From fdabe8c9ba68e1b6267cccf221bd8e21ea6ab561 Mon Sep 17 00:00:00 2001
From: sagebei <bei.zhou@imperial.ac.uk>
Date: Fri, 16 Aug 2024 16:14:12 +0100
Subject: [PATCH] connection_to_ccta

---
 .../CemrgAppModule/include/CemrgCommandLine.h |   2 +
 .../CemrgAppModule/src/CemrgCommandLine.cpp   |  29 ++++
 .../src/internal/AtrialStrainMotionView.cpp   | 146 ++++++++++++++++--
 .../src/internal/AtrialStrainMotionView.h     |  14 +-
 .../AtrialStrainMotionViewControls.ui         |  14 +-
 5 files changed, 185 insertions(+), 20 deletions(-)

diff --git a/CemrgApp/Modules/CemrgAppModule/include/CemrgCommandLine.h b/CemrgApp/Modules/CemrgAppModule/include/CemrgCommandLine.h
index 54c7aee..38f5d5a 100644
--- a/CemrgApp/Modules/CemrgAppModule/include/CemrgCommandLine.h
+++ b/CemrgApp/Modules/CemrgAppModule/include/CemrgCommandLine.h
@@ -110,6 +110,8 @@ class MITKCEMRGAPPMODULE_EXPORT CemrgCommandLine: public QObject {
     std::string PrintFullCommand(QString command, QStringList arguments);
     bool ExecuteCommand(QString executableName, QStringList arguments, QString outputPath, bool isOutputFile = true);
 
+    QString DockerCctaMultilabelSegmentation(QString dir, QString path_to_f, bool saveas_nifti);
+
 protected slots:
 
     void UpdateStdText();
diff --git a/CemrgApp/Modules/CemrgAppModule/src/CemrgCommandLine.cpp b/CemrgApp/Modules/CemrgAppModule/src/CemrgCommandLine.cpp
index 48d5740..87cdde5 100644
--- a/CemrgApp/Modules/CemrgAppModule/src/CemrgCommandLine.cpp
+++ b/CemrgApp/Modules/CemrgAppModule/src/CemrgCommandLine.cpp
@@ -1413,3 +1413,32 @@ void CemrgCommandLine::FinishedAlert() {
     QString data = process->program() + " Completed!";
     panel->append(data);
 }
+
+QString CemrgCommandLine::DockerCctaMultilabelSegmentation(QString dir, QString path_to_f, bool saveas_nifti) {
+    SetDockerImage("cemrg/ccta:latest");
+    QString executablePath = "";
+#if defined(__APPLE__)
+    executablePath = "/usr/local/bin/";
+#endif
+    QString executableName = executablePath + "docker";
+    QDir home(dir);
+    QFileInfo fi(path_to_f);
+    QString outname = fi.baseName();
+    outname += "_label_maps.nii.gz";
+    QStringList arguments = GetDockerArguments(home.absolutePath());
+    arguments << "--filename" << home.relativeFilePath(path_to_f);
+    arguments << "--device" << "cpu";
+    if (saveas_nifti) {
+        arguments << "--saveas-nifti";
+    }
+    QString outPath = home.absolutePath() + "/" + outname;
+    bool successful = ExecuteCommand(executableName, arguments, outPath);
+    QString res="";
+    if (successful) {
+        MITK_INFO << "Successful mutilabel segmentation";
+        res = outPath;
+    } else {
+        MITK_WARN << "Unsuccessful multilabel segmentation";
+    }
+    return res;
+}
diff --git a/CemrgApp/Plugins/kcl.cemrgapp.atrialstrainmotion/src/internal/AtrialStrainMotionView.cpp b/CemrgApp/Plugins/kcl.cemrgapp.atrialstrainmotion/src/internal/AtrialStrainMotionView.cpp
index c5d2b05..9531eb4 100644
--- a/CemrgApp/Plugins/kcl.cemrgapp.atrialstrainmotion/src/internal/AtrialStrainMotionView.cpp
+++ b/CemrgApp/Plugins/kcl.cemrgapp.atrialstrainmotion/src/internal/AtrialStrainMotionView.cpp
@@ -41,34 +41,95 @@ OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 * 
 =========================================================================*/
 
-
+#include "kcl_cemrgapp_atrialstrainmotion_Activator.h"
+#include "AtrialStrainMotionView.h"
 
 // Blueberry
 #include <berryISelectionService.h>
 #include <berryIWorkbenchWindow.h>
 
