= Change Log =

Major updates are marked with a "*"

== MCX v2021.2 (Glossy Gluon - 1.9), FangQ <q.fang (a) neu.edu> ==

 2021-01-07 [9811c83] reorder the input data layout to match the change in preprocessing
 2020-10-22 [991910e] add function comment and revert unnecessary changes
 2020-10-22 [3343338]*add benchmarks from SVMC paper to mcxlab
 2020-10-19 [de87cbf] resolve code alignment issue
 2020-10-18 [5acd287] fix photon detection issue for SVMC mode (by Shijie Yan)
 2020-10-18 [61dbf63] fix ray-tracing issue after the initial template implementation
 2020-10-17 [fbb4f8c] initial implementation of template for SVMC mode (by Shijie Yan)
 2020-10-08 [dad83c6] resolve conflict between two branches to elimate mismatch in demo_focus_mirror_bc.m
 2020-10-08 [fb61782]*sync master branch into nuvox(SVMC) branch (by Shijie Yan)
 2020-09-20 [75f08c5] remove empty depends
 2020-09-20 [fa98229] fix incorrect dependency
 2020-09-20 [d748d29] add octave package files for mcxlab and mcxtools
 2020-09-16 [cf3b1f0] fix typo, change default exe path
 2020-09-16 [15e9946]*fix warnings found by debian packaging at https://mentors.debian.net/package/mcx/
 2020-09-16 [04bb0e7] add man pages for other binaries
 2020-09-14 [aca9f97] remove additional debian packging warnings
 2020-09-14 [ce4e341] add desktop icon files
 2020-09-14 [eb0aa9f] allow new lines in string values in json
 2020-09-14 [4b1301a] set default exe folder to /usr/libexec, fall back to ~/bin/
 2020-09-14 [643e4a1]*add photon as unified cmd for mcx/mcxcl/mmc,polish for debian packaging
 2020-09-14 [a67bc6d] updates to ease debian packaging
 2020-09-08 [8983305] Inno Installer Setup paths and file details fixed
 2020-09-07 [a6bc5a9] another attempt to fix #105
 2020-09-07 [ca303dd] change default shortcut group name, fix #105
 2020-09-06 [0313d4c] install mcxstudio to 64bit folder, close #105
 2020-09-04 [37b4914] add demo script for mirror bc
 2020-09-04 [e561890] make mcxplotvol work in matlab 2010 or earlier
 2020-09-04 [9518cfa] handle mirror bc correctly, close #104
 2020-09-04 [64896aa]*reset pattern center position following a failed launch, fix #103
 2020-09-02 [5af2e76] fix -geometry 0x0 error, see https://forum.lazarus.freepascal.org/index.php?topic=40593.0
 2020-09-01 [dd4be78] add cubesph60b to match example/benchmark2
 2020-08-30 [971ffac] fix extended ascii letters
 2020-08-29 [6eb9596] update mcxcreate.m, add mcxplotshapes.m to render json shapes
 2020-08-29 [0199dad] clean up code and add comments for SVMC
 2020-08-29 [94d55a7]*add mcxcreate, force mcxlab return one output
 2020-08-28 [d917751] give an error for unsupported single dash option
 2020-08-28 [093c9ba]*add pre-processing for SVMC mode
 2020-08-28 [a79e116] add mode delphi in carbon unit
 2020-08-27 [63e5a5f] handle det radii less than or equal to 0.5, fix #101
 2020-08-27 [8f93ee2] fix make mex link error
 2020-08-26 [65f0fe4] fix issrcfrom0 offset
 2020-08-26 [79f9d70]*multiply voxelsize with det radius
 2020-08-26 [d5c3c11] fix mcxpreview det radis issue, require srcpos and tend in mcxlab
 2020-08-24 [1af5507] avoid error on mac
 2020-08-24 [2fce8e5] add missing carbon unit for mac
 2020-08-24 [6f11857] add command line option cheatsheet
 2020-08-24 [5046de0] fix cmake command
 2020-08-24 [cea663b] test cmake in travis
 2020-08-24 [782b4a3] massive update of documentation
 2020-08-24 [041e386] massive update to README to describe all output formats

