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-rw-r--r--python/astra/data3d_c.pyx127
1 files changed, 75 insertions, 52 deletions
diff --git a/python/astra/data3d_c.pyx b/python/astra/data3d_c.pyx
index 915c60d..78ed620 100644
--- a/python/astra/data3d_c.pyx
+++ b/python/astra/data3d_c.pyx
@@ -45,12 +45,17 @@ from .PyXMLDocument cimport XMLDocument
cimport utils
from .utils import wrap_from_bytes
-from .pythonutils import geom_size
+from .pythonutils import geom_size, GPULink
import operator
from six.moves import reduce
+include "config.pxi"
+
+cdef extern from "Python.h":
+ void* PyLong_AsVoidPtr(object)
+
cdef CData3DManager * man3d = <CData3DManager * >PyData3DManager.getSingletonPtr()
@@ -65,12 +70,22 @@ def create(datatype,geometry,data=None, link=False):
cdef Config *cfg
cdef CVolumeGeometry3D * pGeometry
cdef CProjectionGeometry3D * ppGeometry
- cdef CFloat32Data3DMemory * pDataObject3D
+ cdef CFloat32Data3D * pDataObject3D
cdef CConeProjectionGeometry3D* pppGeometry
- cdef CFloat32CustomMemory * pCustom
+ cdef CFloat32CustomMemory * pCustom = NULL
+ IF HAVE_CUDA==True:
+ cdef MemHandle3D hnd
- if link and data.shape!=geom_size(geometry):
- raise Exception("The dimensions of the data do not match those specified in the geometry.")
+ if link:
+ geom_shape = geom_size(geometry)
+ if isinstance(data, np.ndarray):
+ data_shape = data.shape
+ elif isinstance(data, GPULink):
+ data_shape = ( data.z, data.y, data.x )
+ else:
+ raise TypeError("data should be a numpy.ndarray or a GPULink object")
+ if geom_shape != data_shape:
+ raise ValueError("The dimensions of the data do not match those specified in the geometry: {} != {}".format(data_shape, geom_shape))
if datatype == '-vol':
cfg = utils.dictToConfig(six.b('VolumeGeometry'), geometry)
@@ -78,15 +93,25 @@ def create(datatype,geometry,data=None, link=False):
if not pGeometry.initialize(cfg[0]):
del cfg
del pGeometry
- raise Exception('Geometry class not initialized.')
+ raise RuntimeError('Geometry class not initialized.')
if link:
- pCustom = <CFloat32CustomMemory*> new CFloat32CustomPython(data)
- pDataObject3D = <CFloat32Data3DMemory * > new CFloat32VolumeData3DMemory(pGeometry, pCustom)
+ if isinstance(data, np.ndarray):
+ pCustom = <CFloat32CustomMemory*> new CFloat32CustomPython(data)
+ pDataObject3D = <CFloat32Data3D * > new CFloat32VolumeData3DMemory(pGeometry, pCustom)
+ elif isinstance(data, GPULink):
+ IF HAVE_CUDA==True:
+ s = geom_size(geometry)
+ hnd = wrapHandle(<float*>PyLong_AsVoidPtr(data.ptr), data.x, data.y, data.z, data.pitch/4)
+ pDataObject3D = <CFloat32Data3D * > new CFloat32VolumeData3DGPU(pGeometry, hnd)
+ ELSE:
+ raise NotImplementedError("CUDA support is not enabled in ASTRA")
+ else:
+ raise TypeError("data should be a numpy.ndarray or a GPULink object")
else:
- pDataObject3D = <CFloat32Data3DMemory * > new CFloat32VolumeData3DMemory(pGeometry)
+ pDataObject3D = <CFloat32Data3D * > new CFloat32VolumeData3DMemory(pGeometry)
del cfg
del pGeometry
- elif datatype == '-sino' or datatype == '-proj3d':
+ elif datatype == '-sino' or datatype == '-proj3d' or datatype == '-sinocone':
cfg = utils.dictToConfig(six.b('ProjectionGeometry'), geometry)
tpe = wrap_from_bytes(cfg.self.getAttribute(six.b('type')))
if (tpe == "parallel3d"):
@@ -98,41 +123,38 @@ def create(datatype,geometry,data=None, link=False):
elif (tpe == "cone_vec"):
ppGeometry = <CProjectionGeometry3D*> new CConeVecProjectionGeometry3D();
else:
- raise Exception("Invalid geometry type.")
