def initSpec(_strSpecVersion, _strSpecStatus, _strSpecAbort):
"""
Initialization of SpecVariable ...
"""
if EDUtilsBioSaxs.specVersion is None:
EDUtilsBioSaxs.__strSpecVersion = _strSpecVersion
EDUtilsBioSaxs.__strSpecStatus = _strSpecStatus
EDUtilsBioSaxs.__strSpecAbort = _strSpecAbort
if SpecVariable:
EDUtilsBioSaxs.__specVarStatus = SpecVariable.SpecVariable(
_strSpecStatus)
EDUtilsBioSaxs.__specVarAbort = SpecVariable.SpecVariable(
_strSpecAbort)
else:
EDVerbose.DEBUG(
"EDUtilsBioSaxs initSpec called whereas it was already set-up")
if EDUtilsBioSaxs.__strSpecVersion != _strSpecVersion:
EDVerbose.WARNING(
"EDUtilsBioSaxs initSpec specVersion %s whereas configured with %s"
% (_strSpecVersion, EDUtilsBioSaxs.__strSpecVersion))
if EDUtilsBioSaxs.__strSpecStatus != _strSpecStatus:
EDVerbose.WARNING(
"EDUtilsBioSaxs initSpec specStatus %s whereas configured with %s"
% (_strSpecVersion, EDUtilsBioSaxs.__strSpecVersion))
if EDUtilsBioSaxs.__strSpecAbort != _strSpecAbort:
EDVerbose.WARNING(
"EDUtilsBioSaxs initSpec specAbort %s whereas configured with %s"
% (_strSpecVersion, EDUtilsBioSaxs.__strSpecVersion))
def DataColl(self, Delt, Nu, KphiS, KphiE, StpN, TimNE):
flgon = 1
flgon = self.epicswarning(self.Delt, self.warn1, '13BMC:m37', flgon)
flgon = self.epicswarning(self.Nu, self.warn2, '13BMC:m38', flgon)
flgon = self.epicswarning(self.KphiStart, self.warn3, '13BMC:m33',
flgon)
flgon = self.epicswarning(self.KphiEnd, self.warn4, '13BMC:m33', flgon)
flgon = self.stepwarning(self.StpN, self.warn5, flgon)
flgon = self.speedwarning(self.TimperFrm, self.warn6, self.KphiStart,
self.KphiEnd, self.StpN, flgon)
if flgon:
self.Detmov(Delt, Nu)
xtalcmd = SpecCommand.SpecCommandA(
'', 'corvette.cars.aps.anl.gov:6780')
kphivelo = epics.caget('13BMC:m33.VELO')
kphiini = epics.caget('13BMC:m33.VAL')
cmdcon = "xtal kphi " + KphiS.text() + ' ' + KphiE.text(
) + ' ' + StpN.text() + ' ' + TimNE.text()
eval("xtalcmd.executeCommand(\"%s\")" % cmdcon)
Ttem = np.abs(kphiini - float(KphiS.text())) / kphivelo + float(
TimNE.text()) * float(StpN.text()) + 3
time.sleep(Ttem)
if (int(StpN.text()) > 1) and (self.SUMCK.isChecked() == True):
time.sleep(2)
DummyPath = SpecVariable.SpecVariable(
'SCANLOG_PATH',
'corvette.cars.aps.anl.gov:6780').getValue()
DummyN = SpecVariable.SpecVariable(
'SCAN_N', 'corvette.cars.aps.anl.gov:6780').getValue()
DumS = 'S' + (3 - len(str(DummyN))) * '0' + str(DummyN) + '/'
L = re.split('/', DummyPath)
# For Win7 system
# FL = 'T:/'+ L[5]+'/'+ L[6]+'/'+ L[7]+'/'+ L[8]+'/'+ L[9]+'/'+ L[10]+'/'+ L[11]+'/images/'+ L[13]+'/'+DumS
# For Win10 system
FL = '//cars5/data/' + L[5] + '/' + L[6] + '/' + L[
7] + '/' + L[8] + '/' + L[9] + '/' + L[10] + '/' + L[
11] + '/images/' + L[13] + '/' + DumS
files = []
# r=root, d=directories, f = files
for r, d, f in os.walk(FL):
for file in f:
if '.cbf' in file:
files.append(os.path.join(r, file))
elif '.tif' in file:
files.append(os.path.join(r, file))
img = fabio.open(files[0])
for file in files[1:]:
data = fabio.open(file).data
img.data = img.data + data
for xi in range(1043):
for xj in range(981):
if img.data[xi, xj] < 0:
img.data[xi, xj] = -1
IML = FL + 'sum.cbf'
img.write(IML)
self.lastscan(self.LogL1, 'templog.txt')
def __init__(self, parent=None):
super(calibUI, self).__init__(parent)
self.setupUi(self)
Dist0 = SpecVariable.SpecVariable('BMCPilatusDist', 'corvette.cars.aps.anl.gov:6780').getValue()
self.T1.setText(str(Dist0))
beamX0 = SpecVariable.SpecVariable('BMCPilatusBeamX', 'corvette.cars.aps.anl.gov:6780').getValue()
self.T2.setText(str(beamX0))
beamY0 = SpecVariable.SpecVariable('BMCPilatusBeamY', 'corvette.cars.aps.anl.gov:6780').getValue()
self.T3.setText(str(beamY0))
self.R2.setChecked(True)
###################### Define actions #############
self.B1.clicked.connect(lambda: self.update_clicked())
def nextscan(self, widget1, tempfile):
# only use after press newsample
LogPath = SpecVariable.SpecVariable('SCANLOG_PATH', 'corvette.cars.aps.anl.gov:6780').getValue()
MajorPath = SpecVariable.SpecVariable('STARTUP_PROJECT_PATH', 'corvette.cars.aps.anl.gov:6780').getValue()
len1 = len(MajorPath+"scandata/")
dummy = LogPath[len1:-1]
cmdcon = time.asctime()+'\n New data will be saved in folder: ' + dummy + '\n'
f = open(tempfile, 'a+')
dummy2 = f.read()
f.close()
os.remove(tempfile)
dummy3 = cmdcon + dummy2
f = open(tempfile, 'a+')
f.write(dummy3)
f.close()
widget1.setText(dummy3)
def findfolder(self):
ProjPath = SpecVariable.SpecVariable(
'STARTUP_PROJECT_PATH',
'corvette.cars.aps.anl.gov:6780').getValue()
temp = ProjPath[25::]
temp1 = 'T:' + temp + 'images/'
self.FolderN.setText(temp1)
time.sleep(0.3)
def lastscan(self, widget1, tempfile):
