Improve Plot Interfaces (#17)

kip-hart · web-flow · commit 41ccfa7358ad · 2020-05-13T21:39:30.000-05:00
diff --git a/CHANGELOG.rst b/CHANGELOG.rst
@@ -8,11 +8,19 @@ and this project adheres to `Semantic Versioning`_.
 
 `Unreleased`_ - 2020-05-11
 --------------------------
+Added
+'''''
+- Options to shorten input keyword argument lists for plot methods
+  (addresses `#14`_)
+
 Changed
 '''''''
-- Removed support for Python 2.7.
 - Ellipse of best fit method calls the `lsq-ellipse`_ package.
 
+Removed
+'''''''
+- Removed support for Python 2.7.
+
 `1.1.2`_ - 2019-11-07
 ---------------------
 Fixed
@@ -74,3 +82,5 @@ Added
 .. _`Keep a Changelog`: https://keepachangelog.com/en/1.0.0/
 .. _`lsq-ellipse`: https://pypi.org/project/lsq-ellipse
 .. _`Semantic Versioning`: https://semver.org/spec/v2.0.0.html
+
+.. _`#14`: https://github.com/kip-hart/MicroStructPy/issues/14
diff --git a/LICENSE.rst b/LICENSE.rst
@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) 2019 Georgia Tech Research Corporation
+Copyright (c) 2020 Georgia Tech Research Corporation
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal
diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -25,7 +25,7 @@
 # -- Project information -----------------------------------------------------
 
 project = 'MicroStructPy'
-copyright = '2019, Georgia Tech Research Corporation'
+copyright = '2020, Georgia Tech Research Corporation'
 author = 'Kenneth Hart'
 
 # The short X.Y version
diff --git a/src/microstructpy/__init__.py b/src/microstructpy/__init__.py
@@ -5,5 +5,5 @@
 import microstructpy.verification
 from microstructpy._vs import _ver_str
 
-__version__ = '1.1.2'
+__version__ = '1.2.0'
 __version__ = _ver_str(__version__)
diff --git a/src/microstructpy/_misc.py b/src/microstructpy/_misc.py
@@ -1,6 +1,6 @@
 """Miscellaneous functions
 
-This private module contains miscalleaneous functions.
+This private module contains miscellaneous functions.
 """
 import numpy as np
 
@@ -17,6 +17,9 @@
 demo_needs = {'basalt_circle.xml': ['aphanitic_cdf.csv', 'olivine_cdf.csv'],
               'from_image.py': ['aluminum_micro.png']}
 
+mpl_plural_kwargs = {'edgecolors', 'facecolors', 'linewidths', 'antialiaseds',
+                     'offsets'}
+
 
 # --------------------------------------------------------------------------- #
 #                                                                             #
diff --git a/src/microstructpy/cli.py b/src/microstructpy/cli.py
@@ -21,7 +21,6 @@
 import numpy as np
 import scipy.stats
 import xmltodict
-from matplotlib import patches
 from mpl_toolkits.mplot3d import Axes3D
 
 from microstructpy import _misc
@@ -619,21 +618,11 @@ def plot_seeds(seeds, phases, domain, plot_files=[], plot_axes=True,
 
     # Plot seeds
     edge_kwargs.setdefault('edgecolors', {2: 'k', 3: 'none'}[n_dim])
-    seeds.plot(facecolors=seed_colors, **edge_kwargs)
-
-    # Add legend
-    custom_seeds = [None for _ in phases]
-    for seed in seeds:
-        phase_num = seed.phase
-        if custom_seeds[phase_num] is None:
-            c = _phase_color(phase_num, phases)
-            lbl = phase_names[phase_num]
-            phase_patch = patches.Patch(fc=c, ec='k', label=lbl)
-            custom_seeds[phase_num] = phase_patch
-
     if given_names and color_by == 'material':
-        handles = [h for h in custom_seeds if h is not None]
-        ax.legend(handles=handles, loc=4)
+        seeds.plot(material=phase_names, facecolors=seed_colors, loc=4,
+                   **edge_kwargs)
+    else:
+        seeds.plot(facecolors=seed_colors, **edge_kwargs)
 
