sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
9a745ca10980b042fbd44292efbe28b8b3d984f4143b3edb5f6df2e6fc556fee | Python | 14,293 | 380 | # Copyright 2024 Google LLC
#
# 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
#
# https://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, ... |
62c97acb7bffb9a153736735bea7c9af22c1f0f889c0d068a65256fa6406a579 | Python | 14,295 | 406 | """Provide regularization functions and classes for ddf."""
from typing import Callable, Tuple
import tensorflow as tf
from deepreg.registry import REGISTRY
from deepreg.model import layer_util
def gradient_dx(fx: tf.Tensor) -> tf.Tensor:
"""
Calculate gradients on x-axis of a 3D tensor using central finite... |
ae7d3ed2adf423a8d43d479e00cde1efeea48d883e657cff67a7f42968be6406 | Python | 14,295 | 322 |
# This script take as input a gtf file, a sam file input folder, a sample ID file, and the number of cores, then run
# the count exons and genes in parallel, and then output the report file and output file into the output file
import itertools
import collections
import numpy as np
import pandas as pd
from multiproces... |
9f02b2f11ce3f6f0d25dae85e70bb3f1bb48775c8c7ae7cea69a5072d33fbbc8 | Python | 14,310 | 401 | import pdb
import typing
import bisect
import functools
import traceback
from .config import ObservableCollection, ObservableDict, ObservableList
from .qt import *
def get_selected_rows(qlist: QListView) -> typing.List[int]:
return sorted(set(i.row() for i in qlist.selectedIndexes()), reverse=True)
class FlatObser... |
e7e2a3c676bd1d26fcc5cd27ccbb63852dffc086911b7a1088e2633a57d1e82e | Python | 14,315 | 352 | import argparse
import time
import warnings
import torch
import os, time
import sys
import yaml
import datetime
import logging
import random
import numpy as np
import pandas as pd
import transformers
import json
import torch.nn as nn
from torch.utils.data import DataLoader
from numpy import nan
from typing import *
# f... |
f677dad434230ee1e9222bf989abe90597d7fcdc185490fbaeae6f728865c102 | Python | 14,315 | 456 | # -*- coding: utf-8 -*-
#
# test_domain_decompositions.py
import unittest
import arbor as arb
from .. import cases
# check Arbor's configuration of mpi and gpu
mpi_enabled = arb.__config__["mpi"]
gpu_enabled = arb.__config__["gpu"]
"""
all tests for distributed arb.domain_decomposition
"""
# Dummy recipe
class ho... |
f13c2e4a9e167574414f212cc41022299cc83f9a81124e0fa2db2be1d950c517 | Python | 14,316 | 282 | # Generate output file name by request
import pandas as pd
#===============================================================================
#
# Output files for each run
#
#===============================================================================
def outfn_sbcd_per_fc(main_dirs, df_run):
outfn= {
... |
31d6c15029d758d21147eb56a4de79e21c215eb306d810ca7264950aa849dcfc | Python | 14,322 | 276 | """Execute skill examples and scripted agent actions without a live scheduler/LLM."""
import json
import os
from pathlib import Path
import shlex
import socket
import subprocess
import sys
import pytest
from deepagents.backends import LocalShellBackend
from langchain_core.messages import AIMessage, HumanMessage
from ... |
fb38661d6d1e77daede0c2db75f5d2b08cc13841fa09ef130308455381dca332 | Python | 14,323 | 382 | """
FCS file processing functions adapted from the original codebase.
Handles FCS file reading, compensation, and transformation.
"""
import numpy as np
import logging
from pathlib import Path
from typing import List, Optional, Dict, Any
import flowkit as fk
logger = logging.getLogger(__name__)
def read_fcs_file(
... |
4fd4d2966b46bc2eb39b2b12949f9c6923dfa7076b19cef9436c81b35b863469 | Python | 14,329 | 375 | """
Copyright (c) Facebook, Inc. and its affiliates.
This source code is licensed under the MIT license found in the
LICENSE file in the root directory of this source tree.
"""
import torch
from torch import nn
from torch.nn import functional as F
# %%
class Unet(nn.Module):
"""
PyTorch implementation of a ... |
ce6cfbb65a33784657a9639ed78b01283c3cc92d195a1184b1c604138dc5675e | Python | 14,331 | 360 | import time
import numpy as np
import argparse
from copy import deepcopy
from scipy import interpolate
parser = argparse.ArgumentParser('Preprocessing: Generate training/validation/testing features from pdb')
parser.add_argument('--MDfolder', type=str, default="data/pdb/",
help='folder of pdb MD')
... |
51756d14a094f859f684e80a3a7072a245a69ea5d19997a1d5a50e6c8786701a | Python | 14,333 | 331 | from __future__ import annotations
import csv
import datetime
import os
import pickle
import re
import pandas as pd
from biom import Table, load_table
import qiime2 as q2
from skbio import TreeNode
from Bio import Phylo
from .utilities import ReadsData, run_cmd, download_classifier_url, check_conda_qiime2
nodes_nam... |
134841258093fcefe02d517c6e69c35d47111b44c47d6766144c2af54b2f5ad7 | Python | 14,335 | 329 | #!/usr/bin/env python3
import numpy as np
import pandas as pd
import argparse
import os
from datetime import datetime
import pyBigWig
import multiprocessing as mp
import qtl.annotation
import qtl.norm
import qtl.io
def time_now():
"""Return time"""
return datetime.now().strftime("%c")
#----------------------... |
17bdcecd88b97ade35aee0a44e161506dc57d4d052154bd6a0420c0db97173f0 | Python | 14,336 | 223 | from __future__ import annotations
import argparse
import json
import os
import shlex
import shutil
import signal
import subprocess
import threading
import time
import urllib.error
import urllib.request
from importlib.resources import files
from pathlib import Path
from chemgraph.academy.dashboard import serve_dashbo... |
eecab386467ea78cec0cd032676f926c85ee3975fe349a9666fead81124b150d | Python | 14,343 | 353 | """Does the correlation structure among tracked cells survive across days?
