sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
c781c2270f4ff7ec94aed77b16e4a0a29e73b11ee15f10ad4cf8ceeebdbe570a | Python | 9,466 | 223 | #!/usr/bin/env python3
import os
import pickle
import time
import sys
import numpy as np
import matplotlib.pyplot as plt
from scipy import interpolate
import scipy.stats
import tensorflow as tf
import LNODEs
from utilities import *
# Set double precision in TensorFlow.
tf.keras.backend.set_floatx('float64')
# Set... |
da89b8a479da3114385e895fb5e3b8d20a4754c9a125f879462c71597d4e1c84 | Python | 9,467 | 254 | import numpy as np
import pandas as pd
from scipy import signal
import copy
def matriz_shifteada(features, delays):
features = np.array(features).reshape(len(features), 1)
nt, ndim = features.shape
dstims = []
for di, d in enumerate(delays):
dstim = np.zeros((nt, ndim))
if d ... |
66758dc24cdd6d457f4459e32a319e07f23a025950560dbbca4da72b3e701492 | Python | 9,471 | 231 |
'''
Contains input/output functions for clutter stimuli
'''
import os
import csv
import time
from shutil import rmtree
import numpy as np
from PIL import Image
from scipy.io import savemat
from character_mod import Character
from Clutter_mod import Clutter
from utils_mod import shlex_cmd, DIGITS
import warnings
warni... |
09a8af3c3ca6899893556ded1c55a84dce6a129b66e0e127352f8bce1f95be07 | Python | 9,474 | 274 | """Testing the Template GUI."""
# ------------------------------------------------------------------------------
# Imports
# ------------------------------------------------------------------------------
import logging
import re
import unittest
from pathlib import Path
import numpy as np
from phylib.io.model import ... |
f7a6f892a5d8a00b252d53081f17c74d49b2f939f9cc41c587537def02e867b8 | Python | 9,474 | 283 | import contextlib
from io import (
BytesIO,
StringIO,
)
import sqlite3
import sys
import types
import numpy as np
import pytest
from pandas.compat._optional import (
VERSIONS,
import_optional_dependency,
)
import pandas as pd
import pandas._testing as tm
def test_import_optional():
match = "Imp... |
2aad4b0400531bc823bb88b2fded7abad0f0dfd2de91170a89d61c50f2d0eb0d | Python | 9,479 | 270 | import inspect
import pydoc
import numpy as np
import pytest
import pandas as pd
import pandas._testing as tm
class TestSeriesMisc:
def test_tab_completion(self):
# GH 9910
s = pd.Series(list("abcd"))
# Series of str values should have .str but not .dt/.cat in __dir__
assert "str... |
33415c9eb9fe61a644dc255dad3940b5cffa4b7a3884ebd7a3641d75c2ac6f1c | Python | 9,483 | 268 | from typing import Iterable, List, Literal, Optional, Sequence, Tuple, Union
import matplotlib as mpl
import numpy as np
import pandas as pd
import pyBigWig
import tqdm
from matplotlib import pyplot as plt
from matplotlib.axes import Axes
_signaltype = Optional[Literal["mean", "median", "min", "max", "sum", "std"]]
... |
757bba6f9b9b9c5cd647c48b1888b05fe8f53b4661f62f2cd1d8f995c3fd7895 | Python | 9,486 | 285 | import logging
from multiprocessing import Process
import os
from atropos.commands.trim import (
ResultHandler,
WorkerResultHandler,
WriterResultHandler,
)
from atropos.commands.multicore import (
Control,
PendingQueue,
ParallelPipelineRunner,
MulticoreError,
wait_on_process,
enqueue... |
0e6e6e039743d13ec859d885393c73902e7734b207b9c86b077f3456aab52738 | Python | 9,488 | 230 | import numpy as np
import random
import tensorflow as tf
import keras
from keras.models import Sequential
from keras.layers import Dense, Dropout, SpatialDropout1D
from keras.layers import Activation, Flatten, Input, Masking
from keras.layers import Convolution1D, MaxPooling1D
from keras.utils import np_utils
from ker... |
07644852a5d32f48894724325aa742de4900b97484f41738e4c34eebdfe5de83 | Python | 9,494 | 177 |
'''
This script creates json files which can be used to render Manhattan plots.
'''
