Merge pull request #78 from bwohlberg/master

New geometry class and some minor fixes

Author: carterbox

docs/source/api/xdesign.geometry.rst

@@ -53,6 +53,7 @@ Two dimensional entities
       Curve
       Circle
       Polygon
+      RegularPolygon
       Triangle
       Rectangle
       Square

docs/source/conf.py

@@ -57,6 +57,9 @@
 napoleon_use_param = False
 napoleon_use_rtype = False
 
+# Bibtex settings
+bibtex_bibfiles = ['bibtex/cite.bib', 'bibtex/refs.bib']
+
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ['_templates']
 

setup.py

@@ -46,8 +46,19 @@
 # POSSIBILITY OF SUCH DAMAGE.                                             #
 # #########################################################################
 
+import os
 from setuptools import setup, find_packages
 
+long_desc = """
+XDesign is an open-source Python package for generating configurable
+x-ray imaging phantoms, simulating data acquisition, and benchmarking x-ray
+tomographic image reconstruction.
+"""
+
+with open(os.path.join("requirements.txt")) as f:
+    lines = f.readlines()
+install_requires = [line.strip() for line in lines]
+
 setup(
     name='xdesign',
     packages=find_packages('src'),
@@ -56,7 +67,9 @@
     use_scm_version=True,
     author='Daniel Ching, Doga Gursoy',
     description='Benchmarking and optimization tools for tomography.',
+    long_description=long_desc,
     include_package_data=True,
+    install_requires=install_requires,
     url='http://github.com/tomography/xdesign.git',
     keywords=['xdesign', 'tomography'],
     license='BSD-3',

src/xdesign/acquisition.py

@@ -113,7 +113,7 @@ def __repr__(self):
         )
 
     def __str__(self):
-        """Return the string respresentation of the Beam."""
+        """Return the string representation of the Beam."""
         return "Probe(" + super(Probe, self).__str__() + ")"
 
     def distance(self, other):

src/xdesign/geometry/area.py

@@ -7,6 +7,7 @@
     'Curve',
     'Circle',
     'Polygon',
+    'RegularPolygon',
     'Triangle',
     'Rectangle',
     'Square',
@@ -290,12 +291,18 @@ class Polygon(Entity):
     vertices : List of Points
     sign : int (-1 or 1)
         The sign of the area
+
+    Raises
+    ------
+    ValueError : If the number of vertices is less than three.
     """
 
     def __init__(self, vertices, sign=1):
         for v in vertices:
             if not isinstance(v, Point):
                 raise TypeError("vertices must be of type Point.")
+        if len(vertices) < 3:
+            raise ValueError("A Polygon has at least three vertices.")
         super(Polygon, self).__init__()
         self.vertices = vertices
         self._dim = vertices[0].dim
@@ -533,6 +540,42 @@ def contains(self, other):
             return np.logical_not(border.contains_points(np.atleast_2d(x)))
 
 
+class RegularPolygon(Polygon):
+    """A regular polygon in 2D cartesian space.
+
+    It is defined by the polynomial center, order, and radius.
+
+    By default (i.e. when the ``angle`` parameter is zero), the regular
+    polygon is oriented so that one of the vertices is at coordinates
+    :math:`(x + r, x)` where :math:`x` is the x-coordinate of
+    ``center`` and :math:`r` = ``radius``. The ``angle`` parameter is
+    only meaningful modulo :math:`2\pi /` ``order`` since rotation by
+    :math:`2\pi /` ``order`` gives a result equivalent to no rotation.
+
+    Parameters
+    ----------
+    center : :class:`Point`
+        The center of the polygon
+    radius : float
+        Distance from polygon center to vertices
+    order : int
+        Order of the polygon (e.g. order 6 is a hexagon).
+    angle : float
+        Optional rotation angle in radians.
+    sign : int (-1 or 1)
+        Optional sign of the area (see :class:`Polygon`)
+    """
+
+    def __init__(self, center, radius, order, angle=0, sign=1):
+        vertex_angles = (np.linspace(0, 2 * np.pi, order, endpoint=False) +
+                         angle)
+        vertices = [
+            Point([radius * np.cos(theta), radius * np.sin(theta)]) + center
+            for theta in vertex_angles
+        ]
+        super(RegularPolygon, self).__init__(vertices, sign=sign)
+
+
 class Triangle(Polygon):
     """Triangle in 2D cartesian space.
 
@@ -566,7 +609,7 @@ class Rectangle(Polygon):
 
     Defined by a point and a vector to enforce perpendicular sides.
 
-    Attributes
+    Parameters
     ----------
     side_lengths : array
         The lengths of the sides

src/xdesign/geometry/intersect.py

@@ -37,8 +37,8 @@ def halfspacecirc(d, r):
     f : scalar
         The proportion of the circle in the smaller half-space
 
-    Reference
-    ---------
+    References
+    ----------
     Glassner, A. S. (Ed.). (2013). Graphics gems. Elsevier.
 
     """

src/xdesign/geometry/point.py

@@ -78,7 +78,7 @@ def calc_standard(A):
     Return
     ------
     c0 : :py:class:`np.array` (..., N)
-        The first N coeffients for the hyper-plane
+        The first N coefficients for the hyper-plane
     c1 : :py:class:`np.array` (..., 1)
         The last coefficient for the hyper-plane
 
@@ -186,7 +186,7 @@ def rotate(self, theta, point=None, axis=None):
         self._x += center
 
     def scale(self, vector):
-        """SScale the ambient space in each dimension according to vector.
+        """Scale the ambient space in each dimension according to vector.
 
