index 3 is out of bounds for dimension 1 with size 2 deformetrica

[Zicheng Zhu]

Hello, 

I tried to run the examples/atlas/landmark/3d/brain_structures

command: "deformetrica estimate model.xml data_set.xml -p optimization_parameters.xml"

problem: 

self.centers, self.normals = SurfaceMesh._get_centers_and_normals(

  File "/Users/Ricky/opt/anaconda3/lib/python3.8/site-packages/deformetrica/core/observations/deformable_objects/landmarks/surface_mesh.py", line 61, in _get_centers_and_normals

    c = points[triangles[:, 3]]

IndexError: index 3 is out of bounds for dimension 1 with size 3.

When I run 2d example, it was fine. 

[Zicheng Zhu]

hello again,

The same problem happened again when I ran my 2d models. I wanted to combine two 2d vtk files together. 

data_set.xml:

<?xml version="1.0"?>

<data-set>

    <subject id="00-1-AP-15L0214">

        <visit id="experiment">

            <filename object_id="NR-00-1-AP">Data/mc115L0214.vtk</filename>

            <filename object_id="NR-00-1-AP">Data/tpm15L0214.vtk</filename>

        </visit>

    </subject>

    <subject id="00-1-AP-15L0222">

        <visit id="experiment">

            <filename object_id="NR-00-1-AP">Data/mc115L0222.vtk</filename>

            <filename object_id="NR-00-1-AP">Data/tpm15L0222.vtk</filename>

        </visit>

    </subject>

</data-set>

model.xml:

<?xml version="1.0"?>

<model>

    <model-type>DeterministicAtlas</model-type>

    <dimension>2</dimension>

    <template>

        <object id="NR-00-1-AP">

            <deformable-object-type>SurfaceMesh</deformable-object-type>

            <attachment-type>Varifold</attachment-type>

            <noise-std>1</noise-std>

            <kernel-width>3</kernel-width>

            <kernel-type>keops</kernel-type>

            <filename>Data/FM_template-AP.vtk</filename>

        </object>

        <object id="NR-00-1-AP">

            <deformable-object-type>SurfaceMesh</deformable-object-type>

            <attachment-type>Varifold</attachment-type>

            <noise-std>1</noise-std>

            <kernel-width>3</kernel-width>

            <kernel-type>keops</kernel-type>

            <filename>Data/TPM_template-AP.vtk</filename>

        </object>

    </template>

    <deformation-parameters>

        <kernel-width>4</kernel-width>

        <kernel-type>keops</kernel-type>

        <number-of-timepoints>10</number-of-timepoints>

    </deformation-parameters>

</model>

optimization_parameters:

<?xml version="1.0"?>

<optimization-parameters>

    <optimization-method-type>GradientAscent</optimization-method-type>

<!--    <max-iterations>300</max-iterations>-->

<!--    <convergence-tolerance>1e-5</convergence-tolerance>-->

<!--    <use-sobolev-gradient>On</use-sobolev-gradient>-->

<!--    <freeze-template>On</freeze-template>-->

</optimization-parameters>