sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
1a744b13b3333e5c1856025c7f447dc0440a4395eae0c264fd1cb3515368715f | Python | 3,160 | 81 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Mon Sep 16 12:41:34 2019
@author: mmolina
"""
import os
import numpy as np
from config import cfg, cfg_from_file, cfg_from_list, get_output_dir
import scipy.io as sio
import matplotlib.pyplot as plt
from sklearn.metrics import roc_auc_score, roc_curve
# ... |
da8e82ca9f452cd418c2199d2f817bd280e9ca80b039b0e040378c347284a4e7 | Python | 3,160 | 89 | # lexical_selection_generate.py
# Reads manually revieved dix elements
# Creates lexical selection rules for them in a new file.
from argparse import ArgumentParser
from collections import defaultdict
# importing element tree
# under the alias of ET
import xml.etree.ElementTree as ET
def write_variants(file_name,si... |
5ac3a0c20948f0dedf6122e94cb1162ce5d0870a49b118110f5f6e9cee3ec8de | Python | 3,162 | 88 | import multiprocessing
import re
from typing import Any, Callable, Dict, Union
from chromadb.types import Metadata
Validator = Callable[[Union[str, int, float]], bool]
param_validators: Dict[str, Validator] = {
"hnsw:space": lambda p: bool(re.match(r"^(l2|cosine|ip)$", str(p))),
"hnsw:construction_ef": lamb... |
ea36af833ce44188f497f943c038a221eafcd84e48d2e842512d3868ef94423d | Python | 3,162 | 83 | # 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 app... |
0de8ecceeaa06efb880b457805830739680eb3a41534cf297ef685aa54a8f34c | Python | 3,166 | 108 | # test.py
#test_path ='/n/groups/marks/users/david/res/model_save/model2/RES_1639761348.356219_25.pt'
test_path = '/n/groups/marks/users/david/res/model_save/model2/RES_1646945484.3030427_8.pt'
model_id = test_path.split('/')[-1][:-3]
f_path_out = '/n/groups/marks/users/david/res/out/{}.txt'.format(model_id)
import... |
83b04f104b3c67f9c8932207b5f57440df00058c1edf85e3a3f7d0c13ce4e12f | Python | 3,167 | 88 | # SPDX-License-Identifier: BSD-3-Clause
# Copyright (c) 2020-2026, Christian Gaser. See LICENSE.
"""
Drop-in replacement for nilearn's TFCE.
nilearn computes TFCE by stepping the height over a grid and summing
(``nilearn.mass_univariate._utils.calculate_tfce``, 100 steps by default,
following fslmaths). That costs a s... |
6ff737be1c3240c57bb2b0f599b6ea80ab584800e70e274efc8d30e0e385b2da | Python | 3,168 | 100 | import math
import pytest
import geomstats.backend as gs
from .base import VectorSpaceOpenSetTestData
from .riemannian_metric import RiemannianMetricTestData
LN_2 = math.log(2.0)
EXP_1 = math.exp(1.0)
EXP_2 = math.exp(2.0)
class PositiveRealsTestData(VectorSpaceOpenSetTestData):
def belongs_test_data(self):
... |
47526cdf4a44a00a79f043d7b0f1eaf7ed90e426ab8284e4f5ee122a275a1b9a | Python | 3,169 | 86 | """
Is it really a drop-in for nilearn?
nilearn computes TFCE by stepping the height (``calculate_tfce`` in
``nilearn.mass_univariate._utils``). The function here has the same signature and
returns the same thing, computed exactly. The checks are therefore about the
*contract*, not about agreeing numerically with nile... |
75ec8a03022a03f430e5264d90835d5a25a953a84722532eaffee5c9b0f6393c | Python | 3,171 | 92 | # -*- coding: utf-8 -*-
"""
Created on Wed Aug 24 14:00:53 2022
@author: Tom
"""
import tensorflow as tf
from tensorflow import keras as k
tf.config.list_physical_devices()
import os
os.environ['CONDA_DLL_SEARCH_MODIFICATION_ENABLE'] = '1'
import shutil
import numpy as np
from scipy.stats import mode
import config
f... |
486aa724fa9ea3cfeb569aa882bfce2a1b63275232f2cd7ba7035d6462a5b9b9 | Python | 3,172 | 85 | """
Offsets the signal in all channels by a fixed value.
"""
import argparse
from pathlib import Path
import matplotlib.pyplot as plt
from utils.io_utils import load_neo, write_neo, save_plot
from utils.parse import none_or_int, none_or_float, none_or_str
from utils.neo_utils import time_slice
CLI = argparse.Argument... |
8c4c7199f8beaad73180e6436bcbcdbf1e1e8137c168c74cb72aea0bc0961460 | Python | 3,172 | 89 | #!/usr/bin/env python
import sys, gzip
msFile = sys.argv[1]
def isSnp(samples, i):
alleleH = {}
for j in range(len(samples)):
if samples[j][i] != "N":
alleleH[samples[j][i]] = 1
return len(alleleH.keys()) > 1
def processSimulation(samples, positions):
newPositions = []
newSamp... |
f1d0f197b6249097a164dde43589df74d817e0a0effbc85301c5c47a493f504b | Python | 3,172 | 73 | from typing import Tuple
import torch
from torch import nn
class GraphLoss(nn.Module):
"""
Loss that compares two graphs.
Arguments:
node_factor: Weight for node classification loss.
edge_factor: Weight for edge classification loss.
