SHOW:
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- or go back to the newest paste.
| 1 | """ | |
| 2 | note on np.unique | |
| 3 | ||
| 4 | this module expands on a the functionality one would currently bootstrap from np.unique | |
| 5 | to facilitate the functionality implemented in this module, a generalization of unique is proposed | |
| 6 | that is, the version of unique implemented here also takes a lex-sortable tuple, | |
| 7 | or multidimensional array viewed along one of its axes as a valid input; ie: | |
| 8 | ||
| 9 | #stack of 4 images | |
| 10 | images = np.random.rand(4,64,64) | |
| 11 | #shuffle the images; this is a giant mess now; how to find the unique ones? | |
| 12 | shuffled = images[np.random.randint(0,4,200)] | |
| 13 | #there you go | |
| 14 | print unique(shuffled, axis=0) | |
| 15 | ||
| 16 | furthermore, some np.unique related functions are proposed, with a more friendly interface | |
| 17 | (multiplicity, count) | |
| 18 | """ | |
| 19 | ||
| 20 | ||
| 21 | """ | |
| 22 | A note on pandas | |
| 23 | This module has substantial overlap with pandas' grouping functionality. | |
| 24 | So whats the reason for implementing it in numpy? | |
| 25 | ||
| 26 | Primarily; the concept of grouping is far more general than pandas' dataframe. | |
| 27 | There is no reason why numpy ndarrays should not have a solid core of grouping functionality. | |
| 28 | ||
| 29 | The recently added ufunc support make that we can now express grouping operations in pure numpy; | |
| 30 | that is, without any slow python loops or cumbersome C-extensions. | |
| 31 | ||
| 32 | I was not aware of pandas functionalty on this front when starting working on it; | |
| 33 | so i am somewhat pleased to say that many core design elements have turned out the same. | |
| 34 | I take that to mean these design decision probably make sense. | |
| 35 | ||
| 36 | It does raise the question as to where the proper line between pandas and numpy lies. | |
| 37 | I would argue that evidently, most of pandas functionality has no place in numpy. | |
| 38 | Then how is grouping different? I feel what lies at the heart of pandas is a permanent conceptual | |
| 39 | association between various pieces of data, assembled in a dataframe and all its metadata. | |
| 40 | I think numpy ought to stay well clear of that. | |
| 41 | On the other hand, you dont want want to go around creating a pandas dataframe | |
| 42 | just to plot a radial reduction; These kind of transient single-statement associations | |
| 43 | between keys and values are very useful, entirely independently of some heavyweight framework | |
| 44 | ||
| 45 | Further questions raised from pandas: should we have some form of merge/join functionality too? | |
| 46 | or is this getting too panda-ey? all the use cases i can think of fail to be pressed | |
| 47 | in some kind of standard mould, but i might be missing something here | |
| 48 | """ | |
| 49 | ||
| 50 | ||
| 51 | import numpy as np | |
| 52 | import itertools | |
| 53 | ||
| 54 | ||
| 55 | ||
| 56 | ||
| 57 | ||
| 58 | ||
| 59 | """ | |
| 60 | this toggle switches between preferred or backwards compatible semantics | |
| 61 | for dealing with key objects. current behavior for the arguments to functions | |
| 62 | like np.unique is to flatten any input arrays. | |
| 63 | i think a more unified semantics is achieved by interpreting all key arguments as | |
| 64 | sequences of key objects, whereby non-flat arrays are simply sequences of keys, | |
| 65 | whereby the keys themselves are ndim-1-arrays | |
| 66 | for reasons of backwards compatibility, it is probably wise to retain the default, | |
| 67 | but at least an axis keyword to toggle this behavior would be a welcome addition | |
| 68 | """ | |
| 69 | backwards_compatible = False | |
| 70 | if backwards_compatible: | |
| 71 | axis_default = None | |
| 72 | else: | |
| 73 | axis_default = 0 | |
| 74 | ||
| 75 | ||
| 76 | ||
| 77 | """ | |
| 78 | some utility functions | |
| 79 | """ | |
| 80 | ||
| 81 | def as_struct_array(*cols): | |
| 82 | """pack a bunch of columns as a struct""" | |
| 83 | cols = [np.asarray(c) for c in cols] | |
| 84 | rows = len(cols[0]) | |
| 85 | data = np.empty(rows, [('f'+str(i), c.dtype, c.shape[1:]) for i,c in enumerate(cols)])
| |
| 86 | for i,c in enumerate(cols): | |
| 87 | data['f'+str(i)] = c | |
| 88 | return data | |
| 89 | ||
| 90 | def axis_as_object(arr, axis=-1): | |
| 91 | """ | |
| 92 | cast the given axis of an array to a void object | |
| 93 | if the axis to be cast is contiguous, a view is returned, otherwise a copy | |
| 94 | this is useful for efficiently sorting by the content of an axis, for instance | |
| 95 | """ | |
| 96 | shape = arr.shape | |
| 97 | arr = np.ascontiguousarray(np.swapaxes(arr, axis, -1)) | |
| 98 | return arr.view(np.dtype((np.void, arr.dtype.itemsize * shape[axis]))).reshape(np.delete(shape, axis)) | |
| 99 | def object_as_axis(arr, dtype, axis=-1): | |
| 100 | """cast an array of void objects to a typed axis""" | |
| 101 | return np.swapaxes(arr.view(dtype).reshape(arr.shape+(-1,)), axis, -1) | |
| 102 | ||
| 103 | ||
| 104 | def array_as_object(arr): | |
| 105 | """view everything but the first axis as a void object""" | |
| 106 | arr = arr.reshape(len(arr),-1) | |
| 107 | return axis_as_object(arr) | |
| 108 | def array_as_typed(arr, dtype, shape): | |
| 109 | """unwrap a void object to its original type and shape""" | |
| 110 | return object_as_axis(arr, dtype).reshape(shape) | |
| 111 | ||
| 112 | ##def array_as_struct(arr): | |
| 113 | ## return np.ascontiguousarray(arr).view([('f0', arr.dtype, arr.shape[1:])])#.flatten()
| |
| 114 | ##def struct_as_array(arr): | |
| 115 | ## return arr.view(arr['f0'].dtype) | |
| 116 | ||
| 117 | ||
| 118 | ||
| 119 | ||
| 120 | ||
| 121 | """ | |
| 122 | class hierarchy for indexing a set of keys | |
| 123 | the class hierarchy allows for code reuse, while providing specializations for different | |
| 124 | types of key objects, yielding maximum flexibility and performance | |
| 125 | """ | |
| 126 | ||
| 127 | """ | |
| 128 | A note on naming: 'Index' here refers to the fact that the goal of these classes is to | |
| 129 | perform and store precomputations on a set of keys, | |
| 130 | such as to accelerate subsequent operations involving these keys. | |
| 131 | They are not 'logical' indexes as in pandas; | |
| 132 | they are not permanently associated with any other data objects | |
| 133 | ||
| 134 | Note that these classes are not primarily intended to be used directly from the numpy namespace, | |
| 135 | but rather are intended for code reuse within a family of higher level operations, | |
| 136 | only the latter need to be part of the numpy API. | |
| 137 | ||
| 138 | That said, these classes can also be very useful | |
| 139 | in those places where the standard operations do not quite cover your needs, | |
| 140 | saving your from completely reinventing the wheel. | |
| 141 | """ | |
| 142 | ||
| 143 | ||
| 144 | class BaseIndex(object): | |
| 145 | """ | |
| 146 | minimal indexing functionality | |
| 147 | only provides unique and counts, but with optimal performance | |
| 148 | no grouping, or lex-keys are supported, | |
| 149 | or anything that would require an indirect sort | |
| 150 | """ | |
| 151 | def __init__(self, keys): | |
| 152 | """ | |
| 153 | keys is a flat array of possibly compsite type | |
| 154 | """ | |
| 155 | self.keys = np.asarray(keys).flatten() | |
| 156 | self.sorted = np.sort(self.keys) | |
| 157 | #the slicing points of the bins to reduce over | |
| 158 | self.flag = self.sorted[:-1] != self.sorted[1:] | |
| 159 | self.slices = np.concatenate(( | |
| 160 | [0], | |
| 161 | np.flatnonzero(self.flag)+1, | |
| 162 | [self.size])) | |
| 163 | ||
| 164 | @property | |
| 165 | def start(self): | |
| 166 | """start index of all bins""" | |
| 167 | return self.slices[:-1] | |
| 168 | @property | |
| 169 | def stop(self): | |
| 170 | """stop index of all bins""" | |
| 171 | return self.slices[1:] | |
| 172 | @property | |
| 173 | def groups(self): | |
| 174 | return len(self.start) | |
| 175 | @property | |
| 176 | def size(self): | |
| 177 | return self.keys.size | |
| 178 | ||
| 179 | ||
| 180 | @property | |
| 181 | def unique(self): | |
| 182 | """the first entry of each bin is a unique key""" | |
| 183 | return self.sorted[self.start] | |
| 184 | @property | |
| 185 | def uniques(self): | |
| 186 | """number of unique keys""" | |
| 187 | return len(self.slices)-1 | |
| 188 | ||
| 189 | @property | |
| 190 | def count(self): | |
| 191 | """number of times each key occurs""" | |
| 192 | return np.diff(self.slices) | |
| 193 | @property | |
| 194 | def uniform(self): | |
| 195 | """returns true if each key occurs an equal number of times""" | |
| 196 | return not np.any(np.diff(self.count)) | |
| 197 | ||
| 198 | ||
| 199 | class Index(BaseIndex): | |
| 200 | """ | |
| 201 | index object over a set of keys | |
| 202 | adds support for more extensive functionality, notably grouping | |
| 203 | """ | |
| 204 | def __init__(self, keys): | |
| 205 | """ | |
| 206 | keys is a flat array of possibly composite type | |
| 207 | """ | |
| 208 | self.keys = np.asarray(keys) | |
| 209 | #find indices which sort the keys | |
| 210 | self.sorter = np.argsort(self.keys) | |
| 211 | #computed sorted keys | |
| 212 | self.sorted = self.keys[self.sorter] | |
| 213 | #the slicing points of the bins to reduce over | |
| 214 | self.flag = self.sorted[:-1] != self.sorted[1:] | |
| 215 | self.slices = np.concatenate(( | |
| 216 | [0], | |
| 217 | np.flatnonzero(self.flag)+1, | |
| 218 | [self.size])) | |
| 219 | ||
| 220 | @property | |
| 221 | def index(self): | |
| 222 | """ive never run into any use cases for this; | |
| 223 | perhaps it was intended to be used to do group_by(keys).first(values)? | |
| 224 | in any case, included for backwards compatibility with np.unique""" | |
| 225 | return self.sorter[self.start] | |
| 226 | @property | |
| 227 | def rank(self): | |
| 228 | """how high in sorted list each key is""" | |
| 229 | return self.sorter.argsort() | |
| 230 | @property | |
| 231 | def sorted_group_rank_per_key(self): | |
| 232 | """find a better name for this? enumeration of sorted keys. also used in median implementation""" | |
| 233 | return np.cumsum(np.concatenate(([False], self.flag))) | |
| 234 | @property | |
| 235 | def inverse(self): | |
| 236 | """return index array that maps unique values back to original space""" | |
| 237 | return self.sorted_group_rank_per_key[self.rank] | |
| 238 | ||
| 239 | ||
| 240 | ## def where(self, other): | |
| 241 | ## """ | |
| 242 | ## determine at which indices a second set equals a first | |
| 243 | ## """ | |
| 244 | ## return np.searchsorted(self.unique, other) | |
| 245 | ||
| 246 | ||
| 247 | ||
| 248 | class ObjectIndex(Index): | |
| 249 | """ | |
| 250 | given axis enumerates the keys | |
| 251 | all other axes form the keys | |
| 252 | groups will be formed on the basis of bitwise equality | |
| 253 | ||
| 254 | should we retire objectindex? | |
| 255 | this can be integrated with regular index ala lexsort, no? | |
| 256 | not sure what is more readable though | |
| 257 | """ | |
| 258 | def __init__(self, keys, axis): | |
| 259 | self.axis = axis | |
| 260 | self.dtype = keys.dtype | |
| 261 | ||
| 262 | keys = np.swapaxes(keys, axis, 0) | |
| 263 | self.shape = keys.shape | |
| 264 | keys = array_as_object(keys) | |
| 265 | ||
| 266 | super(ObjectIndex, self).__init__(keys) | |
| 267 | ||
| 268 | @property | |
| 269 | def unique(self): | |
| 270 | """the first entry of each bin is a unique key""" | |
| 271 | sorted = array_as_typed(self.sorted, self.dtype, self.shape) | |
| 272 | return np.swapaxes(sorted[self.start], self.axis, 0) | |
| 273 | ||
| 274 | ||
| 275 | class LexIndex(Index): | |
| 276 | """ | |
| 277 | index object based on lexographic ordering of a tuple of key-arrays | |
| 278 | key arrays can be any type, including multi-dimensional, structed or voidobjects | |
| 279 | however, passing such fancy keys to lexindex may not be ideal from a performance perspective, | |
| 280 | as lexsort does not accept them as arguments directly, so we have to index and invert them first | |
| 281 | ||
| 282 | should you find yourself with such complex keys, it may be more efficient | |
| 283 | to place them into a structured array first | |
| 284 | ||
| 285 | note that multidimensional columns are indexed by their first column, | |
| 286 | and no per-column axis keyword is supplied, | |
| 287 | customization of column layout will have to be done at the call site | |
| 288 | ||
| 289 | """ | |
| 290 | def __init__(self, keys): | |
| 291 | self.keys = tuple(np.asarray(key) for key in keys) | |
| 292 | self.dtypes = tuple(key.dtype for key in self.keys) | |
| 293 | self.shapes = tuple(key.shape for key in self.keys) | |
| 294 | ||
| 295 | keyviews = tuple(array_as_object(key) if key.ndim>1 else key for key in self.keys) | |
| 296 | #find indices which sort the keys; complex keys which lexsort does not accept are bootstrapped from Index | |
| 297 | self.sorter = np.lexsort(tuple(Index(key).inverse if key.dtype.kind is 'V' else key for key in keyviews)) | |
| 298 | #computed sorted keys | |
| 299 | self.sorted = tuple(key[self.sorter] for key in keyviews) | |
| 300 | #the slicing points of the bins to reduce over | |
| 301 | self.flag = reduce( | |
| 302 | np.logical_or, | |
| 303 | (s[:-1] != s[1:] for s in self.sorted)) | |
| 304 | self.slices = np.concatenate(( | |
| 305 | [0], | |
| 306 | np.flatnonzero(self.flag)+1, | |
| 307 | [self.size])) | |
| 308 | ||
| 309 | @property | |
| 310 | def unique(self): | |
| 311 | """returns a tuple of unique key columns""" | |
| 312 | return tuple( | |
| 313 | (array_as_typed(s, dtype, shape) if len(shape)>1 else s)[self.start] | |
| 314 | for s, dtype, shape in zip(self.sorted, self.dtypes, self.shapes)) | |
| 315 | ||
| 316 | @property | |
| 317 | def size(self): | |
| 318 | return self.sorter.size | |
| 319 | ||
| 320 | class LexIndexSimple(Index): | |
| 321 | """ | |
| 322 | simplified LexIndex, which only accepts 1-d arrays of simple dtypes | |
| 323 | the more expressive LexIndex only has some logic overhead, | |
| 324 | in case all columns are indeed simple. not sure this is worth the extra code | |
| 325 | """ | |
| 326 | def __init__(self, keys): | |
| 327 | self.keys = tuple(np.asarray(key) for key in keys) | |
| 328 | self.sorter = np.lexsort(self.keys) | |
| 329 | #computed sorted keys | |
| 330 | self.sorted = tuple(key[self.sorter] for key in self.keys) | |
| 331 | #the slicing points of the bins to reduce over | |
| 332 | self.flag = reduce( | |
| 333 | np.logical_or, | |
| 334 | (s[:-1] != s[1:] for s in self.sorted)) | |
| 335 | self.slices = np.concatenate(( | |
| 336 | [0], | |
| 337 | np.flatnonzero(self.flag)+1, | |
| 338 | [self.size])) | |
| 339 | ||
| 340 | @property | |
| 341 | def unique(self): | |
| 342 | """the first entry of each bin is a unique key""" | |
| 343 | return tuple(s[self.start] for s in self.sorted) | |
| 344 | ||
| 345 | @property | |
| 346 | def size(self): | |
| 347 | return self.sorter.size | |
| 348 | ||
| 349 | ||
| 350 | ||
| 351 | def as_index(keys, axis = axis_default, base=False): | |
| 352 | """ | |
| 353 | casting rules for a keys object to an index | |
| 354 | ||
| 355 | the preferred semantics is that keys is a sequence of key objects, | |
| 356 | except when keys is an instance of tuple, | |
| 357 | in which case the zipped elements of the tuple are the key objects | |
| 358 | ||
| 359 | the axis keyword specifies the axis which enumerates the keys | |
| 360 | if axis is None, the keys array is flattened | |
| 361 | if axis is 0, the first axis enumerates the keys | |
| 362 | which of these two is the default depends on whether backwards_compatible == True | |
| 363 | ||
| 364 | if base==True, the most basic index possible is constructed. | |
| 365 | this avoids an indirect sort; if it isnt required, this has better performance | |
| 366 | """ | |
| 367 | if isinstance(keys, Index): | |
| 368 | return keys | |
| 369 | if isinstance(keys, tuple): | |
| 370 | return LexIndex(keys) | |
| 371 | try: | |
| 372 | keys = np.asarray(keys) | |
| 373 | except: | |
| 374 | raise TypeError('Given object does not form a valid set of keys')
| |
| 375 | if axis is None: | |
| 376 | keys = keys.flatten() | |
| 377 | if keys.ndim==1: | |
| 378 | if base: | |
| 379 | return BaseIndex(keys) | |
| 380 | else: | |
| 381 | return Index(keys) | |
| 382 | else: | |
| 383 | return ObjectIndex(keys, axis) | |
| 384 | ||
| 385 | ||
| 386 | ||
| 387 | ||
| 388 | ||
| 389 | """ | |
| 390 | public API starts here | |
| 391 | """ | |
| 392 | ||
| 393 | ||
| 394 | class GroupBy(object): | |
| 395 | """ | |
| 396 | supports ufunc reduction | |
| 397 | should any other form of reduction be supported? | |
| 398 | not sure it should; more cleanly written externally i think, on a grouped iterables | |
| 399 | """ | |
| 400 | def __init__(self, keys, axis = 0): | |
| 401 | #we could inherit from Index, but the multiple specializations make | |
| 402 | #holding a reference to an index object more appropriate | |
| 403 | # note that we dont have backwards compatibility issues with groupby, | |
| 404 | #so we are going to use axis = 0 as a default | |
| 405 | #the multi-dimensional structure of a keys object is usualy meaningfull, | |
| 406 | #and value arguments are not automatically flattened either | |
| 407 | ||
| 408 | self.index = as_index(keys, axis) | |
| 409 | ||
| 410 | #forward interesting/'public' index properties | |
| 411 | @property | |
| 412 | def unique(self): | |
| 413 | return self.index.unique | |
| 414 | @property | |
| 415 | def count(self): | |
| 416 | return self.index.count | |
| 417 | @property | |
| 418 | def inverse(self): | |
| 419 | return self.index.inverse | |
| 420 | @property | |
| 421 | def rank(self): | |
| 422 | return self.index.rank | |
| 423 | ||
| 424 | ||
| 425 | #some different methods of chopping up a set of values by key | |
| 426 | #not sure they are all equally relevant, but i actually have real world use cases for most of them | |
| 427 | ||
| 428 | def as_iterable_from_iterable(self, values): | |
| 429 | """ | |
| 430 | grouping of an iterable. memory consumption depends on the amount of sorting required | |
| 431 | worst case, if index.sorter[-1] = 0, we need to consume the entire value iterable, | |
| 432 | before we can start yielding any output | |
| 433 | but to the extent that the keys come presorted, the grouping is lazy | |
| 434 | """ | |
| 435 | values = iter(enumerate(values)) | |
| 436 | cache = dict() | |
| 437 | def get_value(ti): | |
| 438 | try: | |
| 439 | return cache.pop(ti) | |
| 440 | except: | |
| 441 | while True: | |
| 442 | i, v = next(values) | |
| 443 | if i==ti: | |
| 444 | return v | |
| 445 | cache[i] = v | |
| 446 | s = iter(self.index.sorter) | |
| 447 | for c in self.count: | |
| 448 | yield (get_value(i) for i in itertools.islice(s, c)) | |
| 449 | ||
| 450 | def as_outoforder(self, values): | |
| 451 | """ | |
| 452 | group values, without regard for the ordering of self.index.unique | |
| 453 | consume values as they come, and yield key-group pairs as soon as they complete | |
