sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
fade0a6b881f14e21c447161046a599bd2e66e1d3a841d1b46d71cc012501b0a | Python | 14,205 | 271 | """Junction-nucleotide inference (#461): call resolution, determinism, and back-translation."""
from __future__ import annotations
import polars as pl
import pytest
from vdjdb.annotate import junction
class FakeModel:
"""Just the ``genomic`` tables :func:`junction._resolver` reads."""
def __init__(self) ->... |
6ae1d7bc072943131efa894504e3921b70cf751efa700433cdf2b483ea03a68f | Python | 14,220 | 345 | import matplotlib
matplotlib.use('Qt5Agg')
import matplotlib.pyplot as plt
from PymoNNto.NetworkBehavior.Input.Activator import *
from PymoNNto.NetworkCore.Neuron_Group import *
import PymoNNto.Exploration.Evolution_Old.NetworkEvaluationFunctions as EvalF
class visualization_recorder(Behavior):
def __init__(se... |
e9489231672b205a8dda75aceecf782b78f93f5d58f4e720faf3e258e043ec97 | Python | 14,227 | 366 | from __future__ import annotations
import math
import torch
import torch.nn.functional as F
from e3nn import o3
from e3nn.nn._fc import _Layer as E3NNFCLayer
from torch import nn
def build_lora_irreps(
irreps_in: o3.Irreps, irreps_out: o3.Irreps, rank: int
) -> o3.Irreps:
"""
Choose an equivariant bottl... |
0f3498307102dae215935dca049e3a02dda6ab630951305c153fbf273c620680 | Python | 14,229 | 271 | """Structure association preserves context; optional domain proof checks complete sequences."""
from __future__ import annotations
import io
import tarfile
import polars as pl
import pytest
from vdjdb.assemble.evidence import structures
ALPHA = ('GQNIDQPTEMTATEGAIVQINCTYQTSGFNGLFWYQQHAGEAPTFLSYNVLDGLEEKGRFSSFLSRSKG... |
382d988cb5ab289180da14c3c849b3bf694ebb8c959e2a8ee071d95e8699c4df | Python | 14,236 | 506 | """
Generate 2D feature matrix using SMILES
Author: Son Gyo Jung
Email: sgj13@cam.ac.uk
"""
import numpy as np
import pandas as pd
import re
import joblib
import pickle
import os
from rdkit import Chem
from rdkit.Chem import rdchem
from rdkit.Chem import AllChem
from deepchem.feat.smiles_tokenizer import BasicSmile... |
991dad4fd426fa01f7289ff86584e29b6026e7e722f2cc1f7bcb309b1340a4b1 | Python | 14,236 | 231 | # -*- coding: utf-8 -*-
# Form implementation generated from reading ui file 'mainwindow.ui'
#
# Created by: PyQt5 UI code generator 5.12.1
#
# WARNING! All changes made in this file will be lost!
from PyQt5 import QtCore, QtGui, QtWidgets
class Ui_MainWindow(object):
def setupUi(self, MainWindow):
Main... |
24052c107d2bac4083b2ec8b2ac9fe3356a8c91a348a861189e9aab880141c9d | Python | 14,239 | 466 | import argparse
import gcsfs
import nobrainer
import os
import os.path as op
import tensorflow as tf
def build_multi_input_model(
width=128,
height=128,
depth=128,
n_image_channels=3,
n_qc_metrics=31,
neglect_qc=False,
):
"""Build a multi-input model that concatenates a 3D convolutional ne... |
d9df387a2518d51643dc5c11cd646bc8dddf6a18f7aae7709164585818362b27 | Python | 14,246 | 358 | # Copyright 2020-2025 Intel Corporation
# SPDX-License-Identifier: Apache-2.0
"""DirectorGRPCServer module."""
import asyncio
import logging
import uuid
from pathlib import Path
from typing import AsyncIterator, Optional, Union
import grpc
from grpc import aio, ssl_server_credentials
from openfl.experimental.workfl... |
68f894a6b308169f1c48419c563729cf6a53159e462ceffa96dff003268e44aa | Python | 14,255 | 495 | import os.path
import pandas as pd
from uniprotparser.betaparser import UniprotSequence
import base64
from cryptography.hazmat.backends import default_backend
from cryptography.hazmat.primitives.asymmetric import rsa
from cryptography.hazmat.primitives.ciphers import Cipher, algorithms, modes
from cryptography... |
789fb3290c3aa86afd7dabe22ed37835586a090bf25ce105ede06984aa164ec3 | Python | 14,257 | 366 | import torch
from torch import nn
from torch.autograd import Variable
from torch.utils.data import DataLoader, Dataset
import os
from DeepPurpose import utils, dataset
from datetime import datetime
import copy
import wandb
from DeepPurpose.utils import *
class EarlyStopping:
'''Early stops the training if validat... |
9c4488a69b39ee6b2b21c5792d1f94c40e83c9bde2ef44f427045f901fb2c25a | Python | 14,265 | 443 | from __future__ import print_function
import copy
import pprint
import torch
import numpy as np
import matplotlib.pyplot as plt
import utils
import analysis_utils
from dataset_learning_trainable import DatasetLearningTrainable
import torch.nn as nn
import torch.nn.functional as F
import torch.optim as optim
from to... |
58d23a24fedb0a4211df6202e8f32d944c985e5f83150bde7d4c656df6746fbc | Python | 14,291 | 389 | # Copyright (c) 2021 PaddlePaddle 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 appli... |
3577aff1c2a0f2c96173f808444bcfb480b510657b350e59ba83487b7b8aa8c1 | Python | 14,303 | 439 | # ==============================================================================
