named labels

#!/usr/bin/env python3

#!/usr/bin/env python3

'''

import struct

/**

import numpy

 * @file imagej_tiff_saver.py

import tifffile

 * @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

import math

# DO NOT USE?

def imagej_metadata_tags(metadata, byteorder):

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

    """Return IJMetadata and IJMetadataByteCounts tags from metadata dict.

def __get_IJ_IFD(t,z,c):

    The tags can be passed to the TiffWriter.save function as extratags.

  #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()

    header = [{'>': b'IJIJ', '<': b'JIJI'}[byteorder]]

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

    bytecounts = [0]

    body = []

  ijheader = [

    'ImageJ=',

    def writestring(data, byteorder):

    'hyperstack=true',

        return data.encode('utf-16' + {'>': 'be', '<': 'le'}[byteorder])

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

    'channels='+str(c),

    def writedoubles(data, byteorder):

    'slices='+str(z),

        return struct.pack(byteorder+('d' * len(data)), *data)

    'frames='+str(t),

    'loop=false'

    def writebytes(data, byteorder):

  ]

        return data.tobytes()

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

    metadata_types = (

        ('Info', b'info', 1, writestring),

  ijlabl = [

        ('Labels', b'labl', None, writestring),

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

        ('Ranges', b'rang', 1, writedoubles),

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

        ('LUTs', b'luts', None, writebytes),

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

        ('Plot', b'plot', 1, writebytes),

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

        ('ROI', b'roi ', 1, writebytes),

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

        ('Overlays', b'over', None, writebytes))

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

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

    for key, mtype, count, func in metadata_types:

  ]

        if key not in metadata:

            continue

  #for i in range()

        if byteorder == '<':

            mtype = mtype[::-1]

  #ifd[50838] = (20,10)

        values = metadata[key]

  #ifd[50839] = (20,10)

        if count is None:

  ifd_50838_list = []

            count = len(values)

  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:

        else:

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

            values = [values]

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

        header.append(mtype + struct.pack(byteorder+'I', count))

        for value in values:

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

            data = func(value, byteorder)

            body.append(data)

    imlist = []

            bytecounts.append(len(data))

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

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

    body = b''.join(body)

    header = b''.join(header)

    data = header + body

    bytecounts[0] = len(header)

    bytecounts = struct.pack(byteorder+('I' * len(bytecounts)), *bytecounts)

    return ((50839, 'B', len(data), data, True),

            (50838, 'I', len(bytecounts)//4, bytecounts, True))

    #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):

def hamming_window(x,N):

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

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

hw = hamming_window

hw = hamming_window

  NT = 5

image =  numpy.array([[(255-0*25)*hw(i,512)*hw(j,512) for i in range(512)] for j in range(512)],numpy.float32)

  NC = 1

image = image[numpy.newaxis,...]

  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

ijtags = imagej_metadata_tags({'Labels':["Name1","Name2","Name3","Name4","Name5"]}, '<')

print(ijtags)

with tifffile.TiffWriter("multipage_test.tiff", bigtiff=False,imagej=True) as tif:

  for i in range(5):

    tif.save(image, metadata={'version':'20180905', 'loop':False}, extratags=ijtags)