sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
3f3b88e57397ffebd127c0526b7c5e1ede92bc0e63e27f64804dc62f51e0a800 | Python | 58,846 | 1,474 | """Contains the base Layer class, from which all layers inherit.
"""
from __future__ import print_function
from __future__ import absolute_import
from __future__ import division
import re
from six.moves import zip
import threading
from .. import backend as K
from .. import initializers
from ..utils.layer_utils import... |
912555920a77f72ded07839efa33fcceecc79f3523abbec783f0be46ee2c55c2 | Python | 58,921 | 1,223 | # Copyright (c) Meta Platforms, Inc. and affiliates.
# All rights reserved.
# This source code is licensed under the license found in the
# LICENSE file in the root directory of this source tree.
import warnings
from collections import OrderedDict
import torch
import torch.nn.functional as F
from tqdm import tqdm
... |
9aeffa607de0debe3d62896f8c298308b56129b795a79b14600e4e394f98bd43 | Python | 58,944 | 1,150 |
# -*- coding: utf-8 -*-
"""
Created on Thu Apr 25 14:41:11 2024
@author: guill
"""
import numpy as np
import scipy.sparse as sparse
import scipy.stats as stats
from numba import jit
class SpikingNetwork():
def __init__(self, N_pyr=1000, N_mit=2250, N_fbi=125, N_ffi=125, v_reset=-0.065, v_re... |
de15c24a67f80381627f9be9072f45199e3c83d80f0d46469082397c0df58dc7 | Python | 59,254 | 1,136 | from collections import defaultdict
from datetime import datetime
from itertools import chain
from functools import reduce
from typing import Dict, List, Optional, Set, DefaultDict
from enum import Enum
from catmaid.control.common import set_log_level
from catmaid.control.annotation import (get_annotated_entities,
... |
34ffba89e9ae9cea259bae6386b1be5bf9b69eeb194ef9a2eba950ff132bafd7 | Python | 59,454 | 1,313 | import ast
import gzip
import logging
from collections import Counter, defaultdict
import jsonlines
import requests
import src.datahandlers.mesh as mesh
import src.datahandlers.umls as umls
from src.babel_utils import (
get_prefixes,
get_user_agent,
glom,
read_identifier_file,
remove_overused_xref... |
cf6e978e7c02e39b4d3a0975e71a484f72862a3eb3c8da189562aee76fa106ee | Python | 59,687 | 1,335 | # -*- coding: utf-8 -*-
import json
from io import StringIO
from operator import itemgetter
from django.shortcuts import get_object_or_404
from guardian.shortcuts import assign_perm
from catmaid.control.authentication import (can_edit_all_or_fail,
can_edit_or_fail, PermissionError)
from catmaid.control.common i... |
6b4d2cf3e13efb2f128c2f4f5d734502a3a533047e19ca8de0a90ff574ac3998 | Python | 60,382 | 1,565 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Eigenmode resampling on the cortex
"""
from .utils import (
_get_eigengroups,
eigen_decomposition,
transform_to_spheroid,
transform_to_ellipsoid,
normalize_data,
)
import os
from .geometry import (calc_surface_eigenmodes,
... |
d05a96c8040f0c945b229bf426d84b44c539c4f7906cdca007c8af45a8f560ae | Python | 60,387 | 1,502 | # -*- coding: utf-8 -*-
from datetime import timedelta, datetime
from dateutil import parser as dateparser
import json
import os
import pytz
import time
from typing import Any, Dict
from django.conf import settings
from django.http import HttpRequest, JsonResponse
from django.db.models.aggregates import Count
from dj... |
040d6e55b90479972a786b20eff86b21f4aa7b3e6edae5c548269c0f68accd2d | Python | 60,508 | 1,822 | import h5py
import numpy as np
import pathlib as pl
from matplotlib import pyplot as plt
from myphdlib.general.toolkit import psth2
from myphdlib.figures.analysis import AnalysisBase, g
from myphdlib.figures.modulation import BasicSaccadicModulationAnalysis
from myphdlib.figures.analysis import convertSaccadeDirectionT... |
5f93cea1af54de92f4749167144608919f4e61ec57e1fd1ae17d01a8fb068fb1 | Python | 60,533 | 1,554 | # Image stack importer
# Author: David Young, 2017, 2020
"""Imports image stacks using Bioformats.
Bioformats is access through Python-Bioformats and Javabridge.
Images will be imported into a 4/5D Numpy array.
Attributes:
PIXEL_DTYPE: Dictionary of corresponding data types for
output given by Bioformats... |
7c47a224fb40fde4b7cfcb7c58b4e0b879f76806a8ef8b7c48e2fc1149c5feaa | Python | 60,694 | 1,425 | # 2D overlaid plot editor
# Author: David Young, 2018, 2020
"""Editor for 2D plot with overlaid planes.
Integrates with :class:``atlas_editor.AtlasEditor`` for synchronized 3D
view of orthogonal planes.
