tests/testthat/test_DatFiles.R

In kevin-allen/relectro: Analysis of electrophysiological data

library(relectro)
library(testthat)
context("DatFiles")
test_that("DatFiles",{
  
  nChannels<-5
  nSamples<-10
  f<-file("k01.dat","wb")
  writeBin(object=rep(c(1:nChannels),nSamples),con=f,size=2) # 5 channels, 6
  close(f)
  f<-file("k02.dat","wb")
  writeBin(object=rep(c((1:nChannels)),nSamples*2),con=f,size=2) # 5 channels, 6
  close(f)
  f1.size<-file.info("k01.dat")$size
  f2.size<-file.info("k02.dat")$size
  s<-c(f1.size,f2.size)
  
  
  ## check size of files and samples
  df<-new("DatFiles")
  df<-datFilesSet(df,fileNames=c("k01.dat","k02.dat"),path="",nChannels=5)
  expect_equal(sum(df@size),sum(s))
  expect_equal(sum(df@samples),nSamples+nSamples*2)
  
  ## check data read 
  ## channel 0 contains only 1s
  d<-datFilesGetOneChannel(df,channelNo=0,firstSample=0,lastSample=sum(df@samples)-1)
  expect_equal(sum(d),nSamples+2*nSamples)
  ## channel 4 contains only 5s
  d<-datFilesGetOneChannel(df,channelNo=4,firstSample=0,lastSample=sum(df@samples)-1)
  expect_equal(sum(d),(nSamples+2*nSamples)*5)
  
  ## check function to read several channels
  d<-datFilesGetChannels(df,channels = 0,firstSample = 0,lastSample = sum(df@samples)-1)
  expect_equal(sum(d),nSamples+2*nSamples)
  d<-datFilesGetChannels(df,channels = 4,firstSample = 0,lastSample = sum(df@samples)-1)
  expect_equal(sum(d),(nSamples+2*nSamples)*5)
  d<-datFilesGetChannels(df,channels = c(0,4),firstSample = 0,lastSample = sum(df@samples)-1)
  expect_equal(sum(d),(nSamples+2*nSamples)*5+nSamples+2*nSamples)
  
  
  f<-file("k01.dat","wb")
  writeBin(object=rep(c(1:5),each=nChannels),con=f,size=2) # 5 channels, 6
  close(f)
  f<-file("k02.dat","wb")
  writeBin(object=rep(c(6:11),each=nChannels),con=f,size=2) # 5 channels, 6
  close(f)
  
  ## check that it reads the correct samples
  df<-datFilesSet(df,fileNames=c("k01.dat","k02.dat"),path="",nChannels=5)
  d<-datFilesGetOneChannel(df,channelNo=0,firstSample=0,lastSample=sum(df@samples)-1)
  expect_equal(any(diff(d)!=1),FALSE)
  d<-datFilesGetChannels(df,channels=0,firstSample=0,lastSample=sum(df@samples)-1)
  expect_equal(any(diff(d)!=1),FALSE)
  
  
  ## with different start index
  d<-datFilesGetOneChannel(df,channelNo=0,firstSample=3,lastSample=5)
  expect_equal(d,c(4,5,6))
  d<-datFilesGetChannels(df,channels=0,firstSample=3,lastSample=5)
  expect_equal(d[,1],c(4,5,6))
  
  ## with several indices
  d<-datFilesGetOneChannel(df,channelNo=0,firstSample=c(3,2),lastSample=c(5,4))
  expect_equal(d,c(4,5,6,3,4,5))
  d<-datFilesGetChannels(df,channels=0,firstSample=c(3,2),lastSample=c(5,4))
  expect_equal(d[,1],c(4,5,6,3,4,5))
  
  ## arrays out of bound, 11 samples, 10 is the last index
  expect_error(datFilesGetOneChannel(df,channelNo=0,firstSample=0,lastSample=11))
  expect_error(datFilesGetChannels(df,channels=0,firstSample=0,lastSample=11))
  
  
  file.remove("k01.dat","k02.dat")
  rm(nChannels,nSamples,f,f1.size,f2.size,s,df,d)
})

test_that("DatFiles transposed",{
  
  nChannels<-5
  nSamples<-10
  f<-file("k01.dat","wb")
  writeBin(object=rep(c(1:nChannels),each=nSamples),con=f,size=2) # 5 channels, 6
  close(f)
  f<-file("k02.dat","wb")
  writeBin(object=rep(c((1:nChannels)),each=nSamples*2),con=f,size=2) # 5 channels, 6
  close(f)
  f1.size<-file.info("k01.dat")$size
  f2.size<-file.info("k02.dat")$size
  s<-c(f1.size,f2.size)
  
  ## check size of files and samples
  df<-new("DatFiles")
  df<-datFilesSet(df,fileNames=c("k01.dat","k02.dat"),path="",nChannels=5,transposed = TRUE)
  expect_equal(sum(df@size),sum(s))
  expect_equal(sum(df@samples),nSamples+nSamples*2)
  
