sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
c2738b45027e90e5f7e38a55fae4187456f50c611969a21107cb9e73db6c3bab | Python | 11,840 | 336 | # _*_ encoding: utf-8 _*_
__author__ = 'wjk'
__date__ = '2020/6/30 10:32'
import math
import numpy as np
import torch
import torch.nn as nn
# from einops import rearrange
import torch.nn.functional as F
from .model_Transformer import GPTDecoderLayer, GPTDecoder
from MCMG_utils.utils import Variable
device = torch.... |
a73e72ac4c1deea67230abb64abe8b2b872c4d2808cb226e236c1325104f89c1 | Python | 11,842 | 341 | import numpy as np
#import curves
from base.curves import Curve, remesh
from base import loggingUtils
from base.kernelFunctions import Kernel
from base.curveMatching import CurveMatchingParam, CurveMatching
import matplotlib
matplotlib.use("qt5agg")
import matplotlib.pyplot as plt
def compute(model='default', dirOut=... |
435adc1f1f760aaa86a73344280c9b193f1038843ff390c3938fc62dfbf5f5f7 | Python | 11,843 | 334 | import numpy as np
import logging
from . import conjugateGradient as cg
from . import bfgs
from .gridscalars import GridScalars, saveImage
from .diffeo import multilinInterp, multilinInterpGradient, multilinInterpGradientVectorField, jacobianDeterminant, \
multilinInterpDual, imageGradient, idMesh, multilinInterpVe... |
5cdac59af8d65c0f07fe89205ee905024471f14507aa2329091adfeb735f65a0 | Python | 11,847 | 288 | '''
Created on Mar 30, 2012
@author: regger
'''
import numpy as np
#import reader
#import writer
#import cell_parser
class SynapseMapper(object):
'''
SynapseMapper assigns synapses to neuron morphology
self.cell is neuron SpatialGraph
self.synDist is average synapse distribution (3D scalar field)
... |
5547830c171a4bfe22a040b1e382987ce617b864b91e5ede785e937d10f180e6 | Python | 11,865 | 274 | # Copyright 2026 Xanadu Quantum Technologies 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 agre... |
e6dc55762bf854f0c111b7d56fc8b5467dd422d89f14a3755962fd03e3e43fd0 | Python | 11,866 | 302 | # load_trackmate.py
from initialization.initialization import *
from initialization.config import *
from data_processing.cleaning_formatting_filtering import *
from data_processing.migration_calculations import *
import re
import tqdm
import pandas as pd
import numpy as np
# Thanks to Guillaume Jacquemet for the follo... |
ba1f161b7ff080dcef94bcd234f3dd1fc5a3ff2728900ff1c5eb3d2bc620894b | Python | 11,869 | 265 | import os
from unittest import TestCase, mock
import dynast.align as align
import dynast.config as config
import dynast.utils as utils
from tests import mixins
class TestAlign(mixins.TestMixin, TestCase):
def test_STAR_solo(self):
with mock.patch('dynast.align.utils.get_STAR_binary_path', return_value='... |
c317238fb530a657781d2a1f972569555ba3eb16347c07e8d7f17125cc34599f | Python | 11,872 | 287 | #!/usr/bin/env python
__author__ = 'etseng@pacb.com'
"""
Should be used *after* summarize_sample_GFF_junctions.py is called to generate junction report.
Looks through the junction reports and scrub it, retaining only junctions that
meet one or more of the following criteria:
(a). be the only junction in that "label... |
5a096214cdaee43e2a12fa578efb953b91ea6b5eafd78058fd4a725dfc08fabd | Python | 11,873 | 319 | import datetime
import dateutil
import numpy as np
import pytest
from pandas.errors import Pandas4Warning
import pandas as pd
import pandas._testing as tm
class TestDataFrameMissingData:
@pytest.mark.filterwarnings("ignore:The inplace keyword in DataFrame.dropna")
def test_dropEmptyRows(self, float_frame):... |
b1a9cda8ff84639ee5ee43a86f5ce6db9a956d194643dd1ea2355c90d8a71284 | Python | 11,876 | 334 | # Copyright 2025 Xanadu Quantum Technologies 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 agre... |
6f3b7575d212669df348e16a17cbd75a223f95e772cea8e284afe84ecab74098 | Python | 11,877 | 329 | from models.model import input_dim, output_dim
import numpy as np
import os
import time
import cv2
import sys
from PIL import Image
from inference.segment_brain_gauss import loss_inference
import csv
import json
import re
from utilities.utilities import *
# Will need to be adjusted depending on the GPU
batch_size = 1... |
83beb608864b7c78c04f24713b3a8de98453f594beac78e941d119ca4c01c2da | Python | 11,882 | 309 | r"""
Angular math utils that contain calculations of angles.
"""
__all__ = ['RotationRepresentation', 'to_rotation_matrix', 'radian_to_degree', 'degree_to_radian', 'normalize_angle',
'angle_difference', 'angle_between', 'svd_rotate', 'generate_random_rotation_matrix',
'axis_angle_to_r... |
ce0328ab27be20e5a719f2baed7c545c252e875534a066b9d7a11e0223706a78 | Python | 11,884 | 339 | """This script runs the first-level GLM-Spectra and prepares the group data.
