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Support for writing and executing MATLAB/Octave scripts
This commit is contained in:
Timothy Kassis
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scientific-skills/matlab/references/data-import-export.md
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479
scientific-skills/matlab/references/data-import-export.md
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# Data Import and Export Reference
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## Table of Contents
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1. [Text and CSV Files](#text-and-csv-files)
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2. [Spreadsheets](#spreadsheets)
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3. [MAT Files](#mat-files)
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4. [Images](#images)
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5. [Tables and Data Types](#tables-and-data-types)
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6. [Low-Level File I/O](#low-level-file-io)
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## Text and CSV Files
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### Reading Text Files
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```matlab
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% Recommended high-level functions
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T = readtable('data.csv'); % Read as table (mixed types)
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M = readmatrix('data.csv'); % Read as numeric matrix
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C = readcell('data.csv'); % Read as cell array
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S = readlines('data.txt'); % Read as string array (lines)
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str = fileread('data.txt'); % Read entire file as string
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% With options
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T = readtable('data.csv', 'ReadVariableNames', true);
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T = readtable('data.csv', 'Delimiter', ',');
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T = readtable('data.csv', 'NumHeaderLines', 2);
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M = readmatrix('data.csv', 'Range', 'B2:D100');
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% Detect import options
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opts = detectImportOptions('data.csv');
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opts.VariableNames = {'Col1', 'Col2', 'Col3'};
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opts.VariableTypes = {'double', 'string', 'double'};
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opts.SelectedVariableNames = {'Col1', 'Col3'};
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T = readtable('data.csv', opts);
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```
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### Writing Text Files
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```matlab
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% High-level functions
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writetable(T, 'output.csv');
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writematrix(M, 'output.csv');
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writecell(C, 'output.csv');
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writelines(S, 'output.txt');
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% With options
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writetable(T, 'output.csv', 'Delimiter', '\t');
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writetable(T, 'output.csv', 'WriteVariableNames', false);
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writematrix(M, 'output.csv', 'Delimiter', ',');
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```
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### Tab-Delimited Files
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```matlab
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% Reading
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T = readtable('data.tsv', 'Delimiter', '\t');
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T = readtable('data.txt', 'FileType', 'text', 'Delimiter', '\t');
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% Writing
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writetable(T, 'output.tsv', 'Delimiter', '\t');
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writetable(T, 'output.txt', 'FileType', 'text', 'Delimiter', '\t');
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```
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## Spreadsheets
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### Reading Excel Files
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```matlab
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% Basic reading
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T = readtable('data.xlsx');
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M = readmatrix('data.xlsx');
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C = readcell('data.xlsx');
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% Specific sheet
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T = readtable('data.xlsx', 'Sheet', 'Sheet2');
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T = readtable('data.xlsx', 'Sheet', 2);
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% Specific range
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M = readmatrix('data.xlsx', 'Range', 'B2:D100');
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M = readmatrix('data.xlsx', 'Sheet', 2, 'Range', 'A1:F50');
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% With options
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opts = detectImportOptions('data.xlsx');
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opts.Sheet = 'Data';
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opts.DataRange = 'A2';
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preview(opts.VariableNames) % Check column names
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T = readtable('data.xlsx', opts);
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% Get sheet names
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[~, sheets] = xlsfinfo('data.xlsx');
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```
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### Writing Excel Files
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```matlab
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% Basic writing
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writetable(T, 'output.xlsx');
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writematrix(M, 'output.xlsx');
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writecell(C, 'output.xlsx');
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% Specific sheet and range
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writetable(T, 'output.xlsx', 'Sheet', 'Results');
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writetable(T, 'output.xlsx', 'Sheet', 'Data', 'Range', 'B2');
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writematrix(M, 'output.xlsx', 'Sheet', 2, 'Range', 'A1');
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% Append to existing sheet (use Range to specify start position)
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writetable(T2, 'output.xlsx', 'Sheet', 'Data', 'WriteMode', 'append');
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```
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## MAT Files
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### Saving Variables
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```matlab
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% Save all workspace variables
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save('data.mat');
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% Save specific variables
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save('data.mat', 'x', 'y', 'results');
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% Save with options
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save('data.mat', 'x', 'y', '-v7.3'); % Large files (>2GB)
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save('data.mat', 'x', '-append'); % Append to existing file
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save('data.mat', '-struct', 's'); % Save struct fields as variables
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% Compression options
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save('data.mat', 'x', '-v7'); % Compressed (default)
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save('data.mat', 'x', '-v6'); % Uncompressed, faster
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```
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### Loading Variables
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```matlab
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% Load all variables
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load('data.mat');
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% Load specific variables
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load('data.mat', 'x', 'y');
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% Load into structure
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S = load('data.mat');
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S = load('data.mat', 'x', 'y');
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x = S.x;
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y = S.y;
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% List contents without loading
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whos('-file', 'data.mat');
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vars = who('-file', 'data.mat');
