s2-rut-python 0.0.1__py3-none-any.whl

docs/conf.py

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+#!/usr/bin/env python
+#
+# s2_rut_python 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.
+
+import s2_rut_python
+
+project_title = "s2_rut_python".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",
+]
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ["_templates"]
+
+# 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 = "Jacob Fahy"
+author = "Jacob Fahy"
+
+# 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 = s2_rut_python.__version__
+# The full version, including alpha/beta/rc tags.
+release = s2_rut_python.__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"
+
+# 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 = {
+    "announcement": "<strong>Beta Version:</strong> This software is a beta version, results should be used with caution. Please share any feedback you have after using the tool.",
+}
+
+# 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 = "s2_rut_pythondoc"
+
+
+# -- 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 = [
+    (
+        "content/user/user_guide",
+        "user_manual.tex",
+        "{}: User Guide".format(project_title),
+        "Jacob Fahy",
+        "manual",
+    ),
+    (
+        "content/user/atbd",
+        "atbd.tex",
+        "{}: Algorithm Theoretical Basis Document".format(project_title),
+        "Jacob Fahy",
+        "manual",
+    ),
+]

examples/run_example.py

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+"""example: read a Sentinel-2 L1C SAFE product and run S2-RUT."""
+
+import os
+import glob
+import socket
+
+import matplotlib.pyplot as plt
+from eoio import read
+from shapely import wkt
+
+from s2_rut_python.interface import S2RUTTool
+
+if (
+    socket.gethostname() == "lyon.npl.co.uk"
+    or socket.gethostname() == "leipzig.npl.co.uk"
+    or "leiden" in socket.gethostname()
+):
+    DATA_DIRECTORY = "/mnt/t/data/"
+else:
+    DATA_DIRECTORY = r"T:\ECO\EOServer\data"
+
+
+# Define input path from test datasets
+SAFE_PATH = os.path.join(
+    DATA_DIRECTORY,
+    "unittest_datasets",
+    "S2MSIL1C",
+    "S2A_MSIL1C_20251128T111431_N0511_R137_T30UXE_20251128T121631.SAFE",
+)
+print("SAFE PATH:", SAFE_PATH)
+
+# Define ROI
+roi_string = "POLYGON ((\
+ -0.913910 53.786950,\
+ -0.382900 53.776490,\
+ -0.406240 53.464690,\
+ -0.925060 53.474770,\
+ -0.913910 53.786950\
+))"
+
+geom = wkt.loads(roi_string)
+
+# Read the dataset with eoio, selecting only a few bands and auxiliary variables for efficiency.
+bands = ["B01", "B03", "B09"]
+ds = read(
+    SAFE_PATH,
+    vars_sel={
+        "meas": bands,
+        "aux": [
+            "solar_zenith_angle",
+            "solar_azimuth_angle",
+            "viewing_zenith_angle",
+            "viewing_azimuth_angle",
+        ],
+    },
+    read_params={
+        "use_chunks": True,
+        "metadata_level": "all",
+        "save_extracted": True,
+        "ave_va_det": True,
+    },
+    subset={"roi": geom, "roi_crs": "EPSG:4326"},
+    processors={
+        "interpolate": {
+            "coords": ["y_5000m", "x_5000m"],
+            "data_vars": ["solar_zenith_angle"],
+            "target_grid": [["y_60m", "y_10m"], ["x_60m", "x_10m"]],
+            "method": "linear",
+            "inplace": False,
+        }
+    },
+)
+
+# Run S2-RUT on the dataset, computing both random and systematic uncertainties.
+print("Running S2-RUT")
+rut = S2RUTTool()
+ds_out = rut.run(ds=ds, data_vars=bands, group_unc=True)
+
+
+# Create a single grid plot: rows = bands, columns = [reflectance, random [%], systematic [%]].
+fig, axes = plt.subplots(
+    nrows=len(bands),
+    ncols=3,
+    figsize=(15, 4 * len(bands)),
+)
+
+# Handle single band case (axes is 1D instead of 2D).
+if len(bands) == 1:
+    axes = axes.reshape(1, -1)
+
+for i, band in enumerate(bands):
+    # Column 0: Reflectance
+    ds_out[band].plot(ax=axes[i, 0], robust=True)
+    axes[i, 0].set_title(f"{band} Reflectance")
+    axes[i, 0].set_xlabel("")
+    axes[i, 0].set_ylabel("")
+
+    # Column 1: Random uncertainty [%]
+    random_unc_pct = 100.0 * ds_out[f"u_random_{band}"] / ds_out[band]
+    random_unc_pct.plot(ax=axes[i, 1], robust=True)
+    axes[i, 1].set_title(f"{band} Random Uncertainty [%]")
+    axes[i, 1].set_xlabel("")
+    axes[i, 1].set_ylabel("")
+
+    # Column 2: Systematic uncertainty [%]
+    sys_unc_pct = 100.0 * ds_out[f"u_systematic_{band}"] / ds_out[band]
+    sys_unc_pct.plot(ax=axes[i, 2], robust=True)
+    axes[i, 2].set_title(f"{band} Systematic Uncertainty [%]")
+    axes[i, 2].set_xlabel("")
+    axes[i, 2].set_ylabel("")
+
+plt.tight_layout()
+plt.savefig("s2rut_example.png")
+
+
+if __name__ == "__main__":
+    pass

