Merge branch 'master' into parallel_vec

10 files changed, 167 insertions, 39 deletions

diff --git a/python/astra/PyIncludes.pxd b/python/astra/PyIncludes.pxd
index bba47f3..84469aa 100644
--- a/python/astra/PyIncludes.pxd
+++ b/python/astra/PyIncludes.pxd
@@ -156,6 +156,10 @@ cdef extern from "astra/ReconstructionAlgorithm2D.h" namespace "astra":
     cdef cppclass CReconstructionAlgorithm2D:
         bool getResidualNorm(float32&)
 
+cdef extern from "astra/ReconstructionAlgorithm3D.h" namespace "astra":
+    cdef cppclass CReconstructionAlgorithm3D:
+        bool getResidualNorm(float32&)
+
 cdef extern from "astra/Projector2D.h" namespace "astra":
     cdef cppclass CProjector2D:
         bool isInitialized()
@@ -211,7 +215,6 @@ cdef extern from "astra/Float32Data3DMemory.h" namespace "astra":
         CFloat32Data3DMemory()
         void updateStatistics()
         float32 *getData()
-        float32 ***getData3D()
         THREEEDataType getType()
 
 
diff --git a/python/astra/__init__.py b/python/astra/__init__.py
index b73fff5..5e52a1c 100644
--- a/python/astra/__init__.py
+++ b/python/astra/__init__.py
@@ -27,6 +27,7 @@ from . import matlab as m
 from .creators import astra_dict,create_vol_geom, create_proj_geom, create_backprojection, create_sino, create_reconstruction, create_projector,create_sino3d_gpu, create_backprojection3d_gpu
 from .functions import data_op, add_noise_to_sino, clear, move_vol_geom
 from .extrautils import clipCircle
+from .astra import set_gpu_index, get_gpu_info
 from . import data2d
 from . import astra
 from . import data3d
@@ -38,11 +39,12 @@ from . import plugin
 from . import plugins
 from . import log
 from .optomo import OpTomo
+from .tests import test_noCUDA, test_CUDA
 
-__version__ = '1.8'
+__version__ = '1.8.3'
 
 import os
 
 if 'ASTRA_GPU_INDEX' in os.environ:
     L = [ int(x) for x in os.environ['ASTRA_GPU_INDEX'].split(',') ]
-    astra.set_gpu_index(L)
+    set_gpu_index(L)
diff --git a/python/astra/algorithm_c.pyx b/python/astra/algorithm_c.pyx
index 9ed0634..161fe98 100644
--- a/python/astra/algorithm_c.pyx
+++ b/python/astra/algorithm_c.pyx
@@ -44,7 +44,8 @@ from .utils import wrap_from_bytes
 cdef CAlgorithmManager * manAlg = <CAlgorithmManager * >PyAlgorithmManager.getSingletonPtr()
 
 cdef extern from *:
-    CReconstructionAlgorithm2D * dynamic_cast_recAlg "dynamic_cast<astra::CReconstructionAlgorithm2D*>" (CAlgorithm * ) except NULL
+    CReconstructionAlgorithm2D * dynamic_cast_recAlg2D "dynamic_cast<astra::CReconstructionAlgorithm2D*>" (CAlgorithm * )
+    CReconstructionAlgorithm3D * dynamic_cast_recAlg3D "dynamic_cast<astra::CReconstructionAlgorithm3D*>" (CAlgorithm * )
 
 
 def create(config):
@@ -79,12 +80,18 @@ def run(i, iterations=0):
 
 def get_res_norm(i):
     cdef CReconstructionAlgorithm2D * pAlg2D
+    cdef CReconstructionAlgorithm3D * pAlg3D
     cdef CAlgorithm * alg = getAlg(i)
     cdef float32 res = 0.0
-    pAlg2D = dynamic_cast_recAlg(alg)
-    if pAlg2D == NULL:
-        raise Exception("Operation not supported.")
-    if not pAlg2D.getResidualNorm(res):
+    pAlg2D = dynamic_cast_recAlg2D(alg)
+    pAlg3D = dynamic_cast_recAlg3D(alg)
+    if pAlg2D != NULL:
+        if not pAlg2D.getResidualNorm(res):
+            raise Exception("Operation not supported.")
+    elif pAlg3D != NULL:
+        if not pAlg3D.getResidualNorm(res):
+            raise Exception("Operation not supported.")
+    else:
         raise Exception("Operation not supported.")
     return res
 
diff --git a/python/astra/astra.py b/python/astra/astra.py
index 3804d51..434ccb9 100644
--- a/python/astra/astra.py
+++ b/python/astra/astra.py
@@ -45,6 +45,16 @@ def set_gpu_index(idx, memory=0):
     """
     a.set_gpu_index(idx, memory)
 
