sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
5f4a149a6fbf95eb6d62e76c985b05dcc9bd0897faa11fc2bb50d045f44266b1 | Python | 25,536 | 627 | #!/usr/bin/env python
#
# Copyright (c) 2019 10X Genomics, Inc. All rights reserved.
#
from __future__ import annotations
import os
import re
import string
from collections import OrderedDict
from collections.abc import Iterable
from re import Pattern
from typing import NamedTuple
from six import ensure_binary, ensu... |
4129ac2a17948e1d15fa23a726df1725d3ae6fffd11b98b59ed7df4985d58bd2 | Python | 25,543 | 551 |
# 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 o... |
ff6d434ca18e162341e3d7a90096e71795521d04416da549351477726ddf27bf | Python | 25,543 | 789 | # This code is part of OpenFE and is licensed under the MIT license.
# For details, see https://github.com/OpenFreeEnergy/openfe
"""
Search methods for generating Geometry objects
TODO
----
* Add relevant duecredit entries.
"""
import warnings
from itertools import combinations, groupby
from typing import Optional, U... |
d3eda2a3013cf3d2f3360d72108501deb062cb12fba73ff4c991fbfb83cae950 | Python | 25,592 | 671 | import copy
import cv2
import numpy as np
import torch
from skimage.restoration import denoise_tv_chambolle
from typing import List, Tuple
import random
torch.manual_seed(123)
random.seed(123)
def graph_numpy2tensor(graphs: List[np.ndarray]) -> torch.Tensor:
"""
Convert a list of np arrays to a pytorch tens... |
52173f8065379a2dbab34c157d77d979d1789191f35a6cd510eb570267762426 | Python | 25,688 | 309 | #python3 genListPRM.py
import pandas as pd
import numpy as np
from openpyxl import Workbook
from openpyxl.styles import Font, PatternFill, Alignment, Border, Side
from openpyxl.utils import get_column_letter
import warnings; warnings.filterwarnings("ignore")
# ── LOAD ORIGINAL PANEL ──────────────────────────────────... |
3234976caafe04f4300c27758a61a7ed711a31a361ce43cbfb883b7fcac2079b | Python | 25,697 | 713 | # This code is part of OpenFE and is licensed under the MIT license.
# For details, see https://github.com/OpenFreeEnergy/openfe
"""Equilibrium Free Energy Protocols input settings.
This module implements base settings necessary to run
free energy calculations using OpenMM +/- Tools, such
as :mod:`openfe.protocols.ope... |
aa89dba7e6577f778ef904f113065891df8b976462877892393bf9c78fd944ae | Python | 25,757 | 507 | # Get force field parameters with trained model
import torch
import torch.nn as nn
import torch.nn.functional as F
from torch_geometric.data import Data
from torch_geometric.nn.conv import SAGEConv
from openmm.app import ForceField, NoCutoff, CutoffNonPeriodic, CutoffPeriodic, Ewald, PME, LJPME
from openmm.unit import... |
de6c49e9c31704143eabde238e6d3831645509ef551d56603ceb4b443bd8bde4 | Python | 25,841 | 574 | import os
import sys
import numpy as np
import pandas as pd
import matplotlib
import matplotlib.pyplot as plt
import anndata as ad
import scanpy as sc
from scipy.io import mmwrite, mmread
import seaborn as sns
import scipy
import torch
from torch.func import vmap
import pytorch_lightning as pl
from pytorch_lightning.ca... |
7b3fcca352c002364278d0e8bcc2bc0c7bcd660b191367bc1af0f2980bada85b | Python | 25,859 | 721 | # 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... |
9b2d2916d09b3cd08e8ea0de39bf02fb560dd8418ee73b57bed98bb602ecd5c3 | Python | 25,868 | 725 | # This code is part of OpenFE and is licensed under the MIT license.
# For details, see https://github.com/OpenFreeEnergy/openfe
"""OpenMM MD Protocol --- :mod:`openfe.protocols.openmm_md.plain_md_methods`
===========================================================================================
This module implemen... |
944d70d100dae86e0e0a997212ab9f78ce165c50c58bd67573c62d45ccdd9ab1 | Python | 25,871 | 697 | import tensorflow as tf
import numpy as np
import matplotlib.pyplot as plt
import math
import pandas as pd
from sklearn.model_selection import train_test_split
from PIL import Image
import tqdm
import cv2
import os
#tf.enable_eager_execution() #eager execution
""" 设置使用GPU """
gpus = tf.config.experiment... |
939d68cd4d9715cb572bd90f2dc925fddd3f6aafc3249e2e42556845b705cc2d | Python | 25,892 | 718 | """Tests for XGBoost models, config, training, and model bundles."""
