OSMAPOSLParameters :=
; example file for running OSEM with interfiltering
; filter specific things are at the end

objective function type:=PoissonLogLikelihoodWithLinearKineticModelAndDynamicProjectionData
PoissonLogLikelihoodWithLinearKineticModelAndDynamicProjectionData Parameters:=

input file := ${INPUT}

; if disabled, defaults to maximum segment number in the file
maximum absolute segment number to process := ${MAXSEG}
; see User's Guide to see when you need this
zero end planes of segment 0:= 0

;zoom := .15645
;xy output image size (in pixels) := 21
;z output image size (in pixels) := 17
;z offset (in mm) := 0

projector pair type := Matrix
  Projector Pair Using Matrix Parameters :=
  Matrix type := Ray Tracing
  Ray tracing matrix parameters :=
  End Ray tracing matrix parameters :=
  End Projector Pair Using Matrix Parameters :=

Bin Normalisation type := From ProjData
  Bin Normalisation From ProjData :=
    normalisation projdata filename := all_ones.hs
  End Bin Normalisation From ProjData :=

; we need this for backwards compatibility with the testing script
use subset sensitivities:=0
sensitivity filename:= sens.img
; if next is set to 1, sensitivity will be recomputed
; and written to file (if "sensitivity filename" is set)
recompute sensitivity := 1

; specify additive projection data to handle randoms or so
; see User's Guide for more info
additive sinograms := 0

; patlak related files
Kinetic Model type := Patlak Plot
Patlak Plot Parameters :=
time frame definition filename := time.fdef
starting frame := 23
calibration factor := 9432.31
blood data filename := plasma.if 
Time Shift := 0
In total counts := 1
;In correct scale := 0
end Patlak Plot Parameters :=

end PoissonLogLikelihoodWithLinearKineticModelAndDynamicProjectionData Parameters:=

; Number of subsets should be a divisor of num_views/4
number of subsets:=${NUMSUBS}
; Use for starting the numbering from something else than 1
start at subiteration number:=1
; Use if you want to start from another subset than 0 (but why?)
start at subset:= 0
number of subiterations:= ${ITER}
save estimates at subiteration intervals:= ${SAVITER}

initial estimate := ${INIT}
; enable this when you read an initial estimate with negative data
enforce initial positivity condition:=1

inter-update filter subiteration interval:= 0
inter-update filter type := None

inter-iteration filter subiteration interval:= 0

post-filter type := None

output filename prefix:=POSMAPOSL

END :=
