diff --git a/lightmotif-py/lightmotif/lib.rs b/lightmotif-py/lightmotif/lib.rs
index 054bab463f649a0c587bf15717e864d2c9b25849..802d7f2dd24d5fa92a9bfc0effa1476ed626dc4c 100644
--- a/lightmotif-py/lightmotif/lib.rs
+++ b/lightmotif-py/lightmotif/lib.rs
@@ -14,7 +14,6 @@ use lightmotif::pli::Score;
use pyo3::exceptions::PyBufferError;
use pyo3::exceptions::PyIndexError;
-use pyo3::exceptions::PyKeyError;
use pyo3::exceptions::PyTypeError;
use pyo3::exceptions::PyValueError;
use pyo3::ffi::Py_ssize_t;
@@ -390,7 +389,7 @@ impl From<lightmotif::pli::StripedScores<C>> for StripedScores {
let shape = [cols as Py_ssize_t, rows as Py_ssize_t];
let strides = [
std::mem::size_of::<f32>() as Py_ssize_t,
- (cols.next_power_of_two() * std::mem::size_of::<f32>()) as Py_ssize_t,
+ (scores.matrix().stride() * std::mem::size_of::<f32>()) as Py_ssize_t,
];
// mask the remaining positions that are outside the sequence length
let length = scores.len();
diff --git a/lightmotif/src/dense.rs b/lightmotif/src/dense.rs
index c1eef30b7ee01d0a36d1c3428129dab93d37a3dc..0a823fd13cce32b04a2ee79f95d019a8bdd61711 100644
--- a/lightmotif/src/dense.rs
+++ b/lightmotif/src/dense.rs
@@ -21,7 +21,7 @@ pub type DefaultAlignment = _DefaultAlignment;
// --- DenseMatrix -------------------------------------------------------------
-/// An aligned dense matrix of with a constant number of columns.
+/// A memory-aligned dense matrix with a constant number of columns.
#[derive(Debug, Clone, PartialEq, Eq)]
pub struct DenseMatrix<T: Default + Copy, C: Unsigned, A: Unsigned = DefaultAlignment> {
data: Vec<T>,
@@ -101,9 +101,21 @@ impl<T: Default + Copy, C: Unsigned, A: Unsigned> DenseMatrix<T, C, A> {
C::USIZE
}
- /// The effective number of columns in the matrix, counting alignment.
+ /// The stride of the matrix, as a number of elements.
+ ///
+ /// This may be different from the number of columns to account for memory
+ /// alignment constraints. Multiply by `std::mem::size_of::<T>()` to obtain
+ /// the stride in bytes.
+ ///
+ /// # Example
+ /// ```rust
+ /// # use typenum::{U43, U32};
+ /// # use lightmotif::dense::DenseMatrix;
+ /// let d = DenseMatrix::<u8, U43, U32>::new(0);
+ /// assert_eq!(d.stride(), 64);
+ /// ```
#[inline]
- pub const fn columns_effective(&self) -> usize {
+ pub const fn stride(&self) -> usize {
let x = std::mem::size_of::<T>();
let c = C::USIZE * x;
let b = c + (A::USIZE - c % A::USIZE) * ((c % A::USIZE) > 0) as usize;
@@ -119,7 +131,7 @@ impl<T: Default + Copy, C: Unsigned, A: Unsigned> DenseMatrix<T, C, A> {
/// Change the number of rows of the matrix.
pub fn resize(&mut self, rows: usize) {
// Always over-allocate columns to avoid alignment issues.
- let c: usize = self.columns_effective();
+ let c: usize = self.stride();
// Cache previous dimensions
let previous_rows = self.rows;
@@ -167,7 +179,7 @@ impl<T: Default + Copy, C: Unsigned, A: Unsigned> Index<usize> for DenseMatrix<T
type Output = [T];
#[inline]
fn index(&self, index: usize) -> &Self::Output {
- let c = self.columns_effective();
+ let c = self.stride();
let row = self.offset + c * index;
&self.data[row..row + C::USIZE]
}
@@ -176,7 +188,7 @@ impl<T: Default + Copy, C: Unsigned, A: Unsigned> Index<usize> for DenseMatrix<T
impl<T: Default + Copy, C: Unsigned, A: Unsigned> IndexMut<usize> for DenseMatrix<T, C, A> {
#[inline]
fn index_mut(&mut self, index: usize) -> &mut Self::Output {
- let c = self.columns_effective();
+ let c = self.stride();
let row = self.offset + c * index;
&mut self.data[row..row + C::USIZE]
}
@@ -233,7 +245,7 @@ where
#[inline]
fn get(&mut self, i: usize) -> &'a [T] {
- let c = self.matrix.columns_effective();
+ let c = self.matrix.stride();
let row = self.matrix.offset + c * i;
unsafe { std::slice::from_raw_parts(self.data.as_ptr().add(row), C::USIZE) }
}
@@ -270,7 +282,7 @@ where
#[inline]
fn get(&mut self, i: usize) -> &'a mut [T] {
- let c = self.matrix.columns_effective();
+ let c = self.matrix.stride();
let row = self.matrix.offset + c * i;
unsafe { std::slice::from_raw_parts_mut(self.data.as_ptr().add(row), C::USIZE) }
}
@@ -338,27 +350,27 @@ mod test {
use super::*;
#[test]
- fn test_columns_effective() {
