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Merge pull request #1 from Andlon/matrixmarket-io-fixes 

Matrixmarket IO changes
This commit is contained in:
huihantao 2021-12-01 15:00:44 +01:00 committed by GitHub
parent 920bd75b82 9ddd09017d
commit 6cd009988c
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8 changed files with 285 additions and 170 deletions
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4
.github/workflows/nalgebra-ci-build.yml vendored
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@ -65,10 +65,10 @@ jobs:
- name: test nalgebra-sparse
# Manifest-path is necessary because cargo otherwise won't correctly forward features
# We increase number of proptest cases to hopefully catch more potential bugs
run: PROPTEST_CASES=10000 cargo test --manifest-path=nalgebra-sparse/Cargo.toml --features compare,proptest-support
run: PROPTEST_CASES=10000 cargo test --manifest-path=nalgebra-sparse/Cargo.toml --features compare,proptest-support,io
- name: test nalgebra-sparse (slow tests)
# Unfortunately, the "slow-tests" take so much time that we need to run them with --release
run: PROPTEST_CASES=10000 cargo test --release --manifest-path=nalgebra-sparse/Cargo.toml --features compare,proptest-support,slow-tests slow
run: PROPTEST_CASES=10000 cargo test --release --manifest-path=nalgebra-sparse/Cargo.toml --features compare,proptest-support,io,slow-tests slow
test-nalgebra-macros:
runs-on: ubuntu-latest
steps:

2
nalgebra-sparse/Cargo.toml
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@ -15,6 +15,8 @@ license = "Apache-2.0"
[features]
proptest-support = ["proptest", "nalgebra/proptest-support"]
compare = [ "matrixcompare-core" ]
# Enable matrix market I/O
io = [ "pest", "pest_derive" ]
# Enable to enable running some tests that take a lot of time to run

364
nalgebra-sparse/src/io/matrix_market.rs
View File

@ -4,7 +4,6 @@
use crate::coo::CooMatrix;
use crate::SparseFormatError;
use crate::SparseFormatErrorKind;
use nalgebra::base::Scalar;
use nalgebra::Complex;
use pest::iterators::Pairs;
use pest::Parser;
@ -27,11 +26,12 @@ pub struct MatrixMarketError {
}
/// Errors produced by functions that expect well-formed matrix market format data.
/// > _NOTE:_ Since the matrix market design didn't mention if multiple sparse entries with the same coordiantes are allowed or not, so, it's allowed here.
#[non_exhaustive]
#[derive(Copy, Clone, Debug, PartialEq)]
pub enum MatrixMarketErrorKind {
/// Indicates that some word is not known to MM format
/// Parsing failure.
///
/// Indicates that the parser failed, for example due to an unexpected string.
///
/// Examples
/// --------
@ -39,17 +39,17 @@ pub enum MatrixMarketErrorKind {
/// # use nalgebra_sparse::io::load_coo_from_matrix_market_str;
/// # use nalgebra_sparse::io::MatrixMarketErrorKind;
/// let str = r#"
/// %%MatrixMarket whatever whatever whatever whatever
/// %%MatrixMarket invalid invalid invalid invalid
/// 1 1 1
/// 1 1 5
/// "#;
/// let matrix_error = load_coo_from_matrix_market_str::<f64>(str);
/// assert_eq!(matrix_error.is_err(), true);
/// assert_eq!(matrix_error.unwrap_err().kind(),MatrixMarketErrorKind::ParsingError);
/// let matrix_result = load_coo_from_matrix_market_str::<f64>(str);
/// assert_eq!(matrix_result.is_err(), true);
/// assert_eq!(matrix_result.unwrap_err().kind(), MatrixMarketErrorKind::ParsingError);
/// ```
ParsingError,
/// Indicates that header is not valid
/// Indicates that the matrix market header is invalid.
///
/// Examples
/// --------
@ -62,13 +62,13 @@ pub enum MatrixMarketErrorKind {
/// 1 1 1
/// 1 1 5
/// "#;
/// let matrix_error = load_coo_from_matrix_market_str::<f64>(str);
/// assert_eq!(matrix_error.is_err(), true);
/// assert_eq!(matrix_error.unwrap_err().kind(),MatrixMarketErrorKind::InvalidHeader);
/// let matrix_result = load_coo_from_matrix_market_str::<f64>(str);
/// assert_eq!(matrix_result.is_err(), true);
/// assert_eq!(matrix_result.unwrap_err().kind(),MatrixMarketErrorKind::InvalidHeader);
/// ```
InvalidHeader,
/// Indicates that the data entries in .mtx file are more or less than entries specified in .mtx file
/// Indicates that the number of data entries in the matrix market file does not match the header.
///
/// Examples
/// --------
@ -82,13 +82,14 @@ pub enum MatrixMarketErrorKind {
/// 2 2 2
/// 2 3 2
/// "#;
/// let matrix_error = load_coo_from_matrix_market_str::<f64>(str);
/// assert_eq!(matrix_error.is_err(), true);
/// assert_eq!(matrix_error.unwrap_err().kind(),MatrixMarketErrorKind::EntryNumUnmatched);
/// let matrix_result = load_coo_from_matrix_market_str::<f64>(str);
/// assert_eq!(matrix_result.is_err(), true);
/// assert_eq!(matrix_result.unwrap_err().kind(),MatrixMarketErrorKind::EntryMismatch);
/// ```
EntryNumUnmatched,
EntryMismatch,
/// Indicates that the type T is not matched with the function it called.
/// Indicates that the scalar type requested is not compatible with the scalar type stored
/// in the matrix market file.
