sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
3e041623cfecd4061a8d0d268ce7b6e101f0c2ca9b73995fad91fbc7c0b71966 | Python | 10,448 | 340 | # --- THIS FILE IS AUTO-GENERATED ---
# Modifications will be overwitten the next time code generation run.
from plotly.basedatatypes import BaseTraceHierarchyType as _BaseTraceHierarchyType
import copy as _copy
class Tickfont(_BaseTraceHierarchyType):
_parent_path_str = "scatterternary.marker.... |
15d918b114392e5e203b7aa436cde10420da737865fa4012ff41e91103ee7ffb | Python | 10,449 | 272 | from typing import Optional, Union
try:
from typing import Literal
except ImportError:
from typing_extensions import Literal
import gpytorch
import numpy as np
import pandas as pd
import torch
from anndata import AnnData
from gpytorch.likelihoods import GaussianLikelihood
from numpy import ndarray
from scipy.... |
585e99f9c705a5924f28a5496bb026e0a7e7b3dcd936f16a94d2cc743a5a9069 | Python | 10,449 | 316 | __author__ = 'quentin'
import os
import logging
import datetime
import json
import traceback
import random
import subprocess
import time
import urllib.request, urllib.error, urllib.parse
import http.client
class WrongMachineID(Exception):
pass
try:
from netifaces import ifaddresses, AF_INET, AF_LINK
excep... |
96c91a05ca9fddb3d9ba91b4df67ee2dfefa418bf9c29010ea3b225da739e818 | Python | 10,450 | 264 | from __future__ import absolute_import
import collections
import logging
import os
import re
from pip._vendor import pkg_resources, six
from pip._vendor.packaging.utils import canonicalize_name
from pip._vendor.pkg_resources import RequirementParseError
from pip._internal.exceptions import InstallationError
from pip... |
9a5cf13f742ae3f2b760eb8f334110c6df756ebb030f575890fda446ee0a31d4 | Python | 10,450 | 341 | # --- THIS FILE IS AUTO-GENERATED ---
# Modifications will be overwitten the next time code generation run.
from plotly.basedatatypes import BaseTraceHierarchyType as _BaseTraceHierarchyType
import copy as _copy
class Textfont(_BaseTraceHierarchyType):
_parent_path_str = "histogram2dcontour"
... |
3ae7da1c666c715d8df4f6e2b9af702964abf2c12872d55bdbd5c094c99bbf14 | Python | 10,452 | 297 | import os
import re
from datetime import datetime, timedelta, timezone
from time import monotonic, sleep
from unittest.mock import ANY
import pytest
from celery import uuid
from celery.utils.nodenames import anon_nodename
from celery.worker import state as worker_state
from .tasks import add, sleeping
NODENAME = an... |
90b45ec144014697b3629d4322448cb8ccf009106d19fb8b00b30eb006839125 | Python | 10,455 | 346 | from anndata import AnnData
from typing import Optional, Union
import numpy as np
import pandas as pd
import networkx as nx
from scipy.spatial.distance import cdist
from stlearn.utils import _read_graph
from sklearn.metrics import pairwise_distances
def global_level(
adata: AnnData,
use_label: str = "louvain"... |
8614ddf0101ae1907a5de25ea727919c8a110082939e426a65c3473103d51563 | Python | 10,457 | 258 | import glob
import os
import numpy as np
import pandas
from astropy.stats import circmean
from mne import fit_dipole, create_info, EvokedArray, make_ad_hoc_cov
from mp_dip.old.config import RESAMPLING_FREQUENCY
from mp_dip.utils.interpolate_head_features import INTERP_SIZE
from scipy.signal import convolve2d
from sc... |
3479b04b21df5dba7ecc0bc8792bc941afd4f098b8372a3a2d0949fe857ffc2f | Python | 10,458 | 232 | import os
import torch
from collections import OrderedDict
from abc import ABC, abstractmethod
from . import networks
class BaseModel(ABC):
"""This class is an abstract base class (ABC) for models.
To create a subclass, you need to implement the following five functions:
-- <__init__>: ... |
50ff349455d9c59d4318e275f24b8e7e6ad856726183910d0b8d6488c1845cc6 | Python | 10,459 | 271 | #!/usr/bin/env python3
from DeepRegFinder.preprocessing_functions import _bed_to_saf, process_histones, ChannNormDataset
from DeepRegFinder.prediction_functions import *
from DeepRegFinder.traineval_functions import prediction_loop
from DeepRegFinder.nn_models import create_model
from torch.utils.data import Dataset, T... |
c82ffe723c18d5f88065d50538d25244902c19a4f3ae30bd2de765d72421a4e5 | Python | 10,462 | 214 | from typing import Optional
import pytorch_lightning as pl
from pytorch_lightning import Callback
from pl_bolts.models.regression import LogisticRegression
from torchmetrics.functional import pairwise_cosine_similarity
import torch
from torch.utils.data import TensorDataset, DataLoader
from metrics.metrics import co... |
42fc4b1a4f8fe3502dfaca6e2d1a52d970bda385a774445e5c1ef59cb3ce3c30 | Python | 10,465 | 325 | from __future__ import annotations
import json
import os
import random
from copy import deepcopy
import matplotlib.pyplot as plt
import numpy as np
from tqdm.auto import tqdm
from ..utils import COLORS
from ..utils import transform_gt_into_pr
from .count_curve import calc_scores
from .count_curve import count_point
... |
630311db14475a70d687d070a90019a93576960b1aaf9c670aecef12301294dd | Python | 10,465 | 258 | #!/usr/bin/env python
# coding: utf-8
# overall goal ------------------------
# the goal is to put only one HLA allele in testing data, while make sure that
# the tcrs in training + validation do not have overlap with those in test
# still want to sample according to frequency matching
# put one target HLA allele in ... |
abfbb16f7774820a2e8cf69cf15ae04209bc49d44c4de1b68825938262e4ef82 | Python | 10,469 | 214 | import numpy as np
import os
import sys
import ntpath
import time
from . import util
from . import html
from subprocess import Popen, PIPE
if sys.version_info[0] == 2:
VisdomExceptionBase = Exception
else:
VisdomExceptionBase = ConnectionError
def save_images(webpage, images, names, image_path, aspect_ratio... |
bf8a597da51053c88e5336af57f7fd7cb6a99b11945d382d5c934bc103afbc12 | Python | 10,469 | 258 | """A09 listA row 24: every tabular/file export carries capture-honesty facts.
