Merge pull request #16 from dmpelt/python-interface

Add Python interface

1 files changed, 241 insertions, 0 deletions

diff --git a/python/astra/data2d_c.pyx b/python/astra/data2d_c.pyx
new file mode 100644
index 0000000..ec1b478
--- /dev/null
+++ b/python/astra/data2d_c.pyx
@@ -0,0 +1,241 @@
+#-----------------------------------------------------------------------
+#Copyright 2013 Centrum Wiskunde & Informatica, Amsterdam
+#
+#Author: Daniel M. Pelt
+#Contact: D.M.Pelt@cwi.nl
+#Website: http://dmpelt.github.io/pyastratoolbox/
+#
+#
+#This file is part of the Python interface to the
+#All Scale Tomographic Reconstruction Antwerp Toolbox ("ASTRA Toolbox").
+#
+#The Python interface to the ASTRA Toolbox is free software: you can redistribute it and/or modify
+#it under the terms of the GNU General Public License as published by
+#the Free Software Foundation, either version 3 of the License, or
+#(at your option) any later version.
+#
+#The Python interface to the ASTRA Toolbox is distributed in the hope that it will be useful,
+#but WITHOUT ANY WARRANTY; without even the implied warranty of
+#MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+#GNU General Public License for more details.
+#
+#You should have received a copy of the GNU General Public License
+#along with the Python interface to the ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>.
+#
+#-----------------------------------------------------------------------
+# distutils: language = c++
+# distutils: libraries = astra
+
+import six
+
+cimport cython
+from cython cimport view
+
+cimport PyData2DManager
+from .PyData2DManager cimport CData2DManager
+
+cimport PyXMLDocument
+from .PyXMLDocument cimport XMLDocument
+
+import numpy as np
+
+cimport numpy as np
+np.import_array()
+
+
+from .PyIncludes cimport *
+cimport utils
+from .utils import wrap_from_bytes
+
+
+cdef CData2DManager * man2d = <CData2DManager * >PyData2DManager.getSingletonPtr()
+
+
+def clear():
+    man2d.clear()
+
+
+def delete(ids):
+    try:
+        for i in ids:
+            man2d.remove(i)
+    except TypeError:
+        man2d.remove(ids)
+
+
+def create(datatype, geometry, data=None):
+    cdef XMLDocument * xml
+    cdef Config cfg
+    cdef CVolumeGeometry2D * pGeometry
+    cdef CProjectionGeometry2D * ppGeometry
+    cdef CFloat32Data2D * pDataObject2D
+    if datatype == '-vol':
+        xml = utils.dict2XML(six.b('VolumeGeometry'), geometry)
+        cfg.self = xml.getRootNode()
+        pGeometry = new CVolumeGeometry2D()
+        if not pGeometry.initialize(cfg):
+            del xml
+            del pGeometry
+            raise Exception('Geometry class not initialized.')
+        pDataObject2D = <CFloat32Data2D * > new CFloat32VolumeData2D(pGeometry)
+        del xml
+        del pGeometry
+    elif datatype == '-sino':
+        xml = utils.dict2XML(six.b('ProjectionGeometry'), geometry)
+        cfg.self = xml.getRootNode()
+        tpe = wrap_from_bytes(cfg.self.getAttribute(six.b('type')))
+        if (tpe == 'sparse_matrix'):
+            ppGeometry = <CProjectionGeometry2D * >new CSparseMatrixProjectionGeometry2D()
+        elif (tpe == 'fanflat'):
+            ppGeometry = <CProjectionGeometry2D * >new CFanFlatProjectionGeometry2D()
+        elif (tpe == 'fanflat_vec'):
+            ppGeometry = <CProjectionGeometry2D * >new CFanFlatVecProjectionGeometry2D()
+        else:
+            ppGeometry = <CProjectionGeometry2D * >new CParallelProjectionGeometry2D()
+        if not ppGeometry.initialize(cfg):
+            del xml
+            del ppGeometry
+            raise Exception('Geometry class not initialized.')
+        pDataObject2D = <CFloat32Data2D * > new CFloat32ProjectionData2D(ppGeometry)
+        del ppGeometry
+        del xml
+    else:
+        raise Exception("Invalid datatype.  Please specify '-vol' or '-sino'.")
+
+    if not pDataObject2D.isInitialized():
+        del pDataObject2D
+        raise Exception("Couldn't initialize data object.")
+
+    fillDataObject(pDataObject2D, data)
+
+    return man2d.store(pDataObject2D)
+
+cdef fillDataObject(CFloat32Data2D * obj, data):
+    if data is None:
+        fillDataObjectScalar(obj, 0)
+    else:
+        if isinstance(data, np.ndarray):
+            fillDataObjectArray(obj, np.ascontiguousarray(data,dtype=np.float32))
+        else:
+            fillDataObjectScalar(obj, np.float32(data))
+
+cdef fillDataObjectScalar(CFloat32Data2D * obj, float s):
+    cdef int i
+    for i in range(obj.getSize()):
+        obj.getData()[i] = s
+
+@cython.boundscheck(False)
+@cython.wraparound(False)
