sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
242cb45910bc8b06b9e0cc5b139ccb86eb7b80e153f5aea5804a7ef8998bfa1b | Python | 10,259 | 315 | import glob
import os
import socketserver
import threading
import tempfile
from urllib.parse import urlparse
from typing import Dict, Tuple
from cloudvolume import CloudVolume
from cloudvolume.server import ViewerServerHandler
import napari
from napari import Viewer
import fastremap
import numpy as np
import neurogl... |
0fae0ee8dc33881a61b5d1bdb749be66e2945b2c56b73980d839e508eacf6653 | Python | 10,260 | 251 | import collections
from typing import ClassVar, NamedTuple, Literal
import numpy as np
import polars as pl
from rscvp.util.cli import SelectionOptions, CodeAlias, HEADER, get_headers_from_code
from scipy.stats import zscore
from typing_extensions import Self
from argclz import argument
from neuralib.typing import fla... |
9f0984cface875a3365ec6f60524b1eac28b7a3003e2df5a206599d3a46fb96c | Python | 10,260 | 238 | import os
import pandas as pd
import json
import nibabel as nib
import numpy as np
import re
import glob
from nipype import Node, Workflow, MapNode
from nipype.interfaces.utility import IdentityInterface, Merge, Function
from cvdproc.pipelines.dmri.lqt.lqt_nipype import LQT
from cvdproc.bids_data.rename_bids_file imp... |
eadbced952cd6e229d6833551d5dca2d3d0beaf814a6893088b5efb264aebb68 | Python | 10,260 | 189 |
import pygame
import time
import re
import numpy as np
##############################
# training
##############################
def practice(screen_width, screen_height, window, application_path, stimuli_width, stimuli_height,
give_a_fixed_time_interval, from_xy_to_position, position_x_list, position_y_... |
a61f29e810e929b172f2e9be2e11e54ab49e432bfa2f452ad3406a3abfc0fcf2 | Python | 10,261 | 281 | import os
import shutil
def importElastix():
# Import Elastix
import sys, os
sys.path.insert(0, '/home/acorver/ClearMap2/')
_cwd = os.getcwd()
os.chdir('/home/acorver/ClearMap2/')
from ClearMap.Environment import elx, res, p3d
os.chdir(_cwd)
# Return modules
return elx... |
e95969575bdbcff5855b55d02f4eb930004319deec4c1d98f86ee2178237f9dc | Python | 10,262 | 254 | """
MSI Delocalization Scoring Pipeline
────────────────────────────────────
Quantifies lipid delocalization from tissue into the background region
using spatial metrics (mean distance, nonzero area).
Workflow:
1. Load overlaid h5ad (with tissue mask from the annotation tool)
2. TIC-normalise intensities
3. Remo... |
f423a4d6c7ed28eedc2add0eec2f52c7b7383dcf837a4705684911b6bd375aaf | Python | 10,269 | 254 | from brainscore_core.supported_data_standards.brainio.assemblies import PropertyAssembly
from brainscore_vision import data_registry, stimulus_set_registry, load_stimulus_set
from brainscore_core.supported_data_standards.brainio.s3 import load_assembly_from_s3, load_stimulus_set_from_s3
BIBTEX = """@article{malania2... |
0ed59fd38ece28fb546ba1d64d3ba71a8feb353bb3a17c98ea1ea59a4dde9835 | Python | 10,270 | 225 | import pandas as pd
import shutil, os
import os.path as osp
import torch
import numpy as np
from dgl.data.utils import load_graphs, save_graphs, Subset
import dgl
from ogb.utils.url import decide_download, download_url, extract_zip
from ogb.io.read_graph_dgl import read_graph_dgl, read_heterograph_dgl
from ogb.io.read_... |
a60f060099b1340273060a989e2d68c5740036339de81b73b4710f5968bc8b98 | Python | 10,273 | 327 | '''
Models used across multiple scripts.
'''
import sys, time
import numpy as np
import rsa
from typing import Any, Union, Callable
class InformationTheoretic:
'''
Placeholder class to obtain IT measures
through inheritance.
'''
def __init__(self) -> None:
'''
Never used.
... |
0d06581c319bbaaea7c6c748e0de02a403ce413681606444e886097235216184 | Python | 10,276 | 218 | import warnings
warnings.filterwarnings("ignore", message="It is not recommended to directly access")
import os
import argparse
import numpy as np
import pandas as pd
import torch
import torch.nn as nn
import torch.optim as optim
from torch_geometric.data import DataLoader
from model import HimNet
from dataset import s... |
0c7aa01177d5996c8f69e34ba2debfb20a10c174aa2e4de84ee5e2060625c81a | Python | 10,282 | 280 | import torch
import torch.nn as nn
import torch.nn.functional as F
from torchvision import models
from torch.nn import Module, Conv2d, Parameter, Softmax
from collections import OrderedDict
def conv3otherRelu(in_planes, out_planes, kernel_size=None, stride=None, padding=None):
# 3x3 convolution with padding and r... |
c21010972895d5b48d640d248a82a9a9d9512072225e3f53bbe222c094b7dcbd | Python | 10,283 | 259 | import os
import pandas as pd
import numpy as np
import torch
import librosa
import librosa.display
import matplotlib.pyplot as plt
from torch.utils.data import Dataset
from torchvision import transforms
import sys
sys.path.append(os.path.abspath(os.path.join(os.path.dirname(__file__), '..')))
from da... |
7e6bb833372e104199234cfa13b3ee20995a9196b37a14e9d8c18e39a926bfaf | Python | 10,285 | 235 | import os
from typing import List
import pandas as pd
# Variant-level SNV TSV file name, which is used for implementing the following
# known column display order change:
# - Move Variant_ID_hg38 and Protein_change columns after the
# Gene_symbol column
VARIANT_SNV_FN = "variant-level-snv-consensus-annotated-mut-fr... |
7adac492c22620f8e8eb7d86c8803d43056ba320572d6f9f53d8d9fbbfb6739f | Python | 10,290 | 259 | import os
import h5py
import yaml
import sys
import numpy as np
from copy import deepcopy
trans_fac = 1.5 #stds from mean applied on #(transients) to include/exclude transients
ditch_lonely_offperiods = False
maxdist_lonelies = 2.
ww_smooth_trans_s = 0.1
thr2_perc = 50 #to detect network transient bursts, percentage... |
5d9233472f1003ec59580b6c16a2187d97a44c13b3d665ecd8f1f74d8d0942b5 | Python | 10,292 | 261 | """
This is a demo function for very basic grid search style parameter selction.
By default a 3 X 3 X 3 paramater space is searched and the Sprod performance is
prioritized based on the qualities of the constructed latent graph. Parameter sets
that preserve the overall spot physical struction and image similarity bett... |
79aa828a655fc7253b05dd7f04b0620c791d081c4c747159d86d5e038fe209fc | Python | 10,292 | 321 | """
Validation and test data generation script with 1000M photons
(10x regular photon count).
This script generates validation and test datasets with increased photon counts
for more accurate Monte Carlo simulations. It supports both physiological and
physical parameter types and can be run on cluster environments.
"... |
cda68c70b74ee05db278c83d409614c68709fe73d2028d8a680f657ab2e13e0f | Python | 10,300 | 271 | import os
import time
import copy
import argparse
import torch
import torchvision
from torchvision import datasets, transforms, models
from torch.utils.data import DataLoader, random_split, Dataset
import matplotlib.pyplot as plt
import seaborn as sns
from tensorboardX import SummaryWriter
import numpy as np
from torch... |
8ffe7214a598210e78022a83df82a643a38521ad066885857ccc5a0ad518c94d | Python | 10,301 | 204 | import os
import random
import argparse
import numpy as np
import os.path as op
import torch
from torchinfo import summary
import torch.nn as nn
import torch.optim as optim
from torch.utils.data import DataLoader
from sklearn.model_selection import StratifiedKFold
from sklearn.utils.class_weight import compute_class_w... |
8cdb15af2b57699d368c98019088f6d0d84acfa5fb7077b61b2ddcbacb809372 | Python | 10,303 | 276 | """
foundcog_glm.py — Subject-level GLM pipeline for the FOUNDCOG dataset (pictures task).
This script builds and runs a NiPype workflow that fits a General Linear Model
for each subject/session/run in the BIDS dataset. For each run it:
1. Resolves file paths (functional image, events, motion parameters)
2. Builds... |
1a80117866ad443c9b18f30d6ae140bb5e2c76f5e0370dc2b3d065f4dd7a2bb3 | Python | 10,306 | 221 | import os
import numpy as np
import skimage.io as io
import glob
from natsort import natsorted
import json
import tqdm
from helper import reading_data
import shutil
def extract_cubes_for_hyperparams_search(im_stack, cube_dict, save_dir, padding=32):
im = im_stack
max_z, max_y, max_x = im.shape
save_path = ... |
40a641855cdea49b34514ef2bf70e48c9da14480e50c5bb7d8afd91b495677bf | Python | 10,306 | 176 | """Validate manifest structure and reconstructed OpenPlant output against it."""
from __future__ import annotations
import argparse
import json
import os
import sys
from collections import Counter
from pathlib import Path
from PIL import Image
from .rebuild import IMAGE_EXTENSIONS, atomic_write, manifest_statistics,... |
addc14171c71a8b8d72be8b2d4bd6c5e2c1237001fa9396f1cb6aa559fa3c02b | Python | 10,315 | 251 | import inspect
import warnings
from typing import Any, Callable, Dict, Final, List, Optional, Union
import torch
import torch.nn.functional as F
from torch import Tensor
from torch.nn import Identity
from torch_geometric.nn.dense.linear import Linear
from torch_geometric.nn.resolver import (
activation_resolver,
... |
4295d9574827f1bd03847d2fed2b29f507bcf68301d58a92ca3f3014268bec04 | Python | 10,316 | 250 | import os
from copy import deepcopy
from typing import Optional, Union, Dict
import torch_geometric.utils
from omegaconf import OmegaConf, open_dict
import pytorch_lightning as pl
from overrides import overrides
from pytorch_lightning.utilities import rank_zero_only
from torch_geometric.utils import to_dense_adj, to_de... |
ca7ed5d03b86719341b46fc199c63b7576e6dcaa2e95183200821000bc61b6be | Python | 10,316 | 206 | # add the path of custom functions
import sys
from pathlib import Path
import os
script_dir = Path(__file__).parent
project_root = script_dir
while not (project_root / 'Deps').exists() and project_root.parent != project_root:
project_root = project_root.parent
# Add project root to the Python path if it's not alre... |
0c753fa2096d1881105df336953923a6be85e199cd974c40e7fbaf4a94449da7 | Python | 10,320 | 232 | from __future__ import annotations
import torch
from torch import Tensor, nn
from torch.nn import functional as F
class CNN(nn.Module):
def __init__(self, features: nn.Module, readout: nn.Module):
super().__init__()
self.features = features
self.readout = readout
def forward(self, in... |
5b31a3ba92aed44a3f4af706325c37ea7e074e4a01bbca7c7c88106ecff40e79 | Python | 10,323 | 356 | ###############################################################################
#################### Boilerplate ########################
###############################################################################
import pandas as pd
import matplotlib.pyplot as plt
import os
import matplotlib... |
3765a10b379e94c73b181a25ea128b1aa760d0f6f14550f01b2994a5beaac741 | Python | 10,324 | 283 | """ Image to Patch Embedding using Conv2d
A convolution based approach to patchifying a 2D image w/ embedding projection.
Based on code in:
* https://github.com/google-research/vision_transformer
* https://github.com/google-research/big_vision/tree/main/big_vision
Hacked together by / Copyright 2020 Ross Wightma... |
8c60cda8c54784631ee77e09d72e7ff8681162c04a18d5f9e53d5c9c319a10ab | Python | 10,329 | 291 | from __future__ import annotations
from dataclasses import replace
from typing import TYPE_CHECKING, Any, Callable
import napari.layers
import numpy as np
from PyQt5.QtWidgets import QApplication
from brainways.pipeline.brainways_params import AtlasRegistrationParams, BrainwaysParams
from brainways.ui.controllers.ba... |
c702fa823f93191739400c4bd709806d4bdf04311b9d79a73e9f14462c66841d | Python | 10,330 | 267 | '''
Quick script to aggregate results from increasing k
analysis in encoders.
All options supported by `subject_rsa_enc.py` are
also available here, of course.
NOTE: The output report created by this script isn't
necessarily going to include the prettiest figures; it's
mostly to get a quick overview & to get all the ... |
6550e9d1bf1f4cd79290224fb54692134fad840856dabe4901a667bb78cd26eb | Python | 10,332 | 249 | '''
Quick script to collect data from rERP models in learning task
and perform statistical inference.
All options supported by `subject_rerp_mt1.py` are
also available here, of course.
NOTE: The output report created by this script isn't
necessarily going to include the prettiest figures; it's
mostly to get a quick o... |
b11460289a2808a79becdd65fba5d11947935843542f5a987e2c273c63114427 | Python | 10,334 | 255 | """
DMC-BrainMap widget for padding .tif files to match atlas resolution.
2024 - FJ
"""
from qtpy.QtCore import Signal
from qtpy.QtWidgets import QPushButton, QWidget, QVBoxLayout, QMessageBox, QProgressBar
from napari import Viewer
from napari.qt.threading import thread_worker
from napari.utils.notificatio... |
093522bd65f58272826c6e3b3bee8f8c4b992b168493e2cd6d7f8be76c617225 | Python | 10,342 | 248 | #! /usr/bin/env python
# -*- coding: utf-8 -*-
"""
Script to compute Multishell Multi-tissue Constrained Spherical Deconvolution
ODFs.
By default, will output all possible files, using default names.
Specific names can be specified using the file flags specified in the
"File flags" section.
If --not_all is set, only ... |
d01bad6cd46910c7979a09c96e49526ecfadbf574c832527cc1af67d39b6885d | Python | 10,342 | 250 | import sys
import numpy as np
import yaml
import os
import matplotlib as mpl
from matplotlib import pyplot as plt
pathpath = 'PATHS/filepaths_carlen.yml'
fformat = 'svg'
with open(pathpath, 'r') as myfile: pathdict = yaml.safe_load(myfile)
sys.path.append(os.path.join(pathdict['code']['workspace'],'pfcmap','python',... |
139bf749402ff56ada5d7f8a61d95e31b55bf83433448adaa6afb1e605368d60 | Python | 10,344 | 297 | from argparse import Namespace
from pathlib import Path
from typing import TYPE_CHECKING
import numpy as np
import pandas as pd
import torch
from eir.setup.output_setup_modules.survival_output_setup import (
ComputedSurvivalOutputInfo,
)
from eir.setup.schemas import SurvivalOutputTypeConfig
from eir.train_utils.... |
e819e5026b53f330566292d3537b09421699ac2a22d0a1c6f623d6e30e63dabc | Python | 10,359 | 210 | # 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... |
f0656d1073a5cc6d2c387c04b0e5ad454ccea2cb7e31caf21ee2233aa19a55bc | Python | 10,361 | 216 | import argparse
from os.path import join
import pickle
import keras
from keras.optimizers import Adam
from keras.callbacks import EarlyStopping, ReduceLROnPlateau
import utils
import h5py
from model_zoo import DeepSTARR
import pandas as pd
import wandb
from wandb.integration.keras import WandbMetricsLogger
import yaml
... |
1f1ad5872f942f90902ee2fd5c20c06d248a29d218e91d0822674ac7c00b1cec | Python | 10,363 | 278 | """
This module implements a Residual Network
Author:
Burhaneddin Yaman
Zhengguo Tan <zhengguo.tan@gmail.com>
"""
import torch
import torch.nn as nn
from typing import Tuple, Union
# %%
class ComplexBatchNorm2d(nn.Module):
def __init__(self, num_features):
super().__init__()
self.real_bn... |
811cc62fd9edccbbe40cc3bb0dc897a6c2e1edba733bdbdd3db886b6f1df58b1 | Python | 10,363 | 239 | """Backend-agnostic, lazily configured single-component gRASPA-SYCL MCP server."""
import asyncio
import math
from pathlib import Path, PurePath, PurePosixPath, PureWindowsPath
import uuid
from chemgraph.execution.base import TaskSpec
from chemgraph.mcp.cg_fastmcp import CGFastMCP
from chemgraph.schemas.graspa_schema... |
0b884f5214cc88f22657b28a3deb69b7ab33974b107796c4f8a3d2592d0e5c29 | Python | 10,370 | 341 | #####################################################################################################
### Utility functions for different purposes, mainly regarding the processing of simulation data. ###
#####################################################################################################
### Copyright... |
8fe40dae2a270c3813a3bbdd3208be4d581a7b3d317728b932eb4fb7b8172fbc | Python | 10,370 | 329 | # -*- coding: utf-8 -*-
"""
Created on Thu Mar 26 17:12:40 2020
Collection of functions for dealing with two-photon recordings and suite2p
outputs.
