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.hg_archival.txt
View file @ fac60a36
repo: 4a7a53257c7df5a97aea39377b8c9a6e815c9763
node: 38d12348a1534ecb5f7c428aa5dd5235b76df338
branch: OrthancWSI-0.5
node: dd736430e3a4c9f6816dd3a54d4d0f4716123c71
branch: OrthancWSI-0.6
latesttag: null
latesttagdistance: 146
changessincelatesttag: 148
latesttagdistance: 159
changessincelatesttag: 162
AUTHORS
View file @ fac60a36
......@@ -5,7 +5,7 @@ Orthanc for Whole-Slide Imaging
Authors
-------
* Sebastien Jodogne <s.jodogne@gmail.com>
* Sebastien Jodogne <s.jodogne@orthanc-labs.com>
Overall design and lead developer.
......
Applications/ApplicationToolbox.cpp
View file @ fac60a36
......@@ -2,7 +2,7 @@
* Orthanc - A Lightweight, RESTful DICOM Store
* Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics
* Department, University Hospital of Liege, Belgium
* Copyright (C) 2017-2018 Osimis S.A., Belgium
* Copyright (C) 2017-2019 Osimis S.A., Belgium
*
* This program is free software: you can redistribute it and/or
* modify it under the terms of the GNU Affero General Public License
......@@ -22,13 +22,14 @@
#include "ApplicationToolbox.h"
#include "../Framework/Inputs/OpenSlideLibrary.h"
#include "../Framework/MultiThreading/BagOfTasksProcessor.h"
#include <Core/DicomParsing/FromDcmtkBridge.h>
#include <Core/HttpClient.h>
#include <Core/Logging.h>
#include <Core/MultiThreading/BagOfTasksProcessor.h>
#include <Core/OrthancException.h>
#include <Core/SystemToolbox.h>
#include <Core/Toolbox.h>
#include <boost/filesystem.hpp>
#include <boost/lexical_cast.hpp>
......@@ -63,7 +64,7 @@ namespace OrthancWSI
void GlobalInitialize()
{
Orthanc::Logging::Initialize();
Orthanc::HttpClient::InitializeOpenSsl();
Orthanc::Toolbox::InitializeOpenSsl();
Orthanc::HttpClient::GlobalInitialize();
Orthanc::FromDcmtkBridge::InitializeDictionary(false /* don't load private dictionary */);
assert(DisplayPerformanceWarning());
......@@ -74,7 +75,7 @@ namespace OrthancWSI
{
OrthancWSI::OpenSlideLibrary::Finalize();
Orthanc::HttpClient::GlobalFinalize();
Orthanc::HttpClient::FinalizeOpenSsl();
Orthanc::Toolbox::FinalizeOpenSsl();
}
......@@ -217,12 +218,12 @@ namespace OrthancWSI
<< path << " " << ORTHANC_WSI_VERSION << std::endl
<< "Copyright (C) 2012-2016 Sebastien Jodogne, "
<< "Medical Physics Department, University Hospital of Liege (Belgium)" << std::endl
<< "Copyright (C) 2017-2018 Osimis S.A. (Belgium)" << std::endl
<< "Copyright (C) 2017-2019 Osimis S.A. (Belgium)" << std::endl
<< "Licensing AGPL: GNU AGPL version 3 or later <http://gnu.org/licenses/agpl.html>." << std::endl
<< "This is free software: you are free to change and redistribute it." << std::endl
<< "There is NO WARRANTY, to the extent permitted by law." << std::endl
<< std::endl
<< "Written by Sebastien Jodogne <s.jodogne@gmail.com>" << std::endl;
<< "Written by Sebastien Jodogne <s.jodogne@orthanc-labs.com>" << std::endl;
}
......@@ -279,8 +280,8 @@ namespace OrthancWSI
if (options.count(OPTION_USERNAME) &&
options.count(OPTION_PASSWORD))
{
parameters.SetUsername(options[OPTION_USERNAME].as<std::string>());
parameters.SetPassword(options[OPTION_PASSWORD].as<std::string>());
parameters.SetCredentials(options[OPTION_USERNAME].as<std::string>(),
options[OPTION_PASSWORD].as<std::string>());
}
if (options.count(OPTION_TIMEOUT))
......
