def importTomogramsStep(self, pattern, samplingRate):
""" Copy images matching the filename pattern
Register other parameters.
"""
self.info("Using pattern: '%s'" % pattern)
# Create a Volume template object
tomo = Tomogram()
tomo.setSamplingRate(samplingRate)
imgh = ImageHandler()
tomoSet = self._createSetOfTomograms()
tomoSet.setSamplingRate(samplingRate)
self._parseAcquisitionData()
for fileName, fileId in self.iterFiles():
x, y, z, n = imgh.getDimensions(fileName)
if fileName.endswith('.mrc') or fileName.endswith('.map'):
fileName += ':mrc'
if z == 1 and n != 1:
zDim = n
n = 1
else:
zDim = z
else:
zDim = z
origin = Transform()
if self.setOrigCoord.get():
origin.setShiftsTuple(self._getOrigCoord())
else:
origin.setShifts(x / -2. * samplingRate,
y / -2. * samplingRate,
zDim / -2. * samplingRate)
tomo.setOrigin(origin) # read origin from form
newFileName = _getUniqueFileName(self.getPattern(),
fileName.split(':')[0])
tsId = removeExt(newFileName)
tomo.setTsId(tsId)
if fileName.endswith(':mrc'):
fileName = fileName[:-4]
createAbsLink(fileName, abspath(self._getExtraPath(newFileName)))
tomo.setAcquisition(self._extractAcquisitionParameters(fileName))
if n == 1: # One volume per file
tomo.cleanObjId()
tomo.setFileName(self._getExtraPath(newFileName))
tomoSet.append(tomo)
else: # A stack of volumes per file (not common)
for index in range(1, n + 1):
tomo.cleanObjId()
tomo.setLocation(index, self._getExtraPath(newFileName))
tomoSet.append(tomo)
self._defineOutputs(outputTomograms=tomoSet)
def createOutputStep(self, tsObjId):
ts = self.inputSetOfTiltSeries.get()[tsObjId]
tsId = ts.getTsId()
extraPrefix = self._getExtraPath(tsId)
outputSetOfTomograms = self.getOutputSetOfTomograms()
newTomogram = Tomogram()
newTomogram.setLocation(os.path.join(extraPrefix, ts.getFirstItem().parseFileName(extension=".mrc")))
# Set tomogram origin
ih = ImageHandler()
xDim, yDim, zDim, _ = \
ih.getDimensions(os.path.join(extraPrefix, ts.getFirstItem().parseFileName(extension=".mrc")))
origin = Transform()
sr = self.inputSetOfTiltSeries.get().getSamplingRate()
origin.setShifts(xDim / -2. * sr,
yDim / -2. * sr,
zDim / -2 * sr)
newTomogram.setOrigin(origin)
# Set tomogram acquisition
acquisition = TomoAcquisition()
acquisition.setAngleMin(ts.getFirstItem().getTiltAngle())
acquisition.setAngleMax(ts[ts.getSize()].getTiltAngle())
acquisition.setStep(self.getAngleStepFromSeries(ts))
newTomogram.setAcquisition(acquisition)
outputSetOfTomograms.append(newTomogram)
outputSetOfTomograms.update(newTomogram)
outputSetOfTomograms.write()
self._store()
def importSubTomogramsStep(self, pattern, samplingRate):
""" Copy images matching the filename pattern
Register other parameters.
