sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
bfa5c6fe13277a4cbe0079994714d2458d5dc85b6b72f092114471b5b5e9c56b | Python | 2,273 | 54 | #!/usr/bin/env python
import os
import pandas as pd
## location of main project directory on HPC
proj_path = '/project/3011157.03/Simon/proj_2022_CABB_movie/'
## location of R output files to visualize
r_path = os.path.join(proj_path, 'Scripts', 'MovVar_CommsBio_Revision01', 'control_ISRSA', 'r_output_nocontrol')
## l... |
142cd5bcac1a31743252fe32e88e9e84d6555ff950cf9c668522503bcbc8cd28 | Python | 2,274 | 55 | # This file is to give neurons stimulus
from network.Network import Network
from network.Connection import Connection
from network.Cell import Cell
from network.Segment import Segment
from network.init import *
from network_assemble.data_structure import Circuit, Neuron, Connect, make_connect
from network_assemble.da... |
c379a86a36e227d6db12cf9ade216f6262fb475985a06d3742ee28407bd1cec1 | Python | 2,274 | 68 | import numpy as np
from itertools import cycle
class Lines:
def __init__(self, resolution=20, smooth=None):
self.COLORS = cycle(
[
"#377eb8",
"#e41a1c",
"#4daf4a",
"#984ea3",
"#ff7f00",
"#ffff33",
... |
1dd1cd5cbbcfe7caf9ba09652b5cd9d869f28c17f1c1190bd65bb0b3d6d2999f | Python | 2,275 | 47 | # 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... |
3d769ed747625c2d2ddbef6298dc01af792866f659134020b79f2c4d06663959 | Python | 2,275 | 67 | # processing.py (ES_Adaptive class definition)
import numpy as np
import networkx as nx
import sys
sys.path.append('../Model/tES/')
sys.path.append('./MouseBrainLib/')
# wrapper.py (Wrapper class and network creation)
import networkx as nx
from tES_Adaptive import tES_Adaptive
from DataUtils import DataUtils
class M... |
4b73c3ecffd7da0f29181c38d4d36a04edabaec081159d7d75ed90624f04fd40 | Python | 2,275 | 79 | import torch.nn as nn
from segmentation_models_pytorch.base import modules
class TransposeX2(nn.Sequential):
def __init__(self, in_channels, out_channels, use_batchnorm=True):
super().__init__()
layers = [
nn.ConvTranspose2d(in_channels, out_channels, kernel_size=4, stride=2, padding=... |
c84570b235e6affcc36e7c03f638d28cc9ac67b8fbc5a1599d713c3b13874af8 | Python | 2,275 | 73 | # 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... |
f474fe48152143e45fb5ed53cf53e95edfac536f2ed873c5e7a17bb4cd983e0a | Python | 2,275 | 64 | import os
import numpy as np
from .mask import roiSlice
from yacs.config import CfgNode
from .sitk_tile import sitkTile
from tiffile import imread, imwrite
from .transformation import computeTform, warpAll
def saveMask(cfg: CfgNode):
'''
save masked image volume in the results directory
'''
print(f'Re... |
343909c7699f3f80ca5046476bdb6f403e0cfbf338f59c7888e09c95ab062492 | Python | 2,276 | 59 | #!/bin/python
from IlluminaBeadArrayFiles import GenotypeCalls, BeadPoolManifest
from datetime import datetime
import sys, os, argparse
parser = argparse.ArgumentParser("Generate a final report from a directory of GTC files")
parser.add_argument("manifest", help="BPM manifest file")
parser.add_argument("gtc_directory... |
347dd5b80aab0c802245948f0eb0e84d381a4ade17a96a274ddb39526dfa6944 | Python | 2,276 | 63 | # 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... |
b75fa6ac6d313500b648888071bf281ae478342f8c43657ffca147803794b7cc | Python | 2,276 | 68 | # 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... |
58423719f1458c85265f7456da74d8fa8c5467bb9843445b052b6a37d6ef4b28 | Python | 2,277 | 76 | """
:author: Chinchien Lin
:summary: create neuroglancer single resolution mesh.
ref: https://neurodata.io/help/precomputed/
dependencies:
- neuroglancer==1.1.6
"""
import json
import sys
from pathlib import Path
import numpy as np
import tifffile as tiff
import neuroglancer
def crea... |
6e7f5072be518b0a7aec5028cedf253376055e678555b0472be39681acd9b011 | Python | 2,277 | 61 | # -*- coding: utf-8 -*-
def _qm9_spec(label_map):
"""Returns format dict for the QM9 dataset"""
ds_spec = {
'elems': {'dtype': 'int32', 'shape': [None]},
'coord': {'dtype': 'float', 'shape': [None, 3]}}
for k, v in label_map.items():
ds_spec[k] = {'dtype': 'float', 'shape': []... |
52db59023287614c3539523cbcf990e7290471dd1cc94ff8407fb5f06b7e8cc0 | Python | 2,278 | 67 | """
Pure-Python helpers for cellpose_sam GUI command building and model discovery.
