sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
f616b1c5b2c1fad304fd05b5b0cce1d17ff158c47da6945dfc0c80a84fad8214 | Python | 5,537 | 121 | """
Small python script to extract read counts from illumina NovaSeq X demultiplexing and display them in a table and bar chart.
"""
import argparse
import matplotlib.pyplot as plt
import numpy as np
import seaborn as sns
import pandas as pd
def parse_args():
parser = argparse.ArgumentParser(description="Script... |
05327929944d168e81a938cdbde5f5b93bb9007e5ab6c865cbae07e59fd3b199 | Python | 5,541 | 176 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
'''
usage:
python <name.py> --v root.vtk --folder '/Users/jiangshengdian/Desktop/Daily/PhD_project/Platform/fullmorpho/data/morpho_showdata_for_clusters/3/*'
python full_morpho/analyses/viz_swc_in_vtk_ccfbrain.py --v full_morpho/analyses/root.vtk --folder 'D:/mygitcode/ful... |
7f4ee042016722f09009f289368d8c6e0277d2b6d80470f7dc57c7ff79d4d151 | Python | 5,541 | 180 | # Computes the Purcell enhancement factor of an in-plane dipole in a planar
# dielectric cavity with lossless metallic walls. The result is computed in
# cylindrical and 3D coordinates and compared with the analytic result from:
# I. Abram et al., IEEE J. Quantum Electronics, Vol. 34, pp. 71-76 (1998).
# tutorial refe... |
5d1b70a1f4531eaaf61cd48a63451c75a5999c8af87444fef0dd305e79b19a69 | Python | 5,542 | 171 | '''
author: @emma
compute importance scores for each brain ROI based on a saliency map
importance score = (#salient voxels in region)/(#total voxels in region) x 100%
JMI paper code modified to SimBA data 2023/07/04
'''
import os
import vtk
import argparse
import pandas as pd
import numpy as np
... |
923842ef8606096330b5b6d815cac063dbe085b6bdab17ff92959711dcaa0ea9 | Python | 5,545 | 136 | import os
import pandas as pd
from scipy.io import loadmat
from sklearn.model_selection import train_test_split
from datasets.SequenceDatasets import dataset
from datasets.sequence_aug import *
from tqdm import tqdm
signal_size = 1024
ADBdata_source=[['KA05'],['KA03'],['KI03']]
ADBdata_target=[['KA01',... |
c0e42f141cf52f42cfe5ceb201e7ce9c992c3c94cfb78b1c10ec12cc9fb38c0c | Python | 5,546 | 107 | #!/usr/bin/env python
# relion_run_topaz
# This is to run Topaz-Denoise training (https://github.com/tbepler/topaz) from Relion as an External job type
# Rafael Fernandez-Leiro 2020 - CNIO - rfleiro@cnio.es
# Alex J. Noble 2020 - NYSBC - anoble@nysbc.org
# Run with relion external job
# Provide executable in the gui... |
117db25dfa39a926d2ab112aa5e34860dcff6b54bb22cde53b9248ef23446258 | Python | 5,547 | 180 | from __future__ import annotations
import pandas as pd
import numpy as np
from numpy._typing import NDArray
from typing import Iterable, Optional
import logging
logger = logging.getLogger(__name__)
def max_col(X: pd.DataFrame | NDArray) -> NDArray:
max_col_index = np.argmax(X, axis=1)
if not isinstance(X, pd... |
82a5ac4b62255144c1d430a9f93e0179ab729a668e9144ef930bcd2d5a50f6c3 | Python | 5,547 | 149 | import torch
import torch.nn as nn
from elasticai.creator.nn.integer.concatenate.design import (
Concatenate as ConcatenateDesign,
)
from elasticai.creator.nn.integer.design_creator_module import DesignCreatorModule
from elasticai.creator.nn.integer.math_operations.math_operations import MathOperations
from elasti... |
0de653ddee24297caa53ef35004522c47b4b736ad3b44687ad93b757d41b3799 | Python | 5,548 | 158 | """Model inversion for stimulus estimation from photocurrent.
Port of EstimateStmFromPhotocurrent.m
"""
from dataclasses import dataclass
import numpy as np
from scipy.signal import lfilter
from scipy.signal.windows import gaussian
@dataclass
class InversionResult:
"""Results from model inversion."""
esti... |
13f7ffe469fb0a978d97da597989a4ddd5812b6d2a12745b61105eecc779518d | Python | 5,551 | 189 | # coding=utf-8
# Copyright 2026 The Google Research Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicab... |
0a811068be7bbce7c7a4aad4f84d0882b1046cc9c642d0a4f0e4de7ef179f14d | Python | 5,552 | 153 | import numpy as np
import matplotlib.pyplot as plt
from hippo.environments.w_maze import get_wmaze
from hippo.environments.action_perception import action_perception_loop
from hippo.environments.sequences import EvaluationSequences3x3WMaze
from hippo.visualization import visualize_trajectories, plot_B
from hippo.agent... |
8b6c9224edf2d179751e0caf583c1911f647abda2760fdd799532f49d584e765 | Python | 5,552 | 126 | import numpy as np
import jax
import jax.random as jr
import jax.numpy as jnp
import pandas as pd
import pickle
import os
from matplotlib import pyplot as plt
from dynamax.hidden_markov_model import GaussianHMM, DiagonalGaussianHMM
from BEBE.models.preprocess import static_acc_filter, load_wavelet_transformed_data
fr... |
602d40c890937b49cd5ab9d56f72d6a43e201006b5bcea22010041b67fcf1ca7 | Python | 5,553 | 150 | """Compare two CCF-editor sessions and summarise where they differ.
