sofar 1.2.1__py3-none-any.whl

sofar/io.py

@@ -0,0 +1,427 @@
+"""Module for reading and writing Sofa files with sofar."""
+import contextlib
+import os
+import numpy as np
+from netCDF4 import Dataset, chartostring, stringtochar
+import warnings
+import pathlib
+from packaging.version import parse
+import sofar as sf
+from .utils import _verify_convention_and_version, _atleast_nd
+
+
+def read_sofa(filename, verify='auto', verbose=True):
+    """
+    Read SOFA file from disk and convert it to SOFA object.
+
+    Numeric data is returned as floats or numpy float arrays unless they have
+    missing data, in which case they are returned as numpy masked arrays.
+
+    If you want to read only parts of the data of a large sofa file use
+    :class:`SofaStream` instead.
+
+    Parameters
+    ----------
+    filename : str
+        The full path to the sofa data.
+    verify : bool, optional
+        Verify and update the SOFA object by calling :py:func:`~Sofa.verify`.
+        This helps to find potential errors in the default values and is thus
+        recommended. If reading a file does not work, try to call `Sofa` with
+        ``verify=False``. The default is ``'auto'`` defaults to ``True`` for
+        stable conventions with versions of 1.0 or higher and to ``False``
+        otherwise.
+    verbose : bool, optional
+        Print the names of detected custom variables and attributes. The
+        default is ``True``
+
+    Returns
+    -------
+    sofa : Sofa
+        Object containing the data from `filename`.
+
+    Notes
+    -----
+    1. Missing dimensions are appended when writing the SOFA object to disk.
+       E.g., if ``sofa.Data_IR`` is of shape (1, 2) it is written as an array
+       of shape (1, 2, 1) because the SOFA standard AES69 defines it as a
+       three dimensional array with the dimensions (`M: measurements`,
+       `R: receivers`, `N: samples`)
+    2. When reading data from a SOFA file, array data is always returned as
+       numpy arrays and singleton trailing dimensions are discarded (numpy
+       default). I.e., ``sofa.Data_IR`` will again be an array of shape (1, 2)
+       after writing and reading to and from disk.
+    3. One dimensional arrays with only one element will be converted to scalar
+       values. E.g. ``sofa.Data_SamplingRate`` is stored as an array of shape
+       (1, ) inside SOFA files (according to the SOFA standard AES69) but
+       will be a scalar inside SOFA objects after reading from disk.
+    """
+
+    return _read_netcdf(filename, verify, verbose, mode="sofa")
+
+
+def read_sofa_as_netcdf(filename):
+    """
+    Read corrupted SOFA data from disk.
+
+    .. note::
+        `read_sofa_as_netcdf` is intended to read and fix corrupted SOFA data
+        that could not be read by :py:func:`~read_sofa`. The recommend workflow
+        is
+
+        - Try to read the data with `read_sofa` and ``verify=True``
+        - If this fails, try the above with ``verify=False``
+        - If this fails, use `read_sofa_as_netcdf`
+
+        The SOFA object  returned by `read_sofa_as_netcdf` may not work
+        correctly before the issues with the data were fixed, i.e., before the
+        data are in agreement with the SOFA standard AES-69.
+
+    Numeric data is returned as floats or numpy float arrays unless they have
+    missing data, in which case they are returned as numpy masked arrays.
+
+    Parameters
+    ----------
+    filename : str
+        The full path to the NetCDF data.
+
+    Returns
+    -------
+    sofa : Sofa
+        Object containing the data from `filename`.
+
+    Notes
+    -----
+    1. Missing dimensions are appended when writing the SOFA object to disk.
+       E.g., if ``sofa.Data_IR`` is of shape (1, 2) it is written as an array
+       of shape (1, 2, 1) because the SOFA standard AES69 defines it as a
+       three dimensional array with the dimensions (`M: measurements`,
+       `R: receivers`, `N: samples`)
+    2. When reading data from a SOFA file, array data is always returned as
+       numpy arrays and singleton trailing dimensions are discarded (numpy
+       default). I.e., ``sofa.Data_IR`` will again be an array of shape (1, 2)
+       after writing and reading to and from disk.
