Date: 2021-09-19

# make-data_for_v01

Satoshi Kume*

*satoshi.kume.1984@gmail.com

#### 2021-09-19

#### Package

BioImageDbs 1.0.5

# Contents

Compiled: Sun Sep 19 02:35:27 2021

This script for the v01 dataset

# 1 Load the package

    #Install
    #devtools::install_github( "kumeS/BioImageDbs", force = TRUE )
    library(BioImageDbs)
    library(EBImage)
    library(magick)
    library(purrr)
    library(magrittr)
    library(filesstrings)
    library(animation)

# 2 Convert the images to the array data in R

## 2.1 EM_id0001_Brain_CA1_hippocampus_region

    #Set parameters
    DataFolder <- "EM_id0001_Brain_CA1_hippocampus_region"
    Ori <- "OriginalData"
    GT <- "mitochondria_GT"
    WIDTH00 <- 1024; HEIGHT00 <- 768; CHANNELS00 <- 1

    #Run the conversion
    DataImport_3d_seg(WIDTH = WIDTH00, HEIGHT = HEIGHT00, Z=-1, CHANNELS = CHANNELS00,
               data="./BioImageDbs_Data",
               path01=DataFolder,
               Original_path=Ori,
               GroundTruth_path=GT,
               FileName=paste0(DataFolder, "_5dTensor"))

    filesstrings::file.move(files=paste0(DataFolder, "_5dTensor.Rds"),
                            destinations="./BioImageDbs_Output",
                            overwrite = TRUE)

    Dat <- readRDS( paste0("./BioImageDbs_Output/", DataFolder, "_5dTensor.Rds") )
    #str(Dat); str(Dat$Train)
    for(n in 1:dim(Dat$Train$Train_Original)[1]){
    Sample <- paste0(DataFolder, "_5dTensor_train_dataset_",  n)
    ImageView3D(Dat$Train, Name=, Sample=n, Interval = 0.5)
    filesstrings::file.move(files=paste0(Sample, ".gif"), destinations="./DL_analysis_v01",
                            overwrite = TRUE)
    }

## 2.2 EM_id0002_Drosophila_brain_region

    #Set parameters
    DataFolder <- "EM_id0002_Drosophila_brain_region"
    WIDTH00 <- 512; HEIGHT00 <- 512; CHANNELS00 <- 1

    #Run the conversion
    DataImport_3d_seg(WIDTH = WIDTH00, HEIGHT = HEIGHT00, Z=-1, CHANNELS = CHANNELS00,
               data="./BioImageDbs_Data",
               path01=DataFolder,
               Original_path="OriginalData",
               GroundTruth_path="membrane_GT_inv",
               OriginalDataOnlyinTest=TRUE,
               FileName=paste0(DataFolder, "_5dTensor"))

    filesstrings::file.move(files=paste0(DataFolder, "_5dTensor.Rds"),
                            destinations="./BioImageDbs_Output",
                            overwrite = TRUE)
    Dat <- readRDS( paste0("./BioImageDbs_Output/", DataFolder, "_5dTensor.Rds") )
    str(Dat); str(Dat$Train)
    ImageView3D(Dat$Train, Interval=0.4, Name=paste0(DataFolder, "_5dTensor_train_dataset"))
    filesstrings::file.move(files=paste0(DataFolder, "_5dTensor_train_dataset.gif"),
                            destinations="./BioImageDbs_Output",
                            overwrite = TRUE)

## 2.3 EM_id0003_Drosophila_brain_region

    #Set parameters
    DataFolder <- "EM_id0003_J558L"
    WIDTH00 <- 1024; HEIGHT00 <- 1024; CHANNELS00 <- 1

    #Run the conversion
    DataImport_2d_seg(WIDTH = WIDTH00, HEIGHT = HEIGHT00, CHANNELS = CHANNELS00,
                      data="./BioImageDbs_Data",
                      path01=DataFolder,
                      Original_path="OriginalData",
                      GroundTruth_path="GroundTruth_8b",
                      FileName=paste0(DataFolder, "_4dTensor"))

    filesstrings::file.move(files=paste0(DataFolder, "_4dTensor.Rds"),
                            destinations="./BioImageDbs_Output",
                            overwrite = TRUE)
    Dat <- readRDS( paste0("./BioImageDbs_Output/", DataFolder, "_4dTensor.Rds") )
    #str(Dat); str(Dat$Train)
    #table(Dat$Train$Train_GroundTruth)
    Dat$Train$Train_GroundTruth[Dat$Train$Train_GroundTruth < 0.4] <- 0
    ImageView2D(Dat$Train, Interval=0.8, Name=paste0(DataFolder, "_4dTensor_train_dataset"))
    filesstrings::file.move(files=paste0(DataFolder, "_4dTensor_train_dataset.gif"),
                            destinations="./BioImageDbs_Output",
                            overwrite = TRUE)

