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dicominfo2.m
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dicominfo2.m
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			function metadata = dicominfo2(filename, varargin)
			%DICOMINFO Read metadata from DICOM message.
			% INFO = DICOMINFO(FILENAME) reads the metadata from the compliant
			% DICOM file specified in the string FILENAME.
			%
			% INFO = DICOMINFO(FILENAME, 'dictionary', D) uses the data dictionary
			% file given in the string D to read the DICOM message. The file in D
			% must be on the MATLAB search path. The default value is dicom-dict.mat.
			%
			% Example:
			%
			% info = dicominfo('CT-MONO2-16-ankle.dcm');
			%
			% See also DICOMREAD, DICOMWRITE, DICOMDISP, DICOMDICT, DICOMUID.

			% Copyright 1993-2014 The MathWorks, Inc.
			% MODIFIED by Rapha? Obrist (line 54)


			% Parse input arguments.
			if (nargin < 1)

			error(message('images:dicominfo:tooFewInputs'))

			end

			% Set the dictionary.
			args = parseInputs(varargin{:});
			dicomdict('set_current', args.Dictionary)
			dictionary = dicomdict('get_current');

			% Get the metadata.
			try

			% Get details about the file to read.
			fileDetails = getFileDetails(filename);

			% Ensure the file is actually DICOM.
			if (~isdicom(fileDetails.name))
			error(message('images:dicominfo:notDICOM'))
			end

			% Parse the DICOM file.
			attrs = dicomparse(fileDetails.name, ...
			fileDetails.bytes, ...
			getMachineEndian, ...
			false, ...
			dictionary);

			% Process the raw attributes.
			[metadata,attrNames] = processMetadata(attrs, true, dictionary);
			metadata = dicom_set_imfinfo_values(metadata);
			metadata = setMoreImfinfoValues(metadata, fileDetails);
			%metadata = processOverlays(metadata, dictionary);
			metadata = processCurveData(metadata, attrs, attrNames);

			pixelDataField = dicomlookup_actions('7fe0', '0010', dictionary);
			if (isfield(metadata, pixelDataField))
			metadata = rmfield(metadata, pixelDataField);
			end

			catch ME

			dicomdict('reset_current');
			rethrow(ME)

			end

			% Reset the dictionary.
			dicomdict('reset_current');



			function [metadata,attrNames] = processMetadata(attrs, isTopLevel, dictionary)

			if (isempty(attrs))
			metadata = [];
			return
			end

			% Create a structure for the output and get the names of attributes.
			[metadata, attrNames] = createMetadataStruct(attrs, isTopLevel, dictionary);

			% Fill the metadata structure, converting data along the way.
			for currentAttr = 1:numel(attrNames)

			this = attrs(currentAttr);
			metadata.(attrNames{currentAttr}) = convertRawAttr(this, dictionary);

			end



			function processedAttr = convertRawAttr(rawAttr, dictionary)

			% Information about whether to swap is contained in the attribute.
			swap = needToSwap(rawAttr);

			% Determine the correct output encoding.
			if (isempty(rawAttr.VR))

			% Look up VR for implicit VR files. Use 'UN' for unknown
			% tags. (See PS 3.5 Sec. 6.2.2.)
			vr = findVRFromTag(rawAttr.Group, rawAttr.Element, dictionary);
			if (~isempty(vr))

			% Some attributes have a conditional VR. Pick the first.
			rawAttr.VR = vr;
			if (numel(rawAttr.VR) > 2)
			rawAttr.VR = rawAttr.VR(1:2);
			end

			else
			rawAttr.VR = 'UN';
			end

			end

			% Convert raw data. (See PS 3.5 Sec. 6.2 for full VR details.)
			switch (rawAttr.VR)
			case {'AE','AS','CS','DA','DT','LO','LT','SH','ST','TM','UI','UT'}

			processedAttr = deblankAndStripNulls(char(rawAttr.Data));

			case {'AT'}

			% For historical reasons don't transpose AT.
			processedAttr = dicom_typecast(rawAttr.Data, 'uint16', swap);

			case {'DS', 'IS'}

			processedAttr = sscanf(char(rawAttr.Data), '%f\\');

			case {'FL', 'OF'}

			processedAttr = dicom_typecast(rawAttr.Data, 'single', swap)';

			case 'FD'

			processedAttr = dicom_typecast(rawAttr.Data, 'double', swap)';

			case 'OB'

			processedAttr = rawAttr.Data';

			case {'OW', 'US'}

			processedAttr = dicom_typecast(rawAttr.Data, 'uint16', swap)';

			case 'PN'

			processedAttr = parsePerson(deblankAndStripNulls(char(rawAttr.Data)));

			case 'SL'

			processedAttr = dicom_typecast(rawAttr.Data, 'int32', swap)';

			case 'SQ'

			processedAttr = parseSequence(rawAttr.Data, dictionary);

			case 'SS'

			processedAttr = dicom_typecast(rawAttr.Data, 'int16', swap)';

			case 'UL'

			processedAttr = dicom_typecast(rawAttr.Data, 'uint32', swap)';

			case 'UN'

