[2253] | 1 | """ |
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| 2 | The format for a Points dictionary is: |
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| 3 | |
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| 4 | ['pointlist'] a 2 column array describing points. 1st column x, 2nd column y. |
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| 5 | ['attributelist'], a dictionary of 1D arrays, representing attribute values |
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| 6 | at the point. The dictionary key is the attribute header. |
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[2257] | 7 | ['geo_reference'] a Geo_refernece object. Use if the point information |
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| 8 | is relative. This is optional. |
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[2253] | 9 | eg |
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| 10 | dic['pointlist'] = [[1.0,2.0],[3.0,5.0]] |
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| 11 | dic['attributelist']['elevation'] = [[7.0,5.0] |
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| 12 | |
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[6074] | 13 | |
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[2253] | 14 | The dict format for IO with mesh files is; |
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| 15 | (the triangulation) |
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| 16 | vertices: [[x1,y1],[x2,y2],...] (lists of doubles) |
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| 17 | vertex_attributes: [[a11,a12,...],[a21,a22],...] (lists of doubles) |
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| 18 | vertex_attribute_titles:[A1Title, A2Title ...] (A list of strings) |
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[6074] | 19 | segments: [[v1,v2],[v3,v4],...] (lists of integers) |
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[2253] | 20 | segment_tags : [tag,tag,...] list of strings |
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| 21 | triangles : [(v1,v2,v3), (v4,v5,v6),....] lists of points |
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[6074] | 22 | triangle_tags: [s1,s2,...] A list of strings |
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[2253] | 23 | triangle_neighbors: [[t1,t2,t3], [t4,t5,t6],..] lists of triangles |
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[6074] | 24 | |
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| 25 | (the outline) |
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[2253] | 26 | points: [[x1,y1],[x2,y2],...] (lists of doubles) |
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| 27 | point_attributes: [[a11,a12,...],[a21,a22],...] (lists of doubles) |
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[6074] | 28 | outline_segments: [[point1,point2],[p3,p4],...] (lists of integers) |
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[2253] | 29 | outline_segment_tags : [tag1,tag2,...] list of strings |
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| 30 | holes : [[x1,y1],...](List of doubles, one inside each hole region) |
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| 31 | regions : [ [x1,y1],...] (List of 4 doubles) |
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| 32 | region_tags : [tag1,tag2,...] (list of strings) |
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| 33 | region_max_areas: [ma1,ma2,...] (A list of doubles) |
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| 34 | {Convension: A -ve max area means no max area} |
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[2257] | 35 | geo_reference: a Geo_refernece object. Use if the point information |
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| 36 | is relative. This is optional. |
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[2253] | 37 | |
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[4663] | 38 | Points files are .csv for ascii and .pts for NetCDF |
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[2253] | 39 | Mesh files are .tsh for ascii and .msh for NetCDF |
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| 40 | |
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| 41 | Note: point att's have no titles - that's currently ok, since least |
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| 42 | squares adds the point info to vertices, and they have titles |
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| 43 | |
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| 44 | The format for a .tsh file is (FIXME update this) |
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[6074] | 45 | |
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[2253] | 46 | First line: <# of vertices> <# of attributes> |
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| 47 | Following lines: <vertex #> <x> <y> [attributes] |
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[6074] | 48 | One line: <# of triangles> |
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| 49 | Following lines: <triangle #> <vertex #> <vertex #> <vertex #> |
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| 50 | <neigbouring triangle #> <neigbouring triangle #> |
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| 51 | <neigbouring triangle #> [attribute of region] |
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| 52 | One line: <# of segments> |
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[2253] | 53 | Following lines: <segment #> <vertex #> <vertex #> [boundary tag] |
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| 54 | """ |
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[6360] | 55 | |
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[2253] | 56 | ##FIXME (DSG-DSG) Is the dict format mentioned above a list of a numeric array? |
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| 57 | # Needs to be defined |
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| 58 | |
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| 59 | |
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| 60 | from string import find, rfind |
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| 61 | from os.path import splitext |
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[6360] | 62 | import exceptions |
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[2253] | 63 | |
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[6074] | 64 | from anuga.coordinate_transforms.geo_reference import Geo_reference, TITLE, \ |
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| 65 | TitleError |
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[6086] | 66 | from anuga.config import netcdf_mode_r, netcdf_mode_w, netcdf_mode_a |
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[6304] | 67 | from anuga.config import netcdf_float, netcdf_char, netcdf_int |
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[6074] | 68 | |
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[6360] | 69 | from Scientific.IO.NetCDF import NetCDFFile |
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[6086] | 70 | |
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[6360] | 71 | import numpy as num |
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[6304] | 72 | |
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[6360] | 73 | |
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[2253] | 74 | class TitleAmountError(exceptions.Exception): pass |
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| 75 | |
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[6074] | 76 | |
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[2253] | 77 | NOMAXAREA=-999 |
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| 78 | |
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[6074] | 79 | |
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| 80 | ## |
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| 81 | # @brief Read a mesh file (.tsh or .msh) and return a dictionary. |
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| 82 | # @param ofile Path to the file to read. |
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| 83 | # @return A dictionary of data from the input file. |
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| 84 | # @note Throws IOError if can't read file. |
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| 85 | # @note This is used by pmesh. |
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[2253] | 86 | def import_mesh_file(ofile): |
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[6304] | 87 | """Read a mesh file, either .tsh or .msh |
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[6074] | 88 | |
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[2253] | 89 | Note: will throw an IOError if it can't load the file. |
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| 90 | """ |
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[6304] | 91 | |
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[2253] | 92 | try: |
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[6304] | 93 | if ofile[-4:] == ".tsh": |
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[2253] | 94 | dict = _read_tsh_file(ofile) |
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[6304] | 95 | elif ofile[-4:] == ".msh": |
