sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
1da1917cc1df93bd42f10e87e5d454aab3d006998a107a1922dda5e044a359ec | Python | 3,099 | 119 | import os
import sys
import pandas as pd
#sys.path.append('C:/Users/User/Dropbox/PC (2)/Documents/GitHub/BBC')
# define starting datafolder
#this is the directory
import os
import platform
platform.system()
# define starting datafolder
if platform.system()=='Darwin':
os.chdir('/Volumes/BBC/BBC/WP1/data/EEG... |
cd41317345ab1df5b19c55026ff2252a404c20b5a8abf024757c83b1ba477ffa | Python | 3,100 | 75 | # fit probablistic representation manifold (PRM) of the grid cell population in different speed bins
import numpy as np
import matplotlib.pyplot as plt
import os
import copy
import hickle as hkl
from grid_cell.speed_partition_processor import Speed_Partition_Processor
from grid_cell.manifold_fitter import GP_Fitter
fro... |
163e20ec90b3afd9b3b8b2c92cc3f49885a8b16e81c6d6e07844f92e20118f83 | Python | 3,101 | 76 | import numpy as np
import pandas as pd
from enum import Enum
import tensorflow as tf
from tensorflow import one_hot
from tensorflow.python.keras.layers import Concatenate
from utils.constants import GLM_HMM_SIMULUS_VALUES
class CognitiveModel(Enum):
PRL4 = 1
PRL_foraging_dynamic = 2
HRL2 = 3
GLM_HMM... |
645235a338bc6dec8765570fa239393406ee6cd89315b54522a147a0856e8f07 | Python | 3,101 | 92 | from medperf.exceptions import InvalidArgumentError
import pytest
from medperf.tests.mocks.dataset import TestDataset
from medperf.tests.mocks.training_exp import TestTrainingExp
from medperf.commands.dataset.associate_training import AssociateTrainingDataset
PATCH_ASSOC = "medperf.commands.dataset.associate_training... |
ac84352fb28bc0ea5ab0d441358d1c6d85a49d7f9f737e65178524a6466e41b6 | Python | 3,101 | 94 | """Unit tests for FrameSourceRead provider."""
import ase
import msgpack
import numpy as np
import pytest
from zndraw.providers.frame_source import FrameSourceRead
@pytest.fixture
def water():
"""Simple water molecule for testing."""
return ase.Atoms("H2O", positions=[[0, 0, 0], [1, 0, 0], [0, 1, 0]])
@py... |
cfd374d0917a052f5f52937531b0f1bd04797f0d25536c077ec164913d833920 | Python | 3,101 | 93 | # Script to fit the maximum correlation between diffraction patterns to solve for strain, tilt_lr, and tilt_ud
# This method was developed by Tao Zhou (tzhou@anl.gov)
import os
import numpy as np
from math import *
import time
from skimage import io
# Data folder
folder = '/SOME_PATH/NanobeamNN/data'
# Load the expe... |
f3440ed22ade871052886cd0a692d22318648a9f9fca5877a5c972543e0104f6 | Python | 3,101 | 80 | #!/usr/bin/env python
# Noise2Void - 2D Example for RGB Data"
# Using TensorFlow backend
from n2v.models import N2VConfig, N2V
import numpy as np
from csbdeep.utils import plot_history
from n2v.utils.n2v_utils import manipulate_val_data
from n2v.internals.N2V_DataGenerator import N2V_DataGenerator
from matplotlib impor... |
5729d20b7d9101bba6e6fb9b5d7d2be27612a2473d09abb2ae79290e866b8129 | Python | 3,102 | 87 | from collections.abc import Mapping, Sequence
from typing import List, Optional, Union
import torch.utils.data
from torch.utils.data.dataloader import default_collate
from .batch import Batch
from .data import Data
from .dataset import Dataset
class Collater:
def __init__(self, follow_batch, exclude_keys):
... |
86ac8d0ab2db585087d524a61a1cab612b4d2d21b6333e55af48086582e08ae1 | Python | 3,102 | 107 | # Configuration file for the Sphinx documentation builder.
# -- Project information
from os.path import dirname, abspath, join
from sys import path as syspath
# import time
# from datetime import datetime
from sphinx.application import Sphinx
# If extensions (or modules to document with autodoc) are in another direc... |
baf19318f473eb25a4c8c9f5a6e18f3098efb77c634d0f1d7cc48a02cdc77bca | Python | 3,102 | 80 | #!/usr/bin/env python
# Noise2Void - 2D Example for RGB Data"
# Using TensorFlow backend
from n2v.models import N2VConfig, N2V
import numpy as np
from csbdeep.utils import plot_history
from n2v.utils.n2v_utils import manipulate_val_data
from n2v.internals.N2V_DataGenerator import N2V_DataGenerator
from matplotlib impor... |
52af3086407d5ff135aa1e2f16c89c2e80069569bfa7599c6e41d70cc3e96b82 | Python | 3,105 | 73 | """Shared plumbing for serving a pipeline step's result view on the persistent main app.