The script can be set to preprocess just the single example subject by changing
'subj' in the main body.
If the group-level data collation is run, then all glm-spectrum datasets found
in the output dir are collated.
"""
import glob
import ... |
d44944d331e6b998b918ee82bb5555fb16236d2e9e93f8dfad8e5650a0a3d29f | Python | 11,884 | 331 | from __future__ import annotations
import math
from collections import defaultdict, deque
from dataclasses import dataclass, field
from pathlib import Path
from typing import Dict, FrozenSet, List, Optional, Set, Tuple
@dataclass
class Node:
label: Optional[str] = None
length: Optional[float] = None
chil... |
656f0c6ebc1b3d0a8807cd58d97f8b90487f190736d8d814dcf7dbc78bdc04f1 | Python | 11,885 | 324 | import numpy as np
import pytest
from pandas._libs.tslibs import (
iNaT,
is_supported_dtype,
)
from pandas._libs.tslibs.dtypes import NpyDatetimeUnit
from pandas._libs.tslibs.np_datetime import (
OutOfBoundsDatetime,
OutOfBoundsTimedelta,
add_overflowsafe,
astype_overflowsafe,
is_unitless,
... |
093cd672a1c84b5a659a1b5e67ac337de50a85316dc1dcf22807b91e62f92f15 | Python | 11,887 | 299 | """
Tests for the following offsets:
- BQuarterBegin
- BQuarterEnd
"""
from __future__ import annotations
from datetime import datetime
import pytest
from pandas.tests.tseries.offsets.common import (
assert_is_on_offset,
assert_offset_equal,
)
from pandas.tseries.offsets import (
BQuarterBegin,
BQu... |
4775988dfaeb7aad5960d9209458fc2da12a5ea9e2f74642cb1b5c284198b137 | Python | 11,893 | 289 | #!/usr/bin/env python
# -*- coding: UTF-8 -*-
"""
Step S1p: Merge closely related bins within the same assembly group.
This module analyses paired-end connection files, depth matrices, and
CheckM statistics to identify candidate bin pairs that likely belong
to the same genome, and records them for downstream merging.... |
10bd0c98e406e577640592c8ff6a6a045ec52b5e5a077dc313f53c853910b281 | Python | 11,897 | 379 | # -*- coding: utf-8 -*-
"""
Created on Tue Mar 14 15:29:22 2023
@author: jeanbaptiste
"""
import json
import numpy as np
import matplotlib
import matplotlib.pyplot as plt
from scipy.spatial import distance
import tensorflow as tf
import tensorflow.keras
from tqdm import tqdm
import deepcellcontrol as dcc
matplotli... |
62296a64271a3edc65d71806193c3a585c2d00c2a8d16420f890117c1a994ffe | Python | 11,915 | 406 | """
test cython .agg behavior
"""
import numpy as np
import pytest
from pandas.errors import Pandas4Warning
from pandas.core.dtypes.common import (
is_float_dtype,
is_integer_dtype,
)
import pandas as pd
import pandas._testing as tm
@pytest.mark.parametrize(
"op_name",
[
"count",
"... |
52a6ced74ee5803e940b47fa52301ee4e2d0ad9dc3f23ff2a27e2554828fc5a0 | Python | 11,920 | 428 | # -*- coding: utf-8 -*-
# @File name: plot_firing_rate.py
# @Author: Alicia Garrido-Peña
# @Date: 2023-08-10 21:29:51
# @Contact: alicia.garrido@uam.es
# "Copyright (c) 2023 Alicia Garrido-Peña. All Rights Reserved."
# Use of this source code is govern by GPL-3.0 license that
# can be found in the LICENSE file
# C... |
4420781ee54ac99b0777641a76eb661a3e0c4e0dd5d6cdb127bcb73b65c4888e | Python | 11,924 | 375 | import numpy as np
import pytest
from pandas.errors import UnsortedIndexError
import pandas as pd
import pandas._testing as tm
from pandas.core.indexes.frozen import FrozenList
def test_sortlevel(idx):
tuples = list(idx)
np.random.default_rng(2).shuffle(tuples)
index = pd.MultiIndex.from_tuples(tuples)... |
7157a21f05567fcef20569f4d9fcaba727ece3e921763d5c66d00c62e19b1648 | Python | 11,929 | 286 | from __future__ import annotations
from os import PathLike
from typing import TYPE_CHECKING
import numpy as np
import pandas as pd
import xarray as xr
from pcntoolkit.math_functions.velocity import (
compute_thriveline_y,
compute_thriveline_z,
thrivelines_to_dataframe,
)
from .correlation_matrix import ... |
d404db92dabcb00861d88d4c3463e7e2f3ab420be0a43f10b3967a20eab3f019 | Python | 11,935 | 265 | import scipy as sp
import scipy.io
import os
import numpy as np
import pandas as pd
import glob
import csv
import random as rand
from tqdm import tnrange, tqdm_notebook
from collections import Iterable
import matplotlib.pylab as mpl
import random as rand
from ipywidgets import *
import colorlover as cl
from scipy impor... |
45e76a412340b1925556fc642713d962a393faf0a30331718ba0d4e7d83ae583 | Python | 11,953 | 328 | """
Copyright (c) Facebook, Inc. and its affiliates.