Applications/ApplicationToolbox.h
View file @ fac60a36
......@@ -2,7 +2,7 @@
* Orthanc - A Lightweight, RESTful DICOM Store
* Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics
* Department, University Hospital of Liege, Belgium
* Copyright (C) 2017-2018 Osimis S.A., Belgium
* Copyright (C) 2017-2019 Osimis S.A., Belgium
*
* This program is free software: you can redistribute it and/or
* modify it under the terms of the GNU Affero General Public License
......@@ -21,7 +21,8 @@
#pragma once
#include <Core/MultiThreading/BagOfTasks.h>
#include "../Framework/MultiThreading/BagOfTasks.h"
#include <Core/WebServiceParameters.h>
#include <string>
......
Applications/CMakeLists.txt
View file @ fac60a36
......@@ -100,14 +100,15 @@ set(ORTHANC_WSI_SOURCES
${ORTHANC_WSI_DIR}/Framework/Inputs/TiledPyramidStatistics.cpp
${ORTHANC_WSI_DIR}/Framework/Jpeg2000Reader.cpp
${ORTHANC_WSI_DIR}/Framework/Jpeg2000Writer.cpp
${ORTHANC_WSI_DIR}/Framework/Targets/FolderTarget.cpp
${ORTHANC_WSI_DIR}/Framework/Targets/OrthancTarget.cpp
${ORTHANC_WSI_DIR}/Framework/MultiThreading/BagOfTasksProcessor.cpp
${ORTHANC_WSI_DIR}/Framework/Outputs/DicomPyramidWriter.cpp
${ORTHANC_WSI_DIR}/Framework/Outputs/HierarchicalTiffWriter.cpp
${ORTHANC_WSI_DIR}/Framework/Outputs/InMemoryTiledImage.cpp
${ORTHANC_WSI_DIR}/Framework/Outputs/MultiframeDicomWriter.cpp
${ORTHANC_WSI_DIR}/Framework/Outputs/PyramidWriterBase.cpp
${ORTHANC_WSI_DIR}/Framework/Outputs/TruncatedPyramidWriter.cpp
${ORTHANC_WSI_DIR}/Framework/Targets/FolderTarget.cpp
${ORTHANC_WSI_DIR}/Framework/Targets/OrthancTarget.cpp
)
EmbedResources(
......@@ -119,6 +120,7 @@ EmbedResources(
add_definitions(
-DHAS_ORTHANC_EXCEPTION=1
-DORTHANC_ENABLE_LOGGING_PLUGIN=0
)
......
Applications/DicomToTiff.cpp
View file @ fac60a36
......@@ -2,7 +2,7 @@
* Orthanc - A Lightweight, RESTful DICOM Store
* Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics
* Department, University Hospital of Liege, Belgium
* Copyright (C) 2017-2018 Osimis S.A., Belgium
* Copyright (C) 2017-2019 Osimis S.A., Belgium
*
* This program is free software: you can redistribute it and/or
* modify it under the terms of the GNU Affero General Public License
......
