Iterative SIRT working

pydbt/example.py

@@ -16,6 +16,7 @@
 from functions.initialConfig import initialConfig
 
 from functions.FBP import FDK as FBP
+from functions.SIRT import SIRT
 
 
 #%% Call function for initial configurations
@@ -36,19 +37,23 @@
 
 #%% Set specific recon parameters
 
+nIter = [2];                 # Number of iterations (SIRT)
 filterType = 'FBP';          # Filter type: 'BP', 'FBP'
 cutoff = 0.75;               # Percentage until cut off frequency (FBP)
 
 #%%
 
 print("Starting reconstruction...")
 
-vol = FBP(proj, geo, filterType, cutoff, libFiles)
+#                       ## Uncomment to use ##
+# vol = FBP(proj, geo, filterType, cutoff, libFiles)
 
+vol = SIRT(proj, geo, nIter, libFiles)
 
 plt.figure()
 plt.title('Reconstructed slice')
 plt.imshow(vol[:,:,50] , cmap=plt.get_cmap('gist_gray'))
+plt.imsave('output/Reconstructed_slice.tiff',vol[:,:,50] , cmap=plt.get_cmap('gist_gray'))
 
 # print("Starting projection...")
 # proj = projectionDDb(vol, geo, libFiles) 

pydbt/functions/SIRT.py

@@ -0,0 +1,59 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+"""
+Created on Tue Feb  4 07:50:36 2020
+
+@author: Rodrigo
+"""
+
+import numpy as np
+import time
+
+from functions.backprojectionDDb import backprojectionDDb
+from functions.projectionDDb import projectionDDb
+
+def SIRT(proj, geo, nIter, libFiles):
+
+    highestValue = (2**16) - 1 
+
+    # Initial estimated data 
+    reconData3d = np.zeros([geo.ny, geo.nx, geo.nz]) 
+
+    # Pre calculation of Projection normalization
+    proj_norm = projectionDDb(np.ones([geo.ny, geo.nx, geo.nz]), geo, libFiles) 
+
+    # Pre calculation of Backprojection normalization
+    vol_norm = backprojectionDDb(np.ones([geo.nv, geo.nu, geo.nProj]), geo, libFiles) 
+
+    print('----------------\nStarting SIRT Iterations... \n\n')
+
+    # Start Iterations
+    for iter in range(nIter[-1]):
+
+        startTime = time.time()
+
+        # Error between raw data and projection of estimated data  
+        proj_diff = proj - projectionDDb(reconData3d, geo, libFiles)  
+
+        # Projection normalization
+        proj_diff = proj_diff / proj_norm  
+        proj_diff[np.isnan(proj_diff)] = 0 
+        proj_diff[np.isinf(proj_diff)] = 0 
+
+        upt_term = backprojectionDDb(proj_diff, geo, libFiles) 
+        upt_term = upt_term / vol_norm  # Volume normalization
+        upt_term[np.isnan(upt_term)] = 0 
+        upt_term[np.isinf(upt_term)] = 0 
+
+        # Updates the previous estimation
+        reconData3d = reconData3d + upt_term   
+
+        endTime = time.time()
+
+        # Truncate to highest and minimum value        
+        reconData3d[reconData3d > highestValue] = 0 
+        reconData3d[reconData3d < 0] = 0 
+
+        print('Itaration %d Time: %.2fs\n\n' % (iter , endTime-startTime)) 
+
+    return reconData3d