nii_io

package
v0.4.0 Latest Latest
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 Go to latest Published: Jan 18, 2023 License: GPL-3.0 Imports: 14 Imported by: 0

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Index

Constants

View Source 
const (
	INVALID = "INVALID"
	UNKNOWN = "UNKNOWN"
	ILLEGAL = "ILLEGAL"
)

Variables

This section is empty.

Functions

func IsValidDatatype 

func IsValidDatatype(datatype int32) bool

IsValidDatatype checks whether the datatype is valid for NIFTI format

func NewNiiWriter 

func NewNiiWriter(filePath string, options ...func(*niiWriter)) (*niiWriter, error)

NewNiiWriter returns a new write for export

func WithCompression 

func WithCompression(withCompression bool) func(writer *niiWriter)

WithCompression sets the option to write compressed NIfTI image to a single file (.nii.gz)

If true, the whole file will be compressed. Default is false.

func WithHeader 

func WithHeader(header *Nii1Header) func(*niiWriter)

WithHeader sets the option to allow user to provide predefined NIfTI-1 header structure.

If no header provided, the header will be converted from the NIfTI image structure

func WithHeaderCompression 

func WithHeaderCompression(headerCompression bool) func(*niiWriter)

WithHeaderCompression sets the option to write compressed NIfTI header structure to file (.hdr.gz)

If true, the header will be compressed. It only works when WithWriteHeaderFile is provided with option `true`. Default is false.

func WithHeaderFile 

func WithHeaderFile(headerFile string) func(*niiReader) error

WithHeaderFile allows option to specify the separate header file

func WithInMemory 

func WithInMemory(inMemory bool) func(*niiReader) error

WithInMemory allows option to read the whole file into memory

func WithNIfTIData 

func WithNIfTIData(data *Nii) func(writer *niiWriter)

WithNIfTIData sets the option to allow user to provide predefined NIfTI-1 data structure.

func WithRetainHeader 

func WithRetainHeader(retainHeader bool) func(*niiReader) error

WithRetainHeader allows option to keep the header after parsing instead of just keeping the NIfTI data structure

func WithWriteHeaderFile 

func WithWriteHeaderFile(writeHeaderFile bool) func(*niiWriter)

WithWriteHeaderFile sets the option to write NIfTI image to a header/image (.hdr/.img) file pair

If true, output will be two files for the header and the image. Default is false.

Types

type Nifti1Ext 

type Nifti1Ext struct {
	ECode int32
	Edata []byte
	ESize int32
}

type Nii 

type Nii struct {
	NDim          int64            // last dimension greater than 1 (1..7)
	Nx            int64            // dimensions of grid array
	Ny            int64            // dimensions of grid array
	Nz            int64            // dimensions of grid array
	Nt            int64            // dimensions of grid array
	Nu            int64            // dimensions of grid array
	Nv            int64            // dimensions of grid array
	Nw            int64            // dimensions of grid array
	Dim           [8]int64         // dim[0] = ndim, dim[1] = nx, etc
	NVox          int64            // number of voxels = nx*ny*nz*...*nw
	NByPer        int32            // bytes per voxel, matches datatype (Datatype)
	Datatype      int32            // type of data in voxels: DT_* code
	Dx            float64          // grid spacings
	Dy            float64          // grid spacings
	Dz            float64          // grid spacings
	Dt            float64          // grid spacings
	Du            float64          // grid spacings
	Dv            float64          // grid spacings
	Dw            float64          // grid spacings tEStataILSTERIOn
	PixDim        [8]float64       // pixdim[1]=dx, etc
	SclSlope      float64          // scaling parameter: slope
	SclInter      float64          // scaling parameter: intercept
	CalMin        float64          // calibration parameter: minimum
	CalMax        float64          // calibration parameter: maximum
	QformCode     int32            // codes for (x,y,z) space meaning
	SformCode     int32            // codes for (x,y,z) space meaning
	FreqDim       int32            // indices (1,2,3, or 0) for MRI
	PhaseDim      int32            // directions in dim[]/pixdim[]
	SliceDim      int32            // directions in dim[]/pixdim[]
	SliceCode     int32            // code for slice timing pattern
	SliceStart    int64            // index for start of slices
	SliceEnd      int64            // index for end of slices
	SliceDuration float64          // time between individual slices
	QuaternB      float64          // Quaternion transform parameters [when writing a dataset, these are used for qform, NOT qto_xyz]
	QuaternC      float64          // Quaternion transform parameters [when writing a dataset, these are used for qform, NOT qto_xyz]
	QuaternD      float64          // Quaternion transform parameters [when writing a dataset, these are used for qform, NOT qto_xyz]
	QoffsetX      float64          // Quaternion transform parameters [when writing a dataset, these are used for qform, NOT qto_xyz]
	QoffsetY      float64          // Quaternion transform parameters [when writing a dataset, these are used for qform, NOT qto_xyz]
	QoffsetZ      float64          // Quaternion transform parameters [when writing a dataset, these are used for qform, NOT qto_xyz]
	QFac          float64          // Quaternion transform parameters [when writing a dataset, these are used for qform, NOT qto_xyz]
	QtoXYZ        matrix.DMat44    // qform: transform (i,j,k) to (x,y,z)
	QtoIJK        matrix.DMat44    // qform: transform (x,y,z) to (i,j,k)
	StoXYZ        matrix.DMat44    // sform: transform (i,j,k) to (x,y,z)
	StoIJK        matrix.DMat44    // sform: transform (x,y,z) to (i,j,k)
	TOffset       float64          // time coordinate offset
	XYZUnits      int32            // dx,dy,dz units: NIFTI_UNITS_* code
	TimeUnits     int32            // dt units: NIFTI_UNITS_* code
	NiftiType     int32            // 0==Analyze, 1==NIFTI-1 (file), 2==NIFTI-1 (2 files), 3==NIFTI-ASCII (1 file)
	IntentCode    int32            // statistic type (or something)
	IntentP1      float64          // intent parameters
	IntentP2      float64          // intent parameters
	IntentP3      float64          // intent parameters
	IntentName    [16]byte         // optional description of intent data
	Descrip       [80]byte         // optional text to describe dataset
	AuxFile       [24]byte         // auxiliary filename
	FName         *byte            // header filename
	IName         *byte            // image filename
	INameOffset   int32            // offset into IName where data start
	SwapSize      int32            // swap unit in image data (might be 0)
	ByteOrder     binary.ByteOrder // byte order on disk (MSB_ or LSB_FIRST)
	Volume        []byte           // slice of data: nbyper*nvox bytes
	NumExt        int32            // number of extensions in extList
	Nifti1Ext     []Nifti1Ext      // array of extension structs (with data)
	IJKOrtient    [3]int32         // self-add. Orientation ini, j, k coordinate
	Affine        matrix.DMat44    // self-add. Affine matrix
	VoxOffset     float64          // self-add. Voxel offset
	Version       int              // self-add. Used for version identification when writing
}

