More experienced users can skip the graphical interface and create a parameter
file directly by editing a file from a previous reconstruction. A parameter file
for HST looks like this
! HST_SLAVE PARAMETER FILE
RECONSTRUCT_FROM_SINOGRAMS = NO
! Parameters defining the projection file series
FILE_PREFIX = /hmi/rack/Bessy_Okt03/alex_AlSi7_16wpTiH2_beh/radios/radio
NUM_FIRST_IMAGE = 0 ! No. of first projection file
NUM_LAST_IMAGE = 899 ! No. of last projection file
NUMBER_LENGTH_VARIES = NO
LENGTH_OF_NUMERICAL_PART = 4 ! No. of characters
FILE_POSTFIX = .edf
FILE_INTERVAL = 1 ! Interval between input files
! Parameters defining the projection file format
NUM_IMAGE_1 = 991 ! Number of pixels horizontally
NUM_IMAGE_2 = 1251 ! Number of pixels vertically
IMAGE_PIXEL_SIZE_1 = 3.59 ! Pixel size horizontally (microns)
IMAGE_PIXEL_SIZE_2 = 3.59 ! Pixel size vertically
! Parameters defining background treatment
SUBTRACT_BACKGROUND = NO ! No background subtraction
BACKGROUND_FILE = N.A.
! Parameters defining flat-field treatment
CORRECT_FLATFIELD = NO ! No flat-field correction
FLATFIELD_FILE = N.A.
FLATFIELD_CHANGING = N.A.
FF_PREFIX = N.A.
FF_NUM_FIRST_IMAGE = N.A.
FF_NUM_LAST_IMAGE = N.A.
FF_NUMBER_LENGTH_VARIES = N.A.
FF_LENGTH_OF_NUMERICAL_PART = N.A.
FF_POSTFIX = N.A.
FF_FILE_INTERVAL = N.A.
TAKE_LOGARITHM = NO
! Parameters defining experiment
ANGLE_BETWEEN_PROJECTIONS = 0.20000 ! Increment angle in degrees
ROTATION_VERTICAL = YES
ROTATION_AXIS_POSITION = 568 ! Position in pixels
! Parameters defining reconstruction
OUTPUT_SINOGRAMS = NO ! Output sinograms to files or not
OUTPUT_RECONSTRUCTION = YES ! Reconstruct and save or not
START_VOXEL_1 = 1 ! X-start of reconstruction volume
START_VOXEL_2 = 1 ! Y-start of reconstruction volume
START_VOXEL_3 = 210 ! Z-start of reconstruction volume
END_VOXEL_1 = 990 ! X-end of reconstruction volume
END_VOXEL_2 = 990 ! Y-end of reconstruction volume
END_VOXEL_3 = 210 ! Z-end of reconstruction volume
OVERSAMPLING_FACTOR = 4 ! 0 = Linear, 1 = Nearest pixel
ANGLE_OFFSET = -5.000000 ! Reconstruction rotation offset angle in degrees
CACHE_KILOBYTES = 4096 ! Size of processor cache (L2) per processor (Kbytes)
SINOGRAM_MEGABYTES = 800 ! Maximum size of sinogram storage (megabytes)
! Parameters defining output file / format
OUTPUT_FILE = /hmi/rack/Bessy_Okt03/alex_AlSi7_16wpTiH2_beh/alex.vol
! Reconstruction program options
DISPLAY_GRAPHICS = NO ! No images
Section-by-Section description:
! HST_SLAVE PARAMETER FILE
RECONSTRUCT_FROM_SINOGRAMS = NO
toggles if input files are in radiographic style or as sinograms written, sinograms (at
the time this manual was written) can only be used with hst_slave, not with PyHST
! Parameters defining the projection file series
FILE_PREFIX = /hmi/rack/Bessy_Okt03/alex_AlSi7_16wpTiH2_beh/radios/radio
NUM_FIRST_IMAGE = 0 ! No. of first projection file
NUM_LAST_IMAGE = 899 ! No. of last projection file
NUMBER_LENGTH_VARIES = NO
LENGTH_OF_NUMERICAL_PART = 4 ! No. of characters
FILE_POSTFIX = .edf
FILE_INTERVAL = 1 ! Interval between input files
widely self-explaining, "FILE_PREFIX" should be set to the path where you
data image files are located plus "radio", the rest should be left unchanged
as long as you use bam2hst to create EDF files. "FILE_INTERVAL" is
necessary if you want to reconstruct quick&dirty, eg setting it to "2" makes
hst recognizing only half of input files.