Owns:
- Model-file discovery constants and ``_discover_custom_cellpose_models()``
- The sentinel value used by the model combo-box to trigger a file-browser
No Qt imports - everything here is testable without a QApplication.
""... |
f7385e988a68b0942a767580b6ae184313e77fa4f45aaeaa934550755723c429 | Python | 2,278 | 65 |
import pytest
import numpy as np
from cobolt.model.clustering import ClusterUtil
class TestClusterUtil:
def test_check_version(self):
obj = ClusterUtil(20, 30)
assert not obj.check_version(10, 30)
assert not obj.check_version(20, 10)
assert not obj.check_version(0, 0)
def tes... |
10ef0b6d5680db79e8b3adc37bb69f3a17fb9874349b084493ef54ebc89465d9 | Python | 2,279 | 75 | """Slab recipes for EMT."""
from __future__ import annotations
from typing import TYPE_CHECKING
from quacc import flow
from quacc.recipes.common.slabs import bulk_to_slabs_subflow
from quacc.recipes.emt.core import relax_job, static_job
from quacc.wflow_tools.customizers import customize_jobs
if TYPE_CHECKING:
... |
0020cd6b97ed983c6dc952b6d15fe4dd5f5ea84d4681092d3f8c261a292b1bb9 | Python | 2,280 | 74 | import datetime
import os
import random
import binutil
from dreamcoder.dreamcoder import commandlineArguments, ecIterator
from dreamcoder.grammar import Grammar
from dreamcoder.program import Primitive
from dreamcoder.task import Task
from dreamcoder.type import arrow, tint
from dreamcoder.utilities import numberOfCP... |
0b7e77a54e86da6b37db5e4ee61f6b40356976b3d99996bdf294b5d1a653a495 | Python | 2,280 | 79 | 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
# write down test data path
data_path = 'data/test_sequences.txt'
def p... |
828dc7f8953899f74868a78943327794c10d40ea045a19f3f4779934f7033eca | Python | 2,280 | 82 | """Verilog implementation of HDL abstractions."""
from elasticai.creator.hdl_ir import Node
from elasticai.creator.ir2verilog import (
BaseWire,
Instance,
NullWire,
TemplateDirector,
VectorWire,
Wire,
)
from .protocols import HDLInstance, HDLTemplateDirector, Template
# Verilog wire types al... |
f9307e02e710a31711279ab950c9c83ffd518de1a64d9369b5c59912cce20cf5 | Python | 2,280 | 58 | import torch
import torch.nn as nn
from torch import Generator
from typing import List
from collections import OrderedDict
from ..prixfixe import CoreBlock
from .add_blocks import ConvBlock
class BHICoreBlock(CoreBlock):
"""
The coreBlock of the BHI model.
Consists of a bidirectional LSTM layer, mult... |
47d875b9894bb723d7aee79ca115776de4bf119a44c704ff54b6627ddb3d7c41 | Python | 2,282 | 84 | # Node-group asset "VDW Radii" (GeometryNodeTree), dumped by nodebpy.assets.dump_library.
# Rebuild the library with nodebpy.assets.build_library (nodebpy build).
# _build_group() is the source of truth: the docstring, __init__ and accessors are regenerated from it on the next dump.
from typing import TYPE_CHECKING
fro... |
b6500d66cab1327c22bfdd8516dbcc6d6297de76d1a3222ca3eb544a0baf8663 | Python | 2,282 | 68 | import numpy as np
import seaborn as sns
from matplotlib import pyplot as plt
def get_palette(num_classes):
palette = {0: (0, 0, 0)}
for k, color in enumerate(sns.color_palette("hls", num_classes)):
palette[k + 1] = tuple(np.asarray(255 * np.array(color), dtype="uint8"))
return palette
# --------... |
319ab9c63deaae78f6099b0bdce63be6934c197a354055dab153f46d88501780 | Python | 2,283 | 72 | """"""
"""
Prosper_nn provides implementations for specialized time series forecasting
neural networks and related utility functions.
Copyright (C) 2022 Nico Beck, Julia Schemm, Henning Frechen, Jacob Fidorra,
Denni Schmidt, Sai Kiran Srivatsav Gollapalli
This file is part of Propser_nn.
