s2-rut-python 0.0.1__tar.gz

s2_rut_python-0.0.1/LICENSE

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+GNU LESSER GENERAL PUBLIC LICENSE
+                       Version 3, 29 June 2007
+
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s2_rut_python-0.0.1/MANIFEST.in

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+include versioneer.py
+include s2_rut_python/_version.py

s2_rut_python-0.0.1/PKG-INFO

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+Metadata-Version: 2.4
+Name: s2_rut_python
+Version: 0.0.1
+Summary: Pure Python port of ESA's Sentinel-2 radiometric uncertainty tool
+Author-email: Maddie Stedman <maddie.stedman@npl.co.uk>
+Project-URL: Homepage, http://gitlab.npl.co.uk/eco/tools/s2_rut_python
+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
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy
+Requires-Dist: matplotlib
+Requires-Dist: xarray
+Requires-Dist: obsarray
+Requires-Dist: processor_tools
+Provides-Extra: dev
+Requires-Dist: pre-commit; extra == "dev"
+Requires-Dist: tox; extra == "dev"
+Requires-Dist: sphinx; extra == "dev"
+Requires-Dist: sphinx_book_theme; extra == "dev"
+Requires-Dist: sphinx_rtd_theme; extra == "dev"
+Requires-Dist: ipython; extra == "dev"
+Requires-Dist: sphinx_design; extra == "dev"
+Dynamic: license-file
+
+# s2_rut_python
+
+Pure Python portion of Javi's Sentinel-2 radiometric uncertainty tool.
+
+## Beta Version
+
+**WARNING:** This software is a beta version, results should be used with caution. Please share any feedback you have after using the tool.
+
+## Usage
+
+Files are read into an xarray format for use with our other tools. eoio capabilities are used for accessing and extracting the metadata, used for calculating the uncertainties.
+
+Band selection takes one band or a list of **Sentinel-2 band names**: B01, B02, B03, B04, B05, B06, B07, B08, B8A, B09, B10, B11, B12.
+
+The current interface entry point is `S2RUTTool` and uncertainties can be returned either:
+
+* grouped by correlation component (`u_systematic_<band>`, `u_random_<band>`), or
+* per contributor (for example `u_noise_<band>`).
+
+Each individual type of components is categorised according to Gorrono *et al.* (2017).
+
+Usage of this module is as follows:
+
+```python
+from s2_rut_python.interface import S2RUTTool
+
+s2rut = S2RUTTool()
+ds_out = s2rut.run(
+    ds=s2_ds,
+    data_vars=['B01'],
+    group_unc=True,
+)
+```
+
+To run per-contributor uncertainties:
+
+```python
+ds_out = s2rut.run(
+    ds=s2_ds,
+    data_vars=['B01'],
+    group_unc=False,
+)
+```
+
+To limit contributors to a subset:
+
+```python
+ds_out = s2rut.run(
+    ds=s2_ds,
+    data_vars=['B01'],
+    group_unc=False,
+    subset_unc=['noise', 'adc', 'gamma'],
+)
+```
+
+Uncertainty variables are stored in the obsarray uncertainty accessor (for example `ds_out.unc['B01']`). Reflectance zero-values are masked to `NaN` before return.
+
+## Example
+
+An up-to-date runnable example is available in `examples/run_example.py`. It demonstrates reading Sentinel-2 L1C data with eoio, selecting an ROI subset for the current product, running `S2RUTTool.run(...)`, and plotting reflectance, random uncertainty [%], and systematic uncertainty [%].
+
+### Virtual environment
+
+It's always recommended to make a virtual environment for each of your python projects. Use your preferred virtual environment manager if you want and activate it for the rest of these commands. If you're unfamiliar, read https://realpython.com/python-virtual-environments-a-primer/. You can set one up using:
+
+```bash
+python -m venv venv
+```
+
+and then activate it on Windows by using `venv/Scripts/activate`.
+
+## Installation
+
+Install your package and its dependencies by using:
+
+```bash
+pip install -e .
+```
+
+## Development
+
+For developing the package, you'll want to install the pre-commit hooks as well. Type:
+
+```bash
+pre-commit install
+```
+
+Note that from now on when you commit, `black` will check your code for styling errors. If it finds any it will correct them, but the commit will be aborted. This is so that you can check its work before you continue. If you're happy, just commit again.
+
+## Compatibility
+
+## Authors
+
+s2_rut_python has been developed by `Rasma Ormane <rasma.ormane@npl.co.uk>`_. `Sam Hunt <sam.hunt@npl.co.uk>`_. and `Maddie Stedman <maddie.stedman@npl.co.uk>`_.
+
+## Citations
+
+Gorrono, J.; Fomferra, N.; Peters, M.; Gascon, F.; Underwood, C.I.; Fox, N.P.; Kirches, G.; Brockmann, C.
+A Radiometric Uncertainty Tool for the Sentinel 2 Mission. Remote Sens. 2017, 9, 178. https://doi.org/10.3390/rs9020178

s2_rut_python-0.0.1/README.md

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+# s2_rut_python
+
+Pure Python portion of Javi's Sentinel-2 radiometric uncertainty tool.
+
+## Beta Version
+
+**WARNING:** This software is a beta version, results should be used with caution. Please share any feedback you have after using the tool.
+
+## Usage
+
+Files are read into an xarray format for use with our other tools. eoio capabilities are used for accessing and extracting the metadata, used for calculating the uncertainties.
+
+Band selection takes one band or a list of **Sentinel-2 band names**: B01, B02, B03, B04, B05, B06, B07, B08, B8A, B09, B10, B11, B12.
+
+The current interface entry point is `S2RUTTool` and uncertainties can be returned either:
+
+* grouped by correlation component (`u_systematic_<band>`, `u_random_<band>`), or
+* per contributor (for example `u_noise_<band>`).
+
+Each individual type of components is categorised according to Gorrono *et al.* (2017).
+
+Usage of this module is as follows:
+
+```python
+from s2_rut_python.interface import S2RUTTool
+
+s2rut = S2RUTTool()
+ds_out = s2rut.run(
+    ds=s2_ds,
+    data_vars=['B01'],
+    group_unc=True,
+)
+```
+
+To run per-contributor uncertainties:
+
+```python
+ds_out = s2rut.run(
+    ds=s2_ds,
+    data_vars=['B01'],
+    group_unc=False,
+)
+```
+
+To limit contributors to a subset:
+
+```python
+ds_out = s2rut.run(
+    ds=s2_ds,
+    data_vars=['B01'],
+    group_unc=False,
+    subset_unc=['noise', 'adc', 'gamma'],
+)
+```
+
+Uncertainty variables are stored in the obsarray uncertainty accessor (for example `ds_out.unc['B01']`). Reflectance zero-values are masked to `NaN` before return.
+
+## Example
+
+An up-to-date runnable example is available in `examples/run_example.py`. It demonstrates reading Sentinel-2 L1C data with eoio, selecting an ROI subset for the current product, running `S2RUTTool.run(...)`, and plotting reflectance, random uncertainty [%], and systematic uncertainty [%].
+
+### Virtual environment
+
+It's always recommended to make a virtual environment for each of your python projects. Use your preferred virtual environment manager if you want and activate it for the rest of these commands. If you're unfamiliar, read https://realpython.com/python-virtual-environments-a-primer/. You can set one up using:
+
+```bash
+python -m venv venv
+```
+
+and then activate it on Windows by using `venv/Scripts/activate`.
+
+## Installation
+
+Install your package and its dependencies by using:
+
+```bash
+pip install -e .
+```
+
+## Development
+
+For developing the package, you'll want to install the pre-commit hooks as well. Type:
+
+```bash
+pre-commit install
+```
+
+Note that from now on when you commit, `black` will check your code for styling errors. If it finds any it will correct them, but the commit will be aborted. This is so that you can check its work before you continue. If you're happy, just commit again.
+
+## Compatibility
+
+## Authors
+
+s2_rut_python has been developed by `Rasma Ormane <rasma.ormane@npl.co.uk>`_. `Sam Hunt <sam.hunt@npl.co.uk>`_. and `Maddie Stedman <maddie.stedman@npl.co.uk>`_.
+
+## Citations
+
+Gorrono, J.; Fomferra, N.; Peters, M.; Gascon, F.; Underwood, C.I.; Fox, N.P.; Kirches, G.; Brockmann, C.
+A Radiometric Uncertainty Tool for the Sentinel 2 Mission. Remote Sens. 2017, 9, 178. https://doi.org/10.3390/rs9020178

s2_rut_python-0.0.1/docs/conf.py

@@ -0,0 +1,149 @@
+#!/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",
+    ),
+]

s2_rut_python-0.0.1/examples/run_example.py

@@ -0,0 +1,117 @@
+"""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