clawhdf5-netcdf4: phony dimensions, skipped types and order as netCDF-C
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
@@ -36,23 +36,46 @@ let values: Vec<f64> = temp.read_f64()?;
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| Item | What |
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|---|---|
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| `NetCDF4File` | `open`, `from_bytes`, `dimensions`, `variables`, `variable_names`, `variable`, `global_attrs`, `group`, `group_names`, `nc_properties`, and `hdf5_file` for the underlying `clawhdf5::File` |
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| `NetCDF4File` | `open`, `from_bytes`, `dimensions`, `variables`, `variable_names`, `variable` (a name or a path into a subgroup), `global_attrs`, `group` (a name or a path), `group_names`, `nc_properties`, and `hdf5_file` for the underlying `clawhdf5::File` |
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| `NetCDF4Group` | the same for a sub-group (`dimensions`, `variables`, `variable_names`, `attrs`, nested `group`) |
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| `Variable` | `name`, `shape`, `stored_shape`, `dimensions`, `nc_type`, `is_coordinate`, `attrs`, `cf_attributes`; `read_f64` (CF scale/offset and fill applied), `read_raw_f32`/`_f64`/`_i32`/`_i64`/`_u64`, `read_string`, `read_raw` |
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| `Dimension` | `name`, `size`, `is_unlimited` (an unlimited dimension's `size` is its current length as netCDF-C reports it: the largest extent of the variables using it) |
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| `CfAttributes` | CF convention attributes: `units`, `long_name`, `standard_name`, `fill_value` (`_FillValue`), `missing_value`, `scale_factor`, `add_offset`, `valid_range`, `calendar`, `axis` |
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| `NcType` | the NetCDF type of a variable |
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| `NcType` | the NetCDF type of a variable: an atomic type (`Byte` ... `UInt64`, `Float`, `Double`, `Char`, `String`) or the class of a user-defined one (`Enum`, `Compound`, `VLen`, `Opaque`); `#[non_exhaustive]` |
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Variables and dimensions follow netCDF-C:
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Groups, dimensions and variables are what netCDF-C 4.9.3 reports
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(`libhdf5/hdf5open.c`), names, order and types included. The first call
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that needs them reads the metadata of the whole file, as `nc_open` does:
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- A variable's dimensions are the ones the file names: the ids in its
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`_Netcdf4Coordinates` attribute, else the dimension scales its
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`DIMENSION_LIST` references, found in its group or a parent group. Only
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an axis the file names no dimension for (an HDF5 file not written by a
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netCDF library) gets the first dimension of the group of the same size,
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else an anonymous `dim_<size>`.
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- Dimension scales that are only dimensions are not variables; a dataset
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- Order: a group's links in creation order when it tracks it (netCDF-4
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files do), else in name order (h5py's default); groups and variables in
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that order, dimensions by id.
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- A dimension scale defines a dimension (its `_Netcdf4Dimid`, else the
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next free id; unlimited when its first axis is or its length is 0);
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scales that are only dimensions are not variables, and a dataset
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`_nc4_non_coord_<name>` is the variable `<name>`.
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- A variable's dimensions are the ones the file names: the ids in its
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`_Netcdf4Coordinates` attribute (any group), else — when its first axis
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has one — the dimension scales its `DIMENSION_LIST` attaches, found in
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its group or a parent group.
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- Otherwise (an HDF5 file not written by a netCDF library) its axes get
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netCDF-C's **phony dimensions** `phony_dim_<n>`: per axis, the first
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dimension of the variable's group with the same length and
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unlimitedness that an earlier axis of the variable does not use, else a
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new one. The numbers run file-wide, a group's subgroups before its own
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variables.
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- Datasets of types netCDF-C cannot represent are not variables:
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references, bit fields, time and array types, and compounds, enums and
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VLENs over members or base types that are not netCDF atomic types (4-
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and 8-byte floats only) or types netCDF-C has read before in the file.
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Enum, compound, VLEN and opaque datasets are variables of those classes
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(netCDF4-python itself leaves out opaque ones).
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- Two deliberate differences: floats of other than 4 or 8 bytes (half,
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bfloat16, 4/6/8-bit floats, `long double`) are `Float`/`Double` and
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read as numbers, where netCDF-C 4.9.3 on libhdf5 1.14.6 labels them
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`NC_STRING`; and an axis netCDF-C leaves without a dimension (an id or
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scale it cannot find, or no scale on an axis after a first one that has
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one, where it reads uninitialised memory) gets one by the phony rule.
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- A variable along an unlimited dimension has the dimension's length:
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`shape` is that length, and the reads return that many values, the
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records the variable has not written as its fill value (`_FillValue`,
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@@ -60,11 +83,23 @@ Variables and dimensions follow netCDF-C:
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`stored_shape` is the HDF5 dataset's extent.
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No cargo features. Tests compare against files written by netCDF4-python,
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h5py dimension scales, h5netcdf and xarray, variable by variable with what
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netCDF4-python reads (`tests/interop_tests.rs`; the CI job requires them
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with `CLAWHDF5_REQUIRE_INTEROP=1`; the h5netcdf cases skip when h5netcdf is
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not installed). What the HDF5 reader underneath cannot read is listed in
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[`docs/known-issues.md`](../../docs/known-issues.md).
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h5py (with and without dimension scales, every HDF5 type class), h5netcdf
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and xarray, with what netCDF4-python reads and with what netCDF-C itself
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reports (`tests/interop_tests.rs`; `tests/netcdf_c_view.py` calls the
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libnetcdf netCDF4-python bundles; the CI job requires them with
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`CLAWHDF5_REQUIRE_INTEROP=1`; the h5netcdf cases skip when h5netcdf is not
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installed). `tests/corpus_vs_netcdf_c.rs` compares every file of a corpus
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netCDF-C opens, when `CLAWHDF5_NETCDF_CORPUS` names one: over the
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conformance corpus, 420 of 429 files match (tank, 2026-09-29), and the
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other 9 are explained in `tests/corpus_known_differences.txt`:
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```sh
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CLAWHDF5_NETCDF_CORPUS=conformance/.cache/corpus CLAWHDF5_PYTHON=$PWD/.venv/bin/python \
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cargo test -p clawhdf5-netcdf4 --test corpus_vs_netcdf_c -- --nocapture
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```
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The differences from netCDF-C, and what the HDF5 reader underneath cannot
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read, are listed in [`docs/known-issues.md`](../../docs/known-issues.md).
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## License
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@@ -1,16 +1,15 @@
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//! NetCDF-4 dimension representation.
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//!
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//! Dimensions in NetCDF-4 are stored as HDF5 datasets with the CLASS=DIMENSION_SCALE
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//! attribute and a `_Netcdf4Dimid` attribute. Unlimited dimensions are detected via
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//! the HDF5 dataspace max_dimensions (u64::MAX indicates unlimited); their length
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//! is the largest extent of the variables attached to them.
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//! attribute and a `_Netcdf4Dimid` attribute; variables name theirs in
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//! `_Netcdf4Coordinates` and `DIMENSION_LIST`. A file without them gets
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//! netCDF-C's phony dimensions. How they are put together is in
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//! `crate::model`.
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use std::collections::HashMap;
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use clawhdf5::AttrValue;
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use crate::error::Error;
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/// A NetCDF-4 dimension.
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#[derive(Debug, Clone, PartialEq, Eq)]
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pub struct Dimension {
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@@ -22,202 +21,10 @@ pub struct Dimension {
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pub is_unlimited: bool,
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}
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/// A dimension scale of one group: the dataset that defines a dimension.
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#[derive(Debug, Clone)]
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pub(crate) struct Scale {
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/// Object header address of the scale's dataset (what a variable's
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/// `DIMENSION_LIST` references).
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pub address: u64,
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/// Its `_Netcdf4Dimid` (what a variable's `_Netcdf4Coordinates` lists).
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pub dimid: Option<i64>,
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/// Index of its dimension in [`GroupDims::dims`].
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pub dim: usize,
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}
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/// The dimensions a group defines, with the scales that define them.
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#[derive(Debug, Clone, Default)]
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pub(crate) struct GroupDims {
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/// The group's dimensions, in `_Netcdf4Dimid` order (then discovery order).
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pub dims: Vec<Dimension>,
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/// The dimension scales behind `dims`; empty when the group has no
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/// dimension scale and `dims` were inferred from 1-D datasets.
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pub scales: Vec<Scale>,
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}
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impl GroupDims {
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/// The dimension defined by the scale at `address`.
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pub fn by_address(&self, address: u64) -> Option<&Dimension> {
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self.scales
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.iter()
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.find(|s| s.address == address)
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.map(|s| &self.dims[s.dim])
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}
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/// The dimension whose scale has `_Netcdf4Dimid` `id`.
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pub fn by_dimid(&self, id: i64) -> Option<&Dimension> {
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self.scales
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.iter()
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.find(|s| s.dimid == Some(id))
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.map(|s| &self.dims[s.dim])
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}
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}
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/// The dimensions of an HDF5 group (root or subgroup).
