update documentation, prepare for v2023 release

.github/workflows/build_all.yml

@@ -150,7 +150,7 @@ jobs:
             otool -L ../bin/mcx
           else
             make static
-            #objdump -p ../bin/mcx | grep "DLL Name:"
+            objdump -p ../bin/mcx | grep "DLL Name:"
           fi
       - name: Build mcxstudio
         if: ${{ runner.os != 'macOS' }}

AUTHORS.txt

@@ -1,5 +1,5 @@
-Monte Carlo eXtreme (MCX) is written by Qianqian Fang.
-Qianqian is currently an Associate Professor in the 
+Monte Carlo eXtreme (MCX) is primarily developed by Qianqian Fang.
+Qianqian is currently Associate Professor in the 
 Department of Bioengineering at Northeastern University, USA.
 
 Address: Dept. of Bioengineering
@@ -11,3 +11,27 @@ Email: <q.fang at neu.edu>
 MCX Website : http://mcx.space
 MCX Wiki:     http://mcx.space/wiki
 Source Code:  http://github.com/fangq/mcx
+
+
+
+Other key contributors of MCX include
+
+* Shijie Yan
+** Email: <yan.shiji at northeastern.edu> 
+** Shijie is a PhD student at Northeastern University, Dept of EECS, under the supervision of Dr. Fang. He has made the follow major contributions
+*** split-voxel MC (SVMC)
+*** modeling of polarized light
+*** photon-sharing
+*** MCX-Cloud server-side development
+*** numerous bug fixes and code improvement
+
+* Matin Raayai Ardakani
+** Email: <raayaiardakani.m at northeastern.edu>
+** Matin is a PhD student at Northeastern University, Dept of EECS, co-supervised by Dr. David Kaeli and Dr. Fang. He has made the follow major contributions
+*** development of pmcx (Python binding for MCX)
+*** development of Github action CI system
+
+* Yaoshen Yuan
+** Email: <yuan.yaos at northeastern.edu>
+** Yaoshen was a PhD student at Northeastern University, Dept of EECS, under the supervision of Dr. Fang. He completed his PhD degree in 2020. He has made the follow major contributions
+*** GPU based Adptive non-local-means (ANLM) filter

ChangeLog.txt

@@ -2,8 +2,89 @@
 
 Major updates are marked with a "*"
 
