niraluser / groups Goto Github PK

Group wise registration for 3d-models

License: Apache License 2.0

CMake 12.23% C++ 72.54% Python 15.23%

3d-slicer-extension registration 3d-models

groups's Issues

Update tutorial to indicate naming requirements

The tutorial linked to in SlicerSALT does not make clear the file naming requirements enforced by the following code. Update the tutorial accordingly:

GROUPS/Modules/Scripted/RigidAlignmentModule/RigidAlignmentModule.py

Lines 101 to 103 in 71daa95

 models = self.inputDir.glob('*_pp_surf_SPHARM.vtk') 

 fiducials = self.fiducialsDir.glob('*_fid.fcsv') 

 unitSphere = next(self.commonSphereDir.glob('*_surf_para.vtk'))

Fix -Wunused-variable in GroupwiseRegistration.cpp

/tmp/GROUPS/Modules/CLI/Groups/GroupwiseRegistration.cpp: In member function ‘void GroupwiseRegistration::initProperties(int, const char**, int)’:
/tmp/GROUPS/Modules/CLI/Groups/GroupwiseRegistration.cpp:572:6: warning: unused variable ‘nFace’ [-Wunused-variable]
  int nFace = m_spharm[subj].sphere->nFace();
      ^
/tmp/GROUPS/Modules/CLI/Groups/GroupwiseRegistration.cpp: In member function ‘void GroupwiseRegistration::updateDeformation(int)’:
/tmp/GROUPS/Modules/CLI/Groups/GroupwiseRegistration.cpp:953:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (int i = 0; i < m_spharm[subject].vertex.size() && !updated; i++)
                    ^
/tmp/GROUPS/Modules/CLI/Groups/GroupwiseRegistration.cpp:957:16: warning: unused variable ‘v0’ [-Wunused-variable]
   const float *v0 = v->fv();
                ^
/tmp/GROUPS/Modules/CLI/Groups/GroupwiseRegistration.cpp: In member function ‘void GroupwiseRegistration::updateLandmark()’:
/tmp/GROUPS/Modules/CLI/Groups/GroupwiseRegistration.cpp:977:8: warning: unused variable ‘id’ [-Wunused-variable]
    int id = m_spharm[subj].landmark[i]->id;
        ^
/tmp/GROUPS/Modules/CLI/Groups/GroupwiseRegistration.cpp: In member function ‘void GroupwiseRegistration::updateLandmarkMedian()’:
/tmp/GROUPS/Modules/CLI/Groups/GroupwiseRegistration.cpp:1019:8: warning: unused variable ‘id’ [-Wunused-variable]
    int id = m_spharm[subj].landmark[i]->id;
        ^
/tmp/GROUPS/Modules/CLI/Groups/GroupwiseRegistration.cpp: At global scope:
/tmp/GROUPS/Modules/CLI/Groups/GroupwiseRegistration.cpp:1165:42: warning: unused parameter ‘coeff’ [-Wunused-parameter]
 float GroupwiseRegistration::cost(float *coeff, int statusStep)
                                          ^
/tmp/GROUPS/Modules/CLI/Groups/GroupwiseRegistration.cpp: In member function ‘void GroupwiseRegistration::optimization()’:
/tmp/GROUPS/Modules/CLI/Groups/GroupwiseRegistration.cpp:1229:6: warning: unused variable ‘n2’ [-Wunused-variable]
  int n2 = m_csize * 2 - n1;
      ^

Update FindVcvars.cmake

The version of FindVcvars.cmake used here is a bit out-of-date and does not support any VS 2019 build.

In particular, I am on VS 1929, which would be added by this PR: scikit-build/cmake-FindVcvars#1

It would also be helpful to update FindVcvars in Slicer proper once the above PR is merged; both on the master and v4.11 branches.

Associate 3d-slicer-extension topic with the repository

Could you associate the 3d-slicer-extension GitHub topic so that it is listed here: https://github.com/topics/3d-slicer-extension

To learn more about topic, read https://help.github.com/en/articles/about-topics

Re-fork repositories to avoid confusion

@ilwoolyu To avoid confusion, could you delete your project ilwoolyu/GROUPS and re-fork the one hosted in the NIRALUser organization. See https://github.com/NIRALUser/GROUPS

The fork graph currently shows this:

Thanks 🙏

GroupwiseRegistration::optimization doesn't make use of cost_function

In the GroupwiseRegistration::optimization function, the cost_function is not used hence the warning reported below.

