anuga 1.3.5__zip

Users/steve/Miniconda/envs/anuga/Lib/site-packages/anuga/alpha_shape/alpha_shape.py

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+"""Alpha shape
+Determine the shape of a set of points.
+
+From website by Kaspar Fischer:
+As mentionned in Edelsbrunner's and Muecke's paper, one can
+intuitively think of an alpha-shape as the following:
+
+Imagine a huge mass of ice-cream making up the space and containing
+the points S as ``hard'' chocolate pieces. Using one of these
+sphere-formed ice-cream spoons we carve out all parts of the ice-cream
+block we can reach without bumping into chocolate pieces, even
+carving out holes in the inside (eg. parts not reachable by simply
+moving the spoon from the outside). We will eventually end up with a
+(not necessarily convex) object bounded by caps, arcs and points. If
+we now straighten all ``round'' faces to triangles and line segments,
+we have an intuitive description of what is called the alpha-shape.
+
+Author: Vanessa Robins, ANU
+"""
+
+import exceptions
+import random
+
+from anuga.load_mesh.loadASCII import export_boundary_file
+from anuga.geospatial_data.geospatial_data import Geospatial_data
+
+import numpy as num
+
+
+class AlphaError(exceptions.Exception):pass
+class PointError(AlphaError): pass
+class FlagError(AlphaError): pass
+
+OUTPUT_FILE_TITLE = "# The alpha shape boundary defined by point index pairs of edges"
+INF = pow(10,9)
+EPSILON = 1.0e-12
+
+def alpha_shape_via_files(point_file, boundary_file, alpha= None):
+    """
+    Load a point file and return the alpha shape boundary as a boundary file.
+    
+    Inputs:
+    point_file: File location of the input file, points format (.csv or .pts)
+    boundary_file: File location of the generated output file
+    alpha: The alpha value can be optionally specified.  If it is not specified
+    the optimum alpha value will be used.
+    """
+    geospatial = Geospatial_data(point_file)
+    points = geospatial.get_data_points(absolute=False)
+    
+    AS = Alpha_Shape(points, alpha)
+    AS.write_boundary(boundary_file)
+    
+
+class Alpha_Shape:
+
+    def __init__(self, points, alpha = None):
+        """
+        An Alpha_Shape requires input of a set of points. Other class routines
+        return the alpha shape boundary.
+        
+        Inputs:       
+          points: List of coordinate pairs [[x1, y1],[x2, y2]..] 
+          alpha: The alpha value can be optionally specified.  If it is
+          not specified the optimum alpha value will be used.
+        """
+        self._set_points(points)
+        self._alpha_shape_algorithm(alpha)
+
+    def _set_points(self, points):
+        """
+        Create self.points array, do Error checking
+        Inputs:       
+          points: List of coordinate pairs [[x1, y1],[x2, y2]..] 
+        """
+        if len (points) <= 2:
+            raise PointError, "Too few points to find an alpha shape"
+        if len(points)==3:
+            #check not in a straight line
+            # FIXME check points 1,2,3 if straingt, check if points 2,3,4, ect
+            x01 = points[0][0] - points[1][0]
+            y01 = points[0][1] - points[1][1]
+            x12 = points[1][0] - points[2][0]
+            y12 = points[1][1] - points[2][1]
+            crossprod = x01*y12 - x12*y01
+            if crossprod==0:
+                raise PointError, "Three points on a straight line"
+        
+        #Convert input to numeric arrays
+        self.points = num.array(points, num.float)
+
+    
+    def write_boundary(self,file_name):
+        """
+        Write the boundary to a file
+        """
+        export_boundary_file(file_name, self.get_boundary(),
+                             OUTPUT_FILE_TITLE, delimiter = ',')
+    
+    def get_boundary(self):
+        """
+        Return a list of tuples.
+        Each tuple represents a segment in the boundary
+        by the index of its two end points.
+        The list of tuples represents the alpha shape boundary.
+        """
+        return self.boundary
+
+    def set_boundary_type(self,raw_boundary=True,
+                          remove_holes=False,
+                          smooth_indents=False,
+                          expand_pinch=False,
+                          boundary_points_fraction=0.2):
+        """
+        Use the flags to set constraints on the boundary:
+        raw_boundary    Return raw boundary i.e. the regular edges of the
+                        alpha shape. 
