obsarray 0.2.4__tar.gz → 0.2.6__tar.gz

{obsarray-0.2.4 → obsarray-0.2.6}/.gitignore

@@ -76,8 +76,8 @@ instance/
 .scrapy
 
 # Sphinx documentation
-docs/sphinx/_build/
-docs/sphinx/content/api
+docs/_build/
+docs/content/user/generated/
 
 # PyBuilder
 target/

{obsarray-0.2.4/obsarray.egg-info → obsarray-0.2.6}/PKG-INFO

@@ -1,7 +1,7 @@
 Metadata-Version: 2.1
 Name: obsarray
-Version: 0.2.4
-Summary: Measurement uncertainty handling in Python
+Version: 0.2.6
+Summary: Measurement data handling in Python
 Home-page: https://github.com/comet-toolkit/obsarray
 Author: CoMet Toolkit Team
 Author-email: team@comet-toolkit.org
@@ -9,9 +9,10 @@ License: GPLv3
 Platform: UNKNOWN
 Classifier: Development Status :: 2 - Pre-Alpha
 Classifier: Programming Language :: Python
-Classifier: Programming Language :: Python :: 3.6
-Classifier: Programming Language :: Python :: 3.7
 Classifier: Programming Language :: Python :: 3.8
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
 Provides-Extra: dev
 License-File: LICENSE
 

obsarray-0.2.6/docs/conf.py

@@ -0,0 +1,181 @@
+#!/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/comet_logo.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",
+    ),
+]

obsarray-0.2.6/docs/index.rst

@@ -0,0 +1,66 @@
+obsarray: Measurement data handling in Python
+=============================================
+
+**obsarray** is an extension to `xarray <https://docs.xarray.dev/en/stable/>`_ to support defining, storing and interfacing with measurement data - in particular, measurement uncertainty information using standardised metadata. It is designed to work well with `netCDF <https://www.unidata.ucar.edu/software/netcdf/>`_ files and for the Earth Observation community.
+
+**obsarray** is part of the `CoMet Toolkit <https://www.comet-toolkit.org>`_ (community metrology toolkit), and can combined with the  `punpy <https://punpy.readthedocs.io/en/latest/>`_ (propagating uncertainties in python) module for very simple propagation of defined data uncertainties through arbitrary python functions.
+
+.. grid:: 2
+    :gutter: 2
+
+    .. grid-item-card::  Quickstart Guide
+        :link: content/user/quickstart
+        :link-type: doc
+
+        New to *obsarray*? Check out the quickstart guide for an introduction.
+
+    .. grid-item-card::  User Guide
+        :link: content/user/user_guide
+        :link-type: doc
+
+        The user guide provides a documentation and examples how to use **obsarray** to handle measurement data.
+
+    .. grid-item-card::  API Reference
+        :link: content/user/api
+        :link-type: doc
+
+        The API Reference contains a description the **obsarray** API.
+
+    .. grid-item-card::  Developer Guide
+        :link: content/developer/developer_guide
+        :link-type: doc
+
+        Guide for contributing to **obsarray** (under development).
+
+
+Acknowledgements
+----------------
+
+obsarray has been developed by `Sam Hunt <https://github.com/shunt16>`_.
+
+The development has been funded by:
+
+* The UK's Department for Business, Energy and Industrial Strategy's (BEIS) National Measurement System (NMS) programme
+* The IDEAS-QA4EO project funded by the European Space Agency.
+
+
+Project status
+--------------
+
+obsarray is under active development. It is beta software.
+
+.. toctree::
+   :maxdepth: 2
+   :hidden:
+   :caption: For users
+
+   Quickstart <content/user/quickstart>
+   User Guide <content/user/user_guide>
+   API Reference <content/user/api>
+
+.. toctree::
+   :maxdepth: 2
+   :hidden:
+   :caption: For developers/contributors
+
+   Developer Guide <content/developer/developer_guide>

{obsarray-0.2.4 → obsarray-0.2.6}/obsarray/__init__.py

@@ -8,6 +8,7 @@ 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-0.2.4 → obsarray-0.2.6}/obsarray/_version.py

@@ -8,11 +8,11 @@ import json
 
 version_json = '''
 {
- "date": "2023-03-06T21:45:43+0000",
+ "date": "2024-03-26T17:59:27+0000",
  "dirty": false,
  "error": null,
- "full-revisionid": "f73bc4314bb5f5dca1e7ee619ae4c20527ed1d87",
- "version": "v0.2.4"
+ "full-revisionid": "3f90a44048e43a24a7ec1115d7b727944416ba9f",
+ "version": "v0.2.6"
 }
 '''  # END VERSION_JSON
 

{obsarray-0.2.4 → obsarray-0.2.6}/obsarray/err_corr.py

@@ -1,7 +1,7 @@
 """err_corr_forms - module for the defintion of error-correlation parameterisation forms"""
 
 import abc
-from typing import Callable, Type, Union
+from typing import Callable, Type, Union, List
 import numpy as np
 from comet_maths.linear_algebra.matrix_conversion import expand_errcorr_dims
 
@@ -69,23 +69,79 @@ class BaseErrCorrForm(abc.ABC):
         """Form name"""
         pass
 
-    def expand_dim_matrix(self, submatrix, sli):
+    def expand_dim_matrix(
+        self, submatrix: np.ndarray, submatrix_dim: Union[str, List[str]], sli: tuple
+    ):
         return expand_errcorr_dims(
             in_corr=submatrix,
-            in_dim=self.dims,
+            in_dim=submatrix_dim,
             out_dim=list(self._obj[self._unc_var_name][sli].dims),
-            dim_sizes={
-                dim: self._obj.dims[dim]
-                for dim in self._obj[self._unc_var_name][sli].dims
-            },
+            dim_sizes=self.get_sliced_dim_sizes_uncvar(sli),
         )
 
