From 6ce8b7b14aa86942f0fa47347e452db65c34ab0d Mon Sep 17 00:00:00 2001
From: David Sarrut <david.sarrut@gmail.com>
Date: Thu, 27 Oct 2011 15:54:16 +0200
Subject: [PATCH] Add first version of clitkRelativePositionDataBaseAnalyzer

---
 ...tkRelativePositionDataBaseAnalyzerFilter.h |  78 +++++++++++
 ...RelativePositionDataBaseAnalyzerFilter.txx | 131 ++++++++++++++++++
 .../clitkRelativePositionDataBaseAnalyzer.cxx |  48 +++++++
 .../clitkRelativePositionDataBaseAnalyzer.ggo |  14 ++
 4 files changed, 271 insertions(+)
 create mode 100644 itk/clitkRelativePositionDataBaseAnalyzerFilter.h
 create mode 100644 itk/clitkRelativePositionDataBaseAnalyzerFilter.txx
 create mode 100644 tools/clitkRelativePositionDataBaseAnalyzer.cxx
 create mode 100644 tools/clitkRelativePositionDataBaseAnalyzer.ggo

diff --git a/itk/clitkRelativePositionDataBaseAnalyzerFilter.h b/itk/clitkRelativePositionDataBaseAnalyzerFilter.h
new file mode 100644
index 0000000..7066c63
--- /dev/null
+++ b/itk/clitkRelativePositionDataBaseAnalyzerFilter.h
@@ -0,0 +1,78 @@
+/*=========================================================================
+  Program:   vv                     http://www.creatis.insa-lyon.fr/rio/vv
+
+  Authors belong to: 
+  - University of LYON              http://www.universite-lyon.fr/
+  - Léon Bérard cancer center       http://www.centreleonberard.fr
+  - CREATIS CNRS laboratory         http://www.creatis.insa-lyon.fr
+
+  This software is distributed WITHOUT ANY WARRANTY; without even
+  the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+  PURPOSE.  See the copyright notices for more information.
+
+  It is distributed under dual licence
+
+  - BSD        See included LICENSE.txt file
+  - CeCILL-B   http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
+  ===========================================================================**/
+
+#ifndef CLITKRELATIVEPOSITIONANALYZERFILTER_H
+#define CLITKRELATIVEPOSITIONANALYZERFILTER_H
+
+// clitk
+#include "clitkFilterWithAnatomicalFeatureDatabaseManagement.h"
+#include "clitkFilterBase.h"
+#include "clitkRelativePositionDataBase.h"
+
+namespace clitk {
+  
+  //--------------------------------------------------------------------
+  /*
+    Load a database of relative positions. Analyze it and provide
+    common relative position for each patient. 
+  */
+  //--------------------------------------------------------------------
+  
+  class RelativePositionDataBaseAnalyzerFilter:
+    public virtual clitk::FilterBase,
+    public clitk::FilterWithAnatomicalFeatureDatabaseManagement
+  {
+
+  public:
+    RelativePositionDataBaseAnalyzerFilter();
+    virtual ~RelativePositionDataBaseAnalyzerFilter() {}
+    
+    // Input
+    itkGetConstMacro(DatabaseFilename, std::string);
+    itkSetMacro(DatabaseFilename, std::string);
+    itkGetConstMacro(StationName, std::string);
+    itkSetMacro(StationName, std::string);
+    itkGetConstMacro(ObjectName, std::string);
+    itkSetMacro(ObjectName, std::string);
+    itkGetConstMacro(OutputFilename, std::string);
+    itkSetMacro(OutputFilename, std::string);
+    
+    // For debug
+    void PrintOptions();
+    
+    // Go !