| 454 | thi spproach is lazy, insofar as grouped values are close in their iterable | |
| 455 | """ | |
| 456 | from collections import defaultdict | |
| 457 | cache = defaultdict(list) | |
| 458 | count = self.count | |
| 459 | unique = self.unique | |
| 460 | key = (lambda i: unique[i]) if isinstance(unique, np.ndarray) else (lambda i: tuple(c[i] for c in unique)) | |
| 461 | for i,v in itertools.izip(self.inverse, values): | |
| 462 | cache[i].append(v) | |
| 463 | if len(cache[i]) == count[i]: | |
| 464 | yield key(i), cache.pop(i) | |
| 465 | ||
| 466 | def as_iterable_from_sequence(self, values): | |
| 467 | """ | |
| 468 | this is the preferred method if values has random access, | |
| 469 | but we dont want it completely in memory. | |
| 470 | like a big memory mapped file, for instance | |
| 471 | """ | |
| 472 | s = iter(self.index.sorter) | |
| 473 | for c in self.count: | |
| 474 | yield (values[i] for i in itertools.islice(s, c)) | |
| 475 | ||
| 476 | def as_array(self, values): | |
| 477 | """ | |
| 478 | return grouped values as an ndarray | |
| 479 | returns an array of shape [groups, groupsize, ungrouped-axes] | |
| 480 | this is only possible if index.uniform==True | |
| 481 | """ | |
| 482 | assert(self.index.uniform) | |
| 483 | values = np.asarray(values) | |
| 484 | values = values[self.index.sorter] | |
| 485 | return values.reshape(self.index.groups, self.count[0], *values.shape[1:]) | |
| 486 | ||
| 487 | def as_list(self, values): | |
| 488 | """return grouped values as a list of arrays, or a jagged-array""" | |
| 489 | values = np.asarray(values) | |
| 490 | values = values[self.index.sorter] | |
| 491 | return np.split(values, self.index.slices[1:-1], axis=0) | |
| 492 | ||
| 493 | def group(self, values): | |
| 494 | try: | |
| 495 | return self.as_array(values) | |
| 496 | except: | |
| 497 | return self.as_list(values) | |
| 498 | ||
| 499 | def __call__(self, values): | |
| 500 | """ | |
| 501 | not sure how i feel about this. explicit is better than implict | |
| 502 | but group_by(keys).group(values) does not sit too well with me either | |
| 503 | """ | |
| 504 | return self.unique, self.group(values) | |
| 505 | ||
| 506 | ||
| 507 | # ufunc based reduction methods | |
| 508 | ||
| 509 | def reduce(self, values, operator = np.add): | |
| 510 | """ | |
| 511 | reduce the values over identical key groups, using the ufunc operator | |
| 512 | reduction is over the first axis, which should have elements corresponding to the keys | |
| 513 | all other axes are treated indepenently for the sake of this reduction | |
| 514 | note that this code is only C-vectorized over the first axis | |
| 515 | that is fine is this inner loop is significant, but not so much if it isnt | |
| 516 | if we have only few keys, but values[0].size is substantial, a reduction via | |
| 517 | as_list may be preferable | |
| 518 | """ | |
| 519 | values = values[self.index.sorter] | |
| 520 | if values.ndim>1: | |
| 521 | return np.apply_along_axis( | |
| 522 | lambda slc: operator.reduceat(slc, self.index.start), | |
| 523 | 0, values) | |
| 524 | else: | |
| 525 | return operator.reduceat(values, self.index.start) | |
| 526 | ||
| 527 | def sum(self, values, axis=0): | |
| 528 | """compute the sum over each group""" | |
| 529 | values = np.asarray(values) | |
| 530 | if axis: values = np.rollaxis(values, axis) | |
| 531 | return self.unique, self.reduce(values) | |
| 532 | ||
| 533 | def mean(self, values, axis=0): | |
| 534 | """compute the mean over each group""" | |
| 535 | values = np.asarray(values) | |
| 536 | if axis: values = np.rollaxis(values, axis) | |
| 537 | count = self.count.reshape(-1,*(1,)*(values.ndim-1)) | |
| 538 | return self.unique, self.reduce(values) / count | |
| 539 | ||
| 540 | def var(self, values, axis=0): | |
| 541 | """compute the variance over each group""" | |
| 542 | values = np.asarray(values) | |
| 543 | if axis: values = np.rollaxis(values, axis) | |
| 544 | count = self.count.reshape(-1,*(1,)*(values.ndim-1)) | |
| 545 | mean = self.reduce(values) / count | |
| 546 | err = values - mean[self.inverse] | |
| 547 | return self.unique, self.reduce(err**2) / count | |
| 548 | ||
| 549 | def std(self, values, axis=0): | |
| 550 | """standard deviation over each group""" | |
| 551 | unique, var = self.var(values, axis) | |
| 552 | return unique, np.sqrt(var) | |
| 553 | ||
| 554 | def median(self, values, axis=0, average=True): | |
| 555 | """ | |
| 556 | compute the median value over each group. | |
| 557 | when average is true, the average is the two cental values is taken | |
| 558 | for groups with an even key-count | |
| 559 | """ | |
| 560 | values = np.asarray(values) | |
| 561 | ||
| 562 | mid_2 = self.index.start + self.index.stop | |
| 563 | hi = (mid_2 ) // 2 | |
| 564 | lo = (mid_2 - 1) // 2 | |
