From 1b32573046f33050b9300324e6c74e10abb6caaf Mon Sep 17 00:00:00 2001
From: "Daniel M. Pelt" <D.M.Pelt@cwi.nl>
Date: Thu, 9 Apr 2015 15:44:01 +0200
Subject: Add 'link' feature to Python (for 2D and 3D data)
---
python/astra/CFloat32CustomPython.h | 17 +++++++++++++++++
python/astra/PyIncludes.pxd | 8 ++++++++
python/astra/data2d.py | 21 +++++++++++++++++++++
python/astra/data2d_c.pyx | 21 +++++++++++++++++----
python/astra/data3d.py | 22 ++++++++++++++++++++++
python/astra/data3d_c.pyx | 27 ++++++++++++++++++++++-----
6 files changed, 107 insertions(+), 9 deletions(-)
create mode 100644 python/astra/CFloat32CustomPython.h
(limited to 'python/astra')
diff --git a/python/astra/CFloat32CustomPython.h b/python/astra/CFloat32CustomPython.h
new file mode 100644
index 0000000..d8593fc
--- /dev/null
+++ b/python/astra/CFloat32CustomPython.h
@@ -0,0 +1,17 @@
+class CFloat32CustomPython : public astra::CFloat32CustomMemory {
+public:
+ CFloat32CustomPython(PyObject * arrIn)
+ {
+ arr = arrIn;
+ // Set pointer to numpy data pointer
+ m_fPtr = (float *)PyArray_DATA(arr);
+ // Increase reference count since ASTRA has a reference
+ Py_INCREF(arr);
+ }
+ virtual ~CFloat32CustomPython() {
+ // Decrease reference count since ASTRA object is destroyed
+ Py_DECREF(arr);
+ }
+private:
+ PyObject* arr;
+};
\ No newline at end of file
diff --git a/python/astra/PyIncludes.pxd b/python/astra/PyIncludes.pxd
index 7df02c5..13329d1 100644
--- a/python/astra/PyIncludes.pxd
+++ b/python/astra/PyIncludes.pxd
@@ -63,10 +63,14 @@ cdef extern from "astra/VolumeGeometry2D.h" namespace "astra":
float32 getWindowMaxY()
Config* getConfiguration()
+cdef extern from "astra/Float32Data2D.h" namespace "astra":
+ cdef cppclass CFloat32CustomMemory:
+ pass
cdef extern from "astra/Float32VolumeData2D.h" namespace "astra":
cdef cppclass CFloat32VolumeData2D:
CFloat32VolumeData2D(CVolumeGeometry2D*)
+ CFloat32VolumeData2D(CVolumeGeometry2D*, CFloat32CustomMemory*)
CVolumeGeometry2D * getGeometry()
int getWidth()
int getHeight()
@@ -130,6 +134,7 @@ cdef extern from "astra/ParallelProjectionGeometry2D.h" namespace "astra":
cdef extern from "astra/Float32ProjectionData2D.h" namespace "astra":
cdef cppclass CFloat32ProjectionData2D:
CFloat32ProjectionData2D(CProjectionGeometry2D*)
+ CFloat32ProjectionData2D(CProjectionGeometry2D*, CFloat32CustomMemory*)
CProjectionGeometry2D * getGeometry()
void changeGeometry(CProjectionGeometry2D*)
int getDetectorCount()
@@ -207,6 +212,7 @@ cdef extern from "astra/ProjectionGeometry3D.h" namespace "astra":
cdef extern from "astra/Float32VolumeData3DMemory.h" namespace "astra":
cdef cppclass CFloat32VolumeData3DMemory:
CFloat32VolumeData3DMemory(CVolumeGeometry3D*)
+ CFloat32VolumeData3DMemory(CVolumeGeometry3D*, CFloat32CustomMemory*)
CVolumeGeometry3D* getGeometry()
@@ -231,6 +237,8 @@ cdef extern from "astra/Float32ProjectionData3DMemory.h" namespace "astra":
cdef cppclass CFloat32ProjectionData3DMemory:
CFloat32ProjectionData3DMemory(CProjectionGeometry3D*)
CFloat32ProjectionData3DMemory(CConeProjectionGeometry3D*)
+ CFloat32ProjectionData3DMemory(CProjectionGeometry3D*, CFloat32CustomMemory*)
+ CFloat32ProjectionData3DMemory(CConeProjectionGeometry3D*, CFloat32CustomMemory*)
CProjectionGeometry3D* getGeometry()
cdef extern from "astra/Float32Data3D.h" namespace "astra":
diff --git a/python/astra/data2d.py b/python/astra/data2d.py
index 8c4be03..f119f05 100644
--- a/python/astra/data2d.py
+++ b/python/astra/data2d.py
@@ -24,6 +24,7 @@
#
#-----------------------------------------------------------------------
from . import data2d_c as d
+import numpy as np
def clear():
"""Clear all 2D data objects."""
