sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
b6d26bd4228e28e0033e29187bdf715da5745f5b581056052711967aba266f1c | Python | 7,677 | 192 | # Copyright (c) 2020 10x Genomics, Inc. All rights reserved.
"""Basic python interface for creating a websummary.
If run as "python summarize.py example" it
creates an example HTML websummary using the template in
example/summary.html and the data in example/data.json.
"""
from __future__ import annotations
import... |
48398083244bddf4c881f30f7a73ea76e13102cf898fcb1f77e17c5f37b85a22 | Python | 7,689 | 183 |
############################################################################
# Copyright (c) 2022-2026 University of Helsinki
# All Rights Reserved
# See file LICENSE for details.
############################################################################
# Usage: python3 misc/isoseq_quantification.py -o examples --... |
ab8d6b97dc608a292ebc962b6c58e4d35f33edadd5388ed6b743299b8a153845 | Python | 7,689 | 169 | import matplotlib
import matplotlib.pyplot as plt
import numpy as np
import pytest
from openfe.analysis.plotting import (
plot_2D_rmsd,
plot_lambda_transition_matrix,
)
MBAR_HIGH_FLOAT_PREC = np.array([
[4.04963280e-01, 2.64851626e-01, 1.55960834e-01,
8.70071466e-02, 4.65819362e-02, 2.21166590e-02,
... |
2f9645ce7532d19fbfd226842370232d9c065f7b47cb35da4865a32b18865515 | Python | 7,691 | 207 | from dataclasses import InitVar, dataclass, field
from typing import Iterable, NamedTuple, Sequence
import numpy as np
import torch
from torch import Tensor
from chemprop.data.datasets import CuikBatchedDatum, Datum, MolAtomBondDatum
from chemprop.data.molgraph import MolGraph
from chemprop.featurizers.molgraph.molec... |
14da7db362c338fcd9276ff55358b46c8eb446a1153ab3a438ecc6e4eeafc9f8 | Python | 7,692 | 174 | from copy import deepcopy
from typing import Union, Tuple, List
import numpy as np
import torch
from einops import rearrange
from torch.nn import functional as F
from nnunetv2.configuration import ANISO_THRESHOLD
from nnunetv2.imageio.simpleitk_reader_writer import SimpleITKIO
from nnunetv2.preprocessing.resampling.d... |
358af186fdbf82c989a72d4d186c2a56a0099446760c59228b6f87888acc39f7 | Python | 7,701 | 155 | '''
Prepares the data necessary for the PRC extraciton
the actual PRC extraction goes in prc_extraction/run_prc_extraction.py
'''
from rCPGswCPG.Network import firing_rate
from rCPGswCPG.utils.sp_utils import *
from rCPGswCPG.Network import construct_model
from rCPGswCPG.model_params.config_loader import load_model_cfg... |
71f9758da572a14cdb6e5107033ac05cdfebac1192cbec1e82ff702e76e681ae | Python | 7,705 | 178 | import copy
import numpy as np
import torch_geometric.nn as gnn
import torch
from torch import nn
from torch.nn import functional as F
from sklearn.feature_selection import SelectKBest, f_classif
class GraphConvNet(nn.Module):
def __init__(self, input_size, output_size, hidden_size, alpha):
super().__init... |
5bc9201a903c6ecd9ff35872dcd66c6be14bbb1eb23b0f58c662b0262ecc5a9d | Python | 7,710 | 255 | # Configuration file for the Sphinx documentation builder.
#
# This file only contains a selection of the most common options. For a full
# list see the documentation:
# https://www.sphinx-doc.org/en/master/usage/configuration.html
# -- Path setup --------------------------------------------------------------
# If ex... |
992bbc4ecf895cadacb220fcadca12de1c94a78e45f9272d39330ea8980416f7 | Python | 7,710 | 186 | #
# Copyright (c) 2025 10X Genomics, Inc. All rights reserved.
#
"""Structify cell annotation outs."""
import os
from dataclasses import asdict, dataclass
import martian
from cellranger.cr_io import hard_link, recursive_hard_link_dict
__MRO__ = """
struct CellTypeWebSummaryBundle(
string cell_annotati... |
58577b375f3ff7f5b9d83c27815439bd6ffce2c4a6ee027caeb6c9213bae4553 | Python | 7,718 | 238 | #
# Copyright (c) 2020 10X Genomics, Inc. All rights reserved.
#
from __future__ import annotations
import functools
from collections.abc import Callable, Iterable
from html import unescape
import h5py
import numpy as np
from six import ensure_str
import cellranger.h5_constants as h5_constants
from cellranger.wrap... |
e72f38db2fe350f3383d78e28c7a82ea8a27e02a0ecddf2a5f18997d9f16be55 | Python | 7,722 | 215 | #!/usr/bin/env python
#
# Copyright (c) 2019 10X Genomics, Inc. All rights reserved.
#
from __future__ import annotations
import json
import os
import subprocess
from typing import TYPE_CHECKING
import martian
import numpy as np
import cellranger.cr_io as cr_io
import tenkit.log_subprocess as tk_subproc
if TYPE_CH... |
3fb8b76f3a556fb1faed954f34921872cc37cfd422e0f329c781dbd3a3f72550 | Python | 7,725 | 200 | # Garnet tests
from garnetff import garnet, get_equivalent_atom_types
from openff.toolkit.topology import Molecule, Topology
from openff.pablo import topology_from_pdb
from openmm import HarmonicBondForce, LangevinMiddleIntegrator
from openmm.app import PME, HBonds, Simulation, PDBFile, PDBxFile, ForceField
from openm... |
0da49334733dfc0657f7eb7ecf64fde7b216648b06085e16b4851465ea91ec8b | Python | 7,731 | 221 | 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 aumc_sql.psql_wrapper as psql_aumc
import yaml
"""
To extract demographic and patient characteristic of MIMIC-III and Ams... |
02d6fab8082181c7729c7fc8b56348387433162423025001551ed3f71851005f | Python | 7,740 | 253 | """XGBoost model wrapper for molecular property prediction.
Provides a thin wrapper around ``xgboost.XGBClassifier`` and
``xgboost.XGBRegressor`` that exposes ``model_family = "xgboost"``
for dispatch compatibility with the existing training and inference
pipeline.
"""
import logging
from contextlib import contextman... |
0b89f0708da10db61efccea6a684655c9bb2542047fb9ac873306e57c0252dd0 | Python | 7,741 | 214 | """ Vox2Cortex """
__author__ = "Fabi Bongratz"
__email__ = "fabi.bongratz@gmail.com"
from itertools import chain
from typing import Union, Tuple, Sequence
from deprecated import deprecated
import torch
import torch.nn as nn
from pytorch3d.structures import MeshesXD
import logger
from utils.mesh import vff_to_Meshe... |
be5e884a7078c7ead8e7c12283a0cd5c69601a5d5c64dacae0dd5c713a4b7d5d | Python | 7,747 | 203 | # Copyright (c) 2019 10X Genomics, Inc. All rights reserved.
"""Code to make the web summary for AGGR runs of (Space|Cell) Ranger."""
from __future__ import annotations
from typing import TYPE_CHECKING
import numpy as np
import cellranger.rna.library as rna_library
import cellranger.websummary.sample_properties as ... |
8630ae3b6f9b1a4413182e4b73d80fe0fab8723b721baebb8b3e4b03a9655947 | Python | 7,751 | 233 | from composer import Trainer
from composer.models import ComposerModel
from composer.utils import dist, reproducibility
from glob import glob
import numpy as np
import os
import pandas as pd
from pathlib import Path
from transformers import AutoTokenizer
import torch
from tqdm import tqdm
from train_modules import Tra... |
024db93ab96bf9577b8fcf3b4bfeb44987ffadbd16678ee756f5a1e36117356d | Python | 7,762 | 241 | from pathlib import Path
from typing import List, Dict
from dataclasses import dataclass
import argparse
import matplotlib.pyplot as plt
import numpy as np
import torch
import torchvision.transforms as transforms
from tqdm import tqdm
from . import config
from .utils.activation_manager import ActivationManager
from .... |
45d7b7ea3e66fc2100b387c49f239c5b7a289fdd97658ca0f13fa1f74d942255 | Python | 7,766 | 210 | # Copyright (c) Facebook, Inc. and its affiliates.
import numpy as np
import unittest
from copy import copy
import cv2
import torch
from fvcore.common.benchmark import benchmark
from torch.nn import functional as F
from detectron2.layers.roi_align import ROIAlign, roi_align
class ROIAlignTest(unittest.TestCase):
... |
d915511bfdbe101bf09f5ef0a347e7905d2cbdad782a5b4ea17dffcfcbf3dbea | Python | 7,783 | 158 | import os, re
import pandas as pd
import numpy as np
import matplotlib.pyplot as plt
import seaborn as sns
import functools
from smma.src.utilities import closest_node, find_pairs
from smma.src.visualise import plot_colocalisation
from loguru import logger
logger.info('Import OK')
input_path = 'results/spot_detecti... |
f8983edc0f990967ecfa6ccd7afdefacc07eab270bca713f9020b61402d1e984 | Python | 7,792 | 199 | import networkx as nx
import numpy as np
import mesa
from mesa.examples.advanced.alliance_formation.agents import AllianceAgent
from mesa.experimental.scenarios import Scenario
from mesa.meta_agents import MetaAgents
class AllianceScenario(Scenario):
"""Scenario for the Alliance model."""
n: int = 50
me... |
0495729278fbb6fd55e9e68323d8fec676872830a7e84bc6e6be357e312a998e | Python | 7,814 | 197 | import argparse
import pandas as pd
import numpy as np
from scipy.stats import ttest_rel as _ttest_rel, wilcoxon as _wilcoxon
from datetime import datetime
from tqdm import tqdm
import sys
import os
import warnings
warnings.filterwarnings("ignore", category=RuntimeWarning)
# One-sided wrappers: scipy >= 1.7.0 suppor... |
9df12559b9bfc8181a7fe96ad84fd004c0efea375ba19c90fde3961976247a79 | Python | 7,814 | 188 | """
loaders/axion_loader.py
-----------------------
Loader for Axion BioSystems Maestro MEA recordings.
Axion AxIS exports spike data as a CSV with an interleaved layout:
- Columns 0-1: metadata key-value pairs (left side)
- Columns 2-4: Time (s), Electrode, Amplitude (mV) (right side)
Both sides share the same ... |
8548f445890643e85d8c7aec83ea2c83d53a7a513e198c3f4fb2479a70061902 | Python | 7,820 | 162 | import sys
from pathlib import Path
if len(sys.argv)!=2: sys.exit("USAGE: python evidenceScoreProtMap.py <path to tab-sep-peptide-hits>, \n e.g.,\npython evidenceScoreProtMap.py L:\promec\TIMSTOF\LARS\2021\Oktober\211031FinnFinal\")
pathFiles = Path(sys.argv[1])
#pathFiles = Path("L:/promec/TIMSTOF/LARS/2021/Oktober... |
507982156403829ceaf13e285e1a1c87088ed14c17b3a55d4ae17a6171729ddc | Python | 7,821 | 187 | # Copyright (c) Facebook, Inc. and its affiliates.
import json
import logging
import os
from detectron2.data import DatasetCatalog, MetadataCatalog
from detectron2.data.datasets.builtin_meta import CITYSCAPES_CATEGORIES
from detectron2.utils.file_io import PathManager
"""
This file contains functions to register the ... |
61cd8fb88ddb7fb2f1ef72cb9c9b9ec7ebcffbbde629bf59f9557c4f907877f9 | Python | 7,821 | 191 | '''
pre-processing script for Vox2Cortex
This script is adapted from DeepCSR https://bitbucket.csiro.au/projects/CRCPMAX/repos/deepcsr/browse/preprop.py
This script registers an image (orig.mgz file from FreeSurfer outputs) to MNI space (using niftyreg),
the corresponding affine transformation matrix is then used to w... |
dce967a0cf7c3d2b73f9dbda4ba39b3e6de151cf98c865d8f5fd2f8cbedadb62 | Python | 7,833 | 204 | #!/usr/bin/env python
#
# Copyright (c) 2020 10X Genomics, Inc. All rights reserved.
#
"""A helper stage to pipe through map called stages to sidestep martian issue."""
from __future__ import annotations
from typing import TYPE_CHECKING, Any
import martian
import cellranger.cr_io as cr_io
from cellranger.fast_utils... |
34e7e8bd2aeb8fd09f3811f8d2ea84d1ff08fd4cd562b74847bbf119f0b45fdf | Python | 7,835 | 204 | # 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... |
7d5a1938aefc192f673111b4da6fb7dab0266f04b47fdf11d7485de731aeaf1a | Python | 7,835 | 296 | # noqa: D100
import gc
import weakref
import pytest
from mesa.examples import (
BoidFlockers,
BoltzmannWealth,
ConwaysGameOfLife,
EpsteinCivilViolence,
MultiLevelAllianceModel,
PdGrid,
Schelling,
SugarscapeG1mt,
TransitSystem,
VirusOnNetwork,
WolfSheep,
)
from mesa.examples... |
6aa223eb5e7edbf13efad5838f9fea392d69cf019292fc4602ec731b007883e6 | Python | 7,836 | 220 | # Copyright (c) Facebook, Inc. and its affiliates.
import atexit
import bisect
import multiprocessing as mp
from collections import deque
import cv2
import torch
from detectron2.data import MetadataCatalog
from detectron2.engine.defaults import DefaultPredictor
from detectron2.utils.video_visualizer import VideoVisual... |
84fe93fa8979e07d4a7e14817d50c3a51342a918693c9c8540782a7f80dd3753 | Python | 7,844 | 183 | import utils
import numpy as np
import pandas as pd
import scipy
import math
import os
import sys
#Helper functions
# separate actin point into cells based on their distances to the two membranes
def separate(actin, memb1, memb2, cutoff, voxel_size = 1.34808):
#generate kd tree
memb_1_kd_tree = scipy.spatial.K... |
253dcd43ffa9a7cc7b8ffa85236db0e8a721a2f4274726c86dc6fe30f802f6ce | Python | 7,846 | 220 | # Copyright (c) Facebook, Inc. and its affiliates.
import fvcore.nn.weight_init as weight_init
import torch
import torch.nn.functional as F
from detectron2.layers import Conv2d, FrozenBatchNorm2d, get_norm
from detectron2.modeling import BACKBONE_REGISTRY, ResNet, ResNetBlockBase
from detectron2.modeling.backbone.resn... |
790d7a663f7e6898f99ec7ccf38ac63e69719688aa527f775bc77e58bce0a04c | Python | 7,846 | 220 | # This code is part of OpenFE and is licensed under the MIT license.
# For details, see https://github.com/OpenFreeEnergy/openfe
from typing import List
import click
from openfecli import OFECommandPlugin
from openfecli.parameters import (
MAPPER,
MOL_DIR,
N_PROTOCOL_REPEATS,
NCORES,
OUTPUT_DIR,... |
18a9f204003830aa3a2cb7617628859db559034fbef327bf872f1f9836869f6b | Python | 7,850 | 211 | import sys
import argparse
import os
import shutil
import time
import numpy as np
import sys
import torch
import torch.nn as nn
import torch.nn.parallel
import torch.backends.cudnn as cudnn
import torch.distributed as dist
import torch.optim
import torch.utils.data
import torch.utils.data.distributed
import torchvision... |
5216036aa0ba32de7d546dfb82382c8aa547d86633d15ea49fa0da60d455c4e9 | Python | 7,858 | 226 | """
Skeletons
=========
<!-- difficulty: beginner -->
Load and save skeletons from SWC and other formats, or build them from scratch.
Skeletons are probably the most common representation of neurons and are stored as a series
of connected nodes (the "skeleton"). In {{ navis }}, skeletons are represented by the
[`navi... |
7495e0659063127ffe17e01aed8e9f59f42e5cd69fed72c3cf3b639c7e8f3597 | Python | 7,862 | 280 | import json
import pickle
import sys
from pathlib import Path
import torch
import stoic.predict_stoichiometry as ps
class DummyStoicModel:
def __init__(self):
self.device = None
self.eval_called = False
self.enabled_full_length = None
self.predict_calls = []
def to(self, dev... |
77f7064ddc89cb61231e45a7f375f7b0c417f618040b06b463b0b611a08ad4bc | Python | 7,863 | 172 | from qcportal import PortalClient
