Merge pull request #106 from twitzelbos/feature/write-complex-valued-…

…data

Feature/write complex valued data

Cargo.toml

@@ -22,8 +22,10 @@ flate2 = "1.0"
 num-derive = "0.3"
 num-traits = "0.2"
 quick-error = "2.0"
-safe-transmute = "0.11"
 either = "1.6"
+num-complex = {version = "0.4.3", features=["bytemuck"]} 
+rgb = "0.8.36"
+bytemuck = {version = "1.13.1", features=["extern_crate_alloc"]}
 
 [dependencies.nalgebra]
 optional = true

src/error.rs

@@ -83,6 +83,11 @@ quick_error! {
             display("Could not reserve {} bytes of memory for extended data", bytes)
             source(err)
         }
+
+        /// Attempted a type conversion that is not supported by this crate
+        InvalidTypeConversion(from: NiftiType, to: &'static str) {
+            display("Invalid type conversion from {:?} to {}", from, to)
+        }
     }
 }
 

src/typedef.rs

@@ -5,7 +5,7 @@
 //! converted to these types and vice-versa.
 
 use crate::error::{NiftiError, Result};
-use crate::volume::element::{DataElement, LinearTransform};
+use crate::volume::element::{DataElement, NiftiDataRescaler};
 use byteordered::{Endian, Endianness};
 use num_derive::FromPrimitive;
 use std::io::Read;
@@ -96,88 +96,90 @@ impl NiftiType {
         T: Mul<Output = T>,
         T: Add<Output = T>,
         T: DataElement,
+        T: NiftiDataRescaler<T>,
     {
         match self {
             NiftiType::Uint8 => {
                 let raw = u8::from_raw(source, endianness)?;
-                Ok(<u8 as DataElement>::Transform::linear_transform(
+                Ok(<u8 as DataElement>::DataRescaler::nifti_rescale(
                     T::from_u8(raw),
                     slope,
                     inter,
                 ))
             }
             NiftiType::Int8 => {
                 let raw = i8::from_raw(source, endianness)?;
-                Ok(<i8 as DataElement>::Transform::linear_transform(
+                Ok(<i8 as DataElement>::DataRescaler::nifti_rescale(
                     T::from_i8(raw),
                     slope,
                     inter,
                 ))
             }
             NiftiType::Uint16 => {
                 let raw = endianness.read_u16(source)?;
-                Ok(<u16 as DataElement>::Transform::linear_transform(
+                Ok(<u16 as DataElement>::DataRescaler::nifti_rescale(
                     T::from_u16(raw),
                     slope,
                     inter,
                 ))
             }
             NiftiType::Int16 => {
                 let raw = endianness.read_i16(source)?;
-                Ok(<i16 as DataElement>::Transform::linear_transform(
+                Ok(<i16 as DataElement>::DataRescaler::nifti_rescale(
                     T::from_i16(raw),
                     slope,
                     inter,
                 ))
             }
             NiftiType::Uint32 => {
                 let raw = endianness.read_u32(source)?;
-                Ok(<u32 as DataElement>::Transform::linear_transform(
+                Ok(<u32 as DataElement>::DataRescaler::nifti_rescale(
                     T::from_u32(raw),
                     slope,
                     inter,
                 ))
             }
             NiftiType::Int32 => {
                 let raw = endianness.read_i32(source)?;
-                Ok(<i32 as DataElement>::Transform::linear_transform(
+                Ok(<i32 as DataElement>::DataRescaler::nifti_rescale(
                     T::from_i32(raw),
                     slope,
                     inter,
                 ))
             }
             NiftiType::Uint64 => {
                 let raw = endianness.read_u64(source)?;
-                Ok(<u64 as DataElement>::Transform::linear_transform(
+                Ok(<u64 as DataElement>::DataRescaler::nifti_rescale(
                     T::from_u64(raw),
                     slope,
                     inter,
                 ))
             }
             NiftiType::Int64 => {
                 let raw = endianness.read_i64(source)?;
-                Ok(<i64 as DataElement>::Transform::linear_transform(
+                Ok(<i64 as DataElement>::DataRescaler::nifti_rescale(
                     T::from_i64(raw),
                     slope,
                     inter,
                 ))
             }
             NiftiType::Float32 => {
                 let raw = endianness.read_f32(source)?;
-                Ok(<f32 as DataElement>::Transform::linear_transform(
+                Ok(<f32 as DataElement>::DataRescaler::nifti_rescale(
                     T::from_f32(raw),
                     slope,
                     inter,
                 ))
             }
             NiftiType::Float64 => {
                 let raw = endianness.read_f64(source)?;
-                Ok(<f64 as DataElement>::Transform::linear_transform(
+                Ok(<f64 as DataElement>::DataRescaler::nifti_rescale(
                     T::from_f64(raw),
                     slope,
                     inter,
                 ))
             }
+
             // TODO(#3) add support for more data types
             _ => Err(NiftiError::UnsupportedDataType(self)),
         }

src/util.rs

@@ -6,28 +6,24 @@ use crate::NiftiHeader;
 use byteordered::Endian;
 use either::Either;
 use flate2::bufread::GzDecoder;
-use safe_transmute::{transmute_vec, TriviallyTransmutable};
 use std::borrow::Cow;
 use std::fs::File;
 use std::io::{BufReader, Read, Result as IoResult, Seek};
 use std::mem;
 use std::path::{Path, PathBuf};
-
 /// A trait that is both Read and Seek.
 pub trait ReadSeek: Read + Seek {}
 impl<T: Read + Seek> ReadSeek for T {}
 
 pub fn convert_bytes_to<T, E>(mut a: Vec<u8>, e: E) -> Vec<T>
 where
-    T: TriviallyTransmutable,
+    T: bytemuck::Pod,
     E: Endian,
 {
     adapt_bytes_inline::<T, _>(&mut a, e);
-    match transmute_vec(a) {
+    match bytemuck::allocation::try_cast_vec(a) {
         Ok(v) => v,
-        Err(safe_transmute::Error::IncompatibleVecTarget(e)) => e.copy(),
-        Err(safe_transmute::Error::Unaligned(e)) => e.copy(),
-        _ => unreachable!(),
+        Err((_, v)) => bytemuck::allocation::pod_collect_to_vec(&v),
     }
 }