The per-cell fingerprint asks whether *one* match is real, and answers weakly:
AUC 0.68 against a co-located different cell, which is not enough to decide an
individual match. This asks a different question of the same data -- whether the
**set... |
1694cb6e0c75298906002c87b178ac27f96b82f373b5ecbbd0985f5730f384f4 | Python | 14,345 | 354 | """
@file QFAlignmentDialog.py
@description Alignment and image-difference detection dialog for the QF module.
- Reuses AISE's :class:`ImageAlignmentWidget` without the AISE-specific business
logic (grouping, summation, Result Tab).
- Shares the :class:`ProcessingWorkspace` owned by :class:`QuadrantFoldingGUI`:
* ... |
de7474eb6dd21e41f8cf8a3643bc9c023c97eb7293007592a2fadca3f3014c82 | Python | 14,345 | 324 | """
EEGNet Multi-class Training Script
- Load .npy preprocessed data
- Sliding window data augmentation
- 5-fold stratified cross-validation
- Output per-fold and average accuracy, F1, etc.
"""
import copy
import random
import os
import numpy as np
import torch
import torch.nn as nn
import torch.optim as... |
15b58996efdf52a1a1e29c7f5259b8c7d95dd375a618ec93bb35aefceda0a201 | Python | 14,351 | 295 | import os
import tempfile
from unittest import mock, TestCase
from unittest.mock import call
import kb_python.compile as compile
from tests.mixins import TestMixin
class TestCompile(TestMixin, TestCase):
def test_get_latest_github_release_tag(self):
with mock.patch('kb_python.compile.requests') as reque... |
9f5f948d6099710cd7e35e915376cbc1d9b70a247c9c95188fc88db5bb0f3940 | Python | 14,353 | 393 | import os
from PySide6.QtWidgets import (
QDialog,
QVBoxLayout,
QHBoxLayout,
QTableWidget,
QTableWidgetItem,
QPushButton,
QHeaderView,
QAbstractItemView,
QLabel,
QProgressBar,
QSizePolicy,
QMenu,
QRadioButton,
QSpinBox,
QWidget,
QSplitter,
QScrollArea,... |
f12716985e06ba61499dd2efb3bcd36d6811ad7f0b4c64e3fc829bf675da791d | Python | 14,355 | 277 | # Copyright (c) 2026 Rohit Jena. All rights reserved.
#
# This file is part of FireANTs, distributed under the terms of
# the FireANTs License version 1.0. A copy of the license can be found
# in the LICENSE file at the root of this repository.
#
# IMPORTANT: This code is part of FireANTs and its use, reproduction, or... |
1e30e7067990e56ed1cb22bff0ed19de7bd199087e34d69f124dd2c35f16f5ce | Python | 14,357 | 503 | import math
import random
import numpy as np
from . import colorblind
# pre-define interesting colours/points at corners, edges, faces and interior of
# r,g,b cube
WHITE = (1.0, 1.0, 1.0)
BLACK = (0.0, 0.0, 0.0)
RED = (1.0, 0.0, 0.0)
GREEN = (0.0, 1.0, 0.0)
BLUE = (0.0, 0.0, 1.0)
CYAN = (0.0, 1.0, 1.0)
YELLOW = (1.0... |
ca4df06c92651f069d601fe217a42c9896635a18f2fa17bfd6af5c2a8322ea5c | Python | 14,358 | 369 | from typing import Literal
import polars as pl
import seaborn as sns
from matplotlib.axes import Axes
from scipy.stats import wilcoxon, mannwhitneyu
from argclz import as_argument, argument
from neuralib.plot import plot_figure
from neuralib.util.verbose import publish_annotation
from rscvp.statistic.core import Stat... |
5d5b99cf5cf37944961a07bcfc8a20bc6ca4e06e00a8cf4a6e48d2e80e23eac1 | Python | 14,359 | 308 | import os
import pandas as pd
import json
import nibabel as nib
import numpy as np
import re
from nipype import Node, Workflow, MapNode
from nipype.interfaces.utility import IdentityInterface, Merge, Function
from cvdproc.pipelines.dmri.nemo.nemo_postprocess_nipype import NemoCorticalMetrics, NemoChacovol, NemoChacoco... |
9b1f1bf79d72996df8b8e6f92889746ed5de6880820df9d04d6044078fdecefb | Python | 14,360 | 309 | #!/usr/bin/env python
# coding: utf-8
# # Data preparation for protein-protein interfaces
#
# ## Introduction
#
# <img style="margin-left: 1.5rem" align="right" src="images/data_generation_ppi.png" width="400">
#
# This tutorial will demonstrate the use of DeepRank2 for generating protein-protein interface (PPI) g... |
d725f234217a243a6c23c697a26c99029c1e3ca460190ffd9c73736cc02e7533 | Python | 14,360 | 309 | #!/usr/bin/env python
# coding: utf-8
# # Data preparation for protein-protein interfaces
#
# ## Introduction
#
# <img style="margin-left: 1.5rem" align="right" src="images/data_generation_ppi.png" width="400">
#
# This tutorial will demonstrate the use of DeepRank2 for generating protein-protein interface (PPI) g... |
3a6ebc6fbf6fa2ba404f52f7ee5773db497dbf7f4aa5681350ee18da8c463020 | Python | 14,362 | 309 | #!/usr/bin/env python
# coding: utf-8
# # Data preparation for protein-protein interfaces
#
# ## Introduction
#
# <img style="margin-left: 1.5rem" align="right" src="images/data_generation_ppi.png" width="400">
#
# This tutorial will demonstrate the use of DeepRank2 for generating protein-protein interface (PPI) g... |
f1fa8dd26466c11ffd46f4c340d69778f205258fd8b178fb0863da86a17cc33a | Python | 14,362 | 309 | #!/usr/bin/env python
