sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
147757a60ada80370603a4662440fdab2756c55e8272f54e85f58519eb7ba879 | Python | 1,647 | 49 | """Batch-2D DeepSlice auto-fill: predicts each row's CCF index into the table."""
import os
os.environ.setdefault("QT_QPA_PLATFORM", "offscreen")
import pytest
pytest.importorskip("PySide6")
from unittest.mock import MagicMock
from PySide6.QtWidgets import QApplication
_app = QApplication.instance() or... |
2aebd6d0b77939c11e476471bb00ea5692c22c242a5b6a8a659b2da65a5d52a1 | Python | 1,647 | 62 | #! /usr/bin/env python
# -*- coding: utf-8 -*-
from downward import suites
from common_setup import IssueConfig, IssueExperiment
REVS = ["issue648-base", "issue648-v1"]
SUITE=suites.suite_satisficing()
SUITE.extend(suites.suite_ipc14_sat())
CONFIGS = [
# Test lazy search with randomization
IssueConfig("laz... |
5ac136caf735f0fcd6f59ff861bfd37ec7e5b7c810b172a71c14ada9cd4e0f78 | Python | 1,647 | 59 | def update_param(name, param):
if name == 'weak_learner_params':
param['type'] = 'KeyValue'
param['default_value'] = None
return param
return None # param untouched
extensions = dict(
__imports__="""
import ast
import json
from h2o.estimators.estimator_base import H2OEstimator
from... |
d305790a2b5d1c2a8f15d6758050ba8c986845e81a4bfe4dfa4f0c6b10e63837 | Python | 1,647 | 46 | #! /usr/bin/env python
# -*- coding: utf-8 -*-
import os
from lab.environments import LocalEnvironment, BaselSlurmEnvironment
import common_setup
from common_setup import IssueConfig, IssueExperiment
from relativescatter import RelativeScatterPlotReport
DIR = os.path.dirname(os.path.abspath(__file__))
BENCHMARKS_DI... |
425f62c27b7df00bbefb7075f3cbe13d9b04ad154008285405a2adb7b5cd99ce | Python | 1,648 | 54 | from elasticai.creator import graph as gr
from elasticai.creator.graph.vf2.state import State
def test_update_in_nodes():
state = State(graph=gr.BaseGraph().add_edge("a", "b"))
state.add_pair("a", "first")
state.next_depth()
in_nodes = [state.order_back[i] for i, d in enumerate(state.in_nodes) if d ==... |
8ead6eb653fc72fba301f1ea8f169f1c918009daaefb5a6f0e3bfc398d314696 | Python | 1,648 | 52 | from contextlib import suppress
from .util import subvals
def unary_to_nary(unary_operator):
@wraps(unary_operator)
def nary_operator(fun, argnum=0, *nary_op_args, **nary_op_kwargs):
assert type(argnum) in (int, tuple, list), argnum
@wrap_nary_f(fun, unary_operator, argnum)
def nary_... |
04830ac3d11ed68e3d0e942cfbeabcec5689afedc4b8af0537b273a4f62cee68 | Python | 1,650 | 51 | # 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... |
1f23f1845f318879b72771cfc3767ed5441bab283051b6cb85e18ee48fc587be | Python | 1,650 | 41 | """
Automatically create all the behavioral files
@author: trianaa1
"""
import pandas as pd
import sys, os
sys.path.append('/m/cs/scratch/networks-pm/effects_externalfactors_on_functionalconnectivity/src/analysis')
from utils import get_behav_data, get_behav_data_15days, get_behav_data_tasks, get_behav_data_movie
be... |
3db40516bb58e7036b99bf27240b51e05fb8629ea94c2270acd4a492555a5afb | Python | 1,650 | 47 | """Auto-generated registration output folder names must be ANTs-safe.
Microscope exports often name files after a comma-separated channel list
(e.g. "..._DAPI, FITC, ORNG_06_ORNG_05"); commas in the resulting output path
break ANTs point transformation (ITK mis-parses the [transform,invert] bracket
argument). _sa... |
688867eb71bf5744fd75ae9ba46c2ff9768102f14aa80329436a73d5a5d15124 | Python | 1,650 | 37 | # Create a list of all possible pairs of participants,
# and indicate if the pair is real or pseudo based on the real pair list.
import pandas as pd
from itertools import combinations, permutations
# Load the CSV file containing real pairs
real_pairs_df = pd.read_csv("/project/3011157.03/Simon/proj_2022_CABB_movie/MRI... |
f2c641b13989949a0c28ef9f50484a08267570221a66aab07d3a4c45b05a17dd | Python | 1,651 | 17 | """posthoc_dominant_in_census_2026-10-02.py — POST HOC, descriptive (2 Oct night). The dominant inputs (DOMINANT_INPUTS) of
populations inside the two censuses' circuits (receptor neurons, projection neurons, Kenyon cells): is a wrong sign harmful?"""
