sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
03a545d360323c4eebc0ba13b6fe22a36ceab30af5ee5f8beb933983e0d66287 | Python | 1,482 | 57 | from typing import Callable, Dict, List
from ..base_transform import BaseTransform
class Lambda(BaseTransform):
r'''
Apply a user-defined lambda as a transform.
.. code-block:: python
transform = Lambda(targets=['y'], lambda x: x + 1)
transform(y=1)['y']
>>> 2
Args:
... |
058a5e0411175843c1b4526d2a1fd782e913a2c9720aa3d3ea07a2fa7832538f | Python | 1,482 | 60 | # Copyright (c) OpenMMLab. All rights reserved.
import torch.nn as nn
from mmcv import build_from_cfg
from .registry import BACKBONES, COMPONENTS, LOSSES, MODELS
def build(cfg, registry, default_args=None):
"""Build module function.
Args:
cfg (dict): Configuration for building modules.
regis... |
7fff38d9d49d55718ab8e07dcb0412de703052dd947815759683c80944a06700 | Python | 1,482 | 41 | # coding=utf-8
# Copyright 2026 The Google Research Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicab... |
d5b1a8a3b4ac296cd6f158a6bc7f585229aeb7803913b32c12d0104c51c7dfeb | Python | 1,483 | 56 | #! /usr/bin/env python
# -*- coding: utf-8 -*-
from downward.suites import suite_optimal_with_ipc11
from downward.configs import default_configs_optimal
from downward.reports.scatter import ScatterPlotReport
import common_setup
REVS = ["issue214-base", "issue214-v2"]
CONFIGS = default_configs_optimal()
# remove co... |
dd5eb45b23fecdb8f3ccfb56d758baae55ebd30e160dfa0411d3c8e05b923dde | Python | 1,483 | 37 | #
# MIT License
#
# Copyright (c) 2022 GT4SD team
#
# 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, modify, merge,... |
a22d83c2869173869f24c3a5aaf07f8a50cacd350afced9312cf0f95cbe30f4e | Python | 1,484 | 53 | from sys import argv
import numpy as np
import os
def extract_geometries(filename):
#extract the xyz-geometries and writes it to an external file
#the first line should contain the number of atoms
initconds=open(filename,"r").readlines()
geom=int(1)
line_for_geom=int(0)
for line in initconds:
#get ... |
e0f7d9221508ac2eeb7e8f194555335e7d00380ab5b4d7ef8be3c77f9793874f | Python | 1,484 | 40 | import pandas as pd
from sklearn.metrics import confusion_matrix, accuracy_score, f1_score, roc_auc_score
def load_model(model_path):
# Assuming the model is a pickled sklearn model, modify as necessary
import joblib
return joblib.load(model_path)
def load_test_data(file_path):
return pd.read... |
e71f180f9c36135d7c839ad825d31e350a10f11ac2ff97959bef6de35affe531 | Python | 1,484 | 74 | """To see the steady-state activation/inactivation variables and time constants in KQT3"""
import numpy as np
import math
import matplotlib.pyplot as plt
import os
x = np.arange(-90, 90, 0.1)
vhm = -12.8
ka = 15.8
vhw = -1.1
kiw = 28.8
aw = 0.5
bw = 0.5
vhs = -45.3
kis = 12.3
ass = 0.3
bs = 0.7
atmf = 395.3
btmf = 38... |
977d42e299aec8792107c268350fef037e60b5e9f478954fb2d740d5b4d03787 | Python | 1,485 | 39 | import torch
import torch.nn as nn
from torch import Tensor
from scipy.spatial.distance import cosine
def cal_reliable(spatial_df: Tensor, reliable_X: Tensor, reliable_test_X: Tensor):
"""
Args:
spatial_df: [torch.Tensor] normalized and logarithmized original spatial data (cell by gene)... |
221c2a7d60b387ad98b2f3428dc4ad6a25df607a5d459e6a38cde2a4845c9723 | Python | 1,486 | 49 | import matplotlib.pyplot as plt
import numpy as np
import os
import pandas as pd
import seaborn as sns
from src.analyze.utils import init_mpl
init_mpl(sns_style='ticks', colorpalette='muted')
def get_errors(results_dir, rotation_angles=None):
errors = []
for rot in rotation_angles:
prefix = f"rot={r... |
249052bfb17c5f4bdf1fdedd00466d29e0c26f092e714d94c6e71572e502b71f | Python | 1,486 | 49 | from __future__ import annotations
from shutil import which
import pytest
from quacc import get_settings
pytestmark = pytest.mark.skipif(
which(str(get_settings().QCHEM_CMD)) is None, reason="QChem not installed"
)
from pathlib import Path
from ase.build import molecule
from quacc.recipes.qchem.core import re... |
4711989822eacedb583f0c07726327257b08d547b85bebb19cc1ba463a565a83 | Python | 1,487 | 50 | #! /usr/bin/env python
# -*- coding: utf-8 -*-
import os
from lab.environments import LocalEnvironment, BaselSlurmEnvironment
from lab.reports import Attribute, finite_sum
import common_setup
from common_setup import IssueConfig, IssueExperiment
DIR = os.path.dirname(os.path.abspath(__file__))
BENCHMARKS_DIR = os.e... |
8c797b0a86e3b995610cca2ca476a9b019ec1a6a0e9677259a867f97684515fd | Python | 1,487 | 50 | #! /usr/bin/env python
# -*- coding: utf-8 -*-
import os
from lab.environments import LocalEnvironment, BaselSlurmEnvironment
from lab.reports import Attribute, finite_sum
import common_setup
from common_setup import IssueConfig, IssueExperiment
DIR = os.path.dirname(os.path.abspath(__file__))
BENCHMARKS_DIR = os.e... |
a7d721378b24e4212e4eeebda989c2fc60ce6c438a4e78570cf90f10ce88bc75 | Python | 1,487 | 45 | import sys, os, random, math
