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Python
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# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*- # vi: set ft=python sts=4 ts=4 sw=4 et: """Set of interfaces that allow interaction with data. Currently available interfaces are: DataSource: Generic nifti to named Nifti interface DataSink: Generic named output from interfaces to data store XN...
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Python
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from __future__ import annotations import copy import locale import logging import os import platform import random import re import string import time import traceback from decimal import Decimal from functools import partial, wraps from logging import Logger from types import ModuleType from typing import ( TYPE...
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""" This script is used for path analysis of the worm trajectory. There are several visualization helper functions. """ import numpy as np from scipy.ndimage import center_of_mass import pickle import matplotlib.pyplot as plt from matplotlib.colors import LinearSegmentedColormap from scipy.spatial.distance import eucl...
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from keras.src import backend from keras.src import ops from keras.src.api_export import keras_export from keras.src.backend import KerasTensor from keras.src.backend import any_symbolic_tensors from keras.src.ops.operation import Operation from keras.src.ops.operation_utils import compute_conv_output_shape class RGB...
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Python
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from __future__ import annotations from typing import Dict, Tuple import logging import os import pickle as pkl import random import time import warnings from neurobench.benchmarks import Benchmark from neurobench.metrics.static import ( Footprint, ConnectionSparsity, ) from neurobench.metrics.work...
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Python
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""" Package resource API -------------------- A resource is a logical file contained within a package, or a logical subdirectory thereof. The package resource API expects resource names to have their path parts separated with ``/``, *not* whatever the local path separator is. Do not use os.path operations to manipul...
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Python
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# coding: utf-8 """ Package resource API -------------------- A resource is a logical file contained within a package, or a logical subdirectory thereof. The package resource API expects resource names to have their path parts separated with ``/``, *not* whatever the local path separator is. Do not use os.path opera...
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Python
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# Companion to plot_auc_summary.py: instead of one AUC per dataset (pooling # every across-session unit-pair together regardless of how far apart the two # sessions were recorded), bin across-session unit-pairs by signed delta-days # (date(RecSes 2) - date(RecSes 1)) and compute AUC per bin per score, # pooling across ...
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Python
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# -*- coding: utf-8 -*- # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*- # vi: set ft=python sts=4 ts=4 sw=4 et: """ Set of interfaces that allow interaction with data. Currently available interfaces are: DataSource: Generic nifti to named Nifti interface DataSink: Generic named ou...
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# -*- coding: utf-8 -*- """ Created on Thu May 2 18:55:54 2024 @author: Hiroto """ import tensorflow as tf from tensorflow.keras.layers import AbstractRNNCell from tensorflow.python.keras import backend, activations, constraints, initializers, regularizers #from tensorflow.keras.ops import ops # Clear all previou...
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# coding: utf-8 """ Package resource API -------------------- A resource is a logical file contained within a package, or a logical subdirectory thereof. The package resource API expects resource names to have their path parts separated with ``/``, *not* whatever the local path separator is. Do not use os.path opera...
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# coding: utf-8 """ Package resource API -------------------- A resource is a logical file contained within a package, or a logical subdirectory thereof. The package resource API expects resource names to have their path parts separated with ``/``, *not* whatever the local path separator is. Do not use os.path opera...
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from datetime import datetime from pprint import pprint from typing import Any, Callable, Dict, List, Optional, Tuple, Union import pytest from great_expectations.core import ExpectationValidationResult from great_expectations.expectations.expectation_configuration import ( ExpectationConfiguration, ) from great_...
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Python
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from typing import ( Tuple, Union, Optional, Type, TypeVar, ClassVar, Any, List, Generator, Dict, Iterable, Sequence ) from numpy import ndarray, dtype from merit.ipd.regions import GenotypeProb try: from typing import Self except ImportError: from typing_extensions import Self from abc import ( ...
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Python
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#!/usr/bin/env python3 """Generate Python documentation in HTML or text for interactive use. At the Python interactive prompt, calling help(thing) on a Python object documents the object, and calling help() starts up an interactive help session. Or, at the shell command line outside of Python: Run "pydoc <name>" to ...