! Parameters defining the projection file format
NUM_IMAGE_1 = 991 ! Number of pixels horizontally
NUM_IMAGE_2 = 1251 ! Number of pixels vertically
IMAGE_PIXEL_SIZE_1 = 3.59 ! Pixel size horizontally (microns)
IMAGE_PIXEL_SIZE_2 = 3.59 ! Pixel size vertically
the first two values can be found in any of your EDF files (belonging to your current
reconstruction) header - use head -c 1024 radio0000.edf to display header
information and then Dim_1 = NUM_IMAGE_1 and Dim_2 = NUM_IMAGE_2, the image pixel size
is the resolution used (usally something like 3.6, 5.5 or 11 microns) and can be found
in your BAM headerfile, see "Scandx=..." [mm]
! Parameters defining background treatment
SUBTRACT_BACKGROUND = NO ! No background subtraction
BACKGROUND_FILE = N.A.
! Parameters defining flat-field treatment
CORRECT_FLATFIELD = NO ! No flat-field correction
FLATFIELD_FILE = N.A.
FLATFIELD_CHANGING = N.A.
FF_PREFIX = N.A.
FF_NUM_FIRST_IMAGE = N.A.
FF_NUM_LAST_IMAGE = N.A.
FF_NUMBER_LENGTH_VARIES = N.A.
FF_LENGTH_OF_NUMERICAL_PART = N.A.
FF_POSTFIX = N.A.
FF_FILE_INTERVAL = N.A.
can be left unchanged as long as BAM software as well as bam2hst is used, the
flatfield and dark correction is already applied there
TAKE_LOGARITHM = NO
should be left unchanged, the logarithm is taken by bam2hst, in some cases it
might be helpful to take the logarithm twice in order to improve the contrast but it
can also lead to unexpectable errors
! Parameters defining experiment
ANGLE_BETWEEN_PROJECTIONS = 0.20000 ! Increment angle in degrees
ROTATION_VERTICAL = YES
ROTATION_AXIS_POSITION = 568 ! Position in pixels
"ANGLE_BETWEEN_PROJECTIONS" usually is 180 / number_of_projections
and can also be found in your BAM headerfile, see "WinkelIncr=...", the
"ROTATION_VERTICAL" is always "YES", the "ROTATION_AXIS_POSITION"
can be determined with hst_master (see above), during the measurements, by running /hmi/bin/center_of_image -fit
in the directory where your EDF files are stored and/or later (should always be) optimised by hand (see below)
! Parameters defining reconstruction
OUTPUT_SINOGRAMS = NO ! Output sinograms to files or not
OUTPUT_RECONSTRUCTION = YES ! Reconstruct and save or not
START_VOXEL_1 = 1 ! X-start of reconstruction volume
START_VOXEL_2 = 1 ! Y-start of reconstruction volume
START_VOXEL_3 = 210 ! Z-start of reconstruction volume
END_VOXEL_1 = 990 ! X-end of reconstruction volume
END_VOXEL_2 = 990 ! Y-end of reconstruction volume
END_VOXEL_3 = 210 ! Z-end of reconstruction volume
OVERSAMPLING_FACTOR = 4 ! 0 = Linear, 1 = Nearest pixel
ANGLE_OFFSET = -5.000000 ! Reconstruction rotation offset angle in degrees
CACHE_KILOBYTES = 4096 ! Size of processor cache (L2) per processor (Kbytes)
SINOGRAM_MEGABYTES = 800 ! Maximum size of sinogram storage (megabytes)
"OUTPUT_SINOGRAMS" can be used to create sinograms instead of using bam2hst
or xdisp but only works with hst_slave, not with PyHST (sinograms
will be stored in EDF format (1024 byte textheader plus binary data) and can be displayed with ImageJ); "OUTPUT_RECONSTRUCTION" should always be set to "YES" (otherwise no data
will be saved), "START_VOXEL_..." and "END_VOXEL_..." defining the 3D
region of interest (see below), the "ANGLE_OFFSET" is explained
in detail in the next step and the rest should be left unchanged
! Parameters defining output file / format
OUTPUT_FILE = /hmi/rack/Bessy_Okt03/alex_AlSi7_16wpTiH2_beh/alex.vol
the file where the reconstructed data should be written to, please use
the suffix .vol !
! Reconstruction program options
DISPLAY_GRAPHICS = NO ! No images
should be set per default to no.
The latest generation of PyHST understands some more parameters which are listed
here .
Eg a Median filter can be used (only with PyHST) by adding the following lines to your
parameter file
#konditionaler Medianfilter
DO_CCD_FILTER= YES
CCD_FILTER = "CCD_Filter"
CCD_FILTER_PARA={"threshold": 0.0005 } #Bedingung/Schwellwert
Via the threshold parameter one can control how strong the filter works on the image, entering
-1.0 means max filtering. The path to the compiled object can be set via
CCD_FILTER_PARA ={}
in case you are running into conflicting versions or want to try on your own. To be done: Parameter
for chosing filte application for or after flatfield correction or both