| 565 | ||
| 566 | #need this indirection for lex-index compatibility | |
| 567 | sorted_group_rank_per_key = self.index.sorted_group_rank_per_key | |
| 568 | ||
| 569 | def median1d(slc): | |
| 570 | #place values at correct keys; preconditions the upcoming lexsort | |
| 571 | slc = slc[self.index.sorter] | |
| 572 | #refine value sorting within each keygroup | |
| 573 | sorter = np.lexsort((slc, sorted_group_rank_per_key)) | |
| 574 | slc = slc[sorter] | |
| 575 | return (slc[lo]+slc[hi]) / 2 if average else slc[hi] | |
| 576 | ||
| 577 | values = np.asarray(values) | |
| 578 | if axis: values = np.rollaxis(values, axis) | |
| 579 | if values.ndim>1: #is trying to skip apply_along_axis somewhat premature optimization? | |
| 580 | values = np.apply_along_axis(median1d, 0, values) | |
| 581 | else: | |
| 582 | values = median1d(values) | |
| 583 | return self.unique, values | |
| 584 | ||
| 585 | def min(self, values, axis=0): | |
| 586 | """return the minimum within each group""" | |
| 587 | values = np.asarray(values) | |
| 588 | if axis: values = np.rollaxis(values, axis) | |
| 589 | return self.unique, self.reduce(values, np.minimum) | |
| 590 | ||
| 591 | def max(self, values, axis=0): | |
| 592 | """return the maximum within each group""" | |
| 593 | values = np.asarray(values) | |
| 594 | if axis: values = np.rollaxis(values, axis) | |
| 595 | return self.unique, self.reduce(values, np.maximum) | |
| 596 | ||
| 597 | def first(self, values, axis=0): | |
| 598 | """return values at first occurance of its associated key""" | |
| 599 | values = np.asarray(values) | |
| 600 | if axis: values = np.rollaxis(values, axis) | |
| 601 | return self.unique, values[self.index.sorter[self.index.start]] | |
| 602 | ||
| 603 | def last(self, values, axis=0): | |
| 604 | """return values at last occurance of its associated key""" | |
| 605 | values = np.asarray(values) | |
| 606 | if axis: values = np.rollaxis(values, axis) | |
| 607 | return self.unique, values[self.index.sorter[self.index.stop-1]] | |
| 608 | ||
| 609 | ||
| 610 | ||
| 611 | #implement iter interface? could simply do zip( group_by(keys)(values)), no? | |
| 612 | ||
| 613 | #just an alias, for those who dont like camelcase | |
| 614 | group_by = GroupBy | |
| 615 | #could also turn this into a function with optional values and reduction func. | |
| 616 | def group_by(keys, values=None, reduction=None, axis=0): | |
| 617 | g = GroupBy(keys, axis) | |
| 618 | if values is None: | |
| 619 | return g | |
| 620 | groups = g.group(values) | |
| 621 | if reduction is None: | |
| 622 | return groups | |
| 623 | return [reduction(group) for group in groups] | |
| 624 | ||
| 625 | ||
| 626 | ||
| 627 | """ | |
| 628 | some demonstration of the duplicity between this code and np.unique | |
| 629 | they share a lot of common functionality | |
| 630 | we cant quite bootstrap grouping from unique as is | |
| 631 | but unique can easily be reimplemented using the Index class | |
| 632 | """ | |
| 633 | ||
| 634 | def unique(keys, return_index = False, return_inverse = False, return_count = False, axis = axis_default): | |
| 635 | """ | |
| 636 | backwards compatible interface with numpy.unique | |
| 637 | in the long term i think the kwargs should be deprecated though | |
| 638 | cleaner to call index and its properties directly, | |
| 639 | should you want something beyond the interface provided | |
| 640 | """ | |
| 641 | index = as_index(keys, axis, base = not (return_index or return_inverse)) | |
| 642 | ||
| 643 | ret = index.unique, | |
| 644 | if return_index: | |
| 645 | ret = ret + (index.index,) | |
| 646 | if return_inverse: | |
| 647 | ret = ret + (index.inverse,) | |
| 648 | if return_count: | |
| 649 | ret = ret + (index.count,) | |
| 650 | return ret[0] if len(ret) == 1 else ret | |
| 651 | ||
| 652 | def count(keys, axis = axis_default): | |
| 653 | """numpy work-alike of collections.Counter""" | |
| 654 | index = as_index(keys, axis, base = True) | |
| 655 | return index.unique, index.count | |
| 656 | ||
| 657 | def multiplicity(keys, axis = axis_default): | |
| 658 | """ | |
| 659 | return the multiplicity of each key, or how often it occurs in the set | |
| 660 | note that we are not interested in the unique values for this operation, | |
| 661 | casting doubt on the current numpy design which places np.unique | |
| 662 | at the center of the interface for this kind of operation | |
| 663 | given how often i use multiplicity, id like to have it in the numpy namespace | |
| 664 | """ | |
| 665 | index = as_index(keys, axis) | |
| 666 | return index.count[index.inverse] | |
| 667 | ||
| 668 | def rank(keys, axis = axis_default): | |
| 669 | """ | |
| 670 | where each item is in the pecking order. | |
| 671 | not sure this should be part of the public api, cant think of any use-case right away | |
