[vtkusers] image header size confusion

[Alyassin, Abdalmajeid M (Research)]

If the CT data contains only header information + image data, you do NOT need to specify the header
size. However, you only need to specify the header size ONLY if the data contains a trailer. Try to
read the data without specifying the header size, if it does not look ok, then your data file
contains trailer information & therefore you need to specify exactly the header size.

Hope this helps
Abdalmajeid

-----Original Message-----
From: John Hunter [mailto:jdhunter at ace.bsd.uchicago.edu]
Sent: Monday, January 06, 2003 1:32 PM
To: VTK Users
Subject: [vtkusers] image header size confusion



I am using vtkImageReader to read in some CT data, and am experiencing
some confusion over how to handle the header with vtk.

The data are 512 x 512 x 2bytes.  To compute the header size, I take
the file size and subtract the number of pixels times the pixel size,
which is

  529720 - 512*512*2 = 5432 bytes

When I load the file in matlab using these assumptions, it displays
properly.  That is, I discard the first 5432 bytes of the file and
then read in the next 512*512 values as 2 byte unsigned ints.

However when I try to load it in vtk, I get a file load error when I
make the header size (with SetHeaderSize) larger than 3382 (which is
the value returned by GetHeaderSize if I do not set it manually).  If
I use this default value, the data loads, but is skewed due to the
incorrect header size information.

So, what exactly is the HeaderSize in vtk, and how should I set it for
this file.  Is it bytes from the beginning of the file to the pixel
data?  The man pages for SetHeaderSize say 

  void SetHeaderSize (int size); If there is a tail on the file, you
  want to explicitly set the header size.

which refers to a *tail*.  This confuses me.


Here is the python code -- perhaps the values in the error message
will provide a clue.

    # Image pipeline
    reader = vtkImageReader()
    reader.SetDataByteOrderToBigEndian()
    reader.SetDataExtent(0,512,0,512,2,225)

    reader.SetFilePrefix("Ser397")
    reader.SetFilePattern("%s/I.%03d")
    reader.SetDataScalarTypeToUnsignedShort()
    reader.SetHeaderSize(5432)

    Generic Warning: In /home/bellet/rpm/BUILD/VTK/IO/vtkImageReader.cxx, line 298
    File operation failed. row = 0, Tried to Read = 1026, Read = 0, Skip0 = -2052, Skip1 = 1052676,
FilePos = 530744

Guidance appreciated!
John Hunter

vtk nightly src from 2003-01-06 using vtkpython
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