Error utilizing parfor loops with MTEX calcGrains function

Hi All,

I am segmenting regions within my ebsd data under the mtex toolbox, and then using the parallel computing toolbox (parfor loop) to utilize calcGrains within each segmented region. I am able to run the calcGrains function within the command window, or within separate code, but when I include it in my parfor loop, it throws some odd errors.

**Here is my code:**

%% Specify Crystal and Specimen Symmetries

% crystal symmetry
CS = {... 
    'notIndexed',...
    crystalSymmetry('m-3m', [4 4 4], 'mineral', 'Aluminum'),...
    'notIndexed',...
    'notIndexed'};
%% convention

% plotting convention
setMTEXpref('xAxisDirection','east');
setMTEXpref('zAxisDirection','intoPlane');

%% Specify File Names

% path to files
pname = 'C:\Users\Cole\Desktop\Code\6061_EBSD_Analysis';

% which files to be imported
fname = [pname '\Retreating.ctf'];

%% Import the Data

% create an EBSD variable containing the data
ebsd = EBSD.load(fname,CS,'interface','ctf',...
    'convertEuler2SpatialReferenceFrame');

%% convention

% plotting convention
setMTEXpref('xAxisDirection','east');
setMTEXpref('zAxisDirection','intoPlane');

%% Segment Regions
% Define the dimensions of the entire data set
totalWidth = 1300; % in microns
totalHeight = 3000; % in microns

% Define the step size
stepSize = 100; % in microns

% Calculate the number of regions
numRegions = floor(totalHeight / stepSize);

% Initialize a cell array to store the EBSD regions
ebsdRegions = cell(1, numRegions);

% Iterate over the regions
for regionIndex = 1:numRegions
    % Calculate the ymin and ymax for the current region
    ymin = (regionIndex - 1) * stepSize;
    ymax = regionIndex * stepSize;
    
    % Define the region of interest
    region = [400 ymin 1300 (ymax - ymin)];
    
    % Use inpolygon to conditionally select data within the region
    condition = inpolygon(ebsd, region);
    
    % Create a new EBSD data set containing data within the region
    ebsdRegion = ebsd(condition);
    
    % Store the ebsdRegion in a variable with the desired syntax
    variableName = ['ebsd' num2str(ymin)];
    eval([variableName ' = ebsdRegion;']);
    
    % Store the ebsdRegion in the cell array
    ebsdRegions{regionIndex} = ebsdRegion;
end

%% Compute Grains for each 100 um region
% Set the number of iterations
N = 30;
stepSize = 100; % Step size in microns

% Preallocate arrays to store the results
grains = cell(1, N);
grainIds = cell(1, N);

% Store ebsd variables in a cell array
ebsdData = cell(1, N);
for i = 1:N
    ymin = (i - 1) * stepSize; % Calculate the ymin for the current region
    variableName = ['ebsd' num2str(ymin)];
    ebsdData{i} = evalin('base', variableName); % Retrieve the EBSD region
end

%% Parallel loop
% Preallocate arrays to store the results
tempGrains = cell(1, N);

% Parallel loop
parfor i = 1:N
    ymin = (i - 1) * stepSize; % Calculate the ymin for the current region
    ebsdRegion = ebsdData{i}; % Retrieve the EBSD region
    
    ebsdRegion = ebsdRegion('Aluminum'); % Apply necessary filters
    
    % Perform calculations in parallel
    tempGrains{i} = calcGrains(ebsdRegion);
end

% Assign the results to the cell array
grains = cell(1, N);
parfor i = 1:N
    grains{i} = tempGrains{i};
end

% Access the results from grains and grainIds arrays
for i = 1:N
    ymin = (i - 1) * stepSize; % Calculate the ymin for the current region
    variableName = ['grains' num2str(ymin)];
    assignin('base', variableName, grains{i});
end

**Here is the error that is thrown:**

Error using euler2quat

Invalid default value for property 'CS' in class 'orientation':

SWITCH expression must be a scalar or a character vector.

Error in rotation.byEuler (line 27)

q = euler2quat(varargin{:});

Error in symmetry/calcQuat (line 186)

rot = {rotation.byEuler(0,0,0)};

Error in crystalSymmetry (line 158)

if isempty(rot), rot = symmetry.calcQuat(id,axes); end

Error in gbc_angle (line 4)

d = angle(orientation(q(Dl),CS),orientation(q(Dr),CS));

Error in EBSD/calcGrains/doSegmentation (line 210)

connect(ndx) = feval(['gbc_' gbc],...

Error in EBSD/calcGrains (line 74)

[A_Db,I_DG] = doSegmentation(I_FD,ebsd,varargin{:});

Error in Retreating_Grain_Step (line 100)

parfor i = 1:N

I would really appreciate any help. Thank-you

Answer 1

[Walter Roberson]

parfor operates in a different process that does not have access to the base workspace established by the client.

[Cole Franz]

Is there a way I can explicitely give the parfor loop access to my workspace? One confusing aspect to this problem is that the code worked for me a month or two ago, but since then it has been giving me issues.

[Walter Roberson]

No. There is no way to give parfor access to shared memory (other than to use operating system facilities to create shared memory segments... or perhaps memmap a file)

If you need variables from the base workspace to be available to the workers then use parfevalOnAll() to run a function that initializes the local base workspaces with appropriate values.