One shared source (torchlens._capture_honesty) feeds every exporter in
torchlens.export, the debug DataFrames, Trace.to_pandas, the accessor tables,
and the fastlog tables -- through the format-appropriate slot (comment
preamble, metadata bl... |
01a932ac6a62ac9c77cd949bb3cb21d6a8be739cbeb7a10013a67d77cd8302d4 | Python | 10,470 | 226 | # 均匀采样效果较差
import json
import numpy as np
import os, sys
import random
from collections import Counter
from sklearn import preprocessing
from sklearn.metrics import f1_score
from sklearn.metrics import confusion_matrix
import torch
import torch.nn as nn
import torch.nn.utils.rnn as rnn_utils
import torch.nn.functional ... |
bf0857d7991194a0434c156f1084976735438c456dc299668fc361eefab1eec6 | Python | 10,472 | 159 | from __future__ import print_function
import sys
from bisect import bisect_left
from collections import defaultdict
from math import pow, sqrt
from svim.SVSignature import SignatureTranslocation, SignatureInsertionFrom, SignatureClusterBiLocal
from svim.SVCandidate import CandidateDuplicationInterspersed
from svim.SV... |
efdf04d8073379f88459b4064cd0a45879d19abed8c19086b4f59fd9518d129e | Python | 10,475 | 254 | from __future__ import print_function, unicode_literals, absolute_import, division
from six.moves import range, zip, map, reduce, filter
from six import string_types
import numpy as np
import argparse
import warnings
from packaging.version import Version
from ..utils.tf import keras_import, BACKEND as K
keras = kera... |
194d6be2c2b9798a6e32c8a27f196b0fc6a430d3e529e30f6a3b16643a753bdb | Python | 10,477 | 252 | """Tests for how XCP-D derivatives are written.
The 4D denoised BOLD outputs are written in worker processes rather than on
nipype's main thread, and every derivative niworkflows rewrites or copies is
compressed with ISA-L instead of zlib.
"""
import gzip
import nibabel as nb
import numpy as np
import pytest
from ni... |
1cdab4db672d7302ccba8905ae74f07e0641df5f03652b4132a3ef29184fc482 | Python | 10,479 | 262 | # -*- coding: utf-8 -*-
"""
Created on Tue Aug 2 14:47:43 2022
@author: Lenovo
"""
from scipy import signal
import numpy as np
import math
import matplotlib.pyplot as plt
from random import randint,seed
import os
class tools:
def __init__(self):
self.my_dict={10:{0:{"Idle":[[1.73,5.014],... |
4aae17dfe6606c118327c9998d129d570c70889ad86f6120ce712a789f0d7ab7 | Python | 10,480 | 319 | from collections import Counter
import itertools
from permacache import permacache, stable_hash
import tqdm.auto as tqdm
import numpy as np
from sklearn.linear_model import LogisticRegression
from modular_splicing.data_for_experiments.standardized_sample import (
standardized_sample,
)
from modular_splicing.eval... |
cddbe1ee424458e63c30949173d78c977e23bdc7721c16743e3e4af7ff398c16 | Python | 10,480 | 416 | """Statistical-mechanics neural machines, 1980-2002.
Paper: Gardner 1988, "The space of interactions in neural network models";
Kinzel and Kanter 2002, "Interacting neural networks and cryptography".
Tiny sign, erf, parity, and spin-glass modules expose the canonical order
parameters and energies while omitting traini... |
0388a094129a577f1e9fd958915fce361b679f0bb7cf760ccf21b381ecc25b07 | Python | 10,481 | 286 | #!/usr/bin/env python
"""
tune_servo.py -- Interactive servo angle tuning for Rev D Magpi hopper.
Run this script directly on the Raspberry Pi to find the correct up_angle
and down_angle values for a panel's hopper servo. Once you have good values
the script can write them into this box's own panel_config.json as
hopp... |
978dd26bf7ebdea4cd767dfb45588d3a3db511c90a22ffa02710ed575bf33c14 | Python | 10,482 | 270 | #!/usr/bin/env python3
"""
Hard-reject commit messages or push payloads that contain semantic-release
major-bump triggers (Conventional Commits ``!`` markers or ``BREAKING CHANGE:``
footers).
TorchLens stays on the 2.x family per the locked project release policy.
The PyPI 1.0.0 and 2.0.0 slots have already been burne... |
8ffb496c76cd9cffb2c4060b18e9caeb16deae3998a74a67b2bbe2d18f25144e | Python | 10,483 | 263 | """Round-18 PARAM host-escape parity: bring PARAMETER host-escape handling to parity with the
(already-correct) registered-BUFFER handling on BOTH axes -- untracked host WRITE and read-only
host READ.