@@ -52,6 +53,26 @@ def create(datatype, geometry, data=None):
"""
return d.create(datatype,geometry,data)
+def link(datatype, geometry, data):
+ """Link a 2D numpy array with the toolbox.
+
+ :param datatype: Data object type, '-vol' or '-sino'.
+ :type datatype: :class:`string`
+ :param geometry: Volume or projection geometry.
+ :type geometry: :class:`dict`
+ :param data: Numpy array to link
+ :type data: :class:`numpy.ndarray`
+ :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")
+ return d.create(datatype,geometry,data,True)
+
def store(i, data):
"""Fill existing 2D object with data.
diff --git a/python/astra/data2d_c.pyx b/python/astra/data2d_c.pyx
index b9c105e..ac54898 100644
--- a/python/astra/data2d_c.pyx
+++ b/python/astra/data2d_c.pyx
@@ -49,6 +49,10 @@ from .utils import wrap_from_bytes
cdef CData2DManager * man2d = <CData2DManager * >PyData2DManager.getSingletonPtr()
+cdef extern from "CFloat32CustomPython.h":
+ cdef cppclass CFloat32CustomPython:
+ CFloat32CustomPython(arrIn)
+
def clear():
man2d.clear()
@@ -61,11 +65,12 @@ def delete(ids):
man2d.remove(ids)
-def create(datatype, geometry, data=None):
+def create(datatype, geometry, data=None, link=False):
cdef Config *cfg
cdef CVolumeGeometry2D * pGeometry
cdef CProjectionGeometry2D * ppGeometry
cdef CFloat32Data2D * pDataObject2D
+ cdef CFloat32CustomMemory * pCustom
if datatype == '-vol':
cfg = utils.dictToConfig(six.b('VolumeGeometry'), geometry)
pGeometry = new CVolumeGeometry2D()
@@ -73,7 +78,11 @@ def create(datatype, geometry, data=None):
del cfg
del pGeometry
raise Exception('Geometry class not initialized.')
- pDataObject2D = <CFloat32Data2D * > new CFloat32VolumeData2D(pGeometry)
+ if link:
+ pCustom = <CFloat32CustomMemory*> new CFloat32CustomPython(data)
+ pDataObject2D = <CFloat32Data2D * > new CFloat32VolumeData2D(pGeometry, pCustom)
+ else:
+ pDataObject2D = <CFloat32Data2D * > new CFloat32VolumeData2D(pGeometry)
del cfg
del pGeometry
elif datatype == '-sino':
@@ -91,7 +100,11 @@ def create(datatype, geometry, data=None):
del cfg
del ppGeometry
raise Exception('Geometry class not initialized.')
- pDataObject2D = <CFloat32Data2D * > new CFloat32ProjectionData2D(ppGeometry)
+ if link:
+ pCustom = <CFloat32CustomMemory*> new CFloat32CustomPython(data)
+ pDataObject2D = <CFloat32Data2D * > new CFloat32ProjectionData2D(ppGeometry, pCustom)
+ else:
+ pDataObject2D = <CFloat32Data2D * > new CFloat32ProjectionData2D(ppGeometry)
del ppGeometry
del cfg
else:
@@ -101,7 +114,7 @@ def create(datatype, geometry, data=None):
del pDataObject2D
raise Exception("Couldn't initialize data object.")
