Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Segmentation: refactoring #25

Open
wants to merge 55 commits into
base: master
Choose a base branch
from
Open

Segmentation: refactoring #25

wants to merge 55 commits into from

Commits on Feb 4, 2016

  1. wip: orion_multiscaleLaplacianFilter: implement multiscale processing 

    TODO: fix the FFT to treat data for ifftn as conjugate symmetric. This
will fix the code for finding the maximum response.
    @zmughal
    zmughal committed Feb 4, 2016
    Configuration menu
    Copy the full SHA
    a237f3e View commit details
    Browse the repository at this point in the history

  2. add notes on the construction of the Laplacian in the Fourier domain

    @zmughal
    zmughal committed Feb 4, 2016
    Configuration menu
    Copy the full SHA
    ac96bd8 View commit details
    Browse the repository at this point in the history

  3. WIP: stub out multiscale Laplacian filter

    @zmughal
    zmughal committed Feb 4, 2016
    Configuration menu
    Copy the full SHA
    04664d4 View commit details
    Browse the repository at this point in the history

Commits on Mar 18, 2016

  1. Rename volume parameter for orion_readNegativeSamples

    @zmughal
    zmughal committed Mar 18, 2016
    Configuration menu
    Copy the full SHA
    9b5c7fa View commit details
    Browse the repository at this point in the history

Commits on Mar 28, 2016

  1. Finalise the multiscale Laplacian filter

    @zmughal
    zmughal committed Mar 28, 2016
    Configuration menu
    Copy the full SHA
    cd7ace1 View commit details
    Browse the repository at this point in the history

  2. Implement readNegativeSamples

    @zmughal
    zmughal committed Mar 28, 2016
    Configuration menu
    Copy the full SHA
    8d5c472 View commit details
    Browse the repository at this point in the history

  3. Add comment about getFeatures function

    @zmughal
    zmughal committed Mar 28, 2016
    Configuration menu
    Copy the full SHA
    9a74027 View commit details
    Browse the repository at this point in the history

  4. Remove TODO

    @zmughal
    zmughal committed Mar 28, 2016
    Configuration menu
    Copy the full SHA
    7df9471 View commit details
    Browse the repository at this point in the history

Commits on Mar 31, 2016

  1. Add notes about the contents of the Laplacian response

    @zmughal
    zmughal committed Mar 31, 2016
    Configuration menu
    Copy the full SHA
    55f3491 View commit details
    Browse the repository at this point in the history

  2. Compute features with scales adjusted by the volume spacing

    @zmughal
    zmughal committed Mar 31, 2016
    Configuration menu
    Copy the full SHA
    73dc304 View commit details
    Browse the repository at this point in the history

  3. Helper function to compute features

    @zmughal
    zmughal committed Mar 31, 2016
    Configuration menu
    Copy the full SHA
    b58fe55 View commit details
    Browse the repository at this point in the history

  4. Translate the Gaussian response into feature vectors

    @zmughal
    zmughal committed Mar 31, 2016
    Configuration menu
    Copy the full SHA
    e2575b8 View commit details
    Browse the repository at this point in the history

  5. ndarray3 function to compute minimum and maximum values

    @zmughal
    zmughal committed Mar 31, 2016
    Configuration menu
    Copy the full SHA
    9c975c7 View commit details
    Browse the repository at this point in the history

  6. build: fix for linking of binary with ITK dep

    @zmughal
    zmughal committed Mar 31, 2016
    Configuration menu
    Copy the full SHA
    9a4f5e9 View commit details
    Browse the repository at this point in the history

  7. Add function to reset array container size to zero 

    This allows for reusing a container.
    @zmughal
    zmughal committed Mar 31, 2016
    Configuration menu
    Copy the full SHA
    4bd97ae View commit details
    Browse the repository at this point in the history

  8. Export the filepath function for concatenating paths

    @zmughal
    zmughal committed Mar 31, 2016
    Configuration menu
    Copy the full SHA
    fce3af8 View commit details
    Browse the repository at this point in the history

  9. Add struct member for classifying background voxels by Laplacian resp… 

    …onse
    @zmughal
    zmughal committed Mar 31, 2016
    Configuration menu
    Copy the full SHA
    846be22 View commit details
    Browse the repository at this point in the history

