# HG changeset patch
# User Sebastien Jodogne <s.jodogne@gmail.com>
# Date 1688972380 -7200
# Node ID c72fbdecdc382876c14ce542538df1a15e6e8b50
# Parent  35c241231af2599f86a6cede481e47224f9c19de
reorganization

diff -r 35c241231af2 -r c72fbdecdc38 ViewerPlugin/CMakeLists.txt
--- a/ViewerPlugin/CMakeLists.txt	Mon Jul 10 08:31:50 2023 +0200
+++ b/ViewerPlugin/CMakeLists.txt	Mon Jul 10 08:59:40 2023 +0200
@@ -183,6 +183,7 @@
 
 set(ORTHANC_WSI_SOURCES
   DicomPyramidCache.cpp
+  IIIF.cpp
   OrthancPluginConnection.cpp
   Plugin.cpp
   RawTile.cpp
diff -r 35c241231af2 -r c72fbdecdc38 ViewerPlugin/DicomPyramidCache.cpp
--- a/ViewerPlugin/DicomPyramidCache.cpp	Mon Jul 10 08:31:50 2023 +0200
+++ b/ViewerPlugin/DicomPyramidCache.cpp	Mon Jul 10 08:59:40 2023 +0200
@@ -23,10 +23,15 @@
 #include "../Framework/PrecompiledHeadersWSI.h"
 #include "DicomPyramidCache.h"
 
+#include "OrthancPluginConnection.h"
+
 #include <Compatibility.h>  // For std::unique_ptr
 
 #include <cassert>
 
+static std::unique_ptr<OrthancWSI::DicomPyramidCache>  singleton_;
+
+
 namespace OrthancWSI
 {
   DicomPyramid* DicomPyramidCache::GetCachedPyramid(const std::string& seriesId)
@@ -67,8 +72,9 @@
     // time-consuming operation, we don't want it to block other clients)
     lock.unlock();
 
+    assert(orthanc_.get() != NULL);
     std::unique_ptr<DicomPyramid> pyramid
-      (new DicomPyramid(orthanc_, seriesId, true /* use metadata cache */));
+      (new DicomPyramid(*orthanc_, seriesId, true /* use metadata cache */));
 
     {
       // The pyramid is constructed: Store it into the cache
@@ -112,11 +118,15 @@
   }
 
 
-  DicomPyramidCache::DicomPyramidCache(OrthancStone::IOrthancConnection& orthanc,
+  DicomPyramidCache::DicomPyramidCache(OrthancStone::IOrthancConnection* orthanc /* takes ownership */,
                                        size_t maxSize) :
     orthanc_(orthanc),
     maxSize_(maxSize)
   {
+    if (orthanc == NULL)
+    {
+      throw Orthanc::OrthancException(Orthanc::ErrorCode_NullPointer);
+    }
   }
 
 
@@ -135,6 +145,45 @@
   }
 
 
+  void DicomPyramidCache::InitializeInstance(size_t maxSize)
+  {
+    if (singleton_.get() == NULL)
+    {
+      singleton_.reset(new DicomPyramidCache(new OrthancWSI::OrthancPluginConnection, maxSize));
+    }
+    else
+    {
+      throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls);
+    }
+  }
+
+
+  void DicomPyramidCache::FinalizeInstance()
+  {
+    if (singleton_.get() == NULL)
+    {
+      throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls);
+    }
+    else
+    {
+      singleton_.reset(NULL);
+    }
+  }
+
+
+  DicomPyramidCache& DicomPyramidCache::GetInstance()
+  {
+    if (singleton_.get() == NULL)
+    {
+      throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls);
+    }
+    else
+    {
+      return *singleton_;
+    }
+  }
+
+
   void DicomPyramidCache::Invalidate(const std::string& seriesId)
   {
     boost::mutex::scoped_lock  lock(mutex_);
@@ -151,10 +200,10 @@
   }
 
 
-  DicomPyramidCache::Locker::Locker(DicomPyramidCache& cache,
-                                    const std::string& seriesId) :
-    lock_(cache.mutex_),
-    pyramid_(cache.GetPyramid(seriesId, lock_))
+  DicomPyramidCache::Locker::Locker(const std::string& seriesId) :
+    cache_(DicomPyramidCache::GetInstance()),
+    lock_(cache_.mutex_),
+    pyramid_(cache_.GetPyramid(seriesId, lock_))
   {
   }
 }
diff -r 35c241231af2 -r c72fbdecdc38 ViewerPlugin/DicomPyramidCache.h
--- a/ViewerPlugin/DicomPyramidCache.h	Mon Jul 10 08:31:50 2023 +0200
+++ b/ViewerPlugin/DicomPyramidCache.h	Mon Jul 10 08:59:40 2023 +0200
@@ -27,6 +27,8 @@
 #include <Cache/LeastRecentlyUsedIndex.h>
 
 #include <boost/thread/mutex.hpp>
+#include <string>
+
 
 namespace OrthancWSI
 {
@@ -35,11 +37,14 @@
   private:
     typedef Orthanc::LeastRecentlyUsedIndex<std::string, DicomPyramid*>  Cache;
 
-    boost::mutex                       mutex_;
-    OrthancStone::IOrthancConnection&  orthanc_;
-    size_t                             maxSize_;
-    Cache                              cache_;
+    std::unique_ptr<OrthancStone::IOrthancConnection>  orthanc_;
 
+    boost::mutex  mutex_;
+    size_t        maxSize_;
+    Cache         cache_;
+
+    DicomPyramidCache(OrthancStone::IOrthancConnection* orthanc /* takes ownership */,
+                      size_t maxSize);
 
     DicomPyramid* GetCachedPyramid(const std::string& seriesId);
 
@@ -47,22 +52,25 @@
                              boost::mutex::scoped_lock& lock);
 
   public:
-    DicomPyramidCache(OrthancStone::IOrthancConnection& orthanc,
-                      size_t maxSize);
+    ~DicomPyramidCache();
+
+    static void InitializeInstance(size_t maxSize);
 
-    ~DicomPyramidCache();
+    static void FinalizeInstance();
+
+    static DicomPyramidCache& GetInstance();
 
     void Invalidate(const std::string& seriesId);
 
     class Locker : public boost::noncopyable
     {
     private:
+      DicomPyramidCache&         cache_;
       boost::mutex::scoped_lock  lock_;
       DicomPyramid&              pyramid_;
 
     public:
-      Locker(DicomPyramidCache& cache,
-             const std::string& seriesId);
+      Locker(const std::string& seriesId);
 
