--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/OrthancFramework/Sources/DicomParsing/DicomWebJsonVisitor.cpp	Wed Jun 10 20:30:34 2020 +0200
@@ -0,0 +1,673 @@
+/**
+ * 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 General Public License as
+ * published by the Free Software Foundation, either version 3 of the
+ * License, or (at your option) any later version.
+ *
+ * In addition, as a special exception, the copyright holders of this
+ * program give permission to link the code of its release with the
+ * OpenSSL project's "OpenSSL" library (or with modified versions of it
+ * that use the same license as the "OpenSSL" library), and distribute
+ * the linked executables. You must obey the GNU General Public License
+ * in all respects for all of the code used other than "OpenSSL". If you
+ * modify file(s) with this exception, you may extend this exception to
+ * your version of the file(s), but you are not obligated to do so. If
+ * you do not wish to do so, delete this exception statement from your
+ * version. If you delete this exception statement from all source files
+ * in the program, then also delete it here.
+ * 
+ * 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
+ * General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see <http://www.gnu.org/licenses/>.
+ **/
+
+
+#include "../PrecompiledHeaders.h"
+#include "DicomWebJsonVisitor.h"
+
+#include "../OrthancException.h"
+#include "../Toolbox.h"
+#include "FromDcmtkBridge.h"
+
+#include <boost/math/special_functions/round.hpp>
+#include <boost/lexical_cast.hpp>
+
+
+static const char* const KEY_ALPHABETIC = "Alphabetic";
+static const char* const KEY_IDEOGRAPHIC = "Ideographic";
+static const char* const KEY_PHONETIC = "Phonetic";
+static const char* const KEY_BULK_DATA_URI = "BulkDataURI";
+static const char* const KEY_INLINE_BINARY = "InlineBinary";
+static const char* const KEY_SQ = "SQ";
+static const char* const KEY_TAG = "tag";
+static const char* const KEY_VALUE = "Value";
+static const char* const KEY_VR = "vr";
+
+
+namespace Orthanc
+{
+#if ORTHANC_ENABLE_PUGIXML == 1
+  static void DecomposeXmlPersonName(pugi::xml_node& target,
+                                     const std::string& source)
+  {
+    std::vector<std::string> tokens;
+    Toolbox::TokenizeString(tokens, source, '^');
+
+    if (tokens.size() >= 1)
+    {
+      target.append_child("FamilyName").text() = tokens[0].c_str();
+    }
+            
+    if (tokens.size() >= 2)
+    {
+      target.append_child("GivenName").text() = tokens[1].c_str();
+    }
+            
+    if (tokens.size() >= 3)
+    {
+      target.append_child("MiddleName").text() = tokens[2].c_str();
+    }
+            
+    if (tokens.size() >= 4)
+    {
+      target.append_child("NamePrefix").text() = tokens[3].c_str();
+    }
+            
+    if (tokens.size() >= 5)
+    {
+      target.append_child("NameSuffix").text() = tokens[4].c_str();
+    }
+  }
+  
+  static void ExploreXmlDataset(pugi::xml_node& target,
+                                const Json::Value& source)
+  {
+    // http://dicom.nema.org/medical/dicom/current/output/chtml/part18/sect_F.3.html#table_F.3.1-1
+    assert(source.type() == Json::objectValue);
+
+    Json::Value::Members members = source.getMemberNames();
+    for (size_t i = 0; i < members.size(); i++)
+    {
+      const DicomTag tag = FromDcmtkBridge::ParseTag(members[i]);
+      const Json::Value& content = source[members[i]];
+
+      assert(content.type() == Json::objectValue &&
+             content.isMember(KEY_VR) &&
+             content[KEY_VR].type() == Json::stringValue);
+      const std::string vr = content[KEY_VR].asString();
+
+      const std::string keyword = FromDcmtkBridge::GetTagName(tag, "");
+    
+      pugi::xml_node node = target.append_child("DicomAttribute");
+      node.append_attribute(KEY_TAG).set_value(members[i].c_str());
+      node.append_attribute(KEY_VR).set_value(vr.c_str());
+
+      if (keyword != std::string(DcmTag_ERROR_TagName))
+      {
+        node.append_attribute("keyword").set_value(keyword.c_str());
+      }   
+
+      if (content.isMember(KEY_VALUE))
+      {
+        assert(content[KEY_VALUE].type() == Json::arrayValue);
+        
+        for (Json::Value::ArrayIndex j = 0; j < content[KEY_VALUE].size(); j++)
+        {
+          std::string number = boost::lexical_cast<std::string>(j + 1);
+
+          if (vr == "SQ")
+          {
