# Extract surface meshes from groundtruth and deformed/predicted volumetric meshes
**URL:** https://discourse.vtk.org/t/extract-surface-meshes-from-groundtruth-and-deformed-predicted-volumetric-meshes/12053
**Category:** Support
**Tags:** python
**Created:** [July 28, 2023, 8:30am UTC](https://discourse.vtk.org/t/extract-surface-meshes-from-groundtruth-and-deformed-predicted-volumetric-meshes/12053 "2023-07-28T08:30:17Z")
**Posts on this page:** 5
**Page:** 1
### Author:  [@isuruwi](https://discourse.vtk.org/u/isuruwi)
#### Post date: [July 28, 2023, 8:30am UTC](https://discourse.vtk.org/t/extract-surface-meshes-from-groundtruth-and-deformed-predicted-volumetric-meshes/12053/1 "2023-07-28T08:30:17Z")
Hi,
I have two volumetric meshes that have same number of nodes and connectivities (cells). The only difference is that one mesh is kind of a deformed version of the other. This means only the node positions are sligtly different.
What I want is that extract the surface meshes from those two and save back to the disk for further processing. However, when I attempt to extract by using vtk.geometryFilter (see below sample code) I enconter that the face ids are somehow different to each other.
How can I extract the surface meshes which compatible to each other so that I can compare them. This indicates only the node positions are different but the faces/tirangles ids are exactly the same.
Am I missed anything or any steps here ? If so can you elaborate the steps with an example please ?
I herewith attached a sample groundtruth mesh and its deformed/predicted version for your further reference.
```auto
import os
import vtk
def getSurfaceMesh(vol_mesh_path, out_save_path):
meshReader = vtk.vtkUnstructuredGridReader()
meshReader.SetFileName(vol_mesh_path)
meshReader.ReadAllVectorsOn()
meshReader.ReadAllScalarsOn()
meshReader.Update()
meshGeometryFilter = vtk.vtkGeometryFilter()
meshGeometryFilter.SetInputData(meshReader.GetOutput())
meshGeometryFilter.Update()
stlWriter = vtk.vtkSTLWriter()
stlWriter.SetFileName(out_save_path)
stlWriter.SetInputConnection(meshGeometryFilter.GetOutputPort())
stlWriter.Write()
volumetric_mesh_path = "F:/gt_scan_1.vtk"
surface_save_path = "F:/surface_meshes/gt_scan_1.stl"
pred_volumetric_mesh_path = "F:/pred_scan_1.vtk"
pred_surface_save_path = "F:/surface_meshes/pred_scan_1.stl"
getSurfaceMesh(volumetric_mesh_path, surface_save_path)
getSurfaceMesh(pred_volumetric_mesh_path, pred_surface_save_path)
```
---
### Author:  [@lassoan](https://discourse.vtk.org/u/lassoan)
#### Post date: [July 29, 2023, 6:19pm UTC](https://discourse.vtk.org/t/extract-surface-meshes-from-groundtruth-and-deformed-predicted-volumetric-meshes/12053/2 "2023-07-29T18:19:29Z")
vtkGeometryFilter can pass through original point and cell IDs.
---
### Author:  [@isuruwi](https://discourse.vtk.org/u/isuruwi)
#### Post date: [July 30, 2023, 9:07am UTC](https://discourse.vtk.org/t/extract-surface-meshes-from-groundtruth-and-deformed-predicted-volumetric-meshes/12053/3 "2023-07-30T09:07:55Z")
Hi Andras,
I just modified my script by adding below two lines to the code.
```auto
meshGeometryFilter.SetPassThroughCellIds(1)
meshGeometryFilter.SetPassThroughPointIds(1)
```
However, I encounter an error message saying that there is no attributes specified with SetPassThroughCellIds and SetPassThroughPointIds in vtkGeometryFilter.
**AttributeError: ‘vtkmodules.vtkFiltersGeometry.vtkGeometryFilter’ object has no attribute ‘SetPassThroughCellIds’**
**How can I set original point and cell IDs to the vtkGeometry Filter. Could you please elaborate this with a simple example code ?**
Modified code:
```auto
def getSurfaceMesh(vol_mesh_path, out_save_path):
meshReader = vtk.vtkUnstructuredGridReader()
meshReader.SetFileName(vol_mesh_path)
meshReader.ReadAllVectorsOn()
meshReader.ReadAllScalarsOn()
meshReader.Update()
meshGeometryFilter = vtk.vtkGeometryFilter()
meshGeometryFilter.SetInputData(meshReader.GetOutput())
meshGeometryFilter.SetPassThroughCellIds(1)
meshGeometryFilter.SetPassThroughPointIds(1)
meshGeometryFilter.Update()
stlWriter = vtk.vtkSTLWriter()
stlWriter.SetFileName(out_save_path)
stlWriter.SetInputConnection(meshGeometryFilter.GetOutputPort())
stlWriter.Write()
```
---
### Author:  [@lassoan](https://discourse.vtk.org/u/lassoan)
#### Post date: [July 30, 2023, 12:37pm UTC](https://discourse.vtk.org/t/extract-surface-meshes-from-groundtruth-and-deformed-predicted-volumetric-meshes/12053/4 "2023-07-30T12:37:04Z")
What VTK version do you use? If it is older than 3 years then you may need to update.
---
### Author:  [@mwestphal](https://discourse.vtk.org/u/mwestphal)
#### Post date: [November 5, 2023, 9:48am UTC](https://discourse.vtk.org/t/extract-surface-meshes-from-groundtruth-and-deformed-predicted-volumetric-meshes/12053/5 "2023-11-05T09:48:21Z")
data removed as asked by @isuruwi