Propser_nn is free softw... |
967d85b626ed39387d9c04ab75dc8efe21d6132eca73948d53523d0e9027f5e6 | Python | 2,283 | 77 | import numpy as np
from pyclamp.dsp.channel import *
def si16read(fn, datatype = 'h'):
f = open(fn, 'rb')
Data = np.fromfile(file=f, dtype = datatype)
f.close();
return Data
class SI16: # a fairly primitive short-data binary type reader
IntData = None
fileName = None
chinfo = None
nChan = 0 # number o... |
dece331ccf6769c7317af588c3fdf7652ca8c9e3d05c67083b94648753a94776 | Python | 2,284 | 50 | import os
import subprocess
import numpy as np
import pandas as pd
import glob
import sys
from multiprocessing import Pool
import multiprocessing
###########################
# This script will lift over your sumstats from hg19 to hg38
# 10.04.2023 (provided by Yasmina Mekki)
# https://github.com/hakyimlab/summary-gwas... |
2485dfc844ed99a339aada801df17c259f150f430278e893146c55333d549b10 | Python | 2,285 | 37 | MDATA_BIN_FILE_NAME = "mdata.bin" # name of binary metadata file
MDATA_BIN_FILE_VERSION = 2 # version of binary metadata file
MC_MDATA_BIN_FILE_NAME = "cmap.bin" # name of binary metadata file for multichannel volumes
FORMAT_MDATA_FILE_NAME = ".iim.format" # name of format metadata file
CHANNEL_PREFIX = "CH_" # pr... |
52069b290d582637c890cf5d266f14079e7cffaeacd40a9caf411cae9e43b419 | Python | 2,285 | 62 | from collections import deque
from heapq import heappop, heappush
from recordclass import recordclass
import numpy as np
from .utils import INF
Node = recordclass('Node', ['g', 'parent'])
def retrace(visited, q):
if q is None:
return []
return retrace(visited, visited[tuple(q)].parent) + [q]
def ... |
fcb886698189fd01ce594e2a03e47b921c474b45cd3e559288634ec693d7fd21 | Python | 2,285 | 69 | __author__ = "Zoe Wefers"
__credits__ = ["Ryan Huang"]
__version__ = "1.0.0"
__maintainer__ = "Zoe Wefers"
__email__ = "zoe.wefers@mail.mcgill.ca"
"""Purpose: Object definitions for various cellular compartments."""
import ui
class Dendrite:
def __init__(self, img_name):
self.img_name = img... |
52fbe82d7b2cfcfd23e7ac41872024625618e93e716de2274897a9c74367e7dc | Python | 2,287 | 44 | """Example C: one plugin, three contributions (interface, panel, experiment) sharing one id prefix."""
from liquidaion_fly.plugin_api import Parameter
from .gated_interface import GatedSteeringInterface
INTERFACE = "example_research_interface.gated"
def make_interface(context):
return GatedSteeringInterface(con... |
674430f0d4bb41e247d04f98c0fe68f77436e09e2784d4bef244ca8762091484 | Python | 2,287 | 68 | """
Small script that moves the final results of the subjects
For safekeeping and backup reasons.
"""
import click
import shutil
import os
import pandas as pd
import numpy as np
@click.command(
help="Move the results folder to create a backup on the desired folder ."
)
@click.option("--pip_csv", type=click.STRIN... |
744c4914a9342041ff29c8043bc9436dcefbdf56bd59f8eb50f10e5b90217011 | Python | 2,287 | 59 | # -*- coding: utf-8 -*-
"""This module tests that trained models and checkes that the
evaluation matches what is saved in the evaluation log.
Versioned regression test data is stored at:
https://www.dropbox.com/scl/fo/tkq0zumunvofp7dckfta5/AC_WcVOW-ihchdKTTVOHrno?rlkey=6nz86x7eflli58rlajfspzf8v&dl=0
Upon a breaking... |
9e3229d58cd01dd6d236b29e4bb13bdd2f8ae9576d95b33064c10563aeea2b41 | Python | 2,287 | 60 | # 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... |
a7347f3b26b14e43302af08a3208e75a9117997f6ecf95d7a4193a5a7f81cf75 | Python | 2,287 | 94 | from __future__ import annotations
import numpy as np
import pytest
from quacc import flow, job
from quacc.wflow_tools.job_patterns import (
kwarg_map,
map_partition,
map_partitioned_lists,
partition,
)
def test_partition():
@job
def simple_list():
return list(range(10))
@flow
... |
345e12e5e15f3c5cb6d36dee9bc0977b63e6ad525f8c85e0c253ee742399d27d | Python | 2,288 | 55 | import torch
import torch.nn as nn
from .base_converter import BaseConverter
from ..utils import _triple_same
class Conv3dConverter(BaseConverter):
"""
Decorator class for converting 2d convolution modules
to corresponding 3d version in any networks.
Args:
model (torch.nn.module): model th... |
83f5845f0b29df7a1a760d63d22fce090254736fb3520babc0b62ad659c3e843 | Python | 2,288 | 94 | # Functions used to run simulations to evaluate ideal time-step
from neuron import h
import numpy as np
h.load_file('stdrun.hoc')
h.load_file('negative_init.hoc')
#################################
# Custom simulation initializer #
#################################
def initsim(v_init=-65, cvode=1, atol=5e-5,... |
a3cc15b74db2ca294153e6c4ef415d32235e9f392543e50d30d8c842e1e19767 | Python | 2,288 | 68 | # Configuration file for the Sphinx documentation builder.
#
# This file only contains a selection of the most common options. For a full
# list see the documentation:
# https://www.sphinx-doc.org/en/master/usage/configuration.html
# -- Path setup --------------------------------------------------------------
# If ex... |
ba52565fc8d3dca8463a1e5f08ea7499ccab1831cc8cf8cc25b86a28c9d71bba | Python | 2,289 | 42 | # script to replace values of the @chrs, @StartSites, @StopSites perl variables with suzukii contig information
import os
import re
env_vars = ['Altitude', \
'Annual_mean_wind_speed', \
'Annual_Precipitation', 'Precipitation_Seasonality', \
'Mean_Diurnal_Range', 'Mean_Temperature_of_Coldest_Quarter', 'Mea... |
c5e146827c14e7336a09f6a048ead89508d4dc622ed729c3c069b5b299646330 | Python | 2,289 | 98 | #!/usr/bin/env python3
"""
Run a blocked flickering checkerboard stimulus.
