README.md

In stnava/patchMatchR: Local patch matching with flexible transformation models in n-dimensional images

patchMatchR

very basic patch matching functionality based on ANTsR -- see documentation

installation

devtools::install_github( "stnava/patchMatchR")

or if you have ANTsR etc installed then clone the repo and do:

cd patchMatchR
R CMD INSTALL .

getting started

in R

2D

library( ANTsR )
library( patchMatchR )
img <- ri( 1 )  %>% iMath( "Normalize" )
img2 <- ri( 2 )%>% resampleImage( 2 ) %>% iMath( "Normalize" )
mask = randomMask( getMask( img ), 10 )
match = patchMatch( img2, img, mask, visualize=T, verbose=T )
myMatches = matchedPatches( img2, img, match, verbose = TRUE )
plot( myMatches[[1]][[4]] * 100 )
plot( myMatches[[2]][[4]] * 100 )

2D with pre-existing mapping

library( ANTsR )
library( patchMatchR )
img <- ri( 1 )  %>% iMath( "Normalize" )
img2 <- ri( 2 )%>% resampleImage( 2 ) %>% iMath( "Normalize" )
ireg = antsRegistration( img, img2, "SyNCC" )
mask = randomMask( getMask( img ), 10 )
match = patchMatch( img2, img, mask, visualize=T, verbose=T,
  initialMap = ireg )
myMatches = matchedPatches( img2, img, match, verbose = TRUE )
plot( myMatches[[1]][[4]] * 100 )
plot( myMatches[[2]][[4]] * 100 )

3D

library( ANTsR )
library( patchMatchR )
img <- antsImageRead( getANTsRData( "ch2" ) ) %>% resampleImage( 1 ) %>%
  iMath( "Normalize" )
img2 <- resampleImage( img, 2 ) %>% iMath( "Normalize" )
mask = randomMask( getMask( img ), 25 )
myr = 15
match = patchMatch( img2, img, mask, visualize=T, verbose=T,
  fixedPatchRadius = myr )
myMatches = matchedPatches( img2, img, match, verbose = TRUE,
  fixedPatchRadius = myr+1  )
plot( myMatches[[1]][[4]] * 100 )
plot( myMatches[[2]][[4]] * 100 )

TODO

• allow a probabilistic representation of matching

• provide a method for generating transforms from the matched landmarks (my RANSAC implementation is weak)

• test on GPU

• compare to SIFT

• pass a transform to deepPatchMatch s.t. moving point distance can be calculated wrt tx

• multi-resolution strategy and/or localized refinement of matching

stnava/patchMatchR documentation built on March 23, 2022, 6:47 a.m.