import pandas as pd
R = 'D:/eucys'; D = pd.read_csv(f'{R}/06-OUTPUT/... |
f401a71f56e767842af60d33f7b751d20a5c2f134df6c842c49cc250644683d2 | Python | 1,651 | 58 | # 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... |
3fef6f2c630f16a2738c19d15da23ff94348217f7685a64af81190f23b3230c4 | Python | 1,652 | 52 | # 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... |
4ea89f471efeb0ba28c819da3c2fc93ca1a989984b893e730bbb8cb62b99896b | Python | 1,652 | 51 | import os
from torch.utils import data as torch_data
from torchdrug import data, utils
from torchdrug.core import Registry as R
@R.register("datasets.BetaLactamase")
@utils.copy_args(data.ProteinDataset.load_lmdbs, ignore=("target_fields",))
class BetaLactamase(data.ProteinDataset):
"""
The activity values ... |
5d05657b13dab5a467c1fd1a95de6aac77188d90b24326667e352b4f8a19052b | Python | 1,652 | 52 | import numpy as np
import yacs.config
class Cutout:
def __init__(self, config: yacs.config.CfgNode):
aug_config = config.augmentation.cutout
self.p = aug_config.prob
self.mask_size = aug_config.mask_size
self.cutout_inside = aug_config.cut_inside
self.mask_color = aug_confi... |
69f1da372c78a6ad96d260a999cafb375d3740bc59f16973bb0b765999f8fe61 | Python | 1,652 | 56 | #!/usr/bin/env python
import sys, os, subprocess, platform, re
from glob import glob
from utils import execute
BIOSHELL_DIR = "./"
BUILD_DIR = "./build"
if sys.platform.startswith("linux"): # Ubuntu settings
CMAKE_C_COMPILER = "clang-6.0"
CMAKE_CXX_COMPILER = "clang++-6.0"
elif sys.platform == "darwin": #MacO... |
7e94f5beae3dbab2964740c140b6d716e95183af12df992c8ec6ad38446fafbd | Python | 1,652 | 48 | import numpy as np
import os
import time
import torch
from skimage import color, filters, io
from constants import DEFAULT_CANVAS_SIZE
from src.preprocessing.helpers import cutdown, resize_padded
def preprocess_image_v0(image, simulate_augment=False):
# convert to grayscale
image_preprocessed = color.rgb2gra... |
216465ef47954535b0e8a7b18fa4b4cd4e8b4995432ac590e9acb4baa7878285 | Python | 1,653 | 44 | #============================================================
#
# Artifact reduction from ECG
# Download datasets
#
# author: Ahmed Shaheen
# email: ahmed.shaheen@oulu.fi
# github id: AhmedAShaheen
#
#===========================================================
import os
import zipfile
import argparse
import numpy... |
0f8313dd36e55e1e485232ab2c1d02d930179f15061a5b0071aecc949e66095d | Python | 1,655 | 57 | #! /usr/bin/env python
# -*- coding: utf-8 -*-
from downward import suites
from lab.reports import Attribute, gm
from common_setup import IssueConfig, IssueExperiment
from relativescatter import RelativeScatterPlotReport
def main(revisions=None):
suite = suites.suite_optimal_with_ipc11()
configs = {
... |
cbaa6ae6a3adab062a6d22f5a3f3d197618e98897a6565dee3c9db25b3325400 | Python | 1,655 | 43 | """Arrange multiple single-page PDFs into a grid on one page (replaces pdfjam --nup)."""
import argparse
from pypdf import PageObject, PdfReader, PdfWriter, Transformation
def arrange_pdfs_in_grid(input_files, output_file, cols, rows):
"""Read the first page from each input PDF and tile them into a cols x rows ... |
120b721e5cd5aa0af93ab5d77cb3285d89a17533d3092f9393cf8e42df8f4c24 | Python | 1,656 | 60 | import contextlib
from importlib import import_module
from importlib.util import find_spec
from ._base import LinearModelBase, MethodBase
from ._edger import EdgeR
from ._simple_tests import PermutationTest, SimpleComparisonBase, TTest, WilcoxonTest
def __getattr__(name: str):
deps = {
"PyDESeq2": ["pyde... |
6be8dfd67a9fa10c0a80ecc6ece5cc79b45b323819d6ace29cd1434a432555b5 | Python | 1,657 | 32 | # 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... |
a3cc445a342ea6b6888a5d7dea3cba1cb3ae395e047a23e75630203f99ca23cf | Python | 1,657 | 46 | # EyeNED OCT-ONH segmentation and feature extraction
# Copyright (C) 2024 Erasmus MC
# 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, either version 3 of the License, or
# (at your optio... |
b4f9a11f52a57de5492329f5dc926bffe2794844505cdbc5b424c183b10e558c | Python | 1,657 | 43 | import os.path
import gzip
from ckg.graphdb_builder import builder_utils
#########################
# PathwayCommons #
#########################
def parser(databases_directory, download=True):
config = builder_utils.get_config(config_name="pathwayCommonsConfig.yml", data_type='databases')
url = config['p... |
b6c38dd11f765d1624b0cff7858552eebc277316e873fbb60c78a534591d0a71 | Python | 1,657 | 40 | import numpy as np
from pertpy._types import CSBase
def check_is_numeric_matrix(array: np.ndarray | CSBase) -> None:
"""Check if a matrix is numeric and only contains finite/non-NA values.
Args:
array: Dense or sparse matrix to check.
