sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
26ca0e620c1d7b9c874703f03fdb5db9cd83adf73f0c83935141067145e5a42a | Python | 6,351 | 181 | from __future__ import annotations
from io import StringIO
from pathlib import Path
from typing import TYPE_CHECKING, cast
from ase.io import read
from ase.units import Hartree
if TYPE_CHECKING:
from typing import Any
from ase.atoms import Atoms
from quacc.types import MRCCEnergyInfo
def read_geom_mr... |
9dcd47a6da011d8e90619f652e8a178374a15f60abba0ef9808c88e445ae3ea1 | Python | 6,351 | 203 | import anndata as ad
import h5py
import numpy as np
import pytest
import zarr
from anndata._core.sparse_dataset import sparse_dataset
from anndata.tests.helpers import (
array_bool_subset,
array_int_subset,
assert_equal,
slice_int_subset,
subset_func,
)
from scipy import sparse
subset_func2 = subse... |
34a76038a8a7c9e858b75becef124f0baba5d94ee9d7d468b0a80507fc96f4bb | Python | 6,352 | 145 | #----Figure_03_G,H_preparation--------------------------------------------------
#-------------------------------------------------------------------------------
# This is the code which has to be run in preparation for Figure 03 Panel G and H
# for the connectivity analysis for Reinhard and Fukuda et al. 2024
# ru... |
5d42200581e1b15397f2b5aed47752d4894d81ee9754733da97c811f8051869d | Python | 6,353 | 194 | from __future__ import print_function, division
import numpy as np
class ScaledGaussianMixture:
def __init__(self, ncomponents=2, scale_prior=0.5, tol=1e-6):
self.ncomponents = ncomponents
self.weights = np.ones(ncomponents)/ncomponents
self.means = np.zeros(ncomponents)
self.vari... |
7c3d35408fc3fbd276127e6eb3001fca3e198eadda394ae121c4bc2cf1901068 | Python | 6,353 | 154 | # Loops calling adapted from:
# https://github.com/XiaoTaoWang/HiCPeaks
import lightning.pytorch as pl
from hicdiffusion_model import HiCDiffusion
import matplotlib.pyplot as plt
import matplotlib
import lightning.pytorch as pl
from hicdiffusion_model import HiCDiffusion
import datasets
import numpy as np
import math
... |
825e05b378ffc1bc5814bb748c222258aab46af872f12a0f318471a2a0da14f9 | Python | 6,356 | 149 | #!/usr/bin/env python
#================================================================
# Copyright (C) 2023 Yufeng Liu (Braintell, Southeast University). All rights reserved.
#
# Filename : predict_types.py
# Author : Yufeng Liu
# Date : 2023-02-05
# Description :
#
#=================... |
c72676dac34f86ed9b44eef68f37cd004954d5a0fe2a057d8c74323e6f99f63c | Python | 6,357 | 180 | import tensorflow as tf
from tensorflow import keras
import tensorflow.keras.backend as K
from tensorflow.keras.models import Model
import os
os.environ['TF_CPP_MIN_LOG_LEVEL'] = '2'
import numpy as np
import pandas as pd
import kl_tools
from adv_model import train_adv
from loss import adv_loss
from utils import oneho... |
128ffab403cb674d23d20263f477df371bcd8d414720bffdfb24f70d506dbb0d | Python | 6,358 | 176 | """Common modules for FastGlioma training, evaluation, and inference.
Copyright (c) 2024 University of Michigan. All rights reserved.
Licensed under the MIT License. See LICENSE for license information.
"""
import os
import math
import logging
import argparse
from shutil import copy2
from datetime import datetime
fro... |
2e99dd16200e39f02e03346b8f0b2f6aef22938ff8b8e4e56416b8093276234f | Python | 6,358 | 218 | # -*- coding: utf-8 -*-
import csv
import logging
import os
from pathlib import Path
from subprocess import check_output
class DEFAULT(object):
""" Default values of the package"""
doc = "Documentation at https://unfmontreal.github.io/Dcm2Bids/"
link_bids_validator = "https://github.com/bids-standard/... |
abda71f88852eb2212559dc16d01974f56257f93e1e1dc90357930ab57cc9209 | Python | 6,358 | 219 | # 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... |
b42b6ab5b0570d45af4aca0e8c8b51ecb0560206211a7c2879f2adc90d4b4dc4 | Python | 6,358 | 195 | import os
import torch
import torch.nn as nn
import torch.nn.functional as F
import matplotlib.pyplot as plt
import pandas as pd
from tqdm import tqdm
import argparse
import torch_geometric
from SpiderUtils.dataset import SpiderDataset
from SpiderUtils.models import Spider
from SpiderUtils.Cosine_warm import CosineWar... |
f804d8356137c4fa778878e174331efabaa9658d19f862beee563b891f58e7ed | Python | 6,358 | 172 | # Script to save smoothed population rates obtained during TVAT search
from mpi4py import MPI
comm = MPI.COMM_WORLD
rank = comm.Get_rank()
nhost = comm.Get_size()
import sys
sys.path.append("..")
