obsarray 1.0.2__py3-none-any.whl

docs/conf.py

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+#!/usr/bin/env python
+#
+# obsarray documentation build configuration file, created by
+# cookiecutter
+#
+# This file is execfile()d with the current directory set to its
+# containing dir.
+#
+# Note that not all possible configuration values are present in this
+# autogenerated file.
+#
+# All configuration values have a default; values that are commented out
+# serve to show the default.
+
+
+# If extensions (or modules to document with autodoc) are in another
+# directory, add these directories to sys.path here. If the directory is
+# relative to the documentation root, use os.path.abspath to make it
+# absolute, like shown here.
+
+import sphinx_autosummary_accessors
+import obsarray
+
+project_title = "obsarray".replace("_", " ").title()
+
+
+# -- General configuration ---------------------------------------------
+
+# If your documentation needs a minimal Sphinx version, state it here.
+#
+# needs_sphinx = '1.0'
+
+# Attempt to make links automatially
+default_role = "code"
+
+# Add any Sphinx extension module names here, as strings. They can be
+# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
+# CFAB added napolean to support google-style docstrings
+extensions = [
+    "sphinx.ext.autodoc",
+    "sphinx.ext.autosummary",
+    "sphinx.ext.intersphinx",
+    "sphinx.ext.viewcode",
+    "sphinx.ext.napoleon",
+    "IPython.sphinxext.ipython_directive",
+    "IPython.sphinxext.ipython_console_highlighting",
+    "sphinx_design",
+    "sphinx_autosummary_accessors",
+]
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ["_templates", sphinx_autosummary_accessors.templates_path]
+
+# The suffix(es) of source filenames.
+# You can specify multiple suffix as a list of string:
+#
+# source_suffix = ['.rst', '.md']
+source_suffix = ".rst"
+
+# The master toctree document.
+master_doc = "index"
+
+# General information about the project.
+project = project_title
+copyright = "CoMet Toolkit Team"
+author = "CoMet Toolkit Team"
+
+# The version info for the project you're documenting, acts as replacement
+# for |version| and |release|, also used in various other places throughout
+# the built documents.
+#
+# The short X.Y version.
+version = obsarray.__version__
+# The full version, including alpha/beta/rc tags.
+release = obsarray.__version__
+
+# The language for content autogenerated by Sphinx. Refer to documentation
+# for a list of supported languages.
+#
+# This is also used if you do content translation via gettext catalogs.
+# Usually you set "language" from the command line for these cases.
+language = None
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This patterns also effect to html_static_path and html_extra_path
+exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"]
+
+# The name of the Pygments (syntax highlighting) style to use.
+pygments_style = "sphinx"
+
+rst_prolog = """
+.. role:: python(code)
+    :language: python
+    :class: highlight
+"""
+
+# If true, `todo` and `todoList` produce output, else they produce nothing.
+todo_include_todos = False
+
+
+# -- Options for HTML output -------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+#
+html_theme = "sphinx_book_theme"
+
+# Theme options are theme-specific and customize the look and feel of a
+# theme further.  For a list of options available for each theme, see the
+# documentation.
+#
+# html_theme_options = {}
+
+html_logo = "figs/obsarray.png"
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+html_static_path = ["_static"]
+
+# -- Options for HTMLHelp output ---------------------------------------
+
+# Output file base name for HTML help builder.
+htmlhelp_basename = "obsarraydoc"
+
+
+# -- Options for LaTeX output ------------------------------------------
+
+latex_elements = {
+    # The paper size ('letterpaper' or 'a4paper').
+    #
+    # 'papersize': 'letterpaper',
+    # The font size ('10pt', '11pt' or '12pt').
+    #
+    # 'pointsize': '10pt',
+    # Additional stuff for the LaTeX preamble.
+    #
+    # 'preamble': '',
+    # Latex figure (float) alignment
+    #
+    # 'figure_align': 'htbp',
+}
+
+# Grouping the document tree into LaTeX files. List of tuples
+# (source start file, target name, title, author, documentclass
+# [howto, manual, or own class]).
+latex_documents = [
+    (
+        master_doc,
+        "user_manual.tex",
+        "{} Documentation".format(project_title),
+        "CoMet Toolkit Team",
+        "manual",
+    ),
+]
+
+
+# -- Options for manual page output ------------------------------------
+
+# One entry per manual page. List of tuples
+# (source start file, name, description, authors, manual section).
+man_pages = [(master_doc, "obsarray", "obsarray Documentation", [author], 1)]
+
+
+# -- Options for Texinfo output ----------------------------------------
+
+# Grouping the document tree into Texinfo files. List of tuples
+# (source start file, target name, title, author,
+#  dir menu entry, description, category)
+texinfo_documents = [
+    (
+        master_doc,
+        "obsarray",
+        "obsarray Documentation",
+        author,
+        "obsarray",
+        "Extension to xarray for handling uncertainty quantified observation data",
+        "Miscellaneous",
+    ),
+]