Applications/Dicomizer.cpp
View file @ fac60a36
......@@ -2,7 +2,7 @@
* Orthanc - A Lightweight, RESTful DICOM Store
* Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics
* Department, University Hospital of Liege, Belgium
* Copyright (C) 2017-2018 Osimis S.A., Belgium
* Copyright (C) 2017-2019 Osimis S.A., Belgium
*
* This program is free software: you can redistribute it and/or
* modify it under the terms of the GNU Affero General Public License
......@@ -29,12 +29,12 @@
#include "../Framework/Inputs/TiledJpegImage.h"
#include "../Framework/Inputs/TiledPngImage.h"
#include "../Framework/Inputs/TiledPyramidStatistics.h"
#include "../Framework/MultiThreading/BagOfTasksProcessor.h"
#include "../Framework/Outputs/DicomPyramidWriter.h"
#include "../Framework/Outputs/TruncatedPyramidWriter.h"
#include <Core/DicomParsing/FromDcmtkBridge.h>
#include <Core/Logging.h>
#include <Core/MultiThreading/BagOfTasksProcessor.h>
#include <Core/OrthancException.h>
#include <Core/SystemToolbox.h>
......
Framework/Algorithms/PyramidReader.cpp
View file @ fac60a36
......@@ -2,7 +2,7 @@
* Orthanc - A Lightweight, RESTful DICOM Store
* Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics
* Department, University Hospital of Liege, Belgium
* Copyright (C) 2017-2018 Osimis S.A., Belgium
* Copyright (C) 2017-2019 Osimis S.A., Belgium
*
* This program is free software: you can redistribute it and/or
* modify it under the terms of the GNU Affero General Public License
......@@ -61,7 +61,8 @@ namespace OrthancWSI
assert(tileY_ * that_.sourceTileHeight_ < that_.levelHeight_);
unsigned int bottom = that_.levelHeight_ - tileY_ * that_.sourceTileHeight_;
Orthanc::ImageAccessor a = decoded_->GetRegion(0, bottom,
Orthanc::ImageAccessor a;
decoded_->GetRegion(a, 0, bottom,
that_.sourceTileWidth_,
that_.sourceTileHeight_ - bottom);
ImageToolbox::Set(a,
......@@ -77,7 +78,8 @@ namespace OrthancWSI
assert(tileX_ * that_.sourceTileWidth_ < that_.levelWidth_);
unsigned int right = that_.levelWidth_ - tileX_ * that_.sourceTileWidth_;
Orthanc::ImageAccessor a = decoded_->GetRegion(right, 0,
Orthanc::ImageAccessor a;
decoded_->GetRegion(a, right, 0,
that_.sourceTileWidth_ - right,
that_.sourceTileHeight_);
ImageToolbox::Set(a,
......@@ -283,16 +285,18 @@ namespace OrthancWSI
}
Orthanc::ImageAccessor PyramidReader::GetDecodedTile(unsigned int tileX,
void PyramidReader::GetDecodedTile(Orthanc::ImageAccessor& target,
unsigned int tileX,
unsigned int tileY)
{
if (tileX * targetTileWidth_ >= levelWidth_ ||
tileY * targetTileHeight_ >= levelHeight_)
{
// Accessing a tile out of the source image
return GetOutsideTile();
GetOutsideTile().GetReadOnlyAccessor(target);
}
else
{
SourceTile& source = AccessSourceTile(MapTargetToSourceLocation(tileX, tileY));
const Orthanc::ImageAccessor& tile = source.GetDecodedTile();
......@@ -308,12 +312,10 @@ namespace OrthancWSI
reinterpret_cast<const uint8_t*>(tile.GetConstRow(yy * targetTileHeight_)) +
GetBytesPerPixel(tile.GetFormat()) * xx * targetTileWidth_;
Orthanc::ImageAccessor region;
region.AssignReadOnly(tile.GetFormat(),
target.AssignReadOnly(tile.GetFormat(),
targetTileWidth_,
targetTileHeight_,
tile.GetPitch(), bytes);
return region;
}
}
}
Framework/Algorithms/PyramidReader.h
View file @ fac60a36
......@@ -2,7 +2,7 @@
* Orthanc - A Lightweight, RESTful DICOM Store
* Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics
* Department, University Hospital of Liege, Belgium
* Copyright (C) 2017-2018 Osimis S.A., Belgium
* Copyright (C) 2017-2019 Osimis S.A., Belgium
*
* This program is free software: you can redistribute it and/or
* modify it under the terms of the GNU Affero General Public License
......@@ -88,7 +88,8 @@ namespace OrthancWSI
unsigned int tileX,
unsigned int tileY);
Orthanc::ImageAccessor GetDecodedTile(unsigned int tileX,
void GetDecodedTile(Orthanc::ImageAccessor& target,
unsigned int tileX,
unsigned int tileY);
};
}
Framework/Algorithms/ReconstructPyramidCommand.cpp
View file @ fac60a36
......@@ -2,7 +2,7 @@
* Orthanc - A Lightweight, RESTful DICOM Store
* Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics
* Department, University Hospital of Liege, Belgium
* Copyright (C) 2017-2018 Osimis S.A., Belgium
* Copyright (C) 2017-2019 Osimis S.A., Belgium
*
* This program is free software: you can redistribute it and/or
* modify it under the terms of the GNU Affero General Public License
......@@ -50,7 +50,8 @@ namespace OrthancWSI
if (level == 0)
{
result.reset(new Orthanc::ImageAccessor(source_.GetDecodedTile(x, y)));
result.reset(new Orthanc::ImageAccessor);
source_.GetDecodedTile(*result, x, y);
ImageCompression compression;
const std::string* rawTile = source_.GetRawTile(compression, x, y);
......
Framework/Algorithms/ReconstructPyramidCommand.h
View file @ fac60a36
......@@ -2,7 +2,7 @@
* Orthanc - A Lightweight, RESTful DICOM Store
* Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics
* Department, University Hospital of Liege, Belgium
* Copyright (C) 2017-2018 Osimis S.A., Belgium
* Copyright (C) 2017-2019 Osimis S.A., Belgium
*
* This program is free software: you can redistribute it and/or
* modify it under the terms of the GNU Affero General Public License
......@@ -23,7 +23,7 @@
#include "PyramidReader.h"
#include "../Outputs/IPyramidWriter.h"
#include <Core/MultiThreading/BagOfTasks.h>
#include "../MultiThreading/BagOfTasks.h"
namespace OrthancWSI
......
Framework/Algorithms/TranscodeTileCommand.cpp
View file @ fac60a36
......@@ -2,7 +2,7 @@
* Orthanc - A Lightweight, RESTful DICOM Store
* Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics
* Department, University Hospital of Liege, Belgium
* Copyright (C) 2017-2018 Osimis S.A., Belgium
* Copyright (C) 2017-2019 Osimis S.A., Belgium
*
* This program is free software: you can redistribute it and/or
* modify it under the terms of the GNU Affero General Public License
......@@ -73,7 +73,8 @@ namespace OrthancWSI
}
else
{
Orthanc::ImageAccessor tile = source_.GetDecodedTile(x, y);
Orthanc::ImageAccessor tile;
source_.GetDecodedTile(tile, x, y);
// Re-encoding the file
target_.EncodeTile(tile, level_, x, y);
......
Framework/Algorithms/TranscodeTileCommand.h
View file @ fac60a36
......@@ -2,7 +2,7 @@
* Orthanc - A Lightweight, RESTful DICOM Store
* Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics
* Department, University Hospital of Liege, Belgium
* Copyright (C) 2017-2018 Osimis S.A., Belgium
* Copyright (C) 2017-2019 Osimis S.A., Belgium
*
* This program is free software: you can redistribute it and/or
* modify it under the terms of the GNU Affero General Public License
......@@ -23,8 +23,7 @@
#include "PyramidReader.h"
#include "../Outputs/IPyramidWriter.h"
#include <Core/MultiThreading/BagOfTasks.h>
#include "../MultiThreading/BagOfTasks.h"
namespace OrthancWSI
{
......
