tested only for (t,z,h,w,c) shapes

__license__   = "GPL-3.0+"

__email__     = "oleg@elphel.com"

'''

Usage example:

  import imagej_tiffwriter

  import numpy as np

  # have a few images in the form of numpy arrays

  # make sure to stack them as:

  #   - (t,z,h,w,c)

  #   - (z,h,w,c)

  #   - (h,w,c)

  #   - (h,w)

  imagej_tiffwriter.save(path,images)

'''

from PIL import Image, TiffImagePlugin

import numpy as np

import math

# DO NOT USE?

# thing is the old ImageJs <1.52d poorly handle tags directories or something like that

def __get_IJ_IFD(t,z,c):

  ifd = TiffImagePlugin.ImageFileDirectory_v2()

  ijheader = [

    'ImageJ=',

    'hyperstack=true',

    'images='+str(t*z*c),

    'channels='+str(c),

    'slices='+str(z),

    'frames='+str(t),

    'loop=false'

  ]

  ifd[270] = ("\n".join(ijheader)+"\n")

  #is_hyperstack = 'true' if len(shape)>1 else 'false'

  #if (len(shape)>0):

  return ifd

def save(path,images,force_stack=False,force_hyperstack=False):

#def save(path,images,force_stack=False,force_hyperstack=False):

def save(path,images):

  # Got images, analyze shape:

  #   - possible formats (c == depth):

  #     -- (h,w,c)

  #     -- (h,w)

  # save single layer image

  # 0 or 1 images.shapes are not handled

  #

  # save single channel image in the form of numpy array

  #   -

  if   len(images.shape)==2:

    # (h,w) -> (h,w,c=1)

    images = images[:,:,np.newaxis]

    image = Image.fromarray(images)

    image.save(path)

  elif len(images.shape)>2:

    # do nothing

    pass

  else:

    # (w,) -> (h=1,w,c=1)

    images = images[np.newaxis,:,np.newaxis]

  #imlist = np.ravel(Image.fromarray(images))

  t,z,h,w,c  = images.shape

    h,w,c  = images.shape[-3:]

    if len(images.shape)==3:

      images = np.reshape(images,(1,h,w,c))

    z = images.shape[-4]

    if len(images.shape)==4:

      images = np.reshape(images,(1,z,h,w,c))

    t  = images.shape[-5]

    c_axis = len(images.shape)-1

    if c>1:

      channels = np.squeeze(np.split(images,c,axis=c_axis))

    else:

      channels = np.squeeze(images,axis=c_axis)

    split_channels = np.concatenate(channels,axis=-3)

    images_flat = np.reshape(split_channels,(-1,h,w))

    for i in range(images_flat.shape[0]):

      imlist.append(Image.fromarray(images_flat[i]))

  imlist[0].save(path,save_all=True,append_images=imlist[1:],tiffinfo=__get_IJ_IFD(t,z,c))

    imlist[0].save(path,save_all=True,append_images=imlist[1:])

    # thing is the old ImageJs <1.52d poorly handle tags directories or something like that

    #imlist[0].save(path,save_all=True,append_images=imlist[1:],tiffinfo=__get_IJ_IFD(t,z,c))

# Testing

if __name__ == "__main__":

  def hamming_window(x,N):

    y = 0.54 - 0.46*math.cos(2*math.pi*x/(N-1))

    return y