sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
b6d7d8ef674cc50a3a877e53f489377828beea575177cd42130a44009a358f13 | Python | 11,588 | 324 | # 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... |
c0b2398c00df7408ad3d053fd4a091ca2065aec4016e7458007dc5bd5accba0a | Python | 11,589 | 337 | import numpy as np
import random
import torch
import pandas as pd
import dgl
import networkx as nx
from sklearn.model_selection import StratifiedKFold
import copy
torch.manual_seed(123)
random.seed(123)
def get_adj(edges, size):
edges_tensor = torch.LongTensor(edges).t()
values = torch.ones(len(edges))
a... |
494cbe329caf8568205f1aed284308df7dcdb9ffa243111d0a5617fa2fbd354e | Python | 11,590 | 317 | # 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.
"""
from typing import Annotated, Literal, Optional, TypeAlias
import MDAnalysis as mda
from gufe.settings.typing... |
620fe603521b8c8c039fc7f9f280cad4e01a007657232e205b0ade9c4959bcae | Python | 11,594 | 394 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Common utility functions for patent data preprocessing pipeline.
"""
import os
import json
import logging
from pathlib import Path
from datetime import datetime
import numpy as np
def setup_logging(log_dir=None, log_level=logging.INFO):
"""
Setup logging conf... |
a0727462d035fda3e8426fef94648af7d13cadc73d58bf8cffb3475f1e1db8bf | Python | 11,611 | 291 | from itertools import combinations, product
from typing import Any, Optional, Sequence
import matplotlib.pyplot as plt
import numpy as np
import numpy.typing as npt
import pandas as pd
from matplotlib.axes import Axes
from matplotlib.patches import Patch, Ellipse, Rectangle
from .base import setup_axes, set_figsize
f... |
dae6b7ef03fd332fba5d15c9b5b003de373dc18e0eb3ae55fa605fe7722e580c | Python | 11,628 | 388 | # Copyright (c) 2015 10X Genomics, Inc. All rights reserved.
"""Assorted grab-bag of miscellaneous helper methods.
Do not add to this module. Instead, find or create a module with a name
that indicates to a potential user what sorts of methods they might find
in that module.
"""
from __future__ import annotations
... |
7c531ca8db97ac348405c33fbabdaf3cff3db8fa643368bd227edbe77f442bd0 | Python | 11,630 | 307 | # 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... |
e7a9d36c6ba1de8382e2e0c77c378b06ab4501c66ba93c4be6a26b15d3e7eb19 | Python | 11,633 | 235 | import copy
import pandas as pd
import matplotlib.pyplot as plt
from fafbseg import flywire
import pymaid
import navis as nv
import numpy as np
import seaborn as sns
import scipy.stats as stats
import statsmodels
import scikit_posthocs as sp
import sys
import scipy
import random
import string
def multi_comparisons_... |
c9096e45ebb250f58a632e6e2a0fee43d52b41c427c18df32b1fb52f245907fd | Python | 11,640 | 361 | import numpy as np
import matplotlib.pyplot as plt
from scipy.linalg import eigh
from functools import reduce
import seaborn as sns
# Helper: Kronecker product
def kron(oplist):
return reduce(np.kron, oplist)
# ------------------
# Constants
# ------------------
gamma_e = 1.76086e8 # rad/(s·mT)
... |
2c8cb9a4fb9826d2d2244689f1f921ded2dd3930d74015ed77f1726956d7671c | Python | 11,644 | 356 | # %%
from __future__ import annotations
import mne
import numpy as np
from joblib import delayed
from joblib import Parallel
from scipy.spatial.distance import cdist
from tqdm.autonotebook import tqdm
from tqdm_joblib import tqdm_joblib
from wasabi import msg
from ..utils import get_soi_picks
# %%
class Epo2Rdm:
... |
686dbb945641609abd13bc8e72eba4a7a6e197604872eafc5710dccd7129dcfc | Python | 11,646 | 322 | """ Created on Mon Oct 23 12:23:47 2023
@author: dcupolillo """
import numpy as np
from spyne.core.spines.analysis.segmentation.post_processing_utils import (
threshold_prediction, remove_corner_joints,
remove_distant_spines, remove_small_labels,
calculate_centroid, transform)
from skimage import morph... |
18d9393d631bab8a152b3999a401d18deda6146cc824ede47d4a6bc7f5c39a8e | Python | 11,652 | 332 | """
Configuration File for MorphoScope - Structural Plasticity Analyzer
This module centralizes all application configuration constants and settings,
making it easy to modify behavior without changing core code.
