clawhdf5-netcdf4: phony dimensions, skipped types and order as netCDF-C
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Read a file's metadata the way netCDF-C 4.9.3 does (libhdf5/hdf5open.c),
for the whole file on first use (src/model.rs, replacing src/scope.rs):

- links in creation order when the group tracks it, else name order;
  a group's datasets before its subgroups; dimension ids file-wide;
- variables' dimensions from _Netcdf4Coordinates (file-wide ids), else
  the scales DIMENSION_LIST attaches when the first axis has one, else
  netCDF-C's phony dimensions phony_dim_<id> (create_phony_dims: shared
  by length and unlimitedness within a group, not between two axes of
  one variable, numbered subgroups first, a zero length unlimited);
- datasets of types netCDF-C cannot represent are not variables
  (references, bit fields, time, arrays, compounds/enums/VLENs over
  them), replaying netCDF-C's file-wide type list, failed types
  included;
- unlimited lengths as nc4_find_dim_len (its group and below).

NcType gains Enum, Compound, VLen, Opaque and is #[non_exhaustive];
Variable::nc_type is netCDF-C's type (1-byte strings NC_CHAR). New
clawhdf5_format::group_v2::links_in_creation_order_in.

Tests compare with netCDF-C itself (tests/netcdf_c_view.py calls the
libnetcdf netCDF4-python bundles through ctypes): new interop cases for
h5py files without dimension scales, every type class, link order; and
the gated corpus_vs_netcdf_c (CLAWHDF5_NETCDF_CORPUS): 420 of the 429
conformance-corpus files netCDF-C opens match (main: 68); the other 9
are explained in tests/corpus_known_differences.txt and known-issues.

Co-Authored-By: Claude Opus 5.5 (1M context) <[email protected]>
This commit is contained in:
osobh
2026-09-29 20:38:51 -05:00
co-authored by Claude Opus 5.5
parent 4260af4f70
commit e5d6f59e12
18 changed files with 2263 additions and 524 deletions
+7 -204
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@@ -1,16 +1,15 @@
//! NetCDF-4 dimension representation.
//!
//! Dimensions in NetCDF-4 are stored as HDF5 datasets with the CLASS=DIMENSION_SCALE
//! attribute and a `_Netcdf4Dimid` attribute. Unlimited dimensions are detected via
//! the HDF5 dataspace max_dimensions (u64::MAX indicates unlimited); their length
//! is the largest extent of the variables attached to them.
//! attribute and a `_Netcdf4Dimid` attribute; variables name theirs in
//! `_Netcdf4Coordinates` and `DIMENSION_LIST`. A file without them gets
//! netCDF-C's phony dimensions. How they are put together is in
//! `crate::model`.
use std::collections::HashMap;
use clawhdf5::AttrValue;
use crate::error::Error;
/// A NetCDF-4 dimension.
#[derive(Debug, Clone, PartialEq, Eq)]
pub struct Dimension {
@@ -22,202 +21,10 @@ pub struct Dimension {
pub is_unlimited: bool,
}
/// A dimension scale of one group: the dataset that defines a dimension.
#[derive(Debug, Clone)]
pub(crate) struct Scale {
/// Object header address of the scale's dataset (what a variable's
/// `DIMENSION_LIST` references).
pub address: u64,
/// Its `_Netcdf4Dimid` (what a variable's `_Netcdf4Coordinates` lists).
pub dimid: Option<i64>,
/// Index of its dimension in [`GroupDims::dims`].
pub dim: usize,
}
/// The dimensions a group defines, with the scales that define them.
#[derive(Debug, Clone, Default)]
pub(crate) struct GroupDims {
/// The group's dimensions, in `_Netcdf4Dimid` order (then discovery order).
pub dims: Vec<Dimension>,
/// The dimension scales behind `dims`; empty when the group has no
/// dimension scale and `dims` were inferred from 1-D datasets.
pub scales: Vec<Scale>,
}
impl GroupDims {
/// The dimension defined by the scale at `address`.
pub fn by_address(&self, address: u64) -> Option<&Dimension> {
self.scales
.iter()
.find(|s| s.address == address)
.map(|s| &self.dims[s.dim])
}
/// The dimension whose scale has `_Netcdf4Dimid` `id`.
pub fn by_dimid(&self, id: i64) -> Option<&Dimension> {
self.scales
.iter()
.find(|s| s.dimid == Some(id))
.map(|s| &self.dims[s.dim])
}
}
/// The dimensions of an HDF5 group (root or subgroup).
///
/// NetCDF-4 stores dimensions as datasets with `CLASS=DIMENSION_SCALE`. A fixed
/// dimension's size is the dataset's first (and typically only) shape extent.
/// Unlimited dimensions have `max_dimensions[0] == u64::MAX` in the HDF5 dataspace;
/// their size is computed by `unlimited_len`. A group with no dimension
/// scale at all (not written by a netCDF library) gets one dimension per
/// 1-D dataset instead.
pub(crate) fn group_dims(
file: &clawhdf5::File,
group: &clawhdf5::Group<'_>,
) -> Result<GroupDims, Error> {
let addresses: HashMap<String, u64> = group.entries()?.into_iter().collect();
let dataset_names = group.datasets()?;
// (dimid, dimension, scale address), in discovery order.
let mut found: Vec<(Option<i64>, Dimension, u64)> = Vec::new();
for ds_name in &dataset_names {
let ds = group.dataset(ds_name)?;
let attrs = ds.attrs()?;
if !is_dimension_scale(&attrs) {
continue;
}
let Some(&address) = addresses.get(ds_name) else {
continue;
};
let shape = ds.shape()?;
let is_unlimited = is_unlimited(&ds);
let size = if is_unlimited {
unlimited_len(file, &attrs, &shape)
} else {
shape.first().copied().unwrap_or(0)
};
let dim = Dimension {
name: ds_name.clone(),
size,
is_unlimited,
};
found.push((get_dimid(&attrs), dim, address));
}
if found.is_empty() {
// Fallback: infer dimensions from dataset shapes and names.
// In NetCDF-4, coordinate variables are datasets whose name matches
// a dimension name. If there are no explicit DIMENSION_SCALE attributes,
// we look for 1-D datasets that might be coordinate variables.
let mut dims = Vec::new();
for ds_name in &dataset_names {
let ds = group.dataset(ds_name)?;
let shape = ds.shape()?;
if shape.len() == 1 {
dims.push(Dimension {
name: ds_name.clone(),
size: shape[0],
is_unlimited: is_unlimited(&ds),
});
}
}
return Ok(GroupDims {
dims,
scales: Vec::new(),
});
}
// By dimid; scales without one keep their discovery order after those
// with one (the sort is stable).
found.sort_by_key(|(id, ..)| (id.is_none(), id.unwrap_or(0)));
let mut out = GroupDims::default();
for (i, (dimid, dim, address)) in found.into_iter().enumerate() {
out.dims.push(dim);
out.scales.push(Scale {
address,
dimid,
dim: i,
});
}
Ok(out)
}
/// The start of the `NAME` attribute netCDF-C gives a dimension scale that
/// is only a dimension, not also a (coordinate) variable.
const PURE_DIMENSION_NAME: &str = "This is a netCDF dimension but not a netCDF variable";
/// The current length of an unlimited dimension, as netCDF-C reports it
/// (`NC4_inq_dim` → `nc4_find_dim_len`): the largest current extent, along
/// the dimension, of the variables that use it, in any group; 0 when none
/// has been written. netCDF-C does not extend a dimension scale that is not
/// also a variable, so such a scale's own extent (0) is not counted; a
/// coordinate variable's is. The variables are the scale's attachments,
/// listed with the axis they use in its `REFERENCE_LIST` attribute (the
/// mirror of each variable's `DIMENSION_LIST`). Attachments that cannot be
/// read are skipped; without a readable `REFERENCE_LIST` the length is the
/// scale's own extent, as before.