+    3. One dimensional arrays with only one element will be converted to scalar
+       values. E.g. ``sofa.Data_SamplingRate`` is stored as an array of shape
+       (1, ) inside SOFA files (according to the SOFA standard AES69) but
+       will be a scalar inside SOFA objects after reading from disk.
+    """
+    return _read_netcdf(filename, False, False, mode="netcdf")
+
+
+def _read_netcdf(filename, verify, verbose, mode):
+
+    # check the filename
+    filename = pathlib.Path(filename).with_suffix('.sofa')
+    if not os.path.isfile(filename):
+        raise ValueError(f"{filename} does not exist")
+
+    # attributes that are skipped
+    skip = ["_Encoding"]
+
+    # init list of all and custom attributes
+    all_attr = []
+    custom = []
+
+    # open new NETCDF4 file for reading
+    with Dataset(filename, "r", format="NETCDF4") as file:
+
+        if mode == "sofa":
+            # get convention name and version
+            convention = file.SOFAConventions
+            version = file.SOFAConventionsVersion
+
+            # check if convention and version exist
+            _verify_convention_and_version(version, convention)
+
+            # get SOFA object with default values
+            sofa = sf.Sofa(convention, version=version, verify=verify)
+        else:
+            sofa = sf.Sofa(None)
+
+        # allow writing read only attributes
+        sofa.protected = False
+
+        # load global attributes
+        for attr in file.ncattrs():
+
+            value = getattr(file, attr)
+            all_attr.append(f"GLOBAL_{attr}")
+
+            if not hasattr(sofa, f"GLOBAL_{attr}"):
+                sofa._add_custom_api_entry(
+                    f"GLOBAL_{attr}", value, None, None, "attribute")
+                custom.append(f"GLOBAL_{attr}")
+                sofa.protected = False
+            else:
+                setattr(sofa, f"GLOBAL_{attr}", value)
+
+        # load data
+        for var in file.variables.keys():
+
+            value = _format_value_from_netcdf(file[var][:], var)
+            all_attr.append(var.replace(".", "_"))
+
+            if hasattr(sofa, var.replace(".", "_")):
+                setattr(sofa, var.replace(".", "_"), value)
+            else:
+                dimensions = "".join(list(file[var].dimensions))
+                # SOFA only uses dtypes 'double' and 'S1' but netCDF has more
+                dtype = "string" if file[var].datatype == "S1" else "double"
+                sofa._add_custom_api_entry(var.replace(".", "_"), value, None,
+                                           dimensions, dtype)
+                custom.append(var.replace(".", "_"))
+                sofa.protected = False
+
+            # load variable attributes
+            for attr in [a for a in file[var].ncattrs() if a not in skip]:
+
+                value = getattr(file[var], attr)
+                all_attr.append(var.replace(".", "_") + "_" + attr)
+
+                if not hasattr(sofa, var.replace(".", "_") + "_" + attr):
+                    sofa._add_custom_api_entry(
+                        var.replace(".", "_") + "_" + attr, value, None,
+                        None, "attribute")
+                    custom.append(var.replace(".", "_") + "_" + attr)
+                    sofa.protected = False
+                else:
+                    setattr(sofa, var.replace(".", "_") + "_" + attr, value)
+
+    # remove fields from initial Sofa object that were not contained in NetCDF
+    # file (initial Sofa object contained mandatory and optional fields)
+    attrs = [attr for attr in sofa.__dict__.keys() if not attr.startswith("_")]
+    for attr in attrs:
+        if attr not in all_attr:
+            delattr(sofa, attr)
+
+    # do not allow writing read only attributes any more
+    sofa.protected = True
+
+    # notice about custom entries
+    if custom and verbose:
+        print(("SOFA file contained custom entries\n"
+               "----------------------------------\n"
+               f"{', '.join(custom)}"))
+
+    # set default for verify
+    if verify == 'auto':
+        verify = True if parse(version) >= parse('1.0') else False
+
+    # update api
+    if verify:
+        try:
+            sofa.verify(mode="read")
+        except:  # noqa: E722
+            raise ValueError((
+                "The SOFA object could not be verified, maybe due to erroneous"
+                " data. Call sofa=sofar.read_sofa(filename, verify=False) and "
+                "then sofa.verify() to get more information")) from None
+
+    return sofa
+
+
+def write_sofa(filename: str, sofa: sf.Sofa, compression=4):
+    """
+    Write a SOFA object to disk as a SOFA file.