import json
import tempfile
from pathlib import Path
from unittest.mock import patch
import numpy as np
import pytest
import torch
from sklearn.preprocessing import StandardScaler
from nfml.models.config import XGBoostConfig
from nfml.models.xgboost... |
9c404b700ac4b53f6fbb1353b37c0314356d461be9489cc67eaa8c35dd7cbf87 | Python | 26,101 | 626 | """
Example script for contrast-agnostic registration using SynthSeg
This script demonstrates a full registration pipeline that uses SynthSeg's brain
parcellation to enable registration between images of different contrasts:
1. Generate parcellations of both input and reference images using SynthSeg
2. Register the p... |
2a8cd5cd1d03957c4609a90083c8cab060b8f5665f91501588628b557b3af3cc | Python | 26,119 | 503 | ############################################################################
# Copyright (c) 2022-2026 University of Helsinki
# Copyright (c) 2019-2022 Saint Petersburg State University
# # All Rights Reserved
# See file LICENSE for details.
############################################################################
... |
c24f73130470e8cbfde81ae4343ef688b3ece99a4a34e36c46f196e403846938 | Python | 26,145 | 739 | # -*- coding: utf-8 -*-
"""Functionality for running spatial null models."""
import os
import tempfile
import nibabel as nib
import numpy as np
from scipy import ndimage
from scipy.spatial.distance import cdist
from packaging import version
try:
import brainsmash
from brainsmash.mapgen import Base, Sampled
... |
21b123267c8e4906d95f9bfb6aaecf1ac80d915939e97e18207c12538fc1f39d | Python | 26,159 | 744 | """ Analysis pipeline for spine processing workflows
Created on January 21, 2026
@author: dcupolillo """
from __future__ import annotations
from pathlib import Path
import numpy as np
from spyne.core.imaging.imagingdataset import ImagingDataset
from spyne.core.spines.analysis.segmentation.pipeline import seman... |
8994e3f33624be40846cc4a69ec5c8cbfb7b945b8da15be5742e040bd86c976e | Python | 26,203 | 592 | import os
import numpy as np
import pandas as pd
import matplotlib
import matplotlib.pyplot as plt
import anndata as ad
import scanpy as sc
from scipy.io import mmwrite, mmread
import seaborn as sns
import scipy
from arboreto.algo import grnboost2
import pickle
import collections
import pycistarget
import pyranges as p... |
e16435367a74ea7a3ce0fbb12307e50881cace84d82a90d0a1669d7842ac1cc1 | Python | 26,218 | 578 | #git lfs install
#git clone https://huggingface.co/datasets/animesh/autonlp-data-peptides
#https://www.tensorflow.org/tutorials/load_data/csv
import pandas as pd
peptideCCS_train=pd.read_csv("pepCCS.csv")
peptideCCS_train.head()
peptideCCS_train[' CCS'].hist()
peptideCCS_train_scores = peptideCCS_train.pop(' CCS')
pept... |
2fbb147c4e30e8265c4ee57704ac962202574bfc9eb96968e444e935b8dbb1f3 | Python | 26,237 | 521 | import io
import multiprocessing
import os
import pickle
import unittest
import unittest.mock
from contextlib import redirect_stdout
from tempfile import TemporaryDirectory
import numpy as np
from nnunetv2.preprocessing.preprocessors.default_preprocessor import DefaultPreprocessor
from nnunetv2.preprocessing.sampling... |
5315311535aadac7d63df5f2e560ec1c9227bebaadbc2b00cb177673bdf64a12 | Python | 26,238 | 673 | """
Ablation study for mmVelo:
1. With vs. without KNN smoothing (zdim = 10)
2. Multiple latent dimensionalities: zdim = 5, 10, 30, 50 (with smoothing)
For each condition the script:
- Trains mmVelo from scratch (skips a stage if a checkpoint already exists)
- Generates a latent-space streamline plot using the... |
756c1fa0a921b48cfed050f8b1711d0e3104dcc67e2feb039101b6f6e95454cc | Python | 26,241 | 713 | # 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... |
b6297b7bf51ffde53a0e26de981311a114dd6c3adef1b2463912fd4720645f46 | Python | 26,300 | 751 | #!/usr/bin/env python3
"""Used to draw brain masks on MRI image data (nii.gz).
Usage:
python vol2mask.py path/to/volume.nii.gz
Author:
Tommy Clausner (2020) - tommy.clausner@gmail.com
"""
import argparse
from collections import deque
import json
import os
import sys
from tkinter import Tk, messagebox
from tk... |
4a65f03760cdcf9c620f8a8aadf82e7d6bfe123740636d80bc5c0694fbbad2ea | Python | 26,312 | 609 | # -*- coding: utf-8 -*-
"""
Created on Wed Oct 1 13:41:48 2014
@authors: Luciano Masullo, Federico Barabas
"""
import os
import numpy as np
from scipy import ndimage as ndi
from PIL import Image
import pyqtgraph as pg
from pyqtgraph.Qt import QtCore, QtGui
import ringfinder.utils as utils
from ringfinder.neurosimul... |
80f793ab92664e4731d0fbcdf4326b5a9fd80379231bb70e853fb29bf081ae7a | Python | 26,316 | 758 | # Copyright (c) 2019 10X Genomics, Inc. All rights reserved.
"""Python versions of the React Components available in the web summary.
The Web Summary data is serialized as JSON and for simple objects we just pass
dictionaries around, but also use typed classes for some aspects of the
Components.