"""
def __init__(self, node_factor: float = 1.0... |
4cd4cd909059e6dfb812bb18acf0b59349ff700bce38abeb225bf7b8ddb4f992 | Python | 3,176 | 84 | """Structural result records returned by the nltools estimators."""
from __future__ import annotations
from dataclasses import dataclass
from typing import TYPE_CHECKING, Generic, TypeVar
import numpy as np
if TYPE_CHECKING:
from pathlib import Path
Payload = TypeVar("Payload")
@dataclass(frozen=True)
class... |
0780ca54961e2028de91d0dccf45f6b4a8425f9462850588272770e5473afcc0 | Python | 3,178 | 90 | # Step 1: Imports and configuaration
import SimpleITK as sitk # staple
import matplotlib.pyplot as plt
import numpy as np
import os, sys
import glob
import shutil
from tqdm import tqdm
import nibabel as nib
# Step 2: confgurations and setup
config = dict()
config["post_enhancing"] = True
# BraTS paths
config["br... |
e495cc8c6b550072c9d5d7fee9aa315feff913541b3865043b55c91eabd3e226 | Python | 3,179 | 86 | """The stress mask is shared, and this is what keeps it shared.
``cell_volume_and_mask`` decides per graph whether a virial has a volume to be
normalized by. That decision is only worth anything if every model reaches it,
and a model reaches it by passing ``pbc`` alongside ``cell``. Miss one call
site and that model r... |
0ab087a216e77003bf2dc227b3f79b044a6652da562077908b01582476c83110 | Python | 3,181 | 83 | # Author: Youzhi Luo (yzluo@tamu.edu)
# Updated by: Anmol Anand (aanand@tamu.edu)
import torch
import torch.nn.functional as F
from torch.distributions.bernoulli import Bernoulli
from torch_geometric.data import Data
from torch_geometric.utils import subgraph
from torch_geometric.utils.num_nodes import maybe_num_nodes... |
6e21490f5f74e5b825956dafa98425849ca4efa23ac1c89fb61c03e90a79e5bf | Python | 3,181 | 95 | import glob
import os
import esm
import numpy as np
import tqdm
from model_angelo.utils.apply_sequence_transformer import run_transformer_on_fasta
from model_angelo.utils.fasta_utils import FASTASequence
from model_angelo.utils.protein import (
add_lm_embeddings_to_protein,
dump_protein_to_prot,
get_prote... |
f13d43c6a2eb9deec28c83ecbdd9281c0f42f01f652f780c95efeddf13931415 | Python | 3,181 | 96 | import numpy as np
import copy
def subhist(image_pdf, minimum, maximum, normalize):
"""
Compute the subhistogram between [minimum, maximum] of a given histogram image_pdf
:param image_pdf: numpy.array
:param minimum: int
:param maximum: int
:param normalize: boolean
:return: numpy.array
... |
fa264d3e9c6c449c9d05bac6214d56ddfbd70990bd52a3165853115a5ec4cbf1 | Python | 3,181 | 65 | from sklearn import svm, metrics
from sklearn.datasets import load_svmlight_file
import sys
import numpy as np
#embedding_pt = 'D:/UB/research/dataset/20newsgroups/CoEmbedding/results/Embeddings_K50_iter19.npz'
#embedding_pt = 'D:/UB/research/dataset/20newsgroups/CoEmbedding/topicmodeling/LDA/model-final.theta'
... |
8f484a1a7da3680a1325334210a329b49ee924836811610c4006ed5bc50d417b | Python | 3,182 | 96 | import json
import sys
import os
import numpy as np
import csv
from scipy.stats import poisson
from math import ceil
def import_postsyanptic_network(networkPath):
file = networkPath + '/mTypes.txt'
mFiles = list()
with open(file, newline='') as csvfile:
syns = csv.reader(csvfile, delimiter='\n')
... |
b3987091e1c479c0785e5fa47b530c2cd03b554a5a757878814041726c44b00b | Python | 3,183 | 98 | """
tests for model subparts
"""
import unittest
import torch
from foldingdiff import modelling
class TestPositionalEmbedding(unittest.TestCase):
def setUp(self) -> None:
self.bs = 32 # Batch size
self.d_model = 4
self.seq_len = 512
self.input_shape = (self.bs, self.seq_len, se... |
f368d625b7ccdf2715c8e85bd274159e3aaf2d5903422a80e32b3e3425e4426f | Python | 3,183 | 112 | ####################################
################## DRUGS
import os
import pandas as pd
from tqdm import tqdm
import logging
import json
#import logging
from requests.adapters import HTTPAdapter
from requests.packages.urllib3.util.retry import Retry
import requests
from tqdm import tqdm
import time
def get_drug... |
cdce70a4b73ccba5a7fdbedd53e3f212d27913a058e4ef9f7b98b407b2de04a0 | Python | 3,184 | 91 | #
