def __init__(self, inarr, inangavg, inangavg_Q, filename, filetag="", normalize=False, meanWaveLengthInAngs=eDD.nominalWavelengthInAngs, detectorDistance=eDD.get_detector_dist_in_meters(run_tag)): self.inarr = N.array(inarr).mean(axis=0) self.inarr = self.inarr*(self.inarr>0) self.filename = filename if (filetag != ""): self.filetag = filetag[:] #this is necessary to pass filename by value and not by reference (which would change the input parameters outside of the class) for i in range(len(self.filetag)): self.filetag[i] += ": " else: self.filetag = ["" for i in inangavg] if normalize: self.angavgmax = N.zeros(len(inangavg)) for i in range(len(inangavg)): self.angavgmax[i] = inangavg[i].max() self.angavgmaxindex = self.angavgmax.argmax() self.inangavg = [] for i in range(len(inangavg)): self.inangavg.append(inangavg[i]*self.angavgmax[self.angavgmaxindex]/self.angavgmax[i]) else: self.inangavg = inangavg self.inangavgQ = inangavg_Q self.wavelength = meanWaveLengthInAngs self.detectorDistance = detectorDistance global HIceQ global HIceQLabel global HIceP global colmax global colmin colmax = ((self.inarr<options.maxIntens)*self.inarr).max() colmin = 0
if (typeInStringPos == -1):
foundTypeNumbers[i] = 0
else:
foundTypeNumbers[i] = int(foundTypes[i][typeInStringPos+len("type")])
tcounter = 0
for cDir in foundTypes:
os.chdir(cDir)
updateTypes[tcounter] = int(input("Spline "+cDir+"/ (1 for yes, 0 for no)? "))
foundTypeFiles[tcounter] += G.glob("LCLS*angavg.h5")
foundFiles += G.glob("LCLS*angavg.h5")
os.chdir(originaldir)
tcounter += 1
print "Found %d types (including type0) with %d sorted files." % (numTypes, len(foundFiles))
if (options.verbose):
print "Detector at %lf mm away from the interaction region." % (eDD.get_detector_dist_in_meters(runtag)*1000)
#Check if searchDir already exists and what angavg files it includes
searchDir = ang_avg_dir + runtag
if not os.path.exists(searchDir):
print "There is no directory called %s. Aborting." % (searchDir)
sys.exit(1)
else:
print "Now examining new H5 files in %s/ ..." % (searchDir)
searchstring="LCLS+[a-zA-Z0-9\_]+"+runtag+"[a-z0-9\_]+-angavg.h5"
h5pattern = re.compile(searchstring)
h5files = [x for x in os.listdir(searchDir) if h5pattern.findall(x)]
numFiles = len(h5files)
print "Found %d new H5 files." % (numFiles)
#Check that there are no duplicates in the presorted files
def __init__(self, inarr, inangavg, inangavgQ , filename, meanWaveLengthInAngs=eDD.nominalWavelengthInAngs, detectorDistance=eDD.get_detector_dist_in_meters(runtag)): self.inarr = inarr self.filename = filename self.inangavg = inangavg self.inangavgQ = inangavgQ self.wavelength = meanWaveLengthInAngs self.detectorDistance = detectorDistance global colmax global colmin global storeFlag self.tag = 0
def __init__(self, inarr, inangavg , filename, currTag, meanWaveLengthInAngs=eDD.nominalWavelengthInAngs, detectorDistance=eDD.get_detector_dist_in_meters(runtag)):
self.origarr = inarr.copy()
self.inarr = inarr*(inarr>0)
self.filename = filename
self.inangavg = inangavg
self.wavelength = meanWaveLengthInAngs
self.detectorDistance = detectorDistance
self.HIceQ ={}
global colmax
global colmin
global storeFlag
self.tag = currTag
def __init__(self, inarr, inangavg, inangavg_Q, filename, meanWaveLengthInAngs=eDD.nominalWavelengthInAngs, detectorDistance=eDD.get_detector_dist_in_meters(run_tag)): self.origarr = inarr.copy() self.inarr = inarr*(inarr>0) self.filename = filename self.inangavg = inangavg self.inangavg_Q = inangavg_Q self.wavelength = meanWaveLengthInAngs self.detectorDistance = detectorDistance global HIceQ global HIceQLabel global HIceP global colmax global colmin colmax = ((self.inarr<options.maxIntens)*self.inarr).max() colmin = self.inarr.min()
else:
write_anomaly_dir = write_dir
originaldir=os.getcwd()
foundTypes=[write_dir]
anomalousTypes=G.glob(write_anomaly_dir+"type[1-9]")
if (len(anomalousTypes)>0):
foundTypes+=anomalousTypes
numTypes=len(foundTypes)
for cDir in foundTypes:
os.chdir(cDir)
foundFiles+=G.glob("LCLS*angavg.h5")
os.chdir(originaldir)
print "Found %d types (including type0) with %d files" % (numTypes, len(foundFiles))
if(options.verbose):
print "detector at distance: %lf" % eDD.get_detector_dist_in_meters(runtag)
#Always check the angavg files in searchDir.
searchDir = ang_avg_dir + runtag
print "Now examining H5 files in %s/ ..."%(searchDir)
searchstring="[a-zA-Z0-9\_]+"+runtag+"[a-z0-9\_]+-angavg.h5"
h5pattern = re.compile(searchstring)
h5files = [x for x in os.listdir(searchDir) if h5pattern.findall(x)]
numFiles = len(h5files)
#Check if file sorting has already been done.
if(os.path.exists(canonicalOrderedHitsFN) and os.path.exists(canonicalOrderedIntensInHitsFN)):
print "Found sorted filenames and intens lists."
f = open(canonicalOrderedHitsFN, 'r')
orderedH5Files = N.array(f.read().split())
f.close()
def __init__(self, inarr, inangavg , filename, meanWaveLengthInAngs=eDD.nominalWavelengthInAngs, detectorDistance=eDD.get_detector_dist_in_meters(runtag)):
self.inarr = inarr*(inarr>0)
#cxi74613: invert X-axis to follow CXI-convention
for i in range(len(inarr)):
self.inarr[i] = self.inarr[i][::-1]
self.filename = filename
self.inangavg = inangavg
self.wavelength = meanWaveLengthInAngs
self.detectorDistance = detectorDistance
self.HIceQ ={}
global colmax
global colmin
global storeFlag
self.tag = 0
def __init__(self, inarr, inangavg , filename, meanWaveLengthInAngs=eDD.nominalWavelengthInAngs, detectorDistance=eDD.get_detector_dist_in_meters(runtag)):
self.origarr = inarr.copy()
self.inarr = inarr
self.filename = filename
self.inangavg = inangavg
self.wavelength = meanWaveLengthInAngs
self.detectorDistance = detectorDistance
self.HIceQ ={}
global colmax
global colmin
global storeFlag
colmax = ((self.inarr<options.maxIntens)*self.inarr).max()
colmin = 0
