From b8bf069f375424fd303ad6e594412583633c1110 Mon Sep 17 00:00:00 2001
From: Willem Jan Palenstijn <Willem.Jan.Palenstijn@cwi.nl>
Date: Tue, 23 Jun 2020 11:40:26 +0200
Subject: Refactor cython data3d object creation to prepare
---
python/astra/PyIncludes.pxd | 16 +++++++++---
python/astra/data3d_c.pyx | 38 ++++-----------------------
python/astra/utils.pxd | 3 +++
python/astra/utils.pyx | 62 +++++++++++++++++++++++++++++++++++++++++++++
4 files changed, 82 insertions(+), 37 deletions(-)
(limited to 'python')
diff --git a/python/astra/PyIncludes.pxd b/python/astra/PyIncludes.pxd
index b9a61a9..f964118 100644
--- a/python/astra/PyIncludes.pxd
+++ b/python/astra/PyIncludes.pxd
@@ -236,9 +236,17 @@ cdef extern from "astra/ProjectionGeometry3D.h" namespace "astra":
int getDetectorColCount()
int getDetectorRowCount()
+cdef extern from "astra/Float32VolumeData3D.h" namespace "astra":
+ cdef cppclass CFloat32VolumeData3D(CFloat32Data3D):
+ pass
+
+cdef extern from "astra/Float32ProjectionData3D.h" namespace "astra":
+ cdef cppclass CFloat32ProjectionData3D(CFloat32Data3D):
+ pass
+
cdef extern from "astra/Float32VolumeData3DMemory.h" namespace "astra":
- cdef cppclass CFloat32VolumeData3DMemory:
+ cdef cppclass CFloat32VolumeData3DMemory(CFloat32VolumeData3D):
CFloat32VolumeData3DMemory(CVolumeGeometry3D*)
CFloat32VolumeData3DMemory(CVolumeGeometry3D*, CFloat32CustomMemory*)
CVolumeGeometry3D* getGeometry()
@@ -266,7 +274,7 @@ cdef extern from "astra/ConeVecProjectionGeometry3D.h" namespace "astra":
CConeVecProjectionGeometry3D()
cdef extern from "astra/Float32ProjectionData3DMemory.h" namespace "astra":
- cdef cppclass CFloat32ProjectionData3DMemory:
+ cdef cppclass CFloat32ProjectionData3DMemory(CFloat32ProjectionData3D):
CFloat32ProjectionData3DMemory(CProjectionGeometry3D*)
CFloat32ProjectionData3DMemory(CConeProjectionGeometry3D*)
CFloat32ProjectionData3DMemory(CProjectionGeometry3D*, CFloat32CustomMemory*)
@@ -280,7 +288,7 @@ cdef extern from "astra/Float32ProjectionData3DMemory.h" namespace "astra":
IF HAVE_CUDA==True:
cdef extern from "astra/Float32VolumeData3DGPU.h" namespace "astra":
- cdef cppclass CFloat32VolumeData3DGPU:
+ cdef cppclass CFloat32VolumeData3DGPU(CFloat32VolumeData3D):
CFloat32VolumeData3DGPU(CVolumeGeometry3D*, MemHandle3D)
CVolumeGeometry3D* getGeometry()
void changeGeometry(CVolumeGeometry3D*)
@@ -290,7 +298,7 @@ IF HAVE_CUDA==True:
bool isInitialized()
cdef extern from "astra/Float32ProjectionData3DGPU.h" namespace "astra":
- cdef cppclass CFloat32ProjectionData3DGPU:
+ cdef cppclass CFloat32ProjectionData3DGPU(CFloat32ProjectionData3D):
CFloat32ProjectionData3DGPU(CProjectionGeometry3D*, MemHandle3D)
CProjectionGeometry3D* getGeometry()
void changeGeometry(CProjectionGeometry3D*)
diff --git a/python/astra/data3d_c.pyx b/python/astra/data3d_c.pyx
index 4c8aa62..a1b9138 100644
--- a/python/astra/data3d_c.pyx
+++ b/python/astra/data3d_c.pyx
@@ -44,6 +44,7 @@ from .PyXMLDocument cimport XMLDocument
cimport utils
from .utils import wrap_from_bytes
+from .utils cimport linkVolFromGeometry, linkProjFromGeometry
from .pythonutils import geom_size, GPULink
@@ -53,9 +54,6 @@ from six.moves import reduce
include "config.pxi"
-cdef extern from "Python.h":
- void* PyLong_AsVoidPtr(object)
-
cdef CData3DManager * man3d = <CData3DManager * >PyData3DManager.getSingletonPtr()
@@ -68,16 +66,12 @@ cdef CFloat32Data3DMemory * dynamic_cast_mem_safe(CFloat32Data3D *obj) except NU
raise RuntimeError("Not a memory 3D data object")
return ret
-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 CFloat32Data3D * pDataObject3D
- cdef CConeProjectionGeometry3D* pppGeometry
cdef CFloat32CustomMemory * pCustom = NULL
IF HAVE_CUDA==True:
cdef MemHandle3D hnd
@@ -101,20 +95,9 @@ def create(datatype,geometry,data=None, link=False):
del pGeometry
raise RuntimeError('Geometry class not initialized.')
