[feat] merge nii/jnii/hdf5/tsv reading functions self-contained

getvarfrom.m

@@ -0,0 +1,33 @@
+function p = getvarfrom(ws, name)
+%
+% p=getvarfrom(ws,name)
+%
+% get variable value by name from specified work-space
+%
+% author: Qianqian Fang, <q.fang at neu.edu>
+%
+% input:
+%    ws: name of the work-space, for example, 'base'
+%    name: name string of the variable
+%
+% output:
+%    p: the value of the specified variable, if the variable does not
+%       exist, return empty array
+%
+% -- this function is part of iso2mesh toolbox (http://iso2mesh.sf.net)
+%
+
+wsname = ws;
+if (~iscell(ws))
+    wsname = cell(1);
+    wsname{1} = ws;
+end
+
+p = [];
+for i = 1:length(wsname)
+    isdefined = evalin(wsname{i}, ['exist(''' name ''')']);
+    if (isdefined == 1)
+        p = evalin(wsname{i}, name);
+        break
+    end
+end

loadbidstsv.m

@@ -0,0 +1,92 @@
+function data = loadbidstsv(tsvfile, delim)
+%
+%    data = loadbidstsv(tsvfile)
+%       or
+%    data = loadbidstsv(tsvfile, delim)
+%
+%    Loading a BIDS-formatted .tsv (tab-separated values) or .tsv.gz file as a
+%    struct; numerical fields are converted to floating-point data records
+%    when possible; the header of the file is parsed to define sub-field
+%    names
+%
+%    author: Qianqian Fang (q.fang <at> neu.edu)
+%
+%    input:
+%        tsvfile: the path to the .tsv file
+%        delim: (optional) if not set, tab ('\t') is used as column delimiter
+%
+%    examples:
+%        data = loadbidstsv('participants.tsv');
+%
+%    license:
+%        BSD license, see LICENSE_BSD.txt files for details
+%
+% -- this function is part of JBIDS toolbox (https://neurojson.org/#software)
+%
+
+if (nargin < 2)
+    delim = sprintf('\t');
+end
+
+data = struct;
+
+if (~isempty(regexp(tsvfile, '\.[Gg][Zz]$', 'once')))
+    finput = fopen(tsvfile, 'rb');
+    tsvdata = fread(finput, inf, 'uint8=>uint8');
+    fclose(finput);
+
+    if (~exist('gzipdecode', 'file'))
+        error('To process zipped files, you must install gzipdecode.m from the JSONLab toolbox: http://github.com/fangq/jsonlab');
+    end
+    fid = char(gzipdecode(tsvdata));
+    clear tsvdata;
+    [header, endpos] = regexp(fid, '([^\n\r]*)', 'once', 'tokens', 'end');
+    if (~isempty(header))
+        header = header{1};
+        fid = fid((endpos + 1):end);
+    end
+else
+    fid = fopen(tsvfile, 'rt');
+    header = fgetl(fid);
+    header = regexprep(header, '\s*$', '');
+end
+
+if (isempty(header))
+    return
+end
+
+if (exist('strsplit'))
+    cols = strsplit(header, delim);
+else
+    cols = regexp(header, '\t*([^\t]*)\t*', 'tokens');
+    cols = cellfun(@(x) x{:}, cols, 'uniformoutput', 0);
+end
+cols = cellfun(@encodevarname, cols, 'uniformoutput', 0);
+if (~isempty(cols))
+    body = textscan(fid, [repmat('%s\t', 1, length(cols) - 1), '%s'], 'delimiter', '\t');
+    if (length(body) ~= length(cols))
+        error('invalid tsv');
+    end
+    for i = 1:length(body)
+        try
+            % bodynum = cellfun(@(x) sscanf(regexprep(x,'^n/a$','NaN'), '%f'), body{i}, 'uniformoutput', 0);
+            bodynum = cellfun(@(x) sscanf(x, '%f\t'), body{i}, 'uniformoutput', 0);
+            if (exist('isna'))
+                len = cellfun(@(x) numel(x) * (~isna(sum(x))), bodynum);
+            else
+                len = cellfun(@numel, bodynum);
+            end
+            if (any(len))
+                body{i}(len > 0) = bodynum(len > 0);
+                if (all(len))
+                    body{i} = cell2mat(body{i});
+                end
+            end
+        catch ME
+            warning(ME.message);
+        end
+        data.(cols{i}) = body{i}(:).';
+    end
+end
+
+fclose(fid);