     # Set limits
     lims = domain.limits
@@ -671,6 +660,14 @@ def _phase_color(i, phases):
     return phases[i].get('color', 'C' + str(i % 10))
 
 
+def _phase_color_by(i, phases, color_by='material', colormap='viridis'):
+    if color_by == 'material':
+        return phases[i].get('color', 'C' + str(i % 10))
+    elif color_by == 'material number':
+        n = len(phases)
+        return _cm_color(i / (n - 1), colormap)
+
+
 def _cm_color(f, colormap='viridis'):
     return plt.get_cmap(colormap)(f)
 
@@ -739,7 +736,10 @@ def plot_poly(pmesh, phases, plot_files=['polymesh.png'], plot_axes=True,
     # Plot polygons
     fcs = _poly_colors(pmesh, phases, color_by, colormap, n_dim)
     if n_dim == 2:
-        pmesh.plot(facecolors=fcs)
+        if given_names and color_by == 'material':
+            pmesh.plot(facecolors=fcs, material=phase_names)
+        else:
+            pmesh.plot(facecolors=fcs)
 
         edge_color = edge_kwargs.pop('edgecolors', (0, 0, 0, 1))
         facet_colors = []
@@ -750,22 +750,14 @@ def plot_poly(pmesh, phases, plot_files=['polymesh.png'], plot_axes=True,
                 facet_colors.append('none')
 
         edge_kwargs.setdefault('capstyle', 'round')
-        pmesh.plot_facets(color=facet_colors, **edge_kwargs)
+        pmesh.plot_facets(color=facet_colors, index_by='facet', **edge_kwargs)
     else:
         edge_kwargs.setdefault('edgecolors', 'k')
-        pmesh.plot(facecolors=fcs, **edge_kwargs)
-
-    # add legend
-    if given_names:
-        custom_seeds = [None for _ in phases]
-        for phase_num in pmesh.phase_numbers:
-            if custom_seeds[phase_num] is None:
-                c = phase_colors[phase_num]
-                lbl = phase_names[phase_num]
-                phase_patch = patches.Patch(fc=c, ec='k', label=lbl)
-                custom_seeds[phase_num] = phase_patch
-        handles = [h for h in custom_seeds if h is not None]
-        ax.legend(handles=handles, loc=4)
+        if given_names and color_by == 'material':
+            pmesh.plot(facecolors=fcs, index_by='seed', material=phase_names,
+                       **edge_kwargs)
+        else:
+            pmesh.plot(facecolors=fcs, index_by='seed', **edge_kwargs)
 
