Merge branch 'acr-mode-experimental' into temp-branch

CMakeLists.txt

@@ -13,7 +13,7 @@ SET( ${PROJECT_NAME}_Variant "Full" ) # the particular variant of CaPTk (Full/Ne
 
 SET( PROJECT_VERSION_MAJOR 1 )
 SET( PROJECT_VERSION_MINOR 9 )
-SET( PROJECT_VERSION_PATCH 0 )
+SET( PROJECT_VERSION_PATCH 0.ACRExperimental )
 SET( PROJECT_VERSION_TWEAK ) 
 
 # check for the string "nonRelease" in the PROJECT_VERSION_PATCH variable

azure-pipelines.yml

@@ -4,17 +4,17 @@ schedules:
   displayName: Daily midnight build
   branches:
     include:
-    - master
+    - acr-mode-experimental
 
 trigger:
   batch: true
   branches:
-    include: ['master']
+    include: ['acr-mode-experimental']
 
 # 20200312: apparently this is now explicitly required for azure
 pr:
   branches:
-    include: ['master']
+    include: ['acr-mode-experimental']
 
 jobs:
 - job: 'WindowsBuild'

src/CaPTk.cxx

@@ -56,6 +56,7 @@ int main(int argc, char** argv)
   std::string cmd_inputs, cmd_mask, cmd_tumor, cmd_tissue;
   float cmd_maskOpacity = 1;
   bool comparisonMode = false;
+  bool loadOnStartupWithStudyBrowser = false;
 
   // this is used to populate the available CWL files for the cli  
   auto cwlFolderPath = 
@@ -86,6 +87,10 @@ int main(int argc, char** argv)
   parser.addOptionalParameter("ts", "tissuePt", cbica::Parameter::FILE, ".txt", "Tissue Point file for the image(s) being loaded");
   parser.addOptionalParameter("a", "advanced", cbica::Parameter::BOOLEAN, "none", "Advanced visualizer which does *not* consider", "origin information during loading");
   parser.addOptionalParameter("c", "comparisonMode", cbica::Parameter::BOOLEAN, "true or false", "Enable/Disable comparison mode", "comparison mode during loading");
+
+  // ACR collaboration options, although possibly usable in other contexts
+  parser.addOptionalParameter("acr", "acrExperimentalMode", cbica::Parameter::BOOLEAN, "none", "Enable the ACR collaboration mode, with fewer features and a modified GUI");
+  parser.addOptionalParameter("bs", "browseStudy", cbica::Parameter::BOOLEAN, "none", "Open CaPTk with an experimental study-browser for previewing image information -- requires NIFTIs converted from DICOM and JSON data");
 
   //parser.exampleUsage("-i C:/data/input1.nii.gz,C:/data/input2.nii.gz -m C:/data/inputMask.nii.gz -tu C:/data/init_seed.txt -ts C:/data/init_GLISTR.txt");
   parser.addExampleUsage("-i C:/data/input1.nii.gz,C:/data/input2.nii.gz -m C:/data/inputMask.nii.gz -tu C:/data/init_seed.txt -ts C:/data/init_GLISTR.txt",
@@ -169,6 +174,10 @@ int main(int argc, char** argv)
   {
     parser.getParameterValue("c", comparisonMode);
   }
+  if (parser.isPresent("bs"))
+  {
+      loadOnStartupWithStudyBrowser = true;
+  }
 
 #if defined(__linux__)
   //auto defaultFormat = QVTKOpenGLWidget::defaultFormat();
@@ -251,6 +260,10 @@ int main(int argc, char** argv)
   {
     window.EnableAdvancedVisualizer();
   }
+  if (parser.isPresent("acr"))
+  {
+    window.EnableACRMode();
+  }
 
   // get everything to QString
   std::vector< QString > inputFiles_QString;
@@ -320,9 +333,10 @@ int main(int argc, char** argv)
 #endif
   }
   else
-    window.loadFromCommandLine(inputFiles_QString, comparisonMode, inputMask.toStdString(),
-      cmd_maskOpacity, cmd_tumor, cmd_tissue/*, true*/); // at this point, inputFiles_QString will have at least 1 value
-
+  {
+      window.loadFromCommandLine(inputFiles_QString, comparisonMode, inputMask.toStdString(),
+          cmd_maskOpacity, cmd_tumor, cmd_tissue, loadOnStartupWithStudyBrowser /*, true*/); // at this point, inputFiles_QString will have at least 1 value
+  }
 
