sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
90846a3be3ec95ec40630a65812c38db3d4a60ebeb9f74e2e415e68c4d6e253c | Python | 29,862 | 763 | """
NoClaMe
-------
This script implements a series of metrics for node-classification.
These metrics are for binary node-classification, intended to work
for node-classification on molecular graphs, which usually involves
a large number of relatively small graphs (<50 vertices).
Implemented node-classification me... |
078caf02753590c8ecf161bed0b05a38f6bbcd508f481eb4970c108dd0a291ad | Python | 29,904 | 699 | import os
import numpy as np
import pandas as pd
import matplotlib
import matplotlib.pyplot as plt
import anndata as ad
import scanpy as sc
from scipy.io import mmwrite, mmread
import seaborn as sns
import scipy
np.random.seed(42)
# load anndata
dir_path = "/home/nomura/Proj/mmvelo/experiments/SHARE-seq_hf/2023-08-0... |
0586ec75e5e5c67e6ddbd86c292df4a6348716eeafb7c4520859ad0acb3a0314 | Python | 29,955 | 589 | '''
Created on Nov 7, 2024
@author: voodoocode
'''
import numpy as np
import scipy.signal
import lmfit
import matplotlib
matplotlib.use("Qtagg")
import matplotlib.pyplot as plt
import pandas
import skimage
import csv
import finnpy.file_io.data_manager as dm
import finnpy.feat.cfc as cfc
import finnpy.filters.frequen... |
84d7d8ca1a91692de44361dff74c34805dd92b6f0272a16be5913aa2d986507f | Python | 30,042 | 744 | # Copyright (c) Facebook, Inc. and its affiliates.
# pyre-unsafe
import itertools
import logging
import numpy as np
from collections import UserDict, defaultdict
from dataclasses import dataclass
from typing import Any, Callable, Collection, Dict, Iterable, List, Optional, Sequence, Tuple
import torch
from torch.util... |
3f0dc374811b83ab81c4d5bf0b8d7d6afb86c683a8a67aa9d46ea5a39cacd7f5 | Python | 30,045 | 656 | # Copyright (c) Facebook, Inc. and its affiliates.
from .config import CfgNode as CN
# NOTE: given the new config system
# (https://detectron2.readthedocs.io/en/latest/tutorials/lazyconfigs.html),
# we will stop adding new functionalities to default CfgNode.
# ---------------------------------------------------------... |
a0b507683d2bcf55dd040faa61d4e54facb8bbedb8af486f16af93891351a20f | Python | 30,075 | 845 | # This code is part of OpenFE and is licensed under the MIT license.
# For details, see https://github.com/OpenFreeEnergy/openfe
import itertools
import json
import sys
from math import sqrt
from unittest import mock
import gufe
import mdtraj as mdt
import numpy as np
import pytest
from numpy.testing import assert_all... |
3f2a894d03743d1de032f5163ed93737b1713b50acd0edfc3a1209d6dc6f6371 | Python | 30,132 | 681 |
############################################################################
# Copyright (c) 2022-2026 University of Helsinki
# All Rights Reserved
# See file LICENSE for details.
############################################################################
import csv
import os
import pickle
import gzip
import shutil
... |
bf7662be2374a0431d32af320923af523d5a1650c32044cd7cdbe831729dfd78 | Python | 30,223 | 774 | # This script is part of navis (http://www.github.com/navis-org/navis).
# Copyright (C) 2018 Philipp Schlegel
#
# This program 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 Foundation, either version 3 of... |
88312d23b846f21047f735af3774c740b91603d36089484825ff170e7b79d56b | Python | 30,254 | 738 |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
TST fiberphotometry vs EthoVision Activity (Supplementary Fig. 4b-g)
"""
import os
import re
import json
import glob
import math
import warnings
from collections import defaultdict
import numpy as np
import pandas as pd
from scipy.stats import pearsonr, spearmanr, ... |
8af65718dc553069883c0b9bfec3f5aecf690745c102df37427b12e59607d791 | Python | 30,276 | 623 | import os
import numpy as np
from time import perf_counter
import pyqtgraph as pg
from pyqtgraph.Qt import QtWidgets
from pyqtgraph.Qt import QtCore
from pyqtgraph.console import ConsoleWidget
from pyqtgraph.dockarea.Dock import Dock
from pyqtgraph.dockarea.DockArea import DockArea
from PyQt5.QtWidgets import *
from Py... |
4de9e61cb23ea854d7809fded7c214f3088f7539f95d0114560964313ee8df97 | Python | 30,281 | 745 | #!/usr/bin/env python
from __future__ import division
import pandas as pd
import numpy as np
import os
import sys
import traceback
import gzip
import bz2
import argparse
from scipy.stats import chi2
from ldscore import sumstats
from ldsc import MASTHEAD, Logger, sec_to_str
import time
np.seterr(invalid='ignore')
try:
... |
6c3b61fb0d5e9e4a8cd3986e587cbedc4514de45ea087c66919f7e12b0465adb | Python | 30,315 | 770 | """
Core Image Processor for Structural Plasticity Analysis
Implements the quantification algorithm described in Petsakou et al., 2015:
"Circadian rhythms in Rho1 activity regulate neuronal plasticity and network hierarchy"
This module provides tools to analyze 3D microscopy images of neuronal projections,
qua... |
9bcb853e182774dd6dfac1bb73cb46aeabd7814e46b54ade2caadd7f1f4eba12 | Python | 30,327 | 837 | import os
import re
import sys
from sklearn.model_selection import StratifiedKFold
import torch
import random
import numpy as np
import torch.nn as nn
import torch.optim as optim
from matplotlib import pyplot
from torch.utils.data import Dataset, DataLoader
from sklearn.metrics import accuracy_score,precision_score,rec... |
a935efff1e0d55aae88b6abd8e0d7ccdc794840639da562466dcda5c20e9059a | Python | 30,380 | 846 | # This script is part of navis (http://www.github.com/navis-org/navis).
