sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
012300cc1f707ffead222dbe09a3fe853341f2c088ae4ca2d528900369762258 | C | 4,344 | 137 | /* hfile_gcs.c -- Google Cloud Storage backend for low-level file streams.
Copyright (C) 2016 Genome Research Ltd.
Author: John Marshall <[email protected]>
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to d... |
4f14ddb49ebe8755d0f71df6cecc838948317e732f5beb583c3d729b0372270d | C | 4,361 | 188 | #include <viaio/Vlib.h>
#include <math.h>
#include <stdio.h>
#include <string.h>
#include <stdlib.h>
#include <gsl/gsl_math.h>
#include <gsl/gsl_matrix.h>
#include <gsl/gsl_statistics.h>
#include <gsl/gsl_blas.h>
#include <gsl/gsl_rng.h>
#include <gsl/gsl_randist.h>
#include <gsl/gsl_sort.h>
/* random selection sel... |
23f18f258b34fa4cf9c77404a81589ebb5aa652fef6cfd88fe156ea2dcd60502 | C | 4,383 | 216 | /*
** Various utilities for LISA algorithm
**
** G.Lohmann, Jan 2017
*/
#include <viaio/VImage.h>
#include <viaio/Vlib.h>
#include <viaio/mu.h>
#include <viaio/option.h>
#include <stdio.h>
#include <string.h>
#include <math.h>
#include <stdlib.h>
#include <gsl/gsl_math.h>
#include <gsl/gsl_histogram.h>
#define SQR... |
8940df48bbdc140a5091d1c58fa1052e28e062715e7d4c99668293616bb734d1 | C | 4,387 | 202 | /*! \file
2D Deriche filter for edge detection
\par Reference:
R. Deriche. Fast algorithms for low-level vision.
IEEE Transactions on Pattern Analysis and Machine Intelligence,
1(12):78-88, January 1990.
\par Author:
Gabriele Lohmann, MPI-CBS
*/
/* From the Vista library: */
#include <viaio/Vlib.h>
#include <vi... |
34f607a7d66e8e6e6247ad79fb028dbb8d727d7bc694bf7ed3c204ebfb9a25bd | C | 4,389 | 146 | #include <math.h>
#include <mex.h>
void mexFunction(int nlhs, mxArray *plhs[], int nrhs, const mxArray *prhs[])
{
/*declare variables*/
const mwSize *dims;
mwIndex indx;
int i, numdims;
int numelin;
mxClassID classid;
double *input1r, *input1i, *input2r, *input2i, *output1r, *output1i;
double a, b, c... |
324e37fcf64c7e1f3fc6757c3a56e8a5f0a4783e03da58c3f0dece2a244b4d54 | C | 4,422 | 162 | /*
Copyright (c) 2010, 2013, 2018-2019 Genome Research Ltd.
Author: Andrew Whitwham <[email protected]>
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:
1. Redistributions of source code must retain the above copyright not... |
057a936e1ec6c11c2eb40e1f86b7795eea443b9938c559c7ca625a1c837213fb | C | 4,454 | 201 | /*
** parse second level design file
**
** G.Lohmann
*/
#include <viaio/Vlib.h>
#include <viaio/VImage.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <math.h>
#include <ctype.h>
#include <gsl/gsl_matrix.h>
#include <gsl/gsl_vector.h>
extern int VStringToken(char *, char *, int, int);
#defin... |
f56299fc20b175cb3aed115d958b4636250eed7893450866f6664c51a6146211 | C | 4,470 | 197 | /******************************************************************************
This file is part of the FAST protein structure alignment package,
developed by Jianhua Zhu at the Bioinformatics Program of Boston University.
******************************************************************************/
#include "vote.... |
20ef5ab7b161c13e3cc6b76a9bc9af2eacb5665e496879ec12c617ab7481baa6 | C | 4,477 | 202 | #include <viaio/VImage.h>
#include <viaio/Vlib.h>
#include <gsl/gsl_matrix.h>
#include <gsl/gsl_vector.h>
#include <gsl/gsl_sort.h>
#include <gsl/gsl_statistics.h>
#include <gsl/gsl_math.h>
#include <gsl/gsl_blas.h>
#include <gsl/gsl_sort_vector.h>
#include "../cylutils/cyl.h"
VImage Convert2Repn(VImage src,VImage ... |
5608c667cd394dbe8699cce2f90ecc452384fd1ec0bb9392f40d694891fd878b | C | 4,508 | 161 | /*
* The original plgndr function was implemented using some code from
* Numerical Recipes in C. However, it was not allowed to release that code
* as open source. The new implementation below is using some code from
* the GNU Scientific Library (http://www.gnu.org/software/gsl).
*
* Copyright (C) 2002-2006 ... |
964cd6ec20b8ed4d695bce675f8a76d2f45a8360ec20566cc3a530fe5946f628 | C | 4,516 | 187 | /*
** Read design file
**
** G.Lohmann, MPI-KYB 2018
*/
#include <viaio/Vlib.h>
#include <viaio/VImage.h>
#include <viaio/mu.h>
#include <viaio/option.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <math.h>
#include <gsl/gsl_matrix.h>
#include <gsl/gsl_vector.h>
#include <gsl/gsl_blas.h>
typ... |
653d2c0d0f38363b0a3ae2533d26d05f30b5208f0781ec9c5c7c01e4c1eebdbe | C | 4,531 | 187 | /*
** Read design file
**
** G.Lohmann, MPI-KYB 2018
*/
#include <viaio/Vlib.h>
#include <viaio/VImage.h>
#include <viaio/mu.h>
#include <viaio/option.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <math.h>
#include <gsl/gsl_matrix.h>
#include <gsl/gsl_vector.h>
#include <gsl/gsl_blas.h>
typ... |
36fed87a412dee5caa1eba3800542453abb186f32bbf3d49c52ec8beba1a2352 | C | 4,540 | 134 | /* sample.c -- group data by sample.
