ENH: adds hook for loading directory archetypes

When a directory is added via the Add Data dialog,
it may contain a collection of files that should be
treated as a single MRML data type, such as a series
of image files that get loaded as a volume.

This change allows a qSlicerFileReader subclass to define
a method that can examine the contents of a directory and
filter out any files that should be loaded as a group.  One
of these files then serves as the archetype and the io properties
can be configured such that the files are loaded correctly.

The qSlicerVolumesReader and related classes have been updated
to use the hooks for reading multiple image files as a volume
by default.

Author: pieper

Base/QTCore/qSlicerCoreIOManager.cxx

@@ -781,3 +781,19 @@ void qSlicerCoreIOManager::setDefaultSceneFileType(QString fileType)
   Q_D(qSlicerCoreIOManager);
   d->DefaultSceneFileType = fileType;
 }
+
+//-----------------------------------------------------------------------------
+bool qSlicerCoreIOManager::examineFileInfoList(QFileInfoList &fileInfoList, QFileInfo &archetypeFileInfo, QString &readerDescription, qSlicerIO::IOProperties &ioProperties)const
+{
+  Q_D(const qSlicerCoreIOManager);
+  QList<qSlicerFileReader*> res;
+  foreach(qSlicerFileReader* reader, d->Readers)
+    {
+    if (reader->examineFileInfoList(fileInfoList, archetypeFileInfo, ioProperties))
+      {
+      readerDescription = reader->description();
+      return (true);
+      }
+    }
+  return (false);
+}

Base/QTCore/qSlicerCoreIOManager.h

@@ -22,8 +22,9 @@
 #define __qSlicerCoreIOManager_h
 
 // Qt includes
-#include <QList>
+#include <QFileInfo>
 #include <QImage>
+#include <QList>
 #include <QMap>
 #include <QObject>
 #include <QVariantMap>
@@ -170,6 +171,21 @@ class Q_SLICER_BASE_QTCORE_EXPORT qSlicerCoreIOManager:public QObject
   /// Defines the file format that should be offered by default when the scene is saved.
   Q_INVOKABLE QString defaultSceneFileType()const;
 
+  /// Iterates through readers looking at the fileInfoList to see if there is an entry that can serve as
+  /// an archetype for loading multiple fileInfos.  If so, the reader removes the recognized
+  /// fileInfos from the list and sets the ioProperties so that the corresponding
+  /// loader will read these files. The archetypeEntry will contain the fileInfo
+  /// for the archetype and the method returns true.  If no pattern is recognized
+  /// the method returns false.
+  /// The specific motivating use case is when the file
+  /// list contains a set of related files, such as a list of image files that
+  /// are recognized as a volume. But other cases could also make sense, such as when
+  /// a file format has a set or related files such as textures or material files
+  /// for a surface model.
+  /// \sa qSlicerDataDialog
+  /// \sa qSlicerFileReader
+  Q_INVOKABLE bool examineFileInfoList(QFileInfoList &fileInfoList, QFileInfo &archetypeEntry, QString &readerDescription, qSlicerIO::IOProperties &ioProperties)const;
+
 public slots:
 
   /// Defines the file format that should be offered by default when the scene is saved.

Base/QTCore/qSlicerFileReader.cxx

@@ -119,3 +119,9 @@ QStringList qSlicerFileReader::loadedNodes()const
   Q_D(const qSlicerFileReader);
   return d->LoadedNodes;
 }
+
+//----------------------------------------------------------------------------
+bool qSlicerFileReader::examineFileInfoList(QFileInfoList &fileInfoList, QFileInfo &archetypeFileInfo, qSlicerIO::IOProperties &ioProperties)const
+{
+  return(false);
+}

Base/QTCore/qSlicerFileReader.h

@@ -21,6 +21,9 @@
 #ifndef __qSlicerFileReader_h
 #define __qSlicerFileReader_h
 
+// Qt includes
+#include <QFileInfo>
+
 // QtCore includes
 #include "qSlicerIO.h"
 #include "qSlicerBaseQTCoreExport.h"
@@ -64,6 +67,11 @@ class Q_SLICER_BASE_QTCORE_EXPORT qSlicerFileReader
   /// \sa setLoadedNodes(), load()
   QStringList loadedNodes()const;
 
+  /// Implements the file list examination for the corresponding method in the core
+  /// IO manager.
+  /// \sa qSlicerCoreIOManager
+  virtual bool examineFileInfoList(QFileInfoList &fileInfoList, QFileInfo &archetypeFileInfo, qSlicerIO::IOProperties &ioProperties)const;
+
 protected:
   /// Must be called in load() on success with the list of nodes added into the
   /// scene.

