1 | """ |
---|
2 | The format for a Points dictionary is: |
---|
3 | |
---|
4 | ['pointlist'] a 2 column array describing points. 1st column x, 2nd column y. |
---|
5 | ['attributelist'], a dictionary of 1D arrays, representing attribute values |
---|
6 | at the point. The dictionary key is the attribute header. |
---|
7 | ['geo_reference'] a Geo_refernece object. Use if the point information |
---|
8 | is relative. This is optional. |
---|
9 | eg |
---|
10 | dic['pointlist'] = [[1.0,2.0],[3.0,5.0]] |
---|
11 | dic['attributelist']['elevation'] = [[7.0,5.0] |
---|
12 | |
---|
13 | |
---|
14 | The dict format for IO with mesh files is; |
---|
15 | (the triangulation) |
---|
16 | vertices: [[x1,y1],[x2,y2],...] (lists of doubles) |
---|
17 | vertex_attributes: [[a11,a12,...],[a21,a22],...] (lists of doubles) |
---|
18 | vertex_attribute_titles:[A1Title, A2Title ...] (A list of strings) |
---|
19 | segments: [[v1,v2],[v3,v4],...] (lists of integers) |
---|
20 | segment_tags : [tag,tag,...] list of strings |
---|
21 | triangles : [(v1,v2,v3), (v4,v5,v6),....] lists of points |
---|
22 | triangle_tags: [s1,s2,...] A list of strings |
---|
23 | triangle_neighbors: [[t1,t2,t3], [t4,t5,t6],..] lists of triangles |
---|
24 | |
---|
25 | (the outline) |
---|
26 | points: [[x1,y1],[x2,y2],...] (lists of doubles) |
---|
27 | point_attributes: [[a11,a12,...],[a21,a22],...] (lists of doubles) |
---|
28 | outline_segments: [[point1,point2],[p3,p4],...] (lists of integers) |
---|
29 | outline_segment_tags : [tag1,tag2,...] list of strings |
---|
30 | holes : [[x1,y1],...](List of doubles, one inside each hole region) |
---|
31 | regions : [ [x1,y1],...] (List of 4 doubles) |
---|
32 | region_tags : [tag1,tag2,...] (list of strings) |
---|
33 | region_max_areas: [ma1,ma2,...] (A list of doubles) |
---|
34 | {Convension: A -ve max area means no max area} |
---|
35 | geo_reference: a Geo_refernece object. Use if the point information |
---|
36 | is relative. This is optional. |
---|
37 | |
---|
38 | Points files are .csv for ascii and .pts for NetCDF |
---|
39 | Mesh files are .tsh for ascii and .msh for NetCDF |
---|
40 | |
---|
41 | Note: point att's have no titles - that's currently ok, since least |
---|
42 | squares adds the point info to vertices, and they have titles |
---|
43 | |
---|
44 | The format for a .tsh file is (FIXME update this) |
---|
45 | |
---|
46 | First line: <# of vertices> <# of attributes> |
---|
47 | Following lines: <vertex #> <x> <y> [attributes] |
---|
48 | One line: <# of triangles> |
---|
49 | Following lines: <triangle #> <vertex #> <vertex #> <vertex #> |
---|
50 | <neigbouring triangle #> <neigbouring triangle #> |
---|
51 | <neigbouring triangle #> [attribute of region] |
---|
52 | One line: <# of segments> |
---|
53 | Following lines: <segment #> <vertex #> <vertex #> [boundary tag] |
---|
54 | """ |
---|
55 | ##FIXME (DSG-DSG) Is the dict format mentioned above a list of a numeric array? |
---|
56 | # Needs to be defined |
---|
57 | |
---|
58 | |
---|
59 | from string import find, rfind |
---|
60 | import numpy as num |
---|
61 | from os.path import splitext |
---|
62 | |
---|
63 | from anuga.coordinate_transforms.geo_reference import Geo_reference, TITLE, \ |
---|
64 | TitleError |
---|
65 | |
---|
66 | from Scientific.IO.NetCDF import NetCDFFile |
---|
67 | from anuga.config import netcdf_mode_r, netcdf_mode_w, netcdf_mode_a |
---|
68 | from anuga.config import netcdf_float, netcdf_char, netcdf_int |
---|
69 | |
---|
70 | import exceptions |
---|
71 | |
---|
72 | |
---|
73 | class TitleAmountError(exceptions.Exception): pass |
---|
74 | |
---|
75 | |
---|
76 | NOMAXAREA=-999 |
---|
77 | |
---|
78 | |
---|
79 | ## |
---|
80 | # @brief Read a mesh file (.tsh or .msh) and return a dictionary. |
---|
81 | # @param ofile Path to the file to read. |
---|
82 | # @return A dictionary of data from the input file. |
---|
83 | # @note Throws IOError if can't read file. |
---|
84 | # @note This is used by pmesh. |
---|
85 | def import_mesh_file(ofile): |
---|
86 | """Read a mesh file, either .tsh or .msh |
---|
87 | |
---|
88 | Note: will throw an IOError if it can't load the file. |
---|
89 | Catch these! |
---|
90 | """ |
---|
91 | |
---|
92 | try: |
---|
93 | if ofile[-4:] == ".tsh": |
---|
94 | dict = _read_tsh_file(ofile) |
---|
95 | elif ofile[-4:] == ".msh": |
---|
96 | dict = _read_msh_file(ofile) |
---|
97 | else: |
---|
98 | msg = 'Extension .%s is unknown' % ofile[-4:] |
---|
99 | raise IOError, msg |
---|
100 | #FIXME No test for ValueError |
---|
101 | except (TitleError, SyntaxError, IndexError, ValueError): |
---|
102 | msg = 'File could not be opened' |
---|
103 | raise IOError, msg |
---|
104 | return dict |
---|
105 | |
---|
106 | |
---|
107 | ## |
---|
108 | # @brief Write a mesh file from a dictionary. |
---|
109 | # @param ofile The path of the mesh file to write. |
---|
110 | # @param mesh_dict Dictionary containing data to write to output mesh file. |
---|
111 | # @note Raises IOError if file extension is unrecognized. |
---|
112 | def export_mesh_file(ofile, mesh_dict): |
---|
113 | """Write a mesh file given a dictionary. |
---|
114 | |
---|
115 | First line: <# of vertices> <# of attributes> |
---|
116 | Following lines: <vertex #> <x> <y> [attributes] |
---|
117 | One line: <# of triangles> |
---|
118 | Following lines: <triangle #> <vertex #> <vertex #> <vertex #> |
---|
119 | <neigbouring triangle #> <neigbouring triangle #> |
---|
120 | <neigbouring triangle #> [attribute of region] |
---|
121 | One line: <# of segments> |
---|
122 | Following lines: <segment #> <vertex #> <vertex #> [boundary tag] |
---|
123 | """ |
---|
124 | |
---|
125 | # Ensure that if required key isn't present, we add it with [] value. |
---|
126 | # .setdefault() for dictionaries was added in python 2.0. |
---|
127 | # The only other neat way to do this is to override the dictionary |
---|
128 | # .__getitem__() method to return [] if key not found. |
---|
129 | reqd_keys = ['points', 'point_attributes', 'outline_segments', |
---|
130 | 'outline_segment_tags', 'holes', 'regions', 'region_tags', |
---|
