def __getSubmodule(cls, name, subname):
try:
return importlib.import_module('%s.%s' % (name, subname))
except Exception as e:
msg = str(e)
# FIXME: The following is a quick and dirty way to filter
# when the submodule is not present
if msg != 'No module named %s' % subname:
pwutils.pluginNotFound("%s.%s" % (name, subname), msg)
return None
# * e-mail address '*****@*****.**'
# *
# **************************************************************************
import unittest, sys
from pyworkflow.em import *
from pyworkflow.tests import *
from test_workflow import TestWorkflow
from pyworkflow.utils import pluginNotFound
try:
from xmipp3 import *
from xmipp3.constants import SAME_AS_PICKING
from xmipp3.protocols import *
except:
pluginNotFound('xmipp3', doRaise=True)
try:
from grigoriefflab.protocols import *
except:
pluginNotFound('grigoriefflab', doRaise=True)
try:
from eman2.protocols import *
except:
pluginNotFound('eman2', doRaise=True)
try:
from relion.protocols import *
except:
pluginNotFound('relion', doRaise=True)
# * e-mail address '*****@*****.**'
# *
# **************************************************************************
import unittest, sys
from pyworkflow.em import *
from pyworkflow.tests import *
import pyworkflow.utils as pwutils
from test_workflow import TestWorkflow
from pyworkflow.em.protocol import ProtImportCoordinates
try:
from xmipp3 import *
from xmipp3.protocols import *
except:
pwutils.pluginNotFound('xmipp', doRaise=True)
OTHER = pwutils.importFromPlugin('xmipp3.constants', 'OTHER', doRaise=True)
class TestXmippWorkflow(TestWorkflow):
@classmethod
def setUpClass(cls):
setupTestProject(cls)
cls.dataset = DataSet.getDataSet('xmipp_tutorial')
cls.allCrdsDir = cls.dataset.getFile('posAllDir')
cls.micsFn = cls.dataset.getFile('allMics')
cls.vol1 = cls.dataset.getFile('vol1')
def testXmippWorkflow(self):
#First, import a set of micrographs
from pyworkflow.em.protocol import ProtImportMicrographs, ProtCreateStreamData
from pyworkflow.em.protocol.protocol_create_stream_data import \
SET_OF_MICROGRAPHS
from pyworkflow.protocol import getProtocolFromDb
from xmipp3.protocols import XmippProtPreprocessMicrographs
from xmipp3.protocols.protocol_extract_particles import *
from xmipp3.protocols.protocol_classification_gpuCorr_full import *
ProtCTFFind = importFromPlugin('grigoriefflab.protocols',
'ProtCTFFind',
doRaise=True)
try:
from eman2.protocols.protocol_autopick_sparx import *
except:
pluginNotFound('Eman2', "Eman2 is needed to run this test.", doRaise=True)
# Number of mics to be processed
NUM_MICS = 5
class TestGpuCorrFullStreaming(BaseTest):
@classmethod
def setUpClass(cls):
setupTestProject(cls)
cls.dsRelion = DataSet.getDataSet('relion_tutorial')
def importMicrographs(self):
prot = self.newProtocol(ProtImportMicrographs,
filesPath=self.dsRelion.getFile('micrographs'),
filesPattern='*.mrc',
# **************************************************************************
from os.path import exists
import subprocess
from pyworkflow.tests import *
from pyworkflow.em.protocol import *
from pyworkflow.protocol.launch import schedule
import pyworkflow.utils as pwutils
from pyworkflow.utils.path import *
try:
from relion.protocols import *
from relion.convert import *
except:
pwutils.pluginNotFound('relion')
try:
from xmipp3.protocols import *
from xmipp3.convert import *
except:
pwutils.pluginNotFound('xmipp')
# --- Set this to match with your queue system ---
# json params to fill the queue form, see SCIPION_HOME/config/host.conf
QUEUE_PARAMS = (
u'myslurmqueue',
{
u'JOB_TIME': u'1', # in hours
u'JOB_MEMORY': u'2048', # in Mb
u'QUEUE_FOR_JOBS': u'N',
from pyworkflow.tests import BaseTest, setupTestProject, DataSet
from pyworkflow.utils import importFromPlugin, pluginNotFound
from pyworkflow.em.protocol import (ProtImportAverages, ProtImportMicrographs,
ProtCreateStreamData)
from pyworkflow.em.protocol.protocol_create_stream_data import SET_OF_MICROGRAPHS
from pyworkflow.protocol import getProtocolFromDb
from xmipp3.protocols import XmippProtPreprocessMicrographs
from xmipp3.protocols.protocol_extract_particles import *
from xmipp3.protocols.protocol_classification_gpuCorr_semi import *
ProtCTFFind = importFromPlugin('grigoriefflab.protocols', 'ProtCTFFind', doRaise=True)
try:
from eman2.protocols.protocol_autopick_sparx import *
except:
pluginNotFound('Eman', "Eman is needed to do this test", doRaise=True)
# Number of mics to be processed
NUM_MICS = 5
class TestGpuCorrSemiStreaming(BaseTest):
@classmethod
def setUpClass(cls):
setupTestProject(cls)
cls.dsRelion = DataSet.getDataSet('relion_tutorial')
def importAverages(self):
prot = self.newProtocol(ProtImportAverages,
filesPath=self.dsRelion.getFile(
'import/averages.mrcs'),