sofar 1.1.3__py2.py3-none-any.whl → 1.2.0__py2.py3-none-any.whl

sofar/__init__.py

@@ -1,13 +1,12 @@
 # -*- coding: utf-8 -*-
-
-"""Top-level package for sofar."""
-
 __author__ = """The pyfar developers"""
 __email__ = 'info@pyfar.org'
-__version__ = '1.1.3'
+__version__ = '1.2.0'
 
 from .sofa import Sofa
 
+from .sofastream import SofaStream
+
 from .io import read_sofa, read_sofa_as_netcdf, write_sofa
 
 from .utils import (list_conventions,
@@ -18,6 +17,7 @@ from .update_conventions import update_conventions
 
 
 __all__ = ['Sofa',
+           'SofaStream',
            'update_conventions',
            'list_conventions',
            'read_sofa',

sofar/io.py

@@ -9,13 +9,16 @@ import sofar as sf
 from .utils import _verify_convention_and_version, _atleast_nd
 
 
-def read_sofa(filename, verify=True, verbose=True):
+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
@@ -24,7 +27,9 @@ def read_sofa(filename, verify=True, verbose=True):
         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 ``True``.
+        ``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``
@@ -39,7 +44,7 @@ def read_sofa(filename, verify=True, verbose=True):
 
     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 AES69-2020 defines it as a
+       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
@@ -48,7 +53,7 @@ def read_sofa(filename, verify=True, verbose=True):
        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 AES69-2020) but
+       (1, ) inside SOFA files (according to the SOFA standard AES69) but
        will be a scalar inside SOFA objects after reading from disk.
     """
 
@@ -90,7 +95,7 @@ def read_sofa_as_netcdf(filename):
 
     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 AES69-2020 defines it as a
+       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
@@ -99,7 +104,7 @@ def read_sofa_as_netcdf(filename):
        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 AES69-2020) but
+       (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")
@@ -200,6 +205,10 @@ def _read_netcdf(filename, verify, verbose, mode):
                "----------------------------------\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:
@@ -234,7 +243,7 @@ def write_sofa(filename: str, sofa: sf.Sofa, compression=4):
 
     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 AES69-2020 defines it as a
+       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
@@ -243,7 +252,7 @@ def write_sofa(filename: str, sofa: sf.Sofa, compression=4):
        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 AES69-2020) but
+       (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)
@@ -325,8 +334,7 @@ def _write_sofa(filename: str, sofa: sf.Sofa, compression=4, verify=True):
             if dtype == "f8":
                 tmp_var[:] = value
             else:
-                tmp_var[:] = stringtochar(value)
-                tmp_var._Encoding = "ascii"
+                tmp_var[:] = stringtochar(value, encoding='utf-8')
 
             # write variable attributes
             sub_keys = [k for k in all_keys if k.startswith(f"{key}_")]

sofar/sofa.py

@@ -5,6 +5,7 @@ from datetime import datetime
 import platform
 import numpy as np
 import warnings
+from packaging.version import parse
 from copy import deepcopy
 import sofar as sf
 from .utils import (_nd_newaxis, _atleast_nd, _get_conventions,
@@ -30,7 +31,9 @@ class Sofa():
         Verify the SOFA object by calling :py:func:`~Sofa.verify`. This helps
         to find potential errors in the default values and is thus recommended
         If creating a file does not work, try to call `Sofa` with
-        ``verify=False``. The default is ``True``.
+        ``verify=False``. The default ``'auto'`` defaults to ``True`` for
+        stable conventions with versions of 1.0 or higher and to ``False``
+        otherwise.
 
     Returns
     -------
@@ -60,7 +63,7 @@ class Sofa():
        ``sofa.Data_IR`` is converted to a numpy array of shape (1, 2)
     2. Missing dimensions are appended when writing the SOFA object to disk,
        i.e., ``sofa.Data_IR`` is written as an array of shape (1, 2, 1) because
-       the SOFA standard AES69-2020 defines it as a three dimensional array
+       the SOFA standard AES69 defines it as a three dimensional array
        with the dimensions (`M: measurements`, `R: receivers`, `N: samples`)
     3. When reading data from a SOFA file, array data is always returned as
        numpy arrays and singleton trailing dimensions are discarded (numpy
@@ -68,12 +71,12 @@ class Sofa():
        after writing and reading to and from disk.
     4. 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 AES69-2020) but
+       (1, ) inside SOFA files (according to the SOFA standard AES69) but
        will be a scalar inside SOFA objects after reading from disk.
 