+            if (content[KEY_VALUE][j].type() == Json::objectValue)
+            {
+              pugi::xml_node child = node.append_child("Item");
+              child.append_attribute("number").set_value(number.c_str());
+              ExploreXmlDataset(child, content[KEY_VALUE][j]);
+            }
+          }
+          if (vr == "PN")
+          {
+            bool hasAlphabetic = (content[KEY_VALUE][j].isMember(KEY_ALPHABETIC) &&
+                                  content[KEY_VALUE][j][KEY_ALPHABETIC].type() == Json::stringValue);
+
+            bool hasIdeographic = (content[KEY_VALUE][j].isMember(KEY_IDEOGRAPHIC) &&
+                                   content[KEY_VALUE][j][KEY_IDEOGRAPHIC].type() == Json::stringValue);
+
+            bool hasPhonetic = (content[KEY_VALUE][j].isMember(KEY_PHONETIC) &&
+                                content[KEY_VALUE][j][KEY_PHONETIC].type() == Json::stringValue);
+
+            if (hasAlphabetic ||
+                hasIdeographic ||
+                hasPhonetic)
+            {
+              pugi::xml_node child = node.append_child("PersonName");
+              child.append_attribute("number").set_value(number.c_str());
+
+              if (hasAlphabetic)
+              {
+                pugi::xml_node name = child.append_child(KEY_ALPHABETIC);
+                DecomposeXmlPersonName(name, content[KEY_VALUE][j][KEY_ALPHABETIC].asString());
+              }
+
+              if (hasIdeographic)
+              {
+                pugi::xml_node name = child.append_child(KEY_IDEOGRAPHIC);
+                DecomposeXmlPersonName(name, content[KEY_VALUE][j][KEY_IDEOGRAPHIC].asString());
+              }
+
+              if (hasPhonetic)
+              {
+                pugi::xml_node name = child.append_child(KEY_PHONETIC);
+                DecomposeXmlPersonName(name, content[KEY_VALUE][j][KEY_PHONETIC].asString());
+              }
+            }
+          }
+          else
+          {
+            pugi::xml_node child = node.append_child("Value");
+            child.append_attribute("number").set_value(number.c_str());
+
+            switch (content[KEY_VALUE][j].type())
+            {
+              case Json::stringValue:
+                child.text() = content[KEY_VALUE][j].asCString();
+                break;
+
+              case Json::realValue:
+                child.text() = content[KEY_VALUE][j].asFloat();
+                break;
+
+              case Json::intValue:
+                child.text() = content[KEY_VALUE][j].asInt();
+                break;
+
+              case Json::uintValue:
+                child.text() = content[KEY_VALUE][j].asUInt();
+                break;
+
+              default:
+                break;
+            }
+          }
+        }
+      }
+      else if (content.isMember(KEY_BULK_DATA_URI) &&
+               content[KEY_BULK_DATA_URI].type() == Json::stringValue)
+      {
+        pugi::xml_node child = node.append_child("BulkData");
+        child.append_attribute("URI").set_value(content[KEY_BULK_DATA_URI].asCString());
+      }
+      else if (content.isMember(KEY_INLINE_BINARY) &&
+               content[KEY_INLINE_BINARY].type() == Json::stringValue)
+      {
+        pugi::xml_node child = node.append_child("InlineBinary");
+        child.text() = content[KEY_INLINE_BINARY].asCString();
+      }
+    }
+  }
+#endif
+
+
+#if ORTHANC_ENABLE_PUGIXML == 1
+  static void DicomWebJsonToXml(pugi::xml_document& target,
+                                const Json::Value& source)
+  {
+    pugi::xml_node root = target.append_child("NativeDicomModel");
+    root.append_attribute("xmlns").set_value("http://dicom.nema.org/PS3.19/models/NativeDICOM");
+    root.append_attribute("xsi:schemaLocation").set_value("http://dicom.nema.org/PS3.19/models/NativeDICOM");
+    root.append_attribute("xmlns:xsi").set_value("http://www.w3.org/2001/XMLSchema-instance");
+
+    ExploreXmlDataset(root, source);
+
+    pugi::xml_node decl = target.prepend_child(pugi::node_declaration);
+    decl.append_attribute("version").set_value("1.0");
+    decl.append_attribute("encoding").set_value("utf-8");
+  }
+#endif
+
+
+  std::string DicomWebJsonVisitor::FormatTag(const DicomTag& tag)
+  {
+    char buf[16];
+    sprintf(buf, "%04X%04X", tag.GetGroup(), tag.GetElement());
+    return std::string(buf);
+  }
+
+    
+  Json::Value& DicomWebJsonVisitor::CreateNode(const std::vector<DicomTag>& parentTags,