-    def slice_full_cov(self, full_matrix, sli):
-        mask_array = np.ones(self._obj[self._unc_var_name].shape, dtype=bool)
+    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: 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: 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_full_cov(self, full_matrix: np.ndarray, sli: tuple) -> np.ndarray:
+        return self.slice_flattened_matrix(
+            full_matrix, self._obj[self._unc_var_name].shape, sli
+        )
+
+    def slice_flattened_matrix(self, flattened_matrix, variable_shape, sli):
+        mask_array = np.ones(variable_shape, dtype=bool)
         mask_array[sli] = False
 
         return np.delete(
-            np.delete(full_matrix, mask_array.ravel(), 0), mask_array.ravel(), 1
+            np.delete(flattened_matrix, mask_array.ravel(), 0), mask_array.ravel(), 1
         )
 
     @abc.abstractmethod
@@ -100,6 +156,20 @@ class BaseErrCorrForm(abc.ABC):
         """
         pass
 
+    def build_dot_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
+        """
+
+        return self.expand_dim_matrix(
+            self.build_matrix(sli), self.get_sliced_dims_errcorr(sli), sli
+        )
+
 
 def register_err_corr_form(form_name: str) -> Callable:
     """
@@ -122,7 +192,7 @@ class RandomCorrelation(BaseErrCorrForm):
     form = "random"
     is_random = True
 
-    def build_matrix(self, sli):
+    def build_matrix(self, sli: tuple) -> np.ndarray:
         """
         Returns uncertainty effect error-correlation matrix, populated with error-correlation values defined
         in this parameterisation
@@ -133,16 +203,12 @@ class RandomCorrelation(BaseErrCorrForm):
         """
 
         # evaluate correlation over matrices in form defintion
-        dim_lens = [len(self._obj[dim]) for dim in self.dims]
+        dim_lens = self.get_sliced_shape_errcorr(sli)
         n_elems = int(np.prod(dim_lens))
 
-        dims_matrix = np.eye(n_elems)
-
-        # expand to correlation matrix over all variable dims
-        return self.expand_dim_matrix(dims_matrix, sli)
+        submatrix = np.eye(n_elems)
 
-        # # subset to slice
-        # return self.slice_full_cov(full_matrix, sli)
+        return submatrix
 
 
 @register_err_corr_form("systematic")
@@ -151,7 +217,7 @@ class SystematicCorrelation(BaseErrCorrForm):
     form = "systematic"
     is_systematic = True
 
-    def build_matrix(self, sli):
+    def build_matrix(self, sli: tuple) -> np.ndarray:
         """
         Returns uncertainty effect error-correlation matrix, populated with error-correlation values defined
         in this parameterisation
@@ -162,16 +228,12 @@ class SystematicCorrelation(BaseErrCorrForm):
         """
 
         # evaluate correlation over matrices in form defintion
-        dim_lens = [len(self._obj[dim]) for dim in self.dims]
+        dim_lens = self.get_sliced_shape_errcorr(sli)
         n_elems = int(np.prod(dim_lens))
 
-        dims_matrix = np.ones((n_elems, n_elems))
-
-        # expand to correlation matrix over all variable dims
-        return self.expand_dim_matrix(dims_matrix, sli)
+        submatrix = np.ones((n_elems, n_elems))
 
-        # subset to slice
-        # return self.slice_full_cov(full_matrix, sli)
+        return submatrix
 
 
 @register_err_corr_form("err_corr_matrix")
@@ -179,7 +241,7 @@ class ErrCorrMatrixCorrelation(BaseErrCorrForm):
 
     form = "err_corr_matrix"
 
-    def build_matrix(self, sli):
+    def build_matrix(self, sli: tuple) -> np.ndarray:
         """
         Returns uncertainty effect error-correlation matrix, populated with error-correlation values defined
         in this parameterisation
@@ -189,11 +251,26 @@ class ErrCorrMatrixCorrelation(BaseErrCorrForm):
         :return: populated error-correlation matrix
         """
 
-        # expand to correlation matrix over all variable dims
-        return self.expand_dim_matrix(self._obj[self.params[0]], sli)
+        all_dims = self._obj[self._unc_var_name].dims
+        all_dims_sizes = self._obj.sizes
+
+        sli_submatrix = tuple(
+            [sli[i] for i in range(len(all_dims)) if all_dims[i] in self.dims]
+        )
+
+        sliced_shape = tuple(
+            [
+                all_dims_sizes[all_dims[i]]
+                for i in range(len(all_dims))
+                if all_dims[i] in self.dims
+            ]
+        )
+
+        submatrix = self.slice_flattened_matrix(
+            self._obj[self.params[0]], sliced_shape, sli_submatrix
+        )
 
-        # # subset to slice
-        # return self.slice_full_cov(full_matrix, sli)
+        return submatrix
 
 
 @register_err_corr_form("ensemble")
@@ -201,7 +278,7 @@ class EnsembleCorrelation(BaseErrCorrForm):
 
     form = "ensemble"
 
-    def build_matrix(self, sli):
+    def build_matrix(self, sli: tuple) -> np.ndarray:
         """
         Returns uncertainty effect error-correlation matrix, populated with error-correlation values defined
         in this parameterisation