sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
5dccee429ce49ffb690497b22d78bdaf3be58ba1b3f7c399dd37b5b0c4cf8e77 | Python | 11,317 | 276 | from sklearn.metrics import accuracy_score, precision_score, recall_score, f1_score, confusion_matrix
from matplotlib import pyplot as plt
import numpy as np
import random
import pandas as pd
import seaborn as sns
from scipy.stats import pearsonr
import os
from data.loader import *
import h5py
#from models import mode... |
60a1f59e528572a908af358e44e9a4172bbccf8fedf02ce862661aa0443d8fe8 | Python | 11,325 | 314 | # -------------------------------------------------------------
# Subgrid Optimization
# Copyright (c) 2026
# Dirk Keller, Nick Ramsey's Lab, University Medical Center Utrecht, University Utrecht
# Licensed under the MIT License [see LICENSE for detail]
# ----------------------------------------------------------... |
72c779e936c76c26f62c39ed0af17ec58a6679380d9bf01a08024efc631b3505 | Python | 11,327 | 338 | from collections import defaultdict
import itertools
import json
import os
import posixpath
import re
import requests
import numpy as np
from tqdm import tqdm
from cloudfiles import CloudFiles
from ....lib import red, toiter, Bbox, Vec, first, nvl
from ....mesh import Mesh
from .... import paths
from ..sharding imp... |
a054f8f013c3d8b8229c25385f032b53c1f467a6f20fb7ee38192df6984c1915 | Python | 11,387 | 314 | from PyQt5.QtCore import QTimer, Qt
from PyQt5.QtWidgets import (
QApplication,
QWidget,
QMainWindow,
QDockWidget,
QVBoxLayout,
QGridLayout,
QPushButton,
QLabel,
QProgressBar,
QFileDialog,
QCheckBox,
)
from state import ExperimentState, ScanningParameters, frame_duration
from... |
d8c3fa94868adde27362dccce1157b175b69cf76744ac3ebc9af73dfc4680a6b | Python | 11,392 | 286 | # -*- coding: utf-8 -*-
"""
Created on Tue May 20 13:11:58 2025
@author: Usuario
"""
#Librarires
import os #For importing images and saving figures
import errno # for checking whether the montage direcotry already exists
from cellpose import models, io #Cellpose ML model for single cell segmentation
from c... |
ef1000d34e61a8a837b68962a3630e4ea7e924ef857db207a25938085f88ecf1 | Python | 11,453 | 307 | import json
import pathlib
import typing
from dataclasses import asdict, dataclass
from enum import Enum
class TestResult(str, Enum):
ABORTED = "aborted"
FAILED = "failed"
COMPLETED = "completed"
@dataclass(slots=True)
class TestFile:
name: str
subfolder: str | None
exists_in_ref: bool
e... |
a467aa3d884977ebc8e73382b2cb0d82ffccc5e91e4b2f23f5339581fcd882a1 | Python | 11,462 | 323 | import argparse
import json
import matplotlib.dates as mpd
import matplotlib.pyplot as plt
import os
import pathlib
import typing
from datetime import datetime, timedelta
from tetra.database import DBWrapper
from tetra.utilities import get_env_or_raise
def download_results(project: str, graph_history: int):
# Ma... |
9bc41b8875ef580200f6d7ea4f2125720343177ed87c9a5fb45a3a5ad0672d3c | Python | 11,759 | 362 | #!/usr/bin/env python
"""
TODO:
- define __all__ or limit available functions in some other way.
"""
import numpy as np
import pandas
from argparse import ArgumentParser
try:
# python < 3.3
from collections import Iterable
except ImportError:
# python >= 3.3
from collections.abc import Iterable
from ... |
5b0f41c9cdfd4641bc0d14f6660e21a4578ad93383301a43fbf28d4756beb35c | Python | 11,897 | 354 | """
Precomputed Annotation Reader code adapted from
a mixture of these two repositories:
https://github.com/fcollman/precomputed_python
https://github.com/google/neuroglancer/
"""
from typing import Optional, Union, Iterable
import os
import posixpath
from cloudfiles import CloudFiles
import numpy as np
import nump... |
5837dee3077d295d7609333e5f397782b8b7be7de7a798e526512493c3d554b8 | Python | 12,083 | 332 | # -*- coding: utf-8 -*-
"""
Created on Tue Nov 5 17:19:50 2024
@author: simon
"""
import numpy as np
import matplotlib.pyplot as plt
from plotting_functions import my_style
import seaborn as sns; sns.set_theme()
import pickle
import pandas as pd
import pathlib
# Get the path of the current script
ba... |
3f87dbb5ecf25f34fd2a7d845a3765431f97559d1c2c1712343ea9fd844230cd | Python | 12,107 | 295 | """
Cerebellar normalization and isolation using ANTsPy
@authors: Yaping Wang, Jorn Diedrichsen
"""
import sys
import argparse
import os
import nibabel as nib
import ants
import numpy as np
import pandas as pd
from nibabel.affines import apply_affine
import nitools as nt
from SUITPy.isolation import img_read
def nor... |
33a42a35d17e0b7d62a39e9918c6bacef787c16a71b435a5286f54294a7c9070 | Python | 12,357 | 396 | """nonlinear case."""
import os
os.environ["JAX_PLATFORM_NAME"] = "cuda"
os.environ["XLA_PYTHON_CLIENT_MEM_FRACTION"] = "0.4"
import jax
jax.config.update("jax_enable_x64", True)
import jax.numpy as jnp
import jax.random as jr
import equinox as eqx
import sys
sys.path.append('..')
from utils.sde import SDEIntegrator... |
4813d3c0110ca4d1faa7ca2bb48663abf630d8739db200bff6992ba68a37d392 | Python | 12,441 | 361 | # This script is part of mousebrains (http://www.github.com/schlegelp/navis-mousebrains).
