sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
181302cacad45700009260ea342d1dee18d21d87b22d95e8d715afb503730e94 | Python | 20,773 | 431 | #!/usr/bin/env python3
"""Unit tests for the pure logic of ``scripts/do_schema_release.py``.
Covers the naming rules for the standard schema and a library, version checks, the check that
``hed_add_ids`` only added hedIds, CHANGELOG insertion and extraction, and the replacement of a
schema's rows in ``docs/schemas_over... |
d021fbdc49303ae577a6a30ca81a23f2ab4a68f783f8c50a48e3159f10804748 | Python | 20,773 | 604 | import win32com.client
import os, pdb
import time
import numpy as np
from collections import namedtuple
scanmandata = namedtuple('scanmandata',['img_forward', 'img_backword', 'offset_nm', 'len_nm', 'current','dI_dV'])
latmandata = namedtuple('latmandata',['time','x','y','current','dI_dV','topography'])
dissman... |
4cd49bdcc3806f9acebf7cf96a31e577336a42d082af0b52b13d06e7dbf70d61 | Python | 20,775 | 522 | """
Copright © 2023 Howard Hughes Medical Institute, Authored by Carsen Stringer and Marius Pachitariu.
"""
import os
from fig_utils import *
from matplotlib import patches
def brain_plot(ax, x, y, cweights, cmap, theta=np.pi*0.77, subsample=5,
vmin=None, vmax=None, brain_axes=True):
pos = ax.get_... |
7cc43fd41cfbbb00bab1cab7ce60b09a28ed5fb4d7fcade5f9bf1bdc229274f4 | Python | 20,775 | 571 | # 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... |
76efc5f48d4da7b04b86836c3028081b472e62b793dc6bf0e63af16114e925e0 | Python | 20,784 | 491 | """Utilities for loading and outputting HED schema."""
from __future__ import annotations
import functools
import json
import os
import warnings
from collections import defaultdict
from urllib.error import URLError
from hed.errors.exceptions import HedExceptions, HedFileError
from hed.schema import hed_cache
from he... |
e8e124ddbb78d5653b419a22caea153c6b0a394f89fc16c30e1a2e29b2179b46 | Python | 20,819 | 581 | import functools
import itertools
import logging
import os
import posixpath
import re
import urllib.parse
from dataclasses import dataclass
from typing import (
TYPE_CHECKING,
Any,
Dict,
List,
Mapping,
NamedTuple,
Optional,
Tuple,
Union,
)
from pip._internal.utils.deprecation import... |
2a6faba2c9cf1bffd28c990201684cdec28fa536dbf60b21501bf623e3b91e49 | Python | 20,828 | 528 | from __future__ import print_function
import sys
import torch
import torch.nn as nn
import torch.optim as optim
import torch.nn.functional as F
import torch.backends.cudnn as cudnn
import torchvision
import random
import os
import argparse
import numpy as np
from PreResNet_cifar import *
import dataloader_... |
2458705ae1947c66caa7f8bd867ece3e48c4f275b2b46822bb7aada8a7c94e12 | Python | 20,832 | 509 | # Copyright 2021 DeepMind Technologies Limited
#
# 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 agr... |
1c58831bb2cca1a06cf36f56ba8b6b7c8c1c12b38e13150e47f01e06dc3f4c25 | Python | 20,834 | 508 | # -*- coding: utf-8 -*-
#
# Copyright (C) 2013 Vinay Sajip.
# Licensed to the Python Software Foundation under a contributor agreement.
# See LICENSE.txt and CONTRIBUTORS.txt.
#
import hashlib
import logging
import os
import shutil
import subprocess
import tempfile
try:
from threading import Thread
except ImportErr... |
0de6acb166287cecbdbef7ca059382e902c274f94cde19607d18003b4d622860 | Python | 20,836 | 499 | import os
import argparse
from tqdm import tqdm
import torch
import torch.nn as nn
import torch.optim as optim
import numpy as np
import math
import random
import pandas as pd
from sklearn.metrics import mean_absolute_error, r2_score, accuracy_score, roc_auc_score, f1_score
from sklearn.model_selection import Stratifi... |
851ab0e8e799b1fc72c82c65300ef8d90aeeb94f1a55870515bc479252bdb355 | Python | 20,840 | 373 | import os
import sys
sys.path.append('/home/lifesim/MetaWorm/build/')
import interact
import numpy as np
import os
from neuron import h, load_mechanisms
from eworm.utils import *
from eworm.ghost_in_mesh_sim.worm_neural_network import WormNeuralNetwork
from matplotlib import pyplot as plt
import pickle
def normalize_... |
5f222987298d38a5e99f6e73b024544a4fe193c359397ae3c046f5e79fe26f47 | Python | 20,844 | 542 | # -*- coding: utf-8 -*-
"""sidecars classes"""
import itertools
import logging
import os
import re
from collections import defaultdict, OrderedDict
from fnmatch import fnmatch
from dcm2bids.acquisition import Acquisition
from dcm2bids.utils.io import load_json
from dcm2bids.utils.utils import DEFAULT, convert_dir, c... |
73234828964ccffc451eeba0021e9c82dc98003bcf52d90f274c36386089f4a4 | Python | 20,859 | 478 | """Implementation of transmit card."""