Copyright (C) 2010, 2011 Broad Institute.
Copyright (C) 2013 Genome Research Ltd.
Author: Heng Li <[email protected]>
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to ... |
1c373132fc7ec81938e08f3ac67e4979541d0b2e50b442d027ab29bdc3163a54 | C | 4,576 | 201 | #include <viaio/VImage.h>
#include <viaio/Vlib.h>
#include <viaio/mu.h>
#include <viaio/option.h>
#include <stdio.h>
#include <string.h>
#include <math.h>
#include <stdlib.h>
#include <gsl/gsl_matrix.h>
#include <gsl/gsl_vector.h>
#include <gsl/gsl_errno.h>
#include <gsl/gsl_math.h>
#include <gsl/gsl_fft_real.h>
#inc... |
17b4d6457e46b4fb4ece4f0101fa51d7f49a842f8c98d69f23d876c6ff6623ab | C | 4,601 | 151 | /* sam_utils.c -- various utilities internal to samtools.
Copyright (C) 2014-2016, 2018, 2019 Genome Research Ltd.
Author: John Marshall <[email protected]>
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to d... |
6af5eaeea986d4ef7e1a027bb7e0f51bee4d19b9c969421d205f915cfbbed4f5 | C | 4,603 | 220 | /******************************************************************************
This file is part of the FAST protein structure alignment package,
developed by Jianhua Zhu at the Bioinformatics Program of Boston University.
******************************************************************************/
#include <math.... |
0bcaf9271b5c43f2554a72b4bce828d05281fd97d0ff2f9e76313cf839ec337f | C | 4,632 | 145 | /*
* $Id: ConvertO.c 3177 2008-04-01 14:47:24Z karstenm $
*
* This file contains a routines for converting an image from one pixel
* representation to another by mapping the actual range of source pixel
* values to the full range of destination pixel values.
*/
/*
* Copyright 1993, 1994 University of Briti... |
a03ca963389660367011773918515f1bec75efcdcb02c505e14ab94139e9791d | C | 4,720 | 216 | /*! \file
3D Canny edge detection
\par Reference:
J. Canny (1986). "A computational approach to edge detection",
IEEE-PAMI, Vol.8, No.6. pp.679--698.
\par Author:
Gabriele Lohmann, MPI-CBS
*/
/*
** 3D Canny edge detection
**
** G.Lohmann, 1996
*/
/* From the Vista library: */
#include <viaio/Vlib.h>
#include <vi... |
4725baf16585ce4c4e0417aadf35090b54b4d1bf440e2ad18378acf75fd24063 | C | 4,735 | 188 | /*
Copyright (c) 2009 Genome Research Ltd.
Author: Rob Davies <[email protected]>
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:
1. Redistributions of source code must retain the above copyright notice,
this list of cond... |
09b91cf17b55fe3a33b71e3ac04340f90e2984bc79bd898a80a59a7dff2a5db6 | C | 4,748 | 175 | /*
** TFCE heuristic
**
** M. Kuhlmann, MPI-KYB, Sept 2015
*/
#include <viaio/VImage.h>
#include <viaio/Vlib.h>
#include <viaio/mu.h>
#include <via/via.h>
#include <stdio.h>
#include <string.h>
#include <math.h>
#include <stdlib.h>
#include <gsl/gsl_matrix.h>
#include <gsl/gsl_vector.h>
#include <gsl/gsl_math.h>
#d... |
5c9e4ee5cb6f9fe29b3767bec538218bb1919dc84241e5a4d790d87394f65617 | C | 4,806 | 199 |
/*! \file
A non-linear 3d smoothing filter
The smoothing filter computes the most frequent value in a 6 (or 18)
neighbourhood and replaces the center pixel with this value.
The pixels within the neighbourhood are weighted.
\par Author:
Gabriele Lohmann, MPI-CBS
*/
/* From the Vista library: */
#include <viaio/Vl... |
3472191ffeec89f1e7390ebf6e9c89977925738b0e8f7d38ec9bdd205b698360 | C | 4,837 | 153 | #include <math.h>
#include <mex.h>
void mexFunction(int nlhs, mxArray *plhs[], int nrhs, const mxArray *prhs[])
{
/*declare variables*/
const mwSize *dims;
mwIndex indx;
int i, numdims;
int numelin;
mxClassID classid;
double *input1r, *input1i, *input2r, *input2i, *output1r, *output1i;
double a, b, c... |
85e3db92d223ce46d4ded97d72980e462f3bcc28fc80531008b404554174f29f | C | 4,873 | 213 | /*
** file IO update for lipsia programs
** lipsia programs can read files with extensions .v .v.gz .nii .nii.gz
** lipsia outputs files with extensions .v
**
** G.Lohmann, MPI-KYB, May 2017
*/
#include <stdio.h>
#include <string.h>
#include <stdlib.h>
#include <assert.h>
#include <sys/stat.h>
#include <math.h>
#inc... |
8747f7c09be1fffd47df431c458bfb782ad6fbbed2a4d91cc6823f969dfe7203 | C | 4,877 | 167 | /*
** read and write geometry information
*/
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <viaio/Vlib.h>
#include <viaio/mu.h>
void VCopyGeoInfo(VAttrList src_list,VAttrList dst_list)
{
VAttrListPosn src_posn,dst_posn;
VAttrList geolist=NULL;
VString str=NULL;
for (VFirstAttr (src_lis... |
ff11b9bebb60e5e1f89d01b5a6c7d58b35e753cd6399d3699d8d713f2b7db405 | C | 4,887 | 206 |
#include"ssd1306.h"
// Screenbuffer
static uint8_t SSD1306_Buffer[SSD1306_WIDTH * SSD1306_HEIGHT / 8];
// Screen object
static SSD1306_t SSD1306;
//
// Send a byte to the command register
//
static void ssd1306_WriteCommand(uint8_t command)
{
HAL_I2C_Mem_Write(&hi2c1,SSD1306_I2C_ADDR,0x00,1,&command,1,10);
}
... |
a62a0962b669e1557fdda4d323ead3fe8efaad025077ef0b8c7c1970f6287db9 | C | 4,956 | 181 | /*
* Guillaume Flandin
* Copyright (C) 2005-2022 Wellcome Centre for Human Neuroimaging
*/
#ifndef MATLAB_MEX_FILE
# undef _LARGEFILE64_SOURCE
# define _LARGEFILE64_SOURCE
# include <stdio.h>
# include <sys/stat.h>
# if defined(__APPLE__)
# define structStat struct stat
# define getFileFstat fstat
# define getF... |
d1c72c184a21607b0ab8a7a0bec6ae4a372c9a923d22e2c064d8dbea1184873a | C | 4,969 | 173 | /* bam_color.c -- color-space support.