# For licensing see accompanying LICENSE file.
# Copyright (C) 2022 Apple Inc. All Rights Reserved.
#
from torch import nn, Tensor, Size
from typing import Optional, Union, List
import torch
from . import register_norm_fn
@register_norm_fn(name="layer_norm")
class LayerNorm(nn.LayerNorm):
"""
Applies `Lay... |
f3d6ab979480cf4b0f56ea5619879385707ace2331e75f0e758768eb4509234c | Python | 3,186 | 87 | from kernels import Kernel
from utils import save_model, load_model
import logging
import numpy as np
from sklearn import svm
def train_eval(config, args, X_train, Y_train, X_test=None, Y_test=None):
seed = str(args['seed']) if not args['split_ready'] else ''
model_path = "%s%s_%s.pkl"%(args['model_path']... |
d85f7282ffcf74f719db010ff0e06616960358c8539a3d842df80431cb79d30d | Python | 3,188 | 65 | import os
import tables
import numpy as np
from config_trans import cfg
from model_trans import transxai_model
from data_generator import CustomDataGenerator
from tensorflow.keras.callbacks import CSVLogger, ModelCheckpoint, TensorBoard
def train_model(hdf5_dir, brains_idx_dir, view, batch_size=16, val_batch_size=32,... |
2bda118f9a116797ea64192bb43db0c5759213e48fa270fb77ce8b22e375bbde | Python | 3,189 | 99 | # 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... |
fd29d7ebc4f9a367e4e7c2ec7daa575410a10b7ace0f81f665e560989210f07e | Python | 3,189 | 86 | import numpy as np
import scipy.stats
'''
vocab_pt = 'D:/UB/research/dataset/20newsgroups/CoEmbedding/vocab.txt'
embedding_pt = 'D:/UB/research/dataset/20newsgroups/CoEmbedding/results/Embeddings_K50_iter19.npz'
#embedding_pt = 'D:/UB/research/dataset/20newsgroups/CoEmbedding/word2vec/svd_gradient.npz'
'''
'''... |
79b7774969ef04e2661ed799e8ba49bbc5b227414f233808e7ab71bb2a0ba23e | Python | 3,190 | 102 | import os
import argparse
import warnings
warnings.simplefilter(action="ignore", category=FutureWarning)
import xarray as xr
import tensorflow as tf
tf.compat.v1.logging.set_verbosity(tf.compat.v1.logging.ERROR)
from activation_models.generators import get_activation_models
from custom_model_tools.projection_distance... |
fbe2fe435661a19176d264feec41ff4ea1175cf464bbfdcbcb5924359b851dd5 | Python | 3,190 | 95 | # This file is a part of the `nequip` package. Please see LICENSE and README at the root for information on using it.
import lightning
from lightning.pytorch.callbacks import Callback
from nequip.train import NequIPLightningModule
from nequip.utils.global_state import set_global_state
from typing import Dict, Optional... |
11a05042aff5e0434046b36d7a99c060affeae7dc9b82f46ebf198c860598b8a | Python | 3,191 | 81 |
from sleepy.processing.processor import Algorithm
from sleepy.processing.parameter import Parameter
import numpy as np
class RandomForest(Algorithm):
def __init__(self):
self.name = "RandomForest"
def calc_fs(self,X):
features=np.zeros((X.shape[0],17),dtype='float32')
# Feat... |
3d2f55e7ab26a2d27e429ca9ea063b04816194a95614a4148af48879a4d151d3 | Python | 3,191 | 84 | # -*- coding: utf-8 -*-
import unittest
from unittest.mock import patch, mock_open, Mock, MagicMock
import json
from copy import deepcopy
from io import StringIO
from dival.config import CONFIG_FILENAME, get_config, set_config, CONFIG
class TestConfig(unittest.TestCase):
def test_get_config(self):
c = {
... |
a5444d9b79ff7af18de4cf9e60e55ec83be7b1d3bc48fb1cc3fe8e582a1f6424 | Python | 3,191 | 96 | """Static registry of atlases hosted at `nltools/niftis/atlases`.
Each entry describes an atlas's kind (deterministic vs probabilistic) and
the citation users should cite when they use it. The actual NIfTI + label
files are fetched lazily by `load_atlas` via `fetch_resource`.
Atlases were sourced from atlasreader (BS... |
e738097062368bf60bd982b759cdacd42567d58fb421e5fb5e17dc48c55b270e | Python | 3,196 | 75 |
from sparse_ct.tool import plot_grid
from sparse_ct.data import image_to_sparse_sinogram, ellipses_to_sparse_sinogram
from sparse_ct.reconstructor_2d import (
IRadonReconstructor,
SartReconstructor,
SartTVReconstructor,
Sar... |
3734fd5e4ddd4881ee9f5eaac3f0060f19e9d0721b012a7820af96593f0c289d | Python | 3,197 | 141 | from Purkinje_morpho_1 import Purkinje_Morpho_1
from Purkinje_morpho_1_number import number_ind_1
from neuron import h,gui
import numpy as np
import multiprocessing
import matplotlib.pyplot as plt
import random as rnd
#per disabilitare tutti i generatori random
seed = 123456
rnd.seed(seed)
h.use_mcell_ran4(1)
h.mcell... |
409c948094129e8f53d4a0262c045ea271a71bb574992485e40e02f4e23ede65 | Python | 3,197 | 98 | """Plot a Kernel Density Estimation Classification on the sphere."""
import logging
import os
import matplotlib.pyplot as plt
import numpy as np
import geomstats.backend as gs
import geomstats.visualization as visualization
from geomstats.geometry.hypersphere import Hypersphere
from geomstats.learning.kernel_density... |
bc8121efd9a5e071e397440dc6cfd6abed268e7c0e9bc00ad31470c7b8609feb | Python | 3,197 | 121 | from PymoNNto import *
import matplotlib.pyplot as plt
#https://brian2.readthedocs.io/en/stable/examples/frompapers.Brunel_Hakim_1999.html
tau = 20 #20 # ms
dt=0.2
class Brunel_Hakim_main(Behavior):
def initialize(self, n):
self.Vr = 10 # mV
self.theta = 20 # mV
self.delta = 2 # ms
... |
e1cfefd294cd44f10d7a7d229dd21c84c1016592fe05982e9db1640c2c198ab9 | Python | 3,198 | 90 | # language=rst
"""
This code is directly pulled from the pytorch version found at:
https://github.com/pytorch/pytorch/blob/master/torch/utils/data/_utils/collate.py
Modifications exist to have [time, batch, n_0, ... n_k] instead of batch in dimension 0.
