mirror of
https://github.com/wassname/simpeg.git
synced 2026-07-15 11:26:09 +08:00
VTK example for surface to mesh model - Thanks Gudni!
This commit is contained in:
D Fournier
+81
-3
@@ -389,9 +389,87 @@ def read_GOCAD_ts(tsfile):
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line = fid.readline()
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vrtx = []
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# Run down all the vertices and save in array
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while re.match('VRTX',line):
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l_input = line.split('\s')
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vrtx = np.vstack([vrtx,l_input[1]])
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l_input = re.split('[\s*]',line)
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temp = np.array(l_input[2:5])
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vrtx.append(temp.astype(np.float))
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# Read next line
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line = fid.readline()
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return vrtx
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vrtx = np.asarray(vrtx)
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# Run down the list of triangles
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trgl = []
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# Run down all the vertices and save in array
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while re.match('TRGL',line):
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l_input = re.split('[\s*]',line)
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temp = np.array(l_input[1:4])
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trgl.append(temp.astype(np.int))
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# Read next line
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line = fid.readline()
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trgl = np.asarray(trgl)
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return vrtx, trgl
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def gocad2vtk(gcFile,mesh):
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""""
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Function to read gocad polystructure file and output indexes of mesh with in the structure.
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"""
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import vtk, vtk.util.numpy_support as npsup
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vrtx, trgl = read_GOCAD_ts(gcFile)
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# Adjust the index
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trgl = trgl - 1
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# Make vtk pts
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ptsvtk = vtk.vtkPoints()
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ptsvtk.SetData(npsup.numpy_to_vtk(vrtx,deep=1))
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# Make the polygon connection
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polys = vtk.vtkCellArray()
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for face in trgl:
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poly = vtk.vtkPolygon()
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poly.GetPointIds().SetNumberOfIds(len(face))
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for nrv, vert in enumerate(face):
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poly.GetPointIds().SetId(nrv,vert)
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polys.InsertNextCell(poly)
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# Make the polydata, structure of connections and vrtx
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polyData = vtk.vtkPolyData()
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polyData.SetPoints(ptsvtk)
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polyData.SetPolys(polys)
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# Make implicit func
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ImpDistFunc = vtk.vtkImplicitPolyDataDistance()
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ImpDistFunc.SetInput(polyData)
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# Convert the mesh
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vtkMesh = vtk.vtkRectilinearGrid()
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vtkMesh.SetDimensions(mesh.nNx,mesh.nNy,mesh.nNz)
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vtkMesh.SetXCoordinates(npsup.numpy_to_vtk(mesh.vectorNx,deep=1))
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vtkMesh.SetYCoordinates(npsup.numpy_to_vtk(mesh.vectorNy,deep=1))
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vtkMesh.SetZCoordinates(npsup.numpy_to_vtk(mesh.vectorNz,deep=1))
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# Add indexes
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vtkInd = npsup.numpy_to_vtk(np.arange(mesh.nC),deep=1)
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vtkInd.SetName('Index')
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vtkMesh.GetCellData().AddArray(vtkInd)
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extractImpDistRectGridFilt = vtk.vtkExtractGeometry() # Object constructor
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extractImpDistRectGridFilt.SetImplicitFunction(ImpDistFunc) #
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extractImpDistRectGridFilt.SetInputData(vtkMesh)
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extractImpDistRectGridFilt.ExtractBoundaryCellsOn()
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extractImpDistRectGridFilt.ExtractInsideOn()
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# Executing the pipe
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extractImpDistRectGridFilt.Update()
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insideGrid = extractImpDistRectGridFilt.GetOutput()
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# Return the indexes inside
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return npsup.vtk_to_numpy(insideGrid.GetCellData().GetArray('Index'))
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@@ -48,7 +48,8 @@ ndata = rxLoc.shape[0]
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# Load GOCAD surf
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tsfile = 'SphereA.ts'
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vrtx = PF.BaseMag.read_GOCAD_ts(tsfile)
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[vrtx, trgl] = PF.BaseMag.read_GOCAD_ts(tsfile)
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#%% Run forward modeling
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# Compute forward model using integral equation
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d = PF.Magnetics.Intgrl_Fwr_Data(mesh,B,M,rxLoc,model,actv,'tmi')
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@@ -0,0 +1,76 @@
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import os
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home_dir = '.\Test_tria_2_grid'
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inpfile = 'PYMAG3C_fwr.inp'
