sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
628661b9ec71d243068f132e9415e8e4f65d637987159432dffe09771927f46b | Python | 31,396 | 892 | # 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... |
e2c25fb3979e5179aca4a1034b78b23dbe185a38054ba912ba1e0b5712b0c668 | Python | 31,403 | 731 | try:
import binutil # required to import from dreamcoder modules
except ModuleNotFoundError:
import bin.binutil # alt import if called as module
from dreamcoder.dreamcoder import *
import dill
import matplotlib
matplotlib.use('Agg')
import matplotlib.pyplot as plot
from matplotlib.ticker import MaxNLocator
i... |
8d1327b2d257b867c889f83570c485cf7f9f760a54c732ee951bd8c63c127093 | Python | 31,409 | 864 | """This module contains classes and functions specific to SAMPL6 data files.
The functions are adopted from Bas Rustenburg's Titrato Package, but modified
to calculate relative free energy of microstates between pH 0 and 12."""
import pandas as pd
import numpy as np
from titrato.titrato import TitrationCurve, free_ene... |
eb274dafd0053b191816aacf4338d726d917672b1be83f6b289cac3120068d02 | Python | 31,427 | 429 | import numpy as np
import scipy.stats
from .model_compare_predicted_to_actual import *
def model_compare(target_actvect, model1_actvect, model2_actvect=None, full_report=False, print_report=True, print_by_condition=True, comparison_type='fullcompare_compthenavg', avgthencomp_fixedeffects=False, mean_absolute_error=Tru... |
4a72739bda7f816d0d9a39ae9ecbffb8967be93ae0b5cefd26f72284fea79085 | Python | 31,432 | 543 | ##############################
######## Shallow Grid ########
##############################
#%%# Catalyzer
sup_comp = False # Super Computer?
cellulate = (0, 0) # (cell_layers, layer_cells)
maturity = 48 # {48, 96}
initiate = {'FC_MRNA': 0, 'FC': 0} # {0, ..., 250} # {0, 250, 500, 750, 1000} # Toll!
_initiate = '_'.... |
ca90a1c62662940d2a93ce04cb7082643484e19efe38c4c2ec682f84dc17af2f | Python | 31,432 | 928 | #!/usr/bin/env python
# coding: utf-8
'''
Created on 2023-12-12
@author:fdy
'''
import ctypes
from ctypes import *
from enum import Enum
import time
#加载SDK动态库
# 32bit
#TUSDKdll = OleDLL("./lib/x86/TUCam.dll")
# 64bit
TUSDKdll = cdll.LoadLibrary("libTUCam.so.1")
# class typedef enum TUCAM status:
... |
923dfe568861fcd8d03b16ba775bbc2af4573dd1ca0d7a61e70afb3368b675e1 | Python | 31,439 | 543 | ##############################
######## Shallow Grid ########
##############################
#%%# Catalyzer
sup_comp = False # Super Computer?
cellulate = (0, 0) # (cell_layers, layer_cells)
maturity = 48 # {48, 96}
initiate = {'FC_MRNA': 0, 'FC': 0} # {0, ..., 250} # {0, 250, 500, 750, 1000} # Toll!
_initiate = '_'.... |
604dd5da1962b9bb28441ef66e15bb1b73a52d477f6b3ba2f0281957c0f0e755 | Python | 31,463 | 1,001 | # 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... |
91795335c1f8ba60cd9205305b64ed6a715b839b90a02a71775dbccc20264595 | Python | 31,475 | 708 | import os
import numpy as np
import librosa
from utils.files import flatten_list
from utils.files import get_wav_files as get_files
from config import SE_Config
from random import *
from tqdm import tqdm
import torchaudio
from torch.utils.data import Dataset
import numpy as np
import torch
def gen_log_space(limit, n):... |
147c3dff9c0a2d44ba98a40bb4507664d4cbf763b2f4a73ba2580bd0156a59aa | Python | 31,483 | 918 | # 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... |
da9a16b6d340863dd8e3965d7602153305e335701d51c00e3bfb1cd3087a6a74 | Python | 31,503 | 788 | """distutils.command.build_ext
Implements the Distutils 'build_ext' command, for building extension
modules (currently limited to C extensions, should accommodate C++
extensions ASAP)."""
