Unverified Commit 34c2eb77 authored by stephen scott tucker's avatar stephen scott tucker Committed by GitHub
Browse files

v1.30.5 -- Param errchk (#46) 



* prevented ArgClass Extract from indexing into empty list

* FuncCallClass GetInputs and GetOutputs convenience function for returning strings

* GetProcInputs method returns all properties of ProcInputClass for use with proc stream checking

* Processing stream is only run if Check returns zero, else an error msg is raised

* Changed uses of properties to propnames in ProcInputClass GetProcInputs

* Added default property to ParamClass to store values defined in cfg files and registry

* Parameter definition uses new default property

* EditParam method of ProcStreamClass uses parameter defaults to resolve bad edits

* ProcStreamOptionsGUI is more robust to bad edits

* Added CheckParams method to FuncCallClass which calls errchk function associated with user function if it exists

* Added convenience function to return script-friendly version of param value

* Demo errchk function for hmrR_GLM

* Updated helpstring to reflect new ProcStreamOptionsGUI constraints

* CheckParams called on parameter edit

* CheckParams called on proc stream calc

* prevented ArgClass Extract from indexing into empty list

* FuncCallClass GetInputs and GetOutputs convenience function for returning strings

* GetProcInputs method returns all properties of ProcInputClass for use with proc stream checking

* Processing stream is only run if Check returns zero, else an error msg is raised

* Changed uses of properties to propnames Util fn

* Added explicit list of prereqs to ignore to allow fns like tCCA to work before processing stream has been run

* Added a few more excluded arguments from prereq flagging

* Added Prerequisites to help function

* Registries GetEntryByName function, Proc stream Check rework

* Suppressed debug

* CheckOrder implemented at run, subj, group levels-- only checks runs for now

* Improved string parsing and error dialog on procstream save

* Merge development branch GLM function

* Introduced the Edit method of ParamClass for variable format; removed constraints on parameter length

* Updated hmrR_errchk with c_vector param

* Version 1.30.4

* v1.30.5

Co-authored-by: default avatardejar14 <67239853+dejar14@users.noreply.github.com>
Co-authored-by: default avatarjayd1860 <44243610+jayd1860@users.noreply.github.com>
parent 28a3bbc6

DataTree/ProcStream/FuncCallClass.m

+28 −8
Original line number Original line Diff line number Diff line
@@ -31,7 +31,7 @@ classdef FuncCallClass < handle 
            %        argOut.str: 'dod'

            %        argOut.str: 'dod'

            %         argIn.str: '(dod,t'

            %         argIn.str: '(dod,t'

            %          paramIn: [1x2 ParamClass]

            %          paramIn: [1x2 ParamClass]

            %             help: '  Perform a bandpass filter'

            %             help: '  Perform a bandpass filter�'

            %

            %

            obj.name       = '';

            obj.name       = '';

            obj.nameUI     = '';

            obj.nameUI     = '';
@@ -256,7 +256,7 @@ classdef FuncCallClass < handle 
            %        argOut: 'dod'

            %        argOut: 'dod'

            %         argIn.str: '(dod,t'

            %         argIn.str: '(dod,t'

            %       paramIn: [1x2 ParamClass]

            %       paramIn: [1x2 ParamClass]

            %          help: '  Perform a bandpass filter'

            %          help: '  Perform a bandpass filter�'

            %   

            %   

            obj.err = 0;            

            obj.err = 0;            

            if nargin<2

            if nargin<2
@@ -341,7 +341,8 @@ classdef FuncCallClass < handle 
                            end

                            end

                        end

                        end

                        pvalue = str2num(textstr{ii+2});                       

                        pvalue = str2num(textstr{ii+2});                       

                        obj.paramIn(end+1) = ParamClass(pname, pformat, pvalue);

                        % Save default values in ParamClass

                        obj.paramIn(end+1) = ParamClass(pname, pformat, pvalue, pvalue);

                        obj.GetParamHelp(length(obj.paramIn));

                        obj.GetParamHelp(length(obj.paramIn));

                        flag = 2;

