moved teh Poincare from a plot to an operator

git-svn-id: http://visit.ilight.com/svn/visit/trunk/src@21659 18c085ea-50e0-402c-830e-de6fd14e8384

operators/CMakeLists.txt

@@ -108,6 +108,7 @@ MultiresControl
 OnionPeel
 PDF
 PersistentParticles
+Poincare
 Project
 Reflect
 Replicate

operators/Poincare/CMakeLists.txt

+# DO NOT EDIT THIS FILE! THIS FILE IS AUTOMATICALLY GENERATED BY xml2cmake
+PROJECT(Poincare)
+
+INCLUDE(${VISIT_SOURCE_DIR}/CMake/PluginMacros.cmake)
+
+SET(COMMON_SOURCES
+PoincarePluginInfo.C
+PoincareCommonPluginInfo.C
+PoincareAttributes.C
+)
+
+SET(LIBI_SOURCES 
+PoincarePluginInfo.C
+)
+
+SET(LIBG_SOURCES
+PoincareGUIPluginInfo.C
+QvisPoincareWindow.C
+${COMMON_SOURCES}
+)
+SET(LIBG_MOC_SOURCES
+QvisPoincareWindow.h
+)
+
+SET(LIBV_SOURCES
+PoincareViewerPluginInfo.C
+${COMMON_SOURCES}
+)
+
+SET(LIBE_SOURCES
+PoincareEnginePluginInfo.C
+avtPoincareFilter.C
+FieldlineAnalyzerLib.C
+RationalSurfaceLib.C
+skelet.C
+dir_graph.C
+${COMMON_SOURCES}
+)
+
+
+IF(VISIT_PYTHON_SCRIPTING)
+    SET(PYINCLUDES ${PYTHON_INCLUDE_PATH} ${VISIT_INCLUDE_DIR}/visitpy/visitpy)
+ENDIF(VISIT_PYTHON_SCRIPTING)
+
+INCLUDE_DIRECTORIES(
+${CMAKE_CURRENT_SOURCE_DIR}
+${VISIT_COMMON_INCLUDES}
+${VISIT_INCLUDE_DIR}/avt/DBAtts/MetaData
+${VISIT_INCLUDE_DIR}/avt/DBAtts/SIL
+${VISIT_INCLUDE_DIR}/avt/Database/Database
+${VISIT_INCLUDE_DIR}/avt/Expressions/Abstract
+${VISIT_INCLUDE_DIR}/avt/Expressions/CMFE
+${VISIT_INCLUDE_DIR}/avt/Expressions/Conditional
+${VISIT_INCLUDE_DIR}/avt/Expressions/Derivations
+${VISIT_INCLUDE_DIR}/avt/Expressions/General
+${VISIT_INCLUDE_DIR}/avt/Expressions/ImageProcessing
+${VISIT_INCLUDE_DIR}/avt/Expressions/Management
+${VISIT_INCLUDE_DIR}/avt/Expressions/Math
+${VISIT_INCLUDE_DIR}/avt/Expressions/MeshQuality
+${VISIT_INCLUDE_DIR}/avt/Expressions/TimeIterators
+${VISIT_INCLUDE_DIR}/avt/FileWriter
+${VISIT_INCLUDE_DIR}/avt/Filters
+${VISIT_INCLUDE_DIR}/avt/IVP
+${VISIT_INCLUDE_DIR}/avt/Math
+${VISIT_INCLUDE_DIR}/avt/Pipeline/AbstractFilters
+${VISIT_INCLUDE_DIR}/avt/Pipeline/Data
+${VISIT_INCLUDE_DIR}/avt/Pipeline/Pipeline
+${VISIT_INCLUDE_DIR}/avt/Pipeline/Sinks
+${VISIT_INCLUDE_DIR}/avt/Pipeline/Sources
+${VISIT_INCLUDE_DIR}/avt/Plotter
+${VISIT_INCLUDE_DIR}/avt/QtVisWindow
+${VISIT_INCLUDE_DIR}/avt/View
+${VISIT_INCLUDE_DIR}/avt/VisWindow/Colleagues
+${VISIT_INCLUDE_DIR}/avt/VisWindow/Interactors
+${VISIT_INCLUDE_DIR}/avt/VisWindow/Proxies
+${VISIT_INCLUDE_DIR}/avt/VisWindow/Tools
+${VISIT_INCLUDE_DIR}/avt/VisWindow/VisWindow
+${VISIT_INCLUDE_DIR}/gui
+${VISIT_INCLUDE_DIR}/mdserver/proxy
+${VISIT_INCLUDE_DIR}/mdserver/rpc
+${VISIT_INCLUDE_DIR}/viewer/main
+${VISIT_INCLUDE_DIR}/viewer/proxy
+${VISIT_INCLUDE_DIR}/viewer/rpc
+${VISIT_INCLUDE_DIR}/winutil
+${VISIT_INCLUDE_DIR}/visit_vtk/full
+${VISIT_INCLUDE_DIR}/visit_vtk/lightweight