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[2253] | 96 | dict = _read_msh_file(ofile) |
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[6074] | 97 | else: |
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| 98 | msg = 'Extension .%s is unknown' % ofile[-4:] |
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[2253] | 99 | raise IOError, msg |
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[6074] | 100 | #FIXME No test for ValueError |
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| 101 | except (TitleError, SyntaxError, IndexError, ValueError): |
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[6304] | 102 | msg = 'File could not be opened' |
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| 103 | raise IOError, msg |
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[2253] | 104 | return dict |
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| 105 | |
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| 106 | |
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[6074] | 107 | ## |
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| 108 | # @brief Write a mesh file from a dictionary. |
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| 109 | # @param ofile The path of the mesh file to write. |
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| 110 | # @param mesh_dict Dictionary containing data to write to output mesh file. |
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| 111 | # @note Raises IOError if file extension is unrecognized. |
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| 112 | def export_mesh_file(ofile, mesh_dict): |
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[6304] | 113 | """Write a mesh file given a dictionary. |
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[6074] | 114 | |
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| 115 | First line: <# of vertices> <# of attributes> |
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[2253] | 116 | Following lines: <vertex #> <x> <y> [attributes] |
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[6074] | 117 | One line: <# of triangles> |
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| 118 | Following lines: <triangle #> <vertex #> <vertex #> <vertex #> |
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| 119 | <neigbouring triangle #> <neigbouring triangle #> |
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| 120 | <neigbouring triangle #> [attribute of region] |
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| 121 | One line: <# of segments> |
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[2253] | 122 | Following lines: <segment #> <vertex #> <vertex #> [boundary tag] |
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| 123 | """ |
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[6074] | 124 | |
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| 125 | # Ensure that if required key isn't present, we add it with [] value. |
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| 126 | # .setdefault() for dictionaries was added in python 2.0. |
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| 127 | # The only other neat way to do this is to override the dictionary |
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| 128 | # .__getitem__() method to return [] if key not found. |
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| 129 | reqd_keys = ['points', 'point_attributes', 'outline_segments', |
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| 130 | 'outline_segment_tags', 'holes', 'regions', 'region_tags', |
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| 131 | 'region_max_areas', 'vertices', 'vertex_attributes', |
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| 132 | 'vertex_attribute_titles', 'segments', 'segment_tags', |
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| 133 | 'triangles', 'triangle_tags', 'triangle_neighbors'] |
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| 134 | |
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| 135 | for k in reqd_keys: |
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| 136 | mesh_dict.setdefault(k, []) |
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| 137 | |
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| 138 | # hand-off to appropriate function |
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[2253] | 139 | if (ofile[-4:] == ".tsh"): |
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[6304] | 140 | _write_tsh_file(ofile, mesh_dict) |
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[2253] | 141 | elif (ofile[-4:] == ".msh"): |
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| 142 | _write_msh_file(ofile, mesh_dict) |
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| 143 | else: |
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[6304] | 144 | msg = 'Unknown file type %s ' % ofile |
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[6074] | 145 | raise IOError, msg |
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[2253] | 146 | |
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[6074] | 147 | |
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| 148 | ## |
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[6304] | 149 | # @brief Read a mesh file into a dictionary. |
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[6074] | 150 | # @param ofile Path of the file to read. |
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[6360] | 151 | # @return Points dictionary from the mesh (.tsh) file. |
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[2253] | 152 | def _read_tsh_file(ofile): |
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[6304] | 153 | """Read the text file format for meshes""" |
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[6074] | 154 | |
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| 155 | fd = open(ofile, 'r') |
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[2253] | 156 | dict = _read_triangulation(fd) |
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| 157 | dict_mesh = _read_outline(fd) |
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| 158 | for element in dict_mesh.keys(): |
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| 159 | dict[element] = dict_mesh[element] |
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| 160 | fd.close() |
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[6074] | 161 | |
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[2253] | 162 | return dict |
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| 163 | |
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[6074] | 164 | |
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| 165 | ## |
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[6360] | 166 | # @brief Read triangulation data from a file, leave file open. |
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[6074] | 167 | # @param fd An open descriptor of the file to read. |
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| 168 | # @return A dictionary ... |
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[2253] | 169 | def _read_triangulation(fd): |
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[6304] | 170 | """Read the generated triangulation, NOT the outline.""" |
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[6074] | 171 | |
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[2253] | 172 | delimiter = " " |
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[6074] | 173 | |
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| 174 | # loading the point info |
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[2253] | 175 | line = fd.readline() |
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| 176 | fragments = line.split() |
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[6304] | 177 | if fragments == []: |
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[2253] | 178 | NumOfVertices = 0 |
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| 179 | NumOfVertAttributes = 0 |
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| 180 | else: |
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| 181 | NumOfVertices = fragments[0] |
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| 182 | NumOfVertAttributes = fragments[1] |
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| 183 | points = [] |
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| 184 | pointattributes = [] |
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[6074] | 185 | for index in range(int(NumOfVertices)): |
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[2253] | 186 | fragments = fd.readline().split() |
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[6304] | 187 | fragments.pop(0) # pop off the index |
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[6074] | 188 | |
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[6304] | 189 | # pop the x & y off so we're left with a list of attributes |
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[6074] | 190 | vert = [float(fragments.pop(0)), float(fragments.pop(0))] |
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[2253] | 191 | points.append(vert) |
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| 192 | apointattributes = [] |