Params were inconsistent with buffers:
* Too LOOSE on writes (F2, CRITICAL). A zero-copy numpy alias of a PARAM acqui... |
8638bbad04491b73e70b2e5334e07115eeb1090f17f0e39a3d73026cf6d3fd69 | Python | 10,485 | 267 | from multiprocessing import Pool
from utils import mapper, valid_smiles, read_smiles_csv, get_mol, canonic_smiles, compute_scaffolds, fingerprints, calc_self_tanimoto, side_no_sca_change, mol_passes_filters
import argparse
import pandas as pd
from utils import canonicalize_smiles_from_file
import numpy as np
def fract... |
03f98b55faacd145066a1ebf7d635bdc3293dc6bc185229aeeaa7610102bc966 | Python | 10,486 | 327 | # %%
'''
Perform statistics on connectivity results when considering
the contigency awareness
'''
from nilearn import plotting
from numpy.ma import mask_rowcols
import pingouin as pg
import seaborn as sns
import h5py
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
from bct.nbs import nbs_bct
im... |
d99d942a1ae872a841b4c2d5c60807e0756d79905b106983986710548c783834 | Python | 10,487 | 341 | # --- THIS FILE IS AUTO-GENERATED ---
# Modifications will be overwitten the next time code generation run.
from plotly.basedatatypes import BaseLayoutHierarchyType as _BaseLayoutHierarchyType
import copy as _copy
class Grouptitlefont(_BaseLayoutHierarchyType):
_parent_path_str = "layout.legend... |
33b6f45fed0cbcbba9a79b889ff323294523ce36859b52952ab53e1a689a2262 | Python | 10,488 | 341 | #!/usr/bin/env python
"""
Small library with cheminformatic functions based on openbabel and pgchem.
Copyright 2012, Bjoern Gruening and Xavier Lucas
"""
import glob
import re
import subprocess
import sys
import tempfile
from multiprocessing import Pool
import numpy as np
try:
from galaxy import eggs
... |
4d50125cd6e0257187f4fbd771cc2828c483f5e4261b2a7de9aeaeedd40281af | Python | 10,489 | 224 | #!/usr/bin/env python3 -u
# -*- coding: utf-8 -*-
import os
import argparse
import json
import pandas as pd
import numpy as np
from datetime import datetime
from sklearn.model_selection import train_test_split
from sklearn.svm import SVC
from preprocessing import get_zmap_dataset, features_from_df, preprocess, Featur... |
b1fde9a64e38bec2defa76d3e8e0e302791adcdd2a4927a65311ac05e6ae9e79 | Python | 10,493 | 341 | # --- THIS FILE IS AUTO-GENERATED ---
# Modifications will be overwitten the next time code generation run.
from plotly.basedatatypes import BaseLayoutHierarchyType as _BaseLayoutHierarchyType
import copy as _copy
class Grouptitlefont(_BaseLayoutHierarchyType):
_parent_path_str = "layout.hoverl... |
e29152fde0971d1c099423587c57ebd45ffd8a1599f1ef5337dee773555e830a | Python | 10,493 | 303 | """Saved-graph double-VJP projective gradient regression tests."""
from __future__ import annotations
from collections.abc import Callable
from pathlib import Path
import pytest
import torch
from torch import nn
import torchlens as tl
from torchlens.backends.torch._tl import is_decorated_function
from torchlens.bac... |
650be0c8cd007e69812aad4e74e52503a49ce91b5d2dd8e5a3091b3c41defc04 | Python | 10,495 | 414 | import json
import os
import shlex
import numpy as np
with open("../data/rbnsp_motifs_split.json") as f:
rbnsp_split_half = json.load(f)
with open("../data/rbnsp_motifs_split_90.json") as f:
rbnsp_split_90 = json.load(f)
with open("../data/rbnsn_motifs_split_90.json") as f:
rbnsn_split_90 = json.load(f)... |
4910213e018c790e1983fca9d067b2765f2fc194bf634fb569ec4ec1d7665900 | Python | 10,496 | 377 | #!/usr/bin/env python3
import dataclasses
import re
import secrets
import subprocess
import time
import requests
import typer
from pydantic_settings import BaseSettings, SettingsConfigDict
from typing_extensions import Annotated
# TODO: use pydantic settings
class FiefSettings(BaseSettings):
fief_main_admin_api_... |
de41ee8bb9f904f160de2c8ff56d672d95245e317151e84fae1b684a9f46f9aa | Python | 10,498 | 211 | from __future__ import division
import unittest
import numpy as np
from wyrm.types import Data
from wyrm.processing import segment_dat
from wyrm.processing import swapaxes
class TestSegmentDat(unittest.TestCase):
def setUp(self):
# create 100 samples and tree channels data
ones = np.ones((100,... |
ad67eeba13d927fa82c6898f7e2fd843c2971094e3654b94ac1d35713e347a8a | Python | 10,502 | 341 | # --- THIS FILE IS AUTO-GENERATED ---