== MCX v2020 (Furious Fermion - 1.8), FangQ <q.fang (a) neu.edu> ==

 2020-08-29*[6eb9596] add mcxcreate.m, add mcxplotshapes.m to render json shapes
 2020-08-27 [63e5a5f] handle det radii less than or equal to 0.5, fix #101
 2020-08-24 [6f11857] add command line option cheatsheet
 2020-08-24 [cea663b] test cmake in travis
 2020-08-24 [782b4a3] massive update of documentation
 2020-08-20 [e8e6b58] print an explicit messgae if error 30 is found
 2020-08-19*[883f61b] restore windows progress bar support, disabled in @ae2d60e45
 2020-08-17 [c47de01] allow running testing script on machines without nvidia gpu
 2020-08-16 [0c25958] add more tests for various mcx options
 2020-08-16 [ff2f68f] add sphshell benchmark - see GPU MMC paper
 2020-08-15 [2afab4a] test if media prop count is less than max label
 2020-08-15 [2d71eb7] accept array as Domain.Media json input
 2020-08-15*[433df1f] accept json modifier via --json for easy testing
 2020-08-14 [09adbd0] support --bc or cfg.bc to set an entire bounding face as detector
 2020-08-11*[e095dbb] speed up by 1.6x on 1080Ti by restoring source template for pencil beam only
 2020-08-11 [a220cc2] autoblock size no less than 64, speed up on Turing GPU by doubling threads
 2020-08-04 [71d4196] fix incorrect detpt column when savedetflag/issaveexit are both set
 2020-08-04 [20c596a] retrieve energy tot and abs regardless of isnormalized
 2020-08-03*[30e01a1] add standalone script to submit to mcx speed contest
 2020-07-31 [d9a5953] avoid autoblock is 0 when driver fails, close #99
 2020-07-28 [daa9d56] fix inaccurate core count on Volta, Turing and Pascal
 2020-07-25 [37793ae] fix -b 0 -B rrrrrr crash, thanks to @ShijieYan
 2020-07-22*[f844fe8] add automated building script via travis-ci
 2020-07-22*[cbf0225] add unit testing script
 2020-07-09 [5b038a7] add winget manifest
 2020-07-04*[4bda593] inno windows installer
 2020-07-02 [38529a7] accept -f in mcxshow and mcxviewer
 2020-07-02 [34ecf5f] add glscene directly to the source code
 2020-07-01*[f1828d3] add manpage for mcx
 2020-06-29 [cd4acb8] visual studio project file updated
 2020-06-29 [b22025d] update vs project file
 2020-06-28 [71bedc5] add benchmark options, add jnii/bnii output formats
 2020-05-02 [e7ce8f7] compiles lzma on windows, #94
 2020-05-02*[e56fa2b] add UBJ support, output .bnii files, close #95
 2020-05-01 [ed80ad5] now support lzma and lzip compression
 2020-05-01 [f136bc9] upgrade all built-in binary files to JData formatted JSON files #94
 2020-04-29 [0d9c162] save detected photon data in JSON/JData format, close #94
 2020-04-25 [045a3de] update json schema
 2020-04-25 [e8aae66] initialize gsrcpattern
 2020-04-23*[8086175] add built-in colini27 data,add --dumpjson, add -F jnii output format
 2020-04-19*[da73b8d] add mcx built in benchmarks
 2020-03-21*[b8fb79a] plot data in x/y/z slices,add axis labels and grid
 2020-03-20 [d7e6203] add axis lable and scaling to volume viewer
 2020-03-14*[b91dc5a] update mcxstudio gui to support gpu mmc
 2020-02-18*[8c37911] adding pymcx written by Maxime Baillot as submodule
 2020-02-08 [ba78df5] add template to disable continuous medium support, close #89
 2020-01-28 [b7c1982] speed up cone beam photon launch, fix accuracy, close #86
 2020-01-25*[984b2a0] initial support for hybrid optical properties: tissue type label combined with continous optical properties
 2019-11-19 [1c07b16] scale partial-path when getting det photon time and weight, close #83
 2019-08-08 [0bdbef6] allow to browse file folder on windows
 2019-07-26*[8a341ee] update mcxstudio to add the new flags
 2019-07-23 [e3b53dc] add 2d sample script
 2019-07-22*[c4baa84] output fluence/flux in replay, backport changes from mcxcl
 2019-05-24 [02efc62] bug fix for continuous varying media patch

== MCX v2019.10 (Ether Dome RC2 - 1.5.0), FangQ <q.fang (a) neu.edu> ==

 2019-10-27 [a743b47] resolve compiler complaint: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix]
 2019-09-06 [f9ad72b] fix the incorrect short opt flag for savedetflag
 2019-08-21 [d9d5238] allow one to overwrite SaveDataMask from command line
 2019-08-18 [6023d51] debugged builtin ssh
 2019-08-17 [7f98c48] mcxstudio builtin ssh update
 2019-08-15 [cec9ecf] add missing windows unit
 2019-08-15 [1a84b9e] add runssh in a thread
 2019-08-15 [8cb29c4] add run external command in a thread
 2019-08-15 [997f986]*builtin ssh using synapse
 2019-08-15 [1482b0a]*use new template to speed up with specialization
 2019-08-08 [0bdbef6] allow to browse file folder on windows
 2019-08-03 [e34f9c5] change remote folder path separator
 2019-08-03 [1cab6ce] disable event
 2019-08-02 [f4ab7cf] minor gui updates
 2019-08-02 [e2efbf7] query gpu button status correction
 2019-08-02 [6520c4c] enlarge output window, more plotting scripts, fix outputformat default value
 2019-08-02 [3784d0a]*fix missing dosaveref field, swap incorrect short flag
 2019-08-01 [7ec73b7] make settings scrollable, tested remote execution on windows
 2019-08-01 [3bc5994] fix incorrect BC order
 2019-08-01 [87d0261] add user input to use ssh
 2019-07-30 [e3c0b58] make viewer window on top
 2019-07-30 [3cd64f1] show preview window on top
 2019-07-30 [8c902c9] print for debug
 2019-07-30 [74be22c] allow to load old project files
 2019-07-30 [3af9a1c]*fix a few mac bugs
 2019-07-29 [adb194d] fix rendering dimensions
 2019-07-29 [5fbe79f] print matlab commands for plotting
 2019-07-29 [0158d4d] rename macro from exe to app
 2019-07-29 [3e800c6] add a window to stop simulation
 2019-07-29 [973e83a] use DelimitedText for json storage
 2019-07-28 [a760432] enable manual path settings
 2019-07-28 [5c71f34] minor polishing of the gui
 2019-07-27 [39e54fb] change color
 2019-07-27 [cb747d3] minor update from windows
 2019-07-27 [99e697a] add config unit
 2019-07-27 [55a6b8c] add windows unit to compile
 2019-07-26 [8a341ee]*update mcxstudio to add the new flags
 2019-07-26 [f3a3345]*do not print progress bar by default, still causing hanging on certain gpu
 2019-07-25 [74414b3] print progress bar by default
 2019-07-25 [289b40b] update demo script to use the new detphoton format
 2019-07-25 [334d0a2]*accept struct-based detphotons input, #76
 2019-07-25 [5f1d965] print normalization factor in single-det replay for debugging, #76
 2019-07-25 [0142557]*allow to run replay without giving the 2nd output, #76
 2019-07-24 [337c54e] fix wrong pattern number index for single pattern illumination
 2019-07-23 [e3b53dc]*add 2d sample script
 2019-07-22 [c4baa84] output fluence/flux in replay, backport changes from mcxcl
 2019-07-15 [80357fc] remove volumetric mua input in the basic example
 2019-06-25 [4985db6] fix incorrect indexing, #73
 2019-06-24 [d3f3922]*additional changes due to flexible savedetflag detected photon data format, fix #73
 2019-06-20 [4ac001f] fix incorrect detphoton data buffer indexing, fix #73
 2019-05-25 [2b907e2] fix the unitinmm scaling for single/double FP mua/mus
 2019-05-24 [71571e6]*fix half compilation error
 2019-05-24 [33df8bf] fix the missing unitinmm scaling when input is float mua/mus, half2 input still not working
 2019-05-24 [071262b]*allow to update n in continuous media
 2019-05-24 [02efc62]*bug fix for continuous varying media patch
 2019-05-23 [e1b50b6]*convert all volume formats between mcxlab and mcx, fix #67
 2019-05-22 [711bf81]*allow cuda 9/10 to compile mcx
 2019-05-19 [72afd6a] get rid of json editor validation errors
 2019-05-17 [e92d91c] avoid using string class to keep backward compatibility