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| 193 | for fragment in fragments: |
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| 194 | apointattributes.append(float(fragment)) |
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[4902] | 195 | if apointattributes != []: |
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| 196 | pointattributes.append(apointattributes) |
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[6074] | 197 | |
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| 198 | # loading the point title info |
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[2253] | 199 | line = fd.readline() |
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| 200 | vertTitle = [] |
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[6074] | 201 | for index in range(int(NumOfVertAttributes)): |
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| 202 | fragments = fd.readline().strip() |
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[2253] | 203 | vertTitle.append(fragments) |
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[6074] | 204 | |
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| 205 | # loading the triangle info |
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[2253] | 206 | line = fd.readline() |
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| 207 | fragments = line.split() |
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| 208 | NumOfTriangles = fragments[0] |
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| 209 | triangles = [] |
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| 210 | triangleattributes = [] |
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| 211 | triangleneighbors = [] |
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[6074] | 212 | for index in range(int(NumOfTriangles)): |
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[2253] | 213 | line = fd.readline() |
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[6304] | 214 | line.strip() # so we can get the region string |
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[2253] | 215 | fragments = line.split() |
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[6304] | 216 | fragments.pop(0) # pop off the index |
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[6074] | 217 | |
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| 218 | tri = [int(fragments[0]), int(fragments[1]), int(fragments[2])] |
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[2253] | 219 | triangles.append(tri) |
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[6074] | 220 | neighbors = [int(fragments[3]), int(fragments[4]), int(fragments[5])] |
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[2253] | 221 | triangleneighbors.append(neighbors) |
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[6304] | 222 | for x in range(7): # remove index [<vertex #>] [<neigbouring tri #>] |
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| 223 | line = line[find(line, delimiter):] # remove index |
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[2253] | 224 | line = line.lstrip() |
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| 225 | stringtag = line.strip() |
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| 226 | triangleattributes.append(stringtag) |
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[6074] | 227 | |
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| 228 | # loading the segment info |
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[2253] | 229 | line = fd.readline() |
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| 230 | fragments = line.split() |
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| 231 | NumOfSegments = fragments[0] |
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| 232 | segments = [] |
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| 233 | segmenttags = [] |
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[6074] | 234 | for index in range(int(NumOfSegments)): |
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[2253] | 235 | line = fd.readline() |
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[6304] | 236 | line.strip() # to get the segment string |
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[2253] | 237 | fragments = line.split() |
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[6304] | 238 | fragments.pop(0) #pop off the index |
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[6074] | 239 | seg = [int(fragments[0]), int(fragments[1])] |
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[2253] | 240 | segments.append(seg) |
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[6074] | 241 | line = line[find(line, delimiter):] # remove index |
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[2253] | 242 | line = line.lstrip() |
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[6074] | 243 | line = line[find(line, delimiter):] # remove x |
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[2253] | 244 | line = line.lstrip() |
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[6074] | 245 | line = line[find(line, delimiter):] # remove y |
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[2253] | 246 | stringtag = line.strip() |
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| 247 | segmenttags.append(stringtag) |
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| 248 | |
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| 249 | meshDict = {} |
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| 250 | meshDict['vertices'] = points |
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[4902] | 251 | if pointattributes == []: |
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| 252 | meshDict['vertex_attributes'] = None |
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| 253 | else: |
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| 254 | meshDict['vertex_attributes'] = pointattributes |
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[2253] | 255 | meshDict['triangles'] = triangles |
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| 256 | meshDict['triangle_tags'] = triangleattributes |
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[6074] | 257 | meshDict['triangle_neighbors'] = triangleneighbors |
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| 258 | meshDict['segments'] = segments |
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[2253] | 259 | meshDict['segment_tags'] = segmenttags |
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| 260 | meshDict['vertex_attribute_titles'] = vertTitle |
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[6074] | 261 | |
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[2253] | 262 | return meshDict |
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[6074] | 263 | |
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| 264 | |
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| 265 | ## |
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[6360] | 266 | # @brief Read a mesh outline file. |
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[6074] | 267 | # @param fd An open descriptor of the file to read. |
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[6360] | 268 | # @return A Points dictionary. |
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[6074] | 269 | # @note If file has no mesh info, an empty dict will be returned. |
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[2253] | 270 | def _read_outline(fd): |
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[6304] | 271 | """Read a mesh file outline. |
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| 272 | |
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| 273 | Note, if a file has no mesh info, it can still be read - |
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| 274 | the meshdic returned will be 'empty'. |
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[2253] | 275 | """ |
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[6074] | 276 | |
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[6304] | 277 | delimiter = " " # warning: split() calls are using default whitespace |
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[6074] | 278 | |
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| 279 | # loading the point info |
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[2253] | 280 | line = fd.readline() |
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| 281 | fragments = line.split() |
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[6304] | 282 | if fragments == []: |
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[2253] | 283 | NumOfVertices = 0 |
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| 284 | NumOfVertAttributes = 0 |
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| 285 | else: |
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| 286 | NumOfVertices = fragments[0] |
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| 287 | NumOfVertAttributes = fragments[1] |
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| 288 | points = [] |
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| 289 | pointattributes = [] |
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[6074] | 290 | for index in range(int(NumOfVertices)): |
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| 291 | fragments = fd.readline().split() |
