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AlignDescriptor.m
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classdef AlignDescriptor
% Describes a particular way to slice and align trial data in time based off
% of event times in each trial. Typically analog data and neural data are
% aligned relative to the times of certain events before further analysis takes
% place. This class provides a common language for expressing these different
% types of aligning data.
properties
omitRedundantLabel = false; % e.g. when zero=event1, start=event1-20, label start as "-20" rather than "event1-20"
% abbreviate event names to capital/lowercase initials automatically
% override this by calling addEventAbbrev
autoAbbreviateLabels = true;
% use capitalized initials instead of lowercased initials
autoAbbreviateMakeUpper = true;
% for description
name % set manually, or will be auto-populated
end
properties(SetAccess=protected, Hidden)
nameDefault = true; % false if name has been set manually
% how to handle the window falling outside of the trial
outsideOfTrialMode = AlignDescriptor.TRUNCATE; % TRUNCATE or INVALIDATE or IGNORE
% minimum duration to mark as valid
minDuration = 0;
% allow an additional time window around the alignment interval
% see .setPadWindow below
padPre = 0;
padPost = 0;
end
properties(Access=protected)
% ValueMap : eventName -> abbreviatedName, overrides auto abbreviation
% use ad = ad.abbrev(eventName, abbrev) to add an entry
eventAbbrevLookup
end
properties(Hidden, SetAccess=protected) % SetAccess=protected
% slice times >= t_startEvent + startOffset
startEvent;
startEventIndex = 1;
startOffset = 0;
startLabel = '';
startInfo
startMarkData % mark this point on a data trace in drawOnData
startDefault = true;
% slice times <= t_stopEvent + stopOffset
stopEvent;
stopOffset = 0;
stopEventIndex = 1;
stopLabel = '';
stopInfo
stopMarkData
stopDefault = true;
% shift time such that t_zeroEvent + zeroOffset is t=0
zeroEvent;
zeroOffset = 0;
zeroEventIndex = 1;
zeroLabel = '';
zeroInfo
zeroMarkData
zeroDefault = true;
% move interval start forward in time to avoid these times
truncateBeforeEvents = {};
truncateBeforeEventsIndex
truncateBeforeOffsets
% move interval stop backward in time to avoid these times
truncateAfterEvents = {};
truncateAfterEventsIndex
truncateAfterOffsets
% invalidate any trial whose window includes these events
invalidateEvents = {};
invalidateEventsIndex = {};
invalidateOffsets
% purely for annotation, used by getTimeInfo and drawTimeAxis methods
markEvents = {};
markEventsIndex
markOffsets
markLabelsStored = {};
markInfo
markMarkData
% for marking time intervals on the time axis as colored rectangles
intervalEvents = {}; % n x 2 cell array of start/stop events
intervalEventsIndex % n x 2 array of event indices
intervalOffsets % n x 2 array of offsets
intervalLabelsStored = {};
intervalColors = {}; % color of rectangle used for the interval
% 'first' means use events from first trial in each condition
%intevalMultiTrialMode = 'first';
intervalConditionMatch = {}; % n x 1 cell array of structs with .attrName = attrValue(s)
intervalInfo % miscellaneous
end
properties(Constant, Hidden)
TRUNCATE = 'truncate';
INVALIDATE = 'invalidate';
IGNORE = 'ignore';
end
properties(Dependent, Hidden)
padWindow
markLabels
intervalLabels
startUnabbreviatedLabel
stopUnabbreviatedLabel
zeroUnabbreviatedLabel
markUnabbreviatedLabels
intervalUnabbreviatedLabels
truncateBeforeUnabbreviatedLabels
truncateAfterUnabbreviatedLabels
invalidateUnabbreviatedLabels
end
properties(Dependent)
isFixedLength % is the time window guaranteed fixed length
isStartFixedTime % is the start event always at a fixed time relative to zero
isStopFixedTime % is the start event always at a fixed time relative to zero
isMarkFixedTime % is each mark event always at a fixed time relative to zero
isIntervalFixedTime % n x 2 is interval start/end fixed time relative to zero
isStartZero % is the start event always == 0
isStopZero % is the stop event always == 0
isMarkZero % is each mark event always == 0
isZeroOutsideStartStop % is the zero event guaranteed to lie outside the start/stop window
end
methods % Dependent properties
function tf = get.isFixedLength(ad)
% the window is always the same length if the start / stop events are the same
if strcmp(ad.outsideOfTrialMode, ad.INVALIDATE) ||...
