void AMScanDatabaseImportController::copySamples()
{
if(state_ != Importing) return;
emit progressDescription("Copying Samples...");
emit stepProgress(-1);
int totalSteps = s2dSampleIds_.count();
int currentStep = 0;
QMutableMapIterator<int, int> i(s2dSampleIds_);
while (i.hasNext()) {
if(state_ != Importing) return;
i.next();
emit stepProgress(int(100.0*(++currentStep)/totalSteps));
// key is id; value is id in destination database, or -1 if not there yet. (if not there, need to insert)
int sourceId = i.key(), destinationId = i.value();
if(destinationId<1) {
AMSample s;
s.loadFromDb(sourceDb_, sourceId);
if(s.storeToDb(destinationDb_))
i.setValue(s.id());
else
AMErrorMon::report(AMErrorReport(this, AMErrorReport::Alert, -2, "Could not import the sample '" % sourceSamples_.value(sourceId) % "' into the database."));
}
qApp->sendPostedEvents();
qApp->processEvents();
}
}
void AMScanDatabaseImportController::copyExperiments()
{
if(state_ != Importing) return;
emit progressDescription("Copying Experiments...");
emit stepProgress(-1);
int totalSteps = s2dExperimentIds_.count();
int currentStep = 0;
QMutableMapIterator<int, int> i(s2dExperimentIds_);
while (i.hasNext()) {
if(state_ != Importing) return;
i.next();
emit stepProgress(int(100.0*(++currentStep)/totalSteps));
// key is id; value is id in destination database, or -1 if not there yet. (if not there, need to insert)
int sourceId = i.key(), destinationId = i.value();
if(destinationId<1) {
AMExperiment e;
e.loadFromDb(sourceDb_, sourceId);
if(e.storeToDb(destinationDb_))
i.setValue(e.id());
else
AMErrorMon::report(AMErrorReport(this, AMErrorReport::Alert, -2, "Could not import the experiment '" % sourceExperiments_.value(sourceId) % "' into the database."));
}
// TODO: need to update the scans that should be in this experiment. This will be tricky... don't know new scan IDs yet.
qApp->sendPostedEvents();
qApp->processEvents();
}
}
void pdp::ExampleStep::work(LungDataset& input, LungDataset& output)
{
std::cout << "performing the example step!" << std::endl;
const DWORD pause = 1000;
Sleep(pause);
emit stepProgress(0.33f);
Sleep(pause);
emit stepProgress(0.66f);
Sleep(pause);
emit stepProgress(1.00f);
}
void pdp::convexHull::work(LungDataset& input, LungDataset& output)
{
std::cout << "performing the convexHull step!" << std::endl;
typedef itk::PolyLineParametricPath< 2 >::Pointer PathPointer;
for (int i = 0; i < input.slicesContours.size(); ++i)
{
std::vector<PathPointer> paths;
if(input.slicesContours[i].isLeftLung()){
ContourFilter contourFilterLeft(input.slicesContours[i].getLeftLung());
PathPointer hull = contourFilterLeft.convexHull();
input.slicesContours[i].setLeftHull(hull);
input.slicesThickenings[i].addLeftThickening(contourFilterLeft.generateThickenings(20, i));
//std::cout << "number of thickenings detected: " << thicks.size() << std::endl;
}
if(input.slicesContours[i].isRightLung()){
ContourFilter contourFilterRight(input.slicesContours[i].getRightLung());
PathPointer hull = contourFilterRight.convexHull();
input.slicesContours[i].setRightHull(hull);
input.slicesThickenings[i].addRightThickening(contourFilterRight.generateThickenings(20, i));
//std::cout << "number of thickenings detected: " << thicks.size() << std::endl;
}
emit stepProgress(1.0f/input.slicesContours.size()*i);
}
}
void AMScanDatabaseImportController::analyzeFacilitiesForDuplicates()
{
if(state_ != Analyzing) {
return;
}
sourceFacilities_.clear();
s2dFacilityIds_.clear();
emit progressDescription("Checking Facilities...");
emit stepProgress(-1);
// go through facilities in source, and make sure they all exist in destination. Map ids.
