1.29.0 -- Stim update (#32) (a26b5d1e) · Commits · github_fork / Homer3

DataTree/AcquiredData/Nirs/NirsClass.m

+8 −8

Original line number	Diff line number	Diff line
		@@ -34,15 +34,15 @@ classdef NirsClass < AcqDataClass & FileLoadSaveClass
		%
		% NirsClass with properties:
		%
		% SD: [11 struct]
		% t: [126981 double]
		% s: [126982 double]
		% d: [1269818 double]
		% aux: [126981 double]
		% SD: [1�1 struct]
		% t: [12698�1 double]
		% s: [12698�2 double]
		% d: [12698�18 double]
		% aux: [12698�1 double]
		% CondNames: {'1' '2'}
		% filename: './s1/neuro_run01.nirs'
		% fileformat: 'mat'
		% supportedFomats: [11 struct]
		% supportedFomats: [1�1 struct]
		% err: 0
		%

		@@ -686,13 +686,13 @@ classdef NirsClass < AcqDataClass & FileLoadSaveClass


		% ----------------------------------------------------------------------------------
		function SetStimValues(obj, icond, vals)
		function SetStimAmplitudes(obj, icond, vals)
		return;
		end


		% ----------------------------------------------------------------------------------
		function vals = GetStimValues(obj, icond)
		function vals = GetStimAmplitudes(obj, icond)
		vals = [];
		end

DataTree/AcquiredData/Snirf/SnirfClass.m

+46 −39

Original line number	Diff line number	Diff line
		@@ -969,7 +969,7 @@ classdef SnirfClass < AcqDataClass & FileLoadSaveClass
		if ~obj.stim(ii).Exists(t(tidxs(jj)))
		obj.stim(ii).AddStims(t(tidxs(jj)));
		else
		obj.stim(ii).EditValue(t(tidxs(jj)), s(tidxs(jj),ii));
		obj.stim(ii).EditState(t(tidxs(jj)), s(tidxs(jj),ii));
		end
		end
		end
		@@ -978,14 +978,35 @@ classdef SnirfClass < AcqDataClass & FileLoadSaveClass

		% ---------------------------------------------------------
		function s = GetStims(obj, t)
		% Returns a .nirs style stim signal. Stim state marks are
		% interpolated onto the time series t from their respective
		% onset times.
		s = zeros(length(t), length(obj.stim));
		for i=1:length(obj.stim)
		states = obj.stim(i).GetStates();
		if ~isempty(states)
		[~, k] = nearest_point(t, states(:, 1));
		if ~isempty(k)
		s(k,i) = states(:, 2);
		end
		end
		end
		end


		% ---------------------------------------------------------
		function s = GetStimAmps(obj, t)
		% Returns a .nirs style stim signal. Stim amplitudes are
		% interpolated onto the time series t from their respective
		% onset times.
		s = zeros(length(t), length(obj.stim));
		for ii=1:length(obj.stim)
		[ts, v] = obj.stim(ii).GetStim();
		[~, k] = nearest_point(t, ts);
		data = obj.stim.GetData();
		[~, k] = nearest_point(t, data(:, 1));
		if isempty(k)
		continue;
		end
		s(k,ii) = v;
		s(k,ii) = data(:, 3);
		end
		end

		@@ -1240,57 +1261,43 @@ classdef SnirfClass < AcqDataClass & FileLoadSaveClass

		% Find the destination condition to move stims (among the time pts in tPts)
		% to
		j = [];
		idx_dst = [];
		for ii=1:length(obj.stim)
		if strcmp(condition, obj.stim(ii).GetName())
		j=ii;
		idx_dst=ii;
		break;
		end
		end

		% If no destination condition found among existing conditions,
		% then create a new condition to move stims to
		if isempty(j)
		j = length(obj.stim)+1;
		if isempty(idx_dst)
		idx_dst = length(obj.stim)+1;

		% Otherwise we have a new condition to which to add the stims.
		obj.stim(j) = StimClass([], condition);
		obj.stim(idx_dst) = StimClass([], condition);
		obj.SortStims();

		% Recalculate j after sort
		for ii=1:length(obj.stim)
		if strcmp(condition, obj.stim(ii).GetName())
		j=ii;
		idx_dst=ii;
		break;
		end
		end
		end

