Merge branch 'parallel_vec'

5 files changed, 77 insertions, 2 deletions

diff --git a/python/astra/PyIncludes.pxd b/python/astra/PyIncludes.pxd
index ec37d0a..84469aa 100644
--- a/python/astra/PyIncludes.pxd
+++ b/python/astra/PyIncludes.pxd
@@ -128,6 +128,10 @@ cdef extern from "astra/FanFlatVecProjectionGeometry2D.h" namespace "astra":
     cdef cppclass CFanFlatVecProjectionGeometry2D:
         CFanFlatVecProjectionGeometry2D()
 
+cdef extern from "astra/ParallelVecProjectionGeometry2D.h" namespace "astra":
+    cdef cppclass CParallelVecProjectionGeometry2D:
+        CParallelVecProjectionGeometry2D()
+
 cdef extern from "astra/ParallelProjectionGeometry2D.h" namespace "astra":
     cdef cppclass CParallelProjectionGeometry2D:
         CParallelProjectionGeometry2D()
diff --git a/python/astra/creators.py b/python/astra/creators.py
index 1e4d937..85daf82 100644
--- a/python/astra/creators.py
+++ b/python/astra/creators.py
@@ -147,6 +147,13 @@ This method can be called in a number of ways:
 :type angles: :class:`numpy.ndarray`
 :returns: A parallel projection geometry.
 
+``create_proj_geom('parallel_vec', det_count, V)``:
+
+:param det_count: Number of detector pixels.
+:type det_count: :class:`int`
+:param V: Vector array.
+:type V: :class:`numpy.ndarray`
+:returns: A parallel-beam projection geometry.
 
 ``create_proj_geom('fanflat', det_width, det_count, angles, source_origin, origin_det)``:
 