# NOTE: `qval` means `-log10(pvalue)`
# TODO: optimize binning for fold@20 view.
# - if we knew the max_qval before we started (eg, by running qq first), it would be very easy.
# - at present, we set qval bin size well fo... |
98478367358d429ae4596e1482528f71a5964816c4a59feeb49d83aa8504540f | Python | 9,494 | 285 | """
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 heapq
import logging
from itertools import chain
from pathlib import Path
from typing import List, Literal, Protocol, Union, runtime_c... |
5d841778fd677c37b617f385f6ef007216f33e3156473191928ec3f6adf0a277 | Python | 9,496 | 308 | # 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... |
f62112e85f713f1c721120cfea41944d3123c0782a3159dfb91829ef244a808b | Python | 9,501 | 192 | import os
from unittest import TestCase, mock
import pandas as pd
import dynast.preprocessing.conversion as conversion
import dynast.utils as utils
from .. import mixins
class TestConversion(mixins.TestMixin, TestCase):
def test_read_counts(self):
conversion.read_counts(self.umi_counts_path)
def ... |
8e6e51b8addea21d339d3f12a2a355a10b9952dac848b5b9b81b6f6c47913492 | Python | 9,502 | 321 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Thu Mar 16 09:37:52 2023
@author: kellnere
"""
import os
os.environ['CUDA_VISIBLE_DEVICES'] = "3"
import numpy as npss
import tensorflow as tf
import math
from tensorflow.keras import Model
from tensorflow.keras import layers
import matplotlib.pyplot as pl... |
1c7f585ae98da0f0315bf79e349494584a4d6b8c99d2a92c05678b47d2ed698c | Python | 9,503 | 271 | import inspect
import pydoc
import numpy as np
import pytest
import pandas as pd
import pandas._testing as tm
class TestSeriesMisc:
def test_tab_completion(self):
# GH 9910
s = pd.Series(list("abcd"))
# Series of str values should have .str but not .dt/.cat in __dir__
assert "str... |
2fa3656896325ea676ae33c9b689f85eabc523a0cf541b73e034570417c66400 | Python | 9,503 | 196 | # -*- coding: utf-8 -*-
from keras.layers import *
from keras.regularizers import l2
from keras.models import Model
from keras import backend as K # use computable function
from sklearn.metrics import roc_auc_score, accuracy_score, f1_score, precision_recall_curve
import sklearn.metrics as m
from layers import Aggreg... |
6be55b6d5bcac5ff9f63abf2e55997ab46b3c245b9b1d55e601806c7f8e5b1a6 | Python | 9,503 | 278 | from __future__ import annotations
import json
import numpy as np
import cv2
from typing import Tuple, List
import matplotlib.pyplot as plt
import openpyxl as px
import tifffile
from SCTrack.prepare import convert_dtype
class Stack(object):
def __init__(self):
self.start_frame = None
self.end_fr... |
eeb3bf3462c1d7a4ac048e47484637458c4927bd3dbd6473d6c16e73cebf27ec | Python | 9,504 | 243 | """
Creates CA1 pyramidal cell model, sets parameters, runs simulation in NEURON and shows figures.
Title: main.py
Author: Matus Tomko
Mail: matus.tomko __at__ savba.sk
"""
import time
from neuron import h, gui
import libcell as lb
import saveClass as sc
import numpy as np
from CA1_plasticity.io.figures_shower impo... |
21bfe24080a5320ee0cf64262c34a1be603f1e671a18835d3120b1757466113e | Python | 9,505 | 293 | """Run lifecycle integration tests.
Exercises:
- POST /api/v1/experiments/{id}/runs (queue a run)
- GET /api/v1/experiments/{id}/runs (list)
- GET /api/v1/runs/{id} (status)
- POST /api/v1/runs/{id}/wait (block)
- GET /api/v1/runs/{id}/events (replay)
- WS /ap... |
9d3f338f8822f3bffeb6c6f7d257272c764dcff26ab81fee02e77e4c28dec590 | Python | 9,510 | 253 |
# Copyright 2019 Image Analysis Lab, German Center for Neurodegenerative Diseases (DZNE), Bonn
#
# 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-... |
57c25038c1fd15b6ff96d7b03a5d741f357ff0182b964891dd4b1d13a1b913ae | Python | 9,514 | 300 | # 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... |
1337e744e5726bbe2c3c13558512cc6ad54da889688c7f25b8cd78104d1782a5 | Python | 9,515 | 234 | """Session 24 — god-class drain: ``create_model`` (supervised path).
Supervised ``Experiment.create_model`` no longer delegates to
``self._legacy.create_model``. It resolves the estimator from the engine's
model registry, runs cross-validation, refits on the full training set,
and returns a **real sklearn Pipeline** (... |
071ede10ac07fda32fa21971b2ef6c8157d2967a38619f8019a59711910a1734 | Python | 9,516 | 309 | from typing import Optional, cast, Sequence
import logging
import torch
import torch.nn.functional as F
from ..image import Volume, Slice
from ..transform import mat_transform_points
# _cache: Dict = dict()
# _cache_id: Tuple = tuple()
BATCH_SIZE = 64
# def clean_cache(*args) -> None:
# global _cache, _cache_i... |
e511feec1a11a8fe3992f4ab07f308514bb0a02af6f254fde00a761c0aff8e50 | Python | 9,516 | 258 | __all__ = ["MaxQuantReportParser"]
import os
import re
from typing import Iterable, Tuple, Union
import numpy as np
import pandas as pd
from ....chem.pep.aminoacids import AminoAcidCollection
from ....chem.pep.mods import (
ModificationCollection,
ModifiedSequence,
ModPosition,
modified_sequence_to_s... |
e2ba29ec84fc775d84f01fbd2456175dd6f9df19b389c483b729523efa747ce3 | Python | 9,520 | 193 | """Compressed framing/fallback matrix; each bounded child takes about 0.5 s."""
