testing saving imagej-compatible tiffs: le vs be?

#!/usr/bin/env python3

'''

/**

 * @file imagej_tiff_saver.py

 * @brief save tiffs for imagej (1.52d+) - with stacks and hyperstacks

 * @par <b>License</b>:

 *  This program is free software: you can redistribute it and/or modify

 *  it under the terms of the GNU General Public License as published by

 *  the Free Software Foundation, either version 3 of the License, or

 *  (at your option) any later version.

 *

 *  This program is distributed in the hope that it will be useful,

 *  but WITHOUT ANY WARRANTY; without even the implied warranty of

 *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the

 *  GNU General Public License for more details.

 *

 *  You should have received a copy of the GNU General Public License

 *  along with this program.  If not, see <http://www.gnu.org/licenses/>.

*/

'''

__copyright__ = "Copyright 2018, Elphel, Inc."

__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(ifh=b"MM*\x00\x00\x00\x00\x00",prefix= b"MM")

  ifd = TiffImagePlugin.ImageFileDirectory_v2(prefix= b"MM")

  #ifd = TiffImagePlugin.ImageFileDirectory_v2()

  #ifd = TiffImagePlugin.ImageFileDirectory(prefix='MM')

  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")

  ijlabl = [

    b'IJIJinfo\x00\x00\x00\x01labl\x00\x00\x00\x05',

    '<info></info>'.encode('UTF-16-LE'),

    'img1'.encode('UTF-16-LE'),

    'img2'.encode('UTF-16-LE'),

    'img3'.encode('UTF-16-LE'),

    'img4'.encode('UTF-16-LE'),

    'img5'.encode('UTF-16-LE')

  ]

  #for i in range()

  #ifd[50838] = (20,10)

  #ifd[50839] = (20,10)

  ifd_50838_list = []

  ifd_50839 = b"".join(ijlabl)

  for label in ijlabl:

    ifd_50838_list.append(len(label))

  ifd_50838 = tuple(ifd_50838_list)

  #print(ifd_50838)

  #print(ifd_50839)

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

  #if (len(shape)>0):

  ifd[50838] = ifd_50838

  ifd[50839] = ifd_50839

  # override

  #tif = Image.open("test.tiff")

  #tag_50838 = tif.tag[50838]

  #tag_50839 = tif.tag[50839]

  #tag_270 = tif.tag[270]

  #print(tag_50839)

  #ifd[270] = tag_270

  #ifd[50838] = tag_50838

  #ifd[50839] = tag_50839

  return ifd

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

def save(path,images):

  # Got images, analyze shape:

  #   - possible formats (c == depth):

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

  #     -- (t,h,w,c), t or z does not matter

  #     -- (h,w,c)

  #     -- (h,w)

  # 0 or 1 images.shapes are not handled

  #

  # (h,w)

  if len(images.shape)==2:

    image = Image.fromarray(images)

    image.save(path)

  elif len(images.shape)>2:

    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 = -1

    if c==1:

      split_channels = images

    else:

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

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

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

    imlist = []

    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:])

    # 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

  hw = hamming_window

  NT = 5

  NC = 1

  NZ = 1

  NX = 2916

  NY = 2178

  images = np.empty((NT,NZ,NY,NX,NC))

  import time

  print(str(time.time())+": Generating test images")

  for t in range(NT):

    for z in range(NZ):

      for c in range(NC):

        images[t,z,:,:,c] = np.array([[(255-t*25)*hw(i,512)*hw(j,512) for i in range(NX)] for j in range(NY)],np.float32)

  print(str(time.time())+": Test images generated")

  print("Images shape: "+str(images.shape))

  print("1D run")

  imgs = images[:,0,:,:,0]

  print(imgs.shape)

  imlist = []

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

    tmp = Image.fromarray(imgs[i])

    #tmp.mode = "I;32BS"

    imlist.append(tmp)

  TiffImagePlugin.DEBUG = True

  TiffImagePlugin.WRITE_LIBTIFF = False

  #import sys

  #sys.byteorder = "big"

  #imlist[0].mode = "I;16B"

  #print("encoderconfig")

  #print(imlist[0].encoderconfig)

  imlist[0].save("result_1D.tiff",save_all=True,append_images=imlist[1:],tiffinfo=__get_IJ_IFD(NT,NZ,NC))

  #v = save("result_1D.tiff",imgs)

  #tif = Image.open("result_1D.tiff")

  #tag_50838 = tif.tag[50838]

  #tag_50839 = tif.tag[50839]

  #tag_270 = tif.tag[270]

  #print(tag_50839)

  #tif = Image.open("test.tiff")

  #tif.save("test_saved.tiff")

  #print("5D run")

  #v = save("result_5D.tiff",images)

  #print("4D run")

  #v = save("result_4D.tiff",images[0])

  #print("3D run")

  #v = save("result_3D.tiff",images[0,0])

  #print("3D run, 1 channel")

  #tmp_images = images[0,0,:,:,0]

  #v = save("result_3D1C.tiff",tmp_images[:,:,np.newaxis])

  # open test