+cdef fillDataObjectArray(CFloat32Data2D * obj, float [:,::1] data):
+    if (not data.shape[0] == obj.getHeight()) or (not data.shape[1] == 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]]> obj.getData2D()[0]
+    cView[:] = data
+
+cdef CFloat32Data2D * getObject(i) except NULL:
+    cdef CFloat32Data2D * pDataObject = man2d.get(i)
+    if pDataObject == NULL:
+        raise Exception("Data object not found")
+    if not pDataObject.isInitialized():
+        raise Exception("Data object not initialized properly.")
+    return pDataObject
+
+
+def store(i, data):
+    cdef CFloat32Data2D * pDataObject = getObject(i)
+    fillDataObject(pDataObject, data)
+
+
+def get_geometry(i):
+    cdef CFloat32Data2D * pDataObject = getObject(i)
+    cdef CFloat32ProjectionData2D * pDataObject2
+    cdef CFloat32VolumeData2D * pDataObject3
+    if pDataObject.getType() == PROJECTION:
+        pDataObject2 = <CFloat32ProjectionData2D * >pDataObject
+        geom = utils.createProjectionGeometryStruct(pDataObject2.getGeometry())
+    elif pDataObject.getType() == VOLUME:
+        pDataObject3 = <CFloat32VolumeData2D * >pDataObject
+        geom = utils.createVolumeGeometryStruct(pDataObject3.getGeometry())
+    else:
+        raise Exception("Not a known data object")
+    return geom
+
+
+def change_geometry(i, geom):
+    cdef XMLDocument * xml
+    cdef Config cfg
+    cdef CVolumeGeometry2D * pGeometry
+    cdef CProjectionGeometry2D * ppGeometry
+    cdef CFloat32Data2D * pDataObject = getObject(i)
+    cdef CFloat32ProjectionData2D * pDataObject2
+    cdef CFloat32VolumeData2D * pDataObject3
+    if pDataObject.getType() == PROJECTION:
+        pDataObject2 = <CFloat32ProjectionData2D * >pDataObject
+        xml = utils.dict2XML(six.b('ProjectionGeometry'), geom)
+        cfg.self = xml.getRootNode()
+        tpe = wrap_from_bytes(cfg.self.getAttribute(six.b('type')))
+        if (tpe == 'sparse_matrix'):
+            ppGeometry = <CProjectionGeometry2D * >new CSparseMatrixProjectionGeometry2D()
+        elif (tpe == 'fanflat'):
+            ppGeometry = <CProjectionGeometry2D * >new CFanFlatProjectionGeometry2D()
+        elif (tpe == 'fanflat_vec'):
+            ppGeometry = <CProjectionGeometry2D * >new CFanFlatVecProjectionGeometry2D()
+        else:
+            ppGeometry = <CProjectionGeometry2D * >new CParallelProjectionGeometry2D()
+        if not ppGeometry.initialize(cfg):
+            del xml
+            del ppGeometry
+            raise Exception('Geometry class not initialized.')
+        if (ppGeometry.getDetectorCount() != pDataObject2.getDetectorCount() or ppGeometry.getProjectionAngleCount() != pDataObject2.getAngleCount()):
+            del ppGeometry
+            del xml
+            raise Exception(
+                "The dimensions of the data do not match those specified in the geometry.")
+        pDataObject2.changeGeometry(ppGeometry)
+        del ppGeometry
+        del xml
+    elif pDataObject.getType() == VOLUME:
+        pDataObject3 = <CFloat32VolumeData2D * >pDataObject
+        xml = utils.dict2XML(six.b('VolumeGeometry'), geom)
+        cfg.self = xml.getRootNode()
+        pGeometry = new CVolumeGeometry2D()
+        if not pGeometry.initialize(cfg):
+            del xml
+            del pGeometry
+            raise Exception('Geometry class not initialized.')
+        if (pGeometry.getGridColCount() != pDataObject3.getWidth() or pGeometry.getGridRowCount() != pDataObject3.getHeight()):
+            del xml
+            del pGeometry
+            raise Exception(
+                'The dimensions of the data do not match those specified in the geometry.')
+        pDataObject3.changeGeometry(pGeometry)
+        del xml
+        del pGeometry
+    else:
+        raise Exception("Not a known data object")
+
+@cython.boundscheck(False)
+@cython.wraparound(False)
+def get(i):
+    cdef CFloat32Data2D * pDataObject = getObject(i)
+    outArr = np.empty((pDataObject.getHeight(), pDataObject.getWidth()),dtype=np.float32,order='C')
+    cdef float [:,::1] mView = outArr
+    cdef float [:,::1] cView =  <float[:outArr.shape[0],:outArr.shape[1]]> pDataObject.getData2D()[0]
+    mView[:] = cView
+    return outArr
+
+def get_shared(i):
+    cdef CFloat32Data2D * pDataObject = getObject(i)
+    cdef np.npy_intp shape[2]
+    shape[0] = <np.npy_intp> pDataObject.getHeight()
+    shape[1] = <np.npy_intp> pDataObject.getWidth()
+    return np.PyArray_SimpleNewFromData(2,shape,np.NPY_FLOAT32,<void *>pDataObject.getData2D()[0])
+
+
+def get_single(i):
+    raise Exception("Not yet implemented")
+
+
+def info():
+    six.print_(wrap_from_bytes(man2d.info()))