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Python
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"""Tests for the correlation factory module. Tests for key helpers, VariantNotFoundError, CorrelationFactoryBase ABC, NoCacheCorrelationFactory, InMemoryCorrelationFactory, SQLiteCorrelationFactory, and persistence. All tests are written first (RED phase) before implementation (GREEN phase). Fixtures in this file are...
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import os import mne import json import glob import logging from scipy import io import warnings import numpy as np import pandas as pd from collections import Counter from typing import Any, Dict from scipy.stats import zscore from kneed import KneeLocator import matplotlib.pyplot as plt from gedai.gedai.gedai import ...
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Python
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import os import shelve import numpy as np import prody as pr import pandas as pd from tqdm import tqdm from pathlib import Path from typing import Tuple, Dict, Optional, List from collections import defaultdict from sklearn.model_selection import train_test_split import torch from torch_cluster import knn_graph from ...
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# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*- # vi: set ft=python sts=4 ts=4 sw=4 et: """The minc module provides classes for interfacing with the `MINC <http://www.bic.mni.mcgill.ca/ServicesSoftware/MINC>`_ command line tools. This module was written to work with MINC version 2.2.00. Auth...
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#!/usr/bin/env python3 # Kemal Inecik # k.inecik@gmail.com import bisect import copy import itertools import logging import warnings from collections import Counter from collections.abc import Iterable from functools import cached_property from typing import Any, Callable, Optional, Union import networkx as nx impor...
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# -*- coding: utf-8 -*- # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*- # vi: set ft=python sts=4 ts=4 sw=4 et: """The minc module provides classes for interfacing with the `MINC <http://www.bic.mni.mcgill.ca/ServicesSoftware/MINC>`_ command line tools. This module was written to work with MI...
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Python
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# -*- coding: utf-8 -*- # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*- # vi: set ft=python sts=4 ts=4 sw=4 et: """Provides interfaces to various commands provided by FreeSurfer """ import os import os.path as op from glob import glob import shutil import sys import numpy as np from nibabel i...
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import os, warnings import time import tonic from tonic import DiskCachedDataset, RandomChoiceDiskCachedDataset import torch import torch.nn.functional as F import torch.utils import torchvision.datasets as datasets from timm.data import ImageDataset, create_loader, Mixup, FastCollateMixup, AugMixDataset from timm.da...
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""" CA229.py : Reconstructed prefrontal layer V pyramidal neuron with detailed morphology and active channels --- Acker and Antic (2009) Original: https://senselab.med.yale.edu/ModelDB/ShowModel.cshtml?model=117207&file=/acker_antic/Model/CA%20229.hoc#tabs-2 Modified by : Peng Penny Gao <penggao.1987@gmail.com> Feb ...
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Python
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import os import pickle import warnings import matplotlib import matplotlib.pyplot as plt import matplotlib.colors as mcolors import matplotlib.gridspec as grid_spec import numpy as np import pandas as pd import scipy.stats as st import seaborn as sns import statsmodels.api as sm import nibabel as nib import plotly.gra...
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""" Min-cost flow tracking using Google OR-Tools. Also includes implementations of jaqaman et al. 2008 style tracking algorithm and a hungarian tracking style algorithm for comparison purposes. Implements multi-object tracking with: - Distance-based linking - Gap closing - Birth/death handling """ from __future__ im...
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Python
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import math from collections import defaultdict import numpy as np import json import os from decimal import Decimal, ROUND_HALF_UP def new_round(_float, _len): """ Parameters ---------- _float: float _len: int, 指定四舍五入需要保留的小数点后几位数为_len Returns ------- type ==> float, 返回四舍五入后的值 """ ...
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import pickle import io import numpy as np class CheckoutFake: def __init__(self): ## Setup the class for handling the scripting functions of CheckoutCore self._availableDatasets = {'AssayPlate_Greiner_#781956': ['test_Basic_Otsu_Threshold_Thresholded_Pixel_Area', ...