# Copyright (C) 2018 Philipp Schlegel
#
# This program 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 Foundation, either version 3 of... |
b8fbf8cf82986b7b45e31aafbdae7dcabb3cafa934844a132d9fc3f21fdb2b3d | Python | 30,391 | 722 | # Copyright (c) Facebook, Inc. and its affiliates.
import contextlib
import copy
import io
import itertools
import json
import logging
import numpy as np
import os
import pickle
from collections import OrderedDict
import pycocotools.mask as mask_util
import torch
from pycocotools.coco import COCO
from pycocotools.cocoe... |
e4e09bfb23adebcd206cedc1902b428468256133d3d9eef99d805c0daac57daf | Python | 30,433 | 800 | # -*- coding: utf-8 -*-
"""neu_efficient_binary
Automatically generated by Colab.
Original file is located at
https://colab.research.google.com/drive/1SNwdn9MD7Ycldrwo-InD2-RFmpCLBMKT
Transfer-learning EfficientNetV2B0 pipeline for binary frost vs non-frost
classification, with cross-validation, error analysis, ... |
d2fdcf857d0da626406095e9d8aaf3cb7974328e7c98131ceda0aff45cc68235 | Python | 30,497 | 724 | import torch
import torch.nn as nn
import torch.optim as optim
from torch_geometric.loader import DataLoader
from torch_geometric.nn import DataParallel
import os
os.environ["PYTORCH_CUDA_ALLOC_CONF"] = "max_split_size_mb:1024"
import sys
import time
from tqdm import tqdm
import random
import numpy as np
import pand... |
8a1c44cb5d8ed3c04c105d2351728427b45a6d144213548df808fbcba1b39596 | Python | 30,577 | 807 | """Tests for snakemake template formatting utilities."""
from __future__ import annotations
import string
import hypothesis.strategies as st
import more_itertools as itx
import pytest
from hypothesis import assume, example, given
import tests.strategies as sb_st
from snakebids import bids
from snakebids.paths impor... |
87791365f91cdf4a5887548429f1e10977507eec5ec2417c5e5ccff982fe0544 | Python | 30,589 | 777 | # AUTOGENERATED! DO NOT EDIT! File to edit: 02_parsers.ipynb (unless otherwise specified).
__all__ = ['CoverageBigWig', 'BedReader', 'GroupedParser', 'FastaReader', 'SpliceSiteParser']
# Cell
import numpy
import scipy
from matplotlib import pyplot
import seaborn
import pandas as pd
import pyfastx
import pyfaidx
from ... |
67752f51d9701b75469e4e53dce22e96413b82f6469e2c404b585e3c6e717219 | Python | 30,600 | 632 | ############################################################################
# Copyright (c) 2023-2026 University of Helsinki
# # All Rights Reserved
# See file LICENSE for details.
############################################################################
"""
10x Genomics barcode detectors.
Supports 10x Genomics v... |
732713f612257ab5ce0e54c23ca6ef85a001ba835c2d199b7b4927047e089da6 | Python | 30,688 | 805 | # This script is part of navis (http://www.github.com/navis-org/navis).
# Copyright (C) 2018 Philipp Schlegel
#
# This program 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 Foundation, either version 3 of... |
9fbe5b5f593938053d8834a40501b28e38182eba92679081156d11a40b1f516a | Python | 30,721 | 502 | """Stage 1: run the CNN + WideVariant filters and select candidate SNV positions.
This is the only stage that runs the CNN (via ``cnn_pred.CNN_predict``). It writes
``_snv_state.npz`` (the hand-off the later stages read), the raw CNN scores
``snv_table_cnn_raw.tsv``, and ``snv_table_filtered_tmp.tsv``, which stage 2 f... |
db62a866856abd47f29099d638093e6d84b0164beb39c7b1b20161e311d8a163 | Python | 30,790 | 660 | #!/usr/bin/env python
'''
(c) 2014 Brendan Bulik-Sullivan and Hilary Finucane
LDSC is a command line tool for estimating
1. LD Score
2. heritability / partitioned heritability
3. genetic covariance / correlation
'''
from __future__ import division
import ldscore.ldscore as ld
import ldscore.parse as ps
im... |
5a84daee2abb1d96bce59670894eeff7d8e9a8f1b7b0e58bd9ee9c7b83abe6b7 | Python | 30,850 | 773 | #!/usr/bin/env python
#
# Copyright (c) 2019 10X Genomics, Inc. All rights reserved.
#
from __future__ import annotations
import array
import copy
import json
from collections import OrderedDict, defaultdict
from typing import TYPE_CHECKING, Any
import martian
import numpy as np
import scipy.sparse as sp_sparse
impo... |
9922451160d1e99bb7587d292197ac93528c4f1fa3e39bf07805f1f687eb9c78 | Python | 30,988 | 838 | # This script is part of navis (http://www.github.com/navis-org/navis).