# Modifications will be overwitten the next time code generation run.
from plotly.basedatatypes import BaseLayoutHierarchyType as _BaseLayoutHierarchyType
import copy as _copy
class Font(_BaseLayoutHierarchyType):
_parent_path_str = "layout.annotation.hover... |
bad3eb15b99e6a8cd426d012d43d51c6bcecd92d1d6aeb76fd6039a2a8874073 | Python | 10,504 | 276 | import torch
import os
import glob
import subprocess
import flirpy
import flirpy.io.seq
from flirpy.io.fff import Fff
import numpy as np
import imageio.v3 as iio
import cv2
import time
import csv
from datetime import datetime
from tqdm import tqdm
# Define the paths
script_path = r"C:\Users\jland\anaco... |
c14f7fdc83afb82a7e5392480815f3df412db3d2d9bf8e641980fa15b7c9abfc | Python | 10,507 | 359 | import h5py
import numpy as np
import torch
from torch.utils.data import DataLoader
from torch.nn.functional import softmax
import torch.nn as nn
import torch.nn.functional as F
import os
from utils import (
extract_dist,
list2seq,
permute,
)
from random import shuffle
import itertools, operator
from tqd... |
37ea6528af4a233755147aad3a202dc06bf82bdc3d7cfcecdf79e96742a1cd8e | Python | 10,508 | 273 | from typing import Callable, Optional, Tuple, Union, Literal
import numpy as np
import torch
import torch.nn as nn
from pytorch_lightning import seed_everything
from pytorch_lightning.core import LightningModule
from pytorch_lightning.utilities.model_summary import ModelSummary
from tqdm.auto import tqdm
from .base._... |
9798478a6ff53312f8b90f94889e3191591b2df22b031e357afd82920696d00e | Python | 10,508 | 263 | # -*- coding: utf-8 -*-
"""
Created on Tue Aug 2 14:47:43 2022
@author: Lenovo
"""
from scipy import signal
import numpy as np
import math
import matplotlib.pyplot as plt
from random import randint,seed
import os
class tools:
def __init__(self):
self.my_dict={10:{0:{"Idle":[[1.73,5.014],... |
cec8810ffeeb362334737bb08dfd69a8781a5258ae715bf7eb5b6283c748f755 | Python | 10,508 | 289 | from abc import abstractmethod
import numpy as np
import tensorflow as tf
from tensorflow.python.ops import random_ops
from tensorflow.python.ops import stateless_random_ops
from tensorflow.keras.initializers import Initializer
import sys
from pdb import set_trace
# Typing
from typing import Optional
INIT_TECHNIQUES =... |
696dded6668fee33a2c3fed505aa954b983ca79f39a92d456d018ee3306a389f | Python | 10,517 | 324 | """Tigramite causal discovery for time series."""
# Author: Jakob Runge <jakob@jakob-runge.com>
#
# License: GNU General Public License v3.0
from __future__ import print_function
from scipy import stats
import numpy as np
import sys
import warnings
from .independence_tests_base import CondIndTest
class ParCorr(Cond... |
d1d2ea439caf6c03321463432dde4dc951a8838718f147eb5d32cfc58224ce0f | Python | 10,518 | 263 | """
run_pipeline.py — full experiment, healthy controls and post-stroke patients
1. Load data_loader_01 per-subject trial arrays with real labels
2. Reject preprocessing_02 artifact rejection, flatten to (X, y, subj)
3. Phase 1 amplification off, classify, simulate navigation
4. Phase 2 ... |
e1b0d283baf4514a5c7334b28971ee8ce3e55b06e00efdbadb52a94cdd09b177 | Python | 10,519 | 342 | # --- THIS FILE IS AUTO-GENERATED ---
# Modifications will be overwitten the next time code generation run.
from plotly.basedatatypes import BaseTraceHierarchyType as _BaseTraceHierarchyType
import copy as _copy
class Labelfont(_BaseTraceHierarchyType):
_parent_path_str = "contour.contours"
... |
07c5067a575500aee54478337b4dedb5a7269a94261377b7539c269fecaeddc7 | Python | 10,520 | 303 | # coding=utf-8
# Copyright 2022 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... |
e8e5146d754b7577adba1f064d553def6f70ea3da97d19ef5695b9a9e6490b02 | Python | 10,522 | 268 | """
Copy-paste from monai 0.8.1 in order to unselect classification layers and return intermediate outputs
"""
import torch
import torch.nn as nn
from collections import OrderedDict
from typing import Callable, Sequence, Type, Union
from monai.networks.layers.factories import Conv, Dropout, Pool
from monai.networks.l... |
733362fc02a6e5db5e954bae8495f0c2e7dd94906ceb0563443f4c6aff2bbc41 | Python | 10,524 | 280 | import torch
import torch.nn as nn
import torch.nn.functional as F
from torch.optim import Adam
from sklearn.metrics import roc_auc_score, average_precision_score
import scipy.sparse as sp
import numpy as np
def sparse_to_tuple(sparse_mx):
if not sp.isspmatrix_coo(sparse_mx):
sparse_mx = sparse_m... |
c2f39e45fae1a277ce8af661168faae69eb65770e44097e86d81dc1bf7f5a5a7 | Python | 10,527 | 340 | from types import SimpleNamespace
from unittest.mock import patch
import pytest
from codecarbon.core import hardware_cache
from codecarbon.external.hardware import CPU
from codecarbon.external.ram import RAM
def make_tracker(**overrides):
defaults = {
"_tracking_mode": "machine",
"_force_cpu_pow... |
29e7e91d66c2bc159edda7725cc49299d2344eaf802349fcb4194a53c491966e | Python | 10,529 | 244 | """07. Train YOLOv3 on PASCAL VOC
================================
This tutorial goes through the basic steps of training a YOLOv3 object detection model
provided by GluonCV.
Specifically, we show how to build a state-of-the-art YOLOv3 model by stacking GluonCV components.
.. hint::
You can skip the rest of th... |
e80cc5640d086c10da0649ca62ae5756347b5183bf2e51028538d73dc157dfb3 | Python | 10,530 | 286 | """
Test module for verifying proper filtering of invalid devices in the ethoscope scanner.
