view OrthancFramework/Sources/DicomFormat/DicomIntegerPixelAccessor.cpp @ 5911:bfae0fc2ea1b get-scu-test

Started to work on handling errors as warnings when trying to store instances whose SOPClassUID has not been accepted during the negotiation. Work to be finalized later
author Alain Mazy <am@orthanc.team>
date Mon, 09 Dec 2024 10:07:19 +0100
parents f7adfb22e20e
children
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/**
 * Orthanc - A Lightweight, RESTful DICOM Store
 * Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics
 * Department, University Hospital of Liege, Belgium
 * Copyright (C) 2017-2023 Osimis S.A., Belgium
 * Copyright (C) 2024-2024 Orthanc Team SRL, Belgium
 * Copyright (C) 2021-2024 Sebastien Jodogne, ICTEAM UCLouvain, Belgium
 *
 * This program is free software: you can redistribute it and/or
 * modify it under the terms of the GNU Lesser General Public License
 * as published by the Free Software Foundation, either version 3 of
 * the License, or (at your option) any later version.
 *
 * This program is distributed in the hope that it will be useful, but
 * WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
 * Lesser General Public License for more details.
 *
 * You should have received a copy of the GNU Lesser General Public
 * License along with this program. If not, see
 * <http://www.gnu.org/licenses/>.
 **/


#include "../PrecompiledHeaders.h"

#ifndef NOMINMAX
#define NOMINMAX
#endif

#include "DicomIntegerPixelAccessor.h"

#include "../OrthancException.h"
#include <boost/lexical_cast.hpp>
#include <limits>
#include <cassert>
#include <stdio.h>

namespace Orthanc
{
  DicomIntegerPixelAccessor::DicomIntegerPixelAccessor(const DicomMap& values,
                                                       const void* pixelData,
                                                       size_t size) :
    information_(values),
    pixelData_(pixelData),
    size_(size)
  {
    if (information_.GetBitsAllocated() > 32 ||
        information_.GetBitsStored() >= 32)
    {
      // Not available, as the accessor internally uses int32_t values
      throw OrthancException(ErrorCode_NotImplemented);
    }

    frame_ = 0;
    frameOffset_ = information_.GetFrameSize();

    if (information_.GetNumberOfFrames() * frameOffset_ > size)
    {
      throw OrthancException(ErrorCode_BadFileFormat);
    }

    if (information_.IsSigned())
    {
      // Pixels are signed
      mask_ = (1 << (information_.GetBitsStored() - 1)) - 1;
      signMask_ = (1 << (information_.GetBitsStored() - 1));
    }
    else
    {
      // Pixels are unsigned
      mask_ = (1 << information_.GetBitsStored()) - 1;
      signMask_ = 0;
    }

    if (information_.IsPlanar())
    {
      /**
       * Each color plane shall be sent contiguously. For RGB images,
       * this means the order of the pixel values sent is R1, R2, R3,
       * ..., G1, G2, G3, ..., B1, B2, B3, etc.
       **/
      rowOffset_ = information_.GetWidth() * information_.GetBytesPerValue();
    }
    else
    {
      /**
       * The sample values for the first pixel are followed by the
       * sample values for the second pixel, etc. For RGB images, this
       * means the order of the pixel values sent shall be R1, G1, B1,
       * R2, G2, B2, ..., etc.
       **/
      if (information_.GetBitsStored() == 1)
      {
        if (information_.GetChannelCount() == 1 &&
            information_.GetBitsAllocated() == 1)
        {
          assert(information_.GetWidth() % 8 == 0);  // Tested by DicomImageInformation
          rowOffset_ = information_.GetWidth() / 8;
        }
        else
        {
          throw OrthancException(ErrorCode_IncompatibleImageFormat,
                                 "Image not supported (multi-channel black-and-image image)");
        }
      }
      else
      {
        rowOffset_ = information_.GetWidth() * information_.GetBytesPerValue() * information_.GetChannelCount();
      }
    }
  }


