sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
53905bf6e1904edda1a12bb558a5b5f7c59dd6698339f855af8e01e5759e92cf | Python | 5,871 | 164 | """Code in this file is heavily based on the code from the following repository: https://github.com/CompVis/invariances"""
import warnings
import torch
import torch.nn as nn
from torchvision import models
from ldctinv.utils.distributions import DiagonalGaussianDistribution
from ldctinv.vae.blocks import ActNorm, Den... |
b0f1fa0d457bfd9c7ce86b6e73dcd6c64483530f8be46e4c659ea21f83b291e2 | Python | 5,871 | 157 | def dr_seed_fc():
import numpy as np
from os import path
from labbookdb.report.tracking import treatment_group, append_external_identifiers
from samri.plotting.overview import multiplot_matrix, multipage_plot
from samri.utilities import bids_substitution_iterator
from samri.analysis import fc
db_path = '~/syncd... |
120963c7982a07bf01f18d8dc8b87386fa3b537ae3a6a7ddece616a247dde8b3 | Python | 5,873 | 114 | ####################################################################################################
# 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... |
c1530d70a4eff358c4aec83e62e43e2c3bb45a8280a0c750134b618fbe2d8dd6 | Python | 5,875 | 134 | from glob import glob
from os import path
import pandas as pd
import numpy as np
import copy
def get_timing_correction(filey):
problematic_files = ['s568_motorSelectiveStop.csv', 's568_stroop.csv',
's568_surveyMedley.csv', 's568_DPX.csv',
's568_discountFix.csv',
... |
5ae44e0782bebd11215dc8cebd1ce9029aed8b90e27eb9a2fa7bfef502ae713c | Python | 5,880 | 194 | from dataclasses import dataclass, field
from typing import Any, Dict, Optional
import numpy as np
from .node import NIRNode
@dataclass(eq=False)
class CubaLIF(NIRNode):
r"""Current based leaky integrate and-fire-neuron model.
The current based leaky integrate-and-fire neuron model
is defined by the fo... |
84cd860a8bc9308649f5a0cb2225fb3192403bddacd849786c63ee5d81d9891b | Python | 5,880 | 165 | import numpy as np
import torch
from torch import nn
from sinabs.from_torch import from_model
class NestedANN(nn.Module):
def __init__(self):
super().__init__()
seq = [
nn.Conv2d(
2, 8, kernel_size=(2, 2), stride=(2, 2), padding=(0, 0), bias=False
),
... |
9c34d870df7de2ef75f1f3fda45df50d5333a66c7c5a3487bd8af7a44d1f0de2 | Python | 5,880 | 141 | r"""SBOL — the Synthetic Biology Open Language interchange standard.
`SBOL <https://sbolstandard.org/>`_ is the community standard for exchanging
genetic-design data (parts, devices, constructs) between tools and registries
(iGEM, SynBioHub, Benchling…). These helpers bridge an ``ov.synbio`` construct
(a sequence + a ... |
8fc2a100b29fc1eb4fc097d9c30b49c29ca0cc8c64e104067eb28acbe28dfa45 | Python | 5,881 | 142 | # --------------------------------------------------
# load options for CNN lesion segmentation
#
# Options are loaded from a configuration file
#
# --------------------------------------------------
def load_options(default_config, user_config):
"""
map options from user input into the default config
"""... |
ddeb06757010b250c0d4ead74c3e46d41e7c1d4e3b8f3f95b432e3763e08e5b5 | Python | 5,881 | 179 | from __future__ import annotations
from dataclasses import dataclass
from pathlib import Path
from typing import Any, ClassVar, Iterable, NamedTuple, Sequence, TypeAlias
import numpy as np
import pandas as pd
from numpy.typing import NDArray
from siapy.core.exceptions import InvalidInputError, InvalidTypeError
__al... |
0f7664c667dfdae55053f2ef26e4ea6c8c87f04668b49704986930cf27b1e0c3 | Python | 5,882 | 131 | import optuna
import pandas as pd
import pytest
from sklearn.base import BaseEstimator
from sklearn.svm import SVR
from siapy.core.exceptions import InvalidInputError
from siapy.datasets.schemas import RegressionTarget
from siapy.entities import Signatures
from siapy.optimizers.configs import OptimizeStudyConfig, Tabu... |
8cfb7b3643b2fd98ad3be608ff106effed585291e5f93df2d26495dcdbaed19e | Python | 5,884 | 199 |
'''
Code coming from https://github.com/lucidrains/vit-pytorch
'''
import pdb
import torch
from torch import nn
from einops import rearrange
from einops.layers.torch import Rearrange
# helpers
def posemb_sincos_1d(patches, temperature = 10000, dtype = torch.float32):
_, n, dim, device, dtype = *patches.shape... |
a571f8d7019399c3429606f9a3967ae7bcd5e547ff0935d273822487b7bcb576 | Python | 5,884 | 141 | # Copyright 2021 Division of Medical Image Computing, German Cancer Research Center (DKFZ)
# and Applied Computer Vision Lab, Helmholtz Imaging Platform
#
# 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 L... |
636da2b57efbe07409859c13ccec6dee8c92c51456fd51b71bc75a7b9a1a822a | Python | 5,885 | 143 | #!/usr/bin/python
# This file is NOT licensed under the GPLv3, which is the license for the rest
# of YouCompleteMe.
#
# Here's the license text for this file:
#
# This is free and unencumbered software released into the public domain.
#
# Anyone is free to copy, modify, publish, use, compile, sell, or
# distr... |
3ae712bea5355703c8f72e524772133f6fde80c7bc9e5d04be752ed15836a9be | Python | 5,886 | 157 | """Keep the per-file prose doctest lists in doc/BUILD.bazel complete and live.
