sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
de2b475d6f1bcf7a252274a0df46071018a6dd8aa08ac4d564134c6e520a7461 | Python | 950 | 38 | import unittest
import numpy as np
import numpy.testing as npt
import random
import sigpy as sp
from sigpy.mri import retro
from sigpy.mri.dims import *
if __name__ == "__main__":
unittest.main()
class TestApp(unittest.TestCase):
def test_find_nonzero_ky_lines(self):
kdat = np.zeros([1, 1, 40, 1, 1... |
dbf24216747e1335daa6f945081cf3108383f2827808737ef393e441ef080b05 | Python | 953 | 28 | # This script is part of mousebrains (http://www.github.com/schlegelp/navis-mousebrains).
# Copyright (C) 2020 Philipp Schlegel
#
# 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, e... |
8146e60d1e8e291174e2183cc84c786145ccc78033ac7941a825138fa9d0b499 | Python | 970 | 28 | import pysam
import argparse
def parse_args():
parser = argparse.ArgumentParser()
parser.add_argument("in_bam")
parser.add_argument("out_bam")
parser.add_argument("--head-trim", type=int)
parser.add_argument("--tail-trim", type=int)
return parser.parse_args()
if __name__ == "__main__":
arg... |
5baa51de788666d23b559d11178d4b0153f6e8ac3bc00965b7739737cdb74034 | Python | 990 | 25 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
# somnotate --- Automated polysomnography for experimental animal research
# Copyright (C) 2019 Paul Brodersen <paulbrodersen+somnotate@gmail.com>
# Author: Paul Brodersen <paulbrodersen+somnotate@gmail.com>
# This program is free software; you can redistribute it and/o... |
ee8f583176840dc2c1cac125e1e87267b61e368a0f4bbf367bed86907c566d65 | Python | 1,017 | 40 | from argparse import ArgumentParser
from . import __version__
import os
import cothread
from threading import Thread
import cv2
import time
from softioc import builder, softioc
from GoniOwl.GoniOwl_controller import GoniOwlController
__all__ = ["main"]
print("Hello I am setting up")
goniowl_controller = GoniOwlCo... |
e4217da4e889d345f1df52451a145a03092012709f167e5dd78d882c7d0c45b6 | Python | 1,023 | 34 | """Tests classes in modalities module"""
import unittest
from pydantic import BaseModel
from aind_data_schema_models.modalities import Modality
class TestModality(unittest.TestCase):
"""Tests methods in Modality class"""
def test_from_abbreviation(self):
"""Tests modality can be constructed from ab... |
5f8179f9946d3ffbfa55fbf81bd676fc17929c806833684d9d9b14b8e1e99a0f | Python | 1,036 | 33 | import zmq
from lightparam.param_qt import ParameterTree
class ExternalCommunicationSettings(ParameterTree):
def __init__(self):
super().__init__()
class ZMQcomm:
def __init__(self, zmq_tcp_address="tcp://localhost:5555", timeout=2):
self.zmq_tcp_address = zmq_tcp_address
self.timeou... |
9263a4f7bda86ee3dcc10c9129f2c42b9deecdbfab7efda20eee037b44896965 | Python | 1,047 | 31 | from setuptools import setup, find_packages
import os
# Read the contents of your requirements.txt
# This ensures GitHub and Colab install the same libraries you use locally
with open("requirements.txt") as f:
required = f.read().splitlines()
setup(
name="spatchcocking",
version="0.1.0",
author="nchah... |
f2e6ac19d507995b7111e8c938ed0406407feb997a68ad7597162c5f5316cedd | Python | 1,072 | 41 | import json
import sys
def validate_json_stream(stream):
try:
json.load(stream)
return True
except json.JSONDecodeError as e:
print(f"Invalid JSON: {e.msg}", file=sys.stderr)
print(f"Line {e.lineno}, column {e.colno}", file=sys.stderr)
return False
def main() -> int:
... |
b48e9b332d71ba7cd039d9c5e8a216d929c4b107093193033a6e47528b39cf83 | Python | 1,108 | 39 | def abspath(path):
import os
base_path = os.path.abspath(os.path.dirname(__file__))
return os.path.join(base_path, path)
def test_image_nuclei_2d(return_mask=False):
""" Fluorescence microscopy image and mask from the 2018 kaggle DSB challenge
Caicedo et al. "Nucleus segmentation across imaging e... |
ad85119a4351c082fb40597022439318d7e9cf7523f4a6c0c406a4a9fe118a62 | Python | 1,115 | 50 | from cloudvolume import CloudVolume
import numpy as np
from copy import deepcopy
black = CloudVolume('gs://seunglab-test/test_v0/black')
info = deepcopy(black.info)
sizes = (
# [128,128,1],
# [128,128,2],
# [128,128,4],
# [128,128,4],
# [128,128,8],
# [128,128,16],
# [128,128,32],
# [128,128,64],
[128,128,1... |
7b3ba07f8405de292e1f7f42c417152782b51ad87706556fd8dd54821c00b57f | Python | 1,120 | 27 | import os
import pathlib
from tetra.utilities import get_platform
GPU_BUILD = os.getenv("BUILD_CUDA", "off").lower() in ("true", "1", "on")
PLATFORM = get_platform()
ROOT_DIR = pathlib.Path(__file__).parent.parent
_input_folder_override = os.getenv("INPUT_FOLDER")
if _input_folder_override is not None:
INPUT_FOLD... |
9f78e939fec25f1dcc83ab0eaaff00f119b1b60f5c5268036b8e0f8ea155a00b | Python | 1,140 | 31 | import sys
import traceback
import subprocess
from seuronbot import SeuronBot
from bot_utils import replyto, download_file
from airflow_api import set_variable
@SeuronBot.on_message(["update python package", "update python packages"],
description="Install extra python packages before starting th... |
f9d6548f9bf1328ad713b99ea73273df4cc0a1d74a1ff363cc3c0bc0c887bb62 | Python | 1,152 | 50 | import unittest
import numpy as np
import sigpy as sp
import sigpy.mri.rf as rf
from sigpy.mri.rf import linop
if __name__ == "__main__":
unittest.main()
def check_linop_adjoint(A, dtype=np.float32, device=sp.cpu_device):
device = sp.Device(device)
x = sp.randn(A.ishape, dtype=dtype, device=device)
... |
e3770cabd2d198270153b8ca809969a106abccb672bc11ba8da47d154a26a9c0 | Python | 1,186 | 31 | from seuronbot import SeuronBot
from bot_utils import replyto, download_file
from bot_info import broker_url
from kombu_helper import drain_messages
from airflow_api import set_variable, run_dag
@SeuronBot.on_message(["run custom cpu task", "run custom cpu tasks"],
description="Run custom cpu tas... |
fd5f91e94b2dd165e1c8b854bb9ec77a3cb1c97cd3d42df69d29d559c2c0b7bd | Python | 1,227 | 47 | import math
import unittest
import numpy as np
import numpy.testing as npt
import sigpy.mri.rf as rf
if __name__ == "__main__":
unittest.main()
class TestTrajGrad(unittest.TestCase):
def test_min_gradient(self):
t = np.linspace(0, 1, 1000)
kx = np.sin(2.0 * math.pi * t)
ky = np.cos(... |
1e946ddc94cfe68ec24aea7c099ff8083911d1cdd1961a894aaf0bb7296c5df8 | Python | 1,233 | 30 | import os
