static ImageList LoadPreprocessedFiles(FileList files)
{
ImageList images;
for (unsigned int i=0; i < files.size() ; ++i)
{
images.push_back(mitk::IOUtil::LoadImage(files.at(i)));
}
return images;
}
int main( int argc, char* argv[] )
{
// Parse Command-Line Arguments
mitkCommandLineParser parser;
parser.setArgumentPrefix("--","-");
parser.setTitle("Tumor Progression Mapping");
parser.setCategory("Preprocessing Tools");
parser.setContributor("MBI");
parser.setDescription("Convert a set of co-registered and resampled follow-up images into a 2D png overview (and optionally in a 4D NRRD Volume).\nNaming convecntion of files is IDENTIFIER_YYYY-MM-DD_MODALITY.nrrd");
parser.setArgumentPrefix("--","-");
parser.addArgument("input", "i", mitkCommandLineParser::InputDirectory, "Input folder containing all follow ups");
parser.addArgument("output", "o", mitkCommandLineParser::OutputFile,"Output file (PNG)");
parser.addArgument("blanked", "b", mitkCommandLineParser::Bool, "Only Display Morphology");
parser.addArgument("morphology", "m", mitkCommandLineParser::String, "Morphology postfix.", "_T2.nrrd");
parser.addArgument("segmentation", "s", mitkCommandLineParser::String, "Segmentation postfix. Default: _GTV.nrrd", "_GTV.nrrd");
parser.addArgument("4dVolume", "v", mitkCommandLineParser::OutputFile, "Filepath to merged 4d NRRD Volume.");
parser.addArgument("skip", "k", mitkCommandLineParser::Int, "Number of slices to be skipped from top and from button (Default 0)");
parser.addArgument("interval", "n", mitkCommandLineParser::Int, "1 - for all slices, 2 - every second, 3 - every third ...");
parser.addArgument("opacity", "c", mitkCommandLineParser::Float, "Opacity of overlay [0,1] invisible -> visible");
map<string, us::Any> parsedArgs = parser.parseArguments(argc, argv);
if ( parsedArgs.size()==0 )
return EXIT_SUCCESS;
// Show a help message
if (parsedArgs.count("help") || parsedArgs.count("h"))
{
std::cout << parser.helpText();
return EXIT_SUCCESS;
}
std::string outputFile;
std::string inputFolder;
if (parsedArgs.count("input") || parsedArgs.count("i") )
{
inputFolder = us::any_cast<string> (parsedArgs["input"]) + "/";
}
if (parsedArgs.count("output") || parsedArgs.count("o") )
{
outputFile = us::any_cast<string> (parsedArgs["output"]);
}
int skip = 0;
int interval = 1;
float opacity = .3;
if (parsedArgs.count("skip") || parsedArgs.count("k") )
{
skip = us::any_cast<int>(parsedArgs["skip"]);
}
if (parsedArgs.count("interval") || parsedArgs.count("n") )
{
interval = us::any_cast<int>(parsedArgs["interval"]);
}
if (parsedArgs.count("opacity") || parsedArgs.count("c") )
{
opacity = us::any_cast<float>(parsedArgs["opacity"]);
}
FileList morphFiles;
FileList segFiles;
std::string refPattern;
std::string segPattern;
if (parsedArgs.count("morphology") || parsedArgs.count("m") )
{
refPattern = us::any_cast<std::string>(parsedArgs["morphology"]);
}
else
return EXIT_FAILURE;
if (parsedArgs.count("segmentation") || parsedArgs.count("s") )
{
segPattern = us::any_cast<std::string>(parsedArgs["segmentation"]);
}
bool blank = false;
if (parsedArgs.count("blanked") || parsedArgs.count("b"))
{
blank = true;
}
/// END Parsing CL Options
typedef itk::Image<RGBPixelType, 2> OutputImageType;
typedef itk::Image<RGBPixelType, 3> InputImageType;
mitkProgressionVisualization progressVis;
morphFiles = CreateFileList(inputFolder,refPattern);
segFiles = CreateFileList(inputFolder,segPattern);
ImageList morphImages = LoadPreprocessedFiles(morphFiles);
ImageList segImages;
if (segFiles.size()> 0 && blank == false)
segImages = LoadPreprocessedFiles(segFiles);
mitk::Image::Pointer rgbImage;
// define color for overlay image
mitk::Color color;
color.Fill(0);
color[0]=200*opacity;
color[1]=0;
// Set up itk time image filter to contain 0..N-1 images
itk::TileImageFilter<OutputImageType, OutputImageType>::Pointer tileFilter = itk::TileImageFilter<OutputImageType, OutputImageType>::New();
itk::FixedArray< unsigned int, 2 > layout;
unsigned int noOfTimeSteps = morphImages.size();
layout[0] = noOfTimeSteps;
layout[1] = 0; // automatic number of neccessary rows
tileFilter->SetLayout(layout);
// Get Reference image (all images are expected to have exact same dimensions!)
