HST_MASTER: Reconstruction Direct From Sinograms

     

Sometimes it is necessary to treat the sinogram data in a special fashion prior to back-projection. For this, hst_master can command hst_slave to assemble and output a series of sinograms into files, and can instruct hst_slave to directly input the series of sinograms for reconstruction.

The sequence of questions is similar in style, but also somewhat different for direct reconstruction from sinograms.

The the file selection utility asks for SELECT FIRST SINOGRAM IMAGE FILE. This will be similar to Figure 3, Page . When a file is selected it is input and displayed as shown in Figure 11, Page .

  

Figure 11: Display of First Sinogram

The sinogram image should be similar, with the characteristic sinusoidal variation.

When the correct starting sinogram image has been selected, the file selection utility returns to SELECT LAST SINOGRAM TO RECONSTRUCT.

Next the first sinogram reconstruction parameter control form appears, as show in Figure 12, Page .

  

Figure 12: Sinogram Reconstruction Control Form 1

By clicking on the yellow right-hand column of buttons the ``values'' of the variables controlling the reconstruction can be changed. When the ``values'' have all been set appropriately the O.K button can be clicked to move to the second control form.

The basic sense of each control parameter is described in the left-hand column of DESCRIPTIONS. Further explanation is given when the value is being changed.

The parameters are described following the button text:

SINOGRAM INTERVAL   This control parameter allows faster reconstruction by not reconstructing all the sinograms. Hence, the reconstructed volume becomes smaller. For full reconstruction of all sinograms, this item should equal 1. To only use every other sinogram this item should equal 2. To use every third sinogram this item should equal 3, etc. (Note: Unlike the FILE_INTERVAL parameter for raw data reconstruction, values larger than 1 do not lead to reduced data quality within a slice, but will lead to faster reconstruction and smaller volumes, as a smaller number of slices will be reconstructed.)

X-START  

This is the starting X-pixel within a slice to reconstruct. Note: Unlike the raw data reconstruction there is no graphical determination of the region of a slice worth reconstructing.

Y-START  

This is the starting Y-pixel within a slice to reconstruct.

X-END  

This is the end X-pixel within a slice to reconstruct.

Y-END  

This is the end Y-pixel within a slice to reconstruct.

After clicking on O.K. on form 1 SINOGRAM RECONSTRUCTION CONTROL FORM 2 appears. A typical example of this form is shown in Figure 13, Page .

  

Figure 13: Sinogram Reconstruction Control Form 2

This works in a similar fashion to form 1, but the control parameters are different.

The parameters are described following the button text:

TAKE LOG This parameter controls is presently ignored, for sinogram reconstructions. The logarithm of the data will normally have been taken when the sinograms were created.

CACHE KILOBYTES    

This parameter defines the size of the processor cache (L2) per processor in kilobytes. This value is used to to decide whether or not to process more than one slice at the same time. If the cache is large enough it may be more efficient to process two slices at the same time. However, if the cache is not large enough this might result in slower reconstruction owing to the need to write data to and from the RAM.

For the ESRF computer systems the following values are correct:

``alpha'' (Compaq XP-1000 workstation): 4096

``beta'' (Compaq DS-20 server): 8192

Typical PC system: 512

OVER-SAMPLING  

hst_slave can reconstruct efficiently whilst maintaining reconstruction data quality, by over-sampling the detector pixels, and by linearly interpolating   within the over-sampled array. Having done this, the appropriate over-sampled detector pixel which is back-projected into the reconstructed volume can be found without any further need for interpolation. This allows the reconstruction to be almost as fast as a simple nearest pixel algorithm, whilst allowing the data quality of the interpolation method to be maintained. (In fact interpolation methods other than linear could also be applied in this manner with minimal increase in overall reconstruction time.)

This parameter determines the accuracy with which interpolation is applied to back-project into voxel positions which fall between two detector pixel positions. The value 0 means that full linear interpolation will be used; this will result in the reconstruction taking considerably longer time. The value 1 means that very simple nearest pixel  values will be used and no interpolation will take place. This will result in the quickest reconstruction but quality may suffer. Values greater than one means that the detector pixel arrays will be over-sampled and linearly interpolated at the over-sampling factor specified. The reconstruction then takes place using the closest over-sampled pixel. This allows reconstruction almost as fast as nearest pixel reconstruction but with much better data quality, depending on of course using a suitable over-sampling factor. For most data the value of 4 seems to be quite adequate, however even if a larger value needs to be used this will still be faster than linear interpolation for every pixel.

INCREMENT ANGLE   

This is the incremental angle in degrees from one data image to the next. It may be expressed in degrees and fraction of degrees. (The program works in single precision arithmetic, so you may usefully express this value to 6 or 7 significant figures.)

The numbering of the first and last image in the projection file series is used to suggest the default value for this parameter. This assumes the last image is just before the 180 degree rotation image.

OUTPUT FILE  

This parameter is the name of the of file to contain the completed reconstruction. By default it is the same as the first projection file, but with the extension changed to vol.

If you want to change this file name, click of the button, and the file selection utility will allow you to change output directory and select the required file name.

X-PIXEL SIZE  

This is the pixel size in the faster changing direction (horizontal) in microns. The pixel sizes are used to to convert the absorption  into physical units, but are otherwise unimportant. This parameter will be used for data-sets where the rotation axis was vertical (relative to displayed images).

Y-PIXEL SIZE  

This is the size of the pixels in the slower changing direction (vertical) in microns. This parameter will be used for data-sets where the rotation axis was horizontal (relative to displayed images).

OFFSET ANGLE    

This parameter allows the object reconstructed to be arbitrarily rotated by an angle relative to the experimental conditions. This value is expressed in degrees and may also contain fractions of degrees.

OUTPUT GRAPHICS    

If the value is set to YES then during reconstruction, periodically reconstructed slices will be displayed. This may be used to monitor data quality and check that the reconstruction is progressing in a reasonable manner.

AXIS POSITION   

This is a real value which defines the pixel coordinate of the rotation axis position. This is in the 1st direction of the stored sinograms, which is the detector bin direction. This value is measured in units of the detector image pixels, where the left-hand side of the first pixel is defined as 0.0 and the right hand side of the first pixel is defined as 1.0. Thus if the image has 1024 pixels then the right-hand edge of the last pixel is pixel coordinate 1024.0 and the centre of the image is pixel coordinate 512.0.

Finally the file selection utility asks SELECT NAME FOR THE PARAMETER FILE (See Figure 10, Page ). You are likely to need to enter the name of the parameter file from the keyboard (unless you want to over-write an existing file). You may enter any file name and extension, but I recommend using a standard file extension  . so that the purpose is clear e.g. par.

On Windows systems  you can associate hst_slave with a file extension so that you can click on the parameter file to run hst_slave directly using that parameter file.