Each step that shows results after its compute job (preprocess, transients, …) opens a
browser tab on a dedicated route of the always-running main server. The compute job and
the server share the main process, so the per-tab conte... |
fa1040cf252426a466033d46d4ebb487cc8c980e65c2ad0d5f6d37f22130c217 | Python | 3,106 | 118 | import os
import re
import yaml
import time
import numpy as np
import pandas as pd
import pathlib as pl
import subprocess as sp
from matplotlib import pylab as plt
configFilePath = None
def changeWorkingNetwork(network='Gazer'):
"""
"""
if network == 'Gazer':
global configFilePath
configF... |
d33ca598aec67659b2bf5991e166fb21de1f7f1af3a32397af1c68030d30655d | Python | 3,107 | 96 | # -*- coding: utf-8 -*-
"""
Created on Wed Sep 25 11:36:10 2024
@author: AC
"""
import pandas as pd
from sklearn.model_selection import train_test_split
from sklearn.naive_bayes import GaussianNB
from sklearn.metrics import accuracy_score, precision_score, recall_score, f1_score, confusion_matrix, roc_auc_s... |
9d79ea1e5c54f83ca0c1e2c0b25d265f6ef532d4943b6042c4ccf9b5e1ec195a | Python | 3,109 | 67 | import numpy as np
import pandas as pd
import pytest
from guppy.analysis.group_tables import stack_member_tables, summarize_member_tables
@pytest.fixture
def member_tables():
"""Two members' tonic means over the same two epochs, listed in different orders."""
first = pd.DataFrame(
{"mean_zscore": [1.... |
a479981a2ec7da92ce9035d6f458b5df650be6eef2be487e09647a508c6e0e85 | Python | 3,109 | 73 | #!/usr/bin/env python3
"""
after downloading redcap data, convert it into table for Inclusion Enrollment Report
# multiindex
# grab rows that have "Consent" in it. "
# TODO: insert columns
# calculate totals
"""
import os, sys, glob
import itertools
import pandas as pd
import numpy as np
import datetime
from pathlib i... |
5cc2a154fe5be231e1fcc151db78def17947fc466abed077fc23c9b888b408f7 | Python | 3,111 | 69 | #!/usr/bin/env python
"""
extract dvars and fd info from fmriprep_confounds_timeseries
calculate mean and append it with BIDS data
"""
__author__ = "Heejung Jung, Owen Collins"
__copyright__ = "Spatial Topology Project"
__credits__ = [""] # people who reported bug fixes, made suggestions, etc. but did not actually wri... |
9d1061b9b368c9b5aabb47fe3c688205741166abc8fe2c649e5636ce9e0eccfb | Python | 3,111 | 123 | import shutil
import tempfile
from collections.abc import Callable, MutableMapping
from io import StringIO
from typing import cast
import pytest
from cwl_utils.types import CWLObjectType, CWLOutputType
from cwltool.main import main
from cwltool.secrets import SecretStore
from .util import get_data, needs_docker, nee... |
fb7b6563b8b825c4b33a69554dcd62eb1c6234ccd8eabb3eaa7a2d6521a967f3 | Python | 3,111 | 96 | import os
# os.chdir('../..')
import sys
sys.path.append(os.path.abspath("/home/harryc/github/CCF_translator/"))
import os
from brainglobe_atlasapi.bg_atlas import BrainGlobeAtlas
import CCF_translator as CCF_translator
import nibabel as nib
import numpy as np
import nrrd
import requests
import io
import tempfile
... |
8b49e0d057664422e6710acdb9ae32b6dd6fe7d6eefda25a53a6932c91459a38 | Python | 3,112 | 75 | #!/bin/env python
import pickle
import utils
file = open('../database.pickle', 'rb')
database = pickle.load(file, encoding='latin1')
file.close()
utils.convert_to_json('../database.pickle', '../database.json')
#Put it in a nice table for easy parsing. Use semicolons to separate fields, making sure each individual fi... |
cf4d28338c354b8fc5244394dc6ea51b91f0c23acae447d5b29642bbf65a42d1 | Python | 3,112 | 78 | """Utilities for preprocessing sequence data.
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
from keras_preprocessing import sequence
from .. import utils
pad_sequences = sequence.pad_sequences
make_sampling_table = sequence.make_sampling_table
skipgra... |
54054857fe76a564a4dc7f0401fa8a0203355230af84dde1750809a30debb2ac | Python | 3,114 | 88 | from PyQt5 import QtGui, QtWidgets, QtCore
import pyqtgraph as pg
import numpy as np
from copy import deepcopy
from util.conf import fs_fft_params
from util.functions import movingAverage
from features.Feature import Feature
class PowerSpectrum(Feature):
def __init__(self, data, parent=None, liveplot=None):
... |
5a55d441f8f3e63ad9f1b5bdd5e22267e2a512f0b3a623710f98d383cfecc41f | Python | 3,114 | 105 | import os
import sys
import numpy as np
import yaml
# Parameters to randomly screen
num_configs = int(sys.argv[1]) if len(sys.argv) > 1 else 10
mode = sys.argv[2] if len(sys.argv) > 2 else "w" # Default to overwrite mode
output_dir = "screen_configs"
os.makedirs(output_dir, exist_ok=True)
# Initialize RNG for repro... |
96c176b0bd70c06933a97a49475945f82314d60b529ee4ec251cf0c7d773e058 | Python | 3,117 | 110 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
import tensorflow as tf
from tensorflow.keras.losses import Loss
# =============================================================================
# distance calculations
# =============================================================================
de... |
9f431a4ec05abdb6ef0f3341efaabcc8644c0949bbf02dba96a4f3ff04a57d19 | Python | 3,117 | 99 | """Utilities for the XGBoost Dask interface."""