@author: Samuel Failor
"""
from os.path import join
import numpy as np
from . import timelinepy as tl
from . import cortex_lab_utils as clu
import scipy.io as sio
def... |
93324c6f04e5b0a51efbf89412c3077e020b98ea10915ed4d8fb7e8b6bf5ac57 | Python | 10,370 | 202 | import os
import re
import zipfile
from glob import glob
import brainscore_vision
import h5py
import numpy as np
import pandas as pd
import xarray as xr
from brainscore_vision.knownfile import KnownFile as kf
from brainscore_vision.lookup import pwdb
from brainscore_vision.assemblies import AssemblyModel, AssemblySto... |
8db24a608c065953cada5af2e29964054049c17d7742604612902269d327196c | Python | 10,372 | 302 | import os
from types import SimpleNamespace
os.environ.setdefault("QT_QPA_PLATFORM", "offscreen")
import pytest
from magicgui.widgets import FunctionGui
from qtpy.QtWidgets import QApplication
from napari_dmc_brainmap.padding import padding
from napari_dmc_brainmap.params import params
from napari_dmc_brainmap.prepr... |
ccfb25d2d4fd2124962b5c4fd4a2a97b566351aae1481ef7e964edab07260c8a | Python | 10,372 | 258 | import logging
from typing import Optional, Union
import torch
from torch import Tensor
from torch.nn import ReLU, Sequential
from torch_geometric.explain import Explanation
from torch_geometric.explain.algorithm import ExplainerAlgorithm
from torch_geometric.explain.algorithm.utils import clear_masks, set_masks
from... |
79befcdbd1ca2f9f94cf92281818f761be2bd26a2ef91a126200af5b57170a74 | Python | 10,382 | 335 | """Main score_dm extension for predefined diabetes PRS."""
import argparse
import logging
import os
import sys
import pandas as pd
from .grouped_scoring import score_grouped
from .hla_int_grs import score_int_hla
from .SQL.get_dm_sql import get_dm_sql, get_dm_meta
from ..core.score_bcf import score_bcf
from ..core.ut... |
cc7c21105113834a47d66acedba2d7fe4a9faf015d8fd2b9d71685547ef16af1 | Python | 10,385 | 345 | """CLI entry point for ChemGraph evaluation benchmarks.
Usage::
# Quick local evaluation using a profile
chemgraph eval --profile quick --models gpt-4o-mini --judge-model gpt-4o
# Standard evaluation with LLM judge
chemgraph eval --profile standard --models gpt-4o-mini gemini-2.5-flash
# Explici... |
497d86d0e07e3345d12c3dd05a8b844943ad593caf1330756604219887e130b1 | Python | 10,391 | 196 | import mat73
import argparse
import numpy as np
import cebra
from pathlib import Path
from choice_mode_functions.combine_all_trials_all_brain_regions import dataset_all_sessions, choice_sampled_population, ablate_all_regions_except_one
from choice_mode_functions.split_dataset import split_train_test_data
from choice_mo... |
6535db7d58ce01a5757729c3f060e79d0e83b1c08e5aab2cb900b00daca1437f | Python | 10,391 | 311 | """
This script computes three dimensions from neural activity:
switch evidence, actor outcome, and observer outcome, using TDR
Based on these dimensions angles between these are computed.
Each calculation is repeated resulting in a distribution of angles.
"""
import sys
import os
sys.path.insert(0, os.path.dirname(o... |
4842381ff9de7b7fd3b09554f36a908b8b3f3c24dee0b70f0201594e08c6f623 | Python | 10,397 | 197 | import nipype.interfaces.afni as afni
import nipype.interfaces.fsl as fsl
import nipype.interfaces.ants as ants
from PUMI.engine import NestedNode as Node
from PUMI.pipelines.anat.anat2mni import anat2mni_fsl, anat2mni_ants_hardcoded, anat2mni_ants
from PUMI.pipelines.multimodal.masks import create_ventricle_mask, resa... |
d241f1e09a080582fd37ec99e50410cbabfb101a77ee11ef1d384f5e5808bb4d | Python | 10,397 | 283 | import gc
import os
import torch
import tqdm
from scipy.stats import spearmanr
from sklearn.metrics import r2_score
from torch.optim.lr_scheduler import MultiStepLR
from SWOW_prediction.data_preprocessing import construct_property_dataset
from SWOW_prediction.evaluation import evaluate
from SWOW_prediction.models imp... |
29cbc76c2d3a8ea039ea94f36652a3a4bed4e067a7a10950717fb93b3d3f3e43 | Python | 10,398 | 231 | import argparse
from os.path import join
import pickle
import keras
from keras.optimizers import Adam
from keras.callbacks import EarlyStopping, ReduceLROnPlateau
import utils
from model_zoo import DeepSTARR
import plotting
import pandas as pd
import wandb
from wandb.integration.keras import WandbMetricsLogger
import y... |
43fbdff65149c30e502fe07d13fd2b072f70a7ca8cf122bb8eb9832de7e404b8 | Python | 10,399 | 302 | #!/usr/bin/env python3
"""
=============================================================================
Austin Dibble
University of Glasgow
2026
neurofm/inference.py
Core inference logic. The NeuroFM class is the primary user-facing API.
=============================================================================
"... |
0f64c87c000986b561f28ef2db856766df23385cdbcf0f707be64e1dd4f1b903 | Python | 10,404 | 283 | import os
from sklearn import preprocessing as pp
import pandas as pd
import numpy as np
import matplotlib.pyplot as plt
from scipy.stats import pearsonr
from sklearn.metrics import mean_squared_error
from math import sqrt
import scanpy as sc
import torch
import torch.nn as nn
from torch.backends import cudnn
import ra... |
9041cffaacb6168d6c298d40a286e49d30730694fcc2723449e86c1604304f4b | Python | 10,407 | 282 | import math
import typing
from typing import Optional, Tuple, Union
import torch
import torch.nn.functional as F
from torch import Tensor
from torch_geometric.nn.conv import MessagePassing
from torch_geometric.nn.dense.linear import Linear
from torch_geometric.typing import (
Adj,
NoneType,
OptTensor,
... |
697a596a8f2a0c15cf86cf243e242267097b5f398b506722330f8a2cc7118636 | Python | 10,413 | 296 | #!/usr/bin/env python
# Copyright (c) 2015 Tobias Neumann, Philipp Rescheneder.
#
# This file is part of Slamdunk.
#
# Slamdunk is free software: you can redistribute it and/or modify
# it under the terms of the GNU Affero General Public License as
# published by the Free Software Foundation, either version 3 of the
#... |
5eafdc8f1a9395372cb9bdb1313c25a9d174177c478fc1700be263231d5b0ca4 | Python | 10,417 | 329 | # -*- coding: utf-8 -*-
"""
Zebrafish ANATOMICAL ONTOLOGY
"""
import obonet
import numpy as np
import os
import networkx as nx
import matplotlib.pyplot as plt
import pandas as pd
import matplotlib as mpl
from scipy.cluster.hierarchy import dendrogram
from matplotlib import cm
from sklearn.decompositi... |
f94eb6c86195bc0ee696b9b2f1f18b6810eedbb39e511bd6ec969716a67c0530 | Python | 10,420 | 273 | """Electrodermal activity features from the UL-DD EDA channel (Empatica E4, 4 Hz).
Tonic/phasic separation uses cvxEDA (Greco et al., IEEE TBME 63(4):797-804, 2016)
when cvxopt is installed, and falls back to a zero-phase Butterworth split
otherwise. Both paths are exposed so the choice can be reported in the paper.
"... |
fe23bf88b0cd1fbba6b033e9cc683cc5fa690454495bb0b1c1bd630c75fad9a5 | Python | 10,425 | 296 | import argparse
import torch
import torch.nn.functional as F
from torch.utils.data import DataLoader
import torch_geometric.transforms as T
from torch_geometric.nn import GCNConv, SAGEConv
from ogb.linkproppred import PygLinkPropPredDataset, Evaluator
from logger import Logger
class GCN(torch.nn.Module):
def ... |
43bcb8bf4799269f5229f4504291cc165c62ca409507aaf6b3095d3eada9e23d | Python | 10,429 | 321 | import torch
import torch.nn as nn
from einops import rearrange
from einops.layers.torch import Rearrange
def conv_3x3_bn(inp, oup, image_size, downsample=False):
stride = 1 if downsample == False else 2
return nn.Sequential(
nn.Conv2d(inp, oup, 3, stride, 1, bias=False),
nn.BatchNorm2d(oup),... |
6ba7ac0f092de446b38c9b65df20b20dadfd8722afc78c2318c02f28b231f81e | Python | 10,431 | 181 | from PyQt5.QtWidgets import QLabel,QGraphicsScene,QFrame, QGraphicsItemGroup, QGraphicsPixmapItem, QGraphicsEllipseItem
from PyQt5.QtGui import QColor, QPen
from PyQt5.QtCore import Qt
from napari_dmc_brainmap.registration.sharpy_track.sharpy_track.view.QGraphicsViewerMT import QGraphicsViewMT
from napari_dmc_brainmap.... |
aa6199b1f385b9b205280ee5350d098c8be6e214154a1788f457400d97eed916 | Python | 10,439 | 272 | """
lasagna plugin for exploring the Allen Brain Atlas:
1. Display of average template brain.
2. Reporting of brain area name
more stuff...
Rob Campbell
"""
import os
from PyQt5 import QtGui, QtCore
# For the UI
from lasagna.plugins.ara import ara_explorer_UI
# For contour drawing
from lasagna.plugins.ara.ara_pl... |
1e0a6b1920bb5bf7b3262fc8d1d7bb7efc6bf155a4827b29d14689b8ff1facdf | Python | 10,440 | 330 | import numpy as np
import pytest
from brainscore_vision import load_stimulus_set, load_dataset
from brainscore_vision.benchmarks.geirhos2021.benchmark import DATASETS
def test_count():
assert len(DATASETS) == 12 + 5
@pytest.mark.parametrize('assembly_identifier', [
pytest.param('Geirhos2021_colour', marks=... |
0360da7688c3381855acd898a438d446af2d864f5d37099fd5cad60cde1834cb | Python | 10,444 | 223 | import os
from collections import defaultdict
import pandas as pd
import numpy as np
import scipy as sp
from matplotlib import pyplot as plt
import matplotlib as mpl
from .utils import neighbors as nb
from .utils import stat, vis, util, io
def vis_single_edge_stat_traces(edge_trace_stat):
"""
Input:
... |
73bdd48130cd75e43665f1cdb298ebe71c614d3ca7b6553a48381d59f5e8c4b7 | Python | 10,454 | 205 | import nighres
import os
import nibabel
import numpy
import glob
inpath = '/home/pilou/Projects/Cerebellum/Cerebellar-segmentation-ABC/'
prev_sfx = 'nighres/denoise/'
out_sfx = 'nighres/coreg/'
t1map_sfx = '_anat_inv1_s2c10_lcpca-den_qt1map-t1.nii.gz'
t1w_sfx = '_anat_inv1_s2c10_lcpca-den_qt1map-uni.nii.gz'
t1ref_sf... |
9b9e758035547497896ddad3271c4ffa9a2d7cd6e0b56d84f93c20e940297e39 | Python | 10,454 | 302 | from os import mkdir
from os.path import exists, join
from collections import defaultdict
import pylab
from sklearn.datasets import fetch_lfw_people
from sklearn.impute import IterativeImputer
import numpy as np
from fancyimpute import (
SimpleFill,
IterativeSVD,
SoftImpute,
BiScaler,
KNN
)
from ... |
ede5d6881fd053f83987940ccf8cfa56dc95862f1a27928c4c2d5b2c42b4ce2c | Python | 10,454 | 223 | import logging
import os
from pathlib import Path
import pytorch_lightning as pl
import torch.nn as nn
from pytorch_lightning.plugins import DDPPlugin
from project.datasets.PICP.picp_dgl_data_module import PICPDGLDataModule
from project.utils.deepinteract_constants import NODE_COUNT_LIMIT, RESIDUE_COUNT_LIMIT
from pr... |
a49a4bf0f507d40da38ac963914cd371afdf5cf4879c1126ad062ef755d1a3ad | Python | 10,457 | 299 | """
Readers extracting gene (exon and intron) information from bed / gtf / gff
formats.
- GeneReader: yields exons
- CDSReader: yields cds_exons
- FeatureReader: yields cds_exons, introns, exons
For gff/gtf, the start_codon stop_codon line types are merged with CDSs.
"""
import sys
from bx.bitset_utils import (
... |
e84a9af53129c6c4c3b529943e5f9b880d9d809b8fa7bf4de4417d8d56ce3d0c | Python | 10,457 | 281 | """
Module for optimal battery construction
Author: Bassel Arafat
"""
import numpy as np
import pandas as pd
from numpy.linalg import eigh
import torch as pt
import PcmPy as pcm
def eigenval_crit(G, center=True):
"""Computes various criteria based on the eigenvalues and mutual information of a matrix G.
Assum... |
eb74c15c6eb4034a6e954a6117ec9883819564646be42068dd5db529de4081d4 | Python | 10,457 | 254 | """
Loading Data
============
In this tutorial we demonstrate the various options for loading data. This tutorial covers:
1. The Data Class
2. Getting Example Data
3. Loading Data in NumPy Format
4. Loading Data in MATLAB Format
5. Loading Data in fif Format
6. Loading Data in txt Format
"""
#%%
# The Data class
# ^... |
95b1c77acf956c1ae7a7483ae432ec1354c2bb13803b4ebc5e554b1f3553db28 | Python | 10,463 | 201 | # Set CUDA device BEFORE importing torch
import os
os.environ["CUDA_VISIBLE_DEVICES"] = "7"
# add the path of custom functions
import sys
from pathlib import Path
script_dir = Path(__file__).parent
project_root = script_dir
while not (project_root / 'Deps').exists() and project_root.parent != project_root:
project... |
12afe24806d5c6b20c65eee52387ccc93fdc765bd585a11d9ff35af4f2456694 | Python | 10,470 | 288 | import torch
import torch.nn as nn
import torch.nn.functional as F
from torch_geometric.data import Data
import torch.nn as nn
from lib_3d_OT.ottools.utils import log_string
from lib_3d_OT.ottools import ot, reconstruction as R
from lib_3d_OT.ottools.losses import compute_loss_unsupervised,chamfer_loss
from lib_3d_OT.u... |
5a3736e153eafe4063854bf216369445fa46d55e8cbd0cc01f6dd3f37b9fedb7 | Python | 10,470 | 288 | """ AFMmeasurements_timelapse.py
Check/Amend the following:
- Directory of experimental folder (line 34)
- 'App' (approach height) (line 45)
- 'StepHeight' (line 52) which is the height in µm which the AFM head is retracted before moving
to the next measurement position, where it is extended by StepHeight-2µm
- Line... |
b4e40ddcb4fbd79b9758a09983c52b0ff7378f0633c695051cefd13e6441941a | Python | 10,471 | 238 | """Test the lag-independent activity metrics on the CAT-NAP path.
Run from the repo root::
uv run python python/test_catnap_lag_independent.py
``effRank`` and the NMF fields are read off the *activity* matrix, not off any
adjacency matrix, so they live outside ``compute_network_metrics`` — the piece
CAT-NAP and ... |
0272bcc66f5ccf4707e66ea091ddcabb49268b992360ad252094592a41628359 | Python | 10,473 | 272 | #%%