QSqlQuery q = AMDbObjectSupport::s()->select<AMFacility>(sourceDb_, "id, name, description");
q.exec();
int stepIndex = 0;
int totalSteps = q.size();
while(q.next()) {
emit stepProgress(int(100.0*(++stepIndex) / totalSteps)); // if size is not supported in db, then this will be negative... which will trigger a "undefined" progress bar. Perfect.
int id = q.value(0).toInt();
QString name = q.value(1).toString();
QString description = q.value(2).toString();
sourceFacilities_[id] = name % " " % description;
// Find a matching one in destinationDb_.
QSqlQuery q2 = AMDbObjectSupport::s()->select<AMFacility>(destinationDb_, "id", "name = ? AND description = ?");
q2.bindValue(0, name);
q2.bindValue(1, description);
q2.exec();
if(q2.first()) {
// found one.
s2dFacilityIds_[id] = q2.value(0).toInt(); // insert a mapping from source facility IDs to destination facility IDs
}
else {
// none found in destination. Will need to create it.
s2dFacilityIds_[id] = -1;
}
qApp->sendPostedEvents();
qApp->processEvents();
}
emit stepProgress(100);
}
void AMScanDatabaseImportController::analyzeSamplesForDuplicates()
{
if(state_ != Analyzing)
return;
sourceSamples_.clear();
s2dSampleIds_.clear();
emit progressDescription("Reviewing Samples...");
emit stepProgress(-1);
// go through samples in source, and see if any exist in destination
QSqlQuery q = AMDbObjectSupport::s()->select<AMSample>(sourceDb_, "id, name, dateTime");
q.exec();
int stepIndex = 0;
int totalSteps = q.size();
while(q.next()) {
emit stepProgress(int(100.0*(++stepIndex) / totalSteps)); // if size is not supported in db, then this will be negative... which will trigger a "undefined" progress bar. Perfect.
int id = q.value(0).toInt();
QString name = q.value(1).toString();
QDateTime dateTime = q.value(2).toDateTime();
sourceSamples_[id] = name % ", created " % AMDateTimeUtils::prettyDateTime(dateTime);
// Find a matching one in destinationDb_.
QSqlQuery q2 = AMDbObjectSupport::s()->select<AMSample>(destinationDb_, "id", "name = ? AND dateTime = ?");
q2.bindValue(0, name);
q2.bindValue(1, dateTime);
q2.exec();
if(q2.first()) {
// found one.
s2dSampleIds_[id] = q2.value(0).toInt(); // insert a mapping from source sample IDs to destination sample IDs
}
else {
// none found in destination. Will need to create it.
s2dSampleIds_[id] = -1;
}
qApp->sendPostedEvents();
qApp->processEvents();
}
emit stepProgress(100);
state_ = ReadyToImport;
}
void AMScanDatabaseImportController::startDatabaseOperations()
{
if(state_ != ReadyToImport)
return;
destinationDb_->startTransaction();
state_ = Importing;
copyFacilities();
copyRuns();
copyExperiments();
copySamples();
copyScans();
if(state_ == Importing) { // if we were cancelled, don't commit the transaction.
state_ = Finished;
destinationDb_->commitTransaction();
emit progressDescription("Import complete.");
emit stepProgress(100);
}
}
void AMScanDatabaseImportController::copyScans()
{
if(state_ != Importing) return;
emit progressDescription("Copying Scans...");
emit stepProgress(-1);
QString scanTableName = AMDbObjectSupport::s()->tableNameForClass<AMScan>();
QList<int> scanIds = sourceDb_->objectsWhere(scanTableName, QString());
AMScan::setAutoLoadData(false); // disable loading data for performance. It will also fail to load because it's in the wrong spot.
