sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
868fa1d06612aeaace93dc283133db053f815cebf8c5ebe464681ef260eca71c | Python | 8,658 | 211 | # coding=utf-8
# Copyright 2018 Google AI, Google Brain and Carnegie Mellon University Authors and the HuggingFace Inc. team.
# Copyright (c) 2018, NVIDIA CORPORATION. All rights reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the Lice... |
9fffe51a87880ebe45d6fbf9a1048384545b7ef98037da52d8a2274aaffdd655 | Python | 8,658 | 229 | # 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.
from typing import Sequence, Union
import numpy as np
import sklearn.metrics
from numpy import ndarray
import scipy.stats
import math
import ... |
3854c583b0f211a32a6656854dfb6bb9bbe905575d5985d42b02dd513da5ab11 | Python | 8,660 | 187 | import collections.abc
import functools
import json
import typing
import warnings
from pathlib import Path
import typing_extensions
from rnalysis import FROZEN_ENV
from rnalysis.utils import parsing
PARALLEL_BACKENDS = (
('multiprocessing', 'sequential') if FROZEN_ENV else ('multiprocessing', 'loky', 'threading'... |
9b111861ab8fc458254a1c499cc4e223994182fe48da7105cc034e435f51120b | Python | 8,661 | 227 | import numpy as np
import pytest
from scvi.data import synthetic_iid
from scvi.external import RESOLVI
@pytest.fixture(scope="session")
def adata():
adata = synthetic_iid(
generate_coordinates=True,
n_regions=5,
n_proteins=10,
)
adata.obsm["X_spatial"] = adata.obsm["coordinates"]
... |
beebec949688fcbfea335a3f12e46f7d719bea46c96dd5da10179600bf160519 | Python | 8,663 | 231 |
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import numpy as np
from scipy import ndimage
import random
from tractseg.libs import img_utils
def pad_and_scale_img_to_square_img(data, target_size=144, nr_cpus=-1):
"""
Expects 3D or 4D image as i... |
38e2240e6484354088c8e6a8df49fb8a92d31b67b9bd01b5943f3345964baa6a | Python | 8,667 | 189 | """
Name: Robert Kim
Date: 05-14-2023
Email: robert.f.kim@gmail.com
Script to quantify CEBRA-trajectory separation for attended vs. unattended
modality in the 2-modality DMS RNN. Computes bootstrap-style Euclidean
distances between condition centroids in each attention regime, then plots
them side-by-side as boxplots.... |
e74a66c910c6332469c529e02bf2b0a24d218ac0fe87e54eca47c860b4f78469 | Python | 8,667 | 225 | """
This module contains data processors for the training of Garfield model.
"""
from typing import List, Optional, Tuple
import scipy.sparse as sp
import torch
from anndata import AnnData
from torch_geometric.data import Data
from torch_geometric.transforms import RandomNodeSplit, RandomLinkSplit
from torch_geometri... |
b72ce83b577526adcb24db9a67f0d71514aceb29cf5be293c715f55fd63bf6b9 | Python | 8,669 | 241 | import numpy as np
import torch
from torch import Tensor
import torch.nn as nn
# from .._internally_replaced_utils import load_state_dict_from_url
from typing import Type, Any, Callable, Union, List, Optional
import torch.nn.functional as F
device = torch.device("cuda" if torch.cuda.is_available() else "cpu")
def co... |
de77ffb2ac80ddc602afadb87d3cf05df2e49ed351652cab8ddff9c15093336d | Python | 8,669 | 250 | # Copyright (c) 2017-present, Facebook, Inc.
# All rights reserved.
#
# This source code is licensed under the license found in the LICENSE file in
# the root directory of this source tree. An additional grant of patent rights
# can be found in the PATENTS file in the same directory.abs
from dataclasses import datacla... |
531e9046b8db9aa3bd114e3a7df83400ca12b1fd2370ea530f43c9f0c75521a2 | Python | 8,670 | 255 | from __future__ import annotations
import os
from pathlib import Path
from typing import TYPE_CHECKING
import pytest
from cleo.io.buffered_io import BufferedIO
from cleo.io.null_io import NullIO
from packaging.utils import canonicalize_name
from poetry.factory import Factory
from poetry.publishing.publisher import... |
ab903f077b1fb25ef719982783f590949910facadb224d51ae22d3625dd9464b | Python | 8,670 | 230 | import math
from functools import partial
from typing import Dict, Tuple
import haiku as hk
import jax
import jax.numpy as jnp
import optax
from ..device_utils import DEVICE_AXIS, replicate_on_devices, select_one_device
from ..geom import norm
from ..preprocess.augmentation import random_rotation_matrix
from ..types ... |
2275c851c7ebf9740a902a2fd13f2c44630626a817257a4244ff7efec15d4794 | Python | 8,671 | 230 | from typing import Dict, List, Tuple
import numpy as np
import pandas as pd
from BLEval.evaluator import Evaluator
from BLEval.data import EvaluationData
def _normalize(arr: np.ndarray) -> np.ndarray:
"""
Min-max normalize an array to [0, 1].