       DicomPyramid& GetPyramid() const
       {
diff -r 35c241231af2 -r c72fbdecdc38 ViewerPlugin/IIIF.cpp
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ViewerPlugin/IIIF.cpp	Mon Jul 10 08:59:40 2023 +0200
@@ -0,0 +1,424 @@
+/**
+ * Orthanc - A Lightweight, RESTful DICOM Store
+ * Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics
+ * Department, University Hospital of Liege, Belgium
+ * Copyright (C) 2017-2023 Osimis S.A., Belgium
+ * Copyright (C) 2021-2023 Sebastien Jodogne, ICTEAM UCLouvain, Belgium
+ *
+ * This program is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU Affero General Public License
+ * as published by the Free Software Foundation, either version 3 of
+ * the License, or (at your option) any later version.
+ *
+ * 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
+ * Affero General Public License for more details.
+ *
+ * You should have received a copy of the GNU Affero General Public License
+ * along with this program. If not, see <http://www.gnu.org/licenses/>.
+ **/
+
+
+#include "../Framework/PrecompiledHeadersWSI.h"
+#include "IIIF.h"
+
+#include "DicomPyramidCache.h"
+#include "RawTile.h"
+#include "../Resources/Orthanc/Plugins/OrthancPluginCppWrapper.h"
+
+#include <Images/Image.h>
+#include <Images/ImageProcessing.h>
+#include <Logging.h>
+
+#include <boost/regex.hpp>
+#include <boost/math/special_functions/round.hpp>
+
+
+static std::string  iiifPublicUrl_;
+
+
+static void ServeIIIFImageInfo(OrthancPluginRestOutput* output,
+                               const char* url,
+                               const OrthancPluginHttpRequest* request)
+{
+  std::string seriesId(request->groups[0]);
+
+  LOG(INFO) << "IIIF: Image API call to whole-slide pyramid of series " << seriesId;
+
+  OrthancWSI::DicomPyramidCache::Locker locker(seriesId);
+
+  if (locker.GetPyramid().GetLevelCount() == 0)
+  {
+    throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError);
+  }
+
+  if (locker.GetPyramid().GetTileWidth(0) != locker.GetPyramid().GetTileHeight(0))
+  {
+    throw Orthanc::OrthancException(Orthanc::ErrorCode_IncompatibleImageFormat,
+                                    "IIIF doesn't support non-isotropic tile sizes");
+  }
+
+  for (unsigned int i = 1; i < locker.GetPyramid().GetLevelCount(); i++)
+  {
+    if (locker.GetPyramid().GetTileWidth(i) != locker.GetPyramid().GetTileWidth(0) ||
+        locker.GetPyramid().GetTileHeight(i) != locker.GetPyramid().GetTileHeight(0))
+    {
+      throw Orthanc::OrthancException(Orthanc::ErrorCode_IncompatibleImageFormat,
+                                      "IIIF doesn't support levels with varying tile sizes");
+    }
+  }
+
+  Json::Value sizes = Json::arrayValue;
+  Json::Value scaleFactors = Json::arrayValue;
+
+  for (unsigned int i = locker.GetPyramid().GetLevelCount(); i > 0; i--)
+  {
+    /**
+     * Openseadragon seems to have difficulties in rendering
+     * non-integer scale factors. Consequently, we only keep the
+     * levels with an integer scale factor.
+     **/
+    if (locker.GetPyramid().GetLevelWidth(0) % locker.GetPyramid().GetLevelWidth(i - 1) == 0 &&
+        locker.GetPyramid().GetLevelHeight(0) % locker.GetPyramid().GetLevelHeight(i - 1) == 0)
+    {
+      Json::Value level;
+      level["width"] = locker.GetPyramid().GetLevelWidth(i - 1);
+      level["height"] = locker.GetPyramid().GetLevelHeight(i - 1);
+      sizes.append(level);
+
+      scaleFactors.append(static_cast<float>(locker.GetPyramid().GetLevelWidth(0)) /
+                          static_cast<float>(locker.GetPyramid().GetLevelWidth(i - 1)));
+    }
+  }
+
+  Json::Value tiles;
+  tiles["width"] = locker.GetPyramid().GetTileWidth(0);
+  tiles["height"] = locker.GetPyramid().GetTileHeight(0);
+  tiles["scaleFactors"] = scaleFactors;
+
+  Json::Value result;
+  result["@context"] = "http://iiif.io/api/image/2/context.json";
+  result["@id"] = iiifPublicUrl_ + seriesId;
+  result["profile"] = "http://iiif.io/api/image/2/level0.json";
+  result["protocol"] = "http://iiif.io/api/image";
+  result["width"] = locker.GetPyramid().GetLevelWidth(0);
+  result["height"] = locker.GetPyramid().GetLevelHeight(0);
+  result["sizes"] = sizes;
+
+  result["tiles"] = Json::arrayValue;
+  result["tiles"].append(tiles);
+
+  std::string s = result.toStyledString();
+  OrthancPluginAnswerBuffer(OrthancPlugins::GetGlobalContext(), output, s.c_str(), s.size(), "application/json");
+}
+
+
+static unsigned int GetPhysicalTileWidth(const OrthancWSI::ITiledPyramid& pyramid,
+                                         unsigned int level)
+{
+  return static_cast<unsigned int>(boost::math::iround(
+                                     static_cast<float>(pyramid.GetTileWidth(level)) *
+                                     static_cast<float>(pyramid.GetLevelWidth(0)) /
+                                     static_cast<float>(pyramid.GetLevelWidth(level))));
+}
+
+
+static unsigned int GetPhysicalTileHeight(const OrthancWSI::ITiledPyramid& pyramid,
+                                          unsigned int level)
+{
+  return static_cast<unsigned int>(boost::math::iround(
+                                     static_cast<float>(pyramid.GetTileHeight(level)) *
+                                     static_cast<float>(pyramid.GetLevelHeight(0)) /
+                                     static_cast<float>(pyramid.GetLevelHeight(level))));
+}
+
+
+static void ServeIIIFImageTile(OrthancPluginRestOutput* output,
+                               const char* url,
+                               const OrthancPluginHttpRequest* request)
+{
+  std::string seriesId(request->groups[0]);
+  std::string region(request->groups[1]);
+  std::string size(request->groups[2]);
+  std::string rotation(request->groups[3]);
+  std::string quality(request->groups[4]);
+  std::string format(request->groups[5]);
+
+  LOG(INFO) << "IIIF: Image API call to tile of series " << seriesId << ": "
+            << "region=" << region << "; size=" << size << "; rotation="
+            << rotation << "; quality=" << quality << "; format=" << format;
+
+  if (rotation != "0")
+  {
+    throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented, "IIIF - Unsupported rotation: " + rotation);
+  }
+
+  if (quality != "default")
+  {
+    throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented, "IIIF - Unsupported quality: " + quality);
+  }
+
+  if (format != "jpg")
+  {
+    throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented, "IIIF - Unsupported format: " + format);
+  }
+
+  if (region == "full")
+  {
+    OrthancWSI::DicomPyramidCache::Locker locker(seriesId);
+
+    OrthancWSI::ITiledPyramid& pyramid = locker.GetPyramid();
+    const unsigned int level = pyramid.GetLevelCount() - 1;
+
+    Orthanc::Image full(Orthanc::PixelFormat_RGB24, pyramid.GetLevelWidth(level), pyramid.GetLevelHeight(level), false);
+    Orthanc::ImageProcessing::Set(full, 255, 255, 255, 0);
+
+    const unsigned int nx = OrthancWSI::CeilingDivision(pyramid.GetLevelWidth(level), pyramid.GetTileWidth(level));
+    const unsigned int ny = OrthancWSI::CeilingDivision(pyramid.GetLevelHeight(level), pyramid.GetTileHeight(level));
+    for (unsigned int ty = 0; ty < ny; ty++)
+    {
+      const unsigned int y = ty * pyramid.GetTileHeight(level);
+      const unsigned int height = std::min(pyramid.GetTileHeight(level), full.GetHeight() - y);
+
+      for (unsigned int tx = 0; tx < nx; tx++)
+      {
+        const unsigned int x = tx * pyramid.GetTileWidth(level);
+        std::unique_ptr<Orthanc::ImageAccessor> tile(pyramid.DecodeTile(level, tx, ty));
+
+        const unsigned int width = std::min(pyramid.GetTileWidth(level), full.GetWidth() - x);
+
+        Orthanc::ImageAccessor source, target;
+        tile->GetRegion(source, 0, 0, width, height);
+        full.GetRegion(target, x, y, width, height);
+
+        Orthanc::ImageProcessing::Copy(target, source);
+      }
+    }
+
+    std::string encoded;
+    OrthancWSI::RawTile::Encode(encoded, full, Orthanc::MimeType_Jpeg);
+
+    OrthancPluginAnswerBuffer(OrthancPlugins::GetGlobalContext(), output, encoded.c_str(),
+                              encoded.size(), Orthanc::EnumerationToString(Orthanc::MimeType_Jpeg));
+  }
+  else
+  {
+    int regionX, regionY, regionWidth, regionHeight;
+
+    bool ok = false;
+    boost::regex regionPattern("([0-9]+),([0-9]+),([0-9]+),([0-9]+)");
+    boost::cmatch regionWhat;
