CiftiLib
A C++ library for CIFTI-2 and CIFTI-1 files
CiftiFile.h
1#ifndef __CIFTI_FILE_H__
2#define __CIFTI_FILE_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 "Common/AString.h"
32#include "Common/CiftiException.h"
33#include "Common/MultiDimIterator.h"
34#include "Cifti/CiftiXML.h"
35#include "Nifti/nifti1.h"
36
37#include "boost/shared_ptr.hpp"
38
39#include <vector>
40
42namespace cifti
43{
46 {
47 public:
48
49 enum ENDIAN
50 {
51 ANY,//so that writeFile() with default endian argument can do nothing after setWritingFile with any endian argument - uses native if there is no rewrite to avoid
52 NATIVE,//as long as there are more than two options anyway, provide a convenience option so people don't need to figure out the machine endianness for a common case
53 LITTLE,
54 BIG
55 };
56
57 CiftiFile();
58
60 explicit CiftiFile(const AString &fileName);
61
63 void openFile(const AString& fileName);
64
66 void setWritingFile(const AString& fileName, const CiftiVersion& writingVersion = CiftiVersion(), const ENDIAN& endian = NATIVE);
67
69 void writeFile(const AString& fileName, const CiftiVersion& writingVersion = CiftiVersion(), const ENDIAN& endian = ANY);
70
72 void close();
73
75 void convertToInMemory();
76
77 const CiftiXML& getCiftiXML() const { return m_xml; }
78 bool isInMemory() const;
79
81 void getRow(float* dataOut, const std::vector<int64_t>& indexSelect, const bool& tolerateShortRead = false) const;
82 const std::vector<int64_t>& getDimensions() const { return m_dims; }
83
86 {
87 return MultiDimIterator<int64_t>(std::vector<int64_t>(m_dims.begin() + 1, m_dims.end()));
88 }
89
91 void getColumn(float* dataOut, const int64_t& index) const;
92
93 void setCiftiXML(const CiftiXML& xml, const bool useOldMetadata = true);
94 void setRow(const float* dataIn, const std::vector<int64_t>& indexSelect);
95
97 void setColumn(const float* dataIn, const int64_t& index);
98
100 void getRow(float* dataOut, const int64_t& index, const bool& tolerateShortRead = false) const;
101
103 void setRow(const float* dataIn, const int64_t& index);
104
106 void setWritingDataTypeNoScaling(const int16_t& type = NIFTI_TYPE_FLOAT32);
107 void setWritingDataTypeAndScaling(const int16_t& type, const double& minval, const double& maxval);
108
109 //implementation details from here down
111 {
112 public:
113 virtual void getRow(float* dataOut, const std::vector<int64_t>& indexSelect, const bool& tolerateShortRead) const = 0;
114 virtual void getColumn(float* dataOut, const int64_t& index) const = 0;
115 virtual bool isInMemory() const { return false; }
116 virtual ~ReadImplInterface();
117 };
118 //assume if you can write to it, you can also read from it
120 {
121 public:
122 virtual void setRow(const float* dataIn, const std::vector<int64_t>& indexSelect) = 0;
123 virtual void setColumn(const float* dataIn, const int64_t& index) = 0;
124 virtual void close() {}
125 virtual ~WriteImplInterface();
126 };
127 private:
128 std::vector<int64_t> m_dims;
129 boost::shared_ptr<WriteImplInterface> m_writingImpl;//this will be equal to m_readingImpl when non-null
130 boost::shared_ptr<ReadImplInterface> m_readingImpl;
131 AString m_writingFile;
132 CiftiXML m_xml;
133 CiftiVersion m_onDiskVersion;
134 ENDIAN m_endianPref;
135 bool m_doWriteScaling;
136 int16_t m_writingDataType;
137 double m_minScalingVal, m_maxScalingVal;
138
139 void verifyWriteImpl();
140 static void copyImplData(const ReadImplInterface* from, WriteImplInterface* to, const std::vector<int64_t>& dims);
141 };
142
143}
144
145#endif //__CIFTI_FILE_H__
Definition: CiftiFile.h:111
Definition: CiftiFile.h:120
class for reading and writing cifti files
Definition: CiftiFile.h:46
void getColumn(float *dataOut, const int64_t &index) const
for 2D only, will be slow if on disk!
Definition: CiftiFile.cxx:266
void setWritingDataTypeNoScaling(const int16_t &type=NIFTI_TYPE_FLOAT32)
data type and scaling options - should be set before setRow, etc, to avoid rewriting of file
Definition: CiftiFile.cxx:171
void getRow(float *dataOut, const std::vector< int64_t > &indexSelect, const bool &tolerateShortRead=false) const
the tolerateShortRead parameter is useful for on-disk writing when it is easiest to do RMW multiple t...
Definition: CiftiFile.cxx:259
void convertToInMemory()
reads file into memory, closes file
Definition: CiftiFile.cxx:235
void openFile(const AString &fileName)
starts on-disk reading
Definition: CiftiFile.cxx:153
void writeFile(const AString &fileName, const CiftiVersion &writingVersion=CiftiVersion(), const ENDIAN &endian=ANY)
does nothing if filename, version, and effective endianness match file currently open,...
Definition: CiftiFile.cxx:189
void close()
closes the underlying file to flush it, so that exceptions can be thrown
Definition: CiftiFile.cxx:219
void setWritingFile(const AString &fileName, const CiftiVersion &writingVersion=CiftiVersion(), const ENDIAN &endian=NATIVE)
starts on-disk writing
Definition: CiftiFile.cxx:163
MultiDimIterator< int64_t > getIteratorOverRows() const
convenience function for iterating over arbitrary numbers of dimensions
Definition: CiftiFile.h:85
void setColumn(const float *dataIn, const int64_t &index)
for 2D only, will be slow if on disk!
Definition: CiftiFile.cxx:301
Definition: CiftiVersion.h:38
class for retrieving and setting mapping information of cifti files
Definition: CiftiXML.h:49
Definition: MultiDimIterator.h:39
const int32_t NIFTI_TYPE_FLOAT32
Definition: nifti1.h:552
namespace for all CiftiLib functionality
Definition: CiftiBrainModelsMap.h:42