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-rw-r--r--python/astra/PyIncludes.pxd48
-rw-r--r--python/astra/data3d.py8
-rw-r--r--python/astra/data3d_c.pyx53
-rw-r--r--python/astra/experimental.pyx24
-rw-r--r--python/astra/pythonutils.py18
5 files changed, 113 insertions, 38 deletions
diff --git a/python/astra/PyIncludes.pxd b/python/astra/PyIncludes.pxd
index 39f9039..d5da17c 100644
--- a/python/astra/PyIncludes.pxd
+++ b/python/astra/PyIncludes.pxd
@@ -172,6 +172,13 @@ IF HAVE_CUDA==True:
cdef extern from "astra/CudaProjector2D.h" namespace "astra":
cdef cppclass CCudaProjector2D
+ cdef extern from "astra/Float32Data3DGPU.h" namespace "astraCUDA3d":
+ cdef cppclass MemHandle3D:
+ pass
+
+ cdef extern from "astra/Float32Data3DGPU.h" namespace "astraCUDA3d":
+ cdef MemHandle3D wrapHandle(float *D_ptr, unsigned int x, unsigned int y, unsigned int z, unsigned int pitch)
+
cdef extern from "astra/SparseMatrix.h" namespace "astra":
cdef cppclass CSparseMatrix:
@@ -184,14 +191,18 @@ cdef extern from "astra/SparseMatrix.h" namespace "astra":
unsigned int* m_piColIndices
unsigned long* m_plRowStarts
-cdef extern from "astra/Float32Data3DMemory.h" namespace "astra":
- cdef cppclass CFloat32Data3DMemory:
- CFloat32Data3DMemory()
+cdef extern from "astra/Float32Data3D.h" namespace "astra":
+ cdef cppclass CFloat32Data3D:
bool isInitialized()
int getSize()
int getWidth()
int getHeight()
int getDepth()
+
+
+cdef extern from "astra/Float32Data3DMemory.h" namespace "astra":
+ cdef cppclass CFloat32Data3DMemory(CFloat32Data3D):
+ CFloat32Data3DMemory()
void updateStatistics()
float32 *getData()
float32 ***getData3D()
@@ -228,8 +239,6 @@ cdef extern from "astra/Float32VolumeData3DMemory.h" namespace "astra":
int getSliceCount()
bool isInitialized()
-
-
cdef extern from "astra/ParallelProjectionGeometry3D.h" namespace "astra":
cdef cppclass CParallelProjectionGeometry3D:
CParallelProjectionGeometry3D()
@@ -260,12 +269,23 @@ cdef extern from "astra/Float32ProjectionData3DMemory.h" namespace "astra":
int getAngleCount()
bool isInitialized()
-cdef extern from "astra/Float32Data3D.h" namespace "astra":
- cdef cppclass CFloat32Data3D:
- CFloat32Data3D()
- bool isInitialized()
- int getSize()
- int getWidth()
- int getHeight()
- int getDepth()
- void updateStatistics()
+IF HAVE_CUDA==True:
+ cdef extern from "astra/Float32VolumeData3DGPU.h" namespace "astra":
+ cdef cppclass CFloat32VolumeData3DGPU:
+ CFloat32VolumeData3DGPU(CVolumeGeometry3D*, MemHandle3D)
+ CVolumeGeometry3D* getGeometry()
+ void changeGeometry(CVolumeGeometry3D*)
+ int getRowCount()
+ int getColCount()
+ int getSliceCount()
+ bool isInitialized()
+
+ cdef extern from "astra/Float32ProjectionData3DGPU.h" namespace "astra":
+ cdef cppclass CFloat32ProjectionData3DGPU:
+ CFloat32ProjectionData3DGPU(CProjectionGeometry3D*, MemHandle3D)
+ CProjectionGeometry3D* getGeometry()
+ void changeGeometry(CProjectionGeometry3D*)
+ int getRowCount()
+ int getColCount()
+ int getSliceCount()
+ bool isInitialized()
diff --git a/python/astra/data3d.py b/python/astra/data3d.py
index 9c2bea4..a825700 100644
--- a/python/astra/data3d.py
+++ b/python/astra/data3d.py
@@ -26,6 +26,8 @@
from . import data3d_c as d
import numpy as np
+from .pythonutils import GPULink
+
def create(datatype,geometry,data=None):
"""Create a 3D object.
