###########Example workflow 3

###########Renske van Raaphorst - October 2019

##Workflow: get data from supersegger - plot all separate kymographs - save data

## Packages

require(bactMAP)

################################################
## Data to be filled in per time:

## Working directory

#your working directory is the directory where your supersegger data is saved containing
#the folders starting with "xy"
pathToWD <- "Type/the/path/to/your/files/here"

setwd(pathToWD)

## Name of the tiff image stack you want to use (single stack, grey scale)

myImage <- "yourImage.TIFF"

## Name of your output files:

output_name <- "myOutput"

## magnification converter (when 'myConv' is left out, the number will be automatically asked)

myConv = 0.0645
addPixels2um("myObjective", myConv)

################################################

## Import SuperSegger data

#Check the amount of "xy" folders automatically:
xys <- list.files(pattern="xy")
frames <- length(xys)
firstone <- as.numeric(strsplit(xys[order(xys)][1], "xy")[[1]])

superSegData <- extr_SuperSeggerCells(loc= pathToWD, 
                                      frames=frames, 
                                      startframe=firstone, 
                                      mag="myObjective", 
                                      timelapse=TRUE)

################################################

## Take data of interest, remove unused data

cells <- superSegData$mesh
rm(superSegData) #to clear up memory

################################################

## import TIFF

image <- extr_OriginalStack(myImage)

## Connect tiff to cells

cells_image <- extr_OriginalCells(image, cells)$rawdata_turned

################################################

##Make all kymographs

allKymos <- bactKymo(cells_image, 
                     timeD=TRUE, 
                     sizeAV=TRUE,
                     mag="myObjective")

################################################

##Save PDF

cairo_pdf(filename=paste(output_name, "_Kymos.PDF", sep=""), 
          onefile=TRUE, width=6, height=4)

allKymos

dev.off()

save(cells, file=paste(output_name, "_cells.Rda", sep=""))