v1.23.0 (a0260163) · Commits · github_fork / Homer3

DataTree/AcquiredData/DataFiles/FileLoadSaveClass.m

+5 −5

Original line number	Diff line number	Diff line
		@@ -25,7 +25,7 @@ classdef FileLoadSaveClass < matlab.mixin.Copyable


		% ---------------------------------------------------------
		function Load(obj, filename, format, params)
		function Load(obj, filename, params, format)
		if ~exist('filename','var')
		filename = obj.filename;
		end
		@@ -52,16 +52,16 @@ classdef FileLoadSaveClass < matlab.mixin.Copyable


		% ---------------------------------------------------------
		function Save(obj, filename, format, params)
		function Save(obj, filename, params, format)
		if ~exist('filename','var')
		filename = obj.filename;
		end
		if ~exist('format','var')
		format = obj.fileformat;
		end
		if ~exist('params','var')
		params = [];
		end
		if ~exist('format','var')
		format = obj.fileformat;
		end

		switch(lower(format))
		case obj.supportedFomats.matlab

DataTree/AcquiredData/Snirf/SnirfClass.m

+138 −9

Original line number	Diff line number	Diff line
		@@ -259,6 +259,7 @@ classdef SnirfClass < AcqDataClass & FileLoadSaveClass
		end



		% -------------------------------------------------------
		function objnew = CopyMutable(obj, options)
		if nargin==1
		@@ -274,6 +275,8 @@ classdef SnirfClass < AcqDataClass & FileLoadSaveClass
		% Generate new instance of SnirfClass
		objnew = SnirfClass();

		objnew.filename = obj.filename;

		% Copy mutable properties to new object instance;
		objnew.stim = CopyHandles(obj.stim);

		@@ -281,7 +284,6 @@ classdef SnirfClass < AcqDataClass & FileLoadSaveClass
		t = obj.GetTimeCombined();
		objnew.data = DataClass([],t,[]);
		end

		end


		@@ -369,8 +371,16 @@ classdef SnirfClass < AcqDataClass & FileLoadSaveClass


		% -------------------------------------------------------
		function err = LoadStim(obj, fileobj)
		function err = LoadStim(obj, fileobj, options)
		err = 0;
		if ~exist('options','var')
		options = '';
		end

		paramName = 'stim';
		if optionExists(options, 'original') \|\| optionExists(options, 'orig')
		paramName = 'stim0';
		end

		% Since we want to load stims in sorted order (i.e., according to alphabetical order
		% of condition names), first load to temporary variable.
		@@ -379,7 +389,7 @@ classdef SnirfClass < AcqDataClass & FileLoadSaveClass
		if ii > length(obj.stim)
		obj.stim(ii) = StimClass;
		end
		if obj.stim(ii).LoadHdf5(fileobj, [obj.location, '/stim', num2str(ii)]) < 0
		if obj.stim(ii).LoadHdf5(fileobj, [obj.location, '/', paramName, num2str(ii)]) < 0
		obj.stim(ii).delete();
		obj.stim(ii) = [];
		if ii==1
		@@ -525,9 +535,18 @@ classdef SnirfClass < AcqDataClass & FileLoadSaveClass


		% -------------------------------------------------------
		function SaveStim(obj, fileobj)
		function SaveStim(obj, fileobj, options)
		if ~exist('options','var')
		options = '';
		end

		paramName = 'stim';
		if optionExists(options, 'original') \|\| optionExists(options, 'orig')
		paramName = 'stim0';
		end

		for ii=1:length(obj.stim)
		obj.stim(ii).SaveHdf5(fileobj, [obj.location, '/stim', num2str(ii)]);
		obj.stim(ii).SaveHdf5(fileobj, [obj.location, '/', paramName, num2str(ii)]);
		end
		end

		@@ -582,8 +601,118 @@ classdef SnirfClass < AcqDataClass & FileLoadSaveClass

		% Save aux
		obj.SaveAux(fileobj);
		end



		% -------------------------------------------------------
		function [changes, stim0] = UpdateStim(obj, fileobj)
		flags = zeros(length(obj.stim), 1);

