sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
48d021352f9f43308ad315a9d4f42904247e03c8b0516f5b5eca2e0988ca4812 | Python | 4,889 | 148 | import sys
import json
import pickle
import argparse
from lop.nets.ffnn import FFNN
from lop.nets.linear import MyLinear
from lop.algos.bp import Backprop
from lop.algos.cbp import ContinualBackprop
from lop.utils.miscellaneous import *
def expr(params: {}):
agent_type = params['agent']
env_file = params['env... |
4c1716aa326fc44e328c737ede0003a2cd1a1047fde4e4fb26e6251d5940ba6b | Python | 4,890 | 140 | # Modified from https://github.com/dbolya/tide
# This work is licensed under MIT license.
from collections import defaultdict
class Data:
"""A class to hold ground truth or predictions data in an easy to work with
format.
Note: Any time they appear, bounding boxes are [x, y, width, height] and
masks ... |
f0ce756e7ebabe32fb16701814ad66087949f1cd28b117385648ca21f20b2b0a | Python | 4,890 | 138 | import torch
from torch import nn
from torch.nn import functional as F
#from ._utils import _SimpleSegmentationModel
__all__ = ["DeepLabV3"]
class DeepLabHead(nn.Sequential):
def __init__(self, in_channels, num_classes):
super(DeepLabHead, self).__init__(
ASPP(in_channels, [12, 24, 36]),
... |
104dd44eee171421e967d7ee2f3b8038bba51ff3f1ca91217ec0b6692dcd1b5c | Python | 4,891 | 163 | import pdb
import numpy as np
import yaml
from yaml.loader import SafeLoader
import torch
import matplotlib.pyplot as plt
from latent_time_stepping.time_stepping_models.neural_ODE import NODETimeSteppingModel
from latent_time_stepping.time_stepping_training.optimizers import Optimizer
from latent_time_stepping.time_ste... |
8f4ec557705fe7de987b222273ec2bb0b81e8b74a73ec2036979c5560a765afb | Python | 4,893 | 127 | #!/usr/bin/env python
#-------------------------------------------------------------------------------
# Name : subtitle downloader
# Purpose : One step subtitle download
#
# Authors : manoj m j, arun shivaram p, Valentin Vetter, niroyb
# Edited by : Valentin Vetter
# Created :
# Copyright : (c) www.manojmj.... |
d474d7e30f7cd4bbf2b9447490c3f35ea3a54f92c0c391fde8b75eb0d64e7897 | Python | 4,893 | 84 | import wandb
def wandb_initializer(model_config, pretraining_config, finetune_config, method):
"""
Initialize a Weights & Biases (wandb) run for experiment tracking and logging.
This function sets up a wandb run based on the provided method (reconstruction, DEC, IDEC)
and configuration parameters. It... |
54c5b28bbc06899416f737101608f2698346ba5d67512c6bb6ec94be27ca49bd | Python | 4,895 | 164 | import math
import random
from PIL import Image
import numpy as np
from torch.utils.data import DataLoader, Dataset
import scanpy as sc
import torch
import sys
sys.path.append('..')
from ..VAE.VAE_model import VAE
from sklearn.preprocessing import LabelEncoder
def stabilize(expression_matrix):
''' Use Anscombes ... |
93d5a14f631567311bc40b102a5ca441698d519bda4842d98e647ebcc9754df2 | Python | 4,895 | 144 | #!/usr/bin/env python
#!/usr/local/bin/python
print("""
Update:
tf.nn.seq2seq doesn't work as hoped:
It needs a 1D Tensor (chars) as input, not 2D spectrogram/mfcc/...
unless we feed it with very long 1D wave data,
but that is probably not what seq2seq was intended to for.
Fear not: 1D dilated convolution and LST... |
95450b3e500b3c6795d8160cc6c9cef8a653ed02167de173246ea8591d8070f7 | Python | 4,895 | 139 | # __train_model_start__
from sklearn.datasets import make_regression
from sklearn.ensemble import RandomForestRegressor
from sklearn.metrics import mean_squared_error
from sklearn.model_selection import train_test_split
from sklearn.pipeline import Pipeline
from sklearn.preprocessing import StandardScaler
import mlflow... |
a0f4aff6e23abf29571db353f07a9095f0b6bdd6cc40ecd90a6f4d55df0a651e | Python | 4,897 | 147 | import logging
from typing import TYPE_CHECKING, Dict, List, Optional
from ray.data.block import Block, BlockMetadata
from ray.data.datasource.datasource import Datasource, ReadTask
if TYPE_CHECKING:
import pymongoarrow.api
from ray.data.context import DataContext
logger = logging.getLogger(__name__)
clas... |
3a8e5c3be728bb2426c2642cb5bf009ff82dcfde6b6dfd84712f4ab218922f84 | Python | 4,900 | 187 | import unittest
from lisa.core import data_interface
import numpy as np
import tempfile
import os
from scipy import sparse
class TestProjections(unittest.TestCase):
@classmethod
def setUpClass(cls):
cls.data = data_interface.DataInterface('mm10', window_size=1000, path = './test.h5', make_new=True)
... |
95993a4cc83f17299791bfe09ff0db0a07aede76cf0a6cb784f176fa2cf16d33 | Python | 4,900 | 121 | import logging
import time
from typing import Dict, List, Optional
from ray.data._internal.cluster_autoscaler import (
AutoscalingCoordinator,
DefaultAutoscalingCoordinator,
)
from ray.data._internal.cluster_autoscaler.base_cluster_autoscaler import (
ClusterAutoscaler,
)
from ray.data._internal.execution.... |
29422ca41ac9f3b5c583ec665a281b4719c0dd3a3422102077b81cc05756e970 | Python | 4,902 | 106 | #Instruction configuration for Social Doors Task
#Ori Zaff 12/20/22
instruction_hello_door = '''
Hello! This is the Door Feedback Game.