+                                               const std::vector<size_t>& parentIndexes,
+                                               const DicomTag& tag)
+  {
+    assert(parentTags.size() == parentIndexes.size());      
+
+    Json::Value* node = &result_;
+
+    for (size_t i = 0; i < parentTags.size(); i++)
+    {
+      std::string t = FormatTag(parentTags[i]);
+
+      if (!node->isMember(t))
+      {
+        Json::Value item = Json::objectValue;
+        item[KEY_VR] = KEY_SQ;
+        item[KEY_VALUE] = Json::arrayValue;
+        item[KEY_VALUE].append(Json::objectValue);
+        (*node) [t] = item;
+
+        node = &(*node)[t][KEY_VALUE][0];
+      }
+      else if ((*node)  [t].type() != Json::objectValue ||
+               !(*node) [t].isMember(KEY_VR) ||
+               (*node)  [t][KEY_VR].type() != Json::stringValue ||
+               (*node)  [t][KEY_VR].asString() != KEY_SQ ||
+               !(*node) [t].isMember(KEY_VALUE) ||
+               (*node)  [t][KEY_VALUE].type() != Json::arrayValue)
+      {
+        throw OrthancException(ErrorCode_InternalError);
+      }
+      else
+      {
+        size_t currentSize = (*node) [t][KEY_VALUE].size();
+
+        if (parentIndexes[i] < currentSize)
+        {
+          // The node already exists
+        }
+        else if (parentIndexes[i] == currentSize)
+        {
+          (*node) [t][KEY_VALUE].append(Json::objectValue);
+        }
+        else
+        {
+          throw OrthancException(ErrorCode_InternalError);
+        }
+          
+        node = &(*node) [t][KEY_VALUE][Json::ArrayIndex(parentIndexes[i])];
+      }
+    }
+
+    assert(node->type() == Json::objectValue);
+
+    std::string t = FormatTag(tag);
+    if (node->isMember(t))
+    {
+      throw OrthancException(ErrorCode_InternalError);
+    }
+    else
+    {
+      (*node) [t] = Json::objectValue;
+      return (*node) [t];
+    }
+  }
+
+    
+  Json::Value DicomWebJsonVisitor::FormatInteger(int64_t value)
+  {
+    if (value < 0)
+    {
+      return Json::Value(static_cast<int32_t>(value));
+    }
+    else
+    {
+      return Json::Value(static_cast<uint32_t>(value));
+    }
+  }
+
+    
+  Json::Value DicomWebJsonVisitor::FormatDouble(double value)
+  {
+    try
+    {
+      long long a = boost::math::llround<double>(value);
+
+      double d = fabs(value - static_cast<double>(a));
+
+      if (d <= std::numeric_limits<double>::epsilon() * 100.0)
+      {
+        return FormatInteger(a);
+      }
+      else
+      {
+        return Json::Value(value);
+      }
+    }
+    catch (boost::math::rounding_error&)
+    {
+      // Can occur if "long long" is too small to receive this value
+      // (e.g. infinity)
+      return Json::Value(value);
+    }
+  }
+
+
+#if ORTHANC_ENABLE_PUGIXML == 1
+  void DicomWebJsonVisitor::FormatXml(std::string& target) const
+  {
+    pugi::xml_document doc;
+    DicomWebJsonToXml(doc, result_);
+    Toolbox::XmlToString(target, doc);
+  }
+#endif
+
+
+  void DicomWebJsonVisitor::VisitEmptySequence(const std::vector<DicomTag>& parentTags,
+                                               const std::vector<size_t>& parentIndexes,
+                                               const DicomTag& tag)
+  {
+    if (tag.GetElement() != 0x0000)
+    {
+      Json::Value& node = CreateNode(parentTags, parentIndexes, tag);
+      node[KEY_VR] = EnumerationToString(ValueRepresentation_Sequence);
+    }
+  }
+  
+
+  void DicomWebJsonVisitor::VisitBinary(const std::vector<DicomTag>& parentTags,
+                                        const std::vector<size_t>& parentIndexes,
+                                        const DicomTag& tag,
+                                        ValueRepresentation vr,
+                                        const void* data,
+                                        size_t size)
+  {
+    assert(vr == ValueRepresentation_OtherByte ||
+           vr == ValueRepresentation_OtherDouble ||
+           vr == ValueRepresentation_OtherFloat ||
+           vr == ValueRepresentation_OtherLong ||
+           vr == ValueRepresentation_OtherWord ||
+           vr == ValueRepresentation_Unknown);
+
+    if (tag.GetElement() != 0x0000)
+    {
+      BinaryMode mode;
+      std::string bulkDataUri;
+        
+      if (formatter_ == NULL)
+      {
+        mode = BinaryMode_InlineBinary;
+      }
+      else
+      {