"""
import textwrap
import time
from typing import Callable, List, Optional, Sequence, TYPE_CHECKING, Union
from ... |
1919d6bdc155c50d5f44ccc6c2cdafa4f4a60af84dad65bf45a915723d93c964 | Python | 61,029 | 1,602 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Eigenmode resampling on the cortex
"""
from .utils import (
_get_eigengroups,
eigen_decomposition,
transform_to_spheroid,
transform_to_ellipsoid,
normalize_data,
calc_parcellate,
)
import os
import subprocess
from .geometry import calc_su... |
6d2ef64243b7f3c1fe8f4e756e8a49242cc5ad65e9bb2025e9ade91a973f7e59 | Python | 62,773 | 1,733 | #!/usr/bin/env python
#
# Copyright 2007 Neal Norwitz
# Portions Copyright 2007 Google Inc.
#
# 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... |
c7ee84e001c186d060d0e42537192101782a871d487185e7f01b9402ed393357 | Python | 62,831 | 1,781 | """Test functions in heudiconv.bids module."""
from __future__ import annotations
from collections import OrderedDict
from collections.abc import Callable
from datetime import datetime, timedelta
from glob import glob
import itertools
import logging
import os
import os.path as op
from pathlib import Path
from random ... |
ad315c4ec4846141593bf026cb30653f623da7fe85bbe2bdb3917cc82a4c1b3f | Python | 62,837 | 1,525 | """A `Network` is way to compose layers: the topological form of a `Model`.
"""
from __future__ import print_function
from __future__ import absolute_import
from __future__ import division
import numpy as np
import json
import yaml
import warnings
import copy
import os
from six.moves import zip
from . import saving
f... |
c26c35a7bf26e43b2d9abb8dcbfa40985561c5cd7ff3893c24f5b0850e9ecae8 | Python | 62,967 | 1,080 | import subprocess
import json
from .jobHandler import *
import os
from .sample import Sample
from .cluster import Cluster
from .bcolors import Bcolors
import concurrent.futures
import copy
import gzip
#from Bio import SeqIO
class Experiment:
def __init__(self, name="", slurm_path=None, modules_path=None):
... |
79263d8b8a14b1c1eb973dca1683be90e905569407719ada3980a6001b30db7c | Python | 63,436 | 1,367 | import gzip
import os
import re
import shutil
import sqlite3
import subprocess
import tempfile
import time
import traceback
import urllib
from collections import defaultdict
from datetime import datetime, timedelta
from enum import Enum
from ftplib import FTP
from io import BytesIO
from pathlib import Path
from typing ... |
f7fbe08df46c69268aaece97b20592fd6bf8010e5850f871673617cd9e47704d | Python | 63,503 | 1,258 | #!/usr/bin/env python
"""
1. Unlock scans_tsv and update it based on runtype metadata
2. Harmonize discrepancy between nifti and behavioral data
3. Starting from Line 242, Behavioral data conversion to BIDS valid format
Same format occurs for pain, vicarious, cognitive data
convert behavioral file into event lists and ... |
85efc33eb11de28c9dd1c705ad0afce46d1d885b782685890cbb0460eca61a3e | Python | 63,587 | 1,426 | #VNC-Quant/VNC-Dist Colavita & Perkins Lab, Faculty of Medicine UOttawa
import streamlit as st
import tkinter as tk
from tkinter import filedialog, simpledialog, messagebox
import pandas as pd
import matplotlib.pyplot as plt
import math
import sys
import threading
import time
import os
import tempfile
import zipfile... |
340b05edd4da7534b2a594f258ca76f8ec676549609d8f14716549930a93ecb6 | Python | 63,799 | 1,675 | #!/usr/bin/env python
import sys, os, subprocess, signal
import multiprocessing
import platform
import string
import re
from datetime import datetime, date, time
from collections import defaultdict
from argparse import ArgumentParser, FileType
osx_mode = False
if sys.platform == 'darwin':
osx_mode = True
MAX_EDI... |
236f19114a96de8259e0e61b9c879c49653b21d737300715c36220f25cbb7561 | Python | 64,205 | 1,612 | # Plot Support for MagellanMapper
# Author: David Young, 2018, 2023
"""Shared plotting functions with the MagellanMapper package.
"""
import dataclasses
import pathlib
from collections import OrderedDict
import math
import os
import warnings
from typing import Any, Callable, Dict, List, Optional, Sequence, \
TYPE_C... |
8d96b9f4875cab2fbad491e5dd7ee483f143dd465b7be1996fcdd5056a858be5 | Python | 65,143 | 1,432 |
#******************************************************************************#
#-------------------------- Sec. 1: Import Libraries --------------------------#
'''
print("Importing Libraries ...", end = " ")
#import pandas as pd
import numpy as np
import random
import time
import h5py
import mne
import csv
import s... |
60712cecb08a7efd696ed155079abca3e21cf237ef81e0aa716a31f6749b9f1a | Python | 65,881 | 1,329 | """
Unit tests for src/createcompendia/diseasephenotype.py.
Sections:
- ``# --- UMLS semantic-type tree mapping ---`` exercises the UMLS
semantic-type-tree → Biolink category map that ``write_umls_ids`` hands to
``umls.write_umls_ids``. The map is built inline, so we capture it by mocking
the downstream ``umls.... |
76b4c2ee4f8fd7bc46d9740dea1368e46d42351a71e66c65ff12a702976f78b2 | Python | 66,182 | 1,519 | import os
import numpy as np
import tensorflow as tf
import tensorflow.keras.backend as K
from tensorflow.keras.optimizers import Adam
from tensorflow.keras.models import Model, Sequential
from tensorflow.keras.layers import *
from tensorflow.keras.losses import mse
from tensorflow.keras.utils import multi_gpu_model
fr... |
722ca271d4d8be3b89e594a2402ba7532e605fb0cb23b7dce416070b304e17ae | Python | 66,327 | 1,617 | # coding=utf-8
# Copyright 2020 Microsoft and the Hugging Face 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 require... |
b95c3714b65d2bb88b8b62f03a9afbbbd61643d08151cf887b459f659d173bf4 | Python | 66,467 | 1,710 | """
Util functions for statistical analysis and algorithms.
