sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
08d6a7922d3cde50db077de8401de12c2976b741b300d44f189ed6ff377b2cb3 | Python | 23,899 | 556 | """
The framework for cell counting for the U01 workflow GUI.
Andy Thai
andy.thai@uci.edu
"""
# Import standard libraries
import os
import sys
import glob
import time
from natsort import natsorted
from threading import Thread
from regtools import get_project_root
_project_root = get_project_root()
... |
d6821f77f65512775b7a352d7cc7d5de950861623cbdfd52b355d66a5cb6828a | Python | 23,902 | 636 | # Functions used to evaluate particles to match corticospinal response
import numpy as np
from scipy import signal
def butter_bandpass_filter(data, lowcut, highcut, fs, order=2):
nyq = 0.5 * fs
low = lowcut / nyq
high = highcut / nyq
sos = signal.butter(order, [low, high], btype="bandpass... |
648f314f92aa26d588e7f90f3fd5a924beec14a46aa05a5e5a215bfa00b72623 | Python | 23,910 | 650 | # coding=utf-8
# Copyright 2026 The Google Research 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 applicab... |
091c7c398a16792ed7b95752c02c8c98b54fa2a457accb62bf116fedd265e8ae | Python | 23,913 | 455 | import os
import itertools
import numpy as np
import pandas as pd
import seaborn as sns
sns.set_style('darkgrid')
import matplotlib.pyplot as plt
from sklearn.model_selection import train_test_split
from sklearn.metrics import confusion_matrix, classification_report
import tensorflow as tf
from tensorflow... |
73e6c71829a538fb60371e1c0902748fd402838169f6f10bb6a69ec89a7d8838 | Python | 23,919 | 676 | """
Functions that compute burst rate and statistically significant clusters
of burst rate in a time-resolved manner.
"""
import numpy as np
from os.path import join
from mne.stats import permutation_cluster_test
from scipy.ndimage import gaussian_filter, gaussian_filter1d
from help_funcs import significant_features... |
1473f40233d43b43e14a70c654c763e952568c0da04789a79feac59c72eeba81 | Python | 23,927 | 534 | import pickle
import sys
import pandas as pd
sys.path.append('..')
import time
from contextlib import nullcontext
import torch
import torch.distributed as dist
import torch.multiprocessing as mp
from torch.utils.data import DataLoader
import torch.optim as optim
import torch.optim.lr_scheduler as lr_scheduler
from t... |
1b9f2bbabcadb9635357985800ef96a6d466f7cb49b2e0d4a0cf4fc647e7e4f3 | Python | 23,933 | 597 | from __future__ import annotations
from collections.abc import Callable
import numpy as np
from SurvivalEVAL.evaluations.util import (
check_and_convert,
check_and_convert_event_data,
)
from .._concordance_utils import (
_check_has_any_pairs,
_ConcordanceCounts,
_count_directed_risk_pairs,
_... |
00128e099bb003603f48a1f716a2ba4e28fc74486beb81f5e173c1ad9b5f1232 | Python | 23,950 | 818 | # coding=utf-8
# Copyright 2026 The Google Research 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 applicab... |
9873fd2bcda47f2fdddcc7fd868108634a3ae23034ffbef6fcb7f894c97c9021 | Python | 23,970 | 569 | import os
from typing import Callable, Dict, Tuple, Union
import numpy as np
from scipy import signal
from scipy.io import loadmat
from ....utils import get_random_dir_path
from ..base_dataset import BaseDataset
def _apply_notch_filter(eeg_data: np.ndarray, fs: float, notch_freq: float = 50.0) -> np.ndarray:
""... |
6aee7894603460e305b123c88fee2fcd7e7b71a53478306fe9f8e995c481f534 | Python | 23,972 | 728 | # Copyright 2022 The TensorFlow Authors. All Rights Reserved.
#
# 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 applica... |
d5ea828513ee427c43baeb57a7712a3be63f6f0644b2f8c48b36c840c62a3d57 | Python | 23,980 | 542 | import warnings
from typing import Any, Dict, List, Tuple
import pytorch_lightning as pl
import torch
import torch.autograd as autograd
import torch.nn as nn
import torchmetrics
from torch.utils.data import DataLoader
from torchmetrics.image.inception import InceptionScore
from .utils import FrechetInceptionDistance
... |
eaebec269aa1df7e5e6008a1abc9c18afb82acffc37ff9a812ddcbd7c321ba90 | Python | 23,985 | 572 | #!/usr/bin/env python