Copyright (C) 2009, 2012 University of California - Los Angeles.
Author: Nils Homer <[email protected]>
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 S... |
98f97c836b7fa4d63716a0bf346a1c176d2a91cdeb9b7b8c27ef0512263009fd | C | 4,998 | 209 | /* From the Vista library: */
#include <viaio/Vlib.h>
#include <viaio/VImage.h>
#include <viaio/mu.h>
#include <viaio/option.h>
/* From the standard C libaray: */
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#define MAXPARAMLENGTH 500
char* VGetOptionValue (VOptionDescRec *option)
{
char *ret;
in... |
ffcac57b43f19a506ad8d6c2b740b0dc40b2a119c4d030a8eadfff68457838ca | C | 5,010 | 200 | /*! \file
3d chamfer distance transform.
For each background voxel, the length of the shortest
3D path to the nearest foreground voxel is computed.
The chamfer distance metric is an approximation to the
Euclidian distance.
\par References:
G. Borgefors (1984).
"Distance Transforms in arbitrary dimensions",
CVGIP 27, ... |
4705928d76e4e7b170e3a70dec0c8e46786b9fbf51b12997368d4b12f9cfe92b | C | 5,026 | 197 | /*
** detrending, fit polynomial or order 1 (linear), 3 or 5
** G.Lohmann, Aug 2016, MPI-KYB
*/
#include <viaio/VImage.h>
#include <viaio/Vlib.h>
#include <viaio/mu.h>
#include <viaio/option.h>
#include <stdio.h>
#include <string.h>
#include <math.h>
#include <stdlib.h>
#include <gsl/gsl_vector.h>
#include <gsl/gsl_m... |
68b77e2b1ec60e33f42a336e61f3e0b184d0a1aa67f5da82635091ca2a6d57cf | C | 5,049 | 205 | /*
Copyright (c) 2009, 2013, 2015, 2018-2019 Genome Research Ltd.
Author: Rob Davies <[email protected]>
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:
1. Redistributions of source code must retain the above copyright no... |
5747419bfbc388bcd7f058fa66308ecac103aa9c42f5b645d61ca742596db041 | C | 5,057 | 170 | /* test/test_realn.c -- test sam_prob_realn() function
Copyright (C) 2018 Genome Research Ltd.
Author: Rob Davies <[email protected]>
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 with... |
254d42aa8e4a1dd92ea4d5302a000bd281f4db88bfe6480bd3ac43f337a9416a | C | 5,060 | 225 | /*! \file
3D topological thinning.
The algorithm is based on
Tsao's method. However, the order in which voxels are checked for
deletion is governed by distance. We first compute the distance
transform of the image to be thinned such that each foreground voxel recieves
a label indicating its distance from... |
635735c5acbaaf528224dc9fac8a9f3bb0997cc64ce2e1db5489d47a420d6b49 | C | 5,062 | 170 | #include <math.h>
#include <mex.h>
void mexFunction(int nlhs, mxArray *plhs[], int nrhs, const mxArray *prhs[])
{
/*declare variables*/
const mwSize *dims;
mwIndex indx;
int i, numdims, indx1, indx2, indx3;
int numelin;
mxClassID classid;
double *input1r, *input1i, *input2r, *input2i, *output1r, *output1... |
a3e5fdc7a2242166f38c5da93e7948c330738d7209f359d199ebe35e0ea685c2 | C | 5,072 | 186 | /* test/plugins-dlhts.c -- Test plugins with dynamically loaded libhts.
Copyright (C) 2020 University of Glasgow.
Author: John Marshall <[email protected]>
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Softw... |
f09f3232be19935071354c729ed54596b2da4ec067c75497edd140ff17d1c266 | C | 5,074 | 223 | /*
* $Id: ReadPlain.c 3177 2008-04-01 14:47:24Z karstenm $
*
* This file contains routines for reading Vista plain format files.