== MCX v2019.4 (Ether Dome RC1 - 1.4.9), FangQ <q.fang (a) neu.edu> ==

 2019-04-22 [5e0f0c5] add title to mcxplotvol window
 2019-04-15 [a8fa3f5]*combining partial path on the surface
 2019-04-14 [dc5ec7c] assign -K for --mediabyte
 2019-04-14 [357ef7c] add help info for continuous media, accept string input, sanity check
 2019-04-13 [ac10b73]*supports continuously varying media - mua/mus can vary in every voxel
 2019-04-13 [03228c8] add moredouble target
 2019-04-11 [7e31145] compile to dynamic lib, add function to enable library calls
 2019-04-11 [1c2f2e6] add help info in mcx and mcxlab on savedetflag
 2019-04-10 [ada0b8e]*support -w / --savedetflag to specify which det photon data to output
 2019-03-29 [825537c] fix print information for multiptle patterns when cfg.isnormalized==0
 2019-03-28 [43b377a] update json2mcx, add colin27 for mcxlab
 2019-03-28 [b9a053f]*add json2mcx, converting from json file to mcxlab cfg
 2019-03-23 [f71fd39] add the missing verbose flag --workload, although -W was working
 2019-03-20 [3cdfc54] fix empty string test
 2019-03-20 [6b19d01] mcxstudio: merge output window back to main; update infinite slab sample
 2019-03-19 [ac76ff7]*fix cyclic bc, add mcxlab demo

== MCX v2019.3 (Ether Dome beta - 1.4.8), FangQ <q.fang (a) neu.edu> ==
 2019-03-03 [a3462be] add README files for all new benchmarks, add "What's New" in master README
 2019-03-02 [69a7375] use ANSI colors in the output to improve readability
 2019-02-28 [123d11d] add USC 19.5 atlas example, Fig9a in TranYan2019(submitted)
 2019-02-28 [ccdf8e3]*add digimouse example
 2019-02-28 [e36efa0]*add colin27 atlas example using latest v3 segmentation, Fig6 in Fang2009
 2019-02-28 [ae2d60e] fix progress bar error in newer nvidia drivers
 2019-02-27 [6e84e26] fix mcxlab srcpattern input format bug, update mcxlab help info
 2019-02-26 [f1418cd] fix index mismatch between mcx_replay_prep and mcx detphotons output
 2019-02-23 [ae9443f]*copy detected photon post-processing scripts from mmc to mcx
 2019-02-23 [19e88b0] add function to convert fluence and energy deposition
 2019-02-22 [8644714] use USE_MORE_DOUBLE macro to enable additional double precision calls
 2019-02-22 [005ca00] disable linking with iomp5 to avoid matlab2016/2017 crashes
 2019-02-22 [f7be969]*use nan as srcdir.w, i.e. focal length, for isotropic launch
 2019-02-20 [ce1abbe] use double precision for data output,alternative to #41, for sm_60
 2019-02-20 [c647f18] support integer data rendering, support multiple windows
 2019-02-17 [3a3e72d]*mcx volume renderer is now integrated with mcxstudio
 2019-02-16 [70226e6] support output tx3 3D texture file
 2019-02-16 [b968133] add line, slit and cone sources in mcxrender, close #36
 2019-01-18 [335c9a0] fix mcxlab crash due to racing in multi-thread, close #60
 2019-01-10 [b8db72b] add photon's exiting position in the trajectory data
 2018-12-22 [2f8483b] fix mcxlab 'gpuinfo' output error for multiple GPUs
 2018-12-08 [3c8a9c3]*add gpu anlm filter as submodule, detailed in Yao2018 paper
 2018-12-03 [dc594dc]*initial implementation of "photon sharing" - one forward/replay for many patterns, presented in PW2019
 2018-12-02 [da93f29] fix a shared memory buffer length error, introduced in 9a631d15
 2018-11-24 [5e212a6]*setting separate boundary conditions at 6 boundary facets
 2018-11-24 [e6d4932] use char array for boundary condition input in mcxlab
 2018-11-23 [817609e] test if parameter has been initialized in command line
 2018-11-23 [9a631d1] offloading photonseed to sharedmem,move v back to register
 2018-11-23 [e478c37] only use the sign bit to decide detector coverage, like in the old days
 2018-11-14 [405ce9c]*add benchmark from mcxyz skinvessel example
 2018-11-13 [9a2f696] test if gpuid is 0 to avoid mcxlab crashing
 2018-11-12 [3a05df8] fix shared memory allocation size bug
 2018-11-07 [5339563] add help info for the new detphoton fields
 2018-11-07 [7e45ec0]*save initial weight and partial scattering count to match mmc output
 2018-11-07 [01ec192]*isotropic launch if srcdir(4) is -0.f, valid for all src
 2018-10-26 [183742d]*set g to 1 when mus is 0, fix #51
 2018-10-22 [0721ab4] change NULL pointer test order in reading srcpattern
 2018-10-21 [f37e0e2] prepare for nonuniform grid support
 2018-10-13 [cfa8e31]*accummulate momemtum transfer for all detected photons in replay mode
 2018-09-24 [d3df9b2] update Ruoyang Replay paper citation
 2018-09-02 [4d49f3b] add mcxstudio and mcxlab-octave deb packages
 2018-09-01 [75b3f7c]*add nightly build script to help people build mcx
 2018-08-29 [ecd4053] change deb package folder structure, handcode 1.0 keywords
 2018-08-26 [8c86b3e]*add cmake-styled makefile
 2018-08-26 [79a47bf]*remove outdated examples and flags, simplify Makefile for a clean start
 2018-08-20 [e3bb0e8] add README for mcxstudio

