sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
034ee6237084c88f32a968c3d18c821f58d860d915bf78ad98f809f22bd7363e | C/C++ | 1,153 | 52 | #ifndef HELPER_H
#define HELPER_H
#include "time.h"
#include <iostream>
using namespace std;
extern struct timespec t0;
struct timespec elapsed (){
struct timespec ts;
clock_gettime (CLOCK_REALTIME, &ts);
if (ts.tv_nsec < t0.tv_nsec){
ts.tv_nsec = 1000000000 + ts.tv_nsec - t0.tv_nsec;
ts.tv_sec--;
}
ts.tv... |
9fb5717543a21c49e5afaad0f345eea98ad67128f1888952f604c72fa2caac28 | C/C++ | 1,157 | 52 | #ifndef HELPER_H
#define HELPER_H
#include <bits/stdc++.h>
#include "time.h"
using namespace std;
extern struct timespec t0;
struct timespec elapsed (){
struct timespec ts;
clock_gettime (CLOCK_REALTIME, &ts);
if (ts.tv_nsec < t0.tv_nsec){
ts.tv_nsec = 1000000000 + ts.tv_nsec - t0.tv_nsec;
ts.tv_sec--;
}
... |
96da204a256f0720e076bc07055031a209b2d9e641bc09c8d8314a6487104555 | C/C++ | 1,160 | 40 | // ***************************************************************************
// BamDeviceFactory_p.h (c) 2011 Derek Barnett
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
// Last modified: 10 October 2011 (DB)
// ---------------------... |
7631e84d9c9d295aea21ca0adcffe6c0865efd294f48dd68ca9a74764cd71e81 | C/C++ | 1,161 | 32 | /* Copyright (c) 2008-2026 the MRtrix3 contributors.
*
* This Source Code Form is subject to the terms of the Mozilla Public
* License, v. 2.0. If a copy of the MPL was not distributed with this
* file, You can obtain one at http://mozilla.org/MPL/2.0/.
*
* Covered Software is provided under this License on an "a... |
05efa017fabd21a0f8313bd3ac604d83dc4026a346a6ef0303dbd167fe862376 | C/C++ | 1,165 | 44 | /* Copyright (c) 2008-2026 the MRtrix3 contributors.
*
* This Source Code Form is subject to the terms of the Mozilla Public
* License, v. 2.0. If a copy of the MPL was not distributed with this
* file, You can obtain one at http://mozilla.org/MPL/2.0/.
*
* Covered Software is provided under this License on an "a... |
bfb65879047116a3f7ea40d6f36fcbb51d9bf7b7901de679b4b17f74ff04ee35 | C/C++ | 1,165 | 49 | /*
Copyright (C) 2014 Sergey Demyanov.
contact: sergey@demyanov.net
http://www.demyanov.net
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 the License, or
(at your option) any l... |
604e9ee50671ccbb7a5e9da62c715618769706b5a0084bd5f0346a32817b5f86 | C/C++ | 1,166 | 50 | /* Copyright (c) 2008-2026 the MRtrix3 contributors.
*
* This Source Code Form is subject to the terms of the Mozilla Public
* License, v. 2.0. If a copy of the MPL was not distributed with this
* file, You can obtain one at http://mozilla.org/MPL/2.0/.
*
* Covered Software is provided under this License on an "a... |
cb7da46ab978994dd6e49ae287cf13556018c8af1d79c6cc576de4cac2d91445 | C/C++ | 1,166 | 46 | /* Copyright (c) 2008-2026 the MRtrix3 contributors.
*
* This Source Code Form is subject to the terms of the Mozilla Public
* License, v. 2.0. If a copy of the MPL was not distributed with this
* file, You can obtain one at http://mozilla.org/MPL/2.0/.
*
* Covered Software is provided under this License on an "a... |
c8b59701b8b7c4ab65cfa1cf3b7bba2051f2fcda6f94f9e345c6ff3efa5ba717 | C/C++ | 1,174 | 39 | #pragma once
#include "Core.h"
#include "InvocationState.h"
namespace rayx {
struct Rand;
/**
turn the normal vector through x_rad and z_rad
@params: normal: the normal vector
x_rad: angle in rad for x-axis
z_rad: angle in rad for z-axis
returns modified normal vector
*/
RAYX_FN_ACC glm::d... |
3a2136cf461613a12235cdc646d37b2fc0d161545b5f27cb5a1e01f0dcacaee5 | C/C++ | 1,176 | 44 | /* Copyright (c) 2008-2026 the MRtrix3 contributors.
*
* This Source Code Form is subject to the terms of the Mozilla Public
* License, v. 2.0. If a copy of the MPL was not distributed with this
* file, You can obtain one at http://mozilla.org/MPL/2.0/.
*
* Covered Software is provided under this License on an "a... |
831e7185ae12738ef924ec57af8bb015fbed4c48686ea5aa11bab9d7cc21eacb | C/C++ | 1,188 | 35 | /*
* Copyright (C) 2010 Regents of the University of Michigan
*
* 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 the License, or
* (at your option) any later v... |
baca99534a398804ca122e791b749aa97837fa326aeea6885c46ba7a8799fe36 | C/C++ | 1,190 | 44 | /* Copyright (c) 2008-2026 the MRtrix3 contributors.
