Merge pull request #52 from wjp/change_geometry3d

Add data3d('change_geometry')

8 files changed, 218 insertions, 1 deletions

diff --git a/include/astra/Float32ProjectionData3D.h b/include/astra/Float32ProjectionData3D.h
index 79b762e..329c9a4 100644
--- a/include/astra/Float32ProjectionData3D.h
+++ b/include/astra/Float32ProjectionData3D.h
@@ -196,6 +196,11 @@ public:
 	 * @return pointer to projection geometry.
 	 */
 	virtual CProjectionGeometry3D* getGeometry() const;
+
+	/** Change the projection geometry.
+	 *  Note that this can't change the dimensions of the data.
+	 */
+	virtual void changeGeometry(CProjectionGeometry3D* pGeometry);
 };
 
 
diff --git a/include/astra/Float32VolumeData3D.h b/include/astra/Float32VolumeData3D.h
index d8f0ae9..07df78f 100644
--- a/include/astra/Float32VolumeData3D.h
+++ b/include/astra/Float32VolumeData3D.h
@@ -214,6 +214,11 @@ public:
 	 * @return The geometry describing the data stored in this volume
 	 */
 	virtual CVolumeGeometry3D* getGeometry() const;
+
+	/** Change the projection geometry.
+	 *  Note that this can't change the dimensions of the data.
+	 */
+	virtual void changeGeometry(CVolumeGeometry3D* pGeometry);
 };
 
 //----------------------------------------------------------------------------------------
diff --git a/matlab/mex/astra_mex_data3d_c.cpp b/matlab/mex/astra_mex_data3d_c.cpp
index 7efbdab..6096adc 100644
--- a/matlab/mex/astra_mex_data3d_c.cpp
+++ b/matlab/mex/astra_mex_data3d_c.cpp
@@ -310,6 +310,112 @@ void astra_mex_data3d_get_geometry(int nlhs, mxArray* plhs[], int nrhs, const mx
 }
 
 //-----------------------------------------------------------------------------------------
+/** astra_mex_data3d('change_geometry', id, geom);
+ *
+ * Change the geometry of a 3d data object.
+ * id: identifier of the 3d data object as stored in the astra-library.
+ * geom: the new geometry struct, as created by astra_create_vol/proj_geom
+ */
+void astra_mex_data3d_change_geometry(int nlhs, mxArray* plhs[], int nrhs, const mxArray* prhs[])
+{
+	// parse input
+	if (nrhs < 3) {
+		mexErrMsgTxt("Not enough arguments.  See the help document for a detailed argument list. \n");
+		return;
+	}
+
+	// get data object
+	CFloat32Data3DMemory* pDataObject = NULL;
+	if (!checkID(mxGetScalar(prhs[1]), pDataObject)) {
+		mexErrMsgTxt("Data object not found or not initialized properly.\n");
+		return;
+	}
+
+	const mxArray * const geometry = prhs[2];
+
+	if (!checkStructs(geometry)) {
+		mexErrMsgTxt("Argument 3 is not a valid MATLAB struct.\n");
+		return;
+	}
+
+	CFloat32ProjectionData3D* pProjData = dynamic_cast<CFloat32ProjectionData3D*>(pDataObject);
+	if (pProjData) {
+		// Projection data
+
+		// Read geometry
+		astra::Config* cfg = structToConfig("ProjectionGeometry3D", geometry);
+		// FIXME: Change how the base class is created. (This is duplicated
+		// in Projector3D.cpp.)
+		std::string type = cfg->self->getAttribute("type");
+		astra::CProjectionGeometry3D* pGeometry = 0;
+		if (type == "parallel3d") {
+			pGeometry = new astra::CParallelProjectionGeometry3D();
+		} else if (type == "parallel3d_vec") {
+			pGeometry = new astra::CParallelVecProjectionGeometry3D();
+		} else if (type == "cone") {
+			pGeometry = new astra::CConeProjectionGeometry3D();
+		} else if (type == "cone_vec") {
+			pGeometry = new astra::CConeVecProjectionGeometry3D();
+		} else {
+			mexErrMsgTxt("Invalid geometry type.\n");
+			return;
+		}
+
+		if (!pGeometry->initialize(*cfg)) {
+			mexErrMsgTxt("Geometry class not initialized. \n");
+			delete pGeometry;
+			delete cfg;
+			return;
+		}
+		delete cfg;
+
+		// Check dimensions
+		if (pGeometry->getDetectorColCount() != pProjData->getDetectorColCount() ||
+		    pGeometry->getProjectionCount() != pProjData->getAngleCount() ||
+		    pGeometry->getDetectorRowCount() != pProjData->getDetectorRowCount())
+		{
+			mexErrMsgTxt("The dimensions of the data do not match those specified in the geometry. \n");
+			delete pGeometry;
+			return;
+		}
+
+		// If ok, change geometry
+		pProjData->changeGeometry(pGeometry);
+		delete pGeometry;
+	} else {
+		// Volume data
+		CFloat32VolumeData3D* pVolData = dynamic_cast<CFloat32VolumeData3D*>(pDataObject);
+		assert(pVolData);
+
+		// Read geometry
+		astra::Config* cfg = structToConfig("VolumeGeometry3D", geometry);
+		astra::CVolumeGeometry3D* pGeometry = new astra::CVolumeGeometry3D();
+		if (!pGeometry->initialize(*cfg))
+		{
+			mexErrMsgTxt("Geometry class not initialized. \n");
+			delete pGeometry;
+			delete cfg;
+			return;
+		}
+		delete cfg;
+
+				// Check dimensions
+		if (pGeometry->getGridColCount() != pVolData->getColCount() ||
+		    pGeometry->getGridRowCount() != pVolData->getRowCount() ||
+		    pGeometry->getGridSliceCount() != pVolData->getSliceCount())
+		{
+			mexErrMsgTxt("The dimensions of the data do not match those specified in the geometry. \n");
+			delete pGeometry;
+			return;
+		}
+
+		// If ok, change geometry
+		pVolData->changeGeometry(pGeometry);
+		delete pGeometry;
+	}
+}
+
+//-----------------------------------------------------------------------------------------
 /**
  * astra_mex_data3d('delete', did1, did2, ...);
  */
@@ -351,7 +457,7 @@ static void printHelp()
 {
 	mexPrintf("Please specify a mode of operation.\n");
 	mexPrintf("Valid modes: create, get, get_single, delete, clear, info\n");
-	mexPrintf("             dimensions\n");
+	mexPrintf("             dimensions, get_geometry, change_geometry\n");
 }
 
