sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
bce06ca813a3647f4bef07d6293b4c8ae3a19b59702c7cd4440fe98c11907629 | Python | 11,402 | 341 | from __future__ import annotations
import asyncio
import json
import pathlib
import shutil
import time
from collections import Counter
from typing import Any
from chemgraph.academy.observability.event_log import CampaignEvent
from chemgraph.academy.observability.event_log import read_events
from chemgraph.academy.obs... |
116c84221ed9526bf2823b0ba94da692cb66785c3b7e650a3b16fff784887b57 | Python | 11,403 | 372 | import itertools
from typing import Any
import obspy
import torch
import torch.nn as nn
import torch.nn.functional as F
from .base import GroupingHelper, WaveformModel
class PhaseTEAM(WaveformModel):
"""
A multi-station phase picking model, based on a combination of the PhaseNet and the TEAM architecture.
... |
139f1d8639529b16f830c868c0485c47daf6ed579ed38672727a20df9ad9f11c | Python | 11,403 | 300 | import torch
import numpy as np
import matplotlib.pyplot as plt
from scipy import signal
import os
from tqdm import tqdm
from config import Config
from model import SMoE_DOA_Estimator
from data_generator import DataGenerator
class Evaluator:
def __init__(self, config, model_path):
self.config... |
be256a6e4dc6b27e6eae8c7ec853a2421b61b849231e83a181d5619cd3ed42bd | Python | 11,404 | 303 | from __future__ import annotations
import argparse
import os
import random
from typing import Dict, List, Tuple
import numpy as np
import torch
import torch.nn as nn
from torch.utils.data import DataLoader, random_split
from torchvision import datasets, transforms
from tqdm import tqdm
from mps.utils import set_seed... |
4a112c79ad6594e3370c4e0e3add9c98af67a54adc85a15294590d2b2036798c | Python | 11,406 | 430 | # Copyright 2017 Calico LLC
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# https://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, ... |
5e2ef4000cd0b6bf8b9f02e9de8098d8668e62d0a000b925157ecf4dbd618640 | Python | 11,407 | 355 | from copy import deepcopy
import pytest
import torch
from torch import nn
from eir.models import model_training_utils
from eir.models.input.array import models_cnn
from eir.models.input.array.models_cnn import ConvParamSuggestion
@pytest.fixture
def create_test_util_model():
class TestModel(nn.Module):
... |
1aef1ff3604511775fab651d1f4f2dbd2d77aa69f9aca9dfaeaf13273be1b649 | Python | 11,408 | 311 | # Copyright (c) 2019, NVIDIA CORPORATION. All rights reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by ... |
8a1a85f09124bd30e9af75fcce2a28a9d80fd4f63bb16d7794b219b633e67a18 | Python | 11,408 | 268 | import logging
import nibabel as nib
import numpy as np
import pandas as pd
from brainsmash.mapgen import Base
from joblib import Parallel, delayed
from neuromaps.images import load_gifti, load_nifti
from neuromaps.nulls.nulls import _get_distmat
from scipy.spatial.distance import cdist
from tqdm.auto import tqdm
fro... |
b1c15ad8b3bd12a298f97287dd6570dcc9289910c886b63fe319d1093edbcd59 | Python | 11,408 | 311 | # Copyright (c) 2019, NVIDIA CORPORATION. All rights reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by ... |
a9451071d87fdc9751d6fef616ad0559919c91d21f7a6891e67ca95452ecd3cb | Python | 11,409 | 311 | # Copyright (c) 2019, NVIDIA CORPORATION. All rights reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by ... |
0b0dcfc27cfe96fb98a48b5f50090e7ad1fc83bd48ebffdb6e811de76acddbeb | Python | 11,411 | 346 | #!/usr/bin/env python3
"""
Early & Late Integration (Majority Vote) Runner
- Early integration: concatenate all modality features and train a single model.
- Late integration: train one model per modality and combine hard predictions (0/1) by majority vote.
Models included:
- L1 Logistic Regression (L1)
- Linear ... |
6f185ba6041eec79c0507b2dd08a5a2e261f461a8621022db45945666c66ddb1 | Python | 11,412 | 317 | """Argo endpoints for its Anthropic-native and OpenAI-compatible protocols.
Claude-prefixed Argo models use Anthropic Messages. Other Argo models use the
OpenAI-compatible chat-completions interface. This module owns their shared
wire-name mapping, credential resolution, base URLs, and endpoint quirks.
"""
from __fut... |
dd2ea0eb83db7e7654d3398c7dea9f7bc8c36c333135a5bb825839795fcdded5 | Python | 11,414 | 211 | import os
import warnings
import matplotlib.pyplot as plt
import mlflow
import yaml
import numpy as np
import torch
import torch.nn as nn
from utils.models import WindTurbineModel
from utils.env_config import path_check_and_join, path_dissect_and_join
from utils.metrics import prediction_refactoring
from captum.attr im... |
ad002e80927e11fb39eb24c064a798e4e0fcf1619f40779f79c5c88462361e1e | Python | 11,415 | 253 | import matplotlib.pyplot as plt
import numpy as np
from matplotlib.colors import LightSource
import matplotlib.patheffects as PathEffects
from mpl_toolkits.mplot3d import Axes3D
import matplotlib.patches as mpatches
from matplotlib.collections import PatchCollection
import matplotlib
from . import plot_utils
... |
2f625d42c589e4d2da9c0864aafdf13ee34f82a386a57d8a03ce9b8448d9968c | Python | 11,416 | 245 | #!/usr/bin/env python
"""
Handles the management of one or more camera / feed displays.
