diff Core/DicomFormat/DicomMap.cpp @ 2007:655489d9165d

DicomMap::ParseDicomMetaInformation()
author Sebastien Jodogne <s.jodogne@gmail.com>
date Thu, 09 Jun 2016 15:46:33 +0200
parents b1291df2f780
children dc82c754dcaa
line wrap: on
line diff
--- a/Core/DicomFormat/DicomMap.cpp	Thu Jun 09 14:48:40 2016 +0200
+++ b/Core/DicomFormat/DicomMap.cpp	Thu Jun 09 15:46:33 2016 +0200
@@ -36,6 +36,7 @@
 #include <stdio.h>
 #include <memory>
 #include "DicomArray.h"
+#include "../Endianness.h"
 #include "../OrthancException.h"
 
 
@@ -292,7 +293,7 @@
 
     for (size_t i = 0; i < count; i++)
     {
-      result.SetValue(tags[i], "");
+      result.SetValue(tags[i], "", false);
     }
   }
 
@@ -304,8 +305,8 @@
   void DicomMap::SetupFindStudyTemplate(DicomMap& result)
   {
     SetupFindTemplate(result, studyTags, sizeof(studyTags) / sizeof(DicomTag));
-    result.SetValue(DICOM_TAG_ACCESSION_NUMBER, "");
-    result.SetValue(DICOM_TAG_PATIENT_ID, "");
+    result.SetValue(DICOM_TAG_ACCESSION_NUMBER, "", false);
+    result.SetValue(DICOM_TAG_PATIENT_ID, "", false);
 
     // These main DICOM tags are only indirectly related to the
     // General Study Module, remove them
@@ -317,9 +318,9 @@
   void DicomMap::SetupFindSeriesTemplate(DicomMap& result)
   {
     SetupFindTemplate(result, seriesTags, sizeof(seriesTags) / sizeof(DicomTag));
-    result.SetValue(DICOM_TAG_ACCESSION_NUMBER, "");
-    result.SetValue(DICOM_TAG_PATIENT_ID, "");
-    result.SetValue(DICOM_TAG_STUDY_INSTANCE_UID, "");
+    result.SetValue(DICOM_TAG_ACCESSION_NUMBER, "", false);
+    result.SetValue(DICOM_TAG_PATIENT_ID, "", false);
+    result.SetValue(DICOM_TAG_STUDY_INSTANCE_UID, "", false);
 
     // These tags are considered as "main" by Orthanc, but are not in the Series module
     result.Remove(DicomTag(0x0008, 0x0070));  // Manufacturer
@@ -339,10 +340,10 @@
   void DicomMap::SetupFindInstanceTemplate(DicomMap& result)
   {
     SetupFindTemplate(result, instanceTags, sizeof(instanceTags) / sizeof(DicomTag));
-    result.SetValue(DICOM_TAG_ACCESSION_NUMBER, "");
-    result.SetValue(DICOM_TAG_PATIENT_ID, "");
-    result.SetValue(DICOM_TAG_STUDY_INSTANCE_UID, "");
-    result.SetValue(DICOM_TAG_SERIES_INSTANCE_UID, "");
+    result.SetValue(DICOM_TAG_ACCESSION_NUMBER, "", false);
+    result.SetValue(DICOM_TAG_PATIENT_ID, "", false);
+    result.SetValue(DICOM_TAG_STUDY_INSTANCE_UID, "", false);
+    result.SetValue(DICOM_TAG_SERIES_INSTANCE_UID, "", false);
   }
 