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///
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/// NetCDF-4 stores dimensions as datasets with `CLASS=DIMENSION_SCALE`. A fixed
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/// dimension's size is the dataset's first (and typically only) shape extent.
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/// Unlimited dimensions have `max_dimensions[0] == u64::MAX` in the HDF5 dataspace;
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/// their size is computed by `unlimited_len`. A group with no dimension
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/// scale at all (not written by a netCDF library) gets one dimension per
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/// 1-D dataset instead.
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pub(crate) fn group_dims(
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file: &clawhdf5::File,
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group: &clawhdf5::Group<'_>,
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) -> Result<GroupDims, Error> {
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let addresses: HashMap<String, u64> = group.entries()?.into_iter().collect();
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let dataset_names = group.datasets()?;
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// (dimid, dimension, scale address), in discovery order.
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let mut found: Vec<(Option<i64>, Dimension, u64)> = Vec::new();
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for ds_name in &dataset_names {
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let ds = group.dataset(ds_name)?;
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let attrs = ds.attrs()?;
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if !is_dimension_scale(&attrs) {
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continue;
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}
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let Some(&address) = addresses.get(ds_name) else {
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continue;
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};
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let shape = ds.shape()?;
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let is_unlimited = is_unlimited(&ds);
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let size = if is_unlimited {
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unlimited_len(file, &attrs, &shape)
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} else {
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shape.first().copied().unwrap_or(0)
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};
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let dim = Dimension {
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name: ds_name.clone(),
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size,
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is_unlimited,
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};
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found.push((get_dimid(&attrs), dim, address));
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}
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if found.is_empty() {
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// Fallback: infer dimensions from dataset shapes and names.
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// In NetCDF-4, coordinate variables are datasets whose name matches
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// a dimension name. If there are no explicit DIMENSION_SCALE attributes,
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// we look for 1-D datasets that might be coordinate variables.
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let mut dims = Vec::new();
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for ds_name in &dataset_names {
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let ds = group.dataset(ds_name)?;
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let shape = ds.shape()?;
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if shape.len() == 1 {
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dims.push(Dimension {
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name: ds_name.clone(),
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size: shape[0],
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is_unlimited: is_unlimited(&ds),
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});
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}
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}
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return Ok(GroupDims {
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dims,
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scales: Vec::new(),
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});
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}
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// By dimid; scales without one keep their discovery order after those
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// with one (the sort is stable).
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found.sort_by_key(|(id, ..)| (id.is_none(), id.unwrap_or(0)));
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let mut out = GroupDims::default();
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for (i, (dimid, dim, address)) in found.into_iter().enumerate() {
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out.dims.push(dim);
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out.scales.push(Scale {
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address,
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dimid,
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dim: i,
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});
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}
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Ok(out)
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}
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/// The start of the `NAME` attribute netCDF-C gives a dimension scale that
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/// is only a dimension, not also a (coordinate) variable.
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const PURE_DIMENSION_NAME: &str = "This is a netCDF dimension but not a netCDF variable";
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/// The current length of an unlimited dimension, as netCDF-C reports it
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/// (`NC4_inq_dim` → `nc4_find_dim_len`): the largest current extent, along
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/// the dimension, of the variables that use it, in any group; 0 when none
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/// has been written. netCDF-C does not extend a dimension scale that is not
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/// also a variable, so such a scale's own extent (0) is not counted; a
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/// coordinate variable's is. The variables are the scale's attachments,
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/// listed with the axis they use in its `REFERENCE_LIST` attribute (the
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/// mirror of each variable's `DIMENSION_LIST`). Attachments that cannot be
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/// read are skipped; without a readable `REFERENCE_LIST` the length is the
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/// scale's own extent, as before.
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fn unlimited_len(file: &clawhdf5::File, attrs: &HashMap<String, AttrValue>, shape: &[u64]) -> u64 {
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let own = shape.first().copied().unwrap_or(0);
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let is_variable = !is_pure_dimension(attrs);
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let Some(refs) = reference_list(file, attrs) else {
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return own;
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};
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refs.into_iter()
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.filter_map(|(address, axis)| {
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let shape = file.dataset_at(address).ok()?.shape().ok()?;
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shape.get(usize::try_from(axis).ok()?).copied()
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})
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.chain(is_variable.then_some(own))
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.max()
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.unwrap_or(0)
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}
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/// The `(dataset address, axis)` pairs of a dimension scale's
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/// `REFERENCE_LIST` attribute (HDF5 dimension scales: a compound of an
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/// object reference `dataset` and an integer `dimension`), or `None` when it
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/// is missing or not in that form.
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fn reference_list(
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file: &clawhdf5::File,
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attrs: &HashMap<String, AttrValue>,
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) -> Option<Vec<(u64, u64)>> {
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use clawhdf5_format::data_read::{read_compound_field, read_object_references};
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use clawhdf5_format::datatype::{Datatype, DatatypeByteOrder};
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let Some(AttrValue::Raw { datatype, data, .. }) = attrs.get("REFERENCE_LIST") else {
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return None;
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};
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let dataset = read_compound_field(data, datatype, "dataset").ok()?;
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let addresses = read_object_references(
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&dataset.raw_data,
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&dataset.datatype,
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file.superblock().offset_size,
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)
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.ok()?;
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let dimension = read_compound_field(data, datatype, "dimension").ok()?;
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let Datatype::FixedPoint {
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size, byte_order, ..
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} = dimension.datatype
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else {
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return None;
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};
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let size = usize::try_from(size).ok().filter(|s| (1..=8).contains(s))?;
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let axes = dimension.raw_data.chunks_exact(size).map(|b| {
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let mut v = [0u8; 8];
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match byte_order {
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DatatypeByteOrder::BigEndian => {
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v[8 - size..].copy_from_slice(b);
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u64::from_be_bytes(v)
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}
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_ => {
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v[..size].copy_from_slice(b);
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u64::from_le_bytes(v)
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}
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}
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});
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if axes.len() != addresses.len() {
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return None;
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}
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Some(addresses.into_iter().map(|r| r.address).zip(axes).collect())
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}
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/// The dimension scale attached to each axis of a variable, from its
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/// `DIMENSION_LIST` attribute (HDF5 dimension scales: one variable-length
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/// sequence of object references per axis) — the address of the scale
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@@ -281,13 +88,9 @@ pub(crate) fn is_dimension_scale(attrs: &HashMap<String, AttrValue>) -> bool {
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pub(crate) fn get_dimid(attrs: &HashMap<String, AttrValue>) -> Option<i64> {
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match attrs.get("_Netcdf4Dimid") {
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Some(AttrValue::I64(id)) => Some(*id),
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Some(AttrValue::U64(id)) => Some(*id as i64),
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Some(AttrValue::U64(id)) => i64::try_from(*id).ok(),
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Some(AttrValue::I64Array(ids)) if ids.len() == 1 => Some(ids[0]),
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Some(AttrValue::U64Array(ids)) if ids.len() == 1 => i64::try_from(ids[0]).ok(),
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_ => None,
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}
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}
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/// Whether a dataset's first axis is unlimited (`max_dimensions[0] ==
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/// u64::MAX` in its dataspace).
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fn is_unlimited(ds: &clawhdf5::Dataset<'_>) -> bool {
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matches!(ds.max_dimensions(), Ok(Some(max_dims)) if max_dims.first() == Some(&u64::MAX))
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}
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@@ -7,36 +7,36 @@ use std::collections::HashMap;
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use clawhdf5::AttrValue;
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use crate::dimension::{self, Dimension};
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use crate::dimension::Dimension;
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use crate::error::Error;
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use crate::scope::{self, Scope};
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use crate::model::Model;
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use crate::variable::Variable;
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/// A NetCDF-4 group corresponding to an HDF5 group.
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pub struct NetCDF4Group<'f> {
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/// Group name.
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name: String,
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/// Path of the group from the root (`/`-separated).
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path: String,
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/// Underlying HDF5 file.
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file: &'f clawhdf5::File,
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/// Underlying HDF5 group.
