--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/OrthancFramework/Sources/DicomFormat/DicomStreamReader.cpp	Wed Sep 30 15:33:47 2020 +0200
@@ -0,0 +1,599 @@
+/**
+ * Orthanc - A Lightweight, RESTful DICOM Store
+ * Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics
+ * Department, University Hospital of Liege, Belgium
+ * Copyright (C) 2017-2020 Osimis S.A., 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"
+#include "DicomStreamReader.h"
+
+#include "../OrthancException.h"
+
+namespace Orthanc
+{
+  static uint16_t ReadUnsignedInteger16(const char* dicom,
+                                        bool littleEndian)
+  {
+    const uint8_t* p = reinterpret_cast<const uint8_t*>(dicom);
+
+    if (littleEndian)
+    {
+      return (static_cast<uint16_t>(p[0]) |
+              (static_cast<uint16_t>(p[1]) << 8));
+    }
+    else
+    {
+      return (static_cast<uint16_t>(p[1]) |
+              (static_cast<uint16_t>(p[0]) << 8));
+    }
+  }
+
+
+  static uint32_t ReadUnsignedInteger32(const char* dicom,
+                                        bool littleEndian)
+  {
+    const uint8_t* p = reinterpret_cast<const uint8_t*>(dicom);
+
+    if (littleEndian)
+    {
+      return (static_cast<uint32_t>(p[0]) |
+              (static_cast<uint32_t>(p[1]) << 8) |
+              (static_cast<uint32_t>(p[2]) << 16) |
+              (static_cast<uint32_t>(p[3]) << 24));
+    }
+    else
+    {
+      return (static_cast<uint32_t>(p[3]) |
+              (static_cast<uint32_t>(p[2]) << 8) |
+              (static_cast<uint32_t>(p[1]) << 16) |
+              (static_cast<uint32_t>(p[0]) << 24));
+    }
+  }
+
+
+  static DicomTag ReadTag(const char* dicom,
+                          bool littleEndian)
+  {
+    return DicomTag(ReadUnsignedInteger16(dicom, littleEndian),
+                    ReadUnsignedInteger16(dicom + 2, littleEndian));
+  }
+
+
+  static bool IsShortExplicitTag(ValueRepresentation vr)
+  {
+    /**
+     * Are we in the case of Table 7.1-2? "Data Element with
+     * Explicit VR of AE, AS, AT, CS, DA, DS, DT, FL, FD, IS, LO,
+     * LT, PN, SH, SL, SS, ST, TM, UI, UL and US"
+     * http://dicom.nema.org/medical/dicom/current/output/chtml/part05/chapter_7.html#sect_7.1.2
+     **/
+    return (vr == ValueRepresentation_ApplicationEntity   /* AE */ ||
+            vr == ValueRepresentation_AgeString           /* AS */ ||
+            vr == ValueRepresentation_AttributeTag        /* AT */ ||
+            vr == ValueRepresentation_CodeString          /* CS */ ||
+            vr == ValueRepresentation_Date                /* DA */ ||
+            vr == ValueRepresentation_DecimalString       /* DS */ ||
+            vr == ValueRepresentation_DateTime            /* DT */ ||
+            vr == ValueRepresentation_FloatingPointSingle /* FL */ ||
+            vr == ValueRepresentation_FloatingPointDouble /* FD */ ||
+            vr == ValueRepresentation_IntegerString       /* IS */ ||
+            vr == ValueRepresentation_LongString          /* LO */ ||
+            vr == ValueRepresentation_LongText            /* LT */ ||
+            vr == ValueRepresentation_PersonName          /* PN */ ||
+            vr == ValueRepresentation_ShortString         /* SH */ ||
+            vr == ValueRepresentation_SignedLong          /* SL */ ||
+            vr == ValueRepresentation_SignedShort         /* SS */ ||
+            vr == ValueRepresentation_ShortText           /* ST */ ||
+            vr == ValueRepresentation_Time                /* TM */ ||
