sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
4a5bfd50f8571077c55e00e2f4b238de82ee077a8f85b8726756a118d23f77a8 | Python | 6,795 | 180 | # -*- coding: utf-8 -*-
"""
Created on Mon Oct 20 16:18:57 2025
@author: simon
"""
import numpy as np
import matplotlib.pyplot as plt
from plotting_functions import my_style
from matplotlib.gridspec import GridSpec
import seaborn as sns; sns.set_theme()
import pickle
import pandas as pd
import shap
imp... |
66b7b90cdaa47f9e1a70a6a2a36322311a2e6bdafb4d016ff121b34ddd676394 | Python | 6,873 | 253 | import unittest
import numpy as np
import numpy.testing as npt
from sigpy import alg, linop
if __name__ == "__main__":
unittest.main()
class TestAlg(unittest.TestCase):
def Ax_setup(self, n):
A = np.eye(n) + 0.1 * np.ones([n, n])
x = np.arange(n, dtype=np.float32)
return A, x
d... |
8856c8c25dbee089d6154fda4d50e91d509f5adb4c189c919ce1f07d286c94f9 | Python | 6,876 | 229 | # -*- coding: utf-8 -*-
"""MRI linear operators.
This module mainly contains the Sense linear operator,
which integrates multi-channel coil sensitivity maps and
discrete Fourier transform.
"""
import numpy as np
import sigpy as sp
def Sense(
mps,
coord=None,
weights=None,
tseg=None,
ishape=None,... |
0d44dc4a03aea1bbc09267dc43047af7af5ad5d3adb25fb25c06033c487e40af | Python | 6,888 | 182 | from common import GlobalComputeUrl, ZonalComputeUrl, GenerateBootDisk, GenerateNetworkInterface, GenerateAirflowVar
from common import INSTALL_DOCKER_CMD, INSTALL_OPS_AGENT, INSTALL_NVIDIA_DOCKER_CMD, CELERY_CMD, PARALLEL_CMD
def GenerateEnvironVar(context, hostname_manager):
if "postgres" in context.properties:... |
8c430c8e82d2e476f5c1468b64020da975153b968f08efe6cc86a98a2bfceafc | Python | 6,896 | 198 | import torch
import torch.nn as nn
import torch.nn.functional as F
from torch.autograd import Variable
from utils.tgcn import ConvTemporalGraphical
from utils.graph import Graph
class Model(nn.Module):
r"""Spatial temporal graph convolutional networks.
Args:
in_channels (int): Number of channels in ... |
d2d12ea36f074db7dd6ef438d7c1bb94261b35b4b19d3dddcf25bbdffd42c089 | Python | 6,928 | 212 | """Training commands."""
from __future__ import annotations
import re
from datetime import datetime
from typing import Optional
from seuronbot import SeuronBot
from airflow_api import run_dag
from bot_utils import replyto, download_json
from airflow_api import get_variable, set_variable
from common import docker_help... |
75947f48f4d98c3de86dd88bccca11c1ce8ab7a257c1fd2764541ca531fd3eaf | Python | 7,039 | 186 | """Dev utils tests"""
import unittest
from unittest.mock import patch, MagicMock
from aind_data_schema_models._generators.dev_utils import to_class_name, to_class_name_underscored, update_harp_types
class TestDevUtils(unittest.TestCase):
"""Tests for dev_utils module"""
def test_to_class_name(self):
... |
14a6ea73e4bd7b6c183585febb547c3dd5fac29d31ecaef0101664cd89bd1537 | Python | 7,093 | 255 | import queue as Queue
from functools import partial
import threading
import time
from tqdm import tqdm
DEFAULT_THREADS = 20
class ThreadedQueue(object):
"""Grant threaded task processing to any derived class."""
def __init__(self, n_threads, queue_size=0, progress=None):
self._n_threads = n_threads
self... |
9587a7e5a056c6fbafbf01b4e4cb9b411b349a4488c6e4caa7511f6c4c2e2de3 | Python | 7,112 | 171 | import pathlib
from collections import defaultdict
from tetra.data_frame_utils import check_pandas_equal, load_sorted_data_frame
from tetra.regression_manager import TestData
from tetra.sequence_utils import compare_alignment_files, compare_fastq_files
try:
from tetra.output_validation import setup_validator
exce... |
f92a98521d41dae12704ba33730b2ea498f558facc01377488271574fd082f69 | Python | 7,146 | 197 | from common import ZonalComputeUrl, GenerateDisk, GenerateBootDisk, GenerateScratchDisk, GenerateNetworkInterface, INSTALL_DOCKER_CMD, INSTALL_OPS_AGENT, GenerateAirflowVar
from workers import GenerateDockerCommand, GenerateCeleryWorkerCommand, GenerateEnvironVar
def GenerateNFSServerStartupScript(context, hostname_m... |
94ecd568339ba41ad096b489f16234ba40391b5def8baad2741d518b5ccaddea | Python | 7,197 | 194 | import sys
import socket
import logging
import psutil
from enum import Enum
import os
import redis
from datetime import datetime, timedelta
from time import sleep
from kombu_helper import put_message
from common.google_api import gce_hostname, get_project_id, get_zone, delete_instances, get_created_by
class RedisHealt... |
a005c75e1d58ae1548a589c092d643040800f3320f524ea185ede740a9cfd7ed | Python | 7,231 | 232 | import unittest
from airflow.operators.custom_plugin import MultiTriggerDagRunOperator
from airflow.utils.state import State
from airflow import settings
from tests.utils.mock_helpers import patch_plugin_file
try:
import unittest.mock as mock
except ImportError:
import mock
from datetime import datetime, tim... |
aa7fa569144fd043ba6e2e641af9293f7303b7713cf86d235b2845eed88ba045 | Python | 7,232 | 174 | import sys
import os
import yaml
from yaml import Loader
import numpy as np
import quantities as pq
from elephant.conversion import BinnedSpikeTrain
from elephant.spade import concepts_mining
from utils import concatenate_spiketrains, compute_isi_based_bin_firing_probability, generate_simulated_spiketrains
# Exampl... |
df93b0551f210bdc0d0eaf0a67fb3cc8b1f6da87cdc133ee047b26700151f428 | Python | 7,277 | 181 | #!/usr/bin/env python
"""Determine intervals with missing data in the raw time series data.