std::string fileName = morphFiles.at(0);
mitk::Image* referenceImg = morphImages.at(0);
mitk::Image::Pointer merged4D;
std::string volumeFile;
if (parsedArgs.count("4dVolume") || parsedArgs.count("v") )
{
volumeFile = us::any_cast<string>(parsedArgs["4dVolume"]);
if (volumeFile != "")
{
unsigned int* dims = new unsigned int[4];
dims[0] = referenceImg->GetDimensions()[0];
dims[1] = referenceImg->GetDimensions()[1];
dims[2] = referenceImg->GetDimensions()[2];
dims[3] = morphImages.size();
merged4D = mitk::Image::New();
merged4D->Initialize( referenceImg->GetPixelType() ,4,dims);
merged4D->GetTimeGeometry()->Expand(noOfTimeSteps);
}
}
unsigned int* dim = referenceImg->GetDimensions();
unsigned int sliceMaxAxial=dim[2];
// Now iterate over all data sets, extract overlay and add it to reference image
mitk::Image* morphImage;
mitk::Image* segmentationImage = NULL;
for (unsigned int i =0; i < noOfTimeSteps; i++)
{
MITK_INFO << "File : " << i << " of /" << noOfTimeSteps;
int currentSliceNo = 0;
// Retrieve images of current time step
fileName = morphFiles.at(i);
morphImage = morphImages.at(i);
// Create 4D Volume image
if ( volumeFile != "")
{
mitk::ImagePixelReadAccessor<InputPixelType,3> readAc(morphImage);
merged4D->GetGeometry(i)->SetSpacing(referenceImg->GetGeometry()->GetSpacing());
merged4D->GetGeometry(i)->SetOrigin(referenceImg->GetGeometry()->GetOrigin());
merged4D->GetGeometry(i)->SetIndexToWorldTransform(referenceImg->GetGeometry()->GetIndexToWorldTransform());
merged4D->SetVolume(readAc.GetData(),i);
}
MITK_INFO << "-- Convert to RGB";
rgbImage = progressVis.ConvertToRGBImage(morphImage);
// Add current seg in red
color.Fill(0);
color[0]=200*opacity;
if (!blank )
{
segmentationImage = segImages.at(i);
if (segmentationImage != NULL)
{
MITK_INFO << "-- Add Overlay";
progressVis.AddColouredOverlay(rgbImage,segmentationImage, color);
}
}
// Add Segmentation of next time step in red
if (i == 0)
{
MITK_INFO << "Skipping retro view in first time step";
}
else
{
color.Fill(0);
// Add previous in green
color[1]=200*opacity;
if (!blank)
{
mitk::Image* nextSeg = segImages.at(i-1);
MITK_INFO << "-- Add Overlay of next Step";
progressVis.AddColouredOverlay(rgbImage, nextSeg , color);
}
}
// Now save all slices from overlay in output folder
MITK_INFO << "-- Extract Slices";
for ( int slice = sliceMaxAxial - skip -1 ; slice > skip; slice -= interval)//sliceMaxAxial/40.0f))
{
InputImageType::Pointer itkImage = InputImageType::New();
InputImageType::Pointer itkImage2;
mitk::CastToItkImage(rgbImage, itkImage);
typedef itk::ImageDuplicator< InputImageType > DuplicatorType;
DuplicatorType::Pointer duplicator = DuplicatorType::New();
duplicator->SetInputImage(itkImage);
duplicator->Update();
itkImage2 = duplicator->GetOutput();
itk::Image<RGBPixelType,2>::Pointer extractedSlice = itk::Image<RGBPixelType,2>::New() ;
extractedSlice->Graft( progressVis.ExtractSlice(itkImage2,slice));
tileFilter->SetInput(((currentSliceNo+1)*(noOfTimeSteps)+i),extractedSlice );
tileFilter->SetInput(i,progressVis.TextAsImage(GetDate(fileName)) );
currentSliceNo++;
}
}
MITK_INFO << "Tile Filter Update";
tileFilter->Update();
// Write the output image
typedef itk::ImageFileWriter< OutputImageType > WriterType;
WriterType::Pointer writer = WriterType::New();
writer->SetInput( tileFilter->GetOutput() );
std::string patientName;
patientName = GetName(fileName);
if (blank)
writer->SetFileName(outputFile);
else
writer->SetFileName(outputFile);
writer->Update();
if (volumeFile != "")
mitk::IOUtil::Save(merged4D, volumeFile);
return EXIT_SUCCESS;
}
void IsisMain() {
// Get the list of cubes to process
FileList imageList;
UserInterface &ui = Application::GetUserInterface();
