1 | """Classes implementing general 2D triangular mesh with neighbour structure. |
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2 | |
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3 | This structure is purely geometrical. Anything relating to quantities |
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4 | or timestepping is implemented in subclass domain.py. |
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5 | |
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6 | Ole Nielsen, Stephen Roberts, Duncan Gray, Christopher Zoppou |
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7 | Geoscience Australia, 2004 |
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8 | """ |
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9 | |
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10 | from general_mesh import General_mesh |
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11 | from math import pi, sqrt |
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12 | |
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13 | |
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14 | class Mesh(General_mesh): |
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15 | """Collection of triangular elements (purely geometric) |
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16 | |
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17 | A triangular element is defined in terms of three vertex ids, |
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18 | ordered counter clock-wise, |
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19 | each corresponding to a given coordinate set. |
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20 | Vertices from different elements can point to the same |
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21 | coordinate set. |
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22 | |
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23 | Coordinate sets are implemented as an N x 2 Numeric array containing |
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24 | x and y coordinates. |
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25 | |
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26 | |
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27 | To instantiate: |
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28 | Mesh(coordinates, triangles) |
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29 | |
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30 | where |
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31 | |
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32 | coordinates is either a list of 2-tuples or an Mx2 Numeric array of |
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33 | floats representing all x, y coordinates in the mesh. |
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34 | |
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35 | triangles is either a list of 3-tuples or an Nx3 Numeric array of |
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36 | integers representing indices of all vertices in the mesh. |
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37 | Each vertex is identified by its index i in [0, M-1]. |
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38 | |
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39 | |
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40 | Example: |
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41 | a = [0.0, 0.0] |
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42 | b = [0.0, 2.0] |
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43 | c = [2.0,0.0] |
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44 | e = [2.0, 2.0] |
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45 | |
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46 | points = [a, b, c, e] |
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47 | triangles = [ [1,0,2], [1,2,3] ] #bac, bce |
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48 | mesh = Mesh(points, triangles) |
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49 | |
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50 | #creates two triangles: bac and bce |
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51 | |
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52 | |
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53 | Mesh takes the optional third argument boundary which is a |
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54 | dictionary mapping from (element_id, edge_id) to boundary tag. |
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55 | The default value is None which will assign the default_boundary_tag |
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56 | as specified in config.py to all boundary edges. |
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57 | """ |
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58 | |
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59 | #FIXME: Maybe rename coordinates to points (as in a poly file) |
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60 | #But keep 'vertex_coordinates' |
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61 | |
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62 | #FIXME: Put in check for angles less than a set minimum |
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63 | |
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64 | |
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65 | def __init__(self, coordinates, triangles, |
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66 | boundary=None, |
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67 | tagged_elements=None, |
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68 | geo_reference=None, |
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69 | use_inscribed_circle=False, |
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70 | verbose=False): |
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71 | """ |
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72 | Build triangles from x,y coordinates (sequence of 2-tuples or |
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73 | Mx2 Numeric array of floats) and triangles (sequence of 3-tuples |
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74 | or Nx3 Numeric array of non-negative integers). |
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75 | """ |
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76 | |
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77 | |
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78 | |
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79 | from Numeric import array, zeros, Int, Float, maximum, sqrt, sum |
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80 | |