Framework/DicomToolbox.cpp
View file @ fac60a36
......@@ -2,7 +2,7 @@
* Orthanc - A Lightweight, RESTful DICOM Store
* Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics
* Department, University Hospital of Liege, Belgium
* Copyright (C) 2017-2018 Osimis S.A., Belgium
* Copyright (C) 2017-2019 Osimis S.A., Belgium
*
* This program is free software: you can redistribute it and/or
* modify it under the terms of the GNU Affero General Public License
......
Framework/DicomToolbox.h
View file @ fac60a36
......@@ -2,7 +2,7 @@
* Orthanc - A Lightweight, RESTful DICOM Store
* Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics
* Department, University Hospital of Liege, Belgium
* Copyright (C) 2017-2018 Osimis S.A., Belgium
* Copyright (C) 2017-2019 Osimis S.A., Belgium
*
* This program is free software: you can redistribute it and/or
* modify it under the terms of the GNU Affero General Public License
......
Framework/DicomizerParameters.cpp
View file @ fac60a36
......@@ -2,7 +2,7 @@
* Orthanc - A Lightweight, RESTful DICOM Store
* Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics
* Department, University Hospital of Liege, Belgium
* Copyright (C) 2017-2018 Osimis S.A., Belgium
* Copyright (C) 2017-2019 Osimis S.A., Belgium
*
* This program is free software: you can redistribute it and/or
* modify it under the terms of the GNU Affero General Public License
......
Framework/DicomizerParameters.h
View file @ fac60a36
......@@ -2,7 +2,7 @@
* Orthanc - A Lightweight, RESTful DICOM Store
* Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics
* Department, University Hospital of Liege, Belgium
* Copyright (C) 2017-2018 Osimis S.A., Belgium
* Copyright (C) 2017-2019 Osimis S.A., Belgium
*
* This program is free software: you can redistribute it and/or
* modify it under the terms of the GNU Affero General Public License
......
Framework/Enumerations.cpp
View file @ fac60a36
......@@ -2,7 +2,7 @@
* Orthanc - A Lightweight, RESTful DICOM Store
* Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics
* Department, University Hospital of Liege, Belgium
* Copyright (C) 2017-2018 Osimis S.A., Belgium
* Copyright (C) 2017-2019 Osimis S.A., Belgium
*
* This program is free software: you can redistribute it and/or
* modify it under the terms of the GNU Affero General Public License
......
Framework/Enumerations.h
View file @ fac60a36
......@@ -2,7 +2,7 @@
* Orthanc - A Lightweight, RESTful DICOM Store
* Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics
* Department, University Hospital of Liege, Belgium
* Copyright (C) 2017-2018 Osimis S.A., Belgium
* Copyright (C) 2017-2019 Osimis S.A., Belgium
*
* This program is free software: you can redistribute it and/or
* modify it under the terms of the GNU Affero General Public License
......
Framework/ImageToolbox.cpp
View file @ fac60a36
......@@ -2,7 +2,7 @@
* Orthanc - A Lightweight, RESTful DICOM Store
* Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics
* Department, University Hospital of Liege, Belgium
* Copyright (C) 2017-2018 Osimis S.A., Belgium
* Copyright (C) 2017-2019 Osimis S.A., Belgium
*
* This program is free software: you can redistribute it and/or
* modify it under the terms of the GNU Affero General Public License
......@@ -68,8 +68,10 @@ namespace OrthancWSI
unsigned int h = std::min(source.GetHeight(), target.GetHeight() - y);
unsigned int w = std::min(source.GetWidth(), target.GetWidth() - x);
Orthanc::ImageAccessor targetRegion = target.GetRegion(x, y, w, h);
Orthanc::ImageAccessor sourceRegion = source.GetRegion(0, 0, w, h);
Orthanc::ImageAccessor targetRegion, sourceRegion;
target.GetRegion(targetRegion, x, y, w, h);
source.GetRegion(sourceRegion, 0, 0, w, h);
Orthanc::ImageProcessing::Copy(targetRegion, sourceRegion);
}
......