Commit 684ce5dd authored by Oleg Dzhimiev's avatar Oleg Dzhimiev

named labels, some error to fix

parent 4ecd26fe
...@@ -40,36 +40,77 @@ Usage example: ...@@ -40,36 +40,77 @@ Usage example:
''' '''
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.
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 = TiffImagePlugin.ImageFileDirectory_v2()
ijheader = [ #def save(path,images,force_stack=False,force_hyperstack=False):
'ImageJ=', def save(path,images,labels=None,label_prefix="Label"):
'hyperstack=true',
'images='+str(t*z*c),
'channels='+str(c),
'slices='+str(z),
'frames='+str(t),
'loop=false'
]
ifd[270] = ("\n".join(ijheader)+"\n")
#is_hyperstack = 'true' if len(shape)>1 else 'false'
#if (len(shape)>0):
return ifd
'''
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 +119,33 @@ def save(path,images): ...@@ -78,46 +119,33 @@ 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)
image.save(path) # now the shape length is 3
if len(images.shape)==3:
elif len(images.shape)>2: # 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]]
h,w,c = images.shape[-3:] images = np.reshape(images,(images.shape[0],1,images.shape[1],images.shape[2]))
if len(images.shape)==3: labels_list = []
images = np.reshape(images,(1,h,w,c)) if labels is None:
for i in range(images.shape[0]):
z = images.shape[-4] labels_list.append(label_prefix+str(i))
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)) labels_list = labels
split_channels = np.concatenate(channels,axis=-3)
images_flat = np.reshape(split_channels,(-1,h,w)) print(labels_list)
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)) print(images[i].shape)
tif.save(images[i], metadata={'version':'1.11a',' loop':False}, extratags=ijtags)
# Testing # Testing
if __name__ == "__main__": if __name__ == "__main__":
...@@ -129,34 +157,15 @@ if __name__ == "__main__": ...@@ -129,34 +157,15 @@ 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))
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-t*25)*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-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(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])
...@@ -69,8 +69,6 @@ image = image[numpy.newaxis,...] ...@@ -69,8 +69,6 @@ image = image[numpy.newaxis,...]
ijtags = imagej_metadata_tags({'Labels':["Name1","Name2","Name3","Name4","Name5"]}, '<') ijtags = imagej_metadata_tags({'Labels':["Name1","Name2","Name3","Name4","Name5"]}, '<')
print(ijtags)
with tifffile.TiffWriter("multipage_test.tiff", bigtiff=False,imagej=True) as tif: with tifffile.TiffWriter("multipage_test.tiff", bigtiff=False,imagej=True) as tif:
for i in range(5): for i in range(5):
tif.save(image, metadata={'version':'20180905', 'loop':False}, extratags=ijtags) tif.save(image, metadata={'version':'20180905', 'loop':False}, extratags=ijtags)
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