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+config: 1e167dd1dd46aaceff1d959b66b825f5
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_sources/api/core/compress.rst.txt

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+:html_theme.sidebar_secondary.remove:
+
+**************************
+Compression
+**************************
+.. automodule:: s2scat.core.compress
+   :members: 

_sources/api/core/index.rst.txt

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+
+**************************
+Core Functions
+**************************
+
+.. list-table:: Scattering Operations
+   :widths: 25 25
+   :header-rows: 1
+
+   * - Function Name
+     - Description
+   * - :func:`~s2scat.core.scatter.directional`
+     - Compute directional scattering covariances on the sphere (Mousset et al 2024).
+   * - :func:`~s2scat.core.scatter.directional_c`
+     - Compute directional scattering covariances on the sphere using a custom C backend (Mousset et al 2024).
+
+.. list-table:: Compression Operations
+   :widths: 25 25
+   :header-rows: 1
+
+   * - Function Name
+     - Description
+   * - :func:`~s2scat.core.compress.C01_C11_to_isotropic`
+     - Convert scattering covariances to their isotropic counterpart.
+
+.. list-table:: Synthesis Operations
+   :widths: 25 25
+   :header-rows: 1
+
+   * - Function Name
+     - Description
+   * - :func:`~s2scat.core.synthesis.fit_jaxopt_scipy`
+     - Minimises the declared loss function starting at params using jaxopt.
+   * - :func:`~s2scat.core.synthesis.fit_optax`
+     - Minimises the declared loss function starting at params using optax (adam).
+   * - :func:`~s2scat.core.synthesis.l2_covariance_loss`
+     - L2 loss wrapper for the scattering covariance.
+   * - :func:`~s2scat.core.synthesis.l2_loss`
+     - L2 loss for a single scattering covariance.
+   * - :func:`~s2scat.core.synthesis.get_P00prime`
+     - Computes P00prime which is the averaged power within each wavelet scale.
+
+.. toctree::
+   :hidden:
+   :maxdepth: 2
+   :caption: Core Functions
+
+   scatter
+   compress 
+   synthesis
+

_sources/api/core/scatter.rst.txt

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+:html_theme.sidebar_secondary.remove:
+
+**************************
+Scattering
+**************************
+.. automodule:: s2scat.core.scatter
+   :members: 

_sources/api/core/synthesis.rst.txt

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+
+**************************
+Synthesis
+**************************
+.. automodule:: s2scat.core.synthesis
+   :members: 

_sources/api/index.rst.txt

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+:html_theme.sidebar_secondary.remove:
+
 **************************
-Namespaces
+API
 **************************
-Automatically generated documentation for **<Project-name>** APIs. All functionality is accessible through a pip installation of the **<Project-name>** package.
+Automatically generated documentation for ``S2SCAT`` APIs. All functionality is accessible 
+through a pip installation of the ``S2SCAT`` package. Below is an overview of the 
+directory structure for the software.
 
-.. tabs:: 
-
-	.. tab:: Logs
+Directory structure 
+--------------------
 
-		.. include:: logs.rst
-
-	.. tab:: some
+.. code-block:: bash
 
-	.. tab:: other
+   s2scat/  
+   ├── core/               # Top-level functionality:
+   │      ├─ scatter.py            # - Scattering covariance transform.
+   │      ├─ compress.py           # - Statistical compression functions.
+   │      ├─ synthesis.py          # - Synthesis optimisation functions. 
+   │    
+   ├── operators/          # Internal functionality:
+   │      ├─ spherical.py          # - Specific spherical operations, e.g. batched SHTs.
+   │      ├─ matrices.py           # - Wrappers to generate cached values. 
+   │
+   ├── utility/            # Convenience functionality:
+   │      ├─ reorder.py            # - Reindexing and converting list and arrays.
+   │      ├─ statistics.py         # - Calculation of covariance statistics. 
+   │      ├─ normalisation.py      # - Normalisation functions for covariance statistics. 
+   │      ├─ plotting.py           # - Plotting functions for signals and statistics.
 
-	.. tab:: apis
+.. toctree::
+   :hidden:
+   :maxdepth: 1
+   :caption: Namespaces
+
+   core/index
+   operators/index
+   utility/index

_sources/api/operators/index.rst.txt

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+
+**************************
+Internal Functions
+**************************
+
+.. list-table:: Spherical Operations
+   :widths: 25 25
+   :header-rows: 1
+
+   * - Function Name
+     - Description
+   * - :func:`~s2scat.operators.spherical.make_flm_full`
+     - Reflects real harmonic coefficients to a complete set of coefficients using hermitian symmetry.
+   * - :func:`~s2scat.operators.spherical.make_flm_real`
+     - Compresses harmonic coefficients of a real signal into positive coefficients only which leverages hermitian symmetry.
+   * - :func:`~s2scat.operators.spherical.quadrature`
+     - Generates spherical quadrature weights associated with McEwen-Wiaux sampling.
+
+.. list-table:: Precompute helpers
+   :widths: 25 25
+   :header-rows: 1
+
+   * - Function Name
+     - Description
+   * - :func:`~s2scat.operators.matrices.generate_precompute_matrices`
+     - Generates the full set of precompute matrices for the scattering transform with :math:`\mathcal{O}(NL^3)` memory overhead.
+   * - :func:`~s2scat.operators.matrices.generate_recursive_matrices`
+     - Generates a small set of recursive matrices for underlying Wigner-d recursion algorithms with a modest :math:`\mathcal{O}(NL^2)` memory overhead.
+
+.. toctree::
+   :hidden:
+   :maxdepth: 2
+   :caption: Internal Functions
+
+   spherical
+   matrices 
+