131 | 'region_max_areas', 'vertices', 'vertex_attributes', |
---|
132 | 'vertex_attribute_titles', 'segments', 'segment_tags', |
---|
133 | 'triangles', 'triangle_tags', 'triangle_neighbors'] |
---|
134 | |
---|
135 | for k in reqd_keys: |
---|
136 | mesh_dict.setdefault(k, []) |
---|
137 | |
---|
138 | # hand-off to appropriate function |
---|
139 | if (ofile[-4:] == ".tsh"): |
---|
140 | _write_tsh_file(ofile, mesh_dict) |
---|
141 | elif (ofile[-4:] == ".msh"): |
---|
142 | _write_msh_file(ofile, mesh_dict) |
---|
143 | else: |
---|
144 | msg = 'Unknown file type %s ' % ofile |
---|
145 | raise IOError, msg |
---|
146 | |
---|
147 | |
---|
148 | ## |
---|
149 | # @brief Read a mesh file into a dictionary. |
---|
150 | # @param ofile Path of the file to read. |
---|
151 | # @return Data dictionary from the mesh (.tsh) file. |
---|
152 | def _read_tsh_file(ofile): |
---|
153 | """Read the text file format for meshes""" |
---|
154 | |
---|
155 | fd = open(ofile, 'r') |
---|
156 | dict = _read_triangulation(fd) |
---|
157 | dict_mesh = _read_outline(fd) |
---|
158 | for element in dict_mesh.keys(): |
---|
159 | dict[element] = dict_mesh[element] |
---|
160 | fd.close() |
---|
161 | |
---|
162 | return dict |
---|
163 | |
---|
164 | |
---|
165 | ## |
---|
166 | # @brief ?? |
---|
167 | # @param fd An open descriptor of the file to read. |
---|
168 | # @return A dictionary ... |
---|
169 | def _read_triangulation(fd): |
---|
170 | """Read the generated triangulation, NOT the outline.""" |
---|
171 | |
---|
172 | delimiter = " " |
---|
173 | |
---|
174 | # loading the point info |
---|
175 | line = fd.readline() |
---|
176 | fragments = line.split() |
---|
177 | if fragments == []: |
---|
178 | NumOfVertices = 0 |
---|
179 | NumOfVertAttributes = 0 |
---|
180 | else: |
---|
181 | NumOfVertices = fragments[0] |
---|
182 | NumOfVertAttributes = fragments[1] |
---|
183 | points = [] |
---|
184 | pointattributes = [] |
---|
185 | for index in range(int(NumOfVertices)): |
---|
186 | fragments = fd.readline().split() |
---|
187 | fragments.pop(0) # pop off the index |
---|
188 | |
---|
189 | # pop the x & y off so we're left with a list of attributes |
---|
190 | vert = [float(fragments.pop(0)), float(fragments.pop(0))] |
---|
191 | points.append(vert) |
---|
192 | apointattributes = [] |
---|
193 | for fragment in fragments: |
---|
194 | apointattributes.append(float(fragment)) |
---|
195 | if apointattributes != []: |
---|
196 | pointattributes.append(apointattributes) |
---|
197 | |
---|
198 | # loading the point title info |
---|
199 | line = fd.readline() |
---|
200 | vertTitle = [] |
---|
201 | for index in range(int(NumOfVertAttributes)): |
---|
202 | fragments = fd.readline().strip() |
---|
203 | vertTitle.append(fragments) |
---|
204 | |
---|
205 | # loading the triangle info |
---|
206 | line = fd.readline() |
---|
207 | fragments = line.split() |
---|
208 | NumOfTriangles = fragments[0] |
---|
209 | triangles = [] |
---|
210 | triangleattributes = [] |
---|
211 | triangleneighbors = [] |
---|
212 | for index in range(int(NumOfTriangles)): |
---|
213 | line = fd.readline() |
---|
214 | line.strip() # so we can get the region string |
---|
215 | fragments = line.split() |
---|
216 | fragments.pop(0) # pop off the index |
---|
217 | |
---|
218 | tri = [int(fragments[0]), int(fragments[1]), int(fragments[2])] |
---|
219 | triangles.append(tri) |
---|
220 | neighbors = [int(fragments[3]), int(fragments[4]), int(fragments[5])] |
---|
221 | triangleneighbors.append(neighbors) |
---|
222 | for x in range(7): # remove index [<vertex #>] [<neigbouring tri #>] |
---|
223 | line = line[find(line, delimiter):] # remove index |
---|
224 | line = line.lstrip() |
---|
225 | stringtag = line.strip() |
---|
226 | triangleattributes.append(stringtag) |
---|
227 | |
---|
228 | # loading the segment info |
---|
229 | line = fd.readline() |
---|
230 | fragments = line.split() |
---|
231 | NumOfSegments = fragments[0] |
---|
232 | segments = [] |
---|
233 | segmenttags = [] |
---|
234 | for index in range(int(NumOfSegments)): |
---|
235 | line = fd.readline() |
---|
236 | line.strip() # to get the segment string |
---|
237 | fragments = line.split() |
---|
238 | fragments.pop(0) #pop off the index |
---|
239 | seg = [int(fragments[0]), int(fragments[1])] |
---|
240 | segments.append(seg) |
---|
241 | line = line[find(line, delimiter):] # remove index |
---|
242 | line = line.lstrip() |
---|
243 | line = line[find(line, delimiter):] # remove x |
---|
244 | line = line.lstrip() |
---|
245 | line = line[find(line, delimiter):] # remove y |
---|
246 | stringtag = line.strip() |
---|
247 | segmenttags.append(stringtag) |
---|
248 | |
---|
249 | meshDict = {} |
---|
250 | meshDict['vertices'] = points |
---|
251 | if pointattributes == []: |
---|
252 | meshDict['vertex_attributes'] = None |
---|
253 | else: |
---|
254 | meshDict['vertex_attributes'] = pointattributes |
---|
255 | meshDict['triangles'] = triangles |
---|
256 | meshDict['triangle_tags'] = triangleattributes |
---|
257 | meshDict['triangle_neighbors'] = triangleneighbors |
---|
258 | meshDict['segments'] = segments |
---|
259 | meshDict['segment_tags'] = segmenttags |
---|
260 | meshDict['vertex_attribute_titles'] = vertTitle |
---|
261 | |
---|
262 | return meshDict |
---|
263 | |
---|
264 | |
---|
265 | ## |
---|
266 | # @brief |
---|
267 | # @param fd An open descriptor of the file to read. |
---|
268 | # @return A dictionary ... |
---|
269 | # @note If file has no mesh info, an empty dict will be returned. |
---|
270 | def _read_outline(fd): |
---|
271 | """Read a mesh file outline. |
---|
272 | |
---|
273 | Note, if a file has no mesh info, it can still be read - |
---|
274 | the meshdic returned will be 'empty'. |
---|
275 | """ |
---|
276 | |
---|
277 | delimiter = " " # warning: split() calls are using default whitespace |
---|
278 | |
---|
279 | # loading the point info |
---|
280 | line = fd.readline() |
---|
281 | fragments = line.split() |
---|
282 | if fragments == []: |
---|
283 | NumOfVertices = 0 |
---|
284 | NumOfVertAttributes = 0 |
---|
285 | else: |
---|
286 | NumOfVertices = fragments[0] |
