Merge pull request #44 from tomography/RCv0.3

RCv0.3
AdvancedPhotonSource · May 23, 2017 · e6036dd · e6036dd
2 parents f78b713 + 7597008
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diff --git a/docs/demos/FullReferenceMetrics.ipynb b/docs/demos/FullReferenceMetrics.ipynb
diff --git a/docs/demos/NoReferenceMetrics.ipynb b/docs/demos/NoReferenceMetrics.ipynb
diff --git a/docs/demos/Shepp.ipynb b/docs/demos/Shepp.ipynb
diff --git a/docs/demos/StandardPatterns.ipynb b/docs/demos/StandardPatterns.ipynb
diff --git a/docs/source/api.rst b/docs/source/api.rst
@@ -7,8 +7,9 @@ API
 
    api/xdesign.acquisition
    api/xdesign.algorithms
-   api/xdesign.feature
    api/xdesign.geometry
+   api/xdesign.constants
+   api/xdesign.formats
    api/xdesign.material
    api/xdesign.metrics
    api/xdesign.phantom
@@ -17,4 +18,4 @@ API
 .. automodule:: xdesign
    :members:
    :undoc-members:
-   :show-inheritance: 
+   :show-inheritance:
diff --git a/docs/source/api/xdesign.acquisition.rst b/docs/source/api/xdesign.acquisition.rst
@@ -2,20 +2,22 @@
 ==========================
 
 .. automodule:: xdesign.acquisition
-   :members:
-   :show-inheritance:
-   :undoc-members:
-   :synopsis: Defines objects related to collection and organization of probe data.
+  :members:
+  :show-inheritance:
+  :undoc-members:
 
-   .. rubric:: **Functions:**
+  .. rubric:: **Classes:**
 
-   .. autosummary::
+  .. autosummary::
 
-      Beam
-      Probe
-      sinogram
-      angleogram
-      raster_scan
-      angle_scan
+    Beam
+    Probe
 
-.. moduleauthor:: Doga Gursoy <dgursoy@aps.anl.gov>
+  .. rubric:: **Functions:**
+
+  .. autosummary::
+
+    sinogram
+    angleogram
+    raster_scan
+    angle_scan
diff --git a/docs/source/api/xdesign.algorithms.rst b/docs/source/api/xdesign.algorithms.rst
@@ -5,16 +5,13 @@
    :members:
    :show-inheritance:
    :undoc-members:
-   :synopsis: Defines methods for reconstructing data from the :mod:`.acquisition` module.
 
    .. rubric:: **Functions:**
 
    .. autosummary::
 
-      reconstruct
       art
       sirt
       mlem
       stream
-
-.. moduleauthor:: Doga Gursoy <dgursoy@aps.anl.gov>
+      update_progress
diff --git a/docs/source/api/xdesign.constants.rst b/docs/source/api/xdesign.constants.rst
@@ -0,0 +1,4 @@
+:mod:`xdesign.constants`
+========================
+
+.. automodule:: xdesign.constants
diff --git a/docs/source/api/xdesign.feature.rst b/docs/source/api/xdesign.feature.rst
diff --git a/docs/source/api/xdesign.formats.rst b/docs/source/api/xdesign.formats.rst
@@ -0,0 +1,11 @@
+:mod:`xdesign.formats`
+======================
+
+.. automodule:: xdesign.formats
+   :members:
+   :show-inheritance:
+   :undoc-members:
+
+   .. rubric:: **Functions:**
+
+   .. autosummary::
diff --git a/docs/source/api/xdesign.geometry.rst b/docs/source/api/xdesign.geometry.rst
@@ -2,15 +2,14 @@
 =======================
 
 .. automodule:: xdesign.geometry
-   :members:
-   :show-inheritance:
-   :inherited-members:
-   :undoc-members:
-   :synopsis: Defines geometric objects for the purpose of supporting :class:`.Feature` definition and calculating intersections for the :mod:`.acquisition` module.
+    :members:
+    :show-inheritance:
+    :inherited-members:
 
-   .. rubric:: **Classes:**
+    .. rubric:: **Classes:**
+
+    .. autosummary::
 
-   .. autosummary::
       Entity
       Point
       Circle
@@ -20,6 +19,3 @@
       Square
       Polygon
       Mesh
-
-.. moduleauthor:: Doga Gursoy <dgursoy@aps.anl.gov>
-.. moduleauthor:: Daniel J Ching <daniel.j.ching@gmail.com>
diff --git a/docs/source/api/xdesign.material.rst b/docs/source/api/xdesign.material.rst
@@ -5,13 +5,13 @@
    :members:
    :show-inheritance:
    :undoc-members:
-   :synopsis: Defines objects which auto-generate a parameterized :class:`.Phantom`.
 
