espadon (version 1.11.3)

vol.repair: repairing missing planes of volumes

Description

The vol.repair function repairs missing planes in volumes.

Usage

vol.repair(vol, alias = "", description = NULL)

Value

Returns a "volume" class object (see espadon.class

for class definitions), with no missing plane, if vol is to be repaired. Returns vol otherwise.

Arguments

vol

"volume" class object.

alias

Character string, $alias of the created object.

description

Character string, describing the created object. If description = NULL (default value), it will be set to paste (vol$object.alias, "repair").

Details

Missing planes at download can generate errors or unpredictible results in espadon processing. The vol.repair function detects such missing planes and recreates their value by interpolation.

Examples

step <- 4
patient <- toy.load.patient (modality = c("ct", "mr", "rtstruct", "rtdose"),
                             roi.name  = "",
                             dxyz = rep (step, 3), beam.nb = 3)
CT <- patient$ct[[1]]

# this function removes a plane in a volume in order to simulate
# a dicom transfer issue
remove.plane <- function (vol, k) {
  idx <- which (vol$k.idx == k)
  vol$n.ijk[3] <- vol$n.ijk[3] - 1
  vol$xyz0 <- vol$xyz0[-idx, ]
  vol$k.idx <- vol$k.idx[-idx]
  vol$missing.k.idx <- TRUE
  vol$vol3D.data <- vol$vol3D.data[, , -idx]
  return (vol)
}

# Creation of CT.damaged without the 29th slice.
CT.damaged<- remove.plane (CT, 29)
CT.fix <- vol.repair (CT.damaged)

# Display 
par (mfrow=c(3, 3))
for (k in 28:30) {
display.kplane (CT, k, main = paste("CT @ k =",k),interpolate = FALSE)
display.kplane (CT.damaged, k, main = "damaged CT",interpolate = FALSE)
display.kplane (CT.fix, k, main = "fixed CT", interpolate = FALSE)
}