== MCX v2018 (Dark Matter - 1.0 Final), FangQ <q.fang (a) neu.edu> ==

 2018-08-18 [	    ] MCX 1.0 (v2018) is fully baked! create release packages
 2018-08-18 [ed0612e] add Yu2018 citation, minor gui update
 2018-08-17 [eb9a2e6] fix momentum transfer saving bug, need to clear buffer for each new photon
 2018-08-17 [b11dae9] add help menu with papers and web resources
 2018-08-15 [13ab6f2] add more demo script for mc data processing showcase
 2018-08-14 [1e3eaa9] fix a bug in 2D simulations
 2018-08-14 [e99e5ef] allow saving photon trajectory in command line, add plotting function, bump limit to 1e7
 2018-07-21 [7850c32]*support photon numbers over 2^31, new limit 2^63-1 after fixing #41
 2018-07-20 [db5a349]*use extra global memory to help reduce roundoff error, fix #41
 2018-07-02 [8aba23b] fix a regression introduced in 29ea426, fix #40
 2018-06-04 [d9bdb33] fix incorrect column number when momentum transfer is recorded
 2018-06-04 [cf81b30] read RNGSeed field from the JSON file
 2018-06-04 [8cd8a69] support autopilot flag in JSON, fix typo
 2018-06-04 [c90b8b3] add specular reflection flag, passing more session flags via the JSON file
 2018-06-04 [3e5a1d8]*add mcxlab cfg to json input file converter
 2018-05-19 [d28c36e] use load_nii compatible output, make sure nii is read-only
 2018-05-19 [78ee1ec]*add built-in loadnii support
 2018-05-19 [1854eee] fix normalization bug in replayall mode
 2018-05-19 [7f1b574]*positive respin now means repeat-to run more than 2e9 photons; negative respin means divide
 2018-05-15 [a7632bc] fix bugs in checking replaydet values
 2018-05-15 [e5db8cd] output 5-dim fluence when replaydet=-1,two replay test script,add help for replaydet
 2018-05-14 [651c53f]*replay for all detectors with -Y -1
 2018-05-03 [91765e1] fix issue #38, revert the regression introduced in commit 95b43708
 2018-05-03 [6743d25] partially fixing issue #38
 2018-04-07 [b537309]*complete momentum transfer feature, adapt Stefan's generate_g1 with the new output struct
 2018-04-07 [63bce2b] initial port of mmc momentum transfer calculations for DCS
 2018-04-07 [acef0cf] GUI update on high-res displays
 2018-04-02 [6ea1171] set default output format to mc2 again
 2018-03-31 [4884ab1] make mcxstudio work for mmc
 2018-03-30 [8af5a37] disable button event on the mac
 2018-03-30 [dbbe943] prevent double execution
 2018-03-29 [cbaaed7] fix double execution when clicking Run
 2018-03-29 [ac6c972] make mcxlab to call mcxcl without error
 2018-03-29 [b42b51b] fix dumpmask not working on mcxcl bug
 2018-03-27 [13fd3f8] fix mac remote execution path
 2018-03-27 [4b3af81] fix mac run cmd path bug
 2018-03-27 [053c9b1] replace ssh with scp;debug search path on mac
 2018-03-27 [ccccab8] fix mac run issue
 2018-03-27 [1d1242b] allow both plink and sshpass to download files
 2018-03-26 [9b5c010] set default path for mac to home dir
 2018-03-26 [07de76e] replace ssh to scp in sshpass remote file download
 2018-03-25 [1566fb0] fix typo after replacement
 2018-03-25 [b90a66d] do not print password, add matlab path
 2018-03-25 [5d1e4ac] use parameter and executable to define command line
 2018-03-25 [c7c1445] add longer delay in matlab launching
 2018-03-25 [b2a1152] use TProcess for Mac for execution and matlab
 2018-03-25 [e08f041] use TProcess on mac to call external commands
 2018-03-25 [c633d87] give an error if the executable is not found
 2018-03-23 [4766639] use home dir to write output on mac
 2018-03-22 [5c64bfa] fix default matlab path; fix search path for mac
 2018-03-22 [9844842] fix minor bugs in mcxplotvol
 2018-03-21 [2864522] enable src editor for mcxcl
 2018-03-21 [cb6c185] update atomic flag
 2018-03-21 [9769f8a] move help info from title to a help button
 2018-03-21 [cb2fa99] update mcxstudio folder structure
 2018-03-21 [6a17a9c] change default mcxsuite folder structure
 2018-03-17 [5b083b4]*make mcxlab compatible with mcxlabcl to call opencl
 2018-03-12 [1014527] fix crash due to incorrect column number
 2018-03-12 [f5bf5b8] make mcxstudio compile on windows
 2018-03-11 [74723b1] add ID column for media and detector, addpath to matlab
 2018-03-11 [74b2d57] fix #32: unknown verbose option --root bug
 2018-03-11 [a0d445b] fix Windows low quality host RNG due to 15bit rand(), fix #31
 2018-03-09 [521fb85] compile on lazarus 1.8.2 with glscene svn 7114
 2018-03-09 [f29aa12] enable GUI scaling for high dpi displays
 2018-03-09 [e38bcab] remove memory leak in domain window
 2018-03-02 [5a43a1d] avoid casting double in xor and xoro RNGs
 2018-03-02 [1624105] change default RNG to xoroshiro128+, about 5% faster
 2018-02-28 [ae22a57] make posix RNG work again
 2018-02-28 [a78999d] output trajectory photon id in interger format
 2018-02-19 [779b27e] avoid out-of-bound error when saving diffuse reflectance
 2018-02-09 [95b4370] fix diffuse reflectance bug - must be performed after boundary reflection
 2018-02-09 [d719e78] mcxstudio update
 2018-01-31 [f90ee6e] support 3d pattern source in mcxstudio, automatic increase media count
 2018-01-31 [589ce45] support 3D pattern with type 'pattern3d'
