Fixed issue with PatchGenerator blocking when no patches are generated. It now throws an exception instead.

Author: smistad

source/FAST/Algorithms/ImagePatch/PatchGenerator.cpp

@@ -307,14 +307,23 @@ void PatchGenerator::generateStream() {
             throw Exception("Unsupported data object given to PatchGenerator");
         }
         // Add final patch, and mark it has last frame
-        previousPatch->setLastFrame(getNameOfClass());
-		previousPatch->setFrameData("streaming", "yes"); // Since we are not propagating frame data, we have to set this
-        try {
-            addOutputData(0, previousPatch, false, false);
-        } catch(ThreadStopped &e) {
+        if(!previousPatch) {
+            // No patches have been created
+            reportInfo() << "No patches were generated." << reportEnd();
+            frameAdded(); // Unlock blocking execute()
+            for(const auto& channel : mOutputConnections[0]) {
+                channel.lock()->stop("No patches were created by the PatchGenerator");
+            }
+        } else {
+            previousPatch->setLastFrame(getNameOfClass());
+            previousPatch->setFrameData("streaming", "yes"); // Since we are not propagating frame data, we have to set this
+            try {
+                addOutputData(0, previousPatch, false, false);
+            } catch(ThreadStopped &e) {
 
+            }
+            reportInfo() << "Done generating patches" << reportEnd();
         }
-        reportInfo() << "Done generating patches" << reportEnd();
     } catch(std::exception &e) {
         // Exception happened in thread. Stop pipeline, and propagate error message.
         for(auto item : mOutputConnections) {

source/FAST/Algorithms/ImagePatch/Tests.cpp

@@ -59,6 +59,29 @@ TEST_CASE("Patch generator on 2D image", "[fast][PatchGenerator]") {
     REQUIRE(nrOfPatches == counter);
 }
 
+
+TEST_CASE("Patch generator with no patches", "[fast][PatchGenerator]") {
+    auto importer = WholeSlideImageImporter::create(Config::getTestDataPath() + "/WSI/CMU-1.svs");
+    auto wsi = importer->runAndGetOutputData<ImagePyramid>();
+
+    auto segmentation = TissueSegmentation::create(true)->connect(wsi)->runAndGetOutputData<Image>();
+    segmentation->fill(0); // Empty segmentation will mean no patches
+    const int width = 256;
+    const int height = 256;
+    auto generator = PatchGenerator::create(width, height, 1, 2)
+            ->connect(importer)
+            ->connect(1, segmentation);
+    auto stream = DataStream(generator);
+    int counter = 0;
+    CHECK_THROWS(
+    while(!stream.isDone()) {
+        auto image = stream.getNextFrame<Image>();
+        ++counter;
+    }
+    );
+    REQUIRE(counter == 0);
+}
+
 TEST_CASE("Patch generator on 3D image", "[fast][PatchGenerator]") {
     auto importer = ImageFileImporter::create(Config::getTestDataPath() + "/CT/CT-Thorax.mhd");
     auto image = importer->runAndGetOutputData<Image>();

source/FAST/Exception.hpp

@@ -1,5 +1,4 @@
-#ifndef EXCEPTIONS_HPP_
-#define EXCEPTIONS_HPP_
+#pragma once
 
 #include "FASTExport.hpp"
 #include <exception>
@@ -129,7 +128,4 @@ class FAST_EXPORT ThreadStopped : public Exception {
         bool m_error = false; // Whether thread was stopped due to an error or not.
 };
 
-} // end namespace fast
-
-
-#endif /* EXCEPTIONS_HPP_ */
+} // end namespace fast

source/FAST/Python/Tests/test_data_stream_object.py

@@ -2,6 +2,21 @@
 import numpy as np
 import pytest
 
+
+def test_data_stream_empty():
+    importer = fast.WholeSlideImageImporter.create(fast.Config.getTestDataPath() + '/WSI/CMU-1.svs')
+
+    segmentation = fast.TissueSegmentation.create(False).connect(importer).runAndGetOutputData()
+    segmentation.fill(0) # Empty segmentation, means no patches
+    generator = fast.PatchGenerator.create(256, 256, level=2).connect(importer).connect(1, segmentation)
+
+    counter = 0
+    with pytest.raises(RuntimeError):
+        for image in fast.DataStream(generator):
+            counter += 1
+    assert(counter == 0)
+
+
 def test_data_stream_single():
     streamer = fast.ImageFileStreamer\
         .create(fast.Config.getTestDataPath() + "/US/Heart/ApicalFourChamber/US-2D_#.mhd")
@@ -17,6 +32,7 @@ def test_data_stream_single():
         counter += 1
     assert counter == 100
 
+
 def test_data_stream_multiple():
     streamer1 = fast.ImageFileStreamer \
         .create(fast.Config.getTestDataPath() + "/US/Heart/ApicalFourChamber/US-2D_#.mhd")