# Copyright (c) 2019 Intel Corporation
#
# This work is licensed under the terms of the MIT license.
# For a copy, see <https://opensource.org/licenses/MIT>.
"""
This module provides Challenge routes as standalone scenarios
"""
from __future__ import print_function
import os
import math
import... |
bc36a5820fa16b0f2ccda4f9f4ffa65cd8fc3b7ff1500cd4bb85b769142b5fd8 | Python | 23,990 | 526 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
# Copyright 2024 Clinic for Diagnositic and Interventional Radiology, University Hospital Bonn, 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 ... |
7ebb831574b46c264f7f2e30be6758168810043cd1452263d81377e35bbca404 | Python | 24,000 | 489 | from collections.abc import Iterable
from typing import TYPE_CHECKING, Dict, List, Optional, Tuple, Union
import numpy as np
from ..data import SquadExample, SquadFeatures, squad_convert_examples_to_features
from ..file_utils import add_end_docstrings, is_tf_available, is_torch_available
from ..modelcard import Model... |
87d553e295ff6817b53efd25c4d0cd7b4b991bbdb671fee8fa8208e4ce706b29 | Python | 24,020 | 602 | class AFMimg():
"""A class that contains the x-, y-, z-values, filename and directory of the raw AFM file
Attributes
----------
xvalues : ndarray
N dimensional array with type float that contains the x-values of the igor pro height trace data
yvalues : ndarray
N dimensional arra... |
04a0074b8725d826df691cbd8ad05dc8a9f4249185871713bda0197db6d1bff9 | Python | 24,033 | 489 | import argparse
import torch
import torch_geometric
from torch_geometric.utils import from_networkx
import networkx as nx
import pandas as pd
import numpy as np
import scipy as sp
from sklearn.preprocessing import StandardScaler
from models import *
from data import *
from utils import *
from tqdm import tqdm
impo... |
fd7cb35da2e798aff041817f8147a157c5f61f1483a3f426695e1f25c81b6a9d | Python | 24,035 | 573 | from argparse import ArgumentParser, Namespace, FileType
from Bio.PDB import PDBParser,PDBIO
import os,copy
import numpy as np
from multiprocessing import Pool
import tqdm
import time
from tqdm.contrib.concurrent import process_map # or thread_map
from scipy.spatial.distance import cdist
from rdkit.Chem import AllCh... |
2da3bbe7914d6edb7578828216ee7a372d4111bad16176074bd02fc090bd937f | Python | 24,064 | 561 | import io
import json
import os
import unittest
import urllib.error
from hed import HedFileError, HedString, Sidecar, load_schema_version
from hed.errors import ErrorHandler, SchemaWarnings, get_printable_issue_string
from hed.models import DefinitionDict
from hed.schema import from_string
from hed.validator import He... |
d3838c3e737f591b1b7f28cf476e0c05fe9e1ad27ce0902580a925400d0f3fcf | Python | 24,071 | 549 | import logging
import warnings
from typing import Any, Dict, List, Tuple
import pytorch_lightning as pl
import torch
import torch.autograd as autograd
import torch.nn as nn
import torchmetrics
from torch.utils.data import DataLoader
from torchmetrics.image.inception import InceptionScore
from .utils import FrechetInc... |
b46581622c270fcf942f50a7fa2990833641a0d1b2189ef945b1c1d240bf6c54 | Python | 24,112 | 526 | """tkinter installer wizard - a thin shell over installer.{environment,steps,
drift,platform_win}. All install logic lives in those modules; this file only
renders screens and calls them. build_plan() is the unit-testable core."""
import os
import queue
import sys
import threading
import tkinter as tk
from co... |
b508e533a4d6b24d85bff0d4981808aef03a073185b7eedcfaf360603686e0ba | Python | 24,120 | 612 | # -*- coding: utf-8 -*-
"""
Created on Thu Feb 9 17:28:36 2023
@author: Dustin Garner
"""
import os
import copy
import math
import collections
import itertools
import numpy as np
import pandas as pd
from pydantic import BaseModel
import matplotlib.pyplot as plt
import seaborn as sns
from fafbseg import flywire
impo... |
6ce7f4c5120fe4c9e036054442ba7e15c75b1d5bc133957b6d93f28f98aa312b | Python | 24,122 | 531 | import numpy as np
import itertools
from skimage import transform
from typing import Dict
from typing import List
import pandas
from sklearn.model_selection import train_test_split
from sklearn.linear_model import LogisticRegression
import merlin
from merlin.analysis import decode
from merlin.util import decoding
from... |
96f81fca05aa40c3a7bf41ac0511361592ecd4388a680b58c3ca3ee0504d9c9b | Python | 24,124 | 771 | """Various metrics based on Type I and Type II errors.
References:
https://en.wikipedia.org/wiki/Confusion_matrix
Example:
.. code-block:: python
import segmentation_models_pytorch as smp
# lets assume we have multilabel prediction for 3 classes
output = torch.rand([10, 3, 256, 256... |
460a807604ea97a86672a16af83c6dd0fcbfce9fba46ac52d881ad74ca8da76c | Python | 24,125 | 531 | import numpy as np
import itertools
from skimage import transform
from typing import Dict
from typing import List
import pandas
from sklearn.model_selection import train_test_split
from sklearn.linear_model import LogisticRegression
import merlin
from merlin.analysis import decode
from merlin.util import decoding
from... |
b61f9e4cf22f6de71f25a52c76b6c7d5a1d0bc3576c8213e461aeba6c26129b1 | Python | 24,128 | 600 | """Dependency Resolution
The dependency resolution in pip is performed as follows:
for top-level requirements:
a. only one spec allowed per project, regardless of conflicts or not.
otherwise a "double requirement" exception is raised
b. they override sub-dependency requirements.
