[aa6989b] | 1 | #!/usr/bin/env python |
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[782dd1f] | 2 | """ |
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| 3 | Application to explore the difference between sasview 3.x orientation |
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| 4 | dispersity and possible replacement algorithms. |
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| 5 | """ |
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[aa6989b] | 6 | from __future__ import division, print_function |
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| 7 | |
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| 8 | import sys, os |
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| 9 | sys.path.insert(0, os.path.dirname(os.path.dirname(os.path.realpath(__file__)))) |
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[8678a34] | 10 | |
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[bcb5594] | 11 | import argparse |
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| 12 | |
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[782dd1f] | 13 | import mpl_toolkits.mplot3d # Adds projection='3d' option to subplot |
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| 14 | import matplotlib.pyplot as plt |
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| 15 | from matplotlib.widgets import Slider, CheckButtons |
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| 16 | from matplotlib import cm |
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| 17 | import numpy as np |
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| 18 | from numpy import pi, cos, sin, sqrt, exp, degrees, radians |
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| 19 | |
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[8678a34] | 20 | def draw_beam(ax, view=(0, 0)): |
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[aa6989b] | 21 | """ |
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| 22 | Draw the beam going from source at (0, 0, 1) to detector at (0, 0, -1) |
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| 23 | """ |
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[782dd1f] | 24 | #ax.plot([0,0],[0,0],[1,-1]) |
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| 25 | #ax.scatter([0]*100,[0]*100,np.linspace(1, -1, 100), alpha=0.8) |
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| 26 | |
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| 27 | steps = 25 |
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| 28 | u = np.linspace(0, 2 * np.pi, steps) |
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| 29 | v = np.linspace(-1, 1, steps) |
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| 30 | |
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| 31 | r = 0.02 |
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| 32 | x = r*np.outer(np.cos(u), np.ones_like(v)) |
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| 33 | y = r*np.outer(np.sin(u), np.ones_like(v)) |
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[8678a34] | 34 | z = 1.3*np.outer(np.ones_like(u), v) |
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| 35 | |
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| 36 | theta, phi = view |
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| 37 | shape = x.shape |
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| 38 | points = np.matrix([x.flatten(), y.flatten(), z.flatten()]) |
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| 39 | points = Rz(phi)*Ry(theta)*points |
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| 40 | x, y, z = [v.reshape(shape) for v in points] |
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[782dd1f] | 41 | |
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| 42 | ax.plot_surface(x, y, z, rstride=4, cstride=4, color='y', alpha=0.5) |
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[85190c2] | 43 | |
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[aa6989b] | 44 | def draw_jitter(ax, view, jitter, dist='gaussian', size=(0.1, 0.4, 1.0)): |
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| 45 | """ |
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| 46 | Represent jitter as a set of shapes at different orientations. |
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| 47 | """ |
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| 48 | # set max diagonal to 0.95 |
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| 49 | scale = 0.95/sqrt(sum(v**2 for v in size)) |
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| 50 | size = tuple(scale*v for v in size) |
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[8678a34] | 51 | draw_shape = draw_parallelepiped |
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| 52 | #draw_shape = draw_ellipsoid |
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[85190c2] | 53 | |
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[782dd1f] | 54 | #np.random.seed(10) |
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[85190c2] | 55 | #cloud = np.random.randn(10,3) |
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[782dd1f] | 56 | cloud = [ |
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| 57 | [-1, -1, -1], |
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| 58 | [-1, -1, 0], |
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| 59 | [-1, -1, 1], |
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| 60 | [-1, 0, -1], |
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| 61 | [-1, 0, 0], |
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| 62 | [-1, 0, 1], |
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| 63 | [-1, 1, -1], |
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| 64 | [-1, 1, 0], |
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| 65 | [-1, 1, 1], |
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| 66 | [ 0, -1, -1], |
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| 67 | [ 0, -1, 0], |
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| 68 | [ 0, -1, 1], |
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| 69 | [ 0, 0, -1], |
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| 70 | [ 0, 0, 0], |
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| 71 | [ 0, 0, 1], |
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| 72 | [ 0, 1, -1], |
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| 73 | [ 0, 1, 0], |
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| 74 | [ 0, 1, 1], |
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| 75 | [ 1, -1, -1], |
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| 76 | [ 1, -1, 0], |
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| 77 | [ 1, -1, 1], |
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| 78 | [ 1, 0, -1], |
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| 79 | [ 1, 0, 0], |
