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//! This module contains multiple types defined by the standard. //! At the moment, not all of them are used internally (`NiftiType` //! makes the exception, which also provides a safe means of //! reading voxel values). However, primitive integer values can be //! converted to these types and vice-versa. use byteorder::ReadBytesExt; use error::{Result, NiftiError}; use std::io::Read; use std::ops::{Add, Mul}; use util::{Endianness, raw_to_value}; use num::Num; /// Data type for representing a NIFTI value type in a volume. /// Methods for reading values of that type from a source are also included. #[derive(Debug, PartialEq, Eq, Hash, Clone, Copy, FromPrimitive)] pub enum NiftiType { /// unsigned char. // NIFTI_TYPE_UINT8 2 Uint8 = 2, /// signed short. // NIFTI_TYPE_INT16 4 Int16 = 4, /// signed int. // NIFTI_TYPE_INT32 8 Int32 = 8, /// 32 bit float. // NIFTI_TYPE_FLOAT32 16 Float32 = 16, /// 64 bit complex = 2 32 bit floats. // NIFTI_TYPE_COMPLEX64 32 Complex64 = 32, /// 64 bit float = double. // NIFTI_TYPE_FLOAT64 64 Float64 = 64, /// 3 8 bit bytes. // NIFTI_TYPE_RGB24 128 Rgb24 = 128, /// signed char. // NIFTI_TYPE_INT8 256 Int8 = 256, /// unsigned short. // NIFTI_TYPE_UINT16 512 Uint16 = 512, /// unsigned int. // NIFTI_TYPE_UINT32 768 Uint32 = 768, /// signed long long. // NIFTI_TYPE_INT64 1024 Int64 = 1024, /// unsigned long long. // NIFTI_TYPE_UINT64 1280 Uint64 = 1280, /// 128 bit float = long double. // NIFTI_TYPE_FLOAT128 1536 Float128 = 1536, /// 128 bit complex = 2 64 bit floats. // NIFTI_TYPE_COMPLEX128 1792 Complex128 = 1792, /// 256 bit complex = 2 128 bit floats // NIFTI_TYPE_COMPLEX256 2048 Complex256 = 2048, /// 4 8 bit bytes. // NIFTI_TYPE_RGBA32 2304 Rgba32 = 2304, } impl NiftiType { /// Read a primitive voxel value from a source. pub fn read_primitive_value<S, T>(&self, mut source: S, endianness: Endianness, slope: f32, inter: f32) -> Result<T> where S: Read, T: From<f32>, T: Num, T: Add<Output = T>, T: Mul<Output = T> { let slope: T = slope.into(); let inter: T = inter.into(); match *self { NiftiType::Uint8 => { let raw = source.read_u8()?; Ok(raw_to_value(raw as f32, slope, inter)) }, NiftiType::Uint16 => { let raw = endianness.read_u16(source)?; Ok(raw_to_value(raw as f32, slope, inter)) }, NiftiType::Int16 => { let raw = endianness.read_i16(source)?; Ok(raw_to_value(raw as f32, slope, inter)) }, NiftiType::Uint32 => { let raw = endianness.read_u32(source)?; Ok(raw_to_value(raw as f32, slope, inter)) }, NiftiType::Int32 => { let raw = endianness.read_i32(source)?; Ok(raw_to_value(raw as f32, slope, inter)) }, NiftiType::Uint64 => { // TODO find a way to not lose precision let raw = endianness.read_u64(source)?; Ok(raw_to_value(raw as f32, slope, inter)) }, NiftiType::Int64 => { // TODO find a way to not lose precision let raw = endianness.read_i64(source)?; Ok(raw_to_value(raw as f32, slope, inter)) }, NiftiType::Float32 => { let raw = endianness.read_f32(source)?; Ok(raw_to_value(raw, slope, inter)) }, NiftiType::Float64 => { // TODO find a way to not lose precision let raw = endianness.read_f64(source)?; Ok(raw_to_value(raw as f32, slope, inter)) }, // TODO add support for more data types _ => Err(NiftiError::UnsupportedDataType(*self)) } } } /// An enum type which represents a unit type. #[derive(Debug, PartialEq, Eq, Hash, Clone, Copy, FromPrimitive)] pub enum Unit { /// NIFTI code for unspecified units. Unknown = 0, /* Space codes are multiples of 1. */ /// NIFTI code for meters. Meter = 1, /// NIFTI code for millimeters. Mm = 2, /// NIFTI code for micrometers. Micron = 3, /* Time codes are multiples of 8. */ /// NIFTI code for seconds. Sec = 8, /// NIFTI code for milliseconds. Msec = 16, /// NIFTI code for microseconds. Usec = 24, /* These units are for spectral data: */ /// NIFTI code for Hertz. Hz = 32, /// NIFTI code for ppm. Ppm = 40, /// NIFTI code for radians per second. Rads = 48, } /// An enum type for representing a NIFTI intent code. #[derive(Debug, PartialEq, Eq, Hash, Clone, Copy, FromPrimitive)] pub enum Intent { /// default: no intention is indicated in the header. None = 0, /// nifti1 intent