fn unlimited_len(file: &clawhdf5::File, attrs: &HashMap<String, AttrValue>, shape: &[u64]) -> u64 {
let own = shape.first().copied().unwrap_or(0);
let is_variable = !is_pure_dimension(attrs);
let Some(refs) = reference_list(file, attrs) else {
return own;
};
refs.into_iter()
.filter_map(|(address, axis)| {
let shape = file.dataset_at(address).ok()?.shape().ok()?;
shape.get(usize::try_from(axis).ok()?).copied()
})
.chain(is_variable.then_some(own))
.max()
.unwrap_or(0)
}
/// The `(dataset address, axis)` pairs of a dimension scale's
/// `REFERENCE_LIST` attribute (HDF5 dimension scales: a compound of an
/// object reference `dataset` and an integer `dimension`), or `None` when it
/// is missing or not in that form.
fn reference_list(
file: &clawhdf5::File,
attrs: &HashMap<String, AttrValue>,
) -> Option<Vec<(u64, u64)>> {
use clawhdf5_format::data_read::{read_compound_field, read_object_references};
use clawhdf5_format::datatype::{Datatype, DatatypeByteOrder};
let Some(AttrValue::Raw { datatype, data, .. }) = attrs.get("REFERENCE_LIST") else {
return None;
};
let dataset = read_compound_field(data, datatype, "dataset").ok()?;
let addresses = read_object_references(
&dataset.raw_data,
&dataset.datatype,
file.superblock().offset_size,
)
.ok()?;
let dimension = read_compound_field(data, datatype, "dimension").ok()?;
let Datatype::FixedPoint {
size, byte_order, ..
} = dimension.datatype
else {
return None;
};
let size = usize::try_from(size).ok().filter(|s| (1..=8).contains(s))?;
let axes = dimension.raw_data.chunks_exact(size).map(|b| {
let mut v = [0u8; 8];
match byte_order {
DatatypeByteOrder::BigEndian => {
v[8 - size..].copy_from_slice(b);
u64::from_be_bytes(v)
}
_ => {
v[..size].copy_from_slice(b);
u64::from_le_bytes(v)
}
}
});
if axes.len() != addresses.len() {
return None;
}
Some(addresses.into_iter().map(|r| r.address).zip(axes).collect())
}
/// The dimension scale attached to each axis of a variable, from its
/// `DIMENSION_LIST` attribute (HDF5 dimension scales: one variable-length
/// sequence of object references per axis) — the address of the scale
@@ -281,13 +88,9 @@ pub(crate) fn is_dimension_scale(attrs: &HashMap<String, AttrValue>) -> bool {
pub(crate) fn get_dimid(attrs: &HashMap<String, AttrValue>) -> Option<i64> {
match attrs.get("_Netcdf4Dimid") {
Some(AttrValue::I64(id)) => Some(*id),
Some(AttrValue::U64(id)) => Some(*id as i64),
Some(AttrValue::U64(id)) => i64::try_from(*id).ok(),
Some(AttrValue::I64Array(ids)) if ids.len() == 1 => Some(ids[0]),
Some(AttrValue::U64Array(ids)) if ids.len() == 1 => i64::try_from(ids[0]).ok(),
_ => None,
}
}
/// Whether a dataset's first axis is unlimited (`max_dimensions[0] ==
/// u64::MAX` in its dataspace).
fn is_unlimited(ds: &clawhdf5::Dataset<'_>) -> bool {
matches!(ds.max_dimensions(), Ok(Some(max_dims)) if max_dims.first() == Some(&u64::MAX))
}
+35 -31
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@@ -7,36 +7,36 @@ use std::collections::HashMap;
use clawhdf5::AttrValue;
use crate::dimension::{self, Dimension};
use crate::dimension::Dimension;
use crate::error::Error;
use crate::scope::{self, Scope};
use crate::model::Model;
use crate::variable::Variable;
/// A NetCDF-4 group corresponding to an HDF5 group.
pub struct NetCDF4Group<'f> {
/// Group name.
name: String,
/// Path of the group from the root (`/`-separated).
path: String,
/// Underlying HDF5 file.
file: &'f clawhdf5::File,
/// Underlying HDF5 group.
hdf5_group: clawhdf5::Group<'f>,
/// The file's groups, dimensions and variables.
model: &'f Model,
/// This group's index in `model`.
index: usize,
}
impl<'f> NetCDF4Group<'f> {
/// Create a new NetCDF4Group from an HDF5 group.
/// The group `index` of `model`.
pub(crate) fn new(
name: String,
path: String,
file: &'f clawhdf5::File,
hdf5_group: clawhdf5::Group<'f>,
model: &'f Model,
index: usize,
) -> Self {
Self {
name,
path,
file,
hdf5_group,
model,
index,
}
}
@@ -45,52 +45,56 @@ impl<'f> NetCDF4Group<'f> {
&self.name
}
/// List dimensions defined in this group (not those of its parent
/// groups, which its variables can also use).
/// List dimensions defined in this group, in dimension-id order (not
/// those of its parent groups, which its variables can also use).
pub fn dimensions(&self) -> Result<Vec<Dimension>, Error> {
Ok(dimension::group_dims(self.file, &self.hdf5_group)?.dims)
Ok(self.model.dimensions(self.index))
}
/// List variables in this group: its datasets, except the dimension
/// scales that are only dimensions. Their dimensions can be defined in
/// this group or a parent group.
/// List variables in this group, in netCDF-C's order: its datasets,
/// except the dimension scales that are only dimensions and datasets
/// of types netCDF-C cannot represent. Their dimensions can be defined
/// in this group or a parent group.
pub fn variables(&self) -> Result<Vec<Variable<'f>>, Error> {
Scope::new(self.file, &self.path)?.variables()
self.model.variables(self.file, self.index)
}
/// Get a specific variable by name.
/// Get a specific variable by name (or by path, `"sub/var"`).
pub fn variable(&self, name: &str) -> Result<Variable<'f>, Error> {
scope::variable_at(self.file, &self.path, name)
self.model.variable(self.file, self.index, name)
}
/// Read all attributes of this group.
pub fn attrs(&self) -> Result<HashMap<String, AttrValue>, Error> {
Ok(self.hdf5_group.attrs()?)
Ok(self
.file
.group_at(self.model.group_address(self.index))
.attrs()?)
}
/// List subgroup names.
/// List subgroup names, in netCDF-C's order.
pub fn group_names(&self) -> Result<Vec<String>, Error> {
Ok(self.hdf5_group.groups()?)
Ok(self.model.group_names(self.index))
}
/// Get a subgroup by name.
/// Get a subgroup by name (or by path, `"a/b"`).
pub fn group(&self, name: &str) -> Result<NetCDF4Group<'f>, Error> {
let hdf5_group = self
.hdf5_group
.group(name)
.map_err(|_| Error::GroupNotFound(name.to_string()))?;
let index = self
.model
.find_group(self.index, name)
.ok_or_else(|| Error::GroupNotFound(name.to_string()))?;
Ok(NetCDF4Group::new(
name.to_string(),
format!("{}/{name}", self.path),
self.file,
hdf5_group,
self.model,
index,
))
}
/// The names of this group's variables (see
/// [`variables`](Self::variables)).
pub fn variable_names(&self) -> Result<Vec<String>, Error> {
Scope::new(self.file, &self.path)?.variable_names()
Ok(self.model.variable_names(self.index))
}
}
+48 -23
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@@ -27,7 +27,7 @@ pub mod cf;
pub mod dimension;
pub mod error;
pub mod group;
mod scope;
mod model;
pub mod types;
pub mod variable;
@@ -40,26 +40,49 @@ pub use types::NcType;
pub use variable::Variable;
use std::collections::HashMap;
use std::sync::OnceLock;
use model::Model;
/// A NetCDF-4 file reader.