# only use after one scan is done. Newsample command creates a new logPath.
LogPath = SpecVariable.SpecVariable('SCANLOG_PATH', 'corvette.cars.aps.anl.gov:6780').getValue()
FilePath = SpecVariable.SpecVariable('SCANLOG_FILE', 'corvette.cars.aps.anl.gov:6780').getValue()
len1 = len(LogPath)
dummy = FilePath[len1:-4]
dummy1 = re.split('_', dummy)
cmdcon = time.asctime()+'\n '+ dummy1[2] +' done, saved in folder: '+ dummy1[0]+'_'+dummy1[1]+'\n'
f = open(tempfile, 'a+')
dummy2 = f.read()
f.close()
os.remove(tempfile)
dummy3 = cmdcon + dummy2
f = open(tempfile, 'a+')
f.write(dummy3)
f.close()
widget1.setText(dummy3)
def Reprocess(pDetector, pOperation, pDirectory, pPrefix, pRunNumber, pFrameFirst, pFrameLast, pConcentration, pComments, pCode, \
pMaskFile, pDetectorDistance, pWaveLength, pPixelSizeX, pPixelSizeY, pBeamCenterX, pBeamCenterY, pNormalisation, pBeamStopDiode, \
pMachineCurrent, pKeepOriginal, pTimeOut, pSPECVersion, pSPECVariableStatus, pSPECVariableAbort, pTerminal):
if pSPECVersion is not None:
if pSPECVariableStatus is not None:
globals()["REPROCESS_STATUS"] = SpecVariable.SpecVariable(
pSPECVariableStatus, pSPECVersion)
if pSPECVariableAbort is not None:
globals()["REPROCESS_ABORT"] = SpecVariable.SpecVariable(
pSPECVariableAbort, pSPECVersion)
if pDetector not in ("0", "1"):
showMessage(4, "Invalid detector '%s'!" % pDetector)
return
if pOperation not in ("-2", "-1", "0", "1", "2", "3"):
showMessage(4, "Invalid operation '%s'!" % pOperation)
return
if not os.path.exists(pDirectory):
showMessage(4, "Directory '%s' not found!" % pDirectory)
return
if not os.path.exists(pDirectory + "/1d"):
try:
os.mkdir(pDirectory + "/1d")
except Exception:
showMessage(
4, "Could not create directory '1d' in '%s'!" % pDirectory)
return
if not os.path.exists(pDirectory + "/2d"):
try:
os.mkdir(pDirectory + "/2d")
except Exception:
showMessage(
4, "Could not create directory '2d' in '%s'!" % pDirectory)
return
if not os.path.exists(pDirectory + "/misc"):
try:
os.mkdir(pDirectory + "/misc")
except Exception:
showMessage(
4, "Could not create directory 'misc' in '%s'!" % pDirectory)
return
runNumberList = []
if pRunNumber == "":
for filename in os.listdir(pDirectory + "/raw"):
if os.path.isfile(pDirectory + "/raw/" + filename):
prefix, run, frame, extra, extension = getFilenameDetails(
filename)
if prefix == pPrefix and run != "" and frame != "" and (
pDetector == "0" and extension == "edf"
or pDetector == "1" and extension == "gfrm"):
try:
runNumberList.index(run)
except Exception:
runNumberList.append(run)
else:
list = pRunNumber.split(",")
for runNumber in list:
runNumber = "%03d" % int(runNumber)
try:
runNumberList.index(runNumber)
except Exception:
runNumberList.append(runNumber)
if len(runNumberList) == 0:
showMessage(4, "There are no runs for prefix '%s'!" % pPrefix)
return
else:
runNumberList.sort()
edf = EDF.EDF()
spec = SPEC.SPEC()
hdfDictionary = HDFDictionary.HDFDictionary()
if pDetector == "0":
dictionaryEDF = "EDF_PILATUS"
else:
dictionaryEDF = "EDF_VANTEC"
status, dictionary = hdfDictionary.get(
os.path.join(sys.path[0], "Reprocess.xml"), dictionaryEDF)
if status != 0:
showMessage(3, "Could not get '%s' dictionary!" % dictionaryEDF)
#print dictionary
if pKeepOriginal == "0":
directory1D_REP = ""
directory2D_REP = ""
directoryMISC_REP = ""
else:
i = 0
while True:
directory1D_REP = pDirectory + "/1d/reprocess" + str(i)
if os.path.exists(directory1D_REP):
i += 1
else:
try:
os.mkdir(directory1D_REP)
except Exception:
showMessage(
3, "Could not create reprocess directory '%s'!" %
directory1D_REP)
break
i = 0
while True:
directory2D_REP = pDirectory + "/2d/reprocess" + str(i)
if os.path.exists(directory2D_REP):
i += 1
else:
try:
os.mkdir(directory2D_REP)
except Exception:
showMessage(
3, "Could not create reprocess directory '%s'!" %
directory2D_REP)
break
i = 0
while True:
directoryMISC_REP = pDirectory + "/misc/reprocess" + str(i)
if os.path.exists(directoryMISC_REP):
i += 1
else:
try:
os.mkdir(directoryMISC_REP)
except Exception:
showMessage(
3, "Could not create reprocess directory '%s'!" %
directoryMISC_REP)
break
print
for runNumber in runNumberList:
if __terminal or pSPECVersion is not None: # reprocess was launched from terminal or from BsxCuBE while reprocessing data
frameList = []
for filename in os.listdir(pDirectory + "/raw"):
if os.path.isfile(pDirectory + "/raw/" + filename):
prefix, run, frame, extra, extension = getFilenameDetails(
filename)
if prefix == pPrefix and run == runNumber and frame != "":
if (pFrameFirst == "" or int(frame) >= int(pFrameFirst)
) and (pFrameLast == ""
or int(frame) <= int(pFrameLast)):
if pDetector == "0" and extension == "edf" or pDetector == "1" and extension == "gfrm":
try:
frameList.index(frame)
except Exception:
frameList.append(frame)
else: # reprocess was launched from BsxCuBE while collecting data
frameList = ["%02d" % int(pFrameLast)]
if len(frameList) == 0:
showMessage(3, "There are no frames for run '%s'!" % runNumber)
else:
frameList.sort()
for frame in frameList:
if pDetector == "0": # Pilatus
filenameRAW = "%s/raw/%s_%s_%s.edf" % (pDirectory, pPrefix,
runNumber, frame)
sizeRAW = 4090000
sizeNOR = 4100000
else: # Vantec
filenameRAW = "%s/raw/%s_%s_%s.gfrm" % (
pDirectory, pPrefix, runNumber, frame)
sizeRAW = 4200000
sizeNOR = 16780000
if pKeepOriginal == "0":
filenameNOR = "%s/2d/%s_%s_%s.edf" % (pDirectory, pPrefix,
runNumber, frame)
filenameLOG = "%s/misc/%s_%s_%s.log" % (
pDirectory, pPrefix, runNumber, frame)
filenameMSK = "%s/misc/%s_%s_%s.msk" % (
pDirectory, pPrefix, runNumber, frame)
filenameANG = "%s/misc/%s_%s_%s.ang" % (
pDirectory, pPrefix, runNumber, frame)
filenameDAT = "%s/1d/%s_%s_%s.dat" % (pDirectory, pPrefix,
runNumber, frame)
else:
filenameNOR = "%s/%s_%s_%s.edf" % (
directory2D_REP, pPrefix, runNumber, frame)
filenameLOG = "%s/%s_%s_%s.log" % (
directoryMISC_REP, pPrefix, runNumber, frame)
filenameMSK = "%s/%s_%s_%s.msk" % (
directoryMISC_REP, pPrefix, runNumber, frame)
filenameANG = "%s/%s_%s_%s.ang" % (
directoryMISC_REP, pPrefix, runNumber, frame)
filenameDAT = "%s/%s_%s_%s.dat" % (
directory1D_REP, pPrefix, runNumber, frame)