"""
from __future__ ... |
489a6cea38276a87363c17510ec9d98412d15a35e38753352d270958d6a043ab | Python | 26,457 | 622 | import os
import numpy as np
import pandas as pd
import matplotlib
import matplotlib.pyplot as plt
import anndata as ad
import scanpy as sc
from scipy.io import mmwrite, mmread
import seaborn as sns
import scipy
np.random.seed(42)
# load anndata
dir_path = "/home/nomura/Proj/mmvelo/experiments/SHARE-seq_hf/2023-08-0... |
a12365cc13a0273b3b8fccd791de536beefa91ab7ff626034dc34d5357197a47 | Python | 26,525 | 511 | from __future__ import annotations
import copy
import random
import numpy as np
import pandas as pd
import torch
from bpnn_training import BPNNTrainingConfig
def _initialize_ensemble(model_count: int, input_dim: int, hidden_width: int, seeds: list[int], device):
hidden_weights = []
hidden_biases = []
o... |
5fc4320d77d88dcb0e8cdab4b5095be1b0df528ab1d751ecb4f5efc769370b12 | Python | 26,561 | 681 | """
Ablation study for mmVelo (SHARE-seq_hf dataset):
1. With vs. without KNN smoothing (zdim = 10)
2. Multiple latent dimensionalities: zdim = 5, 10, 30, 50 (with smoothing)
For each condition the script:
- Trains mmVelo from scratch (skips a stage if a checkpoint already exists)
- Generates a latent-space st... |
f580d1ec2c993f6611ea44abbfbbd347c0ad887ced6fc358d18519853992753c | Python | 26,637 | 773 | """Core implementation of Mesa's reactive programming system.
This module provides the foundational classes for Mesa's observable/reactive programming
functionality:
- BaseObservable: Abstract base class defining the interface for all observables
- Observable: Main class for creating observable properties that emit c... |
36d28515f881e2fe46ebd6826aad696edd34640f857b32fd7a50fbfddd0002ae | Python | 26,642 | 621 | #!/usr/bin/env python3
"""
Statistical Analysis Tables Generator
This script generates comprehensive statistical analysis tables for the AL Project
experimental results, following the statistical framework described in the paper.
For each of the 4 settings (Hard_Mode/Hide_The_Label, Hard_Mode/Open_Race,
Regular_Mode... |
2cabc36a5255ab8483723ffdbd3c3b8c04d2a40e8436e4a5c895068d7102a885 | Python | 26,702 | 672 | #!/usr/bin/env python
#
# Copyright (c) 2022 10X Genomics, Inc. All rights reserved.
#
from __future__ import annotations
import os
import socket
import sys
from typing import TYPE_CHECKING, NamedTuple
import martian
import cellranger.constants as cr_constants
import cellranger.env as cr_env
import cellranger.refere... |
a9bc812b2b09f2035fbc109b83562afa5318f2f4963288996a6ad044e2f9ee9f | Python | 26,704 | 594 | 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... |
9dfbf946936cbdd67d1526318e9a3f8b7e2fac9ad3e7e3b8c6a6c304b62ea1cb | Python | 26,831 | 660 | ############################################################################
# Copyright (c) 2025-2026 University of Helsinki
# All Rights Reserved
# See file LICENSE for details.
############################################################################
"""
String interning for memory optimization.
Replaces duplic... |
891c8e92e1812719db1f3671f9c66b37850ed5404d0e2aaea6faa9a32942ff86 | Python | 26,832 | 709 | import numpy as np
from spikeinterface import full as si
import os
import pickle
from scipy.signal import find_peaks, peak_prominences, peak_widths
import matplotlib.pyplot as plt
import hashlib
import batch_process.util.template_util as template_util
# Module for waveform acceptance criteria
def get_MAD... |
3b72e58ee7432e12ee406cb34e570547b340ae51750521a41a5fbe9e2fc64a99 | Python | 26,877 | 472 | ############################################################################
# Copyright (c) 2022-2026 University of Helsinki
# Copyright (c) 2020-2022 Saint Petersburg State University
# # All Rights Reserved
# See file LICENSE for details.
############################################################################
... |
7e31d894fb2750920c5c3cca91cc63f2065ceca57a404b28ac4edc46f938347d | Python | 26,898 | 721 | """mesa.experimental.actions: Timed, interruptible actions for Mesa agents.
An Action represents something an agent does over time. It integrates with
Mesa's event scheduling system for precise timing and supports interruption
with progress tracking and optional resumption.
Actions are subclassable: override on_start... |
84c4c12bb49b4780faa0842d4399fa6d63d6dbff57e37080ee5dfeeaa0057ea7 | Python | 26,901 | 482 | import os
import numpy as np
import pandas as pd
import torch
import torch.nn as nn
import torch.nn.functional as F
from torch.cuda import device
from ndreamer.model_DL import NDreamer_generator,Discriminator,set_seed
from ndreamer.DL_loss_func import CrossEntropy, create_triplets_within_groups, IndependenceL... |
d71e049bf929574afaa0bc33bec80988705315741c4b90fa0c2b9d985911b9ae | Python | 26,933 | 670 | """
Python snippets and functions to help facilitate saving and loading volumetric and surface data to be used with NMF.