Author: Hanna M. Tolle
Date: 2025-02-12
License: BSD-3-Clause
"""
import os
from typing import List, Dict
from dominance_analysis import Dominance
from sklearn.linear_model import LinearRegression
from sklearn.cross_decomposition import PLSRegression
from sk... |
2a52a57a2c00ed18166a0e1b28934d787d5f298fd3355b115ec0de6d4a9d4473 | Python | 66,712 | 1,940 | # -*- coding: utf-8 -*-
# transformations.py
# Copyright (c) 2006-2018, Christoph Gohlke
# Copyright (c) 2006-2018, The Regents of the University of California
# Produced at the Laboratory for Fluorescence Dynamics
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modifica... |
77800845764d7c496166d4ab51bb587e3fcb732a7c2e5ce1fd6bbef6b0aaf273 | Python | 67,834 | 1,731 | import os
import numpy as np
import scipy
import matplotlib.pyplot as plt
# import seaborn as sns
import matplotlib as mpl
from statsmodels.stats.multitest import multipletests
import matplotlib.patches as mpatches
from functools import reduce
# local imports
from auditory_cortex import results_dir, utils, DNN_MODEL... |
c164ec32bdc13b6f1db22a211fc1ff84c50cb8888b091e889f2126b40adc1e61 | Python | 68,084 | 1,355 | """
This module contains the find_lewis() function and associated helper functions to find the
best resonance structures for yarpecules.
"""
import sys
import itertools
import numpy as np
from copy import copy,deepcopy
from ReactBench.utils.taffi_functions import adjmat_to_adjlist,return_rings,graph_seps
from ReactB... |
f5757068361b30bfbe2ee93af8228718fcafe24708e648dc3bb333fff8f860db | Python | 68,359 | 1,117 | """
Deals with models for deepseg module. Available models are listed under MODELS.
Important: model names (onnx or pt files) should have the same name as the enclosing folder.
Copyright (c) 2020 Polytechnique Montreal <www.neuro.polymtl.ca>
License: see the file LICENSE
"""
import os
import json
import logging
impo... |
41e53ca4bdcedefff7feac7cead89aaa7b63a051fe95f6066742d9a66bb46cd6 | Python | 68,755 | 1,651 | #!/usr/bin/env python
# 2D plot image and graph plotter
# Author: David Young, 2017, 2020
"""Plot 2D views of imaging data and graphs."""
import os
import textwrap
from typing import Callable, Optional, Sequence, TYPE_CHECKING, Tuple, Union, Dict, Any
import numpy as np
from matplotlib import colors as mat_colors, gr... |
3595864a6cd177529a8f4b8b392921f2bef4e5e7e44bb3f49c4c2aacc10cf438 | Python | 68,960 | 1,176 | #!/usr/bin/python
import collections
import math
import msprime
import numpy
def OOA(params, inds, length=1e6, mutation_rate=1.45e-8, recombination_rate=1e-8, replicates=300):
"""
This is the Model from Gravel et al. 2013 PNAS for Out of Africa
:param params: all the parameters necessary for this model ... |
1858e659b6caa7e451661336d2e7940a665094233df3d865c2104f70ac41ea9e | Python | 68,975 | 1,534 | # ROI Editor with serial 2D viewer and annotator
# Author: David Young, 2018, 2023
"""ROI editing GUI in the MagellanMapper package.
Attributes:
verify: If true, verification mode is turned on, which for now
simply turns on interior borders as the picker remains on
by default.
"""
from collections ... |
9a94823be4b39f705c061edeeaa5e64c54561d02ab0af64d6a1cc970b7814f18 | Python | 69,487 | 1,585 | """Implementation of CommandLineTool."""
import copy
import hashlib
import json
import locale
import logging
import os
import re
import shlex
import shutil
import threading
import urllib
import urllib.parse
from collections.abc import Generator, Mapping, MutableMapping, MutableSequence
from enum import Enum
from funct... |
48b5ebf1da6af5c033da17885f5e66f4975cc8e457d936f334fdc04566e3fc3f | Python | 69,513 | 1,858 |
# Version: 0.18
"""The Versioneer - like a rocketeer, but for versions.
The Versioneer
==============
* like a rocketeer, but for versions!
* https://github.com/warner/python-versioneer
* Brian Warner
* License: Public Domain
* Compatible With: python2.6, 2.7, 3.2, 3.3, 3.4, 3.5, 3.6, and pypy
* [![Latest Version]
... |
aefe0f2dd216093959d9f2e9bcaf38155925f7a941ec071741ef4a44adefa9d8 | Python | 70,194 | 2,064 | import errno
import json
import logging
import os
import re
import shutil
import stat
import subprocess
import sys
import urllib.parse
from collections.abc import MutableSequence
from io import StringIO
from pathlib import Path
from typing import Any, cast
import cwl_utils.expression as expr
import pydot
import pytest... |
d88ebebf18de9b816747aa34666840e15d4d4cfc4ae4ba9f7c7954b30d8c604b | Python | 71,593 | 1,652 | """
Python API for GuPPy pipeline steps.
Save Input Parameters (automatic provenance)
- Writes GuPPyParamtersUsed.json into each selected data folder.
