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update help info
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fangq committed Sep 15, 2023
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8 changes: 6 additions & 2 deletions README.md
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Expand Up @@ -638,14 +638,18 @@ supported parameters, as shown below:
###############################################################################
# Monte Carlo eXtreme (MCX) -- CUDA #
# Copyright (c) 2009-2023 Qianqian Fang <q.fang at neu.edu> #
# http://mcx.space/ #
# https://mcx.space/ & https://neurojson.org/ #
# #
# Computational Optics & Translational Imaging (COTI) Lab- http://fanglab.org #
# Department of Bioengineering, Northeastern University, Boston, MA, USA #
###############################################################################
# The MCX Project is funded by the NIH/NIGMS under grant R01-GM114365 #
###############################################################################
$Rev::e02c77$ v2023 $Date::2023-08-12 14:16:55 -04$ by $Author::Qianqian Fang$
# Open-source codes and reusable scientific data are essential for research, #
# MCX proudly developed human-readable JSON-based data formats for easy reuse,#
# Please consider using JSON (https://neurojson.org/) for your research data #
###############################################################################
$Rev::ffc8ab$ v2023 $Date::2023-09-13 12:24:07 -04$ by $Author::Qianqian Fang$
###############################################################################
usage: mcx <param1> <param2> ...
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8 changes: 6 additions & 2 deletions README.txt
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Expand Up @@ -614,14 +614,18 @@ supported parameters, as shown below:
<pre>###############################################################################
# Monte Carlo eXtreme (MCX) -- CUDA #
# Copyright (c) 2009-2023 Qianqian Fang <q.fang at neu.edu> #
# http://mcx.space/ #
# https://mcx.space/ & https://neurojson.org/ #
# #
# Computational Optics & Translational Imaging (COTI) Lab- http://fanglab.org #
# Department of Bioengineering, Northeastern University, Boston, MA, USA #
###############################################################################
# The MCX Project is funded by the NIH/NIGMS under grant R01-GM114365 #
###############################################################################
$Rev::e02c77$ v2023 $Date::2023-08-12 14:16:55 -04$ by $Author::Qianqian Fang$
# Open-source codes and reusable scientific data are essential for research, #
# MCX proudly developed human-readable JSON-based data formats for easy reuse,#
# Please consider using JSON (https://neurojson.org/) for your research data #
###############################################################################
$Rev::ffc8ab$ v2023 $Date::2023-09-13 12:24:07 -04$ by $Author::Qianqian Fang$
###############################################################################

usage: mcx <param1> <param2> ...
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38 changes: 27 additions & 11 deletions mcxlab/README.txt
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Expand Up @@ -74,7 +74,7 @@ the verbose command line options in MCX.
cfg: a struct, or struct array. Each element of cfg defines
the parameters associated with a simulation.
if cfg='gpuinfo': return the supported GPUs and their parameters,
if cfg='version': return the version of MCXLAB as a string,
if cfg='version': return the version of mcxlab as a string,
see sample script at the bottom
option: (optional), options is a string, specifying additional options
option='preview': this plots the domain configuration using mcxpreview(cfg)
Expand All @@ -100,29 +100,39 @@ the verbose command line options in MCX.
the 2D plane in such case.
for 2D simulations, Example: <demo_mcxlab_2d.m>