if __terminal or pSPECVersion is not None: # reprocess was launched from terminal or from BsxCuBE while reprocessing data
if pConcentration == "" or pComments == "" or pCode == "" or pMaskFile == "" or pDetectorDistance == "" or pWaveLength == "" or pPixelSizeX == "" or pPixelSizeY == "" or pBeamCenterX == "" or pBeamCenterY == "" or pNormalisation == "" or pBeamStopDiode == "" or pMachineCurrent == "":
filenameNOR_ORG = "%s/2d/%s_%s_%s.edf" % (
pDirectory, pPrefix, runNumber, frame)
if os.path.exists(filenameNOR_ORG):
edf.open(filenameNOR_ORG)
header = edf.getHeader()
history0 = ""
history1 = ""
i = 0
while i < len(header):
if header[i].startswith("History-1 = "):
history0 = header[i][12:]
del header[i]
i -= 1
elif header[i].startswith("History-1~1 = "):
history1 = header[i][14:]
del header[i]
i -= 1
else:
i += 1
header.append("history_combined = " + history0 +
history1)
#print header
status, translate = hdfDictionary.translate(
header, dictionary)
edf.close()
else:
translate = []
showMessage(
3,
"Trying to get values from file '%s' which doesn't exist"
% filenameNOR_ORG)
#print translate
else: # reprocess was launched from BsxCuBE while collecting data
translate = []
if pConcentration == "":
concentration = makeTranslation(translate, "concentration",
"0")
else:
concentration = pConcentration
if pComments == "":
comments = makeTranslation(translate, "comments", "")
else:
comments = pComments
if pCode == "":
code = makeTranslation(translate, "code", "")
else:
code = pCode
if pMaskFile == "":
maskFile = makeTranslation(translate, "mask_file", "")
else:
maskFile = pMaskFile
if pDetectorDistance == "":
detectorDistance = makeTranslation(translate,
"detector_distance",
"0")
else:
detectorDistance = pDetectorDistance
if pWaveLength == "":
waveLength = makeTranslation(translate, "wave_length", "0")
else:
waveLength = pWaveLength
if pPixelSizeX == "":
pixelSizeX = makeTranslation(translate, "pixel_size_X",
"0")
else:
pixelSizeX = pPixelSizeX
if pPixelSizeY == "":
pixelSizeY = makeTranslation(translate, "pixel_size_Y",
"0")
else:
pixelSizeY = pPixelSizeY
if pBeamCenterX == "":
beamCenterX = makeTranslation(translate, "beam_center_X",
"0")
else:
beamCenterX = pBeamCenterX
if pBeamCenterY == "":
beamCenterY = makeTranslation(translate, "beam_center_Y",
"0")
else:
beamCenterY = pBeamCenterY
if pBeamStopDiode == "":
beamStopDiode = makeTranslation(translate, "diode_current",
"0")
else:
beamStopDiode = pBeamStopDiode
if pMachineCurrent == "":
machineCurrent = makeTranslation(translate,
"machine_current", "0")
else:
machineCurrent = pMachineCurrent
if pNormalisation == "":
normalisation = makeTranslation(translate,
"normalization_factor",
"0")
else:
normalisation = pNormalisation
if pOperation in ("-2", "-1", "0", "3"):
print "Normalising EDF frame '%s'..." % filenameNOR
if pKeepOriginal == "0":
os.system("rm -f %s %s 2>/dev/null" %
(filenameNOR, filenameLOG))
status = waitFile(filenameRAW, sizeRAW, pTimeOut)
if status == 0:
if float(beamStopDiode) == 0:
showMessage(
3, "The value of the beam stop diode is zero!")
else:
if pDetector == "0": # Pilatus
command = "saxs_mac +var +pass -omod n -i1err _i1val -i1dum -2 -i1ddum 1.1 -otit \"DiodeCurr=%s, MachCurr=%s mA, Concentration=%s, Comments: %s, Code: %s, Mask: %s, Normalisation: %s\" -i1dis \"%s\" -i1wvl \"%s_nm\" -i1pix %s_um %s_um -i1cen %s %s -ofac %s %s %s > %s 2>/dev/null" % \
(beamStopDiode, machineCurrent, concentration, comments, code, maskFile, normalisation, detectorDistance, waveLength, pixelSizeX, pixelSizeY, beamCenterX, beamCenterY, str(float(normalisation) / float(beamStopDiode)), filenameRAW, filenameNOR, filenameLOG)
else: # Vantec
command = "saxs_mac +var +pass -omod n -i1err _i1val -i1dum -2 -i1ddum 1.1 -otit \"DiodeCurr=%s, MachCurr=%s mA, Concentration=%s, Comments: %s, Code: %s, Mask: %s, Normalisation: %s\" -odis \"%s\" -i1wvl \"%s_nm\" -i1pix %s_um %s_um -i1cen %s %s -ofac %s %s %s > %s 2>/dev/null" % \
(beamStopDiode, machineCurrent, concentration, comments, code, maskFile, normalisation, detectorDistance, waveLength, pixelSizeX, pixelSizeY, beamCenterX, beamCenterY, str(float(normalisation) / float(beamStopDiode)), filenameRAW, filenameNOR, filenameLOG)
#print command
if subprocess.call(command, shell=True) == 0:
showMessage(
2, "The frame '%s' was normalised..." %
filenameNOR, filenameNOR)
else:
showMessage(
3,
"Could not find 'saxs_mac' or it returned an error!"
)
elif status == 1:
print "Aborting data reprocess!"
sys.exit(0)
else:
showMessage(
3,
"File '%s' didn't appear on disk after '%s' seconds."
% (filenameRAW, pTimeOut))
if pOperation in ("-2", "-1", "1", "3"):
print "Generating 1D file '%s'..." % filenameDAT
if pKeepOriginal == "0":
os.system("rm -f %s %s %s 2>/dev/null" %
(filenameDAT, filenameANG, filenameMSK))
status = waitFile(filenameNOR, sizeNOR, pTimeOut)
if status == 0:
command = "saxs_add -omod n %s %s %s > /dev/null 2>/dev/null" % (
filenameNOR, maskFile, filenameMSK)
#print command
if subprocess.call(command, shell=True) == 0:
command = "saxs_angle -omod n -rsys normal -da 360_deg -odim = 1 %s %s > /dev/null 2>/dev/null" % (
filenameMSK, filenameANG)
#print command
if subprocess.call(command, shell=True) == 0:
#command = "saxs_curves -i1err _i1val -scf 2_pi -ext .dat -spc \" \" -prm \"Sample c=%6.2f mg/ml,Concentration: %s,Code: %s\" %s %s" % (float(concentration), concentration, code, filenameANG, filenameDAT)
command = "saxs_curves -scf 2_pi -ext .dat -spc \" \" %s %s > /dev/null 2>/dev/null" % (
filenameANG, filenameDAT)
#print command
if subprocess.call(command, shell=True) == 0:
spec.open(filenameDAT)
header = spec.getHeader()
values = spec.getValues()
spec.close()
header[
1] = " Sample c=%6.2f mg/ml" % float(
concentration)
header.append("Normalisation: %s" %
normalisation)
header.append("Concentration: %s" %
concentration)
header.append("Code: %s" % code)
spec.open(filenameDAT, "w")
spec.write(header, values)
spec.close()
showMessage(
2,
"The 1D file '%s' was generated..." %
filenameDAT, filenameDAT)
else:
showMessage(
3,
"Could not find 'saxs_curves' or it returned an error!"
