Mercurial > hg > orthanc-stone

changeset 2089:63d77859edee dicom-sr

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cont
author Sebastien Jodogne <s.jodogne@gmail.com>
date Tue, 07 Nov 2023 19:30:44 +0100
parents b98d159c7545
children c2dfc253bd04
files Applications/StoneWebViewer/WebAssembly/StoneWebViewer.cpp OrthancStone/Sources/StoneEnumerations.cpp OrthancStone/Sources/StoneEnumerations.h OrthancStone/Sources/Toolbox/DicomStructuredReport.cpp OrthancStone/Sources/Toolbox/DicomStructuredReport.h OrthancStone/UnitTestsSources/UnitTestsMain.cpp
diffstat 6 files changed, 199 insertions(+), 17 deletions(-) [+]
line wrap: on
line diff
--- a/Applications/StoneWebViewer/WebAssembly/StoneWebViewer.cpp	Tue Nov 07 18:12:35 2023 +0100
+++ b/Applications/StoneWebViewer/WebAssembly/StoneWebViewer.cpp	Tue Nov 07 19:30:44 2023 +0100
@@ -82,6 +82,7 @@
 #include "../../../OrthancStone/Sources/Scene2DViewport/ViewportController.h"
 #include "../../../OrthancStone/Sources/StoneException.h"
 #include "../../../OrthancStone/Sources/Toolbox/DicomInstanceParameters.h"
+#include "../../../OrthancStone/Sources/Toolbox/DicomStructuredReport.h"
 #include "../../../OrthancStone/Sources/Toolbox/GeometryToolbox.h"
 #include "../../../OrthancStone/Sources/Toolbox/OsiriX/AngleAnnotation.h"
 #include "../../../OrthancStone/Sources/Toolbox/OsiriX/CollectionOfAnnotations.h"
@@ -102,8 +103,6 @@
 #include <boost/math/special_functions/round.hpp>
 #include <stdio.h>
 
-static const char* const DICOM_COMPREHENSIVE_SR_IOD = "1.2.840.10008.5.1.4.1.1.88.33";
-
 static const double PI = boost::math::constants::pi<double>();
 
 #if !defined(STONE_WEB_VIEWER_EXPORT)
@@ -427,11 +426,18 @@
     {
       for (size_t i = 0; i < message.GetInstancesCount(); i++)
       {
-        std::string sopClassUid;
-        if (message.GetInstance(i).LookupStringValue(sopClassUid, Orthanc::DICOM_TAG_SOP_CLASS_UID, false) &&
-            sopClassUid == DICOM_COMPREHENSIVE_SR_IOD)
+        std::string sopInstanceUid, sopClassUid;
+        if (message.GetInstance(i).LookupStringValue(sopInstanceUid, Orthanc::DICOM_TAG_SOP_INSTANCE_UID, false) &&
+            message.GetInstance(i).LookupStringValue(sopClassUid, Orthanc::DICOM_TAG_SOP_CLASS_UID, false) &&
+            OrthancStone::StringToSopClassUid(sopClassUid) == OrthancStone::SopClassUid_ComprehensiveSR)
         {
-          LOG(ERROR) << "ICI " << message.GetSeriesInstanceUid();
+          std::unique_ptr<OrthancStone::ILoadersContext::ILock> lock(context_.Lock());
+          lock->Schedule(
+            GetSharedObserver(), PRIORITY_NORMAL, OrthancStone::ParseDicomFromWadoCommand::Create(
+              source_, message.GetStudyInstanceUid(), message.GetSeriesInstanceUid(), sopInstanceUid,
+              false /* no transcoding */, Orthanc::DicomTransferSyntax_LittleEndianExplicit /* dummy value */,
+              new InstanceInfo(message.GetStudyInstanceUid(), message.GetSeriesInstanceUid(), OrthancStone::SopClassUid_ComprehensiveSR)));
+          return;
         }
       }
 