This source code is licensed under the MIT license found in the
LICENSE file in the root directory of this source tree.
"""
import math
import torch
from torch_geometric.nn import SchNet
from torch_geometric.nn.models.schnet import GaussianSmearing, InteractionBlo... |
6cc18934c1c3102b38596cc3e2f529866b194c2bf4a8362e96db5c7e3e14b409 | Python | 11,955 | 199 | from botocore.client import Config
import ibm_boto3
from io import StringIO
import os
import pandas as pd
import sys
import json
sys.path.append(os.path.dirname(os.path.dirname(os.path.abspath(__file__))))
sys.path.append(os.path.abspath(os.path.join(os.path.dirname(__file__), "..", "..")))
from config.globals import E... |
35e4905e76811f186d0c8e0911b94754d6fbd9547d6c21a83b1ed9862e693812 | Python | 11,959 | 329 | # Copyright 2024 Xanadu Quantum Technologies 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 agre... |
b4d7a1c0547a65ec6914f3b0a16f7f32a6edeb12b691ac70f972cdd260310033 | Python | 11,961 | 318 | import pandas as pd
import graph_tool.all as gt
import numpy as np
import matplotlib as mpl
import matplotlib.cm as cm
from matplotlib.colors import LinearSegmentedColormap
from tqdm import tqdm
class Network(object):
def __init__(self,
input_dotfile,
cmap=cm.Spectral_r,
... |
d87bd9d70e6b4860cdd4bc02ccc0a5f6878b20b5adb3b4512e02613743c28d76 | Python | 11,962 | 171 | import sys
import os
import argparse
from spit.transform_tx_counts_to_ifs import main as transform_counts
from spit.filter_and_transform_tx_counts import main as filter_counts
from spit.spit_test import main as spit_test
from spit.get_p_cutoff import main as get_p
from spit.dtu_detection import main as detect_dtu
from ... |
fb322bbc3dcb2eecba22d222f09b4033cc92069430b92a7a64f3dd69fab6e0d5 | Python | 11,972 | 313 | __all__ = ["StrucGPReportParser"]
import os
import re
from typing import Iterable, Union
import pandas as pd
from ..filter import GlycoPeptideSpectrumFilter
from .annotation import GlycoPeptideMS2SpectrumAnnotator
from ....chem.gpep.glycans import GlycanNode
from ....chem.gpep.gpmass import GlycoPeptideMassCalcula... |
f6b6b541a245a17cd6ed33b11d07a1e13442ed0c3ebbbf71e4a587ddc6c02dde | Python | 11,977 | 286 | # %% [markdown]
# # Accelerated proximal gradient descent (FISTA) reconstruction using wavelets and $\ell_1$-norm minimization
# %% [markdown]
# ### Image reconstruction
# Here, we use a proximal gradient descent algorithm to reconstruct an image
# from 2D radial k-space data with wavelet regularization.
# In particul... |
079acf7389b7a5ef7f2ed489c6a164dc8aa578e544123b8a5bf62d80baa54354 | Python | 11,980 | 286 | """Models that produce heatmaps of keypoints from images."""
from typing import Any, Literal
import torch
from jaxtyping import Float
from omegaconf import DictConfig, ListConfig
from lightning_pose.data.bboxes import model_to_frame_batch
from lightning_pose.data.datatypes import (
HeatmapLabeledBatchDict,
M... |
ab1822a984e6ae61751f3c404919c842c4f4484cb7dfacf104e705c40c75057f | Python | 11,981 | 349 | # Copyright 2018-2024 Xanadu Quantum Technologies 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... |
6fcd4a02fb0c2b0f18db1bcc9cce83593d3ed4e202afe20404a9f19bf8fa9af4 | Python | 12,008 | 322 | '''
Configuration file.
Fill out this file then run the jupyter notebook to analyze your data
'''
'''
Experiment-specific constants to be filled by user
'''
#
DATA_PATH = 'D:/HERNANDEZ/CSV_files'# Input the path to the folder containing the data
OUTPUT_PATH = 'D:/HERNANDEZ/output' # Input the path to the folder wher... |
4ba7f88b8b31aff78fe5985f47ac5b779f63365ca92e4ced4b2c1643c56dc974 | Python | 12,015 | 389 | # Copyright 2018-2023 Xanadu Quantum Technologies 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... |
a27c64074d44735ae6fe54537e7776506afc0dbe0dbc5d460b2e4d19cacaae74 | Python | 12,021 | 152 | """Clean publication graphics: panel letters only, explanatory text in captions."""
