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 importVolumesStep(self, pattern, samplingRate, setOrigCoord=False):
""" Copy images matching the filename pattern
Register other parameters.
"""
self.info("Using pattern: '%s'" % pattern)
# Create a Volume template object
vol = Volume()
vol.setSamplingRate(samplingRate)
imgh = ImageHandler()
volSet = self._createSetOfVolumes()
volSet.setSamplingRate(samplingRate)
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 setOrigCoord:
origin.setShiftsTuple(self._getOrigCoord())
else:
origin.setShifts(x / -2. * samplingRate,
y / -2. * samplingRate,
zDim / -2. * samplingRate)
vol.setOrigin(origin) # read origin from form
if self.copyFiles or setOrigCoord:
newFileName = abspath(self._getVolumeFileName(fileName, "mrc"))
Ccp4Header.fixFile(fileName, newFileName, origin.getShifts(),
samplingRate, Ccp4Header.ORIGIN)
else:
newFileName = abspath(self._getVolumeFileName(fileName))
if fileName.endswith(':mrc'):
fileName = fileName[:-4]
createAbsLink(fileName, newFileName)
# Make newFileName relative
# https://github.com/I2PC/scipion/issues/1935
newFileName = relpath(newFileName)
if n == 1:
vol.cleanObjId()
vol.setFileName(newFileName)
volSet.append(vol)
else:
for index in range(1, n + 1):
vol.cleanObjId()
vol.setLocation(index, newFileName)
volSet.append(vol)
if volSet.getSize() > 1:
self._defineOutputs(outputVolumes=volSet)
else:
self._defineOutputs(outputVolume=vol)
def extractunitCell(self, sym, offset=0, cropZ=False):
""" 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(XmippProtConvertToPseudoAtoms, **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)