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changeset 77:b8dfde8d64e8

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new dicom tags
author Sebastien Jodogne <s.jodogne@gmail.com>
date Thu, 20 Sep 2012 13:41:18 +0200
parents e2d68529605f
children 10bf2cd24d1d
files Core/DicomFormat/DicomMap.cpp Core/DicomFormat/DicomTag.cpp Core/DicomFormat/DicomTag.h OrthancServer/DicomIntegerPixelAccessor.cpp OrthancServer/DicomProtocol/DicomUserConnection.cpp OrthancServer/OrthancRestApi.cpp OrthancServer/PrepareDatabase.sql OrthancServer/ServerIndex.cpp Resources/CMake/DownloadPackage.cmake
diffstat 9 files changed, 105 insertions(+), 75 deletions(-) [+]
line wrap: on
line diff
--- a/Core/DicomFormat/DicomMap.cpp	Mon Sep 17 17:32:33 2012 +0200
+++ b/Core/DicomFormat/DicomMap.cpp	Thu Sep 20 13:41:18 2012 +0200
@@ -30,54 +30,55 @@
 {
   static DicomTag patientTags[] =
   {
-    DicomTag(0x0010, 0x0010), // PatientName
-    DicomTag(0x0010, 0x0020), // PatientID
-    DicomTag(0x0010, 0x0030), // PatientBirthDate
-    DicomTag(0x0010, 0x0040), // PatientSex
-    DicomTag(0x0010, 0x1000)  // OtherPatientIDs
     //DicomTag(0x0010, 0x1010), // PatientAge
     //DicomTag(0x0010, 0x1040)  // PatientAddress
+    DicomTag(0x0010, 0x0010),   // PatientName
+    DicomTag(0x0010, 0x0030),   // PatientBirthDate
+    DicomTag(0x0010, 0x0040),   // PatientSex
+    DicomTag(0x0010, 0x1000),   // OtherPatientIDs
+    DicomTag::PATIENT_ID
   };
 
   static DicomTag studyTags[] =
   {
-    DicomTag(0x0008, 0x0020), // StudyDate
-    DicomTag(0x0008, 0x0030), // StudyTime
-    DicomTag(0x0008, 0x0050), // AccessionNumber
-    DicomTag(0x0008, 0x1030), // StudyDescription
-    DicomTag(0x0020, 0x000d), // StudyInstanceUID
-    DicomTag(0x0020, 0x0010)  // StudyID
     //DicomTag(0x0010, 0x1020), // PatientSize
     //DicomTag(0x0010, 0x1030)  // PatientWeight
+    DicomTag(0x0008, 0x0020),   // StudyDate
+    DicomTag(0x0008, 0x0030),   // StudyTime
+    DicomTag(0x0008, 0x1030),   // StudyDescription
+    DicomTag(0x0020, 0x0010),   // StudyID
+    DicomTag::ACCESSION_NUMBER,
+    DicomTag::STUDY_INSTANCE_UID
   };
 
   static DicomTag seriesTags[] =
   {
-    DicomTag(0x0008, 0x0021), // SeriesDate
-    DicomTag(0x0008, 0x0031), // SeriesTime
-    DicomTag(0x0008, 0x0060), // Modality
-    DicomTag(0x0008, 0x0070), // Manufacturer
-    DicomTag(0x0008, 0x1010), // StationName
-    DicomTag(0x0008, 0x103e), // SeriesDescription
     //DicomTag(0x0010, 0x1080), // MilitaryRank
-    DicomTag(0x0018, 0x0015), // BodyPartExamined
-    DicomTag(0x0018, 0x0024), // SequenceName
-    DicomTag(0x0018, 0x1030), // ProtocolName
-    DicomTag(0x0020, 0x000e), // SeriesInstanceUID
-    DicomTag(0x0020, 0x0011), // SeriesNumber
-    DicomTag(0x0020, 0x1002), // ImagesInAcquisition
-    DicomTag(0x0054, 0x0081)  // NumberOfSlices
+    DicomTag(0x0008, 0x0021),   // SeriesDate
+    DicomTag(0x0008, 0x0031),   // SeriesTime
+    DicomTag(0x0008, 0x0060),   // Modality
+    DicomTag(0x0008, 0x0070),   // Manufacturer
+    DicomTag(0x0008, 0x1010),   // StationName
+    DicomTag(0x0008, 0x103e),   // SeriesDescription
+    DicomTag(0x0018, 0x0015),   // BodyPartExamined
+    DicomTag(0x0018, 0x0024),   // SequenceName
+    DicomTag(0x0018, 0x1030),   // ProtocolName
+    DicomTag(0x0020, 0x0011),   // SeriesNumber
+    DicomTag::IMAGES_IN_ACQUISITION,
+    DicomTag::NUMBER_OF_SLICES,
+    DicomTag::SERIES_INSTANCE_UID
   };
 