import contextlib
import ctypes
import logging
import threading
import numpy as np
from console.interfaces.acquisition_parameter import Dimensions
from console.interfaces.unrolled_sequence import UnrolledSequence
from console.spcm_control.abstract_device import SpectrumDevice
w... |
6572bd340364681918b5ce171e3b5999e952cacc74ff9134f0a7447d4e4eff05 | Python | 20,860 | 448 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Wed Oct 13 09:11:26 2021
@author: pyess
"""
import numpy as np
import os
import nibabel as nib
from sigfig import round as sfround
import matplotlib.pyplot as plt
import seaborn as sns
import scipy.stats
import itertools
## Syntheitic_P1 is patient ID 'RID... |
08ec1d9800855d7ba9307ed55447f92661e7a9582824c7bcd58b8a44222e3191 | Python | 20,873 | 593 | """
Create a wheel (.whl) distribution.
A wheel is a built archive format.
"""
from __future__ import annotations
import os
import re
import shutil
import stat
import struct
import sys
import sysconfig
import warnings
from email.generator import BytesGenerator, Generator
from email.policy import EmailPolicy
from glo... |
e9b19cb3fadca2663f16d41815f0d912fce74a1195e2c176f59f0e34172ee05e | Python | 20,880 | 622 | #!/usr/bin/env/python
# Copyright (c) Facebook, Inc. and its affiliates.
# All rights reserved.
#
# This source code is licensed under the license found in the
# LICENSE file in the root directory of this source tree.
from torch.utils.data import Dataset, DataLoader
import torch
import numpy as np
import os
import mat... |
616ebfe6b143778db3f628bdcf2c8bc644d97c50a79ec00078a931f723f41c5e | Python | 20,904 | 505 |
import numpy as np
import matplotlib.pyplot as plt
from sklearn.decomposition import PCA
from sklearn.discriminant_analysis import LinearDiscriminantAnalysis as LDA
from sklearn.discriminant_analysis import QuadraticDiscriminantAnalysis as QDA
from sklearn.ensemble import RandomForestClassifier as RF
from sklearn.mode... |
df9e52d105ef7345396b17c82f69604fefd38646ff8faaffc952685ad634b458 | Python | 20,910 | 511 |
from builtins import super
from function import *
import tensorflow.keras as keras
import tensorflow as tf
import numpy as np
def call_model(x):
dic = {'model_12':Model_12(),
'model_7' :Model_7(),
'xception_1d':Xception_1d(),
'xception_1d_2': Xception_1d_2()}
return dic[x]
cla... |
144cb2332035bd77e68cbb1888afc172a2503f5595a1082e468e79f373665fbc | Python | 20,938 | 541 | """
Performs Univariate 2nd order analysis to a SetListTomograms object by tomograms
Input: - A STAR file with a set of ListTomoParticles pickles (SetListTomograms object input)
Output: - Plots by tomograms:
+ Number of particles by list
+ Particles densities by list
... |
950ffa2d1614bd0712af490cb900f80be07a4ffe53d6f2c1819712bc79f16d61 | Python | 20,951 | 563 | # 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... |
c76bd97832c6fa3e0c972e198064c59c99cea07e73efbd68a695942cd4fab67f | Python | 20,957 | 487 | """Figure generation for the Apply Transforms pipeline.
Mirrors the before/after + annotation-overlay figures produced by the main
registration pipeline, but scoped to a single warped input volume.
Produces, next to the warped NIfTI:
- ``<stem>_pair.jpg`` : side-by-side input / warped
- ``<stem>_overla... |
8aecdf519e667f44af77f296f2fec79a60d117792d6deb891e084be8d3b24949 | Python | 20,972 | 427 | """The LiquidAion plugin contracts, registry and discovery (headless; never imports Qt).
One registry holds every replaceable component, built-in or user-provided:
model_adapter language-model family integration (built-in: Qwen3 profiles)
connectome topology and neuron metadata (built-in: FlyWire CX5... |
d9aadb75b3a61c1465e13512d5d290882a301a59ea4c56a04cede2d3628bff0b | Python | 20,977 | 454 | """
Generates a ListTomoParticle object from a input STAR file (translocon project version)
Input: - STAR file for pairing STAR files with particles and particles shapes
Output: - A ListTomoPaticles pickled object for every STAR file row
"""
################# Package import
import os
import vtk
impor... |
8a8c8c58fab6b32ba82c214da584a49b1c55a655285f4f736c179b7dd75b5b60 | Python | 20,995 | 466 | # Parts of this class are from the Scanpy equivalent, see license below
# BSD 3-Clause License
# Copyright (c) 2017 F. Alexander Wolf, P. Angerer, Theis Lab
# All rights reserved.
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions... |
ffccf2550938661150d709964c760cb1529b7c0c05c68e37617b6eed6a122085 | Python | 20,995 | 473 | from __future__ import annotations
from typing import TYPE_CHECKING, Literal, cast
import jax.numpy as jnp
import numpy as np
import numpyro as npy
import numpyro.distributions as npd
from anndata import AnnData
from mudata import MuData
from pertpy._logger import logger
from pertpy._types import cast_matrix
from pe... |
c944b96bd0e115fd5b7b9c3e3e6289ee58fc863cae66767f2211c0b33c2601d4 | Python | 21,010 | 824 | """Workflow decorators."""
