nomad.m - v2.0 - Near-Near-infrared Optode Montage Automated Designer

Dr. Kyle Mathewson, University of Illinois - Feb 7, 2013

% nomad.m - v1.0 - Near-infrared Optode Montage Automated Designer
% Dr. Kyle Mathewson, University of Illinois - Nov 11, 2012

% Formerly Montage_design_2012.m - Interactively design montages, place detectors, srcs, and assign mux numbers
% Modified from earlier Montage_design.m by Kyle Mathewson & Ed Maclin
% Based on Montage Design techniques from Kathy Low

% Copyright Dr. Kyle Mathewson, Beckman Instite, University of Illinois

% Input - uses standard .elp files of the CNL helmets - load from the settings

% Steps

% 1) calls helmet_schem_maker.m to make a schematic and scatterplot of the locations
% 2) Allows the user to choose detectors
% 3) Manually select sources - Automatic works for patches
% 4) Calls assign_mux.m, or another algorithm to assign mux numbers
% 5) Calls FinalSwap.m to move srcs to accomodate new mux numbers

% GUI Steps

% 1) Settings - Set up the montage itself, load your own .elp file or saved structure, number
% of sources and detectors, and the mux number.

% 2) Design Montage - Identify the location of sources and detector
% interactively

% 2) Assign Mux - This is a wrapper for the mux assignment alogrithms for
% the user to interactivly try to assing mux numbers, and check their crosstalk

% 3) Output - This final GUI will let the user save the output files and
% the data structure.


% - Output,
% 1) Schematic of src and det locations and mux's, save as .bmp
% 2) Scatterplot on scalp, histogram of distances, and some stats
% 3) Visualize the Graph
% 4) .mtg files for use by coreg and opt3d
% 5) Graph Definition Files for BOXY aquisition
% 6) Save the mtg structure for future use



%---------------
% Updates
%---------------

% NOMAD - Version 2.0 - Feb 7, 2012

% General
%Reorganized paths and subpaths, elp and examples files in subfolders
%Increased resolution of background images and included EROS helmet

% Setting
%Reorganized SettingsGUI, simplified, included instructions and tips
%IMPORTANT - Custom .elp automatic S and D indentification from the .elp file, the first line of the .elp file must be the SSDDSSDDSS identity of each row
%fixed load button bugs and moved it to more prominent position

% Montage and Schematic
%Created a GUI for the src/det selection, and built the old script into it
%IMPORTANT - Created buttons and instructions to automatically resize the src/det spacing
%IMPORTANT - Created a restart button to refresh the window and start over
%IMPORTANT - included step by step written instructions on the right
%Created a Done button to move forward to mux assignment
%back button to return to settings and make changes
%I HAVE NOT FIXED THE COLOUR PROBLEMS WITH SRC UNDO YET

% Mux Assignment
%Again I revamped the GUI, removed the background image for simplicity
%IMPORTANT - CROSSTALK CHECK - I added an additional check against crosstalk by pressing the orange button
    %this brings up two new figures, the first of which shows the conflict
    %matrix with white dots showning conflict and the second shows, for each mux number, the distance of each
    %src with this mux number from each detector. Red lines show cross talk. Both show warnings when
    %crosstalk is detected.
%IMPORTANT - REMOVED SWAP - this seemed to be causing problems of crosstalk and was removed as an option
%organized it from top to bottom in a temporal order, and numbered
%added colour to the important buttons, and a reminder to color both mtgs


%TODO
% - Save some settings and load them?
% - Change colouring during montage selection
% - Fix undo for source placement, the other source of cross talk problems right now
% - Create buttons to return to detector, right click detector during srcs?
% - Space out detectors in bounding box
% - Space out srcs in bounding box
% - Add funcitonality for patches
% - Update GDF creator with .dll from DENIS for correct BOXY file creation
% - Display lines on surface of convex hull and shade the hull as such
% - Better 2D projection of ELP file for schematic
% - Create output for DENIS and BOXY to visualize signal quality
% - Change shading of src holes
% - Made schematic background grey - JW




% NOMAD - Version 1.02 - Nov11, 2012
% ------------

%Nov 11 -
% make Montage - Fix undo so it removes the white spaces and the gray areas
% Assign mux - Add functionality for dual mtgs - select which one
%       -Make Initial settings match existing montage
% add the head plot and stats to Assign the mux
% 2 wavelength gdf files and distance file
% Create option to resume making montage for mux assign
% Create optoin to resume mux assign / from output
% changed the mtg1 and mtg2 settings to a array of structure mtg with mtg(1) and mtg(2)
% this allows for many mtgs to be combined
% loading old files is somewhat supported


%Nov 10 - Created the mux assignment GUI, Integrated the Setting and OutputGUI
%Included feature to load in saved mtg files
%separated the assign_the_mux from the make_the_montage
%fixed bug to save created colourings to the mtg1 and mtg2 structs


%Nov 6 - KEM
%renamed NOMAD
%Changed montage display to add dual wavelength
%added dual wavelength .mtg files
%added monte carlo tries setting to menu
%added parallel monte carlo options to menu
%deleted many old colour approaches - should consolidate them
%need to make graph definition files and distance graph for dual wavelength- DONE


%Nov 5 - KEM
%Updated GUI to add dual fibre capabillity
%Created new name - NOMAD - and a logo for the GUI
%Moved the detector naming to the schematic maker - helmet_schem_maker
%added custom helmet capabililty - and location to add source detector order for this format
%made graph definition files  and distance diagram work for single oxyplex machine, and single montge
%made .mtg file work for single oxyplex and single montage - combined mtg file for single montage

% March 13 - KEM
% Changed n_try to 10000 - more tries to colour before swapping
% Changed trisurf alpha level to .5 instead of .9 - convex hull is more transparent

% March 14 - KEM
% Added editor cells to increase readability of code

% March 15 - KEM
% Added functionality for multiple mtg's per subject, indicate in Settings
% Moved the head plot and histogram after mtg loop and made a function to plot it over both session
% Added the graph computation to speed mux assignment, put back DESATUR -build
% Added Source Distance Function and Assignment type to advanced settings
% Fixed bug when srcs were right click removed but the detectors were still counting them towards the total allowed
% Fixed bug of the colours going out of range and crashing the program by setting a limit on lower and upper
% Added saving of multiple mtg schematic, saving of all mtgs created

% March 22 - KEM
% Changed .mtg file output for 2 sessions 2 machines to combine all into 1
% Added graph definition file functionality for 2 sessions 2 machines
% Fixed many bugs

% Version 2012b
% -------------

% March 28 - KEM
% Added setting for schematic colors, with options for CNL, DOIL or custom -
% Added titles and labels to schematics
% Additional output matrix page for each opt and session colored by distance

% March 29 - KEM
% Reversed colors to match the bank orientation - JW suggestion
% Changed detectors to match each room, and the proper colours - JW



% TODO Future
% KM 03/2012

% Restrict channels less than the minimum distance - DONE
% - Precompute all distances in helm file and look up throughout the code -DONE
% - Include feature to load your own .elp file - DONE
% - debug DESATUR,include Greedy - DONE
% - Change assign_mux to use the graph instead to speed up - DONE, slower
% - Fix src and det assignment when mouse miss the schematic