"""
import os #for checking if filepaths are reasonable, and files/directories exist
if (os.name == 'nt'):
from asyncio.windows_events import NULL
import sys #check python version, exit upon sani... |
c7665cf31a5c7564957e4efc3dab0d659bd8619b32515bdaaee90f6b6f85a35d | Python | 26,981 | 686 | # 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... |
fe893961c963532939f030f58a92a7bd719dfeeced91831095468026cfc14f7c | Python | 27,004 | 678 | #!/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... |
4560fb41db756c58dd2cc69eb9bdeb60a8a380e7e0a2b93af50fb39c76285a51 | Python | 27,135 | 658 | # 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... |
2f5f8e498d7ccbf92e24076c04eeafa38507f0b476f952f0a51fe0b03968d6c8 | Python | 27,138 | 694 | # Copyright (c) Facebook, Inc. and its affiliates.
import itertools
import logging
import numpy as np
import operator
import pickle
from collections import OrderedDict, defaultdict
from typing import Any, Callable, Dict, List, Optional, Union
import torch
import torch.utils.data as torchdata
from tabulate import tabula... |
e7e51fc063671971365122c01438afddb5f0d00f66db5d82e8a47f1705deafe8 | Python | 27,232 | 628 |
############################################################################
# Copyright (c) 2022-2026 University of Helsinki
# All Rights Reserved
# See file LICENSE for details.
############################################################################
#############################################################... |
48545c93dbdda16b904ef7b394755171937919a917a6a66aceeeaee23dd449a2 | Python | 27,263 | 727 | # Copyright (c) 2018 10X Genomics, Inc. All rights reserved.
"""Tools for managing metrics with metadata attached."""
from __future__ import annotations
# Copied from cellranger-atac (commit 5ccda578ed71e24289c6ea9bb6dec4d9de5d11dc)
import csv
import os
from collections import OrderedDict
import pandas as pd
from six... |
5f44999a3c613104b55be0b790f8846b782cd956d7ad73d899bf323966af83b1 | Python | 27,325 | 736 | # -*- coding: utf-8 -*-
# Copyright (c) Facebook, Inc. and its affiliates.
"""
Implement many useful :class:`Augmentation`.
"""
import numpy as np
import sys
from numpy import random
from typing import Tuple
import torch
from fvcore.transforms.transform import (
BlendTransform,
CropTransform,
HFlipTransform... |
2880adb276008331e2b0a1100ca1743f8f00214a1aa429a298570272aa6d0106 | Python | 27,402 | 705 | """Figure S5 -- Movement control (symmetric 120ms window analysis).
Layout:
A/B/D: Wheel movement traces, single-trial onset detection, onset distribution
C: Movement onset early vs late
E-H: PL mod | NPL mod | PL t2max | NPL t2max
Wheel movement panels are saved separately from the neural modulation pane... |
23699f726ccef97c7078138cc7717d662c5f32515e101446495866da9f731fab | Python | 27,441 | 709 | #python genomeTranslate.py
"""
1. Download nucleotide FASTA from NCBI by accession (via eutils REST, no Biopython)
2. Six-frame translation using a specified NCBI genetic code table (parsed live from NCBI)
3. Download reference proteome from UniProt
4. For each translated segment between stop codons: check if it is a s... |
ceaea404cbbfb0bee164656c2e8443e645ad68f23eb73434ec7f936d73b63499 | Python | 27,465 | 722 | # This code is in parts based on TopologyProposal in perses
# (https://github.com/choderalab/perses)
# The eventual goal is to move this to the OpenFE alchemical topology
# building toolsets.
# LICENSE: MIT
# turn off formatting since this is mostly vendored code
# fmt: off
import itertools
import logging
import warn... |
2558b15cdbdc8f6f60605ee88790c3602f3cfab42cc5acfa65567c0d4e7e47ad | Python | 27,470 | 628 | #!/usr/bin/env python3
"""
LAMAReg: Label Augmented Modality Agnostic Registration
Command-line interface
"""
import argparse
import sys
import os
import tempfile
import shutil
from lamareg.scripts.lamar import lamareg
from lamareg.scripts import synthseg, coregister, apply_warp
from colorama import init, Fore, Style
... |
43d22a42b1361f9605253d274f0e960f93da85ebe07d530df8055c1c3210304b | Python | 27,476 | 668 | """Utility functions used with azimuth. Code taken from panhumanpy and edited."""
import numpy as np
from scipy.sparse import csr_matrix
from sklearn.calibration import LabelEncoder
from cellranger.cell_typing.azimuth.azimuth_ref_paths import (
AZIMUTH_INFERENCE_ENCODERS_PATHS_SORTED_LIST,
)
####################... |
58c2aa25c16137064422927edf12e45664f97d80e600f54a4c8104280c430ee5 | Python | 27,526 | 803 | """Utilities for converting Snakemake apps to BIDS apps."""