                        flag = 2;

                    end

                    end
@@ -415,11 +416,9 @@ classdef FuncCallClass < handle 
                if length(obj.paramIn) ~= length(obj2.paramIn)

                if length(obj.paramIn) ~= length(obj2.paramIn)

                    return;

                    return;

                end

                end

                for ii=1:length(obj.paramIn)

%               Must have the same number of params, but their individual

                    if obj.paramIn(ii) ~= obj2.paramIn(ii)

%               lengths can differ

                        return;



                    end

                end

            elseif isstruct(obj2)

            elseif isstruct(obj2)

                % Name 

                % Name 

                k = find(obj.name=='_');

                k = find(obj.name=='_');
@@ -622,6 +621,27 @@ classdef FuncCallClass < handle 
            nbytes = sum(nbytes);

            nbytes = sum(nbytes);

        end

        end





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

        function errmsg = CheckParams(obj)

            errmsg = '';

            paramValStr = '';

            if exist([obj.name, '_errchk'], 'file')  % If errchk fn is on path

                for i = 1:length(obj.paramIn)  % Assemble list of args

                   paramValStr = [paramValStr, obj.paramIn(i).GetFormattedValue()]; %#ok<AGROW>

                   if i < length(obj.paramIn)

                       paramValStr = [paramValStr, ',']; %#ok<AGROW>

                   end

                end

                % Call the errchk function which returns a non-empty string

                % if there is an error

                eval(['errmsg = ', obj.name, '_errchk(', paramValStr, ')']);

                if ~isempty(errmsg)

                   errmsg = [obj.name, ': ', errmsg];

                end

            else

               return;

            end

        end

        

        

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

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

        function val = GetVar(obj, name)

        function val = GetVar(obj, name)

DataTree/ProcStream/ParamClass.m

+37 −4
Original line number Original line Diff line number Diff line
@@ -2,8 +2,9 @@ classdef ParamClass < matlab.mixin.Copyable 
    

    

    properties

    properties

        name

        name

        value

        value       % Current value of parameter

        format

        default     % Default value loaded from the function helpstring

        format      % printf-format string for scalar(s) in value

        help

        help

    end

    end
@@ -11,11 +12,11 @@ classdef ParamClass < matlab.mixin.Copyable 
        

        

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

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

        function obj = ParamClass(varargin)

        function obj = ParamClass(varargin)

            % FuncCallClass's Encode handles ParamClass construction

            obj.name   = '';

            obj.name   = '';

            obj.value  = [];

            obj.value  = [];

            obj.format = '';

            obj.format = '';

            obj.help   = '';

            obj.help   = '';

            

            if nargin==0

            if nargin==0

                return;

                return;

            elseif nargin==1

            elseif nargin==1
@@ -27,6 +28,11 @@ classdef ParamClass < matlab.mixin.Copyable 
                obj.name   = varargin{1};

                obj.name   = varargin{1};

                obj.format = varargin{2};

                obj.format = varargin{2};

                obj.value  = varargin{3};

                obj.value  = varargin{3};

            elseif nargin==4

                obj.name   = varargin{1};

                obj.format = varargin{2};

                obj.value  = varargin{3};

                obj.default = varargin{4};

            end

            end

        end

        end
@@ -75,6 +81,17 @@ classdef ParamClass < matlab.mixin.Copyable 
            end

            end

        end

        end

        

        

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

        function str = GetFormattedValue(obj)

            % Returns the string version of the value using the format

            % property, including brackets for arrays

            valstr = sprintf(obj.format, obj.value);

            if length(obj.value) > 1

                str = ['[', valstr, ']'];

            else

                str = valstr;

            end

        end

        

        

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

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

        function val = GetName(obj)

        function val = GetName(obj)
@@ -91,6 +108,22 @@ classdef ParamClass < matlab.mixin.Copyable 
            val = obj.format;

            val = obj.format;

        end

        end





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

        function val = GetDefault(obj)

            val = obj.default;

        end



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

        function err = Edit(obj, val)

