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9eb88e9c6fe38cc025515e40e5dd9dc92d5233200129e15810afd6675958f736 | Text | 13,042 | 339 |
# HiC-Pro
### An optimized and flexible pipeline for Hi-C data processing
[](https://travis-ci.com/nservant/HiC-Pro)
[](https://github.com/IBM/aihwkit/actions/workflows/test-and-lint.yml)
[![Documentation Status](https://readthedocs.org/proje... |
1756a610e06a46796e431f8302c1f9ff1cbb95a9109063ad490dbaaf05db2e96 | Text | 13,267 | 244 | .. image:: https://circleci.com/gh/AllenInstitute/deepinterpolation.svg?style=svg
:target: https://circleci.com/gh/AllenInstitute/deepinterpolation
# **Deep Interpolation**
*deepinterpolation* is a Python library to denoise data by removing independent noise. Importantly training does **NOT** require ground tru... |
15145f52fc595257e1655b058bceeb9e6cfa6b5631ed35923d29719efda10ded | Text | 13,289 | 159 | # Calcium Imaging Analysis
These series of scripts takes raw data resulted from FIJI-multi-measure to basic figures, analysis of ISI, max response during each stimuli and responders to each stimuli
## Input data and Folder Structure
Put all scripts in the same folder named whatever you like, e.g. "PythonScripts"
![im... |
5e59f51be3b66aaf99f0b4fbd23020e982d66048180554222ed7670278f5da89 | Text | 13,466 | 304 | # ReadCurrent: A VDCNN-based tool for fast and accurate nanopore selective sequencing
Nanopore selective sequencing allows the targeted sequencing of DNA of interest using computational approaches rather than experimental methods such as targeted multiplex polymerase chain reaction or hybridization capture. Compared t... |
3c4a680175044b0cec4625c92b6f6629992008ada9312e850213aaff9cd53c0a | Text | 13,705 | 147 | # Measuring and reducing the carbon footprint of fMRI preprocessing in fMRIPrep
This repository contains a collection of Python and Shell scripts used for the project '[*Measuring and reducing the carbon footprint of fMRI preprocessing in fMRIPrep*][1]'. This study did not involve novel data collection, but made use o... |
f5c86bcd1d7291e1eb66ecf3b7b84244031090f0371b0410f3db6209a4787243 | Text | 13,906 | 309 | <p align="center">
<picture>
<source media="(prefers-color-scheme: dark)" srcset="docs/assets/fair-chemistry-logo-dark-mode.png">
<source media="(prefers-color-scheme: light)" srcset="docs/assets/fair-chemistry-logo-light-mode.png">
<img src="docs/assets/fair-chemistry-logo-dark-mode.png" width="650" alt=... |
bc85890a6232e6e289e90d2c9139bc2d1b2248e855ca43650694bb311ee3612b | Text | 13,907 | 206 | [](https://zenodo.org/badge/latestdoi/278546123)
<!--# scDRS <!-- omit in toc -->
scDRS (single-cell disease-relevance score) is a method for associating individual cells in single-cell RNA-seq data with disease GWASs, built on top of [AnnData](https://anndata.readthedocs... |
2d353ee63e8de5f9dc87e1ce137b11c425277d25140c4d196887c695aef1fb81 | Text | 13,913 | 274 | # ABCD-HCP BIDS fMRI Pipeline
This software takes a BIDS folder as input and determines parameters
for the DCAN Labs' modified HCP pipeline, calling upon the proper code
to run the subject(s).
### Installation
In order to run this software via a container, you will need to acquire a copy of the FreeSurfer License fo... |
243542242a015c533cda37b713d679d3f90377103d2150eba075a719ded3bd61 | Text | 14,074 | 346 | # Edf2Mat© Matlab Toolbox
Converts EyeLink 1000 Edf files into Matlab
```txt
Adrian Etter
Marc Biedermann
University of Zurich
Department of Economics
Schönberggasse 1
CH-8001 Zurich
```
E-Mail: <it@econ.uzh.ch>
## Abstract
Edf2Mat is a Matlab Toolbox for easy conversion of EyeLink Edf result files. ... |
52abb2393f8e49b6b88b233dd671913cb8338e248658e17a5ab0105d80f00f0e | Text | 14,214 | 265 | [](https://app.cvat.ai)
# CVAT: Computer Vision Annotation Tool
[![Release][release-img]][release-url]
[![GitHub stars][stars-img]][stars-url]
[![License][license-img]][license-url]
[![CI][ci-img]][ci-url]
[![server pulls][docker-server-pulls-img]... |
7e4bb40a2dab339d5d5a506849161beb86456adfc3f0d72813a80dca7144e44f | Text | 14,291 | 235 | # CryoTRANS Overview
CryoTRANS (TRansformations by Artificial NetworkS) is a software that predicts high-resolution maps of rare conformations by constructing a pseudo-trajectory between density maps of varying resolutions for Cryogenic Electron Microscopy (cryo-EM). This trajectory is represented by an ordinary diffe... |
ce221a17c1173683ae469979092d2925db9d65ff485602f3fedafcac8c73401e | Text | 14,421 | 360 | # NicMSlesions
Easy multiple sclerosis white matter lesion segmentation using convolutional deep neural networks.