+        remove_holes    filter to remove small holes
+                        (small is defined by  boundary_points_fraction ) 
+        smooth_indents  remove sharp triangular indents in boundary
+        expand_pinch    test for pinch-off and correct 
+                           i.e. a boundary vertex with more than two edges.
+        """
+
+        if raw_boundary:
+            # reset alpha shape boundary 
+            reg_edge = self.get_regular_edges(self.alpha)
+            self.boundary = [self.edge[k] for k in reg_edge]
+            self._init_boundary_triangles()
+        if remove_holes:
+            #remove small holes
+            self.boundary = self._remove_holes(boundary_points_fraction)
+        if smooth_indents:
+            #remove sharp triangular indents
+            self.boundary = self._smooth_indents()
+        if expand_pinch:
+            #deal with pinch-off
+            self.boundary = self._expand_pinch()
+        
+
+    def get_delaunay(self):
+        """
+        """
+        return self.deltri
+
+    def get_optimum_alpha(self):
+        """
+        """
+        return self.optimum_alpha
+
+    def get_alpha(self):
+        """
+        Return current alpha value.
+        """
+        return self.alpha
+
+    def set_alpha(self,alpha):
+        """
+        Set alpha and update alpha-boundary. 
+        """
+        self.alpha = alpha
+        reg_edge = self.get_regular_edges(alpha)    
+        self.boundary = [self.edge[k] for k in reg_edge]
+        self._init_boundary_triangles()
+    
+            
+    def _alpha_shape_algorithm(self, alpha=None):
+        """
+        Given a set of points (self.points) and an optional alpha value
+        determines the alpha shape boundary (stored in self.boundary,
+        accessed by get_boundary).
+        
+        Inputs:
+          alpha: The alpha value can be optionally specified.  If it is
+          not specified the optimum alpha value will be used.
+        """
+
+        self.alpha = alpha
+
+        ## Build Delaunay triangulation
+        from anuga.mesh_engine.mesh_engine import generate_mesh
+        points = []
+        seglist = []
+        holelist = []
+        regionlist = []
+        pointattlist = []
+        segattlist = []
+
+        points = [(pt[0], pt[1]) for pt in self.points]
+        pointattlist = [ [] for i in range(len(points)) ] 
+        mode = "Qzcn"
+        tridata = generate_mesh(points,seglist,holelist,regionlist,
+                                 pointattlist,segattlist,mode)
+        self.deltri = tridata['generatedtrianglelist']
+        self.deltrinbr = tridata['generatedtriangleneighborlist']
+        self.hulledges = tridata['generatedsegmentlist'] 
+
+        ## Build Alpha table
+        ## the following routines determine alpha thresholds for the
+        ## triangles, edges, and vertices of the delaunay triangulation
+        self._tri_circumradius()
+        self._edge_intervals()
+        self._vertex_intervals()
+
+        if alpha==None:
+            # Find optimum alpha
+            # Ken Clarkson's hull program uses smallest alpha so that
+            # every vertex is non-singular so... 
+            self.optimum_alpha = max([iv[0] for iv in self.vertexinterval \
+                                      if iv!=[] ])
+            alpha = self.optimum_alpha
+        self.alpha = alpha
+        reg_edge = self.get_regular_edges(self.alpha)
+        self.boundary = [self.edge[k] for k in reg_edge]
+        self._init_boundary_triangles()
+        
+        return
+
+    def _tri_circumradius(self):
+        """
+        Compute circumradii of the delaunay triangles
+        """
+        
+        x = self.points[:,0]
+        y = self.points[:,1]
+        ind1 = [self.deltri[j][0] for j in range(len(self.deltri))]
+        ind2 = [self.deltri[j][1] for j in range(len(self.deltri))]
+        ind3 = [self.deltri[j][2] for j in range(len(self.deltri))]
+
+        x1 = num.array([x[j] for j in ind1])
+        y1 = num.array([y[j] for j in ind1])
+        x2 = num.array([x[j] for j in ind2])
+        y2 = num.array([y[j] for j in ind2])
+        x3 = num.array([x[j] for j in ind3])
+        y3 = num.array([y[j] for j in ind3])
+
+        x21 = x2-x1
+        x31 = x3-x1
+        y21 = y2-y1
+        y31 = y3-y1
+
+        dist21 = x21*x21 + y21*y21
+        dist31 = x31*x31 + y31*y31
+
+        denom = x21*y31 - x31*y21
+
+        # dx/2, dy/2 give circumcenter relative to x1,y1. 