A session JSON captures every dragged contour polygon per slice;
two sessions over the same pristine annotation produce two
modified annotations that may differ slice-by-slice. The diff
helper here surfaces:
* slices touched in A but not B (an... |
8d191c5d34536bf237ff11f722c36586238a44797a72594ad68dad42105ad41c | Python | 5,553 | 117 | import os
from typing import Tuple, Union
import numpy as np
import pandas as pd
from sklearn import model_selection
from torcheeg.datasets.module.base_dataset import BaseDataset
from ..utils import get_random_dir_path
from .utils import create_subset, ensure_cache, read_indices, write_indices
def train_test_split_... |
2ed7777d9f21b04f97805cf164f9347d69b43eae55f2635b37474912ebaba354 | Python | 5,554 | 133 | import argparse
from datetime import datetime
from pathlib import Path
from warnings import filterwarnings
import lightning.pytorch as pl
import pandas as pd
import torch
import yaml
from tqdm import tqdm
from dataset import TCGA_Program_Dataset
from datasets_manager import TCGA_Balanced_Datasets_Manager, TCGA_Datase... |
df7745aabd88ebb6cd537ca4ece107e15c3b09eb531fd2c18a42d632df69901d | Python | 5,554 | 77 | #! /usr/bin/env python
# -*- coding: utf-8 -*-
#! /usr/bin/env python
# -*- coding: utf-8 -*-
import os
from lab.environments import LocalEnvironment, MaiaEnvironment
from lab.reports import Attribute, geometric_mean
from common_setup import IssueConfig, IssueExperiment, DEFAULT_OPTIMAL_SUITE, is_test_run
BENCHMAR... |
f5a0f3a2b3848c1ea2a40977cb1b5b91b653f627eb7f791b4ff35f5f2c78afa6 | Python | 5,554 | 137 | import torch
import logging
import os
import Models.model_func as Model_Func
import pickle
from tqdm import tqdm
class ScikitFeatBaseline_Model(torch.nn.Module):
def __init__(self, dataset:str, device:torch.device, input_dim:int, classes:int, lr=0.001):
super().__init__()
assert isinstance(input_d... |
00ea4376607af824f8355937b8b74f5b47478aad9bfaefb9fd08e9ab92552621 | Python | 5,555 | 152 | """
(*)~---------------------------------------------------------------------------
Pupil - eye tracking platform
Copyright (C) 2012-2020 Pupil Labs
Distributed under the terms of the GNU
Lesser General Public License (LGPL v3.0).
See COPYING and COPYING.LESSER for license details.
------------------------------------... |
7322584fdbcfc99209ce4c5913864883ca19b89f2c68090003f8213302c44cfa | Python | 5,556 | 159 | from scipy.integrate import solve_ivp
import matplotlib.pyplot as plt
import numpy as np
import math as m
from mpl_toolkits.mplot3d import Axes3D
import torch
import torch.optim as optim
from Rosenbrock import Rosenbrock_func
from Quadratic import Quadratic_func
from Rastrigin import Rastrigin_func
def ... |
6e881605bdfe6f23082febfbe997fc2a0e9bda6e515055771a97179eef920631 | Python | 5,557 | 161 | import io
from collections import deque
from uuid import uuid1
import bl_ext.blender_org.molecularnodes as mn # type: ignore
import bpy
import matplotlib
import matplotlib.pyplot as plt
from MDAnalysis.core.groups import AtomGroup
from PIL import Image
matplotlib.use("Agg")
# Annotations are auto-registered
# Unregi... |
5570bcb57a7b1f6360ce1aee969c561918184e502bacb2938021890da080a0ec | Python | 5,558 | 191 | #!/usr/bin/env python
# coding: utf-8
# ## p53 feature stability analysis
#
# How stable (in terms of performance, and eventually coefficients) are TP53 mutation prediction models fit on the same dataset? We're particularly interested in how they generalize across domains (in our case tissues/cancer types): can model... |
c9773f9aff27acbe10b1ce54a698ffbdf32456bc3200a111809897ecff6e45da | Python | 5,558 | 124 | # set QT_API environment variable
import os
os.environ["QT_API"] = "pyqt5"
import qtpy
# qt libraries
from qtpy.QtCore import *
from qtpy.QtWidgets import *
from qtpy.QtGui import *
# app specific libraries
import control.widgets as widgets
import control.camera as camera
import control.core as core
import control.c... |
108a5ce24c4fbd7906f58bdb0ed758918915100176ad3d14ee5212b2bbc19922 | Python | 5,559 | 149 | import matplotlib.pyplot as plt
import numpy as np
from skimage.color import rgb2gray
from skimage.io import imsave
from cv2 import imread
import os
from config import DATA_DIR
import shutil
import preprocess
from dataloader import DATA
def visualize_labels(dataset):
n, bins, patches = plt.hist(x=dataset.labels... |
107c14d5e8e2a23058d2f3541a8279fd53fab1cf04afa3b8180db571bdd67d4c | Python | 5,560 | 151 | from typing import List
import numpy as np
import pandas as pd
from pandas.tseries import offsets
from pandas.tseries.frequencies import to_offset
class TimeFeature:
def __init__(self):
pass
def __call__(self, index: pd.DatetimeIndex) -> np.ndarray:
pass
def __repr__(self):
retur... |
69f69cf685d2eebcf2e558738e77f694706e7045e6f18386a41cf696ee5232ed | Python | 5,561 | 174 | # coding=utf-8
# Copyright 2026 The Google Research Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicab... |
5894801f33b579418e4a82f6c4508efe306a9364486079c617661dc9bbcef055 | Python | 5,562 | 181 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
'''
Fig4b
usage:
python Fig4b_cell_viz.py --folder "/Users/jiangshengdian/Desktop/Daily/PhD_project/Platform/fullmorpho/data/morpho_showdata/0/*"
'''
import pandas as pd
import numpy as np
import os
import math
import argparse
import vtk
import vtkmodules.vtkInteractionSt... |
7851fb71a70be8dd12afd5b91f13266d7872d61910ce1d5cec3ed2095af4fb1a | Python | 5,562 | 158 | from typing import cast
import numpy as np
from scipy.optimize import minimize
from scipy.stats import gaussian_kde
from .block_tools import FloatArray, blocking, check, fblocking
class BlockAnalysis:
"""Estimate statistically reliable errors from correlated samples.