 
@@ -479,4 +480,312 @@
       tags.insert(it->first);
     }
   }
+
+
+  static uint16_t ReadUnsignedInteger16(const char* dicom)
+  {
+    return le16toh(*reinterpret_cast<const uint16_t*>(dicom));
+  }
+
+
+  static uint32_t ReadUnsignedInteger32(const char* dicom)
+  {
+    return le32toh(*reinterpret_cast<const uint32_t*>(dicom));
+  }
+
+
+  static bool ValidateTag(const ValueRepresentation& vr,
+                          const std::string& value)
+  {
+    switch (vr)
+    {
+      case ValueRepresentation_ApplicationEntity:
+        return value.size() <= 16;
+
+      case ValueRepresentation_AgeString:
+        return (value.size() == 4 &&
+                isdigit(value[0]) &&
+                isdigit(value[1]) &&
+                isdigit(value[2]) &&
+                (value[3] == 'D' || value[3] == 'W' || value[3] == 'M' || value[3] == 'Y'));
+
+      case ValueRepresentation_AttributeTag:
+        return value.size() == 4;
+
+      case ValueRepresentation_CodeString:
+        return value.size() <= 16;
+
+      case ValueRepresentation_Date:
+        return value.size() <= 18;
+
+      case ValueRepresentation_DecimalString:
+        return value.size() <= 16;
+
+      case ValueRepresentation_DateTime:
+        return value.size() <= 54;
+
+      case ValueRepresentation_FloatingPointSingle:
+        return value.size() == 4;
+
+      case ValueRepresentation_FloatingPointDouble:
+        return value.size() == 8;
+
+      case ValueRepresentation_IntegerString:
+        return value.size() <= 12;
+
+      case ValueRepresentation_LongString:
+        return value.size() <= 64;
+
+      case ValueRepresentation_LongText:
+        return value.size() <= 10240;
+
+      case ValueRepresentation_OtherByte:
+        return true;
+      
+      case ValueRepresentation_OtherDouble:
+        return value.size() <= static_cast<size_t>((1llu << 32) - 8);
+
+      case ValueRepresentation_OtherFloat:
+        return value.size() <= static_cast<size_t>((1llu << 32) - 4);
+
+      case ValueRepresentation_OtherLong:
+        return true;
+
+      case ValueRepresentation_OtherWord:
+        return true;
+
+      case ValueRepresentation_PersonName:
+        return true;
+
+      case ValueRepresentation_ShortString:
+        return value.size() <= 16;
+
+      case ValueRepresentation_SignedLong:
+        return value.size() == 4;
+
+      case ValueRepresentation_Sequence:
+        return true;
+
+      case ValueRepresentation_SignedShort:
+        return value.size() == 2;
+
+      case ValueRepresentation_ShortText:
+        return value.size() <= 1024;
+
+      case ValueRepresentation_Time:
+        return value.size() <= 28;
+
+      case ValueRepresentation_UnlimitedCharacters:
+        return value.size() <= static_cast<size_t>((1llu << 32) - 2);
+
+      case ValueRepresentation_UniqueIdentifier:
+        return value.size() <= 64;
+
+      case ValueRepresentation_UnsignedLong:
+        return value.size() == 4;
+
+      case ValueRepresentation_Unknown:
+        return true;
+
+      case ValueRepresentation_UniversalResource:
+        return value.size() <= static_cast<size_t>((1llu << 32) - 2);
+
+      case ValueRepresentation_UnsignedShort:
+        return value.size() == 2;
+
+      case ValueRepresentation_UnlimitedText:
+        return value.size() <= static_cast<size_t>((1llu << 32) - 2);
+
+      default:
+        // Assume unsupported tags are OK
+        return true;
+    }
+  }
+
+
+  static void RemoveTagPadding(std::string& value,
+                               const ValueRepresentation& vr)
+  {
+    /**
+     * Remove padding from character strings, if need be. For the time
+     * being, only the UI VR is supported.
+     * http://dicom.nema.org/medical/dicom/current/output/chtml/part05/sect_6.2.html
+     **/
+
+    switch (vr)
+    {
+      case ValueRepresentation_UniqueIdentifier:
+      {
+        /**
+         * "Values with a VR of UI shall be padded with a single
+         * trailing NULL (00H) character when necessary to achieve even
+         * length."
+         **/
+
+        if (!value.empty() &&
+            value[value.size() - 1] == '\0')
+        {
+          value.resize(value.size() - 1);
+        }
+