import contextlib
import os
import re
import sys
from ..core import Command
from ..errors import (
DistutilsOptionError,
D... |
6bd771b3faa78169880798c20738e9d4c9de310baecc86570f9e9708dc3b21e2 | Python | 31,531 | 609 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Calibration of VEDB T265
@author: brianszekely, christiansinnott
"""
# from pathlib import Path
import numpy as np
import pandas as pd
import xarray as xr
import matplotlib.pyplot as plt
import pupil_recording_interface as pri
import rigid_body_motion as rbm
import os
... |
6e6a9705a0b2fba827249a5f25bd3dbaf6bf891e0c8d4dc6dbd15ea4724ca031 | Python | 31,531 | 1,215 | from __future__ import annotations
import shutil
from dataclasses import dataclass
from pathlib import Path
from typing import Sequence
import numpy as np
import pandas as pd
import tifffile
from PIL import Image
from ..core.instance_map import validate_instance_map
from ..category import (
CATEGORY_COLUMN,
)
... |
d6c93ed2a5d5516e0e04330d456844561b8b837f652611e0291232d1aea8ad54 | Python | 31,557 | 810 | import numpy as np
import cv2
import os
import logging
import pandas as pd
from matplotlib.backends.backend_agg import FigureCanvasAgg
import matplotlib.pyplot as plt
import seaborn as sns
from typing import List, Dict, Tuple
import argparse
import configparser
import coloredlogs
from scipy.ndimage import gaussian_fil... |
463793c8c8584fac13a69e35c65eba1133ca8f529ea3d478b5029270619a9cc7 | Python | 31,580 | 770 | # coding=utf-8
# Copyright 2021 Facebook AI Research (FAIR), Ross Wightman, The HuggingFace Inc. team. All rights reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.... |
77270b396b406ca0dfa21fe3d1ee00c704c23b9626c77060b0cae0a44cb30744 | Python | 31,605 | 703 | """
Performs Bivariate 2nd order analysis to a SetListTomograms object by tomograms
Input: - A STAR file with a ListTomoParticles pickle (SetListTomograms object input) used as reference
- A STAR file with a set of ListTomoParticles pickles (SetListTomograms object input) to analyze
Output: ... |
d137e72f331c56b566fb2e56a0e7498685e9cadf8c9e88637c01ec25d771f374 | Python | 31,608 | 798 | """
I/O for the reorient tool - handles a heterogeneous mix of inputs:
* **Image volumes**: TIFF, NIfTI, NRRD, NumPy ``.npy`` / ``.npz``, plain
2D images (PNG/JPG/etc.). Loaded via :func:`regtools.utils.io.volume_io.load_volume`.
* **Point clouds**: cellpose CSVs (2D or 3D), napari CSVs, legacy TXT,
or NumP... |
a20177ba6d6a35ba5c0f1e87138508ba767fd5ea0565239f3bc386a0b737e248 | Python | 31,631 | 798 | # 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... |
f8955f9c695d45b62466227f4bcbd22cee98eede2c7de936f4202f4089f39919 | Python | 31,659 | 925 | # 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... |
68367a173fc239617a42888c4d0140fcb11b648a817ffd60553cd2d08265f40d | Python | 31,668 | 697 | import unittest
from hed.errors import ErrorContext, ErrorHandler, ValidationErrors
from hed.models import HedString
from tests.validator.test_tag_validator_base import TestHedBase
class TestTagFormat(TestHedBase):
schema_version = "8.0.0"
class TestConvertTag(TestTagFormat):
def converter_base(self, test_... |
85c7fc7e8d6a1d2c7290c5512f64e2d906015a7ec99d49c12867d3809e8b0685 | Python | 31,677 | 800 | __author__ = 'martinez'
##########################################################################################
#
# Set of classes which follow the VTK filter interface and extend the functionality of VTK
#
##########################################################################################
import vtk
impo... |
45861d85791a98b181bcfd5c158e846742f17049f6dad30f1f142ccb58389559 | Python | 31,679 | 681 | import os
import datetime
import json
import numpy as np
from tqdm import tqdm, trange
import skimage.io
import mrcfile
import tensorflow as tf
from scipy.ndimage import zoom,rotate
try:
from tensorflow.keras import backend as K
from tensorflow.keras.models import Model
from tensorflow.keras.callbacks impo... |
af48cd6f5827677e3f5ca6d64f67612c4662291a5a14c9f22484a50581b8ae89 | Python | 31,682 | 700 | import pickle
from pathlib import Path
import numpy as np
import openturns as ot
import seaborn as sns
ot.Log.Show(ot.Log.NONE)
import matplotlib.pyplot as plt
import scipy.stats
from scipy.interpolate import UnivariateSpline
from sklearn.neighbors import KernelDensity
from uptake.figures.utils import... |
6002ea9595209f4e9cd2b85dd20de4053e69ead040cfc0c22a9d22b1be32903c | Python | 31,723 | 512 | """TWIN.py 2026-10-08. Pre-registration: 04-NOTES/PREREG-2026-10-08b-TWIN.md
A fly twin of the antennal lobe. Shiu et al.'s own file (antennal-lobe cut-out, DELETION_SOURCE.cutout), with three things
real fly neurons do and the model lacks, each set from a measurement:
(1) receptor neurons fire at rest, at their r... |
92ea3edf342a12036c3d62e5b256818167bd82e74e87b3c340f7484affbe56bc | Python | 31,733 | 813 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
"""Module with the model for TGAN.
This module contains two classes:
- :attr:`GraphBuilder`: That defines the graph and implements a Tensorpack compatible API.