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dsep = '\\'
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os.chdir(home_dir)
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#%%
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from SimPEG import np, sp, Utils, mkvc, Maps
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import vtk, vtk.util.numpy_support as npsup
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import simpegPF as PF
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import pylab as plt
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## New scripts to be added to basecode
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#from fwr_MAG_data import fwr_MAG_data
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#from read_MAGfwr_inp import read_MAGfwr_inp
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#%%
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# Read input file
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# Load mesh file
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mesh = Utils.meshutils.readUBCTensorMesh('Mesh_2p5m.msh')
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# Load GOCAD surf
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tsfile = 'Crown.ts'
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#[vrtx, trgl] = PF.BaseMag.read_GOCAD_ts(tsfile)
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indx = PF.BaseMag.gocad2vtk(tsfile,mesh)
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model= np.zeros(mesh.nC)
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model[indx]=1
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Utils.meshutils.writeUBCTensorModel('VTKout.dat',mesh,model)
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# Load model file
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#model = Utils.meshutils.readUBCTensorModel(modfile,mesh)
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# Load in topofile or create flat surface
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#==============================================================================
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# if topofile == 'null':
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#
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# actv = np.ones(mesh.nC)
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#
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# else:
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# topo = np.genfromtxt(topofile,skip_header=1)
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# actv = PF.Magnetics.getActiveTopo(mesh,topo,'N')
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#
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#
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# Utils.writeUBCTensorModel('nullcell.dat',mesh,actv)
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#
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# # Load in observation file
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# [B,M,dobs] = PF.BaseMag.readUBCmagObs(obsfile)
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#
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# rxLoc = dobs[:,0:3]
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# #rxLoc[:,2] += 5 # Temporary change for test
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# ndata = rxLoc.shape[0]
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#==============================================================================
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#%% Run forward modeling
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# Compute forward model using integral equation
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#==============================================================================
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# d = PF.Magnetics.Intgrl_Fwr_Data(mesh,B,M,rxLoc,model,actv,'tmi')
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#
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# # Form data object with coordinates and write to file
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# wd = np.zeros((ndata,1))
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#
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# # Save forward data to file
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# PF.Magnetics.writeUBCobs(home_dir + dsep + 'FWR_data.dat',B,M,rxLoc,d,wd)
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#==============================================================================
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@@ -0,0 +1,56 @@
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GOCAD TSurf 1
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HEADER {
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name:Crown
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*solid*color:1 0.447059 0.337255 1
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ivolmap:false
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imap:false
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painted:on
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*painted*variable:normal
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last_selected_folder:3D property
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vectors3d:true
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*vectors3d*arrow:true
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*vectors3d*color:0.0980392 0.0980392 0.439216 1
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*vectors3d*arrow_size:5
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}
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GOCAD_ORIGINAL_COORDINATE_SYSTEM
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NAME Default
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AXIS_NAME "X" "Y" "Z"
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AXIS_UNIT "m" "m" "m"
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ZPOSITIVE Elevation
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END_ORIGINAL_COORDINATE_SYSTEM
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PROPERTY_CLASS_HEADER Z {
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is_z:on
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}
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PROPERTY_CLASS_HEADER vector3d {
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pclip:99
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low_clip:-0.9956403
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high_clip:0.9905306
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}
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TFACE
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VRTX 1 17.898199081420898 -24.1842041015625 -70.548362731933594
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VRTX 2 -24.411655426025391 -24.1842041015625 -69.894088745117188
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VRTX 3 17.898199081420898 25.8157958984375 -70.548362731933594
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VRTX 4 -24.411655426025391 25.8157958984375 -69.894088745117188
