def convertInputStep(self):
""" Read the input metadatata. """
# Get the converted input micrographs in Xmipp format
makePath(self._getExtraPath("untilted"))
makePath(self._getExtraPath("tilted"))
uSet = self.untiltedSet.get()
tSet = self.tiltedSet.get()
# Get the untilted and tilted coordinates, depending on the input type
if isinstance(uSet, SetOfParticles):
uCoords = uSet.getCoordinates()
tCoords = tSet.getCoordinates()
# If there are not Coordinates associated to particles
# we need to create and fill the set of coordinates
if uCoords is None or tCoords is None:
micTiltedPairs = self.inputMicrographsTiltedPair.get()
uCoords = self._coordsFromParts(micTiltedPairs.getUntilted(),
uSet, '_untilted')
tCoords = self._coordsFromParts(micTiltedPairs.getTilted(),
tSet, '_tilted')
else:
uCoords = uSet
tCoords = tSet
writeSetOfCoordinates(self._getExtraPath("untilted"), uCoords)
writeSetOfCoordinates(self._getExtraPath("tilted"), tCoords)
def writePosFilesStep(self):
""" Write the pos file for each micrograph in metadata format
(both untilted and tilted). """
writeSetOfCoordinates(self._getExtraPath(),
self.inputCoords.getUntilted(),
scale=self.getBoxScale())
writeSetOfCoordinates(self._getExtraPath(),
self.inputCoords.getTilted(),
scale=self.getBoxScale())
# We need to find the mapping by micName (without ext) between the
# micrographs in the SetOfCoordinates and the Other micrographs
if self._micsOther():
micDict = {}
# create tmp set with all mics from coords set
coordMics = SetOfMicrographs(filename=':memory:')
coordMics.copyInfo(self.inputCoords.getUntilted().getMicrographs())
for micU, micT in izip(
self.inputCoords.getUntilted().getMicrographs(),
self.inputCoords.getTilted().getMicrographs()):
micU.cleanObjId()
micT.cleanObjId()
coordMics.append(micU)
coordMics.append(micT)
for mic in coordMics:
micBase = pwutils.removeBaseExt(mic.getFileName())
micPos = self._getExtraPath(micBase + ".pos")
micDict[pwutils.removeExt(mic.getMicName())] = micPos
# now match micDict and inputMics
if any(
pwutils.removeExt(mic.getMicName()) in micDict
for mic in self.inputMics):
micKey = lambda mic: pwutils.removeExt(mic.getMicName())
else:
raise Exception(
'Could not match input micrographs and coordinates '
'by micName.')
for mic in self.inputMics: # micrograph from input (other)
mk = micKey(mic)
if mk in micDict:
micPosCoord = micDict[mk]
if exists(micPosCoord):
micBase = pwutils.removeBaseExt(mic.getFileName())
micPos = self._getExtraPath(micBase + ".pos")
if micPos != micPosCoord:
self.info('Moving %s -> %s' %
(micPosCoord, micPos))
pwutils.moveFile(micPosCoord, micPos)
def writePosFilesStep(self):
""" Write the pos file for each micrograph in metadata format
(both untilted and tilted). """
writeSetOfCoordinates(self._getExtraPath(),
self.inputCoords.getUntilted(),
scale=self.getBoxScale())
writeSetOfCoordinates(self._getExtraPath(),
self.inputCoords.getTilted(),
scale=self.getBoxScale())
# We need to find the mapping by micName (without ext) between the
# micrographs in the SetOfCoordinates and the Other micrographs
if self._micsOther():
micDict = {}
# create tmp set with all mics from coords set
coordMics = SetOfMicrographs(filename=':memory:')
coordMics.copyInfo(self.inputCoords.getUntilted().getMicrographs())
for micU, micT in izip(self.inputCoords.getUntilted().getMicrographs(),
self.inputCoords.getTilted().getMicrographs()):
micU.cleanObjId()
micT.cleanObjId()
coordMics.append(micU)
coordMics.append(micT)
for mic in coordMics:
micBase = pwutils.removeBaseExt(mic.getFileName())
micPos = self._getExtraPath(micBase + ".pos")
micDict[pwutils.removeExt(mic.getMicName())] = micPos
# now match micDict and inputMics
if any(pwutils.removeExt(mic.getMicName()) in micDict for mic in self.inputMics):
micKey = lambda mic: pwutils.removeExt(mic.getMicName())
else:
raise Exception('Could not match input micrographs and coordinates '
'by micName.')
