1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 468 469 470 471 472 473 474 475 476 477 478 479 480 481 482 483 484 485 486 487 488 489 490 491 492 493 494 495 496 497 498 499 500 501 502 503 504 505 506 507 508 509 510 511 512 513 514 515 516 517 518 519 520 521 522 523 524 525 526 527 528 529 530 531 532 533 534 535 536 537 538 539 540 541 542 543 544 545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 571 572 573 574 575 576 577 578 579 580 581 582 583 584 585 586 587 588 589 590 591 592 593 594 595 596 597 598 599 600 601 602 603 604 605 606 607 608 609 610 611 612 613 614 615 616 617 618 619 620 621 622 623 624 625 626 627 628 629 630 631 632 633 634 635 636 637 638 639 640 641 642 643 644 645 646 647 648 649 650 651 652 653 654 655 656 657 658 659 660
|
# -*- coding: utf-8 -*-
"""
Utilities for transforming and validating data types
Given that many of the data transformations involve copying the data, they should
ideally happen in a lazy manner to avoid memory issues.
Created on Tue Nov 3 21:14:25 2015
@author: Suhas Somnath, Chris Smith
"""
from __future__ import division, absolute_import, unicode_literals, print_function
import sys
from warnings import warn
import h5py
import numpy as np
import dask.array as da
__all__ = ['flatten_complex_to_real', 'get_compound_sub_dtypes', 'flatten_compound_to_real', 'check_dtype',
'stack_real_to_complex', 'validate_dtype', 'is_complex_dtype',
'stack_real_to_compound', 'stack_real_to_target_dtype', 'flatten_to_real']
from sidpy.hdf.hdf_utils import lazy_load_array
if sys.version_info.major == 3:
unicode = str
def flatten_complex_to_real(dataset, lazy=False):
"""
Stacks the real values followed by the imaginary values in the last dimension of the given N dimensional matrix.
Thus a complex matrix of shape (2, 3, 5) will turn into a matrix of shape (2, 3, 10)
Parameters
----------
dataset : array-like or :class:`numpy.ndarray`, or :class:`h5py.Dataset`, or :class:`dask.array.core.Array`
Dataset of complex data type
lazy : bool, optional. Default = False
If set to True, will use lazy Dask arrays instead of in-memory numpy arrays
Returns
-------
retval : :class:`numpy.ndarray`, or :class:`dask.array.core.Array`
real valued dataset
Examples
--------
>>> import numpy as np
>>> import sidpy
>>> length = 3
>>> complex_array = np.random.randint(-5, high=5, size=length) + 1j * np.random.randint(-5, high=5, size=length)
>>> print('Complex value: {} has shape: {}'.format(complex_array, complex_array.shape))
Complex value: [2.-2.j 0.-3.j 0.-4.j] has shape: (3,)
>>> stacked_real_array = sidpy.dtype_utils.flatten_complex_to_real(complex_array)
>>> print('Stacked real value: {} has shape: '
>>> '{}'.format(stacked_real_array, stacked_real_array.shape))
Stacked real value: [ 2. 0. 0. -2. -3. -4.] has shape: (6,)
"""
if not isinstance(dataset, (h5py.Dataset, np.ndarray, da.core.Array)):
raise TypeError('dataset should either be a h5py.Dataset or numpy / dask array')
if not is_complex_dtype(dataset.dtype):
raise TypeError("Expected a complex valued dataset")
if isinstance(dataset, da.core.Array):
lazy = True
xp = np
if lazy:
dataset = lazy_load_array(dataset)
xp = da
axis = xp.array(dataset).ndim - 1
if axis == -1:
return xp.hstack([xp.real(dataset), xp.imag(dataset)])
else: # along the last axis