# About:
NicMSlesions makes it easy to accurately segment white matter (WM)
lesions on Magnetic Resonance Images (MRI) using supervised deep
learning. With nicMS... |
922675996245bb797e642fe1c8e1c113ec27917e9999d38718bf50b38013443a | Text | 14,504 | 131 | ## Read me
[](https://mybinder.org/v2/gh/acpennlab/statistics-resampling-online/jammy-docker?urlpath=/lab/tree/statistics-resampling.ipynb) [](https://gnu-octave.github.io/statistics-resampling/) [](https://opensource.org/licenses/MIT) 
- [How to cite](#how-to-cite)
- [What you will need for an empirical analysis](#what-you-will-need)
- [Install instructions](#install-instructions)
- [Usage](#usage)
- [Creating training maps](#creating-training-maps)
- ... |
4e962eaaf46e7b5c43c1f3b56945df692ae2159d17e47b43c539106c39d84211 | Text | 15,695 | 211 | # Taxometer README is [here](https://github.com/RasmussenLab/vamb/blob/taxometer_release/README_Taxometer.md)
# Vamb
Created by Jakob Nybo Nissen and Simon Rasmussen, Technical University of Denmark and Novo Nordisk Foundation Center for Protein Research, University of Copenhagen.
Vamb is a metagenomic binner which ... |
20ae76e0244e3f052854fdee9b42c6ea04f675739b3fd9b4bddad35e3add0bc1 | Text | 15,767 | 185 | <p align="center">
<br>
<img src="./docs/source/en/imgs/diffusers_library.jpg" width="400"/>
<br>
<p>
<p align="center">
<a href="https://github.com/huggingface/diffusers/blob/main/LICENSE">
<img alt="GitHub" src="https://img.shields.io/github/license/huggingface/datasets.svg?color=blue">
</... |
4a6b8e811584c0ff4fce45b606b29e11f6c22b93f856466576e4b984982acd9d | Text | 15,836 | 336 | # KAS-Analyzer
## A new computational framework for exploring KAS-seq data ##
<img src="https://github.com/Ruitulyu/KAS-Analyzer/blob/main/image/KAS-Analyzer.png" height="180" align="right" />
----------------------------------------
Here we introduce KAS-Analyzer, a newly designed, comprehensive methodological frame... |
10b54fc3fadf451e1d20bd30a7def10105a3cb0560e1ff721c0748ff7b7a1dda | Text | 15,993 | 244 | # DeltaSplice
A neural network model to predict splice site usage and splicing-altering mutations
Citation:
Xu, C., Bao, S., Wang, Y., Li, W., Chen, H., Shen, Y., ... & Zhang, C. (2024). Reference-informed prediction of alternative splicing and splicing-altering mutations from sequences. *Genome Research*, 34(7), 1... |
9ac3284ca842f05c4c3a73f2e6dfcfcfe489c6f65b0d99cabdabc98d45ad0db2 | Text | 16,042 | 158 | # Inductive biases of neural network modularity in spatial navigation
This is a project exploring neural architectures for deep reinforcement learning agents. See [paper](https://www.science.org/doi/10.1126/sciadv.adk1256).
All the codes have been tested on Windows machines with Anaconda and CUDA-capable GPUs. The fo... |
d0eafcf3e397c1957cbd03e897f7634ab5a108d70be052710b1c99717dd3081b | Text | 16,057 | 158 | # Inductive biases of neural network modularity in spatial navigation
This is a project exploring neural architectures for deep reinforcement learning agents. See paper https://www.biorxiv.org/content/10.1101/2022.12.07.519515v2.abstract.
All the codes have been tested on Windows machines with Anaconda and CUDA-capab... |
81ca39c045b766e01f7d492a4b41e16981735a9c6949c9a8b32e16bfb3084ee5 | Text | 17,222 | 93 | # pyAGTUM
## Warning:
---
This library and the code are subject to change as this project is ongoing.
