Fix astra wrapper for recent astra versions (#457)

* Add support for recent ASTRA versions in wrapper

* Make ASTRA center of rotation correction similar to Tomopy

source/tomopy/recon/wrappers.py

@@ -151,26 +151,22 @@ def astra(tomo, center, recon, theta, **kwargs):
     vol_geom = astra_mod.create_vol_geom((num_gridx, num_gridy))
 
     # Number of GPUs to use
-    if proj_type == 'cuda':
-        if opts['gpu_list'] is not None:
-            import concurrent.futures as cf
-            gpu_list = opts['gpu_list']
-            ngpu = len(gpu_list)
-            _, slcs = mproc.get_ncore_slices(nslices, ngpu)
-            # execute recon on a thread per GPU
-            with cf.ThreadPoolExecutor(ngpu) as e:
-                for gpu, slc in zip(gpu_list, slcs):
-                    e.submit(astra_rec_cuda, tomo[slc], center[slc], recon[slc],
-                             theta, vol_geom, niter, proj_type, gpu, opts)
-        else:
-            astra_rec_cuda(tomo, center, recon, theta, vol_geom, niter,
-                           proj_type, None, opts)
+    if proj_type == 'cuda' and opts['gpu_list'] is not None:
+        import concurrent.futures as cf
+        gpu_list = opts['gpu_list']
+        ngpu = len(gpu_list)
+        _, slcs = mproc.get_ncore_slices(nslices, ngpu)
+        # execute recon on a thread per GPU
+        with cf.ThreadPoolExecutor(ngpu) as e:
+            for gpu, slc in zip(gpu_list, slcs):
+                e.submit(astra_rec, tomo[slc], center[slc], recon[slc],
+                            theta, vol_geom, niter, proj_type, gpu, opts)
     else:
-        astra_rec_cpu(tomo, center, recon, theta, vol_geom, niter,
-                      proj_type, opts)
+        astra_rec(tomo, center, recon, theta, vol_geom, niter,
+                           proj_type, None, opts)
 
 
-def astra_rec_cuda(tomo, center, recon, theta, vol_geom, niter, proj_type, gpu_index, opts):
+def astra_rec(tomo, center, recon, theta, vol_geom, niter, proj_type, gpu_index, opts):
     # Lazy import ASTRA
     import astra as astra_mod
     nslices, nang, ndet = tomo.shape
@@ -182,19 +178,35 @@ def astra_rec_cuda(tomo, center, recon, theta, vol_geom, niter, proj_type, gpu_i
         cfg['option'] = {}
     if gpu_index is not None:
         cfg['option']['GPUindex'] = gpu_index
-    oc = None
     const_theta = np.ones(nang)
     proj_geom = astra_mod.create_proj_geom(
         'parallel', 1.0, ndet, theta.astype(np.float64))
+    if hasattr(astra_mod, 'geom_postalignment'):
+        proj_geom_orig = proj_geom
     for i in range(nslices):
-        if center[i] != oc:
-            oc = center[i]
-            proj_geom['option'] = {
-                'ExtraDetectorOffset':
-                (center[i] - ndet / 2.) * const_theta}
+        sino = tomo[i]
+        if proj_type=='cuda':
+            if hasattr(astra_mod, 'geom_postalignment'):
+                proj_geom = astra_mod.geom_postalignment(proj_geom_orig, -(center[i] - ndet / 2.))
+            else:
+                proj_geom['option'] = {
+                    'ExtraDetectorOffset':
+                    (center[i] - ndet / 2.) * const_theta}
+        else:
+            shft = int(np.round(ndet / 2. - center[i]))
+            if not shft == 0:
+                sino = np.roll(tomo[i], shft)
+                l = shft
+                r = ndet + shft
+                if l < 0:
+                    l = 0
+                if r > ndet:
+                    r = ndet
+                sino[:, :l] = 0
+                sino[:,  r:] = 0
         pid = astra_mod.create_projector(proj_type, proj_geom, vol_geom)
         cfg['ProjectorId'] = pid
-        sid = astra_mod.data2d.link('-sino', proj_geom, tomo[i])
+        sid = astra_mod.data2d.link('-sino', proj_geom, sino)
         cfg['ProjectionDataId'] = sid
         vid = astra_mod.data2d.link('-vol', vol_geom, recon[i])
         cfg['ReconstructionDataId'] = vid
@@ -206,44 +218,6 @@ def astra_rec_cuda(tomo, center, recon, theta, vol_geom, niter, proj_type, gpu_i
         astra_mod.projector.delete(pid)
 
 
-def astra_rec_cpu(tomo, center, recon, theta, vol_geom, niter, proj_type, opts):
-    # Lazy import ASTRA
-    import astra as astra_mod
-    nslices, nang, ndet = tomo.shape
-    cfg = astra_mod.astra_dict(opts['method'])
-    if 'extra_options' in opts:
-        cfg['option'] = opts['extra_options']
-    proj_geom = astra_mod.create_proj_geom(
-        'parallel', 1.0, ndet, theta.astype(np.float64))
-    pid = astra_mod.create_projector(proj_type, proj_geom, vol_geom)
-    sino = np.zeros((nang, ndet), dtype=np.float32)
-    sid = astra_mod.data2d.link('-sino', proj_geom, sino)
-    cfg['ProjectorId'] = pid
-    cfg['ProjectionDataId'] = sid
-    for i in range(nslices):
-        shft = int(np.round(ndet / 2. - center[i]))
-        if not shft == 0:
-            sino[:] = np.roll(tomo[i], shft)
-            l = shft
-            r = ndet + shft
-            if l < 0:
-                l = 0
-            if r > ndet:
-                r = ndet
-            sino[:, :l] = 0
-            sino[:,  r:] = 0
-        else:
-            sino[:] = tomo[i]
-        vid = astra_mod.data2d.link('-vol', vol_geom, recon[i])
-        cfg['ReconstructionDataId'] = vid
-        alg_id = astra_mod.algorithm.create(cfg)
-        astra_mod.algorithm.run(alg_id, niter)
-        astra_mod.algorithm.delete(alg_id)
-        astra_mod.data2d.delete(vid)
-    astra_mod.data2d.delete(sid)
-    astra_mod.projector.delete(pid)
-
-
 def _process_data(input_task, output_task, sinograms, slices):
     import ufo.numpy as unp
     num_sinograms, num_projections, width = sinograms.shape