# These options can be overridden by setting environment variables with
# the same names before importing tetra.
class ValidationOptions(object):
_instance = None
def __new__(cls):
if cls._instance is None:
cls._instance = super(ValidationOptions, cls).__new__(cls)
c... |
aea4f088f8398db99292c7a0f8364ec3e1bc6e85bdcb82f1fd02580d0339cf65 | Python | 1,274 | 45 | import re
import subprocess
import sys
def get_latest_version():
tags = str(subprocess.check_output('git tag', shell=True))
tags = re.sub("^b'", '', tags)
tags = re.sub("'$", '', tags)
tags = re.split(r'\\n', tags)
tags = [ tuple(map(int, re.split('\.', tag))) for tag in tags if tag ]
tags = sorted(tags, reverse... |
3722419242ce2402803da9169ce9c4254e577318c99fc149baf8eb6680c249aa | Python | 1,279 | 33 | import os
import pysam
test_dir = os.path.dirname(__file__)
seq_lengths = dict()
with pysam.AlignmentFile(os.path.join(test_dir, "resources", "donor_read_sort.bam"), "rb") as in_bam:
with pysam.AlignmentFile(os.path.join(test_dir, "resources", "donor_read_sort_mn_tag.bam"), "wb", template=in_bam) as out_bam:
... |
8c3dd852096cb29ee9840f65872f7dc4bb54f077c616f9235106c5cd11f69d65 | Python | 1,293 | 31 | import pandas as pd
from rdkit import Chem
from rdkit.Chem import AllChem
import joblib
class XGBoostPredictor:
def __init__(self):
self.xgboost_clf = joblib.load('xgboost_model1.pkl')
self.variance_threshold = joblib.load('variance_threshold1.pkl')
def smiles_to_morgan(self, smiles,... |
8fedfb290f7de35a5d58b57e99d674f56ec18673e4aa60f6cee9229ca3d3001e | Python | 1,302 | 42 | from functools import wraps
import os
import re
import inspect
try:
import unittest.mock as mock
except ImportError:
import mock
norm_pattern = re.compile(r'[/|.]')
def patch_plugin_file(*patch_args, **patch_kwargs):
"""
Decorator used to search for in items:
"""
root, filename = os.path.spli... |
39fa24aab9c9ee9584bc9d971704c4e56a70c9cb2bb22e844cfe5c277abd821e | Python | 1,342 | 27 | import streamlit as st
def show_mission():
st.markdown("## 🌍 Our Mission - SRTA City")
st.markdown("""
### 🔬 **Who We Are**
We are a research-driven team at **SRTA City**, dedicated to advancing **drug discovery** using Artificial Intelligence.
### 🎯 **Our Goals**
- **Predict IC50 & pI... |
473ea44839d76d46a764472812b8a77fb8215f5e96cb8a83df11019d7c35f561 | Python | 1,343 | 53 | """Module for computer system and architecture definitions"""
from enum import Enum
class OperatingSystem(str, Enum):
"""Operating systems"""
WINDOWS_8 = "Windows 8"
WINDOWS_10 = "Windows 10"
WINDOWS_11 = "Windows 11"
MACOS_BIG_SUR = "MacOS Big Sur"
MACOS_MONTEREY = "MacOS Monterey"
MACO... |
519d41ccc899f218f3090813030ace10ac104e5be7a064257edd4cd4deab6fa4 | Python | 1,345 | 31 | import pandas as pd
from rdkit import Chem
from rdkit.Chem import AllChem
import joblib
class XGBoostIC50Predictor:
def __init__(self):
self.xgboost_clf_ic50 = joblib.load('xgboost_model1_IC50.pkl')
self.variance_threshold_ic50 = joblib.load('variance_threshold1_IC50.pkl')
def smiles... |
b9186f63f7161bbd3e371cd2fb53a6cf7d4d2b0d8299b0f7433f91a92ee4cd47 | Python | 1,371 | 39 | """The core module contains functions and classes for signal processing.
SigPy provides simple interfaces to commonly used signal processing functions,
including convolution, FFT, NUFFT, wavelet transform, and thresholdings.
All functions, except wavelet transform, can run on both CPU and GPU.
