# read in and display ImagePlus object(s)
from ij.io import OpenDialog
from ij import IJ
import os
import sys

imctool_dir = os.path.join(IJ.getDirectory('plugins'),'imctools')
sys.path.append(os.path.realpath(imctool_dir))

import imctools.imagej.library as lib

def view_image5d_ome(img, ome_meta):
    """

    :param img:
    :param ome_meta:
    :return:
    """
    nchannels = ome_meta.getChannelCount(0)
    channel_names = [ome_meta.getChannelName(0,i) for i in range(nchannels)]

    img = lib.get_image5d(imgName=ome_meta.getImageName(0),
                 img_stack=img.getStack(),
                 channel_names = channel_names)


    img.show()

def load_and_view(file_name):
    (imag, omeMeta) = lib.load_ome_img(file_name)
    view_image5d_ome(imag, omeMeta)



op = OpenDialog('Choose multichannel TIFF')
file = os.path.join(op.getDirectory(), op.getFileName())
load_and_view(file_name=file)

8b5db9dcb62b174c68f9a8943400dff4ed337695
<mask token>

<mask token>
sys.path.append(os.path.realpath(imctool_dir))
<mask token>


def view_image5d_ome(img, ome_meta):
    """

    :param img:
    :param ome_meta:
    :return:
    """
    nchannels = ome_meta.getChannelCount(0)
    channel_names = [ome_meta.getChannelName(0, i) for i in range(nchannels)]
    img = lib.get_image5d(imgName=ome_meta.getImageName(0), img_stack=img.
        getStack(), channel_names=channel_names)
    img.show()


def load_and_view(file_name):
    imag, omeMeta = lib.load_ome_img(file_name)
    view_image5d_ome(imag, omeMeta)


<mask token>
load_and_view(file_name=file)

<mask token>
imctool_dir = os.path.join(IJ.getDirectory('plugins'), 'imctools')
sys.path.append(os.path.realpath(imctool_dir))
<mask token>


def view_image5d_ome(img, ome_meta):
    """

    :param img:
    :param ome_meta:
    :return:
    """
    nchannels = ome_meta.getChannelCount(0)
    channel_names = [ome_meta.getChannelName(0, i) for i in range(nchannels)]
    img = lib.get_image5d(imgName=ome_meta.getImageName(0), img_stack=img.
        getStack(), channel_names=channel_names)
    img.show()


def load_and_view(file_name):
    imag, omeMeta = lib.load_ome_img(file_name)
    view_image5d_ome(imag, omeMeta)


op = OpenDialog('Choose multichannel TIFF')
file = os.path.join(op.getDirectory(), op.getFileName())
load_and_view(file_name=file)

from ij.io import OpenDialog
from ij import IJ
import os
import sys
imctool_dir = os.path.join(IJ.getDirectory('plugins'), 'imctools')
sys.path.append(os.path.realpath(imctool_dir))
import imctools.imagej.library as lib


def view_image5d_ome(img, ome_meta):
    """

    :param img:
    :param ome_meta:
    :return:
    """
    nchannels = ome_meta.getChannelCount(0)
    channel_names = [ome_meta.getChannelName(0, i) for i in range(nchannels)]
    img = lib.get_image5d(imgName=ome_meta.getImageName(0), img_stack=img.
        getStack(), channel_names=channel_names)
    img.show()


def load_and_view(file_name):
    imag, omeMeta = lib.load_ome_img(file_name)
    view_image5d_ome(imag, omeMeta)


op = OpenDialog('Choose multichannel TIFF')
file = os.path.join(op.getDirectory(), op.getFileName())
load_and_view(file_name=file)

# read in and display ImagePlus object(s)
from ij.io import OpenDialog
from ij import IJ
import os
import sys

imctool_dir = os.path.join(IJ.getDirectory('plugins'),'imctools')
sys.path.append(os.path.realpath(imctool_dir))

import imctools.imagej.library as lib

def view_image5d_ome(img, ome_meta):
    """

    :param img:
    :param ome_meta:
    :return:
    """
    nchannels = ome_meta.getChannelCount(0)
    channel_names = [ome_meta.getChannelName(0,i) for i in range(nchannels)]

    img = lib.get_image5d(imgName=ome_meta.getImageName(0),
                 img_stack=img.getStack(),
                 channel_names = channel_names)


    img.show()

def load_and_view(file_name):
    (imag, omeMeta) = lib.load_ome_img(file_name)
    view_image5d_ome(imag, omeMeta)



op = OpenDialog('Choose multichannel TIFF')
file = os.path.join(op.getDirectory(), op.getFileName())
load_and_view(file_name=file)