 
@@ -398,6 +504,8 @@ void mexFunction(int nlhs, mxArray* plhs[],
 		astra_mex_data3d_dimensions(nlhs, plhs, nrhs, prhs); 
 	} else if (sMode == std::string("get_geometry")) {
 		astra_mex_data3d_get_geometry(nlhs, plhs, nrhs, prhs);
+	} else if (sMode == std::string("change_geometry")) {
+		astra_mex_data3d_change_geometry(nlhs, plhs, nrhs, prhs);
 	} else {
 		printHelp();
 	}
diff --git a/python/astra/PyIncludes.pxd b/python/astra/PyIncludes.pxd
index 13329d1..1d8285b 100644
--- a/python/astra/PyIncludes.pxd
+++ b/python/astra/PyIncludes.pxd
@@ -201,12 +201,18 @@ cdef extern from "astra/VolumeGeometry3D.h" namespace "astra":
 		CVolumeGeometry3D()
 		bool initialize(Config)
 		Config * getConfiguration()
+		int getGridColCount()
+		int getGridRowCount()
+		int getGridSliceCount()
 
 cdef extern from "astra/ProjectionGeometry3D.h" namespace "astra":
 	cdef cppclass CProjectionGeometry3D:
 		CProjectionGeometry3D()
 		bool initialize(Config)
 		Config * getConfiguration()
+		int getProjectionCount()
+		int getDetectorColCount()
+		int getDetectorRowCount()
 
 
 cdef extern from "astra/Float32VolumeData3DMemory.h" namespace "astra":
@@ -214,6 +220,11 @@ cdef extern from "astra/Float32VolumeData3DMemory.h" namespace "astra":
 		CFloat32VolumeData3DMemory(CVolumeGeometry3D*)
 		CFloat32VolumeData3DMemory(CVolumeGeometry3D*, CFloat32CustomMemory*)
 		CVolumeGeometry3D* getGeometry()
+		void changeGeometry(CVolumeGeometry3D*)
+		int getRowCount()
+		int getColCount()
+		int getSliceCount()
+
 
 
 cdef extern from "astra/ParallelProjectionGeometry3D.h" namespace "astra":
@@ -240,6 +251,10 @@ cdef extern from "astra/Float32ProjectionData3DMemory.h" namespace "astra":
 		CFloat32ProjectionData3DMemory(CProjectionGeometry3D*, CFloat32CustomMemory*)
 		CFloat32ProjectionData3DMemory(CConeProjectionGeometry3D*, CFloat32CustomMemory*)
 		CProjectionGeometry3D* getGeometry()
+		void changeGeometry(CProjectionGeometry3D*)
+		int getDetectorColCount()
+		int getDetectorRowCount()
+		int getAngleCount()
 
 cdef extern from "astra/Float32Data3D.h" namespace "astra":
 	cdef cppclass CFloat32Data3D:
diff --git a/python/astra/data3d.py b/python/astra/data3d.py
index 4fdf9d7..e5ef6b0 100644
--- a/python/astra/data3d.py
+++ b/python/astra/data3d.py
@@ -112,6 +112,17 @@ def get_geometry(i):
     """
     return d.get_geometry(i)
 
+def change_geometry(i, geometry):
+    """Change the geometry of a 3D object.
+
+    :param i: ID of object.
+    :type i: :class:`int`
+    :param geometry: Volume or projection geometry.
+    :type geometry: :class:`dict`
+
+    """
+    return d.change_geometry(i, geometry)
+
 def dimensions(i):
     """Get dimensions of a 3D object.
 