for sub-dependencies
... |
e95f7414dcaa46b687792f3a717dfa575c83ce8240382973d08da5ca8d0b05be | Python | 24,139 | 592 | from collections import OrderedDict
import torch
import torch.nn as nn
import torch.nn.functional as F
'''
# --------------------------------------------
# Advanced nn.Sequential
# https://github.com/xinntao/BasicSR
# --------------------------------------------
'''
def sequential(*args):
"""Advanced nn.Sequent... |
4ca147ac0296be67baf41c4c6871b422c38c5534dc2418943c991240b1b09f48 | Python | 24,155 | 559 | """Original implementation from https://github.com/tensorflow/tensor2tensor/blob/master/tensor2tensor/utils/adafactor.py """
import re
import tensorflow as tf
from tensorflow import keras
from tensorflow.keras import backend as K
from tensorflow.python.ops import math_ops
# from https://github.com/Smokrow/addons/blob... |
4c1f2ab1d2e3178e9d941631580e52df99268808c5bb8914b9dbd279bb4f4f3c | Python | 24,157 | 577 | """
Coronal TIFF Export - simple GUI
================================
A small standalone PySide6 window around
:func:`regtools.utils.io.coronal_tiff_export.export_coronal_tiffs`:
* pick an input volume and an output folder,
* **scrub coronal slices** with a slider to preview before exporting
(contrast-matc... |
ac7f388028f796910e76ca3d1d53ed14e3d833041d271f0a370a3a05ff3f0e67 | Python | 24,164 | 548 | import pandas as pd
import numpy as np
import matplotlib.pyplot as plt
import os
import sys
import subprocess
import rdkit.Chem as Chem
pd.set_option("display.max_rows", 100)
pd.set_option('display.max_columns', 100)
import torch
torch.set_num_threads(1)
torch.multiprocessing.set_sharing_strategy('file_system')
from ... |
2da9f7149e144b63fee715fb8fe5154e96bf9aa230d176c91e923d528ef0c4e1 | Python | 24,168 | 525 | from functools import partial
import torch
import torch.nn as nn
from torch.nn import functional as F
def conv3d(in_channels, out_channels, kernel_size, bias, padding):
return nn.Conv3d(in_channels, out_channels, kernel_size, padding=padding, bias=bias)
def create_conv(in_channels, out_channels, kernel_size, o... |
a5ea9cc167a86e1e26889cfa42e2c9aeae270b51d315c0621fb222ac2ee8c91f | Python | 24,175 | 652 | #!/bin/env python3
"""
Log files
---------
Parse ithildin log files. The class Log is used to make the contents of a logfile easily accessible.
"""
from typing import Dict, Tuple, List, Union
import datetime
import re
import os
import yaml
import numpy as np
import warnings
def log_to_dict(s:str) -> Dict:
"""
... |
f5cbacf2a9b80f39df31aaf093b75aaaa0fbc4c38a288a8d8010131154d575da | Python | 24,180 | 530 | #
# User-exposed interface of acme
#
# Copyright © 2020-2025 Ernst Strüngmann Institute (ESI) for Neuroscience
# in Cooperation with Max Planck Society
# Copyright © 2026 Ernst Strüngmann Institute (ESI) of the Max Planck Society
#
# SPDX-License-Identifier: BSD-3-Clause
#
# Builtin/3rd party package imports
import in... |
efd673549727163e914fd5d15276233de784bdb24df9ae302249da1970e5f194 | Python | 24,182 | 718 | """Manages the optimization domain and holds points."""
from __future__ import annotations
from copy import deepcopy
from typing import TYPE_CHECKING, Any
from warnings import warn
import numpy as np
from colorama import Fore
from bayes_opt.constraint import ConstraintModel
from bayes_opt.exception import NotUnique... |
f428bce35e712bd8f7c0654348930c58b516b8ae507dd02c7ad8744bd96e8ca2 | Python | 24,195 | 562 | """Orginally implementation from https://github.com/tensorflow/tensor2tensor/blob/master/tensor2tensor/utils/adafactor.py """
import os
import re
import math
import argparse
import tensorflow as tf
from tensorflow import keras
from tensorflow.keras import backend as K
from tensorflow.python.ops import math_ops
# from... |
685cc683102b86645a47b8520cef6c3669ac5105894515455c1ac87f580fe48c | Python | 24,213 | 599 | import logging
import time
import math
import numpy as np
import torch
import torch.nn as nn
from torch_scatter import scatter_mean
from pyexpat.model import XML_CQUANT_OPT
from ocpmodels.common.registry import registry
from ocpmodels.common.utils import conditional_grad
from ocpmodels.models.base import BaseModel
fro... |
7ae09b0b240eac1acb507352eaf9ed2b9d6e4d073215a3f6ccb3c4e3704fb0cd | Python | 24,214 | 1,383 | from __future__ import annotations
from pathlib import Path
from typing import Mapping, Sequence
import matplotlib.pyplot as plt
import numpy as np
import pandas as pd
import math
from PIL import Image, ImageDraw, ImageFont
from matplotlib.colors import to_rgb
from ..plots.style import (
mg_color,
)
# =========... |
9f19833a8605f4d5ee2da198cb4d6d2858e4351796265ac616e24d584893a3ce | Python | 24,215 | 656 | # mypy: ignore-errors
import railroad
from pip._vendor import pyparsing
import typing
from typing import (
List,
NamedTuple,
Generic,
TypeVar,
Dict,
Callable,
Set,
Iterable,