return xp.concatenate([xp.real(dataset), xp.imag(dataset)], axis=axis)
def flatten_compound_to_real(dataset, lazy=False):
"""
Flattens the individual components in a structured array or compound valued hdf5 dataset along the last axis to form
a real valued array. Thus a compound h5py.Dataset or structured numpy matrix of shape (2, 3, 5) having 3 components
will turn into a real valued matrix of shape (2, 3, 15), assuming that all the sub-dtypes of the matrix are real
valued. ie - this function does not handle structured dtypes having complex values
Parameters
----------
dataset : :class:`numpy.ndarray`, or :class:`h5py.Dataset`, or :class:`dask.array.core.Array`
Numpy array that is a structured array or a :class:`h5py.Dataset` of compound dtype
lazy : bool, optional. Default = False
If set to True, will use lazy Dask arrays instead of in-memory numpy arrays
Returns
-------
retval : :class:`numpy.ndarray`, or :class:`dask.array.core.Array`
real valued dataset
Examples
--------
>>> import numpy as np
>>> import sidpy
>>> num_elems = 5
>>> struct_dtype = np.dtype({'names': ['r', 'g', 'b'],
>>> 'formats': [np.float32, np.uint16, np.float64]})
>>> structured_array = np.zeros(shape=num_elems, dtype=struct_dtype)
>>> structured_array['r'] = np.random.random(size=num_elems) * 1024
>>> structured_array['g'] = np.random.randint(0, high=1024, size=num_elems)
>>> structured_array['b'] = np.random.random(size=num_elems) * 1024
>>> print('Structured array is of shape {} and have values:'.format(structured_array.shape))
>>> print(structured_array)
Structured array is of shape (5,) and have values:
[(859.62445, 54, 1012.22256219) (959.5565 , 678, 296.19788769)
(383.20737, 689, 192.45427816) (201.56635, 889, 939.01082338)
(334.22015, 467, 980.9081472 )]
>>> real_array = sidpy.dtype_utils.flatten_compound_to_real(structured_array)
>>> print("This array converted to regular scalar matrix has shape: {} and values:".format(real_array.shape))
>>> print(real_array)
This array converted to regular scalar matrix has shape: (15,) and values:
[ 859.62445068 959.55651855 383.20736694 201.56634521 334.22015381
54. 678. 689. 889. 467.
1012.22256219 296.19788769 192.45427816 939.01082338 980.9081472 ]
"""
if isinstance(dataset, h5py.Dataset):
if len(dataset.dtype) == 0:
raise TypeError("Expected compound h5py dataset")
if lazy:
xp = da
dataset = lazy_load_array(dataset)
else:
xp = np
warn('HDF5 datasets will be loaded as Dask arrays in the future. ie - kwarg lazy will default to True in future releases of sidpy')
return xp.concatenate([xp.array(dataset[name]) for name in dataset.dtype.names], axis=len(dataset.shape) - 1)
elif isinstance(dataset, (np.ndarray, da.core.Array)):
if isinstance(dataset, da.core.Array):
lazy = True
xp = np
if lazy:
dataset = lazy_load_array(dataset)
xp = da
if len(dataset.dtype) == 0:
raise TypeError("Expected structured array")
if dataset.ndim > 0:
return xp.concatenate([dataset[name] for name in dataset.dtype.names], axis=dataset.ndim - 1)
else:
return xp.hstack([dataset[name] for name in dataset.dtype.names])
elif isinstance(dataset, np.void):
return np.hstack([dataset[name] for name in dataset.dtype.names])
else:
raise TypeError('Datatype {} not supported'.format(type(dataset)))
def flatten_to_real(ds_main, lazy=False):
"""