///
/// Wraps a clawhdf5 File and provides NetCDF-4 semantics: dimensions,
/// variables with CF attributes, groups, and type mapping.
///
/// The groups, dimensions and variables are what netCDF-C reports for the
/// file (see the crate README): the first call that needs them reads the
/// metadata of the whole file, as `nc_open` does, and keeps it; the values
/// are read when asked for.
pub struct NetCDF4File {
hdf5: clawhdf5::File,
model: OnceLock<Model>,
}
impl NetCDF4File {
/// Open a NetCDF-4 file from a filesystem path.
pub fn open<P: AsRef<std::path::Path>>(path: P) -> Result<Self, Error> {
let hdf5 = clawhdf5::File::open(path)?;
Ok(Self { hdf5 })
Ok(Self::from_hdf5(clawhdf5::File::open(path)?))
}
/// Open a NetCDF-4 file from in-memory bytes.
pub fn from_bytes(data: Vec<u8>) -> Result<Self, Error> {
let hdf5 = clawhdf5::File::from_bytes(data)?;
Ok(Self { hdf5 })
Ok(Self::from_hdf5(clawhdf5::File::from_bytes(data)?))
}
fn from_hdf5(hdf5: clawhdf5::File) -> Self {
Self {
hdf5,
model: OnceLock::new(),
}
}
/// The file's groups, dimensions and variables, read on first use.
fn model(&self) -> Result<&Model, Error> {
if let Some(model) = self.model.get() {
return Ok(model);
}
let model = Model::build(&self.hdf5)?;
Ok(self.model.get_or_init(|| model))
}
/// Get the _NCProperties root attribute, if present.
@@ -74,27 +97,29 @@ impl NetCDF4File {
}
}
/// List dimensions defined in the root group.
/// List dimensions defined in the root group, in dimension-id order.
pub fn dimensions(&self) -> Result<Vec<Dimension>, Error> {
Ok(dimension::group_dims(&self.hdf5, &self.hdf5.root())?.dims)
Ok(self.model()?.dimensions(0))
}
/// List all variables in the root group: its datasets, except the
/// dimension scales that are only dimensions (netCDF-C does not list
/// them either).
/// List the variables of the root group, in netCDF-C's order: its
/// datasets, except the dimension scales that are only dimensions and
/// datasets of types netCDF-C cannot represent (see
/// [`NcType`]).
pub fn variables(&self) -> Result<Vec<Variable<'_>>, Error> {
scope::Scope::new(&self.hdf5, "/")?.variables()
self.model()?.variables(&self.hdf5, 0)
}
/// The names of the root group's variables (see
/// [`variables`](Self::variables)).
pub fn variable_names(&self) -> Result<Vec<String>, Error> {
scope::Scope::new(&self.hdf5, "/")?.variable_names()
Ok(self.model()?.variable_names(0))
}
/// Get a specific variable by name from the root group.
/// Get a specific variable by name from the root group; the name may be
/// a path into a subgroup (`"sub/var"`).
pub fn variable(&self, name: &str) -> Result<Variable<'_>, Error> {
scope::variable_at(&self.hdf5, "", name)
self.model()?.variable(&self.hdf5, 0, name)
}
/// Read all global (root group) attributes.
@@ -102,22 +127,22 @@ impl NetCDF4File {
Ok(self.hdf5.root().attrs()?)
}
/// List subgroup names in the root group.
/// List subgroup names in the root group, in netCDF-C's order.
pub fn group_names(&self) -> Result<Vec<String>, Error> {
Ok(self.hdf5.root().groups()?)
Ok(self.model()?.group_names(0))
}
/// Get a subgroup by name.
/// Get a subgroup by name (or by path, `"a/b"`).
pub fn group(&self, name: &str) -> Result<NetCDF4Group<'_>, Error> {
let hdf5_group = self
.hdf5
.group(name)
.map_err(|_| Error::GroupNotFound(name.to_string()))?;
let model = self.model()?;
let index = model
.find_group(0, name)
.ok_or_else(|| Error::GroupNotFound(name.to_string()))?;
Ok(NetCDF4Group::new(
name.to_string(),
name.to_string(),
&self.hdf5,
hdf5_group,
model,
index,
))
}
+853
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@@ -0,0 +1,853 @@
//! A file's groups, dimensions and variables, as netCDF-C reads them.
//!
//! netCDF-C (`libhdf5/hdf5open.c`, 4.9.3) reads a file in two passes, and
//! the names, order and sharing of the dimensions depend on both, so this
//! module replays them for the whole file at once:
//!
//! 1. `rec_read_metadata`: each group's links in creation order when the
//! group tracks it, else in name order; a group's datasets and named
//! datatypes before its subgroups, which follow in the same order. A
//! dimension scale (`CLASS` `DIMENSION_SCALE`) defines a dimension with
//! the id in its `_Netcdf4Dimid`, else the next free id (ids are
//! file-wide), its first extent as length, unlimited when that axis is
//! (or the length is 0); it is a variable too unless its `NAME` says it
//! is only a dimension. Every other dataset is a variable, unless its
//! type is one netCDF-C cannot represent ([`VarTypes::nc_type`]); a
//! dataset `_nc4_non_coord_<name>` is the variable `<name>`.
//! 2. `rec_match_dimscales`, subgroups first, then the group's variables in
//! order: a variable gets the dimensions whose ids its
//! `_Netcdf4Coordinates` lists (looked up file-wide), else — when its
//! `DIMENSION_LIST` attaches a scale to its first axis — the scales that
//! list attaches, looked up in its group and then each parent, else
//! "phony" dimensions (`create_phony_dims`): per axis, the first
//! dimension of the variable's group of that length and unlimitedness
//! not already used by an earlier axis of the variable, else a new one
//! called `phony_dim_<id>`.
//!
//! An unlimited dimension's length is the largest extent, along it, of the
//! variables that use it in its group and the groups below
//! (`nc4_find_dim_len`).
//!
//! Where netCDF-C 4.9.3 leaves an axis without a dimension (an id or a scale
//! it cannot find, or an axis without a scale of a variable whose first
//! axis has one — there it reads uninitialised memory), netCDF4-python
//! cannot open the file; this crate gives such an axis a dimension by the
//! phony rule instead.
use std::collections::HashMap;
use clawhdf5::AttrValue;
use clawhdf5_format::datatype::{Datatype, DatatypeByteOrder};
use clawhdf5_format::object_header::{ObjectClass, ObjectHeader};
use crate::dimension::{self, Dimension};
use crate::error::Error;
use crate::types::NcType;
use crate::variable::Variable;
/// The prefix netCDF-C gives the dataset of a variable that has a
/// dimension's name but is not that dimension's coordinate variable (the
/// dimension's scale holds the name).
const NON_COORD_PREFIX: &str = "_nc4_non_coord_";
/// Groups read at most, a guard against files whose groups are hard-linked
/// into each other many times over (netCDF-C reads each link as its own
/// group).
const MAX_GROUPS: usize = 100_000;
/// A file as netCDF-C sees it.