from __future__ import annotations
import json
import logging
import os
import re
import warnings
from collections import defaultdict
from collections.abc import Iterable
from pathlib import Path
from typing import (
Any,
Literal,
overload,
)
im... |
fcd828a650a13e1c99fde93ff9765761e785301d7231eb3744f449697594b78e | Python | 27,566 | 802 | """ Created on Thu Feb 13 11:08:11 2025
@author: dcupolillo """
from __future__ import annotations
from pathlib import Path
import flammkuchen as fl
from tqdm import tqdm
import numpy as np
from functools import cache
import tensorflow as tf
from spyne.core.electrophysiology.config import EphyDatasetConfig
from sp... |
32e4737bb0127e4b28405b52d42ac16a9333c0465619a830307e6d7387de7736 | Python | 27,617 | 601 | import os
import numpy as np
import pandas as pd
import matplotlib
import matplotlib.pyplot as plt
import anndata as ad
import scanpy as sc
from scipy.io import mmwrite, mmread
import seaborn as sns
import scipy
from arboreto.algo import grnboost2
import pickle
import collections
import pycistarget
import pyranges as p... |
768f1c44a30b0a3ad20201a71472107c3b0e7ed6e78b04c93a0c4a0ae67e1206 | Python | 27,640 | 713 | from abc import ABC, abstractmethod
import logging
import math
from typing import Self
import numpy as np
from scipy.optimize import fmin
from scipy.special import expit, logit, softmax
from sklearn.isotonic import IsotonicRegression
import torch
from torch import Tensor
from chemprop.utils.registry import ClassRegis... |
331ee2117e1de7269ef31f70a7f4496b62b1e27797194ea4af8e030fe161d0d5 | Python | 27,686 | 647 | # AUTOGENERATED! DO NOT EDIT! File to edit: 43_experimental_diagnostics.ipynb (unless otherwise specified).
__all__ = ['posterior_dict_to_table', 'extract_variable_names', 'compute_rhat', 'rank_normal_transformation',
'folded_rank_normal_transformation', 'summarize_parameter_convergence_with_rhat', 'compute... |
0e8beb86476618c038d15ea7686ad46f10009efa61555a379b5d4dada61d880a | Python | 27,703 | 687 | # -*- coding: utf-8 -*-
"""Helper code for running spatial nulls models."""
from pathlib import Path
import warnings
import numpy as np
from scipy import optimize, spatial
try: # scipy >= 1.8.0
from scipy.ndimage._measurements import _stats, labeled_comprehension
except ImportError: # scipy < 1.8.0
from sci... |
fd424261e83362880c91cf67b8d90d7ca3947ff2b645d46f72d4c5ef524acac4 | Python | 27,866 | 714 | """
Helper functions for using kalmax
"""
from typing import Callable, Tuple, Any
import numpy as np
import statistics
import jax.numpy as jnp
from jax import vmap
import kalmax
from kalmax.kde import kde
from kalmax.kalman import KalmanFilter
from kalmax.kernels import gaussian_kernel
from kalmax.utils import gaussia... |
eeed02f54bb368353d8f0cab85da5219016b32695781d4b1969476ccae1fc4ef | Python | 27,905 | 677 | """PyTorch Lightning module for stoichiometry prediction training."""
import gc
from typing import Any, Dict, List, Literal, Optional, Tuple, Type
import numpy as np
import torch
import torch.nn as nn
from lightning import LightningModule
from loguru import logger
from torchmetrics import MetricCollection
from torchm... |
5c50e87d8afa797e8ccaa2f15952dd00d264f388b4234fe63413e20f4aba507e | Python | 27,908 | 750 | # -*- coding: utf-8 -*-
"""long_tail
Automatically generated by Colab.
Original file is located at
https://colab.research.google.com/drive/1DrbUfVBgFblytXlraa_xaabPD22UmHaY
Score-CAM comparative analysis across five binary frost vs non-frost models
(CNN, BNN, MobileNetV2, EfficientNetV2B0, ResNet50), producing s... |
e2a5bab198767b4ff0c5d7a31633d064922ea83f5f59cd7e094ac7d0a3c18622 | Python | 27,911 | 801 | # -*- coding: utf-8 -*-
"""
Created on Tue Mar 22 16:30:55 2022
@author: Joseph Vermeil
BeadsCalibration.py -
Joseph Vermeil, 2022
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 o... |
2fa80f2cd9b433bdd601164b1c637f2dc776190ee049a8b48959c70af593f7bd | Python | 27,913 | 641 | # 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... |
acd1986a8cdee6429a54ad118cd4711b10e3196e75a59dcb1dd8d8d64b0d5aa7 | Python | 27,963 | 725 | # 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... |
925339898ebd40d4d307d63e2ba11a880f029270234c579aae42f2fe045a07cf | Python | 28,066 | 755 | # 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... |
7ff5be21fb78fe25e7fff0b9dd0e376640ae74a970a53dab2c54dd6ffa000ad0 | Python | 28,127 | 443 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
import numpy as np
import pylab
import re
import os
import glob
import matplotlib.pyplot as plt
import matplotlib.gridspec as gridspec
from mpl_toolkits.axes_grid1.inset_locator import inset_axes
from optparse import OptionParser
SEQUENCE_INDEX = "0"
SEQ_NUM = 10
ITERATIO... |
e6fb2a3130b987394562f7a9f4056e063dc6e23dfa159957cb81bfbee11bdd12 | Python | 28,157 | 772 | import numpy as np
import pandas
import matplotlib as mpl
import matplotlib.pyplot as plt
import scipy
import argparse
from fit_to_sjostrom import gen_spike_trains_dt, gen_spike_trains, gen_continuos_spike_trains
print(scipy.__version__)
plt.rcParams['text.usetex'] = True
# Set global font settings
fsize = 10
markersi... |
17e6f1d2698d432e3b380d204e1c3a76858e906ca0edcde5be64cf43bca25258 | Python | 28,205 | 586 | """
Storage and retrieval of foreground sampling locations.