imageList.Read(ui.GetFilename("FROMLIST"));
// Read to list if one was entered
FileList outList;
if (ui.WasEntered("TOLIST")) {
outList.Read(ui.GetFilename("TOLIST"));
}
// Check for user input errors and return the file list sorted by CCD numbers
ErrorCheck(imageList, outList);
// Adds statistics for whole and side regions of every cube
for (int img=0; img<(int)imageList.size(); img++) {
g_s.Reset();
g_sl.Reset();
g_sr.Reset();
iString maxCube ((int)imageList.size());
iString curCube (img+1);
ProcessByLine p;
p.Progress()->SetText("Gathering Statistics for Cube " +
curCube + " of " + maxCube);
CubeAttributeInput att;
const std::string inp = imageList[img];
p.SetInputCube(inp, att);
p.StartProcess(GatherStatistics);
p.EndProcess();
g_allStats.push_back(g_s);
g_leftStats.push_back(g_sl);
g_rightStats.push_back(g_sr);
}
// Initialize the object that will calculate the gains and offsets
g_oNorm = new OverlapNormalization(g_allStats);
// Add the known overlaps between two cubes, and apply a weight to each
// overlap equal the number of pixels in the overlapping area
for (int i=0; i<(int)imageList.size()-1; i++) {
int j = i+1;
g_oNorm->AddOverlap(g_rightStats[i], i, g_leftStats[j], j,
g_rightStats[i].ValidPixels());
}
// Read in and then set the holdlist
FileList holdList;
holdList.Read(ui.GetFilename("HOLD"));
for (unsigned i=0; i<holdList.size(); i++) {
int index = -1;
for (unsigned j=0; j<imageList.size(); j++) {
std::string curName = imageList.at(j);
if (curName.compare(holdList[i]) == 0) {
index = j;
g_oNorm->AddHold(index);
}
}
}
// Attempt to solve the least squares equation
g_oNorm->Solve(OverlapNormalization::Both);
// Apply correction to the cubes if desired
bool applyopt = ui.GetBoolean("APPLY");
if (applyopt) {
// Loop through correcting the gains and offsets by line for every cube
for (int img=0; img<(int)imageList.size(); img++) {
g_imageNum = img;
ProcessByLine p;
iString max_cube ((int)imageList.size());
iString cur_cube (img+1);
p.Progress()->SetText("Equalizing Cube " + cur_cube + " of " + max_cube);
CubeAttributeInput att;
const std::string inp = imageList[img];
Cube *icube = p.SetInputCube(inp, att);
Filename file = imageList[img];
// Establish the output file depending upon whether or not a to list
// was entered
std::string out;
if (ui.WasEntered("TOLIST")) {
out = outList[img];
}
else {
Filename file = imageList[img];
out = file.Path() + "/" + file.Basename() + ".equ." + file.Extension();
}
CubeAttributeOutput outAtt;
p.SetOutputCube(out,outAtt,icube->Samples(),icube->Lines(),icube->Bands());
p.StartProcess(Apply);
p.EndProcess();
}
}
// Setup the output text file if the user requested one
if (ui.WasEntered("OUTSTATS")) {
std::string out = Filename(ui.GetFilename("OUTSTATS")).Expanded();
std::ofstream os;
os.open(out.c_str(),std::ios::app);
// Get statistics for each cube with PVL
Pvl p;
PvlObject equ("EqualizationInformation");
for (int img=0; img<(int)imageList.size(); img++) {
std::string cur = imageList[img];
PvlGroup a("Adjustment");
a += PvlKeyword("FileName", cur);
a += PvlKeyword("Average", g_oNorm->Average(img));
a += PvlKeyword("Base", g_oNorm->Offset(img));
a += PvlKeyword("Multiplier", g_oNorm->Gain(img));
equ.AddGroup(a);
}
p.AddObject(equ);
os << p << std::endl;
}
PvlGroup results ("Results");
for (int img=0; img<(int)imageList.size(); img++) {
results += PvlKeyword("FileName", imageList[img]);
results += PvlKeyword("Average", g_oNorm->Average(img));
results += PvlKeyword("Base", g_oNorm->Offset(img));
results += PvlKeyword("Multiplier", g_oNorm->Gain(img));
}
Application::Log(results);
// Clean-up for batch list runs
delete g_oNorm;
g_oNorm = NULL;
g_allStats.clear();
g_leftStats.clear();
g_rightStats.clear();
}