notebook/test_register_err_corr_form.py

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+from obsarray.err_corr import register_err_corr_form, BaseErrCorrForm
+import xarray as xr
+import numpy as np
+import obsarray
+
+
+@register_err_corr_form("new")
+class NewForm(BaseErrCorrForm):
+
+    form = "new"
+    is_systematic = True
+
+    def build_matrix(self, idx: np.ndarray) -> np.ndarray:
+        return "abc"
+
+
+# ds = xr.open_dataset("obs_example.nc")
+#
+# ds.unc["temperature"]["u_sys_temperature"] = (
+#     ["x", "y", "time"],
+#     ds.temperature * 0.03,
+#     {
+#         "err_corr": [
+#             {
+#                 "dim": "x",
+#                 "form": "new",
+#                 "params": [],
+#             },
+#             {
+#                 "dim": "y",
+#                 "form": "systematic",
+#                 "params": [],
+#             },
+#             {
+#                 "dim": "time",
+#                 "form": "systematic",
+#                 "params": [],
+#             },
+#         ]
+#     },
+# )
+#
+# p = ds.unc["temperature"]["u_sys_temperature"]
+#
+# pass

obsarray/__init__.py

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+"""obsarray - Extension to xarray for handling uncertainty-quantified observation data"""
+
+__author__ = "Sam Hunt <sam.hunt@npl.co.uk>"
+__all__ = []
+
+from ._version import get_versions
+from obsarray import unc_accessor, flag_accessor
+from obsarray.err_corr import err_corr_forms
+from obsarray.templater.template_util import create_ds
+from obsarray.templater.dstemplater import DSTemplater
+from obsarray.templater.dswriter import DSWriter
+
+__version__ = get_versions()["version"]
+del get_versions

obsarray/_version.py

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+
+# This file was generated by 'versioneer.py' (0.29) from
+# revision-control system data, or from the parent directory name of an
+# unpacked source archive. Distribution tarballs contain a pre-generated copy
+# of this file.
+
+import json
+
+version_json = '''
+{
+ "date": "2025-04-25T14:06:04+0100",
+ "dirty": false,
+ "error": null,
+ "full-revisionid": "b26b43a5d2e41ccb9a5e73c00e6d16a28a8515a9",
+ "version": "1.0.2"
+}
+'''  # END VERSION_JSON
+
+
+def get_versions():
+    return json.loads(version_json)