///
/// Examples
/// --------
@ -97,18 +98,20 @@ pub enum MatrixMarketErrorKind {
/// # use nalgebra_sparse::io::MatrixMarketErrorKind;
/// let str = r#"
/// %%matrixmarket matrix coordinate real general
/// % it should be called by load_coo_from_matrix_market_str::<f64>(str), or f32;
/// % it should be loaded with load_coo_from_matrix_market_str::<f64>(str) (or f32)
/// 3 3 2
/// 2 2 2.22
/// 2 3 2.22
/// "#;
/// let matrix_error = load_coo_from_matrix_market_str::<i32>(str);
/// assert_eq!(matrix_error.is_err(), true);
/// assert_eq!(matrix_error.unwrap_err().kind(),MatrixMarketErrorKind::TypeUnmatched);
/// let matrix_result = load_coo_from_matrix_market_str::<i32>(str);
/// assert_eq!(matrix_result.is_err(), true);
/// assert_eq!(matrix_result.unwrap_err().kind(),MatrixMarketErrorKind::TypeMismatch);
/// ```
TypeUnmatched,
TypeMismatch,
/// Indicates that zero has been used as an index in the data, or the shape of the matrix, which is not allowed.
/// Indicates that zero has been used as an index in the data.
///
/// **Note**: The matrix market format uses 1-based indexing.
///
/// Examples
/// --------
@ -120,13 +123,14 @@ pub enum MatrixMarketErrorKind {
/// 1 1 1
/// 0 0 10
/// "#;
/// let matrix_error = load_coo_from_matrix_market_str::<f64>(str);
/// assert_eq!(matrix_error.is_err(), true);
/// assert_eq!(matrix_error.unwrap_err().kind(),MatrixMarketErrorKind::ZeroError);
/// let matrix_result = load_coo_from_matrix_market_str::<f64>(str);
/// assert_eq!(matrix_result.is_err(), true);
/// assert_eq!(matrix_result.unwrap_err().kind(),MatrixMarketErrorKind::ZeroError);
/// ```
ZeroError,
/// Indicates [SparseFormatError], while creating the sparse matrix.
/// Indicates [SparseFormatError] while creating the sparse matrix.
///
///
/// Examples
/// --------
@ -139,13 +143,14 @@ pub enum MatrixMarketErrorKind {
/// 1 1 1
/// 4 2 10
/// "#;
/// let matrix_error = load_coo_from_matrix_market_str::<f64>(str);
/// assert_eq!(matrix_error.is_err(), true);
/// assert_eq!(matrix_error.unwrap_err().kind(),MatrixMarketErrorKind::SparseFormatError(SparseFormatErrorKind::IndexOutOfBounds));
/// let matrix_result = load_coo_from_matrix_market_str::<f64>(str);
/// assert_eq!(matrix_result.is_err(), true);
/// assert_eq!(matrix_result.unwrap_err().kind(),
/// MatrixMarketErrorKind::SparseFormatError(SparseFormatErrorKind::IndexOutOfBounds));
/// ```
SparseFormatError(SparseFormatErrorKind),
/// Indicates that a wrong diagonal element has been provieded to the matrix
/// Indicates that a wrong diagonal element has been provided to the matrix.
///
/// Examples
/// --------
@ -160,9 +165,9 @@ pub enum MatrixMarketErrorKind {
/// 1 1 10
/// 2 1 5
/// "#;
/// let matrix_error = load_coo_from_matrix_market_str::<f64>(str);
/// assert_eq!(matrix_error.is_err(), true);
/// assert_eq!(matrix_error.unwrap_err().kind(),MatrixMarketErrorKind::DiagonalError);
/// let matrix_result = load_coo_from_matrix_market_str::<f64>(str);
/// assert_eq!(matrix_result.is_err(), true);
/// assert_eq!(matrix_result.unwrap_err().kind(),MatrixMarketErrorKind::DiagonalError);
///
/// let str = r#"
/// %%matrixmarket matrix coordinate complex hermitian
@ -171,28 +176,27 @@ pub enum MatrixMarketErrorKind {
/// 1 1 10 2
/// 2 1 5 2
/// "#;
/// let matrix_error = load_coo_from_matrix_market_str::<Complex<f64>>(str);
/// assert_eq!(matrix_error.is_err(), true);
/// assert_eq!(matrix_error.unwrap_err().kind(),MatrixMarketErrorKind::DiagonalError);
/// let matrix_result = load_coo_from_matrix_market_str::<Complex<f64>>(str);
/// assert_eq!(matrix_result.is_err(), true);
/// assert_eq!(matrix_result.unwrap_err().kind(),MatrixMarketErrorKind::DiagonalError);
/// ```
/// Here the skew matrix shouldn't have an element on the diagonal
/// Here the skew matrix shouldn't have an element on the diagonal.
DiagonalError,
/// Indicates [io error](`std::io::Error`), while reading the data from file.
/// Indicates an [IO error](`std::io::Error`) while reading the data from file.
///
/// Examples
/// --------
/// ```rust
/// # use nalgebra_sparse::io::load_coo_from_matrix_market_file;
/// # use nalgebra_sparse::io::MatrixMarketErrorKind;
/// let file_name = "whatever.mtx";
/// let matrix_error = load_coo_from_matrix_market_file::<f64,_>(file_name);
/// assert_eq!(matrix_error.is_err(), true);
/// assert_eq!(matrix_error.unwrap_err().kind(),MatrixMarketErrorKind::IOError(std::io::ErrorKind::NotFound));
/// let matrix_result = load_coo_from_matrix_market_file::<f64,_>("matrix.mtx");
/// assert_eq!(matrix_result.is_err(), true);
/// assert_eq!(matrix_result.unwrap_err().kind(),MatrixMarketErrorKind::IOError(std::io::ErrorKind::NotFound));
/// ```
IOError(std::io::ErrorKind),
/// Indicates (skew-)symmetric (or hermitian) matrix is not lower triangle matrix.
/// Indicates that a (skew-)symmetric (or hermitian) matrix is not a lower triangular matrix.