If *any* signal appears to have missing values, the corresponding
interval is marked as missing.
EEG/EMG/LFP recordings often contain intervals with missing
data.
These events typically have one of two origins:
1) Missing va... |
143b95caddf09b446c7ea1b776e58ffe7dd035c7900939d21fff2b4e45771b3d | Python | 7,299 | 176 | #!/usr/bin/env python
"""Train and test in a hold-one-out fashion on data sets for which a
manual created state annotation exists.
"""
import numpy as np
import matplotlib.pyplot as plt
from sklearn.metrics import confusion_matrix as get_confusion_matrix
from somnotate._automated_state_annotation import StateAnnota... |
54a36402742277435ab68ddc015b1edc84617ebc21e88ac88dbf28ece104277f | Python | 7,303 | 164 | import torch
import wandb
import os
import warnings
from sklearn.model_selection import StratifiedGroupKFold
from utils import get_count, get_TrainData, get_dataLoader, reset_wandb_env, get_balancedDF
from train import train
# Define sweep configuration
train_dir_dict = {'parent_dir' : "Data",
's... |
9c6a65bae02496fba00e4760e235e4e7fd50e0516fef58a2ec3565977f899427 | Python | 7,327 | 179 | import numpy as np
class Graph():
""" The Graph to model the skeletons extracted by the openpose
Args:
strategy (string): must be one of the follow candidates
- uniform: Uniform Labeling
- distance: Distance Partitioning
- spatial: Spatial Configuration
For more informa... |
c82c13ca7475b4ec80057d7871181f0a74667f7a1fe66ebf1a203027693e428f | Python | 7,329 | 276 | import os
import numpy as np
import pytest
from cloudfiles import CloudFiles
from cloudvolume import Vec, Bbox, CloudVolume, Storage, Mesh
@pytest.fixture
def unsharded_vol():
test_dir = os.path.dirname(os.path.abspath(__file__))
test_dir = os.path.join(test_dir, "test_seg_unsharded")
print(test_dir)
return ... |
5cad11f81d16d3f8c091a3fa9828afc07f88d402bcb396a12c3035879d7bc620 | Python | 7,349 | 208 | import plotly.graph_objects as go
def plotly_grid(file_dict, spp_code, spp_name, ai_range_dict, samp_key):
ai_range = ai_range_dict[spp_code]
fig = go.Figure()
z_index_unhashable = list(reversed([list(range(i,i+5)) for i in range(0,60,5)]))
z_index_hashable = [z for z_list in z_index_unhashable... |
33b532e016e3728b15faa4786f42ac1ba5f95a50e89d696d6acc5ca9b23419eb | Python | 7,355 | 259 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
import argparse
import numpy as np
import pandas as pd
import statsmodels.api as sm
from pathlib import Path
import matplotlib.pyplot as plt
from matplotlib.ticker import MaxNLocator
def parse_args():
ap = argparse.ArgumentParser()
ap.add_argument("--in-tsv", re... |
7f917c976934f76438a2d38d9511b86782c1d402e23a3536b68de6b166769988 | Python | 7,437 | 215 | from __future__ import print_function, unicode_literals, absolute_import, division
import numpy as np
import warnings
from skimage.measure import regionprops
from skimage.draw import polygon
from csbdeep.utils import _raise
from ..utils import path_absolute, _is_power_of_2, _normalize_grid
from ..matching import _che... |
655446b1abc35f731b962147e88535e085998a8f633a44cdc37275b7e09ea33e | Python | 7,445 | 295 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Wed Apr 13 17:07:10 2022
@author: spiros
"""
import numpy as np
import matplotlib.pyplot as plt
from scipy.ndimage.filters import gaussian_filter1d
from matplotlib.colors import LinearSegmentedColormap
def my_style():
"""
Create custom plotting s... |
460d3f888364e7b01bd2b68793875d9f8dc6c8167caff61c3b60e431f1e287a5 | Python | 7,446 | 241 | # -*- coding: utf-8 -*-
"""
Created on Wed Jul 30 18:09:39 2025
@author: Usuario
"""
# -*- coding: utf-8 -*-
"""
Created on Mon Jul 7 10:11:04 2025
@author: Usuario
"""
# Masks vs True positive
import os #For importing images and saving figures
import errno # for checking whether the montage direco... |
23514de09d0ad9f92affa10f0fe22eeea2cfd435b555afd68eefbbfaf87e320a | Python | 7,483 | 232 | #!/usr/bin/env python
"""
User defined variables and functions that are used across all scripts.