@@ -234,6 +241,12 @@ This method can be called in a number of ways:
             raise Exception(
                 'not enough variables: astra_create_proj_geom(parallel, detector_spacing, det_count, angles)')
         return {'type': 'parallel', 'DetectorWidth': args[0], 'DetectorCount': args[1], 'ProjectionAngles': args[2]}
+    elif intype == 'parallel_vec':
+        if len(args) < 2:
+            raise Exception('not enough variables: astra_create_proj_geom(parallel_vec, det_count, V)')
+        if not args[1].shape[1] == 6:
+            raise Exception('V should be a Nx6 matrix, with N the number of projections')
+        return {'type':'parallel_vec', 'DetectorCount':args[0], 'Vectors':args[1]}
     elif intype == 'fanflat':
         if len(args) < 5:
             raise Exception('not enough variables: astra_create_proj_geom(fanflat, det_width, det_count, angles, source_origin, origin_det)')
diff --git a/python/astra/data2d_c.pyx b/python/astra/data2d_c.pyx
index 9c88073..1b1125d 100644
--- a/python/astra/data2d_c.pyx
+++ b/python/astra/data2d_c.pyx
@@ -111,6 +111,8 @@ def create(datatype, geometry, data=None, link=False):
             ppGeometry = <CProjectionGeometry2D * >new CFanFlatProjectionGeometry2D()
         elif (tpe == 'fanflat_vec'):
             ppGeometry = <CProjectionGeometry2D * >new CFanFlatVecProjectionGeometry2D()
+        elif (tpe == 'parallel_vec'):
+            ppGeometry = <CProjectionGeometry2D * >new CParallelVecProjectionGeometry2D()
         else:
             ppGeometry = <CProjectionGeometry2D * >new CParallelProjectionGeometry2D()
         if not ppGeometry.initialize(cfg[0]):
@@ -225,6 +227,8 @@ def change_geometry(i, geom):
             ppGeometry = <CProjectionGeometry2D * >new CFanFlatProjectionGeometry2D()
         elif (tpe == 'fanflat_vec'):
             ppGeometry = <CProjectionGeometry2D * >new CFanFlatVecProjectionGeometry2D()
+        elif (tpe == 'parallel_vec'):
+            ppGeometry = <CProjectionGeometry2D * >new CParallelVecProjectionGeometry2D()
         else:
             ppGeometry = <CProjectionGeometry2D * >new CParallelProjectionGeometry2D()
         if not ppGeometry.initialize(cfg[0]):
diff --git a/python/astra/functions.py b/python/astra/functions.py
index 7277de5..b3a470d 100644
--- a/python/astra/functions.py
+++ b/python/astra/functions.py
@@ -172,7 +172,27 @@ def geom_2vec(proj_geom):
     :param proj_geom: Projection geometry to convert
     :type proj_geom: :class:`dict`
     """
-    if proj_geom['type'] == 'fanflat':
+
+    if proj_geom['type'] == 'parallel':
+        angles = proj_geom['ProjectionAngles']
+        vectors = np.zeros((len(angles), 6))
+        for i in range(len(angles)):
+
+            # source
+            vectors[i, 0] = np.sin(angles[i])
+            vectors[i, 1] = -np.cos(angles[i])
+
+            # center of detector
+            vectors[i, 2] = 0
+            vectors[i, 3] = 0
+
+            # vector from detector pixel 0 to 1
+            vectors[i, 4] = np.cos(angles[i]) * proj_geom['DetectorWidth']
+            vectors[i, 5] = np.sin(angles[i]) * proj_geom['DetectorWidth']
+        proj_geom_out = ac.create_proj_geom(
+        'parallel_vec', proj_geom['DetectorCount'], vectors)
+
+    elif proj_geom['type'] == 'fanflat':
         angles = proj_geom['ProjectionAngles']
         vectors = np.zeros((len(angles), 6))
         for i in range(len(angles)):
@@ -251,3 +271,37 @@ def geom_2vec(proj_geom):
         raise ValueError(
         'No suitable vector geometry found for type: ' + proj_geom['type'])
     return proj_geom_out
+
+
+def geom_postalignment(proj_geom, factor):
+    """Returns the size of a volume or sinogram, based on the projection or volume geometry.
+
+    :param proj_geom: input projection geometry (vector-based only, use astra.geom_2vec to convert conventional projection geometries)
+    :type proj_geom: :class:`dict`
+    :param factor: Optional axis index to return
+    :type factor: :class:`float`
+    """
+
+    if proj_geom['type'] == 'parallel_vec' or proj_geom['type'] == 'fanflat_vec':
+        for i in range(proj_geom['Vectors'].shape[0]):
+            proj_geom['Vectors'][i,2] = proj_geom['Vectors'][i,2] + factor * proj_geom['Vectors'][i,4];
+            proj_geom['Vectors'][i,3] = proj_geom['Vectors'][i,3] + factor * proj_geom['Vectors'][i,5];
+
+    elif proj_geom['type'] == 'parallel3d_vec' or proj_geom['type'] == 'cone_vec':
+
+        if len(factor) == 1:
+            for i in range(proj_geom['Vectors'].shape[0]):
+                proj_geom['Vectors'][i,3] = proj_geom['Vectors'][i,3] + factor * proj_geom['Vectors'][i,6];
+                proj_geom['Vectors'][i,4] = proj_geom['Vectors'][i,4] + factor * proj_geom['Vectors'][i,7];
+                proj_geom['Vectors'][i,5] = proj_geom['Vectors'][i,5] + factor * proj_geom['Vectors'][i,8];
+
+        elif len(factor) > 1:
+            for i in range(proj_geom['Vectors'].shape[0]):
+                proj_geom['Vectors'][i,3] = proj_geom['Vectors'][i,3] + factor[0] * proj_geom['Vectors'][i,6] + factor[1] * proj_geom['Vectors'][i, 9];
+                proj_geom['Vectors'][i,4] = proj_geom['Vectors'][i,4] + factor[0] * proj_geom['Vectors'][i,7] + factor[1] * proj_geom['Vectors'][i,10];
+                proj_geom['Vectors'][i,5] = proj_geom['Vectors'][i,5] + factor[0] * proj_geom['Vectors'][i,8] + factor[1] * proj_geom['Vectors'][i,11];
+    else:
+        raise ValueError('No suitable geometry for postalignment: ' + proj_geom['type'])
+
+    return proj_geom
+
diff --git a/python/astra/pythonutils.py b/python/astra/pythonutils.py
index 27fa8fd..1028a0a 100644
--- a/python/astra/pythonutils.py
+++ b/python/astra/pythonutils.py
@@ -51,7 +51,7 @@ def geom_size(geom, dim=None):
     elif geom['type'] == 'parallel3d' or geom['type'] == 'cone':
         s = (geom['DetectorRowCount'], len(
             geom['ProjectionAngles']), geom['DetectorColCount'])
-    elif geom['type'] == 'fanflat_vec':
+    elif geom['type'] == 'fanflat_vec' or geom['type'] == 'parallel_vec':
         s = (geom['Vectors'].shape[0], geom['DetectorCount'])
     elif geom['type'] == 'parallel3d_vec' or geom['type'] == 'cone_vec':
         s = (geom['DetectorRowCount'], geom[