import logging
import warnings
from typing import Any, Dict, Optional, Tuple
import distributed
from ..collective import Config
LOGGER = logging.getLogger("[xgboost.dask]")
def get_n_threads(local_param: Dict[str, Any], worker: "distributed.Worker") -> int:
"""G... |
1e6ac473b4e918b296b4d9417dc67ec0735896795b9c65d2039ec21a1582cabd | Python | 3,118 | 81 | import csv
import logging
import requests
from src.babel_utils import make_local_name
from src.util import ensure_parent_dir
def readlabels(which):
swissname = make_local_name(f"UniProtKB/uniprot_{which}.fasta")
swissprot_labels = {}
with open(swissname) as inf:
for line in inf:
if l... |
3b76efba132a953033268bcd62a6faca16b8841b61684ba25a0fc90c247bd3a4 | Python | 3,120 | 85 | import torch
import torch.nn as nn
from nnunet_mednext.network_architecture.custom_modules.custom_networks.nnFormer.nnFormer_tumor import nnFormer as nnFormer_Orig
from nnunet_mednext.training.network_training.nnUNet_variants.architectural_variants.nnUNetTrainerV2_noDeepSupervision import \
nnUNetTrainerV2_noDeepSu... |
77fc2b7949cc523a7085902a5cb31ab45b808efdfa2a690193dcf8c30c6c4b00 | Python | 3,121 | 88 | # -*- coding: utf-8 -*-
import urllib, json
import http.cookiejar as cj
class CatmaidInstance:
""" A class giving access to a CATMAID instance.
"""
def __init__(self, srv, catmaid_usr, catmaid_pwd,
http_usr=None, http_pwd=None):
# Store server and user information
self.server ... |
ba2bafe39001818a7d80002ada5b77766d99545d9cce2779704de9df37a52b9e | Python | 3,121 | 108 | # SPDX-License-Identifier: Apache-2.0
import cv2
import numpy as np
from skimage import transform as trans
def parse_lst_line(line):
'''
Helper function for line parsing
'''
vec = line.strip().split("\t")
assert len(vec)>=3
aligned = int(vec[0])
image_path = vec[1]
label = int(vec[2])
bbox = None
... |
e09081fc552544f4dadcc9f61979486d4bf19e6b66c50add0bf0b49a8357a6e3 | Python | 3,121 | 89 | # Atlas-related PyQt5 threads
from typing import Any, Callable, Optional, Sequence, TYPE_CHECKING
from PyQt5 import QtCore
from magmap.atlas import ontology
from magmap.settings import config
if TYPE_CHECKING:
from magmap.plot import plot_support
_logger = config.logger.getChild(__name__)
class RemapLevelThre... |
3e1c7bced382f7f471ccf8f1ddd5607c026e2778a4a0e568f63efa3d5d8d1685 | Python | 3,122 | 121 | # -*- coding: utf-8 -*-
# @Author: Theo Lemaire
# @Date: 2023-11-10 17:02:12
# @Last Modified by: Theo Lemaire
# @Last Modified time: 2023-11-21 15:03:15
import re
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
import seaborn as sns
'''
Reproduction of experimental data from:
Owen et al., ... |
5d2793b873ce5b9dee48275ee399eb1bc7e7d4d07bf093efc2082c87d8cbe91e | Python | 3,122 | 77 | import os
from medperf.entities.dataset import Dataset
from medperf.utils import sanitize_path, tar, generate_tmp_path
import medperf.config as config
from medperf.exceptions import ExecutionError, MedperfException
import yaml
class ExportDataset:
@classmethod
def run(cls, dataset_id: str, output_path: str):
... |
823085b654b38a51edb0653cf7559579f928b824fb98cf592216983269091325 | Python | 3,123 | 69 | import torch
import torch.nn.functional as F
from fengshen.models.transfo_xl_paraphrase import TransfoXLModel
from fengshen.utils import top_k_logits, get_masks_and_position_ids
from transformers import T5Tokenizer
def get_batch(context_tokens, mem_length, batch_size=1):
tokens = context_tokens
tokens = token... |
b2c05a69e5214c1c5e5d037b8fab708cb00d8d33e1551ebfc633a5acc30e5a01 | Python | 3,125 | 111 | """Checking the gradient steps for pypesto"""
import amici
import matplotlib as mpl
import numpy as np
import time
import petab
import logging
import pypesto.optimize as optimize
import pypesto.petab
import pypesto.profile as profile
import pypesto.sample as sample
import pypesto.store as store
import pypesto.visualiz... |
94b70bfd06c164221df8e45abe644a0609dba172d1bd58f0edcab50ae6891a97 | Python | 3,127 | 86 | import numpy as np
import time
from . import _eval_protocols as eval_protocols
def generate_pred_samples(features, data, pred_len, drop=0):
n = data.shape[1]
features = features[:, :-pred_len]
labels = np.stack([ data[:, i:1+n+i-pred_len] for i in range(pred_len)], axis=2)[:, 1:]
features = features[:,... |
3bfbffee384ebe42c1caaed422fda18ee18b92ab76d230dd1096d8f73283e0bd | Python | 3,129 | 81 | import pyoxigraph
from src.babel_utils import parse_rdf_literal, pull_via_urllib
from src.categories import MOLECULAR_ACTIVITY
from src.prefixes import EC
def pull_ec():
pull_via_urllib("https://ftp.expasy.org/databases/enzyme/", "enzyme.rdf", subpath="EC", decompress=False)
class ECgraph:
"""Load the mesh... |
49f14f3153c2d1baa579c6c0dc6d0f1193e8c3085332e5e9e936e27bd9d858db | Python | 3,129 | 76 | import numpy as np
import gpflow
import tensorflow as tf
from tensorflow_probability import distributions as tfd
from grid_cell.gaussian_wishart.src.likelihoods.WishartProcessLikelihood import WishartLikelihood
from grid_cell.gaussian_wishart.src.models .SVGP_deprecated import SVGP_deprecated
class WishartProcessBase(... |
c87f45c9b8d754d1b6bbf5f2804f7e48b6cdb8926c72eedb40bb66972368a48e | Python | 3,130 | 107 | import os
import pytest
from kgx.transformer import Transformer
from tests import RESOURCE_DIR, TARGET_DIR
from tests.unit import clean_database
from kgx.config import get_logger
from tests.integration import (
check_neo4j_container,
NEO4J_CONTAINER_NAME,
DEFAULT_NEO4J_URL,
DEFAULT_NEO4J_USERNAME,
... |
56e2c99478a249bc9efdc0d0a9cee0d09ac80b774f30b424511e611fd6fa44be | Python | 3,134 | 101 | from .ProvenanceObject import ProvenanceObject
from .attribute import Attribute
from .extractor import Extractor
from .set_type import SetType
class Set(ProvenanceObject):
"""
This class defines a dataflow set.
