sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
ab117214ffa8d10a71d5d39c088bb610279b146dbf5a89bd1997d6479d66cd59 | Python | 26,920 | 537 | """
Reading and writing nnU-Net checkpoints.
nnU-Net writes its checkpoints as safetensors files (`checkpoint_final.safetensors`, `checkpoint_best.safetensors`,
`checkpoint_latest.safetensors`). Checkpoints written by older versions are `torch.save` pickles (`.pth`), and these
are still read, exactly as before.
Why n... |
821afd16d5a6c0bf202b4eaf1c00b6a5b78f0d8dd0b38dadc6fcea5feffd948a | Python | 26,942 | 721 | import torch
import torch.nn as nn
import torch.nn.functional as F
import torch.optim as optim
from torchvision import datasets, transforms
from torch.utils.data import Dataset, DataLoader
from copy import deepcopy
import numpy as np
import matplotlib.pyplot as plt
import argparse
import pdb
import os
import sys
import... |
1d9e74fbd2ccfd16eeb469b4cb987ec49c5da751db8be64be92767b1c3c9c326 | Python | 26,952 | 748 | """
A set of functions and scripts to demonstrate camera calibration and
registration.
Notes:
* Parts of this module uses opencv calibration described here:
https://docs.opencv.org/4.0.0/d9/d0c/group__calib3d.html
* and the Chruco board described here:
https://docs.opencv.org/4.0.0/d0/d3c/classcv_1_1aruco_1... |
413e593d4ab87d4e6d33333a401328a9330bfc75204b45ffe3e0827dacc3bbf9 | Python | 26,953 | 610 | # --- START OF FILE app.py ---
import streamlit as st
import ast
import os
import subprocess
import time
import requests
import getpass
import psutil
from datetime import datetime, timezone
from pathlib import Path
from collections import OrderedDict
# Use our centralized logger setup
from logger_setup import logger
... |
8058859f84e5160330325c022d113c67387750ba52efc2ebd272f423acccff72 | Python | 26,955 | 787 | """
Copyright (c) Meta Platforms, Inc. and affiliates.
This source code is licensed under the MIT license found in the
LICENSE file in the root directory of this source tree.
"""
from __future__ import annotations
import copy
import math
from typing import TYPE_CHECKING
import torch
import torch.nn as nn
from torch... |
0e988bc0ec382adfec51e2bbf552f5dfcf46bc84560a3b81d8437796fd9a0503 | Python | 27,016 | 735 |
import gym
import json
import os
import gym_sted
import pfrl
import torch
import sys
import random
import pickle
import logging
import functools
import numpy
import h5py
from tqdm.auto import trange, tqdm
from matplotlib import pyplot
from collections import defaultdict
from skimage import io
while "../.." in sys.pa... |
d2fdb98bd9de645701121582e615c183dbc3afb55ea004e9a2ada6012422b226 | Python | 27,037 | 595 | import numpy as np
import os
import tifffile as tiff
import random
import math
import torch
from torch.utils.data import Dataset
from skimage import io
def random_transform(input, target):
"""
The function for data augmentation. Randomly select one method among five
transformation methods (including rota... |
158f68a5eab8b30b927a0353dc8439b20190539de7df9abc4441d98975de7798 | Python | 27,039 | 643 | import exputils as eu
import ipywidgets
import pandas as pd
import qgrid
import os
from exputils.gui.jupyter.base_widget import BaseWidget
import IPython
import warnings
# TODO: Feature - allow to filter datasources that should be loaded
# TODO: Feature - progress bar during data loading
# TODO: Bugfix - If the order ... |
226172343fcfdfd93ecd85625a934df919a9731ff60553b28b9cc6f374c49519 | Python | 27,039 | 649 | ####################################################################################################
# Copyright (c) 2016 - 2024, EPFL / Blue Brain Project
# Author(s): Marwan Abdellah <marwan.abdellah@epfl.ch>
#
# This file is part of NeuroMorphoVis <https://github.com/BlueBrain/NeuroMorphoVis>
#
# This program is fre... |
61bb21fa47031ec97fc88804b422e6aed16ee581a8af46738d1d29bf2e431efb | Python | 27,042 | 659 | # Copyright 2021 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, sof... |
253880cb5633cb34c736b1e8f78ffe9c770b13f8d1e68ba9814443c0443bd90d | Python | 27,048 | 713 | import os
import numpy as np
from nibabel import load as load_nii
import nibabel as nib
from operator import itemgetter
from build_model import define_training_layers, fit_model
from operator import add
def train_cascaded_model(model, train_x_data, train_y_data, options):
"""
Train the model using a cascade o... |
ca5afd14fb564a92de2cada9296d4f804f4ccd9fc4c648b0465889ae11dc5061 | Python | 27,061 | 835 | # Copyright 2023 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, sof... |
e9a7f01d3dccc3b0812f05e5b8aef5b421041daeddfe2d876d62b90bc741cdcd | Python | 27,067 | 599 | # Ultralytics YOLO 🚀, GPL-3.0 license
"""
Train a model on a dataset
Usage:
$ yolo mode=train model=yolov8n.pt data=coco128.yaml imgsz=640 epochs=100 batch=16
"""
import os
import subprocess
import time
from collections import defaultdict
from copy import deepcopy
from datetime import datetime
from pathlib import... |
57d2754c095e6e183e2486fb87f9b7225bf2aef5284991796442a1827475d2e7 | Python | 27,082 | 856 | """Abstractions around GCP resources and nodes.
The logic has been abstracted away here to allow for different GCP resources
(API endpoints), which can differ widely, making it impossible to use
the same logic for everything.
Classes inheriting from ``GCPResource`` represent different GCP resources -
API endpoints th... |
a453ff7bee16a2d13f6cb795357faec4b49e7ca86a10d410fb0ac8ecdf65900e | Python | 27,131 | 629 | import torch
import torch.nn as nn
from torch.optim import Optimizer, AdamW
from torch.optim.lr_scheduler import LambdaLR
import numpy as np
from tqdm import tqdm
import os
import platform
from sklearn.model_selection import KFold
from splam_utils import *
from splam_dataset_Chromsome import *
from SPLAM import *
###... |
541d62dfafffb502a10be3d51dd6f24def750b8b447b10e883b888e45e5d428c | Python | 27,159 | 592 | # Copyright 2023 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, sof... |
d3340ebf12488bdafd543d3c7b14ed103d213bc48abaf78eeec53b3fc65c1908 | Python | 27,161 | 849 | """
Segment song motifs by finding maxima in spectrogram cross correlations.
"""
__date__ = "April 2019 - November 2020"
from affinewarp import ShiftWarping
import h5py
from itertools import repeat
from joblib import Parallel, delayed
import matplotlib.pyplot as plt
plt.switch_backend('agg')
try: # Numba >= 0.52
fr... |
5d58c0ca9991436d1ebf7ae18afafe3b464290be824b7510bc779b9cc76f1aa4 | Python | 27,164 | 624 | r"""Image segmentation backends for ``ov.space.seg.segment``.
A backend is built once per call, sees a downsampled copy of the whole image in
:meth:`Backend.prepare` (so intensity scaling is global, not per tile), and is
then called on each window by the tiling engine. Heavy libraries are imported
in ``_build`` only, ... |
16ca9ab4f4d7845a188b5df208f3d51961754ea353ba1a605bcce118dad45291 | Python | 27,165 | 702 | # built-in dependencies
import base64
from importlib.metadata import version as package_version
import os
import shutil
import unittest
from pathlib import Path
from tempfile import TemporaryDirectory
from unittest.mock import MagicMock, patch
# 3rd party dependencies
import gdown
import numpy as np
from flask import ... |
4f59e7e041798b554bb027420eb6edb286d8ebb833c577edd826cc3879f9b7bf | Python | 27,167 | 761 | """Execution tool handlers: execute_code, run_snippet, bash, agent, inspect, search, finish.
Extracted from ``tool_runtime.py`` during Phase 3 decomposition (pass 2).
These handler functions receive explicit dependencies (ctx, executor,
subagent_controller) as parameters rather than accessing ``self`` on
``ToolRuntime... |
9e8c69833542c207709f126326203d1a06f1b09c4d59282b45c31d93249bbf75 | Python | 27,182 | 547 | # Copyright 2023 The HuggingFace Team. 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 applicabl... |
d18ef8a66262dac2407152b3574294fdac1cf47fe60d4ca0c614daf0bb7340b5 | Python | 27,206 | 551 | import numpy as np
import networkx as nx
import os.path
import matplotlib.pyplot as plt
import time
import math
import gc
gc.collect()
import warnings
warnings.filterwarnings("ignore")
import os
os.system('cls' if os.name == 'nt' else 'clear')
plt.rc('font',size=15)
UseDoubleWell=1
RCType=0# Different R... |
e8d21e40bde63c7b29c8db4fef3ec7c8583cc3631526bae661fa84d0dc3541f8 | Python | 27,220 | 558 | import numpy as np
import networkx as nx
import os.path
import matplotlib.pyplot as plt
import time
import math
import gc
gc.collect()
import warnings
warnings.filterwarnings("ignore")
import os
os.system('cls' if os.name == 'nt' else 'clear')
plt.rc('font',size=15)
UseDoubleWell=1
RCType=0# Different R... |
f58c9b50e74c2d153a1685a57ba640a71c27bb5d37c3419bd439786b4bab3de0 | Python | 27,227 | 697 | import asyncio
import logging
from concurrent.futures import ThreadPoolExecutor
from itertools import islice
from typing import List, Optional
import ray.dashboard.memory_utils as memory_utils
from ray import NodeID
from ray._common.utils import get_or_create_event_loop
from ray._private.profiling import chrome_tracin... |
6154db67fc324a56445e0773bc4e186dd0f6530a7586f1b4bfc30ec59234ed62 | Python | 27,235 | 678 | from sklearn.neighbors import NearestNeighbors
from scipy.sparse import diags
from scipy.sparse import csr_matrix
from scipy.spatial.distance import cdist
from .init_pca import init_pca
from .pca import pca
from .mds import mds
import scipy.sparse.linalg as sp_linalg
import numpy as np
import math
from tqdm i... |
09fb6518b507aaa84792f7fa80c93ca7b04cda24f9710f6e6c6ed91ade6ddb5f | Python | 27,236 | 817 | import json
import logging
import os
import shutil
import subprocess
import sys
import tempfile
import time
from pathlib import Path
from typing import Optional
from unittest.mock import patch
import pytest
import yaml
import ray
from ray._common.test_utils import wait_for_condition
from ray._private.runtime_env.pack... |
87921995821a820da97b32467733e7d030927b71cb03a7d572b120699f481cd0 | Python | 27,238 | 694 | ####################################################################################################
# Copyright (c) 2016 - 2024, EPFL / Blue Brain Project
# Author(s): Marwan Abdellah <marwan.abdellah@epfl.ch>
#
# This file is part of NeuroMorphoVis <https://github.com/BlueBrain/NeuroMorphoVis>
#
# This program is fre... |
deb6564228658682e8314b428029cbb05bb49bc3b73649444320a3f6294276a8 | Python | 27,253 | 622 | # Copyright 2023 TSAIL Team and The HuggingFace Team. 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 requir... |
2cbf7af26e9128268d344c2bb039f04df78269460b2c6c35f95947cd2bfe8bb4 | Python | 27,259 | 638 | ####################################################################################################
# Copyright (c) 2016 - 2024, EPFL / Blue Brain Project
# Author(s): Marwan Abdellah <marwan.abdellah@epfl.ch>
#
# This file is part of NeuroMorphoVis <https://github.com/BlueBrain/NeuroMorphoVis>
#
# This program is fre... |
f325d370d64ec8eda463d4193b93b49a2b781dfbbf574bd66cbe229ef4c9e7ec | Python | 27,259 | 726 | import sys, os
import math
import time
import numpy as np
from pathlib import Path
ROOT_DIR = Path(__file__).parent
import tensorflow as tf
from apnet.keras_pair_model import KerasPairModel
from apnet import constants
class PairDataLoader:
""" todo """
def __init__(self, dimers, energies, r_cut, r_cut_im):... |
1f7f3e01cbf1575a48e5d1de67fa1259168b1e860e8e3c6e818123e93370064d | Python | 27,260 | 682 | import glob
import torch.utils.data as data
from PIL import Image
import torch
import sys
import os
import numpy as np
from tifffile import imread
sys.path.append('..')
from csbdeep.utils import normalize, axes_dict, axes_check_and_normalize, backend_channels_last, move_channel_for_backend
from csbdeep.io import load_t... |
157fa570bd9e61dca9af21df245a65337de06fcdea61f4e45b492159611e46ae | Python | 27,267 | 703 | import os, time, glob, shutil
import multiprocessing as mp
import matplotlib
# NOTE: we intentionally do NOT force a non-interactive backend at import time. Doing so
# (matplotlib.use('Agg')) used to silently break inline plotting in notebooks that imported
# motionmapperpy. The few functions here that *save* figures ... |
aff04a7191f27ac6ef58698effe8c6bd742cae30338f4e3ed5d592dbf3893d1c | Python | 27,298 | 472 | import abc
import datetime
import queue
import os
import statistics
import tarfile
import time
import projectmetis.python.utils.proto_messages_factory as proto_messages_factory
from fabric import Connection
from google.protobuf.json_format import MessageToDict
from pebble import ThreadPool
from projectmetis.python.ut... |
699dfc8dd7e97463f85a4fd2bdc4081e41473b250252b226de26760e12410444 | Python | 27,303 | 834 | import numpy as np
import matplotlib.pyplot as plt
from matplotlib.widgets import TextBox,Button
from matplotlib.animation import FuncAnimation
from tqdm import tqdm
from scipy import optimize
import os
import json
SpineWidth = 1000
class SpatialModel():
def __init__(self,CParams,P0Params,gamma,zetaS,FParams,C0Pa... |
c4b9d5352c9dda567513dfe26d8da8fd192af3f740fb949d478ac2356af86cc0 | Python | 27,312 | 773 | import math
from functools import partial
from typing import Optional, Tuple, Union, Sequence
import numpy as np
import torch
import torch.nn.functional as F
from einops import rearrange, repeat
from torch import nn
from x_transformers.x_transformers import (
TokenEmbedding,
AbsolutePositionalEmbedding,
de... |
c9cb9b19782ecda7ab0bbdd138e36ec9f2e3153e4d0619b559ae46deb5ea3b82 | Python | 27,323 | 719 | """I/O for single-cell immune-repertoire (AIRR-seq) data.
This module reads TCR / BCR sequencing output into an :class:`anndata.AnnData`
object using a clean, documented per-cell receptor data model — an
omicverse-style reimplementation of the relevant parts of scirpy's reader.
Data model
----------
After reading, th... |
e4c1fc371b1cd8c53b067c50c35dd794d3f8f257860e9a949708bee781797037 | Python | 27,354 | 926 | import numpy as np
import matplotlib.pyplot as plt
import os
import pickle
import settings
import matplotlib.collections as mcoll
from numba import njit, jit
from scipy.ndimage import gaussian_filter
from sklearn.linear_model import LinearRegression
from math import remainder
@njit(parallel=True, fastmath=True, nogil... |
b841d8d14b305aad95170ae3ca59d12a93ef6807b4e2d6cc6ad900efe5cf86fb | Python | 27,392 | 756 | # Copyright 2026 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, ... |
ea5c6b38014670e4bf38792255b8d392725ce816db46f61fc799686a0e752c3d | Python | 27,398 | 712 | # Copyright 2021 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, sof... |
91de04af473ef437fa9dfd10b4821c67f2448d6d73488bf0bbba57ff50549a6a | Python | 27,402 | 467 | import numpy as np
import sys
class BeliefHistoryTabularRL():
# state is a concatenated string of previous history observations
# separator is used to separate observations
separator = '*'
def __init__(self, env, policy=1, alpha=0.1, epsilon=0.1, seed=None,
exploration_decay=False, exp... |
fd17b83c10cf216fe405104271c9becabb083f72e64bedf549b660f1bc87fa81 | Python | 27,402 | 651 | ####################################################################################################
# Copyright (c) 2020, EPFL / Blue Brain Project
# Author(s): Marwan Abdellah <marwan.abdellah@epfl.ch>
#
# This file is part of NeuroMorphoVis <https://github.com/BlueBrain/NeuroMorphoVis>
#
# This program is free softw... |
04eb6dcf5038b07ebc2a1a422d64ecb8e2d3ed6c1117a04e86be7ccaa9e80a35 | Python | 27,448 | 778 | ####################################################################################################
# Copyright (c) 2016 - 2024, EPFL / Blue Brain Project
# Author(s): Marwan Abdellah <marwan.abdellah@epfl.ch>
#
# This file is part of NeuroMorphoVis <https://github.com/BlueBrain/NeuroMorphoVis>
#
# This program is fre... |
48e592eb2d9a0bf57ceef22f17be5466188743e857c245acb8644c24f0656986 | Python | 27,471 | 685 | import base64
import ipaddress
import logging
import os
import random
import string
from enum import Enum
from threading import RLock
from typing import Any, Dict, Optional, Tuple
from kubernetes import client, config
from ray.autoscaler.tags import (
NODE_KIND_HEAD,
NODE_KIND_WORKER,
STATUS_SETTING_UP,
... |
77680620948815a65cf62b6932cc8738ef3c0db3eff50849732322c589b4cb75 | Python | 27,484 | 652 | ####################################################################################################
# Copyright (c) 2020, EPFL / Blue Brain Project
# Author(s): Marwan Abdellah <marwan.abdellah@epfl.ch>
#
# This file is part of NeuroMorphoVis <https://github.com/BlueBrain/NeuroMorphoVis>
#
# This program is free softw... |
e35d00976566dbad5ff684b122c051b4be43839a2f6c122bd315e87e46258bf0 | Python | 27,487 | 685 | from __future__ import annotations
import logging
import math
import numbers
from collections.abc import Callable, Iterable
from dataclasses import dataclass
from typing import TYPE_CHECKING, Any, List, Optional
import numpy as np
from ray.data._internal.delegating_block_builder import DelegatingBlockBuilder
from ra... |
13920964546a022b9ea4128c26ef48cea3c23beaf3724600dbaa66c9560771a0 | Python | 27,494 | 744 | # 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, ... |
ebb00297368d2b1e7a52b6a8857c9c6b8f1fad1f5a0bff8da97da9976f482cc3 | Python | 27,534 | 642 | import json
import time
from pathlib import Path
from typing import Dict, Iterable, List, Literal, Optional, Union
import inspect
import numpy as np
import pandas as pd
from scipy import sparse
from omicverse.external.scTenifold.core._networks import *
from omicverse.external.scTenifold.core._networks import anndata_... |
cff20de0f80bc4fd7d186c8d359c226f7700a24a5c897a0fb78da09c03d15505 | Python | 27,538 | 672 | # -*- coding: utf-8 -*-
# (C) Copyright 2026 IBM. All Rights Reserved.
#
# Licensed under the MIT license. See LICENSE file in the project root for details.
"""Weight Programming Optimization implementation which is similar to the framework
reported in the following paper:
C. Mackin, et al., "Optimised weight pr... |
eeebaaeb804a5bac7fe38f97387b9c8117039127bb6b0f8f3f083b92b6d67073 | Python | 27,589 | 624 | #!/usr/bin/env python
# ================================
# @auther: Rongbin Zheng
# @email: Rongbin.Zheng@childrens.harvard.edu
# @date: May 2022
# ================================
import os,sys
import time
import pickle as pk
from datetime import datetime
import numpy as np
import pandas as pd
import traceback
from ... |
b6120b0540a87fba9ce74863335effe2856c32f3f42f35d3a28f6fb0d70d4597 | Python | 27,600 | 736 | #
# CEBRA: Consistent EmBeddings of high-dimensional Recordings using Auxiliary variables
# © Mackenzie W. Mathis & Steffen Schneider (v0.4.0+)
# Source code:
# https://github.com/AdaptiveMotorControlLab/CEBRA
#
# Please see LICENSE.md for the full license document:
# https://github.com/AdaptiveMotorControlLab/CEBRA/bl... |
d0d8ef969e629155d06ba059a40d3d409872a3b5c014d6d499cc4fc3ca3990a5 | Python | 27,642 | 660 | r"""Terminator strength, and compiling a truth table into DNA.
Two holes at the circuit layer.