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81 | General_mesh.__init__(self, coordinates, triangles, |
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82 | geo_reference, verbose=verbose) |
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83 | |
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84 | if verbose: print 'Initialising mesh' |
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85 | |
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86 | N = self.number_of_elements |
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87 | |
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88 | self.use_inscribed_circle = use_inscribed_circle |
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89 | |
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90 | #Allocate space for geometric quantities |
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91 | self.centroid_coordinates = zeros((N, 2), Float) |
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92 | |
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93 | self.radii = zeros(N, Float) |
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94 | |
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95 | self.neighbours = zeros((N, 3), Int) |
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96 | self.neighbour_edges = zeros((N, 3), Int) |
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97 | self.number_of_boundaries = zeros(N, Int) |
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98 | self.surrogate_neighbours = zeros((N, 3), Int) |
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99 | |
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100 | #Get x,y coordinates for all triangles and store |
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101 | V = self.vertex_coordinates # Relative coordinates |
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102 | |
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103 | #Initialise each triangle |
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104 | if verbose: print 'Mesh: Computing centroids and radii' |
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105 | for i in range(N): |
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106 | if verbose and i % ((N+10)/10) == 0: print '(%d/%d)' %(i, N) |
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107 | |
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108 | x0 = V[i, 0]; y0 = V[i, 1] |
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109 | x1 = V[i, 2]; y1 = V[i, 3] |
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110 | x2 = V[i, 4]; y2 = V[i, 5] |
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111 | |
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112 | #Compute centroid |
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113 | centroid = array([(x0 + x1 + x2)/3, (y0 + y1 + y2)/3]) |
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114 | self.centroid_coordinates[i] = centroid |
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115 | |
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116 | |
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117 | if self.use_inscribed_circle == False: |
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118 | #OLD code. Computed radii may exceed that of an |
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119 | #inscribed circle |
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120 | |
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121 | #Midpoints |
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122 | m0 = array([(x1 + x2)/2, (y1 + y2)/2]) |
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123 | m1 = array([(x0 + x2)/2, (y0 + y2)/2]) |
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124 | m2 = array([(x1 + x0)/2, (y1 + y0)/2]) |
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125 | |
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126 | #The radius is the distance from the centroid of |
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127 | #a triangle to the midpoint of the side of the triangle |
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128 | #closest to the centroid |
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129 | d0 = sqrt(sum( (centroid-m0)**2 )) |
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130 | d1 = sqrt(sum( (centroid-m1)**2 )) |
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131 | d2 = sqrt(sum( (centroid-m2)**2 )) |
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132 | |
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133 | self.radii[i] = min(d0, d1, d2) |
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134 | |
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135 | else: |
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136 | #NEW code added by Peter Row. True radius |
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137 | #of inscribed circle is computed |
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138 | |
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139 | a = sqrt((x0-x1)**2+(y0-y1)**2) |
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140 | b = sqrt((x1-x2)**2+(y1-y2)**2) |
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141 | c = sqrt((x2-x0)**2+(y2-y0)**2) |
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142 | |
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143 | self.radii[i]=2.0*self.areas[i]/(a+b+c) |
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144 | |
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145 | |
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146 | #Initialise Neighbours (-1 means that it is a boundary neighbour) |
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147 | self.neighbours[i, :] = [-1, -1, -1] |
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148 | |
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149 | #Initialise edge ids of neighbours |
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150 | #In case of boundaries this slot is not used |
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151 | self.neighbour_edges[i, :] = [-1, -1, -1] |
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152 | |
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153 | |
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154 | #Build neighbour structure |
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155 | if verbose: print 'Mesh: Building neigbour structure' |
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156 | self.build_neighbour_structure() |
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157 | |
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158 | #Build surrogate neighbour structure |
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159 | if verbose: print 'Mesh: Building surrogate neigbour structure' |