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[6304] | 292 | fragments.pop(0) # pop off the index |
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| 293 | # pop the x & y off so we're left with a list of attributes |
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[6074] | 294 | vert = [float(fragments.pop(0)), float(fragments.pop(0))] |
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[2253] | 295 | points.append(vert) |
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[6074] | 296 | apointattributes = [] |
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[2253] | 297 | for fragment in fragments: |
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| 298 | apointattributes.append(float(fragment)) |
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| 299 | pointattributes.append(apointattributes) |
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| 300 | |
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[6074] | 301 | # loading the segment info |
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[2253] | 302 | line = fd.readline() |
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| 303 | fragments = line.split() |
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[6304] | 304 | if fragments == []: |
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[2253] | 305 | NumOfSegments = 0 |
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| 306 | else: |
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| 307 | NumOfSegments = fragments[0] |
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| 308 | segments = [] |
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| 309 | segmenttags = [] |
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[6074] | 310 | for index in range(int(NumOfSegments)): |
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[2253] | 311 | line = fd.readline() |
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| 312 | fragments = line.split() |
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[6304] | 313 | fragments.pop(0) # pop off the index |
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[6074] | 314 | seg = [int(fragments[0]), int(fragments[1])] |
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[2253] | 315 | segments.append(seg) |
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[6074] | 316 | line = line[find(line, delimiter):] # remove index |
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[2253] | 317 | line = line.lstrip() |
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[6074] | 318 | line = line[find(line, delimiter):] # remove x |
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[2253] | 319 | line = line.lstrip() |
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[6074] | 320 | line = line[find(line, delimiter):] # remove y |
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[2253] | 321 | stringtag = line.strip() |
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[6074] | 322 | segmenttags.append(stringtag) |
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[2253] | 323 | |
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[6074] | 324 | # loading the hole info |
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[2253] | 325 | line = fd.readline() |
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| 326 | fragments = line.split() |
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[6074] | 327 | if fragments == []: |
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[2253] | 328 | numOfHoles = 0 |
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| 329 | else: |
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| 330 | numOfHoles = fragments[0] |
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| 331 | holes = [] |
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[6074] | 332 | for index in range(int(numOfHoles)): |
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[2253] | 333 | fragments = fd.readline().split() |
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| 334 | fragments.pop(0) #pop off the index |
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[6074] | 335 | hole = [float(fragments[0]), float(fragments[1])] |
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[2253] | 336 | holes.append(hole) |
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| 337 | |
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[6074] | 338 | # loading the region info |
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[2253] | 339 | line = fd.readline() |
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| 340 | fragments = line.split() |
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[6074] | 341 | if fragments == []: |
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[2253] | 342 | numOfRegions = 0 |
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| 343 | else: |
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| 344 | numOfRegions = fragments[0] |
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| 345 | regions = [] |
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| 346 | regionattributes = [] |
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| 347 | for index in range(int(numOfRegions)): |
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| 348 | line = fd.readline() |
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| 349 | fragments = line.split() |
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[6304] | 350 | fragments.pop(0) # pop off the index |
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[6074] | 351 | region = [float(fragments[0]), float(fragments[1])] |
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[2253] | 352 | regions.append(region) |
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| 353 | |
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[6074] | 354 | line = line[find(line, delimiter):] # remove index |
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[2253] | 355 | line = line.lstrip() |
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[6074] | 356 | line = line[find(line, delimiter):] # remove x |
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[2253] | 357 | line = line.lstrip() |
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[6074] | 358 | line = line[find(line, delimiter):] # remove y |
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[2253] | 359 | stringtag = line.strip() |
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| 360 | regionattributes.append(stringtag) |
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[6074] | 361 | |
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[2253] | 362 | regionmaxareas = [] |
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| 363 | line = fd.readline() |
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[6304] | 364 | for index in range(int(numOfRegions)): # Read in the Max area info |
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[2253] | 365 | line = fd.readline() |
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| 366 | fragments = line.split() |
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| 367 | # The try is here for format compatibility |
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| 368 | try: |
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[6304] | 369 | fragments.pop(0) # pop off the index |
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| 370 | if len(fragments) == 0: # no max area |
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[2253] | 371 | regionmaxareas.append(None) |
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| 372 | else: |
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| 373 | regionmaxareas.append(float(fragments[0])) |
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| 374 | except IndexError, e: |
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| 375 | regionmaxareas.append(None) |
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| 376 | |
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| 377 | try: |
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| 378 | geo_reference = Geo_reference(ASCIIFile=fd) |
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| 379 | except: |
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[6074] | 380 | #geo_ref not compulsory |
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[2253] | 381 | geo_reference = None |
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[6074] | 382 | |
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[2253] | 383 | meshDict = {} |
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| 384 | meshDict['points'] = points |
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| 385 | meshDict['point_attributes'] = pointattributes |
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[6074] | 386 | meshDict['outline_segments'] = segments |
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[2253] | 387 | meshDict['outline_segment_tags'] = segmenttags |
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| 388 | meshDict['holes'] = holes |
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| 389 | meshDict['regions'] = regions |
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| 390 | meshDict['region_tags'] = regionattributes |
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| 391 | meshDict['region_max_areas'] = regionmaxareas |