from miscFuncs import *
baseOutDir, filePrefix, numReps = sys.argv[1:]
numReps = int(numReps)
def selectVal(minVal, maxVal):
size = maxVal-minVal
return (random.random()*size)+minVal
msOutDir = "%s/sims" %(baseOutDir)
logDir = "%s/logs" %(baseOutDir)
msOutPath = msOutDir+"/"+file... |
9d222c35f55789b4269f34b23c0147a04d3ca6d9bebf518c2fef88e9bcb1f7ce | Python | 1,489 | 27 | # Copyright 2020 Division of Medical Image Computing, German Cancer Research Center (DKFZ), Heidelberg, Germany
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# ht... |
d01aedcf1a034481b5e8bc0b22eb6518871b80e5e8b1747916009c191a57912c | Python | 1,489 | 46 | #! /usr/bin/env python
# -*- coding: utf-8 -*-
import os
from lab.environments import LocalEnvironment, BaselSlurmEnvironment
import common_setup
from common_setup import IssueConfig, IssueExperiment
from relativescatter import RelativeScatterPlotReport
DIR = os.path.dirname(os.path.abspath(__file__))
BENCHMARKS_DI... |
2a21af46e74d952790866e1ed70816bcbdce6c5624dd4f6059b106a51606440f | Python | 1,490 | 47 | # coding=utf-8
# Copyright 2026 The Google Research Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicab... |
4921d0a9a0f48bee208dcced5aa1a8ff5c4e9764fd83aa86b0a9a3feff5122b1 | Python | 1,490 | 60 | import networkx as nx
import pandas as pd
import numpy as np
def edges_to_graph(df, multi=False):
if multi:
G = nx.MultiDiGraph()
else:
G = nx.DiGraph()
for k, row in df.iterrows():
G.add_node(row['pre'])
G.add_node(row['post'])
G.add_edge(row['pre'], row['post'])
... |
51af9725fd0380a7380a5999ad2650ffbd39897e40b09d74c4b99c81da5c1601 | Python | 1,490 | 38 | import base64, io, os
from PIL import Image
from regtools.registration.report import _img_data_uri
def _big_png(path, size=(1700, 1700)):
# Random noise, not a solid fill: PNG crushes a uniform fill to well
# under _EMBED_MIN_BYTES, so a solid image never reaches the
# optimization gate this test ... |
6cc5a57ddf8f6ab9f4896c371766c700d2e2a931bac9303830eb8a3154b76204 | Python | 1,490 | 47 | from __future__ import print_function
import platform
# from multiprocessing import Pool, TimeoutError, cpu_count
from torch.multiprocessing import Pool, Process, set_start_method,TimeoutError, cpu_count
try:
set_start_method('spawn')
except RuntimeError:
pass
DATE_FORMAT = '%y-%m-%d_%H-%M-%S'
def get_max_co... |
99a865a40552d247cf5f50ba6af515c4145838c6e8f9281586510130aa6e1f31 | Python | 1,490 | 47 | # coding=utf-8
# Copyright 2026 The Google Research Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicab... |
f834c62a9ea79e73b0a6cf79f86449aec50fe4159c5509d6d94e5ad39d36946d | Python | 1,490 | 50 | # -*- coding: utf-8 -*-
"""
Created on Fri May 11 19:47:20 2018
@author: Francois
"""
def updateStylePatched(self):
r = '3px'
if self.dim:
fg = '#466e82'
bg = '#466e82' #dark blue
border = '#466e82' #dark blue
# border = '#7cf3ac'
else:
fg = '#43b1e... |
22766fb7aaa63dc55d5fb9f9650a748933222f65651b13c6e7b12b5467ebb588 | Python | 1,491 | 42 | import matplotlib.pyplot as plt
import autograd.numpy as np
from autograd import elementwise_grad as egrad
"""
Mathematically we can only take gradients of scalar-valued functions, but
autograd's elementwise_grad function also handles numpy's familiar vectorization
of scalar functions, which is used in this example.
... |
48a825a1f7bd054d9e7b4da4b89e1fa9d78a1544ffbdb449b675c9e41ecac381 | Python | 1,491 | 54 | from typing import Callable, Tuple, Any
import numpy as np
import netket as nk
import jax
import jax.numpy as jnp
import flax.linen as nn
from typing import Any, Tuple
from flax import struct
from netket.utils.types import DType, PyTree, Array, Callable
import copy
from functools import partial
import numpy as np
impor... |
d19eea9a9fe84df6e73054632d644380822ba5f8b9695d6bff17b3e14f3fdceb | Python | 1,491 | 39 | """Implementation of CLI convert command."""
import numpy as np
from treem import Node, SWC, Morph
def convert(args):
"""Converts input data to compliant SWC format."""
vprint = print if not args.quiet else lambda *a, **k: None
nam = 'I', 'T', 'X', 'Y', 'Z', 'R', 'P'
fmt = 'i', 'i', 'f', 'f', 'f', '... |
ed2f665735a3d4ab3b8864e20e9efecbb856da07799e73d442027c169735cacb | Python | 1,492 | 46 | import numpy as np
import pytest
from regtools.geometry_registration.pipeline import apply_orientation
from regtools.geometry_registration.types import RunParams
def test_runparams_orientation_defaults():
p = RunParams(tiff_path="x.tif", ccf_index=1)
assert p.rotate_k == 0
assert p.flip_h is Fa... |
f35f1afbfc92e960c01d44721e6c2d52f1fa6f872f9ae35c5e5b524bc60c6589 | Python | 1,492 | 56 | from .tools import Tools
class GraphElement:
"""Base class for elements of a graph."""
def __init__(self, features: dict = {}, label: str = None, id: str = None):
"""Constructor
Args:
features (list[float]: List containing edge features that characterise the edge).