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| 80 | [ 1, 0, 1], |
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| 81 | [ 1, 1, -1], |
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| 82 | [ 1, 1, 0], |
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| 83 | [ 1, 1, 1], |
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| 84 | ] |
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[8678a34] | 85 | dtheta, dphi, dpsi = jitter |
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[1b693ba] | 86 | if dtheta == 0: |
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| 87 | cloud = [v for v in cloud if v[0] == 0] |
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| 88 | if dphi == 0: |
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| 89 | cloud = [v for v in cloud if v[1] == 0] |
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| 90 | if dpsi == 0: |
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| 91 | cloud = [v for v in cloud if v[2] == 0] |
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[8678a34] | 92 | draw_shape(ax, size, view, [0, 0, 0], steps=100, alpha=0.8) |
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[bcb5594] | 93 | scale = {'gaussian':1, 'rectangle':1/sqrt(3), 'uniform':1/3}[dist] |
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[782dd1f] | 94 | for point in cloud: |
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[aa6989b] | 95 | delta = [scale*dtheta*point[0], scale*dphi*point[1], scale*dpsi*point[2]] |
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[8678a34] | 96 | draw_shape(ax, size, view, delta, alpha=0.8) |
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[782dd1f] | 97 | for v in 'xyz': |
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| 98 | a, b, c = size |
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| 99 | lim = np.sqrt(a**2+b**2+c**2) |
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| 100 | getattr(ax, 'set_'+v+'lim')([-lim, lim]) |
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| 101 | getattr(ax, v+'axis').label.set_text(v) |
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| 102 | |
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[8678a34] | 103 | def draw_ellipsoid(ax, size, view, jitter, steps=25, alpha=1): |
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[aa6989b] | 104 | """Draw an ellipsoid.""" |
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[782dd1f] | 105 | a,b,c = size |
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| 106 | u = np.linspace(0, 2 * np.pi, steps) |
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| 107 | v = np.linspace(0, np.pi, steps) |
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| 108 | x = a*np.outer(np.cos(u), np.sin(v)) |
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| 109 | y = b*np.outer(np.sin(u), np.sin(v)) |
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| 110 | z = c*np.outer(np.ones_like(u), np.cos(v)) |
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[8678a34] | 111 | x, y, z = transform_xyz(view, jitter, x, y, z) |
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[782dd1f] | 112 | |
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| 113 | ax.plot_surface(x, y, z, rstride=4, cstride=4, color='w', alpha=alpha) |
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| 114 | |
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[8678a34] | 115 | draw_labels(ax, view, jitter, [ |
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| 116 | ('c+', [ 0, 0, c], [ 1, 0, 0]), |
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| 117 | ('c-', [ 0, 0,-c], [ 0, 0,-1]), |
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| 118 | ('a+', [ a, 0, 0], [ 0, 0, 1]), |
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| 119 | ('a-', [-a, 0, 0], [ 0, 0,-1]), |
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| 120 | ('b+', [ 0, b, 0], [-1, 0, 0]), |
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| 121 | ('b-', [ 0,-b, 0], [-1, 0, 0]), |
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| 122 | ]) |
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[782dd1f] | 123 | |
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[8678a34] | 124 | def draw_parallelepiped(ax, size, view, jitter, steps=None, alpha=1): |
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[aa6989b] | 125 | """Draw a parallelepiped.""" |
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[8678a34] | 126 | a,b,c = size |
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[782dd1f] | 127 | x = a*np.array([ 1,-1, 1,-1, 1,-1, 1,-1]) |
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| 128 | y = b*np.array([ 1, 1,-1,-1, 1, 1,-1,-1]) |
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| 129 | z = c*np.array([ 1, 1, 1, 1,-1,-1,-1,-1]) |
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| 130 | tri = np.array([ |
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| 131 | # counter clockwise triangles |
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| 132 | # z: up/down, x: right/left, y: front/back |
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| 133 | [0,1,2], [3,2,1], # top face |
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| 134 | [6,5,4], [5,6,7], # bottom face |
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| 135 | [0,2,6], [6,4,0], # right face |
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| 136 | [1,5,7], [7,3,1], # left face |
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| 137 | [2,3,6], [7,6,3], # front face |
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| 138 | [4,1,0], [5,1,4], # back face |
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| 139 | ]) |
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| 140 | |
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[8678a34] | 141 | x, y, z = transform_xyz(view, jitter, x, y, z) |
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[782dd1f] | 142 | ax.plot_trisurf(x, y, triangles=tri, Z=z, color='w', alpha=alpha) |
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| 143 | |
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[8678a34] | 144 | draw_labels(ax, view, jitter, [ |
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| 145 | ('c+', [ 0, 0, c], [ 1, 0, 0]), |
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| 146 | ('c-', [ 0, 0,-c], [ 0, 0,-1]), |
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| 147 | ('a+', [ a, 0, 0], [ 0, 0, 1]), |
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| 148 | ('a-', [-a, 0, 0], [ 0, 0,-1]), |
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| 149 | ('b+', [ 0, b, 0], [-1, 0, 0]), |
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| 150 | ('b-', [ 0,-b, 0], [-1, 0, 0]), |
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| 151 | ]) |
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[782dd1f] | 152 | |