## 2.4 EM_id0004_PrHudata

    #Set parameters
    DataFolder <- "EM_id0004_PrHudata"
    WIDTH00 <- 1024; HEIGHT00 <- 1024; CHANNELS00 <- 1
    #Run the conversion
    DataImport_2d_seg(WIDTH = WIDTH00, HEIGHT = HEIGHT00, CHANNELS = CHANNELS00,
                      data="./BioImageDbs_Data",
                      path01=DataFolder,
                      Original_path="OriginalData",
                      GroundTruth_path="GroundTruth_8b",
                      FileName=paste0(DataFolder, "_4dTensor"))

    filesstrings::file.move(files=paste0(DataFolder, "_4dTensor.Rds"),
                            destinations="./BioImageDbs_Output",
                            overwrite = TRUE)
    Dat <- readRDS( paste0("./BioImageDbs_Output/", DataFolder, "_4dTensor.Rds") )
    #str(Dat); str(Dat$Train)
    #table(Dat$Train$Train_GroundTruth)
    Dat$Train$Train_GroundTruth[Dat$Train$Train_GroundTruth < 0.4] <- 0
    ImageView2D(Dat$Train, Interval=0.8, Name=paste0(DataFolder, "_4dTensor_train_dataset"))
    filesstrings::file.move(files=paste0(DataFolder, "_4dTensor_train_dataset.gif"),
                            destinations="./BioImageDbs_Output",
                            overwrite = TRUE)

## 2.5 LM_id0001_DIC_C2DH_HeLa

    #Set parameters
    DataFolder <- "LM_id0001_DIC_C2DH_HeLa"
    WIDTH00 <- 512; HEIGHT00 <- 512; CHANNELS00 <- 1
    #Run the conversion
    #Multi-label / 4d-tensor
    DataImport_2d_seg(WIDTH = WIDTH00, HEIGHT = HEIGHT00, CHANNELS = CHANNELS00,
                      data="./BioImageDbs_Data",
                      path01=DataFolder,
                      Original_path="OriginalData",
                      GroundTruth_path="Cell_GroundTruth_8b",
                      FileName=paste0(DataFolder, "_4dTensor"))

    filesstrings::file.move(files=paste0(DataFolder, "_4dTensor.Rds"),
                            destinations="./BioImageDbs_Output",
                            overwrite = TRUE)
    Dat <- readRDS( paste0("./BioImageDbs_Output/", DataFolder, "_4dTensor.Rds") )
    str(Dat); str(Dat$Train)
    ImageView2D(Dat$Train, Interval=0.25, Name=paste0(DataFolder, "_4dTensor_train_dataset"))
    filesstrings::file.move(files=paste0(DataFolder, "_4dTensor_train_dataset.gif"),
                            destinations="./BioImageDbs_Output",
                            overwrite = TRUE)
    #ImageViewGif("LM_id0001_DIC_C2DH_HeLa.gif")

    #Binary label / 4d-tensor
    DataImport_2d_seg(WIDTH = WIDTH00, HEIGHT = HEIGHT00, CHANNELS = CHANNELS00,
                      data="./BioImageDbs_Data",
                      path01=DataFolder,
                      Original_path="OriginalData",
                      GroundTruth_path="Cell_GroundTruth_8b",
                      FileName=paste0(DataFolder, "_4dTensor"),
                      Binary=TRUE)
    filesstrings::file.move(files=paste0(DataFolder, "_4dTensor_Binary.Rds"),
                            destinations="./BioImageDbs_Output",
                            overwrite = TRUE)
    Dat <- readRDS( paste0("./BioImageDbs_Output/", DataFolder, "_4dTensor_Binary.Rds") )
    str(Dat); str(Dat$Train)
    ImageView2D(Dat$Train, Interval=0.25, Name=paste0(DataFolder, "_4dTensor_Binary_train_dataset"))
    filesstrings::file.move(files=paste0(DataFolder, "_4dTensor_Binary_train_dataset.gif"),
                            destinations="./BioImageDbs_Output",
                            overwrite = TRUE)