)
from jinja2 import Template
from io import StringIO
import inspect
jinja2_template_source = """\
{% if not emb... |
ee9b39fecb90162f5194d73631819d048c9c0f5bc6b3c4e6127d0a7b214b0e47 | Python | 24,225 | 655 | # coding=utf-8
# Copyright 2026 The Google Research 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 applicab... |
fa71e89c1cab9599fb68578e1566cc39f243004dc824ef5af7af9d30ddf02752 | Python | 24,227 | 616 | import numpy as np
from scipy.sparse import csr_matrix
from ..constants import hpro_rng
from .. import config as CFG
from ..utils.mpi import MPI, comm
class PairsInfo:
'''
This class is used to deal with atom pairs. The first atom in the pair is always assumed to be in the unit cell at (0, 0, 0),
and the... |
2c8331e4c24f0763c40d13c2f7cc320db0e500ea537247b8c1e3ee8da5b42040 | Python | 24,232 | 545 | ###########################
######## Utilities ########
###########################
#%%# Catalyzer
import os
import re
import numpy as np
from scipy import interpolate
import torch
from sbi.inference import simulate_for_sbi
import time
import pickle
import matplotlib
import matplotlib.pyplot as plt
plt.rcParams['fig... |
88d5c9ae24d5f832f967e42637f11fc9cc62bea7c9767e4580addc96d05adf05 | Python | 24,242 | 715 | # coding=utf-8
# Copyright 2026 The Google Research 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 applicab... |
5cb9c9105bdc5776e3695ccc3542627a6de7f25bef23d4c9e4f4eef881b6b938 | Python | 24,247 | 739 | from enum import IntEnum
from functools import lru_cache
from itertools import filterfalse
from logging import getLogger
from operator import attrgetter
from typing import (
TYPE_CHECKING,
Dict,
Iterable,
List,
NamedTuple,
Optional,
Sequence,
Tuple,
Type,
Union,
)
from .cells im... |
47dd397306314da75a319487fd6f0ab7c1a088ac670ed511a5a45bd1a8f5bad6 | Python | 24,277 | 498 | import numpy as np
from .utils.mpi import mpi_watch, is_master, comm
from .utils.misc import simple_timer, index_traverse
from .matao.findpairs import pairs_within_cutoff
from .matao.matao import MatAO
from .io.aodata import AOData
from .io.struio import load_structure, from_qexml, from_bgw, from_poscar, from_gpaw
from... |
7f0762f31912ae502fcdd71d0eca52cd775e1ac597d072462c2d1cbce6525a1c | Python | 24,278 | 600 | import logging
import time
import math
import numpy as np
import torch
import torch.nn as nn
from torch_scatter import scatter_mean
from pyexpat.model import XML_CQUANT_OPT
from ocpmodels.common.registry import registry
from ocpmodels.common.utils import conditional_grad
from ocpmodels.models.base import BaseModel
fro... |
95d40c571214f110dff923c5f5875dd02ad041b53d045f630a95728dbfe3f3ef | Python | 24,278 | 600 | import logging
import time
import math
import numpy as np
import torch
import torch.nn as nn
from torch_scatter import scatter_mean
from pyexpat.model import XML_CQUANT_OPT
from ocpmodels.common.registry import registry
from ocpmodels.common.utils import conditional_grad
from ocpmodels.models.base import BaseModel
fro... |
d099b5fa02087fb56f4300c4d18a4d2cb55fa220e37f484fa5dfda114f5c1139 | Python | 24,282 | 607 | """Schema entry classes representing individual nodes in the HED vocabulary."""
from __future__ import annotations
import itertools
import math
from typing import Any
import inflect
from hed.schema.hed_schema_constants import ANY_UNITS_CLASS, HedKey, HedSectionKey
pluralize = inflect.engine()
pluralize.defnoun("he... |
47c916249547902c8fdbb494e4835fce146ffb2e75851ad4fa112e3f98684fe7 | Python | 24,287 | 921 | # parsers.py
import sys
import argparse
from fba import __version__
def coords(s):
try:
# from itertools import chain
# s = ''.join([i.strip() for i in chain.from_iterable(s)]).split(',')
# return [int(i) for i in s]
return [int(i) for i in s.split(',')]
except TypeError:
... |
87e433004473f136fc329db831168ef04f4c997700860e7278f868424e43bf3d | Python | 24,297 | 1,047 | import unittest
import filecmp
import subprocess
import os
class TestReform(unittest.TestCase):
def setUp(self):
self.wd = os.getcwd()
self.cleanup() # Clean up before each test case
def tearDown(self):
os.chdir(self.wd)
self.cleanup() # Clean up after each test case
def cleanup(self):
print("Clean Up... |
3a91aa06831d1a4a60615f75ed26522e25847622590d27777a36eec9a291ae2e | Python | 24,306 | 415 | from e3nn import o3
import torch
from torch import nn
from torch.nn import functional as F
from torch_cluster import radius, radius_graph
from torch_scatter import scatter_mean
import numpy as np
from models.score_model import AtomEncoder, TensorProductConvLayer, GaussianSmearing
from utils import so3, torus
from data... |
076dacd50056ee922e9ef8200a1fb460a207a4d31f1220a366259f64b0088d3d | Python | 24,320 | 657 | #!/bin/env python3
"""
Log files
---------
Parse ithildin log files. The class Log is used to make the contents of a logfile easily accessible.