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VRTX 5 16.807741165161133 25.8157958984375 -9.4825878143310547
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VRTX 6 -4.565277099609375 -24.1842041015625 -28.674692153930664
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VRTX 7 16.807741165161133 -24.1842041015625 -9.4825878143310547
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VRTX 8 -24.629745483398438 -24.1842041015625 -12.972057342529297
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VRTX 9 -24.629745483398438 25.8157958984375 -12.972057342529297
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VRTX 10 -4.565277099609375 25.8157958984375 -28.674692153930664
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TRGL 8 6 9
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TRGL 7 1 5
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TRGL 1 2 3
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TRGL 9 6 10
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TRGL 10 7 5
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TRGL 2 8 4
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TRGL 5 1 3
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TRGL 3 2 4
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TRGL 10 5 3
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TRGL 4 9 10
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TRGL 7 6 1
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TRGL 6 2 1
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TRGL 4 10 3
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TRGL 4 8 9
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TRGL 8 2 6
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TRGL 6 7 10
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END
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@@ -0,0 +1,5 @@
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20 20 20
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0 0 0
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0.50 0.50 0.50 0.50 0.50 0.50 0.50 0.50 0.50 0.50 0.50 0.50 0.50 0.50 0.50 0.50 0.50 0.50 0.50 0.50
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0.50 0.50 0.50 0.50 0.50 0.50 0.50 0.50 0.50 0.50 0.50 0.50 0.50 0.50 0.50 0.50 0.50 0.50 0.50 0.50
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0.50 0.50 0.50 0.50 0.50 0.50 0.50 0.50 0.50 0.50 0.50 0.50 0.50 0.50 0.50 0.50 0.50 0.50 0.50 0.50
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@@ -0,0 +1,5 @@
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80 40 40
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-100.00 -50.00 0.00
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2.50 2.50 2.50 2.50 2.50 2.50 2.50 2.50 2.50 2.50 2.50 2.50 2.50 2.50 2.50 2.50 2.50 2.50 2.50 2.50 2.50 2.50 2.50 2.50 2.50 2.50 2.50 2.50 2.50 2.50 2.50 2.50 2.50 2.50 2.50 2.50 2.50 2.50 2.50 2.50 2.50 2.50 2.50 2.50 2.50 2.50 2.50 2.50 2.50 2.50 2.50 2.50 2.50 2.50 2.50 2.50 2.50 2.50 2.50 2.50 2.50 2.50 2.50 2.50 2.50 2.50 2.50 2.50 2.50 2.50 2.50 2.50 2.50 2.50 2.50 2.50 2.50 2.50 2.50 2.50
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2.50 2.50 2.50 2.50 2.50 2.50 2.50 2.50 2.50 2.50 2.50 2.50 2.50 2.50 2.50 2.50 2.50 2.50 2.50 2.50 2.50 2.50 2.50 2.50 2.50 2.50 2.50 2.50 2.50 2.50 2.50 2.50 2.50 2.50 2.50 2.50 2.50 2.50 2.50 2.50
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2.50 2.50 2.50 2.50 2.50 2.50 2.50 2.50 2.50 2.50 2.50 2.50 2.50 2.50 2.50 2.50 2.50 2.50 2.50 2.50 2.50 2.50 2.50 2.50 2.50 2.50 2.50 2.50 2.50 2.50 2.50 2.50 2.50 2.50 2.50 2.50 2.50 2.50 2.50 2.50
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@@ -0,0 +1,157 @@
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GOCAD TSurf 1
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HEADER {
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name:SphereA_test
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*solid*color:#00ffff
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ivolmap:false
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imap:false
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painted:on
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*painted*variable:normal
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mesh:true
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}
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GOCAD_ORIGINAL_COORDINATE_SYSTEM
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NAME Default
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AXIS_NAME "X" "Y" "Z"
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AXIS_UNIT "m" "m" "m"
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ZPOSITIVE Elevation
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END_ORIGINAL_COORDINATE_SYSTEM
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PROPERTY_CLASS_HEADER Z {
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is_z:on
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}
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PROPERTY_CLASS_HEADER vector3d {
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low_clip:-1
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high_clip:1
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pclip:99
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}
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TFACE
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VRTX 1 -2.2919261455535889 -19.314384460449219 -17.626590728759766
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VRTX 2 6.6298894882202148 -23.695545196533203 -28.910013198852539
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VRTX 3 -15.073513984680176 -19.314384460449219 -38.307632446289063
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VRTX 4 -12.506924629211426 -11.605335235595703 -51.606067657470703
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VRTX 5 -19.863996505737305 -8.0631170272827148 -46.194423675537109
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VRTX 6 -22.580167770385742 3.788722038269043 -23.29432487487793
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VRTX 7 -11.330929756164551 -18.19896125793457 -20.47222900390625
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VRTX 8 6.5996670722961426 -16.974418640136719 -50.459728240966797
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VRTX 9 -17.014554977416992 -8.2651615142822266 -16.98731803894043
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VRTX 10 21.977100372314453 -7.0079841613769531 -23.695110321044922
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VRTX 11 17.244131088256836 0 -15.232500076293945
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VRTX 12 13.95079517364502 10.135844230651855 -51.434154510498047
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VRTX 13 22.229457855224609 -8.2651615142822266 -41.241447448730469
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VRTX 14 -5.8128781318664551 14.548799514770508 -13.851467132568359
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VRTX 15 9.7651596069335937 -2.9769551753997803 -56.153919219970703
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VRTX 16 -13.742574691772461 5.0091938972473145 -53.607688903808594