+        # dx = (y31*dist21 - y21*dist31)/denom
+        # dy = (x21*dist31 - x31*dist21)/denom
+        # first need to check for near-zero values of denom 
+        delta = 0.00000001
+        zeroind = [k for k in range(len(denom)) if \
+                   (denom[k]< EPSILON and  denom[k] > -EPSILON)]
+        # if some denom values are close to zero,
+        # we perturb the associated vertices and recalculate 
+        while zeroind!=[]:
+            random.seed()
+            log.critical("Warning: degenerate triangles found in alpha_shape.py, results may be inaccurate.")
+            for d in zeroind:
+                x1[d] = x1[d]+delta*(random.random()-0.5)
+                x2[d] = x2[d]+delta*(random.random()-0.5)
+                x3[d] = x3[d]+delta*(random.random()-0.5)
+                y1[d] = y1[d]+delta*(random.random()-0.5)
+                y2[d] = y2[d]+delta*(random.random()-0.5)
+                y3[d] = y3[d]+delta*(random.random()-0.5)
+            x21 = x2-x1
+            x31 = x3-x1
+            y21 = y2-y1
+            y31 = y3-y1
+            dist21 = x21*x21 + y21*y21
+            dist31 = x31*x31 + y31*y31
+            denom = x21*y31 - x31*y21
+            zeroind = [k for k in range(len(denom)) if \
+                       (denom[k]< EPSILON and  denom[k] > -EPSILON)]
+
+        if num.any(denom == 0.0):
+            raise AlphaError
+
+        dx = num.divide(y31*dist21 - y21*dist31, denom)
+        dy = num.divide(x21*dist31 - x31*dist21, denom)
+
+        self.triradius = 0.5*num.sqrt(dx*dx + dy*dy)
+
+    def _edge_intervals(self):
+        """
+         for each edge, find triples
+         (length/2, min_adj_triradius, max_adj_triradius) if unattached
+         (min_adj_triradius, min_adj_triradius, max_adj_triradius) if attached.
+         An edge is attached if it is opposite an obtuse angle 
+        """
+        
+        # It should be possible to rewrite this routine in an array-friendly
+        # form like _tri_circumradius()  if we need to speed things up.
+        # Hard to do though.
+
+        edges = []
+        edgenbrs = []
+        edgeinterval = []
+        for t in range(len(self.deltri)):
+            tri = self.deltri[t]
+            trinbr = self.deltrinbr[t]
+            dx = num.array([self.points[tri[(i+1)%3],0] -
+                            self.points[tri[(i+2)%3],0] for i in [0,1,2]])
+            dy = num.array([self.points[tri[(i+1)%3],1] -
+                            self.points[tri[(i+2)%3],1] for i in [0,1,2]])
+            elen = num.sqrt(dx*dx+dy*dy)
+            # really only need sign - not angle value:
+            anglesign = num.array([(-dx[(i+1)%3]*dx[(i+2)%3]-
+                                    dy[(i+1)%3]*dy[(i+2)%3]) for i in [0,1,2]])
+            
+            for i in [0,1,2]:
+                j = (i+1)%3
+                k = (i+2)%3
+                if trinbr[i]==-1:
+                    edges.append((tri[j], tri[k]))
+                    edgenbrs.append((t, -1))
+                    edgeinterval.append([0.5*elen[i], self.triradius[t], INF])
+                elif (tri[j]<tri[k]):
+                    edges.append((tri[j], tri[k]))
+                    edgenbrs.append((t, trinbr[i]))
+                    edgeinterval.append([0.5*elen[i],\
+                       min(self.triradius[t],self.triradius[trinbr[i]]),\
+                          max(self.triradius[t],self.triradius[trinbr[i]]) ])
+                else:
+                    continue
+                if anglesign[i] < 0: 
+                    edgeinterval[-1][0] = edgeinterval[-1][1]
+                    
+        self.edge = edges
+        self.edgenbr = edgenbrs
+        self.edgeinterval = edgeinterval
+
+    def _vertex_intervals(self):
+        """
+        for each vertex find pairs
+        (min_adj_triradius, max_adj_triradius)
+        """
+        nv = len(self.points)