   static DicomTag instanceTags[] =
   {
-    DicomTag(0x0008, 0x0012), // InstanceCreationDate
-    DicomTag(0x0008, 0x0013), // InstanceCreationTime
-    DicomTag(0x0008, 0x0018), // SOPInstanceUID
-    DicomTag(0x0020, 0x0012), // AcquisitionNumber
-    DicomTag(0x0020, 0x0013), // InstanceNumber
-    DicomTag(0x0028, 0x0008), // NumberOfFrames
-    DicomTag(0x0054, 0x1330)  // ImageIndex
+    DicomTag(0x0008, 0x0012),   // InstanceCreationDate
+    DicomTag(0x0008, 0x0013),   // InstanceCreationTime
+    DicomTag(0x0020, 0x0012),   // AcquisitionNumber
+    DicomTag::CARDIAC_NUMBER_OF_IMAGES,
+    DicomTag::IMAGE_INDEX,
+    DicomTag::INSTANCE_NUMBER,
+    DicomTag::NUMBER_OF_FRAMES,
+    DicomTag::SOP_INSTANCE_UID
   };
 
 
@@ -227,7 +228,7 @@
     SetupFindTemplate(result, seriesTags, sizeof(seriesTags) / sizeof(DicomTag));
     result.SetValue(DicomTag::ACCESSION_NUMBER, "");
     result.SetValue(DicomTag::PATIENT_ID, "");
-    result.SetValue(DicomTag::STUDY_UID, "");
+    result.SetValue(DicomTag::STUDY_INSTANCE_UID, "");
   }
 
   void DicomMap::SetupFindInstanceTemplate(DicomMap& result)
@@ -235,8 +236,8 @@
     SetupFindTemplate(result, instanceTags, sizeof(instanceTags) / sizeof(DicomTag));
     result.SetValue(DicomTag::ACCESSION_NUMBER, "");
     result.SetValue(DicomTag::PATIENT_ID, "");
-    result.SetValue(DicomTag::STUDY_UID, "");
-    result.SetValue(DicomTag::SERIES_UID, "");
+    result.SetValue(DicomTag::STUDY_INSTANCE_UID, "");
+    result.SetValue(DicomTag::SERIES_INSTANCE_UID, "");
   }
 
 
--- a/Core/DicomFormat/DicomTag.cpp	Mon Sep 17 17:32:33 2012 +0200
+++ b/Core/DicomFormat/DicomTag.cpp	Thu Sep 20 13:41:18 2012 +0200
@@ -61,11 +61,18 @@
 