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```
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### MAT-File Object (Large Files)
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```matlab
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% Create MAT-file object for partial access
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m = matfile('data.mat');
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m.Properties.Writable = true;
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% Read partial data
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x = m.bigArray(1:100, :); % First 100 rows only
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% Write partial data
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m.bigArray(1:100, :) = newData;
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% Get variable info
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sz = size(m, 'bigArray');
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```
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## Images
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### Reading Images
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```matlab
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% Read image
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img = imread('image.png');
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img = imread('image.jpg');
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img = imread('image.tiff');
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% Get image info
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info = imfinfo('image.png');
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info.Width
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info.Height
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info.ColorType
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info.BitDepth
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% Read specific frames (multi-page TIFF, GIF)
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img = imread('animation.gif', 3); % Frame 3
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[img, map] = imread('indexed.gif'); % Indexed image with colormap
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```
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### Writing Images
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```matlab
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% Write image
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imwrite(img, 'output.png');
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imwrite(img, 'output.jpg');
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imwrite(img, 'output.tiff');
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% With options
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imwrite(img, 'output.jpg', 'Quality', 95);
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imwrite(img, 'output.png', 'BitDepth', 16);
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imwrite(img, 'output.tiff', 'Compression', 'lzw');
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% Write indexed image with colormap
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imwrite(X, map, 'indexed.gif');
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% Append to multi-page TIFF
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imwrite(img1, 'multipage.tiff');
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imwrite(img2, 'multipage.tiff', 'WriteMode', 'append');
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```
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### Image Formats
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```matlab
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% Supported formats (partial list)
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% BMP - Windows Bitmap
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% GIF - Graphics Interchange Format
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% JPEG - Joint Photographic Experts Group
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% PNG - Portable Network Graphics
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% TIFF - Tagged Image File Format
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% PBM, PGM, PPM - Portable bitmap formats
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% Check supported formats
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formats = imformats;
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```
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## Tables and Data Types
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### Creating Tables
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```matlab
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% From variables
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T = table(var1, var2, var3);
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T = table(var1, var2, 'VariableNames', {'Col1', 'Col2'});
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% From arrays
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T = array2table(M);
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T = array2table(M, 'VariableNames', {'A', 'B', 'C'});
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% From cell array
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T = cell2table(C);
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T = cell2table(C, 'VariableNames', {'Name', 'Value'});
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% From struct
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T = struct2table(S);
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```
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### Accessing Table Data
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```matlab
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% By variable name
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col = T.VariableName;
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col = T.('VariableName');
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col = T{:, 'VariableName'};
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% By index
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row = T(5, :); % Row 5
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col = T(:, 3); % Column 3 as table
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data = T{:, 3}; % Column 3 as array
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subset = T(1:10, 2:4); % Subset as table
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data = T{1:10, 2:4}; % Subset as array
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% Logical indexing
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subset = T(T.Value > 5, :);
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```
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### Modifying Tables
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```matlab
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% Add variable
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T.NewVar = newData;
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T = addvars(T, newData, 'NewName', 'Col4');
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T = addvars(T, newData, 'Before', 'ExistingCol');
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% Remove variable
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T.OldVar = [];
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T = removevars(T, 'OldVar');
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T = removevars(T, {'Col1', 'Col2'});
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% Rename variable
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T = renamevars(T, 'OldName', 'NewName');
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T.Properties.VariableNames{'OldName'} = 'NewName';
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% Reorder variables
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T = movevars(T, 'Col3', 'Before', 'Col1');
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T = T(:, {'Col2', 'Col1', 'Col3'});
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```
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### Table Operations
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```matlab
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% Sorting
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T = sortrows(T, 'Column');
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T = sortrows(T, 'Column', 'descend');
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T = sortrows(T, {'Col1', 'Col2'}, {'ascend', 'descend'});
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% Unique rows
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T = unique(T);
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T = unique(T, 'rows');
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% Join tables
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T = join(T1, T2); % Inner join on common keys
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T = join(T1, T2, 'Keys', 'ID');
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T = innerjoin(T1, T2);
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T = outerjoin(T1, T2);
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% Stack/unstack
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T = stack(T, {'Var1', 'Var2'});
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T = unstack(T, 'Values', 'Keys');
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% Group operations
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G = groupsummary(T, 'GroupVar', 'mean', 'ValueVar');
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G = groupsummary(T, 'GroupVar', {'mean', 'std'}, 'ValueVar');
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```