These functions are wra... |
0494a74014db13def37b6a119d6c43a0718cf151dcd7e68cc41bb5a4be0ce8c4 | Python | 1,397 | 65 | import matplotlib.pyplot as plt
import numpy as np
import csv
import sys
from collections import defaultdict
rows = []
filename = sys.argv[1]
with open(filename, 'r') as csvfile:
votereader = csv.reader(csvfile, delimiter='\t', quotechar=None)
for row in votereader:
rows.append(row)
headers = rows.pop... |
0b2a9699db064a28409dcc1a1ded668d374688c95b04113d004f5baea2e88516 | Python | 1,406 | 40 | """Dev utilities for constructing models from CSV files"""
import re
import yaml
import requests
import pandas as pd
from pathlib import Path
def to_class_name_underscored(name: str) -> str:
"""Convert a name to a class name by capitalizing and removing non-alphanumeric characters.
Always prefixes the strin... |
137f74b039107f14f128920f1d1fe290b4bb6e261f40b39621ba0c5cf409d1f6 | Python | 1,425 | 45 | import unittest
import numpy as np
import numpy.testing as npt
from sigpy.mri import samp
if __name__ == "__main__":
unittest.main()
class TestPoisson(unittest.TestCase):
"""Test poisson undersampling defined in `sigpy.mri.samp.poisson`."""
def test_numpy_random_state(self):
"""Verify that ran... |
768cbb312ba34fde09e82c723d3cc48ff5bf0c9d7930e6f88df4285095c7370a | Python | 1,492 | 63 | import json
from pathlib import Path
import os
import glob
from pathlib import Path
from typing import List, Optional, Sequence
def load_json(path: str | Path) -> dict:
with open(path, "r") as f:
return json.load(f)
def find_setting_subfolders(
main_path: str | Path,
subname: str,
setting_... |
6e0d37aefc86f12f0ee5e911a1609d42af29f35b3625cfb342079c1f9b7ce0fd | Python | 1,500 | 54 | from typing import Optional
from .sharded import GrapheneShardedMeshSource
from .unsharded import GrapheneUnshardedMeshSource
from .metadata import GrapheneMeshMetadata
from ..metadata import GrapheneMetadata
from ....cacheservice import CacheService
from ....paths import strict_extract
from ....cloudvolume import Sh... |
e1911363b973308b2f26bdf428680e74056d147e4c41ae2c4cdc4dba241f79fc | Python | 1,518 | 30 | def worker_op(**kwargs):
from custom.docker_custom import DockerWithVariablesOperator
dag = kwargs['dag']
default_args = kwargs.get("default_args", dag.default_args)
return DockerWithVariablesOperator(
variables=kwargs["variables"],
mount_point=kwargs.get("mount_point", None),
ta... |
0d966e55819fb6ea2a071b2204023ee372f371f575842e283c920d77e467b1bb | Python | 1,523 | 48 | import pandas as pd
import numpy as np
import argparse
import sys
import os
import re
def main():
parser = argparse.ArgumentParser(description='Generate FreeSurfer alike stats2table files from radiomics.csv (see radiomics_extractor).')
parser.add_argument(
'--file_prefix',
type=str,
... |
856ebb3c8506737d5f46da756c427fd6ebdacebc2d8119b9faaa897ad977d69a | Python | 1,531 | 44 | from kombu import Connection
import requests
def check_queue(queue):
ret = requests.get("http://rabbitmq:15672/api/queues/%2f/{}".format(queue), auth=('guest', 'guest'))
if not ret.ok:
raise RuntimeError("Cannot connect to rabbitmq management interface")
queue_status = ret.json()
return queue_s... |
2d2629409cbfcf75128d11cbfd8fdc988104714b8ed708e4489ce39a086e9828 | Python | 1,543 | 54 | import argparse
import pathlib
import sys
from ont_output_specification_validator import (
errors,
settings,
validate_file,
validators,
)
from ont_output_specification_validator.specification import (
load_local_specification_bundle,
)
from ont_output_specification_validator.validators.fastq impo... |
a14d9dc2660e83ff6b6a3fb21c25dc8ab9cc69e5dc39d56365d37260195600e9 | Python | 1,547 | 52 | import unittest
import numpy as np
import numpy.testing as npt
from sigpy import app, util
from sigpy.mri import dce
if __name__ == '__main__':
unittest.main()
class TestDCE(unittest.TestCase):
def test_dce(self):
# %% DCE Sample Time
acq_time = 10 # total acquisition time (minute)
t... |
9dc97e4101212d1e1a946d715184d6bab8153559cb3a705d2165a5f95c28e3b5 | Python | 1,550 | 46 | import os
import pathlib
import subprocess
import typing
DEBUG = os.getenv("BUILD_TYPE", "Release").upper() == "DEBUG"
def run_dorado(
cmd_args: list,
timeout: int,
outfile: typing.IO | None = None,
errfile: typing.IO | None = None,
):
print("Dorado command line: ", " ".join(cmd_args))
out = ... |
4cb8f403c57fa4295be357240f0e35c21ad81bbf21aa5d827b5a679086dbf8a6 | Python | 1,571 | 53 | import os
import pathlib
import platform
import subprocess
from datetime import datetime
ROOT_DIR = pathlib.Path(__file__).parent.parent
def get_env_or_raise(name: str) -> str:
val = os.getenv(name)
if val is None:
raise Exception(f"Couldn't find environment variable {name}")
return val
def get... |
1d9fca43771c59d1b6e1196a59296c66367d350dba44c455548fd072a00469ae | Python | 1,593 | 47 | import pathlib
import unittest