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hdf5_group: clawhdf5::Group<'f>,
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/// The file's groups, dimensions and variables.
|
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model: &'f Model,
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/// This group's index in `model`.
|
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index: usize,
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}
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impl<'f> NetCDF4Group<'f> {
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/// 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))
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
@@ -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,
|
||||
))
|
||||
}
|
||||
|
||||
|
||||
@@ -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
|
||||
}
|
||||
@@ -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,
|
||||
}
|
||||
}
|
||||
@@ -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
|
||||
}
|
||||
}
|
||||
|
||||
@@ -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),
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
@@ -0,0 +1,281 @@
|
||||
//! clawhdf5-netcdf4 compared with netCDF-C itself: `tests/netcdf_c_view.py`
|
||||
//! prints what netCDF-C (the libnetcdf netCDF4-python bundles) reports for
|
||||
//! a file, and [`differences`] lists how clawhdf5-netcdf4's reading differs.
|
||||
#![allow(dead_code)]
|
||||
|
||||
use std::collections::{BTreeMap, BTreeSet};
|
||||
use std::path::{Path, PathBuf};
|
||||
use std::process::Command;
|
||||
use std::sync::atomic::{AtomicUsize, Ordering};
|
||||
|
||||
use clawhdf5_netcdf4::{NcType, NetCDF4File, NetCDF4Group, Variable};
|
||||
|
||||
/// The Python with netCDF4-python (`CLAWHDF5_PYTHON`, else `python3`).
|
||||
pub fn python() -> String {
|
||||
std::env::var("CLAWHDF5_PYTHON").unwrap_or_else(|_| "python3".to_string())
|
||||
}
|
||||
|
||||
/// netCDF-C's view of one file.
|
||||
#[derive(Default)]
|
||||
pub struct View {
|
||||
/// `G`, `D` and `V` lines, in order.
|
||||
pub meta: Vec<String>,
|
||||
/// `(group, variable)` → values, from the `X` lines.
|
||||
pub values: BTreeMap<(String, String), Vec<f64>>,
|
||||
}
|
||||
|
||||
/// netCDF-C's view of each file (`None`: netCDF-C cannot open it), from
|
||||
/// `tests/netcdf_c_view.py`.
|
||||
pub fn netcdf_c_views(files: &[PathBuf]) -> BTreeMap<PathBuf, Option<View>> {
|
||||
let dir = tempfile::tempdir().unwrap();
|
||||
let list = dir.path().join("files.txt");
|
||||
let mut paths = String::new();
|
||||
for f in files {
|
||||
paths.push_str(&f.to_string_lossy());
|
||||
paths.push('\n');
|
||||
}
|
||||
std::fs::write(&list, paths).unwrap();
|
||||
let script = Path::new(env!("CARGO_MANIFEST_DIR")).join("tests/netcdf_c_view.py");
|
||||
let out = Command::new(python())
|
||||
.arg(&script)
|
||||
.arg("--list")
|
||||
.arg(&list)
|
||||
.output()
|
||||
.expect("failed to run python");
|
||||
assert!(
|
||||
out.status.success(),
|
||||
"netcdf_c_view.py failed: {}",
|
||||
String::from_utf8_lossy(&out.stderr)
|
||||
);
|
||||
parse_views(&String::from_utf8_lossy(&out.stdout))
|
||||
}
|
||||
|
||||
/// The views in the output of `tests/netcdf_c_view.py`.
|
||||
pub fn parse_views(text: &str) -> BTreeMap<PathBuf, Option<View>> {
|
||||
let mut views = BTreeMap::new();
|
||||
let mut current: Option<(PathBuf, Option<View>)> = None;
|
||||
for line in text.lines() {
|
||||
let fields: Vec<&str> = line.split('\t').collect();
|
||||
match fields[0] {
|
||||
"FILE" => current = Some((PathBuf::from(fields[1]), Some(View::default()))),
|
||||
"END" => {
|
||||
let (path, view) = current.take().expect("END without FILE");
|
||||
views.insert(path, view);
|
||||
}
|
||||
"ERROR" => current.as_mut().expect("ERROR without FILE").1 = None,
|
||||
"X" => {
|
||||
let view = current.as_mut().and_then(|c| c.1.as_mut()).unwrap();
|
||||
let vals = if fields[3] == "-" {
|
||||
Vec::new()
|
||||
} else {
|
||||
fields[3]
|
||||
.split(' ')
|
||||
.map(|v| v.parse().expect("value"))
|
||||
.collect()
|
||||
};
|
||||
view.values
|
||||
.insert((fields[1].to_string(), fields[2].to_string()), vals);
|
||||
}
|
||||
_ => {
|
||||
let view = current.as_mut().and_then(|c| c.1.as_mut()).unwrap();
|
||||
view.meta.push(line.to_string());
|
||||
}
|
||||
}
|
||||
}
|
||||
views
|
||||
}
|
||||
|
||||
/// Variables whose type is labelled as netCDF-C labels it rather than as
|
||||
/// clawhdf5-netcdf4 does (see [`nc_type_label`]).
|
||||
pub static RELABELLED: AtomicUsize = AtomicUsize::new(0);
|
||||
/// Values not compared because this build of the HDF5 reader lacks a
|
||||
/// filter (a cargo feature).
|
||||
pub static FILTER_SKIPPED: AtomicUsize = AtomicUsize::new(0);
|
||||
|
||||
/// The same `G`/`D`/`V` lines from clawhdf5-netcdf4.
|
||||
pub fn our_meta(file: &NetCDF4File) -> Result<Vec<String>, String> {
|
||||
let e = |e: clawhdf5_netcdf4::Error| e.to_string();
|
||||
let mut out = Vec::new();
|
||||
out.push("G\t/".to_string());
|
||||
push_group(
|
||||
&mut out,
|
||||
file.hdf5_file(),
|
||||
"/",
|
||||
file.dimensions().map_err(e)?,
|
||||
file.variables().map_err(e)?,
|
||||
)?;
|
||||
for name in file.group_names().map_err(e)? {
|
||||
walk(
|
||||
&mut out,
|
||||
file.hdf5_file(),
|
||||
&format!("/{name}"),
|
||||
&file.group(&name).map_err(e)?,
|
||||
)?;
|
||||
}
|
||||
Ok(out)
|
||||
}
|
||||
|
||||
fn walk(
|
||||
out: &mut Vec<String>,
|
||||
hdf5: &clawhdf5::File,
|
||||
path: &str,
|
||||
group: &NetCDF4Group<'_>,
|
||||
) -> Result<(), String> {
|
||||
let e = |e: clawhdf5_netcdf4::Error| e.to_string();
|
||||
out.push(format!("G\t{path}"));
|
||||
push_group(
|
||||
out,
|
||||
hdf5,
|
||||
path,
|
||||
group.dimensions().map_err(e)?,
|
||||
group.variables().map_err(e)?,
|
||||
)?;
|
||||
for name in group.group_names().map_err(e)? {
|
||||
walk(
|
||||
out,
|
||||
hdf5,
|
||||
&format!("{path}/{name}"),
|
||||
&group.group(&name).map_err(e)?,
|
||||
)?;
|
||||
}
|
||||
Ok(())
|
||||
}
|
||||
|
||||
/// The type of variable `name` of the group at `path` as the `V` line
|
||||
/// shows it: its `NcType`, except for the one deliberate difference from
|
||||
/// netCDF-C — a float of other than 4 or 8 bytes (half, bfloat16, the 4-,
|
||||
/// 6- and 8-bit floats, `long double`), `NC_FLOAT`/`NC_DOUBLE` here, is
|
||||
/// labelled `NC_STRING` by netCDF-C 4.9.3 on libhdf5 1.14.6; such a
|
||||
/// variable is shown as netCDF-C shows it, and counted.
|
||||
fn nc_type_label(hdf5: &clawhdf5::File, path: &str, var: &Variable<'_>) -> Result<String, String> {
|
||||
let nc_type = var.nc_type().map_err(|e| e.to_string())?;
|
||||
if matches!(nc_type, NcType::Float | NcType::Double) {
|
||||
let dataset = format!("{}/{}", path.trim_end_matches('/'), var.name());
|
||||
if let Ok(ds) = hdf5.dataset(&dataset)
|
||||
&& let Ok(clawhdf5_format::datatype::Datatype::FloatingPoint { size, .. }) =
|
||||
ds.raw_datatype()
|
||||
&& size != 4
|
||||
&& size != 8
|
||||
{
|
||||
RELABELLED.fetch_add(1, Ordering::Relaxed);
|
||||
return Ok("NC_STRING".to_string());
|
||||
}
|
||||
}
|
||||
Ok(nc_type.to_string())
|
||||
}
|
||||
|
||||
fn push_group(
|
||||
out: &mut Vec<String>,
|
||||
hdf5: &clawhdf5::File,
|
||||
path: &str,
|
||||
dims: Vec<clawhdf5_netcdf4::Dimension>,
|
||||
vars: Vec<Variable<'_>>,
|
||||
) -> Result<(), String> {
|
||||
for d in dims {
|
||||
out.push(format!(
|
||||
"D\t{path}\t{}\t{}\t{}",
|
||||
d.name,
|
||||
d.size,
|
||||
u8::from(d.is_unlimited)
|
||||
));
|
||||
}
|
||||
for v in vars {
|
||||
let dims: Vec<&str> = v.dimensions().iter().map(|d| d.name.as_str()).collect();
|
||||
let shape: Vec<String> = v
|
||||
.shape()
|
||||
.map_err(|e| e.to_string())?
|
||||
.iter()
|
||||
.map(u64::to_string)
|
||||
.collect();
|
||||
let or_dash = |s: String| if s.is_empty() { "-".to_string() } else { s };
|
||||
out.push(format!(
|
||||
"V\t{path}\t{}\t{}\t{}\t{}",
|
||||
v.name(),
|
||||
nc_type_label(hdf5, path, &v)?,
|
||||
or_dash(dims.join(",")),
|
||||
or_dash(shape.join(","))
|
||||
));
|
||||
}
|
||||
Ok(())
|
||||
}
|
||||
|
||||
/// The values of variable `name` of group `group`.
