sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
b4f610785efa6dcc7c0a864fc4bdd9cd546a0f2907c3ed351dd6b4f1a5e10154 | Python | 1,795 | 61 | import numpy as np
from pysteps.noise import fftgenerators
from pysteps.tests.helpers import get_precipitation_fields
PRECIP = get_precipitation_fields(
num_prev_files=0,
num_next_files=0,
return_raw=False,
metadata=False,
upscale=2000,
)
PRECIP = PRECIP.filled()
def test_noise_param_2d_fft_filt... |
91acc1a9805b8cac2f6afd477551d8269855dd5526619f40734021469e2740da | Python | 1,796 | 54 | import tensorflow as tf
class ResidualUnit(tf.keras.layers.Layer):
def __init__(self,units,activation='tanh',kernel_initializer='he_normal',**kwagrs):
super().__init__(**kwagrs)
self.activation = tf.keras.activations.get(activation)
self.main_layers = [
tf.keras.layers.Dense(un... |
1bfec3167a83455a1117c3abe5b53fa49fc6b5d444b3ab62b7347700e67c0857 | Python | 1,797 | 28 | def test_filter_spike_trains():
"""Test filtering of spike train dict"""
import neurodynex3.tools.spike_tools as spike_tools
from brian2 import ms
from brian2 import ms
st0 = [0, 1, 2] * ms
st1 = [10, 11] * ms
st2 = [2, 3, 4, 5] * ms
spike_trains = dict()
spike_trains[0] = st0
sp... |
b0d655482c2aa399f72dc6e0c4de60df203fc53d575c4721279fd58a486f77ab | Python | 1,798 | 54 | import tensorflow as tf
class ResidualUnit(tf.keras.layers.Layer):
def __init__(self,units,activation='tanh',kernel_initializer='he_normal',**kwagrs):
super().__init__(**kwagrs)
self.activation = tf.keras.activations.get(activation)
self.main_layers = [
tf.keras.layers.Dense(un... |
fed92652ddb875feb6b8b97d14c1cddc1a550986d21e9844c5beda4c1f764d57 | Python | 1,798 | 59 | from __future__ import annotations
import json
from pathlib import Path
import numpy as np
import pandas as pd
from datamonger import FetchResult, Registry, SparseDataset, fetch_data
ROOT = Path(__file__).resolve().parents[3]
SELECTOR = ROOT / "registry" / "releases" / "proof-0001" / "selector.json"
def _registry... |
3a7acb2de757609cb68b3a106063fe7b4d7bb7dd82907e03dbc93a415f4009a4 | Python | 1,800 | 39 | from src.models.tabular.widedeep.base import WDBaseModel
from pytorch_widedeep.models import SAINT
class WDSAINTModel(WDBaseModel):
def __init__(self, **kwargs):
super().__init__(**kwargs)
def build_network(self):
self.model = SAINT(
column_idx=self.hparams.column_idx,
... |
583190410e979cdd695c52cbb4d3296d312c305bd2116575916429fb088b75aa | Python | 1,800 | 49 | import numpy as np
import os.path as osp
import scipy.io
def roi(list_of_labels):
"""Mask for the selection of the region of interest in the surface
template.
Args:
list_of_labels (list): list with the file name (.mat) containing the
region of interest (from both L and R hemispheres)
... |
9c51e7e217698d725a3ef9e94b27cf0315a077b5178b47d45203ea125dba0826 | Python | 1,802 | 36 | # coding=utf-8
"""
ErodeImage module for the CellProfiler library.
This module contains the core algorithms for morphological erosion operations.
"""
from pydantic import validate_call, ConfigDict, Field
from typing import Union, Tuple, Annotated
from cellprofiler_library.types import ImageAny, StructuringElement
fr... |
15d09cea7f8b303151307f9d3ace37ae225d853068940d478a8d014d5dd2cf2e | Python | 1,806 | 61 | import numpy as np
import sys
sys.path.append('..')
from functions.def_ROIs_EarlyVisualAreas import roi
from functions.individual_variability import grab_data
def generate_eccentricity_mask(path):
"""
Generate a mask for eccentricity values between 1 and 8.
Args:
path (str): path to the data
... |
693a4f7c13ce682b860279ecb12da3103d697ac4886420eb25756b998b2b9584 | Python | 1,806 | 58 | """ tools.py - cpfigure tools that do not depend on WX
"""
import io
import centriole.cpmorphology
import imageio
import matplotlib
import matplotlib.figure
import matplotlib.transforms
import numpy
def figure_to_image(figure, *args, **kwargs):
"""Convert a figure to a numpy array"""
#
# Save the figure... |
e0cf54864eedd6e66fbdf17cd4f81f38630cb74084cc4ea97cb1becf6f466a4b | Python | 1,806 | 53 | # This file is part of pyunicorn.
# Copyright (C) 2008--2026 Jonathan F. Donges and pyunicorn authors
# URL: <https://www.pik-potsdam.de/members/donges/software-2/software>
# License: BSD (3-clause)
#
# Please acknowledge and cite the use of this software and its authors
# when results are used in publications or publi... |
02ae44d0596c3ceb8f8b43f37e4f2705c32a22efa82033242b8ed19fa27b6a6e | Python | 1,809 | 48 | #!/usr/bin/env python
