a LoadSpec needs to know if it is intended to use an image sequence

allen-cell-animated · Aug 4, 2024 · 5096e29 · 5096e29
1 parent 12aad22
commit 5096e29
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Showing 6 changed files with 24 additions and 6 deletions.
diff --git a/agave_app/TimelineDockWidget.cpp b/agave_app/TimelineDockWidget.cpp
@@ -83,7 +83,7 @@ QTimelineWidget::OnTimeChanged(int newTime)
     loadSpec.time = newTime;
 
     if (!m_reader) {
-      m_reader = std::shared_ptr<IFileReader>(FileReader::getReader(loadSpec.filepath));
+      m_reader = std::shared_ptr<IFileReader>(FileReader::getReader(loadSpec.filepath, loadSpec.isImageSequence));
       if (!m_reader) {
         LOG_ERROR << "Could not find a reader for file " << loadSpec.filepath;
         return;

diff --git a/agave_app/agaveGui.cpp b/agave_app/agaveGui.cpp
@@ -725,6 +725,7 @@ agaveGui::open(const std::string& file, const Serialize::ViewerState* vs, bool i
     LoadDialog* loadDialog = new LoadDialog(file, multiscaledims, sceneToLoad, this);
     if (loadDialog->exec() == QDialog::Accepted) {
       loadSpec = loadDialog->getLoadSpec();
+      loadSpec.isImageSequence = isImageSequence;
       dims = multiscaledims[loadDialog->getMultiscaleLevelIndex()].getVolumeDimensions();
       keepCurrentUISettings = loadDialog->getKeepSettings();
     } else {

diff --git a/renderlib/IFileReader.h b/renderlib/IFileReader.h
@@ -14,6 +14,7 @@ struct MultiscaleDims;
 struct LoadSpec
 {
   std::string filepath;
+  bool isImageSequence;
   // important for zarr multiscale
   // (TODO should store multiscale index instead?  ...and then find subpath from metadata)
   std::string subpath;
@@ -33,7 +34,8 @@ struct LoadSpec
     , miny(0)
     , maxy(0)
     , minz(0)
-    , maxz(0)
+    , maxz(0),
+      isImageSequence(false)
   {
   }
 

diff --git a/renderlib/command.cpp b/renderlib/command.cpp
@@ -476,7 +476,7 @@ LoadVolumeFromFileCommand::execute(ExecutionContext* c)
   struct STAT64_STRUCT buf;
   if (STAT64_FUNCTION(m_data.m_path.c_str(), &buf) == 0) {
     // TODO load metadata dims first
-
+    // TODO can we load time sequences of separate files here?
     std::unique_ptr<IFileReader> reader(FileReader::getReader(m_data.m_path));
     if (!reader) {
       LOG_ERROR << "Could not find a reader for file " << m_data.m_path;
@@ -563,7 +563,7 @@ SetTimeCommand::execute(ExecutionContext* c)
   std::shared_ptr<ImageXYZC> image;
   try {
 
-    std::unique_ptr<IFileReader> reader(FileReader::getReader(loadSpec.filepath));
+    std::unique_ptr<IFileReader> reader(FileReader::getReader(loadSpec.filepath, loadSpec.isImageSequence));
     if (!reader) {
       LOG_ERROR << "Could not find a reader for file " << loadSpec.filepath;
       image = nullptr;
@@ -663,6 +663,7 @@ LoadDataCommand::execute(ExecutionContext* c)
   c->m_loadSpec.minz = m_data.m_zmin;
   c->m_loadSpec.maxz = m_data.m_zmax;
 
+  // TODO can we load time sequences of separate files here?
   std::unique_ptr<IFileReader> reader(FileReader::getReader(m_data.m_path));
   if (!reader) {
     LOG_ERROR << "Could not find a reader for file " << m_data.m_path;

diff --git a/renderlib/io/FileReader.cpp b/renderlib/io/FileReader.cpp
@@ -201,6 +201,9 @@ LoadSpec::toString() const
   if (!subpath.empty()) {
     stream << " " << subpath;
   }
+  if (isImageSequence) {
+	stream << " (sequence)";
+  }
   stream << " : scene " << scene << " time " << time;
   stream << " : channels [";
   for (auto i : channels) {

diff --git a/renderlib/io/FileReaderImageSequence.cpp b/renderlib/io/FileReaderImageSequence.cpp
@@ -28,27 +28,38 @@ FileReaderImageSequence::FileReaderImageSequence(const std::string& filepath)
 {
   m_sequence = initializeSequence(filepath);
 }
+
 FileReaderImageSequence::~FileReaderImageSequence() {}
 
 std::shared_ptr<ImageXYZC>
 FileReaderImageSequence::loadFromFile(const LoadSpec& loadSpec)
 {
   LoadSpec sequenceSpec = loadSpec;
   sequenceSpec.filepath = m_sequence[loadSpec.time];
+  sequenceSpec.time = 0;
   return m_tiffReader->loadFromFile(sequenceSpec);
 }
+
 VolumeDimensions
 FileReaderImageSequence::loadDimensions(const std::string& filepath, uint32_t scene)
 {
-  return m_tiffReader->loadDimensions(filepath, scene);
+    VolumeDimensions vd = m_tiffReader->loadDimensions(filepath, scene);
+    vd.sizeT = m_sequence.size();
+    return vd;
 }
+
 uint32_t
 FileReaderImageSequence::loadNumScenes(const std::string& filepath)
 {
   return m_tiffReader->loadNumScenes(filepath);
 }
+
 std::vector<MultiscaleDims>
 FileReaderImageSequence::loadMultiscaleDims(const std::string& filepath, uint32_t scene)
 {
-  return m_tiffReader->loadMultiscaleDims(filepath, scene);
+    std::vector<MultiscaleDims> dims = m_tiffReader->loadMultiscaleDims(filepath, scene);
+    for (auto& d : dims) {
+      d.shape[0] = m_sequence.size();
+	}
+	return dims;
 }