from contextlib import contextmanager
from tetra.regression_manager import RegressionManager, TestResult
from tetra.timestamped_context import TimestampedContext
class TestContext(object):
def __init__(
self, test_name: str, manager: RegressionManager, output_folder: pathli... |
0381378337435564d232384e29987fa64b5f8db3f1c1c35f3d83f87bd67e0d63 | Python | 1,596 | 48 | import nibabel as nib
import nibabel.processing as nib_processing
import nibabel.orientations as nib_orientations
import nibabel.funcs as nib_funcs
import numpy as np
import argparse
if __name__ == '__main__':
parser = argparse.ArgumentParser(description='Reorient to LIA and resample to 1mm iso-voxel resolution i... |
f22d63f17db58450b48fc255a13249a2d463ffa7e36c44b68903aa3be76113c1 | Python | 1,596 | 19 | #!/usr/bin/env python3
import pandas as pd, os, sys, argparse
#for line in open(sys.argv[1], "r"):
metadata = pd.read_csv(sys.argv[1])
for row in range(len(metadata)):
SAMPLE = str(metadata.loc[row,"SRM_sample_number"]) + "_" + str(metadata.loc[row,"Submitted_sample_name"])
ID = str(metadata.loc[row... |
09e089cabcbd267007a0800ec69a156d34040fdb29321af8637aad5fd3a0700d | Python | 1,601 | 50 | import time
from seuronbot import SeuronBot
from bot_utils import replyto, send_message
from common.google_api import get_project_data, get_instance_data, get_instance_metadata, set_instance_metadata
import tenacity
@SeuronBot.on_message("redeploy docker stack",
description="Restart the manager ... |
f33100bc16a554409c7886450d33bcbc3c34e50a358035377184d5f537680030 | Python | 1,627 | 54 | import os
import pickle
import gzip
import argparse
import mudata
import warnings
from scenicplus.simulation import simulate_perturbation
def load_object(filename):
with open(filename, 'rb') as f:
return pickle.load(f)
def save_object(obj, filename):
with gzip.open(filename + '.gz', 'wb') as f:
... |
879dc809f99de6cfc6b675cb9dc15dc300267c10b65caff304eda6490840e716 | Python | 1,630 | 62 | import tenacity
from tqdm import tqdm
from cloudvolume.connectionpools import S3ConnectionPool, GCloudBucketPool
from cloudvolume.threaded_queue import ThreadedQueue
from cloudfiles import CloudFiles
S3_POOL = S3ConnectionPool('s3', 'seunglab-test')
GC_POOL = GCloudBucketPool('seunglab-test')
retry = tenacity.retry... |
5f768a697f7885725866c5cfee746396e052a2652ec3ed47cdb47fd7a8a91783 | Python | 1,645 | 51 | from setuptools import setup, find_packages
import re
VERSIONFILE = "mousebrains/__version__.py"
verstrline = open(VERSIONFILE, "rt").read()
VSRE = r"^__version__ = ['\"]([^'\"]*)['\"]"
mo = re.search(VSRE, verstrline, re.M)
if mo:
verstr = mo.group(1)
else:
raise RuntimeError("Unable to find version string i... |
7cdcef040e87114ffed9dbd41b33df07d62da6a1b2aa252817e03e594559afc6 | Python | 1,674 | 48 | import pytest
import sys
import numpy as np
import cloudvolume
# Basic test of sharded meshes
# The following test files are used from https://storage.googleapis.com:
# /neuroglancer-janelia-flyem-hemibrain/v1.0/segmentation/info
# /fafb-ffn1-20190805/segmentation/mesh/info
# /neuroglancer-janelia-flyem-hemib... |
55d3a8f886de2bcd62f6f3c67f9829ecbb58c325a550523e666dd2b9b1461be1 | Python | 1,701 | 60 | from typing import Optional
import os
from .metadata import PrecomputedSkeletonMetadata
from .sharded import ShardedPrecomputedSkeletonSource
from .unsharded import UnshardedPrecomputedSkeletonSource
from ..metadata import PrecomputedMetadata
from ....cacheservice import CacheService
from ....paths import strict_ext... |
bba3fba1f8c5608e2ab4bec5cfcf91ddcb86918d22c16655ececfddf15d028a8 | Python | 1,701 | 61 | import time
import pendulum
from airflow.decorators import dag, task
@dag(
schedule=None,
start_date=pendulum.datetime(2021, 1, 1, tz="UTC"),
catchup=False,
tags=["maintenance, segmentation, inference"],
)
def easyseg_dag():
@task(queue="cluster", priority_weight=1000)
def start_worker():
... |
1bf476337050a2a46b379a8bd51936bcfb2d52e72f05f459bc0c0775367ad511 | Python | 1,718 | 65 | # -*- coding: utf-8 -*-
"""
Created on Wed Jul 30 15:51:23 2025
@author: Usuario
"""
# -*- coding: utf-8 -*-
"""
Created on Tue May 20 13:11:58 2025
@author: Usuario
"""
#Librarires
import os #For importing images and saving figures
import errno # for checking whether the montage direcotry already exi... |
54509592f635cbd177acf0ef386ac4212f2a4e1e7c60d4bf1dd8554a66687921 | Python | 1,729 | 70 | # -*- coding: utf-8 -*-
"""Methods for computing the geometry factor (g-map)
Author:
Zhengguo Tan <zhengguo.tan@gmail.com>
"""
import copy
import numpy as np
from sigpy import backend, util
from sigpy.mri import app
def pseudo_replica(app, y, mps,
normalize=True, replicas=10):
r"""
Per... |
a98438fbd22a6445641e655ad44984e57d70d64a8fb0147e6457a4f023b43ab1 | Python | 1,733 | 56 | """This MRI submodule contains functions and classes for MRI pulse design.