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160 | self.build_surrogate_neighbour_structure() |
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161 | |
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162 | #Build boundary dictionary mapping (id, edge) to symbolic tags |
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163 | if verbose: print 'Mesh: Building boundary dictionary' |
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164 | self.build_boundary_dictionary(boundary) |
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165 | |
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166 | #Build tagged element dictionary mapping (tag) to array of elements |
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167 | if verbose: print 'Mesh: Building tagged elements dictionary' |
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168 | self.build_tagged_elements_dictionary(tagged_elements) |
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169 | |
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170 | #Update boundary indices FIXME: OBSOLETE |
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171 | #self.build_boundary_structure() |
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172 | |
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173 | #FIXME check integrity? |
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174 | if verbose: print 'Mesh: Done' |
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175 | |
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176 | def __repr__(self): |
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177 | return 'Mesh: %d triangles, %d elements, %d boundary segments'\ |
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178 | %(self.coordinates.shape[0], len(self), len(self.boundary)) |
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179 | |
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180 | |
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181 | def set_to_inscribed_circle(self,safety_factor = 1): |
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182 | #FIXME phase out eventually |
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183 | N = self.number_of_elements |
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184 | V = self.vertex_coordinates |
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185 | |
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186 | #initialising min and max ratio |
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187 | i=0 |
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188 | old_rad = self.radii[i] |
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189 | x0 = V[i, 0]; y0 = V[i, 1] |
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190 | x1 = V[i, 2]; y1 = V[i, 3] |
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191 | x2 = V[i, 4]; y2 = V[i, 5] |
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192 | a = sqrt((x0-x1)**2+(y0-y1)**2) |
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193 | b = sqrt((x1-x2)**2+(y1-y2)**2) |
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194 | c = sqrt((x2-x0)**2+(y2-y0)**2) |
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195 | ratio = old_rad/self.radii[i] |
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196 | max_ratio = ratio |
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197 | min_ratio = ratio |
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198 | |
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199 | for i in range(N): |
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200 | old_rad = self.radii[i] |
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201 | x0 = V[i, 0]; y0 = V[i, 1] |
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202 | x1 = V[i, 2]; y1 = V[i, 3] |
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203 | x2 = V[i, 4]; y2 = V[i, 5] |
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204 | a = sqrt((x0-x1)**2+(y0-y1)**2) |
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205 | b = sqrt((x1-x2)**2+(y1-y2)**2) |
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206 | c = sqrt((x2-x0)**2+(y2-y0)**2) |
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207 | self.radii[i]=self.areas[i]/(2*(a+b+c))*safety_factor |
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208 | ratio = old_rad/self.radii[i] |
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209 | if ratio >= max_ratio: max_ratio = ratio |
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210 | if ratio <= min_ratio: min_ratio = ratio |
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211 | return max_ratio,min_ratio |
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212 | |
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213 | def build_neighbour_structure(self): |
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214 | """Update all registered triangles to point to their neighbours. |
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215 | |
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216 | Also, keep a tally of the number of boundaries for each triangle |
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217 | |
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218 | Postconditions: |
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219 | neighbours and neighbour_edges is populated |
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220 | number_of_boundaries integer array is defined. |
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221 | """ |
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222 | |
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223 | #Step 1: |
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224 | #Build dictionary mapping from segments (2-tuple of points) |
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225 | #to left hand side edge (facing neighbouring triangle) |
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226 | |
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227 | N = self.number_of_elements |
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228 | neighbourdict = {} |
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229 | for i in range(N): |
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230 | |
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231 | #Register all segments as keys mapping to current triangle |
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232 | #and segment id |
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233 | a = self.triangles[i, 0] |
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234 | b = self.triangles[i, 1] |
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235 | c = self.triangles[i, 2] |