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[aa6989b] | 153 | def draw_sphere(ax, radius=10., steps=100): |
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| 154 | """Draw a sphere""" |
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| 155 | u = np.linspace(0, 2 * np.pi, steps) |
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| 156 | v = np.linspace(0, np.pi, steps) |
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| 157 | |
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| 158 | x = radius * np.outer(np.cos(u), np.sin(v)) |
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| 159 | y = radius * np.outer(np.sin(u), np.sin(v)) |
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| 160 | z = radius * np.outer(np.ones(np.size(u)), np.cos(v)) |
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| 161 | ax.plot_surface(x, y, z, rstride=4, cstride=4, color='w') |
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| 162 | |
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[bcb5594] | 163 | PROJECTIONS = [ |
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| 164 | 'equirectangular', 'azimuthal_equidistance', 'sinusoidal', |
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| 165 | ] |
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| 166 | def draw_mesh(ax, view, jitter, radius=1.2, n=11, dist='gaussian', |
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| 167 | projection='equirectangular'): |
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[aa6989b] | 168 | """ |
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| 169 | Draw the dispersion mesh showing the theta-phi orientations at which |
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| 170 | the model will be evaluated. |
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[bcb5594] | 171 | |
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| 172 | jitter projections |
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| 173 | <https://en.wikipedia.org/wiki/List_of_map_projections> |
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| 174 | |
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| 175 | equirectangular (standard latitude-longitude mesh) |
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| 176 | <https://en.wikipedia.org/wiki/Equirectangular_projection> |
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| 177 | Allows free movement in phi (around the equator), but theta is |
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| 178 | limited to +/- 90, and points are cos-weighted. Jitter in phi is |
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| 179 | uniform in weight along a line of latitude. With small theta and |
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| 180 | phi ranging over +/- 180 this forms a wobbling disk. With small |
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| 181 | phi and theta ranging over +/- 90 this forms a wedge like a slice |
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| 182 | of an orange. |
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| 183 | azimuthal_equidistance (Postel) |
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| 184 | <https://en.wikipedia.org/wiki/Azimuthal_equidistant_projection> |
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| 185 | Preserves distance from center, and so is an excellent map for |
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| 186 | representing a bivariate gaussian on the surface. Theta and phi |
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| 187 | operate identically, cutting wegdes from the antipode of the viewing |
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| 188 | angle. This unfortunately does not allow free movement in either |
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| 189 | theta or phi since the orthogonal wobble decreases to 0 as the body |
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| 190 | rotates through 180 degrees. |
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| 191 | sinusoidal (Sanson-Flamsteed, Mercator equal-area) |
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| 192 | <https://en.wikipedia.org/wiki/Sinusoidal_projection> |
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| 193 | Preserves arc length with latitude, giving bad behaviour at |
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| 194 | theta near +/- 90. Theta and phi operate somewhat differently, |
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| 195 | so a system with a-b-c dtheta-dphi-dpsi will not give the same |
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| 196 | value as one with b-a-c dphi-dtheta-dpsi, as would be the case |
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| 197 | for azimuthal equidistance. Free movement using theta or phi |
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| 198 | uniform over +/- 180 will work, but not as well as equirectangular |
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| 199 | phi, with theta being slightly worse. Computationally it is much |
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| 200 | cheaper for wide theta-phi meshes since it excludes points which |
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| 201 | lie outside the sinusoid near theta +/- 90 rather than packing |
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[d73a5ac] | 202 | them close together as in equirectangle. Note that the poles |
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| 203 | will be slightly overweighted for theta > 90 with the circle |
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| 204 | from theta at 90+dt winding backwards around the pole, overlapping |
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| 205 | the circle from theta at 90-dt. |
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[bcb5594] | 206 | Guyour (hemisphere-in-a-square) **not implemented** |
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| 207 | <https://en.wikipedia.org/wiki/Guyou_hemisphere-in-a-square_projection> |
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| 208 | Promising. With tiling should allow rotation in phi or theta |
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| 209 | through +/- 180, preserving almost disk-like behaviour in either |
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| 210 | direction (phi rotation will not be as uniform as it is in |
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| 211 | equirectangular; not sure about theta). Unfortunately, distortion |
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| 212 | is not restricted to the corners of the theta-phi mesh, so this will |
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| 213 | not be as good as the azimuthal equidistance project for gaussian |