+            vr == ValueRepresentation_UniqueIdentifier    /* UI */ ||
+            vr == ValueRepresentation_UnsignedLong        /* UL */ ||
+            vr == ValueRepresentation_UnsignedShort       /* US */);
+  }
+
+
+  static void PrintBlock(const std::string& block)
+  {
+    for (size_t i = 0; i < block.size(); i++)
+    {
+      printf("%02x ", static_cast<uint8_t>(block[i]));
+      if (i % 16 == 15)
+        printf("\n");
+    }
+    printf("\n");
+  }
+    
+
+
+  bool DicomStreamReader::IsLittleEndian() const
+  {
+    return (transferSyntax_ != DicomTransferSyntax_BigEndianExplicit);
+  }
+
+
+  void DicomStreamReader::HandlePreamble(IVisitor& visitor,
+                                         const std::string& block)
+  {
+    //printf("PREAMBLE:\n");
+    //PrintBlock(block);
+
+    assert(block.size() == 144u);
+    assert(reader_.GetProcessedBytes() == 144u);
+
+    /**
+     * The "DICOM file meta information" is always encoded using
+     * "Explicit VR Little Endian Transfer Syntax"
+     * http://dicom.nema.org/medical/dicom/current/output/chtml/part10/chapter_7.html
+     **/
+    if (block[128] != 'D' ||
+        block[129] != 'I' ||
+        block[130] != 'C' ||
+        block[131] != 'M' ||
+        ReadTag(block.c_str() + 132, true) != DicomTag(0x0002, 0x0000) ||
+        block[136] != 'U' ||
+        block[137] != 'L' ||
+        ReadUnsignedInteger16(block.c_str() + 138, true) != 4)
+    {
+      throw OrthancException(ErrorCode_BadFileFormat);
+    }
+
+    uint32_t length = ReadUnsignedInteger32(block.c_str() + 140, true);
+
+    reader_.Schedule(length);
+    state_ = State_MetaHeader;
+  }
+
+    
+  void DicomStreamReader::HandleMetaHeader(IVisitor& visitor,
+                                           const std::string& block)
+  {
+    //printf("META-HEADER:\n");
+    //PrintBlock(block);
+
+    size_t pos = 0;
+    const char* p = block.c_str();
+
+    bool hasTransferSyntax = false;
+
+    while (pos + 8 <= block.size())
+    {
+      DicomTag tag = ReadTag(p + pos, true);
+        
+      ValueRepresentation vr = StringToValueRepresentation(std::string(p + pos + 4, 2), true);
+
+      if (IsShortExplicitTag(vr))
+      {
+        uint16_t length = ReadUnsignedInteger16(p + pos + 6, true);
+
+        std::string value;
+        value.assign(p + pos + 8, length);
+
+        if (tag.GetGroup() == 0x0002)
+        {
+          visitor.VisitMetaHeaderTag(tag, vr, value);
+        }                  
+
+        if (tag == DICOM_TAG_TRANSFER_SYNTAX_UID)
+        {
+          // Remove possible padding byte
+          if (!value.empty() &&
+              value[value.size() - 1] == '\0')
+          {
+            value.resize(value.size() - 1);
+          }
+            
+          if (LookupTransferSyntax(transferSyntax_, value))
+          {
+            hasTransferSyntax = true;
+          }
+          else
+          {
+            throw OrthancException(ErrorCode_NotImplemented, "Unsupported transfer syntax: " + value);
+          }
+        }
+          
+        pos += length + 8;
+      }
+      else if (pos + 12 <= block.size())
+      {
+        uint16_t reserved = ReadUnsignedInteger16(p + pos + 6, true);
+        if (reserved != 0)
+        {
+          break;
+        }
+          
+        uint32_t length = ReadUnsignedInteger32(p + pos + 8, true);
+
+        std::string value;
+        value.assign(p + pos + 12, length);
+
+        if (tag.GetGroup() == 0x0002)
+        {
+          visitor.VisitMetaHeaderTag(tag, vr, value);
+        }                  
+          
