CiftiBrainModelsMap.h
#ifndef __CIFTI_BRAIN_MODELS_MAP_H__
#define __CIFTI_BRAIN_MODELS_MAP_H__
/*LICENSE_START*/
/*
* Copyright (c) 2014, Washington University School of Medicine
* All rights reserved.
*
* Redistribution and use in source and binary forms, with or without modification,
* are permitted provided that the following conditions are met:
*
* 1. Redistributions of source code must retain the above copyright notice,
* this list of conditions and the following disclaimer.
*
* 2. Redistributions in binary form must reproduce the above copyright notice,
* this list of conditions and the following disclaimer in the documentation
* and/or other materials provided with the distribution.
*
* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
* AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
* THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
* ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
* FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
* (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
* LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
* ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
* (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE,
* EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
*/
#include "CiftiMappingType.h"
#include "Common/Compact3DLookup.h"
#include "StructureEnum.h"
#include "VolumeSpace.h"
#include <map>
#include <utility>
#include <vector>
namespace cifti
{
class CiftiBrainModelsMap : public CiftiMappingType
{
public:
enum ModelType
{
SURFACE,
VOXELS
};
struct SurfaceMap
{
int64_t m_ciftiIndex;
int64_t m_surfaceNode;
};
struct VolumeMap
{
int64_t m_ciftiIndex;
int64_t m_ijk[3];
};
struct ModelInfo
{
ModelType m_type;
StructureEnum::Enum m_structure;
int64_t m_indexStart, m_indexCount;//these are intended only for summary info, use getSurfaceMap, etc for the index to vertex/voxel mappings
};
struct IndexInfo
{
ModelType m_type;
StructureEnum::Enum m_structure;
int64_t m_surfaceNode;//only one of these two will be valid
int64_t m_ijk[3];
};
bool hasVolumeData() const;
bool hasVolumeData(const StructureEnum::Enum& structure) const;
bool hasSurfaceData(const StructureEnum::Enum& structure) const;
int64_t getIndexForNode(const int64_t& node, const StructureEnum::Enum& structure) const;
int64_t getIndexForVoxel(const int64_t* ijk, StructureEnum::Enum* structureOut = NULL) const;
int64_t getIndexForVoxel(const int64_t& i, const int64_t& j, const int64_t& k, StructureEnum::Enum* structureOut = NULL) const;
IndexInfo getInfoForIndex(const int64_t index) const;
std::vector<SurfaceMap> getSurfaceMap(const StructureEnum::Enum& structure) const;
std::vector<VolumeMap> getFullVolumeMap() const;
std::vector<VolumeMap> getVolumeStructureMap(const StructureEnum::Enum& structure) const;
const VolumeSpace& getVolumeSpace() const;
int64_t getSurfaceNumberOfNodes(const StructureEnum::Enum& structure) const;
std::vector<StructureEnum::Enum> getSurfaceStructureList() const;
std::vector<StructureEnum::Enum> getVolumeStructureList() const;
const std::vector<int64_t>& getNodeList(const StructureEnum::Enum& structure) const;//useful for copying mappings to a new dense mapping
const std::vector<int64_t>& getVoxelList(const StructureEnum::Enum& structure) const;
std::vector<ModelInfo> getModelInfo() const;
CiftiBrainModelsMap() { m_haveVolumeSpace = false; m_ignoreVolSpace = false; }
void addSurfaceModel(const int64_t& numberOfNodes, const StructureEnum::Enum& structure, const float* roi = NULL);
void addSurfaceModel(const int64_t& numberOfNodes, const StructureEnum::Enum& structure, const std::vector<int64_t>& nodeList);
void addVolumeModel(const StructureEnum::Enum& structure, const std::vector<int64_t>& ijkList);
void setVolumeSpace(const VolumeSpace& space);
void clear();
CiftiMappingType* clone() const { return new CiftiBrainModelsMap(*this); }
MappingType getType() const { return BRAIN_MODELS; }
int64_t getLength() const;
bool operator==(const CiftiMappingType& rhs) const;
bool approximateMatch(const CiftiMappingType& rhs, AString* explanation = NULL) const;
void readXML1(XmlReader& xml);
void readXML2(XmlReader& xml);
void writeXML1(XmlWriter& xml) const;
void writeXML2(XmlWriter& xml) const;
private:
struct BrainModelPriv
{
ModelType m_type;
StructureEnum::Enum m_brainStructure;
int64_t m_surfaceNumberOfNodes;
std::vector<int64_t> m_nodeIndices;
std::vector<int64_t> m_voxelIndicesIJK;
int64_t m_modelStart, m_modelEnd;//stuff only needed for optimization - models are kept in sorted order by their index ranges
std::vector<int64_t> m_nodeToIndexLookup;
bool operator==(const BrainModelPriv& rhs) const;
bool operator!=(const BrainModelPriv& rhs) const { return !((*this) == rhs); }
void setupSurface(const int64_t& start);
};
VolumeSpace m_volSpace;
bool m_haveVolumeSpace, m_ignoreVolSpace;//second is needed for parsing cifti-1
std::vector<BrainModelPriv> m_modelsInfo;
std::map<StructureEnum::Enum, int> m_surfUsed, m_volUsed;
Compact3DLookup<std::pair<int64_t, StructureEnum::Enum> > m_voxelToIndexLookup;//make one unified lookup rather than separate lookups per volume structure
int64_t getNextStart() const;
struct ParseHelperModel
{//specifically to allow the parsed elements to be sorted before using addSurfaceModel/addVolumeModel
ModelType m_type;
StructureEnum::Enum m_brainStructure;
int64_t m_surfaceNumberOfNodes;
std::vector<int64_t> m_nodeIndices;
std::vector<int64_t> m_voxelIndicesIJK;
int64_t m_offset, m_count;
bool operator<(const ParseHelperModel& rhs) const
{
if (m_offset < rhs.m_offset) return true;
if (m_offset > rhs.m_offset) return false;//get the common cases first
if (m_count < rhs.m_count) return true;//in case we have a zero-length model - this shouldn't happen, usually
return false;
}
void parseBrainModel1(XmlReader& xml);
void parseBrainModel2(XmlReader& xml);
static std::vector<int64_t> readIndexArray(XmlReader& xml);
};
};
}
#endif //__CIFTI_BRAIN_MODELS_MAP_H__
cifti::CiftiBrainModelsMap
Definition CiftiBrainModelsMap.h:44
cifti::CiftiMappingType
Definition CiftiMappingType.h:39
cifti::StructureEnum::Enum
Enum
Definition StructureEnum.h:49
cifti::VolumeSpace
Definition VolumeSpace.h:42
cifti
namespace for all CiftiLib functionality
Definition CiftiBrainModelsMap.h:42
cifti::CiftiBrainModelsMap::IndexInfo
Definition CiftiBrainModelsMap.h:68
cifti::CiftiBrainModelsMap::ModelInfo
Definition CiftiBrainModelsMap.h:62
cifti::CiftiBrainModelsMap::SurfaceMap
Definition CiftiBrainModelsMap.h:52
cifti::CiftiBrainModelsMap::VolumeMap
Definition CiftiBrainModelsMap.h:57