 
   //window.setFixedSize(QSize(2735, 1538)); // useful when doing video recording from SP4 and maintain 16x9 ratio

src/applications/FeatureExtraction/src/FeatureExtraction.hxx

@@ -1251,6 +1251,15 @@ void FeatureExtraction< TImage >::SetSelectedROIsAndLabels(std::string roi, std:
     {
       m_roiLabels = tempstr2;
     }
+    if (m_roiLabels.size() < m_roi.size())
+    {
+        auto labelsInitialSize = m_roiLabels.size();
+        auto missingLabelsCount = m_roi.size() - m_roiLabels.size();
+        for (unsigned int i = 0; i < missingLabelsCount; i++)
+        {
+            m_roiLabels.push_back("Label" + std::to_string(m_roi[labelsInitialSize + i]));
+        }
+    }
   }
 
   if (m_debug)

src/applications/GeodesicTraining/src/GeodesicTrainingCaPTkApp.h

@@ -11,6 +11,9 @@
 //#include "ApplicationBase.h"
 #include <QObject>
 
+// Do this to make sure we can connect signals/slots across threads with std::strings
+Q_DECLARE_METATYPE(std::string)
+
 class GeodesicTrainingApplicationBase : public QObject
 {
 	Q_OBJECT
@@ -30,7 +33,9 @@ public slots:
 	//void GeodesicTrainingFinished3D(typename itk::Image<int, 3>::Pointer result);
 	//void GeodesicTrainingFinished2D(typename itk::Image<int, 2>::Pointer result);
 	void GeodesicTrainingFinishedWithError(QString errorMessage);
+	void GeodesicTrainingFinishedWithError(); // For when no error message is published
 	void GeodesicTrainingProgressUpdate(int progress, std::string message, int max);
+	//void GeodesicTrainingProgressUpdate(int progress, QString message, int max);
 
 protected:
 	std::thread m_Thread;
@@ -47,7 +52,10 @@ class GeodesicTrainingCaPTkApp :
     typedef itk::Image<int, Dimensions>       LabelsImageType;
     typedef typename LabelsImageType::Pointer LabelsImagePointer;
 
-    explicit GeodesicTrainingCaPTkApp(QObject* parent = nullptr) : GeodesicTrainingApplicationBase(parent) {}
+    explicit GeodesicTrainingCaPTkApp(QObject* parent = nullptr) : GeodesicTrainingApplicationBase(parent) 
+	{
+		qRegisterMetaType<std::string>(); // Needs to be done at runtime to allow these connections
+	}
 
 	virtual ~GeodesicTrainingCaPTkApp() {}
 
@@ -61,6 +69,8 @@ class GeodesicTrainingCaPTkApp :
 	/** Overriden from GeodesicTrainingSegmentation class */
 	void progressUpdate(std::string message, int progress) override
 	{
+		// use QString to avoid argument queuing issues across threads
+		// (see https://stackoverflow.com/a/17083775)
 		emit GeodesicTrainingProgressUpdate(progress, message, 100);
 	}
 
@@ -73,6 +83,8 @@ class GeodesicTrainingCaPTkApp :
         this->SetLabels(labelsImage);
 		this->SetSaveAll(true);
 		this->SetProcessing(true, 6, true, false, false, 5000000); // Disable pixel limit, all else default.
+		emit GeodesicTrainingProgressUpdate(10, "Geodesic Training Segmentation in progress...", 100);
+
         auto executeResult = this->Execute();
 
         if (executeResult->ok) {

src/view/gui/CMakeLists.txt

@@ -55,6 +55,7 @@ SET( GUI
   CaPTkDockWidget
   fBiasCorrectionDialog
   fBraTSSegmentation
+  fStudyBrowserDialog
   #fSegmentationPanel
   #fHelpAppDialog
 )

src/view/gui/fDrawingPanel.cpp

@@ -42,6 +42,8 @@ fDrawingPanel::fDrawingPanel(QWidget * parent) : QWidget(parent)
   connect(HelpButton, SIGNAL(clicked()), this, SLOT(helpClicked()));
   connect(changeButton, SIGNAL(clicked()), this, SLOT(ChangeLabelValuesClicked()));
   connect(applyMaskButton, SIGNAL(clicked()), this, SLOT(OnApplyMaskButtonClicked()));
+  connect(runGeodesicTrainingSegmentationButton, SIGNAL(clicked()), this, SLOT(OnRunGTSButtonClicked()));
+  connect(finalizeSegmentationButton, SIGNAL(clicked()), this, SLOT(OnFinalizeSegmentationButtonClicked()));
 }
 