+def get_gpu_info(idx=-1):
+    """Get GPU info.
+    
+    :param idx: GPU index, or -1 for current device
+    :type idx: :class:`int`
+    :returns: :class:`str` -- GPU info
+    """
+    return a.get_gpu_info(idx)
+
+
 def delete(ids):
     """Delete an astra object.
     
diff --git a/python/astra/astra_c.pyx b/python/astra/astra_c.pyx
index 6de10da..f25fc2a 100644
--- a/python/astra/astra_c.pyx
+++ b/python/astra/astra_c.pyx
@@ -40,11 +40,15 @@ cdef extern from "astra/Globals.h" namespace "astra":
     bool cudaEnabled()
 
 IF HAVE_CUDA==True:
-  cdef extern from "../cuda/2d/darthelper.h" namespace "astraCUDA":
+  cdef extern from "../cuda/2d/astra.h" namespace "astraCUDA":
       bool setGPUIndex(int)
+      string getCudaDeviceString(int)
 ELSE:
   def setGPUIndex():
     pass
+  def getCudaDeviceString(idx):
+    pass
+
 cdef extern from "astra/CompositeGeometryManager.h" namespace "astra":
     cdef cppclass SGPUParams:
         vector[int] GPUIndices
@@ -85,9 +89,13 @@ IF HAVE_CUDA==True:
         ret = setGPUIndex(params.GPUIndices[0])
         if not ret:
             six.print_("Failed to set GPU " + str(params.GPUIndices[0]))
+  def get_gpu_info(idx=-1):
+    return wrap_from_bytes(getCudaDeviceString(idx))
 ELSE:
   def set_gpu_index(idx, memory=0):
     raise NotImplementedError("CUDA support is not enabled in ASTRA")
+  def get_gpu_info(idx=-1):
+    raise NotImplementedError("CUDA support is not enabled in ASTRA")
 