\n\nPress the with your right pointer finger button to continue.
'''
instruction_hello_face = '''
Hello! This is the Peer Feedback Game.
\n\nPress with your right pointer finger to ... |
18833b39f31f86584ceb980c45557f09ea2c8b42c675df2e445e50d029c1428c | Python | 4,904 | 128 | # Vendored from `decoupler` (https://github.com/scverse/decoupler) by
# omicverse for in-tree GPU acceleration work. Original copyright by
# the decoupler authors, redistributed under decoupler's GPL-3.0
# license. Cross-module imports rewritten from `decoupler.*` to
# `omicverse.es.*` (see scripts/vendor_decoupler.py)... |
f122fe5956599216166ed88d5dc88cebd3e49a9cf03ae18c79823934fac9ae8e | Python | 4,905 | 130 | import os
import argparse
# Implementation note:
# This code implements the same python code in the CalculateCpxEvidences task without alterations.
def sample_svid_readin(filein):
out = {}
fin = open(filein)
for line in fin:
pin = line.strip().split()
if not pin[1] in out.keys():
... |
d731b86f1178a8c6b9e169ec1d986a26038a112804d0d8e4e4734580a800f6b7 | Python | 4,906 | 111 | ####################################################################################################
# Copyright (c) 2016 - 2024, EPFL / Blue Brain Project
# Author(s): Marwan Abdellah <marwan.abdellah@epfl.ch>
#
# This file is part of NeuroMorphoVis <https://github.com/BlueBrain/NeuroMorphoVis>
#
# This program is fre... |
f36c07a81c05df6ac9eec731659807386921d1d8f8ef15626014d7b7eeed23de | Python | 4,906 | 164 | #
# CEBRA: Consistent EmBeddings of high-dimensional Recordings using Auxiliary variables
# © Mackenzie W. Mathis & Steffen Schneider (v0.4.0+)
# Source code:
# https://github.com/AdaptiveMotorControlLab/CEBRA
#
# Please see LICENSE.md for the full license document:
# https://github.com/AdaptiveMotorControlLab/CEBRA/bl... |
4c4b11acecad27f68564033449d79bcf8951d4773cce2b20ee8b5f979e4cd2f0 | Python | 4,907 | 160 | from typing import Callable, Optional
import jax
import jax.numpy as jnp
from jax.lax import cond
from jax.scipy.linalg import solve, eigh
from jax.scipy.sparse.linalg import cg
class lstsq_shift_cg:
def __init__(
self,
diag_shift: float = 0.01,
tol: float = 1e-5,
atol: float = 0.0... |
79c3659a299864b715d0685dc85c8df8fa3f68bce4a62701fcafd4089d5f786d | Python | 4,907 | 163 | """ This camera object can inherit from the same genreal class as
basler and flir, but with some pecularities.
- Azures should await a trigger from the arduino before starting
- The camera grabs multiple images. RGB, IR, and depth.
- ???
"""
from multicamera_acquisition.interfaces.camera_base import BaseCamera, Came... |
896ff8555a66d2ee664c5120782eed986082ef171db3e23e6729532613c431dd | Python | 4,907 | 110 | import gzip
import argparse
import logging
"""
Reformats an SV BED file for VaPoR.
* Outputs headerless BED file containing columns chrom, start, end, name, svtype
* Extracts contig of interest
* Keeps DEL, DUP, INS, INV, and CTX but drops BND, CPX, and CNV types
* Appends SVLEN to INS
* Extracts sites in sample of i... |
653faa98dc8013e3783cf9355a96a6822fc368126742c20353e3646da3bcb7f6 | Python | 4,909 | 169 | """
Copyright (c) Meta Platforms, Inc. and affiliates.
This source code is licensed under the MIT license found in the
LICENSE file in the root directory of this source tree.
Node-to-edge gather + Wigner transform + L→M permutation operation.
This operation is the first step in the edge message passing pipeline:
1. ... |
8e0525613aba114c9038ea3e7c6ab66221080b56781b001b526938e5710b9e67 | Python | 4,909 | 101 | import os
import numpy as np
import argparse
import pickle
def main(args):
fmri_path = os.path.join(args.dataset_root,"derivatives", "versionB", "fsLR32k","GLM")
subject = f"sub-{int(args.subject):02}"
print(f"starting {subject}")
betas_tmp = {f"vid{stim:04}": [] for stim in range(1,1103)}
beta_ty... |
1bf1cccca3bbe9a89318cd22deef8f8cc12b1d8b3b3a59ddaf63cc33c9304239 | Python | 4,910 | 134 | # -*- coding: utf-8 -*-
"""
Created on Tue Apr 23 19:44:26 2024
@author: Leyang Xue
"""
import sys
import networkx as nx
# Add package path
packagepath = '../kcorePercolation' # Manually specify the path to your script
sys.path.append(packagepath)
from utils import kcorePercolation as kp # Import custom utility fu... |
2b022f00489bcbd26437653f3cc896b41e80386afd98ab7999d7c5dfba709632 | Python | 4,910 | 126 | import math
import threading
import time
from typing import Dict, List
import ray
# Resource requests are considered stale after this number of seconds, and
# will be purged.
RESOURCE_REQUEST_TIMEOUT = 60
PURGE_INTERVAL = RESOURCE_REQUEST_TIMEOUT * 2
# When the autoscaling is driven by memory pressure and there are ... |
6a7a237cb299932c8303ad0f8cfa475dd91f0b244d54d6f8837410ce2569cdda | Python | 4,910 | 150 | import numpy as np
class CameraError(Exception):
pass
class BaseCamera(object):
"""
A class used to encapsulate a Camera.
