Final changes to astra

Author: nicwade

savu/plugins/base_recon.py

@@ -154,7 +154,7 @@ def setup(self):
 
         shape = list(in_dataset[0].get_shape())
         shape[dim_volX] = shape[dim_volZ]
-
+        
         out_dataset[0].create_dataset(axis_labels=axis_labels,
                                       shape=tuple(shape))
 

savu/plugins/reconstructions/astra_recons/astra_recon_gpu.py

@@ -38,8 +38,8 @@ class AstraReconGpu(BaseAstraRecon, GpuPlugin):
     :param res_norm: Output the residual norm at each iteration\
         (Error in the solution). Default: False.
     :param reconstruction_type: Reconstruction type (FBP_CUDA|SIRT_CUDA|\
-        SART_CUDA|CGLS_CUDA|FP_CUDA|BP_CUDA|SIRT3D_CUDA|\
-        CGLS3D_CUDA). Default: 'FBP_CUDA'.
+        SART_CUDA (not currently working)|CGLS_CUDA|FP_CUDA|BP_CUDA|\
+        SIRT3D_CUDA|CGLS3D_CUDA). Default: 'FBP_CUDA'.
     """
 
     def __init__(self):
@@ -92,6 +92,7 @@ def setup_3D(self):
         self.manual_mask = True if not self.parameters['sino_pad'] else False
 
     def astra_3D_recon(self, sino, cors, angles, vol_shape, init):
+        sino = sino[:,:,10:]
 #        while len(cors) is not self.sino_shape[self.slice_dir]:
 #            cors.append(0)
         proj_id = False

savu/plugins/reconstructions/base_astra_recon.py

@@ -53,7 +53,7 @@ def get_parameters(self):
     def setup(self):
         super(BaseAstraRecon, self).setup()
         out_dataset = self.get_out_datasets()
-        # is res_norm is required then setup another output dataset
+        # if res_norm is required then setup another output dataset
         if len(out_dataset) is 2:
             self.res = True
             out_pData = self.get_plugin_out_datasets()
@@ -71,8 +71,6 @@ def setup(self):
                                            self.get_max_frames(), fixed=True)
 
     def pre_process(self):
-        # *****check here if there are deviations in the cor and determine the algorithm***
-        # perhaps do the above in base pre-process
         self.alg, self.iters = self.get_parameters()
         if '3D' in self.alg:
             self.setup_3D()
@@ -189,9 +187,11 @@ def set_config(self, rec_id, sino_id, proj_geom, vol_geom):
             proj_id = astra.create_projector(
                 self.parameters['projector'], proj_geom, vol_geom)
             cfg['ProjectorId'] = proj_id
-#        if self.mask_id:
-#            cfg['option'] = {}
-#            cfg['option']['ReconstructionMaskId'] = self.mask_id
+        # mask not currently working correctly for SIRT or SART algorithms
+        sirt_or_sart = [a for a in ['SIRT', 'SART'] if a in self.alg]
+        if self.mask_id and not sirt_or_sart:
+            cfg['option'] = {}
+            cfg['option']['ReconstructionMaskId'] = self.mask_id
         cfg = self.set_options(cfg)
         return cfg
 
@@ -227,7 +227,6 @@ def array_pad(self, ctr, nPixels):
         return np.array([int(p_low), int(p_high)])
 
     def get_max_frames(self):
-        #return 8 if "3D" in self.get_parameters()[0] else 1
         return 8
 
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