from figure_style import *
TOTAL='Midlands Province';YEAR=2022
from matplotlib.lines import Line2D
prov=annual[annual.area==TOTAL].sort_values('year')
unit_names=[n for n in bounds]
latest=annual[(annual.year==YEAR)&(annual.area!=TOTAL)... |
ad551a409a36c85aa7f99b3b280866f832d0630752741e8196c9b7be8c704c15 | Python | 12,029 | 372 | from __future__ import annotations
from collections import defaultdict
import datetime
import json
from typing import (
TYPE_CHECKING,
Any,
overload,
)
from pandas.io.excel._base import ExcelWriter
from pandas.io.excel._util import (
combine_kwargs,
validate_freeze_panes,
)
if TYPE_CHECKING:
... |
8211f26987a0df5df8f83d30fb06060337d0ab29b0e4358bcd579a10bd6c2a17 | Python | 12,034 | 328 | # --------------------------------------------------------
# Based on BEiT, timm, DINO and DeiT code bases
# https://github.com/microsoft/unilm/tree/master/beit
# https://github.com/rwightman/pytorch-image-models/tree/master/timm
# https://github.com/facebookresearch/deit
# https://github.com/facebookresearch/dino
# --... |
6f0793ef57f62d25c8dba51d27c726ad30804d4776466eabca383fc6cc5df655 | Python | 12,039 | 207 | #! /usr/bin/env python
import argparse
import os
import sys
from time import strftime
import pysam
from hashed_read_genome_array import HashedReadBAMGenomeArray, ReadKeyMapFactory, read_length_nmis #, get_hashed_counts
from plastid.genomics.roitools import SegmentChain, positionlist_to_segments
import multiprocessing... |
9126a2cd45af7fa79a15a06126ce94f61868be2d810a326b705a79075e751490 | Python | 12,042 | 256 | """
Trainer for inducing predicate vectors and cued association transition model
Some code is adapted from the DGL implementation of RGCN link prediction:
https://github.com/dmlc/dgl/tree/master/examples/pytorch/rgcn
"""
import sys, configparser, torch, utils
import numpy as np
import torch.nn as nn
import to... |
bf3f2a48606c47224423ea40e5d5752e49724f653bffefc7a8e2bc23247dfbab | Python | 12,047 | 354 | try:
if INIT:
print("Initialized.")
except:
from pyNN.nest import *
from pyNN.random import RandomDistribution
import matplotlib.pyplot as plt
import numpy as np
from scipy.signal import find_peaks
import pickle
import pandas as pd
INIT=True
def OUProcess(tau,tstop,dt):
rng = ... |
0781d5256543b4468150bad44b1d9f27f04451702bef98158f4a915fb12ca441 | Python | 12,048 | 281 | """Regression tests for the release-preparation correctness fixes: the
central value normalizer prior (default from the CV's own geometry; explicit
count from central_value_config, else the top-level key), the player's vecenv
fallback for creator-less registrations, and discrete PPO honoring
multi_gpu_scheduler_kl: 'lo... |
dc0557443f41cb1e4213b5f4175c70798a2489c6dd186071be896e349915fc99 | Python | 12,050 | 309 | r"""
Spatial math utils that combine linear and angular calculations for rigid bodies.
Also contains utils for articulated body kinematics.
"""
__all__ = ['transformation_matrix_np', 'adjoint_transformation_matrix_np', 'transformation_matrix',
'decode_transformation_matrix', 'inverse_transformation... |
a9dc51cf4e51dcad0c021b7031a29d0621643cc8dc8b7901011ad3ddfc94c097 | Python | 12,054 | 332 | from typing import Any
import pytest
import torch
from mrpro.operators import EinsumOp, LinearOperator, MagnitudeOp
from mrpro.operators.LinearOperatorMatrix import LinearOperatorMatrix
from mrpro.utils import RandomGenerator
from tests import dotproduct_adjointness_test
def random_linearop(size, rng):
"""Creat... |
84a62dc760711dccbbeb69eaff2b5e59fab98c750c8b8ecac2e43ba185f2b1b5 | Python | 12,058 | 295 | #-----------------------------------------------------------------------------
# Bridging Water Features
#-----------------------------------------------------------------------------
import os
import sys
import numpy as np
from DXGB.get_pdbinfo import *
#get the structural information of water molecules and get the ... |
e112ec67466f88cdd27b1bc8989a0865fc40d4bc0b01779434510155400c428f | Python | 12,063 | 274 | # -*- coding: utf-8 -*-
import torch
#from sdna.net.core.channel import MarkovModelKL
def train(model, optimizer, args, epoch=1, mode="encoder", warmup=False):
"""
Trains the model depending on the mode and optimizer.
:param model: The entire model or rather the network.
:param optimizer: The optimi... |
5ae1e6b60505c2c04f5dbe23af2a8a9435f8c08cdeaaa5f1d166ef9f6f2ecef1 | Python | 12,069 | 275 | # Copyright 2019 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
#
# http://w... |
6ede35f48747eb8cb31df1bd6315485bfaa6033029ae79adee81c5eafb9c19ed | Python | 12,069 | 337 | import numpy as np
import pytest
import pandas as pd
import pandas._testing as tm
class TestDataFrameNonuniqueIndexes:
def test_setattr_columns_vs_construct_with_columns(self):
# assignment
# GH 3687
arr = np.random.default_rng(2).standard_normal((3, 2))
idx = list(range(2))
... |
97d19c6d122ee6703b5dac0770f7dbbf617b4f76797bc04f7bf6f21232b7622d | Python | 12,071 | 319 | # Copyright 2016 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... |
b8a062e20fa56a19e7b45df17934706732034a89a5c53164ac66cad65ac985fc | Python | 12,074 | 326 | # Copyright 2025 Xanadu Quantum Technologies 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 agre... |
9bd79b22952de5212ea5e97015773ab48cfe3a185fa114c5ef4b2598f908aa24 | Python | 12,079 | 272 | # Copyright 2025 Xanadu Quantum Technologies 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 agre... |
e31a8b644f76dbd059aa4d1f3c82b0798532978a4c954ffd603a7e5c5590177c | Python | 12,081 | 388 | import numpy as np
import pytest
from pandas.errors import (
DataError,
Pandas4Warning,
SpecificationError,
)
import pandas as pd
import pandas._testing as tm
def test_getitem(step):
frame = pd.DataFrame(np.random.default_rng(2).standard_normal((5, 5)))
r = frame.rolling(window=5, step=step)
... |
13b4c0ef00ef23a02cfb278d784090e2b5961d2adcda41f8e323d71c01bd265a | Python | 12,087 | 337 | """
This file contains a minimal set of tests for compliance with the extension
array interface test suite, and should contain no other tests.