+    if (regex_match(region.c_str(), regionWhat, regionPattern))
+    {
+      try
+      {
+        regionX = boost::lexical_cast<int>(regionWhat[1]);
+        regionY = boost::lexical_cast<int>(regionWhat[2]);
+        regionWidth = boost::lexical_cast<int>(regionWhat[3]);
+        regionHeight = boost::lexical_cast<int>(regionWhat[4]);
+        ok = (regionX >= 0 &&
+              regionY >= 0 &&
+              regionWidth > 0 &&
+              regionHeight > 0);
+      }
+      catch (boost::bad_lexical_cast&)
+      {
+      }
+    }
+
+    if (!ok)
+    {
+      throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented, "IIIF - Not a (x,y,width,height) region: " + region);
+    }
+
+    int cropWidth;
+    boost::regex sizePattern("([0-9]+),");
+    boost::cmatch sizeWhat;
+    if (regex_match(size.c_str(), sizeWhat, sizePattern))
+    {
+      try
+      {
+        cropWidth = boost::lexical_cast<int>(sizeWhat[1]);
+        ok = (cropWidth > 0);
+      }
+      catch (boost::bad_lexical_cast&)
+      {
+      }
+    }
+
+    if (!ok)
+    {
+      throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented, "IIIF - Not a (width,) size: " + size);
+    }
+
+    std::unique_ptr<OrthancWSI::RawTile> rawTile;
+    std::unique_ptr<Orthanc::ImageAccessor> toCrop;
+
+    {
+      OrthancWSI::DicomPyramidCache::Locker locker(seriesId);
+
+      OrthancWSI::ITiledPyramid& pyramid = locker.GetPyramid();
+
+      unsigned int level;
+      for (level = 0; level < pyramid.GetLevelCount(); level++)
+      {
+        const unsigned int physicalTileWidth = GetPhysicalTileWidth(pyramid, level);
+        const unsigned int physicalTileHeight = GetPhysicalTileHeight(pyramid, level);
+
+        if (regionX % physicalTileWidth == 0 &&
+            regionY % physicalTileHeight == 0 &&
+            regionWidth <= physicalTileWidth &&
+            regionHeight <= physicalTileHeight &&
+            regionX + regionWidth <= pyramid.GetLevelWidth(0) &&
+            regionY + regionHeight <= pyramid.GetLevelHeight(0))
+        {
+          break;
+        }
+      }
+
+      if (level == pyramid.GetLevelCount())
+      {
+        throw Orthanc::OrthancException(Orthanc::ErrorCode_BadRequest, "IIIF - Cannot locate the level of interest");
+      }
+      else if (cropWidth > pyramid.GetTileWidth(level))
+      {
+        throw Orthanc::OrthancException(Orthanc::ErrorCode_BadRequest, "IIIF - Request for a cropping that is too large for the tile size");
+      }
+      else
+      {
+        rawTile.reset(new OrthancWSI::RawTile(locker.GetPyramid(), level,
+                                              regionX / GetPhysicalTileWidth(pyramid, level),
+                                              regionY / GetPhysicalTileHeight(pyramid, level)));
+
+        if (cropWidth < pyramid.GetTileWidth(level))
+        {
+          toCrop.reset(rawTile->Decode());
+          rawTile.reset(NULL);
+        }
+      }
+    }
+
+    if (rawTile.get() != NULL)
+    {
+      assert(toCrop.get() == NULL);
+
+      // Level 0 Compliance of IIIF expects JPEG files
+      rawTile->Answer(output, Orthanc::MimeType_Jpeg);
+    }
+    else if (toCrop.get() != NULL)
+    {
+      assert(rawTile.get() == NULL);
+      assert(cropWidth < toCrop->GetWidth());
+
+      Orthanc::ImageAccessor cropped;
+      toCrop->GetRegion(cropped, 0, 0, cropWidth, toCrop->GetHeight());
+
+      std::string encoded;
+      OrthancWSI::RawTile::Encode(encoded, cropped, Orthanc::MimeType_Jpeg);
+
+      OrthancPluginAnswerBuffer(OrthancPlugins::GetGlobalContext(), output, encoded.c_str(),
+                                encoded.size(), Orthanc::EnumerationToString(Orthanc::MimeType_Jpeg));
+    }
+    else
+    {
+      throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError);
+    }
+  }
+}
+
+
+static void ServeIIIFManifest(OrthancPluginRestOutput* output,
+                              const char* url,
+                              const OrthancPluginHttpRequest* request)
+{
+  /**
+   * This is based on IIIF cookbook: "Support Deep Viewing with Basic
+   * Use of a IIIF Image Service."
+   * https://iiif.io/api/cookbook/recipe/0005-image-service/
+   **/
+
+  std::string seriesId(request->groups[0]);
+
+  LOG(INFO) << "IIIF: Presentation API call to whole-slide pyramid of series " << seriesId;
+
+  Json::Value study, series;
+  if (!OrthancPlugins::RestApiGet(series, "/series/" + seriesId, false) ||
+      !OrthancPlugins::RestApiGet(study, "/series/" + seriesId + "/study", false))
+  {
+    throw Orthanc::OrthancException(Orthanc::ErrorCode_UnknownResource);
+  }
+
+  unsigned int width, height;
+
+  {
+    OrthancWSI::DicomPyramidCache::Locker locker(seriesId);
+    width = locker.GetPyramid().GetLevelWidth(0);
+    height = locker.GetPyramid().GetLevelHeight(0);
+  }
+
+  const std::string base = iiifPublicUrl_ + seriesId;
+
+  Json::Value service;
+  service["id"] = base;
+  service["profile"] = "level0";
+  service["type"] = "ImageService3";
+
+  Json::Value body;
+  body["id"] = base + "/full/max/0/default.jpg";
+  body["type"] = "Image";
+  body["format"] = Orthanc::EnumerationToString(Orthanc::MimeType_Jpeg);
+  body["height"] = height;
+  body["width"] = width;
+  body["service"].append(service);
+
+  Json::Value annotation;
+  annotation["id"] = base + "/annotation/p0001-image";
+  annotation["type"] = "Annotation";
+  annotation["motivation"] = "painting";
+  annotation["body"] = body;
+  annotation["target"] = base + "/canvas/p1";
+
+  Json::Value annotationPage;
+  annotationPage["id"] = base + "/page/p1/1";
+  annotationPage["type"] = "AnnotationPage";
+  annotationPage["items"].append(annotation);
+
+  Json::Value canvas;
+  canvas["id"] = annotation["target"];
+  canvas["type"] = "Canvas";
+  canvas["width"] = width;
+  canvas["height"] = height;
+
+  Json::Value labels = Json::arrayValue;
+  labels.append(series["MainDicomTags"]["SeriesDate"].asString() + " - " +
+                series["MainDicomTags"]["SeriesDescription"].asString());
+  canvas["label"]["en"] = labels;
+
+  canvas["items"].append(annotationPage);
+
+  Json::Value manifest;
+  manifest["@context"] = "http://iiif.io/api/presentation/3/context.json";
+  manifest["id"] = base + "/manifest.json";
+  manifest["type"] = "Manifest";
+
+  labels = Json::arrayValue;
+  labels.append(study["MainDicomTags"]["StudyDate"].asString() + " - " +
+                study["MainDicomTags"]["StudyDescription"].asString());
+  manifest["label"]["en"] = labels;
+
+  manifest["items"].append(canvas);
+
+  std::string s = manifest.toStyledString();
+  OrthancPluginAnswerBuffer(OrthancPlugins::GetGlobalContext(), output, s.c_str(), s.size(), "application/json");
+}
+
+
+void InitializeIIIF(const std::string& iiifPublicUrl)
+{
+  iiifPublicUrl_ = iiifPublicUrl;
+
+  OrthancPlugins::RegisterRestCallback<ServeIIIFImageInfo>("/wsi/iiif/([0-9a-f-]+)/info.json", true);
+  OrthancPlugins::RegisterRestCallback<ServeIIIFImageTile>("/wsi/iiif/([0-9a-f-]+)/([0-9a-z,:]+)/([0-9a-z,!:]+)/([0-9,!]+)/([a-z]+)\\.([a-z]+)", true);
+  OrthancPlugins::RegisterRestCallback<ServeIIIFManifest>("/wsi/iiif/([0-9a-f-]+)/manifest.json", true);
+}
diff -r 35c241231af2 -r c72fbdecdc38 ViewerPlugin/IIIF.h
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ViewerPlugin/IIIF.h	Mon Jul 10 08:59:40 2023 +0200
@@ -0,0 +1,27 @@
+/**
+ * Orthanc - A Lightweight, RESTful DICOM Store
+ * Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics
+ * Department, University Hospital of Liege, Belgium
+ * Copyright (C) 2017-2023 Osimis S.A., Belgium
+ * Copyright (C) 2021-2023 Sebastien Jodogne, ICTEAM UCLouvain, Belgium
+ *
+ * This program is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU Affero General Public License
+ * as published by the Free Software Foundation, either version 3 of
+ * the License, or (at your option) any later version.
+ *
+ * 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
+ * Affero General Public License for more details.
+ *
+ * You should have received a copy of the GNU Affero General Public License
+ * along with this program. If not, see <http://www.gnu.org/licenses/>.
+ **/
+
+
+#pragma once
+
+#include <string>
+
+void InitializeIIIF(const std::string& iiifPublicUrl);
diff -r 35c241231af2 -r c72fbdecdc38 ViewerPlugin/Plugin.cpp
--- a/ViewerPlugin/Plugin.cpp	Mon Jul 10 08:31:50 2023 +0200
+++ b/ViewerPlugin/Plugin.cpp	Mon Jul 10 08:59:40 2023 +0200
@@ -23,7 +23,7 @@
 #include "../Framework/PrecompiledHeadersWSI.h"
 