            % Assign a new value to the parameter, affecting both the value

            % and format

            obj.value = val;

            eachformat = strsplit(obj.format);

            formatlen = length(val);

            obj.format = strtrim(repmat([eachformat{1}, ' '], 1, formatlen));

            err = 0;  % Error checking i.e. max length

        end

        

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

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

        function str = Encode(obj)

        function str = Encode(obj)

            str = '';

            str = '';

DataTree/ProcStream/ProcStreamClass.m

+4 −2
Original line number Original line Diff line number Diff line
@@ -192,7 +192,9 @@ classdef ProcStreamClass < handle 
        

        

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

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

        function str = EditParam(obj, iFcall, iParam, val)

        function str = EditParam(obj, iFcall, iParam, val)

            % Returns "" if the edit is rejected or the string 

            str = '';

            str = '';

            param = obj.fcalls(iFcall).paramIn(iParam);

            if isempty(iFcall)

            if isempty(iFcall)

                return;

                return;

            end

            end
@@ -205,8 +207,8 @@ classdef ProcStreamClass < handle 
            if isempty(obj.fcalls(iFcall).paramIn)

            if isempty(obj.fcalls(iFcall).paramIn)

                return;

                return;

            end

            end

            obj.fcalls(iFcall).paramIn(iParam).value = val;

            param.Edit(val);

            str = sprintf(obj.fcalls(iFcall).paramIn(iParam).format, val);

            str = sprintf(param.format, val);

        end

        end

FuncRegistry/UserFunctions/hmrR_GLM.m

+2 −6
Original line number Original line Diff line number Diff line
@@ -44,7 +44,7 @@ 
%                Defaults: p=8.6 q=0.547

%                Defaults: p=8.6 q=0.547

%                The peak is at time p*q.  The FWHM is about 2.3*sqrt(p)*q.

%                The peak is at time p*q.  The FWHM is about 2.3*sqrt(p)*q.

% paramsBasis - Parameters for the basis function depends on idxBasis

% paramsBasis - Parameters for the basis function depends on idxBasis

%               idxBasis=1 [stdev step] where stdev is the width of the

%               idxBasis=1 [stdev step ~ ~ ~ ~] where stdev is the width of the

%                  gaussian and step is the temporal spacing between

%                  gaussian and step is the temporal spacing between

%                  consecutive gaussians

%                  consecutive gaussians

%               idxBasis=2. [tau sigma T] applied to both HbO and HbR

%               idxBasis=2. [tau sigma T] applied to both HbO and HbR
@@ -259,11 +259,7 @@ for iBlk=1:length(data_y) 
        

        

    elseif idxBasis==2

    elseif idxBasis==2

        % Modified Gamma

        % Modified Gamma

        if length(paramsBasis)==3

            nConc = 1;

        elseif length(paramsBasis)==6

        nConc = 2;

        nConc = 2;

        end

        

        

        nB = 1;

        nB = 1;

        tbasis = zeros(ntHRF,nB,nConc);

        tbasis = zeros(ntHRF,nB,nConc);

FuncRegistry/UserFunctions/hmrR_GLM_errchk.m

0 → 100644
+20 −0
Original line number Original line Diff line number Diff line 
% PARAMETERS:

% trange: [-2.0, 20.0]

% glmSolveMethod: 1

% idxBasis: 1

% paramsBasis: [1.0 1.0 0.0 0.0 0.0 0.0], maxnum: 6

% rhoSD_ssThresh: 15.0

% flagNuisanceRMethod: 1

% driftOrder: 3

% c_vector: 0

function errmsg = hmrR_GLM_errchk(trange, glmSolveMethod, idxBasis, paramsBasis, rhoSD_ssThresh, flagNuisanceRMethod, driftOrder, c_vector)

    errmsg = '';

    % Define parameter error cases below and return an informative message

    if idxBasis > 4 || idxBasis < 1

       errmsg = 'Select a valid basis function (0-4)';

       return

    elseif glmSolveMethod > 2 || glmSolveMethod < 1

       errmsg = 'Select a valid solve method (1-2)'

       return

    end

end
 
 No newline at end of file

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