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Fixes for MATLAB code #13

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Fixes for MATLAB code #13

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6da76ef
Fixes for MATLAB code
aforren1 Nov 21, 2016
09e13eb
update from comment
aforren1 Nov 28, 2016
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192 changes: 95 additions & 97 deletions matlab/KRload.m
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Original file line number Diff line number Diff line change
@@ -1,113 +1,111 @@
%load in kinereach data (new cpp code), parsing the header file and the
%raw data

function [data,header,varargout] = KRload(varargin)
%clear all;
if nargin == 0
[fname,fpath] = uigetfile('*.*','Select data file to analyze');
else
fpath = varargin{1};
fname = '';
end
function [data, header, filename, filepath] = KRload(filename, filepath)
% KRLOAD Load in kinereach data (new c++ code),
% parsing the header file and the raw data.
%
% [data, header, filename, filepath] = KRLOAD(filename)
% The filename is the name of the file, e.g. 'mydata.dat', and
% the filepath is the full path to the data, e.g. 'C:/Users/data/'.
%
% If the filename and path is unspecified, a UI will open to allow
% manual selection of the file. If just the path is unspecified, the
% current working directory is assumed (and a warning emitted).
%

if nargin == 0
[filename, filepath] = uigetfile('*.*', 'Select data file to analyze.');
elseif ~exist('filename')
error('Must provide a filename.');
elseif ~exist('filepath')
warning('Assuming the current path is correct, may fail.');
filepath = pwd;
end

fid = fopen([fpath fname],'r');
fid = fopen([filepath filename], 'r');

doloop = 1;
while (doloop)
temp = fgetl(fid);
if strcmp(temp,'--')
%detect the end of the header
doloop = true;
while doloop
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@aforren1 aforren1 Nov 28, 2016 •
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This bit should probably just be

while true
    ...
    if condition
        break
    end
end

temp = fgetl(fid);
header.cols = textscan(temp,'%s');
header.cols = header.cols{1};
fgetl(fid);
doloop = 0;
else
hvals = textscan(temp,'%s %s');
if ~isempty(str2num(char(hvals{2})))
hvals = textscan(temp,'%s %d');
tmp = strrep(char(hvals{1}),':','');
eval(sprintf('header.%s = %d;',tmp,hvals{2}));
if strcmp(temp, '--')
%detect the end of the header
temp = fgetl(fid);
header.cols = textscan(temp, '%s');
header.cols = header.cols{1};
fgetl(fid);
doloop = false;
else
tmp = strrep(char(hvals{1}),':','');
tmp1 = strrep(char(hvals{2}),'.txt','');
eval(sprintf('header.%s = ''%s'';',tmp,char(tmp1)));
hvals = textscan(temp, '%s %s');
if ~isempty(str2num(char(hvals{2})))
hvals = textscan(temp, '%s %d');
tmp = strrep(char(hvals{1}), ':', '');
eval(sprintf('header.%s = %d;', tmp, hvals{2}));
else
tmp = strrep(char(hvals{1}), ':', '');
tmp1 = strrep(char(hvals{2}), '.txt', '');
eval(sprintf('header.%s = ''%s'';', tmp, char(tmp1)));
end
end

end
end

% %unknown columns, use this code for complete flexiblity
readstr = '';
for a = 1:length(header.cols)
switch(char(header.cols{a}))
case {'Device_Num','FakeTime','Time'}
readstr = [readstr '%d '];
case {'HandX','HandY','HandZ','HandYaw','HandPitch','HandRoll','Theta'}
readstr = [readstr '%f '];
case {'StartX','StartY','TargetX','TargetY'}
readstr = [readstr '%f '];
case 'Trace'
readstr = [readstr '%d '];
case 'Keymap'
readstr = [readstr '%s '];
otherwise
readstr = [readstr '%f '];
% unknown columns, use this code for complete flexiblity
readstr = '';
for a = 1:length(header.cols)
switch(char(header.cols{a}))
case {'Device_Num', 'FakeTime', 'Time'}
readstr = [readstr '%d '];
case {'HandX', 'HandY', 'HandZ', 'HandYaw', 'HandPitch', 'HandRoll', 'Theta'}
readstr = [readstr '%f '];
case {'StartX', 'StartY', 'TargetX', 'TargetY'}
readstr = [readstr '%f '];
case 'Trace'
readstr = [readstr '%d '];
case 'Keymap'
readstr = [readstr '%s '];
otherwise
readstr = [readstr '%f '];
end
end
end