## About:
---
**pyAGTUM** is a program for controlling a Leica UC7 ultramicrotome and a modified version of the RMC automated tape collecting machine (ATUM) and a New Era Pump Systems syringe pump. The modifi... |
a8a312886361cd264b98ccfd0d4b81248ac4aef240e22cc9e2d10555ae11c649 | Text | 17,258 | 321 | # MOCA
Modular Optode Configuration Analyzer
<img src="images/flowchart.png" width="400" >
MOCA is a matlab-based workflow to design new and analyze existing fNIRS modules and their associated probes. It provides researchers with a command-line-based approach to define modules, contains functions to assist in tessell... |
264ba31615ffdeac48e3a1269d1c3327a756acc18f8536cf9e82974f2a8e7059 | Text | 17,260 | 362 | # UAlign
Official implementation for paper:
[UAlign: Pushing the Limit of Template-free Retrosynthesis Prediction with Unsupervised SMILES Alignment](https://jcheminf.biomedcentral.com/articles/10.1186/s13321-024-00877-2)
## Updates
- Refactored the repository layout: reusable model code is under `models/`, trainin... |
0eb71b6a720f8596ca5e069a0e5e66def5b8188fbc5dbe297b91f8c43239d115 | Text | 17,518 | 327 | [](https://doi.org/10.5281/zenodo.7754275)
# DS3231 Library
An Arduino library for the DS3231 real-time clock (RTC).
## Description
The library provides easy-to-use methods to:
* set and read the current date and time;
* set, clear, and detect two, ind... |
c83c5420097c0831ca1e4b83b9b402cee0ed950668bb229f3682919b5ab9a9d6 | Text | 18,200 | 622 | <div align="center">
# 🌴 PalmNet
### Gabor-PCA Convolutional Networks for Touchless Palmprint Recognition
[](https://www.mathworks.com/products/matlab.html)
[](https://pypi.python.org/pypi/tedana/)
[](https://pypi.python.org/pypi/tedana/)
[](https://badge.fury.io/py/pyBigWig) [](https://travis-ci.org/dpryan79/pyBigWig.svg?branch=master) [![bioconda-badge](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg... |
7547004966ee06653d74bce6019dfdfce0f60e0d63cf2d3d182f2d57709e374f | Text | 19,025 | 524 | ## The landscape of RNA 3D structure modeling with transformer networks
by Sumit Tarafder, Rahmatullah Roche, Debswapna Bhattacharya
<a href="https://doi.org/10.5281/zenodo.12533828"><img src="https://zenodo.org/badge/DOI/10.5281/zenodo.12533828.svg" alt="DOI"></a>
published in [Biology Methods and Protocols](https:... |
88b804e0ff5f4650a53a613b4a4742e3093a9fa191a91f74418ec728853079a7 | Text | 19,472 | 342 | # FlowSig
Python package to infer directed intercellular flows described by ligand-receptor interactions driving tissue-scale gene expression patterning.
FlowSig requires:
1. Single-cell RNA-sequencing (scRNA-seq) data with cell state annotations that compare a baseline control to one or more perturbed conditions, e... |
b02a208404101adb9faaa47c9a23b2f20c342cab7b65ab8047fe2058bbdcee22 | Text | 19,635 | 306 | # fg-data-profiling
> **`ydata-profiling` is now `fg-data-profiling`.** This package has been renamed to `fg-data-profiling`. Please follow the [Migration Guide](#migration-guide) as soon as possible — the old package will no longer receive updates or bug fixes.
[](https://doi.org/10.5281/zenodo.10079215)
## RNA-seq analysis with Snakemake
[Snakemake](https://snakemake.readthedocs.io/en/stable/) is a workflow manager system for
creating reproducible and scalable pipelines. See a < 2 min
[video presentation](ht... |
eea1775882b1ce645a109376f33d5d0291ad9355601c62f455092e409b7fbcf8 | Text | 20,307 | 438 | [](https://zenodo.org/doi/10.5281/zenodo.10076235)
[](https://opensource.org/licenses/BSD-3-Clause)
[](https://github.com/CSDGroup... |
d53b0fb24c9b33f7d3ff176b3b7a2cf2123a62eb37849b619520716027eba084 | Text | 20,442 | 209 |
## Citing
"An exploration into CTEPH medications: Combining natural language processing, embedding learning, in vitro models, and real-world evidence for drug repurposing"
https://doi.org/10.1371/journal.pcbi.1012417
## Introduction:
We tackled the challenge of keeping up with the ... |
b4735a61db8caf3e9c676a75e627b45d70607e8ae3fbaf02c20e80ac52efad85 | Text | 20,821 | 323 | # LDBlockShow
### 1 Introduction
<b>LDBlockShow</b> is a fast and effective tool to generate linkage disequilibrium (LD) heatmap from VCF files. It is more time and memory saving than other current tools. LDBlockShow can generate the plots of LD heatmap and interested statistics or annotation results simultaneously. I... |
7dc96ffda044668c83a5232942570c58515d1c41f4d99363a8becf6bc3bbc3d4 | Text | 20,929 | 280 | # Note
As the Blue Brain Project has been concluded in December 2024, this repository is archived. For any support or inquiries, please contact abdellah.marwan@gmail.com.
