EASYconsole.m rewrite
This commit is contained in:
@@ -3,57 +3,134 @@
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% Updated 240724 Bryan C Roessler to improve file operations and portability
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%
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function varargout = EASYconsole(varargin)
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% initialize global variables for function EASYconsole
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%global ExpOutmat
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%global ExpPath
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%global fhconsole
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%global resDir
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global wCodeDir
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%global ImParMat
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global startDir
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global easyDir
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global easySuffix
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global scansDir
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global easyResultsDir
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global easyResultsDirName
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global matDir
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global matFile
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global userName
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wCodeDir=pwd;
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% Initialize some variables from matlab
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startDir=pwd;
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easyPath=which(mfilename);
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[easyDir,easy_filename]=fileparts(easyPath);
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easyDir=fullfile(easyDir)
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[parentDir, ~]=fileparts(easyDir);
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userName=system('whoami');
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% changing directory to wCodeDir
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% returnStartDir
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% Set scansDir intelligently (project scans directory)
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% Allow users to specify a PROJECT=/mnt/data/ExpJobs/Job directory to analyze with EASY
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% This better enables running the new EASY in standalone mode
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if exist('PROJECT', 'env')
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scansDir=get_env('PROJECT');
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disp(strcat('Using project path: ', scansDir, ' from environment variable PROJECT'));
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disp('This usually indicates that we are in standalone mode');
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elseif exist('SCANS_DIR', 'env')
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scansDir=get_env('SCANS_DIR');
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disp(strcat('Using scans directory: ', scansDir, ' from environment variable SCANS_DIR'));
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disp('This usually indicates that we are in module mode');
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else
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scansDir=fullfile(parentDir,'ExpJobs'); % relative to easy script dir
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disp(strcat('Using scans directory: ', scansDir, ' from hardcoded default'));
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disp('This usually indicates that we are in standalone mode');
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end
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disp(getenv('SCANS_DIR'));
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%% GUI INTERFACE DESIGN %%
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% beginning of GUI formation & design, see help GUI or help GUIDE in
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% command window for more information
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gui_Singleton = 1;
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gui_State = struct('gui_Name', mfilename, ...
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'gui_Singleton', gui_Singleton, ...
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'gui_OpeningFcn', @EASYconsole_OpeningFcn, ...
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'gui_OutputFcn', @EASYconsole_OutputFcn, ...
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'gui_LayoutFcn', [] , ...
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'gui_Callback', []);
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if nargin && ischar(varargin{1})
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gui_State.gui_Callback = str2func(varargin{1});
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% If we don't have the EASY_SUFFIX from the module, generate it from scanDir
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if exist('EASY_SUFFIX', 'env')
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easySuffix=get_env('EASY_SUFFIX');
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else
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[dirName, ~]=fileparts(scansDir);
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[date, userNameScans, easySuffix]=strsplit(dirName, '_');
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% The following is handled by the workflow script that calls this module
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% Reimplementing here for stand-alone mode
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% While the easySuffix directory exists, increment by one and try again
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if exist(easySuffix, 'dir')
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oldSuffix=easySuffix
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while exist(easySuffix, 'dir')
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count=1;
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easySuffix=strcat(oldSuffix,'.', num2str(count));
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end
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end
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if nargout
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[varargout{1:nargout}] = gui_mainfcn(gui_State, varargin{:});
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else
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gui_mainfcn(gui_State, varargin{:});
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% Might as well check this too
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if userName ~= userNameScans
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disp('WARNING: userName does not match userNameScans');
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disp("This usually means that you are attempting to run an EASY analysis on another user's project data scans");
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end
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% For happiness
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if datestr(now, 'yyyymmdd') == date
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disp("Early bird gets the worm")
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end
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end
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% Helpful variables for running in workflow mode that I'll probably have to reimplement in matlab anyways for standalone mode
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if exist('EASY_DIR','env')
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EASY_DIR=fullfile(get_env('EASY_DIR'))
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if easyDir ~= EASY_DIR % sanity check
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disp("WARNING: EASY_DIR does not match this script's default EASY location");
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easyDir=EASY_DIR
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end
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disp(strcat('Using EASY script directory: ', easyDir, ' from environment variable EASY_DIR'));
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else