"""
import torch
from torch._six import string_classes
int_clas... |
0fc91c4028865df25aff030e69ce642212c06262b52ff505ee00f0980c25e9fc | Python | 3,200 | 100 | # 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... |
1e6b5b2940863dc97fc169f95d72e212ceefe7b2ae6444472259a2f73e2941ba | Python | 3,200 | 107 | import geomstats.backend as gs
from geomstats.test.data import TestData
from .base import LevelSetTestData, MatrixVectorSpaceTestData
from .euclidean import EuclideanMetricTestData
class SymmetricMatricesTestData(MatrixVectorSpaceTestData):
pass
class SymmetricMatrices1TestData(TestData):
def basis_test_da... |
36985cc0af8810f672ebb9da26362f16fcfb78fab5f7dfded51c868971a929cc | Python | 3,201 | 96 | """
Patch for Tensorboard add_histogram
"""
import numpy as np
import torch
from torch.utils.tensorboard import SummaryWriter
from torch.utils.tensorboard._convert_np import make_np
from tensorboard.compat.proto.summary_pb2 import Summary, HistogramProto
def add_histogram(
self,
tag,
values,
global_s... |
3f9ddf31b0e6c75e2c6e71f055e8f978b18fa70da60bff191a77c9e720842b9f | Python | 3,202 | 90 | import unittest
import pytest
import torch
import torch.utils.data as tud
from reinvent.models.transformer.core.dataset.dataset import Dataset
from reinvent.models.transformer.core.enums.sampling_mode_enum import SamplingModesEnum
from reinvent.models.transformer.core.vocabulary import SMILESTokenizer
from reinvent.m... |
bc84f46d873a7f041516f87ed4781c140ccb5cf3326b776f39508fa2bef472bd | Python | 3,207 | 100 | # Add up to 2M records until the log-is-full message is seen.
import threading
from concurrent.futures import ThreadPoolExecutor, as_completed
import pytest
from chromadb.api import ClientAPI
from chromadb.errors import RateLimitError
from chromadb.test.conftest import (
reset,
skip_if_not_cluster,
)
EXPECT... |
1c525114ebc1244d61b8ee90c008c3ace18693266e852675b16dec8344af6828 | Python | 3,209 | 103 | import asyncio
import sys
import uuid
from pathlib import Path
import chromadb
import xai_sdk
from pypdf import PdfReader
from langchain_text_splitters import RecursiveCharacterTextSplitter, SentenceTransformersTokenTextSplitter
from tqdm import tqdm
from chromadb.utils.embedding_functions.sentence_transformer_embedd... |
a987fa98968bdcfe1fbb2db8be894c2cdef5a00e9784bdcd9ca14726a5009dbb | Python | 3,209 | 109 | ## IMPORT BASIC LIBS FOR SCRIPT
import scipy as sc
from scipy import io, stats
import bstates as bs
import sklearn as sk
from sklearn import cluster, metrics
import pickle
import numpy as np
import h5py
import feather
import pandas as pd
import os
from sys import argv
## TREATING ARGV VARS
nPats = int(argv[1]) # NU... |
8a9a3422c05722dc89b22d463a55c336e572775ef4962fcf22fbdf68cc596a5b | Python | 3,210 | 99 | #evaluation funcitons for multi-class, single-label problems
from sklearn.metrics import multilabel_confusion_matrix
import torch
import matplotlib.pyplot as plt
import numpy as np
import pandas as pd
from scipy import stats
import compare_auc_delong_xu as DeLongAUC
import os
import sklearn
def AddImplicitClass(out,th... |
b41281e0d0abf15f2e41e5f3d88e4b6d70e448834dbf3e3315ff9fadc19406c1 | Python | 3,211 | 108 |
# ```python
# #PymoNNto/Examples_Docs/speed #initialize
# src = np.random.rand(5000) < 0.01 # 5k pre synaptic neurons (1% spikes)
# dst = np.random.rand(10000) < 0.01 # 10k post synaptic neurons (1% spikes)
# ```
#search all markdown files
#select code sections
#check and extract first code line (path to ... |
6e2a24bc9535fc256a3cecdf72613e1a260a57906f3fbf4688e4b00ad0bf1273 | Python | 3,212 | 125 | # -*- coding: utf-8 -*-
"""
Functions to facilitate reporting.
