# HG changeset patch # User Sebastien Jodogne # Date 1444664963 -7200 # Node ID 9980875edc7cabc2cedd6841d79df328d31c6489 # Parent 4aaaecae580372883363630aa7b8873831dca01f started work on SliceOrdering diff -r 4aaaecae5803 -r 9980875edc7c CMakeLists.txt --- a/CMakeLists.txt Mon Oct 12 14:47:58 2015 +0200 +++ b/CMakeLists.txt Mon Oct 12 17:49:23 2015 +0200 @@ -146,21 +146,28 @@ set(ORTHANC_SERVER_SOURCES + OrthancServer/DatabaseWrapper.cpp + OrthancServer/DatabaseWrapperBase.cpp + OrthancServer/DicomDirWriter.cpp + OrthancServer/DicomFindQuery.cpp + OrthancServer/DicomModification.cpp OrthancServer/DicomProtocol/DicomFindAnswers.cpp OrthancServer/DicomProtocol/DicomServer.cpp OrthancServer/DicomProtocol/DicomUserConnection.cpp OrthancServer/DicomProtocol/RemoteModalityParameters.cpp OrthancServer/DicomProtocol/ReusableDicomUserConnection.cpp - OrthancServer/DicomModification.cpp + OrthancServer/ExportedResource.cpp OrthancServer/FromDcmtkBridge.cpp - OrthancServer/ParsedDicomFile.cpp - OrthancServer/DicomDirWriter.cpp OrthancServer/Internals/CommandDispatcher.cpp + OrthancServer/Internals/DicomImageDecoder.cpp OrthancServer/Internals/FindScp.cpp OrthancServer/Internals/MoveScp.cpp OrthancServer/Internals/StoreScp.cpp - OrthancServer/Internals/DicomImageDecoder.cpp + OrthancServer/LuaScripting.cpp + OrthancServer/OrthancFindRequestHandler.cpp + OrthancServer/OrthancHttpHandler.cpp OrthancServer/OrthancInitialization.cpp + OrthancServer/OrthancMoveRequestHandler.cpp OrthancServer/OrthancPeerParameters.cpp OrthancServer/OrthancRestApi/OrthancRestAnonymizeModify.cpp OrthancServer/OrthancRestApi/OrthancRestApi.cpp @@ -169,21 +176,15 @@ OrthancServer/OrthancRestApi/OrthancRestModalities.cpp OrthancServer/OrthancRestApi/OrthancRestResources.cpp OrthancServer/OrthancRestApi/OrthancRestSystem.cpp - OrthancServer/ServerIndex.cpp - OrthancServer/ToDcmtkBridge.cpp - OrthancServer/DatabaseWrapper.cpp - OrthancServer/DatabaseWrapperBase.cpp + OrthancServer/ParsedDicomFile.cpp + OrthancServer/QueryRetrieveHandler.cpp + OrthancServer/ResourceFinder.cpp OrthancServer/ServerContext.cpp OrthancServer/ServerEnumerations.cpp + OrthancServer/ServerIndex.cpp OrthancServer/ServerToolbox.cpp - OrthancServer/OrthancFindRequestHandler.cpp - OrthancServer/OrthancMoveRequestHandler.cpp - OrthancServer/ExportedResource.cpp - OrthancServer/ResourceFinder.cpp - OrthancServer/DicomFindQuery.cpp - OrthancServer/QueryRetrieveHandler.cpp - OrthancServer/LuaScripting.cpp - OrthancServer/OrthancHttpHandler.cpp + OrthancServer/SliceOrdering.cpp + OrthancServer/ToDcmtkBridge.cpp # From "lua-scripting" branch OrthancServer/DicomInstanceToStore.cpp diff -r 4aaaecae5803 -r 9980875edc7c Core/DicomFormat/DicomMap.cpp --- a/Core/DicomFormat/DicomMap.cpp Mon Oct 12 14:47:58 2015 +0200 +++ b/Core/DicomFormat/DicomMap.cpp Mon Oct 12 17:49:23 2015 +0200 @@ -83,7 +83,8 @@ DICOM_TAG_NUMBER_OF_TEMPORAL_POSITIONS, DICOM_TAG_NUMBER_OF_SLICES, DICOM_TAG_NUMBER_OF_TIME_SLICES, - DICOM_TAG_SERIES_INSTANCE_UID + DICOM_TAG_SERIES_INSTANCE_UID, + DICOM_TAG_IMAGE_ORIENTATION_PATIENT // New in db v6 }; static DicomTag instanceTags[] = @@ -95,7 +96,8 @@ DICOM_TAG_INSTANCE_NUMBER, DICOM_TAG_NUMBER_OF_FRAMES, DICOM_TAG_TEMPORAL_POSITION_IDENTIFIER, - DICOM_TAG_SOP_INSTANCE_UID + DICOM_TAG_SOP_INSTANCE_UID, + DICOM_TAG_IMAGE_POSITION_PATIENT // New in db v6 }; diff -r 4aaaecae5803 -r 9980875edc7c Core/DicomFormat/DicomTag.h --- a/Core/DicomFormat/DicomTag.h Mon Oct 12 14:47:58 2015 +0200 +++ b/Core/DicomFormat/DicomTag.h Mon Oct 12 17:49:23 2015 +0200 @@ -134,6 +134,8 @@ static const DicomTag DICOM_TAG_PIXEL_REPRESENTATION(0x0028, 0x0103); static const DicomTag DICOM_TAG_PLANAR_CONFIGURATION(0x0028, 0x0006); static const DicomTag DICOM_TAG_PHOTOMETRIC_INTERPRETATION(0x0028, 0x0004); + static const DicomTag DICOM_TAG_IMAGE_ORIENTATION_PATIENT(0x0020, 0x0037); + static const DicomTag DICOM_TAG_IMAGE_POSITION_PATIENT(0x0020, 0x0032); // Tags related to date and time static const DicomTag DICOM_TAG_ACQUISITION_DATE(0x0008, 0x0022); diff -r 4aaaecae5803 -r 