# coding: utf-8
# # Data preparation for protein-protein interfaces
#
# ## Introduction
#
# <img style="margin-left: 1.5rem" align="right" src="images/data_generation_ppi.png" width="400">
#
# This tutorial will demonstrate the use of DeepRank2 for generating protein-protein interface (PPI) g... |
f3a10421244a1e2c12f5276f64536a05cf03380bd16b85146fb8f2f08f8fb3c0 | Python | 14,362 | 309 | #!/usr/bin/env python
# coding: utf-8
# # Data preparation for protein-protein interfaces
#
# ## Introduction
#
# <img style="margin-left: 1.5rem" align="right" src="images/data_generation_ppi.png" width="400">
#
# This tutorial will demonstrate the use of DeepRank2 for generating protein-protein interface (PPI) g... |
6e498bdee87a1ebf9a83383848570dd730bdc432b77e3edf316f313737e88a56 | Python | 14,367 | 436 | import pickle
from collections.abc import Callable
from copy import deepcopy
from dataclasses import dataclass
from pathlib import Path
from typing import TYPE_CHECKING, Optional, Protocol, Union
import numpy as np
import pandas as pd
from aislib.misc_utils import ensure_path_exists
from eir.interpretation.interpreta... |
25311c951cfb720c0896b0ba098b083ddc70ed64053695e8380ce11f7f116fdf | Python | 14,368 | 365 | """Tests for keypoint fidelity: physical consistency and registration landmark error.
- Helpers create 2D square / 3D cube images (grid + threshold) and return keypoints in pixel and torch space.
- Physical-consistency tests assert as_physical_coordinates() match for pixel vs torch keypoints.
- Registration tests run ... |
a1a374f60490b76f3bbe97d5a7bd3ed9fb581dcbd9936bd708b45c9cf935db2b | Python | 14,368 | 378 | #!/usr/bin/env python
"""
Base class / functionality for controlling a motorized stage.
Hazen 04/17
"""
from PyQt5 import QtCore
import storm_control.hal4000.halLib.halMessage as halMessage
import storm_control.sc_hardware.baseClasses.hardwareModule as hardwareModule
import storm_control.sc_library.parameters as pa... |
b65c2cb8785594f84e72cc5c41301bd0d0453e36369c17bb8a34c10833278c48 | Python | 14,369 | 570 | #!/usr/bin/python3
#
import os
import sys
import argparse
import shutil
import numpy as np
from sklearn.neighbors import NearestNeighbors
from uac.element import Element
from uac import utils
# Create the parser
my_parser = argparse.ArgumentParser(description="UAC fibre mapping")
# Add the arguments
my_parser.add_ar... |
096bf594eff50279a5f2407ad3e586e26fc02b5aefa8fd63c11395ead1d68afa | Python | 14,383 | 277 | from typing import Callable, Dict, List, Optional, Tuple, Union
from torch_geometric.data import Data, FeatureStore, GraphStore, HeteroData
from torch_geometric.loader.link_loader import LinkLoader
from torch_geometric.sampler import NegativeSampling, NeighborSampler
from torch_geometric.sampler.base import SubgraphTy... |
829713d7f1950623dbdb8b1d3453c627599853391729b158344a2f927469a852 | Python | 14,384 | 371 | import numpy as np
import datajoint as dj
from getpass import getpass
class DJServer:
"""
DataJoint connection class which stores a connection to the specified
database and automatically adds expected schemas as attributes.
Args:
host (str) : String containing the URL of the databas... |
a650d87fc5dfd7be01d1f395c72380aa2ce0731d5ed39063d2dfe8cce4a25ccc | Python | 14,387 | 376 | from pathlib import Path
import numpy as np
import nibabel as nib
from dipy.core.gradients import gradient_table
from dipy.core.sphere import disperse_charges, HemiSphere
from dipy.io import read_bvals_bvecs
from dipy.reconst.dti import (TensorModel, fractional_anisotropy,
mean_diffusivity... |
777327ce65b58e013ae37806dd2e05751fe772498d517b4f4bcdd7b556dd94c2 | Python | 14,391 | 426 | # Copyright (c) Facebook, Inc. and its affiliates.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
import os
from typing import Sequence, Tuple, List, Union
import pickle
import re
import shutil
import torch
from pathlib import Path
import B... |
5f9dc4848cf30c8b5b381a8d96271a7bf69977f1bedefbe9cc54ffbf5cb987ca | Python | 14,392 | 393 | import glob
import math
import os.path
import tensorflow as tf
#Functions in this file is mostly based on https://towardsdatascience.com/a-practical-guide-to-tfrecords-584536bc786c
# and tensorflow docs
def _bytes_feature(value):
"""Returns a bytes_list from a string / byte."""
if isinstance(value, type(tf.c... |
7afd31353f6bc2b3530cc5b05308bba1a6872ccea7954b7922d257434b7f31e7 | Python | 14,398 | 469 | # coding=utf-8
import glob
import logging
import os
import re
import struct
from dipy.io.utils import is_header_compatible
import nibabel as nib
import numpy as np
from scilpy.gradients.bvec_bval_tools import str_to_axis_index
def load_fdf(file_path):
"""
Load a Varian FDF file.