- In the GUI this snapshot is now written automatically by each numbered step;
``save_parameters_snapshot`` exposes the same write directly for tests/scripts.
This m... |
602cf3a5c033293396916fc8bec4dad965307db627309d1d794fd2363835e560 | Python | 71,673 | 1,226 | import numpy as np
import os
from freesurfer.samseg.Samseg import Samseg
from freesurfer.samseg.utilities import Specification
from freesurfer.samseg.SamsegUtility import *
from freesurfer.samseg import gems
import nibabel as nib
from os.path import join
import logging
from freesurfer.samseg.merge_alphas import kvlMerg... |
e758f0be03cdc3040534c0484d4c78c724e094430c2c9172b681c9fddd64ce64 | Python | 71,679 | 1,815 | """XGBoost pyspark integration submodule for core code."""
import base64
# pylint: disable=fixme, protected-access, no-member, invalid-name
# pylint: disable=too-many-lines, too-many-branches
import json
import logging
import os
from collections import namedtuple
from dataclasses import asdict
from typing import (
... |
8401a90e25d25da621076c9857d7657214e052921159e19febbf202de4526cbe | Python | 71,726 | 1,746 | # -*- coding: utf-8 -*-
from collections import defaultdict
import json
import math
from typing import Any, DefaultDict, Dict, List, Set, Tuple
from django.db import connection
from django.shortcuts import get_object_or_404
from django.utils.decorators import method_decorator
from catmaid.control.authentication impo... |
1e61204338835cc8f9cb5d1384b89d207b1e3f29969ab9ef6c5adbb8efd518d6 | Python | 71,843 | 1,826 | """
Neural network models.
License: BSD 3-Clause
Authors: Hanna M. Tolle, Lewis J. Ng
Date: 2024-11-02
"""
import sys
sys.path.append('../')
import abc
from typing import Dict, Optional
import torch
from torch_geometric.utils import to_dense_adj, scatter, to_dense_batch
from torch_geometric.data import Data, Batch
fr... |
f4e542d45faf347fc9adfe0545b09a571a8d7ada182907a94ddc4c5268b07060 | Python | 72,234 | 1,856 | import sys, tempfile, os, subprocess, time, logging
import h5py
import numpy as np
import pytraj as pt
from . import utils, commands, constants, chemtools # local modules
from . import printit, config # local static methods/objects
# TODO:
# - Add description of each features in the docstring
logger = loggin... |
3ab1699447616845424608d2b4d1125e3d0c3ab9b0d314ba96eaf1c6bd12ab0e | Python | 72,504 | 1,522 | import json
import logging
import os
from pathlib import Path
import numpy as np
import pandas as pd
import panel as pn
from .dandi_file_panel import DandiFilePanel
from .frontend_utils import default_root_path
from ..settings import remember_root_folders, remembered_root_folders
from ..utils.utils import (
commo... |
d1d0d08c66df2e2d205115c2e1d0f003053aa7feaf6e64c7f8d16a261a7e7c94 | Python | 72,566 | 1,559 | """
MetaWIBELE Workflow: characterization module
A collection of tasks for characterization workflow
Copyright (c) 2019 Harvard School of Public Health
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Soft... |
c12348f842577e396dea0fa6a3c1c9192e32ced415800c30c7860859423958fd | Python | 72,669 | 1,648 | import json
import math
from fnmatch import fnmatch
from pathlib import Path
from types import SimpleNamespace
import numpy as np
import pandas as pd
import panel as pn
import pytest
from guppy.frontend.input_parameters import (
ParameterForm,
_table_heading,
_titled_box,
)
from guppy.settings import reme... |
be7a631353d24fc4b57c7cd51aba787c9f2f56672e967052e92dd01ecaa81428 | Python | 72,747 | 1,385 | # coding: utf-8
# Copyright 2019 Sinovation Ventures AI Institute
#
# 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 app... |
7f02f21364ec5b5339ac6173e87cdb523c01ce90949420280e72b72d04de4171 | Python | 73,112 | 1,803 | # -*- coding: utf-8 -*-
"""
Created on Sat May 23 10:38:20 2020
@author: george.dickinson@gmail.com
This program is a Python script developed to analyze the motion of intracellular Piezo1 proteins labeled with a fluorescent tag.