... |
f95ba6361927f935538b0674b04e820a2e643d7931efd3897690cde28edebdc6 | Python | 1,492 | 41 | #!/usr/bin/python
#"usage: 3piece_read_split.py Input_file First_piece_size(bp) Last_piece_size(bp) upstream_to_trim(bp) downstream_to_trim(bp)"
import gzip
import sys
fn1=sys.argv[1]
if 'gz' in fn1:
dfh1=gzip.open(fn1,'r')
if 'gz' not in fn1:
dfh1=open(fn1,'r')
ID1=dfh1.readline().split()
line1=dfh1.readl... |
02d02be0f1e4e8c3865620d9d1c51c78d84c70125c17a176ea5d21c3a3dfad38 | Python | 1,494 | 53 | """
toposampling - Topology-assisted sampling and analysis of activity data
Copyright (C) 2020 Blue Brain Project / EPFL & University of Aberdeen
This program is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as
published by the Free Software Foundation... |
39926976ef52dc2245869ac241af50f868e766790fb66bce19a854167dfb28a6 | Python | 1,494 | 45 | import dolfin
from smart import mesh_tools
def test_save_load_mesh(tmp_path):
mesh = dolfin.UnitCubeMesh(3, 3, 3)
mf_cell = dolfin.MeshFunction("size_t", mesh, 3)
mf_cell.array()[:] = 1
mf_facet = dolfin.MeshFunction("size_t", mesh, 2)
mf_facet.array()[:] = 2
mesh_tools.write_mesh(
me... |
568185b43aaa9e62dfafcd447f7084579ae0fc5a5847034ee72e1ad4d3136259 | Python | 1,494 | 48 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Tue Sep 29 15:43:24 2020
@author: usingh
Use this script to benchmark runtimes of different tools
args[1]<-input_fasta_file
args[2]<-out dir
[3]<-Num trials
[4]<-Min len of ORF should be multiple of 3 for orfm to work
"""
from pyrpipe import pyrpipe_engi... |
a045e9b7e766ce71acd1ecd07c1fd38b3f96700b5c966e55596c04c1e7e55598 | Python | 1,494 | 46 | import logging
import logging.config
from pathlib import Path
from ..util import read_json
LOG_LEVELS = {
'DEBUG': logging.DEBUG,
'INFO': logging.INFO,
'WARNING': logging.WARNING,
'ERROR': logging.ERROR,
'CRITICAL': logging.CRITICAL
}
def setup_logging(log_dir, log_config='utils/logger/logger_co... |
d24ca40e9db784d7e6ee06f453294aaed03ef61d9e3206d9f489417aec10d380 | Python | 1,494 | 50 | #! /usr/bin/env python
# -*- coding: utf-8 -*-
from downward import suites
import common_setup
REVS = ["issue455"]
SUITE = suites.suite_satisficing_with_ipc11()
CONFIGS = {
"01-ff": [
"--heuristic",
"hff=ff(cost_type=one)",
"--search",
"lazy(alt([single(hff),single(hff, ... |
e7d80a7a95116a8bacbd511a571706dd8cc0b97de34ed5df32ffa258bfa2a169 | Python | 1,494 | 41 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
# Copyright 2024 Clinic for Diagnositic and Interventional Radiology, University Hospital Bonn, Germany
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy ... |
5a9e5bbeaa318bf9dc4e563840e8af748aa67fdfdbeb94b4af2ca80040b1c07c | Python | 1,495 | 47 | # coding=utf-8
# Copyright 2026 The Google Research Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicab... |
81fd79d78d903fb2cbd95529f2dfc21b16d792160f326af42cb38fa2af823949 | Python | 1,495 | 41 | """Tests for the --reg_spacing option plumbing (downsample registration grid)."""
import os
import sys
PROJECT_ROOT = os.path.abspath(os.path.join(os.path.dirname(__file__), ".."))
if PROJECT_ROOT not in sys.path:
sys.path.insert(0, PROJECT_ROOT)
import inspect
import pytest
from regtools.registration... |
2506e057d0e9e8bfabb53ec46a451f74382d00f39d6d41b00f7f4189c3e3ca07 | Python | 1,496 | 54 | """
This script converts NeSys .xyz files containing in-brain coordinates
to MeshView JSON format (https://meshview.apps.hbp.eu/).
