parfor with temporary variable worning
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I need expert's help.
I attached a code below:
The worning signal indicated "temp_info".
I want to stack CT images as a 3D volume.
But, position information of each slice is on the temp_info (loaded by dicominfo fn.)
I will handle few hundreds patient data.
Seriously, i need your help...
Best regards
Wonjoong Cheon
function [outputArg1] = dicomread3D(path_)
%UNTITLED2 Summary of this function goes here
% Detailed explanation goes here
ct_list = dir(fullfile(path_, '*.dcm'));
num = length(ct_list);
temp_img_size = dicomread(fullfile(ct_list(1).folder, ct_list(1).name));
dcm_stack = zeros(temp_img_size(1), temp_img_size(2), num);
f = waitbar(0,'Please wait...');
parfor iter2 = 1: num
temp_img = dicomread(fullfile(ct_list(iter2).folder, ct_list(iter2).name));
temp_info = dicominfo(fullfile(ct_list(iter2).folder, ct_list(iter2).name));
ct_location = temp_info.InstanceNumber;
dcm_stack(:,:,ct_location) = temp_img;
waitbar(iter2/num, f, 'Load 3D medical images...');
end
close(f)
try
outputArg1 = (dcm_stack.*temp_info.RescaleSlope)+temp_info.RescaleIntercept;
catch
outputArg1 = dcm_stack;
disp('Rescale information is empty')
end
end
采纳的回答
Edric Ellis
2022-11-24
I think there are a couple of problems here. Firstly, I think you need to change the way you're assigning into dcm_stack because as written, you are not satisfying the "sliced variable" requirement for a parfor loop output. I think you can fix this by storing an additional sliced output containing the the ct_location, I think you should apply the slope and intercept inside the parfor loop. Here's a sketch:
ct_list = dir(fullfile(path_, '*.dcm'));
num = length(ct_list);
temp_img_size = dicomread(fullfile(ct_list(1).folder, ct_list(1).name));
dcm_stack = zeros(temp_img_size(1), temp_img_size(2), num);
% Additional output for the parfor loop:
ct_locations = zeros(1, num);
parfor iter2 = 1: num
temp_img = dicomread(fullfile(ct_list(iter2).folder, ct_list(iter2).name));
temp_info = dicominfo(fullfile(ct_list(iter2).folder, ct_list(iter2).name));
% Store information from temp_info
ct_locations(iter2) = temp_info.InstanceNumber;
% Note we must store in stack indexed using "iter2":
dcm_stack(:,:,iter2) = (temp_img .* temp_info.RescaleSlope) + temp_info.RescaleIntercept;
end
% You can now re-order the "pages" in dcm_stack like this:
dcm_stack = dcm_stack(:,:,ct_locations);
7 个评论
Walter Roberson
2022-11-24
Each different file could potentially have its own slope and rescale (or be missing them) so I do recommend doing the transform inside the loop. Maybe
if ~isfield(temp_info, 'RescaleSlope'); temp_info.RescaleSlope = 1; end
if ~isfield(temp_info, 'RescaleIntercept'); temp_info.RescaleIntercept = 0; end
just before the assignment to dcm_stack(:,:,iter2)
wonjoong cheon
2022-11-25
编辑：wonjoong cheon
2022-11-25
Walter Roberson
2022-11-25
I need to block access from other threads such as gate keeper
If you are using parfor() then the only other thread that exists is the client, unless you used java to create threads, or you used system() or System.Diagnostics.Process to create additional processes
The parfor communications mechanisms ensure that different workers do not overwrite each other when setting variables that are indexed by the parfor index variable.
wonjoong cheon
2022-11-25
编辑：wonjoong cheon
2022-11-25
Walter Roberson
2022-11-25
Why isn't the reodering
[~, sortorder] = sort(sliceInfo);
dcm_stackN = dcm_stack(:,:,sortorder);
Walter Roberson
2022-11-25
outputArg1 = (dcm_stackN.*temp_infomation .RescaleSlope)+temp_infomation .RescaleIntercept;
No, every file could have a different rescale slope and intercept (or not have the information.) You should be rescaling inside the parfor.
temp_img = dicomread(fullfile(ct_list(iter2).folder, ct_list(iter2).name));
temp_info = dicominfo(fullfile(ct_list(iter2).folder, ct_list(iter2).name));
sliceInfo(iter2) = temp_info.InstanceNumber;
if ~isfield(temp_info, 'RescaleSlope'); temp_info.RescaleSlope = 1; end
if ~isfield(temp_info, 'RescaleIntercept'); temp_info.RescaleIntercept = 0; end
dcm_stack(:,:,iter2) = (temp_img .* temp_info.RescaleSlope) + temp_info.RescaleIntercept;
wonjoong cheon
2022-11-25
更多回答（1 个）
Walter Roberson
2022-11-24
0 个投票
temp_info is assigned to inside the parfor in a way that is not indexed by the loop variable. parfor automatically makes it a temporary variable, and that means it cannot be used after the loop.
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