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| 392 | meshDict['geo_reference'] = geo_reference |
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[6074] | 393 | |
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[2253] | 394 | return meshDict |
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| 395 | |
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[6074] | 396 | |
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| 397 | ## |
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| 398 | # @brief Write an ASCII triangulation file. |
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| 399 | # @param fd An open descriptor to the file to write. |
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| 400 | # @param gen_dict Dictionary containing data to write. |
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| 401 | def _write_ASCII_triangulation(fd, gen_dict): |
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[2253] | 402 | vertices = gen_dict['vertices'] |
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| 403 | vertices_attributes = gen_dict['vertex_attributes'] |
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| 404 | try: |
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[6074] | 405 | vertices_attribute_titles = gen_dict['vertex_attribute_titles'] |
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[2253] | 406 | except KeyError, e: |
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[6074] | 407 | #FIXME is this the best way? |
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[2253] | 408 | if vertices_attributes == [] or vertices_attributes[0] == []: |
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| 409 | vertices_attribute_titles = [] |
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| 410 | else: |
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[6074] | 411 | raise KeyError, e |
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| 412 | |
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[2253] | 413 | triangles = gen_dict['triangles'] |
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| 414 | triangles_attributes = gen_dict['triangle_tags'] |
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| 415 | triangle_neighbors = gen_dict['triangle_neighbors'] |
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[6074] | 416 | |
---|
[2253] | 417 | segments = gen_dict['segments'] |
---|
| 418 | segment_tags = gen_dict['segment_tags'] |
---|
[6074] | 419 | |
---|
[2253] | 420 | numVert = str(len(vertices)) |
---|
[4902] | 421 | # Don't understand why we have to do vertices_attributes[0] is None, |
---|
| 422 | # but it doesn't work otherwise... |
---|
[6304] | 423 | if (vertices_attributes == None or |
---|
| 424 | numVert == "0" or |
---|
| 425 | len(vertices_attributes) == 0): |
---|
[2253] | 426 | numVertAttrib = "0" |
---|
| 427 | else: |
---|
| 428 | numVertAttrib = str(len(vertices_attributes[0])) |
---|
| 429 | |
---|
[6074] | 430 | fd.write(numVert + " " + numVertAttrib + |
---|
| 431 | " # <# of verts> <# of vert attributes>, next lines <vertex #> " |
---|
| 432 | "<x> <y> [attributes] ...Triangulation Vertices...\n") |
---|
| 433 | |
---|
| 434 | #<vertex #> <x> <y> [attributes] |
---|
[4496] | 435 | index = 0 |
---|
[2253] | 436 | for vert in vertices: |
---|
| 437 | attlist = "" |
---|
[6074] | 438 | |
---|
| 439 | if vertices_attributes == None or vertices_attributes == []: |
---|
[4496] | 440 | attlist = "" |
---|
| 441 | else: |
---|
| 442 | for att in vertices_attributes[index]: |
---|
[6074] | 443 | attlist = attlist + str(att) + " " |
---|
[2253] | 444 | attlist.strip() |
---|
[6074] | 445 | fd.write(str(index) + " " + str(vert[0]) + " " + str(vert[1]) |
---|
| 446 | + " " + attlist + "\n") |
---|
[2253] | 447 | index += 1 |
---|
| 448 | |
---|
[6074] | 449 | # write comments for title |
---|
| 450 | fd.write("# attribute column titles ...Triangulation Vertex Titles...\n") |
---|
[2253] | 451 | for title in vertices_attribute_titles: |
---|
| 452 | fd.write(title + "\n") |
---|
[6074] | 453 | |
---|
[6304] | 454 | # <# of triangles> |
---|
[2253] | 455 | n = len(triangles) |
---|
[6074] | 456 | fd.write(str(n) |
---|
| 457 | + " # <# of triangles>, next lines <triangle #> [<vertex #>] " |
---|
| 458 | "[<neigbouring triangle #>] [attribute of region] ..." |
---|
| 459 | "Triangulation Triangles...\n") |
---|
| 460 | |
---|
| 461 | # <triangle #> <vertex #> <vertex #> <vertex #> <neigbouring triangle #> |
---|
| 462 | # <neigbouring triangle #> <neigbouring triangle #> [attribute of region] |
---|
[2253] | 463 | for index in range(n): |
---|
| 464 | neighbors = "" |
---|
| 465 | tri = triangles[index] |
---|
[4496] | 466 | if triangle_neighbors == []: |
---|
| 467 | neighbors = "-1 -1 -1 " |
---|
| 468 | else: |
---|
| 469 | for neighbor in triangle_neighbors[index]: |
---|
| 470 | if neighbor: |
---|
| 471 | neighbors += str(neighbor) + " " |
---|
[2253] | 472 | else: |
---|
[4496] | 473 | if neighbor == 0: |
---|
| 474 | neighbors += "0 " |
---|
| 475 | else: |
---|
| 476 | neighbors += "-1 " |
---|
[6304] | 477 | # Warning even though a list is passed, only the first value |
---|
| 478 | # is written. There's an assumption that the list only |
---|
[2253] | 479 | # contains one item. This assumption is made since the |
---|
[6304] | 480 | # dict that's being passed around is also be used to communicate |
---|
[2253] | 481 | # with triangle, and it seems to have the option of returning |
---|
| 482 | # more than one value for triangle attributex |
---|
[6304] | 483 | if (triangles_attributes == None or |
---|
| 484 | triangles_attributes == [] or |
---|
| 485 | triangles_attributes[index] == ['']): |
---|
[2253] | 486 | att = "" |
---|
| 487 | else: |
---|
| 488 | att = str(triangles_attributes[index]) |
---|
| 489 | fd.write(str(index) + " " |
---|
[6074] | 490 | + str(tri[0]) + " " |
---|
| 491 | + str(tri[1]) + " " |
---|
| 492 | + str(tri[2]) + " " |
---|
[2253] | 493 | + neighbors + " " |
---|
| 494 | + att + "\n") |
---|
[6074] | 495 | |
---|
[6304] | 496 | # One line: <# of segments> |
---|
[6074] | 497 | fd.write(str(len(segments)) + |
---|
| 498 | " # <# of segments>, next lines <segment #> <vertex #> " |
---|
| 499 | "<vertex #> [boundary tag] ...Triangulation Segments...\n") |
---|
| 500 | |
---|
[6304] | 501 | # Following lines: <segment #> <vertex #> <vertex #> [boundary tag] |
---|
[2253] | 502 | for i in range(len(segments)): |
---|
| 503 | seg = segments[i] |
---|
| 504 | fd.write(str(i) + " " |
---|
[6074] | 505 | + str(seg[0]) + " " |
---|
| 506 | + str(seg[1]) + " " |
---|
[2253] | 507 | + str(segment_tags[i]) + "\n") |
---|
| 508 | |
---|
| 509 | |
---|
[6074] | 510 | ## |
---|
| 511 | # @brief Write triangulation and outline to a .tsh file. |
---|
| 512 | # @param ofile Path of the file to write. |
---|
| 513 | # @mesh_dict Dictionary of data to write. |
---|
| 514 | def _write_tsh_file(ofile, mesh_dict): |
---|
| 515 | fd = open(ofile, 'w') |
---|
| 516 | _write_ASCII_triangulation(fd, mesh_dict) |
---|
| 517 | _write_ASCII_outline(fd, mesh_dict) |
---|
| 518 | fd.close() |
---|
[2253] | 519 | |
---|
[6074] | 520 | |
---|
| 521 | ## |
---|
| 522 | # @brief Write an ASCII outline to a file. |
---|
| 523 | # @param fd An open descriptor of the file to write. |
---|
| 524 | # @param dict Dictionary holding data to write. |
---|
| 525 | def _write_ASCII_outline(fd, dict): |
---|
[2253] | 526 | points = dict['points'] |
---|
| 527 | point_attributes = dict['point_attributes'] |
---|
| 528 | segments = dict['outline_segments'] |
---|
| 529 | segment_tags = dict['outline_segment_tags'] |
---|
| 530 | holes = dict['holes'] |
---|
| 531 | regions = dict['regions'] |
---|
| 532 | region_tags = dict['region_tags'] |
---|
| 533 | region_max_areas = dict['region_max_areas'] |
---|
[6074] | 534 | |
---|
[2253] | 535 | num_points = str(len(points)) |
---|
[6304] | 536 | if (num_points == '0'): |
---|
| 537 | num_point_atts = '0' |
---|
[2253] | 538 | else: |
---|
| 539 | num_point_atts = str(len(point_attributes[0])) |
---|
[6074] | 540 | |
---|
[6304] | 541 | fd.write(num_points + ' ' + num_point_atts + |
---|
| 542 | ' # <# of verts> <# of vert attributes>, next lines <vertex #> ' |
---|
| 543 | '<x> <y> [attributes] ...Mesh Vertices...\n') |
---|
[6074] | 544 | |
---|
[2253] | 545 | # <x> <y> [attributes] |
---|
[6304] | 546 | for i, point in enumerate(points): |
---|
| 547 | attlist = '' |
---|
[2253] | 548 | for att in point_attributes[i]: |
---|
[6304] | 549 | attlist = attlist + str(att) + ' ' |
---|
[2253] | 550 | attlist.strip() |
---|
[6304] | 551 | fd.write(str(i) + ' ' + str(point[0]) + ' ' + str(point[1]) + ' ' + |
---|
| 552 | attlist + '\n') |
---|
[6074] | 553 | |
---|
[6304] | 554 | # One line: <# of segments> |
---|
[6074] | 555 | fd.write(str(len(segments)) + |
---|
[6304] | 556 | ' # <# of segments>, next lines <segment #> <vertex #> ' |
---|
| 557 | '<vertex #> [boundary tag] ...Mesh Segments...\n') |
---|
[6074] | 558 | |
---|
[6304] | 559 | # Following lines: <vertex #> <vertex #> [boundary tag] |
---|
[2253] | 560 | for i,seg in enumerate(segments): |
---|
[6304] | 561 | fd.write(str(i) + ' ' + str(seg[0]) + ' ' + str(seg[1]) + ' ' + |
---|
| 562 | str(segment_tags[i]) + '\n') |
---|
[2253] | 563 | |
---|
[6304] | 564 | # One line: <# of holes> |
---|
