catsim-test 0.0.5__cp313-cp313-manylinux_2_31_x86_64.whl

gecatsim/pyfiles/GetMu.py

@@ -0,0 +1,68 @@
+# Copyright 2024, GE Precision HealthCare. All rights reserved. See https://github.com/xcist/main/tree/master/license
+
+from ctypes import *
+from gecatsim.pyfiles.ReadMaterialFile import ReadMaterialFile
+from gecatsim.pyfiles.CommonTools import *
+
+def GetMu(materialFile, Evec):
+
+    #----------------- load dll lib and material data path
+    clib = load_C_lib()
+
+    #----------------- initialize cross-section data
+    # the format of this path is finicky and using os.path.join, os.pathsep or changing all \\ to /
+    # does not seem to work on the C code side
+    MaterialDirectory = my_path.paths["material"] + "/"
+
+    c_MaterialDirectory = c_char_p(bytes(MaterialDirectory, 'utf-8'))
+    # b_MaterialDirectory = b"./data/materials/" # bytes, python3
+
+    clib.InitializeCrossSectionDB.argtypes = [POINTER(c_char), c_int] # here c_char_p = POINTER(c_char)
+    clib.InitializeCrossSectionDB.restype = None
+    
+    PairProductionFlag = int(np.max(Evec)>1024)
+
+    # clib.InitializeCrossSectionDB(MaterialDirectory, PairProductionFlag) # not working
+    clib.InitializeCrossSectionDB(c_MaterialDirectory, PairProductionFlag) # works
+    # clib.InitializeCrossSectionDB(b_MaterialDirectory, PairProductionFlag) # works
+
+    #----------------- read material file
+    try:
+        materialFile = my_path.find("material", materialFile, '')
+    except:
+        materialFile = my_path.find("material", materialFile.capitalize(), '') # temp solution to be compatible with old material files
+    
+    (numberOfElements, density, atomicNumbers, massFractions) = ReadMaterialFile(materialFile)
+    atomicNumbers = (c_int*numberOfElements)(*atomicNumbers)
+    massFractions = (c_float*numberOfElements)(*massFractions)
+
+    #----------------- X-ray energy vector
+    isNumpy = isinstance(Evec, np.ndarray)
+    if isNumpy:
+        origShape = Evec.shape
+        Evec = list(Evec.ravel())
+    elif isinstance(Evec, (int, float)):
+        Evec = [Evec]
+    numberOfEnergies = len(Evec)
+    energies = (c_float*numberOfEnergies)(*Evec)
+        
+    #----------------- GetMAC
+    MAC = (c_float*numberOfEnergies)()
+    clib.GetCrossSectionMAC.argtypes = [c_int, POINTER(c_int), POINTER(c_float), c_int, POINTER(c_float), POINTER(c_float)]
+    clib.GetCrossSectionMAC.restype = None
+    clib.GetCrossSectionMAC(numberOfElements, atomicNumbers, massFractions, numberOfEnergies, energies, MAC)
+    
+    mu = []
+    for ii in range(0, numberOfEnergies):
+        mu.append(MAC[ii]*density)
+
+    if isNumpy:
+        mu = np.array(mu,dtype=np.single)
+        mu = mu.reshape(origShape)
+    return mu
+
+# if __name__ == '__main__':
+#     Evec = range(10, 70, 10)
+#     # Evec = np.array([(20, 30, 40), (50, 60, 70)], dtype=np.single)
+#     mu = GetMu('water', Evec)
+#     print(mu, type(mu))

gecatsim/pyfiles/LowSignalCorr.py

@@ -0,0 +1,32 @@
+# Copyright 2024, GE Precision HealthCare. All rights reserved. See https://github.com/xcist/main/tree/master/license
+
+from gecatsim.pyfiles.CommonTools import *
+from scipy.ndimage import convolve1d
+from ctypes import *
+from numpy.ctypeslib import ndpointer
+
+# low signal correction
+def LowSignalCorr(cfg, prep):
+    print("Applying LSC...", end="")
+    inshape = prep.shape
+    lsc_prep = prep.reshape(cfg.protocol.viewCount, cfg.scanner.detectorRowCount, cfg.scanner.detectorColCount)
+    # find negative values and replace them with conv data
+    if np.min(lsc_prep) <= 0:
+        neg_mask = lsc_prep <= 0
+        kernel = [0.5, 0, 0.5]
+        tmpprep = convolve1d(lsc_prep, kernel, axis=2) # perform conv in the col direction
+        lsc_prep[neg_mask] = tmpprep[neg_mask]
+
+    # now perform real LSC
+    func = cfg.clib.negative_log
+    func.argtypes = [c_int, c_int, ndpointer(c_float), ndpointer(c_float), c_int]
+    func.restype = None
+    lsc_prep = np.float32(lsc_prep)
+    for i in range(lsc_prep.shape[0]):
+        thisview = np.copy(lsc_prep[i], order='C')
+        thisviewout = np.zeros(thisview.shape, dtype=np.float32)
+        func(lsc_prep.shape[1], lsc_prep.shape[2], thisview, thisviewout, 1)
+        lsc_prep[i] = thisviewout
+
+    print("done.\n")
+    return lsc_prep.reshape(inshape)