Doc prose is tested by `doctest_each()` over explicit lists of pages, not
directory globs, so that every target tests something. Each library (Core,
Data, RLlib, Serve, Train, and Tune) has its own list, and prose that no library
owns is in... |
43ba53f3b54f6f2479f149bb95d007de2d4341bba9eb0e7e54011384d6d7f492 | Python | 5,886 | 187 | import argparse
import sys
import samtools
import re
import shutil
import os.path
from ngs_mapper.bam import sortbam, indexbam
import log
logger = log.setup_logger('tagreads',log.get_config())
# Exception for when headers exist
class HeaderExists(Exception): pass
# The next 3 tuples have to be the same length and ea... |
45517ddbd62d2126e7f724af2b4d6a3016518f247b399e145d76f4410c0eccce | Python | 5,886 | 166 | import os
import time
from pathlib import Path
import pandas as pd
try:
from anndata.io import read_h5ad as _anndata_read_h5ad
except ImportError:
from anndata import read_h5ad as _anndata_read_h5ad
from ..._registry import register_function
def _log_rust_read(path: str, size_mb: float | None, elapsed: flo... |
e73241e29a151c8ffe4d10b4047b73aead2696bc11d53327639bb686ef87fdde | Python | 5,886 | 152 | # External dependencies
import argparse
import glob
import logging
import os
from merlin.core.compat import cupy, numpy
from merlin.io import Dataset
# we can control how much memory to give tensorflow with this environment variable
# IMPORTANT: make sure you do this before you initialize TF's runtime, otherwise
# TF... |
3f734d6c232b2165a6c08fc5020702ebc8c8f2640debdef903d3663591c72022 | Python | 5,887 | 159 | import subprocess
from subprocess import Popen, PIPE
import os
import sys
import time
from typing import List
import psutil
import pynvml
import time
import copy
import signal
from urllib import request, parse
UNIT = 1024 * 1024
pynvml.nvmlInit()
stop = False
def my_handler(signum, frame):
global stop
stop = ... |
bb44686d0256661b3880fc357392be61f004312347f344f9c508e97ef36bde82 | Python | 5,889 | 157 | import unittest
import numpy as np
from neuron_morphology.morphology_builder import MorphologyBuilder
from neuron_morphology.transforms.affine_transform import (
AffineTransform, rotation_from_angle, affine_from_translation,
affine_from_transform, affine_from_transform_translation)
class TestAffine(unittest... |
d144f8a048ca4145c214319a669d55811aeb59ef6302c6738a6f22d7a6c04bdd | Python | 5,889 | 124 | import numpy as np
from scipy.optimize import linear_sum_assignment
from sklearn.metrics import matthews_corrcoef, accuracy_score, f1_score, \
precision_score, recall_score
def kuhn_munkres_algorithm(true_lab, pred_lab):
"""
Function that implements the Kuhn-Munkres algorithm method.
It selects the be... |
3b33dd54089af1a0f7a493d18e013717273936a16a80724175140b90d3477dbd | Python | 5,891 | 164 | import numpy as np
import torch
from ..base import Transform, as_range, randint, to_batched, uniform
from ..ops import fill
def neurokit_peaks(signal, fs):
"""Detect R peaks with neurokit2 (install with `pip install ecg-augmentations[peaks]`)."""
try:
import neurokit2 as nk
except ImportError as ... |
93878a7a83a18e7e8280431727ae711d5182b4b79cb641d0141b94de5e1c22cd | Python | 5,891 | 110 | import numpy as np
import sys
import os
import scipy.io as sio
import time
from scipy import sparse
sys.path.insert(1, '../SUNS2') # the path containing "suns" folder
from suns.PostProcessing.combine import piece_neurons_IOU, piece_neurons_consume
from suns.PostProcessing.evaluate import GetPerformance_Jaccard_2
# da... |
d26b60a119d3b2c0d7723a1a4a95efca2165ccc2faefac4cc654d924c446b816 | Python | 5,891 | 142 | """Thin wrapper around ``pyscdblfinder`` for omicverse's QC pipeline.
Exposes a single ``scdblfinder(adata, ...)`` function used by ``ov.pp.qc``
with ``doublets_method='scdblfinder'``. Writes two columns to
``adata.obs`` so the existing `filter_doublets` codepath (which keys off
``predicted_doublet``) works unchanged:... |
e215c6ff33f33e79f3b1fe1a5a3b9d4fad5ea3b5885dbf5a84ce99bdb5485e65 | Python | 5,891 | 147 | #!/usr/bin/env python
# import
from __future__ import print_function
## batteries
import os
import shutil
import argparse
import logging
## package
from bin import __version__
import gtdb2td
# argparse
desc = 'Convert GTDB taxonomy to input for "diamond makedb --taxonmap"'
epi = """DESCRIPTION:
Convert Genome Taxonomy... |
6c49ac3b69e7b1e7b877c9785fb34da902e59f2aee0abf0c17b27359b79a1412 | Python | 5,893 | 146 | # -*- coding: utf-8 -*-
"""Utility functions for differential phase contrast (DPC) imaging.