			% It's possible that the attribute contains a private sequence
			% with implicit VR; in which case the Data field contains the
			% parsed sequence.
			if (isstruct(rawAttr.Data))
			processedAttr = parseSequence(rawAttr.Data, dictionary);
			else
			processedAttr = rawAttr.Data';
			end

			otherwise

			% PS 3.5-1999 Sec. 6.2 indicates that all unknown VRs can be
			% interpretted as UN.
			processedAttr = rawAttr.Data';

			end

			% Change empty arrays to 0-by-0.
			if isempty(processedAttr)
			processedAttr = reshape(processedAttr, [0 0]);
			end



			function byteOrder = getMachineEndian

			persistent endian

			if (~isempty(endian))
			byteOrder = endian;
			return
			end

			[~, ~, endian] = computer;
			byteOrder = endian;



			function args = parseInputs(varargin)

			% Set default values
			args.Dictionary = dicomdict('get');

			% Parse arguments based on their number.
			if (nargin > 1)

			paramStrings = {'dictionary'};

			% For each pair
			for k = 1:2:length(varargin)
			param = lower(varargin{k});


			if (~ischar(param))
			error(message('images:dicominfo:parameterNameNotString'));
			end

			idx = strmatch(param, paramStrings);

			if (isempty(idx))
			error(message('images:dicominfo:unrecognizedParameterName', param));
			elseif (length(idx) > 1)
			error(message('images:dicominfo:ambiguousParameterName', param));
			end

			switch (paramStrings{idx})
			case 'dictionary'

			if (k == length(varargin))
			error(message('images:dicominfo:missingDictionary'));
			else
			args.Dictionary = varargin{k + 1};
			end

			end % switch

			end % for

			end



			function personName = parsePerson(personString)
			%PARSEPERSON Get the various parts of a person name

			% A description and examples of PN values is in PS 3.5-2000 Table 6.2-1.

			pnParts = {'FamilyName'
			'GivenName'
			'MiddleName'
			'NamePrefix'
			'NameSuffix'};

			if (isempty(personString))
			personName = makePerson(pnParts);
			return
			end

			people = tokenize(personString, '\\'); % Must quote '\' for calls to STRREAD.

			personName = struct([]);

			for p = 1:length(people)

			% ASCII, ideographic, and phonetic characters are separated by '='.
			components = tokenize(people{p}, '=');

			if (isempty(components))
			personName = makePerson(pnParts);
			return
			end


			% Only use ASCII parts.

			if (~isempty(components{1}))

			% Get the separate parts of the person's name from the component.
			componentParts = tokenize(components{1}, '^');

			% The DICOM standard requires that PN values have five or fewer
			% values separated by "^". Some vendors produce files with more
			% than these person name parts.
			if (numel(componentParts) <= 5)

			% If there are the correct numbers, put them in separate fields.
			for q = 1:length(componentParts)

			personName(p).(pnParts{q}) = componentParts{q};

			end

			else

			% If there are more, just return the whole string.
			personName(p).FamilyName = people{p};

			end

			else

			% Use full string as value if no ASCII is present.
			if (~isempty(components))
			personName(p).FamilyName = people{p};
			end

			end

			end



			function personStruct = makePerson(pnParts)
			%MAKEPERSON Make an empty struct containing the PN fields.

			for p = 1:numel(pnParts)
			personStruct.(pnParts{p}) = '';
			end



			function processedStruct = parseSequence(attrs, dictionary)

			numItems = countItems(attrs);
			itemNames = getItemNames(numItems);

			% Initialize the structure to contain this structure.
			structInitializer = cat(1, itemNames, cell(1, numItems));
			processedStruct = struct(structInitializer{:});

			% Process each item (but not delimiters).
			item = 0;
			for idx = 1:numel(attrs)

			this = attrs(idx);
			if (~isDelimiter(this))
			item = item + 1;
			processedStruct.(itemNames{item}) = processMetadata(this.Data, false, dictionary);
			end

			end



			function header = getImfinfoFields

			header = {'Filename', ''
			'FileModDate', ''
			'FileSize', []
			'Format', 'DICOM'
			'FormatVersion', 3.0
			'Width', []
			'Height', []
			'BitDepth', []
			'ColorType', ''}';



			function metadata = setMoreImfinfoValues(metadata, d)

			metadata.Filename = d.name;
			metadata.FileModDate = d.date;
			metadata.FileSize = d.bytes;



			function details = getFileDetails(filename)

