Check in version of ffmpeg source code that is known to work, since t…

…he released version do not. Generalize loading of single volumes, not just movies. Rearranged mutex locking in certain AnnotationWidget methods, in hope of avoiding sporadic hanging observed by Tanya. Created stubs for manual loading of reference and neuron mask. Not working yet.
Vaa3D · Jun 7, 2012 · cff4fa1 · cff4fa1
1 parent 3846a30
commit cff4fa1
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Showing 11 changed files with 215 additions and 41 deletions.
diff --git a/v3d.config b/v3d.config
@@ -1,2 +1,2 @@
 // ADD PREDEFINED MACROS HERE!
-#define ENABLE_FFMPEG
+#define USE_FFMPEG
diff --git a/v3d_main/neuron_annotator/CMakeLists.txt b/v3d_main/neuron_annotator/CMakeLists.txt
@@ -98,9 +98,11 @@ if(USE_FFMPEG)
     )
     set(av_dir "${CMAKE_CURRENT_BINARY_DIR}/libavcodec")
     ExternalProject_Add(
-        LibAvcodec-0-11
+        LibAvcodec-0-10-2-head2012Apr25
         DEPENDS Yasm-1-2-0
-        URL http://ffmpeg.org/releases/ffmpeg-0.11.tar.gz
+        # URL http://ffmpeg.org/releases/ffmpeg-0.10.3.tar.gz
+        # Use the exact distribution I developed against
+        URL ${CMAKE_CURRENT_SOURCE_DIR}/utility/ffmpeg-HEAD-cab15f9.tar.gz
         SOURCE_DIR ${av_dir}/src
         BINARY_DIR ${av_dir}/build
         INSTALL_DIR ${av_dir}/install
@@ -113,20 +115,20 @@ if(USE_FFMPEG)
             --extra-cflags="-D__STDC_CONSTANT_MACROS"
     )
     set(AVCODEC_INCLUDE_DIR "${av_dir}/install/include")
-    set(AVDEVICE_LIBRARY ${av_dir}/install/lib/libavdevice.a)
-    set(AVFORMAT_LIBRARY ${av_dir}/install/lib/libavformat.a)
-    set(AVFILTER_LIBRARY ${av_dir}/install/lib/libavfilter.a)
-    set(AVCODEC_LIBRARY ${av_dir}/install/lib/libavcodec.a)
-    set(SWSCALE_LIBRARY ${av_dir}/install/lib/libswscale.a)
-    set(AVUTIL_LIBRARY ${av_dir}/install/lib/libavutil.a)
+    set(AVDEVICE_LIBRARY ${av_dir}/install/lib/libavdevice.a CACHE INTERNAL "path to a library")
+    set(AVFORMAT_LIBRARY ${av_dir}/install/lib/libavformat.a CACHE INTERNAL "path to a library")
+    set(AVFILTER_LIBRARY ${av_dir}/install/lib/libavfilter.a CACHE INTERNAL "path to a library")
+    set(AVCODEC_LIBRARY ${av_dir}/install/lib/libavcodec.a CACHE INTERNAL "path to a library")
+    set(SWSCALE_LIBRARY ${av_dir}/install/lib/libswscale.a CACHE INTERNAL "path to a library")
+    set(AVUTIL_LIBRARY ${av_dir}/install/lib/libavutil.a CACHE INTERNAL "path to a library")
 
     find_package(ZLIB)
 
     include_directories(${AVCODEC_INCLUDE_DIR})
     add_definitions(-DUSE_FFMPEG)
     add_definitions(-D__STDC_CONSTANT_MACROS)
 
