I see- thank you!

Here is a piece of code that creates a coil wrapped onto a torus, using lines defined from 3D parametric equations.

It makes use of Law(), Curve(), CreateWireBody() and SweepAlongPath() from the XCoreModeling package.

import numpy as np import s4l_v1.document as document import s4l_v1.model as model import XCoreModeling def create_toroidal_coil(R, r, m, n=1, i=1, name="Toroid"): """ Create a spline model object with a spiral shape. The shape is defined from a 3D parametric equation. """ # equation b = 2. * np.pi * float(i) / float(m) x_component = "({R}-{r}*cos({b} + {n}*t)) * cos(t)".format(R=str(R), r=str(r), b=str(b), n=str(n)) y_component = "({R}-{r}*cos({b} + {n}*t)) * sin(t)".format(R=str(R), r=str(r), b=str(b), n=str(n)) z_component = "{r}*sin({b}+{n}*t)".format(r=str(r), b=str(b), n=str(n)) path = XCoreModeling.Law("vec({}, {}, {})".format(x_component, y_component, z_component)) curve = XCoreModeling.Curve(path, 0.0, 2.*np.pi) # Create a spline wire body to visualize wire = XCoreModeling.CreateWireBody( curve ) wire.Name = name torus_centerline = model.CreateCircle(model.Vec3(0,0,0), model.Vec3(0,0,1), 10) torus_centerline.Name = 'Centerline' torus = model.CreateSolidCylinder(model.Vec3(10,0,0),model.Vec3(10,0,0), 3) torus.ApplyTransform(model.Rotation(model.Vec3(1,0,0), np.pi/2)) XCoreModeling.SweepAlongPath(torus, torus_centerline, make_solid=True, cut_off_end=True) # Theoretical self-inductance: area = np.pi * (r*1e-3)**2 L_theoretical = 4.0e-7 * np.pi * n * n * area/ (2.0* np.pi *R * 1e-3) print(L_theoretical * 40) return wire, torus if __name__=="__main__": wire, torus = create_toroidal_coil(10,3,1, n=100)

when you write inventor, do you mean "Autodesk Inventor" or "Open Inventor"?

I guess the file is some kind of assembly, which is exported as a single STL file. STL does not support multi-part models, so you would need to export each part a separate STL file (or other format supported by Sim4Life), or you export it to a file format that supports multiple parts (ACIS .sab/.sat, STEP .step, ... VTK .vtm (multiblock)).

STL also only supports triangle surface representations, so if you had a NURBS CAD file, you loose the that by exporting to STL.

Searching for the topic I found this information for Autodesk Inventor to export as a multibody sab file:
https://knowledge.autodesk.com/support/inventor/troubleshooting/caas/sfdcarticles/sfdcarticles/How-to-convert-Inventor-Assembly-file-to-a-multi-body-part-file.html

btw. if the points in different parts aren't coincident, you may be lucky with your single STL file: try Modeling -> Mesh Tools -> Separate Meshes. This could separate disconnected parts.

Yes, there is. Create a sphere, then use the "Move" tool and look for the "Stretch" button on the right side of the 3D window.
You can then stretch any of the 3 principal axis of the sphere.

To comment on this case. The surface extraction in iSEG is inferior to the surface extraction in Sim4Life. So you probably want to export the labelfield as voxels (e.g. in Nifty, Nrrd or Metaheader format - the VTK format does not preserve the transformations correctly). You can also extract the tissue list as txt file in iSEG in order to set the tissue names e.g. via a python script in Sim4Life.

@Jexyll_S Oh perhaps, thanks!

Hi Micol and Frodi,

One free alternative is to use the shell provided with the Fitness Tracker tutorial. This is the skin shell of the model Billie. It is not license protected and can be exported to any one of the available export formats.

Best,
Habib

Hi, when sweeping an object along a path, the normal of the cross-section should in principle follow the path. This, however, does not prevent having self-intersections in locations where the curvature of the path is too large compared to the size of the cross-section.

The best way to experiment (different geometries, different paths, etc...) is to use the Python API:

import s4l_v1.model as model from s4l_v1.model import Vec3 import XCoreModeling spline1 = model.CreateSpline([Vec3(0,0,0), Vec3(50,0,0), Vec3(50,50,50)]) section = model.CreateCircle(Vec3(0,0,0), Vec3(1,0,0), 10) region1 = XCoreModeling.SweepAlongPath(section, spline1, make_solid=True)

@PeterStijnman Thank you so much for your solution,I will try it.

@LCL You are welcome! Enjoy the Helix tool and do not hesitate to post some screenshots on this forum if you create some nice looking helixes 🙂

Those look llike ghost voxels (i.e. voxels produced by a bug in the voxeler). Look at the regularity of those voxels. If this is reproducible, can you please provide a project file with that model in it and report a bug case?

just to comment on doing booleans with licensed models. this is completely possible, as Suchit says. Sometimes I think users get confused by the lock symbols shown in the model. These locks are not related to the license protection at all, they are there because the model is posable and modifying individual parts would break the posability.

For you I would suggest to download the shell (surface enclosing the complete model) of DUKE and do the boolean operation with the shell only. For Duke you could use: https://itis.swiss/virtual-population/virtual-population/vip2/duke/duke-whole-body-shell-v2-0/

Since the shell is not license protected you can modify it, save it as STL or whatever format and load it other software tools if needed (e.g. MATLAB). To make it a solid the easiest method is to import the STL file and check the box "Import as Solid".

We are planning to restructure the downloads soon, and I want to add the shell surface by default to the zip file containing the full V3.x model, since it is often useful, e.g. to create uniform thickness offset surfaces (skin layers), and other operations.

The list is actually quite a bit longer.

For surface meshes is includes:

VTK PLY OBJ OFF DAT (iSEG/ViP surface format)

For image data it includes:

PRJ (iSEG project files) NIFTY (NII, NII.GZ) DICOM MHA/MHD NRRD

For unstructured meshes it includes:

Exodus II VTU NASTRAN (partial support)

You would have to define the polylines in a supported file format, e.g. VTK.

To create such a file from Python, you could do something like this:

import vtk # define points x1,y1,z1, etc. # add the actual points points = vtk.vtkPoints() points.InsertNextPoint(x1,y1,z1) points.InsertNextPoint(x2,y2,z2) points.InsertNextPoint(x3,y3,z3) # define the lines lines = vtk.vtkCellArray() lines.InsertNextCell(3) # next line is composed of 3 vertices lines.InsertCellPoint(0) # vertex 1 lines.InsertCellPoint(1) # vertex 2 lines.InsertCellPoint(2) # vertex 3 # assemble as surface mesh mesh = vtk.vtkPolyData() mesh.SetPoints(points) mesh.SetLines(lines) # write to file, supported by Sim4Life, Paraview, etc. writer = vtk.vtkDataSetWriter() writer.SetInputData(mesh) writer.SetFileName(r"E:\temp\Foo.vtk") writer.Write()

@pcrespo By the way. Converting to Solid (using either method) only works well when
a) the mesh resolution is not too high (else it will take forever and use huge amounts of memory)
b) the surface mesh is manifold and has no self-intersections. these defects can be identified and often fixed using the Mesh Doctor ("Automatically Fix").

0_1525763901226_d38bb2c1-efd5-4038-b84a-605be284dda1-image.png

0_1525763910904_3d828313-84bb-4410-9be9-d584b6318823-image.png

got it:

wire = GetWires(spline)[0] curve = wire.GetGeometry(transform_to_model_space=True) law = curve.GetLaw() t0 = curve.MinDistParameter(point_start)