Usage
-----
Import at the start of your main application:
from config import Config, setup_lo... |
28f7214e82c6ab74eb565ab5662ae753886f067875fe96ea1ff07d7ccacd04e7 | Python | 11,678 | 231 | from collections import OrderedDict
from copy import deepcopy
from typing import Union, Tuple, List
import numpy as np
import pandas as pd
import torch
from batchgenerators.augmentations.utils import resize_segmentation
from scipy.ndimage import map_coordinates
from skimage.transform import resize
from nnunetv2.config... |
1a4e20f731ecc7816d60ae0d68392fcc7f30950128beb2404b6289b533fdcdac | Python | 11,680 | 252 | import os
import sys
from argparse import ArgumentParser
import numpy as np
import scanpy as sc
import torch
import pytorch_lightning as pl
from pytorch_lightning.callbacks.model_checkpoint import ModelCheckpoint
from pytorch_lightning import loggers as pl_loggers
sys.path.append("/home/nomura/Proj/mmvelo/src")
from m... |
97a407ac864da7bf5c9989c42e90beb4ee22ea8f68e88fc0789e28d9c27e8630 | Python | 11,681 | 247 | #!/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... |
c71ceefabf1fcf5beaa05a4a9438a1bb2f251d2f47ea31dc068a40727a77bb8d | Python | 11,681 | 365 |
""" Graph (sub-)networks """
__author__ = "Fabi Bongratz"
__email__ = "fabi.bongratz@gmail.com"
from typing import Union, Tuple, Sequence
import torch
from torch import nn
from torch.cuda.amp import autocast
from pytorch3d.structures import MeshesXD
import logger
from utils.graph_conv import Features2FeaturesResid... |
aecf5e5182f96688790c78e529bd7a1c5d768fa4001d11727aa484cbea0b4e67 | Python | 11,686 | 304 | import torch
import torch.nn as nn
import torch.nn.functional as F
import dgl
import dgl.function as fn
import numpy as np
class FreqEncoLayer(nn.Module):
def __init__(self, in_dim, out_dim, num_heads, dropout=0.0, layer_norm=False, batch_norm=True, residual=True, use_bias=False,
freq_enhance_rat... |
f9be2654289d1c02f5d105fff603ef7b1f463df64c5b34c4ee0a1d040c52ad25 | Python | 11,691 | 351 | # -*- coding: utf-8 -*-
"""
Spyder Editor
"""
import os
import pandas as pd
# === Folder containing your CSV files ===
folder = "/Users/u0135006/Desktop/Rabies_sum"
# === Find all CSV files in the folder ===
csv_files = [f for f in os.listdir(folder) if f.lower().endswith(".csv")]
if not csv_files:
raise Syst... |
81f16bc695110dd45575bb64d8b1d84efbed4d13ab1acb44d2b0d00e88f2daae | Python | 11,707 | 259 | # Copyright (c) Facebook, Inc. and its affiliates.
import torch
from torch.nn import functional as F
from detectron2.layers import cat, shapes_to_tensor
from detectron2.structures import BitMasks, Boxes
"""
Shape shorthand in this module:
N: minibatch dimension size, i.e. the number of RoIs for instance segmena... |
e79f5e560cda401a94006df85fa18626d7e2ca375782682ef02589b80327531c | Python | 11,708 | 312 | #!/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... |
0d69d567250277d334ae9bafb743f3acd0eccdc6d4e42486e9ec6ef2b198d704 | Python | 11,709 | 276 | import os
import numpy as np
import nibabel as nib
import os.path as op
from glob import glob
from time import time
import pandas as pd
from scipy.spatial import cKDTree
import matplotlib.colors as mcolors
import matplotlib.pyplot as plt
import nibabel as nib
import nipype.interfaces.freesurfer as fs
from nipype.int... |
ac2e60f8102a64d18aaae6f291e26abd6352f4b4dab7eae18de3059ee4d6d973 | Python | 11,710 | 294 | # gene 方向に p, u, s を concat して解析しようとした script
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
... |
9476b6b86ea8e6e160ebf6e5b6e3b5364fca14e556e08709cb9b9a174ffcd11c | Python | 11,726 | 302 | # ------------------------------------------------------------------------------
# Title: Maturation Model for CM Data
# Author: Yiran Song
# Date: March 18, 2025
# Description:
# This script trains a machine learning model to predict CM (cardiomyocyte) maturation
# using multiple datasets. It includes data preprocess... |
24a4fb696f44ff457c225c4bc37dd4dafae7de0d9591dfe7a28e6e2aea3c55db | Python | 11,727 | 239 |
############################################################################
# Copyright (c) 2022-2026 University of Helsinki
# All Rights Reserved
# See file LICENSE for details.
############################################################################
import subprocess
import pytest
import os
import shutil
de... |
ff3ab3d65a499302ed12237a2d69cbddf9418ff0473be2a40e897afb1d7f5549 | Python | 11,749 | 236 | 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 scanpy.external as sce
np.random.seed(42)
# load anndata
dir_path = "/home/nomura/Proj/mmvelo/experiments/multiome_brain_rep_wo_IN/2023-05-07T15:19:02_s43_k... |
57144c9ce7e223a75b37653a963a5047bd63611150879d36edbfa9ac0fe993fc | Python | 11,753 | 322 | import tensorflow as tf
import numpy as np
import math
from sklearn import preprocessing
from scipy.linalg import toeplitz
dim=3000
eta=0.2
elimination_rate=1
def data(dim):
t=[pow(0.5,i) for i in range(dim)]
Sigmainv=toeplitz(t)
Sigma=np.linalg.inv(Sigmainv)
X=np.random.multivariate_normal(np.zeros(... |
18830ab1788661168a442a4c50d8e3e1445f717c57a7f713e8415fa778103b34 | Python | 11,759 | 332 | """
NEURON simulator
================
<!-- difficulty: advanced -->
Run compartment-model simulations of neurons and networks via the NEURON simulator.