  10. Fix Laplacian adjusted scale creation

    @zmughal
    zmughal committed Mar 31, 2016
    Configuration menu
    Copy the full SHA
    70b9321 View commit details
    Browse the repository at this point in the history

  11. Add debug logging for multiscale Laplacian filter function

    @zmughal
    zmughal committed Mar 31, 2016
    Configuration menu
    Copy the full SHA
    90aa001 View commit details
    Browse the repository at this point in the history

  12. Read ORION3 configuration format to set parameters for segmentation

    @zmughal
    zmughal committed Mar 31, 2016
    Configuration menu
    Copy the full SHA
    ed05617 View commit details
    Browse the repository at this point in the history

  13. Initialise multiscale segmentation to zero

    @zmughal
    zmughal committed Mar 31, 2016
    Configuration menu
    Copy the full SHA
    f13e145 View commit details
    Browse the repository at this point in the history

  14. Show usage when tool is not given any arguments

    @zmughal
    zmughal committed Mar 31, 2016
    Configuration menu
    Copy the full SHA
    2c5fdb9 View commit details
    Browse the repository at this point in the history

  15. Add list of Debian packages required for building

    @zmughal
    zmughal committed Mar 31, 2016
    Configuration menu
    Copy the full SHA
    7453e9d View commit details
    Browse the repository at this point in the history

Commits on Apr 1, 2016

  1. Use more general FFT that does not require even dimensions

    @zmughal
    zmughal committed Apr 1, 2016
    Configuration menu
    Copy the full SHA
    0079ec3 View commit details
    Browse the repository at this point in the history

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

    @zmughal
    zmughal committed Apr 1, 2016
    Configuration menu
    Copy the full SHA
    85eea22 View commit details
    Browse the repository at this point in the history

  3. Fix two memory bugs 

    - One function did not return the correct variable.
- Another called a function before the container length was set.
    @zmughal
    zmughal committed Apr 1, 2016
    Configuration menu
    Copy the full SHA
    5f67276 View commit details
    Browse the repository at this point in the history

Commits on Apr 7, 2016

  1. Add PD KISS99 RNG code 

    Taken from <http://www.cse.yorku.ca/~oz/marsaglia-rng.html>.
    @zmughal
    zmughal committed Apr 7, 2016
    Configuration menu
    Copy the full SHA
    4c3a94d View commit details
    Browse the repository at this point in the history

  2. Refactor the KISS99 RNG code 

    Wrap all the seed values inside a struct
    @zmughal
    zmughal committed Apr 7, 2016
    Configuration menu
    Copy the full SHA
    2291b9f View commit details
    Browse the repository at this point in the history

Commits on Apr 11, 2016

  1. Organise the KISS99 RNG headers and tests

    @zmughal
    zmughal committed Apr 11, 2016
    Configuration menu
    Copy the full SHA
    1d8a420 View commit details
    Browse the repository at this point in the history

  2. Remove unused variable

    @zmughal
    zmughal committed Apr 11, 2016
    Configuration menu
    Copy the full SHA
    811515f View commit details
    Browse the repository at this point in the history

  3. Add structure member to segmentation parameters for RNG state

    @zmughal
    zmughal committed Apr 11, 2016
    Configuration menu
    Copy the full SHA
    953ecdd View commit details
    Browse the repository at this point in the history

Commits on Apr 16, 2016

  1. Add function to free RNG state

    @zmughal
    zmughal committed Apr 16, 2016
    Configuration menu
    Copy the full SHA
    f077520 View commit details
    Browse the repository at this point in the history

  2. initialise the RNG when starting the segmentation

    @zmughal
    zmughal committed Apr 16, 2016
    Configuration menu
    Copy the full SHA
    0ca88ca View commit details
    Browse the repository at this point in the history

  3. Project specific Vim settings with autocmd

    @zmughal
    zmughal committed Apr 16, 2016
    Configuration menu
    Copy the full SHA
    39c203d View commit details
    Browse the repository at this point in the history

  4. Add algorithm for sampling without replacement

    @zmughal
    zmughal committed Apr 16, 2016
    Configuration menu
    Copy the full SHA
    821a7d9 View commit details
    Browse the repository at this point in the history

  5. Add test for uniform RNG (mean and variance)

    @zmughal
    zmughal committed Apr 16, 2016
    Configuration menu
    Copy the full SHA
    11469a8 View commit details
    Browse the repository at this point in the history

