sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
b908b921035979be40fcf37050db3729372723054f712db128510a114377207f | Python | 22,160 | 394 | ############################################################################
# Copyright (c) 2022-2026 University of Helsinki
# Copyright (c) 2020-2022 Saint Petersburg State University
# # All Rights Reserved
# See file LICENSE for details.
############################################################################
... |
98ab45853b30d3014274b29fad583e2991efd0d9ac144e869c3e0d4e14bc2512 | Python | 22,215 | 602 |
""" Loss function collection for convenient calculation over multiple classes
and/or instances of meshes.
Notation:
- B: batch size
- S: number of instances, e.g. steps/positions where the loss is computed in
the model
- C: number of channels (= number of classes usually)
-... |
346e63e87915b8e911cd97d4da74b36021acdff23d35c6a01478604081a55115 | Python | 22,223 | 613 | """Grid-based cell space implementations with different connection patterns.
Provides several grid types for organizing cells:
- OrthogonalMooreGrid: 8 neighbors in 2D, (3^n)-1 in nD
- OrthogonalVonNeumannGrid: 4 neighbors in 2D, 2n in nD
- HexGrid: 6 neighbors in hexagonal pattern (2D only)
Each grid type supports o... |
f301f605d3f5303fd9927eb020c7138c78c5eb4b0af1d220a4d6721ab2fa19b9 | Python | 22,238 | 650 | # -*- coding: utf-8 -*-
import numpy as np
import cv2
import torch
from functools import partial
import random
from scipy import ndimage
import scipy
import scipy.stats as ss
from scipy.interpolate import interp2d
from scipy.linalg import orth
import albumentations
import ldm.modules.image_degradation.utils_image as ... |
bd21bcea05b9a5ef87ac70e24edf55e8f775c9be009a126bf77ced36c548e33e | Python | 22,289 | 652 | #!/usr/bin/env python3
#
# Copyright (c) 2014 10X Genomics, Inc. All rights reserved.
#
# Utilities for manipulating fasta and fastq files
#
from __future__ import annotations
import glob
import gzip
import os
import re
import sys
from typing import IO, TYPE_CHECKING, BinaryIO, Literal, TextIO, overload
import numpy... |
20d941bd3e1b94c150a267609c237ee0c920df5dadaa2ce682c5ddb20482bbbe | Python | 22,292 | 512 | from __future__ import print_function
import json, time, os, sys, glob
import shutil
import numpy as np
import torch
from torch import optim
from torch.utils.data import DataLoader
from torch.utils.data.dataset import random_split, Subset
import torch.utils
import torch.utils.checkpoint
import copy
import torch.nn as ... |
d43d0c6d71066530dd6001504fa37fe5bfc943165830f79d7800d0fe0353c7ac | Python | 22,294 | 621 | # -*- coding: utf-8 -*-
"""Functionality for transforming files between spaces."""
import os
from pathlib import Path
import nibabel as nib
from nilearn import image as nimage
import numpy as np
from scipy.interpolate import interpn
from neuromaps.datasets import (ALIAS, DENSITIES, fetch_atlas,
... |
8aa9842905fdb5013f741c793ec76e1430a635b32de4d2255d3ed9ce2c730141 | Python | 22,356 | 732 | """
Base wrapper for VTK objects.
"""
# Author: Oualid Benkarim <oualid.benkarim@mcgill.ca>
# License: BSD 3 clause
import numpy as np
import vtk
from vtk import (vtkAbstractArray, vtkStringArray, vtkIdList, vtkVariantArray,
vtkDataArray)
from vtk.numpy_interface import dataset_adapter as dsa
from ... |
79c6091310ce368cc35aeb4e7d2c21d143376e4c5b0dbbb5ace949200098efd0 | Python | 22,383 | 569 | from __future__ import annotations
import io
import logging
from typing import Iterable
from lightning import pytorch as pl
import torch
from torch import Tensor, nn, optim
from chemprop.conf import LIGHTNING_26_COMPAT_ARGS
from chemprop.data import BatchMolAtomBondGraph, BatchMolGraph, MolAtomBondTrainingBatch
from... |
457840952069d4f3f064b7ea7f6ca5cb2858dd19fbe63a6e5ab2f17b6309a7fa | Python | 22,409 | 661 | """ Created on Mon Sep 15 11:49:07 2025
@author: dcupolillo """
from __future__ import annotations
import pandas as pd
import numpy as np
from spyne.core.spines.analysis.spatial_distances import (
distance_along_neurite, get_path_to_root, path_distance,
prepare_neurite_distance_tools)
from typing import T... |
8a90c5277aea7e73c3e7233238552d62bf71c3498110237a053a3a266fe71bcd | Python | 22,450 | 625 | #!/usr/bin/env python3
############################################################################
# Copyright (c) 2025-2026 University of Helsinki
# All Rights Reserved
# See file LICENSE for details.
############################################################################
"""
Barcode calling quality assessment ... |
2fcd2076338511af24d2b55b31dffd6072734184efa5334f57e6a2ab4cd4980b | Python | 22,456 | 625 | #!/usr/bin/env python3
############################################################################
# Copyright (c) 2025-2026 University of Helsinki
# All Rights Reserved
# See file LICENSE for details.
############################################################################
"""
Barcode calling quality assessment ... |
776572f713d6eef4bebc050437e6019387aa667853baade0ddb117e2ab31c188 | Python | 22,457 | 570 | """
This code is taken from kalmax.kde (https://github.com/TomGeorge1234/KalMax/blob/main/kalmax/kde.py)
and modified by masahiro Nakano
"""
from typing import Callable
import jax
import jax.numpy as jnp
from jax import vmap, jit
from kalmax.utils import gaussian_pdf
from kalmax.kernels import gaussian_kernel
from f... |
95c056a92d672516850ae2e4cd3fc9add8a3f979843a4c1c5b89cf40e934fd30 | Python | 22,497 | 576 | # Copyright (c) Facebook, Inc. and its affiliates.
