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-rw-r--r--python/astra/PyIncludes.pxd16
-rw-r--r--python/astra/data2d.py7
-rw-r--r--python/astra/data3d.py7
-rw-r--r--python/astra/data3d_c.pyx38
-rw-r--r--python/astra/experimental.pyx57
-rw-r--r--python/astra/pythonutils.py15
-rw-r--r--python/astra/utils.pxd3
-rw-r--r--python/astra/utils.pyx64
8 files changed, 159 insertions, 48 deletions
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/data2d.py b/python/astra/data2d.py
index 188ff69..6ab458f 100644
--- a/python/astra/data2d.py
+++ b/python/astra/data2d.py
@@ -65,12 +65,7 @@ def link(datatype, geometry, data):
: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")
+ checkArrayForLink(data)
return d.create(datatype,geometry,data,True)
def store(i, data):
diff --git a/python/astra/data3d.py b/python/astra/data3d.py
index b0d54b2..3eea0e3 100644
--- a/python/astra/data3d.py
+++ b/python/astra/data3d.py
@@ -26,7 +26,7 @@
from . import data3d_c as d
import numpy as np
-from .pythonutils import GPULink
+from .pythonutils import GPULink, checkArrayForLink
def create(datatype,geometry,data=None):
"""Create a 3D object.
@@ -57,10 +57,7 @@ def link(datatype, geometry, data):
if not isinstance(data,np.ndarray) and not isinstance(data,GPULink):
raise TypeError("Input should be a numpy ndarray or GPULink object")
if isinstance(data, np.ndarray):
- if 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")
+ checkArrayForLink(data)
return d.create(datatype,geometry,data,True)
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/experimental.pyx b/python/astra/experimental.pyx
index 8f8e47d..08d907d 100644
--- a/python/astra/experimental.pyx
+++ b/python/astra/experimental.pyx
@@ -65,6 +65,8 @@ IF HAVE_CUDA==True:
cdef CData3DManager * man3d = <CData3DManager * >PyData3DManager.getSingletonPtr()
def do_composite(projector_id, vol_ids, proj_ids, mode, t):
+ if mode != MODE_ADD and mode != MODE_SET:
+ raise RuntimeError("internal error: wrong composite mode")
cdef vector[CFloat32VolumeData3D *] vol
cdef CFloat32VolumeData3D * pVolObject
cdef CFloat32ProjectionData3D * pProjObject
@@ -121,3 +123,58 @@ IF HAVE_CUDA==True:
cdef CProjector3D * projector = manProj.get(projector_id) # may be NULL
if not m.doFDK(projector, pVolObject, pProjObject, False, NULL, MODE_ADD):
raise Exception("Failed to perform FDK")
+
+ cimport utils
+ from .utils cimport linkVolFromGeometry, linkProjFromGeometry
+
+ def direct_FPBP3D(projector_id, vol, proj, mode, t):
+ if mode != MODE_ADD and mode != MODE_SET:
+ raise RuntimeError("internal error: wrong composite mode")
+ cdef CProjector3D * projector = manProj.get(projector_id)
+ if projector == NULL:
+ raise Exception("Projector not found")
+ cdef CVolumeGeometry3D *pGeometry = projector.getVolumeGeometry()
+ cdef CProjectionGeometry3D *ppGeometry = projector.getProjectionGeometry()
+ cdef CFloat32VolumeData3D * pVol = linkVolFromGeometry(pGeometry, vol)
+ cdef CFloat32ProjectionData3D * pProj = linkProjFromGeometry(ppGeometry, proj)
+ cdef vector[CFloat32VolumeData3D *] vols
+ cdef vector[CFloat32ProjectionData3D *] projs
+ vols.push_back(pVol)
+ projs.push_back(pProj)
+ cdef CCompositeGeometryManager m
+ try:
+ if t == "FP":
+ if not m.doFP(projector, vols, projs, mode):
+ raise Exception("Failed to perform FP")
+ elif t == "BP":
+ if not m.doBP(projector, vols, projs, mode):
+ raise Exception("Failed to perform BP")
+ else:
+ raise RuntimeError("internal error: wrong op type")
+ finally:
+ del pVol
+ del pProj
+
+ def direct_FP3D(projector_id, vol, proj):
+ """Perform a 3D forward projection with pre-allocated input/output.
+
+ :param projector_id: A 3D projector object handle
+ :type datatype: :class:`int`
+ :param vol: The input data, as either a numpy array, or a GPULink object
+ :type datatype: :class:`numpy.ndarray` or :class:`astra.data3d.GPULink`
+ :param proj: The pre-allocated output data, either numpy array or GPULink
+ :type datatype: :class:`numpy.ndarray` or :class:`astra.data3d.GPULink`
+ """
+ direct_FPBP3D(projector_id, vol, proj, MODE_SET, "FP")
+
+ def direct_BP3D(projector_id, vol, proj):
+ """Perform a 3D back projection with pre-allocated input/output.
+
+ :param projector_id: A 3D projector object handle
+ :type datatype: :class:`int`
+ :param vol: The pre-allocated output data, as either a numpy array, or a GPULink object
+ :type datatype: :class:`numpy.ndarray` or :class:`astra.data3d.GPULink`
+ :param proj: The input data, either numpy array or GPULink
+ :type datatype: :class:`numpy.ndarray` or :class:`astra.data3d.GPULink`
+ """
+ direct_FPBP3D(projector_id, vol, proj, MODE_SET, "BP")
diff --git a/python/astra/pythonutils.py b/python/astra/pythonutils.py
index 715df30..ef49f97 100644
--- a/python/astra/pythonutils.py
+++ b/python/astra/pythonutils.py
@@ -29,6 +29,8 @@
"""
+import numpy as np
+
def geom_size(geom, dim=None):
"""Returns the size of a volume or sinogram, based on the projection or volume geometry.
@@ -62,6 +64,19 @@ def geom_size(geom, dim=None):
return s
+def checkArrayForLink(data):
+ """Check if a numpy array is suitable for direct usage (contiguous, etc.)
+
+ This function raises an exception if not.
+ """
+
+ if not isinstance(data, np.ndarray):
+ raise ValueError("Numpy array should be numpy.ndarray")
+ if 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")
+
class GPULink(object):
"""Utility class for astra.data3d.link with a CUDA pointer
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..12fc38c 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, checkArrayForLink
+
+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 +242,55 @@ 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):
+ checkArrayForLink(data)
+ 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):
+ checkArrayForLink(data)
+ 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
+
+
generated by cgit v1.2.3 (git 2.25.1) at 2024-11-08 15:48:02 +0000