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

[Dr. Daniel James White PhD]

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