# Copyright 2025 Technical University of Denmark
# Author: Nikolas Borrel-Jensen
#
# All Rights Reserved.
#
# Licensed under the MIT License.
# ==============================================================================
"""End-to-end in... |
6ace2d97ace7ed0ee3cc12068a54c6f08702240beefa1216f58828c59b59baa7 | Python | 14,310 | 365 | import torch
import torch.nn as nn
import torchvision
from torch.hub import load_state_dict_from_url
__all__ = ['ResNet', 'resnet18', 'resnet34', 'resnet50', 'resnet101',
'resnet152', 'resnext50_32x4d', 'resnext101_32x8d',
'wide_resnet50_2', 'wide_resnet101_2']
model_urls = {
'resnet18': '... |
6532b65a69d42a77ef3c7de60291bd71375280dc32c66b0355550aadf1a4c03e | Python | 14,321 | 401 | """
Test backend abstraction for CPU/GPU operations.
Part of functional core - tests pure backend selection and device management.
Following model-spec.md Phase 1 implementation.
"""
import numpy as np
import pytest
# ============================================================================
# Helper Functions
# ... |
7a4ccb6d5ccc69b02b989d6d49e44224f1fb284b9ab1bd5b5d05ddc7934492b8 | Python | 14,328 | 326 | """Reported observations survive predictions, flank comparisons and missing coverage."""
from __future__ import annotations
import hashlib
import os
import polars as pl
import pytest
from vdjdb.assemble import assessment as A
from vdjdb.schema import EPITOPE_ASSESSMENT_COLUMNS
def records() -> pl.DataFrame:
re... |
626aa490f67a46c8f28c31cc6eb39934b839d2fde4afa692f0c05f1ac3f19098 | Python | 14,329 | 381 | import numpy as np
import networkx as nx
import matplotlib.pyplot as plt
import igraph as ig # may have to pip install
import itertools
from tqdm import tqdm
def type_mat_rearrange(input_mat):
typee = type(input_mat[0,0])
rearranged = np.zeros(input_mat.shape).astype(typee)
if input_mat.shape[0]==4:
... |
b60e2660eb6d53b7065aa8a3a60415cb6b70b0de983197a9adcac1e0b009b1cd | Python | 14,329 | 371 | from multiprocessing.connection import Connection
import os
import shutil
import tempfile
from typing import Generator, List, Tuple, Dict, Any, Callable, Type
from hypothesis import given, settings
import hypothesis.strategies as st
import pytest
import json
from urllib import request
from chromadb import config
from c... |
ead3410ae50367b2c21f53f02275f05e2e2ab6cbad6ca8bd7f465a788ca378c7 | Python | 14,340 | 378 | from __future__ import absolute_import
import os
import pandas as pd
import numpy as np
from scipy import stats
from pysurvival import utils
from pysurvival.models import BaseModel
from pysurvival.models._non_parametric import _KaplanMeierModel
from pysurvival.models._non_parametric import _KernelModel
class NonParam... |
39a5d3756d5f8895fc504b2d1890ab2dd959c4d847c9b11b52b541011e41aff6 | Python | 14,360 | 275 | """Is the rewritten motif stage equivalent to or better than the one that shipped?
Marked ``release``: needs ``VDJDB_REFERENCE_ZIP``, built tables (``VDJDB_TABLES``, default
``out/tables``) and built motif files (``VDJDB_MOTIFS``, default ``out/motifs``).
The motif stage is the one place where byte reproduction is ne... |
f76dac384c7f5c26ab8537dcc94e45161487f5a60462f58bfd3c7fb218e6ccd0 | Python | 14,366 | 374 | # Copyright (c) 2021 PaddlePaddle 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 appli... |
bad43c703adb85aebcc122bdd818b5da5a374e5789233781ef32c6230574f0d6 | Python | 14,367 | 251 | """The evidence table: one row per piece of support for a record.
Long, not wide. A record may have any number of pieces of evidence of any number of kinds -- a
motif cluster per method, a structure per PDB entry, a supporting publication per replication -- and
the wide form would be a table of mostly-empty boolean co... |
3dbf5c174173e43d0f09b133c7325278e02fd0becc9562f6a32b1c97323f5c33 | Python | 14,371 | 242 | """
Parameter continuation and bifurcation detection
================================================
In this tutorial, you will learn how to perform a 1D
`numerical parameter continuation <http://www.scholarpedia.org/article/Numerical_analysis#Numerical_solution_of_
differential_and_integral_equations>`_ in PyRates w... |
c2e8eb66f67a1dcbe5be1b1c27f73257b1edb15e0c82aa68c36979a1396b2e20 | Python | 14,373 | 386 | import time
import torch
from pymonntorch.NetworkCore.Base import *
from pymonntorch.NetworkCore.Behavior import Behavior
from pymonntorch.NetworkCore.SynapseGroup import *
class Network(NetworkObject):
"""This is the class to construct a neural network.
