[vtkusers] Image volume conversion

[James Carroll]

After looking at the VTK source for TIFFReader I see that it has no
support for multi-tiff.

But I see the ITK does, so I'll try ITK next.

 

-Jim

 

________________________________

From: vtkusers-bounces+jim=microbrightfield.com at vtk.org
[mailto:vtkusers-bounces+jim=microbrightfield.com at vtk.org] On Behalf Of
James Carroll
Sent: Wednesday, June 08, 2005 1:45 PM
To: vtkusers at vtk.org
Subject: [vtkusers] Image volume conversion

 

 

Hi,

 

I'm trying to do an image stack conversion from a 16bit TIFF with 50
different (multi-tiff style) z planes in it to an 8 bit TIFF, and I'll
want to do some math as a filter in-between.

 

How can I have it read, filter and write an entire volume?  The
SetFileDimensionality(3) doesn't seem to pick up the different images in
the multi-tiff.

 

The weired part is that the format is 16 bit unsigned integer, but vtk
GetScalarRange() gives 3.0 to 11.0 which is really narrow, and floating
point?  I know there are more than 8 different pixel intensities.

 

tiffinfo gives me the following information:

TIFF Directory at offset 0xfaa

  Subfile Type: (0 = 0x0)

  Image Width: 1360 Image Length: 1036

  Resolution: 72, 72 pixels/inch

  Bits/Sample: 16

  Sample Format: unsigned integer

  Compression Scheme: None

  Photometric Interpretation: min-is-black

  Samples/Pixel: 1

  Rows/Strip: 1036

  Planar Configuration: single image plane

 

Here's my best guess so far, 

 

import vtk

 

reader = vtk.vtkTIFFReader()

reader.SetFileDimensionality(3)

reader.SetFileName("D:/TestStack.tiff")

 

# iterate over the entire stack, and see what the min/max of the pixel

# values really is

reader.Update()

minmax = reader.GetOutput().GetScalarRange()

print "The pixel values fall between", minmax

# this prints float 3.0 to 11.0

# I'm confused why an unsigned integer tiff gives a float scalar

# range, if it's really integer 3 - 11 that's too narrow a dynamic
range.

 

bounds = reader.GetOutput().GetBounds()

print "The Bounds are", bounds

# prints (0.0, 1359.0, 0.0, 1035.0, 0.0, 0.0)

# I'd expect the z bounds to be 0.0  to 49.0

 

# eventually...

#scale = vtk.vtkImageShiftScale()

# shift all the 16 bit pixels eight bits to the left

#scale.SetScale(256.0) 

#scale.SetOutputScalarTypeToChar (   ) 

 

 

# write an 8 bit grayscale tiff stack for the entire volume

writer = vtk.vtkTIFFWriter()

writer.SetFileName("D://wood.tiff")

 

writer.SetInput(reader.GetOutput())

writer.Write()

# only one plane gets written, and it's totally black

 

Thanks for the help!

-Jim

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