+ * \brief computes the length (in bytes) we must ALLOCATE to receive the
+ * image(s) pixels (multiframes taken into account)
+ * \warning : it is NOT the group 7FE0 length
+ * (no interest for compressed images).
+ */
+int File::ComputeDecompressedPixelDataSizeFromHeader()
+{
+ // see PS 3.3-2003 : C.7.6.3.2.1
+ //
+ // MONOCHROME1
+ // MONOCHROME2
+ // PALETTE COLOR
+ // RGB
+ // HSV (Retired)
+ // ARGB (Retired)
+ // CMYK (Retired)
+ // YBR_FULL
+ // YBR_FULL_422 (no LUT, no Palette)
+ // YBR_PARTIAL_422
+ // YBR_ICT
+ // YBR_RCT
+
+ // LUT's
+ // ex : gdcm-US-ALOKA-16.dcm
+ // 0028|1221 [OW] [Segmented Red Palette Color Lookup Table Data]
+ // 0028|1222 [OW] [Segmented Green Palette Color Lookup Table Data]
+ // 0028|1223 [OW] [Segmented Blue Palette Color Lookup Table Data]
+
+ // ex : OT-PAL-8-face.dcm
+ // 0028|1201 [US] [Red Palette Color Lookup Table Data]
+ // 0028|1202 [US] [Green Palette Color Lookup Table Data]
+ // 0028|1203 [US] [Blue Palette Color Lookup Table Data]
+
+ int numberBitsAllocated = HeaderInternal->GetBitsAllocated();
+ // Number of "Bits Allocated" is fixed to 16 when:
+ // - it is not defined (i.e. it's value is 0)
+ // - it's 12, since we will expand the image to 16 bits (see
+ // PixelConvert::ConvertDecompress12BitsTo16Bits() )
+ if ( numberBitsAllocated == 0 || numberBitsAllocated == 12 )
+ {
+ numberBitsAllocated = 16;
+ }
+
+ int DecompressedSize = HeaderInternal->GetXSize()
+ * HeaderInternal->GetYSize()
+ * HeaderInternal->GetZSize()
+ * ( numberBitsAllocated / 8 )
+ * HeaderInternal->GetSamplesPerPixel();
+
+ return DecompressedSize;
+}
+
+/**
+ * \brief - Allocates necessary memory,
+ * - Reads the pixels from disk (uncompress if necessary),
+ * - Transforms YBR pixels, if any, into RGB pixels
+ * - Transforms 3 planes R, G, B, if any, into a single RGB Plane
+ * - Transforms single Grey plane + 3 Palettes into a RGB Plane
+ * - Copies the pixel data (image[s]/volume[s]) to newly allocated zone.
+ * @return Pointer to newly allocated pixel data.
+ * NULL if alloc fails
+ */
+uint8_t* File::GetImageData()
+{
+ if ( ! GetDecompressed() )
+ {
+ // If the decompression failed nothing can be done.
+ return 0;
+ }
+
+ uint8_t* pixelData;
+ if ( HeaderInternal->HasLUT() && PixelConverter->BuildRGBImage() )
+ {
+ pixelData = PixelConverter->GetRGB();
+ }
+ else
+ {
+ // When no LUT or LUT conversion fails, return the decompressed
+ pixelData = PixelConverter->GetDecompressed();
+ }
+
+// PIXELCONVERT CLEANME
+ // Restore the header in a disk-consistent state
+ // (if user asks twice to get the pixels from disk)
+ if ( PixelRead != -1 ) // File was "read" before
+ {
+ RestoreInitialValues();
+ }
+ if ( PixelConverter->GetRGB() )
+ {
+ // now, it's an RGB image
+ // Lets's write it in the Header
+ std::string spp = "3"; // Samples Per Pixel
+ HeaderInternal->SetEntryByNumber(spp,0x0028,0x0002);
+ std::string rgb = "RGB "; // Photometric Interpretation
+ HeaderInternal->SetEntryByNumber(rgb,0x0028,0x0004);
+ std::string planConfig = "0"; // Planar Configuration
+ HeaderInternal->SetEntryByNumber(planConfig,0x0028,0x0006);
+ PixelRead = 0; // no PixelRaw
+ }
+ else
+ {
+ if ( HeaderInternal->HasLUT() )
+ {
+ // The LUT interpretation failed
+ std::string photometricInterpretation = Util::DicomString("MONOCHROME1");
+ HeaderInternal->SetEntryByNumber( photometricInterpretation,
+ 0x0028, 0x0004 );
+ PixelRead = 0; // no PixelRaw
+ }
+ else
+ {
+ if ( PixelConverter->IsDecompressedRGB() )
+ {
+ ///////////////////////////////////////////////////
+ // now, it's an RGB image
+ // Lets's write it in the Header
+ // Droping Palette Color out of the Header
+ // has been moved to the Write process.