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236 | if neighbourdict.has_key((a,b)): |
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237 | msg = "Edge 2 of triangle %d is duplicating edge %d of triangle %d.\n" %(i,neighbourdict[a,b][1],neighbourdict[a,b][0]) |
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238 | raise Exception, msg |
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239 | if neighbourdict.has_key((b,c)): |
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240 | msg = "Edge 0 of triangle %d is duplicating edge %d of triangle %d.\n" %(i,neighbourdict[b,c][1],neighbourdict[b,c][0]) |
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241 | raise msg |
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242 | if neighbourdict.has_key((c,a)): |
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243 | msg = "Edge 1 of triangle %d is duplicating edge %d of triangle %d.\n" %(i,neighbourdict[c,a][1],neighbourdict[c,a][0]) |
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244 | raise msg |
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245 | |
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246 | neighbourdict[a,b] = (i, 2) #(id, edge) |
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247 | neighbourdict[b,c] = (i, 0) #(id, edge) |
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248 | neighbourdict[c,a] = (i, 1) #(id, edge) |
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249 | |
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250 | |
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251 | #Step 2: |
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252 | #Go through triangles again, but this time |
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253 | #reverse direction of segments and lookup neighbours. |
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254 | for i in range(N): |
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255 | a = self.triangles[i, 0] |
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256 | b = self.triangles[i, 1] |
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257 | c = self.triangles[i, 2] |
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258 | |
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259 | self.number_of_boundaries[i] = 3 |
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260 | if neighbourdict.has_key((b,a)): |
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261 | self.neighbours[i, 2] = neighbourdict[b,a][0] |
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262 | self.neighbour_edges[i, 2] = neighbourdict[b,a][1] |
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263 | self.number_of_boundaries[i] -= 1 |
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264 | |
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265 | if neighbourdict.has_key((c,b)): |
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266 | self.neighbours[i, 0] = neighbourdict[c,b][0] |
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267 | self.neighbour_edges[i, 0] = neighbourdict[c,b][1] |
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268 | self.number_of_boundaries[i] -= 1 |
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269 | |
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270 | if neighbourdict.has_key((a,c)): |
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271 | self.neighbours[i, 1] = neighbourdict[a,c][0] |
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272 | self.neighbour_edges[i, 1] = neighbourdict[a,c][1] |
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273 | self.number_of_boundaries[i] -= 1 |
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274 | |
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275 | |
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276 | def build_surrogate_neighbour_structure(self): |
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277 | """Build structure where each triangle edge points to its neighbours |
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278 | if they exist. Otherwise point to the triangle itself. |
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279 | |
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280 | The surrogate neighbour structure is useful for computing gradients |
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281 | based on centroid values of neighbours. |
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282 | |
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283 | Precondition: Neighbour structure is defined |
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284 | Postcondition: |
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285 | Surrogate neighbour structure is defined: |
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286 | surrogate_neighbours: i0, i1, i2 where all i_k >= 0 point to |
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287 | triangles. |
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288 | |
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289 | """ |
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290 | |
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291 | N = self.number_of_elements |
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292 | for i in range(N): |
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293 | #Find all neighbouring volumes that are not boundaries |
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294 | for k in range(3): |
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295 | if self.neighbours[i, k] < 0: |
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296 | self.surrogate_neighbours[i, k] = i #Point this triangle |
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297 | else: |
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298 | self.surrogate_neighbours[i, k] = self.neighbours[i, k] |
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299 | |
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300 | |
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301 | |
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302 | def build_boundary_dictionary(self, boundary = None): |
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303 | """Build or check the dictionary of boundary tags. |
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304 | self.boundary is a dictionary of tags, |
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305 | keyed by volume id and edge: |
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306 | { (id, edge): tag, ... } |
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307 | |
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308 | Postconditions: |
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309 | self.boundary is defined. |
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310 | """ |