examples/temporary_example.py

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+import sys
+import os
+
+import matplotlib
+from eoio import read
+
+import s2_rut_python._vendor  # noqa: F401
+
+from S2RUT import S2RUT_L1
+
+import os
+
+this_directory = os.path.dirname(__file__)
+
+file = os.path.abspath(
+    os.path.join(
+        os.path.dirname(this_directory),
+        "third-party",
+        "Data",
+        "S2A_MSIL1C_20210310T084801_N0500_R107_T33KWP_20230525T152740.SAFE",
+    )
+)
+# Open product using eoio
+ds = read(
+    file,
+    vars_sel={
+        "meas": ["B01"],  # Read only a few bands for efficiency
+        "aux": [
+            "solar_zenith_angle",
+            "solar_azimuth_angle",
+            "viewing_zenith_angle",
+            "viewing_azimuth_angle",
+        ],
+    },
+    read_params={
+        "use_chunks": False,
+        "metadata_level": "all",
+        "save_extracted": True,
+        "ave_va_det": True,  # Average over the detector dimension for the angle variables
+    },
+    processors={
+        "interpolate": {
+            "coords": ["y_5000m", "x_5000m"],
+            "data_vars": ["solar_zenith_angle"],
+            "target_grid": ["y_60m", "x_60m"],
+            "method": "linear",
+            "inplace": True,
+        },
+    },
+)
+
+print(ds.data_vars)
+# print(ds['solar_zenith_angle'])
+print(ds.coords)
+
+# Compute uncertainty (absolute value, in reflectance dimension)
+input_contributors = os.path.abspath(
+    os.path.join(
+        os.path.dirname(this_directory), "third-party", "Data", "unc_contributors.json"
+    )
+)
+
+metadata = {
+    "spacecraft": None,
+    "quant": None,
+    "A": [],
+    "offset": [],
+    "alpha": {},
+    "beta": {},
+    "Esun": [],
+    "Usun": None,
+    "refined": False,
+}  # this dictionary contains the relevant metadata parameters
+# read required metadata from ds.attrs and fill the metadata dictionary
+METADATA_MAP = {
+    "spacecraft": "platform",
+    "quant": "quantification_level",
+    "Usun": "reflectance_conversion_u",
+}
+VAR_MTD_MAP = {
+    "Esun": "solar_irradiance",
+    "alpha": "noise_model_alpha",
+    "beta": "noise_model_beta",
+    "A": "physical_gains",
+    "offset": "radiometric_offset",
+}
+
+for key, path in METADATA_MAP.items():
+    if path in ds.attrs:
+        metadata[key] = ds.attrs[path]
+    elif path in ds.attrs["product_metadata"]:
+        metadata[key] = ds.attrs["product_metadata"][path]
+    else:
+        raise KeyError(
+            f"Required metadata parameter '{key}' not found in dataset attributes at path '{path}'."
+        )
+
+for key, path in VAR_MTD_MAP.items():
+    metadata[key] = {
+        band: ds[band].attrs["product_metadata"][path]
+        for band in ds.data_vars
+        if "B" in band
+    }
+
+print("Metadata extracted for uncertainty calculation:", metadata)
+RUTl1 = S2RUT_L1(input_contributors)
+u_ref, u_cont = RUTl1.unc_calculation_abs(
+    ds["B01"].values,
+    "B01",
+    0,
+    metadata,
+    [ds["solar_zenith_angle"].values],
+    do_contributor=True,
+)
+
+
+print("Uncertainty calculated for B01:", u_ref, u_cont)
+print("Shape of u_ref:", u_ref.shape)
+print("u_cont keys:", u_cont.keys())
+
+
+from s2_rut_python.interface import S2RUTTool
+
+rut_processor = S2RUTTool()
+ds = rut_processor.run(
+    ds,
+    data_vars=["B01"],
+    group_unc=False,  # set to True to compute group uncertainties (systematic and random)
+)
+
+# Check the resulting dataset
+print("Data variables in resulting dataset:", ds.data_vars)
+print(ds.unc)
+
+# compare with reference uncertainty
+import matplotlib.pyplot as plt
+
+# plt.imshow(ds.B01.values)
+# plt.title("B01 reflectance")
+# plt.colorbar()
+# plt.show()
+# for unc in ds.data_vars:
+#     if 'u_' in unc:
+#         print(f"Comparing {unc} with reference uncertainty...")
+#         if unc.split('_B01')[0] in u_cont:
+#             plt.imshow(ds[unc].values - u_cont[unc.split('_B01')[0]])
+#             plt.title(f"Difference between {unc} and reference uncertainty")
+#             plt.colorbar()
+#             plt.show()
+
+ds = read(
+    file,
+    vars_sel={
+        "meas": ["B01"],  # Read only a few bands for efficiency
+        "aux": [
+            "solar_zenith_angle",
+            "solar_azimuth_angle",
+            "viewing_zenith_angle",
+            "viewing_azimuth_angle",
+        ],
+    },
+    read_params={
+        "use_chunks": False,
+        "metadata_level": "all",
+        "save_extracted": True,
+        "ave_va_det": True,  # Average over the detector dimension for the angle variables
+    },
+    processors={
+        "interpolate": {
+            "coords": ["y_5000m", "x_5000m"],
+            "data_vars": ["solar_zenith_angle"],
+            "target_grid": ["y_60m", "x_60m"],
+            "method": "linear",
+            "inplace": True,
+        },
+        "s2_rut": {
+            "data_vars": ["B01"],
+            "group_unc": True,  # set to True to compute group uncertainties (systematic and random)
+        },
+    },
+)
+
+print("Data variables in resulting dataset after s2_rut processor:", ds.data_vars)
+print(ds.unc)
+
+for unc in ds.data_vars:
+    if "u_" in unc:
+        print(f"Comparing {unc} with reference uncertainty...")
+        if unc.split("_B01")[0] in u_cont:
+            plt.imshow(ds[unc].values - u_cont[unc.split("_B01")[0]])
+            plt.title(f"Difference between {unc} and reference uncertainty")
+            plt.colorbar()
+            plt.show()
+        else:
+            import numpy as np
+
+            (100 * ds[unc] / ds["B01"]).plot(
+                robust=True
+            )  # , vmin=np.nanpercentile(100*ds[unc].values / ds['B01'].values, 1), vmax=np.nanpercentile(100*ds[unc].values / ds['B01'].values, 99))  # relative uncertainty in percentage
+            plt.title(f"{unc} (no reference uncertainty available)")
+            # plt.colorbar()
+            plt.show()

s2_rut_python/__init__.py

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+"""s2_rut_python - Pure Python port of SNAP's Sentinel-2 radiometric uncertainty tool"""
+
+__author__ = "Sam Hunt <sam.hunt@npl.co.uk>"
+__all__: list = []
+
+from ._version import get_versions
+
+__version__ = get_versions()["version"]
+del get_versions

s2_rut_python/_vendor.py

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+"""
+Internal helper to make vendored third-party S2-RUT code importable.
+
+This module adjusts sys.path to include the vendored subtree.
+Do not modify without updating the subtree integration.
+"""
+
+import os
+import sys
+
+_BASE_DIR = os.path.abspath(os.path.dirname(os.path.dirname(__file__)))
+_VENDOR_DIR = os.path.join(
+    _BASE_DIR,
+    "third-party",
+    "Source",
+)
+
+if _VENDOR_DIR not in sys.path:
+    sys.path.insert(0, _VENDOR_DIR)

s2_rut_python/_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": "2026-04-11T21:23:36+0100",
+ "dirty": false,
+ "error": null,
+ "full-revisionid": "53f4b6263d29cba0b31d24f7520fab6bd921c56a",
+ "version": "0.0.1"
+}
+'''  # END VERSION_JSON
+
+
+def get_versions():
+    return json.loads(version_json)