)
else:
showMessage(
3,
"Could not find 'saxs_angle' or it returned an error!"
)
else:
showMessage(
3,
"Could not find 'saxs_add' or it returned an error!"
)
elif status == 1:
print "Aborting data reprocess!"
sys.exit(0)
else:
showMessage(
3,
"File '%s' didn't appear on disk after '%s' seconds."
% (filenameNOR, pTimeOut))
if pOperation in ("-2", "1", "2", "3"):
if pKeepOriginal == "0":
filenameDAT_AVE = "%s/1d/%s_%s_ave.dat" % (
pDirectory, pPrefix, runNumber)
filenameANG_AVE = "%s/misc/%s_%s_ave.ang" % (
pDirectory, pPrefix, runNumber)
filenameLOG_AVE = "%s/misc/%s_%s_ave.log" % (
pDirectory, pPrefix, runNumber)
filenamePattern = "%s/misc/%s_%s_%s.ang" % (
pDirectory, pPrefix, runNumber, "%%")
else:
filenameDAT_AVE = "%s/%s_%s_ave.dat" % (directory1D_REP,
pPrefix, runNumber)
filenameANG_AVE = "%s/%s_%s_ave.ang" % (directoryMISC_REP,
pPrefix, runNumber)
filenameLOG_AVE = "%s/%s_%s_ave.log" % (directoryMISC_REP,
pPrefix, runNumber)
filenamePattern = "%s/%s_%s_%s.ang" % (
directoryMISC_REP, pPrefix, runNumber, "%%")
print "Generating average '%s' from 1D files..." % filenameDAT_AVE
if pKeepOriginal == "0":
os.system(
"rm -f %s %s %s 2>/dev/null" %
(filenameDAT_AVE, filenameANG_AVE, filenameLOG_AVE))
if pFrameFirst == "":
frameFirst = int(frameList[0])
else:
frameFirst = int(pFrameFirst)
if pFrameLast == "":
frameLast = int(frameList[-1])
else:
frameLast = int(pFrameLast)
#command = "saxs_mac -omod n -i1err _i1val -var -add %d -ofac %f %s,%d,%d %s > %s" % (frameLast - frameFirst + 1, 1 / float(frameLast - frameFirst + 1), filenamePattern, frameFirst, frameLast, filenameANG_AVE, filenameLOG_AVE)
command = "saxs_mac -omod n +var -add %d -ofac %s %s,%d,%d %s > %s 2>/dev/null" % (
frameLast - frameFirst + 1,
str(1 / float(frameLast - frameFirst + 1)),
filenamePattern, frameFirst, frameLast, filenameANG_AVE,
filenameLOG_AVE)
#print command
if subprocess.call(command, shell=True) == 0:
#command = "saxs_curves -i1err _i1val -scf 2_pi -ext .dat -spc \" \" -prm \"Sample c=%6.2f mg/ml,Concentration: %s,Code: %s\" %s %s" % (float(concentration), concentration, code, filenameANG_AVE, filenameDAT_AVE)
command = "saxs_curves -scf 2_pi -ext .dat -spc \" \" %s %s > /dev/null 2>/dev/null" % (
filenameANG_AVE, filenameDAT_AVE)
#print command
if subprocess.call(command, shell=True) == 0:
spec.open(filenameDAT_AVE)
header = spec.getHeader()
values = spec.getValues()
spec.close()
header[1] = " Sample c=%6.2f mg/ml" % float(
concentration)
header.append("Normalisation: %s" % normalisation)
header.append("Concentration: %s" % concentration)
header.append("Code: %s" % code)
spec.open(filenameDAT_AVE, "w")
spec.write(header, values)
spec.close()
showMessage(
2, "The average file '%s' was generated..." %
filenameDAT_AVE, filenameDAT_AVE)
else:
showMessage(
3,
"Could not find 'saxs_curves' or it returned an error!"
)
else:
showMessage(
3,
"Could not find 'saxs_mac' or it returned an error!")
if __terminal or pSPECVersion is not None:
showMessage(0, "The data reprocessing is done!")
def __ltinitFinished(self, *args):
table = self._widgetTree.child('__gridTable')
stringVal = table.text(0, 0)
nbColumn, valid = stringVal.toInt()
if not valid:
dialog = qt.QErrorMessage(self)
dialog.message('Interval must be integer')
return
nbColumn += 1
self._logArgs['scan_type'] = 'lookup'
posMot1 = []
posMot2 = []
pointMatchNb = 0
matchPointId = []
for i, (match, point) in enumerate(
itertools.izip(self._matchPoints, self.__gridPoints)):
if match:
posMot1.append(point[0, 0])
posMot2.append(point[0, 1])
matchPointId.append((i / nbColumn, pointMatchNb))
pointMatchNb += 1
if posMot1:
mot1Widget = self._widgetTree.child('__motor1')
mot2Widget = self._widgetTree.child('__motor2')
timeWidget = self._widgetTree.child('__time')
ctime, valid = timeWidget.text().toFloat()
mot1 = self.__getMotor(mot1Widget.currentText(),
self._horizontalMotors)
mot2 = self.__getMotor(mot2Widget.currentText(),
self._verticalMotors)
posMot1 = numpy.array(posMot1)
posMot1 -= self._beamx
posMot1 *= (self._XSize / mot1.getProperty('unit'))
posMot1 += mot1.getPosition()
posMot2 = numpy.array(posMot2)
posMot2 -= self._beamy
posMot2 *= (self._YSize / mot2.getProperty('unit'))
posMot2 += mot2.getPosition()
lineStartStop = []
lastLineId = -1
currentPointInLine = []
for lineId, pointId in matchPointId:
if lineId != lastLineId:
if currentPointInLine:
lineStartStop.append(currentPointInLine)
currentPointInLine = [pointId]
lastLineId = lineId
else:
currentPointInLine.append(pointId)
if currentPointInLine:
lineStartStop.append(currentPointInLine)
startIndex = []
stopIndex = []
for line in lineStartStop:
startIndex.append(line[0])
stopIndex.append(line[-1])
startIndex = numpy.array(startIndex)
stopIndex = numpy.array(stopIndex)
specVersion = self._ltinit.specVersion
for motor_name, pos_motor in zip(
[str(mot1Widget.currentText()),
str(mot2Widget.currentText())], [posMot1, posMot2]):
ho = self.getHardwareObject(self["command"])
MOTOR_ARRAY = ho.addChannel(
{
"type": "spec",
"version": specVersion,
"name": "MOTOR_ARRAY",
"dispatchMode": None
}, "%s_ltscan_arr" % motor_name)
MOTOR_ARRAY.setValue(SpecArray.SpecArray(pos_motor.ravel()))
LT_START = SpecVariable.SpecVariable('LT_START', specVersion)
LT_START.setValue(SpecArray.SpecArray(startIndex))
LT_STOP = SpecVariable.SpecVariable('LT_STOP', specVersion)
LT_STOP.setValue(SpecArray.SpecArray(stopIndex))
LT_LINE = SpecVariable.SpecVariable('LT_LINE', specVersion)
LT_LINE.setValue(len(stopIndex))