 
     For more examples refer to the `Quick tour of SOFA and sofar` at
-    https://sofar.readthedocs.io/en/latest/
+    https://sofar.readthedocs.io/en/stable/
     """
 
     # these have to be set here, because they are used in __setattr__ and
@@ -85,7 +88,7 @@ class Sofa():
     _read_only_attr = []
 
     def __init__(self, convention, mandatory=False, version="latest",
-                 verify=True):
+                 verify='auto'):
         """See class docstring"""
 
         # get convention
@@ -100,11 +103,24 @@ class Sofa():
             # add attributes with default values
             self._convention_to_sofa(mandatory)
 
+            # set default for verify
+            version = \
+                self._convention['GLOBAL_SOFAConventionsVersion']['default']
+            if verify == 'auto':
+                verify = True if parse(version) >= parse('1.0') else False
+
             # add and update the API
             # (mandatory=False can not be verified because some conventions
             # have default values that have optional variables as dependencies)
             if verify and not mandatory:
                 self.verify(mode="read")
+            # warning for preliminary conventions if verification is bypassed
+            elif parse(version) < parse('1.0'):
+                warnings.warn(UserWarning((
+                    f"Detected preliminary conventions version {version}. "
+                    "Upgrade data to version >= 1.0 if possible. Preliminary "
+                    "conventions might change in the future, which could "
+                    "invalidate data that was written before the changes.")))
 
             self.protected = True
         else:
@@ -168,7 +184,7 @@ class Sofa():
         M
             number of measurements
         N
-            number of samles, frequencies, SOS coefficients
+            number of samples, frequencies, SOS coefficients
             (depending on self.GLOBAL_DataType)
         R
             Number of receivers or SH coefficients
@@ -188,7 +204,7 @@ class Sofa():
         # Check if the dimensions can be updated
         self._update_dimensions()
 
-        # get verbose description for dimesion N
+        # get verbose description for dimension N
         if self.GLOBAL_DataType.startswith("FIR"):
             N_verbose = "samples"
         elif self.GLOBAL_DataType.startswith("TF"):
@@ -392,7 +408,7 @@ class Sofa():
             console.
         issue_handling : str, optional
             Defines how issues detected during verification of the SOFA object
-            are handeled (see :py:func:`~sofar.sofar.Sofa.verify`)
+            are handled (see :py:func:`~sofar.sofar.Sofa.verify`)
 
             ``'raise'``
                 Warnings and errors are raised if issues are detected
@@ -403,7 +419,7 @@ class Sofa():
             ``'ignore'``
                 Issues are ignored, i.e., not raised, printed, or returned.
 
-            The default is ``print'``.
+            The default is ``'print'``.
         """
 
         # update the private attribute `_convention` to make sure the required
@@ -538,7 +554,7 @@ class Sofa():
             # add numeric data
             sofa.add_variable("Temperature", 25.1, "double", "MI")
 
-            # add GLOBAL and Variable attribtue
+            # add GLOBAL and Variable attribute
             sofa.add_entry(
                 "GLOBAL_DateMeasured", "8.08.2021", "attribute", None)
             sofa.add_entry(
@@ -569,7 +585,7 @@ class Sofa():
             import sofar as sf
             sofa = sf.Sofa("GeneralTF")
 
-            # add GLOBAL and Variable attribtue
+            # add GLOBAL and Variable attribute
             sofa.add_attribute("GLOBAL_DateMeasured", "8.08.2021")
             sofa.add_attribute("Data_Real_Units", "Pascal")
 
@@ -695,7 +711,7 @@ class Sofa():
         setattr(self, key, value)
         self.protected = True
 
-    def upgrade_convention(self, target=None, verify=True):
+    def upgrade_convention(self, target=None, verify='auto'):
         """
         Upgrade Sofa data to newer conventions.
 
@@ -713,7 +729,9 @@ class Sofa():
             conventions to which the data can be updated.
         verify : bool, optional
             Flag to specify if the data should be verified after the upgrade
-            using :py:func:`~Sofa.verify`. The default is ``True``.
+            using :py:func:`~Sofa.verify`. The default ``'auto'`` defaults to
+            ``True`` for stable conventions with versions of 1.0 or higher and
+            to ``False`` otherwise.
 
