Murat4

.gitignore

@@ -1,130 +1,64 @@
+# macOS
 .DS_Store
-sac_MSH/.DS_Store
-Utilities_Matlab/.DS_Store
 
-# MATLAB / Simulink ---------------------------------------------------------
-# Temporary files and backups
-*~ 
+# MATLAB/Simulink temporary, backup, and user files
 *.asv
-*.bak
-*.tmp
 *.autosave
+*~
+*.bak
+*.mat
+*.fig
+*.mltbx
+*.mlsettings
+.matlab/
+.history
 
-# MATLAB specific
-*.mlappinstall
-*.mlappinstallinfo
-*.mltbx            # MATLAB toolbox archive (optionally track if you want)
-*.mltbxmanifest
-*.mldatx           # Simulink data dictionary (if you want to ignore local copies)
-*.mlpkginstall
-*.prj              # generic project files (ignore if you keep projects in repo)
-*.mlproj
-matlab.prf         # MATLAB preferences
-*.mlpkg
-*.mlapp            # App Designer saved files (keep or ignore depending on policy)
+# MATLAB build / generated code / caches
+slprj/
+codegen/
+rtw/
+build/
+*_ert_rtw/
+*/.slx-cache/
+*.slxc
+*.slxautosave
 
-# Compiled and binary artifacts
+# Compiled / binary / object files
 *.mex*
-*.mexa64
-*.mexmaci64
-*.mexw64
-*.mexw32
-*.p                # protected code
 *.dll
 *.so
 *.dylib
-*.exe
 *.o
 *.obj
+*.pdb
 
-# Simulink generated & build files
-slprj/
-*_grt_rtw/
-*_ert_rtw/
-*_slprj/
-*.slxc
-*.slxp
-build/
-CodeGenReport/
-rtwtypes.h
-rtw_*.c
-rtw_*.h
+# Large data directories (keep out of repo)
+sac_MSH/
+sac_Romania/
+sac_Toba/
 
-# Simulink coverage and test artifacts
-coverage/
-coverage_*.xml
-modelCoverageReport/
-slcovreport/
-
-# Auto-generated files (Simulink Designer/Requirements)
-requirements/
-reqs/
-TraceabilityReports/
-*.reqs
+# Binaries, archives, generated distributions
+bin/
+*.zip
+*.tar
+*.tar.gz
+*.tgz
 
-# Test results and logs
-TestResults/
-tests_results/
-*.tap
-*.trx
-*.junit.xml
+# Logs, test results, coverage
 *.log
-*.out
-
-# Documentation build artifacts
-docs/_build/
-doc/build/
-html/
-*.pdf
-*.chm
-
-# MATLAB toolbox packaging / installation artifacts
-*.mltbx
-*.mlappinstall
+TestResults/
+coverage/
 
-# Editor / IDE
+# IDE / editor
 .vscode/
-.idea/
 *.sublime-workspace
 *.sublime-project
+*.swp
 
-# OS files
-.DS_Store
-Thumbs.db
-desktop.ini
+# Git metadata / lock files
+.gitattributes.lock
 
-# Python interop (if used)
+# Python cache (if any)
 __pycache__/
 *.pyc
-*.pyo
-env/
-venv/
-.venv/
-
-# Node / web tooling (if used in docs)
-node_modules/
-dist/
-build/
-
-# Containers / CI
-*.tgz
-*.tar.gz
-
-# MATLAB Online specific
-.matlab_history
-.matlab_crash_dump_*
-
-# Optional: user-specific MATLAB files
-history.m
-preferences.mat
-
-# Optional: large data files (enable if you don't want data in repo)
-# data/
-# datasets/
-# *.mat
 
-# Keep Git from trying to track generated files from builds
-# (uncomment and adapt if you build artifacts locally)
-# /bin/
-# /lib/
-# /build/