from __future__ import annotations
from collections.abc import Callable
from functools import partial, wraps
from typing import TYPE_CHECKING, Any, ParamSpec, TypeVar, overload
from quacc.settings import change_settings_wrap
from quacc.wflow_tools.context import NodeType, tracked
if TYPE_... |
72e6c49db75a98c3caef8e3215f1d1b426c918d6f8b2fe061b46646c582b745c | Python | 21,027 | 523 | # 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... |
dafb27e140c60b6c5e495847682b9b812084895add52679198ec37f4a14b4d7d | Python | 21,029 | 507 | """
Performs Bivariate 2nd order analysis between ListTomoParticles pairs
Input: - Two STAR file with a set of ListTomoParticles pickles
Output: - Plots with the analysis
- Matrix with the analysis for further post-processing
"""
################# Package import
import os
import pickle
im... |
654ee9ab657014a6cd38af31619a59a25c4c3063180ebcdee1be496ad29be613 | Python | 21,033 | 603 | """Competing-risk Brier scores checked against direct subject-wise calculations."""
import importlib
import tracemalloc
from unittest.mock import patch
import matplotlib.pyplot as plt
import numpy as np
import pytest
from scipy.integrate import simpson, trapezoid
from scipy.interpolate import PchipInterpolator
from ... |
9ae93fb8eb959fad03a152f25eaee34e061847697c4141164d9890b9f6d402b7 | Python | 21,035 | 387 | from typing import Any, Callable, Dict, Optional, Text, Union, Iterable
import tensorflow.experimental.numpy as tnp
import tensorflow as tf
from tensorflow.keras import layers as kl
from src.layers.layers import *
import tensorflow_addons as tfa
from tensorflow.keras import regularizers
from tensorflow.keras.layers.exp... |
ce10fb477ec8dbe97bb45e31be3d623fd405cecca3984ee095139e06de7ac7ef | Python | 21,036 | 594 | from collections import defaultdict
from functools import lru_cache
from random import choice
from codex.data.connections import Connections
from codex.data.neurotransmitters import NEURO_TRANSMITTER_NAMES
from codex.data.search_index import SearchIndex
from codex.data.structured_search_filters import (
make_stru... |
f38216f641cda8cd87b5bd9eebafa85230d6f281a7ac3655a2b70c939f76221b | Python | 21,037 | 848 | from __future__ import annotations
from dataclasses import dataclass
import numpy as np
import pandas as pd
from scipy import stats
from sklearn.decomposition import PCA
from sklearn.neighbors import NearestNeighbors
from sklearn.preprocessing import RobustScaler, StandardScaler
from .config import DimensionalityRed... |
5c75b4c0be71c274b46298b97c633a33c9b13a9e687a980d64b1dacf92f0ddcf | Python | 21,068 | 534 | """
Performs Univariate 2nd order analysis to a SetListTomograms object by tomograms (Translocon version)
Input: - A STAR file with a set of ListTomoParticles pickles (SetListTomograms object input)
Output: - Plots by tomograms:
+ Number of particles by list
+ Particles d... |
11bbcdfac96f46353e0fc7fde00656e01d8e974adb34cc01f77cee463060ec8f | Python | 21,089 | 482 | import numpy as np
from scipy.io import wavfile
from scipy.linalg import toeplitz, norm
from scipy.fftpack import fft
import math
from scipy import signal
from pesq import pesq
'''
This is a python script which can be regarded as implementation of matlab script "compute_metrics.m".
Usage:
pesq, csig, cbak, covl... |
886352e77924d1cb03df43cf2060aec23aa88d38fc7be369ccfece583628c71c | Python | 21,090 | 380 | from __future__ import print_function
import copy
from collections import defaultdict, namedtuple
from pddlstream.algorithms.downward import get_problem, task_from_domain_problem, get_cost_scale, \
conditions_hold, apply_action, scale_cost, fd_from_fact, make_domain, make_predicate, evaluation_from_fd, \
pla... |
4ce4adb447b695924bec169a93579e780aca6f34d2597819199dd7595523ebc9 | Python | 21,098 | 516 | """MobileNet v2 models for Keras.
MobileNetV2 is a general architecture and can be used for multiple use cases.
