sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
86c1c33b9d70bd299dadb0fe6fcf0411f0cb0fa453efa564c390b00b20b8235e | C/C++ | 6,818 | 122 | /* 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... |
c88855efd0d4ca05c2941a6186eea45ca0d4e99822ef2e6d8f7ef00823df1755 | C/C++ | 6,819 | 205 | /*
* 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... |
80cef0285352da134ab3f09ed7542261fbe3b1b6c12259cfe1ccb2410aad1b65 | C/C++ | 6,846 | 281 | // ***************************************************************************
// BamMultiMerger_p.h (c) 2010 Derek Barnett
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
// Last modified: 10 October 2011 (DB)
// -----------------------... |
d9427bc4488281e558cc099e54595cfcf4bed3b90ca4875deefcb2ff74c4e252 | C/C++ | 6,853 | 123 | /****************************************************************************
**
** Copyright (c) 2009-2015 C.B. Barber. All rights reserved.
** $Id: //main/2015/qhull/src/libqhullcpp/QhullHyperplane.h#4 $$Change: 2079 $
** $DateTime: 2016/02/07 17:43:34 $$Author: bbarber $
**
******************************************... |
2d0c134695908bb287d5c6b8d33cee12e9a62cb2463e7a4e7ae7b2e58ad10946 | C/C++ | 6,875 | 186 | /* 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... |
a733e4c07c972cab95531d473476c8304708a804cc3289c0292a18aa8497f114 | C/C++ | 6,879 | 201 | /* 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... |
57010f64b4c7b7ad9fd856eac4718d5be973c566d17bee2a47827d29a20755c8 | C/C++ | 6,908 | 181 | /* 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... |
51cecaba83f687da120cbae5cff6af82eadf6742cf9b704808ba4532db518d46 | C/C++ | 6,965 | 188 | /* 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... |
ceab40beb0bd95a825d5347359e54b8e70e0e83da5df0542b1ea4890f3c9948c | C/C++ | 6,994 | 128 | /*
Copyright 2010-2011, D. E. Shaw Research.
All rights reserved.
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are
met:
* Redistributions of source code must retain the above copyright
notice, this list of conditions, and the f... |
ca4ea0b66c3de7ede276b8c87d7c64e149b7c9fd32f7139b8153561439e19d24 | C/C++ | 7,023 | 201 | /*
* 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... |
72e40a19087990cf0c5642cab76ba49e51937203980840285f6fd2146669da21 | C/C++ | 7,031 | 174 | /* 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... |
24d976ad6acf84793ca64159f9c65d3b57d8c45de4e9d1ebcbff8397d3c7f344 | C/C++ | 7,064 | 244 | /* 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... |
d4d4023850767f4f60cb191a923337f435d775e555e730de73884136c0616858 | C/C++ | 7,114 | 136 | /*
Copyright 2010-2011, D. E. Shaw Research.
All rights reserved.
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are
met:
* Redistributions of source code must retain the above copyright
notice, this list of conditions, and the f... |
d34b6b9db5e92a114c08cb33c50152ec7c9d78725d26eb3dad398aaf6adfd733 | C/C++ | 7,154 | 151 | /****************************************************************************
**
** Copyright (c) 2008-2015 C.B. Barber. All rights reserved.
** $Id: //main/2015/qhull/src/libqhullcpp/QhullFacet.h#4 $$Change: 2079 $
** $DateTime: 2016/02/07 17:43:34 $$Author: bbarber $
**
***********************************************... |
0b8b147037bfffa013762273f049eb624e11fe69cbe4b04f551e96e0c5bef59a | C/C++ | 7,192 | 176 | /*<html><pre> -<a href="qh-geom.htm"
>-------------------------------</a><a name="TOP">-</a>
geom.h
header file for geometric routines
see qh-geom.htm and geom.c
Copyright (c) 1993-2015 The Geometry Center.