-== MCX v2022.10 (Heroic Hexagon - 1.9.7), FangQ <q.fang (a) neu.edu> ==
-
+== MCX v2023 (Heroic Hadron - 2.0), FangQ <q.fang (a) neu.edu> ==
+ 2023-08-07 [ac893cd] mcxplotvol: allow keeping x/y/z slice when switching between 4th dimension
+ 2023-08-07 [9aaba97] fix photon sharing 0 output issue in negative patterns
+ 2023-08-05 [da0beda] padding -0 instead of 0 when saving dref with mua_float medium
+ 2023-08-04 [82367f0] simplify dref/flux separation
+ 2023-08-04 [97fff3e] update zmatlib, use miniz, drop zlib for easy deployment
+ 2023-08-03 [4fbb4d6] bump pmcx version to 0.0.14
+ 2023-08-03 [aaedf35] handle mirror bc in the reflection code
+ 2023-08-03*[198cd34] initial support of negative source and negative-patterns some test still fails, but feature is mostly working, need more work
+ 2023-07-27 [081c382] parse outputtype in json2mcx
+ 2023-07-21 [87167cb] simplify mua->0 approximation, drop high order term, #164
+ 2023-07-21 [f063fd6] disable macos runner, macos no longer supports CUDA see https://github.com/actions/runner-images/discussions/7838
+ 2023-07-21 [3067a26] fix incorrect handling of near-zero mus, fix #174, fix test
+ 2023-06-30 [ac06b05] CI: compress with upx on Linux
+ 2023-06-29 [527a5cc] add header, format with black, update action runners, #172
+ 2023-05-21*[540931d] support trajectory-only mode with debuglevel=T
+ 2023-05-20*[0100212] mcxplotphotons: plotting photon tracks with patch and show weights
+ 2023-05-20 [615af1b] avoid recursion and segfault when resetting device
+ 2023-05-16 [c327541] add demo to build RF Jacobians using replay, by Pauliina Hirvi
+ 2023-05-05 [bd44f65] reformat pmcx python units with black
+ 2023-05-05 [c12310b] added cwdref function to compute CW diffuse reflectance
+ 2023-05-05 [0bd643e] added detweight function (using only numpy) to the utils.py in pmcx
+ 2023-05-04 [31c0fa3] fix incorrect stat.unitinmm output
+ 2023-04-29 [0c6b358] use svg vector graphs in mcxlab tutorial
+ 2023-04-29 [bed8f08] Update plots with GPU runtime outputs
+ 2023-04-29 [688ac78] Support mcxlabcl for non-GPU runtime on colab, add srctype tutorial
+ 2023-04-28 [4f53e12] add examples on getting trajectory data
+ 2023-04-27 [f271501] Update mcxlab jupyter notebook based tutorial
+ 2023-04-27*[be5a420] add jupyter-notebook based mcxlab tutorial
+ 2023-04-26 [eb68720] make static linking default on Windows
+ 2023-04-25 [e315dfe] fix incorrect comment regarding gaussian src, fix #165
+ 2023-04-16 [b78c4e3] fix inaccurate output unit for energy output time
+ 2023-04-15 [2fd3594] accept jobs submitted from https://mcx.space/cloud
+ 2023-04-15*[7515611] fix mcxcloud job max duration bug, kill runtime>1min
+ 2023-04-13 [70b3b5e] Add photon replay demo codes for pmcx in jupyter notebook
+ 2023-04-13 [855aa40] pmcx: support photon replay, accept detphotons input
+ 2023-04-13 [8a49fe3] switch from cmake back to Makefile
+ 2023-04-01 [c2591aa] ask cmake to create Makefile
+ 2023-03-22 [67d1128] add pmcx jupyter notebook tutorial
+ 2023-03-22 [291adf5] allow mus=0, avoid unnecessary casting of scalars to double
+ 2023-03-17 [3a4f7ed] fix fluence for mua -> 0
+ 2023-03-15 [46b4311] remove explicit dependency to GLScene in mcxstudio
+ 2023-03-10 [193158c] make volume rendering window available on main gui
+ 2023-03-10 [2d09e54] allow Open project dialog to also load nii and jnii files for rendering
+ 2023-03-09 [63a626d] fix progress bar stalling when setting cfg.issavedet to 3
+ 2023-03-08 [8cab50f] add descriptions on how to start mcxstudio on an Mac, fix #162
+ 2023-03-08 [da49503] allow early termination if -d 3 or cfg.issavedet=3 is set
+ 2023-03-04 [5d4d3c6] transition from openjdata.org to neurojson.org, fix #161
+ 2023-03-02*[3c29fa5] mcxstudioL: loading and rendering jnifti based volume file
+ 2023-03-01 [b99f9a9] mcxstudioL: loading portable JSON/JNIFTI based MCX output data files
+ 2023-02-09 [32e3aef] fix RF replay in mcx binary, allow tweaking replay Jacobian for Born approx
+ 2023-02-05*[9abd3f3] adding additional native python pmcx functions
+ 2023-02-05 [63b80f4] add missing pmcx file
+ 2023-02-05 [e77ff2f] allow pmcx to use mixed binary extension and native function
+ 2023-02-01*[d9b2f2b] fix unmatched unit for RF replay, thanks to Pauliina Hirvi
+ 2023-02-01 [ce2a65c] add the l/length option in help info
+ 2023-02-01 [e67feed] support outputtype=length/l for saving total path lengths per voxel
+ 2023-01-25 [4344574] fix windows compilation error
+ 2023-01-25 [a7ce222] permit 3D plotting of DMMC output double-precision nii files
+ 2023-01-22 [cdabf68] automatically replace RCS keywords in pmcx action
+ 2023-01-22 [e527f4b] fix incomplete handling bc and isreflect setting combinations, fix #160
+ 2023-01-20 [daa1dea] use standard CFLAGS and CPPFLAGS in compilation, remove --std99 error for g++
+ 2023-01-11 [def38f6] Merge pull request #159 from matinraayai/master
+ 2023-01-11 [e077f86] Bump pmcx version to 0.0.7.
+ 2023-01-10 [7af2ea2] bump pmcx version to 0.0.6
+ 2023-01-10 [820ce88] build macos binary wheels
+ 2023-01-09 [4f969d1] Removed the macOS builder VM.
+ 2023-01-09 [dd47cda] Updated README.md for pmcx.
+ 2023-01-09 [82ef430] Final version.
+ 2022-12-08 [eb9322f] Added Windows Wheel building job + fixed compilation errors for windows.
+ 2022-11-18 [d5a9beb] Update build_linux_manywheel.yml
+ 2022-11-18 [816c55f] Added Github workflow.
+ 2022-10-15 [084ffc1] update cmake file and remove zmat from pymcx and mex
+ 2022-10-14 [04000e2] remove zmatlib and ubj as dependency to mex and oct
+ 2022-10-14 [d033520] fix negative respin number bug
+ 2022-10-13 [ec4a29d] update version strings
+ 2022-10-13 [a3fe4ce] remove warning on replay output
+ 2022-10-10 [660dd31] update three.js to r145, fix volume render, fix thumbnail
+
+== MCX v2022.10 (only released to MCX'23 workshop participants), FangQ <q.fang (a) neu.edu> ==
+
+ 2022-10-08 [eaedca7] update installer to 2022.10
+ 2022-10-08 [c31a0e2] update mcx version number to v2022.10
  2022-10-05 [dc42951] prevent nan where log(rand) is calculated
  2022-10-05 [63ffc1e] fix nan in detected photon data when using hyperboloid src, see https://groups.google.com/g/mcx-users/c/vyfHbzEO-0M/m/JzlpEZ3TBwAJ
  2022-09-07 [e281f3e] allow to preview continuously varying medium (4D cfg.vol)

