[vtkusers] Can you Fix my very simple problem? convert tiff series/stack to .vtk file with python script?

[Christopher M. Navarro]

Maybe use vtkImageDataGeometryFilter which takes imagedata as input and 
write the output (vtkPolyData) with the vtkPolyDataWriter?

-chris


On Fri, 10 Oct 2003, Dr. Daniel James White PhD wrote:

> Hi all,
> 
> A very simple problem I'm sure only takes a moment to fix......
> 
> I'm trying to write a python script to convert series/stacks of tiff  
> images from our confocal microscope
> into some .vtk file that can be then read by VTK / MayaVi / VolView /  
> ParaView etc
> 
> The Data sets are slices through living cells etc, and need to be  
> reconstructed into a 3D data set for visualisation
> 
> Here is what I have so far..... I think it reads the stack/series of  
> tiff files into a 3D image OK,
> but it fails at the point of conversion of the image data into a
> structured grid (is this the right thing to do?) which can then be  
> written as a vtkStructuredGrid
> with vtkStructuredGridWriter.
> 
> what am I doing wrong...... I'm sure its very simple...
> 
> cheers
> 
> Dan
> 
> 
> #!/usr/bin/env python
> 
> # tiffstack2vtk.py
> # tiff series to .vtk conversion script
> # Dan White 2003
> 
> #----------------------------------------------------------------------- 
> ----
> # Code begins
> 
> import types,sys
> 
> if sys.argv[1:]:
>    filename = sys.argv[1]
> else:
>    filename = "whatnofilename.tif" # default filename
> 
> from vtkpython import *
> 
> # Build the vtk pipeline
> 
> # Data reader
> 
> reader1 = vtkTIFFReader ()
> reader1.SetFilePrefix(filename)
> reader1.SetFilePattern("%s%02i.tif")    #change to fit filename
> reader1.SetDataExtent(0,182,0,212,0,24) #change to fit image size
> reader1.SetDataSpacing(1,1,2.45)        #change to fit z spacing vs x,y
> reader1.SetDataByteOrderToBigEndian     #only needed if more than one  
> byte per pixel
> 
> reader = vtkImageLuminance ()
> reader.SetInput (reader1.GetOutput())
> 
> # Convert image to structured grid, I think I need to do this right?
> 
> converter = vtkDataSetToStructuredGridFilter ()   # OK this like  
> doesn't work as it is an abstract class
> converter.SetInput(reader.GetOutput())                 # so how should  
> I do it then?
> 
> 
> # Data writer
> 
> writer = vtk.vtkStructuredGridWriter()    #or should it be something  
> else
> writer.SetFileName('vtkfileout.vtk')      #change vtkfileout to  
> whatever filename you want
> writer.SetInput(converter.GetOutput())
> 
> # write the file to disk...
> writer.Write()
> 
> 
> 
> 
> Dr. Daniel James White BSc. (Hons.) PhD
> Cell Biology
> Department of biological and environmental science
> PO Box  35
> University of Jyväskylä
> Jyväskylä FIN 40014
> Finland
> +358 (0)14 260 4183 (work)
> +358 (0)414740463 (mob)
> 
> http://www.chalkie.org.uk
> dan at chalkie.org.uk
> white at cc.jyu.fi
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