play with mri data

mri.R

library(OpenImageR)
library(oro.dicom)
library(dplyr)
library(magrittr)
library(magick)

dicompath = '/home/omancarci/Dropbox/MRI'

imageFiles = list.files(file.path(dicompath,'DICOM'),recursive = TRUE,full.names = TRUE)


metadata = oro.dicom::readDICOMFile(file.path(dicompath,'DICOMDIR'))
imagesInOrder = metadata$hdr %>% filter(name=='ReferencedFileID' & grepl('IM',value)) %$% value %>% gsub(' ','/',.)
# imagesInOrder[1:10]

dir.create('out')

imagePaths = file.path(dicompath,imagesInOrder)
images = seq_along(imagePaths) %>% lapply(function(i){
    print(i)
    x = imagePaths[i]
    image = oro.dicom::readDICOMFile(x)
    if(i ==2){
        return(NULL)
    }
    image$img %>% ogbox::scale01() %>% writeImage(paste0('out/',i,'.jpg'))
    return(NULL)
})


imStart = 1394
imEnd = 1521
imFiles = list.files('out',full.names = TRUE)
imFiles = imFiles[imFiles %in% paste0('out/',imStart:imEnd,'.jpg')]
images = imFiles %>% lapply(image_read)

sideBySide = 1:ceiling(length(images)/12) %>% lapply(function(i){
    image_append(do.call(c,images[(i*12-11):(i*12)]))
}) 

sideBySide %>% do.call(c,.) %>% image_append(stack = TRUE) %>% image_write('brainMozaic.jpg')


brainspriteR::brainsprite('brainMozaic.jpg',spriteHeight = 512,spriteWidth = 512)