self._SpecCmd(str(mot1Widget.currentText()),
str(mot2Widget.currentText()), ctime)
def Reprocess(pDetector, pOperation, pDirectory, pPrefix, pRunNumber, pFrameFirst, pFrameLast, pConcentration, pComments, pCode, \
pMaskFile, pDetectorDistance, pWaveLength, pPixelSizeX, pPixelSizeY, pBeamCenterX, pBeamCenterY, pNormalisation, pBeamStopDiode, \
pMachineCurrent, pKeepOriginal, pTimeOut, pSPECVersion, pSPECVariableStatus, pSPECVariableAbort, pTerminal):
if pSPECVersion is not None:
if pSPECVariableStatus is not None:
globals()["REPROCESS_STATUS"] = SpecVariable.SpecVariable(pSPECVariableStatus, pSPECVersion)
if pSPECVariableAbort is not None:
globals()["REPROCESS_ABORT"] = SpecVariable.SpecVariable(pSPECVariableAbort, pSPECVersion)
if pDetector not in ("0", "1"):
showMessage(4, "Invalid detector '%s'!" % pDetector)
return
if pOperation not in ("-2", "-1", "0", "1", "2", "3"):
showMessage(4, "Invalid operation '%s'!" % pOperation)
return
if not os.path.exists(pDirectory):
showMessage(4, "Directory '%s' not found!" % pDirectory)
return
if not os.path.exists(pDirectory + "/1d"):
try:
os.mkdir(pDirectory + "/1d")
except:
showMessage(4, "Could not create directory '1d' in '%s'!" % pDirectory)
return
if not os.path.exists(pDirectory + "/2d"):
try:
os.mkdir(pDirectory + "/2d")
except:
showMessage(4, "Could not create directory '2d' in '%s'!" % pDirectory)
return
if not os.path.exists(pDirectory + "/misc"):
try:
os.mkdir(pDirectory + "/misc")
except:
showMessage(4, "Could not create directory 'misc' in '%s'!" % pDirectory)
return
runNumberList = []
if pRunNumber == "":
for filename in os.listdir(pDirectory + "/raw"):
if os.path.isfile(pDirectory + "/raw/" + filename):
prefix, run, frame, extra, extension = getFilenameDetails(filename)
if prefix == pPrefix and run != "" and frame != "" and (pDetector == "0" and extension == "edf" or pDetector == "1" and extension == "gfrm"):
try:
runNumberList.index(run)
except:
runNumberList.append(run)
else:
list = pRunNumber.split(",")
for runNumber in list:
runNumber = "%03d" % int(runNumber)
try:
runNumberList.index(runNumber)
except:
runNumberList.append(runNumber)
if len(runNumberList) == 0:
showMessage(4, "There are no runs for prefix '%s'!" % pPrefix)
return
else:
runNumberList.sort()
spec = SPEC()
if pDetector == "0":
dictionaryEDF = "EDF_PILATUS"
else:
dictionaryEDF = "EDF_VANTEC"
if pKeepOriginal == "0":
directory1D_REP = ""
directory2D_REP = ""
directoryMISC_REP = ""
else:
i = 0
while True:
directory1D_REP = pDirectory + "/1d/reprocess" + str(i)
if os.path.exists(directory1D_REP):
i += 1
else:
try:
os.mkdir(directory1D_REP)
except:
showMessage(3, "Could not create reprocess directory '%s'!" % directory1D_REP)
break
i = 0
while True:
directory2D_REP = pDirectory + "/2d/reprocess" + str(i)
if os.path.exists(directory2D_REP):
i += 1
else:
try:
os.mkdir(directory2D_REP)
except:
showMessage(3, "Could not create reprocess directory '%s'!" % directory2D_REP)
break
i = 0
while True:
directoryMISC_REP = pDirectory + "/misc/reprocess" + str(i)
if os.path.exists(directoryMISC_REP):
i += 1
else:
try:
os.mkdir(directoryMISC_REP)
except:
showMessage(3, "Could not create reprocess directory '%s'!" % directoryMISC_REP)
break
print
for runNumber in runNumberList:
print """
========================
<Starting RUN> run %s
========================
""" % runNumber
if __terminal or pSPECVersion is not None: # reprocess was launched from terminal or from BsxCuBE while reprocessing data
frameList = []
for filename in os.listdir(pDirectory + "/raw"):
if os.path.isfile(pDirectory + "/raw/" + filename):
prefix, run, frame, extra, extension = getFilenameDetails(filename)
if prefix == pPrefix and run == runNumber and frame != "":
if (pFrameFirst == "" or int(frame) >= int(pFrameFirst)) and (pFrameLast == "" or int(frame) <= int(pFrameLast)):
if pDetector == "0" and extension == "edf" or pDetector == "1" and extension == "gfrm":
try:
frameList.index(frame)
except:
frameList.append(frame)
else: # reprocess was launched from BsxCuBE while collecting data
frameList = ["%05d" % int(pFrameLast)]
if len(frameList) == 0:
showMessage(3, "There are no frames for run '%s'!" % runNumber)
else:
frameList.sort()
for frame in frameList:
print "\n<Processing Frame> No. %s" % frame
if pDetector == "0": # Pilatus
filenameRAW = "%s/raw/%s_%s_%s.edf" % (pDirectory, pPrefix, runNumber, frame)
sizeRAW = 4090000
sizeNOR = 4100000
else: # Vantec
filenameRAW = "%s/raw/%s_%s_%s.gfrm" % (pDirectory, pPrefix, runNumber, frame)
sizeRAW = 4200000
sizeNOR = 16780000
if pKeepOriginal == "0":
filenameNOR = "%s/2d/%s_%s_%s.edf" % (pDirectory, pPrefix, runNumber, frame)
filenameLOG = "%s/misc/%s_%s_%s.log" % (pDirectory, pPrefix, runNumber, frame)
filenameMSK = "%s/misc/%s_%s_%s.msk" % (pDirectory, pPrefix, runNumber, frame)
filenameANG = "%s/misc/%s_%s_%s.ang" % (pDirectory, pPrefix, runNumber, frame)
filenameDAT = "%s/1d/%s_%s_%s.dat" % (pDirectory, pPrefix, runNumber, frame)
else:
filenameNOR = "%s/%s_%s_%s.edf" % (directory2D_REP, pPrefix, runNumber, frame)
filenameLOG = "%s/%s_%s_%s.log" % (directoryMISC_REP, pPrefix, runNumber, frame)
filenameMSK = "%s/%s_%s_%s.msk" % (directoryMISC_REP, pPrefix, runNumber, frame)
filenameANG = "%s/%s_%s_%s.ang" % (directoryMISC_REP, pPrefix, runNumber, frame)
filenameDAT = "%s/%s_%s_%s.dat" % (directory1D_REP, pPrefix, runNumber, frame)
if __terminal or pSPECVersion is not None: # reprocess was launched from terminal or from BsxCuBE while reprocessing data