		% Load original unedited stim, rename it and save it if it
		% doesn't already exist
		snirf = SnirfClass();
		snirf.LoadStim(fileobj, 'orig');
		if snirf.stim.Error()<0
		obj.stim.SaveStim('orig');
		end

		% Now load current stim from file and update it
		snirf.LoadStim(fileobj);
		stim0 = snirf.stim;

		% Update original stims from file with edited stims
		for ii = 1:length(obj.stim)
		for jj = 1:length(stim0)
		if strcmp(obj.stim(ii).GetName(), stim0(jj).GetName())
		if obj.stim(ii) ~= stim0(jj)
		stim0(jj).Copy(obj.stim(ii));
		stim0(jj).SaveHdf5(fileobj, [obj.location, '/stim', num2str(jj)]);
		end
		flags(ii) = 1;
		break;
		end
		end
		if ~flags(ii)
		% We have new stimulus condition added
		if ~obj.stim(ii).IsEmpty()
		stim0(jj+1) = StimClass(obj.stim(ii));
		stim0(jj+1).SaveHdf5(fileobj, [obj.location, '/stim', num2str(jj+1)]);
		end
		end
		end
		changes = sum(flags);
		end



		% -------------------------------------------------------
		function changes = StimChangesMade(obj)
		% Load original unedited stims from file
		snirf = SnirfClass();
		snirf.LoadStim(obj.filename);
		stim0 = snirf.stim;

		flags = zeros(length(obj.stim), 1);

		% Update original stims from file with edited stims
		for ii = 1:length(obj.stim)
		for jj = 1:length(stim0)
		if strcmp(obj.stim(ii).GetName(), stim0(jj).GetName())
		if obj.stim(ii) ~= stim0(jj)
		flags(ii) = 1;
		else
		flags(ii) = -1;
		end
		break;
		end
		end
		if flags(ii)==0
		% We have new stimulus condition added
		if ~obj.stim(ii).IsEmpty()
		flags(ii) = 1;
		end
		end
		end
		flags(flags ~= 1) = 0;
		changes = sum(flags)>0;
		end



		% -------------------------------------------------------
		function b = DataModified(obj)
		b = obj.StimChangesMade();
		end



		% -------------------------------------------------------
		function err = SaveMutable(obj, fileobj)
		if isempty(obj)
		return
		end
		% Arg 1
		if ~exist('fileobj','var') \|\| ~exist(fileobj,'file')
		fileobj = '';
		end

		% Error checking
		if ~isempty(fileobj) && ischar(fileobj)
		obj.filename = fileobj;
		elseif isempty(fileobj)
		fileobj = obj.filename;
		end
		if isempty(fileobj)
		err = -1;
		return;
		end

		% Update original stims and save back to file
		obj.UpdateStim(fileobj);
		end




		% -------------------------------------------------------

DataTree/AcquiredData/Snirf/StimClass.m

+3 −0

Original line number	Diff line number	Diff line
		@@ -419,6 +419,9 @@ classdef StimClass < FileLoadSaveClass
		if isempty(obj.name)
		return;
		end
		if isempty(obj.data)
		return;
		end
		b = false;
		end

DataTree/GroupClass.m

+21 −0

Original line number	Diff line number	Diff line
		@@ -630,6 +630,27 @@ classdef GroupClass < TreeNodeClass



		% ----------------------------------------------------------------------------------
		function SaveAcquiredData(obj)
		for ii = 1:length(obj.subjs)
		obj.subjs(ii).SaveAcquiredData();
		end
		end



		% ----------------------------------------------------------------------------------
		function b = AcquiredDataModified(obj)
		b = false;
		for ii = 1:length(obj.subjs)
		if obj.subjs(ii).AcquiredDataModified()
		b = true;
		end
		end
		end



		% ----------------------------------------------------------------------------------
		function ExportHRF(obj, procElemSelect, iBlk)
		if ~exist('procElemSelect','var') \|\| isempty(procElemSelect)