It contains functions to design a variety of RF pulses for MRI, such as SLR,
adiabatic, parallel transmit, multibanded, and others. The submodule also
includes other functions to assist with pulse design, such as I/O functions,
trajectory/gradi... |
7e89c233068a12edb2a7464d0477383c79999ab83c5ab298c314ad8e676f635a | Python | 1,740 | 30 | from __future__ import absolute_import, print_function
import warnings
def format_warning(message, category, filename, lineno, line=''):
import pathlib
return f"{pathlib.Path(filename).name} ({lineno}): {message}\n"
warnings.formatwarning = format_warning
del warnings
from .version import __version__
# TODO:... |
88842f2a3fa0e698304a396d40615e1bbe5cbdd44c04e88dcd8aa7d7d9bfd5a8 | Python | 1,747 | 70 | """Coordinate enums for data schema"""
from enum import Enum
class Origin(str, Enum):
"""Origin positions for coordinate systems"""
ORIGIN = "Origin" # only exists in Atlases / Images
BREGMA = "Bregma"
LAMBDA = "Lambda"
BETWEEN_C1_C2 = "Between_C1-C2"
BETWEEN_C2_C3 = "Between_C2-C3"
BET... |
042ab3b8f6966032b66fc1011245b6732427188d51c5fd2bbd37f96cdaeda596 | Python | 1,759 | 59 | import unittest
import numpy as np
import numpy.testing as npt
from sigpy.mri import sms
if __name__ == '__main__':
unittest.main()
class TestSms(unittest.TestCase):
def test_slice_order(self):
list_NS = [15, 94, 114, 60, 159, 141, 117]
list_MB = [ 1, 2, 3, 2, 3, 3, 3]
f... |
d98bc43e80f199a15c493f6c79ad5edb211844414b7c9f92444f5b506467f46b | Python | 1,771 | 54 | """Configuration file for the Sphinx documentation builder."""
#
# For the full list of built-in configuration values, see the documentation:
# https://www.sphinx-doc.org/en/master/usage/configuration.html
from datetime import date
# -- Path Setup --------------------------------------------------------------
from o... |
dbbb57db17cd81fcdc1fbd2d940d848f20eb9270a129258fc1275218c9c5d3a2 | Python | 1,775 | 62 | # -*- coding: utf-8 -*-
"""Configuration.
This module contains flags to turn on and off optional modules.
"""
import warnings
from importlib import util
import torch
cuda_avail = torch.cuda.is_available()
cupy_enabled = (util.find_spec("cupy") is not None) and cuda_avail
if cupy_enabled:
try:
import cup... |
e591c2563024ab87f1dd621efdd7e7c43ab946cae79bb039b8096d42db111c26 | Python | 1,788 | 60 | import pathlib
from pandas import concat, read_csv
from pandas.errors import EmptyDataError
from tetra.error_display import pretty_print_diffs
TOLERANCE = 0.0008 # 0.08%
def load_sorted_data_frame(path: pathlib.Path):
df = None
try:
df = read_csv(path, sep="\t", index_col="read_id", keep_default_n... |
426a677a023b06d9f5d205d4e5ca1cb8121e06821ccbd1bf40784b19efdb7267 | Python | 1,833 | 70 | from airflow_api import set_variable
from bot_info import slack_token, slack_app_token
from seuronbot import SeuronBot
import os
import logging
import sys
from bot_utils import send_message
import subprocess
if os.environ.get("VENDOR", None) == "Google":
from common.google_api import gce_external_ip
else:
imp... |
3c3a96db8e4b1d13b2c60d12dac0de4ae2b51f55143132e408c59b64f130e891 | Python | 1,834 | 54 | """Genes"""
import re
import requests
from pydantic import BaseModel, ConfigDict
from aind_data_schema_models.registries import Registry
class NucleotideModel(BaseModel):
"""Nucleotide model"""
model_config = ConfigDict(frozen=True)
name: str
description: str
registry: Registry = Registry.GENB... |
f6ff4cd59f5750c9879877c6a8f5f57db5e75c8b7b387cc593ec991fe7f620ee | Python | 1,834 | 59 | import streamlit as st
def show_readme():
st.markdown("## 📖 ReadMe - Bioactivity Prediction")
st.markdown("""
### ℹ️ **Overview**
This application predicts the bioactivity of chemical compounds using Machine Learning models.
### 📝 **Instructions**
1. Enter a **SMILES string** manually or **... |
d8cbfaa7596160fcc50bd94bf955f648e744c2803b2ea0fe6f6df60c34406518 | Python | 1,837 | 68 | import nibabel as nib
import numpy as np
import argparse
def get_crop(volume):
nonempty = np.argwhere(volume)
top_left = nonempty.min(axis=0)
bottom_right = nonempty.max(axis=0)
return (top_left, bottom_right)
def apply_crop(volume, crop):
top_left, bottom_right = crop
cropped = volume[... |
f0e9156a7292c7882eb7bc77fdd7c3ae703bbb65554032ffd4d8d2ede475cfc5 | Python | 1,845 | 54 | #! /usr/bin/env python3
import pathlib
import shutil
import unittest
from tetra.compare_platforms import PlatformCompare, SpecialCase, compare_platforms
class TestComparePlatforms(unittest.TestCase):
def setUp(self):
self.data_dir = pathlib.Path(__file__).parent / "data"
self.input_data = self.... |
c2e63ef3fe1e287d8ce787ae695116207068cc82df75d3179544cf6a6b485f5e | Python | 1,858 | 69 | import unittest
import numpy as np
import numpy.testing as npt
from sigpy.learn import app
if __name__ == "__main__":
unittest.main()
class TestApp(unittest.TestCase):
def test_ConvSparseDecom(self):
lamda = 1e-9
L = np.array([[1, 1], [1, -1]], dtype=float) / 2**0.5
y = np.array([[1... |
cebf8fd8005a6d53ca565595de37b8b65c4ff865af99aa7e6b8359fd5bdf803d | Python | 1,869 | 65 | import argparse
import pathlib
import sys
from ont_output_specification_validator import (
errors,
settings,
validate_file,
validators,
)
from ont_output_specification_validator.specification import (
load_local_specification_bundle,
)
from ont_output_specification_validator.validators.bam import... |
7641a7894eecd7c01fde5b744d825fdeb54f5679242a52c721b5bbc75954cbf7 | Python | 1,876 | 74 | """Density compensation functions.