strcmp(ad.outsideOfTrialMode, ad.IGNORE) && ...
isempty(ad.truncateBeforeEvents) && isempty(ad.truncateAfterEvents)
tf = strcmp(ad.startEvent, ad.stopEvent) && ad.startEventIndex == ad.stopEventIndex;
else
tf = false;
end
end
function tf = get.isStartFixedTime(ad)
tf = strcmp(ad.zeroEvent, ad.startEvent) && isequal(ad.zeroEventIndex, ad.startEventIndex);
end
function tf = get.isStopFixedTime(ad)
tf = strcmp(ad.zeroEvent, ad.stopEvent) && isequal(ad.zeroEventIndex, ad.stopEventIndex);
end
function tf = get.isMarkFixedTime(ad)
tf = strcmp(ad.zeroEvent, ad.markEvents) & isequal(ad.zeroEventIndex, ad.markEventsIndex);
end
function tf = get.isIntervalFixedTime(ad)
tf = strcmp(ad.zeroEvent, ad.intervalEvents) & isequal(ad.zeroEventIndex, ad.intervalEventsIndex);
end
function tf = get.isStartZero(ad)
tf = strcmp(ad.zeroEvent, ad.startEvent) && isequal(ad.zeroEventIndex, ad.startEventIndex) && ...
ad.zeroOffset == ad.startOffset;
end
function tf = get.isStopZero(ad)
tf = strcmp(ad.zeroEvent, ad.stopEvent) && isequal(ad.zeroEventIndex, ad.stopEventIndex) && ...
ad.zeroOffset == ad.stopOffset;
end
function tf = get.isMarkZero(ad)
tf = strcmp(ad.zeroEvent, ad.markEvents) & isequal(ad.markEventsIndex, ad.stopEventIndex) & ...
ad.markOffsets == ad.zeroOffset;
end
function tf = get.isZeroOutsideStartStop(ad)
tf = (ad.isStartFixedTime && ad.startOffset > 0) || (ad.isStopFixedTime && ad.stopOffset < 0);
end
function name = get.name(ad)
if isempty(ad.name)
name = ad.getStartStopZeroDescription();
else
name = ad.name;
end
end
function ad = set.name(ad, name)
ad.name = name;
ad.nameDefault = isempty(name);
end
function padWindow = get.padWindow(ad)
padWindow = [ad.padPre ad.padPost];
end
end
methods % Auto-generated / manually set abbreviated labels
function str = get.startLabel(ad)
if isempty(ad.startLabel)
if ad.isStartFixedTime && ~ad.isStartZero && ad.omitRedundantLabel
str = ad.buildLabel('', [], ad.startOffset);
else
str = ad.buildLabel(ad.startEvent, ad.startEventIndex, ad.startOffset);
end
else
str = ad.startLabel;
end
end
function str = get.stopLabel(ad)
if isempty(ad.stopLabel)
if ad.isStopFixedTime && ~ad.isStopZero && ad.omitRedundantLabel
str = ad.buildLabel('', [], ad.stopOffset);
else
str = ad.buildLabel(ad.stopEvent, ad.stopEventIndex, ad.stopOffset);
end
else
str = ad.stopLabel;
end
end
function str = get.zeroLabel(ad)
if isempty(ad.zeroLabel)
str = ad.buildLabel(ad.zeroEvent, ad.zeroEventIndex, ad.zeroOffset);
else
str = ad.zeroLabel;
end
end
function markLabels = get.markLabels(ad)
if isempty(ad.markLabelsStored)
ad.markLabelsStored = cell(length(ad.markEvents), 1);
end
markLabels = cell(length(ad.markLabelsStored), 1);
for iMark = 1:length(ad.markLabelsStored)
if ~isempty(ad.markLabelsStored{iMark})
% manual label
markLabels{iMark} = ad.markLabelsStored{iMark};
elseif ad.isMarkFixedTime(iMark) && ad.omitRedundantLabel
% same as zero, just include the offset (e.g. '+100')
markLabels{iMark} = ad.buildLabel('', [], ad.markOffsets(i));
else
% full label string
markLabels{iMark} = ad.buildLabel(ad.markEvents{iMark}, ...