Hazen 3/17
"""
from PyQt5 import QtWidgets
import storm_control.sc_library.parameters as params
import storm_control.hal4000.camera.cameraControl as cameraControl
import storm_control.hal4000.display.cameraViewers as cameraViewe... |
820d2b0e70f814bbc168a4a82c0919c1588041f9612de7c99bafcc8eee5d990b | Python | 11,416 | 294 | from typing import Optional, Tuple
import torch
from torch import Tensor
import torch_geometric.typing
from torch_geometric import is_compiling
from torch_geometric.deprecation import deprecated
from torch_geometric.typing import OptTensor
from torch_geometric.utils import cumsum, degree, sort_edge_index, subgraph
fr... |
bf19bc5a6ffbc9a706a2c7c0eeafafcdd170aa6b44869f3f1326641e25cd10c0 | Python | 11,418 | 323 | # Copyright (c) Meta Platforms, Inc. and affiliates. All Rights Reserved
import math
from typing import Dict, List, Optional
import torch
import torch.nn as nn
import torch.nn.functional as F
import torch.utils.checkpoint as checkpoint
from .model_misc import MLP
class LinearPresenceHead(nn.Sequential):
def __... |
dae77214754de1f4b4ec16256da784cbad4234bdd2290706e2be748742e96454 | Python | 11,423 | 342 | """Atomistic LIne Graph Neural Network.
A prototype crystal line graph network dgl implementation.
"""
from typing import Tuple, Union, List
import dgl
import dgl.function as fn
import numpy as np
import torch
from dgl.nn import AvgPooling
# from dgl.nn.functional import edge_softmax
from pydantic.typing import Lite... |
4176d577b6f5e587a4182fe771872e4a4fa61327196514699065c61e7a8639c8 | Python | 11,424 | 258 | import argparse
import torch
import torch.utils.data
from motion.dataset import MotionDataset
from model.eghn import EGHN
import os
from torch import nn, optim
import json
import random
import numpy as np
parser = argparse.ArgumentParser(description='VAE MNIST Example')
parser.add_argument('--exp_name', type=str, def... |
0787e3edfca90019e60749a3d83a1cc6eb0c5574a2ec513e7855c82308fb4710 | Python | 11,425 | 261 | #!/usr/bin/env python2
# -*- coding: utf-8 -*-
"""
Created on Tue Mar 30 19:47:48 2021
@author: laurayoung
"""
import numpy
import sys
from PIL import Image
from ERICA import aberration_rendering, ERICA_toolkit
def createPinhole(psf_size, pinhole_add, oversampling, ph_scale_up = 10.):
'''Creates a pinhole ma... |
feb8789863d8c1c47d62a911a9a273b9f1147602acddf0117abea8324542590a | Python | 11,425 | 278 | #!/usr/bin/env python
"""
'Tile' the blocks of a maf file over each of a set of intervals. The
highest scoring block that covers any part of a region will be used, and
pieces not covered by any block filled with "-" or optionally "*".
This version uses synteny annotation if found on the alignment blocks, and
will att... |
9700b395126b836d37b7bdb2012bc92d6a97ab8739a91afda7bd21c268062a07 | Python | 11,429 | 316 | """
Copyright 1999 Illinois Institute of Technology
Permission is hereby granted, free of charge, to any person obtaining
a copy of this software and associated documentation files (the
"Software"), to deal in the Software without restriction, including
without limitation the rights to use, copy, modify, merge, publis... |
71f51528e86b1bfb66d62855f8e20b63353b05c9cbda3ec194a9b1577070867a | Python | 11,433 | 342 | import torch
import torch.nn as nn
from einops import rearrange
from einops.layers.torch import Rearrange
import torch.nn.functional as F
class SoftPooling2D(torch.nn.Module):
def __init__(self, kernel_size, stride=None, padding=0):
super(SoftPooling2D, self).__init__()
self.avgpool = torch.nn.Avg... |
48eea3267ac89c231095e121386d8b8a8fe340e4295656c6524f75d62265a946 | Python | 11,436 | 385 | # FetMRQC: Quality control for fetal brain MRI
#
# Copyright 2023 Medical Image Analysis Laboratory (MIAL)
#
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/lice... |
728f34f3926bc0796af3d1f79057f953d8f8ce24a9b61f2c8f1c8c9fdc638f4d | Python | 11,437 | 292 | import jax.numpy as jnp
import numpy as np
import json
import glob
import sys
import matplotlib.pyplot as plt
from matplotlib.ticker import LogLocator
import matplotlib.ticker as ticker
import argparse
import plot_utils
import os
import matplotlib as mpl
import re
plt.rcParams["font.sans-serif"] = ["DejaVu Sans"]... |
5597fbc6efef42e05c5d3d009e2767dff09b4936de7c50b7f18c80cc00f72e06 | Python | 11,438 | 352 | import os
import re
import numpy as np
import pandas as pd
import nibabel as nib
import matplotlib.pyplot as plt
from matplotlib.colors import Normalize
from matplotlib.cm import ScalarMappable
try:
from nilearn.image import resample_to_img
except Exception:
resample_to_img = None
# =========================... |
53bfd6df3d9cb2360db5d5b5799b207ea00c9c3b4326652e7684392a96d7814f | Python | 11,439 | 322 | import pytest
import pathlib
import json
import csv
# import datetime
import numpy as np
from phantoms.MR_XCAT_qMRI.sim_ivim_sig import phantom
import warnings
from tests.IVIMmodels.unit_tests.test_ivim_fit import PerformanceWarning
warnings.simplefilter("always", PerformanceWarning)
def pytest_addoption(parser):
... |
b11c4d0a6b4066d9331e5a09f0b19c8c0c7b16d03a31e4efd4f4bdcb6564ba0b | Python | 11,440 | 334 | #!/usr/bin/env python