[](https://doi.org/10.1093/bioinformatics/bty231)
<p align="center">
<img src="https... |
94939413aaf4e4b812287a0e81c1533ab58041e2b413df9bd49ee276e221841f | Text | 22,523 | 386 | <img src="Cinnamon-Gui-Logo.png" alt="logo" style="display:block; margin:auto; width:200px; height:auto;">
# CINNAMON-GUI
### Convolutional Neural Network And Multimodal Learning with Graphic User Interface for Digital Pathology
## Version 0.5.0
CINNAMON-GUI is an advanced digital pathology tool that leverages the po... |
2345434fbb89a4305f261b99ec817f506ab8cf81d32a44625388bccaf0a7a327 | Text | 23,021 | 734 | Version: FIBSI 1.0.1
# Frequency Independent Biological Signal Identification
-----
FIBSI
Version 1.0.1
By Ryan Michael Cassidy (rmcassidy@pm.me) and Max Odem (Max.Odem@uth.tmc.edu; max.neuro.odem@gmail.com)
This is the program described in the publication:
>Cassidy RM, Bavencoffe AG, Lopez ER, Cheruvu SS, Walters ... |
316a99d9a1cf930249b741beddabb91ddf05cbbfe05104180a82761dfcda5274 | Text | 26,776 | 434 | # RunAssociationTesting (DNAnexus Platform App)
This is the source code for an app that runs on the DNAnexus Platform.
For more information about how to run or modify it, see
https://documentation.dnanexus.com/.
### Table of Contents
- [Introduction](#introduction)
* [Background](#background)
* [Dependencies](#d... |
71c7ec0abe4d4fdc07d1cd6dc80378a1b56a04a0be44bba475eac3678134ad8d | Text | 27,620 | 436 | # deepface
<div align="center">
[](https://pepy.tech/project/deepface)
[![Stars](https://img.shields.io/github/stars/serengil/deepface?color=yellow&style=flat&... |
64d435f6be55bd6b95aced72b8f9b1a216604757deb042e82241118c607eabfc | Text | 27,999 | 394 |
<img src="https://raw.githubusercontent.com/Starlitnightly/ImageStore/main/omicverse_img/ovbanner.png" >
<div align="center">
<a href="READMEM/README_CN.md">中文</a> | <a href="READMEM/README_ES.md">Español</a> | <a href="READMEM/README_JP.md">日本語</a> | <a href="READMEM/README_DE.md">Deutsch</a> | <a href="READMEM/RE... |
50b1a1d1fbebf87a833a8b0a5ece7cbdc7da59cc9045f33545c0ec0e355f93b2 | Text | 30,329 | 310 | # Swin Transformer
[](https://paperswithcode.com/sota/object-detection-on-coco?p=swin-transformer-v2-scaling-up-capacity-and)
[![PWC](https://img.shields.io/endpoint.svg?... |
184aa64761f8057d19eca4f26c7af3d654aad53e6a32f618c9ec6c39569df0b3 | Text | 31,036 | 353 | <div align="center">
# Bio-Diffusion
<a href="https://pytorch.org/get-started/locally/"><img alt="PyTorch" src="https://img.shields.io/badge/PyTorch-ee4c2c?logo=pytorch&logoColor=white"></a>
<a href="https://pytorchlightning.ai/"><img alt="Lightning" src="https://img.shields.io/badge/-Lightning-792ee5?logo=pytorchlig... |
2e748aef708201df20d55dc55d9740ba3f7f6384d69a4b0480e3306e142ebeed | Text | 31,722 | 487 | [](https://badge.fury.io/py/connected-components-3d) [](https://zenodo.org/badge/latestdoi/146368855)
# cc3d: Connected Components on Multilabel 3D Images
<p style="font-style: italics;" align="center">
... |
df3b96c16a7cc643f3e2b68697869beba222546109673d7e07de05ae38111daa | Text | 34,503 | 594 | # Vision Transformer and MLP-Mixer Architectures
In this repository we release models from the papers
- [An Image is Worth 16x16 Words: Transformers for Image Recognition at Scale](https://arxiv.org/abs/2010.11929)
- [MLP-Mixer: An all-MLP Architecture for Vision](https://arxiv.org/abs/2105.01601)
- [How to train you... |
f0e2e92cceab0322f9eb6029d9a5132727547b83e15c3a133e63131d94806ee9 | Text | 35,325 | 327 | <p align="center">
<img src="https://raw.githubusercontent.com/BojarLab/CandyCrunch/main/images/candycrunch_logo_light_banner_pt.svg" style="height:100%;width:100%;">
</p>
# CandyCrunch
[](https://doi.org/10.5281/zenodo.7940046)
[
[](https://pypi.org/project/hic3defdr)
[](https://lifecycle.r-lib.org/articles/stages.html#maturing)
[](https://anaconda.org/bioconda/fastp)
[](https://anaconda.org/bioconda/fastp)
[![DebianBadge](
https://badges.debian.net/badges/debian/unstable/fastp/version.sv... |
0ab0e76bd5e36a71f356d35c0d401ce777a5e5875f1add2e653689227fd7b013 | TypeScript | 27 | 1 | export * from "./Metrics";
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84010f32ad71741a33aa4cdd47a5322096d0751cda72bc3a83c5ea0cb3b3148e | TypeScript | 31 | 1 | export * from "./ProgressBar";
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2f46c9e105cd8186b12c340319951f71df1234fba6b7c0a9b09d3733a30c1442 | TypeScript | 32 | 1 | export * from "./DurationText";