///
/// Examples
/// --------
@ -205,13 +209,13 @@ pub enum MatrixMarketErrorKind {
/// 1 1 10
/// 2 3 5
/// "#;
/// let matrix_error = load_coo_from_matrix_market_str::<i32>(str);
/// assert_eq!(matrix_error.is_err(), true);
/// assert_eq!(matrix_error.unwrap_err().kind(),MatrixMarketErrorKind::NotLowerTriangle);
/// let matrix_result = load_coo_from_matrix_market_str::<i32>(str);
/// assert_eq!(matrix_result.is_err(), true);
/// assert_eq!(matrix_result.unwrap_err().kind(),MatrixMarketErrorKind::NotLowerTriangle);
/// ```
NotLowerTriangle,
/// Indicates (skew-)symmetric (or hermitian) matrix is not square matrix.
/// Indicates that a (skew-)symmetric (or hermitian) matrix is not a square matrix.
///
/// Examples
/// --------
@ -224,11 +228,11 @@ pub enum MatrixMarketErrorKind {
/// 1 1 10
/// 2 3 5
/// "#;
/// let matrix_error = load_coo_from_matrix_market_str::<i32>(str);
/// assert_eq!(matrix_error.is_err(), true);
/// assert_eq!(matrix_error.unwrap_err().kind(),MatrixMarketErrorKind::NotSquareMatrix);
/// let matrix_result = load_coo_from_matrix_market_str::<i32>(str);
/// assert_eq!(matrix_result.is_err(), true);
/// assert_eq!(matrix_result.unwrap_err().kind(),MatrixMarketErrorKind::NonSquare);
/// ```
NotSquareMatrix,
NonSquare,
}
impl MatrixMarketError {
@ -239,7 +243,7 @@ impl MatrixMarketError {
}
}
/// The operation error kind.
/// The matrix market error kind.
#[must_use]
pub fn kind(&self) -> MatrixMarketErrorKind {
self.error_kind
@ -254,7 +258,7 @@ impl MatrixMarketError {
impl fmt::Display for MatrixMarketError {
fn fmt(&self, f: &mut Formatter<'_>) -> fmt::Result {
write!(f, "Matrix Market load error: ")?;
write!(f, "Matrix Market error: ")?;
match self.kind() {
MatrixMarketErrorKind::ParsingError => {
write!(f, "ParsingError,")?;
@ -262,11 +266,11 @@ impl fmt::Display for MatrixMarketError {
MatrixMarketErrorKind::InvalidHeader => {
write!(f, "InvalidHeader,")?;
}
MatrixMarketErrorKind::EntryNumUnmatched => {
MatrixMarketErrorKind::EntryMismatch => {
write!(f, "EntryNumUnmatched,")?;
}
MatrixMarketErrorKind::TypeUnmatched => {
write!(f, "TypeUnmatched,")?;
MatrixMarketErrorKind::TypeMismatch => {
write!(f, "TypeMismatch,")?;
}
MatrixMarketErrorKind::SparseFormatError(_) => {
write!(f, "SparseFormatError,")?;
@ -283,23 +287,24 @@ impl fmt::Display for MatrixMarketError {
MatrixMarketErrorKind::NotLowerTriangle => {
write!(f, "NotLowerTriangle,")?;
}
MatrixMarketErrorKind::NotSquareMatrix => {
MatrixMarketErrorKind::NonSquare => {
write!(f, "NotSquareMatrix,")?;
}
}
write!(f, " Message: {}", self.message)
write!(f, " message: {}", self.message)
}
}
impl std::error::Error for MatrixMarketError {}
impl<T: fmt::Debug + std::hash::Hash + std::marker::Copy + Ord> From<pest::error::Error<T>>
for MatrixMarketError
{
fn from(err: pest::error::Error<T>) -> Self {
impl MatrixMarketError {
fn from_pest_error<T>(error: pest::error::Error<T>) -> Self
where
T: fmt::Debug + std::hash::Hash + std::marker::Copy + Ord
{
Self::from_kind_and_message(
MatrixMarketErrorKind::ParsingError,
format!("Can't parse the data.\n Error: {}", err),
format!("Can't parse the data.\n Error: {}", error),
)
}
}
@ -334,9 +339,9 @@ impl From<std::io::Error> for MatrixMarketError {
impl From<TryFromIntError> for MatrixMarketError {
fn from(err: TryFromIntError) -> Self {
Self::from_kind_and_message(
MatrixMarketErrorKind::TypeUnmatched,
MatrixMarketErrorKind::TypeMismatch,
format!(
"Please consider using a larger integery type. Error message: {}",
"Please consider using a larger integer type. Error message: {}",
&err
),
)
@ -348,7 +353,7 @@ impl From<TryFromIntError> for MatrixMarketError {
impl From<Infallible> for MatrixMarketError {
fn from(_err: Infallible) -> Self {
Self::from_kind_and_message(
MatrixMarketErrorKind::TypeUnmatched,
MatrixMarketErrorKind::TypeMismatch,
format!("This won't happen"),
)
}
@ -431,7 +436,11 @@ impl FromStr for StorageScheme {
/// Precheck if it's a valid header.
///
/// For more details, please check Boisvert, Ronald F., Roldan Pozo, and Karin A. Remington. The matrix market formats: Initial design. Technical report, Applied and Computational Mathematics Division, NIST, 1996. Section 3.
/// For more details, please check
///
/// Boisvert, Ronald F., Roldan Pozo, and Karin A. Remington.
/// The matrix market formats: Initial design.
/// Technical report, Applied and Computational Mathematics Division, NIST, 1996. Section 3.
fn typecode_precheck(tc: &Typecode) -> Result<(), MatrixMarketError> {
match tc {
Typecode {
@ -479,13 +488,17 @@ fn typecode_precheck(tc: &Typecode) -> Result<(), MatrixMarketError> {
}
}
/// Base trait for matrix market types.
pub trait MatrixMarketScalar: Scalar {
/// When matrix is an Integer matrix, it will convert a [i128] number to this type.