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311 | |
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312 | from anuga.config import default_boundary_tag |
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313 | |
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314 | if boundary is None: |
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315 | boundary = {} |
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316 | for vol_id in range(self.number_of_elements): |
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317 | for edge_id in range(0, 3): |
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318 | if self.neighbours[vol_id, edge_id] < 0: |
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319 | boundary[(vol_id, edge_id)] = default_boundary_tag |
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320 | else: |
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321 | #Check that all keys in given boundary exist |
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322 | for vol_id, edge_id in boundary.keys(): |
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323 | msg = 'Segment (%d, %d) does not exist' %(vol_id, edge_id) |
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324 | a, b = self.neighbours.shape |
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325 | assert vol_id < a and edge_id < b, msg |
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326 | |
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327 | #FIXME: This assert violates internal boundaries (delete it) |
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328 | #msg = 'Segment (%d, %d) is not a boundary' %(vol_id, edge_id) |
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329 | #assert self.neighbours[vol_id, edge_id] < 0, msg |
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330 | |
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331 | #Check that all boundary segments are assigned a tag |
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332 | for vol_id in range(self.number_of_elements): |
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333 | for edge_id in range(0, 3): |
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334 | if self.neighbours[vol_id, edge_id] < 0: |
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335 | if not boundary.has_key( (vol_id, edge_id) ): |
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336 | msg = 'WARNING: Given boundary does not contain ' |
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337 | msg += 'tags for edge (%d, %d). '\ |
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338 | %(vol_id, edge_id) |
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339 | msg += 'Assigning default tag (%s).'\ |
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340 | %default_boundary_tag |
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341 | |
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342 | #FIXME: Print only as per verbosity |
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343 | #print msg |
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344 | |
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345 | #FIXME: Make this situation an error in the future |
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346 | #and make another function which will |
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347 | #enable default boundary-tags where |
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348 | #tags a not specified |
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349 | boundary[ (vol_id, edge_id) ] =\ |
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350 | default_boundary_tag |
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351 | |
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352 | |
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353 | |
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354 | self.boundary = boundary |
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355 | |
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356 | |
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357 | def build_tagged_elements_dictionary(self, tagged_elements = None): |
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358 | """Build the dictionary of element tags. |
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359 | self.tagged_elements is a dictionary of element arrays, |
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360 | keyed by tag: |
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361 | { (tag): [e1, e2, e3..] } |
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362 | |
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363 | Postconditions: |
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364 | self.element_tag is defined |
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365 | """ |
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366 | from Numeric import array, Int |
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367 | |
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368 | if tagged_elements is None: |
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369 | tagged_elements = {} |
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370 | else: |
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371 | #Check that all keys in given boundary exist |
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372 | for tag in tagged_elements.keys(): |
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373 | tagged_elements[tag] = array(tagged_elements[tag]).astype(Int) |
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374 | |
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375 | msg = 'Not all elements exist. ' |
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376 | assert max(tagged_elements[tag]) < self.number_of_elements, msg |
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377 | #print "tagged_elements", tagged_elements |
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378 | self.tagged_elements = tagged_elements |
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379 | |
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380 | def build_boundary_structure(self): |
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381 | """Traverse boundary and |
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382 | enumerate neighbour indices from -1 and |
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383 | counting down. |
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384 | |
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385 | Precondition: |
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386 | self.boundary is defined. |
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387 | Post condition: |