# Copyright (C) 2020 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, ei... |
de634b292ce6737acffd785dcfebe54990cef5685c3d0032acb8b4f549a632d7 | Python | 12,520 | 306 | import argparse
import pathlib
import shutil
from dataclasses import dataclass
from enum import Enum
from tetra.reformat_files import reformat_files
from tetra.regression_manager import ManagerData, RegressionManager, TestResult
"""
To update regression test reference data:
1) Run the regression test(s) to produc... |
7a53a7f3864fe8da9bfa8e9a5cd9c9e2079d50f9ad295e4d14d8a10e290a30f1 | Python | 12,542 | 349 | from __future__ import print_function, unicode_literals, absolute_import, division
import numpy as np
import os
from skimage.measure import regionprops
from csbdeep.utils import _raise
from tqdm import tqdm
from ..utils import path_absolute, _normalize_grid
from ..matching import _check_label_array
# from ..lib.stard... |
c242207a234b40ef37e97d43c86db0066c4fa9f3f273cef59c62561290c73d9f | Python | 12,647 | 411 | from typing import Optional
import copy
import re
import os
import numpy as np
from cloudfiles import CloudFiles
import cloudfiles.compression
from .. import (
autocropfn, readonlyguard,
ImageSourceInterface, check_grid_aligned,
generate_chunks
)
from ...types import CompressType, MipType
from ... import com... |
a9d9eb5e1c69319b822b3969ab8e070ec3a238a6e9b8b56bd6281710d945e84d | Python | 12,713 | 323 | from dataclasses import dataclass
import os
import pathlib
import contextlib
import subprocess
import shutil
import typing
import unittest
from copy import deepcopy
from data_paths import (
PLATFORM,
INPUT_FOLDER,
OUTPUT_FOLDER,
REFERENCE_FOLDER,
)
from utilities import DEBUG, run_dorado, make_summary... |
98bcc0b1fb9aedf4ac6ca7fea275219fe41d9e016a5d075c0345db57b9442350 | Python | 12,809 | 319 | #! /usr/bin/env python3
import pathlib
import shutil
import unittest
from tetra.data_checker import DataChecker
from tetra.regression_manager import TestData, TestFile
from tetra.sequence_utils import USE_PYSAM
class TestDataChecker(unittest.TestCase):
KEEP_OUTPUT_DATA = False # Set to True to keep files for ... |
33932d7850646d9241f0ce56d70a2a7ef128bbb3b3fe0cafad76a57635a55481 | Python | 12,987 | 467 | # -*- coding: utf-8 -*-
"""MRI non-linear operators.
This module contains these non-linear operators:
* Nlinv,
joint coil sensitivity maps and image content.
* Diffusion,
exponential diffusion modelling and parallel imaging sampling.
* MGRE,
multi gradient echoes.
Author:
* ... |
2d3f309cadc245a3a534444ae706c9e2e69d3c2489656d921b366c1c6b395d22 | Python | 13,002 | 297 | ################################################################################
# 1. INITIATE ENVIRONMENT #
################################################################################
import streamlit as st
from streamlit_extras.stylable_container import stylab... |
d244913be4b7babfc2224c923913d58d935621bd7d9b2406eac836b48e1fd856 | Python | 13,062 | 421 | """20D nonlinear case.
The target uses one double-well coordinate coupled to the remaining
coordinates through a nonlinear 20D potential.
"""
import os
os.environ.setdefault("JAX_PLATFORM_NAME", "cuda")
os.environ.setdefault("XLA_PYTHON_CLIENT_MEM_FRACTION", "0.48")
import jax
jax.config.update("jax_enable_x64", Tr... |
e8a990ba6c853041b644766bcf6f6522a181a11cc20214772f5518bb96339694 | Python | 13,081 | 346 | # -------------------------------------------------------------
# Subgrid Optimization
# Copyright (c) 2026
# Dirk Keller, Nick Ramsey's Lab, University Medical Center Utrecht, University Utrecht
# Licensed under the MIT License [see LICENSE for detail]
# ----------------------------------------------------------... |
8569c57035aaa0141b49f93fdfd5161348dfdb3a4391a1ef16b100c6526b8401 | Python | 13,166 | 359 | """
Read all CSV log files from /dls_sw/i23/logs/GoniOwl, run fresh GoniOwl
inference on each ECAM_6 image, and produce:
- Annotated images saved as {confidence}_{decision}_{original}.png
- A CSV summary of all results
- Confidence histograms split by human decision (pin on vs pin off)
Example:
python infer_al... |
e7a083774f088d8fb195291583d03d543d05330e87fc5b8d5285b5589d99e51b | Python | 13,179 | 343 | import pathlib
import typing
from collections import defaultdict
from Bio import SeqIO
from tetra.utilities import get_platform
USE_PYSAM = True
try:
import pysam
except Exception:
USE_PYSAM = False
def compare_fastq_files(file_a: pathlib.Path, file_b: pathlib.Path) -> tuple[bool, str]:
record_dict_a =... |
04353e2ec49f97d1c6378aba381f44a59379ca662c112fe4373f746356ec052e | Python | 13,205 | 358 | ###############################################################################
# This library provides utilities for duplicating two-sided and exchange
# reactions in a SBML model. Examples of use are given in the notebook
# Duplicate_Model.ipynb
# Author: Leon Faure, leon.faure@inrae.fr
#############################... |
5e310c8d2a482a7d3a45aea96a4cee232fdb308bf6cbebc26c48fe34d4a1d56e | Python | 13,288 | 332 | """Drosophila developmental stage"""