"""
from typing import Dict, Tuple, List, Union
import datetime
import re
import os
import yaml
import numpy as np
import warnings
def log_to_dict(s:str) -> Dict:
"""
... |
2e35fae61025a5e9018f3701e42771b9c30b5e81bcf990e0d3e01f2994064e5a | Python | 24,325 | 886 | from __future__ import annotations
"""
Configuration for MorphoGlia's combined analytical stage.
Internal sequence:
feature preparation
-> dimensionality reduction
-> multiresolution clustering
-> resolution decision
"""
# ===============================================================... |
72b334dbb90867d29bb288b0e3fa174cbc66633e827c6b69949f7347604503f5 | Python | 24,333 | 529 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
Created by : Alpha Renner (alpren@ini.uzh.ch)
"""
import os
import re
import time
import warnings
import numpy as np
import nxsdk.api.n2a as nx
from SFC_backprop.input_data import generate_input_data
from SFC_backprop.loihi_groups import calc_spiketimes_from_input_ar... |
3ada88d0d066f148ba8406905ffdbec460012f0c85a15853ed247b73698edb29 | Python | 24,334 | 539 | from wsilearn.compress.compression_augm import patch_encoding_map
from wsilearn.utils.cool_utils import print_mp
from wsilearn.dataconf import DataConf
from wsilearn.utils.flexparse import FlexArgumentParser
print = print_mp
print('entered compress.py')
import torch
import torch.nn.parallel
from wsilearn.utils.cool... |
42aebaf1dbbc7cefa4ba6a61df20b653274ad8466fa874cf5041e478cf61294f | Python | 24,338 | 674 | # coding=utf-8
# Copyright 2020 Microsoft and the HuggingFace Inc. team.
#
# 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... |
ab57d9700e9f2726ccafaa58864b6c59218c2a1d9ea1f5d0b4dc5e7d590e76d0 | Python | 24,342 | 447 | """
Modules containing function works for transformation between config,
DetailedCircuit, AbstractCircuit, PointCircuit
config ---> DetailedCircuit: config2detailed
DetailedCircuit ---> AbstractCircuit: detailed2abstract
---> PointCircuit: detailed2point
---> DetailedCircuit (connectio... |
91672406b80ec663ba5e1336724cba01a28deb6244b8491c68f407128d3f540f | Python | 24,344 | 652 | """
Backend integrator and backends definitions. Currently supported are following
backends:
- `jitcdde`: (just-in-time compilation into C) which uses `jitcdde`
which translates symbolic derivatives into C code and then calls C functions
from Python interface:
- very reliable
- uses adaptive `dt` hence... |
ddf381899f1b7753adb8e313a54be4140f9c8ef8ef0b59b12ae3d832e0e99226 | Python | 24,351 | 749 | """
Download Waxholm Space Atlas of the Sprague Dawley Rat Brain.
Downloads the atlas pack from NITRC and extracts the atlas annotation, label
file, and MRI templates.
Directory layout after download + post-processing:
data/templates/waxholm_atlas/
├── WHS_SD_rat_atlas_v4.label (structu... |
013105626973be8cd5f06d0aa9781f96c11606b73921818225af32e4def474d0 | Python | 24,353 | 532 | # trace generated using paraview version 5.5.1
# Apply a preset using its name. Note this may not work as expected when presets have duplicate names.
#### import the simple module from the paraview
from paraview.simple import *
#### disable automatic camera reset on 'Show'
paraview.simple._DisableFirstRenderCameraReset... |
607298529c15ffe91093bc10094c5013e376a2c7c2f4dedbb2423a4c97f8a1fd | Python | 24,377 | 552 | # -*- coding: utf-8 -*-
#
# Test basic functionality of ComputationalRoutine class
#
# Builtin/3rd party package imports
import os
import tempfile
import time
import pytest
import numpy as np
from glob import glob
from scipy import signal
import dask.distributed as dd
# Local imports
from syncopy.datatype import Anal... |
66308e056b310bb1e0e4ed7fa2f42ff442adde4039fac4f40b43bd13bade1b58 | Python | 24,380 | 493 | """
DeepLabCut2.0 Toolbox (deeplabcut.org)
copyright A. & M. Mathis Labs
https://github.com/AlexEMG/DeepLabCut
Please see AUTHORS for contributors.