+        break;
+      }
+
+      /**
+       * TODO implement other VR
+       **/
+
+      default:
+        // No padding is applicable to this VR
+        break;
+    }
+  }
+
+
+  static bool ReadNextTag(DicomTag& tag,
+                          ValueRepresentation& vr,
+                          std::string& value,
+                          const char* dicom,
+                          size_t size,
+                          size_t& position)
+  {
+    /**
+     * http://dicom.nema.org/medical/dicom/current/output/chtml/part05/chapter_7.html#sect_7.1.2
+     * This function reads a data element with Explicit VR encoded using Little-Endian.
+     **/
+
+    if (position + 6 > size)
+    {
+      return false;
+    }
+
+    tag = DicomTag(ReadUnsignedInteger16(dicom + position),
+                   ReadUnsignedInteger16(dicom + position + 2));
+
+    vr = StringToValueRepresentation(std::string(dicom + position + 4, 2), true);
+    if (vr == ValueRepresentation_NotSupported)
+    {
+      return false;
+    }
+
+    if (vr == ValueRepresentation_OtherByte ||
+        vr == ValueRepresentation_OtherDouble ||
+        vr == ValueRepresentation_OtherFloat ||
+        vr == ValueRepresentation_OtherLong ||
+        vr == ValueRepresentation_OtherWord ||
+        vr == ValueRepresentation_Sequence ||
+        vr == ValueRepresentation_UnlimitedCharacters ||
+        vr == ValueRepresentation_UniversalResource ||
+        vr == ValueRepresentation_UnlimitedText ||
+        vr == ValueRepresentation_Unknown)    // Note that "UN" should never appear in the Meta Information
+    {
+      if (position + 12 > size)
+      {
+        return false;
+      }
+
+      uint32_t length = ReadUnsignedInteger32(dicom + position + 8);
+
+      if (position + 12 + length > size)
+      {
+        return false;
+      }
+
+      value.assign(dicom + position + 12, length);
+      position += (12 + length);
+    }
+    else
+    {
+      if (position + 8 > size)
+      {
+        return false;
+      }
+
+      uint16_t length = ReadUnsignedInteger16(dicom + position + 6);
+
+      if (position + 8 + length > size)
+      {
+        return false;
+      }
+
+      value.assign(dicom + position + 8, length);
+      position += (8 + length);
+    }
+
+    if (!ValidateTag(vr, value))
+    {
+      return false;
+    }
+
+    RemoveTagPadding(value, vr);
+
+    return true;
+  }
+
+
+  bool DicomMap::ParseDicomMetaInformation(DicomMap& result,
+                                           const char* dicom,
+                                           size_t size)
+  {
+    /**
+     * http://dicom.nema.org/medical/dicom/current/output/chtml/part10/chapter_7.html
+     * According to Table 7.1-1, besides the "DICM" DICOM prefix, the
+     * file preamble (i.e. dicom[0..127]) should not be taken into
+     * account to determine whether the file is or is not a DICOM file.
+     **/
+
+    if (size < 132 ||
+        dicom[128] != 'D' ||
+        dicom[129] != 'I' ||
+        dicom[130] != 'C' ||
+        dicom[131] != 'M')
+    {
+      return false;
+    }
+
+
+    /**
+     * The DICOM File Meta Information must be encoded using the
+     * Explicit VR Little Endian Transfer Syntax
+     * (UID=1.2.840.10008.1.2.1).
+     **/
+
+    result.Clear();
+
+    // First, we read the "File Meta Information Group Length" tag
+    // (0002,0000) to know where to stop reading the meta header
+    size_t position = 132;
+
+    DicomTag tag(0x0000, 0x0000);  // Dummy initialization
+    ValueRepresentation vr;
+    std::string value;
+    if (!ReadNextTag(tag, vr, value, dicom, size, position) ||
+        tag.GetGroup() != 0x0002 ||
+        tag.GetElement() != 0x0000 ||
+        vr != ValueRepresentation_UnsignedLong ||
+        value.size() != 4)
+    {
+      return false;
+    }
+
+    size_t stopPosition = position + ReadUnsignedInteger32(value.c_str());
+    if (stopPosition > size)
+    {
+      return false;
+    }
+
+    while (position < stopPosition)
+    {
+      if (ReadNextTag(tag, vr, value, dicom, size, position))
+      {
+        result.SetValue(tag, value, IsBinaryValueRepresentation(vr));
+      }
+      else
+      {
+        return false;
+      }
+    }
+
+    return true;
+  }
 }