Raises:
ValueError: If the matrix is not numeric or ... |
e7f646b8833b86eddc869b8b3bf2bee5f0ac5261c29534b5712475c855f2e81f | Python | 1,657 | 55 | #! /usr/bin/env python
# -*- coding: utf-8 -*-
import os
from downward import suites
from lab.environments import LocalEnvironment, MaiaEnvironment
from common_setup import IssueConfig, IssueExperiment, is_test_run
REVS = ["issue551-base", "issue551-v4"]
BENCHMARKS = os.path.expanduser('~/downward-benchmarks')
SUI... |
bc568ccd6ed242124e5be8ef7c0d81dfe67669fe9bffa9fdd7386096acb1dadd | Python | 1,658 | 46 | from typing import cast
from elasticai.creator.arithmetic import FxpArithmetic, FxpParams
from elasticai.creator.base_modules.leaky_relu import LeakyReLU as LeakyReLUBase
from elasticai.creator.nn.design_creator_module import DesignCreatorModule
from elasticai.creator.nn.fixed_point.math_operations import MathOperatio... |
007697c2d3e4c6eed2eae376c3c9876b2eac4d24a5db09a51152c490b4f05e41 | Python | 1,659 | 49 | # 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... |
d0d72940c166ee9a0457122345f5ac3ff7aff55b264eabf2ab86e485d7c110c9 | Python | 1,659 | 49 | #! /usr/bin/env python
# -*- coding: utf-8 -*-
import os
from lab.environments import LocalEnvironment, BaselSlurmEnvironment
from downward.reports.compare import ComparativeReport
import common_setup
from common_setup import IssueConfig, IssueExperiment
from relativescatter import RelativeScatterPlotReport
DIR = ... |
f521b1401945be435f8042704ef429e11a1ae6678b8c67dffa5264d46bf4da12 | Python | 1,659 | 49 | #!/bin/env python3
"""
Example script to test ithildin.filament
"""
import ithildin as ith
import ithildin.filament as fil
import matplotlib.pyplot as plt
import sys
from itertools import chain
# filaments = fil.read_filaments("results/pdl2D_6_tipdata.txt")
# filaments = fil.read_filaments("results/ratchet_20_tipdata... |
50b0a18cf2b49b04c041415d98fd942aab2c5dccfb9817a358a2ee63046a4423 | Python | 1,661 | 44 | import pickle
# - ((CancerMedian - cutoff)/CancerSD) * ((NormalMedian - cutoff)/NormalSD)
cutoff = 0.3
for tissue in ["Bladder", "Kidney", "Prostate"]:
#tissue = "Prostate"
with open("/home/fruitdragon/workspace/NeuralClassifier/old/data/MIXED/"+tissue+"_Tree10.pkl", 'rb') as cancerFile:
patients = p... |
9195ce5e027bb0a01391f79ba67df418675cfb5e8f813a22bf55918ff3adbc8a | Python | 1,661 | 56 | # 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... |
058c8402b2ae2af096085e486da8e7535c6a9f0c9f03693f8d3c686e42236ea0 | Python | 1,662 | 44 | from torch.utils.data import DataLoader, Dataset
import torch
import numpy as np
class Dataset(Dataset):
def __init__(self, root, train=True,to_tensor=True, preprocess_data = False):
self.preprocess_data = preprocess_data
if preprocess_data:
self.Atmax, self.Atmin, self.Stmax,... |
c0e2a2e2315aacab6a028aa3540c6cfde63fba8788b2eabf65ce2595ea792518 | Python | 1,664 | 51 | # 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... |
4ac9528333b39a600c1ebd2735d6b2c1efcec44d93227ebd3b2a68ff2919f70c | Python | 1,665 | 62 | import cv2
import numpy as np
import random
import merlin.util.deconvolve as deconvolve
import merlin.util.matlab as matlab
decon_sigma = 2
decon_filter_size = 9
def decon_diff(image, gt_image):
on_gt = np.sum(image[(gt_image > 0)])
off_gt = np.sum(image[gt_image == 0])
return (on_gt/(on_gt + off_gt))... |
b3081c4ca3a6ddd68b7974d6eafe41512d938b646f1271914181ffc835e4940a | Python | 1,665 | 52 | """
This code wraps the vendored appdirs module to so the return values are
compatible for the current pip code base.
The intention is to rewrite current usages gradually, keeping the tests pass,
and eventually drop this after all usages are changed.
"""
import os
import sys
from typing import List
from pip._vendor ... |
c66ee9968bf89fc691a36ff4cd5faed4edd6c2591d94f1a591684d59e2844e51 | Python | 1,665 | 50 | from matplotlib import pyplot as plt
import pytorch_lightning as L
import sys
sys.path.append("../..")
from shapelearningtheory.datasets import make_dataset
L.seed_everything(0)
def normalize_image(img):
minimum = min(img.min(), 0.)
maximum = max(img.max(), 1.0)
return (img - minimum) / (maximum - minimum... |
e08242b52c7050446c372e8de0c80cafb02708080d8b69065c3a49ad19bb651a | Python | 1,665 | 42 | """
This script reads organizes the scores given in the post-scanner scores.
