Merge pull request #11 from CEA-COSMIC/develop

Version 0.0.2 patch release

.gitignore

@@ -1,19 +1,142 @@
-# Compiled source #
-###################
-*.o
-*.so
-*.pyc
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
 
-# Logs and temporaries #
-########################
-*.log
-*~
-.coverage
+# C extensions
+*.so
 
-# Folders #
-###########
+# Distribution / packaging
+.Python
 build/
+develop-eggs/
 dist/
-pysap_astro.egg-info/
-__pycache__/
+downloads/
+eggs/
 .eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+pytest.xml
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+docs/source/fortuna.*
+docs/source/scripts.*
+docs/source/*.nblink
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/

README.rst

@@ -2,10 +2,10 @@
 PySAP-Astro
 ===============
 
-|travis| |codecov| |pypi|
+|CI| |codecov| |pypi|
 
-.. |travis| image:: https://travis-ci.org/CEA-COSMIC/pysap-astro.svg?branch=master
-  :target: https://travis-ci.org/CEA-COSMIC/pysap-astro
+.. |CI| image:: https://github.com/CEA-COSMIC/pysap-astro/workflows/CI/badge.svg
+  :target: https://github.com/CEA-COSMIC/pysap-astro/actions?query=workflow%3ACI
 
 .. |codecov| image:: https://codecov.io/gh/CEA-COSMIC/pysap-astro/branch/master/graph/badge.svg?token=XHJIQXV7AX
   :target: https://codecov.io/gh/CEA-COSMIC/pysap-astro
@@ -18,7 +18,7 @@ Python Sparse data Analysis Package external ASTRO plugin.
   This package is part of the PySAP plug-in framework and is not intended to
   work as a stand-alone package.
 
-This work is made available by a community of people, amoung which the
+This work is made available by a community of people, among which the
 CEA Neurospin UNATI and CEA CosmoStat laboratories, in particular A. Grigis,
 J.-L. Starck, P. Ciuciu, and S. Farrens.
 
@@ -27,4 +27,4 @@ Important links
 ===============
 
 - Official PySAP source code repo: https://github.com/CEA-COSMIC/pysap
-- PySAP HTML documentation (last stable release): https://python-pysap.readthedocs.io/en/latest/
+- PySAP HTML documentation (last stable release): https://cea-cosmic.github.io/pysap

astro/__init__.py

@@ -7,13 +7,13 @@
 # for details.
 ##########################################################################
 
-"""Module defines all the Astro related plugins."""
+"""PYSAP-ASTRO.
 
-__all__ = ['deconvolution', 'denoising']
+This plug-in provides tools for astrophysical data processing.
+
+"""
 
-from . import *
-from .deconvolution import *
-from .denoising import *
+__all__ = ['deconvolution', 'denoising']
 
-version_info = (0, 0, 0)
+version_info = (0, 0, 2)
 __version__ = '.'.join(str(c) for c in version_info)

astro/deconvolution/__init__.py

@@ -7,8 +7,10 @@
 # for details.
 ##########################################################################
 
-"""Module defines all the Astro deconvolution plugins."""
+"""DECONVOLUTION.
 
-__all__ = ['deconvolve', 'linear', 'wavelet_filters']
+This module provides tools for astrophysical image deconvolution.
+
+"""
 
-from . import *
+__all__ = ['deconvolve', 'linear', 'wavelet_filters']

astro/deconvolution/deconvolve.py

@@ -7,7 +7,12 @@
 # for details.
 ##########################################################################
 
-"""CONDA-VU Galaxy Image Deconvolution."""
+"""DECONVOLVE.
+
+This module defines functions to perform galaxy image deconvolution using the
+Condat-Vu algorithm.
+
+"""
 
 # System import
 import pysap
@@ -31,18 +36,21 @@
 def psf_convolve(data, psf, psf_rot=False):
     """PSF Convolution.
 
+    Convolve the input data with the PSF provided.
+
     Parameters
     ----------
-    data : np.ndarray
+    data : numpy.ndarray
         Input data, 2D image
-    psf : np.ndarray
+    psf : numpy.ndarray
         Input PSF, 2D image
     psf_rot : bool, optional
-        Option to rotate the input PSF (default is False)
+        Option to rotate the input PSF, default is ``False``
 
     Returns
     -------
-    np.ndarray convolved image
+    numpy.ndarray
+        Convolved image
 
     """
     if psf_rot:
@@ -54,21 +62,25 @@ def psf_convolve(data, psf, psf_rot=False):
 def get_weights(data, psf, filters, wave_thresh_factor=np.array([3, 3, 4])):
     """Get Sparsity Weights.
 