"""
import argparse
import subprocess
import os.path as op
def cli_parser():
"""
Parse command line arguments to generate a call to my LOVE flickering checkerboard experiment.
"""
parser = argparse.ArgumentParser(description=__... |
d73476db7aa6dbd39107137ecf81e14c40a933a9f80089d501e3e1ed0cdcfbe2 | Python | 2,289 | 29 | """posthoc_realscan_size_2026-10-02.py (post hoc; v2LN30's value was seen first). REAL_SIGN_SCAN (29 Sept, Seki's real PNs):
flipping each inhibitory local-neuron type to excitatory lowers the fit; is v2LN30's drop larger than its output size predicts?
Output: 06-OUTPUT/posthoc_realscan_size.txt"""
import sys, os
s... |
a78c76ff8b0776cbe2e5d4bd853d870f17887aa3d299f3e257bbc7dcf2243114 | Python | 2,290 | 68 | # Configuration file for the Sphinx documentation builder.
#
# This file only contains a selection of the most common options. For a full
# list see the documentation:
# https://www.sphinx-doc.org/en/master/usage/configuration.html
# -- Path setup --------------------------------------------------------------
# If ex... |
548db6ba86de3536155334fb653327271edb92d421534bbc9f118b88600b62a3 | Python | 2,291 | 68 | # Configuration file for the Sphinx documentation builder.
#
# This file only contains a selection of the most common options. For a full
# list see the documentation:
# https://www.sphinx-doc.org/en/master/usage/configuration.html
# -- Path setup --------------------------------------------------------------
# If ex... |
8c678b55a01ad5217e8f4c4add230df8800545c4fbd949f1285f05bf7acefdd1 | Python | 2,292 | 71 | """Functions for parsing text from dataframes/text formats"""
import re
# Might need separate version again for wiki
header_attr_expression = '([^ ,]+?)="(.*?)"'
attr_re = re.compile(header_attr_expression)
def _parse_header_attributes_line(version_line):
matches = {}
unmatched = []
last_end = 0
fo... |
2ec6d0a3c64bacc78e7aa59038a3188c37b8fc516979169e89a1d2b2597449ac | Python | 2,293 | 72 | from typing import cast
from elasticai.creator.file_generation.in_memory_path import InMemoryFile, InMemoryPath
from elasticai.creator.nn.fixed_point.precomputed.silu import SiLU
def test_vhdl_code_matches_expected_silu() -> None:
expected = """library ieee;
use ieee.std_logic_1164.all;
use ieee.numeric_std.all;... |
3f2149616e1354eced1f445ac61d1b98e260e760033d3564f09134b5b801154c | Python | 2,293 | 85 | 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... |
93b9b55a2d9c258955d783b4acbfd6ad6bc454739fb43e5c1840f4c13c6045ff | Python | 2,293 | 74 | # 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... |
5843685e918ca87a8b59499a21e0744a223f60fb1f6a29fefb0004f162b28fd1 | Python | 2,294 | 59 | from elasticai.creator.file_generation.savable import Path
from elasticai.creator.file_generation.template import (
InProjectTemplate,
module_to_package,
)
from elasticai.creator.nn.integer.ram.design import Ram
from elasticai.creator.nn.sequential.design import Sequential as _SequentialDesign
from elasticai.cr... |
5908992dcabd4afdefe23a7dba9cc6e3ba5bbdcd151efbaee6a4165eef431d45 | Python | 2,294 | 71 | import elasticai.creator_plugins.lutron_filter.rules._ir as _ir
import pytest
from elasticai.creator.ir import attribute
from elasticai.creator.ir.datagraph_impl import DefaultIrFactory as Factory
from elasticai.creator.ir.serializer import IrSerializer
@pytest.fixture
def factory():
return Factory()
_serializ... |
cc989386fb7c4f1108c53319d61b552feba49bb87cded55a5998858581de980a | Python | 2,294 | 72 | from typing import cast
from elasticai.creator.file_generation.in_memory_path import InMemoryFile, InMemoryPath
from elasticai.creator.nn.fixed_point.precomputed.tanh import Tanh
def test_vhdl_code_matches_expected_tanh() -> None:
expected = """library ieee;
use ieee.std_logic_1164.all;
use ieee.numeric_std.all;... |
fcc7686db2cfc99e9b3b6601f404638de6744a086da3a3a32e0cab098238c22e | Python | 2,294 | 81 | # 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... |
705e3a512492d0ef0afeed5891c6a3d7713d0a9e207611aa605003f5f6c0955a | Python | 2,295 | 71 | #! /usr/bin/env python
# -*- coding: utf-8 -*-
import itertools
import os
from lab.environments import LocalEnvironment, MaiaEnvironment
from downward.reports.compare import ComparativeReport
import common_setup
from common_setup import IssueConfig, IssueExperiment, RelativeScatterPlotReport
DIR = os.path.dirname... |
dbc1783508451416230a15a84579932867198b448e4c5f398a8e32ae2d79d397 | Python | 2,295 | 54 | import binutil
from dreamcoder.domains.arc import arcPrimitivesIC2
import numpy as np
import pytest
grid_test_case = arcPrimitivesIC2.Grid(np.array([[0, 0, 0], [0, 1, 0], [3, 0, 3], [4, 4, 5]]))
grid_test_case2 = arcPrimitivesIC2.Grid(np.array([[0, 0, 0], [0, 1, 8], [3, 0, 3], [4, 4, 5]]))
pos_test_case = (1, 5)
size... |
0a69e36c6a671629ae164cd325bc9411467db4afcc11bee187047b6f5bc3c240 | Python | 2,296 | 87 | # Node-group asset "Is Boundary Edge" (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_CHECK... |
0c819e6a35a84b3a7e0bdbc3d5f8d8e9f4136c1846efe16a2ea06f483fe45a6d | Python | 2,296 | 57 | import csv
import numpy as np
from unittest.mock import patch
def test_registration_2d_forwards_edit_params(monkeypatch):