Attributes
----------
cam : PySpin Camera
running : bool
True if acquiring images
camera_attributes : dictionary
Contains links to all of the came... |
e834a0b62998db60d28cb6dcbd9e03fa32e29215d167accd92c145678495fd01 | Python | 4,911 | 124 | import torch
from torch import nn
from torch import distributions
from torch.nn.parameter import Parameter
use_cuda = torch.cuda.is_available()
device = torch.device('cuda:0') if use_cuda else torch.device('cpu')
class Simple_Spring_Model():
def __init__(self, device, R=3):
self.device = device
... |
da06690ea67cc059fd29c5d8c3b6895323d0b88415a9fffd6f5ff6967b912b33 | Python | 4,912 | 134 | # -*- coding: utf-8 -*-
"""
Created on Tue Apr 23 19:44:26 2024
@author: Leyang Xue
"""
import sys
import networkx as nx
# Add package path
packagepath = '../kcorePercolation' # Manually specify the path to your script
sys.path.append(packagepath)
from utils import kcorePercolation as kp # Import custom utility fu... |
f2dab2b7e17656e1e6de9e60b4f9d84dc0c5e8051f548ee3008c5dfce3e3ecea | Python | 4,915 | 151 | from typing import Dict, Optional, List, Any, Union
import logging
import copy as cp
import numpy as np
import pandas as pd
import warnings
from argschema.argschema_parser import ArgSchemaParser
from neuron_morphology.transforms.scale_correction._schemas import (
InputParameters, OutputParameters)
from neuron_mor... |
6a115be4b996944ce53a642919938a9db8aa2521415b806c48e3500f71c616c2 | Python | 4,916 | 131 | import copy
import os
from typing import Any, Dict, Tuple
from ray._common.utils import get_default_ray_temp_dir
from ray.autoscaler._private.cli_logger import cli_logger
unsupported_field_message = "The field {} is not supported for on-premise clusters."
LOCAL_CLUSTER_NODE_TYPE = "local.cluster.node"
def prepare_... |
e19f40a640235fc2d4fa368380a050419972f4ec6565869e6337d88465bdb43c | Python | 4,918 | 137 | import torch
from diffusers import UnCLIPScheduler
from .test_schedulers import SchedulerCommonTest
# UnCLIPScheduler is a modified DDPMScheduler with a subset of the configuration.
class UnCLIPSchedulerTest(SchedulerCommonTest):
scheduler_classes = (UnCLIPScheduler,)
def get_scheduler_config(self, **kwarg... |
4133d1e3f86e7e8cb305228e24549941ed9e114c08315c524caa20a5fbe7edf3 | Python | 4,920 | 148 | import argparse
import glob
import os
from time import time
import cupy
import nvtabular as nvt
import torch
import torch.distributed as dist
from nvtabular.framework_utils.torch.models import Model
from nvtabular.framework_utils.torch.utils import process_epoch
from nvtabular.loader.torch import DLDataLoader, TorchAs... |
83aa27a6b7883b89c695b0bbc8f14cd562d017b9ebcafc6716df65064d3e074a | Python | 4,920 | 155 | # This file is part of the INTREPPPID programme.
# Copyright (c) 2023 Joseph Szymborski.
#
# This programme 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, version 3.
#
# This programme is distributed i... |
a8230286ea258ba41afa8c0f01b9be36c4ff04513164bcd44cd6127277d88699 | Python | 4,925 | 124 |
MRI_DIRS = [
"/gpfs/data/oermannlab/private_data/ObermannNeuro/dicom/",
"/gpfs/data/oermannlab/private_data/ObermannNeuro2/dicom/",
"/gpfs/data/oermannlab/ObermannNeuro3/dicom/"]
RT_DIRS = [
"/gpfs/data/oermannlab/private_data/temporalMRI/gammaplan/",
"/gpfs/data/oermannlab/private_... |
c94718b58a1089ce2597bd0614e367bdd3fb1e723ebacd546661ddbc89ccfff1 | Python | 4,926 | 132 | # Copyright 2023 Google LLC
# 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
# https://www.apache.org/licenses/LICENSE-2.0
# Unless required by applicable law or agreed to in writing, sof... |
033757fda5904defe1676692335e82925f2c30b8d4698fdef463518b6c0b9619 | Python | 4,927 | 108 | #-----------------------------------------------------------------------------------------
#Author: Brandon S Coventry
#Date: 12/18/23
#Purpose: Demonstrate the role of sample size on two comparison t-tests and Bayes t-tests
#Requires: Data from DBS_LFP_GenData.py
#------------------------------------------------------... |
86689cae2bf8d81fff38297b451bb1892e9e16633015c70b1207910dc1093ec9 | Python | 4,928 | 104 | import torch
import torch.nn as nn
from DWonder.RMBG.buildingblocks import Encoder, Decoder, FinalConv, DoubleConv, ExtResNetBlock, SingleConv
from DWonder.RMBG.utils import create_feature_maps
class UNet3D(nn.Module):
"""
3DUnet model from
`"3D U-Net: Learning Dense Volumetric Segmentation from Sparse A... |
d153060d41d1fe8368c6bd73d7fdc209f14ac48da4bd9862afa54741e366d7dc | Python | 4,930 | 101 | __author__ = "Simon Andermatt"
__copyright__ = "Copyright (C) 2017 Simon Andermatt"
import numpy as np
import tensorflow as tf
from mdgru.helper import argget, generate_defaults_info
from mdgru.helper import compile_arguments
from mdgru.model import batch_norm, get_modified_xavier_method
# CaffeMDGRU is not supported... |
dbcd81e2bbaafef3f1b3a34fdd82361d50b0d84da1cba7f09948baa692d5a81f | Python | 4,932 | 163 | # mypy: ignore-errors
"""Correlations between variables."""