@@ -533,6 +539,30 @@
           {
             LOG(ERROR) << "Unable to extract PDF from series: " << info.GetSeriesInstanceUid();
           }
+
+          break;
+        }
+
+        case OrthancStone::SopClassUid_ComprehensiveSR:
+        {
+          try
+          {
+            OrthancStone::DicomStructuredReport sr(message.GetDicom());
+
+            std::list<OrthancStone::DicomStructuredReport::Frame> frames;
+            sr.ExportOrderedFrames(frames);
+
+            for (std::list<OrthancStone::DicomStructuredReport::Frame>::const_iterator
+                   it = frames.begin(); it != frames.end(); ++it)
+            {
+              LOG(ERROR) << "YOU " << it->GetSopInstanceUid() << " " << it->GetFrameNumber();
+            }
+          }
+          catch (Orthanc::OrthancException& e)
+          {
+            LOG(ERROR) << "Cannot decode DICOM-SR: " << e.What();
+          }
+          break;
         }
 
         default:
--- a/OrthancStone/Sources/StoneEnumerations.cpp	Tue Nov 07 18:12:35 2023 +0100
+++ b/OrthancStone/Sources/StoneEnumerations.cpp	Tue Nov 07 19:30:44 2023 +0100
@@ -65,6 +65,10 @@
     {
       return SopClassUid_DicomSeg;
     }
+    else if (s == "1.2.840.10008.5.1.4.1.1.88.33")
+    {
+      return SopClassUid_ComprehensiveSR;
+    }
     else
     {
       //LOG(INFO) << "Other SOP class UID: " << source;
--- a/OrthancStone/Sources/StoneEnumerations.h	Tue Nov 07 18:12:35 2023 +0100
+++ b/OrthancStone/Sources/StoneEnumerations.h	Tue Nov 07 19:30:44 2023 +0100
@@ -116,7 +116,8 @@
     SopClassUid_VideoEndoscopicImageStorage,
     SopClassUid_VideoMicroscopicImageStorage,
     SopClassUid_VideoPhotographicImageStorage,
-    SopClassUid_DicomSeg
+    SopClassUid_DicomSeg,
+    SopClassUid_ComprehensiveSR
   };
 
   enum SeriesThumbnailType
--- a/OrthancStone/Sources/Toolbox/DicomStructuredReport.cpp	Tue Nov 07 18:12:35 2023 +0100
+++ b/OrthancStone/Sources/Toolbox/DicomStructuredReport.cpp	Tue Nov 07 19:30:44 2023 +0100
@@ -118,6 +118,19 @@
 
 namespace OrthancStone
 {
+  void DicomStructuredReport::ReferencedInstance::AddFrame(unsigned int frame)
+  {
+    if (frame == 0)
+    {
+      throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange);
+    }
+    else
+    {
+      frames_.insert(frame);
+    }
+  }
+
+
   class DicomStructuredReport::Structure : public boost::noncopyable
   {
   private:
@@ -369,7 +382,7 @@
 
           if (instancesInformation_.find(sopInstanceUid) == instancesInformation_.end())
           {
-            instancesInformation_[sopInstanceUid] = ReferencedInstance(studyInstanceUid, seriesInstanceUid, sopClassUid);
+            instancesInformation_[sopInstanceUid] = new ReferencedInstance(studyInstanceUid, seriesInstanceUid, sopClassUid);
           }
           else
           {
@@ -468,12 +481,16 @@
                     }
 
                     std::string sopInstanceUid = GetStringValue(*instances.getItem(0), DCM_ReferencedSOPInstanceUID);
-                    if (instancesInformation_.find(sopInstanceUid) == instancesInformation_.end())
+                    std::map<std::string, ReferencedInstance*>::iterator instanceInformation = instancesInformation_.find(sopInstanceUid);
+
+                    if (instanceInformation == instancesInformation_.end())
                     {
                       throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat,
                                                       "Referencing unknown instance in DICOM-SR: " + sopInstanceUid);
                     }
 