#[derive(Debug)]
pub(crate) struct Model {
/// Every group; the root is the first.
groups: Vec<Group>,
/// Every dimension, in the order they were created.
dims: Vec<Dim>,
}
#[derive(Debug)]
struct Group {
/// Object header address of the HDF5 group.
address: u64,
/// Its subgroups, `(name, index in Model::groups)`, in netCDF-C's order.
children: Vec<(String, usize)>,
parent: Option<usize>,
/// The dimensions it defines (indexes in `Model::dims`), in creation
/// order.
dims: Vec<usize>,
/// Its variables, in netCDF-C's order.
vars: Vec<Var>,
}
#[derive(Debug)]
struct Dim {
id: i64,
name: String,
/// The length it was created with (for an unlimited dimension, replaced
/// by its current length once every variable has its dimensions).
len: u64,
unlimited: bool,
/// Object header address of its dimension scale; `None` for a phony
/// dimension.
scale: Option<u64>,
}
#[derive(Debug)]
struct Var {
/// The netCDF name.
name: String,
/// Whether its dataset is `_nc4_non_coord_<name>`.
non_coord: bool,
address: u64,
nc_type: NcType,
extent: Vec<u64>,
/// Whether each axis is unlimited in the dataspace.
unlimited: Vec<bool>,
/// How netCDF-C finds its dimensions.
source: DimSource,
/// Its dimensions (indexes in `Model::dims`), one per axis, once found.
dims: Vec<usize>,
}
#[derive(Debug)]
enum DimSource {
/// A one-dimensional coordinate variable: its own scale's dimension.
OwnScale(usize),
/// The ids in `_Netcdf4Coordinates`; for a multi-dimensional coordinate
/// variable, also its own dimension (for the first axis, should an id
/// not be found).
Coordinates(Vec<i64>, Option<usize>),
/// The scale `DIMENSION_LIST` attaches to each axis (the first has one).
Scales(Vec<Option<u64>>, Option<usize>),
/// None: phony dimensions.
Phony(Option<usize>),
}
impl Model {
/// Read the metadata of `file` as netCDF-C does.
pub fn build(file: &clawhdf5::File) -> Result<Self, Error> {
let mut builder = Builder {
file,
model: Model {
groups: Vec::new(),
dims: Vec::new(),
},
next_id: 0,
types: VarTypes::default(),
};
let root = file.superblock().root_group_address;
builder.model.groups.push(Group {
address: root,
children: Vec::new(),
parent: None,
dims: Vec::new(),
vars: Vec::new(),
});
builder.read_group(0, &mut vec![root])?;
builder.match_dims(0);
builder.unlimited_lengths();
Ok(builder.model)
}
/// The group at `path` (`/`-separated names), from the group `from`.
pub fn find_group(&self, from: usize, path: &str) -> Option<usize> {
path.split('/')
.filter(|p| !p.is_empty())
.try_fold(from, |g, name| {
self.groups[g]
.children
.iter()
.find(|(n, _)| n == name)
.map(|&(_, i)| i)
})
}
/// The object header address of group `g`.
pub fn group_address(&self, g: usize) -> u64 {
self.groups[g].address
}
/// The names of group `g`'s subgroups, in netCDF-C's order.
pub fn group_names(&self, g: usize) -> Vec<String> {
self.groups[g]
.children
.iter()
.map(|(n, _)| n.clone())
.collect()
}
/// The dimensions group `g` defines, in id order (as `nc_inq_dimids`).
pub fn dimensions(&self, g: usize) -> Vec<Dimension> {
let mut dims: Vec<&Dim> = self.groups[g].dims.iter().map(|&d| &self.dims[d]).collect();
dims.sort_by_key(|d| d.id);
dims.into_iter().map(Dim::dimension).collect()
}
/// The names of group `g`'s variables, in netCDF-C's order.
pub fn variable_names(&self, g: usize) -> Vec<String> {
self.groups[g].vars.iter().map(|v| v.name.clone()).collect()
}
/// Group `g`'s variables, in netCDF-C's order.
pub fn variables<'f>(
&self,
file: &'f clawhdf5::File,
g: usize,
) -> Result<Vec<Variable<'f>>, Error> {
self.groups[g]
.vars
.iter()
.map(|v| self.open(file, v))
.collect()
}
/// The variable `name` of group `g`; `name` may be a path (`"sub/var"`)
/// relative to it. Of two variables of one name (datasets `<name>` and
/// `_nc4_non_coord_<name>`), the second.
pub fn variable<'f>(
&self,
file: &'f clawhdf5::File,
g: usize,
name: &str,
) -> Result<Variable<'f>, Error> {
let not_found = || Error::VariableNotFound(name.to_string());
let trimmed = name.trim_start_matches('/');
let (g, leaf) = match trimmed.rsplit_once('/') {
Some((dir, leaf)) => (self.find_group(g, dir).ok_or_else(not_found)?, leaf),
None => (g, trimmed),
};
let vars = &self.groups[g].vars;
let var = vars
.iter()
.find(|v| v.name == leaf && v.non_coord)
.or_else(|| vars.iter().find(|v| v.name == leaf))
.ok_or_else(not_found)?;
self.open(file, var)
}
fn open<'f>(&self, file: &'f clawhdf5::File, var: &Var) -> Result<Variable<'f>, Error> {
let ds = file.dataset_at(var.address)?;
let attrs = ds.attrs().unwrap_or_default();
let dims = var.dims.iter().map(|&d| self.dims[d].dimension()).collect();
Ok(Variable::new(
var.name.clone(),
ds,
dims,
attrs,
var.nc_type,
))
}
}
impl Dim {
fn dimension(&self) -> Dimension {
Dimension {
name: self.name.clone(),
size: self.len,
is_unlimited: self.unlimited,
}
}
}
struct Builder<'f> {
file: &'f clawhdf5::File,
model: Model,
/// netCDF-C's `next_dimid`.
next_id: i64,
types: VarTypes,
}
impl Builder<'_> {
/// Pass 1 for group `g` and, after its own links, its subgroups.
/// `ancestors` holds the addresses of the groups from the root to `g`,
/// so that a group linked into itself is not read forever.
fn read_group(&mut self, g: usize, ancestors: &mut Vec<u64>) -> Result<(), Error> {
let address = self.model.groups[g].address;
let sb = self.file.superblock();
let mut subgroups = Vec::new();
for (name, child) in ordered_entries(self.file, address)? {
let Ok(header) =
ObjectHeader::parse_in(self.file.storage(), child, sb.offset_size, sb.length_size)
else {
continue;
};
match header.object_class() {
Some(ObjectClass::Dataset) => self.read_dataset(g, name, child),
Some(ObjectClass::NamedDatatype) => {
if let Some(dt) = header_datatype(&header) {
self.types.named(&dt);
}
}
_ if is_group(&header) => subgroups.push((name, child)),
_ => {}
}
}
for (name, child) in subgroups {
if ancestors.contains(&child) || self.model.groups.len() >= MAX_GROUPS {
continue;
}
let index = self.model.groups.len();
self.model.groups.push(Group {
address: child,
children: Vec::new(),
parent: Some(g),
dims: Vec::new(),
vars: Vec::new(),
});
self.model.groups[g].children.push((name, index));
ancestors.push(child);
let read = self.read_group(index, ancestors);
ancestors.pop();
read?;
}
Ok(())
}
/// `read_dataset`: a dimension for a dimension scale, a variable for
/// the rest. A dataset that cannot be opened is skipped.