import math
from typing import Dict
import torch
import torch.nn.functional as F
from detectron2.layers import ShapeSpec, cat
from detectron2.layers.roi_align_rotated import ROIAlignRotated
from detectron2.modeling import poolers
from detectron2.modeling.proposal_gen... |
b5e10bda04c6a4adc501307d4ee89fc6f3c762148e9f42ef68bdabd2b0e8520d | Python | 22,505 | 650 | #!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Cox Cure Rate Model Training
This script trains a Cox proportional hazards model with cure fraction (cure rate model).
The model assumes that a portion of the population will never experience the event (cured),
while the remaining population follows a Cox proportional... |
0aed6248fece3909d1a80728e7b6fea28c67c054d086a2b3036db451f1cbfb53 | Python | 22,521 | 455 | from copy import deepcopy
from typing import Literal, Tuple, Union, List
import torch
from batchgenerators.utilities.file_and_folder_operations import isfile
from dynamic_network_architectures.architectures.abstract_arch import AbstractDynamicNetworkArchitectures
from torch._dynamo import OptimizedModule
from nnunetv2... |
67859afe90fa340592e6921d1e190f41bb1da87630a2f8e05126c9a3588e210f | Python | 22,581 | 440 | import os
import numpy as np
import pandas as pd
import umap
import matplotlib.pyplot as plt
import anndata as ad
import scanpy as sc
import scvelo as scv
import multivelo as mv
from scvelo.preprocessing.moments import get_moments
# load anndata
dir_path = "/home/nomura/Proj/mmvelo/experiments/multiome_brain_rep_wo_IN... |
aedd8170ebfd72a54de9fd0432c19546a5024607584dd9fd31171dcbc2b1fe98 | Python | 22,618 | 478 | import numpy as np
import pandas as pd
import mrcfile
from skimage.morphology import skeletonize_3d, medial_axis, remove_small_objects
from skimage.color import label2rgb
from scipy.ndimage import morphology, label, binary_erosion, convolve
from scipy.spatial import distance
from scipy.interpolate import splprep, splev... |
8520fd77e5d2c1f69985e3f02483f131dc225e1d4c1d43317ccb45006a7dfcec | Python | 22,653 | 482 | """Stage 4: compute dN/dS from the annotated final table.
Reads ``snv_table_final.tsv`` + the reference from the group dir; writes
``dNdS_out/data_dNdS.npz``, the same numbers as ``dnds_genomewide.tsv``, and the per-gene
breakdown ``dnds_per_gene.tsv`` to the analysis dir. Includes the mutation-spectrum /
expected-vs-... |
3d7b98a567f83fe93763d49298f70b9d9a538ef3382b35b7c48409b10b1f17da | Python | 22,697 | 639 | """Behavioural contracts for the graph primitives fastcore implements.
These were differential tests: every function was run with and without
navis-fastcore and the two answers compared. Both fallbacks and oracle are gone
(fastcore is a hard requirement now) - and the oracle was the weaker one anyway,
since two implem... |
1ccad474820ab9238281b8284ecda478cb2a4856b7c877dbc17a0b590ee0c81a | Python | 22,698 | 550 | from matplotlib.gridspec import GridSpec
from matplotlib.widgets import CheckButtons
from sklearn.neural_network import MLPClassifier
from xgboost import XGBClassifier
import batch_process.util.template_util as template_util
import batch_process.util.curate_util as curate_util
from spikeinterface import full as s... |
c96caf6378efa5f5c3992d9037d87b1187cebf0ac9929efe44b74442bd90bcc4 | Python | 22,712 | 552 | #!/usr/bin/env python
#
# Copyright (c) 2023 10X Genomics, Inc. All rights reserved.
#
"""Code to produce isotype control plots for the websummary."""
from __future__ import annotations
from collections import OrderedDict
from typing import TYPE_CHECKING
import altair as alt
import numpy as np
import pandas as pd
fro... |
608314fd9a203af9133f2830794d7609660371bbcbd3b78cec57e486db5ec1ff | Python | 22,737 | 561 | #!/usr/bin/env python3
"""Consistency checks for timestamped output folders and a one-image pipeline smoke test."""
from __future__ import annotations
import json
import os
import sys
import tempfile
import unittest
import zipfile
from datetime import datetime
from io import BytesIO
ROOT = os.path.abspath(os.path.jo... |
34ade6b68670c0585d2102c43726a874b7016a8c01ae699e34eacf444057d435 | Python | 22,839 | 588 | """Code taken from Azimuth panhuman.
Azimuth Cell Annotation: Neural network-based hierarchical cell type
annotation for single-cell RNA-seq data.
