def _validate(self):
errors = ProtAlignMovies._validate(self)
# Although getFirstItem is not recommended in general, here it is
# used only once, for validation purposes, so performance
# problems not should be appear.
if not self.inputMovies.get() is None:
inputSet = self.inputMovies.get()
movie = inputSet.getFirstItem()
if (not movie.hasAlignment()) and self.useAlignment:
errors.append(
"Your movies have no alignment. Please, set *No* "
"the parameter _Use previous movie alignment to SUM"
" frames?_")
if self.doApplyDoseFilter:
doseFrame = inputSet.getAcquisition().getDosePerFrame()
if doseFrame == 0.0 or doseFrame is None:
errors.append(
'Dose per frame for input movies is 0 or not '
'set. You cannot apply dose filter.')
if self.numberOfThreads > 1 and self.useGpu:
errors.append("GPU and Parallelization can not be used together")
ofCpu = Plugin.getHome("bin", "xmipp_movie_optical_alignment_cpu")
ofGpu = Plugin.getHome("bin", "xmipp_movie_optical_alignment_gpu")
if not (exists(ofGpu) or exists(ofCpu)):
errors.append(
"It seems that Xmipp Optical Alignment is not installed. "
"Please make sure that _scipion/config/scipion.config_ "
"contains *OPENCV=True* and OpenCV is in your system.\n"
"Then, re-install Xmipp by running "
"'scipion installb xmippSrc'.")
else:
if self.useGpu and not exists(ofGpu):
errors.append(
"It seems that Xmipp Optical Alignment has not been "
"compiled with CUDA.\nPlease, try with *GPU=No*.\n"
"Error: '%s' not found." % ofGpu)
if not self.useGpu and not exists(ofCpu):
errors.append(
"It seems that Xmipp Optical Alignment has been "
"compiled with CUDA.\nPlease, try with *GPU=Yes*.\n"
"Error: '%s' not found." % ofCpu)
return errors
def getCLTomoEnviron(self):
env = Plugin.getEnviron()
env.set(
'PYTHONPATH',
os.path.join(os.environ['SCIPION_HOME'], 'software', 'lib',
'python2.7', 'site-packages', 'sh_alignment'),
Environ.BEGIN)
return env
def applyCTF(self, setPartMd):
writeSetOfParticles(self.partSet, setPartMd)
md1 = xmippLib.MetaData()
md1.setColumnFormat(False)
idctf = md1.addObject()
_acquisition = self.partSet.getAcquisition()
for part in self.partSet:
baseFnCtf = self.proj.getTmpPath(
"kk") #self._getTmpPath("ctf_%d.param"%mic)
md1.setValue(xmippLib.MDL_CTF_SAMPLING_RATE, samplingRate, idctf)
md1.setValue(xmippLib.MDL_CTF_VOLTAGE, 200., idctf)
ctf = part.getCTF()
udefocus = ctf.getDefocusU()
vdefocus = ctf.getDefocusV()
angle = ctf.getDefocusAngle()
md1.setValue(xmippLib.MDL_CTF_DEFOCUSU, udefocus, idctf)
md1.setValue(xmippLib.MDL_CTF_DEFOCUSV, vdefocus, idctf)
md1.setValue(xmippLib.MDL_CTF_DEFOCUS_ANGLE,
180.0 * random.random(), idctf)
md1.setValue(xmippLib.MDL_CTF_CS, 2., idctf)
md1.setValue(xmippLib.MDL_CTF_Q0, 0.07, idctf)
md1.setValue(xmippLib.MDL_CTF_K, 1., idctf)
md1.write(baseFnCtf)
##writeSetOfParticles(self.partSet, setPartMd)
#apply ctf
args = " -i %s" % setPartMd
args += " -o %s" % self.proj.getTmpPath(setPartCtfName)
args += " -f ctf %s" % baseFnCtf
args += " --sampling %f" % samplingRate
Plugin.runXmippProgram("xmipp_transform_filter", args)
args = " -i %s" % setPartMd
args += " -o %s" % self.proj.getTmpPath(setPartCtfPosName)
args += " -f ctfpos %s" % baseFnCtf
args += " --sampling %f" % samplingRate
Plugin.runXmippProgram("xmipp_transform_filter", args)
def _validate(self):
errors = []
nmaBin = Plugin.getVar(NMA_HOME)
nma_programs = [
'nma_check_modes', 'nma_diag_arpack', 'nma_diagrtb',
'nma_elnemo_pdbmat'
]
# Check Xmipp was compiled with NMA flag to True and
# some of the nma programs are under the Xmipp/bin/ folder
for prog in nma_programs:
if not exists(join(nmaBin, prog)):
errors.append(
"Some NMA programs are missing in the NMA folder.")
errors.append(
"Check that Scipion was installed with NMA: 'scipion install nma'"
)
break
from pyworkflow.utils.which import which
if which("csh") == "":
errors.append("Cannot find csh in the PATH")
return errors
def _validate(self):
errors = []
nmaBin = Plugin.getVar(NMA_HOME)
nma_programs = [
'nma_check_modes', 'nma_diag_arpack', 'nma_diagrtb',
'nma_elnemo_pdbmat'
]
# Check Xmipp was compiled with NMA flag to True and
# some of the nma programs are under the Xmipp/bin/ folder
for prog in nma_programs:
if not exists(join(nmaBin, prog)):
errors.append(
"Some NMA programs are missing in the NMA folder.")
#errors.append("Check that Scipion was installed with NMA: 'scipion installb nma'")
errors.append("Check that Scipion was installed with NMA")
break
from pyworkflow.utils.which import which
if (which("csh") == "") and (which("bash") == ""):
errors.append(
"Please install csh (can be a link to tcsh) or bash (e.g., on Ubuntu 'sudo apt-get install csh' or 'sudo apt-get install bash')"
)
return errors
def getNMAEnviron():
""" Create the needed environment for NMA programs. """
from xmipp3 import Plugin
environ = Plugin.getEnviron()
environ.update({'PATH': Plugin.getVar(NMA_HOME)}, position=Environ.BEGIN)
return environ
def getMLTomoEnviron(self):
env = Plugin.getEnviron()
return env
def projectPhantom(featFileName, paramFileName, particlesFileName):
args = "-i %s -o %s" % (featFileName, particlesFileName)
args += " --params %s" % paramFileName
runJob(None, "xmipp_phantom_project", args, env=Plugin.getEnviron())
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)