- :attr:`TGANModel`: The public API for the model, that offers a simplified interface for the
underlying oper... |
b7b1b387e8021facbd4b9ce570f994760018e00be5513308e5ec6ce42c0c2caa | Python | 31,740 | 507 | from json_loading import *
from datetime import datetime
import pandas as pd
import os
import json
import gzip
import pandas as pd
import math
import sys
sample = snakemake.wildcards.sample
folder = snakemake.wildcards.folder
sys.stdout = open("{}/{}/Console_outputs/Nirvana_JsonDecoding.{}.out".format(fold... |
f65477d9c1c4b6aa73454b6b4080ce66a0d4cf4a2aa6e4d57f42aa4294cc2493 | Python | 31,742 | 932 | #%%
import torch
import torch.nn as nn
import torch.nn.functional as F
import math
"""
Model 구조의 선택권 : 1. Linear, 2. Conv
VAE에서의 ... -> Linearity를 고민할 수 있음. -> Manifold mixup in VAE의 latent vector
추가 term으로 임의의 2개 label (동일 structure)에 대해 manifold mixup 해버리자. (기대하는 것 : 동일한 structure에 대해서 label의 lin... |
91e69b7abc598e3d860464bfb6ec09b5334381a36d0bb91e8efad73704e2b2e8 | Python | 31,768 | 668 | #!/bin/env python3
"""
Phase defect fields
-------------------
A *phase defect*
is a (more or less) discontinuous jump in phase. In the context of cardiology,
conduction blocks, for instance, can lead to such phase defect. They can be
observed in the center of a vortex.
This submodule contains algorithms to calculate... |
3a9df01beaa396ed57df1a04e810deed1f90255f4012a9270b6c3615d6608ba6 | Python | 31,780 | 1,069 | ##
# \file input_argparser.py
# \brief Class holding a collection of possible arguments to parse for
# scripts
#
# \author Michael Ebner (michael.ebner.14@ucl.ac.uk)
# \date August 2017
#
import os
import re
import six
import sys
import inspect
import argparse
import platform
import datetime... |
739e8a97a0fbe4ceff76618ba7a19d40915bc5a8ed3ea339c4119e1eade9d32a | Python | 31,793 | 846 | #!/bin/env python3
"""
Visualisation with Matplotlib
-----------------------------
Collection of functions related to visualisation of various ithildin data.
These functions are supposed to be minimal. For more advanced plotting, create
a dedicated script.
Design of drawing functions is such that they can be plugged... |
7056296270f7ab2c1ba09aa254409fdc0e8fcfd0ac3600fbbcca933c307411f6 | Python | 31,809 | 769 | """Smoke + signature tests for ome_zarr_converter functions.
The points submodule is covered in test_ome_zarr_points.py; this file
covers the volume converter (TIFF -> OME-Zarr / Neuroglancer precomputed)
and the points converter helper (convert_points_file).
ng_viewer gets bare-import smoke tests that guard ag... |
d43218d6b403da8152325f17e69885e0a3530cfdd87e34ae730602e464e6370e | Python | 31,810 | 801 | # Numpy implementation of the Lagrange model (RtDeep). Trainable only with single samples. Not used, but kept for understanding the model.
#
#
# Authors: Benjamin Ellenberger (benelot@github)
import time
import numpy as np
# for optimization with root solver
from scipy.optimize import root
from model.network_params ... |
f0120c0a911ef9f089bddf518d8389aa68502a7e52a48e68b505ae578d8b3add | Python | 31,810 | 790 |
"""Base model class."""
import numpy as np
from sklearn.metrics import roc_auc_score, average_precision_score
import torch
import torch as th
import torch.nn as nn
import torch.nn.functional as F
from layers.layers import FermiDiracDecoder
import layers.hyp_layers as hyp_layers
import manifolds
import models.encoder... |
83399a2df13f1bc3cd80ee1bcef5e76c52f11a22f9461976bfb1b7f520bad535 | Python | 31,833 | 847 | #!/bin/env python3
"""
Visualisation with Matplotlib
-----------------------------
Collection of functions related to visualisation of various ithildin data.
These functions are supposed to be minimal. For more advanced plotting, create
a dedicated script.
Design of drawing functions is such that they can be plugged... |
1a9e0cce4d72743bfe03d4296aa1c7077825561b223feee52a47c7a68f8c4dc6 | Python | 31,838 | 582 | """Attractor diagnostic: does recurrent Fly coupling drive Qwen into a repetitive regime?
Runs real greedy inference through the observatory engine under matched controls and
writes structured JSON/CSV results plus plots. Nothing here applies repetition
penalties or other decoding changes; decoding is the same greedy ... |
aef90b9ddbba3173a364fb09824c4c63232f8427994f1fc9c8ce05df2224e5e4 | Python | 31,850 | 897 | import matplotlib
matplotlib.use("Agg")
import matplotlib.pyplot as plt
import numpy as np
import pandas as pd
import pytest
from SurvivalEVAL.evaluations.calibration.distributional import ksd_calibration
from SurvivalEVAL.evaluations.calibration.single_time import one_calibration
from SurvivalEVAL.evaluations.util ... |
0ee8d039c551d32949ebc3bc89719a1f7696bdde74873bca71ea1c71595210cc | Python | 31,872 | 672 | from __future__ import print_function
import argparse
import datetime
import os
import sys
import time
import random
import math
import numpy as np
cwd = os.getcwd()
pwd = os.path.abspath(os.path.join(os.getcwd(), ".."))
sys.path.extend([pwd,'../pddlstream','../ss-pybullet'])
from collections import Counter
from ite... |
86acd148586703bbdf9a4e0e7bb502281dd4f842c37a09724aaeee686291206e | Python | 31,874 | 583 | """Attractor diagnostic: does recurrent Fly coupling drive Qwen into a repetitive regime?