Flattens complex / compound / real valued arrays to real valued arrays
Parameters
----------
ds_main : :class:`numpy.ndarray`, or :class:`h5py.Dataset`, or :class:`dask.array.core.Array`
Compound, complex or real valued numpy array or HDF5 dataset
lazy : bool, optional. Default = False
If set to True, will use lazy Dask arrays instead of in-memory numpy arrays
Returns
----------
ds_main : :class:`numpy.ndarray`, or :class:`dask.array.core.Array`
Array raveled to a float data type
Examples
--------
>>> import numpy as np
>>> import sidpy
>>> num_elems = 5
>>> struct_dtype = np.dtype({'names': ['r', 'g', 'b'],
>>> 'formats': [np.float32, np.uint16, np.float64]})
>>> structured_array = np.zeros(shape=num_elems, dtype=struct_dtype)
>>> structured_array['r'] = np.random.random(size=num_elems) * 1024
>>> structured_array['g'] = np.random.randint(0, high=1024, size=num_elems)
>>> structured_array['b'] = np.random.random(size=num_elems) * 1024
>>> print('Structured array is of shape {} and have values:'.format(structured_array.shape))
>>> print(structured_array)
Structured array is of shape (5,) and have values:
[(859.62445, 54, 1012.22256219) (959.5565 , 678, 296.19788769)
(383.20737, 689, 192.45427816) (201.56635, 889, 939.01082338)
(334.22015, 467, 980.9081472 )]
>>> real_array = sidpy.dtype_utils.flatten_to_real(structured_array)
>>> print('This array converted to regular scalar matrix has shape: {} and values:'.format(real_array.shape))
>>> print(real_array)
This array converted to regular scalar matrix has shape: (15,) and values:
[ 859.62445068 959.55651855 383.20736694 201.56634521 334.22015381
54. 678. 689. 889. 467.
1012.22256219 296.19788769 192.45427816 939.01082338 980.9081472 ]
"""
if not isinstance(ds_main, (h5py.Dataset, np.ndarray, da.core.Array)):
ds_main = np.array(ds_main)
if is_complex_dtype(ds_main.dtype):
return flatten_complex_to_real(ds_main, lazy=lazy)
elif len(ds_main.dtype) > 0:
return flatten_compound_to_real(ds_main, lazy=lazy)
else:
return ds_main
def get_compound_sub_dtypes(struct_dtype):
"""
Returns a dictionary of the dtypes of each of the fields in the given structured array dtype
Parameters
----------
struct_dtype : :class:`numpy.dtype`
dtype of a structured array
Returns
-------
dtypes : dict
Dictionary whose keys are the field names and values are the corresponding dtypes
Examples
--------
>>> import numpy as np
>>> import sidpy
>>> struct_dtype = np.dtype({'names': ['r', 'g', 'b'],
>>> 'formats': [np.float32, np.uint16, np.float64]})
>>> sub_dtypes = sidpy.dtype_utils.get_compound_sub_dtypes(struct_dtype)
>>> for key, val in sub_dtypes.items():
>>> print('{} : {}'.format(key, val))
g : uint16
r : float32
b : float64
"""
if not isinstance(struct_dtype, np.dtype):
raise TypeError('Provided object must be a structured array dtype')
dtypes = dict()
for field_name in struct_dtype.fields:
dtypes[field_name] = struct_dtype.fields[field_name][0]
return dtypes
def check_dtype(h5_dset):
"""
Checks the datatype of the input HDF5 dataset and provides the appropriate
function calls to convert it to a float
Parameters
----------
h5_dset : :class:`h5py.Dataset`
Dataset of interest
Returns
-------
func : callable
function that will convert the dataset to a float
is_complex : bool
is the input dataset complex?
is_compound : bool
is the input dataset compound?