| 672 | plus, we have a namespace conflict | |
| 673 | """ | |
| 674 | index = as_index(keys, axis) | |
| 675 | return index.rank | |
| 676 | ||
| 677 | ||
| 678 | def incidence(boundary): | |
| 679 | """ | |
| 680 | given an Nxm matrix containing boundary info between simplices, | |
| 681 | compute indidence info matrix | |
| 682 | not to be part of numpy API, to be sure, just something im playing with | |
| 683 | """ | |
| 684 | return group_by(boundary).group(np.arange(boundary.size) // boundary.shape[1]) | |
| 685 | ||
| 686 | ||
| 687 | ||
| 688 | ||
| 689 | def test_basic(): | |
| 690 | ||
| 691 | keys = ["e", "b", "b", "c", "d", "e", "e", 'a'] | |
| 692 | values = [1.2, 4.5, 4.3, 2.0, 5.67, 8.08, 9.01,1] | |
| 693 | ||
| 694 | ## keys = np.array(["a", "b", "b", "c", "d", "e", "e",'d','a','c']) | |
| 695 | ## values = np.array([1.2, 4.5, 4.3, 2.0, 5.67, 8.08, 9.01, 1,2,3]) | |
| 696 | ||
| 697 | print 'two methods of computing non-reducing group' | |
| 698 | print 'as iterable' | |
| 699 | g = group_by(keys) | |
| 700 | for k,v in zip(g.unique, g.as_iterable_from_sequence(values)): | |
| 701 | print k, list(v) | |
| 702 | print 'as list' | |
| 703 | for k,v in zip(*group_by(keys)(values)): | |
| 704 | print k, v | |
| 705 | ||
| 706 | print 'some reducing group operations' | |
| 707 | g = group_by(keys) | |
| 708 | unique_keys, reduced_values = g.median(values) | |
| 709 | print 'per group median' | |
| 710 | print reduced_values | |
| 711 | unique_keys, reduced_values = g.mean(values) | |
| 712 | print 'per group mean' | |
| 713 | print reduced_values | |
| 714 | unique_keys, reduced_values = g.std(values) | |
| 715 | print 'per group std' | |
| 716 | print reduced_values | |
| 717 | reduced_values = g.reduce(np.array(values), np.minimum) #alternate way of calling | |
| 718 | print 'per group min' | |
| 719 | print reduced_values | |
| 720 | unique_keys, reduced_values = g.max(values) | |
| 721 | print 'per group max' | |
| 722 | print reduced_values | |
| 723 | ||
| 724 | ||
| 725 | ##test_basic() | |
| 726 | ##quit() | |
| 727 | ||
| 728 | ||
| 729 | def test_lex_median(): | |
| 730 | """ | |
| 731 | for making sure i squased all bugs related to fancy-keys and median filter implementation | |
| 732 | """ | |
| 733 | keys1 = ["e", "b", "b", "c", "d", "e", "e", 'a'] | |
| 734 | keys2 = ["b", "b", "b", "d", "e", "e", 'e', 'e'] | |
| 735 | ## keys3 = np.random.randint(0,2,(8,2)) | |
| 736 | values = [1.2, 4.5, 4.3, 2.0, 5.6, 8.8, 9.1, 1] | |
| 737 | ||
| 738 | unique, median = group_by((keys1, keys2)).median(values) | |
| 739 | for i in zip(zip(*unique), median): | |
| 740 | print i | |
| 741 | ||
| 742 | ##test_lex_median() | |
| 743 | ##quit() | |
| 744 | ||
| 745 | ||
| 746 | def test_fancy_keys(): | |
| 747 | """ | |
| 748 | test Index subclasses | |
| 749 | """ | |
| 750 | keys = np.random.randint(0, 2, (20,3)).astype(np.int8) | |
| 751 | values = np.random.randint(-1,2,(20,4)) | |
| 752 | ||
| 753 | ||
| 754 | #all these various datastructures should produce the same behavior | |
| 755 | #multiplicity is a nice unit test, since it draws on most of the low level functionality | |
| 756 | if backwards_compatible: | |
| 757 | assert(np.all( | |
| 758 | multiplicity(keys, axis=0) == #void object indexing | |
| 759 | multiplicity(tuple(keys.T)))) #lexographic indexing | |
| 760 | assert(np.all( | |
| 761 | multiplicity(keys, axis=0) == #void object indexing | |
| 762 | multiplicity(as_struct_array(keys)))) #struct array indexing | |
| 763 | else: | |
| 764 | assert(np.all( | |
| 765 | multiplicity(keys) == #void object indexing | |
| 766 | multiplicity(tuple(keys.T)))) #lexographic indexing | |
| 767 | assert(np.all( | |
| 768 | multiplicity(keys) == #void object indexing | |
| 769 | multiplicity(as_struct_array(keys)))) #struct array indexing | |
| 770 | ||
| 771 | #lets go mixing some dtypes! | |
| 772 | floatkeys = np.zeros(len(keys)) | |
| 773 | floatkeys[0] = 8.8 | |
| 774 | print 'sum per group of identical rows using struct key' | |
| 775 | g = group_by(as_struct_array(keys, floatkeys)) | |
| 776 | for e in zip(g.count, *g.sum(values)): | |
| 777 | print e | |
| 778 | print 'sum per group of identical rows using lex of nd-key' | |
| 779 | g = group_by(( keys, floatkeys)) | |
| 780 | for e in zip(zip(*g.unique), g.sum(values)[1]): | |
| 781 | print e | |
| 782 | print 'sum per group of identical rows using lex of struct key' | |
| 783 | g = group_by((as_struct_array( keys), floatkeys)) | |
| 784 | for e in zip(zip(*g.unique), g.sum(values)[1]): | |
| 785 | print e | |
| 786 | ||
| 787 | #showcase enhanced unique functionality | |
| 788 | images = np.random.rand(4,4,4) | |
| 789 | #shuffle the images; this is a giant mess now; how to find the unique ones? | |
| 790 | shuffled = images[np.random.randint(0,4,200)] | |