This is the placeholder of all neural network compon... |
6202d566a7d553e708ddef01f1fbfc751a557a241a3ca1d77f4d0d7834b8cff3 | Python | 14,377 | 242 | """
Parameter continuation and bifurcation detection
================================================
In this tutorial, you will learn how to perform a 1D
`numerical parameter continuation <http://www.scholarpedia.org/article/Numerical_analysis#Numerical_solution_of_
differential_and_integral_equations>`_ in PyRates w... |
3654189bc7878fe18c4079f43a6782ba95af4e1bafbb4c1145e201a9cda31367 | Python | 14,378 | 317 | '''
Module focused on the reduction of the ANN and implementation of the
training and testing phases.
'''
import torch
import torch.nn as nn
import numpy as np
from smithers.ml.models.rednet import RedNet
from smithers.ml.models.fnn import FNN, training_fnn
from smithers.ml.utils_rednet import PossibleCutIdx, spatial... |
a43e82eb3a8bead0ddb9ae2374d7c384e1f1c039c54d6fd8a7d153d1516dd914 | Python | 14,385 | 372 | import torch
import itertools
import copy
import numpy as np
def get_peak(x, eps=1.E-3, randomize=False):
# x_in is shape BxXxY
d = x.shape[-1]
peak = torch.zeros((x.shape[0], 2), device=x.device, dtype=torch.long)
for b in range(x.shape[0]):
m = x[b].argmax()
initial_peak = [int(m /... |
f39cd2d0ba08fe66e24cf1cdea54189d802555cc5720d0046e95f71b242f31f5 | Python | 14,386 | 435 | # %%
"""
#### ## ## ######## ####### ######## ######## ######
## ### ### ## ## ## ## ## ## ## ## ##
## #### #### ## ## ## ## ## ## ## ##
## ## ### ## ######## ## ## ######## ## ######
## ## ## ## ## ## ## ## ... |
590d604c27bc26a130c1ee610e754c7960f806ae22b4d4b477abbb10bce6ae86 | Python | 14,391 | 293 | import os
import sys
import json
import re
import pandas as pd
from tqdm import tqdm
from soma import aims
p = os.path.abspath('../')
if p not in sys.path:
sys.path.append(p)
q = os.path.abspath('../../')
if q not in sys.path:
sys.path.append(q)
from vae import *
from preprocess import SkeletonDataset
import... |
5e9a16c3a34847432f81fc9831e57197d3b5d1973841bc212339fd573ed4ccef | Python | 14,422 | 540 | #!/opt/conda/bin/python
import argparse
import dask.dataframe as dd
import matplotlib.pyplot as plt
import nibabel as nib
import numpy as np
import os
import os.path as op
import pandas as pd
import plotly.graph_objects as go
import seaborn as sns
import warnings
from glob import glob
from plot_formatting import set_... |
189e8d605c31d49b8bfe7a97df2a4e8d3ba507f9f652beea7e21873fb454a272 | Python | 14,430 | 399 | # regression_test.py - Testing JAGS fits of HDDM models with participant-level regressors in JAGS using pyjags in Python 3
#
# Copyright (C) 2020 Michael D. Nunez, <m.d.nunez@uva.nl>
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as publis... |
569ec02c11eecdaf3c6500a52f8719353709796f36e2c3243b770960d4863d9f | Python | 14,430 | 399 | """Read and write DesignMatrix objects.
Loads BIDS events and tabular confound files into the frame a `DesignMatrix`
wraps, exports NumPy arrays, and round-trips through TSV/CSV or HDF5
(which also preserves the metadata). A private pandas adapter serves nilearn.
"""
from __future__ import annotations
from pathlib i... |
dbd4a87a4c707619f1b66f699ced4973caa523f5163101b80870c98c46d78b84 | Python | 14,436 | 411 | """`mace_finetuning_select` through its command line.
`tests/workflows/test_finetuning_select.py` builds `SelectionSettings` in-process,
which covers the selection logic and leaves the CLI itself unexercised: nothing
passed `--model`, `--output`, `--device`, `--default_dtype`, `--seed` or the YAML
`--config`, so a fla... |
3d166a2c4f8ef449f78b3b092b39376ba6d710725da03323ff574dc842ee238d | Python | 14,452 | 368 | # Copyright (c) 2022 PaddlePaddle 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 appli... |
85c16de5f37472aff6fee677c1deb2158a269932537e943a983e01f64dcc8407 | Python | 14,454 | 425 | import os
import numpy as np
import collections
import torch
import torch.nn as nn
import torch.nn.functional as F
from skimage.transform import rescale
from functools import reduce
import subprocess
from torch.nn.parameter import Parameter
from cloudvolume import CloudVolume
import torch
from torch.nn.functional impo... |
5963738fb791859c9d2bdd792f7ed5d5369df460be1ffda95f258085a34fda57 | Python | 14,456 | 382 | import torch
import torch.nn as nn
import torch.nn.functional as F
from .mol_tree import MolTree, MolTreeNode
from .chemutils import enum_assemble, set_atommap
from .nnutils import create_var, GRU
MAX_NB = 15
MAX_DECODE_LEN = 100
class JTNNDecoder(nn.Module):
def __init__(self, vocab, hidden_size, latent_size, ... |
9aad3fa87937cbdbcdd071857ae662bdae043eb2e46c1f3fc85d91071aa6e532 | Python | 14,470 | 487 | import random
import numpy as np
import pytest
import scipy
import geomstats.backend as gs
from geomstats.test.test_case import TestCase
from geomstats.test.vectorization import generate_vectorization_data
# TODO: use new strategy for vectorization tests
def _convert_gs_to_np(value):
if gs.is_array(value):
... |
33d5e0b31327255d79365e6a851655381029b2b8674af076e44951cf3d9e9113 | Python | 14,472 | 310 | """PubMed records and abstracts: one client, one tokeniser, two committed inputs.