The input series may represent one or m... |
e359636519e8c749802a1abd0701fc3474025dbf889526f9731446dc9482219d | Python | 5,562 | 188 | from nose.tools import *
from pyccg.chart import *
from pyccg.lexicon import Lexicon
from pyccg.logic import *
def _make_lexicon_with_derived_category():
lex = Lexicon.fromstring(r"""
:- S, NP
the => S/NP {\x.unique(x)}
foo => NP {\x.foo(x)}
bar => NP {\x.bar(x)}
baz => NP {\x.baz(x)}
""", include_se... |
b05d42b77cd0339ffe55011c9f2fd4103be4bd729b5846fce8cb850f74a5137e | Python | 5,563 | 94 | """NORMALISATION.py 2026-10-01. Pre-registration: 04-NOTES/PREREG-2026-10-01a-NORMALISATION.md
Divisive normalisation (Olsen, Bhandawat & Wilson 2010) in the antennal-lobe cut-out of Shiu et al.'s file: a test input to
DL5 or VM7d with and without a mask on every other glomerulus, five sign/deletion conditions, fit of ... |
4f185fe34885214833cdd782d5fb403b19200b3333be2b3bb861140569efe355 | Python | 5,564 | 131 | #! /usr/bin/env python3
import os
import subprocess
import logging
#import APT_interface
import pickle
import numpy as np
import torch
from argparse import Namespace
import random
import time
import mmcv
import mmpose.utils
class cd :
"""Context manager for changing the current working directory, and automagica... |
8940621743f03743e53d3a908c5281c406981f029b1ae131d51013549d47fbd9 | Python | 5,564 | 154 | # coding=utf-8
# Copyright 2026 The Google Research Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicab... |
04d6956dbebd54ae95ba32cc2f51a317c1aef42f45f11fda2ec57d42d20de275 | Python | 5,565 | 160 | # ----------------------------------------------------------------------
# Copyright (C) 2016, Numenta, Inc. Unless you have an agreement
# with Numenta, Inc., for a separate license for this software code, the
# following terms and conditions apply:
#
# This program is free software: you can redistribute it and/or mo... |
82bb5ce4ae8463e7974cfddd53f2d5dd35a8566ea46607148587cd8fbc8ac600 | Python | 5,565 | 138 | import lightning.pytorch as pl
import torch.nn as nn
import torch
from lightning.pytorch.utilities import grad_norm
from torchmetrics.classification import BinaryAccuracy, BinaryAUROC, BinaryRecall, BinaryPrecision, BinaryF1Score
from torchmetrics import MetricCollection
from hicdiffusion_encoder_decoder_model import H... |
748f34f3cb8eee11d9d49f6792768f9e74a20a7b250e0a600c41005e32529161 | Python | 5,566 | 152 | # pylint: disable=too-many-statements, too-many-locals, invalid-name, unbalanced-tuple-unpacking, no-value-for-parameter
"""Script for running experiments: tuning and testing hypertuned models"""
import os
from copy import deepcopy
from omegaconf import OmegaConf, DictConfig
import hydra
import pandas as pd
import nu... |
e95afee5d0b883312d6769328cb17a4b7d92163a7e4a3bae3ea3c17fbd0cc8db | Python | 5,566 | 156 | from typing import List
import numpy as np
import pandas as pd
import statsmodels.api as sm
import scipy.stats as st
class UVMRbased:
def __init__(self, pv_iv: float = 5e-8, min_ivs: int = 5, fwer_exp: float = 0.05):
"""
Initialize the UVMRbased instance with parameters for the analysis.