"""
import os
import json
def parse_xyz(fname):
jsondata = []
obj = {}
triplets = []
with open(fname,"r") as xyz:
for line in xyz:
li... |
548d05e1268c9eaf1c89454fb978237fcd67315f32ecb9cb4d6f01acfcc3ec88 | Python | 1,496 | 49 | import torch
import torch.nn as nn
from torch.optim import Adam
from rocf_scoring.models.model import CNN, weights_init
from scripts.training import train, get_dataloaders, directory_setup, initialize_training_csv
import os
from rocf_scoring.helpers.helpers import visualize_training
def train_CNN():
# setup dirct... |
8ddbab7d44e56aab5e4b537d7599682cdef8e42bba8ac38d9f5a9932f9bc1035 | Python | 1,496 | 18 | """INDEP_CHECK.py 2026-09-29 (methods check, descriptive): does an independent LIF implementation (INDEP_LIF.py, written
from the equations only) reproduce the olfactory runaway and its fix on the AL cut-out? DL5 ORNs at 150 Hz, 1 s."""
import sys, time; sys.path.insert(0, 'D:/eucys/03-CODE')
import numpy as np, scipy.... |
8e33412ba1786f1a5a6ee25a2d2666ed8e6fb8d7e3f1c389c54781e88bc52b03 | Python | 1,496 | 26 | # coding=utf-8
# Copyright 2026 The Google Research Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicab... |
24feee3b5182aab796e16a57a1b80484f202910ad029223d9d191adafa569858 | Python | 1,497 | 58 | # pylint: disable=too-many-function-args, invalid-name, unused-argument
""" HCP ROI dataset loading script"""
import numpy as np
import pandas as pd
from omegaconf import DictConfig
from src.settings import DATA_ROOT
def load_data(
cfg: DictConfig,
dataset_path: str = DATA_ROOT.joinpath("hcp_roi"),
):
"... |
cde62e56ee21b8382a9af0ac10293d6e51e6250bc24c745c517683e5b87db636 | Python | 1,497 | 37 | from typing import List
from dataclasses import dataclass
from sitetack.app.kmer import Kmer
@dataclass(frozen=True)
class Sequence:
""" Represents a sequence in a fasta file."""
""" UniProtID, such as 'RNase_1' """
sequence_name: str
""" The sequence, such as 'MTEITAAMVKELRESTGAGMMDCKNALSETNGDFDKAV... |
0bd7562ae19191519e9df479c721a458567c20f9ff7bc91e62988456782ff901 | Python | 1,498 | 61 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Initialize TFR model
Created on Thu Jun 13 2019
@author: jmagraner
"""
# %%
import autograd.numpy.random as npr
def initparams_random(specs,*unused):
sc=0.01
ndim, tdim, mdim, cdim, cxdim = specs['data dims']
udim, xdim, cohdim, tiodim = ... |
1d5657d22f9b3399487e17a3e15724d28f1933a5bac3a3045cba825dc0bd9582 | Python | 1,498 | 42 | """For backward compatibility, expose main functions from
``setuptools.config.setupcfg``
"""
from functools import wraps
from typing import Callable, TypeVar, cast
from ..warnings import SetuptoolsDeprecationWarning
from . import setupcfg
Fn = TypeVar("Fn", bound=Callable)
__all__ = ('parse_configuration', 'read_con... |
862566e0028a5e6bd1102d266375650fa66baf4a4a997d587a65d209e0d07132 | Python | 1,499 | 45 | # install boto3 and set up aws cli
import boto3
description = 'AMI for Bransonlab APT backend'
source_ami_id = 'ami-0f31a10294d11388a'
source_region = 'us-east-1'
name = 'bransonlab_apt_ami_tf113_20190419'
owner_id = '535416095125'
##
client = boto3.client('ec2')
regions = client.describe_regions()['Regions']
filter... |
17a2492fe810a7f951dae6a2c1e94a71d75cfda779ab180c4cf636ce668a6b1e | Python | 1,500 | 45 | import torch
from torch.nn import Linear as Lin, Sequential as Seq
import torch.nn.functional as F
from torch import nn
class PAE(torch.nn.Module):
def __init__(self, input_dim, dropout=0.2):
super(PAE, self).__init__()
hidden=128
self.parser =nn.Sequential(
nn.Lin... |
9c3b409ea090046d7d305dfc32f5ae97331e8720701f6dceef20883ec4e13820 | Python | 1,500 | 51 | #!/usr/bin/env python
import os, sys, time, datetime
def getDate():
return time.strftime("%a, %d %b %Y %H:%M:%S %Z")
def formatTime(seconds):
return str(datetime.timedelta(seconds = seconds))
"""def runCommand(command, output_filename):
if os.path.exists(output_filename) and os.path.getsize(output_filename)... |
a746e78e3a3a16e038e150eeb2cb151be118946a3cb557a50c3192102c1c7bd2 | Python | 1,500 | 58 | import json
import numpy as np
def extract_meter_values(meters):
ret = { }
for split in meters.keys():
ret[split] = { }
for field,meter in meters[split].items():
ret[split][field] = meter.value()[0]
return ret
def render_meter_values(meter_values):
field_info = []
fo... |
34e56e019aab901c6d93259740c36a349eadc33a0a4d2b66c28ed6e60e25c2f6 | Python | 1,501 | 57 | import random
import unittest
import torch
import torch.nn as nn
from torch.utils.data import Dataset
from torch.utils.data.dataloader import DataLoader
from torcheeg.trainers import ContrastiveTrainer
class DummyDataset(Dataset):
def __init__(self, length: int = 101):
self.length = length
def __le... |
d5ef1b01eb0a942a82c64422012b455e7bc85b8602f4badc17d019b900c81941 | Python | 1,501 | 37 | import os
# Enable JAX persistent compilation cache before importing jax
# This caches compiled XLA programs to disk, eliminating ~5s of JIT
# compilation overhead on subsequent runs
# Cache dir is given by an environment variable, or a fallback if not set
# Explicitly setting the environment variable is recommended i... |
d8a07fdd60019685081d4aa52f9bfab24412e5372cada9fcef303fa9f3c3aa17 | Python | 1,501 | 41 | import torch
from elasticai.creator.nn.integer.quant_utils.simulate_bitshifting import (
simulate_bitshifting,
)
def test_simulate_bitshifting_basic():
x_q = torch.tensor([10], dtype=torch.int32)
m_q_shift = torch.tensor([2], dtype=torch.int32)
