sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
77994e14f0ead64c26f5a75e3861bc69f3c2ac34c953b782c04093ad930b7a2e | Python | 13,417 | 301 | """
apply_SDC - Susceptibility Distortion Correction for diffusion MRI
Part of the micaflow processing pipeline for neuroimaging data.
This module applies susceptibility distortion correction (SDC) to diffusion MRI images
by using a pre-calculated displacement field to unwarp geometric distortions caused by
ma... |
e6b1687ad5ceec0eedbe493975aee919c2b7830bc9e62c5bec439257ec4e6c9b | Python | 13,423 | 338 | # Copyright (c) Facebook, Inc. and its affiliates.
import copy
import glob
import json
import os
import random
import tempfile
import unittest
import zipfile
import torch
from torch import Tensor, nn
from detectron2 import model_zoo
from detectron2.config import get_cfg
from detectron2.config.instantiate import dump_... |
82d189c1b377967aa05fc3f1f53356b4d36c4a83ae5040ea065f83d3fc01318f | Python | 13,424 | 403 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Data Transformation and Feature Engineering Script
This script applies the final transformations to prepare data for model training:
1. Load scaling parameters and vocabularies
2. Apply min-max scaling to numeric features and embeddings
3. Convert categorical features... |
9ba2159ca51a2e6b775bb4a536705ddb91dac6a288ada41008a39a26070066fa | Python | 13,442 | 380 | """
Leave-One-WSI-Out (LOWO) Cross-Validation
Runs LOWO cross-validation for axon segmentation by iteratively leaving out one
whole-slide image (WSI) from training and evaluating with stratified per-tile
metrics on the held-out test set.
Usage:
python train_lowo.py --config model_config_lowo.yaml # all ... |
0db2d212090c2199fd24c90fd29cc1442b87b3404fec09e486d2261f78b9dedd | Python | 13,460 | 291 | ############################################
# ---------- Core NBS Functions ---------- #
############################################
import random
import networkx as nx
import pandas as pd
import scipy.stats as stats
import numpy as np
import numpy.matlib as matlib
from scipy.optimize import nnls
from multiprocessin... |
f60061396488cb6bf08ab8737edbd9904b9c99afd4d2a153c70f053c5f043c27 | Python | 13,466 | 281 | ############################################################################
# Copyright (c) 2022-2026 University of Helsinki
# Copyright (c) 2020-2022 Saint Petersburg State University
# # All Rights Reserved
# See file LICENSE for details.
############################################################################
... |
73939d29546cbc429c06c6e635aa1d98f4e876076096afd64337f7ab5da1020a | Python | 13,476 | 287 | from copy import deepcopy
from typing import Literal, Tuple, Union, List
import torch
from batchgenerators.utilities.file_and_folder_operations import isfile
from dynamic_network_architectures.architectures.abstract_arch import AbstractDynamicNetworkArchitectures
from torch._dynamo import OptimizedModule
from nnunetv2... |
5b39b1a375cff41a01fe66209dc4cdbfc3981bb37ab13a74f4f6c3e6bb806f03 | Python | 13,481 | 333 | ############################################################################
# Copyright (c) 2023-2026 University of Helsinki
# # All Rights Reserved
# See file LICENSE for details.
############################################################################
"""
Dict-based flexible detection result for universal molec... |
145ff806c6a3fca44b88dee2d2a4eee996d4953df5e6d48670dae9867a475e2a | Python | 13,494 | 238 | # flake8: noqa
import sys
import numpy as np
import pytest
from rdkit import Chem
from chemprop.featurizers import (
MorganBinaryFeaturizer,
MorganCountFeaturizer,
RDKit2DFeaturizer,
V1RDKit2DFeaturizer,
V1RDKit2DNormalizedFeaturizer,
)
@pytest.fixture
def mol():
return Chem.MolFromSmiles("F... |
593c445c114e25ebb9cbe5eb506775c444be2df7f1dae4e59aa87eb7736266ef | Python | 13,503 | 322 | """YouTube → mp3 downloader for the TAPA pipeline.
Two-library fallback chain to maximize success on Colab / cloud IPs that
YouTube routinely bot-checks:
1. yt-dlp (default) — alternate player_client list to dodge most bot checks,
plus optional cookies file / browser cookies for stubborn videos.
2. pytubefix... |
dd0db3902d58833532bd025ced3c8874b77cc85483848e44decaab588530d5b8 | Python | 13,509 | 307 | # -*- coding: utf-8 -*-
"""
Supplemental analyses
"""
import numpy as np
import matplotlib.pyplot as plt
import matplotlib.patches as patches
from matplotlib.colors import ListedColormap
import seaborn as sns
from netneurotools import datasets, plotting
from scipy.stats import zscore, pearsonr
from sklearn.linear_model... |
4ffb5c3695622daabf6cf62fc5aa8d2b495b38fe02589a701b28bbaf5b81151c | Python | 13,516 | 341 | import torch
import torch.nn as nn
import torch.nn.functional as F
import random
from Contrast import Contrast
from freq_encoder import FreqEnco, FreqHenco
from wave_evolution import WEL
import numpy as np
import pandas as pd
from sklearn.metrics.pairwise import cosine_similarity
import dgl
random.seed(2025)
torch.man... |
c050a7d1cc2547d95cd6a7812a6aea687661478d246df5f9416da9aff4585c65 | Python | 13,534 | 307 | """Reproduce Supplementary Tables S8 and S9 (SAGAT reliability analysis).
Table S8: Cronbach's alpha for the SAGAT perception scale (Q1-Q4) and its
AV-state (Q2, Q4) and world-state (Q1, Q3) subscales, computed both
classically and ordinally. Because the items are binary, the ordinal alpha
uses tetrachoric inter-item ... |
ba76963bd5b4b8233e6c299d0c52b98963730ef6fbda1415b696024653403a9d | Python | 13,539 | 388 | from __future__ import annotations
import abc
import functools as ft
import re
from collections.abc import Iterable, Mapping, Sequence
from typing import TYPE_CHECKING, Any, Final, TypeAlias, cast
import attrs
import more_itertools as itx
from bids.layout import BIDSLayout, Query
from bids.layout.models import BIDSFi... |
e223ae102a611da646d60e33162d87c4773d9dab165b3a2202af583e6ce967b6 | Python | 13,539 | 417 | # %%
# System Libraries
from __future__ import annotations
import contextlib
import io
import math
import os
import os.path as op
import shutil
import sys
import warnings
from collections import defaultdict
from pathlib import Path
import matplotlib.patches as patches
import matplotlib.pyplot as plt
import mne
import... |
4eef356caa261aeccccf4187278d01da1aeab82e36db0387930da9fccd3089c7 | Python | 13,544 | 334 | import os
import numpy as np
from sklearn.base import BaseEstimator
from .alignment import ProcrustesAlignment, aligned_lambdas as _aligned_lambdas
from .kernels import compute_affinity
from .embedding import PCAMaps, LaplacianEigenmaps, DiffusionMaps
def _is_path_like(x):
"""Return True if `x` looks like a fi... |
7d00634bed9b2e20e1c5fd284306826274a16ddb84aebce55fc2bcffdbf87149 | Python | 13,566 | 343 | from inits import *
import tensorflow as tf
import sys
flags = tf.app.flags
FLAGS = flags.FLAGS
EOS = 1e-9
# global unique layer ID dictionary for layer name assignment
_LAYER_UIDS = {}
def get_layer_uid(layer_name=''):
"""Helper function, assigns unique layer IDs."""
if layer_name not in _LAYER_UIDS:
... |
8d8a2af1986c11cf3946f5abe8bf11019b56f1db1d8c30d6d848427512c785a6 | Python | 13,566 | 289 | import glob
import os
import shutil
import numpy as np
import tifffile
import torch
from albumentations import (
ShiftScaleRotate, GaussNoise,
RandomBrightnessContrast, Compose, RandomRotate90)
from skimage import morphology, transform
from torch.utils.data import Dataset
class DataProcess(Dataset):
"""
... |
9ba1377f3cb7923abb2ec53570890be64cd44bcf2aacc4fedae6f4ac2bef6eed | Python | 13,581 | 332 | ############################################################################
# Copyright (c) 2023-2026 University of Helsinki
# # All Rights Reserved
# See file LICENSE for details.
############################################################################
"""
Shared memory k-mer indexer for parallel processing of l... |
719523cd569ffff742e7b13e6ecf346b09d0daff5516024f800c7208e5da6a66 | Python | 13,583 | 425 | # %%
from __future__ import annotations
import contextlib
import io
import math
import os
import os.path as op
import shutil
import sys
import warnings
from collections import defaultdict
from pathlib import Path
from pprint import pprint
import matplotlib.patches as patches
import matplotlib.pyplot as plt
import mne... |
f375efaca55a665cf76f2c05d9d69a2f9024d47e206bc5676b9bfb9317c46dee | Python | 13,628 | 376 | ## By Anoushka Joglekar
## Created 2018. Edited AS 2019. Edited AJ 2020
import sys
import argparse
import gzip
import pandas as pd
import os
import multiprocessing as mp
import re
from traceback import print_exc
def revComp(my_seq): ## obtain reverse complement of a sequence
base_comp = {'A':'T', '... |
56791e1d5c789167a0121f9347f44248828d682ce1c621db19a8cc7b03e77799 | Python | 13,646 | 360 | # uv run evidenceIntSum.py $HOME/promec/promec/Animesh/Download/BSA/evidence.txt $HOME/promec/promec/Animesh/Download/BSA/proteinGroups.txt
# Usage:
# python evidenceIntSum.py evidence.txt proteinGroups.txt
# python evidenceIntSum.py evidence.txt proteinGroups.txt mqpar.xml
#
# This script keeps the corrected max... |
82f5fdd54995f9af52d7ce3a8cc06966d6376b90ff9c54a7f5d80dc76c4f446c | Python | 13,679 | 299 | import os
import sys
import json
from typing import Optional
from argparse import ArgumentParser
import numpy as np
import pickle
from pathlib import Path
from tempfile import mkdtemp
import datetime
import scanpy as sc
import scvelo as scv
import umap
import matplotlib.pyplot as plt
import seaborn as sns
import torch
... |
19c9e47e48629e8aa8dd0ec4ef06d3f9c1f08cf20d60f35b79ee4f1b249c9d83 | Python | 13,711 | 269 | from typing import Dict, Tuple, Union
import torch
from torch import nn
class FirstVGGBlock(nn.Module):
"""VGG block with Instance Normalization for the first layer"""
def __init__(self, in_channels, middle_channels, out_channels, dropout=0.):
super().__init__()
self.relu = nn.LeakyReLU(nega... |
1a358d7a562697cb13e4cbece3f31eae942fe8db1d65b5c5e139d8dcc8382027 | Python | 13,711 | 441 | """ Test mesh operations """
import pytest
import os
import numpy as np
import shutil
import gzip
import vtk
from vtk.util.vtkConstants import VTK_TRIANGLE, VTK_LINE, VTK_VERTEX
from brainspace.vtk_interface import wrap_vtk
from brainspace.vtk_interface.wrappers import BSPolyData
from brainspace.mesh import mesh_io... |
821afc4164d458f205ea1ecf1ad055b2228feadc81e0af65046efac726f4d7ca | Python | 13,713 | 365 | # Stabilized HiDe-MK
import time
import math
import csv
import sys, os
import pickle
import random
import pandas as pd
import numpy as np
import tensorflow as tf
print('The TF version is {}.'.format(tf.__version__))
import keras
print('The Keras version is {}.'.format(keras.__version__))
from keras impor... |
5d2da17927e701f87dbbbfe8aeda91dff5bd62b53090c63efad91a5eb1d7fc45 | Python | 13,726 | 269 | import numpy as np
import mimic_iii_sql.psql_wrapper as psql_mimic
import aumc_sql.psql_wrapper as psql_aumc
from keras.utils import Sequence
"""
Version 3: Standardisation and imputation after train-test split to rectify data leakage
Version 2: Add train and validate in MIMIC-III, predict in MIIMC-III and AUMC
... |
2673a4199c27f17ce7386659abeaec10208b271066aa79edfaccf64a91d32c3a | Python | 13,801 | 353 | # Copyright (c) Facebook, Inc. and its affiliates.
import torch
import torch.distributed as dist
from fvcore.nn.distributed import differentiable_all_reduce
from torch import nn
from torch.nn import functional as F
from detectron2.utils import comm, env
from .wrappers import BatchNorm2d
class FrozenBatchNorm2d(nn.M... |
c613a368326b21db210d5c32c7f2f2ca22bd116faa641ccd3e539e89c8771d70 | Python | 13,803 | 355 | #!/usr/bin/python3
##################################################################################
#
# MIT License
#
# Copyright (c) 2025 Kevin Rockenbach, Agnieszka Golicz
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "So... |
626af97230c3c25fbf84c1e57185c303f89fabbb5a0cd9d967c3cfc89e548f98 | Python | 13,892 | 347 | #!/usr/bin/env python
"""
train_densenet_fc_age.py
Train a DenseNet-style CNN with attention blocks (HFAB/ERB) to predict a
continuous target (e.g. age, episodic-memory score) from square functional
connectivity (FC) matrices stored as .mat files.
M. Esmaeili et al. (2026), Brain-Cognitive Gaps in relation to Dopamine... |
9ce299f942e52de1c881d734def4b827bd81b6b31b7b883423f406e46450edc9 | Python | 13,894 | 270 | import numpy as np
import mimic_iii_sql.psql_wrapper as psql_mimic
import aumc_sql.psql_wrapper as psql_aumc
from keras.utils import Sequence
"""
Version 3: Standardisation and imputation after train-test split to rectify data leakage
Version 2: Add train and validate in MIMIC-III, predict in MIIMC-III and AUMC
... |
9b9b8b178292bb5e5953901ae0a6101a3e52e7b96c9ced9584beb113d2a5460c | Python | 13,896 | 341 | # Copyright (c) Facebook, Inc. and its affiliates.
import logging
import numpy as np
from typing import Dict, List, Optional, Tuple
import torch
from torch import nn
from detectron2.config import configurable
from detectron2.data.detection_utils import convert_image_to_rgb
from detectron2.layers import move_device_lik... |
568fdcaaa87910d9fd859cc30359c41a8e515816568bb9f58ad704a089b81da0 | Python | 13,936 | 479 | """ Created on Wed Oct 16 11:56:28 2024
@author: dcupolillo """
import matplotlib.pyplot as plt
import matplotlib.cm as cm
from matplotlib.patches import Rectangle
import numpy as np
import seaborn as sns
from sklearn.metrics import confusion_matrix
from sklearn.metrics import average_precision_score
from sklearn.... |
ca54453183c170e1461effbd7e0b6b62d85c8b4ccfd16be31e2c88634b88f8d1 | Python | 13,941 | 340 | # Very slightly adapted from perses https://github.com/choderalab/perses
# License: MIT
# OpenFE note: eventually we aim to move this to openmmtools where possible
# turn off formatting since this is mostly vendored code
# fmt: off
import copy
import warnings
import numpy as np
from openmmtools.alchemy import Alchem... |
5e66735a62aaf17b8b9bfa6520ecccf3c47ae554495557e2045bd73be2899719 | Python | 13,956 | 314 | """
Written by Tom George and Masahiro Nakano
"""
import ratinabox
from ratinabox.Agent import Agent
import numpy as np
import copy
from scipy.interpolate import interp1d
import warnings
class SubAgent(Agent):
"""SubAgents take as input, and are "subservient" to, another Agent (the LeadAgent). The key thing ide... |
0d84ff43e6a9c57566b8c2907e2b403810b415f03e4a86394800941682f6b41d | Python | 13,965 | 293 | """
Created on 10/08/2017
@author: Niklas Pallast
Neuroimaging & Neuroengineering
Department of Neurology
University Hospital Cologne
"""
import sys,os
import numpy as np
import nibabel as nii
import glob
import subprocess
import shlex
sys.path.insert(0, os.path.abspath(os.path.join(os.path.dirname(__file__), os.p... |
40a211b3b6143b26b26314786c7dc7d59cdb7563613ee886f7a83d703b92fe47 | Python | 13,987 | 323 | # Copyright (c) Facebook, Inc. and its affiliates.
import logging
import unittest
from copy import deepcopy
import torch
from torch import nn
from detectron2 import model_zoo
from detectron2.config import get_cfg
from detectron2.export.torchscript_patch import (
freeze_training_mode,
patch_builtin_len,
pat... |
0191b4e39ad87fc7daddb1377594cf9df0c4821fdf48fce11ae34ac4574b0cea | Python | 14,008 | 295 | import argparse
from math import inf
#### Argument parser ####
def setup_shared_args(parser):
"""
Sets up the argparse object for the qm9 dataset
Parameters
----------
parser : :class:`argparse.ArgumentParser`
Argument Parser with arguments.