Commits on Apr 25, 2016

  1. Return the sample array

    @zmughal
    zmughal committed Apr 25, 2016
    Configuration menu
    Copy the full SHA
    3f4f731 View commit details
    Browse the repository at this point in the history

  2. Update the discriminant function code

    @zmughal
    zmughal committed Apr 25, 2016
    Configuration menu
    Copy the full SHA
    e4087ba View commit details
    Browse the repository at this point in the history

  3. Use die() instead of exit() for failures in _orion_rand_seeds

    @zmughal
    zmughal committed Apr 25, 2016
    Configuration menu
    Copy the full SHA
    f15e982 View commit details
    Browse the repository at this point in the history

  4. Add platform-specific defines

    @zmughal
    zmughal committed Apr 25, 2016
    Configuration menu
    Copy the full SHA
    7ee10ec View commit details
    Browse the repository at this point in the history

  5. Configuration generator output needs warning about editing

    @zmughal
    zmughal committed Apr 25, 2016
    Configuration menu
    Copy the full SHA
    fb29a59 View commit details
    Browse the repository at this point in the history

  6. Add NOECHO setting to decrease build output 

    This helps avoid having to see the long series of compiler flags.
    @zmughal
    zmughal committed Apr 25, 2016
    Configuration menu
    Copy the full SHA
    9405b05 View commit details
    Browse the repository at this point in the history

  7. Add a macro to increment ndarray3 elements

    @zmughal
    zmughal committed Apr 25, 2016
    Configuration menu
    Copy the full SHA
    8ccb0e4 View commit details
    Browse the repository at this point in the history

Commits on Apr 26, 2016

  1. Add functions to init and manipulate the 2D histogram

    @zmughal
    zmughal committed Apr 26, 2016
    Configuration menu
    Copy the full SHA
    b10251d View commit details
    Browse the repository at this point in the history

Commits on Apr 27, 2016

  1. Improve indexing of histogram

    @zmughal
    zmughal committed Apr 27, 2016
    Configuration menu
    Copy the full SHA
    79c0e10 View commit details
    Browse the repository at this point in the history

Commits on Jun 8, 2016

  1. VTK build configuration

    @zmughal
    zmughal committed Jun 8, 2016
    Configuration menu
    Copy the full SHA
    8a9b234 View commit details
    Browse the repository at this point in the history

Commits on Jun 10, 2016

  1. Move the generated ITK/VTK make configuration into the BUILDDIR 

    This ensures that the configuration does not stay with the source code.
    @zmughal
    zmughal committed Jun 10, 2016
    Configuration menu
    Copy the full SHA
    52ee36d View commit details
    Browse the repository at this point in the history

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

    @zmughal
    zmughal committed Jun 10, 2016
    Configuration menu
    Copy the full SHA
    3e17468 View commit details
    Browse the repository at this point in the history

Commits on Jun 11, 2016

  1. Travis-CI: build in trusty environment

    @zmughal
    zmughal committed Jun 11, 2016
    Configuration menu
    Copy the full SHA
    2dff9bb View commit details
    Browse the repository at this point in the history

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

    @zmughal
    zmughal committed Jun 11, 2016
    Configuration menu
    Copy the full SHA
    de503ea View commit details
    Browse the repository at this point in the history

  3. build: Add support for VTK C++ compilation

    @zmughal
    zmughal committed Jun 11, 2016
    Configuration menu
    Copy the full SHA
    f9c5cf6 View commit details
    Browse the repository at this point in the history

Commits on Jun 29, 2016

  1. Identify TODO items

    @zmughal
    zmughal committed Jun 29, 2016
    Configuration menu
    Copy the full SHA
    9642be5 View commit details
    Browse the repository at this point in the history

  2. VTK linking and histogram normalisation work

    @zmughal
    zmughal committed Jun 29, 2016
    Configuration menu
    Copy the full SHA
    82fea6a View commit details
    Browse the repository at this point in the history

Commits on Dec 23, 2016

  1. Set up Doxygen

    @zmughal
    zmughal committed Dec 23, 2016
    Configuration menu
    Copy the full SHA
    94de3fe View commit details
    Browse the repository at this point in the history

  2. Change Doxygen settings for this project

    @zmughal
    zmughal committed Dec 23, 2016
    Configuration menu
    Copy the full SHA
    4c4d700 View commit details
    Browse the repository at this point in the history