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-rw-r--r--include/astra/Float32ProjectionData2D.h25
-rw-r--r--include/astra/Float32VolumeData2D.h25
-rw-r--r--python/astra/CFloat32CustomPython.h17
-rw-r--r--python/astra/PyIncludes.pxd8
-rw-r--r--python/astra/data2d.py21
-rw-r--r--python/astra/data2d_c.pyx21
-rw-r--r--python/astra/data3d.py22
-rw-r--r--python/astra/data3d_c.pyx27
-rw-r--r--src/Float32ProjectionData2D.cpp19
-rw-r--r--src/Float32VolumeData2D.cpp20
10 files changed, 196 insertions, 9 deletions
diff --git a/include/astra/Float32ProjectionData2D.h b/include/astra/Float32ProjectionData2D.h
index 7461491..bb99f4b 100644
--- a/include/astra/Float32ProjectionData2D.h
+++ b/include/astra/Float32ProjectionData2D.h
@@ -101,6 +101,19 @@ public:
* Copy constructor
*/
CFloat32ProjectionData2D(const CFloat32ProjectionData2D& _other);
+
+ /** Constructor. Create an instance of the CFloat32ProjectionData2D class with pre-allocated memory.
+ *
+ * Creates an instance of the CFloat32ProjectionData2D class. Memory
+ * is pre-allocated and passed via the abstract CFloat32CustomMemory handle
+ * class. The handle will be deleted when the memory can be freed.
+ * You should override the destructor to provide custom behaviour on free.
+ *
+ * @param _pGeometry Projection Geometry object. This object will be HARDCOPIED into this class.
+ * @param _pCustomMemory custom memory handle
+ *
+ */
+ CFloat32ProjectionData2D(CProjectionGeometry2D* _pGeometry, CFloat32CustomMemory* _pCustomMemory);
/**
* Assignment operator
@@ -148,6 +161,18 @@ public:
* @param _fScalar scalar value to be put at each index.
*/
bool initialize(CProjectionGeometry2D* _pGeometry, float32 _fScalar);
+
+ /** Initialization. Initializes an instance of the CFloat32ProjectionData2D class with pre-allocated memory.
+ *
+ * Memory is pre-allocated and passed via the abstract CFloat32CustomMemory handle
+ * class. The handle will be deleted when the memory can be freed.
+ * You should override the destructor to provide custom behaviour on free.
+ *
+ * @param _pGeometry Projection Geometry object. This object will be HARDCOPIED into this class.
+ * @param _pCustomMemory custom memory handle
+ *
+ */
+ bool initialize(CProjectionGeometry2D* _pGeometry, CFloat32CustomMemory* _pCustomMemory);
/** Get the number of detectors.
*
diff --git a/include/astra/Float32VolumeData2D.h b/include/astra/Float32VolumeData2D.h
index 4f44a8c..abecebf 100644
--- a/include/astra/Float32VolumeData2D.h
+++ b/include/astra/Float32VolumeData2D.h
@@ -92,6 +92,19 @@ public:
* Copy constructor
*/
CFloat32VolumeData2D(const CFloat32VolumeData2D& _other);
+
+ /** Constructor. Create an instance of the CFloat32VolumeData2D class with pre-allocated memory.
+ *
+ * Creates an instance of the CFloat32VolumeData2D class. Memory
+ * is pre-allocated and passed via the abstract CFloat32CustomMemory handle
+ * class. The handle will be deleted when the memory can be freed.
+ * You should override the destructor to provide custom behaviour on free.
+ *
+ * @param _pGeometry Volume Geometry object. This object will be HARDCOPIED into this class.
+ * @param _pCustomMemory custom memory handle
+ *
+ */
+ CFloat32VolumeData2D(CVolumeGeometry2D* _pGeometry, CFloat32CustomMemory* _pCustomMemory);
/**
* Assignment operator
@@ -132,6 +145,18 @@ public:
* @param _fScalar scalar value to be put at each index.
*/
bool initialize(CVolumeGeometry2D* _pGeometry, float32 _fScalar);
+
+ /** Initialization. Initializes an instance of the CFloat32VolumeData2D class with pre-allocated memory.
+ *
+ * Memory is pre-allocated and passed via the abstract CFloat32CustomMemory handle
+ * class. The handle will be deleted when the memory can be freed.
+ * You should override the destructor to provide custom behaviour on free.
+ *
+ * @param _pGeometry Volume Geometry object. This object will be HARDCOPIED into this class.
+ * @param _pCustomMemory custom memory handle
+ *
+ */
+ bool initialize(CVolumeGeometry2D* _pGeometry, CFloat32CustomMemory* _pCustomMemory);
/** Destructor.
*/
diff --git a/python/astra/CFloat32CustomPython.h b/python/astra/CFloat32CustomPython.h
new file mode 100644
index 0000000..d8593fc
--- /dev/null
+++ b/python/astra/CFloat32CustomPython.h
@@ -0,0 +1,17 @@
+class CFloat32CustomPython : public astra::CFloat32CustomMemory {
+public:
+ CFloat32CustomPython(PyObject * arrIn)
+ {
+ arr = arrIn;
+ // Set pointer to numpy data pointer
+ m_fPtr = (float *)PyArray_DATA(arr);
+ // Increase reference count since ASTRA has a reference
+ Py_INCREF(arr);
+ }
+ virtual ~CFloat32CustomPython() {
+ // Decrease reference count since ASTRA object is destroyed
+ Py_DECREF(arr);
+ }
+private:
+ PyObject* arr;
+}; \ No newline at end of file
diff --git a/python/astra/PyIncludes.pxd b/python/astra/PyIncludes.pxd
index a581f88..1d8285b 100644
--- a/python/astra/PyIncludes.pxd
+++ b/python/astra/PyIncludes.pxd
@@ -63,10 +63,14 @@ cdef extern from "astra/VolumeGeometry2D.h" namespace "astra":
float32 getWindowMaxY()
Config* getConfiguration()
+cdef extern from "astra/Float32Data2D.h" namespace "astra":
+ cdef cppclass CFloat32CustomMemory:
+ pass
cdef extern from "astra/Float32VolumeData2D.h" namespace "astra":
cdef cppclass CFloat32VolumeData2D:
CFloat32VolumeData2D(CVolumeGeometry2D*)
+ CFloat32VolumeData2D(CVolumeGeometry2D*, CFloat32CustomMemory*)
CVolumeGeometry2D * getGeometry()
int getWidth()
int getHeight()
@@ -130,6 +134,7 @@ cdef extern from "astra/ParallelProjectionGeometry2D.h" namespace "astra":
cdef extern from "astra/Float32ProjectionData2D.h" namespace "astra":
cdef cppclass CFloat32ProjectionData2D:
CFloat32ProjectionData2D(CProjectionGeometry2D*)
+ CFloat32ProjectionData2D(CProjectionGeometry2D*, CFloat32CustomMemory*)
CProjectionGeometry2D * getGeometry()
void changeGeometry(CProjectionGeometry2D*)
int getDetectorCount()
@@ -213,6 +218,7 @@ cdef extern from "astra/ProjectionGeometry3D.h" namespace "astra":
cdef extern from "astra/Float32VolumeData3DMemory.h" namespace "astra":
cdef cppclass CFloat32VolumeData3DMemory:
CFloat32VolumeData3DMemory(CVolumeGeometry3D*)
+ CFloat32VolumeData3DMemory(CVolumeGeometry3D*, CFloat32CustomMemory*)
CVolumeGeometry3D* getGeometry()
void changeGeometry(CVolumeGeometry3D*)
int getRowCount()
@@ -242,6 +248,8 @@ cdef extern from "astra/Float32ProjectionData3DMemory.h" namespace "astra":
cdef cppclass CFloat32ProjectionData3DMemory:
CFloat32ProjectionData3DMemory(CProjectionGeometry3D*)
CFloat32ProjectionData3DMemory(CConeProjectionGeometry3D*)
+ CFloat32ProjectionData3DMemory(CProjectionGeometry3D*, CFloat32CustomMemory*)
+ CFloat32ProjectionData3DMemory(CConeProjectionGeometry3D*, CFloat32CustomMemory*)
CProjectionGeometry3D* getGeometry()
void changeGeometry(CProjectionGeometry3D*)
int getDetectorColCount()
diff --git a/python/astra/data2d.py b/python/astra/data2d.py
index 8c4be03..f119f05 100644
--- a/python/astra/data2d.py
+++ b/python/astra/data2d.py
@@ -24,6 +24,7 @@
#
#-----------------------------------------------------------------------
from . import data2d_c as d
+import numpy as np
def clear():
"""Clear all 2D data objects."""