... |
dd82124968e6f1d851a4f0a9056aae0638d050dfb829a14ce7ac6ece7f6189b0 | Python | 5,567 | 161 | import numpy as np
from neurolib.utils.collections import dotdict
params = dotdict({})
params.LIMIT_DIFF = 1e-4
params.LIMIT_DIFF_ID = 1e-12
params.TEST_DURATION_6 = 0.6
params.TEST_DURATION_8 = 0.8
params.TEST_DURATION_10 = 1.0
params.TEST_DURATION_12 = 1.2
params.TEST_DELAY = 0.2
params.ITERATIONS = 10000
params.LO... |
55ec2c5c003df1a1752049c17e295305976137a534886c2fc8081834f5f4aa3a | Python | 5,568 | 160 | # coding=utf-8
# Copyright 2026 The Google Research Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicab... |
5c4ae39c51e41d71dd98abaee4615bb740141e06d35de1e2b5a923d431dd6322 | Python | 5,568 | 134 | import json
import os
import pandas as pd
import scipy.sparse
import tiledb
from anndata import AnnData
from cirrocumulus.abstract_dataset import AbstractDataset
class TileDBDataset(AbstractDataset):
def get_suffixes(self):
return ["cxg"]
def get_schema(self, filesystem, path):
# path is to... |
1b4aad541b9415f41326a76534d78bc19fb17a0d8eac4cb58a0516eff4ee88c9 | Python | 5,569 | 123 | import os
import sys
import glob
import argparse
import numpy as np
import torch
from inference import WSIInference
def evaluate_dataset(pipeline, test_dir, output_dir=None):
"""Evaluate model performance on a dataset of WSI slides.
Args:
pipeline: Initialized WSIInference pipeline
test_di... |
5d590b8bc5c37abd801c93848566af06b107e046fabc7bbd6a747923741b8b73 | Python | 5,569 | 92 | """KEYSTONE_ROBUST.py 2026-10-02. Pre-registration: 04-NOTES/PREREG-2026-10-02-KEYSTONE-ROBUST.md (parts R2-R4)
R2: the flip of v2LN30 root 720575940635945919 (the left one; the prereg calls it "right") across synaptic weight x receptor drive (rate theory). R3: excitatory only onto projection neurons,
or only onto ev... |
86ab73e90e8a2394706b656d6473d378b1f5808dc2e1db954867c500ba0028b1 | Python | 5,571 | 200 | """Core recipes for Q-Chem."""
from __future__ import annotations
from importlib.util import find_spec
from typing import TYPE_CHECKING
from quacc import job
from quacc.recipes.qchem._base import run_and_summarize, run_and_summarize_opt
from quacc.utils.dicts import recursive_dict_merge
has_sella = bool(find_spec("... |
23c64afe605606a3b39ae841d0556b7bf09513e1633f53044210abbc0c04b444 | Python | 5,572 | 129 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""build_flywire_variant.py —— 从 FlyWire 源 CSV 重建连接组二进制（含等价性自检），
并生成"谷氨酸抑制"变体（符号必要性实验）。
背景：复审 R1/伸展项——MaleCNS 的正向符号翻转（glut 抑制→兴奋）已证明充分性，
本脚本提供 FlyWire 一侧的必要性检验（glut 兴奋→抑制）。
管线（复现 vendor/snedea-flybrain/scripts/build_connectome.py 的聚合逻辑）：
1. neurons.csv.gz 行序 = 原始索引（与 s... |
7e2982ee5c302e59ed8b0b1e7a46feff5a7772e20ab2c1721d0ad4a4bccaa9eb | Python | 5,573 | 124 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
''' Statistical comparison of listening and imagination, and of sound1 and sound3 in source space '''
import mne
import numpy as np
from matplotlib import pyplot as plt
from stormdb.access import Query
from pickle import load
from scipy import stats
from mne.datasets impor... |
2e31235f366524e63a14478a253d4fe53a5d418abb63eec3e8f6a63e88f7d860 | Python | 5,574 | 160 | # coding=utf-8
# Copyright 2026 The Google Research Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicab... |
4bcecd6d15cb23074e58c7ed94b40add9d19dddb9b3845bb8b17d5485315075e | Python | 5,574 | 161 | """
Stimulus optimization
=====================
This script shows how to optimize the stimulus presentation by means of selecting the optimal subset of stimuli from a
set of candidate stimuli and how to select an optimal layout to allocate them to a stimulus grid. For more information
on the optimization of such subset... |
5db61cc03ec6a08cc837d75fe1a79238aae4a3da69967ffcfd89bfb9dbc53d59 | Python | 5,577 | 136 | import os
import glob
import pandas as pd
import re
import matplotlib.pyplot as plt
import numpy as np
from sklearn.metrics import mean_absolute_error, r2_score
# Dir
directory = "Results_files/KMER_gamma_free_0.1-1-10/"
files = glob.glob(os.path.join(directory, "KMER_prediction_*.txt"))
# Leer el archivo de caracte... |
34b2b19221efa7606c197fdd7d36530a259d37cd6aa2f77e84597be0a69d604e | Python | 5,578 | 133 | import os
import unittest
import hed
from hed.errors import HedFileError
from hed.models import HedTag
from hed.schema import HedKey, HedSchemaGroup, get_hed_xml_version, load_schema, load_schema_version
class TestHedSchema(unittest.TestCase):
@classmethod
def setUpClass(cls):
cls.hed_xml_3g = os.pat... |
956c6a2b4239e0f0c5c997ae31eef9dde664a4e6864510e6875fe1679357f057 | Python | 5,578 | 173 | from wonambi import Wonambi
from PyQt5.QtWidgets import QAction
from os.path import basename, splitext
import csv
from pytest import approx
from .test_scroll_data import (channel_make_group,
find_in_qt,
screenshot,
)
from .pa... |
3f17eb4ec2f74475802cf08f17f2c659a70938de0f2da60966a5822e090d6e70 | Python | 5,579 | 126 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""export_sign_tables.py —— 为对照实验（probe_controls.mjs）导出"按递质拆分"的中间表。
背景：v5.1 的符号干预翻转的是整条递质规则。要回答"起作用的是谷氨酸身份，还是任何
同等规模、同等位置的符号改变"，需要能按神经元、按递质任意组合地重新赋号。本脚本
把两份数据导出为可在 Node 里快速重新赋号的中间表（产物已 .gitignore，随时可重建）。
输出（game/data/derived/）：
1. flywire-pair-nt.bin.gz —— FlyWire 源表 c... |
9ae30b1bb1c73641a22a4a27d3089b8eee68a345384f3a92cf3e5149ba22a5f2 | Python | 5,579 | 184 | """
Various utilities for neural networks.
