel using shfl
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simplifying GMMFindSplit kernel with shfl instructions
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more efficient final warp reductions using shfl
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Commits on Mar 15, 2021

Moving to JIT
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Moving to use of compile time constants
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generalising reduction kernel to any channel count
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Generalised reduction finalisation
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Commits on Mar 16, 2021

determinant calculation for channels 0-4
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handling edge cases in loader and ading force build mode
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fixing determinant warp reduction
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implementing matrix inverse for channels 1-3
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Commits on Mar 17, 2021

generalising everthing but eigenvector calculation
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eigenpair estimation using power iteration
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fixing det and inv errors
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code formmatting
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Commits on Mar 18, 2021

fixing missed elements in reduction
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throwing exception when run with a cpu tensor
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cleaning up python gmm class
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fixing 4 channel matrix inverse term coeffs
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Commits on Mar 19, 2021

Fixing eigenpair approximation
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updating reduction finalize shared memory size
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Commits on Mar 24, 2021

Initial batch generalisation
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fixing batching
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fixing issue with mutable dictionary as default arg
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fixing None check
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fixing type in directory name and adding __init__.py
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fixing typo
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Merge branch 'master' into gmm-implementation
charliebudd
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updating public api test to ignore _extensions folder
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Commits on Apr 1, 2021

moving to cholesky factorization for matrix det and inv, allowing higher channel dimensions
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cleaning up interupted builds
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adding docstring
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removing unused import
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Commits on Apr 6, 2021

removing 255 normalisation
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adding epsilon to nudge distributions with 0 variance
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gmm unit tests
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fixing compiler warnings for int->uint conversion
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tagging .so file
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reformatting
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Merge branch 'master' into gmm-implementation
charliebudd
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updating docs with gmm
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Merge branch 'gmm-implementation' of https://github.com/charliebudd/MONAI into gmm-implementation
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removing skip if no cpp extention decorator
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moving extention call into autograd function
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fixing flake8 error
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fixing typo
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adding manual lock check to prevent hung build
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docstring formatting
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Commits on Apr 7, 2021

adding extention source code to package_data
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code formatting
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Commits on Apr 20, 2021

fixing common term normalisation across mixtures
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unifying reduction schema
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Commits on Apr 21, 2021

Moving to an object orientaited approach
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Commits on Apr 29, 2021

tidying up
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Commits on May 4, 2021

Merge remote-tracking branch 'upstream/dev' into gmm-implementation
chaliebudd
committed

Commits on May 12, 2021

Merge branch 'dev' into gmm-implementation
wyli
authored

Commits on May 24, 2021

Commits on May 25, 2021

updating timeout in loader
chaliebudd
committed
Merge branch 'gmm-implementation' of https://github.com/charliebudd/MONAI into gmm-implementation
chaliebudd
committed

Commits on May 26, 2021

throwing exception if named module is missing
chaliebudd
committed
Merge branch 'dev' into gmm-implementation
charliebudd
authored

Commits on Jun 8, 2021

Merge branch 'dev' into gmm-implementation
wyli
authored

Commits on Jun 18, 2021

changing to pytorch default build directory
chaliebudd
committed

Commits on Jun 19, 2021

Merge branch 'dev' into gmm-implementation
wyli
authored

Commits on Jun 20, 2021