LICENSE.txt

@@ -2,7 +2,7 @@
 =            Monte Carlo eXtreme (MCX) -- CUDA              =
 =============================================================
 
-Copyright (c) 2010-2021  Qianqian Fang <q.fang at neu.edu>
+Copyright (c) 2010-2023  Qianqian Fang <q.fang at neu.edu>
 
 =============================================================
 

Makefile

@@ -5,7 +5,7 @@
 ############################################################
 
 PKGNAME=mcx
-VERSION=1.9.7
+VERSION=2.0.0
 SOURCE=src
 GUI=mcxstudio
 

NOTICE.txt

@@ -1,15 +1,15 @@
 =============================================================
              Monte Carlo eXtreme (MCX) Suite
-                    version 2022.10
+                    version 2023
 =============================================================
 
-Copyright (c) 2010-2022  Qianqian Fang <q.fang at neu.edu>
+Copyright (c) 2010-2023  Qianqian Fang <q.fang at neu.edu>
 
 - Computational Optics & Translational Imaging (COTI) Lab (http://fanglab.org)
 - Department of Bioengineering, Northeastern University
 - 360 Huntington Ave, ISEC 206, Boston, MA 02115, USA
 - Website: http://mcx.space
-- Github: http://github.com/mcextreme/
+- Github: https://github.com/mcx/
 
 =============================================================
 :: Acknowledgement:
@@ -94,6 +94,10 @@ cite the relevant papers in your publications.
 
 === General MC algorithm ===
 
+[Hirvi2023] Hirvi P, Kuutela T, Fang Q, Hannukainen A, Hyvonen N, Nissilä I. Effects of atlas-based anatomy on modelled light transport in the neonatal head. Phys Med Biol. 2023 May 11. doi: 10.1088/1361-6560/acd48c. PMID: 37167982.
+*Summary: RF replay and neonatal brain atlas
+*Download: https://doi.org/10.1088/1361-6560/acd48c
+
 [RaayaiArdakani2022] Matin Raayai Ardakani, Leiming Yu, David R. Kaeli, Qianqian Fang, "Framework for Denoising Monte Carlo Photon Transport Simulations Using Deep Learning," J Biomed Opt. 2022 May;27(8):083019. doi: 10.1117/1.JBO.27.8.083019
 *Summary: DL-based MC denoising
 *Download: https://doi.org/10.1117/1.jbo.27.8.083019