  void DicomIntegerPixelAccessor::GetExtremeValues(int32_t& min, 
                                                   int32_t& max) const
  {
    if (information_.GetHeight() == 0 || information_.GetWidth() == 0)
    {
      min = max = 0;
      return;
    }

    min = std::numeric_limits<int32_t>::max();
    max = std::numeric_limits<int32_t>::min();

    const unsigned int height = information_.GetHeight();
    const unsigned int width = information_.GetWidth();
    const unsigned int channels = information_.GetChannelCount();
    
    for (unsigned int y = 0; y < height; y++)
    {
      for (unsigned int x = 0; x < width; x++)
      {
        for (unsigned int c = 0; c < channels; c++)
        {
          int32_t v = GetValue(x, y, c);
          if (v < min)
            min = v;
          if (v > max)
            max = v;
        }
      }
    }
  }


  int32_t DicomIntegerPixelAccessor::GetValue(unsigned int x, 
                                              unsigned int y,
                                              unsigned int channel) const
  {
    assert(x < information_.GetWidth() && 
           y < information_.GetHeight() && 
           channel < information_.GetChannelCount());

    const uint8_t* pixel = (reinterpret_cast<const uint8_t*>(pixelData_) + 
                            y * rowOffset_ + frame_ * frameOffset_);
    
    if (information_.GetBitsStored() == 1)
    {
      // New in Orthanc 1.10.0, notably for DICOM SEG
      assert(information_.GetBitsAllocated() == 1 &&
             information_.GetChannelCount() == 1 &&
             !information_.IsPlanar());
      
      uint8_t b = pixel[x / 8];

      if (b & (1 << (x % 8)))
      {
        return 255;
      }
      else
      {
        return 0;
      }
    }
    else
    {
      // http://dicom.nema.org/medical/dicom/current/output/html/part03.html#sect_C.7.6.3.1.3
      if (information_.IsPlanar())
      {
        /**
         * Each color plane shall be sent contiguously. For RGB images,
         * this means the order of the pixel values sent is R1, R2, R3,
         * ..., G1, G2, G3, ..., B1, B2, B3, etc.
         **/
        assert(frameOffset_ % information_.GetChannelCount() == 0);
        pixel += channel * frameOffset_ / information_.GetChannelCount() + x * information_.GetBytesPerValue();
      }
      else
      {
        /**
         * The sample values for the first pixel are followed by the
         * sample values for the second pixel, etc. For RGB images, this
         * means the order of the pixel values sent shall be R1, G1, B1,
         * R2, G2, B2, ..., etc.
         **/
        pixel += channel * information_.GetBytesPerValue() + x * information_.GetChannelCount() * information_.GetBytesPerValue();
      }

      uint32_t v;
      v = pixel[0];
      if (information_.GetBytesPerValue() >= 2)
        v = v + (static_cast<uint32_t>(pixel[1]) << 8);
      if (information_.GetBytesPerValue() >= 3)
        v = v + (static_cast<uint32_t>(pixel[2]) << 16);
      if (information_.GetBytesPerValue() >= 4)
        v = v + (static_cast<uint32_t>(pixel[3]) << 24);

      v = v >> information_.GetShift();

      if (v & signMask_)
      {
        // Signed value
        // http://en.wikipedia.org/wiki/Two%27s_complement#Subtraction_from_2N
        return -static_cast<int32_t>(mask_) + static_cast<int32_t>(v & mask_) - 1;
      }
      else
      {
        // Unsigned value
        return static_cast<int32_t>(v & mask_);
      }
    }
  }


  void DicomIntegerPixelAccessor::SetCurrentFrame(unsigned int frame)
  {
    if (frame >= information_.GetNumberOfFrames())
    {
      throw OrthancException(ErrorCode_ParameterOutOfRange);
    }

    frame_ = frame;
  }

}