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| 214 | distributions. |
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| 215 | azimuthal_equal_area **incomplete** |
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| 216 | <https://en.wikipedia.org/wiki/Lambert_azimuthal_equal-area_projection> |
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| 217 | Preserves the relative density of the surface patches. Not that |
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| 218 | useful and not completely implemented |
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| 219 | Gauss-Kreuger **not implemented** |
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| 220 | <https://en.wikipedia.org/wiki/Transverse_Mercator_projection#Ellipsoidal_transverse_Mercator> |
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| 221 | Should allow free movement in theta, but phi is distorted. |
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[aa6989b] | 222 | """ |
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[8678a34] | 223 | theta, phi, psi = view |
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| 224 | dtheta, dphi, dpsi = jitter |
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[aa6989b] | 225 | |
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[bcb5594] | 226 | t = np.linspace(-1, 1, n) |
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| 227 | weights = np.ones_like(t) |
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[aa6989b] | 228 | if dist == 'gaussian': |
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[bcb5594] | 229 | t *= 3 |
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[782dd1f] | 230 | weights = exp(-0.5*t**2) |
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[aa6989b] | 231 | elif dist == 'rectangle': |
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| 232 | # Note: uses sasmodels ridiculous definition of rectangle width |
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[bcb5594] | 233 | t *= sqrt(3) |
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| 234 | elif dist == 'uniform': |
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| 235 | pass |
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[782dd1f] | 236 | else: |
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[bcb5594] | 237 | raise ValueError("expected dist to be gaussian, rectangle or uniform") |
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[782dd1f] | 238 | |
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[bcb5594] | 239 | if projection == 'equirectangular': |
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[87a6591] | 240 | def rotate(theta_i, phi_j): |
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| 241 | return Rx(phi_j)*Ry(theta_i) |
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| 242 | def weight(theta_i, phi_j, wi, wj): |
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[bcb5594] | 243 | return wi*wj*cos(radians(theta_i)) |
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| 244 | elif projection == 'azimuthal_equidistance': |
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[87a6591] | 245 | def rotate(theta_i, phi_j): |
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| 246 | latitude = sqrt(theta_i**2 + phi_j**2) |
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| 247 | longitude = degrees(np.arctan2(phi_j, theta_i)) |
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| 248 | #print("(%+7.2f, %+7.2f) => (%+7.2f, %+7.2f)"%(theta_i, phi_j, latitude, longitude)) |
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| 249 | return Rz(longitude)*Ry(latitude) |
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| 250 | def weight(theta_i, phi_j, wi, wj): |
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[5b5ea20] | 251 | # Weighting for each point comes from the integral: |
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| 252 | # \int\int I(q, lat, log) sin(lat) dlat dlog |
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| 253 | # We are doing a conformal mapping from disk to sphere, so we need |
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| 254 | # a change of variables g(theta, phi) -> (lat, long): |
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| 255 | # lat, long = sqrt(theta^2 + phi^2), arctan(phi/theta) |
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| 256 | # giving: |
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| 257 | # dtheta dphi = det(J) dlat dlong |
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| 258 | # where J is the jacobian from the partials of g. Using |
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| 259 | # R = sqrt(theta^2 + phi^2), |
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| 260 | # then |
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| 261 | # J = [[x/R, Y/R], -y/R^2, x/R^2]] |
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| 262 | # and |
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| 263 | # det(J) = 1/R |
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| 264 | # with the final integral being: |
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| 265 | # \int\int I(q, theta, phi) sin(R)/R dtheta dphi |
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| 266 | # |
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| 267 | # This does approximately the right thing, decreasing the weight |
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| 268 | # of each point as you go farther out on the disk, but it hasn't |
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| 269 | # yet been checked against the 1D integral results. Prior |
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| 270 | # to declaring this "good enough" and checking that integrals |
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| 271 | # work in practice, we will examine alternative mappings. |
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| 272 | # |
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| 273 | # The issue is that the mapping does not support the case of free |
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| 274 | # rotation about a single axis correctly, with a small deviation |
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| 275 | # in the orthogonal axis independent of the first axis. Like the |
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| 276 | # usual polar coordiates integration, the integrated sections |
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| 277 | # form wedges, though at least in this case the wedge cuts through |
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| 278 | # the entire sphere, and treats theta and phi identically. |
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[87a6591] | 279 | latitude = sqrt(theta_i**2 + phi_j**2) |