Parameters
----------
arr : np.ndarray
1-D a... |
0805102ab244f2bc2fa7a76af910de65779422627e1ce09cab96ef08cc65323f | Python | 8,678 | 281 | from scipy.spatial import KDTree
import numpy as np
from matplotlib.lines import Line2D
from matplotlib.patches import Patch
from graph_tool.all import Graph
from graph_tool.topology import max_cardinality_matching
from .figure_Tools import point_value_PMF_1darray
def nn_PMFs(ax, group, df, x0, x1, n_bins, n_boots):... |
b4fa7002cb01bfb80598754f0b8278fd0e37bab6f8fd5cc6f14fc67188bfea66 | Python | 8,688 | 226 | # /usr/bin/env python
'''
Written by Kong Xiaolu and CBIG under MIT license:
https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
'''
import os
import scipy.io as sio
import numpy as np
import time
import torch
import CBIG_pMFM_basic_functions as fc
def get_init(myelin_data, gradient_data, highest_order, init... |
479a6d8073def046639f4ef898fb8a02e442c7723efeee406da7ce4b1e2de5b5 | Python | 8,689 | 282 | from scipy.spatial import KDTree
import numpy as np
from matplotlib.lines import Line2D
from matplotlib.patches import Patch
import jax
from graph_tool.all import Graph
from graph_tool.topology import max_cardinality_matching
from .figure_Tools import point_value_PMF_1darray
def nn_PMFs(ax, group, df, x0, x1, n_bins... |
322bbbd29ab1a406d16204fcb324ab5a6c6f129a4e9210893a1692aa8fb26947 | Python | 8,690 | 261 | # -*- coding: utf-8 -*-
"""
Created on Mon Jul 15 15:16:22 2019
@author: 俊男
"""
# In[] Define the class for Simple Regressor
from sklearn.linear_model import LinearRegression
import pandas as pd
class SimpleRegressor:
__regressor = None
__y_columns = None
def __init__(self):
self.__regressor = L... |
b8c8d65ddaf84aa1f2dfde26b990ab83236bf769f817157745b90fab0f7f9a6d | Python | 8,690 | 283 | from scipy.spatial import KDTree
import numpy as np
from matplotlib.lines import Line2D
from matplotlib.patches import Patch
import jax
from graph_tool.all import Graph
from graph_tool.topology import max_cardinality_matching
from .figure_Tools import point_value_PMF_1darray
def nn_PMFs(ax, group, df, x0, x1, n_bin... |
cbc2ae7dffc5c1d605f832815fe18436c905e80e77140e9591f6072f87330e14 | Python | 8,690 | 229 | from pathlib import Path
import cv2
import numpy as np
import matplotlib.pyplot as plt
import xarray as xr
from skimage.segmentation import mark_boundaries
import dask.array as da
import decord
import click
from matplotlib.widgets import RadioButtons
from .lookup_utils import build_lookup_table, segment_image_with_lo... |
283fcd97dc81a9cebfa0e8a2e70f1436b652458c48f8cd4340921f49423d0838 | Python | 8,691 | 271 | """Pure unit tests for `d3text.schema`.
No data files, no network, no GPU: the schema is a leaf module over plain
dataclasses.
"""
import dataclasses
import pathlib
import pytest
from d3text.schema import EntityType, RelationType, Schema
ENZYMES = EntityType(name="enzymes", prefix="enz")
BACTERIA = EntityType(name... |
7d656bff8eedb1c5a925d964701389dee471301c41f92e9ac2022c75f455f38c | Python | 8,694 | 223 | import os
import glob
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
from scipy.io import loadmat
from scipy.stats import kruskal
import scikit_posthocs as sp
fig_dir = '/home/shared/instruction_timing/figures/fig6_review/'
os.makedirs(fig_dir, exist_ok=True)
# Models without feedforward inhib... |
ca293ab0d6bbec60cbec29b0d55d750ef2e63bbb8bdf250d32e30f42c085e0ff | Python | 8,694 | 226 | # /usr/bin/env python
'''
Written by Kong Xiaolu and CBIG under MIT license:
https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
'''
import os
import scipy.io as sio
import numpy as np
import time
import torch
import CBIG_pMFM_basic_functions as fc
def get_init(myelin_data, gradient_data, highest_order, init... |
160d065a452fc1e61181d0abb41e669ef55791d5844c5455ece43ed436f01864 | Python | 8,695 | 225 | """Reclassify organisms in the `other_organisms` fields of the doc database.
When one of those organisms is a bacteria in the NCBI taxonomy, move it to the
bacteria field of the document and add an entry for it in the `bacteria` table
of the database.
Similarly, if one of those organisms is a bacterial strain, move i... |
27f099b33c2c1ef235461a44ff77173c12909060ca1cf230b0a22ec6ac735958 | Python | 8,697 | 239 | """Tests for hessian.find_out_idx.
Pin down current behavior so a faster rewrite can be validated against it.
"""
import jax
import jax.numpy as jnp
import numpy as np
import pytest
from folx.api import (
JAC_DIM,
FunctionFlags,
FwdJacobian,
FwdLaplArgs,
FwdLaplArray,
)
from folx.hessian import f... |
6fabd8f07fa3b98f55ec98ef816e782d47b73e9cb2395df86abb1cb1ddbe83e4 | Python | 8,700 | 227 | # /usr/bin/env python
'''
Written by Kong Xiaolu and CBIG under MIT license:
https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
'''
import os
import scipy.io as sio
import numpy as np
import time
import torch
import CBIG_pMFM_basic_functions as fc
def get_init(myelin_data, gradient_data, highest_order, init... |
1336532453316465fdc0f165b8e2be2fde3cc9c5d30291b1d488d1e3b37372e5 | Python | 8,702 | 226 | # /usr/bin/env python
'''
Written by Kong Xiaolu and CBIG under MIT license:
https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
'''
import os
import scipy.io as sio
import numpy as np
import time
import torch
import CBIG_pMFM_basic_functions as fc
def get_init(myelin_data, gradient_data, highest_order, init... |
631b22deae0107f2e5957e154a73db88fbe009fd9fbb853a31b0b2c930c9344e | Python | 8,703 | 207 | """
config.py — Configuration for the cross-session pipeline.