import h5py
import numpy as np
import pso_comp
from SensitivityAnalysis import SensitivityAnalysis
import time as cookie
f... |
8a7f52ae8dd89269bcfaa82f54c2a04e6ff5f2524fa1976c6e99e1a6f6dc2059 | Python | 6,359 | 204 | import sys; import os
sys.path.insert(0, os.path.abspath('../eyewire'))
from shove import Shove
import numpy as np
from matplotlib import pyplot
import pickle
import mesh
import scipy.stats
dataset = Shove("lite://tmp/dataset_b","lite://:memory:")
def histagram_average_displacements():
bins = np.linspace(0.0, 1.0... |
a8420940ef17f74dcd768489e8816fc9391f4e3cb45d816b1fa6782a83e54ab0 | Python | 6,360 | 165 | """The input pane's edge letters, per input type.
A section-shaped input gets CONSTANT L/R/S/I - the convention the run assumes
after the user's orientation settings. The labels deliberately do not follow a
flip: a label that moves with the image always agrees with it, so a mirrored
section would never look wrong... |
6cfe8ef625220421b50f97337d7568a90601d50ed294de9e57878a124ed0c658 | Python | 6,361 | 154 | """Public damage/tear detection for the Laplacian ``exterior_damage_aware`` mode.
The silhouette comes from the project's current masker -- the seeded
Multi-Otsu-4 GrabCut in :mod:`regtools.tissue_masking.core.grabcut`
(``compute_entropy_grabcut``) -- NOT from the vendored engine's old
canny/gaussian/``threshold_... |
72e2db9ec6e48f0fe54e156971ac8921bc97ec299f5719258494fa497b9434ac | Python | 6,361 | 139 | import sys
import os
class Deconvolutions:
def __init__(self, RNA_file = None, RNA_h5ad = None, RNA_h5Seurat = None, Spatial_file = None, Spatial_h5ad = None, Spatial_h5Seurat = None, celltype_key = None, celltype_file = None, python_path = None, output_path = None):
"""
@author: wen zhang
... |
9ea4eaa6b4a9b6103ed0fa47337dfa642cd453de58732d904cf81e5e2cc179fa | Python | 6,362 | 151 | """
KNOWN_NT_MATCHED.py - written 2026-09-17, immediately after KNOWN_NT_VALIDATION.py.
WHY THIS FILE EXISTS. KNOWN_NT_VALIDATION.py reported AUC 0.720 for class C (a transmitter
on the menu plus one off it) against class A (single in-vocabulary), cell types as the unit.
Then the composition was inspected and th... |
6d82331d2f50a4b57224bdf9efaf78c72934cf2a1ef4a0f31c225b17dc47231d | Python | 6,363 | 161 | '''Preprocess nback scores. Reads all available logs from the nback task and
computes the scores (median RT, number of correct, wrong, and missing answers)
The input should be done in the following order:
- folder path where the files are
- savefile where the proprocessed data will be s... |
85a6b1fbcd774873917373e4ae60af5f9c415ddbbf140362ad1368a15c2fe295 | Python | 6,363 | 132 | from collections.abc import Sequence
import torch
from torch import nn
from torch_scatter import scatter_add
from torchdrug import core, layers
from torchdrug.core import Registry as R
@R.register("models.GearNet")
class GeometryAwareRelationalGraphNeuralNetwork(nn.Module, core.Configurable):
"""
Geometry A... |
ab4097c016ab03231c945977372def94a78c637845612b8492630f34f6e8a4f3 | Python | 6,363 | 177 | import os
import re
from typing import List, Tuple
from glob import glob
import math
import numpy as np
import h5py as h5
from tqdm import tqdm
import click
from torch.utils.data import DataLoader
import torch
from cl_3d.datamodules.components.data import SectionDataset
from cl_3d.models.contrastive_module import Co... |
f3e8ccaa9e51d1fc71c96561c0d6f918f93a014806bfee4046bd20844551140b | Python | 6,363 | 127 | # 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... |
9a37764320a6ebb86ee5d022ea1110c3abc7f7df257b80a95b4fdb1b6c2249dd | Python | 6,365 | 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... |
d3ce678a4ee29b347cc4436a4d7447f0ce024eb7e5495f211b5a709af1ddf1e9 | Python | 6,365 | 210 | # -*- coding: utf-8 -*-
#
# Configuration file for the Sphinx documentation builder.
#
# This file does only contain a selection of the most common options. For a
# full list see the documentation:
# http://www.sphinx-doc.org/en/master/config
# -- Path setup ------------------------------------------------------------... |
c8917e8dae99cc6137e1ec2755b315d3f915b2ebf56de0f58325fc91f0fea8cd | Python | 6,367 | 232 | #!/usr/bin/env python
# coding: utf-8
# In[1]:
import numpy as np
import matplotlib.pyplot as plt
import pandas as pd
import seaborn as sns
from sklearn.decomposition import PCA
from tqdm.auto import tqdm
import torch
from umap import UMAP
import pancancer_evaluation.config as cfg
from csd_simulations import simula... |
c83bcc841c8fd9eb2ca9fc3795418172b93b5c0799ea0372b79f00b0c87d83c0 | Python | 6,368 | 126 | from typing import List
import torch
import torch.nn as nn
from .mmd_like import _MMDLikeTrainer
def guassian_kernel(x_source,
x_target,
mul_kernel=2.0,
num_kernels=5,
sigma=None):
n_samples = int(x_source.shape[0]) + int(x_target.s... |
1f2cf080b229023daebf545c4162cbeda3669eb31e6858706d18d9f884d40855 | Python | 6,369 | 200 | """
Structured perceptron algorithm for learning CCG weights.
