Struct nifti::header::NiftiHeader [−][src]
pub struct NiftiHeader {}Show fields
pub sizeof_hdr: i32, pub data_type: [u8; 10], pub db_name: [u8; 18], pub extents: i32, pub session_error: i16, pub regular: u8, pub dim_info: u8, pub dim: [u16; 8], pub intent_p1: f32, pub intent_p2: f32, pub intent_p3: f32, pub intent_code: i16, pub datatype: i16, pub bitpix: i16, pub slice_start: i16, pub pixdim: [f32; 8], pub vox_offset: f32, pub scl_slope: f32, pub scl_inter: f32, pub slice_end: i16, pub slice_code: u8, pub xyzt_units: u8, pub cal_max: f32, pub cal_min: f32, pub slice_duration: f32, pub toffset: f32, pub glmax: i32, pub glmin: i32, pub descrip: Vec<u8>, pub aux_file: [u8; 24], pub qform_code: i16, pub sform_code: i16, pub quatern_b: f32, pub quatern_c: f32, pub quatern_d: f32, pub quatern_x: f32, pub quatern_y: f32, pub quatern_z: f32, pub srow_x: [f32; 4], pub srow_y: [f32; 4], pub srow_z: [f32; 4], pub intent_name: [u8; 16], pub magic: [u8; 4], pub endianness: Endianness,
Expand description
The NIFTI-1 header data type. All fields are public and named after the specification’s header file. The type of each field was adjusted according to their use and array limitations.
Examples
use nifti::{NiftiHeader, Endianness}; let hdr1 = NiftiHeader::from_file("0000.hdr")?; let hdr2 = NiftiHeader::from_file("0001.hdr.gz")?; let hdr3 = NiftiHeader::from_file("4321.nii.gz")?;
Or to build one yourself:
let mut hdr = NiftiHeader::default(); hdr.cal_min = 0.; hdr.cal_max = 128.; hdr.datatype = 4; assert_eq!(hdr.cal_min, 0.); assert_eq!(hdr.cal_max, 128.); assert_eq!(hdr.data_type().unwrap(), NiftiType::Int16);
Fields
sizeof_hdr: i32
Header size, must be 348
data_type: [u8; 10]
Unused in NIFTI-1
db_name: [u8; 18]
Unused in NIFTI-1
extents: i32
Unused in NIFTI-1
session_error: i16
Unused in NIFTI-1
regular: u8
Unused in NIFTI-1
dim_info: u8
MRI slice ordering
dim: [u16; 8]
Data array dimensions
intent_p1: f32
1st intent parameter
intent_p2: f32
2nd intent parameter
intent_p3: f32
3rd intent parameter
intent_code: i16
NIFTI_INTENT_* code
datatype: i16
Defines the data type!
bitpix: i16
Number of bits per voxel
slice_start: i16
First slice index
pixdim: [f32; 8]
Grid spacings
vox_offset: f32
Offset into .nii file to reach the volume
scl_slope: f32
Data scaling: slope
scl_inter: f32
Data scaling: offset
slice_end: i16
Last slice index
slice_code: u8
Slice timing order
xyzt_units: u8
Units of pixdim[1..4]
cal_max: f32
Max display intensity
cal_min: f32
Min display intensity
slice_duration: f32
Time for 1 slice
toffset: f32
Time axis shift
glmax: i32
Unused in NIFTI-1
glmin: i32
Unused in NIFTI-1
descrip: Vec<u8>
Any text you like
aux_file: [u8; 24]
Auxiliary filename
qform_code: i16
NIFTI_XFORM_* code
sform_code: i16
NIFTI_XFORM_* code
quatern_b: f32
Quaternion b param
quatern_c: f32
Quaternion c param
quatern_d: f32
Quaternion d param
quatern_x: f32
Quaternion x shift
quatern_y: f32
Quaternion y shift
quatern_z: f32
Quaternion z shift
srow_x: [f32; 4]
1st row affine transform
srow_y: [f32; 4]
2nd row affine transform
srow_z: [f32; 4]
3rd row affine transform
intent_name: [u8; 16]
‘name’ or meaning of data
magic: [u8; 4]
Magic code. Must be b"ni1\0"
or b"ni+\0"
endianness: Endianness
Original data Endianness
Implementations
Retrieve a NIFTI header, along with its byte order, from a file in the file system. If the file’s name ends with “.gz”, the file is assumed to need GZip decoding.
Read a NIfTI-1 header, along with its byte order, from the given byte stream. It is assumed that the input is currently at the start of the NIFTI header.
Fix some commonly invalid fields.
Currently, only the following problems are fixed:
- If
pixdim[0]
isn’t equal to -1.0 or 1.0, it will be set to 1.0
Retrieve and validate the dimensions of the volume. Unlike how NIfTI-1
stores dimensions, the returned slice does not include dim[0]
and is
clipped to the effective number of dimensions.
Error
NiftiError::InconsistentDim
if dim[0]
does not represent a valid
dimensionality, or any of the real dimensions are zero.
Retrieve and validate the number of dimensions of the volume. This is
dim[0]
after the necessary byte order conversions.
Error
NiftiError::
if dim[0]
does not represent a valid dimensionality
(it must be positive and not higher than 7).
Get the spatial units type as a validated unit enum.
Get the time units type as a validated unit enum.
Get the xyzt units type as a validated pair of space and time unit enum.
Get the slice order as a validated enum.
Get the qform coordinate mapping method as a validated enum.
Get the sform coordinate mapping method as a validated enum.
Ensure that the current descrip
field is valid and is exactly equal to 80 bytes.
Descriptions shorter than 80 bytes will be extended with trailing zeros.
Safely set the descrip
field using a buffer.
Retrieve best of available transformations.
Return the ‘sform’ transformation if sform_code
has a valid value, ‘qform’ transformation
if qform_code
has a valid value, otherwise return a “base” transformation, constructed
from the declared shape and zooms.
If sform_code
and qform_code
both have valid values, the ‘sform’ affine transformation
is prioritized.
Retrieve affine transformation from ‘sform’ fields.
Retrieve affine transformation from qform-related fields.
pub fn set_affine<T>(&mut self, affine: &Matrix4<T>) where
T: RealField,
T: SubsetOf<f64>,
T: ToPrimitive,
[src]
pub fn set_affine<T>(&mut self, affine: &Matrix4<T>) where
T: RealField,
T: SubsetOf<f64>,
T: ToPrimitive,
[src]Set affine transformation.
Will set both affine transformations to avoid interoperability problems:
- ‘sform’ from unmodified
affine
, withsform_code
set toAlignedAnat
. - ‘qform’ from a quaternion built from
affine
. However, the ‘qform’ won’t be used by most nifti readers because theqform_code
will be set toUnknown
.
Trait Implementations
Returns the “default value” for a type. Read more
This method tests for self
and other
values to be equal, and is used
by ==
. Read more
This method tests for !=
.
Auto Trait Implementations
impl RefUnwindSafe for NiftiHeader
impl Send for NiftiHeader
impl Sync for NiftiHeader
impl Unpin for NiftiHeader
impl UnwindSafe for NiftiHeader
Blanket Implementations
Mutably borrows from an owned value. Read more
type Output = T
type Output = T
Should always be Self
The inverse inclusion map: attempts to construct self
from the equivalent element of its
superset. Read more
Checks if self
is actually part of its subset T
(and can be converted to it).
Use with care! Same as self.to_subset
but without any property checks. Always succeeds.
The inclusion map: converts self
to the equivalent element of its superset.