# HG changeset patch
# User Sebastien Jodogne <s.jodogne@gmail.com>
# Date 1666936075 -7200
# Node ID 2034ae383cfda04c4ccbec490a93aea42a419487
# Parent  0661115af9392760ea6bb5f5390cd38c7d11277d# Parent  79fdc3b1f031c288d282f8593aa1863d614aad13
integration default->deep-learning

diff -r 79fdc3b1f031 -r 2034ae383cfd Applications/StoneWebViewer/WebApplication/app.js
--- a/Applications/StoneWebViewer/WebApplication/app.js	Fri Oct 28 07:36:31 2022 +0200
+++ b/Applications/StoneWebViewer/WebApplication/app.js	Fri Oct 28 07:47:55 2022 +0200
@@ -463,7 +463,10 @@
       series: [],
       studies: [],
       seriesIndex: {},  // Maps "SeriesInstanceUID" to "index in this.series"
-      virtualSeriesThumbnails: {}
+      virtualSeriesThumbnails: {},
+
+      deepLearningReady: false,
+      deepLearningProgress: 0  // Floating-point number in the range [0..1]
     }
   },
   computed: {
@@ -1102,6 +1105,11 @@
           alert('Cannot find the study in Orthanc');
         });
       
+    },
+
+    ApplyDeepLearning: function()
+    {
+      stone.ApplyDeepLearningModel(this.GetActiveCanvas());
     }
   },
   
@@ -1381,3 +1389,17 @@
     }
   }
 });
+
+
+window.addEventListener('DeepLearningInitialized', function() {
+  stone.LoadDeepLearningModel('model.message');
+});
+
+window.addEventListener('DeepLearningModelReady', function() {
+  app.deepLearningReady = true;
+  app.deepLearningProgress = 0;
+});
+
+window.addEventListener('DeepLearningStep', function(args) {
+  app.deepLearningProgress = args.detail.progress;
+});
diff -r 79fdc3b1f031 -r 2034ae383cfd Applications/StoneWebViewer/WebApplication/index.html
--- a/Applications/StoneWebViewer/WebApplication/index.html	Fri Oct 28 07:36:31 2022 +0200
+++ b/Applications/StoneWebViewer/WebApplication/index.html	Fri Oct 28 07:47:55 2022 +0200
@@ -310,11 +310,23 @@
 
             </div>        
             <div class="wvLayoutLeft__contentBottom">
+              <div v-if="deepLearningReady">
+                <div style="width:100%;padding:10px;text-align:center;">
+                  <button class="btn btn-primary" @click="ApplyDeepLearning()">Apply deep learning</button>
+                </div>
+                
+                <div style="padding: 10px; position: relative; width:100%;">
+                  <div style="background-color: #007000; position: relative; height: 10px;">    
+                    <div v-bind:style="{ 'background-color': '#00ff00', position: 'absolute', height: '100%', width: (deepLearningProgress*100) + '%' }"></div>
+                  </div>
+                </div>
+              </div>
+                
               <div style="width:100%;padding:10px;text-align:center;"
                    v-if="globalConfiguration.InstitutionLogo != ''">
                 <img style="max-width:100%" v-bind:src="globalConfiguration.InstitutionLogo" />
               </div>
-            </div>        
+            </div>
           </div>
         </div>
         <div class="wvLayout__main"
diff -r 79fdc3b1f031 -r 2034ae383cfd Applications/StoneWebViewer/WebAssembly/CMakeLists.txt
--- a/Applications/StoneWebViewer/WebAssembly/CMakeLists.txt	Fri Oct 28 07:36:31 2022 +0200
+++ b/Applications/StoneWebViewer/WebAssembly/CMakeLists.txt	Fri Oct 28 07:47:55 2022 +0200
@@ -24,6 +24,8 @@
 project(OrthancStone)
 include(${CMAKE_SOURCE_DIR}/../Version.cmake)
 
+include(${CMAKE_SOURCE_DIR}/deep-learning/WebAssembly/Protobuf.cmake)  # TODO
+
 set(ORTHANC_STONE_INSTALL_PREFIX "${CMAKE_SOURCE_DIR}/../../../wasm-binaries/StoneWebViewer" CACHE PATH "Where to put the WebAssembly binaries")
 
