# HST_SLAVE PARAMETER FILE 

FILE_PREFIX = /data/id17/inhouse/MRT/2012/July/md656/883_pink/Radios/Proj_

BACKGROUND_FILE = /data/id17/inhouse/MRT/2012/July/md656/883_pink/Radios/ThreadedBackground.edf
FLATFIELD_FILE = /data/id17/inhouse/MRT/2012/July/md656/883_pink/Radios/ThreadedFlatField.edf
OUTPUT_FILE = nocorr.vol


NUM_FIRST_IMAGE = 0 # No. of first projection file 
NUM_LAST_IMAGE = 1199 # 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 = 1300 # Number of pixels horizontally 
NUM_IMAGE_2 = 980 # Number of pixels vertically 

IMAGE_PIXEL_SIZE_1 = 46.6000 # Pixel size horizontally (microns) 
IMAGE_PIXEL_SIZE_2 = 46.6000 # Pixel size vertically 

# Parameters defining background treatment 
SUBTRACT_BACKGROUND = YES # Subtract background from data 
# Parameters defining flat-field treatment 
CORRECT_FLATFIELD = YES # Divide by flat-field image 
FLATFIELD_CHANGING = NO # Series of flat-field files 
TAKE_LOGARITHM = YES # Take log of projection values 
# Parameters defining experiment 

ANGLE_BETWEEN_PROJECTIONS = 0.15 # Increment angle in degrees 

ROTATION_VERTICAL = YES 
ROTATION_AXIS_POSITION =  883-150 # Position in pixels 

START_VOXEL_1 =      1 # X-start of reconstruction volume 
START_VOXEL_2 =      1 # Y-start of reconstruction volume 
START_VOXEL_3 =   122 # Z-start of reconstruction volume 
END_VOXEL_1 =   1300 # X-end of reconstruction volume 
END_VOXEL_2 =   1300# Y-end of reconstruction volume 
END_VOXEL_3 =   122 # Z-end of reconstruction volume 


OVERSAMPLING_FACTOR = 4 # 0 = Linear, 1 = Nearest pixel 
ANGLE_OFFSET = 0.000000 # Reconstruction rotation offset angle in degrees 
CACHE_KILOBYTES = 4096 # Size of processor cache (L2) per processor (KBytes) 
SINOGRAM_MEGABYTES = 400 # Maximum size of sinogram storage (megabytes) 
# Parameters extra features PyHST 
DO_CCD_FILTER = NO # CCD filter (spike 
CCD_FILTER = "CCD_Filter" 
CCD_FILTER_PARA =  {"threshold": 0.040000 } 

DO_RING_FILTER = NO # Sinogram filter (rings)
RING_FILTER = "RING_Filter"
ar = Numeric.ones(1300,'f')
ar[0]=0.0
RING_FILTER_PARA = {"FILTER": ar, "threshold":0.15 }

DO_AXIS_CORRECTION = NO # Axis correction  
AXIS_CORRECTION_FILE = correct.txt  

OPTIONS= { 'padding':'E' , 'axis_to_the_center':'Y' , 'avoidhalftomo':'Y'} # Padding and position axis 

# Parameters for Paganin reconstruction 
# delta over beta ratio for Paganin phase retrieval = 200.00  
DO_PAGANIN = 1
PAGANIN_Lmicron = 1050
PAGANIN_MARGE = 20  
DO_OUTPUT_PAGANIN = 0 
OUTPUT_PAGANIN_FILE = paga_cufft  
OUTPUT_PAGANIN_START=0 
OUTPUT_PAGANIN_END  =20 
PAGANIN_TRY_CUFFT = 1  
PAGANIN_TRY_FFTW = 1  
# Parameters for unsharp masking on the radiographs 
UNSHARP_LOG = 1  
PUS = 0.000000  
PUC = 2.000000  

PENTEZONE=300 
ZEROCLIPVALUE = 0.0000000001 # Minimum value of radiographs after flat / before log 




FBFILTER=1      