  
  ## check data read 
  ## channel 0 contains only 1s
  d<-datFilesGetOneChannel(df,channelNo=0,firstSample=0,lastSample=sum(df@samples)-1)
  expect_equal(sum(d),nSamples+2*nSamples)
  ## channel 4 contains only 5s
  d<-datFilesGetOneChannel(df,channelNo=4,firstSample=0,lastSample=sum(df@samples)-1)
  expect_equal(sum(d),(nSamples+2*nSamples)*5)
  
  ## check function to read several channels
  d<-datFilesGetChannels(df,channels = 0,firstSample = 0,lastSample = sum(df@samples)-1)
  expect_equal(sum(d),nSamples+2*nSamples)
  d<-datFilesGetChannels(df,channels = 4,firstSample = 0,lastSample = sum(df@samples)-1)
  expect_equal(sum(d),(nSamples+2*nSamples)*5)
  d<-datFilesGetChannels(df,channels = c(0,4),firstSample = 0,lastSample = sum(df@samples)-1)
  expect_equal(sum(d),(nSamples+2*nSamples)*5+nSamples+2*nSamples)
  
  
  f<-file("k01.dat","wb")
  writeBin(object=rep(c(1:5),each=nChannels),con=f,size=2) # 5 channels, 6
  close(f)
  f<-file("k02.dat","wb")
  writeBin(object=rep(c(6:11),each=nChannels),con=f,size=2) # 5 channels, 6
  close(f)
  
  ## check that it reads the correct samples
  df<-datFilesSet(df,fileNames=c("k01.dat","k02.dat"),path="",nChannels=5)
  d<-datFilesGetOneChannel(df,channelNo=0,firstSample=0,lastSample=sum(df@samples)-1)
  expect_equal(any(diff(d)!=1),FALSE)
  d<-datFilesGetChannels(df,channels=0,firstSample=0,lastSample=sum(df@samples)-1)
  expect_equal(any(diff(d)!=1),FALSE)
  
  
  ## with different start index
  d<-datFilesGetOneChannel(df,channelNo=0,firstSample=3,lastSample=5)
  expect_equal(d,c(4,5,6))
  d<-datFilesGetChannels(df,channels=0,firstSample=3,lastSample=5)
  expect_equal(d[,1],c(4,5,6))
  
  ## with several indices
  d<-datFilesGetOneChannel(df,channelNo=0,firstSample=c(3,2),lastSample=c(5,4))
  expect_equal(d,c(4,5,6,3,4,5))
  d<-datFilesGetChannels(df,channels=0,firstSample=c(3,2),lastSample=c(5,4))
  expect_equal(d[,1],c(4,5,6,3,4,5))
  
  ## arrays out of bound, 11 samples, 10 is the last index
  expect_error(datFilesGetOneChannel(df,channelNo=0,firstSample=0,lastSample=11))
  expect_error(datFilesGetChannels(df,channels=0,firstSample=0,lastSample=11))
  
  
  ## compare tdat and dat
  nChannels<-5
  nSamples<-200
  f<-file("k01.dat","wb")
  writeBin(object=rep(c(1:nChannels),nSamples),con=f,size=2) # 5 channels, 6
  close(f)
  f<-file("k02.dat","wb")
  writeBin(object=rep(c((1:nChannels)),nSamples),con=f,size=2) # 5 channels, 6
  close(f)
  
  f<-file("k01.tdat","wb")
  writeBin(object=rep(c(1:nChannels),each=nSamples),con=f,size=2) # 5 channels, 6
  close(f)
  f<-file("k02.tdat","wb")
  writeBin(object=rep(c((1:nChannels)),each=nSamples),con=f,size=2) # 5 channels, 6
  close(f)
  
  ## check size of files and samples
  df<-new("DatFiles")
  df<-datFilesSet(df,fileNames=c("k01.dat","k02.dat"),path="",nChannels=5,transposed = FALSE)
  dft<-new("DatFiles")
  dft<-datFilesSet(df,fileNames=c("k01.tdat","k02.tdat"),path="",nChannels=5,transposed = TRUE)
  d<-datFilesGetOneChannel(df,channelNo=1,firstSample=0,lastSample=nSamples-1)
  dt<-datFilesGetOneChannel(dft,channelNo=1,firstSample=0,lastSample=nSamples-1)
  expect_equal(d,dt)
  
  ##
  d<-datFilesGetChannels(df,channels=c(3,4),firstSample=0,lastSample=nSamples-1)
  dt<-datFilesGetChannels(dft,channels=c(3,4),firstSample=0,lastSample=nSamples-1)
  expect_equal(dim(d),dim(dt))
  expect_equal(sum(d),sum(dt))
  
  file.remove("k01.dat","k02.dat","k01.tdat","k02.tdat")
  rm(nChannels,nSamples,f,f1.size,f2.size,s,df,d,dt,dft)
})