"""
import numpy as np
import matplotlib.pyplot as plt
from scipy.signal import (
sosfilt,
iirfilter,
# cheby1,
)
from functools import partial
from somnotate._plotting import plot_signals, plot_states
from so... |
011c38d915a8383ae2b152986d3fe7b9ee6995d7f8ad6692f39fdad8b0ee3fc9 | Python | 7,506 | 276 | import pytest
import os
import shutil
import zarr
from cloudvolume import CloudVolume, Bbox
import numpy as np
TEST_DIR = os.path.dirname("/tmp/removeme/cloudvolume/")
def create_simple_dataset():
test_location = os.path.join(TEST_DIR, "zarr3_simple_unsharded.zarr")
if os.path.exists(test_location):
... |
6bc3046edb455c11e6889d0778b664aa844eb7b225c7de31ce7db1dffd5afbea | Python | 7,557 | 212 | # -*- coding: utf-8 -*-
"""
Created on Tue Jun 27 20:44:25 2023
@author: simon
"""
from neuron import h, gui
from neuron.units import mV, ms
from Class_CA1_Pyr_standardized import Cell
import numpy as np
import pandas as pd
from scipy.spatial import distance_matrix
from timeit import default_timer as tim... |
04242e8c6a9f3a9d9bb7845a7d33742aca7843910c3bdcd131c659a521ad0475 | Python | 7,572 | 177 | #!/usr/bin/env python
import numpy as np
import matplotlib.pyplot as plt
from scipy.signal import welch
import matplotlib
matplotlib.rcParams['path.simplify'] = True
matplotlib.rcParams['path.simplify_threshold'] = 1.0
matplotlib.rcParams['agg.path.chunksize'] = 10000
# import matplotlib.style as mplstyle
# mplstyle.... |
73ef87db9df6186f2a26705c321dfe9b915d72ea6d957fefdb85342c6bf93d6f | Python | 7,600 | 250 | from airflow.operators.python import PythonOperator
from airflow.utils.weight_rule import WeightRule
from airflow.models import Variable
from slack_message import slack_message
from param_default import default_args
if Variable.get("vendor") == "Google":
import google_api_helper as cluster_api
else:
cluster_ap... |
6df8c6681f7a2b8a88fc2c8640fbc1459c13d2d016171bc39150220ae6c08984 | Python | 7,602 | 253 | """Webknossos interface."""
from __future__ import annotations
import json
from datetime import datetime
import requests
from airflow import DAG
from airflow.utils.weight_rule import WeightRule
from airflow.operators.python import PythonOperator
from airflow.models import Variable, BaseOperator as Operator
from work... |
24a9767a50304cf1e31a77cefc909b4130730003a5bd8b4e40d82f744aa5ec70 | Python | 7,707 | 263 | """Functions for Dynamic Contrast Enhanced (DCE) MRI
Author: Zhengguo Tan <zhengguo.tan@gmail.com>
"""
import numpy as np
import sigpy as sp
from sigpy import backend
def arterial_input_function(sample_time,
A = [0.7668, 0.3309],
T = [0.1710, 0.4079],
... |
f9ec947bba16955a1becca885e3d2c5d03637ed7974db2584b4b5c88d63923c8 | Python | 7,808 | 171 | from typing import Union, List, Optional, Literal
import numpy as np
import pynwb
from spikeinterface import BaseRecording, SortingAnalyzer
def _get_electrode_group_indices_by_channel(recording, nwbfile):
"""
Like neuroconv's _get_electrode_group_indices but returns one NWB electrode index
per recording... |
e1cbdeb09230341c1bbe6a9fc13877e44ae6b515ec211c859f9daee44677e9ac | Python | 7,822 | 183 | from matplotlib import pyplot as plt
import numpy as np
import os
import time
import sys
import argparse
import errno
from collections import OrderedDict, defaultdict, Counter
import tensorboardX
from tqdm import tqdm
import random
import torch
import torch.nn as nn
import torch.nn.functional as F
import torch.optim a... |
b9df1d176506c4a53184438590d557c9a771df23116c34c8dea134838d69a2c9 | Python | 7,846 | 190 | # %% Imports
import os
import sys
import yaml
from yaml import Loader
import numpy as np
import quantities as pq
from elephant.spade import concepts_mining
from elephant.conversion import BinnedSpikeTrain
from utils import concatenate_spiketrains, compute_isi_based_bin_firing_probability
# %% Parse the command line ... |
c077971b63d230b4ff274667671c9b779bbe45a7e6e48fc6f632798467cba95e | Python | 7,929 | 161 | # -*- coding: utf-8 -*-
"""
Created on Tue Sep 5 12:44:32 2023
@author: simon
"""
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
from collections import defaultdict
import io
class SWCExplorer():
def __init__(self, swc=None, df=None, eswc=False):
self.eswc = eswc
... |
5f35de4faab0bf78e3a9f08d08334e92864f934ffd92e28598663b2c223ccb82 | Python | 7,977 | 257 | import os
import pickle
import jax
import equinox as eqx
import sys
sys.path.append('..')
from omegaconf import DictConfig
from datasets import Dataset, Features, Array2D, load_from_disk
sys.path.append('../..')
from UIDD.dynamics import UIDD2
from UIDD.models import DiffusionCholeskyMLP, PotentialResMLP_scaleV2
... |
6069eec2d54c8380e139360d8afc755a4855b89c515bbb39970f58990bc9ca3a | Python | 7,995 | 193 | #!/usr/bin/env python
"""
Example script demonstrating how to preprocess a set of datasets and saving out the results.
TODO:
- provide different entry point by command line argument parsing using argparse
- fix plotting (`time` encapsulated at the moment...)
"""
import numpy as np
import matplotlib.pyplot as plt
tr... |
9c14dfb11555755fec3e7055955893a0ba3a461f2cebf1b2aab97e4985734b6d | Python | 8,003 | 212 | import cv2
import os
from datetime import date
import random
from tqdm import tqdm
from concurrent.futures import ProcessPoolExecutor, as_completed
import multiprocessing
import glob
import shutil
import argparse
import logging
# Logging
def setup_logging(level: str = "INFO", log_file: str | None = None) -> None:
... |
60941cff7d428d4634ca25228c675dece828c7f6937d95360430fc23e3324d0a | Python | 8,031 | 209 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Cobra Reaction ID Cleaner (2)
This script cleans and standardizes reaction IDs in an enzyme-constrained (ec)
model, particularly one that has been processed by a preliminary fixing script.
It is designed to be run from the command line.
