sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
ea9560ca5f2210d26043cd483566d610686d16d312ae3ac689ce414cb28004d8 | C/C++ | 853 | 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... |
7ee184434ce8e9c03a3bbef8913051600ad35f07ea0f45a990f889c6cc1eab45 | C/C++ | 857 | 27 | #pragma once
#include "Core.h"
#include "Element/Behaviour.h"
#include "Ray.h"
namespace rayx {
/** variable line spacing for gratings
@params
lineDensity: general line density?
z: z-coordinate of ray position
vls[6]: 6 vls parameters given by user
@returns line density specifically for this z-coordinate... |
2f6f0c34583aff188c0c2a0332161ee6fb1cbdbda527a37616090e31a5738b47 | C/C++ | 859 | 25 | /*
* 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... |
d4b2ca772b5677accb76cca67d5d23692741e48e534bcbb53687c087595a8827 | C/C++ | 860 | 25 | /*
* 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... |
a412bb9e465df93425346408b56eda8d1f1c86a69831e87eafb4aeb4d7e1d918 | C/C++ | 861 | 34 | #pragma once
#include "LightSource.h"
#include "Shader/Rand.h"
namespace rayx {
class RAYX_API CircleSource : public LightSourceBase {
public:
CircleSource(const DesignSource&);
RAYX_FN_ACC detail::Ray genRay(const int rayPathIndex, const int sourceId, const EnergyDistributionDataVariant& __restrict energ... |
e76028ec01fd7f2d26c2b77b8c3942b03f4c01dd0a5b9c3254a63c3eadfa4102 | C/C++ | 863 | 17 | #pragma once
#include <string>
#include <iostream>
#include <fstream>
#include <assert.h>
#include "util.h"
#include "TriMesh_algo.h"
#include "util.h"
#include "libs/magicavoxel_file_writer/VoxWriter.h"
size_t get_file_length(const std::string base_filename);
void read_binary(void* data, const size_t lengt... |
8dccda9c448c98218b9c93233d50df1b19ecf6415f832a784dcadda18c82a369 | C/C++ | 876 | 41 | /**
* 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 parser class for the case where we have features
* to represent labels. It overrides a few key functions such ... |
2a26c3d4b985098cdaf1c34689a73a57a954a5a3876d7cbf4f39a0e41389eb15 | C/C++ | 878 | 29 | #pragma once
#include "Debug/Debug.h"
namespace rayx {
enum class GratingMount { Deviation, Incidence };
enum class ParaboloidType { Focussing, Collimate };
enum class CurvatureType {
Plane,
Toroidal,
Spherical,
Cubic,
Cone,
Cylinder,
Ellipsoid,
Paraboloid,
Quadric,
RzpSphere
}... |
a4585acc3066ed0895d2459ac741efb8cb35dbd3bfad08b8376a8d62bb6f0f42 | C/C++ | 879 | 26 | /*
* 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... |
b8145ceafa70c2f63ec60f7cdd4a480a4938f3ce5a201353cfeebbb0affe040d | C/C++ | 887 | 40 | #pragma once
#include <vector>
#include "Core.h"
#include "Variant.h"
namespace rayx {
enum class SurfaceCoatingType {
SubstrateOnly, // No coating, only substrate
OneCoating, // One coating layer
MultipleCoatings // Multiple coating layers
};
namespace detail {
struct CoatingTypes {
stru... |
31d189eb3b5ea6700099945186b0879a54371814273bee939712c1675ffc1d05 | C/C++ | 888 | 24 | /*
* 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... |
77d84f9b8d117949c2acd3176708b68d5a025e695832fc016cc200d6323c369e | C/C++ | 892 | 36 | /* 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... |
228965bf671e2c7694c1a4b175cb03eb5b11d7c8fd77a336a4da3228fffceab5 | C/C++ | 894 | 33 | #include "filter.h"
///////////////////////////////////////////////////////////////////////////////////////////
class NonlinearFilter : public Filter
{
private:
double *h;
char* type;
list *lst;
int w, alpha, beta;
int initializedflag;
protected:
public:
//constructor
//the vectors b,a with l... |
2e79f3791efc9f989ed19a90bb9b84a3c028870b67e4f173204120dd0e6f5075 | C/C++ | 896 | 26 | /*
* Copyright (C) 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 later v... |
f65793b94ff2d6523d03a96d333d3b5db712360c06de1da1f6b8a32d4faa64c2 | C/C++ | 900 | 31 | /*
* 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... |
3480bc3a11d6e3dbc48f18f902a154b06e12e81f8538fd0d7f184d0bfd54eccc | C/C++ | 902 | 29 | /*
* 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... |
