def merge_kymographs(kym1_imp, kym2_imp, params):
"""Merge two kymographs"""
mrg_imp = RGBStackMerge().mergeChannels([kym1_imp, kym2_imp], True)
mrg_imp.setTitle("Merged " + params.labeled_species +
" intensity and curvature kymograph")
mrg_imp.show()
return mrg_imp
def makemontage(imp, hsize=5, vsize=5, increment=1):
"""Makes a montage of a multichannel ImagePlus object.
Args:
imp (ImagePlus): An ImagePlus object.
hsize (int, optional): Size of the horizontal axis. Defaults to 5.
vsize (int, optional): Size of the vertical axis. Defaults to 5.
increment (int, optional): The increment between images. Allows for dropping of e.g. every second frame. Defaults to 1.
Returns:
ImagePlus: The montage as ImagePlus object.
"""
gridsize = hsize * vsize
def _listProduct(inlist):
"""Calculates the product of all elements in a list.
Args:
inlist (list): A list of numbers.
Returns:
int or double: The product of all list elements.
"""
product = 1
for element in inlist:
if isinstance(element, (int, float)):
product = element * product
return product
def _channelmontage(_imp):
"""Makes a montage of a single channel ImagePlus object.
Args:
_imp (ImagePlus): A single channel ImagePlus object.
Returns:
ImagePlus: A montage of the one input channel.
"""
dims = _imp.getDimensions(
) # width, height, nChannels, nSlices, nFrames
frames = _listProduct(dims[2:])
if frames > gridsize: frames = gridsize
_montage = MontageMaker().makeMontage2(_imp, hsize, vsize, 1.00, 1,
frames, increment, 0, True)
return _montage
name = imp.getTitle()
channels = ChannelSplitter().split(imp)
montages = [_channelmontage(channel) for channel in channels]
montage = RGBStackMerge().mergeChannels(montages, False)
montage.setTitle(name)
return montage
# for each channel.
channels = {}
for image_file in image_files:
channel = re.search('channel(\d+)_', image_file).group(1)
if channel in channels:
channels[channel] += 1
else:
channels[channel] = 1
if len(channels) > 7:
print 'Images with more than 7 channels are not currently supported by the Merge Channels operation.'
sys.exit(1)
# Open an image sequence for each channel.
stacks = []
for channel in channels:
num_frames = channels[channel]
IJ.run('Image Sequence...', 'open=%s file=channel%s sort' % (image_files[0], channel))
stack = IJ.getImage()
stack.setTitle(channel)
stack.setDimensions(1, 1, num_frames) # TODO Don't hardcode the number of slices
stacks.append(stack)
merged_image = RGBStackMerge().mergeChannels(stacks, False)
merged_image.setTitle(dir_name)
# TODO Alternatively, we could upload directly to OMERO. But that probably
# would not work in headless mode.
IJ.run(merged_image, 'OME-TIFF...', 'save=%s.ome.tif compression=Uncompressed' % image_dir_path)