 
   const DicomTag DicomTag::ACCESSION_NUMBER = DicomTag(0x0008, 0x0050);
-  const DicomTag DicomTag::IMAGE_INDEX = DicomTag(0x0054, 0x1330);
-  const DicomTag DicomTag::INSTANCE_UID = DicomTag(0x0008, 0x0018);
-  const DicomTag DicomTag::NUMBER_OF_SLICES = DicomTag(0x0054, 0x0081);
+  const DicomTag DicomTag::SOP_INSTANCE_UID = DicomTag(0x0008, 0x0018);
   const DicomTag DicomTag::PATIENT_ID = DicomTag(0x0010, 0x0020);
-  const DicomTag DicomTag::SERIES_UID = DicomTag(0x0020, 0x000e);
-  const DicomTag DicomTag::STUDY_UID = DicomTag(0x0020, 0x000d);
+  const DicomTag DicomTag::SERIES_INSTANCE_UID = DicomTag(0x0020, 0x000e);
+  const DicomTag DicomTag::STUDY_INSTANCE_UID = DicomTag(0x0020, 0x000d);
   const DicomTag DicomTag::PIXEL_DATA = DicomTag(0x7fe0, 0x0010);
+
+  const DicomTag DicomTag::INSTANCE_NUMBER = DicomTag(0x0020, 0x0013);
+  const DicomTag DicomTag::IMAGE_INDEX = DicomTag(0x0054, 0x1330);
+
+  const DicomTag DicomTag::NUMBER_OF_SLICES = DicomTag(0x0054, 0x0081);
+  const DicomTag DicomTag::NUMBER_OF_FRAMES = DicomTag(0x0028, 0x0008);
+  const DicomTag DicomTag::CARDIAC_NUMBER_OF_IMAGES = DicomTag(0x0018, 0x1090);
+  const DicomTag DicomTag::IMAGES_IN_ACQUISITION = DicomTag(0x0020, 0x1002);
+
 }
--- a/Core/DicomFormat/DicomTag.h	Mon Sep 17 17:32:33 2012 +0200
+++ b/Core/DicomFormat/DicomTag.h	Thu Sep 20 13:41:18 2012 +0200
@@ -58,14 +58,20 @@
 
     friend std::ostream& operator<< (std::ostream& o, const DicomTag& tag);
 
-    // Alias for the most useful tags
+    // Aliases for the most useful tags
     static const DicomTag ACCESSION_NUMBER;
+    static const DicomTag SOP_INSTANCE_UID;
+    static const DicomTag PATIENT_ID;
+    static const DicomTag SERIES_INSTANCE_UID;
+    static const DicomTag STUDY_INSTANCE_UID;
+    static const DicomTag PIXEL_DATA;
+
+    static const DicomTag INSTANCE_NUMBER;
     static const DicomTag IMAGE_INDEX;
-    static const DicomTag INSTANCE_UID;
+
     static const DicomTag NUMBER_OF_SLICES;
-    static const DicomTag PATIENT_ID;
-    static const DicomTag SERIES_UID;
-    static const DicomTag STUDY_UID;
-    static const DicomTag PIXEL_DATA;
+    static const DicomTag NUMBER_OF_FRAMES;
+    static const DicomTag CARDIAC_NUMBER_OF_IMAGES;
+    static const DicomTag IMAGES_IN_ACQUISITION;
   };
 }
--- a/OrthancServer/DicomIntegerPixelAccessor.cpp	Mon Sep 17 17:32:33 2012 +0200
+++ b/OrthancServer/DicomIntegerPixelAccessor.cpp	Thu Sep 20 13:41:18 2012 +0200
@@ -25,12 +25,19 @@
 #endif
 
 #include "../Core/OrthancException.h"
-#include "FromDcmtkBridge.h"
 #include <boost/lexical_cast.hpp>
 #include <limits>
 
 namespace Orthanc
 {
+  static const DicomTag COLUMNS(0x0028, 0x0011);
+  static const DicomTag ROWS(0x0028, 0x0010);
+  static const DicomTag SAMPLES_PER_PIXEL(0x0028, 0x0002);
+  static const DicomTag BITS_ALLOCATED(0x0028, 0x0100);
+  static const DicomTag BITS_STORED(0x0028, 0x0101);
+  static const DicomTag HIGH_BIT(0x0028, 0x0102);
+  static const DicomTag PIXEL_REPRESENTATION(0x0028, 0x0103);
+
   DicomIntegerPixelAccessor::DicomIntegerPixelAccessor(const DicomMap& values,
                                                        const void* pixelData,
                                                        size_t size) :
@@ -44,13 +51,13 @@
 