This module provides tools for hierarchical cell type annotation and
interpretation based on single-cell RNA-seq data using the Azimuth
neural network model trained on ann... |
0b4dfb97f7ae5ad697f11aa68f93df918179a835f389e2a0edac8b9ffe6436ad | Python | 22,963 | 549 | #!/usr/bin/env python
# Copyright 2016-2026 Biomedical Imaging Group Rotterdam, Departments of
# Medical Informatics and Radiology, Erasmus MC, Rotterdam, The Netherlands
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obt... |
b6b638614e661cfff6d637ac2a06a223469990a4f2e138c5d22070d3d853646b | Python | 22,996 | 549 | #!/usr/bin/env python3
import os, re, glob, argparse
from dataclasses import dataclass
from typing import List, Tuple, Dict, Optional
import numpy as np
import pandas as pd
from tqdm import tqdm
import matplotlib.pyplot as plt
import freesasa
from Bio.PDB import PDBParser, Selection
MAX_ASA_TIEN = {
"ALA": 129.0... |
f6b8ad45e226787b1cfb5d90c5730d0c1ae38036266b04626fa9e35143695675 | Python | 23,032 | 589 | import os
import numpy as np
import pandas as pd
import anndata as ad
import numpy as np
import scanpy as sc
import time
import matplotlib.pyplot as plt
def scv_analysis(adata, figure_folder=None, recompute_velocity=True):
if recompute_velocity:
selected_genes_mask = adata.var['selected_genes']
a... |
c11c331e52deb8aa2e3f1759a5a99cae8e9df451ba9fde8ff7ec9c88dce69efd | Python | 23,077 | 528 | import os
import numpy as np
import pandas as pd
import umap
import matplotlib.pyplot as plt
import anndata as ad
import scanpy as sc
import scvelo as scv
import cellrank as cr
import scanpy.external as sce
from scipy.io import mmwrite, mmread
import statsmodels.api as sm
np.random.seed(42)
# peak-gene linkage matrix... |
e0b11941b53a21e72dfadf4a38dfa043184e48f543179880b22f5f05c828b619 | Python | 23,147 | 611 | """Tests for the mesh operations that are not rebuilds - `fix_mesh`,
`smooth_mesh` and `points_to_mesh`.
For `fix_mesh` there are two things worth pinning. One is the trimesh-version
gate: `Trimesh.remove_duplicate_faces`/`.remove_degenerate_faces` were replaced
by `.unique_faces()`/`.nondegenerate_faces()` in trimesh... |
67f3060582058017f1e3b44d996f86819cfdcb65fcb6bcab8649bfbf4d753727 | Python | 23,152 | 644 | import logging
from os import PathLike
from typing import Literal, Mapping, Sequence
import numpy as np
import pandas as pd
from torch import nn
from chemprop.data.datapoints import (
LazyMoleculeDatapoint,
LazyReactionDatapoint,
MolAtomBondDatapoint,
MoleculeDatapoint,
ReactionDatapoint,
)
from c... |
8203b03eaa57d66817aac85ee2d84060f528f9ddf7973bfc94984a0e06406641 | Python | 23,166 | 662 | """
If you use this code, please cite one of the SynthSeg papers:
https://github.com/BBillot/SynthSeg/blob/master/bibtex.bib
Copyright 2020 Benjamin Billot
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 Lice... |
5a7a57f11f2eb67bf7a7fb686818029b3e20c48b267ee144cb6b54aa8a1f9fc5 | Python | 23,173 | 688 | ####### DISCLAIMER ############
# All the code below was adapted from https://github.com/Pella86/DenoiseAverage
# It contains helper functions for handling images, computing their Fourier transforms,
# and applying masks to them to implement the low-, high-, and band-pass filters.
# -*- coding: utf-8 -*-
"""
Created ... |
5fb573adf4a93a7aa3b4278581e5404e5357de4b7a7e0b0a320ee8867b13a048 | Python | 23,177 | 620 | import os
import copy
import torch
import random
import logging
import numpy as np
import torch.nn as nn
from scipy import stats
from torch.utils.data import Dataset, DataLoader
from importlib.resources import files
from accusnv.downstream import snv
log = logging.getLogger('accusnv')
def setup_seed(seed):
torch.... |
843c7faee5913e82b78c218ed5aecc5a96f766bfcb974f9b6b49d57b1bcb4142 | Python | 23,209 | 735 | # %%
from __future__ import annotations
import numpy as np
from joblib import delayed
from joblib import Parallel
from numpy.typing import NDArray
from scipy.stats import kendalltau
from scipy.stats import spearmanr
from tqdm_joblib import tqdm_joblib
# %%
class RSA:
"""Perform RSA between RDMs.
Parameters
... |
51a5a996e8d347ad58657ccc3fbeff749ed205196eb615243ce5427cb3e7733a | Python | 23,261 | 613 | """Tests for the element-axis schema (`navis.core.schema`).
Two kinds of test live here:
- `test_schema_is_complete` guards the schema itself. Missing a field in an
`AXES` declaration means that field silently survives a subset unfiltered, so
the schema being complete is a property worth checking mechanically rat... |
28e4fd6bc2b34689b5f074c1461e27ac777d60772bf2f7cd7949547e34db7f4e | Python | 23,263 | 638 | import argparse, os, sys, datetime, glob, importlib
from omegaconf import OmegaConf
import numpy as np
from PIL import Image
import torch
import torchvision
from torch.utils.data import random_split, DataLoader, Dataset
import pytorch_lightning as pl
from pytorch_lightning import seed_everything
from pytorch_lightning.... |
79576cdad97b04c1f712eb8342b53d76880aea1c5e17eddb500307d2f42ec4b9 | Python | 23,330 | 662 | # -*- coding: utf-8 -*-
# Copyright (c) Facebook, Inc. and its affiliates.
"""
Common data processing utilities that are used in a
typical object detection data pipeline.