[NEURON](https://neuron.yale.edu/neuron/) is a simulation environment for modeling neurons and networks.
It's powerful but fairly low-level, so building models tends ... |
b6b4db66f92c2470c20ad6fefe2a58ae8589c154e37f74162201b11a948551d3 | Python | 11,759 | 257 | '''
Created on 29.09.2020
Author:
Michael Diedenhofen
Max Planck Institute for Metabolism Research, Cologne
'''
from __future__ import print_function
import csv
import os
import sys
import numpy as np
import nibabel as nib
from calendar import month_name
from datetime import datetime
from zoneinfo import ZoneInfo
... |
4b42a617632fad5f9f703c74da55c74dd506c7452e1cae377f767b84c7a52c28 | Python | 11,769 | 334 | """
Configuration File for MorphoScope - Structural Plasticity Analyzer
This module centralizes all application configuration constants and settings,
making it easy to modify behavior without changing core code.
Usage
-----
Import at the start of your main application:
from config import Config, setup_lo... |
757f746e23839004b227536818170a71bd78de9ac4a9cce8d9b4de0ae19b4634 | Python | 11,769 | 213 | ############################################################################
# Copyright (c) 2022-2026 University of Helsinki
# Copyright (c) 2020-2022 Saint Petersburg State University
# # All Rights Reserved
# See file LICENSE for details.
############################################################################
... |
b86648878dfc1d8ef7bdf20c051ef0c6ae5f1710521c9b67c1b9469a58bb39a4 | Python | 11,775 | 323 | import tensorflow as tf
import numpy as np
import math
from sklearn import preprocessing
from scipy.linalg import toeplitz
dim=2000
eta=0.2
elimination_rate=1
def data(dim):
t=[pow(0.5,i) for i in range(dim)]
Sigmainv=toeplitz(t)
Sigma=np.linalg.inv(Sigmainv)
X=np.random.multivariate_normal(np.zeros(... |
096a6e043dc7cb3dd79dc9140bb22092d37689ac30671436b8e88c2345a62907 | Python | 11,785 | 290 | # 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... |
ae4053ca6d61c31563ef4be2301dc2dc8a16c198d1aee0a587de9082cd975420 | Python | 11,790 | 375 | # -*- coding: utf-8 -*-
# pyNBS_stability.py
# Python 2.7-compatible stability metrics for pyNBS consensus clustering
import os
import numpy as np
import pandas as pd
try:
from sklearn.metrics import silhouette_samples, silhouette_score
SKLEARN_SILHOUETTE_AVAILABLE = True
except ImportError:
SKLEARN_SILH... |
8dd0c69807c70ab27332345533ca798ffa9e864648e64f65e27a77e3036df388 | Python | 11,791 | 260 | import glob
import os
import shutil
from skimage import morphology
from albumentations import (
ShiftScaleRotate, GaussNoise,
RandomBrightnessContrast, Compose, RandomRotate90)
import numpy as np
import tifffile
import torch
from torch.utils.data import Dataset
class DataProcess(Dataset):
"""
Class f... |
b281d488392060d076773c69b6778cafd14ba47418e4c062027331454b24608e | Python | 11,797 | 265 | import os
import sys
import json
from typing import Optional
from argparse import ArgumentParser
import numpy as np
import pickle
from pathlib import Path
from tempfile import mkdtemp
import datetime
import scanpy as sc
import scvelo as scv
import umap
import matplotlib.pyplot as plt
import seaborn as sns
import torch
... |
23b9795d05a9f9b7e53854739bfa08594250234de8f980da0eb5b34ca596278a | Python | 11,799 | 345 | import copy
import os
import pickle
from pathlib import Path
from typing import Optional
import lightning
import numpy as np
import pandas as pd
import torch
from loguru import logger
from torch_geometric.data import Dataset
from torch_geometric.loader import DataLoader
from torch_geometric.utils.convert import from_n... |
7eac886d229a3a4ef7b47a559baf29c1bf471e62cf087a5e18b26cde9d8571e7 | Python | 11,807 | 354 | """Tests for `navis.connected_components` - the one primitive everything else
in the component family now goes through.
The properties worth pinning down are the ones the API *promises*: the labels
are a partition of the elements, they are sorted largest-first (so `== 0` is
always the biggest piece), `element` decides... |
f398a7ec3b1ab92257a7472548b2ab3f66e2566f26981dc160129a20eab0d5fa | Python | 11,807 | 330 | # Copyright (c) Facebook, Inc. and its affiliates.
import collections
from dataclasses import dataclass
from typing import Callable, List, Optional, Tuple
import torch
from torch import nn
from detectron2.structures import Boxes, Instances, ROIMasks
from detectron2.utils.registry import _convert_target_to_string, loca... |
5939ac2e677db96be4a77a4f5d4acb0c1cdd2fd0819b36f0c9a07d16bcdd44da | Python | 11,811 | 289 | from abc import abstractmethod
from lightning.pytorch.core.mixins import HyperparametersMixin
import torch
from torch import Tensor, nn
from chemprop.conf import DEFAULT_ATOM_FDIM, DEFAULT_BOND_FDIM, DEFAULT_HIDDEN_DIM
from chemprop.data import BatchMolGraph
from chemprop.exceptions import InvalidShapeError
from chem... |
b6614f4fff5b0c628147848616f4dce981fe2fbe7b9867e91370cc6fe34aea6c | Python | 11,814 | 332 | """
core/criticality.py
-------------------
Criticality metrics: power-law exponents, DCC, branching ratio, shape collapse.