from collections import defaultdict
from rdkit import Chem
import argparse
import numpy as np
import h5py
import yaml
# Units for a variety of fields that can be downloaded.
units = {'dft_total_energy': 'hartree',
'dft_total_gradient': 'hartree/bohr',
'mbis_charges'... |
498ae143dd3efb449ae9760e41dbc0c14b568e1632f07eab911178de11817a38 | Python | 7,867 | 217 | #code https://towardsdatascience.com/creating-an-email-parser-with-python-and-sql-c79cb8771dac
#data outlooks mail copied to folder
#check https://sqlite.org/cli.html
#pip install sqlalchemy
db = sqlite3.connect("emails.db")
# Create empty tables
db.execute("""
CREATE TABLE IF NOT EXISTS "articles" (
"id" INTEGER,
"tit... |
ca0fe5c9a4ca7b4c5c8202d33f820568c30dd533000cbdc6c5812e37b201c058 | Python | 7,889 | 208 | import pandas as pd
import pytest
import torch
import stoic_train.dataset as dataset_module
from stoic_train.dataset import StoichiometryDataModule
class DummyGraph:
def __init__(self, quantity_value: int, interact_value: int):
self.quantity = torch.tensor([quantity_value], dtype=torch.long)
self... |
d7bce845c7cd3827f22687d4b035fd830490f960dce4423484570192d573e9f2 | Python | 7,890 | 229 | # Copyright (c) Facebook, Inc. and its affiliates.
"""
Backward compatibility of configs.
Instructions to bump version:
+ It's not needed to bump version if new keys are added.
It's only needed when backward-incompatible changes happen
(i.e., some existing keys disappear, or the meaning of a key changes)
+ To bump... |
2913c110b142c54081700530ff8b70fa1f2083ddab60bb1e89a50efb99dccc50 | Python | 7,893 | 200 | #!/usr/bin/env python
#
# Copyright (c) 2018 10x Genomics, Inc. All rights reserved.
#
"""Aggr preflight check + convert legacy molecule info h5 to current version."""
from __future__ import annotations
import os
import shutil
from typing import TYPE_CHECKING
import martian
import cellranger.constants as cr_constan... |
9b53ff271b32dece05914bc9cec0174e57acd67e522a746846650b1731ceba63 | Python | 7,898 | 129 | '''
Created on Feb 7, 2025
@author: voodoocode
'''
import scrubber.database4
import scrubber.database6
import scipy.signal
import matplotlib
matplotlib.use("Qtagg")
import matplotlib.pyplot as plt
import numpy as np
minF = 1
maxF1 = 500
maxF2 = 5000
def db4():
path = "/mnt/data/Professional/LMU/data/Beta-prev... |
31e18573cba93395b6ed4d5802ed5c75f5609e7f763b74695b347833746bf710 | Python | 7,921 | 280 |
""" Evaluation metrics. Those metrics are typically computed directly from the
model prediction, i.e., in normalized coordinate space unless specified
otherwise."""
__author__ = "Fabi Bongratz"
__email__ = "fabi.bongratz@gmail.com"
from abc import ABC, abstractmethod
import numpy as np
import torch
import pandas as... |
43e992e99ae9197c3874f279237bfe4800f69bb22e6b16a1a42343d88f0ea0d4 | Python | 7,927 | 201 | # -*- coding: utf-8 -*-
"""
Created on Tue Jul 19 11:52:35 2022
@author: Joseph Vermeil
GraphicStyles.py - state the graphic styles elements of CortExplore programs,
to be imported with "import GraphicStyles as gs" and call content with
"gs.my_graphic_style_thingy".
Joseph Vermeil, 2022
This program is free softwar... |
069b1bb87e5f940cfc5672ebd56b0fb93d0dfa619163b553c343ff4a9680add7 | Python | 7,941 | 210 | # 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... |
9905d89ea41bc366f5e451e2f835a0c0d49bed79e3d3e2c6edc83837320de093 | Python | 7,941 | 167 | import torch
from torch import nn
import torch.nn.functional as F
from einops import repeat
from taming.modules.discriminator.model import NLayerDiscriminator, weights_init
from taming.modules.losses.lpips import LPIPS
from taming.modules.losses.vqperceptual import hinge_d_loss, vanilla_d_loss
def hinge_d_loss_with_... |
bb3ebd9643a85d8d3d35b251579f336d8f0872a30e406c2a5a491d28cf2210df | Python | 7,942 | 216 | """
Run the v3 response pipeline on ICMS83 sessions.
ICMS83 uses a different data layout than experimental animals:
- Data on E:/ICMS83/ instead of C:/data/
- trial_df from CSV instead of DataLoader
- Analyzer at batch_sort/stage3/analyzer_final.zarr instead of merge/hmerge_analyzer.zarr
Usage:
python -m batch_pr... |
93614d6fc635811c794ab2ee364430f1046a93322283ffd58eb0667a3d934249 | Python | 7,946 | 231 | """Copyright 2013 Michael Kane and Bryan Lewis.
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at
http://www.apache.org/licenses/LICENSE-2.0
Unless required by applicable law or agreed to in writ... |
272077647aa88a3df8aa5f2a765f8e92c3077527873cf278c6bd965538efa43d | Python | 7,950 | 207 | #!/usr/bin/env python3
"""Create RAVEN-compatible 3D HDF5 patch datasets from NIfTI volumes."""
from __future__ import annotations
import argparse
import csv
import json
from pathlib import Path
import sys
import h5py
import nibabel as nib
import numpy as np
SCHEMA = (
"orig_dataset_imgs",
"orig_zooms_x",
... |
f711f2caaff760a4c4fbe12bdd32787a9cd9f22539ccf8943d5484dee76b9fce | Python | 7,958 | 241 | """Tests for the Brain Image Library interface.
These are deliberately network-free: we only exercise the pure helpers
(the autoindex parser, the URL mapping, the record flattening and the field
validation). Anything that talks to BIL is left to manual testing, in line
with how the other interfaces are handled.
Note ... |
3e2b420ef56ec055a9ce2a6e5e713b0d4c715cb48214dfd8cc00543f30043607 | Python | 7,961 | 221 | #!/usr/bin/env python
# Copyright (c) Facebook, Inc. and its affiliates.
"""
Detectron2 training script with a plain training loop.
This script reads a given config file and runs the training or evaluation.
It is an entry point that is able to train standard models in detectron2.
In order to let one script support tr... |
d8f9b685b52e2bde1663ca30cee7da3a561f8f09face80c0ed1688f466f1517c | Python | 7,964 | 277 | """
@Article{li2014multiplicative,
author = {Li, Chunming and Gore, John C and Davatzikos, Christos},
title = {Multiplicative intrinsic component optimization (MICO) for MRI bias field estimation and tissue segmentation},
journal = {Magnetic resonance imaging},
year = {2014},
volume = {32},
... |
67733215fa138ead79cbfde7301eabf57adf7a926615b18b0ae8d045a04101ba | Python | 7,979 | 158 | #%%
import sys
sys.path.append('/mnt/obob/staff/fschmidt/cardiac_1_f')
from utils.pymc_utils import coefficients2pcorrs
from os import listdir
from os.path import join
import pandas as pd
import bambi as bmb
import pymc as pm
import joblib
from scipy.stats import zscore
import arviz as az
from plus_slurm import Job... |
b341eff116027dc57b204561fe359e1dd465a95dcbf6136279ad6f0fbafa7760 | Python | 7,980 | 182 | from tristan_pipeline.utils.analysis_utils import *
from tristan_pipeline.io.params import *
from tristan_pipeline.utils.loading_utils import *
from tristan_pipeline.utils.preproc_utils import *
from tristan_pipeline.utils.glm_utils import *
from nilearn.glm import threshold_stats_img
from nilearn import image
import n... |
50e8d967d72f358fa276c9a4f6c5dd7c970788be7b5858dcad26778802f35076 | Python | 8,000 | 252 | import nibabel as nib
import numpy as np
import naturalneighbor
from scipy.stats import zscore
logfile = open(snakemake.log[0], "w")
print(f"Start", file=logfile, flush=True)
def convert_warp_to_itk(warp):
"""Convert warp to ITK convention by negating X and Y"""
warp_itk = warp.copy()
warp_itk[:, :, :, 0... |
b2fe61b940048ce8abe1240c89ff2e41f18b991c14078db5d7df1d2b8dc1a942 | Python | 8,005 | 167 | import sys
from pathlib import Path
if len(sys.argv)!=2: sys.exit("USAGE: python pepXscoreProtMap.py <path to tab-sep-peptide-hits>, \n e.g.,\npython pepXscoreProtMap.py L:\promec\TIMSTOF\LARS\2021\Oktober\211031FinnFinal\gluCtryP")
pathFiles = Path(sys.argv[1])
#pathFiles = Path("L:/promec/TIMSTOF/LARS/2021/Novembe... |
8f205f2434e3f46f82388b77a57fb75d6648f65526e5ea9d47c97e96df37541a | Python | 8,008 | 213 | ############################################################################
# Copyright (c) 2023 University of Helsinki
# # All Rights Reserved
# See file LICENSE for details.
############################################################################
import math
import os
import sys
import argparse
from Bio import S... |
925e0f9e230a184517467a6e73255754aca77ed0293094671b43553c177f0d10 | Python | 8,011 | 186 | # Copyright (c) 2021 10X Genomics, Inc. All rights reserved.
from __future__ import annotations
from typing import TYPE_CHECKING
import numpy as np
import cellranger.rna.library as rna_library
from cellranger.feature.utils import get_feature_counts_as_df
if TYPE_CHECKING:
import pandas as pd
from cellrang... |
509b478f473e1ff13717e310aeddc57b2680cd7feb3c085fe8db1fccd546930d | Python | 8,016 | 197 | import warnings
import numpy as np
import pandas as pd
import nibabel as nib
import pytest
from neuroHarmonize import harmonizationLearn, harmonizationApply
from neuroHarmonize.harmonizationApply import applyModelOne
from neuroHarmonize.harmonizationNIFTI import applyModelNIFTIs, flattenNIFTIs, createMaskNIFTI
@pytes... |
8898c259b9f227d9643c4c125e3f9b7efac3770834ae94d30bc3c491e787d8ae | Python | 8,036 | 223 | import numpy as np
import matplotlib.pyplot as plt
import warnings
def fitSmoothingKernelBandwidth(full_traindict, total_trial_len):
"""Fits a spike smoothing kernel to spike train data using
the improved Sheather-Jones (ISJ) algorithm:
Z. I. Botev, J. F. Grotowski, and D. P. Kroese.
“Kernel dens... |
2a32b61948c77de1557c3a12f22218be8a14c7141b9acbb9f2018412c1d5cf1b | Python | 8,042 | 221 | import torch
import torch.nn as nn
import torch.optim as optim
import numpy as np
from torch.utils.data import DataLoader, TensorDataset, Subset
import pandas as pd
from sklearn.metrics import mean_absolute_error,mean_squared_error,r2_score
NCGCN_embedding_train = np.load('../AMP_dataset/embedding/NCGCN_embedding_trai... |
46d31a10b4e2dc9522c7ebff03714e9a411264226fbe1a48d5a2d9b91716f7d5 | Python | 8,044 | 301 | # -*- coding: utf-8 -*-
import os
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
def plot_cluster_stability(cluster_stab_df, out_fn=None, title=None):
"""
Barplot of within-cluster vs between-cluster consensus.
Input:
cluster_stab_df = output of cluster_stability_table()
... |
cd3446c99489aa05943c3ce27ff1d28772431054bd7cc0ca5d52c0974fa7a60d | Python | 8,060 | 278 | # This code is part of OpenFE and is licensed under the MIT license.
# For details, see https://github.com/OpenFreeEnergy/openfe
"""Pydantic models for the definition of advanced CLI options"""
import warnings
from collections import namedtuple
from typing import Any, Optional
import click
import yaml
from plugcli.pa... |
7ea81b08e7197ab4e4be853b1f64ce7684ee9e0da0716f8dc9179684c58b0e5c | Python | 8,062 | 227 | """Tests for conformer disk caching and parallel generation."""
import tempfile
from pathlib import Path
from unittest.mock import patch
import numpy as np
import pytest
from rdkit import Chem
from nfml.data.fingerprints import (
_ConformerCache,
_generate_conformers,
_generate_single_conformer,
compu... |
a5094cef4fed29b6327d2e0fc8a23b6ef2a7a6cb633aec160f7a0f183a03583a | Python | 8,066 | 228 | """
Stratified Tile-Level Evaluation Metrics
Accumulates patch-level predictions across batches, groups them by tile ID,
and computes segmentation metrics per tile. Supports aggregation to WSI level.
Components:
StratifiedMetricsCalculator — main accumulator class
compute_wsi_level_metrics — aggregate tile ... |
232326df52baecf4e5d72c911bab5514c1c2ce86087429a584d55f4ccf3b82a0 | Python | 8,069 | 206 | import os
import numpy as np
import pandas as pd
import umap
import matplotlib.pyplot as plt
import anndata as ad
import scanpy as sc
import scvelo as scv
import cellrank as cr
import scanpy.external as sce
from scipy.io import mmwrite, mmread
import statsmodels.api as sm
from sklearn.cluster import AgglomerativeCluste... |
74013029de7e82bc071d7739be46a13e0a47941f698996401cd51339b8689808 | Python | 8,069 | 251 |
""" Test procedure """
__author__ = "Fabi Bongratz"
__email__ = "fabi.bongratz@gmail.com"
import re
import os
import sys
import logging
import json
from copy import deepcopy
import wandb
import torch
import numpy as np
import logger
from data.dataset_split_handler import dataset_split_handler
from models.model_han... |
2da6c843ffa493728a17ed7bbf4fec2cf3cab2319c65bc060269f17d1de36c84 | Python | 8,070 | 177 | import os
import numpy as np
import pandas as pd
import umap
import matplotlib.pyplot as plt
import seaborn as sns
import anndata as ad
import scanpy as sc
import scvelo as scv
import scanpy.external as sce
from scipy.io import mmwrite, mmread
import statsmodels.api as sm
np.random.seed(42)
# peak-gene linkage matrix... |
124641f80c389c24f6e7edc3c76288073c20b1b672ae82982b88b33698a0cf68 | Python | 8,071 | 198 | #!/usr/bin/env python
# Copyright 2016-2025 Biomedical Imaging Group Rotterdam, Department of
# Radiology and Nuclear Medicine, Erasmus MC, Rotterdam, The Netherlands
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain ... |
45cba821150be0d1e2cc57d85339c8713a00391a5c803e05e51f77dff59ef715 | Python | 8,072 | 223 | """Tests for `navis.graph.geodesic_clusters`.
Runs on `navis_fastcore.geodesic_clusters`. The greedy carve-out is
deterministic, so these pin what the partition must *be* - every node within
`max_dist` of its cluster's seed, every cluster connected - rather than
comparing against a second implementation.
"""
import n... |
e54a0e0af3788847c3f112cd835ba4ba5202ffb770d82ce8c86b13ec46850b22 | Python | 8,072 | 216 | #!/usr/bin/env python3
"""
Bulk runner for map_active_sites_to_pdb.py over a CSV, including pdb_resseq in the master summary.
Usage :
python run_bulk_mapping_from_csv_with_resseq.py \
--csv mapping_ready.csv \
--pdb-dir ./pdbs \
--outdir ./mapped_results \
--mapper-path ./map_active_sites_to_pdb.py \... |
9b497f02b3836725cc7d2fc4913ab2923fb075f31d1cbb58523f185a75a710ce | Python | 8,074 | 237 | import pandas as pd
import numpy as np
def _compute_bounds(totals, target=0.2, low=0.18, high=0.22):
"""
Compute integer lower/upper bounds for each semantic.
"""
lb = np.floor(totals * low).astype(int)
ub = np.ceil(totals * high).astype(int)
tgt = np.round(totals * target).astype(int)
# E... |
84dcc67a948ec3f17f1908638f01e52e91b0e3599833bc86c13b164d42edb9ee | Python | 8,078 | 222 | """Agent related classes.
Core Objects: Agent.
"""
# Postpone annotation evaluation to avoid NameError from forward references (PEP 563). Remove once Python 3.14+ is required.
from __future__ import annotations
import contextlib
import itertools
from random import Random
from typing import TYPE_CHECKING, ClassVar
i... |
3d83e862ec52fbdda732845131e82c4f079630ff38afdd63d0d359e6736e06ee | Python | 8,088 | 195 | #cluster https://nbviewer.jupyter.org/github/KrishnaswamyLab/PHATE/blob/master/Python/tutorial/EmbryoidBody.ipynb
#!pip install --user phate matplotlib==3.1 scprep
#demo https://www.krishnaswamylab.org/projects/phate/eb-web-tool
import sys
base_path = os.path.expanduser("~")
print(base_path)
from pathlib import Path
pa... |
ca3ebe09d428ff638b2930e4f13003239e069aa592afe132e7113b45464c8c6c | Python | 8,093 | 172 | import glob
import os
from typing import Union
import torch
import torch.optim as optim
from torch.utils.data import DataLoader, random_split
from tqdm import tqdm
from bio_image_unet.siam_unet import BCEDiceLoss
from . import logcoshTverskyLoss, TverskyLoss, weightedBCELoss
from .predict import Predict
from .siam_un... |
ec119d6ad79e9db3eace880775325b77b22e8897518ff5017031355a8c827ebe | Python | 8,096 | 274 | #%%
import pandas as pd
import mne
import scipy.signal as dsp
import joblib
from pathlib import Path
from os.path import join
import scipy.stats as stats
import matplotlib.pyplot as plt
import seaborn as sns
import numpy as np
import pingouin as pg
from fooof import FOOOFGroup
from fooof.utils.params import compute_kne... |
5c43b89727bb4423387666de2d3c830d98663f3ed220f0a0d8fec95c1a7b3ea1 | Python | 8,121 | 227 | #%%
import os
import re
import argparse
import numpy as np
import pickle as pk
import MDAnalysis as mda
from os import path
from src.hbonds import karplus_dict, backbone_torsions, karplus_J, karplus_hbonds, backbone_amide_hbond_between, karplus_extrema
if __name__ == "__main__":
parser = argp... |
85865bb0fbfa777c39fa45d7f870a88f962fd81107d13afeb9fc29542235c442 | Python | 8,121 | 176 | import os
import json
import albumentations
import numpy as np
from PIL import Image
from tqdm import tqdm
from torch.utils.data import Dataset
from taming.data.sflckr import SegmentationBase # for examples included in repo
class Examples(SegmentationBase):
def __init__(self, size=256, random_crop=False, interpo... |
59e8218ffbdb1021ede0ca01b78c7ea0948f6d6edca294bf12e5423fbba2491c | Python | 8,123 | 153 | # This file contains the main code for extracting resampled center line coordinates out of a binary filament segmentation
# It is to be used with the sample config file
import numpy as np
import pandas as pd
import mrcfile
from skimage.morphology import skeletonize_3d, medial_axis, remove_small_objects
from skimage.co... |
67ed6e6e75a5a8e059584cd2521944e311bd5592e6fdc9f7509fe2ceb51898b7 | Python | 8,124 | 192 | # Read molecules and record elements, formal charges, aromatic atoms,
# n bonded atoms, bonds, angles, propers, impropers and molecule indices
# Output uses one-based indexing
# See also https://github.com/openmm/spice-models/blob/main/five-et/createSpiceDataset.py
# This is for the GEMS data and uses MDAnalysis to d... |
ac6a0bb279ada57c96ce06640acf10198e4822427701842a965c78b2599af407 | Python | 8,126 | 250 | """
Wrappers for VTK classes needed for rendering.
"""
# Author: Oualid Benkarim <oualid.benkarim@mcgill.ca>
# License: BSD 3 clause
from .base import BSVTKObjectWrapper, wrap_vtk
from .actor import BSActor, BSActor2D, BSScalarBarActor, BSTextActor
###############################################################
# ... |
b98ea9f27b1b644711c917c908ff66385cd92bf30ce04b45175d3517409d7734 | Python | 8,127 | 207 | #c:\Users\animeshs\scripts>python boltz2JSON.py
from pathlib import Path
import sys
import json
import csv
import glob
import re
import os
in_arg = sys.argv[1] if len(sys.argv) > 1 else ""
out_path = Path(sys.argv[2]) if len(sys.argv) > 2 else Path("boltz2.combined.csv")
def load_file(p: Path):
with p.open("r", ... |
bce2d079a32630bed889c5763e5d9d0d7d389f24095af97324f4324d550e0535 | Python | 8,128 | 205 | # Copyright (c) Facebook, Inc. and its affiliates.
import logging
import math
from typing import List, Tuple, Union
import torch
from detectron2.layers import batched_nms, cat, move_device_like
from detectron2.structures import Boxes, Instances
logger = logging.getLogger(__name__)
def _is_tracing():
# (fixed in... |
3cad832a0e096edadbac067bfcd26cf47e1d2df4964925112cda58cf736cdd68 | Python | 8,129 | 205 | from __future__ import annotations
from copy import copy
from typing import Any, Hashable, Iterable, Optional
import numpy as np
import numpy.typing as npt
import pandas as pd
import xarray as xr
from pandas.core.groupby.generic import DataFrameGroupBy
from .base import attach_labels, get_midx, get_proj_layer_mappin... |
3b6765b4a5deeae6454d117a477587f1c5f6c8e3ecb71ea914ba56f263968a7f | Python | 8,136 | 224 | # ruff: noqa: PLR2004
from __future__ import annotations
import re
from math import inf
import pyparsing as pp
from hypothesis import assume, given
from hypothesis import strategies as st
import tests.strategies as sb_st
from snakebids import bids
from snakebids.core.datasets import BidsComponent, BidsDataset
from s... |
4bcaac738591419fa0b01862424562bd37bc30648dc0ec3599b0676f0d5c015c | Python | 8,152 | 185 | # type: ignore
import pandas as pd
from ..base import get_proj_layer_mapping, get_midx
from . import _utils
pidx = pd.IndexSlice
def get_structural_indices(nrn: int, layer: int, syn_params: pd.DataFrame,
w_min: float = 0.5, tol: float = 3.0) -> pd.MultiIndex:
"""Gets network (layer, n... |
e89cf5242941aebdafe26fcfa2b587c8d89fce95f04b88d379d69a06d663bbc2 | Python | 8,158 | 292 | """ Created on Wed Oct 16 11:36:39 2024
@author: dcupolillo """
import numpy as np
import torch
from torch.utils.data import (
DataLoader, SubsetRandomSampler, WeightedRandomSampler)
from sklearn.model_selection import train_test_split
import random
def set_device():
return "cuda" if torch.cuda.is_availa... |
825d814339645f7ddf5c3375ed1d29f9d5861a0cd0af6ab71ea03bb6817a31fa | Python | 8,161 | 221 | import pandas as pd
import numpy as np
import nibabel as nib
from scipy.ndimage import binary_dilation
from nilearn import image
from scipy.stats import mannwhitneyu, ttest_ind, ttest_rel
from statsmodels.stats.multitest import multipletests
from scipy.stats import permutation_test
def consecutive_blocks_(task_vector... |
b60ac5b3346f8692c1eee66be88b536e94656b691e6b4b71e4c07a035a975cc1 | Python | 8,165 | 168 | import math
import random
import warnings
from itertools import cycle
from typing import List, Optional, Tuple, Callable
from PIL import Image as pil_image, ImageDraw as pil_img_draw, ImageFont
from more_itertools.recipes import grouper
from taming.data.conditional_builder.utils import COLOR_PALETTE, WHITE, GRAY_75, B... |
9bf8999668937bfdf3a14394d443fb8fe94f007e30d35db466f5deb090d0b109 | Python | 8,168 | 170 |
import sys
#export
import os, argparse, sys, datetime
os.environ['TF_CPP_MIN_LOG_LEVEL'] = '3'
import seaborn
from matplotlib import pyplot
import numpy, scipy
from katmap.mikesmaps import GroupedKatmapModels, AnalysisSpecification, FeatureTable
from katmap.parsers import FastaReader
from katmap.rnamap import RNAm... |
d7db732f0c52c18044f61a45af8b90f450ee055f09d4010bcb1f62a8aa35ed20 | Python | 8,169 | 191 | # Copyright (c) Facebook, Inc. and its affiliates.
import copy
import logging
import numpy as np
from typing import List, Optional, Union
import torch
from detectron2.config import configurable
from . import detection_utils as utils
from . import transforms as T
"""
This file contains the default mapping that's appl... |
4eb41fc5acd0d852f4375d0a6ff74fbdadc38d6bc0b8bf4b63ea193efb60a24f | Python | 8,174 | 226 | # -*- coding: utf-8 -*-
"""
Figure 4: Dynamics
"""
import numpy as np
import matplotlib.pyplot as plt
from netneurotools import stats
from scipy.stats import zscore, pearsonr, ttest_ind
import seaborn as sns
from matplotlib.colors import ListedColormap
from scipy.spatial.distance import squareform, pdist
from sklearn.... |
8a3598417d25cf537119127cbbdd880d0d46256d50c417ee2aea216488f43686 | Python | 8,186 | 181 | """Postprocessing for general analysis of detected PNGs.
"""
import numpy as np
import numpy.typing as npt
import xarray as xr
from hsnn.core.record import SpikeRecord
from hsnn.core.types import SpikeTrains
from hsnn import ops
from .base import PNG
__all__ = [
"get_spike_trains",
"get_polygrp_trains",
... |
265c9ecf94fae75f53d036f000785f7e359057c21e4d5a32a01c90b6e23889d8 | Python | 8,191 | 201 | #%%
from plus_slurm import Job
#%%
import os
from os import listdir
from os.path import join
from mne_bids import BIDSPath, read_raw_bids
import mne
import pandas as pd
import numpy as np
from autoreject import Ransac # noqa
import pyriemann
import joblib
from scipy.signal import welch
import h5py
from fooof import... |
460344571795f33ad6080caaa3f31832e9c2fcfcbeabfb1168f01e1833181ba4 | Python | 8,193 | 236 | from typing import Iterable, Optional, NamedTuple
from ..core import Skeleton
import networkx as nx
import pandas as pd
import numpy as np
from ..config import get_logger
logger = get_logger(__name__)
OTHER = "__OTHER__"
class Edge(NamedTuple):
connector_id: int
source_name: str
target_name: str
sou... |
734f02b49731f3abd168de79a38c68fbce7c32191a81e0221a0dc7b2f417e9b0 | Python | 8,200 | 204 | """
Axon-Dendrite Splits
====================
<!-- difficulty: intermediate -->
Split a neuron into axon and dendrite from synapse flow centrality.
## Background
Neurons, generally, have two main compartments: axon and dendrites. In textbooks, the axon is the
part of the neuron that sends signals to other neurons, w... |
ac09c0112ee2eb7e12e5f41d4bd8a18502024c3a89b52d7a06aefc8df3cc6dc5 | Python | 8,208 | 161 | """Compare held-out XGBoost TreeSHAP and GA-BPNN DeepSHAP summaries."""
from __future__ import annotations
import argparse
import json
from itertools import product
from pathlib import Path
from typing import Sequence
import numpy as np
import pandas as pd
DEFAULT_COUNTRIES = ("AUS", "BEL", "CZE", "FIN", "GBR", "I... |
b37df4710dd48850da1fa3756768b7560de77333a0b996c783c4a178744c8652 | Python | 8,212 | 241 | #!/usr/bin/env python
#
# Copyright (c) 2014 10X Genomics, Inc. All rights reserved.
#
# Code for estimating tile-extents on a lane
#
from __future__ import annotations
import re
import xml.etree.ElementTree as etree
from collections.abc import Iterable
from typing import ClassVar, Literal, NamedTuple
import tenkit.s... |
ba0c616efd175eca7b67d559785096307286c9ae761c1019749e73bd59e178fc | Python | 8,212 | 288 | # Copyright (c) 2022 10X Genomics, Inc. All rights reserved.
"""Utility functions for working with aligned segments."""
from __future__ import annotations
from typing import TYPE_CHECKING
import numpy as np
from six import ensure_binary
import cellranger.bam_constants as bam_constants
import cellranger.constants a... |
b2e29d168fb6acd431a0db62ac803bf9c34e041da782dd043975519e9e78956d | Python | 8,214 | 298 | import torch
import torch.nn as nn
import torch.nn.functional as F
class BCELoss(nn.Module):
"""
Binary Cross-Entropy Loss.
Parameters
----------
weight : torch.Tensor, optional
A manual rescaling weight given to the loss of each batch element.
size_average : bool, optional
By... |
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