[6074] | 565 | fd.write(str(len(holes)) + |
---|
[6304] | 566 | ' # <# of holes>, next lines <Hole #> <x> <y> ...Mesh Holes...\n') |
---|
[2253] | 567 | # <x> <y> |
---|
| 568 | for i,h in enumerate(holes): |
---|
[6304] | 569 | fd.write(str(i) + ' ' + str(h[0]) + ' ' + str(h[1]) + '\n') |
---|
[6074] | 570 | |
---|
[6304] | 571 | # One line: <# of regions> |
---|
[6074] | 572 | fd.write(str(len(regions)) + |
---|
[6304] | 573 | ' # <# of regions>, next lines <Region #> <x> <y> <tag>' |
---|
| 574 | '...Mesh Regions...\n') |
---|
[6074] | 575 | |
---|
[2253] | 576 | # <index> <x> <y> <tag> |
---|
| 577 | for i,r in enumerate(regions): |
---|
[6304] | 578 | fd.write(str(i) + ' ' + str(r[0]) + ' ' + str(r[1])+ ' ' + |
---|
| 579 | str(region_tags[i]) + '\n') |
---|
[6074] | 580 | |
---|
[6304] | 581 | # <index> [<MaxArea>|''] |
---|
[6074] | 582 | |
---|
[6304] | 583 | # One line: <# of regions> |
---|
[6074] | 584 | fd.write(str(len(regions)) + |
---|
[6304] | 585 | ' # <# of regions>, next lines <Region #> [Max Area] ' |
---|
| 586 | '...Mesh Regions...\n') |
---|
[2253] | 587 | for i,r in enumerate(regions): |
---|
| 588 | area = str(region_max_areas[i]) |
---|
[6074] | 589 | |
---|
[6304] | 590 | fd.write(str(i) + ' ' + area + '\n') |
---|
[2253] | 591 | |
---|
| 592 | # geo_reference info |
---|
| 593 | if dict.has_key('geo_reference') and not dict['geo_reference'] is None: |
---|
| 594 | dict['geo_reference'].write_ASCII(fd) |
---|
| 595 | |
---|
[6074] | 596 | |
---|
| 597 | ## |
---|
| 598 | # @brief Write a .msh file. |
---|
| 599 | # @param file Path to the file to write. |
---|
| 600 | # @param mesh Dictionary holding data to write. |
---|
[2253] | 601 | def _write_msh_file(file_name, mesh): |
---|
[6074] | 602 | """Write .msh NetCDF file |
---|
[2253] | 603 | |
---|
| 604 | WARNING: This function mangles the mesh data structure |
---|
| 605 | """ |
---|
[6074] | 606 | |
---|
[4899] | 607 | # FIXME(Ole and John): We ran into a problem on Bogong (64 bit) |
---|
| 608 | # where integers appeared as arrays. This may be similar to |
---|
| 609 | # problem seen by Steve in changeset:2778 where he had to wrap |
---|
| 610 | # them in int. Now we are trying with the native Integer format |
---|
| 611 | # (Int == 'l' == Int64). However, that caused casting errors, when |
---|
| 612 | # 64bit arrays are to be assigned to their NetCDF counterparts. It |
---|
| 613 | # seems that the NetCDF arrays are 32bit even though they are |
---|
| 614 | # created with the type Int64. Need to look at the NetCDF library |
---|
| 615 | # in more detail. |
---|
[6074] | 616 | |
---|
[6304] | 617 | IntType = num.int32 |
---|
[4099] | 618 | #IntType = Int |
---|
[6074] | 619 | |
---|
[2253] | 620 | #the triangulation |
---|
[6304] | 621 | mesh['vertices'] = num.array(mesh['vertices'], num.float) |
---|
[4902] | 622 | if mesh['vertex_attributes'] != None: |
---|
| 623 | mesh['vertex_attributes'] = \ |
---|
[6304] | 624 | num.array(mesh['vertex_attributes'], num.float) |
---|
[6074] | 625 | mesh['vertex_attribute_titles'] = \ |
---|
[6304] | 626 | num.array(mesh['vertex_attribute_titles'], num.character) |
---|
[6166] | 627 | mesh['segments'] = num.array(mesh['segments'], IntType) |
---|
[6360] | 628 | print ("Before num.array(), mesh['segment_tags']=%s" |
---|
| 629 | % str(mesh['segment_tags'])) |
---|
[6304] | 630 | mesh['segment_tags'] = num.array(mesh['segment_tags'], num.character) |
---|
[6360] | 631 | print ("After num.array(), mesh['segment_tags']=%s" |
---|
| 632 | % str(mesh['segment_tags'])) |
---|
| 633 | print "mesh['segment_tags'].shape=%s" % str(mesh['segment_tags'].shape) |
---|
[6166] | 634 | mesh['triangles'] = num.array(mesh['triangles'], IntType) |
---|
[6304] | 635 | mesh['triangle_tags'] = num.array(mesh['triangle_tags']) |
---|
[6074] | 636 | mesh['triangle_neighbors'] = \ |
---|
[6166] | 637 | num.array(mesh['triangle_neighbors'], IntType) |
---|
[6074] | 638 | |
---|
| 639 | #the outline |
---|
[6304] | 640 | mesh['points'] = num.array(mesh['points'], num.float) |
---|
| 641 | mesh['point_attributes'] = num.array(mesh['point_attributes'], num.float) |
---|
[6166] | 642 | mesh['outline_segments'] = num.array(mesh['outline_segments'], IntType) |
---|
[6074] | 643 | mesh['outline_segment_tags'] = \ |
---|
[6304] | 644 | num.array(mesh['outline_segment_tags'], num.character) |
---|
| 645 | mesh['holes'] = num.array(mesh['holes'], num.float) |
---|
| 646 | mesh['regions'] = num.array(mesh['regions'], num.float) |
---|
| 647 | mesh['region_tags'] = num.array(mesh['region_tags'], num.character) |
---|
| 648 | mesh['region_max_areas'] = num.array(mesh['region_max_areas'], num.float) |
---|
[6074] | 649 | |
---|
[2253] | 650 | # NetCDF file definition |
---|
| 651 | try: |
---|
[6086] | 652 | outfile = NetCDFFile(file_name, netcdf_mode_w) |
---|
[2253] | 653 | except IOError: |
---|
[6074] | 654 | msg = 'File %s could not be created' % file_name |
---|
[6304] | 655 | raise Exception, msg |
---|
[6074] | 656 | |
---|
[2253] | 657 | #Create new file |
---|
| 658 | outfile.institution = 'Geoscience Australia' |
---|
[6304] | 659 | outfile.description = 'NetCDF format for compact and portable storage ' + \ |
---|
[6074] | 660 | 'of spatial point data' |
---|
| 661 | |
---|
[2253] | 662 | # dimension definitions - fixed |
---|
[6304] | 663 | outfile.createDimension('num_of_dimensions', 2) # This is 2d data |
---|
| 664 | outfile.createDimension('num_of_segment_ends', 2) # Segs have two points |
---|
[2253] | 665 | outfile.createDimension('num_of_triangle_vertices', 3) |
---|
| 666 | outfile.createDimension('num_of_triangle_faces', 3) |
---|
| 667 | outfile.createDimension('num_of_region_max_area', 1) |
---|
| 668 | |
---|
| 669 | # Create dimensions, variables and set the variables |
---|
[6074] | 670 | |
---|
[2253] | 671 | # trianglulation |
---|
| 672 | # vertices |
---|
| 673 | if (mesh['vertices'].shape[0] > 0): |
---|
| 674 | outfile.createDimension('num_of_vertices', mesh['vertices'].shape[0]) |
---|
[6304] | 675 | outfile.createVariable('vertices', netcdf_float, ('num_of_vertices', |
---|
| 676 | 'num_of_dimensions')) |
---|
[2253] | 677 | outfile.variables['vertices'][:] = mesh['vertices'] |
---|
[6304] | 678 | if (mesh['vertex_attributes'] != None and |
---|
| 679 | (mesh['vertex_attributes'].shape[0] > 0 and |
---|
| 680 | mesh['vertex_attributes'].shape[1] > 0)): |
---|
[2253] | 681 | outfile.createDimension('num_of_vertex_attributes', |
---|
| 682 | mesh['vertex_attributes'].shape[1]) |
---|
| 683 | outfile.createDimension('num_of_vertex_attribute_title_chars', |
---|
| 684 | mesh['vertex_attribute_titles'].shape[1]) |
---|
| 685 | outfile.createVariable('vertex_attributes', |
---|
[6304] | 686 | netcdf_float, |
---|
[2253] | 687 | ('num_of_vertices', |
---|
[6074] | 688 | 'num_of_vertex_attributes')) |
---|
[2253] | 689 | outfile.createVariable('vertex_attribute_titles', |
---|
[6304] | 690 | netcdf_char, |
---|
[6074] | 691 | ('num_of_vertex_attributes', |
---|
| 692 | 'num_of_vertex_attribute_title_chars')) |
---|
[2253] | 693 | outfile.variables['vertex_attributes'][:] = \ |
---|
[6074] | 694 | mesh['vertex_attributes'] |
---|
[2253] | 695 | outfile.variables['vertex_attribute_titles'][:] = \ |
---|
| 696 | mesh['vertex_attribute_titles'] |
---|
[6074] | 697 | |
---|
[2253] | 698 | # segments |
---|
[6074] | 699 | if (mesh['segments'].shape[0] > 0): |
---|
| 700 | outfile.createDimension('num_of_segments', mesh['segments'].shape[0]) |
---|
[6304] | 701 | outfile.createVariable('segments', netcdf_int, |
---|
[2253] | 702 | ('num_of_segments', 'num_of_segment_ends')) |
---|
| 703 | outfile.variables['segments'][:] = mesh['segments'] |
---|
[6304] | 704 | if mesh['segment_tags'].shape[1] > 0: |
---|
[2253] | 705 | outfile.createDimension('num_of_segment_tag_chars', |
---|
| 706 | mesh['segment_tags'].shape[1]) |
---|
| 707 | outfile.createVariable('segment_tags', |
---|
[6304] | 708 | netcdf_char, |
---|
[2253] | 709 | ('num_of_segments', |
---|
| 710 | 'num_of_segment_tag_chars')) |
---|
| 711 | outfile.variables['segment_tags'][:] = mesh['segment_tags'] |
---|
[6074] | 712 | |
---|
| 713 | # triangles |
---|
[2253] | 714 | if (mesh['triangles'].shape[0] > 0): |
---|
[6074] | 715 | outfile.createDimension('num_of_triangles', mesh['triangles'].shape[0]) |
---|
[6304] | 716 | outfile.createVariable('triangles', netcdf_int, |
---|
[6074] | 717 | ('num_of_triangles', 'num_of_triangle_vertices')) |
---|
[6304] | 718 | outfile.createVariable('triangle_neighbors', netcdf_int, |
---|
[6074] | 719 | ('num_of_triangles', 'num_of_triangle_faces')) |
---|
[2253] | 720 | outfile.variables['triangles'][:] = mesh['triangles'] |
---|
| 721 | outfile.variables['triangle_neighbors'][:] = mesh['triangle_neighbors'] |
---|
[6304] | 722 | if (mesh['triangle_tags'] != None and |
---|
| 723 | (mesh['triangle_tags'].shape[1] > 0)): |
---|
[2253] | 724 | outfile.createDimension('num_of_triangle_tag_chars', |
---|
[6074] | 725 | mesh['triangle_tags'].shape[1]) |
---|
[6304] | 726 | outfile.createVariable('triangle_tags', netcdf_char, |
---|
[2253] | 727 | ('num_of_triangles', |
---|
| 728 | 'num_of_triangle_tag_chars')) |
---|
| 729 | outfile.variables['triangle_tags'][:] = mesh['triangle_tags'] |
---|
| 730 | |
---|
| 731 | # outline |
---|
| 732 | # points |
---|
| 733 | if (mesh['points'].shape[0] > 0): |