*
* This Source Code Form is subject to the terms of the Mozilla Public
* License, v. 2.0. If a copy of the MPL was not distributed with this
* file, You can obtain one at http://mozilla.org/MPL/2.0/.
*
* Covered Software is provided under this License on an "a... |
4e615d6df84b22a269e70af1776f81a7e75a80b49db088c27c55a15873ffda32 | C/C++ | 1,203 | 49 | /* Copyright (c) 2008-2026 the MRtrix3 contributors.
*
* This Source Code Form is subject to the terms of the Mozilla Public
* License, v. 2.0. If a copy of the MPL was not distributed with this
* file, You can obtain one at http://mozilla.org/MPL/2.0/.
*
* Covered Software is provided under this License on an "a... |
9d1e634ee384b2fbb2fa538f6eff6e1ff2619b7ada4864943d3092de4f2d8ece | C/C++ | 1,215 | 44 | /*
* Copyright (C) 2010 Regents of the University of Michigan
*
* 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 the License, or
* (at your option) any later v... |
26a2724a79ebdcdd5f04a1feb5506397cd98879c98ba20af41d0503408b20f53 | C/C++ | 1,221 | 46 | /* Copyright (c) 2008-2026 the MRtrix3 contributors.
*
* This Source Code Form is subject to the terms of the Mozilla Public
* License, v. 2.0. If a copy of the MPL was not distributed with this
* file, You can obtain one at http://mozilla.org/MPL/2.0/.
*
* Covered Software is provided under this License on an "a... |
e0a0c0039bd0ce30105db1f29dd0c75d0685fe0d9628dbae3c58d904b8e2a09a | C/C++ | 1,222 | 51 | #pragma once
/**
* Defining the RAYX_API macro, which helps with
* building the library (context based import/export of code).
*/
#if defined(RAYX_PLATFORM_MSVC) // Microsoft
#ifdef RAYX_BUILD_DLL
#define RAYX_API __declspec(dllexport)
#else
#define RAYX_API __declspec(dllimport)
#endif
#elif defined(RAYX_PLATF... |
586c83b1621d7375e330c6cedaf6b43cef76d5ae2e09a06ed93f62a9819dd8c8 | C/C++ | 1,231 | 45 | // def,table.h
// header for table-based NUFFT interpolators
#include <stdio.h>
#include "mex.h"
#ifndef Fail
#define Fail(msg) { \
(void)fprintf(stderr, "FAIL %s %d: %s\n", __FILE__, __LINE__, msg); \
(void)fflush(stderr); \
return 0; }
#endif
#ifndef Note1
#define Note1(msg, arg) { \
(void) fprintf(stdout, "No... |
bf73aa46b2452ef5dee917a5357f667e9fe2e1d30faa594b52d358354d67581c | C/C++ | 1,234 | 35 | /*
* Copyright (C) 2010 Regents of the University of Michigan
*
* 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 the License, or
* (at your option) any later v... |
576280e19cb99e9d06c97f089820ee90c73b72209970017de49cae181cf1ed03 | C/C++ | 1,242 | 52 | /* Copyright (c) 2008-2026 the MRtrix3 contributors.
*
* This Source Code Form is subject to the terms of the Mozilla Public
* License, v. 2.0. If a copy of the MPL was not distributed with this
* file, You can obtain one at http://mozilla.org/MPL/2.0/.
*
* Covered Software is provided under this License on an "a... |
6fdc5e5d490335219ebb90325c683ee8e953cabb87d36aa83cfb2c8ff905904e | C/C++ | 1,248 | 53 | /* Copyright (c) 2008-2026 the MRtrix3 contributors.
*
* This Source Code Form is subject to the terms of the Mozilla Public
* License, v. 2.0. If a copy of the MPL was not distributed with this
* file, You can obtain one at http://mozilla.org/MPL/2.0/.
*
* Covered Software is provided under this License on an "a... |
b0ac52866331378178df838eb8a3b04fa9607810392db130855b80902d0b94c7 | C/C++ | 1,248 | 49 | /* Copyright (c) 2008-2026 the MRtrix3 contributors.
*
* This Source Code Form is subject to the terms of the Mozilla Public
* License, v. 2.0. If a copy of the MPL was not distributed with this
* file, You can obtain one at http://mozilla.org/MPL/2.0/.
*
* Covered Software is provided under this License on an "a... |
718dc2a28a2d3eec92f98b7aff09a29df5db841e0bb60e97396c1510de6ab365 | C/C++ | 1,252 | 18 | /*
* Copyright <2012> <Vincent Le Guilloux,Peter Schmidtke, Pierre Tuffery>
* Copyright <2013-2018> <Peter Schmidtke, Vincent Le Guilloux>
Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without... |
245b9e9d03fe72eae5f32855416c1895e67c2b4267c5628a118a8d043eddb88c | C/C++ | 1,256 | 46 | /* Copyright (c) 2008-2026 the MRtrix3 contributors.
*
* This Source Code Form is subject to the terms of the Mozilla Public
* License, v. 2.0. If a copy of the MPL was not distributed with this
* file, You can obtain one at http://mozilla.org/MPL/2.0/.
*
* Covered Software is provided under this License on an "a... |
899b803a5eca98334e553fc50a7f0312b48cadae87b49166394e460269fda029 | C/C++ | 1,260 | 49 | /* Copyright (c) 2008-2026 the MRtrix3 contributors.