"""
self.info("Using pattern: '%s'" % pattern)
# Create a Volume template object
subtomo = SubTomogram()
subtomo.setSamplingRate(samplingRate)
imgh = ImageHandler()
self.subtomoSet = self._createSetOfSubTomograms()
self.subtomoSet.setSamplingRate(samplingRate)
# if self.importCoordinates.get():
# self.coords = []
# for coord3D in self.importCoordinates.get().iterCoordinates():
# self.coords.append(coord3D.clone())
# self.subtomoSet.setCoordinates3D(self.importCoordinates)
self._parseAcquisitionData()
for fileName, fileId in self.iterFiles():
x, y, z, n = imgh.getDimensions(fileName)
if fileName.endswith('.map'):
fileName += ':mrc'
if fileName.endswith('.mrc') or fileName.endswith(':mrc'):
if z == 1 and n != 1:
zDim = n
n = 1
else:
zDim = z
else:
zDim = z
origin = Transform()
origin.setShifts(x / -2. * samplingRate, y / -2. * samplingRate,
zDim / -2. * samplingRate)
subtomo.setOrigin(origin) # read origin from form
newFileName = _getUniqueFileName(self.getPattern(), fileName)
# newFileName = abspath(self._getVolumeFileName(fileName))
if fileName.endswith(':mrc'):
fileName = fileName[:-4]
createAbsLink(fileName, self._getExtraPath(newFileName))
if n == 1:
self._addSubtomogram(subtomo, self._getExtraPath(fileName),
self._getExtraPath(newFileName))
else:
for index in range(1, n + 1):
self._addSubtomogram(subtomo,
self._getExtraPath(fileName),
self._getExtraPath(newFileName),
index=index)
def generateOutputStackStep(self, tomoObjId):
tomo = self.inputSetOfTomograms.get()[tomoObjId]
tomoId = os.path.splitext(os.path.basename(tomo.getFileName()))[0]
extraPrefix = self._getExtraPath(tomoId)
outputProjectedSetOfTiltSeries = self.getOutputProjectedSetOfTiltSeries(
)
newTs = tomoObj.TiltSeries(tsId=tomoId)
newTs.copyInfo(tomo)
newTs.setTsId(tomoId)
# Add origin to output tilt-series
origin = Transform()
outputProjectedSetOfTiltSeries.append(newTs)
tiltAngleList = self.getTiltAngleList()
for index in range(self.getProjectionRange()):
newTi = tomoObj.TiltImage()
newTi.setTiltAngle(tiltAngleList[index])
newTi.setTsId(tomoId)
newTi.setLocation(
index + 1,
os.path.join(extraPrefix,
os.path.basename(tomo.getFileName())))
newTi.setSamplingRate(
self.inputSetOfTomograms.get().getSamplingRate())
newTs.append(newTi)
ih = ImageHandler()
x, y, z, _ = ih.getDimensions(newTs.getFirstItem().getFileName())
newTs.setDim((x, y, z))
# Set origin to output tilt-series
origin.setShifts(
x / -2. * self.inputSetOfTomograms.get().getSamplingRate(),
y / -2. * self.inputSetOfTomograms.get().getSamplingRate(), 0)
newTs.setOrigin(origin)
newTs.write(properties=False)
outputProjectedSetOfTiltSeries.update(newTs)
outputProjectedSetOfTiltSeries.updateDim()
outputProjectedSetOfTiltSeries.write()
self._store()
def _createCoordinate3D(self):
# Tomogram associated to Coordinate3D
self.Tomo = Tomogram()
self.Tomo.setSamplingRate(1)
self.Tomo.setLocation(self.TomogramPath)
x, y, z = self.Tomo.getDim()
origin = Transform()
origin.setShifts(x / -2., y / -2., z / -2.)
self.Tomo.setOrigin(origin)
# Coordinate3D
self.coord = Coordinate3D()
self.coord.setBoxSize(32)
self.coord.setVolume(self.Tomo)
self.coord.setPosition(0, 0, 0, const.BOTTOM_LEFT_CORNER)
self.coord.setMatrix(np.eye(4))
def createOutputStep(self):
vol = Volume()
vol.setLocation(self._getOutputVol())
sampling = self.inputVolumes.get().getSamplingRate()
vol.setSamplingRate(sampling)
#
ccp4header = Ccp4Header(self._getOutputVol(), readHeader=True)
t = Transform()
x, y, z = ccp4header.getOrigin() # origin output vol
# coordinates
t.setShifts(x, y, z)
vol.setOrigin(t)
#
self._defineOutputs(outputVolume=vol)
self._defineSourceRelation(self.inputVolumes, self.outputVolume)
def createOutputStep(self):
inputVol = self.inputStructure.get()