fn read_dataset(&mut self, g: usize, name: String, address: u64) {
let Ok(ds) = self.file.dataset_at(address) else {
return;
};
let attrs = ds.attrs().unwrap_or_default();
let Ok(extent) = ds.shape() else {
return;
};
let max = ds.max_dimensions().ok().flatten();
let unlimited: Vec<bool> = (0..extent.len())
.map(|i| matches!(&max, Some(m) if m.get(i) == Some(&u64::MAX)))
.collect();
let mut own = None;
if dimension::is_dimension_scale(&attrs) && !extent.is_empty() {
// read_scale
let id = match dimension::get_dimid(&attrs) {
Some(id) => {
if id >= self.next_id {
self.next_id = id.saturating_add(1);
}
id
}
None => self.take_id(),
};
let len = extent[0];
own = Some(self.add_dim(
g,
Dim {
id,
name: name.clone(),
len,
unlimited: unlimited[0] || len == 0,
scale: Some(address),
},
));
if dimension::is_pure_dimension(&attrs) {
return;
}
}
// read_var: a type netCDF-C cannot represent drops the variable
// (the dimension of a scale stays).
let Some(nc_type) = ds
.raw_datatype()
.ok()
.and_then(|dt| self.types.nc_type(&dt))
else {
return;
};
let rank = extent.len();
let coordinates = coordinates(&attrs).filter(|ids| ids.len() == rank && rank > 0);
let source = match (own, coordinates) {
(Some(dim), _) if rank == 1 => DimSource::OwnScale(dim),
(_, Some(ids)) => DimSource::Coordinates(ids, own),
_ => match dimension::dimension_list(self.file, &attrs) {
Some(scales)
if scales.len() == rank && scales.first().is_some_and(Option::is_some) =>
{
DimSource::Scales(scales, own)
}
_ => DimSource::Phony(own),
},
};
let (name, non_coord) = match name.strip_prefix(NON_COORD_PREFIX) {
Some(rest) if !rest.is_empty() => (rest.to_string(), true),
_ => (name, false),
};
self.model.groups[g].vars.push(Var {
name,
non_coord,
address,
nc_type,
extent,
unlimited,
source,
dims: Vec::new(),
});
}
fn take_id(&mut self) -> i64 {
let id = self.next_id;
self.next_id = self.next_id.saturating_add(1);
id
}
fn add_dim(&mut self, g: usize, dim: Dim) -> usize {
let index = self.model.dims.len();
self.model.dims.push(dim);
self.model.groups[g].dims.push(index);
index
}
/// Pass 2 (`rec_match_dimscales`): subgroups first, then the group's
/// variables in order.
fn match_dims(&mut self, g: usize) {
let children: Vec<usize> = self.model.groups[g]
.children
.iter()
.map(|&(_, c)| c)
.collect();
for child in children {
self.match_dims(child);
}
for v in 0..self.model.groups[g].vars.len() {
let var = &self.model.groups[g].vars[v];
let rank = var.extent.len();
let mut found: Vec<Option<usize>> = vec![None; rank];
match &var.source {
DimSource::OwnScale(dim) => found[0] = Some(*dim),
DimSource::Coordinates(ids, own) => {
for (slot, id) in found.iter_mut().zip(ids) {
*slot = self.dim_by_id(*id);
}
if found[0].is_none() {
found[0] = *own;
}
}
DimSource::Scales(scales, own) => {
for (slot, scale) in found.iter_mut().zip(scales) {
*slot = scale.and_then(|s| self.dim_by_scale(g, s));
}
if found[0].is_none() {
found[0] = *own;
}
}
DimSource::Phony(own) => {
if rank > 0 {
found[0] = *own;
}
}
}
let mut dims: Vec<usize> = Vec::with_capacity(rank);
for (axis, found) in found.into_iter().enumerate() {
let dim = match found {
Some(dim) => dim,
None => {
let var = &self.model.groups[g].vars[v];
let (len, unlimited) = (var.extent[axis], var.unlimited[axis]);
self.phony_dim(g, len, unlimited, &dims)
}
};
dims.push(dim);
}
self.model.groups[g].vars[v].dims = dims;
}
}
/// The dimension with id `id`: the last one created with it
/// (`nc4_find_dim` looks ids up in a file-wide table, where a later
/// dimension of the same id replaces an earlier one).
fn dim_by_id(&self, id: i64) -> Option<usize> {
self.model.dims.iter().rposition(|d| d.id == id)
}
/// The dimension of the scale at `address`, in group `g` or the nearest
/// parent that has it.
fn dim_by_scale(&self, g: usize, address: u64) -> Option<usize> {
let mut group = Some(g);
while let Some(i) = group {
let found = self.model.groups[i]
.dims
.iter()
.copied()
.find(|&d| self.model.dims[d].scale == Some(address));
if found.is_some() {
return found;
}
group = self.model.groups[i].parent;
}
None
}
/// `create_phony_dims` for one axis: the first dimension of group `g`
/// of length `len` and unlimitedness `unlimited` that no earlier axis
/// of the variable uses (`taken`), else a new `phony_dim_<id>`.
fn phony_dim(&mut self, g: usize, len: u64, unlimited: bool, taken: &[usize]) -> usize {
let dims = &self.model.dims;
let existing = self.model.groups[g].dims.iter().copied().find(|&d| {
let dim = &dims[d];
dim.len == len
&& dim.unlimited == unlimited
&& !taken.iter().any(|&t| dims[t].id == dim.id)
});
if let Some(dim) = existing {
return dim;
}
let id = self.take_id();
self.add_dim(
g,
Dim {
id,
name: format!("phony_dim_{id}"),
len,
// `nc4_dim_list_add`: a length of 0 is NC_UNLIMITED.
unlimited: unlimited || len == 0,
scale: None,
},
)
}
/// Each unlimited dimension's length: the largest extent along it of
/// the variables using it in its group and the groups below.
fn unlimited_lengths(&mut self) {
let mut owner = vec![0usize; self.model.dims.len()];
for (g, group) in self.model.groups.iter().enumerate() {
for &d in &group.dims {
owner[d] = g;
}
}
let mut lens = vec![0u64; self.model.dims.len()];
for (g, group) in self.model.groups.iter().enumerate() {
for var in &group.vars {
for (&d, &e) in var.dims.iter().zip(&var.extent) {
if self.model.dims[d].unlimited && self.is_within(g, owner[d]) {
lens[d] = lens[d].max(e);
}
}
}
}
for (dim, len) in self.model.dims.iter_mut().zip(lens) {
if dim.unlimited {
dim.len = len;
}
}
}
/// Whether group `g` is `ancestor` or below it.
fn is_within(&self, g: usize, ancestor: usize) -> bool {
let mut group = Some(g);
while let Some(i) = group {
if i == ancestor {
return true;
}
group = self.model.groups[i].parent;
}
false
}
}
/// A group's entries in netCDF-C's order: creation order when the group
/// tracks it, else the byte order of the names.
fn ordered_entries(file: &clawhdf5::File, address: u64) -> Result<Vec<(String, u64)>, Error> {
let mut entries = file.group_at(address).entries()?;
let order = clawhdf5_format::group_v2::links_in_creation_order_in(
file.storage(),
file.superblock(),
address,
)
.ok()
.flatten();
match order {
Some(names) => {
let position: HashMap<&str, usize> = names
.iter()
.enumerate()
.map(|(i, n)| (n.as_str(), i))
.collect();
entries.sort_by_key(|(n, _)| position.get(n.as_str()).copied().unwrap_or(usize::MAX));
}
None => entries.sort_by(|a, b| a.0.as_bytes().cmp(b.0.as_bytes())),
}
Ok(entries)
}
fn is_group(header: &ObjectHeader) -> bool {
use clawhdf5_format::message_type::MessageType;
header.messages.iter().any(|m| {
matches!(
m.msg_type,
MessageType::LinkInfo | MessageType::Link | MessageType::SymbolTable
)
})
}
/// The datatype a named datatype's header holds.