for mic in self.inputMics: # micrograph from input (other)
mk = micKey(mic)
if mk in micDict:
micPosCoord = micDict[mk]
if exists(micPosCoord):
micBase = pwutils.removeBaseExt(mic.getFileName())
micPos = self._getExtraPath(micBase + ".pos")
if micPos != micPosCoord:
self.info('Moving %s -> %s' % (micPosCoord, micPos))
pwutils.moveFile(micPosCoord, micPos)
def convertInputStep(self):
""" Read the input metadatata.
"""
# Get the converted input micrographs in Xmipp format
makePath(self._getExtraPath("untilted"))
makePath(self._getExtraPath("tilted"))
if self.typeOfSet.get() == TYPE_PARTICLES:
U_set = self.untiltPar.get().getCoordinates()
T_set = self.tiltPar.get().getCoordinates()
if (U_set or T_set) is None:
U_set = self._createSetOfCoordinates(self.tiltpair.get().getUntilted(),
suffix='_untilted')
T_set = self._createSetOfCoordinates(self.tiltpair.get().getTilted(),
suffix='_tilted')
untiltPar = self.untiltPar.get()
for particle_u in untiltPar:
newCoord = particle_u.getCoordinate().clone()
newCoord.copyObjId(particle_u)
U_set.append(newCoord)
#
tiltPar = self.tiltPar.get()
for particle_t in tiltPar:
newCoord = particle_t.getCoordinate().clone()
newCoord.copyObjId(particle_t)
T_set.append(newCoord)
aux = self.untiltPar.get()
aux2 = aux[1]
bos, y_, z_ = aux2.getDim()
U_set.setBoxSize(bos)
T_set.setBoxSize(bos)
else:
U_set = self.untiltCoor.get()
T_set = self.tiltCoor.get()
writeSetOfCoordinates(self._getExtraPath("untilted"), U_set)
writeSetOfCoordinates(self._getExtraPath("tilted"), T_set)
def writePosFilesStep(self):
""" Write the pos file for each micrograph on metadata format. """
#self.posFiles = writeSetOfCoordinates(self._getExtraPath(), self.inputCoords)
writeSetOfCoordinates(self._getExtraPath(), self.inputCoords)
# We need to find the mapping (either by micName or micId)
# between the micrographs in the SetOfCoordinates and
# the micrographs (if we are in a different case than 'same as picking'
if self.downsampleType != SAME_AS_PICKING:
micDict = {}
coordMics = self.inputCoords.getMicrographs()
for mic in coordMics:
micBase = removeBaseExt(mic.getFileName())
micPos = self._getExtraPath(micBase + ".pos")
micDict[mic.getMicName()] = micPos
micDict[mic.getObjId()] = micPos
if any(mic.getMicName() in micDict for mic in self.inputMics):
micKey = lambda mic: mic.getMicName()
elif any(mic.getObjId() in micDict for mic in self.inputMics):
self.warning(
'Could not match input micrographs and coordinates '
'micrographs by micName, using micId.')
micKey = lambda mic: mic.getObjId()
else:
raise Exception(
'Could not match input micrographs and coordinates '
'neither by micName or micId.')
