def xmippMicrographsToEmx(micMd, emxData, emxDir):
""" Export micrographs from xmipp metadata to EMX.
"""
#acquisionInfo = findAcquisitionInfo(self.SelFileNameInitial)
from protlib_particles import readPosCoordinates
md = MetaData(micMd)
acquisionInfo = findAcquisitionInfo(md.getValue(MDL_MICROGRAPH, md.firstObject()))
micFn = 'mic%06d.mrc'
index = 0
pIndex = 0
img = Image()
hasCtf = md.containsLabel(MDL_CTF_MODEL)
filesRoot = dirname(micMd)
#assume sam pixelspacing for every micrograph
acquisionInfo = findAcquisitionInfo(md.getValue(MDL_MICROGRAPH, md.firstObject()))
if not acquisionInfo is None:
mdAux = MetaData(acquisionInfo)
pixelSpacing = mdAux.getValue(MDL_SAMPLINGRATE, mdAux.firstObject())
else:
pixelSpacing = 1.
for objId in md:
fnIn = md.getValue(MDL_MICROGRAPH, objId)
index += 1
fnOut = micFn % index
img.read(fnIn)
img.write(join(emxDir, fnOut))
micrograph = EmxMicrograph(fnOut)
# Set CTF parameters if present
if hasCtf:
xmippCtfToEmx(md, objId, micrograph)
posFile = join(filesRoot, 'extra', replaceBasenameExt(fnIn, POSENDING))
if exists(posFile):
mdPos = readPosCoordinates(posFile)
for pId in mdPos:
pIndex += 1
# We are using here a dummy filename, since not make sense
# for particles with just coordinates
particle = EmxParticle("", pIndex)
particle.set('centerCoord__X', mdPos.getValue(MDL_XCOOR, pId))
particle.set('centerCoord__Y', mdPos.getValue(MDL_YCOOR, pId))
particle.setMicrograph(micrograph)
emxData.addObject(particle)
micrograph.set('pixelSpacing__X',pixelSpacing)
micrograph.set('pixelSpacing__Y',pixelSpacing)
micrograph.set(COMMENT,'original filename=%s'%fnIn)
emxData.addObject(micrograph)
# Write EMX particles
_writeEmxData(emxData, join(emxDir, 'micrographs.emx'))
def emxParticlesToXmipp(emxData,
outputFileName=PARTFILE,
filesPrefix=None,
ctfRoot='',
_2D=False):
""" This function will iterate over the EMX particles and create
the equivalent Xmipp 'images.xmd' with the list of particles.
If CTF information is found, for each particle will contains information about the CTF
"""
#iterate though emxData
md = MetaData()
mdMic = MetaData()
if ctfRoot:# is None:
ctfRoot = dirname(outputFileName)
samplingRate = 0.
voltage = 0.
cs = 0.
amplitudeContrast = 0.
oldSamplingRate = -1.
oldVoltage = -1.
oldCs = -1.
oldAmplitudeContrast = -1.0
for particle in emxData.iterClasses(PARTICLE):
pIndex = particle.get(INDEX)
pFileName = particle.get(FILENAME)
if pFileName is None:
raise Exception("emxParticlesToXmipp: Xmipp doesn't support Particles without filename")
if filesPrefix is not None:
pFileName = join(filesPrefix, pFileName)
if pIndex is not None:
pFileName = '%06d@%s' % (pIndex, pFileName)
# pIndex is ignored now, in a more general solution
# Xmipp should be able to handle particles in a stack
# where the index has sense....
objId = md.addObject()
md.setValue(MDL_IMAGE, pFileName, objId)
mic = particle.getMicrograph()
if mic is not None:
micFileName = mic.get(FILENAME)
if filesPrefix is not None:
micFileName = join(filesPrefix, micFileName)
md.setValue(MDL_MICROGRAPH, micFileName, objId)
####
ctf = CTF()
for var in CTF.ctfVarLabels.keys():
setattr(ctf, var, mic.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.defocusU is not None:
for var, label in CTF.ctfVarLabels.iteritems():
v = getattr(ctf, var)
if v is not None:
md.setValue(label, float(v), objId)
md.setValue(MDL_CTF_K, 1.0, objId)
if particle.has('centerCoord__X'):
md.setValue(MDL_XCOOR, int(particle.get('centerCoord__X')), objId)
md.setValue(MDL_YCOOR, int(particle.get('centerCoord__Y')), objId)
if particle.has('transformationMatrix__t11'):
emxTransformToXmipp(md, objId, particle,_2D)
if particle.has('defocusU'):
md.setValue(MDL_CTF_DEFOCUSU, particle.get('defocusU')*10., objId)
if particle.has('defocusV'):
md.setValue(MDL_CTF_DEFOCUSV, particle.get('defocusV')*10., objId)
else:
md.setValue(MDL_CTF_DEFOCUSV, particle.get('defocusU')*10., objId)
if particle.has('defocusUAngle'):
md.setValue(MDL_CTF_DEFOCUS_ANGLE, particle.get('defocusUAngle'), objId)
# Sort metadata by particle name
md.sort(MDL_IMAGE)
# Write particles metadata
md.write('Particles@' + outputFileName)
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