``promoter_strength`` and ``rbs_strength`` existed; the third part of every
transcription unit did not. :func:`terminator_strength` scores intrinsic
(Rho-independent) terminators from their structure — hairpin stem stabilit... |
41a680ed30ba40fa6abcb138931bc4440956a5c5d80c89e40797050008a907bd | Python | 27,690 | 706 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
""" functions that creates image from a video file
Primarily intended for plotting, returns correlation images ( local or max )
See Also:
------------
@author andrea giovannucci
"""
from builtins import range
import cv2
import logging
import numpy as np
from scipy.ndim... |
d46d2a0b50d866a5b7acd55c34a42b4787564244ca921960fd06fce26ffc8bb2 | Python | 27,696 | 673 | import threading
from collections import OrderedDict
from random import Random
from typing import Dict, Iterator, List, Optional, Union
import numpy as np
from torch.utils.data import DataLoader, Dataset, Sampler
from rdkit import Chem
from .scaler import StandardScaler
from GR_pKa.features import get_features_genera... |
432b389f20800da1a98479a285a093578d4573dfdaf3aa6e270553f6a757145f | Python | 27,699 | 811 | import os
import logging
import random
from math import sqrt
import networkx as nx
import numpy as np
import torch
import torch.nn as nn
import torch.nn.functional as F
from rdkit.Chem import AllChem
from scipy import stats
from sklearn.metrics import roc_auc_score
from datasets import (
graph_data_obj_to_nx_simpl... |
e3b640a397837cbb6c549d1e8db70f664dfc1b0036782a8da6d1f32499e592db | Python | 27,699 | 618 | #!/usr/bin/env python3.7
"""Defines Query class.
The copyrights of this software are owned by Duke University.
Please refer to the LICENSE and README.md files for licensing
instructions. The source code can be found on the following GitHub
repository: https://github.com/wmglab-duke/ascent
"""
import os
import pickle... |
b2e2f71192f0a0554b27b0de5b1af1c2ff268ce9637d75b5cacfd065cf980f96 | Python | 27,700 | 587 | import matplotlib
import matplotlib.pyplot as plt
import networkx as nx
import seaborn as sns
import scanpy as sc
import numpy as np
import pandas as pd
from typing import Union, Sequence, List, Tuple, Optional, Iterable
from matplotlib.axes import Axes
palette_network = list(sns.color_palette("tab20") \
... |
dd64ba4b1ba1f40bb2e959506f9d978e82793053a8de2e99c53a82f4901179cc | Python | 27,711 | 890 | import numpy as np
import pyro
import torch
import scipy.stats as sts
import sklearn.preprocessing as skp
import sklearn.metrics.pairwise as skmp
import pyro.contrib.gp as gp
import general.pyro_utility as gpu
import general.neural_analysis as na
import general.utility as u
import pyro.distributions as distribs
import... |
b585897fd86e5762b7e057ec45811da1b1daddb0943f5af1814535c184210c14 | Python | 27,712 | 470 | # Copyright 2021 Division of Medical Image Computing, German Cancer Research Center (DKFZ)
# and Applied Computer Vision Lab, Helmholtz Imaging Platform
#
# 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 L... |
5c383b55ffd31153c8095689c72ac57fbe9a1bfd6368533c569bf8a79bb69cd8 | Python | 27,716 | 744 | # 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, ... |
a84cf64465889a1f1d7d7cbd900ec1d16f9b806b38af61f04a95be426bbec55a | Python | 27,716 | 726 | """GPU providers for monitoring GPU usage in Ray dashboard.
This module provides an object-oriented interface for different GPU providers
(NVIDIA, AMD) to collect GPU utilization information.
"""
import abc
import enum
import logging
import os
import re
import subprocess
import time
from typing import Dict, List, Opt... |
9c03048219de0466cbc5fb04bf7514983d7353262c6d95352832cb690b92286c | Python | 27,722 | 697 | """
Copyright (c) Meta Platforms, Inc. and affiliates.
This source code is licensed under the MIT license found in the
LICENSE file in the root directory of this source tree.
"""
from __future__ import annotations
import functools
import logging
import types
import warnings
from typing import TYPE_CHECKING
import n... |
81220b5eca8644299ac87588e18e87a63b8b39acaf7b0c9af84549a1541dc117 | Python | 27,739 | 509 | import torch
import torch.nn as nn
import numpy as np
from tqdm import trange
class gru_prepare(nn.Module):
def __init__(self, input_size, hidden_size, output_size, num_layers=1):
super(gru_prepare, self).__init__()
self.input_size = input_size
self.output_size = output_size
... |
9195e2c9048c196e9f7f13a0f424f1f89e5d58b522fe99dc796a80e81e65f7c9 | Python | 27,756 | 594 | import math
import numpy as np
#from vedo import *
import random
import sys
import argparse
import copy
from pyknotid.spacecurves import Knot
from pyknotid.spacecurves import Link
import top_funcs
import networkx as nx
visitedList = []
ring_links = []
def compute_linking_number(K,L):
K = np.asarray(K)
L = np... |
18c3635a25a65aca11301baa5faa5b02027d26f2db93a11509f91e0403958906 | Python | 27,764 | 1,053 | import numpy as np
import matplotlib
import matplotlib.pyplot as plt
import settings
import os
import pickle
from utils.grid_funcs import (
traj,
traj_pwl,
gridpop_clustering,
gen_offsets
)
from utils.utils import (
grid_meanfr,
get_hexsym,
get_pathsym,
convert_to_rhombus,
ax_pos
)
f... |
49f0ec648bf4efc0691ad012484be221413924f46da5531a4db656f241a9fec9 | Python | 27,768 | 675 | import gym
import numpy
import random
import pysted.base
from gym import error, spaces, utils
from gym.utils import seeding
from matplotlib import pyplot
from collections import OrderedDict
import gym_sted
from gym_sted import rewards, defaults
from gym_sted.utils import SynapseGenerator, MicroscopeGenerator, get_for... |
70d62fb71af634335bdcc26869ff4f42019e58e4d5153a1d022b8430709d1f93 | Python | 27,769 | 862 | #!/usr/bin/env python
import fmm3dpy as fmm
import numpy as np
import numpy.linalg as la
def main():
test_lfmm()
def test_lfmm():
ntests = 54
testres = np.zeros(ntests)
#
# This is a testing code for making sure all the
# fmm routines are accessible through fmm3d.py
#
n = 2000
... |
884b794d0c39d67c1858b636dcb61504c81b8df83ba70fc5c5ffeb008bba4827 | Python | 27,805 | 606 | import torch
from torch import Tensor
import torchvision
import torch.nn as nn
#from .utils import load_state_dict_from_url
from typing import Type, Any, Callable, Union, List, Optional
__all__ = ['ResNet', 'resnet18', 'resnet34', 'resnet50', 'resnet101',
'resnet152', 'resnext50_32x4d', 'resnext101_32x8d',... |
ffa1f72c9a0d66c6218cdf30705cb079ab719b5c9fc87f1417a7c954912de8c1 | Python | 27,814 | 710 | import pandas as pd
import numpy as np
import plotly
import os
import matplotlib as mpl
import matplotlib.pyplot as plt
import networkx as nx
from sklearn.neighbors import NearestNeighbors
from sklearn.preprocessing import normalize
from scipy.stats import norm
def get_cmap_qualitative(cmap_name, n_colors=None):
"... |
f11a345f8ff886e83a57ff20ad2bd2eb27183834731e5941f2a37ddee40d6f37 | Python | 27,848 | 896 | """Additional classes and functions needed for slab handling."""
import pathlib
from typing import Callable, NamedTuple, Tuple
import ase.atoms
import numpy as np
import numpy.typing as npt
from ase.build import sort
from ase.calculators.calculator import Calculator
from ase.constraints import FixAtoms
from ase.geome... |
f83006d35ef56888fba4382ecf83d8592100e1f3721f9925d4b47caf9ab63286 | Python | 27,862 | 600 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
# -------------------------------------------------------------------------
# Created By : Kangjoo Lee (kangjoo.lee@yale.edu)
# Last Updated: 08/06/2024
# -------------------------------------------------------------------------
# =========================================... |
2dbd24451d5dd1430b95ce772f901c3b609c8eda0795e1a7da8d8f931b57a9f1 | Python | 27,876 | 762 | import logging
import random
from typing import (
TYPE_CHECKING,
Any,
Callable,
Dict,
Iterator,
List,
Mapping,
Optional,
Tuple,
TypeVar,
Union,
)
import numpy as np
import pandas as pd
import pyarrow
from packaging.version import parse as parse_version
from ray._common.util... |
5a93c3f58f7a7fc3890ea30d320fc01526ef62bc179649df279d98300759aa16 | Python | 27,923 | 648 | ####################################################################################################
# Copyright (c) 2016 - 2024, EPFL / Blue Brain Project
# Author(s): Marwan Abdellah <marwan.abdellah@epfl.ch>
#
# This file is part of NeuroMorphoVis <https://github.com/BlueBrain/NeuroMorphoVis>
#
# This program is fre... |
76dbaa04bc7d8b943c5e6c46f4dd1291fc89f4c0fa36f86f6be7602ce48141ce | Python | 27,924 | 751 | # Modified from https://github.com/dbolya/tide
# This work is licensed under MIT license.
import math
import os
from collections import OrderedDict, defaultdict
import numpy as np
from pycocotools import mask as mask_utils
from .ap import ClassedAPDataObject
from .data import Data
from .errors import (BackgroundError... |
0f90c3889ebe0bc5e8a2ba42fd3468a4607741b011f5ae7f8b0907cb47523aa6 | Python | 27,930 | 709 | import argparse
import hashlib
import logging
import math
import os
from pathlib import Path
from typing import Optional
import jax
import jax.numpy as jnp
import numpy as np
import optax
import torch
import torch.utils.checkpoint
import transformers
from flax import jax_utils
from flax.training import train_state
fro... |
1682e41fd890febd7e5197842fdd07cb0ba12b425fc42e08e8d1e62df0e3a587 | Python | 27,960 | 739 | """Autoscaler monitoring loop daemon."""
import argparse
import json
import logging
import os
import signal
import sys
import time
import traceback
from collections import Counter
from dataclasses import asdict
from typing import Any, Callable, Dict, Iterable, List, Optional, Union
import ray
import ray._private.ray_... |
85bfd5218a6378475af6bdcbfe7962f55c2462a33c4479c7ca4fc5a1ea7a0545 | Python | 27,982 | 882 | import logging
import pickle
from dataclasses import dataclass
from functools import wraps
from typing import (
TYPE_CHECKING,
Dict,
Generator,
Iterable,
List,
Optional,
Tuple,
TypeVar,
Union,
)
import matplotlib.pyplot as plt
import numpy as np
import numpy.typing as npt
from matpl... |
95d4e88aeec47190c3084f3c7e2532b0643635989e233929412d8be7f572767d | Python | 28,001 | 654 | # -*- coding: utf-8 -*-
"""General utility functions and dynamic simulation tools used in neural space-time model paper."""
from typing import Tuple, Union, List
from os import path
import yaml
import numpy as np
from PIL import Image
from flax.struct import dataclass
from skimage import data, transform
import skimage... |
e251c157714610bee81881ef37d61c35f25f40d8f41363dfb3e255f517f5595d | Python | 28,008 | 711 | # --------------------------------------------
# Class for computing modules on adata object:
# Updated: 06/13/21
# OUTDATED, use SCMODULE package instead
# --------------------------------------------
import glob
import h5py
import re
import gzip
import numpy as np
import pandas as pd
import time
import gc
import os
i... |
f2564f1280dcb7bfd03df0084e09148ce748babb411d8a400458f6a4bba1ad75 | Python | 28,010 | 726 | # -*- coding: utf-8 -*-
# (C) Copyright 2020, 2021, 2022, 2023, 2024, 2025 IBM. All Rights Reserved.
#
# Licensed under the MIT license. See LICENSE file in the project root for details.
# pylint: disable=too-many-locals, too-many-arguments, possibly-used-before-assignment
"""Low level implementation of torch-based ... |
9ec8b6faf50155f6c16911453efdd393842f8ad8001f54f6fea0c92aef6bcb59 | Python | 28,032 | 682 | import math
import numpy as np
import torch
from ..utils import common_functions as c_f
# input must be 2D
def logsumexp(x, keep_mask=None, add_one=True, dim=1):
if keep_mask is not None:
x = x.masked_fill(~keep_mask, c_f.neg_inf(x.dtype))
if add_one:
zeros = torch.zeros(x.size(dim - 1), dty... |
884534005036f901f3f977babf0be469c6de559715e0389c6eebd2ec4fc8e119 | Python | 28,045 | 784 | """Phase diagram analysis
"""
import multiprocessing as mp
from itertools import repeat
import numpy as np
import matplotlib.pyplot as plt
def fit_pmem(data, iter_max : int = 5000000, error_max=1e-8, eta=.05,
method='donders', init_zero=False, verbose=False):
"""Fit binary multichannel data to the ... |
2ed519e9dd2584310e5736edb6d8a21f623179203776e93f407fe656a33844a4 | Python | 28,054 | 838 | #
# CEBRA: Consistent EmBeddings of high-dimensional Recordings using Auxiliary variables
# © Mackenzie W. Mathis & Steffen Schneider (v0.4.0+)
# Source code:
# https://github.com/AdaptiveMotorControlLab/CEBRA
#
# Please see LICENSE.md for the full license document:
# https://github.com/AdaptiveMotorControlLab/CEBRA/bl... |
2a1679826b22ab4fb0cd706cd9779a358292027cdf0998c55d7d9908bb101622 | Python | 28,083 | 747 | """
Data reading functions for OmicVerse.
This module provides functions for reading spatial transcriptomics data,
particularly from SpaceRanger output (both bin-level and cell segmentation data).
"""
import pandas as pd
import numpy as np
import json
import os
import sys
from pathlib import Path
from typing import L... |
f2fd475addc4a587e3ed4c046e081b2c62fb67b3f0e94092cf53f2c1da13c39d | Python | 28,103 | 591 | ####################################################################################################
# Copyright (c) 2016 - 2024, EPFL / Blue Brain Project
# Author(s): Marwan Abdellah <marwan.abdellah@epfl.ch>
#
# This file is part of NeuroMorphoVis <https://github.com/BlueBrain/NeuroMorphoVis>
#
# This program is fre... |
2821babc9dea88910dfd71ad05e37a043dfa87c6e540bb7f117311d6cd99261d | Python | 28,111 | 670 | #!/usr/bin/env python
#### OBSOLETE
#### OBSOLETE
#### OBSOLETE
#### OBSOLETE
#### OBSOLETE
import argparse
import os
import sys
import json
import itertools
import dxpy
import dxencode as dxencode
#from dxencode import dxencode as dxencode
import json
# NOTES: This command-line utility will run the long RNA-seq pipe... |
8b5316b9d210f9ab0ce3b56b5ba55c54a9411aee059ad7af689b0778577e1c88 | Python | 28,141 | 508 | # -*- coding: utf-8 -*-
import math
import copy
import os
import torch
import random
import anndata
#import cmcrameri
import numpy as np
import scanpy as sc
import networkx as nx
import torch.nn as nn
import matplotlib.pyplot as plt
from scipy.spatial import distance_matrix
from torch_geometric.nn import GCNConv, Deep... |
7d0b5a87bd3bb95ca595bac3f98d0638245fd82573f1a4c354cc4c5530e1e183 | Python | 28,145 | 546 | # -*- coding: utf-8 -*-
"""
# # SCRIPT: TRAINING THE DECODING MODEL USING FMRI DATA
# # PROJECT: FMRIREPLAY
# # WRITTEN BY QI HUANG 2022
# # REFERENCED TO LENNART WITTKUHN, SCHUCK NICOLAS, 2021
# # CONTACT: STATE KEY LABORATORY OF COGNITIVE NEUROSCIENCE AND LEARNING, BEIJING NORMAL UNIVERSITY
"""
# In[1]: import releva... |
73b1f918d8ca77f7aa15382f6be1d807b49560bd326e37700c4bab6abff249d0 | Python | 28,159 | 879 | #######################################################################################################################
# This script handels the loading and processing of the input dataset for cell segmentation with Unet #
# Contains the pytorch lightning DataModule ... |
dc32d3414e29173b2af582683c2399d128b00645fe6d33bc23c6f03bf734bae1 | Python | 28,168 | 739 | from __future__ import annotations