@@ -52,6 +53,26 @@ def create(datatype, geometry, data=None):
"""
return d.create(datatype,geometry,data)
+def link(datatype, geometry, data):
+ """Link a 2D numpy array with the toolbox.
+
+ :param datatype: Data object type, '-vol' or '-sino'.
+ :type datatype: :class:`string`
+ :param geometry: Volume or projection geometry.
+ :type geometry: :class:`dict`
+ :param data: Numpy array to link
+ :type data: :class:`numpy.ndarray`
+ :returns: :class:`int` -- the ID of the constructed object.
+
+ """
+ if not isinstance(data,np.ndarray):
+ raise ValueError("Input should be a numpy array")
+ if not data.dtype==np.float32:
+ raise ValueError("Numpy array should be float32")
+ if not (data.flags['C_CONTIGUOUS'] and data.flags['ALIGNED']):
+ raise ValueError("Numpy array should be C_CONTIGUOUS and ALIGNED")
+ return d.create(datatype,geometry,data,True)
+
def store(i, data):
"""Fill existing 2D object with data.
diff --git a/python/astra/data2d_c.pyx b/python/astra/data2d_c.pyx
index b9c105e..ac54898 100644
--- a/python/astra/data2d_c.pyx
+++ b/python/astra/data2d_c.pyx
@@ -49,6 +49,10 @@ from .utils import wrap_from_bytes
cdef CData2DManager * man2d = <CData2DManager * >PyData2DManager.getSingletonPtr()
+cdef extern from "CFloat32CustomPython.h":
+ cdef cppclass CFloat32CustomPython:
+ CFloat32CustomPython(arrIn)
+
def clear():
man2d.clear()
@@ -61,11 +65,12 @@ def delete(ids):
man2d.remove(ids)
-def create(datatype, geometry, data=None):
+def create(datatype, geometry, data=None, link=False):
cdef Config *cfg
cdef CVolumeGeometry2D * pGeometry
cdef CProjectionGeometry2D * ppGeometry
cdef CFloat32Data2D * pDataObject2D
+ cdef CFloat32CustomMemory * pCustom
if datatype == '-vol':
cfg = utils.dictToConfig(six.b('VolumeGeometry'), geometry)
pGeometry = new CVolumeGeometry2D()
@@ -73,7 +78,11 @@ def create(datatype, geometry, data=None):
del cfg
del pGeometry
raise Exception('Geometry class not initialized.')
- pDataObject2D = <CFloat32Data2D * > new CFloat32VolumeData2D(pGeometry)
+ if link:
+ pCustom = <CFloat32CustomMemory*> new CFloat32CustomPython(data)
+ pDataObject2D = <CFloat32Data2D * > new CFloat32VolumeData2D(pGeometry, pCustom)
+ else:
+ pDataObject2D = <CFloat32Data2D * > new CFloat32VolumeData2D(pGeometry)
del cfg
del pGeometry
elif datatype == '-sino':
@@ -91,7 +100,11 @@ def create(datatype, geometry, data=None):
del cfg
del ppGeometry
raise Exception('Geometry class not initialized.')
- pDataObject2D = <CFloat32Data2D * > new CFloat32ProjectionData2D(ppGeometry)
+ if link:
+ pCustom = <CFloat32CustomMemory*> new CFloat32CustomPython(data)
+ pDataObject2D = <CFloat32Data2D * > new CFloat32ProjectionData2D(ppGeometry, pCustom)
+ else:
+ pDataObject2D = <CFloat32Data2D * > new CFloat32ProjectionData2D(ppGeometry)
del ppGeometry
del cfg
else:
@@ -101,7 +114,7 @@ def create(datatype, geometry, data=None):
del pDataObject2D
raise Exception("Couldn't initialize data object.")
- fillDataObject(pDataObject2D, data)
+ if not link: fillDataObject(pDataObject2D, data)
return man2d.store(pDataObject2D)
diff --git a/python/astra/data3d.py b/python/astra/data3d.py
index 4679489..e5ef6b0 100644
--- a/python/astra/data3d.py
+++ b/python/astra/data3d.py
@@ -24,6 +24,7 @@
#
#-----------------------------------------------------------------------
from . import data3d_c as d
+import numpy as np
def create(datatype,geometry,data=None):
"""Create a 3D object.