9980875edc7c NEWS --- a/NEWS Mon Oct 12 14:47:58 2015 +0200 +++ b/NEWS Mon Oct 12 17:49:23 2015 +0200 @@ -5,6 +5,7 @@ * "/tools/create-dicom": Support of binary tags encoded using data URI scheme * "/tools/create-dicom": Support of hierarchical structures (creation of sequences) * "/modify" can insert/modify sequences +* "/series/.../ordered-slices" to order the slices of a 2D+t, 3D or 3D+t image * New URIs for attachments: ".../compress", ".../uncompress" and ".../is-compressed" Plugins diff -r 4aaaecae5803 -r 9980875edc7c OrthancServer/OrthancRestApi/OrthancRestResources.cpp --- a/OrthancServer/OrthancRestApi/OrthancRestResources.cpp Mon Oct 12 14:47:58 2015 +0200 +++ b/OrthancServer/OrthancRestApi/OrthancRestResources.cpp Mon Oct 12 17:49:23 2015 +0200 @@ -39,6 +39,7 @@ #include "../ResourceFinder.h" #include "../DicomFindQuery.h" #include "../ServerContext.h" +#include "../SliceOrdering.h" namespace Orthanc @@ -1093,6 +1094,16 @@ } + static void OrderSlices(RestApiGetCall& call) + { + const std::string id = call.GetUriComponent("id", ""); + + ServerIndex& index = OrthancRestApi::GetIndex(call); + SliceOrdering ordering(index, id); + + } + + void OrthancRestApi::RegisterResources() { Register("/instances", ListResources); @@ -1187,5 +1198,7 @@ Register("/series/{id}/instances-tags", GetChildInstancesTags); Register("/instances/{id}/content/*", GetRawContent); + + Register("/series/{id}/ordered-slices", OrderSlices); } } diff -r 4aaaecae5803 -r 9980875edc7c OrthancServer/SliceOrdering.cpp --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/OrthancServer/SliceOrdering.cpp Mon Oct 12 17:49:23 2015 +0200 @@ -0,0 +1,215 @@ +/** + * Orthanc - A Lightweight, RESTful DICOM Store + * Copyright (C) 2012-2015 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 General Public License as + * published by the Free Software Foundation, either version 3 of the + * License, or (at your option) any later version. + * + * In addition, as a special exception, the copyright holders of this + * program give permission to link the code of its release with the + * OpenSSL project's "OpenSSL" library (or with modified versions of it + * that use the same license as the "OpenSSL" library), and distribute + * the linked executables. You must obey the GNU General Public License + * in all respects for all of the code used other than "OpenSSL". If you + * modify file(s) with this exception, you may extend this exception to + * your version of the file(s), but you are not obligated to do so. If + * you do not wish to do so, delete this exception statement from your + * version. If you delete this exception statement from all source files + * in the program, then also delete it here. + * + * 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 + * General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program. If not, see . + **/ + + +#include "PrecompiledHeadersServer.h" +#include "SliceOrdering.h" + +#include "../Core/Toolbox.h" + +#include + + +namespace Orthanc +{ + static bool TokenizeVector(std::vector& result, + const std::string& value, + unsigned int expectedSize) + { + std::vector tokens; + Toolbox::TokenizeString(tokens, value, '\\'); + + if (tokens.size() != expectedSize) + { + return false; + } + + result.resize(tokens.size()); + + for (size_t i = 0; i < tokens.size(); i++) + { + try + { + result[i] = boost::lexical_cast(tokens[i]); + } + catch (boost::bad_lexical_cast&) + { + return false; + } + } + + return true; + } + + + static bool TokenizeVector(std::vector& result, + const DicomMap& map, + const DicomTag& tag, + unsigned int expectedSize) + { + const DicomValue* value = map.TestAndGetValue(tag); + + if (value == NULL || + value->IsNull()) + { + return false; + } + else + { + return TokenizeVector(result, value->AsString(), expectedSize); + } + } + + + struct SliceOrdering::Instance + { + std::string instanceId_; + bool hasPosition_; + Vector position_; + bool hasIndexInSeries_; + size_t indexInSeries_; + + Instance(ServerIndex& index, + const std::string& instanceId) : + instanceId_(instanceId) + { + DicomMap