# (This is an example similar to an example from the Adafruit fork
# to show the similarities. Most important difference currently is, that
# this library wants RGB mode.)
#
# A more complex RGBMatrix example works with the Python Imaging Library,
# demonstrating a few graphics primitives and i... |
754236f89cef7b78ec8f950aadcd84df0e4e2f99eb71fa306f1f31e6e7ca6067 | Python | 1,809 | 90 | import numpy
import numpy.random
import numpy.testing
from cellprofiler_core.image import Image
class TestImage:
def test_multichannel(self):
x = numpy.zeros((224, 224, 3), numpy.float32)
image = Image(x)
assert image.multichannel
def test_volumetric(self):
x = numpy.zeros(... |
17b61d771d83da21e975289039d7db3d2b46f29bc0d501438b551284350f627f | Python | 1,810 | 67 | import os
from Utils.cal_utils import readfq
# 遍历文件夹及其子文件夹中的文件，并存储在一个列表中
# 输入文件夹路径、空文件列表[]
# 返回 文件列表Filelist,包含文件名（完整路径）
def get_filelist(dir, Filelist):
if os.path.isfile(dir):
Filelist.append(dir)
# # 若只是要返回文件文，使用这个
# Filelist.append(os.path.basename(dir))
elif ... |
4d2c676f1dfbf80ae8788694352df0c9beddb4c4f7e14d59ec9cb1fdf2d37726 | Python | 1,812 | 42 | import numpy as np
class HH:
def __init__(self, n_neurons=50, v_init=-65.0, n_init=0.3177, m_init=0.0529, h_init=0.5961):
self.v = np.full(n_neurons, v_init)
self.n = np.full(n_neurons, n_init)
self.m = np.full(n_neurons, m_init)
self.h = np.full(n_neurons, h_init)
self.C = ... |
f66741dc5b7b9ae0a402b4dc11e6ecf83cfbfcfb60dd866c74bd6a92bf4aff4a | Python | 1,812 | 37 | # coding=utf-8
"""
DilateImage module for the CellProfiler library.
This module contains the core algorithms for morphological dilation operations.
"""
from pydantic import validate_call, ConfigDict, Field
from typing import Union, Tuple, Annotated
from cellprofiler_library.types import ImageAny, StructuringElement
... |
de3153b2d0f3cbe42a8c456bfd6cfcecb933dea1519525db8eee14df2a21134c | Python | 1,813 | 63 | # -*- coding: utf-8 -*-
import numpy as np
import pytest
from numpy.testing import assert_array_almost_equal
from pysteps.tests.helpers import get_precipitation_fields
from pysteps.verification import ensscores
precip = get_precipitation_fields(num_next_files=10, return_raw=True)
np.random.seed(42)
# rankhist
test_... |
b5f1fdd60626771d835fdab862543ca7c7e85154986a741257bd2fe035d579b2 | Python | 1,814 | 34 | from simulate import SimulationDataset
import torch
import numpy as np
# 设置模拟的次数ns（运行很快，可以设大数值）、force种类sim、节点数目n、时间数目nt
sim = 'spring'
ns, nt, n, dim = 10, 1000, 10, 2
# 预定义的六种force下的超参数，包括时间间隔dt、时间数目nt、节点数目n和维度dim
sim_sets = [{'sim': 'r1', 'dt': [5e-3], 'nt': [1000], 'n': [4, 8], 'dim': [2, 3]},
{'sim': ... |
b551697f49289ee32c17367fdfce3cb7dbae1a7d4bdfcdd47f68b82f293d2efb | Python | 1,815 | 66 | """
Module that implements watershed functionality as a two stage process where
1. watershed is performed per-slice, in a 2D domain, obtaining the fragments mask
2. watershed is performed at a volume level, in a 3D domain, and uses the previously generated fragments mask
"""
import numpy as np
import waterz
import z... |
b6fa52713937b95478258b6b9426a36811bc807a2760fc0ffb3f025e6428279c | Python | 1,815 | 62 | # -*- coding: utf-8 -*-
# (C) Copyright 2020, 2021, 2022, 2023 IBM. All Rights Reserved.
#
# This code is licensed under the Apache License, Version 2.0. You may
# obtain a copy of this license in the LICENSE.txt file in the root directory
# of this source tree or at http://www.apache.org/licenses/LICENSE-2.0.
#
# Any... |
cf68008b34ef4dfa69844b5735674b47288c27d11f9fa9ebef4aa2ba22108af4 | Python | 1,818 | 51 | # -*- coding: utf-8 -*-
"""
Created on Fri May 31 15:16:20 2019
@author: Xiaoxuan Jia
"""
import numpy as np
from scipy import signal
import matplotlib.pyplot as plt
#The periodogram can be efficiently computed using the fast Fourier transform (FFT).
# There is a variety of methods, such as Welch and Blackman-Tukey m... |
ff168254a13bf4bef8366ea3ad3d9bc3902173b86aaf7785140ba4dd58293429 | Python | 1,821 | 50 | import centriole.cpmorphology
import matplotlib
import matplotlib.collections
import numpy
import scipy.ndimage
class OutlineArtist(matplotlib.collections.LineCollection):
"""An artist that is a plot of the outline around an object
This class is here so that we can add and remove artists for certain
outl... |
80d458f562eaed74524bd2c353549b0acd95a29c52d6e1d9d04ed98632f3c5af | Python | 1,822 | 53 | # This file is part of pyunicorn.
