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 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 468 469 470 471 472 473 474 475 476 477 478 479 480 481 482 483 484 485 486 487 488 489 490 491 492 493 494 495 496 497 498 499 500 501 502 503 504 505 506 507 508 509 510 511 512 513 514 515 516 517 518 519 520 521 522 523 524 525 526 527 528 529 530 531 532 533 534 535 536 537 538 539 540 541 542 543 544 545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 571 572 573 574 575 576 577 578 579 580 581 582 583 584 585 586 587 588 589 590 591 592 593 594 595 596 597 598 599 600 601 602 603 604 605 606 607 608 609 610 611 612 613 614 615 616 617 618 619 620 621 622 623 624 625 626 627 628 629 630 631 632 633 634 635 636 637 638 639 640 641 642 643 644 645 646 647 648 649 650 651 652 653 654 655 656 657 658 659 660 661 662 663 664 665 666 667 668 669 670 671 672 673 674 675 676 677 678 679 680 681 682 683 684 685 686 687 688 689 690 691 692 693 694 695 696 697 698 699 700 701 702 703 704 705 706 707 708 709 710 711 712 713 714 715 716 717 718 719 720 721 722 723 724 725 726 727 728 729 730 731 732 733 734 735 736 737 738 739 740 741 742 743 744 745 746 747 748 749 750 751 752 753 754 755 756 757 758 759 760 761 762 763 764 765 766 767 768 769 770 771 772 773 774 775 776 777 778 779 780 781 782 783 784 785 786 787 788 789 790 791 792 793 794 795 796 797 798 799 800 801 802 803 804 805 806 807 808 809 810 811 812 813 814 815 816 817 818 819 820 821 822 823 824 825 826 827 828 829 830 831 832 833 834 835 836 837 838 839 840 841 842 843 844 845 846 847 848 849 850 851 852 853 854 855 856 857 858 859 860 861 862 863 864 865 866 867 868 869 870 871 872 873 874 875 876 877 878 879 880 881 882 883 884 885 886 887 888 889 890 891 892 893 894 895 896 897 898 899 900 901 902 903 904 905 906 907 908 909 910 911 912 913 914 915 916 917 918 919 920 921 922 923 924 925 926 927 928 929 930 931 932 933 934 935 936 937 938 939 940 941 942 943 944 945 946 947 948 949 950 951 952 953 954 955 956 957 958 959 960 961 962 963 964 965 966 967 968 969 970 971 972 973 974 975 976 977 978 979 980 981 982 983 984 985 986 987 988 989 990 991 992 993 994 995 996 997 998 999 1000 1001 1002 1003 1004 1005 1006 1007 1008 1009 1010 1011 1012 1013
|
"""Attributes common to PolyData and Grid Objects."""
from __future__ import annotations
from abc import abstractmethod
from collections import UserDict
from collections import defaultdict
from pathlib import Path
from typing import TYPE_CHECKING
from typing import cast
import warnings
import numpy as np
import pyvista
from pyvista._deprecate_positional_args import _deprecate_positional_args
from pyvista.typing.mypy_plugin import promote_type
from . import _vtk_core as _vtk
from .datasetattributes import DataSetAttributes
from .pyvista_ndarray import pyvista_ndarray
from .utilities.arrays import FieldAssociation
from .utilities.arrays import _JSONValueType
from .utilities.arrays import _SerializedDictArray
from .utilities.fileio import PICKLE_EXT
from .utilities.fileio import read
from .utilities.fileio import save_pickle
from .utilities.fileio import set_vtkwriter_mode
from .utilities.helpers import wrap
from .utilities.misc import _NoNewAttrMixin
from .utilities.misc import abstract_class
if TYPE_CHECKING:
from types import FunctionType
from typing import Any
from typing import ClassVar
from typing_extensions import Self
from ._typing_core import NumpyArray
from .utilities.fileio import _VTKWriterAlias
# vector array names
DEFAULT_VECTOR_KEY = '_vectors'
USER_DICT_KEY = '_PYVISTA_USER_DICT'
@promote_type(_vtk.vtkDataObject)
@abstract_class
class DataObject(_NoNewAttrMixin, _vtk.DisableVtkSnakeCase, _vtk.vtkPyVistaOverride):
"""Methods common to all wrapped data objects.
Parameters
----------
*args :
Any extra args are passed as option to all wrapped data objects.
**kwargs :
Any extra keyword args are passed as option to all wrapped data objects.