---|
287 | NumOfVertAttributes = fragments[1] |
---|
288 | points = [] |
---|
289 | pointattributes = [] |
---|
290 | for index in range(int(NumOfVertices)): |
---|
291 | fragments = fd.readline().split() |
---|
292 | fragments.pop(0) # pop off the index |
---|
293 | # pop the x & y off so we're left with a list of attributes |
---|
294 | vert = [float(fragments.pop(0)), float(fragments.pop(0))] |
---|
295 | points.append(vert) |
---|
296 | apointattributes = [] |
---|
297 | for fragment in fragments: |
---|
298 | apointattributes.append(float(fragment)) |
---|
299 | pointattributes.append(apointattributes) |
---|
300 | |
---|
301 | # loading the segment info |
---|
302 | line = fd.readline() |
---|
303 | fragments = line.split() |
---|
304 | if fragments == []: |
---|
305 | NumOfSegments = 0 |
---|
306 | else: |
---|
307 | NumOfSegments = fragments[0] |
---|
308 | segments = [] |
---|
309 | segmenttags = [] |
---|
310 | for index in range(int(NumOfSegments)): |
---|
311 | line = fd.readline() |
---|
312 | fragments = line.split() |
---|
313 | fragments.pop(0) # pop off the index |
---|
314 | seg = [int(fragments[0]), int(fragments[1])] |
---|
315 | segments.append(seg) |
---|
316 | line = line[find(line, delimiter):] # remove index |
---|
317 | line = line.lstrip() |
---|
318 | line = line[find(line, delimiter):] # remove x |
---|
319 | line = line.lstrip() |
---|
320 | line = line[find(line, delimiter):] # remove y |
---|
321 | stringtag = line.strip() |
---|
322 | segmenttags.append(stringtag) |
---|
323 | |
---|
324 | # loading the hole info |
---|
325 | line = fd.readline() |
---|
326 | fragments = line.split() |
---|
327 | if fragments == []: |
---|
328 | numOfHoles = 0 |
---|
329 | else: |
---|
330 | numOfHoles = fragments[0] |
---|
331 | holes = [] |
---|
332 | for index in range(int(numOfHoles)): |
---|
333 | fragments = fd.readline().split() |
---|
334 | fragments.pop(0) #pop off the index |
---|
335 | hole = [float(fragments[0]), float(fragments[1])] |
---|
336 | holes.append(hole) |
---|
337 | |
---|
338 | # loading the region info |
---|
339 | line = fd.readline() |
---|
340 | fragments = line.split() |
---|
341 | if fragments == []: |
---|
342 | numOfRegions = 0 |
---|
343 | else: |
---|
344 | numOfRegions = fragments[0] |
---|
345 | regions = [] |
---|
346 | regionattributes = [] |
---|
347 | for index in range(int(numOfRegions)): |
---|
348 | line = fd.readline() |
---|
349 | fragments = line.split() |
---|
350 | fragments.pop(0) # pop off the index |
---|
351 | region = [float(fragments[0]), float(fragments[1])] |
---|
352 | regions.append(region) |
---|
353 | |
---|
354 | line = line[find(line, delimiter):] # remove index |
---|
355 | line = line.lstrip() |
---|
356 | line = line[find(line, delimiter):] # remove x |
---|
357 | line = line.lstrip() |
---|
358 | line = line[find(line, delimiter):] # remove y |
---|
359 | stringtag = line.strip() |
---|
360 | regionattributes.append(stringtag) |
---|
361 | |
---|
362 | regionmaxareas = [] |
---|
363 | line = fd.readline() |
---|
364 | for index in range(int(numOfRegions)): # Read in the Max area info |
---|
365 | line = fd.readline() |
---|
366 | fragments = line.split() |
---|
367 | # The try is here for format compatibility |
---|
368 | try: |
---|
369 | fragments.pop(0) # pop off the index |
---|
370 | if len(fragments) == 0: # no max area |
---|
371 | regionmaxareas.append(None) |
---|
372 | else: |
---|
373 | regionmaxareas.append(float(fragments[0])) |
---|
374 | except IndexError, e: |
---|
375 | regionmaxareas.append(None) |
---|
376 | |
---|
377 | try: |
---|
378 | geo_reference = Geo_reference(ASCIIFile=fd) |
---|
379 | except: |
---|
380 | #geo_ref not compulsory |
---|
381 | geo_reference = None |
---|
382 | |
---|
383 | meshDict = {} |
---|
384 | meshDict['points'] = points |
---|
385 | meshDict['point_attributes'] = pointattributes |
---|
386 | meshDict['outline_segments'] = segments |
---|
387 | meshDict['outline_segment_tags'] = segmenttags |
---|
388 | meshDict['holes'] = holes |
---|
389 | meshDict['regions'] = regions |
---|
390 | meshDict['region_tags'] = regionattributes |
---|
391 | meshDict['region_max_areas'] = regionmaxareas |
---|
392 | meshDict['geo_reference'] = geo_reference |
---|
393 | |
---|
394 | return meshDict |
---|
395 | |
---|
396 | |
---|
397 | ## |
---|
398 | # @brief Clean up a line with delimited fields. |
---|
399 | # @param line The string to be cleaned. |
---|
400 | # @param delimiter String used a delimiter when splitting 'line'. |
---|
401 | # @return A list of delimited fields with white-space removed from ends. |
---|
402 | # @note Will also remove any field that was originally ''. |
---|
403 | def clean_line(line, delimiter): |
---|
404 | """Clean up a line - return fields with end space removed.""" |
---|
405 | |
---|
406 | line = line.strip() |
---|
407 | numbers = line.split(delimiter) |
---|
408 | i = len(numbers) - 1 |
---|
409 | while i >= 0: |
---|
410 | if numbers[i] == '': |
---|
411 | numbers.pop(i) |
---|
412 | else: |
---|
413 | numbers[i] = numbers[i].strip() |
---|
414 | |
---|
415 | i += -1 |
---|
416 | |
---|
417 | return numbers |
---|
418 | |
---|
419 | |
---|
420 | ## |
---|
421 | # @brief Write an ASCII triangulation file. |
---|
422 | # @param fd An open descriptor to the file to write. |
---|
423 | # @param gen_dict Dictionary containing data to write. |
---|
424 | def _write_ASCII_triangulation(fd, gen_dict): |
---|
425 | vertices = gen_dict['vertices'] |
---|
426 | vertices_attributes = gen_dict['vertex_attributes'] |
---|
427 | try: |
---|
428 | vertices_attribute_titles = gen_dict['vertex_attribute_titles'] |
---|
429 | except KeyError, e: |
---|
430 | #FIXME is this the best way? |
---|
431 | if vertices_attributes == [] or vertices_attributes[0] == []: |
---|
432 | vertices_attribute_titles = [] |
---|
433 | else: |
---|
434 | raise KeyError, e |
---|
435 | |
---|
436 | triangles = gen_dict['triangles'] |
---|
437 | triangles_attributes = gen_dict['triangle_tags'] |
---|
438 | triangle_neighbors = gen_dict['triangle_neighbors'] |
---|
439 | |
---|
440 | segments = gen_dict['segments'] |
---|
441 | segment_tags = gen_dict['segment_tags'] |
---|
442 | |
---|
443 | numVert = str(len(vertices)) |
---|
444 | # Don't understand why we have to do vertices_attributes[0] is None, |
---|
445 | # but it doesn't work otherwise... |
---|
446 | if (vertices_attributes == None or |
---|
447 | numVert == "0" or |
---|
448 | len(vertices_attributes) == 0): |
---|
449 | numVertAttrib = "0" |
---|
450 | else: |
---|
451 | numVertAttrib = str(len(vertices_attributes[0])) |
---|
452 | |
---|
453 | fd.write(numVert + " " + numVertAttrib + |
---|
454 | " # <# of verts> <# of vert attributes>, next lines <vertex #> " |
---|
455 | "<x> <y> [attributes] ...Triangulation Vertices...\n") |
---|
456 | |
---|
457 | #<vertex #> <x> <y> [attributes] |
---|
458 | index = 0 |
---|
459 | for vert in vertices: |
---|
460 | attlist = "" |
---|
461 | |
---|
462 | if vertices_attributes == None or vertices_attributes == []: |
---|
463 | attlist = "" |
---|
464 | else: |
---|
465 | for att in vertices_attributes[index]: |
---|
466 | attlist = attlist + str(att) + " " |
---|
467 | attlist.strip() |
---|
468 | fd.write(str(index) + " " + str(vert[0]) + " " + str(vert[1]) |
---|
469 | + " " + attlist + "\n") |
---|
470 | index += 1 |
---|
471 | |
---|
472 | # write comments for title |
---|
473 | fd.write("# attribute column titles ...Triangulation Vertex Titles...\n") |
---|
474 | for title in vertices_attribute_titles: |
---|
475 | fd.write(title + "\n") |
---|
476 | |
---|
477 | # <# of triangles> |
---|
478 | n = len(triangles) |
---|
479 | fd.write(str(n) |
---|
480 | + " # <# of triangles>, next lines <triangle #> [<vertex #>] " |
---|
481 | "[<neigbouring triangle #>] [attribute of region] ..." |
---|
482 | "Triangulation Triangles...\n") |
---|
483 | |
---|
484 | # <triangle #> <vertex #> <vertex #> <vertex #> <neigbouring triangle #> |
---|
485 | # <neigbouring triangle #> <neigbouring triangle #> [attribute of region] |
---|
486 | for index in range(n): |
---|
487 | neighbors = "" |
---|
488 | tri = triangles[index] |
---|
489 | if triangle_neighbors == []: |
---|
490 | neighbors = "-1 -1 -1 " |
---|
491 | else: |
---|
492 | for neighbor in triangle_neighbors[index]: |
---|
493 | if neighbor: |
---|
494 | neighbors += str(neighbor) + " " |
---|
495 | else: |
---|
496 | if neighbor == 0: |
---|
497 | neighbors += "0 " |
---|
498 | else: |
---|
499 | neighbors += "-1 " |
---|
500 | # Warning even though a list is passed, only the first value |
---|
501 | # is written. There's an assumption that the list only |
---|
502 | # contains one item. This assumption is made since the |
---|
503 | # dict that's being passed around is also be used to communicate |
---|
504 | # with triangle, and it seems to have the option of returning |
---|
505 | # more than one value for triangle attributex |
---|
506 | if (triangles_attributes == None or |
---|
507 | triangles_attributes == [] or |
---|
508 | triangles_attributes[index] == ['']): |
---|
509 | att = "" |
---|
510 | else: |
---|
511 | att = str(triangles_attributes[index]) |
---|
512 | fd.write(str(index) + " " |
---|
513 | + str(tri[0]) + " " |
---|
514 | + str(tri[1]) + " " |
---|
515 | + str(tri[2]) + " " |
---|
516 | + neighbors + " " |
---|
517 | + att + "\n") |
---|
518 | |
---|
519 | # One line: <# of segments> |
---|
520 | fd.write(str(len(segments)) + |
---|
521 | " # <# of segments>, next lines <segment #> <vertex #> " |
---|
522 | "<vertex #> [boundary tag] ...Triangulation Segments...\n") |
---|
523 | |
---|
524 | # Following lines: <segment #> <vertex #> <vertex #> [boundary tag] |
---|
525 | for i in range(len(segments)): |
---|
526 | seg = segments[i] |
---|
527 | fd.write(str(i) + " " |
---|
528 | + str(seg[0]) + " " |
---|
529 | + str(seg[1]) + " " |
---|
530 | + str(segment_tags[i]) + "\n") |
---|
531 | |
---|
532 | |
---|
533 | ## |
---|
534 | # @brief Write triangulation and outline to a .tsh file. |
---|
535 | # @param ofile Path of the file to write. |
---|
536 | # @mesh_dict Dictionary of data to write. |
---|
537 | def _write_tsh_file(ofile, mesh_dict): |
---|
538 | fd = open(ofile, 'w') |
---|
539 | _write_ASCII_triangulation(fd, mesh_dict) |
---|
540 | _write_ASCII_outline(fd, mesh_dict) |
---|
541 | fd.close() |
---|
542 | |
---|
543 | |
---|
544 | ## |
---|
545 | # @brief Write an ASCII outline to a file. |
---|
546 | # @param fd An open descriptor of the file to write. |
---|
547 | # @param dict Dictionary holding data to write. |
---|
548 | def _write_ASCII_outline(fd, dict): |
---|
549 | points = dict['points'] |
---|
550 | point_attributes = dict['point_attributes'] |
---|
551 | segments = dict['outline_segments'] |
---|
552 | segment_tags = dict['outline_segment_tags'] |
---|
553 | holes = dict['holes'] |
---|
554 | regions = dict['regions'] |
---|
555 | region_tags = dict['region_tags'] |
---|
556 | region_max_areas = dict['region_max_areas'] |
---|
557 | |
---|
558 | num_points = str(len(points)) |
---|
559 | if (num_points == '0'): |
---|
560 | num_point_atts = '0' |
---|
561 | else: |
---|
562 | num_point_atts = str(len(point_attributes[0])) |
---|
563 | |
---|
564 | fd.write(num_points + ' ' + num_point_atts + |
---|
565 | ' # <# of verts> <# of vert attributes>, next lines <vertex #> ' |
---|
566 | '<x> <y> [attributes] ...Mesh Vertices...\n') |
---|
567 | |
---|
568 | # <x> <y> [attributes] |
---|
569 | for i, point in enumerate(points): |
---|
570 | attlist = '' |
---|
571 | for att in point_attributes[i]: |
---|
572 | attlist = attlist + str(att) + ' ' |
---|
573 | attlist.strip() |
---|
574 | fd.write(str(i) + ' ' + str(point[0]) + ' ' + str(point[1]) + ' ' + |
---|
575 | attlist + '\n') |
---|
576 | |
---|
577 | # One line: <# of segments> |
---|
578 | fd.write(str(len(segments)) + |
---|
579 | ' # <# of segments>, next lines <segment #> <vertex #> ' |
---|
580 | '<vertex #> [boundary tag] ...Mesh Segments...\n') |
---|
581 | |
---|
582 | # Following lines: <vertex #> <vertex #> [boundary tag] |
---|
583 | for i,seg in enumerate(segments): |
---|
584 | fd.write(str(i) + ' ' + str(seg[0]) + ' ' + str(seg[1]) + ' ' + |
---|
585 | str(segment_tags[i]) + '\n') |
---|
586 | |
---|
587 | # One line: <# of holes> |
---|
588 | fd.write(str(len(holes)) + |
---|
589 | ' # <# of holes>, next lines <Hole #> <x> <y> ...Mesh Holes...\n') |
---|
590 | # <x> <y> |
---|
591 | for i,h in enumerate(holes): |
---|
592 | fd.write(str(i) + ' ' + str(h[0]) + ' ' + str(h[1]) + '\n') |
---|
593 | |
---|
594 | # One line: <# of regions> |
---|
595 | fd.write(str(len(regions)) + |
---|
596 | ' # <# of regions>, next lines <Region #> <x> <y> <tag>' |
---|
597 | '...Mesh Regions...\n') |
---|
598 | |
---|
599 | # <index> <x> <y> <tag> |
---|
600 | for i,r in enumerate(regions): |
---|
601 | fd.write(str(i) + ' ' + str(r[0]) + ' ' + str(r[1])+ ' ' + |
---|
602 | str(region_tags[i]) + '\n') |
---|
603 | |
---|
604 | # <index> [<MaxArea>|''] |
---|
605 | |
---|
606 | # One line: <# of regions> |
---|
607 | fd.write(str(len(regions)) + |
---|
608 | ' # <# of regions>, next lines <Region #> [Max Area] ' |
---|
609 | '...Mesh Regions...\n') |
---|
610 | for i,r in enumerate(regions): |
---|
611 | area = str(region_max_areas[i]) |
---|
612 | |
---|
613 | fd.write(str(i) + ' ' + area + '\n') |
---|
614 | |
---|
615 | # geo_reference info |
---|
616 | if dict.has_key('geo_reference') and not dict['geo_reference'] is None: |
---|
617 | dict['geo_reference'].write_ASCII(fd) |
---|
618 | |
---|
619 | |
---|
620 | ## |
---|
621 | # @brief Write a .msh file. |
---|
622 | # @param file Path to the file to write. |
---|
623 | # @param mesh Dictionary holding data to write. |
---|
624 | def _write_msh_file(file_name, mesh): |
---|
625 | """Write .msh NetCDF file |
---|
626 | |
---|
627 | WARNING: This function mangles the mesh data structure |
---|
628 | """ |
---|
629 | |
---|
630 | # FIXME(Ole and John): We ran into a problem on Bogong (64 bit) |
---|
631 | # where integers appeared as arrays. This may be similar to |
---|
632 | # problem seen by Steve in changeset:2778 where he had to wrap |
---|
633 | # them in int. Now we are trying with the native Integer format |
---|
634 | # (Int == 'l' == Int64). However, that caused casting errors, when |
---|
635 | # 64bit arrays are to be assigned to their NetCDF counterparts. It |
---|
636 | # seems that the NetCDF arrays are 32bit even though they are |
---|
637 | # created with the type Int64. Need to look at the NetCDF library |
---|
638 | # in more detail. |
---|
639 | |
---|
640 | IntType = num.int32 |
---|
641 | #IntType = Int |
---|
642 | |
---|
643 | #the triangulation |
---|
644 | mesh['vertices'] = num.array(mesh['vertices'], num.float) |
---|
645 | if mesh['vertex_attributes'] != None: |
---|
646 | mesh['vertex_attributes'] = \ |
---|
647 | num.array(mesh['vertex_attributes'], num.float) |
---|
648 | mesh['vertex_attribute_titles'] = \ |
---|
649 | num.array(mesh['vertex_attribute_titles'], num.character) |
---|
650 | mesh['segments'] = num.array(mesh['segments'], IntType) |
---|
651 | mesh['segment_tags'] = num.array(mesh['segment_tags'], num.character) |
---|
652 | mesh['triangles'] = num.array(mesh['triangles'], IntType) |
---|
653 | mesh['triangle_tags'] = num.array(mesh['triangle_tags']) |
---|
654 | mesh['triangle_neighbors'] = \ |
---|
655 | num.array(mesh['triangle_neighbors'], IntType) |
---|
656 | |
---|
657 | #the outline |
---|
658 | mesh['points'] = num.array(mesh['points'], num.float) |
---|
659 | mesh['point_attributes'] = num.array(mesh['point_attributes'], num.float) |
---|
660 | mesh['outline_segments'] = num.array(mesh['outline_segments'], IntType) |
---|
661 | mesh['outline_segment_tags'] = \ |
---|
662 | num.array(mesh['outline_segment_tags'], num.character) |
---|
663 | mesh['holes'] = num.array(mesh['holes'], num.float) |
---|
664 | mesh['regions'] = num.array(mesh['regions'], num.float) |
---|
665 | mesh['region_tags'] = num.array(mesh['region_tags'], num.character) |
---|
666 | mesh['region_max_areas'] = num.array(mesh['region_max_areas'], num.float) |
---|
667 | |
---|
668 | # NetCDF file definition |
---|
669 | try: |
---|
670 | outfile = NetCDFFile(file_name, netcdf_mode_w) |
---|
671 | except IOError: |
---|
672 | msg = 'File %s could not be created' % file_name |
---|
673 | raise Exception, msg |
---|
674 | |
---|
675 | #Create new file |
---|
676 | outfile.institution = 'Geoscience Australia' |
---|
677 | outfile.description = 'NetCDF format for compact and portable storage ' + \ |
---|
678 | 'of spatial point data' |
---|
679 | |
---|
680 | # dimension definitions - fixed |
---|
681 | outfile.createDimension('num_of_dimensions', 2) # This is 2d data |
---|
682 | outfile.createDimension('num_of_segment_ends', 2) # Segs have two points |
---|
683 | outfile.createDimension('num_of_triangle_vertices', 3) |
---|
684 | outfile.createDimension('num_of_triangle_faces', 3) |
---|
685 | outfile.createDimension('num_of_region_max_area', 1) |
---|
686 | |
---|
687 | # Create dimensions, variables and set the variables |
---|
688 | |
---|
689 | # trianglulation |
---|
690 | # vertices |
---|
691 | if (mesh['vertices'].shape[0] > 0): |
---|
692 | outfile.createDimension('num_of_vertices', mesh['vertices'].shape[0]) |
---|
693 | outfile.createVariable('vertices', netcdf_float, ('num_of_vertices', |
---|
694 | 'num_of_dimensions')) |
---|
695 | outfile.variables['vertices'][:] = mesh['vertices'] |
---|
696 | if (mesh['vertex_attributes'] != None and |
---|
697 | (mesh['vertex_attributes'].shape[0] > 0 and |
---|
698 | mesh['vertex_attributes'].shape[1] > 0)): |
---|
699 | outfile.createDimension('num_of_vertex_attributes', |
---|
700 | mesh['vertex_attributes'].shape[1]) |
---|
701 | outfile.createDimension('num_of_vertex_attribute_title_chars', |
---|
702 | mesh['vertex_attribute_titles'].shape[1]) |
---|
703 | outfile.createVariable('vertex_attributes', |
---|
704 | netcdf_float, |
---|
705 | ('num_of_vertices', |
---|
706 | 'num_of_vertex_attributes')) |
---|
707 | outfile.createVariable('vertex_attribute_titles', |
---|
708 | netcdf_char, |
---|
709 | ('num_of_vertex_attributes', |
---|
710 | 'num_of_vertex_attribute_title_chars')) |
---|
711 | outfile.variables['vertex_attributes'][:] = \ |
---|
712 | mesh['vertex_attributes'] |
---|
713 | outfile.variables['vertex_attribute_titles'][:] = \ |
---|
714 | mesh['vertex_attribute_titles'] |
---|
715 | |
---|
716 | # segments |
---|
717 | if (mesh['segments'].shape[0] > 0): |
---|
718 | outfile.createDimension('num_of_segments', mesh['segments'].shape[0]) |
---|
719 | outfile.createVariable('segments', netcdf_int, |
---|
720 | ('num_of_segments', 'num_of_segment_ends')) |
---|
721 | outfile.variables['segments'][:] = mesh['segments'] |
---|
722 | if mesh['segment_tags'].shape[1] > 0: |
---|
723 | outfile.createDimension('num_of_segment_tag_chars', |
---|
724 | mesh['segment_tags'].shape[1]) |
---|
725 | outfile.createVariable('segment_tags', |
---|
726 | netcdf_char, |
---|
727 | ('num_of_segments', |
---|
728 | 'num_of_segment_tag_chars')) |
---|
729 | outfile.variables['segment_tags'][:] = mesh['segment_tags'] |
---|
730 | |
---|
731 | # triangles |
---|
732 | if (mesh['triangles'].shape[0] > 0): |
---|
733 | outfile.createDimension('num_of_triangles', mesh['triangles'].shape[0]) |
---|
734 | outfile.createVariable('triangles', netcdf_int, |
---|
735 | ('num_of_triangles', 'num_of_triangle_vertices')) |
---|
736 | outfile.createVariable('triangle_neighbors', netcdf_int, |
---|
737 | ('num_of_triangles', 'num_of_triangle_faces')) |
---|
738 | outfile.variables['triangles'][:] = mesh['triangles'] |
---|
739 | outfile.variables['triangle_neighbors'][:] = mesh['triangle_neighbors'] |
---|
740 | if (mesh['triangle_tags'] != None and |
---|
741 | (mesh['triangle_tags'].shape[1] > 0)): |
---|
742 | outfile.createDimension('num_of_triangle_tag_chars', |
---|
743 | mesh['triangle_tags'].shape[1]) |
---|
744 | outfile.createVariable('triangle_tags', netcdf_char, |
---|
745 | ('num_of_triangles', |
---|
746 | 'num_of_triangle_tag_chars')) |
---|
747 | outfile.variables['triangle_tags'][:] = mesh['triangle_tags'] |
---|
748 | |
---|
749 | # outline |
---|
750 | # points |
---|
751 | if (mesh['points'].shape[0] > 0): |
---|
752 | outfile.createDimension('num_of_points', mesh['points'].shape[0]) |
---|
753 | outfile.createVariable('points', netcdf_float, |
---|
754 | ('num_of_points', 'num_of_dimensions')) |
---|
755 | outfile.variables['points'][:] = mesh['points'] |
---|
756 | if mesh['point_attributes'].shape[0] > 0 \ |
---|
757 | and mesh['point_attributes'].shape[1] > 0: |
---|
758 | outfile.createDimension('num_of_point_attributes', |
---|
759 | mesh['point_attributes'].shape[1]) |
---|
760 | outfile.createVariable('point_attributes', netcdf_float, |
---|
761 | ('num_of_points', 'num_of_point_attributes')) |
---|
762 | outfile.variables['point_attributes'][:] = mesh['point_attributes'] |
---|
763 | |
---|
764 | # outline_segments |
---|
765 | if mesh['outline_segments'].shape[0] > 0: |
---|
766 | outfile.createDimension('num_of_outline_segments', |
---|
767 | mesh['outline_segments'].shape[0]) |
---|
768 | outfile.createVariable('outline_segments', netcdf_int, |
---|
769 | ('num_of_outline_segments', |
---|
770 | 'num_of_segment_ends')) |
---|
771 | outfile.variables['outline_segments'][:] = mesh['outline_segments'] |
---|
772 | if (mesh['outline_segment_tags'].shape[1] > 0): |
---|
773 | outfile.createDimension('num_of_outline_segment_tag_chars', |
---|
774 | mesh['outline_segment_tags'].shape[1]) |
---|
775 | outfile.createVariable('outline_segment_tags', netcdf_char, |
---|
776 | ('num_of_outline_segments', |
---|
777 | 'num_of_outline_segment_tag_chars')) |
---|
778 | outfile.variables['outline_segment_tags'][:] = \ |
---|
779 | mesh['outline_segment_tags'] |
---|
780 | |
---|
781 | # holes |
---|
782 | if (mesh['holes'].shape[0] > 0): |
---|
783 | outfile.createDimension('num_of_holes', mesh['holes'].shape[0]) |
---|
784 | outfile.createVariable('holes', netcdf_float, |
---|
785 | ('num_of_holes', 'num_of_dimensions')) |
---|
786 | outfile.variables['holes'][:] = mesh['holes'] |
---|
787 | |
---|
788 | # regions |
---|
789 | if (mesh['regions'].shape[0] > 0): |
---|
790 | outfile.createDimension('num_of_regions', mesh['regions'].shape[0]) |
---|
791 | outfile.createVariable('regions', netcdf_float, |
---|
792 | ('num_of_regions', 'num_of_dimensions')) |
---|
793 | outfile.createVariable('region_max_areas', netcdf_float, |
---|
794 | ('num_of_regions',)) |
---|
795 | outfile.variables['regions'][:] = mesh['regions'] |
---|
796 | outfile.variables['region_max_areas'][:] = mesh['region_max_areas'] |
---|
797 | if (mesh['region_tags'].shape[1] > 0): |
---|
798 | outfile.createDimension('num_of_region_tag_chars', |
---|
799 | mesh['region_tags'].shape[1]) |
---|
800 | outfile.createVariable('region_tags', netcdf_char, |
---|
801 | ('num_of_regions', |
---|
802 | 'num_of_region_tag_chars')) |
---|
803 | outfile.variables['region_tags'][:] = mesh['region_tags'] |
---|
804 | |
---|
805 | # geo_reference info |
---|
806 | if mesh.has_key('geo_reference') and not mesh['geo_reference'] == None: |
---|
807 | mesh['geo_reference'].write_NetCDF(outfile) |
---|
808 | |
---|
809 | outfile.close() |
---|
810 | |
---|
811 | |
---|
812 | ## |
---|
813 | # @brief Read a mesh file. |
---|
814 | # @param file_name Path to the file to read. |
---|
815 | # @return A dictionary containing the .msh file data. |
---|
816 | # @note Throws IOError if file not found. |
---|
817 | def _read_msh_file(file_name): |
---|
818 | """ Read in an msh file.""" |
---|
819 | |
---|
820 | #Check contents. Get NetCDF |
---|
821 | fd = open(file_name, 'r') |
---|
822 | fd.close() |
---|
823 | |
---|
824 | # throws prints to screen if file not present |
---|
825 | fid = NetCDFFile(file_name, netcdf_mode_r) |
---|
826 | mesh = {} |
---|
827 | |
---|
828 | # Get the variables - the triangulation |
---|
829 | try: |
---|
830 | mesh['vertices'] = fid.variables['vertices'][:] |
---|
831 | except KeyError: |
---|
832 | mesh['vertices'] = num.array([], num.int) #array default# |
---|
833 | |
---|
834 | try: |
---|
835 | mesh['vertex_attributes'] = fid.variables['vertex_attributes'][:] |
---|
836 | except KeyError: |
---|
837 | mesh['vertex_attributes'] = None |
---|
838 | |
---|
839 | mesh['vertex_attribute_titles'] = [] |
---|
840 | try: |
---|
841 | titles = fid.variables['vertex_attribute_titles'][:] |
---|
842 | for i, title in enumerate(titles): |
---|
843 | mesh['vertex_attribute_titles'].append(titles[i].tostring().strip()) |
---|
844 | except KeyError: |
---|
845 | pass |
---|
846 | |
---|
847 | try: |
---|
848 | mesh['segments'] = fid.variables['segments'][:] |
---|
849 | except KeyError: |
---|
850 | mesh['segments'] = num.array([], num.int) #array default# |
---|
851 | |
---|
852 | mesh['segment_tags'] =[] |
---|
853 | try: |
---|
854 | tags = fid.variables['segment_tags'][:] |
---|
855 | for i, tag in enumerate(tags): |
---|
856 | mesh['segment_tags'].append(tags[i].tostring().strip()) |
---|
857 | except KeyError: |
---|
858 | for ob in mesh['segments']: |
---|
859 | mesh['segment_tags'].append('') |
---|
860 | |
---|
861 | try: |
---|
862 | mesh['triangles'] = fid.variables['triangles'][:] |
---|
863 | mesh['triangle_neighbors'] = fid.variables['triangle_neighbors'][:] |
---|
864 | except KeyError: |
---|
865 | mesh['triangles'] = num.array([], num.int) #array default# |
---|
866 | mesh['triangle_neighbors'] = num.array([], num.int) #array default# |
---|
867 | |
---|
868 | mesh['triangle_tags'] = [] |
---|
869 | try: |
---|
870 | tags = fid.variables['triangle_tags'][:] |
---|
871 | for i, tag in enumerate(tags): |
---|
872 | mesh['triangle_tags'].append(tags[i].tostring().strip()) |
---|
873 | except KeyError: |
---|
874 | for ob in mesh['triangles']: |
---|
875 | mesh['triangle_tags'].append('') |
---|
876 | |
---|
877 | #the outline |
---|
878 | try: |
---|
879 | mesh['points'] = fid.variables['points'][:] |
---|
880 | except KeyError: |
---|
881 | mesh['points'] = [] |
---|
882 | |
---|
883 | try: |
---|
884 | mesh['point_attributes'] = fid.variables['point_attributes'][:] |
---|
885 | except KeyError: |
---|
886 | mesh['point_attributes'] = [] |
---|
887 | for point in mesh['points']: |
---|
888 | mesh['point_attributes'].append([]) |
---|
889 | |
---|
890 | try: |
---|
891 | mesh['outline_segments'] = fid.variables['outline_segments'][:] |
---|
892 | except KeyError: |
---|
893 | mesh['outline_segments'] = num.array([], num.int) #array default# |
---|
894 | |
---|
895 | mesh['outline_segment_tags'] =[] |
---|
896 | try: |
---|
897 | tags = fid.variables['outline_segment_tags'][:] |
---|
898 | for i, tag in enumerate(tags): |
---|
899 | mesh['outline_segment_tags'].append(tags[i].tostring().strip()) |
---|
900 | except KeyError: |
---|
901 | for ob in mesh['outline_segments']: |
---|
902 | mesh['outline_segment_tags'].append('') |
---|
903 | |
---|
904 | try: |
---|
905 | mesh['holes'] = fid.variables['holes'][:] |
---|
906 | except KeyError: |
---|
907 | mesh['holes'] = num.array([], num.int) #array default# |
---|
908 | |
---|
909 | try: |
---|
910 | mesh['regions'] = fid.variables['regions'][:] |
---|
911 | except KeyError: |
---|
912 | mesh['regions'] = num.array([], num.int) #array default# |
---|
913 | |
---|
914 | mesh['region_tags'] =[] |
---|
915 | try: |
---|
916 | tags = fid.variables['region_tags'][:] |
---|
917 | for i, tag in enumerate(tags): |
---|
918 | mesh['region_tags'].append(tags[i].tostring().strip()) |
---|
919 | except KeyError: |
---|
920 | for ob in mesh['regions']: |
---|
921 | mesh['region_tags'].append('') |
---|
922 | |
---|
923 | try: |
---|
924 | mesh['region_max_areas'] = fid.variables['region_max_areas'][:] |
---|
925 | except KeyError: |
---|
926 | mesh['region_max_areas'] = num.array([], num.int) #array default# |
---|
927 | |
---|
928 | try: |
---|
929 | geo_reference = Geo_reference(NetCDFObject=fid) |
---|
930 | mesh['geo_reference'] = geo_reference |
---|
931 | except AttributeError, e: |
---|
932 | #geo_ref not compulsory |
---|
933 | mesh['geo_reference'] = None |
---|
934 | |
---|
935 | fid.close() |
---|
936 | |
---|
937 | return mesh |
---|
938 | |
---|
939 | |
---|
940 | ## |
---|
941 | # @brief Export a boundary file. |
---|
942 | # @param file_name Path to the file to write. |
---|
943 | # @param points List of point index pairs. |
---|
944 | # @paran title Title string to write into file (first line). |
---|
945 | # @param delimiter Delimiter string to write between points. |
---|
946 | # @note Used by alpha shapes |
---|
947 | def export_boundary_file(file_name, points, title, delimiter=','): |
---|
948 | """Export a boundary file. |
---|
949 | |
---|
950 | Format: |
---|
951 | First line: Title variable |
---|
952 | Following lines: [point index][delimiter][point index] |
---|
953 | |
---|
954 | file_name - the name of the new file |
---|
955 | points - List of point index pairs [[p1, p2],[p3, p4]..] |
---|
956 | title - info to write in the first line |
---|
957 | """ |
---|
958 | |
---|
959 | fd = open(file_name, 'w') |
---|
960 | |
---|
961 | fd.write(title + '\n') |
---|
962 | |
---|
963 | # [point index][delimiter][point index] |
---|
964 | for point in points: |
---|
965 | fd.write(str(point[0]) + delimiter + str(point[1]) + '\n') |
---|
966 | |
---|
967 | fd.close() |
---|
968 | |
---|
969 | |
---|
970 | ################################################################################ |
---|
971 | # IMPORT/EXPORT POINTS FILES |
---|
972 | ################################################################################ |
---|
973 | |
---|
974 | ## |
---|
975 | # @brief |
---|
976 | # @param point_atts |
---|
977 | def extent_point_atts(point_atts): |
---|
978 | """Returns 4 points representing the extent |
---|
979 | This loses attribute info. |
---|
980 | """ |
---|
981 | |
---|
982 | point_atts['pointlist'] = extent(point_atts['pointlist']) |
---|
983 | point_atts['attributelist'] = {} |
---|
984 | |
---|
985 | return point_atts |
---|
986 | |
---|
987 | |
---|
988 | ## |
---|
989 | # @brief Get an extent array for a set of points. |
---|
990 | # @param points A set of points. |
---|
991 | # @return An extent array of form [[min_x, min_y], [max_x, min_y], |
---|
992 | # [max_x, max_y], [min_x, max_y]] |
---|
993 | def extent(points): |
---|
994 | points = num.array(points, num.float) |
---|
995 | |
---|
996 | max_x = min_x = points[0][0] |
---|
997 | max_y = min_y = points[0][1] |
---|
998 | |
---|
999 | for point in points[1:]: |
---|