Parameters
----------
p... |
4092733b85385b9188d645b8b0df02cfcc23b5057ce328c777c768d681dd6ec8 | Python | 14,008 | 377 | """
Stage 4: build session responses + extract modulation / pulse-locking metrics.
Generates session_responses (pkl), stim_condition_results (CSV), and per-unit
figures from batch_sort/stage3/analyzer_final.zarr + trial_df.csv.
Usage:
python -m batch_process.stage4_postprocess <session_folder> [<session_folder> .... |
8246d902a688b33977027b979776d7c5293a4fc6cf1d329c46e03392fe8f084f | Python | 14,009 | 426 | # This script is part of navis (http://www.github.com/navis-org/navis).
# Copyright (C) 2018 Philipp Schlegel
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of... |
7af1de52247ba7c06e0a7d211f44db6930abd650ed5aab7329128f87cf34eb63 | Python | 14,022 | 354 | #!/opt/env/bin/python
"""
Created on 10/08/2017
@author: Niklas Pallast
Neuroimaging & Neuroengineering
Department of Neurology
University Hospital Cologne
"""
from __future__ import print_function
import atexit
import argparse
import os
import glob
import shutil
import gzip
import subprocess
import sys
sys.path.ins... |
2137c47ad08e786df894d8195622cab96442dc6cbe0b09a432036c956a44d408 | Python | 14,061 | 268 | import numpy as np
import mimic_iii_sql.psql_wrapper as psql_mimic
import aumc_sql.psql_wrapper as psql_aumc
from keras.utils import Sequence
class PoolBatchGenerator(Sequence):
"""Custom Keras sequence generator for getting data batches from MIMIC-III and AmsterdamUMC PSQL DB."""
def __init__(self, admissio... |
13f780ae7a525e2d552d81195545ee78f7825111926cbc18e82f55dfd9ecd8ca | Python | 14,070 | 412 | """Toy self-driving demo of the CW-Net algorithm (Code Ocean capsule entrypoint).
Trains a CW-Net (concept classifier + ranker) on latent states of a pre-trained
PPO CarRacing agent (weights/agent_weights.pt, from JinayJain/deep-racing), then
runs the wrapped agent in simulation and saves losses, a concept confusion
m... |
1ed038c173f2270e7fc075ee7e664525a3a491cbe5b8474a328737c07c4c629e | Python | 14,100 | 348 | import pandas as pd
import torch
from torch_geometric.data import Dataset, Data
import numpy as np
import os
from tqdm import tqdm
from constants import ALL_ATOM_LABELS, DICT_AA_SELECTION, SELECTED_ATOMS
from utils import is_connected, extract_pqr_data, build_edges_blockwise_less_atoms, get_atom_indices_type_aa_type_... |
0db2a372a094393fafbfd11557a1a4d345ff491f515f0e156afb7b95b96b5731 | Python | 14,116 | 380 | # -*- coding: utf-8 -*-
# Copyright (c) Facebook, Inc. and its affiliates.
import inspect
import numpy as np
import pprint
from typing import Any, List, Optional, Tuple, Union
from fvcore.transforms.transform import Transform, TransformList
"""
See "Data Augmentation" tutorial for an overview of the system:
https://d... |
b7fbcd257711a0b80718006d0a26fd602f1045cd817a4dbf274eb4bea7c79591 | Python | 14,146 | 405 | import numpy as np
import pandas as pd
import seaborn as sns
import os
import matplotlib.pyplot as plt
from scipy.stats import mannwhitneyu
import mimic_iii_sql.psql_wrapper as psql_mimic
import adam_sql.psql_wrapper as psql_adam
import yaml
"""
To extract demographic and patient characteristic of MIMIC-III and Ams... |
d221d17bb3a5d018fea612a2077e35e779a0ab11cafb7fefa9d8473a00c9063a | Python | 14,146 | 371 | """Test space drawer classes for various grid types."""
import random
from unittest.mock import MagicMock, patch
import altair as alt
import networkx as nx
import pytest
from matplotlib.collections import LineCollection
from mesa.discrete_space import HexGrid, Network, OrthogonalMooreGrid, VoronoiGrid
from mesa.expe... |
c570dd00ad5b66175053e60159e1fcb0d67dee3c9fa8da9c11a65817db21131a | Python | 14,149 | 433 | import os
import pathlib
import sys
from typing import List, Literal
import click
import numpy as np
import pandas as pd
from cinnabar import FEMap, Measurement
from openff.units import unit
from openfecli import OFECommandPlugin
from openfecli.clicktypes import HyphenAwareChoice
from openfecli.commands.gather import... |
67ab177f1b708d72993e006cec13a4e557120bd2662738519ac66cad4658d2ba | Python | 14,163 | 336 | #python compareDIffExprDIANNvalues.py DDAreport.parquet_Ms1_Area_pivot_all_protein_data.csv reportDDA.parquet_Ms1_Area_pivot_all_protein_data.csv
import sys
import pandas as pd
import numpy as np
import matplotlib.pyplot as plt
import seaborn as sns
from pathlib import Path
from scipy import stats
if len(sys.argv) !=... |
9203d4571a7df9c2d992a30978ceadb47cd10b39b727aed57c54ec1be57acf4c | Python | 14,165 | 482 | #!/usr/bin/env python
# coding: utf-8
# # [setup](https://www.kaggle.com/yujiariyasu/plot-3positive-classes )
#!pip install pandas
#!pip install pydicom
#!pip install tqdm
#!pip install skimage
#!pip install scikit-image
#!pip install cv2
#!pip install opencv
#!pip install opencv-python
#!pip install GDCM
#!pip install... |
15f7edd55febd6c24c2ac2d3b99d6725f9f8fffc61466309f2c8681a4a3ac003 | Python | 14,166 | 344 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Open Race Optimizers Compatibility Layer
This module wraps our existing optimizers to make them compatible with the open race competition.
The key differences are:
- Open race uses continuous function evaluation, not hidden points
- Optimizers need to propose points w... |
9919372ccb4d1e6e9985e7cc5628dba58bf253ace93e0ab47715739946a5f1ed | Python | 14,176 | 293 | # Copyright (c) Facebook, Inc. and its affiliates.
# pyre-unsafe
from typing import Any, List
import torch
from torch.nn import functional as F
from detectron2.config import CfgNode
from detectron2.structures import Instances
from .mask_or_segm import MaskOrSegmentationLoss
from .registry import DENSEPOSE_LOSS_REGI... |
36bd9571500fa0ed9fe37f64bea3b6f627c606370d5e0ec785a9b030d22bbf1a | Python | 14,203 | 281 | # type: ignore
"""Verification tests for low-level feature completeness / coverage (`completeness.py`).
A tiny, fully hand-worked static fixture (five layer-1 neurons forming the informative pool, and
seven anchor-layer-2 PNGs) makes every recruitment count, coverage figure and any-vs-matched
agreement checkable by ey... |
5a781175fbf99c2517ad3e181acb8e846ad69554745baefaa713198cef444274 | Python | 14,203 | 419 | """
author:CBJ
"""
import torch
import torch.nn as nn
class MultiScale1DCNN(nn.Module):
"""
Multi-Scale 1D Convolutional Neural Network
Contains three parallel paths:
- Short-term path: kernel_size=7 (corresponds to FFMC, rapid weather-driven response)
- Medium-term path: kernel_size=30 (corresponds to ... |
fea0aa41f400ad11648468b0514ec4de56b836a000c9be67a7cecb9daddb35e0 | Python | 14,209 | 417 | # This script is part of navis (http://www.github.com/navis-org/navis).
# Copyright (C) 2018 Philipp Schlegel
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of... |
845762fd35d0f59377e1f0b8e077737fa6714a08eab3ee529f325606278f5238 | Python | 14,211 | 309 | import os
import argparse
from calendar import month_name
from datetime import datetime
from pathlib import Path
from zoneinfo import ZoneInfo
os.environ.setdefault("MPLCONFIGDIR", "/tmp/matplotlib")
os.environ.setdefault("XDG_CACHE_HOME", "/tmp")
Path(os.environ["MPLCONFIGDIR"]).mkdir(parents=True, exist_ok=True)
im... |
ee454feafbf5e6aa4e8d69c1b08f7643b17e437c1dce8aa7c8047d717fdbe848 | Python | 14,218 | 336 | import logging
from os import PathLike
from lightning.pytorch import __version__
from lightning.pytorch.utilities.parsing import AttributeDict
import torch
from chemprop.nn.agg import AggregationRegistry
from chemprop.nn.message_passing import (
AtomMessagePassing,
BondMessagePassing,
MulticomponentMessag... |
3ecfd8f33ad255b7c52a03623d2a5b652e3b63055dd06b51f35927c1d87aad3a | Python | 14,221 | 296 |
"""
Created on 10/08/2017
@author: Niklas Pallast
Neuroimaging & Neuroengineering
Department of Neurology
University Hospital Cologne
"""
import csv
import os,sys
import nibabel as nii
import glob
import numpy as np
import scipy.io as sc
sys.path.insert(0, os.path.abspath(os.path.join(os.path.dirname(__file__), ... |
0d2cb619821a4c1b794bd9bfef0b8ae50988c367799f02ef2bc8dfb832e03c8b | Python | 14,253 | 357 | # Script that makes use of more advanced feature selection techniques
# by Alberto Tonda, 2017
import copy
import datetime
import logging
import numpy as np
import os
import sys
from sklearn.ensemble import AdaBoostClassifier
from sklearn.ensemble import BaggingClassifier
from sklearn.ensemble import ExtraTreesClassi... |
35c400af2523d478f1f2487e713a765f103dd54e86af13d3f805c8319ddc53dc | Python | 14,336 | 348 | #!/usr/bin/env python3
# /// script
# requires-python = ">=3.10"
# dependencies = ["mcp[cli]<2", "pywin32; sys_platform == 'win32'"]
# ///
"""MCP server over the charted evidence of Leimroth et al. 2026,
"Exploring EEG and ECG in Music Listening: A Scoping Review"
(Psychophysiology 63(9) e70385, doi:10.1111/psyp.70385)... |
2a033261e3de80ac8826e4f00b3ef6a0650063d0e18857421cd68556b990ee16 | Python | 14,353 | 406 | """
Created on 10/08/2017
@author: Niklas Pallast
Neuroimaging & Neuroengineering
Department of Neurology
University Hospital Cologne
"""
import sys, os
import nipype.interfaces.fsl as fsl
import nibabel as nii
import numpy as np
import glob
import shutil
import regress
import getSingleRegTable
import cv2
import cr... |
5e6a1332af428de8e8665cd1b3da039f78ca3fdeb9b62580025a2a2a5f33d991 | Python | 14,354 | 383 | from abc import ABC, abstractmethod
from typing import List, Optional, Tuple
import torch
import torch.nn as nn
from loguru import logger
from stoic.layers import Identity
class MaskedInstanceNorm1d(nn.Module):
"""InstanceNorm1d that ignores padding positions when computing statistics.
Standard InstanceNor... |
2f659a9c4378670266a6beda5ff5d3d8d5c82978a86b4100a9f269ab903c1264 | Python | 14,356 | 355 | ## utils.py
import logging
import os
import numpy as np
import nibabel as nib
import matplotlib.pyplot as plt
from matplotlib.transforms import Bbox
from matplotlib.gridspec import SubplotSpec
from numpy.fft import fftn, ifftn, fftshift, ifftshift
import math
import csv
from scipy import signal
def saveImage(data :... |
c0ae6b963149c6f509db0d62b298ab970dbdab687899b74ecf2278ab47f71e0c | Python | 14,363 | 443 | # This code is part of OpenFE and is licensed under the MIT license.
# For details, see https://github.com/OpenFreeEnergy/openfe
"""Settings class for equilibrium AFE Protocols using OpenMM + OpenMMTools
This module implements the necessary settings necessary to run absolute free
energies using OpenMM.
See Also
----... |
f5bbf6ec4363513323b8303883e9eeaa328155818a2195fc531b9603d1bc5a5f | Python | 14,368 | 356 | # This code is part of OpenFE and is licensed under the MIT license.
# For details, see https://github.com/OpenFreeEnergy/openfe
import os
import pathlib
import MDAnalysis as mda
import pooch
import pytest
from openff.units import unit
from rdkit import Chem
from openfe.protocols.restraint_utils.geometry.boresch.geom... |
11f15dce3c24345732534fb32ef4808ebc725fa80b144cda3d55f8c681b6ab24 | Python | 14,369 | 430 | """
Spectral analysis of neuronal responses.
## Functions
- `whitenoise()`: band-limited white noise.
- `rate()`: firing rate computed by kernel convolution.
- `spectra()`: stimulus- and response power spectra, and cross spectrum.
- `susceptibilities()`: stimulus- and response spectra up to second order.
- `diag_proj... |
5462027cfff20f861be3340b907affe9a246a2b642f96b6ee867b034f44b6231 | Python | 14,385 | 389 | # This code is part of OpenFE and is licensed under the MIT license.
# For details, see https://github.com/OpenFreeEnergy/openfe
import abc
import warnings
from typing import Callable, Iterable, Optional, Type
from gufe import (
AlchemicalNetwork,
ChemicalSystem,
LigandAtomMapping,
LigandNetwork,
P... |
8f21d8e5b9ea14d46babd2b074335fa8b6dbb27c4311959552fe1dca0622bdf6 | Python | 14,389 | 401 | """Tests for the IVSCC features in `navis.morpho.ivscc`.
Correctness is pinned against a small hand-built neuron whose geometry we can
work out on paper. The example (insect) neurons are only used to smoke-test the
plumbing and to cross-check features against navis' own implementations of the
same quantity - IVSCC fea... |
2c0e4e1ccb7d4f665cfb1a4205109752efea401f90e46fa22bf73e13906b0311 | Python | 14,399 | 376 | import tensorflow as tf
import numpy as np
import math
from sklearn import preprocessing
eta=0.1
#elimination_rate=1
#print('squ',64,eta,elimination_rate,'\n')
def IN():
n_dim=train_X.shape[1]
W1=0.01*np.random.randn(n_dim,n_hidden1).astype(np.float32)
B1=np.random.randn(n_hidden1).astype(np.float32)
... |
dceeb6248df071f961c9cb9ff5b6659876ac966075efff151ae99467081fc84b | Python | 14,401 | 340 | from __future__ import annotations
import copy
import random
from dataclasses import dataclass
import numpy as np
import torch
from torch import nn
from torch.utils.data import DataLoader, TensorDataset
@dataclass(frozen=True)
class BPNNTrainingConfig:
dropout: float = 0.4
learning_rate: float = 0.005
w... |
82e5ee1149cc39446b9536adcbbe7ef4673fe3374c5c0b3467bc1034aeb0e81b | Python | 14,405 | 416 | # -*- coding: utf-8 -*-
"""Functions for fetching annotations (from the internet, if necessary)."""
from collections import defaultdict
from pathlib import Path
import re
import shutil
import pandas as pd
import warnings
try:
# nilearn 0.10.3
from nilearn.datasets._utils import fetch_single_file as _fetch_fil... |
ca8c2c19be10c7ee5270d6dee185bb4e574f7ef5f65cf57f4aac3ade5ed7f49d | Python | 14,419 | 387 | """User functional API for running PNG analysis using SPADE as backend method.
"""
from itertools import combinations
from typing import Any, Optional, Iterable, Sequence
import numpy as np
import pandas as pd
from hsnn import ops
from hsnn.core.logger import get_logger
from ..base import get_midx
from ..spikesdb im... |
c5534724c49f67a907c1da6d9f80f9a2897c053e59b59428eb2970f4549cb4db | Python | 14,426 | 339 | # This script is part of navis (http://www.github.com/navis-org/navis).
# Copyright (C) 2018 Philipp Schlegel
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of... |
d597561ee888c4066a22c2a87bd1bab412bce4259acb7771e9a427a3ff1d1e86 | Python | 14,429 | 425 | # Copyright (c) Facebook, Inc. and its affiliates.
import math
import numpy as np
from enum import IntEnum, unique
from typing import List, Tuple, Union
import torch
from torch import device
_RawBoxType = Union[List[float], Tuple[float, ...], torch.Tensor, np.ndarray]
@unique
class BoxMode(IntEnum):
"""
Enum... |
74991bb4db48c5da4b5dd2d0865e95810659fb88656ae70dcb5476348a460b21 | Python | 14,435 | 404 | ############################################################################
# Copyright (c) 2025-2026 University of Helsinki
# All Rights Reserved
# See file LICENSE for details.
############################################################################
import pytest
from isoquant_lib.barcode_calling.indexers impor... |
28acae7f2d28cb0447ef000e08f3a09a0df240d90ea4bcd20e5b5395b639f56c | Python | 14,472 | 339 | """
velocity_off_manifold.py
Quantifying the off-manifold instability of latent dynamics in mmVelo.