import requests
from pydantic import BaseModel, ConfigDict
from aind_data_schema_models.registries import Registry
"""Drosophila developmental stage"""
class DrosophilaDevelopmentalStageModel(BaseModel):
"""Base model for drosophila developmental stage"""
model_config ... |
a1355fd6d5ae9ca4d1a911232fb2c163e9410f89c6818324b9adb8e39b11d9a7 | Python | 13,364 | 556 | import pytest
import operator
from functools import reduce
from cloudvolume import CloudVolume, Skeleton
from cloudvolume.storage import SimpleStorage
from cloudvolume.datasource.precomputed.image.common import (
gridpoints
)
from cloudvolume.datasource.precomputed.common import (
compressed_morton_code
)
from cl... |
6f6f7cf3d31e0f045b43fa541f48594368258a61918a359ccf48717d51ee4e2d | Python | 13,473 | 327 | #! /usr/bin/env python3
import pathlib
import shutil
import subprocess
import unittest
from datetime import datetime
from tetra.sequence_utils import USE_PYSAM
def run_with_timeout(cmd_args: list[str], timeout: int, verbose: bool):
try:
if verbose:
print("Command line:", " ".join(cmd_args))
... |
37bdce0bc1012fd7197096eca6c59510d5d4a6716ceceb817407bbb447d266e8 | Python | 13,733 | 394 | import os
import shutil
import json
import socket
from time import sleep
from docker import APIClient as Client
from docker.types import Mount
import docker
from airflow.exceptions import AirflowException
from airflow.plugins_manager import AirflowPlugin
from airflow.models import Variable
from airflow.providers.docker... |
75460ee123536b3e08508158190bf9b42a6ce7134c625f1f827505fd7b1d1df3 | Python | 13,762 | 475 | from functools import partial
import fastremap
import numpy as np
import psutil
from tqdm import tqdm
from cloudfiles import CloudFiles, reset_connection_pools, compression
from cloudvolume import lib, chunks
from cloudvolume.exceptions import AlignmentError
from cloudvolume.lib import (
mkdir, clamp, xyzrange, V... |
1c4d06ff8f91c04e28a22d61c7dea5055ce4661aa9a04f497efe8c81c2b193d8 | Python | 13,891 | 480 | from typing import Literal, NamedTuple, Optional, Union, Any, cast, Iterable
from collections import OrderedDict
from dataclasses import dataclass
import posixpath
import os
from cloudfiles import CloudFiles
import numpy as np
import numpy.typing as npt
from ....types import CacheType, StrEnum
from ....lib import ... |
aab548c9b041945f5b4ce4fe84ad0f15c94716a2a3d45cd6da34c32e6769949a | Python | 14,165 | 451 | '''
pymmh3 was written by Fredrik Kihlander and enhanced by Swapnil Gusani, and is placed in the public
domain. The authors hereby disclaim copyright to this source code.
pure python implementation of the murmur3 hash algorithm
https://code.google.com/p/smhasher/wiki/MurmurHash3
This was written for the times when y... |
4cc7a40684ed207fc8ee1ebad47769abdb0cf542fd8517437f104fe695f3baa1 | Python | 14,172 | 465 | import posixpath
from collections import namedtuple
import json
import re
import requests
import urllib
import numpy as np
from ...lib import Vec, Bbox
from ... import exceptions
from ... import paths
from ...secrets import cave_credentials
from ..precomputed import PrecomputedMetadata
VERSION_ORDERING = [
'1.0'... |
2f68e82aa1c02c2346b3f51495af1f00ea57810a6859b48b2db178dcc7fb476a | Python | 14,273 | 364 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Thu Jun 26 11:09:21 2025
@author: joaquin
"""
import os
import errno # for checking whether the montage direcotry already exists
import matplotlib.pyplot as plt
import skimage.morphology as morph
from skimage.filters import threshold_local, threshold_otsu, ... |
d2acf6b6170841ecc801d448ba140438b8f61fca30220a19cefc497337e1d3b7 | Python | 14,616 | 343 | """ Quality control for ecephys pipeline """
import os
import sys
import argparse
import json
import numpy as np
import time
import logging
from pathlib import Path
import spikeinterface as si
import spikeinterface.preprocessing as spre
# AIND
from aind_data_schema.core.processing import Processing
from aind_data_s... |
8a3cc540784ef81b0434cb9fb3f5aa69ce52831bc716bc3ee2fd8cf0714a6832 | Python | 14,907 | 355 | import opensoundscape
from opensoundscape.preprocess.preprocessors import SpectrogramPreprocessor
from opensoundscape.ml.datasets import AudioFileDataset
from opensoundscape.ml.utils import collate_audio_samples_to_tensors
import torch
import torch.nn as nn
import numpy as np
import pandas as pd
import sklearn
import ... |
1a7c61d16609a11623f1cb4709fdfd62278ed7588d925602aa6ebeab86d88bdc | Python | 14,968 | 361 | """Human developmental stage"""
import requests
from pydantic import BaseModel, ConfigDict
from aind_data_schema_models.registries import Registry
"""Human developmental stage"""
class HumanDevelopmentalStageModel(BaseModel):
"""Base model for human developmental stage"""
model_config = ConfigDict(frozen=... |
f01e341091742426828d555ca2c715589985cbad73538fc11ea6308b0aa96a47 | Python | 14,996 | 375 | #!/usr/bin/env python
"""
Automated state annotation using a combination of linear
discriminant analysis (LDA) and hidden Markov model (HMM).