+    virtual void Update();
+
+  protected:
+    std::string m_DatabaseFilename;
+    std::string m_StationName;
+    std::string m_ObjectName;
+    std::string m_OutputFilename;
+    clitk::RelativePositionDataBase db;
+
+    bool ComputeOptimalThreshold(RelativePositionDataBaseIndexType & index, double & threshold);
+
+  }; // end class
+  //--------------------------------------------------------------------
+
+} // end namespace clitk
+//--------------------------------------------------------------------
+
+#include "clitkRelativePositionDataBaseAnalyzerFilter.txx"
+
+#endif
diff --git a/itk/clitkRelativePositionDataBaseAnalyzerFilter.txx b/itk/clitkRelativePositionDataBaseAnalyzerFilter.txx
new file mode 100644
index 0000000..6aa5f3a
--- /dev/null
+++ b/itk/clitkRelativePositionDataBaseAnalyzerFilter.txx
@@ -0,0 +1,131 @@
+/*=========================================================================
+  Program:   vv                     http://www.creatis.insa-lyon.fr/rio/vv
+
+  Authors belong to: 
+  - University of LYON              http://www.universite-lyon.fr/
+  - Léon Bérard cancer center       http://www.centreleonberard.fr
+  - CREATIS CNRS laboratory         http://www.creatis.insa-lyon.fr
+
+  This software is distributed WITHOUT ANY WARRANTY; without even
+  the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+  PURPOSE.  See the copyright notices for more information.
+
+  It is distributed under dual licence
+
+  - BSD        See included LICENSE.txt file
+  - CeCILL-B   http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
+  ===========================================================================**/
+
+//--------------------------------------------------------------------
+clitk::RelativePositionDataBaseAnalyzerFilter::
+RelativePositionDataBaseAnalyzerFilter():
+  clitk::FilterBase(),
+  clitk::FilterWithAnatomicalFeatureDatabaseManagement()
+{
+  VerboseFlagOff();
+  SetDatabaseFilename("default.dbrp");
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+void 
+clitk::RelativePositionDataBaseAnalyzerFilter::
+PrintOptions() 
+{
+  DD("TODO");
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+void 
+clitk::RelativePositionDataBaseAnalyzerFilter::
+Update() 
+{
+  // Load DB of relative position
+  db.Read(GetDatabaseFilename());
+
+  // Get list of objects, list of orientation
+  std::vector<std::string> m_ListOfObjects;
+  db.GetListOfObjects(GetStationName(), m_ListOfObjects);
+  
+  // Set initial index in the DB
+  clitk::RelativePositionDataBase::IndexType index;
+  index.station = GetStationName();
+
+  // Loop over objects
+  std::vector<double> m_ListOfThresholds;
+  for(int i=0; i<m_ListOfObjects.size(); i++) {
+    // DD(i);
+    // DD(m_ListOfObjects[i]);
+    // Set current index
+    index.object = m_ListOfObjects[i];
+    // Get the list of orientation
+    std::vector<clitk::RelativePositionOrientationType> m_ListOfOrientations;
+    db.GetListOfOrientations(GetStationName(), index.object, m_ListOfOrientations);
+    
+    // Loop over orientation
+    for(int j=0; j<m_ListOfOrientations.size(); j++) {
+      // DD(j);
+      // m_ListOfOrientations[j].Println();
+      // Set current index
+      index.orientation = m_ListOfOrientations[j];
+      // Compute the best RelPos parameters 
+      double threshold;
+      bool ok = ComputeOptimalThreshold(index, threshold);
+      m_ListOfThresholds.push_back(threshold);
+      
+      // Print debug FIXME
+      if (ok) {
+        std::cout << m_ListOfObjects[i] << " ";
+        m_ListOfOrientations[j].Print();
+        std::cout << " " << threshold << " " << ok << std::endl;
+      }
+    }
+  }
+}    
+//--------------------------------------------------------------------
+    
+
+//--------------------------------------------------------------------
+bool
+clitk::RelativePositionDataBaseAnalyzerFilter::
+ComputeOptimalThreshold(RelativePositionDataBaseIndexType & index, double & threshold) 
+{
+  // Get list of patient
+  std::vector<std::string> & ListOfPatients = db.GetListOfPatients(index);
+  //  DD(ListOfPatients.size());
+  // index.orientation.Println();
+
+  // For a given station, object, orientation
+  bool stop=false;
+  int i=0;
+  if (index.orientation.notFlag) threshold = 0.0;
+  else threshold = 1.0;
+  while (!stop && (i<ListOfPatients.size())) {
+    // DD(i);
+    index.patient = ListOfPatients[i];
+    // std::cout << i << " " << index.patient << " ";
+    // Check index
+    if (!db.CheckIndex(index)) {
+      std::cout << "Warning index does not exist in the DB. index = "; 
+      index.Println(std::cout);
+    }
+    else {
+      // index = patient station object, orientation = angle1 angle2 notFlag
+      if (db.GetAreaGain(index) == 1.0) stop = true;
+      else {
+        if (index.orientation.notFlag) threshold = std::max(db.GetThreshold(index), threshold);
+        else threshold = std::min(db.GetThreshold(index), threshold);
+        // std::cout << db.GetThreshold(index) << " opt=" << threshold;
+      } 
+    }
+    ++i;
+  }
+  // std::cout << std::endl;
+  // DD(threshold);
+  // DD(stop);
+  return !stop; // if stop before the end, this orientation is not useful.