+${QT_INCLUDE_DIR}
+${QT_QTCORE_INCLUDE_DIR}
+${QT_QTGUI_INCLUDE_DIR}
+${VTK_INCLUDE_DIRS} 
+${PYINCLUDES}
+)
+
+
+LINK_DIRECTORIES(${VISIT_LIBRARY_DIR} ${QT_LIBRARY_DIR} ${GLEW_LIBRARY_DIR} ${VTK_LIBRARY_DIRS} )
+
+ADD_LIBRARY(IPoincareOperator ${LIBI_SOURCES})
+TARGET_LINK_LIBRARIES(IPoincareOperator visitcommon)
+SET(INSTALLTARGETS IPoincareOperator)
+
+IF(NOT VISIT_SERVER_COMPONENTS_ONLY AND NOT VISIT_ENGINE_ONLY AND NOT VISIT_DBIO_ONLY)
+    QT_WRAP_CPP(GPoincareOperator LIBG_SOURCES ${LIBG_MOC_SOURCES})
+    ADD_LIBRARY(GPoincareOperator ${LIBG_SOURCES})
+    TARGET_LINK_LIBRARIES(GPoincareOperator visitcommon gui )
+
+    ADD_LIBRARY(VPoincareOperator ${LIBV_SOURCES})
+    TARGET_LINK_LIBRARIES(VPoincareOperator visitcommon viewer )
+    SET(INSTALLTARGETS ${INSTALLTARGETS} GPoincareOperator VPoincareOperator)
+
+    IF(VISIT_PYTHON_SCRIPTING)
+        SET(LIBS_SOURCES
+            PoincareScriptingPluginInfo.C
+            PyPoincareAttributes.C
+            ${COMMON_SOURCES}
+        )
+        ADD_LIBRARY(SPoincareOperator ${LIBS_SOURCES})
+        TARGET_LINK_LIBRARIES(SPoincareOperator visitcommon visitpy ${PYTHON_LIBRARY})
+        SET(INSTALLTARGETS ${INSTALLTARGETS} SPoincareOperator)
+    ENDIF(VISIT_PYTHON_SCRIPTING)
+
+    IF(VISIT_JAVA)
+        ADD_CUSTOM_TARGET(JavaPoincare ALL ${CMAKE_Java_COMPILER} ${CMAKE_Java_FLAGS} -d ${VISIT_BINARY_DIR}/java -classpath ${VISIT_BINARY_DIR}/java PoincareAttributes.java)
+        ADD_DEPENDENCIES(JavaPoincare JavaClient)
+    ENDIF(VISIT_JAVA)
+ENDIF(NOT VISIT_SERVER_COMPONENTS_ONLY AND NOT VISIT_ENGINE_ONLY AND NOT VISIT_DBIO_ONLY)
+
+ADD_LIBRARY(EPoincareOperator_ser ${LIBE_SOURCES})
+TARGET_LINK_LIBRARIES(EPoincareOperator_ser visitcommon avtexpressions_ser avtfilters_ser avtpipeline_ser )
+SET(INSTALLTARGETS ${INSTALLTARGETS} EPoincareOperator_ser)
+
+IF(VISIT_PARALLEL)
+    ADD_PARALLEL_LIBRARY(EPoincareOperator_par ${LIBE_SOURCES})
+    TARGET_LINK_LIBRARIES(EPoincareOperator_par visitcommon avtexpressions_par avtfilters_par avtpipeline_par )
+    SET(INSTALLTARGETS ${INSTALLTARGETS} EPoincareOperator_par)
+ENDIF(VISIT_PARALLEL)
+
+VISIT_INSTALL_OPERATOR_PLUGINS(${INSTALLTARGETS})
+VISIT_PLUGIN_TARGET_RTOD(operators ${INSTALLTARGETS})
+VISIT_PLUGIN_TARGET_FOLDER(operators Poincare ${INSTALLTARGETS})
+

operators/Poincare/FieldlineAnalyzerLib.h

+/*
+   For more information, please see: http://software.sci.utah.edu
+
+   The MIT License
+
+   Copyright (c) 2009 Scientific Computing and Imaging Institute,
+   University of Utah.
+
+   License for the specific language governing rights and limitations under
+   Permission is hereby granted, free of charge, to any person obtaining a
+   copy of this software and associated documentation files (the "Software"),
+   to deal in the Software without restriction, including without limitation