-   .. rubric:: **Functions:**
+   .. rubric:: **Classes:**
 
    .. autosummary::
 
       Material
+      XDesignDefault
       HyperbolicConcentric
       DynamicRange
       DogaCircles
@@ -25,5 +25,3 @@
       SoftBiomaterial
       Electronics
       FiberComposite
-
-.. moduleauthor:: Daniel J Ching <daniel.j.ching@gmail.com>
diff --git a/docs/source/api/xdesign.metrics.rst b/docs/source/api/xdesign.metrics.rst
@@ -5,21 +5,23 @@
    :members:
    :show-inheritance:
    :undoc-members:
-   :synopsis: Objects and methods for computing the quality of reconstructions.
 
-   .. rubric:: **Functions:**
+   .. rubric:: **Classes:**
 
    .. autosummary::
 
       ImageQuality
-      probability_mask
-      compute_quality
+
+   .. rubric:: **Functions:**
+
+   .. autosummary::
+
       compute_PCC
       compute_likeness
       compute_background_ttest
       compute_mtf
-      compute_mtf_siemens
-      compute_nps
-      compute_neq
-
-.. moduleauthor:: Daniel J Ching <daniel.j.ching@gmail.com>
+      compute_mtf_ffst
+      compute_mtf_lwkj
+      compute_nps_ffst
+      compute_neq_d
+      compute_quality
diff --git a/docs/source/api/xdesign.phantom.rst b/docs/source/api/xdesign.phantom.rst
@@ -5,12 +5,9 @@
    :members:
    :show-inheritance:
    :undoc-members:
-   :synopsis: Defines an object for organizing :class:`.Feature`.
 
-   .. rubric:: **Functions:**
+   .. rubric:: **Classes:**
 
    .. autosummary::
 
       Phantom
-
-.. moduleauthor:: Daniel J Ching <daniel.j.ching@gmail.com>
diff --git a/docs/source/api/xdesign.plot.rst b/docs/source/api/xdesign.plot.rst
@@ -5,7 +5,6 @@
    :members:
    :show-inheritance:
    :undoc-members:
-   :synopsis: Contains functions for visualizing :class:`.Phantom` and :class:`.ImageQuality` metrics.
 
    .. rubric:: **Functions:**
 
@@ -14,13 +13,10 @@
       sidebyside
       discrete_phantom
       plot_phantom
-      plot_feature
       plot_mesh
       plot_polygon
       plot_curve
       plot_metrics
       plot_mtf
       plot_nps
       plot_neq
-
-.. moduleauthor:: Daniel J Ching <daniel.j.ching@gmail.com>
diff --git a/docs/source/bibtex/cite.bib b/docs/source/bibtex/cite.bib
@@ -1,6 +1,6 @@
-@Article{ching:17,	
-author  = "Ching, Daniel J. and G{\"{u}}rsoy, Do{\v{g}}a",	
-title   = "{{\it XDesign}: an open-source software package for designing X-ray imaging phantoms and experiments}",	
+@Article{ching:17,
+author  = "Ching, Daniel J. and G{\"{u}}rsoy, Do{\v{g}}a",
+title   = "{XDesign: an open-source software package for designing X-ray imaging phantoms and experiments}",	
 journal = "Journal of Synchrotron Radiation",
 year    = "2017",
 volume  = "24",

diff --git a/docs/source/bibtex/refs.bib b/docs/source/bibtex/refs.bib
@@ -39,6 +39,15 @@ @article{Sufian:15
 year    = {2015}
 }
 