#
# A file transfer utility specialized for storm-control. It's
# primary difference is that it waits until HAL has finished
# acquiring a movie before transferring. The finished state
# is indicated by the presence of the corresponding XML file
# for the movie.
#
# Hazen 08/16
#
import datetime
... |
d688b2590ba4d52a8752be9d22a94e864efe406813d326f50fecb97b2611b21c | Python | 11,442 | 299 | #!/usr/bin/env python3
# coding=utf-8
# amalgamate.py - Amalgamate C source and header files.
# Copyright (c) 2012, Erik Edlund <erik.edlund@32767.se>
#
# Redistribution and use in source and binary forms, with or without modification,
# are permitted provided that the following conditions are met:
#
# * Redistribu... |
b25668bd716a89bbd07571bad3bb2dc04c1f893149520d74dec717441071f695 | Python | 11,447 | 330 | from typing import List, Final
import torch
from mlcg.nn import MLP
from mlcg.geometry import compute_distance_vectors
from mlcg.nn.angular_basis.spherical_harmonics import SphericalHarmonics
from .base import RANGE
from ..blocks import (
RANGEInteractionBlock,
AggregationBlock,
BroadcastBlock,
So3kr... |
2639ed509c629008159aecd1994345300adab8755633ce6d3aca5ea7a65cb8b5 | Python | 11,449 | 255 | import torch
import torch.nn as nn
from torch_geometric.nn import radius_graph
from torch_geometric.nn import global_mean_pool, global_add_pool
from ocpmodels.common.registry import registry
from ocpmodels.models.base import BaseModel
from ocpmodels.common.utils import (
get_pbc_distances,
radius_graph_pbc,
)
... |
7bfb559e90823b8b56a59deeab14e1cbe61eee581a8e0e415806564fa5613c7d | Python | 11,450 | 329 | from copy import copy
import argparse
from tqdm import tqdm
import torch
import torch.nn.functional as F
from torch.nn import ModuleList, Linear, ParameterDict, Parameter
from torch_sparse import SparseTensor
from torch_geometric.utils import to_undirected
from torch_geometric.data import Data, GraphSAINTRandomWalkSam... |
f416375304510d3bc9fc3ea8a4966a304c6d34f584d539592d6258f6901e46b1 | Python | 11,450 | 350 | # Copyright 2024 Google LLC
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# https://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, ... |
3226908dd469356c901e986973ee2ce36a3b7a08c5892f3f39f9c507202970d2 | Python | 11,451 | 229 | """
If you use this code, please the SynthSR paper in:
https://github.com/BBillot/SynthSR/blob/master/bibtex.bib
Copyright 2020 Benjamin Billot
Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in
compliance with the License. You may obtain a copy of the License at
http:... |
0856d3b2b16e5897466def784219fd7da0c10fb9d34050247ac82eebeedc1340 | Python | 11,454 | 355 | import argparse
import h5py
import os
import numpy as np
import sigpy as sp
import torchvision.transforms as T
from sigpy.mri import retro, app, sms, muse, mussels
from os.path import exists
DIR = os.path.dirname(os.path.realpath(__file__))
HOME_DIR = DIR.rsplit('/', 1)[0]
print('> HOME: ', HOME_DIR)
DATA_DIR = HO... |
a9979dd5827e49e985e90455bdbe8598e38a4f10facf1d4050ac084d1ca7184c | Python | 11,455 | 341 | from abc import abstractmethod
from typing import Optional, List
import warnings
from PySide6.QtWidgets import QWidget, QMenuBar, QMainWindow, QFormLayout, QVBoxLayout, QLabel, QHBoxLayout, QGridLayout, QPushButton, QCheckBox, QSlider, QTableWidget, QTableWidgetItem, QTabWidget, QGroupBox, QSpinBox, QDoubleSpinBox, QFi... |
5da8f5efa34c734f67f69e81c443445f86f20e08bcc5247690bc77f4706460db | Python | 11,457 | 109 | from train_AE import init_from_config
from brainvoice.configuration.configuration import Configuration
from brainvoice.models.utils import load_model_checkpoint
import argparse
import torch
from torch.autograd import Variable
import os
import pathlib
import numpy as np
from tqdm import tqdm
"""
python ... |
9cf1d8f33bc784bf8a44dc58a78576c859c1b2411a237b553646c20e2c8ccb9a | Python | 11,457 | 350 | # Copyright 2024 Google LLC
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# https://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, ... |
eb74c73e0441fe771358e663eb4af2ddd67635efe1e18b1331c7e3ed7ae7d3cf | Python | 11,461 | 272 | # Ultralytics 🚀 AGPL-3.0 License - https://ultralytics.com/license
import os
from itertools import product
from pathlib import Path
import pytest
import torch
from tests import CUDA_DEVICE_COUNT, CUDA_IS_AVAILABLE, MODEL, SOURCE
from ultralytics import YOLO
from ultralytics.cfg import TASK2DATA, TASK2MODEL, TASKS
f... |
33ba2d06d26b6887a40cb95e291bd5efc0d21bbbff96e7290074e1dec5bbdad9 | Python | 11,463 | 283 | ##
#Load Modules
import numpy as np
from numba import njit
import pdb
from EPGMotion import *
@njit()
def Jacobian_MotionCorrection(theta, opt):
# Cache frequently used values
nTR = opt["nTR"].astype(np.int32)[0]
steadyStateTR = opt["SteadyStateTR"].astype(np.int32)[0]
nDummy = opt['nDummy'].astype(np.... |
39c120db21fe6b5923ec97decc68f1edeafa42b6b33b540e5d49fe85b575c987 | Python | 11,467 | 299 | """Classes for simulating a soft mixture of modes."""