Runs real greedy inference through the observatory engine under matched controls and
writes structured JSON/CSV results plus plots. Nothing here applies repetition
penalties or other decoding changes; decoding is the same greedy ... |
7a79e6337560f74755fcf2f69b00ae966d4b65ea2582f71a58d1186f5bf9d177 | Python | 31,898 | 808 | """
This module provides the methods used in our paper to conduct Connectome Spatial
Smoothing (CSS).
The module contains the folowing functionalities:
- Code to map high-resolution and atlas-resolution connetomes
- Code to perform CSS
Python implementation of connectome-based smoothing
Author: Sina Mansour L... |
ae8672884fd21307db60616c0c61520e90ae3f341edeaf0ef9eb8d8852039e4c | Python | 31,906 | 674 | """The mirror functions in segmentation_stats.py and apply_transforms_figures.py
must reproduce the SAME 2-D annotation slice the run itself cropped -
otherwise the annotation silently misaligns against the warped output by
exactly the correction Task 7 introduces. Neither module has any other test
coverage in this... |
f22e5d07959b9737926d802493badaaa6bdde9310dfcd6a488e20437420face3 | Python | 31,931 | 736 | import pandas as pd
import numpy as np
import torch
import argparse
import vcf as pyvcf
import tqdm
from old_annotator_pytorch import Annotator, get_gene, get_genes, initialization
def visualize_snp(_chr, _snp_pos, _strand, _ref, _alt, _mutation_result='', use_spliceai=False, save_folder=None):
import matplotlib.... |
dabca41e830ab8db6d992240a2bfbfda8a6ec0f2bf84573fb413231ff4870bea | Python | 32,007 | 959 | import os
from tqdm import tqdm
import random
import numpy as np
import matplotlib.pyplot as plt
# PyTorch
import torch
from torch.utils.data import Dataset, DataLoader, SubsetRandomSampler,RandomSampler
from torch.cuda import amp
from PIL import Image
from torch import nn
from torch import optim
import torchvision
fr... |
f9d0d407b975ea37dc49f973c1960babe950ef3f359136f5287999ea0935b2c7 | Python | 32,013 | 867 | from __future__ import annotations
import os
import pytest
pytestmark = pytest.mark.skipif(
os.environ.get("GITHUB_ACTIONS") and os.name == "nt",
reason="Skipping this test on Windows in GitHub Actions.",
) # this works locally on Windows, but no clue why it fails on GitHub Actions
from importlib import ut... |
c2a75c9f8b9bdff1d24841852713296741748c39ae1c855c1e4d05a7a694445b | Python | 32,021 | 716 | '''
Description:
Conduct in silico perturbation in scNODE latent space.
Author:
Jiaqi Zhang <jiaqi_zhang2@brown.edu>
'''
import copy
import scipy.interpolate
import torch
import numpy as np
import pandas as pd
from tqdm import tqdm
from sklearn.neighbors import NearestNeighbors
from sklearn.ensem... |
ad2f14706ac3a83a877ae9e28b61a23e9d2499d2d1a1b4bfac79fa0f368c211a | Python | 32,022 | 709 | #!/bin/env python
"""
OXASL - MOdule to calculate M0 value or image for calibration
Copyright (c) 2008 University of Nottingham
"""
import os
import math
from optparse import OptionGroup
import numpy as np
import scipy.ndimage
from fsl.data.image import Image
from fsl.data.atlases import AtlasRegistry
from oxasl i... |
d0041d1beb957706ec02142a65d094d3af02135962c2c149e71aedea1fe94711 | Python | 32,026 | 630 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Thu Apr 16 08:00:51 2020
@author: daltonm
"""
#%matplotlib notebook
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
import pickle
import dill
import os
import glob
import math
import seaborn as sns
from sklearn.decomposition import ... |
28c3fc853ddc04991e44b07352ea939acd224cf318dd975bf5486b7af5724349 | Python | 32,032 | 643 | # -*- coding: utf-8 -*-
import torch
import torch.nn as nn
from torch.utils.data import Dataset
import numpy as np
import pandas as pd
import torch.nn.functional as F
import random
from torch.utils.data import DataLoader
from scipy.stats import pearsonr, spearmanr
import math
from pathlib import Path
from ignite.eng... |
910ba95a7f9e135bd0be8bb3659c9d4a4720e65d1b3a6bed2c61046125b9d6e8 | Python | 32,036 | 671 | from pyclbr import Function
from dolfin import *
import numpy as np
import matplotlib.pyplot as plt
import sys
import os
from IPython import embed
mpi_comm = MPI.comm_world
def read_xdmf(infile, mesh, order, tag, patient, comp):
V = FunctionSpace(mesh, "CG", order)
p = Function(V)
p_xdmf = XDMFFile(... |
1c9fcb0c2e742055bc73ebab72c587a545f45cb8f34baa497413399d799cd149 | Python | 32,048 | 654 | #!/usr/bin/env python
# =============================================================================
# GLOBAL IMPORTS
# =============================================================================
import os
import numpy as np
import pandas as pd
from typeI_analysis import mae, rmse, barplot_with_CI_errorbars
from ty... |
1b7bfeb40003ffcf4a86002115fba5050a8a3df20a4be1846cddba674315ff6a | Python | 32,107 | 955 | # 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... |
335c2aa25ee46959844a72647448863bb069ebffa893dc5e56a1a0ba37c646b8 | Python | 32,138 | 509 | import os
import torch
import logging
import numpy as np
import torch.nn as nn
from torch.optim import lr_scheduler
from torch.nn.utils import vector_to_parameters, parameters_to_vector
from torchdrug.utils import comm
from torchdrug.layers import functional
from torchdrug import core, utils, datasets, model... |
e1975146a6aa6580be28d2032e182baa89eeed270ec359f2ea1deb71a827b239 | Python | 32,156 | 682 | import numpy as np
import cupy as cp
import opt_einsum as oe
from neuron import h
from utils.func import load_json
import pickle
class SynInfo(object):
def __init__(self, id, point, syn, p=-1):
self.id = id
self.point = point
self.syn = syn
self.p = p
class Network(object):
d... |
029e62420b9334b4a30d8b1074f9c7dae4078e7a9b40f45485e8a3e18bbad3cd | Python | 32,160 | 932 | # simulation.py
