diff --git a/Plugins/org.mitk.gui.qt.xnat/CMakeLists.txt b/Plugins/org.mitk.gui.qt.xnat/CMakeLists.txt index 95bffa7abc..df70e7afd7 100644 --- a/Plugins/org.mitk.gui.qt.xnat/CMakeLists.txt +++ b/Plugins/org.mitk.gui.qt.xnat/CMakeLists.txt @@ -1,8 +1,8 @@ project(org_mitk_gui_qt_xnat) MACRO_CREATE_MITK_CTK_PLUGIN( - DEPENDS Poco + PACKAGE_DEPENDS Poco|Zip MODULE_DEPENDS MitkXNAT EXPORT_DIRECTIVE XNAT_EXPORT EXPORTED_INCLUDE_SUFFIXES src ) diff --git a/Plugins/org.mitk.gui.qt.xnat/src/internal/QmitkXnatEditor.cpp b/Plugins/org.mitk.gui.qt.xnat/src/internal/QmitkXnatEditor.cpp index cdf7e540eb..4ef358f2a1 100644 --- a/Plugins/org.mitk.gui.qt.xnat/src/internal/QmitkXnatEditor.cpp +++ b/Plugins/org.mitk.gui.qt.xnat/src/internal/QmitkXnatEditor.cpp @@ -1,581 +1,558 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #include "QmitkXnatEditor.h" // Qmitk #include "QmitkXnatObjectEditorInput.h" #include "org_mitk_gui_qt_xnatinterface_Activator.h" // CTK XNAT Core #include "ctkXnatObject.h" #include "ctkXnatDataModel.h" #include "ctkXnatFile.h" #include "ctkXnatResource.h" #include "ctkXnatScan.h" #include "ctkXnatScanFolder.h" #include "ctkXnatAssessor.h" #include "ctkXnatAssessorFolder.h" #include "ctkXnatReconstruction.h" #include "ctkXnatReconstructionFolder.h" // CTK XNAT Widgets #include "ctkXnatListModel.h" // Blueberry #include #include #include // Qt #include #include #include #include +#include #include // MITK #include #include // Poco -#include +#include const QString QmitkXnatEditor::EDITOR_ID = "org.mitk.editors.xnat.browser"; QmitkXnatEditor::QmitkXnatEditor() : m_DownloadPath(berry::Platform::GetPreferencesService()-> GetSystemPreferences()->Node("/XnatConnection")->Get("Download Path", "")), m_ListModel(new ctkXnatListModel()), m_Session(0), m_DataStorageServiceTracker(mitk::org_mitk_gui_qt_xnatinterface_Activator::GetContext()), m_SelectionListener(new berry::SelectionChangedAdapter(this, &QmitkXnatEditor::SelectionChanged)) { m_DataStorageServiceTracker.open(); if (m_DownloadPath.isEmpty()) { QString xnatFolder = "XNAT_DOWNLOADS"; QDir dir(mitk::org_mitk_gui_qt_xnatinterface_Activator::GetContext()->getDataFile("").absoluteFilePath()); dir.mkdir(xnatFolder); dir.setPath(dir.path() + "/" + xnatFolder); m_DownloadPath = dir.path() + "/"; } } QmitkXnatEditor::~QmitkXnatEditor() { delete m_ListModel; berry::ISelectionService* s = GetSite()->GetWorkbenchWindow()->GetSelectionService(); s->RemoveSelectionListener(m_SelectionListener.data()); m_DataStorageServiceTracker.close(); } bool QmitkXnatEditor::IsDirty() const { return false; } bool QmitkXnatEditor::IsSaveAsAllowed() const { return false; } void QmitkXnatEditor::Init(berry::IEditorSite::Pointer site, berry::IEditorInput::Pointer input) { this->SetSite(site); berry::QtEditorPart::SetInput(input); this->SetInput(input); } void QmitkXnatEditor::DoSave() { } void QmitkXnatEditor::DoSaveAs() { } void QmitkXnatEditor::SetInput(berry::IEditorInput::Pointer input) { QmitkXnatObjectEditorInput::Pointer oPtr = input.Cast(); if (oPtr.IsNotNull()) { berry::QtEditorPart::SetInput(oPtr); this->GetEditorInput().Cast()->GetXnatObject()->fetch(); } } void QmitkXnatEditor::SetFocus() { } void QmitkXnatEditor::CreateQtPartControl(QWidget *parent) { // create GUI widgets from the Qt Designer's .ui file m_Controls.setupUi(parent); m_Controls.buttonDownload->setEnabled(false); m_Controls.labelDownload->setText("Select a xnat file, resource, scan, or scan folder to download..."); GetSite()->GetWorkbenchWindow()->GetSelectionService()->AddSelectionListener(m_SelectionListener.data()); connect(m_Controls.treeView, SIGNAL(activated(const QModelIndex&)), this, SLOT(OnObjectActivated(const QModelIndex&))); connect(m_Controls.buttonDownload, SIGNAL(clicked()), this, SLOT(DownloadResource())); connect(m_Controls.buttonDataModel, SIGNAL(clicked()), this, SLOT(OnDataModelButtonClicked())); connect(m_Controls.buttonProject, SIGNAL(clicked()), this, SLOT(OnProjectButtonClicked())); connect(m_Controls.buttonSubject, SIGNAL(clicked()), this, SLOT(OnSubjectButtonClicked())); connect(m_Controls.buttonExperiment, SIGNAL(clicked()), this, SLOT(OnExperimentButtonClicked())); connect(m_Controls.buttonKindOfData, SIGNAL(clicked()), this, SLOT(OnKindOfDataButtonClicked())); connect(m_Controls.buttonSession, SIGNAL(clicked()), this, SLOT(OnSessionButtonClicked())); connect(m_Controls.buttonResource, SIGNAL(clicked()), this, SLOT(OnResourceButtonClicked())); connect(m_Controls.treeView, SIGNAL(clicked(const QModelIndex&)), SLOT(itemSelected(const QModelIndex&))); m_Tracker = new mitk::XnatSessionTracker(mitk::org_mitk_gui_qt_xnatinterface_Activator::GetXnatModuleContext()); connect(m_Tracker, SIGNAL(AboutToBeClosed(ctkXnatSession*)), this, SLOT(CleanListModel(ctkXnatSession*))); connect(m_Tracker, SIGNAL(Opened(ctkXnatSession*)), this, SLOT(UpdateSession(ctkXnatSession*))); m_Tracker->Open(); // Makes the breadcrumb feature invisible for (int i = 0; i < m_Controls.breadcrumbHorizontalLayout->count() - 1; i++) { QLayoutItem* child = m_Controls.breadcrumbHorizontalLayout->itemAt(i); child->widget()->setVisible(false); } for (int i = 0; i < m_Controls.breadcrumbDescriptionLayout->count() - 1; i++) { QLayoutItem* child = m_Controls.breadcrumbDescriptionLayout->itemAt(i); child->widget()->setVisible(false); } QmitkXnatObjectEditorInput::Pointer oPtr = GetEditorInput().Cast(); if (oPtr.IsNotNull()) { UpdateList(); } else { ctkXnatSession* session; try { session = mitk::org_mitk_gui_qt_xnatinterface_Activator::GetXnatModuleContext()->GetService( mitk::org_mitk_gui_qt_xnatinterface_Activator::GetXnatModuleContext()->GetServiceReference()); } catch (std::invalid_argument) { session = 0; } UpdateSession(session); } } void QmitkXnatEditor::UpdateList() { QmitkXnatObjectEditorInput::Pointer xoPtr(GetEditorInput().Cast()); if (xoPtr.IsNull()) return; ctkXnatObject* inputObject = xoPtr->GetXnatObject(); if (inputObject == NULL) return; m_Controls.treeView->setModel(m_ListModel); m_ListModel->setRootObject(inputObject); m_Controls.treeView->reset(); // recursive method to check parents of the inputObject m_ParentCount = ParentChecker(inputObject); // breadcrumb labels for (int i = 0; i < m_Controls.breadcrumbHorizontalLayout->count() - 1; i++) { QLayoutItem* child = m_Controls.breadcrumbHorizontalLayout->itemAt(i); child->widget()->setVisible(false); } for (int i = 0; i < m_Controls.breadcrumbDescriptionLayout->count() - 1; i++) { QLayoutItem* child = m_Controls.breadcrumbDescriptionLayout->itemAt(i); child->widget()->setVisible(false); } ctkXnatObject* parent = NULL; for (int i = m_ParentCount * 2; i >= 0; i--) { if (i > 12) break; m_Controls.breadcrumbDescriptionLayout->itemAt(i)->widget()->setVisible(true); QLayoutItem* child = m_Controls.breadcrumbHorizontalLayout->itemAt(i); child->widget()->setVisible(true); if (i > 0) { m_Controls.breadcrumbHorizontalLayout->itemAt(i - 1)->widget()->setVisible(true); m_Controls.breadcrumbDescriptionLayout->itemAt(i - 1)->widget()->setVisible(true); } if (parent == NULL) { parent = inputObject; } // create breadcrumb button QPushButton* breadcrumbButton = dynamic_cast(child->widget()); breadcrumbButton->setText(parent->id()); parent = parent->parent(); i--; } m_Controls.buttonDataModel->setText("root"); m_Controls.buttonDownload->setEnabled(false); m_Controls.labelDownload->setVisible(true); } void QmitkXnatEditor::SelectionChanged(const berry::IWorkbenchPart::Pointer& sourcepart, const berry::ISelection::ConstPointer& selection) { // check for null selection if (selection.IsNull()) { return; } // exclude own selection events and check whether this kind of selection can be handled if (sourcepart != this && selection.Cast()) { berry::IStructuredSelection::ConstPointer currentSelection = selection.Cast(); // iterates over the selection for (berry::IStructuredSelection::iterator itr = currentSelection->Begin(); itr != currentSelection->End(); ++itr) { if (berry::SmartPointer objectPointer = itr->Cast()) { // get object of selected ListWidgetElement ctkXnatObject* object = objectPointer->GetQModelIndex().data(Qt::UserRole).value(); // if a file is selected, don't change the input and list view if (dynamic_cast(object) == NULL) { QmitkXnatObjectEditorInput::Pointer oPtr(new QmitkXnatObjectEditorInput(object)); berry::IEditorInput::Pointer editorInput(oPtr); if (!(editorInput == this->GetEditorInput())) this->SetInput(editorInput); UpdateList(); } } } } } void QmitkXnatEditor::DownloadResource() { if (!m_Controls.treeView->selectionModel()->hasSelection()) return; const QModelIndex index = m_Controls.treeView->selectionModel()->currentIndex(); QVariant variant = m_ListModel->data(index, Qt::UserRole); if (variant.isValid()) { ctkXnatObject* resource = variant.value(); if (dynamic_cast(resource) == NULL) { MITK_INFO << "Download started ..."; MITK_INFO << "..."; QString resourceName = m_ListModel->data(index, Qt::DisplayRole).toString(); QString resourcePath = m_DownloadPath + resourceName + ".zip"; resource->download(resourcePath); // Testing if the path exists QDir downDir(m_DownloadPath); if (downDir.exists(resourceName + ".zip")) { MITK_INFO << "Download of " << resourceName.toStdString() << ".zip was completed!"; } else { MITK_INFO << "Download of " << resourceName.toStdString() << ".zip failed!"; } } else { InternalFileDownload(index); } } } void QmitkXnatEditor::ToHigherLevel() { ctkXnatObject* parent = GetEditorInput().Cast()->GetXnatObject()->parent(); if (parent == NULL) { return; } QmitkXnatObjectEditorInput::Pointer oPtr(new QmitkXnatObjectEditorInput(parent)); berry::IEditorInput::Pointer editorInput(oPtr); this->SetInput(editorInput); UpdateList(); } void QmitkXnatEditor::OnObjectActivated(const QModelIndex &index) { if (!index.isValid()) return; ctkXnatObject* child = GetEditorInput().Cast()->GetXnatObject()->children().at(index.row()); if (child != NULL) { ctkXnatFile* file = dynamic_cast(child); if (file != NULL) { // Download file and put into datamanager InternalFileDownload(index); mitk::IDataStorageService* dsService = m_DataStorageServiceTracker.getService(); if (dsService != NULL) { QString name = file->property("Name"); + QString filePath = m_DownloadPath + name; if (file->property("collection") == "DICOM") { - ctkXnatObject* grandParent = file->parent()->parent(); - name = grandParent->property("ID") + "-" + grandParent->property("series_description") + "/" + name; + QDirIterator it(m_DownloadPath, QStringList() << name, QDir::Files, QDirIterator::Subdirectories); + while (it.hasNext()) { + it.next(); + filePath = it.filePath(); + } } - mitk::DataNode::Pointer node = mitk::IOUtil::LoadDataNode((m_DownloadPath + name).toStdString()); + mitk::DataNode::Pointer node = mitk::IOUtil::LoadDataNode(filePath.toStdString()); if ((node.IsNotNull()) && (node->GetData() != NULL)) { dsService->GetDataStorage()->GetDataStorage()->Add(node); mitk::BaseData::Pointer basedata = node->GetData(); mitk::RenderingManager::GetInstance()->InitializeViews( basedata->GetTimeGeometry(), mitk::RenderingManager::REQUEST_UPDATE_ALL, true); } } } else { // Updates the root item QmitkXnatObjectEditorInput::Pointer oPtr(new QmitkXnatObjectEditorInput(child)); berry::IEditorInput::Pointer editorInput(oPtr); this->SetInput(editorInput); this->GetEditorInput().Cast()->GetXnatObject()->fetch(); UpdateList(); } } } void QmitkXnatEditor::InternalFileDownload(const QModelIndex& index) { QVariant variant = m_ListModel->data(index, Qt::UserRole); if (variant.isValid()) { ctkXnatFile* file = dynamic_cast(variant.value()); if (file != NULL) { // Testing if the file exists QDir downDir(m_DownloadPath); if (downDir.exists(file->property("Name"))) { MITK_INFO << "File exists already!"; return; } if (file->property("collection") == QString("DICOM")) { ctkXnatObject* parent = file->parent(); - QList list = parent->children(); - - ctkXnatObject* grandParent = parent->parent(); - QString gpName = grandParent->property("ID") + "-" + grandParent->property("series_description"); - for (int i = 0; i < list.count(); i++) - { - ctkXnatFile* child = dynamic_cast(list.at(i)); - MITK_INFO << "Download started ..."; - MITK_INFO << "..."; - - if (child == NULL) - { - MITK_INFO << "Download failed! Not a file."; - continue; - } + QString filePath = m_DownloadPath + parent->property("label") + ".zip"; + parent->download(filePath); - QDir downDir(m_DownloadPath); - QString name = child->property("Name"); - QString newDownDir = m_DownloadPath + gpName + "/"; + std::ifstream in(filePath.toStdString().c_str(), std::ios::binary); + poco_assert(in); - if (downDir.mkpath(newDownDir)) - { - QString filePath = newDownDir + name; - child->download(filePath); - } - else - { - MITK_INFO << "Download failed! No subdirectory created."; - } + // decompress to XNAT_DOWNLOAD dir + Poco::Zip::Decompress dec(in, Poco::Path(m_DownloadPath.toStdString())); + dec.decompressAllFiles(); - // Testing if the file exists - if (downDir.exists(newDownDir + name)) - { - MITK_INFO << "Download of " << child->name().toStdString() << " was completed!"; - } - else - { - MITK_INFO << "Download of " << child->name().toStdString() << " failed!"; - } - } + in.close(); + QFile::remove(filePath); } else { MITK_INFO << "Download started ..."; MITK_INFO << "..."; QString name = file->property("Name"); QString filePath = m_DownloadPath + name; file->download(filePath); // Testing if the file exists QDir downDir(m_DownloadPath); if (downDir.exists(name)) { MITK_INFO << "Download of " << file->name().toStdString() << " was completed!"; } else { MITK_INFO << "Download of " << file->name().toStdString() << " failed!"; } } } else { MITK_INFO << "Selection was not a file!"; } } } int QmitkXnatEditor::ParentChecker(ctkXnatObject* child) { int sum; if (child->parent() == NULL) { return 0; } else { sum = 1 + ParentChecker(child->parent()); } return sum; } void QmitkXnatEditor::OnDataModelButtonClicked() { for (int i = m_ParentCount; i > 0; i--) { ToHigherLevel(); } } void QmitkXnatEditor::OnProjectButtonClicked() { for (int i = m_ParentCount - 1; i > 0; i--) { ToHigherLevel(); } } void QmitkXnatEditor::OnSubjectButtonClicked() { for (int i = m_ParentCount - 2; i > 0; i--) { ToHigherLevel(); } } void QmitkXnatEditor::OnExperimentButtonClicked() { for (int i = m_ParentCount - 3; i > 0; i--) { ToHigherLevel(); } } void QmitkXnatEditor::OnKindOfDataButtonClicked() { for (int i = m_ParentCount - 4; i > 0; i--) { ToHigherLevel(); } } void QmitkXnatEditor::OnSessionButtonClicked() { for (int i = m_ParentCount - 5; i > 0; i--) { ToHigherLevel(); } } void QmitkXnatEditor::OnResourceButtonClicked() { for (int i = m_ParentCount - 6; i > 0; i--) { ToHigherLevel(); } } void QmitkXnatEditor::UpdateSession(ctkXnatSession* session) { GetSite()->GetWorkbenchWindow()->GetSelectionService()->RemoveSelectionListener(m_SelectionListener.data()); if (session != 0 && session->isOpen()) { m_Controls.labelInfo->setText("Current Position:"); m_Controls.labelInfo->setStyleSheet("QLabel { color: black; }"); // Fill model and show in the GUI QmitkXnatObjectEditorInput::Pointer xoPtr(new QmitkXnatObjectEditorInput(session->dataModel())); berry::IEditorInput::Pointer editorInput(xoPtr); this->SetInput(editorInput); this->GetEditorInput().Cast()->GetXnatObject()->fetch(); UpdateList(); } else { m_Controls.labelInfo->setText("Please check the Preferences of the XNAT Connection.\nMaybe they are not ok."); m_Controls.labelInfo->setStyleSheet("QLabel { color: red; }"); } GetSite()->GetWorkbenchWindow()->GetSelectionService()->AddSelectionListener(m_SelectionListener.data()); } void QmitkXnatEditor::CleanListModel(ctkXnatSession* session) { if (session != 0) { m_Controls.treeView->setModel(0); m_ListModel->setRootObject(0); m_Controls.treeView->reset(); } } void QmitkXnatEditor::itemSelected(const QModelIndex &index) { ctkXnatObject* xnatObject = m_ListModel->data(index, Qt::UserRole).value(); bool downloadable = false; downloadable |= dynamic_cast(xnatObject) != NULL; downloadable |= dynamic_cast(xnatObject) != NULL; downloadable |= dynamic_cast(xnatObject) != NULL; downloadable |= dynamic_cast(xnatObject) != NULL; downloadable |= dynamic_cast(xnatObject) != NULL; downloadable |= dynamic_cast(xnatObject) != NULL; downloadable |= dynamic_cast(xnatObject) != NULL; downloadable |= dynamic_cast(xnatObject) != NULL; m_Controls.buttonDownload->setEnabled(downloadable); m_Controls.labelDownload->setVisible(!downloadable); }