# registration_2d -> register_ndim: assert the two params arrive at register_ndim.
import regtools.registration.registration_2d as r2d
captured = {}
def fake_register_... |
43782369e793a1204c3453dfd90ed961a7065ede1059da11c62d2f4052aa0ca5 | Python | 2,297 | 87 | #!/usr/bin/env python3
## create personality distance matrix (correlation distance across 5 traits)
import os
import pandas as pd
import numpy as np
import seaborn as sns
import matplotlib.pyplot as plt
from sklearn.metrics import pairwise_distances
# ------------------------------------------------------------------... |
b3107646d652483a77cc76331de26df33958e9d62a958f902326d57b7c0e7fdc | Python | 2,297 | 66 | import json
import torch
import tqdm
import numpy as np
import torch.nn as nn
from pathlib import Path
from typing import Any
from ..prixfixe import Trainer, PrixFixeNet, DataProcessor, DEFAULT_METRICS
class AutosomeTrainer(Trainer):
def __init__(
self,
model: PrixFixeNet,
dataprocessor... |
0265f07b34871f42fc5337d55b049505039bcbae7dcf2fbe824fff07d215f54a | Python | 2,298 | 83 | # Node group "Override Index" (GeometryNodeTree), 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 regenerat... |
2f14516079ffbf0d7ec46b615e3fc7ba47f9473affeb2e45baef8d373709142a | Python | 2,298 | 77 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
@author: A.Akdogan
"""
import matplotlib.pyplot as plt
import numpy as np
def visualize(**images):
"""
Plot images in one row
"""
n_images = len(images)
plt.figure(figsize=(20,8))
for idx, (name, image) in enumerate(images.items()):
plt... |
4da172ad0309864f187286d93cd760cd20e6580adf5143e33e558c93ee77459b | Python | 2,298 | 56 | #! /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 = ... |
6aa98db279597c5a72713c86c2587919760a8db2da2ae089ebb81216854582f1 | Python | 2,298 | 80 | import pytest
import numpy as np
from scipy.stats import ortho_group
from sella.linalg import NumericalHessian
from test_utils import poly_factory
@pytest.mark.parametrize("dim,subdim,order,threepoint",
[(3, None, 1, False),
(3, None, 1, True),
... |
77f6b83132bf81c725e9a41844c92260bf7ecf83e19db441df10bb81ca72c501 | Python | 2,298 | 88 | from __future__ import annotations
import numpy as np
import pytest
from quacc import job
from quacc.wflow_tools.job_patterns import (
kwarg_map,
map_partition,
map_partitioned_lists,
partition,
)
def test_partition():
@job
def simple_list():
return list(range(10))
partitioned_l... |
9e80dbd21df642375f07bab07e00d0152a61044b3aea323fc41c992af4ad4538 | Python | 2,299 | 62 | """
Modified from torch.utils.data.distributed.DistributedSampler
Support enlarging the dataset for *iteration-oriented* training, for saving time when restart the
dataloader after each epoch
"""
import math
import torch
from torch.utils.data.sampler import Sampler
import torch.distributed as dist
class DistIterSampl... |
b4c88aa45893413fba028e0691d8a36fa2b07c3e226fb89da4083ae6b3356c8e | Python | 2,299 | 99 | """A script for running the correlation analysis on the marged data set."""
