def __init__(self, inputFile, **kwargs):
# Small trick to handle .vol Spider volumes
if inputFile.endswith('.vol'):
inputFile += ":spi"
CommandView.__init__(self, 'bshow "%s" &' % inputFile,
env=bsoft.Plugin.getEnviron(), **kwargs)
def __init__(self, volfile, sendEnd=True, **kwargs):
if volfile.endswith('.mrc'):
volfile += ':mrc'
self.kwargs = kwargs
if volfile is None:
raise ValueError(volfile)
if '@' in volfile:
[index, file] = volfile.split('@')
else:
file = volfile
if ':' in file:
file = file[0:file.rfind(':')]
if not os.path.exists(file):
raise Exception("File %s does not exists" % file)
self.volfile = volfile
self.voxelSize = self.kwargs.get('voxelSize', None)
# ChimeraServer is the basic server. There are other
# than inherit from it.
serverName = self.kwargs.get('ChimeraServer', 'ChimeraServer')
self.address = ''
self.port = getFreePort()
serverfile = pw.join('em', 'chimera_server.py')
command = CommandView(
"chimera --script '%s %s %s' &" %
(serverfile, self.port, serverName),
env=getChimeraEnviron(),
).show()
self.authkey = 'test'
self.client = Client((self.address, self.port), authkey=self.authkey)
self.initVolumeData()
self.openVolumeOnServer(self.vol, sendEnd)
self.initListenThread()
def _visualize(self, obj, **args):
cls = type(obj)
if issubclass(cls, Volume) or issubclass(cls, Image):
fn = obj.getFileName()
if pwutils.getExt(fn) in ['.stk', '.vol', '.xmp']:
# eman2 expects spider files with .spi extension only
pwutils.createLink(fn, pwutils.replaceExt(fn, 'spi'))
fn = pwutils.replaceExt(fn, 'spi')
view = CommandView("%s %s &" %
(Plugin.getProgram('e2display.py'), fn),
env=Plugin.getEnviron())
return [view]
elif isinstance(obj, EmanProtBoxing):
coords = obj.getCoords()
if coords:
return DataViewer._visualize(self, obj.outputCoordinates)
elif isinstance(obj, EmanProtInitModel):
obj = obj.outputVolumes
fn = obj.getFileName()
labels = 'id enabled comment _filename '
objCommands = "'%s' '%s' '%s'" % (OBJCMD_CLASSAVG_PROJS,
OBJCMD_PROJS, OBJCMD_INITVOL)
self._views.append(
ObjectView(self._project,
obj.strId(),
fn,
viewParams={
showj.MODE: showj.MODE_MD,
showj.VISIBLE: labels,
showj.RENDER: '_filename',
showj.OBJCMDS: objCommands
}))
return self._views
elif isinstance(obj, EmanProtInitModelSGD):
obj = obj.outputVolumes
fn = obj.getFileName()
labels = 'id enabled comment _filename '
objCommands = "'%s'" % OBJCMD_CLASSAVG_PROJS
self._views.append(
ObjectView(self._project,
obj.strId(),
fn,
viewParams={
showj.MODE: showj.MODE_MD,
showj.VISIBLE: labels,
showj.RENDER: '_filename',
showj.OBJCMDS: objCommands
}))
return self._views
def __init__(self, vmdCommand, **kwargs):
CommandView.__init__(self,
'vmd %s' % vmdCommand,
env=getVmdEnviron(),
**kwargs)
def __init__(self, inputFile, **kwargs):
CommandView.__init__(self,
'chimera "%s" &' % inputFile,
env=getChimeraEnviron(),
**kwargs)
def __init__(self, vmdCommand, **kwargs):
CommandView.__init__(self, 'vmd %s' % vmdCommand,
env=getVmdEnviron(), **kwargs)
def __init__(self, inputFile, **kwargs):
CommandView.__init__(self, 'chimera "%s" &' % inputFile,
env=getChimeraEnviron(), **kwargs)