ad.markEventsIndex{iMark}, ad.markOffsets(iMark));
end
end
end
function intervalLabels = get.intervalLabels(ad)
nIntervals = size(ad.intervalEvents, 1);
if isempty(ad.intervalLabelsStored)
ad.intervalLabelsStored = cell(nIntervals, 1);
end
intervalLabels = cell(length(ad.intervalLabelsStored), 1);
for i = 1:nIntervals
if ~isempty(ad.intervalLabelsStored{i})
% manual label
intervalLabels{i} = ad.intervalLabelsStored{i};
else
if ad.isIntervalFixedTime(i, 1) && ad.omitRedundantLabel
% same as zero, just include the offset (e.g. '+100')
label1 = ad.buildLabel('', [], ad.intervalOffsets(i, 1));
else
label1 = ad.buildLabel(ad.intervalEvents{i, 1}, ad.intervalEventsIndex{i,1}, ad.intervalOffsets(i, 1));
end
if ad.isIntervalFixedTime(i, 2) && ad.omitRedundantLabel
% same as zero, just include the offset (e.g. '+100')
label2 = ad.buildLabel('', [], ad.intervalOffsets(i, 2));
else
label2 = ad.buildLabel(ad.intervalEvents{i, 2}, ad.intervalEventsIndex{i,2}, ad.intervalOffsets(i, 2));
end
intervalLabels{i} = sprintf('%s : %s', label1, label2);
end
end
end
end
methods % Unabbreviated raw labels
function str = get.startUnabbreviatedLabel(ad)
str = ad.buildUnabbreviatedLabel(ad.startEvent, ad.startEventIndex, ad.startOffset);
end
function str = get.stopUnabbreviatedLabel(ad)
str = ad.buildUnabbreviatedLabel(ad.stopEvent, ad.stopEventIndex, ad.stopOffset);
end
function str = get.zeroUnabbreviatedLabel(ad)
str = ad.buildUnabbreviatedLabel(ad.zeroEvent, ad.zeroEventIndex, ad.zeroOffset);
end
function strCell = get.markUnabbreviatedLabels(ad)
strCell = cellfun(@ad.buildUnabbreviatedLabel, ad.markEvents, ...
ad.markEventsIndex, num2cell(ad.markOffsets), 'UniformOutput', false);
end
function strCell = get.intervalUnabbreviatedLabels(ad)
% TODO fix this
strCell = cellfun(@ad.buildUnabbreviatedLabel, ad.intervalEvents, ...
ad.intervalEventsIndex, num2cell(ad.intervalOffsets), 'UniformOutput', false);
end
function strCell = get.invalidateUnabbreviatedLabels(ad)
strCell = cellfun(@ad.buildUnabbreviatedLabel, ad.invalidateEvents, ...
ad.invalidateEventsIndex, num2cell(ad.invalidateOffsets), 'UniformOutput', false);
end
function strCell = get.truncateBeforeUnabbreviatedLabels(ad)
strCell = cellfun(@ad.buildUnabbreviatedLabel, ad.truncateBeforeEvents, ...
ad.truncateBeforeEventsIndex, num2cell(ad.truncateBeforeOffsets), 'UniformOutput', false);
end
function strCell = get.truncateAfterUnabbreviatedLabels(ad)
strCell = cellfun(@ad.buildUnabbreviatedLabel, ad.truncateAfterEvents, ...
ad.truncateAfterEventsIndex, num2cell(ad.truncateAfterOffsets), 'UniformOutput', false);
end
end
methods % constructor, manual event specification
function ad = AlignDescriptor(varargin)
ad.eventAbbrevLookup = ValueMap('KeyType', 'char', 'ValueType', 'char');
ad.startEvent = 'TrialStart';
ad.stopEvent = 'TrialEnd';
ad.zeroEvent = 'TrialStart';
% either use named property value pairs or string syntax
if nargin == 1 && ischar(varargin{1});
ad = ad.parseDescriptionString(varargin{1});
else
ad = structargs(ad, varargin);
end
end
function ad = update(ad)
ad.warnIfNoArgOut(nargout);
% does nothing here, used primarily in AlignInfo
end
% return a list of event names this AlignDescriptor references, plus 'start' and 'end'
function eventList = getEventList(ad)
eventList = unique({ad.startEvent ad.stopEvent ad.zeroEvent ...