-// Qmitk
-#include "kcl_cemrgapp_atrialstrainmotion_Activator.h"
-#include "AtrialStrainMotionView.h"
+//Micro services
+#include <usModuleRegistry.h>
+#ifdef _WIN32
+// _WIN32 = we're in windows
+#include <winsock2.h>
+#else
+// or linux/mac
+#include <arpa/inet.h>
+#endif
+
+//VTK
+#include <vtkFieldData.h>
+#include <vtkCleanPolyData.h>
+#include <vtkPolyDataNormals.h>
+#include <vtkPolyDataConnectivityFilter.h>
+#include <vtkWindowedSincPolyDataFilter.h>
+#include <vtkImplicitPolyDataDistance.h>
+#include <vtkBooleanOperationPolyDataFilter.h>
+#include <vtkClipPolyData.h>
+#include <vtkDecimatePro.h>
+
+//ITK
+#include <itkAddImageFilter.h>
+#include <itkRelabelComponentImageFilter.h>
+#include <itkConnectedComponentImageFilter.h>
+#include <itkImageRegionIteratorWithIndex.h>
+#include "itkLabelObject.h"
+#include "itkLabelMap.h"
+#include "itkLabelImageToLabelMapFilter.h"
+#include "itkLabelMapToLabelImageFilter.h"
+#include "itkLabelSelectionLabelMapFilter.h"
 
 // Qt
 #include <QMessageBox>
+#include <QFileDialog>
+#include <QInputDialog>
+#include <QDirIterator>
+#include <QDate>
+#include <QFile>
 
-// mitk image
+// mitk
+#include <QmitkIOUtil.h>
 #include <mitkImage.h>
+#include <mitkLog.h>
+#include <mitkProgressBar.h>
+#include <mitkIDataStorageService.h>
+#include <mitkNodePredicateNot.h>
+#include <mitkNodePredicateProperty.h>
+#include <mitkDataStorageEditorInput.h>
+#include <mitkImageCast.h>
+#include <mitkITKImageImport.h>
+#include <mitkBoundingObject.h>
+#include <mitkCuboid.h>
+#include <mitkAffineImageCropperInteractor.h>
+#include <mitkImagePixelReadAccessor.h>
+#include <mitkUnstructuredGrid.h>
+#include <mitkManualSegmentationToSurfaceFilter.h>
+
+//CemrgAppModule
+#include <CemrgCommonUtils.h>
+#include <CemrgCommandLine.h>
+#include <CemrgMeasure.h>
+#include <CemrgScar3D.h>
+
 
 const std::string AtrialStrainMotionView::VIEW_ID = "org.mitk.views.atrialstrainmotionview";
 
 void AtrialStrainMotionView::SetFocus()
 {
-  m_Controls.button_step_1->setFocus();
+  m_Controls.segment_extract->setFocus();
 }
 
 void AtrialStrainMotionView::CreateQtPartControl(QWidget *parent)
 {
   // create GUI widgets from the Qt Designer's .ui file
   m_Controls.setupUi(parent);
-  connect(m_Controls.button_step_1, &QPushButton::clicked, this, &AtrialStrainMotionView::DoImageProcessing);
+  // Step 1: Segment and Extract
+  connect(m_Controls.segment_extract, SIGNAL(clicked()), this, SLOT(SegmentExtract()));
+
+
+  // Set default variables
+  atrium = std::unique_ptr<CemrgAtrialTools>(new CemrgAtrialTools());
 }
 
 void AtrialStrainMotionView::OnSelectionChanged(berry::IWorkbenchPart::Pointer /*source*/,
@@ -80,13 +141,13 @@ void AtrialStrainMotionView::OnSelectionChanged(berry::IWorkbenchPart::Pointer /
     if (node.IsNotNull() && dynamic_cast<mitk::Image *>(node->GetData()))
     {
       m_Controls.labelWarning->setVisible(false);
-      m_Controls.button_step_1->setEnabled(true);
+      m_Controls.segment_extract->setEnabled(true);
       return;
     }
   }
 
   m_Controls.labelWarning->setVisible(true);
-  m_Controls.button_step_1->setEnabled(false);
+  m_Controls.segment_extract->setEnabled(false);
 }
 
 void AtrialStrainMotionView::DoImageProcessing()
@@ -129,3 +190,70 @@ void AtrialStrainMotionView::DoImageProcessing()
     }
   }
 }
+
+bool AtrialStrainMotionView::RequestProjectDirectoryFromUser() {
+
+  bool succesfulAssignment = true;
+
+  //Ask the user for a dir to store data
+  if (directory.isEmpty()) {
+
+    MITK_INFO << "Directory is empty. Requesting user for directory.";
+    directory = QFileDialog::getExistingDirectory( NULL, "Open Project Directory",
+        mitk::IOUtil::GetProgramPath().c_str(),QFileDialog::ShowDirsOnly|QFileDialog::DontUseNativeDialog);
+
+    MITK_INFO << ("Directory selected:" + directory).toStdString();
+    atrium->SetWorkingDirectory(directory);
+
+    if (directory.isEmpty() || directory.simplified().contains(" ")) {
+      MITK_WARN << "Please select a project directory with no spaces in the path!";
+      QMessageBox::warning(NULL, "Attention", "Please select a project directory with no spaces in the path!");
+      directory = QString();
+      succesfulAssignment = false;
+    }//_if
+
+    if (succesfulAssignment){
+      QString now = QDate::currentDate().toString(Qt::ISODate);
+      QString logfilename = directory + "/afib_log" + now + ".log";
+      std::string logfname_str = logfilename.toStdString();
+
+      mitk::LoggingBackend::SetLogFile(logfname_str.c_str());
+      MITK_INFO << ("Changed logfile location to: " + logfilename).toStdString();
+    }
+
+  } else {
+    MITK_INFO << ("Project directory already set: " + directory).toStdString();
+  }//_if
+
+
+  return succesfulAssignment;
+}
+
+void AtrialStrainMotionView::SegmentExtract() {
+
+    MITK_INFO << "[AnalysisChoice]";
+    bool testRpdfu = RequestProjectDirectoryFromUser();
+    MITK_INFO(testRpdfu) << "Should continue";
+    if (!RequestProjectDirectoryFromUser()) return; // if the path was chosen incorrectly -> returns.
+    MITK_INFO << "After directory selection checkup";
+
+    // TODO: select the first image and segment it
+    QString nifti_dir = directory + "/nifti/";
+    QString input_file = nifti_dir + "dcm-0.nii";
+    std::unique_ptr<CemrgCommandLine> cmd(new CemrgCommandLine());
+
+    MITK_INFO(QFile::copy(input_file, directory + "/dcm-0.nii")) << "QFile::Copy successful";
+    // MITK_INFO << successful;
+
+    // get pathToNifti file!
+    QFileInfo file(input_file);
+
+    cmd->SetUseDockerContainers(true);
+    QString pathToSegmentation = cmd->DockerCctaMultilabelSegmentation(directory, directory + "/dcm-0.nii", false);
+    MITK_INFO << pathToSegmentation;
+    // TODO: build a docker image for extracting LA
+
+
+
+
+}
\ No newline at end of file
diff --git a/CemrgApp/Plugins/kcl.cemrgapp.atrialstrainmotion/src/internal/AtrialStrainMotionView.h b/CemrgApp/Plugins/kcl.cemrgapp.atrialstrainmotion/src/internal/AtrialStrainMotionView.h
index 9547586..d5829f6 100644
--- a/CemrgApp/Plugins/kcl.cemrgapp.atrialstrainmotion/src/internal/AtrialStrainMotionView.h
+++ b/CemrgApp/Plugins/kcl.cemrgapp.atrialstrainmotion/src/internal/AtrialStrainMotionView.h
@@ -52,6 +52,8 @@ OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 
 #include "ui_AtrialStrainMotionViewControls.h"
 
+
+#include "CemrgAtrialTools.h"
 /**
   \brief AtrialStrainMotionView
 
@@ -67,6 +69,8 @@ class AtrialStrainMotionView : public QmitkAbstractView {
 
 public:
   static const std::string VIEW_ID;
+  bool RequestProjectDirectoryFromUser();
+
 
 protected:
   virtual void CreateQtPartControl(QWidget *parent) override;
@@ -77,11 +81,19 @@ class AtrialStrainMotionView : public QmitkAbstractView {
   virtual void OnSelectionChanged(berry::IWorkbenchPart::Pointer source,
                                   const QList<mitk::DataNode::Pointer> &nodes) override;
 
+  Ui::AtrialStrainMotionViewControls m_Controls;
+
   /// \brief Called when the user clicks the GUI button
+
+
 protected slots:
   void DoImageProcessing();
+  void SegmentExtract();
 
-  Ui::AtrialStrainMotionViewControls m_Controls;
+
+private:
+  QString directory;
+  std::unique_ptr<CemrgAtrialTools> atrium;
 };
 
 #endif // AtrialStrainMotionView_h
diff --git a/CemrgApp/Plugins/kcl.cemrgapp.atrialstrainmotion/src/internal/AtrialStrainMotionViewControls.ui b/CemrgApp/Plugins/kcl.cemrgapp.atrialstrainmotion/src/internal/AtrialStrainMotionViewControls.ui
index ea747f5..8e8279e 100644
--- a/CemrgApp/Plugins/kcl.cemrgapp.atrialstrainmotion/src/internal/AtrialStrainMotionViewControls.ui
+++ b/CemrgApp/Plugins/kcl.cemrgapp.atrialstrainmotion/src/internal/AtrialStrainMotionViewControls.ui
@@ -7,7 +7,7 @@
     <x>0</x>
     <y>0</y>
     <width>222</width>
-    <height>161</height>
+    <height>555</height>
    </rect>
   </property>
   <property name="minimumSize">
@@ -26,20 +26,14 @@
       <string notr="true">QLabel { color: rgb(255, 0, 0) }</string>
      </property>
      <property name="text">
-      <string>Please select an image!</string>
+      <string>Model Creation Pipeline</string>
      </property>
     </widget>
    </item>
    <item>
-    <widget class="QPushButton" name="button_step_1">
-     <property name="toolTip">
-      <string>Do image processing</string>
-     </property>
-     <property name="styleSheet">
-      <string notr="true">text-align: left;</string>
-     </property>
+    <widget class="QPushButton" name="segment_extract">
      <property name="text">
-      <string>   Step 1: Do Something </string>
+      <string>Segment and Extract</string>
      </property>
     </widget>
    </item>