# Copyright (C) 2018 Philipp Schlegel
#
# This program 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 Foundation, either version 3 of... |
2e2e29e5c325e1a4ba31e210a367600ab03e238c71cbccc5e3ec04103c2a44d2 | Python | 31,031 | 759 | #utils
import collections
import os
import tarfile
import urllib
import zipfile
from pathlib import Path
from torch.utils.data import Dataset
import h5py
import numpy as np
import torch
from taming.data.helper_types import Annotation
# from torch._six import string_classes
from torch.utils.data._utils.collate import np... |
2718bf80a00a18bb0f6b5c98ad728ccb36404f391498d1ebb65e42eec55621d2 | Python | 31,069 | 951 | ############################################################################
# Copyright (c) 2022-2026 University of Helsinki
# Copyright (c) 2020-2022 Saint Petersburg State University
# # All Rights Reserved
# See file LICENSE for details.
############################################################################
... |
8f5615b884390aef61a1855ab0b1ccaeb92dc649deafbb228808dacd599f8e60 | Python | 31,075 | 753 | import sys
sys.path.insert(0, '..') # for model.py
import os
import argparse
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
import plottools.plottools as pt
from scipy.optimize import curve_fit
from model import simulate, load_models
from eods import plot_eod_interval_hist
from baseline impor... |
15a749ef3c12a203fd730033f0a0d089d31c693ea0b268e275cac9b438343134 | Python | 31,163 | 810 | # -*- coding: utf-8 -*-
"""
Autoradiography
"""
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
from matplotlib import patches
import seaborn as sns
from netneurotools import datasets, metrics, stats, plotting
from scipy.stats import zscore, pearsonr
from scipy.optimize import curve_fit
from ma... |
25121a5053b0089f9ea3caec72b13be82400c6bb2b817607f1a5dec659534c09 | Python | 31,173 | 873 | """Tests for the pluggable parallel backends in `navis.compute`.
Two halves: the registry (which backend gets picked, and why) and the dispatch
seam (chunking, ordering, failure handling). The seam is exercised through a
recording dummy backend so the interesting properties - notably that results
are reordered correct... |
2baf91cdc083b27eb5b4d1c77cdfe67c104a9c5d41ae69ae5724e411592c05f7 | Python | 31,248 | 886 |
""" Training procedure """
__author__ = "Fabi Bongratz"
__email__ = "fabi.bongratz@gmail.com"
import os
import re
from copy import deepcopy
import json
import wandb
import torch
import torch.multiprocessing as mp
import torch.distributed as dist
import numpy as np
from torch.nn.parallel import DistributedDataParall... |
a2c6e6061ddec58b6175877c637a3fc1962b31ddd6fd6922ab9b08707f302cd5 | Python | 31,284 | 797 | #!/usr/bin/env python
#
# Copyright (c) 2019 10X Genomics, Inc. All rights reserved
#
"""Utils for summarizing and computing statistics on RNA reads and UMIs from molecule_info."""
from __future__ import annotations
from collections.abc import Iterable
from copy import deepcopy
from typing import Any
import h5py as ... |
fc0e197ac19324f4ede3ed33f6f2714d1194742e5e1ed9f0d93f1ce4fa7c2eb1 | Python | 31,344 | 701 | import torch
import random
from itertools import combinations
import torch.nn as nn
import torch.nn.functional as F
from torch.distributions import Normal, kl_divergence as kl
# Acknowledgement to scCRAFT from Chuan He (https://www.biorxiv.org/content/10.1101/2024.10.22.619682v1)
def count_labels_per_gro... |
c87d584f2f4af4944a99d3c631e01bb0286ea87c02ad9d9e4d2338176a389683 | Python | 31,539 | 829 | """
Control Spike Sorting Pipeline - Stage 2 (Waveform Curation)
=============================================================
Run AFTER reviewing PPTs from stage1_sort.py and editing curation_config.json.
This stage:
1. Reads curation_config.json for rescue_ids / remove_ids
2. Selects accepted units from analyzer_raw... |
f50c54b44bcbcecf5b9c861684efa159eb48ee04488066c31ee43f0cc3e856f3 | Python | 31,549 | 1,106 | """Tests for DataRecorders."""
import json
import os
import tempfile
from pathlib import Path
from unittest.mock import Mock
import numpy as np
import pandas as pd
import pytest
from mesa.agent import Agent
from mesa.experimental.data_collection import (
DataRecorder,
DataRegistry,
DataSet,
DatasetCo... |
bf282a0e9c51ebf929b740dfa334d2dc9533896fb23989c0331166e04eeb5cfe | Python | 31,569 | 824 | # This script is part of navis (http://www.github.com/navis-org/navis).
# Copyright (C) 2018 Philipp Schlegel
#
# This program 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 Foundation, either version 3 of... |
0a9b38dbfe2ef2643da6c4f5c6e3ee51759f00f17130e137b3b04910e08e4137 | Python | 31,675 | 1,096 | """ Created on Mon Oct 30 13:59:21 2023
@author: dcupolillo """
from __future__ import annotations
from pathlib import Path
from typing import Union
import numpy as np
import matplotlib.pyplot as plt
from matplotlib.colors import Normalize
from functools import cache
import ROIpy as rp
from spyne.core.imaging.vi... |
99c8952b1bea2ac668d84dee052528c5ae862bca48f7bc7554e26f3f3d9284fd | Python | 31,725 | 857 | """Helper functions for drawing mesa spaces with matplotlib.