Inputs: file
Outputs: csv file
@author: trianaa1
"""
import os, glob, sys
import pandas as pd
import numpy as np
file = "/m/cs/archive/networks-pm/behavioral/questionnaires/post-scanner.xlsx"
save_file = "/m/cs/scratch/networks-pm/eff... |
5e6852e888def08632da7741b952d8a8a899ce89eb5e473e3e037518bed95ee2 | Python | 1,666 | 60 | import numpy as np
from pymdp.maths import (
softmax_obj_arr,
spm_MDP_G,
spm_log_single,
compute_accuracy,
spm_dot,
)
from pymdp.utils import to_obj_array
def free_energy(qs, prior, likelihood=None):
free_energy = 0
# Neg-entropy of posterior marginal H(q[f])
negH_qs = qs.dot(np.log(q... |
0351de12a46b080ed4aec38ec1e152b7ce7fec2c16747529dda668ebad36e150 | Python | 1,667 | 48 | import numpy as np
import pandas as pd
from anndata import AnnData
from sklearn.metrics import silhouette_score
import pertpy as pt
def _blobs(rng):
labels = np.array(["control", "target1", "target2"]).repeat(8)
centers = {"control": 0.0, "target1": 10.0, "target2": 30.0}
X = np.vstack([rng.normal(center... |
8610e0ed0b2a95d35e7ba8cf4f41270596bb72fc8a7f9caa48a4cf84aba86336 | Python | 1,667 | 53 | from __future__ import annotations
from shutil import which
import pytest
from quacc import get_settings
pytestmark = pytest.mark.skipif(
which(str(get_settings().VASP_CMD)) is None, reason="VASP not installed"
)
import numpy as np
from ase.build import bulk
from numpy.testing import assert_equal
from quacc.r... |
798de5f81353c9d9da44dad73edfebafe26132da582bd19b382b1d25a07ae62a | Python | 1,668 | 36 | # Perform Signal Space Projection
# Mainly working from tutorial https://mne.tools/stable/auto_tutorials/preprocessing/50_artifact_correction_ssp.html
# SSP uses singular value decomposition to create the projection matrix
# Apply SSP to anteriorly rereferenced data
import os
import mne
import numpy as np
import panda... |
478d886b00173d262a43f5cd423b9739ca29bc99b0d228828718313d6c01a512 | Python | 1,669 | 56 | from os.path import exists
from pathlib import Path
import torch
from elasticai.creator.arithmetic import (
FxpArithmetic,
)
from elasticai.creator.file_generation import find_project_root
from elasticai.creator.file_generation.on_disk_path import OnDiskPath
from elasticai.creator.testing import (
build_repor... |
5261894978b595c634a1b0eef0506ec7b5726bb7d0163898c3b85b0b09b45d72 | Python | 1,670 | 49 | from typing import cast
import torch
from elasticai.creator.base_modules.conv1d import MathOperations as Conv1dOps
from elasticai.creator.base_modules.linear import MathOperations as LinearOps
from elasticai.creator.base_modules.lstm_cell import MathOperations as LSTMOps
from .round_to_float import RoundToFloat
cl... |
7802115c66a65aca20d4f4c3216400cf45cbdc1c49d57893fe208a881713500d | Python | 1,670 | 69 | import numpy as np
from .basic_euclidean import eucl_dist
from .basic_spherical import great_circle_distance
######################
# Euclidean Geometry #
######################
def e_dtw(t0, t1):
"""
Usage
-----
The Dynamic-Time Warping distance between trajectory t0 and t1.
Parameters
----... |
cff74cc5acd3ea188855add590bf6e03681142a59cad2d1f5bd55d878e96643b | Python | 1,670 | 67 | import os
import pandas as pd
from calvados.cfg import Config, Job, Components
import subprocess
import numpy as np
from argparse import ArgumentParser
parser = ArgumentParser()
parser.add_argument('--name',nargs='?',required=True,type=str)
args = parser.parse_args()
cwd = os.getcwd()
sysname = f'{args.name:s}'
# se... |
d0c6cf7babda3b24b0071e31ad4bb881cbd1d45b25d8a66b2ada3e03d1c857aa | Python | 1,670 | 64 | import os
import tempfile
# see tests/conftest.py, this has to be set before bpy is first imported
os.environ.setdefault(
"BLENDER_USER_EXTENSIONS", tempfile.mkdtemp(prefix="mn-benchmark-extensions-")
)
import subprocess # noqa: E402
import sys # noqa: E402
from argparse import Namespace # noqa: E402
from path... |
e11c31b946bfbdf4fafe66794abd77d74d87f56d48b64204263135c1dbbe76bb | Python | 1,670 | 46 | from typing import Any
from torch import Tensor
from torch.nn import BatchNorm2d as TorchBatchNorm2d
from torch.nn import Module
from torch.nn.utils import parametrize as P
class BatchNorm2d(TorchBatchNorm2d):
"""A BatchNorm2d.