1b27759aee5d09a3f97568fe72fe943a7908ac58749dd43cc55b0ee93f3c98e2 | C/C++ | 903 | 38 | // ***************************************************************************
// bamtools_sort.h (c) 2010 Derek Barnett, Erik Garrison
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
// Last modified: 7 April 2011 (DB)
// --------------... |
41363a33a1cabb69203bf2fbe8d1a74a7a1f8ad4888a78d8bd2ade77a02c4038 | C/C++ | 903 | 24 | /*
* 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... |
e6aef3cdfcd4ca19603d8c684ca159323c723323622e0cb87cf9e541eb557ead | C/C++ | 905 | 29 | /*
* 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... |
39204d621d3b55159b5f5d21bdbbee020c0308fd74c74868f0632c2971dd3a02 | C/C++ | 909 | 23 | /*
* Copyright (C) 2011-2013 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... |
07e0f76390158b45febd8ec8449c3afe6ede5e44e55790e70fea1ccb5c5e6b60 | C/C++ | 910 | 28 | #pragma once
#include "Beamline/Beamline.h"
#include "BundleHistory.h"
#include "Tracer/Tracer.h"
#include "UserInterface/Settings.h"
class Simulator {
public:
Simulator();
void runSimulation();
void setSimulationParameters(const std::filesystem::path& RMLPath, const rayx::Beamline& beamline, const UISi... |
fa6548c96660aeb3216ba2d7909200e6b74203cf67b906db8934356750c4e33a | C/C++ | 915 | 35 | #pragma once
#include <array>
#include <glm.hpp>
#include <string>
#include <vector>
#include "Core.h"
#include "Element/Element.h"
#include "EnergyDistributions/EnergyDistribution.h"
#include "Rml/xml.h"
#include "Shader/Ray.h"
namespace rayx {
enum class SourceDist { Uniform, Gaussian, Thirds, Circle }; // Sourc... |
e6cb0435ef90a706f233931f4d1e5a3d61067bcbd2ef01bd51d510efca9c392e | C/C++ | 918 | 38 | // ***************************************************************************
// bamtools_index.h (c) 2010 Derek Barnett, Erik Garrison
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
// Last modified: 7 April 2011
// ------------------... |
70f5307e2238be46cd21828213fc98c61767382d97a850ce61e7524b415b06ac | C/C++ | 926 | 37 | // Resampler.h: interface for the Resampler class.
/*
% Revision History:
% 2012: First release
% 2023: Renamed from deprecated version Resampler.cpp
%
% Reza Sameni, 2012-2023 The Open-Source Electrophysiological Toolbox
% https://github.com/alphanumericslab/OSET
*/
///////////////////////////////////... |
26f52ee4706a1095aa84369dc42c21e664a5face049af1531147e578c61a3ce8 | C/C++ | 928 | 38 | // ***************************************************************************
// bamtools_merge.h (c) 2010 Derek Barnett, Erik Garrison
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
// Last modified: 7 April 2011
// ------------------... |
57fc070d5ad6a69db5ff1690410d60d66114cdbbfc74b18bd0c61a3f6efb0c28 | C/C++ | 929 | 31 | /*
* 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... |
60944a38ae6c0dd3c77941cc5abccbe96f0fb3269c37f7cb081d55c31098789f | C/C++ | 932 | 38 | // ***************************************************************************
// bamtools_count.h (c) 2010 Derek Barnett, Erik Garrison
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
// Last modified: 7 April 2011
// ------------------... |
16dfe1b26b68027f0bf0ccd8214526b75756fc4b2140d0e1453db68b02446406 | C/C++ | 934 | 31 | /*
* 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... |
6240553f8a40a474a713900b2caf9f63e5c4ef37b1f16943c3302e6f79d2270a | C/C++ | 934 | 31 | /*
* 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... |
ecd35534e609591c7a7afe104e45ff7802583b00fc0d7562dc2a77d2a7a2bd89 | C/C++ | 941 | 38 | // ***************************************************************************
// bamtools_stats.h (c) 2010 Derek Barnett, Erik Garrison
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
// Last modified: 7 April 2011
// ------------------... |
bee6ad0f3faca93f76a2e6d5ab7ed2592e15129fa326baf3254bf9468c812e66 | C/C++ | 943 | 32 | /*
*! @title Main application for bioemus
*! @file bioemus.h
*! @author Romain Beaubois
*! @date 10 Aug 2022
*! @copyright
*! SPDX-FileCopyrightText: © 2022 Romain Beaubois <refbeaubois@yahoo.com>
*! SPDX-License-Identifier: GPL-3.0-or-later
*!