fn header_datatype(header: &ObjectHeader) -> Option<Datatype> {
use clawhdf5_format::message_type::MessageType;
let msg = header
.messages
.iter()
.find(|m| m.msg_type == MessageType::Datatype)?;
Datatype::parse_in_header(&msg.data, header.version)
.ok()
.map(|(dt, _)| dt)
}
/// A variable's `_Netcdf4Coordinates`: the id of the dimension of each
/// axis.
fn coordinates(attrs: &HashMap<String, AttrValue>) -> Option<Vec<i64>> {
match attrs.get("_Netcdf4Coordinates")? {
AttrValue::I64Array(ids) => Some(ids.clone()),
AttrValue::I64(id) => Some(vec![*id]),
AttrValue::U64Array(ids) => ids.iter().map(|&id| i64::try_from(id).ok()).collect(),
AttrValue::U64(id) => Some(vec![i64::try_from(*id).ok()?]),
_ => None,
}
}
/// The user-defined types netCDF-C has read so far, and the netCDF type of
/// a dataset.
///
/// netCDF-C keeps every type `read_type` meets in a file-wide list and
/// finds one again by `H5Tequal` on the native types — also a type it
/// failed to read: `read_type` adds the type (with its class, for a
/// compound, enum, variable-length or opaque type) before it looks at the
/// members or base type, and does not remove it when one of those fails.
/// So a dataset of a type netCDF-C skipped once becomes a variable the
/// second time (a compound with a reference member, say), and a compound
/// member of a type it skipped (a bit field) is accepted. This replays
/// that, except that a dataset whose skipped type has no class (a bit
/// field, time, array or complex type) stays hidden: netCDF-C lists the
/// second such dataset with an invalid type (class 0).
#[derive(Debug, Default)]
pub(crate) struct VarTypes {
/// Every type read, with its class when it has one netCDF knows.
known: Vec<(Datatype, Option<NcType>)>,
}
impl VarTypes {
/// The netCDF type netCDF-C gives a dataset of type `dt`
/// (`get_type_info2`), or `None` when it skips the dataset
/// (`NC_EBADTYPID`): a reference, bit field, time or array type, a
/// compound with a member, or an enum or variable-length type with a
/// base type, that is not a netCDF atomic type or a type read before
/// (see the type docs).
///
/// Floats other than 4 and 8 bytes (half floats, bfloat16, the 4-, 6-
/// and 8-bit floats, `long double`) are `Float` (up to 4 bytes) and
/// `Double` here; netCDF-C 4.9.3 on libhdf5 1.14.6 labels them
/// `NC_STRING` (their native type matches none of its own).
pub fn nc_type(&mut self, dt: &Datatype) -> Option<NcType> {
match dt {
Datatype::FixedPoint { size, signed, .. } => int_type(*size, *signed),
Datatype::FloatingPoint { size, .. } => Some(if *size <= 4 {
NcType::Float
} else {
NcType::Double
}),
Datatype::String { size, .. } => Some(if *size > 1 {
NcType::String
} else {
NcType::Char
}),
Datatype::VariableLength {
is_string: true, ..
} => Some(NcType::String),
_ => match self.find(dt) {
Some(class) => class,
None => self.read_type(dt),
},
}
}
/// A named datatype of the file (`read_type` on a committed type).
pub fn named(&mut self, dt: &Datatype) {
if self.find(dt).is_none() {
self.read_type(dt);
}
}
/// The type read before that is `dt`, by its class.
fn find(&self, dt: &Datatype) -> Option<Option<NcType>> {
self.known
.iter()
.find(|(k, _)| native_eq(k, dt))
.map(|&(_, class)| class)
}
/// `read_type`: remember `dt` (not a reference type), then its class if
/// netCDF-C can represent its members or base type.
fn read_type(&mut self, dt: &Datatype) -> Option<NcType> {
let class = match dt {
Datatype::Reference { .. } => return None,
Datatype::Compound { .. } => Some(NcType::Compound),
Datatype::VariableLength { .. } => Some(NcType::VLen),
Datatype::Opaque { .. } => Some(NcType::Opaque),
Datatype::Enumeration { .. } => Some(NcType::Enum),
_ => None,
};
self.known.push((dt.clone(), class));
let parts_ok = match dt {
Datatype::Compound { members, .. } => members.iter().all(|m| match &m.datatype {
Datatype::Array { base_type, .. } => self.is_member_type(base_type),
other => self.is_member_type(other),
}),
Datatype::VariableLength { base_type, .. }
| Datatype::Enumeration { base_type, .. } => self.is_member_type(base_type),
_ => true,
};
class.filter(|_| parts_ok)
}
/// `get_netcdf_type`: whether netCDF-C takes `dt` as the type of a
/// compound member or the base of an enum or variable-length type — an
/// atomic type (4- and 8-byte floats only) or a type read before.
fn is_member_type(&self, dt: &Datatype) -> bool {
match dt {
Datatype::FixedPoint { size, signed, .. } => int_type(*size, *signed).is_some(),
Datatype::FloatingPoint { size: 4 | 8, .. }
| Datatype::String { .. }
| Datatype::VariableLength {
is_string: true, ..
} => true,
_ => self.find(dt).is_some(),
}
}
}
/// The netCDF integer type of an HDF5 integer: the native integer libhdf5
/// converts it to (`H5Tget_native_type`: the smallest at least as wide).
fn int_type(size: u32, signed: bool) -> Option<NcType> {
Some(match (size, signed) {
(1, true) => NcType::Byte,
(1, false) => NcType::UByte,
(2, true) => NcType::Short,
(2, false) => NcType::UShort,
(3..=4, true) => NcType::Int,
(3..=4, false) => NcType::UInt,
(5..=8, true) => NcType::Int64,
(5..=8, false) => NcType::UInt64,
_ => return None,
})
}
/// Whether two datatypes have the same native type (`H5Tequal` after
/// `H5Tget_native_type`): byte order, padding and compound member offsets
/// do not count.
fn native_eq(a: &Datatype, b: &Datatype) -> bool {
use Datatype as D;
match (a, b) {
(
D::FixedPoint {
size: s1,
signed: g1,
..
},
D::FixedPoint {
size: s2,
signed: g2,
..
},
) => g1 == g2 && int_type(*s1, *g1) == int_type(*s2, *g2),
(D::FloatingPoint { size: s1, .. }, D::FloatingPoint { size: s2, .. }) => s1 == s2,
(
D::String {
size: s1,
padding: p1,
charset: c1,
},
D::String {
size: s2,
padding: p2,
charset: c2,
},
) => s1 == s2 && p1 == p2 && c1 == c2,
(
D::VariableLength {
is_string: i1,
base_type: b1,
charset: c1,
..
},
D::VariableLength {
is_string: i2,
base_type: b2,
charset: c2,
..
},
) => i1 == i2 && if *i1 { c1 == c2 } else { native_eq(b1, b2) },
(D::Compound { members: m1, .. }, D::Compound { members: m2, .. }) => {
m1.len() == m2.len()
&& m1
.iter()
.zip(m2)
.all(|(x, y)| x.name == y.name && native_eq(&x.datatype, &y.datatype))
}
(
D::Enumeration {
base_type: b1,
members: m1,
..