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[5b5ea20] | 280 | w = sin(radians(latitude))/latitude if latitude != 0 else 1 |
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| 281 | return w*wi*wj if latitude < 180 else 0 |
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[bcb5594] | 282 | elif projection == 'sinusoidal': |
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| 283 | def rotate(theta_i, phi_j): |
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| 284 | latitude = theta_i |
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| 285 | scale = cos(radians(latitude)) |
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| 286 | longitude = phi_j/scale if abs(phi_j) < abs(scale)*180 else 0 |
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| 287 | #print("(%+7.2f, %+7.2f) => (%+7.2f, %+7.2f)"%(theta_i, phi_j, latitude, longitude)) |
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| 288 | return Rx(longitude)*Ry(latitude) |
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| 289 | def weight(theta_i, phi_j, wi, wj): |
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| 290 | latitude = theta_i |
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| 291 | scale = cos(radians(latitude)) |
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| 292 | w = 1 if abs(phi_j) < abs(scale)*180 else 0 |
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| 293 | return w*wi*wj |
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| 294 | elif projection == 'azimuthal_equal_area': |
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[87a6591] | 295 | def rotate(theta_i, phi_j): |
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| 296 | R = min(1, sqrt(theta_i**2 + phi_j**2)/180) |
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| 297 | latitude = 180-degrees(2*np.arccos(R)) |
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| 298 | longitude = degrees(np.arctan2(phi_j, theta_i)) |
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| 299 | #print("(%+7.2f, %+7.2f) => (%+7.2f, %+7.2f)"%(theta_i, phi_j, latitude, longitude)) |
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| 300 | return Rz(longitude)*Ry(latitude) |
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| 301 | def weight(theta_i, phi_j, wi, wj): |
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[5b5ea20] | 302 | latitude = sqrt(theta_i**2 + phi_j**2) |
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| 303 | w = sin(radians(latitude))/latitude if latitude != 0 else 1 |
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| 304 | return w*wi*wj if latitude < 180 else 0 |
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[b9578fc] | 305 | else: |
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[bcb5594] | 306 | raise ValueError("unknown projection %r"%projection) |
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[b9578fc] | 307 | |
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[8678a34] | 308 | # mesh in theta, phi formed by rotating z |
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| 309 | z = np.matrix([[0], [0], [radius]]) |
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[87a6591] | 310 | points = np.hstack([rotate(theta_i, phi_j)*z |
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[8678a34] | 311 | for theta_i in dtheta*t |
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[b9578fc] | 312 | for phi_j in dphi*t]) |
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| 313 | # select just the active points (i.e., those with phi < 180 |
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[87a6591] | 314 | w = np.array([weight(theta_i, phi_j, wi, wj) |
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| 315 | for wi, theta_i in zip(weights, dtheta*t) |
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| 316 | for wj, phi_j in zip(weights, dphi*t)]) |
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[5b5ea20] | 317 | #print(max(w), min(w), min(w[w>0])) |
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[87a6591] | 318 | points = points[:, w>0] |
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| 319 | w = w[w>0] |
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[5b5ea20] | 320 | w /= max(w) |
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[87a6591] | 321 | |
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| 322 | if 0: # Kent distribution |
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| 323 | points = np.hstack([Rx(phi_j)*Ry(theta_i)*z for theta_i in 30*t for phi_j in 60*t]) |
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| 324 | xp, yp, zp = [np.array(v).flatten() for v in points] |
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| 325 | kappa = max(1e6, radians(dtheta)/(2*pi)) |
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| 326 | beta = 1/max(1e-6, radians(dphi)/(2*pi))/kappa |
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| 327 | w = exp(kappa*zp) #+ beta*(xp**2 + yp**2) |
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| 328 | print(kappa, dtheta, radians(dtheta), min(w), max(w), sum(w)) |
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| 329 | #w /= abs(cos(radians( |
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| 330 | #w /= sum(w) |
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[b9578fc] | 331 | |
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[8678a34] | 332 | # rotate relative to beam |
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| 333 | points = orient_relative_to_beam(view, points) |
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[782dd1f] | 334 | |
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[8678a34] | 335 | x, y, z = [np.array(v).flatten() for v in points] |
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[87a6591] | 336 | #plt.figure(2); plt.clf(); plt.hist(z, bins=np.linspace(-1, 1, 51)) |
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[b9578fc] | 337 | ax.scatter(x, y, z, c=w, marker='o', vmin=0., vmax=1.) |
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[782dd1f] | 338 | |
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[aa6989b] | 339 | def draw_labels(ax, view, jitter, text): |
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| 340 | """ |
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| 341 | Draw text at a particular location. |
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| 342 | """ |
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| 343 | labels, locations, orientations = zip(*text) |
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| 344 | px, py, pz = zip(*locations) |
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| 345 | dx, dy, dz = zip(*orientations) |
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| 346 | |
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| 347 | px, py, pz = transform_xyz(view, jitter, px, py, pz) |
