From 1b32573046f33050b9300324e6c74e10abb6caaf Mon Sep 17 00:00:00 2001 From: "Daniel M. Pelt" Date: Thu, 9 Apr 2015 15:44:01 +0200 Subject: Add 'link' feature to Python (for 2D and 3D data) --- python/astra/CFloat32CustomPython.h | 17 +++++++++++++++++ python/astra/PyIncludes.pxd | 8 ++++++++ python/astra/data2d.py | 21 +++++++++++++++++++++ python/astra/data2d_c.pyx | 21 +++++++++++++++++---- python/astra/data3d.py | 22 ++++++++++++++++++++++ python/astra/data3d_c.pyx | 27 ++++++++++++++++++++++----- 6 files changed, 107 insertions(+), 9 deletions(-) create mode 100644 python/astra/CFloat32CustomPython.h (limited to 'python') 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 7df02c5..13329d1 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() @@ -207,6 +212,7 @@ 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() @@ -231,6 +237,8 @@ cdef extern from "astra/Float32ProjectionData3DMemory.h" namespace "astra": cdef cppclass CFloat32ProjectionData3DMemory: CFloat32ProjectionData3DMemory(CProjectionGeometry3D*) CFloat32ProjectionData3DMemory(CConeProjectionGeometry3D*) + CFloat32ProjectionData3DMemory(CProjectionGeometry3D*, CFloat32CustomMemory*) + CFloat32ProjectionData3DMemory(CConeProjectionGeometry3D*, CFloat32CustomMemory*) CProjectionGeometry3D* getGeometry() cdef extern from "astra/Float32Data3D.h" namespace "astra": 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 = 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 = new CFloat32VolumeData2D(pGeometry) + if link: + pCustom = new CFloat32CustomPython(data) + pDataObject2D = new CFloat32VolumeData2D(pGeometry, pCustom) + else: + pDataObject2D = 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 = new CFloat32ProjectionData2D(ppGeometry) + if link: + pCustom = new CFloat32CustomPython(data) + pDataObject2D = new CFloat32ProjectionData2D(ppGeometry, pCustom) + else: + pDataObject2D = 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 a2e9201..4fdf9d7 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 4b069f7..f2c6e26 100644 --- a/python/astra/data3d_c.pyx +++ b/python/astra/data3d_c.pyx @@ -50,12 +50,17 @@ cdef CData3DManager * man3d = PyData3DManager.getSingletonPtr cdef extern from *: CFloat32Data3DMemory * dynamic_cast_mem "dynamic_cast" (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 = new CFloat32VolumeData3DMemory(pGeometry) + if link: + pCustom = new CFloat32CustomPython(data) + pDataObject3D = new CFloat32VolumeData3DMemory(pGeometry, pCustom) + else: + pDataObject3D = 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 = new CFloat32ProjectionData3DMemory(ppGeometry) + if link: + pCustom = new CFloat32CustomPython(data) + pDataObject3D = new CFloat32ProjectionData3DMemory(ppGeometry, pCustom) + else: + pDataObject3D = 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 = new CFloat32ProjectionData3DMemory(pppGeometry) + if link: + pCustom = new CFloat32CustomPython(data) + pDataObject3D = new CFloat32ProjectionData3DMemory(pppGeometry, pCustom) + else: + pDataObject3D = 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() -- cgit v1.2.3