"""
import pickle
import numpy as np
from pomegranate import (
MultivariateGaussianDistribution,
HiddenMarkovModel,
)
from sklearn.discriminant_analysis import LinearDi... |
5d85bb48b0b71c4a98a20e3cd38570971db8f26433730c23555b6a8e2570b597 | Python | 15,044 | 405 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Module to importing cerebellar atlases and templates from the [cerebellar atlas
repository](https://github.com/DiedrichsenLab/cerebellar_atlases)
@authors: Jorn Diedrichsen, Vahid Ashkani
"""
import os
import json
import numpy as np
import nibabel as nib
import pandas... |
45fd72aafbb296ec2b4c943d3c7e1c9bd5b4a1fa317a838bf87a28d50cd3ce01 | Python | 15,086 | 525 | from collections import defaultdict
import json
import os.path
import posixpath
import re
import boto3
import botocore
from glob import glob
import google.cloud.exceptions
from google.cloud.storage import Batch, Client
import requests
import tenacity
from cloudvolume.connectionpools import S3ConnectionPool, GCloudBuc... |
851ec23449831acda158ac666268fcde8c787e2d4ae786618caba61af1e0d673 | Python | 15,110 | 344 | import math
import random
from sklearn.base import TransformerMixin
from sklearn.preprocessing import StandardScaler, RobustScaler, MinMaxScaler, LabelEncoder
from torch.utils.data import Dataset, DataLoader, TensorDataset, ConcatDataset
import matplotlib.pyplot as plt
import scipy
import statistics as st
import os
imp... |
8f17b0bb4e615e104f962c5cfbf6eada064420ab4ecef0e18bec7eef8c400712 | Python | 15,153 | 547 | # -*- coding: utf-8 -*-
"""
Created on Fri Jul 14 23:28:15 2017.
@author: spiros
"""
import numpy as np
import sys
import pandas as pd
from scipy import signal
def spatial_info(rate_matrix, time_bin):
"""
Spatial information index.
Parameters
----------
rate_matrix : np.ndarray
Firing-r... |
12241edea1637687e761021421415812b07e0d63628f107689b5dba0865837cb | Python | 15,455 | 513 | from functools import partial
import tempfile
import cloudvolume
import numpy as np
import shutil
import posixpath
import pytest
import os
from scipy import sparse
import sys
import json
import re
tempdir = tempfile.mkdtemp()
TEST_PATH = "file://{}".format(tempdir)
TEST_DATASET_NAME = "testvol"
PRECOMPUTED_MESH_TEST_... |
00992e40dc428e41a780bd3518f90530dda62c894df2a230274c27b3eab4d218 | Python | 15,551 | 476 | """
MUSE Reconstruction.
Author: Zhengguo Tan <zhengguo.tan@gmail.com>
"""
import numpy as np
import sigpy as sp
from sigpy import backend
from sigpy.mri import app, retro, sms
from sigpy.mri.dims import *
# %%
def _denoising(input, full_img_shape=None, use_iter=True, max_iter=5):
"""
Args:
input: ... |
91339c2a188e31912f63671856efbcf3ae5e862fc0edc52d4a238f6009e9f4c9 | Python | 15,605 | 493 | import copy
from typing import Dict, Tuple, Sequence, Union, Optional
import numpy as np
from tqdm import tqdm
from cloudfiles import CloudFiles, compression
from cloudvolume import lib, exceptions
from ....types import CompressType, MipType
from ....lib import Bbox, Vec, sip, first, BboxLikeType, toiter, xyzrange
f... |
1956361c647b09ca270263372c48169bdd6151e696baccfca4afabfb93e5d64a | Python | 15,848 | 382 | import numpy as np
import os
import time
import sys
import argparse
import errno
from collections import OrderedDict, defaultdict, Counter
from tqdm import tqdm
import random
import torch
import torch.nn as nn
import torch.optim as optim
from torch.utils.data import Dataset, DataLoader, TensorDataset, ConcatDataset
... |
e31c957f4665dea86cbbcbd2a4b71a13e5c1d4bc170682a6699628d038a0a914 | Python | 15,891 | 527 | import copy
import re
import struct
import sys
import numpy as np
from .exceptions import MeshDecodeError
from .lib import Vec, Bbox
def is_draco_chunk_aligned(verts, chunk_size, draco_grid_size):
"""
Return a mask that for each vertex is true iff it is within
half a draco_grid_size from a chunk border.