All runtime settings are loaded from default.yaml (or a user-supplied YAML).
The Config dataclass defaults below are fallbacks only — edit default.yaml
to change behaviour.
Quick reference (see default.yaml for full documentation):
Datasets: bnci004 ... |
20b058b95c561beb08dd29fb580b351ac13e624ddaa3e04c1b77367d43edd090 | Python | 8,706 | 184 | from md.Simulator import Simulator
import openmm as mm
from openmm import unit as u
from openff.toolkit import Molecule
import argparse
import os
def submit_ligand(name, c1_idx, checkpoint_folder, output_folder, time, cpu, memory, idx, steps, force_constant, xi_0, start, number, ligand, seed):
simulation_folder = ... |
f86345bc7cf3fbd609c74130ddeeeebe4d499d7da06749f3752da87e0344b135 | Python | 8,706 | 222 | """Joint Embedding VAE module."""
from __future__ import annotations
from typing import TYPE_CHECKING
import torch
from scvi import REGISTRY_KEYS
from scvi.external.joint_embedding_scvi._utils import (
binomial_split,
cross_correlation_loss,
sample_thinning_probs,
variance_loss,
)
from scvi.module._... |
4bbe7f62fa5a2ccabb50a75fff34b099184e4e6fdb1e5c7719eb9fb50d126d24 | Python | 8,707 | 283 | from scipy.spatial import KDTree
import numpy as np
from matplotlib.lines import Line2D
from matplotlib.patches import Patch
import jax
import jax.numpy
from graph_tool.all import Graph
from graph_tool.topology import max_cardinality_matching
from .figure_Tools import point_value_PMF_1darray
def nn_PMFs(ax, group, ... |
7bea7370aa59cdd297bb5e91db82193567484b5b102c4bcefbef85280ad2d696 | Python | 8,707 | 222 | """
Extract HIPPIE latent embeddings for one or more datasets.
This example uses the public ``hippie.inference`` API. By default it pulls the
pretrained checkpoint from the HuggingFace Hub (``Jesusgf23/hippie``); pass
``--checkpoint`` to use a local ``.ckpt`` file instead.
Datasets must follow the canonical HIPPIE CS... |
eabb9dc1de1e4b9cb1292a251f43e0045763e2bdeccfc412a10a7e737f4a7c4b | Python | 8,709 | 313 | #Illustration of the spatial-jitter simulation pipeline
#%%
# Imports
import os.path as op
import numpy as np
import pyvista as pv
import mne
from pyvistaqt import BackgroundPlotter
from bfieldtools import sphtools as sph
import functions
import trimesh
import pkg_resources
import matplotlib.pyplot as plt
#%%
fon... |
3d2994207a5ed0379e58ada41281cad395862695f08f09f6568c91a836f13b6d | Python | 8,711 | 194 | """Real Qt items/events and actual mask autosave, without SAM2 inference."""
import os
from pathlib import Path
import sys
import tempfile
import unittest
os.environ.setdefault("QT_QPA_PLATFORM", "offscreen")
os.environ.setdefault("SEGREF3D_DISABLE_SAM2", "1")
sys.path.insert(0, str(Path(__file__).resolve().parents[1]... |
7eb9d53591d7cb5d868b6c76ecec279783d74e7efea2df0532eec0f28c927d5e | Python | 8,711 | 291 | #!/opt/anaconda3/bin/python3
import streamlit as st
import glob
import os
import read_lif
import numpy as np
import cv2
import matplotlib.pyplot as plt
import math
import plotly.graph_objects as go
import SessionState
from plotly.offline import plot
from skimage.measure import label, regionprops
from skimage import da... |
124192839069cbf972d51eb5adb74e2d795a737cb572726de3c464baa25a3b86 | Python | 8,713 | 283 | from scipy.spatial import KDTree
import numpy as np
from matplotlib.lines import Line2D
from matplotlib.patches import Patch
import jax
import jax.numpy as jnp
from graph_tool.all import Graph
from graph_tool.topology import max_cardinality_matching
from .figure_Tools import point_value_PMF_1darray
def nn_PMFs(ax, g... |
18eaf965e8a57cfd6f3793fe7d67a990088288b4b434f94c8b4c1d28005c2d36 | Python | 8,715 | 227 | # /usr/bin/env python
'''
Written by Kong Xiaolu and CBIG under MIT license:
https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
'''
import os
import scipy.io as sio
import numpy as np
import time
import torch
import CBIG_pMFM_basic_functions as fc
def get_init(myelin_data, gradient_data, highest_order, init... |
f0c7066c3e93ed786a081c10537d34d4f887ceacc83de19e0f70ef9be6ddee11 | Python | 8,715 | 205 | import os
import gzip
import pandas as pd
import numpy as np
import GEOparse
import json
import mygene
dest_dir = "__MS_GEO_ROOT__/Expression_Data"
def fast_parse_metadata(soft_path):
# Instead of reading the entire multi-GB array table, we just parse the soft file headers to get MS vs HC metadata
metadata = ... |
203ded2bda25edf64162019f862d8904970cfa4fb4b581442ef5cfd12baabdd4 | Python | 8,718 | 245 | from __future__ import annotations
import pytest
import torch
from torch import nn
import scvi.nn._base_components as base_components_module
from scvi.nn import FCLayers
# ---------------------------------------------------------------------------
# Basic forward behaviour
# -----------------------------------------... |
590898cb247223a92acdbdd0e48fb4a7cccc3afed1e64e23b57f15d7678cd94e | Python | 8,718 | 240 | import logging
import pandas
from patsy import dmatrices
import numpy
from numpy import dot as _dot, diag as _diag
import statsmodels.api as sm
from .. import Exceptions
from ..misc import Math
class Context(object):
def __init__(self): raise Exceptions.ReportableException("Tried to instantiate abstract Multi Ti... |
05fb2f0bfb0ab1136f0c66a7e6905507b9c470e7f78d295a7fb4c80f8f9a50fe | Python | 8,719 | 237 | """Fit OCE on perovskite or MOF feature matrices and report headline metrics.
