def __init__(self,data,order=['x','y','z'],phantomdim=[20,10],phantomvolume=9500,dose=75,dosecaltime='000000',remdose=0,remdosecaltime='000000'):
print order
self.xind = order.index('x')
self.yind = order.index('y')
self.zind = order.index('z')
axes = [self.xind,self.yind,self.zind]
print data
pixelsize,array,info = niq.loaddata(data)
print info
self.pixel_size = pixelsize
print "pixelsize: ", pixelsize
self.phantomvolume = float(phantomvolume)
self.dose = float(dose)
self.dosecaltime = str(dosecaltime)
self.remdose = float(remdose)
self.remdosecaltime = str(remdosecaltime)
self.rows = info.info["0028","0010"].value
self.cols = info.info["0028","0011"].value
self.vendor = info.info["0008","0070"].value
if self.vendor == 'Philips Medical Systems':
self.suvfactor = info.info["7053","1009"].value
else:
self.suvfactor = 1.0
self.weight = info.info["0010","1030"].value
print "Acquisition date",info.info["0008","0022"].value #Date
acqtime = info.info["0008","0032"].value.split('.')[0] #Acq. Time and we remove the microseconds
print "Acquisition time: ", acqtime
print "Activity calibrated: %s at %s "%(self.dose,self.dosecaltime)
print "Remainder activity: %s at %s "%(self.remdose,self.remdosecaltime)
self.fmt = '%H%M%S'
self.fmt2 = '%H%M'
t1 = datetime.strptime(acqtime, self.fmt) #acquisition time dcmhdr
t2 = datetime.strptime(self.dosecaltime, self.fmt) #act. cal time
t3 = datetime.strptime(self.remdosecaltime, self.fmt)#remaining activity cal time
# Activity concentration at acquisitiontime:
deltat0 = float((t1 - t2).seconds/60.) #minutes
deltatr = float((t2 - t3).seconds/60.) #minutes
self.currconc = niqlib.calc_act_con(self.phantomvolume,self.dose,deltat0,self.remdose,deltatr)
print "Net activity at acquisition : %s "%self.currconc
def __init__(self,data,order=['x','y','z'],phantomdim=[20,10],phantomvolume=9500,dose=75,dosecaltime='000000',remdose=0,remdosecaltime='000000'):
print order
self.xind = order.index('x')
self.yind = order.index('y')
self.zind = order.index('z')
axes = [self.xind,self.yind,self.zind]
print data
pixelsize,array,info = niq.loaddata(data)
print info
self.pixel_size = pixelsize
print "pixelsize: ", pixelsize
self.phantomvolume = float(phantomvolume)
self.dose = float(dose)
self.dosecaltime = str(dosecaltime)
self.remdose = float(remdose)
self.remdosecaltime = str(remdosecaltime)
self.rows = info.info["0028","0010"].value
self.cols = info.info["0028","0011"].value
self.vendor = info.info["0008","0070"].value
if self.vendor == 'Philips Medical Systems':
self.suvfactor = info.info["7053","1009"].value
else:
self.suvfactor = 1.0
self.weight = info.info["0010","1030"].value
print "Acquisition date",info.info["0008","0022"].value #Date
acqtime = info.info["0008","0032"].value.split('.')[0] #Acq. Time and we remove the microseconds
print "Acquisition time: ", acqtime
print "Activity calibrated: %s at %s "%(self.dose,self.dosecaltime)
print "Remainder activity: %s at %s "%(self.remdose,self.remdosecaltime)
self.fmt = '%H%M%S'
self.fmt2 = '%H%M'
t1 = datetime.strptime(acqtime, self.fmt) #acquisition time dcmhdr
t2 = datetime.strptime(self.dosecaltime, self.fmt) #act. cal time
t3 = datetime.strptime(self.remdosecaltime, self.fmt)#remaining activity cal time
# Activity concentration at acquisitiontime:
deltat0 = float((t1 - t2).seconds/60.) #minutes
deltatr = float((t2 - t3).seconds/60.) #minutes
self.currconc = niqlib.calc_act_con(self.phantomvolume,self.dose,deltat0,self.remdose,deltatr)
print "Net activity at acquisition : %s "%self.currconc
#float(indata.info["0028","0030"].value[0])
self.bgradius = 4
self.data = np.array(array)
print type(self.data)
print type(self.data[0])
tmpshape = np.shape(self.data)
print tmpshape
self.ddimz = tmpshape[self.zind]
self.ddimy = tmpshape[self.yind]
self.ddimx = tmpshape[self.xind]
self.maxdata = self.data.max()
self.volume = np.zeros(np.shape(data))
# self.mode = mode
self.z = self.z_init()
self.thrdata = copy.deepcopy(self.data)
lowind = (self.thrdata < np.max(self.thrdata[self.z,:,:])*0.2)
self.thrdata[lowind] = 0.0
highind = (self.thrdata >= np.max(self.thrdata[self.z,:,:])*0.2)
self.thrdata[highind] = 10
self.bgdata = copy.deepcopy(self.data)
self.roughcom = ndimage.measurements.center_of_mass(self.data[self.z,:,:])
print "rough com location:", self.roughcom
self.cor = self.roughcom
self.bgspheres = {}
self.set_bg_spheres()