+ // TODO : move 'values' modification to the write process
+ // : save also (in order to be able to restore)
+ // : 'high bit' -when not equal to 'bits stored' + 1
+ // : 'bits allocated', when it's equal to 12 ?!
+ std::string spp = "3"; // Samples Per Pixel
+ std::string photInt = "RGB "; // Photometric Interpretation
+ std::string planConfig = "0"; // Planar Configuration
+ HeaderInternal->SetEntryByNumber(spp,0x0028,0x0002);
+ HeaderInternal->SetEntryByNumber(photInt,0x0028,0x0004);
+ HeaderInternal->SetEntryByNumber(planConfig,0x0028,0x0006);
+ }
+ PixelRead = 1; // PixelRaw
+ }
+ }
+
+ // We say the value *is* loaded.
+ SetPixelData(pixelData);
+// END PIXELCONVERT CLEANME
+
+ return pixelData;
+}
+
+/**
+ * \brief
+ * Read the pixels from disk (uncompress if necessary),
+ * Transforms YBR pixels, if any, into RGB pixels
+ * Transforms 3 planes R, G, B, if any, into a single RGB Plane
+ * Transforms single Grey plane + 3 Palettes into a RGB Plane
+ * Copies at most MaxSize bytes of pixel data to caller allocated
+ * memory space.
+ * \warning This function allows people that want to build a volume
+ * from an image stack *not to* have, first to get the image pixels,
+ * and then move them to the volume area.
+ * It's absolutely useless for any VTK user since vtk chooses
+ * to invert the lines of an image, that is the last line comes first
+ * (for some axis related reasons?). Hence he will have
+ * to load the image line by line, starting from the end.
+ * VTK users have to call GetImageData
+ *
+ * @param destination Address (in caller's memory space) at which the
+ * pixel data should be copied
+ * @param maxSize Maximum number of bytes to be copied. When MaxSize
+ * is not sufficient to hold the pixel data the copy is not
+ * executed (i.e. no partial copy).
+ * @return On success, the number of bytes actually copied. Zero on
+ * failure e.g. MaxSize is lower than necessary.
+ */
+size_t File::GetImageDataIntoVector (void* destination, size_t maxSize)
+{
+ if ( ! GetDecompressed() )
+ {
+ // If the decompression failed nothing can be done.
+ return 0;
+ }
+
+ if ( HeaderInternal->HasLUT() && PixelConverter->BuildRGBImage() )
+ {
+ if ( PixelConverter->GetRGBSize() > maxSize )
+ {
+ dbg.Verbose(0, "File::GetImageDataIntoVector: pixel data bigger"
+ "than caller's expected MaxSize");
+ return 0;
+ }
+ memcpy( destination,
+ (void*)PixelConverter->GetRGB(),
+ PixelConverter->GetRGBSize() );
+ return PixelConverter->GetRGBSize();
+ }
+
+ // Either no LUT conversion necessary or LUT conversion failed
+ if ( PixelConverter->GetDecompressedSize() > maxSize )
+ {
+ dbg.Verbose(0, "File::GetImageDataIntoVector: pixel data bigger"
+ "than caller's expected MaxSize");
+ return 0;
+ }
+ memcpy( destination,
+ (void*)PixelConverter->GetDecompressed(),
+ PixelConverter->GetDecompressedSize() );
+ return PixelConverter->GetDecompressedSize();
+}
+
+/**
+ * \brief Allocates necessary memory,
+ * Transforms YBR pixels (if any) into RGB pixels
+ * Transforms 3 planes R, G, B (if any) into a single RGB Plane
+ * Copies the pixel data (image[s]/volume[s]) to newly allocated zone.