_sources/api/operators/matrices.rst.txt

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+:html_theme.sidebar_secondary.remove:
+
+**************************
+Precomputations
+**************************
+.. automodule:: s2scat.operators.matrices
+   :members: 

_sources/api/operators/spherical.rst.txt

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+
+**************************
+Spherical Operations
+**************************
+.. automodule:: s2scat.operators.spherical
+   :members: 

_sources/api/utility/config.rst.txt

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+
+**************************
+Configuration Wrappers
+**************************
+.. automodule:: s2scat.utility.config
+   :members: 

_sources/api/utility/index.rst.txt

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+:html_theme.sidebar_secondary.remove:
+
+**************************
+Helper Functions
+**************************
+
+.. list-table:: Configuration Functions 
+   :widths: 25 25
+   :header-rows: 1
+
+   * - Function Name
+     - Description
+   * - :func:`~s2scat.utility.config.run_config`
+     - Generates and caches all precomputed arrays.
+
+.. list-table:: Statistics Functions
+   :widths: 25 25
+   :header-rows: 1
+
+   * - Function Name
+     - Description
+   * - :func:`~s2scat.utility.statistics.compute_mean_variance`
+     - Computes the mean and variance of spherical harmonic coefficients :math:`f_{\ell m}`.
+   * - :func:`~s2scat.utility.statistics.normalize_map`
+     - Normalises a spherical map to zero mean and unit variance.
+   * - :func:`~s2scat.utility.statistics.compute_P00`
+     - Stand alone function to compute the second order power statistics.
+   * - :func:`~s2scat.utility.statistics.compute_C01_and_C11`
+     - Stand alone function to compute the fourth and sixth order covariance statistics.
+   * - :func:`~s2scat.utility.statistics.add_to_S1`
+     - Computes and appends the mean field statistic :math:`\text{S1}_j = \langle |\Psi^\lambda f| \rangle` at scale :math:`j`.
+   * - :func:`~s2scat.utility.statistics.add_to_P00`
+     - Computes and appends the second order power statistic :math:`\text{P00}_j = \langle |\Psi^\lambda f|^2 \rangle` at scale :math:`j`.
+   * - :func:`~s2scat.utility.statistics.add_to_C01`
+     - Computes and appends the fourth order covariance statistic :math:`\text{C01}_j = \text{Cov}\big [ \Psi^{\lambda_1} f, \Psi^{\lambda_1} | \Psi^{\lambda_2} f | \big ]` at scale :math:`j`.
+   * - :func:`~s2scat.utility.statistics.add_to_C11`
+     - Computes and appends the sixth order covariance statistic :math:`\text{C11}_j = \text{Cov}\big [ \Psi^{\lambda_1} | \Psi^{\lambda_3} f |, \Psi^{\lambda_1} | \Psi^{\lambda_2} f | \big ]` at scale :math:`j`.
+   * - :func:`~s2scat.utility.statistics.apply_norm`
+     - Applies normalisation to a complete list of covariance statistics.
+
+.. list-table:: Statistical Normalisation Functions 
+   :widths: 25 25
+   :header-rows: 1
+
+   * - Function Name
+     - Description
+   * - :func:`~s2scat.utility.normalisation.compute_norm`
+     - Computes normalisation for the scattering covariance statistics.
+   * - :func:`~s2scat.utility.normalisation.apply_norm`
+     - Applies normalisation to a complete list of covariance statistics.
+
+.. list-table:: Reindexing Functions 
+   :widths: 25 25
+   :header-rows: 1
+
+   * - Function Name
+     - Description
+   * - :func:`~s2scat.utility.reorder.nested_list_to_list_of_arrays`
+     - Specific reindexing function which switches covariance wavelet scale list ordering.
+   * - :func:`~s2scat.utility.reorder.list_to_array`
+     - Converts list of covariance statistics to array of statistics for e.g. Loss functions.
+
+.. toctree::
+   :hidden:
+   :maxdepth: 2
+   :caption: Helper Functions
+
+   statistics
+   reorder 
+   normalisation
+   config
+

_sources/api/utility/normalisation.rst.txt

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+
+**************************
+Normalisation
+**************************
+.. automodule:: s2scat.utility.normalisation
+   :members: 

_sources/api/utility/reorder.rst.txt

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+
+**************************
+List operations
+**************************
+.. automodule:: s2scat.utility.reorder
+   :members: 

_sources/api/utility/statistics.rst.txt

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+
+**************************
+Statistics
+**************************
+.. automodule:: s2scat.utility.statistics
+   :members: