sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
4e2fea7bcc3b5f18f20ad8de70ad25e72c97f6bc1f5542b57eec8831fd4c8994 | Python | 6,755 | 284 | """This tests the CLI functionality of training and predicting a regression model on a single molecule.
"""
import pytest
from chemprop.cli.main import main
from chemprop.models.model import MPNN
pytestmark = pytest.mark.CLI
@pytest.fixture
def data_path(data_dir):
return str(data_dir / "classification" / "mol... |
e171c3426d01749a105410bf6bdd064eb5f42e25d9cd66b7319b3a18d3a8eab6 | Python | 6,757 | 177 | #!/usr/bin/env python3
"""Rebuild aggregate dashboard PNG + per-panel PDFs from a saved ``ALL_FOLDERS_MASTER_RESULTS*.csv``.
Does not re-read CZI files. Panel 6 (Friedman / zone densities) needs per-image columns
``File``, ``Density_early_NMJ_like``, ``Density_Muscle_associated``, ``Density_Neuron_associated``, ``Dens... |
4e4f8e84286e9b5ab36755b92b388120ec3df09388661396febd0625b4ddcfb6 | Python | 6,762 | 235 | from config import ALGORITHMS, COUNTRIES
from data import load_modeling_data
from evaluation import (
heldout_bootstrap_summary,
metric_row,
permutation_importance_rows,
positive_scores,
)
from results import make_result_tables
from selection import select_model_by_cv_auprc, select_model_by_optimism_cor... |
a9d4d0aa5856efe2279d4dff4e9be91bf2bda4fb9da0e74eba81942b42299ba8 | Python | 6,765 | 140 | import logging
from typing import List, Optional
logger = logging.getLogger('IsoQuant')
class FusionMetadata:
def __init__(self, detector) -> None:
self.detector = detector
def process_all(self, min_support: int = 1) -> None:
"""Iterate over fusion candidates and apply gating, gene assignmen... |
637b85cd0cd47b43a08717b5edd6a7e64c5157d47495033d5f410d518a15ad1d | Python | 6,767 | 167 | ############################################################################
# Copyright (c) 2025-2026 University of Helsinki
# All Rights Reserved
# See file LICENSE for details.
############################################################################
import pytest
from isoquant_lib.barcode_calling.umi_filtering ... |
d269508b5aea98075fa8cf0b261449af0319817f8201812a92b88a413c0ab31d | Python | 6,769 | 173 | from __future__ import annotations
from dataclasses import dataclass, field
from typing import Any
from rdkit import Chem
from src.protonation.base import ProtonationError
@dataclass(slots=True)
class DimorphiteProtonator:
"""Protonation backend using Dimorphite-DL.
Dimorphite-DL applies SMARTS-based pKa ... |
8729c3c5688f9769f31236541d3c96717cf51b3e1d08ceb831d291aee4ce5961 | Python | 6,770 | 181 | # 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... |
cff9fcaa1a846f5786e38d3f2cc0db93c73aa2ad6ba6f865d4833130bcbc3fcf | Python | 6,771 | 160 | # Copyright (c) Facebook, Inc. and its affiliates.
import numpy as np
import unittest
from copy import deepcopy
from typing import Dict
import torch
from detectron2.config import CfgNode as CfgNode_
from detectron2.config import instantiate
from detectron2.structures import Boxes, Instances
from detectron2.tracking.ba... |
e7c78c7e5e80ec9b92863f53d47cced50826f8278968c3e94a8a3f3a59668c36 | Python | 6,771 | 212 | """ Created on Tue Aug 27 16:25:15 2024
@author: dcupolillo """
from PyQt5.QtWidgets import QPushButton
from PyQt5.QtCore import Qt, pyqtSignal
from PyQt5.QtWidgets import (
QMainWindow, QGridLayout, QFrame, QLabel)
class CustomToggleButton(QPushButton):
def __init__(
self,
text:... |
4b3ae8e4d4d03c46a2dab8355ca68779dad0574ad97ce3d4906405313552890d | Python | 6,783 | 236 | from functools import partial
import composer.utils.dist as comp_dist
from omegaconf import DictConfig
import os
import pandas as pd
import torch
from torch.utils.data import Dataset, DataLoader
from transformers import PreTrainedTokenizer, AutoTokenizer, BatchEncoding
from typing import Optional, Dict
def build_toke... |
04e73a75c6e05e1c0d847c072d84f6e1b653e820603f2ba8fe1ac597f2db3e37 | Python | 6,789 | 155 | import os
import glob
import random
from itertools import product
from .AttackCNN.utils.condition import Condition
def init_conditions(user, config_cond):
# make conditions from yaml config
user.list_conditions_name, user.list_convergence = make_conditions_from_lists(config_cond)
random.shuffle(user.lis... |
153f3550c1cae8cd8580d8b847173e7964d39d13159e56739065685a0415ea24 | Python | 6,790 | 152 | #!/usr/bin/env python
# Copyright 2016-2024 Biomedical Imaging Group Rotterdam, Departments of
# Medical Informatics and Radiology, 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 obt... |
6aa44f5dd55e07701f8258c35b0a1ca87c01f84a81a643fefe20399c356701d3 | Python | 6,792 | 211 | from functools import partial
import logging
import multiprocessing as mp
import os
import pandas as pd
import re
from tqdm import tqdm
from typing import Optional
logger = logging.getLogger("no_interpolation_ds")
def filter_seqs(
recs: pd.DataFrame,
min_len: Optional[float] = 0.5,
max_len: Optional[flo... |
46669a427ffdc5a84219423130059e02b9bb71c47b9ef11b5c61bb754e32bf4e | Python | 6,794 | 171 | #>python compareDDAnDIA.py intensity_IBAQ "Z:\Download\nDDA\nDDA_quantified_protein_fdr.tsv" "Z:\Download\nDDA\nDIA_quantified_protein_fdr.tsv"
import os
import sys
import pandas as pd
import numpy as np
import matplotlib.pyplot as plt
intensity_col = 'intensity_IBAQ'
dda_path = r'L:\promec\TIMSTOF\LARS\2026\260518_So... |
365e15525ef4ce8e68ddc53384203af417c49ac82d6337dcecef7be3d4079b74 | Python | 6,800 | 178 | import torch
import torch.nn as nn
import numpy as np
import modules
from util import aa_sequences_to_padded_onehot, pad_feature_matrices
device = torch.device("cuda" if torch.cuda.is_available() else "cpu")
class BaselineRINAMI(nn.Module):
def __init__(
self,
device=device,
dropout=0... |
96f04a332ba8b7996482de54f340b98e9a5c91654e80be65e719f29aa36d5bdf | Python | 6,801 | 174 | # Copyright (c) Facebook, Inc. and its affiliates.
# pyre-unsafe
import random
from typing import Any, Callable, Dict, Iterable, Iterator, List, Optional, Tuple
import torch
from torch import nn
SampledData = Any
ModelOutput = Any
def _grouper(iterable: Iterable[Any], n: int, fillvalue=None) -> Iterator[Tuple[Any]... |
2cafd2e0242414d57c260428ab4ede2c5f1bb4ae2b1ad78700e313c3f4e46a61 | Python | 6,802 | 210 | """Exceptions for the scenarios module."""
from __future__ import annotations
from dataclasses import dataclass
from enum import Enum
from typing import TYPE_CHECKING, Any
from mesa.exceptions import MesaException
if TYPE_CHECKING:
from mesa.experimental.scenarios.scenario import Scenario
from mesa.experime... |
5c58db5b72d99090be38f21acdf591da0ccbbac569a6bcced05dd6d1ffde01e5 | Python | 6,805 | 185 | # This code is part of OpenFE and is licensed under the MIT license.
# For details, see https://github.com/OpenFreeEnergy/openfe
import pathlib
import numpy as np
import pytest
from gufe.protocols import execute_DAG
from numpy.testing import assert_allclose
from openff.units import unit
import openfe
from openfe.prot... |
24265e64cfb7f7ad16e23aa280e5284aef0328e45d2c446999224579667cc33f | Python | 6,806 | 167 | """
Label Propagation
=================
<!-- difficulty: intermediate -->
Spread a sparse set of labels across a neuron using its topology.
One of the most intuitive applications for this is to try to label the axon and dendrite of a neuron based on
the distribution of pre- and postsynapses alone.
## Background
The... |
9a28fd5c91aec266f1c38f1cba0827eae67ba29b7f0662a601edc412ee034f56 | Python | 6,812 | 135 | from __future__ import annotations
import argparse
import json
import os
import time
from concurrent.futures import ProcessPoolExecutor, as_completed
from pathlib import Path
import numpy as np
import pandas as pd
from pipeline_core import fit_base_imputer, fit_preprocessor, make_group_split
from screening import we... |
9fbb7550a44f409bf97ab8375b0ef9268852e9cbcf4e8d1ae7d19ead4ee59a42 | Python | 6,830 | 124 | import zipfile
from nnunetv2.utilities.file_path_utilities import *
def export_pretrained_model(dataset_name_or_id: Union[int, str], output_file: str,
configurations: Tuple[str] = ("2d", "3d_lowres", "3d_fullres", "3d_cascade_fullres"),
trainer: str = 'nnUNetTr... |
833e66ac964eed2022b93b9fbf3f9c407d092663a2179e662794d265d00b109a | Python | 6,832 | 171 | #!/usr/bin/env python
# Copyright 2016-2020 Biomedical Imaging Group Rotterdam, Departments of
# Medical Informatics and Radiology, 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 obt... |
cf65f50213603c34874705230828c3fe1edba72c669b18c77794f07f8a4f0e67 | Python | 6,841 | 188 | # -*- coding: utf-8 -*-
from sklearn.preprocessing import MinMaxScaler
from tqdm import tqdm
import scanpy as sc
import torch.optim as optim
import os
from torch.backends import cudnn
import random
import numpy as np
import torch
import torch.nn as nn
import torch.nn.functional as F
def fix_seed(seed):
... |
13a35a1f4cf74a4c0bec6264f1beb605d0dd334b9f3cc53675301c469bbc8d78 | Python | 6,848 | 190 | #!/usr/bin/env python
#
# Copyright (c) 2022 10X Genomics, Inc. All rights reserved.
#
from __future__ import annotations
import json
import os
import shutil
from typing import TYPE_CHECKING
import martian
import cellranger.report as cr_report
import cellranger.webshim.common as cr_webshim
import cellranger.websumma... |
2397da69d095fb614321d2ccd509324c830f70a427c84ec1463029d059a167bf | Python | 6,860 | 195 | """Tests for closing the holes cut into a mesh.
Entry points, with deliberately different scope:
- `navis.fill_holes` closes every opening the mesh has.
- `subset_neuron(..., cap_holes=True)` closes only the ones that call made,
which means it has to leave pre-existing openings alone.
- `Volume.fill_holes` is `navi... |
a68d6edb2f58706f910e72678c49aeab8f9af7bff38ec73a4a575771faa895ec | Python | 6,860 | 148 | ############################################################################
# Copyright (c) 2022-2026 University of Helsinki
# Copyright (c) 2020-2022 Saint Petersburg State University
# # All Rights Reserved
# See file LICENSE for details.
############################################################################
... |
9b9982b325208e3ac329d8532db5e328599f64b8cf63c4abc8a1e65c2dd8e535 | Python | 6,863 | 196 | """
This script crawls the package space and generates .md files in
the references directory of the mkdocs site. For example:
```
# side/reference/connectivity/adjacency.md
::: connectivity.adjacency
```
It also generates a SUMMARY.MD file that contains the
navigation structure of the generated .md files. We
then use... |
af126f268be34661bd7e13561325186e2d7d975879f5c976a7b088220635e4c3 | Python | 6,872 | 202 | import torch
import torch.nn as nn
from functools import partial
import clip
from einops import rearrange, repeat
import kornia
from ldm.modules.x_transformer import Encoder, TransformerWrapper # TODO: can we directly rely on lucidrains code and simply add this as a reuirement? --> test
class AbstractEncoder(nn.Mo... |
4ccad100cd585b3f4344eec08df6e0d93bdc85885d2909b606263860fb285f85 | Python | 6,874 | 170 | import torch as tc
import numpy as np
def gmm_mse(X: tc.Tensor, gmm_weights: tc.Tensor, means: tc.Tensor, scaling: tc.Tensor = None) -> tc.Tensor:
if scaling is not None:
means = means * scaling
X = X * scaling
n_components = gmm_weights.shape[0]
diff = 0
for i in range(n_components):... |
4ed1ba4d471d2124617c34e3b2a098a7e645d073d20e91c8a2e91320a1d6eb81 | Python | 6,881 | 216 | """ Created on Tue Jan 23 11:02:59 2024
@author: dcupolillo """
import numpy as np
import matplotlib.pyplot as plt
def modify_frames(
frames: np.ndarray,
deviating_rows_dict: dict
) -> np.ndarray:
"""
Apply interpolation by averaging neighboring frames
to the frames showing deviating ... |
523ca2fee57c2855ff39b2226d8be1bb24670596f1d4c2b33189ad38134bfb39 | Python | 6,881 | 194 | # 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... |
52c9da9ec49b936801efc65d9c4a1e9a512f4fc0d44924f15cbfe2d4ab65d392 | Python | 6,881 | 185 | import os
import pandas as pd
import numpy as np
import matplotlib.pyplot as plt
import seaborn as sns
from loguru import logger
logger.info('Import OK')
input_folder = 'results/super-res/measurements/'
output_folder = 'results/super-res/summary/'
if not os.path.exists(output_folder):
os.makedirs(output_folder)
... |
4e644a7324b3a6eb793a4086b90c239292bc849c89a48c394efea2c536fa9a88 | Python | 6,883 | 203 | # Copyright (c) Facebook, Inc. and its affiliates.
# pyre-unsafe
import logging
from typing import List, Optional, Sequence, Tuple
import torch
from detectron2.layers.nms import batched_nms
from detectron2.structures.instances import Instances
from densepose.converters import ToChartResultConverterWithConfidences
fr... |
4232c70b1cc3a4f64b865a748fada43190aa5467a33e864ff40db9e5bd693447 | Python | 6,891 | 190 | import pandas as pd
import matplotlib.pyplot as plt
import numpy as np
from scipy import stats
import re
import os
import subprocess
import sys
def download_file(url, filename):
if os.path.exists(filename):
print(f"{filename} already exists. Skipping download.")
return
print(f"Downloading ... |
7bb7a5fc9a4fc0a66242baed8489d45c85d308be2a87129c603a179ed9c8c1d4 | Python | 6,892 | 223 | # ruff: noqa: PLR2004
from __future__ import annotations
import argparse
from typing import Any
import pytest
from pytest_mock import MockerFixture
from snakebids import bidsapp, plugins
from snakebids.bidsapp.args import ArgumentGroups
class TestRunner:
def setup_method(self):
self.hooks_run = 0
... |
30fa66b4d5e8bce10aea074a0be272861c8e1384437b17dfb8c2a6ab72a69cc5 | Python | 6,895 | 222 | """
utils/inspect_file.py
---------------------
Tools for inspecting unknown MEA data files.
Designed for new users who want to:
1. See the full internal structure of any HDF5 or BXR file
before writing a loader for a new manufacturer.
