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Segmentation: refactoring#25

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zmughal wants to merge 55 commits intomasterCBL-ORION/orion:masterfrom segmentationCBL-ORION/orion:segmentationCopy head branch name to clipboard

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Commits on Feb 4, 2016

• wip: orion_multiscaleLaplacianFilter: implement multiscale processing

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• add notes on the construction of the Laplacian in the Fourier domain

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• WIP: stub out multiscale Laplacian filter

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Commits on Mar 18, 2016

• Rename volume parameter for orion_readNegativeSamples

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Commits on Mar 28, 2016

• Finalise the multiscale Laplacian filter

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• Implement readNegativeSamples

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• Add comment about getFeatures function

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• Remove TODO

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Commits on Mar 31, 2016

• Add notes about the contents of the Laplacian response

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• Compute features with scales adjusted by the volume spacing

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• Helper function to compute features

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• Translate the Gaussian response into feature vectors

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• ndarray3 function to compute minimum and maximum values

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• build: fix for linking of binary with ITK dep

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• Add function to reset array container size to zero

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• Export the filepath function for concatenating paths

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• Add struct member for classifying background voxels by Laplacian response

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• Fix Laplacian adjusted scale creation

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• Add debug logging for multiscale Laplacian filter function

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• Read ORION3 configuration format to set parameters for segmentation

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• Initialise multiscale segmentation to zero

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• Show usage when tool is not given any arguments

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• Add list of Debian packages required for building

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Commits on Apr 1, 2016

• Use more general FFT that does not require even dimensions

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• Use more general n-d FFT functions when applying Laplacian filter

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• Fix two memory bugs

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Commits on Apr 7, 2016

• Add PD KISS99 RNG code

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• Refactor the KISS99 RNG code

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Commits on Apr 11, 2016

• Organise the KISS99 RNG headers and tests

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• Remove unused variable

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• Add structure member to segmentation parameters for RNG state

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Commits on Apr 16, 2016

• Add function to free RNG state

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• initialise the RNG when starting the segmentation

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• Project specific Vim settings with autocmd

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• Add algorithm for sampling without replacement

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• Add test for uniform RNG (mean and variance)

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Commits on Apr 25, 2016

• Return the sample array

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• Update the discriminant function code

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• Use die() instead of exit() for failures in _orion_rand_seeds

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• Add platform-specific defines

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• Configuration generator output needs warning about editing

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• Add NOECHO setting to decrease build output

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• Add a macro to increment ndarray3 elements

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Commits on Apr 26, 2016

• Add functions to init and manipulate the 2D histogram

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Commits on Apr 27, 2016

• Improve indexing of histogram

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Commits on Jun 8, 2016

• VTK build configuration

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Commits on Jun 10, 2016

• Move the generated ITK/VTK make configuration into the BUILDDIR

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• Travis-CI: Add libvtk5-dev to the list of packages

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Commits on Jun 11, 2016

• Travis-CI: build in trusty environment

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• Travis-CI: install ITK/VTK version from trusty packages

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• build: Add support for VTK C++ compilation

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Commits on Jun 29, 2016

• Identify TODO items

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• VTK linking and histogram normalisation work

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Commits on Dec 23, 2016

• Set up Doxygen

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• Change Doxygen settings for this project

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