The corpus needs a title and an abstract per reference, and the text is an input to the build rather
than an output of it (hard rule 5). So this module fetches the records, tokenises them, and writes two
files that are **committed, revie... |
e45e47a335279b54bcc79ee18eeef9bf9e6df2fa64c3c19e8de3bcc30cf0edad | Python | 14,481 | 356 | from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
from pprint import pprint
import tensorflow as tf
from tensorflow.python.ops import array_ops
from tensorflow.python.ops import math_ops
import tensorflow_probability as tfp
from sleeprnn.common import check... |
181078609bd94e06437f0525b22efa4259135b5f47c2696881b34e884c6cc30e | Python | 14,495 | 371 | import json
import logging
import pickle
import sqlite3
from threading import Lock
from typing import Dict, Optional
import numpy as np
from openfl.utilities import TensorKey
logger = logging.getLogger(__name__)
__all__ = ["PersistentTensorDB"]
class PersistentTensorDB:
"""
The PersistentTensorDB class im... |
45795e773c460fd937944f6d1dc17a16c47ebcd6a0960a6e82a3b7daf6510aab | Python | 14,497 | 388 | """
eeg_preproc.py
Author
------
Daniel Schonhaut
Computational Memory Lab
University of Pennsylvania
daniel.schonhaut@gmail.com
Description
-----------
Functions for reading and processing time domain EEG.
Last Edited
-----------
1/26/22
"""
import sys
import os
import os.path as op
from collections import Ordere... |
96ed7ae5779d3c591b6e2fb66097fc47053b9069d491068060de511fa9ec0068 | Python | 14,500 | 390 | #
# This module contains functions of autoencoder to apply regression on
# the EFI measurements.
#
from __future__ import absolute_import, division
from __future__ import print_function, unicode_literals
import numpy as np
import tensorflow as tf
K = tf.keras.backend
# For a simple tutorial/example, see e.g.
# https... |
3b69420a0974430e2506ba0307e3a5e4065710c77fb1ab5a0eb23f5956da5c97 | Python | 14,502 | 346 | # 2026-10-16
# Reprocess deposited ITRAP count tables with the dCODE chain-graph caller.
# The model specification is unchanged; each donor is fitted afresh. These loaders only
# reshape deposited GEM or 10x matrices into the frames that caller expects.
# ITRAP1 raw.csv has no empty droplets and no negative-control dex... |
db89623a0338898a1dca722c424155cc2b410a7b498eb964cf2a25d894c4e080 | Python | 14,503 | 345 | # This file is a part of the `nequip` package. Please see LICENSE and README at the root for information on using it.
import torch
from torchmetrics import Metric
from . import AtomicDataDict
from .modifier import BaseModifier, PerAtomModifier, NumNeighbors
from .stats import Mean, RootMeanSquare, StandardDeviation
fr... |
84ac9992934be32fdacc877556a09fec36d6c1dba84be8acb244eea3b8b3ec52 | Python | 14,513 | 390 | # This file is a part of the `nequip` package. Please see LICENSE and README at the root for information on using it.
from dataclasses import dataclass
from typing import Any, Callable, Dict, Final, List, Optional, Union, Tuple
import numpy as np
import packaging.version
import torch
from . import AtomicDataDict
imp... |
d596ad956239a8e936fe4c2da4f4203fe31932b06e32f4cce6ab40e167137799 | Python | 14,527 | 308 | from PymoNNto.Exploration.Network_UI.TabBase import *
from PymoNNto.NetworkBehavior.Recorder.Recorder import *
#from Testing.Common.Grammar_Helper import *
class sidebar_module_quick_access(TabBase):
def __init__(self, module_label='my_module', module_tag='module_tag'):
self.module_label = module_label
... |
0da3207203a334b31d0cfc1796fe896f9deee398becba20927a415618b06c3f1 | Python | 14,529 | 356 | import torch.optim as optim
import torch
import torch.nn as nn
import torch.nn.functional as f
import torchvision.transforms as transforms
import torchvision as tv
import torch.utils.data as data
import os
import matplotlib.pyplot as plt
import random
from torch.utils.data import Dataset, DataLoader
import time
import ... |
1992441ad89c6a8f9c2f22da1b90d655affd2a279dd32d8aa64c11edfe31b7ba | Python | 14,532 | 366 | import numpy as np
import tensorflow as tf
from tensorflow.keras.layers import Input, LeakyReLU, Concatenate, Activation, BatchNormalization, Bidirectional, LSTM, Dense, Dropout, Conv1D, MaxPooling1D, Flatten, Embedding
from tensorflow.keras.callbacks import EarlyStopping
from tensorflow.keras import Model
from sklearn... |
41dae5985a1085157108f53a19ab310b94ff91f32a35ecc2ab961788a0306e63 | Python | 14,555 | 345 | # This file is a part of the `nequip` package. Please see LICENSE and README at the root for information on using it.