 def delete(ids):
     import collections
diff --git a/python/astra/creators.py b/python/astra/creators.py
index 4ddaf0c..85daf82 100644
--- a/python/astra/creators.py
+++ b/python/astra/creators.py
@@ -81,37 +81,19 @@ This method can be called in a number of ways:
     if len(varargin) == 1 and isinstance(varargin[0], int) == 1:
         vol_geom['GridRowCount'] = varargin[0]
         vol_geom['GridColCount'] = varargin[0]
-        vol_geom['option']['WindowMinX'] = -varargin[0] / 2.
-        vol_geom['option']['WindowMaxX'] = varargin[0] / 2.
-        vol_geom['option']['WindowMinY'] = -varargin[0] / 2.
-        vol_geom['option']['WindowMaxY'] = varargin[0] / 2.
     # astra_create_vol_geom([row_count col_count])
     elif len(varargin) == 1 and len(varargin[0]) == 2:
         vol_geom['GridRowCount'] = varargin[0][0]
         vol_geom['GridColCount'] = varargin[0][1]
-        vol_geom['option']['WindowMinX'] = -varargin[0][1] / 2.
-        vol_geom['option']['WindowMaxX'] = varargin[0][1] / 2.
-        vol_geom['option']['WindowMinY'] = -varargin[0][0] / 2.
-        vol_geom['option']['WindowMaxY'] = varargin[0][0] / 2.
     # astra_create_vol_geom([row_count col_count slice_count])
     elif len(varargin) == 1 and len(varargin[0]) == 3:
         vol_geom['GridRowCount'] = varargin[0][0]
         vol_geom['GridColCount'] = varargin[0][1]
         vol_geom['GridSliceCount'] = varargin[0][2]
-        vol_geom['option']['WindowMinX'] = -varargin[0][1] / 2.
-        vol_geom['option']['WindowMaxX'] = varargin[0][1] / 2.
-        vol_geom['option']['WindowMinY'] = -varargin[0][0] / 2.
-        vol_geom['option']['WindowMaxY'] = varargin[0][0] / 2.
-        vol_geom['option']['WindowMinZ'] = -varargin[0][2] / 2.
-        vol_geom['option']['WindowMaxZ'] = varargin[0][2] / 2.
     # astra_create_vol_geom(row_count, col_count)
     elif len(varargin) == 2:
         vol_geom['GridRowCount'] = varargin[0]
         vol_geom['GridColCount'] = varargin[1]
-        vol_geom['option']['WindowMinX'] = -varargin[1] / 2.
-        vol_geom['option']['WindowMaxX'] = varargin[1] / 2.
-        vol_geom['option']['WindowMinY'] = -varargin[0] / 2.
-        vol_geom['option']['WindowMaxY'] = varargin[0] / 2.
     # astra_create_vol_geom(row_count, col_count, min_x, max_x, min_y, max_y)
     elif len(varargin) == 6:
         vol_geom['GridRowCount'] = varargin[0]
@@ -136,6 +118,17 @@ This method can be called in a number of ways:
         vol_geom['option']['WindowMaxY'] = varargin[6]
         vol_geom['option']['WindowMinZ'] = varargin[7]
         vol_geom['option']['WindowMaxZ'] = varargin[8]
+
+    # set the window options, if not set already.
+    if not 'WindowMinX' in vol_geom['option']:
+        vol_geom['option']['WindowMinX'] = -vol_geom['GridColCount'] / 2.
+        vol_geom['option']['WindowMaxX'] =  vol_geom['GridColCount'] / 2.
+        vol_geom['option']['WindowMinY'] = -vol_geom['GridRowCount'] / 2.
+        vol_geom['option']['WindowMaxY'] =  vol_geom['GridRowCount'] / 2.
+        if 'GridSliceCount' in vol_geom:
+            vol_geom['option']['WindowMinZ'] = -vol_geom['GridSliceCount'] / 2.
+            vol_geom['option']['WindowMaxZ'] =  vol_geom['GridSliceCount'] / 2.
+
     return vol_geom
 
 
diff --git a/python/astra/data3d_c.pyx b/python/astra/data3d_c.pyx
index 78ed620..897634b 100644
--- a/python/astra/data3d_c.pyx
+++ b/python/astra/data3d_c.pyx
@@ -60,7 +60,13 @@ cdef extern from "Python.h":
 cdef CData3DManager * man3d = <CData3DManager * >PyData3DManager.getSingletonPtr()
 
 cdef extern from *:
-    CFloat32Data3DMemory * dynamic_cast_mem "dynamic_cast<astra::CFloat32Data3DMemory*>" (CFloat32Data3D * ) except NULL
+    CFloat32Data3DMemory * dynamic_cast_mem "dynamic_cast<astra::CFloat32Data3DMemory*>" (CFloat32Data3D * )
+
+cdef CFloat32Data3DMemory * dynamic_cast_mem_safe(CFloat32Data3D *obj) except NULL:
+    cdef CFloat32Data3DMemory *ret = dynamic_cast_mem(obj)
+    if not ret:
+        raise RuntimeError("Not a memory 3D data object")
+    return ret
 
 cdef extern from "CFloat32CustomPython.h":
     cdef cppclass CFloat32CustomPython:
@@ -154,12 +160,12 @@ def create(datatype,geometry,data=None, link=False):
         raise RuntimeError("Couldn't initialize data object.")
 
     if not link:
-        fillDataObject(dynamic_cast_mem(pDataObject3D), data)
+        fillDataObject(dynamic_cast_mem_safe(pDataObject3D), data)
 
     return man3d.store(<CFloat32Data3D*>pDataObject3D)
 
 def get_geometry(i):
-    cdef CFloat32Data3DMemory * pDataObject = dynamic_cast_mem(getObject(i))
+    cdef CFloat32Data3DMemory * pDataObject = dynamic_cast_mem_safe(getObject(i))
     cdef CFloat32ProjectionData3DMemory * pDataObject2
     cdef CFloat32VolumeData3DMemory * pDataObject3
     if pDataObject.getType() == THREEPROJECTION:
@@ -173,7 +179,7 @@ def get_geometry(i):
     return geom
 