import gzip
import hashlib
import json
import multiprocessing
import os
from pathlib import Path
import random
import signal
import subprocess
import sys
import pytest
from conftest import macs3_env
from MACS3.Utilities.Constants import ... |
53e20136a8415e520089494e0537cb9eff173751ca3e1022cf1854267bbe90f8 | Python | 9,524 | 295 | from typing import Optional
from deepglyco.chem.common.elements import ElementCollection
from deepglyco.chem.gpep.fragments import GlycanFragmentTypeCollection
from deepglyco.chem.gpep.glycans import MonosaccharideCollection
from deepglyco.chem.pep.aminoacids import AminoAcidCollection
from deepglyco.chem.pep.fragment... |
437b0e2528db1c271f18b69cf04651b6e57bd3f7e2a110a33db1f9d91deed487 | Python | 9,525 | 287 | """`pycaret-server` CLI entry point.
Usage:
pycaret-server init [--data-dir ./data]
pycaret-server serve [--host 0.0.0.0] [--port 8020] [--reload]
pycaret-server migrate [--url sqlite:///...] [--revision head] [--reset-dev]
pycaret-server worker [--queues default,gpu] [--worker-id pyc-1]
pycaret-se... |
0d6dd3d78e817eb2476f0404ff8bcf9284004e5ae292c90996799e63e0a7b420 | Python | 9,527 | 230 | # -*- coding: utf-8 -*-
"""
Created on Fri Oct 2 11:52:36 2020
@author: Wladek
"""
import numpy as np
import pylab as py
from mayavi import mlab
from scipy.integrate import simps
from joblib.parallel import Parallel, delayed
def remove_points(mtrx, xpos, ypos, zpos, tp, thr):
idx_to_remove = np.where(abs(mtrx[:,... |
8f296589f07a2b41f2a0dd1bddf3235c3efdc65b048771778e4cab0f2f5b7f88 | Python | 9,530 | 257 | # 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... |
a7427cc60ef713bda4cdf53c376c1d291599ac8915a3f1a06ef75d4af5ebf211 | Python | 9,530 | 244 | """
Creates CA1 pyramidal cell model, sets parameters, runs simulation in NEURON and shows figures.
Title: main.py
Author: Matus Tomko
Mail: matus.tomko __at__ savba.sk
"""
import time
from neuron import h, gui
import libcell as lb
import saveClass as sc
import numpy as np
from CA1_plasticity.io.figures_shower impo... |
cfb4aaedaeaaee1cf64ac74ba72ca9e785f871da3997880cc2069ff7b5932a91 | Python | 9,537 | 310 | import numpy as np
import pytest
import pandas as pd
import pandas._testing as tm
from pandas.tseries import offsets
# suppress warnings about empty slices, as we are deliberately testing
# with a 0-length Series
pytestmark = pytest.mark.filterwarnings(
"ignore:.*(empty slice|0 for slice).*:RuntimeWarning"
)
d... |
442d1c395a3883b7fa769ef40276ec0ca542ed1777a0f34f19c477eecbe96e5a | Python | 9,541 | 218 | #!/usr/bin/env python
import argparse
import pandas as pd
from common import *
def main():
parser = argparse.ArgumentParser()
parser.add_argument("-i", "--input", default="-")
parser.add_argument("-o", "--output")
parser.add_argument(
"-f", "--formats", choices=('txt', 'svg', 'pickle'), nargs="... |
b9a2ea2cf25260eacea0fd925d0b144b638e727b8a66d62d0446266da633a432 | Python | 9,542 | 303 | # 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... |
6888f265edff82f6d2e530b547a2f6f751bacc2084bcd2b6f5247689eab794b4 | Python | 9,544 | 223 | """Phase 0: pivot Trial/Run model — Trial owns Runs, not the other way around
Revision ID: f0a1b2c3d4e5
Revises: e5f6a7b8c9d0
Create Date: 2026-05-12 20:00:00.000000+00:00
The platform's mental model flips here:
- Pre-Phase 0: ``Run`` owned the compare invocation; ``Trial`` was a row
inside a Run's leaderboard.