 2018-01-29 [1b9493b]*add mcxpreview to preview the simulation domain settings
 2018-01-28 [5f748de] fix crash when saving diffuse reflectance
 2018-01-26 [6b55b4b] fix bug to properly scale Jacobian output with voxel size
 2018-01-24 [de1b62f] mcxstudio - render disk and planar source types
 2018-01-24 [f587194] mcxstudio - add mcxrender window to preview domain shapes
 2018-01-24 [b113840] mcxstudio - support displaying source and detectors
 2018-01-16 [6b34910]*mcxstudio - add shape visualization utility
 2018-01-13 [f6fd6a0]*rename mcxlab.mex to mcx.mex, use mcxlab.m to do pre and post processing
 2018-01-11 [ae8bd9a]*fix bug related to absorption fraction changed after fixing 1st scattering handling in #4b33a6f
 2017-12-31 [7e6e081]*add doxygen-format comments for thorough documtation of the source code
 2017-12-28 [57ccb84] allow saving large data files using 64bit size_t for buffer length
 2017-12-02 [b98d728] matlab fails to clear mex variable memory, force setting to NULL
 2017-11-29 [3e25d2d] revert to the old way of finding detector id, new approach gives partially detected optodes
 2017-11-22 [2267ad7] need to round half coordinates before calling nextafter
 2017-11-18 [14bb584]*half precision ray tracer support
 2017-10-30 [9958e32] simplify htime update in hitgrid
 2017-10-26 [4b33a6f] fix 2 bugs: condition for initial scattering, and v.nscat due to focal length input
 2017-10-05 [7703420] port mmc commit 07b33f3 to mcx to compile with matlab 2017
 2017-10-05 [c7895a6] change dir vector to transmission direction before terminating a photon
 2017-10-04 [ac6fa0e] print a message before exit when det mask is dumped
 2017-08-20 [56edc0d] mcxstudio - update app bundle icon
 2017-08-20 [dff89ab]*mcxstudio - mac osx app bundle for mcxstudio
 2017-08-10 [2fe8029]*apply mirror boundary condition when background n is less than 1
 2017-08-07 [53b13e5] mcxstudio - use matlab even in the desktop mode
 2017-08-04 [1bb1b26] avoid calling directory instead of executable under linux
 2017-08-03 [4779504] avoid output window no show on low-res displays
 2017-08-03 [85ee081] avoid output window no show
 2017-08-03 [485ca67] plot using matlab on windows
 2017-08-01 [275ff8c] mcxstudio - search mcx_core.cl dynamically
 2017-07-30 [2371eab] mcxstudio - tested with mcxcl
 2017-07-30 [eac9717] avoid windows compilation warnings from VS
 2017-07-30 [bd61e4f] mcxstudio - update database when config changes,add link to tutorials,accept enter in windows
 2017-07-30 [658906d] mcxstudio - display total frame count in mcxplotvol
 2017-07-27 [08014e3] mcxstudio - support multiple time gates in mcxplotvol
 2017-07-26 [85d6fa1] mcxstudio use mc2 as default output
 2017-07-26 [6d25ddb] mcxstudio - download output files using pscp and scp, help context to online documentation
 2017-07-25 [2ed5363] mcxstudio - add context help file for mcxstudio, support matlab for plotting
 2017-07-25 [0decc1c] dump mask independent of photon detection
 2017-07-25 [3929c80] fix volume mask saving bug
 2017-07-25 [44dcfb3] mcxstudio - add plotting functions for mcx
 2017-07-25 [7cb2015] mcxstudio - add help database and viewer, save user input history
 2017-07-24 [9819eda] mcxstudio - add plotting feature using octave
 2017-07-22 [71bbc40] make mkpath windows friendly
 2017-07-21 [60c971b] mcxstudio command line quotation,remote execution, user input
 2017-07-21 [0503732] recursively create output folder if does not exist
 2017-07-20 [6e839ef] handle progress bar for matlab 2014b or newer as the return value is now object
 2017-07-20 [eed619f] fix matlab2017a crash when using multiple GPUs
 2017-07-20 [b4a37d2] avoid windows compilation error due to mkdir and stat
 2017-07-16 [8d1d9cd] mcxstudio - add remote exec tab,correct save data dialog,define current session icons,renaming conflict check,oneditdone to update
 2017-07-15 [0fae21a] avoid static TLS error in matlab by linking with libiomp5 instead of libgomp, like mmc commit [10c8a27]
 2017-07-15 [d4f2ae1] fix mcxlab for octave crash due to an octave bug #48678
 2017-07-14 [a97e9c5] mcxstudio - fix remote cmd changing bug
 2017-07-14 [7752896] mcxstudio - add middle docking site
 2017-07-14 [2845d7e]*make true remote execution possible by passing json input via -f
 2017-07-14 [2012c0a] Merge branch 'master' of https://github.com/fangq/mcx
 2017-07-14 [35cfcec] mcxstudio - windows browse work folder,search remote command path,robust cmd output capture
 2017-07-14 [3081762] mcxstudio - support inline json input with -f, create root folder if --root is given
 2017-07-13 [21ef382] mcxstudio - lock GPU
 2017-07-13 [e71659d] mcxstudio - make output window dockable, lock GPU list when use ssh
 2017-07-11 [c08a29a] fix mcxstudio GPU name crop bug, fix window drag problem, make media/detector editor autoaddrow
 2017-07-09 [c672643]*use int to represent det and media index; increase max media + max det from 128+1024 to 4000, close #21
 2017-07-08 [bf9aa22]*mcx now supports 2D simulations, just set one dimension to a thickness of 1
 2017-07-05 [dd1026c] mcxstudio - fix source editor bug
 2017-07-05 [d1186aa]*successfully built RPM

