sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
238ede770552f6ff012ec035f192699263f6e805665727006a30a65e60f6d27d | Python | 44,652 | 907 | """
PLS Discriminant analysis script.
Includes bootstrap and permutation. Examples in run.py as run_pls*(...)
"""
import numpy as np
import pandas as pd
import scanpy as sc
import matplotlib.pyplot as plt
from joblib import Parallel, delayed
from numpy.random import default_rng
from scipy.stats import pearsonr, ke... |
50ac5efa8b8be1cf10f409c1e62bb01659caf3d02397531243192a7d0aeb0d9b | Python | 44,698 | 1,178 | from contextlib import nullcontext
import os
from pathlib import Path
from types import SimpleNamespace
from unittest.mock import MagicMock, Mock
from chemgraph.models.supported_models import supported_argo_models
from ui._pages import main_interface as main_ui
from ui.message_utils import extract_molecular_structure,... |
e9229c92a86536956dacf30ee4a1c6e5bbe471ca67c463952f917be0e7ac62b0 | Python | 44,820 | 1,186 | """Functions in this module are responsible for mapping type annotations to widgets."""
from __future__ import annotations
import datetime
import inspect
import itertools
import os
import pathlib
import sys
import types
import warnings
from collections import defaultdict
from collections.abc import Callable, Iterator... |
b7e1479ecca2aabc1a00fb777933f5f65aac4c5ec29a30067754c4e57d9b4429 | Python | 44,855 | 1,193 | # Copyright (c) Meta Platforms, Inc. and affiliates. All Rights Reserved
import contextlib
import fnmatch
import gc
import json
import logging
import math
import os
import time
from collections import OrderedDict
from dataclasses import dataclass, field
from typing import Any, Dict, List, Mapping, Optional
import num... |
daf6f832099986864d87adfec62d69d2127399ca7b96f0ebbd2ce18caab55742 | Python | 44,855 | 1,193 | # Copyright (c) Meta Platforms, Inc. and affiliates. All Rights Reserved
import contextlib
import fnmatch
import gc
import json
import logging
import math
import os
import time
from collections import OrderedDict
from dataclasses import dataclass, field
from typing import Any, Dict, List, Mapping, Optional
import num... |
42f413e4de36b4cbb539f09270f6ef04ad80b1ce4a26a6a79724312a1f9f2cff | Python | 44,873 | 1,022 | # Generated by the protocol buffer compiler. DO NOT EDIT!
from google.protobuf import descriptor
from google.protobuf import message
from google.protobuf import reflection
from google.protobuf import descriptor_pb2
# @@protoc_insertion_point(imports)
DESCRIPTOR = descriptor.FileDescriptor(
name='vgg_caffe.proto'... |
a7144247839a9e0af79bddd553063ee99d102bfbf8c429f56c56cb052ef1b5fe | Python | 44,884 | 1,305 | # Copyright 2019 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, ... |
032478aa44f3d8edd14382f1a527cf880ce7c1879421a8639af477da6bdab84d | Python | 44,886 | 981 | """Run cross-day cell tracking over a dataset.
Ties the pieces together in the order the design requires:
1. group recordings into chains (``chains``)
2. rasterise iscell-filtered footprints (``footprint``)
3. solve robust per-session offsets (``register``)
4. **gate**: chains in which no session would move by ``min_... |
95eb477dcabf63c64948bfa8af5baf6819c9f01deda8d7e6545bd0addac96a15 | Python | 44,937 | 975 | """A local web viewer for a ``.meanap`` bundle.
Express mode ships data instead of pictures; this serves the pictures back on
demand. The front end is HTML so the figures live where people already read
things, and so vector output is a click away rather than a file dialog; the
back end is the same Python that drew the... |
b42ae8a60b019f0f437c9f363f2021f3fa2d007fe3c1e937c3c0c079f5303956 | Python | 44,943 | 1,108 | from sklearn.cluster import AgglomerativeClustering
from sklearn.decomposition import PCA
from sklearn.cluster import KMeans
from scipy.stats import rankdata
import scanpy as sc
import pandas as pd
from anndata import AnnData
import warnings
from builtins import int
warnings.filterwarnings('ignore')
import losses, mi... |
d8bdba31cf6dcc495678974fc39d8ae5893d63fc73229715c879584b6f6f1dbe | Python | 44,943 | 969 | import torch
torch.multiprocessing.set_sharing_strategy('file_system')
import matplotlib
matplotlib.use('Agg')
import os
import os.path as osp
from torch.utils.data import DataLoader
import sys
os.chdir('/project/roysam/rwmills/repos/cluster-contrast-reid/')
print(os.getcwd())
# print(os.listdir())
import os #RWM
prin... |
3ffadaf81e629c319dfd36eec179ec8fd1300472e94f8ae8083c50ae772903ef | Python | 44,968 | 1,462 | import warnings
import matplotlib as mpl
import matplotlib.gridspec as gridspec
import matplotlib.pyplot as plt
import numpy as np
from matplotlib.collections import LineCollection
from scipy import signal
from .. import auxiliary, core
from . import utils # import plotting/utils
from .helpers import RasterLabelData... |
c3bb43e7f30f0298c94d1f2f5a27022f807fcf815a7893c88163411527f2eac0 | Python | 45,090 | 1,144 | #############################################################################
# Copyright (C) 2020-2026 MEmilio
#
# Authors:
#
# Contact: Martin J. Kuehn <Martin.Kuehn@DLR.de>
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may... |
abee69ff4af3519da4301a4249315106ded591fb414ce9fe4bdf44aab2137c05 | Python | 45,130 | 933 | import numpy as np
import pandas as pd
import scipy as s
import sys
from time import sleep
from time import time
from typing import List, Optional, Union
from itertools import chain
from mofapy2.core.BayesNet import *
from mofapy2.core import gpu_utils
from mofapy2.build_model.build_model import *
from mofapy2.build_m... |
11dd6a1116d809c627e973cb0ed7c06e96c484ff908328f7f63ecf22ebc3dc2e | Python | 45,159 | 1,167 | import time
import os
import numpy as np
import scipy.stats as stats
from typing import Union
try:
from importlib.resources import files
tmp = files("encore.gui")
except (TypeError, ImportError): # Python < 3.10
from importlib_resources import files
from encore.validators.algorithm_parameters import vali... |
62d69200a195dc8de43baaad808a027d77de1cdc9e43ea5eed495fe7e1e00a8f | Python | 45,236 | 1,207 | """Core simulation functions — the single source of truth.
Every callable here is a plain Python function (no LangChain ``@tool``,
no MCP ``@mcp.tool``, no Parsl ``@python_app``). Framework-specific
wrappers in ``ase_tools.py``, ``mcp_tools.py``, and ``parsl_tools.py``
simply delegate to these functions.
"""
from __... |
48818c8428e29cb22bc60e41e86689d6d410066c6464a676e754b47aa8f49673 | Python | 45,279 | 1,078 | import logging
import vtk
import numpy as np
from ccf_streamlines.angle import find_closest_streamline
from ccf_streamlines.coordinates import coordinates_to_voxels
from neuron_morphology.transforms.affine_transform import (
rotation_from_angle, affine_from_transform_translation, affine_from_translation, Affi... |
9ea7c8864652e1097d62f0c4fbb13a22d9f640948c88c63d5e5a57c1dfcd1226 | Python | 45,335 | 1,213 | """Observation models for simulations."""
from typing import Optional, Tuple, Union
import numpy as np
from osl_dynamics.utils import array_ops
class MVN:
"""Class that generates data from a multivariate normal distribution.
Parameters
----------
means : np.ndarray or str
Mean vector for e... |
9da638ba9b73491a8f51f7fee51b739048c3c7ef831b32cabfb9045390242ef8 | Python | 45,337 | 849 | import itertools
import math
import pickle
import importlib
import brainscore
import xarray as xr
from PIL import Image
from pixelmatch.contrib.PIL import pixelmatch
from brainscore_core.supported_data_standards.brainio.assemblies import NeuroidAssembly
from pathlib import Path
import copy
import numpy as np
import... |
3c08e6cafbd9c5be555b4f2b5f04dc6a8a59988dc1b3e74f54915e26df6f1594 | Python | 45,399 | 1,199 | #######################################################################################
### Functions that serve to analyze the connectivity, early- and late-phase weights ###
### in a network that contains multiple cell assemblies ###
########################################################... |
a25cab81ce4a5d4a2ece809fb3388f7826d9a9b48a4e71b43829c5f5bb3aee87 | Python | 45,403 | 1,199 | #######################################################################################
### Functions that serve to analyze the connectivity, early- and late-phase weights ###
### in a network that contains multiple cell assemblies ###
########################################################... |
13e341f94d6e2ebb17c433f063e4a29cbad6d018f4f710693f9e4d4579881063 | Python | 45,406 | 1,208 | # Copyright (C) CVAT.ai Corporation
#
# SPDX-License-Identifier: MIT
from __future__ import annotations
import itertools
import json
from abc import ABC, abstractmethod
from collections import Counter
from collections.abc import Sequence
from copy import deepcopy
from typing import TYPE_CHECKING, Any, cast
import at... |
f4f9abb221849ae80c14961989f78f4393c24284aa77e1d81cec52876aeee456 | Python | 45,427 | 1,287 | """
tensorflow/keras utilities for the neuron project
If you use this code, please cite
Dalca AV, Guttag J, Sabuncu MR
Anatomical Priors in Convolutional Networks for Unsupervised Biomedical Segmentation,
CVPR 2018
or for the transformation/interpolation related functions:
Unsupervised Learning for Fast Probabilis... |
e1f956b934bb862379040f60a8b3f42b61f9c90c60ce77a17feb788a0cb9e08d | Python | 45,460 | 1,151 | #############################################################################
# Copyright (C) 2020-2026 MEmilio
#
# Authors:
#
# Contact: Martin J. Kuehn <Martin.Kuehn@DLR.de>
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may... |
e9a28f4ca67c8725a41e12a5d7e8a2dd6b6847e92b52ac3a7ce4620cbc6be3bb | Python | 45,495 | 671 | '''
Aln
'''
import numpy as np
import sys
def intro():
print("""
SHORT List of potential energy surfaces for Aln:
P: potential energy, G: Gradient, D: Nonadiabatic coupling vector
This is listed at the end of description to show the availability.