import warnings
from typing import Dict, List, Optional, Sized, no_type_check
import numpy as np
import pandas as pd
from data_profiling.config import Settings
try:
from pandas.core.base import DataError
except ImportError:
from pandas.errors impo... |
3809614092bd4535364608facb62a38dceeba1b7f542667f87b651bba548a1cc | Python | 4,933 | 148 | import random
from typing import Any, Callable, Dict, Iterable, Optional, Set, Tuple, Union
import ray
_ResultCallback = Callable[[Any], None]
_ErrorCallback = Callable[[Exception], None]
class RayEventManager:
"""Event manager for Ray futures.
The event manager can be used to track futures and invoke call... |
6ba33c6ff5d72babca11c5ad10d7315fa72ba11204209f25097cf74c678efc7d | Python | 4,935 | 95 | from .bioprocessor import BioProcessor
import pysolr
from bionlp.processors.utils import unique_terms
import re
import os
class DiseaseProcessor(BioProcessor):
def __init__(self, model_name):
super().__init__(model_name)
self.solr_url = os.getenv('SOLR_URL','http://localhost:8983/solr/')
... |
0f9d447b95ca2c7b19275a9a40d1e659defeaed0ce54e7f85b3757967c903af7 | Python | 4,938 | 148 | # Copyright 2023 Google LLC
# 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
# https://www.apache.org/licenses/LICENSE-2.0
# Unless required by applicable law or agreed to in writing, sof... |
f68b99c77fa7ab3e605cb464202306a3f033398a47ab8e3a87100ecb84c7cfa3 | Python | 4,940 | 197 | # This file is autogenerated by the command `make fix-copies`, do not edit.
from ..utils import DummyObject, requires_backends
class FlaxControlNetModel(metaclass=DummyObject):
_backends = ["flax"]
def __init__(self, *args, **kwargs):
requires_backends(self, ["flax"])
@classmethod
def from_c... |
1fbb091e2271d43b57f02d61efeb05eb5562269b38b8eae30c2b447eb2d3464b | Python | 4,941 | 136 | # -*- coding: utf-8 -*-
# (C) Copyright 2026 IBM. All Rights Reserved.
#
# Licensed under the MIT license. See LICENSE file in the project root for details.
"""Analog Modules that contain children Modules."""
# pylint: disable=unused-argument, arguments-differ
from types import new_class
from typing import Any, Opti... |
5e8cb3d30156152bd38da65f85d569c7508374f29358984c533b1e5252c83647 | Python | 4,942 | 139 | from utils.tool import read_img, save_img
import time
import os
import numpy as np
import argparse
def alpha(x):
return 0.8*(2**(x/6)-1)
def beta(x):
return 0.5*x-7
def clip(x,min,max):
if x < min:
x = min
if x > max:
x = max
return x
def judge_filter(p1,p0,q0,q1,index_a,index_b,... |
94da32b5a8df67358af4e0a2c752a249cd455f466021e73befec15f7c9743982 | Python | 4,942 | 132 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Python version: 3.10.9
pandas version: 1.5.0
seaborn version: 0.11.0
matplotlib version: 3.6.3
pingouin version: 0.5.3
ptitprince version: 0.2.6
scipy version: 1.11.4
"""
#%% Import Modules
import pandas as pd
import glob
import seaborn as sns
import matplotlib.pylab... |
9aaf916d2c2352fac1ef6c2f87975f81b965c1123ea9c7e66111e5bb1d21f42f | Python | 4,943 | 148 | import os
import torch
from setuptools import setup
from torch.utils.cpp_extension import BuildExtension, CUDAExtension
import sys
SCRIPT_DIR = os.path.dirname(os.path.realpath(__file__))
ROOT_DIR = os.path.dirname(os.path.dirname(SCRIPT_DIR))
# Find version of tinycudann by scraping CMakeLists.txt
with o... |
ea4373400b5c97e05d2c3e7f1a49145df456bc8c4083c068d04d213f128f2421 | Python | 4,943 | 142 | #
# CEBRA: Consistent EmBeddings of high-dimensional Recordings using Auxiliary variables
# © Mackenzie W. Mathis & Steffen Schneider (v0.4.0+)
# Source code:
# https://github.com/AdaptiveMotorControlLab/CEBRA
#
# Please see LICENSE.md for the full license document:
# https://github.com/AdaptiveMotorControlLab/CEBRA/bl... |
0ac5d20fc91448445fe394acbe6a04fdecf02fa5a8ecea8543b6d9f736f7b592 | Python | 4,945 | 145 | import numpy as np
import pytest
import torch
from datamate import set_root_context
from flyvis.network.directories import NetworkDir
from flyvis.solver import MultiTaskSolver
from flyvis.utils.config_utils import get_default_config
@pytest.fixture(scope="module")
def solver(mock_sintel_data, tmp_path_factory) -> Mu... |
7a21235b606518b86486b8435db5e0d7e2e2056a5aa40f228009f70cd07cb99b | Python | 4,945 | 141 | #------------------------------------------------------------------------------
# Libraries
#------------------------------------------------------------------------------
import torch
import torch.nn as nn
import torch.nn.functional as F
#----------------------------------------------------------------------------... |
a1cf87d5f848a4d24a5534d8550dc02ab5e2627de994dd287170eac69f57c5a4 | Python | 4,946 | 118 | from __future__ import annotations
import numpy as np
def _check_shape(x, y):
"""Check that x and y have the correct shapes."""
