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[feat] add -N/--net to download simulations from NeuroJSON.io, add -Q
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@fangq
fangq committed Jan 22, 2025
1 parent 4f20523 commit 12071fd
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2 changes: 1 addition & 1 deletion src/Makefile
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Original file line number Diff line number Diff line change
Expand Up @@ -79,7 +79,7 @@ CPPFLAGS+=-g -Wall #-pedantic #-DNO_LZMA # -DUSE_OS_TIMER
OBJSUFFIX=.o
EXESUFFIX=

FILES=mcx_core mcx_utils mcx_shapes mcx_tictoc mcx mcx_bench mcx_mie cjson/cJSON ubj/ubjw
FILES=mcx_core mcx_utils mcx_shapes mcx_tictoc mcx mcx_bench mcx_neurojson mcx_mie cjson/cJSON ubj/ubjw

ifeq ($(findstring _NT-,$(PLATFORM)), _NT-)
CC=nvcc
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68 changes: 68 additions & 0 deletions src/mcx_neurojson.cpp
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@@ -0,0 +1,68 @@
/***************************************************************************//**
** \mainpage Mesh-based Monte Carlo (MMC) - a 3D photon simulator
**
** \author Qianqian Fang <q.fang at neu.edu>
** \copyright Qianqian Fang, 2010-2024
**
** \section sref Reference:
** \li \c (\b Fang2010) Qianqian Fang, <a href="http://www.opticsinfobase.org/abstract.cfm?uri=boe-1-1-165">
** "Mesh-based Monte Carlo Method Using Fast Ray-Tracing
** in Plucker Coordinates,"</a> Biomed. Opt. Express, 1(1) 165-175 (2010).
** \li \c (\b Fang2012) Qianqian Fang and David R. Kaeli,
** <a href="https://www.osapublishing.org/boe/abstract.cfm?uri=boe-3-12-3223">
** "Accelerating mesh-based Monte Carlo method on modern CPU architectures,"</a>
** Biomed. Opt. Express 3(12), 3223-3230 (2012)
** \li \c (\b Yao2016) Ruoyang Yao, Xavier Intes, and Qianqian Fang,
** <a href="https://www.osapublishing.org/boe/abstract.cfm?uri=boe-7-1-171">
** "Generalized mesh-based Monte Carlo for wide-field illumination and detection
** via mesh retessellation,"</a> Biomed. Optics Express, 7(1), 171-184 (2016)
** \li \c (\b Fang2019) Qianqian Fang and Shijie Yan,
** <a href="http://dx.doi.org/10.1117/1.JBO.24.11.115002">
** "Graphics processing unit-accelerated mesh-based Monte Carlo photon transport
** simulations,"</a> J. of Biomedical Optics, 24(11), 115002 (2019)
** \li \c (\b Yuan2021) Yaoshen Yuan, Shijie Yan, and Qianqian Fang,
** <a href="https://www.osapublishing.org/boe/fulltext.cfm?uri=boe-12-1-147">
** "Light transport modeling in highly complex tissues using the implicit
** mesh-based Monte Carlo algorithm,"</a> Biomed. Optics Express, 12(1) 147-161 (2021)
**
** \section slicense License
** GPL v3, see LICENSE.txt for details
*******************************************************************************/

#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include "mcx_neurojson.h"

#define ALLOC_CHUNK 4096

int runcommand(char* cmd, char* param, char** output) {
int len = ALLOC_CHUNK, pos = 0;
char buffer[256] = {'\0'}, fullcmd[ALLOC_CHUNK] = {'\0'};

snprintf(fullcmd, ALLOC_CHUNK, "%s%s", cmd, param);
FILE* pipe = popen(fullcmd, "r");

if (!pipe) {
return -1;
}

free(*output);
*output = (char*)calloc(ALLOC_CHUNK, 1);

while (fgets(buffer, sizeof(buffer), pipe) != NULL) {
int buflen = strlen(buffer);

if (buflen > len - pos - 1) {
*output = (char*)realloc(*output, len + ALLOC_CHUNK);
len += ALLOC_CHUNK;
}