1000 | x = point[0] |
---|
1001 | if x > max_x: |
---|
1002 | max_x = x |
---|
1003 | if x < min_x: |
---|
1004 | min_x = x |
---|
1005 | |
---|
1006 | y = point[1] |
---|
1007 | if y > max_y: |
---|
1008 | max_y = y |
---|
1009 | if y < min_y: |
---|
1010 | min_y = y |
---|
1011 | |
---|
1012 | extent = num.array([[min_x, min_y], |
---|
1013 | [max_x, min_y], |
---|
1014 | [max_x, max_y], |
---|
1015 | [min_x, max_y]]) |
---|
1016 | |
---|
1017 | return extent |
---|
1018 | |
---|
1019 | |
---|
1020 | ## |
---|
1021 | # @brief Reduce a points file until number of points is less than limit. |
---|
1022 | # @param infile Path to input file to thin. |
---|
1023 | # @param outfile Path to output thinned file. |
---|
1024 | # @param max_points Max number of points in output file. |
---|
1025 | # @param verbose True if this function is to be verbose. |
---|
1026 | def reduce_pts(infile, outfile, max_points, verbose = False): |
---|
1027 | """Reduce a points file until less than given size. |
---|
1028 | |
---|
1029 | Reduces a points file by removing every second point until the # of points |
---|
1030 | is less than max_points. |
---|
1031 | """ |
---|
1032 | |
---|
1033 | # check out pts2rectangular in least squares, and the use of reduction. |
---|
1034 | # Maybe it does the same sort of thing? |
---|
1035 | point_atts = _read_pts_file(infile) |
---|
1036 | |
---|
1037 | while point_atts['pointlist'].shape[0] > max_points: |
---|
1038 | if verbose: print "point_atts['pointlist'].shape[0]" |
---|
1039 | point_atts = half_pts(point_atts) |
---|
1040 | |
---|
1041 | export_points_file(outfile, point_atts) |
---|
1042 | |
---|
1043 | |
---|
1044 | ## |
---|
1045 | # @brief |
---|
1046 | # @param infile |
---|
1047 | # @param max_points |
---|
1048 | # @param delimiter |
---|
1049 | # @param verbose True if this function is to be verbose. |
---|
1050 | # @return A list of |
---|
1051 | def produce_half_point_files(infile, max_points, delimiter, verbose=False): |
---|
1052 | point_atts = _read_pts_file(infile) |
---|
1053 | root, ext = splitext(infile) |
---|
1054 | outfiles = [] |
---|
1055 | |
---|
1056 | if verbose: print "# of points", point_atts['pointlist'].shape[0] |
---|
1057 | |
---|
1058 | while point_atts['pointlist'].shape[0] > max_points: |
---|
1059 | point_atts = half_pts(point_atts) |
---|
1060 | |
---|
1061 | if verbose: print "# of points", point_atts['pointlist'].shape[0] |
---|
1062 | |
---|
1063 | outfile = root + delimiter + str(point_atts['pointlist'].shape[0]) + ext |
---|
1064 | outfiles.append(outfile) |
---|
1065 | export_points_file(outfile, point_atts) |
---|
1066 | |
---|
1067 | return outfiles |
---|
1068 | |
---|
1069 | |
---|
1070 | ## |
---|
1071 | # @brief |
---|
1072 | # @param point_atts Object with attribute of 'pointlist'. |
---|
1073 | # @return |
---|
1074 | def point_atts2array(point_atts): |
---|
1075 | # convert attribute list to array of floats |
---|
1076 | point_atts['pointlist'] = num.array(point_atts['pointlist'], num.float) |
---|
1077 | |
---|
1078 | for key in point_atts['attributelist'].keys(): |
---|
1079 | point_atts['attributelist'][key] = \ |
---|
1080 | num.array(point_atts['attributelist'][key], num.float) |
---|
1081 | |
---|
1082 | return point_atts |
---|
1083 | |
---|
1084 | |
---|
1085 | ## |
---|
1086 | # @brief ?? |
---|
1087 | # @param point_atts ?? |
---|
1088 | # @return ?? |
---|
1089 | def half_pts(point_atts): |
---|
1090 | point_atts2array(point_atts) |
---|
1091 | point_atts['pointlist'] = point_atts['pointlist'][::2] |
---|
1092 | |
---|
1093 | for key in point_atts['attributelist'].keys(): |
---|
1094 | point_atts['attributelist'][key] = point_atts['attributelist'][key][::2] |
---|
1095 | |
---|
1096 | return point_atts |
---|
1097 | |
---|
1098 | ## |
---|
1099 | # @brief ?? |
---|
1100 | # @param dic ?? |
---|
1101 | # @return ?? |
---|
1102 | def concatinate_attributelist(dic): |
---|
1103 | """ |
---|
1104 | giving a dic[attribute title] = attribute |
---|
1105 | return list of attribute titles, array of attributes |
---|
1106 | """ |
---|
1107 | |
---|
1108 | point_attributes = num.array([], num.float) |
---|
1109 | keys = dic.keys() |
---|
1110 | key = keys.pop(0) |
---|
1111 | point_attributes = num.reshape(dic[key], (dic[key].shape[0], 1)) |
---|
1112 | for key in keys: |
---|
1113 | reshaped = num.reshape(dic[key], (dic[key].shape[0], 1)) |
---|
1114 | point_attributes = num.concatenate([point_attributes, reshaped], axis=1) |
---|
1115 | |
---|
1116 | return dic.keys(), point_attributes |
---|
1117 | |
---|
1118 | |
---|
1119 | ## |
---|
1120 | # @brief |
---|
1121 | # @param dict |
---|
1122 | # @param indices_to_keep |
---|
1123 | # @return |
---|
1124 | # @note FIXME(dsg), turn this dict plus methods into a class? |
---|
1125 | def take_points(dict, indices_to_keep): |
---|
1126 | dict = point_atts2array(dict) |
---|
1127 | dict['pointlist'] = num.take(dict['pointlist'], indices_to_keep) |
---|
1128 | |
---|
1129 | for key in dict['attributelist'].keys(): |
---|
1130 | dict['attributelist'][key] = num.take(dict['attributelist'][key], |
---|
1131 | indices_to_keep) |
---|
1132 | |
---|
1133 | return dict |
---|
1134 | |
---|
1135 | ## |
---|
1136 | # @brief ?? |
---|
1137 | # @param dict1 ?? |
---|
1138 | # @param dict2 ?? |
---|
1139 | # @return ?? |
---|
1140 | def add_point_dictionaries(dict1, dict2): |
---|
1141 | """ |
---|
1142 | """ |
---|
1143 | |
---|
1144 | dict1 = point_atts2array(dict1) |
---|
1145 | dict2 = point_atts2array(dict2) |
---|
1146 | |
---|
1147 | combined = {} |
---|
1148 | combined['pointlist'] = num.concatenate((dict2['pointlist'], |
---|
1149 | dict1['pointlist']), axis=0) |
---|
1150 | |
---|
1151 | atts = {} |
---|
1152 | for key in dict2['attributelist'].keys(): |
---|
1153 | atts[key]= num.concatenate((dict2['attributelist'][key], |
---|
1154 | dict1['attributelist'][key]), axis=0) |
---|
1155 | combined['attributelist'] = atts |
---|
1156 | combined['geo_reference'] = dict1['geo_reference'] |
---|
1157 | |
---|
1158 | return combined |
---|
1159 | |
---|
1160 | |
---|
1161 | if __name__ == "__main__": |
---|
1162 | pass |
---|