     # format axes
     lims = np.array([np.min(pmesh.points, 0), np.max(pmesh.points, 0)]).T
@@ -790,35 +782,37 @@ def plot_poly(pmesh, phases, plot_files=['polymesh.png'], plot_axes=True,
 def _poly_colors(pmesh, phases, color_by, colormap, n_dim):
     if n_dim == 2:
         if color_by == 'material':
-            return [_phase_color(n, phases) for n in pmesh.phase_numbers]
+            r_colors = [_phase_color(n, phases) for n in pmesh.phase_numbers]
         elif color_by == 'seed number':
             n = max(pmesh.seed_numbers) + 1
-            return [_cm_color(s / (n - 1), colormap) for s in
-                    pmesh.seed_numbers]
+            r_colors = [_cm_color(s / (n - 1), colormap) for s in
+                        pmesh.seed_numbers]
         elif color_by == 'material number':
             n = len(phases)
-            return [_cm_color(p / (n - 1), colormap) for p in
-                    pmesh.phase_numbers]
+            r_colors = [_cm_color(p / (n - 1), colormap) for p in
+                        pmesh.phase_numbers]
+        n_seeds = max(pmesh.seed_numbers) + 1
+        s_colors = ['none' for i in range(n_seeds)]
+        for seed_num, r_c in zip(pmesh.seed_numbers, r_colors):
+            s_colors[seed_num] = r_c
+        return s_colors
     else:
-        poly_fcs = []
-        for n_pair in pmesh.facet_neighbors:
-            if min(n_pair) < 0:
-                n_int = max(n_pair)
-                if color_by == 'material':
-                    phase_num = pmesh.phase_numbers[n_int]
-                    color = _phase_color(phase_num, phases)
-                elif color_by == 'seed number':
-                    n_seed = max(pmesh.seed_numbers) + 1
-                    seed_num = pmesh.seed_numbers[n_int]
-                    color = _cm_color(seed_num / (n_seed - 1), colormap)
-                elif color_by == 'material number':
-                    n_phases = len(phases)
-                    phase_num = pmesh.phase_numbers[n_int]
-                    color = _cm_color(phase_num / (n_phases - 1), colormap)
+        s2p = {s: p for s, p in zip(pmesh.seed_numbers, pmesh.phase_numbers)}
+        n = max(s2p.keys()) + 1
+        colors = []
+        for s in range(n):
+            if color_by == 'material':
+                phase_num = s2p[s]
+                color = _phase_color(phase_num, phases)
+            elif color_by == 'seed number':
+                color = _cm_color(s / (n - 1), colormap)
+            elif color_by == 'material number':
+                n_phases = len(phases)
+                color = _cm_color(s2p[s] / (n_phases - 1), colormap)
             else:
                 color = 'none'
-            poly_fcs.append(color)
-        return poly_fcs
+            colors.append(color)
+        return colors
 
 
 # --------------------------------------------------------------------------- #
@@ -883,27 +877,56 @@ def plot_tri(tmesh, phases, seeds, pmesh, plot_files=[], plot_axes=True,
             ax._axis3don = False
     fig.add_axes(ax)
 
-    # determine triangle element colors
-    fcs = _tri_colors(tmesh, seeds, pmesh, phases, color_by, colormap, n_dim)
-    phase_nums = range(len(phases))
-
     # plot triangle mesh
     edge_kwargs.setdefault('linewidths', {2: 0.5, 3: 0.1}[n_dim])
     edge_kwargs.setdefault('edgecolors', 'k')
-    tmesh.plot(facecolors=fcs, **edge_kwargs)
-
-    # add legend
-    if any([given_names[phase_num] for phase_num in phase_nums]):
-        custom_seeds = [None for _ in phases]
-        for seed_num in tmesh.element_attributes:
-            phase_num = seeds[seed_num].phase
-            if custom_seeds[phase_num] is None:
-                c = phase_colors[phase_num]
-                lbl = phase_names[phase_num]
-                phase_patch = patches.Patch(fc=c, ec='k', label=lbl)
-                custom_seeds[phase_num] = phase_patch
-        handles = [h for h in custom_seeds if h is not None]
-        ax.legend(handles=handles, loc=4)
+    if given_names and color_by in ('material', 'material number'):
+        n = len(phases)
+        cs = [_phase_color_by(i, phases, color_by, colormap) for i in range(n)]
+
+        old_e_att = np.copy(tmesh.element_attributes)
+        old_f_att = np.copy(tmesh.facet_attributes)
+        tmesh.element_attributes = [seeds[i].phase for i in old_e_att]
+
+        # Determine which facets are visible
+        visible_facets = [i for i, fn in enumerate(pmesh.facet_neighbors)
+                          if min(fn) < 0]
+        f_frontier = set(visible_facets)
+        f_expl = set()
+        r_expl = set(range(-6, 0))
+        while f_frontier:
+            new_facets = set()
+            for f_num in f_frontier:
+                regions = pmesh.facet_neighbors[f_num]
+                new_regions = set(regions) - r_expl
+                for r in new_regions:
+                    phase = phases[pmesh.phase_numbers[r]]
+                    p_type = phase.get('material_type', 'solid')
+                    if p_type in _misc.kw_void:
+                        new_facets |= set(pmesh.regions[r])
+                        r_expl.update(r)
+            f_expl |= f_frontier
+
+            f_frontier |= new_facets
+            f_frontier -= f_expl
+
+        plot_facets = [i for i, fn in enumerate(pmesh.facet_neighbors) if
+                       len(set(fn) - r_expl) == 1]
+        plot_regions = [list(set(pmesh.facet_neighbors[i]) - r_expl)[0] for i
+                        in plot_facets]
+        poly_phases = [pmesh.phase_numbers[r] for r in plot_regions]
+        p_dict = {f: p for f, p in zip(plot_facets, poly_phases)}
+        plot_phases = [p_dict.get(f, n) for f in tmesh.facet_attributes]
+        tmesh.facet_attributes = plot_phases
+
+        tmesh.plot(facecolors=cs, index_by='attribute', material=phase_names,
+                   **edge_kwargs)
+
+        tmesh.element_attributes = old_e_att
+        tmesh.facet_attributes = old_f_att
+    else:
+        fcs = _poly_colors(pmesh, phases, color_by, colormap, n_dim)
+        tmesh.plot(facecolors=fcs, index_by='attribute', **edge_kwargs)
 
