parseInputs(varargin{:}) related questions

I am trying to calculate the deformation displacement of two MRI images. My code has been shown below:

function [u, cc] = DVC(varargin)

% Parse inputs and create meshgrid
[I,m,mSize,sSize,MTF,M,ccThreshold] = parseInputs(varargin{:});

% Initialize variables
mSize_ = prod(mSize);
u123 = zeros(mSize_,3);
cc = zeros(mSize_,1);

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
wb = findall(0,'Tag','TMWWaitbar'); wb = wb(1);

waitbar(1/7,wb,'Estimating Displacements (Time Remaining: )');

for k = 1:mSize_

      tStart = tic; % begin timer
      %--------------------------------------------------------------------------
      % grab the moving subset from the images
      A = I{1}(m{1}(k,:),m{2}(k,:),m{3}(k,:));
      B = I{2}(m{1}(k,:),m{2}(k,:),m{3}(k,:));

      % multiply by the modular transfer function to alter frequency content
      A = MTF.*A; B = MTF.*B;

      % run cross-correlation
      A = xCorr3(A,B,sSize);

      % find maximum index of the cross-correlaiton
      [cc(k), maxIdx] = max(A(:));

      % compute voxel resolution displacements
      [u1, u2, u3] = ind2sub(sSize,maxIdx);

      % gather the 3x3x3 voxel neighborhood around the peak
      try xCorrPeak = reshape(A(u1 + (-1:1), u2 + (-1:1), u3 + (-1:1)),27,1);        
          % last squares fitting of the peak to calculate sub-voxel displacements
          du123 = lsqPolyFit3(xCorrPeak, M{1}, M{2});       
          u123(k,:) = [u1 u2 u3] + du123' - sSize/2 - 1;
          %--------------------------------------------------------------------------
      catch
          u123(k,:) = nan;
      end    
  %     xCorrPeak = reshape(A(u1 + (-1:1), u2 + (-1:1), u3 + (-1:1)),27,1);
  %     
  %     % least squares fitting of the peak to calculate sub-voxel displacements
  %     du123 = lsqPolyFit3(xCorrPeak, M{1}, M{2});
  %     u123(k,:) = [u1 u2 u3] + du123' - (sSize/2) - 1;
      %--------------------------------------------------------------------------

      % waitbar calculations (update only every 100 iterations)
      if rem(k,100) == 0
          tRemaining = (toc(tStart)*(mSize_ - k)); % Time remaining for waitbar
          waitbar(1/7*(k/mSize_ + 1),wb,['Estimating Displacements (Time Remaining: ', datestr(datenum(0,0,0,0,0,tRemaining),'MM:SS'),')'])
      end
  end
  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
  % Reshape displacements and set bad correlations to zero
  waitbar(2/7,wb,'Removing Bad Correlations')
  %
  cc = reshape(double(cc),mSize);
  % cc = permute(cc,[2 1 3]);
  [cc, ccMask] = removeBadCorrelations(I,cc,ccThreshold);
  %
  % u = cell(1,3);
  % for i = 1:3
  %     u{i} = reshape(double(u123(:,i)),mSize).*ccMask;
  %     u{i} = permute(u{i},[2 1 3]);
  % end
  u{1} = reshape(double(u123(:,2)),mSize).*ccMask;
  u{2} = reshape(double(u123(:,1)),mSize).*ccMask;
  u{3} = reshape(double(u123(:,3)),mSize).*ccMask;
  end

It gets error like

Error in DVC (line 29)
[I,mSize,sSize,ccThreshold] = parseInputs(varargin{:});

[per isakson]

• parseInputs what is that?
• full error message please. Line 29 doesn't refer to the function in the question?

[tao wang]

I followed the instruction :" Parse inputs and create meshgrid" so I put parseInputs over there; Line 29 is where the parseinputs are.

Thank you.

[Adam]

Instruction from where? Coding would certainly be a lot easier if all we needed to do was just make a call to a function with the name given in a written instruction and the function would magically create itself and know exactly what we want it to do! But parseInputs is not part of base Matlab or any toolbox I have and you haven't shown us any implementation of it so based on the information you give this function simply doesn't exist.

[tao wang]

That is true. I am very new to this part of matlab. I need to do 3D analysis of MRI images. Based on Frank Lab's FIDVC toolbox, they created a method to do 3D images analysis. Their instructions are:

function [u, cc] = DVC(varargin)
% [du, cc] = DVC(I,sSize,sSpacing,ccThreshold) estimates
% displacements between two volumetric images through digital volume
% correlation.
%
% INPUTS
%   I: cell containing the undeformed, I{1}, and deformed, I{2} 3-D images
%   sSize: interrogation window (subset) size
%   sSpacing: interrogation window (subset) spacing.  Determines window
%             overlap factor
%   ccThreshold: threshold value that defines a bad cross-correlation
%
% OUTPUTS
%   u: cell containing the displacement field (u{1:3} = {u_x, u_y, u_z})
%   cc: peak values of the cross-correlation for each interrogation
%
% NOTES
% all functions are self contained
% If used please cite:
% Bar-Kochba E., Toyjanova J., Andrews E., Kim K., Franck C. (2014) A fast 
% iterative digital volume correlation algorithm for large deformations. 
% Experimental Mechanics. doi: 10.1007/s11340-014-9874-2
%
% Parse inputs and create meshgrid
%
[I,m,mSize,sSize,MTF,M,ccThreshold] = parseInputs(varargin{:});
% Initialize variables
mSize_ = prod(mSize);
u123 = zeros(mSize_,3);
cc = zeros(mSize_,1);

Thank you!

[Adam]

Well, if it is a toolbox then I assume the function is defined in the toolbox, or probably further down that particular file.

Answer 1

[Fangjun Jiang]

Regarding parse inputs, you can type "doc parse" in MATLAB and see an example. It is a better way to write a function to have some checks on the input arguments.

If you are new to MATLAB, just ignore this part and provide all the necessary and needed inputs.

Answer 2

[BA]

it could be a hidden function which can be accessed via

which -all parseInputs

hope this helps https://de.mathworks.com/matlabcentral/answers/375690-general-usage-of-parseinputs