+
+    Parameters
+    ----------
+    filename : str
+        The filename. '.sofa' is appended to the filename, if it is not
+        explicitly given.
+    sofa : object
+        The SOFA object that is written to disk
+    compression : int
+        The level of compression with ``0`` being no compression and ``9``
+        being the best compression. The default of ``9`` optimizes the file
+        size but increases the time for writing files to disk.
+
+    Notes
+    -----
+    1. Missing dimensions are appended when writing the SOFA object to disk.
+       E.g., if ``sofa.Data_IR`` is of shape (1, 2) it is written as an array
+       of shape (1, 2, 1) because the SOFA standard AES69 defines it as a
+       three dimensional array with the dimensions (`M: measurements`,
+       `R: receivers`, `N: samples`)
+    2. When reading data from a SOFA file, array data is always returned as
+       numpy arrays and singleton trailing dimensions are discarded (numpy
+       default). I.e., ``sofa.Data_IR`` will again be an array of shape (1, 2)
+       after writing and reading to and from disk.
+    3. One dimensional arrays with only one element will be converted to scalar
+       values. E.g. ``sofa.Data_SamplingRate`` is stored as an array of shape
+       (1, ) inside SOFA files (according to the SOFA standard AES69) but
+       will be a scalar inside SOFA objects after reading from disk.
+    """
+    _write_sofa(filename, sofa, compression, verify=True)
+
+
+def _write_sofa(filename: str, sofa: sf.Sofa, compression=4, verify=True):
+    """
+    Private write function for writing invalid SOFA files for testing. See
+    write_sofa for documentation.
+    """
+
+    # check the filename
+    filename = pathlib.Path(filename).with_suffix('.sofa')
+
+    if verify:
+        # check if the latest version is used for writing and warn otherwise
+        # if case required for writing SOFA test data that violates the
+        # conventions
+        if sofa.GLOBAL_SOFAConventions != "invalid-value":
+            latest = sf.Sofa(sofa.GLOBAL_SOFAConventions)
+            latest = latest.GLOBAL_SOFAConventionsVersion
+            current = sofa.GLOBAL_SOFAConventionsVersion
+
+            if parse(current) < parse(latest):
+                warnings.warn((
+                    "Writing SOFA object with outdated Convention "
+                    f"version {current}. It is recommend to upgrade "
+                    " data with Sofa.upgrade_convention() before "
+                    "writing to disk if possible."), stacklevel=2)
+
+    # setting the netCDF compression parameter
+    use_zlib = compression != 0
+
+    # update the dimensions
+    if verify:
+        sofa.verify(mode="write")
+
+    # list of all attribute names
+    all_keys = [key for key in sofa.__dict__.keys() if not key.startswith("_")]
+
+    # open new NETCDF4 file for writing
+    with Dataset(filename, "w", format="NETCDF4") as file:
+
+        # write dimensions
+        for dim in sofa._api:
+            file.createDimension(dim, sofa._api[dim])
+
+        # write global attributes
+        keys = [key for key in all_keys if key.startswith("GLOBAL_")]
+        for key in keys:
+            setattr(file, key[7:], str(getattr(sofa, key)))
+
+        # write data
+        for key in all_keys:
+
+            # skip attributes
+            # Note: The used definition of attributes is lax. The strict
+            # definition would parse `key` and assume an attribute if
+            # 1. "_" is in key and key does not start with "DATA_", or
+            # 2. key contains more than one "_"
+            #
+            # The strict definition is implicitly included in the SOFA standard
+            # since underscores only occur for variables starting with Data_