Nii defines the structure of the NIFTI-1 data for I/O purpose

type Nii1Header 

type Nii1Header struct {
	SizeofHdr      int32
	DataTypeUnused [10]uint8
	DbName         [18]uint8
	Extents        int32
	SessionError   int16
	Regular        uint8
	DimInfo        uint8
	Dim            [8]int16
	IntentP1       float32
	IntentP2       float32
	IntentP3       float32
	IntentCode     int16
	Datatype       int16
	Bitpix         int16
	SliceStart     int16
	Pixdim         [8]float32
	VoxOffset      float32
	SclSlope       float32
	SclInter       float32
	SliceEnd       int16
	SliceCode      uint8
	XyztUnits      uint8
	CalMax         float32
	CalMin         float32
	SliceDuration  float32
	Toffset        float32
	Glmax          int32
	Glmin          int32
	Descrip        [80]uint8
	AuxFile        [24]uint8
	QformCode      int16
	SformCode      int16
	QuaternB       float32
	QuaternC       float32
	QuaternD       float32
	QoffsetX       float32
	QoffsetY       float32
	QoffsetZ       float32
	SrowX          [4]float32
	SrowY          [4]float32
	SrowZ          [4]float32
	IntentName     [16]uint8
	Magic          [4]uint8
}

Nii1Header defines the structure of the NIFTI-1 header

func MakeNewNii1Header 

func MakeNewNii1Header(inDim *[8]int16, inDatatype int32) *Nii1Header

type Nii2Header 

type Nii2Header struct {
	SizeofHdr     int32
	Magic         [8]uint8
	Datatype      int16
	Bitpix        int16
	Dim           [8]int64
	IntentP1      float64
	IntentP2      float64
	IntentP3      float64
	Pixdim        [8]float64
	VoxOffset     int64
	SclSlope      float64
	SclInter      float64
	CalMax        float64
	CalMin        float64
	SliceDuration float64
	Toffset       float64
	SliceStart    int64
	SliceEnd      int64
	Descrip       [80]uint8
	AuxFile       [24]uint8
	QformCode     int32
	SformCode     int32
	QuaternB      float64
	QuaternC      float64
	QuaternD      float64
	QoffsetX      float64
	QoffsetY      float64
	QoffsetZ      float64
	SrowX         [4]float64
	SrowY         [4]float64
	SrowZ         [4]float64
	SliceCode     int32
	XyztUnits     int32
	IntentCode    int32
	IntentName    [16]uint8
	DimInfo       uint8
	UnusedStr     [15]uint8
}

Nii2Header defines the structure of the NIFTI-2 header

type NiiReader 

type NiiReader interface {
	// Parse returns the input NIFTI as header and image data
	Parse() error
	// GetOrientation returns the image orientation
	GetOrientation() [3]string
	// GetSliceCode returns the slice code
	GetSliceCode() string
	// GetDatatype returns the datatype of the NIFTI image
	GetDatatype() string
	// GetSFormCode returns the SForm code string
	GetSFormCode() string
	// GetQFormCode returns the QForm code string
	GetQFormCode() string
	// GetImgShape returns the image shape [x, y, z, t]
	GetImgShape() [4]int64
	// GetAt returns the value at [x, y, z, t] as float64
	GetAt(x, y, z, t int64) float64
	// GetBinaryOrder returns the binary order of the NIFTI image
	GetBinaryOrder() binary.ByteOrder
	// GetUnitsOfMeasurements returns the spatial and temporal units of the NIFTI image
	GetUnitsOfMeasurements() ([2]string, error)
	// GetTimeSeries returns the time series of value at [x, y, z]
	GetTimeSeries(x, y, z int64) ([]float64, error)
	// GetSlice returns the X-Y slice at [z, t]
	GetSlice(z, t int64) ([][]float64, error)
	// GetVolume returns the image data as 3-D matrix
	GetVolume(t int64) ([][][]float64, error)
	// GetAffine returns the affine matrix of the NIFTI image
	GetAffine() matrix.DMat44
	// QuaternToMatrix converts the quarternions parameters to matrix
	QuaternToMatrix() matrix.DMat44
	// GetNiiData returns the raw NIFTI header and image data
	GetNiiData() *Nii
}

func NewNiiReader 

func NewNiiReader(filePath string, options ...func(*niiReader) error) (NiiReader, error)

NewNiiReader receives a path to the NIFTI file and returns a new reader to parse the file

Source Files

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