+}
+//--------------------------------------------------------------------
diff --git a/tools/clitkRelativePositionDataBaseAnalyzer.cxx b/tools/clitkRelativePositionDataBaseAnalyzer.cxx
new file mode 100644
index 0000000..b74cec4
--- /dev/null
+++ b/tools/clitkRelativePositionDataBaseAnalyzer.cxx
@@ -0,0 +1,48 @@
+/*=========================================================================
+  Program:   vv                     http://www.creatis.insa-lyon.fr/rio/vv
+
+  Authors belong to:
+  - University of LYON              http://www.universite-lyon.fr/
+  - Léon Bérard cancer center       http://www.centreleonberard.fr
+  - CREATIS CNRS laboratory         http://www.creatis.insa-lyon.fr
+
+  This software is distributed WITHOUT ANY WARRANTY; without even
+  the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+  PURPOSE.  See the copyright notices for more information.
+
+  It is distributed under dual licence
+
+  - BSD        See included LICENSE.txt file
+  - CeCILL-B   http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
+===========================================================================**/
+
+// clitk
+#include "clitkRelativePositionDataBaseAnalyzer_ggo.h"
+#include "clitkIO.h"
+#include "clitkRelativePositionDataBaseAnalyzerFilter.h"
+
+//--------------------------------------------------------------------
+int main(int argc, char * argv[]) {
+
+  // Init command line
+  GGO(clitkRelativePositionDataBaseAnalyzer, args_info);
+  CLITK_INIT;
+
+  // Filter
+  typedef clitk::RelativePositionDataBaseAnalyzerFilter FilterType;
+  FilterType filter;  
+  filter.SetDatabaseFilename(args_info.db_arg);
+  filter.SetStationName(args_info.station_arg);
+  // filter.SetStationName(args_info.object_arg);//FIXME
+  filter.SetOutputFilename(args_info.output_arg);
+
+  try {
+    filter.Update();
+  } catch(std::runtime_error e) {
+    std::cout << e.what() << std::endl;
+    return EXIT_FAILURE;
+  }
+
+  return EXIT_SUCCESS;
+} // This is the end, my friend
+//--------------------------------------------------------------------
diff --git a/tools/clitkRelativePositionDataBaseAnalyzer.ggo b/tools/clitkRelativePositionDataBaseAnalyzer.ggo
new file mode 100644
index 0000000..0da0bcd
--- /dev/null
+++ b/tools/clitkRelativePositionDataBaseAnalyzer.ggo
@@ -0,0 +1,14 @@
+#File clitkRelativePositionDataBaseAnalyzer.ggo
+package "clitkRelativePositionDataBaseAnalyzer"
+version "1.0"
+purpose "Analyze a DB of relative positions for several patient and structures"
+
+section "General options"
+option "config"	  	-	"Config file"			  string  	no
+option "verbose"   	v   	"Verbose"			  flag		off
+
+section "Input/Output"
+option "db"             i	"Input database of RelPost"	  string  	yes
+option "station"	s	"Studied station name"	          string  	yes
+option "object"	        -	"Studied object/struct name"      string  	no
+option "output"    	o   	"Output rpl file"		  string 	yes
-- 
2.45.1