 #include "DicomPyramidCache.h"
-#include "OrthancPluginConnection.h"
+#include "IIIF.h"
 #include "RawTile.h"
 
 #include <Compatibility.h>  // For std::unique_ptr
@@ -38,12 +38,6 @@
 #include <EmbeddedResources.h>
 
 #include <cassert>
-#include <boost/regex.hpp>
-#include <boost/math/special_functions/round.hpp>
-
-static std::unique_ptr<OrthancWSI::OrthancPluginConnection>  orthanc_;
-static std::unique_ptr<OrthancWSI::DicomPyramidCache>        cache_;
-static std::string                                           publicIIIFUrl_;
 
 static void AnswerSparseTile(OrthancPluginRestOutput* output,
                              unsigned int tileWidth,
@@ -85,7 +79,7 @@
   OrthancPluginLogInfo(OrthancPlugins::GetGlobalContext(), tmp);
   
 
-  OrthancWSI::DicomPyramidCache::Locker locker(*cache_, seriesId);
+  OrthancWSI::DicomPyramidCache::Locker locker(seriesId);
 
   unsigned int totalWidth = locker.GetPyramid().GetLevelWidth(0);
   unsigned int totalHeight = locker.GetPyramid().GetLevelHeight(0);
@@ -154,14 +148,14 @@
   }
 
   // Retrieve the raw tile from the WSI pyramid
-  std::unique_ptr<RawTile> rawTile;
+  std::unique_ptr<OrthancWSI::RawTile> rawTile;
 
   {
-    OrthancWSI::DicomPyramidCache::Locker locker(*cache_, seriesId);
-    rawTile.reset(new RawTile(locker.GetPyramid(),
-                              static_cast<unsigned int>(level),
-                              static_cast<unsigned int>(tileX),
-                              static_cast<unsigned int>(tileY)));
+    OrthancWSI::DicomPyramidCache::Locker locker(seriesId);
+    rawTile.reset(new OrthancWSI::RawTile(locker.GetPyramid(),
+                                          static_cast<unsigned int>(level),
+                                          static_cast<unsigned int>(tileX),
+                                          static_cast<unsigned int>(tileY)));
   }
 
   /**
@@ -185,7 +179,7 @@
     sprintf(tmp, "New instance has been added to series %s, invalidating it", resourceId);
     OrthancPluginLogInfo(OrthancPlugins::GetGlobalContext(), tmp);
 
-    cache_->Invalidate(resourceId);
+    OrthancWSI::DicomPyramidCache::GetInstance().Invalidate(resourceId);
   }
 
