named labels

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 struct
+import numpy
+import tifffile
 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
-
-
-
-
-
-
+def imagej_metadata_tags(metadata, byteorder):
+    """Return IJMetadata and IJMetadataByteCounts tags from metadata dict.
+
+    The tags can be passed to the TiffWriter.save function as extratags.
+
+    """
+    header = [{'>': b'IJIJ', '<': b'JIJI'}[byteorder]]
+    bytecounts = [0]
+    body = []
+
+    def writestring(data, byteorder):
+        return data.encode('utf-16' + {'>': 'be', '<': 'le'}[byteorder])
+
+    def writedoubles(data, byteorder):
+        return struct.pack(byteorder+('d' * len(data)), *data)
+
+    def writebytes(data, byteorder):
+        return data.tobytes()
+
+    metadata_types = (
+        ('Info', b'info', 1, writestring),
+        ('Labels', b'labl', None, writestring),
+        ('Ranges', b'rang', 1, writedoubles),
+        ('LUTs', b'luts', None, writebytes),
+        ('Plot', b'plot', 1, writebytes),
+        ('ROI', b'roi ', 1, writebytes),
+        ('Overlays', b'over', None, writebytes))
+
+    for key, mtype, count, func in metadata_types:
+        if key not in metadata:
+            continue
+        if byteorder == '<':
+            mtype = mtype[::-1]
+        values = metadata[key]
+        if count is None:
+            count = len(values)
+        else:
+            values = [values]
+        header.append(mtype + struct.pack(byteorder+'I', count))
+        for value in values:
+            data = func(value, byteorder)
+            body.append(data)
+            bytecounts.append(len(data))
+
+    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))
+
+
+def hamming_window(x,N):
+  y = 0.54 - 0.46*math.cos(2*math.pi*x/(N-1))
+  return y
+
+hw = hamming_window
+
+image =  numpy.array([[(255-0*25)*hw(i,512)*hw(j,512) for i in range(512)] for j in range(512)],numpy.float32)
+image = image[numpy.newaxis,...]
+
+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)