import matplotlib
import matplotlib.pyplot as plt
import pandas as pd
import seaborn as sns
font = {"size": 10, "weight": "bold"}
matplotlib.rc("font", **font)
import imp
plot = imp.load_source("plot", "src/plot.py")
df = pd.read_csv("data... |
e5be2ca1f700d51c9ae9a5cccc854cbbad0c80f8742e873ebe4b64e870f1770c | Python | 2,299 | 69 | #! /usr/bin/env python
# -*- coding: utf-8 -*-
import itertools
import os
from lab.environments import LocalEnvironment, MaiaEnvironment
from downward.reports import compare
import common_setup
from common_setup import IssueConfig, IssueExperiment
DIR = os.path.dirname(os.path.abspath(__file__))
BENCHMARKS_DIR = o... |
fdbe95c886d07e97fec1172f9fc2134facdbd805974446623d8e96a5d3eac174 | Python | 2,299 | 56 | import wsgiref.simple_server
from opentelemetry import metrics
from opentelemetry.exporter.otlp.proto.http.metric_exporter import OTLPMetricExporter
from opentelemetry.instrumentation.sqlalchemy import SQLAlchemyInstrumentor
from opentelemetry.instrumentation.wsgi import OpenTelemetryMiddleware
from opentelemetry.sdk.... |
6982a39a548232f7f35423e654f1aad87b1f4dbdedd448fc858137638fe024ad | Python | 2,300 | 59 | import json
import torch
from torch import optim
from constants import (
RESNET18_CONFIG,
RESNET50_CONFIG,
RESNET101_CONFIG,
RESNEXT50_CONFIG,
EFFICIENTNET_B0,
EFFICIENTNET_L2
)
__all__ = ['get_train_setup']
class TrainSetup:
def __init__(self, epochs, learning_rate, lr_decay, lr_schedul... |
69e1bf3d660a28878449447722b842435127aae104c91e4bd8521c44e724ab0d | Python | 2,300 | 88 | from __future__ import annotations
import numpy as np
import pytest
from quacc import flow, job
from quacc.wflow_tools.job_patterns import (
kwarg_map,
map_partition,
map_partitioned_lists,
partition,
)
def test_partition():
@job
def simple_list():
return list(range(10))
@flow
... |
c9d55971708333dc1c05272292677505c9ad0fe2881a793017f3ee63a70023bc | Python | 2,300 | 70 | # 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... |
d2f21b89e496c7eb24608700d6e645c01c19cdffe98ed4a842e4ba2f833d062a | Python | 2,300 | 94 | from unittest import TestCase
import numpy as np
import matplotlib.pyplot as plt
from soundsig.timefreq import power_spectrum_jn
from soundsig.spikes import simulate_poisson, plot_raster, spike_trains_to_matrix
class SpikeFFTestCase(TestCase):
def setUp(self):
pass
def tearDown(self):
pas... |
5c161f0ff8d89128cb49e44ed978fb8cb1f6a08518b30961337a80cbe40b1b75 | Python | 2,301 | 82 | #! /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... |
6608e68bbb93e03cd83bb7246541dbfa74d78c21ed2ef1b394af8bf0d2aac0b7 | Python | 2,301 | 86 | # 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... |
95a7f35ae7035e007abe8b8386ad231e594f1de128959592aad4e28c99176574 | Python | 2,301 | 61 | from typing import Union, Dict, List
import numpy as np
from ..base_transform import EEGTransform
class Downsample(EEGTransform):
r'''
Downsample the EEG signal to a specified number of data points.
.. code-block:: python
transform = Downsample(num_points=32, axis=-1)
# normalize along... |
0c61b691c119bf40db33b6acf04628b87f1225761c8a0e23d196a7dd2ac6d228 | Python | 2,302 | 46 | # 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... |
46b00fd8da9c9c4399e75894264ea6b93f82fa8c32da2b410f302e74f14f15e7 | Python | 2,302 | 89 | from __future__ import annotations
import logging
import pytest
from quacc import Remove
from quacc.utils.dicts import finalize_dict, recursive_dict_merge, remove_dict_entries
LOGGER = logging.getLogger(__name__)
LOGGER.propagate = True
def test_remove_dict_entries():
d = {
"output": {
"ou... |
ff7af86f099839c07dfd9411eb29748ca389bf6f2f8a76f63c20dd73b51a5c80 | Python | 2,302 | 83 | # Manuel A. Morales (mmoraleq@bidmc.harvard.edu)
# Beth Israel Deaconess Medical Center
# Harvard Medical School
import os
import datetime
import torch
import torch.backends.cudnn as cudnn
import torch.nn as nn
import torch.optim as optim
from Models import *
import sys
# ============================================... |
641e4e6831dafc45a30e995cb4fa9da0f387a157df700e55369a1bdd046a5284 | Python | 2,303 | 60 | # Credits: https://github.com/davda54/sam
import torch
class SAM(torch.optim.Optimizer):
def __init__(self, params, base_optimizer, rho=0.05, adaptive=False, **kwargs):
assert rho >= 0.0, f"Invalid rho, should be non-negative: {rho}"
defaults = dict(rho=rho, adaptive=adaptive, **kwargs)
s... |
51bde2667e7eb757df74bb3449bc102088c1042643609fc36f3cef67477a2f4b | Python | 2,304 | 46 | # 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... |
abf928b53663ac3a774531025261e5b1e039031122c653739e7c00681fa827fa | Python | 2,304 | 75 | """Elastic constants recipes for EMT."""