DataTree/ProcStream/ProcInputClass.m

+48 −30

Original line number	Diff line number	Diff line
		@@ -6,8 +6,7 @@ classdef ProcInputClass < handle
		properties
		tIncMan; % Manually include/excluded time points
		mlActMan; % Manually include/excluded time points
		acquiredEditable; % Copy of acquisition parameters that are editable
		% through manual GUI operations.
		acquired; % Modifiable acquisition parameters initally copied from acquisition files
		stimValSettings; % Derived stim values
		misc;
		end
		@@ -30,7 +29,7 @@ classdef ProcInputClass < handle
		if isempty(acquired)
		return;
		end
		obj.acquiredEditable = acquired.CopyMutable(copyOptions);
		obj.acquired = acquired.CopyMutable(copyOptions);
		end


		@@ -56,7 +55,10 @@ classdef ProcInputClass < handle
		% CopyHandles instead of plain old assignment statement
		eval( sprintf('obj.misc.%s = CopyHandles(obj2.misc.%s, obj.misc.%s);', fields{ii}, fields{ii}) );
		end
		obj.acquiredEditable = CopyHandles(obj2.acquiredEditable, obj.acquiredEditable);
		if isempty(obj.acquired)
		return;
		end
		obj.acquired.Copy(obj2.acquired);
		end


		@@ -90,7 +92,7 @@ classdef ProcInputClass < handle
		elseif isproperty(obj.misc, varname)
		eval(sprintf('varval = obj.misc.%s;', varname));
		else
		varval = obj.acquiredEditable.GetVar(varname);
		varval = obj.acquired.GetVar(varname);
		end
		if ~isempty(varval) && exist('iBlk','var')
		if iscell(varval)
		@@ -120,14 +122,27 @@ classdef ProcInputClass < handle
		nbytes(2) = sizeof(obj.mlActMan);
		nbytes(3) = sizeof(obj.misc);
		nbytes(4) = sizeof(obj.stimValSettings);
		if isempty(obj.acquiredEditable)
		if isempty(obj.acquired)
		nbytes(5) = 0;
		else
		nbytes(5) = obj.acquiredEditable.MemoryRequired();
		nbytes(5) = obj.acquired.MemoryRequired();
		end
		nbytes = sum(nbytes);
		end



		% ----------------------------------------------------------------------------------
		function SaveAcquiredData(obj)
		obj.acquired.SaveMutable();
		end


		% ----------------------------------------------------------------------------------
		function b = AcquiredDataModified(obj)
		b = obj.acquired.DataModified();
		end

		end


		@@ -188,7 +203,7 @@ classdef ProcInputClass < handle
		if nargin==1
		t = [];
		end
		s = obj.acquiredEditable.GetStims(t);
		s = obj.acquired.GetStims(t);
		end


		@@ -200,7 +215,7 @@ classdef ProcInputClass < handle
		if isempty(condition)
		return;
		end
		obj.acquiredEditable.AddStims(tPts, condition);
		obj.acquired.AddStims(tPts, condition);
		end


		@@ -212,7 +227,7 @@ classdef ProcInputClass < handle
		if ~exist('condition','var')
		condition = '';
		end
		obj.acquiredEditable.DeleteStims(tPts, condition);
		obj.acquired.DeleteStims(tPts, condition);
		end


		@@ -224,7 +239,7 @@ classdef ProcInputClass < handle
		if ~exist('condition','var')
		condition = '';
		end
		obj.acquiredEditable.ToggleStims(tPts, condition);
		obj.acquired.ToggleStims(tPts, condition);
		end


		@@ -236,7 +251,7 @@ classdef ProcInputClass < handle
		if ~exist('condition','var')
		condition = '';
		end
		obj.acquiredEditable.MoveStims(tPts, condition);
		obj.acquired.MoveStims(tPts, condition);
		end


		@@ -250,7 +265,7 @@ classdef ProcInputClass < handle

		% ----------------------------------------------------------------------------------
		function SetStimTpts(obj, icond, tpts)
		obj.acquiredEditable.SetStimTpts(icond, tpts);
		obj.acquired.SetStimTpts(icond, tpts);
		end


		@@ -259,13 +274,13 @@ classdef ProcInputClass < handle
		if ~exist('icond','var')
		icond=1;
		end
		tpts = obj.acquiredEditable.GetStimTpts(icond);
		tpts = obj.acquired.GetStimTpts(icond);
		end