"""
import logging
import numpy as np
from typing import List, Union
import pycocotools.mask as mask_util
import torch
from PIL import Image
from d... |
ac5a1d228cd1bcd24b2005100de2b2e0cd6b3fa4a3421d1131351b83037f40d3 | Python | 23,348 | 762 | from pathlib import Path
import matplotlib.pyplot as plt
import matplotlib
import numpy as np
import pandas as pd
import seaborn as sns
import matplotlib.patches as mpatches
from scipy.stats import mannwhitneyu, pearsonr
from sklearn.metrics import roc_curve, r2_score, mean_squared_error, roc_auc_score, auc, \
pre... |
7fe45dbd4837411d301479b11f251287c6aa957a689d6016efc6aec0c7f3e784 | Python | 23,375 | 640 | import tensorflow as tf
import numpy as np
import matplotlib.pyplot as plt
import math
import pandas as pd
from sklearn.model_selection import train_test_split
from PIL import Image
import tqdm
import cv2
import os
#tf.enable_eager_execution() #eager execution
""" 设置使用GPU """
gpus = tf.config.experiment... |
bc63b21a340a33a3555525d3caa489aa1211e7cd01414abd0d9781ce7e388198 | Python | 23,401 | 520 | import os
import sys
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
import anndata as ad
import scanpy as sc
import scvelo as scv
from scipy.io import mmwrite, mmread
import seaborn as sns
import scipy
np.random.seed(42)
dir_path = "/home/nomura/Proj/mmvelo/experiments/Greenleaf_multiome_Cond_... |
8eb1a33a961ff0ad31f7232c9aa60ba486b1bdc59d53aa500df932983e60a551 | Python | 23,412 | 567 | """
IVSCC morphometrics on EM data
==============================
<!-- difficulty: advanced -->
Turn MICrONS reconstructions into something [`navis.ivscc_features`][] can measure.
!!! important "This example is not executed"
Like the [IVSCC tutorial](zzz_tutorial_morpho_05_ivscc), this one is *not* run when the d... |
8b236f376117591a3408c1b9e28513327ff2285a747f8df535c31cce380a7d99 | Python | 23,449 | 595 | # uv add xlrd openpyxl
# uv run pepIntSum.py
#
# REPL-friendly MaxLFQ trace script.
#
# Purpose:
# Trace every step from an exported MaxQuant peptide table to reconstructed LFQ,
# then compare against proteinGroups.txt.
#
# Designed for your small last example:
# peptides opy.txt
# proteinGroups - Copy.txt
#
#... |
8ffcabd3ce772bebf429589210c1ba6c61a7f6feaae89b9b00994836d9a29042 | Python | 23,461 | 589 | #!/usr/bin/env python3
"""
normalize_intensity - Percentile-based Intensity Normalization for MRI Data
Part of the micaflow processing pipeline for neuroimaging data.
This module performs intensity normalization on MRI data using percentile-based clamping
and rescaling. Intensity normalization is crucial for improvin... |
d4a8cfe1793a9079ac33a41b9836c18ac4c54d42d3533a8c442822f09ee751c0 | Python | 23,509 | 546 | ############################################################################
# Copyright (c) 2022-2026 University of Helsinki
# Copyright (c) 2020-2022 Saint Petersburg State University
# # All Rights Reserved
# See file LICENSE for details.
############################################################################
... |
4d45bc4b3928244de76e24acaf937f097ef0e313dc883b557036fc0e9ac3e5ff | Python | 23,513 | 572 | # Copyright (c) Facebook, Inc. and its affiliates.
import numpy as np
from typing import Callable, Dict, List, Union
import fvcore.nn.weight_init as weight_init
import torch
from torch import nn
from torch.nn import functional as F
from detectron2.config import configurable
from detectron2.data import MetadataCatalog
... |
e31c7396299b707f259827966636c373ea3499c03509f81e64a2c3616452938e | Python | 23,540 | 607 | #!/usr/bin/env python3
"""
Batch experiment orchestrator for Bielschowsky axon segmentation.
Reads axon_inference_instructions.csv and processes every block in three phases:
Phase 1 – Inference
Runs inference_wsi.run_axon_infer() on each block's
Data/CLAHE-Enhanced/wsi_clahe_enhanced.npy
→ writes Data/A... |
52a47ca717ff7cf84fd3dc6a180eaa2d693676ed611b81af63c01033ab1c1a67 | Python | 23,575 | 643 | """
This function trains a regressor network to predict Dice scores between segmentations (typically obtained with an
automated algorithm), and their ground truth (to which wwe typically do not have access at test time).
If you use this code, please cite one of the SynthSeg papers:
https://github.com/BBillot/SynthSeg... |
fbfd29019000f9f81c72c297f3366e600183bc557c24e8799626d5774f4591ca | Python | 23,612 | 701 | #!/usr/bin/env python
# Copyright 2016-2021 Biomedical Imaging Group Rotterdam, Departments of
# Medical Informatics and Radiology, Erasmus MC, Rotterdam, The Netherlands
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obt... |
d0b42e0da1964aeb4a3d6c05a2ecdf2c96ca5c2472110601b51fcc8ff38e26b9 | Python | 23,631 | 556 | # Copyright (c) Facebook, Inc. and its affiliates.
import contextlib
import datetime
import io
import json
import logging
import numpy as np
import os
import shutil
import pycocotools.mask as mask_util
from fvcore.common.timer import Timer
from iopath.common.file_io import file_lock
from PIL import Image
from detectro... |
276cd5d4ece258652e28930f423cb638c3e12cbb59acfdb2bd1718ea6247420c | Python | 23,654 | 561 | from __future__ import annotations
from dataclasses import dataclass
import numpy as np
from bpnn_batch import evaluate_candidate_matrix
from bpnn_training import BPNNTrainingConfig, SingleHiddenBPNN, flatten_model_parameters
@dataclass(frozen=True)
class GAGPUConfig:
population_size: int = 30
generations:... |
999f3471e04f9edce81c586cf58f5bebe3a99447a8f9ddb4d3a5236ead71af7b | Python | 23,656 | 694 | # Copyright (c) Facebook, Inc. and its affiliates.
import numpy as np
import fvcore.nn.weight_init as weight_init
import torch
import torch.nn.functional as F
from torch import nn
from detectron2.layers import (
CNNBlockBase,
Conv2d,
DeformConv,
ModulatedDeformConv,
ShapeSpec,
get_norm,
)
from... |
c7ca538141f52f5affd5ea411b5b09bb0ed8444429672a45c36998a88339c920 | Python | 23,667 | 584 | """Dr.VOT backend for stop-VOT measurement.