n_features : Unsigned int
Unsigned integer - the length of the 2nd dimension of the data after `func` is called on it
type_mult : Unsigned int
multiplier that converts from the typesize of the input :class:`~numpy.dtype` to the
typesize of the data after func is run on it
Examples
--------
>>> import numpy as np
>>> import h5py
>>> import sidpy
>>> struct_dtype = np.dtype({'names': ['r', 'g', 'b'],
>>> 'formats': [np.float32, np.uint16, np.float64]})
>>> file_path = 'dtype_utils_example.h5'
>>> if os.path.exists(file_path):
>>> os.remove(file_path)
>>> with h5py.File(file_path, mode='w') as h5_f:
>>> num_elems = (5, 7)
>>> structured_array = np.zeros(shape=num_elems, dtype=struct_dtype)
>>> structured_array['r'] = 450 * np.random.random(size=num_elems)
>>> structured_array['g'] = np.random.randint(0, high=1024, size=num_elems)
>>> structured_array['b'] = 3178 * np.random.random(size=num_elems)
>>> _ = h5_f.create_dataset('compound', data=structured_array)
>>> _ = h5_f.create_dataset('real', data=450 * np.random.random(size=num_elems), dtype=np.float16)
>>> _ = h5_f.create_dataset('complex', data=np.random.random(size=num_elems) + 1j * np.random.random(size=num_elems),
>>> dtype=np.complex64)
>>> h5_f.flush()
>>> # Now, lets test the the function on compound-, complex-, and real-valued HDF5 datasets:
>>> def check_dataset(h5_dset):
>>> print('\tDataset being tested: {}'.format(h5_dset))
>>> func, is_complex, is_compound, n_features, type_mult = sidpy.dtype_utils.check_dtype(h5_dset)
>>> print('\tFunction to transform to real: %s' % func)
>>> print('\tis_complex? %s' % is_complex)
>>> print('\tis_compound? %s' % is_compound)
>>> print('\tShape of dataset in its current form: {}'.format(h5_dset.shape))
>>> print('\tAfter flattening to real, shape is expected to be: ({}, {})'.format(h5_dset.shape[0], n_features))
>>> print('\tByte-size of a single element in its current form: {}'.format(type_mult))
>>> with h5py.File(file_path, mode='r') as h5_f:
>>> print('Checking a compound-valued dataset:')
>>> check_dataset(h5_f['compound'])
>>> print('')
>>> print('Checking a complex-valued dataset:')
>>> check_dataset(h5_f['complex'])
>>> print('')
>>> print('Checking a real-valued dataset:')
>>> check_dataset(h5_f['real'])
>>> os.remove(file_path)
Checking a compound-valued dataset:
Dataset being tested: <HDF5 dataset "compound": shape (5, 7), type "|V14">
Function to transform to real: <function flatten_compound_to_real at 0x112c130d0>
is_complex? False
is_compound? True
Shape of dataset in its current form: (5, 7)
After flattening to real, shape is expected to be: (5, 21)
Byte-size of a single element in its current form: 12
- - - - - - - - - - - - - - - - - -
Checking a complex-valued dataset:
Dataset being tested: <HDF5 dataset "complex": shape (5, 7), type "<c8">
Function to transform to real: <function flatten_complex_to_real at 0x112c13048>
is_complex? True
is_compound? False
Shape of dataset in its current form: (5, 7)
After flattening to real, shape is expected to be: (5, 14)
Byte-size of a single element in its current form: 8
- - - - - - - - - - - - - - - - - -
Checking a real-valued dataset:
Dataset being tested: <HDF5 dataset "real": shape (5, 7), type "<f2">
Function to transform to real: <class 'numpy.float32'>
is_complex? False
is_compound? False
Shape of dataset in its current form: (5, 7)
After flattening to real, shape is expected to be: (5, 7)
Byte-size of a single element in its current form: 4
"""
if not isinstance(h5_dset, h5py.Dataset):
raise TypeError('h5_dset should be a h5py.Dataset object')