https://github.com/AlexEMG/DeepLabCut/blob/master/AUTHORS
Licensed under GNU Lesser General Public License v3.0
"""
import os
import click
from pathlib import Path
import... |
c3474abdddd7e88ffb280ecd20441307adb83b6bcbf4314febe5d56babe77554 | Python | 24,382 | 618 | import time
import os
import subprocess
import sys
import re
import argparse
import collections
import gzip
import math
import shutil
import matplotlib.pyplot as plt
import wandb
import numpy as np
from datetime import datetime
import random
import multiprocessing
#import logging
#from silence_tensorflow import silen... |
5e284ace99909a97a1119e2906a92c3d67f4a104bc0d82fafc50494c1df5783e | Python | 24,395 | 599 | import os
import cv2
import time
import random
import re
import string
import numpy as np
import pandas as pd
import torch
import torch.nn.functional as F
from torch.utils.data import DataLoader, Dataset
from torch.nn.utils.rnn import pad_sequence, pack_padded_sequence
import albumentations as A
from albumentations.pyt... |
03f5a015b6beb42a6a57b7cd0a57dc4ef55b18af9e91a17bc3495d5bd4d78962 | Python | 24,403 | 693 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
'''
Hybrid LFP scheme example script, applying the methodology with a model
implementation similar to:
Nicolas Brunel. "Dynamics of Sparsely Connected Networks of Excitatory and
Inhibitory Spiking Neurons". J Comput Neurosci, May 2000, Volume 8,
Issue 3, pp 183-208
Synop... |
b5a2fe79472d0dd97b035113e79b13992c6b2cfaf5acaf23d7708458f530758f | Python | 24,411 | 606 | import numpy as np #needs install
import os
import pandas #needs install
import sys
import argparse
import mpi4py
class Alya_output_parse():
def __init__(self, project_name):
self.project_name = project_name
self.actmap = []
self.relmap = []
self.maxamp = []
self.maxfound... |
fe2fec52d910a751496213763f0570a345a3fd03933403d0c8927c525f5aa40e | Python | 24,426 | 610 | # coding=utf-8
# Copyright 2026 The Google Research 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 applicab... |
d2ab74d966456987840cc11fdd7ffeb766b5b02e5d5ddf2a913c207b5b4d6d29 | Python | 24,431 | 661 | ################################################################################
# Copyright (c) 2021-2024, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
# Written by D. Jones <djones@llnl.gov> and UCSD collaborators in listed in CONTRIB.md
#
# All rights reserved.... |
649540b99fd38ed735eb2ba1390290b5893115ad1bf22ccd45da7d0d23053f57 | Python | 24,446 | 672 | # coding=utf-8
# Copyright 2026 The Google Research 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 applicab... |
51bbf9e3aa78aeb164334db1006f732f2570b19b0d878c0d62efe2a9ec56dc12 | Python | 24,449 | 485 | # 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... |
a5f352fe88ff1b5ec6630142c9869340a6350934c7651e23725f0218115d56b6 | Python | 24,465 | 539 | #!/bin/env python
from libraries import *
from models_GCAMP_torch import OpGCAMP, ImageGenerator, LatentVector, OpEquilibrium
from GCAMPparam import get_param
torch.manual_seed(0)
par = get_param()
print('Saving in {}'.format(par.fold_res))
makedirs(par.fold_res)
if par.gpu>=0:
ordi = platform.system()
if or... |
060ec55f38ed4eebd1f773813212d38f4ed8ee0fd2d8472855cad70670422525 | Python | 24,482 | 648 | # -*- coding: utf-8 -*-
import os
import random
import subprocess
import sys
import time
from sys import exit as _exit
from sys import platform as _platform
import numpy as np
import tensorflow as tf
import tensorlayer as tl
from . import _logging as logging
from . import iterate
__all__ = [
'fit',
'test',
... |
dbe36f803fa0b93db59d57d6208cf7058d35fafaaf38cc0a3cfe13577791a013 | Python | 24,484 | 574 | # ----------------------------------------------------------------------------
# Contributors: Thiago O. Bezerra
# Antonio C. Roque
# ----------------------------------------------------------------------------
# File description:
#
# Functions to run the astrocyte model from text file, load astrocyte mor... |
7dff44c9218ee32efab2bde4d54cdd3eb57241598b51f2ae0fbf1d70ac098416 | Python | 24,492 | 561 | """Generating synthetic data to test HMP."""
import os
import os.path as op
from copy import deepcopy
from warnings import warn
import mne
import numpy as np
import xarray as xr
from scipy.stats import gamma
from hmp.io import read_mne_raw
from hmp.models.event import EventModel
from hmp.patterndata import PatternDa... |
24242e16c894f00e4f6833d46a39e9b3d9342b537b36819f16b47e5a640e09d7 | Python | 24,493 | 557 | import os,sys
os.environ['TF_CPP_MIN_LOG_LEVEL'] = '3'
import tensorflow as tf
#import numpy as np
import logging
logging.getLogger('tensorflow').setLevel(logging.ERROR)
#
# Input size (batch_size, fid_length, features)
# Features include [time, real, imag]
#
# Functions to generate Poisson-Gap sampling scheme
#... |
a74deb219ab1c136cfa5a5a9a1bd2af6b532ce7ffb9933e860086e226b838a27 | Python | 24,494 | 682 | """The io module handles most file input and output in the `tedana` workflow.
Other functions in the module help write outputs which require multiple
data sources, assist in writing per-echo verbose outputs, or act as helper
functions for any of the above.