These functions are used by the provided matplotlib components, but can also be used to quickly visualize
a space with matplotlib for example when creating a mp4 of a movie run or when needing a figure
for a paper.
"""
import itertools
import os
import war... |
494d26b37cdb1c04f084ca1c8f1658a03d56066b182700da141c35d96a5e55b4 | Python | 31,811 | 926 | # This script is part of navis (http://www.github.com/navis-org/navis).
# Copyright (C) 2018 Philipp Schlegel
#
# This program 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 Foundation, either version 3 of... |
d80cfec971e84280be857cb7597b89c2a35fe9406ecfef877320bd6376765306 | Python | 31,878 | 755 | import os
import numpy as np
import pandas as pd
import umap
import matplotlib.pyplot as plt
import anndata as ad
import scanpy as sc
import scvelo as scv
import cellrank as cr
import scanpy.external as sce
from scipy.io import mmwrite, mmread
import statsmodels.api as sm
np.random.seed(42)
# peak-gene linkage matrix... |
29757564953cf5aa56af7c75576c7d33bff7661631f1ac706aa3926c8775f8e2 | Python | 32,016 | 711 | """
Attaching Data
==============
<!-- difficulty: advanced -->
Carry your own data through subsetting, masking and pruning.
!!! example "New in {{ navis }} 2.0"
`attach` and `attach_link` are new and we are keen to hear how they hold up on
real data. Please read [Caveats](#caveats) and [Antipatterns](#antipa... |
ee5cb8c5974cdb8241a9fc587798f3872d22dfac7f375134003f192311311910 | Python | 32,045 | 901 | # This script is part of navis (http://www.github.com/navis-org/navis).
# Copyright (C) 2018 Philipp Schlegel
#
# This program 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 Foundation, either version 3 of... |
511930f1b9dbf8eb7c805492afe5de21499f38c568dbdf482dc57579b34ab1d4 | Python | 32,072 | 1,110 | """Tests for mesa_signals."""
import doctest
from unittest.mock import Mock, patch
import pytest
from mesa import Agent, Model
from mesa.experimental.mesa_signals import (
ALL,
HasEmitters,
ListSignals,
Observable,
ObservableList,
ObservableSignals,
SignalType,
computed_property,
... |
ed0f74a22e99f13576b7619c5024cebcbc38d361068423eddd0aee7b49bad57d | Python | 32,078 | 661 | ############################################################################
# Copyright (c) 2024-2026 University of Helsinki
# # All Rights Reserved
# See file LICENSE for details.
############################################################################
import logging
import math
from collections import defaultdi... |
ac073b3467de1ff94b1df61df94b45392f6929862de8b39ce6300f717a41aa47 | Python | 32,309 | 803 | # Copyright (c) 2019 10x Genomics, Inc. All rights reserved.
# Keeping the annotation import for now until PEP 563 is mandatory in a future Python version
# Check: https://peps.python.org/pep-0563/
# Check: https://github.com/astral-sh/ruff/issues/7214
from __future__ import annotations
import csv
import sys
from coll... |
c716039dc7f68902d28aa68300b91bea3c8928fe7f948c464ff5d70dbc6eb880 | Python | 32,312 | 596 | ###########################################################################
# Copyright (c) 2026 University of Helsinki
# # All Rights Reserved
# See file LICENSE for details.
############################################################################
import logging
import math
import sys
from ..indexers import Arra... |
f41b6c895d28a500711e6923bef1f3cf7db60c10f91c1d52f0f13e77ae2eef7f | Python | 32,324 | 816 | # /// script
# requires-python = ">=3.13"
# dependencies = [
# "marimo>=0.23.3",
# "numpy>=2.5.1",
# "pandas>=3.0.3",
# "plotly>=6.9.0",
# "scipy>=1.18.0",
# ]
# ///
#local view: uv run marimo run maxLFQmo.py
#server edit: animeshs@ubuntu:~/scripts$ uv run marimo edit maxLFQmo.py --host 0.0.0.0 --po... |
2cfaac0610720403ad6b514067dd4b1e31b68f7d6c834db78021ddbeddb1ce32 | Python | 32,339 | 808 | #!/usr/bin/env python
#
# Copyright (c) 2022 10X Genomics, Inc. All rights reserved.
#
#
"""Generate antigen specificity scores and antigen assignments."""
from __future__ import annotations
import csv
from ast import literal_eval
from collections import Counter, OrderedDict, defaultdict, namedtuple
from enum import E... |
c52b212e8aba56d5dcd24748a25eb03cd488c5071b2aa0db6e0adcf24299a877 | Python | 32,346 | 755 | # -*- coding: utf-8 -*-
"""
Created on Fri Jul 15 12:25:40 2016
@author: Luciano Masullo, Federico Barabas
# TODO: QTHREADS ARE NOT WORKING AS THEY WERE SUPPOSED TO
"""
import os
import time
import numpy as np
from scipy import ndimage as ndi
import tifffile as tiff
from PIL import Image
import matplotlib.pyplot as ... |
7a1702df64f2b46d2b7474d33dc2f2b2ce50f3f8d594dce5898193aa9e3269da | Python | 32,455 | 814 | #!/usr/bin/env python
#
# Copyright (c) 2019 10X Genomics, Inc. All rights reserved.
#
"""This file shows plots in the analysis tab that aren't related to the outputs of the SC_RNA_ANALYZER pipeline.
e.g. targeted UMI plots, sequencing saturation plots, etc
splitting things up in this way allows turing repo to utilize... |
36931cd3620933751c79a46ff072158064f18acd69418f9ccea8621537b4cf8a | Python | 32,500 | 775 | """
coregister - Image Registration for Aligning Neuroimaging Data
Part of the micaflow processing pipeline for neuroimaging data.