# Copyright (C) 2008--2026 Jonathan F. Donges and pyunicorn authors
# URL: <https://www.pik-potsdam.de/members/donges/software-2/software>
# License: BSD (3-clause)
#
# Please acknowledge and cite the use of this software and its authors
# when results are used in publications or publi... |
e6ee671882d893a1f7af4936f8c6c8dda68c0f23914df9074da537ee32a22119 | Python | 1,823 | 68 | """
java.py - CellProfiler-specific JVM utilities
"""
import logging
import os
import scyjava
import cellprofiler_core.preferences
LOGGER = logging.getLogger(__name__)
def start_java():
"""Start CellProfiler's JVM via Javabridge
JVM parameters are harvested from preferences and
the environment variabl... |
4fec66604f3fdb5c291421f91db093007bb993903dfb904bdd3a144a9383c4f6 | Python | 1,824 | 56 | from typing import Literal
import numpy
from ..functions.object_processing import (
watershed as library_watershed,
)
# Simple wrapper for the object_procceing watershed function
def watershed(
input_image: numpy.ndarray,
mask: numpy.ndarray = None,
watershed_method: Literal["distance", "intensity", ... |
9906fd5a4cb2a0602b91896e4c29a733dbd305e0da452b93d88d40238444c104 | Python | 1,828 | 56 | import yaml
import pickle
import os
def recover_config(modelDir: str, outputFile: str) -> bool:
"""
This function recovers the configuration file from a model directory.
Args:
modelDir (str): The model directory with the configuration file and the model.
outputFile (str): The output file ... |
28df700416d81fb6699f5de6a2b23c541565f689fb0da99c78da995ff29337a4 | Python | 1,829 | 64 | from .._subscriber import Subscriber
from ..._validation_error import ValidationError
class ListSubscriber(Subscriber):
"""
Stores name provider names as a list
"""
def __init__(
self,
text,
group,
value=None,
can_be_blank=False,
blank_text="Leave blank... |
c0bd63d55346fa9f08a3ebd1f2360dcdca0ce98f80da12387a12cb18baccf62a | Python | 1,829 | 58 | """
DilateObjects
=============
**DilateObjects** expands objects based on the structuring element provided.
This function is similar to the "Expand" function of **ExpandOrShrinkObjects**,
with two major distinctions-
1. **DilateObjects** supports 3D objects, unlike **ExpandOrShrinkObjects**.
2. In **ExpandOrShrinkO... |
52d881821ec05ddb9104c907b2fd8bd2eec56b23827da079f2a146355206b243 | Python | 1,833 | 31 | from pydantic import Field, validate_call, ConfigDict
from typing import Annotated, List, Union, Optional
from ..opts.colortogray import ImageChannelType
from ..types import Image2DColor, Image2DGrayscale
from ..functions.image_processing import combine_colortogray, split_hsv, split_rgb, split_multichannel
@validate_... |
e91a9a4bdbf82de20351ff203c11f886004296fe20df6ab2caea2b163b20c4ff | Python | 1,835 | 57 | # -*- coding: utf-8 -*-
"""
pysteps.tracking.interface
===========================
Interface to the tracking module. It returns a callable function for tracking
features.
.. autosummary::
:toctree: ../generated/
get_method
"""
from pysteps.tracking import lucaskanade
from pysteps.tracking import tdating
_t... |
b84e85f69b5af25545e8a8ec6e0190c5244dde498c8386533167971630a4cb57 | Python | 1,836 | 35 | import brian2 as b2
from neurodynex3.brunel_model import LIF_spiking_network
print("b2.__version__={}".format(b2.__version__))
def test_LIF_spiking_network():
"""Test LIF spiking network: simulate_brunel_network(short pulse, 1ms, default values)"""
rate_monitor, spike_monitor, voltage_monitor, idx_monitored_... |
ef8ab84ec0158a58210c0813d11ebc2c595af27705d5f891fff63b979b585408 | Python | 1,838 | 63 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
"""Tests for metal.py"""
from __future__ import print_function
from __future__ import unicode_literals
from __future__ import division
import logging
from rdkit import Chem
from molvs.metal import MetalDisconnector
from molvs.standardize import standardize_smiles
loggi... |
a3899609c586a676c9875f77dd3149e8817492ba282c3bee0b2230af227b0632 | Python | 1,839 | 58 |
"""
ClinicalASL - Clinical Arterial Spin Labeling processing pipeline
ASL T1-from-M0 computation module.
Repository: https://github.com/JSIERO/ClinicalASL
Author: Jeroen Siero
Institution: UMCU (University Medical Center Utrecht), The Netherlands
Contact: j.c.w.siero@umcutrecht.nl
Description:
This module... |
422188337bdf88d4a9ef1b8dada20ddecf6dfb64012953f12bde763b8c7d0954 | Python | 1,841 | 48 | import numpy as np
import os.path as osp
import scipy.io
def roi(list_of_labels):
"""Mask for the selection of the region of interest in the surface
template.
Args:
list_of_labels (list): list with file names of visual areas masks (
.mat), from both L and R hemispheres to be merged to... |
9a280a42dd6ef52120fce0abdcd4272581af1ccd210c9f516a9c111572b0e5a8 | Python | 1,844 | 57 | import numpy as np
import matplotlib.pyplot as plt
import scipy.signal as spsn
def butter_lowpass(highcut, fs, order=5):
nyq = 0.5 * fs
high = highcut / nyq
b, a = spsn.butter(order, high, btype='low')
return b, a
def butter_highpass(lowcut, fs, order=5):
nyq = 0.5 * fs
low = lowcut / nyq
... |
80f1d68a90c549196a6b227ba1a5302e6eabf8d761779672831598a70b2e2df1 | Python | 1,845 | 57 | # Inheritaed from open-mmlab/mmclassification
# Modified by Hangyu LIN
#
import json
import logging
from collections import defaultdict
import torch.distributed as dist
from .logging import get_logger
def get_root_logger(log_file=None, log_level=logging.INFO):
"""Get root logger.