for mic in self.inputMics: # micrograph from input (other)
mk = micKey(mic)
if mk in micDict:
micPosCoord = micDict[mk]
if exists(micPosCoord):
micBase = removeBaseExt(mic.getFileName())
micPos = self._getExtraPath(micBase + ".pos")
if micPos != micPosCoord:
self.info('Moving %s -> %s' %
(micPosCoord, micPos))
moveFile(micPosCoord, micPos)
def writePosFilesStep(self):
""" Write the pos file for each micrograph on metadata format. """
writeSetOfCoordinates(self._getExtraPath(), self.inputCoords,
scale=self.getBoxScale())
# We need to find the mapping (either by micName (without ext) or micId)
# between the micrographs in the SetOfCoordinates and
# the Other micrographs if necessary
if self._micsOther():
micDict = {}
coordMics = self.inputCoords.getMicrographs()
for mic in coordMics:
micBase = pwutils.removeBaseExt(mic.getFileName())
micPos = self._getExtraPath(micBase + ".pos")
micDict[pwutils.removeBaseExt(mic.getMicName())] = micPos
micDict[mic.getObjId()] = micPos
if any(pwutils.removeBaseExt(mic.getMicName()) in micDict
for mic in self.inputMics):
micKey = lambda mic: pwutils.removeBaseExt(mic.getMicName())
elif any(mic.getObjId() in micDict for mic in self.inputMics):
self.warning('Could not match input micrographs and coordinates'
' micrographs by micName, using micId.')
micKey = lambda mic: mic.getObjId()
else:
raise Exception('Could not match input micrographs and '
'coordinates neither by micName or micId.')
for mic in self.inputMics: # micrograph from input (other)
mk = micKey(mic)
if mk in micDict:
micPosCoord = micDict[mk]
if exists(micPosCoord):
micBase = pwutils.removeBaseExt(mic.getFileName())
micPos = self._getExtraPath(micBase + ".pos")
if micPos != micPosCoord:
self.info('Moving %s -> %s' % (micPosCoord, micPos))
pwutils.moveFile(micPosCoord, micPos)
def writePosFilesStep(self):
""" Write the pos file for each micrograph on metadata format. """
#self.posFiles = writeSetOfCoordinates(self._getExtraPath(), self.inputCoords)
writeSetOfCoordinates(self._getExtraPath(), self.inputCoords)
# We need to find the mapping (either by micName or micId)
# between the micrographs in the SetOfCoordinates and
# the micrographs (if we are in a different case than 'same as picking'
if self.downsampleType != SAME_AS_PICKING:
micDict = {}
coordMics = self.inputCoords.getMicrographs()
for mic in coordMics:
micBase = removeBaseExt(mic.getFileName())
micPos = self._getExtraPath(micBase + ".pos")
micDict[mic.getMicName()] = micPos
micDict[mic.getObjId()] = micPos
if any(mic.getMicName() in micDict for mic in self.inputMics):
micKey = lambda mic: mic.getMicName()
elif any(mic.getObjId() in micDict for mic in self.inputMics):
self.warning('Could not match input micrographs and coordinates '
'micrographs by micName, using micId.')
micKey = lambda mic: mic.getObjId()
else:
raise Exception('Could not match input micrographs and coordinates '
'neither by micName or micId.')