 void fDrawingPanel::helpClicked()
@@ -137,4 +139,20 @@ void fDrawingPanel::FillButtonFunctionality()
 void fDrawingPanel::OnApplyMaskButtonClicked()
 {
 	emit ApplyMask();
+}
+
+void fDrawingPanel::EnableACRMode()
+{
+    applyMaskButton->hide();
+    algorithmGroup->setHidden(false);
+}
+
+void fDrawingPanel::OnRunGTSButtonClicked()
+{
+    emit runGTSButtonClicked();
+}
+
+void fDrawingPanel::OnFinalizeSegmentationButtonClicked()
+{
+    emit finalizeSegmentationButtonClicked();
 }

src/view/gui/fDrawingPanel.h

@@ -65,6 +65,7 @@ class fDrawingPanel : public QWidget, private Ui::fDrawingPanel
   }
 
   int getCurrentOpacity() { return m_currentOpacity; };
+  void EnableACRMode();
 
 signals :
   void clearMask(int label=-1);
@@ -76,8 +77,11 @@ signals :
   void CurrentMaskOpacityChanged(int); // multiLabel related change
   void helpClicked_Interaction(std::string);
   void sig_ChangeLabelValuesClicked(const std::string, const std::string);
+  void runGTSButtonClicked();
+  void finalizeSegmentationButtonClicked();
   void ApplyMask();
 
+
 public slots :
 
   //! Enable voxel based erase functionality
@@ -118,6 +122,8 @@ public slots :
 
   //! Apply mask
   void OnApplyMaskButtonClicked();
+  void OnRunGTSButtonClicked();
+  void OnFinalizeSegmentationButtonClicked();
 
 private:
   int m_currentOpacity; // set default to the tenth spinbox selection (1.0 mask opacity)

src/view/gui/fFeaturePanel.cpp

@@ -272,7 +272,7 @@ void fFeaturePanel::computeFeature(int type)
     }
   }
 
-  ((fMainWindow*)m_listener)->updateProgress(30, "Calculating and exporting features", images.size());
+  ((fMainWindow*)m_listener)->updateProgress(30, "Calculating and exporting features", 100); // last param used to be images.size()???
 
   if (images[0]->GetLargestPossibleRegion().GetSize()[2] == 1)
   {
@@ -378,6 +378,7 @@ void fFeaturePanel::computeFeature(int type)
   }
 
