# ----------------------------------------------------------------------- # Copyright: 2010-2016, iMinds-Vision Lab, University of Antwerp # 2013-2016, CWI, Amsterdam # # Contact: astra@uantwerpen.be # Website: http://sf.net/projects/astra-toolbox # # This file is part of the ASTRA Toolbox. # # # The ASTRA Toolbox is free software: you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by # the Free Software Foundation, either version 3 of the License, or # (at your option) any later version. # # The ASTRA Toolbox is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY; without even the implied warranty of # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the # GNU General Public License for more details. # # You should have received a copy of the GNU General Public License # along with the ASTRA Toolbox. If not, see . # # ----------------------------------------------------------------------- # # distutils: language = c++ # distutils: libraries = astra import six cimport cython from cython cimport view cimport PyData2DManager from .PyData2DManager cimport CData2DManager cimport PyProjector2DManager from .PyProjector2DManager cimport CProjector2DManager cimport PyXMLDocument from .PyXMLDocument cimport XMLDocument import numpy as np cimport numpy as np np.import_array() from .PyIncludes cimport * cimport utils from .utils import wrap_from_bytes from .pythonutils import geom_size import operator from six.moves import reduce cdef CData2DManager * man2d = PyData2DManager.getSingletonPtr() cdef CProjector2DManager * manProj = PyProjector2DManager.getSingletonPtr() cdef extern from "CFloat32CustomPython.h": cdef cppclass CFloat32CustomPython: CFloat32CustomPython(arrIn) def clear(): man2d.clear() def delete(ids): try: for i in ids: man2d.remove(i) except TypeError: man2d.remove(ids) def create(datatype, geometry, data=None, link=False): cdef Config *cfg cdef CVolumeGeometry2D * pGeometry cdef CProjectionGeometry2D * ppGeometry cdef CFloat32Data2D * pDataObject2D cdef CFloat32CustomMemory * pCustom if link and data.shape!=geom_size(geometry): raise Exception("The dimensions of the data do not match those specified in the geometry.") if datatype == '-vol': cfg = utils.dictToConfig(six.b('VolumeGeometry'), geometry) pGeometry = new CVolumeGeometry2D() if not pGeometry.initialize(cfg[0]): del cfg del pGeometry raise Exception('Geometry class not initialized.') if link: pCustom = new CFloat32CustomPython(data) pDataObject2D = new CFloat32VolumeData2D(pGeometry, pCustom) else: pDataObject2D = new CFloat32VolumeData2D(pGeometry) del cfg del pGeometry elif datatype == '-sino': cfg = utils.dictToConfig(six.b('ProjectionGeometry'), geometry) tpe = wrap_from_bytes(cfg.self.getAttribute(six.b('type'))) if (tpe == 'sparse_matrix'): ppGeometry = new CSparseMatrixProjectionGeometry2D() elif (tpe == 'fanflat'): ppGeometry = new CFanFlatProjectionGeometry2D() elif (tpe == 'fanflat_vec'): ppGeometry = new CFanFlatVecProjectionGeometry2D() elif (tpe == 'parallel_vec'): ppGeometry = new CParallelVecProjectionGeometry2D() else: ppGeometry = new CParallelProjectionGeometry2D() if not ppGeometry.initialize(cfg[0]): del cfg del ppGeometry raise Exception('Geometry class not initialized.') if link: pCustom = new CFloat32CustomPython(data) pDataObject2D = new CFloat32ProjectionData2D(ppGeometry, pCustom) else: pDataObject2D = new CFloat32ProjectionData2D(ppGeometry) del ppGeometry del cfg else: raise Exception("Invalid datatype. Please specify '-vol' or '-sino'.") if not pDataObject2D.isInitialized(): del pDataObject2D raise Exception("Couldn't initialize data object.") if not link: fillDataObject(pDataObject2D, data) return man2d.store(pDataObject2D) cdef fillDataObject(CFloat32Data2D * obj, data): if data is None: fillDataObjectScalar(obj, 0) else: if isinstance(data, np.ndarray): fillDataObjectArray(obj, np.ascontiguousarray(data,dtype=np.float32)) else: fillDataObjectScalar(obj, np.float32(data)) cdef fillDataObjectScalar(CFloat32Data2D * obj, float s): cdef int i for i in range(obj.getSize()): obj.getData()[i] = s @cython.boundscheck(False) @cython.wraparound(False) cdef fillDataObjectArray(CFloat32Data2D * obj, float [:,::1] data): if (not data.shape[0] == obj.getHeight()) or (not data.shape[1] == obj.getWidth()): raise Exception( "The dimensions of the data do not