         Returns
         -------
@@ -745,7 +763,6 @@ class Sofa():
 
         # check for upgrades --------------------------------------------------
         if is_deprecated:
-            version_matched = False
             # check if upgrade is available for this convention
             if convention_current not in upgrade:
                 print((f"Convention {convention_current} v{version_current} is"
@@ -755,7 +772,6 @@ class Sofa():
             # check if upgrade is available for this version
             for from_to in upgrade[convention_current]["from_to"]:
                 if version_current in from_to[0]:
-                    version_matched = True
                     targets = from_to[1]
 
                     if target in targets:
@@ -773,9 +789,6 @@ class Sofa():
                         print(upgrades)
                         return targets
                     break
-            if not version_matched:
-                print((f"Convention {convention_current} v{version_current} is"
-                       " outdated but is missing upgrade rules"))
         else:
             print((f"Convention {convention_current} v{version_current} "
                    "is up to date"))
@@ -856,6 +869,10 @@ class Sofa():
         if upgrade["message"] is not None:
             print(upgrade["message"])
 
+        # set default for verify
+        if verify == 'auto':
+            version = self.GLOBAL_SOFAConventionsVersion
+            verify = True if parse(version) >= parse('1.0') else False
         if verify:
             self.verify()
 
@@ -905,7 +922,7 @@ class Sofa():
         Parameters
         ----------
         issue_handling : str, optional
-            Defines how detected issues are handeled
+            Defines how detected issues are handled
 
             ``'raise'``
                 Warnings and errors are raised if issues are detected
@@ -992,22 +1009,21 @@ class Sofa():
                         f"- {key} must be string but is {type(value)}\n"
 
             elif dtype == "double":
-                # multiple checks needed because sofar does not force the user
-                # to initally pass data as numpy arrays
-                if not isinstance(value,
-                                  (np.int_, np.float_, np.double, np.ndarray)):
-                    current_error += (f"- {key} must be int, float or numpy "
-                                      f"array but is {type(value)}\n")
-
-                if isinstance(value, np.ndarray) and not (
-                        str(value.dtype).startswith('int') or
-                        str(value.dtype).startswith('float')):
+                # All variables can be of type float or int, and are converted
+                # to float when writing.
+                # sofar does not force the user to pass data as numpy arrays.
+                # We thus check for allowed instances (int, float, numpy) and
+                # specifically for the type of numpy arrays.
+                if not isinstance(
+                        value, (int, float, np.ndarray, np.number)) or \
+                        (isinstance(value, (np.ndarray, np.number)) and
+                         value.dtype.kind not in ['i', 'f']):
                     current_error += (f"- {key} must be int or float "
-                                      f"but is {type(value.dtype)}\n")
+                                      f"but is {type(value)}\n")
 
             elif dtype == "string":
                 # multiple checks needed because sofar does not force the user
-                # to initally pass data as numpy arrays
+                # to initially pass data as numpy arrays
                 if not isinstance(value, (str, np.ndarray)):
                     current_error += (f"- {key} must be string or numpy array "
                                       f"but is {type(value)}\n")
@@ -1100,7 +1116,7 @@ class Sofa():
         current_error = ""
         for key in keys:
 
-            # AES69-2020 Sec. 4.7.1
+            # AES69 Sec. 4.7.1
             if key.startswith("PRIVATE") or key.startswith("API"):
                 current_error += "- " + key + "\n"
             if (key.startswith("GLOBAL") and not key.startswith("GLOBAL_")) or\
@@ -1215,7 +1231,7 @@ class Sofa():
                     [self._api[d.upper()] if d != "S" else 1 for d in dim])
 
                 # get shape for comparison to correct length by cropping and
-                # appending singelton dimensions if required
+                # appending singleton dimensions if required
                 shape_compare = shape_act[:len(shape_ref)]
                 for _ in range(len(shape_ref) - len(shape_compare)):
                     shape_compare += (1, )
@@ -1294,7 +1310,7 @@ class Sofa():
             for key_dep, ref_dep in items:
 
                 if key_dep == "_dimensions":
-                    # requires specific dimension(s) to have a vertain size
+                    # requires specific dimension(s) to have a certain size
                     for dim in rules[key]["specific"][test]["_dimensions"]:
                         # possible sizes
                         dim_ref = \
@@ -1391,7 +1407,7 @@ class Sofa():
     @staticmethod
     def _verify_value(test, ref, unit_aliases, key):
         """
-        Check a value agains the SOFA standard for Sofa.verify()
+        Check a value against the SOFA standard for Sofa.verify()
 