- ... |
3460aff68411ae08ec604769057cf0d5f148cbbc8a740db5356497bc87226355 | Python | 9,545 | 260 | """
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 pathlib
from argparse import ArgumentParser
from collections import defaultdict
from DL_reconstruction import save_reconstructions
im... |
e31932d655d6b4bd5d132dda9ced0a02ad3832e303f00b5894ef56f5f23a179c | Python | 9,547 | 240 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
#importing required libraries
import torch
import torch.nn as nn
#from utils import get_data, SeqsDataset
from torch.utils.data import Dataset
import numpy as np
from torch.nn.utils.rnn import pad_sequence
from esm import pretrained
import esm
from typing import Union, Op... |
6ca97014814baef163d61ce9a10c398f05c48df47975e395602caff80468fd24 | Python | 9,554 | 262 | __all__ = [
"NonRedundantSpectraProto",
"NonRedundantSpectraFirstOccurrence",
"NonRedundantSpectraBestScore",
"NonRedundantSpectraConsensus",
]
import os
from typing import (
Any,
Generic,
Iterable,
List,
Optional,
Protocol,
TypeVar,
Union,
cast,
)
import numpy as n... |
e6783f3fc552973fd1218d4f0ef13f8819fb4ed03a6096b1cb00508de00a455f | Python | 9,558 | 249 | import os
import gc
import sys
import traceback
from typing import Set, DefaultDict, List
from collections import defaultdict
import ray
import pydantic
import rapidjson
import neuronbridge.model as model
# Directory to store log files
LOG_DIR = "logs2"
# Print debug messages on the workers
DEBUG = False
# Maximum... |
462af9ce40d88d386db22d8783d7c4e2eb0ceb0a46bc94aa56559798d3db1d01 | Python | 9,559 | 326 | """
Sequence statistical energy and mutation effect computation
protocols
Authors:
Thomas A. Hopf
Anna G. Green (complex)
"""
import pandas as pd
import matplotlib.pyplot as plt
from bokeh.io import save, output_file
from evcouplings.couplings.model import (
CouplingsModel
)
from evcouplings.couplings.mappin... |
4720305ed3e711ca7e685432c9db187138d19b82859b783282c652645ed60a12 | Python | 9,559 | 268 | #%%
#Imports
import numpy as np
import os
import matplotlib.pyplot as plt
import matplotlib.animation as animation
from matplotlib.gridspec import GridSpec
import matplotlib.backends.backend_pdf
matplotlib.rcParams['lines.linewidth'] = 0.5
matplotlib.rcParams['lines.markersize'] = 1
matplotlib.rcParams['pdf.fonttype'] ... |
a12f5b421a5831a1de8a6e2df381464120995420c641ba2a1c969e73892da189 | Python | 9,559 | 257 | import numpy as np
import os
from kcsd import csd_profile as CSD
from kcsd import KCSD2D
from scipy.integrate import simps
from scipy.interpolate import griddata
from figure_properties import *
import matplotlib.pyplot as plt
import matplotlib.cm as cm
def integrate_2d(csd_at, true_csd, ele_pos, h, csd_lims):
csd_... |
2a82632c056c87b592bef706507b1c35c7c4e6cbafaf13fb56f5136e52be8d4f | Python | 9,560 | 286 | #
# File to train networks built from the hnn.py class.
#
# This file establishes the clebsch gordan coefficients, sets up an hnn with given parameters,
# loads holograms from .npy files, and then tests the network via a function call.
#
from argparse import ArgumentParser
import logging
import os
import sys
import ... |
dfd1693291e295f2b5a20db7941928e2eeb75f4591c99b397a77e8c50087b03c | Python | 9,561 | 252 | # MIT License
#
# Copyright (c) 2024 EPFL Biorobotics Laboratory (BioRob).
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# ... |
37e041f2d5ae7050b03d58faba6cb7706da231b5c3009fa6accad70a8bd76e24 | Python | 9,564 | 244 | #!/usr/bin/env python
"""Summarizes trimming accuracy for simulated reads."""
from argparse import ArgumentParser
import csv
import os
from common import *
# Either of these will work
from editdistance import eval as editdistance
#from Levenshtein import distance as editdistance
summary_fields = (
"program", "pr... |
81d094c35c6865a7f0319059c3dbac805b2cd449bc7ae5e8e1094cf1dd4c313b | Python | 9,568 | 228 | # 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 ... |
654db2f7f11345249800e53854c1cf922b6918485eac07bbee5eeeb2b9bc1b77 | Python | 9,569 | 354 | """Test gui."""
# ------------------------------------------------------------------------------
# Imports
# ------------------------------------------------------------------------------
import logging
from phylib.utils import connect, emit, unconnect
from pytest import raises
from phy.plot import BaseCanvas
from... |
7e732b81d3bbad725b24c973d0b06e24c94d5077319216b8128215fe8870a2a3 | Python | 9,571 | 229 | import numpy as np
import matplotlib.pyplot as plt
from matplotlib.patches import ArrowStyle
from pathlib import Path
from typing import Optional
from scipy.io.wavfile import read as wavread
def render_hga_feature_computation_plot(data_snippet: np.ndarray, out_filename: Optional[Path] = None, dpi=300):
fig = plt.... |
ecd8ef16829ce6ffa97ba1c73e4601f481b5f5436220af5359dcc052afd0c026 | Python | 9,572 | 246 | # -*- coding: utf-8 -*-
"""
Created on Tue Feb 14 11:11:06 2023
@author: lonya
"""
#%% Load Data
import tkinter as tk
import tkinter.filedialog as fd
from tkinter import messagebox
import numpy as np
from scipy.stats import pearsonr
import pandas as pd
import scipy.io as sio
import my_funcs as mf
import... |
a9445fa5a46a8b1c5b4dd19342d742ddc32e4bf42b70c4a66048e94a1fe3c7f3 | Python | 9,573 | 180 | import argparse
import os
import pysam
import pandas as pd
import seaborn as sns
import matplotlib.pyplot as plt
def get_args():
"""
Get arguments from command line with argparse.