For example: P/G means both potential energy and g... |
2d778abe530d42de2a4cb1492a2d6c0631e7d1c0c7d1656bc47988b00c4e53e1 | Python | 45,551 | 1,092 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Tue Mar 5 14:55:41 2019
@author: lferiani
"""
#%% import statements
import re
import cv2
import pdb
import tables
import itertools
import numpy as np
import pandas as pd
import scipy.optimize
from pathlib import Path
from matplotlib import cm
from matpl... |
aeaee8623d1e6ba741cd8e8f46b08440427c3b1714996af9f1817105fa5ee163 | Python | 45,556 | 1,062 | """
ProtoECGNet Fusion Inference Script
This script provides standalone inference capabilities for trained ProtoECGNet fusion models
that combine 1D rhythm, 2D partial morphology, and 2D global branches.
Usage:
python inference_fusion.py --target-ecg 65 # will do inference on only ECG 65 (ensure that you choose a... |
fc135a6d4b7b783e0ff7e058dd1d460cb5880af1ee4b6b6d0923e6a7420557ce | Python | 45,604 | 1,342 | """Processing functions for dannce."""
import numpy as np
from skimage.color import rgb2gray
from skimage.transform import downscale_local_mean as dsm
import imageio
import os
import dannce.engine.serve_data_DANNCE as serve_data_DANNCE
import PIL
from six.moves import cPickle
import scipy.io as sio
from scipy.ndimage.f... |
4a572054b13578735e48cb7a78c464abba8cb779ed170e6048ede68cee1d97bd | Python | 45,699 | 1,177 | # Copyright (C) 2020-2022 Intel Corporation
# Copyright (C) CVAT.ai Corporation
#
# SPDX-License-Identifier: MIT
import itertools
import json
import os.path as osp
import tempfile
import zipfile
from io import BytesIO
import datumaro
import numpy as np
from datumaro.components.annotation import Mask
from datumaro.com... |
223fa85b563cd5be3dc1b1a6f6323371cf15db6d8720e388f5c4a79dc60bc2b4 | Python | 45,713 | 830 | """
Script to perform correlation analyses. Examples in run.py as run_corr_*(...)
"""
import pandas as pd
import matplotlib.pyplot as plt
import seaborn as sns
from joblib import Parallel, delayed
import scipy
from matplotlib.colors import TwoSlopeNorm
from end2endPLS import PermutationGeneList, GeneListFromExpre... |
86bf58c0e4f4349fae2aafd4b0cc06f850e103458566ec3513437a46781860cb | Python | 45,826 | 1,226 | # Copyright 2025 BrainX Ecosystem Limited. 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 appli... |
35a861cd5de3a756362e6e909cde5ee56e6de84172529303dc18c66524ec2593 | Python | 45,837 | 801 | """Contains the tests for the REST server of ViRelAy."""
import glob
import io
import os
import re
import numpy
from flask import Flask
from flask.testing import FlaskClient
from PIL import Image
from virelay.server import format_exception, http_bad_request, http_not_found, http_ok, send_image_file
NUMBER_OF_CLASSE... |
f244c42dda70e3fbcaa52499c17f6024147509aa3ae0315f53534bdb4d13ea24 | Python | 45,889 | 1,144 | from collections import defaultdict
from itertools import count
from operator import attrgetter
from os import path as op
import matplotlib.pyplot as plt
import pandas as pd
import numpy as np
from tqdm import tqdm
import pickle
from ..exceptions import PipelineException
try:
import cv2
except ImportError:
pr... |
3894513071a07da447a4053b2d02693f4851577edfadc8f5aa1cf4892626e3aa | Python | 45,980 | 1,229 | from .trainer import *
from flair.training_utils import store_teacher_predictions
from flair.list_data import ListCorpus
import math
import random
import pdb
import copy
from flair.datasets import CoupleDataset
from ..custom_data_loader import ColumnDataLoader
from torch.optim.adam import Adam
import torch.nn.functiona... |
4e13a2f538cf02ab56144eb2a91ca48a4024ce64faaae790ab9ff1c3f399b473 | Python | 46,028 | 6 | standard_train_fold=['hh04W3xXa5s', 'GdFP_p4eQX0', '4iG0ffmnCOw', '81406', 'qyJiDgtj6YE', 'KI2sU-mhM44', 'qXisb7w9LjM', 'CLkTjujFVKU', 'aMtFBGh2wKI', '2OLVF-KEaZU', 'Or-9Nc_GAq8', '72tXTrSXoMk', 'hSgKOKK3L8M', 'YVHJpAROBvQ', 'pVzHaakhKAw', '127470', 'wY8JbFOsp5E', '-iRBcNs9oI8', 'sLaTZtL0ZIk', 'txjqbr6FoZs', 'jVayR0VCl... |
dee3cee426eb79ffc4de7bc60b7cdf47f367f07bda61ccaec1ca6e53634e6dbd | Python | 46,130 | 1,034 | """Top-level pipeline runner, orchestrating steps to mirror ``MEApipeline.m``."""
from __future__ import annotations
import datetime
import json
import shutil
import time
from pathlib import Path
from typing import Callable
from meanap.params import (
GENERATE_CSV_STEP, PARAMS_FILENAME, Params, default_cache_dir... |
4185374330f16192b7d513b49dc12a435400e18c35391fee1c484e6132fdbb3c | Python | 46,182 | 1,165 | # Copyright (C) CVAT.ai Corporation
#
# SPDX-License-Identifier: MIT
from __future__ import annotations
import itertools
import math
from collections.abc import Callable, Sequence
from functools import partial
from typing import Any, NamedTuple, TypeAlias, TypedDict, TypeVar, cast
import datumaro as dm
import datuma... |
425fa4a5aab889020ebd8126dd2c970f5c6bde02b09edc3520d6e8b3a799bab2 | Python | 46,231 | 957 | import torch
import datajoint as dj
from featurevis import models
from featurevis import ops
from featurevis import utils
import featurevis
from staticnet_analyses import multi_mei
from staticnet_experiments import configs
from staticnet_experiments import models as static_models
schema = dj.schema('neurostatic_cros... |
beedd563f516bf1773d77cc39638dfd57cba56128c59523a50235624ee30c947 | Python | 46,264 | 1,048 | """Can genotype or age be read back out of the features? — ports ``doClassification.m``
and ``doLDA.m``.
MATLAB fits five classifiers, cross-validates each, shuffles each feature in
turn to rank importance, and shuffles the labels 200 times to get a null. The
structure is kept. What changes is who is allowed to be in ... |
3420c17c0326b93e1ed6a8dba509c7d62315f09df5d6faa7355f0094c2cf98fe | Python | 46,376 | 1,022 | # coding=utf-8
# Copyright 2022 the HuggingFace Datasets Authors.
#
# 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 app... |
f87207ddde5675c771f7c64c220fd3333ec02a048ff68ffbd2d37ea9081c59a2 | Python | 46,401 | 1,302 | # Kai Sandbrink
# 2023-05-09
# This script shows
# %% LIBRARY IMPORT
import numpy as np
import ast, glob
from matplotlib.ticker import FuncFormatter
import matplotlib.pyplot as plt
from utils import format_axis
import pandas as pd
import os
from scipy import stats
from utils import Config
# %% PLOTTING FUNCTIONS
d... |
4fed753d8811d8d30c7047cc552feacdb9975bd8fb672589efce89b1d34e1561 | Python | 46,419 | 1,451 | # 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
# distributed under t... |
5e5a50fb2fa1ac03f8ec7306f1b2276eaea6e0a59684f597f6b94d05c495f887 | Python | 46,469 | 1,096 | #!/usr/bin/env python3
"""
graphpancake: electronic structure theory-based molecular graphs, because computers haven't taken organic chemistry class
Usage:
graphpancake <command> [options]
Commands:
create-db Create a new molecular graph database
load-data Load QM data for a single molecule
quer... |
0508f1657243f60d2ec2f403d8541f73615a66e5de311cfc7d1e1dde8dbe0c34 | Python | 46,517 | 1,026 | """LAION-fMRI Brain-Score benchmark.
Wraps the LAION-fMRI 7T volumetric dataset (Zerbe et al., VSS 2026) using the
bundled re:vision train/test splits (`tau`, `ood`, `cluster_k5_*`, plus per-OOD-category
sub-variants) on the Allen2022-style **shared pool** (1,492 stimuli seen by every
subject). Mirrors `Hebart2023_fmr... |
f4a66a80c24ea959a5bb5eba562b5d2fca9538dd672739640f457b977af70099 | Python | 46,557 | 803 | # Copyright (c) 2026 Rohit Jena. All rights reserved.
#
# This file is part of FireANTs, distributed under the terms of
# the FireANTs License version 1.0. A copy of the license can be found
# in the LICENSE file at the root of this repository.
#
# IMPORTANT: This code is part of FireANTs and its use, reproduction, or
... |
1e9d450faa6647b4ef797e011940ace4b942e05a37d53db1e7c7890e28d4a729 | Python | 46,562 | 1,305 | __all__ = ["IntervalArray", "EpochArray", "SpaceArray"]
import copy
import logging
import numbers
from sys import float_info
import numpy as np
from numba import jit
from .. import formatters, utils, version
from ..utils_.decorators import keyword_equivalence
#######################################################... |
469b751d94692223cbd37edac3e73c06c3be4212c55dd634295abc21fac11a16 | Python | 46,674 | 1,193 | # -*- coding: utf-8 -*-
"""
Landmark Transform Pipeline for 3D Slicer
A modular, open-access tool for transforming anatomical landmarks and segmentations
from template space to subject space using ANTs registrations.
Features:
- Cross-platform path handling (Windows/Mac/Linux)
- Configurable via YAML or CLI
- R... |
dd04e1a04d7373a865c178ff3850bcc03b9edd2411017f3efb7de74c42bf79e1 | Python | 46,694 | 1,318 | # 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, sof... |
f867d8142ab56e1fed0ec4efe0d5c07b575a287a1b07ddb7e630f80d1dd90a97 | Python | 46,694 | 960 | from qtpy.QtCore import Signal
from pathlib import Path
from napari import Viewer
from napari.qt.threading import thread_worker
from natsort import natsorted
import cv2
from superqt import QCollapsible
from qtpy.QtWidgets import QPushButton, QWidget, QVBoxLayout, QMessageBox, QProgressBar
from magicgui import magicgui
... |
6bbbef3992bbf2a240387d36ba020fa4c03efaede87efe704a95867746566088 | Python | 46,715 | 977 | import random
from math import cos, radians, sin, sqrt
import numpy as np
from gym import spaces
from utils import *
if __name__ == "__main__": # pretend to overload the memory
import pygame
class Molecule:
def __init__(self, position=(0, 0), shape='square', size = 140, state=0, angle=0):
... |
5e7feef88337cee668fbad665b2d489894cde44e73af414dc26dc27e8e7f8655 | Python | 46,783 | 1,403 | import re
import sys
import argparse
import asyncio
import typing
import json
import bisect
import time
import datetime
import copy
import dataclasses
import grpc
import numpy
import scipy.spatial.transform
import scipy.optimize
from thalamus.qt import *
from thalamus import thalamus_pb2
from thalamus import thalamu... |
f9aa7bde9872b52676720f62e05f876c0c939053aa812ab96ff47d6231846877 | Python | 46,789 | 1,290 | # coding=utf-8
# Copyright 2018 The Google AI Language Team Authors.
#
# 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 ... |
ee49f411a88060f82e79b604122b6e90b914df911292ffb128a53df61fbd4e76 | Python | 46,855 | 907 | # Copyright (c) Meta Platforms, Inc. and affiliates.
# All rights reserved.
# This source code is licensed under the license found in the
# LICENSE file in the root directory of this source tree.
import torch
import torch.distributed
import torch.nn.functional as F
from torch.nn.init import trunc_normal_
from .sam.... |
5a9219d10908f3bb61beb2e5952e4bcd40cef96209d48d595d1cdc6a4b2cd05a | Python | 47,040 | 862 |
import datajoint as dj
import featurevis
import numpy as np
import itertools
from functools import partial
from itertools import product, repeat
from tqdm import tqdm
import torch
from torch import nn
from torch.nn import functional as F
import random
import os
from staticnet_invariance.toy import ToyNeuron, GroupAss... |
5537124c5530c513f71987c67ef7f0fe2cba27020d1a0ceddd01666b1480924e | Python | 47,170 | 739 | SYSTEM_PROMPT_FINDINGS_CHINESE = """系统角色： 你是一名顶级的医学影像报告（MRI脑部）AI助手，专门负责将非结构化的MRI报告文本，按照预设规则和标准，转化为结构化、标准化的数据。
核心任务： 对输入的MRI脑部检查报告进行深度清理、信息提取、特征增强及标准化输出。
I. 标准化疾病列表 (共16类 + 肿瘤亚型):
结论必须严格从以下列表中选择。若原始报告提及的疾病不在列表内，则不予采纳或尝试映射到最接近的类别（需谨慎）。
1. 正常
2. 白质高信号（"缺血灶"、"脑白质变性"映射至此）
3. 脑萎缩(特别注意：原始报告中出现的"老年脑"、"脑实质老年性改变"或类似描述年龄相关性脑改... |
67672dff390e7be173e1987c1948944e962e26bf1992ea60ce201ee63b821e70 | Python | 47,223 | 1,204 | #!/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 os
import h5py
import pandas as pd
import numpy as np
import matplotlib.pyplot as plt
import seaborn as sns
import multiprocessing as mp
from ar... |
2d1a6ce4c6eb402c2fb2978b7a3841c3403c092930a558b76012d1df0cc3da0c | Python | 47,255 | 1,156 | import cv2
import numpy as np
import csv
import os
import glob
from ultralytics import YOLO
import configparser
import time
import shutil
import tkinter as tk
from tkinter import messagebox, filedialog
import subprocess
# ~ import config_watcher
import sys
import box_geometry as bg
from kalman_tracker import KalmanTrac... |
94df07d18da6a942b07446e36ed064e801e7fa22937fab470d422ab740988586 | Python | 47,310 | 1,260 | # Copyright (C) CVAT.ai Corporation
#
# SPDX-License-Identifier: MIT
import json
from http import HTTPStatus
from time import sleep, time
import pytest
from deepdiff import DeepDiff
from shared.fixtures.data import Container
from shared.fixtures.init import CVAT_DB_DIR, CVAT_ROOT_DIR, container_exec_cvat
from shared... |
55ba9cb7687f57be12614989058834a0024dad4c194200f8bd075bc8357c278e | Python | 47,346 | 1,298 | # -*- coding: utf-8 -*-
import argparse
import json
import logging
import os
import multiprocessing
import re
import shutil
import sys
import xml.etree.ElementTree as ET
import nibabel as nib
import numpy as np
from dipy.data import SPHERE_FILES
from dipy.io.stateful_tractogram import Origin, Space
from dipy.io.util... |
cb4472bfb389e7b3d136d29a4c90d324bbde67e6144db7c0c752775be42ab5a2 | Python | 47,358 | 1,487 | """CLI tests for the long-lived main-agent workflow."""
import importlib
from types import SimpleNamespace
import pytest
import toml
from chemgraph.agent.main_session import MainAgentTurnResult, PendingInterrupt
from chemgraph.cli import commands
from chemgraph.cli.formatting import console
from chemgraph.memory.sch... |
807b05daba593e5788691c64297b0e8b1d34821371ae8a76f14da125de3fa1cc | Python | 47,453 | 1,558 | import logging
import dipy.core.gradients as dpg
import dipy.reconst.dki as dpy_dki
import dipy.reconst.dti as dpy_dti
import dipy.reconst.fwdti as dpy_fwdti
import dipy.reconst.msdki as dpy_msdki
import immlib
import nibabel as nib
import numpy as np
from dipy.align import resample
from dipy.data import get_sphere
fr... |
51b2a64cf807f47ca5485a059848014a8ee72260ae92ffae7036a0331cd6ea70 | Python | 47,460 | 722 |
import h5py as h5
import numpy as np
import sys
import ArgParser as argp
from scipy.signal import find_peaks
import PatchAnalPlots as pu
import spike_utilities as su
HEADSTAGE_V={'H1':'_S2_', 'H2':'_S4_'}
HV_VAL_KEY={v:k for k,v in HEADSTAGE_V.items()}
HEADSTAGE_I={'H1':'_S1_', 'H2':'_S3_'}
CURRENT_THRESH=5e-12 #det... |
e0c3f370c387d7b2378849feb15e8bb8f3ac77c1d1a86474f4e2fff45e59ab14 | Python | 47,572 | 1,236 | #!/usr/bin/env python3
"""
Batch Hyperparameter Optimization Script
Submits multiple hyperparameter optimization jobs with different combinations of:
- Model types (RandomForest, XGBoost, LightGBM, EBM)
- Optimization metrics (precision, recall, f1, roc_auc, pr_auc)
- Various parameter combinations
Based on the hyper... |
5a0f9bff065930abca35c22b233905f031d1c07e63e3a9edba747e3b200b71db | Python | 47,581 | 701 | import os
class CactiConfig:
def __init__(self):
# content = f.readlines()
# self.baseline_config = ['# power gating\n',
# '-Array Power Gating - "false"\n',
# '-WL Power Gating - "false"\n',
# '-CL Po... |
7a8812010467429b0b31707e757c2818ed1e1cd09bf5a89c9525db8641146073 | Python | 47,590 | 1,205 | #!/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 os
import h5py
import pandas as pd
import numpy as np
import matplotlib.pyplot as plt
import seaborn as sns
import multiprocessing as mp
import ... |
97e64356903c3d8f7d570d71bba8ba39d083e0b4ec90f364d037e1610e56dc86 | Python | 47,605 | 1,205 | #!/usr/bin/env python
# author: Jannes Spangenberg
# github: https://github.com/JannesSP
# website: https://jannessp.github.io
import os
import h5py
import pandas as pd
import numpy as np
import matplotlib.pyplot as plt
import seaborn as sns
import multiprocessing as mp
import sys
from argparse import ArgumentDefaults... |
73f5afd75a6ceeb83a8d8498419338b6f3308e18d6d7f48405ce044bbc6cdd01 | Python | 47,659 | 1,046 | import sys
import os
import json
import shutil
import random
from PyQt5.QtWidgets import (QApplication, QGroupBox, QWidget, QLineEdit, QPushButton, QVBoxLayout, QFileDialog, QProgressBar, QCheckBox, QHBoxLayout, QMessageBox, QSpinBox, QDialog, QFormLayout, QDialogButtonBox, QLabel, QStackedWidget)
from PyQt5.QtCo... |
9fd567e4a1d2f14c21e62907701e4b377b1efafa2819bf97753ce9c979868dd5 | Python | 47,709 | 1,262 | import logging
import numpy as np
import matplotlib.pyplot as plt
import matplotlib.patches as patches
from scipy.ndimage import zoom, gaussian_filter
import scipy
from .base import Model
from nems.registry import layer
from nems.layers.tools import require_shape, pop_shape
from nems.layers import (
WeightChannel... |
0f8ce9a7257d3b9ad041d43f130b3999f4114e1b456bc4e41152e888c4e15e22 | Python | 47,740 | 1,028 | # Ultralytics 🚀 AGPL-3.0 License - https://ultralytics.com/license
from __future__ import annotations
import os
import random
import subprocess
import time
import zipfile
from pathlib import Path
from tarfile import is_tarfile
from typing import Any
from uuid import uuid4
import cv2
import numpy as np
from PIL impo... |
f1e78876d3f56219fdc209624c1553894d8b370e0a5fc5c453c9210c6b80258e | Python | 47,794 | 1,041 | from collections import defaultdict
import warnings
import pandas as pd
import numpy as np
import scipy as sp
from scipy.stats import binomtest, beta
from scipy.optimize import curve_fit
from matplotlib import pyplot as plt
from sklearn.linear_model import HuberRegressor
from .utils import neighbors as nb
from .ut... |
7456269f5fc5a89cd164a65fb9916538ed1fda41575076cf9def26fcbe30f453 | Python | 47,839 | 1,214 | import os
import sys
sys.path.append(os.path.join(os.path.dirname(__file__), '..'))
import json
import torch
import torch.nn as nn
import pandas as pd
import numpy as np
import matplotlib.pyplot as plt
from functools import partial
from .modules import (
optimizers_dict,
MultiPropDecoder,
activation_dict
)
... |
f752a15ce52c86de519f1ac78d36a127879ebd17b344872695f4792307553529 | Python | 47,875 | 1,186 | import math
import pathlib
import typing
import numpy as np
from matplotlib import pyplot, pyplot as plt
from matplotlib.lines import Line2D
from neuron import h, nrn
import numpy.typing as npt
from scipy.linalg import svd
from scipy.spatial.transform import Rotation
from neuron.units import um
from .. import cells
f... |
ab42f76c437212fa3f0462cfc193d5ce1ef7d006a4eac43bc97a1ac0f80cef61 | Python | 47,982 | 1,186 | import copy
import re
import warnings
from collections import defaultdict, namedtuple
from collections.abc import Mapping
from itertools import chain
from typing import Any, Dict, List, NamedTuple, Optional, Tuple, Union
import torch
from torch import Tensor
from typing_extensions import Self
from torch_geometric imp... |
f8cbce853853f77815370d4c62b1f5c8bd6d6a43cbfb8be34c9c11c47ada1854 | Python | 47,990 | 928 | from napari import Viewer
from napari.qt.threading import thread_worker
from natsort import natsorted
import cv2
from napari_dmc_brainmap.utils import get_info, load_params
from superqt import QCollapsible
from qtpy.QtWidgets import QPushButton, QWidget, QVBoxLayout
from magicgui import magicgui
from magicgui.widgets i... |
dd6b40884ba70725ff0df11edc7a7b1c5096b3ee4cd0d27c98c9a4e80276c124 | Python | 48,346 | 640 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Tue Feb 11 14:26:32 2020
This is a pytorch implementation of the Tolman-Eichenbaum Machine,
written by Jacob Bakermans after the original by James Whittington.