Args:
log_file (st... |
780392a52f16df1209d5e8dce7dd49fafc0d1c26e32aebc8c53b43d5c32ffe27 | Python | 1,846 | 63 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
import numpy as np
import TDBG
import os
import re
# get the name of the folder
cwd2 = os.path.split(os.getcwd())[1]
print(str(re.findall("\d+", cwd2)))
cwd2int = int("".join(filter(str.isdigit, cwd2)))
npzfile = f"temptest{cwd2int}.npz"
print(npzfile)
# ---------------... |
649c1127a3a67c29e1059fdf4a40acf39ab81f2f240ebdfb849d4ef405752cde | Python | 1,847 | 48 | import numpy as np
import os.path as osp
import scipy.io
def roi(list_of_labels):
"""Mask for the selection of the region of interest in the surface
template.
Args:
list_of_labels (list): list with file names of visual areas masks (
.mat), from both L and R hemispheres to be merged to... |
6035300e219e36dc25f5801f82fdcefc35951aabf0bc0497750ae02203761174 | Python | 1,848 | 31 | import tensorflow as tf
import config
def _parse_function(filename, label):
filename = config.DATA_DIR + '/' + filename
image_string = tf.read_file(filename)
image_decoded = tf.image.decode_jpeg(image_string, channels=3)
image_height = tf.shape(image_decoded)[0]
image_width = tf.shape(image_decoded... |
66b20a49e312a8ae5b2bdfb242284c16bdeb7fee06acc985b84e9cae470a576f | Python | 1,850 | 71 | from functools import partial
from numpy import (apply_along_axis,
diag,
eye,
flip,
isclose,
trace,
zeros,
moveaxis)
from numpy.linalg import eigh
def vec_to_tens(dt, convention=(0, 1... |
0b50e7444f95fd1ced654483504f824c6818cc13bf759a8b08b886f64f12dfba | Python | 1,853 | 59 | import numpy as np
from scipy import signal
from scipy.io import wavfile
from load import load_filter
def filter_wavfile(wavpath, outwavpath, lfilter_path, rfilter_path):
"""Apply sensimetrics filters to a WAV file, saving out a filtered version.
Parameters
----------
wavpath : str
Path t... |
3e89c9e5a1d7a0339841b57939c10adb4b746782a96acfa7ce01429811167af9 | Python | 1,854 | 50 | import dotenv
import hydra
from omegaconf import DictConfig
import pyrootutils
# load environment variables from `.env` file if it exists
# recursively searches for `.env` in all folders starting from work dir
dotenv.load_dotenv(override=True)
# project root setup
# searches for root indicators in parent dirs, like "... |
c388891de832d71aa72257c938300517a6cab0dae935cbcf1fc81d48ce11a001 | Python | 1,854 | 48 | import os
from ._multichoice import MultiChoice
from .._validation_error import ValidationError
from ..text import Directory
class SubdirectoryFilter(MultiChoice):
"""A setting that indicates which subdirectories should be excluded from an operation
The subdirectory filter holds a collection of subdirectori... |
05c0e473d3b00972e1fad4c053eccd40b684fe24265d37a7dac43977fe6b5be6 | Python | 1,857 | 74 | """
Module that implements utility functions:
- volume reading wrapper to handle h5 and tiff volumes
- volume writing wrapper to handle h5 and tiff volumes
"""
import os
import h5py
import imageio
import pathlib
import numpy as np
def ensure_dir(dpath):
head, tail = os.path.split(dpath)
if not os.path.exis... |
228f9e591dc22eb9e9da849995dcbd75fa6c854202f08eb0568a6dd3627980ba | Python | 1,857 | 60 | import csv
import math
import os
import sys
def get_alignment(lines):
alignment = []
seq = ""
for line in lines:
if ">" in line and len(seq) != 0:
alignment.append(seq)
seq = ""
elif ">" not in line:
seq = seq + line
if len(seq) != 0:
alignment.append(seq)
return alignment
in... |
e7a55093e176410e3bb1ac0f4760be3d1ddd741a28373ce1ebaddfa391ec1d19 | Python | 1,857 | 51 | #!/usr/bin/python3
def coex(dt, dc, **ka):
"""Performs co-expression analyses for all gene pairs.
Performs parallel computation with multiple processes on the same machine.
Model for co-expression between genes i & j:
X_i=gamma*X_j+alpha*C+epsilon,
epsilon~i.i.d. N(0,sigma**2).
Test statistic: conditional... |
db35f53d2d43c69ff7ecf44f111421e7c8c7d3d1d0959f91b7f883c7b1780f19 | Python | 1,858 | 55 | import math
import torch
import torch.nn as nn
import torch.nn.functional as F
from modules.clones import clones
def attention(query, key, value, mask=None, dropout=None):
"Compute 'Scaled Dot Product Attention'"
d_k = query.size(-1)
scores = torch.matmul(query, key.transpose(-2, -1)) \
/ math.s... |
74a6af99c13b70bb7d8adc1b572f3a63fa46d364644ec2d354f10a22257a06a1 | Python | 1,859 | 74 | #!/usr/bin/env python3
import os
import sys
from itertools import product
import numpy as np
from etspredict.job_submission import HTCSubmissionTemplate
subjects = list(
# np.loadtxt(os.path.join("..", "non_na_subjects.txt"), dtype=str)
np.loadtxt(os.path.join("..", "remaining.txt"), dtype=str)
)
session... |
5a19af8f1ef4ad3de5ce5852581d0b8b4a864671d4816af2fadf46635e812c31 | Python | 1,861 | 56 | import os
from unittest import TestCase
from config import ENDOSTROKE_DIR
from pathlib import Path
import numpy as np
import matplotlib.pyplot as plt
from .gendostroke import load_nifti, get_files_patient_path, calculate_total
class LoadingDataTest(TestCase):
def test_load_nifti(self):
files = [f for f i... |
bfae105a7af11a7f52ec7fcf08e639baa3e2219a7deca41a6f2805cecb0ccc28 | Python | 1,861 | 53 | from main import run
import sys
import subprocess
import argparse
parser = argparse.ArgumentParser()
parser.add_argument('--visible_gpus', type=str,
default="",
help='Determines the CUDA devices visible to ' +
'the script. A string of comma ' +
... |
feaa5ea6b868f69bab0dbf614d14fc1018f58992ddedbcff6cc012742bcde46c | Python | 1,864 | 50 | from ._multichoice import MultiChoice
from ...constants.setting import get_name_provider_choices
class SubscriberMultiChoice(MultiChoice):
"""A multi-choice setting that gets its choices through providers
This setting operates similarly to the name subscribers. It gets
its choices from the name providers... |
6e4b9ada58bb593a933a69a86141f8398432487a440bbc1257fcf50aa2b4711e | Python | 1,865 | 71 | # -*- coding: utf-8 -*-