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0f7c387ba0a067f87cb37194d299fc795bcf726363ca53aff16126dd8593d22e | TypeScript | 35 | 1 | export * from "./MetadataSection";
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7171909c7d7e68450b844694c7085b40a8a6ad05da4104bfff771c4c70ab7bfd | TypeScript | 36 | 1 | export * from "./CodeDialogButton";
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c35e5da95d7b0c63539515159cdb320195909b0bcdf2c22379c9cb07506611dc | TypeScript | 39 | 1 | export * from "./AdvancedProgressBar";
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efa439ad0286f6b9517c2c13d2928333e58ee1ab69ac58cc6810678dcb4705ab | TypeScript | 44 | 1 | export * from "./JobTaskNameProgressTable";
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297ca4dcc48b18365581c2107003dfdac94d88c7521cfc3fadd0f97c2a948a2d | TypeScript | 118 | 7 | export type ClassNameProps = {
className?: string;
};
export type DataTestIdProps = {
"data-testid"?: string;
};
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c117384afeb9a3962cdf3909f60774a098c03d2ce34c4de40232bbe63eeed5d9 | TypeScript | 118 | 6 | export const orientationLabelMap = {
off: 0, // set text height to 0
small: 0.02,
medium: 0.04,
large: 0.06
}
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047d975a7de92b60c867a0b551da3ca5a7c15850b7d950e2d6c93dbbe06d7513 | TypeScript | 157 | 9 | // vitest.config.ts
import { defineConfig } from 'vitest/config'
export default defineConfig({
test: {
environment: 'jsdom',
globals: true
}
})
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08dbe7c4c508ea1b5fa4884e78e3417eb09227ef817248d1562689c55fedc210 | TypeScript | 161 | 8 | declare module '@niivue/dcm2niix' {
export class Dcm2niix {
init(): Promise<void>
input(files: File[]): {
run: () => Promise<File[]>
}
}
}
|
f3c9fa3a6e41465eab37c6626a5d5757fcdf61af1f2e2e7eeaa9aed0cd5ae712 | TypeScript | 174 | 6 | import { RayConfigRsp } from "../type/config";
import { get } from "./requestHandlers";
export const getRayConfig = () => {
return get<RayConfigRsp>("api/ray_config");
};
|
64b5d1c8dbab4d9a1cd2746bdfa20c6849de911b033967152049fad5c296ca12 | TypeScript | 206 | 8 | export const baseName = (path: string): string => {
if (!path) {
return ''
}
const pathSep = path.includes('/') ? '/' : '\\'
const parts = path.split(pathSep)
return parts[parts.length - 1]
}
|
d9e84cebfa5e8030accb504596c1348962addc816bf228a51c2705f11269e893 | TypeScript | 206 | 4 | export const API_REFRESH_INTERVAL_MS = 4000;
// Per job page refresh interval.
export const PER_JOB_PAGE_REFRESH_INTERVAL_MS = 10000;
export const DASHBOARD_DATA_LOADED_EVENT = "ray-dashboard-data-loaded";
|
ece5aa290e52c134a198cfc8cd0a3c3f99f9e50cbca918096e4418e51dbfb367 | TypeScript | 206 | 6 | import { DatasetResponse } from "../type/data";
import { get } from "./requestHandlers";
export const getDataDatasets = (jobId: string) => {
return get<DatasetResponse>(`api/data/datasets/${jobId}`);
};
|
ff93e455af69b009a7f89410d25215675a7027337e71cdcbb47127268bdac33b | TypeScript | 206 | 6 | import { ServeApplicationsRsp } from "../type/serve";
import { get } from "./requestHandlers";
export const getServeApplications = () => {
return get<ServeApplicationsRsp>("api/serve/applications/");
};
|
71ab74dd9d89a284ff2f006291bad47dd80c386168f4383daaf45322f5438bce | TypeScript | 208 | 7 | import { MULTIPLANAR_TYPE } from '@niivue/niivue'
export const layouts = {
Auto: MULTIPLANAR_TYPE.AUTO,
'2x2 grid': MULTIPLANAR_TYPE.GRID,
Row: MULTIPLANAR_TYPE.ROW,
Column: MULTIPLANAR_TYPE.COLUMN
}
|
8ea9cf0606c5fc71b203ed4ad798596b704661e881fd3277664baef4acfd80f0 | TypeScript | 236 | 13 | import { defineConfig } from 'tsup'
export default defineConfig({
entry: ['src/index.ts'],
outDir: 'dist',
target: 'es2020',
splitting: false,
format: 'esm',
sourcemap: true,
clean: true,
dts: true,
metafile: true
})
|
667379f8ecb45da1303c86ad9a8e6f368a6573cf53f6ecbdb0056eb0b9739f73 | TypeScript | 255 | 13 | import { get } from "./requestHandlers";
export type RayStatusResp = {
result: boolean;
message: string;
data: {
clusterStatus: string;
};
};
export const getRayStatus = () => {
return get<RayStatusResp>("api/cluster_status?format=1");
};
|
b3d039e6a76a1398ba8ca47ad90eda78f05d29905a354f77d7f12819fd3726a4 | TypeScript | 256 | 8 | import './style.css'
import { setupNiivue } from './setupNiivue.js'
document.querySelector('#app')!.innerHTML = `
<div style="width: 100vw; height: 100vh">
<canvas id="nvCanvas" ></canvas>
</div>
`
setupNiivue(document.querySelector('#nvCanvas')!)
