Merge pull request #23 from LaurentRDC/develop

Develop
LaurentRDC · Aug 18, 2017 · 189fc9d · 189fc9d
2 parents aeb207f + 78b72da
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diff --git a/.gitignore b/.gitignore
@@ -104,3 +104,4 @@ ENV/
 # PyCharm
 .idea/
 benchmark.py
+potential_map.py
diff --git a/README.rst b/README.rst
@@ -29,8 +29,8 @@ from various sources is easy::
 
 The ``Crystal`` object encodes multiple attributes and methods related to space-group, symmetry, and scattering.
 
-Another important part of ultrafast electron diffraction is image processing. Image-alignment, 
-streaming image operations, exploitation of symmetry and more are included.
+Another important part of ultrafast electron diffraction is image processing. Image-alignment, exploitation of 
+symmetry, azimuthal average of polycrystalline data, and more, are included.
 
 Baseline-determination in polycrystalline data is a cornerstone of this package. Using the dual-tree complex 
 wavelet transform, time-varying baselines can be extracted with high accuracy, even in cases where diffraction
@@ -60,6 +60,12 @@ using the standard library's `unittest` module.
 
 After installing scikit-ued you can use it like any other Python module as ``skued``.
 
+Optional dependencies
+---------------------
+
+While it is not strictly required, the fourier transform routines from ``pyfftw`` will be preferred If
+``pyfftw`` is installed.
+
 Citations
 ---------
 

diff --git a/appveyor.yml b/appveyor.yml
@@ -15,7 +15,7 @@ environment:
       TEST_CMD: "python -m unittest discover --verbose"
 
       CONDA_DEPENDENCIES: "numpy scipy cython scikit-image"
-      PIP_DEPENDENCIES: "pywavelets spglib pycifrw ase"
+      PIP_DEPENDENCIES: "pywavelets spglib pycifrw ase npstreams"
 
   matrix:
 

diff --git a/docs/source/api.rst b/docs/source/api.rst
@@ -1,80 +1,138 @@
+.. include:: references.txt
+
 .. _api:
 
 *************
 Reference/API
 *************
 
-Parallel Utilities
-==================
-.. autofunction:: skued.pmap
+.. currentmodule:: skued
 
-.. autofunction:: skued.preduce
+Baseline-determination
+======================
 
-Plot Utilities
-==============
-.. autofunction:: skued.spectrum_colors
+Please refer to the :ref:`tutorial on baseline-determination <baseline_tutorial>` for some examples.
 
-.. autofunction:: skued.rgb_sweep
+.. autosummary::
+    :toctree: functions/
 
-Array Utilities
-===============
-.. automodule:: skued.array_utils
+    baseline_dt
+    baseline_dwt
 
-Iteration/Generator Utilities
-=============================
-.. automodule:: skued.iter_utils
+Dual-tree Complex Wavelet Transform
+-----------------------------------
+.. autosummary::
+    :toctree: functions/
 
-Quantities
-==========
-.. automodule:: skued.quantities
+    dtcwt
+    idtcwt
 
-Voigt Profile
-=============
-.. automodule:: skued.voigt
+Image Analysis
+==============
 
-Affine Transforms
-=================
-.. automodule:: skued.affine
+Combine the routines in the :mod:`skued.image` module with
+`npstreams`_ to process diffraction data in parallel. Please refer 
+to the :ref:`tutorial on image manipulation <image_analysis_tutorial>` 
+for some examples.
+
+.. autosummary::
+    :toctree: functions/
+
+    image.angular_average
+    image.powder_center
+    image.align
+    image.ialign
+    image.diff_register
+    image.shift_image
+    image.nfold
+    image.mnxc2
 
 Crystal structure
 =================
 Handling crystal structure information is crucial for many data analysis and modelling tasks.
 See the :ref:`Structure tutorial <structure_tutorial>` for some examples on how to use the following
 classes.
 
-.. autoclass:: skued.Crystal
-   :members:
+.. autosummary::
+    :toctree: classes/
+
+    Crystal
+    Atom
+    Lattice
 
-   .. autoattribute:: skued.Crystal.lattice_vectors
+.. autosummary::
+    :toctree: functions/
 
-   .. autoattribute:: skued.Crystal.lattice_parameters
+    skued.structure.symmetry_expansion
 
-.. autoclass:: skued.Atom
-   :members:
+Simulation
+==========
 
-.. autoclass:: skued.Lattice
-   :members:
+.. autosummary::
+    :toctree: functions/
 
-.. autofunction:: skued.structure.symmetry_expansion
+    skued.simulation.powdersim
 
-Simulation
+Plot Utilities
+==============
+
+.. autosummary::
+    :toctree: functions/
+
+    spectrum_colors
+    rgb_sweep
+
+Array Utilities
+===============
+
+.. autosummary::
+    :toctree: functions/
+
+    mirror
+    repeated_array
+
+Structure Parsing
+=================
+
+.. autosummary::
+    :toctree: classes/
+
+    structure.CIFParser
+    structure.PDBParser
+
+Quantities
 ==========
-.. autofunction:: skued.simulation.powdersim
 
-Baseline-determination
-======================
-.. autofunction:: skued.baseline_dt
+.. autosummary::
+    :toctree: functions/
 
-.. autofunction:: skued.baseline_dwt
+    electron_wavelength
+    interaction_parameter
+    lorentz
 
-Image Analysis
-==============
-.. automodule:: skued.image.powder
+Voigt Profile
+=============
 