codes, to describe intended meaning of dataset contents Correl = 2, /// [C2, chap 28] Student t statistic (1 param): p1 = DOF. Ttest = 3, /// [C2, chap 27] Fisher F statistic (2 params): /// p1 = numerator DOF, p2 = denominator DOF. Ftest = 4, /// [C1, chap 13] Standard normal (0 params): Density = N(0,1). Zscore = 5, /// [C1, chap 18] Chi-squared (1 param): p1 = DOF. /// Density(x) proportional to exp(-x/2) * x^(p1/2-1). Chisq = 6, /// [C2, chap 25] Beta distribution (2 params): p1=a, p2=b. /// Density(x) proportional to x^(a-1) * (1-x)^(b-1). Beta = 7, /// [U, chap 3] Binomial distribution (2 params): /// p1 = number of trials, p2 = probability per trial. /// Prob(x) = (p1 choose x) * p2^x * (1-p2)^(p1-x), for x=0,1,...,p1. Binom = 8, /// [C1, chap 17] Gamma distribution (2 params): /// p1 = shape, p2 = scale. /// Density(x) proportional to x^(p1-1) * exp(-p2*x). Gamma = 9, /// [U, chap 4] Poisson distribution (1 param): p1 = mean. /// Prob(x) = exp(-p1) * p1^x / x! , for x=0,1,2,.... Poisson = 10, /// [C1, chap 13] Normal distribution (2 params): /// p1 = mean, p2 = standard deviation. Normal = 11, /// [C2, chap 30] Noncentral F statistic (3 params): /// p1 = numerator DOF, p2 = denominator DOF, /// p3 = numerator noncentrality parameter. FtestNonc = 12, /// [C2, chap 29] Noncentral chi-squared statistic (2 params): /// p1 = DOF, p2 = noncentrality parameter. ChisqNonc = 13, /// [C2, chap 23] Logistic distribution (2 params): /// p1 = location, p2 = scale. /// Density(x) proportional to sech^2((x-p1)/(2*p2)). Logistic = 14, /// [C2, chap 24] Laplace distribution (2 params): /// p1 = location, p2 = scale. /// Density(x) proportional to exp(-abs(x-p1)/p2). Laplace = 15, /// [C2, chap 26] Uniform distribution: p1 = lower end, p2 = upper end. Uniform = 16, /// [C2, chap 31] Noncentral t statistic (2 params): /// p1 = DOF, p2 = noncentrality parameter. TtestNonc = 17, /// [C1, chap 21] Weibull distribution (3 params): /// p1 = location, p2 = scale, p3 = power. /// Density(x) proportional to /// ((x-p1)/p2)^(p3-1) * exp(-((x-p1)/p2)^p3) for x > p1. Weibull = 18, /// [C1, chap 18] Chi distribution (1 param): p1 = DOF. /// Density(x) proportional to x^(p1-1) * exp(-x^2/2) for x > 0. /// p1 = 1 = 'half normal' distribution /// p1 = 2 = Rayleigh distribution /// p1 = 3 = Maxwell-Boltzmann distribution. Chi = 19, /// [C1, chap 15] Inverse Gaussian (2 params): /// p1 = mu, p2 = lambda /// Density(x) proportional to /// exp(-p2*(x-p1)^2/(2*p1^2*x)) / x^3 for x > 0. Invgauss = 20, /// [C2, chap 22] Extreme value type I (2 params): /// p1 = location, p2 = scale /// cdf(x) = exp(-exp(-(x-p1)/p2)). Extval = 21, /// Data is a 'p-value' (no params). Pval = 22, /// Data is ln(p-value) (no params). /// To be safe, a program should compute p = exp(-abs(this_value)). /// The nifti_stats.c library returns this_value /// as positive, so that this_value = -log(p). Logpval = 23, /// Data is log10(p-value) (no params). /// To be safe, a program should compute p = pow(10.,-abs(this_value)). /// The nifti_stats.c library returns this_value /// as positive, so that this_value = -log10(p). Log10pval = 24, /* --- these values aren't for statistics --- */ /// To signify that the value at each voxel is an estimate /// of some parameter, set intent_code = `NIFTI_INTENT_ESTIMATE`. /// The name of the parameter may be stored in intent_name. Estimate = 1001, /// To signify that the value at each voxel is an index into /// some set of labels, set intent_code = `NIFTI_INTENT_LABEL`. /// The filename with the labels may stored in aux_file. Label = 1002, /// To signify that the value at each voxel is an index into the /// NeuroNames labels set, set intent_code = `NIFTI_INTENT_NEURONAME`. Neuroname = 1003, /// To store an M x N matrix at each voxel: /// - dataset must have a 5th dimension (dim[0]=5 and dim[5]>1) /// - intent_code must be `NIFTI_INTENT_GENMATRIX` /// - dim[5] must be M*N /// - intent_p1 must be M (in float format) /// - intent_p2 must be N (ditto) /// - the matrix values A[i][[j] are stored in row-order: /// - A[0][0] A[0][1] ... A[0][N-1] /// - A[1][0] A[1][1] ... A[1][N-1] /// - etc., until /// - A[M-1][0] A[M-1][1] ... A[M-1][N-1] Genmatrix = 1004, /// To store an NxN symmetric matrix at each voxel: /// - dataset must have a 5th dimension /// - intent_code must be `NIFTI_INTENT_SYMMATRIX` /// - dim[5] must be N*(N+1)/2 /// - intent_p1 must be N (in float format) /// - the matrix values A[i][[j] are stored in row-order: /// - A[0][0] /// - A[1][0] A[1][1] /// - A[2][0] A[2][1] A[2][2] /// - etc.: row-by-row Symmatrix = 1005, /// To signify that the vector value at each voxel is to be taken /// as a displacement field or vector: /// - dataset must have a 5th dimension /// - intent_code must be `NIFTI_INTENT_DISPVECT` /// - dim[5] must be the dimensionality of the displacment /// vector (e.g., 3 for spatial displacement, 2 for in-plane) /// /// (specifically for displacements) Dispvect = 1006, /// (for any other type of vector) Vector = 1007, /// To signify that the vector value at each voxel is really a /// spatial coordinate (e.g., the vertices or nodes of a surface mesh): /// - dataset must have a 5th dimension /// - intent_code must be `NIFTI_INTENT_POINTSET` /// - dim[0] = 5 /// - dim[1] = number of points /// - dim[2] = dim[3] = dim[4] = 1 /// - dim[5] must be the dimensionality of space (e.g., 3 => 3D space). /// - intent_name may describe the object these points come from /// (e.g., "pial", "gray/white" , "EEG", "MEG"). Pointset = 1008, /// To signify that the vector value at each voxel is really a triple /// of indexes (e.g., forming a triangle) from a pointset dataset: /// - dataset must have a 5th dimension /// - intent_code must be `NIFTI_INTENT_TRIANGLE` /// - dim[0] = 5 /// - dim[1] = number of triangles /// - dim[2] = dim[3] = dim[4] = 1 /// - dim[5] = 3 /// - datatype should be an integer type (preferably `NiftiType::Int32`) /// - the data values are indexes (0,1,...) into a pointset dataset. Triangle = 1009, /// To signify that the vector value at each voxel is a quaternion: /// - dataset must have a 5th dimension /// - intent_code must be `NIFTI_INTENT_QUATERNION` /// - dim[0] = 5 /// - dim[5] = 4 /// - datatype should be a floating point type Quaternion = 1010, /// Dimensionless value - no params - although, as in `_ESTIMATE` /// the name of the parameter may be stored in intent_name. Dimless = 1011, /* --- these values apply to GIFTI datasets --- */ /// To signify that the value at each location is from a time series. TimeSeries = 2001, /// To signify that the value at each location is a node index, from /// a complete surface dataset. NodeIndex = 2002, /// To signify that the vector value at each location is an RGB triplet, /// of whatever type. /// - dataset must have a 5th dimension /// - dim[0] = 5 /// - dim[1] = number of nodes /// - dim[2] = dim[3] = dim[4] = 1 /// - dim[5] = 3 RgbVector = 2003, /// To signify that the vector value at each location is a 4 valued RGBA /// vector, of whatever type. /// - dataset must have a 5th dimension /// - dim[0] = 5 /// - dim[1] = number of nodes /// - dim[2] = dim[3] = dim[4] = 1 /// - dim[5] = 4 RgbaVector = 2004, /// To signify that the value at each location is a shape value, such /// as the curvature. Shape = 2005, } impl Intent { /// Check whether this intent code are used for statistics. pub fn is_statcode(&self) -> bool { *self as i16 >= 2 && *self as i16 <= 24 } } /// An enum type for representing a NIFTI XForm. #[derive(Debug, PartialEq, Eq, Hash, Clone, Copy, FromPrimitive)] pub enum XForm { /// Arbitrary coordinates (Method 1). Unknown = 0, /// Scanner-based anatomical coordinates ScannerAnat = 1, /// Coordinates aligned to another file's, /// or to anatomical "truth". AlignedAnat = 2, /// Coordinates aligned to Talairach-Tournoux /// Atlas; (0,0,0)=AC, etc. Talairach = 3, /// MNI 152 normalized coordinates. Mni152 = 4, } /// An enum type for representing the slice order. #[derive(Debug, PartialEq, Eq, Hash, Clone, Copy, FromPrimitive)] pub enum SliceOrder { /// NIFTI_SLICE_UNKNOWN Unknown = 0, /// NIFTI_SLICE_SEQ_INC SeqInc = 1, /// NIFTI_SLICE_SEQ_DEC SeqDec = 2, /// NIFTI_SLICE_ALT_INC AltInc = 3, /// NIFTI_SLICE_ALT_DEC AltDec = 4, /// NIFTI_SLICE_ALT_INC2 AltInc2 = 5, /// NIFTI_SLICE_ALT_DEC2 AltDec2 = 6, }