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Cleaning up kernel file

master
Trevor Irons 7 년 전
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56bca80f3b
1개의 변경된 파일35개의 추가작업 그리고 31개의 파일을 삭제
  1. 35
    31
      include/KernelV0.h

+ 35
- 31
include/KernelV0.h 파일 보기

@@ -54,8 +54,9 @@ namespace Lemma {
54 54
 
55 55
     /**
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      * \ingroup Merlin
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-     * \brief
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-     * \details
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+     * \brief  Calculated the initial amplitude imaging kernel of a sNMR experiment
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+     * \details This class calculates the imaging kernel for a free induction decay
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+     *          pulse. The methodology follows from Weichman et al., 2000.
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      */
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     class KernelV0 : public LemmaObject {
61 62
 
@@ -108,7 +109,7 @@ namespace Lemma {
108 109
          */
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         virtual YAML::Node Serialize() const;
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-        /*
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+        /**
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          *  Factory method for generating concrete class.
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          *  @return a std::shared_ptr of type KernelV0
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          */
@@ -125,6 +126,32 @@ namespace Lemma {
125 126
         // ====================  OPERATIONS    =======================
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         /**
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+         *   Calculates a single imaging kernel, however, phased arrays are supported
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+         *   so that more than one transmitter and/or receiver can be specified.
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+         *   @param[in] tx is the list of transmitters to use for a kernel, use the same labels as
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+         *              used in PushCoil.
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+         *   @param[in] rx is the list of receivers to use for a kernel, use the same labels as
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+         *              used in PushCoil. @see PushCoil
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+         *   @param[in] vtkOutput generates a VTK hyperoctree file as well, useful for visualization.
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+         *              requires compilation of Lemma with VTK. The VTK files can become very large.
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+         */
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+        void CalculateK0 (const std::vector< std::string >& tx, const std::vector< std::string >& rx,
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+                bool vtkOutput=false );
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+
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+        /**
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+         *  Aligns the kernel settings with an Akvo Processed dataset.
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+         */
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+        void AlignWithAkvoDataset( const YAML::Node& node ) ;
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+
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+        /**
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+         *   Assign transmiter coils
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+         */
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+        inline void PushCoil( const std::string& label, std::shared_ptr<PolygonalWireAntenna> ant ) {
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+            TxRx[label] = ant;
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+        }
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+
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+        // ====================  INQUIRY       =======================
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+        /**
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          * @return std::shared_ptr<LayeredEarthEM>
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          */
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         inline std::shared_ptr<LayeredEarthEM> GetSigmaModel (  ) {
@@ -171,31 +198,6 @@ namespace Lemma {
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         }		// -----  end of method KernelV0::SetIntegrationOrigin  -----
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         /**
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-         *  Aligns the kernel settings with an Akvo Processed dataset.
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-         */
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-        void AlignWithAkvoDataset( const YAML::Node& node ) ;
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-
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-        /**
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-         *   Assign transmiter coils
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-         */
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-        inline void PushCoil( const std::string& label, std::shared_ptr<PolygonalWireAntenna> ant ) {
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-            TxRx[label] = ant;
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-        }
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-
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-        /**
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-         *   Calculates a single imaging kernel, however, phased arrays are supported
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-         *   so that more than one transmitter and/or receiver can be specified.
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-         *   @param[in] tx is the list of transmitters to use for a kernel, use the same labels as
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-         *              used in PushCoil.
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-         *   @param[in] rx is the list of receivers to use for a kernel, use the same labels as
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-         *              used in PushCoil. @see PushCoil
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-         *   @param[in] vtkOutput generates a VTK hyperoctree file as well, useful for visualization.
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-         *              requires compilation of Lemma with VTK. The VTK files can become very large.
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-         */
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-        void CalculateK0 (const std::vector< std::string >& tx, const std::vector< std::string >& rx,
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-                bool vtkOutput=false );
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-
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-        /**
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          *  Sets the temperature, which has implications in calculation of \f$ M_N^{(0)}\f$. Units in
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          *  Kelvin.
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          */
@@ -205,12 +207,15 @@ namespace Lemma {
205 207
 
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         /**
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          *  Sets the tolerance to use for making the adaptive mesh
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-         *
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+         *  @param[in] ttol is the tolerance to use
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          */
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         inline void SetTolerance(const Real& ttol) {
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             tol = ttol;
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         }
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+        /**
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+         *  @param[in] taup sets the pulse duration
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+         */
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         inline void SetPulseDuration(const Real& taup) {
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             Taup = taup;
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         }
@@ -223,7 +228,6 @@ namespace Lemma {
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             Interfaces = iface;
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         }
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-        // ====================  INQUIRY       =======================
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         /**
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          *  Returns the name of the underlying class, similiar to Python's type
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          *  @return string of class name
@@ -302,7 +306,7 @@ namespace Lemma {
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         MatrixXcr   Kern;
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         std::shared_ptr< LayeredEarthEM >         SigmaModel = nullptr;
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-        std::shared_ptr< FieldPoints >            cpoints;
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+        std::shared_ptr< FieldPoints >            cpoints = nullptr;
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         std::map< std::string , std::shared_ptr< PolygonalWireAntenna > >  TxRx;
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         std::map< std::string , std::shared_ptr< EMEarth1D > >             EMEarths;

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