This module performs comprehensive image registration between two images using the
Advanced Normalization Tools (ANTs) SyNRA algorithm, which combines rigid, affine,
and symmetric normali... |
08d37ad6ae8a05112d89ddd37e4e51e6b557455b93ee7d79adbea463bc3728a7 | Python | 32,546 | 888 | """
Created on 10/08/2017
@author: Niklas Pallast
Neuroimaging & Neuroengineering
Department of Neurology
University Hospital Cologne
Documentation preface, added 23/05/09 by Victor Vera Frazao:
This document is currently in revision for improvement and fixing.
Specifically changes are made to allow compatibility of ... |
59f6824c313ae584cebed0c61c9962e2802628f97c4e3c4c27a48b4cdf6bcf00 | Python | 32,618 | 837 | # This script is part of navis (http://www.github.com/navis-org/navis).
# Copyright (C) 2018 Philipp Schlegel
#
# This program 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 Foundation, either version 3 of... |
99bdba165dfb1e219575773d3e7568c003607ebf15ee41c314e67e3765c93897 | Python | 32,671 | 840 | # This script is part of navis (http://www.github.com/navis-org/navis).
# Copyright (C) 2018 Philipp Schlegel
#
# This program 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 Foundation, either version 3 of... |
dddb4d1f017e4f26ef195a7c805bf23039d18445b3785b8d8c420c7b3f969d17 | Python | 32,718 | 886 | # -*- coding: utf-8 -*-
"""bnn_binary
Automatically generated by Colab.
Original file is located at
https://colab.research.google.com/drive/1VUekM0LLYNzbyz9LEeoRQt6aZ7v0Htnk
"""
!pip install tf-keras-vis
"""End-to-end Bayesian CNN pipeline for frost vs non-frost image classification
with MC Dropout uncertainty ... |
a38217e08844d3a57405f0ad811b87374622f90d4cd9c28b321086da082054c9 | Python | 32,896 | 959 | # This script is part of navis (http://www.github.com/navis-org/navis).
# Copyright (C) 2018 Philipp Schlegel
#
# This program 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 Foundation, either version 3 of... |
89c785fd9adfc8355357ec62cb2da2677d39ea3d93fee5f24e4a8c5293694a61 | Python | 33,298 | 810 | #utils
import collections
import os
import tarfile
import urllib
import zipfile
from pathlib import Path
from torch.utils.data import Dataset
import h5py
import numpy as np
import torch
from taming.data.helper_types import Annotation
# from torch._six import string_classes
from torch.utils.data._utils.collate import np... |
ffeadf0eda16f7d0347723468c9a8fe95c290818e715b482eaf436309e704c50 | Python | 33,319 | 1,118 | """Tests for Event, EventList, Schedule, and EventGenerator."""
# ruff: noqa: D101, D102
import gc
import pickle
from collections.abc import Callable
from functools import partial
from unittest.mock import MagicMock
import pytest
from mesa import Model
from mesa.time import (
Event,
EventGenerator,
Event... |
debcadab1d5d6ce4f50a597f3b42fffc4852baa03e44edd6b7d26606f7c9792f | Python | 33,364 | 726 | ############################################################################
# Copyright (c) 2022-2026 University of Helsinki
# Copyright (c) 2021-2022 Saint Petersburg State University
# # All Rights Reserved
# See file LICENSE for details.
############################################################################
... |
043ff43c4d4304f7259419d1bd4529445da71661b5362653ecd174bd4342c413 | Python | 33,409 | 835 | # pytorch_diffusion + derived encoder decoder
import math
import torch
import torch.nn as nn
import numpy as np
from einops import rearrange
from ldm.util import instantiate_from_config
from ldm.modules.attention import LinearAttention
def get_timestep_embedding(timesteps, embedding_dim):
"""
This matches th... |
03713fb2b1f9d673087e46679f7d1b25b28f4d216714e45c54b2f8084fa94895 | Python | 33,426 | 874 | """Hosts the GearToolkitContext class. Provides gear helper functions."""
import argparse
import json
import logging
import os
import pathlib
import sys
import tempfile
import typing as t
import warnings
from pprint import pformat
from shutil import rmtree
try:
import flywheel
HAVE_FLYWHEEL = True
except (Mod... |
8f507fb3263b89fd3811990fa8efd11d331d0c526efd46161160dfcd221159a0 | Python | 33,513 | 863 | #!/usr/bin/env python3
#
# Copyright (c) 2021 10X Genomics, Inc. All rights reserved.
#
"""Identify partitions that contain cells."""
from __future__ import annotations
import dataclasses
import json
import math
import os
from collections import defaultdict
from typing import TYPE_CHECKING, Any, NamedTuple
import ma... |
9bf53d4359ace4ac36c6d31df36189ed2060bd8fc5696546277a953d2fa8cdde | Python | 33,538 | 850 | """
If you use this code, please cite one of the SynthSeg papers:
https://github.com/BBillot/SynthSeg/blob/master/bibtex.bib
Copyright 2020 Benjamin Billot
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 Lice... |
488aa8324cc904473fec426bea389a46a960592949a14cb8f3fda90be34b5a6b | Python | 33,675 | 803 | # This script is part of navis (http://www.github.com/navis-org/navis).