This module contains the utility functions for differential phase contrast (DPC) imaging. The functions include loading
illumination patterns, generating source patterns, generating transfer functions, and conventional Tikhonov... |
39f5c33dee5f270deede7ce802fcb82f66a8cf2a9e79d846486e1e782c687e5a | Python | 5,898 | 139 | import matplotlib.pyplot as plt
import pickle
import numpy as np
import os
import sys
# from Step_7_util import *
from sklearn.metrics import accuracy_score, confusion_matrix, roc_auc_score, roc_curve, precision_recall_curve
def main():
# SUBSET = 9900
# TARGETS = ["pos_MANE", "pos_ALTS", "neg_1", "neg_rando... |
7d3a95074f169ad379611bd97d57c2432a82a7f0e3bb0cca441f787af92f5775 | Python | 5,899 | 192 | """
Implementing "a complex network structure" example in https://github.com/synsense/sinabs/issues/181
"""
import torch
import torch.nn as nn
from sinabs.activation.surrogate_gradient_fn import PeriodicExponential
from sinabs.layers import IAFSqueeze, Merge, SumPool2d
class SNN(nn.Module):
def __init__(self, b... |
b347989813f8cadfdc7a3a25aa8711c478db64396bd7e8c96a230750cd6c09ec | Python | 5,899 | 141 | #!/bin/env python
import argparse
from collections import Counter
import json
import gzip
import pysam
import sys
from typing import List, Text, Optional
import numpy as np
def load_json(path):
with open(path) as f:
training_sites = json.load(f)
return {
s: {'good_variant_ids': set(training_... |
1cf446a73798b94b7d060bf648f6c8da4d1d03944d7a6a2230d9443a08e91a12 | Python | 5,902 | 127 | # Modified from https://github.com/open-mmlab/mmdetection/blob/main/mmdet/utils/setup_env.py # noqa: E501
import datetime
import logging
import os
import platform
import warnings
import cv2
import torch.multiprocessing as mp
from mmengine import DefaultScope
from mmengine.logging import print_log
from mmengine.utils ... |
6e1f9d4a6fd5a2816753bb4e8fa3e8aae53c0b157bb3dfc53cd9a77a267c87a4 | Python | 5,903 | 154 | import sys
import torch
sys.path.append("../utils")
class GAT(torch.nn.Module):
def __init__(self, node_dim, n_head, pair_dim):
super().__init__()
self.node_dim = node_dim
self.n_head = n_head
self.head_dim = node_dim // n_head
# * to alpha
self.query = torch.nn... |
d09894c4f3dc348c9326b3c7e5b7c76d656089d1433105aa654aa65477c4f1d2 | Python | 5,904 | 166 | # compare SOTA algorithms
from sklearn.naive_bayes import GaussianNB
from sklearn.ensemble import RandomForestClassifier
from sklearn.linear_model import RidgeClassifier
from sklearn.neighbors import KNeighborsClassifier
from sklearn.linear_model import LogisticRegression
from sklearn.neural_network import MLPClassifi... |
6cb4917516550272ac6004d05afe686dba85d5318841d35091361ee1a71d2e78 | Python | 5,905 | 139 | # -*- coding: utf-8 -*-
import numpy as np
import numpy.random
import keras
import csv
import keras.layers
from sak.disambiguator import select_kernel_initializer
from sak.modules import StemModule
from sak.modules import AtrousMiddleModule
from sak.modules import LevelModule
from sak.modules import PoolingModule
from... |
153a8764282f01e1c9b09cc2f38c2be2b7416d01f4b8e3b79e6ba02dffbc6fb8 | Python | 5,908 | 197 | from functools import partial
import torch
import torch.nn as nn
import torch.nn.functional as F
from torch.autograd import Variable
def conv3x3x3(in_planes, out_planes, stride=1, dilation=1):
# 3x3x3 convolution with padding
return nn.Conv3d(
in_planes,
out_planes,
kernel_size=3,
... |
dd17972a14bd1048c30266890464d0a6306098630b9d23e42ac55b4b6f63b114 | Python | 5,913 | 193 |
import numpy as np
from data_assimilation.forward_model import BaseForwardModel
from data_assimilation.model_error import BaseModelError
from data_assimilation.observation_operator import BaseObservationOperator
import pdb
import matplotlib.pyplot as plt
class ModelError(BaseModelError):
def __init__(self, params... |
d5948bfceb1799009f9283a6d037471834a098b606b8be961c4f14730dbeb267 | Python | 5,914 | 167 | # Copyright (c) 2017-present, Facebook, Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed... |
9583eb2ddfe8153c2caa7a306bda70f58413b139e549d79d9015eb6b4369abb6 | Python | 5,917 | 181 | from collections import defaultdict
from functools import lru_cache
import boto3
from boto3.exceptions import ResourceNotExistsError
from boto3.resources.base import ServiceResource
from botocore.client import BaseClient
from botocore.config import Config
from ray.autoscaler._private.cli_logger import cf, cli_logger
... |
a3daec32838e2074ac023ff2fec6d24207c751b014dad90aaecb399a9a5d0399 | Python | 5,917 | 167 | import basetest_dqn_like as base
import numpy as np
import pytest
import torch
# IQN does not support the actor-learner interface for now
# from basetest_training import _TestActorLearnerTrainingMixin
from basetest_training import _TestBatchTrainingMixin
from torch import nn
import pfrl
from pfrl.agents import iqn
fr... |
3ad0cccef5c17a0c9e61bb9d5a8be79c075634ebaedca37b3555b2ec6f041623 | Python | 5,918 | 114 | import os