- fillDataObject(pDataObject2D, data)
+ if not link: fillDataObject(pDataObject2D, data)
return man2d.store(pDataObject2D)
diff --git a/python/astra/data3d.py b/python/astra/data3d.py
index a2e9201..4fdf9d7 100644
--- a/python/astra/data3d.py
+++ b/python/astra/data3d.py
@@ -24,6 +24,7 @@
#
#-----------------------------------------------------------------------
from . import data3d_c as d
+import numpy as np
def create(datatype,geometry,data=None):
"""Create a 3D object.
@@ -39,6 +40,27 @@ def create(datatype,geometry,data=None):
"""
return d.create(datatype,geometry,data)
+def link(datatype, geometry, data):
+ """Link a 3D numpy array with the toolbox.
+
+ :param datatype: Data object type, '-vol' or '-sino'.
+ :type datatype: :class:`string`
+ :param geometry: Volume or projection geometry.
+ :type geometry: :class:`dict`
+ :param data: Numpy array to link
+ :type data: :class:`numpy.ndarray`
+ :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")
+ return d.create(datatype,geometry,data,True)
+
+
def get(i):
"""Get a 3D object.
diff --git a/python/astra/data3d_c.pyx b/python/astra/data3d_c.pyx
index 4b069f7..f2c6e26 100644
--- a/python/astra/data3d_c.pyx
+++ b/python/astra/data3d_c.pyx
@@ -50,12 +50,17 @@ cdef CData3DManager * man3d = <CData3DManager * >PyData3DManager.getSingletonPtr
cdef extern from *:
CFloat32Data3DMemory * dynamic_cast_mem "dynamic_cast<astra::CFloat32Data3DMemory*>" (CFloat32Data3D * ) except NULL
-def create(datatype,geometry,data=None):
+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 CFloat32Data3DMemory * pDataObject3D
cdef CConeProjectionGeometry3D* pppGeometry
+ cdef CFloat32CustomMemory * pCustom
if datatype == '-vol':
cfg = utils.dictToConfig(six.b('VolumeGeometry'), geometry)
pGeometry = new CVolumeGeometry3D()
@@ -63,7 +68,11 @@ def create(datatype,geometry,data=None):
del cfg
del pGeometry
raise Exception('Geometry class not initialized.')
- pDataObject3D = <CFloat32Data3DMemory * > new CFloat32VolumeData3DMemory(pGeometry)
+ if link:
+ pCustom = <CFloat32CustomMemory*> new CFloat32CustomPython(data)
+ pDataObject3D = <CFloat32Data3DMemory * > new CFloat32VolumeData3DMemory(pGeometry, pCustom)
+ else:
+ pDataObject3D = <CFloat32Data3DMemory * > new CFloat32VolumeData3DMemory(pGeometry)
del cfg
del pGeometry
elif datatype == '-sino' or datatype == '-proj3d':
@@ -84,7 +93,11 @@ def create(datatype,geometry,data=None):
del cfg
del ppGeometry
raise Exception('Geometry class not initialized.')
- pDataObject3D = <CFloat32Data3DMemory * > new CFloat32ProjectionData3DMemory(ppGeometry)
+ if link:
+ pCustom = <CFloat32CustomMemory*> new CFloat32CustomPython(data)
+ pDataObject3D = <CFloat32Data3DMemory * > new CFloat32ProjectionData3DMemory(ppGeometry, pCustom)
+ else:
+ pDataObject3D = <CFloat32Data3DMemory * > new CFloat32ProjectionData3DMemory(ppGeometry)
del ppGeometry
del cfg
elif datatype == "-sinocone":
@@ -94,7 +107,11 @@ def create(datatype,geometry,data=None):
del cfg
del pppGeometry
raise Exception('Geometry class not initialized.')
- pDataObject3D = <CFloat32Data3DMemory * > new CFloat32ProjectionData3DMemory(pppGeometry)
+ 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'.")
@@ -102,7 +119,7 @@ def create(datatype,geometry,data=None):
del pDataObject3D
raise Exception("Couldn't initialize data object.")
- fillDataObject(pDataObject3D, data)
+ if not link: fillDataObject(pDataObject3D, data)
pDataObject3D.updateStatistics()
--
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