# (C) Copyright 2020, 2021, 2022, 2023 IBM. All Rights Reserved.
#
# This code is licensed under the Apache License, Version 2.0. You may
# obtain a copy of this license in the LICENSE.txt file in the root directory
# of this source tree or at http://www.apache.org/licenses/LICENSE-2.0.
#
# Any... |
a21dd11066ca94c01cf7083c687cad1b40e64a9dbd31ead2e72b76d2d4746926 | Python | 1,866 | 61 | from ._setting import Setting
from ._validation_error import ValidationError
class Coordinates(Setting):
"""A setting representing X and Y coordinates on an image
"""
def __init__(self, text, value=(0, 0), *args, **kwargs):
"""Initialize an integer range
text - helpful text to be display... |
9ee137fe5ef27720fb29135a6a414f1824a49acc24e109229dcced6e4ad38d8d | Python | 1,869 | 74 | #!/usr/bin/env python3
import os
import sys
from itertools import product
import numpy as np
from etspredict.job_submission import HTCSubmissionTemplate
subjects = list(np.loadtxt("subjects_hcp_aging.txt", dtype=str))
missing_subs = list(np.loadtxt("missing_subs.txt", dtype=str))
subjects = [x for x in subjects i... |
1a102afaec7a8ff839337f0f133b64edb08cf6a7213b4cd0bbfd096671a7c9b7 | Python | 1,870 | 74 | class Alignment(object):
def __init__(self, method, parameters, library_templates, \
statistics = {}, id = 0):
self._method = method
self._parameters = parameters
self._library_templates = library_templates
self._statistics = statistics
from . import Database as db... |
5a73efe81a37dc53a8ed4f9775eb95305a90a6661bbbdfc7eb41080fc93bea5a | Python | 1,873 | 67 | from qutip import*
import numpy as np
from qutip.qip.circuit import QubitCircuit, Gate
from qutip.qip.operations import phasegate, rx, gate_sequence_product, cnot, sqrtswap, csign
from scipy import optimize,integrate
list = [ [[1,3]], [[3,2]], [[2,4]], [[4,6]], [[6,5]] ] ;
depth = 6 ;
width = 1 ;
num_qubit_total = ... |
8bf0aa710076ca4836051f2cca617bc7f8e21e1719a7f26f8afd5ca910a8bb3a | Python | 1,876 | 53 | """Smoke tests: the package imports, the quickstart runs, Predict_cord returns
the documented output, and Fit_cord is reproducible under a fixed seed."""
import os
import subprocess
import sys
import numpy as np
import pandas as pd
import scanpy as sc
import torch
ROOT = os.path.dirname(os.path.dirname(os.path.abspat... |
8d4deab72ada045f02b9cc1712af5b5ae05e5362dc70a9826d1305194d94fc32 | Python | 1,876 | 60 | from multiprocessing import cpu_count
from os.path import basename
from traitlets import Dict, Float,Integer
from mrHARDI.base.application import (mask_arg,
mrHARDIBaseApplication,
output_prefix_argument,
... |
98a6fe0d98562336dff25f071a1b0a5178d9a1bc95b79451ca025166cde5b377 | Python | 1,876 | 50 | import prov.model as pm
from .AcquisitionObject import AcquisitionObject
from ..core import Constants
class AssessmentObject(AcquisitionObject):
"""Class for NIDM-Experimenent generic AssessmentAcquisitionObject-Level Objects.
Default constructor uses empty graph with namespaces added from NIDM/Scripts/Const... |
3e0dca3a828a7a00e9b3f605f86f9d24c9f8e6f781ba1c4cd5a85016e3dd0de2 | Python | 1,877 | 70 | import json
import tensorflow as tf
import os
import datetime as dt
import pandas as pd
import numpy as np
from lib.regional_data_builder import rescale_df
# functions to save and load optimization steps
def load_steps(save_dir, optimizer):
try:
file = open(save_dir+'optimiser_results.json', 'r')
... |
69140e81512afd4459edd17a6c55800d8352fa8aca569d827239faaccb6fdc82 | Python | 1,879 | 55 | import os
import os.path as osp
from numpy.testing import assert_equal
import pytest
def get_rhino_root():
"""Return where the root directory structure is for data. Works by checking
some common places and looking for ``/etc/hostname``.