# so we need a comment?
import os
from argparse import ArgumentParser
import torch
from model import BERT_GAT
from torch.utils.data import Dataset
from torch_geometric.data import Data
from torch_geometric.loader import NeighborLoader
import pytorch_lightning as pl
from pytorch_lightning.callbacks import EarlySt... |
4995647941c05996922e5d4f591916d9a9f5440e9120086f15e71848236963db | Python | 10,474 | 260 | # -*- coding: utf-8 -*-
import os
import re
import sys
def extract_reference_values(ref_pcr_path):
values = {
'zero': '',
'bg_coeffs': [],
'scale': '',
'u': '',
'v': '',
'w': ''
}
try:
with open(ref_pcr_path, 'r') as file:
lines = f... |
29a9e9d48062fb56df3646052f3e2fd90650a5abd6e00f2ca39e02920fb7a475 | Python | 10,475 | 284 | import torch
import torch.nn as nn
import torch.nn.functional as F
import os, wget
from .functions import ReverseLayerF
import gdown
def init_layer(layer):
"""Initialize a Linear or Convolutional layer. """
nn.init.xavier_uniform_(layer.weight)
if hasattr(layer, 'bias'):
if layer.bias is not None... |
ea36b5359520aad7cb50b6d293e2639d14612e2f426737467895fb360575231c | Python | 10,477 | 256 | #############################################################################
# Copyright (C) 2020-2026 MEmilio
#
# Authors: Maximilian Betz
#
# 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 Li... |
ddb4f52a6ba9ce54719ec1804bc01ce6121545078bd697e585578a45d24545df | Python | 10,482 | 206 | from sklearn.metrics import accuracy_score, f1_score, precision_score, recall_score, roc_auc_score
from torch_geometric.nn import HGTConv
import pytorch_lightning as pl
from torch import nn
import torch
from Dataset import BotDataset
from torch.utils.data import DataLoader
import argparse
from torch.optim.lr_scheduler ... |
17e4f5ea321be5fd6425a7960d0b538c0c86b73add69d1bb952e4ea7030ad4b8 | Python | 10,484 | 281 | from typing import Optional, Union, Dict
import os
import shutil
import os.path as osp
import torch
import numpy as np
from ogb.utils.url import decide_download, download_url, extract_zip, makedirs
class WikiKG90MDataset(object):
def __init__(self, root: str = 'dataset'):
self.original_root = root
... |
21c7ab43df8d1f96d282396f3ded8ce7dc69fee689057a7ac0797b4764648b95 | Python | 10,486 | 280 | from __future__ import annotations
import argparse
import asyncio
import pathlib
import signal
from typing import Any
from academy.handle import Handle
from academy.runtime import Runtime
from academy.runtime import RuntimeConfig
from chemgraph.academy.core.peer_protocol import build_message
from chemgraph.academy.r... |
b9e3fd2b730e78395c6552d7622038402d9aa796dbb4ea5a57c038769ffe821b | Python | 10,489 | 285 | import os
import SimpleITK as sitk
import numpy as np
from PIL import ImageDraw, ImageFont
import torch
from torch.utils.data.dataset import Dataset
from torchvision.transforms import Compose, RandomCrop, ToTensor, ToPILImage, CenterCrop, Resize, InterpolationMode, Normalize
import torch.nn.functional as F
def is_ni... |
10ea951fe2f9555465635e42b2bc4a51a1ad3566f965f5adfe60fe4c9f935b14 | Python | 10,490 | 256 | '''
Quick script to collect data from rERP models in final task
and perform statistical inference.
All options supported by `subject_rerp_mt2.py` are
also available here, of course.
NOTE: The output report created by this script isn't
necessarily going to include the prettiest figures; it's
mostly to get a quick over... |
be1cfd1063ee110d8b033546230d89e2a51318ab9c39ea7c91d4c6b434193939 | Python | 10,492 | 263 | import os
import json
import pandas as pd
from openai import OpenAI
import concurrent.futures
import time
from tqdm import tqdm
from prompt import SYSTEM_PROMPT_FINDINGS_CHINESE, SYSTEM_PROMPT_FINDINGS_ENGLISH
import argparse
ROOT_DIR = os.path.dirname(os.path.dirname(os.path.abspath(__file__)))
removed_case_list = [... |
272726d7061b9f263185b4877f59993bcb6cfdf79d7a196b408b7e7fca9c94e5 | Python | 10,494 | 270 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
This script is intended to score many versions of a same bundle, compared to
ONE ground truth / gold standard.
All tractograms must be in the same space (aligned to one reference).
Our bundle tractometry analysis scripts
---------------------------------------
- scil... |
5ecbdd9293c208ef0f530646664d3057ae2df665a1e3162ad82a1ead958d0b4c | Python | 10,498 | 284 | from qtpy.QtWidgets import (
QApplication,
QGroupBox,
QHBoxLayout, QVBoxLayout,
QLabel, QLineEdit,
QPushButton, QSpinBox, QDoubleSpinBox, QCheckBox,
QWidget
)
from qtpy.QtCore import QThread, Signal
import napari
from typing import TYPE_CHECKING
if TYPE_CHECKING:
import napari
from ._inpu... |
f6842ddc86d1ae1b6b5b3e9fdb1e7247fba63c9d8ac217aecdbe412872fb504f | Python | 10,499 | 293 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Tue Aug 8 12:34:39 2023
@author: rl05
"""
import os
import os.path as op
project = 'fake_diamond'
cbu_repo_meg = op.join('/megdata/cbu', project)
project_repo = op.join('/imaging/hauk/rl05/', project)
bids_root = op.join(project_repo, 'data', 'raw')
# d... |
67ec6febb2fa8bd6c9928cd1a1f68b978fb7bf994115f621a0cabf3914e568a5 | Python | 10,500 | 274 | # This file is part of connectome-manipulator.
#
# SPDX-License-Identifier: Apache-2.0
# Copyright (c) 2024 Blue Brain Project/EPFL
"""Useful converters for circuits data"""
import glob
import os
import subprocess
from pathlib import Path
import numpy as np
import pyarrow as pa
import pyarrow.parquet as pq
from .. ... |
796593b64913ec0ed143c94a097805e556be12534205ee0bc02794bfb639844f | Python | 10,500 | 290 | from typing import Any
import numpy as np
import obspy
import torch
import torch.nn as nn
import seisbench.util as sbu
from .eqtransformer import (
EQTransformer,
SeqSelfAttention,
Decoder,
Encoder,
ResCNNStack,
Transformer,
ActivationLSTMCell,
CustomLSTM,
)
class EQTP(EQTransformer)... |
9a2da484c7502284ec819b6bc6c588fc9ad93b43925ca84494abb7ed2c535e04 | Python | 10,500 | 283 | """
Metrics that quantify how a candidate adapter compares to the reference.