     # format axes
     lims = np.array([np.min(tmesh.points, 0), np.max(tmesh.points, 0)]).T
diff --git a/src/microstructpy/geometry/ellipsoid.py b/src/microstructpy/geometry/ellipsoid.py
@@ -107,6 +107,8 @@ def __init__(self, **kwargs):
             ratio_bc = 1 / kwargs['ratio_cb']
         if 'size' in kwargs:
             size = kwargs['size']
+        elif 'volume' in kwargs:
+            size = 2 * np.cbrt(3 * kwargs['volume'] / (4 * np.pi))
         if 'axes' in kwargs:
             self.a, self.b, self.c = kwargs['axes']
 
@@ -166,6 +168,21 @@ def __init__(self, **kwargs):
                 self.a = r3 / (self.b * self.c)
             elif (self.a is not None) and (self.c is not None):
                 self.b = r3 / (self.a * self.c)
+            elif (self.a is not None) and (ratio_bc is not None):
+                r2 = r3 / self.a
+                # r2 = b * c
+                # r2 = c * ratio_bc * c = ratio_bc * c^2
+                # c = sqrt(r2 / ratio_bc) and b = ratio_bc * c
+                self.c = np.sqrt(r2 / ratio_bc)
+                self.b = ratio_bc * self.c
+            elif (self.b is not None) and (ratio_ac is not None):
+                r2 = r3 / self.b
+                self.c = np.sqrt(r2 / ratio_ac)
+                self.a = ratio_ac * self.c
+            elif (self.c is not None) and (ratio_ab is not None):
+                r2 = r3 / self.c
+                self.b = np.sqrt(r2 / ratio_ab)
+                self.a = ratio_ab * self.b
             else:
                 # r3 = a * b * c
                 # r3 = a * (a / ratio_ab) * (a / ratio_ac)
@@ -589,7 +606,7 @@ def approximate(self, x1=None):
             return np.array([self.bound_max])
 
         if x1 is None:
-            x1 = 0.75 * min(self.axes)
+            x1 = 0.25 * min(self.axes)
 
         # Perform approximation such that a > b > c
         if (self.a >= self.b) and (self.b >= self.c):
diff --git a/src/microstructpy/meshing/polymesh.py b/src/microstructpy/meshing/polymesh.py
diff --git a/src/microstructpy/meshing/trimesh.py b/src/microstructpy/meshing/trimesh.py
diff --git a/src/microstructpy/seeding/seedlist.py b/src/microstructpy/seeding/seedlist.py