It allows the user to load raw data from a series of image files and track the movement o... |
e3aa3e3de20e7ed263501ee5e27dfeb191f4b839735157bcedc2c5eeb3180d3e | Python | 73,141 | 1,516 | import os
import skeletor as sk
import traceback
import time
import numpy as np
import trimesh
import navis as ns
import subprocess
import pandas
import networkx as nx
import math
from itertools import chain
from trimesh.exchange.obj import export_obj
import tempfile
from typing import Any, List, Iterator
from django.... |
bedfacae69e5a19c04a6e599856a4289be8a6be4edda318caf79b0e4f599f9f8 | Python | 73,224 | 1,454 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Thu Aug 5 11:31:48 2021
@author: schwab
"""
import os
import sys
import time
from pathlib import Path
from typing import Optional
import numpy as np
import torch
import mrcfile
import typer
from tqdm import tqdm
from torch.utils.data import DataLoader
f... |
3c00411456535509194355c9ea2e19f5f7db2213e611727b75a540adc7c31a60 | Python | 73,535 | 1,681 | # -*- coding: utf-8 -*-
from collections import defaultdict
import json
import logging
import numpy as np
from typing import Any, DefaultDict, Dict, List, Optional, Set, Tuple, Union
from django import forms
from django.db import connection
from django.db.models import Q
from django.conf import settings
from django.... |
ef6fcb0fa8b87e16eec17053310197407e468d4ac4a378bad75ed4b8d41758a8 | Python | 73,672 | 2,020 | import json
import unittest
from prov.constants import PROV_TYPE,PROV_RECORD_IDS_MAP
from prov.model import ProvDocument
from provdbconnector.db_adapters.baseadapter import BaseAdapter, METADATA_KEY_IDENTIFIER, METADATA_KEY_TYPE_MAP, METADATA_KEY_NAMESPACES, METADATA_KEY_PROV_TYPE
from provdbconnector.exceptions.datab... |
3b33d6c445a52176138ce3339a57da266bb4e26dd84cb9e8854f9e7380eddfbf | Python | 73,958 | 1,639 | # -*- coding: utf-8 -*-
from datetime import datetime
import gc
from itertools import chain
import logging
import math
import numpy
import os
import progressbar
import re
import subprocess
from typing import Any, Dict, List, Tuple
from django.db import connection
from django.conf import settings
from django.http impo... |
e043631856cc756644ec143ceea2c45df538adab4fe2631c8331970bf1732061 | Python | 74,509 | 1,349 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Fri Feb 7 17:57:52 2025
@author: natalie
"""
import brian2 as b2
import json
import numpy as np
import matplotlib.pyplot as plt
import matplotlib
import matplotlib.gridspec as gridspec
import pandas as pd
import pickle
import os
import scipy
from scipy.... |
1fcf6f3b14d1ebea29d0e16c4037374aaa37a1e6e44f48c47a23f071d242dd7d | Python | 74,516 | 1,735 | #!/usr/bin/env python3
"""Data-centred state-transition model for tumour-cell extravasation across BBB models.
The program separates two levels that must not be confused:
1. experimental models (pillar-based endothelial interface or perfused cylinder);
2. the mathematical model (an observed-state process and discrete... |
293008d4e8ba8bf20f643cc736c7da2e9cb398a1bc9fab58c052f1134c6f5c9f | Python | 74,615 | 1,574 | import os
import re
import sys
import textwrap
from pathlib import Path
import PyQt5.QtCore as Core
import matplotlib.colors as colors
import matplotlib.pyplot as plt
import numpy as np
import pyqtgraph as pg
from PyQt5 import QtCore
from PyQt5.QtCore import Qt
from PyQt5.QtGui import QBrush, QIcon, QFont, QPixmap, QC... |
c622288f36c257ca60c2e5be34e261e606093f6e3d374da6dd881d6cfb5e1d5c | Python | 75,175 | 2,048 | """
Copyright (c) Facebook, Inc. and its affiliates.
This source code is licensed under the MIT license found in the
LICENSE file in the root directory of this source tree.
"""
import logging
import torch.nn as nn
# from typing import Dict, Optional, Union
from typing import Callable, Dict, Optional, Tuple, Union
fro... |
11284e6a9d9b44dcce89718acbadec8a852d70650f94b211a441329a5a42d56b | Python | 75,391 | 1,913 | # This is where all the ultility functions are stored
# The first function is to load in the data
import dask.array as darr
import numpy as np
import pandas as pd
import xarray as xr
import zarr as zr
from os.path import isdir, isfile
from os.path import join as pjoin
from os import listdir
from typing import Callable... |
9b6d9e080079b9f14eb404bfc2129d61d3a4af3ec32205e293749bf7eff69752 | Python | 75,504 | 1,983 | """Built-in metrics.
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import abc
import numpy as np
import six
import types
from . import backend as K
from .layers import Layer
from .losses import mean_squared_error
from .losses import mean_absolute_erro... |
5562ae1ae682e0138137c600b28db5715edccf49043343e9ca0f50d1858f64ad | Python | 75,522 | 1,502 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Mon Jan 15 14:13:05 2024
@author: schwab
"""
import os
import sys
import time
from pathlib import Path
from typing import Optional
import numpy as np
import torch
import mrcfile
import typer
from tqdm import tqdm
from torch.utils.data import DataLoader
... |
87533e78391edf6426269f9176508ee616be775986220dd381d115a03f1f0d52 | Python | 75,879 | 1,619 | from __future__ import print_function
from __future__ import division
from future import standard_library
standard_library.install_aliases()
#from builtins import str
from builtins import range
from quantities.quantity import Quantity
import sciunit
from sciunit import Test,Score
try:
from sciunit import Observatio... |
c3c1b45e3e75eeaffe3c7cbf56966712735565f28b011f720ee2e473cf16cf83 | Python | 75,882 | 1,789 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
@author: Rui Peixoto and Michael Janecek
"""
#%% Choose file & define QC criteria
# Define criteria as dictionary where the key is the column name and the value is a tuple (condition, threshold)
criteria_QC = {
#'LR': ('=', ["Right","Left"]), # use 'LR':('=',"L... |
19b1211a35d5c525eb8a81557cb2d1ec9efffbba903a204eb9cfa663f7c7b15b | Python | 76,694 | 2,048 | # /// script
# requires-python = ">=3.10"
# dependencies = [
# "matplotlib",
# "numpy",
# "scipy",
# ]
# ///
"""Generate SVG figures for the isosbestic-correction explanation page.