+        vertexnbrs = [ [] for i in range(nv)]
+        vertexinterval = [ [] for i in range(nv)] 
+        for t in range(len(self.deltri)):
+            for j in self.deltri[t]:
+                vertexnbrs[int(j)].append(t)
+        for h in range(len(self.hulledges)):
+            for j in self.hulledges[h]:
+                vertexnbrs[int(j)].append(-1)
+        
+        for i in range(nv):
+            radii = [ self.triradius[t] for t in vertexnbrs[i] if t>=0 ]
+            try:
+                vertexinterval[i] = [min(radii), max(radii)]
+                if vertexnbrs[i][-1]==-1:
+                    vertexinterval[i][1]=INF
+            except ValueError:
+                raise AlphaError
+
+        self.vertexnbr = vertexnbrs
+        self.vertexinterval = vertexinterval
+        
+    def get_alpha_triangles(self,alpha):
+        """
+        Given an alpha value,
+        return indices of triangles in the alpha-shape
+        """
+        def tri_rad_lta(k):
+            return self.triradius[k]<=alpha
+
+        return filter(tri_rad_lta, range(len(self.triradius)))
+
+    def get_regular_edges(self,alpha):
+        """
+        Given an alpha value,
+        return the indices of edges on the boundary of the alpha-shape
+        """
+        def reg_edge(k):
+            return self.edgeinterval[k][1]<=alpha and \
+                   self.edgeinterval[k][2]>alpha
+
+        return filter(reg_edge, range(len(self.edgeinterval)))
+
+    def get_exposed_vertices(self,alpha):
+        """
+        Given an alpha value,
+        return the vertices on the boundary of the alpha-shape
+        """
+        def exp_vert(k):
+            return self.vertexinterval[k][0]<=alpha and \
+                   self.vertexinterval[k][1]>alpha
+
+        return filter(exp_vert, range(len(self.vertexinterval)))        
+
+    def _vertices_from_edges(self,elist):
+        """
+        Returns the list of unique vertex labels from edges in elist
+        """
+
+        v1 = [elist[k][0] for k in range(len(elist))]
+        v2 = [elist[k][1] for k in range(len(elist))]
+        v = v1+v2
+        v.sort()
+        vertices = [v[k] for k in range(len(v)) if v[k]!=v[k-1] ]
+        return vertices
+
+    def _init_boundary_triangles(self):
+        """
+        Creates the initial list of triangle indices
+        exterior to and touching the boundary of the alpha shape
+        """
+        def tri_rad_gta(k):
+            return self.triradius[k]>self.alpha
+
+        extrind = filter(tri_rad_gta, range(len(self.triradius)))
+
+        bv = self._vertices_from_edges(self.boundary)
+        
+        btri = []
+        for et in extrind:
+            v0 = self.deltri[et][0]
+            v1 = self.deltri[et][1]
+            v2 = self.deltri[et][2]
+            if v0 in bv or v1 in bv or v2 in bv:
+                btri.append(et)
+
+        self.boundarytriangle = btri
+  
+       
+    def _remove_holes(self,small):
+        """
+        Given the edges in self.boundary, finds the largest components.
+        The routine does this by implementing a union-find algorithm. 
+        """
+
+        bdry = self.boundary
+        
+        def findroot(i):
+            if vptr[i] < 0:
+                return i
+            k = findroot(vptr[i])
+            vptr[i] = k    # this produces "path compression" in the
+                           # union-find tree. 
+            return k
+
+
+
+        # get a list of unique vertex labels:
+        verts = self._vertices_from_edges(bdry)
+
+        # vptr represents the union-find tree.
+        # if vptr[i] = EMPTY < 0, the vertex verts[i] has not been visited yet
+        # if vptr[i] = j > 0, then j verts[j] is the parent of verts[i].
+        # if vptr[i] = n < 0, then verts[i] is a root vertex and
+        #                       represents a connected component of n vertices.