The output of the batchnorm is fake quantized. The weights and bias are fake quan... |
43c4765c266c847a11ac568fc0be92d64dbe399d01c6ffbb2103f8819f25354b | Python | 1,671 | 48 | import torch
from torch_geometric.data import InMemoryDataset,Data
from os.path import join, isfile
from os import listdir
import numpy as np
import os.path as osp
from imports.read_abide_stats_parall import read_data
class ABIDEDataset(InMemoryDataset):
def __init__(self, root, name, transform=None, pre_transfor... |
925b1669ee5bb36378f9723f949093b374d94e77ac16874268dec287ea442e45 | Python | 1,671 | 52 | from __future__ import annotations
from pathlib import Path
import pytest
from ase.build import bulk, molecule
from monty.json import MontyDecoder, jsanitize
from pymatgen.io.ase import AseAtomsAdaptor
from quacc.schemas.atoms import atoms_to_metadata
@pytest.fixture()
def test_cifs():
file_dir = Path(__file__... |
941083921114c0c4670768c7727fcb786529e58941033336b1de9163b4230409 | Python | 1,671 | 47 | """
Created on Wed Jan 26 12:55:10 2022
@author: Haotian Teng
"""
import os,sys,argparse
from tqdm import tqdm
import h5py
import numpy as np
from xron.utils.seq_op import fast5_iter
from pathlib import Path
def retrive_fastq(seq_h):
try:
seq = np.asarray(seq_h['BaseCalled_template']['Fastq']).tobytes().... |
9e0122632c10519af940302b91622cd9b85ad9f9015a40297e513f8d3d2dbe86 | Python | 1,671 | 48 | #! /usr/bin/env python
# -*- coding: utf-8 -*-
from downward import suites, configs
from downward.reports.compare import CompareConfigsReport
import common_setup
REVISIONS = ["issue425-base", "issue425-v1"]
exp = common_setup.IssueExperiment(
search_revisions=REVISIONS,
configs=configs.default_configs_satis... |
c3eb237d5f10fdad99407e1cd8feb815bc9f833bfacba0e765fbd0f4b6fd2c8d | Python | 1,671 | 54 | import os
from opentelemetry.context import Context
from opentelemetry.exporter.otlp.proto.http.trace_exporter import OTLPSpanExporter
from opentelemetry.sdk.resources import Resource
from opentelemetry.sdk.trace import ReadableSpan, Span, SpanLimits, TracerProvider
from opentelemetry.sdk.trace.export import (
Bat... |
62b47b6222ba93aa1b4bb8ee0f667b09d82b0f6bd672a46f7ffa47f49edcf280 | Python | 1,672 | 67 | import os
import pandas as pd
from calvados.cfg import Config, Job, Components
import subprocess
import numpy as np
from argparse import ArgumentParser
parser = ArgumentParser()
parser.add_argument('--name',nargs='?',required=True,type=str)
args = parser.parse_args()
cwd = os.getcwd()
sysname = f'{args.name:s}'
# se... |
45f2fe043df3f9c1170a234af54a63053450c1dbed51388b4010dfca3d6642cb | Python | 1,673 | 47 | #
# MIT License
#
# Copyright (c) 2022 GT4SD team
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge,... |
067c5179107af0fcd709fee5a166d5ade5e239fa42b15c6d78e283dfe4e404e4 | Python | 1,674 | 73 | import argparse
from pathlib import Path
def add_run_mito_arguments(parser: argparse.ArgumentParser) -> None:
parser.add_argument(
"--mesh-file",
type=Path,
default=Path("mito_mesh.h5")
)
parser.add_argument(
"--curv-file",
type=Path,
default=Path("mito_curv.... |
71f990f579105a14f18aec398dfe10f1440795e31cd672634134c9ed1cffeca5 | Python | 1,674 | 52 | #! /usr/bin/env python
# -*- coding: utf-8 -*-
import os
import suites
from lab.reports import Attribute, gm
from common_setup import IssueConfig, IssueExperiment
try:
from relativescatter import RelativeScatterPlotReport
matplotlib = True
except ImportError:
print 'matplotlib not available, scatter plots... |
83ad183cd88e6c308ec4ccb51f5e752c682f8e53a10a8fc0335b2bc7ffda2f72 | Python | 1,674 | 63 | # Node group ".MN_mask_transparent" (ShaderNodeTree), dumped by nodebpy.assets.dump_library.
# Rebuild the library with nodebpy.assets.build_library (nodebpy build).
# Shared by several assets, which import it; not an asset itself.
# _build_group() is the source of truth: the docstring, __init__ and accessors are regen... |
47c4b88922a4da879aa933afd498028eee665a851fc88ddcc2f870826a49f1a7 | Python | 1,675 | 65 | import autograd.numpy as np
import autograd.numpy.random as npr
from autograd import grad
from autograd import isinstance as ag_isinstance
from autograd import tuple as ag_tuple
from autograd.test_util import check_grads
npr.seed(1)
def test_getter():
def fun(input_tuple):
A = np.sum(input_tuple[0])
... |
d851fd272969ba447f1f4c4f2e057ea6a5561d2cf17c3325e7e88a711657febf | Python | 1,675 | 71 | import matplotlib.pyplot as plt
import numpy as np
import meep as mp
# set up the geometry
eps = 13
w = 1.2
r = 0.36
d = 1.4
N = 3
sy = 6
pad = 2
dpml = 1
sx = (2 * (pad + dpml + N)) + d - 1
fcen = 0.25
df = 0.2
nfreq = 500
cell = mp.Vector3(sx, sy, 0)
blk = mp.Block(size=mp.Vector3(mp.inf, w, mp.inf), material=mp.... |
f2bd6bb56e94a8dccb8c2120b85cfb48c4b4c06912b1ddbd80a7442d43489755 | Python | 1,675 | 54 | #! /usr/bin/env python
# -*- coding: utf-8 -*-
import os
from lab.environments import LocalEnvironment, BaselSlurmEnvironment
import common_setup
from common_setup import IssueConfig, IssueExperiment
from relativescatter import RelativeScatterPlotReport
DIR = os.path.dirname(os.path.abspath(__file__))
BENCHMARKS_D... |
45336220cba617bdf17e7c18bf897041777e35a30909fc3da7344a844a665e3a | Python | 1,676 | 48 | from __future__ import (absolute_import, division,
print_function, unicode_literals)
import json
import os
import argparse
parser = argparse.ArgumentParser(description="Setup all parameters for slice time correction file generation for FSL")
parser.add_argument("jsonfile",help="location of json... |
75fe98a2c8395f9b8f1989543d07d7b93c57e38c3d8f619e8d54c15559c32030 | Python | 1,676 | 52 | #! /usr/bin/env python
# -*- coding: utf-8 -*-
import os
import suites
from lab.reports import Attribute, gm
from common_setup import IssueConfig, IssueExperiment
try:
from relativescatter import RelativeScatterPlotReport
matplotlib = True
except ImportError:
print 'matplotlib not available, scatter plots... |
39e1f50fc1d05daf395d41e43d8d5c8585bfec07d3c53ff859c5aa6e730eebca | Python | 1,678 | 54 | # 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... |
4176fc0357af9b3381a929e8592cc06e72d385d184034a14ad0360afa4e57560 | Python | 1,678 | 53 | def update_param(name, param):
if name == 'weak_learner_params':
param['default_value'] = None
return param
return None # param untouched
extensions = dict(
skip_default_set_params_for=['training_frame', 'ignored_columns', 'response_column',
'max_confusion... |
68058dec8688d4293cbc5827b440e8874a8d930547ae0bd81e61384b67443503 | Python | 1,678 | 17 | """Post hoc (6 Oct, after FLYVIS_CENSUS F2 PARTLY): the pre-registered predictor pooled input over all 8 T4/T5 types, which
dilutes inputs that reach only T4 (Mi4, Mi9) or only T5. Here: a source type's largest share onto any single T4/T5 type."""