Depending on the use case, it can use different input layer size and
different width factors. This allows different width models to reduce
the number of multiply-adds and thereby
reduce inference cost on mob... |
000880fdf27251b7d9e09d821b69e5406b8732b849867babab2cf43951295e59 | Python | 21,099 | 460 | # Copyright 2020 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
#
# ht... |
9556b3347abe1f2e73d72a7b714d724e07dfb2c8cdafd3bd66a9cd4926748823 | Python | 21,109 | 439 | #!/usr/bin/env python
# =============================================================================
# GLOBAL IMPORTS
# =============================================================================
import os
import numpy as np
import pandas as pd
from logP_analysis import mae, rmse, barplot_with_CI_errorbars
from log... |
c80867c9489bb470c1ddc7d881c6e2a31f9f59e77cee87c20482034a087da2b4 | Python | 21,112 | 433 | import torch
import torch.nn as nn
from torch.utils.data import DataLoader
from torch.autograd import Variable
import torchvision.transforms.functional as VF
from torchvision import transforms
import sys, argparse, os, copy, itertools, glob, datetime
import pandas as pd
import numpy as np
from scipy.stats import mode
... |
924fc500498662b815541110c39dc7899793c45e21a9d9d46b6bec918539cf66 | Python | 21,113 | 432 | #!/usr/bin/env python
"""Robust local test runner for RegTools.
Wraps pytest with the settings that survive this repo's Windows quirks, learned
the hard way, and a watchdog that recovers from the one quirk flags can't fix.
Failure modes and their fixes:
* Machine sleeps mid-run. A suspend/resume wedges xdi... |
aaae5b9dbac7e8451be30e23f96ea7689934167d6fed99e91d238f33931b763a | Python | 21,113 | 630 | import logging
import os
from datetime import datetime
from random import shuffle
import numpy as np
import pandas as pd
import scipy
import torch
from pyedflib import highlevel
from scipy.signal import decimate
from torch.utils.data import Dataset, Sampler, WeightedRandomSampler
log = logging.getLogger(__name__)
... |
3b75b023bdca3d75f483faf9d19a1f0f1334363274af3804ad73a0bbdb069b14 | Python | 21,116 | 541 | # 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... |
e35cd1b4116952213ea583d516091352511ddcc172276c3fb490d7af78c6df04 | Python | 21,116 | 455 | """
Generates a ListTomoParticle object from a input STAR file (translocon project version)
Input: - STAR file for pairing STAR files with particles and particles shapes
Output: - A ListTomoPaticles pickled object for every STAR file row
"""
################# Package import
import os
import vtk
impor... |
812b73b2218f425fd123052efc9dd301cc04401b4535dadea73606616f579e12 | Python | 21,146 | 485 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Mon Aug 7 13:57:01 2023
@author: MegNParker
"""
import mne
import pandas as pd
import glob
import os, os.path as op
import numpy as np
import copy
#%%
subjid="..."
session=1
sessions=[1,2]
surf_flag=True #FALSE
bids_dir="..."
subjects_dir=op.join(bids_... |
f8faa468eb3373da3eecb4d1d5aa8e2f84aa8b20306c675444a565807b87b9d8 | Python | 21,147 | 614 | """Automatic discovery of Python modules and packages (for inclusion in the
distribution) and other config values.
For the purposes of this module, the following nomenclature is used:
- "src-layout": a directory representing a Python project that contains a "src"
folder. Everything under the "src" folder is meant t... |
0f94ccb244db580f56ed2dd30f42d5ad750d6c7983926841bf65a8f794b2835a | Python | 21,148 | 649 | """Topology optimization of a waveguide mode converter.
The worst-case optimization is based on minimizing the maximum of {R, 1-T} where
R (reflectance) is $|S_{11}|^2$ for mode 1 and T (transmittance) is $|S_{21}|^2$
for mode 2 across six different wavelengths. The optimization uses the
Conservative Convex Separable ... |
9f47860559506411749f0acad9e9edc3b6072aee3546286d673856625b4fa10d | Python | 21,148 | 575 | ##
# \file tikhonov_solver.py
# \brief Implementation to get an approximate solution of the SRR
# problem using Tikhonov-regularization
#
# \author Michael Ebner (michael.ebner.14@ucl.ac.uk)
# \date July 2016
#
import scipy
import numpy as np
import SimpleITK as sitk
from nsol.definitions i... |
8d95be71f6c08bfda015ca400d6e11ab0cc9982308770d5167953c16aec606e2 | Python | 21,181 | 557 | # 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... |
bdf035f997b7a6c40e37d1932b1411d4a18c9e3474c5a7f6f9d2a9d28c3c5ad9 | Python | 21,188 | 399 | import argparse
import json
import os
from tqdm import tqdm
import numpy as np
import torch
import torch.distributed as dist
import torch.optim as optim
from torch.utils.data import DataLoader
from torch.utils.tensorboard import SummaryWriter
from config import GlobalConfig
from model import LidarCenterNet
from data ... |
c5dcd8b321ff4dc618f24430ab02fa587bc496c7ffe098a53a2fd7d580e69779 | Python | 21,193 | 534 | """SMART module interfacing with PETSc SNES solver"""
import logging
from typing import Dict, List, Optional
import dolfin as d