# Copyright (C) 2018 Philipp Schlegel
#
# This program 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 Foundation, either version 3 of... |
c6180fe6c76b0b2892e0160a0dd1e4d1333ab4f85dfe0b48fc5bb479de4bf120 | Python | 33,716 | 769 | # This script is part of navis (http://www.github.com/navis-org/navis).
# Copyright (C) 2018 Philipp Schlegel
#
# This program 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 Foundation, either version 3 of... |
daa1f4a784f0cc9ab891d876ee7b3e0d169782ab844716eec836d4f50ecdd73d | Python | 33,779 | 877 | from abc import ABC, abstractmethod
import types
from typing import Iterable
from lightning import pytorch as pl
import torch
from torch import Tensor
from torch.utils.data import DataLoader
from chemprop.conf import LIGHTNING_26_COMPAT_ARGS
from chemprop.models import MPNN, MolAtomBondMPNN
from chemprop.utils.regist... |
9380dcf6bb5ea9146f517a59749a0c8ce387deb40af505b8b6fe94e196257c25 | Python | 33,818 | 931 | """Mesa visualization module for creating interactive model visualizations.
This module provides components to create browser- and Jupyter notebook-based visualizations of
Mesa models, allowing users to watch models run step-by-step and interact with model parameters.
Key features:
- SolaraViz: Main component for... |
3a034d4f99688d26298efe0b09ebecdbab53444cbce958b518d4184a35590426 | Python | 33,986 | 976 | """
Functions on PointData and CellData.
"""
# Author: Oualid Benkarim <oualid.benkarim@mcgill.ca>
# License: BSD 3 clause
import warnings
import numpy as np
from scipy.stats import mode
from scipy.spatial import KDTree
from scipy.sparse.csgraph import laplacian, connected_components
from sklearn.utils.extmath imp... |
8c8a66278fb7593e2685d9632124c9b30648e895173de934d544a8383190ebd1 | Python | 33,986 | 981 | """Unified k-fold cross-validation training for GNN and VAE models.
Critically, regression target scaling is done **inside** the fold loop
to prevent data leakage.
Supports GNN models (operating on PyG graph data) and VAE models
(operating on flattened molecular tensor representations).
"""
import copy
import logging... |
d9dfd29ce7789b4ce533e739a4e6fb0ba40fa4acefb27c737f0ae7ae01523a82 | Python | 34,037 | 757 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Harder Hide-the-Label Competition Framework
This module implements a harder version of the hide-the-label competition
that makes it more difficult for Bayesian optimizers by using non-GP models
and adding various difficulty factors.
Methods implemented:
1. Non-GP Typ... |
c37bb500e9ddd414beff4fae76992af847a8bfeef4b1dace3a052e5fba751554 | Python | 34,337 | 603 | import shutil
from copy import deepcopy
from typing import List, Union, Tuple
import numpy as np
import torch
from batchgenerators.utilities.file_and_folder_operations import load_json, join, save_json, isfile, maybe_mkdir_p
from dynamic_network_architectures.architectures.unet import PlainConvUNet
from dynamic_networ... |
3a1f95ae2dce94d7a9f58f64fa042ad2796794af7cfa31851b7c534e59caaee2 | Python | 34,419 | 786 | # This script is part of navis (http://www.github.com/navis-org/navis).
# Copyright (C) 2018 Philipp Schlegel
#
# This program 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 Foundation, either version 3 of... |
8858be0c8b3886d62040c63631e1fffd809395d40162f06813ba70aa5a191881 | Python | 34,516 | 935 | """Test the DataCollector."""
import unittest
import warnings
from functools import partial
import pandas as pd
import pytest
from mesa import Agent, Model
from mesa.datacollection import DataCollector
from mesa.exceptions import TableMissingException
class MockAgent(Agent):
"""Minimalistic agent for testing p... |
73337679c5a6ee0499f2c45a3daacf11164262e732e41867e6d4a7b4902a3f23 | Python | 34,619 | 842 | #!/usr/bin/env python
# Copyright 2016-2023 Biomedical Imaging Group Rotterdam, Departments of
# Medical Informatics and Radiology, Erasmus MC, Rotterdam, The Netherlands
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obt... |
bdf22cf85cebb556aa8c0c48dfe9325fb96b6a2de55cf94358a82c48d2ee1e02 | Python | 34,770 | 910 | # This script is part of navis (http://www.github.com/navis-org/navis).
# Copyright (C) 2018 Philipp Schlegel
#
# This program 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 Foundation, either version 3 of... |
89a09c850f53cf2b1a9e340b627ede2ec76f9ff158b55a9c449394cae3189465 | Python | 34,871 | 884 | # This script is part of navis (http://www.github.com/navis-org/navis).
