--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Applications/DicomToTiff.cpp	Sat Oct 22 21:48:33 2016 +0200
@@ -0,0 +1,321 @@
+/**
+ * Orthanc - A Lightweight, RESTful DICOM Store
+ * Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics
+ * Department, University Hospital of Liege, 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/DicomToolbox.h"
+#include "../Framework/ImageToolbox.h"
+#include "../Framework/Inputs/DicomPyramid.h"
+#include "../Framework/Messaging/CurlOrthancConnection.h"
+#include "../Framework/Orthanc/Core/Logging.h"
+#include "../Framework/Orthanc/Core/OrthancException.h"
+#include "../Framework/Outputs/HierarchicalTiffWriter.h"
+
+#include "ApplicationToolbox.h"
+
+#include <boost/program_options.hpp>
+
+
+static bool ParseParameters(int& exitStatus,
+                            boost::program_options::variables_map& options,
+                            int argc, 
+                            char* argv[])
+{
+  // Declare the supported parameters
+  boost::program_options::options_description generic("Generic options");
+  generic.add_options()
+    ("help", "Display this help and exit")
+    ("verbose", "Be verbose in logs")
+    ;
+
+  boost::program_options::options_description source("Options for the source DICOM image");
+  source.add_options()
+    ("orthanc", boost::program_options::value<std::string>()->default_value("http://localhost:8042/"),
+     "URL to the REST API of the target Orthanc server")
+    ("username", boost::program_options::value<std::string>(), "Username for the target Orthanc server")
+    ("password", boost::program_options::value<std::string>(), "Password for the target Orthanc server")
+    ;
+
+  boost::program_options::options_description target("Options for the target TIFF image");
+  target.add_options()
+    ("color", boost::program_options::value<std::string>(), "Color of the background for missing tiles (e.g. \"255,0,0\")")
+    ("reencode", boost::program_options::value<bool>(), 
+     "Whether to reencode each tile in JPEG (no transcoding, much slower) (Boolean)")
+    ("jpeg-quality", boost::program_options::value<int>(), "Set quality level for JPEG (0..100)")
+    ;
+
+  boost::program_options::options_description hidden;
+  hidden.add_options()
+    ("input", boost::program_options::value<std::string>(), "Orthanc identifier of the input series of interest")
+    ("output", boost::program_options::value<std::string>(), "Output TIFF file");
+  ;
+
+  boost::program_options::options_description allWithoutHidden;
+  allWithoutHidden.add(generic).add(source).add(target);
+
+  boost::program_options::options_description all = allWithoutHidden;
+  all.add(hidden);
+
+  boost::program_options::positional_options_description positional;
+  positional.add("input", 1);
+  positional.add("output", 1);
+
+  bool error = false;
+
+  try
+  {
+    boost::program_options::store(boost::program_options::command_line_parser(argc, argv).
+                                  options(all).positional(positional).run(), options);
+    boost::program_options::notify(options);    
+  }
+  catch (boost::program_options::error& e)
+  {
+    LOG(ERROR) << "Error while parsing the command-line arguments: " << e.what();
+    error = true;
+  }
+
+  if (!error &&
+      options.count("help") == 0)
+  {
+    if (options.count("input") != 1)
+    {
+      LOG(ERROR) << "No input series was specified";
+      error = true;
+    }
+
+    if (options.count("output") != 1)
+    {
+      LOG(ERROR) << "No output file was specified";
+      error = true;
+    }
+  }
+
+  if (error || options.count("help")) 
+  {
+    std::cout << std::endl
+              << "Usage: " << argv[0] << " [OPTION]... [INPUT] [OUTPUT]"
+              << std::endl
+              << "Orthanc, lightweight, RESTful DICOM server for healthcare and medical research."
+              << std::endl << std::endl
+              << "Convert a DICOM for digital pathology stored in some Orthanc server as a standard hierarchical TIFF."
