Corrected default processing stream generation code to new OD2Conc handle;... (563346d0) · Commits · github_fork / Homer3

DataTree/ProcStream/ProcStreamClass.m

+1 −1

Original line number	Diff line number	Diff line
		@@ -1181,7 +1181,7 @@ classdef ProcStreamClass < handle
		obj.reg.funcReg(iR).GetUsageStrDecorated(['hmrR_Intensity2OD',suffix]); ...
		obj.reg.funcReg(iR).GetUsageStrDecorated(['hmrR_BandpassFilt',suffix],'aux'); ...
		obj.reg.funcReg(iR).GetUsageStrDecorated(['hmrR_BandpassFilt',suffix],'dod'); ...
		obj.reg.funcReg(iR).GetUsageStrDecorated(['hmrR_OD2Conc_new',suffix]); ...
		obj.reg.funcReg(iR).GetUsageStrDecorated(['hmrR_OD2Conc',suffix]); ...
		obj.reg.funcReg(iR).GetUsageStrDecorated(['hmrR_BlockAvg',suffix],'dcAvg'); ...
		};
		k=[]; kk=1;

FuncRegistry/UserFunctions/Archive/hmrR_OD2Conc_Nirs.m

+24 −9

Original line number	Diff line number	Diff line
		% SYNTAX:
		% dc = hmrR_OD2Conc_Nirs( dod, SD, ppf )
		% dc = hmrR_OD2Conc_new_Nirs( dod, SD, ppf )
		%
		% UI NAME:
		% OD_to_Conc
		@@ -14,22 +14,23 @@
		% of data, then this is a vector of 2 elements. Typical value is ~6 for each
		% wavelength if the absorption change is uniform over the volume of tissue measured.
		% To approximate the partial volume effect of a small localized absorption change
		% within an adult human head, this value could be as small as 0.1. It is recommended
		% to use default values of “1 1” which will result in concentration units of
		% “molar ppf” such that the user can then divide by an estimated ppf at any future
		% point to estimate what the molar concentration change would be.%
		% within an adult human head, this value could be as small as 0.1. Convention is
		% becoming to set ppf=1 and to not divide by the source-detector separation such that
		% the resultant "concentration" is in units of Molar mm (or Molar cm if those are the
		% spatial units). This is becoming wide spread in the literature but there is no
		% fixed citation. Use a value of 1 to choose this option.
		%
		% OUTPUTS:
		% dc: the concentration data (#time points x 3 x #SD pairs
		% 3 concentrations are returned (HbO, HbR, HbT)
		%
		% USAGE OPTIONS:
		% Delta_OD_to_Conc: dc = hmrR_OD2Conc_Nirs( dod, SD, ppf )
		% Delta_OD_to_Conc: dc = hmrR_OD2Conc_new_Nirs( dod, SD, ppf )
		%
		% PARAMETERS:
		% ppf: [1.0, 1.0]
		%
		function dc = hmrR_OD2Conc_Nirs( dod, SD, ppf )
		function dc = hmrR_OD2Conc_new_Nirs( dod, SD, ppf )

		nWav = length(SD.Lambda);
		ml = SD.MeasList;
		@@ -40,10 +41,20 @@ if length(ppf)~=nWav
		return
		end

		if ~isempty(find(ppf==1))
		ppf = ones(size(ppf));
		end

		nTpts = size(dod,1);

		e = GetExtinctions( SD.Lambda );
		if ~isfield(SD,'SpatialUnit')
		e = e(:,1:2) / 10; % convert from /cm to /mm
		elseif strcmpi(SD.SpatialUnit,'mm')
		e = e(:,1:2) / 10; % convert from /cm to /mm
		elseif strcmpi(SD.SpatialUnit,'cm')
		e = e(:,1:2) ;
		end
		einv = inv( e'e )e';