Parameters
-------... |
d028a0ad5901daef1c0d8c1f628fcf39fe5254d4997150d50a2b39b0aa4441a3 | Python | 14,399 | 325 | """Tests for the LAION-fMRI benchmark registry and basic load paths.
The headline registry is 24 variants — 8 shared-pool ridge, 8 persubject-pool
ridge, 4 shared-pool RSA, and 4 shared-pool linear CKA. Non-headline variants (cluster_k5, per-OOD-category,
IT_full) live as factory functions and are exercised separately... |
4ef5da09089b4df5c659ceaf31b45cf32b4464d67b748d1110b3ecd34c1fad10 | Python | 14,401 | 357 | # -*- coding: utf-8 -*-
"""
Created on Fri Oct 21 15:03:57 2022
@author: lcmmichielsen
"""
from pathlib import Path
import argparse
import json
import numpy as np
import pandas as pd
from sklearn.model_selection import GroupKFold
import pysam
import tensorflow as tf
from basenji.dna_io import dna_1hot
parser = argp... |
b47ce53b8c47bcc975ad8339b1f8eb1ff82b6958772bbcd0338a8d72a3c5c051 | Python | 14,418 | 263 | import numpy as np
import torch
import torch.nn as nn
from torch.cuda.amp import autocast
import os
import wget
import timm
from copy import deepcopy
from timm.models.layers import to_2tuple,trunc_normal_
from .functions import ReverseLayerF
# override the timm package to relax the input shape constraint.
class Patc... |
06afde65ad33368cfa5033b6c5fa5c565253a0f61eedcbd9fbf982688c300442 | Python | 14,419 | 395 | # Copyright (c) Meta Platforms, Inc. and affiliates.
# All rights reserved.
# This source code is licensed under the license found in the
# LICENSE file in the root directory of this source tree.
import torch
import torch.nn as nn
import torch.nn.functional as F
from typing import Optional, Tuple, Type
from .common... |
db2684a753611f3221426c8d775819857923d6718cb1fc93c9916fb3857c4383 | Python | 14,419 | 380 | #! /usr/bin/env python3
"""
Implements function find_layer_contrast_roi and corresponding nipype interface FindLayerContrastRoi and command line interface.
"""
import sys
import os
from scipy.optimize import bisect, brentq
from nipype.interfaces.workbench import MetricResample
from nipype.interfaces.base import (
... |
1665ada2902722c9a8cd566c840e324d623ef2b12f7d9ae9f38b24aed0e39886 | Python | 14,420 | 395 | # Copyright (c) Meta Platforms, Inc. and affiliates.
# All rights reserved.
# This source code is licensed under the license found in the
# LICENSE file in the root directory of this source tree.
import torch
import torch.nn as nn
import torch.nn.functional as F
from typing import Optional, Tuple, Type
from .common... |
a58055c6ee2f34485736efe480a6eb0474048888a45c09028c794ee3e800dfbd | Python | 14,420 | 405 |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
SPDX-License-Identifier: MIT
SPDX-FileCopyrightText: © 2022 Boris Lenseigne, Renaud Bastien, Stephane Sanchez <stephane.sanchez@ut-capitole.fr>
Université Toulouse Capitole - Institut de Recherche en Informatique de Toulouse
Real Expression Artificial Life (REVA) Re... |
ef4f5743256bef90c02f8c578c5aa7480d4775c42bdc702a18ab5549b9f52879 | Python | 14,425 | 438 | # Copyright (C) CVAT.ai Corporation
#
# SPDX-License-Identifier: MIT
from __future__ import annotations
import json
from abc import ABC
from collections.abc import Callable, Sequence
from copy import deepcopy
from pathlib import Path
from typing import TYPE_CHECKING, Any, Generic, Literal, TypeVar, overload
from typ... |
839c9449d1a90a451a467a8bbcc3c779874c8c420beaf8c761b9c79f07cfe6d8 | Python | 14,427 | 289 | """Tests for correctness of Keypoints and BatchedKeypoints in fireants.io.keypoints."""
import pytest
import numpy as np
import SimpleITK as sitk
import torch
from fireants.io.image import Image
from fireants.io.keypoints import (
Keypoints,
BatchedKeypoints,
compute_keypoint_distance,
_compute_keypoi... |
37823dd461947a2edaddf9e324d09a98431a2fea5c096f97b44482bf130678bc | Python | 14,434 | 379 | """Backend-agnostic general ASE MCP server.
Uses :class:`~chemgraph.mcp.cg_fastmcp.CGFastMCP`. Tool functions are
plain computation -- the framework handles backend submission, future
resolution, and async job tracking.
This mirrors :mod:`chemgraph.mcp.mace_mcp_hpc` but exposes the full ASE
surface (selectable calcul... |
16f3ff65e01ba27d886614c082d37d68c9b8b1c17493999fc60a4ea81c27666c | Python | 14,436 | 443 | """ Sin-cos, fourier, rotary position embedding modules and functions
Hacked together by / Copyright 2022 Ross Wightman
"""
import math
from typing import List, Tuple, Optional, Union
import torch
from torch import nn as nn
from .grid import ndgrid
from .trace_utils import _assert
def pixel_freq_bands(
num... |
9441eba0948589792b5150d88e4532786a8f4adc78cd0424689cebec455e296f | Python | 14,437 | 248 | from brainvoice.visualization import gen_spectrogram_cmap, plot_spectrogram_on_axis, save_borderless
from brainvoice.spectrogram_utils import linearspectrogram, inv_linear_spectrogram, get_better_synth_hparams
from brainvoice.waveform_utils import write_waveform
from brainvoice.data.brainvoice_loaders import load_label... |
88ef68fb84853ee20f00ad191280d835e3ca10790a3a504e7e4a65e893438c92 | Python | 14,442 | 379 | """
EEG Multi-class Classification Script
=================================================
- Load preprocessed .npy data
- Feature extraction: Multi-band CSP , global stats , frequency features
- Classifier: KNN with grid search
- 5-fold stratified cross-validation, per-subject best results output
"""
import... |
f1468e61e61e3b8e1e983fa177f784157eb8ae72fc7179ac27f47fd8c93a8f66 | Python | 14,446 | 410 | """Convenience functions for model loading and prediction."""
