| 1 | """Alpha shape |
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| 2 | """ |
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| 3 | |
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| 4 | import exceptions |
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| 5 | from Numeric import array, Float, divide_safe, sqrt |
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| 6 | from load_mesh.loadASCII import load_xya_file, export_boundary_file |
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| 7 | |
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| 8 | class PointError(exceptions.Exception): pass |
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| 9 | |
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| 10 | OUTPUT_FILE_TITLE = "# The alpha shape boundary defined by point index pairs of edges" |
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| 11 | INF = pow(10,9) |
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| 12 | |
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| 13 | def alpha_shape_via_files(point_file, boundary_file, alpha= None): |
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| 14 | |
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| 15 | from load_mesh.loadASCII import load_xya_file |
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| 16 | |
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| 17 | point_dict = load_xya_file(point_file) |
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| 18 | points = point_dict['pointlist'] |
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| 19 | #title_string = point_dict['title'] |
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| 20 | |
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| 21 | alpha = Alpha_Shape(points) |
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| 22 | alpha.write_boundary(boundary_file) |
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| 23 | |
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| 24 | class Alpha_Shape: |
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| 25 | |
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| 26 | def __init__(self, points, alpha = None): |
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| 27 | |
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| 28 | """ |
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| 29 | Inputs: |
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| 30 | |
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| 31 | points: List of coordinate pairs [[x1, y1],[x2, y2]..] |
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| 32 | |
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| 33 | alpha: alpha shape parameter |
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| 34 | |
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| 35 | """ |
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| 36 | self._set_points(points) |
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| 37 | self._alpha_shape_algorithm(alpha) |
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| 38 | |
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| 39 | |
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| 40 | def _set_points(self, points): |
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| 41 | """ |
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| 42 | """ |
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| 43 | # print "setting points" |
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| 44 | if len (points) <= 2: |
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| 45 | raise PointError, "Too few points to find an alpha shape" |
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| 46 | |
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| 47 | #Convert input to Numeric arrays |
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| 48 | self.points = array(points).astype(Float) |
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| 49 | |
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| 50 | |
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| 51 | def write_boundary(self,file_name): |
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| 52 | """ |
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| 53 | Write the boundary to a file |
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| 54 | """ |
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| 55 | #print " this info will be in the file" |
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| 56 | export_boundary_file(file_name, self.get_boundary(), |
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| 57 | OUTPUT_FILE_TITLE, delimiter = ',') |
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| 58 | |
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| 59 | def get_boundary(self): |
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| 60 | """ |
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| 61 | """ |
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| 62 | #print "getting boundary" |
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| 63 | return self.boundary |
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| 64 | |
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| 65 | def get_delaunay(self): |
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| 66 | """ |
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| 67 | """ |
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| 68 | return self.deltri |
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| 69 | |
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| 70 | |
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| 71 | def _alpha_shape_algorithm(self,alpha): |
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| 72 | |
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| 73 | # A python style guide suggests using _[function name] to |
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| 74 | # specify internal functions |
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| 75 | # - this is the first time I've used it though - DSG |
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| 76 | |
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| 77 | #print "starting alpha shape algorithm" |
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| 78 | |
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| 79 | # Build Delaunay triangulation |
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| 80 | import triang |
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| 81 | points = [] |
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| 82 | seglist = [] |
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| 83 | holelist = [] |
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| 84 | regionlist = [] |
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| 85 | pointattlist = [] |
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| 86 | segattlist = [] |
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| 87 | trilist = [] |