"""
from collections import Counter
import logging
import numpy as np
from pyccg import chart
from pyccg.util import softmax, NoParsesError
L = logging.getLogger(__name__)
def update_perceptron_batch(lexicon, data, learning_rate=0.1, parser=None):
"""... |
abacbc1a8cd54ba34fb2d727b424e40f42813d0b307e07c28097eeb580c392d5 | Python | 6,369 | 183 | # 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... |
4960575357800b230ceecc6d18db11827c8db2af404117ce6adf1f1f39208636 | Python | 6,370 | 187 | # Node-group asset "Color Rainbow" (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.
import math
from typing import T... |
c87d3d8660ed971066b408ed82d45f18a844e5ee9aa763d6c97ea82f070389f3 | Python | 6,370 | 164 | # coding=utf-8
# Copyright 2020 The Google AI Language Team Authors, Allegro.pl, Facebook Inc. and the HuggingFace Inc. team.
#
# 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://ww... |
b95a287245ae0f2f7be2e5edfe297237acac57b175df7a835d4d9c2f2260629a | Python | 6,371 | 165 | # -*- coding: utf-8 -*-
r"""This file implements the atomic charge dipole model.
Atomic property predictions from the network are interpreted as atomic charges.
A charge neutrality constraint is applied to enfore a charge of zero on the
charge neutral entity by equivalently spreading the excess charge out over the
at... |
15350c847ef35eacd33cd35cdf06bb63cf98f25370dd92736627a5082bff4a63 | Python | 6,372 | 208 | import torch
import torch.nn as nn
import numpy as np
import math
from torch import nn, Tensor
class PositionalEncoder(nn.Module):
def __init__(self, dropout=0.1, max_seq_len: int=5000, d_model: int=512, batch_first: bool=True):
super().__init__()
self.d_model = d_model
self.dropo... |
61a00592c214ab6b4dc23af77ec3e4afaa514d1ff9e3ffb0713ce0d7a184beb6 | Python | 6,372 | 135 | # 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... |
7c8aa7d02a667e57fe49258228ed1e0536c3c9354a57dbbabfa0e4b3cf59e6d5 | Python | 6,373 | 152 | from typing import Any, Optional, Dict
import numpy as np
from models.kan_layers import FastKANConvLayer, KAN
from models.model import Model
import torch
import torch.optim as optim
import torch.nn as nn
from torch.nn import init
import torch.nn.functional as F
class Luo3DCNN_KAN_Net(nn.Module):
"""
HSI-CNN... |
c90092b21a6985a7fb48b1b7e382575d523e8f15e4f54cdc7af5ecfc57d62348 | Python | 6,373 | 160 | from __future__ import print_function
import argparse
import os
import numpy as np
from skimage.morphology import skeletonize_3d
from scipy import ndimage as ndi
from lib.dvn.utils import get_itk_array, make_itk_image, write_itk_image, get_itk_image
def parse_args():
parser = argparse.ArgumentParser(description='E... |
1f0af98b7e94417a21ada764df4222d5003c78019eeead09089c62e1d66b1500 | Python | 6,374 | 147 | """End-to-end test for ccf_boundary_editor.apply_slice_edits.
Exercises the full pipeline:
SliceEditState -> get_backend -> fit_pull_field -> applyDeformationField
The unit tests in test_ccf_boundary_contour_edit.py cover build_components and
correspondences_from_state at a finer grain; this file confirms t... |
2c9cb8fd378c12e771c2ab36e220dad1edaabd07c7e5e055d401326d926b6781 | Python | 6,374 | 223 | #!/usr/bin/env python
import os
import sys
import time
import boto
import boto.ec2
# Environment variables you MUST set (either here or by passing them in).
# -----------------------------------------------------------------------
#
os.environ['AWS_ACCESS_KEY_ID'] = ''
os.environ['AWS_SECRET_ACCESS_KEY'] = ''
os.env... |
4c963cc594c3be2ff0f48a85c0705b50d9f647e43651036255b82333d608054c | Python | 6,375 | 241 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
import matplotlib.pyplot as plt
import numpy as np
import analysis_params
#######################################
### PLOTTING ###
#######################################
def add_gdf_to_dot_display(ax, gdf, color='0.', alpha=1.):
plt.sca(ax)
... |
aa1abee1dbe520df4c8899adf3f6e416bae446edaeda4dda9a94bca6790b1c08 | Python | 6,375 | 170 | """Utilities used in HED validation/loading using a HED schema."""