if link:
- 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")
+ pDataObject3D = linkVolFromGeometry(pGeometry, data)
else:
- pDataObject3D = <CFloat32Data3D * > new CFloat32VolumeData3DMemory(pGeometry)
+ pDataObject3D = new CFloat32VolumeData3DMemory(pGeometry)
del cfg
del pGeometry
elif datatype == '-sino' or datatype == '-proj3d' or datatype == '-sinocone':
@@ -136,20 +119,9 @@ def create(datatype,geometry,data=None, link=False):
del ppGeometry
raise RuntimeError('Geometry class not initialized.')
if link:
- 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")
+ pDataObject3D = linkProjFromGeometry(ppGeometry, data)
else:
- pDataObject3D = <CFloat32Data3DMemory * > new CFloat32ProjectionData3DMemory(ppGeometry)
+ pDataObject3D = new CFloat32ProjectionData3DMemory(ppGeometry)
del ppGeometry
del cfg
else:
diff --git a/python/astra/utils.pxd b/python/astra/utils.pxd
index ea3da86..69f4e96 100644
--- a/python/astra/utils.pxd
+++ b/python/astra/utils.pxd
@@ -33,3 +33,6 @@ from .PyIncludes cimport *
cdef configToDict(Config *)
cdef Config * dictToConfig(string rootname, dc) except NULL
+cdef CFloat32VolumeData3D* linkVolFromGeometry(CVolumeGeometry3D *pGeometry, data) except NULL
+cdef CFloat32ProjectionData3D* linkProjFromGeometry(CProjectionGeometry3D *pGeometry, data) except NULL
+
diff --git a/python/astra/utils.pyx b/python/astra/utils.pyx
index b534d72..3b6e3ff 100644
--- a/python/astra/utils.pyx
+++ b/python/astra/utils.pyx
@@ -45,6 +45,18 @@ from .PyXMLDocument cimport XMLDocument
from .PyXMLDocument cimport XMLNode
from .PyIncludes cimport *
+from .pythonutils import GPULink
+
+cdef extern from "CFloat32CustomPython.h":
+ cdef cppclass CFloat32CustomPython:
+ CFloat32CustomPython(arrIn)
+
+cdef extern from "Python.h":
+ void* PyLong_AsVoidPtr(object)
+
+
+include "config.pxi"
+
cdef Config * dictToConfig(string rootname, dc) except NULL:
cdef Config * cfg = new Config()
@@ -230,3 +242,53 @@ cdef XMLNode2dict(XMLNode node):
inc(it)
if len(opts)>0: dct['options'] = opts
return dct
+
+cdef CFloat32VolumeData3D* linkVolFromGeometry(CVolumeGeometry3D *pGeometry, data) except NULL:
+ cdef CFloat32VolumeData3D * pDataObject3D = NULL
+ geom_shape = (pGeometry.getGridSliceCount(), pGeometry.getGridRowCount(), pGeometry.getGridColCount())
+ if isinstance(data, np.ndarray):
+ data_shape = data.shape
+ elif isinstance(data, GPULink):
+ data_shape = (data.z, data.y, data.x)
+ 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 isinstance(data, np.ndarray):
+ pCustom = <CFloat32CustomMemory*> new CFloat32CustomPython(data)
+ pDataObject3D = new CFloat32VolumeData3DMemory(pGeometry, pCustom)
+ elif isinstance(data, GPULink):
+ IF HAVE_CUDA==True:
+ hnd = wrapHandle(<float*>PyLong_AsVoidPtr(data.ptr), data.x, data.y, data.z, data.pitch/4)
+ pDataObject3D = 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")
+ return pDataObject3D
+
+cdef CFloat32ProjectionData3D* linkProjFromGeometry(CProjectionGeometry3D *pGeometry, data) except NULL:
+ cdef CFloat32ProjectionData3D * pDataObject3D = NULL
+ geom_shape = (pGeometry.getDetectorRowCount(), pGeometry.getProjectionCount(), pGeometry.getDetectorColCount())
+ if isinstance(data, np.ndarray):
+ data_shape = data.shape
+ elif isinstance(data, GPULink):
+ data_shape = (data.z, data.y, data.x)
+ 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 isinstance(data, np.ndarray):
+ pCustom = <CFloat32CustomMemory*> new CFloat32CustomPython(data)
+ pDataObject3D = new CFloat32ProjectionData3DMemory(pGeometry, pCustom)
+ elif isinstance(data, GPULink):
+ IF HAVE_CUDA==True:
+ hnd = wrapHandle(<float*>PyLong_AsVoidPtr(data.ptr), data.x, data.y, data.z, data.pitch/4)
+ pDataObject3D = new CFloat32ProjectionData3DGPU(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")
+ return pDataObject3D
+
+
--
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