import os
import warnings
import lightning as pl
import numpy as np
import torch
from hydra.utils import get_class, instantiate
from omegaconf import DictConfig, OmegaConf
from rich.progress import track
from mcmlnet.training.data_loading.preprocessing im... |
f164544932b3fc8f1423b60bbaca56eb78767cfb990c0481fb5c4f1e1179ac8c | Python | 14,446 | 488 | """Function related to TensorFlow datasets."""
import logging
import os
from typing import Dict, List, Optional, Tuple, Union
import numpy as np
from osl_dynamics.utils import misc
_logger = logging.getLogger("osl-dynamics")
def get_n_sequences(
arr: np.ndarray, sequence_length: int, step_size: Optional[int] ... |
f7bed85a7b27da6fa0fe06f95dd9798372dde45fc50a56a15fc2586ba8b54bdc | Python | 14,471 | 465 | # Copyright (c) Meta Platforms, Inc. and affiliates. All Rights Reserved
import json
from collections import defaultdict
from typing import Dict, List, Tuple
import torch
from pycocotools import mask as mask_util
# ============================================================================
# Utility Functions
# ==... |
b38f5f6ead3152194e9ac8e69ea2aca938d64f6d240fd26b393aaee1d62d4bb9 | Python | 14,474 | 468 | """GLM base class."""
from typing import Dict, List, Optional, Union
from dataclasses import dataclass
import numpy as np
from osl_dynamics.glm.ols import osl_fit, get_degree_of_freedom
# Helper functions for validation
def _validate_name(name: str) -> str:
if not isinstance(name, str):
raise TypeError(... |
fcc0ac42b692610bdccf7a6841b11d445cbac740199c928ce80c33f906e289ab | Python | 14,474 | 349 | ################## PURPOSE #################
# This script is to do PAIR comparisons using the three 3 caller CNVs files
# This script takes in the 3 caller CNVs files and put their content in to a nested dictionary.
# There are 3 dictionaries within the bigger dictionary , each dictionary is the content of a singular... |
1f5accdbf6a270738bb73be0abbdfbbe5081df5ff9a826820a3a850d381ad696 | Python | 14,475 | 329 | #!/usr/bin/python
# ----------------------------------------------------------------------------------------
# A class to load and parse predefined pump commands.
# ----------------------------------------------------------------------------------------
# Jeff Moffitt
# 2/16/14
# jeffmoffitt@gmail.com
# --------------... |
79c860ececb98938b80da7ec5e01dda4209f886c20e5137707310d8baae3917c | Python | 14,475 | 470 | from collections.abc import Sequence
from dataclasses import dataclass
from pathlib import Path
from typing import Any
import polars as pl
from sklearn.preprocessing import KBinsDiscretizer, StandardScaler
from eir.data_load import label_setup
from eir.data_load.label_setup import (
TabularFileInfo,
al_label_... |
fc732eeb03502738c712d8beed08e57222303ba2f415769f1fde2c0dfab48f2a | Python | 14,478 | 379 | import typing
from typing import Optional, Tuple, Union
import torch
import torch.nn.functional as F
from torch import Tensor
from torch.nn import Parameter
from torch_geometric.nn.conv import MessagePassing
from torch_geometric.nn.dense.linear import Linear
from torch_geometric.nn.inits import glorot, zeros
from tor... |
901822ef46881a4d6ac92637090495e81ba2da0757ca16e0f2537e76fc41fa1f | Python | 14,479 | 345 | import torch
import pandas as pd
import os
import csv # Add this import for CSV writer
from tqdm import tqdm # Import tqdm
def compute_rmse(predictions, targets):
"""
Compute Root Mean Square Error between predictions and targets.
