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Segmentation: refactoring #25

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Segmentation: refactoring #25

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a237f3e
wip: orion_multiscaleLaplacianFilter: implement multiscale processing
zmughal Nov 5, 2015
ac96bd8
add notes on the construction of the Laplacian in the Fourier domain
zmughal Jan 2, 2016
04664d4
WIP: stub out multiscale Laplacian filter
zmughal Jan 21, 2016
9b5c7fa
Rename volume parameter for orion_readNegativeSamples
zmughal Mar 18, 2016
cd7ace1
Finalise the multiscale Laplacian filter
zmughal Mar 28, 2016
8d5c472
Implement readNegativeSamples
zmughal Mar 28, 2016
9a74027
Add comment about getFeatures function
zmughal Mar 28, 2016
7df9471
Remove TODO
zmughal Mar 28, 2016
55f3491
Add notes about the contents of the Laplacian response
zmughal Mar 31, 2016
73dc304
Compute features with scales adjusted by the volume spacing
zmughal Mar 31, 2016
b58fe55
Helper function to compute features
zmughal Mar 31, 2016
e2575b8
Translate the Gaussian response into feature vectors
zmughal Mar 31, 2016
9c975c7
ndarray3 function to compute minimum and maximum values
zmughal Mar 31, 2016
9a4f5e9
build: fix for linking of binary with ITK dep
zmughal Mar 31, 2016
4bd97ae
Add function to reset array container size to zero
zmughal Mar 31, 2016
fce3af8
Export the filepath function for concatenating paths
zmughal Mar 31, 2016
846be22
Add struct member for classifying background voxels by Laplacian resp…
zmughal Mar 31, 2016
70b9321
Fix Laplacian adjusted scale creation
zmughal Mar 31, 2016
90aa001
Add debug logging for multiscale Laplacian filter function
zmughal Mar 31, 2016
ed05617
Read ORION3 configuration format to set parameters for segmentation
zmughal Mar 31, 2016
f13e145
Initialise multiscale segmentation to zero
zmughal Mar 31, 2016
2c5fdb9
Show usage when tool is not given any arguments
zmughal Mar 31, 2016
7453e9d
Add list of Debian packages required for building
zmughal Mar 31, 2016
0079ec3
Use more general FFT that does not require even dimensions
zmughal Apr 1, 2016
85eea22
Use more general n-d FFT functions when applying Laplacian filter
zmughal Apr 1, 2016
5f67276
Fix two memory bugs
zmughal Apr 1, 2016
4c3a94d
Add PD KISS99 RNG code
zmughal Apr 7, 2016
2291b9f
Refactor the KISS99 RNG code
zmughal Apr 7, 2016
1d8a420
Organise the KISS99 RNG headers and tests
zmughal Apr 11, 2016
811515f
Remove unused variable
zmughal Apr 11, 2016
953ecdd
Add structure member to segmentation parameters for RNG state
zmughal Apr 11, 2016
f077520
Add function to free RNG state
zmughal Apr 16, 2016
0ca88ca
initialise the RNG when starting the segmentation
zmughal Apr 16, 2016
39c203d
Project specific Vim settings with autocmd
zmughal Apr 16, 2016
821a7d9
Add algorithm for sampling without replacement
zmughal Apr 16, 2016
11469a8
Add test for uniform RNG (mean and variance)
zmughal Apr 16, 2016
3f4f731
Return the sample array
zmughal Apr 17, 2016
e4087ba
Update the discriminant function code
zmughal Apr 25, 2016
f15e982
Use die() instead of exit() for failures in _orion_rand_seeds
zmughal Apr 25, 2016
7ee10ec
Add platform-specific defines
zmughal Apr 25, 2016
fb29a59
Configuration generator output needs warning about editing
zmughal Apr 25, 2016
9405b05
Add NOECHO setting to decrease build output
zmughal Apr 25, 2016
8ccb0e4
Add a macro to increment ndarray3 elements
zmughal Apr 25, 2016
b10251d
Add functions to init and manipulate the 2D histogram
zmughal Apr 26, 2016
79c0e10
Improve indexing of histogram
zmughal Apr 26, 2016
8a9b234
VTK build configuration
zmughal May 24, 2016
52ee36d
Move the generated ITK/VTK make configuration into the BUILDDIR
zmughal Jun 10, 2016
3e17468
Travis-CI: Add libvtk5-dev to the list of packages
zmughal Jun 10, 2016
2dff9bb
Travis-CI: build in trusty environment
zmughal Jun 11, 2016
de503ea
Travis-CI: install ITK/VTK version from trusty packages
zmughal Jun 11, 2016
f9c5cf6
build: Add support for VTK C++ compilation
zmughal Jun 11, 2016
9642be5
Identify TODO items
zmughal Jun 29, 2016
82fea6a
VTK linking and histogram normalisation work
zmughal Jun 29, 2016
94de3fe
Set up Doxygen
zmughal Dec 23, 2016
4c4d700
Change Doxygen settings for this project
zmughal Dec 23, 2016
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Fix Laplacian adjusted scale creation
@zmughal
zmughal committed Mar 31, 2016
commit 70b9321a31a0a2106126ba8941e24a6b3539ddae
2 changes: 1 addition & 1 deletion lib/kitchen-sink/01_Segmentation/dendrites_main/DetectTrainingSet/readNegativeSamples.c
View file
Original file line number Diff line number Diff line change
@@ -20,7 +20,7 @@ orion_readNegativeSamples(
size_t n_scales = array_length_float( param->scales );
array_float* Lap = array_new_float( n_scales );
for( size_t Lap_idx = 0; Lap_idx < n_scales; Lap_idx++ ) {
array_set_float( Lap, Lap_idx,
array_add_float( Lap,
0.66 / array_get_float( param->scales, Lap_idx ) );
}