# A class representing simulation data from a .mat file.
# TODO: Add docstrings
# imports
from os import PathLike
from pathlib import Path
from typing import Callable, Iterator
import h5py
import numpy as np
import numpy.typing as npt
import pandas as pd
import scipy.io as sio
import matplotlib.pypl... |
e043907b0d79e97465626d22319ef6bcfecc061df8ee723cbe4534cea05dc30e | Python | 32,167 | 727 | """
Script for computing/analysis and plotting peri-event-time histogram.
Contains the following:
align_spktrain function; puts together aligned whisker variable and spike
counts (binsize equal to frame) of each cluster; it returns data for
plot_psth function.
spike_train function: used by align_spktrain to compute s... |
3b833cb695d998b2c119532a696601fa95c960c2e13292115e29a39b5c403c87 | Python | 32,174 | 920 | """Tests for coglet Python bindings."""
import queue
import re
import socket
import subprocess
import sys
import threading
import time
from pathlib import Path
import coglet
import pytest
import requests
# =============================================================================
# Module structure tests (no serv... |
69c5727e34f8fbb84c0205651cfb62e06c4f0632099feffc4b3882b304972439 | Python | 32,185 | 793 | import os
import sys
import h5py
import numpy as np
import scipy.interpolate
import scipy.signal
import scipy.fftpack
def rms(x):
'''
Returns root mean square amplitude of x (raises ValueError if NaN).
'''
out = np.sqrt(np.mean(np.square(x)))
if np.isnan(out):
raise ValueError('rms calcula... |
1e03762a8879f19bf1248712b87a500972a8ca6c5cca59b95006ec0701da7ae1 | Python | 32,227 | 800 | #!/usr/bin/env python
#================================================================
# Copyright (C) 2023 Yufeng Liu (Braintell, Southeast University). All rights reserved.
#
# Filename : generate_me_map.py
# Author : Yufeng Liu
# Date : 2023-02-09
# Description :
#
#===============... |
588de18185dbd5b45ed6dd8fd9d6e7975683c71ed6198f234f05f1914c07ff9c | Python | 32,287 | 767 | # Import libraries
import torch
from torch import nn
from torch.utils.data import DataLoader
import torch.optim as optim
import pandas as pd
import numpy as np
from sklearn.model_selection import train_test_split
from sklearn.model_selection import StratifiedKFold
from torch.utils.data import Dataset
from torch.utils.t... |
0c9a380b5ec4b967dd303549300478f51a0107b31df1d35287c575a3627de87c | Python | 32,302 | 736 | """Allows output of HedSchema objects as .json format"""
import json
import pandas as pd
from hed.schema.hed_schema_constants import HedKey, HedSectionKey
from hed.schema.schema_io import df_constants, json_constants
from hed.schema.schema_io.schema2base import Schema2Base
class Schema2JSON(Schema2Base):
"""Co... |
708fa54833d9beb515459f19fd0c73a0a0de0dc742ee4c479b36a780a94c230b | Python | 32,312 | 742 | # -*- coding: utf-8 -*-
"""
Created on Jun 22 2023
@author: Jonas A. Thiele
"""
###Training of prediction models with FC (100 node parcellation) of the main sample (610 subjects, 5-fold cross-validation)
###Training with different numbers of the most relevant links (edges)
#%% Imports
import pandas as p... |
14356749677cb7ed053755175c33a416e553cd3f80d7554b315dec0c07ed3082 | Python | 32,326 | 539 | #####################################
######## 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... |
74bd316a9414fe6b3935cf5594892dfeb988474a4254e14101f6e3d3205fa5bb | Python | 32,335 | 944 | """Classes for plotting.
