Fix pixel data read logic.

src/src/IO/DICOM/DICOMPixelDataHelper.cpp

@@ -61,10 +61,10 @@ void DICOMPixelDataHelper::GetPixelData(const char * path, void *data, unsigned
     DcmFileFormat *fileFormat = new DcmFileFormat();//读取文件获取传输语法
     if (fileFormat->loadFile(path).good()) {
         DcmDataset *dset = fileFormat->getDataset();
-        DicomImage* dcmImage = new DicomImage(fileFormat, dset->getOriginalXfer(),CIF_MayDetachPixelData);
+        DicomImage dcmImage(fileFormat, dset->getOriginalXfer(), CIF_MayDetachPixelData);
-        const DiPixel* pixelData = dcmImage->getInterData();//rescaled
+        const DiPixel *pixelData = dcmImage.getInterData();//rescaled
         unsigned long dataBits = 1;
-        switch (pixelData->getRepresentation()){
+        switch (pixelData->getRepresentation()) {
             case EPR_Uint8:
             case EPR_Sint8:
                 break;
@@ -77,12 +77,10 @@ void DICOMPixelDataHelper::GetPixelData(const char * path, void *data, unsigned
                 dataBits = 4;
                 break;
         }
-
+        const void *dd = pixelData->getData();
-        const void * dd = pixelData->getData();
+        length = pixelData->getCount();
-        length = pixelData->getCount() ;
+        length = length * dataBits;
-        length = length*dataBits;
+        memcpy(data, dd, length);
-        memcpy(data,dd, length);
-        delete dcmImage;
     } else{
         length=-1;
     }
@@ -100,8 +98,8 @@ void convertAndRescale(const void* input, void* output, double slope, double int
 }
 
 
-void* DICOMPixelDataHelper::GetPixelDataFloat(const char *path, unsigned long &length) {
+void DICOMPixelDataHelper::GetPixelDataFloat(const char *path, void *data, unsigned long &length) {
-    void* data = nullptr;
+    void* temp = nullptr;
     DcmFileFormat *fileFormat = new DcmFileFormat();
     if (fileFormat->loadFile(path).good()) {
         DcmDataset *dataset = fileFormat->getDataset();
@@ -109,36 +107,51 @@ void* DICOMPixelDataHelper::GetPixelDataFloat(const char *path, unsigned long &l
         const DiPixel* pixelData = dcmImage.getInterData();//no rescaled
         length = pixelData->getCount();
         const void* pData = pixelData->getData();
-        data = new float [length];
+        double slope = 1.0;
-        double slope= 1.0;
         dataset->findAndGetFloat64(DcmTagKey(0x0028, 0x1053), slope);
-        double intercept= 0.0;
+        double intercept = 0.0;
         dataset->findAndGetFloat64(DcmTagKey(0x0028, 0x1052), intercept);
         switch (pixelData->getRepresentation()){
             case EPR_Uint8:
-                convertAndRescale<Uint8>(pData,data,slope,intercept,length);
+                convertAndRescale<Uint8>(pData, data, slope, intercept, length);
                 break;
             case EPR_Sint8:
-                convertAndRescale<Sint8>(pData,data,slope,intercept,length);
+                convertAndRescale<Sint8>(pData, data, slope, intercept, length);
                 break;
             case EPR_Uint16:
-                convertAndRescale<Uint16>(pData,data,slope,intercept,length);
+                convertAndRescale<Uint16>(pData, data, slope, intercept, length);
                 break;
             case EPR_Sint16:
-                convertAndRescale<Sint16>(pData,data,slope,intercept,length);
+                convertAndRescale<Sint16>(pData, data, slope, intercept, length);
                 break;
             case EPR_Uint32:
-                convertAndRescale<Uint32>(pData,data,slope,intercept,length);
+                convertAndRescale<Uint32>(pData, data, slope, intercept, length);
                 break;
             case EPR_Sint32:
-                convertAndRescale<Sint32>(pData,data,slope,intercept,length);
+                convertAndRescale<Sint32>(pData, data, slope, intercept, length);
                 break;
         }
+        length = length * sizeof(float);
+    } else{
+        length=-1;
+    }
+    delete fileFormat;
+}
+
+void DICOMPixelDataHelper::GetRGBPixelData(const char *path, void *data, unsigned long &length) {
+    DcmFileFormat *fileFormat = new DcmFileFormat();//读取文件获取传输语法
+    if (fileFormat->loadFile(path).good()) {
+        DcmDataset *dset = fileFormat->getDataset();
+        DicomImage dcmImage(fileFormat, dset->getOriginalXfer(), CIF_MayDetachPixelData);
+        dcmImage.hideAllOverlays();
+        length = dcmImage.getOutputDataSize(8);
+        const void *dd = dcmImage.getOutputData(8);
+        memcpy(data, dd, length);
+        dcmImage.deleteOutputData();
     } else{
         length=-1;
     }
     delete fileFormat;
-    return data;
 }
 
 void DICOMPixelDataHelper::GetOverlayData(const char *path, void *data,

src/src/IO/DICOM/DICOMPixelDataHelper.h

@@ -7,6 +7,9 @@
 
 class ExtendMedicalImageProperties;
 