if pConcentration == "" or \
pComments == "" or \
pCode == "" or \
pMaskFile == "" or \
pDetectorDistance == "" or \
pWaveLength == "" or \
pPixelSizeX == "" or \
pPixelSizeY == "" or \
pBeamCenterX == "" or \
pBeamCenterY == "" or \
pNormalisation == "" or \
pBeamStopDiode == "" or \
pMachineCurrent == "":
filenameNOR_ORG = "%s/2d/%s_%s_%s.edf" % (pDirectory, pPrefix, runNumber, frame)
if os.path.exists(filenameNOR_ORG):
valdict = valuesFromHeader(filenameNOR_ORG)
print "terminal ", __terminal
print "pSPECVersion ", pSPECVersion
print filenameNOR_ORG
else: # reprocess was launched from BsxCuBE while collecting data
valdict = []
# Concentration
if pConcentration == "":
if 'Concentration' in valdict:
concentration = valdict['Concentration']
else:
print "concentration not in header"
else:
concentration = pConcentration
# Comments
if pComments == "":
if 'Comments' in valdict:
comments = valdict['Comments']
else:
print "comments not in header"
comments = ""
else:
comments = pComments
# Code
if pCode == "":
if 'Code' in valdict:
code = valdict['Code']
else:
print "code not in header"
code = ""
else:
code = pCode
# Mask
if pMaskFile == "":
if 'Mask' in valdict:
maskFile = valdict['Mask']
else:
print "maskFile not in header"
else:
maskFile = pMaskFile
# Detectordistance
if pDetectorDistance == "":
if 'SampleDistance' in valdict:
detectorDistance = valdict['SampleDistance']
else:
print "DetectorDistance not in header"
else:
detectorDistance = pDetectorDistance
# Wavelength
if pWaveLength == "":
if 'WaveLength' in valdict:
# the program wants nanometers. the header contains meters
waveLength = valdict['WaveLength']
waveLength = float(waveLength) * 1e9
else:
print "Wavelength not in header"
else:
waveLength = pWaveLength
# PSize X
if pPixelSizeX == "":
if 'PSize_1' in valdict:
# the program wants micrometers the header contains meters
pixelSizeX = valdict['PSize_1']
pixelSizeX = float(pixelSizeX) * 1e6
else:
print "pixelSizeX not in header"
else:
pixelSizeX = pPixelSizeX
# PSize Y
if pPixelSizeY == "":
if 'PSize_2' in valdict:
# the program wants micrometers the header contains meters
pixelSizeY = valdict['PSize_2']
pixelSizeY = float(pixelSizeY) * 1e6
else:
print "pixelSizeY not in header"
else:
pixelSizeY = pPixelSizeY
# Beamcenter X
if pBeamCenterX == "":
if 'Center_1' in valdict:
beamCenterX = valdict['Center_1']
else:
print "beamCenterX not in header"
else:
beamCenterX = pBeamCenterX
# Beamcenter Y
if pBeamCenterY == "":
if 'Center_2' in valdict:
beamCenterY = valdict['Center_2']
else:
print "beamCenterY not in header"
else:
beamCenterY = pBeamCenterY
# Beam stop diode
if pBeamStopDiode == "":
if 'DiodeCurr' in valdict:
beamStopDiode = valdict['DiodeCurr']
else:
print "beamStopDiode not in header"
else:
beamStopDiode = pBeamStopDiode
# Machine current
if pMachineCurrent == "":
if 'MachCurr' in valdict:
machineCurrent = valdict['MachCurr']
else:
print "machineCurrent not in header"
else:
machineCurrent = pMachineCurrent
# Normalisation
if pNormalisation == "":
if 'Normalisation' in valdict:
normalisation = valdict['Normalisation']
else:
print "normalisation not in header"
else:
normalisation = pNormalisation
# print "Concentration is: %s " % concentration
# print "Comments are: %s " % comments
# print "Code is: %s " % code
# print "Maskfile is: %s " % maskFile
# print "Detector distance is: %s " % detectorDistance
# print "Wavelength is: %s " % waveLength
# print "pixelSizeX is: %s " % pixelSizeX
# print "pixelSizeY is: %s " % pixelSizeY
# print "beamCenterX is: %s " % beamCenterX
# print "beamCenterY is: %s " % beamCenterY
# print "beamDiodeCurrent is: %s " % beamStopDiode
# print "machineCurrent is: %s " % machineCurrent
# print "normalisation is: %s " % normalisation
if pOperation in ("-2", "-1", "0", "3"):
print " - Normalising EDF frame '%s'..." % filenameNOR
if pKeepOriginal == "0":
os.system("rm -f %s %s 2>/dev/null" % (filenameNOR, filenameLOG))
status = waitFile(filenameRAW, sizeRAW, pTimeOut)
if status == 0:
if float(beamStopDiode) == 0:
showMessage(3, "The value of the beam stop diode is zero!")
else:
if pDetector == "0": # Pilatus
command = "%s +var +pass -omod n -i1err _i1val -i1dum -2 -i1ddum 1.1 -otit \"DiodeCurr=%s, MachCurr=%s mA, Concentration=%s, Comments: %s, Code: %s, Mask: %s, Normalisation: %s\" -i1dis \"%s\" -i1wvl \"%s_nm\" -i1pix %s_um %s_um -i1cen %s %s -ofac %s %s %s > %s 2>/dev/null" % \
(saxs_mac, beamStopDiode, machineCurrent, concentration, comments, code, maskFile, normalisation, detectorDistance, waveLength, pixelSizeX, pixelSizeY, beamCenterX, beamCenterY, str(float(normalisation) / float(beamStopDiode)), filenameRAW, filenameNOR, filenameLOG)
else: # Vantec
command = "%s +var +pass -omod n -i1err _i1val -i1dum -2 -i1ddum 1.1 -otit \"DiodeCurr=%s, MachCurr=%s mA, Concentration=%s, Comments: %s, Code: %s, Mask: %s, Normalisation: %s\" -odis \"%s\" -i1wvl \"%s_nm\" -i1pix %s_um %s_um -i1cen %s %s -ofac %s %s %s > %s 2>/dev/null" % \
(saxs_mac, beamStopDiode, machineCurrent, concentration, comments, code, maskFile, normalisation, detectorDistance, waveLength, pixelSizeX, pixelSizeY, beamCenterX, beamCenterY, str(float(normalisation) / float(beamStopDiode)), filenameRAW, filenameNOR, filenameLOG)
if subprocess.call(command, shell = True) == 0:
showMessage(2, " - Done. frame '%s' was normalised." % filenameNOR, filenameNOR)
else:
showMessage(3, "Could not find 'saxs_mac' or it returned an error!")
elif status == 1:
print "Aborting data reprocess!"