This module tests that devices with empty names, empty IPs, or empty device IDs
are properly filtered out and do not appear in the device list.
"""
import time
from threading import Lock
from unittest.mock import MagicMock, Mo... |
5a710f3164b5d6cec43aca3a811b9f036a727cada8ccbfebad23b58ca76fe536 | Python | 10,531 | 288 | """Extraction planner, plan table, run door, and npz oracles (F20).
The brainpipe centerpiece (memo section 3): two real probes, per-site
linear byte fits with batch-invariant detection, budget arithmetic that
refuses instead of shrinking (D-10), full-signature plan keying (D-15),
the trace-only engine gate (D-11), th... |
6f221fa5272f202dcd0b97de5b6bcd655b6e3e80c710f16796c31ca96b8c6878 | Python | 10,531 | 259 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Fri Nov 5 16:22:54 2021
@author: fcheng
"""
import glob
import os
import numpy as np
import pandas as pd
from eval.image_process import img_process
from eval.identify_line_orientation import principalOrient_Radon_var, create_region_mask, crop_region
... |
0717fbbf4bfde47edb2e0a99c4cedcbc41ba3984d84ee8ca67c44b041fb7da71 | Python | 10,532 | 318 | """Corpus fixture loaders + the O14 admissibility instrument (memo B9/B10).
The vendored fast path is 32 distinct CC0/public-domain photographs
(licensing verified per image; see ``MANIFEST.jsonl`` + ``LICENSES.md``),
deterministically expanded to a 128-row fixture through seeded crops, flips,
and channel gains. The p... |
7ae69efd1c3627ca1fdd32b9af5548cd08ca1bb5c1f8dce4aaf0ff581c6852ef | Python | 10,532 | 341 | # --- THIS FILE IS AUTO-GENERATED ---
# Modifications will be overwitten the next time code generation run.
from plotly.basedatatypes import BaseLayoutHierarchyType as _BaseLayoutHierarchyType
import copy as _copy
class Font(_BaseLayoutHierarchyType):
_parent_path_str = "layout.scene.annotation... |
b3fc9c24bfbde9d59bf1fa5fdc64a89b3297ad338624aa9fe4f904ed0ec2c3f4 | Python | 10,533 | 247 | """
This module contains the _Flamelet2D class that provides a high-level interface for nonpremixed three-stream flamelets.
This is unsupported at the moment but it's pretty close to being useful...
"""
# Spitfire - a Python-C++ library for building tabulated chemistry models and solving differential equations
# Copyr... |
33de18bc635155c313d872200e954c4b9f0603e22edf460b96cc42c621410e1c | Python | 10,537 | 240 | import os
import torch
import torch.nn as nn
import torchvision
import json
from torchvision.models import resnet50, ResNet50_Weights
from torchvision.models.detection import MaskRCNN
from torchvision.models.detection.rpn import AnchorGenerator
from src.data.Data_alignment import prepare_dataloader
from src.utils.utils... |
d99abb6b4a3146728fbcea1d01b2de0d309f383b9a7e00bf742356115f7eb675 | Python | 10,537 | 318 | from typing import List, Literal, Optional, Tuple, Union, cast
import numpy as np
import polars as pl
import pysam
import seqpro as sp
import zarr
from more_itertools import split_when
from numcodecs import (
Blosc,
VLenBytes,
VLenUTF8,
blosc, # type: ignore
)
from numpy.typing import NDArray
from tqd... |
afa7d3e91aa62422b6aef0a776c5bba025795187c4babae25cf58a0fdcd5b680 | Python | 10,539 | 287 | # -*- coding: utf-8 -*-
"""
Scipy version > 0.18 is needed, due to 'mode' option from scipy.misc.imread function
"""
import os
import glob
import h5py
import random
import matplotlib.pyplot as plt
from PIL import Image # for loading images as YCbCr format
import scipy.misc
import scipy.ndimage
import numpy as np
im... |
1945cb2cfb30527d86f05443e02b1e78a36c26021ed6adb707e8dc1b1a1caa36 | Python | 10,541 | 290 | #!/usr/bin/env python
# =============================================================================
# MODULE DOCSTRING
# =============================================================================
"""
Utility classes to wrap command line tools.
The module provides a class :class:`.CLITool` that provides boilerp... |
6f93adba39a10d3af9152ab440a4011e51841bcbf60640984c03b4e95b39d479 | Python | 10,545 | 278 | #!/usr/bin/env python3
"""
File: plot_double_total_ieqtl_barplot.py
Created: 2022/07/06
Last Changed:
Author: M.Vochteloo
Copyright (C) 2020 University Medical Center Groningen.
