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rINSTCONTROL/@MyLog/MyLog.m
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MyLog.m
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% Class to store data versus time.
% Data can be continuously appended and saved. It is possible to add
% labels (time marks) for particular moments in time. Data can be saved
% and plotted with the time marks.
% Metadata for this class is stored independently.
% If instantiated as MyLog(load_path) then
% the content is loaded from file
classdef MyLog < matlab.mixin.Copyable
properties (Access = public, SetObservable = true)
% Save time as posixtime up to ms precision
time_fmt = '%14.3f'
% Save data as reals with up to 14 decimal digits. Trailing zeros
% are removed by %g
data_fmt = '%.14g'
% Data column and line separators
column_sep = '\t'
line_sep = '\r\n'
% File extension that is appended by default when saving the log
% if a different one is not specified explicitly
data_file_ext = '.log'
% File extension for metadata
meta_file_ext = '.meta'
% Formatting options for the metadata
metadata_opts = {}
file_name = '' % Used to save or load the data
data_headers = {} % Cell array of column headers
length_lim = Inf % Keep the log length below this limit
% Format for string representation of timestamps
datetime_fmt = 'yyyy-MMM-dd HH:mm:ss'
save_cont = false % If true changes are continuously saved
end
properties (GetAccess = public, SetAccess = protected, ...
SetObservable = true)
timestamps % Times at which data was aqcuired
data % Array of measurements
% Structure array that stores labeled time marks
TimeLabels = struct( ...
'time', {}, ... % datetime object
'time_str', {}, ... % time in text format
'text_str', {}); % message string
% Structure array that stores all the axes the log is plotted in
PlotList = struct( ...
'Axes', {}, ... % axes handles
'DataLines',{}, ... % data line handles
'LbLines', {}, ... % label line handles
'BgLines', {}); % label line background handles
% First timestamp that was saved in the current file. This value
% is used to decide which time labels to retain under when the log
% data is being trimmed.
FirstSaveTime = datetime.empty()
end
properties (Dependent = true)
channel_no % Number of data colums
data_line_fmt % Format specifier for one data row to be printed
column_headers % Time column header + data column headers
data_file_name % File name with extension for data saving
meta_file_name % File name with extension for metadata saving
timestamps_num % Timestamps converted to numeric format
end
methods (Access = public)
function this = MyLog(varargin)
P = MyClassParser(this);
processInputs(P, this, varargin{:});
end
% save the entire data record
function save(this, filename)
% File name can be either supplied explicitly or given as the
% file_name property
if nargin() < 2
filename = this.file_name;
else
this.file_name = filename;
end
assert(~isempty(filename), 'File name is not provided.');
datfname = this.data_file_name;
stat = createFile(datfname);
if ~stat
return
end
fid = fopen(datfname, 'w');
% Write column headers
str = printDataHeaders(this);
fprintf(fid, '%s', str);
% Write the bulk of data
fmt = this.data_line_fmt;
for i = 1:length(this.timestamps)
fprintf(fid, fmt, this.timestamps_num(i), this.data(i,:));
end
fclose(fid);
this.FirstSaveTime = this.timestamps(1);
% Save time labels in a separate file
saveMetadata(this);
end
%% Plotting
% Plot the log data with time labels. Reurns plotted line objects.
function Pls = plot(this, varargin)
[~, ncols] = size(this.data);
p = inputParser();
% Axes in which log should be plotted
addOptional(p, 'Axes', [], @(x)assert( ...
isa(x,'matlab.graphics.axis.Axes')||...
isa(x,'matlab.ui.control.UIAxes'),...
'Argument must be axes or uiaxes.'));
% If time labels are to be displayed
addParameter(p, 'time_labels', true, @islogical);
% If legend is to be displayed
addParameter(p, 'legend', true, @islogical);
% Logical vector defining the data columns to be displayed
addParameter(p, 'isdisp', true(1,ncols), @(x) assert(...
islogical(x) && isvector(x) && length(x)==ncols, ...
['''isdisp'' must be a logical vector of the size ',...
'equal to the number of data columns.']));
parse(p, varargin{:});
if ~isempty(p.Results.Axes)
Axes = p.Results.Axes;
else
Axes = gca();
end
% Find out if the log was already plotted in these axes. If
% not, appned Ax to the PlotList.
ind = findPlotInd(this, Axes);
if isempty(ind)
l = length(this.PlotList);
this.PlotList(l+1).Axes = Axes;
ind = l+1;
end
% Plot data
if isempty(this.PlotList(ind).DataLines)
% If the log was never plotted in Ax,
% plot using default style and store the line handles
Pls = line(Axes, this.timestamps, this.data);
this.PlotList(ind).DataLines = Pls;
else
% Replace existing data
Pls = this.PlotList(ind).DataLines;
for i = 1:length(Pls)
% Set new data and timestamps at the same time to
% prevent a conflict of array sizes
set(Pls(i), ...