+ fn test_stride() {
let d1 = DenseMatrix::<u8, U32, U32>::new(0);
- assert_eq!(d1.columns_effective(), 32);
+ assert_eq!(d1.stride(), 32);
let d2 = DenseMatrix::<u8, U16, U32>::new(0);
- assert_eq!(d2.columns_effective(), 32);
+ assert_eq!(d2.stride(), 32);
let d3 = DenseMatrix::<u32, U32, U32>::new(0);
- assert_eq!(d3.columns_effective(), 32);
+ assert_eq!(d3.stride(), 32);
let d4 = DenseMatrix::<u32, U8, U32>::new(0);
- assert_eq!(d4.columns_effective(), 8);
+ assert_eq!(d4.stride(), 8);
let d5 = DenseMatrix::<u32, U16, U32>::new(0);
- assert_eq!(d5.columns_effective(), 16);
+ assert_eq!(d5.stride(), 16);
let d6 = DenseMatrix::<u32, U3, U16>::new(0);
- assert_eq!(d6.columns_effective(), 4);
+ assert_eq!(d6.stride(), 4);
let d7 = DenseMatrix::<u8, U15, U8>::new(0);
- assert_eq!(d7.columns_effective(), 16);
+ assert_eq!(d7.stride(), 16);
}
#[test]
diff --git a/lightmotif/src/pli/platform/avx2.rs b/lightmotif/src/pli/platform/avx2.rs
index b39802aa186830170d9773c7b2653a2493544fa7..f9e76d6312e2493c609c96e55351502363f6a9b5 100644
--- a/lightmotif/src/pli/platform/avx2.rs
+++ b/lightmotif/src/pli/platform/avx2.rs
@@ -98,8 +98,8 @@ unsafe fn score_avx2(
s3 = _mm256_add_ps(s3, b3);
s4 = _mm256_add_ps(s4, b4);
// advance to next row in PSSM and sequence matrices
- seqptr = seqptr.add(seq.data.columns_effective());
- pssmptr = pssmptr.add(pssm.weights().columns_effective());
+ seqptr = seqptr.add(seq.data.stride());
+ pssmptr = pssmptr.add(pssm.weights().stride());
}
// permute lanes so that scores are in the right order
let r1 = _mm256_permute2f128_ps(s1, s2, 0x20);
@@ -166,7 +166,7 @@ unsafe fn best_position_avx2(scores: &StripedScores<<Avx2 as Backend>::LANES>) -
s3 = _mm256_blendv_ps(s3, r3, c3);
s4 = _mm256_blendv_ps(s4, r4, c4);
// advance to next row
- dataptr = dataptr.add(data.columns_effective());
+ dataptr = dataptr.add(data.stride());
}
// find the global maximum across all columns
let mut x: [u32; 32] = [0; 32];
@@ -275,7 +275,7 @@ unsafe fn threshold_avx2(
x3 = _mm256_add_epi32(x3, ones);
x4 = _mm256_add_epi32(x4, ones);
// Advance data pointer to next row
- dataptr = dataptr.add(data.columns_effective());
+ dataptr = dataptr.add(data.stride());
}
}
diff --git a/lightmotif/src/pli/platform/neon.rs b/lightmotif/src/pli/platform/neon.rs
index 3d89d6493663c2621a61c85657e625e7d2e28a63..0e356a78577e71085eefd56bb572ab3137fa1a53 100644
--- a/lightmotif/src/pli/platform/neon.rs
+++ b/lightmotif/src/pli/platform/neon.rs
@@ -78,8 +78,8 @@ unsafe fn score_neon<A, C>(
s.3 = vaddq_f32(s.3, vreinterpretq_f32_u32(vandq_u32(lut, p4)));
}
// advance to next row in sequence and PSSM matrices
- dataptr = dataptr.add(seq.data.columns_effective());
- pssmptr = pssmptr.add(pssm.weights().columns_effective());
+ dataptr = dataptr.add(seq.data.stride());
+ pssmptr = pssmptr.add(pssm.weights().stride());
}
// record the score for the current position
let row = &mut data[i];
diff --git a/lightmotif/src/pli/platform/sse2.rs b/lightmotif/src/pli/platform/sse2.rs
index 5ce58f62f2797082c796cea40626bed550afff5b..897a037abea513ef61b4e6b5cb6e25c7a96c113e 100644
--- a/lightmotif/src/pli/platform/sse2.rs
+++ b/lightmotif/src/pli/platform/sse2.rs
@@ -77,8 +77,8 @@ unsafe fn score_sse2<A, C>(
s4 = _mm_add_ps(s4, _mm_and_ps(lut, p4));
}
// advance to next row in sequence and PSSM matrices
- dataptr = dataptr.add(seq.data.columns_effective());
- pssmptr = pssmptr.add(pssm.weights().columns_effective());
+ dataptr = dataptr.add(seq.data.stride());
+ pssmptr = pssmptr.add(pssm.weights().stride());
}
// record the score for the current position
let row = &mut data[i];
@@ -154,7 +154,7 @@ where
s3 = _mm_or_ps(_mm_andnot_ps(c3, s3), _mm_and_ps(r3, c3));
s4 = _mm_or_ps(_mm_andnot_ps(c4, s4), _mm_and_ps(r4, c4));
// advance to next row
- dataptr = dataptr.add(data.columns_effective());
+ dataptr = dataptr.add(data.stride());
}
// find the global maximum across all columns
_mm_storeu_si128(
@@ -274,7 +274,7 @@ where
x3 = _mm_add_epi32(x3, ones);
x4 = _mm_add_epi32(x4, ones);
// Advance data pointer to next row
- dataptr = dataptr.add(data.columns_effective());
+ dataptr = dataptr.add(data.stride());
}
}
}