+   the rights to use, copy, modify, merge, publish, distribute, sublicense,
+   and/or sell copies of the Software, and to permit persons to whom the
+   Software is furnished to do so, subject to the following conditions:
+
+   The above copyright notice and this permission notice shall be included
+   in all copies or substantial portions of the Software.
+
+   THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
+   OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+   FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+   THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+   LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+   FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+   DEALINGS IN THE SOFTWARE.
+*/
+
+
+/*
+ *  FieldlineAnalyzer.h:
+ *
+ *  Written by:
+ *   Allen Sanderson
+ *   SCI Institute
+ *   University of Utah
+ *   September 2006
+ *
+ */
+
+#if !defined(FieldlineAnalyzerLib_h)
+#define FieldlineAnalyzerLib_h
+
+#define STRAIGHTLINE_SKELETON 1
+
+#ifdef STRAIGHTLINE_SKELETON
+#include "skelet.h"
+#endif
+
+#include <avtVector.h>
+#include <DebugStream.h>
+
+typedef avtVector Point ;
+typedef avtVector Vector;
+
+#include <vector>
+
+struct WindingPairStat {
+  unsigned int toroidal;
+  unsigned int poloidal;
+  double stat;
+  int ranking;
+};
+
+
+class FieldlineProperties;
+
+#include <avtPoincareIC.h>
+
+#ifndef POINCARE_FIELDLINE_PROPERTIES_H
+#define POINCARE_FIELDLINE_PROPERTIES_H
+
+class WindingPair {
+
+public:
+  WindingPair( unsigned int t, unsigned int p )
+  {
+    toroidal = t;
+    poloidal = p;
+  };
+
+  unsigned int toroidal;
+  unsigned int poloidal;  
+};
+
+
+class FieldlineProperties {
+
+public:
+
+  FieldlineProperties()
+  {
+    type = FieldlineProperties::UNKNOWN_TYPE;
+
+    analysisMethod = FieldlineProperties::DEFAULT_METHOD;
+    searchState    = FieldlineProperties::NO_SEARCH;
+    analysisState  = FieldlineProperties::UNKNOWN_ANALYSIS;
+
+    source = FieldlineProperties::UNKNOWN_TYPE;
+    
+    iteration = 0;
+
+    safetyFactor = 0;
+
+    toroidalWinding = 0;
+    poloidalWinding = 0;
+
+    toroidalWindingP = 0;
+    poloidalWindingP = 0;
+
+    toroidalResonance = 0;
+    poloidalResonance = 0;
+
+    windingGroupOffset = 0;
+    islands = 0;
+    islandGroups = 0;
+
+    nnodes  = 0;
+    
+    rationalSurfaceTolerance = 0;
+
+    maxPunctures      = 0;
+    numPunctures      = 0;
+    nPuncturesNeeded  = 0;
+
+    parentOPointIC = 0;
+    childOPointIC = 0;
+  };
+
+enum FieldlineType { UNKNOWN_TYPE  = 0,
+
+                     PERIODIC = 0x0010,
+                     RATIONAL = 0x0010,
+
+                     O_POINT  = 0x0011,
+                     X_POINT  = 0x0012,
+
+                     
+                     QUASI_PERIODIC = 0x0060,