+            if sofa._convention[key]["type"] == "attribute":
+                continue
+
+            # get the data and type and shape
+            value, dtype = _format_value_for_netcdf(
+                getattr(sofa, key), key, sofa._convention[key]["type"],
+                sofa._dimensions[key], sofa._api["S"])
+
+            # create variable and write data
+            shape = list(sofa._dimensions[key])
+            tmp_var = file.createVariable(
+                key.replace("Data_", "Data."), dtype, shape,
+                zlib=use_zlib, complevel=compression)
+            if dtype == "f8":
+                tmp_var[:] = value
+            else:
+                tmp_var[:] = stringtochar(value, encoding='utf-8')
+
+            # write variable attributes
+            sub_keys = [k for k in all_keys if k.startswith(f"{key}_")]
+            for sub_key in sub_keys:
+                setattr(tmp_var, sub_key[len(key)+1:],
+                        str(getattr(sofa, sub_key)))
+
+
+def _format_value_for_netcdf(value, key, dtype, dimensions, S):
+    """
+    Format value from SOFA object for saving in a NETCDF4 file.
+
+    Parameters
+    ----------
+    value : str, array like
+        The value to be formatted
+    key : str
+        The name of the current attribute. Needed for verbose errors.
+    dtype : str
+        The the data type of value
+    dimensions : str
+        The intended dimensions from ``sofa.dimensions``
+    S : int
+        Length of the string array.
+
+    Returns
+    -------
+    value : str, numpy array
+        The formatted value.
+    netcdf_dtype : str
+        The data type as a string for writing to a NETCDF4 file ('attribute',
+        'f8', or 'S1').
+    """
+    # copy value
+    with contextlib.suppress(AttributeError):
+        value = value.copy()
+
+    # parse data
+    if dtype == "attribute":
+        value = str(value)
+        netcdf_dtype = "attribute"
+    elif dtype == "double":
+        value = _atleast_nd(value, len(dimensions))
+        netcdf_dtype = "f8"
+    elif dtype == "string":
+        value = np.array(value, dtype=f"S{str(S)}")
+        value = _atleast_nd(value, len(dimensions))
+        netcdf_dtype = 'S1'
+    else:
+        raise ValueError(f"Unknown type {dtype} for {key}")
+
+    return value, netcdf_dtype
+
+
+def _format_value_from_netcdf(value, key):
+    """
+    Format value from NETCDF4 file for saving in a SOFA object.
+
+    Parameters
+    ----------
+    value : np.array of dtype float or S
+        The value to be formatted
+    key : str
+        The variable name of the current value. Needed for verbose errors.
+
+    Returns
+    -------
+    value : str, number, numpy array
+        The formatted value.
+    """
+
+    if "float" in str(value.dtype) or "int" in str(value.dtype):
+        if np.ma.is_masked(value):
+            warnings.warn(f"Entry {key} contains missing data", stacklevel=3)
+        else:
+            # Convert to numpy array or scalar
+            value = np.asarray(value)
+    elif str(value.dtype)[1] in ["S", "U"]:
+        # string arrays are stored in masked arrays with empty strings '' being
+        # masked. Convert to regular arrays with unmasked empty strings
+        if str(value.dtype)[1] == "S":
+            value = chartostring(value, encoding="ascii")
+        value = np.atleast_1d(value).astype("U")
+    else:
+        raise TypeError(
+            f"{key}: value.dtype is {value.dtype} but must be float, S or, U")
+
+    # convert arrays to scalars if they do not store data that is usually used
+    # as scalar metadata, e.g., the SamplingRate
+    data_keys = ["Data_IR", "Data_Real", "Data_Imag", "Data_SOS" "Data_Delay"]
+    if value.size == 1 and key not in data_keys:
+        value = value[0]
+
+    return value