import json, os, numpy as np, pandas as pd
from scipy.stats import rankd... |
cf840e022cdbd2ac64eeb3783fbfdaa430915b3c7f51a7485a2eed3d938b605f | Python | 1,678 | 43 | """
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... |
e1a124d082ee08a693c05bbf33e8dd5ddcf8063e21204c7de35007f4e0d60340 | Python | 1,678 | 56 | #! /usr/bin/env python
# -*- coding: utf-8 -*-
import os
from lab.environments import LocalEnvironment, BaselSlurmEnvironment
import common_setup
from common_setup import IssueConfig, IssueExperiment
DIR = os.path.dirname(os.path.abspath(__file__))
BENCHMARKS_DIR = os.environ["DOWNWARD_BENCHMARKS"]
REVISIONS = ["i... |
37f00a260d1d8bc581bb525e1f886fed1c049c6f63c524de9faa7b076fa2713f | Python | 1,679 | 82 | """This file doesn't import the numpy wrapper, to check if core works
on basic operations even without numpy."""
import warnings
from autograd.core import make_vjp
from autograd.wrap_util import unary_to_nary
@unary_to_nary
def grad(fun, x):
vjp, _ = make_vjp(fun, x)
return vjp(1.0)
# Non-numpy gradient c... |
807b36e2b54b2ff6ff2c5940fa6c2e7033f0f12cb58881c3f2824290bea8101b | Python | 1,679 | 52 | #! /usr/bin/env python
# -*- coding: utf-8 -*-
import os
import suites
from lab.reports import Attribute, gm
from common_setup import IssueConfig, IssueExperiment
try:
from relativescatter import RelativeScatterPlotReport
matplotlib = True
except ImportError:
print 'matplotlib not available, scatter plots... |
98995d76ccc6aa07b59f600b2ef27553bb08dd60579e913dc47e06fa139b89ae | Python | 1,679 | 52 | #! /usr/bin/env python
# -*- coding: utf-8 -*-
import os
import suites
from lab.reports import Attribute, gm
from common_setup import IssueConfig, IssueExperiment
try:
from relativescatter import RelativeScatterPlotReport
matplotlib = True
except ImportError:
print 'matplotlib not available, scatter plots... |
d2808c7b820f5fc5fa4f8204a8937a298b016ad566d4b4f9397dee4a6323bc02 | Python | 1,679 | 52 | #! /usr/bin/env python
# -*- coding: utf-8 -*-
import os
import suites
from lab.reports import Attribute, gm
from common_setup import IssueConfig, IssueExperiment
try:
from relativescatter import RelativeScatterPlotReport
matplotlib = True
except ImportError:
print 'matplotlib not available, scatter plots... |
74425e295ea7f6a30e8e856f2a6b65f972c84e6f23c378eeb54f629269403482 | Python | 1,680 | 54 | # 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... |
c77fba02fa3a54a2978d2802861088a791e2a5e1eee016aed0f99cbdb7c57cfe | Python | 1,680 | 61 | # ******************************************
#
# 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 ... |
fed1def235f2c66cf4a9f67eb7b294ac4bdbb6e8fc4febb2c1ecc0d14d04591f | Python | 1,680 | 54 | """Download Dreem datasets. Modified from
https://github.com/Dreem-Organization/dreem-learning-open/blob/master/download_data.py
"""
import argparse
import boto3
import tqdm
from botocore import UNSIGNED
from botocore.client import Config
from pathlib import Path
def download_data(dst_dir: Path):
client = boto3.... |
998403db95d480777d089d1fbc32ddeb39425a45cf976f65d74c8532505df137 | Python | 1,681 | 65 | # -*- coding: utf-8 -*-
#
# Simple script for testing Syncopy w/o pip-installing it
#
# Builtin/3rd party package imports
import numpy as np
import os
import sys
# Import package
import syncopy as spy
# Import artificial data generators
from syncopy import synthdata
# Prepare code to be executed using, e.g., iPytho... |
b59088e04e02be4885bc0ea51e000803bee47d2b857044f14819925ad9986833 | Python | 1,681 | 59 | import tensorflow as tf
import tensorflow_addons as tfa
import os
import numpy as np
import matplotlib.pyplot as plt
from skimage.morphology import area_closing
# from tensorflow.kera
import utils
# Specify entire folder, not saved_model.pb
loaded = tf.keras.models.load_model(r'C:\Users\leroy.volmer\PycharmProjects\Bo... |
ead8a25243c6bffc8e977f04660a5233eebe917be4ec5028d5cad87091660eea | Python | 1,681 | 46 | from elasticai.creator.arithmetic import FxpArithmetic, FxpParams
from elasticai.creator.base_modules.leaky_relu2 import LeakyReLU2 as LeakyReLU2Base
from elasticai.creator.nn.design_creator_module import DesignCreatorModule
from elasticai.creator.nn.fixed_point.math_operations import MathOperations