+ raise ValueError("Invalid geometry type.")
if not ppGeometry.initialize(cfg[0]):
del cfg
del ppGeometry
- raise Exception('Geometry class not initialized.')
+ raise RuntimeError('Geometry class not initialized.')
if link:
- pCustom = <CFloat32CustomMemory*> new CFloat32CustomPython(data)
- pDataObject3D = <CFloat32Data3DMemory * > new CFloat32ProjectionData3DMemory(ppGeometry, pCustom)
+ if isinstance(data, np.ndarray):
+ pCustom = <CFloat32CustomMemory*> new CFloat32CustomPython(data)
+ pDataObject3D = <CFloat32Data3D * > new CFloat32ProjectionData3DMemory(ppGeometry, pCustom)
+ elif isinstance(data, GPULink):
+ IF HAVE_CUDA==True:
+ s = geom_size(geometry)
+ hnd = wrapHandle(<float*>PyLong_AsVoidPtr(data.ptr), data.x, data.y, data.z, data.pitch/4)
+ pDataObject3D = <CFloat32Data3D * > new CFloat32ProjectionData3DGPU(ppGeometry, hnd)
+ ELSE:
+ raise NotImplementedError("CUDA support is not enabled in ASTRA")
+ else:
+ raise TypeError("data should be a numpy.ndarray or a GPULink object")
else:
pDataObject3D = <CFloat32Data3DMemory * > new CFloat32ProjectionData3DMemory(ppGeometry)
del ppGeometry
del cfg
- elif datatype == "-sinocone":
- cfg = utils.dictToConfig(six.b('ProjectionGeometry'), geometry)
- pppGeometry = new CConeProjectionGeometry3D()
- if not pppGeometry.initialize(cfg[0]):
- del cfg
- del pppGeometry
- raise Exception('Geometry class not initialized.')
- 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'.")
+ raise ValueError("Invalid datatype. Please specify '-vol' or '-proj3d'.")
if not pDataObject3D.isInitialized():
del pDataObject3D
- raise Exception("Couldn't initialize data object.")
-
- if not link: fillDataObject(pDataObject3D, data)
+ raise RuntimeError("Couldn't initialize data object.")
- pDataObject3D.updateStatistics()
+ if not link:
+ fillDataObject(dynamic_cast_mem(pDataObject3D), data)
return man3d.store(<CFloat32Data3D*>pDataObject3D)
@@ -147,7 +169,7 @@ def get_geometry(i):
pDataObject3 = <CFloat32VolumeData3DMemory * >pDataObject
geom = utils.configToDict(pDataObject3.getGeometry().getConfiguration())
else:
- raise Exception("Not a known data object")
+ raise RuntimeError("Not a known data object")
return geom
def change_geometry(i, geom):
@@ -168,18 +190,18 @@ def change_geometry(i, geom):
elif (tpe == "cone_vec"):
ppGeometry = <CProjectionGeometry3D*> new CConeVecProjectionGeometry3D();
else:
- raise Exception("Invalid geometry type.")
+ raise ValueError("Invalid geometry type.")
if not ppGeometry.initialize(cfg[0]):
del cfg
del ppGeometry
- raise Exception('Geometry class not initialized.')
+ raise RuntimeError('Geometry class not initialized.')
del cfg
- if (ppGeometry.getDetectorColCount() != pDataObject2.getDetectorColCount() or \
- ppGeometry.getProjectionCount() != pDataObject2.getAngleCount() or \
- ppGeometry.getDetectorRowCount() != pDataObject2.getDetectorRowCount()):
+ geom_shape = (ppGeometry.getDetectorRowCount(), ppGeometry.getProjectionCount(), ppGeometry.getDetectorColCount())
+ obj_shape = (pDataObject2.getDetectorRowCount(), pDataObject2.getAngleCount(), pDataObject2.getDetectorColCount())
+ if geom_shape != obj_shape:
del ppGeometry
- raise Exception(
- "The dimensions of the data do not match those specified in the geometry.")
+ raise ValueError(
+ "The dimensions of the data do not match those specified in the geometry: {} != {}".format(obj_shape, geom_shape))
pDataObject2.changeGeometry(ppGeometry)
del ppGeometry
@@ -190,19 +212,19 @@ def change_geometry(i, geom):
if not pGeometry.initialize(cfg[0]):
del cfg
del pGeometry
- raise Exception('Geometry class not initialized.')
+ raise RuntimeError('Geometry class not initialized.')
del cfg
- if (pGeometry.getGridColCount() != pDataObject3.getColCount() or \
- pGeometry.getGridRowCount() != pDataObject3.getRowCount() or \
- pGeometry.getGridSliceCount() != pDataObject3.getSliceCount()):
+ geom_shape = (pGeometry.getGridSliceCount(), pGeometry.getGridRowCount(), pGeometry.getGridColCount())
+ obj_shape = (pDataObject3.getSliceCount(), pDataObject3.getRowCount(), pDataObject3.getColCount())
+ if geom_shape != obj_shape:
del pGeometry
- raise Exception(
- "The dimensions of the data do not match those specified in the geometry.")
+ raise ValueError(
+ "The dimensions of the data do not match those specified in the geometry.".format(obj_shape, geom_shape))
pDataObject3.changeGeometry(pGeometry)
del pGeometry
else:
- raise Exception("Not a known data object")
+ raise RuntimeError("Not a known data object")
cdef fillDataObject(CFloat32Data3DMemory * obj, data):
@@ -210,6 +232,10 @@ cdef fillDataObject(CFloat32Data3DMemory * obj, data):
fillDataObjectScalar(obj, 0)
else:
if isinstance(data, np.ndarray):
+ obj_shape = (obj.getDepth(), obj.getHeight(), obj.getWidth())
+ if data.shape != obj_shape:
+ raise ValueError(
+ "The dimensions of the data do not match those specified in the geometry: {} != {}".format(data.shape, obj_shape))
fillDataObjectArray(obj, np.ascontiguousarray(data,dtype=np.float32))
else:
fillDataObjectScalar(obj, np.float32(data))
@@ -222,18 +248,15 @@ cdef fillDataObjectScalar(CFloat32Data3DMemory * obj, float s):
@cython.boundscheck(False)
@cython.wraparound(False)
cdef fillDataObjectArray(CFloat32Data3DMemory * obj, float [:,:,::1] data):
- if (not data.shape[0] == obj.getDepth()) or (not data.shape[1] == obj.getHeight()) or (not data.shape[2] == obj.getWidth()):
- raise Exception(
- "The dimensions of the data do not match those specified in the geometry.")
cdef float [:,:,::1] cView = <float[:data.shape[0],:data.shape[1],:data.shape[2]]> obj.getData3D()[0][0]
cView[:] = data
cdef CFloat32Data3D * getObject(i) except NULL:
cdef CFloat32Data3D * pDataObject = man3d.get(i)
if pDataObject == NULL:
- raise Exception("Data object not found")
+ raise ValueError("Data object not found")
if not pDataObject.isInitialized():
- raise Exception("Data object not initialized properly.")
+ raise RuntimeError("Data object not initialized properly.")
return pDataObject
@cython.boundscheck(False)
@@ -256,7 +279,7 @@ def get_shared(i):
return np.PyArray_SimpleNewFromData(3,shape,np.NPY_FLOAT32,<void *>pDataObject.getData3D()[0][0])
def get_single(i):
- raise Exception("Not yet implemented")
+ raise NotImplementedError("Not yet implemented")
def store(i,data):
cdef CFloat32Data3D * pDataObject = getObject(i)
generated by cgit v1.2.3 (git 2.25.1) at 2024-09-21 23:09:02 +0000