     try
     {
-      width_ = boost::lexical_cast<unsigned int>(FromDcmtkBridge::GetValue(values, "Columns").AsString());
-      height_ = boost::lexical_cast<unsigned int>(FromDcmtkBridge::GetValue(values, "Rows").AsString());
-      samplesPerPixel_ = boost::lexical_cast<unsigned int>(FromDcmtkBridge::GetValue(values, "SamplesPerPixel").AsString());
-      bitsAllocated = boost::lexical_cast<unsigned int>(FromDcmtkBridge::GetValue(values, "BitsAllocated").AsString());
-      bitsStored = boost::lexical_cast<unsigned int>(FromDcmtkBridge::GetValue(values, "BitsStored").AsString());
-      highBit = boost::lexical_cast<unsigned int>(FromDcmtkBridge::GetValue(values, "HighBit").AsString());
-      pixelRepresentation = boost::lexical_cast<unsigned int>(FromDcmtkBridge::GetValue(values, "PixelRepresentation").AsString());
+      width_ = boost::lexical_cast<unsigned int>(values.GetValue(COLUMNS).AsString());
+      height_ = boost::lexical_cast<unsigned int>(values.GetValue(ROWS).AsString());
+      samplesPerPixel_ = boost::lexical_cast<unsigned int>(values.GetValue(SAMPLES_PER_PIXEL).AsString());
+      bitsAllocated = boost::lexical_cast<unsigned int>(values.GetValue(BITS_ALLOCATED).AsString());
+      bitsStored = boost::lexical_cast<unsigned int>(values.GetValue(BITS_STORED).AsString());
+      highBit = boost::lexical_cast<unsigned int>(values.GetValue(HIGH_BIT).AsString());
+      pixelRepresentation = boost::lexical_cast<unsigned int>(values.GetValue(PIXEL_REPRESENTATION).AsString());
     }
     catch (boost::bad_lexical_cast)
     {
@@ -60,7 +67,7 @@
     frame_ = 0;
     try
     {
-      numberOfFrames_ = boost::lexical_cast<unsigned int>(FromDcmtkBridge::GetValue(values, "NumberOfFrames").AsString());
+      numberOfFrames_ = boost::lexical_cast<unsigned int>(values.GetValue(DicomTag::NUMBER_OF_FRAMES).AsString());
     }
     catch (OrthancException)
     {
--- a/OrthancServer/DicomProtocol/DicomUserConnection.cpp	Mon Sep 17 17:32:33 2012 +0200
+++ b/OrthancServer/DicomProtocol/DicomUserConnection.cpp	Thu Sep 20 13:41:18 2012 +0200
@@ -370,7 +370,7 @@
 
     s.CopyTagIfExists(fields, DicomTag::PATIENT_ID);
     s.CopyTagIfExists(fields, DicomTag::ACCESSION_NUMBER);
-    s.CopyTagIfExists(fields, DicomTag::STUDY_UID);
+    s.CopyTagIfExists(fields, DicomTag::STUDY_INSTANCE_UID);
 
     Find(result, FindRootModel_Series, s);
   }
@@ -384,8 +384,8 @@
 
     s.CopyTagIfExists(fields, DicomTag::PATIENT_ID);
     s.CopyTagIfExists(fields, DicomTag::ACCESSION_NUMBER);
-    s.CopyTagIfExists(fields, DicomTag::STUDY_UID);
-    s.CopyTagIfExists(fields, DicomTag::SERIES_UID);
+    s.CopyTagIfExists(fields, DicomTag::STUDY_INSTANCE_UID);
+    s.CopyTagIfExists(fields, DicomTag::SERIES_INSTANCE_UID);
 