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disp(strcat('Using EASY script directory: ', easyDir, ' from hardcoded default'));
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end
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if exist('EASY_RESULTS_DIR', 'env')
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easyResultsDir=fullfile(get_env('EASY_RESULTS_DIR'));
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disp(strcat('Using project prefix: ', easyResultsDir, ' from environment variable EASY_RESULTS_DIR'))
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else
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easyResultsDirName=strcat('Results_',datestr(now, 'yyyymmdd'),'_',easySuffix);
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easyResultsDir=fullfile(scansDir,easyResultsDirName);
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scansDir=fullfile(parent_dir,'ExpJobs') % relative to easy script dir
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disp(strcat('Using project prefix: ', PROJECT_PREFIX, ' from environment variable PROJECT_PREFIX'))
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end
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if exist('PROJECT_USER', 'env')
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if get_env('PROJECT_USER') ~= userName % sanity check
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disp("WARNING: PROJECT_USER does not match the current namespace");
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end
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end
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matDir=fullfile(easyResultsDir,'matResults');
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matFile=fullfile(matDir,strcat(easyResultsDirName,'.mat'));
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% Play around with making some common variables from our input data
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% resDirName=fullfile(SCANS_DIR,'Results',strcat(datestr(now, 'yyyymmdd'),'_', PROJECT_SUFFIX);
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% resDir=fullfile(SCANS_DIR,resDirName);
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% ExpOutmat=fullfile(matDir,strcat(datestr(now,29),newExpfile));
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% ExpPath=fullfile(newExppath);
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% ExpFile=fullfile(matDir,)
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% GUI interface design
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gui_Singleton=1;
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gui_State=struct('gui_Name', mfilename, ...
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'gui_Singleton', gui_Singleton, ...
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'gui_OpeningFcn', @EASYconsole_OpeningFcn, ...
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'gui_OutputFcn', @EASYconsole_OutputFcn, ...
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'gui_LayoutFcn', [] , ...
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'gui_Callback', []);
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if nargin && ischar(varargin{1})
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gui_State.gui_Callback=str2func(varargin{1});
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end
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if nargout
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[varargout{1:nargout}]=gui_mainfcn(gui_State, varargin{:});
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else
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gui_mainfcn(gui_State, varargin{:});
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end
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end
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% Try to enter WCodeDir
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% To remove?
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% Try to enter
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function returnStartDir
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global wCodeDir
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global
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try
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cd(wCodeDir)
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cd(SCANS_DIR)
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catch
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msgbox('Failed to enter selected default directory so starting search at root.');
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if ispc
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cd('C:\');
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elseif (isunix || ismac)
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cd('/mnt/data');
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else
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msgbox('Unknown platform')
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end
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msgbox('Failed to enter the project directory so starting search from where we started.');
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cd(start_dir)
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end
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end
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@@ -65,40 +142,40 @@ end
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% handles--structure with handles and user data (see GUIDATA)
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% varargin--input arguments to EASYconsole (see VARARGIN)
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function EASYconsole_OpeningFcn(hObject, ~, handles, varargin)
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%global ExpOutmat
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%global ExpPath
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global fhconsole
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global resDir
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%global ImParMat
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global fhconsole
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global easyResultsDir
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% Choose default command line output for EASYconsole
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handles.output = hObject;
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% Choose default command line output for EASYconsole
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handles.output = hObject;
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% Update handles structure
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guidata(hObject, handles);
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% Update handles structure
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guidata(hObject, handles);
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%Figure header, Toolbar, etc. Setup
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fhconsole=gcf;
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set(fhconsole,'Toolbar','none');
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fhconsole=gcf;
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%Figure header, Toolbar, etc. Setup
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fhconsole=gcf;
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set(fhconsole,'Toolbar','none');
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fhconsole=gcf;
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if exist('resDir','var')&&~isempty(resDir)
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set(fhconsole,'Name',strcat('EASYconsole- ',char(resDir)));
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else
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set(fhconsole,'Name','EASYconsole -Exp. Analysis NOT selected.')
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end
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% BCR this is set in the global function so I think we're good here
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% easyResultsDirName=strcat('Results',datestr(now, 'yyyymmdd'),newExpfilePref);
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if exist('easyResultsDir','var') && ~isempty(easyResultsDir)
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set(fhconsole,'Name',strcat('EASYconsole- ',char(easyResultsDir)));
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else
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set(fhconsole,'Name','EASYconsole -Exp. Analysis NOT selected.')