Report: /home/isensee/git_repos/random_projects/projects/2026-09_preprocessing_io_speedups/REPORT.md
Covers this store and the resampling fix on the same branch. Records why preallocating and
memory-mapped writing made the store *slower* on NFS, what the pari... |
2fc446c9ea613eea2624198ea045fe3b758eb03f54832e0164c0887765ca5986 | Python | 28,212 | 780 | import navis
import pytest
import struct
import tempfile
import numpy as np
from pathlib import Path
def _can_write_r():
"""Check whether the installed `rdata` can write .rds/.rda files."""
import rdata
# Writing arrived in rdata 1.0, which requires Python >= 3.11. On 3.10 we
# install the last vers... |
ff3d0fb893ea262407ce2266e74704599b86ef99893a91638d1db73b5476ca15 | Python | 28,310 | 593 | """
coregister - Label-Augmented Image Registration for Aligning Neuroimaging Data
Part of the micaflow processing pipeline for neuroimaging data.
This module performs comprehensive image registration between two images using LAMAReg
(Label-Augmented Modality-Agnostic Registration), which combines anatomical im... |
9b3bee84cdc8d911a10c33ec6e5d3ad4f44b8085695aa8810c35e0b8127a056b | Python | 28,318 | 483 | #!/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... |
91dcf72f32eeff5afb71ee691e653c02e2a9a35e4ddbc0f0ffc6ea6d2d9646d7 | Python | 28,354 | 796 | # This script is part of navis (http://www.github.com/navis-org/navis).
# Copyright (C) 2017 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... |
7db2f9de1a6d7941a35f693f534fb4287c3959737c63ac6e0f232a0278330e63 | Python | 28,363 | 574 | ############################################################################
# Copyright (c) 2023-2026 University of Helsinki
# # All Rights Reserved
# See file LICENSE for details.
############################################################################
"""
Stereo-seq barcode detectors.
Stereo-seq uses spatial b... |
e42dd35c5ffc2d8557e764fa8c1c500ad2ea71684fd9b04a9941b7b9115795e2 | Python | 28,400 | 732 | from __future__ import annotations
import logging
import os
import statistics
import time
from collections.abc import Callable
from dataclasses import dataclass, field
from datetime import datetime, timezone
from pathlib import Path
from typing import Any
from rdkit import Chem
from src.database.spreadsheet_source i... |
4a6124fa20f376caf497db3b17cc3c7a266289e213b6302c52ded3f7a6cfe0d4 | Python | 28,424 | 751 | # -*- coding: utf-8 -*-
# Copyright (c) Facebook, Inc. and its affiliates.
"""
This file contains components with some default boilerplate logic user may need
in training / testing. They will not work for everyone, but many users may find them useful.
The behavior of functions/classes in this file is subject to chang... |
e03bec20c64e8366b834e37904841cdcd14ae12008a10d8d983cfce2152baf80 | Python | 28,468 | 606 | """
This function is very similar to training.py, as we train a UNet with synthetic data. In addition to the input image,
the UNet now also takes new inputs: soft probability maps for the target labels. These represent prior information, that
would typically be obtained at test time with a first segmenter.
If you use... |
83233b5212947cda0ed4f893ce5f410130f13644a78c2bcd07f7e72b4e314930 | Python | 28,469 | 740 | # 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... |
520da1736e3966b306a8602c2f66c089e0ff236b636a7d5f17789f14cddd49e1 | Python | 28,581 | 751 | #!/usr/bin/env python
#
# Copyright (c) 2015 10X Genomics, Inc. All rights reserved.
#
from __future__ import annotations
import collections
import csv
import itertools
import json
import os
import re
import subprocess
from typing import Any, NamedTuple
import numpy as np
from six import ensure_binary, ensure_str
i... |
e94a5155200d77f06753ace83d509d5e1e72e544985118108f6f2db3a8ad21a7 | Python | 28,642 | 860 | from dataclasses import dataclass, field
from functools import cached_property
import logging
from typing import NamedTuple, TypeAlias
import numpy as np
from numpy.typing import ArrayLike
from rdkit import Chem
from rdkit.Chem import Mol
from sklearn.preprocessing import StandardScaler
from torch.utils.data import Da... |
21da3b8b26f51d1c173ba6ee6a44bb8869153db660dfb293ea5be64ab7fccf4a | Python | 28,709 | 784 | # This code is part of OpenFE and is licensed under the MIT license.
