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python3-imagej-tiff
Commit 38b9513f authored by Andrey Filippov's avatar Andrey Filippov
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Merge branch 'master' of git@git.elphel.com:Elphel/python3-imagej-tiff.git

parents cdd98c34 091eaecb
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imagej_tiffwriter.py
View file @ 38b9513f
......@@ -2,7 +2,7 @@
'''
/**
* @file imagej_tiff_saver.py
* @file imagej_tiffwriter.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
......@@ -29,47 +29,88 @@ 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)
Have a few images in the form of numpy arrays np.float32:
- (h,w)
- (n,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 struct
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()
ijheader = [
'ImageJ=',
'hyperstack=true',
'images='+str(t*z*c),
'channels='+str(c),
'slices='+str(z),
'frames='+str(t),
'loop=false'
]
# from here: https://stackoverflow.com/questions/50258287/how-to-specify-colormap-when-saving-tiff-stack
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))
ifd[270] = ("\n".join(ijheader)+"\n")
#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:
# - possible formats (c == depth):
......@@ -78,46 +119,30 @@ def save(path,images):
# -- (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
images = images[np.newaxis,...]
# now the shape length is 3
if len(images.shape)==3:
# 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]]
images = np.reshape(images,(images.shape[0],1,images.shape[1],images.shape[2]))
labels_list = []
if labels is None:
for i in range(images.shape[0]):
labels_list.append(label_prefix+str(i+1))
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))
labels_list = labels
imlist = []
for i in range(images_flat.shape[0]):
imlist.append(Image.fromarray(images_flat[i]))
ijtags = imagej_metadata_tags({'Labels':labels_list}, '<')
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))
with tifffile.TiffWriter(path, bigtiff=False,imagej=True) as tif:
for i in range(images.shape[0]):
tif.save(images[i], metadata={'version':'1.11a','loop': False}, extratags=ijtags)
# Testing
if __name__ == "__main__":
......@@ -129,34 +154,15 @@ if __name__ == "__main__":
hw = hamming_window
NT = 5
NC = 2
NZ = 3
NX = 512
NY = 512
images = np.empty((NT,NZ,NY,NX,NC))
images = np.empty((NT,NY,NX),np.float32)
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)
images[t,:,:] = 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("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])
v = save("tiffwriter_test.tiff",images)
imagej_tiffwriter_test.py deleted 100644 → 0
View file @ cdd98c34
#!/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
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