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| 88 | |
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| 89 | points = [(pt[0], pt[1]) for pt in self.points] |
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| 90 | pointattlist = [ [] for i in range(len(points)) ] |
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| 91 | mode = "Qzcn" |
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| 92 | print "computing delaunay triangulation ... \n" |
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| 93 | tridata = triang.genMesh(points,seglist,holelist,regionlist,pointattlist,segattlist,trilist,mode) |
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| 94 | #print tridata |
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| 95 | #print "point attribute list: ", tridata['generatedpointattributelist'],"\n" |
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| 96 | #print "hull segments: ", tridata['generatedsegmentlist'], "\n" |
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| 97 | self.deltri = tridata['generatedtrianglelist'] |
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| 98 | self.deltrinbr = tridata['generatedtriangleneighborlist'] |
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| 99 | self.hulledges = tridata['generatedsegmentlist'] |
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| 100 | |
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| 101 | print "Number of delaunay triangles: ", len(self.deltri), "\n" |
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| 102 | #print "deltrinbrs: ", self.deltrinbr, "\n" |
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| 103 | |
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| 104 | # Build Alpha table |
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| 105 | print "Building alpha table ... \n" |
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| 106 | self._tri_circumradius() |
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| 107 | print "Largest circumradius ", max(self.triradius) |
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| 108 | self._edge_intervals() |
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| 109 | self._vertex_intervals() |
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| 110 | |
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| 111 | if alpha==None: |
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| 112 | # Find optimum alpha |
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| 113 | # Ken Clarkson's hull program uses smallest alpha so that |
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| 114 | # every vertex is non-singular so... |
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| 115 | self.optimum_alpha = max([ interval[0] for interval in self.vertexinterval]) |
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| 116 | print "optimum alpha ", self.optimum_alpha |
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| 117 | |
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| 118 | #alpha_tri = self.get_alpha_triangles(self.optimum_alpha) |
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| 119 | #print "alpha shape triangles ", alpha_tri |
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| 120 | |
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| 121 | reg_edge = self.get_regular_edges(self.optimum_alpha) |
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| 122 | #print "alpha boundary edges", reg_edge |
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| 123 | else: |
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| 124 | reg_edge = self.get_regular_edges(alpha) |
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| 125 | |
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| 126 | self.boundary = [self.edge[k] for k in reg_edge] |
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| 127 | #print "alpha boundary edges ", self.boundary |
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| 128 | |
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| 129 | # this produces a baaad boundary |
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| 130 | #boundary = [] |
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| 131 | #for point_index in range(len(self.points)-1): |
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| 132 | # boundary.append([point_index,point_index +1]) |
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| 133 | #boundary.append([len(self.points)-1,0]) |
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| 134 | #self.boundary = boundary |
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| 135 | return |
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| 136 | |
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| 137 | def _tri_circumradius(self): |
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| 138 | |
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| 139 | # compute circumradii of the delaunay triangles |
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| 140 | x = self.points[:,0] |
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| 141 | y = self.points[:,1] |
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| 142 | ind1 = [self.deltri[j][0] for j in range(len(self.deltri))] |
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| 143 | ind2 = [self.deltri[j][1] for j in range(len(self.deltri))] |
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| 144 | ind3 = [self.deltri[j][2] for j in range(len(self.deltri))] |
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| 145 | |
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| 146 | x1 = array([ x[j] for j in ind1 ]) |
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| 147 | y1 = array([ y[j] for j in ind1 ]) |
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| 148 | x2 = array([ x[j] for j in ind2 ]) |
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| 149 | y2 = array([ y[j] for j in ind2 ]) |
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| 150 | x3 = array([ x[j] for j in ind3 ]) |
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| 151 | y3 = array([ y[j] for j in ind3 ]) |
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| 152 | |
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| 153 | x21 = x2-x1 |
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| 154 | x31 = x3-x1 |
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| 155 | y21 = y2-y1 |
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| 156 | y31 = y3-y1 |
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| 157 | |
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| 158 | dist21 = x21*x21 + y21*y21 |
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| 159 | dist31 = x31*x31 + y31*y31 |
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| 160 | |
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| 161 | denom = x21*y31 - x31*y21 |
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| 162 | #print "denom = ", denom |
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| 163 | |