|
||||
fn our_values(file: &NetCDF4File, group: &str, name: &str) -> Result<Vec<f64>, String> {
|
||||
let var = if group == "/" {
|
||||
file.variable(name)
|
||||
} else {
|
||||
file.variable(&format!("{}/{name}", group.trim_start_matches('/')))
|
||||
}
|
||||
.map_err(|e| e.to_string())?;
|
||||
match var.nc_type().map_err(|e| e.to_string())? {
|
||||
NcType::String | NcType::Char => Err("not numeric".into()),
|
||||
_ => var.read_raw_f64().map_err(|e| e.to_string()),
|
||||
}
|
||||
}
|
||||
|
||||
/// How clawhdf5-netcdf4's reading of `path` differs from `want`; empty
|
||||
/// when it does not.
|
||||
pub fn differences(path: &Path, want: &View) -> Vec<String> {
|
||||
let file = match NetCDF4File::open(path) {
|
||||
Ok(f) => f,
|
||||
Err(e) => return vec![format!("netCDF-C opens it, clawhdf5-netcdf4 does not: {e}")],
|
||||
};
|
||||
let meta = match std::panic::catch_unwind(std::panic::AssertUnwindSafe(|| our_meta(&file))) {
|
||||
Ok(Ok(meta)) => meta,
|
||||
Ok(Err(e)) => return vec![format!("error: {e}")],
|
||||
Err(_) => return vec!["panic".to_string()],
|
||||
};
|
||||
let mut diffs = Vec::new();
|
||||
if meta != want.meta {
|
||||
let ours: BTreeSet<&String> = meta.iter().collect();
|
||||
let theirs: BTreeSet<&String> = want.meta.iter().collect();
|
||||
for line in want.meta.iter().filter(|l| !ours.contains(l)) {
|
||||
diffs.push(format!("netCDF-C: {line}"));
|
||||
}
|
||||
for line in meta.iter().filter(|l| !theirs.contains(l)) {
|
||||
diffs.push(format!("ours: {line}"));
|
||||
}
|
||||
if diffs.is_empty() {
|
||||
diffs.push("same lines, different order".to_string());
|
||||
}
|
||||
}
|
||||
for ((group, name), want) in &want.values {
|
||||
let got = std::panic::catch_unwind(std::panic::AssertUnwindSafe(|| {
|
||||
our_values(&file, group, name)
|
||||
}))
|
||||
.unwrap_or_else(|_| Err("panic".to_string()));
|
||||
match got {
|
||||
Ok(got) => {
|
||||
let same = got.len() == want.len()
|
||||
&& got
|
||||
.iter()
|
||||
.zip(want)
|
||||
.all(|(a, b)| a.to_bits() == b.to_bits() || (a.is_nan() && b.is_nan()));
|
||||
if !same {
|
||||
diffs.push(format!("values of {group} {name} differ"));
|
||||
}
|
||||
}
|
||||
Err(e) if e.contains("this build lacks the") => {
|
||||
FILTER_SKIPPED.fetch_add(1, Ordering::Relaxed);
|
||||
}
|
||||
Err(e) => diffs.push(format!("values of {group} {name}: {e}")),
|
||||
}
|
||||
}
|
||||
diffs
|
||||
}
|
||||
|
||||
/// clawhdf5-netcdf4 reads the file at `path` as netCDF-C does: the same
|
||||
/// groups, dimensions, variables and values (see [`differences`]).
|
||||
pub fn assert_matches_netcdf_c(path: &Path) {
|
||||
let views = netcdf_c_views(&[path.to_path_buf()]);
|
||||
let Some(Some(want)) = views.get(path) else {
|
||||
panic!("netCDF-C cannot open {}", path.display());
|
||||
};
|
||||
let diffs = differences(path, want);
|
||||
assert!(
|
||||
diffs.is_empty(),
|
||||
"{} differs from netCDF-C:\n{}",
|
||||
path.display(),
|
||||
diffs.join("\n")
|
||||
);
|
||||
}
|
||||
@@ -0,0 +1,26 @@
|
||||
# Files of the conformance corpus (conformance/.cache/corpus) that netCDF-C
|
||||
# opens and clawhdf5-netcdf4 reads differently, with the reason.
|
||||
# <path relative to the corpus root><TAB><reason>
|
||||
# Read by tests/corpus_vs_netcdf_c.rs; see docs/known-issues.md
|
||||
# ("NetCDF-4: differences from netCDF-C").
|
||||
#
|
||||
# External links: libhdf5 follows them into the other file (present in the
|
||||
# corpus); clawhdf5 does not follow external links (known-issues: "External
|
||||
# links and external raw data are not followed"), so the linked groups and
|
||||
# datasets are missing and, in files without dimension scales, the phony
|
||||
# dimension numbers after them shift.
|
||||
hdf5/test/testfiles/be_extlink1.h5 external link not followed
|
||||
hdf5/test/testfiles/le_extlink1.h5 external link not followed
|
||||
hdf5/tools/test/testfiles/h5diff_ext2softlink_src.h5 external link not followed
|
||||
hdf5/tools/test/testfiles/h5diff_grp_recurse_ext2-1.h5 external link not followed
|
||||
hdf5/tools/test/testfiles/h5diff_grp_recurse_ext2-2.h5 external link not followed
|
||||
#
|
||||
# Values the HDF5 reader refuses and libhdf5 1.14.6 (the netCDF4-python
|
||||
# wheel's) returns; metadata matches. The first three are the scale-offset
|
||||
# and N-Bit ref-bug / our-error files of CONFORMANCE.md (libhdf5 reads past
|
||||
# the stored data); bad_nbit_decompress.h5 is not in the conformance run and
|
||||
# is not investigated yet.
|
||||
cve_hdf5/cvefiles/cve-2025-2308.h5 values: scale-offset chunk shorter than its values (libhdf5 over-read)
|
||||
cve_hdf5/cvefiles/cve-2025-44904.h5 values: unfiltered chunks shorter than a chunk (libhdf5 over-read)
|
||||
hdf5/test/testfiles/bad_nbit_parms_walk.h5 values: N-Bit parameters too short (conformance our-error/ref-bug)
|
||||
hdf5/test/testfiles/bad_nbit_decompress.h5 values: N-Bit chunk refused ("element count exceeds chunk size"); not investigated
|
||||
@@ -0,0 +1,173 @@
|
||||
//! Every file of a corpus that netCDF-C opens, read by clawhdf5-netcdf4 and
|
||||
//! compared with what netCDF-C reports: groups (order), dimensions (names,
|
||||
//! lengths, unlimited, order), variables (names, order, types, dimensions,
|
||||
//! shapes) and the values of numeric variables of at most 5000 elements.
|
||||
//!
|
||||
//! Gated: set `CLAWHDF5_NETCDF_CORPUS` to a directory (relative to the
|
||||
//! workspace root, or absolute) — the conformance corpus
|
||||
//! (`conformance/.cache/corpus`) or any tree of HDF5/netCDF-4 files — and
|
||||
//! `CLAWHDF5_PYTHON` to a Python with netCDF4-python (whose bundled
|
||||
//! libnetcdf `tests/netcdf_c_view.py` calls). Without the variable the test
|
||||
//! does nothing. netCDF-C reads each file in its own process (4 at a time,
|
||||
//! `CLAWHDF5_NETCDF_JOBS`), under a 60 s timeout and a 4 GiB address-space
|
||||
//! limit: 40 s to 3 minutes for the conformance corpus on tank.
|
||||
//! `CLAWHDF5_NETCDF_VIEW` may name the saved output of an earlier
|
||||
//! `netcdf_c_view.py --list <file of paths>` run over the same (absolute)
|
||||
//! paths, to skip that.
|
||||
//!
|
||||
//! A file whose differences are explained is listed, with the reason, in
|
||||
//! `tests/corpus_known_differences.txt` (and in `docs/known-issues.md`); a
|
||||
//! listed file that matches fails the test too, so the list stays true.
|
||||
//!
|
||||
//! ```sh
|
||||
//! CLAWHDF5_NETCDF_CORPUS=conformance/.cache/corpus CLAWHDF5_PYTHON=$PWD/.venv/bin/python \
|
||||
//! cargo test -p clawhdf5-netcdf4 --test corpus_vs_netcdf_c -- --nocapture
|
||||
//! ```
|
||||
|
||||
mod common;
|
||||
|
||||
use std::collections::BTreeMap;
|
||||
use std::path::{Path, PathBuf};
|
||||
use std::sync::atomic::Ordering;
|
||||
|
||||
use common::{FILTER_SKIPPED, RELABELLED, differences, netcdf_c_views, parse_views};
|
||||
|
||||
/// The file extensions `conformance/list_files.py` sweeps.
|
||||
const EXTS: [&str; 7] = ["h5", "hdf5", "he5", "nc", "nc4", "hdf", "h5f"];
|
||||
|
||||
/// The files of the corpus: those with an HDF5/netCDF-4 extension, except
|
||||
/// netCDF classic files (magic `CDF`), following directory symlinks, in
|
||||
/// byte order of their paths.