2. Compare two files side by side (e.g. two manufacturers)
to find wh... |
8f1343c81bd1f749c670eb0a12bd675355d70592166d8e14d0087d670a2eced1 | Python | 6,895 | 225 | """
Functions to handle padding and unpadding of images for batch processing
of the various analysis backends. Ensures that images are padded to the required
dimensions for neural network models and that predictions are unpadded to restore
original dimensions. Also includes utility functions for saving padded images to... |
007f8eb0c34d9c3c66ac341d130258668ae043d10cf7e3f0d415c523a56c8bf2 | Python | 6,901 | 216 | import torch
import torch.utils.data
from torch import nn, optim
from torch.nn import functional as F
# from torchvision import datasets, transforms
import collections
import sys
from torch.utils.data import TensorDataset, DataLoader
from sklearn.model_selection import train_test_split
from AE.utility import create_act... |
8022a6e5d8aa9e86569e2acf02a69e217a92f8cbbea1d3f2566344045b96af48 | Python | 6,908 | 152 | from __future__ import annotations
import argparse
import json
import time
from pathlib import Path
import numpy as np
import pandas as pd
import torch
from bpnn_batch import fit_predict_pvs_batched
from bpnn_training import BPNNTrainingConfig, SingleHiddenBPNN, flatten_model_parameters
from gpu_metaheuristics impor... |
496ac1212ee304620496bf49f3ad52173faa6b2beecf1d375ff4b1b45715b4ba | Python | 6,923 | 200 | import torch
import torch.nn as nn
from einops import rearrange
import torch.nn.functional as F
from torchvision.models import resnet18
from self_attention_cv import TransformerEncoder
class ViT(nn.Module):
def __init__(
self,
img_dim,
in_channels=1,
patch_dim=16,
num_class... |
60928ced0b0898f365118b517e8ebcb3ebe8458ac4e5c296299dfe22b0e0fcc8 | Python | 6,925 | 227 | #!/usr/bin/env python3
#
# Copyright (c) 2016 10x Genomics, Inc. All rights reserved.
"""Diagnostic tar file uploader."""
from __future__ import annotations
import json
import math
import os
import ssl
import sys
import time
import xml.etree.ElementTree as ET
from http.client import HTTPSConnection
from typing import... |
4561905fd6821bc339102d9d4d0fa8bfe71a2369ddb46004402612e034795d08 | Python | 6,929 | 202 | import logging
import os
import torch
import tarfile
from torch.nn.utils.rnn import pad_sequence
charge_dict = {'H': 1, 'C': 6, 'N': 7, 'O': 8, 'F': 9}
def split_dataset(data, split_idxs):
"""
Splits a dataset according to the indices given.
Parameters
----------
data : dict
Dictionary t... |
4e687e61668f201fb789dd55d89b810b6b0aa69afa5ec30a25594e08d8cf5efc | Python | 6,931 | 170 | import numpy as np
import parasail
from concurrent.futures import ProcessPoolExecutor, as_completed
import logging
from math import sqrt
logging.basicConfig(filename='parasail_0_all.log', level=logging.INFO,
format='%(asctime)s - %(levelname)s - %(message)s')
def read_sequences(file_path):
l... |
4c0781e20d83701579e9a0dfe147f7ce3b3ac8d43c3aec17e7097aef739f6749 | Python | 6,938 | 180 | #!/usr/bin/env python
# Copyright 2016-2021 Biomedical Imaging Group Rotterdam, Departments of
# Medical Informatics and Radiology, 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 obt... |
ac4202bdd98486e8eca88f9d25b294697eecd3bc4d9d0032ba7a4322e5b2b069 | Python | 6,938 | 224 | from typing import Tuple
from os.path import join
import gym
import numpy as np
import torch
from torch import nn, optim
from torch.distributions import Beta
from torch.utils.data import DataLoader
from os import path
from time import sleep
from memory import Memory
device = torch.device("cuda" if torch.cuda.is_avail... |
d3bcb33d81e8b27f9535e3714367cf5237da8fe64c38c88c7f22e1eae15b1b92 | Python | 6,939 | 210 | """
Module to perform CARE denoising using CSBDeep backend.
This module provides a modular denoising pipeline that separates workflow
logic from orchestration, similar to the segmentation pipeline structure.
The main function is `denoising_pipeline()`, which handles:
1) Image collection and padding
2) Backend executi... |
2d999e6ac3c05800c9746c649ebe422be62529f196226b9d3a044ddd1d91cc70 | Python | 6,944 | 162 | import os
import sys
import pytest
from unittest.mock import patch, MagicMock
import subprocess
# Import the CLI main function
from micaflow.cli import main as cli_main
# List of all available commands in the micaflow CLI
COMMANDS = [
"pipeline",
"apply_warp",
"bet",
"bias_correction",
"calculate_d... |
a092b006f30314465398e578a13b80f59de7c9fd3c8d8ff7b826bad693f6d1a9 | Python | 6,944 | 197 | import numpy as np
import pytest
from neuroHarmonize import harmonizationLearn
class TestRandomSeedDeterminism:
"""
Tests to verify that the random seed parameter works correctly.
This tests the bug fix where seed logic was inverted.
"""
def test_same_seed_produces_identical_results(
self... |
8230052bd20880ad7476ee4b3f58135df39e781d5e40d2c86b9d1d7838d1225a | Python | 6,951 | 162 | import os
import numpy as np
import torch as tc
from torch.utils.data import Dataset
import os
from analyses.analysis_utils import data_path
def load_data(args, test_trials=False):
assert os.path.exists(os.path.join(data_path, args.data_path))
data = np.load(os.path.join(data_path, args.data_path),
... |
70724336ed17b3761bcde5f0ebeb92b5eda39bc34083852d5069e4f82b54a7f0 | Python | 6,958 | 217 | """some summary"""
import os
from pathlib import Path
import torch
import pandas as pd
from eeg_visual_classification.utils.lib import (
create_parser,
extract_model_options,
get_dataloaders,
get_model_hash,
save_checkpoint,
load_checkpoint,
)
from ..models import MODEL_REGISTRY
torch.utils.... |
bfe657ad0fb8f12a4ee0ef5e478f0984085f9039ac540d7aa642a41fe97c0a90 | Python | 6,959 | 295 | """This tests the CLI functionality of training and predicting a regression model on a multi-molecule.