*! @brief
*!
*! @details
*! > **10 Aug 2022** : file ... |
55169fd27d3889cb9a10fbc4eb614a61b5755ab4326e6cb43ce228500149a595 | C/C++ | 947 | 34 | /*<html><pre> -<a href="qh-geom.htm"
>-------------------------------</a><a name="TOP">-</a>
random.h
header file for random and utility routines
see qh-geom.htm and random.c
Copyright (c) 1993-2015 The Geometry Center.
$Id: //main/2015/qhull/src/libqhull/random.h#2 $$Ch... |
1c869349e2fae27fbe213066e212c7a2d08da79c46f5dd1140bbefadc7d4000e | C/C++ | 948 | 34 | //
// tlnewick.h
// treelib
//
// Created by mbrazeau on 08/04/2017.
// Copyright © 2017 brazeaulab. All rights reserved.
//
#ifndef tlnewick_h
#define tlnewick_h
#include <string.h>
#include <stdlib.h>
#include <ctype.h>
#define NWKROOTCMD "[&"
#define NWKTKNSYMB " _\'\""
typedef struct {
unsigned int maxl... |
2c60ee34f01a8d2f8eff36e9a792a9f6146eec46907e81fb72742f2b0522111b | C/C++ | 951 | 36 | #pragma once
#include "Core.h"
#include "InvocationState.h"
namespace rayx {
struct Rand;
// Calculates the factorial of n: n!
RAYX_FN_ACC double RAYX_API fact(int n);
/**returns first bessel function of parameter v*/
RAYX_FN_ACC double RAYX_API bessel1(double v);
/**
calculates the Bessel diffraction effects on ... |
b4a008822d1438f12601ce9b3a74ab8fa814f425aa95c7459700176c9093e04e | C/C++ | 952 | 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... |
a069c56573e1da9f230026c41ee7ae2ff2c91fdfa4368d94307f2d1981017bf7 | C/C++ | 953 | 29 | /*
* 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... |
f6ac1c0f9e6a5bb37ed53e88340d35ea20677f9452c30057b88fb23c3792c921 | C/C++ | 955 | 36 | /* 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... |
0b9a487c3130309ebfd4876d1c2bff5cfaf10946966e07f50d36353e19a3dba5 | C/C++ | 960 | 38 | // ***************************************************************************
// bamtools_random.h (c) 2010 Derek Barnett, Erik Garrison
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
// Last modified: 7 April 2010 (DB)
// ------------... |
19ebf025c88f1d513349661f55bb9ebb02f96bec4bd4495bf802749fe94a68aa | C/C++ | 960 | 33 | /*
* Copyright (C) 2010, 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 your... |
5f0eab8fe9d329649d17159a4fbbd397d1289b7142ff13e77168354725fd8c0d | C/C++ | 962 | 37 | /* 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... |
71f025343237acc326bba79d9d2b8e39462aee768cf728abcd1ea4f78f8e505b | C/C++ | 965 | 38 | // ***************************************************************************
// bamtools_convert.h (c) 2010 Derek Barnett, Erik Garrison
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
// Last modified: 9 July 2010
// -----------------... |
c3b34c9ac8bea3f44b0c99dce203c2b3572a4d60c9614d388025d5702fcac124 | C/C++ | 965 | 38 | // ***************************************************************************
// bamtools_revert.h (c) 2010 Derek Barnett, Alistair Ward
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
// Last modified: 7 April 2011
// -----------------... |
b5d94119d01569c323391696c97b198f341297035da65d57915721d6275343b0 | C/C++ | 967 | 38 | // ***************************************************************************
