updated ellipse/ellipsoid exp. volume, fixed bug in verif. module

Author: kip-hart

CHANGELOG.rst

@@ -6,11 +6,17 @@ All notable changes to this project will be documented in this file.
 The format is based on `Keep a Changelog`_,
 and this project adheres to `Semantic Versioning`_.
 
-`Unreleased`_
+`1.3.1`_ - 2020-07-09
 --------------------------
 Added
 '''''
 - VTK output for seed lists and polyhedral meshes.
+- Option to compute expected area of ellipse from area distribution.
+- Option to compute expected volume of ellipsoid from volume distribution.
+
+Fixed
+'''''
+- Error in verification module for 2D uniform random orientations.
 
 `1.3.0`_ - 2020-06-25
 --------------------------
@@ -113,7 +119,8 @@ Added
 
 .. LINKS
 
-.. _`Unreleased`: https://github.com/kip-hart/MicroStructPy/compare/v1.3.0...HEAD
+.. _`Unreleased`: https://github.com/kip-hart/MicroStructPy/compare/v1.3.1...HEAD
+.. _`1.3.1`: https://github.com/kip-hart/MicroStructPy/compare/v1.3.0...v1.3.1
 .. _`1.3.0`: https://github.com/kip-hart/MicroStructPy/compare/v1.2.2...v1.3.0
 .. _`1.2.2`: https://github.com/kip-hart/MicroStructPy/compare/v1.2.1...v1.2.2
 .. _`1.2.1`: https://github.com/kip-hart/MicroStructPy/compare/v1.2.0...v1.2.1

src/microstructpy/__init__.py

@@ -4,4 +4,4 @@
 import microstructpy.seeding
 import microstructpy.verification
 
-__version__ = '1.3.0'
+__version__ = '1.3.1'

src/microstructpy/geometry/ellipse.py

@@ -76,6 +76,8 @@ def __init__(self, **kwargs):
             self.center = (0, 0)
 
         # axes
+        if 'area' in kwargs:
+            kwargs['size'] = 2 * np.sqrt(kwargs['area'] / np.pi)
         if ('a' in kwargs) and ('b' in kwargs):
             assert kwargs['a'] > 0
             assert kwargs['b'] > 0
@@ -369,10 +371,17 @@ def area_expectation(cls, **kwargs):
 
             if type(s_dist) in (float, int):
                 return 0.25 * np.pi * s_dist * s_dist
-            else:
-                return 0.25 * np.pi * s_dist.moment(2)
+            return 0.25 * np.pi * s_dist.moment(2)
+
+        if 'area' in kwargs:
+            a_dist = kwargs['area']
+            try:
+                a_exp = a_dist.moment(1)
+            except AttributeError:
+                a_exp = a_dist
+            return a_exp
 
-        elif ('a' in kwargs) and ('b' in kwargs):
+        if ('a' in kwargs) and ('b' in kwargs):
             exp = np.pi
             for kw in ('a', 'b'):
                 dist = kwargs[kw]
@@ -382,7 +391,8 @@ def area_expectation(cls, **kwargs):
                     mu = dist.moment(1)
                 exp *= mu
             return exp
-        elif ('b' in kwargs) and ('aspect_ratio' in kwargs):
+
+        if ('b' in kwargs) and ('aspect_ratio' in kwargs):
             exp = np.pi
             try:
                 exp *= kwargs['b'].moment(2)
@@ -394,7 +404,8 @@ def area_expectation(cls, **kwargs):
             except AttributeError:
                 exp *= kwargs['aspect_ratio']
             return exp
-        elif ('a' in kwargs) and ('aspect_ratio' in kwargs):
+
+        if ('a' in kwargs) and ('aspect_ratio' in kwargs):
             n = 1000
             try:
                 a = kwargs['a'].rvs(size=n)
@@ -406,10 +417,10 @@ def area_expectation(cls, **kwargs):
             except AttributeError:
                 k = np.full(n, kwargs['aspect_ratio'])
             return np.pi * np.mean((a * a) / k)
-        else:
-            e_str = 'Could not calculate expected area from keywords '
-            e_str += str(kwargs.keys()) + '.'
-            raise KeyError(e_str)
+
+        e_str = 'Could not calculate expected area from keywords '
+        e_str += str(kwargs.keys()) + '.'
+        raise KeyError(e_str)
 
     # ----------------------------------------------------------------------- #
     # Bounding Circles                                                        #

src/microstructpy/geometry/ellipsoid.py

@@ -533,8 +533,15 @@ def volume_expectation(cls, **kwargs):
             s_dist = kwargs['size']
             if type(s_dist) in (float, int):
                 return 0.5 * np.pi * s_dist * s_dist * s_dist / 3
-            else:
-                return 0.5 * np.pi * s_dist.moment(3) / 3
+            return 0.5 * np.pi * s_dist.moment(3) / 3
+
+        if 'volume' in kwargs:
+            v_dist = kwargs['volume']
+            try:
+                v_exp = v_dist.moment(1)
+            except AttributeError:
+                v_exp = v_dist
+            return v_exp
 
         # check for a, b, and c distribution
         try:

src/microstructpy/verification.py

@@ -893,6 +893,11 @@ def error_stats(fit_seeds, seeds, phases, poly_mesh=None, verif_mask=None):
         i_phase = init_phases[i]
         o_phase = outp_phases[i]
         phase = phases[i]
+        for kw in phase:
+            if kw in ('angle', 'angle_deg') and phase[kw] == 'random':
+                phase[kw] = scipy.stats.uniform(loc=0, scale=360)
+            if kw == 'angle_rad':
+                phase[kw] = scipy.stats.uniform(loc=0, scale=2 * np.pi)
 
         err_io = {kw: _kw_errs(i_phase[kw], o_phase[kw]) for kw in i_phase}
         err_po = {kw: _kw_stats(phase[kw], o_phase[kw]) for kw in o_phase}