"""
import json
import sys
import pytest
from chemprop.cli.main import main
pytestmark = pytest.mark.CLI
@pytest.fixture
def data_path(data_dir):
return (
str(data_dir / "regression" / "mol+mol" / "m... |
e4c411140f636eec5099ee74487854030452228103db3269056e0a707ba32468 | Python | 6,971 | 186 | # Copyright (c) Facebook, Inc. and its affiliates.
# pyre-unsafe
from dataclasses import dataclass
from typing import Any, Optional, Tuple
import torch
@dataclass
class DensePoseChartResult:
"""
DensePose results for chart-based methods represented by labels and inner
coordinates (U, V) of individual ch... |
087493d12fbed3315765a550e5416df9b6b35789e0e28e671c08e6e55feaee55 | Python | 6,973 | 176 | # Copyright (c) Facebook, Inc. and its affiliates.
import copy
import numpy as np
import os
import unittest
import pycocotools.mask as mask_util
from detectron2.data import MetadataCatalog, detection_utils
from detectron2.data import transforms as T
from detectron2.structures import BitMasks, BoxMode
from detectron2.... |
bf95d463c38c8e7bcd247930c179aab0d21d9a544eded7d047af8cd0d8fe5e2e | Python | 6,980 | 205 | # 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... |
76a5096c7e76da397fc1de8378d6a0a186f2cc3d04dea83efc5b5d61ff96a084 | Python | 6,987 | 196 | """Hit vs miss PSTHs with cluster-based permutation test.
Median +/- IQR traces, gold cluster shading, red onset line.
"""
import sys
from pathlib import Path
sys.path.insert(0, str(Path(__file__).resolve().parents[1]))
import matplotlib
matplotlib.use('Agg')
import matplotlib.pyplot as plt
import numpy as np
import ... |
3eeb04fe0ce51cba80bfd173979781f7aa21a4eb06f1bb420bf0516b55a405f5 | Python | 6,989 | 205 | import numpy as np
from matplotlib import pyplot as plt
from scipy import signal
from sklearn.cluster import KMeans, DBSCAN
from copy import copy as cp
def flip(zeros_and_ones):
return -(zeros_and_ones - 0.5) + 0.5
def relabel(raw_labels, lookup_table):
return [cp(lookup_table[int(raw_label)]) for raw_label i... |
0deeab524020e4a6987c9d84cc46b3d3ac8e06c71df0c47cd9f9de7d2f3f56c6 | Python | 6,993 | 200 |
""" Graph conv blocks.
Implementation based on https://github.com/cvlab-epfl/voxel2mesh.
"""
__author__ = "Fabi Bongratz"
__email__ = "fabi.bongratz@gmail.com"
import torch
import torch.nn as nn
import torch.nn.functional as F
import torch_geometric.nn as gnn
import pytorch3d.ops as py3dnn
from torch_sparse import ... |
df5eecd88836ca92e4c278b5fd02d954fc3d1c187703dcc18da4031ec1f9c3f4 | Python | 7,005 | 148 | ##############################################
# ---------- NBS Wrapper Function ---------- #
##############################################
from pyNBS import pyNBS_core as core
from pyNBS import network_propagation as prop
import networkx as nx
import numpy as np
import pandas as pd
import random
# Wrapper function ... |
d0ebd195a2f68b134d16ad68e5de5b64383bc951d37635aacddb2595f7c00d02 | Python | 7,011 | 209 | """
Loss Functions for Axon Segmentation
Implements three loss functions suited for binary segmentation with class imbalance,
plus a comprehensive metrics function for evaluation.
Loss functions:
DiceLoss — overlap-based loss robust to class imbalance
TverskyLoss — Dice variant with separate FP... |
9d7b60ea65aec4b70f5a9434bd44a639073eaa8862ea76dd1ec02cc706cbf6d2 | Python | 7,014 | 203 | # This code is part of OpenFE and is licensed under the MIT license.
# For details, see https://github.com/OpenFreeEnergy/openfe
"""
Settings for adding restraints.
TODO
----
* Rename from host/guest to molA/molB?
* Add all the restraint settings entries.
"""
from typing import Annotated, Literal, Optional, TypeAlias... |
40ffbee67f3526d197a9cdc5e81fcf3b8a1d802a4d10c1ca8c9cda75fc970957 | Python | 7,018 | 181 | import torch
from torch import nn
class AttentionUnet(nn.Module):
"""
Neural network for semantic image segmentation U-Net (PyTorch), with attention mechanism during decoding
Parameters
----------
n_filter : int
Number of convolutional filters (commonly 16, 32, or 64)
"""
def __in... |
fa142fedc12c27a96a93d4ca2b9e6474477acda787366b26da7c2cb7d2c7568a | Python | 7,019 | 154 | """
loaders/cl1_loader.py
---------------------
Loader for Cortical Labs CL1 .h5 files.
Both the standard recording and the game recording are supported.
The game recording contains additional /data_stream/ groups (ball position,
paddle, motor regions, etc.) which are silently ignored — only /spikes is used.
HDF5 str... |
705b57b53bb0a3a1333b2811bdcef66618e939c466141f313eeb1fbf372eb3fa | Python | 7,020 | 150 | """
Meshes
======
<!-- difficulty: intermediate -->
Light mesh neurons properly - which is what a real renderer is for.