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388 | neighbour array has unique negative indices for boundary |
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389 | boundary_segments array imposes an ordering on segments |
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390 | (not otherwise available from the dictionary) |
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391 | |
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392 | Note: If a segment is listed in the boundary dictionary |
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393 | it *will* become a boundary - even if there is a neighbouring triangle. |
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394 | This would be the case for internal boundaries |
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395 | """ |
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396 | |
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397 | #FIXME: Now Obsolete - maybe use some comments from here in |
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398 | #domain.set_boundary |
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399 | |
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400 | if self.boundary is None: |
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401 | msg = 'Boundary dictionary must be defined before ' |
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402 | msg += 'building boundary structure' |
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403 | raise msg |
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404 | |
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405 | |
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406 | self.boundary_segments = self.boundary.keys() |
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407 | self.boundary_segments.sort() |
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408 | |
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409 | index = -1 |
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410 | for id, edge in self.boundary_segments: |
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411 | |
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412 | #FIXME: One would detect internal boundaries as follows |
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413 | #if self.neighbours[id, edge] > -1: |
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414 | # print 'Internal boundary' |
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415 | |
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416 | self.neighbours[id, edge] = index |
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417 | index -= 1 |
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418 | |
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419 | |
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420 | def get_boundary_tags(self): |
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421 | """Return list of available boundary tags |
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422 | """ |
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423 | |
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424 | tags = {} |
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425 | for v in self.boundary.values(): |
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426 | tags[v] = 1 |
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427 | |
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428 | return tags.keys() |
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429 | |
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430 | |
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431 | def get_boundary_polygon(self, verbose=False): |
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432 | """Return bounding polygon for mesh (counter clockwise) |
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433 | |
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434 | Using the mesh boundary, derive a bounding polygon for this mesh. |
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435 | If multiple vertex values are present, the algorithm will select the |
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436 | path that contains the mesh. |
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437 | |
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438 | All points are in absolute UTM coordinates |
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439 | """ |
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440 | |
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441 | from Numeric import allclose, sqrt, array, minimum, maximum |
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442 | from anuga.utilities.numerical_tools import angle, ensure_numeric |
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443 | |
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444 | |
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445 | # Get mesh extent |
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446 | xmin, xmax, ymin, ymax = self.get_extent(absolute=True) |
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447 | pmin = ensure_numeric([xmin, ymin]) |
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448 | pmax = ensure_numeric([xmax, ymax]) |
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449 | |
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450 | |
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451 | # Assemble dictionary of boundary segments and choose starting point |
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452 | segments = {} |
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453 | inverse_segments = {} |
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454 | p0 = None |
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455 | mindist = sqrt(sum((pmax-pmin)**2)) #Start value across entire mesh |
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456 | for i, edge_id in self.boundary.keys(): |
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457 | # Find vertex ids for boundary segment |
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458 | if edge_id == 0: a = 1; b = 2 |
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459 | if edge_id == 1: a = 2; b = 0 |
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460 | if edge_id == 2: a = 0; b = 1 |
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461 | |
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462 | A = self.get_vertex_coordinate(i, a, absolute=True) # Start |
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463 | B = self.get_vertex_coordinate(i, b, absolute=True) # End |
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464 | |
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465 | |