		% Find all stims for any conditions which match the time points.
		for ii=1:length(tPts)
		for kk=1:length(obj.stim)
		d = obj.stim(kk).GetData();
		if isempty(d)
		continue;
		end
		k = find(d(:,1)==tPts(ii));
		if ~isempty(k)
		if kk==j
		continue;
		end

		% If stim at time point tPts(ii) exists in stim
		% condition kk, then move stim from obj.stim(kk) to
		% obj.stim(j)
		obj.stim(j).AddStims(tPts(ii), d(k(1),2), d(k(1),3));

		% After moving stim from obj.stim(kk) to
		% obj.stim(j), delete it from obj.stim(kk)
		d(k(1),:)=[];
		obj.stim(kk).SetData(d);

		% Move on to next time point
		break;
		for i=1:length(obj.stim)
		data = obj.stim(i).GetData();
		for j=1:size(data, 1)
		onset = data(j, 1);
		if onset > min(tPts) & onset < max(tPts)
		% Delete the stim from its condition and add it to selected dst
		duration = data(j, 2);
		amplitude = data(j, 3);
		more = data(j, 4:end);
		obj.stim(i).DeleteStims(onset);
		obj.stim(idx_dst).AddStims(onset, duration, amplitude, more);
		end
		end
		end
		@@ -1330,19 +1337,19 @@ classdef SnirfClass < AcqDataClass & FileLoadSaveClass


		% ----------------------------------------------------------------------------------
		function SetStimValues(obj, icond, vals)
		obj.stim(icond).SetValues(vals);
		function SetStimAmplitudes(obj, icond, amps)
		obj.stim(icond).SetAmplitudes(amps);
		end



		% ----------------------------------------------------------------------------------
		function vals = GetStimValues(obj, icond)
		function vals = GetStimAmplitudes(obj, icond)
		if icond>length(obj.stim)
		vals = [];
		return;
		end
		vals = obj.stim(icond).GetValues();
		vals = obj.stim(icond).GetAmplitudes();
		end

DataTree/AcquiredData/Snirf/StimClass.m

+552 −449

Original line number	Diff line number	Diff line
		@@ -3,11 +3,13 @@ classdef StimClass < FileLoadSaveClass
		properties
		name
		data
		dataLabels
		states % Stim marks enabled/disabled. Not part of SNIRF
		end

		% Properties not part of the SNIRF spec. These parameters aren't loaded or saved to files
		properties (Access = private)
		errmargin
		errmargin % Margin for interpolating onset times. Not part of SNIRF
		end

		methods
		@@ -16,8 +18,8 @@ classdef StimClass < FileLoadSaveClass
		function obj = StimClass(varargin)
		% Set class properties not part of the SNIRF format
		obj.SetFileFormat('hdf5');
		obj.errmargin = 1e-3;

		obj.errmargin = 1e-2;
		obj.states = [];
		if nargin==1
		if isa(varargin{1}, 'StimClass')
		obj.Copy(varargin{1});
		@@ -28,19 +30,22 @@ classdef StimClass < FileLoadSaveClass
		else
		obj.name = varargin{1};
		obj.data = [];
		obj.dataLabels = {'Onset', 'Duration', 'Amplitude'};
		end
		end
		elseif nargin==2
		if ischar(varargin{1})
		obj.SetFilename(varargin{1});
		obj.Load(varargin{1}, obj.fileformat, varargin{2});
		% Note that states are not loaded from file
		else
		t = varargin{1};
		CondName = varargin{2};
		obj.name = CondName;
		for ii=1:length(t)
		obj.data(end+1,:) = [t(ii), 5, 1];
		obj.data(end+1,:) = [t(ii), 10, 1];
		end
		obj.dataLabels = {'Onset', 'Duration', 'Amplitude'};
		end
		elseif nargin==3
		s = varargin{1};
		@@ -48,12 +53,16 @@ classdef StimClass < FileLoadSaveClass
		CondName = varargin{3};
		obj.name = CondName;
		k = s>0 \| s==-1 \| s==-2; % Include stim marks with these values
		obj.data = [t(k), 5*ones(length(t(k)),1), s(k)];
		obj.data = [t(k), 10*ones(length(t(k)),1), ones(length(t(k)),1)];
		obj.states = [t(k) s(k)];
		obj.dataLabels = {'Onset', 'Duration', 'Amplitude'};
		elseif nargin==0
		obj.name = '';
		obj.data = [];
		obj.dataLabels = {'Onset', 'Duration', 'Amplitude'};
		end

		obj.SortTpts();
		obj.updateStates(); % Generates enabled states to match the data array
		end


