Refactor module structure

Broke large modules into multiple files.
Fixed broken demo notebooks.
Added Azure Pipelines as a CI service.
Used YAPF to format all code.

README.rst

@@ -17,36 +17,47 @@ XDesign
    :target: https://codeclimate.com/github/tomography/xdesign
    :alt: Code Climate
 
-**XDesign** is an open-source Python package for generating
-configurable simulation phantoms for benchmarking tomographic
-image reconstruction.
+**XDesign** is an open-source Python package for generating configurable
+x-ray imaging `phantoms <https://en.wikipedia.org/wiki/Imaging_phantom>`_,
+simulating `data acquisition <https://en.wikipedia.org/wiki/Data_acquisition>`_,
+and benchmarking x-ray `tomographic image reconstruction
+<https://en.wikipedia.org/wiki/Tomography>`_.
 
-Current Scope
+
+Goals
 =====
+* Assist faster development of new generation tomographic reconstruction methods
+* Allow quantitative comparison of different reconstruction methods
+* Create a framework for designing x-ray imaging experiments
+
+
+Current Scope
+=============
 * Customizable 2D phantoms constructed from circles and convex polygons
 * Quantitative reconstruction quality and probe coverage metrics
 * Attenuation interactions with X-ray probes of uniform flux
 * Use of analytic (exact) solutions for algorithms and computation
 
+
 Contribute
 ==========
 * Issue Tracker: https://github.com/tomography/xdesign/issues
 * Documentation: https://github.com/tomography/xdesign/tree/master/docs
 * Source Code: https://github.com/tomography/xdesign/tree/master/xdesign
 * Tests: https://github.com/tomography/xdesign/tree/master/tests
 
+
 License
 =======
 The project is licensed under the
 `BSD-3 <https://github.com/tomography/xdesign/blob/master/LICENSE.txt>`_ license.
 
+
 Install
 =======
-
-First, install XDesign's dependencies using pip. Then install XDesign
-in the usual way. Using pip or by running setup.py.
+Since version 0.5, XDesign is available on the conda-forge channel. Install it
+in the usual way:
 
 .. code-block:: bash
 
-  $ pip install -r requirements.txt
-  $ pip install .
+  $ conda install xdesign -c conda-forge

azure-pipelines.yml

@@ -0,0 +1,34 @@
+# Python package
+# Create and test a Python package on multiple Python versions.
+# Add steps that analyze code, save the dist with the build record, publish to a PyPI-compatible index, and more:
+# https://docs.microsoft.com/azure/devops/pipelines/languages/python
+
+jobs:
+
+- job: 'Test'
+  pool:
+    vmImage: 'Ubuntu-16.04'
+  strategy:
+    matrix:
+      Python35:
+        python.version: '3.5'
+      Python36:
+        python.version: '3.6'
+      Python37:
+        python.version: '3.7'
+    maxParallel: 4
+
+  steps:
+  - task: UsePythonVersion@0
+    inputs:
+      versionSpec: '$(python.version)'
+      architecture: 'x64'
+
+  - script: python -m pip install --upgrade pip && pip install -r requirements.txt nose python-coveralls
+    displayName: 'Install dependencies'
+
+  - script: python setup.py install
+    displayName: 'Install XDesign'
+
+  - script: nosetests
+    displayName: 'nosetests'

docs/source/api.rst

@@ -1,21 +1,14 @@
-API
-===
-
-.. rubric:: **XDesign Modules:**
-
-.. toctree::
-
-   api/xdesign.acquisition
-   api/xdesign.algorithms
-   api/xdesign.geometry
-   api/xdesign.constants
-   api/xdesign.formats
-   api/xdesign.material
-   api/xdesign.metrics
-   api/xdesign.phantom
-   api/xdesign.plot
+API Documentation
+=================
 
 .. automodule:: xdesign
    :members:
    :undoc-members:
    :show-inheritance:
+
+.. toctree::
+   :maxdepth: 4
+   :hidden:
+   :glob:
+
+   api/*

docs/source/api/xdesign.constants.rst

@@ -2,3 +2,6 @@
 ========================
 
 .. automodule:: xdesign.constants
+  :members:
+  :show-inheritance:
+  :undoc-members:

docs/source/api/xdesign.geometry.rst

@@ -6,16 +6,70 @@
     :show-inheritance:
     :inherited-members:
 
