[4127] | 1 | """Class Quantity - Implements values at each triangular element |
---|
| 2 | |
---|
| 3 | To create: |
---|
| 4 | |
---|
| 5 | Quantity(domain, vertex_values) |
---|
| 6 | |
---|
| 7 | domain: Associated domain structure. Required. |
---|
| 8 | |
---|
| 9 | vertex_values: N x 3 array of values at each vertex for each element. |
---|
| 10 | Default None |
---|
| 11 | |
---|
| 12 | If vertex_values are None Create array of zeros compatible with domain. |
---|
| 13 | Otherwise check that it is compatible with dimenions of domain. |
---|
| 14 | Otherwise raise an exception |
---|
| 15 | """ |
---|
| 16 | |
---|
| 17 | from Numeric import array, zeros, Float, less, concatenate, NewAxis,\ |
---|
[4704] | 18 | argmax, argmin, allclose, take, reshape |
---|
[4130] | 19 | |
---|
[4127] | 20 | from anuga.utilities.numerical_tools import ensure_numeric, is_scalar |
---|
[4583] | 21 | from anuga.utilities.polygon import inside_polygon |
---|
| 22 | |
---|
[4127] | 23 | from anuga.geospatial_data.geospatial_data import Geospatial_data |
---|
[4130] | 24 | from anuga.fit_interpolate.fit import fit_to_mesh |
---|
[4254] | 25 | from anuga.config import points_file_block_line_size as default_block_line_size |
---|
[4815] | 26 | from anuga.config import epsilon |
---|
[4127] | 27 | |
---|
| 28 | class Quantity: |
---|
| 29 | |
---|
| 30 | def __init__(self, domain, vertex_values=None): |
---|
| 31 | |
---|
| 32 | from anuga.abstract_2d_finite_volumes.neighbour_mesh import Mesh |
---|
| 33 | |
---|
| 34 | msg = 'First argument in Quantity.__init__ ' |
---|
| 35 | msg += 'must be of class Mesh (or a subclass thereof)' |
---|
| 36 | assert isinstance(domain, Mesh), msg |
---|
| 37 | |
---|
| 38 | if vertex_values is None: |
---|
| 39 | N = len(domain) # number_of_elements |
---|
| 40 | self.vertex_values = zeros((N, 3), Float) |
---|
| 41 | else: |
---|
| 42 | self.vertex_values = array(vertex_values).astype(Float) |
---|
| 43 | |
---|
| 44 | N, V = self.vertex_values.shape |
---|
| 45 | assert V == 3,\ |
---|
| 46 | 'Three vertex values per element must be specified' |
---|
| 47 | |
---|
| 48 | |
---|
| 49 | msg = 'Number of vertex values (%d) must be consistent with'\ |
---|
| 50 | %N |
---|
| 51 | msg += 'number of elements in specified domain (%d).'\ |
---|
| 52 | %len(domain) |
---|
| 53 | |
---|
| 54 | assert N == len(domain), msg |
---|
| 55 | |
---|
| 56 | self.domain = domain |
---|
| 57 | |
---|
[5394] | 58 | # Allocate space for other quantities |
---|
[4127] | 59 | self.centroid_values = zeros(N, Float) |
---|
| 60 | self.edge_values = zeros((N, 3), Float) |
---|
| 61 | |
---|
[5394] | 62 | # Allocate space for Gradient |
---|
[4957] | 63 | self.x_gradient = zeros(N, Float) |
---|
[5162] | 64 | self.y_gradient = zeros(N, Float) |
---|
[4957] | 65 | |
---|
[5394] | 66 | # Allocate space for Limiter Phi |
---|
[5162] | 67 | self.phi = zeros(N, Float) |
---|
| 68 | |
---|
[5394] | 69 | # Intialise centroid and edge_values |
---|
[4127] | 70 | self.interpolate() |
---|
| 71 | |
---|
[5394] | 72 | # Allocate space for boundary values |
---|
[4957] | 73 | L = len(domain.boundary) |
---|
| 74 | self.boundary_values = zeros(L, Float) |
---|
[4127] | 75 | |
---|
[5394] | 76 | # Allocate space for updates of conserved quantities by |
---|
| 77 | # flux calculations and forcing functions |
---|
[4127] | 78 | |
---|
[5394] | 79 | # Allocate space for update fields |
---|
[4957] | 80 | self.explicit_update = zeros(N, Float ) |
---|
| 81 | self.semi_implicit_update = zeros(N, Float ) |
---|
[5162] | 82 | self.centroid_backup_values = zeros(N, Float) |
---|
[4957] | 83 | |
---|
[5162] | 84 | self.beta = 1.0 |
---|
[4957] | 85 | |
---|
| 86 | |
---|
[5162] | 87 | |
---|
[5394] | 88 | # Methods for operator overloading |
---|
[4127] | 89 | def __len__(self): |
---|
| 90 | return self.centroid_values.shape[0] |
---|
| 91 | |
---|
| 92 | |
---|
| 93 | def __neg__(self): |
---|
| 94 | """Negate all values in this quantity giving meaning to the |
---|
| 95 | expression -Q where Q is an instance of class Quantity |
---|
| 96 | """ |
---|
| 97 | |
---|
| 98 | Q = Quantity(self.domain) |
---|
| 99 | Q.set_values(-self.vertex_values) |
---|
| 100 | return Q |
---|
| 101 | |
---|
| 102 | |
---|
| 103 | def __add__(self, other): |
---|
| 104 | """Add to self anything that could populate a quantity |
---|
| 105 | |
---|
| 106 | E.g other can be a constant, an array, a function, another quantity |
---|
| 107 | (except for a filename or points, attributes (for now)) |
---|
| 108 | - see set_values for details |
---|
| 109 | """ |
---|
| 110 | |
---|
| 111 | Q = Quantity(self.domain) |
---|
| 112 | Q.set_values(other) |
---|
| 113 | |
---|
| 114 | result = Quantity(self.domain) |
---|
| 115 | result.set_values(self.vertex_values + Q.vertex_values) |
---|
| 116 | return result |
---|
| 117 | |
---|
| 118 | def __radd__(self, other): |
---|
| 119 | """Handle cases like 7+Q, where Q is an instance of class Quantity |
---|
| 120 | """ |
---|
| 121 | return self + other |
---|
| 122 | |
---|
| 123 | |
---|
| 124 | def __sub__(self, other): |
---|
| 125 | return self + -other #Invoke __neg__ |
---|
| 126 | |
---|
| 127 | def __mul__(self, other): |
---|
| 128 | """Multiply self with anything that could populate a quantity |
---|
| 129 | |
---|
| 130 | E.g other can be a constant, an array, a function, another quantity |
---|
| 131 | (except for a filename or points, attributes (for now)) |
---|
| 132 | - see set_values for details |
---|
| 133 | """ |
---|
| 134 | |
---|
[4815] | 135 | if isinstance(other, Quantity): |
---|
| 136 | Q = other |
---|
| 137 | else: |
---|
| 138 | Q = Quantity(self.domain) |
---|
| 139 | Q.set_values(other) |
---|
[4127] | 140 | |
---|
| 141 | result = Quantity(self.domain) |
---|
[4815] | 142 | |
---|
| 143 | # The product of vertex_values, edge_values and centroid_values |
---|
| 144 | # are calculated and assigned directly without using |
---|
| 145 | # set_values (which calls interpolate). Otherwise |
---|
| 146 | # edge and centroid values wouldn't be products from q1 and q2 |
---|
| 147 | result.vertex_values = self.vertex_values * Q.vertex_values |
---|
| 148 | result.edge_values = self.edge_values * Q.edge_values |
---|
| 149 | result.centroid_values = self.centroid_values * Q.centroid_values |
---|
| 150 | |
---|
[4127] | 151 | return result |
---|
| 152 | |
---|
| 153 | def __rmul__(self, other): |
---|
| 154 | """Handle cases like 3*Q, where Q is an instance of class Quantity |
---|
| 155 | """ |
---|
| 156 | return self * other |
---|
| 157 | |
---|
[4815] | 158 | def __div__(self, other): |
---|
| 159 | """Divide self with anything that could populate a quantity |
---|
| 160 | |
---|
| 161 | E.g other can be a constant, an array, a function, another quantity |
---|
| 162 | (except for a filename or points, attributes (for now)) |
---|
| 163 | - see set_values for details |
---|
| 164 | |
---|
| 165 | Zero division is dealt with by adding an epsilon to the divisore |
---|
| 166 | FIXME (Ole): Replace this with native INF once we migrate to NumPy |
---|
| 167 | """ |
---|
| 168 | |
---|
| 169 | if isinstance(other, Quantity): |
---|
| 170 | Q = other |
---|
| 171 | else: |
---|
| 172 | Q = Quantity(self.domain) |
---|
| 173 | Q.set_values(other) |
---|
| 174 | |
---|
| 175 | result = Quantity(self.domain) |
---|
| 176 | |
---|
| 177 | # The quotient of vertex_values, edge_values and centroid_values |
---|
| 178 | # are calculated and assigned directly without using |
---|
| 179 | # set_values (which calls interpolate). Otherwise |
---|
| 180 | # edge and centroid values wouldn't be quotient of q1 and q2 |
---|
| 181 | result.vertex_values = self.vertex_values/(Q.vertex_values + epsilon) |
---|
| 182 | result.edge_values = self.edge_values/(Q.edge_values + epsilon) |
---|
| 183 | result.centroid_values = self.centroid_values/(Q.centroid_values + epsilon) |
---|
| 184 | |
---|
| 185 | return result |
---|
| 186 | |
---|
| 187 | def __rdiv__(self, other): |
---|
| 188 | """Handle cases like 3/Q, where Q is an instance of class Quantity |
---|
| 189 | """ |
---|
| 190 | return self / other |
---|
| 191 | |
---|
[4127] | 192 | def __pow__(self, other): |
---|
| 193 | """Raise quantity to (numerical) power |
---|
| 194 | |
---|
| 195 | As with __mul__ vertex values are processed entry by entry |
---|
| 196 | while centroid and edge values are re-interpolated. |
---|
| 197 | |
---|
| 198 | Example using __pow__: |
---|
| 199 | Q = (Q1**2 + Q2**2)**0.5 |
---|
| 200 | |
---|
| 201 | """ |
---|
| 202 | |
---|
[4815] | 203 | if isinstance(other, Quantity): |
---|
| 204 | Q = other |
---|
| 205 | else: |
---|
| 206 | Q = Quantity(self.domain) |
---|
| 207 | Q.set_values(other) |
---|
| 208 | |
---|
[4127] | 209 | result = Quantity(self.domain) |
---|
[4815] | 210 | |
---|
| 211 | # The power of vertex_values, edge_values and centroid_values |
---|
| 212 | # are calculated and assigned directly without using |
---|
| 213 | # set_values (which calls interpolate). Otherwise |
---|
| 214 | # edge and centroid values wouldn't be correct |
---|
| 215 | result.vertex_values = self.vertex_values ** other |
---|
| 216 | result.edge_values = self.edge_values ** other |
---|
| 217 | result.centroid_values = self.centroid_values ** other |
---|
| 218 | |
---|
[4127] | 219 | return result |
---|
| 220 | |
---|
[4815] | 221 | #def __sqrt__(self, other): |
---|
| 222 | # """Define in terms of x**0.5 |
---|
| 223 | # """ |
---|
| 224 | # pass |
---|
| 225 | |
---|
[4127] | 226 | |
---|
| 227 | def interpolate(self): |
---|
| 228 | """Compute interpolated values at edges and centroid |
---|
| 229 | Pre-condition: vertex_values have been set |
---|
| 230 | """ |
---|
[4728] | 231 | |
---|
[4791] | 232 | # FIXME (Ole): Maybe this function |
---|
| 233 | # should move to the C-interface? |
---|
| 234 | # However, it isn't called by validate_all.py, so it |
---|
| 235 | # may not be that important to optimise it? |
---|
| 236 | |
---|
[4127] | 237 | N = self.vertex_values.shape[0] |
---|
| 238 | for i in range(N): |
---|
| 239 | v0 = self.vertex_values[i, 0] |
---|
| 240 | v1 = self.vertex_values[i, 1] |
---|
| 241 | v2 = self.vertex_values[i, 2] |
---|
| 242 | |
---|
| 243 | self.centroid_values[i] = (v0 + v1 + v2)/3 |
---|
| 244 | |
---|
| 245 | self.interpolate_from_vertices_to_edges() |
---|
| 246 | |
---|
| 247 | |
---|
| 248 | def interpolate_from_vertices_to_edges(self): |
---|
[5394] | 249 | # Call correct module function |
---|
| 250 | # (either from this module or C-extension) |
---|
[4127] | 251 | interpolate_from_vertices_to_edges(self) |
---|
| 252 | |
---|
[4886] | 253 | def interpolate_from_edges_to_vertices(self): |
---|
[5394] | 254 | # Call correct module function |
---|
| 255 | # (either from this module or C-extension) |
---|
[4886] | 256 | interpolate_from_edges_to_vertices(self) |
---|
[4127] | 257 | |
---|
| 258 | |
---|
| 259 | |
---|
[4886] | 260 | |
---|
[4735] | 261 | # New leaner interface to setting values |
---|
[4127] | 262 | def set_values(self, |
---|
[5518] | 263 | numeric=None, # List, numeric array or constant |
---|
| 264 | quantity=None, # Another quantity |
---|
| 265 | function=None, # Callable object: f(x,y) |
---|
| 266 | geospatial_data=None, # Arbitrary dataset |
---|
| 267 | points=None, values=None, data_georef=None, # Obsoleted by use of geo_spatial object |
---|
| 268 | filename=None, attribute_name=None, #Input from file |
---|
| 269 | alpha=None, |
---|
| 270 | location='vertices', |
---|
| 271 | polygon=None, |
---|
| 272 | indices=None, |
---|
| 273 | smooth=False, |
---|
| 274 | verbose=False, |
---|
| 275 | use_cache=False): |
---|
[4127] | 276 | |
---|
| 277 | """Set values for quantity based on different sources. |
---|
| 278 | |
---|
| 279 | numeric: |
---|
| 280 | Compatible list, Numeric array (see below) or constant. |
---|
| 281 | If callable it will treated as a function (see below) |
---|
| 282 | If instance of another Quantity it will be treated as such. |
---|
| 283 | If geo_spatial object it will be treated as such |
---|
| 284 | |
---|
| 285 | quantity: |
---|
| 286 | Another quantity (compatible quantity, e.g. obtained as a |
---|
| 287 | linear combination of quantities) |
---|
| 288 | |
---|
| 289 | function: |
---|
| 290 | Any callable object that takes two 1d arrays x and y |
---|
| 291 | each of length N and returns an array also of length N. |
---|
| 292 | The function will be evaluated at points determined by |
---|
| 293 | location and indices in the underlying mesh. |
---|
| 294 | |
---|
| 295 | geospatial_data: |
---|
| 296 | Arbitrary geo spatial dataset in the form of the class |
---|
| 297 | Geospatial_data. Mesh points are populated using |
---|
| 298 | fit_interpolate.fit fitting |
---|
| 299 | |
---|
| 300 | points: |
---|
| 301 | Nx2 array of data points for use with fit_interpolate.fit |
---|
| 302 | If points are present, an N array of attribute |
---|
| 303 | values corresponding to |
---|
| 304 | each data point must be present. |
---|
| 305 | (Obsoleted by geospatial_data) |
---|
| 306 | |
---|
| 307 | values: |
---|
| 308 | If points is specified, values is an array of length N containing |
---|
| 309 | attribute values for each point. |
---|
| 310 | (Obsoleted by geospatial_data) |
---|
| 311 | |
---|
| 312 | data_georef: |
---|
| 313 | If points is specified, geo_reference applies to each point. |
---|
| 314 | (Obsoleted by geospatial_data) |
---|
| 315 | |
---|
| 316 | filename: |
---|
| 317 | Name of a points file containing data points and attributes for |
---|
| 318 | use with fit_interpolate.fit. |
---|
| 319 | |
---|
| 320 | attribute_name: |
---|
| 321 | If specified, any array matching that name |
---|
| 322 | will be used. from file or geospatial_data. |
---|
| 323 | Otherwise a default will be used. |
---|
| 324 | |
---|
| 325 | alpha: |
---|
| 326 | Smoothing parameter to be used with fit_interpolate.fit. |
---|
| 327 | See module fit_interpolate.fit for further details about alpha. |
---|
| 328 | Alpha will only be used with points, values or filename. |
---|
| 329 | Otherwise it will be ignored. |
---|
| 330 | |
---|
| 331 | |
---|
| 332 | location: Where values are to be stored. |
---|
| 333 | Permissible options are: vertices, edges, centroids |
---|
| 334 | Default is 'vertices' |
---|
| 335 | |
---|
| 336 | In case of location == 'centroids' the dimension values must |
---|
| 337 | be a list of a Numerical array of length N, |
---|
| 338 | N being the number of elements. |
---|
| 339 | Otherwise it must be of dimension Nx3 |
---|
| 340 | |
---|
| 341 | |
---|
| 342 | The values will be stored in elements following their |
---|
| 343 | internal ordering. |
---|
| 344 | |
---|
[5518] | 345 | If location is 'unique vertices' indices refers the set |
---|
| 346 | of node ids that the operation applies to. |
---|
| 347 | If location is not 'unique vertices' indices refers the |
---|
| 348 | set of triangle ids that the operation applies to. |
---|
[4127] | 349 | |
---|
[5518] | 350 | |
---|
[4127] | 351 | If selected location is vertices, values for |
---|
| 352 | centroid and edges will be assigned interpolated |
---|
| 353 | values. In any other case, only values for the |
---|
| 354 | specified locations will be assigned and the others |
---|
| 355 | will be left undefined. |
---|
| 356 | |
---|
[4579] | 357 | |
---|
| 358 | polygon: Restrict update of quantity to locations that fall |
---|
| 359 | inside polygon. Polygon works by selecting indices |
---|
| 360 | and calling set_values recursively. |
---|
[4583] | 361 | Polygon mode has only been implemented for |
---|
| 362 | constant values so far. |
---|
[4579] | 363 | |
---|
| 364 | indices: Restrict update of quantity to locations that are |
---|
| 365 | identified by indices (e.g. node ids if location |
---|
[5518] | 366 | is 'unique vertices' or triangle ids otherwise). |
---|
[4579] | 367 | |
---|
[4127] | 368 | verbose: True means that output to stdout is generated |
---|
| 369 | |
---|
| 370 | use_cache: True means that caching of intermediate results is |
---|
| 371 | attempted for fit_interpolate.fit. |
---|
| 372 | |
---|
| 373 | |
---|
| 374 | |
---|
| 375 | |
---|
| 376 | Exactly one of the arguments |
---|
| 377 | numeric, quantity, function, points, filename |
---|
| 378 | must be present. |
---|
| 379 | """ |
---|
| 380 | |
---|
| 381 | from anuga.geospatial_data.geospatial_data import Geospatial_data |
---|
| 382 | from types import FloatType, IntType, LongType, ListType, NoneType |
---|
| 383 | from Numeric import ArrayType |
---|
| 384 | |
---|
[4579] | 385 | |
---|
[4583] | 386 | # Treat special case: Polygon situation |
---|
[4584] | 387 | # Location will be ignored and set to 'centroids' |
---|
[4583] | 388 | # FIXME (Ole): This needs to be generalised and |
---|
| 389 | # perhaps the notion of location and indices simplified |
---|
[5518] | 390 | |
---|
| 391 | # FIXME (Ole): Need to compute indices based on polygon (and location) and |
---|
| 392 | # use existing code after that. |
---|
[4584] | 393 | |
---|
[4583] | 394 | if polygon is not None: |
---|
| 395 | if indices is not None: |
---|
| 396 | msg = 'Only one of polygon and indices can be specified' |
---|
| 397 | raise Exception, msg |
---|
[4579] | 398 | |
---|
[4583] | 399 | msg = 'With polygon selected, set_quantity must provide ' |
---|
| 400 | msg += 'the keyword numeric and it must (currently) be ' |
---|
| 401 | msg += 'a constant.' |
---|
| 402 | if numeric is None: |
---|
| 403 | raise Exception, msg |
---|
| 404 | else: |
---|
| 405 | # Check that numeric is as constant |
---|
| 406 | assert type(numeric) in [FloatType, IntType, LongType], msg |
---|
[4579] | 407 | |
---|
[4583] | 408 | |
---|
| 409 | location = 'centroids' |
---|
| 410 | |
---|
| 411 | |
---|
[4592] | 412 | points = self.domain.get_centroid_coordinates(absolute=True) |
---|
[4583] | 413 | indices = inside_polygon(points, polygon) |
---|
| 414 | |
---|
| 415 | self.set_values_from_constant(numeric, |
---|
| 416 | location, indices, verbose) |
---|
[4897] | 417 | |
---|
| 418 | |
---|
[4583] | 419 | self.extrapolate_first_order() |
---|
[4897] | 420 | |
---|
| 421 | if smooth: |
---|
| 422 | self.smooth_vertex_values() |
---|
| 423 | |
---|
| 424 | |
---|
[4583] | 425 | return |
---|
| 426 | |
---|
| 427 | |
---|
| 428 | |
---|
| 429 | |
---|
| 430 | |
---|
| 431 | |
---|
[4769] | 432 | # General input checks |
---|
[4127] | 433 | L = [numeric, quantity, function, geospatial_data, points, filename] |
---|
| 434 | msg = 'Exactly one of the arguments '+\ |
---|
| 435 | 'numeric, quantity, function, geospatial_data, points, '+\ |
---|
| 436 | 'or filename must be present.' |
---|
| 437 | assert L.count(None) == len(L)-1, msg |
---|
| 438 | |
---|
| 439 | |
---|
| 440 | if location not in ['vertices', 'centroids', 'edges', |
---|
| 441 | 'unique vertices']: |
---|
| 442 | msg = 'Invalid location: %s' %location |
---|
[4166] | 443 | raise Exception, msg |
---|
[4127] | 444 | |
---|
| 445 | |
---|
| 446 | msg = 'Indices must be a list or None' |
---|
| 447 | assert type(indices) in [ListType, NoneType, ArrayType], msg |
---|
| 448 | |
---|
| 449 | |
---|
| 450 | if not(points is None and values is None and data_georef is None): |
---|
| 451 | from warnings import warn |
---|
| 452 | |
---|
| 453 | msg = 'Using points, values or data_georef with set_quantity ' |
---|
| 454 | msg += 'is obsolete. Please use a Geospatial_data object instead.' |
---|
[4735] | 455 | #warn(msg, DeprecationWarning) |
---|
| 456 | raise Exception, msg |
---|
[4127] | 457 | |
---|
| 458 | |
---|
| 459 | |
---|
[4769] | 460 | # Determine which 'set_values_from_...' to use |
---|
[4127] | 461 | |
---|
| 462 | if numeric is not None: |
---|
| 463 | if type(numeric) in [FloatType, IntType, LongType]: |
---|
| 464 | self.set_values_from_constant(numeric, |
---|
| 465 | location, indices, verbose) |
---|
| 466 | elif type(numeric) in [ArrayType, ListType]: |
---|
| 467 | self.set_values_from_array(numeric, |
---|
| 468 | location, indices, verbose) |
---|
| 469 | elif callable(numeric): |
---|
| 470 | self.set_values_from_function(numeric, |
---|
| 471 | location, indices, verbose) |
---|
| 472 | elif isinstance(numeric, Quantity): |
---|
| 473 | self.set_values_from_quantity(numeric, |
---|
| 474 | location, indices, verbose) |
---|
| 475 | elif isinstance(numeric, Geospatial_data): |
---|
| 476 | self.set_values_from_geospatial_data(numeric, |
---|
| 477 | alpha, |
---|
| 478 | location, indices, |
---|
[5518] | 479 | verbose=verbose, |
---|
| 480 | use_cache=use_cache) |
---|
[4127] | 481 | else: |
---|
| 482 | msg = 'Illegal type for argument numeric: %s' %str(numeric) |
---|
| 483 | raise msg |
---|
| 484 | |
---|
| 485 | elif quantity is not None: |
---|
| 486 | self.set_values_from_quantity(quantity, |
---|
| 487 | location, indices, verbose) |
---|
| 488 | elif function is not None: |
---|
| 489 | msg = 'Argument function must be callable' |
---|
| 490 | assert callable(function), msg |
---|
| 491 | self.set_values_from_function(function, |
---|
| 492 | location, indices, verbose) |
---|
| 493 | elif geospatial_data is not None: |
---|
| 494 | self.set_values_from_geospatial_data(geospatial_data, |
---|
| 495 | alpha, |
---|
| 496 | location, indices, |
---|
[5518] | 497 | verbose=verbose, |
---|
| 498 | use_cache=use_cache) |
---|
[4127] | 499 | elif points is not None: |
---|
[4735] | 500 | msg = 'The usage of points in set_values has been deprecated.' +\ |
---|
| 501 | 'Please use the geospatial_data object instead.' |
---|
| 502 | raise Exception, msg |
---|
[4127] | 503 | |
---|
[4735] | 504 | |
---|
| 505 | |
---|
[4127] | 506 | elif filename is not None: |
---|
[4254] | 507 | if hasattr(self.domain, 'points_file_block_line_size'): |
---|
| 508 | max_read_lines = self.domain.points_file_block_line_size |
---|
| 509 | else: |
---|
| 510 | max_read_lines = default_block_line_size |
---|
[4127] | 511 | self.set_values_from_file(filename, attribute_name, alpha, |
---|
| 512 | location, indices, |
---|
[5518] | 513 | verbose=verbose, |
---|
[4254] | 514 | max_read_lines=max_read_lines, |
---|
[5518] | 515 | use_cache=use_cache) |
---|
[4127] | 516 | else: |
---|
| 517 | raise Exception, 'This can\'t happen :-)' |
---|
| 518 | |
---|
| 519 | |
---|
| 520 | |
---|
| 521 | # Update all locations in triangles |
---|
| 522 | if location == 'vertices' or location == 'unique vertices': |
---|
| 523 | # Intialise centroid and edge_values |
---|
| 524 | self.interpolate() |
---|
| 525 | |
---|
| 526 | if location == 'centroids': |
---|
| 527 | # Extrapolate 1st order - to capture notion of area being specified |
---|
| 528 | self.extrapolate_first_order() |
---|
| 529 | |
---|
| 530 | |
---|
| 531 | |
---|
[5394] | 532 | # Specific functions for setting values |
---|
[4127] | 533 | def set_values_from_constant(self, X, |
---|
| 534 | location, indices, verbose): |
---|
| 535 | """Set quantity values from specified constant X |
---|
| 536 | """ |
---|
| 537 | |
---|
[4579] | 538 | # FIXME (Ole): Somehow indices refer to centroids |
---|
| 539 | # rather than vertices as default. See unit test |
---|
| 540 | # test_set_vertex_values_using_general_interface_with_subset(self): |
---|
| 541 | |
---|
[4127] | 542 | |
---|
| 543 | if location == 'centroids': |
---|
| 544 | if indices is None: |
---|
| 545 | self.centroid_values[:] = X |
---|
| 546 | else: |
---|
[5518] | 547 | # Brute force |
---|
[4127] | 548 | for i in indices: |
---|
| 549 | self.centroid_values[i] = X |
---|
| 550 | |
---|
| 551 | elif location == 'edges': |
---|
| 552 | if indices is None: |
---|
| 553 | self.edge_values[:] = X |
---|
| 554 | else: |
---|
[5518] | 555 | # Brute force |
---|
[4127] | 556 | for i in indices: |
---|
| 557 | self.edge_values[i] = X |
---|
| 558 | |
---|
| 559 | elif location == 'unique vertices': |
---|
| 560 | if indices is None: |
---|
[4478] | 561 | self.edge_values[:] = X #FIXME (Ole): Shouldn't this be vertex_values? |
---|
[4127] | 562 | else: |
---|
| 563 | |
---|
[5518] | 564 | # Go through list of unique vertices |
---|
[4127] | 565 | for unique_vert_id in indices: |
---|
| 566 | |
---|
[4478] | 567 | triangles = self.domain.get_triangles_and_vertices_per_node(node=unique_vert_id) |
---|
| 568 | |
---|
[5518] | 569 | # In case there are unused points |
---|
[4478] | 570 | if len(triangles) == 0: |
---|
| 571 | continue |
---|
| 572 | |
---|
[5518] | 573 | # Go through all triangle, vertex pairs |
---|
| 574 | # and set corresponding vertex value |
---|
[4127] | 575 | for triangle_id, vertex_id in triangles: |
---|
| 576 | self.vertex_values[triangle_id, vertex_id] = X |
---|
| 577 | |
---|
[5518] | 578 | # Intialise centroid and edge_values |
---|
[4127] | 579 | self.interpolate() |
---|
| 580 | else: |
---|
| 581 | if indices is None: |
---|
| 582 | self.vertex_values[:] = X |
---|
| 583 | else: |
---|
[5518] | 584 | # Brute force |
---|
[4127] | 585 | for i_vertex in indices: |
---|
| 586 | self.vertex_values[i_vertex] = X |
---|
| 587 | |
---|
| 588 | |
---|
| 589 | |
---|
| 590 | |
---|
| 591 | def set_values_from_array(self, values, |
---|
| 592 | location='vertices', |
---|
| 593 | indices=None, |
---|
| 594 | verbose=False): |
---|
| 595 | """Set values for quantity |
---|
| 596 | |
---|
| 597 | values: Numeric array |
---|
| 598 | location: Where values are to be stored. |
---|
| 599 | Permissible options are: vertices, edges, centroid, unique vertices |
---|
| 600 | Default is 'vertices' |
---|
| 601 | |
---|
| 602 | indices - if this action is carried out on a subset of |
---|
| 603 | elements or unique vertices |
---|
| 604 | The element/unique vertex indices are specified here. |
---|
| 605 | |
---|
| 606 | In case of location == 'centroid' the dimension values must |
---|
| 607 | be a list of a Numerical array of length N, N being the number |
---|
| 608 | of elements. |
---|
| 609 | |
---|
| 610 | Otherwise it must be of dimension Nx3 |
---|
| 611 | |
---|
| 612 | The values will be stored in elements following their |
---|
| 613 | internal ordering. |
---|
| 614 | |
---|
| 615 | If selected location is vertices, values for centroid and edges |
---|
| 616 | will be assigned interpolated values. |
---|
| 617 | In any other case, only values for the specified locations |
---|
| 618 | will be assigned and the others will be left undefined. |
---|
| 619 | """ |
---|
| 620 | |
---|
| 621 | from Numeric import array, Float, Int, allclose |
---|
| 622 | |
---|
| 623 | values = array(values).astype(Float) |
---|
| 624 | |
---|
| 625 | if indices is not None: |
---|
| 626 | indices = array(indices).astype(Int) |
---|
[4768] | 627 | msg = 'Number of values must match number of indices:' |
---|
[5518] | 628 | msg += ' You specified %d values and %d indices'\ |
---|
[4768] | 629 | %(values.shape[0], indices.shape[0]) |
---|
[4127] | 630 | assert values.shape[0] == indices.shape[0], msg |
---|
| 631 | |
---|
| 632 | N = self.centroid_values.shape[0] |
---|
| 633 | |
---|
| 634 | if location == 'centroids': |
---|
| 635 | assert len(values.shape) == 1, 'Values array must be 1d' |
---|
| 636 | |
---|
| 637 | if indices is None: |
---|
| 638 | msg = 'Number of values must match number of elements' |
---|
| 639 | assert values.shape[0] == N, msg |
---|
| 640 | |
---|
| 641 | self.centroid_values = values |
---|
| 642 | else: |
---|
| 643 | msg = 'Number of values must match number of indices' |
---|
| 644 | assert values.shape[0] == indices.shape[0], msg |
---|
| 645 | |
---|
| 646 | #Brute force |
---|
| 647 | for i in range(len(indices)): |
---|
| 648 | self.centroid_values[indices[i]] = values[i] |
---|
| 649 | |
---|
| 650 | elif location == 'edges': |
---|
| 651 | # FIXME (Ole): No mention of indices here. However, I don't |
---|
| 652 | # think we ever need to set values at edges anyway |
---|
| 653 | assert len(values.shape) == 2, 'Values array must be 2d' |
---|
| 654 | |
---|
| 655 | msg = 'Number of values must match number of elements' |
---|
| 656 | assert values.shape[0] == N, msg |
---|
| 657 | |
---|
| 658 | msg = 'Array must be N x 3' |
---|
| 659 | assert values.shape[1] == 3, msg |
---|
| 660 | |
---|
| 661 | self.edge_values = values |
---|
| 662 | |
---|
| 663 | elif location == 'unique vertices': |
---|
| 664 | assert len(values.shape) == 1 or allclose(values.shape[1:], 1),\ |
---|
| 665 | 'Values array must be 1d' |
---|
| 666 | |
---|
| 667 | self.set_vertex_values(values.flat, indices=indices) |
---|
| 668 | |
---|
| 669 | else: |
---|
| 670 | # Location vertices |
---|
| 671 | if len(values.shape) == 1: |
---|
| 672 | self.set_vertex_values(values, indices=indices) |
---|
| 673 | |
---|
| 674 | elif len(values.shape) == 2: |
---|
[5518] | 675 | # Vertex values are given as a triplet for each triangle |
---|
[4127] | 676 | |
---|
| 677 | msg = 'Array must be N x 3' |
---|
| 678 | assert values.shape[1] == 3, msg |
---|
| 679 | |
---|
| 680 | if indices is None: |
---|
| 681 | self.vertex_values = values |
---|
| 682 | else: |
---|
| 683 | for element_index, value in map(None, indices, values): |
---|
| 684 | self.vertex_values[element_index] = value |
---|
| 685 | else: |
---|
| 686 | msg = 'Values array must be 1d or 2d' |
---|
| 687 | raise msg |
---|
| 688 | |
---|
| 689 | |
---|
| 690 | def set_values_from_quantity(self, q, |
---|
| 691 | location, indices, verbose): |
---|
| 692 | """Set quantity values from specified quantity instance q |
---|
| 693 | |
---|
| 694 | Location is ignored - vertices will always be used here. |
---|
| 695 | """ |
---|
| 696 | |
---|
| 697 | |
---|
| 698 | A = q.vertex_values |
---|
| 699 | |
---|
| 700 | from Numeric import allclose |
---|
| 701 | msg = 'Quantities are defined on different meshes. '+\ |
---|
| 702 | 'This might be a case for implementing interpolation '+\ |
---|
| 703 | 'between different meshes.' |
---|
| 704 | assert allclose(A.shape, self.vertex_values.shape), msg |
---|
| 705 | |
---|
| 706 | self.set_values(A, location='vertices', |
---|
| 707 | indices=indices, |
---|
| 708 | verbose=verbose) |
---|
| 709 | |
---|
| 710 | |
---|
| 711 | def set_values_from_function(self, f, |
---|
| 712 | location='vertices', |
---|
| 713 | indices=None, |
---|
| 714 | verbose=False): |
---|
| 715 | """Set values for quantity using specified function |
---|
| 716 | |
---|
| 717 | Input |
---|
| 718 | |
---|
| 719 | f: x, y -> z Function where x, y and z are arrays |
---|
| 720 | location: Where values are to be stored. |
---|
| 721 | Permissible options are: vertices, centroid, edges, |
---|
| 722 | unique vertices |
---|
| 723 | Default is "vertices" |
---|
| 724 | indices: |
---|
| 725 | |
---|
| 726 | |
---|
| 727 | """ |
---|
| 728 | |
---|
[5518] | 729 | # FIXME: Should check that function returns something sensible and |
---|
| 730 | # raise a meaningfull exception if it returns None for example |
---|
[4127] | 731 | |
---|
[5518] | 732 | # FIXME: Should supply absolute coordinates |
---|
[4127] | 733 | |
---|
| 734 | |
---|
| 735 | # Compute the function values and call set_values again |
---|
| 736 | if location == 'centroids': |
---|
| 737 | if indices is None: |
---|
| 738 | indices = range(len(self)) |
---|
| 739 | |
---|
| 740 | V = take(self.domain.get_centroid_coordinates(), indices) |
---|
| 741 | self.set_values(f(V[:,0], V[:,1]), |
---|
| 742 | location=location, |
---|
| 743 | indices=indices) |
---|
| 744 | |
---|
| 745 | elif location == 'vertices': |
---|
| 746 | |
---|
| 747 | M = self.domain.number_of_triangles |
---|
| 748 | V = self.domain.get_vertex_coordinates() |
---|
| 749 | |
---|
| 750 | x = V[:,0]; y = V[:,1]; |
---|
| 751 | values = f(x, y) |
---|
| 752 | |
---|
| 753 | |
---|
| 754 | # FIXME (Ole): This code should replace all the |
---|
| 755 | # rest of this function and it would work, except |
---|
| 756 | # one unit test in test_region fails. |
---|
| 757 | # If that could be resolved this one will be |
---|
| 758 | # more robust and simple. |
---|
| 759 | |
---|
| 760 | #values = reshape(values, (M,3)) |
---|
| 761 | #self.set_values(values, |
---|
| 762 | # location='vertices', |
---|
| 763 | # indices=indices) |
---|
| 764 | |
---|
| 765 | |
---|
| 766 | # This should be removed |
---|
| 767 | if is_scalar(values): |
---|
| 768 | # Function returned a constant value |
---|
| 769 | self.set_values_from_constant(values, |
---|
| 770 | location, indices, verbose) |
---|
| 771 | return |
---|
| 772 | |
---|
| 773 | # This should be removed |
---|
| 774 | if indices is None: |
---|
| 775 | for j in range(3): |
---|
| 776 | self.vertex_values[:,j] = values[j::3] |
---|
| 777 | else: |
---|
| 778 | #Brute force |
---|
| 779 | for i in indices: |
---|
| 780 | for j in range(3): |
---|
| 781 | self.vertex_values[i,j] = values[3*i+j] |
---|
| 782 | |
---|
| 783 | |
---|
| 784 | else: |
---|
| 785 | raise 'Not implemented: %s' %location |
---|
| 786 | |
---|
| 787 | |
---|
| 788 | |
---|
| 789 | def set_values_from_geospatial_data(self, geospatial_data, alpha, |
---|
| 790 | location, indices, |
---|
[5518] | 791 | verbose=False, |
---|
| 792 | use_cache=False): |
---|
[5394] | 793 | # FIXME: Use this function for the time being. Later move code in here |
---|
[4127] | 794 | |
---|
[5518] | 795 | points = geospatial_data.get_data_points(absolute=False) |
---|
[4127] | 796 | values = geospatial_data.get_attributes() |
---|
| 797 | data_georef = geospatial_data.get_geo_reference() |
---|
| 798 | |
---|
| 799 | |
---|
| 800 | |
---|
| 801 | from anuga.coordinate_transforms.geo_reference import Geo_reference |
---|
| 802 | |
---|
| 803 | |
---|
| 804 | points = ensure_numeric(points, Float) |
---|
| 805 | values = ensure_numeric(values, Float) |
---|
| 806 | |
---|
| 807 | if location != 'vertices': |
---|
| 808 | msg = 'set_values_from_points is only defined for '+\ |
---|
| 809 | 'location=\'vertices\'' |
---|
| 810 | raise ms |
---|
| 811 | |
---|
| 812 | coordinates = self.domain.get_nodes() |
---|
| 813 | triangles = self.domain.triangles #FIXME |
---|
| 814 | |
---|
| 815 | |
---|
[5518] | 816 | # Take care of georeferencing |
---|
[4127] | 817 | if data_georef is None: |
---|
| 818 | data_georef = Geo_reference() |
---|
| 819 | |
---|
| 820 | |
---|
| 821 | mesh_georef = self.domain.geo_reference |
---|
| 822 | |
---|
| 823 | |
---|
[4569] | 824 | # Call fit_interpolate.fit function |
---|
[5518] | 825 | # args = (coordinates, triangles, points, values) |
---|
[4779] | 826 | args = (points, ) |
---|
| 827 | kwargs = {'vertex_coordinates': coordinates, |
---|
| 828 | 'triangles': triangles, |
---|
| 829 | 'mesh': None, |
---|
| 830 | 'point_attributes': values, |
---|
| 831 | 'data_origin': data_georef.get_origin(), |
---|
[4127] | 832 | 'mesh_origin': mesh_georef.get_origin(), |
---|
| 833 | 'alpha': alpha, |
---|
| 834 | 'verbose': verbose} |
---|
| 835 | |
---|
[4569] | 836 | vertex_attributes = apply(fit_to_mesh, |
---|
| 837 | args, kwargs) |
---|
[4127] | 838 | |
---|
[4569] | 839 | # Call underlying method using array values |
---|
[4127] | 840 | self.set_values_from_array(vertex_attributes, |
---|
| 841 | location, indices, verbose) |
---|
| 842 | |
---|
[4735] | 843 | |
---|
| 844 | |
---|
| 845 | def set_values_from_points(self, points, values, alpha, |
---|
| 846 | location, indices, |
---|
[5518] | 847 | data_georef=None, |
---|
| 848 | verbose=False, |
---|
| 849 | use_cache=False): |
---|
[4735] | 850 | """ |
---|
| 851 | Set quantity values from arbitray data points using |
---|
| 852 | fit_interpolate.fit |
---|
| 853 | """ |
---|
| 854 | |
---|
| 855 | raise Exception, 'set_values_from_points is obsolete, use geospatial data object instead' |
---|
| 856 | |
---|
| 857 | |
---|
[4127] | 858 | def set_values_from_file(self, filename, attribute_name, alpha, |
---|
| 859 | location, indices, |
---|
[5518] | 860 | verbose=False, |
---|
| 861 | use_cache=False, |
---|
[4252] | 862 | max_read_lines=None): |
---|
[4127] | 863 | """Set quantity based on arbitrary points in a points file |
---|
| 864 | using attribute_name selects name of attribute |
---|
| 865 | present in file. |
---|
| 866 | If attribute_name is not specified, use first available attribute |
---|
| 867 | as defined in geospatial_data. |
---|
| 868 | """ |
---|
| 869 | |
---|
| 870 | from types import StringType |
---|
| 871 | msg = 'Filename must be a text string' |
---|
| 872 | assert type(filename) == StringType, msg |
---|
| 873 | |
---|
[4130] | 874 | |
---|
| 875 | if location != 'vertices': |
---|
[4735] | 876 | msg = 'set_values_from_file is only defined for '+\ |
---|
[4130] | 877 | 'location=\'vertices\'' |
---|
[4149] | 878 | raise msg |
---|
[4130] | 879 | |
---|
[4872] | 880 | if True: |
---|
[4808] | 881 | vertex_attributes = fit_to_mesh(filename, |
---|
[4821] | 882 | mesh=self.domain, |
---|
[4808] | 883 | alpha=alpha, |
---|
| 884 | attribute_name=attribute_name, |
---|
| 885 | use_cache=use_cache, |
---|
| 886 | verbose=verbose, |
---|
| 887 | max_read_lines=max_read_lines) |
---|
| 888 | else: |
---|
| 889 | |
---|
| 890 | coordinates = self.domain.get_nodes(absolute=True) |
---|
| 891 | triangles = self.domain.triangles #FIXME |
---|
| 892 | vertex_attributes = fit_to_mesh(filename, |
---|
| 893 | coordinates, triangles, |
---|
| 894 | alpha=alpha, |
---|
| 895 | attribute_name=attribute_name, |
---|
| 896 | use_cache=use_cache, |
---|
| 897 | verbose=verbose, |
---|
| 898 | max_read_lines=max_read_lines) |
---|
[4253] | 899 | |
---|
[4569] | 900 | # Call underlying method using array values |
---|
[4130] | 901 | self.set_values_from_array(vertex_attributes, |
---|
| 902 | location, indices, verbose) |
---|
[4127] | 903 | |
---|
| 904 | |
---|
[4704] | 905 | def get_extremum_index(self, mode=None, indices=None): |
---|
| 906 | """Return index for maximum or minimum value of quantity (on centroids) |
---|
[4127] | 907 | |
---|
[4704] | 908 | Optional arguments: |
---|
| 909 | mode is either 'max'(default) or 'min'. |
---|
[4127] | 910 | indices is the set of element ids that the operation applies to. |
---|
| 911 | |
---|
| 912 | Usage: |
---|
[4704] | 913 | i = get_extreme_index() |
---|
[4127] | 914 | |
---|
| 915 | Notes: |
---|
[4704] | 916 | We do not seek the extremum at vertices as each vertex can |
---|
[4127] | 917 | have multiple values - one for each triangle sharing it. |
---|
| 918 | |
---|
| 919 | If there are multiple cells with same maximum value, the |
---|
| 920 | first cell encountered in the triangle array is returned. |
---|
| 921 | """ |
---|
| 922 | |
---|
| 923 | V = self.get_values(location='centroids', indices=indices) |
---|
| 924 | |
---|
| 925 | # Always return absolute indices |
---|
[4704] | 926 | if mode is None or mode == 'max': |
---|
| 927 | i = argmax(V) |
---|
| 928 | elif mode == 'min': |
---|
| 929 | i = argmin(V) |
---|
[4127] | 930 | |
---|
[4704] | 931 | |
---|
[4127] | 932 | if indices is None: |
---|
| 933 | return i |
---|
| 934 | else: |
---|
| 935 | return indices[i] |
---|
| 936 | |
---|
[4704] | 937 | |
---|
| 938 | def get_maximum_index(self, indices=None): |
---|
| 939 | """See get extreme index for details |
---|
| 940 | """ |
---|
| 941 | |
---|
| 942 | return self.get_extremum_index(mode='max', |
---|
| 943 | indices=indices) |
---|
| 944 | |
---|
| 945 | |
---|
[4127] | 946 | |
---|
| 947 | def get_maximum_value(self, indices=None): |
---|
| 948 | """Return maximum value of quantity (on centroids) |
---|
| 949 | |
---|
| 950 | Optional argument: |
---|
| 951 | indices is the set of element ids that the operation applies to. |
---|
| 952 | |
---|
| 953 | Usage: |
---|
| 954 | v = get_maximum_value() |
---|
| 955 | |
---|
| 956 | Note, we do not seek the maximum at vertices as each vertex can |
---|
| 957 | have multiple values - one for each triangle sharing it |
---|
| 958 | """ |
---|
| 959 | |
---|
| 960 | |
---|
| 961 | i = self.get_maximum_index(indices) |
---|
| 962 | V = self.get_values(location='centroids') #, indices=indices) |
---|
| 963 | |
---|
| 964 | return V[i] |
---|
| 965 | |
---|
| 966 | |
---|
| 967 | def get_maximum_location(self, indices=None): |
---|
| 968 | """Return location of maximum value of quantity (on centroids) |
---|
| 969 | |
---|
| 970 | Optional argument: |
---|
| 971 | indices is the set of element ids that the operation applies to. |
---|
| 972 | |
---|
| 973 | Usage: |
---|
| 974 | x, y = get_maximum_location() |
---|
| 975 | |
---|
| 976 | |
---|
| 977 | Notes: |
---|
| 978 | We do not seek the maximum at vertices as each vertex can |
---|
| 979 | have multiple values - one for each triangle sharing it. |
---|
| 980 | |
---|
| 981 | If there are multiple cells with same maximum value, the |
---|
| 982 | first cell encountered in the triangle array is returned. |
---|
| 983 | """ |
---|
| 984 | |
---|
| 985 | i = self.get_maximum_index(indices) |
---|
| 986 | x, y = self.domain.get_centroid_coordinates()[i] |
---|
| 987 | |
---|
| 988 | return x, y |
---|
| 989 | |
---|
| 990 | |
---|
[4704] | 991 | def get_minimum_index(self, indices=None): |
---|
| 992 | """See get extreme index for details |
---|
| 993 | """ |
---|
[4127] | 994 | |
---|
[4704] | 995 | return self.get_extremum_index(mode='min', |
---|
| 996 | indices=indices) |
---|
[4127] | 997 | |
---|
[4704] | 998 | |
---|
| 999 | def get_minimum_value(self, indices=None): |
---|
| 1000 | """Return minimum value of quantity (on centroids) |
---|
| 1001 | |
---|
| 1002 | Optional argument: |
---|
| 1003 | indices is the set of element ids that the operation applies to. |
---|
| 1004 | |
---|
| 1005 | Usage: |
---|
| 1006 | v = get_minimum_value() |
---|
| 1007 | |
---|
| 1008 | See get_maximum_value for more details. |
---|
| 1009 | """ |
---|
| 1010 | |
---|
| 1011 | |
---|
| 1012 | i = self.get_minimum_index(indices) |
---|
| 1013 | V = self.get_values(location='centroids') |
---|
| 1014 | |
---|
| 1015 | return V[i] |
---|
| 1016 | |
---|
| 1017 | |
---|
| 1018 | def get_minimum_location(self, indices=None): |
---|
| 1019 | """Return location of minimum value of quantity (on centroids) |
---|
| 1020 | |
---|
| 1021 | Optional argument: |
---|
| 1022 | indices is the set of element ids that the operation applies to. |
---|
| 1023 | |
---|
| 1024 | Usage: |
---|
| 1025 | x, y = get_minimum_location() |
---|
| 1026 | |
---|
| 1027 | |
---|
| 1028 | Notes: |
---|
| 1029 | We do not seek the maximum at vertices as each vertex can |
---|
| 1030 | have multiple values - one for each triangle sharing it. |
---|
| 1031 | |
---|
| 1032 | If there are multiple cells with same maximum value, the |
---|
| 1033 | first cell encountered in the triangle array is returned. |
---|
| 1034 | """ |
---|
| 1035 | |
---|
| 1036 | i = self.get_minimum_index(indices) |
---|
| 1037 | x, y = self.domain.get_centroid_coordinates()[i] |
---|
| 1038 | |
---|
| 1039 | return x, y |
---|
| 1040 | |
---|
| 1041 | |
---|
| 1042 | |
---|
| 1043 | |
---|
[4127] | 1044 | def get_interpolated_values(self, interpolation_points): |
---|
| 1045 | |
---|
| 1046 | # Interpolation object based on internal (discontinuous triangles) |
---|
| 1047 | x, y, vertex_values, triangles = self.get_vertex_values(xy=True, |
---|
| 1048 | smooth=False) |
---|
| 1049 | # FIXME: This concat should roll into get_vertex_values |
---|
| 1050 | vertex_coordinates = concatenate((x[:, NewAxis], y[:, NewAxis]), |
---|
| 1051 | axis=1) |
---|
| 1052 | |
---|
| 1053 | can_reuse = False |
---|
| 1054 | if hasattr(self, 'interpolation_object'): |
---|
| 1055 | # Reuse to save time |
---|
| 1056 | I = self.interpolation_object |
---|
| 1057 | |
---|
| 1058 | if allclose(interpolation_points, I._point_coordinates): |
---|
| 1059 | can_reuse = True |
---|
| 1060 | |
---|
| 1061 | |
---|
| 1062 | if can_reuse is True: |
---|
| 1063 | # Use absence of points to indicate reuse in I.interpolate |
---|
| 1064 | result = I.interpolate(vertex_values) |
---|
| 1065 | else: |
---|
| 1066 | from anuga.fit_interpolate.interpolate import Interpolate |
---|
| 1067 | |
---|
| 1068 | # Create interpolation object with matrix |
---|
| 1069 | I = Interpolate(vertex_coordinates, triangles) |
---|
| 1070 | self.interpolation_object = I |
---|
| 1071 | |
---|
| 1072 | # Call interpolate with points the first time |
---|
| 1073 | interpolation_points = ensure_numeric(interpolation_points, Float) |
---|
| 1074 | result = I.interpolate(vertex_values, interpolation_points) |
---|
| 1075 | |
---|
| 1076 | return result |
---|
| 1077 | |
---|
| 1078 | |
---|
| 1079 | def get_values(self, interpolation_points=None, |
---|
| 1080 | location='vertices', |
---|
| 1081 | indices = None): |
---|
| 1082 | """get values for quantity |
---|
| 1083 | |
---|
| 1084 | return X, Compatible list, Numeric array (see below) |
---|
| 1085 | interpolation_points: List of x, y coordinates where value is |
---|
| 1086 | sought (using interpolation). If points are given, values of |
---|
| 1087 | location and indices are ignored |
---|
| 1088 | |
---|
| 1089 | location: Where values are to be stored. |
---|
[4679] | 1090 | Permissible options are: vertices, edges, centroids |
---|
[4127] | 1091 | and unique vertices. Default is 'vertices' |
---|
| 1092 | |
---|
| 1093 | |
---|
| 1094 | The returned values with be a list the length of indices |
---|
| 1095 | (N if indices = None). |
---|
| 1096 | |
---|
| 1097 | In case of location == 'centroids' the dimension of returned |
---|
| 1098 | values will be a list or a Numerical array of length N, N being |
---|
| 1099 | the number of elements. |
---|
| 1100 | |
---|
| 1101 | In case of location == 'vertices' or 'edges' the dimension of |
---|
| 1102 | returned values will be of dimension Nx3 |
---|
| 1103 | |
---|
| 1104 | In case of location == 'unique vertices' the average value at |
---|
| 1105 | each vertex will be returned and the dimension of returned values |
---|
| 1106 | will be a 1d array of length "number of vertices" |
---|
| 1107 | |
---|
| 1108 | Indices is the set of element ids that the operation applies to. |
---|
| 1109 | |
---|
| 1110 | The values will be stored in elements following their |
---|
| 1111 | internal ordering. |
---|
| 1112 | """ |
---|
| 1113 | from Numeric import take |
---|
| 1114 | |
---|
[4768] | 1115 | # FIXME (Ole): I reckon we should have the option of passing a |
---|
| 1116 | # polygon into get_values. The question becomes how |
---|
| 1117 | # resulting values should be ordered. |
---|
| 1118 | |
---|
[4127] | 1119 | if interpolation_points is not None: |
---|
| 1120 | return self.get_interpolated_values(interpolation_points) |
---|
| 1121 | |
---|
| 1122 | |
---|
| 1123 | |
---|
| 1124 | if location not in ['vertices', 'centroids', 'edges', |
---|
| 1125 | 'unique vertices']: |
---|
| 1126 | msg = 'Invalid location: %s' %location |
---|
| 1127 | raise msg |
---|
| 1128 | |
---|
| 1129 | import types, Numeric |
---|
| 1130 | assert type(indices) in [types.ListType, types.NoneType, |
---|
| 1131 | Numeric.ArrayType],\ |
---|
| 1132 | 'Indices must be a list or None' |
---|
| 1133 | |
---|
| 1134 | if location == 'centroids': |
---|
| 1135 | if (indices == None): |
---|
| 1136 | indices = range(len(self)) |
---|
| 1137 | return take(self.centroid_values,indices) |
---|
| 1138 | elif location == 'edges': |
---|
| 1139 | if (indices == None): |
---|
| 1140 | indices = range(len(self)) |
---|
| 1141 | return take(self.edge_values,indices) |
---|
| 1142 | elif location == 'unique vertices': |
---|
| 1143 | if (indices == None): |
---|
| 1144 | indices=range(self.domain.number_of_nodes) |
---|
| 1145 | vert_values = [] |
---|
[5518] | 1146 | |
---|
[5394] | 1147 | # Go through list of unique vertices |
---|
[4127] | 1148 | for unique_vert_id in indices: |
---|
[4478] | 1149 | triangles = self.domain.get_triangles_and_vertices_per_node(node=unique_vert_id) |
---|
| 1150 | |
---|
[5394] | 1151 | # In case there are unused points |
---|
[4478] | 1152 | if len(triangles) == 0: |
---|
[4127] | 1153 | msg = 'Unique vertex not associated with triangles' |
---|
| 1154 | raise msg |
---|
| 1155 | |
---|
| 1156 | # Go through all triangle, vertex pairs |
---|
| 1157 | # Average the values |
---|
| 1158 | |
---|
| 1159 | # FIXME (Ole): Should we merge this with get_vertex_values |
---|
| 1160 | sum = 0 |
---|
| 1161 | for triangle_id, vertex_id in triangles: |
---|
| 1162 | sum += self.vertex_values[triangle_id, vertex_id] |
---|
| 1163 | vert_values.append(sum/len(triangles)) |
---|
| 1164 | return Numeric.array(vert_values) |
---|
| 1165 | else: |
---|
[4677] | 1166 | if (indices is None): |
---|
[4127] | 1167 | indices = range(len(self)) |
---|
[4677] | 1168 | return take(self.vertex_values, indices) |
---|
[4127] | 1169 | |
---|
| 1170 | |
---|
| 1171 | |
---|
| 1172 | def set_vertex_values(self, A, indices = None): |
---|
| 1173 | """Set vertex values for all unique vertices based on input array A |
---|
| 1174 | which has one entry per unique vertex, i.e. |
---|
[4478] | 1175 | one value for each row in array self.domain.nodes. |
---|
[4127] | 1176 | |
---|
| 1177 | indices is the list of vertex_id's that will be set. |
---|
| 1178 | |
---|
| 1179 | This function is used by set_values_from_array |
---|
| 1180 | """ |
---|
| 1181 | |
---|
| 1182 | from Numeric import array, Float |
---|
| 1183 | |
---|
[5394] | 1184 | # Assert that A can be converted to a Numeric array of appropriate dim |
---|
| 1185 | A = ensure_numeric(A, Float) |
---|
[4127] | 1186 | |
---|
[5394] | 1187 | # print 'SHAPE A', A.shape |
---|
[4127] | 1188 | assert len(A.shape) == 1 |
---|
| 1189 | |
---|
| 1190 | if indices is None: |
---|
| 1191 | assert A.shape[0] == self.domain.get_nodes().shape[0] |
---|
| 1192 | vertex_list = range(A.shape[0]) |
---|
| 1193 | else: |
---|
| 1194 | assert A.shape[0] == len(indices) |
---|
| 1195 | vertex_list = indices |
---|
| 1196 | |
---|
[5394] | 1197 | # Go through list of unique vertices |
---|
[4127] | 1198 | for i_index, unique_vert_id in enumerate(vertex_list): |
---|
| 1199 | |
---|
| 1200 | |
---|
[4478] | 1201 | triangles = self.domain.get_triangles_and_vertices_per_node(node=unique_vert_id) |
---|
| 1202 | |
---|
[5394] | 1203 | # In case there are unused points |
---|
[4478] | 1204 | if len(triangles) == 0: continue |
---|
| 1205 | |
---|
[5394] | 1206 | # Go through all triangle, vertex pairs |
---|
| 1207 | # touching vertex unique_vert_id and set corresponding vertex value |
---|
[4127] | 1208 | for triangle_id, vertex_id in triangles: |
---|
| 1209 | self.vertex_values[triangle_id, vertex_id] = A[i_index] |
---|
| 1210 | |
---|
[5394] | 1211 | # Intialise centroid and edge_values |
---|
[4127] | 1212 | self.interpolate() |
---|
| 1213 | |
---|
| 1214 | |
---|
[4897] | 1215 | def smooth_vertex_values(self): |
---|
| 1216 | """ Smooths vertex values. |
---|
[4127] | 1217 | """ |
---|
| 1218 | |
---|
[5518] | 1219 | A,V = self.get_vertex_values(xy=False, smooth=True) |
---|
[4897] | 1220 | self.set_vertex_values(A) |
---|
[4127] | 1221 | |
---|
| 1222 | |
---|
| 1223 | # Methods for outputting model results |
---|
| 1224 | def get_vertex_values(self, |
---|
| 1225 | xy=True, |
---|
| 1226 | smooth=None, |
---|
[4471] | 1227 | precision=None): |
---|
[4127] | 1228 | """Return vertex values like an OBJ format i.e. one value per node. |
---|
| 1229 | |
---|
| 1230 | The vertex values are returned as one sequence in the 1D float array A. |
---|
| 1231 | If requested the coordinates will be returned in 1D arrays X and Y. |
---|
| 1232 | |
---|
| 1233 | The connectivity is represented as an integer array, V, of dimension |
---|
| 1234 | Mx3, where M is the number of triangles. Each row has three indices |
---|
| 1235 | defining the triangle and they correspond to elements in the arrays |
---|
| 1236 | X, Y and A. |
---|
| 1237 | |
---|
| 1238 | if smooth is True, vertex values corresponding to one common |
---|
[4471] | 1239 | coordinate set will be smoothed by taking the average of vertex values for each node. |
---|
| 1240 | In this case vertex coordinates will be |
---|
[4127] | 1241 | de-duplicated corresponding to the original nodes as obtained from |
---|
| 1242 | the method general_mesh.get_nodes() |
---|
| 1243 | |
---|
| 1244 | If no smoothings is required, vertex coordinates and values will |
---|
| 1245 | be aggregated as a concatenation of values at |
---|
| 1246 | vertices 0, vertices 1 and vertices 2. This corresponds to |
---|
| 1247 | the node coordinates obtained from the method |
---|
| 1248 | general_mesh.get_vertex_coordinates() |
---|
| 1249 | |
---|
| 1250 | |
---|
| 1251 | Calling convention |
---|
| 1252 | if xy is True: |
---|
| 1253 | X,Y,A,V = get_vertex_values |
---|
| 1254 | else: |
---|
| 1255 | A,V = get_vertex_values |
---|
| 1256 | |
---|
| 1257 | """ |
---|
| 1258 | |
---|
| 1259 | from Numeric import concatenate, zeros, Float, Int, array, reshape |
---|
| 1260 | |
---|
| 1261 | |
---|
| 1262 | if smooth is None: |
---|
| 1263 | # Take default from domain |
---|
[4897] | 1264 | try: |
---|
| 1265 | smooth = self.domain.smooth |
---|
| 1266 | except: |
---|
| 1267 | smooth = False |
---|
[4127] | 1268 | |
---|
| 1269 | if precision is None: |
---|
| 1270 | precision = Float |
---|
| 1271 | |
---|
| 1272 | |
---|
| 1273 | if smooth is True: |
---|
[4471] | 1274 | # Ensure continuous vertex values by averaging |
---|
| 1275 | # values at each node |
---|
[4127] | 1276 | |
---|
| 1277 | V = self.domain.get_triangles() |
---|
| 1278 | N = self.domain.number_of_full_nodes # Ignore ghost nodes if any |
---|
[4471] | 1279 | A = zeros(N, Float) |
---|
[4127] | 1280 | points = self.domain.get_nodes() |
---|
[4471] | 1281 | |
---|
| 1282 | if 1: |
---|
| 1283 | # Fast C version |
---|
| 1284 | average_vertex_values(ensure_numeric(self.domain.vertex_value_indices), |
---|
| 1285 | ensure_numeric(self.domain.number_of_triangles_per_node), |
---|
| 1286 | ensure_numeric(self.vertex_values), |
---|
| 1287 | A) |
---|
| 1288 | A = A.astype(precision) |
---|
| 1289 | else: |
---|
[4127] | 1290 | |
---|
[4471] | 1291 | # Slow Python version |
---|
| 1292 | |
---|
| 1293 | current_node = 0 |
---|
| 1294 | k = 0 # Track triangles touching on node |
---|
| 1295 | total = 0.0 |
---|
| 1296 | for index in self.domain.vertex_value_indices: |
---|
[4536] | 1297 | if current_node == N: |
---|
| 1298 | msg = 'Current node exceeding number of nodes (%d) ' %(N) |
---|
| 1299 | raise msg |
---|
| 1300 | |
---|
| 1301 | |
---|
| 1302 | |
---|
[4471] | 1303 | k += 1 |
---|
| 1304 | |
---|
| 1305 | volume_id = index / 3 |
---|
| 1306 | vertex_id = index % 3 |
---|
| 1307 | |
---|
| 1308 | #assert V[volume_id, vertex_id] == current_node |
---|
| 1309 | |
---|
[4127] | 1310 | v = self.vertex_values[volume_id, vertex_id] |
---|
[4471] | 1311 | total += v |
---|
[4127] | 1312 | |
---|
[4471] | 1313 | #print 'current_node=%d, index=%d, k=%d, total=%f' %(current_node, index, k, total) |
---|
| 1314 | if self.domain.number_of_triangles_per_node[current_node] == k: |
---|
| 1315 | A[current_node] = total/k |
---|
| 1316 | |
---|
| 1317 | |
---|
| 1318 | # Move on to next node |
---|
| 1319 | total = 0.0 |
---|
| 1320 | k = 0 |
---|
| 1321 | current_node += 1 |
---|
[4127] | 1322 | |
---|
[4471] | 1323 | |
---|
| 1324 | |
---|
[4127] | 1325 | else: |
---|
| 1326 | # Allow discontinuous vertex values |
---|
| 1327 | V = self.domain.get_disconnected_triangles() |
---|
| 1328 | points = self.domain.get_vertex_coordinates() |
---|
| 1329 | A = self.vertex_values.flat.astype(precision) |
---|
| 1330 | |
---|
| 1331 | |
---|
| 1332 | # Return |
---|
| 1333 | if xy is True: |
---|
| 1334 | X = points[:,0].astype(precision) |
---|
| 1335 | Y = points[:,1].astype(precision) |
---|
| 1336 | |
---|
| 1337 | return X, Y, A, V |
---|
| 1338 | else: |
---|
| 1339 | return A, V |
---|
| 1340 | |
---|
| 1341 | |
---|
| 1342 | |
---|
| 1343 | def extrapolate_first_order(self): |
---|
| 1344 | """Extrapolate conserved quantities from centroid to |
---|
[4883] | 1345 | vertices and edges for each volume using |
---|
[4127] | 1346 | first order scheme. |
---|
| 1347 | """ |
---|
| 1348 | |
---|
| 1349 | qc = self.centroid_values |
---|
| 1350 | qv = self.vertex_values |
---|
[4883] | 1351 | qe = self.edge_values |
---|
[4127] | 1352 | |
---|
| 1353 | for i in range(3): |
---|
| 1354 | qv[:,i] = qc |
---|
[4883] | 1355 | qe[:,i] = qc |
---|
[4127] | 1356 | |
---|
[4957] | 1357 | self.x_gradient *= 0.0 |
---|
| 1358 | self.y_gradient *= 0.0 |
---|
[4127] | 1359 | |
---|
[4957] | 1360 | |
---|
[4127] | 1361 | def get_integral(self): |
---|
| 1362 | """Compute the integral of quantity across entire domain |
---|
| 1363 | """ |
---|
| 1364 | integral = 0 |
---|
| 1365 | for k in range(len(self.domain)): |
---|
| 1366 | area = self.domain.areas[k] |
---|
| 1367 | qc = self.centroid_values[k] |
---|
| 1368 | integral += qc*area |
---|
| 1369 | |
---|
| 1370 | return integral |
---|
| 1371 | |
---|
[4957] | 1372 | def get_gradients(self): |
---|
| 1373 | """Provide gradients. Use compute_gradients first |
---|
| 1374 | """ |
---|
[4127] | 1375 | |
---|
[4957] | 1376 | return self.x_gradient, self.y_gradient |
---|
[4127] | 1377 | |
---|
| 1378 | |
---|
| 1379 | def update(self, timestep): |
---|
[5394] | 1380 | # Call correct module function |
---|
| 1381 | # (either from this module or C-extension) |
---|
[4127] | 1382 | return update(self, timestep) |
---|
| 1383 | |
---|
| 1384 | def compute_gradients(self): |
---|
[5394] | 1385 | # Call correct module function |
---|
| 1386 | # (either from this module or C-extension) |
---|
[4127] | 1387 | return compute_gradients(self) |
---|
| 1388 | |
---|
| 1389 | def limit(self): |
---|
[5394] | 1390 | # Call correct module depending on whether |
---|
| 1391 | # basing limit calculations on edges or vertices |
---|
[4883] | 1392 | limit_old(self) |
---|
[4127] | 1393 | |
---|
[4897] | 1394 | def limit_vertices_by_all_neighbours(self): |
---|
[5394] | 1395 | # Call correct module function |
---|
| 1396 | # (either from this module or C-extension) |
---|
[4897] | 1397 | limit_vertices_by_all_neighbours(self) |
---|
[4883] | 1398 | |
---|
[4897] | 1399 | def limit_edges_by_all_neighbours(self): |
---|
[5394] | 1400 | # Call correct module function |
---|
| 1401 | # (either from this module or C-extension) |
---|
[4897] | 1402 | limit_edges_by_all_neighbours(self) |
---|
[4883] | 1403 | |
---|
[4897] | 1404 | def limit_edges_by_neighbour(self): |
---|
[5394] | 1405 | # Call correct module function |
---|
| 1406 | # (either from this module or C-extension) |
---|
[4897] | 1407 | limit_edges_by_neighbour(self) |
---|
[4883] | 1408 | |
---|
[4127] | 1409 | def extrapolate_second_order(self): |
---|
[5394] | 1410 | # Call correct module function |
---|
| 1411 | # (either from this module or C-extension) |
---|
[4957] | 1412 | compute_gradients(self) |
---|
| 1413 | extrapolate_from_gradient(self) |
---|
[5162] | 1414 | |
---|
[5306] | 1415 | def extrapolate_second_order_and_limit_by_edge(self): |
---|
[5394] | 1416 | # Call correct module function |
---|
| 1417 | # (either from this module or C-extension) |
---|
[5306] | 1418 | extrapolate_second_order_and_limit_by_edge(self) |
---|
[4990] | 1419 | |
---|
[5306] | 1420 | def extrapolate_second_order_and_limit_by_vertex(self): |
---|
[5394] | 1421 | # Call correct module function |
---|
| 1422 | # (either from this module or C-extension) |
---|
[5306] | 1423 | extrapolate_second_order_and_limit_by_vertex(self) |
---|
| 1424 | |
---|
[5162] | 1425 | def bound_vertices_below_by_constant(self, bound): |
---|
[5394] | 1426 | # Call correct module function |
---|
| 1427 | # (either from this module or C-extension) |
---|
[5162] | 1428 | bound_vertices_below_by_constant(self, bound) |
---|
| 1429 | |
---|
| 1430 | def bound_vertices_below_by_quantity(self, quantity): |
---|
[5394] | 1431 | # Call correct module function |
---|
| 1432 | # (either from this module or C-extension) |
---|
[5162] | 1433 | |
---|
[5394] | 1434 | # check consistency |
---|
[5162] | 1435 | assert self.domain == quantity.domain |
---|
| 1436 | bound_vertices_below_by_quantity(self, quantity) |
---|
| 1437 | |
---|
[4712] | 1438 | def backup_centroid_values(self): |
---|
[5394] | 1439 | # Call correct module function |
---|
| 1440 | # (either from this module or C-extension) |
---|
[4712] | 1441 | backup_centroid_values(self) |
---|
[4127] | 1442 | |
---|
[4712] | 1443 | def saxpy_centroid_values(self,a,b): |
---|
[5394] | 1444 | # Call correct module function |
---|
| 1445 | # (either from this module or C-extension) |
---|
[4712] | 1446 | saxpy_centroid_values(self,a,b) |
---|
| 1447 | |
---|
[4962] | 1448 | #Conserved_quantity = Quantity |
---|
[4712] | 1449 | |
---|
[4957] | 1450 | class Conserved_quantity(Quantity): |
---|
| 1451 | """Class conserved quantity being removed, use Quantity |
---|
| 1452 | |
---|
| 1453 | """ |
---|
| 1454 | |
---|
| 1455 | def __init__(self, domain, vertex_values=None): |
---|
| 1456 | #Quantity.__init__(self, domain, vertex_values) |
---|
| 1457 | |
---|
| 1458 | msg = 'ERROR: Use Quantity instead of Conserved_quantity' |
---|
| 1459 | |
---|
| 1460 | raise Exception, msg |
---|
| 1461 | |
---|
| 1462 | |
---|
| 1463 | |
---|
[4127] | 1464 | from anuga.utilities import compile |
---|
[4769] | 1465 | if compile.can_use_C_extension('quantity_ext.c'): |
---|
| 1466 | # Underlying C implementations can be accessed |
---|
[4127] | 1467 | |
---|
[4883] | 1468 | from quantity_ext import \ |
---|
| 1469 | average_vertex_values,\ |
---|
| 1470 | backup_centroid_values,\ |
---|
| 1471 | saxpy_centroid_values,\ |
---|
| 1472 | compute_gradients,\ |
---|
| 1473 | limit_old,\ |
---|
[4897] | 1474 | limit_vertices_by_all_neighbours,\ |
---|
| 1475 | limit_edges_by_all_neighbours,\ |
---|
| 1476 | limit_edges_by_neighbour,\ |
---|
[4957] | 1477 | limit_gradient_by_neighbour,\ |
---|
| 1478 | extrapolate_from_gradient,\ |
---|
[5306] | 1479 | extrapolate_second_order_and_limit_by_edge,\ |
---|
| 1480 | extrapolate_second_order_and_limit_by_vertex,\ |
---|
[5162] | 1481 | bound_vertices_below_by_constant,\ |
---|
| 1482 | bound_vertices_below_by_quantity,\ |
---|
[4883] | 1483 | interpolate_from_vertices_to_edges,\ |
---|
[4886] | 1484 | interpolate_from_edges_to_vertices,\ |
---|
[4883] | 1485 | update |
---|
[4769] | 1486 | else: |
---|
| 1487 | msg = 'C implementations could not be accessed by %s.\n ' %__file__ |
---|
| 1488 | msg += 'Make sure compile_all.py has been run as described in ' |
---|
| 1489 | msg += 'the ANUGA installation guide.' |
---|
| 1490 | raise Exception, msg |
---|
| 1491 | |
---|
| 1492 | |
---|
| 1493 | |
---|