import os
import torch
from nequip.data import AtomicDataDict
from .graph_model import GraphModel
from ._graph_mixin import GraphModuleMixin
from nequip.utils.dtype import (
test_model_output_simil... |
04683b8358cfa12f210668ff5aa4b613281db5dc36a47a827d68eb198c6dd8a9 | Python | 14,583 | 403 | # Copyright (c) 2018 PaddlePaddle 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 app... |
0f6330958f3d58ee9bdc2cfb59ea990988519f6a1926a6741dfbf4b0d1125426 | Python | 14,596 | 363 | # -*- coding: utf-8 -*-
"""
Created on Fri Jul 10 16:58:54 2020
@author: Tom
"""
from tensorflow import keras as k
import pandas as pd
import numpy as np
import preprocess_crop #courtesy of Rustam Aliyev
import matplotlib.pyplot as plt
from image_data_generator_pat import ImageDataGeneratorPat
from negative_log_likel... |
1a2f6535dfc17a027b979c451f3386954b6341b678fe1706839690e96b0bb1d5 | Python | 14,602 | 398 | import matplotlib
matplotlib.use("Agg")
import pytest
import nibabel as nib
from nltools.data.simulator import Simulator, SimulateGrid
import numpy as np
def _small_mask():
"""A tiny all-ones brain mask for fast Simulator smoke tests."""
return nib.Nifti1Image(np.ones((12, 12, 12), dtype=np.float32), affine... |
7770821c33ead1e95f4ec45879fbc4c92b60abb7f509140244181979d2bc584c | Python | 14,604 | 374 | from PymoNNto.Exploration.Network_UI.Network_UI import *
from PymoNNto.Exploration.Network_UI.TabBase import *
class UI_sidebar_network_selector():
def __init__(self, add_color_dict={'output': (255, 255, 255)}):
if type(add_color_dict) is str:
add_color_dict={add_color_dict:(255,255,255)}
... |
12c02f02bcffbb30c3582e3fc9a73ad336e051022d2e1cb11a8cca455983494f | Python | 14,616 | 423 | """
Motor imagery testing.
After setting experimental parameters, it runs a trial with feedback
by calling the classify() method of a Feedback class object.
Trials are repeated until the set number of trials are achieved.
Kyuhwa Lee, 2015
Swiss Federal Institute of Technology (EPFL)
This program is free software: ... |
772456f1fbd3f0e9f54fcf40b9a42247b6615d7c6ceb506c0b116cedc39d04b5 | Python | 14,622 | 361 | import math
import numpy as np
import torch
import torch_geometric
from torch_cluster import radius_graph
from torch_scatter import scatter
from utils import get_iso_permuted_dataset
from utils import get_scalar_density_comparisons
from utils import get_iso_permuted_dataset_lpop_scale
from e3nn.nn.models.gate_points_21... |
ba97e273da5c83c978343d26e7822e2aec32f622cfd430d7ce1bebd46b04ce3d | Python | 14,631 | 367 | import torch.utils.data as data
import torchvision.transforms as transforms
from PIL import Image
import os
import os.path
import numpy as np
try:
import accimage
except ImportError:
accimage = None
import pdb
from mapcrop import MapCrop
from augmentation import RandAugment
IMG_EXTENSIONS = ['.jpg', '.jpeg', '... |
0a2c077711702728e7c246d657c4ccdd6d4f55ae361a5fbbd5348be2a8abb14e | Python | 14,634 | 359 | # Copyright 2020-2023 Intel Corporation
# SPDX-License-Identifier: Apache-2.0
import os
import yaml
import logging
import tests.end_to_end.utils.defaults as defaults
import tests.end_to_end.utils.exceptions as ex
import tests.end_to_end.utils.helper as helper
import tests.end_to_end.utils.ssh_helper as ssh
log = log... |
3fc5a6d5ae6c5fd67fd08760b529486324ad64b3cb712e4b067699bae4f9d088 | Python | 14,636 | 464 | import copy
import torch
from tqdm import tqdm
from corgie import constants, exceptions
from corgie.log import logger as corgie_logger
from corgie.boundingcube import BoundingCube
from corgie.layers.base import register_layer_type, BaseLayerType
from corgie import helpers
def get_extra_interpolate_parameters():
... |
119258b1ae55490b1abd9d619ddce59497d4ac38b291d30b5d10a9b1b7453360 | Python | 14,640 | 382 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Tue Mar 14 12:18:38 2023
@author: egemo
"""
from .core import core
from .group import synapsegroup,neurongroup
from .component_utils import (LS_time_dep,
LIF_time_dep,
quick_activator,
... |
224036424283c7acc46875f956c106f3af1377fc7f9db18b36235149691c04dc | Python | 14,640 | 395 | """Plotting functions for Adjacency matrices."""
import numpy as np
def _divergent_heatmap_defaults(square):
"""Heatmap keywords that anchor a signed matrix at zero, or none if one-signed.
