Merge pull request #20 from wvaarle/matlab-get-geometry

'get_geometry' functions in the matlab layer

14 files changed, 98 insertions, 41 deletions

diff --git a/include/astra/ConeProjectionGeometry3D.h b/include/astra/ConeProjectionGeometry3D.h
index 2a0474d..00e72ce 100644
--- a/include/astra/ConeProjectionGeometry3D.h
+++ b/include/astra/ConeProjectionGeometry3D.h
@@ -40,8 +40,8 @@ namespace astra
  * \par XML Configuration
  * \astra_xml_item{DetectorRowCount, int, Number of detectors for each projection.}
  * \astra_xml_item{DetectorColCount, int, Number of detectors for each projection.}
- * \astra_xml_item{DetectorWidth, float, Width of each detector.}
- * \astra_xml_item{DetectorHeight, float, Width of each detector.}
+ * \astra_xml_item{DetectorSpacingX, float, Width of each detector.}
+ * \astra_xml_item{DetectorSpacingY, float, Width of each detector.}
  * \astra_xml_item{ProjectionAngles, vector of float, projection angles in radians.}
  * \astra_xml_item{DistanceOriginDetector, float, Distance between the center of rotation and the detectorarray.}
  * \astra_xml_item{DistanceOriginSource, float, Distance between the center of rotation the the x-ray source.}
@@ -51,8 +51,8 @@ namespace astra
  *		proj_geom = astra_struct('cone');\n
  *		proj_geom.DetectorRowCount = 512;\n
  *		proj_geom.DetectorColCount = 512;\n
- *		proj_geom.DetectorWidth = 1.0;\n
- *		proj_geom.DetectorHeight = 1.0;\n
+ *		proj_geom.DetectorSpacingX = 1.0;\n
+ *		proj_geom.DetectorSpacingY = 1.0;\n
  *		proj_geom.ProjectionAngles = linspace(0,pi,100);\n
  *		proj_geom.DistanceOriginDetector = 10000;\n
  *		proj_geom.DistanceOriginSource = 10000;\n
@@ -148,6 +148,12 @@ public:
 	 */
 	virtual bool isEqual(const CProjectionGeometry3D*) const;
 
+	/** Get all settings in a Config object.
+	 *
+	 * @return Configuration Object.
+	 */
+	virtual Config* getConfiguration() const;
+
 	/** Returns true if the type of geometry defined in this class is the one specified in _sType.
 	 *
 	 * @param _sType geometry type to compare to.
@@ -155,12 +161,6 @@ public:
 	 */
 	virtual bool isOfType(const std::string& _sType) const;
 
-	/** Turn this object into an XML object.
-	 *
-	 * @param _sNode The XML object to fill.
-	 */
-	virtual void toXML(XMLNode* _sNode) const;
-
 	/** Returns the distance from the origin of the coordinate system to the source.
 	 *
 	 * @return Distance from the origin of the coordinate system to the source
diff --git a/include/astra/ConeVecProjectionGeometry3D.h b/include/astra/ConeVecProjectionGeometry3D.h
index 68a80ef..e82a411 100644
--- a/include/astra/ConeVecProjectionGeometry3D.h
+++ b/include/astra/ConeVecProjectionGeometry3D.h
@@ -56,7 +56,7 @@ namespace astra
  * to a single projection, and consists of:
  * ( srcX, srcY, srcZ, dX, dY, dZ, uX, uY, uZ, vX, vY, vZ )
  *      src: the ray source
- *      d  : the corner of the detector
+ *      d  : the centre of the detector plane
  *      u  : the vector from detector pixel (0,0) to (0,1)
  *      v  : the vector from detector pixel (0,0) to (1,0)
  */
@@ -128,6 +128,12 @@ public:
 	 */
 	virtual bool isEqual(const CProjectionGeometry3D*) const;
 
+	/** Get all settings in a Config object.
+	 *
+	 * @return Configuration Object.
+	 */
+	virtual Config* getConfiguration() const;
+
 	/** Returns true if the type of geometry defined in this class is the one specified in _sType.
 	 *
 	 * @param _sType geometry type to compare to.
@@ -135,12 +141,6 @@ public:
 	 */
 	 virtual bool isOfType(const std::string& _sType) const;
 