# For details, see https://github.com/OpenFreeEnergy/openfe
"""
Restraint Geometry classes
TODO
----
* Add relevant duecredit entries.
"""
import warnings
from typing import Optional
import MDAnalysis as mda
import numpy as np
import numpy.typing a... |
e1b446e93626041c3b3c5a0a9c7c2e4e8a6a1c6a113c77748d8de14384ac5e84 | Python | 28,726 | 737 | #!/usr/bin/env python
#
# Copyright (c) 2017 10X Genomics, Inc. All rights reserved.
#
"""Types for loading, saving, and using feature reference data."""
from __future__ import annotations
import csv
import os
from collections.abc import Collection, Generator, ItemsView, Iterable, KeysView
from dataclasses import da... |
9ed1e1a8ee4b553e190c6cfcf095a28b3c69796f07009baab11b60a91c8aef28 | Python | 28,753 | 764 | """Chemprop unit tests for chemprop/models/loss.py"""
import numpy as np
import pytest
import torch
from chemprop.nn.metrics import (
SID,
BCELoss,
BinaryMCCLoss,
BoundedMSE,
CrossEntropyLoss,
DirichletLoss,
EvidentialLoss,
MulticlassMCCLoss,
MVELoss,
NLogProbEn... |
54ea471897bdda2cc9f70acdfa3c4baf19ac5f81a2ad5f4fa538b8ada5011f1a | Python | 28,783 | 812 | # 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 sys
from typing import List, Literal
import click
import gufe
import pandas as pd
from openfecli import OFECommandPlugin
from openfecli.clicktypes import Hy... |
6f386be654cd4bbcbc6706be4e1f99cce1480075d9f6457bde8aaa0fd7cc0849 | Python | 28,860 | 832 | """
Data Preprocessing Pipeline for Axon Segmentation
Processes large Bielschowsky-stained image tiles and their corresponding axon
masks into 128×128 tiles with optional data augmentation.
Features:
- Grid-based and random tile extraction with configurable overlap
- Probabilistic augmentation chain (geometric, inten... |
40df38ccb97b2952f08494ad43804cc092759f02760e89240bfec8c1b8a31086 | Python | 28,943 | 878 | """
tensorflow/keras utilities for the neuron project
If you use this code, please cite
Dalca AV, Guttag J, Sabuncu MR
Anatomical Priors in Convolutional Networks for Unsupervised Biomedical Segmentation,
CVPR 2018
Contact: adalca [at] csail [dot] mit [dot] edu
License: GPLv3
"""
import sys
from lamareg.ext.neuron ... |
e7deb515ef7c1f2bf80d28485eeeb0c4e2b8767fa5f68309c7c83ec752fa512b | Python | 29,024 | 916 | import os
import math
import random
import numpy as np
import torch
import cv2
from torchvision.utils import make_grid
from datetime import datetime
#import matplotlib.pyplot as plt # TODO: check with Dominik, also bsrgan.py vs bsrgan_light.py
os.environ["KMP_DUPLICATE_LIB_OK"]="TRUE"
'''
# ----------------------... |
6e131018e73c8981973d118781fba5c656f61b47a6569810c324d036940a3e6d | Python | 29,028 | 732 | ############################################################################
# Copyright (c) 2022-2026 University of Helsinki
# Copyright (c) 2020-2022 Saint Petersburg State University
# # All Rights Reserved
# See file LICENSE for details.
############################################################################
... |
dc2783234356223f6d6b8e3d5d67ac312c5aa927c573f74fbcb288fb60afbfa5 | Python | 29,039 | 707 | import numpy as np
import math
import pandas as pd
import os
import batch_process.util.file_util as file_util
# Lazy import: dataloader pulls in psignifit which isn't always available.
# Only needed by get_stim_data() for experimental data loading.
dataloader_module = None
from collections import namedtuple
fr... |
ec9f4de5bd1b24af188e3237dd29bf1e2e1afd064db540f635cdb7803ed5a478 | Python | 29,183 | 1,170 | """This tests the CLI functionality of training and predicting a regression model on a single molecule.
"""
import sys
import numpy as np
import pytest
from chemprop.cli.hpopt import NO_HYPEROPT, NO_OPTUNA, NO_RAY
from chemprop.cli.main import main
from chemprop.cli.utils.MAB_parsing import build_MAB_data_from_files
... |
b02db1729126bd79a40f33ad7225c5cd4f32f2d722a61b5441d92f196286817b | Python | 29,234 | 852 | """Mesa visualization space drawers.
This module provides the core logic for drawing spaces in Mesa, supporting
orthogonal grids, hexagonal grids, networks, continuous spaces, and Voronoi grids.
It includes implementations for both Matplotlib and Altair backends.