 
@@ -131,6 +133,8 @@
 add_executable(StoneWebViewer
   ${ORTHANC_STONE_SOURCES}
   ${AUTOGENERATED_SOURCES}
+  ${PROTOBUF_SOURCES}  # TODO
+  ${CMAKE_SOURCE_DIR}/deep-learning/WebAssembly/Worker.pb.cc  # TODO
   StoneWebViewer.cpp
   )
 
diff -r 79fdc3b1f031 -r 2034ae383cfd Applications/StoneWebViewer/WebAssembly/StoneWebViewer.cpp
--- a/Applications/StoneWebViewer/WebAssembly/StoneWebViewer.cpp	Fri Oct 28 07:36:31 2022 +0200
+++ b/Applications/StoneWebViewer/WebAssembly/StoneWebViewer.cpp	Fri Oct 28 07:47:55 2022 +0200
@@ -1590,6 +1590,7 @@
   static const int LAYER_REFERENCE_LINES = 3;
   static const int LAYER_ANNOTATIONS_OSIRIX = 4;
   static const int LAYER_ANNOTATIONS_STONE = 5;
+  static const int LAYER_DEEP_LEARNING = 6;
 
   
   class ICommand : public Orthanc::IDynamicObject
@@ -2008,6 +2009,10 @@
   // the center of the top-left pixel
   boost::shared_ptr<OrthancStone::AnnotationsSceneLayer>  stoneAnnotations_;
 
+  boost::shared_ptr<Orthanc::ImageAccessor>  deepLearningMask_;
+  std::string deepLearningSopInstanceUid_;
+  unsigned int deepLearningFrameNumber_;
+  
 
   void ScheduleNextPrefetch()
   {
@@ -2229,6 +2234,28 @@
       }
     }
 
+    std::unique_ptr<OrthancStone::LookupTableTextureSceneLayer> deepLearningLayer;
+
+    if (deepLearningMask_.get() != NULL &&
+        deepLearningSopInstanceUid_ == instance.GetSopInstanceUid() &&
+        deepLearningFrameNumber_ == frameIndex)
+    {
+      std::vector<uint8_t> lut(4 * 256);
+      for (unsigned int v = 128; v < 256; v++)
+      {
+        lut[4 * v] = 196;
+        lut[4 * v + 1] = 0;
+        lut[4 * v + 2] = 0;
+        lut[4 * v + 3] = 196;
+      }
+      
+      deepLearningLayer.reset(new OrthancStone::LookupTableTextureSceneLayer(*deepLearningMask_));
+      deepLearningLayer->SetLookupTable(lut);
+      deepLearningLayer->SetPixelSpacing(pixelSpacingX, pixelSpacingY);
+      deepLearningLayer->SetFlipX(flipX_);
+      deepLearningLayer->SetFlipY(flipY_);
+    }
+
     StoneAnnotationsRegistry::GetInstance().Load(*stoneAnnotations_, instance.GetSopInstanceUid(), frameIndex);
 
     // Orientation markers, new in Stone Web viewer 2.4
@@ -2305,6 +2332,15 @@
         scene.DeleteLayer(LAYER_ORIENTATION_MARKERS);
       }
 
+      if (deepLearningLayer.get() != NULL)
+      {
+        scene.SetLayer(LAYER_DEEP_LEARNING, deepLearningLayer.release());
+      }
+      else
+      {
+        scene.DeleteLayer(LAYER_DEEP_LEARNING);
+      }
+
       stoneAnnotations_->Render(scene);  // Necessary for "FitContent()" to work
 
       if (fitNextContent_)
@@ -2331,7 +2367,7 @@
     {
       const size_t cursorIndex = cursor_->GetCurrentIndex();
       const OrthancStone::DicomInstanceParameters& instance = frames_->GetInstanceOfFrame(cursorIndex);
-      const size_t frameNumber = frames_->GetFrameNumberInInstance(cursorIndex);
+      const unsigned int frameNumber = frames_->GetFrameNumberInInstance(cursorIndex);
 