*
* This Source Code Form is subject to the terms of the Mozilla Public
* License, v. 2.0. If a copy of the MPL was not distributed with this
* file, You can obtain one at http://mozilla.org/MPL/2.0/.
*
* Covered Software is provided under this License on an "a... |
3669199917017fe032d9a41d06332d8024856ae0772d90d7baff9c1c7be60daf | C/C++ | 1,265 | 51 | /**
* Copyright (c) Facebook, Inc. and its affiliates.
*
* This source code is licensed under the MIT license found in the
* LICENSE file in the root directory of this source tree.
*/
/**
* This is the internal data handler class for the case where we
* have features to represent labels. It overrides a few key ... |
be6345920b1c3907b102dad814c0975a3ee5877a81baab721df906bd0b4af386 | C/C++ | 1,265 | 31 | // Copyright 2024 DeepMind Technologies Limited
//
// AlphaFold 3 source code is licensed under the Apache License, Version 2.0
// (the "License"); you may not use this file except in compliance with the
// License. You may obtain a copy of the License at
//
// http://www.apache.org/licenses/LICENSE-2.0
//
// Unless re... |
60ec63665dfd3d0ced50d78fa67f2ecffade9165142436e9177245cb5821703b | C/C++ | 1,268 | 31 | // Copyright 2024 DeepMind Technologies Limited
//
// AlphaFold 3 source code is licensed under the Apache License, Version 2.0
// (the "License"); you may not use this file except in compliance with the
// License. You may obtain a copy of the License at
//
// http://www.apache.org/licenses/LICENSE-2.0
//
// Unless re... |
c35ea77eba41cc12ac8e7141573dd4e339d8acb63fd904b3714193078118ad3e | C/C++ | 1,272 | 31 | // Copyright 2026 DeepMind Technologies Limited
//
// AlphaFold 3 source code is licensed under the Apache License, Version 2.0
// (the "License"); you may not use this file except in compliance with the
// License. You may obtain a copy of the License at
//
// http://www.apache.org/licenses/LICENSE-2.0
//
// Unless re... |
3850e847c2701a5f96434eb2979f882725de5756299ca764e846d5bea03fdf8b | C/C++ | 1,273 | 44 | /*
* Copyright (C) 2010 Regents of the University of Michigan
*
* 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 the License, or
* (at your option) any later v... |
332477cb900ee8ec8890b8a89700323d69e4865a1f477f44c25b7702be278147 | C/C++ | 1,277 | 44 | /*
* Copyright (C) 2011 Regents of the University of Michigan
*
* 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 the License, or
* (at your option) any later v... |
1059f40bb1906781d8472fc7d41026aef87e1623c5f20f3c4506f8faec3d2bb9 | C/C++ | 1,280 | 31 | // Copyright 2024 DeepMind Technologies Limited
//
// AlphaFold 3 source code is licensed under the Apache License, Version 2.0
// (the "License"); you may not use this file except in compliance with the
// License. You may obtain a copy of the License at
//
// http://www.apache.org/licenses/LICENSE-2.0
//
// Unless re... |
eef4f809d58aaa021435663eb292ac6f732340529c2e6705be0e1138ec110ff0 | C/C++ | 1,280 | 62 | #ifndef STD_H
#define STD_H
using namespace std;
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <limits.h>
#include <iostream>
#include <fstream>
#include <sstream>
#include <string>
#include <map>
#include <algorithm>
#include <vector>
#include <deque>
#include <math.h>
#include <ctype.h>
#inclu... |
a3ed3c797e25ec7cfec26c9487f34845e4d42167a176c806f91c534b3459eef2 | C/C++ | 1,281 | 40 | /* Copyright (c) 2008-2026 the MRtrix3 contributors.
*
* This Source Code Form is subject to the terms of the Mozilla Public
* License, v. 2.0. If a copy of the MPL was not distributed with this
* file, You can obtain one at http://mozilla.org/MPL/2.0/.