"""
import math
import torch as th
import torch.nn as nn
# PyTorch 1.7 has SiLU, but we support PyTorch 1.5.
class SiLU(nn.Module):
def forward(self, x):
return x * th.sigmoid(x)
class GroupNorm32(nn.GroupNorm):
def forward(self, x):
return super(... |
cd8e2e2d63ce0db587d7bc31dafaf82d3ffe6ca972f5c769c3350dfd7f665a78 | Python | 5,579 | 142 | import numpy as np
import random
from collections import OrderedDict
from examples.pybullet.utils.pybullet_tools.utils import add_data_path, load_pybullet, set_point, Point, create_box, \
stable_z, HUSKY_URDF, load_model, TURTLEBOT_URDF, joints_from_names, \
set_joint_positions, get_joint_positions, link_from_... |
131788a1db1fcff73bc56ffbf7a69f59d221181b3e1dc4975dc02ac408793398 | Python | 5,581 | 154 | """Embedded, colour-preserving log view for GUI tabs.
Registration runs write ANSI-coloured output to ``<output>/console.log`` while
executing in a detached process. :class:`AnsiLogView` tails that file into an
in-GUI black-background monospace widget, translating ANSI SGR colour codes into
Qt text formatting - s... |
2ef81e37f97b2229a9beb8826f241e09dc54ab162c4b54d3d4801c7ccb636461 | Python | 5,583 | 153 | from collections import deque
from typing import Generator, Optional
import cv2
import torch
from torch import Tensor
from torch.nn import Module
from torchvision import transforms
import random
def resize(vid, size, interpolation='bilinear'):
# NOTE: using bilinear interpolation because we don't wor... |
c20e358e2e3748fbc4fd6c94eaee4d3c624bc9b14269072e6f86e667eef3360d | Python | 5,583 | 124 | from elasticai.creator.file_generation.savable import Path
from elasticai.creator.file_generation.template import (
InProjectTemplate,
module_to_package,
)
from elasticai.creator.vhdl.auto_wire_protocols.port_definitions import create_port
from elasticai.creator.vhdl.design.design import Design
from elasticai.c... |
5c382402c329fe32d7f668fee8449d7fb18affc46e5fd93020bc173a137519a3 | Python | 5,584 | 152 | """distutils.command.build
Implements the Distutils 'build' command."""
import sys
import os
from ..core import Command
from ..errors import DistutilsOptionError
from ..util import get_platform
def show_compilers():
from ..ccompiler import show_compilers
show_compilers()
class build(Command):
descrip... |
e8314e435bd54eeca783b6d3520667b769745d1b638c62183a304433fc932a7a | Python | 5,584 | 181 | import h5py
import click
import numpy as np
import seaborn as sns
import matplotlib.pyplot as plt
from basenji import plots
from basenji import dna_io
@click.command()
@click.option('--score',
'score_files',
required=True,
multiple=True,
type=click.Path(exists=T... |
03fed26f1b33f667a2f7f121e2c7dc4fc14a5d683c5a39fd5eb9d31fd03a6559 | Python | 5,585 | 183 | """Utility functions for dealing with defects."""
from __future__ import annotations
from importlib.util import find_spec
from typing import TYPE_CHECKING
from monty.dev import requires
from pymatgen.core.periodic_table import DummySpecies
from pymatgen.entries.computed_entries import ComputedStructureEntry
from pym... |
3ab546b764a83e9d28034e724cc2705ef605f21438d0893e83097c056f41b664 | Python | 5,585 | 153 | '''
This code is modefied based on a TCN impelemtation by https://github.com/locuslab/TCN
'''
import csv
import json
import math
import joblib
import argparse
from pathlib import Path
from collections import OrderedDict
import numpy as np
import torch
import torch.nn as nn
from torch.nn.utils import we... |
82db9c67147d403ce094f558ea4eb37b6db43bbafc14a7d10992929f0d845355 | Python | 5,585 | 123 | #!/bin/env python
"""
OXASL - Registration for ASL data
Michael Chappell, IBME QuBIc & FMRIB Image Analysis Groups
Copyright (c) 2008 University of Nottingham
"""
from __future__ import unicode_literals
import os
import numpy as np
import fsl.wrappers as fsl
from oxasl import reg
from oxasl.reporting import LineG... |
db4badb5f0be0630bc41ee17ba7530d6b68b271ca986f54f7d6fa5d13f3efbe8 | Python | 5,587 | 154 | # coding=utf-8