Created on Feb 5 2025
@author: Mohammad Torabi
"""
import os
import matplotlib.pyplot as plt
import seaborn as sns
################################# Parameters ####################################
fig_dpi = 120
fig_bbox_inches = "tight"
fig_pad = 0.1
s... |
4642865261b66979ca85e702e0b4f62c81284d04dc4482baf8bb6b275ae215d5 | Python | 3,214 | 67 | """
MIT License
Copyright (c) 2017 Sadeep Jayasumana , Miguel Monteiro
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 Software without restriction, including without limitation the rights
to use, copy, m... |
0af2bc4f4ea69ead399518016964e51f86bd362852307c7cbd43a3bc0ed7ac3a | Python | 3,216 | 80 | import haiku as hk
import jax
from jax import numpy as jnp
from typing import Optional
class Attention(hk.Module):
def __init__(
self,
attention_dim: int,
n_heads: int,
residual: bool,
attention_value_dim: Optional[int] = None,
output_dim: Optional[int] = None,
... |
f22288900d732bf7f1a3f2b9346e016b5148c37f2f3187eaa1dee7836de45e87 | Python | 3,218 | 81 | import pandas as pd
import numpy as np
import pandas as pd
from tqdm import tqdm
from common.adni.utils import INPUT_COLS, TARGET_COLS, NAME2DX, MRI_BIOMARKERS
def standardize_metadata(df, out_filename, dt=6):
n_max_fu = 10
targets = ["DXTARGET", "ADAS13", "Ventricles"]
# avail_cols = df.columns.tolist()... |
f43ce47fa4b5ffd8e56f86fc8e43d6be01116c969504c865aa6d9d72b7f7eca6 | Python | 3,218 | 93 | # /usr/bin/env python3
# coding: utf-8
#
# This software and supporting documentation are distributed by
# Institut Federatif de Recherche 49
# CEA/NeuroSpin, Batiment 145,
# 91191 Gif-sur-Yvette cedex
# France
#
# This software is governed by the CeCILL license version 2 under
# French law and abi... |
f0acb03d4b263f52aa3724a8a637b532fd82b21b52c00882f1b907277d42c4ff | Python | 3,219 | 105 | import pytest
from typing import List, cast, Dict, Any
from chromadb.api.types import Documents, Image, Document, Embeddings
from chromadb.utils.embedding_functions import (
EmbeddingFunction,
register_embedding_function,
)
import numpy as np
def random_embeddings() -> Embeddings:
return cast(
Emb... |
8471c7f17d1e0768aea33e4ec4a3a3a7c2bb877e4581d5a9fd22adaee041e7b2 | Python | 3,222 | 75 | from PymoNNto.Exploration.Network_UI.TabBase import *
class character_activation_tab(TabBase):
def __init__(self, title='char'):
super().__init__(title)
self.title = title
def add_recorder_variables(self, neuron_group, Network_UI):
return
def initialize(self, Network_UI):
... |
55c9980e1dae77ff5d6699491b8582a24ef94c190c3d5beb5109e09470c364d7 | Python | 3,225 | 85 | from typing import Tuple
import torch
from torch import Tensor
import torch_geometric.transforms as T
from torch_geometric.data import Data, Batch
from torch_geometric.datasets import GNNBenchmarkDataset, Yelp, Flickr, Reddit2
from ogb.nodeproppred import PygNodePropPredDataset
def index2mask(idx: Tensor, size: int)... |
d982ec71390a6b03ade3c04b998c39969f496c489f97bcabf89ecf9b79eedcac | Python | 3,227 | 90 | import torch
import torchfields
import numpy as np
import argparse
import h5py
from pathlib import Path
from concurrent.futures import ProcessPoolExecutor, Executor
if __name__ == "__main__":
parser = argparse.ArgumentParser(description="Upsample H5 Field")
parser.add_argument(
"--src_path", type=str,... |
d320debd19dc17034a9ff2212455141d5e4355e09f2dd5348aa424416b6eb22c | Python | 3,228 | 78 | import numpy
def get_sided_masked_array(d, side=None, axis=None, mask_stat="median"):
"""mask array to include values greater than ("right") or less than ("left") a statistic of the set
Parameters
----------
d : :class:`numpy.ndarray`
input data array
side : str or None
"l", "r", ... |
6d996bd87c36558ff24393056458c87189dcdcc1cdaa08c379e163e11c13c211 | Python | 3,229 | 92 | # Copyright 2020-2024 Intel Corporation
# SPDX-License-Identifier: Apache-2.0
"""FedProx Keras optimizer module."""
import tensorflow as tf
import tensorflow.keras as keras
@keras.utils.register_keras_serializable()
class FedProxOptimizer(keras.optimizers.Optimizer):
"""FedProx optimizer (Keras3 based API).
... |
805550d044b161224aadf516532a37e8b70abcd9dfa1c91e14beb5485f02e648 | Python | 3,229 | 93 | """Regenerate the committed goldens.
Goldens are edit-locked. Every artifact under ``tests/golden/`` -- the
fixtures, the anchor checkpoints, the reference JSONs -- is only rewritten by
this script, and only in a change that does nothing else and explains the
physics of what moved. That is why it refuses to run withou... |
8a61c4200d6ee7c85d562a2b28973cb88ca2901778388cbbbad4f6e7fdc63146 | Python | 3,230 | 104 | from collections import defaultdict
from pathlib import Path
import cv2
import numpy as np
import paddle.vision.transforms as T
from openvino.inference_engine import IECore
from ppdet.modeling.mot.tracker import JDETracker
from ppdet.modeling.mot.visualization import plot_tracking_dict
root_path = Path(__file__).pare... |
5d268c155b2bf0623c3ab2633d381f17e0f652721cfb9683d2edbbb82c386ada | Python | 3,231 | 146 | import collections
import random
import numpy as np
import torch
import torch.nn as nn
import torch.nn.functional as F
import predictive_coding as pc
import analysis_utils as au
def plot_mean(df):
df = au.nature_pre(df)
g = au.nature_relplot(
data=df,
x='pc_learning_rate',
y='Mean ... |
89c22c607a6fd4574b93e9bbcbd592d6e953a294aeee92780bb7ccbaffc9f258 | Python | 3,231 | 83 | """
Calculate the period between two consecutive waves for each wave and channel.
"""
import argparse
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
from utils.io_utils import load_neo, save_plot
from utils.parse import none_or_str
from utils.neo_utils import analogsignal_to_imagesequence
CLI ... |
500e92efad6bb8037e90b3c814a8f3727df8bf5f82b571b955e26b9509affa4e | Python | 3,232 | 112 | """Command line setup
FIXME: replace with dataclass and automatic conversion to argparse?
