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//! This module defines the voxel volume API, as well as data //! types for reading volumes from files. //! An integration with `ndarray` allows for more elegant and //! efficient approaches, and should be preferred when possible. //! In order to do so, you must add the `ndarray_volumes` feature //! to this crate. pub mod inmem; pub use self::inmem::*; mod util; use error::{NiftiError, Result}; use typedef::NiftiType; #[cfg(feature = "ndarray_volumes")] pub mod ndarray; /// Public API for NIFTI volume data, exposed as a multi-dimensional /// voxel array. /// /// This API is currently experimental and will likely be subjected to /// various changes and additions in future versions. pub trait NiftiVolume { /// Get 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. fn dim(&self) -> &[u16]; /// Get the volume's number of dimensions. In a fully compliant file, /// this is equivalent to the corresponding header's `dim[0]` field /// (with byte swapping already applied). fn dimensionality(&self) -> usize { self.dim().len() } /// Fetch a single voxel's value in the given voxel index coordinates /// as a double precision floating point value. /// All necessary conversions and transformations are made /// when reading the voxel, including scaling. Note that using this /// function continuously to traverse the volume is inefficient. /// Prefer using iterators or the `ndarray` API for volume traversal. /// /// # Errors /// /// - `NiftiError::OutOfBounds` if the given coordinates surpass this /// volume's boundaries. fn get_f64(&self, coords: &[u16]) -> Result<f64>; /// Get this volume's data type. fn data_type(&self) -> NiftiType; /// Fetch a single voxel's value in the given voxel index coordinates /// as a single precision floating point value. /// All necessary conversions and transformations are made /// when reading the voxel, including scaling. Note that using this /// function continuously to traverse the volume is inefficient. /// Prefer using iterators or the `ndarray` API for volume traversal. /// /// # Errors /// /// - `NiftiError::OutOfBounds` if the given coordinates surpass this /// volume's boundaries. #[inline] fn get_f32(&self, coords: &[u16]) -> Result<f32> { self.get_f64(coords) .map(|v| v as f32) } /// Fetch a single voxel's value in the given voxel index coordinates /// as an unsigned 8-bit value. /// All necessary conversions and transformations are made /// when reading the voxel, including scaling. Note that using this /// function continuously to traverse the volume is inefficient. /// Prefer using iterators or the `ndarray` API for volume traversal. /// /// # Errors /// /// - `NiftiError::OutOfBounds` if the given coordinates surpass this /// volume's boundaries. #[inline] fn get_u8(&self, coords: &[u16]) -> Result<u8> { self.get_f64(coords) .map(|v| v as u8) } /// Fetch a single voxel's value in the given voxel index coordinates /// as a signed 8-bit value. /// All necessary conversions and transformations are made /// when reading the voxel, including scaling. Note that using this /// function continuously to traverse the volume is inefficient. /// Prefer using iterators or the `ndarray` API for volume traversal. /// /// # Errors /// /// - `NiftiError::OutOfBounds` if the given coordinates surpass this /// volume's boundaries. #[inline] fn get_i8(&self, coords: &[u16]) -> Result<i8> { self.get_f64(coords) .map(|v| v as i8) } /// Fetch a single voxel's value in the given voxel index coordinates /// as an unsigned 16-bit value. /// All necessary conversions and transformations are made /// when reading the voxel, including scaling. Note that using this /// function continuously to traverse the volume is inefficient. /// Prefer using iterators or the `ndarray` API for volume traversal. /// /// # Errors /// /// - `NiftiError::OutOfBounds` if the given coordinates surpass this /// volume's boundaries. #[inline] fn get_u16(&self, coords: &[u16]) -> Result<u16> { self.get_f64(coords) .map(|v| v as u16) } /// Fetch a single voxel's value in the given voxel index coordinates /// as a signed 16-bit value. /// All necessary conversions and transformations are made /// when reading the voxel, including scaling. Note that using this /// function continuously to traverse the volume is inefficient. /// Prefer using iterators or the `ndarray` API for volume traversal. /// /// # Errors /// /// - `NiftiError::OutOfBounds` if the given coordinates surpass this /// volume's boundaries. #[inline] fn get_i16(&self, coords: &[u16]) -> Result<i16> { self.get_f64(coords) .map(|v| v as i16) } /// Fetch a single voxel's value in the given voxel index coordinates /// as an unsigned 32-bit value. /// All necessary conversions and transformations are made /// when reading the voxel, including scaling. Note that using this /// function continuously to traverse the volume is inefficient. /// Prefer using iterators or the `ndarray` API for volume traversal. /// /// # Errors /// /// - `NiftiError::OutOfBounds` if the given coordinates surpass this /// volume's boundaries. #[inline] fn get_u32(&self, coords: &[u16]) -> Result<u32> { self.get_f64(coords) .map(|v| v as u32) } /// Fetch a single voxel's value in the given voxel index coordinates /// as a signed 32-bit value. /// All necessary conversions and transformations are made /// when reading the voxel, including scaling. Note that using this /// function continuously to traverse the volume is inefficient. /// Prefer using iterators or the `ndarray` API for volume traversal. /// /// # Errors /// /// - `NiftiError::OutOfBounds` if the given coordinates surpass this /// volume's boundaries. #[inline] fn get_i32(&self, coords: &[u16]) -> Result<i32> { self.get_f64(coords) .map(|v| v as i32) } /// Fetch a single voxel's value in the given voxel index coordinates /// as an unsigned 64-bit value. /// All necessary conversions and transformations are made /// when reading the voxel, including scaling. Note that using this /// function continuously to traverse the volume is inefficient. /// Prefer using iterators or the `ndarray` API for volume traversal. /// /// # Errors /// /// - `NiftiError::OutOfBounds` if the given coordinates surpass this /// volume's boundaries. #[inline] fn get_u64(&self, coords: &[u16]) -> Result<u64> { self.get_f64(coords) .map(|v| v as u64) } /// Fetch a single voxel's value in the given voxel index coordinates /// as a signed 64-bit value. /// All necessary conversions and transformations are made /// when reading the voxel, including scaling. Note that using this /// function continuously to traverse the volume is inefficient. /// Prefer using iterators or the `ndarray` API for volume traversal. /// /// # Errors /// /// - `NiftiError::OutOfBounds` if the given coordinates surpass this /// volume's boundaries. #[inline] fn get_i64(&self, coords: &[u16]) -> Result<i64> { self.get_f64(coords) .map(|v| v as i64) } } /// Interface for a volume that can be sliced. pub trait Sliceable { /// The type of the resulting slice, which is also a volume. type Slice: NiftiVolume; /// Obtain a slice of the volume over a certain axis, yielding a /// volume of N-1 dimensions. fn get_slice(&self, axis: u16, index: u16) -> Result<Self::Slice>; } /// A view over a single slice of another volume. /// Slices are usually created by calling the `get_slice` method (see `Sliceable`). /// This implementation is generic and delegates most operations to the underlying volume. #[derive(Debug, Clone)] pub struct SliceView<T> { volume: T, axis: u16, index: u16, dim: Vec<u16>, } impl<'a, T> Sliceable for &'a T where &'a T: NiftiVolume, { type Slice = SliceView<&'a T>; fn get_slice(&self, axis: u16, index: u16) -> Result<Self::Slice> { let mut coords: Vec<_> = self.dim().into(); if let Some(d) = coords.get(axis as usize) { if *d <= index { return Err(NiftiError::OutOfBounds(util::hot_vector( self.dimensionality(), axis as usize, index, ))); } } else { return Err(NiftiError::AxisOutOfBounds(axis)); } let _ = coords.remove(axis as usize); Ok(SliceView { volume: *self, axis, index, dim: coords, }) } } impl<V> NiftiVolume for SliceView<V> where V: NiftiVolume, { #[inline] fn dim(&self) -> &[u16] { &self.dim } fn get_f32(&self, coords: &[u16]) -> Result<f32> { let mut coords = Vec::from(coords); coords.insert(self.axis as usize, self.index); self.volume.get_f32(&coords) } fn get_f64(&self, coords: &[u16]) -> Result<f64> { let mut coords = Vec::from(coords); coords.insert(self.axis as usize, self.index); self.volume.get_f64(&coords) } fn get_u8(&self, coords: &[u16]) -> Result<u8> { let mut coords = Vec::from(coords); coords.insert(self.axis as usize, self.index); self.volume.get_u8(&coords) } fn get_i8(&self, coords: &[u16]) -> Result<i8> { let mut coords = Vec::from(coords); coords.insert(self.axis as usize, self.index); self.volume.get_i8(&coords) } fn get_u16(&self, coords: &[u16]) -> Result<u16> { let mut coords = Vec::from(coords); coords.insert(self.axis as usize, self.index); self.volume.get_u16(&coords) } fn get_i16(&self, coords: &[u16]) -> Result<i16> { let mut coords = Vec::from(coords); coords.insert(self.axis as usize, self.index); self.volume.get_i16(&coords) } fn get_u32(&self, coords: &[u16]) -> Result<u32> { let mut coords = Vec::from(coords); coords.insert(self.axis as usize, self.index); self.volume.get_u32(&coords) } fn get_i32(&self, coords: &[u16]) -> Result<i32> { let mut coords = Vec::from(coords); coords.insert(self.axis as usize, self.index); self.volume.get_i32(&coords) } fn get_u64(&self, coords: &[u16]) -> Result<u64> { let mut coords = Vec::from(coords); coords.insert(self.axis as usize, self.index); self.volume.get_u64(&coords) } fn get_i64(&self, coords: &[u16]) -> Result<i64> { let mut coords = Vec::from(coords); coords.insert(self.axis as usize, self.index); self.volume.get_i64(&coords) } /// Get this volume's data type. #[inline] fn data_type(&self) -> NiftiType { self.volume.data_type() } }