    #Multi-label / 5d-tensor
    DataImport_3d_seg(WIDTH = WIDTH00, HEIGHT = HEIGHT00, Z=-1, CHANNELS = CHANNELS00,
               data="./BioImageDbs_Data",
               path01=DataFolder,
               Original_path="OriginalData_3D",
               GroundTruth_path="Cell_GroundTruth_8b_3D",
               OriginalDataOnlyinTest=FALSE,
               FileName=paste0(DataFolder, "_5dTensor"))

    filesstrings::file.move(files=paste0(DataFolder, "_5dTensor.Rds"),
                            destinations="./BioImageDbs_Output",
                            overwrite = TRUE)
    Dat <- readRDS( paste0("./BioImageDbs_Output/", DataFolder, "_5dTensor.Rds") )
    str(Dat); str(Dat$Train)
    ImageView3D(Dat$Train, Interval=0.25, Name=paste0(DataFolder, "_5dTensor_train_dataset"))
    filesstrings::file.move(files=paste0(DataFolder, "_5dTensor_train_dataset.gif"),
                            destinations="./BioImageDbs_Output",
                            overwrite = TRUE)

## 2.6 LM_id0002_PhC_C2DH_U373

    #Set parameters
    DataFolder <- "LM_id0002_PhC_C2DH_U373"
    WIDTH00 <- 696; HEIGHT00 <- 520; CHANNELS00 <- 1
    #Multi-label / 4d-tensor
    DataImport_2d_seg(WIDTH = WIDTH00, HEIGHT = HEIGHT00, CHANNELS = CHANNELS00,
                      data="./BioImageDbs_Data",
                      path01=DataFolder,
                      Original_path="OriginalData",
                      GroundTruth_path="Cell_GroundTruth_8b",
                      FileName=paste0(DataFolder, "_4dTensor"))

    filesstrings::file.move(files=paste0(DataFolder, "_4dTensor.Rds"),
                            destinations="./BioImageDbs_Output",
                            overwrite = TRUE)
    Dat <- readRDS( paste0("./BioImageDbs_Output/", DataFolder, "_4dTensor.Rds") )
    str(Dat); str(Dat$Train)
    ImageView2D(Dat$Train, Interval=0.25, Name=paste0(DataFolder, "_4dTensor_train_dataset"))
    filesstrings::file.move(files=paste0(DataFolder, "_4dTensor_train_dataset.gif"),
                            destinations="./BioImageDbs_Output",
                            overwrite = TRUE)
    #ImageViewGif("LM_id0001_DIC_C2DH_HeLa.gif")

    #Binary label / 4d-tensor
    DataImport_2d_seg(WIDTH = WIDTH00, HEIGHT = HEIGHT00, CHANNELS = CHANNELS00,
                      data="./BioImageDbs_Data",
                      path01=DataFolder,
                      Original_path="OriginalData",
                      GroundTruth_path="Cell_GroundTruth_8b",
                      FileName=paste0(DataFolder, "_4dTensor"),
                      Binary=TRUE)
    filesstrings::file.move(files=paste0(DataFolder, "_4dTensor_Binary.Rds"),
                            destinations="./BioImageDbs_Output",
                            overwrite = TRUE)
    Dat <- readRDS( paste0("./BioImageDbs_Output/", DataFolder, "_4dTensor_Binary.Rds") )
    str(Dat); str(Dat$Train)
    ImageView2D(Dat$Train, Interval=0.25, Name=paste0(DataFolder, "_4dTensor_Binary_train_dataset"))
    filesstrings::file.move(files=paste0(DataFolder, "_4dTensor_Binary_train_dataset.gif"),
                            destinations="./BioImageDbs_Output",
                            overwrite = TRUE)

    #Multi-label / 5d-tensor
    DataImport_3d_seg(WIDTH = WIDTH00, HEIGHT = HEIGHT00, Z=-1, CHANNELS = CHANNELS00,
               data="./BioImageDbs_Data",
               path01=DataFolder,
               Original_path="OriginalData_3D",
               GroundTruth_path="Cell_GroundTruth_8b_3D",
               OriginalDataOnlyinTest=FALSE,
               FileName=paste0(DataFolder, "_5dTensor"))

    filesstrings::file.move(files=paste0(DataFolder, "_5dTensor.Rds"),
                            destinations="./BioImageDbs_Output",
                            overwrite = TRUE)
    Dat <- readRDS( paste0("./BioImageDbs_Output/", DataFolder, "_5dTensor.Rds") )
    str(Dat); str(Dat$Train)
    #ImageView3D(Dat$Train, Interval=0.25, Name=paste0(DataFolder, "_5dTensor_train_dataset"))
    #filesstrings::file.move(files=paste0(DataFolder, "_5dTensor_train_dataset.gif"),
    #                        destinations="./BioImageDbs_Output",
    #                        overwrite = TRUE)