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end
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end
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%% EASYconsole OUTPUT FUNCTION %%
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% EASYconsole OUTPUT FUNCTION %%
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% Outputs from this function are returned to the command line.
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% varargout--cell array for returning output args (see VARARGOUT);
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% hObject--handle to figure
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% eventdata reserved - to be defined in a future version of MATLAB
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% handles--structure with handles and user data (see GUIDATA)
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function varargout = EASYconsole_OutputFcn(~, ~, handles)
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% Get default command line output from handles structure
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varargout{1} = handles.output;
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% Get default command line output from handles structure
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varargout{1} = handles.output;
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end
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%% CONSOLE BUTTON INTERFACES %%
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@@ -114,194 +191,179 @@ end
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% New Experiment Button Interface
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function NewExpDat_Callback(~, ~, ~)
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global newExpfile
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global newExppath
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global SWnewExp
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global ExpOutmat
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global ExpPath
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global matDir
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global resDir
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global fhconsole
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global scan
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global SWnewExp
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global matDir
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global matFile
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global easyResultsDir
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global easyResultsDirName
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global fhconsole
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global scan
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global userName
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% put all users on same working directory
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%returnStartDir
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% Create a new experiment
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try
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questdlg('\fontsize{20} NAME the file and NAVIGATE to the directory with the image folders.','File Creation','OK', struct('Default','OK','Interpreter','tex'));
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[inputFile,inputPath]=uiputfile('.mat');
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SWnewExp=1;
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% Create a new experiment
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try
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questdlg('\fontsize{20} NAME the file and NAVIGATE to the directory with the image folders.','File Creation','OK', struct('Default','OK','Interpreter','tex'));
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[newExpfile,newExppath] = uiputfile(' .mat');
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SWnewExp=1;
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inputFileName=strrep(inputFile,'.mat','');
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easyResultsDirName=strcat('Results_',datestr(now,'yyyymmdd'),'_',userName,'_',inputFileName);
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% Set paths
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newExpfilePref= strrep(newExpfile,'.mat','');
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resDir=fullfile(newExppath,resDirName);
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matDir=fullfile(newExppath,resDirName,'matResults');
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ExpOutmat=fullfile(matDir,strcat(datestr(now,29),newExpfile));
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ExpPath=fullfile(newExppath);
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% Set paths
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scansDir=fullfile(inputPath);
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easyResultsDir=fullfile(scansDir,easyResultsDirName);
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matDir=fullfile(easyResultsDir,'matResults');
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matFile=fullfile(matDir,strcat(datestr(now,'yyyymmdd'),'_',userName,'_',inputFile));
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%***Added for 'parfor global' to preallocate 'scan' structure 20-0123*****
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nlist=dir(fullfile(ExpPath,'*'));
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nnn=0;
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for n=1:size(nlist,1)
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if (~isempty(str2num(nlist(n).name)))
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nnn=nnn+1;
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PnumLst(nnn)= (str2num(nlist(n).name));
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sl(nnn,1)={(nlist(n).name)};
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end
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end
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scanSize= size(sl,1);
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scanMax= max(str2double(sl));
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clear scan;
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scan(scanMax)= struct(); %changed for parfor global 20_0118
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save(ExpOutmat,'scan')
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%***Added for 'parfor global' to preallocate 'scan' structure 20-0123*****
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nlist=dir(fullfile(scansDir,'*'));
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nnn=0;
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for n=1:size(nlist,1)
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if (~isempty(str2num(nlist(n).name)))
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nnn=nnn+1;
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PnumLst(nnn)= (str2num(nlist(n).name));
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sl(nnn,1)={(nlist(n).name)};
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end
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end
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scanSize=size(sl,1);
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scanMax=max(str2double(sl));
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clear scan;
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scan(scanMax)=struct(); % changed for parfor global 20_0118
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save(matFile,'scan')
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% BCR rewrote these but moved the functionality into the main workflow script
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% % create supporting dirs
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% dirs = {'PrintResults', 'CFfigs', 'Fotos', 'Fotos/BkUp'};
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% for i = 1:length(dirs)
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% d = dirs{i};
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% if ~exist(fullfile(ExpPath, resDirName, d), 'dir')
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% mkdir(fullfile(ExpPath, resDirName, d));
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% end
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% end
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% % templateDirs are stored in the easy template directory
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% templates = {'figs', 'PTmats'}
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% for i = 1:length(templates)
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% d = dirs{i};
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% if ~exist(fullfile(ExpPath, resDirName, d), 'dir')
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% copyfile((fullfile(wCodeDir,d)), (fullfile(ExpPath,resDirName,d)));
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% end
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% end
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clear sbdg % reduce possible retention of a previous job sdbg
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sbdg= cell(1,scanMax);
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save((fullfile(resDir,'Fotos','Nbdg')),'sbdg');
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catch ME
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% returnStartDir
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disp('Error Creating a New Experiment')
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% create supporting dirs
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% this is also in the workflow script but here for standalone mode
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dirs = {'PrintResults', 'CFfigs', 'Fotos', 'Fotos/BkUp'};
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for i = 1:length(dirs)
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d = dirs{i};
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if ~exist(fullfile(easyResultsDir, d), 'dir')
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mkdir(fullfile(easyResultsDir, d));
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end
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end
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% set the title for fhconsole depending on existence
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if exist('resDir','var')&&~isempty(resDir)
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set(fhconsole,'Name',strcat('EASYconsole- ',char(resDir)))
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else
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set(fhconsole,'Name','EASYconsole -Exp. Analysis NOT selected.')
