def setDefaultParams(self):
params = experiparams(self.experimentName,
self.runNumber,
detectorName=self.detectorName,
outDir=self.outDir)
params.setDefaultPsana()
self.queue = 'psanaq'
self.nodes = 1
self.ncpus = 12
self.outDir = params.cxiDir
self.logFile = params.cxiDir + "/.%J.log"
self.noe = -1
self.jobName = "%s-r%.4d" % (params.experimentName, params.runNumber)
## peak finder algorithm params
self.minPeaks = 15
self.maxPeaks = 2048
self.minRes = -1
self.pkTag = ""
## mask params
self.staticMask = params.cxiDir + '/staticMask.h5'
self.userMask_path = None
## other params
self.clen = params.clenEpics
self.coffset = params.coffset
self.instrument = params.instrument
self.pixelSize = params.pixelSize
self.detectorDistance = params.detectorDistance
def deployCenter(experimentName, runNumber, detectorName, newCx, newCy):
## deploy the new geometry file
## Calculate detector translation in x and y
ds = psana.DataSource("exp=" + experimentName + ":run=" + str(runNumber) +
':idx')
run = ds.runs().next()
det = psana.Detector(detectorName)
times = run.times()
evt = None
counter = 0
while evt is None:
evt = run.event(times[counter]) # guarantee we have a valid event
counter += 1
psanaCx, psanaCy = det.point_indexes(evt, pxy_um=(0, 0))
pixelSize = det.pixel_size(evt)
print "##### current psana center: ", psanaCx, psanaCy
dx = pixelSize * (psanaCx - newCx) # microns
dy = pixelSize * (psanaCy - newCy) # microns
geo = det.geometry(evt)
if 'cspad' in detectorName.lower() and 'cxi' in experimentName:
geo.move_geo('CSPAD:V1', 0, dx=dx, dy=dy, dz=0)
elif 'rayonix' in detectorName.lower() and 'mfx' in experimentName:
top = geo.get_top_geo()
children = top.get_list_of_children()[0]
geo.move_geo(children.oname, 0, dx=dx, dy=dy, dz=0)
elif 'rayonix' in detectorName.lower() and 'xpp' in experimentName:
top = geo.get_top_geo()
children = top.get_list_of_children()[0]
geo.move_geo(children.oname, 0, dx=dx, dy=dy, dz=0)
else:
print "autoDeploy not implemented"
params = experiparams(experimentName=experimentName,
runNumber=runNumber,
detectorName=detectorName)
fname = params.cxiDir + "/" + str(runNumber) + '-end.data'
print "fname: ", fname
geo.save_pars_in_file(fname)
print "#################################################"
print "Deploying psana detector geometry: ", fname
print "#################################################"
cmts = {
'exp': experimentName,
'app': 'psocake',
'comment': 'auto recentred geometry'
}
calibDir = '/reg/d/psdm/' + experimentName[:3] + '/' + experimentName + '/calib'
deploy_calib_file(cdir=calibDir,
src=str(det.name),
type='geometry',
run_start=int(runNumber),
run_end=None,
ifname=fname,
dcmts=cmts,
pbits=0)
def loadPsanaGeo(self):
self.params = experiparams(self.experimentName,
self.runNumber,
detectorName=self.detectorName)
self.params.setDefaultPsana()
self.detectorDistance = self.params.detectorDistance
self.coffset = self.params.coffset
self.clen = self.params.clen
self.geomfile = self.params.cxiDir + "/.temp.geom"
def runmaster(args):
exprun = "exp="+str(args.exp)+":run="+str(args.run)
ds = psana.DataSource(exprun+':idx')
run = ds.runs().next()
det = psana.Detector(args.det)
times = run.times()
evt = None
counter = 0
while evt is None:
evt = run.event(times[counter])
counter += 1
max_img = None
mean_img = None
median_img = None
## counter is a monitor to record how many images have been process in total
## nClients is the number of clients to process the data
counter = 0.