from dolfin.common.timer import timed
import petsc4py.PETSc as p
from .common import Stopwatch
from .model_assembly import Compartment
import numpy as np
logger = logging.getLogger(__name_... |
e78c4634691afe56c9d493f010b80d3dc52acd7aa17d53b511bb79c1a7ee6e03 | Python | 21,193 | 560 | def calc_asymcut(values, coord, ori, imgh, imgrh, imgw, imgrw, centre):
"""Determines the cross-section along the most asymmetric cut through the z_values and shifts
the origin to the geometric centre
Parameters
----------
values : ndarray
N dimensional array with type float that contai... |
e3936fce0bf6320f845b9711e312c43809bffe0338757875591dafb6534063a3 | Python | 21,196 | 522 | from torchvision import transforms
from torchvision import datasets
from torch.utils.data import DataLoader
import torch.nn as nn
import torch
from mpl_toolkits.mplot3d import Axes3D
from sklearn.decomposition import PCA
import matplotlib.pyplot as plt
import matplotlib
import numpy as np
import os
from utils import Lo... |
2f2e81cf211f9718e400709fac6bb35d388f2e7628c2944ed67d483b37ace11e | Python | 21,207 | 418 | import math
import sys
from matplotlib import animation as animation, pyplot as plt
import traceback
from src.utils import parse_config, contain_substr
import pandas as pd
import numpy as np
from scipy.ndimage import gaussian_filter1d
import os
from joblib import Parallel, delayed
import glob
import joblib
import cv2... |
ce6f0b508be602b3dbddd98afbc5f4f70e55665879cdb9be593a87e459c6a393 | Python | 21,231 | 616 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Written by Tong He and CBIG under MIT license:
https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
"""
import os
import time
import pickle
import hashlib
import itertools
import torch
import torch.utils.data
import torch.nn as nn
import torch.nn.init as init
f... |
960556356b72fbd3e99ab5d49f700d929690c8a74280f3b3ca9b8f95b9033f8b | Python | 21,232 | 699 | #!/usr/bin/env python3
# Copyright (c) Facebook, Inc. and its affiliates. All Rights Reserved.
"""Configs."""
from fvcore.common.config import CfgNode
from . import custom_config
# -----------------------------------------------------------------------------
# Config definition
# ------------------------------------... |
5a6f27b7cb9361e794cb1ce12e9c84febac3a7edd7c356d6a40129a8d985d889 | Python | 21,265 | 471 | import os
import os.path as path
import numpy as np
import torch
import numpy.random as nr
from scipy import signal
import matplotlib.pyplot as plt
import _pickle as pickle
import re
from eworm.utils import func
from scipy import interpolate
# weight normalization
"""
Three different weight form ( sample ---- input -... |
ac12e3e4972f3fedee70764f29253a52920c22c345a282a8f477e9d14200e3f6 | Python | 21,274 | 475 | """
Shared dialog classes for the U01 workflow GUI.
"""
import numpy as np
from PySide6.QtWidgets import (
QCheckBox,
QComboBox,
QDialog,
QHBoxLayout,
QLabel,
QPushButton,
QSlider,
QVBoxLayout,
)
from PySide6.QtCore import Qt
import regtools.gui.gui_constants as gc
... |
ce58c9cbd3a1815238484b0de0b08e29e1ca80eaaebe11f4d6f4434103dee9a6 | Python | 21,279 | 630 | """
Set of functions to clean up the non-essential files of each step
of the preprocessing pipeline.
Each step needs to have an own function to properly work
Also, generate comparison images and values that are useful to rapidly assess
the correctness of the preprocessing steps.
Use this class:
https://raamana.gith... |
00a689c2daa31442b5f948fbf63cb8f3bd2b29bed397d8f08f449e453c3b2727 | Python | 21,284 | 602 | import pytest
import torch
from torch.nn import functional as F
from elasticai.creator.nn.integer.linear.linear import Linear
from elasticai.creator.nn.integer.math_operations.math_operations import MathOperations
from elasticai.creator.nn.integer.quant_utils.calculate_quant_params import (
calculate_asymmetric_qu... |
887cb3a69f21f76256ea2e2b4c5759067788dbe40bee92aa413c1090c35ae546 | Python | 21,285 | 433 | import shlex
import sys
import uuid
from unittest.mock import MagicMock
import pytest
import NDATools
from NDATools.clientscripts.vtcmd import validate
from NDATools.upload.cli import ValidatedFile
from NDATools.upload.submission.api import SubmissionHistory, NdaCollection, SubmissionPackage, PackagingStatus, \
S... |
9441aadc420d445d88ef0d046eebaf6ae89742468c78811060705d51b702f7ca | Python | 21,288 | 687 | """
==================================
Extract EEG segments from the data
==================================
Segment EEG data around experimental events
Authors: José C. García Alanis <alanis.jcg@gmail.com>
License: BSD (3-clause)
"""
# %%
# imports
import sys
import os
from pathlib import Path
import numpy as np
... |
f90e3dce7544d0bdfd71500c741ae2cd706e8f95c114fed655df0642a3d2f218 | Python | 21,304 | 484 | import numpy
import pandas
import connalysis
import tqdm
def compress_id_ranges(dfs):
"""
Reindexes values in a DataFrame, compressing them to have [0 ... n] as values, where
n is the number of unique values in the DataFrame.