import numpy as np
from permutations_stats.permutations import friedman
from scipy.stats import wilcoxon
import pandas as pd
import ivim
root = '/path/to/root'
input_root = os.path.join(root,'data')
results_root = os.path.join(root,'results')
subs = [sub for sub in os.listdir(results_root) if sub.startswith... |
81722af8e3a4e48b4d89da6d71abcf12b8bdab7d27837987118dea73d9154cdd | Python | 5,918 | 151 | import unittest
import numpy as np
from neuron_morphology.morphology import Morphology
from neuron_morphology.morphology_builder import MorphologyBuilder
from neuron_morphology.feature_extractor.data import Data
from neuron_morphology.feature_extractor.feature_extractor import FeatureExtractor
from neuron_morphology... |
844556cb1af33bbd02200ef5ee28f3cb4e6d9ad9b88e5fc13e194ef01d3a5200 | Python | 5,920 | 179 | import tempfile
import unittest
from unittest import mock
import pytest
import pfrl
class TestTrainAgent(unittest.TestCase):
def test(self):
outdir = tempfile.mkdtemp()
agent = mock.Mock()
env = mock.Mock()
# Reaches the terminal state after five actions
env.reset.side_... |
fdcdea7904da713e32e392e09638e58011897a3269b6e5024de0a75be37ce0cb | Python | 5,922 | 151 | import torch
from torch import nn
from math import sqrt
def call_reinit(m, i, o):
m.reinit()
def log_features(m, i, o):
with torch.no_grad():
if m.decay_rate == 0:
m.features = i[0]
else:
if m.features is None:
m.features = (1 - m.decay_rate) * i[0]
... |
1866b45427121d5dc99a39450583abaa8dcb2c5d6944cff10a8cfdff7d175ce4 | Python | 5,925 | 132 | import pandas as pd
import numpy as np
import matplotlib.pyplot as plt
def extract_patient_info(version, output_dir):
cols = {} # column names
cols["pd_features"] = ["PATNO", "SXMO","SXYEAR", "PDDXDT", "INFODT", "EVENT_ID"] # first symptom onset month, year, diagnosis date, SC event date
# Subject Characte... |
664d77e4fca9943e6e3ab777e8c585e3377e8d588e771362b83d1844a57a017a | Python | 5,926 | 142 | import os
import numpy as np
from scipy import ndimage
import glob
import pydicom # https://pydicom.github.io/
import dicom_numpy # https://dicom-numpy.readthedocs.io/en/latest/
import numpy as np
import nibabel as nib # https://nipy.org/nibabel/
import pandas as pd
import datetime
from config import config
from ut... |
91804bbf279ff722559eddf6bbdebcfb7d0e52b81922b1c57272495e92d60649 | Python | 5,927 | 205 | import importlib
import torch
import numpy as np
from collections import abc
from einops import rearrange
from functools import partial
import multiprocessing as mp
from threading import Thread
from queue import Queue
from inspect import isfunction
from PIL import Image, ImageDraw, ImageFont
def log_txt_as_img(wh,... |
fdf92bbb0e5250a2d2f0f220fb2a477c822c24e733645f30fac14b5ac31c2879 | Python | 5,928 | 150 | # coding=utf-8
# Copyright 2023 The HuggingFace Inc. team.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable... |
4a13e6556789805ae8753a58ff32591943441edb14d549e480fe40aa35d09df0 | Python | 5,929 | 90 | proj_dir = "/path/to/main_project_folder/" # edit this line
import numpy as np
import pandas as pd
import xarray as xr
import dask.array as da
import glob as glob
from functools import partial
import os
import sys
sys.path.append(proj_dir)
from project_fxns import load_region
from project_fxns import fxns
import impor... |
59cbcca5cb2dcc26e7b93c94e09e2632048044508fcd8b47e1f47e9c82388660 | Python | 5,929 | 155 | import numpy as np
import torch
import torchvision
import torch.nn as nn
from collections import OrderedDict
from torch.autograd import Variable
from utils.prune_utils import ConvLayerRotation, LinearLayerRotation
def print_model_param_nums(model=None):
if model == None:
model = torchvision.models.alexne... |
d14ba377060e1fa3068986b84a2410d12010569cfdc154264a614f9edc6bc31f | Python | 5,929 | 126 | import os
import numpy as np
from basicsr.data.data_util import paired_paths_from_folder, paired_paths_from_lmdb
from basicsr.data.transforms import augment, paired_random_crop
from basicsr.utils import FileClient, imfrombytes, img2tensor
from basicsr.utils.registry import DATASET_REGISTRY
from torch.utils import data ... |
7224865f105ad184641fe382f54439bee598fae79591ca8e7903c96d1d9fe87b | Python | 5,934 | 145 | import numpy as np
import struct
from spinnaker2.neuron_models.application import BaseApplication
from spinnaker2.configuration import PEConfig
from spinnaker2.neuron_models.common import (add_log_memory_region,
collect_routing_targets, format_routing_targets)
from spinnaker2.coordinates import ByteAddr, align... |
c5263ab0c89ee2628f9038ed6a87bb8352d6b2a599959f0ac185cf38343d012c | Python | 5,936 | 179 | r"""
The role of mozaik is to coordinate the workings of number of tools to provide a
consistent workflow experience for the user. Consequently the root mozaik package is very light,
and majority of functionality is in the number of subpackages each addressing different parts of the workflow.