Replaces TAPA's Praat-based ``measure_vot`` with the deep-learning Dr.VOT model
(MLSpeech/Dr.VOT, Shrem et al. 2019) while keeping TAPA's per-token output
schema so downstream averaging/CSV/JSON code is unchanged.
Workflow per recording:
1. For every stop token TAPA's se... |
8de4c56beaa85240a799d8dbc3739a5ac0f2cb5a42d5da1183d00a888a844f9b | Python | 23,684 | 630 | ############################################################################
# Copyright (c) 2025-2026 University of Helsinki
# All Rights Reserved
# See file LICENSE for details.
############################################################################
"""
Tests for molecule structure parsing and element types.
T... |
51100d1b866a2db2e11ef8fc5dbf9ab5abd81577d4e88b243171925d790fa921 | Python | 23,698 | 631 | """Streamlit-free per-image NMJ analysis and NMJ_Plot PNG rendering (shared by batch UI and CLI regen)."""
from __future__ import annotations
import gc
import os
from dataclasses import dataclass
from typing import Any
import matplotlib.pyplot as plt
import numpy as np
import pandas as pd
import seaborn as sns
from ... |
9893740ee23b472fbc43d1cfb06744ede723e21316acee9b5fde5bc06f82d89b | Python | 23,736 | 685 | # This code is part of OpenFE and is licensed under the MIT license.
# For details, see https://github.com/OpenFreeEnergy/openfe
"""
Classes for applying restraints to OpenMM Systems.
Acknowledgements
----------------
Many of the classes here are at least in part inspired from
`Yank <https://github.com/choderalab/yank... |
7ea98f9b46f8e9d18bae85010baacad57c3308e37c6f8fadc50a854835ae7aca | Python | 23,740 | 581 | '''
(c) 2014 Brendan Bulik-Sullivan and Hilary Finucane
This module deals with getting all the data needed for LD Score regression from files
into memory and checking that the input makes sense. There is no math here. LD Score
regression is implemented in the regressions module.
'''
from __future__ import division
imp... |
fa2c32b0cb305a9f4738b4b0e2a8c9d2e62afc32d0e4a45ff41db76caa3ebeca | Python | 23,776 | 477 | """
SlotDeconv: Spatial Transcriptomics Deconvolution via Slot-based Reference Learning
"""
import os
import warnings
import numpy as np
import pandas as pd
import torch
import torch.nn as nn
import torch.nn.functional as F
import torch.optim as optim
from scipy.spatial.distance import cdist
from scipy.optimize import ... |
21437d93fad02ba0eef236c1a297c62af37adcc96183d3bd1c968ae55567ba7c | Python | 23,814 | 533 | # Copyright (c) Facebook, Inc. and its affiliates.
from typing import Dict, List, Optional, Tuple, Union
import torch
import torch.nn.functional as F
from torch import nn
from detectron2.config import configurable
from detectron2.layers import Conv2d, ShapeSpec, cat
from detectron2.structures import Boxes, ImageList, ... |
c2edb4f4842fa6fe74c7b35c869b51b4d1210c3a5ba364a3098e7b769f3524ee | Python | 23,870 | 645 | import tensorflow as tf
import numpy as np
import matplotlib.pyplot as plt
import math
import pandas as pd
from sklearn.model_selection import train_test_split
from PIL import Image
import tqdm
import cv2
import os
#tf.enable_eager_execution() #eager execution
""" 设置使用GPU """
gpus = tf.config.experiment... |
95b4485cca38da4afafdf30ffab54398d7a36011cca4f4d62a35445f874d9392 | Python | 23,887 | 1,017 | """This tests the CLI functionality of training and predicting a regression model on a single molecule.
"""
import json
import sys
import pytest
import torch
from chemprop.cli.hpopt import NO_HYPEROPT, NO_OPTUNA, NO_RAY
from chemprop.cli.main import main
from chemprop.cli.train import FoundationModels, TrainSubcomma... |
7ef72ae90708ecbe18c1a2522a660fa8f6299ba1e7d1735992fa1954144213c2 | Python | 23,915 | 661 | import tensorflow as tf
import numpy as np
import matplotlib.pyplot as plt
import math
import pandas as pd
from sklearn.model_selection import train_test_split
from PIL import Image
import tqdm
import cv2
import os
#tf.enable_eager_execution() #eager execution
""" 设置使用GPU """
gpus = tf.config.experiment... |
ed19a2f7bd0db2f686e5a484df78aa1146d6e65ab4af00714301b9be1501c895 | Python | 23,930 | 639 | import pytest
from isoquant_lib.fusion.fusion_metadata import FusionMetadata
class FakeDetector:
"""Mock detector for testing FusionMetadata."""
def __init__(self):
self.fusion_candidates = {}
self.fusion_breakpoints = {}
self.fusion_metadata = {}
self.fusion_assigned_pairs = ... |
fdfda3c1b404789cfd4cbdba2fe41d59ba16e0e3d5cf5cbc1baabd2fe245464d | Python | 23,933 | 556 | import sys
import numpy as np
import torch
from torch import nn
import torch.nn.functional as F
import torch.distributions as dist
from torch.nn.parameter import Parameter
from torch.nn import init
import pytorch_lightning as pl
from pytorch_lightning.callbacks.early_stopping import EarlyStopping
sys.path.append("./sr... |
8deece92f4d3b2e026e17e4555028eee970c309902dca9d438aa4426b159f16c | Python | 23,970 | 738 | # This script is part of navis (http://www.github.com/navis-org/navis).