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import google.protobuf from packaging.version import Version if Version(google.protobuf.__version__).major >= 5: # -*- coding: utf-8 -*- # Generated by the protocol buffer compiler. DO NOT EDIT! # source: databricks_uc_registry_messages.proto # Protobuf Python Version: 5.26.0 """Generated protocol buffer co...
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from typing import List, Tuple, Union, Optional, Dict, Any, Sequence, Callable import warnings import functools import PIL from pathlib import Path import math import numpy as np import scipy.optimize import scipy.sparse import torch from tqdm.auto import tqdm import cv2 import matplotlib.pyplot as plt from .. impor...
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Python
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""" Main analysis GUI @author: amandaschott """ import os from pathlib import Path import scipy import h5py import numpy as np import pandas as pd import matplotlib import matplotlib.pyplot as plt from matplotlib.backends.backend_qt5agg import FigureCanvasQTAgg as FigureCanvas from matplotlib.backends.backend_qt5agg i...
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#!/usr/bin/env python # -*- coding: utf-8 -*- """ This experiment was created using PsychoPy3 Experiment Builder (v2022.2.5), on May 18, 2023, at 12:47 If you publish work using this script the most relevant publication is: Peirce J, Gray JR, Simpson S, MacAskill M, Höchenberger R, Sogo H, Kastman E, Li...
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Python
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from collections import defaultdict import bisect import numpy as np import json import os def new_round(_float, _len): """ Parameters ---------- _float: float _len: int, 指定四舍五入需要保留的小数点后几位数为_len Returns ------- type ==> float, 返回四舍五入后的值 """ if isinstance(_float, float): ...
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"""Behavioral checks for packaged literature methods, beyond simulation coverage.""" import inspect import json import re import numpy as np import pandas as pd import pytest from scipy.signal import filtfilt, remez import ripple_detection as rd from ripple_detection import literature_methods as lm RIPPLE_TIMES = [...
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"""Live visualization during cross-validation experiments. This module provides real-time plotting of CV results, generating figures similar to those in make_all_figures_training_set_section.py with consistent colors and styling. """ import argparse import os import sys from pathlib import Path from typing import Dic...
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"""Prototype: pial surface reconstruction by forward-integrating the DiReCT velocity field, instead of the shipped FreeSurfer / nighres pial pipeline. STATUS: research prototype, not wired into the CLI or the default pipeline. It is not imported by any other module in this package. Run it directly (see `main()` / `--h...
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#!/usr/bin/env python3 """ Bump Chart / Slope Graph Visualization ====================================== Creates bump charts (slope graphs) showing individual pathway trajectories through the Early → TrajDev → Late stages. Unlike alluvial diagrams that show categorical flows, bump charts show: - Y-axis: NES value (co...
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try: from . import entrypoint_setup except ImportError: import entrypoint_setup import os import tkinter as tk import argparse import base64 import json import queue import subprocess import sys import traceback import webbrowser from types import SimpleNamespace from tkinter import ttk, messagebox, filedialog...
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# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*- # vi: set ft=python sts=4 ts=4 sw=4 et: """AFNI utility interfaces.""" import os import os.path as op import re import numpy as np from ...utils.filemanip import load_json, save_json, split_filename from ..base import ( CommandLineInputSpec...
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"""Post-hoc extraction helpers for pipeline archives.""" from __future__ import annotations import json import math from collections.abc import Mapping from dataclasses import dataclass from enum import Enum from pathlib import Path from typing import Literal import pandas as pd from scipy.stats import chi2 from me...
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""" Controls the bulk loading summary level data: * ``read_gwas`` - Will read in a dataset from a flat file and perform some normalisation on it. This is essentially a wrapper around `pandas.read_csv <https://pandas.pydata.org/pandas-docs/stable/reference/api/pandas.read_csv.html#pandas.read_csv>`__. * ``set_gwas`...
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# -*- coding: utf-8 -*- # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*- # vi: set ft=python sts=4 ts=4 sw=4 et: """AFNI utility interfaces.""" import os import os.path as op import re import numpy as np from ...utils.filemanip import load_json, save_json, split_filename from ..base import ( ...