In future the number of ... |
8a49eb8e55de63aaaf880fb60ce09b929b2de395e200e0a131b1430445df8a71 | Python | 5,937 | 174 | #%% load data and compute metrics
import seaborn as sns
import matplotlib.pyplot as plt
import pandas as pd
import numpy as np
from statannotations.Annotator import Annotator
from scipy.stats import ks_2samp
from matplotlib import rc, rcParams
from sklearn.metrics import accuracy_score, roc_auc_score, average_precision... |
e860b4b4220c00a65eaddac426c351a7a8ab5411c0767d80b35faac9bb8455db | Python | 5,939 | 149 | import csv
from typing import List, Optional, Union
import torch
from tqdm import tqdm
from GR_pKa.args import PredictArgs, TrainArgs
from GR_pKa.data import get_data, get_data_from_smiles, MoleculeDataLoader, MoleculeDataset
from GR_pKa.utils import load_args, load_checkpoint, makedirs, timeit, load_scalers, update_... |
59a7e2439625dd9db1d1e507f537b68520eb7a23c05254f4d8950294aea81f33 | Python | 5,940 | 177 | """This file is a fork from ChainerCV, an MIT-licensed project,
https://github.com/chainer/chainercv/blob/master/chainercv/utils/download.py
"""
import hashlib
import os
import posixpath
import shutil
import sys
import tempfile
import time
import urllib
import zipfile
import filelock
_models_root = os.environ.get(
... |
7b8bb1ef29dd622cb4bd1b0eb6cf6f52ae0e8f149ec4200d79bbd32b72af4393 | Python | 5,941 | 140 | import exputils as eu
import numpy as np
import rlexp.utils as utils
import torch
class DND_SF(torch.nn.Module):
"""
Implementation of a differentiable neural dictionary as introduced in
Neural Episodic Control (Pritzel et. al, 2017) with values being
successor features (SF)
"""
@staticmethod
... |
ea4bcadd707ba609f8a20da23c79874446d8357116318c416fe65d154c0b3cc2 | Python | 5,943 | 186 | # In[]
import numpy as np
import os
import numpy as np
import tensorflow as tf
import keras
from keras import backend as K
import matplotlib.pyplot as plt
import pickle
# In[]
# In[]
import os
folder= "/media/sam/internal_2/behavior/dualNet/v051122_STAGE3_deepScreen/"
folder_restrict= "/media/sam/internal_2/behavio... |
7e28747f9a437dca27ab29febd0d99253deaf99731233aabbd27b69b2f7f4bfd | Python | 5,944 | 183 | import numpy as np
from scipy.optimize import minimize_scalar
from scipy.special import gammaln
from hic3defdr.util.scaled_nb import inverse_mvr, equalize
from hic3defdr.util.binning import equal_bin
from hic3defdr.util.lowess import lowess_fit
def qcml(data, f=None, max_iter=10, tol=1e-4):
"""
Estimates the... |
41032e0552a280e9337724a8f7f5ec1fde8513bf7b403f039181b0deeb960ac9 | Python | 5,945 | 131 | import numpy as np
from sklearn.metrics import zero_one_loss
from reval.utils import kuhn_munkres_algorithm
import logging
logging.basicConfig(format='%(asctime)s, %(levelname)s %(message)s',
datefmt='%H:%M:%S',
level=logging.INFO)
class RelativeValidation:
"""
This cl... |
67dfb9ed123bf7c57e44eecf007359138ba3fe2543f16ebb999096087fde0116 | Python | 5,946 | 142 | """Thin wrapper around ``doubletfinder-py`` for omicverse's QC pipeline.
Exposes a single ``doubletfinder(adata, ...)`` function used by ``ov.pp.qc``
with ``doublets_method="doubletfinder"``. Writes two columns to
``adata.obs``:
* ``predicted_doublet`` — bool, for downstream compatibility with the
scrublet ... |
37021554416dcc01a21c22bdb946ec88379555c5e170d3f0289570596a256627 | Python | 5,947 | 148 | # -------------------------------------------------------------------------------------------------------------------------------------
# Following code curated for Bio-Diffusion (https://github.com/BioinfoMachineLearning/bio-diffusion):
# --------------------------------------------------------------------------------... |
68c9dd4c57ebdee674d3344bcdbbdd6be4ed67d5da763084d57b5f931ef3a90f | Python | 5,947 | 172 | 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
from models import *
import math, sys, random
from optparse import OptionParser
import threading
parser = OptionParser()
parser.add_option("-t", "--train", dest="train_path")
p... |
7a38ec2601aa4c59f155ed8106c6521398dc8051337f9bb6bb99c37074cbc7bc | Python | 5,947 | 150 | # 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... |
f98825678cd5f628d4dd67836370f18d8290087ecf6dc71a107f0dc9703ea0ea | Python | 5,947 | 141 | import scipy.io as sio
import os
import numpy as np
import h5py
import sys
# from skimage import filters
from scipy.ndimage import gaussian_filter
from scipy import sparse
from IoU_2 import IoU_2
import multiprocessing as mp
sys.path.insert(1, '../SUNS2') # the path containing "suns" folder
from suns.PreProcessing.pre... |
d5f5596238b745d66029887105cd4b5c52a1b3c4180caf6745aa98b15690e3fd | Python | 5,950 | 177 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
#
"""
"""
import sys
import datetime
import numpy as np
import scipy.stats as ss
import pandas as pd
import svtk.utils as svu
class PESRTest:
def __init__(self, medians=None, common=False):
self.medians = medians
self.common = common
def test(s... |
af627ef820d9df0180694016330fd7f59bf8ae85a0a3edece04d40bc6c15c520 | Python | 5,951 | 167 | import os
import pickle
import sys
import numpy as np
# with open("./spliceai_result_"+SPLICEAI_VERSION+"/"+output_file+"/d_scores_"+TYPE+".pkl", 'rb') as fw:
# pickle.dump(donor_scores, fw)
# with open("./spliceai_result_"+SPLICEAI_VERSION+"/"+output_file+"/a_scores_"+TYPE+".pkl", 'rb') as fw:
# pickle.dump(... |
ee3088099395eeaa039e862c06f7021be8c07a3d9482cfb19c8656e6f5d5c321 | Python | 5,952 | 106 | from tkinter import *
""" Specifes CLEAR'S user input parameters. CLEAR sets the input parameters as global variables
whose values are NOT changed in any other module (these are CLEAR's only global variables).