|
95c614b2af7f5ef45c905b3e1b6af651686e86ae649fc7632cc7c6f36b21428d | TypeScript | 263 | 11 | import { defineConfig } from 'vitest/config'
export default defineConfig({
test: {
include: ['test/cli/**/*.test.ts'],
testTimeout: 120000,
hookTimeout: 30000,
// CLI tests run in Node environment (no DOM needed)
environment: 'node'
}
})
|
f92fcaf5b973d7af5272a16f65a0a4c2b8ac7dd85b9d6f8503007fb069b9b3d8 | TypeScript | 268 | 10 | import { DRAG_MODE } from '@niivue/niivue'
export const dragModeMap = {
None: DRAG_MODE.none,
Contrast: DRAG_MODE.contrast,
'Pan/Zoom': DRAG_MODE.pan,
Measure: DRAG_MODE.measurement,
Slicer3D: DRAG_MODE.slicer3D,
'ROI selection': DRAG_MODE.roiSelection
}
|
8c1157155a7150c42800313c44c6c5faef482e00e4aec03df5b9d1b6c8ae2edb | TypeScript | 280 | 14 | import { defineConfig } from 'tsup'
export default defineConfig({
entry: ['src/lib/loader.ts', 'src/vox2nii.ts'],
outDir: 'build',
target: 'es2020',
splitting: false,
format: 'esm',
sourcemap: true,
clean: true,
dts: true,
cjsInterop: true,
metafile: true
})
|
81d4a26221166f4c40c31db134157eff97da16053cabee4dcb695e357fdcad74 | TypeScript | 282 | 9 | /**
* Authentication-related constants for the Ray dashboard.
*/
/**
* Event name dispatched when an authentication error occurs (401 or 403).
* Listened to by App.tsx to show the authentication dialog.
*/
export const AUTHENTICATION_ERROR_EVENT = "ray-authentication-error";
|
927ec3a115efc34cf8fb2495a474d52babcedc03eb8f3805297aefd6141883a3 | TypeScript | 285 | 14 | import { Task } from "./task";
export type StateApiResponse<T> = {
result: boolean;
message: string;
data: {
[result: string]: {
[result: string]: T[];
};
};
};
export type AsyncFunction<O> = () => Promise<O>;
export type StateApiTypes = Task | PlacementGroup;
|
1549df551ba5a96f2abb637a027ec032cac0121b93cdc9e2cb594f97473eaa81 | TypeScript | 297 | 7 | // Utility to filter valid enum key-value pairs
export const filterEnum = (enumObj: object): Record<string, number> =>
Object.fromEntries(
Object.entries(enumObj)
.filter(([key]) => isNaN(Number(key)))
.map(([key, value]) => [key.replace(/[-_]/g, ' ').toLowerCase(), value])
)
|
58b61108dd79dc627f7918ae6acbdffa7bbd07c89332363c03f194c8fe074c46 | TypeScript | 301 | 9 | import { PlacementGroup } from "../type/placementGroup";
import { StateApiResponse } from "../type/stateApi";
import { get } from "./requestHandlers";
export const getPlacementGroup = () => {
return get<StateApiResponse<PlacementGroup>>(
"api/v0/placement_groups?detail=1&limit=10000",
);
};
|
33e4b2921cf1c206a52ffb3536fbeef21b7faaa4e46f982f17e84cb7e9d67a69 | TypeScript | 306 | 11 | // Copyright (C) CVAT.ai Corporation
//
// SPDX-License-Identifier: MIT
type CapabilityCallback = (allowed: boolean) => void;
type CapabilityUnsubscribe = () => void;
export function observe(_name: string, callback: CapabilityCallback): CapabilityUnsubscribe {
callback(true);
return () => {};
}
|
bcb54ab01e09d53396968599936310fe5a2743889e65f1a1a33739e9fa1790fa | TypeScript | 307 | 10 | import { NodeDetailRsp, NodeListRsp } from "../type/node";
import { get } from "./requestHandlers";
export const getNodeList = async () => {
return await get<NodeListRsp>("nodes?view=summary");
};
export const getNodeDetail = async (id: string) => {
return await get<NodeDetailRsp>(`nodes/${id}`);
};
|
a225d4654091fe69582751e2273a75eb287b58ef367381598284fb5ba134f1cb | TypeScript | 322 | 19 | // declare module '*.glsl' {
// const value: string
// export default value
// }
declare module '*.png' {
const value: string
export default value
}
declare module '*.png?inline' {
const value: string
export default value
}
declare module '*.png?url' {
const value: string
export default value... |
0c589561fe2af72b612640e621c077ea496dc846d116d1378692472b709ec60e | TypeScript | 333 | 11 | /**
* Interaction modules for handling user input events.
