## ---- echo=FALSE, results="hide"---------------------------------------------- knitr::opts_chunk$set(error=FALSE, warning=FALSE, message=FALSE, fig.retina = 0.75, crop = NULL) library(BiocStyle) ## ----library, echo=FALSE------------------------------------------------------ library(cytomapper) ## ---- message=FALSE----------------------------------------------------------- library(HDF5Array) # Define output directory cur_dir <- getHDF5DumpDir() path.to.images <- system.file("extdata", package = "cytomapper") image.list <- loadImages(path.to.images, pattern = "mask.tiff", on_disk = TRUE, h5FilesPath = cur_dir) # Show list image.list # Scale images image.list <- scaleImages(image.list, value = 2^16 - 1) image.list$E34_mask ## ----------------------------------------------------------------------------- data("pancreasImages") pancreasImages_onDisk <- CytoImageList(pancreasImages, on_disk = TRUE, h5FilesPath = cur_dir) # Image object pancreasImages$E34_imc # HDF5Array object pancreasImages_onDisk$E34_imc # Seed of HDF5Array object seed(pancreasImages_onDisk$E34_imc) # Size in memory format(object.size(pancreasImages), units = "auto") format(object.size(pancreasImages_onDisk), units = "auto") ## ----------------------------------------------------------------------------- pancreasImages_inMemory <- CytoImageList(pancreasImages_onDisk, on_disk = FALSE) # Compare the image data to the original representation identical(as.list(pancreasImages_inMemory), as.list(pancreasImages)) ## ----sanity-check, echo=FALSE------------------------------------------------- stopifnot(identical(as.list(pancreasImages), as.list(pancreasImages_inMemory))) ## ----------------------------------------------------------------------------- # Size of object in memory format(object.size(pancreasImages_onDisk), units = "auto") # Size of object on disk in kB file.info(paste0(cur_dir, "/E34_imc.h5"))[,"size"] / 1000 pancreasImages_norm <- normalize(pancreasImages_onDisk) seed(pancreasImages_norm$E34_imc) # Size of object in memory format(object.size(pancreasImages_norm), units = "auto") # Size of object on disk in kB file.info(paste0(cur_dir, "/E34_imc.h5"))[,"size"] / 1000 ## ----------------------------------------------------------------------------- cur_Images1 <- pancreasImages_onDisk cur_Images2 <- getChannels(pancreasImages_onDisk, 2) channelNames(cur_Images2) <- "CD99_2" setChannels(cur_Images1, 1) <- cur_Images2 format(object.size(cur_Images1), units = "auto") ## ----------------------------------------------------------------------------- channels1 <- getChannels(pancreasImages_onDisk, 1:2) channels2 <- getChannels(pancreasImages_onDisk, 3:4) dir.create(file.path(cur_dir, "test")) cur_path_2 <- file.path(cur_dir, "test") channels3 <- mergeChannels(channels1, channels2, h5FilesPath = cur_path_2) seed(channels3$E34_imc) ## ----sessionInfo, echo=FALSE-------------------------------------------------- sessionInfo()