Initial commit

.gitattributes

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+# Set the default behavior, in case people don't have core.autocrlf set.
+* text=auto
+
+# Explicitly declare text files you want to always be normalized and converted
+# to native line endings on checkout.
+*.c text
+*.h text
+*.m text
+*.sh text
+
+# Denote all files that are truly binary and should not be modified.
+*.png binary
+*.jpg binary
+*.mj2 binary
+*.tif binary

.gitignore

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+*.mj2
+*.tif
+aside
+mj2tif-test-input-folder
+mj2tif-test-output-folder
+repo

is_mj2_same_as_tif.m

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+function result = is_mj2_same_as_tif(mj2_file_name, tif_file_name)
+    % Converts a single .mj2 file at input_file_name to a multi-image .tif
+    % at output_file_name.  Will overwrite pre-existing file at
+    % output_file_name, if present.
+
+    mj2_stack = read_16bit_grayscale_mj2(mj2_file_name) ;
+    tif_stack = read_16bit_grayscale_tif(tif_file_name) ;
+    result = isequal(class(mj2_stack), class(tif_stack)) && isequal(size(mj2_stack), size(tif_stack)) && all(all(all(mj2_stack==tif_stack))) ;
+end

mj2tif.m

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+function mj2tif(input_folder_name, output_folder_name, do_verify)
+    % Converts each .mj2 file in input_folder_name to a multi-image .tif in
+    % output_folder_name.  Will overwrite pre-existing files in
+    % output_folder_name, if present.
+
+    if nargin<3 ,
+        do_verify = false ;
+    end
+
+    if ~exist(output_folder_name, 'dir') ,
+        mkdir(output_folder_name) ;
+    end
+    entity_names = setdiff(simple_dir(input_folder_name), {'.' '..'}) ;
+    entity_count = length(entity_names) ;
+    for i = 1 : entity_count ,
+        entity_name = entity_names{i} ;        
+        entity_path = fullfile(input_folder_name, entity_name) ;
+        if exist(entity_path, 'dir') ,
+            % if a folder, recurse
+            output_entity_path = fullfile(output_folder_name, entity_name) ;
+            mj2tif(entity_path, output_entity_path) ;
+        else
+            % if a normal file, convert to .tif if it's a .mj2, or just
+            % copy otherwise
+            [~,~,ext] = fileparts(entity_path) ;
+            if isequal(ext, '.mj2') ,
+                output_entity_path = fullfile(output_folder_name, replace_extension(entity_name, '.tif')) ;
+                if ~exist(output_entity_path, 'file') ,
+                    fprintf('About to convert %s...', entity_path);
+                    tic_id = tic() ;
+                    mj2tif_single(entity_path, output_entity_path, do_verify) ;
+                    duration  = toc(tic_id) ;
+                    fprintf(' took %g seconds\n', duration) ;
+                end
+            else
+                output_entity_path = fullfile(output_folder_name, entity_name) ;
+                if ~exist(output_entity_path, 'file') ,
+                    copyfile(entity_path, output_entity_path) ;
+                end
+            end
+        end
+    end
+end

mj2tif_single.m

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+function mj2tif_single(input_file_name, output_file_name, do_verify)
+    % Converts a single .mj2 file at input_file_name to a multi-image .tif
+    % at output_file_name.  Will overwrite pre-existing file at
+    % output_file_name, if present.
+
+    if nargin<3 ,
+        do_verify = false ;
+    end
+
+    input_file = VideoReader(input_file_name) ;
+    frame_index = 0 ;
+    while input_file.hasFrame() ,
+        frame_index = frame_index + 1 ; 
+        frame = input_file.readFrame() ;
+        if frame_index == 1 ,
+            imwrite(frame, output_file_name, 'WriteMode', 'overwrite',  'Compression', 'none') ;
+        else
+            imwrite(frame, output_file_name, 'WriteMode', 'append',  'Compression', 'none') ;            
+        end        
+    end    
+
+    if do_verify ,
+        if ~is_mj2_same_as_tif(input_file_name, output_file_name) ,
+            error('%s is not the same as %s\n', output_file_name, input_file_name) ;
+        end
+    end
+end

read_16bit_grayscale_mj2.m

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+function stack = read_16bit_grayscale_mj2(file_name)
+    input_file = VideoReader(file_name) ;
+    n_rows = input_file.Height ;
+    n_cols = input_file.Width ;
+    n_pages_approx = ceil(input_file.FrameRate * input_file.Duration) ;  % hopefully big enough
+    stack = zeros([n_rows n_cols n_pages_approx], 'uint16') ;
+    frame_index = 0 ;
+    while input_file.hasFrame() ,
+        frame_index = frame_index + 1 ; 
+        frame = input_file.readFrame() ;
+        stack(:,:,frame_index) = frame ;
+    end    
+    n_pages = frame_index ;
+    stack = stack(:,:,1:n_pages) ;  
+end

read_16bit_grayscale_tif.m

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+function stack = read_16bit_grayscale_tif(file_name)
+    info = imfinfo(file_name, 'tif') ;
+    n_pages = length(info) ;
+    if n_pages>0 ,
+        first_frame_info = info(1) ;
+        n_cols = first_frame_info.Width;
+        n_rows = first_frame_info.Height;
+    else
+        n_cols = 0 ;
+        n_rows = 0 ;
+    end
+    stack  = zeros([n_rows n_cols n_pages], 'uint16');
+    for i = 1:n_pages ,
+        stack(:,:,i) = imread(file_name, 'Index', i, 'Info', info) ;
+    end
+end

replace_extension.m

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+function result = replace_extension(file_name, new_extension)
+    % Replace the extension of the given file_name with the new_extension
+    [path_to_parent, base_name, ~] = fileparts(file_name) ;
+    result = fullfile(path_to_parent, horzcat(base_name, new_extension)) ;
+end

simple_dir.m

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+function file_names = simple_dir(folder_name)
+    % Does what I wish dir() did: just return a cell array of the directory
+    % entries, without all the other stuff.
+    s = dir(folder_name) ;
+    file_names = {s.name} ;
+end