   m_btnCompute->setEnabled(true);
+  emit computationFinished();
   return;
 }
 
@@ -439,4 +440,119 @@ void fFeaturePanel::onIBSI2Toggled(bool checked)
         msgbox.setText(msg);
         msgbox.exec();
     }
+}
+
+void fFeaturePanel::EnableACRMode()
+{
+    m_doACRCallbackOnFinish = true;
+    // force Image Selection to All Images, hide those options
+    radio1->setChecked(false);
+    radio1->hide();
+    radio2->setChecked(true);
+
+    // For speed, uncheck these by default for now so that demos are done quickly
+    // TBD: Once we address long-running feature extraction, this can be changed back.
+    m_GLCM->setChecked(false);
+    m_GLSZM->setChecked(false);
+    m_GLRLM->setChecked(false);
+    m_NGTDM->setChecked(false);
+    m_LBP->setChecked(false);
+    m_Histogram->setChecked(false);
+    m_Collage->setChecked(false);
+    m_Lattice->setChecked(false);
+
+
+    // Add/replace Compute+save button, hide output file selector
+    // TODO switch to a temp dir and store this location for deletion later
+    QProcessEnvironment env = QProcessEnvironment::systemEnvironment();
+    QString outputDirRoot = env.value("DART_CAPTK_OUTPUT_DIR_ROOT", "NULL");
+    cbica::createDirectory(cbica::normalizePath(outputDirRoot.toStdString() + "/temp/"));
+    QString tmpFeatureFilePath = outputDirRoot + "/temp/tmp_features.csv";
+    m_txtSaveFileName->setText(QString::fromStdString(cbica::normPath(tmpFeatureFilePath.toStdString()))); // will be deleted after each run
+    m_txtSaveFileName->hide();
+    m_btnBrowseSaveFile->hide();
+    saveGroup_file->hide();
+    instructionsGroup->setHidden(false);
+    //m_verticalConcat->hide(); // We may need to hide this if we want all output to be uniform
+    saveGroup->setTitle("Output");
+
+    // Ensure output uniformity in a consistent format for training module
+    m_verticalConcat->setChecked(false);
+    m_verticalConcat->setVisible(false);
+    m_btnCompute->setText("Compute + Save to DART");
+}
+
+std::string fFeaturePanel::GetCurrentOutputPath()
+{
+    return m_txtSaveFileName->text().toStdString();
+}
+
+bool fFeaturePanel::GetSelectedROIValuesAndLabelsVectors(std::vector<int>& vals, std::vector<std::string>& labels)
+{
+    vals.clear();
+    labels.clear();
+    auto roi = m_roi->text().toStdString();
+    auto roi_labels = m_roi_label->text().toStdString();
+    bool roivaluesfound = false;
+    bool roilabelsfound = false;
+
+    if (!roi.empty() && roi != "all")
+    {
+        auto tempstr = cbica::stringSplit(roi, "|");
+        auto tempstr2 = cbica::stringSplit(roi, ",");
+        if (tempstr2.size() > tempstr.size())
+        {
+            tempstr = tempstr2;
+        }
+        for (size_t i = 0; i < tempstr.size(); i++)
+        {
+            vals.push_back(std::stoi(tempstr[i]));
+            if (roi_labels.empty())
+            {
+                labels.push_back(tempstr[i]);
+            }
+        }
+
+        roivaluesfound = true;
+    }
+
+    if (!roi_labels.empty() && roi_labels != "all")
+    {
+        labels = cbica::stringSplit(roi_labels, "|");
+        auto tempstr2 = cbica::stringSplit(roi_labels, ",");
+        if (tempstr2.size() > labels.size())
+        {
+            labels = tempstr2;
+        }
+        if (labels.size() < vals.size())
+        {
+            auto labelsInitialSize = labels.size();
+            auto missingLabelsCount = vals.size() - labels.size();
+            for (unsigned int i = 0; i < missingLabelsCount; i++)
+            {
+                labels.push_back("Label" + std::to_string(vals[labelsInitialSize + i]));
+            }
+        }
+        roilabelsfound = true;
+    }
+
+    return (roivaluesfound && roilabelsfound);
+}
+
+void fFeaturePanel::SetROIValuesAndLabelStrings(std::string valuesString, std::string labelsString)
+{
+    m_roi->setText(QString::fromStdString(valuesString));
+    m_roi_label->setText(QString::fromStdString(labelsString));
+}
+
+bool fFeaturePanel::IBSIFeaturesEnabled()
+{
+    if (m_IBSI2->isChecked())
+    {
+        return true;
+    }
+    else
+    {
+        return false;
+    }
 }

src/view/gui/fFeaturePanel.h

@@ -55,12 +55,25 @@ class fFeaturePanel : public QWidget, private Ui::fFeaturePanel
     m_tempFolderLocation = input_tempFolder;
   }
 
+  void EnableACRMode();
+
+  //! Get the currently selected output filepath.
+  std::string GetCurrentOutputPath();
+
+  //! Populate the 2 given vectors with the ROI values (intensity in mask image) and labels (corresponding region names)
+  // returns true if this actually works, false if nothing is selected or if "all" is typed in
+  bool GetSelectedROIValuesAndLabelsVectors(std::vector<int>& vals, std::vector<std::string>& labels);
+
+  // return true if IBSI features are toggled on. Useful for detecting when to pick up the artifacts.
+  bool IBSIFeaturesEnabled();
 
 signals:
   void m_btnComputeClicked();
   void helpClicked_FeaUsage(std::string);
+  void computationFinished();
 
   public slots :
+  void SetROIValuesAndLabelStrings(std::string valuesString, std::string labelsString);
   void browseOutputFileName();
   void ComputeFunctionality();
   void CancelFunctionality();
@@ -115,7 +128,8 @@ class fFeaturePanel : public QWidget, private Ui::fFeaturePanel
       m_FeatureMaps.push_back(featureMap);
     }
   }
-
+  // Flag for whether to run the ACR callback script (only works in an ACR containerized environment)
+  bool m_doACRCallbackOnFinish; 
 };