for mic in self.inputMics: # micrograph from input (other)
mk = micKey(mic)
if mk in micDict:
micPosCoord = micDict[mk]
if exists(micPosCoord):
micBase = removeBaseExt(mic.getFileName())
micPos = self._getExtraPath(micBase + ".pos")
if micPos != micPosCoord:
self.info('Moving %s -> %s' % (micPosCoord, micPos))
moveFile(micPosCoord, micPos)
def convertInputStep(self):
inputParticles = self.inputParticles.get()
firstCoord = inputParticles.getFirstItem().getCoordinate()
self.hasMicName = firstCoord.getMicName() is not None
inputMics = self._getMicrographs()
self.alignType = inputParticles.getAlignment()
self.downFactor = self.ctfDownFactor.get()
# create a tmp set for matching mics
self.matchingMics = self._createSetOfMicrographs(suffix='_tmp')
self.matchingMics.copyInfo(inputMics)
if self.downFactor != 1.:
self.matchingMics.setDownsample(self.downFactor)
# create a tmp set for coords
coords = self._createSetOfCoordinates(inputMics, suffix='_tmp')
newCoord = Coordinate()
self.scale = inputParticles.getSamplingRate() / inputMics.getSamplingRate()
if self.scale != 1.0:
print "Scaling coordinates by a factor *%0.2f*" % self.scale
# Create the micrograph dicts
micDict = {} # dict with micName or micId
micBaseDict = {} # dict with micName (just basename)
micKey2 = None
insertedMics = {}
for mic in inputMics:
if self.hasMicName:
micKey = mic.getMicName()
micKey2 = pwutils.removeBaseExt(micKey)
else:
micKey = mic.getObjId()
if micKey in micDict:
print ">>> ERROR: micrograph key %s is duplicated!" % micKey
print " Used in micrographs:"
print " - %s" % micDict[micKey].getLocation()
print " - %s" % mic.getLocation()
raise Exception("Micrograph key %s is duplicated!" % micKey)
micDict[micKey] = mic.clone()
if self.hasMicName:
micBaseDict[micKey2] = mic.clone()
# match the mic from coord with micDict
for particle in inputParticles:
coord = particle.getCoordinate() or None
if coord is None:
print "Skipping particle, coordinates not found"
continue
if self.hasMicName:
micKey = coord.getMicName()
micKey2 = pwutils.removeBaseExt(micKey)
else:
micKey = coord.getMicId()
# find the mapping by micName (with or without ext) or micId
mic = micDict.get(micKey, None) or micBaseDict.get(micKey2, None)
if mic is None:
print "Skipping particle, key %s not found" % micKey
else:
newCoord.copyObjId(particle)
x, y = coord.getPosition()
if self.applyShifts:
shifts = getShifts(particle.getTransform(), self.alignType)
xCoor, yCoor = x - int(shifts[0]), y - int(shifts[1])
newCoord.setPosition(xCoor * self.scale, yCoor * self.scale)
else:
newCoord.setPosition(x * self.scale, y * self.scale)
newCoord.setMicrograph(mic)
coords.append(newCoord)
if mic.getObjId() not in insertedMics:
insertedMics[mic.getObjId()] = mic
self.matchingMics.append(mic)
ih = em.ImageHandler()
# We convert matching micrographs if they are not *.mrc
for mic in self.matchingMics:
# Create micrograph dir
micName = mic.getFileName()
micDir = self._getTmpPath(pwutils.removeBaseExt(micName))
pwutils.makePath(micDir)
outMic = pwutils.join(micDir, pwutils.replaceBaseExt(micName, 'mrc'))
if self.downFactor != 1.:
ih.scaleFourier(micName, outMic, self.downFactor)
sps = inputMics.getScannedPixelSize() * self.downFactor
self._params['scannedPixelSize'] = sps
else:
if micName.endswith('.mrc'):
pwutils.createLink(micName, outMic)
else:
ih.convert(micName, outMic)
# Write out coordinate files and sets
writeSetOfCoordinates(self._getTmpPath(), coords, self.matchingMics)
coords.clear()
pwutils.cleanPath(coords.getFileName())
self.matchingMics.write()
self.matchingMics.close()
def writePosFilesStep(self):
""" Write the pos file for each micrograph on metadata format. """
#self.posFiles = writeSetOfCoordinates(self._getExtraPath(), self.inputCoords)
writeSetOfCoordinates(self._getExtraPath(), self.inputCoords)
def writePosFilesStep(self):