Reads:
data/<subset>/features.npz — X (n,p), names, sizes, families
data/<subset>/feature_index.json — column metadata
data/<subset>/structures.json — energy_total_eV (when present)
Splits parent-stratified by `family` (to... |
2d3b64a2dea0d7f63ea0ec1f0eb2dc6c5d80f8e43da95bd2750da682e1020b79 | Python | 8,721 | 226 | # 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.
from functools import lru_cache
import numpy as np
import torch
from fairseq.data import Dictionary, data_utils
from . import BaseWrapperDat... |
e98e2ae1e90bd80d58235681ca2937bfced5117eb75ce92639ceab64d02808dd | Python | 8,723 | 241 | # Source code:
# https://github.com/zbmed-semtec/doc2vec-doc-relevance-training/blob/main/code/train_model/utilities.py
# This file includes the modifications to the source codes according to this project!
import tqdm
import gensim
import logging
import numpy as np
import pandas as pd
from scipy.spatial.distance impo... |
91867ac47a0ce36912d430539844d877964017b6b6ae2b79baf187b57d080b0e | Python | 8,726 | 251 | import os
import copy
import numpy as np
from PIL import Image
import matplotlib.cm as mpl_color_map
import torch
from torch.autograd import Variable
from utils.datasets import *
def convert_to_grayscale(im_as_arr):
"""
Converts 3d image to grayscale
Args:
im_as_arr (numpy arr): ... |
f0ba17d37069a4ebd73baf69c4c65edc42990fe4cd82613b7198655780f79562 | Python | 8,726 | 256 | #
# Copyright 2017 National Technology & Engineering Solutions of Sandia, LLC
# (NTESS). Under the terms of Contract DE-NA0003525 with NTESS, the U.S. Government
# retains certain rights in this software.
#
# See LICENSE for full license details
#
from __future__ import annotations
from dataclasses import dataclass, ... |
fba32a0a7204da2cdce35c7b3b3b4e46dea0b8c5704653a7fa3d65a16bbcf090 | Python | 8,728 | 262 | """
Various utilities for neural networks.
"""
from enum import Enum
import math
from typing import Optional
import torch as th
import torch.nn as nn
import torch.utils.checkpoint
import torch.nn.functional as F
from einops import rearrange, repeat
def equinorm(channels, ksize=5, pad=2):
"""
Make a standard... |
32862e565f4f462b800fb43a3d1e939f57c0103b070e9a0161dadd9e174f4d87 | Python | 8,729 | 226 | # /usr/bin/env python
'''
Written by Kong Xiaolu and CBIG under MIT license:
https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
'''
import numpy as np
import time
import torch
import os
import CBIG_pMFM_basic_functions as fc
def get_init(gradient_pc1, gradient_pc2, highest_order, init_para):
'''
Thi... |
e73e1850577c3e000424228de86c8ab7ce614c8e0223e067b2ff886fdb488f3e | Python | 8,737 | 182 | """R1-C6: stability of the KAN explanation across random seeds, CV folds and preprocessing choices.
Uses the PAPER's pipeline: paper2/loaders.py, the published group hold-out (seed 42, 30%), the
per-food preprocessing, and the compact 8-component equation front-end (interpret_food.EQUATION_NC).
Preprocessing and PLS a... |
1981aa8ec03024f0b59f249fe366118472e5ae153544fe77d8a76266c8099837 | Python | 8,738 | 315 | import argparse
from pathlib import Path
from scgpt.tokenizer import GeneVocab, random_mask_value
import sys
from datasets import Dataset, load_dataset
import os
sys.path.insert(0, "../")
parser = argparse.ArgumentParser()
parser.add_argument(
"-d",
"--data-source",
type=str,
required=True,
help='... |
e64830d7e14adc6db9b02b19e7cb6373e7dfc13e82060d847b6aba2b49c2288c | Python | 8,738 | 219 | """GUI tests for the Training dialog (window_utils.open_training_window).
Tests verify the dialog opens correctly with both panels (Segmentation
and Classification), dataset creation widgets, training parameter entries,
and action buttons.
"""
import pytest
from PyQt6.QtWidgets import (
QDialog, QRadioButton, QLin... |
02c16733a29569e9e2348f46e630af20154000e35b7b272933e0cbf5e1c0e0b1 | Python | 8,742 | 184 | # coding=utf-8
import os
import sys
sys.path.append("..")
sys.path.append("../utils")
import numpy as np
import cv2
import random
import torch
from torch.utils.data import Dataset
import config.cfg_lodet as cfg
import dataloadR.augmentations as DataAug
import utils.utils_basic as tools
from PIL import Image
import mat... |
cbe0058ae9cd2c737d628105a34a9418c7104aa4d4855129c51e45e871c262ec | Python | 8,742 | 268 | """Which compression actually suits the precomputed-embeddings store.