'XData', this.timestamps, ...
'YData', this.data(:,i));
end
end
% Set the visibility of lines
if ~ismember('isdisp', p.UsingDefaults)
for i = 1:ncols
Pls(i).Visible = p.Results.isdisp(i);
end
end
if p.Results.time_labels
% Plot time labels
plotTimeLabels(this, ind);
else
% Hide existing time labels
try
set(this.PlotList(ind).LbLines, 'Visible', 'off');
set(this.PlotList(ind).BgLines, 'Visible', 'off');
catch ME
warning(ME.message)
end
end
% Add legend
if isempty(Axes.Legend)
legend(Axes, 'Location', 'southwest');
end
if p.Results.legend && ~isempty(this.data_headers) && ...
~isempty(this.data)
% Display the legend
Axes.Legend.Visible = 'on';
Axes.Legend.String = this.data_headers;
% Include only those lines that are visible
for i = 1:ncols
Pls(i).Annotation.LegendInformation.IconDisplayStyle = ...
Pls(i).Visible;
end
else
% Hide the legend
Axes.Legend.Visible = 'off';
end
end
% Append data point to the log
function appendData(this, Time, val)
% Format checks on the input data
assert(isa(Time, 'datetime') || isnumeric(Time),...
['''time'' argument must be numeric or ',...
'of the class datetime.']);
assert(isrow(val) && isnumeric(val), ...
'''val'' argument must be a numeric row vector.');
if ~isempty(this.data)
[~, ncols] = size(this.data);
assert(length(val) == ncols,['Length of ''val'' ' ...
'does not match the number of data columns']);
end
% Ensure time format
if isa(Time,'datetime')
Time.Format = this.datetime_fmt;
end
% Append new data and time stamps
this.timestamps = [this.timestamps; Time];
this.data = [this.data; val];
% Ensure the log length is within the length limit
trim(this);
% Optionally save the new data point to file
if this.save_cont
try
if exist(this.data_file_name, 'file') == 2
% Otherwise open for appending
fid = fopen(this.data_file_name, 'a');
else
% If the file does not exist, create it and write
% the column headers
createFile(this.data_file_name);
fid = fopen(this.data_file_name, 'w');
str = printDataHeaders(this);
fprintf(fid, '%s', str);
end
% Convert the new timestamps to numeric form for saving
if isa(Time, 'datetime')
time_num = posixtime(Time);
else
time_num = Time;
end
% Append new data points to file
fprintf(fid, this.data_line_fmt, time_num, val);
fclose(fid);
if isempty(this.FirstSaveTime)
this.FirstSaveTime = Time;
end
catch
warning(['Logger cannot save data at time = ',...
datestr(datetime('now', ...
'Format', this.datetime_fmt))]);
% Try closing fid in case it is still open
try
fclose(fid);
catch
end
end
end
end
%% Time labels
% Add label
function addTimeLabel(this, varargin)
p = inputParser();
addParameter(p, 'Time', datetime('now'), ...
@(x)assert(isa(x, 'datetime'), ['''Time'' must be of ' ...
'the type datetime.']))
addParameter(p, 'text', '', ...
@(x)assert(iscellstr(x) || ischar(x) || isstring(x), ...
'''text'' must be a string or cell array of strings.'))
% If 'index' is specified, then the function configures an
% existing time label instead of adding a new one
addParameter(p, 'index', [], ...
@(x)assert(floor(x)==x && x<=length(this.TimeLabels), ...
['Index must be a positive integer not exceeding the ' ...
'number of time labels.']))
parse(p, varargin{:})
Time = p.Results.Time;
Time.Format = this.datetime_fmt;
if ismember('text', p.UsingDefaults)
% Invoke a dialog to input label time and name
if ismember('index', p.UsingDefaults)
% Default dialog field values
dlg_args = {'', datestr(Time)};
else
% Provide existing values for modification
Tlb = this.TimeLabels(p.Results.index);
dlg_args = {char(Tlb.text_str), Tlb.time_str};
end
answ = inputdlg({'Label text', 'Time'},'Add time label',...