The script performs a serie... |
2416dff3cc44c816f802318381bca2350fa64943b74c3d47512e7bf316427680 | Python | 8,081 | 183 | import torch
from tqdm import tqdm
import wandb
import torchmetrics
import shutil
from utils import EarlyStopping, get_model, ConfigureResnet
def train(train_dataloader, valid_dataloader, config, sweep_id, sweep_run_name, fold, val_ratio, train_ratio, spp):
#Fold name dict converter
abc_dict = {'1':"a", ... |
aed05a8f6ad04b208a0a75707f5d6b40a0fb6e041580e5c4caace20743464c5a | Python | 8,139 | 284 | import unittest
import numpy as np
import numpy.testing as npt
from sigpy import fourier, util
if __name__ == "__main__":
unittest.main()
class TestFourier(unittest.TestCase):
def test_fft(self):
input = np.array([0, 1, 0], dtype=complex)
npt.assert_allclose(
fourier.fft(input)... |
6ad921fc13398df64220202195cf17cb36700af5f39665a6380b3983c99e660c | Python | 8,206 | 254 | """
# Custom loss functions
This module contains custom loss functions for training the models.
The case class `Loss` is an abstract class that defines the interface for loss functions.
Sub-classes must implement the `Loss.compute_sample_loss` method.
# """
import jax
import equinox as eqx
import jax.numpy as jnp
f... |
2df04988675a3d4d3b255aa5a4ebb5a1c1cc9c90a99311871ef7084f3be2b78d | Python | 8,274 | 321 | import pytest
import numpy as np
import cloudvolume.lib as lib
from cloudvolume.lib import Bbox, Vec, xyzrange
def test_xyzrange():
def xyz(*args):
return np.array(list(xyzrange(*args)))
assert list(xyzrange((0,0,0))) == []
assert list(xyzrange((1,0,0))) == []
assert np.all(xyz((1,1,1)) == [Vec(0,0,0)])... |
334b06153cd0d4617e59945189cd1dc8e2ff10f739f5598016c267523ed1da64 | Python | 8,362 | 240 | def slack_message(msg, notification=False, broadcast=False, attachment=None):
from airflow import configuration as conf
import kombu_helper
msg_payload = {
'text': msg,
'notification': notification,
'broadcast': broadcast,
'attachment': attachment,
}
t... |
d044d31bdd691696a9fdefff94d8ab6c61feb30fadb11359358220e72e9a2d94 | Python | 8,371 | 262 | """Training DAGs."""
from __future__ import annotations
import json
import os
import uuid
from datetime import datetime
from airflow import DAG
from airflow.utils.weight_rule import WeightRule
from airflow.operators.python import PythonOperator
from airflow.models import Variable, BaseOperator as Operator
from airflo... |
b32f433ac2bec1b961616934956921058a704f8fd80f986242b502448657f34a | Python | 8,390 | 185 | #!/usr/bin/env python
import numpy as np
import matplotlib.pyplot as plt
from scipy.signal import welch
import matplotlib
matplotlib.rcParams['path.simplify'] = True
matplotlib.rcParams['path.simplify_threshold'] = 1.0
matplotlib.rcParams['agg.path.chunksize'] = 10000
# import matplotlib.style as mplstyle
# mplstyle.... |
0126cbaef6eb958002ce0e6c58711ca32f40ff2c9cf7963b9a2e38286557406d | Python | 8,487 | 238 | import torch
import torch.nn.functional as F
import os
import numpy as np
import torchvision.transforms as transforms
import random
from src.losses.losses import fourier_space_loss, l1_loss, l2_loss, grad_l2_norm_isolated
from typing import Optional
def set_seed(seed = 42):
random.seed(seed)
np.random.seed(see... |
783d8c3ce35bcbd1811105c9df03b0892f12a79de4b2144250a9277136507bc4 | Python | 8,510 | 269 | # -*- coding: utf-8 -*-
"""RF Pulse Simulation Functions.
"""
from sigpy import backend
__all__ = ["abrm", "abrm_nd", "abrm_hp", "abrm_ptx"]
def abrm(rf, x, balanced=False):
r"""1D RF pulse simulation, with simultaneous RF + gradient rotations.
Args:
rf (array): rf waveform input.
x (arra... |
e614a97dbc567f13ad50e883c3a8a273a2f3125d83f289aa857af7933bfc6178 | Python | 8,513 | 349 | from typing import Union
import sys
import threading
import numpy as np
def getsizeof(val:Union[int,str,bytes,list,tuple]) -> int:
"""does sizeof at arbitrary depth for tuples and lists"""
nbytes = 0
if isinstance(val, (tuple, list)):
for elem in val:
nbytes += getsizeof(elem)
elif isinstance(val, n... |
15267532c0c85dea7eef70694d1ea2074cb4d1a7039d0858d258d09e28599e53 | Python | 8,519 | 206 | from common import GlobalComputeUrl, ZonalComputeUrl, GenerateBootDisk, GenerateNetworkInterface, GenerateAirflowVar
from common import INSTALL_DOCKER_CMD, INSTALL_NVIDIA_DOCKER_CMD, INSTALL_OPS_AGENT, DOCKER_CMD, CELERY_CMD, PARALLEL_CMD
GPU_TYPES = ['gpu', 'custom-gpu', 'synaptor-gpu', 'deepem-gpu']
SYNAPTOR_TYPES ... |
60bfad3b85b179784357a4914edd6e830407d1f97615de87eaeae3245294cde3 | Python | 8,540 | 257 | import torch
import torch.nn as nn
from utils.tgcn import ConvTemporalGraphical
from utils import Graph
from nets.utils.graph_frames_withpool_2 import Graph_pool
from nets.non_local_embedded_gaussian import NONLocalBlock2D
inter_channels = [128, 128, 256]
fc_out = inter_channels[-1]
fc_unit = 512
class Model(nn.Mo... |
2b1fca67d522fe5e80305d4d415fb9334ed4b291627e881a62a0b4351e0f34fd | Python | 8,594 | 348 | # -*- coding: utf-8 -*-
"""Methods for Echo-Planar Imaging (EPI) acquisition
with an focus on diffusion tensor/kurtosis imaging.