ad.truncateBeforeEvents{:} ad.truncateAfterEvents{:} ad.invalidateEvents{:} ...
ad.markEvents{:} ad.intervalEvents{:}});
eventList = union(eventList, {'TrialStart', 'TrialEnd'});
end
function ad = start(ad, eventName, varargin)
ad.warnIfNoArgOut(nargout);
p = inputParser;
p.addOptional('offset', 0, @isscalar);
p.addParamValue('index', 1, @(x) ischar(x) || isscalar(x));
p.addParamValue('as', '', @ischar);
p.addParamValue('markData', [], @islogical);
p.KeepUnmatched = true;
p.parse(varargin{:});
offset = p.Results.offset;
ad.startEvent = eventName;
ad.startEventIndex = p.Results.index;
ad.startOffset = offset;
if isempty(p.Results.markData)
ad.startMarkData = offset == 0;
else
ad.startMarkData = p.Results.markData;
end
if ~isempty(p.Results.as)
ad.startLabel = p.Results.as;
end
ad.startInfo = p.Unmatched;
ad.startDefault = false;
% if no zero is specified, determine it from the start event
ad = ad.setDefaultZero();
ad = ad.update();
end
function ad = stop(ad, eventName, varargin)
ad.warnIfNoArgOut(nargout);
p = inputParser;
p.addOptional('offset', 0, @isscalar);
p.addParamValue('index', 1, @(x) ischar(x) || isscalar(x));
p.addParamValue('as', '', @ischar);
p.addParamValue('markData', [], @islogical);
p.KeepUnmatched = true;
p.parse(varargin{:});
offset = p.Results.offset;
ad.stopEvent = eventName;
ad.stopEventIndex = p.Results.index;
ad.stopOffset = offset;
if isempty(p.Results.markData)
ad.stopMarkData = offset == 0;
else
ad.stopMarkData = p.Results.markData;
end
if ~isempty(p.Results.as)
ad.stopLabel = p.Results.as;
end
ad.stopInfo = p.Unmatched;
ad.stopDefault = true;
ad = ad.update();
end
function ad = pad(ad, pre, post, varargin)
ad.warnIfNoArgOut(nargout);
if nargin < 3
ad.padPre = pre(1);
ad.padPost = pre(2);
else
ad.padPre = pre;
ad.padPost = post;
end
ad = ad.update();
end
function ad = zero(ad, eventName, varargin)
ad.warnIfNoArgOut(nargout);
p = inputParser;
p.addOptional('offset', 0, @isscalar);
p.addParamValue('index', 1, @(x) ischar(x) || isscalar(x));
p.addParamValue('as', '', @ischar);
p.addParamValue('markData', [], @islogical);
p.KeepUnmatched = true;
p.parse(varargin{:});
offset = p.Results.offset;
ad.zeroEvent = eventName;
ad.zeroEventIndex = p.Results.index;
ad.zeroOffset = offset;
if isempty(p.Results.markData)
ad.zeroMarkData = offset == 0;
else
ad.zeroMarkData = p.Results.markData;
end
if ~isempty(p.Results.as)
ad.zeroLabel = p.Results.as;
end
ad.zeroInfo = p.Unmatched;
ad.zeroDefault = true;
ad = ad.update();
end
function ad = interval(ad, eventNameStart, offsetStart, eventNameStop, offsetStop, varargin)
ad.warnIfNoArgOut(nargout);
p = inputParser;
p.addParamValue('indexStart', 1, @(x) ischar(x) || isscalar(x));
p.addParamValue('indexEnd', 1, @(x) ischar(x) || isscalar(x));
p.addParamValue('as', '', @ischar);
p.addParamValue('color', 'k', @(x) true);
p.addParamValue('conditionMatch', struct(), @(x) isstruct(x) && isscalar(x));
p.KeepUnmatched = true;
p.parse(varargin{:});
color = p.Results.color;
as = p.Results.as;
conditionMatch = p.Results.conditionMatch;
iInterval = size(ad.intervalEvents,1)+1;
ad.intervalEventsStart{iInterval} = eventNameStart;
ad.intervalEventsStop{iInterval} = eventNameStop;
ad.intervalEventsIndexStart{iInterval} = p.Results.indexStart;
ad.intervalEventsIndexStop{iInterval} = p.Results.indexEnd;
ad.intervalOffsetsStart(iInterval) = offsetStart;
ad.intervalOffsetsStop(iInterval) = offsetStop;
ad.intervalColors{iInterval} = color;
ad.intervalInfo{iInterval} = p.Unmatched;
%ad.intervalConditionMatch{iInterval} = conditionMatch;