for(int i=0, cc=scanIds.count(); i<cc; i++) {
if(state_ != Importing) return;
emit stepProgress(int(100.0*(i+1)/cc));
AMDbObject* object = AMDbObjectSupport::s()->createAndLoadObjectAt(sourceDb_, scanTableName, scanIds.at(i));
if(!object) {
AMErrorMon::report(AMErrorReport(this,
AMErrorReport::Alert,
-3,
QString("Error copying the scan with ID '%1' out of the import database. Your database might be corrupted. Please report this problem to the Acquaman developers.").arg(scanIds.at(i))));
continue;
}
AMScan* scan = qobject_cast<AMScan*>(object);
if(!scan) {
AMErrorMon::report(AMErrorReport(this,
AMErrorReport::Alert,
-4,
QString("Error copying the scan with ID '%1' out of the import database: it wasn't a scan object. Your database might be corrupted. Please report this problem to the Acquaman developers.").arg(scanIds.at(i))));
delete object;
continue;
}
scan->retain(this);
// update scan fields:
scan->setRunId(s2dRunIds_.value(scan->runId(), -1));
scan->setSampleId(s2dSampleIds_.value(scan->sampleId(), -1));
// copy the raw data: filePath and additionalFilePaths
QDir destinationDir(destinationPath_);
// Assuming paths always in relative file format.
QString filePath = scan->filePath();
// Does the file exist already in the destination?
if(destinationDir.exists(filePath)) {
// I know we're not supposed to be a GUI module... but is it okay to prompt here for what to do?
if(userSaysShouldSkipDuplicateScan(scan)) {
scan->release(this);
continue;
}
filePath = makeUniqueFileName(destinationPath_, filePath);
}
copyFileAndMakeFoldersAsRequired(sourcePath_ % "/" % scan->filePath(),
destinationPath_ % "/" % filePath);
scan->setFilePath(filePath);
// Copy additional file paths:
QStringList extraPaths = scan->additionalFilePaths();
for(int j=0, cc=extraPaths.count(); j<cc; j++) {
QString destinationFilePath = extraPaths.at(j);
if(destinationDir.exists(destinationFilePath)) {
destinationFilePath = makeUniqueFileName(destinationPath_, destinationFilePath);
}
copyFileAndMakeFoldersAsRequired(sourcePath_ % "/" % extraPaths.at(j),
destinationPath_ % "/" % destinationFilePath);
extraPaths[j] = destinationFilePath;
}
scan->setAdditionalFilePaths(extraPaths);
// OK. raw data copied and file paths adjusted. Just store this scan in the new db:
if(!scan->storeToDb(destinationDb_, false)) { // HOLD UP! Don't generate those thumbnails... We'll do a direct copy.
AMErrorMon::report(AMErrorReport(this,
AMErrorReport::Alert,
-4,
QString("Error copying the scan with ID '%1' into the new database. Your database might be corrupted. Please report this problem to the Acquaman developers.").arg(scanIds.at(i))));
scan->release(this);
continue;
}
// Copy the thumbnails from the old DB to the new DB:
// find the old thumbnails:
QStringList thumbnailCols;
thumbnailCols << "objectId" << "objectTableName" << "number" << "type" << "title" << "subtitle" << "thumbnail";
int thumbnailFirstId = -1;
int thumbnailCount = 0;
QSqlQuery q = sourceDb_->select(AMDbObjectSupport::thumbnailTableName(),
thumbnailCols.join(","),
"objectId = ? AND objectTableName = ?");
q.bindValue(0, scanIds.at(i));
q.bindValue(1, scanTableName);
if(!q.exec()) {
AMErrorMon::report(AMErrorReport(this,
AMErrorReport::Alert,
-4,
QString("Error copying the the thumbnails for scan with ID '%1' out of the old database. Please report this problem to the Acquaman developers.").arg(scanIds.at(i))));
}
else {
if(q.first()) {
QVariantList thumbnailVals;
thumbnailVals << q.value(0) << q.value(1) << q.value(2) << q.value(3) << q.value(4) << q.value(5) << q.value(6);
thumbnailVals[0] = scan->id(); // update the scan id from old DB to new DB's value
thumbnailFirstId = destinationDb_->insertOrUpdate(0, AMDbObjectSupport::thumbnailTableName(), thumbnailCols, thumbnailVals);
if(thumbnailFirstId > 0)
thumbnailCount++;
else
AMErrorMon::report(AMErrorReport(this,
AMErrorReport::Alert,
-4,
QString("Error copying the the thumbnails for scan with ID '%1' into the new database. Please report this problem to the Acquaman developers.").arg(scanIds.at(i))));
}
while(q.next()) {
QVariantList thumbnailVals;
thumbnailVals << q.value(0) << q.value(1) << q.value(2) << q.value(3) << q.value(4) << q.value(5) << q.value(6);
thumbnailVals[0] = scan->id(); // update the scan id from old DB to new DB's value
if(destinationDb_->insertOrUpdate(0, AMDbObjectSupport::thumbnailTableName(), thumbnailCols, thumbnailVals) > 0)
thumbnailCount++;
}
}
// Finally, update the thumbnail references in the scan object:
// now that we know where the thumbnails are, update this in the object table
if(!destinationDb_->update(scan->id(),
scanTableName,
QStringList() << "thumbnailCount" << "thumbnailFirstId",
QVariantList() << thumbnailCount << thumbnailFirstId)) {
AMErrorMon::report(AMErrorReport(this, AMErrorReport::Alert, AMSCANDATABASEIMPORTCONTROLLER_ERROR_STORING_UPDATED_THUMBNAIL_COUNT_AND_FIRST_ID, QString("While importing, error trying to store the updated thumbnail count and firstThumbnailId for database object %1. Please report this problem to the Acquaman developers.").arg(scanIds.at(i))));
}
// What experiments was this scan in? Need to map and add in new database.
QList<int> experiments = AMExperiment::experimentsContainingScan(scanIds.at(i), sourceDb_);
foreach(int oldExperimentId, experiments) {
int newExperimentId = s2dExperimentIds_.value(oldExperimentId);
if(newExperimentId > 0)
AMExperiment::addScanToExperiment(scan->id(), newExperimentId, destinationDb_);
}
// All done!
scan->release();
qApp->sendPostedEvents();
qApp->processEvents();
}
void pdp::EMClassification::work(LungDataset& input, LungDataset& output)
{
std::cout << "performing the expectation maximization step!" << std::endl;
typedef itk::Image<float, 3> ImageType;
typedef itk::Image<unsigned char, 3> MaskType;
mitk::Image::Pointer mitkImage = input.getImage("Lungs");
mitkImage->DisconnectPipeline();
ImageType::Pointer img;
mitk::CastToItkImage(mitkImage, img);
mitk::Image::Pointer mitkMask = input.getImage("Otsu");
mitkMask->DisconnectPipeline();
MaskType::Pointer mask;
mitk::CastToItkImage(mitkMask, mask);
typedef itk::Vector< double, 1 > MeasurementVectorType;
typedef itk::Statistics::ListSample< MeasurementVectorType > SampleType;
SampleType::Pointer sample = prepareSample(img, mask);
emit stepProgress(0.33f);
//numberOfClasses = 4;
typedef itk::Array< double > ParametersType;
ParametersType params( 2 );
std::vector< ParametersType > initialParameters( numberOfClasses );
params[0] = -920.0;
params[1] = 2500.0;//std = 50
initialParameters[0] = params;
params[0] = -835.0;
params[1] = 1600.0;//std = 40
initialParameters[1] = params;
params[0] = -720.0;
params[1] = 900.0;//std = 30
initialParameters[2] = params;
params[0] = -570.0;
params[1] = 900.0;//std = 30
initialParameters[3] = params;
itk::Array< double > initialProportions(numberOfClasses);
initialProportions[0] = 0.8;
initialProportions[1] = 0.1;
initialProportions[2] = 0.05;
initialProportions[3] = 0.05;
expectationMaximization(initialParameters, initialProportions, sample);
emit stepProgress(0.66f);
MaskType::Pointer nonLungTissueMask = classify(img, mask);
// Cast the ITK -> MITK image and add it to the datatree.
mitk::Image::Pointer mitkOut = mitk::Image::New();
mitk::CastToMitkImage(nonLungTissueMask, mitkOut);
output.addImage(mitkOut, "nonLungTissueMask");
output.getDataStore()->Remove(output.getDataStore()->GetNamedNode("Otsu"));
emit stepProgress(1.00f);
}
void pdp::ThickeningDetector::onStepProgress(float totalpercent)
{
emit stepProgress(totalpercent);
}