from hed.errors.error_reporter import ErrorHandler
from hed.errors.error_types import SchemaWarnings
from hed.schema import hed_schema_constants as constants
from hed.schema.hed_schema_constants import character_types
def validate_schema_tag(hed_entr... |
7799e59b648a373b75e0ca6f2e4ce71f729384468e3aa17cc9a7d7dfbdb91903 | Python | 6,376 | 200 | import torch
import torch.nn as nn
import torch.nn.functional as F
import argparse
import os
#import wandb
import tqdm
import numpy as np
import pandas as pd
import data
import util
import net as networks
from torch.utils.data import DataLoader
"""
Optimized Hyperparameter
conv_out_dim=512
lstm_hidden_size=320
kern... |
ee2d69c271255168a4b7b02df7477e9aa6284d2be4e7a69c655bf7d760b9c4ad | Python | 6,376 | 152 | """Regression tests for the DRY-ed TissueCyte orientation.
The orientation (clamp>=0, transpose spatial axes, flip both) used to be
hand-rolled inline in four places: three TIFF read paths in
``regtools/utils/io/tiff_io.py`` (`_load_image_2d`, and twice in
`_load_image_multipage`) plus the 2D registration loader'... |
707251ffa2a7d57ea167a139a4d7d001a0761c64ec42151a5d8b56393d89c10e | Python | 6,377 | 164 | from typing import Any, List
import torch
from pytorch_lightning import LightningModule
from torchmetrics import MinMetric, MeanMetric
from torchmetrics.classification.accuracy import Accuracy
from torchmetrics import MeanAbsoluteError, MeanSquaredError
class MREBrainLitModule(LightningModule):
"""Example of Ligh... |
a0871ffb7a58188dea724d504a7f34d09bac738a716fbfc7fd7ecfb21c26d94e | Python | 6,377 | 192 | import subprocess
import tomllib
from pathlib import Path
import pytest
import serial
import torch
from elasticai.usbprotocol import UserRemoteControl, get_env5_port
from elasticai.creator.arithmetic import (
FxpArithmetic,
FxpParams,
)
from elasticai.creator.file_generation.on_disk_path import OnDiskPath
fro... |
a584a45968d8cf3f2406a07913d7918f86f557d7d753c2d533babbb9a16d90b0 | Python | 6,377 | 136 | import os
import sys
import torch
import pandas as pd
import numpy as np
import torch.nn.functional as F
import scanpy as sc
import anndata as ad
from .TOSICA_model import scTrans_model as create_model
#model_weight_path = "./weights20220429/model-5.pth"
#mask_path = os.getcwd()+'/mask.npy'
def todense(adata):
i... |
e4b635f422891d649dc97f031cd61e4d51542d8cc6abe928ae6a537a854006cf | Python | 6,377 | 180 | from collections.abc import Callable
from typing import Any, cast
from torch.fx import Node as FxNode
from torch.fx import Tracer
from torch.nn import Module
import elasticai.creator.function_dispatch as FD
import elasticai.creator.ir as ir
from elasticai.creator.ir2torch import DataGraph as DataGraph
from elasticai.... |
de2c89d582014a8fd1510d857b97d21b7e2d75ded85dd8bff555f708134a1cb1 | Python | 6,380 | 125 | """
This script summarizes the significant results for global efficiency, participation
coefficients, and selected links, organizing them and matching the results with
the node coordinates for H1
"""
import os
import pandas as pd
###############################################################################
# Change... |
8d3e1776c5f352491221f4d3631d5c6127faa689ec9128fd4f36c8498ebf6cdd | Python | 6,381 | 199 | # 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... |
ee4e2f2a58080713e3a0087c4c56d49b1653b6bc759254c8387defc822072644 | Python | 6,381 | 153 | # 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... |
103c5ff5571cf21431c89cd73d3d1c6f01463b04ae37759d7bc97aae9a646712 | Python | 6,382 | 226 | from numpy.fft import fftfreq
from scipy.fftpack import fft
import unittest
import numpy as np
from matplotlib import cm
import matplotlib.pyplot as plt
from soundsig.signal import bandpass_filter,lowpass_filter,highpass_filter, mt_power_spectrum, power_spectrum,match_power_spectrum
from soundsig.coherence import cr... |
3842e150488dea4522ecf7654dea056a32107f58c77f8d17072c96646f57ce65 | Python | 6,382 | 149 | from collections import namedtuple, deque
from pddlstream.language.constants import is_plan
from pddlstream.language.external import Result
from pddlstream.language.stream import StreamResult
from pddlstream.utils import INF, implies, neighbors_from_orders, topological_sort, get_connected_components
import gc
# TODO... |
99208cfeb61325bd5f354ff81941f019d02a50c976011865e0b5c3a24e91e0cd | Python | 6,382 | 125 | """
This script summarizes the significant results for global efficiency, participation
coefficients, and selected links, organizing them and matching the results with
the node coordinates for H2
"""
import os
import pandas as pd
###############################################################################
# Change... |
441c72e00ae3caa246fa1d4fe96afab2653389b64e37265bd2a0ef401087074e | Python | 6,385 | 223 | # 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... |
8a0a7409634b7fe2242724524f6fe7b5d869d7a2bbe0560729fbe54a6deb9d8b | Python | 6,385 | 139 | import sys
import os
class Deconvolutions:
def __init__(self, RNA_file = None, RNA_h5ad = None, RNA_h5Seurat = None, Spatial_file = None, Spatial_h5ad = None, Spatial_h5Seurat = None, celltype_key = None, celltype_file = None, my_python_path = None, output_path = None):
"""
@author: wen zhang
... |
aaaaf32566f0e58359ee053fdc5e1f5a28b63a9989aa6090ef212a7719dbb2b3 | Python | 6,386 | 178 | """GUI wiring for the tilt-slice launch button in the registration tab."""