       // Only change the scene if the loaded frame still corresponds to the current cursor
       if (instance.GetSopInstanceUid() == loadedSopInstanceUid &&
@@ -2655,7 +2691,7 @@
       {
         const size_t cursorIndex = cursor_->GetCurrentIndex();
         const OrthancStone::DicomInstanceParameters& instance = frames_->GetInstanceOfFrame(cursorIndex);
-        const size_t frameNumber = frames_->GetFrameNumberInInstance(cursorIndex);
+        const unsigned int frameNumber = frames_->GetFrameNumberInInstance(cursorIndex);
 
         StoneAnnotationsRegistry::GetInstance().Save(instance.GetSopInstanceUid(), frameNumber, *stoneAnnotations_);
 
@@ -2850,7 +2886,7 @@
       const size_t cursorIndex = cursor_->GetCurrentIndex();
 
       const OrthancStone::DicomInstanceParameters& instance = frames_->GetInstanceOfFrame(cursorIndex);
-      const size_t frameNumber = frames_->GetFrameNumberInInstance(cursorIndex);
+      const unsigned int frameNumber = frames_->GetFrameNumberInInstance(cursorIndex);
 
       FramesCache::Accessor accessor(*framesCache_, instance.GetSopInstanceUid(), frameNumber);
       if (accessor.IsValid())
@@ -3352,7 +3388,7 @@
     {
       const size_t cursorIndex = cursor_->GetCurrentIndex();
       const OrthancStone::DicomInstanceParameters& instance = frames_->GetInstanceOfFrame(cursorIndex);
-      const size_t frameNumber = frames_->GetFrameNumberInInstance(cursorIndex);
+      const unsigned int frameNumber = frames_->GetFrameNumberInInstance(cursorIndex);
 
       if (instance.GetSopInstanceUid() == sopInstanceUid &&
           frameNumber == frame)
@@ -3367,6 +3403,43 @@
       }
     }    
   }
+
+
+  bool GetCurrentFrame(std::string& sopInstanceUid /* out */,
+                       unsigned int& frameNumber /* out */) const
+  {
+    if (cursor_.get() != NULL &&
+        frames_.get() != NULL)
+    {
+      const size_t cursorIndex = cursor_->GetCurrentIndex();
+      const OrthancStone::DicomInstanceParameters& instance = frames_->GetInstanceOfFrame(cursorIndex);
+      sopInstanceUid = instance.GetSopInstanceUid();
+      frameNumber = frames_->GetFrameNumberInInstance(cursorIndex);
+      return true;
+    }
+    else
+    {
+      return false;
+    }
+  }
+
+
+  void SetDeepLearningMask(const std::string& sopInstanceUid,
+                           unsigned int frameNumber,
+                           const Orthanc::ImageAccessor& mask)
+  {
+    std::string currentSopInstanceUid;
+    unsigned int currentFrameNumber;
+    if (GetCurrentFrame(currentSopInstanceUid, currentFrameNumber) &&
+        sopInstanceUid == currentSopInstanceUid &&
+        frameNumber == currentFrameNumber)
+    {
+      deepLearningSopInstanceUid_ = sopInstanceUid;
+      deepLearningFrameNumber_ = frameNumber;
+      deepLearningMask_.reset(Orthanc::Image::Clone(mask));
+      Redraw();
+    }
+  }
 };
 