$Id: //main/2015/qhull/src/libqhull/geom.h#1 $$Change: 1981 $
... |
756c3cb807dcc651df288df488898f9fbee7d194fb0b5bf1f14b988f17f40d69 | C/C++ | 7,217 | 183 | #pragma once
#include <functional>
#include <glm.hpp>
#include <memory>
#include <variant>
#include <vector>
#include "Core.h"
#include "Design/DesignElement.h"
#include "Design/DesignSource.h"
#include "Node.h"
namespace rayx {
/**
* A beamline group that can contain child nodes (elements, sources, or other group... |
cc919069dcd5e37111c976fd5da32175b0dd68041d8f3c3568934ff96e79ec15 | C/C++ | 7,301 | 178 | /*<html><pre> -<a href="qh-merge.htm"
>-------------------------------</a><a name="TOP">-</a>
merge.h
header file for merge.c
see qh-merge.htm and merge.c
Copyright (c) 1993-2015 C.B. Barber.
$Id: //main/2015/qhull/src/libqhull/merge.h#1 $$Change: 1981 $
$DateTime: 20... |
a8d408a0fb269d12cb11f00acf387e3f01904d7a8f4f216d964ec568b9c2fc7e | C/C++ | 7,322 | 202 | #pragma once
#include "Complex.h"
#include "Constants.h"
namespace rayx {
using Stokes = glm::dvec4;
using ElectricField = cvec3;
using LocalElectricField = cvec2;
static_assert(std::is_default_constructible_v<ElectricField>);
static_assert(std::is_default_constructible_v<LocalElectricField>);
#ifn... |
2bc977888795f4748d0f1601daf270b5e2a4360d98ae8af0d6bc8e33e8693e87 | C/C++ | 7,361 | 153 | #pragma once
#include <vector>
#include "Core.h"
#include "Shader/ElectricField.h"
#include "Shader/EventType.h"
#include "Shader/Rand.h"
// TODO: all this macros should be invisible to the user
// TODO: implement template based solution instead of macros
#ifdef X
#error macro 'X' must not be defined at this point
... |
42ca765153b8dc43713d1553acc8d428430785d0219cdc4adeda6e80bc3b95f0 | C/C++ | 7,497 | 243 | /* 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... |
74473340ff48a281dee41ca98a076adc6154a3b4cb9a7ac0e8a9ca28d8cb0453 | C/C++ | 7,498 | 246 | /* 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... |
bc0b759951f7c104c735f12e801b6ed327342817e7e9c746292c715900d606e9 | C/C++ | 7,501 | 242 | //
// morphydefs.h
// MorPhy2
//
// Created by mbrazeau on 07/05/2017.
// Copyright © 2017 brazeaulab. All rights reserved.
//
#ifndef morphydefs_h
#define morphydefs_h
#ifdef __cplusplus
extern "C" {
#endif
#include <stdint.h>
#include <stdbool.h>
//#ifdef MPLDBL
typedef double Mflt;
#define MPL_EPSILON DB... |
e91a25e4f3548da03bd587c69f77bbc19a8dda5c61bd3a67360a0bea5a3c74a6 | C/C++ | 7,506 | 201 | /* 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... |
afc2285cd4f5cd0e5e7b86d3449996ebee574337917d50aaf0498bffdeac9b0f | C/C++ | 7,534 | 262 | #pragma once
#include "Beamline/Node.h"
#include "Element/Element.h"
#include "Value.h"
namespace rayx {
class RAYX_API DesignElement : public BeamlineNode {
public:
DesignElement();
DesignElement(std::string name);
~DesignElement() = default;
// Delete copy constructor because shallow copies of D... |
3fd3091d96976e31ce973a9e6b2b8209be1c76c2779f902954c56d11a3346fdc | C/C++ | 7,538 | 240 | /* 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... |
04966b5e80a3a19e1309dabdd69ce32455f4a4b333f69e424cf583eda1b804c2 | C/C++ | 7,617 | 176 | /**************************************************************************/
/*!
