[feat] simulate multiple sources, close #163

ChangeLog.txt

@@ -2,7 +2,7 @@
 
 Major updates are marked with a "*"
 
-== MCX v2023.11 (Interstellar Ion - 2.2), FangQ <q.fang (a) neu.edu> ==
+== MCX v2024.1 (Interstellar Ion - 2.2), FangQ <q.fang (a) neu.edu> ==
 
  2023-11-07 [a710ab3] allow converting integer cfg.vol to json
  2023-10-31 [d6c64e4] [test] fix rng test after make double

NOTICE.txt

@@ -1,6 +1,6 @@
 =============================================================
              Monte Carlo eXtreme (MCX) Suite
-                    version 2023.11
+                    version 2024.1
 =============================================================
 
 Copyright (c) 2009-2023  Qianqian Fang <q.fang at neu.edu>

README.md

@@ -4,7 +4,7 @@ Monte Carlo eXtreme (MCX) - CUDA Edition
 
 -   Author: Qianqian Fang (q.fang at neu.edu)
 -   License: GNU General Public License version 3 (GPLv3)
--   Version: 2.2.pre (v2023.11, Interstellar Ion)
+-   Version: 2.2.pre (v2024.1, Interstellar Ion)
 -   Website: <http://mcx.space>
 
 ![Mex and Binaries](https://github.com/fangq/mcx/actions/workflows/build_all.yml/badge.svg)\

README.txt

@@ -5,7 +5,7 @@
 
 *Author:  Qianqian Fang <q.fang at neu.edu>
 *License: GNU General Public License version 3 (GPLv3)
-*Version: 2.2.pre (v2023.11, Interstellar Ion)
+*Version: 2.2.pre (v2024.1, Interstellar Ion)
 *Website: http://mcx.space
 
 ---------------------------------------------------------------------

example/multisrc/multisrc.json

@@ -0,0 +1,84 @@
+{
+	"Session":{
+		"ID":"multisrc",
+		"DoAutoThread":1,
+		"Photons":10000000
+	},
+	"Forward":{
+		"T0":0,
+		"T1":5e-09,
+		"Dt":5e-09
+	},
+	"Optode":{
+		"Source":{
+			"Pos":[
+				[50,30,0,1],
+				[44.14213562373095,44.14213562373095,0,1],
+				[30,50,0,1],
+				[15.85786437626905,44.14213562373095,0,1],
+				[10,30.00000000000001,0,1],
+				[15.85786437626905,15.85786437626905,0,1],
+				[29.99999999999999,10,0,1],
+				[44.14213562373094,15.85786437626904,0,1],
+				[25,25,0,4]
+			],
+			"Dir":[
+				[-0.5,0,0.8660254037844386,20],
+				[-0.3535533905932738,-0.3535533905932737,0.8660254037844386,20],
+				[-1.110223024625157e-16,-0.5,0.8660254037844386,20],
+				[0.3535533905932737,-0.3535533905932738,0.8660254037844386,20],
+				[0.5,-1.387778780781446e-16,0.8660254037844386,20],
+				[0.3535533905932739,0.3535533905932736,0.8660254037844386,20],
+				[2.220446049250313e-16,0.5,0.8660254037844386,20],
+				[-0.3535533905932736,0.353553390593274,0.8660254037844386,20],
+				[0,0,1,0]
+			],
+			"Param1":[
+				[-8,3,0,0],
+				[-7.778174593052023,-3.535533905932737,0,0],
+				[-3.000000000000002,-8,0,0],
+				[3.535533905932736,-7.778174593052024,0,0],
+				[8,-3.000000000000004,0,0],
+				[7.778174593052025,3.535533905932735,0,0],
+				[3.000000000000004,7.999999999999999,0,0],
+				[-3.535533905932733,7.778174593052025,0,0],
+				[10,0,0,0]
+			],
+			"Param2":[
+				[3,3,0,0],
+				[4.440892098500626e-16,4.242640687119286,0,0],
+				[-3,3.000000000000001,0,0],
+				[-4.242640687119286,1.332267629550188e-15,0,0],
+				[-3.000000000000001,-2.999999999999999,0,0],
+				[-1.77635683940025e-15,-4.242640687119286,0,0],
+				[2.999999999999999,-3.000000000000002,0,0],
+				[4.242640687119286,-2.664535259100376e-15,0,0],
+				[0,10,0,0]
+			],
+			"Type":"planar"
+		}
+	},
+	"Domain":{
+		"OriginType":0,
+		"Media":[
+			{
+				"mua":0,
+				"mus":0,
+				"g":1,
+				"n":1
+			},
+			{
+				"mua":0.005,
+				"mus":0.2,
+				"g":0,
+				"n":1.37
+			}
+		],
+		"MediaFormat":"byte",
+		"Dim":[60,60,40],
+		"VolumeFile":""
+	},
+	"Shapes":[
+		{"Grid": {"Tag":1, "Size":[60,60,40]}}
+	]
+}