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| 348 | dx, dy, dz = transform_xyz(view, jitter, dx, dy, dz) |
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| 349 | |
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| 350 | # TODO: zdir for labels is broken, and labels aren't appearing. |
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| 351 | for label, p, zdir in zip(labels, zip(px, py, pz), zip(dx, dy, dz)): |
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| 352 | zdir = np.asarray(zdir).flatten() |
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| 353 | ax.text(p[0], p[1], p[2], label, zdir=zdir) |
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| 354 | |
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| 355 | # Definition of rotation matrices comes from wikipedia: |
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| 356 | # https://en.wikipedia.org/wiki/Rotation_matrix#Basic_rotations |
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[782dd1f] | 357 | def Rx(angle): |
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[aa6989b] | 358 | """Construct a matrix to rotate points about *x* by *angle* degrees.""" |
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[782dd1f] | 359 | a = radians(angle) |
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[aa6989b] | 360 | R = [[1, 0, 0], |
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| 361 | [0, +cos(a), -sin(a)], |
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| 362 | [0, +sin(a), +cos(a)]] |
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[782dd1f] | 363 | return np.matrix(R) |
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| 364 | |
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| 365 | def Ry(angle): |
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[aa6989b] | 366 | """Construct a matrix to rotate points about *y* by *angle* degrees.""" |
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[782dd1f] | 367 | a = radians(angle) |
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[aa6989b] | 368 | R = [[+cos(a), 0, +sin(a)], |
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| 369 | [0, 1, 0], |
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| 370 | [-sin(a), 0, +cos(a)]] |
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[782dd1f] | 371 | return np.matrix(R) |
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| 372 | |
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| 373 | def Rz(angle): |
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[aa6989b] | 374 | """Construct a matrix to rotate points about *z* by *angle* degrees.""" |
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[782dd1f] | 375 | a = radians(angle) |
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[aa6989b] | 376 | R = [[+cos(a), -sin(a), 0], |
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| 377 | [+sin(a), +cos(a), 0], |
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| 378 | [0, 0, 1]] |
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[782dd1f] | 379 | return np.matrix(R) |
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| 380 | |
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[8678a34] | 381 | def transform_xyz(view, jitter, x, y, z): |
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[aa6989b] | 382 | """ |
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| 383 | Send a set of (x,y,z) points through the jitter and view transforms. |
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| 384 | """ |
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[8678a34] | 385 | x, y, z = [np.asarray(v) for v in (x, y, z)] |
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| 386 | shape = x.shape |
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| 387 | points = np.matrix([x.flatten(),y.flatten(),z.flatten()]) |
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| 388 | points = apply_jitter(jitter, points) |
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| 389 | points = orient_relative_to_beam(view, points) |
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| 390 | x, y, z = [np.array(v).reshape(shape) for v in points] |
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| 391 | return x, y, z |
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| 392 | |
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| 393 | def apply_jitter(jitter, points): |
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[aa6989b] | 394 | """ |
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| 395 | Apply the jitter transform to a set of points. |
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| 396 | |
---|
| 397 | Points are stored in a 3 x n numpy matrix, not a numpy array or tuple. |
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| 398 | """ |
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[8678a34] | 399 | dtheta, dphi, dpsi = jitter |
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[d4c33d6] | 400 | points = Rx(dphi)*Ry(dtheta)*Rz(dpsi)*points |
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[8678a34] | 401 | return points |
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| 402 | |
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| 403 | def orient_relative_to_beam(view, points): |
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[aa6989b] | 404 | """ |
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| 405 | Apply the view transform to a set of points. |
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| 406 | |
---|
| 407 | Points are stored in a 3 x n numpy matrix, not a numpy array or tuple. |
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| 408 | """ |
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[8678a34] | 409 | theta, phi, psi = view |
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| 410 | points = Rz(phi)*Ry(theta)*Rz(psi)*points |
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| 411 | return points |
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| 412 | |
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[aa6989b] | 413 | # translate between number of dimension of dispersity and the number of |
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| 414 | # points along each dimension. |
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| 415 | PD_N_TABLE = { |
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| 416 | (0, 0, 0): (0, 0, 0), # 0 |
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| 417 | (1, 0, 0): (100, 0, 0), # 100 |
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| 418 | (0, 1, 0): (0, 100, 0), |
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| 419 | (0, 0, 1): (0, 0, 100), |
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| 420 | (1, 1, 0): (30, 30, 0), # 900 |
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| 421 | (1, 0, 1): (30, 0, 30), |
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| 422 | (0, 1, 1): (0, 30, 30), |