if len(x.shape) != 2 or len(y.shape) != 2:
raise ValueError("x and y must be 2D arrays.")
if x.shape[0] != y.shape[0]:
raise ValueError("Number of datapoints in... |
936ca60f3ffdb6e66ff804312f10fdb650425695e9936c7d635b9fbfb97f691e | Python | 4,947 | 161 | import numpy as np
from scipy.stats import sem
NULL_RESPONSE = -1
class SimpleTracker():
def __init__(self, size=256):
self.buffer = {}
self.unique = {}
self.size = size
def add(self, ctx_id, value, verbose=False):
# if input is new, create new slots
if not self.ctx_in... |
7183aa8db3a5711de95723027e8f88edadd67be65a706cd48edda1272fcd618f | Python | 4,950 | 114 | import os
from ray._private.ray_constants import env_bool, env_float, env_integer
DASHBOARD_LOG_FILENAME = "dashboard.log"
DASHBOARD_AGENT_ADDR_NODE_ID_PREFIX = "DASHBOARD_AGENT_ADDR_NODE_ID_PREFIX:"
DASHBOARD_AGENT_ADDR_IP_PREFIX = "DASHBOARD_AGENT_ADDR_IP_PREFIX:"
DASHBOARD_AGENT_LOG_FILENAME = "dashboard_agent.log... |
9e97e9193f376e5a9fb6cc11aad4d68b8be18fd4181a6e5d1b64aa895a25ad63 | Python | 4,950 | 160 | """
Copyright (c) Meta Platforms, Inc. and affiliates.
This source code is licensed under the MIT license found in the
LICENSE file in the root directory of this source tree.
"""
from __future__ import annotations
import hashlib
import os
import shutil
import subprocess
import pytest
from fairchem.core.common impo... |
dd89fa7d3f9d2c4b9b7ca54f9d2c1e94bc5a4afda4529cb2f0fc293fa59da584 | Python | 4,951 | 112 | ####################################################################################################
# Copyright (c) 2016 - 2024, EPFL / Blue Brain Project
# Author(s): Marwan Abdellah <marwan.abdellah@epfl.ch>
#
# This file is part of NeuroMorphoVis <https://github.com/BlueBrain/NeuroMorphoVis>
#
# This program is fre... |
37e55c091dfd24a84d291999dc68fcd9ad744c04b8ea55859768bb93486f796d | Python | 4,953 | 148 | import sys
from glob import glob
import skimage
from skimage import measure
import nibabel
import numpy
import os
from math import floor
import argparse
def f(i, j, k, affine):
"""
Returns affine transformed coordinates (i,j,k) -> (x,y,z) Use to set correct coordinates and size for the mesh.
Parameters
----------... |
ef462b1bad8346a0747841cbdec889a4d38d6b5db54f5647d84ed3a5bfa9f412 | Python | 4,954 | 110 | r"""Vendored access to `ThermoMPNN <https://github.com/Kuhlman-Lab/ThermoMPNN>`_
for real thermostability ΔΔG prediction.
ThermoMPNN (Dieckhaus *et al.* 2024, PNAS) is a transfer-learning head on a
frozen ProteinMPNN encoder, trained on the mega-scale stability dataset. It has
no PyPI package and its inference script ... |
2080269e7840228ca692d6583aeab1f901871e8e8d809d0d70b90ac6eed28d55 | Python | 4,955 | 107 | import numpy as np
import statsmodels.api as sm
import statsmodels.formula.api as smf
import pandas as pd
from ..io import SAVED_DIR, load_rates, load_current, load_weights, save_convergence
from ..math import ones
def test_convergence(run_name, directory=SAVED_DIR, conv_trials=100, conv_alpha=0.05, conv_thresh=0.01, ... |
da8274656813ded01077b98b23269ebcb5995f89c2b27c9ceb28826177f8cab3 | Python | 4,956 | 120 | # Copyright 2023 The HuggingFace 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/LICENSE-2.0
#
# Unless required by applicabl... |
ff5199b8ca851f3063c29cffeab5ebd09751aaca2715c72778213ea63c33bf07 | Python | 4,958 | 99 | # camera-ready
import torch
import torch.nn as nn
import torch.nn.functional as F
class ASPP(nn.Module):
def __init__(self, num_classes):
super(ASPP, self).__init__()
self.conv_1x1_1 = nn.Conv2d(512, 256, kernel_size=1)
self.bn_conv_1x1_1 = nn.BatchNorm2d(256)
self.conv_3x3_1 = n... |
13f36921c2bfb6736777fb2f39b4ab83619c61e23be85efa45e58f5a00a8bb10 | Python | 4,959 | 215 | import pytest
import ray
@ray.remote
class Counter:
def __init__(self, init_value=0):
self.i = init_value
def inc(self):
self.i += 1
def get(self):
return self.i
def test_basic_task_dag(shared_ray_instance):
ct = Counter.remote()
@ray.remote
def a():
ray.g... |
a519a3c6ad0a65014d2c54446a75c0f25e84483378388476ec9f01d12fc2f049 | Python | 4,959 | 130 |
import numpy
import matplotlib
from matplotlib import pyplot
class PickIndex:
def __init__(self, idx):
self.idx = idx
def select(thetas, objectives, with_time, times, figsize=(8, 8), borders=None, *args, **kwargs):
"""Asks the user to select the best option by clicking on the points from the
:mo... |
aa5ac895adea0d9e372cdeaa0ebdc802a3c7945a61e089e5a6aabba12b72a9d9 | Python | 4,960 | 111 | # This file is part of the INTREPPPID programme.