| 791 | #there you go | |
| 792 | if backwards_compatible: | |
| 793 | print unique(shuffled, axis=0) | |
| 794 | else: | |
| 795 | print unique(shuffled) | |
| 796 | ||
| 797 | ||
| 798 | ##g = test_fancy_keys() | |
| 799 | ##quit() | |
| 800 | ||
| 801 | ||
| 802 | def test_radial(): | |
| 803 | x = np.linspace(-2,2, 64) | |
| 804 | y = x[:, None] | |
| 805 | x = x[None, :] | |
| 806 | R = np.sqrt( x**2+y**2) | |
| 807 | ||
| 808 | def airy(r, sigma): | |
| 809 | from scipy.special import j1 | |
| 810 | r = r / sigma * np.sqrt(2) | |
| 811 | a = (2*j1(r)/r)**2 | |
| 812 | a[r==0] = 1 | |
| 813 | return a | |
| 814 | def gauss(r, sigma): | |
| 815 | return np.exp(-(r/sigma)**2) | |
| 816 | ||
| 817 | distribution = np.random.choice([gauss, airy])(R, 0.3) | |
| 818 | sample = np.random.poisson(distribution*200+10).astype(np.float) | |
| 819 | ||
| 820 | import matplotlib.pyplot as pp | |
| 821 | #is this an airy or gaussian function? hard to tell with all this noise! | |
| 822 | pp.imshow(sample, interpolation='nearest', cmap='gray') | |
| 823 | pp.show() | |
| 824 | #radial reduction to the rescue! | |
| 825 | #if we are sampling an airy function, you will see a small but significant rise around x=1 | |
| 826 | g = group_by(np.round(R, 5).flatten()) | |
| 827 | pp.errorbar( | |
| 828 | g.unique, | |
| 829 | g.mean(sample.flatten())[1], | |
| 830 | g.std (sample.flatten())[1] / np.sqrt(g.count)) | |
| 831 | pp.xlim(0,2) | |
| 832 | pp.show() | |
| 833 | ||
| 834 | ##test_radial() | |
| 835 | ##quit() | |
| 836 | ||
| 837 | def test_meshing(): | |
| 838 | """ | |
| 839 | meshing example | |
| 840 | demonstrates the use of multiplicity, and group.median | |
| 841 | """ | |
| 842 | #set up some random points, and get their delaunay triangulation | |
| 843 | points = np.random.random((20000,2))*2-1 | |
| 844 | points = points[np.linalg.norm(points,axis=1) < 1] | |
| 845 | from scipy.spatial.qhull import Delaunay | |
| 846 | d = Delaunay(points) | |
| 847 | tris = d.simplices | |
| 848 | ||
| 849 | #the operations provided in this module allow us to express potentially complex | |
| 850 | #computational geometry questions elegantly in numpy | |
| 851 | #Delaunay.neighbors could be used as well, | |
| 852 | #but the point is to express this in pure numpy, without additional library functionaoty | |
| 853 | edges = tris[:,[[0,1],[1,2],[2,0]]].reshape(-1,2) | |
| 854 | sorted_edges = np.where(edges[:,0:1]<edges[:,1:2], edges, edges[:,::-1]) | |
| 855 | #we test to see how often each edge occurs, or how many indicent simplices it has | |
| 856 | #this is a very general method of finding the boundary of any topology | |
| 857 | #and we can do so here with only one simple and readable command, multiplicity == 1 | |
| 858 | if backwards_compatible: | |
| 859 | boundary_edges = edges[multiplicity(sorted_edges, axis=0)==1] | |
| 860 | else: | |
| 861 | boundary_edges = edges[multiplicity(sorted_edges)==1] | |
| 862 | boundary_points = unique(boundary_edges) | |
| 863 | ||
| 864 | if False: | |
| 865 | print boundary_edges | |
| 866 | print incidence(boundary_edges) | |
| 867 | ||
| 868 | ||
| 869 | #create some random values on faces | |
| 870 | #we want to smooth them over the mesh to create a nice hilly landscape | |
| 871 | face_values = np.random.normal(size=d.nsimplex) | |
| 872 | #add some salt and pepper noise, to make our problem more interesting | |
| 873 | face_values[np.random.randint(d.nsimplex, size=10)] += 1000 | |
| 874 | ||
| 875 | #start with a median step, to remove salt-and-pepper noise | |
| 876 | #toggle to mean to see the effect of the median filter | |
| 877 | g = group_by(tris.flatten()) | |
| 878 | prestep = g.median if True else g.mean | |
| 879 | vertex_values = prestep(np.repeat(face_values, 3))[1] | |
| 880 | vertex_values[boundary_points] = 0 | |
| 881 | ||
| 882 | #actually, we can compute the mean without grouping | |
| 883 | tris_per_vert = g.count | |
| 884 | def scatter(x): | |
| 885 | r = np.zeros(d.npoints, x.dtype) | |
| 886 | for idx in tris.T: np.add.at(r, idx, x) | |
| 887 | return r / tris_per_vert | |
| 888 | def gather(x): | |
| 889 | return x[tris].mean(axis=1) | |
| 890 | ||
| 891 | #iterate a little | |
| 892 | for i in range(100): | |
| 893 | face_values = gather(vertex_values) | |
| 894 | vertex_values = scatter(face_values) | |
| 895 | vertex_values[boundary_points] = 0 | |
| 896 | ||
| 897 | ||
| 898 | #display our nicely rolling hills and their boundary | |
| 899 | import matplotlib.pyplot as plt | |
| 900 | x, y = points.T | |
| 901 | plt.tripcolor(x,y, triangles = tris, facecolors = face_values) | |
| 902 | plt.scatter(x[boundary_points], y[boundary_points]) | |
| 903 | plt.xlim(-1,1) | |
| 904 | plt.ylim(-1,1) | |
| 905 | plt.axis('equal')
| |
| 906 | plt.show() | |
| 907 | ||
| 908 | d = test_meshing() |