A [`Mesh`][navis.Mesh] is a surface, and a surface is where 3D earns its keep: the renderer does
occlusion and lighting for you, so none of the [2D machinery](../1b_plotting_2d/tutorial_plotting_2d_... |
e1dd3853b831ee75f3b2c26b4ba08912e83bcb2edb6236bb2bd68448b6cc5a10 | Python | 7,020 | 200 | #!../venv/bin/python
import os
import psutil #edited by Caleb to monitor memory used by Python process
import logging
import argparse
import csv
import yaml
import psycopg2
import psql_wrapper as psql
from datetime import datetime
from tqdm import tqdm
CURR_DIR = os.path.dirname(os.path.realpath(__file__))
CURR_... |
8a60e34a331cbb848398bda1c1f4238903e1fdb8d55d91b23c91384e515c71b0 | Python | 7,032 | 221 | """ Created on Wed Jun 25 13:45:20 2025
@author: dcupolillo """
import sys
from PyQt5 import QtWidgets
from PyQt5.QtWidgets import (
QMainWindow, QGridLayout, QWidget, QMessageBox, QMenu, QAction,
QPushButton)
from spyne.core.imaging.imagingdataset import ImagingDataset
from spyne.GUI.load import LoadFiles... |
467a338c242658840d3af03d6832303364ffdf440023a0a8942296e52fc6de54 | Python | 7,033 | 207 | #!/usr/bin/env python
#
# Copyright (c) 2016 10X Genomics, Inc. All rights reserved.
#
from __future__ import annotations
import os
import shlex
import shutil
import socket
import martian
from six import ensure_str
import tenkit.bcl as tk_bcl
import tenkit.log_subprocess as tk_proc
__MRO__ = """
stage BCL2FASTQ_WI... |
4a3e66e6e8f337db613eebdd4e927d2e984181b89d81df2ac3a43c6500dd063a | Python | 7,038 | 171 | # Copyright (c) Facebook, Inc. and its affiliates.
import logging
import unittest
import torch
from detectron2.layers import ShapeSpec
from detectron2.modeling.box_regression import Box2BoxTransform, Box2BoxTransformRotated
from detectron2.modeling.roi_heads.fast_rcnn import FastRCNNOutputLayers
from detectron2.modeli... |
eb01f3d909772f2b2794b5e5b48ec841f98f87bf9bfe942c31b395661e23acbc | Python | 7,045 | 206 | #
# Copyright (c) 2019 10X Genomics, Inc. All rights reserved.
#
"""Compute extra metrics for multiplexing from the uber molecule info.
and the sets of multiplet and singlet barcodes
- median CMO UMIs over all singlets
- fraction of CMO reads lost to multiplets
- fraction reads in cells on a per-tag basis
"""
from ... |
29a076c73def7d9eb5c269fa88b4929ae25008b50b9e40f5b1d3ebcce021f8d4 | Python | 7,046 | 226 | """This integration test is designed to ensure that the chemprop model can _overfit_ the training
data. A small enough dataset should be memorizable by even a moderately sized model, so this test
should generally pass."""
from lightning import pytorch as pl
import numpy as np
import pytest
import torch
from torch.util... |
1635d7b9df11a990e99a2fb1faf4d6a47a0a8fa95175549f8e7ba8044a58538b | Python | 7,049 | 256 | from pathlib import Path
import click
import click_log
import pandas as pd
from ... import io
from ..._cli.utils import (
OrderedClickGroup,
SteinbockCLIException,
catch_exception,
logger,
)
from ..._steinbock import SteinbockException
from ..._steinbock import logger as steinbock_logger
from .. impor... |
5849979a6736a51cb76bdd1055fc988362ad5579c7febb45ac49786563da46b5 | Python | 7,066 | 275 | """Tests for Model public event scheduling and time advancement API."""
# ruff: noqa: D101 D102 D107
import gc
from functools import partial
import pytest
from mesa import Agent, Model
from mesa.time import Schedule
class StepAgent(Agent):
def __init__(self, model):
super().__init__(model)
self... |
97e1f9eefbbdc5889199d87b263cf75903e896fe0e4977bf81a0bbe0fc686f79 | Python | 7,069 | 207 | import numpy as np
from scipy import ndimage
from tqdm.auto import trange
from .. import core, config
from .base import TransformSequence, BaseTransform
from .h5reg import H5transform
from . import registry
logger = config.get_logger(__name__)
class ImageXformer:
"""Class to render images from a source to a ta... |
5c887f63e82b2099d060fce0d072979a9778ac8becd464a2b9d4f1f6f02fa2b6 | Python | 7,079 | 192 | import numpy as np
import pandas as pd
import pytest
from neuroHarmonize import harmonizationLearn, harmonizationApply
from neuroHarmonize.harmonizationApply import applyModelOne
class TestApplyModelOneConsistency:
"""
Tests to verify applyModelOne produces identical results to harmonizationApply
for sing... |
1df56a000861640ea2e95c77215380a372b3bd3700a6f99c4409f61f4c2fa2c5 | Python | 7,084 | 171 | # -*- coding: utf-8 -*-
# Copyright (c) Facebook, Inc. and its affiliates.
# pyre-unsafe
import copy
import logging
from typing import Any, Dict, List, Tuple
import torch
from detectron2.data import MetadataCatalog
from detectron2.data import detection_utils as utils
from detectron2.data import transforms as T
from ... |
07579d5eecf5eb875519460c441befeff90365d2e3fc3c7acbd9e4637764edd6 | Python | 7,086 | 209 | """Test the spatial lookups and physical positioning of different discrete spaces."""