# Copyright (C) 2018 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, either version 3 of... |
cff4bf81352e19ab5bf96aff72859eaffb20536a9487383eb6691d80218f90fc | Python | 24,312 | 655 | import torch
import torch.nn as nn
import torch.nn.functional as F
import math
from torch.autograd import Variable
from utils import my_softmax, get_offdiag_indices, gumbel_softmax
_EPS = 1e-10
class MLP(nn.Module):
"""Two-layer fully-connected ELU net with batch norm."""
def __init__(self, n_in, n_hid, n_... |
a0e90a624223cf5dfde1f09588c5a7ea560a2cec6a106948c8253ebded924d3a | Python | 24,321 | 692 | from abc import abstractmethod
from typing import Literal
import numpy as np
from numpy.typing import ArrayLike
import torch
from torch import Tensor
from torch.nn import functional as F
import torchmetrics
from torchmetrics.utilities.compute import auc
from torchmetrics.utilities.data import dim_zero_cat
from chempr... |
33b0030cff7e34b84d1858dd6cd7aaa376df7589c2bdd3b166c78a82ef4619d4 | Python | 24,323 | 508 | import os
import numpy as np
import pandas as pd
import matplotlib
import matplotlib.pyplot as plt
import anndata as ad
import scanpy as sc
from scipy.io import mmwrite, mmread
import seaborn as sns
import scipy
from arboreto.algo import grnboost2
import pickle
import collections
import pycistarget
import pyranges as p... |
f37a76e11aa206fd68c2eff0883e71002f4734cd6f33ea245ddcbc0d3539b38a | Python | 24,338 | 712 | # SPDX-License-Identifier: MIT
"""
Spatial plotting utilities for long-read spatial transcriptomics data.
This module provides functions to visualize spatial transcriptomics data
as hexbin overlays, read tree-traversal isoform results, and generate
heatmap tiles with accompanying bar plots.
"""
import os
import numpy ... |
3ef2302edb73fda9e462066224caa61569bd3ec09aeaa41ff38c66fe877393eb | Python | 24,411 | 591 | import torch
import torch.nn as nn
import torch.nn.functional as F
import numpy as np
from torch import einsum
from einops import rearrange
class VectorQuantizer(nn.Module):
"""
see https://github.com/MishaLaskin/vqvae/blob/d761a999e2267766400dc646d82d3ac3657771d4/models/quantizer.py
_____________________... |
a2bb834d8a772ea47fab4281ddc83444d80d194ee84be53ee4ef6e689829695e | Python | 24,441 | 492 | # Copyright 2020 Division of Medical Image Computing, German Cancer Research Center (DKFZ), Heidelberg, Germany
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://w... |
35115c2d77e420045fa2d6ba2702a3e3b9c9541322442bb4fb875bc4ea11ba71 | Python | 24,461 | 574 | import sys
import numpy as np
import torch
from torch import nn
import torch.nn.functional as F
import torch.distributions as dist
from torch.nn.parameter import Parameter
from torch.nn import init
import pytorch_lightning as pl
from pytorch_lightning.callbacks.early_stopping import EarlyStopping
sys.path.append("mmVe... |
01e551bcb642e5b0eb70524dfe855100aa701b8fb8d5c50361ffc2f7b4de7737 | Python | 24,469 | 512 | from copy import deepcopy
import os
import shutil
from typing import Literal, get_args
import torch
import numpy as np
# from numpy.core.multiarray
from nnunetv2.preprocessing.preprocessors.default_preprocessor import DefaultPreprocessor
from nnunetv2.utilities.plans_handling.plans_handler import ConfigurationManager... |
22ae2176de59af506fefb5981eb8474ef251826d56ea7c529a48c9f5626536c8 | Python | 24,495 | 683 |
# This file helps to compute a version number in source trees obtained from
# git-archive tarball (such as those provided by githubs download-from-tag
# feature). Distribution tarballs (built by setup.py sdist) and build
# directories (produced by setup.py build) will contain a much shorter file
# that just contains t... |
58d60e0cb4a4397f719dd8646c190b19de910a751a4509ec21a56e60eaeeada3 | Python | 24,533 | 602 | #!/usr/bin/env python
# Copyright 2020 Biomedical Imaging Group Rotterdam, Departments of
# Medical Informatics and Radiology, Erasmus MC, Rotterdam, The Netherlands
#
# 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... |
b5ec79011647a519ce1e9c2d0b9f218955b3a1709538f518fdc9a9e3697deea3 | Python | 24,576 | 557 | import os
import re
import scipy.io as sio
import numpy as np
from spikeinterface import full as si, extractors as se
import datetime
from pathlib import Path
from util.impedance_analyzer import ImpedanceAnalyzer
import pandas as pd
# Lazy import: psignifit only needed for threshold calculation
# import psign... |
072085b2d5a9d942d90a8ae43e169f5be192480ad655002ffe7c10027afd970d | Python | 24,699 | 723 | # SPDX-License-Identifier: MIT
"""
Utilities for annotating reads in an allinfo file with cell types and constructing sparse isoform matrices.