Tkinter is used to provide some checks on the user's inputs. The file
'Input Parameters for CLEAR.pdf' ... |
03c210b807722b7655f8273de96f3617ce389e9eb1170a5af5a87f476ea210b1 | Python | 5,953 | 178 | import pytest
import ray
from ray.air.execution.resources.fixed import FixedResourceManager
from ray.air.execution.resources.request import ResourceRequest
from ray.util.scheduling_strategies import PlacementGroupSchedulingStrategy
REQUEST_2_CPU = ResourceRequest([{"CPU": 2}])
REQUEST_4_CPU = ResourceRequest([{"CPU":... |
dc39aa5aea55bafd878d33475a15efb7cbfc67a09bfb31b69349b9b32dc46ab4 | Python | 5,954 | 123 | """
From https://github.com/ehoogeboom/e3_diffusion_for_molecules/
"""
import torch
import os
import src.datamodules.components.edm.build_geom_dataset as build_geom_dataset
from omegaconf import DictConfig
from functools import partial
from torch.utils.data.dataloader import DataLoader as TorchDataLoader
from torch... |
6f154d27785b13a7cb5fcbabcb3bd227442994d78f883cc977e3756e42ea7519 | Python | 5,955 | 156 | """
Compare behavioral vs. neural dprimes
"""
import os
rdir = os.path.dirname(os.path.dirname(os.path.dirname(__file__)))
import sys
sys.path.append(rdir)
from helpers.path_helpers import local_results_file
from settings import RESULTS_DIR
import scipy.stats as ss
import pandas as pd
import numpy as np
import matplot... |
78dc1f306aff461d157b4358cd473a051464cf1983189f36c92d70b0c9402806 | Python | 5,956 | 169 | # 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, ... |
6752609753abe71857e99dafb7d64556886b9f9b5e60f16549e38373c74fa894 | Python | 5,957 | 237 | #!/usr/bin/env python3
# SPDX-License-Identifier: BSD-2-Clause
# Copyright (c) 2018 Jakub Červený
def gilbert3d(width, height, depth):
"""
Generalized Hilbert ('Gilbert') space-filling curve for arbitrary-sized
3D rectangular grids. Generates discrete 3D coordinates to fill a cuboid
of size (width x h... |
9111038d1271a67236b6b7151a29af403a77828598b73d9997b26a7e28dacb56 | Python | 5,957 | 181 | # -*- encoding: utf-8 -*-
from __future__ import division, print_function
import numpy as np
from .core import algo
from . import utils
class SegModel(object):
def __init__(self, S, edgemask=None):
self.edgemask = edgemask
if edgemask is not None and np.any(edgemask):
self.score_matri... |
b2d926304f72c493e3fb94f2aec89352cc7eef53e83bc04e81b7e3c0d0015ff2 | Python | 5,958 | 157 | from neuron_morphology.validation.result import NodeValidationError as ve
from neuron_morphology.constants import *
valid_types = {SOMA, AXON, BASAL_DENDRITE, APICAL_DENDRITE}
def validate_count_node_parent(morphology, node_type, parent_type, expected_count):
""" This function validates the number of nodes that... |
c4c486c5939d0d89923316610d085184f514352804862585ca8f03626cd5c7ab | Python | 5,959 | 139 | import numpy as np
from sklearn.metrics import cohen_kappa_score
from statsmodels.stats.inter_rater import fleiss_kappa
if __name__ == "__main__":
las = ["NF", "FR", "FNR", "FRN", "FRN", "NF", "NF", "NF", "NF", "NF", "NF", "NF", "NF", "NF", "FR", "FR", "FNR", "FNR",
"NF", "NF", "FR", "NF", "NF", "FNR", "... |
3311c7faba9ead2c75fe87be85fc3679f62aed4cab3f3e3dbef794a424b7ac2b | Python | 5,960 | 189 | # 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... |
6fefabb4d0198c8002535b3feeb080b31f78dc49718bc742192bb63516fdd32c | Python | 5,962 | 112 | import argparse
import cloudpickle
import json
import os
import numpy as np
import tensorflow as tf
from experiments.utils.data_partitioning import DataPartitioning
from experiments.keras.models.fashion_mnist_fc import FashionMnistModel
from projectmetis.python.driver.driver_session import DriverSession
from projectm... |
ee9a26a42f9ce5412e6f03496a134b416d2e1ab2fa419100532bc123b45082b9 | Python | 5,963 | 183 | #
# 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... |
dff7acdc364493838a16624fd4fb8e826a01c815e2decfea4be03156660efcc3 | Python | 5,964 | 173 | import matplotlib.pyplot as plt
from matplotlib.animation import FuncAnimation, PillowWriter
import numpy as np
def get_init_theta():
return np.array([0.9, 0.9])
def Q_batch(theta):
"""Returns the true function value for a batch of parameters with size (B, 2)"""
return 1.2 - (3 / 4 * theta[:, 0] ** 2 + ... |
b9866cadb1c94e5229e007fb12d3b132c5ac7124a77bbfa433d488acab27e017 | Python | 5,968 | 178 | '''
Averages runs with the same stimulation protocol to boost SNR.
