from __future__ import print_function, division
import SimpleITK as sitk
import numpy as np
from dataprocess.utils import file_name_path
bratshgg_path = "D:\Data\\brats18\HGG"
bratslgg_path = "D:\Data\\brats18\LGG"
flair_name = "_flair.nii.gz"
t1_name = "_t1.nii.gz"
t1ce_name = "_t1ce.nii.gz"
t2_name = "_t2.nii.gz"
mask_name = "_seg.nii.gz"
def getImageSizeandSpacing():
"""
get image and spacing
:return:
"""
pathhgg_list = file_name_path(bratshgg_path)
pathlgg_list = file_name_path(bratslgg_path)
for subsetindex in range(len(pathhgg_list)):
brats_subset_path = bratshgg_path + "/" + str(pathhgg_list[subsetindex]) + "/"
flair_image = brats_subset_path + str(pathhgg_list[subsetindex]) + flair_name
t1_image = brats_subset_path + str(pathhgg_list[subsetindex]) + t1_name
t1ce_image = brats_subset_path + str(pathhgg_list[subsetindex]) + t1ce_name
t2_image = brats_subset_path + str(pathhgg_list[subsetindex]) + t2_name
flair_src = sitk.ReadImage(flair_image, sitk.sitkInt16)
t1_src = sitk.ReadImage(t1_image, sitk.sitkInt16)
t1ce_src = sitk.ReadImage(t1ce_image, sitk.sitkInt16)
t2_src = sitk.ReadImage(t2_image, sitk.sitkInt16)
print('subsetindex:', subsetindex)
print("flair_src image size,flair_src image Spacing:", (flair_src.GetSize(), flair_src.GetSpacing()))
print("t1_src image size,t1_src image Spacing:", (t1_src.GetSize(), t1_src.GetSpacing()))
print("t1ce_src image size,t1ce_src image Spacing:", (t1ce_src.GetSize(), t1ce_src.GetSpacing()))
print("t2_src image size,t2_src image Spacing:", (t2_src.GetSize(), t2_src.GetSpacing()))
for subsetindex in range(len(pathlgg_list)):
brats_subset_path = bratslgg_path + "/" + str(pathlgg_list[subsetindex]) + "/"
flair_image = brats_subset_path + str(pathlgg_list[subsetindex]) + flair_name
t1_image = brats_subset_path + str(pathlgg_list[subsetindex]) + t1_name
t1ce_image = brats_subset_path + str(pathlgg_list[subsetindex]) + t1ce_name
t2_image = brats_subset_path + str(pathlgg_list[subsetindex]) + t2_name
flair_src = sitk.ReadImage(flair_image, sitk.sitkInt16)
t1_src = sitk.ReadImage(t1_image, sitk.sitkInt16)
t1ce_src = sitk.ReadImage(t1ce_image, sitk.sitkInt16)
t2_src = sitk.ReadImage(t2_image, sitk.sitkInt16)
print('subsetindex:', subsetindex)
print("flair_src image size,flair_src image Spacing:", (flair_src.GetSize(), flair_src.GetSpacing()))
print("t1_src image size,t1_src image Spacing:", (t1_src.GetSize(), t1_src.GetSpacing()))
print("t1ce_src image size,t1ce_src image Spacing:", (t1ce_src.GetSize(), t1ce_src.GetSpacing()))
print("t2_src image size,t2_src image Spacing:", (t2_src.GetSize(), t2_src.GetSpacing()))
def getMaskLabelValue():
"""
get max mask value
brats mask have four value:0,1,2,4(0 is backgroud )
:return:
"""
pathhgg_list = file_name_path(bratshgg_path)
pathlgg_list = file_name_path(bratslgg_path)
for subsetindex in range(len(pathhgg_list)):
brats_subset_path = bratshgg_path + "/" + str(pathhgg_list[subsetindex]) + "/"
mask_image = brats_subset_path + str(pathhgg_list[subsetindex]) + mask_name
seg = sitk.ReadImage(mask_image, sitk.sitkUInt8)
segimg = sitk.GetArrayFromImage(seg)
seg_maskimage = segimg.copy()
seg_maskimage = seg_maskimage.flatten()
bcounts = np.bincount(seg_maskimage)
print("mask_value:", bcounts)
print('lgg')
for subsetindex in range(len(pathlgg_list)):
brats_subset_path = bratslgg_path + "/" + str(pathlgg_list[subsetindex]) + "/"
mask_image = brats_subset_path + str(pathlgg_list[subsetindex]) + mask_name
seg = sitk.ReadImage(mask_image, sitk.sitkUInt8)
segimg = sitk.GetArrayFromImage(seg)
seg_maskimage = segimg.copy()
seg_maskimage = seg_maskimage.flatten()
bcounts = np.bincount(seg_maskimage)
print("mask_value:", bcounts)
# getMaskLabelValue()
# getImageSizeandSpacing()