Author:
Zhengguo Tan <zhengguo.tan@gmail.com>
"""
import numpy as np
from sigpy import fourier
MIN_POSITIVE_SIGNAL = 0.0001
def phase_corr(kdat, pcor, topup_dim=-11):
"""perform p... |
9c6214b94e09b902ce8103db6e09bab575b00a94667c03eea465a5a3f8c5a341 | Python | 8,692 | 273 | """linear case."""
import os
os.environ["JAX_PLATFORM_NAME"] = "cuda"
os.environ["XLA_PYTHON_CLIENT_MEM_FRACTION"] = "0.18"
import jax
jax.config.update("jax_enable_x64", True)
import jax.numpy as jnp
import jax.random as jr
import equinox as eqx
import sys
sys.path.append('..')
from utils.sde import SDEIntegrator
f... |
933e40b554a744f58353ea5f521823190263eaee24452a6f3233b5c964bb2bfe | Python | 8,698 | 221 | # -*- coding: utf-8 -*-
"""
Created on Mon Nov 25 15:40:25 2024
@author: simon
"""
import numpy as np
import matplotlib.pyplot as plt
from plotting_functions import my_style
from matplotlib.gridspec import GridSpec
import seaborn as sns; sns.set_theme()
import pickle
import pandas as pd
from matplotlib.... |
a17965d7447fee5807eaba0a030f662538bc6a354c2ec445a89feeb06f076038 | Python | 8,702 | 208 | # Adapted from VideoPose3D (Facebook Research)
# Source: https://github.com/facebookresearch/VideoPose3D/blob/main/common/model.py
#
# Pavllo et al., "3D human pose estimation in video with temporal convolutions and semi-supervised training",
# CVPR 2019.
import torch.nn as nn
class TemporalModelBase(nn.Module):
... |
85e1e274b917f1132c66a1724a4b99e449ad0078a18184b1c96baccd74f00b76 | Python | 8,720 | 281 | import os
import jax
import equinox as eqx
import sys
sys.path.append('..')
from tqdm import tqdm
from omegaconf import DictConfig
from datasets import Dataset, Features, Array2D, load_from_disk
sys.path.append('../..')
from UIDD.dynamics import UIDD2
from UIDD.models import DiffusionCholeskyMLP, PotentialResMLP_scal... |
2b0de4d3cb5cdd8c280f44ae7e0107a7ed3e3c474ec6e13e59b107fbc53728d2 | Python | 8,722 | 211 | import os
import numpy as np
import torch
import torch.nn as nn
from functools import partial
from models.DSTformer import DSTformer
class AverageMeter(object):
"""Computes and stores the average and current value"""
def __init__(self):
self.reset()
def reset(self):
self.val = 0
se... |
4cfdd2ccbdd573199d45c3949de418accecf98e6ef469086d472d7407d3fc030 | Python | 8,909 | 256 | """Mouse developmental stage"""
import requests
from pydantic import BaseModel, ConfigDict
from aind_data_schema_models.registries import Registry
"""Mouse developmental stage"""
class MouseDevelopmentalStageModel(BaseModel):
"""Base model for mouse developmental stage"""
model_config = ConfigDict(frozen=... |
0f97d452b483b72c18c268a53eebd5b6788aa36cea5e363044a4b070920e28ee | Python | 9,092 | 356 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Wed Apr 13 17:07:10 2022
@author: spiros
"""
import numpy as np
import matplotlib.pyplot as plt
from scipy.ndimage.filters import gaussian_filter1d
from matplotlib.colors import LinearSegmentedColormap
from pathlib import Path
from scipy.signal import find... |
a04eace03653f54861309a5f2a72a34d3730b89829b502ddeeecc818d10cccc8 | Python | 9,194 | 255 | from collections import defaultdict
import itertools
import json
import os
import posixpath
import re
import requests
import numpy as np
from tqdm import tqdm
from cloudfiles import CloudFiles
from ....lib import red, toiter, Bbox, Vec, jsonify
from ....mesh import Mesh
from .... import paths
from ....scheduler impo... |
145ec800bfe14daafd9ff138d0d97f2558a7eb0cbe57a9b371b215c5d768cee6 | Python | 9,210 | 245 | import psycopg2
from psycopg2 import sql
from datetime import datetime
from tetra.utilities import get_env_or_raise
# Wrapper around all DB interactions.
class DBWrapper:
def __init__(self, project: str):
DB_HOST = get_env_or_raise("BENCHMARK_DB_HOST")
DB_PASSWRD = get_env_or_raise("BENCHMARK_DB_P... |
4aa344c9d3a8e0d10865793fce5852a4bea375af2a086200f914fadcb3367843 | Python | 9,247 | 233 | # -*- coding: utf-8 -*-
"""
Created on Fri Nov 4 12:28:51 2022
@author: spiros
"""
import os
import numpy as np
from opt_ import gridfield
from poisson_input import poisson_spikes, gaussian_prob
import pathlib
from scipy.stats import multivariate_normal
# Get the path of the current script
base_pat... |
e36c68642cdf357107d35aed640c1c5e40c755fb6bfb5c8aabf5cb5d23113914 | Python | 9,350 | 280 | """
This dag autoscales your cluster. This only works with docker-compose (local)
and Infrakit (swarm).
For Infrakit, the following environment variables must be set:
- INFRAKIT_IMAGE - what docker image to use for infrakit
i.e.infrakit/devbundle:latest
- INFRAKIT_GROUPS_URL - the location of the groups js... |
15cb8f0c173d024f7367cb64d1e5f7ba39f2a72b2aaa289f8ddb548173cf3008 | Python | 9,401 | 330 | # -*- coding: utf-8 -*-
"""Multiband RF Pulse Design functions.