"""
from __future__ import annotations
__all__ = ["parse_command_line"]
import argparse
import os
from pathlib import Path
import logging
import torch
from reinvent import version
from reinvent.utils import config_parse
from ... |
d0a6d1e9bae3aab90941dd6a8ffb64a70514c3acf6c684b433f527baffd03ef9 | Python | 3,234 | 93 | import logging
import os
from time import time
import datetime
import numpy as np
import pandas as pd
from sklearn.linear_model import LinearRegression
import h5py
from PIL import Image
from model_tools.utils import fullname, s3
def properties_to_id(architecture, task, kind, source):
identifier = f'architecture:{... |
d6b691a476a6e0d735c7483c17cfef0418eeec392927898206b794e974cda5a0 | Python | 3,235 | 106 | # 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 nequip.data import AtomicDataDict
from typing import Dict, List, Callable, Union
# === Inputs and Outputs for AOT Compile ===
# standard sets of input and output fields for specific i... |
fab79f9053fc456ec24f86537d537f1803b77e515f34ea1c056b0981b7c58ee6 | Python | 3,235 | 84 | """
Calculate the period between two consecutive waves for each wave and channel.
"""
import argparse
from pathlib import Path
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
from utils.io_utils import load_neo, save_plot
from utils.parse import none_or_path, none_or_str
from utils.neo_utils imp... |
849d99730e4a0db6e33a6e5385bf3675d6f1e624e44a61cc700b404c867c2ebd | Python | 3,238 | 89 | # from main import base_model, get_last_weights
from tensorflow.keras.models import model_from_json, load_model
from tensorflow.keras.preprocessing.image import load_img, img_to_array
import numpy as np, glob, cv2.cv2 as cv2, matplotlib.pyplot as plt, copy
from skimage.segmentation import mark_boundaries
from visualiza... |
8819d6a52ed263152a09c4fdac0934892ab8ac8154f16b36b1daa080bc2ae1b6 | Python | 3,238 | 99 | # 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... |
759b3907946f89387e9384b9bc34ed7c7ff7c2d8834b76720e89a9b7b7988e1f | Python | 3,239 | 94 | from PymoNNto import *
import time
from globparams import *
import scipy as sp
settings = {'dtype': float32, 'synapse_mode': SxD}
class LeakyIntegrateAndFire(Behavior):
def initialize(self, neurons):
neurons.spikes = neurons.vector('bool')
neurons.spikesOld = neurons.vector('bool')
... |
79d1f4553258d9c1fefd80db2ff526f02f38f421000837a5f0e0c55ef8d2a5d4 | Python | 3,240 | 88 | import torch
from torch import nn as tnn
from torch.nn.utils import rnn as tnnur
from reinvent.models.model_parameter_enum import ModelParametersEnum
class Encoder(tnn.Module):
"""
Simple bidirectional RNN encoder implementation.
"""
def __init__(self, num_layers: int, num_dimensions: int, vocabular... |
8259c4f4c1ccd98493b8848461018f9204585ae62d9c206569e0f6f1c9990d22 | Python | 3,242 | 90 | """`--log_level`, which decides what a run says and not what it records.
`setup_logger` puts the root logger at DEBUG and then attaches three handlers:
the console and `<tag>.log` at the requested level, and `<tag>_debug.log` at
DEBUG unconditionally. So the flag quiets two of the three destinations, and the
one it do... |
fd8875f3d1e885d017c1bf7813f50f882db57cd3ad4ffe1f344bdb4d8d29051d | Python | 3,242 | 111 | from pickle import FALSE
from datagenerator_pd import DataGenerator
from sklearn.metrics import confusion_matrix, accuracy_score
from tensorflow.keras.utils import to_categorical
import matplotlib.pyplot as plt
import seaborn as sns
import SimpleITK as sitk
import pandas as pd
import numpy as np
import random
... |
b149c777d4b23b72c127e2781752678c9a30ed3ca3f0df2379f185a2dd513796 | Python | 3,245 | 109 | from contextlib import contextmanager
from functools import wraps
from typing import Callable, Tuple
try:
import torch._dynamo as dynamo
except ImportError:
dynamo = None
from e3nn import get_optimization_defaults, set_optimization_defaults
from torch import autograd, nn
from torch.fx import symbolic_trace
Mo... |
6303ec959f15e7487ab2ad9d109616b9967471f8a299a582bb129d1760538366 | Python | 3,246 | 83 | """
Calculate the period between two consecutive waves for each wave and channel.
"""
import argparse
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
from utils.io_utils import load_neo, save_plot
from utils.parse import none_or_str
from utils.neo_utils import analogsignal_to_imagesequence
CLI ... |
4e04197d0ad37e73dea63276dc208670f71f8133cfe6d3303c8864ae03aa64b9 | Python | 3,250 | 87 | """
Train FBPUNetReconstructor on ``'ellipses'``.