m_q = torch.tensor([4], dtype=torch.int32)
result = ... |
12ad2d92c7a8a0e4f76563cfd0cbbcea4c2c543356c0406a5ddd7d6ce0daa39c | Python | 1,502 | 45 | # coding=utf-8
# Copyright 2026 The Google Research Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicab... |
479134eb7e4a25f64400e614096ea9b3ce69f1ed25e69ff60cbb68b99bbabbf0 | Python | 1,502 | 49 | #! /usr/bin/env python
# -*- coding: utf-8 -*-
import os
from lab.environments import LocalEnvironment, BaselSlurmEnvironment
import common_setup
from common_setup import IssueConfig, IssueExperiment
from relativescatter import RelativeScatterPlotReport
DIR = os.path.dirname(os.path.abspath(__file__))
BENCHMARKS_D... |
c38b6c683f8d4aa9873b48ad769ac125b37aa5276a137eadc95d29da6c636db8 | Python | 1,502 | 58 | import pdb
from typing import Dict, List, Callable
from ..base_transform import BaseTransform
class PDB(BaseTransform):
r'''
For debugging, insert breakpoints in transforms. The transformation itself does not change the input data.
.. code-block:: python
transform = Compose([
ToTens... |
dd1e062046447027e9394a7491639d2de7f407b72dadb074a0929600afb12fb8 | Python | 1,502 | 59 | import torch
from diff_frech_mean.frechetmean.utils import EPS, arcosh
def l_prime(y):
cond = y < 1e-12
val = 4 * torch.ones_like(y)
ret = torch.where(cond, val, 2 * arcosh(1 + 2 * y) / (y.pow(2) + y).sqrt())
return ret
def frechet_ball_forward(X, w, K=-1.0, max_iter=1000, rtol=1e-6, atol=1e-6, ver... |
05420da27cf445d98d3401f14a6e503156961678f1270e7c2e821f27c309dec9 | Python | 1,503 | 37 | '''Since the n-back has 1 and 2-back events and the beta series are computed on
the events type, then we have one network for 1-back and another for 2-back.
Following the GLM contrasts, the final networks are obtained from substracting
the 1-back adjecency matrix from the 2-back adjacency matrix. This script
comput... |
2593f66638d9962c5f1b006f61d918975f3b66a995ee203a2772efa989cb76ab | Python | 1,504 | 29 | __version__ = "1.0.0"
#__picture__ = """
# ____ MiaoNet
# ,' , `. (v.{} RELEASE ฅ^oωo^ ฅ){}___
# ,-+-,.' _ | ,--, ===================================== ,--.'|_
# ,-+-. ; , |,--.... |
32032833c0a51b04074f89e90db903c67fec98640c62412fa2583811c1f7bbf4 | Python | 1,504 | 52 | # --------------------------------------------------------
# DaSiamRPN
# Licensed under The MIT License
# Written by Qiang Wang (wangqiang2015 at ia.ac.cn)
# --------------------------------------------------------
#!/usr/bin/python
import vot
from vot import Rectangle
import sys
import cv2 # imread
import torch
impo... |
67082deef2457ef7f8abfdf16eefd4ba01c89642700df204e79078801a896de0 | Python | 1,504 | 48 | def update_param(name, param):
if name == 'distribution':
param['values'].remove('ordinal')
return param
return None # param untouched
extensions = dict(
extra_params=[('verbose', 'FALSE')],
validate_params="""
# Required maps for different names params, including deprecated params
.g... |
818d3f1d7f5e4bd86cba50aaf62e8f211eaeb9ffa94a3fb12af8c437b529a2fc | Python | 1,504 | 38 | """
toposampling - Topology-assisted sampling and analysis of activity data
Copyright (C) 2020 Blue Brain Project / EPFL & University of Aberdeen
This program is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as
published by the Free Software Found... |
abb457e4a26384b4132fdac84953d203572ebfaddf686e26cd3bf2440f52e9ab | Python | 1,505 | 53 | # coding=utf-8
# Copyright 2026 The Google Research Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicab... |
c8a49b41edd483784016ae55b254991bba071ed1574347ada05580b908829939 | Python | 1,506 | 52 | # coding=utf-8
# Copyright 2026 The Google Research Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicab... |
e125fbb40cbc0d9c88fed983a8f781b61b0c40c3d469807d6c942754e8223683 | Python | 1,506 | 51 | #!/usr/bin/env python3
import cc3d
import numpy as np
from skimage.measure import label
from skimage.measure import regionprops
from skimage.measure import label2rgb
def instance_segnmentation(img, background, arr_type):
'''
Perform instance segmentation of puncta
args: img -> numpy array of the... |
7c72bc86e9de1160e98ae62f3794efbd4b4cf0d0984be7da0044d031f3430e16 | Python | 1,507 | 47 | #! /usr/bin/env python
# -*- coding: utf-8 -*-
import os
from lab.environments import LocalEnvironment, BaselSlurmEnvironment
import common_setup
from common_setup import IssueConfig, IssueExperiment
from relativescatter import RelativeScatterPlotReport
DIR = os.path.dirname(os.path.abspath(__file__))
BENCHMARKS_DI... |
bd889c37553557881866f70a966a7340d4e1b103ece8f20494c12c2e56991a9b | Python | 1,507 | 41 | import torch
import torch.nn as nn
import math
class lap_spatial_param_module(torch.nn.Module):
def __init__(self, channels=None):
super(lap_spatial_param_module, self).__init__()
self.learn_adjust = nn.Parameter(torch.zeros([1, channels, 1, 1]))
self.learn_scale = nn.Parameter(torch.ones(... |
e4c960712ba1d1ececa6d748713f4cadb337963f039b4104db5c9325ccdba291 | Python | 1,508 | 34 | import os
import pandas as pd
from src.utils import contain_substr
from joblib import Parallel, delayed
# load all skel and re-sample
def load_and_sample(path, sample):
input_df = pd.read_csv(path)
return input_df.sample(n=sample)
def pool_features(complete_skel_path='output/skel_complete.txt', output_stat... |
0d9ee6d3e675f9571375c1f772ee90aa19eab117944d6940c5964c9f4aafe808 | Python | 1,509 | 44 | """Unit tests for the reusable MIND descriptor generator."""