*
* Covered Software is provided under this License on an "a... |
5c2a59ac3627fd8a5612293991f05ac5bbde35ef9228432cb2a93bb3a274eda0 | C/C++ | 1,283 | 31 | // Copyright 2024 DeepMind Technologies Limited
//
// AlphaFold 3 source code is licensed under the Apache License, Version 2.0
// (the "License"); you may not use this file except in compliance with the
// License. You may obtain a copy of the License at
//
// http://www.apache.org/licenses/LICENSE-2.0
//
// Unless re... |
e1e1f90b95ba8082032040969a6cbea4b9f9e42c6caeb8cefb8e12cb8348429f | C/C++ | 1,284 | 31 | // Copyright 2024 DeepMind Technologies Limited
//
// AlphaFold 3 source code is licensed under the Apache License, Version 2.0
// (the "License"); you may not use this file except in compliance with the
// License. You may obtain a copy of the License at
//
// http://www.apache.org/licenses/LICENSE-2.0
//
// Unless re... |
3bfbbb59efb5cf29de1d21a6264d0eae4496fb935db0d880be55f896468d5a34 | C/C++ | 1,286 | 45 | // ***************************************************************************
// NetUnix_p.h (c) 2011 Derek Barnett
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
// Last modified: 10 November 2011 (DB)
// -----------------------------... |
0678b903ecdd6156e1fba523339710009861b7a638c8b3ac349fdd73d6cca434 | C/C++ | 1,287 | 51 | /*
Bayesian Functional GWAS --- MCMC (bfGWAS:MCMC)
Copyright (C) 2016 Jingjing Yang
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 the License, or
(at your ... |
3dc688d57b0e7675f26a9c04be9ca50356bbbd178fe170889928b7b5ac5fbff7 | C/C++ | 1,287 | 31 | // Copyright 2024 DeepMind Technologies Limited
//
// AlphaFold 3 source code is licensed under the Apache License, Version 2.0
// (the "License"); you may not use this file except in compliance with the
// License. You may obtain a copy of the License at
//
// http://www.apache.org/licenses/LICENSE-2.0
//
// Unless re... |
94ff03a5c2ed74d450bc8776b1ebb16f3f015d251ec2262b4dd9ab448842f484 | C/C++ | 1,287 | 31 | // Copyright 2024 DeepMind Technologies Limited
//
// AlphaFold 3 source code is licensed under the Apache License, Version 2.0
// (the "License"); you may not use this file except in compliance with the
// License. You may obtain a copy of the License at
//
// http://www.apache.org/licenses/LICENSE-2.0
//
// Unless re... |
6873684aa0eea6311b4fbf1c5baa666952625d5f9957f540dbb205eba6bc119e | C/C++ | 1,289 | 31 | // Copyright 2024 DeepMind Technologies Limited
//
// AlphaFold 3 source code is licensed under the Apache License, Version 2.0
// (the "License"); you may not use this file except in compliance with the
// License. You may obtain a copy of the License at
//
// http://www.apache.org/licenses/LICENSE-2.0
//
// Unless re... |
d0c77b626e004bc0db1ac1eb9b4abe5f4d47aae8cd7704a250966c32b3592f88 | C/C++ | 1,289 | 31 | // Copyright 2024 DeepMind Technologies Limited
//
// AlphaFold 3 source code is licensed under the Apache License, Version 2.0
// (the "License"); you may not use this file except in compliance with the
// License. You may obtain a copy of the License at
//
// http://www.apache.org/licenses/LICENSE-2.0
//
// Unless re... |
17adabbe3d12eb2331a7ffb24aaa7e8243cdf3a909988206b892d8ef35f960aa | C/C++ | 1,292 | 49 | /****************************************************************************
**
** Copyright (c) 2008-2015 C.B. Barber. All rights reserved.
** $Id: //main/2015/qhull/src/libqhullcpp/QhullStat.h#2 $$Change: 2079 $
** $DateTime: 2016/02/07 17:43:34 $$Author: bbarber $
**
************************************************... |
36df9a80748dff20e10837f6a88a737a921e49dc35132deb2758c6ef54ba77fc | C/C++ | 1,293 | 42 | #pragma once
#include <filesystem>
#include <string>
#include <vector>
#include <shared_mutex>
#include <mutex>
#include "Core.h"
namespace rayx {
class RAYX_API ResourceHandler {
public:
static ResourceHandler& getInstance() {
static ResourceHandler instance;
return instance;
}
// Pl... |
4b418ce9306a70f7cca005dc7d1ba404579f7197c7761d49c625987a0a090707 | C/C++ | 1,294 | 45 | /*
Copyright (C) 2014 Sergey Demyanov.
contact: sergey@demyanov.net
http://www.demyanov.net
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 the License, or
(at your option) any l... |
576b6bd502b3eeba521ea60d55221a7f7422ca41302d35281edc9faee3dbb270 | C/C++ | 1,298 | 31 | // Copyright 2024 DeepMind Technologies Limited
//
// AlphaFold 3 source code is licensed under the Apache License, Version 2.0
// (the "License"); you may not use this file except in compliance with the
// License. You may obtain a copy of the License at
//
// http://www.apache.org/licenses/LICENSE-2.0
//
// Unless re... |
7d018c81bf2e974fbb17e9cdc930fafb8e6bf2e682508cafc258a5937e578ad3 | C/C++ | 1,301 | 48 | // ***************************************************************************
// BamPipe_p.h (c) 2011 Derek Barnett
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
// Last modified: 10 November 2011 (DB)
// -----------------------------... |
b5c9be162309028ed9c9816df3a892ebdacd2cbc80d3f3249c5b23e80329f59b | C/C++ | 1,301 | 38 | #pragma once
#include "Rays.h"
namespace rayx {
// this struct is analog to struct Rays. It contains pointers to the attribute arrays
struct RaysPtr {
#define X(type, name, flag) type* __restrict name;
RAYX_X_MACRO_RAY_ATTR
#undef X
RAYX_FN_ACC glm::dvec3 position(const int i) const { return glm::dvec3(pos... |
4746d453ac84b0a304598d3b32ae8db4ae0837f042662a7ae9bb933f3835d50e | C/C++ | 1,306 | 31 | // Copyright 2024 DeepMind Technologies Limited
//
// AlphaFold 3 source code is licensed under the Apache License, Version 2.0
// (the "License"); you may not use this file except in compliance with the
// License. You may obtain a copy of the License at
//
// http://www.apache.org/licenses/LICENSE-2.0
//
// Unless re... |
5c22239c48bbf35755fd733b9b269118967cda6499970bc7833b2760882e7476 | C/C++ | 1,307 | 44 | /*
Copyright (C) 2014 Sergey Demyanov.
contact: sergey@demyanov.net
http://www.demyanov.net
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 the License, or
(at your option) any l... |
422a3b6895e71953fdd31255b892f3fece10c7c983c68ebc4c8f7e2d47eb33d9 | C/C++ | 1,308 | 32 | //
// tlerror.h
// treelib
//
// Created by mbrazeau on 22/04/2017.