},
D::Enumeration {
base_type: b2,
members: m2,
..
},
) => {
native_eq(b1, b2)
&& m1.len() == m2.len()
&& m1.iter().zip(m2).all(|(x, y)| {
x.name == y.name && enum_value(&x.value, b1) == enum_value(&y.value, b2)
})
}
(D::Opaque { size: s1, tag: t1 }, D::Opaque { size: s2, tag: t2 }) => s1 == s2 && t1 == t2,
(
D::Array {
base_type: b1,
dimensions: d1,
},
D::Array {
base_type: b2,
dimensions: d2,
},
) => d1 == d2 && native_eq(b1, b2),
(
D::Reference {
size: s1,
ref_type: r1,
},
D::Reference {
size: s2,
ref_type: r2,
},
) => s1 == s2 && r1 == r2,
(D::BitField { size: s1, .. }, D::BitField { size: s2, .. })
| (D::Time { size: s1, .. }, D::Time { size: s2, .. }) => s1 == s2,
(
D::Complex {
size: s1,
base_type: b1,
},
D::Complex {
size: s2,
base_type: b2,
},
) => s1 == s2 && native_eq(b1, b2),
_ => false,
}
}
/// An enum member's value, in the order of its base type's bytes.
fn enum_value(value: &[u8], base: &Datatype) -> Vec<u8> {
let big = matches!(
base,
Datatype::FixedPoint {
byte_order: DatatypeByteOrder::BigEndian,
..
}
);
let mut v = value.to_vec();
if big {
v.reverse();
}
v
}
-231
View File
@@ -1,231 +0,0 @@
//! A group's variables and the dimensions they are defined on.
//!
//! netCDF-C (`libhdf5/hdf5open.c`) gives a variable its dimensions from the
//! file, never by size: the dimension ids in its `_Netcdf4Coordinates`
//! attribute (each dimension scale's `_Netcdf4Dimid`), else the dimension
//! scales its `DIMENSION_LIST` attribute references, looked up in the
//! variable's group and then each parent group up to the root. Only an axis
//! with neither (a file not written by a netCDF library) gets a dimension
//! by size. Dimension scales that are only dimensions are not variables, and
//! a variable stored as `_nc4_non_coord_<name>` (a variable sharing a
//! dimension's name without being its coordinate variable) is `<name>`.
use std::collections::{HashMap, HashSet};
use clawhdf5::AttrValue;
use crate::dimension::{self, Dimension, GroupDims};
use crate::error::Error;
use crate::variable::Variable;
/// The prefix netCDF-C gives the dataset of a variable that has a
/// dimension's name but is not that dimension's coordinate variable (the
/// dimension's scale holds the name).
const NON_COORD_PREFIX: &str = "_nc4_non_coord_";
/// A group, with the dimensions visible from it.
pub(crate) struct Scope<'f> {
file: &'f clawhdf5::File,
group: clawhdf5::Group<'f>,
/// This group's dimensions, then its parent's, and so on to the root's.
levels: Vec<GroupDims>,
}
impl<'f> Scope<'f> {
/// The group at `path` (`/`-separated from the root; `""` or `"/"` is
/// the root).
pub fn new(file: &'f clawhdf5::File, path: &str) -> Result<Self, Error> {
let parts: Vec<&str> = path.split('/').filter(|p| !p.is_empty()).collect();
let mut levels = Vec::with_capacity(parts.len() + 1);
for n in (0..=parts.len()).rev() {
let group = file.group(&parts[..n].join("/"))?;
levels.push(dimension::group_dims(file, &group)?);
}
let group = file.group(&parts.join("/"))?;
Ok(Self {
file,
group,
levels,
})
}
/// The group's datasets, as `(dataset name, object header address)` in
/// listing order.
fn datasets(&self) -> Result<Vec<(String, u64)>, Error> {
let datasets: HashSet<String> = self.group.datasets()?.into_iter().collect();
Ok(self
.group
.entries()?
.into_iter()
.filter(|(name, _)| datasets.contains(name))
.collect())
}
/// The group's variables: every dataset but the dimension scales that
/// are only dimensions.
pub fn variables(&self) -> Result<Vec<Variable<'f>>, Error> {
let mut variables = Vec::new();
for (ds_name, address) in self.datasets()? {
let ds = self.file.dataset_at(address)?;
let attrs = ds.attrs()?;
if dimension::is_pure_dimension(&attrs) {
continue;
}
variables.push(self.variable_from(nc_name(&ds_name), address, ds, attrs)?);
}
Ok(variables)
}
/// The names of the group's variables.
pub fn variable_names(&self) -> Result<Vec<String>, Error> {
let mut names = Vec::new();
for (ds_name, address) in self.datasets()? {
let attrs = self.file.dataset_at(address)?.attrs()?;
if !dimension::is_pure_dimension(&attrs) {
names.push(nc_name(&ds_name));
}
}
Ok(names)
}
/// The variable called `name`: the dataset `_nc4_non_coord_<name>` if
/// there is one, else the dataset `<name>` unless it is only a
/// dimension.
pub fn variable(&self, name: &str) -> Result<Variable<'f>, Error> {
let not_found = || Error::VariableNotFound(name.to_string());
let datasets = self.datasets()?;
let prefixed = format!("{NON_COORD_PREFIX}{name}");
let address = datasets
.iter()
.find(|(n, _)| *n == prefixed)
.or_else(|| datasets.iter().find(|(n, _)| n == name))
.map(|&(_, address)| address)
.ok_or_else(not_found)?;
let ds = self.file.dataset_at(address)?;
let attrs = ds.attrs()?;
if dimension::is_pure_dimension(&attrs) {
return Err(not_found());
}
self.variable_from(nc_name(name), address, ds, attrs)
}
fn variable_from(
&self,
name: String,
address: u64,
ds: clawhdf5::Dataset<'f>,
attrs: HashMap<String, AttrValue>,
) -> Result<Variable<'f>, Error> {
let shape = ds.shape()?;
let dims = self.variable_dims(address, &attrs, &shape);
Ok(Variable::new(name, ds, dims, attrs))
}
/// The first dimension, searching this group and then its ancestors,
/// that `find` picks.
fn find<'a>(
&'a self,
find: impl Fn(&'a GroupDims) -> Option<&'a Dimension>,
) -> Option<Dimension> {
self.levels.iter().find_map(find).cloned()
}
/// The dimensions of the dataset at `address`, one per axis of `shape`,
/// as netCDF-C resolves them (see the module docs).
fn variable_dims(
&self,
address: u64,
attrs: &HashMap<String, AttrValue>,
shape: &[u64],
) -> Vec<Dimension> {
let rank = shape.len();
let mut dims: Vec<Option<Dimension>> = vec![None; rank];
if rank == 0 {
return Vec::new();
}
// A coordinate variable is the scale of its (first) dimension.
dims[0] = self.levels[0].by_address(address).cloned();
if let Some(ids) = coordinates(attrs).filter(|ids| ids.len() == rank) {
for (slot, id) in dims.iter_mut().zip(ids) {
if slot.is_none() {
*slot = self.find(|level| level.by_dimid(id));
}
}
}
if dims.iter().any(Option::is_none)
&& let Some(scales) =
dimension::dimension_list(self.file, attrs).filter(|s| s.len() == rank)
{
for (slot, scale) in dims.iter_mut().zip(scales) {
if slot.is_none()
&& let Some(scale) = scale
{
*slot = self.find(|level| level.by_address(scale));
}
}
}
// Neither: the first dimension of this group of the same size not
// already taken by another such axis, else an anonymous one.
let own = &self.levels[0].dims;
let mut used = vec![false; own.len()];
dims.into_iter()
.zip(shape)
.map(|(dim, &size)| {
dim.unwrap_or_else(|| {
match own
.iter()
.enumerate()
.find(|&(i, d)| !used[i] && d.size == size)
{
Some((i, d)) => {
used[i] = true;
d.clone()
}
None => Dimension {
name: format!("dim_{size}"),
size,
is_unlimited: false,
},
}
})
})
.collect()
}
}
/// The variable `name` of the group at `group_path`; `name` may itself be
/// a path (`"sub/var"`), relative to that group.
pub(crate) fn variable_at<'f>(
file: &'f clawhdf5::File,
group_path: &str,
name: &str,
) -> Result<Variable<'f>, Error> {
match name.trim_start_matches('/').rsplit_once('/') {
Some((dir, leaf)) => Scope::new(file, &format!("{group_path}/{dir}"))
.map_err(|_| Error::VariableNotFound(name.to_string()))?