		@@ -92,6 +101,7 @@ classdef StimClass < FileLoadSaveClass
		% Load datasets
		obj.name = HDF5_DatasetLoad(gid, 'name');
		obj.data = HDF5_DatasetLoad(gid, 'data', [], '2D');
		obj.dataLabels = HDF5_DatasetLoad(gid, 'dataLabels', {});
		if all(obj.data(:)==0)
		obj.data = [];
		end
		@@ -105,7 +115,7 @@ classdef StimClass < FileLoadSaveClass
		return

		end

		obj.updateStates();
		end


		@@ -132,11 +142,13 @@ classdef StimClass < FileLoadSaveClass
		fid = H5F.create(fileobj, 'H5F_ACC_TRUNC', 'H5P_DEFAULT', 'H5P_DEFAULT');
		H5F.close(fid);
		end

		hdf5write_safe(fileobj, [location, '/name'], obj.name);

		% Since this is a writable writeable parameter AFTER it's creation, we
		% call hdf5write_safe with the 'rw' option
		hdf5write_safe(fileobj, [location, '/data'], obj.data, 'rw:2D');
		hdf5write_safe(fileobj, [location, '/dataLabels'], obj.dataLabels, 'rw');
		end


		@@ -149,6 +161,7 @@ classdef StimClass < FileLoadSaveClass
		end
		hdf5write_safe(fileobj, [location, '/name'], obj.name);
		hdf5write_safe(fileobj, [location, '/data'], obj.data, 'w');
		hdf5write_safe(fileobj, [location, '/dataLabels'], obj.dataLabels, 'w');
		end


		@@ -156,6 +169,8 @@ classdef StimClass < FileLoadSaveClass
		function Copy(obj, obj2)
		obj.name = obj2.name;
		obj.data = obj2.data;
		obj.dataLabels = obj2.dataLabels;
		obj.states = obj2.states;
		end


		@@ -178,6 +193,30 @@ classdef StimClass < FileLoadSaveClass
		B = true;
		end

		function updateStates(obj)
		% Generate or regenerate a state list compatible with the data
		% array. Match up existing states with new list of time points
		if isempty(obj.data)
		return;
		elseif size(obj.states, 1) == size(obj.data, 1)
		obj.states(:, 1) = obj.data(:, 1);
		return;
		end
		old = obj.states;
		obj.states = ones(size(obj.data, 1), 2);
		for i=1:size(obj.data, 1) % For each data row
		if ~isempty(old)
		k = find(abs(obj.data(i,1) - old(:, 1)) < obj.errmargin);
		else
		k = [];
		end
		if isempty(k) % If old state not there, generate new one
		obj.states(i, :) = [obj.data(i, 1), 1];
		else % Get old state if it exists
		obj.states(i, :) = old(k, :);
		end
		end
		end
		end


		@@ -199,6 +238,7 @@ classdef StimClass < FileLoadSaveClass
		% -------------------------------------------------------
		function SetData(obj, val)
		obj.data = val;
		obj.updateStates();
		end

		% -------------------------------------------------------
		@@ -206,6 +246,31 @@ classdef StimClass < FileLoadSaveClass
		val = obj.data;
		end

		% -------------------------------------------------------
		function SetStates(obj, states)
		obj.states = states;
		obj.updateStates();
		end

		% -------------------------------------------------------
		function val = GetStates(obj)
		val = obj.states;
		end

		function SetDataLabels(obj, dataLabels)
		if length(dataLabels) < size(obj.data, 2)
		for i = 1:size(obj.data, 2) - length(dataLabels)
		dataLabels{end + 1} = '';
		end
		end
		obj.dataLabels = dataLabels(1:size(obj.data, 2));
		end