The test suite for the full functionality of the array is located in
`pandas/tests/arrays/`.
The tests in this file are inherited from the BaseExtensionTests, and only
minimal ... |
a598c28b9aa506cd1475f33457fb7756580a3a47b5e11d8debb6cf9cf9e8e6e8 | Python | 12,088 | 348 | import torch
import numpy
import matplotlib.pyplot as plt
import bionetwork
import plotting
import pandas
from scipy.stats import pearsonr
import seaborn as sns
from scipy.stats import mannwhitneyu
import copy
def loadModel(refModel, fileName):
#work around to copy weights and bias values
#because class struc... |
e39da4bcd1f35f382ea0044e2b5f97df234cf42306ae96a9745df406929a774e | Python | 12,088 | 325 | import os
import urllib.request
from collections import Counter, deque
from typing import List
import numpy as np
import onnxruntime as ort
import SimpleITK as sitk
import torch
from .utils import clip_and_rescale_sitk_image, crop_cube, resample_sitk_image
model_urls = {
"RLLandmarkLocalizer": "https://www.resea... |
856f6a893143d6f9c55baf41be47cfcaba0d527e97c582921d37b26784a64cd1 | Python | 12,092 | 330 | import os
import numpy as np
import nrrd
from torch.utils.data import Dataset
from pathlib import Path
import torch
import torch.nn.functional as F
from torchvision import transforms
# Images should be stored with the following file structure. This is after
# they are processed with functions in preprocessing.py
# .
... |
1fa0f09cd259b6af14bd07713befa997d289285cbd093e1ef8329a2cf6187ba3 | Python | 12,098 | 374 | # -*- coding: utf-8 -*-
#
# project-template documentation build configuration file, created by
# sphinx-quickstart on Mon Jan 18 14:44:12 2016.
#
# This file is execfile()d with the current directory set to its
# containing dir.
#
# Note that not all possible configuration values are present in this
# autogenerated fi... |
b9947d14cf9e74dc31eb79f8596e19f27a0c793b8818cd1ac2f4a4f0cf078267 | Python | 12,106 | 323 | import figure_Tbasis as fb
import targeted_basis as tb
import numpy as np
import scipy
import matplotlib.pyplot as plt
import matplotlib.gridspec as gridspec
from figure_properties import *
import os
from sklearn import preprocessing
from kcsd import oKCSD1D
def calculate_eigensources(obj):
try:
e... |
b494aaace6ff80a72edad9c7aa60e865537ec9de91d31eb69fadc9df8007de2b | Python | 12,107 | 275 | """Bounded subprocess driver for compiled public chromosome scheduling calls."""
from concurrent.futures import Future
import faulthandler
import json
import logging
from pathlib import Path
import sys
import numpy as np
import MACS3.Signal.CallPeakUnit as unit
import MACS3.Signal.CallerExecution as execution
from MA... |
eb633f029153e272fad304e80df4d1f058f5062b00a50f9ebfa93c88fc5ca7a1 | Python | 12,107 | 363 | import re
import numpy as np
import pytest
import pandas as pd
import pandas._testing as tm
from pandas.tests.plotting.common import (
_check_axes_shape,
_check_plot_works,
get_x_axis,
get_y_axis,
)
pytest.importorskip("matplotlib")
@pytest.fixture
def hist_df():
df = pd.DataFrame(
np.r... |
a65b254099e4ee21f3fb0c1cb7e93b3e4acb22f9cdec5695e12544bb6a5cdbbc | Python | 12,111 | 330 | ''' backcheck_aws.py
This program will backcheck AWS S3 contents to neuronbridge.neuronMetadata
'''
import argparse
from operator import attrgetter
import sys
from types import SimpleNamespace
import boto3
import MySQLdb
from tqdm import tqdm
import jrc_common.jrc_common as JRC
import neuronbridge_lib as NB
# pyl... |
a8a90bfc42a1e3dc2f1ff1fe48851e29bea711952f0c8c3a65b51d2282edca0a | Python | 12,131 | 313 | # Copyright 2018-2021 Xanadu Quantum Technologies 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... |
cb5567b3fc22dfb89ada6b38d80fa6178f3add4099c51b79f6ca68ec2d8447c6 | Python | 12,140 | 280 | # Copyright 2018-2021 Xanadu Quantum Technologies 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... |
7ee5bef5be9f99def4e6ecd59e8960e87bf18e75950471609da0df2b2f623a64 | Python | 12,145 | 299 | # -------------------------------------------------------------------------------------------------------------------------------------
# Following code curated for GCPNet (https://github.com/BioinfoMachineLearning/GCPNet):
# ----------------------------------------------------------------------------------------------... |
d344a48624336ba8703c90344fc2f63c021ae3edc489a34bf8f44e477154486c | Python | 12,152 | 408 | import numpy as np
from itertools import combinations
from scipy.special import binom
from indices.indices_info import Indices
def _file_name_gen(key):
"""Generate the name of the file containing a given index.