import math
import random
from unittest.mock import patch
import networkx as nx
import numpy as np
import pytest
from mesa.discrete_space import (
Cell,
HexGrid,
Network,
OrthogonalMooreGrid,
VoronoiGrid,
)
de... |
12b411fba1899290d31c1532c05334eda8ea0e47132761976258a00be59d251c | Python | 7,088 | 234 | from typing import Optional, Sequence
import numpy as np
import pandas as pd
from . import _utils
from .base import PNG, Refine
__all__ = [
"Compose",
"DropRepeating",
"Merge",
"FilterBySpan",
"FilterLayers",
"FilterIndex",
"Match",
"FilterMinOcc",
"Structural",
"Connected",
... |
85e6b3d34844ad1362cf5334818332c25445ca00e013e8ba132fc86b50bf4d6f | Python | 7,091 | 192 | import numpy as np
import matplotlib.pyplot as plt
import matplotlib as mpl
import pandas as pd
import os
from elephant.statistics import isi, cv
import quantities as q
import string
from network_simulations.utils.nest_utils import convert_spikes_df2neo
from matplotlib.ticker import LinearLocator, MaxNLocator
from n... |
adb10d8b745dc4e56a8b2e2fee7b3c327795e06d6fd6724272231bbc292b2e3e | Python | 7,091 | 222 | import torch
import torch.nn as nn
import torch.nn.functional as F
from torch.nn.init import uniform_
from torch_geometric.nn.conv import MessagePassing
from torch_geometric.nn.conv.gcn_conv import gcn_norm
from torch_geometric.utils import add_remaining_self_loops
from torch_scatter import scatter_add
from math imp... |
f3dd7be07f14215cf42d60c629123205c30bf7fbdecf4f58a9eb2545edc6a6d3 | Python | 7,092 | 185 | # Copyright (c) Facebook, Inc. and its affiliates.
# pyre-unsafe
"""
MIT License
Copyright (c) 2019 Microsoft
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without... |
a70700c6ea3c5e14630ca49bea85ee1f737038a584eb90467e6f9fffae584f29 | Python | 7,093 | 248 | import torch
import torch.nn as nn
import numpy as np
class AbstractPermuter(nn.Module):
def __init__(self, *args, **kwargs):
super().__init__()
def forward(self, x, reverse=False):
raise NotImplementedError
class Identity(AbstractPermuter):
def __init__(self):
super().__init__()... |
46703e92635e90349073de38733c120065c6fdd4d3fdff17f0f6b33781462d87 | Python | 7,103 | 182 | #!/usr/bin/env python
# Copyright 2016-2022 Biomedical Imaging Group Rotterdam, Departments of
# Medical Informatics and Radiology, 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 obt... |
8350be7f94695345f0c81fbbd25ca78fc2b9f38a53ddf107b594a48c6d142883 | Python | 7,105 | 220 | from composer.core import DataSpec
from composer.models import HuggingFaceModel, ComposerModel
from composer.utils import dist
import gc
from omegaconf import DictConfig
from transformers import PreTrainedTokenizer, AutoModel
import torch
from torch.utils.data import DataLoader
import build_datasets as data_module
imp... |
126e808f648919311abc7f38d46395fb9a3949bcda578ca3686cd2ef77e3124d | Python | 7,115 | 244 | """Model configuration dataclasses for serialisation and loading.
Replaces filename-based regex parsing with proper JSON config files.
"""
import json
from dataclasses import asdict, dataclass, field
from pathlib import Path
from typing import Any, Dict, List, Optional, Union
@dataclass
class GNNConfig:
"""Confi... |
17d981314001243114925dd8247087fa0aedec4330aaa361cd3e68e3d1447a40 | Python | 7,122 | 176 | # 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... |
1b445cb356512814880fa3bffc188cf45e08f1d5c93022ac66dc16327282f1ac | Python | 7,125 | 188 | # 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... |
54e7bf0d83d95a88d448872bda7a92fa0c620d14d9e23d74638ac8a2adeffef8 | Python | 7,126 | 239 | import warnings
from typing import Dict, Iterable, Optional, Tuple, Union
import numpy as np
from matplotlib import pyplot as plt
from matplotlib.colors import rgb2hex
from numpy.typing import NDArray
from rdkit import Chem
from rdkit.Geometry.rdGeometry import Point3D
try:
import py3Dmol
except ImportError:
... |
8a6a0c7983b7b2c1cabcd37bfe7eb2e4782e9967252bda12b6538340677d6de0 | Python | 7,128 | 181 | from dataclasses import dataclass
import math
import json
from typing import Callable
import random
import yaml
from pathlib import Path
from tqdm import tqdm
import numpy as np
from .. import config
from .pgd_attack import AttackParams
from .pca import PCAHandler
from .ica import ICAHandler
from .decomposition_handl... |
3dbdb4a28a8c8e9fcad9378c43792fc3f6e229828f4cafe4ac6e0e646070167d | Python | 7,131 | 187 | """Speaker clustering: silhouette scoring and speaker-count estimation.
Regression cover for two shipped bugs:
* a fixed Ward distance cut made the speaker count grow with recording
length (20 min -> 2 speakers, the same audio at 2 h -> 8);
* singleton clusters scored a perfect silhouette, so 11 segments were ... |
5cae616071a407c2a683ebb58f72343c2da6b31e41113092ed27e62d531ad7af | Python | 7,133 | 158 | '''
Created on May 22, 2025
@author: voodoocode
'''
import bpy
import addon_utils
import numpy as np
STRUCTURES = ["/mnt/data/Professional/LMU/code/Beta_prevalence/spatial/stn.obj"]
VOLUMES = ["/mnt/data/Professional/LMU/code/Beta_prevalence/spatial/heatmap.vdb"]
def load_scene(structures, volumes):
bpy.ops.obj... |
846eeef0446ea2d662465aeac984e59f6a6e8371f09cff29892e4b5e92a493a1 | Python | 7,137 | 211 | """Tests for `navis.patch_caveclient`.