// bamtools_filter.h (c) 2010 Derek Barnett, Erik Garrison
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
// Last modified: 28 August 2010
// ---------------... |
7dd4186b551889c04bed4910498446dac35d9cc3dcf35faa06cbae87880dcbf2 | C/C++ | 968 | 37 | #pragma once
#include "LightSource.h"
#include "Shader/Rand.h"
namespace rayx {
class RAYX_API SimpleUndulatorSource : public LightSourceBase {
public:
SimpleUndulatorSource(const DesignSource&);
RAYX_FN_ACC detail::Ray genRay(const int rayPathIndex, const int sourceId, const EnergyDistributionDataVariant... |
b2881d510d0acd6db89b79bb7137a0cece09228c5ec12b58a286d732f6e41caa | C/C++ | 968 | 43 | /* 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... |
8955991fdc57122b08cdde67396497ac5b08958249817db86a28f5dc3a28735b | C/C++ | 970 | 38 | // ***************************************************************************
// bamtools_coverage.h (c) 2010 Derek Barnett, Erik Garrison
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
// Last modified: 1 August 2010
// --------------... |
0aa53979d28678e86a0c0ab30cf6286f1e9d8e0fa0a9166aa1bdd0ab0255ebab | C/C++ | 971 | 38 | #pragma once
#include <glm.hpp>
#include "Core.h"
#include "ElectricField.h"
#include "EventType.h"
#include "Rand.h"
namespace rayx::detail {
// this struct is for the usage inside a kernel
// it is padded for optimal memory access on the CPU
// the GPU does not care about padding as long as Ray stays in registers... |
f3f80d066d9076f8d14221725a1cb20db4ec106006c6d9a27084fd88020f83b3 | C/C++ | 971 | 31 | /* 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... |
36ca743326e0140620c52f2976d429f841c0c2c017d6a6f650a884346bec2d59 | C/C++ | 974 | 26 | /*
* 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... |
24175f619a91cb22cf857ff01c2bf2ef399ab0d85f64590bb399948e1a265c8c | C/C++ | 975 | 31 | /*
* 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... |
c179aef2f060c4330cca704c0e1ad883714aa8825adada91a176bc48de78c323 | C/C++ | 975 | 31 | /*
* GPReduce_emxutil.h
*
* Code generation for function 'GPReduce_emxutil'
*
* C source code generated on: Sun Aug 23 01:10:26 2015
*
*/
#ifndef __GPREDUCE_EMXUTIL_H__
#define __GPREDUCE_EMXUTIL_H__
/* Include files */
#include <math.h>
#include <stdlib.h>
#include <string.h>
#include "mwmathutil.h"
#include ... |
c9036fd2973fc2dd974e4719ac0c07ab5132f989debc9ce6382e49bbdce9fffa | C/C++ | 975 | 31 | /*
* GPExpand_emxutil.h
*
* Code generation for function 'GPExpand_emxutil'
*
* C source code generated on: Sun Aug 23 01:10:53 2015
*
*/
#ifndef __GPEXPAND_EMXUTIL_H__
#define __GPEXPAND_EMXUTIL_H__
/* Include files */
#include <math.h>
#include <stdlib.h>
#include <string.h>
#include "mwmathutil.h"
#include ... |
3b7019ab1012bebda73ce27fd8730efc20dda1bc586ea36cf81200310755b6f6 | C/C++ | 981 | 33 | #pragma once
#include <memory>
#include <optional>
#include "FrameInfo.h"
#include "GraphicsCore/Device.h"
#include "GraphicsCore/GraphicsPipeline.h"
#include "RenderObject.h"
#include "RenderSystem.h"
struct Line;
/**
* @brief The RayRenderSystem class handles the rendering of a RenderObject representing rays.