+        pos += length + 12;
+      }
+    }
+
+    if (pos != block.size())
+    {
+      throw OrthancException(ErrorCode_BadFileFormat);
+    }
+
+    if (!hasTransferSyntax)
+    {
+      throw OrthancException(ErrorCode_BadFileFormat, "DICOM file meta-header without transfer syntax UID");
+    }
+
+    visitor.VisitTransferSyntax(transferSyntax_);
+
+    reader_.Schedule(8);
+    state_ = State_DatasetTag;
+  }
+    
+
+  void DicomStreamReader::HandleDatasetTag(const std::string& block,
+                                           const DicomTag& untilTag)
+  {
+    static const DicomTag DICOM_TAG_SEQUENCE_ITEM(0xfffe, 0xe000);
+    static const DicomTag DICOM_TAG_SEQUENCE_DELIMITATION_ITEM(0xfffe, 0xe00d);
+    static const DicomTag DICOM_TAG_SEQUENCE_DELIMITATION_SEQUENCE(0xfffe, 0xe0dd);
+
+    assert(block.size() == 8u);
+
+    const bool littleEndian = IsLittleEndian();
+    DicomTag tag = ReadTag(block.c_str(), littleEndian);
+
+    if (sequenceDepth_ == 0 &&
+        tag >= untilTag)
+    {
+      state_ = State_Done;
+      return;
+    }
+      
+    if (tag == DICOM_TAG_SEQUENCE_ITEM ||
+        tag == DICOM_TAG_SEQUENCE_DELIMITATION_ITEM ||
+        tag == DICOM_TAG_SEQUENCE_DELIMITATION_SEQUENCE)
+    {
+      //printf("SEQUENCE TAG:\n");
+      //PrintBlock(block);
+
+      // The special sequence items are encoded like "Implicit VR"
+      uint32_t length = ReadUnsignedInteger32(block.c_str() + 4, littleEndian);
+
+      if (tag == DICOM_TAG_SEQUENCE_ITEM)
+      {
+        for (unsigned int i = 0; i <= sequenceDepth_; i++)
+          printf("  ");
+        if (length == 0xffffffffu)
+        {
+          // Undefined length: Need to loop over the tags of the nested dataset
+          printf("...next dataset in sequence...\n");
+          reader_.Schedule(8);
+          state_ = State_DatasetTag;
+        }
+        else
+        {
+          // Explicit length: Can skip the full sequence at once
+          printf("...next dataset in sequence... %u bytes\n", length);
+          reader_.Schedule(length);
+          state_ = State_DatasetValue;
+        }
+      }
+      else if (tag == DICOM_TAG_SEQUENCE_DELIMITATION_ITEM ||
+               tag == DICOM_TAG_SEQUENCE_DELIMITATION_SEQUENCE)
+      {
+        if (length != 0 ||
+            sequenceDepth_ == 0)
+        {
+          throw OrthancException(ErrorCode_BadFileFormat);
+        }
+
+        if (tag == DICOM_TAG_SEQUENCE_DELIMITATION_SEQUENCE)
+        {
+          for (unsigned int i = 0; i < sequenceDepth_; i++)
+            printf("  ");
+          printf("...leaving sequence...\n");
+
+          sequenceDepth_ --;
+        }
+        else
+        {
+          if (sequenceDepth_ == 0)
+          {
+            throw OrthancException(ErrorCode_BadFileFormat);
+          }
+        }
+
+        reader_.Schedule(8);
+        state_ = State_DatasetTag;          
+      }
+      else
+      {
+        throw OrthancException(ErrorCode_InternalError);
+      }
+    }
+    else
+    {
+      //printf("DATASET TAG:\n");
+      //PrintBlock(block);
+
+      previousTag_ = tag;
+          
+      ValueRepresentation vr = ValueRepresentation_Unknown;
+        
+      if (transferSyntax_ == DicomTransferSyntax_LittleEndianImplicit)
+      {
+        if (sequenceDepth_ == 0)
+        {
+          danglingTag_ = tag;
+          danglingVR_ = vr;
+        }
+
+        uint32_t length = ReadUnsignedInteger32(block.c_str() + 4, true /* little endian */);
+        HandleDatasetExplicitLength(length);
+      }
+      else