Seaborn picks a sequential ramp and data-range limits whenever `center` is
unset, which leaves a matrix straddling ... |
d252542b29ad1b5b326f7bda1549d18695e9618d164822086e0d34a231a49b01 | Python | 14,680 | 490 |
from sleepy.gui.exceptions import UserCancel, NoNavigatorError, NavigatorEmptyError
from sleepy.gui.tagging.control.channels import MultiChannelControl, visualize
from PyQt5.QtWidgets import QMessageBox
import pdb
class TaggingControl(MultiChannelControl):
def __init__(self, parent, settings):
... |
25a5e595ed37459c1ca95c444d8b2300a081621e709d044a36609f8234e2be3c | Python | 14,689 | 393 | ################################################################################
# Import, Set up MPI Variables, Load Necessary Files
################################################################################
import os
from os.path import join
import sys
import matplotlib
import matplotlib.pyplot as plt
from matp... |
95d710a62653b06b4073386d9af888fe99d1c6cca535a3959acf8011ba53f283 | Python | 14,694 | 457 | from __future__ import absolute_import
import numpy as np
import tensorflow as tf
import tensorflow.keras.backend as K
def _crps_tf(y_true, y_pred, factor=0.05):
'''
core of (pseudo) CRPS loss.
y_true: two-dimensional arrays
y_pred: two-dimensional arrays
factor: importanc... |
1a6ca274d15efe3de2e96b72bd3dfb9c44e19bdc63fac01c4bf5bb7ba2ff19f5 | Python | 14,695 | 469 | from typing import Dict, Optional, Union
__version__ = "1.6.0"
import logging
from chromadb.api.client import Client as ClientCreator
from chromadb.api.client import (
AdminClient as AdminClientCreator,
)
from chromadb.api.async_client import AsyncClient as AsyncClientCreator
from chromadb.auth.token_authn import... |
01149770818855f7c86c4c7c16e386563758f10be75fa1e5b0f347565389d768 | Python | 14,700 | 460 | import click
from corgie import exceptions, stack, helpers, scheduling, argparsers
import json
from corgie.log import logger as corgie_logger
from corgie.boundingcube import get_bcube_from_coords
from corgie.argparsers import (
LAYER_HELP_STR,
create_layer_from_dict,
corgie_optgroup,
corgie_option,
... |
5d0a0bfcb044cebc2d63e38049bf31f4f83737d2108dfd2802daae88c07a1dc1 | Python | 14,703 | 406 | """
PyQt5 Canvas for Neurodecode's StreamViewer.
"""
import math
import numpy as np
import pyqtgraph as pg
from PyQt5 import QtCore
# pg.setConfigOptions(antialias=True)
class _BackendPyQt5:
"""
The PyQt5 backend for neurodecode's StreamViewer.
Parameters
----------
scope : neurodecode.stream_v... |
b56776d09b8dc9236d56bf0929e5af4d5e3bba52699b51fa9510570bee35881c | Python | 14,703 | 371 | # Copyright (c) 2022 PaddlePaddle 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 appli... |
060f388cdb19811f434d428f6fe456d1e02083324d0305e88558711fdfae44d6 | Python | 14,708 | 360 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
import numpy as np
import matplotlib.pyplot as plt
from mpl_toolkits.mplot3d import Axes3D
import matplotlib.animation as animation
# Parameters
# -----------------------------------------------------------------------------
dt = 0.1e-3
T = 3. # duration, seconds
tv = np... |
3315c5e059cc934692f2cb6aae2c64021d38d6e58a85e61f0c5a964168e2a081 | Python | 14,710 | 418 | from PymoNNto.Exploration.Network_UI.TabBase import *
from PymoNNto.Exploration.StorageManager.StorageManager import *
from PymoNNto.Exploration.Evolution.TxtHighlighter import *
from PyQt5 import QtCore
from PyQt5.QtGui import *
from PyQt5.QtWidgets import *
import pyqtgraph as pg
import numpy as np
from distutils.dir... |
72eb0bc2c53424bb5604aa0ed2aa285bd08819dfa70f519ca2ce249703ee0cf6 | Python | 14,710 | 370 | # Copyright (c) 2022 PaddlePaddle 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 appli... |
0c3a5f57e828d6bc9a1d00b9d7652672fe1b1aea5bef4c1c37703a31c0ae73b3 | Python | 14,738 | 417 | import jax
import re
import jax.numpy as jnp
import numpy as np
from scipy.special import kl_div
from pathlib import Path
import os
import ast
import logging
from pathlib import Path
from typing import Any, Dict
from pandas import DataFrame
import random
import time
import sys
from colorama import init, Fore, Back, Sty... |
f77b87f9a8cd3559144f6482160cfe5c4eb6bb7eb580e43841555bf5295706e3 | Python | 14,742 | 387 | from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import numpy as np
from scipy.signal import firwin
import tensorflow as tf
from sleeprnn.common import constants
def apply_fir_filter_tf_batch(signals, kernel):
"""For batch of signals"""
signals = s... |
67132cfa73dae1ee5584de08265d3966f5c189b21779b3ffa1d5b55f4f7030cd | Python | 14,752 | 529 | #!/opt/conda/bin/python
import argparse
import dask.dataframe as dd
import json
import matplotlib as mpl
import matplotlib.gridspec as gridspec
import matplotlib.pyplot as plt
import numpy as np
import os.path as op
import pandas as pd
import s3fs
import seaborn as sns
from afqinsight.datasets import AFQDataset
from ... |
adcea0dd3734b10e4c96ab0265fddca23fb67ca9167103fd1851d21a74e15600 | Python | 14,753 | 376 | # Copyright (c) 2021 PaddlePaddle 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 appli... |
2d731c3777f34ed41e080c0bd534ec47582c74946dd103b17d23185db5c4454b | Python | 14,762 | 290 | import numpy as np
from scipy import sparse
from sklearn.metrics import pairwise_distances
from suns.PostProcessing.par3 import fastCOMdistance
def segs_results(segs: list):
'''Pull segmented masks and their properties together from a list of segmentation results from each frame.