/// Scalar types supported by the matrix market parser.
mod internal {
use crate::io::MatrixMarketError;
use na::{Complex, Scalar};
pub trait SupportedMatrixMarketScalar: Scalar {
/// When the matrix is an integer matrix, it will convert a [i128] number to this type.
fn from_i128(i: i128) -> Result<Self, MatrixMarketError>;
/// When matrix is a Real matrix, it will convert a [f64] number to this type.
fn from_f64(f: f64) -> Result<Self, MatrixMarketError>;
/// When matrix is a Complx matrix, it will convert a [Complex<f64>] number to this type.
/// When matrix is a Complex matrix, it will convert a [Complex<f64>] number to this type.
fn from_c64(c: Complex<f64>) -> Result<Self, MatrixMarketError>;
/// When matrix is a Pattern matrix, it will convert a unit type [unit] to this type.
fn from_pattern(p: ()) -> Result<Self, MatrixMarketError>;
@ -493,11 +506,21 @@ pub trait MatrixMarketScalar: Scalar {
fn negative(self) -> Result<Self, MatrixMarketError>;
/// When matrix is a Hermitian matrix, it will convert itself to its conjugate.
fn conjugate(self) -> Result<Self, MatrixMarketError>;
}
}
/// A marker trait for supported matrix market scalars.
///
/// This is a sealed trait; it cannot be implemented by external crates. This is done in order to prevent leaking
/// some of the implementation details we currently rely on. We may relax this restriction in the future.
pub trait MatrixMarketScalar: internal::SupportedMatrixMarketScalar {}
/// Implement MatrixMarketScalar for primitive integer types.
macro_rules! mm_int_impl {
($T:ty) => {
impl MatrixMarketScalar for $T {
impl MatrixMarketScalar for $T {}
impl internal::SupportedMatrixMarketScalar for $T {
#[inline]
fn from_i128(i: i128) -> Result<Self, MatrixMarketError> {
Ok(Self::try_from(i)?)
@ -505,28 +528,28 @@ macro_rules! mm_int_impl {
#[inline]
fn from_f64(_f: f64) -> Result<Self, MatrixMarketError> {
Err(MatrixMarketError::from_kind_and_message(
MatrixMarketErrorKind::TypeUnmatched,
MatrixMarketErrorKind::TypeMismatch,
format!("Int type can't be parsed from f64"),
))
}
#[inline]
fn from_c64(_c: Complex<f64>) -> Result<Self, MatrixMarketError> {
Err(MatrixMarketError::from_kind_and_message(
MatrixMarketErrorKind::TypeUnmatched,
MatrixMarketErrorKind::TypeMismatch,
format!("Int type can't be parsed from Complex<f64>"),
))
}
#[inline]
fn from_pattern(_p: ()) -> Result<Self, MatrixMarketError> {
Err(MatrixMarketError::from_kind_and_message(
MatrixMarketErrorKind::TypeUnmatched,
MatrixMarketErrorKind::TypeMismatch,
format!("Int type can't be parsed from ()"),
))
}
#[inline]
fn conjugate(self) -> Result<Self, MatrixMarketError> {
Err(MatrixMarketError::from_kind_and_message(
MatrixMarketErrorKind::TypeUnmatched,
MatrixMarketErrorKind::TypeMismatch,
format!("Int type has no conjugate"),
))
}
@ -540,11 +563,13 @@ macro_rules! mm_int_impl {
/// Implement MatrixMarketScalar for primitive real types.
macro_rules! mm_real_impl {
($T:ty) => {
impl MatrixMarketScalar for $T {
impl MatrixMarketScalar for $T {}
impl internal::SupportedMatrixMarketScalar for $T {
#[inline]
fn from_i128(_i: i128) -> Result<Self, MatrixMarketError> {
Err(MatrixMarketError::from_kind_and_message(
MatrixMarketErrorKind::TypeUnmatched,
MatrixMarketErrorKind::TypeMismatch,
format!("real type can't be parsed from i128"),
))
}
@ -555,21 +580,21 @@ macro_rules! mm_real_impl {
#[inline]
fn from_c64(_c: Complex<f64>) -> Result<Self, MatrixMarketError> {
Err(MatrixMarketError::from_kind_and_message(
MatrixMarketErrorKind::TypeUnmatched,
MatrixMarketErrorKind::TypeMismatch,
format!("real type can't be parsed from Complex<f64>"),
))
}
#[inline]
fn from_pattern(_p: ()) -> Result<Self, MatrixMarketError> {
Err(MatrixMarketError::from_kind_and_message(
MatrixMarketErrorKind::TypeUnmatched,
MatrixMarketErrorKind::TypeMismatch,
format!("real type can't be parsed from ()"),
))
}
#[inline]
fn conjugate(self) -> Result<Self, MatrixMarketError> {
Err(MatrixMarketError::from_kind_and_message(
MatrixMarketErrorKind::TypeUnmatched,
MatrixMarketErrorKind::TypeMismatch,
format!("real type has no conjugate"),
))
}
@ -580,21 +605,24 @@ macro_rules! mm_real_impl {
}
};
}
/// Implement MatrixMarketScalar for primitive complex types.
macro_rules! mm_complex_impl {
($T:ty) => {
impl MatrixMarketScalar for Complex<$T> {
impl MatrixMarketScalar for Complex<$T> {}
impl internal::SupportedMatrixMarketScalar for Complex<$T> {
#[inline]
fn from_i128(_i: i128) -> Result<Self, MatrixMarketError> {
Err(MatrixMarketError::from_kind_and_message(
MatrixMarketErrorKind::TypeUnmatched,
MatrixMarketErrorKind::TypeMismatch,
format!("Complex type can't be parsed from i128"),
))
}
#[inline]
fn from_f64(_f: f64) -> Result<Self, MatrixMarketError> {
Err(MatrixMarketError::from_kind_and_message(
MatrixMarketErrorKind::TypeUnmatched,
MatrixMarketErrorKind::TypeMismatch,
format!("Complex type can't be parsed from f64"),
))
}
@ -608,7 +636,7 @@ macro_rules! mm_complex_impl {
#[inline]
fn from_pattern(_p: ()) -> Result<Self, MatrixMarketError> {
Err(MatrixMarketError::from_kind_and_message(
MatrixMarketErrorKind::TypeUnmatched,
MatrixMarketErrorKind::TypeMismatch,
format!("Complex type can't be parsed from ()"),
))
}
@ -626,25 +654,27 @@ macro_rules! mm_complex_impl {
/// Implement MatrixMarketScalar for primitive unit types.