import os
import sys
PROJECT_ROOT = os.path.abspath(os.path.join(os.path.dirname(__file__), ".."))
if PROJECT_ROOT not in sys.path:
sys.path.insert(0, PROJECT_ROOT)
import numpy as np
import pytest
from regtools.registration.core.metrics imp... |
4880df00be12324938316616251d41946658f2b941f4883eccc73d74435a0d5f | Python | 1,509 | 44 | # --------------------------------------------------------
# DaSiamRPN
# Licensed under The MIT License
# Written by Qiang Wang (wangqiang2015 at ia.ac.cn)
# --------------------------------------------------------
#!/usr/bin/python
import glob, cv2, torch
import numpy as np
from os.path import realpath, dirname, join... |
aea40b989e072e89d784c6e1d30ce380cc08d6a53d3fc95fdf1c1247c988eca2 | Python | 1,509 | 42 | import os
import pandas as pd
import numpy as np
from dotenv import load_dotenv
load_dotenv() # take environment variables from .env.
BASE_PATH = os.path.join(os.environ['WORKSPACE'], 'results/')
def ch_ds(ch):
locs = {
'cme-bins1': BASE_PATH + 'cme/analysis/mappers_cme_bins1.json',
'cme-bins2': ... |
c224ab73a0f5dc32921988c5f915a8ee00f3a65a2d10318c6e51e689808f446b | Python | 1,509 | 54 | #! /usr/bin/env python
# -*- coding: utf-8 -*-
import os
from lab.environments import LocalEnvironment, BaselSlurmEnvironment
import common_setup
from common_setup import IssueConfig, IssueExperiment
DIR = os.path.dirname(os.path.abspath(__file__))
BENCHMARKS_DIR = os.environ["DOWNWARD_BENCHMARKS"]
REVISIONS = ["is... |
ecde5670910fe43f65c54b3f6315004bb78e7b2771cd8b1caccc0fd48de916b5 | Python | 1,509 | 54 | #! /usr/bin/env python
# -*- coding: utf-8 -*-
import os
from lab.environments import LocalEnvironment, BaselSlurmEnvironment
import common_setup
from common_setup import IssueConfig, IssueExperiment
DIR = os.path.dirname(os.path.abspath(__file__))
BENCHMARKS_DIR = os.environ["DOWNWARD_BENCHMARKS"]
REVISIONS = ["is... |
ee0c08dd4289da8969838e751784a8d754a6f680476ac98da8bb1c1f3544d97f | Python | 1,510 | 38 | ### adapted from Adriano Fonzino et al.
## (ENSG00000160710) ADAR
## (ENSG00000197381) ADARB1
## (ENSG00000185736) ADARB2
import sys, os
print('Sample\tGene\tTPM')
f=open('/media/Scratch_SSD_Voyager/sammi/RNA_editing/fc_TS_v1/counts_all_organize_tpm.txt')
tpm_list={}
for i in f:
if i.startswith('Geneid'):
h=i.s... |
3ef65ebcb000367bbc2a1bdfcaa573a9649d70428f3ea2c013b0819e739492fc | Python | 1,512 | 37 | #
# MIT License
#
# Copyright (c) 2022 GT4SD team
#
# 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, modify, merge,... |
66527570788e8cd7d1534ef24cde72142fe2a7e43dcf78f1bdc1d4aedcd497ed | Python | 1,512 | 44 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Wed May 31 16:52:48 2023
@author: felipe
"""
import numpy as np
import sys
import os
sys.path.append(os.path.abspath('../../../'))
import analysis.frequency as frequency
import analysis.synchronization as synchronization
import scipy.io as sio
import scipy.... |
93e6bc3c1a0fea6f10fec6ec7b1583953060506792ea64dad6b927015d82f2cb | Python | 1,513 | 48 | # flake8: noqa