"""
_WRITERS: ClassVar[dict[str, type[_VTKWriterAlias]]] = {}
def __init__(self: Self, *args, **kwargs) -> None:
"""Initialize the data object."""
try:
super().__init__(*args, **kwargs)
except TypeError:
# super() maps to object
super().__init__()
# Remember which arrays come from numpy.bool arrays, because there is no direct
# conversion from bool to vtkBitArray, such arrays are stored as vtkCharArray.
self._association_bitarray_names: defaultdict[Any, Any] = defaultdict(set)
# view these arrays as complex128 as VTK doesn't support complex types
self._association_complex_names: defaultdict[Any, Any] = defaultdict(set)
def __getattr__(self: Self, item: str) -> Any:
"""Get attribute from base class if not found."""
return super().__getattribute__(item)
def shallow_copy(self: Self, to_copy: Self | _vtk.vtkDataObject) -> None:
"""Shallow copy the given mesh to this mesh.
Parameters
----------
to_copy : DataObject | :vtk:`vtkDataObject`
Data object to perform a shallow copy from.
"""
self.ShallowCopy(to_copy)
def deep_copy(self: Self, to_copy: Self | _vtk.vtkDataObject) -> None:
"""Overwrite this data object with another data object as a deep copy.
Parameters
----------
to_copy : DataObject | :vtk:`vtkDataObject`
Data object to perform a deep copy from.
"""
self.DeepCopy(to_copy)
def _from_file(self: Self, filename: str | Path, **kwargs) -> None:
"""Read data objects from file."""
data = read(filename, **kwargs)
if not isinstance(self, type(data)):
msg = (
f'Reading file returned data of `{type(data).__name__}`, '
f'but `{type(self).__name__}` was expected.'
)
raise TypeError(msg)
self.shallow_copy(data)
self._post_file_load_processing()
def _post_file_load_processing(self: Self) -> None:
"""Execute after loading a dataset from file, to be optionally overridden by subclasses."""
@_deprecate_positional_args(allowed=['filename'])
def save(
self: Self,
filename: Path | str,
binary: bool = True, # noqa: FBT001, FBT002
texture: NumpyArray[np.uint8] | str | None = None,
) -> None:
"""Save this vtk object to file.
.. versionadded:: 0.45
Support saving pickled meshes
See Also
--------
pyvista.read
Parameters
----------
filename : str, pathlib.Path
Filename of output file. Writer type is inferred from
the extension of the filename.
binary : bool, default: True
If ``True``, write as binary. Otherwise, write as ASCII.
texture : str, np.ndarray, optional
Write a single texture array to file when using a PLY
file. Texture array must be a 3 or 4 component array with
the datatype ``np.uint8``. Array may be a cell array or a
point array, and may also be a string if the array already
exists in the PolyData.
If a string is provided, the texture array will be saved
to disk as that name. If an array is provided, the
texture array will be saved as ``'RGBA'``
.. note::
This feature is only available when saving PLY files.
Notes
-----
Binary files write much faster than ASCII and have a smaller
file size.
"""
def _warn_multiblock_nested_field_data(mesh: pyvista.MultiBlock) -> None:
iterator = mesh.recursive_iterator('all', node_type='parent')
for index, name, nested_multiblock in iterator:
if len(nested_multiblock.field_data.keys()) > 0:
# Avoid circular import
from pyvista.core.filters.composite import _format_nested_index
index_fmt = _format_nested_index(index)
warnings.warn(
f"Nested MultiBlock at index {index_fmt} with name '{name}' "
f'has field data which will not be saved.\n'
'See https://gitlab.kitware.com/vtk/vtk/-/issues/19414 \n'
'Use `move_nested_field_data_to_root` to store the field data '
'with the root MultiBlock before saving.'
)
def _check_multiblock_hdf_types(mesh: pyvista.MultiBlock) -> None:
if (9, 4, 0) <= pyvista.vtk_version_info < (9, 5, 0):
if mesh.is_nested:
msg = (
'Nested MultiBlocks are not supported by the .vtkhdf format in VTK 9.4.'
'\nUpgrade to VTK>=9.5 for this functionality.'
)
raise TypeError(msg)
if type(None) in mesh.block_types:
msg = (
'Saving None blocks is not supported by the .vtkhdf format in VTK 9.4.'
'\nUpgrade to VTK>=9.5 for this functionality.'
)
raise TypeError(msg)
supported_block_types: list[type] = [
pyvista.PolyData,
pyvista.UnstructuredGrid,
type(None),
pyvista.MultiBlock,
pyvista.PartitionedDataSet,
]
for id_, name, block in mesh.recursive_iterator('all'):
if type(block) not in supported_block_types:
from pyvista.core.filters.composite import _format_nested_index
index_fmt = _format_nested_index(id_)
msg = (
f"Block at index {index_fmt} with name '{name}' has type "
f'{block.__class__.__name__!r} '
f'which cannot be saved to the .vtkhdf format.\n'
f'Supported types are: {[typ.__name__ for typ in supported_block_types]}.'
)
raise TypeError(msg)
def _warn_imagedata_direction_matrix(mesh: pyvista.ImageData) -> None:
if not np.allclose(mesh.direction_matrix, np.eye(3)):
warnings.warn(
'The direction matrix for ImageData will not be saved using the '
'legacy `.vtk` format.\n'
'See https://gitlab.kitware.com/vtk/vtk/-/issues/19663 \n'
'Use the `.vti` extension instead (XML format).'
)
def _write_vtk(mesh_: DataObject) -> None:
writer = mesh_._WRITERS[file_ext]()
set_vtkwriter_mode(vtk_writer=writer, use_binary=binary)
writer.SetFileName(str(file_path))
writer.SetInputData(mesh_)
if isinstance(writer, _vtk.vtkPLYWriter) and texture is not None: # type: ignore[unreachable]
mesh_ = cast('pyvista.DataSet', mesh_) # type: ignore[unreachable]
if isinstance(texture, str):
writer.SetArrayName(texture)
array_name = texture
elif isinstance(texture, np.ndarray):
array_name = '_color_array'
mesh_[array_name] = texture
writer.SetArrayName(array_name)
# enable alpha channel if applicable
if mesh_[array_name].shape[-1] == 4:
writer.SetEnableAlpha(True)
writer.Write()
if self._WRITERS is None:
msg = ( # type: ignore[unreachable]
f'{self.__class__.__name__} writers are not specified,'
' this should be a dict of (file extension: vtkWriter type)'
)
raise NotImplementedError(msg)
file_path = Path(filename)
file_path = file_path.expanduser()
file_path = file_path.resolve()
file_ext = file_path.suffix
if file_ext == '.vtkhdf' and binary is False:
msg = '.vtkhdf files can only be written in binary format.'
raise ValueError(msg)
# store complex and bitarray types as field data
self._store_metadata()
# warn if data will be lost
if isinstance(self, pyvista.MultiBlock):
_warn_multiblock_nested_field_data(self)
if file_ext == '.vtkhdf':
_check_multiblock_hdf_types(self)
if isinstance(self, pyvista.ImageData) and file_ext == '.vtk':
_warn_imagedata_direction_matrix(self)
writer_exts = self._WRITERS.keys()
if file_ext in writer_exts:
_write_vtk(self)
elif file_ext in PICKLE_EXT:
save_pickle(filename, self)
else:
msg = (
'Invalid file extension for this data type.'
f' Must be one of: {list(writer_exts) + list(PICKLE_EXT)}'
)
raise ValueError(msg)
def _store_metadata(self: Self) -> None:
"""Store metadata as field data."""
fdata = self.field_data
for assoc_name in ('bitarray', 'complex'):
for assoc_type in ('POINT', 'CELL'):
assoc_data = getattr(self, f'_association_{assoc_name}_names')
array_names = assoc_data.get(assoc_type)
if array_names:
key = f'_PYVISTA_{assoc_name}_{assoc_type}_'.upper()
fdata[key] = list(array_names)
def _restore_metadata(self: Self) -> None:
"""Restore PyVista metadata from field data.
Metadata is stored using ``_store_metadata`` and contains entries in
the format of f'_PYVISTA_{assoc_name}_{assoc_type}_'. These entries are
removed when calling this method.
"""
fdata = self.field_data
for assoc_name in ('bitarray', 'complex'):
for assoc_type in ('POINT', 'CELL'):
key = f'_PYVISTA_{assoc_name}_{assoc_type}_'.upper()
if key in fdata:
assoc_data = getattr(self, f'_association_{assoc_name}_names')
assoc_data[assoc_type] = set(fdata[key])
del fdata[key]
@abstractmethod
def get_data_range(
self: Self, name: str | None, preference: FieldAssociation | str
) -> tuple[float, float]: # pragma: no cover
"""Get the non-NaN min and max of a named array."""
msg = f'{type(self)} mesh type does not have a `get_data_range` method.'
raise NotImplementedError(msg)
def _get_attrs(self: Self) -> list[tuple[str, Any, str]]: # pragma: no cover
"""Return the representation methods (internal helper)."""
msg = 'Called only by the inherited class'
raise NotImplementedError(msg)
@_deprecate_positional_args
def head(self: Self, display: bool = True, html: bool | None = None) -> str: # noqa: FBT001, FBT002
"""Return the header stats of this dataset.
If in IPython, this will be formatted to HTML. Otherwise
returns a console friendly string.
Parameters
----------
display : bool, default: True
Display this header in iPython.
html : bool, optional
Generate the output as HTML.
Returns
-------
str
Header statistics.
"""
# Generate the output
if html:
fmt = ''
# HTML version
fmt += '\n'
fmt += "<table style='width: 100%;'>\n"
fmt += f'<tr><th>{type(self).__name__}</th><th>Information</th></tr>\n'
row = '<tr><td>{}</td><td>{}</td></tr>\n'
# now make a call on the object to get its attributes as a list of len 2 tuples
for attr in self._get_attrs():
try:
fmt += row.format(attr[0], attr[2].format(*attr[1]))
except TypeError:
fmt += row.format(attr[0], attr[2].format(attr[1]))
if hasattr(self, 'n_arrays'):
fmt += row.format('N Arrays', self.n_arrays)
fmt += '</table>\n'
fmt += '\n'
if display:
from IPython.display import HTML
from IPython.display import display as _display
_display(HTML(fmt))
return ''
return fmt
# Otherwise return a string that is Python console friendly
fmt = f'{type(self).__name__} ({hex(id(self))})\n'
# now make a call on the object to get its attributes as a list of len 2 tuples
# get longest row header
max_len = max(len(attr[0]) for attr in self._get_attrs()) + 4
# now make a call on the object to get its attributes as a list of len
# 2 tuples
row = f' {{:{max_len}s}}' + '{}\n'
for attr in self._get_attrs():
try:
fmt += row.format(attr[0] + ':', attr[2].format(*attr[1]))
except TypeError:
fmt += row.format(attr[0] + ':', attr[2].format(attr[1]))
if hasattr(self, 'n_arrays'):
fmt += row.format('N Arrays:', self.n_arrays)
return fmt.strip()
def _repr_html_(self: Self) -> str: # pragma: no cover
"""Return a pretty representation for Jupyter notebooks.
This includes header details and information about all arrays.
"""
msg = 'Called only by the inherited class'
raise NotImplementedError(msg)
def copy_meta_from(self: Self, *args, **kwargs) -> None: # pragma: no cover
"""Copy pyvista meta data onto this object from another object.
Intended to be overridden by subclasses.
Parameters
----------
*args : tuple
Positional arguments.
**kwargs : dict, optional
Keyword arguments.
"""
# called only by the inherited class
@_deprecate_positional_args
def copy(self: Self, deep: bool = True) -> Self: # noqa: FBT001, FBT002
"""Return a copy of the object.
Parameters
----------
deep : bool, default: True
When ``True`` makes a full copy of the object. When
``False``, performs a shallow copy where the points, cell,
and data arrays are references to the original object.
Returns
-------
pyvista.DataSet
Deep or shallow copy of the input. Type is identical to
the input.
Examples
--------
Create and make a deep copy of a PolyData object.
>>> import pyvista as pv
>>> mesh_a = pv.Sphere()
>>> mesh_b = mesh_a.copy()
>>> mesh_a == mesh_b
True
"""
thistype = type(self)
newobject = thistype()
if deep:
newobject.deep_copy(self)
else:
newobject.shallow_copy(self)
newobject.copy_meta_from(self, deep=deep)
return newobject
def __eq__(self: Self, other: object) -> bool:
"""Test equivalency between data objects."""
if not isinstance(self, type(other)):
return False
if self is other:
return True
# these attrs use numpy.array_equal
if isinstance(self, pyvista.ImageData):
equal_attrs = ['extent', 'index_to_physical_matrix']
else:
equal_attrs = ['points', 'cells']
if isinstance(self, pyvista.PolyData):
equal_attrs.extend(['verts', 'lines', 'faces', 'strips'])
elif isinstance(self, pyvista.UnstructuredGrid):
equal_attrs.append('celltypes')
for attr in equal_attrs:
# Only check equality for attributes defined by PyVista
# (i.e. ignore any default vtk snake_case attributes)
if hasattr(self, attr) and not _vtk.is_vtk_attribute(self, attr):
if not np.array_equal(getattr(self, attr), getattr(other, attr), equal_nan=True):
return False
# these attrs can be directly compared
attrs = ['field_data', 'point_data', 'cell_data']
for attr in attrs:
if hasattr(self, attr):
if getattr(self, attr) != getattr(other, attr):
return False
return True
__hash__ = None # type: ignore[assignment] # https://github.com/pyvista/pyvista/pull/7671
@_deprecate_positional_args(allowed=['array', 'name'])
def add_field_data(self: Self, array: NumpyArray[float], name: str, deep: bool = True) -> None: # noqa: FBT001, FBT002
"""Add field data.
Use field data when size of the data you wish to associate
with the dataset does not match the number of points or cells
of the dataset.
Parameters
----------
array : sequence
Array of data to add to the dataset as a field array.
name : str
Name to assign the field array.
deep : bool, default: True
Perform a deep copy of the data when adding it to the
dataset.
Examples
--------
Add field data to a PolyData dataset.
>>> import pyvista as pv
>>> import numpy as np
>>> mesh = pv.Sphere()
>>> mesh.add_field_data(np.arange(10), 'my-field-data')
>>> mesh['my-field-data']
pyvista_ndarray([0, 1, 2, 3, 4, 5, 6, 7, 8, 9])
Add field data to a ImageData dataset.
>>> mesh = pv.ImageData(dimensions=(2, 2, 1))
>>> mesh.add_field_data(['I could', 'write', 'notes', 'here'], 'my-field-data')
>>> mesh['my-field-data']
pyvista_ndarray(['I could', 'write', 'notes', 'here'], dtype='<U7')
Add field data to a MultiBlock dataset.
>>> blocks = pv.MultiBlock()
>>> blocks.append(pv.Sphere())
>>> blocks['cube'] = pv.Cube(center=(0, 0, -1))
>>> blocks.add_field_data([1, 2, 3], 'my-field-data')
>>> blocks.field_data['my-field-data']
pyvista_ndarray([1, 2, 3])
"""
if not hasattr(self, 'field_data'):
msg = f'`{type(self)}` does not support field data'
raise NotImplementedError(msg)
self.field_data.set_array(array, name, deep_copy=deep)
@property
def field_data(self: Self) -> DataSetAttributes:
"""Return FieldData as DataSetAttributes.
Use field data when size of the data you wish to associate
with the dataset does not match the number of points or cells
of the dataset.
Returns
-------
DataSetAttributes
FieldData as DataSetAttributes.
Examples
--------
Add field data to a PolyData dataset and then return it.
>>> import pyvista as pv
>>> import numpy as np
>>> mesh = pv.Sphere()
>>> mesh.field_data['my-field-data'] = np.arange(10)
>>> mesh.field_data['my-field-data']
pyvista_ndarray([0, 1, 2, 3, 4, 5, 6, 7, 8, 9])
"""
return DataSetAttributes(
self.GetFieldData(),
dataset=self, # type: ignore[arg-type]
association=FieldAssociation.NONE,
)
def clear_field_data(self: Self) -> None:
"""Remove all field data.
Examples
--------
Add field data to a PolyData dataset and then remove it.
>>> import pyvista as pv
>>> mesh = pv.Sphere()
>>> mesh.field_data['my-field-data'] = range(10)
>>> len(mesh.field_data)
1
>>> mesh.clear_field_data()
>>> len(mesh.field_data)
0
"""
if not hasattr(self, 'field_data'):
msg = f'`{type(self)}` does not support field data'
raise NotImplementedError(msg)
self.field_data.clear()
@property
def user_dict(self: Self) -> _SerializedDictArray:
"""Set or return a user-specified data dictionary.
The dictionary is stored as a JSON-serialized string as part of the mesh's
field data. Unlike regular field data, which requires values to be stored
as an array, the user dict provides a mapping for scalar values.
Since the user dict is stored as field data, it is automatically saved
with the mesh when it is saved in a compatible file format (e.g. ``'.vtk'``).
Any saved metadata is automatically de-serialized by PyVista whenever
the user dict is accessed again. Since the data is stored as JSON, it
may also be easily retrieved or read by other programs.
Any JSON-serializable values are permitted by the user dict, i.e. values
can have type ``dict``, ``list``, ``tuple``, ``str``, ``int``, ``float``,
``bool``, or ``None``. Storing NumPy arrays is not directly supported, but
these may be cast beforehand to a supported type, e.g. by calling ``tolist()``
on the array.
To completely remove the user dict string from the dataset's field data,
set its value to ``None``.
.. note::
The user dict is a convenience property and is intended for metadata storage.
It has an inefficient dictionary implementation and should only be used to
store a small number of infrequently-accessed keys with relatively small
values. It should not be used to store frequently accessed array data
with many entries (a regular field data array should be used instead).
.. warning::
Field data is typically passed-through by dataset filters, and therefore
the user dict's items can generally be expected to persist and remain
unchanged in the output of filtering methods. However, this behavior is
not guaranteed, as it's possible that some filters may modify or clear
field data. Use with caution.
.. versionadded:: 0.44
Returns
-------
UserDict
JSON-serialized dict-like object which is subclassed from
:py:class:`collections.UserDict`.
Examples
--------
Load a mesh.
>>> import pyvista as pv
>>> from pyvista import examples
>>> mesh = examples.load_ant()
Add data to the user dict. The contents are serialized as JSON.
>>> mesh.user_dict['name'] = 'ant'
>>> mesh.user_dict
{"name": "ant"}
Alternatively, set the user dict from an existing dict.
>>> mesh.user_dict = dict(name='ant')
The user dict can be updated like a regular dict.
>>> mesh.user_dict.update(
... {
... 'num_legs': 6,
... 'body_parts': ['head', 'thorax', 'abdomen'],
... }
... )
>>> mesh.user_dict
{"name": "ant", "num_legs": 6, "body_parts": ["head", "thorax", "abdomen"]}
Data in the user dict is stored as field data.
>>> mesh.field_data
pyvista DataSetAttributes
Association : NONE
Contains arrays :
_PYVISTA_USER_DICT str "{"name": "ant",..."
Since it's field data, the user dict can be saved to file along with the
mesh and retrieved later.
>>> mesh.save('ant.vtk')
>>> mesh_from_file = pv.read('ant.vtk')
>>> mesh_from_file.user_dict
{"name": "ant", "num_legs": 6, "body_parts": ["head", "thorax", "abdomen"]}
"""
self._config_user_dict()
return self._user_dict
@user_dict.setter
def user_dict(
self: Self,
dict_: dict[str, _JSONValueType] | UserDict[str, _JSONValueType] | None,
) -> None:
# Setting None removes the field data array
if dict_ is None:
if hasattr(self, '_user_dict'):
del self._user_dict
if USER_DICT_KEY in self.field_data.keys():
del self.field_data[USER_DICT_KEY]
return
self._config_user_dict()
if isinstance(dict_, dict):
self._user_dict.data = dict_
elif isinstance(dict_, UserDict):
self._user_dict.data = dict_.data
else:
msg = ( # type: ignore[unreachable]
f'User dict can only be set with type {dict} or {UserDict}.\n'
f'Got {type(dict_)} instead.'
)
raise TypeError(msg)
def _config_user_dict(self: Self) -> None:
"""Init serialized dict array and ensure it is added to field_data."""
field_data = self.field_data
if not hasattr(self, '_user_dict'):
# Init
object.__setattr__(self, '_user_dict', _SerializedDictArray())
if USER_DICT_KEY in field_data.keys():
if isinstance(array := field_data[USER_DICT_KEY], pyvista_ndarray):
# When loaded from file, field will be cast as pyvista ndarray
# Convert to string and initialize new user dict object from it
self._user_dict = _SerializedDictArray(''.join(array))
elif isinstance(array, str) and repr(self._user_dict) != array: # type: ignore[unreachable]
# Filters may update the field data block separately, e.g.
# when copying field data, so we need to capture the new
# string and re-init
self._user_dict = _SerializedDictArray(array)
else:
# User dict is correctly configured, do nothing
return
# Set field data array directly instead of calling 'set_array'
# This skips the call to '_prepare_array' which will otherwise
# do all kinds of casting/conversions and mangle this array
self._user_dict.SetName(USER_DICT_KEY)
field_data.VTKObject.AddArray(self._user_dict)
field_data.VTKObject.Modified()
@property
def memory_address(self: Self) -> str:
"""Get address of the underlying VTK C++ object.
Returns
-------
str
Memory address formatted as ``'Addr=%p'``.
Examples
--------
>>> import pyvista as pv
>>> mesh = pv.Sphere()
>>> mesh.memory_address
'Addr=...'
"""
return self.GetInformation().GetAddressAsString('')
@property
def actual_memory_size(self: Self) -> int:
"""Return the actual size of the dataset object.
Returns
-------
int
The actual size of the dataset object in kibibytes (1024
bytes).
Examples
--------
>>> from pyvista import examples
>>> mesh = examples.load_airplane()
>>> mesh.actual_memory_size # doctest:+SKIP
93
"""
return self.GetActualMemorySize()
def copy_structure(self: Self, dataset: Self) -> None:
"""Copy the structure (geometry and topology) of the input dataset object.
Parameters
----------
dataset : :vtk:`vtkDataSet`
Dataset to copy the geometry and topology from.
Examples
--------
>>> import pyvista as pv
>>> source = pv.ImageData(dimensions=(10, 10, 5))
>>> target = pv.ImageData()
>>> target.copy_structure(source)
>>> target.plot(show_edges=True)
"""
self.CopyStructure(dataset) if dataset is not self else None
def copy_attributes(self: Self, dataset: Self) -> None:
"""Copy the data attributes of the input dataset object.
Parameters
----------
dataset : pyvista.DataSet
Dataset to copy the data attributes from.
Examples
--------
>>> import pyvista as pv
>>> source = pv.ImageData(dimensions=(10, 10, 5))
>>> source = source.compute_cell_sizes()
>>> target = pv.ImageData(dimensions=(10, 10, 5))
>>> target.copy_attributes(source)
>>> target.plot(scalars='Volume', show_edges=True)
"""
self.CopyAttributes(dataset)
def __getstate__( # type: ignore[return] # noqa: RET503
self: Self,
) -> tuple[FunctionType, tuple[dict[str, Any]]] | dict[str, Any]:
"""Support pickle."""
pickle_format = pyvista.PICKLE_FORMAT
if pickle_format == 'vtk':
return self._serialize_vtk_pickle_format()
elif pickle_format in ['xml', 'legacy']:
return self._serialize_pyvista_pickle_format()
# Invalid format, use the setter to raise an error
pyvista.set_pickle_format(pickle_format)
def _serialize_vtk_pickle_format(
self: Self,
) -> tuple[FunctionType, tuple[dict[str, Any]]]:
# Note: The serialized state has format: ( function, (dict,) )
serialized = _vtk.serialize_VTK_data_object(self)
# Add this object's data to the state dictionary
state_dict = serialized[1][0]
state_dict['_PYVISTA_STATE_DICT'] = self.__dict__.copy()
# Unlike the PyVista formats, we do not return a dict. Instead, return
# the same format returned by the vtk serializer.
return serialized
def _serialize_pyvista_pickle_format(self: Self) -> dict[str, Any]:
"""Support pickle by serializing the VTK object data.
The format of the serialized VTK object data depends on `pyvista.PICKLE_FORMAT`
(case-insensitive).
- If ``'xml'``, the data is serialized as an XML-formatted string.
- If ``'legacy'``, the data is serialized to bytes in VTK's binary format.
.. note::
These formats are custom PyVista legacy formats. The native 'vtk' format is
preferred since it supports more objects (e.g. MultiBlock).
"""
if isinstance(self, pyvista.MultiBlock):
msg = (
"MultiBlock is not supported with 'xml' or 'legacy' pickle formats."
"\nUse `pyvista.PICKLE_FORMAT='vtk'`."
)
raise TypeError(msg)
state = self.__dict__.copy()
if pyvista.PICKLE_FORMAT.lower() == 'xml':
# the generic VTK XML writer `vtkXMLDataSetWriter` currently has a bug where it does
# not pass all settings down to the sub-writers. Until this is fixed, use the
# dataset-specific writers
# https://gitlab.kitware.com/vtk/vtk/-/issues/18661
writers = {
_vtk.vtkImageData: _vtk.vtkXMLImageDataWriter,
_vtk.vtkStructuredGrid: _vtk.vtkXMLStructuredGridWriter,
_vtk.vtkRectilinearGrid: _vtk.vtkXMLRectilinearGridWriter,
_vtk.vtkUnstructuredGrid: _vtk.vtkXMLUnstructuredGridWriter,
_vtk.vtkPolyData: _vtk.vtkXMLPolyDataWriter,
_vtk.vtkTable: _vtk.vtkXMLTableWriter,
}
for parent_type, writer_type in writers.items():
if isinstance(self, parent_type):
writer = writer_type() # type: ignore[unreachable]
break
else:
msg = f'Cannot pickle dataset of type {self.GetDataObjectType()}'
raise TypeError(msg)
writer.SetInputDataObject(self) # type: ignore[unreachable]
writer.SetWriteToOutputString(True)
writer.SetDataModeToBinary()
writer.SetCompressorTypeToNone()
writer.Write()
to_serialize = writer.GetOutputString()
elif pyvista.PICKLE_FORMAT.lower() == 'legacy':
writer = _vtk.vtkDataSetWriter()
writer.SetInputDataObject(self)
writer.SetWriteToOutputString(True)
writer.SetFileTypeToBinary()
writer.Write()
to_serialize = writer.GetOutputStdString()
state['vtk_serialized'] = to_serialize
# this needs to be here because in multiprocessing situations, `pyvista.PICKLE_FORMAT`
# is not shared between processes
state['PICKLE_FORMAT'] = pyvista.PICKLE_FORMAT
return state
def __setstate__(self: Self, state: Any) -> None:
"""Support unpickle."""
def _is_vtk_format(state_: Any) -> bool:
# Note: The vtk state has format ( function, (dict,) )
return (
isinstance(state_, tuple)
and len(state_) == 2
and isinstance(state_[1], tuple)
and len(state_[1]) == 1
and isinstance(state_[1][0], dict)
)
def _is_pyvista_format(state_: Any) -> bool:
return isinstance(state_, dict) and 'vtk_serialized' in state_
if _is_vtk_format(state):
self._unserialize_vtk_pickle_format(state)
elif _is_pyvista_format(state):
self._unserialize_pyvista_pickle_format(state)
else:
msg = f"Cannot unpickle '{self.__class__.__name__}'. Invalid pickle format."
raise RuntimeError(msg)
def _unserialize_vtk_pickle_format(
self: Self, state: tuple[FunctionType, tuple[dict[str, Any]]]
) -> None:
"""Support unpickle of VTK's format."""
# The vtk state has format: ( function, (dict,) )
unserialize_func = state[0]
state_dict = state[1][0]
self.__dict__.update(state_dict['_PYVISTA_STATE_DICT'])
obj = unserialize_func(state_dict)
self.deep_copy(obj)
def _unserialize_pyvista_pickle_format(self: Self, state: dict[str, Any]) -> None:
"""Support unpickle of PyVista 'xml' and 'legacy' formats.
.. note::
These formats are custom PyVista legacy formats. The native 'vtk' format is
preferred since it supports more objects (e.g. MultiBlock).
"""
vtk_serialized = state.pop('vtk_serialized')
pickle_format = state.pop(
'PICKLE_FORMAT',
'legacy', # backwards compatibility - assume 'legacy'
)
self.__dict__.update(state)
if pickle_format.lower() == 'xml':
# the generic VTK XML reader `vtkXMLGenericDataObjectReader` currently has a
# bug where it does not pass all settings down to the sub-readers.
# Until this is fixed, use the dataset-specific readers
# https://gitlab.kitware.com/vtk/vtk/-/issues/18661
readers = {
_vtk.vtkImageData: _vtk.vtkXMLImageDataReader,
_vtk.vtkStructuredGrid: _vtk.vtkXMLStructuredGridReader,
_vtk.vtkRectilinearGrid: _vtk.vtkXMLRectilinearGridReader,
_vtk.vtkUnstructuredGrid: _vtk.vtkXMLUnstructuredGridReader,
_vtk.vtkPolyData: _vtk.vtkXMLPolyDataReader,
_vtk.vtkTable: _vtk.vtkXMLTableReader,
}
for parent_type, reader_type in readers.items():
if isinstance(self, parent_type):
reader = reader_type() # type: ignore[unreachable]
break
else:
msg = f'Cannot unpickle dataset of type {self.GetDataObjectType()}'
raise TypeError(msg)
reader.ReadFromInputStringOn() # type: ignore[unreachable]
reader.SetInputString(vtk_serialized)
reader.Update()
elif pickle_format.lower() == 'legacy':
reader = _vtk.vtkDataSetReader()
reader.ReadFromInputStringOn()
if isinstance(vtk_serialized, bytes):
reader.SetBinaryInputString(vtk_serialized, len(vtk_serialized)) # type: ignore[arg-type]
elif isinstance(vtk_serialized, str):
reader.SetInputString(vtk_serialized)
reader.Update()
mesh = wrap(reader.GetOutput())
# copy data
self.copy_structure(mesh) # type: ignore[arg-type]
self.copy_attributes(mesh) # type: ignore[arg-type]
@property
@abstractmethod
def is_empty(self) -> bool:
"""Return ``True`` if the object is empty."""
|