		% -------------------------------------------------------
		function val = GetDataLabels(obj)
		val = obj.dataLabels;
		end

		end


		@@ -231,48 +296,70 @@ classdef StimClass < FileLoadSaveClass


		% ----------------------------------------------------------------------------------
		function AddStims(obj, tPts, duration, val)
		function AddStims(obj, tPts, duration, amp, more)
		% Add one or more stims to with a given duration, amplitude, and additional
		% column data given by more
		if ~exist('duration','var')
		duration = 5;
		duration = 10;
		end
		if ~exist('val','var')
		val = 1;
		if ~exist('amp','var')
		amp = 1;
		end
		if ~exist('more', 'var') \| isempty(more)
		more = zeros(size(obj.data, 2) - 3);
		end
		if ~isempty(obj.data)
		if ~isempty(more) & length(more) > (size(obj.data, 2) - 3)
		obj.data(:, end+length(more)) = 0; % Pad to accomodate additional data columns
		end
		for i=1:length(tPts)
		if ~obj.Exists(tPts(i))
		obj.data(end+1,:) = [tPts(i), duration, amp, more];
		obj.states(end+1,:) = [tPts(i), 1];
		end
		for ii=1:length(tPts)
		if ~obj.Exists(tPts(ii))
		obj.data(end+1,:) = [tPts(ii), duration, val];
		end
		else % If this stim is being added to an empty condition
		for i=1:length(tPts)
		obj.data = [tPts(i), duration, amp, more];
		obj.states = [tPts(i), 1];
		end
		end
		end


		% ----------------------------------------------------------------------------------
		function EditValue(obj, tPts, val)
		function EditAmplitude(obj, tPts, amp)
		if isempty(obj.data)
		return;
		end
		if ~exist('val','var')
		val = 1;
		if ~exist('amp','var')
		amp = 1;
		end
		for ii=1:length(tPts)
		k = find( abs(obj.data(:,1)-tPts(ii)) < obj.errmargin );
		if isempty(k)
		continue;
		end
		obj.data(k,3) = val;
		obj.data(k,3) = amp;
		end
		end


		% -------------------------------------------------------
		function [ts, v] = GetStim(obj)
		ts = [];
		v = [];
		% ----------------------------------------------------------------------------------
		function EditState(obj, tPts, state)
		if isempty(obj.data)
		return;
		end
		ts = obj.data(:,1);
		v = obj.data(:,3);
		if ~exist('state','var')
		state = 1;
		end
		for ii=1:length(tPts)
		k = find( abs(obj.states(:,1)-tPts(ii)) < obj.errmargin );
		if isempty(k)
		continue;
		end
		obj.states(k,2) = state;
		end
		end


		@@ -288,6 +375,7 @@ classdef StimClass < FileLoadSaveClass
		return;
		end
		obj.data(k,1) = tPts;
		obj.SortTpts();
		end


		@@ -344,12 +432,12 @@ classdef StimClass < FileLoadSaveClass


		% ----------------------------------------------------------------------------------
		function SetValues(obj, vals, tPts)
		function SetAmplitudes(obj, amps, tPts)
		if isempty(obj.data)
		return;
		end
		if ~exist('vals','var')
		vals = 1;
		if ~exist('amps','var')
		amps = 1;
		end
		if ~exist('tPts','var')
		tPts = obj.data(:,1);
		@@ -361,13 +449,13 @@ classdef StimClass < FileLoadSaveClass
		continue;
		end
		end
		obj.data(k,3) = vals;
		obj.data(k,3) = amps;
		end


		% -------------------------------------------------------
		function vals = GetValues(obj, tPts)
		vals = [];
		function amps = GetAmplitudes(obj, tPts)
		amps = [];
		if isempty(obj.data)
		return;
		end
		@@ -378,7 +466,7 @@ classdef StimClass < FileLoadSaveClass
		for ii=1:length(tPts)
		k(ii) = find( abs(obj.data(:,1)-tPts(ii)) < obj.errmargin );
		end
		vals = obj.data(k,3);
		amps = obj.data(k,3);
		end