"""
from tqdm.auto import tqdm
import sigpy as sp
__all__ = ["pipe_menon_dcf"]
def pipe_menon_dcf(
coord,
img_shape=None,
device=sp.cpu_device,
max_iter=30,
n=128,
beta=8,
width=4,
show_pbar=True,
):
r"""Compute Pipe Menon density compensation ... |
18fcb2ff46659ba88af65e61f8d882cb650d8132bcc1bb5996dba9526c9abb67 | Python | 1,885 | 40 | """Integration test for developmental stage ontology lookups (MMUSDV, HSAPDV, FBDV, WBLS)."""
import sys
from aind_data_schema_models.mouse_developmental_stage import MouseDevelopmentalStage
from aind_data_schema_models.human_developmental_stage import HumanDevelopmentalStage
from aind_data_schema_models.drosophila_d... |
75a0c7c9cb3a97767b646c65859a26cc8b7e353d8946e0afda9d681bd1cfbb4c | Python | 1,889 | 57 | import os
import re
import subprocess
from seuronbot import SeuronBot
from airflow_api import get_variable
from slackbot.bot_utils import replyto
def extract_jupyterlab_token():
try:
command_output = subprocess.check_output(["jupyter", "lab", "list"], encoding="utf-8")
except FileNotFoundError:
... |
14e35d7bf1bae9aa7b7b55f3238fa53c4f4a86528c9fad7b669b90b12e2f29e0 | Python | 1,894 | 65 | from typing import Optional
from .image import N5ImageSource
from .metadata import N5Metadata
from ...frontends.precomputed import CloudVolumePrecomputed
from .. import get_cache_path
from ...cacheservice import CacheService
from ...cloudvolume import (
register_plugin, SharedConfiguration,
CompressType, Paralle... |
904b7dd413cf9bdcf57e2dcdbf21906126faf23bd9d73670a0b5c542162587c2 | Python | 1,913 | 67 | import pathlib
def reformat_txt(file: pathlib.Path) -> None:
# Read it all
rows = []
with open(file) as input:
while line := input.readline():
rows.append(line)
# Sort it, ignoring the header line
rows[1:] = sorted(rows[1:])
# Save it
with open(file, "w+") as output:
... |
eb22f283d8a4799bd0ede639063b58c680a6b50e40907054e3d30ddb21786570 | Python | 1,922 | 62 | from typing import Optional, Union
from .image import BossImageSource
from .metadata import BossMetadata
from ...frontends.precomputed import CloudVolumePrecomputed
from .. import get_cache_path
from ...cacheservice import CacheService
from ...cloudvolume import (
register_plugin, SharedConfiguration,
CompressTy... |
cef38de8eb8859abdfbd24cca9f074aa3b3f9c508486c805c2c2b033f47f8731 | Python | 1,959 | 65 | from typing import Optional
from .image import Zarr3ImageSource
from .metadata import Zarr3Metadata
from ...frontends.precomputed import CloudVolumePrecomputed
from .. import get_cache_path
from ...cacheservice import CacheService
from ...cloudvolume import (
register_plugin, SharedConfiguration,
CompressType, P... |
e09789c0e7cacaeb05919023955e5e9fb52ae9d15131619c324d3494405348f2 | Python | 1,959 | 65 | from typing import Optional
from .image import Zarr2ImageSource
from .metadata import Zarr2Metadata
from ...frontends.precomputed import CloudVolumePrecomputed
from .. import get_cache_path
from ...cacheservice import CacheService
from ...cloudvolume import (
register_plugin, SharedConfiguration,
CompressType, P... |
f4d2303d3ff3f36d3d03ec13d0ac261769be5280166f1efdb55c96b107388166 | Python | 1,960 | 57 | from configparser import ConfigParser
from seuronbot import SeuronBot
from airflow_api import set_variable, run_dag
from bot_info import broker_url
from bot_utils import replyto, download_file, download_json
from kombu_helper import put_message
@SeuronBot.on_message("update synaptor parameters",
... |
818e17b09c1db989ad4a5114ce28c8b5af626c4a8d57834dc643c54270b8833d | Python | 1,964 | 56 | import os
from .metadata import PrecomputedMeshMetadata
from .unsharded import UnshardedLegacyPrecomputedMeshSource
from .multilod import ShardedMultiLevelPrecomputedMeshSource, UnshardedMultiLevelPrecomputedMeshSource
from ..metadata import PrecomputedMetadata
from ....cacheservice import CacheService
from ....exce... |
36dc572a99e0c74a695cac6da626ebb9f581681e0718881136b226923e187fab | Python | 1,969 | 52 | # test reslice
"""
test for reslice module
Also test correctness of ANTS deformation file
"""
import SUITPy as suit
import nibabel as nb
def test_reslice_anatomical():
"""This uses the forward deformation"""
T1_file = 'docs/source/tutorials/sub-ex_T1w.nii.gz'
def_file = 'docs/source/tutorials/sub-ex_T1w_to... |
44b1af7912ae46c62c5b74712dae31697afc697e788c8dd9c5050602a2397173 | Python | 1,978 | 43 | """ DropBlock, DropPath
PyTorch implementations of DropBlock and DropPath (Stochastic Depth) regularization layers.
Papers:
DropBlock: A regularization method for convolutional networks (https://arxiv.org/abs/1810.12890)
Deep Networks with Stochastic Depth (https://arxiv.org/abs/1603.09382)
Code:
DropBlock impl inspire... |
099406432f789e509a767919df350f5a182d2776a3cafb58c6b69b9bb86ba62b | Python | 1,986 | 62 | import pytest
import shutil
import numpy as np
import os
from cloudvolume import Storage, CloudVolume
from cloudvolume.lib import Bbox, Vec, min2, max2, find_closest_divisor
TEST_NUMBER = np.random.randint(0, 999999)
CLOUD_BUCKET = 'seunglab-test'
layer_path = '/tmp/removeme/'
def create_storage(layer_name='layer... |
040a87cead40aeafc683b491519de5de7fcfbf72affc148958eea7cb8dc5fe8f | Python | 2,007 | 69 | """Custom layers as equinox modules"""
import jax
import equinox as eqx
from math import sqrt
from ._utils import default_floating_dtype
from jax import Array
from jax.random import PRNGKey
from typing import Optional
from jax.typing import DTypeLike
class ConstantLayer(eqx.Module):
"""Constant layer."""
we... |
aaa2304129c34444039806ef128cd9e47807f97260b5b0d67b7b9137850fad80 | Python | 2,020 | 67 | # -*- coding: utf-8 -*-
"""Wavelet transform functions.
"""
import numpy as np
import pywt
from sigpy import backend, util
__all__ = ["fwt", "iwt"]
def get_wavelet_shape(shape, wave_name="db4", axes=None, level=None):
zshape = [((i + 1) // 2) * 2 for i in shape]
tmp = pywt.wavedecn(
np.zeros(zshape... |
42941db095e044da10f0ada88299b734a1196623f0a4a1648be4082b6a9726cb | Python | 2,032 | 76 | import unittest
import numpy as np
import numpy.testing as npt
import sigpy.mri.rf as rf
if __name__ == "__main__":
unittest.main()
class TestMultiband(unittest.TestCase):
def test_multiband(self):
# slr pulse
tb = 8
N = 512
d1 = 0.01
d2 = 0.01
p_type = "ex"
... |
3cb988769f00631859b542e2ba59c4b12733ae3e24e9402e9b44118fcd177fe6 | Python | 2,038 | 101 | import pytest
from cloudvolume.lru import LRU
import time
import random
import sys
def test_lru_size_w_tuple():
lru = LRU(int(1e6), size_in_bytes=True)
assert lru.nbytes == 0
val = (1, b'0' * 1000, b'1' * 1000)
lru[1] = val
ans = (
sys.getsizeof(val)
+ sys.getsizeof(val[0])
+ sys.getsizeof(va... |
c972a9c46b22e508222fbbf468d466f7eb140f53c0c9bcbf08555bd1e6c1045f | Python | 2,051 | 63 | import numpy as np
from numba import jit
@jit(nopython=True)
def make_arc(cx, cy, radius, n_segments=12, is_left=True):
"""
Make an half-circle arc with the centre cx, cy with n_segments poic
"""
angles = np.linspace(
(3 * np.pi / 2 if is_left else -np.pi / 2), np.pi / 2, n_segments
)
... |
fc599ab04316116c1dca72dcc94afd9933ff4db0e693ba239543dd62cb094a5d | Python | 2,055 | 93 | # -*- coding: utf-8 -*-
"""
Created on Mon May 27 14:28:36 2024
@author: CAG329
"""
# Packages ####################################################################
from brian2 import *
# %matplotlib qt
matplotlib.rcParams.update({'font.size': 13})
# Parameters #######################################################... |
aecace1315bd043f0fc75d612da87905eb5fc99873b50e018a1a246d7ebc2326 | Python | 2,064 | 91 | from cloudvolume.threaded_queue import ThreadedQueue
from functools import partial
def test_threading():
execution_count = 1000
executions = []
def reset_executions():
return [ False for _ in range(execution_count) ]
def addone(idnum, should_be_none):
executions[idnum] = True
assert should_b... |
cc47022928f1327801bf5454418dd86f165991c0b62cb639a4176d76310b1a78 | Python | 2,072 | 53 | import sys
import torch
import torch.nn as nn
import torch.nn.functional as F
import numpy as np
class MLP(nn.Module):
'''
Single layer MLP for either 3D joint angle prediction (regression) or action classification.
Input: (N, M, T, J, C)
'''
def __init__(self, task='regression', num_classe... |
3d7bd6649314ac9e5465a4e9a97e9bae7b1d698da15c716116ccdb735312b0a5 | Python | 2,083 | 59 | # -*- coding: utf-8 -*-
"""
Created on Fri Jan 20 16:31:34 2023
@author: simon
"""
from poisson_input import gaussian_filtered_poisson_spikes
from poisson_input_interneurons import theta_filtered_spikes
import pathlib
import numpy as np
import pandas as pd
# Get the path of the current script
base_pa... |
e56c9b2e3401cdef7de512a95bd5ed6d7f059eef868d69945ff0e3c6235d633d | Python | 2,091 | 57 | # Configuration file for the Sphinx documentation builder.
