Implemented reading of whole directory structure and post-processing of tissue...

Implemented reading of whole directory structure and post-processing of tissue classification into a single multi-channel image into IvusTcDemo pipeline.

modules/ivus_tc/pipelines/ivustcdemo.cpp

@@ -24,8 +24,9 @@
 
 #include "ivustcdemo.h"
 
-#include "tgt/event/keyevent.h"
+#include "tgt/filesystem.h"
 #include "core/datastructures/imagedata.h"
+#include "core/datastructures/genericimagerepresentationlocal.h"
 
 #include "core/classification/geometry1dtransferfunction.h"
 #include "core/classification/tfgeometry1d.h"
@@ -34,14 +35,21 @@ namespace campvis {
 
     IvusTcDemo::IvusTcDemo(DataContainer* dc)
         : AutoEvaluationPipeline(dc)
+        , p_sourceDirectory("SoruceDirectory", "Source Directory", "D:/Medical Data/IVUS/H52 LAD1", StringProperty::DIRECTORY)
+        , p_readImagesButton("ReadImagesButton", "Read Images")
         , _lsp()
         , _imageReader(&_canvasSize)
         , _ve(&_canvasSize)
     {
+        // Use AbstractPipeline overload to avoid automatic evaluation of _imageReader processor
+//        AbstractPipeline::addProcessor(&_imageReader);
+
         addProcessor(&_lsp);
-        addProcessor(&_imageReader);
         addProcessor(&_ve);
 
+        addProperty(p_sourceDirectory);
+        addProperty(p_readImagesButton);
+
         addEventListenerToBack(&_ve);
     }
 
@@ -50,6 +58,8 @@ namespace campvis {
 
     void IvusTcDemo::init() {
         AutoEvaluationPipeline::init();
+        _imageReader.init();
+        p_readImagesButton.s_clicked.connect(this, &IvusTcDemo::readAndProcessImages);
         
         _ve.p_outputImage.setValue("combine");
         _renderTargetID.setValue("combine");
@@ -69,8 +79,68 @@ namespace campvis {
     }
 
     void IvusTcDemo::deinit() {
+        _imageReader.deinit();
+        p_readImagesButton.s_clicked.disconnect(this);
         AutoEvaluationPipeline::deinit();
     }
 
+    void IvusTcDemo::readAndProcessImages() {
+        std::string baseDir = tgt::FileSystem::cleanupPath(p_sourceDirectory.getValue());
+
+        std::string ivusDir = baseDir + "/IVUS";
+        std::string cmDir = baseDir + "/Confidence_Map";
+        std::string calcifiedDir = baseDir + "/Calcified_Map";
+        std::string fibroticDir = baseDir + "/Fibrotic_Map";
+        std::string lipidicDir = baseDir + "/Lipidic_Map";
+        std::string necroticDir = baseDir + "/Necrotic_Map";
+        std::string plaqueDir = baseDir + "/Plaque_Mask";
+
+        // read images
+        readImage(ivusDir, "image.ivus");
+        readImage(cmDir, "image.cm");
+
+        readImage(calcifiedDir, "image.calcified");
+        readImage(fibroticDir , "image.fibrotic" );
+        readImage(lipidicDir  , "image.lipidic"  );
+        readImage(necroticDir , "image.necrotic" );
+
+        readImage(plaqueDir, "image.plaque");
+
+        // fuse TC maps into single 4-channel image
+        typedef uint8_t ivus_t;
+        GenericImageRepresentationLocal<ivus_t, 1>::ScopedRepresentation calcifiedRep(getDataContainer(), "image.calcified");
+        GenericImageRepresentationLocal<ivus_t, 1>::ScopedRepresentation fibroticRep(getDataContainer(), "image.fibrotic");
+        GenericImageRepresentationLocal<ivus_t, 1>::ScopedRepresentation lipidicRep(getDataContainer(), "image.lipidic");
+        GenericImageRepresentationLocal<ivus_t, 1>::ScopedRepresentation necroticRep(getDataContainer(), "image.necrotic");
+
+        if (   (calcifiedRep && fibroticRep && lipidicRep && necroticRep) 
+            && (calcifiedRep->getSize() == fibroticRep->getSize() && fibroticRep->getSize() == lipidicRep->getSize() && lipidicRep->getSize() == necroticRep->getSize())) {
+            ImageData* id = new ImageData(3, calcifiedRep->getSize(), 4);
+            tgt::Vector4<ivus_t>* data = new tgt::Vector4<ivus_t>[tgt::hmul(calcifiedRep->getSize())];
+
+            for (size_t i = 0; i < calcifiedRep->getNumElements(); ++i) {
+                data[i] = tgt::Vector4<ivus_t>(calcifiedRep->getElement(i), fibroticRep->getElement(i), lipidicRep->getElement(i), necroticRep->getElement(i));
+            }
+
+            GenericImageRepresentationLocal<ivus_t, 4>::create(id, data);
+            id->setMappingInformation(calcifiedRep->getParent()->getMappingInformation());
+            getDataContainer().addData("image.tc", id);
+        }
+        else {
+            LERROR("Could not create fused TC image.");
+        }
+
+        getDataContainer().removeData("image.calcified");
+        getDataContainer().removeData("image.fibrotic" );
+        getDataContainer().removeData("image.lipidic"  );
+        getDataContainer().removeData("image.necrotic" );
+    }
+
+    void IvusTcDemo::readImage(const std::string& baseDir, const std::string& id) {
+        _imageReader.p_inputDirectory.setValue(baseDir);
+        _imageReader.p_outputImage.setValue(id);
+        _imageReader.process(getDataContainer());
+    }
+
 
 }
\ No newline at end of file

modules/ivus_tc/pipelines/ivustcdemo.h

@@ -27,7 +27,7 @@
 
 
 #include "core/pipeline/autoevaluationpipeline.h"
-#include "core/properties/cameraproperty.h"
+#include "core/properties/allproperties.h"
 #include "modules/base/processors/lightsourceprovider.h"
 #include "modules/io/processors/mhdimagereader.h"
 #include "modules/io/processors/genericimagereader.h"
@@ -59,6 +59,14 @@ namespace campvis {
         static const std::string getId() { return "IvusTcDemo"; };
 
     protected:
+        /// reads and processes all images from the given directory
+        void readAndProcessImages();
+
+        void readImage(const std::string& baseDir, const std::string& id);
+
+        StringProperty p_sourceDirectory;
+        ButtonProperty p_readImagesButton;
+
         LightSourceProvider _lsp;
         IvusBatchReader _imageReader;
         VolumeExplorer _ve;