Crate netcdf

Rust bindings for Unidata’s libnetcdf

This crate allows one to store and retrieve multi-dimensional arrays from a netCDF supported format, which can be a netCDF file, a subset of hdf5 files, or from a DAP url.

netCDF files are self-contained, they contain metadata about the data contained in them. See the CF Conventions for conventions used for climate and forecast models.

To explore the documentation, see the Functions section, in particular open(), create(), and append().

For more information see:

• The official introduction to netCDF
• The netCDF-c repository

Examples

How to read a variable from a file:

// Open the file `simple_xy.nc`:
let file = netcdf::open("simple_xy.nc")?;

// Get the variable in this file with the name "data"
let var = &file.variable("data").expect("Could not find variable 'data'");

// Read a single datapoint from a 1D variable as a numeric type
let data_i32 = var.get_value::<i32, _>(4)?;
let data_f32 : f32 = var.get_value(5)?;

// If your variable is multi-dimensional you need to use a
// type that supports `Selection`, such as a tuple or array
let data_i32 = var.get_value::<i32, _>([40, 0, 0])?;
let data_i32 = var.get_value::<i32, _>((40, 0, 0))?;

// You can use `values_arr()` to get all the data from the variable.
// This requires the `ndarray` feature
// Passing `..` will give you the entire slice
let data = var.get::<i32, _>(..)?;

// A subset can also be selected, the following will extract the slice at
// `(40, 0, 0)` and get a dataset of size `100, 100` from this
let data = var.get::<i32, _>(([40, 0 ,0], [1, 100, 100]))?;
let data = var.get::<i32, _>((40, ..100, ..100))?;

// You can read into an ndarray to reuse an allocation
let mut data = ndarray::Array::<f32, _>::zeros((100, 100));
var.get_into((0, .., ..), data.view_mut())?;

How to create a new file and write to it:

// Create a new file with default settings
let mut file = netcdf::create("crabs.nc")?;

// We must create a dimension which corresponds to our data
file.add_dimension("ncrabs", 10)?;
// These dimensions can also be unlimited and will be resized when writing
file.add_unlimited_dimension("time")?;

// A variable can now be declared, and must be created from the dimension names.
let mut var = file.add_variable::<i32>(
            "crab_coolness_level",
            &["time", "ncrabs"],
)?;
// Metadata can be added to the variable, but will not be used when
// writing or reading data
var.put_attribute("units", "Kelvin")?;
var.put_attribute("add_offset", 273.15_f32)?;

// Data can then be created and added to the variable
let data : Vec<i32> = vec![42; 10];
var.put_values(&data, (0, ..))?;

// Values can be added along the unlimited dimension, which
// resizes along the `time` axis
var.put_values(&data, (11, ..))?;

// Using the ndarray feature you can also use
let values = ndarray::Array::from_shape_fn((5, 10), |(j, i)| (j * 10 + i) as f32);
var.put((11.., ..), values.view())?;

Modules

• types
  Contains functions and enums describing variable types

Structs

• Attribute
  Extra properties of a variable or a group can be represented with attributes. Primarily added with add_attribute on the variable and group
• Dimension
  Represents a netcdf dimension
• DimensionIdentifier
  Unique identifier for a dimension in a file. Used when names can not be used directly, for example when dealing with nested groups
• File
  Read only accessible file
• FileMemhas-mmap
  The memory mapped file is kept in this structure to extend the lifetime of the buffer.
• FileMut
  Mutable access to file.
• Group
  Main component of the netcdf format. Holds all variables, attributes, and dimensions. A group can always see the parents items, but a parent can not access a childs items.
• GroupMut
  Mutable access to a group.
• Options
  Options for opening, creating, and appending files
• Variable
  This struct defines a netCDF variable.
• VariableMut
  Mutable access to a variable.

Enums

• AttributeValue
  Holds the attribute value which can be inserted and returned from the file
• Endianness
  Enum for variables endianness
• Error
  Various error types that can occur in this crate
• Extent
  An extent of a dimension
• Extents
  A selector for putting and getting data along a dataset

Traits

• NcPutGet
  This trait allow an implicit cast when fetching a netCDF variable. These methods are not be called directly, but used through methods on Variable

Functions

• append
  Open a netCDF file in append mode
• append_with
  Open a netCDF file in append mode with the given options
• create
  Open a netcdf file in create mode
• create_with
  Open a netCDF file in create mode with the given options
• open
  Open a netCDF file in read mode
• open_memhas-mmap
  Open a netCDF file from a buffer
• open_with
  Open a netCDF file in read mode with the given options

Type Aliases

• Result
  Result type used in this crate