sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
fcd44ee0febb4262e3ae548300c06e0edfeee5b9a19c06670ed538c1e1d92595 | Python | 5,278 | 156 | import logging
import numpy as np
from dipy.tracking.streamline import length, set_number_of_points
from scilpy.tractograms.streamline_operations import smooth_line_gaussian
def post_process_labels_discrete(
nb_labels, bundle_label, bundle_mask, bundle_name
):
""" Discretize the labels and apply a mask to t... |
5dbaa3ef5e2a0349204eabaed3b60cd0c5097ea25e2d5ed9b2d521a9cd8fc8af | Python | 5,281 | 184 | import os.path
def parse_tab_separated_value_file(file_path):
header = list()
rows = list()
if not os.path.isfile(file_path):
return header, rows, '{} is not a valid filepath'.format(file_path)
with open(file_path, 'rt') as f_handle:
for i, line in enumerate(f_handle):
tok... |
c1fbfc8be0ab4f79565c99b094cb202e5c9c375dcf8f53ca4fabdb9bbd607dc0 | Python | 5,281 | 171 | """CTF Rest Dataset: Static Network Analysis.
In this script we calculate static network metrics using source
reconstructed resting-state MEG data.
The examples/toolbox_paper/ctf_rest/get_data.py script can be used
to download the training data.
"""
import os
import numpy as np
import pandas as pd
from osl_dynamics... |
0976c75ca0a721cf90f342a77153edcf79aee357fb53b618b35f98d6b127053a | Python | 5,282 | 126 | from scvi.dataset import CsvDataset
import os
import numpy as np
import pandas as pd
from scvi.models import SCANVI
from scvi.inference import SemiSupervisedTrainer
import time as tm
import rpy2.robjects as robjects
def run_scVI(DataPath, LabelsPath, CV_RDataPath, OutputDir, GeneOrderPath = "", NumGenes = 0):... |
f84f93527f8208554d1fc3547e0e5012af4b917122417b2530466df799f04e50 | Python | 5,283 | 173 | import numpy as np
import pandas as pd
from sklearn.metrics import classification_report
from sklearn.metrics.pairwise import cosine_similarity
import sys
from collections import deque
import time
import logging
from sklearn.metrics import roc_curve, auc, matthews_corrcoef
from scipy.spatial import distance
from scipy ... |
5b09dc9662ff1cd3ece81fb76d138dcce05edae88ab0b8ca19813cb9c7b85a61 | Python | 5,284 | 201 | """Functions to process data."""
from typing import Optional
import mne
import numpy as np
from scipy import signal
from osl_dynamics.utils import array_ops
def standardize(x: np.ndarray, axis: int = 0, create_copy: bool = True) -> np.ndarray:
"""Standardizes a time series.
Returns a time series with zero... |
fa9d79f256e6021299c8368b210e52a383657265736557bb7e86018b829473ed | Python | 5,284 | 140 | import sys
import yaml
import os
import numpy as np
from matplotlib import pyplot as plt
pathpath,myrun = sys.argv[1:]
#pathpath = 'PATHS/filepaths_carlen.yml'
#myrun = 'runC00dMP3_brain'
with open(pathpath) as yfile: pathdict = yaml.safe_load(yfile)
rundict_path = pathdict['configs']['rundicts']
srcdir = pathdic... |
835be4f1dc210efaedc950c9f8ced4243fcaa759d60e8eac757057ebf5c8fa6f | Python | 5,285 | 144 | # Kai Sandbrink
# 2023-05-27
# This script compares behavior and transdiagnostic scores
# %% LIBRARY IMPORT
from matplotlib.ticker import FuncFormatter
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
import os
from scipy import stats
import seaborn as sns
from sklearn.decomposition import PCA
... |
8785a0679835bfba74dd1e9833112ea437f6c44612a7487c6e1d37fb44bc7928 | Python | 5,285 | 170 | import numpy as np
class Distribution:
"""Base class for a Distribution."""
# Any subclass of Distribution will be registered here, for use by
# `Distribution.from_json`
subclasses = {}
def __init_subclass__(cls, **kwargs):
super().__init_subclass__(**kwargs)
cls.subclasses[cls.__... |
1404e885ce3c28cccc59c6a57eac0da04d31227920d715a4ab2e8e2b5f5fdc3f | Python | 5,290 | 139 | from pathlib import Path
import zipfile
from io import BytesIO
from typing import Type, Literal
from argclz import AbstractParser
from neuralib.util.tqdm import download_with_tqdm
from neuralib.util.utils import ensure_dir
from rscvp.util.io import RSCVP_CACHE_DIRECTORY
__all__ = [
'DEMO_DATA_SOURCE',
'mkdir... |
bb1bbcb32601081f1026b4587a644a24d91a67a71f5e89b0da1fbaf92798d2f8 | Python | 5,290 | 171 | # utils/metrics.py
# ──────────────────────────────────────────────────────────────
# 多标签分类常用指标集合（纯函数、无任何训练逻辑）
# ──────────────────────────────────────────────────────────────
from __future__ import annotations
from typing import Literal, Dict, Any
import numpy as np
from sklearn.metrics import (
roc_auc_score,
... |
0eb1af4159f68710e0ebfc07550ad34828b7942a8a384e1853cf5603502ebf94 | Python | 5,291 | 154 | import numpy as np
from scipy import stats
import statsmodels.api as sm
import matplotlib.pyplot as plt
from matplotlib.colors import Normalize
from matplotlib.colors import ListedColormap
import matplotlib.pyplot as plt
import seaborn as sns
from nilearn import plotting
sns.set_style("white")
class MidpointNormalize(... |
a1e5e3bf37ca94d809e0131c405c41dcba1c94c1a711f9fb0b0da7ef0b41c19b | Python | 5,291 | 142 | from __future__ import print_function, absolute_import
import time
import collections
from collections import OrderedDict
import numpy as np
import torch
import random
import copy
from .evaluation_metrics import cmc, mean_ap
from .utils.meters import AverageMeter
from .utils.rerank import re_ranking
from .utils import... |
1718ce7a8009f24488be87a01940d5f246a24cd57dcef40e997679734ee9692f | Python | 5,294 | 138 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Save connections of a hdf5 created with
>> scil_tractogram_segment_connections_from_labels.
Useful for quality control and visual inspections.
It can either save all connections (default), individual connections specified
with --edge_keys or connections from specific... |
0ba4fa6036ce9410536d8fa7b9193f274110e73437a10dba8c4456958e33533e | Python | 5,297 | 212 | #real_time_ABRS
# Copyright (c) 2019 Primoz Ravbar UCSB
# Licensed under BSD 2-Clause [see LICENSE for details]
# Written by Primoz Ravbar
import numpy as np
import matplotlib.pyplot as plt
import cv2
import pickle
import msvcrt
from scipy import misc #pip install pillow
import scipy
from scipy impor... |
17591b5f8d2358383bedfacc50db5debe6c0fb02b2ac2427b879f0dc7c66f029 | Python | 5,297 | 120 | """Recompute per-unit split-half (Spearman-Brown) reliability at the FIXED 70-170 ms
window from raw GoodUnit rasters -- the window-matched noise ceiling for the
fixed-window static Li2026 assembly. Streams one session at a time (low RAM).
Output: CSV neuroid_id,reliability_window (neuroid_id = f"{ses}.{u}", GoodUnit... |
dd49a0032f992056d25bdae309e9177d6aabe9689af0b74e0dcfee0cb81dfec2 | Python | 5,297 | 176 | import os, sys, math, random, argparse, numpy as np
import bpy
import bmesh
import json
from math import radians
from mathutils import Matrix
print(os.getcwd())
import blender_util as bu
from lib_alban import *
# parse arguments
parser = argparse.ArgumentParser()
parser.add_argument('--nobjects', type=int, default=1... |
c8f44daae94dfd4f43661c5c42fe6a680422e98c5fccc4974b79d9b0f3dd295a | Python | 5,298 | 147 | # MIT License
# Copyright (c) Kentaro Wada
from __future__ import annotations
import math
import uuid
from typing import TypedDict
import numpy as np
import PIL.Image
import PIL.ImageDraw
from numpy.typing import NDArray
from .._shape import CIRCLE_POINT_COUNT
from .._shape import LINE_POINT_COUNT
from .._shape imp... |
3797733966a2d44c3f7c61a1b641aadaa157c1385e41b8af5c2191f51e8ef788 | Python | 5,299 | 143 | import os
from copy import deepcopy
import numpy as np
import argparse
import innvestigate.utils as iutils
from keras.models import Model
from keras.preprocessing import image
from keras.utils import to_categorical
import keras
import tensorflow as tf
from numpy import average, dot, linalg
from utils import *
from lrp ... |
7d2941a9f55f770391ab43ab147d284b5700186372e3bfccfee5a84d3d2ca40c | Python | 5,299 | 126 | #############################################################################
# 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... |
924520e0ad84601c55bedce935629c05ca27d4639667f903d15de386b9a923d4 | Python | 5,299 | 150 | from copy import deepcopy
from dataclasses import dataclass
from typing import TYPE_CHECKING
from eir.models.input.sequence.transformer_models import SequenceModelConfig
from eir.setup.input_setup_modules import setup_sequence
from eir.setup.input_setup_modules.torchtext_port.vocab import Vocab
from eir.setup.schemas ... |
3898d7dc2387aefc3987a20e8bd461aa7de913d299b855912438bd6388f97fa9 | Python | 5,300 | 115 | """Run the Python MEA-NAP pipeline with parameters matched to the MATLAB
parity run (parityRun/params_matlab_parity.mat), so the two runs' CSV outputs
can be compared field-by-field.
uv run python parityRun/run_python_parity.py
"""
import sys
from pathlib import Path
REPO_ROOT = Path(__file__).parent.parent
sys.... |
51eca7997bf28c99ed4c71ef9cfb535964bbaadf92cf3900298f545184c132b4 | Python | 5,300 | 275 | #! /usr/bin/env python
# aponteeduardo@gmail.com
# copyright (C) 2017
''''
Basic container classes.
'''
from collections import Sequence
import numpy as np
from copy import deepcopy
from scipy.integrate import cumtrapz
class AlgebraicObject(object):
''' A class for the units statistics. '''
fields = [... |
2e07d78b0abc63abb5ddf8dc0c8e0ee8ade0eef2ee38648ccc98c899a534555e | Python | 5,302 | 150 | """Hyperparameter Configuration Space."""
import numpy as np
import random
class Hyperparameter:
"""
Class defines a hyperparameter and its range.
"""
def __init__(self, name, type, range=None, min_value=0, max_value=0, step=1):
self.name = name
self.min_value = min_value
self.... |
d23c2dee19aa96ad3f4a00f41c94c463bae82f9330482b76d95c3e64cd9730a4 | Python | 5,302 | 125 | #############################################################################
# Copyright (C) 2020-2026 MEmilio
#
# Authors: Henrik Zunker
#
# 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 Lice... |
d6f0cd69040816d7fa85512f5c740dc69529343af13112663038823b3feddbcf | Python | 5,302 | 156 | import nibabel as nib
import numpy as np
from nibabel.streamlines import load, Tractogram, save
def _apply_axis_flips_mm(streamlines, img_affine, img_shape,
flip_x=False, flip_y=False, flip_z=False):
"""
Apply optional left-right (X), anterior-posterior (Y), and
inferior-superior (... |
ea6b2e62f5060cfad0a56aec2210d57d76bb2eec8cc7a29c04d985dc43e18063 | Python | 5,302 | 157 | from unittest.mock import Mock, create_autospec, patch
import numpy as np
import pytest
import torch
from scipy.special import softmax
from sklearn.preprocessing import StandardScaler
from eir.models.output.sequence.sequence_output_modules import (
SequenceOutputModuleConfig as SeqOutputModuleConfig,
)
from eir.s... |
1983546c33a42dfa12b0eff7f7c5f8dbc931f737a36d3b52381414ca5f57ae61 | Python | 5,303 | 139 | import torch
from torch import nn, Tensor
from torch.nn import init
import my_setup
from custom_layers.custom_module import BatchEvalModule
from custom_layers.dense import Dense
class RegressorModel(BatchEvalModule):
def __init__(self, num_features=32, config=None):
super(RegressorModel, self).__init__()... |
2aacbe8507b7d2b3f4898d36f59cd76a8eb831b3f9dc06b64a108f93549041a6 | Python | 5,304 | 172 | """
:mod:`ergodic` --- summary measures for ergodic Markov chains
=============================================================
"""
__author__ = "Sergio J. Rey <srey@asu.edu> "
__all__ = ["steady_state", "fmpt"]
import numpy as np
import numpy.linalg as la
def set_self_transition_zero(x):
"""Set cost/length of... |
0f26fe26dc237d796313773a30c28c86c2f0be89cf806ee6226e2316f0c7dd5a | Python | 5,306 | 145 | """LAION-fMRI baseline sweep across the 20 headline benchmark variants.
Default lineup is the 5-model baseline reported in METHODS.md (alexnet,
alexnet_random, resnet50_tutorial, convnext_tiny, resnext101_32x8d_wsl) +
one additional shipped-layermap model (convnext_base). Edit ``MODELS``
below to swap in your own.
Ru... |
bbba7158f50fbe80fe02ecd6c0c4742e0f1d10724c99540c798cd4d27a218460 | Python | 5,307 | 139 | import time
import argparse
import torch
import torch.nn.functional as F
from torch.utils.data import DataLoader
from torch.nn import ModuleList, Linear, BatchNorm1d, Identity
from ogb.lsc import MAG240MDataset, MAG240MEvaluator
from root import ROOT
class MLP(torch.nn.Module):
def __init__(self, in_channels: i... |
28eeebd5b90434fb9465808b48975f860885437e6a92d889316ed113a89c9185 | Python | 5,308 | 94 | from brainscore_vision import metric_registry
from .metric import CrossRegressedCorrelation, pls_regression, ridge_cv_regression, ridge_regression, \
dual_ridge_regression, dual_ridge_cv_regression, single_regression, linear_regression,\
pearsonr_correlation, ReverseCrossRegressedCorrelation, ReverseTrainTestSp... |
40f74a6487b67155edc43b3d47ba9db162f4bcc42faa6d869bd307b8fe9acbe3 | Python | 5,308 | 183 | import torch
import torch.nn as nn
from torch_geometric.nn import global_add_pool
from torch_geometric.nn import (
JumpingKnowledge,
global_add_pool
)
from layers import (
AttentiveLayer,
GATLayer,
GINLayer,
MPNNLayer
)
from activation import get_activation
class Atte... |
5fc4e41315e541e2df37130e6e9cf12e2246593e88608d27d1a3c391f5367904 | Python | 5,308 | 133 | """Hermetic contribution checks for portable and bundled skills."""
import importlib
import json
from pathlib import Path
import shlex
import sys
from markdown_it import MarkdownIt
import pytest
import yaml
from chemgraph.registry import ToolRegistry
from chemgraph.skills.lint import lint_skills
ROOT = Path(__file_... |
a96b4cc35876bb62cc19e6c3595fc7a372389be16493040fff3ca95ce1fc94a4 | Python | 5,308 | 173 | def get_indx(scrub_input, frames_in_1D_file):
"""
Method to get the list of time
frames that are to be included
Parameters:
in_file (str): path to file containing the valid time frames
Returns:
scrub_input_string (str): input string for 3dCalc in scrubbing workflow,
... |
e323747c4bb2a7bc025ec30961cd1796078eda7e99c1bb0fb538abcbe2ce7cb3 | Python | 5,310 | 142 | # Ultralytics 🚀 AGPL-3.0 License - https://ultralytics.com/license
# Copyright (c) Meta Platforms, Inc. and affiliates. All Rights Reserved
"""Necks are the interface between a vision backbone and the rest of the detection model."""