"""
import matplotlib
matplotlib.use("Agg")
import matplotlib.pyplot as plt
from matplotlib import patches
# this is so I can plot graphics on a headless server
plt.ioff()
HORIZONTAL_LEVELS = [1, 2, 3, 4]
class _Plot:
"""Base plotting class"""
def __init__(self, filename="", hei... |
4831f8d86e0d039f49adb1382ee6600f56310f151621197b6333eb97c6481801 | Python | 32,375 | 515 | ##############################
######## Shallow Grid ########
##############################
#%%# 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)
import numpy as np
import... |
688e9644adc296eaa9f397d26e769612d05d64a3a50876e53ad352ca899cdd93 | Python | 32,387 | 701 | import os
import json
from copy import deepcopy
import cv2
import carla
from PIL import Image
from collections import deque
import torch
import numpy as np
import math
from leaderboard.autoagents import autonomous_agent
from model import LidarCenterNet
from config import GlobalConfig
from data import lidar_to_histog... |
fb9297755b01468961bee865e722e8fbad99af4c7e615f21c94c519c8f90a697 | Python | 32,410 | 822 | from abc import abstractmethod
import numpy as np
import uuid
import cv2
from skimage import measure
from typing import List
from typing import Tuple
from typing import Dict
from shapely import geometry
import h5py
import merlin
import pandas
import networkx as nx
import rtree
from scipy.spatial import cKDTree
from m... |
e64a7beb54f7be5ffc3c1056fdab7b2c2eb9d1e420bd233dbc347f464e0ddc58 | Python | 32,453 | 911 | """
Run the "canonical" TE-Dependent ANAlysis workflow.
"""
import argparse
import datetime
import json
import logging
import os
import os.path as op
import shutil
import sys
from glob import glob
import numpy as np
import pandas as pd
from nilearn.masking import compute_epi_mask
from scipy import stats
from threadpoo... |
cadea633f5ece6c32908a8e26be629307754d0835e1554590020338fdfcc10e6 | Python | 32,472 | 613 | """Headless lifecycle and signal checks; fixtures never enter user anatomy caches."""
from __future__ import annotations
import os
import hashlib
import json
os.environ.setdefault("QT_QPA_PLATFORM", "offscreen")
import sys
import types
from pathlib import Path
from types import SimpleNamespace
import numpy as np
impo... |
e1f018ad165a003e9f20ba6344caebfd653a06166fe129d1d530a9b8a522c2c4 | Python | 32,488 | 539 | #####################################
######## 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... |
6765d5335be30383a0612dc8717253f93800e248f6182a242846839f8022bfb4 | Python | 32,495 | 728 | import numpy as np
#### import the simple module from the paraview
from paraview.simple import *
#### disable automatic camera reset on 'Show'
paraview.simple._DisableFirstRenderCameraReset()
################################################################################
# Set visualisation environment:
# get active... |
f180d0785c2830ccd09bfa3da9f73db82dfaf31b7cee3be600211ee9175fac12 | Python | 32,500 | 1,014 | #!/usr/bin/env python3
import os
import re
import shutil
import subprocess
import sys
from importlib import resources
from pathlib import Path
# Imports relocated internally to functions to avoid module-level import errors
# when running visualization subcommands in environments without simulation packages.
SCRIPTS =... |
1d90adc81fc16227b7c7cf04d17fd30af8afac7095bada0c955d84e0704c55cc | Python | 32,503 | 703 | import os
import argparse
import time
import numpy as np
import torch
import torch.nn as nn
import torch.optim as optim
import matplotlib.pyplot as plt
import torch.nn.functional as F
import networkx as nx
import torchdiffeq as ode
import sys
import functools
import scipy.io as scio
from utils import *
import argparse
... |
02f78d0c336472ac1dbd09cbd8fee143f04ce9b959b33c581c484e7c10169fc8 | Python | 32,513 | 783 | #!/usr/bin/env python
# -*- encoding: utf-8 -*-
import re
import textwrap
import bindings as bi
class JavaTypeTranslator(bi.TypeTranslator):
def __init__(self):
bi.TypeTranslator.__init__(self)
self.types["string"] = "String"
type_adapter = JavaTypeTranslator()
def translate_type(h2o_type, schema... |
fb304e31cd1cc915ca598784c20ac654808d17bc608403ec04b7be3e60fc0d37 | Python | 32,526 | 659 | # -*- coding: utf-8 -*-
################################################################################
## Form generated from reading UI file 'dgn_chkres_ctrl.ui'
##
## Created by: Qt User Interface Compiler version 6.8.0
##
## WARNING! All changes made in this file will be lost when recompiling UI file!
###... |
349830c1864d8cb5bda14fcf38d89975cac5e77bf55a61274a7f294326ccac06 | Python | 32,530 | 797 | import math
import os
import random
import re
from collections import namedtuple
from itertools import combinations
import numpy as np
from .pr2_never_collisions import NEVER_COLLISIONS
from .utils import multiply, get_link_pose, set_joint_position, set_joint_positions, get_joint_positions, get_min_limit, get_max_lim... |
91d36895613145b17cf5f27a6a3ed86e676f79eb70229a69b69be6196f16e5a4 | Python | 32,551 | 976 | from functools import partial
import numpy as onp
from autograd.extend import SparseObject, VJPNode, defvjp, defvjp_argnum, primitive, register_notrace, vspace
from ..util import func
from . import numpy_wrapper as anp
from .numpy_boxes import ArrayBox
# ----- Non-differentiable functions -----
nograd_functions = ... |
c422989249a03d6225056c162a44afd06fa0e326364510a5b207f87a791d3acc | Python | 32,554 | 883 | """
CLI entry point for cellpose-SAM cell detection.