---|
| 734 | outfile.createDimension('num_of_points', mesh['points'].shape[0]) |
---|
[6304] | 735 | outfile.createVariable('points', netcdf_float, |
---|
| 736 | ('num_of_points', 'num_of_dimensions')) |
---|
[6074] | 737 | outfile.variables['points'][:] = mesh['points'] |
---|
| 738 | if mesh['point_attributes'].shape[0] > 0 \ |
---|
| 739 | and mesh['point_attributes'].shape[1] > 0: |
---|
[2253] | 740 | outfile.createDimension('num_of_point_attributes', |
---|
| 741 | mesh['point_attributes'].shape[1]) |
---|
[6304] | 742 | outfile.createVariable('point_attributes', netcdf_float, |
---|
[6074] | 743 | ('num_of_points', 'num_of_point_attributes')) |
---|
[2253] | 744 | outfile.variables['point_attributes'][:] = mesh['point_attributes'] |
---|
[6074] | 745 | |
---|
| 746 | # outline_segments |
---|
| 747 | if mesh['outline_segments'].shape[0] > 0: |
---|
[2253] | 748 | outfile.createDimension('num_of_outline_segments', |
---|
| 749 | mesh['outline_segments'].shape[0]) |
---|
[6304] | 750 | outfile.createVariable('outline_segments', netcdf_int, |
---|
[2253] | 751 | ('num_of_outline_segments', |
---|
| 752 | 'num_of_segment_ends')) |
---|
| 753 | outfile.variables['outline_segments'][:] = mesh['outline_segments'] |
---|
| 754 | if (mesh['outline_segment_tags'].shape[1] > 0): |
---|
| 755 | outfile.createDimension('num_of_outline_segment_tag_chars', |
---|
| 756 | mesh['outline_segment_tags'].shape[1]) |
---|
[6304] | 757 | outfile.createVariable('outline_segment_tags', netcdf_char, |
---|
[2253] | 758 | ('num_of_outline_segments', |
---|
| 759 | 'num_of_outline_segment_tag_chars')) |
---|
[6074] | 760 | outfile.variables['outline_segment_tags'][:] = \ |
---|
| 761 | mesh['outline_segment_tags'] |
---|
| 762 | |
---|
[2253] | 763 | # holes |
---|
| 764 | if (mesh['holes'].shape[0] > 0): |
---|
| 765 | outfile.createDimension('num_of_holes', mesh['holes'].shape[0]) |
---|
[6304] | 766 | outfile.createVariable('holes', netcdf_float, |
---|
| 767 | ('num_of_holes', 'num_of_dimensions')) |
---|
[2253] | 768 | outfile.variables['holes'][:] = mesh['holes'] |
---|
[6074] | 769 | |
---|
[2253] | 770 | # regions |
---|
| 771 | if (mesh['regions'].shape[0] > 0): |
---|
| 772 | outfile.createDimension('num_of_regions', mesh['regions'].shape[0]) |
---|
[6304] | 773 | outfile.createVariable('regions', netcdf_float, |
---|
| 774 | ('num_of_regions', 'num_of_dimensions')) |
---|
| 775 | outfile.createVariable('region_max_areas', netcdf_float, |
---|
| 776 | ('num_of_regions',)) |
---|
[2253] | 777 | outfile.variables['regions'][:] = mesh['regions'] |
---|
| 778 | outfile.variables['region_max_areas'][:] = mesh['region_max_areas'] |
---|
| 779 | if (mesh['region_tags'].shape[1] > 0): |
---|
| 780 | outfile.createDimension('num_of_region_tag_chars', |
---|
| 781 | mesh['region_tags'].shape[1]) |
---|
[6304] | 782 | outfile.createVariable('region_tags', netcdf_char, |
---|
[2253] | 783 | ('num_of_regions', |
---|
| 784 | 'num_of_region_tag_chars')) |
---|
| 785 | outfile.variables['region_tags'][:] = mesh['region_tags'] |
---|
| 786 | |
---|
| 787 | # geo_reference info |
---|
| 788 | if mesh.has_key('geo_reference') and not mesh['geo_reference'] == None: |
---|
| 789 | mesh['geo_reference'].write_NetCDF(outfile) |
---|
[6074] | 790 | |
---|
[2253] | 791 | outfile.close() |
---|
| 792 | |
---|
| 793 | |
---|
[6074] | 794 | ## |
---|
| 795 | # @brief Read a mesh file. |
---|
| 796 | # @param file_name Path to the file to read. |
---|
| 797 | # @return A dictionary containing the .msh file data. |
---|
[6304] | 798 | # @note Throws IOError if file not found. |
---|
[2253] | 799 | def _read_msh_file(file_name): |
---|
[6304] | 800 | """ Read in an msh file.""" |
---|
[2253] | 801 | |
---|
[6304] | 802 | #Check contents. Get NetCDF |
---|
[6074] | 803 | fd = open(file_name, 'r') |
---|
[2253] | 804 | fd.close() |
---|
| 805 | |
---|
[6304] | 806 | # throws prints to screen if file not present |
---|
[6086] | 807 | fid = NetCDFFile(file_name, netcdf_mode_r) |
---|
[2253] | 808 | mesh = {} |
---|
[6074] | 809 | |
---|
[6304] | 810 | # Get the variables - the triangulation |
---|
[2253] | 811 | try: |
---|
| 812 | mesh['vertices'] = fid.variables['vertices'][:] |
---|
| 813 | except KeyError: |
---|
[6304] | 814 | mesh['vertices'] = num.array([], num.int) #array default# |
---|
[6074] | 815 | |
---|
[2253] | 816 | try: |
---|
| 817 | mesh['vertex_attributes'] = fid.variables['vertex_attributes'][:] |
---|
| 818 | except KeyError: |
---|
[4902] | 819 | mesh['vertex_attributes'] = None |
---|
[6074] | 820 | |
---|
[2253] | 821 | mesh['vertex_attribute_titles'] = [] |
---|
| 822 | try: |
---|
| 823 | titles = fid.variables['vertex_attribute_titles'][:] |
---|
| 824 | for i, title in enumerate(titles): |
---|
| 825 | mesh['vertex_attribute_titles'].append(titles[i].tostring().strip()) |
---|
| 826 | except KeyError: |
---|
[6074] | 827 | pass |
---|
| 828 | |
---|
[2253] | 829 | try: |
---|
| 830 | mesh['segments'] = fid.variables['segments'][:] |
---|
| 831 | except KeyError: |
---|
[6304] | 832 | mesh['segments'] = num.array([], num.int) #array default# |
---|
[6074] | 833 | |
---|
[2253] | 834 | mesh['segment_tags'] =[] |
---|
| 835 | try: |
---|
| 836 | tags = fid.variables['segment_tags'][:] |
---|
| 837 | for i, tag in enumerate(tags): |
---|
| 838 | mesh['segment_tags'].append(tags[i].tostring().strip()) |
---|
| 839 | except KeyError: |
---|
| 840 | for ob in mesh['segments']: |
---|
| 841 | mesh['segment_tags'].append('') |
---|
[6074] | 842 | |
---|
[2253] | 843 | try: |
---|
| 844 | mesh['triangles'] = fid.variables['triangles'][:] |
---|
| 845 | mesh['triangle_neighbors'] = fid.variables['triangle_neighbors'][:] |
---|
| 846 | except KeyError: |
---|
[6304] | 847 | mesh['triangles'] = num.array([], num.int) #array default# |
---|
| 848 | mesh['triangle_neighbors'] = num.array([], num.int) #array default# |
---|
[6074] | 849 | |
---|
[6304] | 850 | mesh['triangle_tags'] = [] |
---|
[2253] | 851 | try: |
---|
| 852 | tags = fid.variables['triangle_tags'][:] |
---|
| 853 | for i, tag in enumerate(tags): |
---|
| 854 | mesh['triangle_tags'].append(tags[i].tostring().strip()) |
---|
| 855 | except KeyError: |
---|
| 856 | for ob in mesh['triangles']: |
---|
| 857 | mesh['triangle_tags'].append('') |
---|
[6074] | 858 | |
---|
| 859 | #the outline |
---|
[2253] | 860 | try: |
---|
| 861 | mesh['points'] = fid.variables['points'][:] |
---|
| 862 | except KeyError: |
---|
| 863 | mesh['points'] = [] |
---|
[6074] | 864 | |
---|
[2253] | 865 | try: |
---|
| 866 | mesh['point_attributes'] = fid.variables['point_attributes'][:] |
---|
| 867 | except KeyError: |
---|
| 868 | mesh['point_attributes'] = [] |
---|
| 869 | for point in mesh['points']: |
---|
| 870 | mesh['point_attributes'].append([]) |
---|
[6074] | 871 | |
---|
[2253] | 872 | try: |
---|
| 873 | mesh['outline_segments'] = fid.variables['outline_segments'][:] |
---|
| 874 | except KeyError: |
---|
[6304] | 875 | mesh['outline_segments'] = num.array([], num.int) #array default# |
---|
[6074] | 876 | |
---|
[2253] | 877 | mesh['outline_segment_tags'] =[] |
---|
| 878 | try: |
---|
| 879 | tags = fid.variables['outline_segment_tags'][:] |
---|
| 880 | for i, tag in enumerate(tags): |
---|
| 881 | mesh['outline_segment_tags'].append(tags[i].tostring().strip()) |
---|
| 882 | except KeyError: |
---|
| 883 | for ob in mesh['outline_segments']: |
---|
| 884 | mesh['outline_segment_tags'].append('') |
---|
[6074] | 885 | |
---|
[2253] | 886 | try: |
---|
| 887 | mesh['holes'] = fid.variables['holes'][:] |
---|
| 888 | except KeyError: |
---|
[6304] | 889 | mesh['holes'] = num.array([], num.int) #array default# |
---|
[6074] | 890 | |
---|
[2253] | 891 | try: |
---|
| 892 | mesh['regions'] = fid.variables['regions'][:] |
---|
| 893 | except KeyError: |
---|
[6304] | 894 | mesh['regions'] = num.array([], num.int) #array default# |
---|
[6074] | 895 | |
---|
[2253] | 896 | mesh['region_tags'] =[] |
---|
| 897 | try: |
---|
| 898 | tags = fid.variables['region_tags'][:] |
---|
| 899 | for i, tag in enumerate(tags): |
---|
| 900 | mesh['region_tags'].append(tags[i].tostring().strip()) |
---|
| 901 | except KeyError: |
---|
| 902 | for ob in mesh['regions']: |
---|
| 903 | mesh['region_tags'].append('') |
---|
[6074] | 904 | |
---|
[2253] | 905 | try: |
---|
| 906 | mesh['region_max_areas'] = fid.variables['region_max_areas'][:] |
---|
| 907 | except KeyError: |
---|
[6304] | 908 | mesh['region_max_areas'] = num.array([], num.int) #array default# |
---|
[6074] | 909 | |
---|
[2253] | 910 | try: |
---|
| 911 | geo_reference = Geo_reference(NetCDFObject=fid) |
---|
| 912 | mesh['geo_reference'] = geo_reference |
---|
| 913 | except AttributeError, e: |
---|
[6074] | 914 | #geo_ref not compulsory |
---|
[2253] | 915 | mesh['geo_reference'] = None |
---|
[6074] | 916 | |
---|
[2253] | 917 | fid.close() |
---|
[6074] | 918 | |
---|
[2253] | 919 | return mesh |
---|
| 920 | |
---|
[6074] | 921 | |
---|
| 922 | ## |
---|
| 923 | # @brief Export a boundary file. |
---|
| 924 | # @param file_name Path to the file to write. |
---|
| 925 | # @param points List of point index pairs. |
---|
| 926 | # @paran title Title string to write into file (first line). |
---|
| 927 | # @param delimiter Delimiter string to write between points. |
---|
| 928 | # @note Used by alpha shapes |
---|