obsarray/err_corr.py

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+"""err_corr_forms - module for the defintion of error-correlation parameterisation forms"""
+
+import abc
+from typing import Callable, Type, Union, List
+import numpy as np
+from comet_maths.linear_algebra.matrix_conversion import expand_errcorr_dims
+
+__author__ = "Sam Hunt <sam.hunt@npl.co.uk>"
+__all__ = ["err_corr_forms", "register_err_corr_form", "BaseErrCorrForm"]
+
+
+class ErrCorrForms:
+    """
+    Container for error-correlation parameterisation form definition objects
+    """
+
+    def __init__(self):
+        self._forms = {}
+
+    def __setitem__(self, form_name, form_cls):
+        if not issubclass(form_cls, BaseErrCorrForm):
+            raise TypeError(
+                "form must be subclass of " + str(BaseErrCorrForm.__class__)
+            )
+
+        self._forms[form_name] = form_cls
+
+    def __getitem__(self, name):
+        return self._forms[name]
+
+    def __delitem__(self, name):
+        del self._forms[name]
+
+    def keys(self):
+        return self._forms.keys()
+
+
+err_corr_forms = ErrCorrForms()
+
+
+# placeholder currently
+class BaseErrCorrForm(abc.ABC):
+    """
+    Base class for error-correlation parameterisation form defintions
+    """
+
+    is_random = False
+    is_systematic = False
+
+    def __init__(self, xarray_obj, unc_var_name, dims, params, units):
+        self._obj = xarray_obj
+        self._unc_var_name = unc_var_name
+        self.dims = dims if isinstance(dims, list) else [dims]
+        self.params = params if isinstance(params, list) else [params]
+        self.units = units
+
+    def __str__(self):
+        """Custom __str__"""
+
+        return self.form + " " + str(self.params)
+
+    def __repr__(self):
+        """Custom  __repr__"""
+        return str(self)
+
+    @property
+    @abc.abstractmethod
+    def form(self) -> str:
+        """Form name"""
+        pass
+
+    def get_varshape_errcorr(self):
+        """
+        return shape of uncertainty variable, including only dimensions which are included in the current error correlation form.
+
+        :return: shape of included dimensions
+        """
+        all_dims = self._obj[self._unc_var_name].dims
+        all_dims_sizes = self._obj.sizes
+
+        return tuple([all_dims_sizes[dim] for dim in all_dims if dim in self.dims])
+
+    def get_sliced_dim_sizes_uncvar(self, sli: tuple) -> dict:
+        """
+        Return dictionary with sizes of sliced dimensions of unc variable, including all dimensions.
+
+        :param sli: slice (tuple with slice for each dimension)
+        :return: dictionary with shape of included sliced dimensions
+        """
+        uncvar_dims = self._obj[self._unc_var_name][sli].dims
+        uncvar_shape = self._obj[self._unc_var_name][sli].shape
+        return {
+            uncvar_dims[idim]: uncvar_shape[idim] for idim in range(len(uncvar_dims))
+        }
+
+    def get_sliced_dim_sizes_errcorr(self, sli: tuple) -> dict:
+        """
+        Return dictionary with sizes of sliced dimensions of unc variable, including only dimensions which are
+        included in the current error correlation form.
+
+        :param sli: slice (tuple with slice for each dimension)
+        :return: dictionary with shape of included sliced dimensions
+        """
+        uncvar_sizes = self.get_sliced_dim_sizes_uncvar(sli)
+        sliced_dims = self.get_sliced_dims_errcorr(sli)
+
+        return {dim: uncvar_sizes[dim] for dim in sliced_dims}
+
+    def get_sliced_dims_errcorr(self, sli: tuple) -> list:
+        """
+        Return dimensions which are within the slice and included in the current error correlation form.
+
+        :param sli: slice (tuple with slice for each dimension)
+        :return: list with sliced dimensions
+        """
+        all_dims = self._obj[self._unc_var_name].dims
+        return [
+            all_dims[idim]
+            for idim in range(len(all_dims))
+            if (isinstance(sli[idim], slice) and all_dims[idim] in self.dims)
+        ]
+
+    def get_sliced_shape_errcorr(self, sli: tuple) -> tuple:
+        """
+        return shape of sliced uncertainty variable, including only dimensions which are included in the current error correlation form.
+
+        :param sli: slice (tuple with slice for each dimension)
+        :return: shape of included sliced dimensions
+        """
+        uncvar_sizes = self.get_sliced_dim_sizes_uncvar(sli)
+        sliced_dims = self.get_sliced_dims_errcorr(sli)
+
+        return tuple([uncvar_sizes[dim] for dim in sliced_dims])
+
+    def slice_errcorr_matrix(self, err_corr_matrix, variable_shape, sli) -> np.ndarray:
+        """
+        Slice the provided error correlation matrix (typically the error correlation matrix of the
+        BaseErrCorrForm) using the
+
+        :param err_corr_matrix: error correlation matrix to be sliced
+        :param variable_shape: tuple with the length of the dimensions in the error correlation matrix (in correct order for flattening)
+        :param sli: slice of observation variable to return error-correlation matrix for
+        :return: sliced error correlation matrix
+        """
