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Segmentation: refactoring #25

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Segmentation: refactoring #25

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@zmughal zmughal commented Mar 28, 2016

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@zmughal
wip: orion_multiscaleLaplacianFilter: implement multiscale processing
a237f3e 
TODO: fix the FFT to treat data for ifftn as conjugate symmetric. This
will fix the code for finding the maximum response.
@zmughal
add notes on the construction of the Laplacian in the Fourier domain
ac96bd8
@zmughal
WIP: stub out multiscale Laplacian filter
04664d4
@zmughal
Rename volume parameter for orion_readNegativeSamples
9b5c7fa
@zmughal
Finalise the multiscale Laplacian filter
cd7ace1
@zmughal
Implement readNegativeSamples
8d5c472
@zmughal
Add comment about getFeatures function
9a74027
@zmughal
Remove TODO
7df9471
@zmughal
Add notes about the contents of the Laplacian response
55f3491
@zmughal
Compute features with scales adjusted by the volume spacing
73dc304
@zmughal
Helper function to compute features
b58fe55
@zmughal
Translate the Gaussian response into feature vectors
e2575b8
@zmughal
ndarray3 function to compute minimum and maximum values
9c975c7
@zmughal
build: fix for linking of binary with ITK dep
9a4f5e9
@zmughal
Add function to reset array container size to zero
4bd97ae 
This allows for reusing a container.
@zmughal
Export the filepath function for concatenating paths
fce3af8
@zmughal
Add struct member for classifying background voxels by Laplacian resp…
846be22 
…onse
@zmughal
Fix Laplacian adjusted scale creation
70b9321
@zmughal
Add debug logging for multiscale Laplacian filter function
90aa001
@zmughal
Read ORION3 configuration format to set parameters for segmentation
ed05617
@zmughal
Initialise multiscale segmentation to zero
f13e145
@zmughal
Show usage when tool is not given any arguments
2c5fdb9
@zmughal
Add list of Debian packages required for building
7453e9d
@zmughal
Use more general FFT that does not require even dimensions
0079ec3
@zmughal
Use more general n-d FFT functions when applying Laplacian filter
85eea22
@zmughal
Fix two memory bugs
5f67276 
- One function did not return the correct variable.
- Another called a function before the container length was set.
@zmughal
Add PD KISS99 RNG code
4c3a94d 
Taken from <http://www.cse.yorku.ca/~oz/marsaglia-rng.html>.
@zmughal
Refactor the KISS99 RNG code
2291b9f 
Wrap all the seed values inside a struct
@zmughal
Organise the KISS99 RNG headers and tests
1d8a420
@zmughal
Remove unused variable
811515f
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Coverage Status

Coverage increased (+2.4%) to 79.839% when pulling 2dff9bb on segmentation into 03d208f on master.

@coveralls
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Coverage Status

Coverage increased (+2.4%) to 79.839% when pulling de503ea on segmentation into 03d208f on master.

@coveralls
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Coverage Status

Coverage increased (+2.4%) to 79.839% when pulling f9c5cf6 on segmentation into 03d208f on master.

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