CiftiLib
A C++ library for CIFTI-2 and CIFTI-1 files
CiftiBrainModelsMap.h
1#ifndef __CIFTI_BRAIN_MODELS_MAP_H__
2#define __CIFTI_BRAIN_MODELS_MAP_H__
3
4/*LICENSE_START*/
5/*
6 * Copyright (c) 2014, Washington University School of Medicine
7 * All rights reserved.
8 *
9 * Redistribution and use in source and binary forms, with or without modification,
10 * are permitted provided that the following conditions are met:
11 *
12 * 1. Redistributions of source code must retain the above copyright notice,
13 * this list of conditions and the following disclaimer.
14 *
15 * 2. Redistributions in binary form must reproduce the above copyright notice,
16 * this list of conditions and the following disclaimer in the documentation
17 * and/or other materials provided with the distribution.
18 *
19 * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
20 * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
21 * THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
22 * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
23 * FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
24 * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
25 * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
26 * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
27 * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE,
28 * EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
29 */
30
31#include "CiftiMappingType.h"
32
33#include "Common/Compact3DLookup.h"
34#include "StructureEnum.h"
35#include "VolumeSpace.h"
36
37#include <map>
38#include <utility>
39#include <vector>
40
41namespace cifti
42{
44 {
45 public:
46 enum ModelType
47 {
48 SURFACE,
49 VOXELS
50 };
52 {
53 int64_t m_ciftiIndex;
54 int64_t m_surfaceNode;
55 };
56 struct VolumeMap
57 {
58 int64_t m_ciftiIndex;
59 int64_t m_ijk[3];
60 };
61 struct ModelInfo
62 {
63 ModelType m_type;
64 StructureEnum::Enum m_structure;
65 int64_t m_indexStart, m_indexCount;//these are intended only for summary info, use getSurfaceMap, etc for the index to vertex/voxel mappings
66 };
67 struct IndexInfo
68 {
69 ModelType m_type;
70 StructureEnum::Enum m_structure;
71 int64_t m_surfaceNode;//only one of these two will be valid
72 int64_t m_ijk[3];
73 };
74 bool hasVolumeData() const;
75 bool hasVolumeData(const StructureEnum::Enum& structure) const;
76 bool hasSurfaceData(const StructureEnum::Enum& structure) const;
77 int64_t getIndexForNode(const int64_t& node, const StructureEnum::Enum& structure) const;
78 int64_t getIndexForVoxel(const int64_t* ijk, StructureEnum::Enum* structureOut = NULL) const;
79 int64_t getIndexForVoxel(const int64_t& i, const int64_t& j, const int64_t& k, StructureEnum::Enum* structureOut = NULL) const;
80 IndexInfo getInfoForIndex(const int64_t index) const;
81 std::vector<SurfaceMap> getSurfaceMap(const StructureEnum::Enum& structure) const;
82 std::vector<VolumeMap> getFullVolumeMap() const;
83 std::vector<VolumeMap> getVolumeStructureMap(const StructureEnum::Enum& structure) const;
84 const VolumeSpace& getVolumeSpace() const;
85 int64_t getSurfaceNumberOfNodes(const StructureEnum::Enum& structure) const;
86 std::vector<StructureEnum::Enum> getSurfaceStructureList() const;
87 std::vector<StructureEnum::Enum> getVolumeStructureList() const;
88 const std::vector<int64_t>& getNodeList(const StructureEnum::Enum& structure) const;//useful for copying mappings to a new dense mapping
89 const std::vector<int64_t>& getVoxelList(const StructureEnum::Enum& structure) const;
90 std::vector<ModelInfo> getModelInfo() const;
91
92 CiftiBrainModelsMap() { m_haveVolumeSpace = false; m_ignoreVolSpace = false; }
93 void addSurfaceModel(const int64_t& numberOfNodes, const StructureEnum::Enum& structure, const float* roi = NULL);
94 void addSurfaceModel(const int64_t& numberOfNodes, const StructureEnum::Enum& structure, const std::vector<int64_t>& nodeList);
95 void addVolumeModel(const StructureEnum::Enum& structure, const std::vector<int64_t>& ijkList);
96 void setVolumeSpace(const VolumeSpace& space);
97 void clear();
98
99 CiftiMappingType* clone() const { return new CiftiBrainModelsMap(*this); }
100 MappingType getType() const { return BRAIN_MODELS; }
101 int64_t getLength() const;
102 bool operator==(const CiftiMappingType& rhs) const;
103 bool approximateMatch(const CiftiMappingType& rhs, AString* explanation = NULL) const;
104 void readXML1(XmlReader& xml);
105 void readXML2(XmlReader& xml);
106 void writeXML1(XmlWriter& xml) const;
107 void writeXML2(XmlWriter& xml) const;
108 private:
109 struct BrainModelPriv
110 {
111 ModelType m_type;
112 StructureEnum::Enum m_brainStructure;
113 int64_t m_surfaceNumberOfNodes;
114 std::vector<int64_t> m_nodeIndices;
115 std::vector<int64_t> m_voxelIndicesIJK;
116
117 int64_t m_modelStart, m_modelEnd;//stuff only needed for optimization - models are kept in sorted order by their index ranges
118 std::vector<int64_t> m_nodeToIndexLookup;
119 bool operator==(const BrainModelPriv& rhs) const;
120 bool operator!=(const BrainModelPriv& rhs) const { return !((*this) == rhs); }
121 void setupSurface(const int64_t& start);
122 };
123 VolumeSpace m_volSpace;
124 bool m_haveVolumeSpace, m_ignoreVolSpace;//second is needed for parsing cifti-1
125 std::vector<BrainModelPriv> m_modelsInfo;
126 std::map<StructureEnum::Enum, int> m_surfUsed, m_volUsed;
127 Compact3DLookup<std::pair<int64_t, StructureEnum::Enum> > m_voxelToIndexLookup;//make one unified lookup rather than separate lookups per volume structure
128 int64_t getNextStart() const;
129 struct ParseHelperModel
130 {//specifically to allow the parsed elements to be sorted before using addSurfaceModel/addVolumeModel
131 ModelType m_type;
132 StructureEnum::Enum m_brainStructure;
133 int64_t m_surfaceNumberOfNodes;
134 std::vector<int64_t> m_nodeIndices;
135 std::vector<int64_t> m_voxelIndicesIJK;
136 int64_t m_offset, m_count;
137 bool operator<(const ParseHelperModel& rhs) const
138 {
139 if (m_offset < rhs.m_offset) return true;
140 if (m_offset > rhs.m_offset) return false;//get the common cases first
141 if (m_count < rhs.m_count) return true;//in case we have a zero-length model - this shouldn't happen, usually
142 return false;
143 }
144 void parseBrainModel1(XmlReader& xml);
145 void parseBrainModel2(XmlReader& xml);
146 static std::vector<int64_t> readIndexArray(XmlReader& xml);
147 };
148 };
149}
150
151#endif //__CIFTI_BRAIN_MODELS_MAP_H__
Definition CiftiBrainModelsMap.h:44
Definition CiftiMappingType.h:39
Enum
Definition StructureEnum.h:49
Definition VolumeSpace.h:42
namespace for all CiftiLib functionality
Definition CiftiBrainModelsMap.h:42
Definition CiftiBrainModelsMap.h:68
Definition CiftiBrainModelsMap.h:62
Definition CiftiBrainModelsMap.h:52
Definition CiftiBrainModelsMap.h:57