+                     IRRATIONAL     = 0x0060,
+
+                     FLUX_SURFACE   = 0x0020,
+
+                     ISLAND_CHAIN                    = 0x0040,
+
+                     ISLAND_PRIMARY_CHAIN            = 0x0040,
+                     ISLAND_SECONDARY_CHAIN          = 0x0042,
+
+                     ISLAND_PRIMARY_SECONDARY_AXIS   = 0x0041,
+                     ISLAND_SECONDARY_SECONDARY_AXIS = 0x0043,
+                     
+                     CHAOTIC = 30 };
+  
+enum AnalysisMethod { UNKNOWN_METHOD = 0,
+                      DEFAULT_METHOD = 1,
+
+                      RATIONAL_SEARCH   = 10,
+                      RATIONAL_MINIMIZE = 11,
+                      RATIONAL_BRACKET  = 12 }; //Remove a curve from continueExecute logic
+
+enum AnalysisState { UNKNOWN_ANALYSIS = 0,
+
+                     COMPLETED  = 2,
+                     TERMINATED = 3,
+                     
+                     OVERRIDE = 5,
+
+                     DELETE   = 7,
+
+                     ADDING_POINTS = 10,
+
+                     ADD_O_POINTS = 15,
+                     ADD_X_POINTS = 16,
+
+                     ADD_BOUNDARY_POINT = 17 };
+
+enum SearchState { UNKNOWN_SEARCH = 0,
+
+                   NO_SEARCH = 1,
+
+                   ////// Code for island width search
+                   ISLAND_O_POINT,
+                   ISLAND_BOUNDARY_SEARCH,
+
+                   ////// Code for island width search
+                      
+                   ////// Code for rational surface search
+                   ORIGINAL_RATIONAL = 100,
+                   SEARCHING_SEED,
+                   WAITING_SEED,
+                   FINISHED_SEED,
+                   MINIMIZING_A      = 105,  // Used to bracket the minimum
+                   MINIMIZING_B,
+                   MINIMIZING_C,
+                   MINIMIZING_X0     = 110, // Used for Golden search routine
+                   MINIMIZING_X1,
+                   MINIMIZING_X2,
+                   MINIMIZING_X3,
+                   BRACKETING_A      = 120, //Used to bracket the minimum
+                   BRACKETING_B,
+                   BRACKETING_C
+                      ////// Code for rational surface search
+};
+
+public:
+
+  FieldlineType type;
+
+  FieldlineType source;
+
+  ////// Code for rational surface search
+  AnalysisMethod analysisMethod;
+
+  AnalysisState analysisState;
+
+  ////// Code for rational surface search
+  SearchState searchState;
+
+  unsigned int iteration;
+
+  double safetyFactor;
+
+  // Base number of transits
+  unsigned int toroidalWinding;
+  unsigned int poloidalWinding;
+
+  // Secondary axis number of transits
+  unsigned int toroidalWindingP;
+  unsigned int poloidalWindingP;
+
+  // Number of transists when an island to get back to the initial puncture.