Attributes:
- tag (:obj:`str`): Set Tag.
- type (:obj:`SetType`): Set Type.
... |
b44e5c68c41c9fa5f2300cdaf49358b3edf0b87571343b2ee3d02323e3967916 | Python | 3,134 | 87 | import random
import numpy as np
import pandas as pd
from scipy.cluster.hierarchy import leaves_list, linkage, optimal_leaf_ordering
from sklearn.cluster import KMeans
def sub2ind(array_shape, rows, cols):
ind = rows * array_shape[1] + cols
ind[ind < 0] = -1
ind[ind >= array_shape[0] * array_shape[1]] = ... |
e386f335d8ca4df835a6cea1aca5e7397f226c167f15a0a994c3ff6084463df7 | Python | 3,135 | 97 | # tests/test_router_task_claim.py
"""Tests for task claim endpoint using shared fixtures."""
from conftest import make_room_address
from zndraw_joblib.schemas import TaskClaimResponse
def test_claim_task_returns_null_when_empty(seeded_client):
worker_id = seeded_client.seeded_worker_id
response = seeded_cli... |
72fe2cfddb1e9638b141c6be77a0486db9869fd824e26c7560d245dbc610d42b | Python | 3,136 | 97 |
baseFileName = './shellScripts/LIF_TEST'
baseSimTag = 'LIF_2_CLASS_'
def generateCommand(trial_num=0,
num_trials=10,
learning_rate=0.001,
sim_tag='default',
exc_hid_rat=0.5,
epochs=30,
log_file='example.log',
obj_dir='./data/obj',
w1_std=-1,
w1... |
b9afc4219a866fe54bed6c42af74c7028276fc0944ff5dde92032b49ec71a02b | Python | 3,136 | 77 | # import cProfile, pstats
# pr = cProfile.Profile()
# pr.enable()
os.environ['CUDA_VISIBLE_DEVICES'] = '-1' # GPU is not needed for this small dataset
# test the performance of methods depending on the number of datapoints
import numpy as np
import matplotlib.pyplot as plt
import hickle as hkl
import os
from grid_cel... |
beef04a9976d401613c8c349dbe26e30a38a7f7d796ec8edba22c899c48bc555 | Python | 3,137 | 81 | from pathlib import Path
import pandas as pd
import pytest
from guppy.orchestration.import_custom_events import build_custom_events_template
@pytest.fixture
def template(panel_extension, tmp_path):
return build_custom_events_template(str(tmp_path))
def _set_row(config, index, name, text):
while len(config... |
1f726624ed174ffbdd12b0998f77c6505f36203be6a233ca0ec411db9b7265bd | Python | 3,138 | 110 | """
Algorithms to extract various features of interest for outlier detection methods.
"""
from os import makedirs
from os.path import exists as pexists, join as pjoin, splitext
import numpy as np
from visualqc import config as cfg
from visualqc.utils import read_image, scale_0to1
def t1_histogram_whole_scan(in_mr... |
f0a465323bbbed077ed0e3912a9782929028c0e69405425422581ca5d252d47e | Python | 3,138 | 98 | # This file is part of h5py, a Python interface to the HDF5 library.
#
# http://www.h5py.org
#
# Copyright 2008-2013 Andrew Collette and contributors
#
# License: Standard 3-clause BSD; see "license.txt" for full license terms
# and contributor agreement.
"""
Versioning module for h5py.
"""
from typing ... |
c30d1807b775152fa1f0669ba6db36c5c89656bba56ea25c09706c2b1d541a43 | Python | 3,139 | 93 | import glob
import os
import shutil
import string
import subprocess
import tarfile
import random
def generate_random_str(length):
return ''.join(random.choice(string.ascii_lowercase) for _ in range(length))
def copy_matching_paths(src_pattern, dst, root_dir=''):
if type(src_pattern) is str:
matching... |
b13d9457b74bd0d5a453f6c807499f7ba63fc8f8b4a9effb95a6cbf4601cc03d | Python | 3,140 | 73 | import catmaid.fields
from django.conf import settings
import django.contrib.postgres.functions
from django.db import migrations, models
import django.db.models.deletion
forward = """
CREATE TABLE catmaid_writable_stack (
id int GENERATED BY DEFAULT AS IDENTITY PRIMARY KEY,
user_id int REFERENCES ... |
f9e83ad7208cb6f14b454c628c2a3d2eb4db78867d8fa3a4f0dbba5cda33f881 | Python | 3,140 | 95 | """Unit tests for the delta-varint codec (encode_intlist / decode_intlist)."""
import pytest
from eggnogmapper.annotator import encode_intlist, decode_intlist
# ---------------------------------------------------------------------------
# Roundtrip helpers
# ---------------------------------------------------------... |
63a8671e9f79545b6a7184d31188a2047c943bd47784766a3c43663c28b2e560 | Python | 3,143 | 74 | # -*- coding: utf-8 -*-
"""
Created on Mon Jun 10 16:54:02 2024
@author: mbmad
"""
from patchanalysis.measures.measuretools import NoResultError, InvalidRecordingError, \
withinEachSweep, withinEachSweepHzXuYuCu
from patchanalysis import TimeSpan, FullSpan, NullSpan
from scipy.signal import find_peaks
import num... |
82505ec6f9c97aeb0ef6f90587114817407cb75e2d21b1f5c2265146fc2fe57f | Python | 3,144 | 94 | """Shared bootstrap for the default @internal filesystem provider.