.variable(leaf),
None => Scope::new(file, group_path)?.variable(name.trim_start_matches('/')),
}
}
/// The netCDF name of the dataset `ds_name`.
fn nc_name(ds_name: &str) -> String {
ds_name
.strip_prefix(NON_COORD_PREFIX)
.unwrap_or(ds_name)
.to_string()
}
/// A variable's `_Netcdf4Coordinates`: the `_Netcdf4Dimid` of the dimension
/// of each axis.
fn coordinates(attrs: &HashMap<String, AttrValue>) -> Option<Vec<i64>> {
match attrs.get("_Netcdf4Coordinates")? {
AttrValue::I64Array(ids) => Some(ids.clone()),
AttrValue::I64(id) => Some(vec![*id]),
AttrValue::U64Array(ids) => ids.iter().map(|&id| i64::try_from(id).ok()).collect(),
AttrValue::U64(id) => Some(vec![i64::try_from(*id).ok()?]),
_ => None,
}
}
+28 -3
View File
@@ -4,8 +4,16 @@
use clawhdf5::DType;
/// NetCDF-4 data types corresponding to the standard NetCDF type system.
/// NetCDF-4 data types corresponding to the standard NetCDF type system:
/// the atomic types, and the class of a user-defined type.
///
/// A dataset whose type netCDF-C cannot represent — a reference, bit
/// field, time or array type; a compound with such a member, a
/// half-precision float member, or a member of a user-defined type not
/// read before it; an enum or variable-length type over such a base — is
/// not a variable, as in netCDF-C.
#[derive(Debug, Clone, Copy, PartialEq, Eq, Hash)]
#[non_exhaustive]
pub enum NcType {
/// NC_BYTE: signed 8-bit integer
Byte,
@@ -29,8 +37,18 @@ pub enum NcType {
Double,
/// NC_STRING: variable-length string
String,
/// NC_CHAR: fixed-length string / character data
/// NC_CHAR: a fixed-length string of one byte (longer ones are
/// `String`, as netCDF-C reads them)
Char,
/// NC_ENUM: an enumeration (user-defined type)
Enum,
/// NC_COMPOUND: a compound (user-defined type)
Compound,
/// NC_VLEN: a variable-length sequence (user-defined type)
VLen,
/// NC_OPAQUE: an opaque type (user-defined type; netCDF4-python skips
/// such variables)
Opaque,
}
impl std::fmt::Display for NcType {
@@ -48,11 +66,16 @@ impl std::fmt::Display for NcType {
NcType::Double => write!(f, "NC_DOUBLE"),
NcType::String => write!(f, "NC_STRING"),
NcType::Char => write!(f, "NC_CHAR"),
NcType::Enum => write!(f, "NC_ENUM"),
NcType::Compound => write!(f, "NC_COMPOUND"),
NcType::VLen => write!(f, "NC_VLEN"),
NcType::Opaque => write!(f, "NC_OPAQUE"),
}
}
}
/// Map a clawhdf5 DType to a NetCDF type.
/// Map a clawhdf5 DType to a NetCDF type. A variable's own type, as
/// netCDF-C reads it, is [`Variable::nc_type`](crate::Variable::nc_type).
pub fn dtype_to_nctype(dtype: &DType) -> NcType {
match dtype {
DType::I8 => NcType::Byte,
@@ -66,6 +89,8 @@ pub fn dtype_to_nctype(dtype: &DType) -> NcType {
DType::F32 => NcType::Float,
DType::F64 => NcType::Double,
DType::String | DType::VariableLengthString => NcType::String,
DType::Compound(_) => NcType::Compound,
DType::Enum(_) => NcType::Enum,
_ => NcType::Char, // fallback for other types
}
}
+18 -9
View File
@@ -16,7 +16,7 @@ use clawhdf5::AttrValue;
use crate::cf::{self, CfAttributes, FillValue};
use crate::dimension::Dimension;
use crate::error::Error;
use crate::types::{NcType, dtype_to_nctype};
use crate::types::NcType;
/// A NetCDF-4 variable backed by an HDF5 dataset.
pub struct Variable<'f> {
@@ -28,6 +28,8 @@ pub struct Variable<'f> {
dims: Vec<Dimension>,
/// The dataset's attributes.
attrs: HashMap<String, AttrValue>,
/// Its netCDF type.
nc_type: NcType,
}
impl<'f> Variable<'f> {
@@ -37,12 +39,14 @@ impl<'f> Variable<'f> {
dataset: clawhdf5::Dataset<'f>,
dims: Vec<Dimension>,
attrs: HashMap<String, AttrValue>,
nc_type: NcType,
) -> Self {
Self {
name,
dataset,
dims,
attrs,
nc_type,
}
}
@@ -51,11 +55,12 @@ impl<'f> Variable<'f> {
&self.name
}
/// The dimensions of this variable, one per axis: the ones the file
/// gives it (`_Netcdf4Coordinates`, else `DIMENSION_LIST`), found in its
/// group or a parent group. An axis the file gives no dimension (a file
/// not written by a netCDF library) gets the first dimension of the
/// variable's group of the same size, else an anonymous `dim_<size>`.
/// The dimensions of this variable, one per axis, as netCDF-C gives
/// them: the ones the file names (`_Netcdf4Coordinates`, else the
/// scales `DIMENSION_LIST` attaches), found in its group or a parent
/// group; for a dataset without them (a file not written by a netCDF
/// library), netCDF-C's phony dimensions `phony_dim_<n>`, shared by
/// the variables of a group by length.
pub fn dimensions(&self) -> &[Dimension] {
&self.dims
}
@@ -75,10 +80,11 @@ impl<'f> Variable<'f> {
Ok(self.dataset.shape()?)
}
/// The NetCDF data type of this variable.
/// The NetCDF data type of this variable, as netCDF-C reads it (a
/// fixed-length string longer than one byte is `String`, one byte
/// long `Char`).
pub fn nc_type(&self) -> Result<NcType, Error> {
let dtype = self.dataset.dtype()?;
Ok(dtype_to_nctype(&dtype))
Ok(self.nc_type)
}
/// Read all attributes as a HashMap.
@@ -297,6 +303,9 @@ fn default_fill(nc_type: NcType) -> FillValue {
NcType::Double => FillValue::Float(9.969_209_968_386_869e36),
NcType::String => FillValue::String(String::new()),
NcType::Char => FillValue::Int(0),
// User-defined types have no default fill value in netCDF-C; their
// values are not read through these methods.
_ => FillValue::Int(0),
}
}