Commit b1111bca authored by Andrey Filippov's avatar Andrey Filippov

Trying versions and working on new evaluation criteria for FG/BG

parent 2c44046d
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#!/usr/bin/env python3
* @file
* @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
* 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 <>.
__copyright__ = "Copyright 2018, Elphel, Inc."
__license__ = "GPL-3.0+"
__email__ = ""
Usage example:
import imagej_tiffwriter
import numpy as np
Have a few images in the form of numpy arrays np.float32:
- (h,w)
- (n,h,w)
Labels can be provided as a list: ['label1','label2', etc.]
No list length check against number of images,images,labels)
import numpy as np
import struct
import tifffile
import math
# from here:
def imagej_metadata_tags(metadata, byteorder):
"""Return IJMetadata and IJMetadataByteCounts tags from metadata dict.
The tags can be passed to the 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:
if byteorder == '<':
mtype = mtype[::-1]
values = metadata[key]
if count is None:
count = len(values)
values = [values]
header.append(mtype + struct.pack(byteorder+'I', count))
for value in values:
data = func(value, byteorder)
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 save(path,images,force_stack=False,force_hyperstack=False):
def save(path,images,labels=None,label_prefix="Label "):
labels a list or None
(n,h,w) - just create a simple stack
# 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:
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 = labels
ijtags = imagej_metadata_tags({'Labels':labels_list}, '<')
with tifffile.TiffWriter(path, bigtiff=False,imagej=True) as tif:
for i in range(images.shape[0]):[i], metadata={'version':'1.11a','loop': False}, extratags=ijtags)
# 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
NX = 512
NY = 512
images = np.empty((NT,NY,NX),np.float32)
import time
print(str(time.time())+": Generating test images")
for t in range(NT):
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))
v = save("tiffwriter_test.tiff",images)
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