@file Adafruit_TSL2591.h
@author KT0WN (adafruit.com)
This is a library for the Adafruit TSL2591 breakout board
This library works with the Adafruit TSL2591 breakout
----> https://www.adafruit.com/products/1980... |
d322dd05009124292d3deebbe8ef9dfb2cfba09646c31b8363fb5a425a4d5c8f | C/C++ | 7,644 | 186 | /*
* Copyright (C) 2008 The Android Open Source Project
*
* 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 required by applicab... |
b909401ac99c9e4b2845c74e906dbb6e37ab7b3f71f78e41f85222d362be2928 | C/C++ | 7,678 | 234 | // ***************************************************************************
// bamtools_filter_properties.h (c) 2010 Derek Barnett, Erik Garrison
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
// Last modified: 10 October 2011
// ---... |
e513cf5173d38fec32c78e49d61a014d76fc9d5e935960e69af17ea1fa813f6e | C/C++ | 7,702 | 234 | /* 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... |
be35e4f10b2526317a9ba7cb0270a397cacc7c7d6ca5ee917910413951b5517a | C/C++ | 7,705 | 184 | /*<html><pre> -<a href="qh-geom_r.htm"
>-------------------------------</a><a name="TOP">-</a>
geom_r.h
header file for geometric routines
see qh-geom_r.htm and geom_r.c
Copyright (c) 1993-2015 The Geometry Center.
$Id: //main/2015/qhull/src/libqhull_r/geom_r.h#3 $$Chang... |
825ad7636ef9bce38bf683c9490633910b0bced96c4edf59ac459ceadc64d4e1 | C/C++ | 7,707 | 136 | /****************************************************************************
**
** Copyright (c) 2009-2015 C.B. Barber. All rights reserved.
** $Id: //main/2015/qhull/src/libqhullcpp/QhullPoint.h#4 $$Change: 2079 $
** $DateTime: 2016/02/07 17:43:34 $$Author: bbarber $
**
***********************************************... |
7f5eac47e950f74a2250bb2196689999c67adfcf706760f948fb15cba2c46c4b | C/C++ | 7,742 | 206 | /* Copyright (c) 2008-2026 the MRtrix3 contributors.
*
* This Source Code Form is subject to the terms of the Mozilla Public
* License, v. 2.0. If a copy of the MPL was not distributed with this
* file, You can obtain one at http://mozilla.org/MPL/2.0/.
*
* Covered Software is provided under this License on an "a... |
08ed549f59217a92f69d99fea0011747f8b31a28bfd73b90321ca99cf126959c | C/C++ | 7,869 | 186 | /*<html><pre> -<a href="qh-merge_r.htm"
>-------------------------------</a><a name="TOP">-</a>
merge_r.h
header file for merge_r.c
see qh-merge_r.htm and merge_r.c
Copyright (c) 1993-2015 C.B. Barber.
$Id: //main/2015/qhull/src/libqhull_r/merge_r.h#3 $$Change: 2079 $
... |
00f6e3da30d6cca5078e7d008de3327e3d94e4e5dd479e15c34ee5d8b411a13e | C/C++ | 7,890 | 136 | /*
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 yo... |
55e07e08c7f93a94680e06b5238e80f109fb58ddadb2cfd09fdaa740f9fb553a | C/C++ | 7,927 | 200 | /*
Copyright 2011, D. E. Shaw Research.
All rights reserved.
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are
met:
* Redistributions of source code must retain the above copyright
notice, this list of conditions, and the follow... |
c8608f46fcf1e59e7f0b191a605e96fbff9f4278e1b3e7701118fe0b9105b15f | C/C++ | 7,940 | 226 | /* 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... |
f6c578d368b62c0f02d86449e7dd9147177c3bdfc30ea11404683362bedb5d11 | C/C++ | 7,948 | 159 | /*<html><pre> -<a href="qh-io.htm"
>-------------------------------</a><a name="TOP">-</a>
io.h
declarations of Input/Output functions
see README, libqhull.h and io.c
Copyright (c) 1993-2015 The Geometry Center.
$Id: //main/2015/qhull/src/libqhull/io.h#1 $$Change: 1981 $... |
1e23e391da37630f8e5ad7cecf05a76d78862a0bdb16f642a6805251f6ca46cb | C/C++ | 7,951 | 194 | /* Copyright (c) 2008-2026 the MRtrix3 contributors.
*
* This Source Code Form is subject to the terms of the Mozilla Public
* License, v. 2.0. If a copy of the MPL was not distributed with this
* file, You can obtain one at http://mozilla.org/MPL/2.0/.