== MCX v2017.7 (Dark Matter - 1.0-RC2), FangQ <q.fang (a) neu.edu> ==

 2017-07-05 [6144ee4] fix windows progress bar issue
 2017-07-05 [1319828] windows registry fix, fix memory leak, associate .mcxp, use messagedlg, fix VerifyInput bug
 2017-07-04 [71fa54a]*add RPM and DEB packaging scripts, add root-level makefile
 2017-07-03 [3406ea8] fix memory leak caused by the shape JSON editor, mmc compatible, progress bar fixed
 2017-07-02 [       ] automatically build mcxstudio and include the binary in the mcx nightly build
 2017-06-30 [ff5e25f] fix shape editor deletion handling, collapsible groupbox, allow remote execution
 2017-06-30 [139b50d]*unified GUI for mcx, mmc and mcxcl, ligher source designer
 2017-06-29 [1d0f883] initialize tty info to avoid uninitialized values
 2017-06-28 [950f96b]*much improved mcxstudio: simulation designer,volume designer,more options,copy and paste sessions
 2017-06-26 [9606e95] save mc2 file under rootpath if --root is defined
 2017-06-25 [1b7271d] shape editor, json input editor for advanced options, form scaling for high DPI displays
 2017-06-21 [325aa35] update of the GUI, more robust mcx execution, colored output, simulation designer
 2017-06-20 [faad1a1] user specified scattering events to disable anisotropy g
 2017-06-06 [5f42259] fix a bug when using verbose only flags
 2017-05-29 [adddbc5] support pencil beam array
 2017-05-28 [4ef73e1] use environment variable CUDA_PATH on windows
 2017-05-28 [cc22461] add registry key fix for windows
 2017-05-27 [cfe280b] fix matlab crash when using multiple GPUs
 2017-04-10 [b5170e4] fix windows compilation bug for Pascal cards


== MCX v2017.3 (Dark Matter - 1.0-RC1), FangQ <q.fang (a) neu.edu> ==

 2017-01-16 [d5a2cbe] prevent progress bar from stalling
 2017-01-02 [0a28d4e] fix compilation error on windows
 2016-12-21 [63e5e23] fix voxel [0 0 0] is always zero bug, regression since v2016.4
 2016-12-21 [1848321] refresh matlab window when running mcx
 2016-12-21 [8715a40]*fix progress bar in matlab when set debuglevel=P
 2016-12-21 [b53d8ac] avoid hanging in mcxlab when mus=0
 2016-12-11 [c93be5b] fix nan error when scattering coeff is 0
 2016-11-11 [024542c] fix replay bug due to f->ndone initial value as -1
 2016-11-05 [758b8b5]*enable autobuild in both windows and linux
 2016-11-05 [dac3cd0] autobuild for windows
 2016-10-20 [1f5d0ef] fix Jacobian output normalization
 2016-10-13 [84462a3] correct WP replay scaling factor
 2016-10-13 [16ab1c9] normalize scattering count based on total replay weight
 2016-10-12 [df62a0d] removing divergence inside hitgrid, thanks to njuffa
 2016-10-09 [5905e0b]*record diffuse reflectance on the air voxels outside of domain boundaries, close #6
 2016-10-09 [39038bf]*save detected photon position and direction using -x 1, close #16
 2016-10-08 [e8b21b8]*port diverging and converging widefield source beams from MMC to MCX, close #27
 2016-10-05 [ceb6009] fixing mcxlab crash when detps is not given in the replay mode
 2016-10-04 [ead4794] fix Gaussian beam waist radius scaling issue, close #25
 2016-10-03 [42866fa] fix two regressions for replay, returning scattering count in replay
 2016-09-14 [9d70a56] fix memory out-of-bound bug in replay
 2016-09-11 [a6792e7] fix usleep warning
 2016-09-09 [6393a45] save scattering event count in replay
 2016-08-25 [78acd39]*compiling mcx on windows
 2016-08-24 [f19e3d4] update core count for GP104
 2016-08-22 [1c21212] fix core count in Pascal
 2016-08-18 [55e917c] use c++ template to avoid branching in launchnewphoton - by Gustavo Maia and Fanny Paravecino
 2016-08-11 [5da5466] remove -code flags to create arch independent binaries, it also produces faster binaries with cuda 7.5
 2016-07-24 [dbbc4c6]*support Russian roulette
 2016-07-22 [542223d]*compiling mcxlab mex file for Pascal
 2016-07-22 [88441c6] support Pascal
 2016-07-02 [9b5ee49]*elegantly terminate mcxlab when an exception is raised
 2016-07-02 [382aab1] ignore user specified nonexistent devices in workload calculations - bug reported by Nicholas Dana
 2016-07-02 [2b98d3e]*add progress bar when user specify -D P
 2016-06-05 [6a6fe13]*update makefile for autobuild, correct mcxlab RNG seed length
 2016-06-02 [83481ff] add replay demo script
 2016-06-02 [2aed76d] fix replay seed bug for mcxlab
 2016-05-16 [701beec] make mcx gpu contest compatible with octave
 2016-05-16*[a4cb1e1] add debug option to save photon trajectory data
 2016-04-26 [590c596] fix workload and gpuid bug when handeling 0 mask
 2016-04-23 [4c37c0d] test gpu contest script in matlab 2014
 2016-04-22 [bc56e86] make static target on Linux and Mac
 2016-04-22 [f5342f0] update Linux static target command, make total photon number accurate
 2016-04-22*[690406c] fix multi-GPU hanging problem for real, wrap all CUDA calls with error testing, return workload in mcxlab