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from typing import Optional, Tuple, Any, Iterable, Mapping, Union, Dict from tifffile import imread, imwrite, TiffFile import numpy as np import numba as nb from numba import cuda import skimage def get_tiff_metadata(filepath: str, return_all: bool = False) -> dict: """ Read the metadata from a TIFF image. ...
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Python
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import pandas as pd import numpy as np from sklearn.model_selection import GroupShuffleSplit import rdkit from rdkit import Chem from rdkit import Chem, DataStructs from rdkit.Chem import AllChem from rdkit.Chem.MolStandardize import rdMolStandardize from rdkit.Chem.MolStandardize import rdMolStandardize as std from rd...
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"""Functions for the basic normalisation of input files. """ # Standard Python # import pprint as pp import math import re # Standard Python from collections import Counter, namedtuple # 3rd Party packages from scipy.stats import norm # My stuff from gwas_norm import ( constants as con, columns as col, p...
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"""Get useful information from live Python objects. This module encapsulates the interface provided by the internal special attributes (co_*, im_*, tb_*, etc.) in a friendlier fashion. It also provides some help for examining source code and class layout. Here are some of the useful functions provided by this module:...
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Python
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#!/usr/bin/env python3 """ Track metrics + histograms from *_pairs_tracks.csv exports. Adds: - Fix path_length aggregation (use last, not first) """ from __future__ import annotations import argparse import os import sys import glob import re from pathlib import Path from typing import List, Dict, Optional, Tuple im...
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Python
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"""Get useful information from live Python objects. This module encapsulates the interface provided by the internal special attributes (co_*, im_*, tb_*, etc.) in a friendlier fashion. It also provides some help for examining source code and class layout. Here are some of the useful functions provided by this module:...
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Python
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from __future__ import absolute_import, division, unicode_literals from pip._vendor.six import with_metaclass, viewkeys import types from collections import OrderedDict from . import _inputstream from . import _tokenizer from . import treebuilders from .treebuilders.base import Marker from . import _utils from .con...
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"""Commonly-used neural network operations not included in NumPy.""" import warnings from keras.src import backend from keras.src.api_export import keras_export from keras.src.backend import KerasTensor from keras.src.backend import any_symbolic_tensors from keras.src.backend import config from keras.src.backend impo...
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# -*- coding: utf-8 -*- """This module defines plotting functions for protein dynamics analysis. Plotting functions are called by the name of the plotted data/property and are prefixed with ``show``. Function documentations refers to the :mod:`matplotlib.pyplot` function utilized for actual plotting. Arguments and k...
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# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*- # vi: set ft=python sts=4 ts=4 sw=4 et: """Provides interfaces to various commands provided by FreeSurfer""" import os import os.path as op from glob import glob import shutil import sys from looseversion import LooseVersion import numpy as np ...
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""" Post-processing utilities for image and mask data in BiaPy. This module provides functions for instance segmentation refinement, watershed segmentation, morphological filtering, synapse and point detection, ensemble predictions, and other post-processing operations for 2D and 3D biomedical images. It supports adva...
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Python
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""" Tests for the dataset module """ from merit.example_data import dummy_summary_data as dsd from merit.gwas import dataset, utils as data_tools from merit import constants as con, errors from itertools import combinations, permutations from collections import namedtuple from pathlib import Path import numpy as np imp...
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#!/usr/bin/env python3 # -*- coding: utf-8 -*- """ HVG-SINDy Autoencoder for Taijiquan Public Attention Dynamics and System Evolution Modeling date: 2026\1\1 This code implements the following functions: 1.Construct a Horizontal Visibility Graph (HVG) and use the HVG degree distribution exponent λ as a criter...
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#!/usr/bin/env python3 """Prepare TACMAN-compatible homology files from external resources.""" from __future__ import annotations import argparse import gzip import re import shutil import subprocess import sys from pathlib import Path from typing import Dict, Iterable, List, Optional, Sequence, Set, Tuple pd = None...
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"""Tests for core signal processing and utility functions.""" import warnings import numpy as np import pandas as pd import pytest from scipy.signal import filtfilt, freqz from scipy.stats import median_abs_deviation, zscore from ripple_detection.core import ( _get_ripplefilter_kernel, estimate_noise_thresho...