-    .. rubric:: **Classes:**
 
-    .. autosummary::
+Zero dimensional entities
+-------------------------
 
-      Entity
-      Point
+.. automodule:: xdesign.geometry.point
+  :members:
+  :show-inheritance:
+  :undoc-members:
+
+  .. rubric:: **Classes:**
+
+  .. autosummary::
+
+    Point
+
+
+One dimensional entities
+------------------------
+
+.. automodule:: xdesign.geometry.line
+  :members:
+  :show-inheritance:
+  :undoc-members:
+
+  .. rubric:: **Classes:**
+
+  .. autosummary::
+
+    Line
+    Segment
+
+
+Two dimensional entities
+-------------------------
+
+.. automodule:: xdesign.geometry.area
+  :members:
+  :show-inheritance:
+  :undoc-members:
+
+  .. rubric:: **Classes:**
+
+  .. autosummary::
+
+      Curve
       Circle
-      Line
+      Polygon
       Triangle
       Rectangle
       Square
-      Polygon
       Mesh
+
+
+Intersect
+---------
+
+.. automodule:: xdesign.geometry.intersect
+  :members:
+  :show-inheritance:
+  :undoc-members:
+
+  .. rubric:: **Functions:**
+
+  .. autosummary::
+
+    clip_SH
+    halfspacecirc

docs/source/api/xdesign.metrics.rst

@@ -2,25 +2,57 @@
 ======================
 
 .. automodule:: xdesign.metrics
-   :members:
-   :show-inheritance:
-   :undoc-members:
+  :members:
+  :show-inheritance:
+  :undoc-members:
 
-   .. rubric:: **Classes:**
 
-   .. autosummary::
+Coverage metrics
+----------------
 
-      ImageQuality
+.. automodule:: xdesign.metrics.coverage
+  :members:
+  :show-inheritance:
+  :undoc-members:
 
-   .. rubric:: **Functions:**
+  .. rubric:: **Functions:**
 
-   .. autosummary::
+  .. autosummary::
 
-      pcc
-      ssim
-      msssim
-      compute_mtf
-      compute_mtf_ffst
-      compute_mtf_lwkj
-      compute_nps_ffst
-      compute_neq_d
+    coverage_approx
+
+
+Full-reference metrics
+----------------------
+
+.. automodule:: xdesign.metrics.fullref
+  :members:
+  :show-inheritance:
+  :undoc-members:
+
+  .. rubric:: **Functions:**
+
+  .. autosummary::
+
+    pcc
+    ssim
+    msssim
+
+
+Standards-based metrics
+-----------------------
+
+.. automodule:: xdesign.metrics.standards
+  :members:
+  :show-inheritance:
+  :undoc-members:
+
+  .. rubric:: **Functions:**
+
+  .. autosummary::
+
+    compute_mtf
+    compute_mtf_ffst
+    compute_mtf_lwkj
+    compute_nps_ffst
+    compute_neq_d

docs/source/api/xdesign.phantom.rst

@@ -1,28 +1,59 @@
 :mod:`xdesign.phantom`
-=======================
+======================
 
 .. automodule:: xdesign.phantom
-   :members:
-   :show-inheritance:
-   :undoc-members:
-
-   .. rubric:: **Classes:**
-
-   .. autosummary::
-
-      Phantom
-      save_phantom
-      load_phantom
-      pickle_phantom
-      unpickle_phantom
-      XDesignDefault
-      HyperbolicConcentric
-      DynamicRange
-      DogaCircles
-      SlantedSquares
-      UnitCircle
-      Soil
-      WetCircles
-      SiemensStar
-      Foam
-      Softwood
+  :members:
+  :show-inheritance:
+  :undoc-members:
+
+
+Phantoms
+--------
+
+.. automodule:: xdesign.phantom.phantom
+  :members:
+  :show-inheritance:
+  :undoc-members:
+
+  .. autosummary::
+
+    Phantom
+    save_phantom
+    load_phantom
+    pickle_phantom
+    unpickle_phantom
+
+
+Standard phantoms
+-----------------
+
+.. automodule:: xdesign.phantom.standards
+  :members:
+  :show-inheritance:
+  :undoc-members:
+
+  .. autosummary::
+
+    XDesignDefault
+    HyperbolicConcentric
+    DynamicRange
+    DogaCircles
+    SlantedSquares
+    UnitCircle
+    SiemensStar
+
+
+Custom phantoms
+---------------
+
+.. automodule:: xdesign.phantom.custom
+  :members:
+  :show-inheritance:
+  :undoc-members:
+
+  .. autosummary::
+
+    Soil
+    WetCircles
+    Foam
+    Softwood

docs/source/api/xdesign.algorithms.rst → docs/source/api/xdesign.recon.rst

@@ -1,7 +1,7 @@
-:mod:`xdesign.algorithms`
+:mod:`xdesign.recon`
 =========================
 
-.. automodule:: xdesign.algorithms
+.. automodule:: xdesign.recon
    :members:
    :show-inheritance:
    :undoc-members: