wandb 0.19.1rc1__py3-none-musllinux_1_2_aarch64.whl
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- package_readme.md +97 -0
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- wandb/vendor/pygments/lexers/other.py +41 -0
- wandb/vendor/pygments/lexers/parasail.py +79 -0
- wandb/vendor/pygments/lexers/parsers.py +835 -0
- wandb/vendor/pygments/lexers/pascal.py +644 -0
- wandb/vendor/pygments/lexers/pawn.py +199 -0
- wandb/vendor/pygments/lexers/perl.py +620 -0
- wandb/vendor/pygments/lexers/php.py +267 -0
- wandb/vendor/pygments/lexers/praat.py +294 -0
- wandb/vendor/pygments/lexers/prolog.py +306 -0
- wandb/vendor/pygments/lexers/python.py +939 -0
- wandb/vendor/pygments/lexers/qvt.py +152 -0
- wandb/vendor/pygments/lexers/r.py +453 -0
- wandb/vendor/pygments/lexers/rdf.py +270 -0
- wandb/vendor/pygments/lexers/rebol.py +431 -0
- wandb/vendor/pygments/lexers/resource.py +85 -0
- wandb/vendor/pygments/lexers/rnc.py +67 -0
- wandb/vendor/pygments/lexers/roboconf.py +82 -0
- wandb/vendor/pygments/lexers/robotframework.py +560 -0
- wandb/vendor/pygments/lexers/ruby.py +519 -0
- wandb/vendor/pygments/lexers/rust.py +220 -0
- wandb/vendor/pygments/lexers/sas.py +228 -0
- wandb/vendor/pygments/lexers/scripting.py +1222 -0
- wandb/vendor/pygments/lexers/shell.py +794 -0
- wandb/vendor/pygments/lexers/smalltalk.py +195 -0
- wandb/vendor/pygments/lexers/smv.py +79 -0
- wandb/vendor/pygments/lexers/snobol.py +83 -0
- wandb/vendor/pygments/lexers/special.py +103 -0
- wandb/vendor/pygments/lexers/sql.py +681 -0
- wandb/vendor/pygments/lexers/stata.py +108 -0
- wandb/vendor/pygments/lexers/supercollider.py +90 -0
- wandb/vendor/pygments/lexers/tcl.py +145 -0
- wandb/vendor/pygments/lexers/templates.py +2283 -0
- wandb/vendor/pygments/lexers/testing.py +207 -0
- wandb/vendor/pygments/lexers/text.py +25 -0
- wandb/vendor/pygments/lexers/textedit.py +169 -0
- wandb/vendor/pygments/lexers/textfmts.py +297 -0
- wandb/vendor/pygments/lexers/theorem.py +458 -0
- wandb/vendor/pygments/lexers/trafficscript.py +54 -0
- wandb/vendor/pygments/lexers/typoscript.py +226 -0
- wandb/vendor/pygments/lexers/urbi.py +133 -0
- wandb/vendor/pygments/lexers/varnish.py +190 -0
- wandb/vendor/pygments/lexers/verification.py +111 -0
- wandb/vendor/pygments/lexers/web.py +24 -0
- wandb/vendor/pygments/lexers/webmisc.py +988 -0
- wandb/vendor/pygments/lexers/whiley.py +116 -0
- wandb/vendor/pygments/lexers/x10.py +69 -0
- wandb/vendor/pygments/modeline.py +44 -0
- wandb/vendor/pygments/plugin.py +68 -0
- wandb/vendor/pygments/regexopt.py +92 -0
- wandb/vendor/pygments/scanner.py +105 -0
- wandb/vendor/pygments/sphinxext.py +158 -0
- wandb/vendor/pygments/style.py +155 -0
- wandb/vendor/pygments/styles/__init__.py +80 -0
- wandb/vendor/pygments/styles/abap.py +29 -0
- wandb/vendor/pygments/styles/algol.py +63 -0
- wandb/vendor/pygments/styles/algol_nu.py +63 -0
- wandb/vendor/pygments/styles/arduino.py +98 -0
- wandb/vendor/pygments/styles/autumn.py +65 -0
- wandb/vendor/pygments/styles/borland.py +51 -0
- wandb/vendor/pygments/styles/bw.py +49 -0
- wandb/vendor/pygments/styles/colorful.py +81 -0
- wandb/vendor/pygments/styles/default.py +73 -0
- wandb/vendor/pygments/styles/emacs.py +72 -0
- wandb/vendor/pygments/styles/friendly.py +72 -0
- wandb/vendor/pygments/styles/fruity.py +42 -0
- wandb/vendor/pygments/styles/igor.py +29 -0
- wandb/vendor/pygments/styles/lovelace.py +97 -0
- wandb/vendor/pygments/styles/manni.py +75 -0
- wandb/vendor/pygments/styles/monokai.py +106 -0
- wandb/vendor/pygments/styles/murphy.py +80 -0
- wandb/vendor/pygments/styles/native.py +65 -0
- wandb/vendor/pygments/styles/paraiso_dark.py +125 -0
- wandb/vendor/pygments/styles/paraiso_light.py +125 -0
- wandb/vendor/pygments/styles/pastie.py +75 -0
- wandb/vendor/pygments/styles/perldoc.py +69 -0
- wandb/vendor/pygments/styles/rainbow_dash.py +89 -0
- wandb/vendor/pygments/styles/rrt.py +33 -0
- wandb/vendor/pygments/styles/sas.py +44 -0
- wandb/vendor/pygments/styles/stata.py +40 -0
- wandb/vendor/pygments/styles/tango.py +141 -0
- wandb/vendor/pygments/styles/trac.py +63 -0
- wandb/vendor/pygments/styles/vim.py +63 -0
- wandb/vendor/pygments/styles/vs.py +38 -0
- wandb/vendor/pygments/styles/xcode.py +51 -0
- wandb/vendor/pygments/token.py +213 -0
- wandb/vendor/pygments/unistring.py +217 -0
- wandb/vendor/pygments/util.py +388 -0
- wandb/vendor/pynvml/__init__.py +0 -0
- wandb/vendor/pynvml/pynvml.py +4779 -0
- wandb/vendor/watchdog_0_9_0/wandb_watchdog/__init__.py +17 -0
- wandb/vendor/watchdog_0_9_0/wandb_watchdog/events.py +615 -0
- wandb/vendor/watchdog_0_9_0/wandb_watchdog/observers/__init__.py +98 -0
- wandb/vendor/watchdog_0_9_0/wandb_watchdog/observers/api.py +369 -0
- wandb/vendor/watchdog_0_9_0/wandb_watchdog/observers/fsevents.py +172 -0
- wandb/vendor/watchdog_0_9_0/wandb_watchdog/observers/fsevents2.py +239 -0
- wandb/vendor/watchdog_0_9_0/wandb_watchdog/observers/inotify.py +218 -0
- wandb/vendor/watchdog_0_9_0/wandb_watchdog/observers/inotify_buffer.py +81 -0
- wandb/vendor/watchdog_0_9_0/wandb_watchdog/observers/inotify_c.py +575 -0
- wandb/vendor/watchdog_0_9_0/wandb_watchdog/observers/kqueue.py +730 -0
- wandb/vendor/watchdog_0_9_0/wandb_watchdog/observers/polling.py +145 -0
- wandb/vendor/watchdog_0_9_0/wandb_watchdog/observers/read_directory_changes.py +133 -0
- wandb/vendor/watchdog_0_9_0/wandb_watchdog/observers/winapi.py +348 -0
- wandb/vendor/watchdog_0_9_0/wandb_watchdog/patterns.py +265 -0
- wandb/vendor/watchdog_0_9_0/wandb_watchdog/tricks/__init__.py +174 -0
- wandb/vendor/watchdog_0_9_0/wandb_watchdog/utils/__init__.py +151 -0
- wandb/vendor/watchdog_0_9_0/wandb_watchdog/utils/bricks.py +249 -0
- wandb/vendor/watchdog_0_9_0/wandb_watchdog/utils/compat.py +29 -0
- wandb/vendor/watchdog_0_9_0/wandb_watchdog/utils/decorators.py +198 -0
- wandb/vendor/watchdog_0_9_0/wandb_watchdog/utils/delayed_queue.py +88 -0
- wandb/vendor/watchdog_0_9_0/wandb_watchdog/utils/dirsnapshot.py +293 -0
- wandb/vendor/watchdog_0_9_0/wandb_watchdog/utils/echo.py +157 -0
- wandb/vendor/watchdog_0_9_0/wandb_watchdog/utils/event_backport.py +41 -0
- wandb/vendor/watchdog_0_9_0/wandb_watchdog/utils/importlib2.py +40 -0
- wandb/vendor/watchdog_0_9_0/wandb_watchdog/utils/platform.py +57 -0
- wandb/vendor/watchdog_0_9_0/wandb_watchdog/utils/unicode_paths.py +64 -0
- wandb/vendor/watchdog_0_9_0/wandb_watchdog/utils/win32stat.py +123 -0
- wandb/vendor/watchdog_0_9_0/wandb_watchdog/version.py +28 -0
- wandb/vendor/watchdog_0_9_0/wandb_watchdog/watchmedo.py +577 -0
- wandb/wandb_agent.py +588 -0
- wandb/wandb_controller.py +719 -0
- wandb/wandb_run.py +9 -0
- wandb-0.19.1rc1.dist-info/METADATA +223 -0
- wandb-0.19.1rc1.dist-info/RECORD +822 -0
- wandb-0.19.1rc1.dist-info/WHEEL +5 -0
- wandb-0.19.1rc1.dist-info/entry_points.txt +3 -0
- wandb-0.19.1rc1.dist-info/licenses/LICENSE +21 -0
@@ -0,0 +1,241 @@
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import io
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import os
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import pathlib
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from typing import TYPE_CHECKING, Optional, Sequence, Type, Union
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from wandb import util
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from wandb.sdk.lib import runid
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from wandb.sdk.lib.paths import LogicalPath
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from ._private import MEDIA_TMP
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from .base_types.media import BatchableMedia, Media
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if TYPE_CHECKING: # pragma: no cover
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from typing import TextIO
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import rdkit.Chem # type: ignore
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from wandb.sdk.artifacts.artifact import Artifact
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from ..wandb_run import Run as LocalRun
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RDKitDataType = Union[str, "rdkit.Chem.rdchem.Mol"]
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class Molecule(BatchableMedia):
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"""Wandb class for 3D Molecular data.
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Args:
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data_or_path: (string, io)
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Molecule can be initialized from a file name or an io object.
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caption: (string)
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Caption associated with the molecule for display.
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"""
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SUPPORTED_TYPES = {
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"pdb",
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"pqr",
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"mmcif",
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"mcif",
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"cif",
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"sdf",
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"sd",
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"gro",
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"mol2",
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"mmtf",
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}
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SUPPORTED_RDKIT_TYPES = {"mol", "sdf"}
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_log_type = "molecule-file"
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def __init__(
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self,
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data_or_path: Union[str, "TextIO"],
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caption: Optional[str] = None,
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**kwargs: str,
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) -> None:
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super().__init__()
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self._caption = caption
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if hasattr(data_or_path, "name"):
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# if the file has a path, we just detect the type and copy it from there
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data_or_path = data_or_path.name
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if hasattr(data_or_path, "read"):
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if hasattr(data_or_path, "seek"):
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data_or_path.seek(0)
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molecule = data_or_path.read()
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extension = kwargs.pop("file_type", None)
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if extension is None:
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raise ValueError(
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"Must pass file_type keyword argument when using io objects."
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)
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if extension not in Molecule.SUPPORTED_TYPES:
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raise ValueError(
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"Molecule 3D only supports files of the type: "
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+ ", ".join(Molecule.SUPPORTED_TYPES)
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)
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tmp_path = os.path.join(
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MEDIA_TMP.name, runid.generate_id() + "." + extension
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)
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with open(tmp_path, "w") as f:
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f.write(molecule)
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self._set_file(tmp_path, is_tmp=True)
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elif isinstance(data_or_path, str):
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extension = os.path.splitext(data_or_path)[1][1:]
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if extension not in Molecule.SUPPORTED_TYPES:
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raise ValueError(
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"Molecule only supports files of the type: "
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+ ", ".join(Molecule.SUPPORTED_TYPES)
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)
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self._set_file(data_or_path, is_tmp=False)
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else:
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raise ValueError("Data must be file name or a file object")
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@classmethod
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def from_rdkit(
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cls,
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data_or_path: "RDKitDataType",
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caption: Optional[str] = None,
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convert_to_3d_and_optimize: bool = True,
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mmff_optimize_molecule_max_iterations: int = 200,
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) -> "Molecule":
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"""Convert RDKit-supported file/object types to wandb.Molecule.
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Args:
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data_or_path: (string, rdkit.Chem.rdchem.Mol)
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Molecule can be initialized from a file name or an rdkit.Chem.rdchem.Mol object.
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caption: (string)
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Caption associated with the molecule for display.
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convert_to_3d_and_optimize: (bool)
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Convert to rdkit.Chem.rdchem.Mol with 3D coordinates.
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This is an expensive operation that may take a long time for complicated molecules.
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mmff_optimize_molecule_max_iterations: (int)
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Number of iterations to use in rdkit.Chem.AllChem.MMFFOptimizeMolecule
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"""
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rdkit_chem = util.get_module(
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"rdkit.Chem",
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required='wandb.Molecule needs the rdkit-pypi package. To get it, run "pip install rdkit-pypi".',
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)
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rdkit_chem_all_chem = util.get_module(
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"rdkit.Chem.AllChem",
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required='wandb.Molecule needs the rdkit-pypi package. To get it, run "pip install rdkit-pypi".',
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)
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if isinstance(data_or_path, str):
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# path to a file?
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path = pathlib.Path(data_or_path)
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extension = path.suffix.split(".")[-1]
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if extension not in Molecule.SUPPORTED_RDKIT_TYPES:
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raise ValueError(
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"Molecule.from_rdkit only supports files of the type: "
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+ ", ".join(Molecule.SUPPORTED_RDKIT_TYPES)
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)
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# use the appropriate method
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if extension == "sdf":
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with rdkit_chem.SDMolSupplier(data_or_path) as supplier:
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molecule = next(supplier) # get only the first molecule
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else:
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molecule = getattr(rdkit_chem, f"MolFrom{extension.capitalize()}File")(
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data_or_path
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)
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elif isinstance(data_or_path, rdkit_chem.rdchem.Mol):
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molecule = data_or_path
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else:
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raise ValueError(
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"Data must be file name or an rdkit.Chem.rdchem.Mol object"
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)
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if convert_to_3d_and_optimize:
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molecule = rdkit_chem.AddHs(molecule)
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rdkit_chem_all_chem.EmbedMolecule(molecule)
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rdkit_chem_all_chem.MMFFOptimizeMolecule(
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molecule,
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maxIters=mmff_optimize_molecule_max_iterations,
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)
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# convert to the pdb format supported by Molecule
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pdb_block = rdkit_chem.rdmolfiles.MolToPDBBlock(molecule)
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return cls(io.StringIO(pdb_block), caption=caption, file_type="pdb")
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@classmethod
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def from_smiles(
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cls,
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data: str,
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caption: Optional[str] = None,
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sanitize: bool = True,
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convert_to_3d_and_optimize: bool = True,
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mmff_optimize_molecule_max_iterations: int = 200,
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) -> "Molecule":
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"""Convert SMILES string to wandb.Molecule.
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Args:
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data: (string)
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SMILES string.
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caption: (string)
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Caption associated with the molecule for display
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sanitize: (bool)
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Check if the molecule is chemically reasonable by the RDKit's definition.
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convert_to_3d_and_optimize: (bool)
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Convert to rdkit.Chem.rdchem.Mol with 3D coordinates.
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This is an expensive operation that may take a long time for complicated molecules.
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mmff_optimize_molecule_max_iterations: (int)
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Number of iterations to use in rdkit.Chem.AllChem.MMFFOptimizeMolecule
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"""
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rdkit_chem = util.get_module(
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"rdkit.Chem",
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required='wandb.Molecule needs the rdkit-pypi package. To get it, run "pip install rdkit-pypi".',
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)
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molecule = rdkit_chem.MolFromSmiles(data, sanitize=sanitize)
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if molecule is None:
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raise ValueError("Unable to parse the SMILES string.")
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return cls.from_rdkit(
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data_or_path=molecule,
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caption=caption,
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convert_to_3d_and_optimize=convert_to_3d_and_optimize,
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mmff_optimize_molecule_max_iterations=mmff_optimize_molecule_max_iterations,
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)
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@classmethod
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def get_media_subdir(cls: Type["Molecule"]) -> str:
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return os.path.join("media", "molecule")
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def to_json(self, run_or_artifact: Union["LocalRun", "Artifact"]) -> dict:
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json_dict = super().to_json(run_or_artifact)
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json_dict["_type"] = self._log_type
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if self._caption:
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json_dict["caption"] = self._caption
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return json_dict
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@classmethod
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def seq_to_json(
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cls: Type["Molecule"],
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seq: Sequence["BatchableMedia"],
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run: "LocalRun",
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key: str,
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step: Union[int, str],
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) -> dict:
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seq = list(seq)
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jsons = [obj.to_json(run) for obj in seq]
|
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+
|
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for obj in jsons:
|
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expected = LogicalPath(cls.get_media_subdir())
|
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+
if not obj["path"].startswith(expected):
|
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raise ValueError(
|
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+
"Files in an array of Molecule's must be in the {} directory, not {}".format(
|
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+
cls.get_media_subdir(), obj["path"]
|
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+
)
|
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)
|
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+
|
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return {
|
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"_type": "molecule",
|
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+
"filenames": [obj["path"] for obj in jsons],
|
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|
+
"count": len(jsons),
|
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|
+
"captions": Media.captions(seq),
|
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+
}
|
@@ -0,0 +1,470 @@
|
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1
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+
import codecs
|
2
|
+
import itertools
|
3
|
+
import json
|
4
|
+
import os
|
5
|
+
from typing import (
|
6
|
+
TYPE_CHECKING,
|
7
|
+
ClassVar,
|
8
|
+
Literal,
|
9
|
+
Optional,
|
10
|
+
Sequence,
|
11
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+
Set,
|
12
|
+
TextIO,
|
13
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+
Tuple,
|
14
|
+
Type,
|
15
|
+
TypedDict,
|
16
|
+
Union,
|
17
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+
)
|
18
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+
|
19
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+
import wandb
|
20
|
+
from wandb import util
|
21
|
+
from wandb.sdk.lib import runid
|
22
|
+
from wandb.sdk.lib.paths import LogicalPath
|
23
|
+
|
24
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+
from . import _dtypes
|
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from ._private import MEDIA_TMP
|
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+
from .base_types.media import BatchableMedia
|
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+
|
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+
if TYPE_CHECKING: # pragma: no cover
|
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+
import numpy as np
|
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+
import numpy.typing as npt
|
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+
|
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from wandb.sdk.artifacts.artifact import Artifact
|
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+
|
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+
from ..wandb_run import Run as LocalRun
|
35
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+
|
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+
numeric = Union[int, float, np.integer, np.float64]
|
37
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+
FileFormat3D = Literal[
|
38
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+
"obj",
|
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+
"gltf",
|
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+
"glb",
|
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+
"babylon",
|
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+
"stl",
|
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+
"pts.json",
|
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+
]
|
45
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+
Point3D = Tuple[numeric, numeric, numeric]
|
46
|
+
Point3DWithCategory = Tuple[numeric, numeric, numeric, numeric]
|
47
|
+
Point3DWithColors = Tuple[numeric, numeric, numeric, numeric, numeric, numeric]
|
48
|
+
Point = Union[Point3D, Point3DWithCategory, Point3DWithColors]
|
49
|
+
PointCloudType = Literal["lidar/beta"]
|
50
|
+
RGBColor = Tuple[numeric, numeric, numeric]
|
51
|
+
|
52
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+
Quaternion = Tuple[numeric, numeric, numeric, numeric]
|
53
|
+
|
54
|
+
class Box3D(TypedDict):
|
55
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+
corners: Tuple[
|
56
|
+
Point3D,
|
57
|
+
Point3D,
|
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|
+
Point3D,
|
59
|
+
Point3D,
|
60
|
+
Point3D,
|
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|
+
Point3D,
|
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|
+
Point3D,
|
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|
+
Point3D,
|
64
|
+
]
|
65
|
+
label: Optional[str]
|
66
|
+
color: RGBColor
|
67
|
+
score: Optional[numeric]
|
68
|
+
|
69
|
+
class Vector3D(TypedDict):
|
70
|
+
start: Sequence[Point3D]
|
71
|
+
end: Sequence[Point3D]
|
72
|
+
|
73
|
+
class Camera(TypedDict):
|
74
|
+
viewpoint: Sequence[Point3D]
|
75
|
+
target: Sequence[Point3D]
|
76
|
+
|
77
|
+
|
78
|
+
def _install_numpy_error() -> "wandb.Error":
|
79
|
+
return wandb.Error(
|
80
|
+
"wandb.Object3D requires NumPy. To get it, run 'pip install numpy'."