gecatsim/pyfiles/OneScan.py

@@ -0,0 +1,144 @@
+# Copyright 2024, GE Precision HealthCare. All rights reserved. See https://github.com/xcist/main/tree/master/license
+
+import copy, time
+import matplotlib.pyplot as plt
+from gecatsim.pyfiles.CommonTools import *
+from tqdm import tqdm
+from gecatsim.pyfiles.PhantomProjectorWrapper import PhantomWrapper, ProjectorWrapper
+from gecatsim.pyfiles.C_Projector_SetData import C_Projector_SetData
+
+def one_scan(cfg):
+    cfg = initialize_scan(cfg)
+    
+    # view loop
+    if cfg.sim.isPhantomScan:
+        # print('phantom scan view loop...')
+        viewIndex = tqdm(range(cfg.sim.startViewId, cfg.sim.stopViewId+1))
+    else:
+        viewIndex = range(cfg.sim.startViewId, cfg.sim.stopViewId+1)
+    for viewId in viewIndex:
+    # for viewId in range(cfg.sim.startViewId, cfg.sim.stopViewId+1):
+        # detector
+        if viewId == cfg.sim.startViewId or cfg.physics.recalcDet:
+            cfg = feval(cfg.scanner.detectorCallback, cfg)
+
+        # source
+        if viewId == cfg.sim.startViewId or cfg.physics.recalcSrc:
+            cfg = feval(cfg.scanner.focalspotCallback, cfg)
+
+        # ray angles
+        if viewId == cfg.sim.startViewId or cfg.physics.recalcRayAngle:
+            cfg = feval(cfg.physics.rayAngleCallback, cfg)
+
+        # spectrum
+        if viewId == cfg.sim.startViewId or cfg.physics.recalcSpec:
+            cfg = feval(cfg.protocol.spectrumCallback, cfg)
+
+        # filters (bowtie and flat)
+        if viewId == cfg.sim.startViewId or cfg.physics.recalcFilt:
+            cfg = feval(cfg.protocol.filterCallback, cfg)
+
+        # flux
+        if viewId == cfg.sim.startViewId or cfg.physics.recalcFlux:
+            cfg = feval(cfg.physics.fluxCallback, cfg)
+
+        # phantom and material
+        if (viewId == cfg.sim.startViewId or cfg.physics.recalcPht) and cfg.sim.isPhantomScan:
+            cfg = PhantomWrapper(cfg)
+        
+        # Pass det and src to C projectors
+        C_Projector_SetData(cfg, viewId)
+        
+        for subViewId in range(cfg.sim.subViewCount):
+            # initial subview
+            cfg.thisSubView = copy.copy(cfg.detFlux)
+            
+            if cfg.sim.isPhantomScan:
+                # apply gantry rotation and table movement
+                cfg = feval(cfg.protocol.scanTrajectory, cfg, viewId)
+
+                # projector
+                cfg = ProjectorWrapper(cfg, viewId, subViewId)
+
+                # scatter
+                if cfg.physics.scatterCallback:
+                    cfg = feval(cfg.physics.scatterCallback, cfg, viewId, subViewId)
+            
+            # detection, the input: cfg.thisSubView [col-row, energy]
+            #            the output: cfg.thisView [col, row]
+            cfg = feval(cfg.scanner.detectionCallback, cfg, viewId, subViewId)
+
+            cfg = update_scan_time(cfg, subViewId)
+
+        # save cfg.thisView to file
+        cfg = feval(cfg.physics.outputCallback, cfg, viewId)
+        
+    #print("Scan sim time: %.1f s" % (time.time()-cfg.sim.timer))
+    
+    return cfg
+
+def initialize_scan(cfg):
+    # scan type
+    cfg.sim.isAirScan = cfg.sim.thisScanType[0]
+    cfg.sim.isOffsetScan = cfg.sim.thisScanType[1]
+    cfg.sim.isPhantomScan = not(cfg.sim.isAirScan or cfg.sim.isOffsetScan)
+    
+    if cfg.sim.isPhantomScan:
+        cfg.sim.startViewId = cfg.protocol.startViewId
+        cfg.sim.stopViewId = cfg.protocol.stopViewId
+        cfg.sim.subViewCount = cfg.physics.viewSampleCount
+        cfg.sim.enableQuantumNoise = cfg.physics.enableQuantumNoise
+        if cfg.physics.enableElectronicNoise:
+            cfg.sim.eNoise = cfg.scanner.eNoise
+        else:
+            cfg.sim.eNoise = 0
+    else:
+        cfg.sim.startViewId = 0
+        if cfg.sim.isAirScan:
+            cfg.sim.stopViewId = cfg.protocol.airViewCount-1
+        else:
+            cfg.sim.stopViewId = cfg.protocol.offsetViewCount-1
+        cfg.sim.subViewCount = 1
+        cfg.sim.enableQuantumNoise = 0
+        cfg.sim.eNoise = 0
+    cfg.sim.viewCount = cfg.sim.stopViewId-cfg.sim.startViewId+1
+    
+    # scan time
+    startTime = 0
+    viewTime = cfg.protocol.rotationTime/cfg.protocol.viewsPerRotation  # view interval
+    subViewTime = viewTime*cfg.protocol.dutyRatio/cfg.sim.subViewCount  # beam-on time oversampling
+    cfg.time = startTime + cfg.protocol.startViewId*viewTime - 0.5*viewTime + 0.5*subViewTime
+    cfg.viewTime = viewTime
+    cfg.subViewTime = subViewTime
+    
+    # simulation time
+    cfg.sim.timer = time.time()
+    
+    return cfg
+
+def update_scan_time(cfg, subViewId):
+    cfg.time += cfg.subViewTime
+    if cfg.protocol.dutyRatio<1 and subViewId==cfg.sim.subViewCount-1:
+        cfg.time = cfg.time + (1-cfg.protocol.dutyRatio) * cfg.viewTime
+
+    return cfg
+
+# if __name__ == "__main__":
+#
+#     cfg = source_cfg("./cfg/default.cfg")
+#
+#     cfg.sim.thisScanType = [0, 0, 1]
+#     cfg.sim.enableQuantumNoise = 0
+#     cfg.sim.subViewCount = 3
+#     cfg.protocol.startViewId = 0
+#     cfg.protocol.stopViewId = cfg.protocol.viewsPerRotation-1
+#     cfg.protocol.startAngle = 29
+#     cfg.protocol.startZ = 2
+#
+#     cfg = one_scan(cfg)
+#
+#     thisScan = cfg.thisView.reshape(cfg.scanner.detectorColCount, cfg.scanner.detectorRowCount)
+#
+#     check_value(thisScan[400:500, 7])
+#     plt.plot(thisScan[:, 7])
+#     plt.show()

