Python interface — HARP 1.29 documentation

# Python interface

The Python interface consists of a Python package `'harp'` that provides a set of functions to `import` and `export` HARP products. The import can be used to read products using the HARP format or to read non-HARP products of a type supported by HARP. The Python interface depends on the `_cffi_backend` module, which is part of the C foreign function interface (cffi) package. This package must be installed in order to be able to use the Python interface. See the cffi documentation for details on how to install the cffi package.

Products are represented in Python by instances of `harp.Product`, which can be manipulated freely from within Python. A `harp.Product` instance contains a `harp.Variable` instance for each variable contained in the product. A `harp.Product` also contains special entries for the global attributes source_product and history (a `harp.Product` will thus not be able to contain variables with these names). Note that the Conventions, datetime_start and datetime_stop global attributes are not included in a `harp.Product` as these are automatically handled by the import/export functions of HARP.

Products can be `exported` as HARP compliant products in any of the file formats supported by the HARP C library (NetCDF/HDF4/HDF5). Such exported products can subsequently be processed further using the HARP command line tools. Products can also be `converted` to an `OrderedDict`. This can be convenient when there is a need to interface with existing code such as plotting libraries, or when the additional information provided by the `harp.Product` representation is not needed.

## Dimension types

The HARP C library defines several dimension types. Each dimension of a variable is associated with one of these dimension types. The number of dimension types should match the number of dimensions of the data array.

In Python, all dimension types are referred to by name, except the `independent` dimension type. Dimension type names are case-sensitive. The `independent` dimension type is special because variable dimensions associated with this dimension type need not be of the same length (in contrast to all other dimension types). The `independent` dimension type is represented in Python by `None`.

Each `harp.Variable` instance contains an attribute `dimension`, which is a list of dimension types. For each dimension of a variable, the `dimension` attribute indicates the dimension type it is associated with.

The dimension types supported by HARP are:

time

  Temporal dimension; this is the only appendable dimension.

vertical

  Vertical dimension, indicating height or depth.

spectral

  Spectral dimension, associated with wavelength, wavenumber, or frequency.

latitude

  Latitude dimension, only to be used for the latitude axis of a regular (latitude, longitude) grid.

longitude

  Longitude dimension, only to be used for the longitude axis of a regular (latitude, longitude) grid.

independent

  Independent dimension, used to index other quantities, such as the corner coordinates of ground pixel polygons.

## Data types

The HARP Python interface takes care of the conversion of product and variables from the C domain to the Python domain and back. This section describes the relation between types in the C domain and types in the Python domain.

The table below shows the type map that is used to convert the high level concepts product and variable.

C type | Python type
--- | ---
harp_product | harp.Product
harp_variable | harp.Variable

The table below shows the type map that is used when importing a product, i.e. when translating from the C domain to the Python domain.

Variable data arrays are converted to NumPy arrays. The NumPy data type used for the converted array is determined from the HARP data type of the variable according to the type map shown below. Zero-dimensional arrays of length 1 are converted to Python scalars using the `numpy.asscalar()` function. The resulting Python type is also shown in the type map.

Product and variable attributes, being scalars, are converted directly to Python scalars. The Python type is determined from the HARP data type according to the type map.

Zero-terminated C strings are always converted to instances of type `str` in Python. See section Unicode for details on unicode decoding in Python 3.

HARP data type | NumPy dtype | Python type | unicode decoding
--- | --- | --- | ---
harp_type_int8 | numpy.int8 | int |
harp_type_int16 | numpy.int16 | int |
harp_type_int32 | numpy.int32 | int |
harp_type_float | numpy.float32 | float |
harp_type_double | numpy.float64 | float |
harp_type_string | numpy.object_ | str | Python 3

The table below shows the type map that is used when exporting a product, i.e. when translating from the Python domain to the C domain.

NumPy object arrays (that is, NumPy arrays with data type `numpy.object_`) will be converted to arrays of zero-terminated C strings. The elements of a NumPy object array must be all `str` or all `bytes`. (Note that on Python 2, `bytes` is an alias of `str`.) NumPy arrays with data type `numpy.str_` or `numpy.bytes_` will be converted to arrays of zero-terminated C strings as well.

NumPy scalars with data type `numpy.object_`, `numpy.str_`, or `numpy.bytes_` are converted following the same rules as for NumPy arrays. NumPy scalars are treated as NumPy arrays of length 1 in this respect. Python scalars of type `str` or `bytes` will also be converted to zero-terminated C strings.

Unicode encoding is only performed for array elements or scalars of type `str` or `numpy.str_`, and only on Python 3. See section Unicode for details on unicode encoding in Python 3.