instance; + if (!index.GetMainDicomTags(instance, instanceId, ResourceType_Instance, ResourceType_Instance)) + { + throw OrthancException(ErrorCode_UnknownResource); + } + + std::vector tmp; + hasPosition_ = TokenizeVector(tmp, instance, DICOM_TAG_IMAGE_POSITION_PATIENT, 3); + + if (hasPosition_) + { + position_[0] = tmp[0]; + position_[1] = tmp[1]; + position_[2] = tmp[2]; + } + + std::string s; + hasIndexInSeries_ = false; + + try + { + if (index.LookupMetadata(s, instanceId, MetadataType_Instance_IndexInSeries)) + { + indexInSeries_ = boost::lexical_cast(s); + hasIndexInSeries_ = true; + } + } + catch (boost::bad_lexical_cast&) + { + } + } + }; + + + void SliceOrdering::ComputeNormal() + { + DicomMap series; + if (!index_.GetMainDicomTags(series, seriesId_, ResourceType_Series, ResourceType_Series)) + { + throw OrthancException(ErrorCode_UnknownResource); + } + + std::vector cosines; + hasNormal_ = TokenizeVector(cosines, series, DICOM_TAG_IMAGE_ORIENTATION_PATIENT, 6); + + if (hasNormal_) + { + normal_[0] = cosines[1] * cosines[5] - cosines[2] * cosines[4]; + normal_[1] = cosines[2] * cosines[3] - cosines[0] * cosines[5]; + normal_[2] = cosines[0] * cosines[4] - cosines[1] * cosines[3]; + } + } + + + void SliceOrdering::CreateInstances() + { + std::list instancesId; + index_.GetChildren(instancesId, seriesId_); + + instances_.reserve(instancesId.size()); + for (std::list::const_iterator + it = instancesId.begin(); it != instancesId.end(); ++it) + { + instances_.push_back(new Instance(index_, *it)); + } + } + + + bool SliceOrdering::SortUsingPositions() + { + if (!hasNormal_) + { + return false; + } + + for (size_t i = 0; i < instances_.size(); i++) + { + assert(instances_[i] != NULL); + if (!instances_[i]->hasPosition_) + { + return false; + } + } + + + + return true; + } + + + SliceOrdering::SliceOrdering(ServerIndex& index, + const std::string& seriesId) : + index_(index), + seriesId_(seriesId) + { + ComputeNormal(); + CreateInstances(); + } + + + SliceOrdering::~SliceOrdering() + { + for (std::vector::iterator + it = instances_.begin(); it != instances_.end(); ++it) + { + if (*it != NULL) + { + delete *it; + } + } + } +} diff -r 4aaaecae5803 -r 9980875edc7c OrthancServer/SliceOrdering.h --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/OrthancServer/SliceOrdering.h Mon Oct 12 17:49:23 2015 +0200 @@ -0,0 +1,64 @@ +/** + * Orthanc - A Lightweight, RESTful DICOM Store + * Copyright (C) 2012-2015 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 General Public License as + * published by the Free Software Foundation, either version 3 of the + * License, or (at your option) any later version. + * + * In addition, as a special exception, the copyright holders of this + * program give permission to link the code of its release with the + * OpenSSL project's "OpenSSL" library (or with modified versions of it + * that use the same license as the "OpenSSL" library), and distribute + * the linked executables. You must obey the GNU General Public License + * in all respects for all of the code used other than "OpenSSL". If you + * modify file(s) with this exception, you may extend this exception to + * your version of the file(s), but you are not obligated to do so. If + * you do not wish to do so, delete this exception statement from your + * version. If you delete this exception statement from all source files + * in the program, then also delete it here. + * + * 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 + * General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program. If not, see . + **/ + + +#pragma once + +#include "ServerIndex.h" + +namespace Orthanc +{ + class SliceOrdering + { + private: + typedef float Vector[3]; + + struct Instance; + + ServerIndex& index_; + std::string seriesId_; + bool hasNormal_; + Vector normal_; + std::vector instances_; + + void ComputeNormal(); + + void CreateInstances(); + + bool SortUsingPositions(); + + public: + SliceOrdering(ServerIndex& index, + const std::string& seriesId); + + ~SliceOrdering(); + }; +}