Change Reader, reset image pixel data order,change spacing[2] can be negative

src/src/base/vtkDICOMImageReader2.cpp

@@ -2,13 +2,12 @@
 // Created by Krad on 2022/2/8.
 //
 
+#include <vtkErrorCode.h>
 #include "vtkDICOMImageReader2.h"
 #include "vtkDataArray.h"
 #include "vtkImageData.h"
 #include "vtkObjectFactory.h"
-
+#include "vtkPointData.h"
-
-
 
 #include "DICOMAppHelper.h"
 #include "DICOMParser.h"
@@ -25,6 +24,51 @@ vtkDICOMImageReader2::~vtkDICOMImageReader2() {
 
 }
 
+//----------------------------------------------------------------------------
+void vtkDICOMImageReader2::SetupOutputInformation(int num_slices)
+{
+    int width = this->AppHelper->GetWidth();
+    int height = this->AppHelper->GetHeight();
+    int bit_depth = this->AppHelper->GetBitsAllocated();
+    int num_comp = this->AppHelper->GetNumberOfComponents();
+
+    this->DataExtent[0] = 0;
+    this->DataExtent[1] = width - 1;
+    this->DataExtent[2] = 0;
+    this->DataExtent[3] = height - 1;
+    this->DataExtent[4] = 0;
+    this->DataExtent[5] = num_slices - 1;
+
+    bool isFloat = this->AppHelper->RescaledImageDataIsFloat();
+
+    bool sign = this->AppHelper->RescaledImageDataIsSigned();
+
+    if (isFloat)
+    {
+        this->SetDataScalarTypeToFloat();
+    }
+    else if (bit_depth <= 8)
+    {
+        this->SetDataScalarTypeToUnsignedChar();
+    }
+    else
+    {
+        if (sign)
+        {
+            this->SetDataScalarTypeToShort();
+        }
+        else
+        {
+            this->SetDataScalarTypeToUnsignedShort();
+        }
+    }
+    this->SetNumberOfScalarComponents(num_comp);
+
+    this->GetPixelSpacing();
+
+    this->vtkImageReader2::ExecuteInformation();
+}
+
 void vtkDICOMImageReader2::ExecuteInformation() {
     vtkDICOMImageReader::ExecuteInformation();
     if (!this->DirectoryName && !this->FileName && !DICOMFileNames->empty()){
@@ -81,6 +125,155 @@ void vtkDICOMImageReader2::ExecuteInformation() {
     }
 }
 
