save_image_v5.jl

using Images, QuartzImageIO, FileIO, ProgressMeter
#using ImageView

function alignstack(img,dx,dy)
  (xn, yn, zn) = size(img)
  img_m = zeros(xn+zn*dx,yn+zn*dy,zn)
  fill!(img_m, NaN)
  for z = 1:zn
    yaxi = 1:yn
    yaxi = yaxi+(zn-z+1)*dy
    xaxi = 1:xn
    xaxi = xaxi+(zn-z+1)*dx
    img_m[xaxi,yaxi,z]=img[:,:,z]
  end
  return img_m
end

function rm_na(img)
  x=copy(img)
  x[isnan.(x)]=0
  img=x
  return img
end

function rm_bad(img)
  f(img)=img<0.29
  mask = map(f,img[:,:,1])
  sum(mask)
  mask1 = Integer.(mask)
  img = Array(img)
  img_rm=img.*mask1
return img_rm
end


print("Date: ")
date=chomp(readline())
#date="10-28"
#filename="tim-a1T-0-0"
cd("/Volumes/")
files=readdir()
disk=filter(x->contains(x,"xitong_lab"),files)[1]

cd(@sprintf("/Volumes/%s/ocpi/%s/",disk,date))
files=readdir()
x=filter(x->contains(x,".imagine"),files)
k=1
filename=x[k][1:end-8]
exp = load(@sprintf("%s.imagine", filename))


# z = size(exp,3)÷2
# img1 = view(exp,:,:,z+1,1)
# img2 = view(exp,:,:,z,1)
# imgov = colorview(RGB, paddedviews(0, img1, img2, zeroarray)...)
# imshow(imgov)
t = 1

print("time: ")
t=chomp(readline())
t=parse(Int,t)

img1=exp[:,:,:,t]
img3=convert(Array{N0f16}, img1)
img3=colorview(Gray,img3)
QuartzImageIO.save(File{format"TIFF"}(@sprintf("%s-%s.tif", filename,t)), img3)



function drift(dx,dy,zrange=0)

  tp=nimages(exp)
  if zrange==0
    zrange=1:size(exp)[3]
  end

  add = @sprintf("/Volumes/%s/images/%s/%s-%s",disk,date,filename,zrange)
  if !isdir(add)
  mkpath(add)
  end
  cd(add)

  @showprogress for i in 1:tp
    img1 = exp[:,:,zrange,i]
    img1 = rm_bad(img1)
    imgb = imfilter(img1, (KernelFactors.IIRGaussian(2.0),KernelFactors.IIRGaussian(2.0)));
    img2 = alignstack(imgb,dx,dy)
    img2 = rm_na(img2)
    img3 = convert(Array{N0f16}, img2)
    img3 = mapslices(maximum, img3, 3)
    img3 = colorview(Gray,img3)
    QuartzImageIO.save(File{format"TIFF"}(@sprintf("%s-%i.tif", filename,i)), img3)
  end
end