| 1 | |
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| 2 | from string import find, rfind |
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| 3 | |
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| 4 | def mesh_file_to_mesh_dictionary(fileName): |
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| 5 | """Load a pmesh file. Returning the mesh dictionary. |
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| 6 | """ |
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| 7 | try: |
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| 8 | meshdic = import_trianglulation(fileName) |
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| 9 | except IOError, e: |
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| 10 | msg = 'Could not open file %s ' %fileName |
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| 11 | raise IOError, msg |
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| 12 | return meshdic |
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| 13 | |
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| 14 | def import_trianglulation(ofile): |
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| 15 | """ |
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| 16 | reading triangulation and meshoutline info. |
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| 17 | import a file, ofile, with the format |
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| 18 | |
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| 19 | First line: <# of vertices> <# of attributes> |
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| 20 | Following lines: <vertex #> <x> <y> [attributes] |
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| 21 | One line: <# of triangles> |
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| 22 | Following lines: <triangle #> <vertex #> <vertex #> <vertex #> <neigbouring triangle #> <neigbouring triangle #> <neigbouring triangle #> [attribute of region] |
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| 23 | One line: <# of segments> |
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| 24 | Following lines: <segment #> <vertex #> <vertex #> [boundary marker] |
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| 25 | Note: This might throw a can't load file error |
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| 26 | """ |
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| 27 | fd = open(ofile,'r') |
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| 28 | dict = read_trianglulation(fd) |
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| 29 | dict_mesh = read_mesh(fd) |
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| 30 | for element in dict_mesh.keys(): |
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| 31 | dict[element] = dict_mesh[element] |
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| 32 | |
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| 33 | fd.close() |
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| 34 | return dict |
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| 35 | |
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| 36 | |
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| 37 | def read_trianglulation(fd): |
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| 38 | delimiter = " " |
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| 39 | ######### loading the point info |
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| 40 | line = fd.readline() |
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| 41 | #print line |
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| 42 | fragments = line.split() |
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| 43 | #for fragment in fragments: |
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| 44 | # print fragment |
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| 45 | if fragments ==[]: |
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| 46 | NumOfVertices = 0 |
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| 47 | NumOfVertAttributes = 0 |
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| 48 | else: |
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| 49 | NumOfVertices = fragments[0] |
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| 50 | NumOfVertAttributes = fragments[1] |
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| 51 | points = [] |
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| 52 | pointattributes = [] |
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| 53 | for index in range(int(NumOfVertices)): |
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| 54 | #print index |
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| 55 | fragments = fd.readline().split() |
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| 56 | #print fragments |
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| 57 | fragments.pop(0) #pop off the index |
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| 58 | |
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| 59 | # pop the x y off so we're left with a list of attributes |
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| 60 | vert = [float(fragments.pop(0)),float(fragments.pop(0))] |
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| 61 | points.append(vert) |
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| 62 | apointattributes = [] |
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| 63 | #print fragments |
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| 64 | for fragment in fragments: |
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| 65 | apointattributes.append(float(fragment)) |
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| 66 | pointattributes.append(apointattributes) |
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| 67 | |
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| 68 | ######### loading the point title info |
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| 69 | line = fd.readline() |
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| 70 | #print "point title comments",line |
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| 71 | vertTitle = [] |
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| 72 | for index in range(int(NumOfVertAttributes)): |
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| 73 | #print index |
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| 74 | fragments = fd.readline().strip() |
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| 75 | vertTitle.append(fragments) |
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| 76 | #print vertTitle |
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| 77 | |
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| 78 | ######### loading the triangle info |
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| 79 | line = fd.readline() |
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| 80 | #print "triangle comments",line |
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| 81 | fragments = line.split() |
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| 82 | #for fragment in fragments: |
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| 83 | # print fragment |
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| 84 | NumOfTriangles = fragments[0] |
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| 85 | triangles = [] |
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| 86 | triangleattributes = [] |
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| 87 | triangleneighbors = [] |
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| 88 | for index in range(int(NumOfTriangles)): |
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| 89 | #print index |
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| 90 | line = fd.readline() |
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| 91 | line.strip() # so we can get the region string |
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| 92 | fragments = line.split() |