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| 164 | # dx/2, dy/2 give circumcenter relative to x1,y1. |
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| 165 | #dx = (y31*dist21 - y21*dist31)/denom |
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| 166 | #dy = (x21*dist31 - x31*dist21)/denom |
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| 167 | # from Numeric import divide_safe |
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| 168 | try: |
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| 169 | dx = divide_safe(y31*dist21 - y21*dist31,denom) |
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| 170 | dy = divide_safe(x21*dist31 - x31*dist21,denom) |
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| 171 | except ZeroDivisionError: |
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| 172 | print "Found some degenerate triangles." |
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| 173 | raise |
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| 174 | # really need to take care of cases when denom = 0. |
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| 175 | # eg: something like: |
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| 176 | # print "Handling degenerate triangles." |
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| 177 | # ... add some random displacments to trouble points? |
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| 178 | |
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| 179 | self.triradius = 0.5*sqrt(dx*dx + dy*dy) |
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| 180 | #print "triangle radii", self.triradius |
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| 181 | return |
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| 182 | |
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| 183 | def _edge_intervals(self): |
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| 184 | # for each edge, find triples |
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| 185 | # (length/2, min_adj_triradius, max_adj_triradius) if unattached |
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| 186 | # (min_adj_triradius, min_adj_triradius, max_adj_triradius) if attached. |
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| 187 | |
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| 188 | # It should be possible to rewrite this routine in an array-friendly form |
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| 189 | # like _tri_circumradius() if we need to speed things up. |
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| 190 | |
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| 191 | edges = [] |
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| 192 | edgenbrs = [] |
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| 193 | edgeinterval = [] |
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| 194 | for t in range(len(self.deltri)): |
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| 195 | tri = self.deltri[t] |
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| 196 | trinbr = self.deltrinbr[t] |
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| 197 | dx = array([self.points[tri[(i+1)%3],0] - self.points[tri[(i+2)%3],0] for i in [0,1,2]]) |
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| 198 | dy = array([self.points[tri[(i+1)%3],1] - self.points[tri[(i+2)%3],1] for i in [0,1,2]]) |
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| 199 | elen = sqrt(dx*dx+dy*dy) |
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| 200 | #angle = array([(-dx[(i+1)%3]*dx[(i+2)%3]-dy[(i+1)%3]*dy[(i+2)%3])/(elen[(i+1)%3]*elen[(i+2)%3]) for i in [0,1,2]]) |
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| 201 | #angle = arccos(angle) |
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| 202 | # really only need sign - not angle value: |
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| 203 | anglesign = array([(-dx[(i+1)%3]*dx[(i+2)%3]-dy[(i+1)%3]*dy[(i+2)%3]) for i in [0,1,2]]) |
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| 204 | |
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| 205 | #print "dx ",dx,"\n" |
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| 206 | #print "dy ",dy,"\n" |
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| 207 | #print "edge lengths of triangle ",t,"\t",elen,"\n" |
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| 208 | #print "angles ",angle,"\n" |
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| 209 | |
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| 210 | for i in [0,1,2]: |
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| 211 | j = (i+1)%3 |
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| 212 | k = (i+2)%3 |
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| 213 | if trinbr[i]==-1: |
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| 214 | edges.append((tri[j], tri[k])) |
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| 215 | edgenbrs.append((t, -1)) |
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| 216 | edgeinterval.append([0.5*elen[i], self.triradius[t], INF]) |
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| 217 | elif (tri[j]<tri[k]): |
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| 218 | edges.append((tri[j], tri[k])) |
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| 219 | edgenbrs.append((t, trinbr[i])) |
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| 220 | edgeinterval.append([0.5*elen[i],\ |
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| 221 | min(self.triradius[t],self.triradius[trinbr[i]]),\ |
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| 222 | max(self.triradius[t],self.triradius[trinbr[i]]) ]) |
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| 223 | else: |
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| 224 | continue |
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| 225 | #if angle[i]>pi/2: |
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| 226 | if anglesign[i] < 0: |
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| 227 | edgeinterval[-1][0] = edgeinterval[-1][1] |
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| 228 | |
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| 229 | self.edge = edges |
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| 230 | self.edgenbr = edgenbrs |
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| 231 | self.edgeinterval = edgeinterval |
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| 232 | #print "edges: ",edges, "\n" |
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| 233 | #print "edge nbrs:", edgenbrs ,"\n" |
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| 234 | #print "edge intervals: ",edgeinterval , "\n" |
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| 235 | |
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| 236 | def _vertex_intervals(self): |
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| 237 | # for each vertex find pairs |