*/
/*
* Copyright 1993, 1994 University of British Columbia
*
* Permission to use, copy, modify, distribute, and sell this software and its
* documentation for any purpose is he... |
fce1b73e9ce2f3577c9b753a469154aba4da1c07a857f7cfc8f0d91f1fdfac7b | C | 5,100 | 262 | /*
** ECM - eigenvector centrality mapping using full matrix
**
** G.Lohmann, MPI-KYB, Nov 2018
*/
#include <viaio/Vlib.h>
#include <viaio/VImage.h>
#include <viaio/mu.h>
#include <viaio/option.h>
#include <gsl/gsl_matrix.h>
#include <gsl/gsl_vector.h>
#include <gsl/gsl_errno.h>
#include <gsl/gsl_cblas.h>
#include <g... |
c843e0f1e3168ea354ad56b9361231f6147d5ed6a48459abd6ce153bcf1ce1c5 | C | 5,102 | 160 | #include <viaio/VImage.h>
#include <string.h>
#include <gsl/gsl_matrix.h>
#include <viaio/Vlib.h>
#include "gsl_utils.h"
void whitecov(VImage rho_vol, gsl_matrix_float *Y,
gsl_matrix_float* invM, gsl_matrix_float* pinvX,
gsl_matrix_float* X, int numlags, int slice)
{
/* set up variables */
int n... |
dcdeb2e43b11b89246fdd99c6835d685b1dde8c2883e55d937fd3e19be616417 | C | 5,117 | 200 | /*
** ECM - eigenvector centrality mapping, I/O interface
**
** G.Lohmann, MPI-KYB, updated Oct 2018
*/
#include <viaio/Vlib.h>
#include <viaio/VImage.h>
#include <viaio/mu.h>
#include <viaio/option.h>
#include <gsl/gsl_matrix.h>
#include <gsl/gsl_vector.h>
#include <gsl/gsl_errno.h>
#include <gsl/gsl_blas.h>
#includ... |
5132d8a93e154422804c5669a0443a61d7ccfd6130922a8138f49d640d7c74b5 | C | 5,139 | 160 | /* hfile_gcs.c -- Google Cloud Storage backend for low-level file streams.
Copyright (C) 2016, 2021 Genome Research Ltd.
Author: John Marshall <[email protected]>
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software")... |
9c46ec9b6a8ed35bc3f4ced416bf84ee51a2d125c300aac18724586b632176af | C | 5,167 | 151 | /*
Copyright (C) 2017, 2020 Genome Research Ltd.
Author: Petr Danecek <[email protected]>
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 restriction, including without... |
02c88837178009becdb8082f6d96bb714fc3e7adbec5f486dc21ffc798710456 | C | 5,197 | 199 | /*! \file
2D image rotation.
\par Reference:
"A Fast Algorithm for General Raster Rotation"
by Alan Paeth, Graphics Interface '86, pp. 77-81.
\par Author:
Daniel Ko, UBC Laboratory for Computational Intelligence
*/
/*
* This file contains routines for rotating images.
*/
/*
* Copyright 1993, 1994 Univers... |
e69946536189845d0cdc4165ab71b27ea42226422653d49f195d0af36fc14ac9 | C | 5,225 | 188 | /*
* Copyright (c) 2019,2020 Genome Research Ltd.
* Author(s): James Bonfield
*
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
*
* 1. Redistributions of source code must retain the above copyright notice,
* ... |
827f8c9f3a585d73d3875e89ce7e3a36258ad84db27cec549ee0fb3ae7fbe3c1 | C | 5,229 | 175 | /*
** hubness map
** this program expects as input a list of edges produced by "vted"
**
** Ref: Lohmann et al (2016) PLoS One, 11(6):e0158185
**
** G.Lohmann, May 2015
*/
#include <stdio.h>
#include <stdlib.h>
#include <math.h>
#include <string.h>
/* From the Vista library: */
#include <viaio/VImage.h>
#include <v... |
34529b8006e22578dfd500cd1f60b1067593567194fb1ebc3cfdd1bb76409317 | C | 5,277 | 170 | /*
* $Id: GaussConv.c 3181 2008-04-01 15:19:44Z karstenm $
*
* This file contains routines for performing Gaussian convolution.
*/
/*
* Copyright 1993, 1994 University of British Columbia
*
* Permission to use, copy, modify, distribute, and sell this software and its
* documentation for any purpose is her... |
300d7feff9a9767c14e93fef598a01ae6adfe1ace3980398f81878cb0c09e973 | C | 5,345 | 183 | /* vcf_sweep.c -- forward/reverse sweep API.
Copyright (C) 2013 Genome Research Ltd.
Author: Petr Danecek <[email protected]>
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 rest... |
1d3dbcd648b379ef0e109646bc37d0140c16381c3d0f74c610a112fd84546846 | C | 5,350 | 182 | /**
******************************************************************************
* @file stm32f4xx_hal_i2c_ex.c
* @author MCD Application Team
* @brief I2C Extension HAL module driver.
* This file provides firmware functions to manage the following
* functionalities of I2C extensio... |
c5e9e2cdfd957aa5bb73c9f665523f93b7164aa6f00aeb6f95c72e71c6e0d880 | C | 5,396 | 235 | /*
* $Id: Invert.c 3177 2008-04-01 14:47:24Z karstenm $
*
* This file contains routines for inverting and negating images.
*/
/*
* Copyright 1993, 1994 University of British Columbia
*
* Permission to use, copy, modify, distribute, and sell this software and its
* documentation for any purpose is hereby g... |
d0c09a3543aea83e71a89246c5e14503c6527dbd57d7a590c3ecabfdddf37242 | C | 5,422 | 181 | /*
** Cylarim: Cylinder-based Algorithm for Laminar fMRI Data Analysis
**
** G.Lohmann, MPI-KYB, Oct 2024
*/
/* From the standard C library: */
#include <stdio.h>
#include <stdlib.h>
#include <math.h>
/* From the Vista library: */
#include <viaio/VImage.h>
#include <viaio/Vlib.h>
#include <viaio/mu.h>
#include <via... |
a5b05477a3198d0506697362be57b4d62f4d68f46cb5757bcb330be0039e332f | C | 5,434 | 192 | /******************************************************************************
This file is part of the FAST protein structure alignment package,
developed by Jianhua Zhu at the Bioinformatics Program of Boston University.