""" Write the pos file for each micrograph on metadata format (both untilted and tilted). """
writeSetOfCoordinates(self._getExtraPath(), self.inputCoordinatesTiltedPairs.get().getUntilted())
writeSetOfCoordinates(self._getExtraPath(), self.inputCoordinatesTiltedPairs.get().getTilted())
def convertInputStep(self):
inputParticles = self.inputParticles.get()
firstCoord = inputParticles.getFirstItem().getCoordinate()
self.hasMicName = firstCoord.getMicName() is not None
inputMics = self._getMicrographs()
self.alignType = inputParticles.getAlignment()
self.downFactor = self.ctfDownFactor.get()
# create a tmp set for matching mics
self.matchingMics = self._createSetOfMicrographs(suffix='_tmp')
self.matchingMics.copyInfo(inputMics)
if self.downFactor != 1.:
self.matchingMics.setDownsample(self.downFactor)
# create a tmp set for coords
coords = self._createSetOfCoordinates(inputMics, suffix='_tmp')
newCoord = Coordinate()
self.scale = inputParticles.getSamplingRate(
) / inputMics.getSamplingRate()
if self.scale != 1.0:
print "Scaling coordinates by a factor *%0.2f*" % self.scale
# Create the micrograph dicts
micDict = {} # dict with micName or micId
micBaseDict = {} # dict with micName (just basename)
micKey2 = None
insertedMics = {}
for mic in inputMics:
if self.hasMicName:
micKey = mic.getMicName()
micKey2 = pwutils.removeBaseExt(micKey)
else:
micKey = mic.getObjId()
if micKey in micDict:
print ">>> ERROR: micrograph key %s is duplicated!" % micKey
print " Used in micrographs:"
print " - %s" % micDict[micKey].getLocation()
print " - %s" % mic.getLocation()
raise Exception("Micrograph key %s is duplicated!" % micKey)
micDict[micKey] = mic.clone()
if self.hasMicName:
micBaseDict[micKey2] = mic.clone()
# match the mic from coord with micDict
for particle in inputParticles:
coord = particle.getCoordinate() or None
if coord is None:
print "Skipping particle, coordinates not found"
continue
if self.hasMicName:
micKey = coord.getMicName()
micKey2 = pwutils.removeBaseExt(micKey)
else:
micKey = coord.getMicId()
# find the mapping by micName (with or without ext) or micId
mic = micDict.get(micKey, None) or micBaseDict.get(micKey2, None)
if mic is None:
print "Skipping particle, key %s not found" % micKey
else:
newCoord.copyObjId(particle)
x, y = coord.getPosition()
if self.applyShifts:
shifts = getShifts(particle.getTransform(), self.alignType)
xCoor, yCoor = x - int(shifts[0]), y - int(shifts[1])
newCoord.setPosition(xCoor * self.scale,
yCoor * self.scale)
else:
newCoord.setPosition(x * self.scale, y * self.scale)
newCoord.setMicrograph(mic)
coords.append(newCoord)
if mic.getObjId() not in insertedMics:
insertedMics[mic.getObjId()] = mic
self.matchingMics.append(mic)
ih = em.ImageHandler()
# We convert matching micrographs if they are not *.mrc
for mic in self.matchingMics:
# Create micrograph dir
micName = mic.getFileName()
micDir = self._getTmpPath(pwutils.removeBaseExt(micName))
pwutils.makePath(micDir)
outMic = pwutils.join(micDir,
pwutils.replaceBaseExt(micName, 'mrc'))
if self.downFactor != 1.:
ih.scaleFourier(micName, outMic, self.downFactor)
sps = inputMics.getScannedPixelSize() * self.downFactor
self._params['scannedPixelSize'] = sps
else:
if micName.endswith('.mrc'):
pwutils.createLink(micName, outMic)
else:
ih.convert(micName, outMic)
# Write out coordinate files and sets
writeSetOfCoordinates(self._getTmpPath(), coords, self.matchingMics)
coords.clear()
pwutils.cleanPath(coords.getFileName())
self.matchingMics.write()
self.matchingMics.close()
def writePosFilesStep(self):
""" Write the pos file for each micrograph on metadata format (both untilted and tilted). """
writeSetOfCoordinates(self._getExtraPath(), self.inputCoordinatesTiltedPairs.get().getUntilted())
writeSetOfCoordinates(self._getExtraPath(), self.inputCoordinatesTiltedPairs.get().getTilted())