References
----------
Habibollahi et al. (2022) – tplfit MLE method, DCC definition
Beggs & Plenz (2003) – neuronal avalanche framework
Wilting & Priesemann (2018)– branching ratio estimat... |
afdee60cd0473fc3baf4ef77de574c6caacc62e1b7b72935529a9a2828c85228 | Python | 11,826 | 263 | import numpy as np
import sigpy
from .mtypes import DatBasics
from .utils import scalingArray, saveImage
import os
## RMSE coil combine
def coil_combine(dat_basics : DatBasics, data : np.ndarray, var : str, working_path : str, no_reacq: bool) -> None:
Coils_im = np.abs(np.sqrt(np.sum(np.abs(data * np.conj(da... |
4ae972b0e57281d263c2978236c95489d6f4c96410c5b937d6a29ba5f25a9ea7 | Python | 11,828 | 469 |
""" Logging a single experiment. This module is designed to handle a single
experiment at a time."""
__author__ = "Fabi Bongratz"
__email__ = "fabi.bongratz@gmail.com"
import os
import time
import logging
import functools
import copy
import collections
import inspect
import json
import torch
import wandb
import pan... |
fcb2c5e8d68f0f5169c8389d821768162fbc62f8da75c86ec597d40a37c4db17 | Python | 11,838 | 237 | ############################################################################
# Copyright (c) 2022-2024 University of Helsinki
# # All Rights Reserved
# See file LICENSE for details.
############################################################################
# Splice-site error correction for constructed transcript mo... |
07fef880ec349ee3b5b69ac0e815f72d0fb89387ed3a64db8541878290c57c46 | Python | 11,848 | 374 | # noqa: D100
import base64
import playwright.sync_api
import pytest
from IPython.display import display
from mesa.examples import (
BoidFlockers,
BoltzmannWealth,
ConwaysGameOfLife,
EpsteinCivilViolence,
PdGrid,
Schelling,
SugarscapeG1mt,
VirusOnNetwork,
WolfSheep,
)
from mesa.exam... |
5b18ed9775c63905e64b398449badcd6dbf50e544a55b0a6663e3f4fef75a828 | Python | 11,848 | 294 | import numpy as np
from typing import Dict, List, Optional, Tuple
import torch
from torch import Tensor, nn
from detectron2.data.detection_utils import convert_image_to_rgb
from detectron2.layers import move_device_like
from detectron2.modeling import Backbone
from detectron2.structures import Boxes, ImageList, Instan... |
cbfbf004e26a1272cd2db48bc5c89c1c41df06c082498f9501984f3c08334aef | Python | 11,855 | 312 | """Cell spaces based on Voronoi tessellation around seed points.
Creates irregular spatial divisions by building cells around seed points,
where each cell contains the area closer to its seed than any other.
Features:
- Organic-looking spaces from point sets
- Automatic neighbor determination
- Area-based cell capacit... |
ef685c12ae587848895f18a54dac0340a250a8851820520b68a731ea8c022a63 | Python | 11,858 | 276 | #!/usr/bin/env python3
# Copyright 2004-present Facebook. All Rights Reserved.
import copy
import numpy as np
from typing import List
import torch
from detectron2.config import configurable
from detectron2.structures import Boxes, Instances
from detectron2.structures.boxes import pairwise_iou
from ..config.config imp... |
7559c1086a7d04b534999893bd84509f9f30334cb7672640eeb8d0b1e0931e63 | Python | 11,860 | 310 | """Tests for dotprops construction (tangent vectors + alpha).
`make_dotprops` and `Dotprops.recalculate_tangents` compute these via
`navis_fastcore.dotprops` when it is available and fall back to
`scipy.spatial.cKDTree` + numpy SVDs otherwise. Both paths are exercised here.
Note the two backends are *not* expected to... |
c28d507291d1544cd6919bffbec44622c7591807465b1a849f03a317a1f1204a | Python | 11,868 | 226 | import numpy as np
import pandas as pd
import scanpy as sc
import scvelo as scv
import torch
import pytorch_lightning as pl
from scipy.sparse import csr_matrix
from scvelo.preprocessing.moments import get_moments
def split_data(adata, val_ratio=0.1, test_ratio=0.1):
total_num = adata.shape[0]
val_num = int(tot... |
8b33c76c8022cf64f81d6f5f2f45d506e648b5493ec201d79c82f52c95ceba5c | Python | 11,881 | 346 | """ Created on Wed Sep 6 11:31:57 2023
@author: dcupolillo
Visualization and export functions for imaging data.
This module handles frame visualization, video creation, and image export.