 def change_geometry(i, geom):
-    cdef CFloat32Data3DMemory * pDataObject = dynamic_cast_mem(getObject(i))
+    cdef CFloat32Data3DMemory * pDataObject = dynamic_cast_mem_safe(getObject(i))
     cdef CFloat32ProjectionData3DMemory * pDataObject2
     cdef CFloat32VolumeData3DMemory * pDataObject3
     if pDataObject.getType() == THREEPROJECTION:
@@ -248,7 +254,7 @@ cdef fillDataObjectScalar(CFloat32Data3DMemory * obj, float s):
 @cython.boundscheck(False)
 @cython.wraparound(False)
 cdef fillDataObjectArray(CFloat32Data3DMemory * obj, float [:,:,::1] data):
-    cdef float [:,:,::1] cView = <float[:data.shape[0],:data.shape[1],:data.shape[2]]> obj.getData3D()[0][0]
+    cdef float [:,:,::1] cView = <float[:data.shape[0],:data.shape[1],:data.shape[2]]> obj.getData()
     cView[:] = data
 
 cdef CFloat32Data3D * getObject(i) except NULL:
@@ -262,28 +268,28 @@ cdef CFloat32Data3D * getObject(i) except NULL:
 @cython.boundscheck(False)
 @cython.wraparound(False)
 def get(i):
-    cdef CFloat32Data3DMemory * pDataObject = dynamic_cast_mem(getObject(i))
+    cdef CFloat32Data3DMemory * pDataObject = dynamic_cast_mem_safe(getObject(i))
     outArr = np.empty((pDataObject.getDepth(),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],:outArr.shape[2]]> pDataObject.getData3D()[0][0]
+    cdef float [:,:,::1] cView = <float[:outArr.shape[0],:outArr.shape[1],:outArr.shape[2]]> pDataObject.getData()
     mView[:] = cView
     return outArr
 
 def get_shared(i):
-    cdef CFloat32Data3DMemory * pDataObject = dynamic_cast_mem(getObject(i))
+    cdef CFloat32Data3DMemory * pDataObject = dynamic_cast_mem_safe(getObject(i))
     outArr = np.empty((pDataObject.getDepth(),pDataObject.getHeight(), pDataObject.getWidth()),dtype=np.float32,order='C')
     cdef np.npy_intp shape[3]
     shape[0] = <np.npy_intp> pDataObject.getDepth()
     shape[1] = <np.npy_intp> pDataObject.getHeight()
     shape[2] = <np.npy_intp> pDataObject.getWidth()
-    return np.PyArray_SimpleNewFromData(3,shape,np.NPY_FLOAT32,<void *>pDataObject.getData3D()[0][0])
+    return np.PyArray_SimpleNewFromData(3,shape,np.NPY_FLOAT32,<void *>pDataObject.getData())
 
 def get_single(i):
     raise NotImplementedError("Not yet implemented")
 
 def store(i,data):
     cdef CFloat32Data3D * pDataObject = getObject(i)
-    fillDataObject(dynamic_cast_mem(pDataObject), data)
+    fillDataObject(dynamic_cast_mem_safe(pDataObject), data)
 
 def dimensions(i):
     cdef CFloat32Data3D * pDataObject = getObject(i)
diff --git a/python/astra/experimental.pyx b/python/astra/experimental.pyx
index 0af3118..136165b 100644
--- a/python/astra/experimental.pyx
+++ b/python/astra/experimental.pyx
@@ -40,8 +40,8 @@ IF HAVE_CUDA==True:
             bool doBP(CProjector3D *, vector[CFloat32VolumeData3D *], vector[CFloat32ProjectionData3D *])
 
     cdef extern from *:
-        CFloat32VolumeData3D * dynamic_cast_vol_mem "dynamic_cast<astra::CFloat32VolumeData3D*>" (CFloat32Data3D * ) except NULL
-        CFloat32ProjectionData3D * dynamic_cast_proj_mem "dynamic_cast<astra::CFloat32ProjectionData3D*>" (CFloat32Data3D * ) except NULL
+        CFloat32VolumeData3D * dynamic_cast_vol_mem "dynamic_cast<astra::CFloat32VolumeData3D*>" (CFloat32Data3D * )
+        CFloat32ProjectionData3D * dynamic_cast_proj_mem "dynamic_cast<astra::CFloat32ProjectionData3D*>" (CFloat32Data3D * )
 
