Merge branch 'master' of git@git.elphel.com:Elphel/python3-imagej-tiff.git (38b9513f) · Commits · Elphel / python3-imagej-tiff

imagej_tiffwriter.py

+92 −86

Original line number	Original line	Diff line number	Diff line
	@@ -2,7 +2,7 @@

	'''		'''
	/**		/**
	* @file imagej_tiff_saver.py		* @file imagej_tiffwriter.py
	* @brief save tiffs for imagej (1.52d+) - with stacks and hyperstacks		* @brief save tiffs for imagej (1.52d+) - with stacks and hyperstacks
	* @par <b>License</b>:		* @par <b>License</b>:
	* This program is free software: you can redistribute it and/or modify		* This program is free software: you can redistribute it and/or modify
	@@ -29,47 +29,88 @@ Usage example:
	import imagej_tiffwriter		import imagej_tiffwriter
	import numpy as np		import numpy as np

	# have a few images in the form of numpy arrays		Have a few images in the form of numpy arrays np.float32:
	# make sure to stack them as:		- (h,w)
	# - (t,z,h,w,c)		- (n,h,w)
	# - (z,h,w,c)
	# - (h,w,c)
	# - (h,w)

	imagej_tiffwriter.save(path,images)		Labels can be provided as a list: ['label1','label2', etc.]
			No list length check against number of images

			imagej_tiffwriter.save(path,images,labels)

	'''		'''

	from PIL import Image, TiffImagePlugin
	import numpy as np		import numpy as np
			import struct
			import tifffile
	import math		import math

	# DO NOT USE?		# from here: https://stackoverflow.com/questions/50258287/how-to-specify-colormap-when-saving-tiff-stack
	# thing is the old ImageJs <1.52d poorly handle tags directories or something like that		def imagej_metadata_tags(metadata, byteorder):
	def __get_IJ_IFD(t,z,c):		"""Return IJMetadata and IJMetadataByteCounts tags from metadata dict.

	ifd = TiffImagePlugin.ImageFileDirectory_v2()		The tags can be passed to the TiffWriter.save function as extratags.

	ijheader = [		"""
	'ImageJ=',		header = [{'>': b'IJIJ', '<': b'JIJI'}[byteorder]]
	'hyperstack=true',		bytecounts = [0]
	'images='+str(tzc),		body = []
	'channels='+str(c),
	'slices='+str(z),		def writestring(data, byteorder):
	'frames='+str(t),		return data.encode('utf-16' + {'>': 'be', '<': 'le'}[byteorder])
	'loop=false'
	]		def writedoubles(data, byteorder):
			return struct.pack(byteorder+('d' * len(data)), *data)
	ifd[270] = ("\n".join(ijheader)+"\n")
			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))

	#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,labels=None,label_prefix="Label "):

			'''
			labels a list or None
			'''

	#def save(path,images,force_stack=False,force_hyperstack=False):		'''
	def save(path,images):		Expecting:
			(h,w),
			(n,h,w) - just create a simple stack
			'''

	# Got images, analyze shape:		# Got images, analyze shape:
	# - possible formats (c == depth):		# - possible formats (c == depth):
	@@ -78,46 +119,30 @@ def save(path,images):
	# -- (h,w,c)		# -- (h,w,c)
	# -- (h,w)		# -- (h,w)


	# 0 or 1 images.shapes are not handled		# 0 or 1 images.shapes are not handled
	#		#
	# (h,w)		# (h,w)
	if len(images.shape)==2:		if len(images.shape)==2:
			images = images[np.newaxis,...]

	image = Image.fromarray(images)		# now the shape length is 3
	image.save(path)

	elif len(images.shape)>2:

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

	if len(images.shape)==3:		if len(images.shape)==3:
	images = np.reshape(images,(1,h,w,c))		# tifffile treats shape[0] as channel, need to expand to get labels displayed
			#images = images[images.shape[0],np.newaxis,images.shape[1],images.shape[2]]
	z = images.shape[-4]		images = np.reshape(images,(images.shape[0],1,images.shape[1],images.shape[2]))

	if len(images.shape)==4:		labels_list = []
	images = np.reshape(images,(1,z,h,w,c))		if labels is None:
			for i in range(images.shape[0]):
	t = images.shape[-5]		labels_list.append(label_prefix+str(i+1))

	c_axis = -1

	if c==1:
	split_channels = images
	else:		else:
	channels = np.array(np.split(images,c,axis=c_axis))		labels_list = labels
	split_channels = np.concatenate(channels,axis=-3)

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

	imlist = []		ijtags = imagej_metadata_tags({'Labels':labels_list}, '<')
	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:])		with tifffile.TiffWriter(path, bigtiff=False,imagej=True) as tif:
	# thing is the old ImageJs <1.52d poorly handle tags directories or something like that		for i in range(images.shape[0]):
	#imlist[0].save(path,save_all=True,append_images=imlist[1:],tiffinfo=__get_IJ_IFD(t,z,c))		tif.save(images[i], metadata={'version':'1.11a','loop': False}, extratags=ijtags)

	# Testing		# Testing
	if __name__ == "__main__":		if __name__ == "__main__":
	@@ -129,34 +154,15 @@ if __name__ == "__main__":
	hw = hamming_window		hw = hamming_window

	NT = 5		NT = 5
	NC = 2
	NZ = 3
	NX = 512		NX = 512
	NY = 512		NY = 512

	images = np.empty((NT,NZ,NY,NX,NC))		images = np.empty((NT,NY,NX),np.float32)

	import time		import time
	print(str(time.time())+": Generating test images")		print(str(time.time())+": Generating test images")
	for t in range(NT):		for t in range(NT):
	for z in range(NZ):		images[t,:,:] = np.array([[(255-t25)hw(i,512)*hw(j,512) for i in range(NX)] for j in range(NY)],np.float32)
	for c in range(NC):
	images[t,z,:,:,c] = np.array([[(255-t25)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(str(time.time())+": Test images generated")
	print("Images shape: "+str(images.shape))		print("Images shape: "+str(images.shape))
			v = save("tiffwriter_test.tiff",images)
	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])

imagej_tiffwriter_test.py

deleted100644 → 0

+0 −240

Original line number	Original line	Diff line number	Diff line
	#!/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(tzc),
	'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 - 0.46math.cos(2math.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-t25)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

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