# Copyright (c) 2023 Joseph Szymborski.
#
# This programme 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, version 3.
#
# This programme is distributed i... |
e9f03b81455db9ae8b63099b0e197085b5158a911164724f5f69ee21e050994c | Python | 4,960 | 188 | import os
import pdb
from matplotlib import pyplot as plt
import numpy as np
import yaml
from yaml.loader import SafeLoader
import torch
import ray
from latent_time_stepping.oracle import ObjectStorageClientWrapper
from latent_time_stepping.utils import create_directory
from latent_time_stepping.AE_models.VAE_encoder ... |
5aecc3ff856920c22f3a2704b832724b13dca829b7f1584f5f86b453d4be9ff7 | Python | 4,962 | 130 | r"""Plotting for single-cell metabolism results (:class:`ov.single.Metabolism`).
:func:`metabolism_heatmap` summarises the ``adata.obsm['X_metabolism']``
matrix written by any :class:`ov.single.Metabolism` backend
(scMetabolism pathway activity, Compass reaction flux, scFEA module
flux) as a group-mean heatmap.
"""
f... |
5430e9ee616bee9bfcd6be7171b2204dd95cca69e707ceb038dcdbab2f507f7c | Python | 4,963 | 145 | # Modified from https://github.com/DiZhang-XDU/sleepstager-twobranch/blob/main/sleep_models/ResAtt_OneLoss.py
import torch
import torch.nn as nn
import torch.nn.functional as F
class ChannelMask(nn.Module):
def __init__(self, input_channels, ratio=8):
super(ChannelMask, self).__init__()
squ... |
f3c72baace69347fa013028df1a6855def5f7609630ab8645d1b9c0a5b6177db | Python | 4,964 | 165 | import os
import csv
import numpy as np
import itertools
import subprocess
#See conditions nname below
def register_images(subject_dir, subject_id):
fmA_infile =os.path.join(subject_dir)
fmA_outfile = os.path.join(subject_dir, 'model', 'model001','onsets','task002_run001')
fmB_infile =os.path.join(subject_dir)
f... |
05429644b662532aa4ed3f8d99bfa35e35ea112733fce0c846bafa7ae43e2e59 | Python | 4,965 | 109 | import time
from experiments.keras.models.brainage_3dcnn import BrainAge3DCNN
from experiments.keras.models.cifar_cnn import CifarCNN
from experiments.keras.models.fashion_mnist_fc import FashionMnistModel
from projectmetis.proto import learner_pb2_grpc
from projectmetis.python.utils.grpc_services import GRPCChannelMa... |
fa767c029ab988f0fc97987f8c28c4874bd2e925f4833bf0e5a65a43e669292b | Python | 4,966 | 144 | from abc import ABC, abstractmethod
from typing import Any, Dict, Generic, TypeVar
from ray.experimental.channel.accelerator_context import AcceleratorContext
from ray.util.annotations import DeveloperAPI
T = TypeVar("T")
@DeveloperAPI
class DAGOperationFuture(ABC, Generic[T]):
"""
A future representing the... |
bbaa794c194b83bbe868638b779377998f24958e9f2cc9c379c8374b7d809f14 | Python | 4,968 | 130 | import gzip
from csv import reader, DictWriter, DictReader
from pathlib import Path
from typing import Optional
import plyvel
import requests
from rich.progress import Progress
from . import utils
def build_ensembl_pro_to_upkb_db(processed_folder: Path):
db = plyvel.DB(
str(processed_folder / "ensembl_p... |
bbfdff11687a268e61d7f65ef4bc6014806eef15b13f685f375ff1356c15e004 | Python | 4,969 | 124 | from typing import Optional, Sequence, Tuple, Union
import numpy as np
import torch
import torch.nn as nn
from monai.networks.blocks.convolutions import Convolution
from monai.networks.layers.convutils import same_padding
from monai.networks.layers.factories import Conv
class ResidualUnit(nn.Module):
"""
Res... |
4cf6635289fdc492ad2199edb6a43471c89f6e7281e3fa4605f6abf34d33e196 | Python | 4,970 | 151 | import numpy as np
import pandas as pd
from sklearn.neighbors import NearestNeighbors
import itertools
import networkx as nx
# Modified from https://github.com/lkmklsmn/insct
def create_dictionary_mnn(adata, use_rep, batch_name, k = 50, save_on_disk = True, approx = True, verbose = 1, iter_comb = None):
cell_n... |
656bf109e9f0d49a03c1e455b97b67f21748a4a6d310c41b0adeefd09984d640 | Python | 4,970 | 149 | import tensorflow as tf
from utils.nn import linearND, linear
from mol_graph import atom_fdim as adim, bond_fdim as bdim, max_nb, smiles2graph, smiles2graph_test, bond_types
from models import *
import math, sys, random
from optparse import OptionParser
import threading
from multiprocessing import Queue
import rdkit
fr... |
f7bb419029fa62583af5dd4d36ddb05d2482608f187035b20b710eb963ff09e5 | Python | 4,970 | 155 | # Dependencies
# LinAlg / Stats / Plotting Dependencies
import numpy as np
from PIL import Image
# Torch Dependencies
import torch
import torch.multiprocessing
from torchvision import transforms
from einops import rearrange
# Local Dependencies
import vision_transformer as vits
import vision_transformer4k as vits4k
... |
1e910cbde773519162480fd3a0306e8fecb9687a51804f742724a4b51117f21d | Python | 4,973 | 156 | # coding=utf-8
"""
Module for computing The Hartigans' dip statistic.
The dip statistic measures unimodality of a sample from a random process.