******************************************************************************/
/*=============... |
54887b4ba79247e7de06c0dbd7b2f95df7d327f80b9f9b04a9b0daf98977a8a3 | C | 5,450 | 197 | /*
* $Id: Dictionary.c 3177 2008-04-01 14:47:24Z karstenm $
*
* This file contains dictionaries that symbols used in V data files to
* values used internally.
*/
/*
* Copyright 1993, 1994 University of British Columbia
*
* Permission to use, copy, modify, distribute, and sell this software and its
* doc... |
c0c4520e7386307e2f96b706101c2dc5eff918a9a15fdbccbae4d587172bc98a | C | 5,533 | 223 | /*
* Copyright (c) 2016-2020 Genome Research Ltd.
* Author(s): James Bonfield
*
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
*
* 1. Redistributions of source code must retain the above copyright notice,
*... |
67a4e4add11725f6e3c91bdb28012d81c7ab1e6b7879da0bf2ef32956311f638 | C | 5,555 | 206 | /*
* $Id: Edges.c 3177 2008-04-01 14:47:24Z karstenm $
*
* This file provides basic support for edges (the VEdges class).
*/
/*
* Copyright 1993, 1994 University of British Columbia
*
* Permission to use, copy, modify, distribute, and sell this software and its
* documentation for any purpose is hereby gr... |
fc7ea0f7751c392c4fc182677e314cd90b7413be843c779c41aa9a4dad55b7da | C | 5,566 | 185 | /* plugin.c -- low-level path parsing and plugin functions.
Copyright (C) 2015 Genome Research Ltd.
Author: John Marshall <[email protected]>
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 Soft... |
fbf5bb87d8cb47a97d2704563f5b75dda429672b302db42bb2ef96a67d15997a | C | 5,570 | 190 | /* vcf_sweep.c -- forward/reverse sweep API.
Copyright (C) 2013-2014, 2019 Genome Research Ltd.
Author: Petr Danecek <[email protected]>
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 w... |
db2a8472a732ef0dde37c4e9997d914d5de46aed6cf052fd4c786dafbbdc821e | C | 5,583 | 154 | /*
Copyright (c) 2010-2013 Genome Research Ltd.
Author: James Bonfield <[email protected]>
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:
1. Redistributions of source code must retain the above copyright notice,
this lis... |
7eeac790ac5edb8bc4214516137e7d5fab128a15a9fcda40cbd143764e14e70b | C | 5,682 | 198 | #include <stdio.h>
#include <stdlib.h>
#include <math.h>
#include "helpers.h"
void get_total_number_of_synapses(int sizeneurons, int num_neurons[sizeneurons],
int sizever, int sizehor,
double conn_probs[sizever][sizehor], double ratio_syn[sizever][sizehor],
int num_synapse[][sizehor])
/*
Written by... |
c2baf00eafb677aa0ac8c7bc59612274375f6ef0702c02e0e616b45f237bd784 | C | 5,700 | 146 | #include <math.h>
#include <matrix.h>
#include <mex.h>
void mexFunction(int nlhs, mxArray *plhs[], int nrhs, const mxArray *prhs[])
{
/*declare variables*/
const mwSize *dims;
mwSize *dimsout;
mwIndex indx;
int i, j, k, numdims;
int numelin;
mxClassID classid;
double *input1r, *input1i, *output1r, *ou... |
0c9d8c505c0ddee8a9a6e77bac18b796c26f9d3a8b991a19f1f6b3ea37802e63 | C | 5,747 | 227 | /*
** random swap functions
**
** M. Kuhlmann, MPI-KYB, Sept 2015
**/
#include <viaio/Vlib.h>
#include <stdio.h>
#include <string.h>
#include <math.h>
#include <stdlib.h>
#include <gsl/gsl_matrix.h>
#include <gsl/gsl_vector.h>
#include <gsl/gsl_rng.h>
#include <gsl/gsl_math.h>
#include <gsl/gsl_randist.h>
#include <g... |
0a3651722971a42acfde32ff6ec32b39286c6ca5ec0577a96e77d0b2b45c79f4 | C | 5,758 | 216 | /*! \file
Geometric transformations using trilinear interpolation.
This file contains functions for trilinear resampling
and 3D rotations. The transformation equation is:
y = A(x-x0) + b
where x,x0,b,y are 1x3 vectors and A is a 3x3 matrix.
The vector x0 can be used to specify a position that
remains unchanged... |
42e60d54524df8244519d15229b060e6692e80261eadab2f3491e7415ad2434d | C | 5,762 | 243 | #include <viaio/Vlib.h>
#include <math.h>
#include <stdio.h>
#include <string.h>
#include <stdlib.h>
#include <gsl/gsl_math.h>
#include <gsl/gsl_matrix.h>
#include <gsl/gsl_sort.h>
#include <gsl/gsl_sort_vector.h>
#include <gsl/gsl_statistics.h>
#include <gsl/gsl_blas.h>
#include <gsl/gsl_rng.h>
#include <gsl/gsl_ran... |
0f7bfc1c3e79ddae433b2082e2111da4a2d6811317f3af75c58ca03f3ce1f75d | C | 5,803 | 239 | /******************************************************************************
This file is part of the FAST protein structure alignment package,
developed by Jianhua Zhu at the Bioinformatics Program of Boston University.