A copy of the BSD 3-Clause "New" or "Revised" License can be found in the
LICENSE file in the root directory of this sou... |
5b00cf0a1328978886e8bb89035a39f30d6635380ed84ced929890b41533c7cf | Python | 10,546 | 296 | # ruff: noqa: F401
import sys
from typing import TYPE_CHECKING
if TYPE_CHECKING:
from ..graph_objs import Waterfall
from ..graph_objs import Volume
from ..graph_objs import Violin
from ..graph_objs import Treemap
from ..graph_objs import Table
from ..graph_objs import Surface
from ..graph_o... |
9acc804a4e05b94ec7825981d3c2735446f22eff0513adfa89cd0c58f5fd83d8 | Python | 10,546 | 300 | """
@author: Olivier Sigaud
A merge between two sources:
* Adaptation of the MountainCar Environment from the "FAReinforcement" library
of Jose Antonio Martin H. (version 1.0), adapted by 'Tom Schaul, tom@idsia.ch'
and then modified by Arnaud de Broissia
* the gym MountainCar environment
itself from
http://incomple... |
c6cc0543bfe68697539aaaadf7fb812879eda47df9ae25a85cc669b703768a13 | Python | 10,547 | 242 | """
This module define Model_factory
"""
# Obliger d'utiliser le sys path append car le structure de chargement de model_ENCODER
# doit etre la meme que lors de la sauvegarde dans l'ancien projet
import sys
import logging
import torch
from models_architectures.transformer_classif_per_prot import (
TransformerClass... |
63b1df41f46346a98bb97fd77f4e54ce7ca5737af4f3c7a9bbf13ff39d6731dd | Python | 10,548 | 287 | import streamlit as st
import pandas as pd
import networkx as nx
import plotly.graph_objects as go
import altair as alt
import duckdb
@st.cache_resource
def load_data():
"""
Defines the database connection to the NOCICEPTRA duckdb database
"""
try:
print("Try to connect to the database")
... |
b05a829218098b861297281e9bac4e07040ba30a40200f28f627f0d87a51dbe9 | Python | 10,549 | 286 | #!/usr/bin/env python
"""Peak finding for an already-converted XPS NeXus file.
Reads the default NXdata group's signal/axes (energy vs. intensity) out of an
existing NeXus/HDF5 file, runs ``scipy.signal.find_peaks`` on the intensity, and
appends one NXfit/NXpeak group per detected peak carrying the peak's energy
(``da... |
daa4d600e3a2d32f846a528db6170df18ebb879cb6fd277a3821ccc2ba8c7525 | Python | 10,550 | 342 | # --- THIS FILE IS AUTO-GENERATED ---
# Modifications will be overwitten the next time code generation run.
from plotly.basedatatypes import BaseTraceHierarchyType as _BaseTraceHierarchyType
import copy as _copy
class Labelfont(_BaseTraceHierarchyType):
_parent_path_str = "contourcarpet.contour... |
3760f7d47f74e46c7ab7f6ef365a5fa152941912cef3141ce337ef41a8feb8cd | Python | 10,551 | 231 | import os
import gymnasium as gym
try:
import kortex as keras_cortex
except:
import keras_cortex as kortex
import tensorflow as tf
from tensorflow.keras.layers import TimeDistributed as TD
# from tensorflow_core.python.keras.utils import plot_model
from tensorflow.keras.utils import plot_model
from angorapy... |
16f1a0f07cb68d710b230492db4b56a3892a30669eec6576fd2258f7c463798a | Python | 10,553 | 337 | """
Spatial distributions for placing agents and sources.
Generates the initial coordinates of a group of agents or sources, either
along a circle or rectangle, uniformly within a disc, or on a regular grid.
"""
from __future__ import annotations
from typing import Any, List, Optional, Sequence, Tuple
import numpy a... |
411a5d143e0b0402fbaa75135f697ffca9b2c2d0bdf994b088f947d47c7de5ba | Python | 10,553 | 273 | """Phase 0 capture-unification schema and emission tests."""
from __future__ import annotations
from dataclasses import dataclass
from typing import Any
import pytest
import torch
from torch import nn
import torchlens as tl
import torchlens.postprocess._materialize as materialize_mod
from torchlens.ir import Device... |
b7b62f81e96f937f2f51ff0a6c3ede3a4eb49c70d96845c092a6b9a82265cebb | Python | 10,553 | 272 | from functools import partial
from typing import Callable, Optional
import torch
from torch import Tensor, nn
from torch import distributed as torch_dist
from lightly.utils import dist
def negative_mises_fisher_weights(
out0: Tensor, out1: Tensor, sigma: float = 0.5
) -> Tensor:
"""Negative Mises-Fisher wei... |
f176a7c57aa5f33a018b9633dad3a5bf2370e8f56baf355af597959521ee5abd | Python | 10,553 | 284 | """Django-specific customization."""
import contextlib
import os
import sys
import warnings
from datetime import datetime, timezone
from importlib import import_module
from typing import IO, TYPE_CHECKING, Any, List, Optional, cast
from uuid import uuid4
from kombu.utils.imports import symbol_by_name
from kombu.utils.... |
f305413b3f44cd77f73f1f2b608d1f457b8a3fbad34dee2a0e6d591a4d66f887 | Python | 10,555 | 268 | """Tests for spiketools.spatial.occupancy"""
import numpy as np
import pandas as pd
from spiketools.spatial.occupancy import *
###################################################################################################
##########################################################################################... |
6314dd2479a18a03a61facbf250063ea57409325f7cd2d34ddf5dea0fbdf86ea | Python | 10,556 | 305 | import pytest
import numpy as np
from ripser import ripser
from sklearn import datasets
from sklearn.metrics.pairwise import pairwise_distances
from scipy import sparse
import itertools
def makeSparseDM(X, thresh):
"""