Data persistence functions have been moved to dataloader.py for better
separation of concerns.
""... |
8056722eb046dd8e777209dbf0595bcd2444179b4081ce691fa583e7df53a45b | Python | 11,883 | 322 | #!/usr/bin/env python
#
# Copyright (c) 2021 10X Genomics, Inc. All rights reserved
#
"""Assigns tags to cells."""
from __future__ import annotations
import pickle
from typing import TYPE_CHECKING
import martian
import numpy as np
import pandas as pd
import cellranger.feature.multiplexing.metrics_utils as multi_met... |
2577440feffb5620299bc5a3c716cae6d340c56fd64bab44567961c5f0389a4d | Python | 11,888 | 232 | ############################################################################
# Copyright (c) 2022-2026 University of Helsinki
# Copyright (c) 2020-2022 Saint Petersburg State University
# # All Rights Reserved
# See file LICENSE for details.
############################################################################
... |
cac2914729bddacfdc1c604fd0d861e4eb143c51bf1a9f74b7705e5b9085fa20 | Python | 11,892 | 341 | # 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... |
6f35e60da43c9c7c3aa2fd71c52e451ac898265b6c9b1ccf72f9b90d3b0506e4 | Python | 11,919 | 217 | import os
import warnings
from typing import Union, Tuple, List
import numpy as np
import torch
from batchgenerators.dataloading.data_loader import DataLoader
from batchgenerators.utilities.file_and_folder_operations import join, load_json
from threadpoolctl import threadpool_limits
from nnunetv2.paths import nnUNet_... |
f910ae89250bfde555d43d5dd51e86a6fc83a2c99f66d43c453ab4e57dff4a15 | Python | 11,920 | 352 | """
Pipeline for VTK filters.
"""
# Author: Oualid Benkarim <oualid.benkarim@mcgill.ca>
# License: BSD 3 clause
from .decorators import wrap_input
from .wrappers.algorithm import BSAlgorithm
from .wrappers.data_object import BSDataObject
from .wrappers.utils import get_vtk_name
# From https://vtk.org/Wiki/VTK/Tuto... |
dba5285de7349da62bd89d87761089a9fd1598ddd7f13c5819f6478cdab1f4d0 | Python | 11,930 | 282 | # Copyright (c) Facebook, Inc. and its affiliates.
import numpy as np
import fvcore.nn.weight_init as weight_init
import torch
from torch import nn
from torch.nn import functional as F
from detectron2.layers import ShapeSpec, cat
from detectron2.utils.events import get_event_storage
from detectron2.utils.registry impo... |
4006946592212d64aab8cf69097c16b6ed1421c21b38de03401e69556fb3da9b | Python | 11,932 | 316 | from __future__ import annotations
import argparse
import glob
import json
import os
import tkinter as tk
from tkinter import filedialog
from tkinter import messagebox
from tkinter import simpledialog
from tkinter import ttk
from PIL import Image
from PIL import ImageTk
parser = argparse.ArgumentParser(description='... |
5aadc689ba46faa774d68f5c6c04fa47652f1d9b4e675986b55dc8a20b264fac | Python | 11,943 | 294 | # 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... |
c250eedcf5f48c75ff9c3e2f5e1a30e778f24fb1ae1e6ace4b38f0206e31e8cf | Python | 11,946 | 344 | """
Created on 10/08/2017
@author: Niklas Pallast
Neuroimaging & Neuroengineering
Department of Neurology
University Hospital Cologne
"""
from __future__ import print_function
import os,sys
import numpy as np
from dict2xml import createXML
# from string import split
def parsePV(filename):
"""
Parser fo... |
d615633915b62310204d1e1773644798f7517bfc522e0bbd5dd280e56a47b23a | Python | 11,965 | 356 |
# 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 o... |
5fde24d3b05ff4bc782906582003ecb0cdb7100d688218a6b10de4e4a2f694ea | Python | 11,981 | 320 | import numpy as np
import pandas as pd
from typing import Tuple, List
from sklearn.gaussian_process import GaussianProcessRegressor
from sklearn.gaussian_process.kernels import Matern, WhiteKernel, ConstantKernel
from scipy.stats import qmc
import warnings
warnings.filterwarnings('ignore')
import os
# Find the project... |
84f518aed801db3762911a8c203e52534dba1206bc9b2cad19f064729fb75f43 | Python | 11,983 | 279 | # Copyright 2020 Division of Medical Image Computing, German Cancer Research Center (DKFZ), Heidelberg, Germany
#
# 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://w... |
2a8497e8f52347e201a3b143289b7a9c671ddcaa0790fd7e81b2edf8d5a137c6 | Python | 11,987 | 259 | from . nets import *
import torch
from torch import nn, optim
from . utils import calculate_affinity,target_distribution
import numpy as np
from sklearn.cluster import KMeans
from scipy.sparse import coo_matrix
from sklearn.preprocessing import StandardScaler
from itertools import combinations
from sklearn.decompositio... |
538c8fffc35fdddc7b1a843ae145cf7c11a7c63024d891f47a72acb1b348f3ff | Python | 11,989 | 330 | import os
import glob
import time
from collections import defaultdict
import openai
import PyPDF2
import pandas as pd
import docx
from pptx import Presentation
from PIL import Image
import pytesseract
from openai import error as openai_error
import json
from openai.error import RateLimitError
from dotenv import load_do... |
30522f8a4142986e4b17574b724da855bc89e924c68cbc11476f48b3ed5ee93a | Python | 11,999 | 327 | # 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... |
b645bf7832b19981e77f8f63fdfd833e3586c292f0ec67641ebed7a8d0f8a611 | Python | 12,003 | 329 | #%%
from os import listdir
from os.path import join
import numpy as np
import matplotlib.pyplot as plt
import seaborn as sns
import pandas as pd
import joblib
import sys
sys.path.append('/mnt/obob/staff/fschmidt/cardiac_1_f')
from utils.plot_utils import plot_ridge
from utils.trf_utils import do_boosting, trf2pandas,... |
27519366d7be45d92bf7209389e352321abe4111f5a1bead1151fb2c5ea3517d | Python | 12,017 | 245 | """Shape and dtype round-trips through the multi-output predictors.