is_complex = False
is_compound = False
in_dtype = h5_dset.dtype
# TODO: avoid assuming 2d shape - why does one even need n_samples!? We only care about the last dimension!
n_features = h5_dset.shape[-1]
if is_complex_dtype(h5_dset.dtype):
is_complex = True
new_dtype = np.real(h5_dset[0, 0]).dtype
type_mult = new_dtype.itemsize * 2
func = flatten_complex_to_real
n_features *= 2
elif len(h5_dset.dtype) > 0:
"""
Some form of structured numpy is in use
We only support real scalars for the component types at the current time
"""
is_compound = True
# TODO: Avoid hard-coding to float32
new_dtype = np.float32
type_mult = len(in_dtype) * new_dtype(0).itemsize
func = flatten_compound_to_real
n_features *= len(in_dtype)
else:
if h5_dset.dtype not in [np.float32, np.float64]:
new_dtype = np.float32
else:
new_dtype = h5_dset.dtype.type
type_mult = new_dtype(0).itemsize
func = new_dtype
return func, is_complex, is_compound, n_features, type_mult
def stack_real_to_complex(ds_real, lazy=False):
"""
Puts the real and imaginary sections of the provided matrix (in the last axis) together to make complex matrix
Parameters
------------
ds_real : :class:`numpy.ndarray`, :class:`dask.array.core.Array`, or :class:`h5py.Dataset`
n dimensional real-valued numpy array or HDF5 dataset where data arranged as [instance, 2 x features],
where the first half of the features are the real component and the
second half contains the imaginary components
lazy : bool, optional. Default = False
If set to True, will use lazy Dask arrays instead of in-memory numpy arrays
Returns
----------
ds_compound : :class:`numpy.ndarray` or :class:`dask.array.core.Array`
2D complex array arranged as [sample, features]
Examples
--------
>>> import numpy as np
>>> import sidpy
>>> real_val = np.hstack([5 * np.random.rand(6),
>>> 7 * np.random.rand(6)])
>>> print('Real valued dataset of shape {}:'.format(real_val.shape))
>>> print(real_val)
Real valued dataset of shape (12,):
[3.59249723 1.05674621 4.41035214 1.84720102 1.79672691 4.7636207
3.09574246 0.76396171 3.38140637 4.97629028 0.83303717 0.32816285]
>>> comp_val = sidpy.dtype_utils.stack_real_to_complex(real_val)
>>> print('Complex-valued array of shape: {}'.format(comp_val.shape))
>>> print(comp_val)
Complex-valued array of shape: (6,)
[3.59249723+3.09574246j 1.05674621+0.76396171j 4.41035214+3.38140637j
1.84720102+4.97629028j 1.79672691+0.83303717j 4.7636207 +0.32816285j]
"""
if not isinstance(ds_real, (np.ndarray, da.core.Array, h5py.Dataset)):
if not isinstance(ds_real, (tuple, list)):
raise TypeError("Expected at least an iterable like a list or tuple")
ds_real = np.array(ds_real)
if len(ds_real.dtype) > 0:
raise TypeError("Array cannot have a compound dtype")
if is_complex_dtype(ds_real.dtype):
raise TypeError("Array cannot have complex dtype")
if ds_real.shape[-1] / 2 != ds_real.shape[-1] // 2:
raise ValueError("Last dimension must be even sized")
half_point = ds_real.shape[-1] // 2
if isinstance(ds_real, da.core.Array):
lazy = True
if lazy and not isinstance(ds_real, da.core.Array):
ds_real = lazy_load_array(ds_real)
return ds_real[..., :half_point] + 1j * ds_real[..., half_point:]
def stack_real_to_compound(ds_real, compound_type, lazy=False):
"""
Converts a real-valued dataset to a compound dataset (along the last axis) of the provided compound d-type
Parameters
------------
ds_real : :class:`numpy.ndarray`, :class:`dask.array.core.Array`, or :class:`h5py.Dataset`
n dimensional real-valued numpy array or HDF5 dataset where data arranged as [instance, features]
compound_type : :class:`numpy.dtype`
Target complex data-type
lazy : bool, optional. Default = False
If set to True, will use lazy Dask arrays instead of in-memory numpy arrays
Returns
----------
ds_compound : :class:`numpy.ndarray` or :class:`dask.array.core.Array`
N-dimensional complex-valued array arranged as [sample, features]
Examples
--------
>>> import numpy as np
>>> import sidpy
>>> struct_dtype = np.dtype({'names': ['r', 'g', 'b'],
>>> 'formats': [np.float32, np.uint16, np.float64]})
>>> num_elems = 5
>>> real_val = np.concatenate((np.random.random(size=num_elems) * 1024,
>>> np.random.randint(0, high=1024, size=num_elems),
>>> np.random.random(size=num_elems) * 1024))
>>> print('Real valued dataset of shape {}:'.format(real_val.shape))
>>> print(real_val)
Real valued dataset of shape (15,):
[276.65339095 527.80665658 741.38145798 647.06743252 710.41729083
380. 796. 504. 355. 985.