Helper function to make a sparse distance matrix
"""
N = X.shape[0]
D = pairwi... |
b58bef76b4ed955bb88d1840a15fe6f5f97c8837b495d2535b4b95f24aeaa4ba | Python | 10,556 | 295 | # SOURCE: vendored from ZouJiu1/Dorefa_Pact @ fbbab6f7c834fbdad6c55194c0d24bf2a8fcce7e
# Files: quantization/dorefa.py (DorefaWeightQuantizer, needed as a pact.py import
# dependency) + quantization/pact.py (PactActivationQuantizer, QuantConv2d, QuantLinear,
# add_quant_op, prepare) -- the actual PACT (Parameterized Cl... |
66380039f54b586de7e73b468d7ed6addee8a1dbf92e1c1fc505a68f6b20b70b | Python | 10,557 | 146 | #### Master Script 2c: Compile TIL correlations and statistics of different study sub-samples ####
#
# Shubhayu Bhattacharyay
# University of Cambridge
# email address: sb2406@cam.ac.uk
#
### Contents:
# I. Initialisation
# II. Compile and save bootstrapped TIL correlations and statistics
# III. Calculate 95% confidenc... |
5b3a6244c709b4102e921f79a949ac82f0db99efd59e671c464731fdfceab63d | Python | 10,559 | 398 | import importlib.metadata
import click
import pytest
import flask
from flask import appcontext_popped
from flask.cli import ScriptInfo
from flask.globals import _cv_app
from flask.json import jsonify
from flask.testing import EnvironBuilder
from flask.testing import FlaskCliRunner
def test_environ_defaults_from_con... |
517b493bc4b06b1f6aa67f59c47b8a9dbe78b64b6a92cbd8aa22a53b615bf283 | Python | 10,560 | 296 | import itertools
from typing import Tuple
import numpy as np
from matplotlib import pyplot as plt
from .support_function import *
def step2_final_estimation(
basic_estimate_img: np.ndarray,
noisy_image: np.ndarray,
param: tuple,
mask: np.ndarray,
verbose: bool = False,
) -> np.ndarray:
"""
... |
c25177a3727bece2732ad284f519d9335876bab6a37554c4070b4d04a1e61fbe | Python | 10,560 | 383 | import torch
import torch.nn as nn
import warnings
from torch.autograd import Function
from typing import *
from torch.cuda.amp import custom_fwd, custom_bwd
try:
import pointnet2_ops._ext as _ext
except ImportError:
from torch.utils.cpp_extension import load
import glob
import os.path as osp
impo... |
f799a591a82b4df5f1a2a82429250fce26433c28eac021b1226ed3d96002af02 | Python | 10,563 | 351 | """
Base class for every object in a simulation.
Defines the identity, grouping and lifecycle shared by agents, sources and
environment objects, and their registration with the simulation model.
"""
from __future__ import annotations
from typing import Any
import param
from .. import util
from ..param import Neste... |
5a21e3229f1c0788c3bcf7a0dd72cb369c6406bdb8720597fd471593d9b73e60 | Python | 10,564 | 282 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created in November 2018
@author: Nathan de Lara <nathan.delara@polytechnique.org>
@author: Quentin Lutz <qlutz@enst.fr>
@author: Thomas Bonald <bonald@enst.fr>
"""
from typing import Union, Optional
import numpy as np
from scipy import sparse
from sknetwork.clusteri... |
a1accc54a41cf6f52cee25f28e4259d87ad6397bef9ea97837183bd237e114cf | Python | 10,565 | 357 | # coding=utf-8
# Copyright 2025 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... |
49aa36ce5f37f13419755cf51538400bdcf730f2b19b5f0dc721fdca02e99c42 | Python | 10,568 | 268 | """Episode full-surface differential oracle + the gap-9 cross-tier token pin.
Three independent production paths over the SAME episode are compared on
their full public surface:
1. the SESSION product (one wrapped capture, the ruled representation),
2. the FLOOR product (N observer-discipline per-step captures in a B... |
c75774623e076ad42c4bdba9e2e3447bf0baa7d033a1901169096fa93a103776 | Python | 10,569 | 230 | from ipywidgets import widgets, interactive
import matplotlib.pyplot as plt
import urllib.request, json
from model_analysis_folders import all_model_info
from ipywidgets import Output, GridspecLayout
from IPython import display
from IPython.display import Image
from IPython.core.display import HTML
from scipy.io imp... |
98a9e618416ec7609fc5249bfaf17d16c2662bd34239c209db5299216ab1b4d4 | Python | 10,571 | 274 | """
Author: Derek van Tilborg -- TU/e -- 25-05-2022
Code to compute activity cliffs
- ActivityCliffs: Class that takes care of computing activity cliffs
- find_fc(): Calculate the fold change
- get_fc(): Compute the pairwise fold change
... |
ff96a908b868c5b5549cb87f3ddd31fdefc83d1ae3d6a8f793d16b5459e502c2 | Python | 10,573 | 275 | from paddle.nn.initializer import XavierNormal
import paddle.nn as nn
import paddle
import paddle.nn.functional as F
class exchange_bilinear(nn.Layer):
def __init__(self,params):
super(exchange_bilinear,self).__init__()
self.p = params
self.output_dim = self.p.fusion_dim
self.Hidde... |
83181a5b143c4d8e6661e65fa39407d17c0bb2d4af04e1caef233d3bd9c74665 | Python | 10,574 | 220 | #!/usr/bin/env python
"""Hybrid policy networks that utilize both visual and unstructured input data."""
import os
import gymnasium as gym
try:
import kortex as keras_cortex
except:
import keras_cortex as kortex
import tensorflow as tf
from tensorflow.keras.layers import TimeDistributed as TD
# from tensorfl... |
d74250cc4bb8e34750c26ce2055c04a147d74d0ec62719f7a7be958ef10f8730 | Python | 10,574 | 300 | #!/usr/bin/env python3
"""
File: create_ieqtl_upsetplot.py
Created: 2022/07/05
Last Changed:
Author: M.Vochteloo
Copyright (C) 2020 University Medical Center Groningen.