+void vtkDICOMImageReader2::ExecuteDataWithInformation(vtkDataObject *output,
+                                                     vtkInformation *outInfo)
+{
+    vtkImageData *data = this->AllocateOutputData(output, outInfo);
+
+    if (!this->FileName && this->DICOMFileNames->empty())
+    {
+        vtkErrorMacro( << "Either a filename was not specified or the specified directory does not contain any DICOM images.");
+        this->SetErrorCode( vtkErrorCode::NoFileNameError );
+        return;
+    }
+
+    data->GetPointData()->GetScalars()->SetName("DICOMImage");
+
+    this->ComputeDataIncrements();
+
+    if (this->FileName)
+    {
+        vtkDebugMacro( << "Single file : " << this->FileName);
+        this->Parser->ClearAllDICOMTagCallbacks();
+        this->Parser->OpenFile(this->FileName);
+        this->AppHelper->Clear();
+        this->AppHelper->RegisterCallbacks(this->Parser);
+        this->AppHelper->RegisterPixelDataCallback(this->Parser);
+
+        this->Parser->ReadHeader();
+
+        void* imgData = nullptr;
+        DICOMParser::VRTypes dataType;
+        unsigned long imageDataLength;
+
+        this->AppHelper->GetImageData(imgData, dataType, imageDataLength);
+        if( !imageDataLength )
+        {
+            vtkErrorMacro( << "There was a problem retrieving data from: " << this->FileName );
+            this->SetErrorCode( vtkErrorCode::FileFormatError );
+            return;
+        }
+
+        void* buffer = data->GetScalarPointer();
+        if (buffer == nullptr)
+        {
+            vtkErrorMacro(<< "No memory allocated for image data!");
+            return;
+        }
+        // DICOM stores the upper left pixel as the first pixel in an
+        // image. VTK stores the lower left pixel as the first pixel in
+        // an image.  Need to flip the data.
+        vtkIdType rowLength;
+        rowLength = this->DataIncrements[1];
+        unsigned char *b = (unsigned char *)buffer;
+        unsigned char *iData = (unsigned char *)imgData;
+        memcpy(b,imgData,imageDataLength);
+//        iData += (imageDataLength - rowLength); // beginning of last row
+//        for (int i=0; i < this->AppHelper->GetHeight(); ++i)
+//        {
+//            memcpy(b, iData, rowLength);
+//            b += rowLength;
+//            iData -= rowLength;
+//        }
+    }
+    else if (!this->DICOMFileNames->empty())
+    {
+        vtkDebugMacro( << "Multiple files (" << static_cast<int>(this->DICOMFileNames->size()) << ")");
+        this->Parser->ClearAllDICOMTagCallbacks();
+        this->AppHelper->Clear();
+        this->AppHelper->RegisterCallbacks(this->Parser);
+        this->AppHelper->RegisterPixelDataCallback(this->Parser);
+
+        void* buffer = data->GetScalarPointer();
+        if (buffer == nullptr)
+        {
+            vtkErrorMacro(<< "No memory allocated for image data!");
+            return;
+        }
+
+        std::vector<std::string>::iterator fiter;
+
+        int count = 0;
+        vtkIdType numFiles = static_cast<int>(this->DICOMFileNames->size());
+
+        for (fiter = this->DICOMFileNames->begin();
+             fiter != this->DICOMFileNames->end();
+             ++fiter)
+        {
+            count++;
+            const char *file = fiter->c_str();
+            vtkDebugMacro( << "File : " << file );
+            this->Parser->OpenFile( file );
+            this->Parser->ReadHeader();
+
+            void* imgData = nullptr;
+            DICOMParser::VRTypes dataType;
+            unsigned long imageDataLengthInBytes;
+
+            this->AppHelper->GetImageData(imgData, dataType, imageDataLengthInBytes);
+            if( !imageDataLengthInBytes )
+            {
+                vtkErrorMacro( << "There was a problem retrieving data from: " << file );
+                this->SetErrorCode( vtkErrorCode::FileFormatError );
+                return;
+            }
+
+            // DICOM stores the upper left pixel as the first pixel in an
+            // image. VTK stores the lower left pixel as the first pixel in
+            // an image.  Need to flip the data.
+            vtkIdType rowLength;
+            rowLength = this->DataIncrements[1];
+            unsigned char *b = (unsigned char *)buffer;
+            unsigned char *iData = (unsigned char *)imgData;
+            memcpy(b,imgData,imageDataLengthInBytes);
+            buffer = ((char*) buffer) + imageDataLengthInBytes;
+
+            this->UpdateProgress(float(count)/float(numFiles));
+            int len = static_cast<int> (strlen((const char*) (*fiter).c_str()));
+            char* filename = new char[len+1];
+            strcpy(filename, (const char*) (*fiter).c_str());
+            this->SetProgressText(filename);
+            delete[] filename;
+        }
+    }
+}
+
+//避免z轴被强行设置成正增长
+double* vtkDICOMImageReader2::GetPixelSpacing()
+{
+    std::vector<std::pair<float, std::string> > sortedFiles;
+
+    this->AppHelper->GetImagePositionPatientFilenamePairs(sortedFiles, false);
+
+    float* spacing = this->AppHelper->GetPixelSpacing();
+    this->DataSpacing[0] = spacing[0];
+    this->DataSpacing[1] = spacing[1];
+
+    if (sortedFiles.size() > 1)
+    {
+        std::pair<float, std::string> p1 = sortedFiles[0];
+        std::pair<float, std::string> p2 = sortedFiles[1];
+        this->DataSpacing[2] = (p1.first - p2.first);
+//        this->DataSpacing[2] = fabs(p1.first - p2.first);
+    }
+    else
+    {
+        this->DataSpacing[2] = spacing[2];
+    }
+
+    return this->DataSpacing;
+}
+
 void vtkDICOMImageReader2::SetFileNames(const std::vector<std::string>& files) {
 
     this->DICOMFileNames->clear();

src/src/base/vtkDICOMImageReader2.h

@@ -28,10 +28,13 @@ public:
     vtkDICOMImageReaderVector* GetDICOMFileNames(){
         return DICOMFileNames;
     }
+    double* GetPixelSpacing();
 protected:
 
-
+    void SetupOutputInformation(int num_slices);
     void ExecuteInformation() override;
+    void vtkDICOMImageReader2::ExecuteDataWithInformation(vtkDataObject *output,
+                                                          vtkInformation *outInfo) override ;
 
     //
     // Constructor