   return OrthancPluginErrorCode_Success;
@@ -234,383 +228,6 @@
 }
 
 
-
-void ServeIIIFImageInfo(OrthancPluginRestOutput* output,
-                        const char* url,
-                        const OrthancPluginHttpRequest* request)
-{
-  std::string seriesId(request->groups[0]);
-
-  LOG(INFO) << "IIIF: Image API call to whole-slide pyramid of series " << seriesId;
-
-  OrthancWSI::DicomPyramidCache::Locker locker(*cache_, seriesId);
-
-  if (locker.GetPyramid().GetLevelCount() == 0)
-  {
-    throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError);
-  }
-
-  if (locker.GetPyramid().GetTileWidth(0) != locker.GetPyramid().GetTileHeight(0))
-  {
-    throw Orthanc::OrthancException(Orthanc::ErrorCode_IncompatibleImageFormat,
-                                    "IIIF doesn't support non-isotropic tile sizes");
-  }
-
-  for (unsigned int i = 1; i < locker.GetPyramid().GetLevelCount(); i++)
-  {
-    if (locker.GetPyramid().GetTileWidth(i) != locker.GetPyramid().GetTileWidth(0) ||
-        locker.GetPyramid().GetTileHeight(i) != locker.GetPyramid().GetTileHeight(0))
-    {
-      throw Orthanc::OrthancException(Orthanc::ErrorCode_IncompatibleImageFormat,
-                                      "IIIF doesn't support levels with varying tile sizes");
-    }
-  }
-
-  Json::Value sizes = Json::arrayValue;
-  Json::Value scaleFactors = Json::arrayValue;
-
-  for (unsigned int i = locker.GetPyramid().GetLevelCount(); i > 0; i--)
-  {
-    /**
-     * Openseadragon seems to have difficulties in rendering
-     * non-integer scale factors. Consequently, we only keep the
-     * levels with an integer scale factor.
-     **/
-    if (locker.GetPyramid().GetLevelWidth(0) % locker.GetPyramid().GetLevelWidth(i - 1) == 0 &&
-        locker.GetPyramid().GetLevelHeight(0) % locker.GetPyramid().GetLevelHeight(i - 1) == 0)
-    {
-      Json::Value level;
-      level["width"] = locker.GetPyramid().GetLevelWidth(i - 1);
-      level["height"] = locker.GetPyramid().GetLevelHeight(i - 1);
-      sizes.append(level);
-
-      scaleFactors.append(static_cast<float>(locker.GetPyramid().GetLevelWidth(0)) /
-                          static_cast<float>(locker.GetPyramid().GetLevelWidth(i - 1)));
-    }
-  }
-
-  Json::Value tiles;
-  tiles["width"] = locker.GetPyramid().GetTileWidth(0);
-  tiles["height"] = locker.GetPyramid().GetTileHeight(0);
-  tiles["scaleFactors"] = scaleFactors;
-
-  Json::Value result;
-  result["@context"] = "http://iiif.io/api/image/2/context.json";
-  result["@id"] = publicIIIFUrl_ + seriesId;
-  result["profile"] = "http://iiif.io/api/image/2/level0.json";
-  result["protocol"] = "http://iiif.io/api/image";
-  result["width"] = locker.GetPyramid().GetLevelWidth(0);
-  result["height"] = locker.GetPyramid().GetLevelHeight(0);
-  result["sizes"] = sizes;
-
-  result["tiles"] = Json::arrayValue;
-  result["tiles"].append(tiles);
-
-  std::string s = result.toStyledString();
-  OrthancPluginAnswerBuffer(OrthancPlugins::GetGlobalContext(), output, s.c_str(), s.size(), "application/json");
-}
-
-
-static unsigned int GetPhysicalTileWidth(const OrthancWSI::ITiledPyramid& pyramid,
-                                         unsigned int level)
-{
-  return static_cast<unsigned int>(boost::math::iround(
-                                     static_cast<float>(pyramid.GetTileWidth(level)) *
-                                     static_cast<float>(pyramid.GetLevelWidth(0)) /
-                                     static_cast<float>(pyramid.GetLevelWidth(level))));
-}
-
-
-static unsigned int GetPhysicalTileHeight(const OrthancWSI::ITiledPyramid& pyramid,
-                                          unsigned int level)
-{
-  return static_cast<unsigned int>(boost::math::iround(
-                                     static_cast<float>(pyramid.GetTileHeight(level)) *
-                                     static_cast<float>(pyramid.GetLevelHeight(0)) /
-                                     static_cast<float>(pyramid.GetLevelHeight(level))));
-}
-
-
-void ServeIIIFImageTile(OrthancPluginRestOutput* output,
-                        const char* url,
-                        const OrthancPluginHttpRequest* request)
-{
-  std::string seriesId(request->groups[0]);
-  std::string region(request->groups[1]);
-  std::string size(request->groups[2]);
-  std::string rotation(request->groups[3]);
-  std::string quality(request->groups[4]);
-  std::string format(request->groups[5]);
-
-  LOG(INFO) << "IIIF: Image API call to tile of series " << seriesId << ": "
-            << "region=" << region << "; size=" << size << "; rotation="
-            << rotation << "; quality=" << quality << "; format=" << format;
-
-  if (rotation != "0")
-  {
-    throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented, "IIIF - Unsupported rotation: " + rotation);
-  }
-
-  if (quality != "default")
-  {
-    throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented, "IIIF - Unsupported quality: " + quality);
-  }
-
-  if (format != "jpg")
-  {
-    throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented, "IIIF - Unsupported format: " + format);
-  }
-
-  if (region == "full")
-  {
-    OrthancWSI::DicomPyramidCache::Locker locker(*cache_, seriesId);
-
-    OrthancWSI::ITiledPyramid& pyramid = locker.GetPyramid();
-    const unsigned int level = pyramid.GetLevelCount() - 1;
-
-    Orthanc::Image full(Orthanc::PixelFormat_RGB24, pyramid.GetLevelWidth(level), pyramid.GetLevelHeight(level), false);
-    Orthanc::ImageProcessing::Set(full, 255, 255, 255, 0);
-
-    const unsigned int nx = OrthancWSI::CeilingDivision(pyramid.GetLevelWidth(level), pyramid.GetTileWidth(level));
-    const unsigned int ny = OrthancWSI::CeilingDivision(pyramid.GetLevelHeight(level), pyramid.GetTileHeight(level));
-    for (unsigned int ty = 0; ty < ny; ty++)
-    {
-      const unsigned int y = ty * pyramid.GetTileHeight(level);
-      const unsigned int height = std::min(pyramid.GetTileHeight(level), full.GetHeight() - y);
-
-      for (unsigned int tx = 0; tx < nx; tx++)
-      {
-        const unsigned int x = tx * pyramid.GetTileWidth(level);
-        std::unique_ptr<Orthanc::ImageAccessor> tile(pyramid.DecodeTile(level, tx, ty));
-
-        const unsigned int width = std::min(pyramid.GetTileWidth(level), full.GetWidth() - x);
-
-        Orthanc::ImageAccessor source, target;
-        tile->GetRegion(source, 0, 0, width, height);
-        full.GetRegion(target, x, y, width, height);
-
-        Orthanc::ImageProcessing::Copy(target, source);
-      }
-    }
-
-    std::string encoded;
-    RawTile::Encode(encoded, full, Orthanc::MimeType_Jpeg);
-
-    OrthancPluginAnswerBuffer(OrthancPlugins::GetGlobalContext(), output, encoded.c_str(),
-                              encoded.size(), Orthanc::EnumerationToString(Orthanc::MimeType_Jpeg));
-  }
-  else
-  {
-    int regionX, regionY, regionWidth, regionHeight;
-
-    bool ok = false;
-    boost::regex regionPattern("([0-9]+),([0-9]+),([0-9]+),([0-9]+)");
-    boost::cmatch regionWhat;
-    if (regex_match(region.c_str(), regionWhat, regionPattern))
-    {
-      try
-      {
-        regionX = boost::lexical_cast<int>(regionWhat[1]);
-        regionY = boost::lexical_cast<int>(regionWhat[2]);
-        regionWidth = boost::lexical_cast<int>(regionWhat[3]);
-        regionHeight = boost::lexical_cast<int>(regionWhat[4]);
-        ok = (regionX >= 0 &&
-              regionY >= 0 &&
-              regionWidth > 0 &&
-              regionHeight > 0);
-      }
-      catch (boost::bad_lexical_cast&)
-      {
-      }
-    }
-
-    if (!ok)
-    {
-      throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented, "IIIF - Not a (x,y,width,height) region: " + region);
-    }
-
-    int cropWidth;
-    boost::regex sizePattern("([0-9]+),");
-    boost::cmatch sizeWhat;
-    if (regex_match(size.c_str(), sizeWhat, sizePattern))
-    {
-      try
-      {
-        cropWidth = boost::lexical_cast<int>(sizeWhat[1]);
-        ok = (cropWidth > 0);
-      }
-      catch (boost::bad_lexical_cast&)
-      {
-      }
-    }
-
-    if (!ok)
-    {
-      throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented, "IIIF - Not a (width,) size: " + size);
-    }
-
-    std::unique_ptr<RawTile> rawTile;
-    std::unique_ptr<Orthanc::ImageAccessor> toCrop;
-
-    {
-      OrthancWSI::DicomPyramidCache::Locker locker(*cache_, seriesId);
-
-      OrthancWSI::ITiledPyramid& pyramid = locker.GetPyramid();
-
-      unsigned int level;
-      for (level = 0; level < pyramid.GetLevelCount(); level++)
-      {
-        const unsigned int physicalTileWidth = GetPhysicalTileWidth(pyramid, level);
-        const unsigned int physicalTileHeight = GetPhysicalTileHeight(pyramid, level);
-
-        if (regionX % physicalTileWidth == 0 &&
-            regionY % physicalTileHeight == 0 &&
-            regionWidth <= physicalTileWidth &&
-            regionHeight <= physicalTileHeight &&
-            regionX + regionWidth <= pyramid.GetLevelWidth(0) &&
-            regionY + regionHeight <= pyramid.GetLevelHeight(0))
-        {
-          break;
-        }
-      }
-
-      if (level == pyramid.GetLevelCount())
-      {
-        throw Orthanc::OrthancException(Orthanc::ErrorCode_BadRequest, "IIIF - Cannot locate the level of interest");
-      }
-      else if (cropWidth > pyramid.GetTileWidth(level))
-      {
-        throw Orthanc::OrthancException(Orthanc::ErrorCode_BadRequest, "IIIF - Request for a cropping that is too large for the tile size");
-      }
-      else
-      {
-        rawTile.reset(new RawTile(locker.GetPyramid(), level,
-                                  regionX / GetPhysicalTileWidth(pyramid, level),
-                                  regionY / GetPhysicalTileHeight(pyramid, level)));
-
-        if (cropWidth < pyramid.GetTileWidth(level))
-        {
-          toCrop.reset(rawTile->Decode());
-          rawTile.reset(NULL);
-        }
-      }
-    }
-
-    if (rawTile.get() != NULL)
-    {
-      assert(toCrop.get() == NULL);
-
-      // Level 0 Compliance of IIIF expects JPEG files
-      rawTile->Answer(output, Orthanc::MimeType_Jpeg);
-    }
-    else if (toCrop.get() != NULL)
-    {
-      assert(rawTile.get() == NULL);
-      assert(cropWidth < toCrop->GetWidth());
-
-      Orthanc::ImageAccessor cropped;
-      toCrop->GetRegion(cropped, 0, 0, cropWidth, toCrop->GetHeight());
-
-      std::string encoded;
-      RawTile::Encode(encoded, cropped, Orthanc::MimeType_Jpeg);
-
-      OrthancPluginAnswerBuffer(OrthancPlugins::GetGlobalContext(), output, encoded.c_str(),
-                                encoded.size(), Orthanc::EnumerationToString(Orthanc::MimeType_Jpeg));
-    }
-    else
-    {
-      throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError);
-    }
-  }
-}
-
-
-void ServeIIIFManifest(OrthancPluginRestOutput* output,
-                       const char* url,
-                       const OrthancPluginHttpRequest* request)
-{
-  /**
-   * This is based on IIIF cookbook: "Support Deep Viewing with Basic
-   * Use of a IIIF Image Service."
-   * https://iiif.io/api/cookbook/recipe/0005-image-service/
-   **/
-
-  std::string seriesId(request->groups[0]);
-
-  LOG(INFO) << "IIIF: Presentation API call to whole-slide pyramid of series " << seriesId;
-
-  Json::Value study, series;
-  if (!OrthancPlugins::RestApiGet(series, "/series/" + seriesId, false) ||
-      !OrthancPlugins::RestApiGet(study, "/series/" + seriesId + "/study", false))
-  {
-    throw Orthanc::OrthancException(Orthanc::ErrorCode_UnknownResource);
-  }
-
-  unsigned int width, height;
-
-  {
-    OrthancWSI::DicomPyramidCache::Locker locker(*cache_, seriesId);
-    width = locker.GetPyramid().GetLevelWidth(0);
-    height = locker.GetPyramid().GetLevelHeight(0);
-  }
-
-  const std::string base = publicIIIFUrl_ + seriesId;
-
-  Json::Value service;
-  service["id"] = base;
-  service["profile"] = "level0";
-  service["type"] = "ImageService3";
-
-  Json::Value body;
-  body["id"] = base + "/full/max/0/default.jpg";
-  body["type"] = "Image";
-  body["format"] = Orthanc::EnumerationToString(Orthanc::MimeType_Jpeg);
-  body["height"] = height;
-  body["width"] = width;
-  body["service"].append(service);
-
-  Json::Value annotation;
-  annotation["id"] = base + "/annotation/p0001-image";
-  annotation["type"] = "Annotation";
-  annotation["motivation"] = "painting";
-  annotation["body"] = body;
-  annotation["target"] = base + "/canvas/p1";
-
-  Json::Value annotationPage;
-  annotationPage["id"] = base + "/page/p1/1";
-  annotationPage["type"] = "AnnotationPage";
-  annotationPage["items"].append(annotation);
-
-  Json::Value canvas;
-  canvas["id"] = annotation["target"];
-  canvas["type"] = "Canvas";
-  canvas["width"] = width;
-  canvas["height"] = height;
-
-  Json::Value labels = Json::arrayValue;
-  labels.append(series["MainDicomTags"]["SeriesDate"].asString() + " - " +
-                series["MainDicomTags"]["SeriesDescription"].asString());
-  canvas["label"]["en"] = labels;
-
-  canvas["items"].append(annotationPage);
-
-  Json::Value manifest;
-  manifest["@context"] = "http://iiif.io/api/presentation/3/context.json";
-  manifest["id"] = base + "/manifest.json";
-  manifest["type"] = "Manifest";
-
-  labels = Json::arrayValue;
-  labels.append(study["MainDicomTags"]["StudyDate"].asString() + " - " +
-                study["MainDicomTags"]["StudyDescription"].asString());
-  manifest["label"]["en"] = labels;
-
-  manifest["items"].append(canvas);
-
-  std::string s = manifest.toStyledString();
-  OrthancPluginAnswerBuffer(OrthancPlugins::GetGlobalContext(), output, s.c_str(), s.size(), "application/json");
-}
-
-
 extern "C"
 {
   ORTHANC_PLUGINS_API int32_t OrthancPluginInitialize(OrthancPluginContext* context)
@@ -647,7 +264,7 @@
     // hardware threads (e.g. number of CPUs or cores or
     // hyperthreading units)
     unsigned int threads = Orthanc::SystemToolbox::GetHardwareConcurrency();
-    RawTile::InitializeTranscoderSemaphore(threads);
+    OrthancWSI::RawTile::InitializeTranscoderSemaphore(threads);
 