@@ -52,11 +54,11 @@ def link(datatype, geometry, data):
:returns: :class:`int` -- the ID of the constructed object.
"""
- if not isinstance(data,np.ndarray):
+ if not isinstance(data,np.ndarray) and not isinstance(data,GPULink):
raise ValueError("Input should be a numpy array")
- if not data.dtype==np.float32:
+ if not isinstance(data,GPULink) and not data.dtype==np.float32:
raise ValueError("Numpy array should be float32")
- if not (data.flags['C_CONTIGUOUS'] and data.flags['ALIGNED']):
+ if not isinstance(data,GPULink) and 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)
diff --git a/python/astra/data3d_c.pyx b/python/astra/data3d_c.pyx
index 3934f22..56247de 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 +70,19 @@ 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
-
- if link and data.shape!=geom_size(geometry):
- raise Exception("The dimensions of the data do not match those specified in the geometry.")
+ cdef CFloat32CustomMemory * pCustom = NULL
+ IF HAVE_CUDA==True:
+ cdef MemHandle3D hnd
+
+ if link:
+ if isinstance(data, GPULink):
+ s = geom_size(geometry)
+ if geom_size(geometry) != ( data.z, data.y, data.x ):
+ raise Exception("The dimensions of the data do not match those specified in the geometry.")
+ elif 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)
@@ -80,10 +92,18 @@ def create(datatype,geometry,data=None, link=False):
del pGeometry
raise Exception('Geometry class not initialized.')
if link:
- pCustom = <CFloat32CustomMemory*> new CFloat32CustomPython(data)
- pDataObject3D = <CFloat32Data3DMemory * > new CFloat32VolumeData3DMemory(pGeometry, pCustom)
+ if 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:
+ pCustom = <CFloat32CustomMemory*> new CFloat32CustomPython(data)
+ pDataObject3D = <CFloat32Data3D * > new CFloat32VolumeData3DMemory(pGeometry, pCustom)
else:
- pDataObject3D = <CFloat32Data3DMemory * > new CFloat32VolumeData3DMemory(pGeometry)
+ pDataObject3D = <CFloat32Data3D * > new CFloat32VolumeData3DMemory(pGeometry)
del cfg
del pGeometry
elif datatype == '-sino' or datatype == '-proj3d' or datatype == '-sinocone':
@@ -105,8 +125,16 @@ def create(datatype,geometry,data=None, link=False):
del ppGeometry
raise Exception('Geometry class not initialized.')
if link:
- pCustom = <CFloat32CustomMemory*> new CFloat32CustomPython(data)
- pDataObject3D = <CFloat32Data3DMemory * > new CFloat32ProjectionData3DMemory(ppGeometry, pCustom)
+ if 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:
+ pCustom = <CFloat32CustomMemory*> new CFloat32CustomPython(data)
+ pDataObject3D = <CFloat32Data3D * > new CFloat32ProjectionData3DMemory(ppGeometry, pCustom)
else:
pDataObject3D = <CFloat32Data3DMemory * > new CFloat32ProjectionData3DMemory(ppGeometry)
del ppGeometry
@@ -118,8 +146,7 @@ def create(datatype,geometry,data=None, link=False):
del pDataObject3D
raise Exception("Couldn't initialize data object.")
