<reponame>rominashirazi/SpineSegmentation<filename>segmentation_test/Scripts/medpy_zoom_image.py
#!c:\users\hooma\documents\github\spinesegmentation\segmentation_test\scripts\python.exe

"""
Zoom into an image by adding new slices in the z-direction and filling them with interpolated data.

Copyright (C) 2013 <NAME>

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/>.
"""

# build-in modules
import argparse
import logging
import os

# third-party modules
from scipy.ndimage import interpolation

# path changes

# own modules
from medpy.core import Logger
from medpy.io import load, save, header


# information
__author__ = "<NAME>"
__version__ = "r0.2.1, 2012-06-13"
__email__ = "<EMAIL>"
__status__ = "Release"
__description__ = """
                  Zoom into an image by adding new slices in the z-direction and filling
                  them with interpolated data. Overall "enhancement" new slices will be
                  created between every two original slices.
                  
                  If you want to zoom multiple binary objects in an image without
                  interpolating between their values, use the -o switch.
                  
                  Copyright (C) 2013 <NAME>
                  This program comes with ABSOLUTELY NO WARRANTY; This is free software,
                  and you are welcome to redistribute it under certain conditions; see
                  the LICENSE file or <http://www.gnu.org/licenses/> for details.   
                  """

# code
def main():
    args = getArguments(getParser())

    # prepare logger
    logger = Logger.getInstance()
    if args.debug: logger.setLevel(logging.DEBUG)
    elif args.verbose: logger.setLevel(logging.INFO)
    
    # check if output image exists
    if not args.force and os.path.exists(args.output):
        logger.warning('The output image {} already exists. Exiting.'.format(args.output))
        exit(-1)
    
    # load input data
    input_data, input_header = load(args.input)
    
    # if normal mode, perform the zoom
    logger.info('Performing normal zoom...')
    output_data, output_header = zoom(input_data, args.enhancement, args.dimension, hdr=input_header)

    # saving results
    save(output_data, args.output, output_header, args.force)
    
def zoom(image, factor, dimension, hdr = False, order = 3):
    """
    Zooms the provided image by the supplied factor in the supplied dimension.
    The factor is an integer determining how many slices should be put between each
    existing pair.
    If an image header (hdr) is supplied, its voxel spacing gets updated.
    Returns the image and the updated header or false.
    """
    # check if supplied dimension is valid
    if dimension >= image.ndim:
        raise argparse.ArgumentError('The supplied zoom-dimension {} exceeds the image dimensionality of 0 to {}.'.format(dimension, image.ndim - 1))
    
    # get logger
    logger = Logger.getInstance()

    logger.debug('Old shape = {}.'.format(image.shape))

    # perform the zoom
    zoom = [1] * image.ndim
    zoom[dimension] = (image.shape[dimension] + (image.shape[dimension] - 1) * factor) / float(image.shape[dimension])
    logger.debug('Reshaping with = {}.'.format(zoom))
    image = interpolation.zoom(image, zoom, order=order)
        
    logger.debug('New shape = {}.'.format(image.shape))
    
    if hdr:
        new_spacing = list(header.get_pixel_spacing(hdr))
        new_spacing[dimension] = new_spacing[dimension] / float(factor + 1)
        logger.debug('Setting pixel spacing from {} to {}....'.format(header.get_pixel_spacing(hdr), new_spacing))
        header.set_pixel_spacing(hdr, tuple(new_spacing))
    
    return image, hdr
    
def getArguments(parser):
    "Provides additional validation of the arguments collected by argparse."
    return parser.parse_args()

def getParser():
    "Creates and returns the argparse parser object."
    parser = argparse.ArgumentParser(description=__description__, formatter_class=argparse.RawTextHelpFormatter)
    parser.add_argument('input', help='Source volume.')
    parser.add_argument('output', help='Target volume.')
    parser.add_argument('dimension', type=int, help='The dimension along which to zoom.')
    parser.add_argument('enhancement', type=int, help='How many slices to put between each original slice.')
    #parser.add_argument('-o', dest='objects', action='store_true', help='Activate this flag to perform the zoom for any binary object in the image separatly.')
    parser.add_argument('-v', dest='verbose', action='store_true', help='Display more information.')
    parser.add_argument('-d', dest='debug', action='store_true', help='Display debug information.')
    parser.add_argument('-f', dest='force', action='store_true', help='Silently override existing output images.')
    return parser

if __name__ == "__main__":
    main()     

#!c:\users\hooma\documents\github\spinesegmentation\segmentation_test\scripts\python.exe

"""
Zoom into an image by adding new slices in the z-direction and filling them with interpolated data.

Copyright (C) 2013 <NAME>

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/>.
"""

# build-in modules
import argparse
import logging
import os

# third-party modules
from scipy.ndimage import interpolation

# path changes

# own modules
from medpy.core import Logger
from medpy.io import load, save, header


# information
__author__ = "<NAME>"
__version__ = "r0.2.1, 2012-06-13"
__email__ = "<EMAIL>"
__status__ = "Release"
__description__ = """
                  Zoom into an image by adding new slices in the z-direction and filling
                  them with interpolated data. Overall "enhancement" new slices will be
                  created between every two original slices.
                  