The correction math (np.polyfit degree 1, deltaFF) mirrors GuPPy's
src/guppy/analysis/z_score.py exactly, and the synthetic-fa... |
723408642c460756c7a56da0cea2c5518f83ad3b86a24d42a551c9bcfec459ab | Python | 77,018 | 1,899 | # -*- coding: utf-8 -*-
from collections import defaultdict
import dateutil.parser
import re
from typing import Any, DefaultDict, Dict, FrozenSet, List, Optional, Set, Tuple, Union
from django.http import HttpRequest, HttpResponse, JsonResponse
from django.shortcuts import get_object_or_404
from django.db import con... |
8c71533e95118c5f8f3d2288a6f3440a1c4809d605d1121396e02c43b0f902b9 | Python | 77,185 | 1,997 | import glob
import logging
import random
import tempfile
import uuid
from collections import namedtuple
from typing import Generator, Iterable, List, Sequence
import numpy as np
import pytest
from pyspark import SparkConf
from pyspark.ml import Pipeline, PipelineModel
from pyspark.ml.evaluation import BinaryClassifica... |
22218db81c5d743c928913f620388eba6678e1ac8aaf7c729a7d1917b058b20c | Python | 77,380 | 1,551 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
import copy
import math
import random
import torch
import torch.nn as nn
import torch.utils.checkpoint
from torch.nn import CrossEntropyLoss
from typing import List, Optional, Tuple, Union
from transformers.modeling_utils import PreTrainedModel
from transformers.activati... |
6b11fb7c601b2b72101480bab819ae07f260a85dd9f8d241a84236d40fd602ea | Python | 78,708 | 2,249 | """Copyright 2019-2025, XGBoost contributors"""
import asyncio
import json
import os
import pickle
import socket
import tempfile
from concurrent.futures import ThreadPoolExecutor
from functools import partial
from pathlib import Path
from typing import Any, Dict, Generator, Literal, Optional, Tuple, Type, Union
impor... |
668c8245199b508bc4c65cbe944182a8a81527bdc87e5873d628dbb5d5bd0de2 | Python | 78,815 | 2,142 | import threading
import pytest
import numpy as np
import pandas as pd
from numpy.testing import assert_allclose
import sys
import scipy.sparse as sparse
from flaky import flaky
import keras
from keras import losses
from keras import metrics
from keras.layers import Layer, Activation, Dense, Dropout, Conv2D, Concatena... |
aeffd4d10397efa61229c73a2f81fca5401bb598c89b61713fcb96dcaf7d59e7 | Python | 79,783 | 2,038 | # -*- coding: utf-8 -*-
import array
from collections import defaultdict, deque
from datetime import datetime
from functools import partial
import json
import logging
from math import sqrt
import msgpack
import networkx as nx
from psycopg2.extras import DateTimeTZRange
import pytz
import struct
from typing import Any,... |
5a9fbbf61fbb5850be9fbd692588d315406574959503af71d249ee3ea2dafa1f | Python | 79,820 | 1,683 | """
Spinal Cord Registration module
Copyright (c) 2020 Polytechnique Montreal <www.neuro.polymtl.ca>
License: see the file LICENSE
"""
import logging
import os # FIXME
import shutil
import psutil
from math import asin, cos, sin, acos, radians
import numpy as np
from scipy.ndimage import gaussian_filter1d, sobel, co... |
1291f50eb8980e3eb29f388b39b7890db8140a2458f7f1436ccc11fb78228748 | Python | 79,855 | 2,260 | # pylint: disable=too-many-arguments, too-many-locals
# pylint: disable=missing-class-docstring, invalid-name
# pylint: disable=too-many-lines
"""
Dask extensions for distributed training
----------------------------------------
See :doc:`Distributed XGBoost with Dask </tutorials/dask>` for simple tutorial. Also
:doc... |
d9a2c1d25f94691a967731e6319ab86b1d40c01908b2523de4cab8885768486e | Python | 81,279 | 1,829 | # Atlas refinement
# Author: David Young, 2019, 2023
"""Refine atlases in 3D.
"""
from collections import OrderedDict
from enum import Enum
import os
from typing import Dict, List, Optional, Sequence, Tuple, Union, Any
try:
import itk
except ImportError:
itk = None
import numpy as np
import pandas as pd
try:
... |
5592a1259139d2cb0db6c21536a2a15cce48ff3e447f0e14d07c6c8cb9995400 | Python | 81,945 | 1,964 | """
SCT Image API
Copyright (c) 2018 Polytechnique Montreal <www.neuro.polymtl.ca>
License: see the file LICENSE
"""
# TODO: Sort out the use of Image.hdr and Image.header --> they seem to carry duplicated information.
import sys
import os
import errno
import itertools
import warnings
import logging
import math
from... |
02a6eea0a2057aa386a2e30795587cc98503b97dafffa685b9a4835584588432 | Python | 82,240 | 1,954 | # coding=utf-8
# Copyright 2021 The IDEA 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 a... |
e12094040378288f8a89fe615e6bf29ea7c01aa25cf479ffd5aec8a21fda171c | Python | 82,500 | 2,228 | """Evaluation module (adapted from bluepyemodel)."""