Used by both the in-process taskiq worker (``zndraw.database.lifespan``)
and the standalone taskiq worker (``zndraw.broker``). Centralizing the
construction keeps both call sites in lockstep.
"""
from __future__ import annotations
from pathlib import... |
b195d4b84fdeeec683509f6e2cb27cfaeb107ca55ba9ee20b8c9105314d7ddbb | Python | 3,145 | 100 | #!/usr/bin/env python
"""
Trains a model using one or more GPUs.
"""
from multiprocessing import Process
import caffe
def train(
solver, # solver proto definition
snapshot, # solver snapshot to restore
gpus, # list of device ids
timing=False, # show timing info for compute and com... |
64210ca9baa4da400328dc700d629960fd63d4f9bc5e29fe645f203670335e67 | Python | 3,146 | 60 | import os
def create_key(template, outtype=('nii.gz',), annotation_classes=None):
if template is None or not template:
raise ValueError('Template must be a valid format string')
return template, outtype, annotation_classes
def infotodict(seqinfo):
"""Heuristic evaluator for determining which run... |
c80743e78d61296beeb38aecdfcf5a85ec03a5e68b0c9d8807db0d7bb9b7aa73 | Python | 3,146 | 112 | """Light geometry types for scene illumination.
Provides directional, ambient, and hemisphere lights as scene objects.
Lights can be attached to the camera to follow view direction.
"""
from pydantic import BaseModel, ConfigDict, Field
Vec3 = tuple[float, float, float]
class LightPosition(BaseModel):
"""Positi... |
4d5fb1ebda756c51f7b71716016b75612cccadb91a9e483c7f8587e17618ad88 | Python | 3,149 | 75 | from django.conf import settings
from django.db import migrations, models
import django.db.models.deletion
import django.utils.timezone
import catmaid.fields
forward = """
CREATE TYPE volume_origin_source_type AS ENUM ('mesh', 'segmentation');
CREATE TABLE volume_origin (
id int GENERATED BY DEFAULT ... |
5a2432807559a267c33f08af49e812fedfb5f52ce0f12bf5a5142dede4f6bf4c | Python | 3,149 | 103 |
import torch
import torch.nn as nn
import numpy as np
from Bio import SeqIO
import matplotlib.pyplot as plt
import logomaker
import pandas as pd
import os
class CNN(nn.Module):
def __init__(self, channel=7, nb_filter=16, kernel_size=(4, 10), stride=(1, 1), padding=(0, 0)):
super(CNN, self).__init__()
... |
8d35b16ab69016a07c49de03a153c790c1b455357b04b720226967ca908f3eaa | Python | 3,151 | 91 | import torch
import numpy as np
class BirdParticle:
def __init__(self, position, w=1.0, c1=0.8, c2=0.2, minclamp=0.0, maxclamp=1.0, name=None):
"""
Initializes a particle.
Args:
position (torch.Tensor): The initial position of the particle.
w (float): The inertia we... |
d3893326683f6fa02399252994355efacc48496362b0b1da27cc310b61d994c8 | Python | 3,151 | 90 | from rest_framework.generics import GenericAPIView
from rest_framework.response import Response
from rest_framework import status
from .models import EncryptedKey
from .serializers import (
EncryptedKeySerializer,
CreateEncryptedKeyListSerializer,
UpdateEncryptedKeyListSerializer,
)
from .permissions impor... |
c81c174f52cda7faf7d134c899af5533fa9090999e5d447e060cbbb17645de9a | Python | 3,152 | 69 | # %%
# load library
import os
from nilearn import plotting
from nilearn import datasets
from nilearn import image
import matplotlib.pyplot as plt
from pathlib import Path
import itertools
import sys, argparse
# help -----
# https://stackoverflow.com/questions/64331987/removing-hiding-empty-subplots-in-matplotlib-when-p... |
16a14f8e041b747faea536a2603025ff98d28b6b94de7f49efe1f03fcba53064 | Python | 3,156 | 98 | import re
import subprocess
import os
import sys
import readline
from optparse import OptionParser
WD = os.path.abspath(os.path.split(__file__)[0])
os.chdir(WD)
parser = OptionParser()
parser.add_option("--notest", dest="notest", action='store_true')
parser.add_option("--simulate", dest="simulate", action='store_true... |
6b1d1b23b343a4c62c48cee9b2331d25610ddb2f6a16e3487bf1c79ba0722132 | Python | 3,156 | 126 | import queue as Queue
import threading
import torch
from torch.utils.data import DataLoader
class PrefetchGenerator(threading.Thread):
"""A general prefetch generator.