Parameters:
- predictions: Predicted values
- targets: Target... |
4cb920e1260e882cd73f6672c5f635188efa52318adc36a6a28eb8738ec281cb | Python | 14,492 | 353 | import numpy as np
import sys
sys.path.append('/Users/denis/ownCloud/pfc-layers/analysis/fmri-analysis/library')
sys.path.append('/data/p_02389/code/fmri-analysis/library')
import voxeldepths_from_surfaces as vfs
import nibabel as nib
import os
from numba import jit, prange
from skimage.segmentation import expand_label... |
638777fc90684bf5f6bdd162495f11ae0ee0e7a4b99d54302ba83b34ece93df2 | Python | 14,494 | 405 | # Kai Sandbrink
# 2023-02-01
# This script takes a converged network with APE layer and mistrains the efficacy signal
# %% LIBRARY IMPORTS
import numpy as np
from datetime import datetime
import matplotlib.pyplot as plt
import os, random
import time
import wandb
import torch
from torch import nn
import torch.nn.func... |
3bda1e17ac84444e6a4592dcb3bbb8acc6c1a1de27e7bdfcece52abf7cc85c8d | Python | 14,508 | 290 |
class QMException(Exception):
pass
class Calculation:
"""
This class is going to store information about calculation input files
The default calculation run is expected to be like this
"""
multiplicity = 1 # make multiplicity a class variable
#Define solvent properties as a class attrib... |
dd97a09f6bfb2d0dbe20763a1eddac87cdc65edf2d604341a4589e8a2cde7834 | Python | 14,511 | 702 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Segment, mask and bin 'brain-KCc' files
"""
import os
import matplotlib.pyplot as plt
import numpy as np
import mbflim.utils as ut
import mbflim.visualization as vis
import mbflim.image.image_processing as pro
import mbflim.image.image_set_processing as setpro
impo... |
ae23ee58cbbb776f93e6944e77705fb825f23d5beb1a84a2d79eac0b9198505e | Python | 14,513 | 349 | import unittest
import numpy as np
import pandas as pd
from sklearn.datasets import make_classification
from sklearn.linear_model import LogisticRegression, LinearRegression
from causallib.metrics import weighted_roc_auc_error, expected_roc_auc_error
from causallib.metrics import weighted_roc_curve_error, expected_roc... |
ed58f55d311de55b9199062c79d0ec9e0377c9d1b11064c5b484d2ede71b67ec | Python | 14,513 | 417 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
@author: ajaver
"""
import numpy as np
import pandas as pd
event_columns = ['motion_mode', 'food_region', 'turn']
durations_columns = ['event_type', 'region',
'duration', 'timestamp_initial',
'timestamp_final', 'edge_flag']
... |
be7c28b2f60d3580bd0f87196cbc63702178887493c5daf1fb924709c830320e | Python | 14,518 | 293 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Mon Nov 21 09:28:15 2022
@author: mgruenig
"""
import tensorflow as tf
import os
GPU = '3'
os.environ['CUDA_VISIBLE_DEVICES'] = GPU # Use 3rd GPU
gpus = tf.config.experimental.list_physical_devices('GPU')
tf.config.experimental.set_memory_... |
01b6dc4f74db9aa167c3694454b72c1608fdbd342b3a8b5717b3722fb61226f4 | Python | 14,521 | 384 | import unittest
from zigzag.classes.workload.layer_node import LayerNode
class TestLayerNode(unittest.TestCase):
def test_CONV2D_1(self):
test_equation = "O[g][b][k][oy][ox]+=W[g][k][c][fy][fx]*I[g][b][c][ix][iy]"
test_loop_dim_size = {
"B": 2,
"K": 32,
"C": 64... |
3b5f87a402fb8722c115172d41b44dcd7a41c4c2c334089421c74a7c512de646 | Python | 14,522 | 325 | """Read a public Dropbox folder share link, one file at a time.
A folder share link looks like a dead end: the only *documented* unauthenticated
operation is downloading the whole folder as a generated zip, which for a real
dataset means tens of gigabytes and no way to take a part of it. Dropbox's own
web interface ob... |
a45aa24e225baa64f110b522f058f476f9bd51b39c3ea2e3019a72ee189429e8 | Python | 14,522 | 420 | ''' data processing for neuron project '''
# built-in
import sys
import os
import shutil
import six
# third party
import nibabel as nib
import numpy as np
import scipy.ndimage.interpolation
from tqdm import tqdm_notebook as tqdm # for verbosity for forloops
from PIL import Image
import matplotlib.pyplot as plt
# n... |
2cc5ab750b8e279ba5a4e56808c5700e27ced4b8486039d80429fe2d3a6768e7 | Python | 14,524 | 354 | # -*- coding: utf-8 -*-
import logging
from ast import literal_eval
from dipy.core.gradients import gradient_table
from dipy.reconst.csdeconv import (mask_for_response_ssst,
response_from_mask_ssst)
from dipy.reconst.mcsd import mask_for_response_msmt, response_from_mask_msmt
from d... |
e398d59236b4b79a90d570f66f6dfafc9a8b378e456113a0ce473b3eae928629 | Python | 14,527 | 417 | """
Module defining the operator view
"""
import typing
import asyncio
import datetime
import functools
from ..qt import *
import packaging.version
import numpy
PYQT_VERSION = packaging.version.parse(PYQT_VERSION_STR)
USINGLEGACY_QT = PYQT_VERSION < packaging.version.parse('5.11.0')
from .window import Window as Ta... |
0847c2ab55483060f93a45c2c89c3a3f32ae986e20cf065c9c0c0450b9f999a6 | Python | 14,531 | 494 | """
Recorder hooked into :func:`ProjectionProcessor.fitModel`.
Activation
----------
Set ``MUSCLEX_CAPTURE_FITS=1`` to enable. Optional env vars:
* ``MUSCLEX_CAPTURE_DIR`` -- where pickle files are written
(default: ``<repo>/musclex/tests/fitting_ab/fit_cases``).
* ``MUSCLEX_CAPTURE_TAG`` -- a string folded into ea... |
37950877fb45f2f5fff38758b4a58271a7747b6ac0dbfd11da30b5ed585f9417 | Python | 14,535 | 274 | from torch import nn
import torch
import torch.nn.functional as F
from torch_sparse import spmm
from model.basic import EGNN, EquivariantScalarNet, BaseMLP, aggregate, EGMN
class EquivariantEdgeScalarNet(nn.Module):
def __init__(self, n_vector_input, hidden_dim, activation, n_scalar_input=0, norm=True, flat=False... |
4e363b929ef5099e4ca63fef376ee569930a438c10a9c96044594f83b970da38 | Python | 14,549 | 398 | # Copyright (c) Meta Platforms, Inc. and affiliates.
# All rights reserved.
# This source code is licensed under the license found in the
# LICENSE file in the root directory of this source tree.
import torch
import torch.nn as nn
import torch.nn.functional as F
from typing import Optional, Tuple, Type
from .common... |
64f4f98451d4c52246743d9b8c346a0e44996288f309372a1a3f5438454032ab | Python | 14,550 | 398 | #!/usr/bin/env python
"""
Point Grey camera used in the context of a focus lock.
