def createScipionPartView(self, filename, viewParams={}):
inputParticlesId = self.protocol.inputParticles.get().strId()
labels = 'enabled id _size _filename _transform._matrix'
viewParams = {
showj.ORDER: labels,
showj.VISIBLE: labels,
showj.RENDER: '_filename',
'labels': 'id',
}
return em.ObjectView(self._project,
self.protocol.strId(),
filename,
other=inputParticlesId,
env=self._env,
viewParams=viewParams)
def _createVolumesSqlite(self):
""" Write an sqlite with all volumes selected for visualization. """
path = self.protocol._getExtraPath('frealign_viewer_volumes.sqlite')
samplingRate = self.protocol.inputParticles.get().getSamplingRate()
files = []
if self.protocol.IS_REFINE:
for it in self._iterations:
volFn = self.protocol._getFileName('iter_vol', iter=it)
if exists(volFn):
files.append(volFn)
else:
for it in self._iterations:
for ref3d in self._refsList:
volFn = self.protocol._getFileName('iter_vol_class',
iter=it,
ref=ref3d)
if exists(volFn):
files.append(volFn)
self.createVolumesSqlite(files, path, samplingRate)
return [em.ObjectView(self._project, self.protocol.strId(), path)]
def _visualize(self, obj, **args):
cls = type(obj)
def _getMicrographDir(mic):
""" Return an unique dir name for results of the micrograph. """
from pyworkflow.utils.path import removeBaseExt
return obj._getExtraPath(removeBaseExt(mic.getFileName()))
def iterMicrographs(mics):
""" Iterate over micrographs and yield
micrograph name and a directory to process.
"""
for mic in mics:
micFn = mic.getFileName()
micDir = _getMicrographDir(mic)
yield (micFn, micDir, mic)
def visualizeObjs(obj, setOfMics):
if exists(obj._getPath("ctfs_temporary.sqlite")):
os.remove(obj._getPath("ctfs_temporary.sqlite"))
ctfSet = self.protocol._createSetOfCTF("_temporary")
for fn, micDir, mic in iterMicrographs(setOfMics):
samplingRate = mic.getSamplingRate(
) * self.protocol.ctfDownFactor.get()
mic.setSamplingRate(samplingRate)
out = self.protocol._getCtfOutPath(micDir)
psdFile = self.protocol._getPsdPath(micDir)
if exists(out) and exists(psdFile):
ctfModel = em.CTFModel()
readCtfModel(ctfModel, out)
ctfModel.setPsdFile(psdFile)
ctfModel.setMicrograph(mic)
ctfSet.append(ctfModel)
if ctfSet.getSize() < 1:
raise Exception(
"Has not been completed the CTF estimation of any micrograph"
)
else:
ctfSet.write()
ctfSet.close()
self._visualize(ctfSet)
if issubclass(cls, ProtGctf) and not obj.hasAttribute("outputCTF"):
mics = obj.inputMicrographs.get()
visualizeObjs(obj, mics)
elif obj.hasAttribute("outputCTF"):
self._visualize(obj.outputCTF)
else:
fn = obj.getFileName()
if obj.strId() == "None":
objName = fn
else:
objName = obj.strId()
psdLabels = '_psdFile'
labels = 'id enabled comment %s _defocusU _defocusV _defocusAngle _defocusRatio' % psdLabels
labels = labels + ' _gctf_ctfResolution _gctf_crossCorrelation _micObj._filename'
print "objName, ", objName
self._views.append(
em.ObjectView(self._project,
objName,
fn,
viewParams={
showj.MODE: showj.MODE_MD,
showj.ORDER: labels,
showj.VISIBLE: labels,
showj.ZOOM: 50,
showj.RENDER: psdLabels,
showj.OBJCMDS: "'%s'" % OBJCMD_GCTF
}))
return self._views
def createView(self, filename, viewParams={}):
return em.ObjectView(self._project, self.protocol.strId(),
filename, viewParams=viewParams)