Args:
dfs: list of DataFrames with integer values
Returns:
... |
2efac7779ab5e8a6f27e4df3011d605f854a0077b05915b02f2bffdf13c5f4e4 | Python | 21,314 | 387 | #----------------------------------------------------------------------------------------------------------------------------
# Author: Brandon S Coventry CAP Lab Purdue University Weldon School of BME
# Date: 09/02/20
# Revision History: 09/15/20 - Adaptation made for multiprocessor use. On a single RX process... |
9bfd31135a3be0dca02a89c5c346a97b9834ad27e4633d20a82fe854487fc73a | Python | 21,314 | 439 | import copy
import unittest
from hed import load_schema_version
from hed.errors import ErrorHandler
from hed.models import HedString
from hed.schema import HedSectionKey, from_string
from hed.schema.schema_validation import attribute_validators as schema_attribute_validators
from hed.validator import HedValidator
from... |
43c3d551400e4505f1a0e183b6389736c667047f0822c75975273c3422be8018 | Python | 21,320 | 499 | import math
import warnings
from collections import OrderedDict
from functools import partial
import torch
import torch.nn as nn
import torch.nn.functional as F
from einops import rearrange
def _drop_path(x, drop_prob: float = 0., training: bool = False, scale_by_keep: bool = True):
if drop_prob == 0. or not tra... |
5dbeb21b133b39cba8a6aea733142ceb6a33046c53efbb4e455a80ced15b3db7 | Python | 21,320 | 517 | # -*- coding: utf-8 -*-
from __future__ import annotations
import os
import tempfile
from io import StringIO
from typing import TYPE_CHECKING, Iterable, Optional, Sequence, Tuple, Union
from supar.utils.logging import get_logger
from supar.utils.tokenizer import Tokenizer
from supar.utils.transform import Sentence, ... |
9f4d480b942bd2bbef124121fe61cb396eef1b7b2ba02c661f74c71968148bfc | Python | 21,321 | 375 | import numpy as np
import matplotlib.pyplot as plt
from mpl_toolkits.mplot3d import Axes3D
from matplotlib import cm
import matplotlib.animation as animation
import time
import ray
import os
from neuron_model_parallel import NeuronSim
from elec_field import sparse_place_human
from pulse_train import PulseTrain_Sinusoid... |
996c7520535605c4764525d2f9f08821fd14fe9cc599d33cf2353cdd9b42b7e5 | Python | 21,323 | 642 | """Tests for ContourCorrespondenceStore - the pure data model extracted
from the manual contour registration viewer.
All tests are pure Python with no matplotlib, Qt, or Tk dependencies.
"""
import pytest
from regtools.manual_contour_registration.correspondence_store import (
ContourCorrespondenceStore,
... |
dec34470f0dcbb5c6b739067015bfbce806fc78fceb4bf4413e6ec2181cea530 | Python | 21,327 | 380 | from .enums.nbo_type import NboType
from .enums.qm_target import QmTarget
from .enums.node_feature import NodeFeature
from .enums.edge_feature import EdgeFeature
from .enums.graph_feature import GraphFeature
from .enums.hydrogen_mode import HydrogenMode
from .enums.sopa_resolution_mode import SopaResolutionMode
from .e... |
558e997cccc449f70d0a9a10e164ef00e50236dc472b63304a03e1a5bb486784 | Python | 21,333 | 517 | # -*- coding: utf-8 -*-
#
# Syncopy object arithmetics
#
# Builtin/3rd party package imports
import numpy as np
import h5py
import dask.distributed as dd
# Local imports
from syncopy.shared.parsers import data_parser
from syncopy.shared.errors import SPYValueError, SPYTypeError, SPYWarning
from syncopy.shared.computa... |
8d90f0139d74e394fba738cb54330218ffd17a5156c8bc9cc221d8f68d360bee | Python | 21,335 | 639 | """Module contains frequently used functions dealing with channel lists."""
import math
from cmath import sqrt
import mne
import numpy as np
import scipy.interpolate
from mne.surface import _normalize_vectors
from numpy.polynomial.legendre import legval
from psutil import virtual_memory
from scipy import linalg
from s... |
763245e7888f57da0ead4ea6f23f367c8082fcd036ce1877d1eeab83f5c82d11 | Python | 21,336 | 616 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Written by Pansheng Chen, Tong He and CBIG under MIT license:
https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
"""
import os
import time
import pickle
import hashlib
import itertools
import torch
import torch.utils.data
import torch.nn as nn
import torch.nn... |
5b77fe42255068eeb05a1ecf47013dfa384fe58d32800c173bbd5071c066d540 | Python | 21,340 | 361 | """
Populates the graph database with all the files generated by the importer.py module:
Ontologies, Databases and Experiments.