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| 423 | (1, 1, 1): (15, 15, 15), # 3375 |
---|
| 424 | } |
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| 425 | |
---|
| 426 | def clipped_range(data, portion=1.0, mode='central'): |
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| 427 | """ |
---|
| 428 | Determine range from data. |
---|
| 429 | |
---|
| 430 | If *portion* is 1, use full range, otherwise use the center of the range |
---|
| 431 | or the top of the range, depending on whether *mode* is 'central' or 'top'. |
---|
| 432 | """ |
---|
| 433 | if portion == 1.0: |
---|
| 434 | return data.min(), data.max() |
---|
| 435 | elif mode == 'central': |
---|
| 436 | data = np.sort(data.flatten()) |
---|
| 437 | offset = int(portion*len(data)/2 + 0.5) |
---|
| 438 | return data[offset], data[-offset] |
---|
| 439 | elif mode == 'top': |
---|
| 440 | data = np.sort(data.flatten()) |
---|
| 441 | offset = int(portion*len(data) + 0.5) |
---|
| 442 | return data[offset], data[-1] |
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| 443 | |
---|
| 444 | def draw_scattering(calculator, ax, view, jitter, dist='gaussian'): |
---|
| 445 | """ |
---|
| 446 | Plot the scattering for the particular view. |
---|
| 447 | |
---|
| 448 | *calculator* is returned from :func:`build_model`. *ax* are the 3D axes |
---|
| 449 | on which the data will be plotted. *view* and *jitter* are the current |
---|
| 450 | orientation and orientation dispersity. *dist* is one of the sasmodels |
---|
| 451 | weight distributions. |
---|
| 452 | """ |
---|
[bcb5594] | 453 | if dist == 'uniform': # uniform is not yet in this branch |
---|
| 454 | dist, scale = 'rectangle', 1/sqrt(3) |
---|
| 455 | else: |
---|
| 456 | scale = 1 |
---|
[aa6989b] | 457 | |
---|
| 458 | # add the orientation parameters to the model parameters |
---|
| 459 | theta, phi, psi = view |
---|
| 460 | theta_pd, phi_pd, psi_pd = [scale*v for v in jitter] |
---|
| 461 | theta_pd_n, phi_pd_n, psi_pd_n = PD_N_TABLE[(theta_pd>0, phi_pd>0, psi_pd>0)] |
---|
| 462 | ## increase pd_n for testing jitter integration rather than simple viz |
---|
| 463 | #theta_pd_n, phi_pd_n, psi_pd_n = [5*v for v in (theta_pd_n, phi_pd_n, psi_pd_n)] |
---|
| 464 | |
---|
| 465 | pars = dict( |
---|
| 466 | theta=theta, theta_pd=theta_pd, theta_pd_type=dist, theta_pd_n=theta_pd_n, |
---|
| 467 | phi=phi, phi_pd=phi_pd, phi_pd_type=dist, phi_pd_n=phi_pd_n, |
---|
| 468 | psi=psi, psi_pd=psi_pd, psi_pd_type=dist, psi_pd_n=psi_pd_n, |
---|
| 469 | ) |
---|
| 470 | pars.update(calculator.pars) |
---|
| 471 | |
---|
| 472 | # compute the pattern |
---|
| 473 | qx, qy = calculator._data.x_bins, calculator._data.y_bins |
---|
| 474 | Iqxy = calculator(**pars).reshape(len(qx), len(qy)) |
---|
| 475 | |
---|
| 476 | # scale it and draw it |
---|
| 477 | Iqxy = np.log(Iqxy) |
---|
| 478 | if calculator.limits: |
---|
| 479 | # use limits from orientation (0,0,0) |
---|
| 480 | vmin, vmax = calculator.limits |
---|
| 481 | else: |
---|
| 482 | vmin, vmax = clipped_range(Iqxy, portion=0.95, mode='top') |
---|
| 483 | #print("range",(vmin,vmax)) |
---|
| 484 | #qx, qy = np.meshgrid(qx, qy) |
---|
| 485 | if 0: |
---|
| 486 | level = np.asarray(255*(Iqxy - vmin)/(vmax - vmin), 'i') |
---|
| 487 | level[level<0] = 0 |
---|
| 488 | colors = plt.get_cmap()(level) |
---|
| 489 | ax.plot_surface(qx, qy, -1.1, rstride=1, cstride=1, facecolors=colors) |
---|
| 490 | elif 1: |
---|
| 491 | ax.contourf(qx/qx.max(), qy/qy.max(), Iqxy, zdir='z', offset=-1.1, |
---|
| 492 | levels=np.linspace(vmin, vmax, 24)) |
---|
| 493 | else: |
---|
| 494 | ax.pcolormesh(qx, qy, Iqxy) |
---|
| 495 | |
---|
| 496 | def build_model(model_name, n=150, qmax=0.5, **pars): |
---|
| 497 | """ |
---|
| 498 | Build a calculator for the given shape. |
---|
| 499 | |
---|
| 500 | *model_name* is any sasmodels model. *n* and *qmax* define an n x n mesh |
---|
| 501 | on which to evaluate the model. The remaining parameters are stored in |
---|
| 502 | the returned calculator as *calculator.pars*. They are used by |
---|
| 503 | :func:`draw_scattering` to set the non-orientation parameters in the |
---|
| 504 | calculation. |
---|
| 505 | |
---|
| 506 | Returns a *calculator* function which takes a dictionary or parameters and |
---|
| 507 | produces Iqxy. The Iqxy value needs to be reshaped to an n x n matrix |
---|
| 508 | for plotting. See the :class:`sasmodels.direct_model.DirectModel` class |
---|
| 509 | for details. |
---|
| 510 | """ |
---|
| 511 | from sasmodels.core import load_model_info, build_model |
---|
| 512 | from sasmodels.data import empty_data2D |
---|
| 513 | from sasmodels.direct_model import DirectModel |
---|
| 514 | |
---|
| 515 | model_info = load_model_info(model_name) |
---|
| 516 | model = build_model(model_info) #, dtype='double!') |
---|
| 517 | q = np.linspace(-qmax, qmax, n) |
---|
| 518 | data = empty_data2D(q, q) |
---|
| 519 | calculator = DirectModel(data, model) |
---|
| 520 | |
---|
| 521 | # stuff the values for non-orientation parameters into the calculator |
---|
| 522 | calculator.pars = pars.copy() |
---|
| 523 | calculator.pars.setdefault('backgound', 1e-3) |
---|
| 524 | |
---|
| 525 | # fix the data limits so that we can see if the pattern fades |
---|
| 526 | # under rotation or angular dispersion |
---|
| 527 | Iqxy = calculator(theta=0, phi=0, psi=0, **calculator.pars) |
---|
| 528 | Iqxy = np.log(Iqxy) |
---|
| 529 | vmin, vmax = clipped_range(Iqxy, 0.95, mode='top') |
---|
| 530 | calculator.limits = vmin, vmax+1 |
---|
| 531 | |
---|
| 532 | return calculator |
---|
| 533 | |
---|
[59e537a] | 534 | def select_calculator(model_name, n=150, size=(10,40,100)): |
---|
[aa6989b] | 535 | """ |
---|
| 536 | Create a model calculator for the given shape. |
---|
| 537 | |
---|
| 538 | *model_name* is one of sphere, cylinder, ellipsoid, triaxial_ellipsoid, |
---|
| 539 | parallelepiped or bcc_paracrystal. *n* is the number of points to use |
---|
| 540 | in the q range. *qmax* is chosen based on model parameters for the |
---|
| 541 | given model to show something intersting. |
---|
| 542 | |
---|
| 543 | Returns *calculator* and tuple *size* (a,b,c) giving minor and major |
---|
| 544 | equitorial axes and polar axis respectively. See :func:`build_model` |
---|
| 545 | for details on the returned calculator. |
---|
| 546 | """ |
---|
[59e537a] | 547 | a, b, c = size |
---|
[aa6989b] | 548 | if model_name == 'sphere': |
---|
| 549 | calculator = build_model('sphere', n=n, radius=c) |
---|
| 550 | a = b = c |
---|
| 551 | elif model_name == 'bcc_paracrystal': |
---|
| 552 | calculator = build_model('bcc_paracrystal', n=n, dnn=c, |
---|
| 553 | d_factor=0.06, radius=40) |
---|
| 554 | a = b = c |
---|
| 555 | elif model_name == 'cylinder': |
---|
| 556 | calculator = build_model('cylinder', n=n, qmax=0.3, radius=b, length=c) |
---|