import os
import sys
import time
PROJECT_ROOT = os.path.abspath(os.path.join(os.path.dirname(__file__), ".."))
if PROJECT_ROOT not in sys.path:
sys.path.insert(0, PROJECT_ROOT)
os.environ.setdefault("QT_QPA_PLATFORM", "offscreen")... |
4b3847474751d6438339397146d7c3ee48e64f797f6640a154289ef8312842ca | Python | 6,389 | 151 | """
toposampling - Topology-assisted sampling and analysis of activity data
Copyright (C) 2020 Blue Brain Project / EPFL & University of Aberdeen
This program is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as
published by the Free Software Foundation... |
b386a76040a8e39911b035c3407b492f080d639b47a95a68a4683930abc5a3fa | Python | 6,390 | 219 | """Computes the extraction efficiency of a cleaved stack using a 3D sim."""
import argparse
from typing import Tuple
import meep as mp
import matplotlib.pyplot as plt
import numpy as np
RESOLUTION_UM = 25
WAVELENGTH_UM = 1.0
CLADDING_UM = 0.5
ACTIVE_UM = 0.3
SUBSTRATE_UM = 1.0
PML_UM = 0.5
AIR_UM = 1.0
SIDE_UM = 3.... |
5b43aeeab43cf372d546850c4c06917755ac8b47cd4be9b45ad7a3b274cc7a23 | Python | 6,391 | 167 | """Launcher for the CCF boundary editor.
Builds the Qt application, embeds :class:`CCFContourViewer` in an
``AppScaffold`` window, optionally preloads volumes given on the command
line, and starts the event loop. pyqtgraph is PyQt5-native, so napari's
subprocess rule does not apply here.
Usage
-----
pyth... |
680000c2dfb8b0e9c297fc85e0a7189daf6745dd95a060b7b0ea9bb7d53a5575 | Python | 6,391 | 171 | import numpy as np
import jax.numpy as jnp
import scipy.signal.windows
from itertools import product
import jax.scipy as jsc
from jax import jit
from functools import partial
from scipy.optimize import minimize
import matplotlib.pyplot as plt
@jit
def conv(x, filter):
"""filter...
Args:
x ([type]): [... |
8b3dbee2a5ac753344eab8c8667b607930c90655760740d90b94bd13c6b396f6 | Python | 6,391 | 160 | import torch
import torch.nn as nn
import torch.nn.functional as F
class GraphConvolution(nn.Module):
def __init__(self, in_channels: int, out_channels: int, bias: bool=False):
super(GraphConvolution, self).__init__()
self.in_channels = in_channels
self.out_channels = out_channels
... |
befb0dea35c7900fb2e3875c3765582e5ae903a817b6bc402a9f15caab5b1147 | Python | 6,393 | 161 | """Aalen–Johansen estimation from aggregated multi-state transition counts."""
import numpy as np
from numpy.typing import ArrayLike
from SurvivalEVAL.nonparametric_estimator.util import _predict_step
class AalenJohansenMultiState:
"""
Estimate transition matrices for states numbered 0 through n_states - 1.... |
198ebafb4350f685e8a7a4035a2398c2013ff40ca7c8be4ca3dcc35b04d3a418 | Python | 6,394 | 189 | """Radiation pattern of a dipole antenna above a ground plane.
Tutorial reference:
https://meep.readthedocs.io/en/latest/Python_Tutorials/Near_to_Far_Field_Spectra/#antenna-above-a-perfect-electric-conductor-ground-plane
"""
import math
import matplotlib.pyplot as plt
import meep as mp
import numpy as np
RESOLUTI... |
682218d866892fcda81d632ae1bfc067151d3d82d572bed8d87895d2578c9e4b | Python | 6,394 | 119 | import numpy as np
import pandas as pd
import os
import matplotlib.pyplot as plt
plt.switch_backend('agg')
import seaborn as sns
def save_logos(motif_dict, folder='.', input_file='maggie_output_mergedSignificant.tsv'):
if not os.path.exists(folder+'/logos'):
os.mkdir(folder+'/logos')
read_df = p... |
6ae9501c82b2e5e701669228a050d35fc55d10ff63fe5801394127561541d969 | Python | 6,395 | 103 | import numpy as np
from batchgenerators.utilities.file_and_folder_operations import *
from nnunet.dataset_conversion.utils import generate_dataset_json
from nnunet.paths import nnUNet_raw_data, preprocessing_output_dir
from nnunet.utilities.file_conversions import convert_2d_image_to_nifti
if __name__ == '__main... |
3c9b98d132df29623c0fd302d54306652c6a9794bccdb46acfd477fcf49c686c | Python | 6,396 | 221 | """
version 1.0
author: Felix Plasser
description: Procedures for reading and writing files.