"""
import numpy as np
__all__ = ["mb_phs_tab", "mb_rf", "dz_pins"]
from sigpy.mri.rf import slr as slr
from sigpy.mri.rf.trajgrad import trap_grad
def mb_rf(pulse_in, n_bands=3, band_sep=5, phs_0_pt="None"):
r"""Multiband an input RF pulse.
A... |
88de069040537b838ca346dd475fed9e6def07627dc92ebe08c01f233c962d08 | Python | 9,410 | 263 | # %% [markdown]
# # Notebook 05: Spatchcocking — 3D to 2D projection
#
# **Paper section:** Methods — Spatchcocking transformation
# **Paper figures:** Fig. 2 (coordinate system), Figs. 3–6 (heatmaps)
#
# This script flattens the 3D basal surface mesh into a 2D map using the
# spatchcocking transformation, combining al... |
524367661ca05372b1c2f04280916a1b0975f6c0a9a67d2ac216d53aac2d33db | Python | 9,488 | 331 | """Functions for Simultaneous Multi-Slice (SMS) Acquisition
Author: Zhengguo Tan <zhengguo.tan@gmail.com>
"""
import numpy as np
import sigpy as sp
__all__ = ['get_uncollap_slice_idx',
'get_ordered_slice_idx',
'reorder_slices',
'get_sms_phase_shift',
'readout_extended_fov',... |
60d2ad7ba386dbf8dc3edef36587eaeffeeab78dd0762633b01414743c928396 | Python | 9,576 | 291 | # from __future__ import print_function
# from six.moves import range
# import pytest
# import re
# import time
# from cloudvolume.storage import Storage
# from cloudvolume import exceptions, Bbox, chunks
# from layer_harness import delete_layer, TEST_NUMBER
# #TODO delete files created by tests
# def test_read_wri... |
ef4aea03e77ad72a4370b7d32b1c9a01defcd9bff5e4ae0b6341fd6aed8e6afb | Python | 9,708 | 299 | #!/usr/bin/env python
"""
TODO
- consistent variable naming for p, min_percentile, max_percentile
"""
import numpy as np
def robust_normalize(arr, p=1., axis=-1, method='standard score'):
"""
References:
-----------
https://en.wikipedia.org/wiki/Normalization_(statistics)
"""
if method == 'm... |
5a96c37f5711914803d4b8416c92b65cbea0b21e77217c592f69122e4b96b46b | Python | 9,722 | 303 | # -*- coding: utf-8 -*-
""":math:`B_1^{+}`-selective RF Pulse Design functions.
"""
import numpy as np
from sigpy.mri.rf import slr as slr
from sigpy.mri.rf.util import dinf
__all__ = ["dz_b1_rf", "dz_b1_gslider_rf", "dz_b1_hadamard_rf"]
def dz_b1_rf(
dt=2e-6,
tb=4,
ptype="st",
flip=np.pi / 6,
... |
b59e8b2056065cb4005c6919078c2ef8e67ee8903e81aadd8c1a00df28cc39da | Python | 9,755 | 234 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Cobra Model Reversibility Fixer (1)
This script identifies and resolves conflicting reaction reversibility between a
conventional model and an enzyme-constrained (ec) model.
The script performs the following steps:
1. Loads a conventional model and an ec-model fro... |
0b4a21649e501acb440623fa6662709a25e8fa82d4032ac08390af73904d24e4 | Python | 9,773 | 279 | """Batch CaImAn processing for one-photon calcium imaging TIFF files.
This script performs motion correction, CNMF source extraction, seeded CNMF
refinement, component filtering, and export of fluorescence traces and spatial
metadata. Paths, animal identifiers, and day ranges are provided on the command
line so the pi... |
c8e8dd10ac99ed1e0c55500da322b6ce4a698ab7c98036c04ab8b0814841a9b9 | Python | 9,800 | 322 | # -*- coding: utf-8 -*-
"""MRI sampling functions.
"""
import numba as nb
import numpy as np
__all__ = ["poisson", "radial", "spiral"]
def poisson(
img_shape,
accel,
calib=(0, 0),
dtype=complex,
crop_corner=True,
return_density=False,
seed=0,
max_attempts=30,
tol=0.1,
):
"""Ge... |
516e071311229ec9b4bf7497f4a6cedf268dda1c7ad22320244a50cdd41bf99f | Python | 9,856 | 327 | # -*- coding: utf-8 -*-
"""FFT and non-uniform FFT (NUFFT) functions.
"""
from math import ceil
import numpy as np
from sigpy import backend, interp, util
__all__ = [
"fft",
"ifft",
"nufft",
"nufft_adjoint",
"estimate_shape",
"toeplitz_psf",
]
def fft(input, oshape=None, axes=None, center=... |
01f1ac745c6abda1141d666ed3745db754efcc3f6982b2f1b244b3fe8627e3f9 | Python | 9,872 | 300 | """Convert MMD summary NPZ files to Excel workbooks.
This script leaves the source ``.npz`` files untouched. For each input file it
creates up to three ``.xlsx`` files next to the source file:
* ``<stem>_timeseries.xlsx``: 1D arrays aligned by ``ts``.