gecatsim/pyfiles/PhantomProjectorWrapper.py

@@ -0,0 +1,65 @@
+import sys
+from copy import copy, deepcopy
+from gecatsim.pyfiles.CommonTools import *
+
+def CopyCfgPhantom(cfgfrom, cfgto=None):
+    if cfgto is None:
+        cfgto = CFG()
+    cfgto.phantom = deepcopy(cfgfrom.phantom)
+
+    return cfgto
+
+# split cfg.phantom from a list into 
+def SplitCfgPhantom(cfg):
+    cfg_list = []
+    cfgphantom_attrs = [x for x in dir(cfg.phantom) if not x.startswith('__')]
+    for i in range(len(cfg.phantom.filename)):
+        thiscfg = CFG()
+        for thisattr in cfgphantom_attrs:
+            setattr(thiscfg.phantom, thisattr, deepcopy(getattr(cfg.phantom, thisattr)[i]))
+
+        cfg_list.append(thiscfg)
+
+    return cfg_list
+
+def PhantomWrapper(cfg):
+    if isinstance(cfg.phantom.callback, list):
+        # if duplicate phantom callback, raise an error
+        if (len(cfg.phantom.callback) != len(set(cfg.phantom.callback))) and len(cfg.phantom.callback) > 1:
+            print("Error! XCIST does not support repeated phantom types.\n")
+            sys.exit(1)
+
+        cfg_list = SplitCfgPhantom(cfg)
+        origCfgPhantom = CopyCfgPhantom(cfg)
+        cfg_nom_list = []
+        for thiscfg in cfg_list:
+            cfg = CopyCfgPhantom(thiscfg, cfg)
+            cfg = feval(cfg.phantom.callback, cfg)
+            if hasattr(cfg.phantom, 'numberOfMaterials'):
+                cfg_nom_list.append(cfg.phantom.numberOfMaterials)
+                delattr(cfg.phantom, 'numberOfMaterials')
+            else:
+                # ncat does not have such property
+                cfg_nom_list.append(None)
+
+        # restore original CFG
+        cfg = CopyCfgPhantom(origCfgPhantom, cfg)
+        cfg.phantom.numberOfMaterials = cfg_nom_list
+    else:
+        cfg = feval(cfg.phantom.callback, cfg)
+
+    return cfg
+
+def ProjectorWrapper(cfg, viewId, subViewId):
+    if isinstance(cfg.phantom.projectorCallback, list):
+        cfg_list = SplitCfgPhantom(cfg)
+        origCfgPhantom = CopyCfgPhantom(cfg)
+        for thiscfg in cfg_list:
+            cfg = CopyCfgPhantom(thiscfg, cfg)
+            cfg = feval(cfg.phantom.projectorCallback, cfg, viewId, subViewId)
+        # restore original CFG
+        cfg = CopyCfgPhantom(origCfgPhantom, cfg)
+    else:
+        cfg = feval(cfg.phantom.projectorCallback, cfg, viewId, subViewId)
+
+    return cfg