See:
Hartigan, J. A.; Hartigan, P. M. The Dip Test of Unimodality. The Annals
of Statistics 13 (1985), no. 1, 70--84. doi:10.1214/aos/1176346577.
http... |
d326b0e3b9f0e3b52a4ef6186bb6e707dcd2b3167d944889f587bc9ed3c820e3 | Python | 4,976 | 163 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
#
"""
"""
import argparse
import sys
import pysam
import svtk.utils as svu
from svtk.vcfcluster import VCFCluster
from svtk.svfile import SVRecordCluster
def samples_overlap(samplesA, samplesB, upper_thresh=0.8, lower_thresh=0.5):
# Get lists of called samples for ... |
725005a181991710f976109ef5ba4d7b3e402b4c757bcf6d2fbac4d2921d6cba | Python | 4,978 | 125 | """
Copyright (c) Meta Platforms, Inc. and affiliates.
This source code is licensed under the MIT license found in the
LICENSE file in the root directory of this source tree.
"""
from __future__ import annotations
import os
import pytest
import torch
from fairchem.core.common import distutils, gp_utils
from fairch... |
c9debb536bd5e12c3176fd37bd5fd483b65262c5079eec65c64d2ce20e6f9d91 | Python | 4,982 | 126 | ####################################################################################################
# Copyright (c) 2020, EPFL / Blue Brain Project
# Author(s): Marwan Abdellah <marwan.abdellah@epfl.ch>
#
# This file is part of NeuroMorphoVis <https://github.com/BlueBrain/NeuroMorphoVis>
#
# This program is free softw... |
84d9fdd4a4e8bfffb70bb77deec591ac735cf70263f0ec6fc1ef683bfc6a9903 | Python | 4,983 | 168 | # This file is part of the INTREPPPID programme.
# Copyright (c) 2023 Joseph Szymborski.
#
# This programme 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, version 3.
#
# This programme is distributed i... |
c5a74ab3f2f3549f8eef3fbd98675420dbcc567a0be902ef96851b6e33adc609 | Python | 4,983 | 164 | #!/usr/bin/python
import warnings
import numpy as np
from scipy.sparse import coo_matrix
import pandas as pd
def sample_molecules(counts, n):
"""Sample n molecules from a vector of molecular counts
Parameters
----------
counts: ndarray
ngene x 1 count vector
n: int
number of molec... |
408667ae9c514848205c748f296ed1f9357d183782ff3b5070734a43d75393c5 | Python | 4,986 | 131 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
#
"""
"""
import argparse
import heapq
from collections import deque
import pysam
import svtk.utils as svu
def records_match(record, other):
"""
Test if two records are same SV: check chromosome, position, stop, SVTYPE, SVLEN (for insertions),
STRANDS (for B... |
f27298589170ea92bfe2be4eb8b106059ac618cdd91a1ad1fc5af9939749bbd0 | Python | 4,986 | 109 | """
Copyright (c) Meta Platforms, Inc. and affiliates.
This source code is licensed under the MIT license found in the
LICENSE file in the root directory of this source tree.
"""
from __future__ import annotations
import argparse
import os
import pathlib
mapping = {
"fairchem.experimental.foundation_models.unit... |
17f488dbdb094584521a448d518da1fe529aea0176b359a56f70a213948338d7 | Python | 4,987 | 159 | """Transforms on raw wav samples."""
__author__ = 'Yuan Xu'
import random
import numpy as np
import librosa
import torch
from torch.utils.data import Dataset
def should_apply_transform(prob=0.5):
"""Transforms are only randomly applied with the given probability."""
return random.random() < prob
class Load... |
73021605ca640ddc15ecc67aa4421f435ddce1e468060918f1025f6ea2cf6e39 | Python | 4,987 | 148 | from __future__ import annotations
"""
OmicVerse Agent utilities
Public API
----------
seeker(links, *, name=None, description=None, max_pages=30, target="skills", out_dir=None, package=False, package_dir=None)
Create a Claude Agent skill from a link (or list of links) directly from Jupyter.
Examples
--------
>>... |
8ab5210d6ad0d04159a4241b71c4f682ca5c47369d6b9fd52ffd33fcb1583b41 | Python | 4,989 | 172 | """
test 'charge_and_spike' neuron model
"""
import os
import matplotlib.pyplot as plt
import numpy as np
from spinnaker2 import hardware, snn
rng = np.random.default_rng(42)
def v_silent(input_spikes, weights, t):
ts = np.ones_like(input_spikes) * t
t_diff = ts - input_spikes
t_diff = np.maximum(t_diff... |
e17768225f0ea615d78f3e5b9218d55881d35d94c0e4bd2893a0712a561278a1 | Python | 4,989 | 123 | ####################################################################################################
# Copyright (c) 2016 - 2024, EPFL / Blue Brain Project
# Author(s): Marwan Abdellah <marwan.abdellah@epfl.ch>
#
# This file is part of NeuroMorphoVis <https://github.com/BlueBrain/NeuroMorphoVis>
#
# This program is fre... |
196c7a3450489febc64d956a87555bca547cc9df0251a03bf0cc1226af154ddd | Python | 4,991 | 131 | # Copyright 2024 Google LLC
#
# 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
#
# https://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, ... |
f8c05cb5e7863edf023d3eec64f6b69504713ce116513a7dcce5a5fdc5718a4b | Python | 4,991 | 131 | import torch
import torch.distributed as dist
import torch.multiprocessing as mp
import argparse
import os, glob
from sklearn.model_selection import train_test_split
from torch_geometric.loader import DataLoader
import socket
from src import AseReadDatasetAttr
from src import TrainerFineTuneRegression
from equiformer_... |
2d4155db4ee92f640de1211d95986e3244b3d146eb3cfd63514f6356a43ff83f | Python | 4,993 | 91 | # -*- coding: utf-8 -*-
"""Convert .czi image stack (saved by Zeiss microscopes) into .tif image stack.