// Copyright © 2017 brazeaulab. All rights reserved.
//
#ifndef tlerror_h
#define tlerror_h
typedef enum {
ERR_EX_DAT_CONFLICT = -16, /*!< Conflict with existing loaded data */
ERR_SYMBOL = -15, /*!< Unrecognized symbol... |
5a526ee6254776388bcd337a6a7e997c221475c9878969054396283747c76d39 | C/C++ | 1,309 | 36 | #pragma once
#include "Ray.h"
#include "Throw.h"
namespace rayx {
/**
* converts energy (eV) to wavelength (nm)
* @param energy energy of a photon in eV. must not be 0
* @return wavelength of photon in nm
*/
RAYX_FN_ACC inline double RAYX_API energyToWaveLength(double x) { return INV_NM_TO_EVOLT / x; }
/**
* C... |
581ab619bc85aca51b725e4d12475e838f6d2a2846daae923b73628f3f7fde86 | C/C++ | 1,329 | 52 | #pragma once
#include <alpaka/alpaka.hpp>
#include "Debug/Debug.h"
namespace rayx {
template <typename Acc>
constexpr inline auto getBlockSize() {
using Idx = alpaka::Idx<Acc>;
using Dim = alpaka::Dim<Acc>;
auto impl = []() -> Idx {
#if defined(ALPAKA_ACC_GPU_CUDA_ENABLED)
if constexpr (std::is... |
f713da5680ccfe64b7cb523f9b2aa554f1e10d79ea3155191174e26468619fde | C/C++ | 1,339 | 53 | #pragma once
#include <array>
#include <vector>
#include <glm.hpp>
#include "Core.h"
namespace rayx {
/**
* This enum class is the c++ perspective on the Materials stored in
* "materials.xmacro".
* Whenever you want to add a material, just add a line in materials.xmacro:
* everything else is done automagically.... |
436084a60aed80c39d2090f93c9afbdcf1d397950260ec8970214c343ffaf1bd | C/C++ | 1,340 | 30 | /* Copyright (c) 2008-2026 the MRtrix3 contributors.
*
* This Source Code Form is subject to the terms of the Mozilla Public
* License, v. 2.0. If a copy of the MPL was not distributed with this
* file, You can obtain one at http://mozilla.org/MPL/2.0/.
*
* Covered Software is provided under this License on an "a... |
4c0d8254402c9474617098b9f58b2f43c307677496263631681dee3f3e953b5f | C/C++ | 1,340 | 38 | /*
* Copyright (C) 2011 Regents of the University of Michigan,
* Hyun Min Kang, Matthew Flickenger, Matthew Snyder,
* and Goncalo Abecasis
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License... |
84606b6b5bdbf57808263899ef0e810750247be13210a27f3489329a252cdfe5 | C/C++ | 1,340 | 49 | /*
Copyright (C) 2014 Sergey Demyanov.
contact: sergey@demyanov.net
http://www.demyanov.net
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 the License, or
(at your option) any l... |
3250d7299bb606e29eea54ec8fe63dc0bd0c39661bbbedfc51b1c8f225b7d5c2 | C/C++ | 1,341 | 45 | /* Copyright (c) 2008-2026 the MRtrix3 contributors.
*
* This Source Code Form is subject to the terms of the Mozilla Public
* License, v. 2.0. If a copy of the MPL was not distributed with this
* file, You can obtain one at http://mozilla.org/MPL/2.0/.
*
* Covered Software is provided under this License on an "a... |
e30608834911583227b67f834fc1b10cd82a8a40c867b7c607bf72f157aaf895 | C/C++ | 1,341 | 54 | /*
* Copyright (C) 2011 Regents of the University of Michigan
*
* 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 the License, or
* (at your option) any later v... |
a8defc0c797dbe0364359ca4c2424a02f815b04806adf38b763d956fa61a0bef | C/C++ | 1,343 | 41 | /* Copyright (c) 2008-2026 the MRtrix3 contributors.
*
* This Source Code Form is subject to the terms of the Mozilla Public
* License, v. 2.0. If a copy of the MPL was not distributed with this
* file, You can obtain one at http://mozilla.org/MPL/2.0/.
*
* Covered Software is provided under this License on an "a... |
82f52948c8b04ebf3d9f3bcdb926cacd403ac71fd81755a7ad4ccfc6991315c5 | C/C++ | 1,353 | 40 | #pragma once
#include <CLI/CLI.hpp>
#include <optional>
#include <unordered_map>
class CommandParser {
public:
// Custom constructor
CommandParser(int _argc, char* const* _argv);
~CommandParser() = default;
std::shared_ptr<CLI::App> m_cli11;
// CLI Arguments
// Flags initialize to DISABLED
... |
b21259dcfaab7548b0ebf7d5961ecdcc6dbfe2f4df278aced3abe3ebe120990b | C/C++ | 1,355 | 34 | /*
* Copyright (C) 2010 Regents of the University of Michigan
*
* 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 the License, or
* (at your option) any later v... |
1c9892ff335eebb1ed00f83ad91aa023297d05d2024046b3fa2673807acee272 | C/C++ | 1,359 | 41 | /*
* Copyright (C) 2010 Regents of the University of Michigan
*
* 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 the License, or
* (at your option) any later v... |
6764dcc0eabdb3f2f922ef1ae4bc6b6f8bdb0e7599ea6e9f3e972e8b53ed85e5 | C/C++ | 1,359 | 48 | /* Copyright (c) 2008-2026 the MRtrix3 contributors.