The referenced paper is the bioRxiv publication at https://www.biorxiv.org/content/10.1101/770495... |
b60d6227d886b055a1e55e8dd215f19773df6f9745cbea531768296e97a7c77b | Python | 48,428 | 932 |
import warnings
import numpy as np
import scipy
from matplotlib.widgets import Button
from mpl_toolkits.axes_grid1 import make_axes_locatable
from numpy.typing import NDArray
from typing import Tuple
from helper_functions.load_cell_distributions import compute_distribution
from helper_functions.cell_type_lib import Ce... |
63fb512ff51efc088c384ce6432b8cc035af02e54c08e834b022235ddd773c9a | Python | 48,498 | 1,057 | """
This file contains all the utilities used in that project. They are classified in 5 categories:
1- loading/saving functions:
-load_volume
-save_volume
-get_volume_info
-get_list_labels
-load_array_if_path
-write_pickle
-read_pickle
-write_model_summary
2- reformatting functions
-... |
7de6061d09d7ff76b3b4fc504b0659c819cf458a9d217063b5b2df94bd7691c9 | Python | 48,498 | 1,410 | # Copyright (C) CVAT.ai Corporation
#
# SPDX-License-Identifier: MIT
import io
import math
from logging import Logger
from pathlib import Path
from types import SimpleNamespace as namespace
import cvat_sdk.auto_annotation as cvataa
import PIL.Image
import pytest
from cvat_sdk import Client, models
from cvat_sdk.attri... |
8ae2a2658b8d56b1273bb241c4ad2b5a005d12d81942ed8abf23a1b26f0f79d1 | Python | 48,524 | 990 | import numpy as np
import warnings
from collections import defaultdict
import pandas as pd
from scipy.spatial import KDTree
import skimage.morphology as skim
from .utils import neighbors as nb
from .utils import util as util
import network_flow_tracker.LFBFP as LFBFP
import trackpy as tp
from trackpy import linking ... |
66fc3d7df87b338560fef36e26f6bba796635ffaf0672bf44d783daf858b8106 | Python | 48,640 | 1,136 | #!/usr/bin/env python3
"""
chemembed_by_file.py — ChemEmbed annotation module (FAISS GPU edition)
=========================================================================
Iterates over all samples, reads the GNPS/SIRIUS MGF file from each
sample's polarity folder, and produces ChemEmbed predictions.
Speed improveme... |
8c5ee88132768ba3f3f85e259535f40e7a194b8e83414f8a17a566a98795ab63 | Python | 48,685 | 1,225 | # 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, ... |
a573c6c3c4e9ae471c1f6ec0f192d4d49f7ce836eab5fba4eb617deff8c8b466 | Python | 48,691 | 1,027 | import os.path
import unittest
import tests.base_test
import tests.output_parser as output_parser
import tests.test_config
import tests.util
class Test(tests.base_test.BaseTest):
def setUp(self):
super().setUp()
self._test_base_dir = tests.test_config.TEST_BASE_DIR
self._test_dir = os.pa... |
8abee51ec8d6f04b0b7b451c451ab54d39175b0f1a22510cc7d97ad22064f50b | Python | 48,705 | 884 | ############################################################################################
### Functions to analyze and plot weight and activity distributions from simulation data ###
############################################################################################
### Copyright 2019-2022 Jannik Luboe... |
fc5a2d1dd9bd78fa8946ee4e3300d21f4c82096729a07c6be8dbc854e255b221 | Python | 48,706 | 884 | ############################################################################################
### Functions to analyze and plot weight and activity distributions from simulation data ###
############################################################################################
### Copyright 2019-2022 Jannik Luboe... |
4815f8d06646fd31b9ad7a6a004fe58b1128ceef7f477c989096cdd698df2289 | Python | 48,848 | 974 | #! /usr/bin/env python
"""Script to generate all the plots and statistics for the mitochondria ultrastructure
analysis in the surface morphometrics paper."""
__author__ = "Benjamin Barad"
__email__ = "benjamin.barad@gmail.com"
__license__ = "GPLv3"
import os
import pickle
import numpy as np
import time
from morphom... |
12ec75c5463ce1089bc629b6a869cde6e78f4c1a129627e97ce772a2431839d2 | Python | 48,870 | 1,245 | # 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.
"""
Train a network across multiple GPUs.