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| 93 | #print "triangle info", fragments |
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| 94 | fragments.pop(0) #pop off the index |
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| 95 | |
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| 96 | tri = [int(fragments[0]),int(fragments[1]),int(fragments[2])] |
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| 97 | triangles.append(tri) |
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| 98 | neighbors = [int(fragments[3]),int(fragments[4]),int(fragments[5])] |
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| 99 | triangleneighbors.append(neighbors) |
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| 100 | for x in range(7): # remove index [<vertex #>] [<neigbouring tri #>] |
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| 101 | line = line[find(line,delimiter):] # remove index |
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| 102 | line = line.lstrip() |
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| 103 | stringmarker = line.strip() |
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| 104 | triangleattributes.append([stringmarker]) |
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| 105 | |
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| 106 | ######### loading the segment info |
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| 107 | line = fd.readline() |
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| 108 | #print "seg comment line",line |
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| 109 | fragments = line.split() |
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| 110 | #for fragment in fragments: |
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| 111 | # print fragment |
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| 112 | NumOfSegments = fragments[0] |
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| 113 | segments = [] |
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| 114 | segmentmarkers = [] |
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| 115 | for index in range(int(NumOfSegments)): |
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| 116 | #print index |
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| 117 | line = fd.readline() |
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| 118 | line.strip() # to get the segment string |
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| 119 | fragments = line.split() |
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| 120 | #print fragments |
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| 121 | fragments.pop(0) #pop off the index |
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| 122 | seg = [int(fragments[0]),int(fragments[1])] |
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| 123 | segments.append(seg) |
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| 124 | line = line[find(line,delimiter):] # remove index |
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| 125 | line = line.lstrip() |
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| 126 | line = line[find(line,delimiter):] # remove x |
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| 127 | line = line.lstrip() |
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| 128 | line = line[find(line,delimiter):] # remove y |
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| 129 | stringmarker = line.strip() |
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| 130 | segmentmarkers.append(stringmarker) |
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| 131 | meshDict = {} |
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| 132 | meshDict['generatedpointlist'] = points |
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| 133 | meshDict['generatedpointattributelist'] = pointattributes |
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| 134 | meshDict['generatedtrianglelist'] = triangles |
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| 135 | meshDict['generatedtriangleattributelist'] = triangleattributes |
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| 136 | meshDict['generatedtriangleneighborlist'] = triangleneighbors |
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| 137 | meshDict['generatedsegmentlist'] = segments |
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| 138 | meshDict['generatedsegmentmarkerlist'] = segmentmarkers |
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| 139 | meshDict['generatedpointattributetitlelist'] = vertTitle |
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| 140 | return meshDict |
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| 141 | |
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| 142 | def import_mesh(ofile): |
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| 143 | """ |
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| 144 | import a file, ofile, with the format |
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| 145 | |
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| 146 | First line: <# of vertices> <# of attributes> |
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| 147 | Following lines: <x> <y> [attributes] |
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| 148 | One line: <# of segments> |
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| 149 | Following lines: <vertex #> <vertex #> [boundary marker] |
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| 150 | Note: This might throw a can't load file error |
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| 151 | """ |
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| 152 | fd = open(ofile,'r') |
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| 153 | meshDict = read_mesh(fd) |
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| 154 | fd.close() |
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| 155 | return meshDict |
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| 156 | |
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| 157 | def read_mesh(fd): |
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| 158 | """ |
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| 159 | Note, if a file has no mesh info, it can still be read - the meshdic |
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| 160 | returned will be 'empty'. |
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| 161 | """ |
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| 162 | delimiter = " " # warning: split() calls are using default whitespace |
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| 163 | |
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| 164 | ######### loading the point info |
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| 165 | line = fd.readline() |
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| 166 | #print line |
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| 167 | fragments = line.split() |
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| 168 | #for fragment in fragments: |
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| 169 | if fragments ==[]: |
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| 170 | NumOfVertices = 0 |
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| 171 | NumOfVertAttributes = 0 |
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| 172 | else: |
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| 173 | NumOfVertices = fragments[0] |
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| 174 | NumOfVertAttributes = fragments[1] |
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| 175 | points = [] |
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| 176 | pointattributes = [] |
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| 177 | for index in range(int(NumOfVertices)): |
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| 178 | #print index |
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| 179 | fragments = fd.readline().split() |