 
@@ -3696,6 +3769,218 @@
 }
 
 
+#include <emscripten/fetch.h>
+#include "deep-learning/WebAssembly/Worker.pb.h"
+
+enum DeepLearningState
+{
+  DeepLearningState_Waiting,
+  DeepLearningState_Pending,
+  DeepLearningState_Running
+};
+
+static DeepLearningState deepLearningState_ = DeepLearningState_Waiting;
+static worker_handle deepLearningWorker_;
+static std::string deepLearningPendingSopInstanceUid_;
+static unsigned int deepLearningPendingFrameNumber_;
+
+// Forward declaration
+static void DeepLearningCallback(char* data,
+                                 int size,
+                                 void* payload);
+
+static void SendRequestToWebWorker(const OrthancStone::Messages::Request& request)
+{
+  std::string s;
+  if (request.SerializeToString(&s) &&
+      !s.empty())
+  {
+    emscripten_call_worker(deepLearningWorker_, "Execute", &s[0], s.size(), DeepLearningCallback, NULL);
+  }
+  else
+  {
+    throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError,
+                                    "Cannot send command to the Web worker");
+  }
+}
+
+static void DeepLearningSchedule(const std::string& sopInstanceUid,
+                                 unsigned int frameNumber)
+{
+  if (deepLearningState_ == DeepLearningState_Waiting)
+  {
+    LOG(WARNING) << "Starting deep learning on: " << sopInstanceUid << " / " << frameNumber;
+
+    FramesCache::Accessor accessor(*framesCache_, sopInstanceUid, frameNumber);
+    if (accessor.IsValid() &&
+        accessor.GetImage().GetFormat() == Orthanc::PixelFormat_Float32)
+    {
+      const Orthanc::ImageAccessor& image = accessor.GetImage();
+
+      OrthancStone::Messages::Request request;
+      request.set_type(OrthancStone::Messages::RequestType::LOAD_IMAGE);
+      request.mutable_load_image()->set_sop_instance_uid(sopInstanceUid);
+      request.mutable_load_image()->set_frame_number(frameNumber);
+      request.mutable_load_image()->set_width(image.GetWidth());
+      request.mutable_load_image()->set_height(image.GetHeight());
+
+      const unsigned int height = image.GetHeight();
+      const unsigned int width = image.GetWidth();
+      for (unsigned int y = 0; y < height; y++)
+      {
+        const float* p = reinterpret_cast<const float*>(image.GetConstRow(y));
+        for (unsigned int x = 0; x < width; x++, p++)
+        {
+          request.mutable_load_image()->mutable_values()->Add(*p);
+        }
+      }
+
+      deepLearningState_ = DeepLearningState_Running;
+      SendRequestToWebWorker(request);
+    }
+    else
+    {
+      LOG(ERROR) << "Cannot access the frame content, maybe a color image?";
+
+      EM_ASM({
+          const customEvent = document.createEvent("CustomEvent");
+          customEvent.initCustomEvent("DeepLearningStep", false, false,
+                                      { "progress" : "0" });
+          window.dispatchEvent(customEvent);
+        });
+    }
+  }
+  else
+  {
+    deepLearningState_ = DeepLearningState_Pending;
+    deepLearningPendingSopInstanceUid_ = sopInstanceUid;
+    deepLearningPendingFrameNumber_ = frameNumber;
+  }
+}
+
+static void DeepLearningNextStep()
+{
+  switch (deepLearningState_)
+  {
+    case DeepLearningState_Pending:
+      deepLearningState_ = DeepLearningState_Waiting;
+      DeepLearningSchedule(deepLearningPendingSopInstanceUid_, deepLearningPendingFrameNumber_);
+      break;
+      
+    case DeepLearningState_Running:
+    {
+      OrthancStone::Messages::Request request;
+      request.set_type(OrthancStone::Messages::RequestType::EXECUTE_STEP);
+      SendRequestToWebWorker(request);
+      break;
+    }
+
+    default:
+      throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError, "Bad state for deep learning");
+  }
+}
+
+static void DeepLearningCallback(char* data,
+                                 int size,
+                                 void* payload)
+{
+  try
+  {
+    OrthancStone::Messages::Response response;
+    if (response.ParseFromArray(data, size))
+    {
+      switch (response.type())
+      {
+        case OrthancStone::Messages::ResponseType::INITIALIZED:
+          DISPATCH_JAVASCRIPT_EVENT("DeepLearningInitialized");
+          break;
+
+        case OrthancStone::Messages::ResponseType::PARSED_MODEL:
+          LOG(WARNING) << "Number of steps in the model: " << response.parse_model().number_of_steps();
+          DISPATCH_JAVASCRIPT_EVENT("DeepLearningModelReady");
+          break;
+
+        case OrthancStone::Messages::ResponseType::LOADED_IMAGE:
+          DeepLearningNextStep();
+          break;
+
+        case OrthancStone::Messages::ResponseType::STEP_DONE:
+        {
+          EM_ASM({
+              const customEvent = document.createEvent("CustomEvent");
+              customEvent.initCustomEvent("DeepLearningStep", false, false,
+                                          { "progress" : $0 });
+              window.dispatchEvent(customEvent);
+            },
+            response.step().progress()
+            );
+
+          if (response.step().done())
+          {
+            deepLearningState_ = DeepLearningState_Waiting;
+
+            const unsigned int height = response.step().mask().height();
+            const unsigned int width = response.step().mask().width();
+            
+            LOG(WARNING) << "SUCCESS! Mask: " << width << "x" << height << " for frame "
+                         << response.step().mask().sop_instance_uid() << " / "
+                         << response.step().mask().frame_number();
+
+            Orthanc::Image mask(Orthanc::PixelFormat_Grayscale8, width, height, false);
+
+            size_t pos = 0;
+            for (unsigned int y = 0; y < height; y++)
+            {
+              uint8_t* p = reinterpret_cast<uint8_t*>(mask.GetRow(y));
+              for (unsigned int x = 0; x < width; x++, p++, pos++)
+              {
+                *p = response.step().mask().values(pos) ? 255 : 0;
+              }
+            }
+
+            for (Viewports::iterator it = allViewports_.begin(); it != allViewports_.end(); ++it)
+            {
+              assert(it->second != NULL);
+              it->second->SetDeepLearningMask(response.step().mask().sop_instance_uid(),
+                                              response.step().mask().frame_number(), mask);
+            }
+          }
+          else
+          {
+            DeepLearningNextStep();
+          }
+        
+          break;
+        }
+
+        default:
+          LOG(ERROR) << "Unsupported response type from the deep learning worker";
+      }
+    }
+    else
+    {
+      LOG(ERROR) << "Bad response received from the deep learning worker";
+    }
+  }
+  EXTERN_CATCH_EXCEPTIONS;
+}
+
+static void DeepLearningModelLoaded(emscripten_fetch_t *fetch)
+{
+  try
+  {
+    LOG(WARNING) << "Deep learning model loaded: " << fetch->numBytes;
+
+    OrthancStone::Messages::Request request;
+    request.set_type(OrthancStone::Messages::RequestType::PARSE_MODEL);
+    request.mutable_parse_model()->mutable_content()->assign(fetch->data, fetch->numBytes);
+    
+    emscripten_fetch_close(fetch);  // Don't use "fetch" below
+    SendRequestToWebWorker(request);
+  }
+  EXTERN_CATCH_EXCEPTIONS;
+}
+
 extern "C"
 {
   int main(int argc, char const *argv[]) 
@@ -3711,11 +3996,55 @@
     framesCache_.reset(new FramesCache);
     osiriXAnnotations_.reset(new OrthancStone::OsiriX::CollectionOfAnnotations);
 