* These modules provide pure functions for event management.
*/
export * from './EventController'
export * from './MouseController'
export * from './TouchController'
export * from './KeyboardController'
export * from './WheelController'
export * from './Drag... |
26dde141b457143eadd0e67fdbbe5c1aa299601f040f570303e31745a3a069d1 | TypeScript | 335 | 5 | export { nice } from '@/utils/nice'
export { readFileAsDataURL } from '@/utils/file-utils'
export { img2ras16, unpackFloatFromVec4i, intensityRaw2Scaled } from '@/utils/image-utils'
export { tickSpacing, deg2rad, negMinMax, clamp } from '@/utils/math-utils'
export { swizzleVec3, isRadiological, unProject } from '@/util... |
76c931c0483d2187758e53af08f61d7094f274bb0a743efd0e92011230d4fd54 | TypeScript | 348 | 16 | export interface NiivueTestOptions {
isAntiAlias: boolean
forceDevicePixelRatio: number
thumbnail?: string
}
export interface FilePath {
filePath: string
}
export type NiivueTestOptionsFilePath = NiivueTestOptions & FilePath
export const TEST_OPTIONS: NiivueTestOptions = {
isAntiAlias: false,
... |
7881b5edee596dc4e9f1705bcac36891029680c0e4d151bba53964278af42ab9 | TypeScript | 358 | 13 | export { drawUndo } from '@/drawing/undo'
export { encodeRLE, decodeRLE } from '@/drawing/rle'
export {
findBoundarySlices,
extractSlice,
extractIntensitySlice,
insertColorMask,
doGeometricInterpolation,
doIntensityGuidedInterpolation,
smoothSlice,
calculateIntensityWeight,
interpola... |
74af9e8a43ad637ae8b5ca394e8d86518937ab662c3734e1537db61ca3e7d247 | TypeScript | 376 | 14 | import { Niivue } from '@niivue/niivue'
import { vox2nii } from './lib/loader.js'
export async function setupNiivue(element: HTMLCanvasElement) {
const nv = new Niivue()
await nv.attachToCanvas(element)
// supply loader function, fromExt, and toExt (without dots)
nv.useLoader(vox2nii, 'vox', 'nii')
await nv.... |
3f79261bac8c8df44bb9ad3ed56f7c4d01c80c187c9a593d56b4d9b2fb4e509b | TypeScript | 399 | 34 | // TODO: export these from Niivue so we don't have to duplicate them
export const MESH_EXTENSIONS = [
'ASC',
'BYU',
'DFS',
'FSM',
'PIAL',
'ORIG',
'INFLATED',
'SMOOTHWM',
'SPHERE',
'WHITE',
'G',
'GEO',
'GII',
'ICO',
'MZ3',
'NV',
'OBJ',
'OFF',
'PLY',
'SRF',
'STL',
'TCK',
'TRA... |
1b53ecae8ac02724d63fc6f6d4abe3adfa666b78770aa5ef1b102ada76adef6c | TypeScript | 407 | 18 | import { defineConfig } from 'tsup'
export default defineConfig({
entry: ['src/niivue/index.ts', 'src/drawing/index.ts', 'src/utils/index.ts'],
outDir: 'build',
target: 'es2020',
splitting: false,
format: 'esm',
sourcemap: true,
clean: true,
loader: {
'.jpg': 'dataurl',
... |
c20426175580b84a7255972352d91618edabaa73c331df7eb75db5a7189e01b3 | TypeScript | 425 | 15 | import { PlatformEventsRsp } from "../type/platform";
import { get, head } from "./requestHandlers";
export const getPlatformEvents = async () => {
return await get<PlatformEventsRsp>("api/v0/platform_events");
};
export const getPlatformEventsEnabled = async (): Promise<boolean> => {
try {
await head("api/v0... |
9c2a0ccf979b0113e8fa03db30758bdce377f057ae7f9dc4f8cc83460a018f3c | TypeScript | 432 | 22 | export type RayConfig = {
userName: string;
workNodeNumber: number;
headNodeNumber: number;
containerVcores: number;
containerMemory: number;
clusterName: string;
supremeFo: boolean;
jobManagerPort: number;
externalRedisAddresses: string;
envParams: string;
sourceCodeLink: string;
imageUrl: stri... |
88cc57eb09686a68dd5fe622cb64fb3ccbc40a97af0ea18ce69c2ded57eb776c | TypeScript | 484 | 16 | import { test, expect } from '@playwright/test'
import { Niivue } from '../../dist/index.js'
import { httpServerAddress } from './helpers.js'
test.beforeEach(async ({ page }) => {
await page.goto(httpServerAddress)
})
test('niivue utilities arrayEquals', async ({ page }) => {
const val = await page.evaluate((... |
68dfac7688283bba0f3d5be276b0842027560f9cdd832f2fc1eaae794ead3a08 | TypeScript | 497 | 26 | import { ActorDetail } from "../type/actor";
import { get } from "./requestHandlers";
export const getActors = () => {
return get<{
result: boolean;
message: string;
data: {
actors: {
[actorId: string]: ActorDetail;
};
};
}>("logical/actors");
};
export type ActorResp = {
res... |
4c13eb3e253d3ba35055267512c19b70ad3ee82dcdd9ebab71f57cc9dc77637f | TypeScript | 498 | 18 | import { EventGlobalRsp, EventRsp } from "../type/event";
import { axiosInstance } from "./requestHandlers";
export const getEvents = (jobId: string) => {
if (jobId) {
return axiosInstance.get<EventRsp>(`events?job_id=${jobId}`);
}
};
export const getPipelineEvents = (jobId: string) => {
if (jobId) {
re... |
4a2f855d9d1e34f733bf9d8bcb8ccf09a3854348f6d61b285fa0d681f3a9e2a4 | TypeScript | 500 | 15 | export const hexToRgba10 = (hex: string): number[] => {
const r = parseInt(hex.slice(1, 3), 16)
const g = parseInt(hex.slice(3, 5), 16)
const b = parseInt(hex.slice(5, 7), 16)
const a = 255
let rgba = [r, g, b, a]
rgba = rgba.map((c) => c / 255)
return rgba
}
export const rgba10ToHex = (rgba: number[] | ... |
afbdcb01a38f77314fbebe25ee60802850c0e8a511b7799631713a57f6679d5b | TypeScript | 502 | 21 | import useSWR from "swr";
import { PER_JOB_PAGE_REFRESH_INTERVAL_MS } from "../../../common/constants";
import { getActors } from "../../../service/actor";
export const useActorList = () => {
const { data } = useSWR(
"useActorList",
async () => {
const rsp = await getActors();
if (rsp?.data?.dat... |
4320e83222126d2ea487c86800a23fd3dc36e16cda7693030fe2f7cbf420a8f6 | TypeScript | 522 | 19 | declare module '*.png'
declare module '*.svg'
declare module '*.jpeg'
declare module '*.jpg'
// used for custom niivue loaders with drag and drop files
interface FileSystemEntry {
isDirectory: boolean
isFile: boolean
fullPath: string
name: string
}
// used for custom niivue loaders with drag and drop ... |
210200c830591e35a8b4041a91b164a7d91155142dee54d6b778ad4b3e389547 | TypeScript | 529 | 20 | import { defineConfig } from 'tsup'
export default defineConfig({
entry: ['src/niivue/index.ts'],
outDir: 'dist', // use dist for tests so we don't need to modify all test files
target: 'es2020',
splitting: false,
format: 'esm',
sourcemap: true,
clean: true,
loader: {
'.jpg': 'd... |
3db69d1ca7f8b2892c4a7aa2bbdfb7237a7798d585578c31b47032bd9edbde70 | TypeScript | 540 | 27 | export const memoryConverter = (bytes: number) => {
if (bytes < 1024) {
return `${bytes.toFixed(4)}B`;
}
if (bytes < 1024 ** 2) {
return `${(bytes / 1024 ** 1).toFixed(2)}KB`;
}
if (bytes < 1024 ** 3) {
return `${(bytes / 1024 ** 2).toFixed(2)}MB`;
}
if (bytes < 1024 ** 4) {
return `${(... |
ac14d65678ce9f7c488e15d1d87cd2a31027762d65e2ef51b1f930a8fbd2a048 | TypeScript | 565 | 24 | import { get } from "./requestHandlers";
export type UsageStatsEnabledResponse = {
usageStatsEnabled: boolean;
usageStatsPromptEnabled: boolean;
};
export type ClusterMetadataResponse = {
result: boolean;
message: string;
data: {
rayVersion: string;
pythonVersion: string;
sessionId: string;
... |
6a4ae02c8d82ef7ebdfffc99f657d05c26ad501340974d53a637b18a70da80bf | TypeScript | 570 | 17 | import { test, expect } from '@playwright/test'
import { Niivue } from '../../dist/index.js'
import { httpServerAddress } from './helpers.js'
import { TEST_OPTIONS } from './test.types.js'
test.beforeEach(async ({ page }) => {
await page.goto(httpServerAddress)
})
test('niivue calculateMinMaxVoxIdx', async ({ pag... |
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