"""
import os
class dict_plus(dict):
"""
Extension of a dictionary where data can be read from an input file.
"""
def __init__(self, file_name='', revert=False):
if not file_name == '':
if ... |
514cac807ac4c29137cdbaba3318c36dee3e03b959f8b5c6c62cc3172442688d | Python | 6,396 | 125 | from pddlstream.algorithms.downward import make_axiom
from pddlstream.algorithms.disabled import get_free_objects
from pddlstream.algorithms.reorder import get_partial_orders, get_stream_plan_components
from pddlstream.algorithms.scheduling.utils import partition_external_plan
from pddlstream.language.optimizer import ... |
761845106406dd6a4f46150ad4b8f98ee14a57b2971499d428ef334cbd79aa3a | Python | 6,396 | 160 | import pandas as pd
import numpy as np
import seaborn as sns
from matplotlib import pyplot as plt
import matplotlib
import os
from one.api import ONE
one = ONE(silent=True)
one = ONE()
ROOT = one.cache_dir.joinpath('wittenlab/Subjects/fip_').as_posix()# Set folder where data was downloaded
def alf_loader(alfpath):
... |
daf52362ba5f7d73fd84e70cc18278af4d268c65c5893b65c89c0468aff0548c | Python | 6,398 | 133 | # regtools/ccf_boundary_editor/canvas_lock_ui.py
"""Floating annotation-lock control overlaid on the editor canvas.
Replaces the side-panel "Lock annotation" checkbox with a checkable lock button
anchored top-right of the GraphicsLayoutWidget canvas (self._glw), plus read-only
cues shown only when locked: an ambe... |
1aeeab2d9b7a5cfd04a03689c4592575fcd6f0f2334c1e6b5e47b72f3dd33e8c | Python | 6,399 | 168 | from pathlib import Path
import numpy as np
import mne_bids
import shutil
import platform
import os
import requests
from zipfile import ZipFile
import hmp
from hmp import io
from hmp import simulations
from hmp import utils
from hmp.patterndata import PatternData
from hmp.models import EventModel
DATA_DIR = Path("... |
a3262270a824cd9539e961f56c9fedf94a0780d0b6f8095228e09dec82b11500 | Python | 6,399 | 188 | # 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... |
8a324b61b806bd5d9bf8826f84557642cf4cdd1db5a68e05db1d8e4889dd2360 | Python | 6,400 | 166 | # 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... |
8a5650b788662db07fda0e82566697b0aa1b81a1e6ff7a53448f138d00c40975 | Python | 6,400 | 187 | import math
import torch
import torch.nn as nn
import torch.nn.functional as F
def initialize_weights(m):
if isinstance(m, nn.Conv1d):
n = m.kernel_size[0] * m.out_channels
m.weight.data.normal_(0, math.sqrt(2 / n))
if m.bias is not None:
nn.init.constant_(m.bias.data, 0)
... |
fa777717dd22ec6a572e37a12d51ea5411342a55b31af4143c44cb04d9f8a3a5 | Python | 6,400 | 162 | ######################## BEGIN LICENSE BLOCK ########################
# The Original Code is Mozilla Universal charset detector code.
#
# The Initial Developer of the Original Code is
# Netscape Communications Corporation.
# Portions created by the Initial Developer are Copyright (C) 2001
# the Initial Developer. All R... |
4f40e0095b8161c957cb94cb709cc824b04bf5ab57fa5ca139756058f343cb16 | Python | 6,401 | 115 | # ******************************************
#
# SHARC Program Suite
#
# Copyright (c) 2023 University of Vienna
#
# This file is part of SHARC.
#
# SHARC is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software ... |
5030ba2ce562fdbc7d94393ac243909e2d917299c086a92cc74817d4dfbd7674 | Python | 6,401 | 211 | import numpy as np
