## using simpleITK to load and save data.
import SimpleITK as sitk
itk_img = sitk.ReadImage('./nifti.nii.gz')
img = sitk.GetArrayFromImage(itk_img)
print("img shape:",img.shape)

## save 
out = sitk.GetImageFromArray(img)
# # out.SetSpacing(itk_img.GetSpacing())
# # out.SetOrigin(itk_img.GetOrigin())
sitk.WriteImage(out,'simpleitk_save.nii.gz')

import sys
import SimpleITK as sitk
import numpy as np

dcm_directory = "./flair_dicom"
series_ids = sitk.ImageSeriesReader.GetGDCMSeriesIDs(dcm_directory)
print("series ids:",series_ids)

if not series_ids:
 print("ERROR: given directory dose not a DICOM series.")
 sys.exit(1)

series_file_names = sitk.ImageSeriesReader.GetGDCMSeriesFileNames(dcm_directory,series_ids[0])
series_reader = sitk.ImageSeriesReader()
series_reader.SetFileNames(series_file_names)
image3D = series_reader.Execute()
size = image3D.GetSize()
print( "Image size:", size[0], size[1], size[2] )

image_array = sitk.GetArrayFromImage(image3D)

# SimpleITK讀取的圖像數據的坐標順序為zyx，即從多少張切片到單張切片的寬和高；
# 而據SimpleITK Image獲取的origin和spacing的坐標順序則是xyz

origin = image3D.GetOrigin()
spacing = image3D.GetSpacing()
print("origin:",origin," spacing:",spacing)

import SimpleITK as sitk
import numpy as np
image = sitk.ReadImage(slice_path)
image_array = sitk.GetArrayFromImage(image) # z, y, x

/*******************************************************
 
	控制臺運行程序
	輸入：
		程序名稱
		讀取圖像文件名
		保存圖像文件名
	輸出：
		保存另一種類型的圖像
	功能：
		圖像在jpeg和bmp兩種格式之間互換
********************************************************/
 
#include "itkImageFileReader.h"
#include "itkImageFileWriter.h"
#include "itkImageIOFactory.h"
#include "itkBMPImageIOFactory.h"
#include "itkJPEGImageIOFactory.h"
#include <iostream>
 
int main(int argc , char *argv[])
{
	if (argc < 3)
	{
		std::cerr << "Usage: " << std::endl;
		std::cerr << argv[0] << " inputImageFile outputImageFile " << std::endl;
		return EXIT_FAILURE;
	}
 
	itk::BMPImageIOFactory::RegisterOneFactory();
	itk::JPEGImageIOFactory::RegisterOneFactory();
 
	typedef itk::Image< unsigned char, 2 > ImageType;
	typedef itk::ImageFileReader< ImageType > ReaderType;
	typedef itk::ImageFileWriter< ImageType > WriterType;
 
	ReaderType::Pointer reader = ReaderType::New();
	WriterType::Pointer writer = WriterType::New();
 
	const char * inputFilename = argv[1];
	const char * outputFilename = argv[2];
 
	reader->SetFileName( inputFilename );
	writer->SetFileName( outputFilename );
 
	writer->SetInput( reader->GetOutput() );
	try
	{
		writer->Update();
	}
	catch( itk::ExceptionObject & err )
	{
		std::cerr << "ExceptionObject caught !" << std::endl;
		std::cerr << err << std::endl;
		return EXIT_FAILURE;
	}
 
	system("pause");
	return 0;
}