Arguments
---------
key : str
Key of the Indices dict that corresponds to a given ... |
ba75cbfc439ec6e4f3d3beed8e3b414157bbfad7bbc2bf073b32b58571a961c5 | Python | 12,162 | 377 | '''
Created on Nov 3, 2012
@author: regger
'''
import numpy as np
from model_data_base.mdbopen import mdbopen
def vm_mean(vVec, tVec, tStim, dtStim):
'''
computes mean subthreshold voltage from
voltage trace during stimulation time window
[tStim, tStim+dtStim]
'''
t = np.array(tVec)
v = n... |
0ad19bda4b39f06b869426a70462d438a46fdbffcf91d21a247eb203c049128e | Python | 12,165 | 235 | # SPDX-FileCopyrightText: Copyright (c) 2021 NVIDIA CORPORATION & AFFILIATES. All rights reserved.
# SPDX-License-Identifier: BSD-3-Clause
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
#
# 1. Redistributions of sourc... |
e642833122a4ab494abbcebf4af73caccf9dc5074206b06cdf24f8de43817ef7 | Python | 12,172 | 284 | import regex
import unicodedata
import logging
import langcodes
from .language_info import get_language_info, SPACELESS_SCRIPTS, EXTRA_JAPANESE_CHARACTERS
from .preprocess import preprocess_text, smash_numbers
# Placeholders for CJK functions that we'll import on demand
_mecab_tokenize = None
_jieba_tokenize = None
_... |
401b0e289b7f0f138800b15fd79310a3fe2f6ac4785e44a4cc3fa671887331bc | Python | 12,174 | 327 | import numpy as np
from math import ceil
from scipy.special import binom
class BaseComparisons(object):
"""Base class to compare arbitrary numbers of fingerprints.
Attributes
----------
fingerprints : {np.ndrarray, int}
Numpy array with the fingerprints that will be compared.
... |
5b2d2d2e0ce64d0d563d39ec9989b170fbc3ae2b340f363822b18415f453d4d5 | Python | 12,174 | 352 | #!/usr/bin/env python
"""Module Description: Test functions in PileupV2 (weighted p-v pileups).
Every pileup is compared with a small numpy reference: the weighted
coverage of half-open intervals [start, end) accumulated on the
elementary segments between distinct coordinates, written as change
points (pos, value), wh... |
7abcf61c277e595d7301d3ba28324e26f267aad9472542ef1e7eba295a4461fd | Python | 12,182 | 379 | """Plotly-native exploratory data analysis (EDA) plots.
Functions:
- ``column_distribution`` — histogram (numeric) / bar (categorical) for
a single column.
- ``correlation_heatmap`` — Pearson correlation matrix as a heatmap.
- ``missingness_map`` — per-column missing-rate bar.
- ``target_vs_feature`` — joint distri... |
e6e10d95efb62e1b522df376871eaaa371472ee3fdcfdfa6fe05110e8232d1a0 | Python | 12,182 | 353 | import torch
import torch.nn as nn
import torch.nn.functional as F
import numpy as np
import random
import sys
import math
from torch.distributions.categorical import Categorical
from torch.distributions.beta import Beta
from collections import defaultdict
""""vanilla_RNN"""
class RNNnet(nn.Module):
def __init__(... |
bedea78e7cc049165532a2953c5028dcb5d0e4868ea48e56fe11048f39b1ff75 | Python | 12,189 | 383 | # Copyright 2026 Xanadu Quantum Technologies 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 agre... |
93e713d6ef66da536abd52f4f0b46783291ff718d1373b566d505aa1817725c4 | Python | 12,193 | 351 | import numpy as np