-    add_dependencies(NeuronAnnotatorLib LibAvcodec-0-11)
+    add_dependencies(NeuronAnnotatorLib LibAvcodec-0-10-2-head2012Apr25)
     find_package(Threads)
     target_link_libraries(NeuronAnnotatorLib
         ${SWSCALE_LIBRARY}

diff --git a/v3d_main/neuron_annotator/data_model/MipFragmentColors.cpp b/v3d_main/neuron_annotator/data_model/MipFragmentColors.cpp
@@ -36,17 +36,22 @@ void MipFragmentColors::update()
     size_t data_size = 0;
     // qDebug() << "MipFragmentColors::update()" << __FILE__ << __LINE__;
     {
+        DataColorModel::Reader colorReader(dataColorModel); // readlock two of two
+        if (dataColorModel.readerIsStale(colorReader)) return;
+
         MipFragmentData::Reader mipReader(mipFragmentData); // readlock one of two
         if (! mipReader.hasReadLock()) return;
         if (mipReader.getNumberOfDataChannels() == 0) return; // what's the use?
-        DataColorModel::Reader colorReader(dataColorModel); // readlock two of two
-        if (dataColorModel.readerIsStale(colorReader)) return;
+        const Image4DProxy<My4DImage> mipProxy = mipReader.getMipProxy();
+        if (mipProxy.nbytes == 0)
+            return; // upstream data is invalid
+
         if (! (colorReader.getNumberOfDataChannels() == mipReader.getNumberOfDataChannels()) )
         {
             qDebug() << "Error: color model does not match data model";
             return;
         }
-        const Image4DProxy<My4DImage> mipProxy = mipReader.getMipProxy();
+
         const Image4DProxy<My4DImage> intensityProxy = mipReader.getIntensityProxy();
         int refIndex = intensityProxy.sz - 1; // relative to fragment indices
 

diff --git a/v3d_main/neuron_annotator/data_model/NaVolumeData.cpp b/v3d_main/neuron_annotator/data_model/NaVolumeData.cpp
@@ -250,6 +250,27 @@ void NaVolumeData::loadVolumeDataFromFiles()
     emit dataChanged();
 }
 
+/* slot */
+bool NaVolumeData::loadChannels(QString fileName) // includes loading general volumes
+{
+    bool bSucceeded = false;
+    int channel_count = 0;
+    emit progressMessageChanged("Loading single volume file"); // emit outside of lock block
+    {
+        Writer writer(*this);
+        channel_count = writer.loadChannels(fileName);
+        if (channel_count > 0)
+            bSucceeded = true;
+    } // release lock before emitting
+    if (bSucceeded) {
+        emit channelsLoaded(channel_count);
+        emit dataChanged();
+    }
+    else
+        emit progressAborted("Data stack load failed");
+    return bSucceeded;
+}
+
 /* slot */
 bool NaVolumeData::loadSingleImageMovieVolume(QString fileName)
 {
@@ -270,6 +291,59 @@ bool NaVolumeData::loadSingleImageMovieVolume(QString fileName)
     return bSucceeded;
 }
 
+/* slot */
+bool NaVolumeData::loadReference(QString fileName)
+{
+    bool bSucceeded = false;
+    emit progressMessageChanged("Loading reference channel"); // emit outside of lock block
+    {
+        Writer writer(*this);
+        if (writer.loadReference(fileName))
+            bSucceeded = true;
+    }
+
+    if (bSucceeded)
+        emit referenceLoaded();
+    else
+        emit progressAborted("Reference load failed");
+    return bSucceeded;
+}
+
+/* slot */
+bool NaVolumeData::loadOneChannel(QString fileName, int channel_index) // includes loading general volumes
+{
+    bool bSucceeded = false;
+    emit progressMessageChanged(QString("Loading data channel %1").arg(channel_index)); // emit outside of lock block
+    {
+        Writer writer(*this);
+        if (writer.loadOneChannel(fileName, channel_index))
+            bSucceeded = true;
+    }
+    if (bSucceeded)
+        emit channelLoaded(channel_index);
+    else
+        emit progressAborted("Channel load failed");
+    return bSucceeded;
+}
+
+/* slot */
+bool NaVolumeData::loadNeuronMask(QString fileName)
+{
+    bool bSucceeded = false;
+    emit progressMessageChanged("Loading neuron mask"); // emit outside of lock block
+    {
+        Writer writer(*this);
+        if (writer.loadNeuronMask(fileName))
+            bSucceeded = true;
+    }
+    if (bSucceeded)
+        emit neuronMaskLoaded();
+    else
+        emit progressAborted("Neuron mask load failed");
+    return bSucceeded;
+}
+
+
 //////////////////////////////////
 // NaVolumeData::Writer methods //
 //////////////////////////////////
@@ -323,9 +397,25 @@ bool NaVolumeData::Writer::loadSingleImageMovieVolume(QString fileName)
 #endif
 }
 