from __future__ import annotations
from copy import deepcopy
import torch
from to... |
dca453090dfe2e0bf9544b8b08946c9f7937f05ea81132ae2f2219c293356c0c | Python | 5,311 | 154 | #!/usr/bin/env python3
"""
Usage: ./prepare.py --tech nanopore --cohort clinical --proj_dir /path/to/long_read_archive/nobackups/
Author: Mei Wu, https://github.com/projectoriented
"""
import os
import glob
import sys
import logging
import argparse
import pandas as pd
import pysam
LOG = logging.getLogger()
logging.ba... |
7633fd8a56e03ab6975252c941e7d8772aa1ca0ad74ed92706cea5c2491e2f70 | Python | 5,312 | 139 | # -*- coding: utf-8 -*-
"""TODO"""
import numpy as np
import core.core_global as core
from core.core_definitions import simulation_timestep
from core.spiking_group import SpikingGroup
class PoissonPatternGroup(SpikingGroup):
"""TODO"""
def __init__(self, size, rate=1.0, rate_bg=1.0, params={}):
"""... |
05512c0392045d60d85e650b658826fb546e621d641c3628741169ee87359a71 | Python | 5,313 | 109 | import itertools
import numpy as np
from brainscore_core.supported_data_standards.brainio.assemblies import BehavioralAssembly
from brainscore_core import Metric
from brainscore_vision.metrics import Score
from brainscore_vision.metric_helpers.transformations import apply_aggregate
class AccuracyDistance(Metric):
... |
7d58fe43e5fef8551ab936cea73deb949cf5580c7bf60bd5052f4a2f8b32c3cf | Python | 5,313 | 135 | import fcn_megfmri
import numpy as np
import pandas as pd
import seaborn as sns
import scipy.stats as stats
import matplotlib.pyplot as plt
# get custom colormaps
cmap_seq, cmap_seq_r, megcmap, megcmap2, categ_cmap = fcn_megfmri.make_colormaps()
plt.rcParams['svg.fonttype'] = 'none'
plt.rcParams['font.sans-serif'] =... |
1446cc2449ef5c42bfc52453dd8c68d6fea5c7705a85b721e9f0105b480db1b9 | Python | 5,314 | 180 | # Copyright 2015 Numenta Inc.
#
# Copyright may exist in Contributors' modifications
# and/or contributions to the work.
#
# Use of this source code is governed by the MIT
# license that can be found in the LICENSE file or at
# https://opensource.org/licenses/MIT.
"""
Tests the score normalization scheme.
"""
import c... |
5728a8bef3819205c08452e8abf95bee951770f3bbc948fbada40f841b857868 | Python | 5,314 | 144 | from __future__ import absolute_import
from torch import nn
from torch.nn import functional as F
from torch.nn import init
import torchvision
import torch
from .pooling import build_pooling_layer
from .xception_model import *
__all__ = ['Xception', 'xception']
class Xception(nn.Module):
__factory = {
... |
9dc6aabe24ee11835c4ad614fbd900062b344953698eb5c28a2caede3b29137f | Python | 5,315 | 172 | import re
import sys
import enum
import pathlib
import argparse
import warnings
import collections
import pandas
import numpy
from pprint import pformat
from .record_reader2 import RecordReader
class DataFrameBuilder:
class Type(enum.Enum):
Analog = enum.auto()
Text = enum.auto()
Invalid = enum.auto()... |
e437c0674bfbe1e6f2f34379241a02229edb85c3264678a3feb28218e87302ef | Python | 5,318 | 211 | """mobilenet in pytorch
[1] Andrew G. Howard, Menglong Zhu, Bo Chen, Dmitry Kalenichenko, Weijun Wang, Tobias Weyand, Marco Andreetto, Hartwig Adam
MobileNets: Efficient Convolutional Neural Networks for Mobile Vision Applications
https://arxiv.org/abs/1704.04861
"""
import torch
import torch.nn as nn
cl... |
108b0d9cade5a6c72e535c8f249d06cabeb4ad2987c42e7cb6a925a79c22b4a2 | Python | 5,319 | 142 | from brainscore_vision.model_helpers.check_submission import check_models
import functools
from transformers import AutoFeatureExtractor, CvtForImageClassification
from brainscore_vision.model_helpers.activations.pytorch import PytorchWrapper
from PIL import Image
import numpy as np
import torch
"""
Template module fo... |
13d4708804a6a47b1a8608b1ca3e79fae345c42a3ddf2f56183314acaaf7b751 | Python | 5,319 | 180 | #!/usr/bin/env python
"""
split bam file into .shrt.bam and .long.bam
Created by Rongxin Fang
Modified by Armen Abnousi
"""
import sys
import pysam
import collections
from itertools import islice
from itertools import combinations
import time
import os
import subprocess
import shutil
import glob
def main():
input_t... |
b23b906126ca629c19c5e2bdf1970223d6b26e1833aa0ea4bcc89fbb6cc33e0e | Python | 5,319 | 142 | from brainscore_vision.model_helpers.check_submission import check_models
import functools
from transformers import AutoFeatureExtractor, CvtForImageClassification
from brainscore_vision.model_helpers.activations.pytorch import PytorchWrapper
from PIL import Image
import numpy as np
import torch
"""
Template module fo... |
d4447be55855b6bf90696db54bf976f07f812df0a0ccf1042f59f643209dcecd | Python | 5,319 | 122 | import pandas as pd
import matplotlib.pyplot as plt
import numpy as np
import os
import seaborn as sns
# Load the CSV file
file_path = 'INSERT_PATH_HERE'
output_dir = 'INSERT_PATH_HERE'
df = pd.read_csv(file_path)
# Define brain regions and name mapping
brain_regions = [1011, 7, 2, 174, 173, 175, 1030, 17, 1024, 102... |
448d6af7067095e3f9312fe3eefae09f6a7de0d43108a70b8c212f0725e88318 | Python | 5,321 | 119 | import torch
import torch.nn as nn
import torch.optim as optim
from torch.utils.data import DataLoader, TensorDataset, random_split
from sklearn.preprocessing import StandardScaler
import numpy as np
import pandas as pd
import os
import argparse
from model_options import TransformerClassifier, load_compatible_state_dic... |
c31099948fcfddec78f6f3e503ec0889b652404b115527a9539757e3303bf4be | Python | 5,321 | 149 | import os
import numpy as np
import git
import yaml
import sys
pathpath = 'PATHS/sompaths_units_IBLpassive.yml'#
myrun = 'runIBLPasdMP3_brain_pj'
ncluststr = '8'
cmethod = 'ward'
ncl = int(ncluststr)
nshuff = 2000
signif_levels = np.array([0.05,0.01,0.001])
tuning_attr_names = ['stimTuned','choiceTuned','feedbTune... |
e7805cfb96a242f5889a82d69cdfc160d0f9ba5744609de02f64e0a62ec20bc1 | Python | 5,325 | 127 | """Using for merged ab-ig graph
"""
import sys
sys.path.append('..')
import torch
import torch.nn.functional as F
from torch import nn
from torch.nn import Linear
from layers.conv import ConvBlock, GINEConvBlock
from layers.predictor import Predictor, MixtureDensityNetwork
from common import utils
from common.mapping... |
ee2ddec95ffb11c8daa662f2957330ac2ed73e4e74cc64532614c0234fc1caad | Python | 5,326 | 118 | import numpy as np
import pickle
import math
import os
from Functions import load_result
from Functions import save_result
from Trace_Value_Extraction import test_top_value
def NED_SED(c, test_path):
# Calculate NED and SED
# A is related to NED and B is associated with SED
layers = model_layers
Cmodels = class... |
4221b4c172c735707a6e1306b0fd93357058b9bfda40b96bdda304c855dc3d44 | Python | 5,327 | 141 | """Test pipeline Step 4 — network metrics parity with MATLAB.
Run from the repo root::
uv run python python/test_pipeline_step4.py
Only the deterministic metrics in ``meanap.pipeline.network_metrics`` are
checked here (see that module's docstring for what's out of scope — anything
depending on randomized null mo... |
649e4bead9ce9a11cbf80fa463aad04bdebcf193c7711c68a0f8184eef9e3a95 | Python | 5,328 | 153 | """Preprocess BraTS volumes into normalized 3-channel .npy training data."""
from __future__ import annotations
import argparse
from pathlib import Path
import nibabel as nib
import numpy as np
import splitfolders
from sklearn.preprocessing import MinMaxScaler
def parse_args() -> argparse.Namespace:
parser = a... |
24e8b9830196e7a243ef48df6898fe78fc7a9d50fc7fbab91a065bda6efa6634 | Python | 5,331 | 165 | # Copyright (C) CVAT.ai Corporation
#
# SPDX-License-Identifier: MIT
from collections.abc import Sequence
from typing import TypedDict
import attrs
import attrs.validators
import torch
import torch.utils.data
from torch import Tensor
from cvat_sdk.datasets.common import UnsupportedDatasetError
from cvat_sdk.pytorch.... |
d6b10e81b5d5bc1fd5225ed35c5da1ba683d6df42e725fd6db2569d993cb6d01 | Python | 5,331 | 113 | from PUMI.pipelines.func.func2standard import atlas2func
from nipype.interfaces import afni
import nipype.interfaces.utility as utility
from PUMI.engine import GroupPipeline, FuncPipeline, NestedNode as Node, QcPipeline
from PUMI.utils import relabel_atlas, get_reference, TsExtractor, timeseries_carpet_plot
@QcPipeli... |
5f01a0ea230fc8ab937e6a0c15f06666c877da3519df5b4844b131ea24ec33c6 | Python | 5,332 | 71 | # fsl_anat
# Usage: fsl_anat [options] -i <structural image>
# fsl_anat [options] -d <existing anat directory>
# Arguments (You may specify one or more of):
# -i <strucural image> filename of input image (for one image only)
# -d <anat dir> directory name for existing .anat directory... |
71667931eab91874476d24f847e1711ebbf449c3d3fa702b657fa264b4c3744f | Python | 5,333 | 142 | from brainscore_vision.model_helpers.check_submission import check_models
import functools
from transformers import AutoFeatureExtractor, CvtForImageClassification
from brainscore_vision.model_helpers.activations.pytorch import PytorchWrapper
from PIL import Image
import numpy as np
import torch
"""
Template module fo... |
a4e099471b747b9fadf7800a0013a4ba17c213cbcb2eb16b8574c825964c246d | Python | 5,333 | 145 | import os
import logging
import shutil
import xnat
from xnat.mixin import ImageScanData
import dicom2nifti
from dicom2nifti.exceptions import ConversionValidationError
from util.config_vars import config
from util.io import make_dir_if_not_exists
class DataImport:
"""
Imports the MRI-data as DICOMs using sp... |
e5c46ec55498183980bd617b2c69e55be2cad6666d7e5a5c95ce9a93a4ffcadd | Python | 5,333 | 142 | from brainscore_vision.model_helpers.check_submission import check_models
import functools
from transformers import AutoFeatureExtractor, CvtForImageClassification
from brainscore_vision.model_helpers.activations.pytorch import PytorchWrapper
from PIL import Image
import numpy as np
import torch
"""
Template module fo... |
b6affc7a25f98152f6a45df9bc312ce67064bb53bdf269b6b5a912b6a4c58cd4 | Python | 5,334 | 152 | #!/usr/bin/env python
"""
Wraps the pySerial library for RS232 communication.
Hazen 3/09
"""
import serial
import time
class RS232(object):
"""
The basic RS-232 communication object which is used by all the objects
that communicate with their associated hardware using RS-232.
"""
... |
c848865648bfb1a9bff5221b0a9eeb43eb9b7c46752dd35c0784846eab912089 | Python | 5,334 | 152 | from __future__ import division
import numpy.ma as ma
import numpy as np
import scipy as s
import scipy.special as special
from mofapy2.core.utils import *
from mofapy2.core import gpu_utils
# Import manually defined functions
from .variational_nodes import Gamma_Unobserved_Variational_Node
from mofapy2.core.distrib... |
8e77459f74632e73ef7eb76547be8805afca71fb34a838fcba88ce1073faeb25 | Python | 5,335 | 137 | import sys
import numpy as np
from scipy import sparse
import scipy.stats
import tempfile
from pathlib import Path
import subprocess
import multiprocessing
import boto3
import nibabel as nib
import nibabel.processing
import time
import os
import pickle
chunklistfile=sys.argv[1]
parcname=sys.argv[2]
reffile=sys.argv[3... |
4f40f0c7719f4a546596d65872a8a1ba6b84df2df7965534b935fe9d01421c61 | Python | 5,343 | 163 | import random
from typing import Optional, Sequence
from pathlib import Path
import hydra
import numpy as np
import omegaconf
import pytorch_lightning as pl
import torch
from omegaconf import DictConfig
from torch.utils.data import Dataset
from torch_geometric.data import DataLoader
from xrdsol.common.utils import PR... |
98c89ae3b7213ac53a395f84a982aa5cbdf5f0e19235ffaa785486527f280ea9 | Python | 5,345 | 133 | """
Metrics to assess performance of weight models.
Function named as ``*_error`` return a scalar value to minimize:
the lower, the better.
Metrics' interface doesn't strictly follow skleran's metrics interface.
"""
import pandas as pd
import numpy as np
from ..utils.stat_utils import (
calc_weighted_ks2samp,
... |
faa98b8e54222955a6b4779f008204f7b750c4471a05f7ad3099ef81866ec248 | Python | 5,347 | 153 | import glob
import os
import os.path as osp
from typing import Callable, List, Optional
import torch
from torch_geometric.data import (
Data,
InMemoryDataset,
download_url,
extract_zip,
)
from torch_geometric.io import fs, read_off
class ModelNet(InMemoryDataset):
r"""The ModelNet10/40 datasets ... |
1d2ccc7c0d88bcb4675f7f4fd637e66dd0855daea3701d3da3aa3beff132a27f | Python | 5,348 | 186 | #!/usr/bin/env python
"""Python script to run cell model"""
"""
/* Copyright (c) 2015-2022 EPFL-BBP, All rights reserved.
THIS SOFTWARE IS PROVIDED BY THE BLUE BRAIN PROJECT ``AS IS''
AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PA... |
297db13ede7d3deb3fb14a52009f44c55b7721345c0f6e37dfb70f8912a29eae | Python | 5,348 | 186 | #!/usr/bin/env python
"""Python script to run cell model"""
"""
/* Copyright (c) 2015-2022 EPFL-BBP, All rights reserved.
THIS SOFTWARE IS PROVIDED BY THE BLUE BRAIN PROJECT ``AS IS''
AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PA... |
39c95bd357bbf42f358a786f926b4453d5cc6ef89672fcd303192d8b1abea961 | Python | 5,348 | 186 | #!/usr/bin/env python
"""Python script to run cell model"""
"""
/* Copyright (c) 2015-2022 EPFL-BBP, All rights reserved.
THIS SOFTWARE IS PROVIDED BY THE BLUE BRAIN PROJECT ``AS IS''
AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PA... |
917b1aef7a970bfbfc76918b04029983272afdab5a0ef508bbd2e4101222566c | Python | 5,349 | 189 | # %%
import csv
import json
import torch
from argparse import ArgumentParser
import re
import torch
def clean_str(string):
"""
Tokenization/string cleaning for all datasets except for SST.
Original taken from https://github.com/yoonkim/CNN_sentence/blob/master/process_data.py
"""
string = re.sub(r"... |
cf512624ab453208ebf0d50ae5297cad22c4a1d7f1d774afc79948b0c3d5d515 | Python | 5,349 | 139 | import os
import numpy as np
import argparse
import subprocess
import psutil
import re
def kill_process_tree(pid, including_parent=True):
try:
parent = psutil.Process(pid)
children = parent.children(recursive=True)
for child in children:
child.kill()
psutil.wait_procs(... |
343290386c911f835c2eefc6e1381be4e683238a347a183e6c4ee1c1d2db74ad | Python | 5,350 | 186 | #!/usr/bin/env python
"""Python script to run cell model"""
"""
/* Copyright (c) 2015-2022 EPFL-BBP, All rights reserved.
THIS SOFTWARE IS PROVIDED BY THE BLUE BRAIN PROJECT ``AS IS''
AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PA... |
8bb0940afafa8e38b8999edbe85986748fa87937f0df6d6875e121a7ed75438d | Python | 5,350 | 139 | # This file contains experimental modules
import numpy as np
import torch
import torch.nn as nn
try:
from ..models.common import Conv, DWConv
from ..utils.google_utils import attempt_download
except:
from keypoint.models.common import Conv, DWConv
from keypoint.utils.google_utils import attempt_downlo... |
fc5823fab581a7a282a4f2a234d4bcd1b985e3afb7422d044fc7c87b17943fb9 | Python | 5,350 | 141 | #! /usr/bin/env python
"""Summarize what has been computed for each segmentation in a dataset.
``status config.yml`` scans the work_dir and reports, per segmentation and per
membrane surface, which steps have run: meshing, curvature, refinement (and the
accepted iteration), and which distance / orientation / thickness... |
16e715661664d5b4d63fe1dd42727813676300b9dc838a4e60357a89d198d2ea | Python | 5,352 | 171 | # This file is part of connectome-manipulator.