- if not link: fillDataObject(pDataObject3D, data)
-
+ if not link: fillDataObject(dynamic_cast_mem(pDataObject3D), data)
return man3d.store(<CFloat32Data3D*>pDataObject3D)
diff --git a/python/astra/experimental.pyx b/python/astra/experimental.pyx
index b6c7881..0af3118 100644
--- a/python/astra/experimental.pyx
+++ b/python/astra/experimental.pyx
@@ -36,12 +36,20 @@ IF HAVE_CUDA==True:
cdef extern from "astra/CompositeGeometryManager.h" namespace "astra":
cdef cppclass CCompositeGeometryManager:
- bool doFP(CProjector3D *, vector[CFloat32VolumeData3DMemory *], vector[CFloat32ProjectionData3DMemory *])
- bool doBP(CProjector3D *, vector[CFloat32VolumeData3DMemory *], vector[CFloat32ProjectionData3DMemory *])
+ bool doFP(CProjector3D *, vector[CFloat32VolumeData3D *], vector[CFloat32ProjectionData3D *])
+ bool doBP(CProjector3D *, vector[CFloat32VolumeData3D *], vector[CFloat32ProjectionData3D *])
cdef extern from *:
- CFloat32VolumeData3DMemory * dynamic_cast_vol_mem "dynamic_cast<astra::CFloat32VolumeData3DMemory*>" (CFloat32Data3D * ) except NULL
- CFloat32ProjectionData3DMemory * dynamic_cast_proj_mem "dynamic_cast<astra::CFloat32ProjectionData3DMemory*>" (CFloat32Data3D * ) except NULL
+ CFloat32VolumeData3D * dynamic_cast_vol_mem "dynamic_cast<astra::CFloat32VolumeData3D*>" (CFloat32Data3D * ) except NULL
+ CFloat32ProjectionData3D * dynamic_cast_proj_mem "dynamic_cast<astra::CFloat32ProjectionData3D*>" (CFloat32Data3D * ) except NULL
+
+ cdef extern from "astra/Float32ProjectionData3D.h" namespace "astra":
+ cdef cppclass CFloat32ProjectionData3D:
+ bool isInitialized()
+ cdef extern from "astra/Float32VolumeData3D.h" namespace "astra":
+ cdef cppclass CFloat32VolumeData3D:
+ bool isInitialized()
+
cimport PyProjector3DManager
from .PyProjector3DManager cimport CProjector3DManager
@@ -52,9 +60,9 @@ IF HAVE_CUDA==True:
cdef CData3DManager * man3d = <CData3DManager * >PyData3DManager.getSingletonPtr()
def do_composite(projector_id, vol_ids, proj_ids, t):
- cdef vector[CFloat32VolumeData3DMemory *] vol
- cdef CFloat32VolumeData3DMemory * pVolObject
- cdef CFloat32ProjectionData3DMemory * pProjObject
+ cdef vector[CFloat32VolumeData3D *] vol
+ cdef CFloat32VolumeData3D * pVolObject
+ cdef CFloat32ProjectionData3D * pProjObject
for v in vol_ids:
pVolObject = dynamic_cast_vol_mem(man3d.get(v))
if pVolObject == NULL:
@@ -62,7 +70,7 @@ IF HAVE_CUDA==True:
if not pVolObject.isInitialized():
raise Exception("Data object not initialized properly")
vol.push_back(pVolObject)
- cdef vector[CFloat32ProjectionData3DMemory *] proj
+ cdef vector[CFloat32ProjectionData3D *] proj
for v in proj_ids:
pProjObject = dynamic_cast_proj_mem(man3d.get(v))
if pProjObject == NULL:
diff --git a/python/astra/pythonutils.py b/python/astra/pythonutils.py
index 3bd3321..27fa8fd 100644
--- a/python/astra/pythonutils.py
+++ b/python/astra/pythonutils.py
@@ -61,3 +61,21 @@ def geom_size(geom, dim=None):
s = s[dim]
return s
+
+class GPULink(object):
+ """Utility class for astra.data3d.link with a CUDA pointer
+
+ The CUDA pointer ptr must point to an array of floats.
+
+ x is the fastest-changing coordinate, z the slowest-changing.
+
+ pitch is the width in bytes of the memory block. For a contiguous
+ memory block, pitch is equal to sizeof(float) * x. For a memory block
+ allocated by cudaMalloc3D, pitch is the pitch as returned by cudaMalloc3D.
+ """
+ def __init__(self, ptr, x, y, z, pitch):
+ self.ptr = ptr
+ self.x = x
+ self.y = y
+ self.z = z
+ self.pitch = pitch
generated by cgit v1.2.3 (git 2.25.1) at 2024-11-15 03:51:58 +0000