+        mode = formatter_->Format(bulkDataUri, parentTags, parentIndexes, tag, vr);
+      }
+
+      if (mode != BinaryMode_Ignore)
+      {
+        Json::Value& node = CreateNode(parentTags, parentIndexes, tag);
+        node[KEY_VR] = EnumerationToString(vr);
+
+        switch (mode)
+        {
+          case BinaryMode_BulkDataUri:
+            node[KEY_BULK_DATA_URI] = bulkDataUri;
+            break;
+
+          case BinaryMode_InlineBinary:
+          {
+            std::string tmp(static_cast<const char*>(data), size);
+          
+            std::string base64;
+            Toolbox::EncodeBase64(base64, tmp);
+
+            node[KEY_INLINE_BINARY] = base64;
+            break;
+          }
+
+          default:
+            throw OrthancException(ErrorCode_ParameterOutOfRange);
+        }
+      }
+    }
+  }
+
+
+  void DicomWebJsonVisitor::VisitIntegers(const std::vector<DicomTag>& parentTags,
+                                          const std::vector<size_t>& parentIndexes,
+                                          const DicomTag& tag,
+                                          ValueRepresentation vr,
+                                          const std::vector<int64_t>& values)
+  {
+    if (tag.GetElement() != 0x0000 &&
+        vr != ValueRepresentation_NotSupported)
+    {
+      Json::Value& node = CreateNode(parentTags, parentIndexes, tag);
+      node[KEY_VR] = EnumerationToString(vr);
+
+      if (!values.empty())
+      {
+        Json::Value content = Json::arrayValue;
+        for (size_t i = 0; i < values.size(); i++)
+        {
+          content.append(FormatInteger(values[i]));
+        }
+
+        node[KEY_VALUE] = content;
+      }
+    }
+  }
+
+  void DicomWebJsonVisitor::VisitDoubles(const std::vector<DicomTag>& parentTags,
+                                         const std::vector<size_t>& parentIndexes,
+                                         const DicomTag& tag,
+                                         ValueRepresentation vr,
+                                         const std::vector<double>& values)
+  {
+    if (tag.GetElement() != 0x0000 &&
+        vr != ValueRepresentation_NotSupported)
+    {
+      Json::Value& node = CreateNode(parentTags, parentIndexes, tag);
+      node[KEY_VR] = EnumerationToString(vr);
+
+      if (!values.empty())
+      {
+        Json::Value content = Json::arrayValue;
+        for (size_t i = 0; i < values.size(); i++)
+        {
+          content.append(FormatDouble(values[i]));
+        }
+          
+        node[KEY_VALUE] = content;
+      }
+    }
+  }
+
+  
+  void DicomWebJsonVisitor::VisitAttributes(const std::vector<DicomTag>& parentTags,
+                                            const std::vector<size_t>& parentIndexes,
+                                            const DicomTag& tag,
+                                            const std::vector<DicomTag>& values)
+  {
+    if (tag.GetElement() != 0x0000)
+    {
+      Json::Value& node = CreateNode(parentTags, parentIndexes, tag);
+      node[KEY_VR] = EnumerationToString(ValueRepresentation_AttributeTag);
+
+      if (!values.empty())
+      {
+        Json::Value content = Json::arrayValue;
+        for (size_t i = 0; i < values.size(); i++)
+        {
+          content.append(FormatTag(values[i]));
+        }
+          
+        node[KEY_VALUE] = content;
+      }
+    }
+  }
+
+  
+  ITagVisitor::Action
+  DicomWebJsonVisitor::VisitString(std::string& newValue,
+                                   const std::vector<DicomTag>& parentTags,
+                                   const std::vector<size_t>& parentIndexes,
+                                   const DicomTag& tag,
+                                   ValueRepresentation vr,
+                                   const std::string& value)
+  {
+    if (tag.GetElement() == 0x0000 ||
+        vr == ValueRepresentation_NotSupported)
+    {
+      return Action_None;
+    }
+    else
+    {
+      Json::Value& node = CreateNode(parentTags, parentIndexes, tag);
+      node[KEY_VR] = EnumerationToString(vr);
+
+#if 0
+      /**
+       * TODO - The JSON file has an UTF-8 encoding, thus DCMTK
+       * replaces the specific character set with "ISO_IR 192"
+       * (UNICODE UTF-8). On Google Cloud Healthcare, however, the
+       * source encoding is reported, which seems more logical. We
+       * thus choose the Google convention. Enabling this block will
+       * mimic the DCMTK behavior.