+        
+        #initialise vptr to negative number outside range 
+        EMPTY = -max(verts)-len(verts)
+        vptr = [EMPTY for k in range(len(verts))]
+
+        #add edges and maintain union tree
+        for i in range(len(bdry)):
+            vl = verts.index(bdry[i][0])
+            vr = verts.index(bdry[i][1])
+            rvl = findroot(vl)
+            rvr = findroot(vr)
+            if not(rvl==rvr):
+                if (vptr[vl]==EMPTY):
+                    if (vptr[vr]==EMPTY):
+                        vptr[vl] = -2
+                        vptr[vr] = vl
+                    else:
+                        vptr[vl] = rvr
+                        vptr[rvr] = vptr[rvr]-1
+                else:
+                    if (vptr[vr]==EMPTY):
+                        vptr[vr] = rvl
+                        vptr[rvl] = vptr[rvl]-1
+                    else:
+                        if vptr[rvl] > vptr[rvr]:
+                            vptr[rvr] = vptr[rvr] + vptr[rvl]
+                            vptr[rvl] = rvr
+                            vptr[vl] = rvr
+                        else:
+                            vptr[rvl] = vptr[rvl] + vptr[rvr]
+                            vptr[rvr] = rvl
+                            vptr[vr] = rvl 
+        # end edge loop
+
+        if vptr.count(EMPTY):
+            raise FlagError, "We didn't hit all the vertices in the boundary"
+        
+        # discard the edges in the little components
+        # (i.e. those components with less than 'small' fraction of bdry points)
+        cutoff = round(small*len(verts))
+        largest_component = -min(vptr)
+        if cutoff > largest_component:
+            cutoff = round((1-small)*largest_component)
+
+        # littleind has root indices for small components 
+        littleind = [k for k in range(len(vptr)) if \
+                     (vptr[k]<0 and vptr[k]>-cutoff)] 
+        if littleind:
+            # littlecomp has all vptr indices in the small components
+            littlecomp = [k for k in range(len(vptr)) if \
+                          findroot(k) in littleind]
+            # vdiscard has the vertex indices corresponding to vptr indices  
+            vdiscard = [verts[k] for k in littlecomp] 
+            newbdry = [e for e in bdry if \
+                       not((e[0] in vdiscard) and (e[1] in vdiscard))]
+
+            newverts = self._vertices_from_edges(newbdry)
+            # recompute the boundary triangles
+            newbt = []
+            for bt in self.boundarytriangle:
+                v0 = self.deltri[bt][0]
+                v1 = self.deltri[bt][1]
+                v2 = self.deltri[bt][2]
+                if (v0 in newverts or v1 in newverts or v2 in newverts):
+                    newbt.append(bt)
+
+            self.boundarytriangle = newbt           
+        else:
+            newbdry = bdry
+    
+        return newbdry
+
+
+    def _smooth_indents(self):
+        """
+        Given edges in bdry, test for acute-angle triangular indents
+        and remove them.
+        """
+        
+        bdry = self.boundary
+        bdrytri = self.boundarytriangle
+        
+        # find boundary triangles that have two edges in bdry
+        # v2ind has the place index relative to the triangle deltri[ind]  
+        # for the bdry vertex where the two edges meet.
+
+        verts = self._vertices_from_edges(bdry)
+
+        b2etri = []
+        for ind in bdrytri:
+            bect = 0
+            v2ind = [0,1,2]
+            for j in [0,1,2]:
+                eda = (self.deltri[ind][(j+1)%3], self.deltri[ind][(j+2)%3])
+                edb = (self.deltri[ind][(j+2)%3], self.deltri[ind][(j+1)%3])
+                if eda in bdry or edb in bdry:
+                    bect +=1
+                    v2ind.remove(j)
+            if bect==2:
+                b2etri.append((ind,v2ind[0]))
+
+        # test the bdrytri triangles for acute angles 
+        acutetri = []
+        for tind in b2etri:
+            tri = self.deltri[tind[0]]
+            
+            dx = num.array([self.points[tri[(i+1)%3],0] - \
+                           self.points[tri[(i+2)%3],0] for i in [0,1,2]])
+            dy = num.array([self.points[tri[(i+1)%3],1] - \
+                           self.points[tri[(i+2)%3],1] for i in [0,1,2]])
+            anglesign = num.array([(-dx[(i+1)%3]*dx[(i+2)%3]-\
+                                   dy[(i+1)%3]*dy[(i+2)%3]) for i in [0,1,2]])
+            # record any triangle that has an acute angle spanned by
+            #two edges along the boundary..