When this was written, `tensor_to_bytes` used fp16 + BITSHUFFLE + ZSTD
clevel 9 and achieved 1.145x, which is close to not compressing at all for a
second of CPU per document; the `CURRENT` row still measures that scheme. This
sweeps the alternative... |
dd5922ae1c88d60e8f9948342b8096fb71a7482f0107c90075b4d8a56a28b22f | Python | 8,743 | 210 | #!/usr/bin/env python3
"""
@file test_baseline.py
@author Simon Yu
@date 12/02/2024
@brief Script for testing baseline models.
"""
import argparse
import dataset
import header
import logger
import model
import sklearn.metrics
import torch
import tqdm
import type
import utility
import wandb
def getBinaryLabelsAt... |
506ec94547c8a12299722ddb35c6f6adc90580b8f2cab508f0f94add33c9cca7 | Python | 8,744 | 173 | #!/usr/bin/env python3
"""O canal de hibridação corrige o viés dos iodetos?
Protocolo do artigo: alvo `gap_reg` (gapadas sem misto_F), features / n_atomos,
CV agrupada por familia A/B, base wave15 como referencia.
TRES TESTES, em ordem:
1. NOS IODETOS (n~205) -- o regime onde o vies mora e onde o canal deve agir.
... |
a81d5ffa4701866f3c6b3ab8588438d7f6e9f6c99176fe50011744c95878cfd1 | Python | 8,750 | 270 | """
Copyright 2020 The Google Research Authors.
Copyright (c) Microsoft Corporation.
Licensed under the MIT License.
Based on code from https://github.com/yang-song/score_sde_pytorch
which is released under Apache licence.
Abstract SDE classes, Reverse SDE, and VE/VP SDEs.
Key changes:
- Adapted to work on batched p... |
4726d0385905aa1cafd6fb5aeeed1ad77b8d98587054b252c96237c1dc7e6850 | Python | 8,754 | 250 | ## To train model, run below.
import os
import torch
import random
import numpy as np
import time
from colab.utils import random_transform, gen_train_dataloader, DatasetSUPPORT_test_stitch
from colab.model import SUPPORT
from tqdm import tqdm
def train_SUPPORT(img, model_size=4, n_epochs=20):
random.seed(0)
t... |
ac133b20eca13cdb56550cba2d7c20da60d3b8636886e745fbd044cf123e789d | Python | 8,758 | 222 | import importlib.util
from pathlib import Path
import numpy as np
import pandas as pd
SCRIPT = Path(__file__).with_name("parameter_sensitivity_analysis.py")
def load_module():
spec = importlib.util.spec_from_file_location("parameter_sensitivity_analysis", SCRIPT)
module = importlib.util.module_from_spec(sp... |
cedb723ce29d81ab48d50ed54fe16373e73872666e922ebe9ef7fa9819fbdb05 | Python | 8,758 | 197 | # -*- coding: utf-8 -*-
from dipy.data import get_sphere
from dipy.reconst.shm import sh_to_sf_matrix
import numpy as np
from numba import njit
from scilpy.gpuparallel.opencl_utils import CLManager, CLKernel
from itertools import product as iterprod
import logging
class AsymmetricFilter():
def __init__(self, sh_o... |
d5bb5b26193b5215151474acd1ffb8d1b1e564ccd1415d8ccde94fc018401a03 | Python | 8,759 | 231 | """tests for vak.prep.spectrogram_dataset module"""
import pathlib
import pandas as pd
import pytest
import vak.common.annotation
import vak.common.constants
import vak.prep.spectrogram_dataset.prep
import vak.prep.spectrogram_dataset.spect_helper
from ...fixtures.annot import ANNOT_FILE_YARDEN
from ...fixtures.audi... |
2e1e446ae50815d4f4fa0b4a032ddfce37e06b95c76a05286e9e8afc2bb0d4da | Python | 8,763 | 211 | #!/usr/bin/env python3
"""Compare paired gmx_MMPBSA API results from two external result trees.
The comparison is deliberately independent of CSV formatting. It loads each
paired ``_GMXMMPBSA_info`` or ``COMPACT_MMXSA_RESULTS.mmxsa`` file through the
current public API and compares numeric cells in raw data, summarie... |
253b0d8f4de4ba456d83469566367980274ae12782616713ff2def8c40f07922 | Python | 8,765 | 271 | import numpy as np
import tensorflow as tf
import scipy.linalg as splin
from . import utils
def _soft_rectified_tanh(x, gamma=10.0):
return (1 / gamma) * tf.math.log(1 + tf.math.exp(gamma * tf.keras.activations.tanh(x)))
cos = tf.losses.CosineSimilarity()
mse = tf.losses.MeanSquaredError()
def SAD(y_true, y_... |
939ab437863b1ff0ba2bae2ca1b4c1ae5ee4e10b45d1238cf60a7fc27807a1c9 | Python | 8,772 | 268 | #########################
# In this script we train PVGG on ImageNet
# We use the pretrained model and only train feedback connections.
#########################
# %%
import torch
import torchvision
import torchvision.models as models
import torchvision.transforms as transforms
import wandb
from torch.utils.data impor... |
004b6c2dfc2aabbc988bf4bd01a43859b6dbcdae2d022328f170b11a8840f76b | Python | 8,774 | 275 | # 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 unittest
from copy import deepcopy
from dataclasses import dataclass
import pytest
from typing import Optional
from unittest.mock impor... |
ad1bf80fff990c6e482bd3ec779a41daf3a8e74cf4f2d51249f37e82de81684e | Python | 8,776 | 286 | """`batch_progress`: a bar for loaders that cannot report a batch count."""