Estimating local tangent spaces from the kNN neighbors of each cell using batched SVD,
and decomposing posterior d samples into on-manifold and off-manifold components
to evaluate the variance of each component.
Defin... |
1596d3f04a974be2d6d5fc46f74f730d0598a4969865e31f0416b9ef18760b7f | Python | 14,485 | 408 | # This script is part of navis (http://www.github.com/navis-org/navis).
# Copyright (C) 2018 Philipp Schlegel
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of... |
70bdfe62ba3ed528f23b8283b7d4b6d54736ca92a6f90fc1a0cceb32b319ee32 | Python | 14,489 | 325 | import os
from typing import Union
import numpy as np
import tifffile
import torch
from ..multi_output_unet3d.multi_output_unet3d import MultiOutputUnet3D
from ..progress import ProgressNotifier
from ..utils import get_device
from ..utils.model_cache import load_cached_model
from ..utils.tiling import TileBlender, au... |
26afc5dfc55b9bc6ef2201489714d23092b4914aa947b29a0156d48fbd7621ae | Python | 14,491 | 279 | #############################################################################
#### plot_fig4.py
##############################################################################
# -*- coding: utf-8 -*-
"""
Reproduce Figure 4 from Grabot et al. (Traveling Waves in the Human Visual Cortex:
an MEG-EEG Model-Based Appr... |
3e304ffa093d2b495e0f8ba2acfa303090bed944f4d9c62497962ce2f9eb9868 | Python | 14,498 | 434 | import json
import shutil
from importlib import resources
from unittest import mock
import numpy as np
import pytest
from click.testing import CliRunner
from gufe import AlchemicalNetwork, SmallMoleculeComponent
from openff.units import unit
from openff.utilities import skip_if_missing
from openfe.protocols.openmm_ut... |
24c8672e46186bf2f3332b50b9ce13edda60764364afc8e9e32f7fa872eb59ce | Python | 14,503 | 367 | # This script is part of navis (http://www.github.com/navis-org/navis).
# Copyright (C) 2018 Philipp Schlegel
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of... |
29bab022bb77830ff52bc45d3ffa111a4853d651a606f028ccc74591fd68a259 | Python | 14,510 | 342 | # AUTOGENERATED! DO NOT EDIT! File to edit: 51_plotting.ipynb (unless otherwise specified).
__all__ = ['plot_rna_map', 'plot_binding_changes', 'plot_predictions', 'plot_change_in_binding_per_exon', 'plot_motif',
'plot_perturbations', 'plot_perturbation_zscores', 'plot_perturbations_fdr']
# Cell
import nump... |
a5bb94b2050a1a34fa209c800cfb23724d8e1360af6764e238f5b1737db847e9 | Python | 14,526 | 415 | from __future__ import division
import numpy as np
import bitarray as ba
def getBlockLefts(coords, max_dist):
'''
Converts coordinates + max block length to the a list of coordinates of the leftmost
SNPs to be included in blocks.
Parameters
----------
coords : array
Array of coordinat... |
e8803dca79844f4cd5fd60d10c83c09c9006596a856e4bb8be9126446f804d8f | Python | 14,527 | 349 | #!/usr/bin/env python
#
# Copyright (c) 2019 10X Genomics, Inc. All rights reserved.
#
from __future__ import annotations
import os
from collections.abc import Iterable, Mapping
from typing import TYPE_CHECKING
import numpy as np
from six import ensure_str
from sklearn.utils import sparsefuncs
import cellranger.an... |
4a35d7591a7e21f93f6da91599fc7af507226b934ad0aa0f746071505229f7ae | Python | 14,531 | 329 | from __future__ import annotations
import argparse
import hashlib
import importlib.metadata
import json
import json
import textwrap
from collections.abc import Sequence
from itertools import product
from pathlib import Path
from typing import Any
import matplotlib
matplotlib.use("Agg")
import matplotlib.pyplot as pl... |
90447c5f47285fc5c7f4628a0b6b52fafb4f5f13f6b24f49c6340ca314c95eda | Python | 14,546 | 412 | """Tests for `navis.heal_skeleton` and the machinery behind it."""
import tracemalloc
import navis
import numpy as np
import pandas as pd
import pytest
from scipy.sparse import coo_matrix
from scipy.sparse.csgraph import connected_components, minimum_spanning_tree
from scipy.spatial import cKDTree
def fragment(neu... |
13c9ffbc0e3cfd2b266d61e5c0e224201a82cf9d66d540465e089ac531667f97 | Python | 14,547 | 349 | """
train_mouse_brain.py
--------------------
Three-stage training pipeline for Tutorial 1 (embryonic mouse brain).
Monitor keys are hardcoded here — NOT in the notebook — to prevent
misconfiguration:
- Stage 1 & 2 : DREG_PRE.validation_step logs "val_elbo_loss"
- Stage 3 : DREG_DYN.validation_step logs "va... |
2172786cb167ea91d1b53d787b2c037052783c2b78b76cde65fbde34f37d1d30 | Python | 14,557 | 418 | """ Created on March 16, 2026
@author: dcupolillo
Simple manual annotation GUI for test datasets.