ad.intervalLabelsStored{iInterval} =as;
ad = ad.update();
end
function ad = mark(ad, eventName, varargin)
ad.warnIfNoArgOut(nargout);
p = inputParser;
p.addOptional('offset', 0, @isscalar);
p.addParamValue('index', [], @(x) isempty(x) || ischar(x) || isscalar(x));
p.addParamValue('as', '', @ischar);
p.addParamValue('markData', [], @islogical);
p.KeepUnmatched = true;
p.parse(varargin{:});
offset = p.Results.offset;
if isempty(p.Results.index)
index = ':';
else
index = p.Results.index;
end
iMark = length(ad.markEvents)+1;
ad.markEvents{iMark} = eventName;
ad.markEventsIndex{iMark} = index;
ad.markOffsets(iMark) = offset;
if isempty(p.Results.markData)
ad.markMarkData(iMark) = offset == 0;
else
ad.markMarkData(iMark) = p.Results.markData;
end
ad.markInfo{iMark} = p.Unmatched;
if ~isempty(p.Results.as)
% store manual label
ad.markLabelsStored{iMark,1} = p.Results.as;
else
ad.markLabelsStored{iMark,1} = '';
end
ad = ad.update();
end
function ad = truncateBefore(ad, eventName, offset, varargin)
p = inputParser;
p.addOptional('index', [], @(x) isempty(x) || ischar(x) || isscalar(x));
p.parse(varargin{:});
if isempty(p.Results.index)
% choose most conservative default
index = 'end';
else
index = p.Results.index;
end
ad.warnIfNoArgOut(nargout);
ad.truncateBeforeEvents{end+1} = eventName;
ad.truncateBeforeEventsIndex{end+1} = index;
ad.truncateBeforeOffsets(end+1) = offset;
ad = ad.update();
end
function ad = truncateAfter(ad, eventName, offset, varargin)
p = inputParser;
p.addOptional('index', [], @(x) isempty(x) || ischar(x) || isscalar(x));
p.parse(varargin{:});
if isempty(p.Results.index)
index = 1;
else
index = p.Results.index;
end
ad.warnIfNoArgOut(nargout);
ad.truncateAfterEvents{end+1} = eventName;
ad.truncateAfterEventsIndex{end+1} = index;
ad.truncateAfterOffsets(end+1) = offset;
ad = ad.update();
end
function ad = invalidateOverlap(ad, eventName, offset, varargin)
p = inputParser;
p.addOptional('index', [], @(x) isempty(x) || ischar(x) || isscalar(x));
p.parse(varargin{:});
if isempty(p.Results.index)
index = ':';
else
index = p.Results.index;
end
ad.warnIfNoArgOut(nargout);
ad.invalidateEvents{end+1} = eventName;
ad.invalidateEventsIndex{end+1} = index;
ad.invalidateOffsets(end+1) = offset;
ad = ad.update();
end
function ad = setOutsideOfTrialIgnore(ad)
ad.warnIfNoArgOut(nargout);
ad.outsideOfTrialMode = AlignDescriptor.IGNORE;
ad = ad.update();
end
function ad = setOutsideOfTrialInvalidate(ad)
ad.warnIfNoArgOut(nargout);
ad.outsideOfTrialMode = AlignDescriptor.INVALIDATE;
ad = ad.update();
end
function ad = setOutsideOfTrialTruncate(ad)
ad.warnIfNoArgOut(nargout);
ad.outsideOfTrialMode = AlignDescriptor.TRUNCATE;
ad = ad.update();
end
% store an abbreviation for an event name
function ad = abbrev(ad, eventName, abbrev)
ad.warnIfNoArgOut(nargout);
ad.eventAbbrevLookup(eventName) = abbrev;
end
% replace the start and end event with a particular zero-relative
% time window
function ad = windowAroundZero(ad, tStart, tStop, varargin)
ad.warnIfNoArgOut(nargout);
ad = ad.start(ad.zeroEvent, tStart);
ad = ad.stop(ad.zeroEvent, tStop);
end
end
methods % Equivalence to other descriptors
% determine if this align descriptor is functionally equivalent to another AlignDescriptor,
% ignoring appearance-level details (e.g. marks, intervals, label info, abbreviations)
% and focusing only on time alignment and trial validity details
function tf = isCompatibleWith(ad1, ad2)
% check for equivalence of all of the following properties:
props = { ...