+            if anglesign[tind[1]] > 0:
+                acutetri.append(tind[0])
+
+        # adjust the bdry edges and triangles by adding
+        #in the acutetri triangles
+        for pind in acutetri:
+            bdrytri.remove(pind) 
+            tri = self.deltri[pind]
+            for i in [0,1,2]:
+                bdry.append((tri[(i+1)%3], tri[(i+2)%3]))
+
+        newbdry = []
+        for ed in bdry:
+            numed = bdry.count(ed)+bdry.count((ed[1],ed[0]))
+            if numed%2 == 1:
+                newbdry.append(ed)
+        
+        return newbdry
+
+    def _expand_pinch(self):
+        """
+        Given edges in bdry, test for vertices with more than 2 incident edges.
+        Expand by adding back in associated triangles.
+        """
+
+        bdry = self.boundary
+        bdrytri = self.boundarytriangle
+        
+        v1 = [bdry[k][0] for k in range(len(bdry))]
+        v2 = [bdry[k][1] for k in range(len(bdry))]
+        v = v1+v2
+        v.sort()
+        probv = [v[k] for k in range(len(v)) \
+                 if (v[k]!=v[k-1] and v.count(v[k])>2) ]
+
+        # find boundary triangles that have at least one vertex in probv
+        probtri = []
+        for ind in bdrytri:
+            v0 = self.deltri[ind][0]
+            v1 = self.deltri[ind][1]
+            v2 = self.deltri[ind][2]
+            if v0 in probv or v1 in probv or v2 in probv:
+                probtri.append(ind)
+
+
+        # "add in" the problem triangles
+        for pind in probtri:
+            bdrytri.remove(pind) 
+            tri = self.deltri[pind]
+            for i in [0,1,2]:
+                bdry.append((tri[(i+1)%3], tri[(i+2)%3]))
+
+        newbdry = []
+        for ed in bdry:
+            numed = bdry.count(ed)+bdry.count((ed[1],ed[0]))
+            if numed%2 == 1:
+                newbdry.append(ed)
+        
+        return newbdry
+
+
+#-------------------------------------------------------------
+if __name__ == "__main__":
+    """
+    Load in a data point file.
+    Determine the alpha shape boundary
+    Save the boundary to a file.
+
+    usage: alpha_shape.py point_file.csv boundary_file.bnd [alpha]
+    
+    The alpha value is optional.
+    """
+    
+    import os, sys
+    usage = "usage: %s point_file.csv boundary_file.bnd [alpha]"%os.path.basename(sys.argv[0])
+    if len(sys.argv) < 3:
+        print usage
+    else:
+        point_file = sys.argv[1]
+        boundary_file = sys.argv[2]
+        if len(sys.argv) > 4:
+            alpha = sys.argv[3]
+        else:
+            alpha = None
+
+        #print "about to call alpha shape routine \n"
+        alpha_shape_via_files(point_file, boundary_file, alpha)
+        

Users/steve/Miniconda/envs/anuga/Lib/site-packages/anuga/alpha_shape/setup.py

@@ -0,0 +1,21 @@
+from __future__ import division, print_function
+
+import os
+import sys
+
+from os.path import join
+
+def configuration(parent_package='',top_path=None):
+    
+    from numpy.distutils.misc_util import Configuration
+    from numpy.distutils.system_info import get_info
+    
+    config = Configuration('alpha_shape', parent_package, top_path)
+
+    config.add_data_dir('tests')
+
+    return config
+    
+if __name__ == '__main__':
+    from numpy.distutils.core import setup
+    setup(configuration=configuration)

Users/steve/Miniconda/envs/anuga/Lib/site-packages/anuga/alpha_shape/tests/__init__.py

@@ -0,0 +1,8 @@
+"""Make directory available as a Python package
+"""
+
+pass
+
+
+
+