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| 238 | # (min_adj_triradius, max_adj_triradius) |
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| 239 | nv = len(self.points) |
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| 240 | vertexnbrs = [ [] for i in range(nv)] |
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| 241 | vertexinterval = [ [] for i in range(nv)] |
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| 242 | for t in range(len(self.deltri)): |
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| 243 | for j in self.deltri[t]: |
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| 244 | vertexnbrs[j].append(t) |
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| 245 | for h in range(len(self.hulledges)): |
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| 246 | for j in self.hulledges[h]: |
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| 247 | vertexnbrs[j].append(-1) |
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| 248 | |
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| 249 | for i in range(nv): |
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| 250 | radii = [ self.triradius[t] for t in vertexnbrs[i] if t>=0 ] |
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| 251 | try: |
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| 252 | vertexinterval[i] = [min(radii), max(radii)] |
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| 253 | if vertexnbrs[i][-1]==-1: |
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| 254 | vertexinterval[i][1]=INF |
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| 255 | except ValueError: |
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| 256 | print "Vertex %i is isolated?"%i |
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| 257 | print "coords: ",self.points[i] |
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| 258 | print "Vertex nbrs: ", vertexnbrs[i] |
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| 259 | print "nbr radii: ",radii |
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| 260 | vertexinterval[i] = [0,INF] |
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| 261 | pass |
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| 262 | |
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| 263 | self.vertexnbr = vertexnbrs |
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| 264 | self.vertexinterval = vertexinterval |
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| 265 | #print "vertex nbrs ", vertexnbrs, "\n" |
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| 266 | #print "vertex intervals ",vertexinterval, "\n" |
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| 267 | |
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| 268 | def get_alpha_triangles(self,alpha): |
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| 269 | """ |
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| 270 | Given an alpha value, |
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| 271 | return indices of triangles in the alpha-shape |
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| 272 | """ |
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| 273 | def tri_rad_lta(k): |
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| 274 | return self.triradius[k]<=alpha |
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| 275 | |
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| 276 | return filter(tri_rad_lta, range(len(self.triradius))) |
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| 277 | |
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| 278 | def get_regular_edges(self,alpha): |
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| 279 | """ |
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| 280 | Given and alpha value, |
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| 281 | return the edges on the boundary of the alpha-shape |
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| 282 | """ |
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| 283 | def reg_edge(k): |
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| 284 | return self.edgeinterval[k][1]<=alpha and self.edgeinterval[k][2]>alpha |
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| 285 | |
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| 286 | return filter(reg_edge, range(len(self.edgeinterval))) |
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| 287 | |
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| 288 | |
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| 289 | |
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| 290 | #------------------------------------------------------------- |
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| 291 | if __name__ == "__main__": |
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| 292 | """ |
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| 293 | Load in a data point file. |
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| 294 | Determine the alpha shape boundary |
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| 295 | Save the boundary to a file. |
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| 296 | |
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| 297 | usage: alpha_shape.py point_file.xya boundary_file.bnd [alpha] |
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| 298 | |
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| 299 | The alpha value is optional. |
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| 300 | """ |
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| 301 | |
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| 302 | import os, sys |
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| 303 | usage = "usage: %s point_file.xya boundary_file.bnd [alpha]"%os.path.basename(sys.argv[0]) |
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| 304 | # I made up the .bnd affix. Other ideas welcome. -DSG |
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| 305 | if len(sys.argv) < 3: |
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| 306 | print usage |
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| 307 | else: |
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| 308 | point_file = sys.argv[1] |
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| 309 | boundary_file = sys.argv[2] |
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| 310 | if len(sys.argv) > 4: |
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| 311 | alpha = sys.argv[3] |
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| 312 | else: |
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| 313 | alpha = None |
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| 314 | |
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| 315 | print "about to call alpha shape routine \n" |
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| 316 | alpha_shape_via_files(point_file, boundary_file, alpha) |
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| 317 | |
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