******************************************************************************/
#include "basic... |
566cb3718c103b3496a2ad606abf25b446076af3d4551e43f484bd99e7d6b736 | C | 5,804 | 193 | /*
* Copyright (C) 1999-2022 Christophe Phillips
*/
/*
Input : XYZva, XYZvb, trib, weight, defl
Output : Cii
siga==sig[0], sigb==sig[1], sigc==sig[2], sigd==sig[3]
weight = (sig[0]-sig[1])/((sig[2]+sig[3])*2.*pi) ;
*/
#include <math.h>
#include "mex.h"
void Cij_lin(double C[], double XYZva[], int Nverta, ... |
41898fb586b5bddac1dcc7ff56a5c41ecb729108b2822073340887755163b84e | C | 5,939 | 231 | /* USER CODE BEGIN Header */
/**
******************************************************************************
* @file stm32f4xx_it.c
* @brief Interrupt Service Routines.
******************************************************************************
* @attention
*
* <h2><center>© Copyright (c) ... |
c0622d463c023a587b7e18b75c6b799528e7c2c53fea97d69f515c34cc222e60 | C | 5,962 | 294 | /*
** Methods for the volume set (Volumes) data type.
**
** Author:
** G.Lohmann, MPI/CNS, <[email protected]>, Dez. 1995
*/
/* From the Vista library: */
#include <viaio/Vlib.h>
#include <viaio/VImage.h>
#include <viaio/mu.h>
#include <viaio/option.h>
#include <viaio/Volumes.h>
/* From the standard C libaray: */
#i... |
2c148390e67c98c609f799908edb0b3eb1af031c6c6ab9f4a0eb55146ec896e1 | C | 5,987 | 179 | /* dict.c -- create a sequence dictionary file.
Copyright (C) 2015, 2020 Genome Research Ltd.
Author: Shane McCarthy <[email protected]>
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 ... |
3a4c9bffb452c6f3dcd290b3d176904e0d3cb931a2149f884360151f55a8b830 | C | 5,987 | 195 | #include "nanaccum.h"
/* Helper function to find linearized distance between elements on a given
* dimension of a multidimensional array. Lower indices are close in memory
* (column-major or FORTRAN/MATLAB order: */
mwSize stride(int dim, int shape_len, const mwSize *shape)
{
int i, s = 1;
for (i = 0; i < dim; i... |
72393c8a21e1979a2e009e125501e062c99da984372fb03ed0ae8099c8f80206 | C | 5,996 | 296 | /*
** get transformation matrix for co-registration
** Translation, rotation and one scaling parameter (7 degrees of freedom)
**
** G.Lohmann, 2015
*/
#include <viaio/VImage.h>
#include <viaio/Vlib.h>
#include <viaio/mu.h>
#include <viaio/os.h>
#include <stdio.h>
#include <stdlib.h>
#include <math.h>
#include <gsl/... |
e19ad0bb93cf164e55dba89b23bd72e2ca5cc65433e773472ad972c8dc65cbdf | C | 6,007 | 200 | /*
Copyright (c) 2012-2013 Genome Research Ltd.
Author: James Bonfield <[email protected]>
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:
1. Redistributions of source code must retain the above copyright notice,
this lis... |
a77ad90ec4671abca6cdaf711ae14efe0d12ad254db06643a6dd07e978279c13 | C | 6,027 | 172 | /**
******************************************************************************
* @file stm32f4xx_hal_flash_ramfunc.c
* @author MCD Application Team
* @brief FLASH RAMFUNC module driver.
* This file provides a FLASH firmware functions which should be
* executed from internal SRAM... |
e153d9f5768e4eeacb49cf41115376bfa8352be95b822cf4cf87a40a52e6eaca | C | 6,103 | 258 | /******************************************************************************
This file is part of the FAST protein structure alignment package,
developed by Jianhua Zhu at the Bioinformatics Program of Boston University.
******************************************************************************/
/*=============... |
3b921f9535a261df8e57720fb69e8d8fe712a8932901d2c1dee15b637c80bc5f | C | 6,107 | 203 | /* CCGEngine.c
This is a bare-bones C program whos purpose is to compute
Multi-unit cross correlograms quickly. Not intended for
use on its own. It is designed to be wrapped by a MATLAB
function.
Usage - [CCG, PAIRS] = CCGEngine(TIMES, MARKS, BINSIZE, HALFBINS)
TIMES ( is the name of a binary file c... |
6bfddfabbb13010ceae916582bd98eb994fbc61b8bca03773205d7360a67d171 | C | 6,119 | 282 | /*! \file
2D Skeletonization
Perform a topological thinning.
\par Reference:
A.Manzanera,T.Bernard,F.Preteux,B.Longuet:
"nD skeletonization: a unified mathematical framework".
Journal of Electronic Engineering, Vol. 11-1, Jan. 2002, pp.25-37.
\par Author:
Gabriele Lohmann, MPI-CBS
*/
#include <stdio.h>
#includ... |
9ed54c8344c3586f40772b3a4ec706c52c0915d19844d99ead7f709f49fb2a26 | C | 6,163 | 219 | #include <viaio/Vlib.h>
#include <viaio/VImage.h>
#include <math.h>
#include <stdio.h>
#include <string.h>
#include <stdlib.h>
#include <gsl/gsl_math.h>
#include <gsl/gsl_matrix.h>
#include <gsl/gsl_sort.h>
#include <gsl/gsl_sort_vector.h>
#include <gsl/gsl_statistics.h>
#include <gsl/gsl_blas.h>
#include <gsl/gsl_rn... |
4e16d699cf8516651c2f6a41124bdea98716c67d9b090fc17dbd4662f733eca6 | C | 6,177 | 263 | /*! \file
Constrained distance transform.