from __future__ import annotations
from typing import TYPE_CHECKING
from quacc import flow
from quacc.recipes.common.elastic import bulk_to_deformations_subflow
from quacc.recipes.emt.core import relax_job, static_job
from quacc.wflow_tools.customizers import customize_funcs
... |
294e701aeb8f1f6c4977cee3e3e0027a59cae07a0b81f55f53e8cc9c92426947 | Python | 2,305 | 72 | from typing import cast
from elasticai.creator.file_generation.in_memory_path import InMemoryFile, InMemoryPath
from elasticai.creator.nn.fixed_point.precomputed.sigmoid import Sigmoid
def test_vhdl_code_matches_expected_sigmoid() -> None:
expected = """library ieee;
use ieee.std_logic_1164.all;
use ieee.numeric... |
2ba4541822cc3d97258fc65915b98b5e1f01f4e1703402fb104f758e44795308 | Python | 2,305 | 82 | # -*- coding: utf-8 -*-
#
# Syncopy's (deep) copy function
#
# Builtin/3rd party package imports
from copy import copy as py_copy
import shutil
import h5py
import numpy as np
# Syncopy imports
from syncopy.shared.parsers import data_parser
from syncopy.shared.errors import SPYInfo
__all__ = ["copy"]
# Return a dee... |
3f50ae52bc8455f62237f632902a90eaf9d29b691fe99eb28153bdf2b9669490 | Python | 2,305 | 82 |
import os
from calvados.cfg import Config, Job, Components
import subprocess
import numpy as np
from argparse import ArgumentParser
from Bio import SeqIO
parser = ArgumentParser()
parser.add_argument('--name',nargs='?',required=True,type=str)
parser.add_argument('--replica',nargs='?',required=True,type=int)
args = pa... |
48d6a0c972722fc1f666b701895dca955db149f6bfec3118c3992eb7cd8bf8a6 | Python | 2,305 | 66 | import json
import torch
import tqdm
import numpy as np
import torch.nn as nn
from pathlib import Path
from typing import Any
from ..prixfixe import Trainer, PrixFixeNet, DataProcessor, DEFAULT_METRICS
class AutosomeTrainer(Trainer):
def __init__(
self,
model: PrixFixeNet,
dataprocessor... |
b2fd7a743efb795fbbeeb0b06bf0add8d536b0a4662f18293ea11c1f5f37dde1 | Python | 2,305 | 81 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Tue Jan 31 16:54:57 2023
@author: emma
code for fitting PCA model to full velocity fields (for inter-subject variability/subject effects)
"""
# python imports
import os
import glob
import sys
import random
import tensorflow as tf
import numpy as np
os.en... |
ef39d6b679a04662b8602e3baa43d62ca5ab131a619f9dcbd4f1f4f5adacdccf | Python | 2,305 | 161 | # 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... |
9c56ae92152acdad3c29bff5cf64208e42970a9b233cdcc03be01f3e966fbb8a | Python | 2,306 | 70 | # Renamed from types.py to avoid clash with stdlib module.
# In the future, use explicitly relative imports or absolute
# imports as a better solution.
import itertools
def _get_type_predicate_name(type_name):
# PDDL allows mixing types and predicates, but some PDDL files
# have name collisions between types... |
154ab83ed4fce0cd374b816906d77fdf1a0ed0756ea1925d3dff54f314b5b84e | Python | 2,307 | 61 | # 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... |
f3e07ab16477124059aa05ca1ca95fb8f5049621b8967cb2372edf0655e6ca89 | Python | 2,307 | 75 | # Parameters
import argparse
# Create an ArgumentParser object
parser = argparse.ArgumentParser(description='Pretrained models for pseudobulk data')
# Add parameters to the parser
parser.add_argument('--inPath', type=str, help='Folder with the input data')
parser.add_argument('--modelFile', type=str, help='Saved mode... |
407541d9253cdac7030d507c3b5b2f528c475cdc38b9018a604d770dd96b0891 | Python | 2,308 | 65 | import torch.nn as nn
class SFCNBlock(nn.Module):
def __init__(self, c_in:int, c_out:int, act_fn, grouped_maps=1):
"""
Inputs:
c_in - Number of input feature maps from the previous layers
c_red - Dictionary with keys "3x3" and "5x5" specifying the output of the dimensio... |
7db52031bd225250be327824b4c9eb855c7ba741b748a6d438135f3ffb770a70 | Python | 2,308 | 64 | # 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... |
cf49d31dce4fa4694a7fcba9117c0b45a3154a42af8c8543736890e52532f513 | Python | 2,308 | 63 | import sys, math
from pybioshell.core.data.io import Pdb
from pybioshell.std import vector_core_data_basic_Vec3
from pybioshell.core.calc.structural.transformations import *
from pybioshell.utils import LogManager
LogManager.INFO()
if len(sys.argv) < 3 :
print("""
Calculates cRMSD (coordinate Root-Mean-Square De... |