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Python
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"""Execution tests for the code in the agent skills bundled with ``great_expectations``. The skills teach an agent how to drive this library, and every instruction they give is carried by a code snippet. Markdown is not compiled, imported or linted by anything, so a snippet that stopped working would keep being handed...
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Python
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from __future__ import annotations import logging from typing import TYPE_CHECKING, Any, Dict, List, Tuple, Union, Optional, Set, Literal import gc from json import load, dump, dumps from os.path import exists from copy import deepcopy import cv2 import numpy as np import SimpleITK as sitk from mdh_app.data_build...
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Python
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import numpy as np import random import tensorflow as tf from tensorflow.keras.layers import Input, Dense, Concatenate, RNN from tensorflow.keras.models import Model from tensorflow.keras import initializers from tensorflow.keras.regularizers import l2 from tensorflow.keras.initializers import GlorotUniform from sklear...
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from __future__ import annotations import argparse import csv from functools import partial import hashlib import itertools import json import math import os import random import subprocess import time import warnings from collections import Counter, defaultdict from datetime import datetime, timezone from pathlib imp...
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# Copyright 2024 DeepMind Technologies Limited # # AlphaFold 3 source code is licensed under the Apache License, Version 2.0 # (the "License"); you may not use this file except in compliance with the # License. You may obtain a copy of the License at # # http://www.apache.org/licenses/LICENSE-2.0 # # Unless required by...
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""" Classes for mapping variants """ # from time import time from merit.ensembl import variants, constants as ensc from operator import itemgetter from pyaddons import gzopen import sys import csv import re import itertools import pprint as pp # https://stackoverflow.com/questions/15063936 csv.field_size_limit(sys....
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# pylint: disable=W0611, W0612, F0401, R0914, C0302 """General tests of eFEL""" """ Copyright (c) 2015, Blue Brain Project/EPFL Copyright (c) 2025-2026 Open Brain Institute All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the followin...
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__author__ = "Simon Nilsson; sronilsson@gmail.com" import platform from typing import Dict, List, Optional, Tuple, Union import numpy as np try: from typing import Literal except: from typing_extensions import Literal import functools import multiprocessing import os from collections import ChainMap import...
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import math from collections import defaultdict import numpy as np import json import os from decimal import Decimal, ROUND_HALF_UP def new_round(_float, _len): """ Parameters ---------- _float: float _len: int, 指定四舍五入需要保留的小数点后几位数为_len Returns ------- type ==> float, 返回四舍五入后的值 """ ...
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import builtins import collections import functools import math import string import warnings import numpy as np import tensorflow as tf from tensorflow.python.ops.linalg.sparse import sparse_csr_matrix_ops from tensorflow.python.ops.math_ops import is_nan from keras.src import tree from keras.src.backend import conf...
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#!/usr/bin/env python # -*- coding: utf-8 -*- from pip._vendor.chardet.sbcharsetprober import SingleByteCharSetModel # 3: Positive # 2: Likely # 1: Unlikely # 0: Negative RUSSIAN_LANG_MODEL = { 37: { # 'А' 37: 0, # 'А' 44: 1, # 'Б' 33: 1, # 'В' 46: 1, # 'Г' 41: 1, #...
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import sys from . import data, stats, models, simulations, optimize_geometry, md, md_parallel, constants, generate_initial_conditions import numpy as np import os import random import joblib from . import gap_md, namd class Sampler(): def __init__(self,sampler_function=None): if type(sampler_function) is s...
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""" Augmentation utilities for image and mask data in deep learning workflows. This module provides a variety of data augmentation functions for images and masks, including cutout, cutblur, cutmix, cutnoise, misalignment, cropping, flipping, rotation, zoom, gamma/contrast adjustment, blurring, dropout, elastic deforma...
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import copy import inspect import json import logging import math import re from abc import abstractmethod from dataclasses import asdict, dataclass from typing import TYPE_CHECKING, Any, Literal import pydantic if TYPE_CHECKING: from mlflow.genai.utils.type import FunctionCall from mlflow.types.llm import Ch...
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"""Finding sharp-wave ripple events (150-250 Hz) from local field potentials. """ import functools import os import sys import warnings from collections.abc import Generator, Iterable from dataclasses import dataclass from itertools import pairwise from pathlib import Path from typing import Any, Literal, get_args im...
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#!/usr/bin/env python3 """ ANO Final Model Training - ANO Framework Module 8 ================================================= PURPOSE: Module 8 trains final production models using the best configurations from Modules 4-7, then compares their performance to select the best approach. KEY FEATURES: 1. **Best Configura...
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#!/usr/bin/env python3 ''' .. code-block:: !---------------------------------------------------------------------------! ! ML_NEA: ML-nuclear ensemble UV/vis spectra ! ! Implementations by: Bao-Xin Xue ! !------------------------------...
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"""Classes for handling genomic regions, variants and genotypes. """ # Standard imports import re from typing import ( Any, Optional, Union, List, Tuple, TypeVar, ClassVar, Set ) from itertools import zip_longest from enum import Enum # from math import factorial from math import log from copy import deepcopy # 3r...
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__author__ = "Simon Nilsson; sronilsson@gmail.com" import io import os import shutil from copy import copy from functools import lru_cache from typing import Any, Dict, List, Optional, Tuple, Union import cv2 import imutils import matplotlib #matplotlib.use('agg') import matplotlib.pyplot as plt import numpy as np imp...
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""" Metrics and loss functions for BiaPy. This module provides a variety of metrics and loss functions for evaluating and training deep learning models in BiaPy. It includes implementations for Jaccard index (IoU), Dice loss, BCE, Cross-Entropy, contrastive losses, instance segmentation losses, detection metrics, and ...
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"""Unit tests for gget virus module. This test module provides comprehensive validation of the virus function and all helper functions, covering downloads, filtering, parsing, and error handling for viral sequences and metadata from NCBI's virus database. Test Structure: --------------- The test suite uses a hybrid a...
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# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*- # vi: set ft=python sts=4 ts=4 sw=4 et: """Interfaces to assorted Freesurfer utility programs.""" import os import re import shutil from ... import logging from ...utils.filemanip import fname_presuffix, split_filename from ..base import ( ...
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from __future__ import annotations import datetime import functools import logging import re import warnings from abc import ABC, abstractmethod from collections import Counter from copy import deepcopy from inspect import isabstract from numbers import Number from typing import ( TYPE_CHECKING, Any, Calla...
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# -*- coding: utf-8 -*- # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*- # vi: set ft=python sts=4 ts=4 sw=4 et: """Interfaces to assorted Freesurfer utility programs. """ import os import re import shutil from ... import logging from ...utils.filemanip import fname_presuffix, split_filename f...
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""" This file contains functions to edit/preprocess volumes (i.e. not tensors!). These functions are sorted in five categories: 1- volume editing: this can be applied to any volume (i.e. images or label maps). It contains: -mask_volume -rescale_volume -crop_volume -crop_volume_around_reg...
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''' .. code-block:: !---------------------------------------------------------------------------! ! Interface_TorchANI: Interface between TorchANI and MLatom ! ! Implementations by: Fuchun Ge and Max Pinheiro Jr ! ! Defines the MS-ANI model ...
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#!/usr/bin/env python # -*- coding: utf-8 -*- """ This experiment was created using PsychoPy3 Experiment Builder (v2021.1.2), on szeptember 29, 2023, at 15:00 If you publish work using this script the most relevant publication is: Peirce J, Gray JR, Simpson S, MacAskill M, Höchenberger R, Sogo H, Kastman E, Li...
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import pickle import numpy as np import os import pandas as pd import gc import re import matplotlib.pyplot as plt import matplotlib.patches as patches import seaborn as sns import math import DataParser import ET_param_manager import ET_data_extraction import itertools """ The following list is a list of participans ...
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# Copyright (C) 2023 Lorenzo Posani # # This program is free software: you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by # the Free Software Foundation, either version 3 of the License, or # (at your option) any later version. # # This ...
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# Copyright 2017 Google LLC. # # Redistribution and use in source and binary forms, with or without # modification, are permitted provided that the following conditions # are met: # # 1. Redistributions of source code must retain the above copyright notice, # this list of conditions and the following disclaimer. # #...
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# # turtle.py: a Tkinter based turtle graphics module for Python # Version 1.1b - 4. 5. 2009 # # Copyright (C) 2006 - 2010 Gregor Lingl # email: glingl@aon.at # # This software is provided 'as-is', without any express or implied # warranty. In no event will the authors be held liable for any damages # arising from th...
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# # turtle.py: a Tkinter based turtle graphics module for Python # Version 1.1b - 4. 5. 2009 # # Copyright (C) 2006 - 2010 Gregor Lingl # email: glingl@aon.at # # This software is provided 'as-is', without any express or implied # warranty. In no event will the authors be held liable for any damages # arising from th...
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""" Base workflow class for BiaPy. This module defines the Base_Workflow abstract class, which provides the main structure and utility methods for building training and inference workflows in BiaPy. It handles configuration, model preparation, data loading, training, testing, metrics, logging, and post-processing for ...
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#!/usr/bin/env python3 """Build the independently derived external LD reference corpus foundation.""" from __future__ import annotations import argparse import csv import gzip import hashlib import importlib.metadata import json import os import shutil import subprocess import sys import tempfile from dataclasses imp...
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__author__ = "Simon Nilsson; sronilsson@gmail.com" import time start = time.time() import itertools import multiprocessing import numpy as np import pandas as pd from numba import (boolean, float32, float64, int64, jit, njit, prange, typed, types) from numba.typed import Dict, List from numpy.lib....
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# Author: Leland McInnes <leland.mcinnes@gmail.com> # # License: BSD 3 clause from __future__ import print_function import locale from collections import deque from warnings import warn import time from scipy.optimize import curve_fit from sklearn.base import BaseEstimator, ClassNamePrefixFeaturesOutMixin from sklear...
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from __future__ import annotations import argparse import sys from datetime import datetime from typing import Any import pandas as pd # Get current date and time for alphafold default foldername dt_string = datetime.now().strftime("%Y_%m_%d-%H_%M") import json # noqa: E402 import os # noqa: E402 import subproces...
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#!/usr/bin/env python # -*- coding: utf-8 -*- """ This experiment was created using PsychoPy3 Experiment Builder (v2021.1.4), on május 09, 2023, at 09:51 If you publish work using this script the most relevant publication is: Peirce J, Gray JR, Simpson S, MacAskill M, Höchenberger R, Sogo H, Kastman E, Lindelø...
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""" Toothy Purpose: Data ingestion (input data selection and data processing pipeline) Authors: Amanda Schott, Kathleen Esfahany Last updated: 2025-10-08 TODO - Replace icons for the probe selection widget black and white circle - TODO review probe_hanlder - TODO implement view_data_assignments better: should open...
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# -*- coding: utf-8 -*- # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*- # vi: set ft=python sts=4 ts=4 sw=4 et: """AFNI preprocessing interfaces.""" import os import os.path as op from ...utils.filemanip import load_json, save_json, split_filename, fname_presuffix from ..base import ( Co...
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import math import jax import numpy as np import pytest import scipy.ndimage import tensorflow as tf from absl.testing import parameterized from keras.src import backend from keras.src import testing from keras.src.backend.common import dtypes from keras.src.backend.common.keras_tensor import KerasTensor from keras.s...
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# -*- coding: utf-8 -*- __author__ = 'Carlos Ventura' __email__ = ['carlosventura@stonybrook.edu'] import tkinter as tk from tkinter import ttk, filedialog, messagebox import os import subprocess import shutil import glob import sys import ast from pathlib import Path import importlib import gzip import pickle import ...
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""" The ``data_tools`` module is a collection of functions that are designed to make it easier to do common data orientated operations on gwas datasets. These are the sorts of things that will often have to be done prior to an analysis taking place. Many of the functions in this module are used internally by ``read_gw...