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Commit 2e3436b7 authored by Tamino Huxohl's avatar Tamino Huxohl
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invert mu_map and add filtering to recon script

parent 1cd6a5a2
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...@@ -67,18 +67,18 @@ OSMAPOSLParameters := ...@@ -67,18 +67,18 @@ OSMAPOSLParameters :=
; keywords that specify the filtering that occurs after every subiteration ; keywords that specify the filtering that occurs after every subiteration
; warning: do not normally use together with a prior ; warning: do not normally use together with a prior
;inter-iteration filter subiteration interval := 4 inter-iteration filter subiteration interval := 4
;inter-iteration filter type := Separable Gaussian inter-iteration filter type := Separable Gaussian
;post-filter type := Separable Gaussian ;post-filter type := Separable Gaussian
;separable gaussian filter parameters := separable gaussian filter parameters :=
;x-dir filter fwhm (in mm) := 6 x-dir filter fwhm (in mm) := 9.6
;y-dir filter fwhm (in mm) := 6 y-dir filter fwhm (in mm) := 9.6
;z-dir filter fwhm (in mm) := 6 z-dir filter fwhm (in mm) := 9.6
;x-dir maximum kernel size := 129 x-dir maximum kernel size := 128
;y-dir maximum kernel size := 129 y-dir maximum kernel size := 128
;z-dir maximum kernel size := 31 z-dir maximum kernel size := 33
;Normalise filter to 1 := 1 Normalise filter to 1 := 1
;end separable gaussian filter parameters := end separable gaussian filter parameters :=
END := END :=
""" """
...@@ -189,6 +189,11 @@ if __name__ == "__main__": ...@@ -189,6 +189,11 @@ if __name__ == "__main__":
type=str, type=str,
help="a mu map for attenuation correction in DICOM or INTERFILE format", help="a mu map for attenuation correction in DICOM or INTERFILE format",
) )
parser.add_argument(
"--skip_mu_map_z_inv",
action="store_true",
help="per default mu maps need to be inverted in z direction for attenuation correction to work correctly - this parameter can skip this",
)
parser.add_argument( parser.add_argument(
"--out", type=str, help="the filename to store the reconstruction" "--out", type=str, help="the filename to store the reconstruction"
) )
...@@ -215,6 +220,8 @@ if __name__ == "__main__": ...@@ -215,6 +220,8 @@ if __name__ == "__main__":
stir.Verbosity_set(args.verbosity) stir.Verbosity_set(args.verbosity)
mu_map = load_as_interfile(args.mu_map) if args.mu_map else None mu_map = load_as_interfile(args.mu_map) if args.mu_map else None
if not args.skip_mu_map_z_inv:
mu_map = (mu_map[0], mu_map[1][::-1])
mu_map_slices = None if mu_map is None else mu_map[1].shape[0] mu_map_slices = None if mu_map is None else mu_map[1].shape[0]
if args.recon: if args.recon:
......
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