A copy of the BSD 3-Clause "New" or "Revised" License can be found in the
LICENSE file in the root directory of this source tree.... |
11299ea01c7a5364009e1e408f01a38c6059e4eb1befad78968d53d6f4d0f781 | Python | 10,575 | 342 | # --- THIS FILE IS AUTO-GENERATED ---
# Modifications will be overwitten the next time code generation run.
from plotly.basedatatypes import BaseTraceHierarchyType as _BaseTraceHierarchyType
import copy as _copy
class Labelfont(_BaseTraceHierarchyType):
_parent_path_str = "histogram2dcontour.co... |
a6fdba80b5d97c337441d3cf0548ad2d69b8d1d21c21b9656176a440784742d4 | Python | 10,575 | 223 | import sys
from torch.utils.data import DataLoader, TensorDataset
import torch
import torch.nn as nn
import torch.optim as optim
import numpy as np
from sklearn.metrics import roc_auc_score, precision_score, recall_score, average_precision_score, confusion_matrix
import optuna
import build_dataset
import splitters
from... |
7c1af2482baecb097e704d61fc83355cc223b28efecc54f2782f1bc31186aa96 | Python | 10,576 | 348 | from __future__ import annotations
from enum import Enum
from typing import Any, Literal, cast
import numpy as np
from numpy.typing import NDArray
from ._utils import DTYPE, SeqType, cast_seqs, check_axes
from .alphabets._alphabets import NucleotideAlphabet
from .seqpro import _k_shuffle # type: ignore[missing-impo... |
be0226f07465174d065b588c2baa8811156a12cfc272a3aae62bce64c885173f | Python | 10,578 | 253 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Fri Sep 24 10:57:59 2021
@author: Audrey Mazancieux
This script stimates a general linear model (GLM) at the subject level for
all stimuli in the local-global task on several ROIs time series. Other
regressors include V4 time serie, movement parameters,... |
984055fec8fb36f5070087e31897526612da547a9bdf5bed2b966ea0f31c7b10 | Python | 10,579 | 229 | """procrustes.py
Implements full affine and optimally constrained affine fitting with the
same interface as required by scikit-learn.
Copyright (C) 2018-2026 Max Planck Institute for Neurobiology of Behavior
This program is free software: you can redistribute it and/or modify it under
the terms of the GNU General ... |
db2126b7db85158344996b30aaa0e8c84f80cc27274d533ecdb4239ae9e3748a | Python | 10,579 | 254 | # Copyright 2025 Google.
#
# 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 agreed to in writing, soft... |
20fe3ae2e47287b7e57fe2c3c1389555f29eac5ec7b5d7f1d777957729ae29ec | Python | 10,583 | 298 | """F08 auto-ladder acceptance: rungs, folds, elision, multi-pass, partition.
Summary memo 3.1/3.4 build requirements: the identity partition holds at
every depth/fold/elision; the strict fold signature splits on trainability
and dtype drift; elision is deterministic, protected, totals-conserving;
the multi-pass row mo... |
908720c3af6eb3b012f70ca061c497b943d4fe15e4f9ece9478fc5fc07e971ce | Python | 10,584 | 329 | import pickle
import itertools
import os
import sys
import glob
import matplotlib.pyplot as plt
import numpy as np
from pathlib import Path
import matplotlib.pyplot as plt
import matplotlib.backends.backend_pdf
sys.path.append('../../code/')
sys.path.append('../../analysis/')
# import utils
plt.rcParams['figur... |
cbe094ced70f83f6cfa485ea76eedbe23ea1b293c4b227f6171a07bef7ecc667 | Python | 10,586 | 304 | """Evaluation code for BDD100K instance segmentation.
predictions format: BitMasks
"""
import copy
import json
import os
from multiprocessing import Pool
from typing import Dict, List, Tuple
import numpy as np
from PIL import Image
from scalabel.common.parallel import NPROC
from scalabel.common.typing import (
D... |
439cefc5e9678f89bb7ffbb776b7fd9161cf49872e20282af79e7e06668cfab7 | Python | 10,588 | 322 | import numpy as np
from keras.src import initializers
from keras.src import layers
from keras.src import testing
class SimpleRNNTest(testing.TestCase):
def test_basics(self):
self.run_layer_test(
layers.SimpleRNN,
init_kwargs={"units": 3, "dropout": 0.5, "recurrent_dropout": 0.5},... |
1e3585bd4e0ff62f5a07bdce698bf727772ead469cc1a7d6910f72e19167aa65 | Python | 10,590 | 258 | #!/usr/bin/env python3
"""
INGEST_TEMPLATE.py — Scaffold for ingesting a new EEG-AD cohort.
This is a starting point for adapting the methodology to a cohort not
listed in the paper. Fill in the four TODOs below — the rest is
generic wiring. The output is a per-subject feature JSON matching
``docs/INGEST_CONTRACT.md``... |
d6e8c7fec73c05ae55be4aa77eb55ccde494f913ec5bda18de0352d97066d417 | Python | 10,591 | 285 | #!/usr/bin/env python3
from DeepRegFinder.traineval_functions import *
from sklearn.metrics import precision_recall_fscore_support
from DeepRegFinder.nn_models import create_model
from sklearn.preprocessing import label_binarize
import torch
import argparse
import torch.nn as nn
import numpy as np
import pandas as pd
f... |
977b61989fcf18bc9fec41afdc4572712a7bc74311c67e919ac5aa30c497ba5c | Python | 10,592 | 277 | #!/usr/bin/env python3
"""
File: compare_tvalues.py
Created: 2021/11/19
Last Changed: 2022/02/10
Author: M.Vochteloo
Copyright (C) 2020 University Medical Center Groningen.
A copy of the BSD 3-Clause "New" or "Revised" License can be found in the
LICENSE file in the root directory of this source t... |
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