from .design impor... |
4b934221249c3de22b2b021e5d1c1d265de457d4389ea65f9cd3c3c7a1dffff8 | Python | 1,682 | 51 | # Copyright 2016 Julien Danjou
# Copyright 2016 Joshua Harlow
# Copyright 2013-2014 Ray Holder
#
# 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
#... |
9889a30debf1b5c64880506bb310d53d07f7d831abb31da4fa4a2d640e06bd41 | Python | 1,682 | 48 | #! /usr/bin/env python
# -*- coding: utf-8 -*-
import os
from lab.environments import LocalEnvironment, BaselSlurmEnvironment
import common_setup
from common_setup import IssueConfig, IssueExperiment
from relativescatter import RelativeScatterPlotReport
DIR = os.path.dirname(os.path.abspath(__file__))
BENCHMARKS_DI... |
a96c9778485d4e9a7e5dbec1fcdfd0fb78008c4e93275e409dc48f82467b8f83 | Python | 1,682 | 64 | import random
import unittest
import torch
import torch.nn as nn
from torch.utils.data import Dataset
from torch.utils.data.dataloader import DataLoader
from torcheeg.trainers import SimCLRTrainer, BYOLTrainer
class DummyDataset(Dataset):
def __init__(self, length: int = 101):
self.length = length
... |
20c43b3d7aaf8fd324a9aeaae604fa0bd370824ed825d1eb7197a4eff8640a47 | Python | 1,683 | 59 | #! /usr/bin/env python
# -*- coding: utf-8 -*-
from downward import suites
from downward.experiment import FastDownwardExperiment
from downward.reports.compare import CompareConfigsReport
from relativescatter import RelativeScatterPlotReport
import common_setup
REPO = common_setup.get_repo_base()
REV_BASE = 'issue58... |
4f3102899a0228d32a83053be9c3c278a58506a696bc074b31ebf9fdb0a4858f | Python | 1,683 | 85 | """
All of the Enums that are used throughout the chardet package.
:author: Dan Blanchard (dan.blanchard@gmail.com)
"""
from enum import Enum, Flag
class InputState:
"""
This enum represents the different states a universal detector can be in.
"""
PURE_ASCII = 0
ESC_ASCII = 1
HIGH_BYTE = 2
... |
7f36cdedfe9fd763346ff2244b6eb09c9af2adca17ec362ed92b4f9d76277e47 | Python | 1,683 | 43 | import torch
from torch import nn
from torch.nn import functional as F
from wsilearn.dl.models.model_utils import create_bn_act_drop_conv, create_conv_bn_act, create_conv, create_activation
#https://d2l.ai/chapter_convolutional-modern/resnet.html
class ResBlock(nn.Module):
def __init__(self, in_channels, out_chan... |
c9990002e087186be9101a87b2862ee4750234c06dc9e822ce099f104adfc357 | Python | 1,684 | 42 | #------------------------------------------------------------------------------------------------------------------
# Author: Brandon S Coventry Purdue University/Wisconsin Institute for Translational Neuroengineering
# Date: 05/21/24 Nice Cloudy Day today
# Purpose: Setup file for SpikerNet
#------... |
f8689d3123afa6711643dae280d67dae7b0e67424debb5613a42d7b9c04f2298 | Python | 1,684 | 70 | from focal_aug import get_unet
import glob
from cv2 import imread
from PIL import Image
from skimage.transform import resize
import numpy as np
from matplotlib import pyplot as plt
from skimage.morphology import label
from pycocotools import mask as maskUtils
from tqdm import tqdm
import os
import cv2
from keras.layers... |
5110eefc86fb0a499bdb283feb9fe5e21e32745d02e007116a2206f9289b1924 | Python | 1,686 | 49 | # SPDX-FileCopyrightText: 2024 Blue Brain Project / EPFL
#
# SPDX-License-Identifier: AGPL-3.0-or-later
'''
Compute correlations of (sub)population
Last updated: 12.2023
'''
import conntility
from scipy.spatial import distance
import numpy as np
import json
import sys
sys.path.append('../../../library')
from preproce... |
6a003f454dd1fc7c54bc3d3fc7917b0dcce44f2d82c0a9da951f6144826d894e | Python | 1,686 | 56 | r"""Test OpenBabel executables from Python
Note: Python bindings not used
On Windows or Linux, you can run these tests at the commandline
in the build folder with:
"C:\Program Files\CMake 2.6\bin\ctest.exe" -C CTestTestfile.cmake
-R pytest -VV
You could also "chdir" into bu... |
6eae3c8b176d851b291a6eecdb8ebf0416f033b311f99b97e27b6f96a5fd47b7 | Python | 1,686 | 37 | from setuptools import setup
import versioneer
LONG_DESCRIPTION = """Converts nifti files (raw and mask) and mrtrix tck files to DICOM format
readable by Brainlab surgical planning and navigation systems.