example/multisrc/run_multisrc.bat

@@ -0,0 +1 @@
+..\..\bin\mcx.exe -f multisrc.json -D P %*

example/multisrc/run_multisrc.sh

@@ -0,0 +1,2 @@
+#!/bin/sh
+../../bin/mcx -f multisrc.json -D P $@

mcxlab/NEWS

@@ -2,7 +2,7 @@
 
 Major updates are marked with a "*"
 
-== MCX v2023.11 (Interstellar Ion - 2.2), FangQ <q.fang (a) neu.edu> ==
+== MCX v2024.1 (Interstellar Ion - 2.2), FangQ <q.fang (a) neu.edu> ==
 
  2023-11-07 [a710ab3] allow converting integer cfg.vol to json
  2023-10-31 [d6c64e4] [test] fix rng test after make double

mcxlab/README.txt

@@ -2,7 +2,7 @@
 
 Author: Qianqian Fang <q.fang at neu.edu>
 License: GNU General Public License version 3 (GPLv3)
-Version: this package is part of Monte Carlo eXtreme (MCX) v2023.11
+Version: this package is part of Monte Carlo eXtreme (MCX) v2024.1
 
 <toc>
 

mcxlab/examples/demo_multsrc.m

@@ -0,0 +1,82 @@
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% MCXLAB - Monte Carlo eXtreme for MATLAB/Octave by Qianqina Fang
+%
+% In this example, we show how to simultaneously simulate multiple sources
+% of the same type.
+%
+% Specifically, we create a complex source made of an array of 9 planar
+% sources - where 8 of the sources form a circular array by rotating one
+% of the sources around the center of the bottom-face center; the 9th
+% source is manually placed at the center of the array.
+%
+% One can individually control the settings for each of the sources,
+% including the position (srcpos), launch direction (srcdir), and
+% additional parameters (srcparam1/srcparam2).
+
+% By default, each source entry launches an equal fraction of photons,
+% determined by cfg.nphoton/size(cfg.srcpos(1,:)). However, one can set the
+% 4-th element of the srcpos() for each sourc to create different weights
+% for each source. Here, we set the central source 4x of the intensity
+% compared to other circular-array sources (weight of 1). This allows mcx
+% to allocate 4/(8+4) = 1/3 of the total photons (cfg.nphoton) to the central
+% source while each other source launches 1/12 of the total photon packets.
+%
+% Worth to mention that we also set the 4th element of cfg.srcdir, i.e. the
+% focal length, to create a convergent beam for each planar source.
+%
+% This file is part of Monte Carlo eXtreme (MCX) URL:http://mcx.sf.net
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+% only clear cfg to avoid accidentally clearing other useful data
+clear cfg cfgs
+
+cfg.nphoton=1e7;
+cfg.vol=uint8(ones(60,60,40));
+cfg.srctype='planar';
+
+Rs=20;
+delta=pi/4;
+
+ang=0:delta:(2*pi-delta);
+rotmat2d=[cos(delta), -sin(delta); sin(delta), cos(delta)];
+offset2d=[30 30];
+
+% first create an array of planar sources by rotating around origin
+
+% the 4th element of srcpos sets the initial weight
+cfg.srcpos=repmat([Rs, 0, 0, 1], length(ang), 1);
+
+% the 4th element of srcdir sets the focal length (positive: convergent)
+cfg.srcdir=repmat([-0.5, 0, sqrt(3)/2, 20], length(ang), 1);
+cfg.srcparam1=repmat([-8,3,0,0], length(ang), 1);
+cfg.srcparam2=repmat([3,3,0,0], length(ang), 1);
+
+for i=2:length(ang)
+    cfg.srcpos(i,1:2)=(rotmat2d*cfg.srcpos(i-1,1:2)')';
+    cfg.srcdir(i,1:2)=(rotmat2d*cfg.srcdir(i-1,1:2)')';
+    cfg.srcparam1(i,1:2)=(rotmat2d*cfg.srcparam1(i-1,1:2)')';
+    cfg.srcparam2(i,1:2)=(rotmat2d*cfg.srcparam2(i-1,1:2)')';
+end
+
+% translate the circular array to the desired offset
+cfg.srcpos(:,1)=cfg.srcpos(:,1)+offset2d(1);
+cfg.srcpos(:,2)=cfg.srcpos(:,2)+offset2d(2);
+
+% manually add the 9th source to the center
+
+cfg.srcpos(end+1, :)=[offset2d(1)-Rs/4,offset2d(2)-Rs/4,0,4]; % initial weight is 4
+cfg.srcdir(end+1, :)=[0, 0 1 0];
+cfg.srcparam1(end+1, :)=[Rs/2,0,0,0];
+cfg.srcparam2(end+1, :)=[0,Rs/2,0,0];
+
+cfg.gpuid=1;
+% cfg.gpuid='11'; % use two GPUs together
+cfg.autopilot=1;
+cfg.prop=[0 0 1 1;0.005 0.2 0 1.37];
+cfg.tstart=0;
+cfg.tend=5e-9;
+cfg.tstep=5e-9;
+
+flux=mcxlab(cfg);
+
+mcxplotvol(log10(flux.data));

