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  MCX Studio - A graphical user interface for MCX, MMC and MCX-CL
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Author:  Qianqian Fang <q.fang at neu.edu>
License: GNU General Public License version 3 (GPLv3)
Version: 1.0 (v2023)
Website: http://mcx.space

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Table of Content:

<toc>

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== # Introduction ==

MCXStudio is a light-weight graphical user interface (GUI) for MCX, MMC and MCX-CL. 
It gives user an intuitive environment to browse and set parameters for a wide range
of simulations. It also provides functionalities to save, edit and reopen a set of
pre-defined simulations and share among users.

MCXStudio is written in Object Pascal using the open-source Lazarus 
(https://www.lazarus-ide.org/) rapid application development (RAD) 
environment and LCL (Lazarus component library). The OpenGL rendering 
of the GUI is provided by the GLScene Library (http://glscene.org).

MCXStudio is cross-platform and can run on Windows, Linux and Mac OS.
The GUI itself does not contain any Monte Carlo (MC) modeling capability. Instead,
it serves as a shell within which one can launch MC simulations by calling
externally compiled mcx, mmc and mcxcl binaries. 

MCXStudio contains many features that are designed to ease the pre-processing,
simulation and post-processing for MC simulations. It is compatible
with mcx (NVIDIA GPU), mmc (CPU) and mcxcl (cross-vendor CPUs/GPUs). It has a built-in
domain designer, source designer with a convenient panel for media/detector settings. 
It also supports visualization of simulation output data (mc2, nii, hdr/img) using
the built-in 3D volumetric data renderer. One can also launch remote MCX/MMC 
simulations using the Remote Execution panel.

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== # Installation ==

MCXStudio is portable and can be directly executed without installation.
However, in order for MCXStudio to find mcx/mmc/mcxcl binaries, you should use
one of the following methods

# place mcx/mmc/mcxcl executables side-by-side with the mcxstudio executable
# modify system environment variable and add the full paths to mcx/mmc/mcxcl to the PATH variable
# create a MCXSuite/ subfolder in the same directory storing mcxstudio, and \
extract mcx/mmc/mcxcl binary packags inside MCXSuite/ folder, so that one has \
the following folder structure


 MCXStudio/
  |-  MCXSuite/
  |      |- mcx/bin/mcx
  |      |- mcxcl/bin/mcxcl
  |      |- mmc/bin/mmc
  |-  mcxstudio
  |-  mcxshow
  |-  mcxviewer


If you download and unzip the released MCXStudio package, the
above folder structure already exists, and you can simply double click on the 
mcxstudio executable to start the program.

For windows users, the first time to start MCXStudio, you may see a popup window
asking you that your system registry needs to be modified in order for MCX/MCXCL
to run more than 5 seconds. You must click "yes" and then reboot the computer in 
order for this setting to be effective. 

If you click yes and receive a permission error, you have to first quit MCXStudio, 
and then right-click on the mcxstudio executable and select "Run as administrator", 
then accept the prompt.

Alternatively, one should open file browser, navigate into mcx/setup/win64 folder,
and right-click on the "apply_timeout_registry_fix.bat" file and select 
"Run as Administrator".

'''You must reboot your computer for this change to be effective!'''

For Mac users, when double-clicking on the mcxstudio application icon,
if you see a popup window warning "This application 'mcxstudio' can't be opened",
you must first remove the quarantine attribute from the unzipped files before you
can run it. To remove the quarantine attributes from all mcx files, you should
open a Terminal, and run the below commands

  cd /path/to/MCXStudio
  xattr -dr com.apple.quarantine .

After applying the above command, you should be able to start mcxstudio
(and mcxshow, mcxviewer applications) by double-clicking on their icons.

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== # Using MCX Studio GUI ==


Once MCXStudio is launched, it first checks if the mcx
binary presents in the system search paths; if yes, the "GPU" button on the 
toolbar becomes enabled. If you do not have an NVIDIA GPU and intend
to use mcxcl for your simulations, you may click on the "New" button
in the toolbar, and select the 3rd option (NVIDIA/AMD/Inte CPUs/GPUs MCX-CL).
After selecting "OK", and if mcxcl binary presents in your folders, 
the GPU button will also become active.

It is recommended to click on the GPU button once, and verify if you have
compatible GPUs or processors suitables to run MCX or MCXCL simulations.
If you are able to see printed information in a message window, your system 
is ready to run MCX (or mcxcl). If you get an error message or not able
to see any usable GPU, please check the drivers and the binary files.

If your system is verified to support MCX/MCXCL, you can now create new simulations 
by clicking on the "New" button. MCX Studio will ask you to provide a session
name for this new simulation. After a valid session name is provide, MCXStudio
creates the simulation and set all parameters to a ready-to-run default configuration
(containing a 60x60x60 mm^3 homogeneous domain). You should modify the settings
based on your needs. Once you finish the adjustment, you should click the 
"Verify" button to see if there are missing/conflicting settings. If everything looks
ok, the "Run" button will become activated. Clicking on it once will start your
simulation. If you want to abort the current simulation, you can click
the "Stop" button.

You can create multiple tasks with MCX Studio by hitting the "New"
button again. The information for all session configurations can
be saved as a project file (with a ".mcxp" file extension) by clicking the
"Save" button. You can load a previously saved project, containing multiple
simulation sessions, back to MCX Studio by clicking the "Load" button.