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| 180 | #print fragments |
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| 181 | fragments.pop(0) #pop off the index |
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| 182 | # pop the x y off so we're left with a list of attributes |
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| 183 | vert = [float(fragments.pop(0)),float(fragments.pop(0))] |
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| 184 | points.append(vert) |
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| 185 | apointattributes = [] |
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| 186 | #print fragments |
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| 187 | for fragment in fragments: |
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| 188 | apointattributes.append(float(fragment)) |
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| 189 | pointattributes.append(apointattributes) |
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| 190 | |
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| 191 | |
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| 192 | ######### loading the segment info |
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| 193 | line = fd.readline() |
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| 194 | #print line |
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| 195 | fragments = line.split() |
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| 196 | #for fragment in fragments: |
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| 197 | # print fragment |
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| 198 | if fragments ==[]: |
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| 199 | NumOfSegments = 0 |
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| 200 | else: |
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| 201 | NumOfSegments = fragments[0] |
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| 202 | segments = [] |
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| 203 | segmentmarkers = [] |
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| 204 | for index in range(int(NumOfSegments)): |
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| 205 | #print index |
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| 206 | line = fd.readline() |
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| 207 | fragments = line.split() |
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| 208 | #print fragments |
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| 209 | fragments.pop(0) #pop off the index |
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| 210 | |
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| 211 | seg = [int(fragments[0]),int(fragments[1])] |
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| 212 | segments.append(seg) |
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| 213 | line = line[find(line,delimiter):] # remove index |
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| 214 | line = line.lstrip() |
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| 215 | line = line[find(line,delimiter):] # remove x |
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| 216 | line = line.lstrip() |
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| 217 | line = line[find(line,delimiter):] # remove y |
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| 218 | stringmarker = line.strip() |
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| 219 | segmentmarkers.append(stringmarker) |
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| 220 | |
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| 221 | ######### loading the hole info |
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| 222 | line = fd.readline() |
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| 223 | #print line |
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| 224 | fragments = line.split() |
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| 225 | #for fragment in fragments: |
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| 226 | # print fragment |
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| 227 | if fragments ==[]: |
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| 228 | numOfHoles = 0 |
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| 229 | else: |
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| 230 | numOfHoles = fragments[0] |
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| 231 | holes = [] |
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| 232 | for index in range(int(numOfHoles)): |
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| 233 | #print index |
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| 234 | fragments = fd.readline().split() |
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| 235 | #print fragments |
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| 236 | fragments.pop(0) #pop off the index |
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| 237 | hole = [float(fragments[0]),float(fragments[1])] |
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| 238 | holes.append(hole) |
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| 239 | |
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| 240 | |
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| 241 | ######### loading the region info |
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| 242 | line = fd.readline() |
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| 243 | #print line |
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| 244 | fragments = line.split() |
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| 245 | #for fragment in fragments: |
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| 246 | # print fragment |
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| 247 | if fragments ==[]: |
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| 248 | numOfRegions = 0 |
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| 249 | else: |
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| 250 | numOfRegions = fragments[0] |
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| 251 | regions = [] |
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| 252 | regionattributes = [] |
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| 253 | for index in range(int(numOfRegions)): |
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| 254 | line = fd.readline() |
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| 255 | fragments = line.split() |
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| 256 | #print fragments |
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| 257 | fragments.pop(0) #pop off the index |
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| 258 | region = [float(fragments[0]),float(fragments[1])] |
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| 259 | regions.append(region) |
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| 260 | |
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| 261 | line = line[find(line,delimiter):] # remove index |
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| 262 | line = line.lstrip() |
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| 263 | line = line[find(line,delimiter):] # remove x |
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| 264 | line = line.lstrip() |
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| 265 | line = line[find(line,delimiter):] # remove y |
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| 266 | stringmarker = line.strip() |
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| 267 | regionattributes.append(stringmarker) |
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| 268 | regionmaxareas = [] |
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| 269 | line = fd.readline() |
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| 270 | for index in range(int(numOfRegions)): # Read in the Max area info |
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| 271 | line = fd.readline() |