strncpy(*output + pos, buffer, len - pos - 1);
pos += buflen;
}

*output = (char*)realloc(*output, pos + 1);
pclose(pipe);
return pos;
}
44 changes: 44 additions & 0 deletions src/mcx_neurojson.h
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Original file line number Diff line number Diff line change
@@ -0,0 +1,44 @@
/***************************************************************************//**
** \mainpage Mesh-based Monte Carlo (MMC) - a 3D photon simulator
**
** \author Qianqian Fang <q.fang at neu.edu>
** \copyright Qianqian Fang, 2010-2024
**
** \section sref Reference:
** \li \c (\b Fang2010) Qianqian Fang, <a href="http://www.opticsinfobase.org/abstract.cfm?uri=boe-1-1-165">
** "Mesh-based Monte Carlo Method Using Fast Ray-Tracing
** in Plucker Coordinates,"</a> Biomed. Opt. Express, 1(1) 165-175 (2010).
** \li \c (\b Fang2012) Qianqian Fang and David R. Kaeli,
** <a href="https://www.osapublishing.org/boe/abstract.cfm?uri=boe-3-12-3223">
** "Accelerating mesh-based Monte Carlo method on modern CPU architectures,"</a>
** Biomed. Opt. Express 3(12), 3223-3230 (2012)
** \li \c (\b Yao2016) Ruoyang Yao, Xavier Intes, and Qianqian Fang,
** <a href="https://www.osapublishing.org/boe/abstract.cfm?uri=boe-7-1-171">
** "Generalized mesh-based Monte Carlo for wide-field illumination and detection
** via mesh retessellation,"</a> Biomed. Optics Express, 7(1), 171-184 (2016)
** \li \c (\b Fang2019) Qianqian Fang and Shijie Yan,
** <a href="http://dx.doi.org/10.1117/1.JBO.24.11.115002">
** "Graphics processing unit-accelerated mesh-based Monte Carlo photon transport
** simulations,"</a> J. of Biomedical Optics, 24(11), 115002 (2019)
** \li \c (\b Yuan2021) Yaoshen Yuan, Shijie Yan, and Qianqian Fang,
** <a href="https://www.osapublishing.org/boe/fulltext.cfm?uri=boe-12-1-147">
** "Light transport modeling in highly complex tissues using the implicit
** mesh-based Monte Carlo algorithm,"</a> Biomed. Optics Express, 12(1) 147-161 (2021)
**
** \section slicense License
** GPL v3, see LICENSE.txt for details
*******************************************************************************/

#ifndef _MCEXTREME_NEUROJSON_API_H
#define _MCEXTREME_NEUROJSON_API_H

#ifdef __cplusplus
extern "C" {
#endif
int runcommand(char* cmd, char* param, char** output);

#ifdef __cplusplus
}
#endif

#endif
101 changes: 73 additions & 28 deletions src/mcx_utils.c
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Original file line number Diff line number Diff line change
Expand Up @@ -51,6 +51,7 @@
#include "mcx_core.h"
#include "mcx_bench.h"
#include "mcx_mie.h"
#include "mcx_neurojson.h"

#if defined(_WIN32) && defined(USE_OS_TIMER) && !defined(MCX_CONTAINER)
#include "mmc_tictoc.h"
Expand Down Expand Up @@ -108,7 +109,7 @@
const char shortopt[] = {'h', 'i', 'f', 'n', 't', 'T', 's', 'a', 'g', 'b', '-', 'z', 'u', 'H', 'P',
'd', 'r', 'S', 'p', 'e', 'U', 'R', 'l', 'L', '-', 'I', '-', 'G', 'M', 'A', 'E', 'v', 'D',
'k', 'q', 'Y', 'O', 'F', '-', '-', 'x', 'X', '-', 'K', 'm', 'V', 'B', 'W', 'w', '-',
'-', '-', 'Z', 'j', '-', '-', '-', '\0'
'Q', '-', 'Z', 'j', '-', '-', '-', 'N', '\0'
};

/**
Expand All @@ -128,7 +129,7 @@ const char* fullopt[] = {"--help", "--interactive", "--input", "--photon",
"--maxvoidstep", "--saveexit", "--saveref", "--gscatter", "--mediabyte",
"--momentum", "--specular", "--bc", "--workload", "--savedetflag",
"--internalsrc", "--bench", "--dumpjson", "--zip", "--json", "--atomic",
"--srcid", "--trajstokes", ""
"--srcid", "--trajstokes", "--net", ""
};