-	/** Turn this object into an XML object.
-	 *
-	 * @param _sNode The XML object to fill.
-	 */
-	 virtual void toXML(XMLNode* _sNode) const;
-
 	 /**
 	  * Returns a vector giving the projection direction for a projection and detector index
 	  */
diff --git a/include/astra/Config.h b/include/astra/Config.h
index 647462b..9893c90 100644
--- a/include/astra/Config.h
+++ b/include/astra/Config.h
@@ -31,6 +31,7 @@ $Id$
 
 #include "Globals.h"
 #include "XMLNode.h"
+#include "XMLDocument.h"
 
 #include <set>
 
@@ -46,6 +47,8 @@ struct _AstraExport Config {
 	Config(XMLNode* _self);
 	~Config();
 
+	void initialize(std::string rootname);
+
 	XMLNode* self;
 	XMLNode* global;
 };
diff --git a/include/astra/FanFlatProjectionGeometry2D.h b/include/astra/FanFlatProjectionGeometry2D.h
index 8f22c35..180fe68 100644
--- a/include/astra/FanFlatProjectionGeometry2D.h
+++ b/include/astra/FanFlatProjectionGeometry2D.h
@@ -140,6 +140,12 @@ public:
 	 */
 	 virtual bool isOfType(const std::string& _sType);
 
+	/** Get all settings in a Config object.
+	 *
+	 * @return Configuration Object.
+	 */
+	virtual Config* getConfiguration() const;
+
     /** Return true if this geometry instance is the same as the one specified.
 	 *
 	 * @return true if this geometry instance is the same as the one specified.
diff --git a/include/astra/FanFlatVecProjectionGeometry2D.h b/include/astra/FanFlatVecProjectionGeometry2D.h
index 85c994f..ee85408 100644
--- a/include/astra/FanFlatVecProjectionGeometry2D.h
+++ b/include/astra/FanFlatVecProjectionGeometry2D.h
@@ -53,6 +53,14 @@ namespace astra
  *		proj_geom.DetectorCount = 512;\n
  *		proj_geom.Vectors = V;\n
  * }
+ *
+ * \par Vectors
+ * Vectors is a matrix containing the actual geometry. Each row corresponds
+ * to a single projection, and consists of:
+ * ( srcX, srcY, srcZ, dX, dY uX, uY)
+ *      src: the ray source
+ *      d  : the centre of the detector array
+ *      u  : the vector from detector 0 to detector 1
  */
 class _AstraExport CFanFlatVecProjectionGeometry2D : public CProjectionGeometry2D
 {
@@ -126,6 +134,13 @@ public:
 	 */
 	virtual bool isEqual(CProjectionGeometry2D*) const;
 
+	/** Get all settings in a Config object.
+	 *
+	 * @return Configuration Object.
+	 */
+	virtual Config* getConfiguration() const;
+
+
 	/** Get the value for t and theta, based upon the row and column index.
 	 *
 	 * @param _iRow		row index 
diff --git a/include/astra/ParallelProjectionGeometry2D.h b/include/astra/ParallelProjectionGeometry2D.h
index ed9d228..2f7d36f 100644
--- a/include/astra/ParallelProjectionGeometry2D.h
+++ b/include/astra/ParallelProjectionGeometry2D.h
@@ -136,6 +136,12 @@ public:
 	 */
 	 virtual bool isOfType(const std::string& _sType);
 