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VRTX 17 -13.711102485656738 20.304235458374023 -28.35902214050293
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VRTX 18 -7.821871280670166 -18.734676361083984 -47.922031402587891
|
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VRTX 19 13.062463760375977 21.316003799438477 -33.333328247070313
|
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VRTX 20 -14.062309265136719 4.0251598358154297 -13.05897045135498
|
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VRTX 21 24.778470993041992 2.9769551753997803 -31.861873626708984
|
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VRTX 22 20.487052917480469 13.627725601196289 -37.756645202636719
|
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VRTX 23 -6.8588962554931641 -4.9832801818847656 -9.8147735595703125
|
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VRTX 24 9.4985036849975586 16.97282600402832 -49.040065765380859
|
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VRTX 25 19.077316284179688 3.788722038269043 -49.040065765380859
|
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VRTX 26 -24.44097900390625 -4.9556803703308105 -31.578392028808594
|
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VRTX 27 15.63094425201416 11.356545448303223 -17.468194961547852
|
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VRTX 28 2.7494394779205322 22.420015335083008 -22.619619369506836
|
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VRTX 29 5.0962982177734375 -4.9596676826477051 -9.3660707473754883
|
||||
VRTX 30 -2.6028509140014648 18.735876083374023 -49.679340362548828
|
||||
VRTX 31 7.3593044281005859 6.6037797927856445 -10.371823310852051
|
||||
VRTX 32 -21.796012878417969 -12.156011581420898 -31.861873626708984
|
||||
VRTX 33 -5.0962982177734375 -4.9596676826477051 -57.300586700439453
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VRTX 34 18.269777297973633 -16.974418640136719 -31.577091217041016
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VRTX 35 -19.291585922241211 15.273146629333496 -28.910013198852539
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VRTX 36 -23.036630630493164 3.6853373050689697 -42.318424224853516
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VRTX 37 8.4685440063476562 9.8534049987792969 -11.974625587463379
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VRTX 38 16.887338638305664 -14.301387786865234 -44.964668273925781
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VRTX 39 10.637019157409668 -16.68756103515625 -18.056575775146484
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VRTX 40 -4.8257155418395996 24.485654830932617 -34.804782867431641
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VRTX 41 -21.789302825927734 12.130206108093262 -35.089565277099609
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VRTX 42 -9.5504827499389648 18.734676361083984 -46.853691101074219
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VRTX 43 -2.6198656558990479 8.0631160736083984 -56.851882934570312
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VRTX 44 -0.90874701738357544 -24.94017219543457 -34.8037109375
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VRTX 45 -15.073513984680176 19.314384460449219 -38.307632446289063
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TRGL 31 29 11
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TRGL 7 3 44
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TRGL 36 41 45
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TRGL 35 41 6
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TRGL 22 24 19
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TRGL 45 41 35
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TRGL 14 23 31
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TRGL 30 43 42
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TRGL 39 2 34
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TRGL 17 35 14
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TRGL 20 9 23
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TRGL 2 38 34
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TRGL 26 5 32
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TRGL 43 30 24
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TRGL 11 10 21
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TRGL 21 13 25
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TRGL 19 28 27
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TRGL 36 16 5
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TRGL 19 40 28
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TRGL 12 43 24
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TRGL 1 44 2
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TRGL 2 44 8
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TRGL 9 32 7
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TRGL 22 12 24
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TRGL 6 26 9
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TRGL 11 29 39
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TRGL 33 18 4
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TRGL 6 9 20
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TRGL 10 34 13
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TRGL 33 16 43
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TRGL 34 38 13
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TRGL 10 11 39
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TRGL 35 6 20
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TRGL 38 15 25
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TRGL 42 36 45
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TRGL 27 28 37
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TRGL 5 4 3
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TRGL 21 25 22
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TRGL 16 36 42
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TRGL 30 42 40
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TRGL 25 15 12
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TRGL 33 43 15
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TRGL 4 18 3
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TRGL 26 32 9
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TRGL 13 38 25
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TRGL 40 42 45
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TRGL 19 27 22
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TRGL 14 31 37
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TRGL 40 17 28
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TRGL 41 26 6
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TRGL 43 12 15
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TRGL 22 25 12
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TRGL 14 20 23
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TRGL 8 18 33
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TRGL 10 13 21
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TRGL 11 21 27
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TRGL 40 45 17
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TRGL 40 19 24
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TRGL 30 40 24
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Reference in New Issue
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