import matplotlib.pyplot as plt
# ----- #
# Variables.
savepath = "/home/sotpapad/Codes/dreyer_2023/"
savefigs = True # True, False
classification_mode = "incremental" # "incremental", "sliding"
if classification_mode == "incremental":
clm_str = "_tr"
elif classification_mode == "sliding":... |
86d6628cbe80068a5013b6b2c64324714286d4bd9e8705324d573b7e49dd81f2 | Python | 6,401 | 194 | # Node-group asset "Color Attribute Map" (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_CH... |
bfba09f05deb0b953b10fb21890ae7116a58371f66344bce93480ea0f97e87f4 | Python | 6,401 | 144 | # coding=utf-8
# Copyright 2021 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.apache.org/licenses/LICENSE-2.0
#
# Unless r... |
d2602fba4db31225042d59448a0bd9aad091d17dfdd273ae327e9cddf9c63605 | Python | 6,401 | 65 | """PREDICTION_CALIBRATION.py 2026-10-02. How good were my own predictions? Every probability written in a pre-registration from 24 Sept
(the first with numeric predictions) to 2 Oct, against what happened (04-NOTES/PREDICTIONS.csv: one row per stated outcome;
the options of one question are separate rows). Descriptive.... |
c244f14a734fd9cdd9ae0eb316fdbca2f85b390cc388ccee405f63798182fabf | Python | 6,405 | 204 | from brian2 import *
from math import exp, floor, sqrt
from matplotlib.pyplot import *
from setup import izzy, pos_3D, STDP1, reg_synapse, write_video, vectormap, wave_propagation
def Wave(seednum,batch, RATE):
seed(seednum)
vidName = str(batch) + '/' + str(batch) + str(seednum) + '.avi'
fileName1... |
475646619d2a15bd4925141fc9f9ab27269b9e58f0ff2526161bd852091a2c7b | Python | 6,409 | 165 | from __future__ import division
from __future__ import print_function
# coding: utf-8
# In[13]:
#!/usr/bin/python
from builtins import range
from past.utils import old_div
import os
import re
import glob
import sys
import argparse
from subprocess import call
def main(argv):
parser = argparse.ArgumentParse... |
38822678531da331a51a720103548801e7ff166844f1a6ced591a96dd041b370 | Python | 6,411 | 201 | import os
import shutil
import gzip
import pytest
from click.testing import CliRunner
from pandas import read_csv
from scbs.cli import cli
def scan_gzip_contents(path_gz):
contents = []
with gzip.open(path_gz, "rt") as infile:
for line in infile:
contents.append(line.strip())
return ... |
5ef6920ce027672d80ec52426f041cb6a25bb8182573b026347bf0763e3aa2f3 | Python | 6,412 | 178 | import numpy as np
import pickle as pkl
import networkx as nx
import scipy.sparse as sp
from scipy.sparse.linalg.eigen.arpack import eigsh
import sys
def parse_index_file(filename):
"""Parse index file."""
index = []
for line in open(filename):
index.append(int(line.strip())) #strip() 方法用于移除字符串头尾指... |
8ab927f915741dbb60f81cd4970ee0ea3ef0591ddd08cf5cd556ab938a6cc3d3 | Python | 6,414 | 200 | # 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... |
cd3510911bc5ce39c8880a083337712e30e74687994175b802a56c16f8f33556 | Python | 6,417 | 162 | """MNE epoch data format reading.
This module provides functions for reading MNE epoched data format (.fif only)
"""
from copy import deepcopy
from pathlib import Path
from typing import Callable, Optional
import numpy as np
from mne import read_epochs, set_log_level
from mne.channels import DigMontage
from numpy.ty... |
63d84f0945da00e5e1b34ac25cd3e65b3b4ec5a2429635694ed249052732ecb3 | Python | 6,418 | 180 | """
Curates an output STAR file from Relion to work as input for pyseg.pyorg scripts for microtubules
Input: - STAR file with the particles to curate
- STAR file to pair tomograms used for reconstruction with the one segmented used to pick the particles
Output: - A curated output STAR file
... |
67d4803cb47601011464b5f93663efead68f5d3669ea6d3a3fcfa230875349f1 | Python | 6,418 | 144 | import os
import unittest
from hed import schema
from hed.errors import ErrorContext, ErrorHandler, error_reporter
from hed.models.hed_string import HedString
from hed.validator.hed_validator import HedValidator
# todo: update these tests(TagValidator no longer exists)
class TestHedBase(unittest.TestCase):
schem... |
b798e26b8cdc609449672e14fd5a27ef3325d378499a67287e3ea80cd4e78fb6 | Python | 6,419 | 189 | import logging
from optparse import Values
from typing import Generator, Iterable, Iterator, List, NamedTuple, Optional
from pip._vendor.packaging.utils import canonicalize_name
from pip._internal.cli.base_command import Command
from pip._internal.cli.status_codes import ERROR, SUCCESS
from pip._internal.metadata imp... |
06eb3e21cffce834f482afef448f500cbaa13db2c57840e54a568aaffd2b75c4 | Python | 6,420 | 126 | """
Set of classes for dealing with a XML files for loading cellular objects (e.g. filaments)
# Author: Antonio Martinez-Sanchez (University of Goettingen Medical Center)
# Date: 1.02.20
"""
__author__ = 'Antonio Martinez-Sanchez'
import xml.etree.ElementTree as ET
import numpy as np
###############################... |
6580cc1976c8d4ebcdf4b1f26a1da806d3698d7bd28f2ffdc34ee3bb1249e180 | Python | 6,420 | 165 | # -*- coding: utf-8 -*-
"""
Updated on 08.10.2024
@author: Pablo Maceira Elvira
Logistic regression is used for binary classification. However, predictions can be interpreted as a probability, as
the sigmoid (i.e., the logistic function) is bounded between 0 and 1. Ultimately, what I want is to be able to
det... |
05586b7152ae3f451c0d822e1e9ac84074654bcb4196f965556a64ecb5a0cc4c | Python | 6,423 | 115 | # 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... |
cc7063316d53fa020178507ba3a58bfab17cad104b89c8b6debc5be90a0f1fe3 | Python | 6,425 | 140 | rest_api_version = 99
supervised_learning = False
def class_extensions():
def init_for_pipeline(self):
"""
Returns H2OSVD object which implements fit and transform method to be used in sklearn.Pipeline properly.