+	/** Get all settings in a Config object.
+	 *
+	 * @return Configuration Object.
+	 */
+	virtual Config* getConfiguration() const;
+
  	/**
 	 * Returns a vector describing the direction of a ray belonging to a certain detector,
 	 *   the direction is the same for all detectors in one projection 
diff --git a/include/astra/ParallelProjectionGeometry3D.h b/include/astra/ParallelProjectionGeometry3D.h
index da60617..72401e5 100644
--- a/include/astra/ParallelProjectionGeometry3D.h
+++ b/include/astra/ParallelProjectionGeometry3D.h
@@ -41,8 +41,8 @@ namespace astra
  * \par XML Configuration
  * \astra_xml_item{DetectorRowCount, int, Number of detectors for each projection.}
  * \astra_xml_item{DetectorColCount, int, Number of detectors for each projection.}
- * \astra_xml_item{DetectorWidth, float, Width of each detector.}
- * \astra_xml_item{DetectorHeight, float, Width of each detector.}
+ * \astra_xml_item{DetectorSpacingX, float, Width of each detector.}
+ * \astra_xml_item{DetectorSpacingY, float, Width of each detector.}
  * \astra_xml_item{ProjectionAngles, vector of float, projection angles in radians.}
  *
  * \par MATLAB example
@@ -50,8 +50,8 @@ namespace astra
  *		proj_geom = astra_struct('parallel');\n
  *		proj_geom.DetectorRowCount = 512;\n
  *		proj_geom.DetectorColCount = 512;\n
- *		proj_geom.DetectorWidth = 1.0;\n
- *		proj_geom.DetectorHeight = 1.0;\n
+ *		proj_geom.DetectorSpacingX = 1.0;\n
+ *		proj_geom.DetectorSpacingY = 1.0;\n
  *		proj_geom.ProjectionAngles = linspace(0,pi,100);\n
  * }
  */
@@ -129,6 +129,12 @@ public:
 	 */
 	virtual bool isEqual(const CProjectionGeometry3D*) const;
 
+	/** Get all settings in a Config object.
+	 *
+	 * @return Configuration Object.
+	 */
+	virtual Config* getConfiguration() const;
+
 	/** Returns true if the type of geometry defined in this class is the one specified in _sType.
 	 *
 	 * @param _sType geometry type to compare to.
@@ -136,12 +142,6 @@ public:
 	 */
 	 virtual bool isOfType(const std::string& _sType) const;
 
-	/** Turn this object into an XML object.
-	 *
-	 * @param _sNode The XML object to fill.
-	 */
-	 virtual void toXML(XMLNode* _sNode) const;
-
 	 /**
 	  * Returns a vector giving the projection direction for a projection and detector index
 	  */
diff --git a/include/astra/ParallelVecProjectionGeometry3D.h b/include/astra/ParallelVecProjectionGeometry3D.h
index fbc2112..5a63249 100644
--- a/include/astra/ParallelVecProjectionGeometry3D.h
+++ b/include/astra/ParallelVecProjectionGeometry3D.h
@@ -55,7 +55,7 @@ namespace astra
  * to a single projection, and consists of:
  * ( rayX, rayY, rayZ, dX, dY, dZ, uX, uY, uZ, vX, vY, vZ )
  *      ray: the ray direction
- *      d  : the corner of the detector
+ *      d  : the centre of the detector plane
  *      u  : the vector from detector pixel (0,0) to (0,1)
  *      v  : the vector from detector pixel (0,0) to (1,0)
  */
@@ -128,6 +128,12 @@ public:
 	 */
 	virtual bool isEqual(const CProjectionGeometry3D*) const;
 
+	/** Get all settings in a Config object.
+	 *
+	 * @return Configuration Object.
+	 */
+	virtual Config* getConfiguration() const;
+
 	/** Returns true if the type of geometry defined in this class is the one specified in _sType.
 	 *
 	 * @param _sType geometry type to compare to.
@@ -135,12 +141,6 @@ public:
 	 */
 	 virtual bool isOfType(const std::string& _sType) const;
 
-	/** Turn this object into an XML object.
-	 *
-	 * @param _sNode The XML object to fill.
-	 */
-	 virtual void toXML(XMLNode* _sNode) const;
-
 	 /**
 	  * Returns a vector giving the projection direction for a projection and detector index
 	  */
diff --git a/include/astra/ProjectionGeometry2D.h b/include/astra/ProjectionGeometry2D.h
index 303ca0a..b8324e2 100644
--- a/include/astra/ProjectionGeometry2D.h
+++ b/include/astra/ProjectionGeometry2D.h
@@ -157,6 +157,12 @@ public:
 	 */
 	virtual bool isEqual(CProjectionGeometry2D*) const = 0;
 