This script is used to convert .czi image stack into .tif image stack. The .czi file is saved by Zeiss microscopes
and contains 3D SIM data. While the .czi file can be directly loaded by the SIM3DDataLoader class in... |
a1245b1cb54ec10a78f66e85304c426bd22e7dc1b8781431ca97357d9f46ea21 | Python | 4,993 | 132 | # -*- coding: utf-8 -*-
"""
Created on Wed Sep 14 12:18:00 2022
@author: ju-bar
EMD file I/O
This code is part of the 'emilys' repository
https://github.com/ju-bar/emilys
published under the GNU General Publishing License, version 3
"""
import json
import h5py
import numpy as np
def get_data_as_str(data):
d = ... |
354f45becf49a7badc0273315420b30f58ee0465c44e0ed612667ce49b8f894f | Python | 4,994 | 116 | ####################################################################################################
# Copyright (c) 2016 - 2024, EPFL / Blue Brain Project
# Author(s): Marwan Abdellah <marwan.abdellah@epfl.ch>
#
# This file is part of NeuroMorphoVis <https://github.com/BlueBrain/NeuroMorphoVis>
#
# This program is fre... |
90bce2df02d315d34986341ad6a81815b5533046356902d1452a733bdf540fc1 | Python | 4,994 | 100 | import torch
import numpy as np
import nibabel as nib
import torch.nn as nn
import torchio as tio
import kornia.augmentation as K
from torch.utils.data import Dataset
from pytorch3dunet.unet3d.model import UNet3D
from skimage.morphology import closing, cube
model_path = '/space/calico/3/asterion/1/users/lr252/synth_hy... |
3210721a15b18c3c72dbe8eb6ef398b9637a035b292c252167601bc5aa297b5e | Python | 4,995 | 127 | from typing import Dict, TypeVar
from ray.data._internal.execution.interfaces import ExecutionResources
# The math functions defined in this module use a generic type rather than
# `PhysicalOperator` so it's easier to test. We already pass in all of the necessary
# inputs, so the actual type doesn't matter.
T = TypeV... |
d3efa6f3db4830be9cf97a0a7ce3a1feb92e1deaed0dbeab5cd5075c5472865e | Python | 4,995 | 156 | # -*- coding: utf-8 -*-
# (C) Copyright 2026 IBM. All Rights Reserved.
#
# Licensed under the MIT license. See LICENSE file in the project root for details.
"""aihwkit example 21: Fitting a device data to a piecewise step device.
Plots the fitted response of a piecewise step device
"""
# pylint: disable=redefined-o... |
3bbc0aa2e8f3b0e3d5e6737c05f9cb6620ef8f07fc63724f08758006066c70a3 | Python | 4,996 | 161 | # -*- coding: utf-8 -*-
# (C) Copyright 2026 IBM. All Rights Reserved.
#
# Licensed under the MIT license. See LICENSE file in the project root for details.
"""Parsers for the AIHW Composer API."""
from datetime import datetime, timezone
from typing import Any, Dict
from aihwkit.cloud.client.entities import (
C... |
3fbdd9d9f3dd46bc111e48a8893f8d752c845933ca2a72e72c99c24c5e0f9a5f | Python | 4,997 | 128 | # coding=utf-8
# Copyright 2023, Haofan Wang, Qixun Wang, 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 re... |
71052f00f5ff5b886daaa5f329625f3eb0c7bf8b053edb38698d8fbb6516e677 | Python | 4,998 | 113 | import torch
from loss import spearman_loss
from metrics import spearman_corr
class ProcessingData(torch.utils.data.Dataset):
def __init__(self, train_csv, train_pt, dataset_type):
self.train_csv = train_csv
self.train_pt = train_pt
self.dataset_type = dataset_type
def __len__(self)... |
8a671fc1ab2f6c10434b87609bc4737d0a77b92cb3c8c63e3a9cc1355fd43b16 | Python | 4,999 | 150 | import multiprocessing as mp
import tkinter as tk
import PIL
from PIL import Image, ImageTk
import cv2
import numpy as np
import logging
import time
def get_latest(queue, timeout = 0.1 ):
start_time = time.time()
try:
item = queue.get(timeout=timeout)
while True:
try:
... |
dbbfbadfc9535f52decdaf22b52a3f318ceebf7d40bc81e341ddcb6fc6d43c86 | Python | 4,999 | 130 | #!/usr/bin/env python
# coding: utf-8
# In[ ]:
#In order for this code to be executed one needs the detailed spreadsheets that are created after each model's training
#and testing process and contain the individual predictions and probabilities for each patient.
#The code can then read the spreadsheets and calculat... |
58acc1de8efab1d754c7d82b8a5a0b43afa28c304fa85157b21769f408c48803 | Python | 5,002 | 139 | from typing import Tuple
import numpy as np
class ValidateMapping:
def __init__(
self,
input_feature_size: int,
output_feature_size: int,
kernel_size: Tuple[int, int],
stride: Tuple[int, int],
padding: Tuple[int, int],
input_dimension: Tuple[int, int] = [64,... |
d6c16cf07d4d6f3b67e748f5bbca6c5a074017bae74e00bdd84c26b9d29c87c8 | Python | 5,003 | 181 | #!/usr/bin/env python
import os
import numpy as np
from scipy.sparse import coo_matrix
from scipy.io import mmread, mmwrite
from clusterdiffex.distance import spearmanr
import umap
import phenograph
def get_knn(distance, k=20):
""" Get a cell x cell k-nearest neigbors adjacency matrix
Parameters
-------... |
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