我正在运行一个函数,以从100,000+个患者xray dicom文件中提取一些信息。出于安全目的,文件存储在veracrypt加密容器内。为什么Matlab在大量迭代中缓慢进行循环,但快速迭代次数很少?
当我运行一小部分文件时,它的执行速度非常快,但是当我在整个数据集上运行函数时,它的速度相当慢,从每秒几个文件到每秒1个文件(大约)。
,我很困惑,为什么发生这种情况?我曾尝试将数据存储在ssd和普通硬盘上,并且在使用较大数据集时与使用较小数据集相比,速度较慢。
我已经添加下面的参考代码,但还没有完全注释它尚未..这是我的论文,所以我将做到这一点,一旦我得到完成提取..
感谢您的帮助。
function [ DB, corrupted_files ] = extract_from_dcm(folder_name)
%EXTRACT_FROM_DCM Summary of this function goes here
% Detailed explanation goes here
if nargin == 0
folder_name = 'I:\Find and Treat\MXU Old Backup\2005';
end
Database_Check = strcat(folder_name, '\DataBase.mat');
if exist(Database_Check, 'file')
load(Database_Check);
entry_start = length(DB) + 1;
else
entry_start = 1;
[ found_dicoms ] = recursive_search(folder_name);
end
mat_file_location = strcat(folder_name, '\DataBase.mat');
excel_DB_file = strcat(folder_name, '\DataBase.xlsx');
excel_Corrupted_file = strcat(folder_name, '\Corrupted_Files.xlsx');
% the recursive search creates a struct with the path for each
% dcm file found. the list is then recursivly used to locate
% the image and extract the relevant information from it.
fprintf('---------------------------------------------\n');
fprintf('Start Patient Data Extraction\n');
tic
h = waitbar(0,'','Name','Patient Data Extraction');
entry_end = length(found_dicoms);
if entry_end == 0
% set(handles.info_box, 'String', 'No Dicom Files Found in this Folder or its Subfolders');
else
% set(handles.info_box, 'String', 'Congratulations Dicom Files have been found Look Through the Data Base using the Buttons Below....Press Save Button to save the Database. (Database Save format is EXCEL SpreadSheet and MAT file');
for kk = entry_start : entry_end
progress = kk/entry_end;
progress_percent = round(progress * 100);
waitbar(progress,h, sprintf('%d%% %d/%d of images processed', progress_percent, kk, entry_end));
img_full_path = found_dicoms(kk).name;
% search_path = folder_name;
% img_full_path = strrep(img_full_path, search_path, '');
try %# Attempt to perform some computation
dicom_info = dicominfo(img_full_path); %# The operation you are trying to perform goes here
try %# Attempt to perform some computation
dicom_read = dicomread(dicom_info); %# The operation you are trying to perform goes here
old = dicominfo(img_full_path);
DB(kk).StudyDate = old.StudyDate;
DB(kk).StudyTime = old.StudyTime;
if isfield(old.PatientName, 'FamilyName')
DB(kk).Forename = old.PatientName.FamilyName;
else
DB(kk).Forename = 'NA';
end
if isfield(old.PatientName, 'GivenName')
DB(kk).LastName = old.PatientName.GivenName;
else
DB(kk).LastName = 'NA';
end
if isfield(old, 'PatientSex')
DB(kk).PatientSex = old.PatientSex;
else
DB(kk).PatientSex = 'NA';
end
if isempty(old.PatientBirthDate)
DB(kk).PatientBirthDate = '00000000';
else
DB(kk).PatientBirthDate = old.PatientBirthDate;
end
if strcmp(old.Manufacturer, 'Philips Medical Systems')
DB(kk).Van = '1';
else
DB(kk).Van = '0';% section to represent organising by different vans
end
DB(kk).img_Path = img_full_path;
save(mat_file_location,'DB','found_dicoms');
catch exception %# Catch the exception
fprintf('read - file %d corrupt.\n',kk);
continue %# Pass control to the next loop iteration
end
catch exception %# Catch the exception
fprintf('info - file %d corrupt.\n',kk);
continue %# Pass control to the next loop iteration
end
end
end
[ corrupted_files, DB ] = corruption_check(DB, found_dicoms, folder_name);
toc
fprintf('End Patient Data Extraction\n');
fprintf('---------------------------------------------\n');
fprintf('---------------------------------------------\n');
fprintf('Start Saving Extracted Data \n');
tic
save(mat_file_location,'DB','corrupted_files','found_dicoms');
if isempty(DB)
msg = sprintf('No Dicom Files Found');
msgbox(strcat(msg));
else
DB_table = struct2table(DB);
writetable(DB_table, excel_DB_file);
end
close(h);
toc
fprintf('End Saving Extracted Data \n');
fprintf('---------------------------------------------\n');
end
就扔了这一点,有没有任何证据支持:你真的应该预先分配的是'DB'阵列,它看起来并不像你...你知道有多少元素会出现,特别是'entry_end - entry_start + 1'。当你做'DB(kk)'的时候,Matlab应该警告你,因为你会不断改变它的大小(这很慢),因为这会导致重新分配。要确定,运行[profiler](http://www.mathworks.com/help/matlab/ref/profile.html)。 –
更新该等待栏可能会耗费大量执行时间。循环中的图形更新非常昂贵。尝试评论,看看是否有帮助。更好的是,使用探查器。 – siliconwafer
很酷的感谢,你是我打算做预先分配,我会看看waitbar。问题是,作为代码,较大的循环就变得越慢,我不明白为什么这会是这样.. – bilaly