     char info[1024];
     sprintf(info, "The whole-slide imaging plugin will use at most %u threads to transcode the tiles", threads);
@@ -655,19 +272,7 @@
 
     OrthancPluginSetDescription(context, "Provides a Web viewer of whole-slide microscopic images within Orthanc.");
 
-    orthanc_.reset(new OrthancWSI::OrthancPluginConnection);
-    cache_.reset(new OrthancWSI::DicomPyramidCache(*orthanc_, 10 /* Number of pyramids to be cached - TODO parameter */));
-
-    {
-      // TODO => CONFIG
-      publicIIIFUrl_ = "http://localhost:8042/wsi/iiif";
-
-      if (publicIIIFUrl_.empty() ||
-          publicIIIFUrl_[publicIIIFUrl_.size() - 1] != '/')
-      {
-        publicIIIFUrl_ += "/";
-      }
-    }
+    OrthancWSI::DicomPyramidCache::InitializeInstance(10 /* Number of pyramids to be cached - TODO parameter */);
 
     OrthancPluginRegisterOnChangeCallback(OrthancPlugins::GetGlobalContext(), OnChangeCallback);
 
@@ -678,9 +283,18 @@
     OrthancPlugins::RegisterRestCallback<ServePyramid>("/wsi/pyramids/([0-9a-f-]+)", true);
     OrthancPlugins::RegisterRestCallback<ServeTile>("/wsi/tiles/([0-9a-f-]+)/([0-9-]+)/([0-9-]+)/([0-9-]+)", true);
 