macro_rules! mm_pattern_impl {
($T:ty) => {
impl MatrixMarketScalar for $T {
impl MatrixMarketScalar for $T {}
impl internal::SupportedMatrixMarketScalar for $T {
#[inline]
fn from_i128(_i: i128) -> Result<Self, MatrixMarketError> {
Err(MatrixMarketError::from_kind_and_message(
MatrixMarketErrorKind::TypeUnmatched,
MatrixMarketErrorKind::TypeMismatch,
format!("Pattern type can't be parsed from i128"),
))
}
#[inline]
fn from_f64(_f: f64) -> Result<Self, MatrixMarketError> {
Err(MatrixMarketError::from_kind_and_message(
MatrixMarketErrorKind::TypeUnmatched,
MatrixMarketErrorKind::TypeMismatch,
format!("Pattern type can't be parsed from f64"),
))
}
#[inline]
fn from_c64(_c: Complex<f64>) -> Result<Self, MatrixMarketError> {
Err(MatrixMarketError::from_kind_and_message(
MatrixMarketErrorKind::TypeUnmatched,
MatrixMarketErrorKind::TypeMismatch,
format!("Pattern type can't be parsed from Complex<f64>"),
))
}
@ -656,14 +686,14 @@ macro_rules! mm_pattern_impl {
#[inline]
fn conjugate(self) -> Result<Self, MatrixMarketError> {
Err(MatrixMarketError::from_kind_and_message(
MatrixMarketErrorKind::TypeUnmatched,
MatrixMarketErrorKind::TypeMismatch,
format!("Pattern type has no conjugate"),
))
}
#[inline]
fn negative(self) -> Result<Self, MatrixMarketError> {
Err(MatrixMarketError::from_kind_and_message(
MatrixMarketErrorKind::TypeUnmatched,
MatrixMarketErrorKind::TypeMismatch,
format!("Pattern type has no negative"),
))
}
@ -687,16 +717,31 @@ mm_pattern_impl!(());
#[derive(Parser)]
#[grammar = "io/matrix_market.pest"]
struct MMParser;
struct MatrixMarketParser;
/// Parses a Matrix Market file at the given path, and returns the corresponding sparse matrix as CooMatrix format.
/// Parses a Matrix Market file at the given path as a `CooMatrix`.
///
/// The matrix market format specification does not clarify whether duplicate entries are allowed. Our importer
/// assumes that this is permitted and produces a `CooMatrix` with possibly duplicate entries.
///
/// **Note**: A current restriction of the importer is that you must use a compatible scalar type when importing.
/// For example, in order to import a matrix stored as `integer` in the matrix market format, you must
/// import it as an integer matrix, otherwise a [TypeMismatch](MatrixMarketErrorKind::TypeMismatch) error
/// will be returned. This restriction may be lifted in the future, and is
/// tracked by issue [#1038](https://github.com/dimforge/nalgebra/issues/1038).
///
/// Errors
/// --------
///
/// See [MatrixMarketErrorKind] for a list of possible error conditions.
///
/// > _NOTE:_ Here uses strong type requirements, which means if the matrix is an integer matrix, e.g. `%%matrixmarket matrix cooridnate integer general`, then you have to load it by `load_coo_from_matrix_market_file<T>`, where T is an integer type. Trying `load_coo_from_matrix_market_file<f64>` will give [TypeUnmatched](MatrixMarketErrorKind::TypeUnmatched) Error. After loading it, you can cast it into a `f64` matrix, by calling [cast](`nalgebra::base::Matrix::cast()`), but be aware of accuracy lose.
/// Examples
/// --------
/// ```
/// use nalgebra_sparse::io::load_coo_from_matrix_market_file;
/// // Use e.g. `f64` for floating-point matrices
/// let matrix = load_coo_from_matrix_market_file::<i32>("path/to/matrix.mtx")?;
/// ```
pub fn load_coo_from_matrix_market_file<T, P: AsRef<Path>>(
path: P,
) -> Result<CooMatrix<T>, MatrixMarketError>
@ -707,21 +752,36 @@ where
load_coo_from_matrix_market_str(&file)
}
/// Parses a Matrix Market file described by the given string, and returns the corresponding as CooMatrix format.
/// Parses a Matrix Market file described by the given string as a `CooMatrix`.
///
/// See [load_coo_from_matrix_market_file] for more information.
///
/// Errors
/// --------
///
/// See [MatrixMarketErrorKind] for a list of possible error conditions.
///
/// > _NOTE:_ Here uses strong type requirements, which means if the matrix is an integer matrix, e.g. `%%matrixmarket matrix cooridnate integer general`, then you have to load it by `load_coo_from_matrix_market_str<T>`, where T is an integer type. Trying `load_coo_from_matrix_market_str<f64>` will give [TypeUnmatched](MatrixMarketErrorKind::TypeUnmatched) Error. After loading it, you can cast it into a `f64` matrix, by calling [cast](`nalgebra::base::Matrix::cast()`),but be aware of accuracy lose.