+                    assert(instanceInformation->second != NULL);
+
                     if (instances.getItem(0)->tagExists(DCM_ReferencedFrameNumber))
                     {
                       std::string frames = GetStringValue(*instances.getItem(0), DCM_ReferencedFrameNumber);
@@ -490,12 +507,14 @@
                         else
                         {
                           AddStructure(sopInstanceUid, group, true, frame, hasProbabilityOfCancer, probabilityOfCancer);
+                          instanceInformation->second->AddFrame(frame);
                         }
                       }
                     }
                     else
                     {
                       AddStructure(sopInstanceUid, group, false, 0, hasProbabilityOfCancer, probabilityOfCancer);
+                      instanceInformation->second->AddFrame(1);
                     }
                   }
                 }
@@ -515,5 +534,64 @@
       assert(*it != NULL);
       delete *it;
     }
+
+    for (std::map<std::string, ReferencedInstance*>::iterator
+           it = instancesInformation_.begin(); it != instancesInformation_.end(); ++it)
+    {
+      assert(it->second != NULL);
+      delete it->second;
+    }
+  }
+
+
+  void DicomStructuredReport::GetReferencedInstance(std::string& studyInstanceUid,
+                                                    std::string& seriesInstanceUid,
+                                                    std::string& sopInstanceUid,
+                                                    std::string& sopClassUid,
+                                                    size_t i) const
+  {
+    if (i >= orderedInstances_.size())
+    {
+      throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange);
+    }
+
+    sopInstanceUid = orderedInstances_[i];
+
+    std::map<std::string, ReferencedInstance*>::const_iterator found = instancesInformation_.find(sopInstanceUid);
+    if (found == instancesInformation_.end())
+    {
+      throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError);
+    }
+
+    assert(found->second != NULL);
+    studyInstanceUid = found->second->GetStudyInstanceUid();
+    seriesInstanceUid = found->second->GetSeriesInstanceUid();
+    sopClassUid = found->second->GetSopClassUid();
+  }
+
+
+  void DicomStructuredReport::ExportOrderedFrames(std::list<Frame>& frames) const
+  {
+    frames.clear();
+
+    for (size_t i = 0; i < orderedInstances_.size(); i++)
+    {
+      std::map<std::string, ReferencedInstance*>::const_iterator found = instancesInformation_.find(orderedInstances_[i]);
+      if (found == instancesInformation_.end())
+      {
+        throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError);
+      }
+
+      assert(found->second != NULL);
+
+      for (std::set<unsigned int>::const_iterator frame = found->second->GetFrames().begin();
+           frame != found->second->GetFrames().end(); ++frame)
+      {
+        frames.push_back(Frame(found->second->GetStudyInstanceUid(),
+                               found->second->GetSeriesInstanceUid(),
+                               orderedInstances_[i],
+                               found->second->GetSopClassUid(), *frame));
+      }
+    }
   }
 }
--- a/OrthancStone/Sources/Toolbox/DicomStructuredReport.h	Tue Nov 07 18:12:35 2023 +0100
+++ b/OrthancStone/Sources/Toolbox/DicomStructuredReport.h	Tue Nov 07 19:30:44 2023 +0100
@@ -35,6 +35,7 @@
 
 #include <dcmtk/dcmdata/dcitem.h>
 #include <list>
+#include <set>
 
 namespace OrthancStone
 {
@@ -45,12 +46,13 @@
     class Point;
     class Polyline;
 
-    class ReferencedInstance
+    class ReferencedInstance : public boost::noncopyable
     {
     private:
       std::string  studyInstanceUid_;
       std::string  seriesInstanceUid_;
       std::string  sopClassUid_;
+      std::set<unsigned int>  frames_;
 
     public:
       ReferencedInstance(const std::string& studyInstanceUid,
@@ -62,10 +64,6 @@
       {
       }
 