'startEvent', ...
'startEventIndex', ...
'startOffset', ...
'startEventIndex', ...
'stopEvent', ...
'stopEventIndex', ...
'stopOffset', ...
'zeroEvent', ...
'zeroEventIndex', ...
'zeroOffset', ...
'truncateBeforeEvents', ...
'truncateBeforeEventsIndex', ...
'truncateBeforeOffsets', ...
'truncateAfterEvents', ...
'truncateAfterEventsIndex', ...
'truncateAfterOffsets', ...
'invalidateEvents', ...
'invalidateEventsIndex', ...
'invalidateOffsets', ...
'outsideOfTrialMode', ...
'minDuration', ...
};
tf = true;
for i = 1:length(props)
tf = tf && isequal(ad1.(props{i}), ad2.(props{i}));
end
end
end
methods(Access=protected) % Utility methods
function warnIfNoArgOut(obj, nargOut)
if nargOut == 0 && ~ishandle(obj)
message = sprintf('WARNING: %s is not a handle class. If the instance handle returned by this method is not stored, this call has no effect.\\n', ...
class(obj));
expr = sprintf('debug(''%s'')', message);
evalin('caller', expr);
end
end
end
methods(Access=protected) % Defaults, start/stop/zero set dependent on each other if missing
function ad = setDefaultZero(ad)
ad.warnIfNoArgOut(nargout);
% if no zero specified, make zero the start event with no offset
if isempty(ad.zeroEvent) || ad.zeroDefault
ad.zeroEvent = ad.startEvent;
ad.zeroEventIndex = 1;
ad.zeroOffset = 0;
end
end
end
methods % String parsing and building, disp()
function ad = parseDescriptionString(ad, str)
% parse the string in the format:
% startEventName+offset : stopEventName+offset @ zeroEventName+offset, truncateBefore event+offset, truncateAfter event+offset, mark event+offset
ad.warnIfNoArgOut(nargout);
str = strtrim(str);
[startStopZero remain] = strtok(str, ',');
% split the string into start : stop @ zero
pat = '(?<start>[^:]+):(?<stop>[^@]+)(?<zero>@.*)?';
info = regexp(startStopZero, pat, 'names', 'once');
if isempty(info) || isempty(info.start) || isempty(info.stop)
% Try parsing it as just a single event, which would be
% come the zero
%try
[ad.zeroEvent ad.zeroEventIndex ad.zeroOffset ad.zeroLabel] = ...
ad.parseEventOffsetString(startStopZero, 'zero', 'defaultIndex', 1);
ad.zeroDefault = false;
% '@Event' means TrialStart:TrialEnd @ Event (align whole trial to Event), whereas
% 'Event' means Event:Event @ Event (single sample at Event)
if(str(1) ~= '@')
ad = ad.start(ad.zeroEvent, 'index', ad.zeroEventIndex, 'offset', ad.zeroOffset);
ad = ad.stop(ad.zeroEvent, 'index', ad.zeroEventIndex, 'offset', ad.zeroOffset);
end
%catch exc
% otherwise just fail
%error('Error parsing align descriptor %s', string);
%end
end
if ad.zeroDefault
% parse each of the start, stop, and zero strings
[ad.startEvent ad.startEventIndex ad.startOffset ad.startLabel] = ...