		lst = find( ml(:,4)==1 );
		@@ -51,6 +62,10 @@ for idx=1:length(lst)
		idx1 = lst(idx);
		idx2 = find( ml(:,4)>1 & ml(:,1)==ml(idx1,1) & ml(:,2)==ml(idx1,2) );
		rho = norm(SD.SrcPos(ml(idx1,1),:)-SD.DetPos(ml(idx1,2),:));
		if ppf(1)~=1
		dc(:,:,idx) = ( einv * (dod(:,[idx1 idx2'])./(ones(nTpts,1)rhoppf))' )';
		else
		dc(:,:,idx) = ( einv * (dod(:,[idx1 idx2'])./(ones(nTpts,1)))' )';
		end
		end
		dc(:,3,:) = dc(:,1,:) + dc(:,2,:);

FuncRegistry/UserFunctions/Archive/hmrR_OD2Conc_new_Nirs.m

deleted100644 → 0

+0 −71

Original line number	Diff line number	Diff line
		% SYNTAX:
		% dc = hmrR_OD2Conc_new_Nirs( dod, SD, ppf )
		%
		% UI NAME:
		% OD_to_Conc
		%
		% DESCRIPTION:
		% Convert OD to concentrations
		%
		% INPUTS:
		% dod: the change in OD (#time points x #channels)
		% SD: the SD structure
		% ppf: Partial path length factors for each wavelength. If there are 2 wavelengths
		% of data, then this is a vector of 2 elements. Typical value is ~6 for each
		% wavelength if the absorption change is uniform over the volume of tissue measured.
		% To approximate the partial volume effect of a small localized absorption change
		% within an adult human head, this value could be as small as 0.1. Convention is
		% becoming to set ppf=1 and to not divide by the source-detector separation such that
		% the resultant "concentration" is in units of Molar mm (or Molar cm if those are the
		% spatial units). This is becoming wide spread in the literature but there is no
		% fixed citation. Use a value of 1 to choose this option.
		%
		% OUTPUTS:
		% dc: the concentration data (#time points x 3 x #SD pairs
		% 3 concentrations are returned (HbO, HbR, HbT)
		%
		% USAGE OPTIONS:
		% Delta_OD_to_Conc: dc = hmrR_OD2Conc_new_Nirs( dod, SD, ppf )
		%
		% PARAMETERS:
		% ppf: [1.0, 1.0]
		%
		function dc = hmrR_OD2Conc_new_Nirs( dod, SD, ppf )

		nWav = length(SD.Lambda);
		ml = SD.MeasList;

		if length(ppf)~=nWav
		errordlg('The length of PPF must match the number of wavelengths in SD.Lambda');
		dc = zeros(size(dod,1),3,length(find(ml(:,4)==1)));
		return
		end

		if ~isempty(find(ppf==1))
		ppf = ones(size(ppf));
		end

		nTpts = size(dod,1);

		e = GetExtinctions( SD.Lambda );
		if ~isfield(SD,'SpatialUnit')
		e = e(:,1:2) / 10; % convert from /cm to /mm
		elseif strcmpi(SD.SpatialUnit,'mm')
		e = e(:,1:2) / 10; % convert from /cm to /mm
		elseif strcmpi(SD.SpatialUnit,'cm')
		e = e(:,1:2) ;
		end
		einv = inv( e'e )e';

		lst = find( ml(:,4)==1 );
		for idx=1:length(lst)
		idx1 = lst(idx);
		idx2 = find( ml(:,4)>1 & ml(:,1)==ml(idx1,1) & ml(:,2)==ml(idx1,2) );
		rho = norm(SD.SrcPos(ml(idx1,1),:)-SD.DetPos(ml(idx1,2),:));
		if ppf(1)~=1
		dc(:,:,idx) = ( einv * (dod(:,[idx1 idx2'])./(ones(nTpts,1)rhoppf))' )';
		else
		dc(:,:,idx) = ( einv * (dod(:,[idx1 idx2'])./(ones(nTpts,1)))' )';
		end
		end
		dc(:,3,:) = dc(:,1,:) + dc(:,2,:);

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