Hazen 09/19
"""
import numpy
import time
from PyQt5 import QtCore
import storm_control.sc_hardware.utility.af_lock_c as afLC
import storm_control.sc_hardware.utility.sa_lock_peak_finder as slpf
import storm_control.sc_hardware.pointGrey... |
2bb1c801250f87faa90e03a4afba51d99222370ba91839c867b4e5f0c2e347b5 | Python | 14,551 | 273 | from utils.env_config import * # Includes os
import yaml
import torch
from torch.utils.data import DataLoader, ConcatDataset, RandomSampler
from data.dataset import RotorBladeDatasetClean
from data.preanalysis.create_overview_data import filter_csv_by_intervals, plot_histogram_v1
import pandas as pd
import numpy as np... |
6c3bd6b893be456820bedd8ac6158806c7f6c7eef527ec36cd33252a43899dd4 | Python | 14,551 | 420 | """Plot labelled JHU mesh statistics inside an MNI152 glass brain.
Python example
--------------
from cvdproc.utils.python.visualization.plot_JHU_glass_brain import plot_jhu_glass_brain
plot_jhu_glass_brain(values=[...50 values...], output="jhu_stats.png")
plot_jhu_glass_brain(
values=[...50 values...],
signif... |
c388f9ff77740bb50a605c0efd826a8833e9a1bc4b98c2fb80e6205546d99376 | Python | 14,552 | 431 | #! /usr/bin/env python3
import logging
import torch
from sklearn.metrics import adjusted_mutual_info_score, normalized_mutual_info_score
from . import common_functions as c_f
from . import stat_utils
EQUALITY = torch.eq
def maybe_get_avg_of_avgs(accuracy_per_sample, sample_labels, avg_of_avgs):
if avg_of_avgs... |
107d9058ce996778ffae0bcbc91b63e2c4a54cb5f5ed6a0877243892e7804214 | Python | 14,555 | 465 | #Lucas Sancéré -
import csv
import json
import os
#depends on the env, could be
# from collections.abd import MutableMapping
import random
from collections.abc import MutableMapping
import numpy as np
from tqdm import tqdm
### Utils Functions
def checkdownsampling(originalimagepath: str, downsampleimagepath: str, ... |
67b879e688eed1adb307dc64035493f543d8c0b280ae52c3d6a48f19bbca055c | Python | 14,564 | 369 | import datetime
import subprocess
import tempfile
from collections import defaultdict
from pathlib import Path
from typing import Optional
import numpy as np
import pandas as pd
from .util import StationMapper, logger, set_cwd
try:
from obspy.taup import TauPyModel
from obspy.taup.taup_create import build_ta... |
6fd08c019469a87ec82ebeea3024cb40762cc0d9d111af04b7f3530aa5860ece | Python | 14,579 | 370 | """Tests for mcmlnet.utils.mc_runner module."""
import copy
import os
import shutil
import tempfile
import warnings
from itertools import product
from typing import Any
import numpy as np
import pandas as pd
import pytest
import torch
from mcmlnet.utils.mc_runner import RecomputeMC
class TestRecomputeMC:
"""Te... |
af096776fb366173b6be050d961d39b8d3a4d937f9aec796ebbc75e79af9f3ec | Python | 14,579 | 403 | import cv2
import numpy as np
import struct
from PySide6.QtGui import QImage, QPixmap
from PySide6.QtCore import QRunnable, Signal, Slot, QObject, QThreadPool, QThread, QTimer, QEventLoop
class BehavVideo(QObject):
fetch_frame_number = Signal(object)
new_frame_fetched = Signal(object)
run_worker = Signal(... |
14cd16491396e2e1b991b57b5fea4055ac5cf7a45e6625d0a79489f7963d7a39 | Python | 14,580 | 438 | # Copyright (c) Meta Platforms, Inc. and affiliates. All Rights Reserved
import math
from enum import IntEnum, unique
from typing import List, Tuple, Union
import numpy as np
import torch
from torch import device
_RawBoxType = Union[List[float], Tuple[float, ...], torch.Tensor, np.ndarray]
@unique
class BoxMode(In... |
603cc061884c7bae6b571a4c371f21953bac20fe5011a99c23a842df3dc95e38 | Python | 14,582 | 369 | import logging
import math
from functools import partial
import torch
from torch.optim import Optimizer
from torch.optim.optimizer import required
from torch.optim.lr_scheduler import _LRScheduler, ReduceLROnPlateau
log = logging.getLogger("flair")
class SGDW(Optimizer):
r"""Implements stochastic gradient desc... |
1adb76e889e4fec166c0436ca99ac85944e94dd4a39d8ef3d389507b9185bf44 | Python | 14,596 | 375 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
Photometry Control vs Test (portable GitHub-ready; paper-matched)
- Batch process raw CSVs in Control/Test folders
- Photobleaching correction
- Motion correction (405 -> 465 regression)
- Z-score normalization using a global baseline interval
- Saves per-anim... |
a057bdb5677bd787df76e245c4b5904d0071ea2a8947607b8f9e03b04e3609d7 | Python | 14,601 | 285 | import multiprocessing
import os
import socket
from typing import Union, Optional
import nnunetv2
import torch.cuda
import torch.distributed as dist
import torch.multiprocessing as mp
from batchgenerators.utilities.file_and_folder_operations import join, isfile, load_json
from nnunetv2.paths import nnUNet_preprocessed... |
2cae00f0c6b8a76feb991334fa4528345217bdf3be9f3bc512a9771424791156 | Python | 14,603 | 412 | """
Data structures to hold PLS inputs and results objects
"""
from multiprocessing import cpu_count
from textwrap import dedent
from .utils import ResDict
_pls_input_docs = dict(
decomposition_narrative=dedent(
"""\
The singular value decomposition generates mutually orthogonal latent
variables ... |
f5c00a887efe9d890f9b1326747d90d92eb517bfe54b254f59bf7d826aca7b11 | Python | 14,605 | 370 | import numpy as np
import pandas as pd
import os
from sklearn.model_selection import KFold
from sklearn.metrics import accuracy_score, f1_score, hamming_loss, label_ranking_average_precision_score, roc_auc_score, confusion_matrix
from sklearn.utils.class_weight import compute_class_weight
from imblearn.over_sampl... |
85e1310093f7b799dd1b6ab44244e22eb90ddfe1998baa945b0e6ec839c4a7bb | Python | 14,606 | 390 | import numpy as np
from pathlib import Path
import sys
import os
import scipy.io
from scipy.signal import butter, sosfilt
import mne
# For suppressing print statements within a function. Place function after - with HiddenPrints(): From https://stackoverflow.com/questions/8391411/how-to-block-calls-to-print
class Hidd... |
053a5dba8b8c481fe5d11e938d90d45e4bc04ef708192f52fe124b5b3c36fcfb | Python | 14,613 | 404 | from pathlib import Path
import pandas as pd
from tqdm import tqdm
from transformers import RobertaTokenizer, RobertaModel
import torch
import numpy as np
import os
from torch_geometric.data import Data, HeteroData
def get_data_dir(server_id):
if server_id == "206":
return Path("/new_temp/fsb/Twibot22-base... |
46868397a5b7b52531ba80668b3846ee7a5a15c5fb0344fb3505b34e5a6231e6 | Python | 14,614 | 321 | """Frozen, annotation-grounded image recipes for the published OpenPlant release.