In both the unzipped binary packags of mcx and mcxcl, under the folder named
"examples", one can find a pre-created project file (*_examples.mcxp) 
for MCXStudio. Loading these files using the "Load" button allows you to
see these preconfigured simulation.

On Windows, once you start MCXStudio once, the .mcxp suffix becomes automatically
associated with mcxstudio executable. To load a .mcxp file, you can simply
double-click on the file, mcxstudio will be started automatically.

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== # Remote Execution ==

MCXStudio not only supports running mmc/mmc/mcxcl simulations on your local
computer, but also running those remotely on a more powerful server/cluster.
Additional information and video tutorial regarding remote execution can be 
found at

http://mcx.space/wiki/index.cgi?Workshop/MCX18Preparation/MethodB

To use the remote execution feature, one must download and install the 
needed MC simulator (mcx/mmc/mcxcl) in the remote server first, and make sure
those executables can be found by your PATH environment variable. On the client
side, no need to change any software structure. Only the remote copy of mcx/mmc
or mcxcl will be used. They are not restricted by the processors present on your
local computer.

The remote execution is performed using the "ssh" command. One must enable
the ssh sever on the remote server in order to run commands remotely, and install
ssh/scp client on the local computer (your laptop, for example).

On the server side (where mcx/mmc/mcxcl simulations are executed), if it is a 
Linux computer, you can install ssh server by using 

 sudo apt-get install openssh-server
 
or

 sudo dnf install openssh-server
 
If your server is a Mac machine, you should enable SSH access by clicking on
System Preference\Sharing\Remote Login and add your username.

If your remote server is a Windows machine, you can install and enable 
the builtin ssh sever using the instructions below 

https://winscp.net/eng/docs/guide_windows_openssh_server

On the client-side (where mcxstudio is executed, like your laptop), you should
have ssh/scp client software ready. If you use Linux or MacOS, ssh and scp commands are 
typically included by default. If you use Windows, you may download pscp.exe
and plink.exe from the following link

https://www.chiark.greenend.org.uk/~sgtatham/putty/latest.html

and place the two executables in the same folder as mcxstudio.exe (or add to system PATH).

=== Key-based SSH authentication ===

Running mcx/mmc/mcxcl simulations remotely requires one to login a remote server 
using ssh. Typically, one must type password to login. This is the default process
when using MCXStudio. However, if one wants to avoid typing password every time making
a connection, one can setup ssh key-based authentication by following the steps in the
below link 

http://www.linuxproblem.org/art_9.html

=== Clusters with shared file system ===

If your client computer and server computer have a shared file path (i.e., the folder
storing mcxstudio can be both accessed from both computers with the same path,
typical for an NFS-based Linux cluster), then, you should check the "Shared file system"
in the Remote Execution section of MCXStudio window.

If the simulation is launched on a shared file system, your simulation can involve
local files (.bin, meshes etc), and all outputs are stored under MCXStudio/Output/ folder.
You may directly call the menus under the Plot button in MCXStudio to plot the volume
data.

=== Remote servers without shared file system ===

If your client and sever do not have shared file folders, you should uncheck the "Shared file
system". This way, MCXStudio will send all needed setting info via ssh command and create
the output in the ~/Output directory of the server.

In order for a user to plot the output data, one must click on the Plot button in MCXStudio
toolboar, and select one of the Download ... menus to retrieve the file back to your client
drive in order to visualize the results. You must have scp commands available for the file 
transfer to work.


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== #  Acknowledgement ==

The icon set was created by Qianqian Fang, with a style inspired by 
the "Uniform" icon-set 
URL: https://github.com/0rAX0/uniform-icon-theme

The JSON shape editor uses an function "ShowJSONData"  
adapted from the "jsonviewer" example in Lazarus.
URL: http://wiki.freepascal.org/fcl-json#From_JsonViewer

The MCX volume renderer (mcxviewer) was adapted based on the Texture3D Example
provided by the GLScene Project (http://glscene.org). The original author
of this example is Jurgen Abel. The license for GLScene is 

GLScene is distributed under Mozilla Public Licence (MPL 2.0), which means, in short, 
that it is free for both freeware and commercial use. 
The code is still copyrighted (in that it isn't public domain), but you can use it 
in products with closed or open-source freely. The only requirements are:
Acknowledge GLScene is used somewhere in your application (in an about box, credits page or printed manual, etc.
with at least a link to http://glscene.org)
Modifications made to GLScene units must be made public (no need to publish the full code, 
only to state which parts were altered, and how), but feel welcome to open-source your code if you so wish.
Some Delphi units, API headers and DLLs are included in the GLScene package for convenience 
but are not part of GLScene, may use different licensing scheme and have different copyright owners, 
such files have an explicit notice attached to them or placed in their directory.

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== #  Reference ==

[1] Qianqian Fang and David A. Boas, "Monte Carlo Simulation of Photon \
Migration in 3D Turbid Media Accelerated by Graphics Processing Units,"
Optics Express, vol. 17, issue 22, pp. 20178-20190 (2009).

[2] Leiming Yu, Fanny Nina-Paravecino, David Kaeli, Qianqian Fang, \
"Scalable and massively parallel Monte Carlo photon transport simulations \
for heterogeneous computing platforms," J. Biomed. Opt. 23(1), 010504 (2018).

If you use MCX in your research, the author of this software would like
you to cite the above papers in your related publications.