These use tiny randomly-initialised checkpoints rather than trained weights: the
point is that every input shape survives tiling, prediction and stitching, in
particular shapes smaller than the patch, which used to reach the network with
sizes the dec... |
1ee6b1942204ddac777aad978c6b17df67b6d02be588760ea1d392df4a60f2ea | Python | 12,026 | 382 | import os
import matplotlib.patches as mpatches
import matplotlib.pyplot as plt
import numpy as np
import pandas as pd
import seaborn as sns
from src.chem import compute_motif_enrichment_table, motifs
from src.graphs import style_violins, violin_prune_outliers
from src.io import BenchmarkResults
from src.stats import... |
7d3cb320bc862d9bd18d43c90d14b75f7b5f6e09c233dd735bba26d45a9341aa | Python | 12,036 | 305 | # -*- coding: utf-8 -*-
# Copyright (c) Facebook, Inc. and its affiliates.
# pyre-unsafe
import csv
import logging
import numpy as np
from typing import Any, Callable, Dict, List, Optional, Union
import av
import torch
from torch.utils.data.dataset import Dataset
from detectron2.utils.file_io import PathManager
fro... |
ebe0af29e8a77da247e05842de39d1e6e144846dbd486ed34500d7c71fd0e363 | Python | 12,038 | 328 | 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 PyQt5.QtWidgets import *
from PyQt5.QtGui import *
from PyQt5.QtCore import *
import pandas... |
5d2e4f592a795da4a7f549ad2db446057391be150939029649bcd9e7285364c2 | Python | 12,050 | 294 | #!/usr/bin/env python
#
# Copyright (c) 2019 10x Genomics, Inc. All rights reserved.
#
import math
import os
import martian
import cellranger.analysis.constants as analysis_constants
import cellranger.rna.library as rna_library
from cellranger.matrix import CountMatrix
from cellranger.molecule_counter import Molecul... |
3c02d290f45c06b3d517f866ae4b9fc4e7fe39155ce8efc6ed1eafa8525e5900 | Python | 12,058 | 211 | import multiprocessing
import os
from time import sleep
from typing import List, Type, Union
import numpy as np
from batchgenerators.utilities.file_and_folder_operations import load_json, join, save_json, isfile, maybe_mkdir_p
from tqdm import tqdm
from nnunetv2.imageio.base_reader_writer import BaseReaderWriter
from... |
f80bc8f92f173b0ee216137ca23cc1d7c0dfc23184985ca8dcba7ec44f5793c2 | Python | 12,074 | 335 | """
Population coupling analysis for control animals.
Adapted from pop_coupling_v2.py for experimental animals.
Computes STPR (spike-triggered population rate) and shuffle-normalized
population coupling (pc_norm) — matching the experimental pipeline output.
Uses session_responses.pkl for PL/NPL classification ... |
fe11b8241028d0561bbaf2f55a9b1ec88bef516daf839a3f416080b9b922a1df | Python | 12,121 | 278 | #python diffExprDIANN.py F:\promec\TIMSTOF\LARS\2025\250107_Hela_Coli\DDAreport.parquet_Ms1_Area_pivot_all.csv
#python diffExprDIANN.py F:\promec\TIMSTOF\LARS\2025\250107_Hela_Coli\reportDDA.parquet_Ms1_Area_pivot_all.csv
import sys
import pandas as pd
import numpy as np
import matplotlib.pyplot as plt
import seaborn a... |
a72b57b46503be12ad615a832fcaac50c32a8f2aaaef9c6c673ff9feb1a5cbac | Python | 12,141 | 266 | import glob
import os
import shutil
from skimage import morphology
from albumentations import (
ShiftScaleRotate, Blur, MultiplicativeNoise,
RandomBrightnessContrast, Compose, RandomRotate90)
import numpy as np
import tifffile
import torch
from torch.utils.data import Dataset
class DataProcess(Dataset):
... |
ff01cf8d53cac005c77ff543aac2779cc80cb34838423241eadaea2e8eca260f | Python | 12,145 | 267 | '''
Created on Nov 7, 2024
@author: voodoocode
'''
import os
import numpy as np
import scrubber.core
import csv
IN_PATH = "/mnt/data/Professional/LMU/data/Beta-prevalence/database6/original/"
OUT_PATH = "/mnt/data/Professional/LMU/data/Beta-prevalence/database6/scrubbed/"
COLLECTION_META_PATH = "/mnt/data/Professio... |
ac4602b2983ef73c6e6ada8ef5eb5de69a93391b23ed938d95b2ce88f02104a0 | Python | 12,146 | 400 | """
Utility functions for plotting.