No legacy processing script is imported or executed. In particular, this module
never renames source files, randomly splits images, or deletes source data.
"""
from __future__ import annotations
import csv
import gzip
import hashlib
imp... |
7fc9d203fcd95ced98c0a327686731fc2cfed7551d3317dc93e865d01e8c7278 | Python | 14,614 | 355 | from typing import List, Optional, Tuple, Union
import torch
from torch import Tensor
import torch_geometric.typing
from torch_geometric import is_compiling, is_in_onnx_export, warnings
from torch_geometric.typing import torch_scatter
from torch_geometric.utils.functions import cumsum
if torch_geometric.typing.WITH_... |
0124d86b3a167fa9dc195b6fa57f77805ab65361559aff829dc5770604b21574 | Python | 14,618 | 437 | from collections.abc import Callable, Generator, Iterable, Sequence
from copy import copy, deepcopy
from enum import Enum
from typing import (
TYPE_CHECKING,
Any,
Optional,
TypedDict,
)
import torch
from torch import nn
from torch.nn import Module
from torch.utils.data import DataLoader
from eir.setup... |
17d6e65809f62abd4a5fb6946f9631b54f430c0003d4a46df9ac4b021897a79d | Python | 14,622 | 472 | from unittest.mock import patch
import json
import numpy as np
import obspy
import pytest
import torch
import torch.nn.functional as F
from torch.utils.data import DataLoader
import seisbench.generate as sbg
import seisbench.models as sbm
import seisbench.util as sbu
from seisbench.util.dkpn_shared import _feature_a... |
f2965eecac61de3570939d84d37a558b1d6d069d4cc4ecdceeb99ab3279ecd58 | Python | 14,625 | 368 | import argparse
import numpy as np
from scipy.spatial import distance, distance_matrix
import time
from Bio.PDB.PDBParser import PDBParser
from PixelateResidue import *
from pyrosetta import *
init(extra_options="-constant_seed -mute all -read_only_ATOM_entries")
from pyrosetta.rosetta import *
from pyrosetta.rosetta.... |
f94e24a8f1853990b3feedab5d55cb5ef2e47515f5ae12231e6a897d58f3660b | Python | 14,634 | 316 | """ Mixup and Cutmix
Papers:
mixup: Beyond Empirical Risk Minimization (https://arxiv.org/abs/1710.09412)
CutMix: Regularization Strategy to Train Strong Classifiers with Localizable Features (https://arxiv.org/abs/1905.04899)
Code Reference:
CutMix: https://github.com/clovaai/CutMix-PyTorch
Hacked together by / Co... |
2f2d54f3230b55fa1f8d8d30253d46b0a03401aa10d743ce1a53010ee8ac654a | Python | 14,636 | 404 | from pathlib import Path
import pandas as pd
from tqdm import tqdm
from transformers import RobertaTokenizer, RobertaModel
import torch
import numpy as np
import os
from torch_geometric.data import Data, HeteroData
def get_data_dir(server_id):
if server_id == "206":
return Path("/new_temp/Twibot22-baseline... |
51663948ffb9adfbe673c5c6a41407b729cd8a83d80f08e83bab6536197f3dd0 | Python | 14,637 | 384 | #!/usr/bin/env python
from optparse import OptionParser
import glob
import pdb
import os
import random
import h5py
import numpy as np
from scipy.stats import cauchy
from basenji.emerald import EmeraldVCF
'''
sad5.py
Interfaces to normalized and population-adjusted SAD scores.
'''
class SAD5:
def __init__(self,... |
0445a0f877d259e2989c150bc3dbaa327bab0086ffc5b10463244e00dc23db45 | Python | 14,639 | 421 | """resnet in pytorch
[1] Kaiming He, Xiangyu Zhang, Shaoqing Ren, Jian Sun.
Deep Residual Learning for Image Recognition
https://arxiv.org/abs/1512.03385v1
"""
from types import FunctionType
from torch import Tensor
import torch.nn as nn
import numpy as np
import torch
from models import maxout_conv2d
#fro... |
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