Description Usage Arguments Details Value Author(s) Examples

View source: R/getNeighborhood.R

this converts a scalar image to a matrix with rows that contain neighbors around a center voxel

1 2 3 | ```
getNeighborhoodInMask(image, mask, radius, physical.coordinates = FALSE,
boundary.condition = "NA", spatial.info = FALSE,
get.gradient = FALSE)
``` |

`image` |
image object of S4 class |

`mask` |
image object of S4 class |

`radius` |
array of values for neighborhood radius (in voxels) |

`physical.coordinates` |
logical indicating if voxel indices and offsets should be in voxel or physical coordinates |

`boundary.condition` |
string indicating how to handle voxels in a
neighborhood, but not in the mask. See |

`spatial.info` |
a boolean indicating of voxel locations and neighborhood offsets should be returned along with pixel values. |

`get.gradient` |
a boolean indicating if a matrix of gradients (at the center voxel) should be returned in addition to the value matrix (WIP) |

`boundary.condition`

should be one of:

`NA`

: Fill values with`NA`

.`image`

: Use image value, even if not in mask.`mean`

: Use man of all non-`NA`

values for that neighborhood.

if `spatial.info`

is false: a matrix of pixel values where the number of rows
is the size of the neighborhood and there is a column for each voxel

if `spatial.info`

is true, a list containing three matrices:

values: matrix of pixel values where the number of rows is the size of the neighborhood and there is a column for each voxel.

indices: matrix providing the center coordinates for each neighborhood

offsets: matrix providing the offsets from center for each voxel in a neighborhood

Duda JT

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 | ```
r16 <- getANTsRData("r16")
r16 <- antsImageRead(r16,2)
mask <- getMask(r16,lowThresh=mean(r16),cleanup=1)
radius <- rep(2,2)
mat <- getNeighborhoodInMask(r16,mask,radius)
mat <- getNeighborhoodInMask(r16,mask,radius,
boundary.condition ="image")
mat <- getNeighborhoodInMask(r16,mask,radius,
boundary.condition ="mean")
randlist <- getNeighborhoodInMask(r16,mask,radius,
physical.coordinates = TRUE)
arr = as.array(r16)
testthat::expect_error(getNeighborhoodInMask(arr,mask,radius), "antsImage")
testthat::expect_error(getNeighborhoodInMask(r16,as.numeric(mask),radius),
"mask must be")
testthat::expect_error(getNeighborhoodInMask(r16,mask,as.character(radius)),
"radius must be")
# testthat::expect_error(getNeighborhoodInMask(r16,mask,c(radius, 3)),
# "Radius must")
``` |

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