Allows users to label individual calcium imaging traces.
"""
import sys
import numpy as np
import random
from pathlib import Path
from PyQt5.QtWidgets import (
QApplication, QMainWindow, QPushButton,
... |
9d9b9595783e8c7d520f117b742c9184cc587c45e7f019bcfe3b92f43e96e5cc | Python | 14,593 | 428 | # This script is part of navis (http://www.github.com/navis-org/navis).
# Copyright (C) 2018 Philipp Schlegel
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of... |
ebb6d1e08744365496a513ed59fdf75361b0d5a83a7c650998428066115a185d | Python | 14,596 | 296 |
"""
Created on 10/08/2017
@author: Niklas Pallast
Neuroimaging & Neuroengineering
Department of Neurology
University Hospital Cologne
"""
import csv
import os,sys
import nibabel as nii
import glob
import numpy as np
import scipy.io as sc
sys.path.insert(0, os.path.abspath(os.path.join(os.path.dirname(__file__), ... |
bd87da79f003f87c2b6d34722fa619b73af67827976669a6458c9df8b85866c8 | Python | 14,638 | 408 | import random
from typing import NamedTuple
import uuid
import numpy as np
import pytest
from chemprop.featurizers.molgraph import CGRFeaturizer, RxnMode
from chemprop.utils import make_mol
AVAILABLE_RXN_MODE_NAMES = [
"REAC_PROD",
"REAC_PROD_BALANCE",
"REAC_DIFF",
"REAC_DIFF_BALANCE",
"PROD_DIFF... |
a9bab24e2efc4fb8fece00f1c2c800a64d58e989a6b4aaa0e4e75ebd7db8f7a7 | Python | 14,645 | 256 | ############################################################################
# Copyright (c) 2022-2026 University of Helsinki
# Copyright (c) 2020-2022 Saint Petersburg State University
# # All Rights Reserved
# See file LICENSE for details.
############################################################################
... |
a4e3b1fd08d22d33aee90575e2f20885866d2ee00eea9f2cc9d05797b88e299f | Python | 14,651 | 395 | from copy import copy
from typing import Hashable, Optional
import numpy as np
import numpy.typing as npt
import pandas as pd
import xarray as xr
from ._types import CountsArray, RatesArray
from .base import infer_rates
__all__ = [
"get_specific_measures",
"get_sorted_measures_rates",
"get_specific_measu... |
b228d4fd94ccf8e321ada964f8b3c8deec8353c8b307e55fce43452dd04c8b45 | Python | 14,686 | 479 | """ Created on Thu Jun 26 09:56:37 2025
@author: dcupolillo """
import pyqtgraph as pg
import numpy as np
from PyQt5.QtWidgets import (
QMainWindow, QGridLayout, QWidget, QPushButton, QSlider,
QAction, QInputDialog)
from PyQt5.QtCore import Qt
import matplotlib.pyplot as plt
class ImageView(pg.ImageView)... |
29b28e7b19c06c75e85b57605156b305095fbd7b78aab920ee79db790f052750 | Python | 14,700 | 378 | import time
import numpy as np
import argparse
from copy import deepcopy
from scipy import interpolate
parser = argparse.ArgumentParser('Preprocessing: Generate training/validation/testing features from pdb')
parser.add_argument('--MDfolder', type=str, default="data/pdb/",
help='folder of pdb MD')
... |
7767c76deeea5f4efe332fa6904242003a43663c210f9945ca661227239b2ee6 | Python | 14,708 | 384 | #!/usr/bin/env python
#
# Copyright (c) 2018 10x Genomics, Inc. All rights reserved.
#
import pickle
import sys
from collections import defaultdict
import martian
import numpy as np
import cellranger.analysis.batch_correction as cr_batch_correction
import cellranger.analysis.constants as analysis_constants
import cel... |
39ece71a01737f058020133730173988c81f9b57da737a242fe38bce3af0cd8c | Python | 14,712 | 477 | """
Embedding approaches.
"""
# Author: Oualid Benkarim <oualid.benkarim@mcgill.ca>
# License: BSD 3 clause
import warnings
from abc import ABCMeta, abstractmethod
import numpy as np
from scipy import sparse as ssp
from scipy.sparse.linalg import eigsh
from scipy.sparse.csgraph import laplacian
from scipy.sparse.cs... |
4e4ddd7ee469e68e25584777b18402bea0a18f4a36cb48ce9a3a4dd8160f3cf8 | Python | 14,732 | 339 | # type: ignore
"""Verification tests for the role co-membership matrix (`comembership.py`).
Two hand-checkable in-memory fixtures lock in the cell construction (within-layer H-B
switching and the structural mask; cross-layer switch-up/switch-down and the count
identity), and a gated suite asserts the invariants + a co... |
a37ba042eef240c53dcc1d168183365756419693dfe7f82733558c2569bab65b | Python | 14,733 | 411 | """Tests for snakebids.utils.snakemake_templates module."""
from __future__ import annotations
import re
import pytest
from hypothesis import given
from hypothesis import strategies as st
from snakebids.utils.snakemake_templates import SnakemakeFormatter, SnakemakeWildcards
from tests.test_snakemake_templates.strat... |
15224e86a3b78224e5cf94e8bcda3416a94a46f5ea995866566b3c3655711338 | Python | 14,741 | 288 | from argparse import ArgumentError, ArgumentParser, Namespace
import logging
from pathlib import Path
import sys
from chemprop.cli.utils import LookupAction
from chemprop.cli.utils.args import uppercase
from chemprop.featurizers import AtomFeatureMode, MoleculeFeaturizerRegistry, RxnMode
logger = logging.getLogger(__... |
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