# Copyright 2026 The Google Research Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicab... |
ac9a31937e0bfd2f04b1323bf1bb9d643824b97b94b0b293ead941b37d176e67 | Python | 5,588 | 181 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
'''
Fig4b
usage:
python Fig4b_cell_viz.py --folder /Users/jiangshengdian/Desktop/Daily/PhD_project/Platform/fullmorpho/py/morpho_showdata/0
'''
import pandas as pd
import numpy as np
import os
import math
import argparse
import vtk
import vtkmodules.vtkInteractionStyle
im... |
3be62e2ae190a4acfb99a9abf12b859fae4e04a8558897421bbd38e389a5ea9a | Python | 5,589 | 148 | # Build an index dictionary for sequence position -> reference position & signal position
import re
import pysam
import pod5
import pickle
import zlib
import lmdb
from collections import defaultdict
from tqdm import tqdm
import numpy as np
DATA_TYPE = np.int32
START_H_PATTERN = re.compile(r'^(\d+)H')
END_H_PATTERN = r... |
4fb586fa247746e62ec9cea0118d3ee2f78631790561056e8f9ca6b7284432d3 | Python | 5,589 | 129 | import itertools
import numpy as np
import pytest
from MDAnalysis.tests.datafiles import DCD, GRO, PSF, XTC
import molecularnodes as mn
from molecularnodes.nodes.geometry import StyleRibbon, StyleSpheres
from .constants import codes, data_dir
from .utils import GeometrySet
formats = ["pdb", "cif", "bcif"]
@pytest.ma... |
ae97c0da6c0abf0ca476cfae92adfe36eacd5c85829b2497f649a3834ed9eab7 | Python | 5,589 | 136 | #! /usr/bin/env python
# -*- coding: utf-8 -*-
import itertools
import os
from lab.environments import LocalEnvironment, BaselSlurmEnvironment
from downward.reports.compare import ComparativeReport
import common_setup
from common_setup import IssueConfig, IssueExperiment
from relativescatter import RelativeScatterP... |
8731269642ca04b11e7bbbacc8ee3eb96f68393e72b7fa001503485ae5a29fba | Python | 5,590 | 118 | import inspect
from typing import Any, Callable, Dict, Optional, Text, Union, Iterable
import numpy as np
import tensorflow.experimental.numpy as tnp
import tensorflow as tf
#tnp.experimental_enable_numpy_behavior(prefer_float32=True)
from tensorflow.keras import layers as kl
@tf.keras.utils.register_keras_serializab... |
9764adc9c31a91bc6932c5b8118a27804d877da388267d2b92d5e4b98fbb5042 | Python | 5,590 | 168 | """Poincare ball manifold."""
import torch
import numpy as np
from manifolds.base import Manifold
from utils.math_utils import artanh, tanh
class PoincareBall(Manifold):
"""
PoicareBall Manifold class.
We use the following convention: x0^2 + x1^2 + ... + xd^2 < 1 / c
Note that 1/sqrt(c) is the Poin... |
8d9f600343e1a30f886ef52ccf8419818239be03ee15ead880ca545f7b8d494c | Python | 5,591 | 156 | # Acquisition helper functions from PySpin
import PySpin
import numpy as np
import scipy.ndimage
from matplotlib import pyplot as plt
from PIL import Image
from Library import pyspin_helper as psh
import time
class app_variables():
def __init__(self,cam):
self.cam = cam
self.image_result = self.cam... |
8e9b00750bc2042900baf9845d823dd1357890d18ed98d7736a0ebfcfaef7610 | Python | 5,591 | 148 | import re
import functools
import distutils.core
import distutils.errors
import distutils.extension
from .monkey import get_unpatched
def _have_cython():
"""
Return True if Cython can be imported.
"""
cython_impl = 'Cython.Distutils.build_ext'
try:
# from (cython_impl) import build_ext
... |
0ee367da760ba79da0d01b4f727d60da74f69890e391bfa378292b9a0f3b5d90 | Python | 5,593 | 117 | import unittest
from unittest import mock
import os
import pandas as pd
from sklearn.decomposition import PCA
import sys
sys.path.append(os.path.dirname(os.path.realpath(__file__)) + "/../../src")
from hornet.uml import create_pca_dataset
class TestCreatePcaDataset(unittest.TestCase):
def setUp(self):
sel... |
3e70e523a75074be0c98fa366774a1e5d9e080fb8983a7436cb208b82d9323a6 | Python | 5,593 | 123 | import torch
from torch.optim.optimizer import Optimizer, required
class PIDAccOptimizer_SI_AAdRMS(Optimizer):
r"""Implements stochastic gradient descent (optionally with momentum).
Nesterov momentum is based on the formula from
`On the importance of initialization and momentum in deep learning`__.