     Find(result, FindRootModel_Instance, s);
   }
@@ -594,8 +594,8 @@
                                        const DicomMap& findResult)
   {
     DicomMap simplified;
-    simplified.SetValue(DicomTag::STUDY_UID, findResult.GetValue(DicomTag::STUDY_UID));
-    simplified.SetValue(DicomTag::SERIES_UID, findResult.GetValue(DicomTag::SERIES_UID));
+    simplified.SetValue(DicomTag::STUDY_INSTANCE_UID, findResult.GetValue(DicomTag::STUDY_INSTANCE_UID));
+    simplified.SetValue(DicomTag::SERIES_INSTANCE_UID, findResult.GetValue(DicomTag::SERIES_INSTANCE_UID));
     Move(targetAet, simplified);
   }
 
@@ -604,8 +604,8 @@
                                        const std::string& seriesUid)
   {
     DicomMap map;
-    map.SetValue(DicomTag::STUDY_UID, studyUid);
-    map.SetValue(DicomTag::SERIES_UID, seriesUid);
+    map.SetValue(DicomTag::STUDY_INSTANCE_UID, studyUid);
+    map.SetValue(DicomTag::SERIES_INSTANCE_UID, seriesUid);
     Move(targetAet, map);
   }
 
@@ -613,9 +613,9 @@
                                          const DicomMap& findResult)
   {
     DicomMap simplified;
-    simplified.SetValue(DicomTag::STUDY_UID, findResult.GetValue(DicomTag::STUDY_UID));
-    simplified.SetValue(DicomTag::SERIES_UID, findResult.GetValue(DicomTag::SERIES_UID));
-    simplified.SetValue(DicomTag::INSTANCE_UID, findResult.GetValue(DicomTag::INSTANCE_UID));
+    simplified.SetValue(DicomTag::STUDY_INSTANCE_UID, findResult.GetValue(DicomTag::STUDY_INSTANCE_UID));
+    simplified.SetValue(DicomTag::SERIES_INSTANCE_UID, findResult.GetValue(DicomTag::SERIES_INSTANCE_UID));
+    simplified.SetValue(DicomTag::SOP_INSTANCE_UID, findResult.GetValue(DicomTag::SOP_INSTANCE_UID));
     Move(targetAet, simplified);
   }
 
@@ -625,9 +625,9 @@
                                          const std::string& instanceUid)
   {
     DicomMap map;
-    map.SetValue(DicomTag::STUDY_UID, studyUid);
-    map.SetValue(DicomTag::SERIES_UID, seriesUid);
-    map.SetValue(DicomTag::INSTANCE_UID, instanceUid);
+    map.SetValue(DicomTag::STUDY_INSTANCE_UID, studyUid);
+    map.SetValue(DicomTag::SERIES_INSTANCE_UID, seriesUid);
+    map.SetValue(DicomTag::SOP_INSTANCE_UID, instanceUid);
     Move(targetAet, map);
   }
 
--- a/OrthancServer/OrthancRestApi.cpp	Mon Sep 17 17:32:33 2012 +0200
+++ b/OrthancServer/OrthancRestApi.cpp	Thu Sep 20 13:41:18 2012 +0200
@@ -244,7 +244,7 @@
 
     if ((m.GetValue(DicomTag::ACCESSION_NUMBER).AsString().size() <= 2 &&
          m.GetValue(DicomTag::PATIENT_ID).AsString().size() <= 2) ||
-        m.GetValue(DicomTag::STUDY_UID).AsString().size() <= 2)
+        m.GetValue(DicomTag::STUDY_INSTANCE_UID).AsString().size() <= 2)
     {
       return false;
     }        
@@ -300,7 +300,7 @@
           return false;
         }
         m.CopyTagIfExists(studies.GetAnswer(j), DicomTag::PATIENT_ID);
-        m.CopyTagIfExists(studies.GetAnswer(j), DicomTag::STUDY_UID);
+        m.CopyTagIfExists(studies.GetAnswer(j), DicomTag::STUDY_INSTANCE_UID);
 