*
* Covered Software is provided under this License on an "a... |
a95feb3036f21a62055a8c3527bd237f8610a99623dbd491a7f518580ee4267a | C/C++ | 7,957 | 248 | void make_box1(double *x, int N, double scal, int bs,
int *box, int *lis, int *mxi);
/* make one-dimensional box
input
x - input sequence
N - length of the input sequence
scal - renormalization factor, scal=#boxes/(max(x)-min(x))
bs - #boxes
output
box - each element of the array is ordinary num... |
aaf8cd870d90cd03f7363c676cb338969eb308d5ca8c73d187bb72bec0af85b5 | C/C++ | 8,006 | 291 | /* Copyright (c) 2008-2026 the MRtrix3 contributors.
*
* This Source Code Form is subject to the terms of the Mozilla Public
* License, v. 2.0. If a copy of the MPL was not distributed with this
* file, You can obtain one at http://mozilla.org/MPL/2.0/.
*
* Covered Software is provided under this License on an "a... |
f12c92194947f03a69bfe64a5facde8109abb7e1d6b3e46227428c19fa8b80b8 | C/C++ | 8,049 | 161 | /****************************************************************************
**
** Copyright (c) 2009-2015 C.B. Barber. All rights reserved.
** $Id: //main/2015/qhull/src/libqhullcpp/PointCoordinates.h#4 $$Change: 2079 $
** $DateTime: 2016/02/07 17:43:34 $$Author: bbarber $
**
*****************************************... |
df38a02ce603a1c373305782db67b5a1ebf76c5a9c5ec013f9e5fb87984e2913 | C/C++ | 8,054 | 173 | /****************************************************************************
**
** Copyright (c) 2008-2015 C.B. Barber. All rights reserved.
** $Id: //main/2015/qhull/src/libqhullcpp/QhullIterator.h#4 $$Change: 2079 $
** $DateTime: 2016/02/07 17:43:34 $$Author: bbarber $
**
********************************************... |
3671f228e8c94466cc013bd08b00f80fc92be0c369cff3f7eab7870760e99f0c | C/C++ | 8,213 | 262 | #pragma once
/// This file mostly exposes the RAYX_LOG, RAYX_VERB, RAYX_WARN and RAYX_EXIT macros.
/// We mostly use these macros instead of std::cout / std::cerr for convenience reasons.
/// These macros automatically generate a newline at the end, and also print file and line number from where the print originated.
... |
984d704a8f11c2e3e2eed129a83ee407e47cf65bc225db51f5c71fef671ef0ba | C/C++ | 8,261 | 238 | /* 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... |
7d207fcd54910e2fa374fdda81af62e39842dc4ca622a28d1c17a1f267c1c61a | C/C++ | 8,339 | 256 | /* 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... |
cd7c65d777182e175d2bcb511f0c75b5b684b4d00acecb517ad49fc355117104 | C/C++ | 8,342 | 290 | /* 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... |
66433134b40f272abab00d2d243d108ab2dfca30fb8728bed71dc9fc24315422 | C/C++ | 8,436 | 218 | /*
* Copyright (C) 2011-2012 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... |
764f97dd3edc2e14f99eee4f3b7913c5f0037530d4ccc19d91b7fe597622d62d | C/C++ | 8,462 | 238 | // ***************************************************************************
// BamStandardIndex.h (c) 2010 Derek Barnett
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
// Last modified: 10 November 2011 (DB)
// ----------------------... |
6b4f24398d517611ba20126e37e8eb88746e9000dd0ecfe2fa2f503bf791b062 | C/C++ | 8,505 | 215 | /* 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... |
de442423a34540277b535b98c5d068c32571a6effb411ddb7bfe6fec2c6f145b | C/C++ | 8,511 | 283 | /* 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... |
5aa016d35e5666a5d238c53c503d66cb2455712c6344dad7600402d070b2d1cd | C/C++ | 8,658 | 222 | /*<html><pre> -<a href="qh-mem.htm"
>-------------------------------</a><a name="TOP">-</a>
mem.h
prototypes for memory management functions
see qh-mem.htm, mem.c and qset.h
for error handling, writes message and calls
qh_errexit(qhmem_ERRmem, NULL, NULL) if insuffic... |
3865e2f04c516c7a9c2d3f359a8c142ace0dc2241cae8b286d74e89fedb383d0 | C/C++ | 8,676 | 167 | /*<html><pre> -<a href="qh-io_r.htm"
>-------------------------------</a><a name="TOP">-</a>
io_r.h
declarations of Input/Output functions
see README, libqhull_r.h and io_r.c
Copyright (c) 1993-2015 The Geometry Center.