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| 272 | fragments = line.split() |
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| 273 | #print fragments |
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| 274 | # The try is here for format compatibility |
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| 275 | try: |
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| 276 | fragments.pop(0) #pop off the index |
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| 277 | if len(fragments) == 0: #no max area |
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| 278 | regionmaxareas.append(None) |
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| 279 | else: |
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| 280 | regionmaxareas.append(float(fragments[0])) |
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| 281 | except IndexError, e: |
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| 282 | regionmaxareas.append(None) |
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| 283 | |
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| 284 | meshDict = {} |
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| 285 | meshDict['pointlist'] = points |
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| 286 | meshDict['pointattributelist'] = pointattributes |
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| 287 | meshDict['segmentlist'] = segments |
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| 288 | meshDict['segmentmarkerlist'] = segmentmarkers |
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| 289 | meshDict['holelist'] = holes |
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| 290 | meshDict['regionlist'] = regions |
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| 291 | meshDict['regionattributelist'] = regionattributes |
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| 292 | meshDict['regionmaxarealist'] = regionmaxareas |
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| 293 | |
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| 294 | return meshDict |
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| 295 | |
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| 296 | def clean_line(line,delimiter): |
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| 297 | """Remove whitespace |
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| 298 | """ |
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| 299 | #print ">%s" %line |
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| 300 | line = line.strip() |
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| 301 | #print "stripped>%s" %line |
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| 302 | numbers = line.split(delimiter) |
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| 303 | i = len(numbers) - 1 |
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| 304 | while i >= 0: |
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| 305 | if numbers[i] == '': |
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| 306 | numbers.pop(i) |
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| 307 | i += -1 |
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| 308 | #for num in numbers: |
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| 309 | # print "num>%s<" %num |
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| 310 | return numbers |
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| 311 | |
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| 312 | def write_ASCII_trianglulation(fd, |
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| 313 | gen_dict): |
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| 314 | vertices = gen_dict['generatedpointlist'] |
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| 315 | vertices_attributes = gen_dict['generatedpointattributelist'] |
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| 316 | try: |
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| 317 | vertices_attribute_titles = gen_dict['generatedpointattributetitlelist'] |
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| 318 | |
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| 319 | except KeyError, e: |
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| 320 | #FIXME is this the best way? |
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| 321 | if vertices_attributes == [] or vertices_attributes[0] == []: |
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| 322 | vertices_attribute_titles = [] |
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| 323 | else: |
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| 324 | raise KeyError, e |
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| 325 | |
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| 326 | triangles = gen_dict['generatedtrianglelist'] |
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| 327 | triangles_attributes = gen_dict['generatedtriangleattributelist'] |
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| 328 | triangle_neighbors = gen_dict['generatedtriangleneighborlist'] |
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| 329 | |
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| 330 | segments = gen_dict['generatedsegmentlist'] |
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| 331 | segment_markers = gen_dict['generatedsegmentmarkerlist'] |
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| 332 | |
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| 333 | numVert = str(len(vertices)) |
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| 334 | if (numVert == "0"): |
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| 335 | numVertAttrib = "0" |
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| 336 | else: |
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| 337 | numVertAttrib = str(len(vertices_attributes[0])) |
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| 338 | fd.write(numVert + " " + numVertAttrib + " # <vertex #> <x> <y> [attributes] ...Triangulation Vertices..." + "\n") |
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| 339 | |
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| 340 | #<vertex #> <x> <y> [attributes] |
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| 341 | index = 0 |
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| 342 | for vert in vertices: |
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| 343 | attlist = "" |
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| 344 | for att in vertices_attributes[index]: |
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| 345 | attlist = attlist + str(att)+" " |
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| 346 | attlist.strip() |
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| 347 | fd.write(str(index) + " " |
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| 348 | + str(vert[0]) + " " |
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| 349 | + str(vert[1]) + " " |
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| 350 | + attlist + "\n") |
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| 351 | index += 1 |
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| 352 | |
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| 353 | # write comments for title |
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| 354 | fd.write("# attribute column titles ...Triangulation Vertex Titles..." + "\n") |
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| 355 | for title in vertices_attribute_titles: |
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| 356 | fd.write(title + "\n") |
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| 357 | |
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| 358 | #<# of triangles> |
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| 359 | n = len(triangles) |
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| 360 | fd.write(str(n) + " # <triangle #> [<vertex #>] [<neigbouring triangle #>] [attribute of region] ...Triangulation Triangles..." + "\n") |