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% templateDirs are stored in the easy template directory
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templates = {'figs', 'PTmats'}
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for i = 1:length(templates)
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d = dirs{i};
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if ~exist(fullfile(easyResultsDir, d), 'dir')
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copyfile((fullfile(,d)), (fullfile(easyResultsDir,d)));
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end
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end
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clear sbdg % reduce possible retention of a previous job sdbg
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sbdg= cell(1,scanMax);
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save((fullfile(easyResultsDir,'Fotos','Nbdg')),'sbdg');
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catch ME
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% returnStartDir
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disp('Error Creating a New Experiment')
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end
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% set the title for fhconsole depending on existence
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if exist('easyResultsDir','var')&&~isempty(easyResultsDir)
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set(fhconsole,'Name',strcat('EASYconsole- ',char(easyResultsDir)))
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else
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set(fhconsole,'Name','EASYconsole -Exp. Analysis NOT selected.')
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end
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end
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% Load a previous experiment
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function LoadDatFile_Callback(~, ~, ~)
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global openExpfile
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global openExppath
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global SWnewExp
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global ExpOutmat
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global ExpPath
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global matDir
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global resDir
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global fhconsole
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%global ImParMat
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global SWnewExp
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global matDir
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global matFile
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global easyResultsDir
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global easyPath
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global fhconsole
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%global ImParMat
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% TODO this entire try block needs work
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try
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% TODO this whole block is highly questionable
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questdlg('\fontsize{20} Load file from ExpJobs/YourJob/YourResults/matResults','File Creation','OK', struct('Default','OK','Interpreter','tex'));
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[openExpfile,openExppath] = uigetfile('.mat','Open Experiment folder and data storage .mat file name','MultiSelect','off');
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SWnewExp=0;
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ExpOutmat= fullfile(openExppath,openExpfile);
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load(ExpOutmat);
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resdir=fullfile('../',openExppath)
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ExpPath=fullfile('../../',openExppath)
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try
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questdlg('\fontsize{20} Load file from ExpJobs/YourJob/YourResults/matResults','File Creation','OK', struct('Default','OK','Interpreter','tex'));
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[inputFile,inputPath]=uigetfile('.mat','Open Experiment folder and data storage .mat file name','MultiSelect','off');
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SWnewExp=0;
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matDir=fullfile(inputPath)
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matFile=fullfile(inputPath,inputFile);
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load(matFile);
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easyResultsDir=fullfile(matDir,'..')
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scansDir=fullfile(matDir,'..', '..')
