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gather_apex_data.m
3aa2120ee410master

gather_apex_data.m
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			% GATHER_APEX_DATA gathers all the data from APEX compressed archives
			% into individual CSV files that can be loaded by Octave.
			%
			% Blanchoud Group, UNIFR
			% Simon Blanchoud
			% 29/11/2020
			function csv_files = gather_apex_data(fnames)

			% load the required packages
			pkg load io

			% Format the input as a list of cells
			if ~iscell(fnames)
			if (isfile(fnames))
			fnames = {fnames};
			elseif (isfolder(fnames))
			fnames = glob(fullfile(fnames, '*.tgz'));
			end
			end

			% Prepare the temporary folder
			tmpdir = fullfile(pwd, 'TmpData');
			if (length(glob(fullfile(tmpdir, '*.csv')))>0)
			delete(fullfile(tmpdir, '*.csv'));
			end

			% Prepare the output files
			csv_files = {};

			% Loop through all files to gather
			for i=1:length(fnames)

			% Extract the actual files
			files = unpack(fnames{i}, tmpdir, 'tgz');

			% Loop through those files
			for j=1:length(files)
			xml = fullfile(tmpdir,files{j});

			% Make sure this is an actual file
			if isfile(xml)

			% Just try loading it as an XML file, ignore other types
			try
			dom = xmlread(xml);
			catch ME
			disp(ME.message)
			continue;
			end

			% Get the content of the file
			content = dom.getDocumentElement();
			content.normalize();

			% Check which type of file this is
			type = content.getNodeName();
			switch type
			case 'datalog'
			node = 'record';
			target = 'probe';

			% Currently we only parse the datalog
			otherwise
			node = '';
			target = '';
			end

			% Get the nodes that are actually useful
			nodes = content.getElementsByTagName(node);

			% And convert them to CSV
			new_files = convert_xml(nodes, target, tmpdir);
			csv_files = [csv_files; new_files(:)];
			end
			end

			% Delete the temporary files
			[dname, fname, ext] = fileparts(fnames{i});
			delete(fullfile(tmpdir, fname, '*'));
			rmdir(fullfile(tmpdir, fname));
			end

			% Remove duplicates
			csv_files = unique(csv_files);

			return;
			end

			% Here we physically copy the XML data into a CSV file
			function files = convert_xml(xml, target, fdir)

			% Some handlers for the files to be written
			files = {};
			fids = struct();

			% We loop over all the nodes in the XML
			for i=1:xml.getLength()
			item = xml.item(i-1);

			% We loop over all the attributes of each node
			for j=1:item.getLength()
			node = item.item(j-1);

			% We check which type of node this is
			name = node.getNodeName();
			switch name

			% We extract the data from the target type
			case target

			% We get all the data from the child nodes
			content = node2cell(node.getChildNodes());

			% We loop through all the cells and copy the proper data
			name = '';
			type = '';
			val = NaN;
			for k=1:size(content, 1)
			switch content{k,1}
			case 'name'
			name = content{k,2};
			case 'type'
			type = content{k,2};
			case 'value'
			val = str2double(content{k,2});
			end
			end

			% If we got all the data we need, then we write it
			if (~isnan(val) && ~isempty(name))

			% We store the file handlers in a structure, which we
			% need to create if it isn't ready yet
			if (~isfield(fids, name))
			fname = fullfile(fdir, [name '.csv']);
			fids.(name) = fopen(fname, 'a');

			if (fids.(name) > -1)
			files{end+1} = fname;
			else
			error(['Cannot create the proper CSV file at ' fname])
			end
			end

			% Actually write the data on disk
			fprintf(fids.(name), '%d,%f\n', curr_time, val);
			end

			% We store the date for proper ordering of the CSV
			case 'date'
			val = node.getTextContent();
			[curr_time, indx] = strptime(val, '%m/%d/%Y %H:%M:%S');
			if (indx > length(val))
			curr_time = mktime(curr_time);
			else
			error(['Cannot interpret the time format ' val]);
			end
			otherwise
			val = '';
			end
			end
			end

			% We close all the handlers
			fields = fieldnames(fids);
			for i=1:length(fields)
			fclose(fids.(fields{i}));
			end

			return;
			end

			% Here we extract the nodes into a cell matrix
			function data = node2cell(nodes)

			% We populate a {name, text} stucture
			data = cell(0,2);
			for i=1:nodes.getLength()
			node = nodes.item(i-1);
			node.normalize();

			% Get the two fields
			name = node.getNodeName();
			val = node.getTextContent();

			% If there is something, store it
			if (~isempty(name) && name(1)~='#')
			data{end+1, 1} = name;
			data{end, 2} = val;
			end
			end

			return;
			end

SiBoRG/helpers/gather_apex_data.m3aa2120ee410master

gather_apex_data.mView Options

SiBoRG/helpers/gather_apex_data.m
3aa2120ee410master

gather_apex_data.m
View Options