# Copyright (C) 2018 Philipp Schlegel
#
# This program 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 Foundation, either version 3 of... |
e1775043217736a03a104dd61c8e76a3f46985eebb8fbd349dea356d3f80722d | Python | 34,877 | 838 | #!/usr/bin/env python3
#
############################################################################
# Copyright (c) 2022-2026 University of Helsinki
# Copyright (c) 2020-2022 Saint Petersburg State University
# # All Rights Reserved
# See file LICENSE for details.
#####################################################... |
92e0c23ada849f532be12d9be2ebcddd98d3b040aa366981ac5f06c96d53b6af | Python | 34,953 | 961 | from abc import abstractmethod
from functools import partial
import math
from typing import Iterable
import numpy as np
import torch as th
import torch.nn as nn
import torch.nn.functional as F
from ldm.modules.diffusionmodules.util import (
checkpoint,
conv_nd,
linear,
avg_pool_nd,
zero_module,
... |
6d829bd1b98255c051c124bd2388a95dcebedf56559ce1a373549fcd9ea2293c | Python | 35,119 | 862 | """
SDC - Susceptibility Distortion Correction for Echo-Planar Imaging
Part of the micaflow processing pipeline for neuroimaging data.
This module corrects geometric distortions in echo-planar imaging (EPI) MRI data
caused by magnetic field (B0) inhomogeneities. EPI sequences, commonly used for
functional MR... |
ec80a6df89038726724aeead819b0460377554a8976c0a0c1a74d3c59e4f17ac | Python | 35,135 | 821 | import pytest
import logging
from unittest.mock import MagicMock, patch
from isoquant_lib.fusion.fusion_detector import FusionDetector, _CIGAR_CACHE
logger = logging.getLogger('IsoQuant')
class TestFusionDetectorInitialization:
"""Test FusionDetector initialization."""
@patch('isoquant_lib.fusion.fusion_det... |
692ed4b532d0fa2262d5e51fc36dddb00f53287c0f15d93ad6406d617bc1c65b | Python | 35,252 | 910 | #!/usr/bin/env python
#
# Copyright (c) 2018 10X Genomics, Inc. All rights reserved.
#
from __future__ import annotations
import pickle
from collections.abc import Collection
from copy import copy
from typing import TYPE_CHECKING, TypedDict
import numpy as np
import pandas as pd
import cellranger.molecule_counter as... |
fb66a876a254277843caad6d6eeab5317b4c207de8da37567f38b820ed3b6dd1 | Python | 35,490 | 826 | #!/usr/bin/env python3
"""
extract_b0 - B0 Volume Extraction and Dataset Splitting Tool
Part of the micaflow processing pipeline for neuroimaging data.
This module extracts b=0 (non-diffusion-weighted) volumes from diffusion-weighted
images (DWI) and separates them from the diffusion-weighted volumes. B0 volumes are... |
3a8cb9ccf5beab1da93b5c5fa1afafbc8adc235fbe2056933f2242a710042bc6 | Python | 35,517 | 674 | #!/usr/bin/env python
# Copyright 2016-2021 Biomedical Imaging Group Rotterdam, Departments of
# Medical Informatics and Radiology, Erasmus MC, Rotterdam, The Netherlands
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obt... |
568ec74e3068fa964727b0c2f953a2b448ec62f2070172d09ab8eadef9ab1c35 | Python | 35,586 | 823 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Harder Open Race Competition Framework
This module implements a harder version of the open race competition
that makes it more difficult for Bayesian optimizers by using non-GP models
and adding various difficulty factors.
Methods implemented:
1. Non-GP Type 1 Models... |
d6f161e7ebc680e917ea43bb0e120aa73b657d06f6f1714ed23d5f06460d6d91 | Python | 35,682 | 664 | from __future__ import annotations
import csv
import json
import os
from pathlib import Path
import queue
import subprocess
import sys
import threading
import time
import traceback
ROOT = Path(__file__).resolve().parents[1]
APP_TITLE = "Smart Home Intent Classification Experiment Console"
APP_VERSION = "3.0"
def re... |
a531ba6b8941921892753dba5b3ff351c728d10da43df9e3034fbe4706f8b55f | Python | 35,701 | 945 | # This script is part of navis (http://www.github.com/navis-org/navis).
# Copyright (C) 2018 Philipp Schlegel
#
# This program 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 Foundation, either version 3 of... |
6e722ad5d39ff74132e72b80aab1cadebaaf575db99095ffba8d25b23ac95cc3 | Python | 35,827 | 1,068 | #!/usr/bin/env python
#
# Copyright (c) 2016 10x Genomics, Inc. All rights reserved.
#
# Utilities for reading and generating Illumina Experiment Manager sample sheets
#
import csv
import logging
import re
from collections import namedtuple
from six import ensure_text
import tenkit.pandas as pandas
import tenkit.se... |
4081875283f3a8362a5aaa13ad15d48a39aad7dbb918198f2dff7e0f4b99b4c4 | Python | 35,908 | 1,055 | # This code is part of OpenFE and is licensed under the MIT license.