-    OrthancPlugins::RegisterRestCallback<ServeIIIFImageInfo>("/wsi/iiif/([0-9a-f-]+)/info.json", true);
-    OrthancPlugins::RegisterRestCallback<ServeIIIFImageTile>("/wsi/iiif/([0-9a-f-]+)/([0-9a-z,:]+)/([0-9a-z,!:]+)/([0-9,!]+)/([a-z]+)\\.([a-z]+)", true);
-    OrthancPlugins::RegisterRestCallback<ServeIIIFManifest>("/wsi/iiif/([0-9a-f-]+)/manifest.json", true);
+    {
+      // TODO => CONFIG
+      std::string url = "http://localhost:8042/wsi/iiif";
+
+      if (url.empty() ||
+          url[url.size() - 1] != '/')
+      {
+        url += "/";
+      }
+
+      InitializeIIIF(url);
+    }
 
     // Extend the default Orthanc Explorer with custom JavaScript for WSI
     std::string explorer;
@@ -693,9 +307,8 @@
 
   ORTHANC_PLUGINS_API void OrthancPluginFinalize()
   {
-    cache_.reset(NULL);
-    orthanc_.reset(NULL);
-    RawTile::FinalizeTranscoderSemaphore();
+    OrthancWSI::DicomPyramidCache::FinalizeInstance();
+    OrthancWSI::RawTile::FinalizeTranscoderSemaphore();
   }
 
 
diff -r 35c241231af2 -r c72fbdecdc38 ViewerPlugin/RawTile.cpp
--- a/ViewerPlugin/RawTile.cpp	Mon Jul 10 08:31:50 2023 +0200
+++ b/ViewerPlugin/RawTile.cpp	Mon Jul 10 08:59:40 2023 +0200
@@ -37,150 +37,153 @@
 
 static std::unique_ptr<Orthanc::Semaphore>  transcoderSemaphore_;
 
-Orthanc::ImageAccessor* RawTile::DecodeInternal()
+namespace OrthancWSI
 {
-  switch (compression_)
+  Orthanc::ImageAccessor* RawTile::DecodeInternal()
   {
-    case OrthancWSI::ImageCompression_Jpeg:
+    switch (compression_)
     {
-      std::unique_ptr<Orthanc::JpegReader> decoded(new Orthanc::JpegReader);
-      decoded->ReadFromMemory(tile_);
-      return decoded.release();
-    }
-
-    case OrthancWSI::ImageCompression_Jpeg2000:
-    {
-      std::unique_ptr<OrthancWSI::Jpeg2000Reader> decoded(new OrthancWSI::Jpeg2000Reader);
-      decoded->ReadFromMemory(tile_);
-
-      if (photometric_ == Orthanc::PhotometricInterpretation_YBR_ICT)
+      case ImageCompression_Jpeg:
       {
-        OrthancWSI::ImageToolbox::ConvertJpegYCbCrToRgb(*decoded);
+        std::unique_ptr<Orthanc::JpegReader> decoded(new Orthanc::JpegReader);
+        decoded->ReadFromMemory(tile_);
+        return decoded.release();
       }
 
-      return decoded.release();
-    }
+      case ImageCompression_Jpeg2000:
+      {
+        std::unique_ptr<Jpeg2000Reader> decoded(new Jpeg2000Reader);
+        decoded->ReadFromMemory(tile_);
 
-    case OrthancWSI::ImageCompression_None:
-    {
-      unsigned int bpp = Orthanc::GetBytesPerPixel(format_);
-      if (bpp * tileWidth_ * tileHeight_ != tile_.size())
-      {
-        throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
+        if (photometric_ == Orthanc::PhotometricInterpretation_YBR_ICT)
+        {
+          ImageToolbox::ConvertJpegYCbCrToRgb(*decoded);
+        }
+
+        return decoded.release();
       }
 
-      std::unique_ptr<Orthanc::ImageAccessor> decoded(new Orthanc::ImageAccessor);
-      decoded->AssignReadOnly(format_, tileWidth_, tileHeight_, bpp * tileWidth_, tile_.c_str());
+      case ImageCompression_None:
+      {
+        unsigned int bpp = Orthanc::GetBytesPerPixel(format_);
+        if (bpp * tileWidth_ * tileHeight_ != tile_.size())
+        {
+          throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
+        }
 
-      return decoded.release();
+        std::unique_ptr<Orthanc::ImageAccessor> decoded(new Orthanc::ImageAccessor);
+        decoded->AssignReadOnly(format_, tileWidth_, tileHeight_, bpp * tileWidth_, tile_.c_str());
+
+        return decoded.release();
+      }
+
+      default:
+        throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented);
     }
-
-    default:
-      throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented);
   }
-}
 
 
-void RawTile::EncodeInternal(std::string& encoded,
-                             const Orthanc::ImageAccessor& decoded,
-                             Orthanc::MimeType transcodingType)
-{
-  switch (transcodingType)
+  void RawTile::EncodeInternal(std::string& encoded,
+                               const Orthanc::ImageAccessor& decoded,
+                               Orthanc::MimeType transcodingType)
   {
-    case Orthanc::MimeType_Png:
+    switch (transcodingType)
     {
-      Orthanc::PngWriter writer;
-      Orthanc::IImageWriter::WriteToMemory(writer, encoded, decoded);
-      break;
+      case Orthanc::MimeType_Png:
+      {
+        Orthanc::PngWriter writer;
+        Orthanc::IImageWriter::WriteToMemory(writer, encoded, decoded);
+        break;
+      }
+
+      case Orthanc::MimeType_Jpeg:
+      {
+        Orthanc::JpegWriter writer;
+        Orthanc::IImageWriter::WriteToMemory(writer, encoded, decoded);
+        break;
+      }
+
+      default:
+        throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented);
     }
-
-    case Orthanc::MimeType_Jpeg:
-    {
-      Orthanc::JpegWriter writer;
-      Orthanc::IImageWriter::WriteToMemory(writer, encoded, decoded);
-      break;
-    }
-
-    default:
-      throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented);
   }
-}
 
 
-RawTile::RawTile(OrthancWSI::ITiledPyramid& pyramid,
-                 unsigned int level,
-                 unsigned int tileX,
-                 unsigned int tileY) :
-  format_(pyramid.GetPixelFormat()),
-  tileWidth_(pyramid.GetTileWidth(level)),
-  tileHeight_(pyramid.GetTileHeight(level)),
-  photometric_(pyramid.GetPhotometricInterpretation())
-{
-  if (!pyramid.ReadRawTile(tile_, compression_, level, tileX, tileY))
+  RawTile::RawTile(ITiledPyramid& pyramid,
+                   unsigned int level,
+                   unsigned int tileX,
+                   unsigned int tileY) :
+    format_(pyramid.GetPixelFormat()),
+    tileWidth_(pyramid.GetTileWidth(level)),
+    tileHeight_(pyramid.GetTileHeight(level)),
+    photometric_(pyramid.GetPhotometricInterpretation())
   {
-    // Handling of missing tile (for sparse tiling): TODO parameter?
-    // AnswerSparseTile(output, tileWidth, tileHeight); return;
-    throw Orthanc::OrthancException(Orthanc::ErrorCode_UnknownResource);
+    if (!pyramid.ReadRawTile(tile_, compression_, level, tileX, tileY))
+    {
+      // Handling of missing tile (for sparse tiling): TODO parameter?
+      // AnswerSparseTile(output, tileWidth, tileHeight); return;
+      throw Orthanc::OrthancException(Orthanc::ErrorCode_UnknownResource);
+    }
   }
-}
 