+    Get the weights needed for the sparse regularisation term in the
+    deconvolution problem.
+
     Parameters
     ----------
-    data : np.ndarray
+    data : numpy.ndarray
         Input data, 2D image
-    psf : np.ndarray
+    psf : numpy.ndarray
         Input PSF, 2D image
-    filters : np.ndarray
+    filters : numpy.ndarray
         Wavelet filters
-    wave_thresh_factor : np.ndarray, optional
-        Threshold factors for each wavelet scale (default is
-        np.array([3, 3, 4]))
+    wave_thresh_factor : numpy.ndarray, optional
+        Threshold factors for each wavelet scale, default is
+        ``np.array([3, 3, 4])``
 
     Returns
     -------
-    np.ndarray weights
+    numpy.ndarray
+        Weights
 
     """
     noise_est = sigma_mad(data)
@@ -93,24 +105,28 @@ def sparse_deconv_condatvu(
 ):
     """Sparse Deconvolution with Condat-Vu.
 
+    Perform deconvolution using sparse regularisation with the Condat-Vu
+    algorithm.
+
     Parameters
     ----------
-    data : np.ndarray
+    data : numpy.ndarray
         Input data, 2D image
-    psf : np.ndarray
+    psf : numpy.ndarray
         Input PSF, 2D image
     n_iter : int, optional
-        Maximum number of iterations, default is 300
+        Maximum number of iterations, default is ``300``
     n_reweights : int, optional
-        Number of reweightings, default is 1
+        Number of reweightings, default is ``1``
     verbose : bool, optional
-        Verbosity option, default is True
+        Verbosity option, default is ``True``
     progress : bool, optional
-        Option to show progress bar, default is True
+        Option to show progress bar, default is ``True``
 
     Returns
     -------
-    np.ndarray deconvolved image
+    numpy.ndarray
+        Deconvolved image
 
     """
     # Print the algorithm set-up

astro/deconvolution/linear.py

@@ -7,7 +7,11 @@
 # for details.
 ##########################################################################
 
-"""Module contains linears operators classes."""
+"""LINEAR.
+
+This module defines a linears operator class for wavelet convolution.
+
+"""
 
 from modopt.opt.linear import LinearParent
 from modopt.signal.wavelet import filter_convolve
@@ -21,10 +25,10 @@ class WaveletConvolve2(LinearParent):
 
     Parameters
     ----------
-    filters: np.ndarray
+    filters: numpy.ndarray
         Array of wavelet filter coefficients
     method : str {'astropy', 'scipy'}, optional
-        Convolution method (default is 'astropy')
+        Convolution method, default is ``astropy``
 
     """
 

astro/deconvolution/wavelet_filters.py

@@ -7,7 +7,11 @@
 # for details.
 ##########################################################################
 
-"""Module contains methods for getting wavelet transform filters."""
+"""WAVELET FILTER.
+
+This module defines a function for getting wavelet transform filters.
+
+"""
 
 import numpy as np
 from pysap import load_transform
@@ -16,7 +20,7 @@
 def get_cospy_filters(data_shape, transform_name, n_scales=4, coarse=False):
     """Get PySAP transform filters.
 
-    This method obtains wavelet filters by calling cospy
+    This method obtains wavelet filters using the transform name provided.
 
     Parameters
     ----------
@@ -25,13 +29,14 @@ def get_cospy_filters(data_shape, transform_name, n_scales=4, coarse=False):
     transform_name : str
         Name of wavelet transform
     n_scales : int, optional
-        Number of transform scales (default is 4)
+        Number of transform scales, default is ``4``
     coarse : bool, optional
-        Option to keep coarse scale (default is 'False')
+        Option to keep coarse scale, default is ``False``
 
     Returns
     -------
-    np.ndarray 3D array of wavelet filters
+    numpy.ndarray
+        3D array of wavelet filters
 
     """
     # Adjust the shape of the input data.