@@ -39,6 +40,27 @@ def create(datatype,geometry,data=None):
"""
return d.create(datatype,geometry,data)
+def link(datatype, geometry, data):
+ """Link a 3D numpy array with the toolbox.
+
+ :param datatype: Data object type, '-vol' or '-sino'.
+ :type datatype: :class:`string`
+ :param geometry: Volume or projection geometry.
+ :type geometry: :class:`dict`
+ :param data: Numpy array to link
+ :type data: :class:`numpy.ndarray`
+ :returns: :class:`int` -- the ID of the constructed object.
+
+ """
+ if not isinstance(data,np.ndarray):
+ raise ValueError("Input should be a numpy array")
+ if not data.dtype==np.float32:
+ raise ValueError("Numpy array should be float32")
+ if not (data.flags['C_CONTIGUOUS'] and data.flags['ALIGNED']):
+ raise ValueError("Numpy array should be C_CONTIGUOUS and ALIGNED")
+ return d.create(datatype,geometry,data,True)
+
+
def get(i):
"""Get a 3D object.
diff --git a/python/astra/data3d_c.pyx b/python/astra/data3d_c.pyx
index 48af032..84472c1 100644
--- a/python/astra/data3d_c.pyx
+++ b/python/astra/data3d_c.pyx
@@ -50,12 +50,17 @@ cdef CData3DManager * man3d = <CData3DManager * >PyData3DManager.getSingletonPtr
cdef extern from *:
CFloat32Data3DMemory * dynamic_cast_mem "dynamic_cast<astra::CFloat32Data3DMemory*>" (CFloat32Data3D * ) except NULL
-def create(datatype,geometry,data=None):
+cdef extern from "CFloat32CustomPython.h":
+ cdef cppclass CFloat32CustomPython:
+ CFloat32CustomPython(arrIn)
+
+def create(datatype,geometry,data=None, link=False):
cdef Config *cfg
cdef CVolumeGeometry3D * pGeometry
cdef CProjectionGeometry3D * ppGeometry
cdef CFloat32Data3DMemory * pDataObject3D
cdef CConeProjectionGeometry3D* pppGeometry
+ cdef CFloat32CustomMemory * pCustom
if datatype == '-vol':
cfg = utils.dictToConfig(six.b('VolumeGeometry'), geometry)
pGeometry = new CVolumeGeometry3D()
@@ -63,7 +68,11 @@ def create(datatype,geometry,data=None):
del cfg
del pGeometry
raise Exception('Geometry class not initialized.')
- pDataObject3D = <CFloat32Data3DMemory * > new CFloat32VolumeData3DMemory(pGeometry)
+ if link:
+ pCustom = <CFloat32CustomMemory*> new CFloat32CustomPython(data)
+ pDataObject3D = <CFloat32Data3DMemory * > new CFloat32VolumeData3DMemory(pGeometry, pCustom)
+ else:
+ pDataObject3D = <CFloat32Data3DMemory * > new CFloat32VolumeData3DMemory(pGeometry)
del cfg
del pGeometry
elif datatype == '-sino' or datatype == '-proj3d':
@@ -84,7 +93,11 @@ def create(datatype,geometry,data=None):
del cfg
del ppGeometry
raise Exception('Geometry class not initialized.')
- pDataObject3D = <CFloat32Data3DMemory * > new CFloat32ProjectionData3DMemory(ppGeometry)
+ if link:
+ pCustom = <CFloat32CustomMemory*> new CFloat32CustomPython(data)
+ pDataObject3D = <CFloat32Data3DMemory * > new CFloat32ProjectionData3DMemory(ppGeometry, pCustom)
+ else:
+ pDataObject3D = <CFloat32Data3DMemory * > new CFloat32ProjectionData3DMemory(ppGeometry)
del ppGeometry
del cfg
elif datatype == "-sinocone":
@@ -94,7 +107,11 @@ def create(datatype,geometry,data=None):
del cfg
del pppGeometry
raise Exception('Geometry class not initialized.')
- pDataObject3D = <CFloat32Data3DMemory * > new CFloat32ProjectionData3DMemory(pppGeometry)
+ if link:
+ pCustom = <CFloat32CustomMemory*> new CFloat32CustomPython(data)
+ pDataObject3D = <CFloat32Data3DMemory * > new CFloat32ProjectionData3DMemory(pppGeometry, pCustom)
+ else:
+ pDataObject3D = <CFloat32Data3DMemory * > new CFloat32ProjectionData3DMemory(pppGeometry)
else:
raise Exception("Invalid datatype. Please specify '-vol' or '-proj3d'.")
@@ -102,7 +119,7 @@ def create(datatype,geometry,data=None):
del pDataObject3D
raise Exception("Couldn't initialize data object.")
- fillDataObject(pDataObject3D, data)
+ if not link: fillDataObject(pDataObject3D, data)
pDataObject3D.updateStatistics()
diff --git a/src/Float32ProjectionData2D.cpp b/src/Float32ProjectionData2D.cpp
index 85e0cdd..f7f83e3 100644
--- a/src/Float32ProjectionData2D.cpp
+++ b/src/Float32ProjectionData2D.cpp
@@ -75,6 +75,16 @@ CFloat32ProjectionData2D::CFloat32ProjectionData2D(const CFloat32ProjectionData2
m_bInitialized = true;
}
+//----------------------------------------------------------------------------------------
+// Create an instance of the CFloat32ProjectionData2D class with pre-allocated data
+CFloat32ProjectionData2D::CFloat32ProjectionData2D(CProjectionGeometry2D* _pGeometry, CFloat32CustomMemory* _pCustomMemory)
+{
+ m_bInitialized = false;
+ m_bInitialized = initialize(_pGeometry, _pCustomMemory);
+}
+
+
+
// Assignment operator
CFloat32ProjectionData2D& CFloat32ProjectionData2D::operator=(const CFloat32ProjectionData2D& _other)
@@ -119,6 +129,15 @@ bool CFloat32ProjectionData2D::initialize(CProjectionGeometry2D* _pGeometry, flo
}
//----------------------------------------------------------------------------------------
+// Initialization
+bool CFloat32ProjectionData2D::initialize(CProjectionGeometry2D* _pGeometry, CFloat32CustomMemory* _pCustomMemory)
+{
+ m_pGeometry = _pGeometry->clone();
+ m_bInitialized = _initialize(m_pGeometry->getDetectorCount(), m_pGeometry->getProjectionAngleCount(), _pCustomMemory);
+ return m_bInitialized;
+}
+
+//----------------------------------------------------------------------------------------
// Destructor
CFloat32ProjectionData2D::~CFloat32ProjectionData2D()
{
diff --git a/src/Float32VolumeData2D.cpp b/src/Float32VolumeData2D.cpp
index e11c4e4..c903c66 100644
--- a/src/Float32VolumeData2D.cpp
+++ b/src/Float32VolumeData2D.cpp
@@ -72,6 +72,15 @@ CFloat32VolumeData2D::CFloat32VolumeData2D(const CFloat32VolumeData2D& _other) :
m_bInitialized = true;
}
+//----------------------------------------------------------------------------------------
+// Create an instance of the CFloat32VolumeData2D class with pre-allocated data
+CFloat32VolumeData2D::CFloat32VolumeData2D(CVolumeGeometry2D* _pGeometry, CFloat32CustomMemory* _pCustomMemory)
+{
+ m_bInitialized = false;
+ m_bInitialized = initialize(_pGeometry, _pCustomMemory);
+}
+
+
// Assignment operator
CFloat32VolumeData2D& CFloat32VolumeData2D::operator=(const CFloat32VolumeData2D& _other)
@@ -122,6 +131,17 @@ bool CFloat32VolumeData2D::initialize(CVolumeGeometry2D* _pGeometry, float32 _fS
m_bInitialized = _initialize(m_pGeometry->getGridColCount(), m_pGeometry->getGridRowCount(), _fScalar);
return m_bInitialized;
}
+
+//----------------------------------------------------------------------------------------
+// Initialization
+bool CFloat32VolumeData2D::initialize(CVolumeGeometry2D* _pGeometry, CFloat32CustomMemory* _pCustomMemory)
+{
+ m_pGeometry = _pGeometry->clone();
+ m_bInitialized = _initialize(m_pGeometry->getGridColCount(), m_pGeometry->getGridRowCount(), _pCustomMemory);
+ return m_bInitialized;
+}
+
+
//----------------------------------------------------------------------------------------
void CFloat32VolumeData2D::changeGeometry(CVolumeGeometry2D* _pGeometry)
{
generated by cgit v1.2.3 (git 2.25.1) at 2024-11-01 21:33:46 +0000