Any NumPy array, NumPy scalar, or Python scalar that cannot be converted according to the rules described above is assumed to be numeric. An attempt will be made to determine the minimal HARP data type that it, or its elements, can be safely cast to (according to the function `numpy.can_cast()` using the `'safe'` casting option). See the type map for details.

Python type | NumPy dtype | type test | array element type | array element type test | HARP data type | unicode encoding
--- | --- | --- | --- | --- | --- | ---
numpy.ndarray numpy.generic | numpy.object_ | numpy.issubdtype | str | isinstance | harp_type_string | Python 3
bytes | isinstance | harp_type_string | no
numpy.str_ | numpy.issubdtype |  |  | harp_type_string | Python 3
numpy.bytes_ | numpy.issubdtype |  |  | harp_type_string | no
numpy.int8 | numpy.can_cast |  |  | harp_type_int8 |
numpy.int16 | numpy.can_cast |  |  | harp_type_int16 |
numpy.int32 | numpy.can_cast |  |  | harp_type_int32 |
numpy.float32 | numpy.can_cast |  |  | harp_type_float32 |
numpy.float64 | numpy.can_cast |  |  | harp_type_float64 |
str |  | isinstance |  |  | harp_type_string | Python 3
bytes |  | isinstance |  |  | harp_type_string | no
any other type | numpy.int8 | numpy.can_cast |  |  | harp_type_int8 |
numpy.int16 | numpy.can_cast |  |  | harp_type_int16 |
numpy.int32 | numpy.can_cast |  |  | harp_type_int32 |
numpy.float32 | numpy.can_cast |  |  | harp_type_float32 |
numpy.float64 | numpy.can_cast |  |  | harp_type_float64 |

## Unicode

Zero-terminated C strings received from the HARP C library are always converted to instances of type `str` in Python. Type `str` is a byte string in Python 2, but a unicode string in Python 3.

In Python 2, no unicode encoding or decoding is performed by the HARP Python interface.

In Python 3, byte strings received from the HARP C library are decoded using a configurable encoding. Unicode strings (instances of type `str`) are encoded using the same encoding into byte strings, which are sent to the HARP C library. Byte strings (instances of type `bytes`) are passed through without encoding.

The encoding used can be configured by the user, see the `harp.set_encoding()` and `harp.get_encoding()` methods. The default encoding is `'ascii'`.

## Examples

    import harp
    import numpy

    # Create a product in Python and export it as a NetCDF file.
    product = harp.Product()
    harp.export_product(product, "empty.nc")

    # Add some variables to the product.
    product.foo = harp.Variable("foo")
    product.strings = harp.Variable(numpy.array(("foo", "bar", "baz")), ["time"])
    product.temperature = harp.Variable(numpy.ones((3, 5), dtype=numpy.float32),
                                        ["time", None])
    product.temperature.unit = "K"
    product.temperature.description = "temperature"

    # Pretty print information about the product.
    print(product)

    # Pretty print information about the variable 'temperature'.
    print(product.temperature)

    # Set valid minimum value of the variable 'temperature'. Note the use of item
    # access syntax instead of attribute access syntax.
    product["temperature"].valid_min = 0.0
    print(product.temperature)

    # Export the updated product as an HDF4 file.
    harp.export_product(product, "non-empty.hdf", file_format="hdf4")

    # Convert the product to an OrderedDict.
    dict_product = harp.to_dict(product)

    # Import an S5P L2 HCHO product.
    hcho_product = harp.import_product("S5P_NRTI_L2__HCHO___20080808T224727_20080808T234211_21635_01_021797_00000000T000000.nc",
                                       "solar_zenith_angle < 60 [degree]; latitude > 30 [degree_north]; latitude < 60 [degree_north]")

    # Pretty print information about the product.
    print(hcho_product)

    # Export the product as a HARP compliant data product.
    harp.export_product(hcho_product, "hcho.h5", file_format='hdf5', hdf5_compression=6)

## API reference

This section describes the types, functions, and exceptions defined by the HARP Python interface.

### Types

This section describes the types defined by the HARP Python interface.

class harp.Product(source_product='', history='')

  Python representation of a HARP product.

  A product consists of product attributes and variables. Any attribute of a Product instance of which the name does not start with an underscore is either a variable or a product attribute. Product attribute names are reserved and cannot be used for variables.

  The list of names reserved for product attributes is:

  source_product

    Name of the original product this product is derived from.

  history

    New-line separated list of invocations of HARP command line tools that have been performed on the product.

  Variables can be accessed by name using either the attribute access `'.'` syntax, or the item access `'[]'` syntax. For example:

      from __future__ import print_function

      # Alternative ways to access the variable 'HCHO_column_number_density'.
      density = product.HCHO_column_number_density
      density = product["HCHO_column_number_density"]

      # Iterate over all variables in the product. For imported  products, the
      # order of the variables is the same as the order in the source product.
      for name in product:
          print(product[name].unit)

  Product attributes can be accessed in the same way as variables, but are not included when iterating over the variables in a product. For example:

      from __future__ import print_function

      # Print product attributes.
      print(product.source_product)
      print(product.history)

  Parameters:

    - source_product (str) – Name of the original product this product is derived from.