We deliberately keep this small and explicit; the runner calls the public
helpers and lets pandas do the heavy lifting downstream.
"""
from __future__ import annotations
from typing import Dict, Iterable, Iterator, List, Mapping, Optional
... |
c9a43e5267bbca7925aa28b5a3b52c85157693d30ae797754c227b20fac63403 | Python | 10,502 | 353 | import unittest
import warnings
from unittest.mock import patch
from argclz import AbstractParser
# from rscvp.atlas._ccf.main_slice_transform import plot_slice_view_transform
from rscvp.atlas.main_expr_range import RoiExprRangeBatchOptions
from rscvp.atlas.main_roi_atlas import RoiAtlasOptions
from rscvp.atlas.main_r... |
ac5af75a2a6c45dde8951889ea70cc1a4e49c86eeb199a96c4f7817a85d5e5d1 | Python | 10,507 | 306 | '''Generic Object Decoding: Feature prediction
Analysis summary
----------------
- Learning method: Sparse linear regression
- Preprocessing: Normalization and voxel selection
- Data: GenericDecoding_demo
- Results format: Pandas dataframe
'''
from __future__ import print_function
import os
i... |
cb21708ca3a464297cbe060b5c0c23cb86ec4055b94922617d99a4ce16c00aac | Python | 10,508 | 324 | import logging
import os.path as op
from enum import IntEnum
from time import time
import numpy as np
from scipy.ndimage import gaussian_filter
from skimage.segmentation import find_boundaries
from AFQ.data.fetch import afq_home, fetch_synthseg_models
from AFQ.nn.utils import prepare_t1_for_nn, resample_output
logge... |
a6a6f31f74d63747fdb2ae67b3359183840729d4cd624b2efad8ad263c54124a | Python | 10,513 | 231 | # Ultralytics 🚀 AGPL-3.0 License - https://ultralytics.com/license
from __future__ import annotations
import os
from pathlib import Path
import numpy as np
from PIL import Image
from ultralytics.data.utils import IMG_FORMATS
from ultralytics.utils import LOGGER, TORCH_VERSION
from ultralytics.utils.checks import c... |
7748c983b5f63ecb63c748cc081fd53a9a6c21a026ff6b4dbe2f79c801977c4c | Python | 10,515 | 302 | """
Fast KNN implementation using FAISS.
This implementation is significantly faster than scikit-learn's KNN, achieving
speed-ups of over 1000x for typical use cases (1702s with scikit vs 1.5s on GPU).
Supports multiple distance metrics: L2, L1, cosine similarity, spectral angle
mapping (SAM), weighted L2, and hierar... |
0e0ba6214914027b3b56c7c7236cc41cd5319a7abcde6071f14ca2acb1fb295d | Python | 10,520 | 236 | #!/usr/bin/env python3
# -*- coding: utf-8
"""
Script that simulates data for benchmarking of DestVI,
with answers to reviewer's comments.
Created on 2021/08/03
@author romain_lopez
"""
import os
import click
import numpy as np
np.random.seed(0)
from logzero import logger
from utils import get_mean_normal, catego... |
c741bf1f656c7b260d8f9ff9243c1b5b9226595c9476d849f30d1ea819dd26cb | Python | 10,524 | 199 | from src.wrappers.OsipiBase import OsipiBase
import numpy as np
import IVIMNET.deep as deep
import torch
import warnings
from utilities.data_simulation.GenerateData import GenerateData
class IVIM_NEToptim(OsipiBase):
"""
Bi-exponential fitting algorithm by Oliver Gurney-Champion, Amsterdam UMC
"""
# I... |
18a7d7bf9b324bd134e99036f5e55383a003046a1d56a1efd21a1955d842f510 | Python | 10,529 | 224 | #!/usr/bin/env python3
"""Estimate PVeD with ANTs Atropos from MNI-space dtifit maps."""
import argparse
import json
import os
import shutil
import subprocess
import time
import nibabel as nib
import numpy as np
from nibabel.processing import resample_from_to, resample_to_output
from scipy import ndimage
from scipy.s... |
197445704e1b1b093f1d07dda3397353b830c338045e9efc3292cb5e8715c391 | Python | 10,529 | 315 | """Skill inference task.
Project for Setayesh Radkani and Michael Yoo.
"""
#pylint: disable=import-error, no-name-in-module
import numpy as np
import pdb
from moog import action_spaces
from moog import observers
from moog import physics as physics_lib
from moog import game_rules
from moog import tasks
from . import... |
80f17b3e2fc0ad4b9d9eb0851d898ce17997456214214e7dd30930660c5c1b4f | Python | 10,529 | 277 | # 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... |
525824a6246f7d5494417da5f4a690518b1f5fb6c6bb71c2b39b230988c1fb36 | Python | 10,531 | 296 | import argparse
import torch
import torch.nn.functional as F
from torch.utils.data import DataLoader
from torch_geometric.utils import negative_sampling
import torch_geometric.transforms as T
from torch_geometric.nn import GCNConv, SAGEConv
from ogb.linkproppred import PygLinkPropPredDataset, Evaluator
from logger ... |
8fa2381775be0a793fc65139d3f1ca205fabc0ddf27cf9c6f73d360b74d1fe2c | Python | 10,531 | 246 | """ Custom Synaptic Input Test
Author: Aaron Miller
Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig Germany
Brain Networks Group
Tests the custom synaptic input point processes h.SunCur and h.SynCurNMDA, defined by
neuron_interface/neurosim/mechanisms/synCur.mod
neuron_interface/neurosim/mechanism... |
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