def _runAnalysis(self, paramName=None):
program = Plugin.getProgram('analyze')
args = ' %s %d --Apix %0.3f' % (
self.protocol._getFileName("output_dir"),
self._epoch,
self.protocol._getSampling())
hostConfig = self.protocol.getHostConfig()
# Create the steps executor
executor = StepExecutor(hostConfig)
self.protocol.setStepsExecutor(executor)
# Finally run the protocol
self.protocol.runJob(program, args, env=Plugin.getEnviron(),
cwd=None)
def _extraWork():
program = Plugin.getProgram('').split()[:-1] # remove cryodrgn command
fn = self.protocol._getFileName('output_notebook',
epoch=self._epoch)
program.append('jupyter notebook %s' % os.path.basename(fn))
if os.path.exists(fn):
fnDir = os.path.dirname(fn)
hostConfig = self.protocol.getHostConfig()
executor = StepExecutor(hostConfig)
self.protocol.setStepsExecutor(executor)
self.protocol.runJob(" ".join(program), '',
env=Plugin.getEnviron(),
cwd=fnDir)
else:
self.showError('Jupyter notebook not found! Have you run analysis?')
def _getTrainingArgs(self):
args = [
'-o %s ' % self._getFileName('output_dir'),
'--zdim %d' % self.zDim.get(),
'--poses %s' % self._getFileName('input_poses'),
'--ctf %s' % self._getFileName('input_ctf'),
'-n %d' % self.numEpochs.get(), '--relion31 '
]
if Plugin.IS_V03():
if len(self.getGpuList()) > 1:
args.append('--multigpu')
if not self.doInvert:
args.append('--uninvert-data')
args.extend([
'--enc-layers %d' % self.qLayers.get(),
'--enc-dim %d' % self.qDim.get(),
'--dec-layers %d' % self.pLayers.get(),
'--dec-dim %d' % self.pDim.get()
])
else:
if self.doInvert:
args.append('--invert-data')
args.extend([
'--qlayers %d' % self.qLayers.get(),
'--qdim %d' % self.qDim.get(),
'--players %d' % self.pLayers.get(),
'--pdim %d' % self.pDim.get()
])
if self.extraParams.hasValue():
args.append('%s' % self.extraParams.get())
if os.path.exists(self._getFileName('input_stack')):
# input is a downsampled stack
args.append('%s' % self._getFileName('input_stack'))
else:
# input is a star file
args.extend([
'--datadir %s' % self._getDataDir(),
'%s' % self._getFileName('input_parts')
])
return args
def runTrainingStep(self):
""" Call cryoDRGN with the appropriate parameters. """
params = ' '.join(self._getTrainingArgs())
gpus = ",".join(str(i) for i in self.getGpuList())
program = Plugin.getProgram('train_vae', gpus=gpus)
self.runJob(program, params, env=Plugin.getEnviron(), cwd=None)
def runParseCtfStep(self):
""" Call cryoDRGN with the appropriate parameters. """
params = ' '.join(self._getParseCtfArgs())
program = Plugin.getProgram('parse_ctf_star')
self.runJob(program, params, env=Plugin.getEnviron(), cwd=None)
def runDownSampleStep(self):
""" Call cryoDRGN with the appropriate parameters. """
params = ' '.join(self._getDownsampleArgs())
program = Plugin.getProgram('downsample')
self.runJob(program, params, env=Plugin.getEnviron(), cwd=None)
def _runProgram(self, program, args, useGpu=True):
gpus = ','.join(str(i) for i in self.getGpuList())
self.runJob(Plugin.getProgram(program, gpus), ' '.join(args))
def _runProgram(self, program, args):
self.runJob(Plugin.getProgram(program), ' '.join(args))