All parameters defined in self.__params, should be input parameters in H2OSVD.... |
7911d680330e8ac3b2f1d8d1c4c97601f181df11cde7fcea0d8dd5002e77a17b | Python | 6,428 | 141 | import math
import random
from itertools import cycle, count
import numpy as np
from control_tools.execution import ArmTrajectory
from plan_tools.common import Control, Conf, lookup_orientation, STIR_QUATS, get_urdf_from_base
from plan_tools.samplers.generators import get_pairwise_arm_links, set_gripper_position, \
... |
88c1a97a5fbf069f797d5360b8b8ff57e93f32bc602a2886e0cf2f34f6d21164 | Python | 6,428 | 128 | # 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... |
ae1032cba9d28e19162eada2db964b51bf2013482b12ed0a2f33bd977f170af7 | Python | 6,429 | 165 | """
Created on Wed May 11 02:05:35 2022
@author: Haotian Teng
"""
import os
import time
import toml
import torch
import itertools
import numpy as np
from matplotlib import pyplot as plt
from xron.nrhmm.hmm import GaussianEmissions, RHMM
from xron.nrhmm.hmm_input import Kmer2Transition, Kmer_Dataset
from torchvision im... |
4a1da6d969e362d836528db7497ae7ac5e9939d64920c1b9d07202b2b06a032d | Python | 6,430 | 181 | # pylint: disable=invalid-name, missing-function-docstring, missing-class-docstring, unused-argument, too-few-public-methods, no-member, too-many-arguments, line-too-long, too-many-instance-attributes
""" BNT model module from https://github.com/Wayfear/BrainNetworkTransformer"""
import numpy as np
from torch import... |
ac0def1cb031feee5c6079b04a0e64c61b32deafff667b4595dbe8f2377ee63a | Python | 6,430 | 174 | import torch
import torch.nn as nn
from elasticai.creator.nn.integer.addition.design import Addition as AdditionDesign
from elasticai.creator.nn.integer.design_creator_module import DesignCreatorModule
from elasticai.creator.nn.integer.math_operations import MathOperations
from elasticai.creator.nn.integer.quant_utils... |
02af5d9fbfa12e36c5600aafd25ddaf5d6b77f4ee57522e9c819ec6b4fd1ba89 | Python | 6,431 | 371 | from functools import partial
import pytest
import autograd.numpy as np
import autograd.numpy.random as npr
from autograd.test_util import check_grads
npr.seed(1)
### fwd mode not yet implemented
check_grads = partial(check_grads, modes=["rev"])
def test_fft():
def fun(x):
return np.fft.fft(x)
D ... |
0fb11f2e7ad51e6b4046c939a2ad32c0f75c554588cc1e735b01c50fc12189fc | Python | 6,431 | 141 | import os
import re
from typing import Iterator, Dict, List, Tuple, Union
import pandas as pd
from sklearn import model_selection
from torcheeg.datasets.module.base_dataset import BaseDataset
from .base_model_selection import BaseModelSelection
from .utils import create_subset, read_indices, write_indices
class KFo... |
49a7a965024986d4bcd613146da091f15db28beaddf944c2bc6580b1cc158b92 | Python | 6,431 | 161 | import os
import numpy as np
import pytest
pytest.importorskip("pyqtgraph.opengl")
os.environ.setdefault("QT_QPA_PLATFORM", "offscreen")
@pytest.fixture(scope="module")
def qapp():
from PySide6.QtWidgets import QApplication
app = QApplication.instance() or QApplication([])
yield app
de... |
8a0917c2f8975349f3f7ab0a34a271918be9b0b118a669c4b696c09759fb2637 | Python | 6,431 | 132 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Mon Oct 23 18:43:14 2023
@author: daltonm
"""
import dill
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
import seaborn as sns
import itertools
import os
from scipy.stats import binomtest, ttest_rel
marmscode = 'both'
if marmscode... |
aa91e3f55226594bbec2673dd9ceaca8dd5778ba0fd07d6ea2626fbee1732b53 | Python | 6,432 | 188 | import torch
import torch.nn as nn
import torch.nn.functional as F
from segmentation_models_pytorch.base import modules as md
class PAB(nn.Module):
def __init__(self, in_channels, out_channels, pab_channels=64):
super(PAB, self).__init__()
# Series of 1x1 conv to generate attention feature maps
... |
10e7b2255705b0293b810a4bc9a762549232d52b96a5cc1780acdf9a51ace259 | Python | 6,438 | 203 | """Module to plot all the elements in 3d space.
"""
from numpy import (linspace,
nanmax,
mean,
tile,
array,
abs,
)
from vispy.color import get_colormap, ColorArray
from vispy.geometry import MeshData
from v... |
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