#
# This file only contains a selection of the most common options. For a full
# list see the documentation:
# https://www.sphinx-doc.org/en/master/usage/configuration.html
# -- Path setup --------------------------------------------------------------
# If ex... |
14c5f88c65f8353f9865ead3ebca6e4ad2b60df0fa2b36027de2b2f4f841c3f2 | Python | 2,129 | 73 | import unittest
import numpy as np
import numpy.testing as npt
from sigpy import config, thresh
if config.cupy_enabled:
import cupy as cp
if __name__ == "__main__":
unittest.main()
class TestThresh(unittest.TestCase):
def test_l2_proj(self):
x = np.ones(5)
y = np.full(5, 1 / 5**0.5)
... |
ed1e480adaecdd9f2183dfc81155e989b3b84940e2ae1f06e573987802859784 | Python | 2,182 | 63 | #!/usr/bin/env python
"""
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% example script to generate simulated interacting brain regions and
% perform Current-Based Decomposition (CURBD). Ref:
%
% Perich MG et al. Inferring brain-wide interactions using data-constrained
% recurrent neural ... |
94b290e217b0baec6bfd361d77685c1cff9b8ecf735115fcb04b16a0ac4e494a | Python | 2,195 | 67 | import unittest
import numpy as np
import numpy.testing as npt
import sigpy.mri.rf as rf
if __name__ == "__main__":
unittest.main()
class TestB1sel(unittest.TestCase):
def test_b1sel_generic(self):
dt = 2e-6 # sampling period
d1 = 0.01 # passband ripple
d2 = 0.01 # stopband rippl... |
d087d955233591f596f8169d46814b94f9b11a61c4f25363053efce2d433add7 | Python | 2,195 | 70 | """Script to pull developmental stage ontology term names from the EBI OLS4 API.
One-off/manual refresh script (like get_protocols.py) — not run automatically by
run_all.sh. Re-run this and commit the resulting CSVs when an ontology release adds
or renames terms.
"""
import pandas as pd
import requests
API_BASE = "h... |
a1af4d73522fb1b91e1e10e2da72e965048bc7a70a93d1308d9a67fc25d3b60d | Python | 2,290 | 69 | """
This script creates a 2-minute synthetic NWB file with 3 electrical series for testing the pipeline.
Requirements:
- spikeinterface
- pynwb
- neuroconv
"""
import spikeinterface as si
from pathlib import Path
from pynwb import NWBHDF5IO
from pynwb.testing.mock.file import mock_NWBFile, mock_Subject
from neurocon... |
9fa0ecd85108e927327f895f9f98443927b715c51101629f0476935f581cc6c1 | Python | 2,307 | 68 | """Data utilities."""
import jax.numpy as jnp
from datasets import Dataset, Features, Array2D
def shrink_trajectory_len(dataset: Dataset, new_traj_len: int) -> Dataset:
"""Reshapes a dataset to shrink trajectory length and increase number of examples
This is to optimise GPU usage when the trajectory length ... |
61ff3f71b472e6302acc5555dbb156b0a58b0c503c9a752aed1959b68059c7e9 | Python | 2,334 | 75 | # Configuration file for the Sphinx documentation builder.
#
# For the full list of built-in configuration values, see the documentation:
# https://www.sphinx-doc.org/en/master/usage/configuration.html
# -- Project information -----------------------------------------------------
# https://www.sphinx-doc.org/en/master... |
2035a216dbdad698228299b86af498ae97ff9a31fc45294e876dbfc84a8b5e5e | Python | 2,379 | 82 | from intern.remote.boss import BossRemote
from intern.resource.boss.resource import ChannelResource, ExperimentResource, CoordinateFrameResource
from ...secrets import boss_credentials
from cloudvolume.datasource.precomputed.metadata import PrecomputedMetadata
class BossMetadata(PrecomputedMetadata):
def __init__(s... |
a59f70543aef0dd1ef6ea0d539fb196cdac6ef8a424fb32f08113aa5a91413d9 | Python | 2,385 | 75 | def read_chunks(f, s_i, t_j, p_ji):
import struct
unpack_count = struct.Struct('q').unpack
unpack_seg = struct.Struct('qq').unpack
unpack_seg_pair = struct.Struct('qqq').unpack
while True:
count_data = f.read(8)
if count_data:
count, = unpack_count(count_data)
els... |
aa3891d3c0cd74bacae126e779f9e5e0c1392d5c29c153aff01e032fad6f9d74 | Python | 2,402 | 67 |
# The based unit of graph convolutional networks.
import torch
import torch.nn as nn
class ConvTemporalGraphical(nn.Module):
r"""The basic module for applying a graph convolution.
Args:
in_channels (int): Number of channels in the input sequence data
out_channels (int): Number of channels p... |
609c5effcaf70731d70a505587f8ce340def7d4417a92a390f39f82b710b8c33 | Python | 2,410 | 67 | #!/usr/bin/env python
"""Train a model on data sets for which manual annotations exist.
This model can then be loaded at a later time point to automatically
annotate new data sets.
"""
import numpy as np
from data_io import (
ArgumentParser,
load_dataframe,
check_dataframe,
load_state_vector,
loa... |
765250beac342c2437e9be264d40a88441053492dcfe9bbe31926c3dbc06274a | Python | 2,410 | 55 | """Process names"""
from enum import Enum
class ProcessName(str, Enum):
"""Process names"""
ANALYSIS = "Analysis"
COMPRESSION = "Compression"
DENOISING = "Denoising"
EPHYS_CURATION = "Ephys curation"
EPHYS_POSTPROCESSING = "Ephys postprocessing"
EPHYS_PREPROCESSING = "Ephys preprocessing... |
4f5e551e93884b57b1a3bfef5e1a5a04686f3e8f7569d0a844ff1b96194e0072 | Python | 2,422 | 80 | """
Adjust brightness and contrast for images in a directory.
Example:
python adjust_brightness_contrast.py \
--input-dir ./outputs/disagreements \
--output-dir ./outputs/adjusted \
--brightness-delta 20 \
--contrast-delta 0.1
"""
import argparse
import os
from pathlib import Path
import numpy as n... |
f01087cbe4789d421eb133a23b390cd1088fa058a5a53446ec8bdeca8374814d | Python | 2,423 | 58 | # -*- coding: utf-8 -*-
"""
Created on Fri Sep 20 15:41:24 2024
@author: simon
"""
def my_style():
"""
Create custom plotting style.
Returns ------- my_style : dict
Dictionary with matplotlib parameters. """
# color pallette
fsize = 12... |
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