# Format for parameter specification:
# parameter: {
# 'gui_name': text displayed next to edit box in GUI
# 'type': callable datatype for this parameter, like int or float.
# 'min': minimum value allowed (inclusive).
# 'max': maximum value allowed (inclusive).
# 'exclude': list ... |
5ccede2fdf62ec301e636bdee97903646ecf0537ccf944eaa0401a82728bc6e3 | Python | 12,200 | 391 | # Copyright 2018-2021 Xanadu Quantum Technologies 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... |
1a5fed3d9024dcb507e3911c9b0d5c8f7da4a42d0c1a480e30e1567d2b526585 | Python | 12,201 | 278 | # 3D-HSFormer parameter
import os
data_name = '150819_0_8X-cfos_16-55-11'
name = data_name.split('_')
if len(name) == 6:
name_seg = name[1] + str('_') + name[2] + str('_') + name[3] + str('_') + name[4] + str('_') + name[5]
else:
print('Recheck the name of the data')
Raw_data_root = r'G:\cyx/' + data_name + '/... |
9a1c40f6a3a253d9a1c1e191edd380d46a0272b6456eae2887d596a408a5e120 | Python | 12,206 | 358 | import io
import numpy as np
import pytest
import pandas as pd
pytest.importorskip("jinja2")
def bar_grad(a=None, b=None, c=None, d=None):
"""Used in multiple tests to simplify formatting of expected result"""
ret = [("width", "10em")]
if all(x is None for x in [a, b, c, d]):
return ret
ret... |
9061c9841f3c940a23bbcdcc8e782352378f92cefd130cac8fd6fcf0c316dd0e | Python | 12,210 | 341 | # Copyright 2024 Xanadu Quantum Technologies 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 agre... |
dface194df2221da8eb007175bee95a562122ade8392288fa35f1ecb93ff7d89 | Python | 12,210 | 324 | """
Tests for offsets.CustomBusinessHour
"""
from __future__ import annotations
from datetime import (
datetime,
time as dt_time,
)
import numpy as np
import pytest
from pandas._libs.tslibs import Timestamp
from pandas._libs.tslibs.offsets import (
BusinessHour,
CustomBusinessHour,
Nano,
)
from... |
3caebaec2d3a4cf468c732e861521d22e9fb7da2a6da4ab7aa2794b841fddf03 | Python | 12,211 | 363 | import torch
import numpy
import matplotlib.pyplot as plt
import bionetwork
import plotting
import pandas
from scipy.stats import pearsonr
import seaborn as sns
import copy
from matplotlib import cm
from matplotlib.colors import ListedColormap
def loadModel(refModel, fileName):
#work around to copy weights and bia... |
d2879dedfae04e014268a06d298efea94bcbfc9bb5438f4355bb885b501322d7 | Python | 12,214 | 297 | # Copyright 2023 Xanadu Quantum Technologies 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 agre... |
9942c2bc00b783108c2b38c70c6a4e52224ba871cd4ce8a1ab0fd8b14ba98187 | Python | 12,228 | 251 | """Convert the public MIT PAOPAC Conventional release into portable Torch trees.
Build-only dependency: cryptography. The original Windows loader's public string
table supplies its packaging key. No Windows code or arbitrary pickle globals
are executed; a restricted reader retains inert records and NumPy arrays only.
... |
25f43b2daabe539330b6ae36c81d3c45e95e1e8e9cbfeb0efbaf98fada4f06cf | Python | 12,231 | 298 | import numpy as np, matplotlib.pyplot as plt, sys
import pumpprobe as pp, wormdatamodel as wormdm
from scipy.optimize import curve_fit
from multipy import fdr
#this script is to print all the relevant numbers for the paper and save them as latex macros
ds_list = "/projects/LEIFER/francesco/funatlas_list.txt"
ds_tags ... |
aa619db0e19f36fb9c05f16a55223d2fe1ce64d8eb6b26f172a6b994314a6d9b | Python | 12,239 | 343 | import os
import sys
import subprocess
import numpy as np
import tensorflow as tf
from keras.utils import np_utils
from util.pretreatment import max_minNorm
from util.DANN_ import feature_extracter, classifier, Discriminator, DANN
from util.loss import gradient_reversal, loss_domain, early_stop
import matplo... |
ab2ef8c3bae1a9e198eea3cf787f19c5bf61a136a25f9294c16928f34b71541c | Python | 12,240 | 316 | """Heads that produce heatmap predictions for heatmap regression."""
from typing import Literal
import torch
from jaxtyping import Float
from kornia.geometry.subpix import spatial_softmax2d
from torch import nn
from lightning_pose.models.heads import HeatmapHead
from lightning_pose.models.heads.heatmap import run_s... |
2932582dd0501c044ba363e9fdf956f82c1aeb3ee05331d18cc16c610c078dd7 | Python | 12,248 | 301 | """
Script to produce the plots in Figure 5 in the paper.