"""
# Author: Oualid Benkarim <oualid.benkarim@mcgill.ca>
# License: BSD 3 clause
from itertools import product as iter_prod
import collections
from collections import namedtuple
import numpy as np
class PTuple(collections.abc.Sequence):
def __init__(self, *args):
s... |
0ec700eadd2fd43cc7b7e5994c8118f3c80525f14d2ed40aced16e138168fe44 | Python | 12,155 | 289 | import numpy as np
import torch as tc
import torch.nn as nn
from argparse import Namespace
import os
class RNN_Model(nn.Module):
def __init__(self, args: Namespace = None):
super(RNN_Model, self).__init__()
if args is not None:
self.args = args
tc.manual_seed(args.run)
... |
f3f25c4febf64d01ef42f967dc5cf10f6856bf3aa92d26f09803ad408169da9b | Python | 12,164 | 284 | import argparse
from pkg_resources import resource_filename
from pangolin.model import *
import vcf
import gffutils
import pandas as pd
import pyfastx
# import time
# startTime = time.time()
IN_MAP = np.asarray([[0, 0, 0, 0],
[1, 0, 0, 0],
[0, 1, 0, 0],
[0... |
703ddd7ca318d8de48bfb353e5f81f3578ef4d08ebdd7be6580f260ec5049217 | Python | 12,166 | 347 | """
Implementation of Spin permutations.
"""
# Author: Oualid Benkarim <oualid.benkarim@mcgill.ca>
# License: BSD 3 clause
import numpy as np
from scipy.optimize import linear_sum_assignment
from scipy.spatial.distance import cdist
from scipy.spatial import KDTree
from sklearn.utils import check_random_state
from s... |
3bd9ee948e8d4638e6171fbc97c22757e428ff05c86ae36a7cd7bffd9eb5914f | Python | 12,171 | 344 | """Base Scenario class."""
from __future__ import annotations
import warnings
from collections import defaultdict
from collections.abc import Sequence
from functools import partial
from itertools import count
from typing import Any, ClassVar
import numpy as np
import pandas as pd
SeedLike = int | np.integer | Seque... |
4370a06a7fef79ba00780f7e5d0f9854cccf70b26bf8168e36a21be09ac1cf2d | Python | 12,185 | 298 | # Copyright (c) Facebook, Inc. and its affiliates.
from typing import List
import fvcore.nn.weight_init as weight_init
import torch
from torch import nn
from torch.nn import functional as F
from detectron2.config import configurable
from detectron2.layers import Conv2d, ConvTranspose2d, ShapeSpec, cat, get_norm
from d... |
dcbfbc4760dcc5ffadc4a7ea32bb1f1800f8f42ecc31feed68417c9c0267d362 | Python | 12,195 | 351 | # 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... |
5aff7fd59a4d721b805dbd7d5b75a05ec2844094adcb63a53ef77dc1909c0a02 | Python | 12,198 | 358 | from __future__ import division
import munge_sumstats as munge
import unittest
import numpy as np
import pandas as pd
import nose
from pandas.util.testing import assert_series_equal
from pandas.util.testing import assert_frame_equal
from numpy.testing import assert_array_equal, assert_array_almost_equal, assert_allclos... |
c5ce73743ba8be141e2cbe0b065f0852275365f0265380ce46531c0fb454e33a | Python | 12,199 | 287 | # Copyright (c) Facebook, Inc. and its affiliates.
import itertools
import logging
import math
from collections import defaultdict
from typing import Optional
import torch
from torch.utils.data.sampler import Sampler
from detectron2.utils import comm
logger = logging.getLogger(__name__)
class TrainingSampler(Sample... |
c0f65b5b8e871fb6b65996d301213e636bd7993614b91ed6a9706a4acb959c1f | Python | 12,232 | 275 | from __future__ import annotations
from time import sleep
from typing import Optional
import logging
import numpy as np
from concurrent.futures import ThreadPoolExecutor, Future, wait
from queue import Queue
from threading import Thread
from .data_io import load_dat_basics
from .motion import prepare_tcl_data
from .ut... |
c788495d09a957f5b8e07d424af8dbffdebde191618146af1ec641b9b667bb0d | Python | 12,260 | 383 | """Data loading and I/O operations for imaging datasets.