+	/** Get all settings in a Config object.
+	 *
+	 * @return Configuration Object.
+	 */
+	virtual Config* getConfiguration() const = 0;
+
 	/** Get the number of projection angles.
 	 *
 	 * @return Number of projection angles
diff --git a/include/astra/ProjectionGeometry3D.h b/include/astra/ProjectionGeometry3D.h
index 41b1cb7..19ac3ab 100644
--- a/include/astra/ProjectionGeometry3D.h
+++ b/include/astra/ProjectionGeometry3D.h
@@ -187,6 +187,12 @@ public:
 	 */
 	virtual bool isEqual(const CProjectionGeometry3D *) const = 0;
 
+	/** Get all settings in a Config object.
+	 *
+	 * @return Configuration Object.
+	 */
+	virtual Config* getConfiguration() const = 0;
+
 	/** Get the number of projections.
 	 *
 	 * @return Number of projections
@@ -322,12 +328,6 @@ public:
 	 */
 	 virtual bool isOfType(const std::string& _sType) const = 0;
 
-	/** Turn this object into an XML object.
-	 *
-	 * @param _sNode The XML object to fill.
-	 */
-	 virtual void toXML(XMLNode* _sNode) const = 0;
-
 	 /**
 	  * Returns a vector giving the projection direction for a projection and detector index
 	  */
diff --git a/include/astra/SparseMatrixProjectionGeometry2D.h b/include/astra/SparseMatrixProjectionGeometry2D.h
index 36964be..d56f95e 100644
--- a/include/astra/SparseMatrixProjectionGeometry2D.h
+++ b/include/astra/SparseMatrixProjectionGeometry2D.h
@@ -103,7 +103,6 @@ public:
 	 * @param _pMatrix Pointer to a CSparseMatrix. The caller is responsible for keeping this matrix valid until it is no longer required.
 	 * @return initialization successful?
 	 */
-
 	bool setMatrix(CSparseMatrix* _pMatrix);
 
 	/** Get a pointer to the associated sparse matrix.
@@ -128,6 +127,13 @@ public:
 	 */
 	 virtual bool isOfType(const std::string& _sType);
 
+	/** Get all settings in a Config object.
+	 *
+	 * @return Configuration Object.
+	 */
+	virtual Config* getConfiguration() const;
+
+
 	/**
 	 * Returns a vector describing the direction of a ray belonging to a certain detector
 	 *
diff --git a/include/astra/VolumeGeometry2D.h b/include/astra/VolumeGeometry2D.h
index fa0528d..28703d5 100644
--- a/include/astra/VolumeGeometry2D.h
+++ b/include/astra/VolumeGeometry2D.h
@@ -205,6 +205,12 @@ public:
 	 */
 	virtual bool isEqual(CVolumeGeometry2D*) const;
 
+	/** Get all settings in a Config object.
+	 *
+	 * @return Configuration Object.
+	 */
+	virtual Config* getConfiguration() const;
+
 	/** Get the number of columns in the volume grid.
 	 *
 	 * @return Number of columns in the volume grid.
diff --git a/include/astra/VolumeGeometry3D.h b/include/astra/VolumeGeometry3D.h
index d5c8fff..ff94844 100644
--- a/include/astra/VolumeGeometry3D.h
+++ b/include/astra/VolumeGeometry3D.h
@@ -246,6 +246,12 @@ public:
 	 */
 	virtual bool isEqual(const CVolumeGeometry3D*) const;
 
+	/** Get all settings in a Config object.
+	 *
+	 * @return Configuration Object.
+	 */
+	virtual Config* getConfiguration() const;
+
 	/** Get the number of columns in the volume grid.
 	 *
 	 * @return Number of columns in the volume grid.
diff --git a/include/astra/XMLDocument.h b/include/astra/XMLDocument.h
index c6f1b9a..869e1a3 100644
--- a/include/astra/XMLDocument.h
+++ b/include/astra/XMLDocument.h
@@ -86,6 +86,9 @@ public:
 	 */
 	void saveToFile(string sFilename);
 
+	/** convert and XML DOM tree to a string
+	 */
+	std::string toString();
 
 private: