SAR-ARD · johntruckenbrodt · Oct 13, 2023 · Oct 13, 2023
diff --git a/S1_NRB/ard.py b/S1_NRB/ard.py
diff --git a/S1_NRB/metadata/extract.py b/S1_NRB/metadata/extract.py
@@ -593,10 +593,7 @@ def calc_enl(tif, block_size=30, return_arr=False, decimals=2):
 
     References
     ----------
-    .. [1]  S. N. Anfinsen, A. P. Doulgeris and T. Eltoft,
-            "Estimation of the Equivalent Number of Looks in Polarimetric Synthetic Aperture Radar Imagery,"
-            in IEEE Transactions on Geoscience and Remote Sensing, vol. 47, no. 11, pp. 3795-3809, Nov. 2009,
-            doi: 10.1109/TGRS.2009.2019269.
+    :cite:`anfinsen.etal_2009`
     """
     with Raster(tif) as ras:
         arr = ras.array()

diff --git a/docs/about/changelog.rst b/docs/about/changelog.rst
@@ -57,7 +57,7 @@ Changelog
 * New metadata config parameters (`#110 <https://github.com/SAR-ARD/S1_NRB/pull/110>`_)
 * support for scenes acquired in NRT Slicing mode (`#112 <https://github.com/SAR-ARD/S1_NRB/pull/112>`_)
 
-`Full Changelog <https://github.com/SAR-ARD/S1_NRB/compare/v1.3.0...v1.4.0>`_
+`Full v1.4.0 Changelog <https://github.com/SAR-ARD/S1_NRB/compare/v1.3.0...v1.4.0>`_
 
 1.3.0 | 2023-05-24
 ------------------
@@ -70,7 +70,7 @@ Changelog
 * enhanced time filtering (`#84 <https://github.com/SAR-ARD/S1_NRB/pull/84>`_)
 * general processor improvements (`#85 <https://github.com/SAR-ARD/S1_NRB/pull/85>`_)
 
-`Full Changelog <https://github.com/SAR-ARD/S1_NRB/compare/v1.2.0...v1.3.0>`_
+`Full v1.3.0 Changelog <https://github.com/SAR-ARD/S1_NRB/compare/v1.2.0...v1.3.0>`_
 
 1.2.0 | 2022-12-29
 ------------------
@@ -81,7 +81,7 @@ Changelog
 * add DEM as additional output layer (`#70 <https://github.com/SAR-ARD/S1_NRB/pull/70>`_)
 * sigma0 processing and annotation layer configuration (`#74 <https://github.com/SAR-ARD/S1_NRB/pull/74>`_)
 
-`Full Changelog <https://github.com/SAR-ARD/S1_NRB/compare/v1.1.0...v1.2.0>`_
+`Full v1.2.0 Changelog <https://github.com/SAR-ARD/S1_NRB/compare/v1.1.0...v1.2.0>`_
 
 1.1.0 | 2022-09-29
 ------------------
@@ -93,7 +93,7 @@ Changelog
 * documentation update reflecting the recent process restructuring (`#66 <https://github.com/SAR-ARD/S1_NRB/pull/66>`_)
 * renamed processing mode 'snap' to 'rtc' (`#67 <https://github.com/SAR-ARD/S1_NRB/pull/67>`_)
 
-`Full Changelog <https://github.com/SAR-ARD/S1_NRB/compare/v1.0.2...v1.1.0>`_
+`Full v1.1.0 Changelog <https://github.com/SAR-ARD/S1_NRB/compare/v1.0.2...v1.1.0>`_
 
 1.0.2 | 2022-08-24
 ------------------
@@ -106,14 +106,14 @@ Changelog
 * Fix and improve metadata geometry handling (`#57 <https://github.com/SAR-ARD/S1_NRB/pull/57>`_)
 * SNAP 9 compatibility (`#58 <https://github.com/SAR-ARD/S1_NRB/pull/58>`_)
 
-`Full Changelog <https://github.com/SAR-ARD/S1_NRB/compare/v1.0.1...v1.0.2>`_
+`Full v1.0.2 Changelog <https://github.com/SAR-ARD/S1_NRB/compare/v1.0.1...v1.0.2>`_
 
 1.0.1 | 2022-07-03
 ------------------
 
 * dem handling improvements (`#45 <https://github.com/SAR-ARD/S1_NRB/pull/45>`_)
 
-`Full Changelog <https://github.com/SAR-ARD/S1_NRB/compare/v1.0.0...v1.0.1>`_
+`Full v1.0.1 Changelog <https://github.com/SAR-ARD/S1_NRB/compare/v1.0.0...v1.0.1>`_
 
 1.0.0 | 2022-06-23
 ------------------
@@ -125,15 +125,15 @@ Changelog
 * Geolocation accuracy (`#40 <https://github.com/SAR-ARD/S1_NRB/pull/40>`_)
 * various bug fixes and documentation improvements
 
-`Full Changelog <https://github.com/SAR-ARD/S1_NRB/compare/v0.4.2...v1.0.0>`_
+`Full v1.0.0 Changelog <https://github.com/SAR-ARD/S1_NRB/compare/v0.4.2...v1.0.0>`_
 
 0.4.2 | 2022-06-16
 ------------------
 
 * Update documentation (`#27 <https://github.com/SAR-ARD/S1_NRB/pull/27>`_)
 * find unpacked .SAFE scenes in scene_dir (instead of just .zip) (`aea53a5 <https://github.com/SAR-ARD/S1_NRB/commit/aea53a57bc5fa1418fea4f46f69b41b7332909b1>`_)
 
-`Full Changelog <https://github.com/SAR-ARD/S1_NRB/compare/v0.4.1...v0.4.2>`_
+`Full v0.4.2 Changelog <https://github.com/SAR-ARD/S1_NRB/compare/v0.4.1...v0.4.2>`_
 
 0.4.1 | 2022-06-01
 ------------------
@@ -142,7 +142,7 @@ Changelog
 * set dem download authentication via env. variables (`#26 <https://github.com/SAR-ARD/S1_NRB/pull/26>`_)
 * various bug fixes
 
-`Full Changelog <https://github.com/SAR-ARD/S1_NRB/compare/v0.4.0...v0.4.1>`_
+`Full v0.4.1 Changelog <https://github.com/SAR-ARD/S1_NRB/compare/v0.4.0...v0.4.1>`_
 
 0.4.0 | 2022-05-30
 ------------------
@@ -156,7 +156,7 @@ Changelog
 * Set up sphinx documentation (`#23 <https://github.com/SAR-ARD/S1_NRB/pull/23>`_)
 * AOI scene selection (`#24 <https://github.com/SAR-ARD/S1_NRB/pull/24>`_)
 
-`Full Changelog <https://github.com/SAR-ARD/S1_NRB/compare/v0.3.0...v0.4.0>`_
+`Full v0.4.0 Changelog <https://github.com/SAR-ARD/S1_NRB/compare/v0.3.0...v0.4.0>`_
 
 0.3.0 | 2022-03-30
 ------------------
@@ -170,13 +170,9 @@ Changelog
 * Improved RGB composite (`#15 <https://github.com/SAR-ARD/S1_NRB/pull/15>`_)
 * Store DEM/WBM tiles in UTM zones different to the native MGRS zone (`#16 <https://github.com/SAR-ARD/S1_NRB/pull/16>`_)
 
-`Full Changelog <https://github.com/SAR-ARD/S1_NRB/compare/v0.2.0...v0.3.0>`_
+`Full v0.3.0 Changelog <https://github.com/SAR-ARD/S1_NRB/compare/v0.2.0...v0.3.0>`_
 
 0.2.0 | 2022-03-03
 ------------------
 
-`Full Changelog <https://github.com/SAR-ARD/S1_NRB/compare/v0.1.0...v0.2.0>`_
-
-0.1.0 | 2022-01-14
-------------------
-
+`Full v0.2.0 Changelog <https://github.com/SAR-ARD/S1_NRB/compare/v0.1.0...v0.2.0>`_
diff --git a/docs/general/enl.rst b/docs/general/enl.rst
@@ -9,9 +9,9 @@ In case of linear scaled backscatter data, ENL can be calculated as:
 .. math::
     ENL = \frac{\mu^2}{\sigma^2}
 
-where :math:`\mu` is the mean and :math:`\sigma` is the standard deviation of the image. (:footcite:`cls_2016`, section A1.1.7)
+where :math:`\mu` is the mean and :math:`\sigma` is the standard deviation of the image. (:cite:`cls_2016`, section A1.1.7)
 
-The ENL value stored in the metadata of each S1-NRB product is calculated as suggested in :footcite:`anfinsen.etal_2009`, where ENL is first
+The ENL value stored in the metadata of each S1-NRB product is calculated as suggested in :cite:`anfinsen.etal_2009`, where ENL is first
 calculated for small pixel windows over the cross-polarized backscatter image and afterwards the median value of
 the distribution is selected.
 
@@ -40,7 +40,7 @@ the resulting array is shown in Figure 1.
 
 Comparison between GRDH and NRB
 -------------------------------
-:footcite:`cls_2016` provides estimates of ENL for different Sentinel-1 products (average over all swaths), e.g. ENL of 4.4 for GRDH in
+:cite:`cls_2016` provides estimates of ENL for different Sentinel-1 products (average over all swaths), e.g. ENL of 4.4 for GRDH in
 IW mode, and a description of the estimation process in section D1. The following shows a simple comparison between the
 GRDH product:
 
@@ -68,7 +68,3 @@ consistently higher ENL values for the GRDH product (Avg. ENL: 4.81) in comparis
     :alt: Figure 3: Scatter plot comparing ENL values between GRDH and NRB, calculated for selected areas (see Fig. 2).
 
     Figure 3: Scatter plot comparing ENL values between GRDH and NRB, calculated for selected areas (see Fig. 2).
-
-References
-----------
-.. footbibliography::
diff --git a/docs/general/geoaccuracy.rst b/docs/general/geoaccuracy.rst
@@ -2,7 +2,7 @@ Geolocation Accuracy
 ====================
 
 Item 4.3 of the CARD4L NRB specification requires, as minimum, an estimate of the absolute location error (ALE) "as
-bias and standard deviation, provided in slant range/azimuth, or Northing/Easting" [1]. As desired target the accuracy
+bias and standard deviation, provided in slant range/azimuth, or Northing/Easting" :cite:`ceos_2021`. As desired target the accuracy
 is less or equal 0.1 pixels radial root mean square error (rRMSE), which can be defined as:
 
 .. math::
@@ -32,7 +32,7 @@ Currently, the following simplifications need to be considered for the calculati
 of each S1-NRB product:
 
 * Processing induced errors (:math:`RMSE_{proc}`) and the error term related to DEM interpolation are not further considered and assumed to be 0.
-* The DEM accuracy (:math:`\sigma_{DEM}`) is estimated on the global mean accuracy LE90 reported for the COP-DEM [2] under the assumption of gaussian distribution:
+* The DEM accuracy (:math:`\sigma_{DEM}`) is estimated on the global mean accuracy LE90 reported for the COP-DEM :cite:`airbus_2022` under the assumption of gaussian distribution:
 
     * Global: LE90 = 2.57; LE68 :math:`\approx` 1.56
 
@@ -41,8 +41,3 @@ of each S1-NRB product:
 Development Status
 ------------------
 The development status is tracked and discussed in the following Github issue: https://github.com/SAR-ARD/S1_NRB/issues/33
-
-References
------------
-* [1] https://ceos.org/ard/files/PFS/NRB/v5.5/CARD4L-PFS_NRB_v5.5.pdf
-* [2] https://spacedata.copernicus.eu/documents/20126/0/GEO1988-CopernicusDEM-SPE-002_ProductHandbook_I1.00.pdf/082dd479-f908-bf42-51bf-4c0053129f7c?t=1586526993604
diff --git a/docs/index.rst b/docs/index.rst
@@ -7,10 +7,10 @@ Further information about these products can be found
 `here <https://sentinel.esa.int/web/sentinel/sentinel-1-ard-normalised-radar-backscatter-nrb-product>`_.
 
 .. toctree::
-   :maxdepth: 2
+    :maxdepth: 2
 
-   general/index.rst
-   api.rst
-   examples/index.rst
-   about/index.rst
-   tocs.rst
+    general/index.rst
+    api.rst
+    examples/index.rst
+    about/index.rst
+    tocs.rst
diff --git a/docs/references.bib b/docs/references.bib
@@ -31,4 +31,22 @@ @article{anfinsen.etal_2009
     pages = {3795--3809},
     issn = {0196-2892, 1558-0644},
     doi = {10.1109/TGRS.2009.2019269}
+}
+@techreport{ceos_2021,
+  title = {Analysis {{Ready Data}} for {{Land}}: {{Normalized Radar Backscatter}}},
+  author = {CEOS},
+  institution = {CEOS},
+  date = {2021-10-14},
+  year = {2021},
+  number = {5.5},
+  url = {https://ceos.org/ard/files/PFS/NRB/v5.5/CARD4L-PFS_NRB_v5.5.pdf}
+}
+@techreport{airbus_2022,
+  title = {Copernicus {{DEM Product Handbook}}},
+  author = {Airbus},
+  institution = {Airbus},
+  date = {2022-11-29},
+  year = {2022},
+  number = {5.0},
+  url = {https://spacedata.copernicus.eu/documents/20123/122407/GEO1988-CopernicusDEM-SPE-002_ProductHandbook_I5.0+%281%29.pdf/706ee17d-2cce-f1fa-a73e-1686d28f09dd?t=1679657087883}
 }
diff --git a/docs/tocs.rst b/docs/tocs.rst
@@ -1,6 +1,8 @@
-Indices and tables
-==================
+.. only:: html
 
-* :ref:`genindex`
-* :ref:`modindex`
-* :ref:`search`
+    Indices and tables
+    ==================
+
+    * :ref:`genindex`
+    * :ref:`modindex`
+    * :ref:`search`