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### Cell Arrays
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```matlab
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% Create cell array
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C = {1, 'text', [1 2 3]};
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C = cell(m, n); % Empty m×n cell array
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% Access contents
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contents = C{1, 2}; % Contents of cell (1,2)
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subset = C(1:2, :); % Subset of cells (still cell array)
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% Convert
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A = cell2mat(C); % To matrix (if compatible)
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T = cell2table(C); % To table
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S = cell2struct(C, fields); % To struct
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```
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### Structures
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```matlab
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% Create structure
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S.field1 = value1;
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S.field2 = value2;
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S = struct('field1', value1, 'field2', value2);
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% Access fields
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val = S.field1;
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val = S.('field1');
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% Field names
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names = fieldnames(S);
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tf = isfield(S, 'field1');
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% Structure arrays
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S(1).name = 'Alice';
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S(2).name = 'Bob';
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names = {S.name}; % Extract all names
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```
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## Low-Level File I/O
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### Opening and Closing Files
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```matlab
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% Open file
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fid = fopen('file.txt', 'r'); % Read
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fid = fopen('file.txt', 'w'); % Write (overwrite)
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fid = fopen('file.txt', 'a'); % Append
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fid = fopen('file.bin', 'rb'); % Read binary
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fid = fopen('file.bin', 'wb'); % Write binary
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% Check for errors
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if fid == -1
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error('Could not open file');
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end
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% Close file
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fclose(fid);
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fclose('all'); % Close all files
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```
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### Text File I/O
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```matlab
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% Read formatted data
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data = fscanf(fid, '%f'); % Read floats
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data = fscanf(fid, '%f %f', [2 Inf]); % Two columns
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C = textscan(fid, '%f %s %f'); % Mixed types
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% Read lines
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line = fgetl(fid); % One line (no newline)
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line = fgets(fid); % One line (with newline)
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% Write formatted data
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fprintf(fid, '%d, %f, %s\n', intVal, floatVal, strVal);
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fprintf(fid, '%6.2f\n', data);
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% Read/write strings
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str = fscanf(fid, '%s');
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fprintf(fid, '%s', str);
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```
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### Binary File I/O
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```matlab
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% Read binary data
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data = fread(fid, n, 'double'); % n doubles
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data = fread(fid, [m n], 'int32'); % m×n int32s
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data = fread(fid, Inf, 'uint8'); % All bytes
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% Write binary data
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fwrite(fid, data, 'double');
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fwrite(fid, data, 'int32');
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% Data types: 'int8', 'uint8', 'int16', 'uint16', 'int32', 'uint32',
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% 'int64', 'uint64', 'single', 'double', 'char'
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```
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### File Position
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```matlab
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% Get position
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pos = ftell(fid);
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% Set position
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fseek(fid, 0, 'bof'); % Beginning of file
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fseek(fid, 0, 'eof'); % End of file
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fseek(fid, offset, 'cof'); % Current position + offset
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% Rewind to beginning
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frewind(fid);
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% Check end of file
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tf = feof(fid);
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```
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### File and Directory Operations
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```matlab
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% Check existence
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tf = exist('file.txt', 'file');
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tf = exist('folder', 'dir');
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tf = isfile('file.txt');
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tf = isfolder('folder');
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% List files
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files = dir('*.csv'); % Struct array
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files = dir('folder/*.mat');
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names = {files.name};
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% File info
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info = dir('file.txt');
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info.name
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info.bytes
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info.date
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info.datenum
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% File operations
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copyfile('src.txt', 'dst.txt');
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movefile('src.txt', 'dst.txt');
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delete('file.txt');
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% Directory operations
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mkdir('newfolder');
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rmdir('folder');
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rmdir('folder', 's'); % Remove with contents
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cd('path');
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pwd % Current directory
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```
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### Path Operations
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```matlab
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% Construct paths
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fullpath = fullfile('folder', 'subfolder', 'file.txt');
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fullpath = fullfile(pwd, 'file.txt');
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% Parse paths
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[path, name, ext] = fileparts('/path/to/file.txt');
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% path = '/path/to', name = 'file', ext = '.txt'
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% Temporary files/folders
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tmpfile = tempname;
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tmpdir = tempdir;
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```
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