ad.parseEventOffsetString(info.start, 'start', 'defaultIndex', 1);
ad.startDefault = true;
[ad.stopEvent ad.stopEventIndex ad.stopOffset ad.stopLabel] = ...
ad.parseEventOffsetString(info.stop, 'stop', 'defaultIndex', 1);
ad.stopDefault = true;
% deal with event:+100, -100:event cases
if isempty(ad.startEvent) && ~isempty(ad.stopEvent)
ad.startEvent = ad.stopEvent;
elseif isempty(ad.stopEvent) && ~isempty(ad.startEvent)
ad.stopEvent = ad.startEvent;
end
if isfield(info, 'zero') && ~isempty(info.zero)
% zero specified explicitly
info.zero = strtrim(info.zero(2:end)); % remove the leading @
[ad.zeroEvent ad.zeroEventIndex ad.zeroOffset ad.zeroLabel] = ...
ad.parseEventOffsetString(info.zero, 'zero', 'defaultIndex', 1);
ad.zeroDefault = false;
if isempty(ad.startEvent) && isempty(ad.stopEvent)
ad.startEvent = ad.zeroEvent;
ad.stopEvent = ad.zeroEvent;
end
else
% deal with 500:800 case here
if isempty(ad.startEvent) && isempty(ad.stopEvent)
ad.startEvent = 'TrialStart';
ad.stopEvent = 'TrialStart';
end
ad = ad.setDefaultZero();
end
end
% parse the remainder strings one by one to get after, before, mark
while ~isempty(remain)
% grab the next comma-separated token
if remain(1) == ','
remain = strtrim(remain(2:end));
end
[thisToken remain] = strtok(remain, ',');
% parse this as 'typeStr name+offset'
[typeStr name index offset label] = ....
ad.parseTypedEventOffsetString(thisToken);
if ~isempty(typeStr)
% match typeStr against the known types:
switch typeStr
case {'truncateAfter', 'before'}
ad.truncateAfterEvents{end+1} = name;
if isempty(index)
% choose most conservative default, truncate
% everything after the first occurrence
ad.truncateAfterEventsIndex{end+1} = 1;
else
ad.truncateAfterEventsIndex{end+1} = index;
end
ad.truncateAfterOffsets(end+1) = offset;
case {'truncateBefore', 'after'}
ad.truncateBeforeEvents{end+1} = name;
if isempty(index)
% choose most conservative default, truncate
% everything before the last occurrence
ad.truncateBeforeEventsIndex{end+1} = 'end';
else
ad.truncateBeforeEventsIndex{end+1} = index;
end
ad.truncateBeforeOffsets(end+1) = offset;
case {'invalidate', 'exclude', 'excluding'}
ad.invalidateEvents{end+1} = name;
if isempty(index)
% choose most conservative default, any
% occurrence invalidates the trial
ad.invalidateEventsIndex{end+1} = ':';
else
ad.invalidateEventsIndex{end+1} = index;
end
ad.invalidateOffsets(end+1) = offset;
case {'mark', 'indicate'}
ad = ad.mark(name, offset, 'as', label, 'index', index);
otherwise
error('Unknown descriptor keyword %s', typeStr);
end
else
% try parsing pad command
[success, ad.padPre, ad.padPost] = ad.parsePadString(thisToken);
if ~success
error('Could not parse token %s');
end
end
end
ad = ad.update();
end
function [success, padPre, padPost] = parsePadString(ad, str)
pat = 'pad\s*\[?(?<padPre>+?-?\d*):(?<padPost>+?-?\d*)';
str = strtrim(str);
info = regexp(str, pat, 'names', 'once');
if isempty(info)
success = false;
else
success = true;
padPre = str2double(info.padPre);
padPost = str2double(info.padPost);
assert(~isnan(padPre), 'Could not parse padPre %s as number', info.padPre);
assert(~isnan(padPost), 'Could not parse padPost %s as number', info.padPost);
end
end
function [typeStr name index offset label] = parseTypedEventOffsetString(ad, str, varargin)
% looking for something like 'typeStr eventName + offset'
pat = '(?<typeStr>\w+)\s*(?<offsetStr>.+)';
