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segmentation/howToPrepareData.m
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howToPrepareData.m
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%% How to call autoSegment function
%% init
clear all
close all
clc
%% parameters of the segmentation. These parameters are used and you can use them as they are:
% opt.isLeft = true;
opt.isLeft = false;
opt.doSmoothing = true;
opt.ParallelProcess = true;
opt.numTemplates = 5;
opt.threshold = 190;
opt.volThr = 35000;
opt.ransacMaxIter = 5.0e6;
opt.ransacDist = 6; %mm
opt.ransacNo = 4; % number of samples for ransac!
opt.searchWindowSize = [65, 65, 45];
% The folder that contains images to segment
folderIn = '../../../../data/N/2/0/N209-149341/CT-N209-149341-1/';
% folderIn = './sampleData/samplesRight/';
%folderOut = folderIn;
folderOut = ' ../../../../data/N/2/0/N209-149341/CT-N209-149341-1/matlab/';
modelPath = '../Model/';
% This line adds sift feature extraction toolbox to the path
run('../Libraries/SIFT3D-master/build/lib/wrappers/matlab/setupSift3D.m')
% all nenessary functions are stored in the folder fonctions. We add these
% functions to the path
addpath(genpath('./functions'));
%% load model and extract the sift features on the meanShape
model = loadModel(modelPath, opt.isLeft);
%% load samples one by one and perform segmentation and then save the result
% This example assumes that all images are listed in a single folder. or in
% folders inside one folder specified in folderIn. For example, let's say
% folderIn is structured as follows:
% folderIn
% Img1.am
% Img2
% Img2.mhd
% Img2.raw
% Img3
% Img3_0001.dcm
% Img3_0002.dcm
% ...
% Img3_0250.dcm
% Img4.am
% ...
% If the structure of your folders are different, then you should adapt
% this folder
% list of all images in the folder
bones_in = dir([folderIn '*']);
%Exclude "." and ".." from the list. Put dicom images in a folder!
bones_in = bones_in(3:end);
for b = 1 : size(bones_in, 1)
tic
boneName = [folderIn bones_in(b).name];
%if the folder contains DICOMDIR or each image is in one directory!
if (isdir(boneName))
imageFile = dir(boneName);
imageFile = imageFile(3:end);
for file_counter = 1:size(imageFile, 1)
if(strcmp(imageFile(file_counter).name(end-2:end), 'mhd') || strcmp(imageFile(file_counter).name(end-2:end), 'dcm'))
boneName = [boneName, filesep imageFile(3).name];
break;
end
end
end
fname = boneName;
ind = strfind(fname, '.');
if(isempty(ind))
continue;
end
ind = ind(end);
fileFormat = fname(ind+1:end);
% right now I have code for ".am", ".mhd" and ".dcm" file formats. You
% can add more cases here to read data.
switch fileFormat
case 'am'
try
[imgInfo, Img] = LoadData_Amira(boneName);
catch
display([bones_in(b).name ': Problem in reading the file. Check the file and try again later!']);
end
case 'mhd'
try
[imgMHD, info]=read_mhd(boneName);
catch
display([bones_in(b).name ': Problem in reading the file. Check the file and try again later!']);
end
eval(['Img = ' class(imgMHD.data) '(zeros(size(imgMHD.data, 2), size(imgMHD.data, 1), size(imgMHD.data, 3)));']);
for ii = 1:size(imgMHD.data, 3)
Img(:, :, ii) = imgMHD.data(:, :, ii)';
end
imgInfo.BoundingBox.xMin = imgMHD.origin(1);
imgInfo.BoundingBox.yMin = imgMHD.origin(2);
imgInfo.BoundingBox.zMin = imgMHD.origin(3);
imgInfo.PixelSpacing(1) = imgMHD.spacing(1);
imgInfo.PixelSpacing(2) = imgMHD.spacing(2);
imgInfo.SliceThickness = imgMHD.spacing(3);
imgInfo.xSize = imgMHD.size(1);
imgInfo.ySize = imgMHD.size(2);
imgInfo.zSize = imgMHD.size(3);
imgInfo.BoundingBox.xMax = imgMHD.origin(1) + (imgMHD.size(1)-1) * imgInfo.PixelSpacing(1);
imgInfo.BoundingBox.yMax = imgMHD.origin(2) + (imgMHD.size(2)-1) * imgInfo.PixelSpacing(2);
imgInfo.BoundingBox.zMax = imgMHD.origin(3) + (imgMHD.size(3)-1) * imgInfo.SliceThickness;
if imgInfo.BoundingBox.zMax - imgInfo.BoundingBox.zMin > 700
display ([ bones_in(b).name ': skipped processing, due to the large size of scan, please crop this image and then try again (' num2str(size(imgMHD.data)) ')']);
continue;
end
clear imgMHD;
case 'dcm'
dicomDir = strsplit(boneName, filesep);
dicomDir = strjoin(dicomDir(1, 1:end-1), filesep);
[Img, imgInfo] = readDicomStack(dicomDir);
if (isempty(Img))
display ([ bones_in(b).name ': Could not read the dicom images.']);
continue;
end
otherwise
continue;
end
fname = bones_in(b).name;
ind = strfind(fname, '.');
if(isempty(ind))
ind = length(fname)+1;
else
ind = ind(end);
end
finalSurface = autoSegment(Img, imgInfo, model, opt);
simplePlyWrite(finalSurface, [folderOut fname(1:ind-1) '_auto.ply']);
measurements = doMeasurements(finalSurface);
save( [folderOut fname(1:ind-1) '.am'],'measurements');
end
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