import logging
from typing import Any
import pytest
import torch
from d3text import progress
from d3text.data.data import get_batch_loader
class FakeBar:
"""Records what a bar was told, instead of drawing one."""
instances: list["F... |
abc979810d7607cfb704a25e89e84fc6bdf72401d5aa4d8fff686c707a8f6650 | Python | 8,777 | 226 | # /usr/bin/env python
'''
Written by Kong Xiaolu and CBIG under MIT license:
https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
'''
import os
import scipy.io as sio
import numpy as np
import time
import torch
import CBIG_pMFM_basic_functions as fc
def get_init(myelin_data, gradient_data, highest_order, init... |
18b3522e197d72dc9ca037d4babb0d208e5b9be7a483624a44064d3aca9d289a | Python | 8,778 | 227 | # /usr/bin/env python
'''
Written by Kong Xiaolu and CBIG under MIT license:
https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
'''
import os
import scipy.io as sio
import numpy as np
import time
import torch
import CBIG_pMFM_basic_functions as fc
def get_init(myelin_data, gradient_data, highest_order, init... |
5a6d8a153f657118856a8210b814f0d13f2ddf4ae0b29af5d97f608727c85a17 | Python | 8,786 | 267 | from __future__ import annotations
import subprocess
from typing import TYPE_CHECKING
import pytest
from poetry.utils._compat import WINDOWS
if TYPE_CHECKING:
from cleo.testers.application_tester import ApplicationTester
from cleo.testers.command_tester import CommandTester
from pytest_mock import Moc... |
3a42ebf03542278cdd0d393e0cb86a1e8ce604ad57cd14d95d0f8eed92873e54 | Python | 8,789 | 268 | # 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 functools
import operator
import torch
import torch.nn.functional as F
from fairseq.modules.fairseq_dropout import FairseqDropout
from... |
a57e5e57c9b2fbb5338354379656d0ae3f2a81d96164b537b5a7293a49c1dc40 | Python | 8,789 | 227 | # /usr/bin/env python
'''
Written by Kong Xiaolu and CBIG under MIT license:
https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
'''
import os
import scipy.io as sio
import numpy as np
import time
import torch
import CBIG_pMFM_basic_functions as fc
def get_init(myelin_data, gradient_data, highest_order, init... |
135b602477b3c61ee877a55d76d029b3e656e94f0ecaa810bf6eafe607969f0b | Python | 8,791 | 226 | # /usr/bin/env python
'''
Written by Kong Xiaolu and CBIG under MIT license:
https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
'''
import os
import scipy.io as sio
import numpy as np
import time
import torch
import CBIG_pMFM_basic_functions as fc
def get_init(myelin_data, gradient_data, highest_order, init... |
aadac3ca6e1ad3b7a1e10dc56b9d936fb714f8243f1e57ce98f87cd994e25ee6 | Python | 8,794 | 228 | # /usr/bin/env python
'''
Written by Kong Xiaolu and CBIG under MIT license:
https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
'''
import os
import scipy.io as sio
import numpy as np
import time
import torch
import CBIG_pMFM_basic_functions as fc
def get_init(myelin_data, gradient_data, highest_order, init... |
9949e563ffc5940988a320809a4c40ee7e352011beed410dd279eb3285483472 | Python | 8,795 | 169 | # -*- coding: utf-8 -*-
# Form implementation generated from reading ui file 'ScheduleUI/beastScheduleUI.ui'
#
# Created by: PyQt5 UI code generator 5.9.2
#
# WARNING! All changes made in this file will be lost!
from PyQt5 import QtCore, QtWidgets
class Ui_Form(object):
def setupUi(self, Form: QtWidgets.QWidget... |
2a21519eaa796c24e097874a06740ede5a6991fe490ad0e9e36a56e062a5c961 | Python | 8,798 | 198 | import unittest
import sys
import os
import shutil
import re
if "DEBUG" in sys.argv:
sys.path.insert(0, "..")
sys.path.insert(0, "../../")
sys.path.insert(0, ".")
sys.argv.remove("DEBUG")
from metax.Person import Person
class TestPerson(unittest.TestCase):
def testPersonConstructor(self):
... |
1f169f7a30d66f306659fdeeab0852718ff6e8cf0dad25fd9817e78621e86777 | Python | 8,799 | 263 | """Reading a tagger's own spans out of an encodings-store group: the join
that feeds the linker a checkpoint's own detections rather than gold
mentions, from a corpus-prefixed group's windowed token ids to `TaggedSpan`s
grounded in that document's own text."""
import contextlib
import pathlib
import h5py
import numpy... |
0cc26631e9d22d727bbab662249adda84dbf4ad681b4c004b29cc34ff59a9b4f | Python | 8,807 | 287 | # 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 mmap
import os
import shutil
import struct
import typing as tp
from functools import lru_cache
import numpy as np
import torch
from fa... |
bb4acf275ea073c9a6325ae4c02483d6ce698e9e4b44cc2241a8b0ea105e79a2 | Python | 8,810 | 232 | #!/usr/bin/env python
# ENCODE DCC adapter trimmer wrapper
# Author: Jin Lee (leepc12@gmail.com)
import sys
import os
import argparse
import copy
from detect_adapter import detect_most_likely_adapter
from encode_lib_common import (
copy_f_to_dir, copy_f_to_f, log, ls_l, mkdir_p, read_tsv, rm_f,
run_shell_cmd,... |
99483d4a8f466a32a8ca517b6fac124545737e726bf8bb663775d52975bfac5c | Python | 8,812 | 234 | # /usr/bin/env python
'''
Written by Kong Xiaolu and CBIG under MIT license:
https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
'''
import os
import numpy as np
import time
import torch
import CBIG_pMFM_basic_functions_main as fc
import warnings
def get_init(myelin_data, gradient_data, highest_order, init_p... |
adecf64c6bab65b31740c321e568cf174f753d5617745aa5762d842339d68b53 | Python | 8,813 | 250 | #!/usr/bin/env python