		@@ -391,10 +479,12 @@ classdef StimClass < FileLoadSaveClass
		% Find all stims for any conditions which match the time points and
		% delete them from data.
		k = [];
		j = [];
		for ii=1:length(tPts)
		k = [k, find( abs(obj.data(:,1)-tPts(ii)) < obj.errmargin )];
		end
		obj.data(k,:) = [];
		obj.states(k,:) = [];
		end


		@@ -406,12 +496,12 @@ classdef StimClass < FileLoadSaveClass
		end

		% Find all stims for any conditions which match the time points and
		% flip it's value.
		% flip their states
		k = [];
		for ii=1:length(tPts)
		k = [k, find( abs(obj.data(:,1)-tPts(ii)) < obj.errmargin )];
		k = [k, find( abs(obj.states(:,1)-tPts(ii)) < obj.errmargin )];
		end
		obj.data(k,3) = -1*obj.data(k,3);
		obj.states(k,2) = -1*obj.states(k,2);
		end


		@@ -435,13 +525,26 @@ classdef StimClass < FileLoadSaveClass
		end



		% ----------------------------------------------------------------------------------
		function SortTpts(obj)
		try
		[~, idx] = sort(obj.data(:, 1));
		obj.data = obj.data(idx, :);
		obj.states = obj.states(idx, :);
		catch % Index error
		return;
		end
		end


		% ----------------------------------------------------------------------------------
		function nbytes = MemoryRequired(obj)
		nbytes = 0;
		if isempty(obj)
		return
		end
		nbytes = sizeof(obj.name) + sizeof(obj.data) + sizeof(obj.GetFilename()) + sizeof(obj.GetFileFormat()) + sizeof(obj.GetSupportedFormats()) + 8;
		nbytes = sizeof(obj.states) + sizeof(obj.name) + sizeof(obj.data) + sizeof(obj.GetFilename()) + sizeof(obj.GetFileFormat()) + sizeof(obj.GetSupportedFormats()) + 8;
		end

		end

DataTree/ProcStream/ProcInputClass.m

+5 −5

Original line number	Diff line number	Diff line
		@@ -321,7 +321,7 @@ classdef ProcInputClass < handle
		function [tpts, duration, vals] = GetStimData(obj, icond)
		tpts = obj.GetStimTpts(icond);
		duration = obj.GetStimDuration(icond);
		vals = obj.GetStimValues(icond);
		vals = obj.GetStimAmplitudes(icond);
		end


		@@ -356,17 +356,17 @@ classdef ProcInputClass < handle


		% ----------------------------------------------------------------------------------
		function SetStimValues(obj, icond, vals)
		obj.acquired.SetStimValues(icond, vals);
		function SetStimAmplitudes(obj, icond, vals)
		obj.acquired.SetStimAmplitudes(icond, vals);
		end


		% ----------------------------------------------------------------------------------
		function vals = GetStimValues(obj, icond)
		function vals = GetStimAmplitudes(obj, icond)
		if ~exist('icond','var')
		icond=1;
		end
		vals = obj.acquired.GetStimValues(icond);
		vals = obj.acquired.GetStimAmplitudes(icond);
		end

DataTree/ProcStream/ProcStreamClass.m

+5 −5

Original line number	Diff line number	Diff line
		@@ -1385,7 +1385,7 @@ classdef ProcStreamClass < handle
		function [tpts, duration, vals] = GetStimData(obj, icond)
		tpts = obj.GetStimTpts(icond);
		duration = obj.GetStimDuration(icond);
		vals = obj.GetStimValues(icond);
		vals = obj.GetStimAmplitudes(icond);
		end


		@@ -1420,17 +1420,17 @@ classdef ProcStreamClass < handle


		% ----------------------------------------------------------------------------------
		function SetStimValues(obj, icond, vals)
		obj.input.SetStimValues(icond, vals);
		function SetStimAmplitudes(obj, icond, vals)
		obj.input.SetStimAmplitudes(icond, vals);
		end


		% ----------------------------------------------------------------------------------
		function vals = GetStimValues(obj, icond)
		function vals = GetStimAmplitudes(obj, icond)
		if ~exist('icond','var')
		icond=1;
		end
		vals = obj.input.GetStimValues(icond);
		vals = obj.input.GetStimAmplitudes(icond);
		end

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