Merge branch 'develop'

INSTALLATION.md

@@ -42,8 +42,8 @@ for more details.
 ## [PyFFTW][pyfftw]
 
 If installed, PyMKS will use [PyFFTW][pyfftw] to
-computed FFTs instead of [Numpy][numpy]. As long as [Numpy][numpy] is
-not using [Intel MKL][MKL], [PyFFTW][pyfftw] should improvement the
+compute FFTs instead of [Numpy][numpy]. As long as [Numpy][numpy] is
+not using [Intel MKL][MKL], [PyFFTW][pyfftw] should improve the
 performance of PyMKS.
 
 To install [PyFFTW][pyfftw] use pip
@@ -56,11 +56,11 @@ See the [PyFFTW installation instructions](https://github.com/hgomersall/pyFFTW#
 ## Installation on Windows
 
 We recommend you download and install the [Anaconda Python Distribution](http://continuum.io/downloads)
-for Python 2.7 (x64) and then download and install PyMKS using the [windows installer](https://github.com/materialsinnovation/pymks/releases/download/version-0_2_1/PyMKS-x64-anaconda27.exe).
+for Python 2.7 (x64) and then download and install PyMKS, using the [windows installer](https://github.com/materialsinnovation/pymks/releases/download/version-0_2_1/PyMKS-x64-anaconda27.exe).
 
 ## Installation on Mac OS X
 
-We recommend you download and install the [Anaconda Python Distibution](http://continuum.io/downloads)
+We recommend you download and install the [Anaconda Python Distribution](http://continuum.io/downloads)
 for Python 2.7 (x64). Once Anaconda has been installed, follow the above procedures to install SfePy.
 Finally, install PyMKS using `pip` as described above.
 
@@ -74,7 +74,7 @@ use your terminal or shell to install PyMKS using pip.
 
 ## Requirements
 
-The [REQUIREMENTS.md](https://github.com/materialsinnovation/pymks/blob/master/REQUIREMENTS.md) file has a list of required
+The [REQUIREMENTS.md](REQUIREMENTS.html) file has a list of required
 packages in a Python environment used to run tests and examples
 for the current release of PyMKS.
 

LICENSE.md

@@ -2,7 +2,7 @@
 
 The MIT License (MIT)
 
-Copyright (c) 2014, David Brough, Daniel Wheeler, Tony Fast, Surya Kalidindi, Andrew Reid
+Copyright (C) 2014-2015 David Brough, Daniel Wheeler, Tony Fast, Surya Kalidindi, Andrew Reid
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

README.md

@@ -5,7 +5,7 @@
 The Materials Knowledge Systems (MKS) is a novel data science approach
 for solving multiscale materials science problems. It uses techniques
 from physics, machine learning, regression analysis, signal processing,
-and spatial statistics to create structure-property-processing
+and spatial statistics to create processing-structure-property
 relationships. The MKS carries the potential to bridge multiple
 length scales using localization and homogenization linkages, and
 provides a data driven framework for solving inverse material design
@@ -32,16 +32,16 @@ See these references for further reading:
 ### PyMKS
 
 The Materials Knowledge Materials in Python (PyMKS) framework is an
-object oriented set of tools and examples written in Python that
-provide high level access to the MKS framework for rapid creation and
+object-oriented set of tools and examples, written in Python, that
+provide high-level access to the MKS framework for rapid creation and
 analysis of structure-property-processing relationships. A short
-intoduction of how to use PyMKS is outlined below and example cases can
+introduction to how to use PyMKS is outlined below and example cases can
 be found [in the examples section](EXAMPLES.html). Both code and
-example contributions are welcome.
+examples contributions are welcome.
 
 ### Mailing List
 
-Please feel free to ask open ended questions about PyMKS on the
+Please feel free to ask open-ended questions about PyMKS on the
 <[email protected]> list.
 