/**
Expand Down Expand Up @@ -5057,6 +5058,67 @@ void mcx_parsecmd(int argc, char* argv[], Config* cfg) {

break;

case 'Q':
if (i + 1 < argc && isalpha((int)argv[i + 1][0]) ) {
int idx = mcx_keylookup(argv[++i], benchname);

if (idx == -1) {
MCX_ERROR(-1, "Unsupported bechmark.");
}

isinteractive = 0;
jsoninput = (char*)benchjson[idx];
} else {
MCX_FPRINTF(cfg->flog, "Built-in benchmarks:\n");

for (int i = 0; i < sizeof(benchname) / sizeof(char*) - 1; i++) {
MCX_FPRINTF(cfg->flog, "\t%s\n", benchname[i]);
}

exit(0);
}

break;

case 'N':
if (i == argc - 1 || argv[i + 1][0] == '-') {
int j, doclen;
char* jbuf = NULL;
runcommand("curl -s -X GET 'https://neurojson.io:7777/mcx/_all_docs'", "", &jbuf);
cJSON* root = cJSON_Parse(jbuf), *docs = cJSON_GetObjectItem(root, "rows"), *subitem, *tmp;

if (!docs) {
MCX_ERROR(-1, jbuf);
}

doclen = cJSON_GetArraySize(docs);
subitem = docs->child;
printf("Downloading %d simulations from NeuroJSON.io (https://neurojson.org/db/mcx)\n", doclen - 1);

for (j = 0; j < doclen; j++) {
if (strchr(FIND_JSON_KEY("id", "id", subitem, "", valuestring), '_') == NULL) {
printf("\t%s\n", FIND_JSON_KEY("id", "id", subitem, "", valuestring));
}

subitem = subitem->next;
}

free(jbuf);
exit(0);
} else {
if (strstr(argv[i + 1], "http") == argv[i + 1]) {
runcommand("curl -s -X GET ", argv[i + 1], &jsoninput);
} else if (strchr(argv[i + 1], '/')) {
runcommand("curl -s -X GET https://neurojson.io:7777/", argv[i + 1], &jsoninput);
} else {
runcommand("curl -s -X GET https://neurojson.io:7777/mcx/", argv[i + 1], &jsoninput);
}

isinteractive = 2;
}

break;

case '-': /*additional verbose parameters*/
if (strcmp(argv[i] + 2, "maxvoidstep") == 0) {
i = mcx_readarg(argc, argv, i, &(cfg->maxvoidstep), "int");
Expand All @@ -5081,29 +5143,6 @@ void mcx_parsecmd(int argc, char* argv[], Config* cfg) {
} else {
i = mcx_readarg(argc, argv, i, &(cfg->isdumpjson), "int");
}
} else if (strcmp(argv[i] + 2, "bench") == 0) {
if (i + 1 < argc && isalpha(argv[i + 1][0]) ) {
int idx = mcx_keylookup(argv[++i], benchname);

if (idx == -1) {
MCX_ERROR(-1, "Unsupported bechmark.");
}

isinteractive = 0;
jsoninput = (char*)benchjson[idx];
} else {
MCX_FPRINTF(cfg->flog, "Built-in benchmarks:\n");

for (int i = 0; i < MAX_MCX_BENCH - 1; i++) {
if (benchname[i][0] == '\0') {
break;
}

MCX_FPRINTF(cfg->flog, "\t%s\n", benchname[i]);
}

exit(0);
}
} else if (strcmp(argv[i] + 2, "reflectin") == 0) {
i = mcx_readarg(argc, argv, i, &(cfg->isrefint), "char");
} else if (strcmp(argv[i] + 2, "atomic") == 0) {
Expand Down Expand Up @@ -5147,7 +5186,10 @@ void mcx_parsecmd(int argc, char* argv[], Config* cfg) {
}

if (cfg->isgpuinfo != 2) { /*print gpu info only*/
if (isinteractive) {
if (isinteractive == 2 && jsoninput) {
mcx_readconfig(jsoninput, cfg);
free(jsoninput);
} else if (isinteractive) {
mcx_readconfig((char*)"", cfg);
} else if (jsoninput) {
mcx_readconfig(jsoninput, cfg);
Expand Down Expand Up @@ -5450,8 +5492,11 @@ where possible parameters include (the first value in [*|*] is the default)\n\
if the string starts with '{', it is parsed as\n\
an inline JSON input file\n\
or\n\
--bench ['cube60','skinvessel',..] run a buint-in benchmark specified by name\n\
run --bench without parameter to get a list\n\
-Q/--bench [cube60, skinvessel,...] run a buint-in benchmark specified by name\n\
run -Q without parameter to get a list\n\
-N benchmark (--net) get benchmark from NeuroJSON.io, -N only to list\n\
benchmark can be dataset URL,or dbname/benchname\n\
requires 'curl', install from https://curl.se/\n\
\n"S_BOLD S_CYAN"\
== MC options ==\n" S_RESET"\
-n [0|int] (--photon) total photon number (exponential form accepted)\n\
Expand Down

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