Created on January 21, 2026
@author: dcupolillo
"""
from __future__ import annotations
from pathlib import Path
import numpy as np
import flammkuchen as fl
from spyne.core.imaging.load import (
load_metadata_from_tiff, load_imaging_data_from_tiff)
class I... |
d94bfc818bffd42f391bbde687212c64c9e40030731d87d0c98e530de2e8200d | Python | 12,269 | 274 | 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 scanpy.external as sce
from scipy.io import mmwrite, mmread
np.random.seed(42)
# peak-gene linkage matrix
dir_path = "/home/nomura/Proj/mmvelo/data/10x_mult... |
9d27d729b771edc3bc57f2d0140fffd0d314896638b0560aa6d0bc5b43031748 | Python | 12,283 | 200 | import os
import sys
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
import anndata as ad
import scanpy as sc
import scvelo as scv
from scipy.io import mmwrite, mmread
import seaborn as sns
import scipy
np.random.seed(42)
dir_path = "/home/nomura/Proj/mmvelo/experiments/Greenleaf_multiome_Cond_... |
e3c592d36851dca5f76ad363b2229b406b5ddd29c07d048566dd36c03b53506a | Python | 12,305 | 381 | from __future__ import annotations
import platform
import re
import subprocess as sp
import sys
import tempfile
from pathlib import Path
from typing import Any, Final, Literal, TypedDict
import copier
import more_itertools as itx
import pathvalidate
import pytest
import requests_mock
from hypothesis import HealthChec... |
02cfdd25ecdb895a4ffe055418af04449107518fc65764dfbd04d6d9614e800a | Python | 12,307 | 341 | #!/usr/bin/env python
# Copyright 2016-2019 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... |
0f8b1aa40bfb0f4a35283701259315a549ff5bba9ad3d273499ca1fd67c89709 | Python | 12,310 | 345 | """
Created on 10/08/2017
@author: Niklas Pallast
Neuroimaging & Neuroengineering
Department of Neurology
University Hospital Cologne
"""
import sys,os
import nibabel as nii
import numpy as np
import nipype.interfaces.fsl as fsl
import glob
import shutil
#makes sure to import bet.py
sys.path.insert(0, os.path.abspat... |
ba3aac23bf471967ad77535ee6c51bed2b0b93083a0a64d83789a8e279116bb0 | Python | 12,330 | 325 | """Tests for the per-worker thread cap in `navis.compute.threads`.
navis spreads work over processes; navis-fastcore (and BLAS, and OpenMP) spread
it over threads. Nothing tells a worker that it is one of twenty, so without a
cap the two multiply - 20 workers x 224 threads over 224 cores, which measured
*slower* than ... |
9c00fcc7d3951382d67b54ec25803a667174a10afa04272eea42e94eb724fefb | Python | 12,336 | 337 | from copy import deepcopy
import navis
import numpy as np
import pandas as pd
import pytest
def test_deepcopy():
nrn = navis.core.BaseNeuron()
deepcopy(nrn)
@pytest.mark.parametrize("op", ["mul", "truediv", "add", "sub"])
def test_mesh_math_connectors(op):
"""Arithmetic must not choke on integer conne... |
40f63bb6c982a96e4978b679bb52efbf21782bddc52eea306c1eb2325da51eba | Python | 12,353 | 184 | # AUTOGENERATED! DO NOT EDIT! File to edit: 44_inference_summaries.ipynb (unless otherwise specified).
__all__ = ['posterior_dict_to_table', 'invert_dict', 'construct_summary_dict', 'model_fit_summary_to_table',
'construct_target_summary']
# Cell
from ..utilities import progbar
from arviz import psislw
imp... |
98f7731353faeab501a05d6b6a5c676cf40a195fe7e2563be605e287dda2a7ce | Python | 12,376 | 349 | """Tests for `Mesh.extra_edges` - edges that are not part of any face.
These express connectivity that the mesh surface itself does not have (e.g.
bridges between disconnected fragments). Two things need testing: that the
edges survive the things we do to neurons (storage/invariants), and that the
code deriving connec... |
ba67411882aa6ebe580049d5f6d3246368060aee8d87e2639870e47a56fcf963 | Python | 12,378 | 314 | import numpy as np
from sklearn.linear_model import Lasso, LogisticRegression
class ALasso(Lasso):
"""Implementation of the adaptive lasso algorithm (ALasso).
This weighted Lasso updated weights iteratively.
The implementation structure is inspired by the sklearn implementation of the Lasso algorithm.
... |
826072899229a95042adb024eca3fb2b11f2e5c58c8286237bd6d67047a77264 | Python | 12,382 | 321 | # 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... |
35ce2b03d6d4490a58dbce04de24cfa1051cf7218e78446c447ff66e28d9fd9e | Python | 12,384 | 286 | """
calculate_dice - Segmentation Overlap Measurement Tool
Part of the micaflow processing pipeline for neuroimaging data.
This module calculates the DICE coefficient (Sørensen-Dice coefficient) between
two segmentation volumes. The DICE score is a statistic used for comparing the
similarity and diversity of s... |
f30ff521b0ddb06679d131a64189ac0889d2a89bc247d4cd4dc722969bbac44e | Python | 12,397 | 336 | #
# Copyright (c) 2023 10X Genomics, Inc. All rights reserved.
#
"""Code to make a VDJ reference."""
from __future__ import annotations
import collections
import hashlib
import os
import shutil
from typing import AnyStr
import pysam
from six import ensure_binary
from cellranger import constants as cr_constants
from... |
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