Ar... |
9cf447b32a7580e3081cdb10b09ce9d78b30afb3c617682a405c7e775ded18fb | Python | 5,594 | 171 | from typing import Iterable, List, Literal
import bpy
from bpy.types import GeometryNodeTree, Node
from databpy.nodes import append_from_blend, get_output, swap_tree
from nodebpy import TreeBuilder, arrange
from nodebpy import geometry as g
from .. import color
from ..assets import MN_DATA_FILE
from . import geometry a... |
529be11099e7e3f77783a34b5cbe4517e98e4be0976b3b36b5893b2c4a577b04 | Python | 5,595 | 121 | import collections
import gc
from typing import Tuple, List
import numpy as np
import scanpy as sc
import scipy.stats
import sklearn.linear_model
import sklearn.svm
from sklearn.cluster import KMeans
from tqdm.auto import tqdm
from . import types
def get_pca(adata: types.AnnData, n_comps: int = 50) -> np.ndarray:
... |
f762eb2d131aa3463172c7aa5d2f0dd6f1898f7e6d3b94ab5e0bfd108f53be03 | Python | 5,596 | 116 | import os
import glob
import math
import numpy as np
import torch
from torchdrug import core, data
from torchdrug.layers import functional
from torchdrug.core import Registry as R
from siamdiff import rotamer
# the function to create conformers for the siamese diffusion scheme
# a commonly used scheme for sampling... |
dc0373bbeb5ad6b2bf0fd5546b021bf80af641860e0c336c5f39d600ae297b14 | Python | 5,597 | 221 | # -*- coding: utf-8 -*-
#
# Helpers to generate correct data, labels etc. for the plots
# from Syncopy dataypes
#
# Builtin/3rd party package imports
import numpy as np
from copy import deepcopy
import re
import functools
def revert_selection(plotter):
"""
To extract 'meta-information' like time and freq a... |
5e0d8b94e053511c31682afb67cedb4ac7ff128ad5f5d623390c2a16eed0faaf | Python | 5,598 | 151 | # coding=utf-8
# Copyright 2026 The Google Research Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicab... |
75ff2f6e1f97e02655881e08c7e060ade915ad3728911124f8d9f2fb7aee054d | Python | 5,599 | 160 | import numpy as np
import torch
import torch.nn as nn
import torch.nn.functional as F
from skorch import NeuralNet
class LogisticRegression(nn.Module):
"""Model for PyTorch logistic regression."""
def __init__(self, input_size):
super(LogisticRegression, self).__init__()
# one output for bina... |
6df28079546ec7fd90c1c8821d0d072266d6f2e79847de4b9474f4dc10afba1d | Python | 5,600 | 139 | from nnunetv2.training.nnUNetTrainer.variants.network_architecture.nnUNetTrainerNoDeepSupervision import \
nnUNetTrainerNoDeepSupervision
from nnunetv2.utilities.plans_handling.plans_handler import ConfigurationManager, PlansManager
from nnunetv2.training.lr_scheduler.polylr import PolyLRScheduler
from torch import... |
78388a3b6922f26d63132d14f7f8a2102c1a953a98b1d46fe2476e6255974ae2 | Python | 5,600 | 166 | """
Script for filter a MbGraphMCF object by extracting a filament network with cross-linkers between to segmented
regions
Input: - MbGraphMCF (pickle file)
- Cross-linkders setting
Output: - A filtered version of the input MbGraphMCF with the cross-linkers
- A VTP file with ... |
d2e93fab02ec947654f169111a9d2c056fc34b5b8d64e1d0c53686e89e356a83 | Python | 5,600 | 132 | """Read cell-point coordinates from an AnnData ``.h5ad`` with an explicit
field->axis mapping.
See ``docs/superpowers/specs/2026-08-13-h5ad-points-registration-design.md``.
AnnData has no universal spatial-coordinate convention, so the caller must
state which ``obsm`` matrix or ``obs`` columns hold the coordinate... |
90dd49b5da5bd6561deacfbd0ecdc18c14776966352720408dbeb38eaddab922 | Python | 5,603 | 122 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
# Copyright 2024 Clinic for Diagnositic and Interventional Radiology, University Hospital Bonn, Germany
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy ... |
d812743204bff2a953e255243a61cc57a165d0e4805dcb6d1f159e5c0ee37b26 | Python | 5,603 | 115 | import os
from copy import copy
from typing import Union
import numpy as np
import pandas as pd
from sklearn import model_selection
from torcheeg.datasets.module.base_dataset import BaseDataset
def train_test_split_cross_trial(
dataset: BaseDataset,
test_size: float = 0.2,
shuffle: bool = Fal... |
729e968974da11df0b5b0c62ce99c54a66c23928b33cb725007145b2ac51aaab | Python | 5,604 | 172 | """distutils.command.build_scripts
Implements the Distutils 'build_scripts' command."""
import os
import re
from stat import ST_MODE
from distutils import sysconfig
from ..core import Command
from ..dep_util import newer
from ..util import convert_path
from distutils._log import log
import tokenize
shebang_pattern =... |
6fea55e7fc2a8716f85cd1ad284ccfd667e5bf90f37f06423ecd24cb9c34006d | Python | 5,605 | 174 | # Copyright (c) 2021, Ko Sugawara
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
#
# 1. Redistributions of source code must retain the above copyright notice,
# this list of conditions and t... |
e9d1a2cb690edbb725e8737eaa9f56ea86a0ca9aefb22f36078a0c1f836a5d69 | Python | 5,605 | 148 | #
# MIT License
#
# Copyright (c) 2022 GT4SD team
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge,... |
f2e4259fbd072ee81a572f53ce7cb687b2a6a19afa5eef07aea58e55a73cdfb2 | Python | 5,605 | 116 | '''
Average node properties at nodes using the simplicial structure
Author(s): Daniela Egas S.
Last update: 02.2024
'''
# General
import numpy as np
import pandas as pd
import pickle
# Connectomes and network analysis
import conntility
from connalysis.network import stats as nstats
# Specific to this project
impor... |
2c7b71a0ca8f88a0258d69d49e597ecc9e79fc9ba0cb4538faf99c6766ef6cb4 | Python | 5,606 | 185 | #
# MIT License
#
# Copyright (c) 2022 GT4SD team
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge,... |
bd8fc03ce541fb701660530dff6c980b765bdf09e0ce858ee465db18a901f18d | Python | 5,606 | 175 | # coding=utf-8
# Copyright 2026 The Google Research Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicab... |
0488491406259b1c9769a0dbe22874492db233da7c1f6e0fb46c523c033f7476 | Python | 5,607 | 149 | # Node-group asset "oxDNA Vectors" (GeometryNodeTree), dumped by nodebpy.assets.dump_library.