"""
data_roots = [
'/', # rhino
'/Volumes/rhino... |
73daf50d2be2010e99f5f47cbf37c43e00600bb16330be641d6217eefc11f1fb | Python | 1,880 | 60 | from typing import Generator
from numpy import less_equal, clip
from numpy.ma import clump_masked, clump_unmasked, masked_array
from mrHARDI.compute.utils import value_closest, value_first
def serialize_fsl_args(args_dict, separator="\n", bool_as_flags=False):
base_string = ""
if bool_as_flags:
base... |
95c87c90abfc1968f2aa45d7e85e4a80d151eb46d2aa60364329b50073cf2ff0 | Python | 1,880 | 92 | from enum import Enum
from typing import Union
import torch
class Format(str, Enum):
NCHW = 'NCHW'
NHWC = 'NHWC'
NCL = 'NCL'
NLC = 'NLC'
FormatT = Union[str, Format]
def get_spatial_dim(fmt: FormatT):
"""Return spatial dimension indices for a given tensor format.
Args:
fmt: Tenso... |
da8358cec77250b812fbe9b5bdf98df1f29a497aa4ed39bc4ec5f6aab088f175 | Python | 1,880 | 63 | #!/usr/bin/python3
import matplotlib.pyplot as plt
import numpy as np
import sys
import getopt
from scipy import signal
import researchdata1258
subj = 20
startsec = 60
endsec = False
task = False
helptext = 'usage: {} -p participant -s startsec -f noiseredfile.tsv -t task -m -h'.format(sys.argv[0])
helptext = helptex... |
3ddc026c6c7f96af98321ec052c9b4258ee35514b2dc95ec0610d67b10455735 | Python | 1,882 | 50 | import dotenv
import hydra
from omegaconf import DictConfig
import pyrootutils
# load environment variables from `.env` file if it exists
# recursively searches for `.env` in all folders starting from work dir
dotenv.load_dotenv(override=True)
# project root setup
# searches for root indicators in parent dirs, like "... |
90c4b7c18e895df0375c34a5ff0541a787e599edb7232e2d5330dfca23586cb3 | Python | 1,884 | 55 | import pandas as pd
import splitter as sp
import pair_generation_top as pg
import os
from sklearn.model_selection import KFold
import numpy as np
def make_dir(file_name):
ouput_path = file_name + '/'
try:
os.mkdir(ouput_path)
except OSError as error:
print(error)
return ouput_path... |
0e12fa21f09a7abf4c73dc3921853cd7e30a6973855046d3fcf914bf4606e3c2 | Python | 1,886 | 56 | # This file is part of pyunicorn.
# Copyright (C) 2008--2026 Jonathan F. Donges and pyunicorn authors
# URL: <https://www.pik-potsdam.de/members/donges/software-2/software>
# License: BSD (3-clause)
#
# Please acknowledge and cite the use of this software and its authors
# when results are used in publications or publi... |
40c3325213d3e20ef7ff469d310bcb231c553ea5a1ab36c8afc343f08d4b6f22 | Python | 1,887 | 40 | from src.models.tabular.widedeep.base import WDBaseModel
from pytorch_widedeep.models import TabTransformer
class WDTabTransformerModel(WDBaseModel):
def __init__(self, **kwargs):
super().__init__(**kwargs)
def build_network(self):
self.model = TabTransformer(
column_idx=self.hpa... |
9f4d941caeccd190ba7461642fc276eb80996b3085badcc8080c5fb73b2375dd | Python | 1,889 | 49 | from cellprofiler_core.preferences import INTENSITY_MODE_LOG
from cellprofiler_core.preferences import INTENSITY_MODE_NORMAL
from cellprofiler_core.preferences import get_default_colormap
from cellprofiler_core.preferences import get_intensity_mode
from ._workspace_view_row import WorkspaceViewRow
from ..artist import... |
712e22bd095229607325d3bf57ed7fd7a4d4215507dcddab06b93bbb096d1f19 | Python | 1,892 | 52 | # This file is part of pyunicorn.
# Copyright (C) 2008--2026 Jonathan F. Donges and pyunicorn authors
# URL: <https://www.pik-potsdam.de/members/donges/software-2/software>
# License: BSD (3-clause)
#
# Please acknowledge and cite the use of this software and its authors
# when results are used in publications or publi... |
7070851cef9b3d2a2f75e314fdc459de002c9ceb51beced6499ac6bf545d4196 | Python | 1,893 | 55 | # -*- coding: utf-8 -*-
# (C) Copyright 2020, 2021, 2022, 2023 IBM. All Rights Reserved.
#
# This code is licensed under the Apache License, Version 2.0. You may
# obtain a copy of this license in the LICENSE.txt file in the root directory
# of this source tree or at http://www.apache.org/licenses/LICENSE-2.0.
#
# Any... |
e402b6e596f92f8bc1d82f1e5632aa5cb9ef59c7c05a71dc07b2095e7a410918 | Python | 1,894 | 56 | import os
import argparse
import sys
import logging
import pandas as pd
def create_csv(data_path):
"""This function expects `data_path` to be structured in a certain way:
it should contain a list of folders: each one contains a 'image.nii.gz'.
"""
input_data = []
for subjectID in os.listdir(data_p... |
f133d8ed9cd94a78819ea28a652df6f4c6b63f579d3a91b548d6f6888e9e37ce | Python | 1,897 | 56 | """
ClinicalASL - Clinical Arterial Spin Labeling processing pipeline
ASL control/label interleaving module.
Repository: https://github.com/JSIERO/ClinicalASL
Author: Jeroen Siero
Institution: UMCU (University Medical Center Utrecht), The Netherlands
Contact: j.c.w.siero@umcutrecht.nl
Description:
Function for ... |
a7848b7a2e1d5e0abd1b2239196e727da969aadd1fcf2f12b42165416da05537 | Python | 1,899 | 62 | """Plugin modules - redirect module loads to the user's plugin
directory.