[2 40; 1 40], dlg_args);
% If 'Cancel' button is pressed or no input is provided, do
% not modify or add a new label
if isempty(answ) || isempty(answ{1})
return
end
% Convert the inputed value to datetime with proper format
Time = datetime(answ{2}, 'Format', this.datetime_fmt);
% Store multiple lines as cell array
str = cellstr(answ{1});
else
str = cellstr(p.Results.text);
end
if ~isempty(this.timestamps) && (Time < this.timestamps(1))
warning(['The time of label ''%s'' is earlier than ' ...
'the first timestamp in memory. Such time label ' ...
'will not be plotted but will be saved in ' ...
'metadata.'], str{1});
end
if ~isempty(this.FirstSaveTime) && (Time < this.FirstSaveTime)
warning(['The time of label ''%s'' is earlier than ' ...
'the first timestamp in the current data file. ' ...
'Such time label will not be automatically saved ' ...
'in metadata.'], str{1});
end
% Find the index of time label. We do not supply a default
% value for the end of the list in case the length was changed
% over the course of function execution.
if ismember('index', p.UsingDefaults)
ind = length(this.TimeLabels)+1;
else
ind = p.Results.index;
end
this.TimeLabels(ind).time = Time;
this.TimeLabels(ind).time_str = datestr(Time);
this.TimeLabels(ind).text_str = str;
% Order time labels by ascending time
sortTimeLabels(this);
if this.save_cont
saveMetadata(this);
end
end
function deleteTimeLabel(this, ind)
this.TimeLabels(ind) = [];
if this.save_cont
saveMetadata(this);
end
end
% Show the list of labels in a readable format
function lst = printTimeLabels(this)
if isempty(this.TimeLabels)
lst = {};
return
end
if ~isempty(this.timestamps)
% Select only those time labels that are within
% the interval of time of currently stored data
t_ind = ([this.TimeLabels.time] >= this.timestamps(1));
Tl = this.TimeLabels(t_ind);
else
Tl = this.TimeLabels;
end
% The returned output is a list of character strings
lst = cell(length(Tl), 1);
for i = 1:length(Tl)
if ~isempty(Tl(i).text_str)
% Display the first line of label
lbl = Tl(i).text_str{1};
else
lbl = '';
end
lst{i} = [Tl(i).time_str, ' ', lbl];
end
end
%% Misc public functions
% Clear log data and time labels
function clear(this)
% Clear while preserving the array types
this.TimeLabels(:) = [];
% Delete all the data lines and time labels
for i=1:length(this.PlotList)
delete(this.PlotList(i).DataLines);
delete(this.PlotList(i).LbLines);
delete(this.PlotList(i).BgLines);
end
this.PlotList(:) = [];
% Clear data and its type
this.timestamps = [];
this.data = [];
% Switch off continuous saving to prevent the overwriting of
% previously saved data
this.save_cont = false;
end
% Convert the log channel record to trace
function Trace = toTrace(this, varargin)
p = inputParser();
addParameter(p, 'channel', 1, ...
@(x)assert(x>0 && floor(x)==x && x<=this.channel_no, ...
['Channel number must be an integer between 1 and ' ...
num2str(this.channel_no) '.']));
addParameter(p, 'index', []);
% If false, the beginning of x data in the trace is shifted to
% zero
addParameter(p, 'absolute_time', false, @islogical);
parse(p, varargin{:});
n_ch = p.Results.channel;
Trace = MyTrace();
if ismember('index', p.UsingDefaults)
Trace.x = this.timestamps_num;
Trace.y = this.data(:, n_ch);
else
Trace.x = this.timestamps_num(p.Results.index);
Trace.y = this.data(p.Results.index, n_ch);
end
Trace.name_x = 'Time';
Trace.unit_x = 's';
if ~p.Results.absolute_time
% Shift the beginning of data to zero
Trace.x = Trace.x-Trace.x(1);
end
if length(this.data_headers) >= n_ch
% Try extracting the name and unit from the column header.
% The regexp will match anything of the format 'x (y)' with
% any types of brackets, (), [] or {}.
tokens = regexp(this.data_headers{n_ch}, ...
'(.*)[\(\[\{](.*)[\)\]\}]', 'tokens');
if ~isempty(tokens)
% Removes leading and trailing whitespaces
tokens = strtrim(tokens{1});
Trace.name_y = tokens{1};
Trace.unit_y = tokens{2};
else
Trace.name_y = this.data_headers{n_ch};
end
end
end
end
methods (Access = public, Static = true)
% Load log from file. Formatting parameters can be supplied as
% varargin
function L = load(filename, varargin)
assert(exist(filename, 'file') == 2, ...