% %known columns, use this code for proper formatting
% readstr = '%d %d %f %f %f %f %f %f %f %d'; %devNo, time, x, y, theta, startx, starty, tgtx, tgty, trace
dvals = textscan(fid, readstr, inf);

%doloop = 1;
%while (doloop)
dvals = textscan(fid,readstr,inf);
%compute number of birds
numBirds = length(unique(dvals{1}));

%compute number of birds
numBirds = length(unique(dvals{1}));
for a = 1:numBirds

for a = 1:numBirds

%divide data structure into appropriate fields, based on column names
for b = 1:length(header.cols)
eval(sprintf('data{%d}.%s = dvals{%d}(%d:%d:end);',a,char(header.cols{b}),b,a,numBirds));
end

if isfield(header,'Sampling_Rate') && isfield(data{a},'HandX')
data{a}.MakeTime = [0:1:length(data{a}.HandX)-1]'/header.Sampling_Rate*1000;
elseif isfield(data{a},'HandX')
data{a}.MakeTime = [0:1:length(data{a}.HandX)-1]';
elseif isfield(header,'Sampling_Rate') && isfield(data{a},'StickX')
data{a}.MakeTime = [0:1:length(data{a}.StickX)-1]'/header.Sampling_Rate*1000;
elseif isfield(data{a},'StickX')
data{a}.MakeTime = data{a}.SystemTime-data{a}.SystemTime(1);
else %unrecognized trial table type
data{a}.MakeTime = [];
end

%identify devide, if possible
if isfield(data{a},'Device_Num')
data{a}.Device_Num = unique(data{a}.Device_Num);
switch data{a}.Device_Num(1)
case 1
data{a}.BirdName = 'Left_Hand';
case 2
data{a}.BirdName = 'Left_Arm';
case 3
data{a}.BirdName = 'Right_Hand';
case 4
data{a}.BirdName = 'Right_Arm';
end %end switch
end %end if

end %end for loop
%divide data structure into appropriate fields, based on column names
for b = 1:length(header.cols)
eval(sprintf('data{%d}.%s = dvals{%d}(%d:%d:end);', a, char(header.cols{b}), b, a, numBirds));
end

fclose(fid);
if isfield(header, 'Sampling_Rate') && isfield(data{a},'HandX')
data{a}.MakeTime = [0:1:length(data{a}.HandX)-1]'/header.Sampling_Rate*1000;
elseif isfield(data{a}, 'HandX')
data{a}.MakeTime = [0:1:length(data{a}.HandX) - 1]';
elseif isfield(header, 'Sampling_Rate') && isfield(data{a},'StickX')
data{a}.MakeTime = [0:1:length(data{a}.StickX) - 1]'/header.Sampling_Rate*1000;
elseif isfield(data{a}, 'StickX')
data{a}.MakeTime = data{a}.SystemTime - data{a}.SystemTime(1);
else %unrecognized trial table type
data{a}.MakeTime = [];
end

if nargout > 2
varargout{1} = fname;
end
if nargout > 3
varargout{2} = fpath;
end
%identify device, if possible
if isfield(data{a},'Device_Num')
data{a}.Device_Num = unique(data{a}.Device_Num);
switch data{a}.Device_Num(1)
case 1
data{a}.BirdName = 'Left_Hand';
case 2
data{a}.BirdName = 'Left_Arm';
case 3
data{a}.BirdName = 'Right_Hand';
case 4
data{a}.BirdName = 'Right_Arm';
end %end switch
end %end if

end %end for loop

fclose(fid);
end