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| 361 | |
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| 362 | # <triangle #> <vertex #> <vertex #> <vertex #> <neigbouring triangle #> <neigbouring triangle #> <neigbouring triangle #> [attribute of region] |
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| 363 | for index in range(n): |
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| 364 | neighbors = "" |
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| 365 | tri = triangles[index] |
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| 366 | for neighbor in triangle_neighbors[index]: |
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| 367 | if neighbor: |
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| 368 | neighbors += str(neighbor) + " " |
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| 369 | else: |
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| 370 | if neighbor == 0: |
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| 371 | neighbors += "0 " |
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| 372 | else: |
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| 373 | neighbors += "-1 " |
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| 374 | if triangles_attributes[index] == ['']: |
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| 375 | att = "" |
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| 376 | else: |
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| 377 | att = str(triangles_attributes[index]) |
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| 378 | fd.write(str(index) + " " |
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| 379 | + str(tri[0]) + " " |
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| 380 | + str(tri[1]) + " " |
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| 381 | + str(tri[2]) + " " |
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| 382 | + neighbors + " " |
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| 383 | + att + "\n") |
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| 384 | |
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| 385 | #One line: <# of segments> |
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| 386 | fd.write(str(len(segments)) + |
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| 387 | " # <segment #> <vertex #> <vertex #> [boundary marker] ...Triangulation Segments..." + "\n") |
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| 388 | |
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| 389 | #Following lines: <segment #> <vertex #> <vertex #> [boundary marker] |
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| 390 | for i in range(len(segments)): |
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| 391 | seg = segments[i] |
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| 392 | fd.write(str(i) + " " |
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| 393 | + str(seg[0]) + " " |
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| 394 | + str(seg[1]) + " " |
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| 395 | + str(segment_markers[i]) + "\n") |
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| 396 | |
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| 397 | |
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| 398 | def export_trianglulation_file(ofile,gen_dict): |
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| 399 | """ |
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| 400 | write a file, ofile, with the format |
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| 401 | |
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| 402 | First line: <# of vertices> <# of attributes> |
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| 403 | Following lines: <vertex #> <x> <y> [attributes] |
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| 404 | One line: <# of triangles> |
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| 405 | Following lines: <triangle #> <vertex #> <vertex #> <vertex #> <neigbouring triangle #> <neigbouring triangle #> <neigbouring triangle #> [attribute of region] |
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| 406 | One line: <# of segments> |
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| 407 | Following lines: <segment #> <vertex #> <vertex #> [boundary marker] |
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| 408 | """ |
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| 409 | try: |
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| 410 | fd = open(ofile,'w') |
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| 411 | write_ASCII_trianglulation(fd,gen_dict) |
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| 412 | fd.close() |
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| 413 | except IOError, e: |
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| 414 | msg = 'Could not write file %s ' %fileName |
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| 415 | raise IOError, msg |
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| 416 | |
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| 417 | ## used by alpha shapes |
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| 418 | |
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| 419 | def export_boundary_file( file_name, points, title, delimiter = ','): |
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| 420 | """ |
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| 421 | export a file, ofile, with the format |
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| 422 | |
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| 423 | First line: Title variable |
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| 424 | Following lines: [point index][delimiter][point index] |
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| 425 | |
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| 426 | file_name - the name of the new file |
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| 427 | points - List of point index pairs [[p1, p2],[p3, p4]..] |
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| 428 | title - info to write in the first line |
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| 429 | """ |
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| 430 | |
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| 431 | fd = open(file_name,'w') |
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| 432 | |
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| 433 | fd.write(title+"\n") |
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| 434 | #[point index][delimiter][point index] |
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| 435 | for point in points: |
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| 436 | fd.write( str(point[0]) + delimiter |
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| 437 | + str(point[1]) + "\n") |
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| 438 | fd.close() |
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| 439 | |
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| 440 | |
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| 441 | ### |
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| 442 | # LOADING XYA FILES |
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| 443 | ### |
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| 444 | |
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| 445 | |
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| 446 | def load_xya_file(ofile,delimiter = ','): |
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| 447 | """ |
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| 448 | load a file, ofile, with the format |
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| 449 | x,y, [attributes] |
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| 450 | """ |
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| 451 | try: |
