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Questions:

  1. How to determine the width, length and bit depth of TIFF images? 
  2. How to reconstruct just a slab of slices using recon_arrayxml.py?
  3. How to reconstruct a region of interest?

 

 

 

 

 

 

 

Answers to questions:

  1. The width, length and bit depth of TIFF images can be determined in many different ways. For example, the Linux command tiffinfo can be used to print information about the input TIFF file(s) in the following way: tiffinfo [options] input1.tif input2.tif...

    For example,

    Linux command
    tiffinfo 06029.tif

    displays the following summary information:

    Linux output from tiffinfo
    TIFFReadDirectory: Warning, 06029.tif: unknown field with tag 65000 (0xfde8) encountered.
TIFF Directory at offset 0x146d308 (21418760)
  Image Width: 4008 Image Length: 2672
  Bits/Sample: 16
  Sample Format: unsigned integer
  Compression Scheme: None
  Photometric Interpretation: min-is-black
  Samples/Pixel: 1
  Rows/Strip: 2672
  Planar Configuration: single image plane
  Make: Unknown
  Model: Unknown
  Tag 65000: 727733745.824557

  2. It is sometimes desirable to reconstruct a slab of slices rather than the complete set. The recon_arrayxml.py script is capable of accomplishing this task with the help of the F- and L-options. 
    For example,

    Linux command
    python2.6 /dls_sw/i13/software/gda/config/tomography_scripts/recon_arrayxml.py -I settings.xml -o ../../reconstruction/564/ -C 2000.5 -F 1299 -L 1300

    will reconstruct a slab consisting of exactly 1 slice (=1300-1299), namely that indexed 1299.

  3. The contents of your settings.xml file under the ROI tag need to be modified in the following way:

     

    <ROI>
            <Type info="Standard, Rectangle">Rectangle</Type>
            <Xmin>580</Xmin>
            <Xmax>3000</Xmax>
            <Ymin>1225</Ymin>
            <Ymax>1725</Ymax>
            <OutputWidthType info="Standard, Given">Standard</OutputWidthType>
            <OutputWidth>500</OutputWidth>
            <Angle>0.0</Angle>

    </ROI>

     

    where the above values of Xmin, Xmax, Ymin, and Ymax should be changed to whatever values you would like to use (you can use ImageJ to determine those values by looking at the original images).  

     

 

 

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