nii_io

Documentation

Index

• func IsValidDatatype(datatype int32) bool
• func NewNiiWriter(filePath string, options ...func(*niiWriter)) (*niiWriter, error)
• func WithCompression(withCompression bool) func(writer *niiWriter)
• func WithHeader(header *Nii1Header) func(*niiWriter)
• func WithHeaderCompression(headerCompression bool) func(*niiWriter)
• func WithHeaderFile(headerFile string) func(*niiReader) error
• func WithInMemory(inMemory bool) func(*niiReader) error
• func WithNIfTIData(data *Nii) func(writer *niiWriter)
• func WithRetainHeader(retainHeader bool) func(*niiReader) error
• func WithWriteHeaderFile(writeHeaderFile bool) func(*niiWriter)
• type NiiReader
  • func NewNiiReader(filePath string, options ...func(*niiReader) error) (NiiReader, error)

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 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