#
# Copyright 2009, Google Inc.
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are
# met:
#
# * Redistributions of source code must retain the above copyright
# notice, this list... |
6c257bc4d5768d9e9b3fe2fea7c481ea914bee1eded4e81d34925f3fbcc7e10d | Python | 8,815 | 223 | """Phase 9 — off-criticality p sweep.
Vary site-occupation probability p around p_c on the honeycomb lattice
(C-AIREBO) to test whether:
(a) D_f → 91/48 ≈ 1.896 is unique to p = p_c (we expect yes)
(b) γ ≈ 0 holds at all p where the largest cluster grows with L
(we expect yes — it is a "compact dens... |
1ecf4a58e153da67ddc67ba264232642f74f991021323131dc5ff91e4711e1d0 | Python | 8,822 | 200 | import numpy as np
import torch
from torch.utils.data import DataLoader
import time
from pathlib import Path
from input_data_from_mesh import prep_input_data
from fit import fit, fit_with_early_stopping
from optim import *
from plotting import plot_field
def train(field_comp, disp, pffmodel, matprop, crack_dict, numr... |
5f5a82199bdb134e1cd16f89fd5031a0aa77241a957b929b0f271005d4ae4fc0 | Python | 8,825 | 242 | # 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 functools
from typing import Any, Dict, List, Tuple, Union
import torch
import torch.utils.checkpoint as checkpoint
from fairseq impor... |
b1dad386cac52f4730b9d592f0e8e3d188d265ea3a07b4e4b29004d44174155b | Python | 8,828 | 228 | from __future__ import annotations
import argparse
import csv
import json
import math
from pathlib import Path
ROOT = Path(__file__).resolve().parents[1]
MAIN_ROOT = ROOT / "results" / "revision_known_composition_benchmark"
REPEAT_ROOT = ROOT / "results" / "revision_known_composition_seed_repeats"
MANUSCRIPT_TABLE_D... |
c5a56d9fab089b74c694cfa2812429f461d75b678e6ddad04d45125ad96eef1d | Python | 8,832 | 253 | # 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 numpy as np
import torch
from . import FairseqDataset, data_utils
def collate(samples, pad_idx, eos_idx, fixed_pad_length=None, pad_... |
a63fdf3ef5322ed062f94bd958092b4bbfad7a19ad699e1c879dc27bac6fabf8 | Python | 8,834 | 242 | # 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 random
import json
import pickle
from tqdm import tqdm
import os
import numpy as np
class CaptionDedupProcessor(object):
"""remov... |
2a545f178638c7b4a73e7018abf816fcc9859b82a54e46dd81e5df15bcfb4694 | Python | 8,836 | 223 | #!/usr/bin/env python3
"""G2-cross-species — macaque → mouse counterfactual cell-type profiles.
For each overlapping cell type between a source (macaque, Lisberger src=3) and
a reference (mouse, Hausser src=1) dataset:
1. Encode all macaque cells of that type using their true source conditioning
(source_id = s... |
240114a6d6c912e01b45756719a3718245dd95e867e376164a30a7c80d688c16 | Python | 8,837 | 253 | # Copyright (c) Microsoft Corporation.
# Licensed under the MIT License.
import pytest
import torch
from torch_scatter import scatter_add
from mattergen.common.data.chemgraph import ChemGraph
from mattergen.common.data.collate import collate
from mattergen.common.data.transform import set_chemical_system_string
from ... |
745bc82075f7d28d7b3c7b3df461b44330c66393159fa1a58d677ec3bf569f8c | Python | 8,837 | 211 | from __future__ import annotations
from typing import TYPE_CHECKING
import torch
from torch import nn
from torch.distributions import Bernoulli, Normal
from scvi import REGISTRY_KEYS
from scvi.external.vivs._constants import VIVS_REGISTRY_KEYS
from scvi.module import VAE
from scvi.module.base import BaseModuleClass,... |
e2246533dee6508eee8e7529f8fd9ea362844ecd76445d3a227bbc7cd6654dbd | Python | 8,838 | 281 | from __future__ import annotations
import json
import re
from pathlib import Path
from typing import TYPE_CHECKING
from typing import Any
from urllib.parse import urlparse
import pytest
import responses
from packaging.utils import canonicalize_name
from poetry.repositories.legacy_repository import LegacyRepository... |
f3767e70c753786e94a4d7d1d5fc3dfb0114da5051fc186cf5dec5d979b2de84 | Python | 8,840 | 263 | #!/usr/bin/env python3
"""
Profile external models (params/FLOPs/peak memory) with dummy inputs.