 
-void RawTile::Answer(OrthancPluginRestOutput* output,
-                     Orthanc::MimeType transcodingType)
-{
-  if (compression_ == OrthancWSI::ImageCompression_Jpeg)
-  {
-    // The tile is already a JPEG image. In such a case, we can
-    // serve it as such, because any Web browser can handle JPEG.
-    OrthancPluginAnswerBuffer(OrthancPlugins::GetGlobalContext(), output, tile_.c_str(),
-                              tile_.size(), Orthanc::EnumerationToString(Orthanc::MimeType_Jpeg));
-  }
-  else
+  void RawTile::Answer(OrthancPluginRestOutput* output,
+                       Orthanc::MimeType transcodingType)
   {
-    // This is a lossless frame (coming from a JPEG2000 or an
-    // uncompressed DICOM instance), which is not a DICOM-JPEG
-    // instance. We need to decompress the raw tile, then transcode
-    // it to the PNG/JPEG, depending on the "transcodingType".
-
-    std::string transcoded;
-
+    if (compression_ == ImageCompression_Jpeg)
+    {
+      // The tile is already a JPEG image. In such a case, we can
+      // serve it as such, because any Web browser can handle JPEG.
+      OrthancPluginAnswerBuffer(OrthancPlugins::GetGlobalContext(), output, tile_.c_str(),
+                                tile_.size(), Orthanc::EnumerationToString(Orthanc::MimeType_Jpeg));
+    }
+    else
     {
-      // The semaphore is used to throttle the number of simultaneous computations
-      Orthanc::Semaphore::Locker locker(*transcoderSemaphore_);
+      // This is a lossless frame (coming from a JPEG2000 or an
+      // uncompressed DICOM instance), which is not a DICOM-JPEG
+      // instance. We need to decompress the raw tile, then transcode
+      // it to the PNG/JPEG, depending on the "transcodingType".
+
+      std::string transcoded;
+
+      {
+        // The semaphore is used to throttle the number of simultaneous computations
+        Orthanc::Semaphore::Locker locker(*transcoderSemaphore_);
+
+        std::unique_ptr<Orthanc::ImageAccessor> decoded(DecodeInternal());
+        EncodeInternal(transcoded, *decoded, transcodingType);
+      }
+
+      OrthancPluginAnswerBuffer(OrthancPlugins::GetGlobalContext(), output, transcoded.c_str(),
+                                transcoded.size(), Orthanc::EnumerationToString(transcodingType));
+    }
+  }
+
 
-      std::unique_ptr<Orthanc::ImageAccessor> decoded(DecodeInternal());
-      EncodeInternal(transcoded, *decoded, transcodingType);
-    }
+  Orthanc::ImageAccessor* RawTile::Decode()
+  {
+    Orthanc::Semaphore::Locker locker(*transcoderSemaphore_);
+    return DecodeInternal();
+  }
+
 
-    OrthancPluginAnswerBuffer(OrthancPlugins::GetGlobalContext(), output, transcoded.c_str(),
-                              transcoded.size(), Orthanc::EnumerationToString(transcodingType));
+  void RawTile::Encode(std::string& encoded,
+                       const Orthanc::ImageAccessor& decoded,
+                       Orthanc::MimeType transcodingType)
+  {
+    Orthanc::Semaphore::Locker locker(*transcoderSemaphore_);
+    EncodeInternal(encoded, decoded, transcodingType);
+  }
+
+
+  void RawTile::InitializeTranscoderSemaphore(unsigned int maxThreads)
+  {
+    transcoderSemaphore_.reset(new Orthanc::Semaphore(maxThreads));
+  }
+
+
+  void RawTile::FinalizeTranscoderSemaphore()
+  {
+    transcoderSemaphore_.reset(NULL);
   }
 }
-
-
-Orthanc::ImageAccessor* RawTile::Decode()
-{
-  Orthanc::Semaphore::Locker locker(*transcoderSemaphore_);
-  return DecodeInternal();
-}
-
-
-void RawTile::Encode(std::string& encoded,
-                     const Orthanc::ImageAccessor& decoded,
-                     Orthanc::MimeType transcodingType)
-{
-  Orthanc::Semaphore::Locker locker(*transcoderSemaphore_);
-  EncodeInternal(encoded, decoded, transcodingType);
-}
-
-
-void RawTile::InitializeTranscoderSemaphore(unsigned int maxThreads)
-{
-  transcoderSemaphore_.reset(new Orthanc::Semaphore(maxThreads));
-}
-
-
-void RawTile::FinalizeTranscoderSemaphore()
-{
-  transcoderSemaphore_.reset(NULL);
-}
diff -r 35c241231af2 -r c72fbdecdc38 ViewerPlugin/RawTile.h
--- a/ViewerPlugin/RawTile.h	Mon Jul 10 08:31:50 2023 +0200
+++ b/ViewerPlugin/RawTile.h	Mon Jul 10 08:59:40 2023 +0200
@@ -28,40 +28,43 @@
 #include <orthanc/OrthancCPlugin.h>
 
 
-class RawTile : public boost::noncopyable
+namespace OrthancWSI
 {
-private:
-  Orthanc::PixelFormat               format_;
-  unsigned int                       tileWidth_;
-  unsigned int                       tileHeight_;
-  Orthanc::PhotometricInterpretation photometric_;
-  std::string                        tile_;
-  OrthancWSI::ImageCompression       compression_;
+  class RawTile : public boost::noncopyable
+  {
+  private:
+    Orthanc::PixelFormat               format_;
+    unsigned int                       tileWidth_;
+    unsigned int                       tileHeight_;
+    Orthanc::PhotometricInterpretation photometric_;
+    std::string                        tile_;
+    ImageCompression                   compression_;
 
-  Orthanc::ImageAccessor* DecodeInternal();
+    Orthanc::ImageAccessor* DecodeInternal();
 
-  static void EncodeInternal(std::string& encoded,
-                             const Orthanc::ImageAccessor& decoded,
-                             Orthanc::MimeType transcodingType);
+    static void EncodeInternal(std::string& encoded,
+                               const Orthanc::ImageAccessor& decoded,
+                               Orthanc::MimeType transcodingType);
 
-public:
-  RawTile(OrthancWSI::ITiledPyramid& pyramid,
-          unsigned int level,
-          unsigned int tileX,
-          unsigned int tileY);
+  public:
+    RawTile(ITiledPyramid& pyramid,
+            unsigned int level,
+            unsigned int tileX,
+            unsigned int tileY);
 
-  void Answer(OrthancPluginRestOutput* output,
-              Orthanc::MimeType transcodingType);
+    void Answer(OrthancPluginRestOutput* output,
+                Orthanc::MimeType transcodingType);
 
-  Orthanc::ImageAccessor* Decode();
+    Orthanc::ImageAccessor* Decode();
 
-  static void Encode(std::string& encoded,
-                     const Orthanc::ImageAccessor& decoded,
-                     Orthanc::MimeType transcodingType);
+    static void Encode(std::string& encoded,
+                       const Orthanc::ImageAccessor& decoded,
+                       Orthanc::MimeType transcodingType);
 
-  // This semaphore is used to implement throttling for the
-  // decoding/encoding of tiles
-  static void InitializeTranscoderSemaphore(unsigned int maxThreads);
+    // This semaphore is used to implement throttling for the
+    // decoding/encoding of tiles
+    static void InitializeTranscoderSemaphore(unsigned int maxThreads);
 
-  static void FinalizeTranscoderSemaphore();
-};
+    static void FinalizeTranscoderSemaphore();
+  };
+}