-.. automodule:: skued.image.alignment
+.. autosummary::
+    :toctree: functions/
 
-.. automodule:: skued.image.streaming
+    gaussian
+    lorentzian
+    pseudo_voigt
 
-.. automodule:: skued.image.symmetry
+Affine Transforms
+=================
 
-.. automodule:: skued.image.correlation
+.. autosummary::
+    :toctree: functions/
+
+    affine_map
+    transform
+    change_of_basis
+    change_basis_mesh
+    is_basis
+    is_rotation_matrix
+    minimum_image_distance
+    rotation_matrix
+    translation_matrix
+    translation_rotation_matrix
diff --git a/docs/source/classes/skued.Atom.rst b/docs/source/classes/skued.Atom.rst
@@ -0,0 +1,16 @@
+skued\.Atom
+===========
+
+.. currentmodule:: skued
+
+.. autoclass:: Atom
+
+
+   .. automethod:: __init__
+
+
+
+
+
+
+
diff --git a/docs/source/classes/skued.Crystal.rst b/docs/source/classes/skued.Crystal.rst
@@ -0,0 +1,16 @@
+skued\.Crystal
+==============
+
+.. currentmodule:: skued
+
+.. autoclass:: Crystal
+
+
+   .. automethod:: __init__
+
+
+
+
+
+
+
diff --git a/docs/source/classes/skued.Lattice.rst b/docs/source/classes/skued.Lattice.rst
@@ -0,0 +1,16 @@
+skued\.Lattice
+==============
+
+.. currentmodule:: skued
+
+.. autoclass:: Lattice
+
+
+   .. automethod:: __init__
+
+
+
+
+
+
+
diff --git a/docs/source/classes/skued.structure.CIFParser.rst b/docs/source/classes/skued.structure.CIFParser.rst
@@ -0,0 +1,16 @@
+skued\.structure\.CIFParser
+===========================
+
+.. currentmodule:: skued.structure
+
+.. autoclass:: CIFParser
+
+
+   .. automethod:: __init__
+
+
+
+
+
+
+
diff --git a/docs/source/classes/skued.structure.PDBParser.rst b/docs/source/classes/skued.structure.PDBParser.rst
@@ -0,0 +1,16 @@
+skued\.structure\.PDBParser
+===========================
+
+.. currentmodule:: skued.structure
+
+.. autoclass:: PDBParser
+
+
+   .. automethod:: __init__
+
+
+
+
+
+
+
diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -40,11 +40,13 @@
               'sphinx.ext.autodoc',
 			  'sphinx.ext.napoleon',
 			  'sphinx.ext.mathjax',
+              'sphinx.ext.autosummary',
 			  'matplotlib.sphinxext.plot_directive']
 
 intersphinx_mapping = {'numpy': ('http://docs.scipy.org/doc/numpy/', None)}
 
 napoleon_google_docstring = False
+autosummary_generate = True
 
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ['_templates']

diff --git a/docs/source/functions/skued.affine_map.rst b/docs/source/functions/skued.affine_map.rst
@@ -0,0 +1,6 @@
+skued\.affine\_map
+==================
+
+.. currentmodule:: skued
+
+.. autofunction:: affine_map
diff --git a/docs/source/functions/skued.baseline_dt.rst b/docs/source/functions/skued.baseline_dt.rst
@@ -0,0 +1,6 @@
+skued\.baseline\_dt
+===================
+
+.. currentmodule:: skued
+
+.. autofunction:: baseline_dt
diff --git a/docs/source/functions/skued.baseline_dwt.rst b/docs/source/functions/skued.baseline_dwt.rst
@@ -0,0 +1,6 @@
+skued\.baseline\_dwt
+====================
+
+.. currentmodule:: skued
+
+.. autofunction:: baseline_dwt
diff --git a/docs/source/functions/skued.change_basis_mesh.rst b/docs/source/functions/skued.change_basis_mesh.rst
@@ -0,0 +1,6 @@
+skued\.change\_basis\_mesh
+==========================
+
+.. currentmodule:: skued
+
+.. autofunction:: change_basis_mesh
diff --git a/docs/source/functions/skued.change_of_basis.rst b/docs/source/functions/skued.change_of_basis.rst
@@ -0,0 +1,6 @@
+skued\.change\_of\_basis
+========================
+
+.. currentmodule:: skued
+
+.. autofunction:: change_of_basis
diff --git a/docs/source/functions/skued.dtcwt.rst b/docs/source/functions/skued.dtcwt.rst
@@ -0,0 +1,6 @@
+skued\.dtcwt
+============
+
+.. currentmodule:: skued
+
+.. autofunction:: dtcwt
diff --git a/docs/source/functions/skued.electron_wavelength.rst b/docs/source/functions/skued.electron_wavelength.rst
@@ -0,0 +1,6 @@
+skued\.electron\_wavelength
+===========================
+
+.. currentmodule:: skued
+
+.. autofunction:: electron_wavelength
diff --git a/docs/source/functions/skued.gaussian.rst b/docs/source/functions/skued.gaussian.rst
@@ -0,0 +1,6 @@
+skued\.gaussian
+===============
+
+.. currentmodule:: skued
+
+.. autofunction:: gaussian
diff --git a/docs/source/functions/skued.idtcwt.rst b/docs/source/functions/skued.idtcwt.rst
@@ -0,0 +1,6 @@
+skued\.idtcwt
+=============
+
+.. currentmodule:: skued
+
+.. autofunction:: idtcwt