#include <vtkImageReslice.h>
#include<vtkSmartPointer.h>
#include<vtkRenderWindow.h>
#include<vtkRenderer.h>
#include<vtkRenderWindowInteractor.h>
#include<vtkInteractorStyleTrackballCamera.h>
#include<vtkCylinderSource.h>
#include<vtkPolyDataMapper.h>
#include<vtkProperty.h>
#include<vtkActor.h>
#include<vtkDICOMImageReader.h>
#include<vtkMarchingCubes.h>
#include<vtkImageData.h>
#include<vtkPointData.h>
#include<vtkCellData.h>
#include <vtkNIFTIImageReader.h>
#include <vtkNIFTIImageHeader.h>
#include <vtkTransformFilter.h>
#include <vtkPLYReader.h>
#include <vtkAxesActor.h>
#include <vtkCaptionActor2D.h>
#include <vtkTextActor.h>
#include <vtkVertexGlyphFilter.h>
#include <vtkStringArray.h>
#include <vtkTransformPolyDataFilter.h>
#include <vtkDICOMReader.h>
#include <vtkSTLReader.h>
#include <vtkMatrix4x4.h>
#include <vtkNIFTIHeader.h>
#include <vtkNIFTIReader.h>
#include <vtkTransform.h>
#include <vtkInteractorStyleTrackballCamera.h>
#include <vtkNIFTIWriter.h>
#include <vtkDICOMToRAS.h>
#include <vtkNew.h>
#include <vtkCamera.h>
#include <QDir>
#include <qDebug>
#include "vtkAutoInit.h" 
VTK_MODULE_INIT(vtkRenderingOpenGL2); // VTK was built with vtkRenderingOpenGL2
VTK_MODULE_INIT(vtkInteractionStyle);
VTK_MODULE_INIT(vtkRenderingFreeType)


int main(){
	/////////////////////
	//preparing part 1://
	/////////////////////
	//1.1 initialize render window
	vtkNew<vtkRenderer> renderer;
	renderer->SetBackground(0.1804, 0.5451, 0.3412);
	vtkNew<vtkRenderWindow> renderWindow;
	renderWindow->SetSize(1000, 1000);
	renderWindow->AddRenderer(renderer);
	vtkNew<vtkInteractorStyleTrackballCamera> style;
	vtkNew<vtkRenderWindowInteractor> renderWindowInteractor;
	renderer->GetActiveCamera()->SetFocalPoint(50, 100, 80);
	renderer->GetActiveCamera()->SetPosition(-800, 100, 80);
	renderer->GetActiveCamera()->SetViewUp(0, 1, 0);
	renderWindowInteractor->SetInteractorStyle(style);
	renderWindowInteractor->SetRenderWindow(renderWindow);
	//1.2 set transform mat
	double temparray[16] = 
	{ -0.0434782, -0.999054 ,-2.45238e-08, 243.429,
	0.00189944, -8.26871e-05 ,0.999998, 74.5061,
	-0.999053 ,0.0434782, 0.00190124, 174.119,
	0 ,0, 0, 1};
	vtkNew<vtkMatrix4x4> transformMat;
	transformMat->DeepCopy(temparray);
	//1.3 add axes in renderwindow
	vtkNew<vtkAxesActor> actorAxes;
	actorAxes->SetPosition(0, 0, 0);
	actorAxes->SetTotalLength(50, 50, 50);
	actorAxes->SetShaftType(0);
	actorAxes->SetAxisLabels(true);
	actorAxes->GetXAxisCaptionActor2D()->GetTextActor()->SetTextScaleModeToViewport();
	actorAxes->GetYAxisCaptionActor2D()->GetTextActor()->SetTextScaleModeToViewport();
	actorAxes->GetZAxisCaptionActor2D()->GetTextActor()->SetTextScaleModeToViewport();  
	actorAxes->SetCylinderRadius(0.02);
	renderer->AddActor(actorAxes);
	//1.4 read dicom directory
	vtkNew <vtkStringArray>stringfilesOri;
	QDir dirDcmOri("3D-T1_Directory_Path");
	QStringList qstringfilesOri = dirDcmOri.entryList(QStringList("*.dcm"), QDir::Files | QDir::Readable, QDir::Name);
	for (int i = 0; i < qstringfilesOri.size(); i++) {
		stringfilesOri->InsertNextValue((dirDcmOri.absolutePath() + "\\" + qstringfilesOri[i]).toStdString());}
	vtkNew <vtkDICOMReader> readerOri;
	readerOri->SetFileNames(stringfilesOri);
	readerOri->Update();
	//1.5 reslice to transform the image data
	auto reslice = vtkSmartPointer<vtkImageReslice>::New();
	reslice->SetInputConnection(readerOri->GetOutputPort());
	reslice->SetInformationInput(readerOri->GetOutput());
	reslice->SetOutputDimensionality(3);
	reslice->SetResliceAxes(transformMat);
	reslice->SetInterpolationModeToLinear();
	reslice->Update();
	///////////////////
	//working part 2://
	///////////////////
#define IF_TRANSFORM 1
	//2.1 reconstruct imagedata and visualize
	vtkNew <vtkMarchingCubes> mc1;
#if (IF_TRANSFORM == 1)
	mc1->SetInputConnection(reslice->GetOutputPort()); 
#else
	mc1->SetInputConnection(readerOri->GetOutputPort());
#endif
	mc1->ComputeNormalsOn();
	mc1->SetValue(0, 70);
	vtkNew<vtkPolyDataMapper> mapper1;
	mapper1->SetInputConnection(mc1->GetOutputPort());
	mapper1->ScalarVisibilityOff();
	vtkNew<vtkActor> actor1;
	actor1->GetProperty()->SetColor(.3, .3, .3);
	actor1->GetProperty()->SetOpacity(0.1);
	actor1->SetMapper(mapper1);
	renderer->AddActor(actor1);
	//2.2 write imagedata into NIFTI file
	auto writer1 = vtkNIFTIWriter::New();
#if (IF_TRANSFORM == 1)
	writer1->SetInputConnection(reslice->GetOutputPort());
#else
	writer1->SetInputConnection(readerOri->GetOutputPort()); 
#endif
	writer1->SetFileName("testdicom2nii_1.nii");
	writer1->SetQFac(0);
	writer1->Write();
	//2.3 read imagedata from NIFTI file
	auto *readerResult2 = vtkNIFTIReader::New();
	readerResult2->SetFileName("testdicom2nii_1.nii");
	readerResult2->Update();
	//2.4 reconstruct imagedata and visualize
	vtkNew <vtkMarchingCubes> surfaceResult2;
	surfaceResult2->SetInputConnection(readerResult2->GetOutputPort());
	surfaceResult2->ComputeNormalsOn();
	surfaceResult2->SetValue(0, 70);
	vtkNew<vtkPolyDataMapper> mapperResult2;
	mapperResult2->SetInputConnection(surfaceResult2->GetOutputPort());
	mapperResult2->ScalarVisibilityOff();
	vtkNew<vtkActor> actorResult2;
	actorResult2->GetProperty()->SetColor(.1, .1, .8);
	actorResult2->GetProperty()->SetOpacity(.1);
	actorResult2->SetMapper(mapperResult2);
	renderer->AddActor(actorResult2);


	renderWindow->Render();
	renderWindowInteractor->Start();

}