"""
from pathlib import Path
import matplotlib.pyplot as plt
from matplotlib.pyplot import *
from src.np_implementation.data import generate_random_nonlinear_data
from src.np_implementation.model import TPC
plt.style.use('ggplot')
results_path = Path('./res... |
5f76f964ba3859ce8a292ecaed620fbcdd84340714dbaac7c393204fd51f7029 | Python | 12,248 | 226 |
import os
os.environ['TF_CPP_MIN_LOG_LEVEL'] = '2'
import tensorflow as tf
from tensorflow.keras import backend as K
from sklearn.model_selection import StratifiedKFold, StratifiedShuffleSplit
from tensorflow.keras.callbacks import EarlyStopping, LearningRateScheduler
from functions.OneDCNN_models import OneDCNN
fro... |
314539168c265e9c4f4a49faee3a986a6bf03efe03696b4eba0bba4c99ef2aa5 | Python | 12,249 | 306 | import os
import sys
import numpy as np
import pandas as pd
import tensorflow as tf
from dissect.utils.network_fn import network1 as network
from dissect.utils.network_fn import loss
from tqdm import tqdm
import random
from dissect.utils.utils_fn import normalize_per_batch, reproducibility, ccc_fn
from sklearn.metrics ... |
f3703e0406d7f7649254b6b4c66208c2e118c94177912074eea2fcced1acd5b0 | Python | 12,249 | 227 | import argparse
import textwrap
from pgen.esm_msa_sampler import ESM_MSA_sampler
from pgen.pgen_msa_revised import delete_msa_cols
from pgen import models
from pgen.utils import parse_fasta, RawAndDefaultsFormatter, SequenceSubsetter, add_to_msa, write_sequential_fasta, generate_alignment, run_phmmer
import sys
import ... |
dcb196dab1266c434a48121582a4724a16ac7ab244f7b33b81eb592ae66d19e0 | Python | 12,256 | 258 | # Copyright 2025 Xanadu Quantum Technologies 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 agre... |
72cf56dab78a682548011eee43facbef2d2b037219737725f452625566783ad7 | Python | 12,259 | 345 | """Figures for manuscript
"""
#%%
#Imports
import os
from pathlib import Path
import matplotlib
import matplotlib.backends.backend_pdf
import matplotlib.pyplot as plt
import matplotlib.animation as animation
import numpy as np
from matplotlib.gridspec import GridSpec
# style specs
matplotlib.rcParams['lines.linewi... |
f829420d19d2365b71a1404d234771713a2394109f6aa9d9744c63c4827dbf18 | Python | 12,260 | 327 | """Evaluation metrics for assessing pose estimation model quality.
CSV format conventions
----------------------
Labels CSV (DLC format, 3-row MultiIndex header: scorer / bodyparts / coords):
- coord values are ``x``, ``y``, and optionally ``visible``.
- ``visible`` encodes per-keypoint visibility: 2 = labeled, 1 ... |
90641d1fc098781dc5a0a803da063a54259457955d60c49d9c6086e7334854ba | Python | 12,264 | 329 | #! /usr/bin/env python
##############################################################################
## DendroPy Phylogenetic Computing Library.
##
## Copyright 2010-2015 Jeet Sukumaran and Mark T. Holder.
## All rights reserved.
##
## See "LICENSE.rst" for terms and conditions of usage.
##
## If you use this wo... |
75288202cfe4b1d54709f1f587e746a32e6b353baebca93099c5112619c29ef7 | Python | 12,274 | 334 | import pickle
import re
import numpy as np
import pytest
from pandas.compat import HAS_PYARROW
import pandas.util._test_decorators as td
import pandas as pd
import pandas._testing as tm
from pandas.core.arrays.string_ import (
StringArray,
StringDtype,
)
from pandas.core.arrays.string_arrow import (
Arro... |
afccae446c54f35dea6b7978f50fbb4b7c624a4f0d8675e3313c7115ad5df473 | Python | 12,275 | 371 | """Clustering utility functions."""
# ------------------------------------------------------------------------------
# Imports
# ------------------------------------------------------------------------------
import logging
from copy import deepcopy
import numpy as np
from phylib.utils import Bunch, _as_list, _is_lis... |
2471a80cfc0db94cde0e19f30b938ec2c768ce38d4f3241c4547a2bad80fb8f8 | Python | 12,276 | 343 | # Copyright 2018-2022 Xanadu Quantum Technologies 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... |
f205a834211d58f57628b4b316a7cf0f107d208b08201f280d59ba131da556fa | Python | 12,279 | 312 | # Ported from the Isaac Lab rl_games integration (isaaclab_rl); original DexPBT
# implementation from NVIDIA-Omniverse/IsaacGymEnvs (https://arxiv.org/abs/2305.12127).
# Copyright (c) 2022-2026, The Isaac Lab Project Developers.
# SPDX-License-Identifier: BSD-3-Clause
import datetime
import os
import random
import soc... |
e9951530bcaa232da6ad1b2948d68bed5d2d9914242344a644ded66108c988aa | Python | 12,282 | 364 | import ast
import os
from itertools import groupby
import numpy as np
import pandas as pd
import torch
from pymatgen.core.structure import Structure
from torch.utils.data import Dataset
from roost.core import Featurizer
class CrystalGraphData(Dataset):
def __init__(
self,
data_path,
fea_... |
02edbefd1f25113cae66abdce203d61cceda25c9c32c6e91213c8b983f7c733b | Python | 12,290 | 331 | # Copyright 2018-2021 Xanadu Quantum Technologies 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... |
5de505ee24eeb47d9e1d8b4aae4ef68869a8d7bc0cebea16953ae058433515c9 | Python | 12,294 | 388 | from __future__ import annotations
from typing import (
TYPE_CHECKING,
Literal,
cast,
)
import warnings
import numpy as np
from pandas.errors import Pandas4Warning
from pandas.util._decorators import cache_readonly
from pandas.util._exceptions import find_stack_level
from pandas.core.dtypes.common impor... |
1e7e223ac139888c326559043c6351652920c71d918243f2cabd1b027f948ede | Python | 12,306 | 323 | # cython: language_level=3
# Time-stamp: <2024-10-22 17:14:11 Tao Liu>
"""Module
This code is free software; you can redistribute it and/or modify it
under the terms of the BSD License (see the file COPYING included
with the distribution).
"""
# ------------------------------------
# python modules
# ----------------... |
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