+int NaVolumeData::Writer::loadChannels(QString fileName) // includes loading general volumes
+{
+    qDebug() << "NaVolumeData::Writer::loadChannels()" << fileName;
+    My4DImage* img = new My4DImage();
+    ImageLoader loader;
+    if (! loader.loadImage(img, fileName) ) {
+        delete img;
+        return 0;
+    }
+    if (! setSingleImageVolume(img)) {
+        delete img;
+        return 0;
+    }
+    return img->getCDim();
+}
+
 bool NaVolumeData::Writer::setSingleImageVolume(My4DImage* img)
 {
-    qDebug() << "NaVolumeData::Writer::loadSingleImageMovieVolume";
+    qDebug() << "NaVolumeData::Writer::setSingleImageVolume";
     if (m_data->originalImageStack == img)
         return false; // no change
     if (NULL == img)
@@ -340,7 +430,8 @@ bool NaVolumeData::Writer::setSingleImageVolume(My4DImage* img)
         img->updateminmaxvalues();
     m_data->originalImageProxy = Image4DProxy<My4DImage>(m_data->originalImageStack);
     m_data->originalImageProxy.set_minmax(m_data->originalImageStack->p_vmin, m_data->originalImageStack->p_vmax);
-    // Populate histgrams
+    // TODO - for speed, deprecate or move histogram computation
+    // Populate histograms
     m_data->histograms.assign((size_t)(m_data->originalImageProxy.sc), IntensityHistogram());
     for(int c = 0; c < m_data->originalImageProxy.sc; ++c)
         m_data->histograms[c].populate(m_data->originalImageProxy, c);
@@ -475,6 +566,25 @@ bool NaVolumeData::Writer::loadStacks()
     return true;
 }
 
+bool NaVolumeData::Writer::loadReference(QString fileName)
+{
+    assert(false); // TODO
+    return false;
+}
+
+bool NaVolumeData::Writer::loadOneChannel(QString fileName, int channel_index) // includes loading general volumes
+{
+    assert(false); // TODO
+    return false;
+}
+
+bool NaVolumeData::Writer::loadNeuronMask(QString fileName)
+{
+    assert(false); // TODO
+    return false;
+}
+
+
 //////////////////////////////////
 // NaVolumeData::Reader methods //
 //////////////////////////////////

diff --git a/v3d_main/neuron_annotator/data_model/NaVolumeData.h b/v3d_main/neuron_annotator/data_model/NaVolumeData.h
@@ -51,12 +51,25 @@ class NaVolumeData : public NaLockableData
     explicit NaVolumeData();
     virtual ~NaVolumeData();
 
+signals:
+    void referenceLoaded();
+    void channelLoaded(int channel_index);
+    void channelsLoaded(int channel_count);
+    void neuronMaskLoaded();
+
 public slots:
+    bool loadChannels(QString fileName); // includes loading general volumes
+    bool loadSingleImageMovieVolume(QString fileName);
+
+protected slots:
     void loadVolumeDataFromFiles(); // Assumes file name paths have already been set
     void setProgressValue(int progressValue);
     void setProgressMessage(QString message) {emit progressMessageChanged(message);}
     void setStackLoadProgress(int progressValue, int stackIndex);
-    bool loadSingleImageMovieVolume(QString fileName);
+
+    bool loadReference(QString fileName);
+    bool loadOneChannel(QString fileName, int channel_index = 0);
+    bool loadNeuronMask(QString fileName);
 
 private:
     QString originalImageStackFilePath;
@@ -134,6 +147,11 @@ public slots:
         bool loadSingleImageMovieVolume(QString fileName);
         bool setSingleImageVolume(My4DImage* img);
 