'''
import os
import glob
import nibabel as nb
import numpy as np
import sys
sys.path.append('./code/misc')
from computeT1w import *
DATADIR = '/Users/sebastiandresbach/data/neurovascularCouplingVASO/Nifti'
SUBS = ['sub-07']
SESSIONS = ['ses-01',... |
dca1414753af9b571d1bf21951e532be9afb3b8e8bd7cb2f87f9fefefd59fe57 | Python | 5,973 | 220 | hier_struct = {
"exercising": {
"performing_cardio_exercises": [
"jump_rope",
"perform_jumping_jacks",
"do_stair_steps"
],
"performing_resistance_exercises": [
"bicep_curls",
"shoulder_press",
"push_ups",
"si... |
2f5d187fc111ce541659a1d42477e3ba252c72a2749db8a4d8e020f7c25ea687 | Python | 5,974 | 201 |
import numpy as np
from data_assimilation.numpy.forward_model import BaseForwardModel
from data_assimilation.numpy.model_error import BaseModelError
from data_assimilation.numpy.observation_operator import BaseObservationOperator
import pdb
import matplotlib.pyplot as plt
class ModelError(BaseModelError):
def __i... |
102f3166868fd834b2009c81389b2cd4b578710e543d4a201214a02b82e75260 | Python | 5,976 | 151 | import torch
import torch.nn as nn
import torch.nn.functional as F
from torch.nn.utils import spectral_norm
from torch.optim import Adam
import math
import numpy as np
from utils import *
from lookahead import Lookahead
class ProteinInteractionNet(nn.Module):
def __init__(self, protein_dim, hid_dim, dropout, g... |
3575074272c61d09c11b2e369d4af6df517dce782f2774415caaa1f3fe98de1d | Python | 5,981 | 137 | import tensorflow as tf
import pandas as pd
import matplotlib.pyplot as plt
from sklearn.metrics import precision_recall_curve, average_precision_score, auc
import numpy as np
def main():
spliceai_versions = ['1', '2', '3', '4', '5']
spliceai_input_dir = '/ccb/cybertron/khchao/splam-analysis-results/train/resu... |
249606d61dd4c052e04ece62b14e810722e1bf7dec682480c0ea473ca6ff1302 | Python | 5,982 | 208 | # -*- coding: utf-8 -*-
# (C) Copyright 2020, 2021, 2022, 2023, 2024 IBM. All Rights Reserved.
#
# This code is licensed under the Apache License, Version 2.0. You may
# obtain a copy of this license in the LICENSE.txt file in the root directory
# of this source tree or at http://www.apache.org/licenses/LICENSE-2.0.
#... |
42888693f458106c7a1ff84fdddd06af367583bc730f06c952f9feadd1cd0150 | Python | 5,984 | 124 | ####################################################################################################
# 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... |
4b2c9476caaa52d9116bdee87e7e510f0049bf8df12ea8e2167a3c66fe0bcc7f | Python | 5,984 | 189 | from typing import Any, Dict, List
from data_profiling.config import Settings
from data_profiling.report.formatters import fmt, fmt_bytesize, fmt_percent
from data_profiling.report.presentation.core import (
Container,
FrequencyTable,
Image,
Table,
)
from data_profiling.report.presentation.core.variabl... |
7ce1b8334a490911eb04f4fb79d3dc007ecbdfc5d09dad32da7e7af8b80b8722 | Python | 5,986 | 129 | import numpy as np
import argparse
import pickle
from typing import List
from lib.data_utils.dynamic_data_util import JitteredMovieBatchDataloader
from lib.dataset_config_parser.dataset_config_parser import read_config_file
import lib.dataset_config_parser.dataset_config_parser as dcp
import lib.data_utils.dynamic_da... |
82a8262990b463e08f403956928b498652948e75f6722345b395a538be4b1377 | Python | 5,986 | 184 | '''
Home page w/ interactive TWAS table.