"""
parser = argparse.ArgumentParser(
prog='paf-mapping-summary.py',
description="""Summarize mapped read c... |
8b4fae12c1f2677fb46701198ef37e5e49bcad3594d550a99a044e21658ce03a | Python | 9,578 | 298 | from __future__ import annotations
from typing import (
TYPE_CHECKING,
Any,
Literal,
overload,
)
import warnings
import numpy as np
from pandas._libs import (
lib,
missing as libmissing,
)
from pandas.util._exceptions import find_stack_level
from pandas.core.dtypes.cast import maybe_box_nati... |
6194aa5cc899436dd7f3aa8b6d4504e0652d880a42a92a50f23d47b3b7360d9f | Python | 9,584 | 216 | # 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... |
7532a6a48f33c5f0d1691f10906021f3c06158a61f7aa0b79425cf359251b78c | Python | 9,584 | 247 | # 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... |
20470f00b01501705200a6c9e363c6cb292fac0d066080801517e1f5342f8fb7 | Python | 9,589 | 231 | import math
from pathlib import Path
import numpy as np
import pytest
import torch
from pyaging.utils._feature_ranges import get_feature_ranges, load_feature_range_registry, resolve_feature_ranges
WEIGHTS_DIR = Path(__file__).resolve().parents[2] / "clocks" / "weights"
def test_registry_has_schema_version_and_sect... |
390022887b250f27c3741045f26d58e9615a7cbb693e651803155c029a99bb35 | Python | 9,601 | 240 | #!/usr/bin/env python3
"""UltraScan III conventions that neither clang-format nor clang-tidy enforce.
usage: check-conventions.py [--fix] (--staged | <base-ref>)
--staged check the index (pre-commit hook)
<base-ref> check the worktree against <base-ref> (CI: merge-base with origin/main)
--fix append a... |
22371f7f2c041140de219c798fd19e0a773ac02a7046218ef938136b2d2c143b | Python | 9,602 | 257 | import pytest
from pandas._libs.tslibs import to_offset
from pandas._libs.tslibs.offsets import INVALID_FREQ_ERR_MSG
import pandas as pd
import pandas._testing as tm
class TestDatetimeIndexRound:
def test_round_daily(self):
dti = pd.date_range("20130101 09:10:11", periods=5)
result = dti.round("... |
56c07e119b351861f9a5217fcbf6222d0fab7415e6ef0b0946f84b42a5d34ba6 | Python | 9,603 | 238 | """MRI/PET volume loading, frame handling, brain cropping, and resizing.
Ports `process_scan` / `find_brain_bounding_box` / `resize_to_input_shape`
from `Dataset_MRI.ipynb` / `Dataset_PET.ipynb` (see
`docs/legacy-notebooks-inventory.md`), preserving the modality-specific
Otsu tuning as an explicit, named preset rather... |
f643005fa79cbf2854fcbe96fbce164e288d3c605d8edf49f1e92186ac564253 | Python | 9,607 | 340 | """
Expressions
-----------
Offer fast expression evaluation through numexpr
"""
from __future__ import annotations
import operator
from typing import TYPE_CHECKING
import warnings
import numpy as np
from pandas._config.config import _global_config as config
from pandas.util._exceptions import find_stack_level
... |
f7a0eb6a774c87ed2f2c6e67a9e4f97a51f4d7df124838d0093d00b00231aac2 | Python | 9,607 | 256 | """This script creates a summary of the residual autocorrelation."""
import os
import h5py
import matplotlib.pyplot as plt
import mne
import numpy as np
import osl
import sails
import lemon_plotting
from glm_config import cfg
from lemon_support import (get_eeg_data, lemon_make_bads_regressor,
... |
b0a8ddc7495656b6846390a4a211222d9e2d624cf86622b14c5d4b017f7ebbee | Python | 9,608 | 263 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Tue Oct 3 00:51:46 2023
@author: s205272
"""
import numpy as np
def normalize_mi_ma(x, mi, ma, clip=False, eps=1e-20, dtype=np.float32):
if dtype is not None:
x = x.astype(dtype,copy=False)
mi = dtype(mi) if np.isscalar(mi) else mi... |
df2c25e1d9753a0e28684bbe3075f5fd94f2cc395f5077891020aba0b46cd1c5 | Python | 9,608 | 269 | # Copyright 2018-2025 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... |
d591a66c4dd5bec9788afcb8c00e771bc331e7c0b550afc92688516057a45a3f | Python | 9,609 | 264 | from sklearn.linear_model import BayesianRidge, ARDRegression
from sklearn.gaussian_process import GaussianProcessRegressor
from sklearn.gaussian_process.kernels import DotProduct, RBF
from sklearn.compose import ColumnTransformer, make_column_selector, make_column_transformer
from sklearn.svm import LinearSVR
from skl... |