from typing import List, Optional, Union
import numpy as np
from scipy.special import softmax
from osl_dynamics.simulation.obs_mod import MVN, MSess_MVN
from osl_dynamics.simulation.base import Simulation
class MixedSine:
"""Simulates sinusoidal oscilations... |
3b682ed1ebb236189f1a1f6be6de06b37a3bf46cb37e647d22fe3166ca3442bb | Python | 11,471 | 331 | """
Unified metrics for multi-label classification (8 surgical decisions)
and multi-output regression (8 surgical doses).
**2025-06-09 更新**
-------------------
* 修复 `masked_*` 系列函数在 **numpy.ndarray × torch.Tensor** 相乘时的类型冲突：现在会自动把 `mask` 也转换为 NumPy；兼容 CPU/GPU。
* 其他逻辑保持一致（分类指标、整体回归指标）。
"""
from __future__ import annot... |
422f2f926f23a60d20be860ee47acd6c42774905b933f4785e079c2acf8d42ca | Python | 11,471 | 332 | """
Dual-modality fusion experiment: FLAIR + T2 Late Fusion
Uses two trained single-modality models for late fusion
"""
import numpy as np
import pandas as pd
import os
def _roc_auc_score_binary(y_true, y_score):
"""Compute binary classification AUC"""
if len(np.unique(y_true)) < 2:
return 0.0
pos_... |
9634792c00d511a2dc0794becc96d5a449c7945baf723b68c512d6b881ebd890 | Python | 11,471 | 258 | from PUMI.engine import AnatPipeline, QcPipeline
from PUMI.engine import NestedNode as Node
from PUMI.pipelines.multimodal.image_manipulation import vol2png
from PUMI.utils import get_reference, get_config, registration_ants_hardcoded
from nipype.interfaces import fsl
from nipype.interfaces.ants import Registration, Ap... |
11088ae693e33d73386330bdb6b0824702137fc89abf3f062d3d872f5ff8e71e | Python | 11,472 | 260 | from copy import deepcopy
import numpy as np
from time import time
import torch
from skimage.data import camera
from torch.nn.functional import pad, conv3d, conv1d, conv2d
from batchgeneratorsv2.helpers.scalar_type import RandomScalar, sample_scalar
from batchgeneratorsv2.transforms.base.basic_transform import ImageO... |
a3bb40ad63dc0eec29ab2a798c6db5fa772047b95c9627c32eccb3e80a3e3701 | Python | 11,479 | 284 |
import colorsys
import os
import pathlib
import h5py
import numpy as np
import matplotlib
from matplotlib.collections import LineCollection
from matplotlib import colors as mcolors
from mpl_toolkits.axes_grid1 import make_axes_locatable
from neuron import h
from neuron.units import ms, mV
import json
from neuron_inter... |
2734b8d1030ecd4bd988c74464105d20b337a57f766f841542fde7e6b496cd7c | Python | 11,480 | 385 | # Copyright 2024 Google LLC
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# https://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, ... |
44f9e63c041936018699b97d171fab549734fa376fba1c99221cd80842669675 | Python | 11,485 | 325 | #############################################################################
# Copyright (C) 2020-2025 MEmilio
#
# Authors: Agatha Schmidt, Henrik Zunker, Manuel Heger
#
# Contact: Martin J. Kuehn <Martin.Kuehn@DLR.de>
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file exce... |
0573d5248ae255122b3947b5861f117f814d0f980677fe3cb50ea4d489f3a606 | Python | 11,489 | 306 | # Copyright (c) Meta Platforms, Inc. and affiliates. All Rights Reserved
import warnings
from typing import Dict, List
import numpy as np
# Check if Numba is available
HAS_NUMBA = False
try:
import numba as nb
HAS_NUMBA = True
except ImportError:
warnings.warn(
"Numba not found. Using slower pure... |
0119a614bee81c16bd694f70923218afea5c20251366d87e2c925a596f588744 | Python | 11,492 | 229 | import torch
import torch.nn as nn
import numpy as np
from datetime import datetime
import MixDataLoader, SeparatedDataLoader
# import data
device = 'cuda' if torch.cuda.is_available() else 'cpu'
batch_size_train = 100
batch_size_test = 100
worker = 0
num_class = 100
target_extend = torch.arange(num_class)... |
d4f0777158e48011f862264fbe6a14bd056842c4af57de8b2fb0be2786c28b35 | Python | 11,495 | 317 | # -*- coding: utf-8 -*-
import numpy as np
from fury import window
from scilpy.utils.spatial import get_axis_index
from scilpy.viz.backends.fury import (create_scene,
set_display_extent,
set_viewport,
sna... |
b3eedffd716c30a59dd79bb8008b8830692aaa6b7d41f58cef44353cac3af565 | Python | 11,500 | 319 | """Social reversal learning task for MWorks.