+ * DOES NOT transform Grey plane + 3 Palettes into a RGB Plane
+ * @return Pointer to newly allocated pixel data.
+ * \ NULL if alloc fails
+ */
+uint8_t* File::GetImageDataRaw ()
+{
+ uint8_t* decompressed = GetDecompressed();
+ if ( ! decompressed )
+ {
+ return 0;
+ }
+
+// PIXELCONVERT CLEANME
+ // Restore the header in a disk-consistent state
+ // (if user asks twice to get the pixels from disk)
+ if ( PixelRead != -1 ) // File was "read" before
+ {
+ RestoreInitialValues();
+ }
+ if ( PixelConverter->IsDecompressedRGB() )
+ {
+ ///////////////////////////////////////////////////
+ // now, it's an RGB image
+ // Lets's write it in the Header
+ // Droping Palette Color out of the Header
+ // has been moved to the Write process.
+ // TODO : move 'values' modification to the write process
+ // : save also (in order to be able to restore)
+ // : 'high bit' -when not equal to 'bits stored' + 1
+ // : 'bits allocated', when it's equal to 12 ?!
+ std::string spp = "3"; // Samples Per Pixel
+ std::string photInt = "RGB "; // Photometric Interpretation
+ std::string planConfig = "0"; // Planar Configuration
+ HeaderInternal->SetEntryByNumber(spp,0x0028,0x0002);
+ HeaderInternal->SetEntryByNumber(photInt,0x0028,0x0004);
+ HeaderInternal->SetEntryByNumber(planConfig,0x0028,0x0006);
+ }
+
+ // We say the value *is* loaded.
+/* GetHeader()->SetEntryByNumber( GDCM_BINLOADED,
+ GetHeader()->GetGrPixel(), GetHeader()->GetNumPixel());
+
+ // will be 7fe0, 0010 in standard cases
+ GetHeader()->SetEntryBinAreaByNumber( decompressed,
+ GetHeader()->GetGrPixel(), GetHeader()->GetNumPixel());*/
+ SetPixelData(decompressed);
+
+ PixelRead = 1; // PixelRaw
+// END PIXELCONVERT CLEANME
+
+ return decompressed;
+}
+
+uint8_t* File::GetDecompressed()
+{
+ uint8_t* decompressed = PixelConverter->GetDecompressed();
+ if ( ! decompressed )
+ {
+ // The decompressed image migth not be loaded yet:
+ std::ifstream* fp = HeaderInternal->OpenFile();
+ PixelConverter->ReadAndDecompressPixelData( fp );
+ if(fp) HeaderInternal->CloseFile();
+ decompressed = PixelConverter->GetDecompressed();
+ if ( ! decompressed )
+ {
+ dbg.Verbose(0, "File::GetDecompressed: read/decompress of "
+ "pixel data apparently went wrong.");
+ return 0;
+ }
+ }
+
+ return decompressed;
+}
+
+/**
+ * \brief Points the internal Pixel_Data pointer to the callers inData
+ * image representation, BUT WITHOUT COPYING THE DATA.
+ * 'image' Pixels are presented as C-like 2D arrays : line per line.
+ * 'volume'Pixels are presented as C-like 3D arrays : plane per plane
+ * \warning Since the pixels are not copied, it is the caller's responsability
+ * not to deallocate it's data before gdcm uses them (e.g. with
+ * the Write() method.
+ * @param inData user supplied pixel area
+ * @param expectedSize total image size, in Bytes