fe152aa96b7fea3c285e709efa89ee1ae1ae52587006da28a2e633dc5f314272 | Python | 9,610 | 257 | # 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... |
8f6021565e44e3be80649c3efb93831a24c23c1edfdde8a587c1ef583ae78451 | Python | 9,613 | 266 | # 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... |
846b93a19a613f9c71b00a3cb4ae0ddd83d69695d38b80f7bf2e78d88a3d4dcc | Python | 9,614 | 320 | import numpy as np
import pytest
import pandas as pd
import pandas._testing as tm
from pandas.tests.copy_view.util import get_array
def index_view(index_data):
df = pd.DataFrame({"a": index_data, "b": 1.5})
view = df[:]
df = df.set_index("a", drop=True)
idx = df.index
# df = None
return idx, ... |
303fd03120e43db878e03bf308c32bc60ff2c74cd4ffe24c1ab40e71927bd78e | Python | 9,615 | 260 | # -*- coding: utf-8 -*-
"""
Created on Thu Mar 10 16:05:07 2022
1:1 copied implementation from the MATLAB reference implementation found at
https://github.com/YunzheLiu/TDLM
results of both functions are bit wise equivalent
@author: Simon
"""
import math
import numpy as np
def uperms_MATLAB(*args, **kwargs):
... |
37c9ef189a2b0f7f12f98e584d3218a8433e3d00acc9327d79e04fb744d1c265 | Python | 9,615 | 270 | import sys
import io
import numpy as np
import pandas as pd
def get_run(x):
print(x)
trial_start = x.TRIAL_START_TIME
starts = sorted(list(trial_start.unique()))
run = trial_start.apply(lambda x, starts=starts: starts.index(x))
out = pandas.DataFrame({'run': run}, index=x.index)
return out
de... |
3636212be7246379cd13b9a0b5e24afd7a62a6d481bf8aec82969eda44a3073b | Python | 9,618 | 254 | """pickle compat"""
from __future__ import annotations
import pickle
from typing import (
TYPE_CHECKING,
Any,
)
import warnings
from pandas.compat import pickle_compat
from pandas.util._decorators import set_module
from pandas.io.common import get_handle
if TYPE_CHECKING:
from pandas._typing import (
... |
37b95bb99c09f1ecf23bb21c0b7efef2061a8c90609918740ec589e43152ecaa | Python | 9,624 | 310 | """Scheduled-job CRUD.
Routes (under ``/api/v1``):
GET /workspaces/{ws_id}/schedules
POST /workspaces/{ws_id}/schedules
GET /schedules/{id}
PATCH /schedules/{id} (toggle enabled, update cron, update spec)
DELETE /schedules/{id}
POST /schedules/{id}/run-now (fire the handler immediately, o... |
90e65307c9c5aad78646e40743c1b8da24637adca4ea5a34cfeb1318012ef1b1 | Python | 9,633 | 256 | from collections import OrderedDict
import numpy as np
import pytest
from pandas.errors import Pandas4Warning
import pandas as pd
import pandas._testing as tm
class TestFromDict:
# Note: these tests are specific to the from_dict method, not for
# passing dictionaries to DataFrame.__init__
def test_co... |
4945037d2bc2d1d047fbbf62b9662b41e02ad26fa93206baa4348a8a947b8e4b | Python | 9,639 | 326 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Thu May 16 13:50:07 2019
@author: loading
"""
import numpy as np
import os
import shutil
import math
def getBundleNames( bundlefile ):
#get center names from bundle file
ns = dict()
exec(open( bundlefile).read(),None, ns)
bunlist = ns[ 'attribut... |
8af42aaa068e373a5406fc6bee5cc1521670d54fea607b71c695e1dc87f47203 | Python | 9,643 | 288 | import numpy as np
import pytest
import pandas as pd
import pandas._testing as tm
from pandas.api.types import is_integer
from pandas.core.arrays import IntegerArray
from pandas.core.arrays.integer import (
Int8Dtype,
Int32Dtype,
Int64Dtype,
)
@pytest.fixture(params=[pd.array, IntegerArray._from_sequence... |
15a42a35a2ade28ec4afafae5ec2572058c71fef5780a8d58271087a784c44e4 | Python | 9,651 | 300 | # 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... |
44e3ca38b6430d29d6cbf0e14e703739e5dd653685c3cd9c824ffe1935b37a19 | Python | 9,657 | 277 | __all__ = [
"PeptideMS2Data",
"PeptideMS2DataBatch",
"PeptideMS2DataConverter",
"PeptideMS2Dataset",
"unbatch_peptide_fragment_intensity",
"PeptideMS2OutputConverter",
]
import itertools
from typing import Any, List, NamedTuple, Optional, Tuple, Union, overload
import numpy as np
import torch
... |
638a68683b1e338aa0d2174e92d7a669a27a8df0a7853ff07ba524912b4b22df | Python | 9,657 | 264 | """Session 42 — phase 5c (cont.): drain ``TimeSeriesExperiment.compare_models``.
Phase 5b (s40) drained ``create_model``; phase 5c (s41) drained
``predict_model``. This session drains the third TS verb.