"""
... |
3244d1b0590e8bc3d1d1b3190e7c9e5067b01812a7cc7ce06d877823a609f076 | Python | 16,107 | 363 | import torch
import torch.nn as nn
import math
import warnings
import random
import numpy as np
from collections import OrderedDict
from functools import partial
from itertools import repeat
from models.drop import DropPath
def _no_grad_trunc_normal_(tensor, mean, std, a, b):
# Cut & paste from PyTorch official ma... |
4d40c82187e9d8f3f34d216e8e00f17c03d895185c63d4b8785a3e67a2733ddf | Python | 16,158 | 345 | # -*- coding: utf-8 -*-
"""
Created on Tue Aug 5 11:15:40 2025
@author: simon
"""
import numpy as np
import os, sys
import pickle
import pandas as pd
import pathlib
from scipy.signal import find_peaks
from scipy import cluster
# Get the path of the current script
base_path = pathlib.Path().resolve... |
47e0ac4ebb32922f463f854c0d10723a2934067ee6b536332009fe4b8191b64d | Python | 16,316 | 543 | #!/usr/bin/env python
# coding: utf-8
# # P0 Het and Ko analysis Replicate 1
# AT Updated 8/8/24
# ## Section 1: Load in data and concatenate datasets if applicable
# Import libraries
import numpy as np
import pandas as pd
import scanpy as sc
from sklearn.cluster import KMeans
from sklearn.metrics import silhou... |
2f847cd432c9cdaee3926cf303fdfe3db120add17b01110da848ce6b409b26d1 | Python | 16,399 | 470 | """
grouped_pattern.py
GroupedPatternDataset
---------------------
Purpose
^^^^^^^
This Dataset loads **pre-saved PyTorch tensors** (`.pt`) and groups samples by a shared
**Pattern ID (PID)** so you can build pattern-aware batches (e.g., batches containing
multiple different patterns instead of many samples from one ... |
a18cf59482f649e0d7e4a1778a3f37f23dcf49a0b7c8a372f53bb0e8774e6c61 | Python | 16,461 | 517 | #!/usr/bin/env python
# coding: utf-8
# # P0 Het and Ko analysis Replicate 2
# AT Updated 8/8/24
# ## Section 1: Load in data and concatenate datasets if applicable
# Import libraries needed
import numpy as np
import pandas as pd
import scanpy as sc
from sklearn.cluster import KMeans
from sklearn.metrics import... |
7216759a63e399faf160e6c13983eaa54febdb634f3ca990adf37a24b8ef4120 | Python | 16,620 | 408 | import warnings
warnings.filterwarnings("ignore")
# GENERAL IMPORTS
import os
import sys
import argparse
import json
from pathlib import Path
import time
import logging
from copy import deepcopy
from datetime import datetime, timedelta
import numpy as np
import pandas as pd
# SPIKEINTERFACE
import spikeinterface as... |
f9a5fbb589d3a0d0250940ae2e036996e9d63c770270fcad9fd017d9e29dffd5 | Python | 17,003 | 614 | # -*- coding: utf-8 -*-
"""This module contains an abstraction class Prox for proximal operators,
and provides commonly used proximal operators, including soft-thresholding,
l1 ball projection, and box constraints.
"""
import numpy as np
import random
import torch
import torch.nn as nn
from sigpy import backend, util,... |
43f0f179313b1eca1c56cdff1f122b93b551799d7e818862b9c01b005b7f90e2 | Python | 17,067 | 434 | # -*- coding: utf-8 -*-
"""
Created on Tue Oct 7 15:03:11 2025
@author: simon
"""
import numpy as np
import matplotlib.pyplot as plt
from plotting_functions import my_style
from matplotlib.gridspec import GridSpec
from matplotlib.colors import LogNorm
from opt_ import make_maps_spikes
import seaborn as ... |
dcc8face0fefbc48f24ff3abdcb734570578eb9aa606ce48b39219f6c5a89f34 | Python | 17,113 | 533 | # -*- coding: utf-8 -*-
"""Block reshape functions.
"""
import numba as nb
import numpy as np
from sigpy import backend, config, util
__all__ = ["array_to_blocks", "blocks_to_array"]
def array_to_blocks(input, blk_shape, blk_strides):
"""Extract blocks from an array in a sliding window manner.
Args:
... |
e4e9060a3ff240b39950a93b3f590d2ba2b31729e014502ffbfc8dbcc3a69bae | Python | 17,159 | 550 | # -*- coding: utf-8 -*-
"""Convolution functions with multi-dimension, and multi-channel support.
"""
import numpy as np
import scipy.signal as signal
from sigpy import backend, config, util
__all__ = ["convolve", "convolve_data_adjoint", "convolve_filter_adjoint"]
def convolve(data, filt, mode="full", strides=No... |
f859988e69256d8146f535731c6eee05b58692e3cf3753565c336926dbc753bf | Python | 17,355 | 396 | #!/usr/bin/env python3
"""Verify that a pipeline run produced the expected outputs.
The sample dataset contains 3 recordings (main, short, unsigned):
- all 3 are preprocessed
- all 3 have quality control run on them
- the "short" (10s) recording is too short to be spike sorted, so only
2 recordings produce a... |
04bfa606edfd88cb8ba3bb84073030bb5bc58fc858aa859fce508982345a31e4 | Python | 17,536 | 393 | import warnings
warnings.filterwarnings("ignore")
# GENERAL IMPORTS
import os
# this is needed to limit the number of scipy threads
# and let spikeinterface handle parallelization
os.environ["OPENBLAS_NUM_THREADS"] = "1"
import sys
import numpy as np
from pathlib import Path
import shutil
import json
import argpars... |
b0a6d6d56291d471380e7ee2ff2610d5b96aed7fd810239edcd13e98028f1495 | Python | 17,670 | 538 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Sun Mar 14 09:37:20 2021.
@author: spiros
"""
import os
import brian2
import pathlib
import numpy as np
import matplotlib.pyplot as plt
def poisson_spikes(t1, t2, N, rate=10, dt=0.1):
"""
Poisson spike generator.
Parameters
----------
... |
d1146283e0d96d5444e5bec3c4d1123f912d4a4b2c8de96b1ce58fe8959d5f13 | Python | 17,912 | 427 | # -*- coding: utf-8 -*-
"""
Created on Wed Oct 16 10:59:33 2024
@author: simon
"""
import numpy as np
import matplotlib.pyplot as plt
from plotting_functions import my_style
import seaborn as sns; sns.set_theme()
import pickle
import pandas as pd
import pathlib
# Get the path of the current script
ba... |
48cbc730bdfedd0e068b627c7fa20d76bf565e78e0fffcef2ea576a2a851d514 | Python | 17,914 | 485 | r"""
# Basic trainers for SDE models
This module implements basic training routines for SDE models.
The base class is `SDETrainer`, which provides the base training logic.
The sub-classes are required to implement the `SDETrainer.loss_func` that is used to train the model.