Ref:
https://stackoverflow.com/questions/7323664/python-generator-pre-fetch
Args:
generator: Python generator.
num_p... |
e601327a036c5ad6c578212ebb77dcc028e6a094e349f6e0bf553cd16be9d302 | Python | 3,156 | 92 | # Copyright (c) OpenMMLab. All rights reserved.
import argparse
import os.path as osp
from functools import partial
import numpy as np
from mmengine.utils import mkdir_or_exist, scandir, track_parallel_progress
from PIL import Image
from scipy.io import loadmat
AUG_LEN = 10582
def convert_mat(mat_file, in_dir, out_... |
76f27275adadb1f5e48d7e112f47f349f030f4329e9ddc8107102c37c7c9e381 | Python | 3,157 | 101 | # this file imports custom routes into the experiment server
from flask import Blueprint, render_template, request, jsonify, Response, abort, current_app
from jinja2 import TemplateNotFound
from functools import wraps
from sqlalchemy import or_
from psiturk.psiturk_config import PsiturkConfig
from psiturk.experiment_... |
28832527f722729c1e6035d78fa38fac596bc4a8bf34f6ea7ff76dff9842f4e7 | Python | 3,158 | 88 | import logging
import os
from pyalfe.data_structure import Modality, PipelineDataDir
from pyalfe.image_processing import ImageProcessor
from pyalfe.inference import InferenceModel
from pyalfe.tasks import Task
class Skullstripping(Task):
"""This task performs skullstripping for all the modalities.
Attribute... |
f6630026d9ff9d222285713ef7b87b002f324a4cd4f0a75c1948a46c8e40c184 | Python | 3,158 | 97 | from medperf.exceptions import InvalidArgumentError, MedperfException
class CompatibilityTestParamsValidator:
"""Validates the input parameters to the CompatibilityTestExecution class"""
def __init__(
self,
benchmark: int = None,
data_prep: str = None,
model: str = None,
... |
51688573d95f7d8420d82aa5a90dfcd7eed5665d5b03e8fe21d5b647a1d01ac3 | Python | 3,160 | 112 | from luna.paths import LunaPaths
from luna import candidate_info, dataset
from luna.ct import Ct
from luna.prepcache import LunaPrepCacheApp
from torch.utils.data import DataLoader
#from Utils.dataloader import *
from Utils.models import *
from Utils.TrainModelLUNA import *
from Utils.config import *
from multiprocessi... |
eb30efb407b5da9224ad6e92a8ad0d3ad83a85090f141ce43f6ed90e0011f343 | Python | 3,162 | 110 | from medperf.comms.entity_resources.sources.synapse import SynapseSource
import pytest
import os
from medperf.exceptions import (
CommunicationAuthenticationError,
CommunicationRetrievalError,
)
from synapseclient.core.exceptions import (
SynapseNoCredentialsError,
SynapseHTTPError,
SynapseUnmetAcce... |
b6e8181fd68bc113f923fd0d3b8f6ef68d561fa45781b6f14d54f75154bcb979 | Python | 3,163 | 100 | import matplotlib.pyplot as plt
import pandas as pd
import seaborn as sns
import numpy as np
plt.rcParams.update({'font.size': 20}) # Default is usually 10
# Load the data
datapath = "../data_files/"
ages = ["P28", "P21", "P14", "P07", "P04"]
colours = pd.read_csv(f"{datapath}/points_hierarchies.csv")
colour_map = ... |
3725e828aa547e8d2124f737fae669356094f09114ee6851ea647ef577fd8404 | Python | 3,165 | 114 | from rest_framework import status
from medperf.tests import MedPerfTest
from medperf.testing_utils import mock_mlcube, mock_dataset
from parameterized import parameterized
class UserTest(MedPerfTest):
def generic_setup(self):
# setup users
user1 = "user1"
user2 = "user2"
user3 = ... |
8dfd08f3969d4fdf34b903dbf7d11f1d862367c4a72c7bd111f4af483181ce96 | Python | 3,166 | 118 | import logging
import os
import random
import time
from logging import Logger
import numpy as np
import torch
import yaml
from easydict import EasyDict
from tqdm.auto import tqdm
class BlackHole(object):
def __setattr__(self, name, value):
pass
def __call__(self, *args, **kwargs):
return sel... |
e601a5622ba44933df1ac8a53dbb84892a57f8ec31d094385bb0c0e85cefb09d | Python | 3,167 | 78 | from pathlib import Path
import pandas as pd
import pytest
from guppy.extractors.csv_recording_extractor import CsvRecordingExtractor
from guppy.utils.custom_events import (
is_sorted,
parse_pasted_timestamps,
write_custom_event_csv,
)
class TestParsePastedTimestamps:
def test_newline_separated(self... |
f47ef1b5ae696798ea4cb4400d8e23c5e6268dbcff3c275ef5dc48b0e1a18639 | Python | 3,167 | 59 | # Copyright 2020 Division of Medical Image Computing, German Cancer Research Center (DKFZ), Heidelberg, Germany
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://w... |
00d02cd96d1b9c8400ebe87ff7bf79ba83ecd62a6bbfcc67c8e928062cc275e2 | Python | 3,168 | 101 | """Testing code shared by other tests."""
# pylint: disable=invalid-name
import collections
import importlib.util
import json
import os
import tempfile
from typing import Any, Callable, Dict, Type
import numpy as np
import xgboost as xgb
from xgboost._typing import ArrayLike
def validate_leaf_output(leaf: np.ndarr... |
90a1cc78e9ce5fbc4178f31d3c9792b5d777c68317a0fd2d118a76dcccb295ae | Python | 3,169 | 86 | import torch
import torch.nn as nn
import torch.nn.functional as F
class DynamicLSTM(nn.Module):
"""
An Attention-based Bidirectional LSTM (Att-BiLSTM).