+      {
+        // This in an explicit transfer syntax
+
+        vr = StringToValueRepresentation(
+          std::string(block.c_str() + 4, 2), false /* ignore unknown VR */);
+
+        if (vr != ValueRepresentation_Sequence &&
+            sequenceDepth_ > 0)
+        {
+          for (unsigned int i = 0; i <= sequenceDepth_; i++)
+            printf("  ");
+          printf("%s\n", tag.Format().c_str());
+        }
+          
+        if (vr == ValueRepresentation_Sequence)
+        {
+          for (unsigned int i = 0; i <= sequenceDepth_; i++)
+            printf("  ");
+          printf("...entering sequence... %s\n", tag.Format().c_str());
+          sequenceDepth_ ++;
+          reader_.Schedule(4);
+          state_ = State_SequenceExplicitLength;
+        }
+        else if (IsShortExplicitTag(vr))
+        {
+          uint16_t length = ReadUnsignedInteger16(block.c_str() + 6, littleEndian);
+
+          reader_.Schedule(length);
+          state_ = State_DatasetValue;
+        }
+        else
+        {
+          uint16_t reserved = ReadUnsignedInteger16(block.c_str() + 6, littleEndian);
+          if (reserved != 0)
+          {
+            throw OrthancException(ErrorCode_BadFileFormat);
+          }
+
+          reader_.Schedule(4);
+          state_ = State_DatasetExplicitLength;
+        }
+
+        if (sequenceDepth_ == 0)
+        {
+          danglingTag_ = tag;
+          danglingVR_ = vr;
+        }
+      }
+    }
+  }
+
+
+  void DicomStreamReader::HandleDatasetExplicitLength(uint32_t length)
+  {
+    if (length == 0xffffffffu)
+    {
+      /**
+       * This is the case of pixel data with compressed transfer
+       * syntaxes. Schedule the reading of the first tag of the
+       * nested dataset.
+       * http://dicom.nema.org/medical/dicom/current/output/chtml/part05/sect_7.5.html
+       **/
+
+      for (unsigned int i = 0; i <= sequenceDepth_; i++)
+        printf("  ");
+      printf("...entering sequence... %s\n", previousTag_.Format().c_str());
+        
+      state_ = State_DatasetTag;
+      reader_.Schedule(8);
+      sequenceDepth_ ++;
+    }
+    else
+    {
+      reader_.Schedule(length);
+      state_ = State_DatasetValue;
+    }
+  }    
+
+    
+  void DicomStreamReader::HandleDatasetExplicitLength(const std::string& block)
+  {
+    //printf("DATASET TAG LENGTH:\n");
+    //PrintBlock(block);
+
+    assert(block.size() == 4);
+
+    uint32_t length = ReadUnsignedInteger32(block.c_str(), IsLittleEndian());
+    HandleDatasetExplicitLength(length);
+  }
+    
+
+  void DicomStreamReader::HandleSequenceExplicitLength(const std::string& block)
+  {
+    //printf("DATASET TAG LENGTH:\n");
+    //PrintBlock(block);
+
+    assert(block.size() == 4);
+
+    uint32_t length = ReadUnsignedInteger32(block.c_str(), IsLittleEndian());
+    if (length == 0xffffffffu)
+    {
+      state_ = State_DatasetTag;
+      reader_.Schedule(8);
+    }
+    else
+    {
+      for (unsigned int i = 0; i <= sequenceDepth_; i++)
+        printf("  ");
+      printf("...skipping sequence thanks to explicit length... %d\n", length);
+
+      reader_.Schedule(length);
+      state_ = State_SequenceExplicitValue;
+    }
+  }
+
+    
+  void DicomStreamReader::HandleSequenceExplicitValue()
+  {
+    if (sequenceDepth_ == 0)
+    {
+      throw OrthancException(ErrorCode_InternalError);
+    }
+
+    sequenceDepth_ --;
+
+    state_ = State_DatasetTag;
+    reader_.Schedule(8);
+  }
+
+
+  void DicomStreamReader::HandleDatasetValue(IVisitor& visitor,