Perform Chamfer distance transform in 3D while avoiding obstacles, i.e.
get distance from each "inside" point to closest "outside" point
while avoiding "obstacle" points. The distance is measured as the length
of the shortest path to the closest outside point that does not tou... |
8249bc6f2992b9ed153a35e8636a0272b0b71d3e293545373a224da73a421d4a | C | 6,235 | 233 | /*
* John Ashburner
* Copyright (C) 1995-2022 Wellcome Centre for Human Neuroimaging
*/
/*
% add a series of images - a compiled routine
% FORMAT s = spm_add(V,Q,flags)
% V - Vector of mapped volumes (from spm_map or spm_vol).
% Q - Filename for averaged image
% flags - Flags can be:
% 'f' - ... |
bd38d2c2c3153e2245c6cb59e8ddfe92eb6ca076869c7311519247b1831fdda5 | C | 6,445 | 197 | /* errmod.c -- revised MAQ error model.
Copyright (C) 2010 Broad Institute.
Copyright (C) 2012, 2013, 2016 Genome Research Ltd.
Author: Heng Li <[email protected]>
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Softwa... |
fd387965582db94649a8d4be0836d0dedb192dbe410ffd97b14e540f0342702b | C | 6,452 | 249 |
/* From the Vista library: */
#include <viaio/VImage.h>
#include <viaio/Vlib.h>
#include <gsl/gsl_matrix.h>
#include <gsl/gsl_vector.h>
#include <gsl/gsl_sort.h>
#include <gsl/gsl_statistics.h>
#include <gsl/gsl_math.h>
#include <gsl/gsl_blas.h>
#include <gsl/gsl_rng.h>
#include <gsl/gsl_randist.h>
#include <gsl/gsl_... |
a63bdaa58e65e0adb46595eab2d1fda0c63c4ae037c02b8f1d03c2517bfbfff2 | C | 6,476 | 198 | /*
** Implementation of LISA algorithm
** for statistical inference of fMRI images
**
** generic plug-in.
** A file containing a list of all 3D permutation images must be supplied.
**
** G.Lohmann, April 2017
*/
#include <viaio/Vlib.h>
#include <viaio/file.h>
#include <viaio/mu.h>
#include <viaio/option.h>
#include <v... |
686f4d497b405df65defacf6a8f65ab351c7e07c206e609a5e9162e197f7a996 | C | 6,481 | 158 | /* bam.c -- miscellaneous BAM functions.
Copyright (C) 2008-2013, 2015, 2019-2020 Genome Research Ltd.
Portions copyright (C) 2009-2012 Broad Institute.
Author: Heng Li <[email protected]>
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documen... |
d07d2b875b09fc3ced0db0b6cd1ccfa26ff9fdce153f02210b2a32baef389553 | C | 6,501 | 220 | /* plugin.c -- low-level path parsing and plugin functions.
Copyright (C) 2015-2016, 2020 Genome Research Ltd.
Author: John Marshall <[email protected]>
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
... |
ca96472db3e71308c67fe00b72e2af230a3010efac6a28165b7fc7749ec96044 | C | 6,507 | 299 | /*! \file
2D connected component labelling
Each foreground voxel receives a label indicating
its membership in a connected component.
The algorithm is based on depth first search.
\par Reference:
G. Lohmann (1998). "Volumetric Image Analysis",
John Wiley & Sons, Chichester, England.
\par Author:
Gabriele Lohmann, ... |
0dc45dd40ab71c024d5b001a697a45a7bf154f1fa0cd740dc5f961efbb4d4276 | C | 6,510 | 244 | /*! \file
3D binary morphology using distance transforms
3D binary morphological operations are implemented using distance
transforms. This implementation is usually much faster than the
Minkowski addition. However, only structuring elements of spherical
shape are permitted.
\par Reference:
G. Lohmann (1998). "Vol... |
da30be015d743d03b016060ff489d101549ab3b9095d32e0eb1acc8d6f15bbdc | C | 6,526 | 204 | #include <math.h>
#include <mex.h>
void mexFunction(int nlhs, mxArray *plhs[], int nrhs, const mxArray *prhs[])
{
/*declare variables*/
const mwSize *dims;
mwIndex indx;
int i, numdims, indx1, indx2, indx3;
int numelin;
mxClassID classid;
double *input1r, *input1i, *input2r, *input2i, *output1r, *output1... |
62fca53c04f402759c90022b32b098399f741fea24cb28972dc320ce35763b31 | C | 6,609 | 410 |
/*
** gsl routines for double data type
**
** G.Lohmann, July 2004
*/
#include <stdio.h>
#include <stdlib.h>
#include <math.h>
#include <gsl/gsl_cblas.h>
#include <gsl/gsl_matrix.h>
#include <gsl/gsl_vector.h>
#include <gsl/gsl_linalg.h>
#define dvset gsl_vector_set
#define dvget gsl_vector_get
#define dmset gs... |
15334dd3e362f28d004119910fc5ce4bbf7d47e0b652aa841944d07d36d0b4be | C | 6,615 | 201 | #include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include "lif.h"
struct LIF *create_lif(int num, int *lif_neurons, int *group_neurons,
int *total_neurons, int population_id,
double CM, double V_RESET, double V_THRESH,double EL,
double GL, double TAU_M,double TAU_REF){
/*
in... |
44709da9df0295360f096b59804e26941d8eb2793a06868ac79d6a59cd4da09b | C | 6,656 | 221 | /*
* $Id: EdgesType.c 3177 2008-04-01 14:47:24Z karstenm $
*
* This file contains methods for the edge set (VEdges) type.