		% ----------------------------------------------------------------------------------
		function SetStimDuration(obj, icond, duration)
		obj.acquiredEditable.SetStimDuration(icond, duration);
		obj.acquired.SetStimDuration(icond, duration);
		end


		@@ -274,13 +289,13 @@ classdef ProcInputClass < handle
		if ~exist('icond','var')
		icond=1;
		end
		duration = obj.acquiredEditable.GetStimDuration(icond);
		duration = obj.acquired.GetStimDuration(icond);
		end


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


		@@ -289,13 +304,13 @@ classdef ProcInputClass < handle
		if ~exist('icond','var')
		icond=1;
		end
		vals = obj.acquiredEditable.GetStimValues(icond);
		vals = obj.acquired.GetStimValues(icond);
		end


		% ----------------------------------------------------------------------------------
		function CondNames = GetConditions(obj)
		CondNames = obj.acquiredEditable.GetConditions();
		CondNames = obj.acquired.GetConditions();
		end


		@@ -304,13 +319,13 @@ classdef ProcInputClass < handle
		if nargin==1
		return;
		end
		obj.acquiredEditable.SetConditions(CondNames);
		obj.acquired.SetConditions(CondNames);
		end


		% ----------------------------------------------------------------------------------
		function SetStims_MatInput(obj, s, t, CondNames)
		obj.acquiredEditable.SetStims_MatInput(s, t);
		obj.acquired.SetStims_MatInput(s, t);
		end


		@@ -318,7 +333,7 @@ classdef ProcInputClass < handle
		function StimReject(obj, t, iBlk)
		tRange = [-2, 10];

		s = obj.acquiredEditable.GetStims(t);
		s = obj.acquired.GetStims(t);
		dt = (t(end)-t(1))/length(t);
		tRangeIdx = floor(tRange(1)/dt):ceil(tRange(2)/dt);
		smax = max(s,[],2);
		@@ -329,7 +344,7 @@ classdef ProcInputClass < handle
		s(lstS(iS),:) = -1*abs(s(lstS(iS),:));
		end
		end
		obj.acquiredEditable.SetStims_MatInput(s, t);
		obj.acquired.SetStims_MatInput(s, t);
		end


		@@ -337,7 +352,7 @@ classdef ProcInputClass < handle
		function StimInclude(obj, t, iBlk)
		tRange = [-2, 10];

		s = obj.acquiredEditable.GetStims(t);
		s = obj.acquired.GetStims(t);
		dt = (t(end)-t(1))/length(t);
		tRangeIdx = floor(tRange(1)/dt):ceil(tRange(2)/dt);
		for iC = 1:size(s,2)
		@@ -349,29 +364,32 @@ classdef ProcInputClass < handle
		end
		end
		end
		obj.acquiredEditable.SetStims_MatInput(s, t);
		obj.acquired.SetStims_MatInput(s, t);
		end


		% ----------------------------------------------------------------------------------
		function RenameCondition(obj, oldname, newname)
		% Function to rename a condition. Important to remeber that changing the
		% Function to rename a condition. Important to note that changing the
		% condition involves 2 distinct well defined steps:
		%
		% a) For the current element change the name of the specified (old)
		% condition for ONLY for ALL the acquired data elements under the
		% currElem, be it run, subj, or group . In this step we DO NOT TOUCH
		% the condition names of the run, subject or group .
		% condition ONLY for ALL the ACQUIRED data elements under the
		% current element, be it run, subj, or group . In this step we DO NOT TOUCH
		% the derived set of condition names of the run, subject or group .
		% b) Rebuild condition names and tables of all the tree nodes group, subjects
		% and runs same as if you were loading during Homer3 startup from the
		% acquired data.
		%
		% This method only implements step a).
		%
		if ~exist('oldname','var') \|\| ~ischar(oldname)
		return;
		end
		if ~exist('newname','var') \|\| ~ischar(newname)
		return;
		end
		obj.acquiredEditable.RenameCondition(oldname, newname);
		obj.acquired.RenameCondition(oldname, newname);
		end
		end

Admin message