/// Examples
/// --------
/// ```
/// # use nalgebra_sparse::io::load_coo_from_matrix_market_str;
/// # use nalgebra_sparse::io::MatrixMarketErrorKind;
/// let str = r#"
/// %%matrixmarket matrix coordinate integer symmetric
/// 5 4 2
/// 1 1 10
/// 2 3 5
/// "#;
/// let matrix = load_coo_from_matrix_market_str::<i32>(str)?;
/// ```
pub fn load_coo_from_matrix_market_str<T>(data: &str) -> Result<CooMatrix<T>, MatrixMarketError>
where
T: MatrixMarketScalar,
{
// unwrap() in this function are guaranteed by parsing the data
let file = MMParser::parse(Rule::Document, data)?.next().unwrap();
let file = MatrixMarketParser::parse(Rule::Document, data)
.map_err(MatrixMarketError::from_pest_error)?
.next().unwrap();
let mut rows: Vec<usize> = Vec::new();
let mut cols: Vec<usize> = Vec::new();
@ -746,16 +806,16 @@ where
// used when constructing dense matrix.
// If it's sparse matrix, it has no effect.
let mut current_dense_coordiante: (usize, usize) = (0, 0);
let mut current_dense_coordinate: (usize, usize) = (0, 0);
if header_type.storagescheme == StorageScheme::Skew {
// for skew dense matrix, the first element starts from (1,0)
current_dense_coordiante = (1, 0);
current_dense_coordinate = (1, 0);
}
// count how many entries in the matrix data
let count = lines.clone().count();
if count != shape.2 {
return Err(MatrixMarketError::from_kind_and_message(
MatrixMarketErrorKind::EntryNumUnmatched,
MatrixMarketErrorKind::EntryMismatch,
format!(
"{} entries required for the matrix, but {} was provided",
shape.2, count,
@ -800,12 +860,12 @@ where
..
} => {
entry = (
current_dense_coordiante.0,
current_dense_coordiante.1,
current_dense_coordinate.0,
current_dense_coordinate.1,
parse_dense_complex::<T>(&mut data_line.into_inner())?,
);
next_dense_coordiante(
&mut current_dense_coordiante,
next_dense_coordinate(
&mut current_dense_coordinate,
shape,
&header_type.storagescheme,
);
@ -816,13 +876,13 @@ where
..
} => {
entry = (
current_dense_coordiante.0,
current_dense_coordiante.1,
current_dense_coordinate.0,
current_dense_coordinate.1,
parse_dense_real::<T>(&mut data_line.into_inner())?,
);
next_dense_coordiante(
&mut current_dense_coordiante,
next_dense_coordinate(
&mut current_dense_coordinate,
shape,
&header_type.storagescheme,
);
@ -833,12 +893,12 @@ where
..
} => {
entry = (
current_dense_coordiante.0,
current_dense_coordiante.1,
current_dense_coordinate.0,
current_dense_coordinate.1,
parse_dense_int::<T>(&mut data_line.into_inner())?,
);
next_dense_coordiante(
&mut current_dense_coordiante,
next_dense_coordinate(
&mut current_dense_coordinate,
shape,
&header_type.storagescheme,
);
@ -963,7 +1023,7 @@ fn parse_header(inner: &mut Pairs<'_, Rule>) -> Typecode {
// Parse shape starts here-------------------------------------------------
/// Parse a pest structure to sparse shape information, including 3 int, which are number of rols, cols and non-zeros.
/// Parse a pest structure to sparse shape information, including 3 int, which are number of rows, cols and non-zeros.
fn parse_sparse_shape(
inner: &mut Pairs<'_, Rule>,
storagescheme: &StorageScheme,
@ -994,15 +1054,15 @@ fn parse_sparse_shape(
));
}
// check for square matirx, when it's not a general matrix
// check for square matrix, when it's not a general matrix
if *storagescheme != StorageScheme::General && r != c {
return Err(MatrixMarketError::from_kind_and_message(MatrixMarketErrorKind::NotSquareMatrix,format!("(Skew-)Symmetric or hermitian matrix should be square matrix, but it has dimension {} and {}",r,c)));
return Err(MatrixMarketError::from_kind_and_message(MatrixMarketErrorKind::NonSquare, format!("(Skew-)Symmetric or hermitian matrix should be square matrix, but it has dimension {} and {}", r, c)));
}
Ok((r, c, nnz))
}
/// Parse a pest structure to dense shape information, including 2 int, which are number of rols, cols.
/// Parse a pest structure to dense shape information, including 2 int, which are number of rows, cols.
fn parse_dense_shape(
inner: &mut Pairs<'_, Rule>,
storagescheme: &StorageScheme,
@ -1030,9 +1090,9 @@ fn parse_dense_shape(
));
}
// check for square matirx, when it's not a general matrix
// check for square matrix, when it's not a general matrix
if *storagescheme != StorageScheme::General && r != c {
return Err(MatrixMarketError::from_kind_and_message(MatrixMarketErrorKind::NotSquareMatrix,format!("(Skew-)Symmetric or hermitian matrix should be square matrix, but it has dimension {} and {}",r,c)));
return Err(MatrixMarketError::from_kind_and_message(MatrixMarketErrorKind::NonSquare, format!("(Skew-)Symmetric or hermitian matrix should be square matrix, but it has dimension {} and {}", r, c)));
}
let n: usize;
@ -1061,7 +1121,7 @@ fn parse_dense_shape(
// Parse entry starts here-------------------------------------------------
/// Parse a pest structure to sparse real entry, including 2 int, which are number of rols, cols, and a real number as data
/// Parse a pest structure to sparse real entry, including 2 int, which are number of rows, cols, and a real number as data
fn parse_sparse_real<T>(inner: &mut Pairs<'_, Rule>) -> Result<(usize, usize, T), MatrixMarketError>
where
T: MatrixMarketScalar,
@ -1070,17 +1130,17 @@ where
let entry_inner = inner.next().unwrap();
if entry_inner.as_rule() != Rule::SparseReal {
return Err(MatrixMarketError::from_kind_and_message(MatrixMarketErrorKind::ParsingError,format!("
Spare real matrix requires 2 int number as coordiantes and 1 real number as data, but line {} was provided.