$Id: //main/2015/qhull/src/libqhull_r/io_r.h#3 $$Ch... |
a56bc16f40d0c51f74be996b03ff463be5de069437ebd26a27cbd08d9b6a6e0a | C/C++ | 8,691 | 222 | /*
* 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... |
02738b70d3f9ac006acfa6b6a768f6d750df726be470ec66aba1dc213514e226 | C/C++ | 8,796 | 228 | /* 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... |
5d52bffe2f7803816360fb2fc6388e1603abfb3591873bbb83d0bb678df54583 | C/C++ | 8,820 | 230 | /* 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... |
65bc6dd96351348b644bd45e3a4925fe98c77d7160b92dd114590242e6b5693e | C/C++ | 8,823 | 196 | /* 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... |
8ae66f29494c7b8c26be69838038e75eccface8f665de8d77e4a7ea37d74ab7f | C/C++ | 8,906 | 238 | /* 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... |
1654f71660bd44fd04b12170d64518c842f12b935ffe20f98d415b07384a5cc4 | C/C++ | 8,933 | 235 | /* 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... |
81e6d87d3df93ef7af1ce8976110b5f620634467e0a2b49d1872fa97f20a1b7e | C/C++ | 8,955 | 271 | /* 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... |
0f4ec6e9d8edc7a45785ef0363398ce9b9a03e918ddaf8769d044905473ee82d | C/C++ | 8,965 | 177 | /*
* 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... |
928496e76f8bd9cf9f5aa554c857976eec534c6417e9409001ffb730fd7a9c7f | C/C++ | 8,976 | 416 | /*
* Copyright (C) 2010-2012 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 la... |
9807d7dc6a9d0b888199e36a197144e0e5ece71d06705e374f572d83b5e144f8 | C/C++ | 8,976 | 285 | /*
Copyright 2010-2011, D. E. Shaw Research.
All rights reserved.
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are
met:
* Redistributions of source code must retain the above copyright
notice, this list of conditions, and the f... |
2bea6c941c40f5a2268be28f292312ba73aeb9faff2e9ad21ed101345940a54c | C/C++ | 9,104 | 234 | /*<html><pre> -<a href="qh-mem_r.htm"
>-------------------------------</a><a name="TOP">-</a>
mem_r.h
prototypes for memory management functions
see qh-mem_r.htm, mem_r.c and qset_r.h
for error handling, writes message and calls
qh_errexit(qhT *qh, qhmem_ERRmem, NULL... |
e395fd29704089cd3176d0d880e94bd9a1f497c207bf1e6c69a1c0b85591966e | C/C++ | 9,122 | 251 | /* 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... |
976d615dfa1039f13d0a3393e295d8cd982afd1896fcc41b355785854d6ab501 | C/C++ | 9,126 | 256 | #pragma once
#include <iterator>
#include <memory>
#include <string>
#include <unordered_map>
#include <variant>
// Include your other dependencies.