-      ReferencedInstance()
-      {
-      }
-
       const std::string& GetStudyInstanceUid() const
       {
         return studyInstanceUid_;
@@ -80,8 +78,16 @@
       {
         return sopClassUid_;
       }
+
+      void AddFrame(unsigned int frame);
+
+      const std::set<unsigned int>& GetFrames() const
+      {
+        return frames_;
+      }
     };
 
+
     void AddStructure(const std::string& sopInstanceUid,
                       DcmItem& group,
                       bool hasFrameNumber,
@@ -89,13 +95,75 @@
                       bool hasProbabilityOfCancer,
                       float probabilityOfCancer);
 
-    std::map<std::string, ReferencedInstance>  instancesInformation_;
-    std::vector<std::string>                   orderedInstances_;
-    std::list<Structure*>                      structures_;
+    std::map<std::string, ReferencedInstance*>  instancesInformation_;
+    std::vector<std::string>                    orderedInstances_;
+    std::list<Structure*>                       structures_;
 
   public:
+    class Frame
+    {
+    private:
+      std::string  studyInstanceUid_;
+      std::string  seriesInstanceUid_;
+      std::string  sopInstanceUid_;
+      std::string  sopClassUid_;
+      unsigned int frameNumber_;
+
+    public:
+      Frame(const std::string& studyInstanceUid,
+            const std::string& seriesInstanceUid,
+            const std::string& sopInstanceUid,
+            const std::string& sopClassUid,
+            unsigned int frameNumber) :
+        studyInstanceUid_(studyInstanceUid),
+        seriesInstanceUid_(seriesInstanceUid),
+        sopInstanceUid_(sopInstanceUid),
+        sopClassUid_(sopClassUid),
+        frameNumber_(frameNumber)
+      {
+      }
+
+      const std::string& GetStudyInstanceUid() const
+      {
+        return studyInstanceUid_;
+      }
+
+      const std::string& GetSeriesInstanceUid() const
+      {
+        return seriesInstanceUid_;
+      }
+
+      const std::string& GetSopInstanceUid() const
+      {
+        return sopInstanceUid_;
+      }
+
+      const std::string& GetSopClassUid() const
+      {
+        return sopClassUid_;
+      }
+
+      unsigned int GetFrameNumber() const
+      {
+        return frameNumber_;
+      }
+    };
+
     DicomStructuredReport(Orthanc::ParsedDicomFile& dicom);
 
     ~DicomStructuredReport();
+
+    size_t GetReferencedInstancesCount() const
+    {
+      return orderedInstances_.size();
+    }
+
+    void GetReferencedInstance(std::string& studyInstanceUid,
+                               std::string& seriesInstanceUid,
+                               std::string& sopInstanceUid,
+                               std::string& sopClassUid,
+                               size_t i) const;
+
+    void ExportOrderedFrames(std::list<Frame>& frames) const;
   };
 }
--- a/OrthancStone/UnitTestsSources/UnitTestsMain.cpp	Tue Nov 07 18:12:35 2023 +0100
+++ b/OrthancStone/UnitTestsSources/UnitTestsMain.cpp	Tue Nov 07 19:30:44 2023 +0100
@@ -44,6 +44,7 @@
   ASSERT_EQ(SopClassUid_VideoEndoscopicImageStorage, StringToSopClassUid("1.2.840.10008.5.1.4.1.1.77.1.1.1"));
   ASSERT_EQ(SopClassUid_VideoMicroscopicImageStorage, StringToSopClassUid("1.2.840.10008.5.1.4.1.1.77.1.2.1"));
   ASSERT_EQ(SopClassUid_VideoPhotographicImageStorage, StringToSopClassUid("1.2.840.10008.5.1.4.1.1.77.1.4.1"));
+  ASSERT_EQ(SopClassUid_ComprehensiveSR, StringToSopClassUid("1.2.840.10008.5.1.4.1.1.88.33"));
   ASSERT_EQ(SopClassUid_Other, StringToSopClassUid("nope"));
 
   ASSERT_EQ(SeriesThumbnailType_Pdf, GetSeriesThumbnailType(SopClassUid_EncapsulatedPdf));