testing saving imagej-compatible tiffs: le vs be?

imagej_tiffwriter_test.py

+#!/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
+
+
+
+
+
+