|
||||
fn corpus_files(root: &Path) -> Vec<PathBuf> {
|
||||
fn walk(dir: &Path, out: &mut Vec<PathBuf>, depth: usize) {
|
||||
let Ok(entries) = std::fs::read_dir(dir) else {
|
||||
return;
|
||||
};
|
||||
for entry in entries.flatten() {
|
||||
let path = entry.path();
|
||||
if path.file_name().is_some_and(|n| n == ".git") {
|
||||
continue;
|
||||
}
|
||||
let Ok(meta) = std::fs::metadata(&path) else {
|
||||
continue;
|
||||
};
|
||||
if meta.is_dir() && depth < 32 {
|
||||
walk(&path, out, depth + 1);
|
||||
} else if meta.is_file()
|
||||
&& path
|
||||
.extension()
|
||||
.and_then(|e| e.to_str())
|
||||
.is_some_and(|e| EXTS.contains(&e.to_ascii_lowercase().as_str()))
|
||||
{
|
||||
let mut magic = [0u8; 3];
|
||||
let classic = std::fs::File::open(&path)
|
||||
.and_then(|mut f| std::io::Read::read_exact(&mut f, &mut magic))
|
||||
.is_ok()
|
||||
&& &magic == b"CDF";
|
||||
if !classic {
|
||||
out.push(path);
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
let mut out = Vec::new();
|
||||
walk(root, &mut out, 0);
|
||||
out.sort_by(|a, b| {
|
||||
a.as_os_str()
|
||||
.as_encoded_bytes()
|
||||
.cmp(b.as_os_str().as_encoded_bytes())
|
||||
});
|
||||
out
|
||||
}
|
||||
|
||||
/// The files `tests/corpus_known_differences.txt` explains: path relative
|
||||
/// to the corpus root → reason.
|
||||
fn known_differences() -> BTreeMap<String, String> {
|
||||
let list = Path::new(env!("CARGO_MANIFEST_DIR")).join("tests/corpus_known_differences.txt");
|
||||
std::fs::read_to_string(list)
|
||||
.expect("tests/corpus_known_differences.txt")
|
||||
.lines()
|
||||
.filter(|l| !l.trim().is_empty() && !l.starts_with('#'))
|
||||
.map(|l| {
|
||||
let (path, reason) = l.split_once('\t').unwrap_or((l, ""));
|
||||
(path.trim().to_string(), reason.trim().to_string())
|
||||
})
|
||||
.collect()
|
||||
}
|
||||
|
||||
#[test]
|
||||
fn corpus_matches_netcdf_c() {
|
||||
let Ok(root) = std::env::var("CLAWHDF5_NETCDF_CORPUS") else {
|
||||
eprintln!("SKIP: set CLAWHDF5_NETCDF_CORPUS to a corpus directory");
|
||||
return;
|
||||
};
|
||||
// A relative path is from the workspace root (cargo runs the test in
|
||||
// the crate's directory).
|
||||
let root = Path::new(env!("CARGO_MANIFEST_DIR"))
|
||||
.join("../..")
|
||||
.join(root);
|
||||
let root = std::fs::canonicalize(&root).unwrap_or(root);
|
||||
let files = corpus_files(&root);
|
||||
assert!(!files.is_empty(), "no files under {}", root.display());
|
||||
// `CLAWHDF5_NETCDF_VIEW`: the output of an earlier run of
|
||||
// `tests/netcdf_c_view.py` over the same files, which takes a few
|
||||
// minutes over the conformance corpus.
|
||||
let views = match std::env::var("CLAWHDF5_NETCDF_VIEW") {
|
||||
Ok(saved) => parse_views(&std::fs::read_to_string(saved).expect("CLAWHDF5_NETCDF_VIEW")),
|
||||
Err(_) => netcdf_c_views(&files),
|
||||
};
|
||||
let known = known_differences();
|
||||
|
||||
let (mut opened, mut matched) = (0, 0);
|
||||
let mut explained = Vec::new();
|
||||
let mut unexplained = Vec::new();
|
||||
let mut stale = Vec::new();
|
||||
for path in &files {
|
||||
let Some(Some(want)) = views.get(path) else {
|
||||
continue;
|
||||
};
|
||||
opened += 1;
|
||||
let rel = path
|
||||
.strip_prefix(&root)
|
||||
.unwrap_or(path)
|
||||
.to_string_lossy()
|
||||
.into_owned();
|
||||
let diffs = differences(path, want);
|
||||
match (diffs.is_empty(), known.get(&rel)) {
|
||||
(true, None) => matched += 1,
|
||||
(true, Some(_)) => stale.push(rel),
|
||||
(false, Some(reason)) => explained.push((rel, reason.clone(), diffs)),
|
||||
(false, None) => unexplained.push((rel, diffs)),
|
||||
}
|
||||
}
|
||||
eprintln!(
|
||||
"{} files; netCDF-C opens {opened}; {matched} match; {} differ as explained; \
|
||||
{} differ unexplained; {} listed but match; {} variables relabelled \
|
||||
(floats of other than 4 or 8 bytes); {} variables' values not compared \
|
||||
(filter not in this build)",
|
||||
files.len(),
|
||||
explained.len(),
|
||||
unexplained.len(),
|
||||
stale.len(),
|
||||
RELABELLED.load(Ordering::Relaxed),
|
||||
FILTER_SKIPPED.load(Ordering::Relaxed),
|
||||
);
|
||||
for (rel, reason, diffs) in &explained {
|
||||
eprintln!("explained: {rel} ({reason}): {} differences", diffs.len());
|
||||
}
|
||||
for (rel, diffs) in &unexplained {
|
||||
eprintln!("DIFFERS: {rel}");
|
||||
for d in diffs.iter().take(20) {
|
||||
eprintln!(" {d}");
|
||||
}
|
||||
}
|
||||
assert!(
|
||||
unexplained.is_empty(),
|
||||
"{} files differ from netCDF-C unexplained",
|
||||
unexplained.len()
|
||||
);
|
||||
assert!(
|
||||
stale.is_empty(),
|
||||
"listed in corpus_known_differences.txt but match: {stale:?}"
|
||||
);
|
||||
}
|
||||
@@ -2,6 +2,8 @@
|
||||
//!
|
||||
//! Tests are skipped if python3 or netCDF4/xarray Python packages are not available.
|
||||
|
||||
mod common;
|
||||
|
||||
use std::process::Command;
|
||||
|
||||
use clawhdf5_netcdf4::{AttrValue, NcType, NetCDF4File};
|
||||
@@ -842,3 +844,267 @@ ds.to_netcdf({path:?}, engine={engine:?}, unlimited_dims=["time"])
|
||||
assert_same_view(&path);
|
||||
}
|
||||
}
|
||||
|
||||
// ===========================================================================
|
||||
// Compared with netCDF-C itself (tests/netcdf_c_view.py): groups,
|
||||
// dimensions, variables, types and values, in netCDF-C's order
|
||||
// ===========================================================================
|
||||
|
||||
/// The dimensions of the variable `name` (a path) of `file`.
|
||||
fn dim_names(file: &NetCDF4File, name: &str) -> Vec<String> {
|
||||
file.variable(name)
|
||||
.unwrap()
|
||||
.dimensions()
|
||||
.iter()
|
||||
.map(|d| d.name.clone())
|
||||
.collect()
|
||||
}
|
||||
|
||||
/// An h5py file without dimension scales: netCDF-C's phony dimensions,
|
||||
/// numbered file-wide (subgroups before their parent's variables, each
|
||||
/// group's datasets in name order, as h5py does not track creation order),
|
||||
/// shared by length within a group — but not between two axes of one
|
||||
/// variable, nor between a fixed and an unlimited axis — with a length of 0
|
||||
/// always unlimited and never shared with a fixed axis, and the real
|
||||
/// dimension of a scale taken by length too.
|
||||
#[test]
|
||||
fn phony_dimensions_match_netcdf_c() {
|
||||
skip_if_no_netcdf4!();
|
||||
let dir = tempfile::tempdir().unwrap();
|
||||
let path = dir.path().join("phony.h5");
|
||||
run_python(&format!(
|
||||
r#"
|
||||
import h5py
|
||||
import numpy as np
|
||||
with h5py.File({path:?}, "w") as f:
|
||||
f["zz"] = np.arange(12.0).reshape(2, 2, 3)
|
||||
f["aa"] = np.arange(6, dtype="i4").reshape(3, 2)
|
||||
f.create_dataset("un", data=np.ones((2, 3), "f4"), maxshape=(None, 3))
|
||||
f.create_dataset("un2", data=np.ones(2, "f4"), maxshape=(None,))
|
||||
f["zero"] = np.zeros((0,))
|
||||
f.create_dataset("zero_un", (0,), "f4", maxshape=(None,))
|
||||
f["zero2"] = np.zeros((0, 2))
|
||||
f["s"] = 1.5
|
||||
g = f.create_group("g")
|
||||
g["x"] = np.arange(5, dtype="i2")
|
||||
g["y"] = np.arange(2, dtype="u1")
|
||||
g.create_group("h")["q"] = np.arange(7.0)
|
||||
f.create_group("b")["w"] = np.arange(18, dtype="i8").reshape(2, 9)
|
||||
f["sc"] = np.arange(6.0)
|
||||
f["sc"].make_scale("sc")
|
||||
f["second_only"] = np.zeros((2, 6))
|
||||
f["second_only"].dims[1].attach_scale(f["sc"])
|
||||
"#,
|
||||
path = path.display().to_string()
|
||||
));
|
||||
common::assert_matches_netcdf_c(&path);
|
||||
|
||||
let file = NetCDF4File::open(&path).unwrap();
|
||||
// `sc` is dimension 0; /b gets 1 and 2, /g/h 3, /g 4 and 5, / from 6.