42fc91bdfc461a5af1bc97dd5ded0bdc45b32658415ebf8bc5cb68f9324833ce | Python | 2,309 | 65 | """Subject demographics of the EEG LEMON and MEG Cam-CAN datasets
"""
# Set up dependencies
import os
import numpy as np
from sys import argv
from utils import data as Data
if __name__ == "__main__":
# ------- [1] ------- #
# Settings #
# ------------------- #
print("*** STEP 1: SETTINGS ... |
73b93143b866310c59a2c230cbd0da5ed62fd746efbb4677e8ea33c40861c27f | Python | 2,309 | 66 | # ********** a running example **********
# initializa a network
# and give input to the network
# and get the output of the network
# and export the data for visualization
# commond: python run.py --config /home/zhaomengdi/Project/eworm/Celegans_as_deep_net_net/chemotaxis_net/config.json --randseed 0
from cProfile i... |
9e92b4e4000c6ccb2d117309e773e1031b26df42bf273fa4371a6c4781375e64 | Python | 2,309 | 66 | import numpy as np
import numpy.testing as npt
import pytest
from pycudadecon import affineGPU, deskewGPU, rotateGPU
def test_deskew(raw_image, deskewed_image):
"""test basic deskewing of a file acquired on a lattice light sheet"""
deskewed = deskewGPU(raw_image, dzdata=0.3, angle=31.5, pad_val=98)
npt.a... |
bc4903bf7159699a18d76e62c1ee2ce3e4d49888864e95e4016ac07507043f83 | Python | 2,309 | 61 | ### KMeans class
from sklearn.cluster import KMeans
from BEBE.models.model_superclass import BehaviorModel
from BEBE.models.preprocess import whitener_standalone, static_acc_filter, load_wavelet_transformed_data
import yaml
import numpy as np
import pickle
import os
import pandas as pd
class kmeans(BehaviorModel):
... |
c07843dd1d915f4b2cf94c98db2889d747d498f5d47a51ba0beca69545e56b48 | Python | 2,309 | 59 | # -*- coding: utf-8 -*-
# @title Software configuration file
# @file SwConfigFile.py
# @author Romain Beaubois
# @date 01 May 2023
# @copyright
# SPDX-FileCopyrightText: © 2023 Romain Beaubois <refbeaubois@yahoo.com>
# SPDX-License-Identifier: GPL-3.0-or-later
#
# @brief Script to generate... |
e6c01a17944e83b0f380a391d60069181efd570d8fa6123a61a5c41b850046e6 | Python | 2,309 | 81 | import os
from calvados.cfg import Config, Job, Components
import subprocess
import numpy as np
from argparse import ArgumentParser
from Bio import SeqIO
parser = ArgumentParser()
parser.add_argument('--name',nargs='?',required=True,type=str)
parser.add_argument('--gpu_id',nargs='?',required=True,type=int)
parser.add_... |
02521d5ae16046d7efbd95a158a3e10ae17a5f7442face85c3ab032fa42d3bf6 | Python | 2,310 | 66 | import matplotlib.pyplot as plt
from mpl_toolkits.mplot3d import Axes3D
from matplotlib import cm, axes
from scipy import optimize
import numpy as np
def fit_func(x, a, b):
return (a*x+b)
def plotter(matrix, dim, x, fit, outfile, outdir):
num=0
plt.clf()
palette = plt.get_cmap('hsv')
... |
a667ab1ac1147670dcfd2624a7a6385af06c433fb8debc773db3d3c475b4e694 | Python | 2,310 | 73 | from __future__ import print_function,division
import numpy as np
import pandas as pd
import sys
import os
def parse_args():
import argparse
parser = argparse.ArgumentParser('Script for matching predicted particles with a test particle set')
parser.add_argument('path', help='path to predictions')
pars... |
47be8ef7b1f00c611d4fe209686338e54262fb2a1bde338e44af89c48074937b | Python | 2,311 | 88 | # A module for circular statistics
import numpy as np
import scipy.stats as stats
def cang(X, maxx = np.pi): # -pi <= angle <= pi
twopi = 2.*np.pi
x = np.mod(X, twopi)
if maxx >= twopi:
return x
if type(X) is np.ndarray:
if x.ndim:
x[x>maxx] -= twopi
elif x > maxx:
x -= twop... |
7c71466b22b365a5ec7a2fb56e8375e0acc2a9e46df8c17e18219280e54b5e66 | Python | 2,311 | 73 | from importlib.util import find_spec
from typing import Literal
from urllib.error import URLError
import anndata as ad
import numpy as np
import pandas as pd
import pytest
import scipy.sparse as sp
PYDESEQ2_AVAILABLE = find_spec("pydeseq2") is not None
def _load_example_data(modality: Literal["raw_counts", "metadat... |
a397aef489709931a6680d0064347485bf161ca623e98047fa1f872a1321ac3a | Python | 2,311 | 68 | import open_pose4 as op
import os
import pickle
import PoseTools
# import tensorflow
# tensorflow.get_logger().setLevel('ERROR')
# vv = [int(v) for v in tensorflow.__version__.split('.')]
# if vv[0] == 1 and vv[1] > 12:
# tf = tensorflow.compat.v1
# elif vv[0] == 2:
# tf = tensorflow.compat.v1
# tf.disabl... |
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