+                                             const std::string& block)
+  {
+    if (sequenceDepth_ == 0)
+    {
+      bool c;
+        
+      if (!block.empty() &&
+          (block[block.size() - 1] == ' ' ||
+           block[block.size() - 1] == '\0') &&
+          (danglingVR_ == ValueRepresentation_ApplicationEntity ||
+           danglingVR_ == ValueRepresentation_AgeString ||
+           danglingVR_ == ValueRepresentation_CodeString ||
+           danglingVR_ == ValueRepresentation_DecimalString ||
+           danglingVR_ == ValueRepresentation_IntegerString ||
+           danglingVR_ == ValueRepresentation_LongString ||
+           danglingVR_ == ValueRepresentation_LongText ||
+           danglingVR_ == ValueRepresentation_PersonName ||
+           danglingVR_ == ValueRepresentation_ShortString ||
+           danglingVR_ == ValueRepresentation_ShortText ||
+           danglingVR_ == ValueRepresentation_UniqueIdentifier ||
+           danglingVR_ == ValueRepresentation_UnlimitedText))
+      {
+        std::string s(block.begin(), block.end() - 1);
+        c = visitor.VisitDatasetTag(danglingTag_, danglingVR_, s, IsLittleEndian());
+      }
+      else
+      {
+        c = visitor.VisitDatasetTag(danglingTag_, danglingVR_, block, IsLittleEndian());
+      }
+        
+      if (!c)
+      {
+        state_ = State_Done;
+        return;
+      }
+    }
+
+    reader_.Schedule(8);
+    state_ = State_DatasetTag;
+  }
+    
+    
+  DicomStreamReader::DicomStreamReader(std::istream& stream) :
+    reader_(stream),
+    state_(State_Preamble),
+    transferSyntax_(DicomTransferSyntax_LittleEndianImplicit),  // Dummy
+    previousTag_(0x0000, 0x0000),  // Dummy
+    danglingTag_(0x0000, 0x0000),  // Dummy
+    danglingVR_(ValueRepresentation_Unknown),  // Dummy
+    sequenceDepth_(0)
+  {
+    reader_.Schedule(128 /* empty header */ +
+                     4 /* "DICM" magic value */ +
+                     4 /* (0x0002, 0x0000) tag */ +
+                     2 /* value representation of (0x0002, 0x0000) == "UL" */ +
+                     2 /* length of "UL" value == 4 */ +
+                     4 /* actual length of the meta-header */);
+  }
+
+  
+  void DicomStreamReader::Consume(IVisitor& visitor,
+                                  const DicomTag& untilTag)
+  {
+    while (state_ != State_Done)
+    {
+      std::string block;
+      if (reader_.Read(block))
+      {
+        switch (state_)
+        {
+          case State_Preamble:
+            HandlePreamble(visitor, block);
+            break;
+
+          case State_MetaHeader:
+            HandleMetaHeader(visitor, block);
+            break;
+
+          case State_DatasetTag:
+            HandleDatasetTag(block, untilTag);
+            break;
+
+          case State_DatasetExplicitLength:
+            HandleDatasetExplicitLength(block);
+            break;
+
+          case State_SequenceExplicitLength:
+            HandleSequenceExplicitLength(block);
+            break;
+
+          case State_SequenceExplicitValue:
+            HandleSequenceExplicitValue();
+            break;
+
+          case State_DatasetValue:
+            HandleDatasetValue(visitor, block);
+            break;
+
+          default:
+            throw OrthancException(ErrorCode_InternalError);
+        }
+      }
+      else
+      {
+        return;  // No more data in the stream
+      }
+    }
+  }
+
+
+  void DicomStreamReader::Consume(IVisitor& visitor)
+  {
+    DicomTag untilTag(0xffff, 0xffff);
+    Consume(visitor, untilTag);
+  }
+}