# For details, see https://github.com/OpenFreeEnergy/openfe
import copy
import os
import sys
from importlib import resources
from pathlib import Path
from unittest import mock
import numpy as np
import pooch
import pytest
from gufe.settings import Op... |
79753fe1471887cc4d8a8b8e7ffe6da56ad33ae5dc45e343c4b0d116bcee5442 | Python | 35,999 | 1,082 | """Tests for mesa.experimental.scenarios."""
import pickle
from concurrent.futures import ProcessPoolExecutor
import numpy as np
import pandas as pd
import pytest
import scipy.stats.qmc as qmc
from mesa import Agent, Model
from mesa.experimental.data_collection import DataRecorder
from mesa.experimental.scenarios im... |
1430552c048368a98c37f570de9a7c7e7ab707f21dc1bb9421c920db443d8674 | Python | 36,270 | 1,008 | from __future__ import annotations
import copy
import functools as ft
import itertools as it
import operator as op
import re
import string
import warnings
from pathlib import Path
from typing import Any
import more_itertools as itx
import pytest
from hypothesis import assume, example, given
from hypothesis import str... |
1f38ead2a68a78eb83ec04cb184bdda0c5363f7c1c3d41c1108491a9198fcb73 | Python | 36,461 | 960 | # AUTOGENERATED! DO NOT EDIT! File to edit: 06a_seq_summaries.ipynb (unless otherwise specified).
__all__ = ['rbpamp_imported', 'SequenceSummarizer', 'PWM', 'PWMScorer', 'RBPampAffinityModel', 'RBPampMotifScorer',
'generate_sequence_with_all_kmers', 'MultiPWM', 'MultiPWMScorer', 'ProboundModel', 'ProBoundSc... |
965fae6b56725e2c1d05b7fe9ca76ec023482a89b6849a693a4ea709767f0082 | Python | 36,469 | 747 | ############################################################################
# Copyright (c) 2022-2026 University of Helsinki
# Copyright (c) 2020-2022 Saint Petersburg State University
# # All Rights Reserved
# See file LICENSE for details.
############################################################################
... |
c189eaa3ea51d375d18e394159051c3367ac8ecee149f54e92d5c136d14eba05 | Python | 36,520 | 1,010 | # -*- coding: utf-8 -*-
"""photomicrgraphs
Automatically generated by Colab.
Original file is located at
https://colab.research.google.com/drive/1B-m7P9u1keP7_O9S3-G-fRmOpVnUexl-
# Full Photomicrograph Classification + Score‑CAM + Metrics
"""
import os
os.environ["TF_FORCE_GPU_ALLOW_GROWTH"] = "true"
import te... |
ab999afc6198be9dc2b0c62e69f51a7a23ec6e0b2bedbebc5e844bcce91bc83f | Python | 36,578 | 992 | # -*- coding: utf-8 -*-
"""neu_cnn_multiclass
Automatically generated by Colab.
Original file is located at
https://colab.research.google.com/drive/15HYyLD7l-r-kN99mJXIE_pRLxuyy2ria
"""
!pip install tf-keras-vis
"""End-to-end multiclass CNN pipeline for microstructure image classification,
with detailed misclas... |
db0697bb7f0559913806c3bac518b658bde61cd9658529a37b83c43c48720578 | Python | 36,861 | 987 | # -*- coding: utf-8 -*-
"""neu_bnn_multiclass
Automatically generated by Colab.
Original file is located at
https://colab.research.google.com/drive/1MJOewWobpYzWZFNhtajIpRqpjIkOd0FK
"""
!pip install tf-keras-vis
"""End-to-end multiclass Bayesian CNN pipeline for microstructure image
classification with MC Dropo... |
a8896167d53d3e4b807602695a9e63c5465e4f9e7ae9e47e9bddb1d31612bc66 | Python | 37,101 | 948 | from argparse import ArgumentError, ArgumentParser, Namespace
import json
import logging
from pathlib import Path
import sys
from typing import Iterator
from lightning import pytorch as pl
import numpy as np
import pandas as pd
import torch
from chemprop import data
from chemprop.callbacks import CallbackRegistry
fro... |
7aca6881b25469b48726c12676fc1059e9c1f3dd5576d31024af13711a0ffa66 | Python | 37,148 | 760 | from copy import deepcopy
from typing import Literal, Tuple, Union, List
import torch
from batchgenerators.utilities.file_and_folder_operations import isfile
from dynamic_network_architectures.architectures.abstract_arch import AbstractDynamicNetworkArchitectures
from torch._dynamo import OptimizedModule
from nnunetv2... |
912f079de97b6ac7c4157fce665fcccdae22523624e2ad219d8149b754ad777a | Python | 37,576 | 1,034 | import inspect
import json
import multiprocessing as mp
import subprocess
import os
from helpers import (get_fmriname, get_readoutdir, get_realdwelltime,
get_relpath, get_taskname, ijk_to_xyz)
class ParameterSettings(object):
"""
Paths to files and settings required to run DCAN HCP. Cl... |
e72abea05f5039e103b75c092ff82ccad6e826d59e7e2044522a82537dd75c7e | Python | 37,699 | 877 | # Copyright (c) Facebook, Inc. and its affiliates.
import inspect
import logging
import numpy as np
from typing import Dict, List, Optional, Tuple
import torch
from torch import nn
from detectron2.config import configurable
from detectron2.layers import ShapeSpec, nonzero_tuple
from detectron2.structures import Boxes,... |
7a08f309757c5c6ceb7023062c4a18c1aaedeb4635446d0627240dd175c233fe | Python | 37,815 | 816 | import torch
import torch.nn.functional as F
import pytorch_lightning as pl
from main_hdf5 import instantiate_from_config
import numpy as np
from taming.modules.diffusionmodules.model import Encoder, Decoder, EncoderVINN, DecoderVINN
from taming.modules.vqvae.quantize import VectorQuantizer2 as VectorQuantizer
from ta... |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.