## Training routines
We provide here two tr... |
c11e6ee8c7652a762ac697963b1291bdcdfe57202b31c3ccbeb089ad0e3fa1e1 | Python | 17,985 | 528 | from typing import Union, Iterable
from collections import defaultdict
from functools import partial
import re
import struct
import numpy as np
from cloudfiles import CloudFiles
from .common import apply_transform
from .unsharded import UnshardedLegacyPrecomputedMeshSource
from ..sharding import ShardingSpecificati... |
ac8ba5d014b4dc72270d3e2bcdab47136f8d9f7e93703433ac0fce412ae69b32 | Python | 18,268 | 446 | import sys
import time
from typing import Optional, Union, Tuple, Any
import multiprocessing as mp
import numpy as np
from tqdm import tqdm
from cloudfiles import CloudFiles
from cloudfiles.paths import normalize
from .exceptions import UnsupportedFormatError, DimensionError, InfoUnavailableError
from .lib import ge... |
2992b38d702d49ec5e7c808b0366e5e3248ca1d7d38788e89bd78b1674f36417 | Python | 18,395 | 741 | import re
import os
import numpy as np
from cloudfiles import CloudFiles
from cloudvolume.datasource.precomputed.metadata import PrecomputedMetadata
from cloudvolume.lib import jsonify, Vec, Bbox, spatial_unit_in_meters, time_unit_in_seconds
from ... import exceptions
from ...provenance import DataLayerProvenance
... |
7a6ac69b7430ec9417fe6afe9bc9099406fc1028aea00b92d53d1485772e7dd7 | Python | 18,529 | 418 | # -*- coding: utf-8 -*-
"""
Created on Mon Sep 30 15:03:26 2024
@author: simon
"""
import numpy as np
from scipy.ndimage import gaussian_filter1d
import matplotlib.pyplot as plt
from plotting_functions import my_style
from opt_ import make_maps_spikes
from matplotlib.gridspec import GridSpec
from matplot... |
2a4569931f2d5129a873acf10df6cfcbc83bc6fcc46afbf3e19af734fec6727e | Python | 18,533 | 657 | from functools import partial
import json
import os
import posixpath
import shutil
from . import scheduler
from .provenance import DataLayerProvenance
from cloudfiles import CloudFiles, compression
from cloudfiles.interfaces import COMPRESSION_EXTENSIONS
from .lib import (
Bbox, colorize, jsonify, mkdir,
toabs,... |
c4d85b2e71d3cfdcf1fe1e561bf098f84eafba78094918452fbce322f2e63129 | Python | 19,077 | 449 | from airflow import DAG
from airflow.operators.python import PythonOperator
from worker_op import worker_op
from airflow.utils.weight_rule import WeightRule
from datetime import datetime, timedelta
from cloudvolume import CloudVolume
from cloudvolume.lib import Bbox
from airflow.models import Variable
from param_defaul... |
7a4fada7a1016e0ad03b19d70831a85cdf58da8d75eaabccd38015cdaf788d14 | Python | 19,096 | 601 | # @license
# Copyright 2017 The Neuroglancer Authors
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or... |
1edb99fe5b5024c52ea9f8738e0d886e7c2dd7e7e0496a5bfd0f86b898c91b9c | Python | 19,243 | 444 | import unittest
import numpy as np
import numpy.testing as npt
from sigpy import backend, config, conv, util
if __name__ == "__main__":
unittest.main()
dtypes = [np.float32, np.float64, np.complex64, np.complex128]
class TestConv(unittest.TestCase):
def test_convolve_valid(self):
mode = "valid"
... |
5bf3c8f6745b61991ddeaa06dfc8613f7c6e7e7b1b0a1d91df10430bb39a916c | Python | 19,656 | 388 | import streamlit as st
import pandas as pd
import joblib
from rdkit import Chem
from rdkit.Chem import AllChem, Descriptors
import tensorflow as tf
from keras.layers import TFSMLayer
import numpy as np
import chardet # For automatic encoding detection
import hashlib # For generating fixed accuracy and error
from abo... |
56704bc06ee39ae8011312f71b765173fa179b801498cc36f87ad6a3fe2b8279 | Python | 19,991 | 584 | r'''
Dynamical models
```
The `sde` instance can then be used to simulate the dynamics
of the system or perform training.