``exp.compare_models()`` no longer touches ``self._legacy.compare_models``
— it iterates the sktime registry, calls ... |
251ee4a3ce4b780a8e38477aec9f8852a2d9227be6b6fdf14bbd893c535de27a | Python | 9,658 | 276 | # 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... |
d4211423fda4db0d3352f24f72936d337418d4990c50e8c45b887b7e86c0bce2 | Python | 9,659 | 282 | """Test of filter functionalities"""
import copy
import pathlib
import tempfile
import dclab
import numpy as np
from PyQt6 import QtCore, QtWidgets
from PyQt6.QtCore import QEventLoop
from shapeout2.gui.main import ShapeOut2
from shapeout2 import session
import pytest
data_path = pathlib.Path(__file__).parent / "da... |
28ab15e0643351796db4aec1af70741e89ffbb8fe127e3ad184bc0cb6351445c | Python | 9,663 | 250 | # 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... |
fa76b09496cf374f65cb1b92a72ffd5b06324818f96e6b897db672f88938147b | Python | 9,663 | 289 | """
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
from math import pi as PI
from typing import List
import numpy as np
import torch
import torch.nn as nn
from scipy.special impor... |
b048d8e9a4ca63d6d23c12ed9a9f7567d8a86c168b0dd5215e8470ed9f0fab67 | Python | 9,677 | 242 | """Session 35 — drain ``self._legacy.setup()`` for the simple supervised case.
The biggest remaining drain target. When the user passes a basic
classification or regression experiment with no complex preprocessing
flags (``normalize`` / ``transformation`` / ``remove_outliers`` /
``feature_selection``) and no extra ``s... |
66d200b8f1ec1984ebd71f1c5ebada4d0e83d32b525026d99d7101498410aa7c | Python | 9,678 | 214 | from Environment_ui import *
from PySide2.QtWidgets import QWidget, QFileDialog, QTextBrowser, QPushButton, QMessageBox
from PySide2.QtUiTools import QUiLoader
from PySide2.QtCore import Signal, QObject
from threading import Thread
from concurrent.futures import ThreadPoolExecutor
from pages.Data_preprocessing.cutting ... |
191b6a6015767277f78c15eb9b52ac025d6945889dc7e7951ecaad2391e9c0eb | Python | 9,679 | 270 | """orc compat"""
from __future__ import annotations
import io
from typing import (
TYPE_CHECKING,
Any,
Literal,
)
from pandas._libs import lib
from pandas.compat._optional import import_optional_dependency
from pandas.util._decorators import set_module
from pandas.util._validators import check_dtype_back... |
98ddfd74990ff57379bc6f30a12436f79523c59f70d0bff7ef2b899edbb70797 | Python | 9,679 | 213 | """Regression tests for a batch of critical fixes: runner CLI on py3.12+,
max_frames/max_steps handling, LR scheduling, and checkpoint save/restore round-trips."""
import os
import subprocess
import sys
import tempfile
import pytest
import torch
import yaml
REPO = os.path.dirname(os.path.dirname(os.path.abspath(__fil... |
6c34adeeb8e2bc650611de59a9aedc345739261900e4d4ecbbbffd98e4acb73a | Python | 9,688 | 246 | #!/usr/bin/env python3
# -*- coding: UTF-8 -*-
"""Prepare an external binset so refinement and gap filling can resume.
The historical ``-r`` route called outlier removal and ignored ``--module``.
Later stages still expect the checkpoint and list files produced by a normal
autobinning run. This module creates those fi... |
df02a79c6b77090e05601c58c2bf5e5f439da0fca32db8481b4a767102a61787 | Python | 9,690 | 320 | # 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... |
1829c4ab788f3c8e7764415edb9f40f23b3dbc590fbeac33bdf495fa46d3edb4 | Python | 9,694 | 247 | """
Creates CA1 pyramidal cell model, sets parameters, runs simulation in NEURON and shows figures.
Title: main.py
Author: Matus Tomko
Mail: matus.tomko __at__ savba.sk
"""
import time
from neuron import h, gui
import libcell as lb
import saveClass as sc
import numpy as np
from CA1_plasticity.io.figures_shower impo... |
72bb17b054de13ef4e84591b056765de60e900ee63cb99fe5ec915239630c0a2 | Python | 9,695 | 291 | from . import utils
from .utils import PheWebError
from . import conf
#import sys
import itertools
from collections import OrderedDict,Counter
import typing as ty
from typing import Dict,Any
def scientific_int(s:str) -> int:
'''like int(s) but accepts "1.23e2" == 123'''
try:
return int(s)
except ... |
cb9dea4420ed01ef79bd703caea7be62e629e8e4a490f87f1e0182975d42b62f | Python | 9,695 | 254 | """Bounded public FRAG EOF regressions for #765 / #757 item 7."""
import gzip
import struct
import subprocess
import sys
import zlib
import pytest
from conftest import macs3_env
def write_frag(path, data, encoding):
if encoding == "plain":
path.write_bytes(data)
elif encoding == "gzip":
path... |
055730808d1b747e983f2946901809d681fe8c6dadda52b0a36219d187cc1503 | Python | 9,697 | 183 | import sys
sys.path.insert(1, '/media/sda/Anna/brain_age')
import os
import pandas as pd
from HDBET.HD_BET.run import run_hd_bet
os.environ["CUDA_VISIBLE_DEVICES"] = "0"
dataset_dict_metadata = {
#'wu1200':"/media/sda/Anna/brain_age/pytorch/data/datasets/Dataset_WU1200.csv",}
#'ABCD_2023': "/media/sda/Anna/b... |
0dea473d59e1b68c57d0f6051a6648fc66cb5dbd8045972d7801bbe6a9411f0e | Python | 9,701 | 233 | """Compose the Greedy logo from a real greedy registration (see make_logo.sh),
in the same bookshelf layout as the Convert3D logo: the moving image, the moving
image resampled through the warp at several points of the optimization (with the
warped grid drawn on it), and the fixed image."""