+@inproceedings{loebich2007digital,
+  title={Digital camera resolution measurement using sinusoidal Siemens stars},
+  author={Loebich, Christian and Wueller, Dietmar and Klingen, Bruno and Jaeger, Anke},
+  booktitle={Electronic Imaging 2007},
+  pages={65020N--65020N},
+  year={2007},
+  organization={International Society for Optics and Photonics}
+}
+
 @article{Bergamaschi:fv5047,
 author = "Bergamaschi, Antoine and Medjoubi, Kadda and Messaoudi, C{\'{e}}dric and Marco, Sergio and Somogyi, Andrea",
 title = "{{\it MMX-I}: data-processing software for multimodal X-ray imaging and tomography}",

diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -14,6 +14,7 @@
 
 import sys
 import os
+from unittest.mock import MagicMock
 
 # If extensions (or modules to document with autodoc) are in another directory,
 # add these directories to sys.path here. If the directory is relative to the
@@ -23,7 +24,7 @@
 # -- General configuration ------------------------------------------------
 
 # If your documentation needs a minimal Sphinx version, state it here.
-#needs_sphinx = '1.0'
+# needs_sphinx = '1.0'
 
 # Add any Sphinx extension module names here, as strings. They can be
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
@@ -40,6 +41,8 @@
     'sphinx.ext.viewcode',
     'sphinx.ext.napoleon',
     'sphinxcontrib.bibtex',
+    'nbsphinx',
+    'IPython.sphinxext.ipython_console_highlighting',
 ]
 
 # Napoleon settings
@@ -63,7 +66,7 @@
 source_suffix = '.rst'
 
 # The encoding of source files.
-#source_encoding = 'utf-8-sig'
+# source_encoding = 'utf-8-sig'
 
 # The master toctree document.
 master_doc = 'index'
@@ -79,7 +82,7 @@
 #
 # The short X.Y version.
 # The full version, including alpha/beta/rc tags.
-release = '0.1'
+release = '0.3'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
@@ -96,7 +99,7 @@
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
-exclude_patterns = []
+exclude_patterns = ['_build', '**.ipynb_checkpoints']
 
 # The reST default role (used for this markup: `text`) to use for all
 # documents.
@@ -168,7 +171,7 @@
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = ['_static']
+# html_static_path = ['_static']
 
 # Add any extra paths that contain custom files (such as robots.txt or
 # .htaccess) here, relative to this directory. These files are copied
@@ -315,42 +318,24 @@
 # texinfo_no_detailmenu = False
 
 # Example configuration for intersphinx: refer to the Python standard library.
-intersphinx_mapping = {'https://docs.python.org/': None}
+intersphinx_mapping = {'https://docs.python.org/3': None}
 
-# picked from http://read-the-docs.readthedocs.org/en/latest/faq.html
-class Mock(object):
 
-    __all__ = []
+# picked from http://read-the-docs.readthedocs.org/en/latest/faq.html
+class Mock(MagicMock):
+    @classmethod
+    def __getattr__(cls, name):
+            return MagicMock()
 
-    def __init__(self, *args, **kwargs):
-        pass
 
-    def __call__(self, *args, **kwargs):
-        return Mock()
+MOCK_MODULES = ['numpy',
+                'matplotlib', 'matplotlib.pyplot', 'matplotlib.patches',
+                'matplotlib.path', 'matplotlib.patheffects', 'matplotlib.axis',
+                'polytope',
+                'cached_property',
+                'scipy', 'scipy.stats', 'scipy.ndimage', 'scipy.spatial',
+                'cycler',
+                'phasepack',
+                ]
 
-    @classmethod
-    def __getattr__(cls, name):
-        return Mock()
-    def __mul__(self, other):
-        return Mock()
-    def __rmul__(self, other):
-        return Mock()
-    def __pow__(self, other):
-        return Mock()
-    def __div__(self, other):
-        return Mock()
-    def __add__(self, other):
-        return Mock()
-    def __radd__(self, other):
-        return Mock()
-
-MOCK_MODULES = [
-    'cached_property', 'cycler', 'intertools',
-    'matplotlib', 'matplotlib.pyplot', 'matplotlib.patches',
-    'matplotlib.path', 'matplotlib.patheffects', 'matplotlib.axis', 
-    'math', 'numpy', 'numbers', 'phasepack', 'polytope', 
-    'scipy', 'scipy.stats', 'scipy.ndimage', 'scipy.spatial',
-    ]
-
-for mod_name in MOCK_MODULES:
-    sys.modules[mod_name] = Mock()
+sys.modules.update((mod_name, Mock()) for mod_name in MOCK_MODULES)