Base/QTGUI/qSlicerDataDialog.cxx

@@ -163,7 +163,43 @@ void qSlicerDataDialogPrivate::addDirectory(const QDir& directory)
   bool recursive = true;
   QDir::Filters filters =
     QDir::AllDirs | QDir::Files | QDir::Readable | QDir::NoDotAndDotDot;
-  foreach(QFileInfo entry, directory.entryInfoList(filters))
+  QFileInfoList fileInfoList = directory.entryInfoList(filters);
+
+  //
+  // check to see if any readers recognize the directory contents
+  // and provide an archetype.
+  //
+  qSlicerCoreIOManager* coreIOManager =
+    qSlicerCoreApplication::application()->coreIOManager();
+  QString readerDescription;
+  qSlicerIO::IOProperties ioProperties;
+  QFileInfo archetypeEntry;
+  if (coreIOManager->examineFileInfoList(fileInfoList, archetypeEntry, readerDescription, ioProperties))
+    {
+    this->addFile(archetypeEntry);
+    QString filePath = archetypeEntry.absoluteFilePath();
+    QList<QTableWidgetItem *> items = this->FileWidget->findItems(filePath, Qt::MatchExactly);
+    if (items.isEmpty())
+      {
+      qWarning() << "Couldn't add archetype widget for file: " << filePath;
+      }
+    else
+      {
+      QTableWidgetItem *item = items[0];
+      QWidget *cellWidget = this->FileWidget->cellWidget(item->row(), TypeColumn);
+      QComboBox *descriptionComboBox = dynamic_cast<QComboBox *>(cellWidget);
+      descriptionComboBox->setCurrentIndex(descriptionComboBox->findText(readerDescription));
+      cellWidget = this->FileWidget->cellWidget(item->row(), OptionsColumn);
+      qSlicerIOOptionsWidget *ioOptionsWidget = dynamic_cast<qSlicerIOOptionsWidget *> (cellWidget);
+      ioOptionsWidget->updateGUI(ioProperties);
+      }
+    }
+
+  //
+  // now add any files and directories that weren't filtered
+  // out by the ioManager
+  //
+  foreach(QFileInfo entry, fileInfoList)
     {
     if (entry.isFile())
       {

Modules/Loadable/Volumes/qSlicerVolumesIOOptionsWidget.cxx

@@ -223,3 +223,14 @@ void qSlicerVolumesIOOptionsWidget::updateColorSelector()
       }
     }
 }
+
+//------------------------------------------------------------------------------
+void qSlicerVolumesIOOptionsWidget::updateGUI(const qSlicerIO::IOProperties& ioProperties)
+{
+  Q_D(qSlicerVolumesIOOptionsWidget);
+  qSlicerIOOptionsWidget::updateGUI(ioProperties);
+  if (ioProperties.contains("singleFile"))
+    {
+    d->SingleFileCheckBox->setChecked(ioProperties["singleFile"].toBool());
+    }
+}

Modules/Loadable/Volumes/qSlicerVolumesIOOptionsWidget.h

@@ -41,6 +41,11 @@ class Q_SLICER_QTMODULES_VOLUMES_EXPORT qSlicerVolumesIOOptionsWidget :
   qSlicerVolumesIOOptionsWidget(QWidget *parent=0);
   virtual ~qSlicerVolumesIOOptionsWidget();
 
+  /// Allows custom handling of image sets as volumes
+  /// \sa qSlicerVolumesReader
+  /// \sa qSlicerDataDialog::addDirectory
+  void updateGUI(const qSlicerIO::IOProperties& ioProperties);
+
 public slots:
   virtual void setFileName(const QString& fileName);
   virtual void setFileNames(const QStringList& fileNames);

Modules/Loadable/Volumes/qSlicerVolumesReader.cxx

@@ -18,7 +18,12 @@
 
 ==============================================================================*/
 
+// std includes
+#include <vector>
+#include <algorithm>
+
 // Qt includes
+#include <QDebug>
 #include <QFileInfo>
 
 // SlicerQt includes
@@ -39,6 +44,9 @@
 #include <vtkSmartPointer.h>
 #include <vtkStringArray.h>
 
+// ITK includes
+#include <itkArchetypeSeriesFileNames.h>
+
 //-----------------------------------------------------------------------------
 class qSlicerVolumesReaderPrivate
 {
@@ -205,3 +213,40 @@ bool qSlicerVolumesReader::load(const IOProperties& properties)
     }
   return node != 0;
 }
+
+//-----------------------------------------------------------------------------
+bool qSlicerVolumesReader::examineFileInfoList(QFileInfoList &fileInfoList, QFileInfo &archetypeFileInfo, qSlicerIO::IOProperties &ioProperties)const
+{
+
+  //
+  // Check each file to see if it's recognzied as part of a series.  If so,
+  // keep it as the archetype and remove all the others from the list
+  //
+  foreach(QFileInfo fileInfo, fileInfoList)
+    {
+    itk::ArchetypeSeriesFileNames::Pointer seriesNames = itk::ArchetypeSeriesFileNames::New();
+    std::vector<std::string> candidateFiles;
+    seriesNames->SetArchetype(fileInfo.absoluteFilePath().toStdString());
+    candidateFiles = seriesNames->GetFileNames();
+    if (candidateFiles.size() > 1)
+      {
+      archetypeFileInfo = fileInfo;
+      QMutableListIterator<QFileInfo> fileInfoIterator(fileInfoList);
+      while (fileInfoIterator.hasNext())
+        {
+        const QString &path = fileInfoIterator.next().absoluteFilePath();
+        if (path == archetypeFileInfo.absoluteFilePath())
+          {
+          continue;
+          }
+        if (std::find(candidateFiles.begin(), candidateFiles.end(), path.toStdString()) != candidateFiles.end())
+          {
+          fileInfoIterator.remove();
+          }
+        }
+      ioProperties["singleFile"] = false;
+      return true;
+      }
+    }
+  return false;
+}

Modules/Loadable/Volumes/qSlicerVolumesReader.h

@@ -47,6 +47,12 @@ class qSlicerVolumesReader
   virtual qSlicerIOOptions* options()const;
 
   virtual bool load(const IOProperties& properties);
+
+  /// Implements the file list examination for the corresponding method in the core
+  /// IO manager.
+  /// \sa qSlicerCoreIOManager
+  virtual bool examineFileInfoList(QFileInfoList &fileInfoList, QFileInfo &archetypeFileInfo, qSlicerIO::IOProperties &ioProperties)const;
+
 protected:
   QScopedPointer<qSlicerVolumesReaderPrivate> d_ptr;