*... |
17f121f9820cc3f71401600b33959060e2a02c22af201d2c088823d92e30f984 | C/C++ | 983 | 30 | #pragma once
#include <cmath>
#include "Complex.h"
#include "Ray.h"
#include "Utils.h"
namespace rayx {
/**
calculates refracted ray
@params: ray: Ray
normal: normal at intersection point of ray and element -> for planes normal is always the same (0,1,0) -> no need to rotate but we do
anyways. az: line... |
8c2e6d6d3d040cfc186fb24d8aa6c090898dba62a500867685f092184a767b67 | C/C++ | 983 | 36 | /*
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... |
a712e12542dd24b764f6576a09d5147206c6c456567aa7f93fe4a3772f6ea1e0 | C/C++ | 984 | 22 | /*
* 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... |
8301ada37338e409b7159fdbab5fa7986d1de5b3c30487c2300705bd4aa8afd2 | C/C++ | 985 | 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... |
2132b018301a1f71c4a30f1c41d1bbe139ab3bd17f310c2b2ff20290b88b28c5 | C/C++ | 986 | 28 | #ifndef __TL_UTILS__
#define __TL_UTILS__
#include <stdlib.h>
#include <string.h>
#include <stdbool.h>
#include <stdio.h>
#define MAX_TOKEN_SIZE 100
#define NWKDELIM "+(,);"
/* Function prototypes */
void* tl_alloc(size_t size, int setval);
int tl_push_label(TLlabel *newlab, TLstrlist *strlst);
int ... |
a80713c78f24dc641a1dac3a41a31a011b7932e005e33ea5094824e5008bfaae | C/C++ | 989 | 38 | /* 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... |
0cc83cfd54b45a6de4c7dc7cdc1eb4b142ba80b6da71261ba0e60a63f685faaa | C/C++ | 991 | 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... |
580f336ad22cd8687dd883e0184c109feb02d187053e68951c7d2541b9f1c6be | C/C++ | 994 | 36 | #ifndef GENOMULT_H
#define GENOMULT_H
#include <random>
#include "matmult.h"
#include "storage.h"
#include <Eigen/Dense>
#include <Eigen/Core>
#include <Eigen/LU>
#include <Eigen/SVD>
using namespace Eigen;
using namespace std;
#ifdef USE_DOUBLE
typedef Eigen::Matrix<double, Eigen::Dynamic, Eigen::Dynamic, Eigen::Row... |
a4e1c9c94dae8bca3e326ae8f8601fe4f81aa91ade08d1bc686881676aa2b54e | C/C++ | 996 | 38 | /* 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... |
44eef19401840967cc2580ea9bd292b1786bce3cab1cb95e44a84edb072df3e6 | C/C++ | 998 | 39 | // ***************************************************************************
// bamtools_split.h (c) 2010 Derek Barnett, Erik Garrison
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
// Last modified: 7 April 2011 (DB)
// -------------... |
22e79fe0a4657976de666f2f8aa998249362f1cf3d39d1c570c5dacf3401d37b | C/C++ | 1,000 | 31 | /* 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... |
ee73dbe2f7f68ee366e16a3d78a084a6a3e28ca0c373fbec6d280452ffcef36e | C/C++ | 1,000 | 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... |
2c559c199bca632e648f7431c67379b218eab4ba8059f9605cfd961b83fb7ebc | C/C++ | 1,003 | 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... |
f0674f9b5675ce343273159fa1e429b19575b7f817e5356898dda88613693a29 | C/C++ | 1,006 | 39 | #ifndef STATSFN_H
#define STATSFN_H
#include <iostream>
using namespace std;
namespace statsfn {
#ifdef USE_DOUBLE
typedef Eigen::Matrix<double, Eigen::Dynamic, Eigen::Dynamic, Eigen::RowMajor> MatrixXdr;
#else
typedef Eigen::Matrix<float, Eigen::Dynamic, Eigen::Dynamic, Eigen::RowMajor> MatrixXdr;
#endif
... |
913a18730a6c4f868bbff708f5ee8644ec310462c7718cf8d4cd7c9120561738 | C/C++ | 1,008 | 37 | /*
* 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... |
e03699d95c15a285a04f46ff79dba181ca2b57970b7eddf040e612c420a4e84f | C/C++ | 1,012 | 39 | // ***************************************************************************