| 557 | a = b |
---|
| 558 | elif model_name == 'ellipsoid': |
---|
| 559 | calculator = build_model('ellipsoid', n=n, qmax=1.0, |
---|
| 560 | radius_polar=c, radius_equatorial=b) |
---|
| 561 | a = b |
---|
| 562 | elif model_name == 'triaxial_ellipsoid': |
---|
| 563 | calculator = build_model('triaxial_ellipsoid', n=n, qmax=0.5, |
---|
| 564 | radius_equat_minor=a, |
---|
| 565 | radius_equat_major=b, |
---|
| 566 | radius_polar=c) |
---|
| 567 | elif model_name == 'parallelepiped': |
---|
| 568 | calculator = build_model('parallelepiped', n=n, a=a, b=b, c=c) |
---|
| 569 | else: |
---|
| 570 | raise ValueError("unknown model %s"%model_name) |
---|
[8678a34] | 571 | |
---|
[aa6989b] | 572 | return calculator, (a, b, c) |
---|
[8678a34] | 573 | |
---|
[bcb5594] | 574 | SHAPES = [ |
---|
| 575 | 'parallelepiped', 'triaxial_ellipsoid', 'bcc_paracrystal', |
---|
| 576 | 'cylinder', 'ellipsoid', |
---|
| 577 | 'sphere', |
---|
| 578 | ] |
---|
| 579 | |
---|
| 580 | DISTRIBUTIONS = [ |
---|
| 581 | 'gaussian', 'rectangle', 'uniform', |
---|
| 582 | ] |
---|
| 583 | DIST_LIMITS = { |
---|
| 584 | 'gaussian': 30, |
---|
| 585 | 'rectangle': 90/sqrt(3), |
---|
| 586 | 'uniform': 90, |
---|
| 587 | } |
---|
| 588 | |
---|
| 589 | def run(model_name='parallelepiped', size=(10, 40, 100), |
---|
| 590 | dist='gaussian', mesh=30, |
---|
| 591 | projection='equirectangular'): |
---|
[aa6989b] | 592 | """ |
---|
| 593 | Show an interactive orientation and jitter demo. |
---|
[8678a34] | 594 | |
---|
[aa6989b] | 595 | *model_name* is one of the models available in :func:`select_model`. |
---|
| 596 | """ |
---|
| 597 | # set up calculator |
---|
[59e537a] | 598 | calculator, size = select_calculator(model_name, n=150, size=size) |
---|
[8678a34] | 599 | |
---|
[aa6989b] | 600 | ## uncomment to set an independent the colour range for every view |
---|
| 601 | ## If left commented, the colour range is fixed for all views |
---|
| 602 | calculator.limits = None |
---|
| 603 | |
---|
| 604 | ## initial view |
---|
| 605 | #theta, dtheta = 70., 10. |
---|
| 606 | #phi, dphi = -45., 3. |
---|
| 607 | #psi, dpsi = -45., 3. |
---|
| 608 | theta, phi, psi = 0, 0, 0 |
---|
| 609 | dtheta, dphi, dpsi = 0, 0, 0 |
---|
| 610 | |
---|
| 611 | ## create the plot window |
---|
[782dd1f] | 612 | #plt.hold(True) |
---|
| 613 | plt.set_cmap('gist_earth') |
---|
| 614 | plt.clf() |
---|
| 615 | #gs = gridspec.GridSpec(2,1,height_ratios=[4,1]) |
---|
| 616 | #ax = plt.subplot(gs[0], projection='3d') |
---|
| 617 | ax = plt.axes([0.0, 0.2, 1.0, 0.8], projection='3d') |
---|
[36b3154] | 618 | try: # CRUFT: not all versions of matplotlib accept 'square' 3d projection |
---|
| 619 | ax.axis('square') |
---|
| 620 | except Exception: |
---|
| 621 | pass |
---|
[782dd1f] | 622 | |
---|
| 623 | axcolor = 'lightgoldenrodyellow' |
---|
[8678a34] | 624 | |
---|
[aa6989b] | 625 | ## add control widgets to plot |
---|
[782dd1f] | 626 | axtheta = plt.axes([0.1, 0.15, 0.45, 0.04], axisbg=axcolor) |
---|
| 627 | axphi = plt.axes([0.1, 0.1, 0.45, 0.04], axisbg=axcolor) |
---|
| 628 | axpsi = plt.axes([0.1, 0.05, 0.45, 0.04], axisbg=axcolor) |
---|
[1b693ba] | 629 | stheta = Slider(axtheta, 'Theta', -90, 90, valinit=theta) |
---|
[782dd1f] | 630 | sphi = Slider(axphi, 'Phi', -180, 180, valinit=phi) |
---|
| 631 | spsi = Slider(axpsi, 'Psi', -180, 180, valinit=psi) |
---|
[8678a34] | 632 | |
---|
[782dd1f] | 633 | axdtheta = plt.axes([0.75, 0.15, 0.15, 0.04], axisbg=axcolor) |
---|
| 634 | axdphi = plt.axes([0.75, 0.1, 0.15, 0.04], axisbg=axcolor) |
---|
| 635 | axdpsi= plt.axes([0.75, 0.05, 0.15, 0.04], axisbg=axcolor) |
---|
[aa6989b] | 636 | # Note: using ridiculous definition of rectangle distribution, whose width |
---|
| 637 | # in sasmodels is sqrt(3) times the given width. Divide by sqrt(3) to keep |
---|
| 638 | # the maximum width to 90. |
---|
[bcb5594] | 639 | dlimit = DIST_LIMITS[dist] |
---|
[0db85af] | 640 | sdtheta = Slider(axdtheta, 'dTheta', 0, 2*dlimit, valinit=dtheta) |
---|
[aa6989b] | 641 | sdphi = Slider(axdphi, 'dPhi', 0, 2*dlimit, valinit=dphi) |
---|
| 642 | sdpsi = Slider(axdpsi, 'dPsi', 0, 2*dlimit, valinit=dpsi) |
---|
| 643 | |
---|
| 644 | ## callback to draw the new view |
---|
[782dd1f] | 645 | def update(val, axis=None): |
---|
[8678a34] | 646 | view = stheta.val, sphi.val, spsi.val |
---|
| 647 | jitter = sdtheta.val, sdphi.val, sdpsi.val |
---|
[aa6989b] | 648 | # set small jitter as 0 if multiple pd dims |
---|
| 649 | dims = sum(v > 0 for v in jitter) |
---|
[bcb5594] | 650 | limit = [0, 0, 0.5, 5][dims] |
---|
[aa6989b] | 651 | jitter = [0 if v < limit else v for v in jitter] |
---|
[782dd1f] | 652 | ax.cla() |
---|
[8678a34] | 653 | draw_beam(ax, (0, 0)) |
---|
[aa6989b] | 654 | draw_jitter(ax, view, jitter, dist=dist, size=size) |
---|
[d4c33d6] | 655 | #draw_jitter(ax, view, (0,0,0)) |
---|
[bcb5594] | 656 | draw_mesh(ax, view, jitter, dist=dist, n=mesh, projection=projection) |
---|
[aa6989b] | 657 | draw_scattering(calculator, ax, view, jitter, dist=dist) |
---|
[782dd1f] | 658 | plt.gcf().canvas.draw() |
---|
| 659 | |
---|
[aa6989b] | 660 | ## bind control widgets to view updater |
---|
[782dd1f] | 661 | stheta.on_changed(lambda v: update(v,'theta')) |
---|
| 662 | sphi.on_changed(lambda v: update(v, 'phi')) |
---|
| 663 | spsi.on_changed(lambda v: update(v, 'psi')) |
---|
| 664 | sdtheta.on_changed(lambda v: update(v, 'dtheta')) |
---|
| 665 | sdphi.on_changed(lambda v: update(v, 'dphi')) |
---|
| 666 | sdpsi.on_changed(lambda v: update(v, 'dpsi')) |
---|
| 667 | |
---|
[aa6989b] | 668 | ## initialize view |
---|
[782dd1f] | 669 | update(None, 'phi') |
---|
| 670 | |
---|
[aa6989b] | 671 | ## go interactive |
---|
[782dd1f] | 672 | plt.show() |
---|
| 673 | |
---|
[bcb5594] | 674 | def main(): |
---|
| 675 | parser = argparse.ArgumentParser( |
---|
| 676 | description="Display jitter", |
---|
| 677 | formatter_class=argparse.ArgumentDefaultsHelpFormatter, |
---|
| 678 | ) |
---|
| 679 | parser.add_argument('-p', '--projection', choices=PROJECTIONS, default=PROJECTIONS[0], help='coordinate projection') |
---|
| 680 | parser.add_argument('-s', '--size', type=str, default='10,40,100', help='a,b,c lengths') |
---|
| 681 | parser.add_argument('-d', '--distribution', choices=DISTRIBUTIONS, default=DISTRIBUTIONS[0], help='jitter distribution') |
---|
| 682 | parser.add_argument('-m', '--mesh', type=int, default=30, help='#points in theta-phi mesh') |
---|
| 683 | parser.add_argument('shape', choices=SHAPES, nargs='?', default=SHAPES[0], help='oriented shape') |
---|
| 684 | opts = parser.parse_args() |
---|
| 685 | size = tuple(int(v) for v in opts.size.split(',')) |
---|
| 686 | run(opts.shape, size=size, |
---|
| 687 | mesh=opts.mesh, dist=opts.distribution, |
---|
| 688 | projection=opts.projection) |
---|
| 689 | |
---|
[782dd1f] | 690 | if __name__ == "__main__": |
---|
[bcb5594] | 691 | main() |
---|