         DicomFindAnswers series;
         c.FindSeries(series, m);
--- a/OrthancServer/PrepareDatabase.sql	Mon Sep 17 17:32:33 2012 +0200
+++ b/OrthancServer/PrepareDatabase.sql	Thu Sep 20 13:41:18 2012 +0200
@@ -17,7 +17,8 @@
 CREATE TABLE Series(
        uuid TEXT PRIMARY KEY,
        parentStudy TEXT REFERENCES Studies(uuid) ON DELETE CASCADE,
-       dicomSeries TEXT
+       dicomSeries TEXT,
+       numberOfInstances INTEGER
        );
 
 CREATE TABLE Instances(
@@ -27,7 +28,8 @@
        fileUuid TEXT,
        fileSize INTEGER,
        jsonUuid TEXT,
-       distantAet TEXT
+       distantAet TEXT,
+       instanceIndex INTEGER
        );
 
 CREATE TABLE MainDicomTags(
@@ -55,6 +57,9 @@
 CREATE INDEX DicomInstanceIndex ON Instances(dicomInstance);
 
 CREATE INDEX MainDicomTagsIndex ON MainDicomTags(uuid);
+CREATE INDEX MainDicomTagsGroupElement ON MainDicomTags(tagGroup, tagElement);
+CREATE INDEX MainDicomTagsValues ON MainDicomTags(value COLLATE BINARY);
+
 CREATE INDEX ChangesIndex ON Changes(uuid);
 
 CREATE TRIGGER InstanceRemoved
--- a/OrthancServer/ServerIndex.cpp	Mon Sep 17 17:32:33 2012 +0200
+++ b/OrthancServer/ServerIndex.cpp	Thu Sep 20 13:41:18 2012 +0200
@@ -279,10 +279,11 @@
   {
     std::string seriesUuid = Toolbox::GenerateUuid();
 
-    SQLite::Statement s(db_, SQLITE_FROM_HERE, "INSERT INTO Series VALUES(?, ?, ?)");
+    SQLite::Statement s(db_, SQLITE_FROM_HERE, "INSERT INTO Series VALUES(?, ?, ?, ?)");
     s.BindString(0, seriesUuid);
     s.BindString(1, parentStudyUuid);
     s.BindString(2, dicomSeries);
+    s.BindNull(3);
     s.Run();
 
     RecordChange("series", seriesUuid);
@@ -474,9 +475,9 @@
     boost::mutex::scoped_lock scoped_lock(mutex_);
 
     std::string dicomPatientId = dicomSummary.GetValue(DicomTag::PATIENT_ID).AsString();
-    std::string dicomInstance = dicomSummary.GetValue(DicomTag::INSTANCE_UID).AsString();
-    std::string dicomSeries = dicomSummary.GetValue(DicomTag::SERIES_UID).AsString();
-    std::string dicomStudy = dicomSummary.GetValue(DicomTag::STUDY_UID).AsString();
+    std::string dicomInstance = dicomSummary.GetValue(DicomTag::SOP_INSTANCE_UID).AsString();
+    std::string dicomSeries = dicomSummary.GetValue(DicomTag::SERIES_INSTANCE_UID).AsString();
+    std::string dicomStudy = dicomSummary.GetValue(DicomTag::STUDY_INSTANCE_UID).AsString();
 
     try
     {
--- a/Resources/CMake/DownloadPackage.cmake	Mon Sep 17 17:32:33 2012 +0200
+++ b/Resources/CMake/DownloadPackage.cmake	Thu Sep 20 13:41:18 2012 +0200
@@ -55,6 +55,9 @@
       endif()
 
     elseif ("${CMAKE_HOST_SYSTEM_NAME}" STREQUAL "Windows")
+      # How to silently extract files using 7-zip
+      # http://superuser.com/questions/331148/7zip-command-line-extract-silently-quietly
+
       FIND_PROGRAM(ZIP_EXECUTABLE 7z PATHS "$ENV{ProgramFiles}/7-Zip") 
 
       if (("${TMP_EXTENSION}" STREQUAL "gz") OR ("${TMP_EXTENSION}" STREQUAL "tgz"))