Usage:
# Positional arguments
python -m regtools.cellpose_sam section_001.tif results/
# Or with flags
python -m regtools.cellpose_sam --input section_001.tif --output results/
# Directory of stitched sections
python -m regtools.... |
c367e154485fdf74af91f920b9a815a5cea19e2fdd00ca1b5e36b391970234e2 | Python | 32,588 | 780 | # MEGIT data process functions
import copy
import numpy as np
import scipy.ndimage as ndi
import scipy.interpolate as itp
import cv2 as cv
import warnings
"""Function list:
# Image/Video processing functions
get_frm(vid_cap, frm_idx): Get specified frame of video file.
brt_con(img, brt=0, con=0)... |
ab18b8eb4c749020c58411d08ebe187d20917c72f1874f044b002fe17854e51f | Python | 32,591 | 615 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Thu Apr 16 08:00:51 2020
@author: daltonm
"""
#%matplotlib notebook
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
import pickle
import dill
import os
import glob
import math
import seaborn as sns
from sklearn.decomposition import ... |
1357a148af14fab17415e5669814a11b785205c1a1903ce8484ce6c9007ba440 | Python | 32,594 | 605 | # coding=utf-8
# Copyright 2018 The Google AI Language Team Authors and The HuggingFace Inc. team.
# Copyright (c) 2018, NVIDIA CORPORATION. All rights reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a cop... |
3f9eb00adbb1a7f4418e0c05122111be2c222db802ed75335e926f157481578c | Python | 32,635 | 630 |
'''EG2EP'''
# import pandas as pd
# import os
# # 指定数据集文件所在的目录和结果保存目录
# # data_directory = '/home/tjzhang03/zxj/deal_data/data_input/BENGI/Remove-Ambiguous-Pairs.Natural-Ratio/conbine_data/'
# data_directory = '/home/tjzhang03/zxj/deal_data/data_input/BENGI/All-Pairs.Natural-Ratio/'
# # data_directory = '/home/tjzh... |
653f0ce0b8d44455a8b8883284a29dee3fab19b89bd86505857544073f115f43 | Python | 32,659 | 273 | dataset_metadata = {
"mouseID_19030607-191192": "https://download.brainimagelibrary.org/inventory/e9102e30-6863-5c3f-82da-98ea37aad4d6.json",
"mouseID_w19082922-193663": "https://download.brainimagelibrary.org/inventory/6d267b5b-f370-5060-a5ca-cfc0c83c5261.json",
"211061": "https://download.brainimagelibrar... |
6d3d93d1a37427ec55e8aab2f67c8dccfb03238741e2d22d834a151cba118ce3 | Python | 32,710 | 841 | # 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... |
7ca71f1b574a41a186330a944c389032a747e19fdb3d3633f30f0323c0345169 | Python | 32,737 | 872 | """
(*)~---------------------------------------------------------------------------
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.
------------------------------------... |
00ce2aacd358c82757ef65fd0e7123aa393f9e9b8ed2958c066347eec84b87aa | Python | 32,750 | 659 | from typing import Dict, Tuple
import traceback
import cv2
import numpy as np
import torch
# torch.backends.cudnn.enabled=False
import sys
import os
sys.path.append(os.getcwd())
sys.path.append('../pysot')
from pysot.core.config import cfg
from pysot.models.model_builder import ModelBuilder
from pysot.tracker.tracke... |
acefe90d61264580eae5d89e550f0c78a0630386851acd59fda80bdfb96b281f | Python | 32,751 | 919 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Tue Oct 26 13:05:23 2021
@author: joaquin
"""
import matplotlib.pyplot as plt
import seaborn as sns
import numpy as np
import scipy.io
import pandas as pd
import os
import h5py
import mat73
from scipy import signal
from scipy import stats
from sklearn.dec... |
c5ffe468352ea1f4f9fbf0761b407d126835b630c7af6193b0480d704a4af930 | Python | 32,871 | 811 | import logging
import tqdm
from torch.nn import functional as F
import torch
from pyfaidx import Fasta
import numpy as np
import pandas as pd
from pyensembl import Genome
import vcf as pyvcf
from model.model import SpTransformer
from model import SpliceAI
IN_MAP = np.asarray([[0, 0, 0, 0],
[1, 0,... |
e8d4444fb9e876c8e0104b6e61b81e89e0c6c9a170fcfc0295a02c47324ee30c | Python | 32,873 | 767 | """
Defines class CleftRegions that holds cleft-related data (geometry and layers)
from one or more observations (experiments) divided (classified) in groups.
