def getObjectView(self, filename, **kwargs):
""" This is a wrapper around the ObjectView constructor, just to
avoid passing the project and protocol, since both are know
here in the ProtocolViewer.
"""
# We can not import em globally
from pyworkflow.em import ObjectView
return ObjectView(self._project, self.protocol.strId(), filename,
**kwargs)
def objectView(self, filenameOrObject, **kwargs):
""" This is a wrapper around the ObjectView constructor, just to
avoid passing the project and protocol, since both are know
here in the ProtocolViewer.
Params:
filenameOrObject: This parameter can be either a filename or an
object that has 'getFileName' method.
**kwargs: Can receive extra keyword-arguments that will be passed
to the ObjectView constructor
"""
# We can not import em globally
from pyworkflow.em import ObjectView
fn = None
if isinstance(filenameOrObject, basestring):
# If the input is a string filename, we should take the object id
# from the protocol. This assumes that self.protocol have been
# previously set
fn = filenameOrObject
strId = self.getProtocolId()
elif isinstance(filenameOrObject, Object):
if filenameOrObject.getObjId() is None:
strId = self.getProtocolId()
else:
strId = filenameOrObject.strId()
if hasattr(filenameOrObject, 'getLocation'):
# In this case fn will be a location tuple that will be
# correctly handled by the showj DataView
fn = filenameOrObject.getLocation()
elif hasattr(filenameOrObject, 'getFileName'):
# If the input is an object, we can take the id from it
fn = filenameOrObject.getFileName()
if fn is None:
raise Exception("Incorrect input object, it should be 'string' or "
"'Object' (with 'getLocation' or 'getFileName' "
"methods).")
return ObjectView(self._project, strId, fn, **kwargs)
def createScipionPartView(self, partSet, viewParams={}):
from pyworkflow.em import ObjectView
inputParticlesId = self.protocol.inputParticles.get().strId()
filename = partSet.getFileName()
labels = 'enabled id _size _filename _transform._matrix'
viewParams = {
showj.ORDER: labels,
showj.VISIBLE: labels,
showj.RENDER: '_filename',
'labels': 'id',
}
return ObjectView(
self._project,
self.protocol.strId(),
filename,
other=inputParticlesId,
# env=self._env,
viewParams=viewParams)
def viewVolumesSqlite(self, volumes):
path = self.protocol._getExtraPath('viewer_volumes.sqlite')
samplingRate = self.protocol.inputParticles.get().getSamplingRate()
self.createVolumesSqlite(volumes, path, samplingRate)
return [ObjectView(self._project, self.protocol.strId(), path)]