Spare real matrix requires 2 int number as coordinates and 1 real number as data, but line {} was provided.
",entry_inner.as_str() )));
}
let mut inner = entry_inner.into_inner();
let (r, c) = parse_sparse_coordiante(&mut inner)?;
let (r, c) = parse_sparse_coordinate(&mut inner)?;
let d = inner.next().unwrap().as_str().parse::<f64>().unwrap();
Ok((r, c, T::from_f64(d)?))
}
/// Parse a pest structure to sparse integer entry, including 2 int, which are number of rols, cols, and a int number as data
/// Parse a pest structure to sparse integer entry, including 2 int, which are number of rows, cols, and a int number as data
fn parse_sparse_int<T>(inner: &mut Pairs<'_, Rule>) -> Result<(usize, usize, T), MatrixMarketError>
where
T: MatrixMarketScalar,
@ -1093,20 +1153,20 @@ where
MatrixMarketErrorKind::ParsingError,
format!(
"
Spare real matrix requires 3 int number as coordiantes and data, but line {} was provided.
Spare real matrix requires 3 int number as coordinates and data, but line {} was provided.
",
entry_inner.as_str()
),
));
}
let mut inner = entry_inner.into_inner();
let (r, c) = parse_sparse_coordiante(&mut inner)?;
let (r, c) = parse_sparse_coordinate(&mut inner)?;
// Here to guarantee it is an integer number
let d = inner.next().unwrap().as_str().parse::<i128>()?;
Ok((r, c, T::from_i128(d)?))
}
/// Parse a pest structure to sparse pattern entry, including 2 int, which are number of rols, cols
/// Parse a pest structure to sparse pattern entry, including 2 int, which are number of rows, cols
fn parse_sparse_pattern<T>(
inner: &mut Pairs<'_, Rule>,
) -> Result<(usize, usize, T), MatrixMarketError>
@ -1120,18 +1180,18 @@ where
MatrixMarketErrorKind::ParsingError,
format!(
"
Spare real matrix requires 2 int number as coordiantes, but line {} was provided.
Spare real matrix requires 2 int number as coordinates, but line {} was provided.
",
entry_inner.as_str()
),
));
}
let mut inner = entry_inner.into_inner();
let (r, c) = parse_sparse_coordiante(&mut inner)?;
let (r, c) = parse_sparse_coordinate(&mut inner)?;
Ok((r, c, T::from_pattern(())?))
}
/// Parse a pest structure to sparse complex entry, including 2 int, which are number of rols, cols, and 2 real number as complex data
/// Parse a pest structure to sparse complex entry, including 2 int, which are number of rows, cols, and 2 real number as complex data
fn parse_sparse_complex<T>(
inner: &mut Pairs<'_, Rule>,
) -> Result<(usize, usize, T), MatrixMarketError>
@ -1142,11 +1202,11 @@ where
let entry_inner = inner.next().unwrap();
if entry_inner.as_rule() != Rule::SparseComplex {
return Err(MatrixMarketError::from_kind_and_message(MatrixMarketErrorKind::ParsingError,format!("
Spare real matrix requires 2 int number as coordiantes and 2 real number as complex data, but line {} was provided.
Spare real matrix requires 2 int number as coordinates and 2 real number as complex data, but line {} was provided.
",entry_inner.as_str() )));
}
let mut inner = entry_inner.into_inner();
let (r, c) = parse_sparse_coordiante(&mut inner)?;
let (r, c) = parse_sparse_coordinate(&mut inner)?;
let real = inner.next().unwrap().as_str().parse::<f64>().unwrap();
let imag = inner.next().unwrap().as_str().parse::<f64>().unwrap();
let complex = Complex::<f64>::new(real, imag);
@ -1232,8 +1292,8 @@ where
// Parse entry ends here-------------------------------------------------
/// Parse the coordiantes information used for sparse matrix
fn parse_sparse_coordiante(
/// Parse the coordinates information used for sparse matrix
fn parse_sparse_coordinate(
inner: &mut Pairs<'_, Rule>,
) -> Result<(usize, usize), MatrixMarketError> {
// unwrap() in this function are guaranteed by parsing the data
@ -1242,51 +1302,51 @@ fn parse_sparse_coordiante(
if r * c == 0 {
return Err(MatrixMarketError::from_kind_and_message(
MatrixMarketErrorKind::ZeroError,
String::from("The data has to be one-indixed"),
String::from("The data has to be one-indexed"),
));
}
// The coordiantes in matrix market is one-based, but in CooMatrix is zero-based.
// The coordinates in matrix market is one-based, but in CooMatrix is zero-based.
Ok((r - 1, c - 1))
}
/// Calculate the next coordiantes used for dense matrix
fn next_dense_coordiante(
current_dense_coordiante: &mut (usize, usize),
/// Calculate the next coordinates used for dense matrix
fn next_dense_coordinate(
current_dense_coordinate: &mut (usize, usize),
shape: (usize, usize, usize),
storagescheme: &StorageScheme,
) {
// matrix market is column based format.
// so it follows the order (0,0) -> (1,0) -> ... -> (row, 0) -> (0,1) -> ... ->(row,col)
// current_dense_coordiante is (row, column)
// current_dense_coordinate is (row, column)
match storagescheme {
StorageScheme::General => {
if current_dense_coordiante.0 < shape.0 - 1 {
current_dense_coordiante.0 += 1
if current_dense_coordinate.0 < shape.0 - 1 {
current_dense_coordinate.0 += 1
} else {
// jump to next column, reset row to 1, column add 1
current_dense_coordiante.0 = 0;
current_dense_coordiante.1 += 1;
current_dense_coordinate.0 = 0;
current_dense_coordinate.1 += 1;
}
}
StorageScheme::Symmetric | StorageScheme::Hermitian => {
if current_dense_coordiante.0 < shape.0 - 1 {
current_dense_coordiante.0 += 1
if current_dense_coordinate.0 < shape.0 - 1 {
current_dense_coordinate.0 += 1
} else {
// jump to next column, column add 1, then set row equals to current column
// for example (0,0) -> (1,0) -> ... -> (row, 0) -> (1,1) -> ...