Highly cited in speech and audio processing literature because the attention
mechanism allows the model to weigh the importance of different time fra... |
7419e7eb817f178c86ebf12431bf7b6702c3f4286519d0b7a92300d4f68a8283 | Python | 3,170 | 61 | # Copyright 2020 Division of Medical Image Computing, German Cancer Research Center (DKFZ), Heidelberg, Germany
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://w... |
a487caf0d54433f2975c74a78324b8b06b6edfbbdd2af79c28405130c5e6b0fe | Python | 3,170 | 97 | # -*- coding: utf-8 -*-
"""
Created on Tue Sep 24 13:46:09 2024
@author: AC
"""
import pandas as pd
from sklearn.model_selection import train_test_split
from sklearn.linear_model import LogisticRegression
from sklearn.metrics import accuracy_score, precision_score, recall_score, f1_score, confusion_matrix, ... |
0a646ba2800d247d755d2ae97ae8e556cefb69efcfdf1a5e34c1b550a11f8287 | Python | 3,172 | 89 | # Copyright 2020 Division of Medical Image Computing, German Cancer Research Center (DKFZ), Heidelberg, Germany
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://w... |
1d4ba22322077a7991ddbd116a39a87e8ad687ab91fb55fc19029af9c92d158d | Python | 3,172 | 97 | import pytest
from hypothesis import assume, given, note, settings, strategies
import xgboost as xgb
from xgboost import testing as tm
pytestmark = tm.timeout(10)
parameter_strategy = strategies.fixed_dictionaries(
{
"booster": strategies.just("gblinear"),
"eta": strategies.floats(0.01, 0.25),
... |
fd2661d29b7d29586cddd7a0c11f64ccf7a9d8ff600ff125ef2172e727a998e8 | Python | 3,172 | 107 | """Data transformation models for filtering geometry properties.
Transformations allow dynamic filtering of geometry data based on frame data.
For example, filtering positions to only show atoms that are constrained.
Also includes CurveAttachment for referencing Curve geometries with progress.
"""
from typing import... |
d4b285979a2b764c7acb03fa2002c3742ac3184027ad2fb8400f4f4b5f87dde9 | Python | 3,175 | 105 | from Utils.dataloader_BrainTumorMRI import *
from Utils.config import *
from Utils.models import *
from Utils.TrainModel import *
from multiprocessing import Process
from codecarbon import EmissionsTracker
def task(lr, data_partition:float=None, run_idx:int=None, backbone:str='dense121'):
_cuda = 'cuda:0'
_im... |
3d946b16fb524863fec74ad2b4a1ca1ad5f8b1de105e0a44871125d8e6147a0d | Python | 3,176 | 100 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
import argparse
import glob
import os
import pandas as pd
import shutil
from dmriqcpy.io.report import Report
from dmriqcpy.io.utils import (add_online_arg, add_overwrite_arg,
assert_inputs_exist, assert_outputs_exist)
from dmriqcpy.viz.uti... |
d03aca6e8c43fd541826be4b97873f883c0f8bc09b71dc486d130e17157f2ccf | Python | 3,176 | 104 | """Xgboost pyspark integration submodule for params."""
from typing import Dict
from pyspark.ml.param import TypeConverters
from pyspark.ml.param.shared import Param, Params
class HasArbitraryParamsDict(Params):
"""
This is a Params based class that is extended by _SparkXGBParams
and holds the variable ... |
b01a5b3a6cbbc3e6fedd66465c04176e2ecf2e91972466c4a29d76aaf1ec8f17 | Python | 3,177 | 75 | # -*- coding: utf-8 -*-
"""Tsodyks-Markram model Evaluator used to fit data from multiple frequency
stimulations. This module contains an evaluator for the Tsodyks-Markram model.
@authors: Andras Ecker and Giuseppe Chindemi
@remark: Copyright (c) 2017, EPFL/Blue Brain Project
This file is part of BluePyOpt <h... |
fcaf2bcb30ceba739ba0308964d2774de9883fa792f042faf001ae1cd76e48a8 | Python | 3,177 | 89 | # An Pytorch implementation of the pafnucy model
# The original model was in outdated TensorFlow 1.x.
from collections import OrderedDict
import torch
from torch import nn
class PafnucyNetwork(nn.Module):
"""
Pytorch implementation of the Pafnucy model.
Original paper:
Stepniewska-Dziubinska, M.M.,... |
bfc4cca926ba011bb77fad70ab4bfbe414169d004250bbcdb628b1f5fe242dc9 | Python | 3,178 | 99 | # Copyright (c) OpenMMLab. All rights reserved.
import argparse
import glob
import math
import os
import os.path as osp
import mmcv
import numpy as np
from mmengine.utils import ProgressBar
def parse_args():
parser = argparse.ArgumentParser(
description='Convert levir-cd dataset to mmsegmentation format'... |
3172c08d05f452d0a6170ed2debc0a135d927e3314915b20ec0d9e246d07146a | Python | 3,179 | 82 | import json
from pathlib import Path
import h5py
import pytest
@pytest.mark.parametrize(
"step3_fixture_name, expected_recording_site, expected_ttl",
[
(
"step3_output_csv",
"region",
"ttl",
),
(
"step3_output_tdt",
"dms",
... |
a2416d84f14f21dd9534ae7914fa166de59b5c54e4c3013c4e0daa2c0087fa4f | Python | 3,179 | 99 | # MLP model
import tensorflow.keras as keras
import tensorflow as tf
import numpy as np
import time
import matplotlib
matplotlib.use('agg')
import matplotlib.pyplot as plt
from utils.utils import save_logs
from utils.utils import calculate_metrics
class Classifier_MLP:
def __init__(self, output_directory, input... |
026ac477150191ad4ae3c37a12f06f429201a106f1d9fb7985ede8cfdb5300a9 | Python | 3,180 | 112 | import subprocess
import sys
import os
import logging
from .utils import which
lgr = logging.getLogger(__name__)
def queue_conversion(queue, iterarg, iterables, queue_args=None):
"""
Write out conversion arguments to file and submit to a job scheduler.
Parses `sys.argv` for heudiconv arguments.