Nhung, Jan 2024
'''
import numpy as np
import pandas as pd
import os
import dash
from dash import Dash, callback, Input, Output
from dash import html, dcc
from dash import dash_table
import dash_bootstrap_components as dbc
################################################... |
2bf92fdf1a2cf9bd4f95bb64a8d7c17e8e258e290360009f52bead4703433311 | Python | 5,990 | 193 | from utils.grid_funcs import (
gridpop_clustering,
gridpop_repsupp,
gridpop_conj,
gen_offsets,
traj_star,
traj_star_delay
)
from utils.utils import get_hexsym, get_pathsym, convert_to_rhombus
import numpy as np
import pickle
import os
import settings
data = {
"path": {},
"conj": {},
... |
58af6b7c9187e4edd6d9dc5454f37190be558dadd3f7fd071b8f6bb8e38512a8 | Python | 5,991 | 165 | import numpy as np
import tensorflow as tf
# from official.common import flags as tfm_flags
from official.vision.beta.projects.movinet.modeling import movinet, movinet_model
learning_rate = 0.0001
hidden_units = 256
dropout_rate = 0.5
temperature = 0.05
class DDGenerator:
def __init__(self, input_dd, output_dd,... |
064fdbdd7ed01c8cda1db59826fbb386974fc1d79324f129f3244756d512b135 | Python | 5,993 | 149 | import os
import re
import subprocess
import sys
from pathlib import Path
from setuptools import Extension, setup
from setuptools.command.build_ext import build_ext
VERSION = "1.0.10"
# Convert distutils Windows platform specifiers to CMake -A arguments
PLAT_TO_CMAKE = {
"win32": "Win32",
"win-amd64": "x64",... |
1c584cda9da33e22b48c5137613a28c6fccb0db7e500cc38f90ee395d4756bbc | Python | 5,993 | 148 | 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_list as _s2g
from models import *
from ioutils import *
import math, sys, random
from collections import Counter
from optparse import OptionParser
from functools import partial
... |
980d0ae98c66007c038a30e44e89882aba311bd34b05560a021503c6bb6347b8 | Python | 5,994 | 195 | # built-in dependencies
from typing import List, Optional, Union, cast
# 3rd party dependencies
import torch
from torch import nn, Tensor
# project dependencies
from deepface.commons import weight_utils
from deepface.models.facial_recognition.pytorch.TorchFacialRecognition import (
TorchFacialRecognition,
loa... |
9df4b7df48633dfc11651c79b3a9a29c8eb916d0ea84a1007502edb4d6b6de5f | Python | 5,995 | 169 | # built-in dependencies
from typing import List, Union, cast, Any
# 3rd party dependencies
from numpy.typing import NDArray
# project dependencies
from deepface.commons import package_utils, weight_utils
from deepface.modules import verification
from deepface.models.FacialRecognition import FacialRecognition
from dee... |
7e05d7cc0669c427d48fd0a37ee63465b75111fefd7db5bd31ebd32aed0f55ca | Python | 5,997 | 191 | import numpy as np
import matplotlib.pyplot as plt
import torch.nn as nn
import torch.optim as optim
import torch
import pdb
from torch.nn.utils import spectral_norm
import time
import math
import torch.nn.functional as F
class PositionalEmbedding(nn.Module):
def __init__(self, embed_dim, max_len=1000):
... |
20a1c7dc7dee167103d998d63f976a6d9fa3ce13240c4522689a1279b1a47016 | Python | 5,998 | 231 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Wed Nov 1 16:29:42 2023
@author: Saad Idrees idrees.sa@gmail.com
jZ Lab, York University
"""
# %% primate cones
def fr_cones_fixed():
pr_params = {}
pr_params['sigma'] = 2.2
pr_params['sigma_scaleFac'] = 10.
pr_params['sigma_train... |
969bc41206cef481545cb3012405caa0293e29dcb92e440d06b85b69991217b4 | Python | 5,998 | 153 | import numpy as np
import scipy
import time
import warnings
warnings.filterwarnings('ignore')
import pandas as pd
import numpy as np
import pickle
import os
import argparse
from glmsingle.glmsingle import GLM_single
import nibabel as nib
#compute glm using glmsingle
# https://github.com/cvnlab/GLMsingle
def interpola... |
8e4674d26645c1665cd1ee945a20126f2d7aec91c93396cd30f3cd1fbf6ab39f | Python | 5,999 | 131 | import matplotlib.pyplot as plt
import numpy as np
import os
import numpy as np
import statsmodels.api as sm
import matplotlib.pyplot as plt
import json
import ivim
root = '/path/to/root'
input_root = os.path.join(root,'data')
results_root = os.path.join(root,'results')
subs = [sub for sub in os.listdir(results_root... |
23f41999a48c7e76aa875bede183fefb3012f0c7d5ed075a673f4699f077c72c | Python | 6,000 | 143 | import numpy as np
from matplotlib import pyplot as plt
import os
import shutil
from tqdm import tqdm
import argparse
import time
def str2bool(v):
if isinstance(v, bool):
return v
if v.lower() in ('yes', 'true', 't', 'y', '1'):
return True
elif v.lower() in ('no', 'false', 'f', 'n', '0'):
... |
f3703a482ee212505e946001f55f6025c4268f02813f24d7ee925ed45b907cc0 | Python | 6,001 | 116 | __author__ = "Simon Andermatt"
__copyright__ = "Copyright (C) 2017 Simon Andermatt"
import logging
from copy import deepcopy
from mdgru.helper import compile_arguments, generate_defaults_info
from mdgru.model_pytorch.crnn import CRNNCell
import torch as th
from torch.nn.parameter import Parameter
from torch.nn import ... |
c198c316d9e08430873176ad9e81a3246f91189acacfad234969592443fbc081 | Python | 6,003 | 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_list as _s2g
from models import *
from ioutils import *
import math, sys, random
from collections import Counter
from optparse import OptionParser
from functools import partial
... |
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