#
# SPDX-License-Identifier: Apache-2.0
# Copyright (c) 2024 Blue Brain Project/EPFL
from dataclasses import dataclass
from pathlib import Path
import json
from click.testing import CliRunner
from connectome_manipulator.cli import app
from bluepysnap.circuit import Circ... |
3c291ed5d836f75785f9ac91e1ad0d2779e36ca571b4c599a64902bcdc3acd18 | Python | 5,352 | 186 | #!/usr/bin/env python
"""Python script to run cell model"""
"""
/* Copyright (c) 2015-2022 EPFL-BBP, All rights reserved.
THIS SOFTWARE IS PROVIDED BY THE BLUE BRAIN PROJECT ``AS IS''
AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PA... |
56a5b7d24087c81c00d7aa29c8d05502acee63243294e047a5d155c7a97722c8 | Python | 5,352 | 186 | #!/usr/bin/env python
"""Python script to run cell model"""
"""
/* Copyright (c) 2015-2022 EPFL-BBP, All rights reserved.
THIS SOFTWARE IS PROVIDED BY THE BLUE BRAIN PROJECT ``AS IS''
AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PA... |
3f7c7952bb8c97535aaa9a813a74e0e183a0cc0e28a3f336f20d490f5d86d901 | Python | 5,353 | 118 | """Which earlier runs this one may read from.
This used to sit on the Paths tab, three groups below the folders it had nothing
to do with, while the switch that turns it on — **Use prior analysis** — was on
another tab entirely. You could fill these in and have them do nothing, or tick
the box and have it fail on a fo... |
be767771de4bde197620b0492d4d48719657324dc4a95cd60c0869c6f292fb7e | Python | 5,353 | 153 | ###############################################################################
#################### Boilerplate ########################
###############################################################################
import pandas as pd
import matplotlib.pyplot as plt
import os
import matplotlib... |
f6243d9afa99f8f1b5672a0e09ae28b786814f420c7094a1881a50cfa1a0f3c4 | Python | 5,355 | 170 | from __future__ import annotations
from dataclasses import dataclass
from functools import cached_property
from typing import Optional, Sequence, Union
import cv2
import numpy as np
import torch
from brainglobe_atlasapi import BrainGlobeAtlas
from numpy.typing import NDArray
from brainways.utils.atlas.slice_atlas im... |
a50a128aa0a777fbfa5dc5bbdf57546e9fcd9ef53e9ffc9058c0720b8f3c699c | Python | 5,356 | 112 | # Ultralytics 🚀 AGPL-3.0 License - https://ultralytics.com/license
from __future__ import annotations
import ast
from urllib.parse import urlsplit
import numpy as np
class TritonRemoteModel:
"""Client for interacting with a remote Triton Inference Server model.
This class provides a convenient interface ... |
b44cf08be7a7510c4bfaa762ea6104d668387573dd7e62e792cffa59d83186f1 | Python | 5,356 | 138 | """A module that contains unit tests for the :py:mod:`corelay.processor.flow` module."""
import pytest
from corelay.processor.base import FunctionProcessor
from corelay.processor.flow import Shaper, Parallel, Sequential
class TestShaper:
"""Contains unit tests for the :py:class:`~corelay.processor.flow.Shaper` ... |
95a0627f216bc9fad73df140266ef8df4f7b5c79a3eda53195783ca9b0693214 | Python | 5,357 | 180 | import base64
from collections.abc import Sequence
from functools import partial
from pathlib import Path
from typing import Any
import numpy as np
from docs.doc_modules.experiments import AutoDocExperimentInfo, run_capture_and_save
from docs.doc_modules.serve_experiments_utils import copy_inputs
from docs.doc_module... |
a351490051f73436b53787d820331b99ce4695001b0afae5a3e3e43c85fef896 | Python | 5,357 | 142 | """LangChain ``@tool`` wrappers for the ALCF IRI Facility API.
Each tool delegates to the pure-Python implementation in
:mod:`chemgraph.tools.alcf_iri_core`.
Seven category tools (facility, status, account, compute, filesystem,
task, auth) instead of one @tool per endpoint. Each accepts an
``action`` enum plus option... |
073038ad5563ca8a57a92748649c6123e7d097e839a1962d3a6c41a61c5d9bc5 | Python | 5,358 | 180 | import numpy as np
import concurrent.futures
from heig.utils import inv
class LDSC:
"""
cross-trait LDSC for estimating the intercept when there is sample overlap
"""
def __init__(
self,
ldr_z,
y2_z,
ldscore,
ldr_heri,
y2_heri,
n1,
n2,
... |
2175f3010de1fb0fc776dfd1941186523bbc8fe48b4a4dc80a4fa90ad70521c5 | Python | 5,358 | 186 | #!/usr/bin/env python
"""Python script to run cell model"""
"""
/* Copyright (c) 2015 EPFL-BBP, All rights reserved.