    - history (str) – New-line separated list of invocations of HARP command line tools that have been performed on the product.

class harp.Variable(data, dimension=[], unit=None, valid_min=None, valid_max=None, description=None, enum=None)

  Python representation of a HARP variable.

  A variable consists of data (either a scalar or NumPy array), a list of dimension types that describe the dimensions of the data, and a number of optional attributes: physical unit, minimum valid value, maximum valid value, human-readable description, and enumeration name list.

  Parameters:

    - data – Value(s) associated with the variable; can be either a scalar or a NumPy array.

    - dimension (list) – List of strings indicating the dimensions the variable depends on.

    - unit (str) – Physical unit the values associated with the variable are expressed in.

    - valid_min – Minimum valid value; any value below this threshold is considered to be invalid.

    - valid_max – Maximum valid value; any value above this threshold is considered to be invalid.

    - description (str) – Humand-readble description of the variable.

    - enum (list) – List of strings with the names of each enumeration value.

### Functions

This section describes the functions defined by the HARP Python library.

harp.import_product(filename, operations='', options='', reduce_operations='', post_operations='')

  Import a product from a file.

  This will first try to import the file as an HDF4, HDF5, or netCDF file that complies to the HARP Data Format. If the file is not stored using the HARP format then it will try to import it using one of the available ingestion modules.

  If the filename argument is a list of filenames, a globbing (glob.glob()) pattern, or a list of globbing patterns then the harp.import_product() function will be called on each individual matching file. All imported products will then be appended into a single merged product and that merged product will be returned.

  If the filename argument is a .pth file, then the products referenced in the .pth file will be treated as a HARP Dataset and its merged content will be returned. Note that the source_product attribute of products in a HARP Dataset needs to be unique; if a dataset contains multiple products with the same source_product value then only the last product in the list will be kept.

  Parameters:

    - filename (str,list) – Filename, file pattern, .pth file, or list of filenames/patterns/.pths of the product(s) to import

    - operations (str) – Actions to apply as part of the import; should be specified as a semi-colon separated string of operations; in case a list of products is ingested these operations will be performed on each product individually before the data is merged.

    - options (str) – Ingestion module specific options; should be specified as a semi-colon separated string of key=value pairs; only used if a file is not in HARP format.

    - reduce_operations (str) – Actions to apply after each append; should be specified as a semi-colon separated string of operations; these operations will only be applied if the filename argument is a file pattern or a list of filenames/patterns; this advanced option allows for memory efficient application of time reduction operations (such as bin()) that would normally be provided as part of post_operations.

    - post_operations (str) – Actions to apply after the list of products is merged; should be specified as a semi-colon separated string of operations; these operations will only be applied if the filename argument is a file pattern or a list of filenames/patterns.

  Returns:

    Imported product.

  Return type:

    harp.Product

harp.import_product_metadata(filename, options='')

  Import specific metadata from a single file.

  This will try to extract the following information from a file.

    - datetime_start

    - datetime_stop

    - dimension lengths for time, latitude, longitude, vertical, and spectral

    - source_product

  If the file is not stored using the HARP format then it will try to import the metadata using one of the available ingestion modules.

  Parameters:

    - filename (str) – Filename of the product from which to extract the metadata

    - options (str) – Ingestion module specific options; should be specified as a semi-colon separated string of key=value pairs; only used if a file is not in HARP format.

  Returns:

    Imported metadata.

  Return type:

    collections.OrderedDict

harp.export_product(product, filename, file_format='netcdf', operations='', hdf5_compression=0)

  Export a HARP compliant product.

  Parameters:

    - product (str) – Product to export.

    - filename (str) – Filename of the exported product.

    - operations (str) – Actions to apply as part of the export; should be specified as a semi-colon separated string of operations.

    - file_format (str) – File format to use; one of ‘netcdf’, ‘hdf4’, or ‘hdf5’.

    - hdf5_compression – Compression level when exporting to hdf5 (0=disabled, 1=low, …, 9=high).

harp.concatenate(productlist)

  Combines all HARP products in the list into a single HARP output product.

  All non-time dependent variables from the input products are made time dependent before concatenating them.

  Trying to merge input products that do not have the same types of variables will result in an error.

  The ‘index’ variable will not be included in the concatenated product.

  The resulting product will not have a ‘source_product’ or ‘history’ global attribute set.

  Parameters:

    productlist (list) – List of harp.Product objects.

  Returns:

    Single product containing concatenated content.