"""
import contextlib
import logging
import os
import sys
import tim... |
74c93b299dc5973c343c2ee422e690a11083bd8b7dc86c4e9fa7d23107732012 | Python | 48,875 | 1,196 | import datetime
import logging
import os
import struct
from abc import ABC, abstractmethod
from pathlib import Path
from typing import Any, Optional, Tuple, Union
import numpy as np
import pandas as pd
import pyproj
from pyproj import CRS, Transformer
from . import _core as backend
logger = logging.getLogger("pyocto... |
ed372b71304b4ba18dcf3af450624e6a6e82564d58e3158f72cf7047d41a1879 | Python | 48,891 | 1,336 | import glob
import os
import tarfile
from collections import defaultdict
from typing import Callable, Dict, List, Optional, Tuple, Union
import ngs_tools as ngs
import pandas as pd
from .config import get_kallisto_binary_path
from .logging import logger
from .utils import (
concatenate_files,
decompress_gzip,... |
10040dbbc870797b34cfc5fca15e057b74c66e95ab22ed426e7eaebd71d5891b | Python | 48,908 | 1,710 | # Copyright 2019 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, ... |
c3b930a4ed22698a2e0e6b03612ef8a17dedd8fbad78d9333da861982ae2697b | Python | 48,983 | 1,035 | """The catalogue of step-5 figures, and how to draw one from stored results.
Three places need to draw these figures: the step itself
(:mod:`meanap.stats.run`), the bundle exporter, and the viewer. Left to
themselves each would carry its own list of which figures exist and how each is
made, and the three lists would d... |
579dfc93a6117617192f44654723507ea863f21f49260364bdb6fef76b823df6 | Python | 49,005 | 1,545 | # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##
#
# See COPYING file distributed along with the PyMVPA package for the
# copyright and license terms.
#
### ### ### ### ###... |
c2d3a2dccb51998f7ace7b02df2742f4f28df6ae70b84994c4acfbeea8a41b70 | Python | 49,051 | 1,515 | """Define networks for dannce."""
from tensorflow.keras.models import Model, load_model
from tensorflow.keras.layers import Input, concatenate, Conv2D, MaxPooling2D
from tensorflow.keras.layers import Conv2DTranspose, Conv3D, Lambda
from tensorflow.keras.layers import MaxPooling3D, Conv3DTranspose
from tensorflow.keras... |
7ae8f6a6c957cc69cc86b9701835706588c80ff85a02898f613547953eb1641a | Python | 49,069 | 1,237 | # Copyright (C) 2019-2022 Intel Corporation
# Copyright (C) CVAT.ai Corporation
#
# SPDX-License-Identifier: MIT
import heapq
import math
from collections.abc import Callable, Container, Generator, Iterable, Iterator, Sequence
from copy import copy, deepcopy
from itertools import chain
from typing import Any
import n... |
3960bde703c0653ae4a657e37fa1b5572e2cc628bb192f6de06a3b207856a8b4 | Python | 49,164 | 1,405 | """Maxfiltering.
This module wraps the Elekta Maxfilter command-line tool for applying
Signal Space Separation (SSS) and temporal SSS (tSSS) to MEG data.
Note
----
This module requires a licensed installation of Elekta/MEGIN MaxFilter.
MaxFilter is proprietary software and is not included with osl-dynamics.
**OHBA u... |
f6b32c075d006d6ca2649c61d937c24d923331d6e85f19b478f47dab797b13cb | Python | 49,183 | 1,141 |
import copy
import gzip
import logging
import os
import pickle
import numpy as np
import pandas as pd
from joblib import Parallel, delayed
from pingouin import compute_effsize
from tqdm.auto import tqdm
from .datasets import get_template
from .io import get_input_data
from .nulls import generate_null_maps
from .stat... |
67d40ba1d1676c382700cb812143efd47f76c59a08499acc6148b904238625f0 | Python | 49,270 | 1,160 | import os
import subprocess
import shutil
import nibabel as nib
import numpy as np
import pandas as pd
from nipype.interfaces.base import BaseInterface, BaseInterfaceInputSpec, TraitedSpec, File, Directory, traits, CommandLineInputSpec, File, TraitedSpec, CommandLine, Directory
from nipype.interfaces.utility import Ide... |
b7c99a34964675314aa17974167f7cae2c4daf3d1263db4cc6be2a886d5e0795 | Python | 49,282 | 1,364 | # import modules
import pandas as pd
import os
from pyliftover import LiftOver
import numpy as np
from sys import argv
import sys
import time
import Query_api
import subprocess
import tempfile
# disable pandas helper messages
pd.options.mode.chained_assignment = None # default='warn'
### Define helper functions
# ... |
8d3a67064624fe081d44ed5c3baf3590d43052ed710039b15689291670bf6059 | Python | 49,292 | 1,354 | #!/usr/bin/env python
# -*- coding : utf-8 -*-
"""Utilities for running various MRtrix3's DWI preprocessing tools"""
import os
import os.path as op
import subprocess
from shutil import copyfile, which
import numpy as np
from ..preprocessing import mrinfoutil, rician, smoothing
from ..system.errors import MRTrixErro... |
cc7704a22a0bafd95e3c981b9ec472e2096937b17f0be7c4a7dcc10e820269a2 | Python | 49,356 | 1,133 | # Dataset utils and dataloaders
import glob
import logging
import math
import os
import random
import shutil
import time
from itertools import repeat
from multiprocessing.pool import ThreadPool
from pathlib import Path
from threading import Thread
import cv2
import numpy as np
import torch
import torch.nn.functional ... |
29bc9c67519899baddc62f54392d47cad31d8cd2c170bea9ca7ce785c8c27c28 | Python | 49,395 | 1,480 | # imagecodecs.py
# Copyright (c) 2008-2026, Christoph Gohlke
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
#
# 1. Redistributions of source code must retain the above copyright notice,
# thi... |
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