- Some simple definition of the potential, dissipation, conservation, and diffusion functions are
provided in `UIDD.models`
- The `ReducedSDE` class includes both an `SDE` component and a dimens... |
5d7ed77cc589e1391c112a6d1a65c30c083dd086b363d63baa9917bee41f4cd8 | Python | 20,093 | 430 | """ top level run script """
# GENERAL IMPORTS
import os
# this is needed to limit the number of scipy threads
# and let spikeinterface handle parallelization
os.environ["OPENBLAS_NUM_THREADS"] = "1"
import argparse
import warnings
import json
import pickle
import numpy as np
from pathlib import Path
import probeint... |
630401c2039231834d995c9bb5c34dc50562ceb7ffab8b96cedf0c1671c321b0 | Python | 20,128 | 616 | """
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% Performs Current-Based Decomposition (CURBD) of multi-region data. Ref:
%
% Perich MG et al. Inferring brain-wide interactions using data-constrained
% recurrent neural network models. bioRxiv. DOI: https://doi.org/10.1101/2020.12.18.42... |
32af04843436ee11ee251813fbba753cb5857e19aa0fabd87a3d3095cc3ccc31 | Python | 20,526 | 494 | from pathlib import Path
try:
from importlib.metadata import requires
except ImportError:
from importlib_metadata import requires
from zipfile import ZipFile
import numpy as np
import tempfile
from packaging.version import Version
from csbdeep.utils import axes_check_and_normalize, normalize, _raise
DEEPIMAGE... |
f1cfa9b41f6be1e1b3e27de17bc300e308f688f4bf2d6d27d02d4527a6de6f99 | Python | 20,897 | 488 | import numpy as np
import sys
import os
import argparse
import csv
import pandas as pd
import nibabel as nib
from collections import OrderedDict
import torch
import torch.nn as nn
import torch.nn.functional as F
from torch.nn import ModuleList, ReplicationPad2d, Dropout
from torch.utils.data.sampler import Sampler, Seq... |
93f19ce24e40e923e22bed0a96f923a8a69a9877e3e9b6695f7afbf83538583a | Python | 20,937 | 822 | import pytest
import copy
import gzip
import json
import math
import numpy as np
import os
import shutil
from cloudvolume import CloudVolume, chunks, Storage, Skeleton
from cloudvolume.storage import SimpleStorage
from cloudvolume.lib import mkdir, Bbox, Vec, jsonify
from cloudvolume.datasource.precomputed.sharding ... |
1a93e0aa12beb49bbd81b4979fc5e99d263d8a0882137e6bb831655997600eaa | Python | 20,942 | 706 | import queue as Queue
from collections import defaultdict
import itertools
import json
import os.path
import posixpath
import re
from functools import partial
import types
from tqdm import tqdm
from cloudvolume import compression
from cloudvolume.exceptions import UnsupportedProtocolError
from cloudvolume.lib import ... |
a2600192eec4a73b115caea3282f815dbbdcb895509969fa18b55a128d1b57f2 | Python | 21,090 | 491 | # -*- coding: utf-8 -*-
"""
Created on Fri Sep 20 16:20:34 2024
@author: simon
"""
import numpy as np
import matplotlib.pyplot as plt
from plotting_functions import my_style
from matplotlib.gridspec import GridSpec
import seaborn as sns; sns.set_theme()
import pickle
import pandas as pd
import pingouin ... |
c81378c6d613b3bfe610cf89e4f76c58631766503c1ac88834c5dc4fbb3e479a | Python | 21,808 | 470 | # -*- coding: utf-8 -*-
"""
Created on Fri Sep 5 16:28:55 2025
@author: simon
"""
import numpy as np
import os, sys
import pickle
import pandas as pd
import pathlib
from scipy.signal import find_peaks
from scipy.interpolate import interp1d
from scipy import cluster
from opt import make_maps
from plac... |
eae8e0f90738c872d05d3e9dc7c295b9aeab4bd6226e9b546ec225cc86e84dfa | Python | 21,920 | 504 | # %%
"""
fem_plane_stress.py
2D plane-stress finite element model of the cranial neural tube cross-section.
Model summary
-------------
- Geometry : half-annulus cross-section (exploits dorso-ventral symmetry).
Inner radius r(θ) and wall thickness t(θ) are parametrized by three
measurements (dorsal, lateral, vent... |
ad471ca18ad7cb6f6f3716cac6d6cf419fc7f5ad71b2d6e22a042b053305cda2 | Python | 22,024 | 540 | # -*- coding: utf-8 -*-
"""
Created on Thu Oct 9 10:43:56 2025
@author: simon
"""
import numpy as np
import matplotlib.pyplot as plt
from plotting_functions import my_style
from matplotlib.gridspec import GridSpec
from matplotlib.colors import LogNorm
from scipy.ndimage import gaussian_filter1d
import s... |
f69b1cd1dcc524e1445d6aee188726b0974ff5956b22c462c91b83b7edd33279 | Python | 22,031 | 643 | import pickle
import unittest
import numpy as np
import numpy.testing as npt
import random
from sigpy import backend, config, fourier, linop, util
if __name__ == "__main__":
unittest.main()
dtypes = [np.float32, np.float64, np.complex64, np.complex128]
devices = [backend.cpu_device]
if config.cupy_enabled:
... |
01ac9cabfe50db67f26196ba6212d9eedfee0d5f6b28d94642b6a4b97cf49299 | Python | 22,159 | 639 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Classification (supporting evidence) with nested CV + CI + permutation test.
UPDATED FIGURES:
- ROC figures PER CLASSIFIER:
Figure5_ROC_LogReg_L2.png
Figure5_ROC_LinearSVM.png
Each figure contains ROC curves for all feature sets:
(1) topology-only (+ opt... |
f7cb60a36d95f3c99282fbb8bd2bb563d32b1bb4341613c5f6c00dceb24144c4 | Python | 22,628 | 530 | from time import sleep
from datetime import datetime, timedelta, timezone
from requests import Response
from airflow.models import Variable
from airflow.hooks.base_hook import BaseHook
from slack_message import slack_message
import json
from common import google_api
def list_managed_instances(instance_group):
re... |
f816bba14d1159fe3db6f57d149f1b46e20bcac6e646823c386d0bad1775e087 | Python | 22,842 | 588 | # -*- coding: utf-8 -*-
"""
Created on Thu Feb 15 17:47:04 2024
@author: simon
"""
from neuron import h
from neuron.units import mV, ms
from Class_CA1_Pyr_standardized import Cell
import matplotlib.pyplot as plt
import numpy as np
import pickle
import pandas as pd
import random
from functools import wr... |
977ac32582d5042eaae4655a9172d665f2fee0930dfabe6c4d08b371b2183c7a | Python | 23,659 | 799 | import copy
import re
import os
import numpy as np
from cloudfiles import CloudFiles
from cloudvolume.datasource.precomputed.metadata import PrecomputedMetadata
from cloudvolume.lib import jsonify, Vec, Bbox, spatial_unit_in_meters, time_unit_in_seconds
from ... import exceptions
from ...provenance import DataLayer... |
af875406d65fc4027d8c24e1ce9e346138128b584f68bef5ebb1416464b853d8 | Python | 24,162 | 554 | """Evaluate trained nonlinear-case models via MMD vs time.