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if isfolder(fullfile(openExppath, '..','..','1')) %If Inovation Vrobot Then
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if exist(fullfile(resDir,'PTmats','NImParameters.mat'), 'file')
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load(fullfile(resDir,'PTmats','NImParameters.mat'));
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else
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curDir=pwd;
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returnStartDir
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load NImParameters.mat
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cd(curDir)
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end
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else %If Epson 10Plate Scans Then>
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if exist(fullfile(resDir,'PTmats','ImParameters.mat'), 'file')
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load(fullfile(resDir,'PTmats','ImParameters.mat'));
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else
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curDir=pwd;
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returnStartDir
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load ImParameters.mat
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cd(curDir)
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end
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end
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mkdir(fullfile(openExppath,'\BkUp'));
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% create supporting dirs
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% dirs = {'PrintResults', 'figs', 'CFfigs', 'PTmats', 'Fotos'}
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% for i = 1:length(dirs)
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% d = dirs{i}
|
||||
% if ~exist(fullfile(resDir, d), 'dir')
|
||||
% mkdir(fullfile(resDir, d));
|
||||
% end
|
||||
% end
|
||||
|
||||
catch
|
||||
returnStartDir
|
||||
if isfolder(fullfile(matDir, '..','..','1')) % If Inovation Vrobot Then
|
||||
if exist(fullfile(easyResultsDir,'PTmats','NImParameters.mat'), 'file')
|
||||
load(fullfile(easyResultsDir,'PTmats','NImParameters.mat'));
|
||||
else
|
||||
load(fullfile(easyPath,'NImParameters.mat'));
|
||||
end
|
||||
else % If Epson 10Plate Scans Then>
|
||||
if exist(fullfile(easyResultsDir,'PTmats','ImParameters.mat'), 'file')
|
||||
load(fullfile(easyResultsDir,'PTmats','ImParameters.mat'));
|
||||
else
|
||||
load(fullfile(easyPath,'ImParameters.mat'));
|
||||
end
|
||||
end
|
||||
|
||||
clear scan
|
||||
mkdir(fullfile(matDir,'BkUp'));
|
||||
|
||||
if exist('resDir','var')&&~isempty(resDir)
|
||||
fhconsole= gcf;
|
||||
set(fhconsole,'Name',strcat('EASYconsole- ',char(resDir)))
|
||||
else
|
||||
set(fhconsole,'Name','EASYconsole -Exp. Analysis NOT selected.')
|
||||
% Create supporting dirs
|
||||
dirs = {'PrintResults', 'figs', 'CFfigs', 'PTmats', 'Fotos'}
|
||||
for i = 1:length(dirs)
|
||||
d = dirs{i}
|
||||
if ~exist(fullfile(easyResultsDir, d), 'dir')
|
||||
mkdir(fullfile(easyResultsDir, d));
|
||||
end
|
||||
end
|
||||
catch
|
||||
returnStartDir
|
||||
end
|
||||
|
||||
clear scan
|
||||
|
||||
if exist('easyResultsDir','var') && ~isempty(easyResultsDir)
|
||||
fhconsole=gcf;
|
||||
set(fhconsole,'Name',strcat('EASYconsole- ',char(easyResultsDir)))
|
||||
else
|
||||
set(fhconsole,'Name','EASYconsole -Exp. Analysis NOT selected.')
|
||||
end
|
||||
end
|
||||
|
||||
|
||||
%% CALLBACKS %%
|
||||
|
||||
% callback for the 'Run' in the dropdown menu
|
||||
function run_Callback(~, ~, ~)
|
||||
|
||||
end
|
||||
|
||||
function runPlateMapPintool_Callback(~, ~, ~)
|
||||
try
|
||||
NImapPT
|
||||
catch ME
|
||||
returnStartDir
|
||||
EASYconsole
|
||||
end
|
||||
try
|
||||
NImapPT
|
||||
catch ME
|
||||
returnStartDir
|
||||
EASYconsole
|
||||
end
|
||||
end
|
||||
|
||||
function NImCFcombo_Callback(~, ~, ~)
|
||||
try
|
||||
par4Gbl_Main8c
|
||||
catch
|
||||
returnStartDir
|
||||
EASYconsole
|
||||
end
|
||||
try
|
||||
par4Gbl_Main8c
|
||||
catch
|
||||
returnStartDir
|
||||
EASYconsole
|
||||
end
|
||||
end
|
||||
|
||||
function runPlateImAnal_Callback(~, ~, ~)
|
||||
try
|
||||
NImStartupOnly
|
||||
catch ME
|
||||
returnStartDir
|
||||
EASYconsole
|
||||
end
|
||||
try
|
||||
NImStartupOnly
|
||||
catch ME
|
||||
returnStartDir
|
||||
EASYconsole
|
||||
end
|
||||
end
|
||||
|
||||
function PlateCFit_Callback(~, ~, ~)
|
||||
%global ExpOutmat
|
||||
try
|
||||
NCstart
|
||||
catch ME
|
||||
returnStartDir
|
||||
end
|
||||
% global matFile % TODO BCR not sure if needed
|
||||
try
|
||||
NCstart
|
||||
catch ME
|
||||
returnStartDir
|
||||
end
|
||||
end
|
||||
|
||||
function GenPrintouts_Callback(~, ~, ~)
|
||||
@@ -311,83 +373,73 @@ function uploadExcelMP2DB_Callback(~, ~, ~)
|
||||
end
|
||||
|
||||
function runDMPexcel_Callback(~, ~, ~)
|
||||
global ExpPath
|
||||
try
|
||||
DMPexcel2mat_2024winLinix %DMPexcel2mat_2023winLinix
|
||||
catch ME
|
||||
returnStartDir
|
||||
EASYconsole
|
||||
end
|
||||
try
|
||||
DMPexcel2mat_2024winLinix %DMPexcel2mat_2023winLinix
|
||||
catch ME
|
||||
returnStartDir
|
||||
EASYconsole
|
||||
end
|
||||
end
|
||||
|
||||
function runResults_DBcombo_Callback(~, ~, ~)
|
||||
|
||||
try
|
||||
DgenResults240430 %similar but semicolons removed to restore so cmdLine display info.
