def close(self):
self.onClose()
# loadavg = os.getloadavg()[0]
# if loadavg > 2.0:
# apDisplay.printMsg("Load average is high "+str(round(loadavg,2)))
# time.sleep(loadavg**2)
apParam.closeFunctionLog(functionname=self.functionname,
logfile=self.logfile, msg=(not self.quiet))
if self.quiet is False:
apDisplay.printMsg("Ended at "+time.strftime("%a, %d %b %Y %H:%M:%S"))
if apDisplay.isDebugOn():
apDisplay.printDebug("Memory increase during run: %.3f MB"%((mem.active()-self.startmem)/1024.0))
apDisplay.printColor("Total run time:\t"+apDisplay.timeString(time.time()-self.t0),"green")
def boxerFrameStack(framestackpath, parttree, outstack, boxsize,framelist):
"""
boxes the particles and returns them as a list of numpy arrays
"""
start_frame = framelist[0]
nframe = len(framelist)
apDisplay.printMsg("boxing %d particles from sum of total %d frames starting from frame %d using mmap" % (len(parttree),nframe,start_frame))
boxedparticles = []
stack = mrc.mmap(framestackpath)
for partdict in parttree:
x1,x2,y1,y2 = getBoxBoundary(partdict, boxsize)
apDisplay.printDebug(' crop range of (x,y)=(%d,%d) to (%d,%d)' % (x1,y1,x2-1,y2-1))
#numpy arrays are rows,cols --> y,x not x,y
boxpart = numpy.sum(stack[tuple(framelist),y1:y2,x1:x2],axis=0)
boxedparticles.append(boxpart)
apImagicFile.writeImagic(boxedparticles, outstack)
return True
def close(self):
self.onClose()
# loadavg = os.getloadavg()[0]
# if loadavg > 2.0:
# apDisplay.printMsg("Load average is high "+str(round(loadavg,2)))
# time.sleep(loadavg**2)
apParam.closeFunctionLog(functionname=self.functionname,
logfile=self.logfile,
msg=(not self.quiet))
if self.quiet is False:
apDisplay.printMsg("Ended at " +
time.strftime("%a, %d %b %Y %H:%M:%S"))
if apDisplay.isDebugOn():
apDisplay.printDebug("Memory increase during run: %.3f MB" %
((mem.active() - self.startmem) / 1024.0))
apDisplay.printColor(
"Total run time:\t" +
apDisplay.timeString(time.time() - self.t0), "green")