Indeed, if we trace the flow, there functions are called:

GroupwiseRegistration::optimization -> min_newuoa -> min_newuoa -> newuoa_ -> newuob_ -> biglag_ -> no use of "func"

void GroupwiseRegistration::optimization(void)
{
	cost_function costFunc(this);
	int prev = 0;
	int step = 1;

	while (m_degree_inc < m_degree)
	{
		nIter = 0;
		int n = (m_degree_inc + 1) * (m_degree_inc + 1) * m_nSubj * 2 - prev;
		min_newuoa(n, &m_coeff[prev], costFunc, 1.0f, 1e-5f, m_maxIter);
		prev = (m_degree_inc + 1) * (m_degree_inc + 1) * m_nSubj * 2;
		m_degree_inc = min(m_degree_inc + step, m_degree);
	}
	
	// the entire optimization together
	nIter = 0;
	min_newuoa(m_csize * 2, m_coeff, costFunc, 1.0f, 1e-6f, m_maxIter);
}

In file included from /home/jcfr/Projects/SlicerSALT-Release-Qt5/GROUPS/Modules/CLI/Groups/GroupwiseRegistration.cpp:19:0:
/home/jcfr/Projects/SlicerSALT-Release-Qt5/GROUPS/Modules/CLI/Groups/newuoa.h: In instantiation of ‘int biglag_(int, int, TYPE*, TYPE*, TYPE*, TYPE*, int*, int*, int*, TYPE*, TYPE*, TYPE*, TYPE*, TYPE*, TYPE*, TYPE*, TYPE*, Func&) [with TYPE = float; Func = cost_function]’:
/home/jcfr/Projects/SlicerSALT-Release-Qt5/GROUPS/Modules/CLI/Groups/newuoa.h:1311:10:   required from ‘TYPE newuob_(int, int, TYPE*, TYPE, TYPE, int*, int, TYPE*, TYPE*, TYPE*, TYPE*, TYPE*, TYPE*, TYPE*, TYPE*, TYPE*, TYPE*, int*, TYPE*, TYPE*, TYPE*, Func&) [with TYPE = float; Func = cost_function]’
/home/jcfr/Projects/SlicerSALT-Release-Qt5/GROUPS/Modules/CLI/Groups/newuoa.h:1709:16:   required from ‘TYPE newuoa_(int, int, TYPE*, TYPE, TYPE, int*, int, TYPE*, Func&) [with TYPE = float; Func = cost_function]’
/home/jcfr/Projects/SlicerSALT-Release-Qt5/GROUPS/Modules/CLI/Groups/newuoa.h:1720:15:   required from ‘TYPE min_newuoa(int, TYPE*, Func&, TYPE, TYPE, int) [with TYPE = float; Func = cost_function]’
/home/jcfr/Projects/SlicerSALT-Release-Qt5/GROUPS/Modules/CLI/Groups/GroupwiseRegistration.cpp:1263:65:   required from here
/home/jcfr/Projects/SlicerSALT-Release-Qt5/GROUPS/Modules/CLI/Groups/newuoa.h:59:42: warning: unused parameter ‘func’ [-Wunused-parameter]
        TYPE *gd, TYPE *s, TYPE *w, Func &func)
                                          ^

Fix -Wsign-compare in GroupwiseRegistration.cpp

xref https://github.com/ilwoolyu/GROUPS/issues/4

Fix -Wsign-compare in Groups.cxx

xref https://github.com/ilwoolyu/GROUPS/issues/3

Simplify RigidAlignmentModule and GroupWiseRegistrationModule

When built against Slicer, the latest version of ShapePopulationViewer (SPV) is built as a loadable module.

This means that models already loaded in Slicer can easily be loaded in SPV, models can also be drag-and-dropped and loaded automatically.

This means that that the workflow in RigidAlignmentModule (or GroupWiseRegistrationModule) should be updated.

Currently the workflow is expected to be the following:

Display shape in shape population viewer by starting the CLI and expect the user to select entries from the CSV dialog. See here
Run rigid alignment CLI (or GROUPS CLI)
Run surf remesh CLI
Display shape in shape population viewer by starting the CLI and expecting the user to select entries from the CSV dialog. See here

A possible workflow could be the following:

Run rigid alignment CLI (or GROUPS CLI)
Run surf remesh CLI
Automatically select SPV and load shapes (without creating intermediate CSV files)

Merge last changes from local repo into NIRAL repo

Please, Mahmoud,

Can you merge your last changes into this repo? We are about to fix the windows compilation issues.
https://github.com/MahmoudMostapha/GROUPS

Thanks,
Bea

Remove LAPACK dependency

It am unable to find where lapack is being used in this extension, and having LAPACK as a dependency is a bit of overhead with needing fortran and all.

niraluser / groups Goto Github PK

groups's Issues

Update tutorial to indicate naming requirements

Fix -Wunused-variable in GroupwiseRegistration.cpp

Update FindVcvars.cmake

Associate 3d-slicer-extension topic with the repository

Re-fork repositories to avoid confusion

GroupwiseRegistration::optimization doesn't make use of cost_function

Fix -Wsign-compare in GroupwiseRegistration.cpp

Fix -Wsign-compare in Groups.cxx

Simplify RigidAlignmentModule and GroupWiseRegistrationModule

Merge last changes from local repo into NIRAL repo

Remove LAPACK dependency

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	models = self.inputDir.glob('*_pp_surf_SPHARM.vtk')
	fiducials = self.fiducialsDir.glob('*_fid.fcsv')
	unitSphere = next(self.commonSphereDir.glob('*_surf_para.vtk'))