"""
from odl.operator import OperatorComp
from torch.multiprocessing import set_start_method, get_start_method
import torch
import odl
import numpy as np
from dival import get_standard_dataset
from dival.measure import PSNR
from dival.reconstructors.fbpunet_reconstructo... |
fedb39a4159945055449203d9d9be0ddfc343f704b50a6c15894221a441b78d8 | Python | 3,251 | 116 | from pymonntorch import Network, SynapseGroup, NeuronGroup, Behavior, EventRecorder
import torch
import time
from globparams import *
import matplotlib.pyplot as plt
settings = {"dtype": torch.float32, "synapse_mode": "SxD", "device": "cuda"}
class TimeResolution(Behavior):
def initialize(self, n):
n.dt ... |
173b5044f4bebb7cd6fa0ffe37d4ca8ff3191fe59f68010c93a2b78add746e04 | Python | 3,252 | 73 | import torch
from torch_geometric.data import Data
from .loading_utils import train_scaler, scale_dataset_aux
TARGET_ID_TO_PROPERTY = {
0: 'First excitation energy (ZINDO)',
1: 'Electron affinity (ZINDO/s)',
2: 'Excitation energy at maximal absorption (ZINDO)',
3: 'Atomization energy (DFT/PBE0)',
... |
40a4c4eb056ee62721adb9be18cdad2768413aba649b9d55fa4e00756f6e69aa | Python | 3,253 | 96 | import geomstats.backend as gs
from geomstats.test.data import TestData
from .base import VectorSpaceOpenSetTestData
from .riemannian_metric import RiemannianMetricTestData
class PoincareHalfSpaceTestData(VectorSpaceOpenSetTestData):
pass
class PoincareHalfSpace2TestData(TestData):
def belongs_test_data(se... |
384c74319ba7a40c71f91a3a66f21128faa018e8a36c74195968d9ebbb2dff10 | Python | 3,257 | 98 | #!/usr/bin/env python3
from pathlib import Path
import numpy as np
import matplotlib.pyplot as plt
import torch
from mlspm.datasets import download_dataset
from mlspm.models import ASDAFMNet
from mlspm.visualization import make_input_plots, make_prediction_plots
def plot_experiment_AFM(list_of_exp):
cols = 10
... |
96eec90069d39a9c637c45f633103a904ef92ab8bb9cdae8ae224a9394f971fe | Python | 3,257 | 104 | """RDKit 2D Pharmacophore Fingerprints"""
from __future__ import annotations
__all__ = ["Pharm2DFP"]
import os
from dataclasses import dataclass
from typing import List
import logging
from rdkit import Chem, DataStructs
from rdkit.Chem import ChemicalFeatures
from rdkit.Chem.Pharm2D import Generate, Gobbi_Pharm2D
f... |
537b5aba31e4053feec7f49b777ac2c01d410e2973aca401b0dfb8aead4208d6 | Python | 3,259 | 133 | """Optimizers implementations."""
import logging
from abc import ABC, abstractmethod
from scipy.optimize import OptimizeResult
import geomstats.backend as gs
class Minimizer(ABC):
"""Minimizer.
Parameters
----------
save_result : bool
Whether to save result.
"""
def __init__(self,... |
22f14fab84e42d52f065c5bb656b08fe63d44509bed908fbb7626e60ee063d25 | Python | 3,260 | 106 | # -*- coding: utf-8 -*-
"""
Configuration of the library.
The module variable :obj:`CONFIG` holds the current configuration.
The library configuration is stored in the file ``~/.dival/config.json``.
If the config file does not exist when the library is imported, it is created
using default values.
Changes made in ``c... |
88220d48c9f6b59d80c98474960ec5dfc1eb96d229e352fb67cf6c201e45a12b | Python | 3,263 | 106 | import lmdb
import torch
import pickle
import pytest
import numpy as np
from nequip.data.dataset import NequIPLMDBDataset
def make_atomic_data(i: int) -> dict:
# Minimal AtomicDataDict with only 'pos' field
return {"pos": torch.tensor([[float(i), float(i), float(i)]], dtype=torch.float)}
def test_save_load_... |
b4a2306b1f9fb428413edc758bee5cdd722e999bf2e58c05bd1c2b08245e5eba | Python | 3,263 | 116 | from pymonntorch import Network, SynapseGroup, NeuronGroup, Behavior, EventRecorder
import torch
import time
from globparams import *
import matplotlib.pyplot as plt
settings = {"dtype": torch.float32, "synapse_mode": "SxD", "device": "cpu"}
class TimeResolution(Behavior):
def initialize(self, n):
n.dt =... |
a089e2752dcb5bb9997f59f152c2d0b8ad158fa7c6cf6ff852b5cfe8b0356093 | Python | 3,264 | 86 | import sys, os
from sklearn.externals import joblib
import numpy as np
import random
from sklearn.ensemble import ExtraTreesClassifier
from time import time
from operator import itemgetter
from sklearn.model_selection import GridSearchCV
trainingSetFileName, classifierPickleFileName = sys.argv[1:3]
statsToUse = sys.ar... |
636ad1c9a05dba2d1e02fbd0b93c3852c3a96d8e952454f279f3b3a6b15ac334 | Python | 3,271 | 89 | from PymoNNto.Exploration.Network_UI.TabBase import *
#from Testing.Common.Classifier_Helper import *
class sidebar_music_module(TabBase):
def add_recorder_variables(self, neuron_group, Network_UI):
if hasattr(neuron_group, 'pattern_index'):
Network_UI.add_recording_variable(neuron_group, 'n.... |
93660910a4ac866160db18b983335a6563c936468c3f35c560fdcec298267448 | Python | 3,272 | 114 | #!/usr/bin/env python3
"""Run a deterministic shard of a pytest selection."""
from __future__ import annotations
import argparse
import os
import subprocess
import sys
import tempfile
from typing import Sequence
def parse_args() -> argparse.Namespace:
parser = argparse.ArgumentParser(description=__doc__)
pa... |
fbee37896b605ed7a4564c4331c49617604577855ce3f3cbff7ba39ba36f93aa | Python | 3,272 | 97 | from pathlib import Path
import mne
from .. import io
from ... import logger
def resample(inst, sfreq, **kwargs):
"""
Resample the inst.
Resample goal is to speed up computation. As it add a jitter to the
trigger/events, it is recommanded to first create the epochs and then
downsample the epochs... |
c7135bfc253c32a3969e30b7ef67ff991ff77a544c89e548c6a80feb5e5c88f5 | Python | 3,273 | 84 | """
Calculate the period between two consecutive waves for each wave and channel.
