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View Code? Open in Web Editor NEWGroup wise registration for 3d-models
License: Apache License 2.0
Group wise registration for 3d-models
License: Apache License 2.0
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
/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;
^
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used here is a bit out-of-date and does not support any VS 2019 build.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.
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
@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 🙏
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)
^
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:
A possible workflow could be the following:
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
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.
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