|
||||
assert_eq!(dim_names(&file, "b/w"), ["phony_dim_1", "phony_dim_2"]);
|
||||
assert_eq!(dim_names(&file, "g/h/q"), ["phony_dim_3"]);
|
||||
let h = file.group("g/h").unwrap();
|
||||
assert_eq!(h.variable_names().unwrap(), ["q"]);
|
||||
assert_eq!(h.dimensions().unwrap()[0].name, "phony_dim_3");
|
||||
assert_eq!(dim_names(&file, "aa"), ["phony_dim_6", "phony_dim_7"]);
|
||||
assert_eq!(
|
||||
dim_names(&file, "zz"),
|
||||
["phony_dim_7", "phony_dim_11", "phony_dim_6"]
|
||||
);
|
||||
assert_eq!(dim_names(&file, "second_only"), ["phony_dim_7", "sc"]);
|
||||
assert_eq!(dim_names(&file, "un"), ["phony_dim_8", "phony_dim_6"]);
|
||||
assert_eq!(dim_names(&file, "un2"), ["phony_dim_8"]);
|
||||
assert_eq!(dim_names(&file, "zero"), ["phony_dim_9"]);
|
||||
assert_eq!(dim_names(&file, "zero_un"), ["phony_dim_9"]);
|
||||
assert_eq!(dim_names(&file, "zero2"), ["phony_dim_10", "phony_dim_7"]);
|
||||
let root: Vec<(String, u64, bool)> = file
|
||||
.dimensions()
|
||||
.unwrap()
|
||||
.into_iter()
|
||||
.map(|d| (d.name, d.size, d.is_unlimited))
|
||||
.collect();
|
||||
assert_eq!(root[0], ("sc".to_string(), 6, false));
|
||||
assert!(root.contains(&("phony_dim_8".to_string(), 2, true)));
|
||||
assert!(root.contains(&("phony_dim_9".to_string(), 0, true)));
|
||||
assert!(root.contains(&("phony_dim_10".to_string(), 0, true)));
|
||||
assert_eq!(
|
||||
file.variable_names().unwrap(),
|
||||
[
|
||||
"aa",
|
||||
"s",
|
||||
"sc",
|
||||
"second_only",
|
||||
"un",
|
||||
"un2",
|
||||
"zero",
|
||||
"zero2",
|
||||
"zero_un",
|
||||
"zz"
|
||||
]
|
||||
);
|
||||
}
|
||||
|
||||
/// Datasets of types netCDF-C cannot represent are not variables:
|
||||
/// references, bit fields, array types, a compound with a reference member
|
||||
/// or a half-float member, a compound nesting a compound not seen before;
|
||||
/// enum, compound, variable-length and opaque types are variables of those
|
||||
/// classes. netCDF-C also remembers a type it failed to read, so the second
|
||||
/// dataset of a compound with a reference member is a variable, and a
|
||||
/// nested compound is accepted once a dataset of the inner type was read.
|
||||
#[test]
|
||||
fn types_netcdf_c_skips_are_not_variables() {
|
||||
skip_if_no_netcdf4!();
|
||||
let dir = tempfile::tempdir().unwrap();
|
||||
let path = dir.path().join("types.h5");
|
||||
run_python(&format!(
|
||||
r#"
|
||||
import h5py
|
||||
import numpy as np
|
||||
inner = np.dtype([("x", "i2"), ("y", "f4")])
|
||||
with h5py.File({path:?}, "w") as f:
|
||||
f["i4"] = np.arange(3, dtype="i4")
|
||||
f["f2"] = np.arange(3, dtype="f2")
|
||||
f["s1"] = np.array([b"a", b"b"], dtype="S1")
|
||||
f["s5"] = np.array([b"abc", b"b"], dtype="S5")
|
||||
f["vs"] = np.array(["x", "yy"], dtype=h5py.string_dtype())
|
||||
f["bool"] = np.array([True, False])
|
||||
f["cmp"] = np.array([(1, 2.0)], dtype=[("a", "i4"), ("b", "f8")])
|
||||
f["en"] = np.array([0, 1], dtype=h5py.enum_dtype({{"A": 0, "B": 1}}, basetype="i1"))
|
||||
d = f.create_dataset("vl", (2,), dtype=h5py.vlen_dtype("i4"))
|
||||
d[0] = [1, 2]
|
||||
d[1] = [3]
|
||||
f["op"] = np.array([b"ab", b"cd"], dtype="V2")
|
||||
f.create_dataset("ref", (1,), dtype=h5py.ref_dtype)[0] = f["i4"].ref
|
||||
f["cref1"] = np.array([(1, f["i4"].ref)], dtype=[("a", "i4"), ("r", h5py.ref_dtype)])
|
||||
f["cref2"] = np.array([(2, f["i4"].ref)], dtype=[("a", "i4"), ("r", h5py.ref_dtype)])
|
||||
f["cmp_f2"] = np.zeros(2, dtype=[("a", "f2")])
|
||||
f["in1"] = np.zeros(2, dtype=inner)
|
||||
f["nested"] = np.zeros(2, dtype=[("a", "i4"), ("in", inner)])
|
||||
f["a_nested"] = np.zeros(2, dtype=[("b", "i4"), ("in", np.dtype([("p", "i1")]))])
|
||||
sid = h5py.h5s.create_simple((2,))
|
||||
h5py.h5d.create(f.id, b"bitf", h5py.h5t.STD_B8LE.copy(), sid)
|
||||
h5py.h5d.create(f.id, b"arr", h5py.h5t.array_create(h5py.h5t.NATIVE_INT32, (3,)), sid)
|
||||
"#,
|
||||
path = path.display().to_string()
|
||||
));
|
||||
common::assert_matches_netcdf_c(&path);
|
||||
|
||||
let file = NetCDF4File::open(&path).unwrap();
|
||||
assert_eq!(
|
||||
file.variable_names().unwrap(),
|
||||
[
|
||||
"bool", "cmp", "cref2", "en", "f2", "i4", "in1", "nested", "op", "s1", "s5", "vl", "vs"
|
||||
]
|
||||
);
|
||||
let nc_type = |name: &str| file.variable(name).unwrap().nc_type().unwrap();
|
||||
assert_eq!(nc_type("bool"), NcType::Enum);
|
||||
assert_eq!(nc_type("cmp"), NcType::Compound);
|
||||
assert_eq!(nc_type("vl"), NcType::VLen);
|
||||
assert_eq!(nc_type("op"), NcType::Opaque);
|
||||
assert_eq!(nc_type("s1"), NcType::Char);
|
||||
assert_eq!(nc_type("s5"), NcType::String);
|
||||
// netCDF-C 4.9.3 on libhdf5 1.14.6 says NC_STRING (deliberate
|
||||
// difference, see the README).
|
||||
assert_eq!(nc_type("f2"), NcType::Float);
|
||||
assert_eq!(
|
||||
file.variable("f2").unwrap().read_raw_f32().unwrap(),
|
||||
[0.0, 1.0, 2.0]
|
||||
);
|
||||
assert!(matches!(
|
||||
file.variable("ref"),
|
||||
Err(clawhdf5_netcdf4::Error::VariableNotFound(_))
|
||||
));
|
||||
}
|
||||
|
||||
/// The order of groups and variables: creation order where the group
|
||||
/// tracks it (every netCDF-4 file; also h5py with `track_order`), compact
|
||||
/// or dense (more than 8 links), else name order (h5py by default).