# There's no way to ignore "F401 '...' imported but unused" warnings in this
# module, but to preserve other warnings. So, don't check this module at all.
# Copyright 2020 The HuggingFace Team. All rights reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use thi... |
8ed01445f3973a10cdbdc1e35d7febb88dc3fd02bd98ad57711c61d44eeeba72 | Python | 1,514 | 36 | """
Training and evaluation parameters
"""
train_params = {
'78 100': {
"workers": 10, "is_binary": 0, "eval_test": True, "id": "final", "epochs": 75, "batch_size": 64, "lr": 0.01,
"gamma": 0.95, "wd": 0, "weighted_sampling": 1, "image_size": [78, 100], "simulated_data": None,
"max_simulat... |
b1e6c3b41ec20413f855650e825d5242408b41c28923587edf71fd0c88cd0e23 | Python | 1,514 | 50 | # coding=utf-8
# Copyright 2026 The Google Research Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicab... |
f5b4f44b858834ffc99fe1840fab350263b7ed4c0bf99e877f07e6927a1ef4cf | Python | 1,514 | 39 | import torch.nn as nn
class PreActResNetBlock(nn.Module):
def __init__(self, c_in, act_fn, subsample=False, c_out=-1, grouped_maps=1):
"""
Inputs:
c_in - Number of input features
act_fn - Activation class constructor (e.g. nn.ReLU)
subsample - If True, we want t... |
fa0acbbca165b5d723dab955872023aae8105169dc0589db19c1acbbe3a201f6 | Python | 1,514 | 48 | # Material dispersion example, from the Meep tutorial. Here, we simply
# simulate homogenous space filled with a dispersive material, and compute
# its modes as a function of wavevector k. Since omega/c = k/n, we can
# extract the dielectric function epsilon(omega) = (ck/omega)^2.
import meep as mp
cell = mp.Vector3... |
202e1dabc81957e5d184987133497463404f4d1b612b5e823bd6b2c4e946723a | Python | 1,515 | 49 | """
A subpackage for reading rotation matrices and translation vectors
for biological assemblies from different file formats.
The central functions are `get_transformations_`
"""
from abc import ABCMeta, abstractmethod
class AssemblyParser(metaclass=ABCMeta):
@abstractmethod
def list_assemblies(self):
... |
25b309cb3d0f5ce3784024be699c3d8cfe59fc0bf617dd6944743db5f456db00 | Python | 1,515 | 48 | from psychopy import prefs
prefs.hardware['audioLib'] = ['PTB']
from psychopy import gui, visual, event, core
from os import system, path, chdir
from random import shuffle
my_path = path.abspath(path.dirname(__file__))
chdir(my_path)
def quit():
win0.close()
core.quit()
event.globalKeys.add(key='escape', fun... |
2a2f8c77868d8093cfd8b8cfc529a37a054abe5b630779905b4c6396923907c1 | Python | 1,515 | 51 |
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
from .scVI_distribution import *
import os
import copy
import random
import numpy as np
import pandas as pd
import scipy
import torch
from torch import nn, optim
import torch.nn.functional as F
import torch.di... |
321c289e1ab826d7ba7fe63bb0409d67bb0d6292eeaade13e1a7184edc065eb3 | Python | 1,515 | 43 | #!/bin/env python3
"""
Compare different kinds of heart rhythms for experiment and simulation
"""
import ithildin as ith
import numpy as np
import matplotlib.pyplot as plt
def compare_exp_theo(it, ax):
drawn = []
drawn.append(ax[0,0].imshow(sd.vars["u"][it+52,0], vmin=-0.5*3, vmax=1.3*3))
drawn.append(a... |
4510fcf07010997b9e334d675c9cfb0ac88ae623b2427755961fd0e2eae5c8b2 | Python | 1,516 | 49 | PaviaU = {
'path_to_hsi': './datasets/PaviaU/PaviaU.mat',
'hsi_key': 'paviaU',
'path_to_mask': './datasets/PaviaU/PaviaU_gt.mat',
'mask_key': 'paviaU_gt',
'train_sample_percentage': 0.2
}
PaviaC = {
'path_to_hsi': './datasets/PaviaC/Pavia.mat',
'hsi_key': 'pavia',
'path_to_mask': './data... |
991fcaa6252388db88c075123658bda8152a9aca10c3893c42283fdb63236cf1 | Python | 1,516 | 53 | import sys
import traceback
import getopt
def main(parameters):
"""
The main function, which starts to software according to the given command line arguments.
:param parameters: the command line parameters:
* -h help
* -c command line
* -g graphic interface
"""
if not parameters:
... |
9da5d9cf7eeac72a86ac8c49961f15223257a9b027473c2fae9b932557636e57 | Python | 1,516 | 46 | from merlin.core import analysistask
class ExportBarcodes(analysistask.AnalysisTask):
"""
An analysis task that filters barcodes based on area and mean
intensity.
"""
def __init__(self, dataSet, parameters=None, analysisName=None):
super().__init__(dataSet, parameters, analysisName)
... |
e7fdf85d97665323237a94cda5f95c255cdf8cd3e4900af8dc564bd0da39d609 | Python | 1,516 | 49 | """Build script for Cython extensions, used by poetry's build system."""
import os
import shutil
from pathlib import Path
def main():
"""Build Cython extensions when invoked by poetry."""
try:
import numpy as np
from Cython.Build import cythonize
from Cython.Distutils import build_ext... |
02579b53faeed6a6acdb7cdd11611f6a52a6459935402573da737f7175a0721c | Python | 1,517 | 51 | # Copyright (c) OpenMMLab. All rights reserved.
import torch.nn as nn
import torch.nn.functional as F
from .sr_backbone_utils import default_init_weights
class PixelShufflePack(nn.Module):
""" Pixel Shuffle upsample layer.