This module provides functions to:
- Label reads with celltype-region labels from segmentation data
- Generate auxiliary CSV outputs for scisorseqr (isoform IDs, counts per cl... |
ad910c2d6866861bcbbc471d2fb04ee8ca7b0ddff69b4d84cbc48ea544eef304 | Python | 24,776 | 517 | import os
import numpy as np
import pandas as pd
import matplotlib
import matplotlib.pyplot as plt
import anndata as ad
import scanpy as sc
from scipy.io import mmwrite, mmread
import seaborn as sns
import scipy
from arboreto.algo import grnboost2
import pickle
import collections
import pycistarget
import pyranges as p... |
eb1c66bd3314473f8b906a9dd394caea496cee9dd7c4883d78710b52677ccc38 | Python | 24,826 | 614 | #!/usr/bin/env python3
#
# Copyright (c) 2015 10X Genomics, Inc. All rights reserved.
#
from __future__ import annotations
import collections
import glob
import os
import re
import shutil
import subprocess
import xml.etree.ElementTree as etree
from collections.abc import Iterable
from enum import Enum, auto, unique
f... |
a966b06d75684b66b9b584d2bba3ca2372f6d099ab8cbfd84efd42ce120f67d3 | Python | 24,837 | 633 | """
Surface plotting functions.
"""
# Author: Oualid Benkarim <oualid.benkarim@mcgill.ca>
# License: BSD 3 clause
import os
import warnings
from itertools import product as iter_prod
import matplotlib.pyplot as plt
import numpy as np
from matplotlib.colors import Colormap
from .base import Plotter
from .colormaps ... |
84dc15e740e27cd50c79a7fb004476db96db0842d557a8f2add6acfcb4182896 | Python | 24,859 | 467 | import argparse
import inspect
import itertools
import multiprocessing
import numpy as np
from os.path import join
from pathlib import Path
from time import time
from typing import Union, List, Tuple
import warnings
import torch
from torch._dynamo import OptimizedModule
from tqdm import tqdm
import openvino as ov
impo... |
30b804b7c1e7ac67dec5c678d33508c0119547bbbfea2e12fbfa81c9a7e77d65 | Python | 24,965 | 522 | '''
Created on Nov 11, 2024
@author: voodoocode
'''
import numpy as np
import scipy.signal
import functools
import finnpy.file_io.data_manager as dm
import matplotlib
matplotlib.use("Qtagg")
import matplotlib.pyplot as plt
import copy
TIMER_DELAY = 200
import pandas
import PyQt6.QtWidgets
import pyqtgraph
import o... |
d53584e63fe3c883314f82547380f1df7234239b06dbd0249d9518ec2465c362 | Python | 24,968 | 1,168 | # -*- coding: utf-8 -*-
"""
PSTN 评估脚本：指标计算与可视化
输入文件：
A_raw_{t}h.npy
scRNA-seq raw counts，形状为 cells × genes
B_{t}h.npy
ST 表达矩阵，已经经过：
normalize_total(1e4) + log1p
形状为 spots × genes
mapping_matrix_{t}h.pt
映射矩阵，预期形状为 cells × spots
预测流程：
pred_raw =... |
20c59a2f524380551ccff52313e72429fbda11aed90bd7efa56955f669c764b6 | Python | 25,014 | 742 | """
Molecular property prediction using single models and ensembles.
Core inference functions for predicting any scalar molecular property
from SMILES strings: phase classification, transition temperatures,
melting points, birefringence, dielectric anisotropy, etc.
Supports single-model and ensemble prediction for bo... |
3cf0f31b721abb20dcf0f637d6c32778f32b682b3a06f3d6efec65bf45b4e8dd | Python | 25,019 | 384 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
import numpy as np
import pylab
import re
import os
import glob
import matplotlib.pyplot as plt
import matplotlib.gridspec as gridspec
from mpl_toolkits.axes_grid1.inset_locator import inset_axes
from optparse import OptionParser
FOLDERNAME_GENERATE = "learning_generation"... |
90f821c0a01c291d7871cb7c142ee0913b0ffb1c2b4bd57b75c46646a456f7f7 | Python | 25,020 | 481 | '''
Created on Oct 6, 2025
@author: voodoocode
'''
import scipy.io
import numpy as np
import warnings
import os
import pyexcel
import pyvista
import finnpy.visualization.volumetric as vol
import finnpy.visualization.atlas_nifti_to_obj
import finnpy.file_io.data_manager as dm
import h5py
MNI_NATIVE_ERR_THRESH = 0.01... |
7a42415430d89a74f4c1dbfdb44df0a8aa3d0859a839e148038aa2c206344191 | Python | 25,037 | 530 | # This script is part of navis (http://www.github.com/navis-org/navis).