|
81
|
+
)
|
82
|
+
|
83
|
+
|
84
|
+
def _normalize_vec(x: "np.ndarray") -> "np.ndarray":
|
85
|
+
"""Normalizes a non-zero 1-dimensional array."""
|
86
|
+
try:
|
87
|
+
import numpy as np
|
88
|
+
except ImportError as e:
|
89
|
+
raise _install_numpy_error() from e
|
90
|
+
|
91
|
+
x = abs(x)
|
92
|
+
argmax = x.argmax()
|
93
|
+
|
94
|
+
if x[argmax] == 0:
|
95
|
+
raise ValueError("Unexpected zero quaternion.")
|
96
|
+
|
97
|
+
# Rescale by the largest component first to be more numerically
|
98
|
+
# stable than dividing by the norm directly.
|
99
|
+
x = x / x[argmax]
|
100
|
+
return x / np.linalg.norm(x)
|
101
|
+
|
102
|
+
|
103
|
+
def _quaternion_to_rotation(quaternion: "np.ndarray") -> "np.ndarray":
|
104
|
+
"""Returns the rotation matrix corresponding to a non-zero quaternion.
|
105
|
+
|
106
|
+
The corresponding rotation matrix transforms column vectors by
|
107
|
+
post-multiplication: `x @ R`. This way, it can be used to
|
108
|
+
transform an Nx3 NumPy array of points as `points @ R`.
|
109
|
+
"""
|
110
|
+
try:
|
111
|
+
import numpy as np
|
112
|
+
except ImportError as e:
|
113
|
+
raise _install_numpy_error() from e
|
114
|
+
|
115
|
+
# Precompute a few products to simplify the expression below.
|
116
|
+
qr, qi, qj, qk = _normalize_vec(quaternion)
|
117
|
+
qii, qjj, qkk = qi**2, qj**2, qk**2
|
118
|
+
qij, qik, qjk = qi * qj, qi * qk, qj * qk
|
119
|
+
qir, qjr, qkr = qi * qr, qj * qr, qk * qr
|
120
|
+
|
121
|
+
return np.array(
|
122
|
+
(
|
123
|
+
(1 - 2 * (qjj + qkk), 2 * (qij + qkr), 2 * (qik - qjr)),
|
124
|
+
(2 * (qij - qkr), 1 - 2 * (qii + qkk), 2 * (qjk + qir)),
|
125
|
+
(2 * (qik + qjr), 2 * (qjk - qir), 1 - 2 * (qii + qjj)),
|
126
|
+
),
|
127
|
+
dtype=np.float64,
|
128
|
+
)
|
129
|
+
|
130
|
+
|
131
|
+
def box3d(
|
132
|
+
*,
|
133
|
+
center: "npt.ArrayLike",
|
134
|
+
size: "npt.ArrayLike",
|
135
|
+
orientation: "npt.ArrayLike",
|
136
|
+
color: "RGBColor",
|
137
|
+
label: "Optional[str]" = None,
|
138
|
+
score: "Optional[numeric]" = None,
|
139
|
+
) -> "Box3D":
|
140
|
+
"""Returns a Box3D.
|
141
|
+
|
142
|
+
Args:
|
143
|
+
center: The center point of the box as a length-3 ndarray.
|
144
|
+
size: The box's X, Y and Z dimensions as a length-3 ndarray.
|
145
|
+
orientation: The rotation transforming global XYZ coordinates
|
146
|
+
into the box's local XYZ coordinates, given as a length-4
|
147
|
+
ndarray [r, x, y, z] corresponding to the non-zero quaternion
|
148
|
+
r + xi + yj + zk.
|
149
|
+
color: The box's color as an (r, g, b) tuple with 0 <= r,g,b <= 1.
|
150
|
+
label: An optional label for the box.
|
151
|
+
score: An optional score for the box.