"""
from itertools import pairwise
import altair as a... |
b34bae07752557f94bad0025242e963b0f53521bfb7bf5eb7dbd1e4b20807de5 | Python | 29,287 | 830 | # 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... |
61f2c519a7f73fa12da9eb90da97b97ec2f8d5f31d42605639c7600cbd321cbe | Python | 29,312 | 469 | import argparse
import os.path
def main(args):
import json, time, os, sys, glob
import shutil
import warnings
import numpy as np
import torch
from torch import optim
from torch.utils.data import DataLoader
from torch.utils.data.dataset import random_split, Subset
import copy
im... |
eb1f19dea4934618b1f84d3a96938034e3bb05f0c7727440a005bbc07f2b053c | Python | 29,385 | 708 | import sys
import numpy as np
import json
from time import perf_counter
import pandas as pd
import pyqtgraph as pg
from pyqtgraph.Qt import QtWidgets
from pyqtgraph.Qt import QtCore
from pyqtgraph.console import ConsoleWidget
from pyqtgraph.dockarea.Dock import Dock
from pyqtgraph.dockarea.DockArea import DockArea
from... |
2aeaa7f087294f470a2dbcb7a26a5960d72766d8c888098e0decbf58b55db915 | Python | 29,403 | 676 | # -*- coding: utf-8 -*-
"""
Created on Fri Jul 15 12:25:40 2016
@author: Luciano Masullo, Federico Barabas
"""
import os
import time
import math
import numpy as np
from scipy import ndimage as ndi
import tifffile as tiff
from PIL import Image
import pyqtgraph as pg
from pyqtgraph.Qt import QtGui, QtCore
import matp... |
3f72e769ed7cacde4807664aa83b420a497ede553d95023a07dd37c70a9b949c | Python | 29,456 | 709 | import argparse
import html
import logging
import os
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(paren... |
06a9ad17f1162ff7821808c663d59cd2e0f8116a997b8446e5a82e81a1076459 | Python | 29,516 | 771 | """ Cortex dataset handler """
__author__ = "Fabi Bongratz"
__email__ = "fabi.bongratz@gmail.com"
import os
import random
import warnings
import collections.abc as abc
from typing import Union, Sequence
from abc import ABC, abstractmethod
import torch
import torchio as tio
import numpy as np
import nibabel as nib
im... |
024e230569e71e9b2e25a5368d0266c345fc34b892ed2bcd7416c3a1f149dc42 | Python | 29,518 | 743 | '''
(c) 2014 Brendan Bulik-Sullivan and Hilary Finucane
Estimators of heritability and genetic correlation.
Shape convention is (n_snp, n_annot) for all classes.
Last column = intercept.
'''
from __future__ import division
import numpy as np
import pandas as pd
from scipy.stats import norm, chi2
import jackknife as ... |
323e901fb579e8cd25945ffbc162830b871f24af8da179844340a6986cb1a601 | Python | 29,588 | 703 | import pytest
from isoquant_lib.fusion.fusion_validator import FusionValidator
class MockDetector:
"""Mock detector object for testing FusionValidator."""
def __init__(self):
self.fusion_metadata = {}
self.fusion_candidates = {}
self.fusion_breakpoints = {}
self.fusion_assigne... |
4c0d0ff1229a71ad7042b980352434dfb75b50b0b3e47656f84915bafbd0cabc | Python | 29,694 | 779 | # This code is part of OpenFE and is licensed under the MIT license.
# For details, see https://github.com/OpenFreeEnergy/openfe
from typing import Callable
import pytest
import openfe
from ..conftest import mol_from_smiles
class BadMapper(openfe.setup.atom_mapping.LigandAtomMapper):
@classmethod
def _def... |
000b157339ad33f859b0b403ec2a9e38699e59c73f13dcffa6458bb2726ffa6d | Python | 29,781 | 611 | import sys
import numpy as np
import torch
from torch import nn
import torch.nn.functional as F
import torch.distributions as dist
from torch.nn.parameter import Parameter
from torch.nn import init
import pytorch_lightning as pl
from pytorch_lightning.callbacks.early_stopping import EarlyStopping
sys.path.append("/mmV... |
2cd12a96139ac016e719e1585f49494465124721caecea8e6709cc01b71345f4 | Python | 29,789 | 611 | #!/usr/bin/env python3
"""AccuSNV pipeline launcher and argparse.
This file parses inputs, writes configs, and runs Snakemake.
accusnv -m {dryrun,slurm,local} -i samples.csv -r ./ref_dir/ -o out/ [-c config.yaml] [-p pipeline.yaml]
Two config files are required for a run:
1. config.yaml - Snakemake execution s... |
53296490641266ff41d272c38c574d4f63e10fd3204c1115a5a78e0a935b1b4f | Python | 29,812 | 522 | """Stage 2: annotate candidate mutations against the reference, merge the annotations with
the CNN+filter table into the unfiltered table, and split those by CNN label into the final
tables. Includes the mutation-annotation library functions inline.
Reads ``_snv_state.npz`` and ``snv_table_filtered_tmp.tsv`` (both fro... |
9a889d9a973178cee4a72d133f1e243a6550768dc2b65589fcd462be72ba658a | Python | 29,845 | 879 | from scipy.stats import mannwhitneyu
from batch_process.util.plotting import add_sig_bracket, p_to_stars
import batch_process.util.template_util as template_util
import seaborn as sns
import batch_process.postprocessing.responses_v2.response_plotting_util as rpu
from batch_process.util import curate_util
import spikein... |
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