MuRAT.m

@@ -0,0 +1,159 @@
+%[text] # MuRAT Multi-Resolution (seismic) Attenuation Tomography
+%[text] **SCOPE**: **A code for 3D attenuation-scattering-absorption tomography**
+%[text] SYSTEM: The program works on all Mac, Windows and Linux computers where it has been tried.
+%[text] MATLAB Version: Matlab 2025b
+%[text] TOOLBOXES:
+%[text] - Curve Fitting Toolbox
+%[text] - Mapping Toolbox
+%[text] - Optimization and Global Optimization Toolboxes
+%[text] - Signal Processing Toolbox.
+%[text] - Parallel Computing Toolbox is highly recommended for speed. \
+%[text] TEMPLATES: Three sample datasets (Mount St. Helens, Romania and Toba) and corresponding inputs are available in the root MuRAT folder.
+%[text] INSTRUCTIONS: The current release (4.0) works following these steps:
+%[text] 1. Download or branch the package at [https://github.com/LucaDeSiena/MuRAT](https://github.com/LucaDeSiena/MuRAT).
+%[text] 2. Build your own input file (.m or .mlx) - each field is described in the attached Documentation.pdf and README.txt.
+%[text] 3. Create your *sac\_data* folder. The codes in the *Utilities\_Matlab* folder, especially those in the *PrePostProcessing* subfolder, can be useful to check data and outputs, especially the necessary parameters are in the headers of the SAC files.
+%[text] 4. Run this file and select the name of the input file you created beforhand. \
+%[text] Author: L. De Siena, January 2026
+%[text] ## INPUTS AND CHECKS
+addpath(fullfile(pwd,'bin'));
+
+r       =   fullfile(pwd,'Utilities_Matlab');
+
+% Split genpath into cell array of full folder paths
+parts   = strsplit(genpath(r), pathsep);
+parts   = parts(~cellfun(@isempty, parts));
+
+% Filters: exclude .git, hidden folders (start with .), and 'private'
+isBad = @(p) contains(p, [filesep '.git' filesep], 'IgnoreCase', true) ...
+           | contains(p, [filesep '.svn' filesep], 'IgnoreCase', true) ...
+           | contains(p, [filesep 'private' filesep], 'IgnoreCase', true) ...
+           | any( startsWith( split(p, filesep), '.' ) );
+
+% Keep folders that pass filter and contain at least one .m file
+keepMask = false(size(parts));
+for k = 1:numel(parts)
+    p = parts{k};
+    if ~isBad(p)
+        % fast check for .m files (not recursive)
+        if ~isempty(dir(fullfile(p,'*.m')))
+            keepMask(k) = true;
+        end
+    end
+end
+
+addList = parts(keepMask);
+if ~isempty(addList)
+    addpath(strjoin(addList, pathsep), '-end');
+end
+
+% Ask user for input file
+[file, path]= uigetfile({'*.m;*.mlx','MuRAT input files (*.m, *.mlx)'; '*.*','All Files'});
+if isequal(file,0)
+    error('No input file selected.');
+end
+inputFile   = fullfile(path, file);
+fprintf('Using input file %s\n', inputFile);
+
+% Run or load input file safely
+[~,~,ext]   = fileparts(file);
+switch lower(ext)
+    case '.mlx'
+        run(inputFile);
+    case '.m'
+        run(inputFile);
+    otherwise
+        error('Unsupported input file extension: %s', ext);
+end
+tStart      = tic;
+
+% --- Validation and ordering ---
+Murat       =   Murat_checks(Murat);
+Murat.input =   orderfields(Murat.input);
+
+% --- Ensure temp folder exists ---
+tempFolder  = fullfile(pwd,'temp');
+if ~exist(tempFolder,'dir'), mkdir(tempFolder); end
+save(fullfile(tempFolder,'Murat_checks.mat'), 'Murat','-v7');
+
+tCheck = toc(tStart);
+fprintf('Time spent on checks: %.2f s\n', tCheck);
+%%
+%[text] ## SEISMIC DATA PROCESSING AND FORWARD MODELLING
+load(fullfile(tempFolder,'Murat_checks.mat'),'Murat');
+
+% Ask user
+useParallel     =   Murat.input.workers;
+
+% Try to prepare parallel pool only if requested
+if ~isempty(useParallel)
+    % Check for Parallel Computing Toolbox
+    hasPCT      =   license('test','Distrib_Computing_Toolbox') || license('test','Parallel_Computing_Toolbox');
+    if ~hasPCT
+        warning('Parallel Computing Toolbox not available. Falling back to sequential.');
+        useParallel =   false;
+    else
+        % Start pool if none exists
+        pool        =   gcp('nocreate');
+        if isempty(pool)
+            try
+                pool= useParallel; % optionally specify NumWorkers
+            catch ME
+                warning('Failed to start parpool: %s. Falling back to sequential.');
+                useParallel = false;
+            end
+        end
+    end
+end
+
+tDataStart = tic;
+
+if useParallel
+    Murat   =   Murat_dataParallelized(Murat);
+else
+    Murat   =   Murat_data(Murat);
+end
+save(fullfile(tempFolder,'Murat_forward.mat'), 'Murat','-v7');
+tData = toc(tDataStart);
+fprintf('Time spent on data processing: %.2f s\n', tData);
+%%
+%[text] ## TOMOGRAPHIC INVERSIONS
+tInvStart   =   tic;
+load(fullfile(tempFolder,'Murat_forward.mat'),'Murat');
+Murat       =   Murat_inversion(Murat);
+% Save with -v7.3 if large
+info        =   whos('Murat');
+if info.bytes > 2e9
+    save(fullfile(tempFolder,'Murat_inverse.mat'),'Murat','-v7.3');
+else
+    save(fullfile(tempFolder,'Murat_inverse.mat'),'Murat','-v7');
+end
+tInv        =   toc(tInvStart);
+fprintf('Inversion completed (%.2f s)\n', tInv);
+%%
+%[text] ## PLOTTING and CLEANING UP
+tPlotStart  =   tic;
+Murat       =   Murat_plot(Murat);
+
+outFolder   =   Murat.input.label;
+
+info        =   whos('Murat'); % re-check size
+if info.bytes > 2e9
+    save(fullfile(outFolder,'Murat.mat'),'Murat','-v7.3');
+else
+    save(fullfile(outFolder,'Murat.mat'),'Murat','-v7');
+end
+
+tPlot       =   toc(tPlotStart);
+fprintf('Plotting completed (%.2f s)\n', tPlot);
+
+totalTime   =   toc(tStart);
+fprintf('Total run time: %.2f s\n', totalTime);
+
+clearvars -except Murat tCheck tData tInv tPlot totalTime
+
+%[appendix]{"version":"1.0"}
+%---
+%[metadata:view]
+%   data: {"layout":"inline","rightPanelPercent":40}
+%---