960.70015068 567.47024098 881.25140299 105.48936013 933.13686734]
>>> comp_val = sidpy.dtype_utils.stack_real_to_compound(real_val, struct_dtype)
>>> print('Structured array of shape: {}'.format(comp_val.shape))
>>> print(comp_val)
Structured array of shape: (5,)
[(276.65338, 380, 960.70015068) (527.80664, 796, 567.47024098)
(741.3815 , 504, 881.25140299) (647.06744, 355, 105.48936013)
(710.4173 , 985, 933.13686734)]
"""
if lazy or isinstance(ds_real, da.core.Array):
raise NotImplementedError('Lazy operation not available due to absence of Dask support')
if not isinstance(ds_real, (np.ndarray, h5py.Dataset)):
if not isinstance(ds_real, (list, tuple)):
raise TypeError("Expected at least an iterable like a list or tuple")
ds_real = np.array(ds_real)
if len(ds_real.dtype) > 0:
raise TypeError("Array cannot have a compound dtype")
elif is_complex_dtype(ds_real.dtype):
raise TypeError("Array cannot have complex dtype")
if not isinstance(compound_type, np.dtype):
raise TypeError('Provided object must be a structured array dtype')
new_spec_length = ds_real.shape[-1] / len(compound_type)
if new_spec_length % 1:
raise ValueError('Provided compound type was not compatible by number of elements')
new_spec_length = int(new_spec_length)
new_shape = list(ds_real.shape) # Make mutable
new_shape[-1] = new_spec_length
xp = np
kwargs = {}
"""
if isinstance(ds_real, h5py.Dataset) and not lazy:
warn('HDF5 datasets will be loaded as Dask arrays in the future. ie - kwarg lazy will default to True in future releases of sidpy')
if isinstance(ds_real, da.core.Array):
lazy = True
if lazy:
xp = da
ds_real = lazy_load_array(ds_real)
kwargs = {'chunks': 'auto'}
"""
ds_compound = xp.empty(new_shape, dtype=compound_type, **kwargs)
for name_ind, name in enumerate(compound_type.names):
i_start = name_ind * new_spec_length
i_end = (name_ind + 1) * new_spec_length
ds_compound[name] = ds_real[..., i_start:i_end]
return ds_compound.squeeze()
def stack_real_to_target_dtype(ds_real, new_dtype, lazy=False):
"""
Transforms real data into the target dtype
Parameters
----------
ds_real : :class:`numpy.ndarray`, :class:`dask.array.core.Array` or :class:`h5py.Dataset`
n dimensional real-valued numpy array or HDF5 dataset
new_dtype : :class:`numpy.dtype`
Target data-type
Returns
----------
ret_val : :class:`numpy.ndarray` or :class:`dask.array.core.Array`
N-dimensional array of the target data-type
Examples
--------
>>> import numpy as np
>>> import sidpy
>>> struct_dtype = np.dtype({'names': ['r', 'g', 'b'],
>>> 'formats': [np.float32, np.uint16, np.float64]})
>>> num_elems = 5
>>> real_val = np.concatenate((np.random.random(size=num_elems) * 1024,
>>> np.random.randint(0, high=1024, size=num_elems),
>>> np.random.random(size=num_elems) * 1024))
>>> print('Real valued dataset of shape {}:'.format(real_val.shape))
>>> print(real_val)
Real valued dataset of shape (15,):
[276.65339095 527.80665658 741.38145798 647.06743252 710.41729083
380. 796. 504. 355. 985.