## 2.7 LM_id0003_Fluo_N2DH_GOWT1

    #Set parameters
    DataFolder <- "LM_id0003_Fluo_N2DH_GOWT1"
    WIDTH00 <- 1024; HEIGHT00 <- 1024; CHANNELS00 <- 1
    #Multi-label / 4d-tensor
    DataImport_2d_seg(WIDTH = WIDTH00, HEIGHT = HEIGHT00, CHANNELS = CHANNELS00,
                      data="./BioImageDbs_Data",
                      path01=DataFolder,
                      Original_path="OriginalData",
                      GroundTruth_path="Cell_GroundTruth_8b",
                      FileName=paste0(DataFolder, "_4dTensor"))

    filesstrings::file.move(files=paste0(DataFolder, "_4dTensor.Rds"),
                            destinations="./BioImageDbs_Output",
                            overwrite = TRUE)
    Dat <- readRDS( paste0("./BioImageDbs_Output/", DataFolder, "_4dTensor.Rds") )
    str(Dat); str(Dat$Train)
    ImageView2D(Dat$Train, Interval=0.25, Name=paste0(DataFolder, "_4dTensor_train_dataset"))
    filesstrings::file.move(files=paste0(DataFolder, "_4dTensor_train_dataset.gif"),
                            destinations="./BioImageDbs_Output",
                            overwrite = TRUE)

    #Binary label / 4d-tensor
    DataImport_2d_seg(WIDTH = WIDTH00, HEIGHT = HEIGHT00, CHANNELS = CHANNELS00,
                      data="./BioImageDbs_Data",
                      path01=DataFolder,
                      Original_path="OriginalData",
                      GroundTruth_path="Cell_GroundTruth_8b",
                      FileName=paste0(DataFolder, "_4dTensor"),
                      Binary=TRUE)
    filesstrings::file.move(files=paste0(DataFolder, "_4dTensor_Binary.Rds"),
                            destinations="./BioImageDbs_Output",
                            overwrite = TRUE)
    Dat <- readRDS( paste0("./BioImageDbs_Output/", DataFolder, "_4dTensor_Binary.Rds") )
    str(Dat); str(Dat$Train)
    ImageView2D(Dat$Train, Interval=0.25, Name=paste0(DataFolder, "_4dTensor_Binary_train_dataset"))
    filesstrings::file.move(files=paste0(DataFolder, "_4dTensor_Binary_train_dataset.gif"),
                            destinations="./BioImageDbs_Output",
                            overwrite = TRUE)

    #Multi-label / 5d-tensor
    DataImport_3d_seg(WIDTH = WIDTH00, HEIGHT = HEIGHT00, Z=-1, CHANNELS = CHANNELS00,
               data="./BioImageDbs_Data",
               path01=DataFolder,
               Original_path="OriginalData_3D",
               GroundTruth_path="Cell_GroundTruth_8b_3D",
               OriginalDataOnlyinTest=FALSE,
               FileName=paste0(DataFolder, "_5dTensor"))

    filesstrings::file.move(files=paste0(DataFolder, "_5dTensor.Rds"),
                            destinations="./BioImageDbs_Output",
                            overwrite = TRUE)
    Dat <- readRDS( paste0("./BioImageDbs_Output/", DataFolder, "_5dTensor.Rds") )
    str(Dat); str(Dat$Train)
    #ImageView3D(Dat$Train, Interval=0.25, Name=paste0(DataFolder, "_5dTensor_train_dataset"))
    #filesstrings::file.move(files=paste0(DataFolder, "_5dTensor_train_dataset.gif"),
    #                        destinations="./BioImageDbs_Output",
    #                        overwrite = TRUE)

## 2.8 Display the GIF animations

    #Set parameters
    #DataFolder <- "EM_id0001_Brain_CA1_hippocampus_region"
    #Display the GIF image
    #id0001 <- Display.GIF(GifFileName=paste0("./BioImageDbs_Output/", DataFolder, "_5dTensor_train_dataset.gif"), View=TRUE)
    #id0001
    #str(id0001)
    #class(id0001)