For every (seed, model) pair, loads `outputs/nonlinear<seed>_<Model>_dt<dt>/<ckpt>`,
simulates trajectories from both the trained model and the exact target SDE
on freshly drawn (independent) initial conditions, and computes the
time-evolution of the Gaussian-... |
6aa251150e0abfec89a2a37b4201ee87238262b43c507ba0ca6d4c99b5aff993 | Python | 24,248 | 556 | """Evaluate trained 20D nonlinear-case models via MMD vs time.
For every (seed, model) pair, loads
`outputs/20Dnonlinear<seed>_<Model>_dt<dt>/<ckpt>`,
simulates trajectories from both the trained model and the exact target SDE
on freshly drawn (independent) initial conditions, and computes the
time-evolution of the Ga... |
d29d77b9a51e60ff98c39f1cf82d5dc32bf79ea16688e6122910ce217ebad5ba | Python | 24,408 | 778 | # -*- coding: utf-8 -*-
"""This module contains an abstract class App for iterative signal processing,
and provides a few general Apps, including a linear least squares App,
and a maximum eigenvalue estimation App.
"""
import time
from tqdm.auto import tqdm
from sigpy import backend, linop, prox, util
from sigpy.alg ... |
8e857129f9f2ef24dccf8480e728650e32136a1c0670fefa07aed8bdb45ebed0 | Python | 24,539 | 545 | # -*- coding: utf-8 -*-
"""
Created on Tue Oct 14 15:55:22 2025
@author: simon
"""
import numpy as np
import os, sys
import pickle
import pandas as pd
import pathlib
from scipy import cluster
from scipy.signal import find_peaks
from sklearn.ensemble import RandomForestRegressor
from sklearn.multioutput... |
632213594d7342ac5e773be83a670e6636ea12e18df91d37b84ef0775e8eff60 | Python | 24,869 | 521 | # -*- coding: utf-8 -*-
"""
Created on Wed Apr 24 12:22:55 2024
@author: simon
"""
import numpy as np
import pickle
import pandas as pd
from scipy.signal import find_peaks
from functools import wraps
import os
import pathlib
# Get the path of the current script
base_path = pathlib.Path().resolve().... |
85390c50e77a3102482eb7c6d4fc87fab070caae845de00891e755e5c3383832 | Python | 25,283 | 624 | import numpy as np
import warnings
import math
from tqdm import tqdm
from skimage.measure import regionprops
from skimage.draw import polygon
from csbdeep.utils import _raise, axes_check_and_normalize, axes_dict
from itertools import product
from .geometry import polygons_to_label_coord, polyhedron_to_label
OBJECT_... |
8704282277bbe17f5a24f498c8dcbec8a02d2906212c6c11203b341aa6217ed1 | Python | 26,485 | 575 | import warnings
warnings.filterwarnings("ignore")
import os
import re
import sys
import argparse
from pathlib import Path
import shutil
import json
import time
from datetime import datetime, timezone, UTC
from packaging.version import parse
import numpy as np
import pandas as pd
import logging
import zarr
import numc... |
e0030b4de6c0f3defefddef9e0014b677c0fd9d355d3ad506ef259131e0b6ff9 | Python | 27,034 | 842 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Compare GLM results with and without node-number adjustment
for both:
1) global topology metrics
2) local-distribution summary metrics
Main outputs:
- global_metrics_per_subject.tsv
- local_metrics_per_subject.tsv
- global_glm_compare_node.tsv
- local_glm_compare_nod... |
86f5146552db9e628eb233054de8aefb295d02862529cdbc621020302da1eb86 | Python | 27,348 | 885 | from typing import List
from collections.abc import Iterable
from functools import reduce
import json
import operator
import os
import posixpath
import json5
import multiprocessing as mp
import numpy as np
from tqdm import tqdm
from cloudfiles import CloudFiles
from ... import exceptions
from ...provenance import ... |
50ed6cdbd73ebc150675ccf768d068b28d9cffae1d0ab797c1901f0a050845c7 | Python | 27,939 | 820 | """
Downloading NeuroImaging datasets: utility functions
source: Nilearn
https://github.com/nilearn/nilearn/blob/main/nilearn/datasets/utils.py
"""
import os
import numpy as np
import collections.abc
import contextlib
import fnmatch
import hashlib
import pickle
import shutil
import time
import sys
import tarfile
import... |
3b6069b7a0231cd1656b4829d306a02af5d0ef0175393c9b0111ee104ad324f2 | Python | 27,977 | 890 | """
The Precomputed format is a neuroscience imaging format
designed for cloud storage. The specification is located
here:
https://github.com/google/neuroglancer/tree/master/src/neuroglancer/datasource/precomputed
This datasource contains the code for manipulating images.
"""
import copy
from typing import Dict, Tup... |
2ec2d83e952c994f1658e4bfed49bfd71e8a2ea5ae1aa031ac970c88a3c75775 | Python | 28,112 | 748 | # -------------------------------------------------------------
# Subgrid Optimization
# Copyright (c) 2026
# Dirk Keller, Nick Ramsey's Lab, University Medical Center Utrecht, University Utrecht
# Licensed under the MIT License [see LICENSE for detail]
# ----------------------------------------------------------... |
eb34e3f55c89da78672031773bc0106475426925db6f1301a1907582b60de651 | Python | 28,313 | 888 | # -*- coding: utf-8 -*-
"""MRI RF excitation pulse design functions,
including SLR and small tip spatial design
"""
import numpy as np
import scipy.linalg as linalg
import scipy.signal as signal
import sigpy as sp
from sigpy.mri.rf.util import dinf
__all__ = [
"dzrf",
"dzls",
"msinc",
"dzmp",
... |
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