The module loads all the entities and relationships defined in the importer files. It
calls Cypher queries defined in the cypher.py module. Further, it generates an hdf object
... |
38de7d90555ae72ecdbd14b944cb95be4d1f62cc2b9a0ca9f5a4f85e180794fc | Python | 21,346 | 498 | #!/usr/bin/env python
# -*- encoding: utf-8 -*-
from copy import deepcopy
from functools import partial
from io import StringIO
from inspect import getsource
from pprint import pformat
import sys
import bindings as bi
from custom import get_customizations_for, reformat_block
str_type = str
get_customizations_for = pa... |
91b991aff20ab0fde0155175aa1913c926b78c36333910d1fdc9fa6ac6243238 | Python | 21,346 | 524 | # 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... |
e4938cacf4be378bfa8bd8f716b9d846747c89e810720545e9838e66640e190a | Python | 21,350 | 327 | """
Connectivity analysis (mostly wrappers around `assemblyfire.topology` functions)
last modified: András Ecker 06.2023
"""
import os
import h5py
from tqdm import tqdm
import numpy as np
import pandas as pd
from conntility.circuit_models import circuit_connection_matrix
from assemblyfire.config import Config
import ... |
5cdf0d9b6c6af5869f34a5ca766830410357436de563e3addfdca5d8cea00cde | Python | 21,351 | 486 | '''
Original Author: Nate Zuniga
Modified by: Yi Jie (Josh) Tseng on 10/01/2023
Software requirement: Python
Python module requirement: scipy, sklearn, numpy, pandas and matplotlib
Purpose:
To perform normalization based on the Aguilan et al. 2020. It includes the following steps:
1. Clean and filter data.... |
f6f67290eb86f13507a647e4af8a98bf80be5107e59c808022f5ddf41390158b | Python | 21,351 | 499 | # -*- coding: utf-8 -*-
from __future__ import annotations
from typing import List, Optional, Tuple
import torch
import torch.nn as nn
import torch.nn.functional as F
from supar.structs import DependencyCRF
from supar.utils.common import MIN
class DependencyMFVI(nn.Module):
r"""
Mean Field Variational Infer... |
a313177b331a84409d428ddc274696bc30edb3dcf9d98ce7af252f935c7f3d8b | Python | 21,358 | 509 | # NOTE: to use the violin_plot_performance function, you'll need to use an virtual
# environment with seaborn version 0.11.0
import os
import pickle
import json
import numpy as np
import networkx as nx
from nilearn import plotting
import matplotlib.ticker as ticker
import pandas as pd
import matplotlib.pyplot as plt... |
509a8c23d84268f87c534f7e53e2e52028130014b836cfffc16d1853b1e69c59 | Python | 21,362 | 444 | ######## Name
######## BiochemSimulMuleRapid
######## Requires
######## {Modules}
import numpy as np
import numba
class BiochemSimulMuleRapid:
"""Class 'BiochemSimul' Illustration!
It is an essential part of the 'BiochemAnalysis' class!
########
Attributes
########
Met... |
9be7dd110695de5f142011d45151018bbb8f3b324b61471bcb94886e9301ec97 | Python | 21,388 | 1,047 | from __future__ import annotations
import matplotlib.pyplot as plt
from matplotlib.colors import to_rgb
import numpy as np
import pandas as pd
from .config import PlotConfig
# ======================================================================
# MORPHOGLIA PALETTE
# ==============================================... |
bb239942e2c3a8477a425ca25d79fa001f474e8d0ad0c5ef3c3ff7121d784ed1 | Python | 21,394 | 529 | # 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... |
f6d7d3081998ecdab75de1e3fe17aca47082182e3a6a13eb39ae9d78759de885 | Python | 21,397 | 648 | from pyclamp.dsp.fpfunc import *
from pyclamp.dsp.optfunc import *
from pyclamp.dsp.nnmod import *
from pyclamp.gui.pgb import *
import numpy as np
SHOWFITS = False
if SHOWFITS:
from mplqt import *
import iplot
import resfunc
# Numerical analysis
class MMA (censca): # Minimum / maximum analysis
numlbl = ... |
288b6fa3b371f4fcad55f1866dc1fe75cb0bc4bbd709e6f83ac342296246bf3b | Python | 21,414 | 700 | import logging
import numpy as np
class BaseAtlas:
"""
Simple base for anatomical atlases. Internal representation as dictionary
{node_num: "name"}.