+        mask_array = np.ones(variable_shape, dtype=bool)
+        mask_array[sli] = False
+
+        return np.delete(
+            np.delete(err_corr_matrix, mask_array.ravel(), 0), mask_array.ravel(), 1
+        )
+
+    @abc.abstractmethod
+    def build_matrix(self, sli: Union[np.ndarray, tuple]) -> np.ndarray:
+        """
+        Returns uncertainty effect error-correlation matrix, populated with error-correlation values defined
+        in this parameterisation
+
+        :param sli: slice of observation variable to return error-correlation matrix for
+
+        :return: populated error-correlation matrix
+        """
+        pass
+
+    def build_dot_matrix(self, sli: Union[np.ndarray, tuple]) -> np.ndarray:
+        """
+        Returns expanded error correlation matrix for use in dot product with error correlation
+        in other dimensions.
+
+        The (sliced) error correlation matrix for this BaseErrCorrForm is expanded from its current
+        (sliced) dimensions (which often don't include all dimensions of the associated uncertainty
+        variable) to the dimensions of the full (sliced) error correlation (i.e. all dimensions of
+        the uncertainty).
+        The returned matrix is not meaningfull unless combined in a dot product with the expanded
+        matrices of other error correlation matrices (together spanning all uncertainty dimensions).
+
+        :param sli: slice of observation variable to return error-correlation matrix for
+        :return: expanded matrix for use in dot product with error correlation in other dimensions.
+        """
+        return expand_errcorr_dims(
+            in_corr=self.build_matrix(sli),
+            in_dim=self.get_sliced_dims_errcorr(sli),
+            out_dim=list(self._obj[self._unc_var_name][sli].dims),
+            dim_sizes=self.get_sliced_dim_sizes_uncvar(sli),
+        )
+
+
+def register_err_corr_form(form_name: str) -> Callable:
+    """
+    Decorator for registering error-correlation parmaterisation form definition to package definition container
+
+    :param form_name: name of error-correlation parmaterisation form e.g. "random"
+    :return: decorator function
+    """
+
+    def decorator(form_cls: Type) -> Type:
+        err_corr_forms[form_name] = form_cls
+        return form_cls
+
+    return decorator
+
+
+@register_err_corr_form("random")
+class RandomCorrelation(BaseErrCorrForm):
+
+    form = "random"
+    is_random = True
+
+    def build_matrix(self, sli: tuple) -> np.ndarray:
+        """
+        Returns uncertainty effect error-correlation matrix, populated with error-correlation values defined
+        in this parameterisation
+
+        :param sli: slice of observation variable to return error-correlation matrix for
+
+        :return: populated error-correlation matrix
+        """
+
+        # evaluate correlation over matrices in form defintion
+        dim_lens = self.get_sliced_shape_errcorr(sli)
+        n_elems = int(np.prod(dim_lens))
+
+        submatrix = np.eye(n_elems)
+
+        return submatrix
+
+
+@register_err_corr_form("systematic")
+class SystematicCorrelation(BaseErrCorrForm):
+
+    form = "systematic"
+    is_systematic = True
+
+    def build_matrix(self, sli: tuple) -> np.ndarray:
+        """
+        Returns uncertainty effect error-correlation matrix, populated with error-correlation values defined
+        in this parameterisation
+
+        :param sli: slice of observation variable to return error-correlation matrix for
+
+        :return: populated error-correlation matrix
+        """
+
+        # evaluate correlation over matrices in form defintion
+        dim_lens = self.get_sliced_shape_errcorr(sli)
+        n_elems = int(np.prod(dim_lens))
+
+        submatrix = np.ones((n_elems, n_elems))
+
+        return submatrix
+
+
+@register_err_corr_form("err_corr_matrix")
+class ErrCorrMatrixCorrelation(BaseErrCorrForm):
+
+    form = "err_corr_matrix"
+
+    def build_matrix(self, sli: tuple) -> np.ndarray:
+        """
+        Returns uncertainty effect error-correlation matrix, populated with error-correlation values defined
+        in this parameterisation
+
+        :param sli: slice of observation variable to return error-correlation matrix for
+
+        :return: populated error-correlation matrix
+        """
+        all_dims = self._obj[self._unc_var_name].dims
+
+        sli_submatrix = tuple(
+            [sli[i] for i in range(len(all_dims)) if all_dims[i] in self.dims]
+        )
+
+        submatrix = self.slice_errcorr_matrix(
+            self._obj[self.params[0]], self.get_varshape_errcorr(), sli_submatrix
+        )
+
+        return submatrix
+
+
+@register_err_corr_form("ensemble")
+class EnsembleCorrelation(BaseErrCorrForm):
+
+    form = "ensemble"
+
+    def build_matrix(self, sli: tuple) -> np.ndarray:
+        """
+        Returns uncertainty effect error-correlation matrix, populated with error-correlation values defined
+        in this parameterisation
+
+        :param sli: slice of observation variable to return error-correlation matrix for
+
+        :return: populated error-correlation matrix
+        """
+
+        raise NotImplementedError
+
+
+if __name__ == "__main__":
+    pass