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466 | # Take the point closest to pmin as starting point |
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467 | # Note: Could be arbitrary, but nice to have |
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468 | # a unique way of selecting |
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469 | dist_A = sqrt(sum((A-pmin)**2)) |
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470 | dist_B = sqrt(sum((B-pmin)**2)) |
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471 | |
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472 | #Find lower leftmost point |
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473 | if dist_A < mindist: |
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474 | mindist = dist_A |
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475 | p0 = A |
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476 | if dist_B < mindist: |
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477 | mindist = dist_B |
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478 | p0 = B |
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479 | |
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480 | |
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481 | # Sanity check |
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482 | if p0 is None: |
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483 | raise Exception('Impossible') |
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484 | |
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485 | |
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486 | # Register potential paths from A to B |
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487 | if not segments.has_key(tuple(A)): |
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488 | segments[tuple(A)] = [] # Empty list for candidate points |
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489 | |
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490 | segments[tuple(A)].append(B) |
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491 | |
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492 | |
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493 | |
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494 | |
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495 | #Start with smallest point and follow boundary (counter clock wise) |
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496 | polygon = [p0] # Storage for final boundary polygon |
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497 | point_registry = {} # Keep track of storage to avoid multiple runs around |
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498 | # boundary. This will only be the case if there are |
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499 | # more than one candidate. |
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500 | # FIXME (Ole): Perhaps we can do away with polygon |
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501 | # and use only point_registry to save space. |
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502 | |
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503 | point_registry[tuple(p0)] = 0 |
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504 | |
---|
505 | #while len(polygon) < len(self.boundary): |
---|
506 | while len(point_registry) < len(self.boundary): |
---|
507 | |
---|
508 | candidate_list = segments[tuple(p0)] |
---|
509 | if len(candidate_list) > 1: |
---|
510 | # Multiple points detected |
---|
511 | # Take the candidate that is furthest to the clockwise direction, |
---|
512 | # as that will follow the boundary. |
---|
513 | |
---|
514 | |
---|
515 | if verbose: |
---|
516 | print 'Point %s has multiple candidates: %s'\ |
---|
517 | %(str(p0), candidate_list) |
---|
518 | |
---|
519 | |
---|
520 | # Choose vector against which all angles will be measured |
---|
521 | if len(polygon) > 1: |
---|
522 | v_prev = p0 - polygon[-2] # Vector that leads to p0 |
---|
523 | else: |
---|
524 | # FIXME (Ole): What do we do if the first point has multiple |
---|
525 | # candidates? |
---|
526 | # Being the lower left corner, perhaps we can use the |
---|
527 | # vector [1, 0], but I really don't know if this is completely |
---|
528 | # watertight. |
---|
529 | # Another option might be v_prev = [1.0, 0.0] |
---|
530 | v_prev = [1.0, 0.0] |
---|
531 | |
---|
532 | |
---|
533 | |
---|
534 | # Choose candidate with minimum angle |
---|
535 | minimum_angle = 2*pi |
---|
536 | for pc in candidate_list: |
---|
537 | vc = pc-p0 # Candidate vector |
---|
538 | |
---|
539 | # Angle between each candidate and the previous vector |
---|
540 | # in [-pi, pi] |
---|
541 | ac = angle(vc, v_prev) |
---|
542 | if ac > pi: ac = pi-ac |
---|
543 | |
---|
544 | # take the minimal angle corresponding to the rightmost vector |
---|
545 | if ac < minimum_angle: |
---|
546 | minimum_angle = ac |
---|
547 | p1 = pc # Best candidate |
---|
548 | |
---|
549 | |
---|
550 | if verbose is True: |
---|
551 | print ' Best candidate %s, angle %f' %(p1, minimum_angle*180/pi) |
---|
552 | |
---|
553 | else: |
---|
554 | p1 = candidate_list[0] |
---|
555 | |
---|
556 | if point_registry.has_key(tuple(p1)): |
---|
557 | # We have completed the boundary polygon - yeehaa |
---|
558 | break |
---|
559 | else: |
---|
560 | point_registry[tuple(p1)] = len(point_registry) |
---|
561 | |
---|
562 | polygon.append(p1) |
---|
563 | p0 = p1 |
---|
564 | |
---|
565 | |
---|
566 | return polygon |
---|
567 | |
---|
568 | |
---|
569 | def check_integrity(self): |
---|
570 | """Check that triangles are internally consistent e.g. |
---|
571 | that area corresponds to edgelengths, that vertices |
---|
572 | are arranged in a counter-clockwise order, etc etc |
---|
573 | Neighbour structure will be checked by class Mesh |
---|
574 | """ |
---|
575 | |
---|
576 | from anuga.config import epsilon |
---|
577 | from anuga.utilities.numerical_tools import anglediff |
---|
578 | |
---|
579 | N = self.number_of_elements |
---|
580 | #Get x,y coordinates for all vertices for all triangles |
---|
581 | V = self.get_vertex_coordinates() |
---|
582 | #Check each triangle |
---|
583 | for i in range(N): |
---|
584 | |
---|
585 | x0 = V[i, 0]; y0 = V[i, 1] |
---|
586 | x1 = V[i, 2]; y1 = V[i, 3] |
---|
587 | x2 = V[i, 4]; y2 = V[i, 5] |
---|
588 | |
---|
589 | #Check that area hasn't been compromised |
---|
590 | area = self.areas[i] |
---|
591 | ref = abs((x1*y0-x0*y1)+(x2*y1-x1*y2)+(x0*y2-x2*y0))/2 |
---|
592 | msg = 'Wrong area for vertex coordinates: %f %f %f %f %f %f'\ |
---|
593 | %(x0,y0,x1,y1,x2,y2) |
---|
594 | assert abs((area - ref)/area) < epsilon, msg |
---|
595 | |
---|
596 | #Check that points are arranged in counter clock-wise order |
---|
597 | v0 = [x1-x0, y1-y0] |
---|
598 | v1 = [x2-x1, y2-y1] |