+/**
+ * DICOM file Pixel Data read helper
+ */
 class DICOMPixelDataHelper {
 public:
     DICOMPixelDataHelper() = default;
@@ -15,13 +18,42 @@ public:
     }
     static void GetThumbnailData(ExtendMedicalImageProperties *property, unsigned char* data,
             unsigned long& length);
-    static void GetPixelData(const char * path, void* data,unsigned long& length);
+    /**
-    static void* GetPixelDataFloat(const char * path,unsigned long& length);
+     * Get Pixel Data with Rescaled, result is calculate as integer, and arrange as integer.
+     * @param path dcm file absolute path
+     * @param data output data buffer pointer
+     * @param length output data length
+     */
+    static void GetPixelData(const char * path, void* data, unsigned long& length);
+
+    /**
+     * Get Pixel Data with Rescaled, result is calculate as Float, and arrange as Float.
+     * @param path dcm file absolute path
+     * @param data output data buffer pointer
+     * @param length output data length
+     */
+    static void GetPixelDataFloat(const char * path, void* data, unsigned long& length);
+
+    /**
+     * Get colorful Pixel Data as three component R,G,B color value.
+     * @param path dcm file absolute path
+     * @param data output data buffer pointer
+     * @param length output data length
+     */
+    static void GetRGBPixelData(const char * path, void* data, unsigned long& length);
+
+
     static void GetOverlayData(const char * path, void* data,
                                unsigned int& width, unsigned int& height,unsigned int plane = 0);
 
+    /**
+     * Init decompress Codecs, must be called before other method.
+     */
     static void InitCodecs();
 
+    /**
+     * Finalize decompress Codecs, must be called after other method have done.
+     */
     static void FinalizeCodecs();
 };
 

src/src/IO/DICOM/ExtendMedicalImageProperties.cpp

@@ -98,11 +98,3 @@ void ExtendMedicalImageProperties::GenerateUniqueID() {
     this->SetUniqueID(uniqueID.c_str());
 }
 
-bool ExtendMedicalImageProperties::RescaledImageDataIsUnsignedChar() {
-    bool charData = BitsAllocated == 8;
-    bool noScale = ((int)(this->RescaleOffset) == 0) && ((int)(this->RescaleSlope) == 1);
-    bool unSign =  (this->PixelRepresentation == 0);
-    bool color = SamplePerPixel == 3;
-    return (color || (charData && unSign && noScale));
-}
-

src/src/IO/DICOM/vtkDICOMImageReader2.cpp

@@ -93,37 +93,33 @@ void vtkDICOMImageReader2::ExecuteDataWithInformation(vtkDataObject *output,
         vtkErrorMacro(<< "No memory allocated for image data!");
         return;
     }
+
+    // init codes to support compressed file
+    DICOMPixelDataHelper::InitCodecs();
+
     for (int i = 0; i < properties->GetFileNames().size(); ++i) {
-        const std::string& path = properties->GetFileNames()[i];
+        const std::string &path = properties->GetFileNames()[i];
-        if (this->DataScalarType == VTK_FLOAT)
-        {
-            void *imgData = nullptr;
 
-            unsigned long imageDataLength;
+        unsigned long imageDataLength;
+
+        if (this->DataScalarType == VTK_FLOAT) {
+
+            DICOMPixelDataHelper::GetPixelDataFloat(path.c_str(), buffer, imageDataLength);
+
+        } else if (NumberOfScalarComponents > 1) {
+
+            DICOMPixelDataHelper::GetRGBPixelData(path.c_str(), buffer, imageDataLength);
+
+        } else {
+
+            DICOMPixelDataHelper::GetPixelData(path.c_str(), buffer, imageDataLength);
 
-            imgData = DICOMPixelDataHelper::GetPixelDataFloat(path.c_str(),imageDataLength);
-            if(imgData){
-                //calc size of float
-                imageDataLength = imageDataLength * sizeof(float);
-                unsigned char *b = (unsigned char *) buffer;
-                unsigned char *iData = (unsigned char *) imgData;
-                memcpy(b, imgData, imageDataLength);
-                buffer = ((char*) buffer) + imageDataLength;
-            }
-            else{
-                vtkErrorMacro(<< "Can't read data from path:"<<path.c_str()<<"!");
-                return;
-            }
-        }
-        else{
-            void *imgData = nullptr;
-
-            unsigned long imageDataLength;
-            unsigned char *b = (unsigned char *) buffer;
-            DICOMPixelDataHelper::GetPixelData(path.c_str(), buffer,imageDataLength);
-            buffer = ((char*) buffer) + imageDataLength;
         }
+        buffer = ((char *) buffer) + imageDataLength;
     }
+
+    // finalize codecs
+    DICOMPixelDataHelper::FinalizeCodecs();
 }
 
 double* vtkDICOMImageReader2::GetPixelSpacing()