The outputs are the segm... |
14c2992fb2771ee4beca2eecfe19e29445e04bb62abd96cce0d4862a3bd53ae4 | Python | 14,776 | 538 | #!/usr/bin/env python
# encoding: utf8
"""
Collaborative Brain Wave Analysis Pipeline (Cobrawap)
"""
import argparse
import inspect
import logging
import os
import re
import shutil
import subprocess
import sys
from pathlib import Path
from pprint import pformat
sys.path.append(str(Path(inspect.getfile(lambda: None)).... |
81b614f47aeffd01c78186ebfeaad6097ce1fc73511d26d7ea3cf623a3bf38fd | Python | 14,793 | 349 | import numpy as np
import cv2
import os
import sys
import glob
from ppdet.utils.logger import setup_logger
import copy
logger = setup_logger('ppdet_cam')
import paddle
from ppdet.engine import Trainer
def get_test_images(infer_dir, infer_img):
"""
Get image path list in TEST mode
"""
assert infer_img... |
76b395927507919bbec83a7a553c927a721da5f03a252b8907fd13675ca42e0b | Python | 14,797 | 449 | # -*- coding: utf-8 -*-
import matplotlib
#matplotlib.use('Agg')
import matplotlib.pyplot as plt
plt.rcParams.update({'font.size': 18})
import numpy as np
import logging
import argparse
import os
import torch
import h5py
import sys
sys.path.insert(0, os.path.join(os.getcwd(), 'src/models'))
from layers import Ne... |
97c67ed9d9253a7a2253a8fa6a20efb4b0a68f84e6dfcb1d7440b655fccb07c4 | Python | 14,798 | 352 | # Copyright (c) 2021 PaddlePaddle 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 appli... |
c429d9581f7c9d385ad4f73ce1584cd8111010d326de1c2357c9d92fc61f16c1 | Python | 14,804 | 352 | # Jun 3rd, 2020. Extracted from
# https://www.tensorflow.org/addons/api_docs/python/tfa/optimizers/AdamW
# Copyright 2019 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... |
d31d93196b231f7015f39e6b89958a7b3572c3df0595d44ed779e89448b7589f | Python | 14,813 | 396 | # Copyright (c) 2022 PaddlePaddle 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 appli... |
c9464391d0e9ff59de8934c6b31032af89fb7f1ab6c81cc277a256ea31ef9502 | Python | 14,816 | 409 | """idmatcher.ai matches identities from two different tracked
sessions, see :ref:`idmatcher.ai`."""
import json
import logging
from argparse import ArgumentParser
from pathlib import Path
import matplotlib.pyplot as plt
import numpy as np
from scipy.optimize import linear_sum_assignment
from idtrackerai import ListO... |
0c34afb45f592c0c276359b7145bd52ed6d203b321c05d07da73f3832bf8450a | Python | 14,828 | 343 | # This file is a part of the `nequip` package. Please see LICENSE and README at the root for information on using it.
import torch
import lightning
from lightning.pytorch.utilities.warnings import PossibleUserWarning
from hydra.utils import instantiate
from hydra.utils import get_method, get_class
from nequip.data impo... |
8e3ea2fd8ed952b484c87a49105b2d0bca2b07045ef027569cb60c074e5f37b4 | Python | 14,831 | 438 | import experiment as exp
from experiment import session_state
from video_system import image_sources, capture_images
import arena
import schedule
import video_system
import cv2 as cv
import numpy as np
import time
import datetime
import bbox
import random
from image_observers.yolo_bbox_detector import BBoxDataCollector... |
ef3862c766d8c8757f9aa0e4088a1d416f101743bb050dfef4294fbaa2d064c5 | Python | 14,852 | 431 | # Authors: George Dang <george_dang@brown.edu>
# Rajat Partani <rajatpartani@gmail.com>
import json
from copy import deepcopy
from pathlib import Path
from time import sleep
from urllib.request import urlretrieve
import numpy as np
import pytest
import hnn_core
from hnn_core import (
simulate_dipole,
... |
81c5bb4af26009630144e86cc478b6b0ca1448dd62d09b5ae127f5d5c4ad2447 | Python | 14,853 | 381 | # Copyright (c) 2021 PaddlePaddle 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 appli... |
2f6ff58a20a2f1797b7e9b1b08fedcb2433d62ba904f08fdfe065c2b8a8a4ab8 | Python | 14,854 | 406 | import logging
import pickle
from collections.abc import Iterable, Iterator, Sequence
from io import BytesIO
from itertools import chain, pairwise, product
from multiprocessing import Pool
from pathlib import Path
import h5py
import numpy as np
from . import Blob
from .utils import (
LOGGING_QUEUE,
Episode,
... |
5251d379599ab8cc205a8bd195979c29ccd0464ac1d03ad7e0f080b75d605fb2 | Python | 14,882 | 323 | # -*- coding: utf-8 -*-
import unittest
from functools import partial
try:
import torch
except ImportError:
TORCH_AVAILABLE = False
else:
TORCH_AVAILABLE = True
from dival.util.torch_utility import (
RandomAccessTorchDataset, GeneratorTorchDataset,
load_state_dict_convert_data_parallel, ... |
57ab3147318a5d192ab2702cacf735519499fb73ebc7d1bdc0da376da1e53064 | Python | 14,885 | 439 | """Estimators wrapped around R-functions.