# Copyright (c) 2022 EPFL-BBP, All rights reserved.
#
# THIS SOFTWARE IS PROVIDED BY THE BLUE BRAIN PROJECT ``AS IS''
# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
# THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
# P... |
0e7663996beb5347824a8ab2218c66495fb5ffbaa14c21b14bbe08dcdef52e07 | Python | 83,373 | 2,211 | import logging
import os
import subprocess
import tempfile
import time
from typing import ClassVar
import h5py
import numpy as np
import pytraj as pt
from . import ( # local modules # local static methods/objects
commands,
config,
constants,
log,
utils,
)
# chemtools pulls in rdkit and openbab... |
ac4736863993bd7f5bd01403f99e2bc3fe72011dbd784ea5487fe158a80bc24e | Python | 83,606 | 2,130 | # -*- coding: utf-8 -*-
"""
Created on Sat May 23 10:38:20 2020
@author: george.dickinson@gmail.com
This program is a Python script developed to analyze the motion of intracellular Piezo1 proteins labeled with a fluorescent tag.
It allows the user to load raw data from a series of image files and track the movement o... |
eee0523c0544572e511bfa9fc9e7c2ee7b7cab3cd9749173f33e3f98db76e86a | Python | 83,702 | 7,636 | """
Copyright (c) Facebook, Inc. and its affiliates.
This source code is licensed under the MIT license found in the
LICENSE file in the root directory of this source tree.
k-hot elemental embeddings from QMOF, motivated by the following Github Issue threads:
https://github.com/txie-93/cgcnn/issues/2
https://github.... |
dab3ff7183bcec6f93110d5c1bcecd65610f809f3c422512a773b23d717382f1 | Python | 84,072 | 2,501 | """
SO3LR Molecular Dynamics Module
This module provides functions for running molecular dynamics simulations
with the SO3LR Machine Learned Force Field.
It includes functionality for:
- NVT simulations
- NPT simulations
- Geometry optimization
- Trajectory output in hdf5 and extxyz formats
- Restart capabilities
"""... |
3dbafc90631bf0e45009ea4febcb0ceeaffdfdddc485441335f1e67278ef3132 | Python | 84,414 | 2,265 | # pylint: disable=too-many-arguments, too-many-locals, invalid-name, fixme, too-many-lines
"""Scikit-Learn Wrapper interface for XGBoost."""
import copy
import json
import os
import warnings
from concurrent.futures import ThreadPoolExecutor
from inspect import signature
from typing import (
Any,
Callable,
D... |
d748a8531673468cc8c9d497a23c4a68450f1180e6e2b459936846a92104cb4d | Python | 85,684 | 2,100 | # -*- coding: utf-8 -*-
import colorsys
from datetime import datetime, timedelta
import enum
import logging
from random import random
import re
import sys
from typing import Any, Dict, Tuple
import urllib
import urllib.parse
import uuid
from django import forms
from django.conf import settings
from django.contrib.aut... |
bc3802dbe0b05cd47d388ce26132175c70015dd99a1a90a7c2888c5674c263d1 | Python | 85,878 | 2,221 | # -*- coding: utf-8 -*-
# tests/test_backmapping_em1_em2.py
################################################################################
# EncoderMap: A python library for dimensionality reduction.
#
# Copyright 2019-2024 University of Konstanz and the Authors
#
# Authors:
# Kevin Sawade, Tobias Lemke
#
# Encoderma... |
d1189d5769c0224e893ce2f70104150cdb61b82078734414bea7af5e84c931f2 | Python | 87,482 | 1,510 | #!/usr/bin/env python
#
# Analyze lesions
#
# Copyright (c) 2014 Polytechnique Montreal <www.neuro.polymtl.ca>
# License: see the file LICENSE
import os
import sys
import pickle
from typing import Sequence
import textwrap
import numpy as np
from skimage.measure import label
from scipy.ndimage import center_of_mass
f... |
2e347b300f195c6f1d565b1475152d7c342a2cc7ed4324cca020cc7335a37798 | Python | 87,539 | 2,358 | # Version: 0.29
"""The Versioneer - like a rocketeer, but for versions.
The Versioneer
==============
* like a rocketeer, but for versions!
* https://github.com/python-versioneer/python-versioneer
* Brian Warner
* License: Public Domain (Unlicense)
* Compatible with: Python 3.7, 3.8, 3.9, 3.10, 3.11 and pypy3
* [![L... |
49e024f344c0e75aaa13b564cdc94ea2b762558dae6b941dd41fad8a49d83d3f | Python | 87,828 | 2,537 | # Copyright (c) OpenMMLab. All rights reserved.
import copy
import inspect
import warnings
from typing import Dict, List, Optional, Sequence, Tuple, Union
import cv2
import mmcv
import mmengine
import numpy as np
from mmcv.transforms import RandomFlip as MMCV_RandomFlip
from mmcv.transforms import Resize as MMCV_Resiz... |
08e44eca1c13ef03cf202c88560ae93e9b45ea81a9a0008607c585b5ea33926e | Python | 89,163 | 2,091 | # -*- coding: utf-8 -*-
# encodermap/misc/backmapping.py
################################################################################
# EncoderMap: A python library for dimensionality reduction.
#
# Copyright 2019-2024 University of Konstanz and the Authors
#
# Authors:
# Kevin Sawade, Tobias Lemke
#
# Encodermap i... |
5a728d27a8fd5951cf4ca05894af0e20c972fcd3c12d4c0904e2af53a3b3201f | Python | 89,420 | 2,258 | # -*- coding: utf-8 -*-
# encodermap/trajinfo/info_single.py
################################################################################
# EncoderMap: A python library for dimensionality reduction.
#
# Copyright 2019-2024 University of Konstanz and the Authors
#
# Authors:
# Kevin Sawade
#
# Encodermap is free sof... |
a891212d1a76657455959a5dec8802708ee3a254cff995a15d75105b1702afbb | Python | 89,915 | 1,975 | # -*- coding: utf-8 -*-
from io import StringIO
import json
import platform
import re
from typing import Any, Dict
from unittest import skipIf
from urllib.parse import urlencode
from django.db import connection, transaction
from django.shortcuts import get_object_or_404
from guardian.shortcuts import assign_perm
fro... |
7ff263ec9bcb09954ce3e58b27a7fbd072fd00cd12f72f9aac81f72b2d678544 | Python | 90,052 | 1,911 | """Training-related part of the Keras engine.