"""
import json
import logging
import os
import os.path as op
... |
666a81d9f9ef211fc2078db1859ff668548bb71a512e87e122173e8735b1cb3b | Python | 24,495 | 603 | import numpy as np
import pandas
from scipy import optimize
from sklearn.neighbors import NearestNeighbors
from scipy.sparse.csgraph import connected_components
from scipy.sparse import csr_matrix
from merlin.core import analysistask
from merlin.analysis import decode
class AbstractFilterBarcodes(decode.BarcodeSavin... |
0b1eb162d81cd6473eb840b1e599ebba2bcb95301a3993ff7fca2e8b7da5629f | Python | 24,533 | 745 | """Parameter-related utilities for the Vasp calculator."""
from __future__ import annotations
from dataclasses import dataclass, field
from importlib.util import find_spec
from logging import INFO, WARNING, getLogger
from typing import TYPE_CHECKING, cast
import numpy as np
import psutil
from ase.calculators.vasp im... |
52de1cbae390543c44186c3f0bb57886cc6990592fcd419e49e9f626969dce02 | Python | 24,537 | 502 | """Implementation of receive card."""
import contextlib
import logging
import threading
import time
from collections.abc import Callable
from ctypes import POINTER, addressof, byref, c_int32, c_short, cast
from dataclasses import dataclass
from itertools import compress
import numpy as np
from console.interfaces.rx_... |
cd4d2ca5a17567722ef035b29e50c54bb80eb1c8c25360dfa0314d6999a1bcd3 | Python | 24,540 | 646 | """
Performs Bivariate 2nd order analysis to a SetListTomograms object by tomograms
Input: - A STAR file with a ListTomoParticles pickle (SetListTomograms object input) used as reference
- A STAR file with a set of ListTomoParticles pickles (SetListTomograms object input) to analyze
Output: ... |
292a073ca595e470fe25af97b3956d5a3f00f658ddf2a23a38022b5f3c803c2c | Python | 24,562 | 509 |
import os
from shutil import copy2 as copyfile
from shutil import rmtree
import pandas as pd
from tqdm import tqdm
from termcolor import cprint
from glob import glob
import time
import torch
import warnings
import SimpleITK as sitk
import numpy as np
import multiprocessing
from natsort import os_sorted
def predict_si... |
cc60e0890338580fc68a1632374c5ba3c7bffe4444a984c6c87111ea1065fb1f | Python | 24,563 | 626 | """
Performs Univariate 2nd order analysis to a SetListTomograms object by tomograms
Input: - A STAR file with a set of ListTomoParticles pickles (SetListTomograms object input)
- Analysis settings
Output: - Plots by tomograms:
+ Number of particles by list
+ ... |
d3135f3ce55b8584ee5d9bd49a8db02c7070fa760802be5744776be3ba005004 | Python | 24,576 | 626 | """
Performs Univariate 2nd order analysis to a SetListTomograms object by tomograms
Input: - A STAR file with a set of ListTomoParticles pickles (SetListTomograms object input)
- Analysis settings
Output: - Plots by tomograms:
+ Number of particles by list
+ ... |
9ad22e97d3c25f6348b4569a626c94c37b729f42c2a42f61fe7ac44c5b93d919 | Python | 24,608 | 585 |
# coding: utf-8
# In[1]:
'''
Mayank Jan 12 2016
Paw detector modified from:
Project: https://github.com/aymericdamien/TensorFlow-Examples/
'''
from __future__ import division
from builtins import str
from builtins import range
from operator import floordiv as old_div
import tensorflow
# Assume TensorFlow 2.x.x
tf =... |
996b380861d3971647486dec159c2fec5f41878bce9983313fdb391f071dc7f5 | Python | 24,612 | 498 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Thu Jul 21 09:32:23 2022
@author: caroline
"""
import argparse
import matplotlib.pyplot as plt
import math
import numpy as np
import pandas as pd
import scipy.stats
import statsmodels.api as sm
from scipy.stats import pearsonr, spearmanr
from sklearn.linea... |
7a0d76149e2dcbf45bd636d05c43dcd8d06d7a895070646944e9e40bdd132491 | Python | 24,614 | 944 | import inspect
import signal
import random
import time
import traceback
import sys
import os
import subprocess
import math
import pickle as pickle
from itertools import chain
import heapq
import hashlib
import wandb
def computeMD5hash(my_string):
#https://stackoverflow.com/questions/13259691/convert-string-to-md5... |
90a3cfa9df4c344d3eaac6e440716a612999072bd0774748ba307394ebb39e13 | Python | 24,615 | 630 | """
Performs Univariate 2nd order analysis to a SetListTomograms object by tomograms
Input: - A STAR file with a set of ListTomoParticles pickles (SetListTomograms object input)
- Analysis settings
Output: - Plots by tomograms:
+ Number of particles by list
+... |
6bac5b91e68dfddd20259825db541788475ccd1576e6ac3ed51ab61dbb808d23 | Python | 24,620 | 558 | # coding=utf-8
# Copyright 2026 The Google Research 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 applicab... |
f25f124d6e18d60320fe21c17b414cf42e51c888c842c0de81a19d3d9e68791c | Python | 24,632 | 697 | #!/usr/bin/env python
# coding: utf-8
# Copyright (C) 2021 Blue Brain Project, EPFL
#
# 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 the License, or
# (at your option) any... |
4f4fd11d9a462bd212133eb1d64581217915b402bae16ecaa71141219effc2f7 | Python | 24,634 | 518 | #!/usr/bin/env python3
"""
Copyright (C) 2018-2020 Intel Corporation
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 applic... |
8e0ebaabb8cb397a071bfe650de0c9d65a1a75207c569545875cb56f59f7f1a3 | Python | 24,635 | 407 | import torch
from torch import nn
import torch.nn.functional as F
import timm
class GeometricFusionBackbone(nn.Module):
"""
image_architecture: Architecture used in the image branch. ResNet, RegNet and ConvNext are supported
lidar_architecture: Architecture used in the lidar branch. ResNet, RegNet and Conv... |
27301e2b30416d7774fe13f498f323c0089de69d413d4d43f278563294cc5c6a | Python | 24,642 | 444 | # Inherits TVATAnalysis
# Adds functions to generate plots from TVAT analysis
from TVATAnalysis import TVATAnalysis
import matplotlib.pyplot as plt
import numpy as np
from colors_paultol import *
from scipy.stats import shapiro, levene, ttest_ind
import plotly.express as px
class TVATPlotting(TVATAnalysis):... |
525f4ea7669373355c56cd5cfe943f64fab496affc1d428e510aae2bf597e04f | Python | 24,648 | 656 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
"""Copyright (C) 2012 Computational Neuroscience Group, NMBU.