"""
import warnings
import itertools
import numbers
import numpy as np
from scipy.stats import pearsonr
from sklearn.base import BaseEstimator
from sklearn.utils import check_array, check_consistent_length
from sklearn.model_selection import check_cv
from sklearn.utils.valida... |
f36481659d21d7a3ab647aa82eff1068b36d9f22e2a46e89291293e3c4e81b03 | Python | 14,891 | 384 | import numpy as np
import os
import pickle
from glob import glob
import torch
import torchvision
from torch.utils.data import Dataset, DataLoader
import torchvision.transforms as T
import torchvision.transforms.functional as F
import torchvision.datasets as ds
import PIL
from PIL import Image, ImageFont, ImageDraw, Ima... |
c5332d7772f4cabaee467430118613145ea501cdea55fbdbb973ec2f77932490 | Python | 14,894 | 403 | """
Notes:
- Something to be aware of when grouping tests inside classes is that each test has
a unique instance of the class. Having each test share the same class instance
would be very detrimental to test isolation and would promote poor test practices.
todo:
- carefully test TS truncate
"""
import time
i... |
ac9d945e7105af6c8e2398461d16936adbe862612e4931114bb79b8ff4d9f3ef | Python | 14,896 | 383 | # 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 math
from typing import Any, Dict, List, Optional
import torch
import torch.nn as nn
from fairseq import utils
from fairseq.distribut... |
7a02ec237405bf45216be24641d347be7c867a5f6b5d29eaf53ae7ea1867f140 | Python | 14,927 | 461 | from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import os
import time
import numpy as np
import pandas as pd
from sleeprnn.common import constants
from sleeprnn.data import utils
from sleeprnn.data import stamp_correction
from sleeprnn.data.dataset import ... |
3113189c86227684e9d8b393a9398e6147969ce337cac184746d79e2c60881d2 | Python | 14,942 | 359 | """The published foundation checkpoints this suite pins, and how it reaches them.
A golden for a foundation model is only worth something if the file it was
taken from is the file the test loads. Everything here exists to make that
identity checkable rather than assumed:
* the **loader call** is data, not prose. ``lo... |
b6530a31c69852cd6fb8395942dc8633c02412bd1c3445e8d42fbef508e1ecdb | Python | 14,947 | 381 | # Copyright (c) 2020 PaddlePaddle 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 appli... |
1fd999cbb30883d44711c41be04496266da0734f13a88033611249a327bb776c | Python | 14,953 | 363 | """Did the vendor kernel actually run?
A backend golden compares numbers, and numbers alone cannot tell an
accelerated kernel from the plain e3nn path that produced the reference in
the first place -- the two are *supposed* to agree. So a value-only assertion
is green in exactly the case the golden exists to catch: th... |
2ccf000782204fa155ecbce1d022c8a90f424926b1bcf9497d1c153bcd382925 | Python | 14,967 | 369 | # Copyright (c) 2021 PaddlePaddle 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
#
# Un... |
3e03a954a4e889091a4dac3d1e4d1a64e55115dec9aa4351dde5ac5757f5e6db | Python | 14,969 | 250 | """Compact confidence features from completed VDJdb build tables.
Use the shipped legacy score, publication/donor totals, motif membership and mean ipTM.
No chunk reconstruction, assay taxonomy, experiment tracing or allele-specific model.
"""
from __future__ import annotations
import math
import polars as pl
from ... |
90ad008fefadf196cb5a35860a885734c160178fe655e2c39908b7d6b12a42b8 | Python | 14,977 | 309 | #!/usr/bin/env python3
__author__ = 'Frederic Escudie'
__edit__ = 'David Baux'
__edit__ = 'Charles Van Goethem'
__copyright__ = 'Copyright (C) 2019 IUCT-O'
__license__ = 'GNU General Public License'
__version__ = '1.1.3a'
__email__ = 'escudie.frederic@iuct-oncopole.fr'
__status__ = 'prod'
import os
import sys
import ... |
119b46c491a5362c4e48739f6eb2991153934441fbe5f01a75ee13412132e261 | Python | 14,985 | 449 | """The n-dimensional hyperbolic space.
The n-dimensional hyperbolic space with Poincare ball model.
Lead author: Hadi Zaatiti.
"""
import math
import geomstats.algebra_utils as utils
import geomstats.backend as gs
from geomstats.geometry._hyperbolic import _Hyperbolic
from geomstats.geometry.base import VectorSpace... |
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