# clawhdf5-netcdf4

Read NetCDF-4 files in pure Rust. NetCDF-4 files are HDF5 files with
conventions for dimensions, coordinate variables and attributes; this crate
reads them through the [`clawhdf5`](../clawhdf5/README.md) facade, with no
libnetcdf or libhdf5. Read-only: NetCDF-3 (classic) files are not HDF5 and
are not supported.

Not on crates.io yet; depend on it from git:

```toml
[dependencies]
clawhdf5-netcdf4 = { git = "https://git.redclaw.dev/quantumclaw/clawhdf5" }
```

## Usage

```rust,no_run
use clawhdf5_netcdf4::NetCDF4File;

let nc = NetCDF4File::open("climate.nc")?;
for dim in nc.dimensions()? {
    println!("{}: {} (unlimited = {})", dim.name, dim.size, dim.is_unlimited);
}
let mut temp = nc.variable("temperature")?;
let dims: Vec<&str> = temp.dimensions().iter().map(|d| d.name.as_str()).collect();
println!("{:?} over {:?}", temp.shape()?, dims);
let cf = temp.cf_attributes()?;
println!("units: {:?}", cf.units);
// scale_factor/add_offset applied; _FillValue and missing_value become NaN
let values: Vec<f64> = temp.read_f64()?;
# Ok::<(), clawhdf5_netcdf4::Error>(())
```

## API

| Item | What |
|---|---|
| `NetCDF4File` | `open`, `from_bytes`, `dimensions`, `variables`, `variable_names`, `variable`, `global_attrs`, `group`, `group_names`, `nc_properties`, and `hdf5_file` for the underlying `clawhdf5::File` |
| `NetCDF4Group` | the same for a sub-group (`dimensions`, `variables`, `variable_names`, `attrs`, nested `group`) |
| `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` |
| `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) |
| `CfAttributes` | CF convention attributes: `units`, `long_name`, `standard_name`, `fill_value` (`_FillValue`), `missing_value`, `scale_factor`, `add_offset`, `valid_range`, `calendar`, `axis` |
| `NcType` | the NetCDF type of a variable |

Variables and dimensions follow netCDF-C:

- A variable's dimensions are the ones the file names: the ids in its
  `_Netcdf4Coordinates` attribute, else the dimension scales its
  `DIMENSION_LIST` references, found in its group or a parent group. Only
  an axis the file names no dimension for (an HDF5 file not written by a
  netCDF library) gets the first dimension of the group of the same size,
  else an anonymous `dim_<size>`.
- Dimension scales that are only dimensions are not variables; a dataset
  `_nc4_non_coord_<name>` is the variable `<name>`.
- A variable along an unlimited dimension has the dimension's length:
  `shape` is that length, and the reads return that many values, the
  records the variable has not written as its fill value (`_FillValue`,
  else netCDF's default for the type; NaN from `read_f64`).
  `stored_shape` is the HDF5 dataset's extent.

No cargo features. Tests compare against files written by netCDF4-python,
h5py dimension scales, h5netcdf and xarray, variable by variable with what
netCDF4-python reads (`tests/interop_tests.rs`; the CI job requires them
with `CLAWHDF5_REQUIRE_INTEROP=1`; the h5netcdf cases skip when h5netcdf is
not installed). What the HDF5 reader underneath cannot read is listed in
[`docs/known-issues.md`](../../docs/known-issues.md).

## License

MIT