sys.exit(0)
else:
showMessage(3, "File '%s' didn't appear on disk after '%s' seconds." % (filenameRAW, pTimeOut))
if pOperation in ("-2", "-1", "1", "3"):
print " - Generating 1D file '%s'..." % filenameDAT
if pKeepOriginal == "0":
os.system("rm -f %s %s %s 2>/dev/null" % (filenameDAT, filenameANG, filenameMSK))
status = waitFile(filenameNOR, sizeNOR, pTimeOut)
if status == 0:
command = "saxs_add -omod n %s %s %s > /dev/null 2>/dev/null" % (filenameNOR, maskFile, filenameMSK)
#print command
if subprocess.call(command, shell = True) == 0:
command = "saxs_angle -omod n -rsys normal -da 360_deg -odim = 1 %s %s > /dev/null 2>/dev/null" % (filenameMSK, filenameANG)
#print command
if subprocess.call(command, shell = True) == 0:
#command = "saxs_curves -i1err _i1val -scf 2_pi -ext .dat -spc \" \" -prm \"Sample c=%6.2f mg/ml,Concentration: %s,Code: %s\" %s %s" % (float(concentration), concentration, code, filenameANG, filenameDAT)
command = "saxs_curves -scf 2_pi -ext .dat -spc \" \" %s %s > /dev/null 2>/dev/null" % (filenameANG, filenameDAT)
#print command
if subprocess.call(command, shell = True) == 0:
spec.open(filenameDAT)
header = spec.getHeader()
values = spec.getValues()
spec.close()
header[1] = " Sample c=%6.2f mg/ml" % float(concentration)
header.append("Normalisation: %s" % normalisation)
header.append("Concentration: %s" % concentration)
header.append("Code: %s" % code)
spec.open(filenameDAT, "w")
spec.write(header, values)
spec.close()
showMessage(2, " - Done. 1D file '%s' was generated." % filenameDAT, filenameDAT)
else:
showMessage(3, "Could not find 'saxs_curves' or it returned an error!")
else:
showMessage(3, "Could not find 'saxs_angle' or it returned an error!")
else:
showMessage(3, "Could not find 'saxs_add' or it returned an error!")
elif status == 1:
print "Aborting data reprocess!"
sys.exit(0)
else:
showMessage(3, "File '%s' didn't appear on disk after '%s' seconds." % (filenameNOR, pTimeOut))
if pOperation in ("-2", "1", "2", "3"):
if pKeepOriginal == "0":
filenameDAT_AVE = "%s/1d/%s_%s_ave.dat" % (pDirectory, pPrefix, runNumber)
filenameANG_AVE = "%s/misc/%s_%s_ave.ang" % (pDirectory, pPrefix, runNumber)
filenameLOG_AVE = "%s/misc/%s_%s_ave.log" % (pDirectory, pPrefix, runNumber)
filenamePattern = "%s/misc/%s_%s_%s.ang" % (pDirectory, pPrefix, runNumber, "%%")
else:
filenameDAT_AVE = "%s/%s_%s_ave.dat" % (directory1D_REP, pPrefix, runNumber)
filenameANG_AVE = "%s/%s_%s_ave.ang" % (directoryMISC_REP, pPrefix, runNumber)
filenameLOG_AVE = "%s/%s_%s_ave.log" % (directoryMISC_REP, pPrefix, runNumber)
filenamePattern = "%s/%s_%s_%s.ang" % (directoryMISC_REP, pPrefix, runNumber, "%%")
print "\n<Averaging>"
print " - Generating average '%s' from 1D files..." % filenameDAT_AVE
if pKeepOriginal == "0":
os.system("rm -f %s %s %s 2>/dev/null" % (filenameDAT_AVE, filenameANG_AVE, filenameLOG_AVE))
if pFrameFirst == "":
frameFirst = int(frameList[0])
else:
frameFirst = int(pFrameFirst)
if pFrameLast == "":
frameLast = int(frameList[-1])
else:
frameLast = int(pFrameLast)
#command = "saxs_mac -omod n -i1err _i1val -var -add %d -ofac %f %s,%d,%d %s > %s" % (frameLast - frameFirst + 1, 1 / float(frameLast - frameFirst + 1), filenamePattern, frameFirst, frameLast, filenameANG_AVE, filenameLOG_AVE)
command = "%s -omod n +var -add %d -ofac %s %s,%d,%d %s > %s 2>/dev/null" % (saxs_mac, frameLast - frameFirst + 1, str(1 / float(frameLast - frameFirst + 1)), filenamePattern, frameFirst, frameLast, filenameANG_AVE, filenameLOG_AVE)
#print command
if subprocess.call(command, shell = True) == 0:
#command = "saxs_curves -i1err _i1val -scf 2_pi -ext .dat -spc \" \" -prm \"Sample c=%6.2f mg/ml,Concentration: %s,Code: %s\" %s %s" % (float(concentration), concentration, code, filenameANG_AVE, filenameDAT_AVE)
command = "saxs_curves -scf 2_pi -ext .dat -spc \" \" %s %s > /dev/null 2>/dev/null" % (filenameANG_AVE, filenameDAT_AVE)
#print command
if subprocess.call(command, shell = True) == 0:
spec.open(filenameDAT_AVE)
header = spec.getHeader()
values = spec.getValues()
spec.close()
header[1] = " Sample c=%6.2f mg/ml" % float(concentration)
header.append("Normalisation: %s" % normalisation)
header.append("Concentration: %s" % concentration)
header.append("Code: %s" % code)
spec.open(filenameDAT_AVE, "w")
spec.write(header, values)
spec.close()
showMessage(2, " - average done.")
else:
showMessage(3, "Could not find 'saxs_curves' or it returned an error!")
else:
showMessage(3, "Could not find 'saxs_mac' or it returned an error!")