# Rebuild the library with nodebpy.assets.build_library (nodebpy build).
# _build_group() is the source of truth: the docstring, __init__ and accessors are regenerated from it on the next dump.
from typing import TYPE_CHECKING... |
33a5291f6f14ac69000890bee404e99670579ea32dc987d8c37eb32b0a453909 | Python | 5,608 | 190 | # Node-group asset "Visualize Angle" (GeometryNodeTree), dumped by nodebpy.assets.dump_library.
# Rebuild the library with nodebpy.assets.build_library (nodebpy build).
# _build_group() is the source of truth: the docstring, __init__ and accessors are regenerated from it on the next dump.
from typing import TYPE_CHECKI... |
58b17f7a37f6653e4924eb22ca73df324e28d1a827693867f77ddf446d6831fa | Python | 5,608 | 220 | from __future__ import annotations
import pytest
ct = pytest.importorskip("covalent")
from ase.build import bulk, molecule
from quacc import flow, job, subflow
from quacc.recipes.emt.core import relax_job, static_job # skipcq: PYL-C0412
from quacc.recipes.emt.slabs import bulk_to_slabs_flow # skipcq: PYL-C0412
... |
681239d4a3d6453561e76425e5cf1f343e6ec06969d7a94c5194710aa44d1d4d | Python | 5,608 | 139 | from nnunetv2.training.nnUNetTrainer.variants.network_architecture.nnUNetTrainerNoDeepSupervision import \
nnUNetTrainerNoDeepSupervision
from nnunetv2.utilities.plans_handling.plans_handler import ConfigurationManager, PlansManager
from nnunetv2.training.lr_scheduler.polylr import PolyLRScheduler
from torch import... |
b8358553a5b8a44bd4f71eccd7a03cab2ba2766c6341131d07eff1446fd78542 | Python | 5,609 | 139 | from nnunetv2.training.nnUNetTrainer.variants.network_architecture.nnUNetTrainerNoDeepSupervision import \
nnUNetTrainerNoDeepSupervision
from nnunetv2.utilities.plans_handling.plans_handler import ConfigurationManager, PlansManager
from nnunetv2.training.lr_scheduler.polylr import PolyLRScheduler
from torch import... |
c0104e97183deb3053a6e9883e2644b6a17c30fff68debfa36f5a53ddaa7a9ce | Python | 5,609 | 170 | """Class to import straight text records.
"""
from logging import getLogger
from numpy import empty, float64, floor
from os import listdir
from os.path import splitext
from pathlib import Path
from .utils import DEFAULT_DATETIME
lg = getLogger(__name__)
class Text:
"""Class to read text format records. The reco... |
c7060c47948cf4f38d83f5b2442687cdd9b7a5f49508739f250e0a4b5b1c7597 | Python | 5,610 | 123 | """
Class to handle synapse nearest neighbour distance results (and storage)
last modified: Michael Reimann 01.2023
"""
import h5py
import numpy as np
import pandas as pd
class SynNNDResults(object):
"""
An object to hold results of synapse Nearest Neighbour Distance (NND) and read/write them from/to an HDF5... |
65d1f00128c36487de0414fdc1d95ca97b613bef694ecad5302236bdc4fd1930 | Python | 5,612 | 143 | """Custom quartodoc renderer for the node class pages.
The node groups are documented twice: GUI pages under `docs/nodes/` (generated
by `docs/generate.py`, holding the long-form prose and demo videos) and the
quartodoc class pages this renderer produces. For each node class this renders
the Inputs / Outputs docstring... |
50b162bfca216628d1f8be047e38b3ad762a910d5b563e6ed8d5d41885c5a21c | Python | 5,613 | 106 | #!/usr/bin/env python
import os
import pandas as pd
import numpy as np
import matplotlib.pyplot as plt
from nltools.data import Brain_Data, Adjacency
from nltools.mask import expand_mask, roi_to_brain
from nltools.stats import threshold
from nilearn import plotting as nplot
from sklearn.metrics import pairwise_distan... |
11d6866d9101042d745a37e6594dea120e84b2b66a62c9d9d3b3efd08ce8ada5 | Python | 5,615 | 172 | # coding=utf-8
# Copyright 2026 The Google Research Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicab... |
48be5d9b1fd9f68e6c471edf184e8d17e3dd519981ab76fa6ec23a2ef8d86192 | Python | 5,615 | 175 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
Example plot for LFPy: Single-synapse contribution to the LFP
Copyright (C) 2017 Computational Neuroscience Group, NMBU.
Execution:
python example_anisotropy.py
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU Ge... |
730ade3ac012cac59647d1ce9716c85251cabd3441f92dd175ddeff0a240dcd1 | Python | 5,615 | 182 | from io import BytesIO
import matplotlib.font_manager as font_manager
import matplotlib.pyplot as plt
import numpy as np
import seaborn as sns
from PIL import Image
class Colors:
def __init__(self):
"""
Constructs all the necessary attributes for the DataPreSetting object.
... |
ed2c84abbc5636cfd9c21f02d16434e0a293a8991a115cb7bc5a4a74c63d0a60 | Python | 5,615 | 136 | #! /usr/bin/env python
# ==============================================================================
# Copyright (c) 2021, Ko Sugawara
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
#
# 1. Re... |
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