mcxlab/mcxlab.m

@@ -78,6 +78,11 @@
 %                      of the srcdir direction; if the focal length is -inf, the launch
 %                      angle will be computed based on the Lambertian (cosine) distribution.
 %
+%      Starting v2024, cfg.{srcpos,srcdir,srcparam1,srcparam2} accept multiple sources,
+%      with each source corresponding to a single row of the array. For all 4 components,
+%      srcpos/srcdir support 3 or 4 columns, and srcparam1/srcparam2 support 4 columns.
+%      If any of the 4 compnents present, they should have matching row number.
+%
 %== MC simulation settings ==
 %      cfg.seed:       seed for the random number generator (integer) [0]
 %                      if set to a uint8 array, the binary data in each column is used 

mcxstudio/README.txt

@@ -4,7 +4,7 @@
 
 Author:  Qianqian Fang <q.fang at neu.edu>
 License: GNU General Public License version 3 (GPLv3)
-Version: 1.2.pre (v2023.11)
+Version: 1.2.pre (v2024.1)
 Website: http://mcx.space
 
 ---------------------------------------------------------------------

pmcx/README.md

@@ -4,7 +4,7 @@
 
 - Copyright: (C) Matin Raayai Ardakani (2022-2023) <raayaiardakani.m at northeastern.edu>, Qianqian Fang (2019-2023) <q.fang at neu.edu>, Fan-Yu Yen (2023) <yen.f at northeastern.edu>
 - License: GNU Public License V3 or later
-- Version: 0.2.8
+- Version: 0.2.9
 - URL: https://pypi.org/project/pmcx/
 - Github: https://github.com/fangq/mcx
 

pmcx/pmcx/__init__.py

@@ -49,7 +49,7 @@
 # from .files import loadmc2, loadmch, load, save
 from .bench import bench
 
-__version__ = "0.2.8"
+__version__ = "0.2.9"
 
 __all__ = (
     "gpuinfo",

pmcx/setup.py

@@ -123,7 +123,7 @@ def build_extension(self, ext):
 setup(
     name="pmcx",
     packages=["pmcx"],
-    version="0.2.8",
+    version="0.2.9",
     requires=["numpy"],
     license="GPLv3+",
     author="Matin Raayai Ardakani, Qianqian Fang, Fan-Yu Yen",

src/Makefile

@@ -74,7 +74,7 @@ NVCCOMP=$(OMP)
 CUDA_STATIC=--cudart static -Xcompiler "-static-libgcc -static-libstdc++"
 
 CFLAGS+=-std=c99
-CPPFLAGS+=-g -Wall #-DNO_LZMA # -DUSE_OS_TIMER
+CPPFLAGS+=-g -Wall -pedantic #-DNO_LZMA # -DUSE_OS_TIMER
 
 OBJSUFFIX=.o
 EXESUFFIX=

src/mcx_const.h

@@ -31,7 +31,7 @@
 #ifndef _MCEXTREME_CONSTANT_H
 #define _MCEXTREME_CONSTANT_H
 
-#define MCX_VERSION        "v2023.11"
+#define MCX_VERSION        "v2024.1"
 #define MCX_VERSION_MAJOR  2
 #define MCX_VERSION_MINOR  2