| 929 | def export_boundary_file(file_name, points, title, delimiter=','): |
---|
[6304] | 930 | """Export a boundary file. |
---|
[6074] | 931 | |
---|
[6304] | 932 | Format: |
---|
[2253] | 933 | First line: Title variable |
---|
[6074] | 934 | Following lines: [point index][delimiter][point index] |
---|
[2253] | 935 | |
---|
| 936 | file_name - the name of the new file |
---|
[6074] | 937 | points - List of point index pairs [[p1, p2],[p3, p4]..] |
---|
[2253] | 938 | title - info to write in the first line |
---|
| 939 | """ |
---|
[6074] | 940 | |
---|
| 941 | fd = open(file_name, 'w') |
---|
| 942 | |
---|
[6304] | 943 | fd.write(title + '\n') |
---|
[6074] | 944 | |
---|
[6304] | 945 | # [point index][delimiter][point index] |
---|
[2253] | 946 | for point in points: |
---|
[6304] | 947 | fd.write(str(point[0]) + delimiter + str(point[1]) + '\n') |
---|
[6074] | 948 | |
---|
[2253] | 949 | fd.close() |
---|
| 950 | |
---|
[6304] | 951 | ################################################################################ |
---|
[2253] | 952 | # IMPORT/EXPORT POINTS FILES |
---|
[6304] | 953 | ################################################################################ |
---|
[2253] | 954 | |
---|
[6074] | 955 | ## |
---|
| 956 | # @brief |
---|
| 957 | # @param point_atts |
---|
[2253] | 958 | def extent_point_atts(point_atts): |
---|
[6304] | 959 | """Returns 4 points representing the extent |
---|
| 960 | This loses attribute info. |
---|
[2253] | 961 | """ |
---|
[6304] | 962 | |
---|
[2253] | 963 | point_atts['pointlist'] = extent(point_atts['pointlist']) |
---|
| 964 | point_atts['attributelist'] = {} |
---|
[6074] | 965 | |
---|
[2253] | 966 | return point_atts |
---|
[6074] | 967 | |
---|
| 968 | |
---|
| 969 | ## |
---|
| 970 | # @brief Get an extent array for a set of points. |
---|
| 971 | # @param points A set of points. |
---|
| 972 | # @return An extent array of form [[min_x, min_y], [max_x, min_y], |
---|
| 973 | # [max_x, max_y], [min_x, max_y]] |
---|
[2253] | 974 | def extent(points): |
---|
[6304] | 975 | points = num.array(points, num.float) |
---|
[6074] | 976 | |
---|
[2253] | 977 | max_x = min_x = points[0][0] |
---|
| 978 | max_y = min_y = points[0][1] |
---|
[6074] | 979 | |
---|
[2253] | 980 | for point in points[1:]: |
---|
[6074] | 981 | x = point[0] |
---|
[6304] | 982 | if x > max_x: |
---|
| 983 | max_x = x |
---|
| 984 | if x < min_x: |
---|
| 985 | min_x = x |
---|
[6074] | 986 | |
---|
| 987 | y = point[1] |
---|
[6304] | 988 | if y > max_y: |
---|
| 989 | max_y = y |
---|
| 990 | if y < min_y: |
---|
| 991 | min_y = y |
---|
[6074] | 992 | |
---|
[6154] | 993 | extent = num.array([[min_x, min_y], |
---|
| 994 | [max_x, min_y], |
---|
| 995 | [max_x, max_y], |
---|
| 996 | [min_x, max_y]]) |
---|
[6074] | 997 | |
---|
[2253] | 998 | return extent |
---|
[6074] | 999 | |
---|
| 1000 | |
---|
| 1001 | ## |
---|
| 1002 | # @brief Reduce a points file until number of points is less than limit. |
---|
| 1003 | # @param infile Path to input file to thin. |
---|
| 1004 | # @param outfile Path to output thinned file. |
---|
| 1005 | # @param max_points Max number of points in output file. |
---|
| 1006 | # @param verbose True if this function is to be verbose. |
---|
[2253] | 1007 | def reduce_pts(infile, outfile, max_points, verbose = False): |
---|
[6304] | 1008 | """Reduce a points file until less than given size. |
---|
| 1009 | |
---|
| 1010 | Reduces a points file by removing every second point until the # of points |
---|
[2253] | 1011 | is less than max_points. |
---|
| 1012 | """ |
---|
[6074] | 1013 | |
---|
[2888] | 1014 | # check out pts2rectangular in least squares, and the use of reduction. |
---|
| 1015 | # Maybe it does the same sort of thing? |
---|
[2253] | 1016 | point_atts = _read_pts_file(infile) |
---|
[6074] | 1017 | |
---|
[2253] | 1018 | while point_atts['pointlist'].shape[0] > max_points: |
---|
| 1019 | if verbose: print "point_atts['pointlist'].shape[0]" |
---|
| 1020 | point_atts = half_pts(point_atts) |
---|
[6074] | 1021 | |
---|
[2253] | 1022 | export_points_file(outfile, point_atts) |
---|
[6074] | 1023 | |
---|
| 1024 | |
---|
| 1025 | ## |
---|
| 1026 | # @brief |
---|
| 1027 | # @param infile |
---|
| 1028 | # @param max_points |
---|
| 1029 | # @param delimiter |
---|
| 1030 | # @param verbose True if this function is to be verbose. |
---|
| 1031 | # @return A list of |
---|
| 1032 | def produce_half_point_files(infile, max_points, delimiter, verbose=False): |
---|
[2253] | 1033 | point_atts = _read_pts_file(infile) |
---|
| 1034 | root, ext = splitext(infile) |
---|
| 1035 | outfiles = [] |
---|
[6074] | 1036 | |
---|
[2253] | 1037 | if verbose: print "# of points", point_atts['pointlist'].shape[0] |
---|
[6074] | 1038 | |
---|
[2253] | 1039 | while point_atts['pointlist'].shape[0] > max_points: |
---|
| 1040 | point_atts = half_pts(point_atts) |
---|
[6074] | 1041 | |
---|
[2253] | 1042 | if verbose: print "# of points", point_atts['pointlist'].shape[0] |
---|
[6074] | 1043 | |
---|
[2253] | 1044 | outfile = root + delimiter + str(point_atts['pointlist'].shape[0]) + ext |
---|
| 1045 | outfiles.append(outfile) |
---|
[6074] | 1046 | export_points_file(outfile, point_atts) |
---|
| 1047 | |
---|
[2253] | 1048 | return outfiles |
---|
[6074] | 1049 | |
---|
| 1050 | |
---|
| 1051 | ## |
---|
| 1052 | # @brief |
---|
[6304] | 1053 | # @param point_atts Object with attribute of 'pointlist'. |
---|
[6074] | 1054 | # @return |
---|
[2253] | 1055 | def point_atts2array(point_atts): |
---|
[6074] | 1056 | # convert attribute list to array of floats |
---|
[6304] | 1057 | point_atts['pointlist'] = num.array(point_atts['pointlist'], num.float) |
---|
[6074] | 1058 | |
---|
[2253] | 1059 | for key in point_atts['attributelist'].keys(): |
---|
[6074] | 1060 | point_atts['attributelist'][key] = \ |
---|
[6304] | 1061 | num.array(point_atts['attributelist'][key], num.float) |
---|
[6074] | 1062 | |
---|
[2253] | 1063 | return point_atts |
---|
[6074] | 1064 | |
---|
| 1065 | |
---|
| 1066 | ## |
---|
| 1067 | # @brief ?? |
---|
| 1068 | # @param point_atts ?? |
---|
| 1069 | # @return ?? |
---|
[2253] | 1070 | def half_pts(point_atts): |
---|
| 1071 | point_atts2array(point_atts) |
---|
| 1072 | point_atts['pointlist'] = point_atts['pointlist'][::2] |
---|
[6074] | 1073 | |
---|
[2253] | 1074 | for key in point_atts['attributelist'].keys(): |
---|
[6074] | 1075 | point_atts['attributelist'][key] = point_atts['attributelist'][key][::2] |
---|
| 1076 | |
---|
[2253] | 1077 | return point_atts |
---|
| 1078 | |
---|
[6074] | 1079 | ## |
---|
| 1080 | # @brief ?? |
---|
| 1081 | # @param dic ?? |
---|
| 1082 | # @return ?? |
---|
[2253] | 1083 | def concatinate_attributelist(dic): |
---|
| 1084 | """ |
---|
| 1085 | giving a dic[attribute title] = attribute |
---|
[6074] | 1086 | return list of attribute titles, array of attributes |
---|
[2253] | 1087 | """ |
---|
[6074] | 1088 | |
---|
[6304] | 1089 | point_attributes = num.array([], num.float) |
---|
[2253] | 1090 | keys = dic.keys() |
---|
| 1091 | key = keys.pop(0) |
---|
[6304] | 1092 | point_attributes = num.reshape(dic[key], (dic[key].shape[0], 1)) |
---|
[2253] | 1093 | for key in keys: |
---|
[6304] | 1094 | reshaped = num.reshape(dic[key], (dic[key].shape[0], 1)) |
---|
[6154] | 1095 | point_attributes = num.concatenate([point_attributes, reshaped], axis=1) |
---|
[6074] | 1096 | |
---|
[2253] | 1097 | return dic.keys(), point_attributes |
---|
| 1098 | |
---|
[6074] | 1099 | |
---|
| 1100 | ## |
---|
| 1101 | # @brief |
---|
| 1102 | # @param dict |
---|
| 1103 | # @param indices_to_keep |
---|
| 1104 | # @return |
---|
[6304] | 1105 | # @note FIXME(dsg), turn this dict plus methods into a class? |
---|
[6074] | 1106 | def take_points(dict, indices_to_keep): |
---|
[2253] | 1107 | dict = point_atts2array(dict) |
---|
[6304] | 1108 | dict['pointlist'] = num.take(dict['pointlist'], indices_to_keep) |
---|
[2253] | 1109 | |
---|
| 1110 | for key in dict['attributelist'].keys(): |
---|
[6304] | 1111 | dict['attributelist'][key] = num.take(dict['attributelist'][key], |
---|
| 1112 | indices_to_keep) |
---|
[6074] | 1113 | |
---|
[2253] | 1114 | return dict |
---|
[6074] | 1115 | |
---|
| 1116 | ## |
---|
| 1117 | # @brief ?? |
---|
| 1118 | # @param dict1 ?? |
---|
| 1119 | # @param dict2 ?? |
---|
| 1120 | # @return ?? |
---|
[6304] | 1121 | def add_point_dictionaries(dict1, dict2): |
---|
[2253] | 1122 | """ |
---|
| 1123 | """ |
---|
[6074] | 1124 | |
---|
[2253] | 1125 | dict1 = point_atts2array(dict1) |
---|
| 1126 | dict2 = point_atts2array(dict2) |
---|
[6074] | 1127 | |
---|
| 1128 | combined = {} |
---|
[6154] | 1129 | combined['pointlist'] = num.concatenate((dict2['pointlist'], |
---|
[6304] | 1130 | dict1['pointlist']), axis=0) |
---|
[6074] | 1131 | |
---|
| 1132 | atts = {} |
---|
[2253] | 1133 | for key in dict2['attributelist'].keys(): |
---|
[6154] | 1134 | atts[key]= num.concatenate((dict2['attributelist'][key], |
---|
| 1135 | dict1['attributelist'][key]), axis=0) |
---|
[6304] | 1136 | combined['attributelist'] = atts |
---|
[2253] | 1137 | combined['geo_reference'] = dict1['geo_reference'] |
---|
[6074] | 1138 | |
---|
[2253] | 1139 | return combined |
---|
[6074] | 1140 | |
---|
| 1141 | |
---|
[2253] | 1142 | if __name__ == "__main__": |
---|
| 1143 | pass |
---|