 

REQUIREMENTS.md

@@ -26,8 +26,9 @@ Packages Required to Run Tests and Examples
  - pytz==2015.4
  - pyzmq==14.6.0
  - setuptools==17.0
+ - scikit-image==0.11.3
  - sfepy==2015.1
  - six==1.9.0
  - sympy==0.7.6
  - tables==3.1.1
- - tornado==4.2
+ - tornado==4.2

doc/EXAMPLES.rst

@@ -7,6 +7,7 @@ Examples
    :maxdepth: 2
 
    spatial_stats.rst
+   structure_analysis.rst
    homogenization.rst
    localization.rst
 

doc/MKSmodels.rst

@@ -1,6 +1,11 @@
 MKS Models
 ==========
 
+MKSStructureAnalysis
+----------------------
+.. autoclass:: pymks.mks_structure_analysis.MKSStructureAnalysis
+   :members:
+
 MKSHomogenizationModel
 ----------------------
 .. autoclass:: pymks.mks_homogenization_model.MKSHomogenizationModel

doc/_static/pymks.css

@@ -65,8 +65,8 @@ a:focus {
 
 /*START OF Change to code reference text in documentation */
 code {
-    font-size: 90%;
-    color: #762a83;
+    font-size: 100%;
+    color: #1f78b4;
 }
 
 /* START OF Change for code blocks*/

doc/bases.rst

@@ -1,17 +1,22 @@
 Microstructure Bases
 ====================
 
-DiscreteIndicatorBasis
-----------------------
-.. autoclass:: pymks.bases.DiscreteIndicatorBasis
-   :members:
-
-ContinuousIndicatorBasis
+PrimitiveBasis
 ------------------------
-.. autoclass:: pymks.bases.ContinuousIndicatorBasis
+.. autoclass:: pymks.bases.PrimitiveBasis
    :members:
 
 LegendreBasis
 -------------
 .. autoclass:: pymks.bases.LegendreBasis
+   :members:
+
+FourierBasis
+-------------
+.. autoclass:: pymks.bases.FourierBasis
+   :members:
+
+GSHBasis
+-------------
+.. autoclass:: pymks.bases.GSHBasis
    :members:

doc/datageneration.rst

@@ -1,38 +1,46 @@
 Data Generation
 ===============
 
+make_microstructure
+-------------------
+.. autofunction:: pymks.datasets.make_microstructure
+
 make_delta_microstructures
 --------------------------
 .. autofunction:: pymks.datasets.make_delta_microstructures
 
-make_elastic_FE_strain_delta
-----------------------------
-.. autofunction:: pymks.datasets.make_elastic_FE_strain_delta
-
-make_elastic_FE_strain_random
------------------------------
-.. autofunction:: pymks.datasets.make_elastic_FE_strain_random
+make_checkerboard_microstructure
+--------------------------------
+.. autofunction:: pymks.datasets.make_checkerboard_microstructure
 
 make_cahn_hilliard
 ------------------
 .. autofunction:: pymks.datasets.make_cahn_hilliard
 
-make_microstructure
--------------------
-.. autofunction:: pymks.datasets.make_microstructure
+Data Generation that Requires SfePy
+-----------------------------------
 
-make_checkerboard_microstructure
---------------------------------
-.. autofunction:: pymks.datasets.make_checkerboard_microstructure
+make_elastic_FE_strain_random
+-----------------------------
+.. autofunction:: pymks.datasets.make_elastic_FE_strain_random
+
+make_elastic_FE_strain_delta
+----------------------------
+.. autofunction:: pymks.datasets.make_elastic_FE_strain_delta
 
 make_elastic_stress_random
 --------------------------
 .. autofunction:: pymks.datasets.make_elastic_stress_random
 
+
 Simulations
 -----------
+Cahn-Hilliard
+-------------
 .. autoclass:: pymks.datasets.cahn_hilliard_simulation.CahnHilliardSimulation
    :members:
 
+Finite Element Elasticity
+-------------------------
 .. autoclass:: pymks.datasets.elastic_FE_simulation.ElasticFESimulation
    :members:

doc/homogenization.rst

@@ -4,4 +4,5 @@ Homogenization
 .. toctree::
    :maxdepth: 1
 
-   rst/stress_homogenization_2D.rst
+   rst/homogenization_stress_2D.rst
+   rst/homogenization_fiber_2D.rst