			% Get the fully qualified path to the file.
			fid = fopen(filename);
			if (fid > 0)

			fullPathFilename = fopen(fid);
			fclose(fid);

			else

			% Look for the file with a different extension.
			file = dicom_create_file_struct;
			file.Filename = filename;
			file = dicom_get_msg(file);

			if (isempty(file.Filename))
			error(message('images:dicominfo:noFileOrMessagesFound', filename));
			end

			% dicom_get_msg looks up the fully qualified path.
			fullPathFilename = file.Filename;

			end

			details = dir(fullPathFilename);
			details.name = fullPathFilename;



			function [metadata, attrNames] = createMetadataStruct(attrs, isTopLevel, dictionary)

			% Get the attribute names.
			totalAttrs = numel(attrs);
			attrNames = cell(1, totalAttrs);

			for currentAttr = 1:totalAttrs
			attrNames{currentAttr} = ...
			dicomlookup_actions(attrs(currentAttr).Group, ...
			attrs(currentAttr).Element, ...
			dictionary);

			% Empty attributes indicate that a public/retired attribute was
			% not found in the data dictionary. This used to be an error
			% condition, but is easily resolved by providing a special
			% attribute name.
			if (isempty(attrNames{currentAttr}))
			attrNames{currentAttr} = sprintf('Unknown_%04X_%04X', ...
			attrs(currentAttr).Group, ...
			attrs(currentAttr).Element);
			end
			end

			% Remove duplicate attribute names. Keep the last appearance of the attribute.
			[tmp, reorderIdx] = unique(attrNames);
			if (numel(tmp) ~= totalAttrs)
			warning(message('images:dicominfo:attrWithSameName'))
			end

			uniqueAttrNames = attrNames(sort(reorderIdx));
			uniqueTotalAttrs = numel(uniqueAttrNames);

			% Create a metadata structure to hold the parsed attributes. Use a
			% cell array initializer, which has a populated section for IMFINFO
			% data and an unitialized section for the attributes from the DICOM
			% file.
			if (isTopLevel)
			structInitializer = cat(2, getImfinfoFields(), ...
			cat(1, uniqueAttrNames, cell(1, uniqueTotalAttrs)));
			else
			structInitializer = cat(1, uniqueAttrNames, cell(1, uniqueTotalAttrs));
			end

			metadata = struct(structInitializer{:});



			function str = deblankAndStripNulls(str)
			%DEBLANKANDDENULL Deblank a string, treating char(0) as a blank.

			if (isempty(str))
			return
			end

			while (~isempty(str) && (str(end) == 0))
			str(end) = '';
			end

			str = deblank(str);



			function vr = findVRFromTag(group, element, dictionary)

			% Look up the attribute.
			attr = dicomlookup_helper(group, element, dictionary);

			% Get the vr.
			if (~isempty(attr))

			vr = attr.VR;

			else

			% Private creator attributes should be treated as CS.
			if ((rem(group, 2) == 1) && (element == 0))
			vr = 'UL';
			elseif ((rem(group, 2) == 1) && (element < 256))
			vr = 'CS';
			else
			vr = 'UN';
			end

			end



			function out = processOverlays(in, dictionary)

			out = in;

			% Look for overlays.
			allFields = fieldnames(in);
			idx = strmatch('OverlayData', allFields);

			if (isempty(idx))
			return
			end

			% Convert each overlay data attribute.
			for p = 1:numel(idx)

			olName = allFields{idx(p)};

			% The overlay fields can be present but empty.
			if (isempty(in.(olName)))
			continue;
			end

			% Which repeating group is this?
			[group, element] = dicomlookup_actions(olName, dictionary);

			% Get relevant details. All overlays are in groups 6000 - 60FE.
			overlay.Rows = double(in.(dicomlookup_actions(group, '0010', dictionary)));
			overlay.Columns = double(in.(dicomlookup_actions(group, '0011', dictionary)));

			sppTag = dicomlookup_actions(group, '0012', dictionary);
			if (isfield(in, sppTag))
			overlay.SamplesPerPixel = double(in.(sppTag));
			else
			overlay.SamplesPerPixel = 1;
			end

			bitsTag = dicomlookup_actions(group, '0100', dictionary);
			if (isfield(in, bitsTag))
			overlay.BitsAllocated = double(in.(bitsTag));
			else
			overlay.BitsAllocated = 1;
			end

			numTag = dicomlookup_actions(group, '0015', dictionary);
			if (isfield(in, numTag))
			overlay.NumberOfFrames = double(in.(numTag));
			else
			overlay.NumberOfFrames = 1;
			end

			% We could potential support more overlays later.
			if ((overlay.BitsAllocated > 1) \|\| (overlay.SamplesPerPixel > 1))

			warning(message('images:dicominfo:unsupportedOverlay', sprintf( '(%04X,%04X)', group, element )));
			continue;

			end

			% Process the overlay.
			for frame = 1:(overlay.NumberOfFrames)

			overlayData = tobits(in.(olName));
			numSamples = overlay.Columns * overlay.Rows * overlay.NumberOfFrames;
			out.(olName) = permute(reshape(overlayData(1:numSamples), ...
			overlay.Columns, ...
			overlay.Rows, ...
			overlay.NumberOfFrames), ...
			[2 1 3]);

			end

			end



			function out = processCurveData(in, attrs, attrNames)
			% Reference - PS 3.3 - 2003 C 10.2. The Curve Data's final data type
			% depends on DataValueRepresentation. Process those attributes here.

			% Passing in attrs because we may need to swap the data depending on the
			% endianness of the machine and the attribute.

			% default
			out = in;

			% Look for Curve Data.
			allFields = fieldnames(in);
			idx = strmatch('CurveData', allFields);

			if (isempty(idx))
			return
			end

			% All the Curve Data attributes will have the same endianness, so we just need
			% to check one attribute and apply that setting to the rest.

			curveDataName = allFields{idx(1)};
			curveDataLoc = strncmp(curveDataName,attrNames, length(curveDataName));
			swap = needToSwap(attrs(curveDataLoc));

			for p = 1 : numel(idx)

			curveDataName = allFields{idx(p)};

			underscore = strfind(curveDataName,'_');
			% The data type of the Curve Data comes from the
			% DataValueRepresentation attribute.
			numOfRepeatedAttr = curveDataName(underscore+1:end);
			dvrName = strcat('DataValueRepresentation','_',numOfRepeatedAttr);

			if ~isfield(in,dvrName)
			% do nothing
			continue;
			else

			dataType = in.(dvrName);
			% See PS 3.3-2003, C 10.2.1.2
			switch dataType
			case 0
			expDataType = 'uint16';
			case 1
			expDataType = 'int16';
			case 2
			expDataType = 'single';
			case 3
			expDataType = 'double';
			case 4
			expDataType = 'int32';
			otherwise
			warning(message('images:dicominfo:unknownDataType', dataType));
			end

			% We need to undo any previous swapping before calling typecast, and do the
			% final swapping afterwards.

			if swap
			out.(curveDataName) = ...
			swapbytes(typecast(swapbytes(in.(curveDataName)), ...
			expDataType));
			else
			out.(curveDataName) = typecast(in.(curveDataName), expDataType);
			end
			end
			end



			function itemNames = getItemNames(numberOfItems)

			% Create a cell array of item names, which can be quickly used.
			persistent namesCell
			if (isempty(namesCell))
			namesCell = generateItemNames(50);
			end

			% If the number of cached names is too small, expand it and recache.
			if (numberOfItems > numel(namesCell))
			namesCell = generateItemNames(numberOfItems);
			end

			% Return the first n item names.
			itemNames = namesCell(1:numberOfItems);



			function namesCell = generateItemNames(numberOfItems)

			namesCell = cell(1, numberOfItems);
			for idx = 1:numberOfItems
			namesCell{idx} = sprintf('Item_%d', idx);
			end



			function tf = needToSwap(currentAttr)

			switch (getMachineEndian)
			case 'L'
			if (currentAttr.IsLittleEndian)
			tf = false;
			else
			tf = true;
			end

			case 'B'
			if (currentAttr.IsLittleEndian)
			tf = true;
			else
			tf = false;
			end

			otherwise
			error(message('images:dicominfo:unknownEndian', getMachineEndian))

			end



			function tf = isDelimiter(attr)

			% True if (FFFE,E00D) or (FFFE,E0DD).
			tf = (attr.Group == 65534) && ...
			((attr.Element == 57357) \|\| (attr.Element == 57565));



			function count = countItems(attrs)

			if (isempty(attrs))
			count = 0;
			else
			% Find the items (FFFE,E000) in the array of attributes (all of
			% which are item tags or delimiters; no normal attributes
			% appear in attrs here).
			idx = find(([attrs(:).Group] == 65534) & ...
			([attrs(:).Element] == 57344));
			count = numel(idx);
			end

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