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import collections
import warnings
import copy
import numpy as np
from .network import Network
from .base_layer import Layer
from . import training_utils
from ... |
85ad7c90b77ac2bf7e53ebcb8a49c9d57d1c613f0312bb9774ff47988cf5684c | Python | 90,234 | 2,086 | # coding=utf-8
# Copyright 2021 The IDEA 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 a... |
3a9dd70cd6e927fe18f1d00ebc7862211849424c824e999b9f1c9674629ba695 | Python | 90,605 | 2,337 | # -*- coding: utf-8 -*-
# encodermap/loading/featurizer.py
################################################################################
# EncoderMap: A python library for dimensionality reduction.
#
# Copyright 2019-2024 University of Konstanz and the Authors
#
# Authors:
# Kevin Sawade
#
# Encodermap is free softw... |
cbd80286b2f45b921a7ace93a352d5130268f97c8b21a494f5a949901f182de8 | Python | 91,342 | 2,151 | import pytest
from numpy.testing import assert_allclose
import numpy as np
import scipy.sparse as sparse
import warnings
from keras import backend as K
from keras.utils.conv_utils import convert_kernel
from keras.backend import numpy_backend as KNP
try:
from keras.backend import cntk_backend as KC
except ImportE... |
e58254dc7b919b695f415c5d56d745dfb57305c0496eb789e6e6d256b734141b | Python | 92,039 | 2,438 | # This file is part of h5py, a Python interface to the HDF5 library.
#
# http://www.h5py.org
#
# Copyright 2008-2013 Andrew Collette and contributors
#
# License: Standard 3-clause BSD; see "license.txt" for full license terms
# and contributor agreement.
"""
Dataset testing operations.
Tests all d... |
1c196c444a6835be43a1d9fc6f307dcf40ddae2fcefb4c9cb3e690daa6f362ae | Python | 92,855 | 2,027 | import numpy as np
import matplotlib.pyplot as plt
import matplotlib.transforms as mtransforms
from fig_utils import *
import os
from matplotlib import scale as mscale
from fig_utils import AsymScale
mscale.register_scale(AsymScale)
import seaborn as sns
from matplotlib import gridspec
import matplotlib.patches as patc... |
8257e2d82207899ab3fe87043efa0827947c8769ae1934f62ab913c6e66e0d52 | Python | 92,878 | 2,041 | """Command line interfaces for SO3LR."""
import os
import sys
import jax
import ase
import time
import yaml
import click
import logging
import warnings
import platform
import numpy as np
from pathlib import Path
from ase.io import read, write
from typing import Dict, List, Tuple, Optional, Union, Any, Callable
from .... |
2a054ad11b09d986e2ac9b8bc8ded88b5579f72364575921ace6703b9ec20601 | Python | 92,972 | 2,921 | from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import cntk as C
import numpy as np
from .common import floatx
from .common import epsilon
from .common import image_data_format
from .common import normalize_data_format
from ..utils.generic_utils import trans... |
bd4ce6aafcca088a64e2a46e25aaf3200d8d94825de3690caf77fa9c920e2d35 | Python | 93,340 | 2,038 | from __future__ import print_function
from __future__ import division
from future import standard_library
standard_library.install_aliases()
#from builtins import str
from builtins import range
from quantities.quantity import Quantity
import sciunit
from sciunit import Test,Score
try:
from sciunit import Observatio... |
7946deaa6ab0e477415bfa237b76d489fcb355ec82f704d471fe801a51c192a7 | Python | 95,475 | 2,495 | # -*- coding: utf-8 -*-
# encodermap/plot/interactive_plotting.py
################################################################################
# EncoderMap: A python library for dimensionality reduction.
#
# Copyright 2019-2024 University of Konstanz and the Authors
#
# Authors:
# Kevin Sawade, Tobias Lemke
#
# Enc... |
39510cc3c1c97b139ab36283920d491ae756b90e215b30456e68259008de7646 | Python | 95,963 | 2,254 | # -*- coding: utf-8 -*-
from django.db import migrations
from django.conf import settings
# This migration will remove all existing history tables and replace them with
# a new version, which also keeps track of transaction IDs. This happens either
# in live tables directly or as part of tracking table (formally tim... |
ccc7be2f24a81feb32c596a05b2b80e1b836b371cc7d950561370a331979deec | Python | 96,038 | 2,206 | """
Event-based shuffling utilities for calcium transient analysis.
This module provides both temporal and spatial shuffling capabilities:
TEMPORAL SHUFFLING:
- Shuffles the timing of calcium transients while preserving spatial relationships
- Uses ITI (inter-transient interval) permutation to maintain realistic timi... |
5e62e85e359275ebc18ed64f08f5099370de1f9aff57561ff1bbad53782e5965 | Python | 96,949 | 2,002 | # coding=utf-8
# Copyright 2021 The IDEA 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 a... |
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