import re
from functools import lru_cache
from pathlib import Path
from typing import Mapping
import numpy as np
import pandas as pd
import scanpy as sc
from .._registry import register_function
_LIANA_PRIMARY_COLUMNS = ("source", "target", "ligand_complex", "receptor_complex")
_... |
7864e23bb3d950cd38ba7b8eb7fcf9767b3cf81998b677d31604f6322177f28b | Python | 28,175 | 741 | import argparse, os, sys, datetime, glob, importlib, csv
import numpy as np
import time
import torch
import torchvision
import pytorch_lightning as pl
from packaging import version
from omegaconf import OmegaConf
from torch.utils.data import random_split, DataLoader, Dataset, Subset
from functools import partial
from ... |
f85d3a861fffcaa6f9c4da54ad4eb8e47610e52f3e3bc13208a7ba0596a47c56 | Python | 28,206 | 697 | import logging
import sys
from pprint import pformat
from scipy.sparse import coo_matrix, vstack
from typing import Dict, List, Optional, Union, Set
import numpy as np
import pandas as pd
import copy
import torch
from deeprvat.utils import calculate_mean_std, standardize_series_with_params
logging.basicConfig(
fo... |
6f6c02b3f7f2527fd19fa1050ffb82cd3f4996fcab3616d5fec440bc10215291 | Python | 28,209 | 538 | from setup import *
def get_general_ts_all(test_type):
"""
A generic function used to get all the rows of a specific general touchscreen test. After the csv is generated, it
will ask for the user to save the file in a directory. Used for Habituation 1 and 2, Initial Touch, Must Touch,
and Mus... |
fed80012c5b7ca4d0ddbce4c37920b09ae7426eb7a13c832076fd6ac5f9efd78 | Python | 28,217 | 874 | import copy
import json
import logging
import os
import re
import time
from functools import partial, reduce
import google_auth_httplib2
import googleapiclient
import httplib2
from google.oauth2 import service_account
from google.oauth2.credentials import Credentials as OAuthCredentials
from googleapiclient import dis... |
dda9830e31c6e4198b3693223e179048af1fe459439ca0a06b20ea9242ee37dd | Python | 28,260 | 720 | #
# CEBRA: Consistent EmBeddings of high-dimensional Recordings using Auxiliary variables
# © Mackenzie W. Mathis & Steffen Schneider (v0.4.0+)
# Source code:
# https://github.com/AdaptiveMotorControlLab/CEBRA
#
# Please see LICENSE.md for the full license document:
# https://github.com/AdaptiveMotorControlLab/CEBRA/bl... |
04c3be0314b32793ea7398cc287cb35a01a9ea1e352b5f9c48da21ff937f3ba8 | Python | 28,267 | 655 | # coding: utf-8
import argparse
import time
import math
import os
import copy
import torch
import torch.onnx
import torch.nn as nn
import torch.optim as optim
import numpy as np
import logging
import random
import data
torch.multiprocessing.set_start_method('spawn')
torch.set_num_threads(16)
###... |
9be07a304bbdd41f1bd6be937ad9a4aebc88d4d6397bffefdf3beae0bed010fd | Python | 28,281 | 771 | """
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 datetime
import errno
import json
import logging
import os
import random
import subprocess
from abc import ABC, abstractmethod
from col... |
3b61f88a62783fa54eda8a7c29afa28128a140649a22f765bac6cecbbdd3dc13 | Python | 28,282 | 730 | r"""
This module contains the definition of the AnalysisDataStructure API and implementation of some basic analysis data structures.
For more documentation refer to :doc:`mozaik.analysis`
"""
import mozaik
import numpy
from mozaik.tools.mozaik_parametrized import MozaikParametrized, SNumber, SInteger, SString
logger ... |
78c37cabed35cc1f1cd652cb42f34d337df47516b0fdf8f81f7d5054f5e62a85 | Python | 28,320 | 718 | import contextlib
import math
import re
import time
import cv2
import numpy as np
import torch
import torch.nn.functional as F
import torchvision
from ultralytics.yolo.utils import LOGGER
from .metrics import box_iou
class Profile(contextlib.ContextDecorator):
"""
YOLOv8 Profile class.
Usage: as a deco... |
4217c2922eb4292209737636343e55e419bfdf2361c93a511b92d9416f98cabf | Python | 28,331 | 582 | ####################################################################################################
# Copyright (c) 2023, EPFL / Blue Brain Project
# Author(s): Nadir Roman <nadir.roman@epfl.ch>
# Adrien Fleury <adrien.fleury@epfl.ch>
# Marwan Abdellah <marwan.abdellah@epfl.ch>
#
# This file is p... |
91dba053c5eeb1f6fbcb0a9c6e522a7492483e178d8435e1644b27fa7fd84d72 | Python | 28,331 | 704 | #!/usr/bin/env python
# ============================
# ===== EXPERIMENT SETUP =====
# ============================
# ----- CALLING PACKAGES -----
from __future__ import absolute_import, division
from psychopy import prefs
from psychopy import sound, gui, visual, core, data, event, logging, clock, colors
from psychopy... |
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