"""
# These examples:
# http://blog.dowski.com/2008/07/31/customizing-the-python-import-system/
# http://www.secomputing.co.uk/2009/05/importing-python-packages-in-memory.html
# were helpful when writing this code.
import glob
import imp
import... |
f472b8d13a4fdc5607dda88d29ac88f5ba85feb95dc080e662b59cfe15dbf98a | Python | 1,899 | 56 | import re
from .._text import Text
from ..._validation_error import ValidationError
class Alphanumeric(Text):
"""A setting for entering text values limited to alphanumeric + _ values
This can be used for measurement names, object names, etc.
"""
def __init__(self, text, value, *args, **kwargs):
... |
7775ee35975352960991b8f99562690d27e95d9d5607827326263f521baec955 | Python | 1,901 | 74 | #!/usr/bin/env python
import os
import h5py
import deeprank.generate
def clean_dataset(fname, feature=True, pdb=True, points=True, grid=False):
# name of the hdf5 file
f5 = h5py.File(fname, 'a')
# get the folder names
mol_names = f5.keys()
for name in mol_names:
mol_grp = f5[name]
... |
7ea692f8c0dc641d8fd49abcecdedfc465130464a5314bb6a87ad611c88a27a0 | Python | 1,901 | 73 | import os
import subprocess
import sys
from typing import List
from test_utils import PY_PACKAGE, ROOT, cd, print_time, record_time
class TypeCheckPaths:
"""The paths mypy runs on."""
MYPY = (
# core
"python-package/",
# tests
"tests/python/generate_models.py",
"tests... |
e4106cd9f6a84e424f19f26f13dfd6cd46e649880952eaf6b19114a281627b3d | Python | 1,901 | 47 |
import importlib
from tensorflow.keras.models import Model
from tensorflow.keras.layers import Dropout, Dense
from tensorflow.keras.optimizers import Adam
from utils.losses import earth_movers_distance
class Nima:
def __init__(self, base_model_name, n_classes=10, learning_rate=0.001, dropout_rate=0, loss=earth_m... |
ecfeddf46916ac44fb48e0cec0b2e8d95412251cbd691970ebafe9507095f72b | Python | 1,901 | 54 | import numpy as np
from numpy import pi,linspace
import cmath, random
from pylab import *
from training_data import *
from forward_backward import *
def mean_fidelity(X):
total_fidelity = 0 ;
for i in range(size_train):
phiout, _ = forward_th(X, train_psi[i]) ;
total_fidelity = total_fidel... |
155db5510ec2e12dc0965577dc03afa1dea97aaf1b6d1e7f9f30e6bc384ad8ff | Python | 1,903 | 56 | import numpy as np
import torch
from lib.graph import grid_tensor
def reshape_square(x, channels=None):
# transform to numpy
if isinstance(x, torch.Tensor):
x = x.cpu().detach().numpy()
N = x.size
if channels is None:
# assumes that there is just one one channel
dimension = N
... |
95fdfb73cbb534f6c9d6a9a0ea601696148a896ac8f31f75f0a75124c9c3ab4a | Python | 1,903 | 122 | import numpy as np
"""Uses the data from https://search.r-project.org/CRAN/refmans/GeDS/html/coalMining.html"""
coal_mining_data = {
"disasters": np.array(
[
5,
4,
1,
0,
4,
3,
4,
0,
6,
3... |
6ba8dc635665f354f491637bd7e03c3aba9fe9d574aa791099681755ee016e4c | Python | 1,904 | 63 | # -*- coding: utf-8 -*-
# (C) Copyright 2020, 2021, 2022, 2023 IBM. All Rights Reserved.
#
# This code is licensed under the Apache License, Version 2.0. You may
# obtain a copy of this license in the LICENSE.txt file in the root directory
# of this source tree or at http://www.apache.org/licenses/LICENSE-2.0.
#
# Any... |
373bab007d8f9909064a1cb1ca0752f09fb4e68ddd471a019cb937065a4a6cee | Python | 1,905 | 54 | """
Command-Line script used to clean segmentations produced by the automatic segmentation pipeline.
It takes as parameters:
1. the minimum segment size
2. the minimum number of segment slices
3. boolean indicating if relabeling is requested
4. path to output segmentation
Then:
1. it removes all segments that are s... |
680e22964d64315a3c41e1915fd488e1e0d7833eb7f8f93d98c0d7f1e4568c7c | Python | 1,905 | 63 | """
RemoveHoles
===========
**RemoveHoles** fills holes smaller than the specified diameter.
This module works best on binary and integer-labeled images (i.e., the output of
**ConvertObjectsToImage** when the color format is *uint16*). Grayscale and multichannel
image data is converted to binary by setting values bel... |
dbfe5c91deaeacf571fd3156811078c3b3e00264ce558c6c8d00111be272b6de | Python | 1,905 | 63 | """ Step Scheduler
Basic step LR schedule with warmup, noise.
Hacked together by / Copyright 2020 Ross Wightman
"""
import math
import torch
from typing import List, Tuple, Union
from .scheduler import Scheduler
class StepLRScheduler(Scheduler):
"""
"""
def __init__(
self,
opt... |
4f29b3adbe166e987345676ac36e19f433b7c183b2c165b0c18a584668dc8353 | Python | 1,906 | 72 | # -*- coding: utf-8 -*-
import numpy as np
import pytest
from numpy.testing import assert_array_almost_equal
from pysteps.extrapolation.semilagrangian import extrapolate
def test_semilagrangian():
"""Test semilagrangian extrapolation with number of timesteps."""