import sys
import numpy as np... |
02bb4c2b2cc9808fa87178240bf9fc69cadb8037017379bcc0222ae36294068d | Python | 9,705 | 273 | from aigarmic.plate import Plate, PlateSet, plate_set_from_dir
from tests.conftest import (DRUG_NAME,
MIN_CONCENTRATION,
MAX_CONCENTRATION,
TARGET_MIC_CSV,
MIC_PLATES_PATH,
basic_p... |
4e8e3f6bd784d207ed318fa7ea5e17d078beaeaca771cb6771f2feb18718cf72 | Python | 9,708 | 272 | # 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... |
c272a8cbd1fff0ec51b03717a78233b5b4f0c5cd889c5e41791e53544cd5949a | Python | 9,708 | 289 | import functools
import os
import numpy as np
import pandas as pd
import torch
from pymatgen.core.composition import Composition
from torch.utils.data import Dataset
from roost.core_pretrain import Featurizer
class CompositionData(Dataset):
"""
The CompositionData dataset is a wrapper for a dataset data poi... |
00ace190f6ac48097055b71469ad25f035574f3b5dbaeff56c37da3a5732e279 | Python | 9,713 | 274 | from datetime import datetime
import zoneinfo
import numpy as np
import pytest
import pandas as pd
import pandas._testing as tm
class TestInsert:
@pytest.mark.parametrize(
"null", [None, np.nan, np.datetime64("NaT", "ns"), pd.NaT, pd.NA]
)
@pytest.mark.parametrize("tz", [None, "UTC", "US/Eastern... |
ef2dcbae7cef7b64771484cfd00d92dd130400053c88478c35a0032ef6b91bb1 | Python | 9,715 | 267 | # An example cifar-10/100-p evaluation script; some imports may not work out-of-the-box
# -*- coding: utf-8 -*-
import numpy as np
import os
import argparse
import time
import torch
import torch.nn as nn
import torch.backends.cudnn as cudnn
import torchvision.transforms as trn
import torchvision.datasets as dset
import... |
0b18b19931bab2f8118f87d56a0a52b6e30f75c4f78e7b1ba3e7eff677fe2b7c | Python | 9,716 | 287 | """Miscellaneous functions used for analyses."""
import logging
import multiprocessing as mp
import os
import nibabel as nib
import numpy as np
from neuromaps.datasets import fetch_atlas
from nibabel.gifti import GiftiDataArray
from scipy.cluster.hierarchy import leaves_list, linkage, optimal_leaf_ordering
from sklea... |
efe00ce50be9fa95e8684ec0cbde8780afa91c612d50741dc7c97565d859a68b | Python | 9,725 | 239 | """Test nimare.meta.kernel (CBMA kernel estimators)."""
import shutil
import nibabel as nib
import numpy as np
import pytest
from scipy.ndimage.measurements import center_of_mass
import nimare
from nimare import extract
from nimare.dataset import Dataset
from nimare.meta import MKDADensity, kernel
from nimare.utils i... |
b8ba53f8284ed4725269077be1e31afe1660cc90229a172ccbe6d559f636b791 | Python | 9,731 | 239 | """Test the predictions module."""
import copy
from unittest.mock import MagicMock, patch
import pandas as pd
import pytest
from omegaconf import OmegaConf
from lightning_pose.losses import get_loss_factories
from lightning_pose.models import get_model
from lightning_pose.utils.predictions import make_dlc_pandas_ind... |
28248922e0d5d1796fea2b31d3f6aac103d81f8346df4bc5ce70cc0ba4a5fc33 | Python | 9,734 | 268 | """TabNet self-supervised pretraining for SIMS.
This module provides :class:`SIMSPretrainer`, a Lightning module that runs
TabNet self-supervised pretraining (random feature obfuscation +
reconstruction loss, as described in section 3.4 of the original TabNet
paper). The encoder learned during pretraining can be trans... |
7ef1a448a6801256ef35d0f68b957726eac40e64d365922dc68ed8995a70df48 | Python | 9,734 | 299 | import numpy as np
from scipy.ndimage.filters import gaussian_filter1d, gaussian_filter
from scipy.ndimage import correlate
from skimage import exposure
import tensorflow as tf
def threshold_detect(signal, threshold):
thresh_signal = signal > threshold
thresh_signal[1:][thresh_signal[:-1] & thresh_sign... |
7d9ae476cd10eaaabff66510f8d130fbea59b5ac5fbd0da4128b18cd3e97e101 | Python | 9,737 | 170 | import numpy as np
import os
import sklearn
from sklearn import metrics
import time
from time import perf_counter
import matplotlib.pyplot as plt
import matplotlib
matplotlib.use('Agg')
from functions_OC import list_files_in_folder, create_save_dir
# The code can require changes if not the same format of folder names i... |
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