*/
/*
* Copyright 1993, 1994 University of British Columbia
*
* Permission to use, copy, modify, distribute, and sell this software and its
* documentation for any purpose is hereby gr... |
6856a6d1b609bc1d3b8c970dfb10571f5598410d35337a7db572fab7b9fc6e49 | C | 6,658 | 305 | /****************************************************************
*
* vpreprocess: SpatialFilter.c
*
* Copyright (C) Max Planck Institute
* for Human Cognitive and Brain Sciences, Leipzig
*
* <[email protected]>
*
* This program is free software; you can redistribute it and/or
* modify it under the terms of ... |
7ee4e37c96efc9414cd0598f1c89eb7562600a9747c13c41029c72820c80447e | C | 6,739 | 215 | /*
* $Id: ImageType.c 3177 2008-04-01 14:47:24Z karstenm $
*
* This file contains methods for the image (VImage) type.
*/
/*
* Copyright 1993, 1994 University of British Columbia
*
* Permission to use, copy, modify, distribute, and sell this software and its
* documentation for any purpose is hereby grant... |
fa60e7ed99ae4b55b34e5f085f54675e71dfc0229e9b1e49890a54bf3aed96ff | C | 6,742 | 190 | /* bam_quickcheck.c -- quickcheck subcommand.
Copyright (C) 2015-2017 Genome Research Ltd.
Author: Joshua C. Randall <[email protected]>
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 Soft... |
cfef086fa5699c9e17d9ca342ebbe391ee39ef188f240a2885869d61e8792ede | C | 6,757 | 208 | /* errmod.c -- revised MAQ error model.
Copyright (C) 2010 Broad Institute.
Copyright (C) 2012, 2013, 2016-2017, 2019 Genome Research Ltd.
Author: Heng Li <[email protected]>
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (... |
99e9b5a50b557d766c0804fdaff9515b003ec4a6a9f8f2e89493db66c686ccd5 | C | 6,785 | 299 | /*! \file
3D binary morphology.
This file contains functions for 3D binary morphology:
ersion, dilation, and generation of 3D structuring elements.
\par Reference:
P. Maragos, R.W. Schafer (1990):
"Morphological Systems for multidimensional signal processing",
Proc. of the IEEE, Vol. 78, No. 4, pp. 690--70... |
433e011419bdab297d2bac4afe14e36088d35e6bb821cb8c188c359a877b8bfa | C | 6,822 | 257 | /*
** read data matrix, map of voxel addresses
**
** G.Lohmann, Jan 2013
*/
#include <stdio.h>
#include <stdlib.h>
#include <math.h>
#include <string.h>
#include <gsl/gsl_matrix.h>
#include <gsl/gsl_vector.h>
#include <gsl/gsl_blas.h>
#include <gsl/gsl_sort.h>
#include "viaio/Vlib.h"
#include "viaio/VImage.h"
#includ... |
8882c6b9b621f44b9eb8aab96269c37b919969d1c50fd0b340d4e23ae8b027b4 | C | 6,877 | 335 | /*! \file
3d Euclidean distance transform.
For each background voxel, the length of the shortest
3D path to the nearest foreground voxel is computed.
\par References:
Toyofumi Saito, Jun-Ichiro Toriwaki (1994).
"New algorithms for euclidean distance transformation of a n-dimensional
picture with applications",
Patte... |
a4688628ef3b8df2fb1d0871373799d30246487c2c82b970e871705430881b69 | C | 6,887 | 265 | /*
* $Id: ConvertC.c 3177 2008-04-01 14:47:24Z karstenm $
*
* This file contains a routine for converting an image from one pixel
* representation to another by simply copying (not mapping) pixel values.
*/
/*
* Copyright 1993, 1994 University of British Columbia
*
* Permission to use, copy, modify, distr... |
f3ed9eb691d7f452965bb90e9b6e9f6a0c953900147d7b83ee71ab38ac50e778 | C | 6,893 | 254 | /*
*
* This file contains methods for the volume set (Volumes) type.
*
* Author: Gabriele Lohmann, MPI/CNS, Nov. 1995
*/
/* From the Vista library: */
#include <viaio/Vlib.h>
#include <viaio/os.h>
#include <viaio/Volumes.h>
/*
* Table of methods.
*/
/* Later in this file: */
static VDecodeMethod VolumesDe... |
c4d7afd1d17869fec5a4eba2ae56bfb84391192aa7e2c20f1ad76d0759d7ae25 | C | 6,929 | 291 | /*! \file
Constrained distance transform.
Perform Chamfer distance transform in 3D while avoiding obstacles, i.e.
get distance from each "inside" point to closest "outside" point
while avoiding "obstacle" points. The distance is measured as the length
of the shortest path to the closest outside point that does not tou... |
82be8896fb91e0bc27c9786c78d33104d268ae3c2ede9f6dcb1aa8eed5c5dd77 | C | 6,951 | 225 | /* bam_lpileup.c -- lplbuf routines.
Copyright (C) 2008, 2009, 2013 Genome Research Ltd.
Author: Heng Li <[email protected]>
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 restr... |
d70077be82bf83c954613d20714055e68d03f82a203307a083b5c5f2eec994cb | C | 6,961 | 282 | /*
** file IO update for lipsia programs
** lipsia programs can read files with extensions .v .v.gz .nii .nii.gz
** lipsia outputs files with extensions .v
**
** G.Lohmann, MPI-KYB, May 2017, updated Feb 2018
*/
#include <stdio.h>
#include <string.h>
#include <stdlib.h>
#include <assert.h>
#include <sys/stat.h>
#inc... |
ae3083918e7f665b579abb1e67be373c4af9fc45f1ec2019ade20208f92d3fbd | C | 6,966 | 233 | /* test-expr.c -- Testing: filter expression parsing and processing.
Copyright (C) 2020 Genome Research Ltd.
Author: James Bonfield <[email protected]>
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... |
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