== MCX v2016.4 (Dark Matter - 1.0-beta), FangQ <q.fang (a) neu.edu> ==

 2016-04-21 [release] finalize and release v2016.04
 2016-04-21*[2b1f22a] add Visual Studio 2013 Nsight project for easy compilation on windows
 2016-04-19 [3b69a1a] fix thread hanging bug when running on multiple GPUs
 2016-04-15*[e71f4c7] kick-off "MCX GPU Contest" for user-contributed hardware benchmarking
 2016-04-06 [c52b470] fix photon detection bug, fix json file crash, fix workload distribution bug, fix hitgrid inf handeling, fix energytot bug
 2016-04-05*[e94087f] add benchmark folder, announce "MCX Speed Challenge"
 2016-03-28 [76f9c5a] reduce memory dependency, yielded a 42% increase in mcx speed for the quicktest benchmark
 2016-03-26*[b14ccf1] simplify RNG interface, two new RNGs: POSIX erand48 and xorshift128+, retiring MT RNG
 2016-02-28 [29ea426] speed up ray tracer with customized nextafterf function and reciprocal of c
 2015-11-09 [1491f4e] Determining block size in autopilot mode using max block per SMX, by Fanny Nina Paravecino
 2015-11-08 [48dfb33] fix refractive index mismatch transmission bug
 2015-09-28*[73dd850] add uniform line source and slit source, suggested by Yu Chen
 2015-09-12 [9da817e] fix bug for wide field sources
 2015-09-11*[c7f9625] make precise ray-tracing default to improve accuracy
 2015-09-11 [a1e781a] update affiliation, Qianqian now moved to Northeastern
 2015-07-12 [3898b14] add nsight project files
 2015-07-27 [cd8f134] use proper epsilon for float roundoff tests
 2015-06-25 [6815577] fix address alignment error for CUDA 6 or higher
 2015-06-25*[60238c4] multiple GPU support!
 2015-06-25*[60238c4] set atomic as default, single binary now contains all features
 2015-06-15 [97cd3e9] return gpu info for better interfacing with matlab
 2015-06-10*[7487e4d] support saving photon seeds and replay
 2015-06-10 [3c8a116] accept endianness input
 2015-05-01 [funding] NIH/NIGMS R01 funding support starts

== MCX 0.9.7-2 (Dark Matter - alpha update 2), FangQ <fangq (a) nmr.mgh.harvard.edu> ==

 2014-09-23 [r325] fix submillimeter voxel scaling bug in the binary mode; fix total simulated photon count
 2014-07-11 [r324] a patch submitted by David Gasperino for rigirously modeling a collimated Gaussian beam
 2014-07-11 [r323] high priority bug fixes submitted by Kim Shultz: transmission angle and oddphoton handling
 2014-01-19 [r322] saving detected photon seed for fast replay and pMC analysis

== MCX 0.9.7-1 (Dark Matter - alpha update 1), FangQ <fangq (a) nmr.mgh.harvard.edu> ==

 2013-10-22 [r320] fix isotropic scattering bug at g=0, a critical bug fix

== MCX 0.9.7 (Dark Matter - alpha), FangQ <fangq (a) nmr.mgh.harvard.edu> ==

 2013-09-16 [r306] MCXLAB srctype demo script
 2013-09-15*[r305-308] wide-field source support, including 9 source types
 2013-09-11 [r305] random number generator performance optimization
 2013-08-29 [r304] loadmch supports the seed data from the latest MMC simulations
 2013-02-11 [r300-302] fix double correction for unitinmm

== MCX 0.8.0 (Charm Quarks - final), FangQ <fangq (a) nmr.mgh.harvard.edu> ==

 2012-08-24 [r297] merge all variants into a single binary for Fermi cards (make fermi)
 2012-08-21 [r296] fix Bug/0005, incorrect returned field and normalization for multiple gate groups (reported by Vivian Pera)
 2012-08-21 [r295] fix Bug/0004. incorrect detected photon buffer pointer in MCXLAB with respin>1 (Vivian Pera)
 2012-08-08 [r291-294] fix Bug/0001, forward scattering bias with automatic reseeding of the RNG (Matt Adams,Okito Yamashita)
 2012-08-08 [r290] backport features from MMCLAB: exception handling and print inside matlab
 2012-07-25 [r287] fix Bug/0002-2, conflict between savedet and share memory cache (Okito Yamashita)
 2012-07-21 [r286] change default MAX_DETECTORS from 256 t0 1024
 2012-07-13 [r282] fix Bug/0002. use srcfrom0 flag to set crop0 and crop1 in mcx_cached (Okito Yamashita)
 2012-07-06 [r280] calculate exact exit point when savedet is true (suggested by Audrey Steever)
 2012-07-04 [r276] fix MP core count bug (patch by Suresh Paidi)

