tests/testthat/test-shootflow.R

In alexanderbates/deformetricar: R wrapper for elements of the Deformetrica registration tool

context("shoot and flow")
test_that("we can run shoot and flow on a matrix",{
  app=try(find_app("ShootAndFlow3"))
  if(inherits(app, 'try-error')) skip("Can't find ShootAndFlow3!")
  vtkfile=system.file("extdata/vtk_files/larval_central_nervous_system.vtk", package = 'deformetricar')
  m<-read.vtk(vtkfile)
  regdir=system.file("extdata/reg_output", package = 'deformetricar')
  expect_is(deform.m<-shootflow(m, regdir), 'matrix')
})

test_that("we can spot bad parameter files",{
  app=try(find_app("ShootAndFlow3"))
  if(inherits(app, 'try-error')) skip("Can't find ShootAndFlow3!")
  regdir=system.file("extdata/reg_output", package = 'deformetricar')
  dir.create(td <- tempfile('badparamtest'))
  on.exit(unlink(td, recursive = TRUE))
  file.copy(dir(regdir, full.names = T), td)
  # overwrite with bad params file for test
  file.copy("testdata/paramDiffeos_badstep.xml",
            file.path(td, "paramDiffeos.xml"), overwrite = TRUE)
  m=matrix(1:6, ncol=2)
  expect_error(shootflow(m, regdir=td), "Invalid number-of-timepoints")
})

test_that("we can run shoot and flow on a neuronlist",{
  app=try(find_app("ShootAndFlow3"))
  if(inherits(app, 'try-error')) skip("Can't find ShootAndFlow3!")
  n3=nat::Cell07PNs[1:3]
  regdir=system.file("extdata/reg_output", package = 'deformetricar')
  expect_is(deform.n3<-shootflow(n3, regdir), 'neuronlist')
})