+    deepLearningWorker_ = emscripten_create_worker("DeepLearningWorker.js");
+    emscripten_call_worker(deepLearningWorker_, "Initialize", NULL, 0, DeepLearningCallback, NULL);
+
     DISPATCH_JAVASCRIPT_EVENT("StoneInitialized");
   }
 
 
   EMSCRIPTEN_KEEPALIVE
+  void LoadDeepLearningModel(const char* uri)
+  {
+    try
+    {
+      LOG(WARNING) << "Loading deep learning model: " << uri;
+
+      emscripten_fetch_attr_t attr;
+      emscripten_fetch_attr_init(&attr);
+      strcpy(attr.requestMethod, "GET");
+      attr.attributes = EMSCRIPTEN_FETCH_LOAD_TO_MEMORY;
+      attr.onsuccess = DeepLearningModelLoaded;
+      attr.onerror = NULL;
+      emscripten_fetch(&attr, uri);
+    }
+    EXTERN_CATCH_EXCEPTIONS;
+  }
+
+
+  EMSCRIPTEN_KEEPALIVE
+  void ApplyDeepLearningModel(const char* canvas)
+  {
+    try
+    {
+      boost::shared_ptr<ViewerViewport> viewport = GetViewport(canvas);
+
+      std::string sopInstanceUid;
+      unsigned int frameNumber;
+      if (viewport->GetCurrentFrame(sopInstanceUid, frameNumber))
+      {
+        DeepLearningSchedule(sopInstanceUid, frameNumber);
+      }
+      else
+      {
+        LOG(WARNING) << "No active frame";
+      }
+    }
+    EXTERN_CATCH_EXCEPTIONS;
+  }
+
+
+  EMSCRIPTEN_KEEPALIVE
   void SetDicomWebRoot(const char* uri,
                        int useRendered)
   {