Implemented support for using TissueSegmentation on Image #199

smistad · Dec 12, 2023 · ca375a6 · ca375a6
1 parent cf3c2db
commit ca375a6
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Showing 3 changed files with 44 additions and 15 deletions.
diff --git a/source/FAST/Algorithms/TissueSegmentation/Tests.cpp b/source/FAST/Algorithms/TissueSegmentation/Tests.cpp
@@ -11,21 +11,42 @@
 using namespace fast;
 
 TEST_CASE("Tissue segmentation", "[fast][wsi][TissueSegmentation][visual]") {
-    auto importer = WholeSlideImageImporter::New();
-    importer->setFilename(Config::getTestDataPath() + "/WSI/CMU-1.svs");
+    auto importer = WholeSlideImageImporter::create(Config::getTestDataPath() + "/WSI/CMU-1.svs");
 
-    auto segmentation = TissueSegmentation::New();
-    segmentation->setInputConnection(importer->getOutputPort());
+    auto segmentation = TissueSegmentation::create()
+            ->connect(importer);
 
-    auto renderer = ImagePyramidRenderer::New();
-    renderer->addInputConnection(importer->getOutputPort());
+    auto renderer = ImagePyramidRenderer::create()
+            ->connect(importer);
 
-    auto segRenderer = SegmentationRenderer::New();
-    segRenderer->addInputConnection(segmentation->getOutputPort());
+    auto segRenderer = SegmentationRenderer::create()
+            ->connect(segmentation);
     segRenderer->setOpacity(0.5);
 
-    auto window = SimpleWindow::New();
-    window->set2DMode();
+    auto window = SimpleWindow2D::create();
+    window->addRenderer(renderer);
+    window->addRenderer(segRenderer);
+    window->setTimeout(2000);
+    window->start();
+}
+
+TEST_CASE("Tissue segmentation on image", "[fast][wsi][TissueSegmentation][visual]") {
+    auto importer = WholeSlideImageImporter::create(Config::getTestDataPath() + "/WSI/CMU-1.svs");
+
+    auto access = importer->runAndGetOutputData<ImagePyramid>()->getAccess(ACCESS_READ);
+    auto image = access->getLevelAsImage(2);
+
+    auto segmentation = TissueSegmentation::create()
+            ->connect(image);
+
+    auto renderer = ImagePyramidRenderer::create()
+            ->connect(importer);
+
+    auto segRenderer = SegmentationRenderer::create()
+            ->connect(segmentation);
+    segRenderer->setOpacity(0.5);
+
+    auto window = SimpleWindow2D::create();
     window->addRenderer(renderer);
     window->addRenderer(segRenderer);
     window->setTimeout(2000);

diff --git a/source/FAST/Algorithms/TissueSegmentation/TissueSegmentation.cpp b/source/FAST/Algorithms/TissueSegmentation/TissueSegmentation.cpp
@@ -62,9 +62,17 @@ bool TissueSegmentation::getFilterZeros() const {
 }
 
 void TissueSegmentation::execute() {
-    auto wsi = getInputData<ImagePyramid>();
-    auto access = wsi->getAccess(ACCESS_READ);
-    auto input = access->getLevelAsImage(wsi->getNrOfLevels()-1);
+    auto image = getInputData<SpatialDataObject>();
+
+    Image::pointer input;
+    if(auto wsi = std::dynamic_pointer_cast<ImagePyramid>(image)) {
+        auto access = wsi->getAccess(ACCESS_READ);
+        input = access->getLevelAsImage(wsi->getNrOfLevels()-1);
+    } else if(auto patch = std::dynamic_pointer_cast<Image>(image)) {
+        input = patch;
+    } else {
+        throw Exception("TissueSegmentation requires an Image or ImagePyramid data object.");
+    }
 
     auto output = Image::createSegmentationFromImage(input);
 

diff --git a/source/FAST/Algorithms/TissueSegmentation/TissueSegmentation.hpp b/source/FAST/Algorithms/TissueSegmentation/TissueSegmentation.hpp
@@ -8,12 +8,12 @@ namespace fast {
  * @brief Segment tissue from a WSI
  *
  * Uses the GPU to perform a simple threshold-based tissue/glass segmentation of a WSI.
- * Since glass is almost white, the thresold is the distance from the pixels color
+ * Since glass is almost white, the threshold is the distance from the pixels color
  * to white (255,255,255).
  * A morphological closing (dilation+erosion) is performed after thresholding.
  *
  * Inputs:
- * - 0: ImagePyramid WSI
+ * - 0: ImagePyramid WSI or Image patch
  *
  * Outputs:
  * - 0: Segmentation tissue mask