The observations are expected to be generated by scripts/cleft.py.
or classify_connections.py.
# Author: Vladan Lucic (Max Planck Institute for Biochemistry)... |
e3838763e21c4b0c9ee8d59d5372347adc203405e27d9775510fec9f612da2eb | Python | 32,889 | 708 | """
DeepLabCut2.0 Toolbox (deeplabcut.org)
copyright A. & M. Mathis Labs
https://github.com/AlexEMG/DeepLabCut
Please see AUTHORS for contributors.
https://github.com/AlexEMG/DeepLabCut/blob/master/AUTHORS
Licensed under GNU Lesser General Public License v3.0
"""
import os
import os.path
import glob
import cv2
import... |
c04fa68f9d7498d662eed19c245a07eeda13a917cffc3b101e4bc27c822ad808 | Python | 32,897 | 830 | #!/usr/bin/env python3
# System imports
import os
from os import listdir
from os import walk
from os.path import isfile, join
from pathlib import Path
import sys
import glob
import numpy as np
import re
import time
import pudb
from sc... |
a9d0a6bc70467e84d86396047b45c7ffd342de44aa398d5d3b4070408e1577eb | Python | 32,926 | 712 | import schnetpack as spk
import torch
import torch.nn as nn
from torch.autograd import grad
from schnetpack import Properties
from schnetpack.atomistic import Atomwise
import schnarc
from schnarc.data import Properties
class StateModel(nn.Module):
def __init__(self, representation, output_modules, mapping=None)... |
c3de77af5314a2cf4a80fdc3f18155fc4206f8cc042669a295f3525518ee116b | Python | 32,963 | 803 | """
Contour extraction, normal estimation, and correspondence matching.
Provides functions for finding contours in brain images, estimating surface
normals, computing 2D correspondences, and performing slice-to-slice
Laplacian registration.
Performance optimizations:
- Parallel slice processing with joblib
-... |
76a57c985e32f1e41ead2cdaccc36290992c4a1a32cad637c2384db410065e4c | Python | 32,965 | 847 | """Single HED schema object representing a loaded vocabulary specification."""
from __future__ import annotations
import json
from pandas import DataFrame
from hed.errors import ErrorHandler
from hed.errors.error_types import ValidationErrors
from hed.errors.exceptions import HedExceptions, HedFileError
from hed.sc... |
826f251339fc996bded82851e1a57eaa901d7384edef4e23cbfa84d3855a947c | Python | 32,968 | 585 | """The four stages of SpreadsheetValidator, their stops, and the DataFrame-free path."""
import io
import json
import os
import unittest
import pandas as pd
from hed import Sidecar, SpreadsheetInput, TabularInput, load_schema, load_schema_version
from hed.errors.error_reporter import ErrorHandler
from hed.errors.err... |
acc91114d47fd8fd3024155725b90277aa7eeb8dbe2f6e0099b5b4441765d322 | Python | 32,980 | 710 | # 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... |
18f86f921e38c1b91c090d1f3cfeef6a1a9442b9cbe14bf1aae7b75510fcb9a4 | Python | 33,038 | 589 | import sys
assert('neuron' not in sys.modules)
import os
nrn_options = "-nogui -NSTACK 100000 -NFRAME 20000"
os.environ["NEURON_MODULE_OPTIONS"] = nrn_options
import numpy as np
import matplotlib.pyplot as plt
from mpl_toolkits.mplot3d import Axes3D
from matplotlib import cm
import matplotlib.animation as animation
imp... |
3cb83634b4b0d22ce3c88fc93f4269f6a5765a369e81fd6ef7721e2b7c6d4f52 | Python | 33,042 | 917 | # -*- coding: utf-8 -*-
"""
Created on Mar 9 2023
@author: Jonas A. Thiele
"""
### Comparisons between results of network-specific link selections in the main sample
#%% Imports
import pandas as pd
import numpy as np
import scipy.stats
import seaborn as sns
from matplotlib import colors
import mat... |
4e3115abd4bc67d9d91cd4e06ec3bc06a8fa9b73b07ab094ae240f965141cb4f | Python | 33,068 | 731 | # 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... |
8691b6f419b63c0abb1bea204dab5970d5208f0b74ce97535edc46c3833f32d5 | Python | 33,084 | 874 | # The following comment should be removed at some point in the future.
# mypy: strict-optional=False
import functools
import logging
import os
import shutil
import sys
import uuid
import zipfile
from optparse import Values
from typing import Any, Collection, Dict, Iterable, List, Optional, Sequence, Union
from pip._v... |
ebf046f2fcdd24dd7b1982995247b03d0ee519c72f85256e050118153047f752 | Python | 33,111 | 809 | # -*- encoding: utf-8 -*-
r"""
pyparser -- module for parsing Python files.
This module provides capabilities for parsing Python files into logical pieces. It relies on standard
module :mod:`tokenize` to break the file into tokens, and then combines those tokens into high-level
code constructs. Unlike :mod:`ast`, this... |
fa205b2d73ab8f9c0c338830f91a0e1b12b3ea2fb558a1979ed1aa69edfcc84e | Python | 33,129 | 645 | #!/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 lo... |
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