# inputs
precip = np.zeros((8, 8))
pre... |
dcaeaed3d40d601bba212358e59ce992f8cec98031a1072c4410354b3b42d879 | Python | 1,906 | 42 | import os
import torch
import random
import numpy as np
from PIL import Image
import torchvision.transforms as transforms
import datasets.data_util as data_util
from pathlib import Path
from DSEC.dataset.provider import DatasetProvider
def DSECEvents(dsec_dir, nr_events_data=1, delta_t_per_data=50, nr_events_window... |
892d640ccbec9e96157aaf40e235cc6f75d3529a0bf27f8866bde6ce6cdb5f95 | Python | 1,910 | 63 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
"""Tests for normalize.py"""
from __future__ import print_function
from __future__ import unicode_literals
from __future__ import division
import logging
from rdkit import Chem
from molvs.normalize import Normalizer
logging.basicConfig(level=logging.DEBUG)
def normal... |
a502f791740f26760def51219d4bcd1f124cc4990d5fd8dd87dbf7cee8857f83 | Python | 1,916 | 64 | #!/usr/bin/env python3
# Copyright 2021 Alexander Meulemans, Matilde Tristany, Maria Cervera
#
# 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
... |
f1db5efe271aa869794756e966b0055f977a32f2aad9c22baa6f2ff96158695b | Python | 1,917 | 50 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
import os
from setuptools import setup
if os.path.exists('README.rst'):
long_description = open('README.rst').read()
else:
long_description = '''MolVS is a molecule validation and standardization tool, written in Python using the RDKit
chemistry framework. Buildi... |
04932f3c4d626654334152c48e7c138913fbf0d8bf764cd45f9460764e6648b1 | Python | 1,924 | 63 | """empty message
Revision ID: a0928ce2eee6
Revises: 11230bf660dc
Create Date: 2021-10-13 16:19:02.318876
"""
from alembic import op
import sqlalchemy as sa
# revision identifiers, used by Alembic.
revision = "a0928ce2eee6"
down_revision = "11230bf660dc"
branch_labels = None
depends_on = None
def upgrade():
# ... |
a41ede3e4230e62a908b46bc32e8e791ea94380e826a4ce81d0bfc260d15cefc | Python | 1,925 | 55 | from __future__ import annotations
from dataclasses import dataclass
from typing import Optional
import pytest
from nidm.experiment.tools.rest import RestParser
from nidm.util import urlretrieve
from ..conftest import BrainVol
@dataclass
class OpenNeuro:
files: list[str]
project_uri: str
@pytest.fixture(sco... |
554243b59245528689fc5b0193fecf126aca68637b8905495f06b457ad040451 | Python | 1,926 | 55 | """
alignReads
"""
import subprocess
import os
import logging
logger = logging.getLogger('root')
logger.propagate = False
def alignReads(cores, BWA_path, genome_path, read1, read2, outfile):
sample_name = os.path.basename(outfile).split('.')[0]
output_folder = os.path.dirname(outfile)
if not os.path.ex... |
dab3066a7f21b276062a2c4111a87001dabff5aa7070199da9dd213e79fd7712 | Python | 1,926 | 47 | import torch
from torch.utils.data import Sampler
from torch._six import int_classes as _int_classes
class SequentialSubsetSampler(Sampler):
"""Samples elements sequentially given a list of indices,
Arguments:
indices (sequence): a sequence of indices
"""
def __init__(self, indices):
... |
9c539bfa249e1e85689b0561f21297e1cbf1753e83b4784f2dc566fd06f4329a | Python | 1,927 | 48 | import itertools
import json
import warnings
from pathlib import Path
from typing import Union
import pandas as pd
from .base import BaseReader
class LocReader(BaseReader):
"""
Reads a localization file ("localization.json") and returns the data it contains as a flat DataFrame.
Nested fields in the JSON... |
791d5219c84a7d2e8d78d319883b04497f9dceed9108eac642b19c9b05fe3fde | Python | 1,930 | 41 | from src.models.tabular.widedeep.base import WDBaseModel
from pytorch_widedeep.models import TabFastFormer
class WDTabFastFormerModel(WDBaseModel):
def __init__(self, **kwargs):
super().__init__(**kwargs)
def build_network(self):
self.model = TabFastFormer(
column_idx=self.hparam... |
1465f07331cc8b623fe0fb26352f786eaf00a375c93417b8edc88707a1a26551 | Python | 1,933 | 57 | # -*- coding: utf-8 -*-
# (C) Copyright 2020, 2021, 2022, 2023 IBM. All Rights Reserved.
#
# This code is licensed under the Apache License, Version 2.0. You may
# obtain a copy of this license in the LICENSE.txt file in the root directory
# of this source tree or at http://www.apache.org/licenses/LICENSE-2.0.
#
# Any... |
a40aa841e6f457e7ae9651f03fb7b6777fc7ef5c15430db7e9c87ca63ba9bcbe | Python | 1,933 | 82 | import pdb
import torch
import torch.nn as nn
class BaseForwardModel(nn.Module):
def __init__(
self,
):
super(BaseForwardModel, self).__init__()
pass
def forward(
self,
num_samples: int,
pars: torch.Tensor,
):
pass
class ... |
52affcf82aeb034e597fb025b86e3626856821d27097d73ac899ede241a7db8f | Python | 1,935 | 50 | #!/usr/bin/env python2
# -*- coding: utf-8 -*-
"""
Created on Fri Apr 13 15:50:27 2018
@author: saskiad
snippet from nicain
"""
from allensdk.brain_observatory.locally_sparse_noise import LocallySparseNoise as LocallySparseNoiseBase
from allensdk.core.brain_observatory_cache import BrainObservatoryCache
import allen... |
aec2fc5e014f89dbb634c080b51648761cf23259b9ba4b8ae43b360e740e309c | Python | 1,937 | 64 | #!/usr/bin/env python3
# Copyright 2021 Alexander Meulemans, Matilde Tristany, Maria Cervera
#
# 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
... |
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