== MCX 0.7.9 (Charm Quarks - beta), FangQ <fangq (a) nmr.mgh.harvard.edu> ==

 2012-01-10 fix a regression introduced in 0.5.3 for accurate exit positions
 2012-01-08 support 3D shape input and and run-time rasterization
 2012-01-07 port JSON-formatted input file support from MMC to MCX

== MCX 0.5.3 (Black Hole - update 3), FangQ <fangq (a) nmr.mgh.harvard.edu> ==

 2012-01-07 fix a minor bug which fails using -1 with -E
 2011-12-21 fix an issue causing forward scattering bias (reported by David Giraud)

== MCX 0.5.2 (Black Hole - update 2), FangQ <fangq (a) nmr.mgh.harvard.edu> ==

 2011-09-21 fix a regression in MCXLAB related to detectors, use exact exit position for radius test
 2011-09-20 add verbose warnings for launch-time-out error and non-surface detectors
 2011-09-19 users can specify srcfrom0 (origin setting) from the input file
 2011-09-19 fix a bug in detector-to-volume mapping, effects all non-integer inputs

== MCX 0.5.1 (Black Hole - update 1), FangQ <fangq (a) nmr.mgh.harvard.edu> ==

 2011-05-03 use the expected absorption for normalization to reduce non-atomic impact
 2011-04-26 fix a serious shared-mem buffer length bug (can cause crash)
 2011-04-26 MCXLAB now accepts crop0/crop1 fields to specify shared-mem region
 2011-03-25 new GPU-ocelot compilation flag

== MCX 0.5.0 (Black Hole), FangQ <fangq (a) nmr.mgh.harvard.edu> ==

 2011-03-18 update documents, get ready to release 0.5.0
 2011-03-18 gracefully handle exceptions in MCXLAB
 2011-03-17 add validation scripts for MCXLAB/MCX, fix a bug for saving flux
 2011-03-16 add MCXLAB example scripts
 2011-03-15 extensive debugging with the --unitinmm flag
 2011-03-09 MCXLAB now returns flux and detected photon in Matlab and Octave
 2011-03-03 add -E to seed RNG from command line
 2010-12-28 use negative -R to enable cachebox defined in the input file, fix time wraping
 2010-08-08 debug make mex option for Linux
 2010-08-09 first import of MCXLAB - MCX for Matlab and Octave
 2010-08-08 debug and test --unitinmm flag
 2010-08-05 initial support for reflection at internal boundaries
 2010-08-05 estimate maxgate when using the autopilot mode
 2010-08-02 fix a bug when saving multiple blocks of mch

== MCX 0.4.9 (Black Hole-beta), FangQ <fangq (a) nmr.mgh.harvard.edu> ==

 2010-08-01 update documentation and release v0.5 beta (aka 0.4.9)
 2010-08-01 fix a critical bug for pre-Fermi cards,validated MCX on CC11,13,20
 2010-07-31 enable -n for photon number, disable -m, report simulation speed
 2010-07-30 fix a bug when reading medium index with detector mask
 2010-07-29 use atomic with shared memory cache to improve accuracy near the source
 2010-07-28 add example for validation of MCX in heterogeneous media
 2010-07-28 use RNG for transmission/reflection test
 2010-07-28 use column major as the internal array format
 2010-07-27 support saving detected photons, but got 25% slower
 2010-07-15 users can use -u to specify voxel edge length in mm
 2010-07-12 fix a bug for indexing error in large volumes
 2010-07-09 fix a bug when appending data for multiple time gate groups
 2010-06-26 use constant memory to pass kernel param, more error info
 2010-06-26 use meaningful struct in the kernel to improve readability
 2010-05-14 allow to select which GPU to use with the -G option
 2010-02-04 fix a minor NaN bug detected by GPU Ocelot
 2010-01-26 add GPU Ocelot makefile for multicore CPU

== MCX 0.2 (Aurora), FangQ <fangq (a) nmr.mgh.harvard.edu> ==

 2009-12-19 polish documentation, add svn keywords and tagged 0.2 final
 2009-12-10 MCX Studio GUI is tested on Linux, Windows, Mac OS X
 2009-12-03 add README.txt file for each example folder
 2009-12-02 complete "bubble" mode to reduce impact from non-atomic write
 2009-10-24 use cuda event timer, use VC compiler for Windows
 2009-10-21 paper published online, added windows support
 2009-10-20 set license to GPLv3, first public release (v0.2 beta)
 2009-10-19 fixed double-precision warning for CUDA 2.3
 2009-10-06 more GUI developments
 2009-09-25 fixed memory leakage, supported verbose options
 2009-09-24 major code clean-up, added GPUDEBUG macro
 2009-07-31 tested on GTX295 with CUDA 2.3
 2009-07-15 used atomicFloatAdd for atomic memory write
 2009-07-13 fixed half-grid shift bug in the validation script
 2009-07-08 reflection for a maximum of 3 interfaces
 2009-06-26 tested non-atomic write racing condition
 2009-05-19 added mcx studio: a GUI for mcx
 2009-05-07 query GPU info
 2009-05-05 added options to print to a log file
 2009-04-30 code clean up and paper submission, tag 0.1.9 (Aurora alpha)
 2009-04-26 new and more robust boundary reflection code
 2009-04-24 build-in fluence normalization (unitary solution)
 2009-04-20 added examples and validation scripts, supported respins
 2009-04-07 energy conservation for normalization of the solution
 2009-04-03 time gating support
 2009-04-01 split the main function to units, add utils. and config file
 2009-03-02 added logistic-map based random number generator
 2009-02-27 early support of boundary reflection
 2009-02-24 MT rand now working fine
 2009-02-21 added MT random number generator initial version
 2009-02-20 translated to Brook+
 2009-02-15 translated to CUDA
 2009-02-14 initial version written in BrookGPU