current_dense_coordiante.1 += 1;
current_dense_coordiante.0 = current_dense_coordiante.1;
current_dense_coordinate.1 += 1;
current_dense_coordinate.0 = current_dense_coordinate.1;
}
}
StorageScheme::Skew => {
if current_dense_coordiante.0 < shape.0 - 1 {
current_dense_coordiante.0 += 1;
if current_dense_coordinate.0 < shape.0 - 1 {
current_dense_coordinate.0 += 1;
} else {
// jump to next column, set row equals to current column, then column add 1
// skew matrix doesn't have element on diagonal
// for example (1,0) -> (2,0) -> ... -> (row, 0) -> (2,1) -> ...
current_dense_coordiante.1 += 1;
current_dense_coordiante.0 = current_dense_coordiante.1 + 1;
current_dense_coordinate.1 += 1;
current_dense_coordinate.0 = current_dense_coordinate.1 + 1;
}
}
}

34
nalgebra-sparse/src/io/mod.rs
View File

@ -1,7 +1,35 @@
//! Parsers for various matrix formats.
//! Functionality for importing and exporting sparse matrices to and from files.
//!
//! ## Matrix Market
//! See the [website](https://math.nist.gov/MatrixMarket/formats.html) or the [paper](https://www.researchgate.net/publication/2630533_The_Matrix_Market_Exchange_Formats_Initial_Design) for more details about matrix market.
//! **Available only when the `io` feature is enabled.**
//!
//! The following formats are currently supported:
//!
//! | Format | Import | Export |
//! | ------------------------------------------------|------------|------------|
//! | [Matrix market](#matrix-market-format) | Yes | No |
//!
//! [Matrix market]: https://math.nist.gov/MatrixMarket/formats.html
//!
//! ## Matrix Market format
//!
//! The Matrix Market format is a simple ASCII-based file format for sparse matrices, and was initially developed for
//! the [NIST Matrix Market](https://math.nist.gov/MatrixMarket/), a repository of example sparse matrices.
//! In later years it has largely been superseded by the
//! [SuiteSparse Matrix Collection](https://sparse.tamu.edu/) (formerly University of Florida Sparse Matrix Collection),
//! which also uses the Matrix Market file format.
//!
//! We currently offer functionality for importing a Matrix market file to an instance of a
//! [CooMatrix](crate::CooMatrix) through the function [load_coo_from_matrix_market_file]. It is also possible to load
//! a matrix stored in the matrix market format with the function [load_coo_from_matrix_market_str].
//!
//! Export is currently not implemented, but [planned](https://github.com/dimforge/nalgebra/issues/1037).
//!
//! Our implementation is based on the [format description](https://math.nist.gov/MatrixMarket/formats.html)
//! on the Matrix Market website and the
//! [following NIST whitepaper](https://math.nist.gov/MatrixMarket/reports/MMformat.ps):
//!
//! > Boisvert, Ronald F., Roldan Pozo, and Karin A. Remington.<br/>
//! > "*The Matrix Market Exchange Formats: Initial Design.*" (1996).
pub use self::matrix_market::{
load_coo_from_matrix_market_file, load_coo_from_matrix_market_str, MatrixMarketError,

1
nalgebra-sparse/src/lib.rs
View File

@ -19,6 +19,7 @@
//! - Sparsity patterns in CSR and CSC matrices are explicitly represented by the
//! [SparsityPattern](pattern::SparsityPattern) type, which encodes the invariants of the
//! associated index data structures.
//! - [Matrix market format support](`io`) when the `io` feature is enabled.
//! - [proptest strategies](`proptest`) for sparse matrices when the feature
//! `proptest-support` is enabled.
//! - [matrixcompare support](https://crates.io/crates/matrixcompare) for effortless

11
nalgebra-sparse/tests/unit.rs
View File

@ -1,6 +1,13 @@
//! Unit tests
#[cfg(any(not(feature = "proptest-support"), not(feature = "compare")))]
compile_error!("Tests must be run with features `proptest-support` and `compare`");
#[cfg(not(all(
feature = "proptest-support",
feature = "compare",
feature = "io",
)))]
compile_error!(
"Please enable the `proptest-support`, `compare` and `io` features in order to compile and run the tests.
Example: `cargo test -p nalgebra-sparse --features proptest-support,compare,io`"
);
mod unit_tests;

18
nalgebra-sparse/tests/unit_tests/matrix_market.rs
View File

@ -4,6 +4,24 @@ use nalgebra::Complex;
use nalgebra_sparse::io::load_coo_from_matrix_market_str;
use nalgebra_sparse::CooMatrix;
#[test]
#[rustfmt::skip]
fn test_matrixmarket_sparse_real_general_empty() {
// Test several valid zero-shapes of a matrix
let shapes = vec![ (0, 0), (1, 0), (0, 1) ];
let strings: Vec<String> = shapes
.into_iter()
.map(|(m, n)| format!("%%MatrixMarket matrix coordinate real general\n {} {} 0", m, n))
.collect();
for string in &strings {
let sparse_mat = load_coo_from_matrix_market_str::<f32>(string).unwrap();
assert_eq!(sparse_mat.nrows(), 0);
assert_eq!(sparse_mat.ncols(), 0);
assert_eq!(sparse_mat.nnz(), 0);
}
}
#[test]
#[rustfmt::skip]
fn test_matrixmarket_sparse_real_general() {

1
nalgebra-sparse/tests/unit_tests/mod.rs
View File

@ -3,7 +3,6 @@ mod convert_serial;
mod coo;
mod csc;
mod csr;
#[cfg(feature = "io")]
mod matrix_market;
mod ops;
mod pattern;