// bamtools_header.h (c) 2010 Derek Barnett, Erik Garrison
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
// Last modified: 7 April 2011
// -----------------... |
8719fce17b70483a11f2fe57b9e55152f8eab40ec84baa1704b6a986ed2989be | C/C++ | 1,019 | 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... |
f6b78b74ac724dc881231ca16c9bb014de775e5b46a3c85ec41739f450636396 | C/C++ | 1,021 | 54 | /* 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... |
3175f3451616dabad9a131aea50ae631a9b98384d9f82927e3970731b12c5ea6 | C/C++ | 1,024 | 36 | // ***************************************************************************
// bamtools_tool.h (c) 2010 Derek Barnett, Erik Garrison
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
// Last modified: 2 June 2010
// --------------------... |
497b4bb0a765b77d250c3dd5de3b7f0d90f6f3762a8fde1d5b52d9e698019120 | C/C++ | 1,024 | 35 | #include <cstdlib>
#include<fstream.h>
#ifndef IIR_FILTER_H_
#define IIR_FILTER_H_
#include "filter.h"
///////////////////////////////////////////////////////////////////////////////////////////
class IIR_filter : public Filter
{
private:
double *b, *a, *pre_x, *pre_y;
int M, N;
protected:
publ... |
56da2a912cf625b88321ca187e7d1babdd273e662bbc3284e3ef6be9e7a9d93f | C/C++ | 1,039 | 42 | /* 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... |
f558c2e88eda6b1032b68daeaa34d273a0fa1689237037b0b7a4e0b84c4569ae | C/C++ | 1,042 | 32 | #ifndef _CHROMOSOME_H_
#define _CHROMOSOME_H_
#include "GenomeSequence.h"
class Chromosome{
public:
explicit Chromosome(GenomeSequence* gs, unsigned int chrosomeIndex);
explicit Chromosome(GenomeSequence* gs, const char* chromosomeName);
explicit Chromosome(const char* genomseSequenceFileName, unsigned in... |
4eb02ffeaab35ffb8711ff7c8054c91f7e3753abe9509b8976c36ed3766c7e8c | C/C++ | 1,045 | 34 | #pragma once
#include <chrono>
#include <filesystem>
#include "Beamline/Beamline.h"
#include "CommandParser.h"
#include "Debug/Instrumentor.h"
#include "Rays.h"
#include "TerminalAppConfig.h"
#include "Tracer/Tracer.h"
class TerminalApp {
public:
TerminalApp(int argc, char** argv);
~TerminalApp();
voi... |
b70fc6ffb9d1736cd859815020a5b74715636263e3ba422643968b126eb89820 | C/C++ | 1,053 | 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... |
992c65473038050a1951b63eb792a8ed8afc0b0ee3299268c1dc1041b5b9e511 | C/C++ | 1,055 | 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... |
c80f35b5ccd1c73d93c5524c1e4873ff8c20a00eb1171f3a25783efa64a00441 | C/C++ | 1,056 | 37 | /*
* 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... |
144fac67a8dd25d86af3d274f3c10ea2b06edbfdc267c42d8d61c5a8c98b2888 | C/C++ | 1,061 | 43 | /* 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... |
adb5f5d901cb8ef3a99e9a9249e8fbe3bfeaff1ca3e7a64e7f5ea310f1a926c2 | C/C++ | 1,064 | 54 | #ifndef _LIST_H_
#define _LIST_H_
// A sorted list class used for trimmed mean and median filtering
/*
% Revision History:
% 2008: First release
% 2023: Renamed from deprecated version List.h
%
% Reza Sameni, 2022-2023 The Open-Source Electrophysiological Toolbox
% https://github.com/alphanumericslab/OSE... |
a28d2f55adc7b0401330f63d29b1d20fa264faf3e741e6f23c7b5c63b887a199 | C/C++ | 1,072 | 41 | /*<html><pre> -<a href="qh-geom_r.htm"
>-------------------------------</a><a name="TOP">-</a>
random.h
header file for random and utility routines
see qh-geom_r.htm and random_r.c
Copyright (c) 1993-2015 The Geometry Center.
