--- /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);
+}