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utils.py
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# -*- coding: utf-8 -*-
import os
import SimpleITK as sitk
from math import ceil
import numpy as np
'''
Data pre-processing
'''
def convert_volumes_into_tiles(volumes_list, tile_size, overlap_size, tiles_path):
for index in range(len(volumes_list)):
print('Data:' + volumes_list[index])
volume = readimage(os.path.abspath(volumes_list[index]))
Origin = volume.GetOrigin()
Spacing = volume.GetSpacing()
Direction = volume.GetDirection()
tiles = volume_to_tiles(volume, tile_size, overlap_size)
write_path = tiles_path + '/' + str(index)
if not os.path.exists(write_path):
os.makedirs(write_path)
for count in range(tiles.shape[0]):
tile_to_write = sitk.GetImageFromArray(tiles[count,:,:,:])
tile_to_write.SetOrigin(Origin)
tile_to_write.SetSpacing(Spacing)
tile_to_write.SetDirection(Direction)
sitk.WriteImage(tile_to_write,write_path+'/'+str(count)+'.nii.gz')
print('Successfully convert into tiles')
def readimage(filename):
reader = sitk.ImageFileReader()
reader.SetFileName(filename)
return reader.Execute()
def volume_to_tiles(volume, tile_size, overlap_size, GT = False):
volume_shape = [volume.GetDepth(),volume.GetHeight(),volume.GetWidth()]
tiles_count = get_tiles_count(volume_shape,tile_size, overlap_size)
tiles = np.zeros(shape = (np.prod(tiles_count), tile_size[0],tile_size[1],tile_size[2]))
padded_volume = pad_volume(volume,tiles_count,tile_size,overlap_size)
padded_volume = sitk.GetArrayFromImage(padded_volume)
if not GT:
mean_value = np.mean(padded_volume)
std_value = np.std(padded_volume)
padded_volume = (padded_volume-mean_value)/std_value
for d in range(tiles_count[0]):
for h in range(tiles_count[1]):
for w in range(tiles_count[2]):
tiles[d*tiles_count[1]*tiles_count[2]+h*tiles_count[2]+w,:,:,:] = padded_volume[int(d*(tile_size[0]-overlap_size[0])):int(d*(tile_size[0]-overlap_size[0])+tile_size[0]),
int(h*(tile_size[1]-overlap_size[1])):int(h*(tile_size[1]-overlap_size[1])+tile_size[1]),
int(w*(tile_size[2]-overlap_size[2])):int(w*(tile_size[2]-overlap_size[2])+tile_size[2])]
return tiles
def get_tiles_count(volume_size, tile_size, overlap_size):
count_depth = int(ceil(float(volume_size[0] - overlap_size[0]) / float(tile_size[0] - overlap_size[0])))
count_height = int(ceil(float(volume_size[1] - overlap_size[1]) / float(tile_size[1] - overlap_size[1])))
count_width = int(ceil(float(volume_size[2] - overlap_size[2]) / float(tile_size[2] - overlap_size[2])))
return [count_depth,count_height,count_width]
def pad_volume(volume, tiles_count, tile_size, overlap_size):
padder = sitk.ConstantPadImageFilter()
padder.SetConstant(0)
depth_pad_l,depth_pad_u = get_pad_value(volume.GetDepth(), tiles_count[0], tile_size[0], overlap_size[0])
height_pad_l,height_pad_u = get_pad_value(volume.GetHeight(), tiles_count[1], tile_size[1], overlap_size[1])
width_pad_l,width_pad_u = get_pad_value(volume.GetWidth(), tiles_count[2], tile_size[2], overlap_size[2])
low_pad = sitk.VectorUInt32()
low_pad.append(width_pad_l)
low_pad.append(height_pad_l)
low_pad.append(depth_pad_l)
up_pad = sitk.VectorUInt32()
up_pad.append(width_pad_u)
up_pad.append(height_pad_u)
up_pad.append(depth_pad_u)
padder.SetPadLowerBound(low_pad)
padder.SetPadUpperBound(up_pad)
return padder.Execute(volume)
def get_pad_value(volume_size, tiles_count, tile_size, overlap_size):
total = tile_size * tiles_count - overlap_size * (tiles_count-1) - volume_size
lowerpad = int(total / 2)
upperpad = int(total - lowerpad)
return lowerpad, upperpad
def standardize_info(volume_path, tile_size, overlap_size):
volume = readimage(os.path.abspath(volume_path))
volume_shape = [volume.GetDepth(),volume.GetHeight(),volume.GetWidth()]
tiles_count = get_tiles_count(volume_shape,tile_size, overlap_size)
padded_volume = pad_volume(volume,tiles_count,tile_size,overlap_size)
padded_volume = sitk.GetArrayFromImage(padded_volume)
mean_value = np.mean(padded_volume)
std_value = np.std(padded_volume)
return mean_value, std_value
'''
Data post-processing
'''
def stitch_tiles(tiles_seg_result, volume_size, tile_size, overlap_size):
tiles_count = get_tiles_count(volume_size, tile_size, overlap_size)
depth_pad_l,depth_pad_u = get_pad_value(volume_size[0], tiles_count[0], tile_size[0], overlap_size[0])
height_pad_l,height_pad_u = get_pad_value(volume_size[1], tiles_count[1], tile_size[1], overlap_size[1])
width_pad_l,width_pad_u = get_pad_value(volume_size[2], tiles_count[2], tile_size[2], overlap_size[2])
padded_volume_size = [volume_size[0] + depth_pad_l + depth_pad_u, volume_size[1] + height_pad_l + height_pad_u, volume_size[2] + width_pad_l + width_pad_u]
padded_volume_seg_result = np.zeros(shape = padded_volume_size)
for d in range(tiles_count[0]):
for h in range(tiles_count[1]):
for w in range(tiles_count[2]):
padded_volume_seg_result[int(d*(tile_size[0]-overlap_size[0])):int(d*(tile_size[0]-overlap_size[0])+tile_size[0]),
int(h*(tile_size[1]-overlap_size[1])):int(h*(tile_size[1]-overlap_size[1])+tile_size[1]),
int(w*(tile_size[2]-overlap_size[2])):int(w*(tile_size[2]-overlap_size[2])+tile_size[2])] = tiles_seg_result[d*tiles_count[1]*tiles_count[2]+h*tiles_count[2]+w,:,:,:]
volume_seg_result = np.zeros(shape = volume_size)
volume_seg_result = padded_volume_seg_result[depth_pad_l:depth_pad_l + volume_size[0], height_pad_l:height_pad_l + volume_size[1], width_pad_l:width_pad_l + volume_size[2]]
return volume_seg_result
# get volume size & [origin spacing]
def ref_info_for_write(ref_img):
ref_volume = readimage(os.path.abspath(ref_img))
volume_size = [ref_volume.GetDepth(),ref_volume.GetHeight(),ref_volume.GetWidth()]
ref_origin = ref_volume.GetOrigin()
ref_spacing = ref_volume.GetSpacing()
ref_direction = ref_volume.GetDirection()
return volume_size, ref_origin, ref_spacing, ref_direction
def write_seg_result(seg_result, ref_origin, ref_spacing, ref_direction, filename):
result_img = sitk.GetImageFromArray(seg_result)
result_img.SetOrigin(ref_origin)
result_img.SetSpacing(ref_spacing)
result_img.SetDirection(ref_direction)
sitk.WriteImage(result_img, filename)
print('Successfully write!')