+              << std::endl;
+
+    std::cout << allWithoutHidden << "\n";
+
+    if (error)
+    {
+      exitStatus = -1;
+    }
+
+    return false;
+  }
+
+  if (options.count("verbose"))
+  {
+    Orthanc::Logging::EnableInfoLevel(true);
+  }
+
+  return true;
+}
+
+
+
+static Orthanc::ImageAccessor* CreateEmptyTile(const OrthancWSI::IPyramidWriter& writer,
+                                               const boost::program_options::variables_map& options)
+{
+  std::auto_ptr<Orthanc::ImageAccessor> tile
+    (OrthancWSI::ImageToolbox::Allocate(writer.GetPixelFormat(), 
+                                        writer.GetTileWidth(), 
+                                        writer.GetTileHeight()));
+
+  uint8_t red = 255;
+  uint8_t green = 255;
+  uint8_t blue = 255;
+
+  if (options.count("color"))
+  {
+    OrthancWSI::ApplicationToolbox::ParseColor(red, green, blue, options["color"].as<std::string>());
+  }
+
+  OrthancWSI::ImageToolbox::Set(*tile, red, green, blue);
+
+  return tile.release();
+}
+
+
+
+static void RunTranscode(OrthancWSI::ITiledPyramid& source,
+                         const boost::program_options::variables_map& options)
+{
+  OrthancWSI::HierarchicalTiffWriter target(options["output"].as<std::string>(),
+                                            source.GetPixelFormat(), 
+                                            source.GetImageCompression(), 
+                                            source.GetTileWidth(), 
+                                            source.GetTileHeight());
+
+  std::auto_ptr<Orthanc::ImageAccessor> empty(CreateEmptyTile(target, options));
+
+  for (unsigned int level = 0; level < source.GetLevelCount(); level++)
+  {
+    LOG(WARNING) << "Creating level " << level << " of size " 
+                 << source.GetLevelWidth(level) << "x" << source.GetLevelHeight(level);
+    target.AddLevel(source.GetLevelWidth(level), source.GetLevelHeight(level));
+  }
+
+  for (unsigned int level = 0; level < source.GetLevelCount(); level++)
+  {
+    LOG(WARNING) << "Transcoding level " << level;
+
+    unsigned int countX = OrthancWSI::CeilingDivision(source.GetLevelWidth(level), source.GetTileWidth());
+    unsigned int countY = OrthancWSI::CeilingDivision(source.GetLevelHeight(level), source.GetTileHeight());
+
+    for (unsigned int tileY = 0; tileY < countY; tileY++)
+    {
+      for (unsigned int tileX = 0; tileX < countX; tileX++)
+      {
+        LOG(INFO) << "Dealing with tile (" << tileX << "," << tileY << ") at level " << level;
+        std::string tile;
+
+        if (source.ReadRawTile(tile, level, tileX, tileY))
+        {
+          target.WriteRawTile(tile, source.GetImageCompression(), level, tileX, tileY);
+        }
+        else
+        {
+          target.EncodeTile(*empty, level, tileX, tileY);
+        }
+      }        
+    }
+
+    target.Flush();
+  }
+}
+
+
+static void RunReencode(OrthancWSI::ITiledPyramid& source,
+                        const boost::program_options::variables_map& options)
+{
+  OrthancWSI::HierarchicalTiffWriter target(options["output"].as<std::string>(),
+                                            source.GetPixelFormat(), 
+                                            OrthancWSI::ImageCompression_Jpeg,
+                                            source.GetTileWidth(), 
+                                            source.GetTileHeight());
+
+  if (options.count("jpeg-quality"))
+  {
+    target.SetJpegQuality(options["jpeg-quality"].as<int>());
+  }
+
+  std::auto_ptr<Orthanc::ImageAccessor> empty(CreateEmptyTile(target, options));
+
+  for (unsigned int level = 0; level < source.GetLevelCount(); level++)
+  {
+    LOG(WARNING) << "Creating level " << level << " of size " 
+                 << source.GetLevelWidth(level) << "x" << source.GetLevelHeight(level);
+    target.AddLevel(source.GetLevelWidth(level), source.GetLevelHeight(level));
+  }
+
+  for (unsigned int level = 0; level < source.GetLevelCount(); level++)
+  {
+    LOG(WARNING) << "Reencoding level " << level;
+
+    unsigned int countX = OrthancWSI::CeilingDivision(source.GetLevelWidth(level), source.GetTileWidth());
+    unsigned int countY = OrthancWSI::CeilingDivision(source.GetLevelHeight(level), source.GetTileHeight());
+
+    for (unsigned int tileY = 0; tileY < countY; tileY++)
+    {
+      for (unsigned int tileX = 0; tileX < countX; tileX++)
+      {
+        LOG(INFO) << "Dealing with tile (" << tileX << "," << tileY << ") at level " << level;
+
+        std::auto_ptr<Orthanc::ImageAccessor> tile(source.DecodeTile(level, tileX, tileY));
+        if (tile.get() == NULL)
+        {
+          target.EncodeTile(*empty, level, tileX, tileY);
+        }
+        else
+        {
+          target.EncodeTile(*tile, level, tileX, tileY);
+        }
+      }        
+    }
+
+    target.Flush();
+  }
+}
+
+
+
+int main(int argc, char* argv[])
+{
+  OrthancWSI::ApplicationToolbox::GlobalInitialize();
+
+  int exitStatus = 0;
+  boost::program_options::variables_map options;
+
+  try
+  {
+    if (ParseParameters(exitStatus, options, argc, argv))
+    {
+      Orthanc::WebServiceParameters params;
+
+      if (options.count("orthanc"))
+      {
+        params.SetUrl(options["orthanc"].as<std::string>());
+      }
+
+      if (options.count("username"))
+      {
+        params.SetUsername(options["username"].as<std::string>());
+      }
+
+      if (options.count("password"))
+      {
+        params.SetPassword(options["password"].as<std::string>());
+      }
+
+      OrthancWSI::CurlOrthancConnection orthanc(params);
+      OrthancWSI::DicomPyramid source(orthanc, options["input"].as<std::string>());
+
+      if (options.count("reencode") &&
+          options["reencode"].as<bool>())
+      {
+        RunReencode(source, options);
+      }
+      else
+      {
+        RunTranscode(source, options);
+      }
+    }
+  }
+  catch (Orthanc::OrthancException& e)
+  {
+    LOG(ERROR) << "Terminating on exception: " << e.What();
+
+    if (options.count("reencode") == 0)
+    {
+      LOG(ERROR) << "Consider using option \"--reencode\"";
+    }
+    
+    exitStatus = -1;
+  }
+
+  OrthancWSI::ApplicationToolbox::GlobalFinalize();
+
+  return exitStatus;
+}