+       **/
+      if (tag == DICOM_TAG_SPECIFIC_CHARACTER_SET)
+      {
+        node[KEY_VALUE].append("ISO_IR 192");
+      }
+      else
+#endif
+      {
+        std::string truncated;
+        
+        if (!value.empty() &&
+            value[value.size() - 1] == '\0')
+        {
+          truncated = value.substr(0, value.size() - 1);
+        }
+        else
+        {
+          truncated = value;
+        }
+
+        if (!truncated.empty())
+        {
+          std::vector<std::string> tokens;
+          Toolbox::TokenizeString(tokens, truncated, '\\');
+
+          if (tag == DICOM_TAG_SPECIFIC_CHARACTER_SET &&
+              tokens.size() > 1 &&
+              tokens[0].empty())
+          {
+            // Specific character set with code extension: Remove the
+            // first element from the vector of encodings
+            tokens.erase(tokens.begin());
+          }
+
+          node[KEY_VALUE] = Json::arrayValue;
+          for (size_t i = 0; i < tokens.size(); i++)
+          {
+            try
+            {
+              switch (vr)
+              {
+                case ValueRepresentation_PersonName:
+                {
+                  Json::Value value = Json::objectValue;
+                  if (!tokens[i].empty())
+                  {
+                    std::vector<std::string> components;
+                    Toolbox::TokenizeString(components, tokens[i], '=');
+
+                    if (components.size() >= 1)
+                    {
+                      value[KEY_ALPHABETIC] = components[0];
+                    }
+
+                    if (components.size() >= 2)
+                    {
+                      value[KEY_IDEOGRAPHIC] = components[1];
+                    }
+
+                    if (components.size() >= 3)
+                    {
+                      value[KEY_PHONETIC] = components[2];
+                    }
+                  }
+                  
+                  node[KEY_VALUE].append(value);
+                  break;
+                }
+                  
+                case ValueRepresentation_IntegerString:
+                {
+                  /**
+                   * The calls to "StripSpaces()" below fix the
+                   * issue reported by Rana Asim Wajid on 2019-06-05
+                   * ("Error Exception while invoking plugin service
+                   * 32: Bad file format"):
+                   * https://groups.google.com/d/msg/orthanc-users/T32FovWPcCE/-hKFbfRJBgAJ
+                   **/
+
+                  std::string t = Orthanc::Toolbox::StripSpaces(tokens[i]);
+                  if (t.empty())
+                  {
+                    node[KEY_VALUE].append(Json::nullValue);
+                  }
+                  else
+                  {
+                    int64_t value = boost::lexical_cast<int64_t>(t);
+                    node[KEY_VALUE].append(FormatInteger(value));
+                  }
+                 
+                  break;
+                }
+              
+                case ValueRepresentation_DecimalString:
+                {
+                  std::string t = Orthanc::Toolbox::StripSpaces(tokens[i]);
+                  if (t.empty())
+                  {
+                    node[KEY_VALUE].append(Json::nullValue);
+                  }
+                  else
+                  {
+                    double value = boost::lexical_cast<double>(t);
+                    node[KEY_VALUE].append(FormatDouble(value));
+                  }
+
+                  break;
+                }
+
+                default:
+                  if (tokens[i].empty())
+                  {
+                    node[KEY_VALUE].append(Json::nullValue);
+                  }
+                  else
+                  {
+                    node[KEY_VALUE].append(tokens[i]);
+                  }
+                  
+                  break;
+              }
+            }
+            catch (boost::bad_lexical_cast&)
+            {
+              std::string tmp;
+              if (value.size() < 64 &&
+                  Toolbox::IsAsciiString(value))
+              {
+                tmp = ": " + value;
+              }
+              
+              LOG(WARNING) << "Ignoring DICOM tag (" << tag.Format()
+                           << ") with invalid content for VR " << EnumerationToString(vr) << tmp;
+            }
+          }
+        }
+      }
+    }
+      
+    return Action_None;
+  }
+}