|
||||
#[test]
|
||||
fn group_and_variable_order_match_netcdf_c() {
|
||||
skip_if_no_netcdf4!();
|
||||
let dir = tempfile::tempdir().unwrap();
|
||||
let nc = dir.path().join("order.nc");
|
||||
let h5 = dir.path().join("order.h5");
|
||||
run_python(&format!(
|
||||
r#"
|
||||
import h5py
|
||||
import netCDF4 as nc
|
||||
import numpy as np
|
||||
names = ["zeta", "alpha", "mid", "beta", "omega", "gamma", "k", "a", "zz", "c"]
|
||||
with nc.Dataset({nc:?}, "w") as f:
|
||||
f.createDimension("x", 2)
|
||||
for i, n in enumerate(names):
|
||||
f.createVariable(n, "i4", ("x",))[:] = [i, i + 1]
|
||||
for n in ["gz", "ga", "gm"]:
|
||||
f.createGroup(n).createVariable("v", "f8", ("x",))[:] = [1, 2]
|
||||
small = f.createGroup("small")
|
||||
for n in ["q", "b", "p"]:
|
||||
small.createVariable(n, "i2", ("x",))[:] = [3, 4]
|
||||
with h5py.File({h5:?}, "w") as f:
|
||||
for i, n in enumerate(names):
|
||||
f[n] = np.arange(i + 1)
|
||||
t = f.create_group("tracked", track_order=True)
|
||||
for i, n in enumerate(names):
|
||||
t[n] = np.arange(3, dtype="i1")
|
||||
for n in ["gz", "ga"]:
|
||||
f.create_group(n)["v"] = np.arange(4.0)
|
||||
"#,
|
||||
nc = nc.display().to_string(),
|
||||
h5 = h5.display().to_string()
|
||||
));
|
||||
common::assert_matches_netcdf_c(&nc);
|
||||
common::assert_matches_netcdf_c(&h5);
|
||||
|
||||
let file = NetCDF4File::open(&nc).unwrap();
|
||||
assert_eq!(
|
||||
file.variable_names().unwrap(),
|
||||
[
|
||||
"zeta", "alpha", "mid", "beta", "omega", "gamma", "k", "a", "zz", "c"
|
||||
]
|
||||
);
|
||||
assert_eq!(file.group_names().unwrap(), ["gz", "ga", "gm", "small"]);
|
||||
let file = NetCDF4File::open(&h5).unwrap();
|
||||
assert_eq!(file.group_names().unwrap(), ["ga", "gz", "tracked"]);
|
||||
assert_eq!(
|
||||
file.variable_names().unwrap(),
|
||||
[
|
||||
"a", "alpha", "beta", "c", "gamma", "k", "mid", "omega", "zeta", "zz"
|
||||
]
|
||||
);
|
||||
assert_eq!(
|
||||
file.group("tracked").unwrap().variable_names().unwrap(),
|
||||
[
|
||||
"zeta", "alpha", "mid", "beta", "omega", "gamma", "k", "a", "zz", "c"
|
||||
]
|
||||
);
|
||||
}
|
||||
|
||||
/// The files of the earlier tests, compared with netCDF-C itself too:
|
||||
/// dimension scales of h5py, netCDF4-python files with groups, unlimited
|
||||
/// dimensions and non-coordinate variables named like a dimension.
|
||||
#[test]
|
||||
fn netcdf4_python_files_match_netcdf_c() {
|
||||
skip_if_no_netcdf4!();
|
||||
let dir = tempfile::tempdir().unwrap();
|
||||
let path = dir.path().join("mixed.nc");
|
||||
run_python(&format!(
|
||||
r#"
|
||||
import netCDF4 as nc
|
||||
import numpy as np
|
||||
with nc.Dataset({path:?}, "w") as f:
|
||||
f.createDimension("time", None)
|
||||
f.createDimension("p", 2)
|
||||
f.createDimension("q", 2)
|
||||
f.createVariable("a", "i4", ("time",))[0:2] = [1, 2]
|
||||
f.createVariable("b", "f4", ("time", "q"))[0:5, :] = np.arange(10).reshape(5, 2)
|
||||
f.createVariable("q", "f4", ("q",))[:] = [0, 1]
|
||||
f.createVariable("p", "f4", ("q", "p"))[:] = np.array([[0, 1], [2, 3]])
|
||||
g = f.createGroup("g")
|
||||
g.createDimension("r", 3)
|
||||
g.createVariable("w", "i4", ("r", "time"))[:, 0:1] = np.ones((3, 1))
|
||||
g.createGroup("h").createVariable("z", "i8", ("p", "r"))[:] = np.arange(6).reshape(2, 3)
|
||||
"#,
|
||||
path = path.display().to_string()
|
||||
));
|
||||
common::assert_matches_netcdf_c(&path);
|
||||
}
|
||||
|
||||
@@ -776,9 +776,12 @@ fn test_pure_dimensions_hidden_and_non_coord_names() {
|
||||
.with_shape(&[2]);
|
||||
let file = NetCDF4File::from_bytes(b.finish().unwrap()).unwrap();
|
||||
|
||||
// `x`, and the phony dimension netCDF-C gives the 3 values of
|
||||
// `_nc4_non_coord_x` (no dimension scale attached).
|
||||
let dims = file.dimensions().unwrap();
|
||||
assert_eq!(dims.len(), 1);
|
||||
assert_eq!(dims[0].name, "x");
|
||||
let names: Vec<&str> = dims.iter().map(|d| d.name.as_str()).collect();
|
||||
assert_eq!(names, ["x", "phony_dim_1"]);
|
||||
assert_eq!(dims[1].size, 3);
|
||||
let mut names = file.variable_names().unwrap();
|
||||
names.sort();
|
||||
assert_eq!(names, ["v", "x"]);
|
||||
@@ -786,7 +789,8 @@ fn test_pure_dimensions_hidden_and_non_coord_names() {
|
||||
assert_eq!(x.name(), "x");
|
||||
assert_eq!(x.read_raw_f64().unwrap(), [1.0, 2.0, 3.0]);
|
||||
assert!(!x.is_coordinate());
|
||||
// No DIMENSION_LIST: `v` gets `x` by size, as before.
|
||||
// No DIMENSION_LIST: `v` gets the group's first dimension of its length
|
||||
// (netCDF-C's phony rule, which also takes real dimensions).
|
||||
assert_eq!(file.variable("v").unwrap().dimensions()[0].name, "x");
|
||||
}
|
||||
|
||||
|
||||
@@ -0,0 +1,238 @@
|
||||
#!/usr/bin/env python3
|
||||
"""netcdf_c_view.py FILE...: print each file as netCDF-C sees it.
|
||||
|
||||
The metadata comes from netCDF-C itself (the libnetcdf that netCDF4-python
|
||||
bundles, called through ctypes), not from netCDF4-python's objects, which
|
||||
leave out variables of types netCDF-C supports but netCDF4-python does not
|
||||
(opaque, compounds of vlen strings, ...). Values come from netCDF4-python.
|
||||
Each file is read in its own process under a timeout, so a file that crashes
|
||||
or hangs libnetcdf only costs that file.
|
||||
|
||||
Output, per file, fields separated by tabs:
|
||||
|
||||
FILE <path>
|
||||
ERROR <message> netCDF-C cannot open it; nothing else
|
||||
G <group> every group, pre-order, children in
|
||||
netCDF-C's order ("/" is the root)
|
||||
D <group> <name> <length> <0|1> its dimensions in dimension-id order
|
||||
(1: unlimited)
|
||||
V <group> <name> <type> <dims> <shape>
|
||||
its variables in netCDF-C's order;
|
||||
<dims> and <shape> comma-separated,
|
||||
"-" when there are none; <type> as
|
||||
clawhdf5_netcdf4::NcType prints it
|
||||
X <group> <name> <values> the values of a numeric variable of
|
||||
at most MAX_VALUES elements, as
|
||||
space-separated Python float reprs
|
||||
("-" when there are none)
|
||||
END
|
||||
|
||||
Used by tests/corpus_vs_netcdf_c.rs (CLAWHDF5_NETCDF_CORPUS).
|
||||
"""
|
||||
import concurrent.futures
|
||||
import ctypes
|
||||
import glob
|
||||
import os
|
||||
import subprocess
|
||||
import sys
|
||||
|
||||
MAX_VALUES = 5000
|
||||
TIMEOUT = 60
|
||||
MEMORY = 4 << 30 # address space of each file's process
|
||||
|
||||
ATOMIC = {
|
||||
1: "NC_BYTE", 2: "NC_CHAR", 3: "NC_SHORT", 4: "NC_INT", 5: "NC_FLOAT",
|
||||
6: "NC_DOUBLE", 7: "NC_UBYTE", 8: "NC_USHORT", 9: "NC_UINT",
|
||||
10: "NC_INT64", 11: "NC_UINT64", 12: "NC_STRING",
|
||||
}
|
||||
USER_CLASS = {13: "NC_VLEN", 14: "NC_OPAQUE", 15: "NC_ENUM", 16: "NC_COMPOUND"}
|
||||
NUMERIC = {"NC_BYTE", "NC_SHORT", "NC_INT", "NC_FLOAT", "NC_DOUBLE",
|
||||
"NC_UBYTE", "NC_USHORT", "NC_UINT", "NC_INT64", "NC_UINT64"}
|
||||
NAME = 257 # NC_MAX_NAME + 1
|
||||
MAXDIMS = 1024
|
||||
|
||||
|
||||
def libnetcdf():
|
||||
"""The libnetcdf netCDF4-python is linked with (same process, same copy)."""