  Return type:

    harp.Product

harp.execute_operations(productlist, operations='', post_operations='')

  Apply operations on the given list of products. ‘productlist’ can be either a single ‘harp.Product()’ instance or a list of ‘harp.Product()’ instances.

  If a list of products is provided then the products will be concatenated/merged after the ‘operations’ on each product has been performed.

  If a ‘post_operations’ parameter is provided then these operations will be applied to the concatenated/merged product before it is returned.

  Warning

  Note that this function will first export all products to the HARP C library and will import the final result back from the C library to the Python domain. This can have a considerable performance impact when products are large. You should therefore only use this function if the operation cannot be performed easily within the Python domain itself. Also, when using this function try to pass a ‘harp.Product()’ instance that contains the minimal set of variables that are needed to execute the operations.

  Parameters:

    - productlist (list) – List of harp.Product objects or single harp.Product object.

    - operations (str) – Actions to apply on the product(s); should be specified as a semi-colon separated string of operations; in case a list of products is provided these operations will be performed on each product individually before the data is merged.

    - post_operations (str) – Actions to apply after the list of products is merged; should be specified as a semi-colon separated string of operations; these operations will only be applied if the productlist parameter is a list of harp.Product objects.

  Returns:

    Single product containing concatenated content with operations being performed.

  Return type:

    harp.Product

harp.convert_unit(from_unit, to_unit, values)

  Perform unit conversion on the list of values. The list of values will be converted to an array of double values after which the HARP C library is used to convert the values from ‘from_unit’ to ‘to_unit’. The function will return a copy of the values with converted units.

  Parameters:

    - from_unit (str) – Existing unit of the data that should be converted (use udunits2 compliant units)

    - to_unit (str) – Unit to which the data should be converted (use udunits2 compliant units).

    - values – an array with values on which unit conversion needs to be applied

  Returns:

    Numpy array of unit converted values

harp.to_dict(product)

  Convert a `harp.Product` instance to an `OrderedDict`.

  The `OrderedDict` representation provides direct access to the data associated with each variable. All product attributes and all variable attributes except the unit attribute are discarded as part of the conversion.

  The unit attribute of a variable is represented by adding a scalar variable of type string with the name of the corresponding variable suffixed with `'_unit'` as name and the unit as value.

  The `OrderedDict` representation can be convenient when there is a need to interface with existing code such as plotting libraries, or when the additional information provided by the Product representation is not needed.

  Note that only `harp.Product` instances can be exported as a HARP product. The `OrderedDict` representation does not contain enough information.

  For example:

      from __future__ import print_function

      # Convert input product to an OrderedDict.
      product = to_dict(input_product)

      # Accessing the variable 'HCHO_column_number_density'.
      product["HCHO_column_number_density"]

      # Accessing the unit attribute of the variable
      # 'HCHO_column_number_density'.
      product["HCHO_column_number_density_unit"]

      # Iterate over all variables in the product. For imported products, the
      # order of the variables is the same as the order in the source product.
      for name, value in product.items():
          print name, value

  Parameters:

    product (harp.Product) – Product to convert.

  Returns:

    Converted product.

  Return type:

    collections.OrderedDict

harp.get_encoding()

  Return the encoding used to convert between unicode strings and C strings (only relevant when using Python 3).

  Returns:

    Encoding currently in use.

  Return type:

    str

harp.set_encoding(encoding)

  Set the encoding used to convert between unicode strings and C strings (only relevant when using Python 3).

  Parameters:

    encoding (str) – Encoding to use.

harp.version()

  Return the version of the HARP C library.

  Returns:

    HARP C library version.

  Return type:

    str

### Exceptions

This sections describes the exceptions defined by the HARP Python interface.

exception harp.Error(*args)

  Exception base class for all HARP Python interface errors.

  Parameters:

    args (tuple) – Tuple of arguments passed to the constructor; usually a single string containing an error message.

exception harp.CLibraryError(errno=None, strerror=None)

  Exception raised when an error occurs inside the HARP C library.

  Parameters:

    - errno (str) – error code; if None, the error code will be retrieved from the HARP C library.

    - strerror (str) – error message; if None, the error message will be retrieved from the HARP C library.

exception harp.UnsupportedTypeError(*args)

  Exception raised when unsupported types are encountered, either on the Python or on the C side of the interface.

  Parameters:

    args (tuple) – Tuple of arguments passed to the constructor; usually a single string containing an error message.

exception harp.UnsupportedDimensionError(*args)

  Exception raised when unsupported dimensions are encountered, either on the Python or on the C side of the interface.

  Parameters:

    args (tuple) – Tuple of arguments passed to the constructor; usually a single string containing an error message.

exception harp.NoDataError

  Exception raised when the product returned from an import contains no variables, or variables without data.