"""
import argparse
from pathlib import Path
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
from utils.io_utils import load_neo, save_plot
from utils.parse import none_or_path, none_or_str
from utils.neo_utils imp... |
c42264ed7865792f9926e6b488f6e5255988d3c802bd0d892a86bf2820faf5dc | Python | 3,275 | 161 | # Copyright 2020-2025 Intel Corporation
# SPDX-License-Identifier: Apache-2.0
"""Module consists of custom exceptions for end to end testing"""
class PersistentStoreCreationException(Exception):
"""Exception for persistent store creation"""
pass
class DockerException(Exception):
"""Exception for docker"... |
5d65076bc7365da6501250068681890c98ab72fc0161ad9c38b2d01a8aeb2457 | Python | 3,278 | 101 | import numpy as np
import pandas as pd
import pyfizi
class AnnotSeries(pd.Series):
@property
def _constructor(self):
return pyfizi.AnnotSeries
@property
def _constructor_expanddim(self):
return pyfizi.Annot
class Annot(pd.DataFrame):
"""
Thin wrapper for a pandas DataFrame ... |
04d7a44f5bcbc6c092a2cd5b5884b29ba1b431e7b7e8328d73defc751f240a30 | Python | 3,280 | 52 | # -*- coding: utf-8 -*-
import functions.rate_coding
import numpy as np
import functions.manifold
import functions.Graphs
import matplotlib.pyplot as plt
import functions.statistics_test as st
#%% Load data
data = np.load('/datapath/dataset.npy', allow_pickle=True).item()
#%% Manifold of all mice
res, ... |
b2344c92278931ef264d482753f7f9e834aae4945669983a23b2818ea6e9c67c | Python | 3,281 | 76 | from collections.abc import Sequence
from qtpy.QtCore import Qt, Signal # type: ignore[reportPrivateImportUsage]
from qtpy.QtWidgets import QCheckBox, QHBoxLayout, QLabel, QMessageBox, QWidget
from idtrackerai.GUI_tools import InvertibleSlider, LabelRangeSlider
class AreaThresholds(QWidget):
valueChanged = Sig... |
32f3c681519d8fd366def5d7188c9e661a3f176c6b5800c399533e395e5e87aa | Python | 3,282 | 112 | import argparse
import os
import pickle
import random
import numpy as np
from src.ECGXMLReader import ECGXMLReader
def parse_args():
parser = argparse.ArgumentParser("Building cross-validation folds")
parser.add_argument(
"--c_avrt_path",
type=str,
required=True,
help="path f... |
2668e43bab54d3daeb9265ab1f359c440ab77b067336d428389a465ed6f11f90 | Python | 3,283 | 128 | #!/usr/bin/env python3
#
# Sniffles2
# A fast structural variant caller for long-read sequencing data
#
# Created: 27.08.2021
# Author: Moritz Smolka
# Contact: moritz.g.smolka@gmail.com
#
import statistics
import math
import sys
import time
class Sniffles2Exit(Exception):
pass
def stdev(nums):
nums=list(nu... |
dd6d6bce8f3970c58e9f275bff03772b21ac0c8a8fadce8d8ded11b96932e760 | Python | 3,285 | 92 | import pytest
from reinvent.chemistry.amino_acids.amino_acids import (
construct_amino_acids_fragments,
add_O_to_endof_fragment_amino_acids,
remove_cyclization,
)
@pytest.mark.parametrize(
"sequences, expected_output",
[
(
[
"N[C@@H](C)C(=O)|N[C@@H](CC(=O)O)C(=O... |
02992fff694e0c5c90bd1d915cebf77682489b3eb2211ae023c0fb1024992bf3 | Python | 3,288 | 92 | """The proprietary-data guard. TCRvdb must never reach the repository or a release."""
from __future__ import annotations
import os
from pathlib import Path
import pytest
from vdjdb.validate import scan_paths, tcrvdb_path
from vdjdb.validate.guard import ENV_VAR
def test_clean_tree_has_no_leaks(tmp_path):
(tmp... |
9dee7b4767ebd4f885a8751abb4e4fdd8a0fac55a3209e1026c31fb5a38c94d3 | Python | 3,292 | 95 | # Copyright 2020-2025 Intel Corporation
# SPDX-License-Identifier: Apache-2.0
"""
This file contains utility functions for Secure Aggregation Shamir's secret
sharing related operations.
"""
from Crypto.Protocol.SecretSharing import Shamir # nosec B413
# The length of each chunk of secret used for creation of share... |
22efec0b67d8e7ba1accd76289d1575024c6f9cced1168970ac2436e0bfe17d3 | Python | 3,298 | 111 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Wed Dec 12 15:25:17 2018
@author: ngritti
"""
from csbdeep.data import RawData, create_patches
from csbdeep.utils import axes_dict
from csbdeep.models import CARE, Config
from csbdeep.io import load_training_data
import time, os, glob
import numpy as np
#... |
3111ad1a9faca2794cef5d692b79cdd41b304e63e9cb1471939cc864d9a026fe | Python | 3,298 | 115 | from errors import MutationError
import pandas
from rdkit import Chem
from rdkit.Chem.EnumerateStereoisomers import EnumerateStereoisomers, StereoEnumerationOptions
def _perform_mutation(mutations, seq):
"""
Main logic for performing mutations.
"""
for mutation in mutations:
# print('->' +... |
e1c9cfe7ea538847098252776b07254da4e1780d8b78bbe6abc6797c9ad20b30 | Python | 3,298 | 101 | import csv
import os
import pytest
from reinvent.runmodes.enumeration.run_enumeration import run_enumeration, PeptideEnumeration
from reinvent.runmodes.enumeration.validation import AAEnumerationConfig
TEST_DIR = os.path.dirname(os.path.abspath(__file__))
MOCK_LIBRARY_FILE = os.path.join(TEST_DIR, "mock_aa_library.csv... |
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