str = strtrim(str);
info = regexp(str, pat, 'names', 'once');
if isempty(info)
typeStr = '';
end
typeStr = info.typeStr;
[name index offset label] = ad.parseEventOffsetString(info.offsetStr, typeStr, varargin{:});
end
function [name index offset label] = parseEventOffsetString(ad, str, errorName, varargin)
% parse a string in a format 'eventName + offset' or 'eventName - offset'
% or possibly 'eventName + offset as label'
% or possibly 'eventName(index) ...' where index is 1,2 or
% end-1, end-2 or 1:end or :
% errorName provides information for printing error message about what we're trying to parse
p = inputParser;
p.addParamValue('defaultIndex', [], @isvector);
p.parse(varargin{:});
% match event name
eventPat = '(?<event>[a-zA-Z]\w+)?';
% match anything like V or V:V where V is '#', 'end', 'end-#'
indexPat = '(?<index>\((end)?-?\d*:?(end)?-?\d*\))?';
% match anything like +# or -#
offsetPat = '(?<offset>[+\-\.e\d\s]+)?';
% match 'as eventLabel'
asPat = '(as)?\s*(?<label>[\w\s\d+\-\.\<\>\?]+)?';
pat = [eventPat indexPat '\s*' offsetPat '\s*' asPat];
str = strtrim(str);
info = regexp(str, pat, 'names', 'once');
if isempty(info)
error('Error parsing %s descriptor "%s"', errorName, str);
end
name = info.event;
if isempty(info.index)
index = p.Results.defaultIndex;
else
indexStr = info.index(2:end-1);
num = str2double(indexStr);
if ~isnan(num)
% convert to number
index = num;
else
% keep as string otherwise
index = indexStr;
end
end
if isempty(info.offset)
offset = 0;
else
info.offset = info.offset(~isspace(info.offset));
offset = str2double(info.offset);
if isnan(offset)
error('Error parsing %s offset %s', errorName, info.offset);
end
end
label = info.label;
end
function str = buildLabel(ad, name, index, offset)
if nargin < 3 || isempty(index)
index = 1;
end
if nargin < 4
offset = 0;
end
% determine the appropriate abbreviation
if isempty(name)
% just the offset
abbrev = '';
elseif ad.eventAbbrevLookup.isKey(name)
% abbrev has been specified via addEventAbbrev
abbrev = ad.eventAbbrevLookup(name);
elseif ad.autoAbbreviateLabels
% auto abbreviate:
% here we assume name is camelCased, we convert it to the capitalized
% initials of each word in the event name
isUpper = upper(name) == name;
isUpper(1) = true;
isSpace = name == ' ';
abbrev = name(isUpper & ~isSpace);
if ad.autoAbbreviateMakeUpper
abbrev = upper(abbrev);
else
abbrev = lower(abbrev);
end
end
% build a parenthetical index string if index ~= 1
if ischar(index)
indexStr = ['(' index ')'];
elseif index == 1
indexStr = '';
else
indexStr = ['(' num2str(index) ')'];
end
% combine eventAbbrev(index)+offset
if offset == 0
str = [abbrev indexStr];
else
str = sprintf('%s%s%+.0f', abbrev, indexStr, offset);
end
end
function str = buildUnabbreviatedLabel(ad, name, index, offset)
if nargin < 3 || isempty(index)
index = 1;
end
if nargin < 4
offset = 0;
end
% build a parenthetical index string if index ~= 1
if ischar(index)
indexStr = ['(' index ')'];
elseif index == 1
indexStr = '';
else
indexStr = ['(' num2str(index) ')'];
end
% combine eventAbbrev(index)+offset
if offset == 0
str = [name indexStr];
else
str = sprintf('%s%s%+.0f', name, indexStr, offset);
end
end
function str = getDescription(ad)
desc = ad.getStartStopZeroDescription();
if strcmp(ad.name, desc)
str = desc;
else
str = sprintf('%s : %s', ad.name, desc);
end
end
function str = getStartStopZeroDescription(ad)