Examples:
# MONAI UNETR (if monai is installed)
python profile_external_models.py \
--model monai.networks.nets.UNETR \
--model-kwargs '{"in_channels":1,"out_channels":3,"img_size":[96,96,96],"feature_size":16}... |
82a1a58c379682b41962792cff9910b736418c432424008bbbec019e51431f8d | Python | 8,842 | 211 | import numpy as np
import numpy.polynomial.polynomial as poly
import matplotlib.pyplot as plt
import sys
def LyE_R(X,Fs,tau,dim,*args):
"""
inputs - X, If this is a single dimentional array the code will use tau
and dim to perform a phase space reconstruction. If this is
... |
82a31ba2809915301d89b991070652b70640f34c9dbd99c9d9a1426dd4534f99 | Python | 8,849 | 234 | # /usr/bin/env python
'''
Written by Kong Xiaolu and CBIG under MIT license:
https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
'''
import os
import numpy as np
import time
import torch
import CBIG_pMFM_basic_functions as fc
import warnings
def get_init(myelin_data, gradient_data, highest_order, init_para):... |
1d101d63efce7fbbbfc643a3865ad24fe3fa6e4c48eeec1d6b627f38edad7cda | Python | 8,855 | 286 | import os
from copy import copy
import itertools
import pandas as pd
import numpy as np
import torch
import torch.nn as nn
import torch.nn.functional as F
import torch.utils.data as data
import torch.distributions as dist
import torch.optim as optim
import torch.utils.data
from tqdm.auto import tqdm
from torchvision i... |
e26a93ce59a9e409788afb0f01c4dfa6f2bec16d9c5cc26b0e6a5cb7a1793478 | Python | 8,857 | 235 | # 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 numpy as np
import torch
import torch.nn as nn
import torch.nn.functional as F
from fairseq import utils
from fairseq.data import encod... |
5c955c96b2bdab816dbb107d4a7cbd6b6419629c89ea0ed01301ec2525855af9 | Python | 8,860 | 268 | #########################
# In this script we train PVGG on ImageNet
# We use the pretrained model and only train feedback connections.
#########################
# %%
import torch
import torchvision
import torchvision.models as models
import torchvision.transforms as transforms
import wandb
from torch.utils.data impor... |
8fecd815bb579644f645f4027d4b41e86fbcac6d075dba333670d75c30d6ac25 | Python | 8,860 | 246 | from __future__ import annotations
import inspect
import logging
import os
import warnings
from typing import TYPE_CHECKING
import anndata
import mudata
import numpy as np
import pandas as pd
import torch
from anndata import AnnData, read_h5ad
from scvi import settings
from scvi.data._constants import _SETUP_METHOD_... |
79efa5308fa60cca390f3448f680d89cb6e4e32436a36b4886b02fbb70bbf806 | Python | 8,861 | 344 | project = "Neuroglancer"
copyright = "2021 The Neuroglancer Authors"
version = ""
release = ""
import typing
from typing import NamedTuple, Optional
import os
import re
import sys
import docutils.nodes
import sphinx.application
import sphinx.addnodes
import sphinx.domains.python
import sphinx.environment
os.environ... |
e7013cd5c2e809ba567414ef4e37d494a855dda46d07ac9f2a8b7ecf3918419b | Python | 8,861 | 241 | import tqdm
import gensim
import numpy as np
import pandas as pd
from scipy.spatial.distance import cosine
from gensim.models.doc2vec import Doc2Vec, TaggedDocument
from typing import Union, List
import logging
# Retrieves cleaned data from RELISH and TREC npy files
def process_data_from_npy(file_path_in: st... |
b93ba217023f1a94e4242899d864e4e664fc03f6cac98906cd5ca644b936a121 | Python | 8,862 | 288 | """
This module contains methods used in analysis windows or in report in Email
module.
Calculation of d' is left as commentar in
weighted_binned_performance method.
"""
"""
Copyright (c) 2019, 2022 [copyright holders here]
This file is part of NoSeMaze.
NoSeMaze is free software: you can redistribute it and/or
mo... |
f54f46e198e8ed6632eafcdb5299a4eec25ab12e0f6252d4dd49e14d87d6b7bb | Python | 8,865 | 234 | # /usr/bin/env python
'''
Written by Kong Xiaolu and CBIG under MIT license:
https://github.com/ThomasYeoLab/CBIG/blob/master/LICENSE.md
'''
import os
import numpy as np
import time
import torch
import CBIG_pMFM_basic_functions as fc
import warnings
def get_init(myelin_data, gradient_data, highest_order, init_para):... |
d81758a334911aa9dd3b0bf5e74af45516b1be2dd010164fe47661ddbdfb848c | Python | 8,866 | 222 | #!/usr/bin/env python3
"""
Author: Ken Chen
Email: chenkenbio@gmail.com
"""
import argparse
from tqdm import tqdm
import os
import sys
import pickle
import numpy as np
import torch
from torch import Tensor
import torch.nn as nn
import torch.nn.functional as F
from torch.utils.data import DataLoader, Dataset, Subset
fr... |
8c0b24277a4d9eaef2176be038af5b082acd071f331922eb075a38fdb3f9c59c | Python | 8,868 | 253 | """
Vocabulary backend compatibility module for scGPT.
This module prefers torchtext as the GeneVocab base class only when it is
actually usable (import succeeds and the Vocab type is subclassable).
Otherwise it falls back to a pure-Python implementation.
Why fallback is needed:
----------------------
torchtext <=0.1... |
a642fb52ac0eb332b9b137f7f64a977ae6db7cab773bf315fea5c567badcc355 | Python | 8,871 | 322 | import networkx as nx
import numpy as np
import pandas as pd
import pytest
from joblib.externals.loky import get_reusable_executor
from pgmpy.estimators import TreeSearch
from pgmpy.example_models import load_model
from pgmpy.factors.discrete import TabularCPD
from pgmpy.models import DiscreteBayesianNetwork
from pgmp... |
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