import argparse
import glob
import os

import numpy as np

from utils import *


def main(args):
	desired_width = args.desired_width
	desired_height = args.desired_height

	img_fn_array = []

	if args.image:
		img_obj = {}
		img_obj["img"] = args.image
		img_obj["out"] = args.out
		img_fn_array.append(img_obj)

	if args.dir:
		normpath = os.path.normpath("/".join([args.dir, '*', '']))
		for img_fn in glob.iglob(normpath, recursive=True):
			if os.path.isfile(img_fn) and True in [ext in img_fn for ext in [".nrrd", ".nii", ".nii.gz", ".gipl", ".gipl.gz"]]:
				img_obj = {}
				img_obj["img"] = img_fn
				img_obj["out"] = os.path.normpath("/".join([args.out]))
				img_fn_array.append(img_obj)


	for img_obj in img_fn_array:
		image = img_obj["img"]
		out = img_obj["out"]

		if not os.path.exists(out):
			os.makedirs(out)
		
		img, _ = ReadFile(image, verbose=1)
		img = Normalize(np.array(img))
		
		print("Deconstruction...")
		Deconstruction(img, image, out, desired_width, desired_height)



if __name__ ==  '__main__':
	parser = argparse.ArgumentParser(description='Label pre-processing', formatter_class=argparse.ArgumentDefaultsHelpFormatter)

	input_group = parser.add_argument_group('Input files')
	input_params = input_group.add_mutually_exclusive_group(required=True)
	input_params.add_argument('--image', type=str, help='Input 3D label')
	input_params.add_argument('--dir', type=str, help='Input directory with 3D labels')

	size_group = parser.add_argument_group('Resizing parameters')
	size_group.add_argument('--desired_width', type=int, help="width of the images", default=512)
	size_group.add_argument('--desired_height', type=int, help="height of the images", default=512)

	output_params = parser.add_argument_group('Output parameters')
	output_params.add_argument('--out', type=str, help='Output directory of the label slices', required=True)

	args = parser.parse_args()

	main(args)

243206b480ce678d5bf66c25ebb2b9dfb59026db
<mask token>

<mask token>


def main(args):
    desired_width = args.desired_width
    desired_height = args.desired_height
    img_fn_array = []
    if args.image:
        img_obj = {}
        img_obj['img'] = args.image
        img_obj['out'] = args.out
        img_fn_array.append(img_obj)
    if args.dir:
        normpath = os.path.normpath('/'.join([args.dir, '*', '']))
        for img_fn in glob.iglob(normpath, recursive=True):
            if os.path.isfile(img_fn) and True in [(ext in img_fn) for ext in
                ['.nrrd', '.nii', '.nii.gz', '.gipl', '.gipl.gz']]:
                img_obj = {}
                img_obj['img'] = img_fn
                img_obj['out'] = os.path.normpath('/'.join([args.out]))
                img_fn_array.append(img_obj)
    for img_obj in img_fn_array:
        image = img_obj['img']
        out = img_obj['out']
        if not os.path.exists(out):
            os.makedirs(out)
        img, _ = ReadFile(image, verbose=1)
        img = Normalize(np.array(img))
        print('Deconstruction...')
        Deconstruction(img, image, out, desired_width, desired_height)


<mask token>

<mask token>


def main(args):
    desired_width = args.desired_width
    desired_height = args.desired_height
    img_fn_array = []
    if args.image:
        img_obj = {}
        img_obj['img'] = args.image
        img_obj['out'] = args.out
        img_fn_array.append(img_obj)
    if args.dir:
        normpath = os.path.normpath('/'.join([args.dir, '*', '']))
        for img_fn in glob.iglob(normpath, recursive=True):
            if os.path.isfile(img_fn) and True in [(ext in img_fn) for ext in
                ['.nrrd', '.nii', '.nii.gz', '.gipl', '.gipl.gz']]:
                img_obj = {}
                img_obj['img'] = img_fn
                img_obj['out'] = os.path.normpath('/'.join([args.out]))
                img_fn_array.append(img_obj)
    for img_obj in img_fn_array:
        image = img_obj['img']
        out = img_obj['out']
        if not os.path.exists(out):
            os.makedirs(out)
        img, _ = ReadFile(image, verbose=1)
        img = Normalize(np.array(img))
        print('Deconstruction...')
        Deconstruction(img, image, out, desired_width, desired_height)