#include "Angle.h"
#include "Beamline/EnergyDistribution.h"
#include "Core.h"
#include "Debug/Debug.h"
#include "Element/Cutout.h"
#include "Element/Surface.h"
#include ... |
0e68bf0d9fbb2327ede07a54cc3e132e524e365dafb9e462760f1b2b15e4d657 | C/C++ | 9,139 | 276 | /* 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... |
851f596c508ee8ad1a211fb2120d74946440b54f63650c8e0fe8a5660260b37f | C/C++ | 9,189 | 361 | /*
* 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... |
632392502ea27961d0ae2545eefa4c71bd7dba6fef66fcd7b2e5b1d44b0ffe67 | C/C++ | 9,282 | 324 | // ***************************************************************************
// BamConstants.h (c) 2011 Derek Barnett
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
// Last modified: 16 October 2011 (DB)
// ---------------------------... |
9391a07bed917910f772422819abc3eeab90e540480b5c175d6a7efcb695c4b8 | C/C++ | 9,305 | 345 | #ifndef MAILMAN_H
#define MAILMAN_H
#include <Eigen/Dense>
#include <Eigen/Core>
#include <Eigen/LU>
#include <Eigen/SVD>
#include <bits/stdc++.h>
#include "storage.h"
#include <assert.h>
#include <emmintrin.h>
namespace mailman {
void fastmultiply_normal(int m, int n , int k, std::vector<int> &p, Eigen::Matrix<do... |
98896ca584b772c9061ca894ecddf5b1234926ee8b3823a99a4bf0477a6a8ee5 | C/C++ | 9,341 | 353 | // ***************************************************************************
// bamtools_filter_ruleparser.h (c) 2010 Derek Barnett, Erik Garrison
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
// Last modified: 10 October 2011
// ---... |
01babe676415290bbaab0c6a8c362d2e45dbebb9461bee5de95ed29d8ac89066 | C/C++ | 9,356 | 353 | #ifndef MAILMAN_H
#define MAILMAN_H
#include <Eigen/Dense>
#include <Eigen/Core>
#include <Eigen/LU>
#include <Eigen/SVD>
#include "storage.h"
#include <assert.h>
#include <iostream>
#if defined(SSE_SUPPORT) && SSE_SUPPORT == 1
#include <emmintrin.h>
#endif
namespace mailman {
#ifdef USE_DOUBLE
typedef Eigen::Ma... |
87088dbcf176508b4816affca3b0bd7d2e5f9c1a611dbfc167b8938b1de62154 | C/C++ | 9,569 | 112 | #pragma once
#include <stdint.h>
// LUT tables to copy to GPU memory for quick morton decode / encode
static const uint32_t host_morton256_x[256] =
{
0x00000000,
0x00000001, 0x00000008, 0x00000009, 0x00000040, 0x00000041, 0x00000048, 0x00000049, 0x00000200,
0x00000201, 0x00000208, 0x00000209, 0x00000240, 0x00000241... |
20777eda7e313b9ec83dff97c9ac349a027eb8a7206064058a4fe8e7cac93e75 | C/C++ | 9,575 | 305 | /* 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... |
dc30909b9cc291d226ba3c11d9eedbf5eefffcab5a828d6bf5189d592d41c86a | C/C++ | 9,628 | 262 | /* 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... |
f799939488467a6902987bd0b3cf55305a17169ea0f3271fcf31f59986c9faf8 | C/C++ | 9,709 | 249 | #include <inttypes.h>
#include <stdio.h>
#include <zlib.h>
#include "htslib/sam.h"
#include "htslib/faidx.h"
#include "bigWig.h"
#if HTS_VERSION < 101100
#error "The minimum supported version of htslib is 1.11!"
#endif
//These are needed to handle multiple threads
extern pthread_mutex_t positionMutex;
extern pthread... |
303bd31e05dae8ed7e04f85fe3578476b9360ea9a8a11e2f8936dbf30418a84d | C/C++ | 9,754 | 302 | /*
* 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... |
05d00807941451e4f86f3272c8528d9c51fa1587f4028ea9bceecb69aaf5743a | C/C++ | 9,757 | 276 | /* 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... |
7e7d66d534ba19178fbd625f6fe96cca25c9bf27a2db969da480ffc114023cee | C/C++ | 9,910 | 278 | /* 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... |
7cb54f71d10ab450a6f29f5da80e19004e91493e1250a46d59ec44b181a74753 | C/C++ | 9,933 | 290 | /* 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... |
70391e8aff4fc76793e1e9a6e7748dbd938588f046edc1531e7d68364dc6d478 | C/C++ | 9,936 | 298 | /* 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... |
7072b2134ca43ba2df26938e9f0a779c40339fc84657b76e6dd4bd8a85a993eb | C/C++ | 9,978 | 233 | /*
* 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... |
9bde154c72eacc3ad881b25b7b66091f592808ece718aa7c8c9d72c895dce799 | C/C++ | 10,047 | 280 | /*
Copyright 2010-2011, D. E. Shaw Research.
All rights reserved.