nClients = comm_size-1
while nClients > 0:
# Remove client if the run ended
md = mpidata()
md.recv()
if max_img is None:
max_img = md.max_img
mean_img = md.mean_img
median_img = md.median_img
else:
max_img = np.maximum(max_img, md.max_img)
mean_img = (mean_img * counter + md.mean_img * md.small.counter)*1.0/(counter + md.small.counter)
counter = counter + md.small.counter
nClients -= 1
print "##### Total number of images: %s/%s " % (str(counter), str(args.noe))
params = experiparams(experimentName=args.exp, runNumber=args.run, outDir=os.path.realpath(args.outDir))
np.save(params.cxiDir+"/"+args.exp+"_"+str(args.run).zfill(4)+"_max_assem.npy", det.image(evt, max_img))
np.save(params.cxiDir+"/"+args.exp+"_"+str(args.run).zfill(4)+"_max.npy", max_img)
np.save(params.cxiDir+"/"+args.exp+"_"+str(args.run).zfill(4)+"_mean_assem.npy", det.image(evt, mean_img/counter))
np.save(params.cxiDir+"/"+args.exp+"_"+str(args.run).zfill(4)+"_mean.npy", mean_img/counter)
print "## saving the average powder pattern to: %s" % params.cxiDir
def checkStartFiles(experimentName, runNumber):
copyParams = experiparams(experimentName=experimentName,
runNumber=runNumber)
cxiDir = copyParams.cxiDir
status = True
if cxiDir is None or not os.path.exists(cxiDir):
print "@@@@@ cxiDir does not exist "
status = False
if not os.path.isfile(cxiDir + '/staticMask.h5'):
print "@@@@@ statisMask.h5 is missing "
status = False
if not os.path.isfile(cxiDir + '/psanaMask.npy'):
print "@@@@@ psanaMask.npy is missing "
status = False
if not os.path.isfile(cxiDir + "/.temp.geom"):
print "@@@@@ .temp.geom is missing "
status = False
return status
def setDefaultParams(self):
params = experiparams(self.experimentName,
self.runNumber,
detectorName=self.detectorName,
outDir=self.outDir)
params.setDefaultPsana()
self.queue = 'psanaq'
### TODO: psocake accept former directory as outDir
self.outDir = params.outDir
### TODO: indexnoe is actually not implemented in psocake
self.indexnoe = -1
self.pkTag = ""
self.instrument = params.instrument
self.pixelSize = params.pixelSize
self.pdbfile = None
self.clenEpics = params.clenEpics
self.likelihood = 0.
self.tag = "index-" + utils.getTime()
type=str)
args = parser.parse_args()
if args.det is None:
from experiment import myExp
runs = [args.run]
exp = myExp(args.exp, runs[0])
try:
exp.Det
except:
pass
args.det = exp.detName
print args.det
if args.img is None and args.mask is None:
params = experiparams(experimentName=args.exp, runNumber=args.run)
args.img = params.cxiDir + "/" + args.exp + "_" + str(
args.run).zfill(4) + "_" + str(args.det) + "_mean_assem.npy"
args.mask = params.cxiDir + "/psanaMask.npy"
image = np.load(args.img)
# assem
if args.assem:
evt, det = experiparams.expdet(args.exp, args.run, args.det)
if evt is None or det is None:
pass
else:
image = det.image(evt, image)
if args.mask is not None and os.path.isfile(args.mask):
def setupNewRun(experimentName=None,
runNumber=None,
detectorName=None,
outDir=None,
copyRun=None):
params = experiparams(experimentName=experimentName,
runNumber=runNumber,
detectorName=detectorName,
outDir=outDir)
copyParams = experiparams(experimentName=experimentName,
runNumber=copyRun,
detectorName=detectorName,
outDir=outDir)
if not os.path.isdir(params.cxiDir):
print params.cxiDir
os.makedirs(params.cxiDir)
if copyRun is not None:
status = checkStartFiles(experimentName, copyRun)
if status:
from shutil import copyfile
copyfile(src=copyParams.cxiDir + '/staticMask.h5',
dst=params.cxiDir + '/staticMask.h5')
copyfile(src=copyParams.cxiDir + '/psanaMask.npy',
dst=params.cxiDir + '/psanaMask.npy')
copyfile(src=copyParams.cxiDir + "/.temp.geom",
dst=params.cxiDir + "/.temp.geom")
copyfile(src=copyParams.cxiDir + "/.temp.geom",
dst=params.cxiDir + "/temp.geom")
print "##### copy file from run %d to %d" % (copyRun, runNumber)
return True
# get the psana mask from the psana server
unassem_img, assem_img = loadPsanaMask(experimentName, runNumber,
detectorName)
np.save(params.cxiDir + '/psanaMask.npy', assem_img)
print "##### save psanaMask: ", params.cxiDir + '/psanaMask.npy'
## save unassem_img to cheetah mask
saveCheetahStaticMask(unassem_img, experimentName, detectorName,
params.cxiDir + '/staticMask.h5')
print "##### save cheetah mask: ", params.cxiDir + '/staticMask.h5'
## load psana geometry
calibFile = findPsanaGeometry(experimentName, runNumber, detectorName)
print "##### load calibFile: ", calibFile
############################
# Sometimes the geom file is not compatible with psocake, we need to modify a little bit
fgeom = params.cxiDir + "/temp.geom"
CalibFileToGeomFile(calibFile, detectorName, fgeom)
print "##### convert calibFile to geometry file"
## load geom file and make a copy to .temp.geom
f = open(fgeom)
lines = f.readlines()
f.close()
f = open(params.cxiDir + "/.temp.geom", 'w')
params.setDefaultPsana()
for i in lines:
#if 'mask' in i:
# f1.write(';'+i)
if 'clen' in i:
f.write(i.split(';')[-1])
elif 'coffset' in i:
f.write(i.split('=')[0] + "= " + str(params.coffset) + '\n')
else:
f.write(i)
f.close()
return True