Tck files are converted to 3D objects that can be manipulated by Brainlab tools.
Label images are converted to a d... |
b5f0175c8383facf77f461d95c82a23c0001fd29aa2b37c3c2936ebc8252f22e | Python | 1,686 | 53 | # import logging
# import warnings
# import datetime
# import numpy as np
# # --------------------------------------------
# # report software running logging
# # --------------------------------------------
#
# # --------------------------------------------
# # MAIN FUNCTION
# # --------------------------------------... |
c5b76956c19934f4ead2329df960332ede4554c4851d080c820eef663ca57d9b | Python | 1,686 | 44 | import os
import numpy as np
import argparse
from cmdstanpy import CmdStanModel
from datetime import datetime
parser = argparse.ArgumentParser(description="index for the mouse id")
parser.add_argument('mouse_idx', type=str, help='index for the mouse id, starting from 0')
args = parser.parse_args()
mouse_idx = int(args... |
e819c09a4d9740b3c0b1fcdb9b6dc92366bf269ee7cbe18d35245805a0001ebc | Python | 1,686 | 50 | from setuptools import setup, find_packages
import re
VERSIONFILE = "cocoa/__version__.py"
verstrline = open(VERSIONFILE, "rt").read()
VSRE = r"^__version__ = ['\"]([^'\"]*)['\"]"
mo = re.search(VSRE, verstrline, re.M)
if mo:
verstr = mo.group(1)
else:
raise RuntimeError("Unable to find version string in %s." ... |
5b75d889d862a98d59256ecf47d07497ddfcbf1a5622c9a281988b731834c362 | Python | 1,687 | 60 | import scanpy as sc
import numpy as np
import pandas as pd
import scvi
from scvi.model import CondSCVI, DestVI
import sys
import os
scrna_path = sys.argv[1]
spatial_path = sys.argv[2]
celltype_key = sys.argv[3]
output_path = sys.argv[4]
sc_adata = sc.read_h5ad(scrna_path)
st_adata = sc.read_h5ad(spatial_path)
# f... |
b5585f94d9b627ec25e295f954c9b2cf7d17f8062ac5fcee21002cb75477a6e0 | Python | 1,687 | 49 | """
Optuna example that runs optimization trials in parallel using Dask.
In this example, we perform hyperparameter optimization on a
RandomForestClassifier which is trained using the handwritten digits
dataset. Trials are run in parallel on a Dask cluster using Optuna's
DaskStorage integration.
To run this example:
... |
f5e551add83428bae30f4790d48ee2f5d0c4c6be4bc3b6172214a4d7c1a982d2 | Python | 1,687 | 46 | #!/usr/bin/env python
from IlluminaBeadArrayFiles import GenotypeCalls, BeadPoolManifest, code2genotype
import sys
import os
import glob
import argparse
parser = argparse.ArgumentParser("Generate a final report from a directory of GTC files")
parser.add_argument("manifest", help="BPM manifest file")
parser.add_argume... |
5022cc1c4779cd7fd7bdce2b9bb2d20791a1cd85eb72ac11853b9b40313c84fa | Python | 1,688 | 54 | """Preprocess empatica data. Reads all empatica data splitted in days,
aggregates them by day, and saves them in the given savepath.
The input should be done in the following order:
Parameters
----------
path : str
path where the raw data is stored
savefile : str
"""
... |
eeebb896bd0145a6957babb3976fddff01f9b6d26bf0ce82f00bd4d8166d6940 | Python | 1,688 | 56 | ######################################################################
#
# wgtRotorSrch.py: weighted rotor search (conformer search)
#
######################################################################
from __future__ import print_function
from openbabel import openbabel
import sys
# Make sure we have a filename
... |
dfaca3f7445e3ef2551e145c982a102fc56f016b650593b0f6d49e0d13f171b9 | Python | 1,689 | 22 | """posthoc_uncalled_share_2026-10-08.py (POST HOC, descriptive). Where do the neurons that FlyWire leaves uncalled sit:
in the circuits the laboratory checked (the 106 SEZ types of the optogenetic screen, the named taste neurons) or in the
antennal lobe's local neurons? Output: 06-OUTPUT/posthoc_uncalled_share.txt"""
i... |
4f5e32dd8d27fcf87bc5d7a58da0bcfea8527acca0e8ce6a04e4850d9af4ee32 | Python | 1,690 | 57 | """Python port of geometry-processing-mouse-brain.
Original MATLAB implementation by Agarwal et al.,
"Geometry Processing of Conventionally Produced Mouse Brain Slice Images"
(Journal of Neuroscience Methods, 2018).
"""
from .atlas import atlas_segmentation
from .edges import (
canny_edge_magnitude,
... |
b1f3056c51aad2c5d19d2a8b2cc0c2852dd021bdef0b0a9948d50688526b1f99 | Python | 1,690 | 69 | import numpy as np
import scipy.io as sio
import torch
import torchvision
from torch.autograd import Variable
import torch.nn as nn
import torch.nn.functional as F
import torch.optim as optim
from models import UNetSAR
import pickle
import os
import matplotlib.pyplot as plt
import json
# config = {
# "batch_size... |
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