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 the License, or
(at you... |
560573970db303024f022febd1f429f076845580197aa30a94e25416e9b65ebe | Python | 24,658 | 557 | #!/usr/bin/env python
"""Utility classes and functions for SAMPLing analysis."""
# =============================================================================
# GLOBAL IMPORTS
# =============================================================================
import os
import csv
import glob
import json
import operat... |
eb8e871513574fc8377caa866b099759ee1d8431efbbb524e8c53990054ef64d | Python | 24,663 | 705 | """ Network sketches
--------------------
Diagrams for illustrating network structure and connectivity.
"""
import mesocircuit
from mesocircuit.parameterization.base_network_params import net_dict
from mesocircuit.parameterization.base_plotting_params import plot_dict
from mesocircuit.parameterization.base_plotting_p... |
efcd9a4a6d713f0d14510dd26d8dcb74ce35abd1877edcd99347b3c2b2507bcc | Python | 24,665 | 627 | """
This module, 'phonons.py', contains recipes for performing phonon calculations using the
ph.x binary from Quantum ESPRESSO via the quacc library.
The recipes provided in this module are jobs and flows that can be used to perform
phonon calculations in different fashion.
"""
from __future__ import annotations
fro... |
1279d7cea4b3c424c76bfe3635805bc7808d3ce6fba667b715afb3154a42042e | Python | 24,669 | 830 | """
Custom types used throughout quacc.
"""
from __future__ import annotations
from typing import TYPE_CHECKING
from pydantic_settings import BaseSettings
class DefaultSetting(BaseSettings):
"""
Type hint for when a default setting will be applied
"""
if TYPE_CHECKING:
from datetime import dateti... |
a7642f5eb040606b09e752566c1ec1ae20d75f413e34033ac201cb504cd36dc1 | Python | 24,675 | 647 | """
Performs Bivariate 2nd order analysis to a SetListTomograms object by tomograms
Input: - A STAR file with a ListTomoParticles pickle (SetListTomograms object input) used as reference
- A STAR file with a set of ListTomoParticles pickles (SetListTomograms object input) to analyze
Output: ... |
b06c1aff267a5f635c4525095b35256247fc6c3123472480137690e4e7b02160 | Python | 24,678 | 650 | import functools
import os
import sys
import sysconfig
from importlib.util import cache_from_source
from typing import Any, Callable, Dict, Generator, Iterable, List, Optional, Set, Tuple
from pip._internal.exceptions import UninstallationError
from pip._internal.locations import get_bin_prefix, get_bin_user
from pip.... |
798bef25f9a8906a25f32029fc3907523f1d33a96a55ede5122cee5212bd21af | Python | 24,688 | 681 | import copy
import numpy as np
import pandas as pd
import neuprint as neu
import networkx as nx
from pathlib import Path
from .janelia import JaneliaDataSet
from .scenes import _get_mcns_scene
from .ds_utils import (
_get_mcns_meta,
_get_neuprint_mcns_client,
_get_mcns_types,
_get_mcns_sides,
_ad... |
14264f88ad51c4b8f03222002faf0d2e1de160cddb0e0932f282696ad84b22c7 | Python | 24,704 | 496 | # -*- coding: utf-8 -*-
"""
Created on Fri May 13 11:53:14 2022
@author: Dalton
"""
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
import matplotlib.colors as colors
from pathlib import Path
import dill
import re
import seaborn as sns
from scipy import sparse
from sklearn.metri... |
2fa91349e2743e343caf743fec43461b409ca049c44bd043deb95d62362e2683 | Python | 24,704 | 630 | """
Performs Univariate 2nd order analysis to a SetListTomograms object by tomograms
Input: - A STAR file with a set of ListTomoParticles pickles (SetListTomograms object input)
- Analysis settings
Output: - Plots by tomograms:
+ Number of particles by list
+ ... |
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