Hello to all,
I have a .csv file with (x,y,z) positions of start and end positions of cylinders.
I would like to import this into paraview and create the cylinders givent the (x,y,z) of start points, and (x,y,z) of end points and specify the radius.
Is this possible?
I will leave an example .csv file:
foo.csv (1.2 KB)
Best regards
The easiest way is to use a programmable source and to write the reading part in python.
Note that the Tube filter creates a cylinder from lines, so you may just create a simple polydata and apply this filter.
In Programmable Source, I tried to use Cylinder Source and it became very complicated. nicolas.vuaille is right, it is much better to use Tube filter.
Just for reference, here is a dirty script for Programmable Source.
import numpy as np
import vtk
# CSV file to define the cylinders
csv_file = 'C:/Users/icem/Desktop/cyl/foo.csv'
# cylinder radius
r = 0.025
# CSV file reading
data = np.genfromtxt(csv_file, skip_header=2, dtype=None, names=['start_x','start_y','start_z','end_x','end_y','end_z'], delimiter=',', autostrip=True)
# obtain starting and ending coordinates of cylinders
start_pnts = np.vstack([data['start_x'],data['start_y'],data['start_z']]).T
end_pnts = np.vstack([data['end_x'],data['end_y'],data['end_z']]).T
appender = vtk.vtkAppendPolyData()
for start_pnt, end_pnt in zip(start_pnts, end_pnts):
# center coordinates of a cylinder
center = (start_pnt + end_pnt)*0.5
# direction vector of a cylinder
direc = end_pnt - start_pnt
# height of cylinder
h = np.linalg.norm(direc)
# define the local coordinate system of a cylinder
dir2 = direc / h
dir1 = np.array([dir2[1], -dir2[0], 0])
dir1 /= np.linalg.norm(dir1)
dir3 = np.cross(dir1, dir2)
# basis transformation matrix of the local coordinate system of a cylinder
T = np.array([dir1, dir2, dir3]).T
T = np.concatenate([T, np.zeros((3,1))], axis=1)
T = np.concatenate([T, np.zeros((1,4))], axis=0)
T[3, 3] = 1.0
# create a cylinder
cyl = vtk.vtkCylinderSource()
cyl.SetCenter([0,0,0])
cyl.SetRadius(r)
cyl.SetHeight(h)
cyl.SetResolution(100)
cyl.Update()
# transforms cylinder along its local coordinate system
transform = vtk.vtkTransform()
transform.PostMultiply()
transform.SetMatrix(T.flatten())
transform.Translate(center)
transformFilter = vtk.vtkTransformPolyDataFilter()
transformFilter.SetInputData(cyl.GetOutput())
transformFilter.SetTransform(transform)
transformFilter.Update()
# add a cylinder to appender
appender.AddInputData(transformFilter.GetOutput())
appender.Update()
output.DeepCopy(appender.GetOutput())
How can I create the polydata?
When using the Tube filter, the Programmable Source script becomes very simple as follows.
import numpy as np
import vtk
# CSV file to define the cylinders
csv_file = 'C:/Users/icem/Desktop/cyl/foo.csv'
# cylinder radius
r = 0.025
# CSV file reading
data = np.genfromtxt(csv_file, skip_header=2, dtype=None, names=['start_x','start_y','start_z','end_x','end_y','end_z'], delimiter=',', autostrip=True)
# obtain starting and ending coordinates of cylinders
start_pnts = np.vstack([data['start_x'],data['start_y'],data['start_z']]).T
end_pnts = np.vstack([data['end_x'],data['end_y'],data['end_z']]).T
appender = vtk.vtkAppendPolyData()
for start_pnt, end_pnt in zip(start_pnts, end_pnts):
# creating the central axis of a cylinder
line = vtk.vtkLineSource()
line.SetPoint1(start_pnt)
line.SetPoint2(end_pnt)
line.SetResolution(1)
line.Update()
# creating a cylinder
tubefilter = vtk.vtkTubeFilter()
tubefilter.SetInputData(line.GetOutput())
tubefilter.SetRadius(r)
tubefilter.SetNumberOfSides(50)
tubefilter.CappingOn()
tubefilter.Update()
# add a cylinder to appender
appender.AddInputData(tubefilter.GetOutput())
appender.Update()
output.DeepCopy(appender.GetOutput())
This worked!
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