mcxlab also accepts 4D arrays to define continuously varying media.
mcxlab also accepts 4D arrays to define continuously varying media.
The following formats are accepted
1 x Nx x Ny x Nz float32 array: mua values for each voxel (must use permute to make 1st dimension singleton)
2 x Nx x Ny x Nz float32 array: mua/mus values for each voxel (g/n use prop(2,:))
4 x Nx x Ny x Nz uint8 array: mua/mus/g/n gray-scale (0-255) interpolating between prop(2,:) and prop(3,:)
2 x Nx x Ny x Nz uint16 array: mua/mus gray-scale (0-65535) interpolating between prop(2,:) and prop(3,:)
1 x Nx x Ny x Nz float32 array: "mua_float"/101 format: mua values for each voxel (must use permute to make 1st dimension singleton)
2 x Nx x Ny x Nz float32 array: "muamus_float"/100 format: mua/mus values for each voxel (g/n use prop(2,:))
3 x Nx x Ny x Nz float32 array: "labelplus"/99 format: {[float32: property_value][float32: property_index i, 0-3][float32: tissue label]},
the optical properties are first read based on the label, then the i-th property is replaced by the property value
3 x Nx x Ny x Nz int16/uint16 array: "mixlabel"/98 format: {[int16 label1][uint16 label2][0-65535 label1 percentage]}
4 x Nx x Ny x Nz uint8 array: "asgn_byte"/103 format: mua/mus/g/n gray-scale (0-255) interpolating between prop(2,:) and prop(3,:)
2 x Nx x Ny x Nz uint16 array: "muamus_short"/104 format: mua/mus gray-scale (0-65535) interpolating between prop(2,:) and prop(3,:)
8 x Nx x Ny x Nz uint8 array: "svmc"/97 format: split-voxel MC (SVMC) hybrid domain, can be created by mcxsvmc.m
Example: <demo_continuous_mua_mus.m>. If voxel-based media are used, partial-path/momentum outputs are disabled
Example: <demo_svmc_*.m> for SVMC related examples
*cfg.prop: an N by 4 array, each row specifies [mua, mus, g, n] in order.
the first row corresponds to medium type 0
(background) which is typically [0 0 1 1]. The
second row is type 1, and so on. The background
medium (type 0) has special meanings: a photon
terminates when moving from a non-zero to zero voxel.
medium (type 0) has special meanings: a photon is terminated
when moving from a non-zero to zero voxel.
*cfg.tstart: starting time of the simulation (in seconds)
*cfg.tstep: time-gate width of the simulation (in seconds)
*cfg.tend: ending time of the simulation (in second)
*cfg.srcpos: a 1 by 3 vector, the position of the source in grid unit
*cfg.srcpos: a 1 by 3 vector, the position of the source in grid unit; if a non-zero
4th element is given, it specifies the initial weight of each photon packet
(or a multiplier in the cases of pattern/pattern3d sources); this initial weight
can be negative - the output fluence is expected to be linearly proportional
to this initial weight (w0) before normalization.
*cfg.srcdir: a 1 by 3 vector, specifying the incident vector; if srcdir
contains a 4th element, it specifies the focal length of
the source (only valid for focuable src, such as planar, disk,
fourier, gaussian, pattern, slit, etc); if the focal length
is nan, all photons will be launched isotropically regardless
of the srcdir direction.
of the srcdir direction; if the focal length is -inf, the launch
angle will be computed based on the Lambertian (cosine) distribution.

== MC simulation settings ==
cfg.seed: seed for the random number generator (integer) [0]
Expand All @@ -149,7 +159,9 @@ the verbose command line options in MCX.
'0': this face is not used to detector photons
'1': this face is used to capture photons (if output detphoton)
see <demo_bc_det.m>
cfg.isnormalized:[1]-normalize the output fluence to unitary source, 0-no reflection
cfg.isnormalized:[1]-normalize the output fluence to unitary source, 0-no reflection.
setting isnormalized to 2 in the replay mode builds the Jacobian
with Born approximation instead of the default Rytov approximation
cfg.isspecular: 1-calculate specular reflection if source is outside, [0] no specular reflection
cfg.maxgate: the num of time-gates per simulation
cfg.minenergy: terminate photon when weight less than this level (float) [0.0]
Expand Down Expand Up @@ -227,6 +239,10 @@ the verbose command line options in MCX.
set by srcparam1(1) (in grid unit); if srcparam1(2) is set to a non-zero
value, this source defines a ring (annulus) shaped source, with
srcparam1(2) denoting the inner circle's radius, here srcparam1(1)>=srcparam1(2)
'ring' [*] - a uniform ring/ring-sector source pointing along srcdir; the outer radius
of the ring is srcparam1(1) (in grid unit) and the inner radius is srcparam1(2);
srcparam1(3) and srcparam1(4) can optionally set the lower and upper angular
bound (in positive rad) of a ring sector if at least one of those is positive.
'fourierx' [*] - a general Fourier source, the parameters are
srcparam1: [v1x,v1y,v1z,|v2|], srcparam2: [kx,ky,phi0,M]
normalized vectors satisfy: srcdir cross v1=v2
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5 changes: 4 additions & 1 deletion mcxstudio/README.txt
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Expand Up @@ -97,6 +97,7 @@ After applying the above command, you should be able to start mcxstudio
(and mcxshow, mcxviewer applications) by double-clicking on their icons.

---------------------------------------------------------------------------

== # Using MCX Studio GUI ==


Expand Down Expand Up @@ -141,6 +142,7 @@ associated with mcxstudio executable. To load a .mcxp file, you can simply
double-click on the file, mcxstudio will be started automatically.

---------------------------------------------------------------------------

== # Remote Execution ==

MCXStudio not only supports running mmc/mmc/mcxcl simulations on your local
Expand Down Expand Up @@ -222,13 +224,14 @@ transfer to work.


---------------------------------------------------------------------------

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

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