|
||||
import netCDF4
|
||||
site = os.path.dirname(os.path.dirname(netCDF4.__file__))
|
||||
found = glob.glob(os.path.join(site, "netcdf4.libs", "libnetcdf*.so*")) + \
|
||||
glob.glob(os.path.join(site, "netCDF4.libs", "libnetcdf*.so*"))
|
||||
if found:
|
||||
return ctypes.CDLL(found[0])
|
||||
return ctypes.CDLL("libnetcdf.so")
|
||||
|
||||
|
||||
def view(path, out):
|
||||
nc = libnetcdf()
|
||||
ncid = ctypes.c_int()
|
||||
rc = nc.nc_open(path.encode(), 0, ctypes.byref(ncid)) # NC_NOWRITE
|
||||
if rc != 0:
|
||||
nc.nc_strerror.restype = ctypes.c_char_p
|
||||
out.append("ERROR\t" + nc.nc_strerror(rc).decode(errors="replace"))
|
||||
return
|
||||
numeric = [] # (group path, variable name)
|
||||
try:
|
||||
walk(nc, ncid.value, "/", out, numeric)
|
||||
finally:
|
||||
nc.nc_close(ncid)
|
||||
values(path, numeric, out)
|
||||
|
||||
|
||||
def check(rc, what):
|
||||
if rc != 0:
|
||||
raise RuntimeError(f"{what} failed: {rc}")
|
||||
|
||||
|
||||
def name_of(fn, *args):
|
||||
buf = ctypes.create_string_buffer(NAME)
|
||||
check(fn(*args, buf), fn.__name__)
|
||||
return buf.value.decode(errors="replace")
|
||||
|
||||
|
||||
def walk(nc, gid, path, out, numeric):
|
||||
out.append(f"G\t{path}")
|
||||
n = ctypes.c_int()
|
||||
ids = (ctypes.c_int * MAXDIMS)()
|
||||
check(nc.nc_inq_dimids(gid, ctypes.byref(n), ids, 0), "nc_inq_dimids")
|
||||
for dimid in ids[: n.value]:
|
||||
length = ctypes.c_size_t()
|
||||
dname = ctypes.create_string_buffer(NAME)
|
||||
check(nc.nc_inq_dim(gid, dimid, dname, ctypes.byref(length)), "nc_inq_dim")
|
||||
out.append(f"D\t{path}\t{dname.value.decode(errors='replace')}\t{length.value}\t"
|
||||
f"{int(is_unlimited(nc, gid, dimid))}")
|
||||
nvars = ctypes.c_int()
|
||||
varids = (ctypes.c_int * 65536)()
|
||||
check(nc.nc_inq_varids(gid, ctypes.byref(nvars), varids), "nc_inq_varids")
|
||||
for varid in varids[: nvars.value]:
|
||||
vname = ctypes.create_string_buffer(NAME)
|
||||
xtype = ctypes.c_int()
|
||||
ndims = ctypes.c_int()
|
||||
dimids = (ctypes.c_int * MAXDIMS)()
|
||||
natts = ctypes.c_int()
|
||||
check(nc.nc_inq_var(gid, varid, vname, ctypes.byref(xtype), ctypes.byref(ndims),
|
||||
dimids, ctypes.byref(natts)), "nc_inq_var")
|
||||
names, shape = [], []
|
||||
for dimid in dimids[: ndims.value]:
|
||||
dname = ctypes.create_string_buffer(NAME)
|
||||
length = ctypes.c_size_t()
|
||||
if nc.nc_inq_dim(gid, dimid, dname, ctypes.byref(length)) != 0:
|
||||
names.append("?")
|
||||
shape.append("?")
|
||||
continue
|
||||
names.append(dname.value.decode(errors="replace"))
|
||||
shape.append(str(length.value))
|
||||
tname = type_name(nc, gid, xtype.value)
|
||||
vn = vname.value.decode(errors="replace")
|
||||
out.append(f"V\t{path}\t{vn}\t{tname}\t{','.join(names) or '-'}\t{','.join(shape) or '-'}")
|
||||
if tname in NUMERIC and "?" not in shape:
|
||||
count = 1
|
||||
for s in shape:
|
||||
count *= int(s)
|
||||
if count <= MAX_VALUES:
|
||||
numeric.append((path, vn))
|
||||
ngrps = ctypes.c_int()
|
||||
grps = (ctypes.c_int * 65536)()
|
||||
check(nc.nc_inq_grps(gid, ctypes.byref(ngrps), grps), "nc_inq_grps")
|
||||
for child in grps[: ngrps.value]:
|
||||
cname = ctypes.create_string_buffer(NAME)
|
||||
check(nc.nc_inq_grpname(child, cname), "nc_inq_grpname")
|
||||
cpath = path.rstrip("/") + "/" + cname.value.decode(errors="replace")
|
||||
walk(nc, child, cpath, out, numeric)
|
||||
|
||||
|
||||
def is_unlimited(nc, gid, dimid):
|
||||
n = ctypes.c_int()
|
||||
ids = (ctypes.c_int * MAXDIMS)()
|
||||
# Unlimited dimensions visible from this group include its parents'.
|
||||
if nc.nc_inq_unlimdims(gid, ctypes.byref(n), ids) != 0:
|
||||
return False
|
||||
return dimid in ids[: n.value]
|
||||
|
||||
|
||||
def type_name(nc, gid, xtype):
|
||||
if xtype in ATOMIC:
|
||||
return ATOMIC[xtype]
|
||||
size = ctypes.c_size_t()
|
||||
base = ctypes.c_int()
|
||||
nfields = ctypes.c_size_t()
|
||||
klass = ctypes.c_int()
|
||||
tname = ctypes.create_string_buffer(NAME)
|
||||
if nc.nc_inq_user_type(gid, xtype, tname, ctypes.byref(size), ctypes.byref(base),
|
||||
ctypes.byref(nfields), ctypes.byref(klass)) != 0:
|
||||
return f"type{xtype}"
|
||||
return USER_CLASS.get(klass.value, f"class{klass.value}")
|
||||
|
||||
|
||||
def values(path, numeric, out):
|
||||
if not numeric:
|
||||
return
|
||||
import numpy as np
|
||||
import netCDF4
|
||||
try:
|
||||
ds = netCDF4.Dataset(path)
|
||||
except Exception: # noqa: BLE001 - netCDF4-python refuses some files netCDF-C opens
|
||||
return
|
||||
with ds:
|
||||
for gpath, name in numeric:
|
||||
try:
|
||||
group = ds if gpath == "/" else ds[gpath]
|
||||
var = group.variables[name]
|
||||
var.set_auto_maskandscale(False)
|
||||
# A whole-variable read through netCDF-C 4.9.3 lays out a
|
||||
# variable shorter than an unlimited dimension that is not its
|
||||
# first wrongly (written values first); reads of one index of
|
||||
# the leading axis are right.
|
||||
if var.ndim >= 2:
|
||||
data = np.stack([np.asarray(var[i]) for i in range(var.shape[0])]) \
|
||||
if var.shape[0] else np.zeros(var.shape)
|
||||
else:
|
||||
data = np.asarray(var[...])
|
||||
flat = np.asarray(data, dtype=np.float64).ravel()
|
||||
except Exception: # noqa: BLE001
|
||||
continue
|
||||
vals = " ".join(repr(float(v)) for v in flat) or "-"
|
||||
out.append(f"X\t{gpath}\t{name}\t{vals}")
|
||||
|
||||
|
||||
def limit_memory():
|
||||
import resource
|
||||
resource.setrlimit(resource.RLIMIT_AS, (MEMORY, MEMORY))
|
||||
|
||||
|
||||
def one(path):
|
||||
"""Run view() for one file in a child process."""
|
||||
try:
|
||||
proc = subprocess.run([sys.executable, __file__, "--one", path],
|
||||
capture_output=True, timeout=TIMEOUT, text=True,
|
||||
preexec_fn=limit_memory)
|
||||
except subprocess.TimeoutExpired:
|
||||
return [f"FILE\t{path}", "ERROR\ttimeout", "END"]
|
||||
lines = proc.stdout.splitlines()
|
||||
if proc.returncode != 0 or not lines or lines[-1] != "END":
|
||||
err = (proc.stderr.strip().splitlines() or [f"exit {proc.returncode}"])[-1]
|
||||
return [f"FILE\t{path}", f"ERROR\tchild failed: {err}", "END"]
|
||||
return lines
|
||||
|
||||
|
||||
def main(argv):
|
||||
if argv and argv[0] == "--one":
|
||||
out = [f"FILE\t{argv[1]}"]
|
||||
try:
|
||||
view(argv[1], out)
|
||||
except Exception as e: # noqa: BLE001
|
||||
out = [f"FILE\t{argv[1]}", f"ERROR\t{e}"]
|
||||
out.append("END")
|
||||
sys.stdout.write("\n".join(out) + "\n")
|
||||
return
|
||||
if argv and argv[0] == "--list":
|
||||
with open(argv[1]) as fh:
|
||||
argv = [line.rstrip("\n") for line in fh if line.strip()]
|
||||
jobs = int(os.environ.get("CLAWHDF5_NETCDF_JOBS", "4"))
|
||||
with concurrent.futures.ThreadPoolExecutor(jobs) as pool:
|
||||
for lines in pool.map(one, argv):
|
||||
sys.stdout.write("\n".join(lines) + "\n")
|
||||
|
||||
|
||||
if __name__ == "__main__":
|
||||
main(sys.argv[1:])
|
||||
Reference in New Issue
Block a user