"""
################################################################################
#### Determine whether on laptop or on rig and update sys.path accordingly
################################################################################
_PYTHON_SITE_PACKAGES = getvar(... |
c2fd82dcaaf9dd94c98bd657db593f525d6759b828cbbacb464c7947700c4001 | Python | 11,501 | 298 | import torch
from torch import nn
from torch.nn import init
import torch.nn.functional as F
class LayerNorm(nn.Module):
def __init__(self, normalized_shape, eps=1e-6, data_format="channels_last"):
super().__init__()
# 创建权重参数，初始化为1
self.weight = nn.Parameter(torch.ones(normalized_shape))
... |
23235ed63e0804ae56ec87c1daadbb4fbc4316b3d5382b295962530018b557a2 | Python | 11,503 | 368 | from pathlib import Path
import torch.nn as nn
import torch
import math
from typing import Union, Tuple
from typing import List
from torch.optim import Optimizer
import flair
from flair.data import Dictionary
class LanguageModel(nn.Module):
"""Container module with an encoder, a recurrent module, and a decoder... |
bd599d8b9f8304c99fb98b90d6ff73d5421acdd53b4cc6826d1c5b4c4f8faa12 | Python | 11,503 | 312 | # Configuration file for the Sphinx documentation builder.
#
# This file only contains a selection of the most common options. For a full
# list see the documentation:
# https://www.sphinx-doc.org/en/master/usage/configuration.html
# -- Path setup --------------------------------------------------------------
# If ex... |
7ea390539291aa5cbc4679b1209dd8f7774f807090b2a2fa8fd927b1565c6620 | Python | 11,504 | 311 | """
Copyright 1999 Illinois Institute of Technology
Permission is hereby granted, free of charge, to any person obtaining
a copy of this software and associated documentation files (the
"Software"), to deal in the Software without restriction, including
without limitation the rights to use, copy, modify, merge, publis... |
6a0097a4e4c29ea75f90b1aa6481926d4a5d5c24877850c71b78d6a9f41f9ac6 | Python | 11,506 | 436 | """
Utilities for nd (n-dimensional) arrays
Tested on Python 3.5
Contact: adalca@csail.mit.edu
"""
import builtins
import numpy as np
import scipy as sp
import scipy.ndimage
from scipy.spatial import ConvexHull
def boundingbox(bwvol):
"""
bounding box coordinates of a nd volume
Parameters
---------... |
dca0b035f984cb6bc9c609763bfac3d94f3ed6a450f524e9b4a2114eae5f3845 | Python | 11,506 | 335 | # Code Reference : https://github.com/d-li14/mobilenetv3.pytorch
# @InProceedings{Howard_2019_ICCV,
# author = {Howard, Andrew and Sandler, Mark and Chu, Grace and Chen, Liang-Chieh and Chen, Bo and Tan, Mingxing and Wang, Weijun and Zhu, Yukun and Pang, Ruoming and Vasudevan, Vijay and Le, Quoc V. and Adam, Hartwig},... |
c05ac375de4ba60f4b0f71cbb14dd25c7b0fc168182c8b753c05def0dcdc10a9 | Python | 11,509 | 282 | """The optional steps: a checkbox each, and each one actually does something.
Run from the repo root::
uv run python python/test_optional_steps.py
``Params.optional_steps_to_run`` used to be a multi-select list box holding one
inert entry — ``generateCSV`` was written into the parameter file and read by
nothing.... |
dea07df6f3474acdee9ddb51337c2b876e95cc90a013c5aa17cb098d420213b6 | Python | 11,513 | 239 | import argparse
from os.path import join
import pickle
import keras
from keras.optimizers import Adam
from keras.callbacks import EarlyStopping, ReduceLROnPlateau
import utils
from model_zoo import lentiMPRA
import plotting
import pandas as pd
import wandb
from wandb.keras import WandbMetricsLogger
import yaml
import n... |
40cd904d88a6c6e3c5ee53f7247e77defa25974c11ad33f4f5d1e559a4df2cf1 | Python | 11,515 | 251 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
The script uses scalars from an anatomy, data_per_point or data_per_streamline
(e.g. commit_weights) to visualize them on the streamlines.
Saves the RGB values in the data_per_point 'color' with 3 values per point:
(color_x, color_y, color_z).
If called with .tck, the... |
d9a8c64131fa9df7bda0996f3d98b6e5a6b4a50045785e654da7421f7f61e248 | Python | 11,518 | 332 | # Copyright 2024 Google LLC
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# https://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, ... |
c50c5e8b174605dfcbae7a14e846ae5d24ef9d78dbafc61d9eace47d9e60ab71 | Python | 11,519 | 240 | """
(C) Copyright 2019 IBM Corp.