"""
name = ""
label = ""
def __init__(self, atlas, coords=None):
"""
:param atlas: anatomical atlas / parcellation
... |
df7e3e323369ce4769aeb059f3781f1ead13f6bac31ec70e30ba4119ab629625 | Python | 21,423 | 449 | from __future__ import print_function
import argparse
import datetime
import math
import os
import sys
import time
import numpy as np
sys.path.extend([
os.path.join(os.getcwd(), 'pddlstream'), # Important to use absolute path when doing chdir
os.path.join(os.getcwd(), 'ss-pybullet'),
])
from collections imp... |
9e2dbd20720eeaa87d642f4d4044df869d46249345f652ecda5dbeb0687d7ced | Python | 21,444 | 371 | #####################################
######## Paper Draft Cartoon ########
#####################################
#%%# Catalyzer
import os
import sys
path = os.path.dirname(os.path.realpath(__file__)) + '/../Resources'
sys.path.append(path)
path = os.path.dirname(os.path.realpath(__file__))
sys.path.append(path)
impo... |
537f63e9c9467a232a19311f1a19b85e3851170ce3caad7aea8b6c569bd17e31 | Python | 21,445 | 639 | #!/usr/bin/env python
#
# Copyright 2005 Google Inc. All Rights Reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are
# met:
#
# * Redistributions of source code must retain the above copyright
# notice, this list of... |
695868f7380754f0573e79c940d0714231eb475602fba61dc5a979a541721eef | Python | 21,447 | 622 | from datetime import datetime, timezone
from logging import getLogger, NOTSET, WARNING, disable
from os import SEEK_SET, SEEK_CUR, SEEK_END
from os.path import splitext
from struct import unpack
from pathlib import Path
from numpy import (asarray, empty, expand_dims, fromfile, iinfo, nan, ones,
resh... |
d60e0eb68c4e5cdd7b2a301faa64c198577fbbd24b135283fe0a0278811f2639 | Python | 21,450 | 485 | import numpy as np
import pandas as pd
import numexpr as ne
import random
import copy
import json
import jsbeautifier
from scipy.integrate import odeint, cumtrapz
from scipy.optimize import root_scalar
import multiprocessing as mp
import time
from clamping import apply_transition, get_feasible_transitions
... |
bbfbf533bdb4bd12f069297d03d6a1376cea2b8adf3b9b0bce6ea8a769e0f875 | Python | 21,455 | 562 | __author__ = 'martinez'
try:
import pexceptions
except:
import pyseg.pexceptions
import numpy as np
try:
import disperse_io
except:
import pyseg.pexceptions
from pyto.io import ImageIO
from abc import *
##########################################################################################
# Clas... |
c3a1f9dc9172c22a0fd8828c93a0669d5369c840e0d705c350d400b774ff206c | Python | 21,483 | 522 | """A segmentation mask drawn over the input pane, like the cell-points overlay.
The overlay exists to answer one question before a registration is spent: does
the mask actually sit on the tissue, and does the orientation chosen keep the two
together? So these tests assert what is DRAWN - alpha where objects are,
... |
e4dac5bcf437a144f0e103f5d2974c0cd8720f80ff36d67a6a38dd2aff6e9ba0 | Python | 21,486 | 553 | import numpy as np
from scipy.sparse import csr_matrix
from .constants import hpro_rng
from .utils import atom_number2name
BASE = 20
class PairsInfo:
'''
This class is used to deal with atom pairs. The first atom in the pair is always assumed to be in the unit cell at (0, 0, 0),
and the second atom is in... |
a453b83f9bf1821168ccda6e33a356250f7698eaed324b4b754306b6c9bddc53 | Python | 21,493 | 548 | """ data augmentation algriothm"""
import albumentations as A
from albumentations.augmentations.geometric.functional import safe_rotate_enlarged_img_size, _maybe_process_in_chunks, \
keypoint_rotate
import cv2
import math
import random
import numpy as np
d... |
35a86a9f810fec6a97baf577432cb8f65ed00749350af1c34703c9f06a3a79b2 | Python | 21,495 | 478 | # ----------------------------------------------------------------------------
# Contributors: Thiago O. Bezerra
# Antonio C. Roque
# ----------------------------------------------------------------------------
# File description:
#
# Functions implementing the current densities and differential equ... |
4fbae98ce99df7c12027cf1cc04019c59402975a5edc47bdfea6f137aa996b21 | Python | 21,508 | 452 | # Copyright 2020 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
#
# ht... |
b7cc79c5602255a89c488946a67c0c22d6c7272a3cd4fb7db7f06692de28ca65 | Python | 21,508 | 492 | """ model components"""
import numpy as np
import torch
import torch.nn as nn
import torch.nn.functional as F
import timm
from MolNexTR.utils import FORMAT_INFO, to_device
from MolNexTR.tokenization import SOS_ID, EOS_ID, PAD_ID, MASK_ID
from MolNexTR.decoding import GreedySearch, BeamSearch
from MolNexTR.models impo... |
0f15cbc7092ec252eb19f0d57b8221d8167e3dc1c0e0976585ee4305830a10b8 | Python | 21,514 | 578 | # 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... |
2fdb22b5605147ca40f02d8d66d85a7d200bf2ccc705d5bf395531c4979a7a5a | Python | 21,518 | 553 | ##
# \file ScatteredDataApproximation.py
# \brief Implementation of two different approaches for Scattered Data
# Approximation (SDA)
#
# \author Michael Ebner (michael.ebner.14@ucl.ac.uk)
# \date April 2016
#
import os
import sys
import itk
import time
import numpy as np
import SimpleITK a... |
51d54110e3928c8fbb407d0a8a4fd9fe7fca0f2cb51808038f121b14462500e8 | Python | 21,526 | 558 | #!/usr/bin/env python3
"""Track tumor instances across timepoints and measure their volume over time.
Each file is a binary segmentation mask for one scan date (may contain
several disconnected instances, e.g. multiple metastases). The scan date is
parsed from the filename (default: "YYYY-MM"/"YYYY_MM" before ".nii.gz... |
72fbcb120fcc3a9aea8f98d2c8769835b2307ef8d8a3661dd9e38db11f2de01d | Python | 21,536 | 1,131 | from __future__ import annotations
from dataclasses import (
asdict,
dataclass,
field,
is_dataclass,
)
from pathlib import Path
from typing import Any
import yaml
from .metadata.config import (
MetadataConfig,
)
from .preprocessing.config import (
PreprocessingConfig,
)
from .segmentation.co... |
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