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| 452 | fd = open(ofile) |
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| 453 | #print "ofile",ofile |
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| 454 | xya_dic = read_xya_file(fd, delimiter) |
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| 455 | fd.close() |
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| 456 | except IOError, e: |
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| 457 | msg = 'Could not open file %s ' %fileName |
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| 458 | raise IOError, msg |
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| 459 | return xya_dic |
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| 460 | |
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| 461 | def read_xya_file(fd, delimiter): |
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| 462 | lines = fd.readlines() |
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| 463 | points = [] |
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| 464 | pointattributes = [] |
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| 465 | if len(lines) <= 1: |
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| 466 | raise SyntaxError |
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| 467 | title = lines.pop(0) # the first (title) line |
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| 468 | attLength = len(clean_line(lines[0],delimiter))-2 |
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| 469 | |
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| 470 | #print "initlegth" |
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| 471 | #print attLength |
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| 472 | for line in lines: |
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| 473 | #print "line >%s" %line |
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| 474 | numbers = clean_line(line,delimiter) |
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| 475 | #print "numbers >%s<" %numbers |
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| 476 | if len(numbers) < 2 and numbers != []: |
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| 477 | raise SyntaxError |
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| 478 | if numbers != []: |
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| 479 | try: |
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| 480 | x = float(numbers[0]) |
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| 481 | y = float(numbers[1]) |
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| 482 | points.append([x,y]) |
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| 483 | numbers.pop(0) |
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| 484 | numbers.pop(0) |
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| 485 | attributes = [] |
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| 486 | if attLength != len(numbers): |
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| 487 | raise SyntaxError |
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| 488 | |
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| 489 | attLength = len(numbers) |
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| 490 | |
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| 491 | for num in numbers: |
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| 492 | num.strip() |
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| 493 | if num != '\n' and num != '': |
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| 494 | attributes.append(float(num)) |
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| 495 | except ValueError: |
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| 496 | raise SyntaxError |
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| 497 | pointattributes.append(attributes) |
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| 498 | xya_dict = {} |
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| 499 | xya_dict['pointlist'] = points |
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| 500 | xya_dict['pointattributelist'] = pointattributes |
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| 501 | xya_dict['title'] = title |
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| 502 | xya_dict['segmentlist'] = [] |
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| 503 | xya_dict['segmentmarkerlist'] = [] |
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| 504 | xya_dict['regionlist'] = [] |
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| 505 | xya_dict['regionattributelist'] = [] |
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| 506 | xya_dict['regionmaxarealist'] = [] |
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| 507 | xya_dict['holelist'] = [] |
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| 508 | |
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| 509 | return xya_dict |
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| 510 | |
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| 511 | |
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| 512 | def export_xya_file( file_name, xya_dict, title, delimiter = ','): |
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| 513 | """ |
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| 514 | export a file, ofile, with the format |
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| 515 | |
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| 516 | First line: Title variable |
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| 517 | Following lines: <vertex #> <x> <y> [attributes] |
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| 518 | |
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| 519 | file_name - the name of the new file |
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| 520 | xya_dict - point and point attribute info in a dictionary |
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| 521 | title - info to write in the first line |
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| 522 | """ |
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| 523 | #FIXME, move the test for this from meshharness to loadasciiharness |
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| 524 | points = xya_dict['pointlist'] |
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| 525 | pointattributes = xya_dict['pointattributelist'] |
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| 526 | |
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| 527 | fd = open(file_name,'w') |
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| 528 | |
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| 529 | fd.write(title+"\n") |
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| 530 | #<vertex #> <x> <y> [attributes] |
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| 531 | for vert, vertatts in map(None, points, pointattributes): |
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| 532 | attlist = "" |
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| 533 | for att in vertatts: |
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| 534 | attlist = attlist + str(att)+ delimiter |
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| 535 | attlist = attlist[0:-len(delimiter)] # remove the last delimiter |
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| 536 | attlist.strip() |
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| 537 | fd.write( str(vert[0]) + delimiter |
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| 538 | + str(vert[1]) + delimiter |
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| 539 | + attlist + "\n") |
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| 540 | fd.close() |
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| 541 | |
|---|
| 542 | if __name__ == "__main__": |
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| 543 | m = import_mesh("tee.txt") |
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| 544 | print m |
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