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at
http://www.apache.org/licenses/LICENSE-2.0
Unless required by applicable law or agreed to in writing, software
... |
217cd58129b8e6c34bece3c2c7fe72f3471e9d79e4c1bbb41a2a99430a342b70 | Python | 11,522 | 268 | from typing import Optional
from bread.data import *
from bread.algo.tracking import AssignmentDataset, GNNTracker, AssignmentClassifier, GraphLoader, accuracy_assignment, f1_assignment
from glob import glob
from pathlib import Path
import datetime, json, argparse
import torch, os
from pprint import pprint
from sklear... |
2d194f7ee7d153e408cf7f02ac63da2076cf8e05ce05c6e7990aac28f4dbf7cb | Python | 11,524 | 198 | #!/usr/bin/env python3
"""
Main training script for RoBep model.
This script provides comprehensive argument parsing and training functionality.
"""
import argparse
import torch
from pathlib import Path
from bce.utils.trainer import Trainer
from bce.utils.tools import set_seed
from bce.utils.results import evaluate_m... |
8465d2c54f59503c9dd6b69ec8b638b2fd7f7ee95f5776f1733671bbfc2e04ca | Python | 11,524 | 337 | """Utilities for visualizing the model fitting process."""
import numpy as np
import matplotlib.pyplot as plt
from .model import input_heatmap
from .tools import standardize_axes
def prediction_vs_target(input, target, model, ax=None, sampling_rate=None,
show_input=False, xlim=None, title=N... |
0a2edf7605ed3bcb11750c373cb2dafae05f804f6db87b36fbffb090d6c884a7 | Python | 11,525 | 334 | import math, copy
import numpy as np
import torch
import torch.nn as nn
import torch.nn.functional as F
from torch.autograd import Variable
from typing import Any, Dict
import hydra
import omegaconf
import pytorch_lightning as pl
from torch_scatter import scatter
from torch_scatter.composite import scatter_softmax
... |
936ed6fba4cccf9c7fdaea8c866cc6f5b17c57690741b3f12ba15bbe9aff2cd7 | Python | 11,531 | 321 | import os
import numpy as np
import cv2
import torch
import yaml
import csv
import argparse
from argparse import Namespace
from monai.transforms import (
Compose,
ToTensord,
ScaleIntensityd,
AsDiscrete
)
from monai.networks.nets import UNet
from torchmetrics import Dice, JaccardIndex
from monai.metrics ... |
27fa0d34e78874ad312fd9c9c1320cce8eb2e83ca102d040b30084f4ab7fdca2 | Python | 11,532 | 302 | #!/usr/bin/env python
# author: Jannes Spangenberg
# e-mail: jannes.spangenberg@uni-jena.de
# github: https://github.com/JannesSP
# website: https://jannessp.github.io
import read5_ont
import multiprocessing as mp
import pysam
import psutil
from argparse import ArgumentDefaultsHelpFormatter, ArgumentParser, Namespace
... |
917e911f9b0753af96d04e12bb6ddc7817331670a2dc908f575bfdca32dcda34 | Python | 11,533 | 299 | #!/usr/bin/env python
"""
Draw the parameter with the correct style.
Provide widgets for editing parameters.
Hazen 04/17
"""
import os
from PyQt5 import QtCore, QtGui, QtWidgets
import storm_control.sc_library.parameters as params
def truncateString(a_string):
max_len = 25
if (len(a_strin... |
556c73f87c3be67fefbdb2a03e87fa88b2862da7cca61ffb31e5d08c82ff5ac3 | Python | 11,535 | 344 | import subprocess
import tempfile
import time
from pathlib import Path
from typing import Literal, Optional
import dolfin as df
import numpy as np
import pymeshfix
import pyvista as pv
import simple_mri as sm
import skimage
import SVMTK as svmtk
from loguru import logger
from scipy.spatial import KDTree
from gmri2fem... |
52d9fe216a55f2f82b49a75cd175f05cfbe4db3c2dd7485eee3e26da0e4a5298 | Python | 11,541 | 214 | import sys
import os
sys.path.append(os.path.dirname(os.path.dirname(__file__)))
import argparse
import os
import pandas as pd
import torch
import numpy as np
from txgnn import TxData
def parse_args():
parser = argparse.ArgumentParser()
parser.add_argument("--seed", help="seed for random split")
parser.a... |
e0b1424d14ca92f7522b10d4e47299752c219ce8dcc6cc9e2ef0b9fb877530c6 | Python | 11,543 | 342 | import torch
import torch.nn as nn
from einops import rearrange
from einops.layers.torch import Rearrange
import torch.nn.functional as F
class SoftPooling2D(torch.nn.Module):
def __init__(self, kernel_size, stride=None, padding=0):
super(SoftPooling2D, self).__init__()
self.avgpool = torch.nn.Avg... |
66021bf2f758674ed85891972783d3e161c21134c3b71e9a47330bb68300a798 | Python | 11,546 | 231 | import argparse
from os.path import join
import pickle
import keras
from keras.optimizers import Adam
from keras.callbacks import EarlyStopping, ReduceLROnPlateau
import utils
from model_zoo import lentiMPRA_v2
import plotting
import pandas as pd
import wandb
from wandb.keras import WandbMetricsLogger
import yaml
impor... |
20dfa2684e1f44e114e0ab1939555baae80285d2d0e0c37340c103d54d7cefd1 | Python | 11,547 | 311 | from logging import raiseExceptions
import os.path as osp
import warnings
from collections import OrderedDict
from functools import reduce
import mmcv
import numpy as np
from mmcv.utils import print_log
from prettytable import PrettyTable
from torch.utils.data import Dataset
from depth.core import pre_eval_to_metrics... |
07a7a83c5eae3e186e9b9577ca52751453c5f9246995f5747c9fe01efa27008b | Python | 11,548 | 293 | import sys
import yaml
import os
import numpy as np
import re
import matplotlib.pyplot as plt
import matplotlib as mpl
import h5py
pathpath,myrun,ncluststr,cmethod = sys.argv[1:]
'''
pathpath = 'PATHS/filepaths_carlen.yml'
myrun = 'runCrespZP_brain'
cmethod = 'ward'
ncluststr = '8'
'''
with open(pathpath, 'r') as my... |
8a0c0264592344337c5e326d99e10a26f9e95070fb0c2ff330250d9ee263c23c | Python | 11,548 | 278 | """
Main manuscript - Figure 3: Field strength differences in orientation-dependent qMRI
Left column: Absolute differences between 9.4T and 3T qMRI parameters, including lower and higher FA bins.
Right column: Subject-specific absolute difference maps for R1, R2, and AI between 9.4T and 3T for one exemplary subject.
... |
827a7b3b0ccf58677ceb3a528815eec0d8533e827523a0cb0b7c212fe5ff5667 | Python | 11,551 | 278 | """ Attention Pool 2D
Implementations of 2D spatial feature pooling using multi-head attention instead of average pool.
Based on idea in CLIP by OpenAI, licensed Apache 2.0
https://github.com/openai/CLIP/blob/3b473b0e682c091a9e53623eebc1ca1657385717/clip/model.py
Hacked together by / Copyright 2021 Ross Wightman
"""... |
91545201e4d191ace4ba3ff5c8c528893f366541935a798a446dd2d7157e105c | Python | 11,553 | 242 | ##############################################################################################
### Script to average data from the same columns in data files stored in different folders ###
### -- v1.2 -- ###
###################################... |
e39b89c38eeb658046bdbdbf2f7d022437195f5af8542bac3185ab2070ce0888 | Python | 11,553 | 342 | # Copyright 2024 Google LLC
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# https://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, ... |
251a24813252ed627f90b0a19b0edb8354ce43f487a42d721ef65c4e9a7444c6 | Python | 11,555 | 242 | ##############################################################################################
### Script to average data from the same columns in data files stored in different folders ###
### -- v1.2 -- ###
###################################... |
1bea370d369fe77444e93a76489d131a2c919321637b1f08ae8aa19a70dfe683 | Python | 11,562 | 382 | import numpy as np
from dataclasses import dataclass, field
from typing import Any, Union
from trigger import Port
# import psychopy and set hardware specs
from psychopy import visual, misc, core, prefs
prefs.hardware['audioLib'] = ['ptb', 'pyo']
prefs.hardware['audioLatencyMode'] = 3
from psychopy import sound
from ... |
368e169c4ee8a09f05a70aedcaa8bd3ebc315f685bad78e473d6becfe3ca2872 | Python | 11,567 | 350 | """1D per-sector cone-background model (Chebyshev polynomial + optional
physical tails) used by the step-0 projection background pass.
Vendored verbatim from the bg-optimization research repo
(``src/bg_removal/gen_bg_fit/fit_sector_var_model.py``). Depends only on
numpy/scipy, so it is self-contained.
"""
import nump... |
c0b8cfb4ccb1bbf84a22891ef94dae941013935033c154b87abec6ac2f637267 | Python | 11,567 | 330 | # Copyright (c) DP Technology.
# Copyright (c) Facebook, Inc. and its affiliates.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
import logging
import os
import warnings
from argparse import Namespace
from typing import Any, Callable, Dict,... |
7a05f64a41be312528f6bdef366ab4ee789ef3e8264936975bdf91205ece50b4 | Python | 11,569 | 311 | import os
import nibabel as nib
import pytest
from unittest.mock import patch, MagicMock
import subprocess
from conftest import load_data
from pydesigner.preprocessing import mrpreproc, mrinfoutil
from pydesigner.system.errors import MRTrixError
DATA = load_data(type="hifi")
PATH_DWI = DATA["nifti"]
PATH_DWI_NO_JSON ... |
06f4b6d89690457b02bebbb284fd3340c4fe52325087e439eb5970f3309357ce | Python | 11,570 | 315 | # -*- coding: utf-8 -*-
import itertools
import logging
import multiprocessing
import numpy as np
from dipy.data import get_sphere
from dipy.reconst.mcsd import MSDeconvFit
from dipy.reconst.multi_voxel import MultiVoxelFit
from dipy.reconst.shm import sh_to_sf_matrix
from scilpy.reconst.utils import find_order_from_... |
677b35230b9ddecc3e387c7d93764a21d9e5ea445e5d7e162dcb196a13e1473b | Python | 11,570 | 260 | '''
Modified from https://raw.githubusercontent.com/DingXiaoH/RepVGG/main/repvgg.py
MIT License
Copyright (c) 2020 DingXiaoH
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, ... |
04cd72dbb682367de3b8d5d48670ec876d1f455df589a217ae53685128107707 | Python | 11,572 | 250 | # Copyright (c) Ankush Kesri/Yangming Ou, Boston Children's Hospital/Harvard Medical School, 2024
# email: Ankush.Kesri@childrens.harvard.edu, Yangming.Ou@childrens.harvard.edu
# Permission is hereby granted, free of charge, to any person obtaining a copy of
# this software and associated documentation files (the "Sof... |
e64f44fe78ffc37cb565662278f653699a491783ccee5bbfaadd1f84c88a957a | Python | 11,572 | 360 | """3-D molecular structure visualisation components for the Streamlit UI."""
import json
import re as _re
import numpy as np
import pandas as pd
import streamlit as st
from ase.data import chemical_symbols
from chemgraph.tools.ase_core import create_ase_atoms, create_xyz_string
# -----------------------------------... |
e042b5263e5d070c30cdd4795572baed563b4f31b9e0f87f59895af2163c03dd | Python | 11,579 | 267 | #! /usr/bin/env python
# -*- coding: utf-8 -*-
"""
Script to compute multi-encoding multi-shell multi-tissue (memsmt)
Constrained Spherical Deconvolution ODFs.