Para... |
b6d1034f7b01e7fa87215f271f58098f3997226475193f31e79f6d62884ee57c | Python | 3,180 | 106 | from medperf.tests.mocks.cube import TestCube
import pytest
import medperf.commands.compatibility_test.utils as utils
import os
import medperf.config as config
PATCH_UTILS = "medperf.commands.compatibility_test.utils.{}"
class TestPrepareCube:
@pytest.fixture(autouse=True)
def setup(self, mocker, fs):
... |
ebf6cc06ccfa42942709d2de3eb9d343e5895c8c5ff0d5e287c87002bb6c030b | Python | 3,180 | 96 | # -*- coding: utf-8 -*-
"""
Created on Wed Sep 25 11:22:25 2024
@author: AC
"""
import pandas as pd
from sklearn.model_selection import train_test_split
from sklearn.ensemble import AdaBoostClassifier
from sklearn.metrics import accuracy_score, precision_score, recall_score, f1_score, confusion_matrix, roc_... |
3061e057e310cab3c4611d2c6339d0876e413def1213508d183cb66c889634af | Python | 3,181 | 105 | import os
import pytest
from rdflib import URIRef, Graph
from pprint import pprint
from kgx.prefix_manager import PrefixManager
from kgx.utils.rdf_utils import infer_category, process_predicate
from tests import RESOURCE_DIR
@pytest.mark.parametrize(
"query",
[
(URIRef("http://purl.obolibrary.org/obo... |
3c880f25a2694bc3eae11579b2791e4461e173ac636d8866804754e4483e0ea1 | Python | 3,181 | 84 | # Model for preparing data: Extract features and labels from csv files
# This module provides utility functions for mapping emotion labels,
# managing emotion lists, and handling device placement for PyTorch tensors.
import torch
def dict_emotions():
"""
Returns an dictionary for the emotions
:return: Dict... |
6165c6cd7e7776bc894f6796fad4973843eaf3456babeb3807d689a55fd68ec8 | Python | 3,181 | 100 | # This file is part of h5py, a Python interface to the HDF5 library.
#
# http://www.h5py.org
#
# Copyright 2008-2013 Andrew Collette and contributors
#
# License: Standard 3-clause BSD; see "license.txt" for full license terms
# and contributor agreement.
"""
Tests the h5py.AttributeManager.create() met... |
4f745fb0ba0c6d888cb885e82c1283910ec5312d3f61dc3596084462e2ad403e | Python | 3,183 | 117 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Tue Feb 28 10:22:58 2023
@author: george
"""
from __future__ import division, unicode_literals, print_function # for compatibility with Python 2 and 3
import matplotlib as mpl
import matplotlib.pyplot as plt
# Optionally, tweak styles.
mpl.rc('figure', ... |
4be365f4193abb83eb935afd99d7dd04cea59a5150cd65439cc682765d3a6983 | Python | 3,184 | 90 | # +
from src import config as cfg
import os
#import scipy.io as sio
#import h5py
import json
#from datetime import datetime as dt
################
# data in
#################
def readfile(path):
print(f'Reading file at {path}')
with open(path, 'r') as f:
lines = f.read()
print(lines)
def loadmat... |
544190e9c4fe020ed0ae01b2b014bb5b4e3459ef7eacc84810ff5e24ac945cf6 | Python | 3,184 | 131 | #!/usr/bin/env python
import sys, os, subprocess, random
from argparse import ArgumentParser, FileType
"""
"""
def reverse_complement(seq):
result = ""
for nt in seq:
base = nt
if nt == 'A':
base = 'T'
elif nt == 'a':
base = 't'
elif nt == 'C':
... |
b05a871de28abddeafe56cce63732f9134d953e8f39ec3fcbc840b1827689e92 | Python | 3,184 | 83 | from __future__ import annotations
import os.path
from typing import TYPE_CHECKING
from zipfile import ZipFile
import pytest
from pymatgen.core import Structure
from chgnet import ROOT
from chgnet.data.dataset import StructureData
from chgnet.utils import parse_vasp_dir
if TYPE_CHECKING:
from pathlib import Pat... |
8f449f973198add42d7c45b756c76d95826f86dfbe66a78c757491acd1e4d114 | Python | 3,186 | 77 | # Copyright (c) OpenMMLab. All rights reserved.
from unittest import TestCase
import torch
from mmengine.structures import InstanceData
from mmseg.models.assigners import HungarianAssigner
class TestHungarianAssigner(TestCase):
def test_init(self):
with self.assertRaises(AssertionError):
Hu... |
afad86bbeed21d520b050f92cc32e7922c9238f38fb8919eb84d19c5cc52edd1 | Python | 3,187 | 119 | import torch.nn as nn
from nnunet_mednext.network_architecture.custom_modules.custom_networks.TransBTS.IntmdSequential import IntermediateSequential
class SelfAttention(nn.Module):
def __init__(
self, dim, heads=8, qkv_bias=False, qk_scale=None, dropout_rate=0.0
):
super().__init__()
s... |
6efae52d577918ea12193cad0264eb840a76fa2bb0e1717e6335a4ad90c98349 | Python | 3,188 | 91 | from __future__ import annotations
import json
from ast import literal_eval
from pathlib import Path
from typing import Mapping, Optional, Union
from xml.etree import ElementTree
import cv2
import numpy as np
import pandas as pd
from numpy.typing import ArrayLike, NDArray
from .base import SoccerTrackMixin
_pathlik... |
6695ee018ce66ab84768d5373256933d3d478e430138acf58167dcb895b5dbdd | Python | 3,191 | 113 | """
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 logging
import os
import random
import numpy as np
import pytest
import torch
from ase.io import read
from ocpmodels.common.registry... |
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