From c23ceeca945c8493c4fbfaf4cca830a560b13fe6 Mon Sep 17 00:00:00 2001
From: David Borland <borland@renci.org>
Date: Mon, 6 Jan 2020 11:13:24 -0500
Subject: [PATCH] Support loading of multi-page TIFF volume files

---
 MainWindow.cxx             |  4 ++--
 VisualizationContainer.cxx | 45 +++++++++++++++++++++++++++++++-------
 2 files changed, 39 insertions(+), 10 deletions(-)

diff --git a/MainWindow.cxx b/MainWindow.cxx
index e808170..6c4e257 100644
--- a/MainWindow.cxx
+++ b/MainWindow.cxx
@@ -81,7 +81,7 @@ void MainWindow::on_actionOpen_Image_File_triggered() {
 	QString fileName = QFileDialog::getOpenFileName(this,
 		"Open Volume",
 		GetDefaultDirectory(defaultImageDirectoryKey),
-		"All files (*.*);;NIfTI (*.nii);;VTK XML ImageData (*.vti)");
+		"All files (*.*);;NIfTI (*.nii);;TIFF (*.tif *.tiff);;VTK XML ImageData (*.vti)");
 
 	// Check for file name
 	if (fileName == "") {
@@ -173,7 +173,7 @@ void MainWindow::on_actionOpen_Segmentation_File_triggered() {
 	QString fileName = QFileDialog::getOpenFileName(this,
 		"Open Segmentation Data",
 		GetDefaultDirectory(defaultSegmentationDirectoryKey),
-		"All files (*.*);;NIfTI (*.nii);;VTK XML ImageData (*.vti)");
+		"All files (*.*);;NIfTI (*.nii);;TIFF (*.tif *.tiff);;VTK XML ImageData (*.vti)");
 
 	// Check for file name
 	if (fileName == "") {
diff --git a/VisualizationContainer.cxx b/VisualizationContainer.cxx
index 4bf5700..bf41f77 100644
--- a/VisualizationContainer.cxx
+++ b/VisualizationContainer.cxx
@@ -132,8 +132,8 @@ VisualizationContainer::FileErrorCode VisualizationContainer::OpenImageFile(cons
 	std::string extension = fileName.substr(fileName.find_last_of(".") + 1);
 
 	// Load the data
-	if (extension == "vti") {
-		vtkSmartPointer<vtkXMLImageDataReader> reader = vtkSmartPointer<vtkXMLImageDataReader>::New();
+	if (extension == "nii") {
+		vtkSmartPointer<vtkNIFTIImageReader> reader = vtkSmartPointer<vtkNIFTIImageReader>::New();
 		reader->SetFileName(fileName.c_str());
 		reader->Update();
 
@@ -141,8 +141,17 @@ VisualizationContainer::FileErrorCode VisualizationContainer::OpenImageFile(cons
 
 		return Success;
 	}
-	else if (extension == "nii") {
-		vtkSmartPointer<vtkNIFTIImageReader> reader = vtkSmartPointer<vtkNIFTIImageReader>::New();
+	else if (extension == "tif" || extension == "tiff") {
+		vtkSmartPointer<vtkTIFFReader> reader = vtkSmartPointer<vtkTIFFReader>::New();
+		reader->SetFileName(fileName.c_str());
+		reader->Update();
+
+		SetImageData(reader->GetOutput());
+
+		return Success;
+	}
+	else if (extension == "vti") {
+		vtkSmartPointer<vtkXMLImageDataReader> reader = vtkSmartPointer<vtkXMLImageDataReader>::New();
 		reader->SetFileName(fileName.c_str());
 		reader->Update();
 
@@ -187,8 +196,8 @@ VisualizationContainer::FileErrorCode VisualizationContainer::OpenSegmentationFi
 	std::string extension = fileName.substr(fileName.find_last_of(".") + 1);
 
 	// Load the data
-	if (extension == "vti") {
-		vtkSmartPointer<vtkXMLImageDataReader> reader = vtkSmartPointer<vtkXMLImageDataReader>::New();
+	if (extension == "nii") {
+		vtkSmartPointer<vtkNIFTIImageReader> reader = vtkSmartPointer<vtkNIFTIImageReader>::New();
 		reader->SetFileName(fileName.c_str());
 
 		vtkSmartPointer<vtkImageCast> cast = vtkSmartPointer<vtkImageCast>::New();
@@ -207,8 +216,28 @@ VisualizationContainer::FileErrorCode VisualizationContainer::OpenSegmentationFi
 			return VolumeMismatch;
 		}
 	}
-	else if (extension == "nii") {
-		vtkSmartPointer<vtkNIFTIImageReader> reader = vtkSmartPointer<vtkNIFTIImageReader>::New();
+	else if (extension == "tif" || extension == "tiff") {
+		vtkSmartPointer<vtkTIFFReader> reader = vtkSmartPointer<vtkTIFFReader>::New();
+		reader->SetFileName(fileName.c_str());
+
+		vtkSmartPointer<vtkImageCast> cast = vtkSmartPointer<vtkImageCast>::New();
+		cast->SetOutputScalarTypeToUnsignedShort();
+		cast->SetInputConnection(reader->GetOutputPort());
+		cast->Update();
+
+		if (SetLabelData(cast->GetOutput())) {
+			LoadRegionMetadata(fileName + ".json");
+
+			qtWindow->updateRegions(regions);
+
+			return Success;
+		}
+		else {
+			return VolumeMismatch;
+		}
+	}
+	else if (extension == "vti") {
+		vtkSmartPointer<vtkXMLImageDataReader> reader = vtkSmartPointer<vtkXMLImageDataReader>::New();
 		reader->SetFileName(fileName.c_str());
 
 		vtkSmartPointer<vtkImageCast> cast = vtkSmartPointer<vtkImageCast>::New();