Args:
in_channels (int): Number of input channels.
out_channels (int)... |
7302ce4bac939874615590e04319ccfd1d19ccd58c558fa6509869a20382159f | Python | 1,518 | 59 | from typing import Callable, Dict, List
from ..base_transform import BaseTransform
class Lambda(BaseTransform):
r'''
Apply a user-defined lambda as a transform.
.. code-block:: python
from torcheeg import transforms
t = transforms.Lambda(targets=['y'], lambda x: x + 1)
t(y=1)['... |
ceda5e159b9664f8380045d5e28d36b7e19c42065423e161bb50eba3f6851e47 | Python | 1,518 | 51 | # -*- coding: utf-8 -*-
"""
Created on Wed Sep 14 22:16:23 2016
downloaded from http://scipy-cookbook.readthedocs.io/items/Matplotlib_HintonDiagrams.html?highlight=hinton%20diagrams
"""
from __future__ import division, print_function
import numpy as N
import pylab as P
def _blob(x,y,area,colour):
"""
Draws a... |
101a4bd4e2834b4a35dbb7f4aa38e753b9c1d85976d485100d9d56de781572e1 | Python | 1,519 | 52 | import io
import cv2
import numpy as np
from decord import VideoReader, cpu
try:
from petrel_client.client import Client
petrel_backend_imported = True
except (ImportError, ModuleNotFoundError):
petrel_backend_imported = False
def get_video_loader(use_petrel_backend: bool = True,
en... |
5739b3b76f501980ecf604df451aef3460f39cbc6052b40123a89f4e559caf5d | Python | 1,519 | 57 | from elasticai.creator.testing.ghdl_report_parsing import parse_report
def test_parse_ghdl_simulation_results_one_liner():
simulation_output = (
"my_test_bench.vhd:64:17:@4ps:(report note):my report message\nsimulation"
" finished\n"
)
expected = [
{
"source": "my_test_... |
cef393d5dd0c9dabb743cc60f8434ad0793cba548859f1995d2f20df2e843f87 | Python | 1,519 | 53 | #! /usr/bin/env python
# -*- coding: utf-8 -*-
import os
from lab.environments import LocalEnvironment, MaiaEnvironment
import common_setup
from common_setup import IssueConfig, IssueExperiment
DIR = os.path.dirname(os.path.abspath(__file__))
BENCHMARKS_DIR = os.environ["DOWNWARD_BENCHMARKS"]
REVISIONS = ["issue68... |
41b52adb400f78b861ed2ee31dce9b81e8b6746b7cca08c6a49e21e946c4e97a | Python | 1,520 | 53 | #!/usr/bin/env python
from __future__ import absolute_import, division, print_function, unicode_literals
import argparse
import logging
import os
import sys
import glob
import re
import tensorflow as tf
tf.keras.backend.clear_session()
from callbacks import CallBacks
from model_factory import GetModel
from preprocess... |
a711a550c254d164b10e2e942f0ae854d93c860072528117aab0b1db69a70cf9 | Python | 1,520 | 38 | #!/usr/bin/env python
# coding=utf-8
# Copyright 2021 The HuggingFace Inc. team. 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/LI... |
cd3e03754b408bcebe246859ebfc390bacbc79e01a52a84150d7504584694a96 | Python | 1,520 | 39 | """3D TIFF orientation is opt-in via --tissuecyte_orient; --no_orient deprecated.
Aligns the 3D CLI path with 2D: TIFF data loads exactly as stored unless the
user opts into the TissueCyte transform. --no_orient is kept for backward
compatibility but no longer controls orientation.
"""
import inspect
from r... |
d6d460c6c7e73b319e0be9759c31b53a3112d6f70522c15cfd16ebc73bab3387 | Python | 1,520 | 36 | # Plots effect sizes and sensitivities for Fig 5C-H
from os.path import join
from get_paths import *
from TVATPlotting import TVATPlotting
import matplotlib.pyplot as plt
if __name__ == "__main__":
save_flag = 0
## Load data
fname_regressions = "data_tvat_polynomialregressions.pickle"
... |
0fe1bd9ce4bc27aa4f5cd196f92898aae202731ad865504ee2984b9809f61073 | Python | 1,521 | 48 | import numpy as np
import scipy.sparse as sp
def sparse_to_tuple(sparse_mx):
"""Convert sparse matrix to tuple representation."""
def to_tuple(mx):
if not sp.isspmatrix_coo(mx):
mx = mx.tocoo()
coords = np.vstack((mx.row, mx.col)).transpose()
values = mx.data
... |
307eb0a55517bcee77334b3ea8b7c3ab4362432ffbf85936e1a8cb3520e8bdf6 | Python | 1,521 | 51 | # pylint: disable=too-many-function-args, invalid-name
""" UKB ICA dataset loading script"""
import numpy as np
import pandas as pd
from omegaconf import DictConfig
def load_data(
cfg: DictConfig,
dataset_path: str = "/data/users2/ppopov1/datasets/ukb/UKB_",
indices_path: str = "/data/users2/ppopov1/data... |
5670c8ce7d3c497343324140f1e63a50ca3c683a1daaa13b8e129f211cbdc34b | Python | 1,522 | 42 | from typing import Dict, Tuple
import numpy as np
import torch
from constants import N_ITEMS
from src.inference.utils import assign_score
def predict_item_presence(input_tensor: torch.Tensor, classifiers: Dict[int, torch.nn.Module]) -> Dict[int, int]:
results = {}
with torch.no_grad():
for i in ran... |
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