In order to operate, the script only needs the data from one type of b-tensor
encoding. However, giving only a spherical one will not produce good fODFs, as
it... |
52e7c3833aa8376a495218f04292b8bedd9a0c04513170d7ff0427849de21856 | Python | 11,580 | 274 | '''A quick example to generate heatmaps for vgg16.'''
import os
from functools import partial
import click
import torch
import numpy as np
from torch.utils.data import DataLoader, Subset
from torchvision.transforms import Compose, Resize, CenterCrop, ToTensor
from torchvision.datasets import ImageFolder
from torchvisi... |
4f279f9406488fe34e98f2b5efe2ff9e81ec1ecebdaa8c359432a1a6d039e5e4 | Python | 11,581 | 319 | """Plot semantic cluster flatmaps, % match between languages, tuning shift per cluster.
Note: Cluster numbers in the paper are flipped and 1-indexed.
Figure 3B, 3C, 5A.
"""
import matplotlib.pyplot as plt
import numpy as np
import os
import pickle
from matplotlib.colors import ListedColormap
from scipy.stats import t... |
6ec33e2260acb9f9853bffd31354497d221c0d1a3f2b74fb470fb1ba1c35c96a | Python | 11,583 | 284 | import matplotlib.pyplot as plt
import matplotlib.ticker as ticker
import jax.numpy as jnp
import jax
import os
import json
import sys
import glob
import matplotlib.colors as mcolors
from matplotlib.colors import to_rgba
from collections import Counter
from scipy.stats import gaussian_kde
plt.rcParams["font.sans-s... |
b6d22a2db05fc3fa7db66c24501d6fbc10ed59e32b757734ab2b841caa4a476b | Python | 11,584 | 296 | """
MSI Delocalization Visualisation Tool
─────────────────────────────────────
Reads a scored h5ad file (produced by the scoring pipeline) and provides
interactive visualisation of individual m/z features:
• Heatmap view – spatial intensity map with tissue contour overlay
• Distance map – arrows from nonzero ... |
872f0d4dbd1bcab4bc911c761a2fc74bd8f1e512abe20bd6db1aa2053617030f | Python | 11,587 | 281 | """Tests pinning the two open contributions.
Each open pull request claims to fix a specific defect. The tests here assert
the *fixed* behaviour and are marked ``xfail(strict=True)``, so:
- on the default branch they xfail, the suite stays green, and CI remains a
useful gate on unrelated work;
- merging the contrib... |
1483670fb8295b48556eba3f10f9457580184ae18032750a5abc78d8e0b0b966 | Python | 11,591 | 314 | import math
import pathlib
from enum import Enum
from typing import Type
import numpy as np
import numpy.typing as npt
from neuron import h
from scipy.io import loadmat
from neuron.units import ms, mV
import neuron_interface.neurosim
from ...spherical_cartesian_conversion import norm_spherical_to_cartesian
from ..ce... |
53e079d2af1b7924c526fcb68bf746c077f7df1d013ae2d853fb2b70caa9d064 | Python | 11,591 | 279 | import numpy as np
import os
import sys
import gc
import cooler
from collections import defaultdict
import matplotlib.pyplot as plt
from scipy.ndimage import zoom
import torch
from . import plot_utils
def get_region(matrix, chrom_name, start, end):
'''Get Hi-C map by genome position'''
block = m... |
6d70bf799e3ef17f9507e72b262d21990860fafea47b3f0bca34b9649b2cbfbb | Python | 11,591 | 275 | from math import factorial
import operator
from tqdm import tqdm
import numpy as np
from sympy.ntheory import factorint
import logging
from zigzag.classes.hardware.architecture.memory_hierarchy import MemoryHierarchy
from zigzag.classes.opt.temporal.loma.multipermute import permutations
from zigzag.classes.opt.tempora... |
001812b8eabfbc33c398e6f5ae2f81a8c35641f93a18483d3371969b18cba7db | Python | 11,595 | 298 | #!/usr/bin/env python2
# -*- coding: utf-8 -*-
#
# MRC CBU PYTHON SCANNING SYNC
#
# This library is intended to allow for easy communication between Python
# experiments and the MEG and MRI scanners at the MRC Cognition and Brain
# Sciences Unit (CBU). The implementation is intended for the CBU setup only,
# and interf... |
f7127f9e7f8e25677daf9180fa37cd889098d3c2e9933870db9a3ee48a68097d | Python | 11,604 | 358 | # Copyright (c) Meta Platforms, Inc. and affiliates. All Rights Reserved
import contextlib
import fnmatch
import logging
from typing import (
Any,
Callable,
Dict,
List,
Mapping,
Optional,
Sequence,
Set,
Tuple,
Union,
)
import numpy as np
import torch
import torch.nn as nn
from... |
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