samplingRate = inputVol.getSamplingRate()
volume = Volume()
volume.setFileName(self._getExtraPath("pseudoatoms_approximation.vol"))
volume.setSamplingRate(samplingRate)
x, y, z = volume.getDim()
xv, yv, zv = inputVol.getOrigin(force=True).getShifts()
t = Transform()
t.setShifts((x / 2. * samplingRate) - xv, (y / 2. * samplingRate) - yv,
(z / 2. * samplingRate) - zv)
volume.setOrigin(inputVol.getOrigin())
self._defineOutputs(outputVolume=volume)
self._defineSourceRelation(self.inputStructure.get(), volume)
pdb = AtomStruct(self._getPath('pseudoatoms.pdb'), pseudoatoms=True)
pdb.setVolume(volume)
pdb.setOrigin(t)
self.createChimeraScript(inputVol, pdb)
self._defineOutputs(outputPdb=pdb)
self._defineSourceRelation(self.inputStructure, pdb)
def extractunitCell(self, sym, offset=0, cropZ=False):
# FlexProtConvertToPseudoAtoms = Domain.importFromPlugin("continuousflex.protocols",
# "FlexProtConvertToPseudoAtoms",
# doRaise=True)
# NMA_MASK_THRE = Domain.importFromPlugin("continuousflex.protocols.pdb.protocol_pseudoatoms_base",
# "NMA_MASK_THRE",
# doRaise=True)
""" extract unit cell from icosahedral phantom
using xmipp_i2 symmetry
"""
# create phantom (3D map)
_samplingRate = 1.34
_, outputFile1 = mkstemp(suffix=".mrc")
command = "xmipp_phantom_create "
args = " -i %s" % self.filename[sym]
args += " -o %s" % outputFile1
runJob(None, command, args, env=Plugin.getEnviron())
ccp4header = Ccp4Header(outputFile1, readHeader=True)
x, y, z = ccp4header.getDims()
t = Transform()
if cropZ:
_, outputFile2 = mkstemp(suffix=".mrc")
args = "-i %s -o %s" % (outputFile1, outputFile2)
args += " --corners "
args += " %d " % (-x / 2.)
args += " %d " % (-y / 2.)
args += " %d " % (0.)
args += " %d " % (+x / 2.)
args += " %d " % (+y / 2.)
args += " %d " % (+z / 2.)
runJob(None,
"xmipp_transform_window",
args,
env=Plugin.getEnviron())
t.setShifts(0, 0, 0)
outputFile = outputFile2
ccp4header = Ccp4Header(outputFile2, readHeader=True)
else:
t.setShifts(0, 0, 0)
outputFile = outputFile1
ccp4header.setSampling(_samplingRate)
ccp4header.setOrigin(t.getShifts())
ccp4header.writeHeader()
# import volume
if cropZ:
args = {
'filesPath': outputFile,
'filesPattern': '',
'samplingRate': _samplingRate,
'copyFiles': True,
'setOrigCoord': True,
'x': 90. * _samplingRate,
'y': 90. * _samplingRate,
'z': 0.
# x, y, z in Angstroms
}
else:
args = {
'filesPath': outputFile,
'filesPattern': '',
'samplingRate': _samplingRate,
'copyFiles': True,
'setDefaultOrigin': False,
}
prot = self.newProtocol(ProtImportVolumes, **args)
prot.setObjLabel('import volume(%s)' % XMIPP_SYM_NAME[sym])
self.launchProtocol(prot)
# execute protocol extract unitCell
args = {
'inputVolumes': prot.outputVolume,
'symmetryGroup': sym,
'symmetryOrder': self.symOrder,
'innerRadius': self.innerRadius,
'outerRadius': self.outerRadius,
'expandFactor': .2,
'offset': offset
}
prot = self.newProtocol(XmippProtExtractUnit, **args)
prot.setObjLabel('extract unit cell')
self.launchProtocol(prot)
# check results
ih = ImageHandler()
xdim, ydim, zdim, ndim = \
ih.getDimensions(prot.outputVolume.getFileName())
self.assertTrue(abs(xdim - self.box[sym][0]) < 2)
self.assertTrue(abs(ydim - self.box[sym][1]) < 2)
self.assertTrue(abs(zdim - self.box[sym][2]) < 2)
# create pdb fileoutput
# args = {'inputStructure': prot.outputVolume,
# 'maskMode': NMA_MASK_THRE,
# 'maskThreshold': 0.5,
# 'pseudoAtomRadius': 1.5
# }
# prot = self.newProtocol(FlexProtConvertToPseudoAtoms, **args)
# prot.setObjLabel('get pdb')
# self.launchProtocol(prot)
# check results
# filenamePdb = prot._getPath('pseudoatoms.pdb')
# self.assertTrue(os.path.isfile(filenamePdb))
# delete temporary files
os.remove(self.filename[sym])
os.remove(outputFile)