Release v0.1.0, with EXE

Author: MingyeWu

EXE/catsim.exe

@@ -0,0 +1,3 @@
+# Phantom
+phantom.filename = 'CatSim_logo.json'       # phantom filename
+phantom.centerOffset = [0.0, 0.0, 0.0]      # offset of phantom center relative to origin (in mm)

EXE/cfg/Phantom.cfg

@@ -0,0 +1,22 @@
+# Geometric and energy sampling
+physics.energyCount = 20
+physics.monochromatic = -1
+physics.colSampleCount = 2
+physics.rowSampleCount = 2
+physics.srcXSampleCount = 2
+physics.srcYSampleCount = 2
+physics.viewSampleCount = 2
+
+# Flags to determine what has to be recalculated each view
+physics.recalcDet = 0
+physics.recalcSrc = 0
+physics.recalcRayAngle = 0
+physics.recalcSpec = 0
+physics.recalcFilt = 0
+physics.recalcFlux = 0
+physics.recalcPht = 0
+physics.recalcDet = 0
+
+# Noise on/off settings
+physics.enableQuantumNoise = 1
+physics.enableElectronicNoise = 1

EXE/cfg/Physics.cfg

@@ -0,0 +1,26 @@
+cfg.resultsName = "./results/simulation_test"
+protocol.scanTypes = [1, 1, 1]              # flags for airscan, offset scan, phantom scan
+
+# Table and gantry
+protocol.viewsPerRotation = 100		        # total numbers of view per rotation
+protocol.viewCount = 100                    # total number of views in scan
+protocol.startViewId = 0		            # index of the first view in the scan
+protocol.stopViewId = protocol.startViewId+protocol.viewCount-1 # index of the last view in the scan
+protocol.airViewCount = 1		            # number of views averaged for air scan
+protocol.offsetViewCount = 1		        # number of views averaged for offset scan
+protocol.rotationTime = 1.0		            # gantry rotation period (in seconds)
+protocol.rotationDirection = 1		        # gantry rotation direction (1=CW, -1 CCW, seen from table foot-end)
+protocol.startAngle = 0		                # relative to vertical y-axis (n degrees)
+protocol.tableSpeed = 0		                # speed of table translation along positive z-axis (in mm/sec)
+protocol.startZ = 0		                    # start z-position of table
+protocol.tiltAngle = 0		                # gantry tilt angle towards negative z-axis (in degrees)
+protocol.wobbleDistance = 0.0		        # focalspot wobble distance
+protocol.focalspotOffset = [0, 0, 0]		# focalspot position offset
+
+# X-ray tube technique and filtration
+protocol.mA = 200		                    # tube current (in mA)
+protocol.spectrumFilename = "tungsten_tar7_120_unfilt.dat" # name of the spectrum file
+protocol.spectrumScaling = 1		        # scaling factor such that spectrum is in photons / mA / s / mm^2 at 1000 mm
+protocol.bowtie = "sample_bowtie.dat"       # name of the bowtie file (or [])
+protocol.flatFilter = ['al', 3.0]           # additional filtration - materials and thicknesses (in mm)
+protocol.dutyRatio = 1.0                    # tube ON time fraction (for pulsed tubes)

EXE/cfg/Protocol.cfg

@@ -0,0 +1,6 @@
+# Reconstruction
+recon.fov = 500.0           # diameter of the reconstruction field-of-view (in mm)
+recon.imageSize = 512       # number of columns and rows to be reconstructed (square)
+recon.sliceCount = 1        # number of slices to reconstruct
+recon.sliceThickness = 1.0  # reconstruction inter-slice interval (in mm)
+recon.centerOffset = [0.0,0.0,0.0] # reconstruction offset relative to center of rotation (in mm)

EXE/cfg/Recon.cfg

@@ -0,0 +1,25 @@
+# Scanner geometry
+scanner.sid = 540.0                         # source-to-iso distance (in mm)
+scanner.sdd = 950.0                         # source-to-detector distance (in mm)
+scanner.detectorColsPerMod = 1              # number of detector columns per module
+scanner.detectorRowsPerMod = 16             # number of detector rows per module
+scanner.detectorColOffset = 0.0             # detector column offset relative to centered position (in detector columns)
+scanner.detectorRowOffset = 0.0             # detector row offset relative to centered position (in detector rows)
+scanner.detectorColSize = 1.0               # detector column pitch or size (in mm)
+scanner.detectorRowSize = 1.0               # detector row pitch or size (in mm)
+scanner.detectorColCount = 900              # total number of detector columns
+scanner.detectorRowCount = scanner.detectorRowsPerMod     # total number of detector rows
+scanner.detectorPrefilter = ['graphite', 1.0]  # detector filter
+
+# X-ray tube
+scanner.targetAngle = 7.0                   # target angle relative to scanner XY-plane (in degrees)
+scanner.focalspotWidth = 1.0
+scanner.focalspotLength = 1.0
+
+# Detector
+scanner.detectorMaterial = "lumex"          # detector sensor material
+scanner.detectorDepth = 3.0                 # detector sensor depth (in mm)
+scanner.detectionGain = 15.0                # factor to convert energy to electrons (electrons / keV)
+scanner.detectorColFillFraction = 0.9       # active fraction of each detector cell in the column direction
+scanner.detectorRowFillFraction = 0.9       # active fraction of each detector cell in the row direction
+scanner.eNoise = 5000.0                     # standard deviation of Gaussian electronic noise (in electrons)

EXE/cfg/Scanner.cfg

@@ -0,0 +1,23 @@
+# Copyright 2020, General Electric Company. All rights reserved. See https://github.com/xcist/code/blob/master/LICENSE
+
+
+##--------- Make changes to parameters or load other cfg files (optional)
+# ct.resultsName = "./results/simulation_test"
+# ct.protocol.viewsPerRotation = 50
+# ct.protocol.viewCount = ct.protocol.viewsPerRotation
+# ct.protocol.stopViewId = ct.protocol.viewCount-1
+# ct.protocol.scanTypes = [1, 0, 0]  # flags for airscan, offset scan, phantom scan
+# ct.load_cfg("Protocol_Sample_axial", "Physics_Sample", "Recon_Sample_2d")  # new cfg overrides existing parameters
+
+##--------- Run simulation
+ct.run_all()  # run the scans defined by protocol.scanTypes
+
+##--------- show results
+import matplotlib.pyplot as plt
+prep = xc.rawread(ct.resultsName+'.prep', [ct.protocol.viewCount, ct.scanner.detectorColCount, ct.scanner.detectorRowCount], 'float')
+prep = prep[-1, :, :]
+plt.plot(prep[:, 7])
+plt.show()
+
+print()
+os.system('pause')

EXE/cfg/sim.py

@@ -28,6 +28,7 @@ def run_all(self, *para):
             cfg = self.phantom_scan(cfg)
         if all(scanTypes):
             cfg = self.prep_view(cfg)
+        print('Simulation is done')
         return cfg
 
     def air_scan(self, *para):

catsim/CatSim.py

@@ -137,7 +137,7 @@ def source_cfg(*para):
     return cfg
 
 def vectornorm(xyz):
-    if xyz.shape[0] is not 3:
+    if xyz.shape[0]!=3:
         print('ERROR : argument of vectornorm has to be of size 3 x n');
         return
     else:

catsim/CommonTools.py

@@ -63,7 +63,7 @@ def one_scan(cfg):
 
         if cfg.sim.viewCount>10 and (viewId+1)%round(cfg.sim.viewCount/10)==0:
             print("Simulated view %d/%d, time: %.1f s" % (viewId+1, cfg.sim.viewCount, time.time()-cfg.sim.timer))
-    print("Total sim time: %.1f s" % (time.time()-cfg.sim.timer))
+    print("Scan sim time: %.1f s" % (time.time()-cfg.sim.timer))
 
     return cfg