diff --git a/python/astra/data3d_c.pyx b/python/astra/data3d_c.pyx
index f2c6e26..84472c1 100644
--- a/python/astra/data3d_c.pyx
+++ b/python/astra/data3d_c.pyx
@@ -139,6 +139,61 @@ def get_geometry(i):
         raise Exception("Not a known data object")
     return geom
 
+def change_geometry(i, geom):
+    cdef CFloat32Data3DMemory * pDataObject = dynamic_cast_mem(getObject(i))
+    cdef CFloat32ProjectionData3DMemory * pDataObject2
+    cdef CFloat32VolumeData3DMemory * pDataObject3
+    if pDataObject.getType() == THREEPROJECTION:
+        pDataObject2 = <CFloat32ProjectionData3DMemory * >pDataObject
+        # TODO: Reduce code duplication here
+        cfg = utils.dictToConfig(six.b('ProjectionGeometry'), geom)
+        tpe = wrap_from_bytes(cfg.self.getAttribute(six.b('type')))
+        if (tpe == "parallel3d"):
+            ppGeometry = <CProjectionGeometry3D*> new CParallelProjectionGeometry3D();
+        elif (tpe == "parallel3d_vec"):
+            ppGeometry = <CProjectionGeometry3D*> new CParallelVecProjectionGeometry3D();
+        elif (tpe == "cone"):
+            ppGeometry = <CProjectionGeometry3D*> new CConeProjectionGeometry3D();
+        elif (tpe == "cone_vec"):
+            ppGeometry = <CProjectionGeometry3D*> new CConeVecProjectionGeometry3D();
+        else:
+            raise Exception("Invalid geometry type.")
+        if not ppGeometry.initialize(cfg[0]):
+            del cfg
+            del ppGeometry
+            raise Exception('Geometry class not initialized.')
+        del cfg
+        if (ppGeometry.getDetectorColCount() != pDataObject2.getDetectorColCount() or \
+            ppGeometry.getProjectionCount() != pDataObject2.getAngleCount() or \
+            ppGeometry.getDetectorRowCount() != pDataObject2.getDetectorRowCount()):
+            del ppGeometry
+            raise Exception(
+                "The dimensions of the data do not match those specified in the geometry.")
+        pDataObject2.changeGeometry(ppGeometry)
+        del ppGeometry
+
+    elif pDataObject.getType() == THREEVOLUME:
+        pDataObject3 = <CFloat32VolumeData3DMemory * >pDataObject
+        cfg = utils.dictToConfig(six.b('VolumeGeometry'), geom)
+        pGeometry = new CVolumeGeometry3D()
+        if not pGeometry.initialize(cfg[0]):
+            del cfg
+            del pGeometry
+            raise Exception('Geometry class not initialized.')
+        del cfg
+        if (pGeometry.getGridColCount() != pDataObject3.getColCount() or \
+            pGeometry.getGridRowCount() != pDataObject3.getRowCount() or \
+            pGeometry.getGridSliceCount() != pDataObject3.getSliceCount()):
+            del pGeometry
+            raise Exception(
+                "The dimensions of the data do not match those specified in the geometry.")
+        pDataObject3.changeGeometry(pGeometry)
+        del pGeometry
+
+    else:
+        raise Exception("Not a known data object")
+
+
 cdef fillDataObject(CFloat32Data3DMemory * obj, data):
     if data is None:
         fillDataObjectScalar(obj, 0)
diff --git a/src/Float32ProjectionData3D.cpp b/src/Float32ProjectionData3D.cpp
index d039c83..2bd0447 100644
--- a/src/Float32ProjectionData3D.cpp
+++ b/src/Float32ProjectionData3D.cpp
@@ -270,4 +270,13 @@ CFloat32ProjectionData3D& CFloat32ProjectionData3D::operator-=(const float32& _f
 	return *this;
 }
 
+void CFloat32ProjectionData3D::changeGeometry(CProjectionGeometry3D* _pGeometry)
+{
+	if (!m_bInitialized) return;
+
+	delete m_pGeometry;
+	m_pGeometry = _pGeometry->clone();
+}
+
+
 } // end namespace astra
diff --git a/src/Float32VolumeData3D.cpp b/src/Float32VolumeData3D.cpp
index ce00a10..bd78001 100644
--- a/src/Float32VolumeData3D.cpp
+++ b/src/Float32VolumeData3D.cpp
@@ -266,4 +266,13 @@ CFloat32VolumeData3D& CFloat32VolumeData3D::operator-=(const float32& _fScalar)
 	return *this;
 }
 
+void CFloat32VolumeData3D::changeGeometry(CVolumeGeometry3D* _pGeometry)
+{
+	if (!m_bInitialized) return;
+
+	delete m_pGeometry;
+	m_pGeometry = _pGeometry->clone();
+}
+
+
 } // end namespace astra