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are
met:
* Redistributions of source code must retain the above copyright
notice, this list of conditions, and the f... |
76d7b9aebe6a4fff507d4f8213d7693ad3cc50f7df29f74faa90df659fed5981 | C/C++ | 10,048 | 265 | #pragma once
#include <algorithm>
#include <glm.hpp>
#include "Core.h"
#if defined(RAYX_CUDA_ENABLED)
#include <cuda/std/complex>
#else
#include <complex>
#endif
namespace rayx {
namespace complex {
template <typename T>
#if defined(RAYX_CUDA_ENABLED)
using tcomplex = cuda::std::complex<T>;
#else
using tcomplex = ... |
032c3079b57cc59df75a3ddc03540f58f38b171d318c9e70cfc7bfc36f9db6d2 | C/C++ | 10,079 | 255 | /* 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... |
310901c4e1e074b9e048cc1f24f0fc04b8534cd595b604341dd4cd9320ef2519 | C/C++ | 10,084 | 327 | /* 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... |
0cda642b05316512c38ee26353e879167c56d6cba34c2ac065b1161112c9ef46 | C/C++ | 10,130 | 236 | /*
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... |
a0d3f20b08ee2372e95cfe21a95238c4179a653e62da93522ea904a39c4b3afc | C/C++ | 10,188 | 300 | /* 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... |
7b49242c298d223ac3d51873d0d3b47426f25c0109c1f59605c1fd06465f3ef8 | C/C++ | 10,263 | 337 | /* 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... |
12b228e9ac2bfb9ce6ba0a648f9cbcaaa45a9bf23173cb2dbd32f10ac384d662 | C/C++ | 10,283 | 400 | /*
* Copyright (C) 2010-2012 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 la... |
4f29deafdb0fb63f81b7b586f27cccce67d637173653971c37d9a0780ebb1219 | C/C++ | 10,314 | 294 | /* 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... |
07b2ddfd7bd4da4bcd3d9bb1c77f9da47d4fdf5e1aa08a9dae70dcf8499283dd | C/C++ | 10,449 | 207 | /*!
* @file Adafruit_TCS34725.h
*
* Software License Agreement (BSD License)
*
* Copyright (c) 2013, Adafruit Industries
* All rights reserved.
*
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are
* met:
* 1. R... |
5659e0a7d185e76425a24a0c081fd0ea3dc2a8c9385b689d4e145de8c7e8c7cb | C/C++ | 10,465 | 254 | /* 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... |
4f41605ed3b1658286511011cd6d9fd34b2786d6ec3d780d53887f6722b410bc | C/C++ | 10,521 | 281 | #pragma once
#include <filesystem>
#include <random>
#include <string>
#include <vector>
#include "Beamline/Beamline.h"
#include "Beamline/Definitions.h"
#include "Beamline/StringConversion.h"
#include "Core.h"
#include "Element/Cutout.h"
namespace rayx {
/**
* Set all Parameters for each optical Element a RML fil... |
c7c94b89a2eff54051b8a33b19a93a153b24acfa003f7d8cd69fb41fba983cfe | C/C++ | 10,547 | 237 | /* 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... |
3ca18a6932d4cd28042e45c21d0305137673cac9d784cf5fa563d130aa179907 | C/C++ | 10,656 | 382 | /*
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 option) any later ve... |
b02526944db4f2ad9b36ee0066a2aeb6faf930c88377f33b040e64c886b2e878 | C/C++ | 10,700 | 399 | // ***************************************************************************
// BamAux.h (c) 2009 Derek Barnett, Michael Str�mberg
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
// Last modified: 25 October 2011 (DB)
// --------------... |
42c9d33512851ae1f20ea34aa7e680db7fd85e13f1eabeb4d68d70fb29016843 | C/C++ | 10,721 | 248 | #pragma once
#include "Constants.h"
#include "ElectricField.h"
#include "Rand.h"
namespace rayx {
struct FresnelCoeffs {
double s;
double p;
};
struct ComplexFresnelCoeffs {
complex::Complex s;
complex::Complex p;
};
/// calculates the angle in rad, between two unit vectors
RAYX_FN_ACC inline doubl... |
55af5ae4ecd1203d5d6955916ea99df84fd358aa52c94b34a395897c420dcb19 | C/C++ | 10,776 | 245 | /*
* Copyright (C) 2010-2012 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... |
f7a4f1a4c4abf7ce90fdd47512008277e07d1786bbc241b3c4961c7f3bbe2683 | C/C++ | 10,833 | 441 | /*
* 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... |
e9ee811d9472c92d9b3472d197ceca8e59e58f0749c052bd715f40b8547a5735 | C/C++ | 10,891 | 293 | /* 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... |
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