match those specified in the geometry.") cdef float [:,::1] cView = obj.getData2D()[0] cView[:] = data cdef CFloat32Data2D * getObject(i) except NULL: cdef CFloat32Data2D * pDataObject = man2d.get(i) if pDataObject == NULL: raise Exception("Data object not found") if not pDataObject.isInitialized(): raise Exception("Data object not initialized properly.") return pDataObject def store(i, data): cdef CFloat32Data2D * pDataObject = getObject(i) fillDataObject(pDataObject, data) def get_geometry(i): cdef CFloat32Data2D * pDataObject = getObject(i) cdef CFloat32ProjectionData2D * pDataObject2 cdef CFloat32VolumeData2D * pDataObject3 if pDataObject.getType() == TWOPROJECTION: pDataObject2 = pDataObject geom = utils.configToDict(pDataObject2.getGeometry().getConfiguration()) elif pDataObject.getType() == TWOVOLUME: pDataObject3 = pDataObject geom = utils.configToDict(pDataObject3.getGeometry().getConfiguration()) else: raise Exception("Not a known data object") return geom cdef CProjector2D * getProjector(i) except NULL: cdef CProjector2D * proj = manProj.get(i) if proj == NULL: raise Exception("Projector not initialized.") if not proj.isInitialized(): raise Exception("Projector not initialized.") return proj def check_compatible(i, proj_id): cdef CProjector2D * proj = getProjector(proj_id) cdef CFloat32Data2D * pDataObject = getObject(i) cdef CFloat32ProjectionData2D * pDataObject2 cdef CFloat32VolumeData2D * pDataObject3 if pDataObject.getType() == TWOPROJECTION: pDataObject2 = pDataObject return pDataObject2.getGeometry().isEqual(proj.getProjectionGeometry()) elif pDataObject.getType() == TWOVOLUME: pDataObject3 = pDataObject return pDataObject3.getGeometry().isEqual(proj.getVolumeGeometry()) else: raise Exception("Not a known data object") def change_geometry(i, geom): cdef Config *cfg cdef CVolumeGeometry2D * pGeometry cdef CProjectionGeometry2D * ppGeometry cdef CFloat32Data2D * pDataObject = getObject(i) cdef CFloat32ProjectionData2D * pDataObject2 cdef CFloat32VolumeData2D * pDataObject3 if pDataObject.getType() == TWOPROJECTION: pDataObject2 = pDataObject cfg = utils.dictToConfig(six.b('ProjectionGeometry'), geom) tpe = wrap_from_bytes(cfg.self.getAttribute(six.b('type'))) if (tpe == 'sparse_matrix'): ppGeometry = new CSparseMatrixProjectionGeometry2D() elif (tpe == 'fanflat'): ppGeometry = new CFanFlatProjectionGeometry2D() elif (tpe == 'fanflat_vec'): ppGeometry = new CFanFlatVecProjectionGeometry2D() elif (tpe == 'parallel_vec'): ppGeometry = new CParallelVecProjectionGeometry2D() else: ppGeometry = new CParallelProjectionGeometry2D() if not ppGeometry.initialize(cfg[0]): del cfg del ppGeometry raise Exception('Geometry class not initialized.') if (ppGeometry.getDetectorCount() != pDataObject2.getDetectorCount() or ppGeometry.getProjectionAngleCount() != pDataObject2.getAngleCount()): del ppGeometry del cfg raise Exception( "The dimensions of the data do not match those specified in the geometry.") pDataObject2.changeGeometry(ppGeometry) del ppGeometry del cfg elif pDataObject.getType() == TWOVOLUME: pDataObject3 = pDataObject cfg = utils.dictToConfig(six.b('VolumeGeometry'), geom) pGeometry = new CVolumeGeometry2D() if not pGeometry.initialize(cfg[0]): del cfg del pGeometry raise Exception('Geometry class not initialized.') if (pGeometry.getGridColCount() != pDataObject3.getWidth() or pGeometry.getGridRowCount() != pDataObject3.getHeight()): del cfg del pGeometry raise Exception( 'The dimensions of the data do not match those specified in the geometry.') pDataObject3.changeGeometry(pGeometry) del cfg del pGeometry else: raise Exception("Not a known data object") @cython.boundscheck(False) @cython.wraparound(False) def get(i): cdef CFloat32Data2D * pDataObject = getObject(i) outArr = np.empty((pDataObject.getHeight(), pDataObject.getWidth()),dtype=np.float32,order='C') cdef float [:,::1] mView = outArr cdef float [:,::1] cView = pDataObject.getData2D()[0] mView[:] = cView return outArr def get_shared(i): cdef CFloat32Data2D * pDataObject = getObject(i) cdef np.npy_intp shape[2] shape[0] = pDataObject.getHeight() shape[1] = pDataObject.getWidth() return np.PyArray_SimpleNewFromData(2,shape,np.NPY_FLOAT32,pDataObject.getData2D()[0]) def get_single(i): raise Exception("Not yet implemented") def info(): six.print_(wrap_from_bytes(man2d.info()))