* ``<stem>_scalars.xlsx``: metadata, aggregate errors, and per-see... |
1ef09a658e95dfc950eec02e2f2dbc4ab0623a937746128026402e003c49247e | Python | 9,894 | 259 | from copy import deepcopy
from datetime import datetime
from seuronbot import SeuronBot
from bot_info import broker_url
from bot_utils import replyto, extract_command, clear_queues, download_json, guess_run_type, latest_param_type, upload_param
from kombu_helper import drain_messages, visible_messages, get_message, put... |
115045a757ec860c0b6d96e339d5c43825e60dd1ad0f548fd5ac11f47c07140d | Python | 9,927 | 197 | # -*- coding: utf-8 -*-
"""
Created on Tue Aug 22 12:28:56 2023
@author: simon
"""
import numpy as np
import matplotlib.pyplot as plt
import seaborn as sns; sns.set_theme()
import pickle
import os,sys
from scipy.signal import find_peaks
from statannot import add_stat_annotation
import pandas as pd
from... |
1e0d8f6b8b7d3933048f970da56b2777a3d751c234e224116756d381d816fb1e | Python | 9,964 | 366 | # -*- coding: utf-8 -*-
"""Functions and classes for getting and setting computing devices.
"""
import numpy as np
from sigpy import config
if config.cupy_enabled:
import cupy as cp
if config.mpi4py_enabled:
from mpi4py import MPI
if config.nccl_enabled:
from cupy.cuda import nccl
__all__ = [... |
2782be83e5333993824ed8dd68bd976ea795080cad4b6e26de642d18ef734c82 | Python | 9,995 | 284 | """Non-technical user segmentation commands ("easy seg")."""
from __future__ import annotations
import re
from typing import Any
from datetime import datetime
import time
import humanize
from seuronbot import SeuronBot
from bot_info import broker_url
from bot_utils import clear_queues, replyto, download_json
from bot... |
30446d710fab1be3314315deeb42fc47a8f2aa7f15cee1d5719a8f7fb1cdb1fd | Python | 10,247 | 227 | ###############################################################################
# This library provide utilities for building experimental datasets.
# The library makes use of scipy, pandas, sklearn, pyDOE2, math,
# For visualization, it makes use of seaborn and matplotlib
# Two main tasks can be performed (examples ... |
33c3059422acbe0797e03d0832d7a96dfe223f533748fb67efe56fbd611ef533 | Python | 10,336 | 307 | # -*- coding: utf-8 -*-
"""
Created on Mon Jul 7 10:11:04 2025
@author: Usuario
"""
# Masks vs True positive
import os #For importing images and saving figures
import errno # for checking whether the montage direcotry already exists
import matplotlib.pyplot as plt
import numpy as np
from skimage import... |
a187ea16ee8aaeb61a3fc44310bcf0b58c6e41af4556c17a88dbce1ce5d8730e | Python | 10,459 | 338 | """utils for reduced polymer dynamics."""
import os
import pickle
import jax
import equinox as eqx
import sys
sys.path.append('..')
from omegaconf import DictConfig
from datasets import Dataset, Features, Array2D
from sklearn.model_selection import train_test_split
sys.path.append('../..')
from UIDD.dynamics import ... |
c9df833230d338ad9da0f7fdc21edb9a7874a5fe03c1d99c8c51b28f912adddb | Python | 10,468 | 315 | from multiprocessing import Process, Event, Queue
from dataclasses import dataclass
from pathlib import Path
from typing import Optional
from queue import Empty
import flammkuchen as fl
import numpy as np
import shutil
import json
import yagmail
from PIL import Image
import os
import time
@dataclass
class SavingParam... |
5103775f5b9c16d2c16b2c99fa8960e3dc04b1a7ef47ee5e993c414db84c2414 | Python | 10,536 | 348 | from typing import Optional
import copy
import re
import os
import numpy as np
from cloudfiles import CloudFiles
import cloudfiles.compression
from .. import (
autocropfn, readonlyguard,
ImageSourceInterface, check_grid_aligned,
generate_chunks
)
from ...types import CompressType, MipType
from ... import com... |
0721491df602fe0a4c2314dbdb58816a1dfdf40fcc4580e8b4bfc3b0d626322b | Python | 10,559 | 228 | import unittest
import numpy as np
import numpy.testing as npt
from sigpy import backend, config, util, linop, prox
# from sigpy.app import NonLinearLeastSquares as sp_nlls
from sigpy.nlls import NonLinearLeastSquares as nlls
from sigpy.mri import nlop, epi, nlrecon
if __name__ == '__main__':
unittest.main()
dev... |
ca71a09013f6ef79ef8051d15e15f6a2962206458e3139513415d17e7e8350ed | Python | 10,613 | 302 | # -*- coding: utf-8 -*-
"""MRI RF excitation pulse design functions,
including SLR and small tip spatial design
"""
import numpy as np
from scipy.interpolate import interp1d
import sigpy as sp
from sigpy import backend
from sigpy.mri import rf as rf
__all__ = ["stspa", "stspk"]
def stspa(
target,
sens,... |
fa0ac92138189ab001f2ae377485b5337caa06c1f6a908f604da2002e020b79f | Python | 10,682 | 346 | from __future__ import annotations
import re
import string
import requests
import json
import json5
import base64
import traceback
from functools import lru_cache
from collections import OrderedDict
from secrets import token_hex
from kombu_helper import put_message, visible_messages
import slack_sdk as slack
from typi... |
ba251b810c57677f1bb92738aa1b49d54a4c13e6b6a9979b4cca0a97e3631761 | Python | 10,696 | 369 | # -*- coding: utf-8 -*-
"""This module contains an abstraction class Nlop for non-linear operators,
and provides commonly used non-linear operator, including exponential.