`caveclient` is an optional dependency and the skeleton service needs both a
network connection and an auth token, so everything here runs against a stub
client that returns the payloads the real service does.
Note this module must stay free of doctests - pytest runs with
`--doc... |
64eba7f1c01c8f3e1ed2ae2c40214791fe4e6c473f5e2aecbab1beab8984c161 | Python | 7,140 | 206 | """Tests for error messages that tell the caller how to fix the problem.
These pin *repair signals*: each message names the way out, not just the
symptom. Three of them exist because the underlying failure used to surface as
a raw third-party exception (pint, pandas, scipy) that mentioned neither navis
nor the paramet... |
0c059425c36efda4572defb5ff2576e2d21a65ba08bb7ad6fcc5c6a811fec60c | Python | 7,149 | 973 | #https://github.com/animesh/scripts/commit/8fd66822b7b85409b88983328ae97d608bc78b4b#diff-d592612aef70515362d5ab69e30a1b7ddff49ae376d5afbba0b286c04ac2452f
#https://api.platform.opentargets.org/api/v4/graphql/browser?operationName=assocs&query=query%20assocs%20%7B%0A%20%20search%28queryString%3A%20%22EIF3C%22%2C%20entity... |
a966f0ba6092a276cb5466ff7198dba08411c9d1647cbc16cf9c29cf522803a5 | Python | 7,149 | 139 | import pandas as pd
import numpy as np
import os
import h5py
from scipy.signal import find_peaks
class AnalysisDataLoader:
def __init__(self):
pass
def load_data(self, database, signal_sampling_rate, start_time, end_time, baseline_correction, peak_detection_width=1, use_zscore=False):
processe... |
ca8e4aea31984683d85c4ccd05a4145c02257660d6ebef1bb0b87c91422cd0fe | Python | 7,153 | 219 | import torch
import torch.nn as nn
def count_params(model):
total_params = sum(p.numel() for p in model.parameters())
return total_params
class ActNorm3D(nn.Module):
def __init__(self, num_features, logdet=False, affine=True, allow_reverse_init=False):
assert affine
super(ActNorm3D, self)... |
5b7f46b4e4b454804348d3b4558922cac0741d7fef7d179fc1578eec3383c385 | Python | 7,169 | 177 | from os import listdir
from os.path import join
from PIL import Image
from torch.utils.data.dataset import Dataset
import torchvision.transforms as T
import torchvision.transforms.functional as TF
import random
from data_loader import utils
import numpy as np
import torchvision
import yaml
from torch.utils... |
ccaa53cec5a440a5175ff77826103a8d72d91126b00306e5390c983486af9558 | Python | 7,169 | 135 | #!/usr/bin/env python3
"""Optional expensive checkpoint and synthetic I/O checks for bundle release."""
from __future__ import annotations
import argparse
import json
from pathlib import Path
import tempfile
CHECKPOINTS = (
"logs/2025-06-18T01-31-51_raven_f2_nfg64_nfd64_dw1e-1_lpw2.0_l1w0.0_lrgtod0.5_3dlpips_AE... |
8e93309042ff66fac208182db4539095cfd8a4b97990d5caf5e431846957ea5f | Python | 7,173 | 175 | # -*- coding: utf-8 -*-
"""
Created on Sun May 9 18:06:56 2021
@author: araba
"""
import numpy as np
from scipy.spatial import Delaunay
from scipy.spatial import Voronoi
import math
from itertools import compress
from matplotlib.patches import Polygon
from matplotlib.collections import PatchCollection
im... |
a775f326ebc16216726b7af29badca3df1c92888ed61350951cdd7ea7e34c164 | Python | 7,175 | 201 | #!/usr/bin/env python
#
# Copyright (c) 2022 10X Genomics, Inc. All rights reserved.
#
"""For a single sample, generate the gene expression clustering/umap plots, antibody clustering/umap plots,.
and sample-level rank plots as plotly JSON, so that they can be passed forward to the
WRITE_MULTI_WEB_SUMMARY stage and ins... |
308473d524de8940dcc881b6c02a1352ab0f8fcb1ca40f95e8d3e2267c65d71f | Python | 7,178 | 219 | from pathlib import Path
pathmura = Path('C:/Users/animeshs/OneDrive - NTNU/MURA-v1.1/MURA-v1.1')
trainlist=list(pathmura.glob('train/*/*/*/*.png'))
import numpy as np
import cv2
from matplotlib import pyplot as plt
img = cv2.imread(str(trainlist[-1]),0)
plt.imshow(img, cmap = 'gray', interpolation = 'bicubic')
... |
cbf124bcfb093516b8066942959a45a1e3bfbcee5b96cc5de369330ee31cdbd2 | Python | 7,178 | 200 | from typing import Callable
import torch
from torch import nn
from torch._dynamo import disable
from nnunetv2.utilities.ddp import AllReduceGrad
@disable # collectives do not belong in a compiled graph
def global_sum(x: torch.Tensor) -> torch.Tensor:
"""Sum x across all DDP ranks, differentiably. Every rank ge... |
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