+  unsigned int toroidalPeriod;
+  unsigned int poloidalPeriod;
+
+  // Resonance periods 
+
+  // When a surface resonances equal 1
+
+  // When a primary island the resonances equal the base number of
+  // windings and the toroidal resonance and the base toroidal winding both
+  // equal the number of islands.
+
+  // When secondary islands the toroial resonance is the total number
+  // of islands and the toroidal resonance divided by the base
+  // toroidal winding equals the number of island on each group.
+
+  unsigned int toroidalResonance;
+  unsigned int poloidalResonance;
+
+  std::vector< WindingPair > windingPairs;
+
+  std::map< WindingPair, unsigned int > topWindingPairs;
+
+  unsigned int windingGroupOffset;
+  unsigned int islands;
+  unsigned int islandGroups;
+
+  // If a surface it's overlap is found geometrically
+  // If an island (primary or secondary) toroidalPeriod / toroidalResonance
+  float nnodes;
+
+  unsigned int maxPunctures;
+  unsigned int numPunctures;
+  unsigned int nPuncturesNeeded;
+
+  // Rational Surface periodicity measures
+  double rationalSurfaceTolerance;
+
+  // Seeds for islands
+  avtVector lastSeedPoint;
+  std::vector< avtVector > seedPoints;
+
+  ////// Code for island width search
+  bool pastFirstSearchFailure;
+  double islandWidth;
+  double searchBaseDelta;
+  double searchDelta;
+  double searchIncrement;
+  double searchMagnitude;
+  avtVector searchNormal;
+  avtPoincareIC* parentOPointIC;
+  avtPoincareIC* childOPointIC;
+
+  unsigned int baseToroidalWinding;
+  unsigned int basePoloidalWinding;
+
+  ////// Code for island width search
+
+  ////// Code for rational surface search
+  // The rational points bounding the location of the minimization action
+  avtVector rationalPt1;
+  avtVector rationalPt2;
+
+  std::vector< avtPoincareIC *> *children;
+  ////// Code for rational surface search
+};
+#endif
+
+
+class FieldlineLib
+{
+public:
+  Point interpert( Point lastPt, Point currPt, double t );
+
+  int ccw( Vector v0, Vector v1 );
+
+  int intersect( Point l0_p0, Point l0_p1,
+                 Point l1_p0, Point l1_p1 );
+
+  void convexHull( std::vector< std::pair< Point, unsigned int > > &hullPts,
+                   unsigned int &m,
+                   unsigned int npts,
+                   int dir );
+
+  bool hullCheck( std::vector< Point > &points,
+                  int &direction);
+
+  unsigned int isPrime( unsigned int a );
+
+  unsigned int GCD( unsigned int a, unsigned int b );
+
+  unsigned int GCD( std::vector< unsigned int > values,
+                    unsigned int &freq,
+                    unsigned int minGCD = 1 );
+
+  unsigned int ResonanceCheck( std::vector< std::pair< unsigned int, double > > &stats,
+                              unsigned int baseResonance,
+                              unsigned int max_samples = 3 );
+
+  Point circle(Point &pt1, Point &pt2, Point &pt3);
+
+  bool IsPerpendicular(Point &pt1, Point &pt2, Point &pt3);
+
+  Point CalcCircle(Point &pt1, Point &pt2, Point &pt3);
+
+  bool
+  IntersectCheck( std::vector< Point >& points,
+                  unsigned int nbins,
+                  unsigned int skip  );
+
+  unsigned int Blankinship( unsigned int toroidalWinding,
+                            unsigned int poloidalWinding,
+                            unsigned int skip   = 1 );
+
+  void rotationalSumStats( std::vector< double > &rotationalSums,
+                           double &averageRotationalSum,
+                           double &stdDev );
+  template< class TYPE >
+  void safetyFactorStats( std::vector< TYPE > &poloidalWindingCounts,
+                          double &averageSafetyFactor,
+                          double &stdDev );
+
+  void SortWindingPairStats( std::vector< WindingPairStat > &windingPairStats,
+                             bool reverse = false );
+
+  void RankWindingPairStats( std::vector< WindingPairStat > &windingPairStats,
+                             bool LT = true );
+
+  void poloidalWindingCheck( std::vector< unsigned int > &poloidalWindingset,
+                             std::vector< WindingPairStat > &windingPairStats );
+
+  void
+  periodicityStats( std::vector< Point >& points,
+                    std::vector< std::pair< unsigned int, double > >& stats,
+                    unsigned int max_period,
+                    unsigned int checkType );
+
+
+  void thresholdStats( std::vector< std::pair< unsigned int, double > >& stats,
+                       bool erase,
+                       unsigned int checkType );
+
+  double
+  calculateSumOfSquares( std::vector< Point >& poloidalWinding_points,
+                         unsigned int poloidalWinding,
+                         unsigned int checkType );
+
+  bool
+  rationalCheck( std::vector< Point >& points,
+                 unsigned int toroidalWinding,
+                 unsigned int &nnodes,
+                 float delta=0.01 );
+
+  bool
+  islandChecks( std::vector< Point >& points,
+                unsigned int toroidalWinding,
+                unsigned int &islands,
+                unsigned int &nnodes,
+                bool &complete );
+
+  void
+  getPunctures( std::vector< Point > &ptList,
+                Vector planeN,
+                std::vector< Point > &puncturePts );
+
+  void
+  getFieldlineBaseValues( std::vector< Point > &ptList,
+                          std::vector< Point > &poloidal_puncture_pts,
+                          std::vector< Point > &ridgeline_points,
+                          std::vector< double > &rotationalSums,
+                          std::vector< unsigned int > &poloidalWindingCounts,
+                          float &delta,
+                          unsigned int OLineToroidalWinding );
+
+  Point getAxisPt( Point pt, double phi, double toroidalBase );
+
+  void
+  GetBaseWindingPairs( std::vector< unsigned int > &poloidalWindingCounts,
+                       std::vector< Point > &poloidal_puncture_pts,
+                       std::vector< WindingPairStat > &baseWindingPairStats,
+                       double &windingPairConfidence,
+                       unsigned int &toroidalWindingMax,
+                       unsigned int &poloidalWindingMax,
+                       unsigned int &windingNumberMatchIndex );
+
+  void
+  GetPeriodWindingPairs( std::vector< WindingPairStat > &baseWindingPairStats,
+                         std::vector< WindingPairStat > &periodWindingPairStats,
+                         std::vector< std::pair< unsigned int, double > > &toroidalStats,
+                         std::vector< std::pair< unsigned int, double > > &poloidalStats );
+
+  void
+  fieldlineProperties( std::vector< Point > &ptList,
+                       FieldlineProperties &properties,
+                       unsigned int overrideToroidalWinding,
+                       unsigned int overridePoloidalWinding,
+                       unsigned int maxToroidalWinding,
+                       double windingPairConfidence,
+                       double rationalSurfaceFactor,
+                       bool detectIslandCenters,
+                       unsigned int OLineToroidalWinding,
+                       std::string OLineAxisFilename );
+
+  void
+  fieldlineProperties2( std::vector< Point > &ptList,
+                        double rationalSurfaceFactor,
+                        FieldlineProperties &fi );
+
+  void findIslandCenters( std::vector< Point > &puncturePts,
+                          unsigned int islands,
+                          unsigned int offset,
+                          unsigned int nnodes,
+                          unsigned int moduloValue,
+                          std::vector< Point > &centers,
+                          std::vector< Vector > &axis );
+
+  Point findSkeletonCenter( Skeleton::Skeleton &s,
+                            unsigned int nHullPts );
+
+  unsigned int
+  islandProperties( std::vector< Point > &points,
+                    Vector &baseCentroid,
+                    unsigned int &startIndex,
+                    unsigned int &middleIndex,
+                    unsigned int &stopIndex,
+                    unsigned int &nodes );