['File ''', filename, ''' is not found.'])
L = MyLog(varargin{:});
L.file_name = filename;
% Load metadata if file is found
if exist(L.meta_file_name, 'file') == 2
Mdt = MyMetadata.load(L.meta_file_name,L.metadata_opts{:});
setMetadata(L, Mdt);
else
disp(['Log metadata file is not found, continuing ' ...
'without it.']);
end
% Read column headers from the data file
fid = fopen(filename,'r');
dat_col_heads = strsplit(fgetl(fid), L.column_sep, ...
'CollapseDelimiters', true);
fclose(fid);
% Assign column headers
if length(dat_col_heads) > 1
L.data_headers = dat_col_heads(2:end);
end
% Read data as delimiter-separated values and convert to cell
% array, skip the first line containing column headers
fulldata = dlmread(filename, L.column_sep, 1, 0);
L.data = fulldata(:, 2:end);
L.timestamps = fulldata(:, 1);
% Convert time stamps to datetime if the time column header
% is 'posixtime'
if ~isempty(dat_col_heads) && ...
contains(dat_col_heads{1}, 'posix', 'IgnoreCase', true)
L.timestamps = datetime(L.timestamps, ...
'ConvertFrom', 'posixtime', 'Format', L.datetime_fmt);
end
L.FirstSaveTime = L.timestamps(1);
end
end
methods (Access = protected)
% Add time labels on the plot given the plot index in PlotList
function plotTimeLabels(this, ind)
Axes = this.PlotList(ind).Axes;
if ~isempty(this.timestamps) && ~isempty(this.TimeLabels)
% Select for plotting only those time labels that are within
% the interval of time of currently stored data
t_ind = ([this.TimeLabels.time] >= this.timestamps(1));
Tl = this.TimeLabels(t_ind);
else
Tl = this.TimeLabels;
end
% Plot labels
for i = 1:length(Tl)
T = Tl(i);
n_lines = max(length(T.text_str), 1);
try
Lbl = this.PlotList(ind).LbLines(i);
% Update the existing label line
Lbl.Value = T.time;
Lbl.Label = T.text_str;
Lbl.Visible = 'on';
% Update the background width - font size times the
% number of lines
Bgl = this.PlotList(ind).BgLines(i);
Bgl.Value = T.time;
Bgl.LineWidth = Lbl.FontSize*n_lines;
Bgl.Visible = 'on';
catch
% Add new background line
this.PlotList(ind).BgLines(i) = xline(Axes, T.time, ...
'LineWidth', 10*n_lines, ...
'Color', [1, 1, 1]);
% Add new label line
this.PlotList(ind).LbLines(i) = xline(Axes, T.time, ...
'-', T.text_str, ...
'LineWidth', 0.5, ...
'LabelHorizontalAlignment', 'center', ...
'FontSize', 10);
end
end
% Remove redundant markers if any
n_tlbl = length(Tl);
if length(this.PlotList(ind).LbLines) > n_tlbl
delete(this.PlotList(ind).LbLines(n_tlbl+1:end));
this.PlotList(ind).LbLines(n_tlbl+1:end) = [];
end
if length(this.PlotList(ind).BgLines) > n_tlbl
delete(this.PlotList(ind).BgLines(n_tlbl+1:end));
this.PlotList(ind).BgLines(n_tlbl+1:end) = [];
end
end
% Ensure the log length is within length limit
function trim(this)
len = length(this.timestamps);
if len <= this.length_lim
return
end
% Remove data points beyond the length limit
dn = len-this.length_lim;
this.timestamps(1:dn) = [];
this.data(1:dn, :) = [];
if isempty(this.TimeLabels)
return
end
% Remove only the time labels which times fall outside the
% range of both a) trimmed data b) data in the current file
BeginTime = min(this.timestamps(1), this.FirstSaveTime);
ind = ([this.TimeLabels.time] < BeginTime);
this.TimeLabels(ind) = [];
end
% Print column names to a string
function str = printDataHeaders(this)
cs = this.column_sep;
str = sprintf(['%s',cs], this.column_headers{:});
str = [str, sprintf(this.line_sep)];
end
% Find out if the log was already plotted in the axes Ax and return
% the corresponding index of PlotList if it was
function ind = findPlotInd(this, Ax)
assert(isvalid(Ax),'Ax must be valid axes or uiaxes')
if ~isempty(this.PlotList)
ind_b = ([this.PlotList.Axes] == Ax);
% Find the index of first match
ind = find(ind_b, 1);
else
ind = [];
end
end
% Re-order the elements of TimeLabels array so that labels
% corresponding to later times have larger index
function sortTimeLabels(this)
times = [this.TimeLabels.time];
[~,ind] = sort(times);
this.TimeLabels = this.TimeLabels(ind);
end
% Create metadata from log properties
function Mdt = getMetadata(this)
if ~isempty(this.FirstSaveTime)
% Select for saving only those time labels that are within
% the interval of time of data in the current file
ind = ([this.TimeLabels.time] >= this.FirstSaveTime);
Tl = this.TimeLabels(ind);
else
Tl = this.TimeLabels;
end
if ~isempty(Tl)
% Add the textual part of TimeLabels structure
Mdt = MyMetadata(this.metadata_opts{:}, ...