---|
599 | v2 = [x0-x2, y0-y2] |
---|
600 | |
---|
601 | a0 = anglediff(v1, v0) |
---|
602 | a1 = anglediff(v2, v1) |
---|
603 | a2 = anglediff(v0, v2) |
---|
604 | |
---|
605 | msg = '''Vertices (%s,%s), (%s,%s), (%s,%s) are not arranged |
---|
606 | in counter clockwise order''' %(x0, y0, x1, y1, x2, y2) |
---|
607 | assert a0 < pi and a1 < pi and a2 < pi, msg |
---|
608 | |
---|
609 | #Check that normals are orthogonal to edge vectors |
---|
610 | #Note that normal[k] lies opposite vertex k |
---|
611 | |
---|
612 | normal0 = self.normals[i, 0:2] |
---|
613 | normal1 = self.normals[i, 2:4] |
---|
614 | normal2 = self.normals[i, 4:6] |
---|
615 | |
---|
616 | for u, v in [ (v0, normal2), (v1, normal0), (v2, normal1) ]: |
---|
617 | |
---|
618 | #Normalise |
---|
619 | l_u = sqrt(u[0]*u[0] + u[1]*u[1]) |
---|
620 | l_v = sqrt(v[0]*v[0] + v[1]*v[1]) |
---|
621 | |
---|
622 | x = (u[0]*v[0] + u[1]*v[1])/l_u/l_v #Inner product |
---|
623 | |
---|
624 | msg = 'Normal vector (%f,%f) is not perpendicular to' %tuple(v) |
---|
625 | msg += ' edge (%f,%f) in triangle %d.' %(tuple(u) + (i,)) |
---|
626 | msg += ' Inner product is %e.' %x |
---|
627 | assert x < epsilon, msg |
---|
628 | |
---|
629 | self.lone_vertices = [] |
---|
630 | #Check that all vertices have been registered |
---|
631 | for v_id, v in enumerate(self.vertexlist): |
---|
632 | |
---|
633 | #msg = 'Vertex %s does not belong to an element.' |
---|
634 | #assert v is not None, msg |
---|
635 | if v is None: |
---|
636 | #print msg%v_id |
---|
637 | self.lone_vertices.append(v_id) |
---|
638 | |
---|
639 | #Check integrity of neighbour structure |
---|
640 | for i in range(N): |
---|
641 | # print i |
---|
642 | for v in self.triangles[i, :]: |
---|
643 | #Check that all vertices have been registered |
---|
644 | assert self.vertexlist[v] is not None |
---|
645 | |
---|
646 | #Check that this triangle is listed with at least one vertex |
---|
647 | assert (i, 0) in self.vertexlist[v] or\ |
---|
648 | (i, 1) in self.vertexlist[v] or\ |
---|
649 | (i, 2) in self.vertexlist[v] |
---|
650 | |
---|
651 | |
---|
652 | |
---|
653 | #Check neighbour structure |
---|
654 | for k, neighbour_id in enumerate(self.neighbours[i,:]): |
---|
655 | |
---|
656 | #Assert that my neighbour's neighbour is me |
---|
657 | #Boundaries need not fulfill this |
---|
658 | if neighbour_id >= 0: |
---|
659 | edge = self.neighbour_edges[i, k] |
---|
660 | msg = 'Triangle %d has neighbour %d but it does not point back. \n' %(i,neighbour_id) |
---|
661 | msg += 'Only points to (%s)' %(self.neighbours[neighbour_id,:]) |
---|
662 | assert self.neighbours[neighbour_id, edge] == i ,msg |
---|
663 | |
---|
664 | |
---|
665 | |
---|
666 | #Check that all boundaries have |
---|
667 | # unique, consecutive, negative indices |
---|
668 | |
---|
669 | #L = len(self.boundary) |
---|
670 | #for i in range(L): |
---|
671 | # id, edge = self.boundary_segments[i] |
---|
672 | # assert self.neighbours[id, edge] == -i-1 |
---|
673 | |
---|
674 | |
---|
675 | #NOTE: This assert doesn't hold true if there are internal boundaries |
---|
676 | #FIXME: Look into this further. |
---|
677 | #FIXME (Ole): In pyvolution mark 3 this is OK again |
---|
678 | #NOTE: No longer works because neighbour structure is modified by |
---|
679 | # domain set_boundary. |
---|
680 | #for id, edge in self.boundary: |
---|
681 | # assert self.neighbours[id,edge] < 0 |
---|
682 | # |
---|
683 | #NOTE (Ole): I reckon this was resolved late 2004? |
---|
684 | # |
---|
685 | #See domain.set_boundary |
---|
686 | |
---|
687 | def get_lone_vertices(self): |
---|
688 | """Return a list of vertices that are not connected to any triangles. |
---|
689 | |
---|
690 | Precondition |
---|
691 | FIXME(DSG - DSG) Pull the code out of check integrity that builds this |
---|
692 | structure. |
---|
693 | check_integrity has to have been called. |
---|
694 | """ |
---|
695 | return self.lone_vertices |
---|
696 | |
---|
697 | def get_centroid_coordinates(self): |
---|
698 | """Return all centroid coordinates. |
---|
699 | Return all centroid coordinates for all triangles as an Nx2 array |
---|
700 | (ordered as x0, y0 for each triangle) |
---|
701 | """ |
---|
702 | return self.centroid_coordinates |
---|
703 | |
---|
704 | |
---|
705 | |
---|
706 | |
---|
707 | def statistics(self): |
---|
708 | """Output statistics about mesh |
---|
709 | """ |
---|
710 | |
---|
711 | from Numeric import arange |
---|
712 | from anuga.utilities.numerical_tools import histogram, create_bins |
---|
713 | |
---|
714 | vertex_coordinates = self.vertex_coordinates # Relative coordinates |
---|
715 | areas = self.areas |
---|
716 | x = vertex_coordinates[:,0] |
---|
717 | y = vertex_coordinates[:,1] |
---|
718 | |
---|
719 | |
---|
720 | #Setup 10 bins for area histogram |
---|
721 | bins = create_bins(areas, 10) |
---|
722 | #m = max(areas) |
---|
723 | #bins = arange(0., m, m/10) |
---|
724 | hist = histogram(areas, bins) |
---|
725 | |
---|
726 | str = '------------------------------------------------\n' |
---|
727 | str += 'Mesh statistics:\n' |
---|
728 | str += ' Number of triangles = %d\n' %self.number_of_elements |
---|
729 | str += ' Extent:\n' |
---|
730 | str += ' x in [%f, %f]\n' %(min(x), max(x)) |
---|
731 | str += ' y in [%f, %f]\n' %(min(y), max(y)) |
---|
732 | str += ' Areas:\n' |
---|
733 | str += ' A in [%f, %f]\n' %(min(areas), max(areas)) |
---|
734 | str += ' number of distinct areas: %d\n' %(len(areas)) |
---|
735 | str += ' Histogram:\n' |
---|
736 | |
---|
737 | hi = bins[0] |
---|
738 | for i, count in enumerate(hist): |
---|
739 | lo = hi |
---|
740 | if i+1 < len(bins): |
---|
741 | #Open upper interval |
---|
742 | hi = bins[i+1] |
---|
743 | str += ' [%f, %f[: %d\n' %(lo, hi, count) |
---|
744 | else: |
---|
745 | #Closed upper interval |
---|
746 | hi = max(areas) |
---|
747 | str += ' [%f, %f]: %d\n' %(lo, hi, count) |
---|
748 | |
---|
749 | N = len(areas) |
---|
750 | if N > 10: |
---|
751 | str += ' Percentiles (10%):\n' |
---|
752 | areas = areas.tolist() |
---|
753 | areas.sort() |
---|
754 | |
---|
755 | k = 0 |
---|
756 | lower = min(areas) |
---|
757 | for i, a in enumerate(areas): |
---|
758 | if i % (N/10) == 0 and i != 0: #For every 10% of the sorted areas |
---|
759 | str += ' %d triangles in [%f, %f]\n' %(i-k, lower, a) |
---|
760 | lower = a |
---|
761 | k = i |
---|
762 | |
---|
763 | str += ' %d triangles in [%f, %f]\n'\ |
---|
764 | %(N-k, lower, max(areas)) |
---|
765 | |
---|
766 | |
---|
767 | str += 'Boundary:\n' |
---|
768 | str += ' Number of boundary segments == %d\n' %(len(self.boundary)) |
---|
769 | str += ' Boundary tags == %s\n' %self.get_boundary_tags() |
---|
770 | str += '------------------------------------------------\n' |
---|
771 | |
---|
772 | |
---|
773 | return str |
---|
774 | |
---|