         Scaling is centered on the origin.
         """

src/xdesign/metrics/standards.py

@@ -33,30 +33,31 @@ def compute_mtf(phantom, image):
     HyperbolicCocentric phantom. Calculate the MTF from the modulation depth
     at each edge on the line from (0.5,0.5) to (0.5,1). MTF = (hi-lo)/(hi+lo)
 
+    .. deprecated:: 0.3
+
+        This method rapidly becomes inaccurate at small wavelenths because the
+        measurement gets out of phase with the waves due to rounding error. Use
+        another one of the MTF functions instead. This method will be removed
+        in xdesign 0.6.
+
+    .. seealso::
+
+        :meth:`compute_mtf_ffst`
+        :meth:`compute_mtf_lwkj`
+
     Parameters
-    ---------------
+    ----------
     phantom : HyperbolicConcentric
         Predefined phantom of cocentric rings whose widths decay parabolically.
     image : ndarray
         The reconstruction of the above phantom.
 
     Returns
-    --------------
+    -------
     wavelength : list
         wavelenth in the scale of the original phantom
     MTF : list
         MTF values
-
-    .. deprecated:: 0.3
-        This method rapidly becomes inaccurate at small wavelenths because the
-        measurement gets out of phase with the waves due to rounding error. Use
-        another one of the MTF functions instead. This method will be removed
-        in xdesign 0.6.
-
-    .. seealso::
-        :meth:`compute_mtf_ffst`
-        :meth:`compute_mtf_lwkj`
-
     """
     warnings.warn(
         'compute_mtf will be removed in xdesign 0.6, use compute_mtf_lwkj or '
@@ -94,6 +95,10 @@ def compute_mtf(phantom, image):
 def compute_mtf_ffst(phantom, image, Ntheta=4):
     '''Calculate the MTF using the method described in :cite:`Friedman:13`.
 
+    .. seealso::
+
+        :meth:`compute_mtf_lwkj`
+
     Parameters
     ----------
     phantom : :py:class:`.UnitCircle`
@@ -111,9 +116,6 @@ def compute_mtf_ffst(phantom, image, Ntheta=4):
         MTF values
     bin_centers : ndarray
         the center of the bins if Ntheta >= 1
-
-    .. seealso::
-        :meth:`compute_mtf_lwkj`
     '''
     if not isinstance(phantom, UnitCircle):
         raise TypeError('MTF requires unit circle phantom.')
@@ -204,6 +206,10 @@ def compute_mtf_lwkj(phantom, image):
     """Calculate the MTF using the modulated Siemens Star method in
     :cite:`loebich2007digital`.
 
+    .. seealso::
+
+        :meth:`compute_mtf_ffst`
+
     Parameters
     ----------
     phantom : :py:class:`.SiemensStar`
@@ -216,9 +222,6 @@ def compute_mtf_lwkj(phantom, image):
         The spatial frequency in cycles per unit length
     M : array
         The MTF values for each frequency
-
-    .. seealso::
-        :meth:`compute_mtf_ffst`
     """
     # Determine which radii to sample. Do not sample linearly because the
     # spatial frequency changes as 1/r
@@ -296,7 +299,7 @@ def fit_sinusoid(value, angle, f, p0=[0.5, 0.25, 0.25]):
     sinusoidal instead of square, contrast values larger than unity are clipped
     back to unity.
 
-    parameters
+    Parameters
     ----------
     value : NxM ndarray
         The value of the function at N angles and M radii
@@ -308,8 +311,8 @@ def fit_sinusoid(value, angle, f, p0=[0.5, 0.25, 0.25]):
     p0 : list, optional
         The initial guesses for the parameters.
 
-    returns:
-    --------
+    Returns
+    -------
     MTFR: 1xM ndarray
         The modulation part of the MTF at each of the M radii
     """
@@ -340,7 +343,7 @@ def errorfunc(p, x, y):
 def periodic_function(p, x):
     """A periodic function for fitting to the spokes of the Siemens Star.
 
-    parameters
+    Parameters
     ----------
     p[0] : scalar
         the mean of the function
@@ -355,7 +358,7 @@ def periodic_function(p, x):
     theta : Nx1 ndarray
         input angles for the function
 
-    returns
+    Returns
     -------
     value : Nx1 array
         the values of the function at phi; cannot return NaNs.
@@ -385,7 +388,7 @@ def compute_nps_ffst(phantom, A, B=None, plot_type='frequency'):
         'histogram' returns a plot binned by radial coordinate wavenumber
         'frequency' returns a wavenumber vs wavenumber plot
 
-    returns
+    Returns
     -------
     bins :
         Bins for the radially binned NPS

tests/test_geometry/test_area.py

@@ -196,6 +196,15 @@ def test_Polygon_contains():
     contains_no_overlap(A, Bn)
 
 
+def test_RegularPolygon_contains():
+    r = 0.5
+    order = 7
+    A = Circle(Point([0, 0]), r)
+    B = RegularPolygon(Point([0, 0]), r - 1e-7, order)
+    A.contains(B)
+    assert A.contains(B)
+
+
 def test_Mesh_contains():
     p0 = Point([0, 0])
     p1 = Point([0, 1])