if __name__ == '__main__':
    parser = argparse.ArgumentParser(description='Label pre-processing',
        formatter_class=argparse.ArgumentDefaultsHelpFormatter)
    input_group = parser.add_argument_group('Input files')
    input_params = input_group.add_mutually_exclusive_group(required=True)
    input_params.add_argument('--image', type=str, help='Input 3D label')
    input_params.add_argument('--dir', type=str, help=
        'Input directory with 3D labels')
    size_group = parser.add_argument_group('Resizing parameters')
    size_group.add_argument('--desired_width', type=int, help=
        'width of the images', default=512)
    size_group.add_argument('--desired_height', type=int, help=
        'height of the images', default=512)
    output_params = parser.add_argument_group('Output parameters')
    output_params.add_argument('--out', type=str, help=
        'Output directory of the label slices', required=True)
    args = parser.parse_args()
    main(args)

import argparse
import glob
import os
import numpy as np
from utils import *


def main(args):
    desired_width = args.desired_width
    desired_height = args.desired_height
    img_fn_array = []
    if args.image:
        img_obj = {}
        img_obj['img'] = args.image
        img_obj['out'] = args.out
        img_fn_array.append(img_obj)
    if args.dir:
        normpath = os.path.normpath('/'.join([args.dir, '*', '']))
        for img_fn in glob.iglob(normpath, recursive=True):
            if os.path.isfile(img_fn) and True in [(ext in img_fn) for ext in
                ['.nrrd', '.nii', '.nii.gz', '.gipl', '.gipl.gz']]:
                img_obj = {}
                img_obj['img'] = img_fn
                img_obj['out'] = os.path.normpath('/'.join([args.out]))
                img_fn_array.append(img_obj)
    for img_obj in img_fn_array:
        image = img_obj['img']
        out = img_obj['out']
        if not os.path.exists(out):
            os.makedirs(out)
        img, _ = ReadFile(image, verbose=1)
        img = Normalize(np.array(img))
        print('Deconstruction...')
        Deconstruction(img, image, out, desired_width, desired_height)


if __name__ == '__main__':
    parser = argparse.ArgumentParser(description='Label pre-processing',
        formatter_class=argparse.ArgumentDefaultsHelpFormatter)
    input_group = parser.add_argument_group('Input files')
    input_params = input_group.add_mutually_exclusive_group(required=True)
    input_params.add_argument('--image', type=str, help='Input 3D label')
    input_params.add_argument('--dir', type=str, help=
        'Input directory with 3D labels')
    size_group = parser.add_argument_group('Resizing parameters')
    size_group.add_argument('--desired_width', type=int, help=
        'width of the images', default=512)
    size_group.add_argument('--desired_height', type=int, help=
        'height of the images', default=512)
    output_params = parser.add_argument_group('Output parameters')
    output_params.add_argument('--out', type=str, help=
        'Output directory of the label slices', required=True)
    args = parser.parse_args()
    main(args)

import argparse
import glob
import os

import numpy as np

from utils import *


def main(args):
	desired_width = args.desired_width
	desired_height = args.desired_height

	img_fn_array = []

	if args.image:
		img_obj = {}
		img_obj["img"] = args.image
		img_obj["out"] = args.out
		img_fn_array.append(img_obj)

	if args.dir:
		normpath = os.path.normpath("/".join([args.dir, '*', '']))
		for img_fn in glob.iglob(normpath, recursive=True):
			if os.path.isfile(img_fn) and True in [ext in img_fn for ext in [".nrrd", ".nii", ".nii.gz", ".gipl", ".gipl.gz"]]:
				img_obj = {}
				img_obj["img"] = img_fn
				img_obj["out"] = os.path.normpath("/".join([args.out]))
				img_fn_array.append(img_obj)


	for img_obj in img_fn_array:
		image = img_obj["img"]
		out = img_obj["out"]

		if not os.path.exists(out):
			os.makedirs(out)
		
		img, _ = ReadFile(image, verbose=1)
		img = Normalize(np.array(img))
		
		print("Deconstruction...")
		Deconstruction(img, image, out, desired_width, desired_height)



if __name__ ==  '__main__':
	parser = argparse.ArgumentParser(description='Label pre-processing', formatter_class=argparse.ArgumentDefaultsHelpFormatter)

	input_group = parser.add_argument_group('Input files')
	input_params = input_group.add_mutually_exclusive_group(required=True)
	input_params.add_argument('--image', type=str, help='Input 3D label')
	input_params.add_argument('--dir', type=str, help='Input directory with 3D labels')

	size_group = parser.add_argument_group('Resizing parameters')
	size_group.add_argument('--desired_width', type=int, help="width of the images", default=512)
	size_group.add_argument('--desired_height', type=int, help="height of the images", default=512)

	output_params = parser.add_argument_group('Output parameters')
	output_params.add_argument('--out', type=str, help='Output directory of the label slices', required=True)

	args = parser.parse_args()

	main(args)