$Id: //main/2015/qhull/src/libqhull_r/random_... |
d6253713fc6bac4b1f40760f3be9d46a4ef37331fc5b82aad66607f66f11008f | C/C++ | 1,076 | 30 | void BatchNormalizationP_forward_cuda(
THCudaTensor *input, THCudaTensor *output,
THCudaTensor *weight, THCudaTensor *bias,
THCudaTensor *running_mean, THCudaTensor *running_var,
THCudaTensor *save_mean, THCudaTensor *save_std,
int train, double momentum, double eps);
void BatchNormalizationP_mean_cuda(
T... |
48b192a9eccdd86ddb92444aece4e0c1ec4810b2f783843ac56a3bf88037d12e | C/C++ | 1,081 | 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... |
940b8bf4883ffce749261b2cd715992f72e3d3f7b14af9b3fde594844b0513d6 | C/C++ | 1,084 | 55 | #ifndef IO_H
#define IO_H
#include "std.h"
#include "printable.h"
class io {
public:
static int debug ;
static void print (const string& s, int level, string file) ;
static void println (const string& s, int level) ;
static void print (const string& s, int level ) ;
static void print (printable &p, int ... |
7c1c8b98589fa6c913c0fd862a6351b97a215fbcc62e102d086d5d2cd1b58dcd | C/C++ | 1,086 | 32 | /************************************************************************/
/* Public implementation follows */
/************************************************************************/
/*--- Defines ----------------------------------------------------------*/
#undef SVDiterations
#define SVDiterations... |
5e76e22f2308941575a000d18e43c2c427b6f8a39a8b872942c94be505e566bf | C/C++ | 1,089 | 36 | #pragma once
#include "Element/Element.h"
#include "RaysPtr.h"
namespace rayx {
/// Expresses whether we force sequential tracing, or we use dynamic tracing.
/// We prefer this over a boolean, as calling eg. the trace function with an argument of `true` has no obvious meaning.
/// On the other hand calling it with `... |
98256b165b52d5d6265bb6b5b5e8d6855b8bd32fc44fd3b0532a9f4ba3d954b0 | C/C++ | 1,090 | 43 | // ***************************************************************************
// bamtools_resolve.h (c) 2011 Derek Barnett
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
// Last modified: 23 June 2011
// -------------------------------... |
ee30baf101823487e0e36f23c794a5ac6647a04ab4c5dad1ef6d5a0c62cce2bb | C/C++ | 1,093 | 38 | /* 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... |
4a7ebb7d0ee05a4e7e2d9642f5e7297331b8c3a9280dec80aa24b7c24f62e48b | C/C++ | 1,103 | 29 | //
// fitch.h
// MorPhy2
//
// Created by mbrazeau on 02/05/2017.
// Copyright © 2017 brazeaulab. All rights reserved.
//
#ifndef fitch_h
#define fitch_h
int mpl_fitch_downpass(MPLndsets* lset, MPLndsets* rset, MPLndsets* nset, MPLpartition* part);
int mpl_fitch_uppass(MPLndsets* lset, MPLndsets* rset, MPLndsets... |
e608187f524c81bd4bc65c252bc4d8427792c5dc5d59d23b356c7d56a18fc70a | C/C++ | 1,109 | 36 | /************************************************************************/
/* Public implementation follows */
/************************************************************************/
/*--- Defines ----------------------------------------------------------*/
#undef FALSE
#define FALSE ((int)(0 != 0... |
ba04455bb586c03b8dbe57621df6615eaa40e368fb47e92ee7f33564be78cc69 | C/C++ | 1,112 | 27 | /* 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... |
92de0439104b91306b0cdb98c5adb44b7c75d0b0254a7463a0803e948d950541 | C/C++ | 1,121 | 38 | /* 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... |
a2d73a558670451f709656c18fb5f8354ead23c07f69065c7c60cdf86f7cb5fb | C/C++ | 1,122 | 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... |
7563c2d0cda08557555fd30f1b1aef8ba169e627976aa54c115b85ac52ea373f | C/C++ | 1,124 | 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... |
c8c3614813be6e1af37fc1545808701ee5c471b3f3a9e3b0fd9449fb67984924 | C/C++ | 1,124 | 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... |
db50337282bee7096f8f25294a45f07bcb9e2d1104ded0e606ee65aed421610b | C/C++ | 1,133 | 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... |
dfb2ae4329ea26e9b9af2ff6677178c773844c9f5663cd739df404b119a34e58 | C/C++ | 1,133 | 33 | /*
* 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... |
013be5aa3f313bfbb0305c3687d5d5e22cf49c863dad096f2af9132a37beae24 | C/C++ | 1,138 | 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... |
9154fc1a394031ddc2458ec3342ee1576ddc610afd523b429884ab48f3a06ba1 | C/C++ | 1,149 | 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... |
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