# Copyright (C) 2018 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, either version 3 of... |
93ce7e03e2432eb788453ab931644bef8a38229f6ccaaa28e3edc2b03dfb36b9 | Python | 25,079 | 683 | from copy import deepcopy
import logging
from pathlib import Path
import shutil
import sys
from configargparse import ArgumentParser, Namespace
from lightning import pytorch as pl
from lightning.pytorch.callbacks import EarlyStopping
import numpy as np
import torch
from chemprop.cli.common import add_common_args, pro... |
791b44effa2cdf5491b5c755c79d6dd2a31038d44997955b61b20fec57a7bfc6 | Python | 25,124 | 747 | #!/usr/bin/python3
#
# Copyright (c) 2024 10X Genomics, Inc. All rights reserved.
#
"""Python Client to run cloud cell annotation."""
import base64
import functools
import hashlib
import logging
import os
import random
import string
import textwrap
import time
from collections import defaultdict
from dataclasses impo... |
2e40e089722e3b442966390210a73c3a0aee7992804f49b459b8cc0c88b1509c | Python | 25,186 | 526 | """
opNMF implemented in python
Current implementation has following options:
opNMF (regular version with XX^T stored in memory)
opNMF (mem version with reduced memory footprint but longer runtime)
qr-opNMF
svd-opNMF
tsvd-opNMF
"""
import sys #check python version, exit upon sanity check failures... |
57e940e89a21ddba9f1e0c12ddd34c0c0811320f594eb7cf2910d1d7b049a955 | Python | 25,198 | 730 | # -*- coding: utf-8 -*-
"""
# --------------------------------------------
# Super-Resolution
# --------------------------------------------
#
# Kai Zhang (cskaizhang@gmail.com)
# https://github.com/cszn
# From 2019/03--2021/08
# --------------------------------------------
"""
import numpy as np
import cv2
import tor... |
c87122fc2990c9b87a50cfbbd3bad327542044eb3d379fafc3084a9233257a50 | Python | 25,202 | 695 | # Copyright (c) Facebook, Inc. and its affiliates. All Rights Reserved
"""
Implementation of Swin models from :paper:`swin`.
This code is adapted from https://github.com/SwinTransformer/Swin-Transformer-Object-Detection/blob/master/mmdet/models/backbones/swin_transformer.py with minimal modifications. # noqa
--------... |
1e7e586c7f45d5045792622caee77227866bf7483a3db54f49155f713b7ca21e | Python | 25,251 | 691 | """DataRecorder for the DataRegistry Architecture.
This module orchestrates data collection from Mesa's DataRegistry, managing
storage and conversion to analysis-ready formats.
Architecture:
DataRegistry → DataRecorder → Analysis
- DataRegistry: Pure extraction (what to collect)
- DataRecorders: Storage ... |
3fbb4448ae7c0f82af8c7ec9d72331c1f93b3d30ed7b3c30257349252f4a1dcc | Python | 25,290 | 616 | """
compute_fa_md - Diffusion Tensor Imaging Metrics Calculator
Part of the micaflow processing pipeline for neuroimaging data.
This module computes diffusion tensor imaging (DTI) scalar metrics, specifically
Fractional Anisotropy (FA) and Mean Diffusivity (MD), from preprocessed diffusion-weighted
images (D... |
a0551c03a03cc8e5e8093a8f6394f91ede9a051a36b8e974bcc5a8081d47a355 | Python | 25,310 | 740 | import matplotlib.pyplot as plt
import matplotlib.gridspec as gridspec
import numpy as np
import pandas as pd
import seaborn as sns
import statsmodels.formula.api as smf
import matplotlib.patches as mpatches
from matplotlib.colors import TwoSlopeNorm
from matplotlib.ticker import FuncFormatter
from statsmodels.stats.mu... |
ebad560f8adcacea671433ed558dfd80200d3179143fd6c75d1512821fe4d9ff | Python | 25,390 | 569 | # Copyright (c) Facebook, Inc. and its affiliates.
import logging
from typing import Callable, Dict, List, Optional, Tuple, Union
import torch
from torch import nn
from torch.nn import functional as F
from detectron2.config import configurable
from detectron2.data.detection_utils import get_fed_loss_cls_weights
from d... |
07a371ba0ee097fc95ffa7e047a7ff3b89efa610bd3ab6763acbde81e591f5a2 | Python | 25,473 | 686 | # This script is part of navis (http://www.github.com/navis-org/navis).
# Copyright (C) 2018 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, either version 3 of... |
7e54b329e2a11108d5603bffff904d2f24c1d7da68abb697ea5b269e1e25ef3e | Python | 25,489 | 630 |
import os
from PIL import Image
import numpy as np
import glob
import cv2
import shutil
from scipy.stats import mode
#from EB_get_segmentation_mask import gaussian_kernel, visualize_segmentation
from itertools import combinations
from EB_transformers_util import get_class_value_map
from collections import defaultdic... |
e96e25d7bf8285016c36575575f4a0fe0eb99c8b3b30f4669fb691510955f0fc | Python | 25,504 | 635 | import ratinabox
from ratinabox.Neurons import PlaceCells
from ratinabox.Agent import Agent
from ratinabox.Environment import Environment
import numpy as np
import matplotlib.pyplot as plt
from tqdm import tqdm
from pathlib import Path
import sys
from matplotlib import colors
import matplotlib
import copy
# root_dir ... |
414bd95026b486a482f8426a2f385b56c2f1bed7390329bb7780cddf0ff0d52a | Python | 25,505 | 690 | # -*- coding: utf-8 -*-
# Copyright (c) Facebook, Inc. and its affiliates.
import datetime
import itertools
import logging
import math
import operator
import os
import tempfile
import time
import warnings
from collections import Counter
import torch
from fvcore.common.checkpoint import Checkpointer
from fvcore.common.... |
7ef8908fa4464a9fee6124ad8384244990187f1d49bbda9d75365c648ec65d3c | Python | 25,511 | 734 | #!/usr/bin/env python3
"""
Synthetic Volume Generator for MorphoScope
==========================================
Generates synthetic 3D volumes with known geometries to:
1. Validate the spread quantification algorithm
2. Help biologists understand what spread measures
3. Demonstrate how different variables affect spre... |
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