From 1d0e10be49f157d4f68bba54c0395d84fafd98a3 Mon Sep 17 00:00:00 2001
From: Jakob Jorgensen <jakob.jorgensen@manchester.ac.uk>
Date: Wed, 7 Mar 2018 10:02:03 +0000
Subject: Extended geoms with channels attribute, added experimental mc demo
 script

---
 Wrappers/Python/ccpi/reconstruction/geoms.py | 45 +++++++++++++++-------------
 Wrappers/Python/test/simple_mc_demo.py       | 43 ++++++++++++++++++++++++++
 2 files changed, 68 insertions(+), 20 deletions(-)
 create mode 100644 Wrappers/Python/test/simple_mc_demo.py

diff --git a/Wrappers/Python/ccpi/reconstruction/geoms.py b/Wrappers/Python/ccpi/reconstruction/geoms.py
index edce3b3..9f81fa0 100644
--- a/Wrappers/Python/ccpi/reconstruction/geoms.py
+++ b/Wrappers/Python/ccpi/reconstruction/geoms.py
@@ -1,16 +1,17 @@
 
 class VolumeGeometry:
     
-    def __init__(self, \
-                 voxel_num_x=None, \
-                 voxel_num_y=None, \
-                 voxel_num_z=None, \
-                 voxel_size_x=None, \
-                 voxel_size_y=None, \
-                 voxel_size_z=None, \
-                 center_x=0, \
-                 center_y=0, \
-                 center_z=0):
+    def __init__(self, 
+                 voxel_num_x=None, 
+                 voxel_num_y=None, 
+                 voxel_num_z=None, 
+                 voxel_size_x=None, 
+                 voxel_size_y=None, 
+                 voxel_size_z=None, 
+                 center_x=0, 
+                 center_y=0, 
+                 center_z=0, 
+                 channels=1):
         
         self.voxel_num_x = voxel_num_x
         self.voxel_num_y = voxel_num_y
@@ -21,6 +22,7 @@ class VolumeGeometry:
         self.center_x = center_x
         self.center_y = center_y
         self.center_z = center_z  
+        self.channels = channels
         
     def getMinX(self):
         return self.center_x - 0.5*self.voxel_num_x*self.voxel_size_x
@@ -43,16 +45,17 @@ class VolumeGeometry:
     
 class SinogramGeometry:
     
-    def __init__(self, \
-                 geom_type, \
-                 dimension, \
-                 angles, \
-                 pixel_num_h=None, \
-                 pixel_size_h=1, \
-                 pixel_num_v=None, \
-                 pixel_size_v=1, \
-                 dist_source_center=None, \
-                 dist_center_detector=None, \
+    def __init__(self, 
+                 geom_type, 
+                 dimension, 
+                 angles, 
+                 pixel_num_h=None, 
+                 pixel_size_h=1, 
+                 pixel_num_v=None, 
+                 pixel_size_v=1, 
+                 dist_source_center=None, 
+                 dist_center_detector=None, 
+                 channels=1
                  ):
         """
         General inputs for standard type projection geometries
@@ -91,6 +94,8 @@ class SinogramGeometry:
         self.pixel_size_h = pixel_size_h
         self.pixel_num_v = pixel_num_v
         self.pixel_size_v = pixel_size_v
+        
+        self.channels = channels
 
         
                 
diff --git a/Wrappers/Python/test/simple_mc_demo.py b/Wrappers/Python/test/simple_mc_demo.py
new file mode 100644
index 0000000..ca6a89e
--- /dev/null
+++ b/Wrappers/Python/test/simple_mc_demo.py
@@ -0,0 +1,43 @@
+
+
+import sys
+
+sys.path.append("..")
+
+from ccpi.framework import *
+from ccpi.reconstruction.algs import *
+from ccpi.reconstruction.funcs import *
+from ccpi.reconstruction.ops import *
+from ccpi.reconstruction.astra_ops import *
+from ccpi.reconstruction.geoms import *
+
+import numpy as np
+import matplotlib.pyplot as plt
+
+test_case = 2   # 1=parallel2D, 2=cone2D
+
+# Set up phantom
+N = 128
+
+numchannels = 3
+
+x = np.zeros((N,N,numchannels))
+
+x[round(N/4):round(3*N/4),round(N/4):round(3*N/4),0] = 1.0
+x[round(N/8):round(7*N/8),round(3*N/8):round(5*N/8),0] = 2.0
+
+x[round(N/4):round(3*N/4),round(N/4):round(3*N/4),1] = 0.7
+x[round(N/8):round(7*N/8),round(3*N/8):round(5*N/8),1] = 1.2
+
+x[round(N/4):round(3*N/4),round(N/4):round(3*N/4),2] = 1.5
+x[round(N/8):round(7*N/8),round(3*N/8):round(5*N/8),2] = 2.2
+
+f, axarr = plt.subplots(1,numchannels)
+for k in numpy.arange(3):
+    axarr[k].imshow(x[:,:,k],vmin=0,vmax=2.5)
+plt.show()
+
+vg = VolumeGeometry(N,N,None, 1,1,None,channels=numchannels)
+
+
+Phantom = VolumeData(x,geometry=vg)
\ No newline at end of file
-- 
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