     cdef extern from "astra/Float32ProjectionData3D.h" namespace "astra":
         cdef cppclass CFloat32ProjectionData3D:
diff --git a/python/astra/tests.py b/python/astra/tests.py
new file mode 100644
index 0000000..32afd36
--- /dev/null
+++ b/python/astra/tests.py
@@ -0,0 +1,97 @@
+# -----------------------------------------------------------------------
+# Copyright: 2010-2017, iMinds-Vision Lab, University of Antwerp
+#            2013-2017, CWI, Amsterdam
+#
+# Contact: astra@uantwerpen.be
+# Website: http://www.astra-toolbox.com/
+#
+# This file is part of the ASTRA Toolbox.
+#
+#
+# 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 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 ASTRA Toolbox. If not, see <http://www.gnu.org/licenses/>.
+#
+# -----------------------------------------------------------------------
+
+from __future__ import print_function, absolute_import
+
+def _basic_par2d_fp(type):
+  import astra
+  import numpy as np
+  vg = astra.create_vol_geom(2, 32)
+  pg = astra.create_proj_geom('parallel', 1, 32, [0])
+  proj_id = astra.create_projector(type, pg, vg)
+  vol = np.random.rand(2, 32)
+  (sino_id, sino) = astra.create_sino(vol, proj_id)
+  astra.data2d.delete(sino_id)
+  astra.projector.delete(proj_id)
+  err = np.max(np.abs(sino[0,:] - np.sum(vol,axis=0)))
+  return err < 1e-6
+
+def _basic_par3d_fp():
+  import astra
+  import numpy as np
+  vg = astra.create_vol_geom(2, 32, 32)
+  pg = astra.create_proj_geom('parallel3d', 1, 1, 32, 32, [0])
+  vol = np.random.rand(32, 2, 32)
+  (sino_id, sino) = astra.create_sino3d_gpu(vol, pg, vg)
+  astra.data3d.delete(sino_id)
+  err = np.max(np.abs(sino[:,0,:] - np.sum(vol,axis=1)))
+  return err < 1e-6
+
+
+def _basic_par2d():
+  print("Testing basic CPU 2D functionality... ", end="")
+  if _basic_par2d_fp('line'):
+    print("Ok")
+    return True
+  else:
+    print("Error")
+    return False
+
+def _basic_par2d_cuda():
+  print("Testing basic CUDA 2D functionality... ", end="")
+  if _basic_par2d_fp('cuda'):
+    print("Ok")
+    return True
+  else:
+    print("Error")
+    return False
+
+def _basic_par3d_cuda():
+  print("Testing basic CUDA 3D functionality... ", end="")
+  if _basic_par3d_fp():
+    print("Ok")
+    return True
+  else:
+    print("Error")
+    return False
+
+def test_noCUDA():
+  """Perform a very basic functionality test, without CUDA"""
+  
+  ok = _basic_par2d()
+  if not ok:
+    raise RuntimeError("Test failed")
+
+def test_CUDA():
+  """Perform a very basic functionality test, including CUDA"""
+  
+  import astra
+  print("Getting GPU info... ", end="")
+  print(astra.get_gpu_info())
+  ok1 = _basic_par2d()
+  ok2 = _basic_par2d_cuda()
+  ok3 = _basic_par3d_cuda()
+  if not (ok1 and ok2 and ok3):
+    raise RuntimeError("Test failed")
diff --git a/python/astra/utils.pyx b/python/astra/utils.pyx
index a40916b..bcff6c3 100644
--- a/python/astra/utils.pyx
+++ b/python/astra/utils.pyx
@@ -171,6 +171,7 @@ def stringToPythonValue(inputIn):
     input = castString(inputIn)
     # matrix
     if ';' in input:
+        input = input.rstrip(';')
         row_strings = input.split(';')
         col_strings = row_strings[0].split(',')
         nRows = len(row_strings)
@@ -185,6 +186,7 @@ def stringToPythonValue(inputIn):
 
     # vector
     if ',' in input:
+        input = input.rstrip(',')
         items = input.split(',')
         out = np.empty(len(items))
         for idx,item in enumerate(items):