THIS SOFTWARE IS PROVIDED BY THE BLUE BRAIN PROJECT ``AS IS''
AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICUL... |
46711a387f6556a257f7b9ccd8bcc849bb055ab19db467bf7993dec647003f22 | Python | 5,358 | 168 | from __future__ import annotations
import dataclasses
import numpy as np
import osam
from loguru import logger
from numpy.typing import NDArray
from .._ai_models import supports_point_prompts
from .._shape import Shape
from ._geometry import _round_bbox_to_int
from ._osam_session import OsamSession
from ._shape_buil... |
6cb01fcc4ed6ae3868c61bbe6b71c2c6157f1ffe9a406036a2830bde45fd640c | Python | 5,358 | 153 | import tempfile
from pathlib import Path
from typing import Optional
import click
import numpy as np
import tqdm
from simple_mri import SimpleMRI, load_mri, save_mri
from loguru import logger
from dti.utils import mri_number_of_frames
from gmri2fem.reslice_4d import reslice_4d
def construct_tensor_from_eigs(
dt... |
baa8552fe76ebfa5aac476c122b4ae682da619a52f85ce25dd71abe235feb8b6 | Python | 5,358 | 181 | # Authors: Lucas Berg and Elnaz
#
# Program that calculates the APD for a single cell in the grid by passing its
# transmembrane potential over the time as input.
#
# This program also works with multiple AP's !
import sys
import subprocess
import time
import numpy as np
def forwarddiff(y, h):
n = len(y)
re... |
cfe274f9759e48dd146d5b3f18b2bd3ee24700d67992d2794c98235f5bd922a1 | Python | 5,358 | 186 | #!/usr/bin/env python
"""Python script to run cell model"""
"""
/* Copyright (c) 2015 EPFL-BBP, All rights reserved.
THIS SOFTWARE IS PROVIDED BY THE BLUE BRAIN PROJECT ``AS IS''
AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICUL... |
e4249d33a65f008d095afde0af78f6f01539a0af9a69978105e028a9aa8b4903 | Python | 5,358 | 186 | #!/usr/bin/env python
"""Python script to run cell model"""
"""
/* Copyright (c) 2015 EPFL-BBP, All rights reserved.
THIS SOFTWARE IS PROVIDED BY THE BLUE BRAIN PROJECT ``AS IS''
AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICUL... |
4f77b238f4231366cc39455aea3c5a8fef6205dfa247eea9ecb0ea01fcdebe77 | Python | 5,359 | 192 | """
This script demonstrates
* the kx-ky sampling pattern in diffusion MRI,
* the ky-diff sampling pattern in diffusion MRI.
Author: Zhengguo Tan <zhengguo.tan@gmail.com>
"""
# %%
import numpy as np
import matplotlib.pyplot as plt
import argparse
# %%
parser = argparse.ArgumentParser(description='plot sampling ... |
0c6c754aa84919cea129350e85e2440ff6c2b398eaeea395412f33896a147d00 | Python | 5,360 | 201 | #!/usr/bin/env python3
"""
Pre-download BigWig/BigBed tracks for Docker image
This script pre-downloads all genomic tracks specified in a bwq_config.yaml file
into a persistent cache directory. Used during Docker build to create "prewarmed"
images with tracks already cached.
Usage:
python predownload_tracks.py <b... |
3ac03556018722d20cb8eb27c15e140c3d78aa6e833aa5a01a0fbbd97f624cc6 | Python | 5,361 | 170 | #!/usr/bin/env python
"""
Generic Obis laser control (RS-232 over USB).
Hazen 7/10
"""
import traceback
import storm_control.sc_hardware.serial.RS232 as RS232
class Obis(RS232.RS232):
"""
This controls a Coherent Obis laser using RS-232.
"""
def __init__(self, **kwds):
"""
... |
b16eaa103560bdbc3e899c8cd749e1e79545ec74e030e80261b94b73151f1a91 | Python | 5,361 | 172 | from dataclasses import dataclass
from pathlib import Path
from typing import Literal, Optional
import numpy as np
import torch
from eir.setup import schemas
from eir.setup.input_setup_modules.common import (
DataDimensions,
get_data_dimension_from_data_source,
get_dtype_from_data_source,
)
from eir.setup... |
545f01fc2baa59842bfe4094b70ec037f1449b06c8555ba2af9539a9d940a9d8 | Python | 5,362 | 186 | #!/usr/bin/env python
"""Python script to run cell model"""
"""
/* Copyright (c) 2015 EPFL-BBP, All rights reserved.
THIS SOFTWARE IS PROVIDED BY THE BLUE BRAIN PROJECT ``AS IS''
AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICUL... |
303d3c1a0912de91bb947709dffabea7ae2bb92df7e4a9b0367e6bb7bbbf907d | Python | 5,363 | 153 | import torch
import torch.nn as nn
import numpy as np
import ase
from ase.io import read
# utils imports
from utils.plot_corr import plot_corr
from utils.neuralnets.FFNet import FFNet
from utils.distances import get_bond_length_hoxa
from utils.kernels import get_1D_kernels_k33
# define options
torch.set_printoptions(... |
7d10ff8fc8165130a1a1914dfa34814fc8287de6b3847e580b1f4e36fc64c9bd | Python | 5,363 | 128 | """ This module contains both standard metrics from libraries and custom ones for evaluation of our models.
The idea is to gather all of them in one module for better imports and referencing.
"""
import os
import numpy as np
from sklearn.metrics import accuracy_score, precision_score, recall_score, f1_score, confu... |
17e3623b9b7cf739ca8cd922c9973dd76347f9b281919ec0284db6bd521629e0 | Python | 5,364 | 147 | # -*- coding: utf-8 -*-
# python standard library inputs
import os
# external inputs
import numpy as np
import nibabel as nb
from nipype.interfaces.fsl import ErodeImage, DilateImage
from scipy.ndimage.morphology import binary_fill_holes
def skullstrip_epi(file_in, roi_size=5, scale=0.75, nerode=2, ndilate=1,
... |
665eb7c6bf936f565fb91aaf56e32c4e1f4211f54e944683da4c239845d76e2f | Python | 5,364 | 186 | #!/usr/bin/env python
"""Python script to run cell model"""
"""
/* Copyright (c) 2015 EPFL-BBP, All rights reserved.
THIS SOFTWARE IS PROVIDED BY THE BLUE BRAIN PROJECT ``AS IS''
AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICUL... |
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