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Update pctbinning.py #93

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0e020e2
ENH: Adapt pctbinning.py to use HoleFillingImageFilter
acoussat Aug 19, 2026
edf464e
ENH: Update pctbinning.py with LMU features
acoussat Aug 19, 2026
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42 changes: 37 additions & 5 deletions applications/pctbinning/pctbinning.py
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Original file line number Diff line number Diff line change
Expand Up @@ -22,6 +22,7 @@ def build_parser():
parser.add_argument(
"-c", "--count", help="Image of count of proton pairs per pixel"
)
parser.add_argument("--variance", help="Image of variance of WEPL values per pixel")
parser.add_argument(
"--scatwepl", help="Image of scattering WEPL of proton pairs per pixel"
)
Expand All @@ -33,6 +34,11 @@ def build_parser():
action="store_true",
default=False,
)
parser.add_argument(
"--particle",
help="Particle used for imaging (proton or alpha)",
default="proton",
)
parser.add_argument(
"-v", "--verbose", help="Verbose execution", action="store_true", default=False
)
Expand Down Expand Up @@ -88,6 +94,12 @@ def build_parser():
action="store_true",
default=False,
)
parser.add_argument(
"--fillvariance",
help="Fill holes, i.e. pixels that were not hit by protons (for variance projections)",
action="store_true",
default=False,
)
parser.add_argument(
"--trackerresolution", help="Tracker resolution in mm", type=float
)
Expand Down Expand Up @@ -159,6 +171,8 @@ def process(args_info: argparse.Namespace):
projection.SetRobust(args_info.robust)
projection.SetComputeScattering(bool(args_info.scatwepl))
projection.SetComputeNoise(bool(args_info.noise))
projection.SetComputeVariance(bool(args_info.variance))
projection.SetParticle(args_info.particle)

if args_info.quadricIn:
# quadric = object surface
Expand Down Expand Up @@ -190,15 +204,14 @@ def process(args_info: argparse.Namespace):

projection.Update()

filler = pct.SmallHoleFiller[OutputImageType]()
hole_filter = pct.HoleFillingImageFilter[OutputImageType].New()
if args_info.fill:
filler.SetImage(projection.GetOutput())
filler.SetHolePixel(0.0)
filler.Fill()
hole_filter.SetInput(projection.GetOutput())
hole_filter.Update()

cii = itk.ChangeInformationImageFilter[OutputImageType].New()
if args_info.fill:
cii.SetInput(filler.GetOutput())
cii.SetInput(hole_filter.GetOutput())
else:
cii.SetInput(projection.GetOutput())
cii.ChangeOriginOn()
Expand All @@ -217,6 +230,25 @@ def process(args_info: argparse.Namespace):
# Write
itk.imwrite(projection.GetCount(), args_info.count)

if args_info.variance:
VarianceImageType = itk.Image[itk.F, 3]
variance_hole_filter = pct.HoleFillingImageFilter[VarianceImageType].New()
if args_info.fillvariance:
variance_hole_filter.SetInput(projection.GetVariance())
variance_hole_filter.Update()
cii_var = itk.ChangeInformationImageFilter[VarianceImageType].New()
if args_info.fillvariance:
cii_var.SetInput(variance_hole_filter.GetOutput())
else:
cii_var.SetInput(projection.GetVariance())
cii_var.ChangeOriginOn()
cii_var.ChangeDirectionOn()
cii_var.ChangeSpacingOn()
cii_var.SetOutputDirection(projection.GetOutput().GetDirection())
cii_var.SetOutputOrigin(projection.GetOutput().GetOrigin())
cii_var.SetOutputSpacing(projection.GetOutput().GetSpacing())
itk.imwrite(cii_var.GetOutput(), args_info.variance)

if args_info.scatwepl:
# Write
itk.imwrite(projection.GetAngle(), args_info.scatwepl)
Expand Down
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