Author: Zhengguo Tan <zhengguo.tan@gmail.com>
"""
import numpy as np
from sigpy import backend, linop
class Nlop():
"""Abstraction for non-li... |
561c721cbe11e38851abd13f7950fd2b4116485329377a1c5fa36ad895ac6abd | Python | 10,705 | 360 | """DAG definition for synaptor workflows."""
from typing import Optional
from datetime import datetime, timedelta
from dataclasses import dataclass
from airflow import DAG
from airflow.operators.python import PythonOperator
from airflow.models import Variable, BaseOperator
from dags.slack_message import slack_message
... |
b8a1394b9fa9cbc2ea7a856c2597794b946df34f1cd72bd13aacef81941ad6fd | Python | 10,746 | 432 | """Harp device types"""
from typing import Literal, Union
from pydantic import BaseModel, ConfigDict, Field
from typing_extensions import Annotated
class HarpDeviceTypeModel(BaseModel):
"""Base model for platform"""
model_config = ConfigDict(frozen=True)
whoami: int = Field(..., title="Harp whoami valu... |
4435b9a149499d1f30cc60e8c1e0cc2e1d539bfe30bc2fb60497e2ff4efa193e | Python | 10,762 | 267 | # -*- 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 exists
from cellpose import models, io #Cellpose ML model for single cell segmentation
from c... |
8f57b3ca36f9d7e87896a608df20fd5eccfaae22b75a6347336fd6fbda991e6e | Python | 10,786 | 351 | """Operator functions for synaptor DAGs."""
from __future__ import annotations
import os
from typing import Optional
from airflow import DAG
from airflow.utils.weight_rule import WeightRule
from airflow.operators.python import PythonOperator
from airflow.models import Variable, BaseOperator
from worker_op import work... |
1dd296c1f19588414233564584f9606e1ee950f0d9fa8d5b29560f01e3dcaab5 | Python | 10,790 | 322 | import argparse
import csv
import io
import os
import pathlib
import re
import dateutil.parser as dateutilparser
from datetime import datetime, timezone
from tetra.database import DBWrapper
from tetra.utilities import get_env_or_raise
# Split <preset>_<config> into parts.
def extract_preset_config(name: str, for_lat... |
3dd5456bdb373f4f5b8513856a53da899e477a5b89b07843b5556e92a480a86a | Python | 10,825 | 321 | """ MISR-GRU for multi-image super resolution """
import torch.nn as nn
import torch
from torch.autograd import Variable
class ResidualBlock(nn.Module):
def __init__(self, channel_size=64, kernel_size=3):
"""
Args:
channel_size : int (c), number of hidden channels
kernel_s... |
0568d0c9f06641ad1d8511327419b115e2dbfcaa1a206be4c8c1b40e5e321a89 | Python | 10,957 | 297 | #!/usr/bin/env python3
"""
prepare_pt_from_tiff.py
Convert simulated TIFF stacks into normalized PyTorch tensors (.pt) in parallel.
Typical use-case in this repo:
- You already generated simulations as TIFF movies (e.g., noisy stacks).
- You want to convert them into `.pt` tensors so training/eval loads fast.
This s... |
5ddad8959c73b102bf62be653c8a0cab02aad98df98fcd53afd6c2d54aa3ddc0 | Python | 11,012 | 371 | from typing import Union, Iterable, Optional
from collections import defaultdict
import itertools
import simdjson
import re
import os
import struct
import numpy as np
from tqdm import tqdm
from cloudfiles import CloudFiles
from .... import exceptions
from ....lib import yellow, red, toiter, sip
from ....mesh import... |
6c301c5d9033fbc7df4260a9f2441731f4a0bff73802f07ece5cc311435b0b63 | Python | 11,036 | 287 | import numpy as np
import os, sys
import pickle
import yaml
from easydict import EasyDict as edict
from typing import Any, IO
from scipy.stats import mode
from collections import Counter
ROOT_PATH = os.path.join(os.path.dirname(os.path.realpath(__file__)), '..')
class TextLogger:
def __init__(self, log_path):
... |
feeea2750cc37ac07ff6647bbd95d107b8adae012800fbf0dd9f6db47ddca8c8 | Python | 11,111 | 296 | from multiprocessing import Event, Process, Queue
import numpy as np
try:
import nidaqmx
from nidaqmx import Task
from nidaqmx.stream_readers import AnalogMultiChannelReader
from nidaqmx.stream_writers import AnalogMultiChannelWriter
from nidaqmx.constants import Edge, AcquisitionType, LineGrouping
... |
2eb8eccaf925467b87dc856d1fc03ac234419a0a6d70cbe1305e960cee4e50b8 | Python | 11,126 | 303 | import os
import re
import functools
import json
import itertools
import difflib
import concurrent.futures
import logging
import time
import tenacity
from threading import Event
from slack_sdk.rtm_v2 import RTMClient
from slack_sdk.socket_mode import SocketModeClient
from slack_sdk.socket_mode.request import SocketMode... |
2a8eb0409de3d960d7538d7bc99a5bde6fac2e19e13953c05bfc3a24cddcb7f5 | Python | 11,185 | 307 | from multiprocessing import Event, Queue
from lightparam import Param, ParameterTree
from lightparam.param_qt import ParametrizedQt
from scanning import (
Scanner,
ScanningParameters,
ScanningState,
RoiParameters,
ImageReconstructor,
frame_duration,
)
from pathlib import Path
from streaming_save... |
33a816d2e585d5a19b6a5728960279d477a6249ddc1e8f628664130bf491872b | Python | 11,237 | 340 | import abc
import os
import typing
import unittest
from dataclasses import dataclass, field
from functools import cache
from data_paths import INPUT_FOLDER, OUTPUT_FOLDER, ROOT_DIR
from tetra.timestamped_context import TimestampedContext
from tetra.utilities import get_platform, run_with_timeout
def _get_benchmarkin... |
63cbc569e3b324fea2fb1dc0310f07cfee152e7e13ba3bded9005cacfffe372b | Python | 11,243 | 476 | # -*- coding: utf-8 -*-
"""Utility functions.
"""
import numpy as np
from sigpy import backend
__all__ = [
"prod",
"vec",
"split",
"rss",
"resize",
"flip",
"circshift",
"downsample",
"upsample",
"dirac",
"randn",
"triang",
"hanning",
"monte_carlo_sure",
"axp... |
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