*
* This Source Code Form is subject to the terms of the Mozilla Public
* License, v. 2.0. If a copy of the MPL was not distributed with this
* file, You can obtain one at http://mozilla.org/MPL/2.0/.
*
* Covered Software is provided under this License on an "a... |
5eb350775be985d8c6d8b9fae52af04badd93e1d667c1ab317cf89bd24fdd056 | C/C++ | 1,362 | 49 | /*
Copyright (C) 2014 Sergey Demyanov.
contact: sergey@demyanov.net
http://www.demyanov.net
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 the License, or
(at your option) any l... |
4057d07d94384d6af60baa1b7a6ba605b614ba13e539aafcbb86963caac95648 | C/C++ | 1,365 | 49 | // ***************************************************************************
// bamtools_fasta.h (c) 2010 Derek Barnett, Erik Garrison
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
// Last modified: 10 October 2011
// ---------------... |
118a889f3e5071ad4494e307fc5acbf879672dc1b7a83938cf77d75129ab8e6e | C/C++ | 1,370 | 63 | // Portable high-precision timer
// Using QueryPerformanceCounter for Win32/Win64
// And POSIX get_clock() for other platforms
#pragma once
#if _MSC_VER
#include <Windows.h>
#elif __GNUC__
#include "time.h"
#endif
using namespace std;
#if _MSC_VER
struct Timer { // High performance Win64 timer using QPC events
dou... |
8facd79a93ea8bfbae263a4ba51e3a5cac58ac511d02ae64125660e2379aeb37 | C/C++ | 1,370 | 34 | #pragma once
#include <filesystem>
#include <vector>
#include "Core.h"
#include "FileIO.h"
namespace rayx {
/// `relPath` is a path relative to the root of the RAY-X git repository (i.e.
/// where .git lies). canonicalizeRepositoryPath(relPath) yields an absolute
/// path representing the same path. Examples:
/// -... |
cb38f61ec62092bf9aceb891565d69828f57c550b147c7a5745deddac5ea063f | C/C++ | 1,376 | 37 | #pragma once
#include <vector>
#include "BundleHistory.h"
#include "Element/Element.h"
#include "RenderObject.h"
/**
* @brief Traces the path of rays through an OpticalElement using a grid-based approach, and returns a RenderObject for visualization.
* @param element The optical element through which rays are trac... |
d5a7c1f14d30ffe6740147b1b867eccc2c669b355d859a485a5f3b80eb1a7c09 | C/C++ | 1,377 | 59 | #ifndef AUXILLARY_H
#define AUXILLARY_H
#include <Eigen/Dense>
#include <Eigen/Core>
#include <Eigen/LU>
#include <Eigen/SVD>
#include <vector>
#ifdef USE_DOUBLE
typedef Eigen::Matrix<double, Eigen::Dynamic, Eigen::Dynamic, Eigen::RowMajor> MatrixXdr;
#else
typedef Eigen::Matrix<float, Eigen::Dynamic, Eigen::Dynami... |
6b56107a3756e581368c6282f707cbe98294d20fc8564c0db1e7c89f973e8175 | C/C++ | 1,378 | 55 | /* Copyright (c) 2008-2026 the MRtrix3 contributors.
*
* This Source Code Form is subject to the terms of the Mozilla Public
* License, v. 2.0. If a copy of the MPL was not distributed with this
* file, You can obtain one at http://mozilla.org/MPL/2.0/.
*
* Covered Software is provided under this License on an "a... |
c64badc154128b3846bb2f69297d9ddb05fef7a5657377bedb29088baf4f995e | C/C++ | 1,380 | 57 | /* Copyright (c) 2008-2026 the MRtrix3 contributors.
*
* This Source Code Form is subject to the terms of the Mozilla Public
* License, v. 2.0. If a copy of the MPL was not distributed with this
* file, You can obtain one at http://mozilla.org/MPL/2.0/.
*
* Covered Software is provided under this License on an "a... |
f1660d2c982880d77d7597dda150b5749f29835f1aeb6c471820553e17d1950d | C/C++ | 1,384 | 56 | /* Copyright (c) 2008-2026 the MRtrix3 contributors.
*
* This Source Code Form is subject to the terms of the Mozilla Public
* License, v. 2.0. If a copy of the MPL was not distributed with this
* file, You can obtain one at http://mozilla.org/MPL/2.0/.
*
* Covered Software is provided under this License on an "a... |
4828ff500f51a0e05614638fb2f23e29af883dbee4d63ea541072e6b3180b864 | C/C++ | 1,394 | 39 | #include <stdlib.h>
#include <stdbool.h>
#include <gsl/gsl_odeiv2.h>
#include <gsl/gsl_roots.h>
int compute_streamline(
gsl_odeiv2_driver *, // GSL ODE solver driver
const double[3], // initial position
const size_t, // streamline index
const double, // integration step size
co... |
2aedd226d5f6b62ee3dfdb02c2c341902ba49c290438c4a54cf5629fd47fa7c0 | C/C++ | 1,395 | 58 | /* Copyright (c) 2008-2026 the MRtrix3 contributors.
*
* This Source Code Form is subject to the terms of the Mozilla Public
* License, v. 2.0. If a copy of the MPL was not distributed with this
* file, You can obtain one at http://mozilla.org/MPL/2.0/.
*
* Covered Software is provided under this License on an "a... |
57d241a15f81d1e3ab03944210216dcb4bdc4e771c821fb8af14c0c8876b301a | C/C++ | 1,397 | 34 | #pragma once
#include "Beamline/EnergyDistribution.h"
#include "Core.h"
#include "Shader/Rand.h"
#include "Variant.h"
namespace rayx {
struct EnergyDistributionList {
double* __restrict prefixWeights;
double* __restrict energies;
double weightSum;
int size;
bool continous;
};
struct EnergyDistri... |
a7137f581f8de9c88724000c9b4254d1fa32f5137fc4ab4d921ee29e8ac0c9ad | C/C++ | 1,400 | 33 | #pragma once
#include <cassert>
#include "Core.h"
#define _throw(string, ...) \
do { \
printf("Error occurred while executing kernel: " string "\n... |
8c01fca8a12cda5e9201794b1f863731d9a975c8829ae3aa3dc27e2a2c2d1d20 | C/C++ | 1,406 | 53 | // ***************************************************************************
// BamFile_p.h (c) 2011 Derek Barnett
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
// Last modified: 10 November 2011 (DB)
// -----------------------------... |
1d892230d75cd74c9f2caceace93d0919663ca4360ff167052dc70fa053822d6 | C/C++ | 1,407 | 45 | /* Copyright (c) 2008-2026 the MRtrix3 contributors.
*
* This Source Code Form is subject to the terms of the Mozilla Public
* License, v. 2.0. If a copy of the MPL was not distributed with this
* file, You can obtain one at http://mozilla.org/MPL/2.0/.
*
* Covered Software is provided under this License on an "a... |
b27c5b5599fb3c0299d45d4355848d9f8b4fd5b7052841771e3a9fabcd91beed | C/C++ | 1,410 | 46 | /*
* Copyright (C) 2011 Regents of the University of Michigan
*
* 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 the License, or
* (at your option) any later v... |
7332032f1b27e3b9b8338935173f1d97a80078a968d2b6b826a8d54e4eda03b5 | C/C++ | 1,413 | 48 | /*
Bayesian Functional GWAS --- MCMC (bfGWAS:MCMC)
Copyright (C) 2016 Jingjing Yang
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 the License, or
(at your ... |
d02b2ae32c4acb2ca1e1ef66ac28943e7071092beddd781c736613d0200c14ce | C/C++ | 1,413 | 50 | /* Copyright (c) 2008-2026 the MRtrix3 contributors.
*
* This Source Code Form is subject to the terms of the Mozilla Public
* License, v. 2.0. If a copy of the MPL was not distributed with this
* file, You can obtain one at http://mozilla.org/MPL/2.0/.
*
* Covered Software is provided under this License on an "a... |
16ee051c0416fc6df222447f007fdc6827cec913e0f44b3a5d8942dc8e4d7daa | C/C++ | 1,416 | 57 | /* Copyright (c) 2008-2026 the MRtrix3 contributors.
*
* This Source Code Form is subject to the terms of the Mozilla Public
* License, v. 2.0. If a copy of the MPL was not distributed with this
* file, You can obtain one at http://mozilla.org/MPL/2.0/.
*
* Covered Software is provided under this License on an "a... |
cd9d5aaf06e542777f06ae8fbf77774a2818f09eefb0109f0263178b47839825 | C/C++ | 1,427 | 51 | /*
Copyright (C) 2014 Sergey Demyanov.
contact: sergey@demyanov.net
http://www.demyanov.net
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 the License, or
(at your option) any l... |
19fb593874057a8da04b7aa243220d619cdb2e68b90064520485f8f28cfba2cc | C/C++ | 1,432 | 58 | /* Copyright (c) 2008-2026 the MRtrix3 contributors.
*
* This Source Code Form is subject to the terms of the Mozilla Public
* License, v. 2.0. If a copy of the MPL was not distributed with this
* file, You can obtain one at http://mozilla.org/MPL/2.0/.
*
* Covered Software is provided under this License on an "a... |
e9c094e5a4c37c92289cdb07f3932093d92514ab9dd69d5081f1bcbda11cff61 | C/C++ | 1,432 | 57 | #ifndef __HW_CONFIG_SYSTEM_H__
#define __HW_CONFIG_SYSTEM_H__
#define HW_VERSION "0.1.1"
#define PRJ_ROOT_PATH "C:/Work/Projects/bioemus-dev/"
#define CLOCK_FREQUENCY_MHZ 400.0
#define HW_FPGA_ARCH "ZYNQMP"
#define HW_FPGA_ARCH_ZYNQMP
#define NB_NRN 1024
#define TIME_STEP_MS 0.03125
// ---
// sfi coding
/... |
76d11af13d72aee32f00aa629d5821031df53bdb95f50c474f7516388b33ecbf | C/C++ | 1,436 | 55 | /* Copyright (c) 2008-2026 the MRtrix3 contributors.
*
* This Source Code Form is subject to the terms of the Mozilla Public
* License, v. 2.0. If a copy of the MPL was not distributed with this
* file, You can obtain one at http://mozilla.org/MPL/2.0/.
*
* Covered Software is provided under this License on an "a... |
a24ae2305b6ae202ea638210ba9b50f146bf4a6bf81af48f4bfb83997c319ad2 | C/C++ | 1,441 | 49 | /* Copyright (c) 2008-2026 the MRtrix3 contributors.
*
* This Source Code Form is subject to the terms of the Mozilla Public
* License, v. 2.0. If a copy of the MPL was not distributed with this
* file, You can obtain one at http://mozilla.org/MPL/2.0/.
*
* Covered Software is provided under this License on an "a... |
d97c59defaf32d1ef2c317c8c0b06bd5a7713f7f7e5b59f01e712fd052325ec0 | C/C++ | 1,442 | 53 | // ***************************************************************************
// ILocalIODevice_p.h (c) 2011 Derek Barnett
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
// Last modified: 10 October 2011 (DB)
// -----------------------... |
12deb08b30922f616e9aca094a76605efa07d56507f24d81254baedba4c565ea | C/C++ | 1,445 | 55 | // ***************************************************************************
// BamException_p.h (c) 2011 Derek Barnett
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
// Last modified: 6 October 2011 (DB)
// --------------------------... |
0029f8631f3657433e45cff42d0cfa89f10f4922a98c057874b7a4093c6e6d76 | C/C++ | 1,448 | 54 | /*
* Copyright (C) 2000-2009, Thomas Maier-Komor
*
* This is the source code of mbuffer.
*
* 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 the License, or
* (at... |
37682a4f3a6f1112080df00571db916d5ca410d94cb6423d09f79d28759fb35c | C/C++ | 1,450 | 62 | /* Copyright (c) 2008-2026 the MRtrix3 contributors.
*
* This Source Code Form is subject to the terms of the Mozilla Public
* License, v. 2.0. If a copy of the MPL was not distributed with this
* file, You can obtain one at http://mozilla.org/MPL/2.0/.
*
* Covered Software is provided under this License on an "a... |
ba46bde163fcc078da3de5da5d5616c9de18fac98b82dea2d11ea03bc3f96b68 | C/C++ | 1,452 | 56 | /* Copyright (c) 2008-2026 the MRtrix3 contributors.
*
* This Source Code Form is subject to the terms of the Mozilla Public
* License, v. 2.0. If a copy of the MPL was not distributed with this
* file, You can obtain one at http://mozilla.org/MPL/2.0/.
*
* Covered Software is provided under this License on an "a... |
84c4c8800044bfd04a9a57d636dd09deeb990865cfae09de8ec4febe76d8b598 | C/C++ | 1,454 | 55 | /* Copyright (c) 2008-2026 the MRtrix3 contributors.
*
* This Source Code Form is subject to the terms of the Mozilla Public
* License, v. 2.0. If a copy of the MPL was not distributed with this
* file, You can obtain one at http://mozilla.org/MPL/2.0/.
*
* Covered Software is provided under this License on an "a... |
c4efdcbf2351665a61bc716b82306de16ce49cd2bf4e79c28d61343da25543e1 | C/C++ | 1,455 | 44 | /*
* Copyright (C) 2010 Regents of the University of Michigan
*
* 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 the License, or
* (at your option) any later v... |
d0072f997babbdfea19fcd1ca56c47e8940f9262074d0650a779e9a17ca74165 | C/C++ | 1,455 | 44 | /*
* Copyright (C) 2010 Regents of the University of Michigan
*
* 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 the License, or
* (at your option) any later v... |
efda45dd2c0b12c06879cf538fc6d8177dc809f8141199e2a1e94219335596b3 | C/C++ | 1,455 | 48 | /*
Copyright (C) 2014 Sergey Demyanov.
contact: sergey@demyanov.net
http://www.demyanov.net
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 the License, or
(at your option) any l... |
0629684740e3603694e38a1e478310ea78698fdaf8e2d250096f9b6225d84395 | C/C++ | 1,466 | 63 | /*
* GPReduce_types.h
*
* Code generation for function 'GPReduce'
*
* C source code generated on: Sun Aug 23 01:10:26 2015
*
*/
#ifndef __GPREDUCE_TYPES_H__
#define __GPREDUCE_TYPES_H__
/* Include files */
#include "rtwtypes.h"
/* Type Definitions */
#ifndef typedef_ResolvedFunctionInfo
#define typedef_Resolv... |
8110f5f6e8ed7737dfe3de926394b01ad885c3c6b6381862745654a264965a87 | C/C++ | 1,466 | 38 | /* test/test.h -- test harness utility routines.
Copyright (C) 2014 Genome Research Ltd.
Author: Martin O. Pollard <mp15@sanger.ac.uk>
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software wi... |
f37c5dd794825d054eb6596c580c3bb542aa4e40a2ea7822098f09fd2cf2659f | C/C++ | 1,469 | 48 | /*
* Copyright (C) 2010 Regents of the University of Michigan
*
* 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 the License, or
* (at your option) any later v... |
0d4325359954db4c32ed7042f65ff577640d3d39546bf4d5f5b865aa464bf8cf | C/C++ | 1,473 | 45 | /*
* Copyright (C) 2010 Regents of the University of Michigan
*
* 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 the License, or
* (at your option) any later v... |
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