'title', 'TimeLabels');
Lbl = struct('time_str', {Tl.time_str}, ...
'text_str', {Tl.text_str});
addParam(Mdt, 'Lbl', Lbl);
else
Mdt = MyMetadata.empty();
end
end
% Save log metadata, owerwriting existing
function saveMetadata(this, Mdt)
if exist('Mdt', 'var') == 0
Mdt = getMetadata(this);
end
if isempty(Mdt)
return
end
metfilename = this.meta_file_name;
% Create or clear the file
stat = createFile(metfilename, 'overwrite', true);
if ~stat
return
end
save(Mdt, metfilename);
end
% Process metadata
function setMetadata(this, Mdt)
% Assign time labels
Tl = titleref(Mdt, 'TimeLabels');
if ~isempty(Tl)
Lbl = Tl.ParamList.Lbl;
for i=1:length(Lbl)
this.TimeLabels(i).time_str = Lbl(i).time_str;
this.TimeLabels(i).time = datetime(Lbl(i).time_str, ...
'Format', this.datetime_fmt);
this.TimeLabels(i).text_str = Lbl(i).text_str;
end
end
end
end
%% Set and get methods
methods
function set.length_lim(this, val)
assert(isreal(val),'''length_lim'' must be a real number');
% Make length_lim non-negative and integer
this.length_lim = max(0, round(val));
% Apply the new length limit to log
trim(this);
end
function set.data_headers(this, val)
assert(iscellstr(val) && isrow(val), ['''data_headers'' must '...
'be a row cell array of character strings.']) %#ok<ISCLSTR>
this.data_headers = val;
end
function set.save_cont(this, val)
this.save_cont = logical(val);
end
function set.file_name(this, val)
assert(ischar(val),'''file_name'' must be a character string.')
if ~isequal(this.file_name, val)
% Reset the first saved timestamp marker
this.FirstSaveTime = datetime.empty(); %#ok<MCSUP>
end
this.file_name = val;
end
% The get function for file_name adds extension if it is not
% already present and also ensures proper file separators
% (by splitting and combining the file name)
function fname = get.data_file_name(this)
fname = this.file_name;
[filepath,name,ext] = fileparts(fname);
if isempty(ext)
ext = this.data_file_ext;
end
fname = fullfile(filepath,[name,ext]);
end
function fname = get.meta_file_name(this)
fname = this.file_name;
[filepath,name,~] = fileparts(fname);
ext = this.meta_file_ext;
fname = fullfile(filepath,[name,ext]);
end
function data_line_fmt = get.data_line_fmt(this)
cs = this.column_sep;
nl = this.line_sep;
if isempty(this.data)
l = 0;
else
[~,l] = size(this.data);
end
data_line_fmt = this.time_fmt;
for i = 1:l
data_line_fmt = [data_line_fmt, cs, this.data_fmt]; %#ok<AGROW>
end
data_line_fmt = [data_line_fmt, nl];
end
function hdrs = get.column_headers(this)
% Add header for the time column
if isa(this.timestamps,'datetime')
time_title_str = 'POSIX time (s)';
else
time_title_str = 'Time';
end
hdrs = [time_title_str, this.data_headers];
end
function time_num_arr = get.timestamps_num(this)
% Convert time stamps to numbers
if isa(this.timestamps, 'datetime')
time_num_arr = posixtime(this.timestamps);
else
time_num_arr = this.timestamps;
end
end
function val = get.channel_no(this)
if isempty(this.data)
val = length(this.data_headers);
else
[~, val] = size(this.data);
end
end
end
end
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