Fixed issue in patch gen causing pipeline test to fail

Author: smistad

source/FAST/Algorithms/ImagePatch/PatchGenerator.cpp

@@ -208,6 +208,7 @@ void PatchGenerator::generateStream() {
                     patch->setFrameData("patch-level", std::to_string(level));
                     m_progress = (float)(patchX+patchY*patchesX)/(patchesX*patchesY);
                     patch->setFrameData("progress", std::to_string(m_progress));
+                    patch->setFrameData("streaming", "yes"); // Since we are not propagating frame data, we have to set this
 
                     mRuntimeManager->stopRegularTimer("create patch");
                     try {
@@ -299,6 +300,7 @@ void PatchGenerator::generateStream() {
                         patch->setFrameData("patch-spacing-z", std::to_string(spacing.z()));
                         m_progress = ((float)(patchX+patchY*patchesX+patchZ*patchesX*patchesY)/(patchesX*patchesY*patchesZ));
                         patch->setFrameData("progress", std::to_string(m_progress));
+                        patch->setFrameData("streaming", "yes"); // Since we are not propagating frame data, we have to set this
                         try {
                             if(previousPatch) {
                                 addOutputData(0, previousPatch, false, false);
@@ -321,6 +323,7 @@ void PatchGenerator::generateStream() {
         }
         // 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) {

source/FAST/Algorithms/TissueSegmentation/TissueSegmentation.cpp

@@ -20,6 +20,7 @@ TissueSegmentation::TissueSegmentation(bool useColorThresholdingMethod, int leve
     createIntegerAttribute("dilate-kernel-size", "Kernel size for dilation", "", m_dilate);
     createIntegerAttribute("erode-kernel-size", "Kernel size for erosion", "", m_erode);
     createBooleanAttribute("filter-zeros", "Include zero values to background/glass class", "", m_filterZeros);
+    createBooleanAttribute("color-thresholding", "Use color thresholding instead of neural network", "", false);
     setThreshold(threshold);
     setDilate(dilationSize);
     setErode(erosionSize);
@@ -34,7 +35,7 @@ void TissueSegmentation::loadAttributes() {
     setDilate(getIntegerAttribute("dilate-kernel-size"));
     setErode(getIntegerAttribute("erode-kernel-size"));
     setFilterZeros(getBooleanAttribute("filter-zeros"));
-
+    setUseColorThresholdingMethod("color-thresholding");
 }
 
 void TissueSegmentation::setThreshold(int thresh) {

source/FAST/Algorithms/TissueSegmentation/TissueSegmentation.hpp

@@ -94,7 +94,7 @@ class FAST_EXPORT TissueSegmentation : public ProcessObject {
         int m_erode = 9;
         int m_thresh = 85;
         int m_level = -1;
-        float m_magnification = 2.5f;
+        float m_magnification = 1.25f;
         bool m_filterZeros = true;
         bool m_useColorThresholdingMethod = false;
 };