960.70015068 567.47024098 881.25140299 105.48936013 933.13686734]
>>> comp_val = sidpy.dtype_utils.stack_real_to_target_dtype(real_val, struct_dtype)
>>> print('Structured array of shape: {}'.format(comp_val.shape))
>>> print(comp_val)
Structured array of shape: (5,)
[(276.65338, 380, 960.70015068) (527.80664, 796, 567.47024098)
(741.3815 , 504, 881.25140299) (647.06744, 355, 105.48936013)
(710.4173 , 985, 933.13686734)]
"""
if is_complex_dtype(new_dtype):
return stack_real_to_complex(ds_real, lazy=lazy)
try:
if len(new_dtype) > 0:
return stack_real_to_compound(ds_real, new_dtype, lazy=lazy)
except TypeError:
return new_dtype(ds_real)
# catching all other cases, such as np.dtype('<f4')
return new_dtype.type(ds_real)
def validate_dtype(dtype):
"""
Checks the provided object to ensure that it is a valid dtype that can be written to an HDF5 file.
Raises a type error if invalid. Returns True if the object passed the tests
Parameters
----------
dtype : object
Object that is hopefully a :class:`h5py.Datatype`, or :class:`numpy.dtype` object
Returns
-------
status : bool
True if the object was a valid data-type
Examples
--------
>>> import numpy as np
>>> import sidpy
>>> for item in [np.float16, np.complex64, np.uint8, np.int16]:
>>> print('Is {} a valid dtype? : {}'.format(item, sidpy.dtype_utils.validate_dtype(item)))
Is <class 'numpy.float16'> a valid dtype? : True
Is <class 'numpy.complex64'> a valid dtype? : True
Is <class 'numpy.uint8'> a valid dtype? : True
Is <class 'numpy.int16'> a valid dtype? : True
# This function is especially useful on compound or structured data types:
>>> struct_dtype = np.dtype({'names': ['r', 'g', 'b'],
>>> 'formats': [np.float32, np.uint16, np.float64]})
>>> print('Is {} a valid dtype? : {}'.format(struct_dtype, sidpy.dtype_utils.validate_dtype(struct_dtype)))
Is [('r', '<f4'), ('g', '<u2'), ('b', '<f8')] a valid dtype? : True
"""
if isinstance(dtype, (h5py.Datatype, np.dtype)):
pass
elif isinstance(np.dtype(dtype), np.dtype):
# This should catch all those instances when dtype is something familiar like - np.float32
pass
else:
raise TypeError('dtype should either be a numpy or h5py dtype')
return True
def is_complex_dtype(dtype):
"""
Checks if the provided dtype is a complex dtype
Parameters
----------
dtype : object
Object that is a class:`h5py.Datatype`, or :class:`numpy.dtype` object
Returns
-------
is_complex : bool
True if the dtype was a complex dtype. Else returns False
Examples
--------
>>> import numpy as np
>>> import sidpy
>>> for dtype in [np.float32, np.float16, np.uint8, np.int16, bool]:
>>> print('Is {} a complex dtype?: {}'.format(dtype, (sidpy.dtype_utils.is_complex_dtype(dtype))))
Is <class 'numpy.float32'> a complex dtype?: False
Is <class 'numpy.float16'> a complex dtype?: False
Is <class 'numpy.uint8'> a complex dtype?: False
Is <class 'numpy.int16'> a complex dtype?: False
Is <class 'bool'> a complex dtype?: False
>>> struct_dtype = np.dtype({'names': ['r', 'g', 'b'],
>>> 'formats': [np.float32, np.uint16, np.float64]})
Is [('r', '<f4'), ('g', '<u2'), ('b', '<f8')] a complex dtype?: False
>>> for dtype in [complex, np.complex64, np.complex128, np.complex256]:
>>> print('Is {} a complex dtype?: {}'.format(dtype, (sidpy.dtype_utils.is_complex_dtype(dtype))))
Is <class 'complex'> a complex dtype?: True
Is <class 'numpy.complex64'> a complex dtype?: True
Is <class 'numpy.complex128'> a complex dtype?: True
Is <class 'numpy.complex256'> a complex dtype?: False
"""
validate_dtype(dtype)
if dtype in [complex, np.complex64, np.complex128]:
return True
return False
|