         Parameters
         ----------
@@ -1463,7 +1479,7 @@ class Sofa():
                 or not isinstance(ref[0], str):
             raise TypeError("ref must be a list of length 1 containing a str")
 
-        # Following the SOFA standard AES69-2020, units may be separated by
+        # Following the SOFA standard AES69, units may be separated by
         # `, ` (comma and space), `,` (comma only), and ` ` (space only).
         # (regexp ', ?' matches ', ' and ',')
         units_ref = re.split(', ?', ref[0])
@@ -1501,7 +1517,7 @@ class Sofa():
         -------
         reference_units : str
         """
-        # Following the SOFA standard AES69-2020, units may be separated by
+        # Following the SOFA standard AES69, units may be separated by
         # `, ` (comma and space), `,` (comma only), and ` ` (space only).
         # (regexp ', ?' matches ', ' and ',')
         units_test = re.split(', ?| ', test.lower())

sofar/sofa_conventions/conventions/AnnotatedEmitterAudio_0.2.csv

@@ -0,0 +1,46 @@
+Name	Default	Flags	Dimensions	Type	Comment
+GLOBAL:Conventions	SOFA	rm		attribute
+GLOBAL:Version	2.1	rm		attribute
+GLOBAL:SOFAConventions	AnnotatedEmitterAudio	rm		attribute
+GLOBAL:SOFAConventionsVersion	0.2	rm		attribute
+GLOBAL:APIName		rm		attribute
+GLOBAL:APIVersion		rm		attribute
+GLOBAL:ApplicationName				attribute
+GLOBAL:ApplicationVersion				attribute
+GLOBAL:AuthorContact		m		attribute
+GLOBAL:Comment				attribute
+GLOBAL:DataType	Audio	rm		attribute
+GLOBAL:History				attribute
+GLOBAL:License	No license provided, ask the author for permission	m		attribute
+GLOBAL:Organization		m		attribute
+GLOBAL:References				attribute
+GLOBAL:RoomType	free field	m		attribute
+GLOBAL:Origin				attribute
+GLOBAL:DateCreated		m		attribute
+GLOBAL:DateModified		m		attribute
+GLOBAL:Title		m		attribute
+ListenerPosition	[0 0 0]	m	IC, MC	double	Position of the head. IC if not tracked, MC if tracked.
+ListenerPosition:Type	cartesian	m		attribute
+ListenerPosition:Units	metre	m		attribute
+ReceiverPosition	[0 0.09 0; 0 -0.09 0]	m	rC, rCM	double	Position of the ears. RC if not tracked, RCM if tracked.
+ReceiverPosition:Type	cartesian	m		attribute
+ReceiverPosition:Units	metre	m		attribute
+SourcePosition	[0 0 0]	m	IC, MC	double	Position of the virtual ensemble. IC if not tracked, MC if tracked.
+SourcePosition:Type	cartesian	m		attribute
+SourcePosition:Units	metre	m		attribute
+EmitterPosition	[0 0 0]	m	eC, eCM	double	Position of the virtual source(s). eC if not tracked, eCM if tracked.
+EmitterPosition:Type	cartesian	m		attribute
+EmitterPosition:Units	metre	m		attribute
+ListenerUp	[0 0 1]	m	IC, MC	double	Must be of the same dimensionality as ListenerView.
+ListenerView	[1 0 0]	m	IC, MC	double	Orientation of the head. IC if not tracked, MC if tracked.
+ListenerView:Type	cartesian	m		attribute
+ListenerView:Units	metre	m		attribute
+Data.Emitter	[0 0]	m	In, En	double	audio data at the emitter(s); n=number of audio samples
+Data.SamplingRate	44100	m	I	double
+Data.SamplingRate:Units	hertz	m		attribute
+M	0	m	m	double	Time stamp of the measurements in M, defines the size of M.
+M:LongName	time	m		attribute	Narrative name for M
+M:Units	second	m		attribute	Units used for M
+Response	{''}		I, C, S	string	the subject’s response
+Response:Type				attribute	type depends on the dimension
+Response:LongName				attribute	narrative description of the response type