|
||||
%Dgen241010qhtcp %par4global -convert 1x1cell of 384cells to be like previous 1x384 cells CFparameter
|
||||
catch ME
|
||||
disp('Error in DgenResults240430')
|
||||
returnStartDir
|
||||
EASYconsole
|
||||
end
|
||||
try
|
||||
DgenResults240430 %similar but semicolons removed to restore so cmdLine display info.
|
||||
%Dgen241010qhtcp %par4global -convert 1x1cell of 384cells to be like previous 1x384 cells CFparameter
|
||||
catch ME
|
||||
disp('Error in DgenResults240430')
|
||||
EASYconsole
|
||||
end
|
||||
end
|
||||
|
||||
function Tools_Callback(~, ~, ~)
|
||||
end
|
||||
|
||||
function runOverlayPlots_Callback(~, ~, ~)
|
||||
try
|
||||
DoverlayPlots2
|
||||
EASYconsole
|
||||
catch ME
|
||||
returnStartDir
|
||||
EASYconsole
|
||||
end
|
||||
try
|
||||
DoverlayPlots2
|
||||
EASYconsole
|
||||
catch ME
|
||||
EASYconsole
|
||||
end
|
||||
end
|
||||
|
||||
function runFotoStrip_Callback(~, ~, ~)
|
||||
try
|
||||
F_NImStartup_CentCir
|
||||
EASYconsole
|
||||
catch ME
|
||||
returnStartDir
|
||||
EASYconsole
|
||||
end
|
||||
try
|
||||
F_NImStartup_CentCir
|
||||
EASYconsole
|
||||
catch ME
|
||||
EASYconsole
|
||||
end
|
||||
end
|
||||
|
||||
function runDisplayFig_Callback(~, ~, ~)
|
||||
try
|
||||
UfigDisplay
|
||||
catch ME
|
||||
returnStartDir
|
||||
EASYconsole
|
||||
end
|
||||
try
|
||||
UfigDisplay
|
||||
catch ME
|
||||
EASYconsole
|
||||
end
|
||||
end
|
||||
|
||||
function runViewParameters_Callback(~, ~, ~)
|
||||
try
|
||||
catch ME
|
||||
returnStartDir
|
||||
EASYconsole
|
||||
end
|
||||
try
|
||||
catch ME
|
||||
EASYconsole
|
||||
end
|
||||
end
|
||||
|
||||
function QkviewN_Callback(~, ~, ~)
|
||||
try
|
||||
QkviewImages
|
||||
catch ME
|
||||
returnStartDir
|
||||
EASYconsole
|
||||
end
|
||||
try
|
||||
QkviewImages
|
||||
catch ME
|
||||
EASYconsole
|
||||
end
|
||||
end
|
||||
|
||||
function CFdisplay_Callback(~, ~, ~)
|
||||
try
|
||||
NCsingleDisplay
|
||||
returnStartDir
|
||||
EASYconsole
|
||||
catch ME
|
||||
returnStartDir
|
||||
EASYconsole
|
||||
end
|
||||
try
|
||||
NCsingleDisplay
|
||||
EASYconsole
|
||||
catch ME
|
||||
EASYconsole
|
||||
end
|
||||
end
|
||||
Reference in New Issue
Block a user