                  If you want to zoom multiple binary objects in an image without
                  interpolating between their values, use the -o switch.
                  
                  Copyright (C) 2013 <NAME>
                  This program comes with ABSOLUTELY NO WARRANTY; This is free software,
                  and you are welcome to redistribute it under certain conditions; see
                  the LICENSE file or <http://www.gnu.org/licenses/> for details.   
                  """

# code
def main():
    args = getArguments(getParser())

    # prepare logger
    logger = Logger.getInstance()
    if args.debug: logger.setLevel(logging.DEBUG)
    elif args.verbose: logger.setLevel(logging.INFO)
    
    # check if output image exists
    if not args.force and os.path.exists(args.output):
        logger.warning('The output image {} already exists. Exiting.'.format(args.output))
        exit(-1)
    
    # load input data
    input_data, input_header = load(args.input)
    
    # if normal mode, perform the zoom
    logger.info('Performing normal zoom...')
    output_data, output_header = zoom(input_data, args.enhancement, args.dimension, hdr=input_header)

    # saving results
    save(output_data, args.output, output_header, args.force)
    
def zoom(image, factor, dimension, hdr = False, order = 3):
    """
    Zooms the provided image by the supplied factor in the supplied dimension.
    The factor is an integer determining how many slices should be put between each
    existing pair.
    If an image header (hdr) is supplied, its voxel spacing gets updated.
    Returns the image and the updated header or false.
    """
    # check if supplied dimension is valid
    if dimension >= image.ndim:
        raise argparse.ArgumentError('The supplied zoom-dimension {} exceeds the image dimensionality of 0 to {}.'.format(dimension, image.ndim - 1))
    
    # get logger
    logger = Logger.getInstance()

    logger.debug('Old shape = {}.'.format(image.shape))

    # perform the zoom
    zoom = [1] * image.ndim
    zoom[dimension] = (image.shape[dimension] + (image.shape[dimension] - 1) * factor) / float(image.shape[dimension])
    logger.debug('Reshaping with = {}.'.format(zoom))
    image = interpolation.zoom(image, zoom, order=order)
        
    logger.debug('New shape = {}.'.format(image.shape))
    
    if hdr:
        new_spacing = list(header.get_pixel_spacing(hdr))
        new_spacing[dimension] = new_spacing[dimension] / float(factor + 1)
        logger.debug('Setting pixel spacing from {} to {}....'.format(header.get_pixel_spacing(hdr), new_spacing))
        header.set_pixel_spacing(hdr, tuple(new_spacing))
    
    return image, hdr
    
def getArguments(parser):
    "Provides additional validation of the arguments collected by argparse."
    return parser.parse_args()

def getParser():
    "Creates and returns the argparse parser object."
    parser = argparse.ArgumentParser(description=__description__, formatter_class=argparse.RawTextHelpFormatter)
    parser.add_argument('input', help='Source volume.')
    parser.add_argument('output', help='Target volume.')
    parser.add_argument('dimension', type=int, help='The dimension along which to zoom.')
    parser.add_argument('enhancement', type=int, help='How many slices to put between each original slice.')
    #parser.add_argument('-o', dest='objects', action='store_true', help='Activate this flag to perform the zoom for any binary object in the image separatly.')
    parser.add_argument('-v', dest='verbose', action='store_true', help='Display more information.')
    parser.add_argument('-d', dest='debug', action='store_true', help='Display debug information.')
    parser.add_argument('-f', dest='force', action='store_true', help='Silently override existing output images.')
    return parser

if __name__ == "__main__":
    main()
#!c:\users\hooma\documents\github\spinesegmentation\segmentation_test\scripts\python.exe Zoom into an image by adding new slices in the z-direction and filling them with interpolated data.  Copyright (C) 2013 <NAME>  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/>. # build-in modules # third-party modules # path changes # own modules # information Zoom into an image by adding new slices in the z-direction and filling                   them with interpolated data. Overall "enhancement" new slices will be                   created between every two original slices.                                      If you want to zoom multiple binary objects in an image without                   interpolating between their values, use the -o switch.                                      Copyright (C) 2013 <NAME>                   This program comes with ABSOLUTELY NO WARRANTY; This is free software,                   and you are welcome to redistribute it under certain conditions; see                   the LICENSE file or <http://www.gnu.org/licenses/> for details. # code # prepare logger # check if output image exists # load input data # if normal mode, perform the zoom # saving results Zooms the provided image by the supplied factor in the supplied dimension.     The factor is an integer determining how many slices should be put between each     existing pair.     If an image header (hdr) is supplied, its voxel spacing gets updated.     Returns the image and the updated header or false. # check if supplied dimension is valid # get logger # perform the zoom #parser.add_argument('-o', dest='objects', action='store_true', help='Activate this flag to perform the zoom for any binary object in the image separatly.')