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ENH: Add method to import selected files into DICOM browser #914

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May 29, 2020
Merged

ENH: Add method to import selected files into DICOM browser #914

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9765f24
ENH: Add method to import selected files into DICOM browser
lassoan May 29, 2020
1f87dc5
BUG: Minor DICOM database fixes
lassoan May 29, 2020
c7d20e1
BUG: Fixed all DICOM tests
lassoan May 29, 2020
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17 changes: 12 additions & 5 deletions Libs/DICOM/Core/Testing/Cpp/ctkDICOMIndexerTest1.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -33,18 +33,25 @@ int ctkDICOMIndexerTest1( int argc, char * argv [] )
{
QCoreApplication app(argc, argv);

// Get data directory from environment
QDir dataDir = QDir(QProcessEnvironment::systemEnvironment().value("CTKData_DIR", ""));
QString dicomDir = dataDir.filePath("Data/DICOM");
if (!QDir(dicomDir).exists())
{
std::cerr << "Directory does not exist: " << qPrintable(dicomDir) << std::endl;
std::cerr << "Make sure CTKData_DIR environment variable is set correctly" << std::endl;
}

ctkDICOMDatabase database;
database.openDatabase(":memory:");
ctkDICOMIndexer indexer;

// Test ctkDICOMIndexer::addDirectory()
// just check if it doesn't crash
// Create block to test batch indexing using indexingBatch helper class.
{
indexer.addDirectory(&database, QString());
// might work (if there are some DCM images in temp
indexer.addDirectory(&database, QDir::tempPath());
// give an invalid destination name
indexer.addDirectory(&database, QDir::tempPath(), true);
indexer.addDirectory(&database, dicomDir, false);
indexer.addDirectory(&database, dicomDir, true);
}

// ensure all concurrent inserts are complete
Expand Down
2 changes: 2 additions & 0 deletions Libs/DICOM/Core/ctkDICOMDatabase.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -1583,6 +1583,7 @@ ctkDICOMDatabase::ctkDICOMDatabase(QObject* parent)
//------------------------------------------------------------------------------
ctkDICOMDatabase::~ctkDICOMDatabase()
{
this->closeDatabase();
}

//------------------------------------------------------------------------------
Expand Down Expand Up @@ -2891,6 +2892,7 @@ bool ctkDICOMDatabase::cleanup(bool vacuum/*=false*/)
QSqlQuery tagcacheCleanup(d->TagCacheDatabase);
seriesCleanup.exec("VACUUM;");
}
d->resetLastInsertedValues();
return true;
}

Expand Down
74 changes: 43 additions & 31 deletions Libs/DICOM/Widgets/Testing/Cpp/ctkDICOMBrowserTest.cpp
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Expand Up @@ -59,6 +59,7 @@ private slots:
private:
void _testImportCommon(ctkDICOMBrowser& browser);

QString DatabaseDirectoryName;
QString TemporaryDatabaseDirectoryName;

QDir DICOMDir;
Expand All @@ -67,47 +68,46 @@ private slots:
// ----------------------------------------------------------------------------
void ctkDICOMBrowserTester::initTestCase()
{
QApplication::instance()->setOrganizationName("commontk");
QApplication::instance()->setOrganizationDomain("commontk.org");
QApplication::instance()->setApplicationName("ctkDICOM");

// Get data directory from environment
QDir dataDir = QDir(
QProcessEnvironment::systemEnvironment().value("CTKData_DIR", ""));
QDir dataDir = QDir(QProcessEnvironment::systemEnvironment().value("CTKData_DIR", ""));
QVERIFY(dataDir.exists());

this->DICOMDir = dataDir.filePath("Data/DICOM");
QVERIFY(this->DICOMDir.exists());

this->DatabaseDirectoryName = QDir::tempPath() + "/ctkDICOMBrowserTest-Database";
this->TemporaryDatabaseDirectoryName =
QString("ctkDICOMBrowserTest.%1.DICOM-Database").arg(QTime::currentTime().toString("hhmmsszzz"));
}

// ----------------------------------------------------------------------------
void ctkDICOMBrowserTester::init()
{
// If any, remove default ./ctkDICOM-Database directory
{
ctkScopedCurrentDir scopedCurrentDir(QDir::tempPath());
ctk::removeDirRecursively("./ctkDICOM-Database");
QCOMPARE(QFileInfo("./ctkDICOM-Database").isDir(), false);
}

// Generate a new database directory name
this->TemporaryDatabaseDirectoryName =
QString("ctkDICOMBrowserTest.%1.DICOM-Database").arg(QTime::currentTime().toString("hhmmsszzz"));
// If any, remove default database directory
ctk::removeDirRecursively(this->DatabaseDirectoryName);
QCOMPARE(QFileInfo(this->DatabaseDirectoryName).isDir(), false);
}

// ----------------------------------------------------------------------------
void ctkDICOMBrowserTester::testDefaults()
{
// Clear left over settings
QSettings().remove("DatabaseDirectory");

ctkDICOMBrowser browser;
browser.setDatabaseDirectory(this->DatabaseDirectoryName);
browser.createNewDatabaseDirectory();

QVERIFY(QFileInfo("./ctkDICOM-Database").isDir());
QVERIFY(QFileInfo("./ctkDICOM-Database/ctkDICOM.sql").isFile());
QVERIFY(QFileInfo("./ctkDICOM-Database/ctkDICOMTagCache.sql").isFile());
QVERIFY(QFileInfo(this->DatabaseDirectoryName).isDir());
QVERIFY(QFileInfo(this->DatabaseDirectoryName+"/ctkDICOM.sql").isFile());
QVERIFY(QFileInfo(this->DatabaseDirectoryName+"/ctkDICOMTagCache.sql").isFile());

QCOMPARE(browser.databaseDirectory(), QString("./ctkDICOM-Database"));
QCOMPARE(browser.databaseDirectory(), this->DatabaseDirectoryName);
QVERIFY(browser.database() != 0);

QCOMPARE(browser.tagsToPrecache(), QStringList());

QVERIFY(browser.dicomTableManager() != 0);

QCOMPARE(browser.displayImportSummary(), true);
Expand All @@ -124,10 +124,12 @@ void ctkDICOMBrowserTester::testDatabaseDirectory()
{
// Check that value from setting is picked up
{
QSettings().setValue("DatabaseDirectory", this->TemporaryDatabaseDirectoryName);
QSettings().setValue("TempDatabaseDirectory", this->TemporaryDatabaseDirectoryName);
QCOMPARE(QFileInfo(this->TemporaryDatabaseDirectoryName).isDir(), false);

ctkDICOMBrowser browser;
browser.setDatabaseDirectorySettingsKey("TempDatabaseDirectory");
browser.createNewDatabaseDirectory();

QCOMPARE(QFileInfo(browser.databaseDirectory()).absoluteFilePath(),
QFileInfo(this->TemporaryDatabaseDirectoryName).absoluteFilePath());
Expand All @@ -138,9 +140,8 @@ void ctkDICOMBrowserTester::testDatabaseDirectory()
// ----------------------------------------------------------------------------
void ctkDICOMBrowserTester::testImportDirectoryMode()
{
QSettings().setValue("DatabaseDirectory", this->TemporaryDatabaseDirectoryName);

ctkDICOMBrowser browser;
browser.setDatabaseDirectory(this->TemporaryDatabaseDirectoryName);

browser.setImportDirectoryMode(ctkDICOMBrowser::ImportDirectoryCopy);
QCOMPARE(browser.importDirectoryMode(), ctkDICOMBrowser::ImportDirectoryCopy);
Expand All @@ -163,11 +164,14 @@ void ctkDICOMBrowserTester::testImportDirectories()
QFETCH(QStringList, directories);
QFETCH(ctkDICOMBrowser::ImportDirectoryMode, importDirectoryMode);

QSettings().setValue("DatabaseDirectory", this->TemporaryDatabaseDirectoryName);

ctkDICOMBrowser browser;
browser.setDatabaseDirectory(this->TemporaryDatabaseDirectoryName);

browser.setDisplayImportSummary(false);
// clear database because if an image is already imported
// then it is not imported again
browser.database()->initializeDatabase();

//browser.setDisplayImportSummary(false);
browser.importDirectories(directories, /* mode= */ importDirectoryMode);

this->_testImportCommon(browser);
Expand All @@ -176,6 +180,8 @@ void ctkDICOMBrowserTester::testImportDirectories()
// ----------------------------------------------------------------------------
void ctkDICOMBrowserTester::_testImportCommon(ctkDICOMBrowser& browser)
{
browser.waitForImportFinished();

QFETCH(int, expectedImporedPatients);
QFETCH(int, expectedImporedStudies);
QFETCH(int, expectedImporedSeries);
Expand Down Expand Up @@ -232,11 +238,14 @@ void ctkDICOMBrowserTester::testImportDirectory()
QFETCH(QStringList, directories);
QFETCH(ctkDICOMBrowser::ImportDirectoryMode, importDirectoryMode);

QSettings().setValue("DatabaseDirectory", this->TemporaryDatabaseDirectoryName);

ctkDICOMBrowser browser;
browser.setDatabaseDirectory(this->TemporaryDatabaseDirectoryName);

// clear database because if an image is already imported
// then it is not imported again
browser.database()->initializeDatabase();

browser.setDisplayImportSummary(false);
//browser.setDisplayImportSummary(false);
browser.importDirectory(directories[0], /* mode= */ importDirectoryMode);

this->_testImportCommon(browser);
Expand Down Expand Up @@ -275,11 +284,14 @@ void ctkDICOMBrowserTester::testOnImportDirectory()
QFETCH(QStringList, directories);
QFETCH(ctkDICOMBrowser::ImportDirectoryMode, importDirectoryMode);

QSettings().setValue("DatabaseDirectory", this->TemporaryDatabaseDirectoryName);

ctkDICOMBrowser browser;
browser.setDatabaseDirectory(this->TemporaryDatabaseDirectoryName);

// clear database because if an image is already imported
// then it is not imported again
browser.database()->initializeDatabase();

browser.setDisplayImportSummary(false);
//browser.setDisplayImportSummary(false);
browser.onImportDirectory(directories[0], /* mode= */ importDirectoryMode);

this->_testImportCommon(browser);
Expand Down
30 changes: 29 additions & 1 deletion Libs/DICOM/Widgets/Testing/Cpp/ctkDICOMBrowserTest1.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -68,17 +68,45 @@ int ctkDICOMBrowserTest1( int argc, char * argv [] )

// [Deprecated]
// make sure copy/link dialog doesn't pop up, always copy on import
/*
QSettings settings;
QString settingsString = settings.value("MainWindow/DontConfirmCopyOnImport").toString();
settings.setValue("MainWindow/DontConfirmCopyOnImport", QString("0")); // QMessageBox::AcceptRole
CHECK_INT(browser.importDirectoryMode(), static_cast<int>(ctkDICOMBrowser::ImportDirectoryCopy));
*/
// [/Deprecated]

// Test import of a few specific files
QDirIterator it(argv[1], QStringList() << "*.IMA", QDir::Files, QDirIterator::Subdirectories);
// Skip a few files
it.next();
it.next();
// Add 3 files
QStringList files;
files << it.next();
files << it.next();
files << it.next();
browser.importFiles(files);
browser.waitForImportFinished();

qDebug() << browser.patientsAddedDuringImport()
<< " " << browser.studiesAddedDuringImport()
<< " " << browser.seriesAddedDuringImport()
<< " " << browser.instancesAddedDuringImport();

CHECK_INT(browser.patientsAddedDuringImport(), 1);
CHECK_INT(browser.studiesAddedDuringImport(), 1);
CHECK_INT(browser.seriesAddedDuringImport(), 1);
CHECK_INT(browser.instancesAddedDuringImport(), 3);

browser.importDirectories(QStringList() << argv[1]);
browser.waitForImportFinished();

qDebug() << "\n\nAdded to database directory: " << files;

// [Deprecated]
// reset to the original copy/import setting
settings.setValue("MainWindow/DontConfirmCopyOnImport", settingsString);
//settings.setValue("MainWindow/DontConfirmCopyOnImport", settingsString);
// [/Deprecated]

CHECK_INT(browser.patientsAddedDuringImport(), 1);
Expand Down
32 changes: 22 additions & 10 deletions Libs/DICOM/Widgets/ctkDICOMAppWidget.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -156,7 +156,7 @@ void ctkDICOMAppWidgetPrivate::showUpdateSchemaDialog()
UpdateSchemaProgress->setMinimumDuration(0);
UpdateSchemaProgress->setValue(0);

//q->connect(UpdateSchemaProgress, SIGNAL(canceled()),
//q->connect(UpdateSchemaProgress, SIGNAL(canceled()),
// DICOMIndexer.data(), SLOT(cancel()));

q->connect(DICOMDatabase.data(), SIGNAL(schemaUpdateStarted(int)),
Expand All @@ -173,7 +173,7 @@ void ctkDICOMAppWidgetPrivate::showUpdateSchemaDialog()
q->connect(DICOMDatabase.data(), SIGNAL(schemaUpdated()),
&DICOMModel, SLOT(reset()));
// reset the database if canceled
q->connect(UpdateSchemaProgress, SIGNAL(canceled()),
q->connect(UpdateSchemaProgress, SIGNAL(canceled()),
&DICOMModel, SLOT(reset()));
}
UpdateSchemaProgress->show();
Expand All @@ -198,11 +198,17 @@ void ctkDICOMAppWidgetPrivate::showIndexerDialog()
IndexerProgress->setMinimumDuration(0);
IndexerProgress->setValue(0);

q->connect(IndexerProgress, SIGNAL(canceled()),
q->connect(IndexerProgress, SIGNAL(canceled()),
DICOMIndexer.data(), SLOT(cancel()));

q->connect(DICOMIndexer.data(), SIGNAL(progress(int)),
IndexerProgress, SLOT(setValue(int)));
// QProgressDialog requires a rate limiter when used from another thread,
// otherwise it crashes with stack overflow
// (see https://bugreports.qt.io/browse/QTBUG-83265).
// Since this feature is obsolete anyway (since ctkDICOMBrowser can now
// has built-in progress reporting of background data import), we just disable it.
// q->connect(DICOMIndexer.data(), SIGNAL(progress(int)),
// IndexerProgress, SLOT(setValue(int)));

q->connect(DICOMIndexer.data(), SIGNAL(progressDetail(QString)),
progressLabel, SLOT(setText(QString)));
q->connect(DICOMIndexer.data(), SIGNAL(progressDetail(QString)),
Expand All @@ -215,13 +221,13 @@ void ctkDICOMAppWidgetPrivate::showIndexerDialog()
q->connect(DICOMIndexer.data(), SIGNAL(indexingComplete(int, int, int, int)),
&DICOMModel, SLOT(reset()));
// stop indexing and reset the database if canceled
q->connect(IndexerProgress, SIGNAL(canceled()),
q->connect(IndexerProgress, SIGNAL(canceled()),
DICOMIndexer.data(), SLOT(cancel()));
q->connect(IndexerProgress, SIGNAL(canceled()),
q->connect(IndexerProgress, SIGNAL(canceled()),
&DICOMModel, SLOT(reset()));

// allow users of this widget to know that the process has finished
q->connect(IndexerProgress, SIGNAL(canceled()),
q->connect(IndexerProgress, SIGNAL(canceled()),
q, SIGNAL(directoryImported()));
q->connect(DICOMIndexer.data(), SIGNAL(indexingComplete(int, int, int, int)),
q, SIGNAL(directoryImported()));
Expand Down Expand Up @@ -490,9 +496,15 @@ void ctkDICOMAppWidget::onFileIndexed(const QString& filePath)
{
// Update the progress dialog when the file name changes
// - also allows for cancel button
QCoreApplication::instance()->processEvents();

// QProgressDialog requires a rate limiter when used from another thread,
// otherwise it crashes with stack overflow
// (see https://bugreports.qt.io/browse/QTBUG-83265).
// Since this feature is obsolete anyway (since ctkDICOMBrowser can now
// has built-in progress reporting of background data import), we just disable it.
//QCoreApplication::instance()->processEvents();

qDebug() << "Indexing \n\n\n\n" << filePath <<"\n\n\n";

}

//----------------------------------------------------------------------------
Expand Down
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