|
152
|
+
"""
|
153
|
+
try:
|
154
|
+
import numpy as np
|
155
|
+
except ImportError as e:
|
156
|
+
raise _install_numpy_error() from e
|
157
|
+
|
158
|
+
center = np.asarray(center, dtype=np.float64)
|
159
|
+
size = np.asarray(size, dtype=np.float64)
|
160
|
+
orientation = np.asarray(orientation, dtype=np.float64)
|
161
|
+
|
162
|
+
assert center.shape == (3,)
|
163
|
+
assert size.shape == (3,)
|
164
|
+
assert orientation.shape == (4,)
|
165
|
+
|
166
|
+
# Precompute the rotation matrix.
|
167
|
+
rot = _quaternion_to_rotation(orientation)
|
168
|
+
|
169
|
+
# Scale, rotate and translate each corner of the unit box.
|
170
|
+
unit_corners = np.array(
|
171
|
+
list(itertools.product((-1, 1), (-1, 1), (-1, 1))),
|
172
|
+
dtype=np.float64,
|
173
|
+
)
|
174
|
+
corners = center + (0.5 * size * unit_corners) @ rot
|
175
|
+
|
176
|
+
return {
|
177
|
+
# Ignore the type because mypy can't infer that the list has length 8:
|
178
|
+
# https://github.com/python/mypy/issues/7509
|
179
|
+
"corners": tuple(tuple(pt) for pt in corners), # type: ignore
|
180
|
+
"color": color,
|
181
|
+
"label": label,
|
182
|
+
"score": score,
|
183
|
+
}
|
184
|
+
|
185
|
+
|
186
|
+
class Object3D(BatchableMedia):
|
187
|
+
"""Wandb class for 3D point clouds.
|
188
|
+
|
189
|
+
Args:
|
190
|
+
data_or_path: (numpy array, string, io)
|
191
|
+
Object3D can be initialized from a file or a numpy array.
|
192
|
+
|
193
|
+
You can pass a path to a file or an io object and a file_type
|
194
|
+
which must be one of SUPPORTED_TYPES
|
195
|
+
|
196
|
+
The shape of the numpy array must be one of either:
|
197
|
+
```
|
198
|
+
[[x y z], ...] nx3
|
199
|
+
[[x y z c], ...] nx4 where c is a category with supported range [1, 14]
|
200
|
+
[[x y z r g b], ...] nx6 where is rgb is color
|
201
|
+
```
|
202
|
+
"""
|
203
|
+
|
204
|
+
SUPPORTED_TYPES: ClassVar[Set[str]] = {
|
205
|
+
"obj",
|
206
|
+
"gltf",
|
207
|
+
"glb",
|
208
|
+
"babylon",
|
209
|
+
"stl",
|
210
|
+
"pts.json",
|
211
|
+
}
|
212
|
+
SUPPORTED_POINT_CLOUD_TYPES: ClassVar[Set[str]] = {"lidar/beta"}
|
213
|
+
_log_type: ClassVar[str] = "object3D-file"
|
214
|
+
|
215
|
+
def __init__(
|
216
|
+
self,
|
217
|
+
data_or_path: Union["np.ndarray", str, "TextIO", dict],
|
218
|
+
**kwargs: Optional[Union[str, "FileFormat3D"]],
|
219
|
+
) -> None:
|
220
|
+
super().__init__()
|
221
|
+
|
222
|
+
if hasattr(data_or_path, "name"):
|
223
|
+
# if the file has a path, we just detect the type and copy it from there
|
224
|
+
data_or_path = data_or_path.name
|
225
|
+
|
226
|
+
if hasattr(data_or_path, "read"):
|
227
|
+
if hasattr(data_or_path, "seek"):
|
228
|
+
data_or_path.seek(0)
|
229
|
+
object_3d = data_or_path.read()
|
230
|
+
|
231
|
+
extension = kwargs.pop("file_type", None)
|
232
|
+
if extension is None:
|
233
|
+
raise ValueError(
|
234
|
+
"Must pass file type keyword argument when using io objects."
|
235
|
+
)
|
236
|
+
if extension not in Object3D.SUPPORTED_TYPES:
|
237
|
+
raise ValueError(
|
238
|
+
"Object 3D only supports numpy arrays or files of the type: "
|
239
|
+
+ ", ".join(Object3D.SUPPORTED_TYPES)
|
240
|
+
)
|
241
|
+
|
242
|
+
extension = "." + extension
|
243
|
+
|
244
|
+
tmp_path = os.path.join(MEDIA_TMP.name, runid.generate_id() + extension)
|
245
|
+
with open(tmp_path, "w") as f:
|
246
|
+
f.write(object_3d)
|
247
|
+
|
248
|
+
self._set_file(tmp_path, is_tmp=True, extension=extension)
|
249
|
+
elif isinstance(data_or_path, str):
|
250
|
+
path = data_or_path
|
251
|
+
extension = None
|
252
|
+
for supported_type in Object3D.SUPPORTED_TYPES:
|
253
|
+
if path.endswith(supported_type):
|
254
|
+
extension = "." + supported_type
|
255
|
+
break
|
256
|
+
|
257
|
+
if not extension:
|
258
|
+
raise ValueError(
|
259
|
+
"File '"
|
260
|
+
+ path
|
261
|
+
+ "' is not compatible with Object3D: supported types are: "
|
262
|
+
+ ", ".join(Object3D.SUPPORTED_TYPES)
|
263
|
+
)
|
264
|
+
|
265
|
+
self._set_file(data_or_path, is_tmp=False, extension=extension)
|
266
|
+
# Supported different types and scene for 3D scenes
|
267
|
+
elif isinstance(data_or_path, dict) and "type" in data_or_path:
|
268
|
+
if data_or_path["type"] == "lidar/beta":
|
269
|
+
data = {
|
270
|
+
"type": data_or_path["type"],
|
271
|
+
"vectors": data_or_path["vectors"].tolist()
|
272
|
+
if "vectors" in data_or_path
|
273
|
+
else [],
|
274
|
+
"points": data_or_path["points"].tolist()
|
275
|
+
if "points" in data_or_path
|
276
|
+
else [],
|
277
|
+
"boxes": data_or_path["boxes"].tolist()
|
278
|
+
if "boxes" in data_or_path
|
279
|
+
else [],
|
280
|
+
}
|
281
|
+
else:
|
282
|
+
raise ValueError(
|
283
|
+
"Type not supported, only 'lidar/beta' is currently supported"
|
284
|
+
)
|
285
|
+
|
286
|
+
tmp_path = os.path.join(MEDIA_TMP.name, runid.generate_id() + ".pts.json")
|
287
|
+
with codecs.open(tmp_path, "w", encoding="utf-8") as fp:
|
288
|
+
json.dump(
|
289
|
+
data,
|
290
|
+
fp,
|
291
|
+
separators=(",", ":"),
|
292
|
+
sort_keys=True,
|
293
|
+
indent=4,
|
294
|
+
)
|
295
|
+
self._set_file(tmp_path, is_tmp=True, extension=".pts.json")
|
296
|
+
elif util.is_numpy_array(data_or_path):
|
297
|
+
np_data = data_or_path
|
298
|
+
|
299
|
+
# The following assertion is required for numpy to trust that
|
300
|
+
# np_data is numpy array. The reason it is behind a False
|
301
|
+
# guard is to ensure that this line does not run at runtime,
|
302
|
+
# which would cause a runtime error if the user's machine did
|
303
|
+
# not have numpy installed.
|
304
|
+
|
305
|
+
if TYPE_CHECKING:
|
306
|
+
assert isinstance(np_data, np.ndarray)
|
307
|
+
|
308
|
+
if len(np_data.shape) != 2 or np_data.shape[1] not in {3, 4, 6}:
|
309
|
+
raise ValueError(
|
310
|
+
"""
|
311
|
+
The shape of the numpy array must be one of either
|
312
|
+
[[x y z], ...] nx3
|
313
|
+
[x y z c], ...] nx4 where c is a category with supported range [1, 14]
|
314
|
+
[x y z r g b], ...] nx6 where rgb is color
|
315
|
+
"""
|
316
|
+
)
|
317
|
+
|
318
|
+
list_data = np_data.tolist()
|
319
|
+
tmp_path = os.path.join(MEDIA_TMP.name, runid.generate_id() + ".pts.json")
|
320
|
+
with codecs.open(tmp_path, "w", encoding="utf-8") as fp:
|
321
|
+
json.dump(
|
322
|
+
list_data,
|
323
|
+
fp,
|
324
|
+
separators=(",", ":"),
|
325
|
+
sort_keys=True,
|
326
|
+
indent=4,
|
327
|
+
)
|
328
|
+
self._set_file(tmp_path, is_tmp=True, extension=".pts.json")
|
329
|
+
else:
|
330
|
+
raise ValueError("data must be a numpy array, dict or a file object")
|
331
|
+
|
332
|
+
@classmethod
|
333
|
+
def from_file(
|
334
|
+
cls,
|
335
|
+
data_or_path: Union["TextIO", str],
|
336
|
+
file_type: Optional["FileFormat3D"] = None,
|
337
|
+
) -> "Object3D":
|
338
|
+
"""Initializes Object3D from a file or stream.
|
339
|
+
|
340
|
+
Args:
|
341
|
+
data_or_path (Union["TextIO", str]): A path to a file or a `TextIO` stream.
|
342
|
+
file_type (str): Specifies the data format passed to `data_or_path`. Required when `data_or_path` is a
|
343
|
+
`TextIO` stream. This parameter is ignored if a file path is provided. The type is taken from the file extension.
|
344
|
+
"""
|
345
|
+
# if file_type is not None and file_type not in cls.SUPPORTED_TYPES:
|
346
|
+
# raise ValueError(
|
347
|
+
# f"Unsupported file type: {file_type}. Supported types are: {cls.SUPPORTED_TYPES}"
|
348
|
+
# )
|
349
|
+
return cls(data_or_path, file_type=file_type)
|
350
|
+
|
351
|
+
@classmethod
|
352
|
+
def from_numpy(cls, data: "np.ndarray") -> "Object3D":
|
353
|
+
"""Initializes Object3D from a numpy array.
|
354
|
+
|
355
|
+
Args:
|
356
|
+
data (numpy array): Each entry in the array will
|
357
|
+
represent one point in the point cloud.
|
358
|
+
|
359
|
+
|
360
|
+
The shape of the numpy array must be one of either:
|
361
|
+
```
|
362
|
+
[[x y z], ...] # nx3.
|
363
|
+
[[x y z c], ...] # nx4 where c is a category with supported range [1, 14].
|
364
|
+
[[x y z r g b], ...] # nx6 where is rgb is color.
|
365
|
+
```
|
366
|
+
"""
|
367
|
+
if not util.is_numpy_array(data):
|
368
|
+
raise ValueError("`data` must be a numpy array")
|
369
|
+
|
370
|
+
if len(data.shape) != 2 or data.shape[1] not in {3, 4, 6}:
|
371
|
+
raise ValueError(
|
372
|
+
"""
|
373
|
+
The shape of the numpy array must be one of either:
|
374
|
+
[[x y z], ...] nx3
|
375
|
+
[x y z c], ...] nx4 where c is a category with supported range [1, 14]
|
376
|
+
[x y z r g b], ...] nx6 where rgb is color
|
377
|
+
"""
|
378
|
+
)
|
379
|
+
|
380
|
+
return cls(data)
|
381
|
+
|
382
|
+
@classmethod
|
383
|
+
def from_point_cloud(
|
384
|
+
cls,
|
385
|
+
points: Sequence["Point"],
|
386
|
+
boxes: Sequence["Box3D"],
|
387
|
+
vectors: Optional[Sequence["Vector3D"]] = None,
|
388
|
+
point_cloud_type: "PointCloudType" = "lidar/beta",
|
389
|
+
# camera: Optional[Camera] = None,
|
390
|
+
) -> "Object3D":
|
391
|
+
"""Initializes Object3D from a python object.
|
392
|
+
|
393
|
+
Args:
|
394
|
+
points (Sequence["Point"]): The points in the point cloud.
|
395
|
+
boxes (Sequence["Box3D"]): 3D bounding boxes for labeling the point cloud. Boxes
|
396
|
+
are displayed in point cloud visualizations.
|
397
|
+
vectors (Optional[Sequence["Vector3D"]]): Each vector is displayed in the point cloud
|
398
|
+
visualization. Can be used to indicate directionality of bounding boxes. Defaults to None.
|
399
|
+
point_cloud_type ("lidar/beta"): At this time, only the "lidar/beta" type is supported. Defaults to "lidar/beta".
|
400
|
+
"""
|
401
|
+
if point_cloud_type not in cls.SUPPORTED_POINT_CLOUD_TYPES:
|
402
|
+
raise ValueError("Point cloud type not supported")
|
403
|
+
|
404
|
+
numpy = wandb.util.get_module(
|
405
|
+
"numpy",
|
406
|
+
required="wandb.Object3D.from_point_cloud requires numpy. Install with `pip install numpy`",
|
407
|
+
)
|
408
|
+
|
409
|
+
data = {
|
410
|
+
"type": point_cloud_type,
|
411
|
+
"points": numpy.array(points),
|
412
|
+
"boxes": numpy.array(boxes),
|
413
|
+
"vectors": numpy.array(vectors) if vectors is not None else numpy.array([]),
|
414
|
+
}
|
415
|
+
|
416
|
+
return cls(data)
|
417
|
+
|
418
|
+
@classmethod
|
419
|
+
def get_media_subdir(cls: Type["Object3D"]) -> str:
|
420
|
+
return os.path.join("media", "object3D")
|
421
|
+
|
422
|
+
def to_json(self, run_or_artifact: Union["LocalRun", "Artifact"]) -> dict:
|
423
|
+
json_dict = super().to_json(run_or_artifact)
|
424
|
+
json_dict["_type"] = Object3D._log_type
|
425
|
+
|
426
|
+
if isinstance(run_or_artifact, wandb.Artifact):
|
427
|
+
if self._path is None or not self._path.endswith(".pts.json"):
|
428
|
+
raise ValueError(
|
429
|
+
"Non-point cloud 3D objects are not yet supported with Artifacts"
|
430
|
+
)
|
431
|
+
|
432
|
+
return json_dict
|
433
|
+
|
434
|
+
@classmethod
|
435
|
+
def seq_to_json(
|
436
|
+
cls: Type["Object3D"],
|
437
|
+
seq: Sequence["BatchableMedia"],
|
438
|
+
run: "LocalRun",
|
439
|
+
key: str,
|
440
|
+
step: Union[int, str],
|
441
|
+
) -> dict:
|
442
|
+
seq = list(seq)
|
443
|
+
|
444
|
+
jsons = [obj.to_json(run) for obj in seq]
|
445
|
+
|
446
|
+
for obj in jsons:
|
447
|
+
expected = LogicalPath(cls.get_media_subdir())
|
448
|
+
if not obj["path"].startswith(expected):
|
449
|
+
raise ValueError(
|
450
|
+
"Files in an array of Object3D's must be in the {} directory, not {}".format(
|
451
|
+
expected, obj["path"]
|
452
|
+
)
|
453
|
+
)
|
454
|
+
|
455
|
+
return {
|
456
|
+
"_type": "object3D",
|
457
|
+
"filenames": [
|
458
|
+
os.path.relpath(j["path"], cls.get_media_subdir()) for j in jsons
|
459
|
+
],
|
460
|
+
"count": len(jsons),
|
461
|
+
"objects": jsons,
|
462
|
+
}
|
463
|
+
|
464
|
+
|
465
|
+
class _Object3DFileType(_dtypes.Type):
|
466
|
+
name = "object3D-file"
|
467
|
+
types = [Object3D]
|
468
|
+
|
469
|
+
|
470
|
+
_dtypes.TypeRegistry.add(_Object3DFileType)
|