def xmippCtfModelToEmx(ctfModel, micrograph):
mdCTF = RowMetaData(ctfModel)
ctf = CTF()
# Set the variables in the dict
for var, label in CTF.ctfVarLabels.iteritems():
setattr(ctf, var, mdCTF.getValue(label))
ctf.defocusU /= 10.
ctf.defocusV /= 10.
while ctf.defocusUAngle < 0:
ctf.defocusUAngle += 180.
while ctf.defocusUAngle > 180.:
ctf.defocusUAngle -= 180.;
#this must be ordered
for var in CTF.ctfVarLabels.keys():
micrograph.set(var, getattr(ctf, var))
def createMicroscope(log, microscopeFn, Voltage, SphericalAberration, SamplingRate, AmplitudeContrast):
md = RowMetaData()
md.setValue(MDL_CTF_VOLTAGE, float(Voltage))
md.setValue(MDL_CTF_CS, float(SphericalAberration))
md.setValue(MDL_CTF_SAMPLING_RATE, float(SamplingRate))
md.setValue(MDL_CTF_Q0, float(AmplitudeContrast))
#md.setValue(MDL_MAGNIFICATION, 60000.0)
md.write(microscopeFn)
def createAcquisition(log, acqFn, SamplingRate):
# Create the acquisition info file
mdAcq = RowMetaData()
mdAcq.setValue(MDL_SAMPLINGRATE, float(SamplingRate))
mdAcq.write(acqFn)
def createMicroscope(log, fnOut, Voltage, SphericalAberration, SamplingRate):
md = RowMetaData()
md.setValue(xmipp.MDL_CTF_VOLTAGE, float(Voltage))
md.setValue(xmipp.MDL_CTF_CS, float(SphericalAberration))
md.setValue(xmipp.MDL_CTF_SAMPLING_RATE, float(SamplingRate))
md.setValue(xmipp.MDL_MAGNIFICATION, 60000.0)
md.write(fnOut)
def createAcquisition(log, fnOut, SamplingRate):
# Create the acquisition info file
mdAcq = RowMetaData()
mdAcq.setValue(xmipp.MDL_SAMPLINGRATE, float(SamplingRate))
mdAcq.write(fnOut)
def emxCTFToXmipp(emxData,
outputFileName=MICFILE,
filesPrefix='', #dirname
ctfRoot='',
_voltage=None,
_sphericalAberration=None,
_samplingRate=None,
_amplitudeContrast=None
):
""" This function will iterate over the EMX micrographs and create
a file .ctfparam for each micrograph.
"""
hasCTFMicro = False
hasCTFParticle = False
if emxData.objLists[PARTICLE] and (emxData.objLists[PARTICLE][0]).get('defocusU') is not None:
hasCTFParticle = True
objectClass = PARTICLE
if (emxData.objLists[MICROGRAPH][0]).get('defocusU') is not None:
hasCTFMicro = True
objectClass = MICROGRAPH
if not (hasCTFParticle or hasCTFMicro):
print "No CTF information available"
return # no ctf info
#fill metadata with CTF info
#objMd = MetaData()
for object in emxData.iterClasses(objectClass):
objIndex = object.get(INDEX)
objFileName = object.get(FILENAME)
if objFileName is None:
raise Exception("emxCTFToXmipp: Xmipp doesn't support Objects without filename")
elif objIndex is not None:
objFileName = join(filesPrefix, "%06d@%s"%(int(objIndex),objFileName))
else:
objFileName = join(filesPrefix, "%s"%(objFileName))
ctfModelFileName = join(ctfRoot, replaceBasenameExt(objFileName, CTFENDING))
ctf = CTFDEFOCUS()
# Set the variables in the dict
for var in CTF.ctfVarLabels.keys():
setattr(ctf, var, object.get(var))
if not ctfRoot:# is None:
ctfRoot = dirname(outputFileName)
for micrograph in emxData.iterClasses(MICROGRAPH):
micIndex = micrograph.get(INDEX)
micFileName = micrograph.get(FILENAME)
samplingRate = 0.
voltage = 0.
cs = 0.
amplitudeContrast = 0.
oldSamplingRate = -1.
oldVoltage = -1.
oldCs = -1.
oldAmplitudeContrast = -1.0
for micrograph in emxData.iterClasses(MICROGRAPH):
micIndex = micrograph.get(INDEX)
micFileName = micrograph.get(FILENAME)
if micFileName is None:
raise Exception("emxMicsToXmipp: Xmipp doesn't support Micrograph without filename")
# if micFileName is None:
# raise Exception("emxCTFToXmipp: Xmipp doesn't support Objects without filename")
elif micIndex is not None:
objFileName = join(filesPrefix, "%06d@%s"%(int(micIndex),micFileName))
else:
objFileName = join(filesPrefix, "%s"%(micFileName))
ctfModelFileName = join(ctfRoot, replaceBasenameExt(micFileName, CTFENDING))
ctf = CTF()
ctf.pixelSpacing__Y = micrograph.get('pixelSpacing__Y')
# Set the variables in the dict
for var in CTF.ctfVarLabels.keys():
setattr(ctf, var, micrograph.get(var))
# Now do some adjusments to vars
if ctf.defocusU is not None:
ctf.defocusU *= 10.
if ctf.defocusV is None:
ctf.defocusV = ctf.defocusU
ctf.defocusUAngle = 0.
else:
ctf.defocusV *= 10.
if ctf.pixelSpacing__Y is not None:
if ctf.pixelSpacing__X != ctf.pixelSpacing__Y:
raise Exception ('pixelSpacingX != pixelSpacingY. Xmipp does not support it')
if ctf.pixelSpacing__X is not None:
samplingRate = ctf.pixelSpacing__X
if (oldSamplingRate > -1):
if oldSamplingRate != samplingRate:
raise Exception ('Xmipp emx import cannot import emx files with different samplingRate')
oldSamplingRate = samplingRate
if ctf.acceleratingVoltage is not None:
voltage = ctf.acceleratingVoltage
if (oldVoltage > -1):
if oldVoltage != voltage:
raise Exception ('Xmipp emx import cannot import emx files with different voltage')
oldVoltage = voltage
if ctf.cs is not None:
cs = ctf.cs
if (oldCs > -1):
if oldCs != cs:
raise Exception ('Xmipp emx import cannot import emx files with different cs')
oldCs = cs
if ctf.amplitudeContrast is not None:
amplitudeContrast = ctf.amplitudeContrast
if (oldAmplitudeContrast > -1):
if oldAmplitudeContrast != amplitudeContrast:
raise Exception ('Xmipp emx import cannot import emx files with different amplitudeContrast')
oldAmplitudeContrast = amplitudeContrast
# Create the .ctfparam, replacing the micrograph name
#write only if ctf information is available
if (ctf.acceleratingVoltage is not None and
ctf.cs is not None and
ctf.amplitudeContrast is not None
):
mdCtf = RowMetaData()
for var, label in CTF.ctfVarLabels.iteritems():
v = getattr(ctf, var)
if v is not None:
mdCtf.setValue(label, float(v))
mdCtf.setValue(MDL_CTF_K, 1.0)
mdCtf.write(ctfModelFileName)
# Sort metadata by micrograph name
#mdMic.sort(MDL_MICROGRAPH)
# Write micrographs metadata
#mdMic.write('Micrographs@' + outputFileName)
return voltage, cs, samplingRate