+        bool loadReference(QString fileName);
+        bool loadOneChannel(QString fileName, int channel_index = 0);
+        int  loadChannels(QString fileName); // includes loading general volumes
+        bool loadNeuronMask(QString fileName);
+
     private:
         NaVolumeData * m_data;
     };

diff --git a/v3d_main/neuron_annotator/gui/AnnotationWidget.cpp b/v3d_main/neuron_annotator/gui/AnnotationWidget.cpp
@@ -679,26 +679,32 @@ void AnnotationWidget::selectEntity(const Entity *entity)
 
 void AnnotationWidget::selectEntity(const Entity *entity, const bool external)
 {
-    QMutexLocker locker(&mutex);
     qDebug() << "AnnotationWidget::selectEntity"<<(entity==0?"None":*entity->name)<<"external?"<<external;
 
-    if ((selectedEntity==entity) || (selectedEntity!=0 && entity!=0 && *selectedEntity->id==*entity->id)) return;
-    selectedEntity = entity;
-    ui->annotatedBranchTreeView->clearSelection();
-    if (entity!=0) ui->annotatedBranchTreeView->selectEntity(*entity->id);
+    {
+        QMutexLocker locker(&mutex);
+
+        if ((selectedEntity==entity) || (selectedEntity!=0 && entity!=0 && *selectedEntity->id==*entity->id)) return;
+        selectedEntity = entity;
+        ui->annotatedBranchTreeView->clearSelection();
+        if (entity!=0) ui->annotatedBranchTreeView->selectEntity(*entity->id);
+    } // release lock before emit
     emit entitySelected(selectedEntity);
 
-    if (!external)
     {
-        if (entity!=0)
+        QMutexLocker locker(&mutex);
+        if (!external)
         {
-            qDebug() << "AnnotationWidget::selectEntity (notifying console)"<<*entity->id;
-            selectEntityThread = new SelectEntityThread(*entity->id);
-            selectEntityThread->start(QThread::NormalPriority);
-        }
-        else
-        {
-            // TODO: deselectEntity event?
+            if (entity!=0)
+            {
+                qDebug() << "AnnotationWidget::selectEntity (notifying console)"<<*entity->id;
+                selectEntityThread = new SelectEntityThread(*entity->id);
+                selectEntityThread->start(QThread::NormalPriority);
+            }
+            else
+            {
+                // TODO: deselectEntity event?
+            }
         }
     }
 }
@@ -726,18 +732,20 @@ void AnnotationWidget::selectEntityById(const qint64 & entityId)
 
 void AnnotationWidget::selectEntityById(const qint64 & entityId, const bool external)
 {
-    QMutexLocker locker(&mutex);
     qDebug() << "AnnotationWidget::selectEntityById"<<entityId<<"external?"<<external;
+    {
+        QMutexLocker locker(&mutex);
 
-    if (annotatedBranch==0) return;
-    Entity *entity = annotatedBranch->getEntityById(entityId);
-    if (entity!=0) selectEntity(entity, external);
+        if (annotatedBranch==0) return;
+        Entity *entity = annotatedBranch->getEntityById(entityId);
+        if (entity!=0) selectEntity(entity, external);
+    }
 }
 
 void AnnotationWidget::selectNeuron(int index)
 {
-    QMutexLocker locker(&mutex);
     qDebug() << "AnnotationWidget::selectNeuron"<<index;
+    QMutexLocker locker(&mutex);
 
     if (!annotatedBranch) return;
 

diff --git a/v3d_main/neuron_annotator/gui/NaMainWindow.cpp b/v3d_main/neuron_annotator/gui/NaMainWindow.cpp
@@ -490,12 +490,17 @@ void NaMainWindow::on_actionOpen_Single_Movie_Stack_triggered()
 /* slot */
 bool NaMainWindow::loadSingleVolumeMovieFile(QString fileName)
 {
+    bool bSucceeded = false; // start pessimistic
     onDataLoadStarted();
     DataFlowModel* dfm = new DataFlowModel();
     setDataFlowModel(*dfm);
-    bool result = dataFlowModel->getVolumeData().loadSingleImageMovieVolume(fileName);
+
+    int num_channels = dataFlowModel->getVolumeData().loadChannels(fileName);
+    if (num_channels > 0)
+        bSucceeded = true;
+
     onDataLoadFinished();
-    return result;
+    return bSucceeded;
 }
 
 /* slot */