if __terminal or pSPECVersion is not None:
showMessage(0, "\n<Data reprocessing DONE>\n")
def Reprocess(pDetector, pOperation, pDirectory, pPrefix, pRunNumber, pFrameFirst, pFrameLast, pConcentration, pComments, pCode, \
pMaskFile, pDetectorDistance, pWaveLength, pPixelSizeX, pPixelSizeY, pBeamCenterX, pBeamCenterY, pNormalisation, pBeamStopDiode, \
pMachineCurrent, pKeepOriginal, pTimeOut, pSPECVersion, pSPECVariableStatus, pSPECVariableAbort, pTerminal):
if pSPECVersion is not None:
if pSPECVariableStatus is not None:
globals()["REPROCESS_STATUS"] = SpecVariable.SpecVariable(
pSPECVariableStatus, pSPECVersion)
if pSPECVariableAbort is not None:
globals()["REPROCESS_ABORT"] = SpecVariable.SpecVariable(
pSPECVariableAbort, pSPECVersion)
if pDetector not in ("0", "1"):
showMessage(4, "Invalid detector '%s'!" % pDetector)
return
if pOperation not in ("-2", "-1", "0", "1", "2", "3"):
showMessage(4, "Invalid operation '%s'!" % pOperation)
return
if not os.path.exists(pDirectory):
showMessage(4, "Directory '%s' not found!" % pDirectory)
return
if not os.path.exists(pDirectory + "/1d"):
try:
os.mkdir(pDirectory + "/1d")
except:
showMessage(
4, "Could not create directory '1d' in '%s'!" % pDirectory)
return
if not os.path.exists(pDirectory + "/2d"):
try:
os.mkdir(pDirectory + "/2d")
except:
showMessage(
4, "Could not create directory '2d' in '%s'!" % pDirectory)
return
if not os.path.exists(pDirectory + "/misc"):
try:
os.mkdir(pDirectory + "/misc")
except:
showMessage(
4, "Could not create directory 'misc' in '%s'!" % pDirectory)
return
runNumberList = []
if pRunNumber == "":
for filename in os.listdir(pDirectory + "/raw"):
if os.path.isfile(pDirectory + "/raw/" + filename):
prefix, run, frame, extra, extension = getFilenameDetails(
filename)
if prefix == pPrefix and run != "" and frame != "" and (
pDetector == "0" and extension == "edf"
or pDetector == "1" and extension == "gfrm"):
try:
runNumberList.index(run)
except:
runNumberList.append(run)
else:
list = pRunNumber.split(",")
for runNumber in list:
runNumber = "%03d" % int(runNumber)
try:
runNumberList.index(runNumber)
except:
runNumberList.append(runNumber)
if len(runNumberList) == 0:
showMessage(4, "There are no runs for prefix '%s'!" % pPrefix)
return
else:
runNumberList.sort()
spec = SPEC()
if pDetector == "0":
dictionaryEDF = "EDF_PILATUS"
else:
dictionaryEDF = "EDF_VANTEC"
if pKeepOriginal == "0":
directory1D_REP = ""
directory2D_REP = ""
directoryMISC_REP = ""
else:
i = 0
print
for runNumber in runNumberList:
if __terminal or pSPECVersion is not None: # reprocess was launched from terminal or from BsxCuBE while reprocessing data
frameList = []
for filename in os.listdir(pDirectory + "/raw"):
if os.path.isfile(pDirectory + "/raw/" + filename):
prefix, run, frame, extra, extension = getFilenameDetails(
filename)
if prefix == pPrefix and run == runNumber and frame != "":
if (pFrameFirst == "" or int(frame) >= int(pFrameFirst)
) and (pFrameLast == ""
or int(frame) <= int(pFrameLast)):
if pDetector == "0" and extension == "edf" or pDetector == "1" and extension == "gfrm":
try:
frameList.index(frame)
except:
frameList.append(frame)
else: # reprocess was launched from BsxCuBE while collecting data
frameList = ["%05d" % int(pFrameLast)]
if len(frameList) == 0:
showMessage(3, "There are no frames for run '%s'!" % runNumber)
else:
frameList.sort()
for frame in frameList:
if pDetector == "0": # Pilatus
filenameRAW = "%s/raw/%s_%s_%s.edf" % (pDirectory, pPrefix,
runNumber, frame)
sizeRAW = 4090000
sizeNOR = 4100000
else: # Vantec
filenameRAW = "%s/raw/%s_%s_%s.gfrm" % (
pDirectory, pPrefix, runNumber, frame)
sizeRAW = 4200000
sizeNOR = 16780000
if __terminal or pSPECVersion is not None: # reprocess was launched from terminal or from BsxCuBE while reprocessing data
if pConcentration == "" or \
pComments == "" or \
pCode == "" or \
pMaskFile == "" or \
pDetectorDistance == "" or \
pWaveLength == "" or \
pPixelSizeX == "" or \
pPixelSizeY == "" or \
pBeamCenterX == "" or \
pBeamCenterY == "" or \
pNormalisation == "" or \
pBeamStopDiode == "" or \
pMachineCurrent == "":
filenameNOR_ORG = "%s/2d/%s_%s_%s.edf" % (
pDirectory, pPrefix, runNumber, frame)
if os.path.exists(filenameNOR_ORG):
valdict = valuesFromHeader(filenameNOR_ORG)
else: # reprocess was launched from BsxCuBE while collecting data
valdict = []
# Concentration
if pConcentration == "":
if 'Concentration' in valdict:
concentration = valdict['Concentration']
else:
print "concentration not in header"
else:
concentration = pConcentration
# Comments
if pComments == "":
if 'Comments' in valdict:
comments = valdict['Comments']
else:
print "comments not in header"
else:
comments = pComments
# Code
if pCode == "":
if 'Code' in valdict:
code = valdict['Code']
else:
print "code not in header"
else:
code = pCode
# Mask
if pMaskFile == "":
if 'Mask' in valdict:
maskFile = valdict['Mask']
else:
print "maskFile not in header"
else:
maskFile = pMaskFile
# Detectordistance
if pDetectorDistance == "":
if 'SampleDistance' in valdict:
detectorDistance = valdict['SampleDistance']
else:
print "DetectorDistance not in header"
else:
detectorDistance = pDetectorDistance
# Wavelength
if pWaveLength == "":
if 'WaveLength' in valdict:
waveLength = valdict['WaveLength']
else:
print "Wavelength not in header"
else:
waveLength = pWaveLength
# PSize X
if pPixelSizeX == "":
if 'PSize_1' in valdict:
pixelSizeX = valdict['PSize_1']
else:
print "pixelSizeX not in header"
else:
pixelSizeX = pPixelSizeX
# PSize Y
if pPixelSizeY == "":
if 'PSize_2' in valdict:
pixelSizeY = valdict['PSize_2']
else:
print "pixelSizeY not in header"
else:
pixelSizeY = pPixelSizeY
# Beamcenter X
if pBeamCenterX == "":
if 'Center_1' in valdict:
beamCenterX = valdict['Center_1']
else:
print "beamCenterX not in header"
else:
beamCenterX = pBeamCenterX
# Beamcenter Y
if pBeamCenterY == "":
if 'Center_2' in valdict:
beamCenterY = valdict['Center_2']
else:
print "beamCenterY not in header"
else:
beamCenterY = pBeamCenterY
# Beam stop diode
if pBeamStopDiode == "":
if 'DiodeCurr' in valdict:
beamStopDiode = valdict['DiodeCurr']
else:
print "beamStopDiode not in header"
else:
beamStopDiode = pBeamStopDiode
# Machine current
if pMachineCurrent == "":
if 'MachCurr' in valdict:
machineCurrent = valdict['MachCurr']
else:
print "machineCurrent not in header"
else:
machineCurrent = pMachineCurrent
# Normalisation
if pNormalisation == "":
if 'Normalisation' in valdict:
normalisation = valdict['Normalisation']
else:
print "normalisation not in header"
else:
normalisation = pNormalisation
print "Concentration is: %s " % concentration
print "Comments are: %s " % comments
print "Code is: %s " % code
print "Maskfile is: %s " % maskFile
print "Detector distance is: %s " % detectorDistance
print "Wavelength is: %s " % waveLength
print "pixelSizeX is: %s " % pixelSizeX
print "pixelSizeY is: %s " % pixelSizeY
print "beamCenterX is: %s " % beamCenterX
print "beamCenterY is: %s " % beamCenterY
print "beamDiodeCurrent is: %s " % beamStopDiode
print "machineCurrent is: %s " % machineCurrent
print "normalisation is: %s " % normalisation
if __terminal or pSPECVersion is not None:
showMessage(0, "The data reprocessing is done!")
