class CoordinatesTiltPair(TiltPairSet):
"""Represents a Coordinates Tilt Pair"""
ITEM_TYPE = TiltPair
def __init__(self, **kwargs):
TiltPairSet.__init__(self, **kwargs)
self._angles = SetOfAngles()
self._micsPair = Pointer()
def getAngles(self):
return self._angles
def getMicsPair(self):
return self._micsPair.get()
def setAngles(self, setAngles):
self._angles = setAngles
def setMicsPair(self, micsPair):
self._micsPair.set(micsPair)
def getFiles(self):
filePaths = TiltPairSet.getFiles(self)
filePaths.update(self.getAngles().getFiles())
filePaths.update(self.getMicsPair().getFiles())
return filePaths
def _loadClassesDict(self):
return globals()
def close(self):
TiltPairSet.close(self)
self.getAngles().close()
class CoordinatesTiltPair(EMSet):
"""Represents a Coordinates Tilt Pair"""
ITEM_TYPE = TiltPair
def __init__(self, **args):
EMSet.__init__(self, **args)
self._tilted = None#SetOfCoordinates()
self._untilted = None#SetOfCoordinates()
self._angles = SetOfAngles()
self._micsPair = Pointer()
def getUntilted(self):
return self._untilted
def getTilted(self):
return self._tilted
def getAngles(self):
return self._angles
def getMicsPair(self):
return self._micsPair.get()
def setUntilted(self, untilted):
self._untilted = untilted
def setTilted(self, tilted):
self._tilted = tilted
def setAngles(self, setAngles):
self._angles = setAngles
def setMicsPair(self, micsPair):
self._micsPair.set(micsPair)
def getFiles(self):
filePaths = set()
filePaths.add(self.getTilted().getFiles)
filePaths.add(self.getUntilted().getFiles)
return filePaths
def _loadClassesDict(self):
return globals()
def close(self):
self._tilted.close()
self._untilted.close()
EMSet.close(self)
class ParticlesTiltPair(TiltPairSet):
"""Represents a Particles Tilt Pair"""
ITEM_TYPE = TiltPair
def __init__(self, **kwargs):
TiltPairSet.__init__(self, **kwargs)
self._coordsPair = Pointer()
def getCoordsPair(self):
return self._coordsPair.get()
def setCoordsPair(self, coordsPair):
self._coordsPair.set(coordsPair)
def getFiles(self):
filePaths = TiltPairSet.getFiles(self)
filePaths.update(self.getCoordsPair().getFiles())
return filePaths
class ParticlesTiltPair(EMSet):
"""Represents a Particles Tilt Pair"""
ITEM_TYPE = TiltPair
def __init__(self, **args):
EMSet.__init__(self, **args)
self._tilted = None#SetOfImages()
self._untilted = None#SetOfImages()
self._coordsPair = Pointer()
def getUntilted(self):
return self._untilted
def getTilted(self):
return self._tilted
def getCoordsPair(self):
return self._coordsPair.get()
def setUntilted(self, untilted):
self._untilted = untilted
def setTilted(self, tilted):
self._tilted = tilted
def setCoordsPair(self, coordsPair):
self._coordsPair.set(coordsPair)
def getFiles(self):
filePaths = set()
filePaths.add(self.getTilted().getFiles)
filePaths.add(self.getUntilted().getFiles)
return filePaths
def _loadClassesDict(self):
return globals()
def close(self):
self._tilted.close()
self._untilted.close()
EMSet.close(self)
class ParticlesTiltPair(TiltPairSet):
"""Represents a Particles Tilt Pair"""
ITEM_TYPE = TiltPair
def __init__(self, **kwargs):
TiltPairSet.__init__(self, **kwargs)
self._coordsPair = Pointer()
def getCoordsPair(self):
return self._coordsPair.get()
def setCoordsPair(self, coordsPair):
self._coordsPair.set(coordsPair)
def getFiles(self):
filePaths = TiltPairSet.getFiles(self)
filePaths.update(self.getCoordsPair().getFiles())
return filePaths
class CoordinatesTiltPair(TiltPairSet):
"""Represents a Coordinates Tilt Pair"""
ITEM_TYPE = TiltPair
def __init__(self, **kwargs):
TiltPairSet.__init__(self, **kwargs)
self._angles = None
self._micsPair = Pointer()
def getAngles(self):
return self._angles
def getBoxSize(self):
return self.getUntilted().getBoxSize()
def getMicsPair(self):
return self._micsPair.get()
def setAngles(self, setAngles):
self._angles = setAngles
def setMicsPair(self, micsPair):
self._micsPair.set(micsPair)
def getFiles(self):
filePaths = TiltPairSet.getFiles(self)
filePaths.update(self.getAngles().getFiles())
filePaths.update(self.getMicsPair().getFiles())
return filePaths
def _loadClassesDict(self):
return globals()
def close(self):
TiltPairSet.close(self)
if self.getAngles():
self.getAngles().close()
def create_service_project(request):
if request.is_ajax():
import os
from pyworkflow.object import Pointer
from pyworkflow.em.protocol import ProtUnionSet, ProtImportAverages
from pyworkflow.em.packages.xmipp3 import XmippProtRansac, XmippProtReconstructSignificant, XmippProtAlignVolumeForWeb
from pyworkflow.em.packages.eman2 import EmanProtInitModel
from pyworkflow.em.packages.simple import ProtPrime
# Create a new project
projectName = request.GET.get('projectName')
# Filename to use as test data
testDataKey = request.GET.get('testData')
#customMenu = os.path.join(os.path.dirname(os.environ['SCIPION_PROTOCOLS']), 'menu_initvolume.conf')
manager = getServiceManager('myfirstmap')
writeCustomMenu(manager.protocols)
project = manager.createProject(projectName, runsView=1,
hostsConf=manager.hosts,
protocolsConf=manager.protocols
)
project.getSettings().setLifeTime(14)
project.saveSettings()
#copyFile(customMenu, project.getPath('.config', 'protocols.conf'))
# 1. Import averages
# If using test data execute the import averages run
# options are set in 'project_utils.js'
dsMDA = DataSet.getDataSet('initial_volume')
if testDataKey :
fn = dsMDA.getFile(testDataKey)
newFn = join(project.uploadPath, basename(fn))
copyFile(fn, newFn)
label_import = 'import averages ('+ testDataKey +')'
protImport = project.newProtocol(ProtImportAverages, objLabel=label_import)
protImport.filesPath.set(newFn)
protImport.samplingRate.set(1.)
project.launchProtocol(protImport, wait=True)
else:
protImport = project.newProtocol(ProtImportAverages, objLabel='import averages')
project.saveProtocol(protImport)
# 2a. Ransac
protRansac = project.newProtocol(XmippProtRansac)
protRansac.setObjLabel('xmipp - ransac')
protRansac.inputSet.set(protImport)
protRansac.inputSet.setExtended('outputAverages')
if testDataKey :
setProtocolParams(protRansac, testDataKey)
project.saveProtocol(protRansac)
# 2b. Eman
protEmanInitVol = project.newProtocol(EmanProtInitModel)
protEmanInitVol.setObjLabel('eman - initial vol')
protEmanInitVol.inputSet.set(protImport)
protEmanInitVol.inputSet.setExtended('outputAverages')
if testDataKey :
setProtocolParams(protEmanInitVol, testDataKey)
project.saveProtocol(protEmanInitVol)
# 2c. Significant
protSignificant = project.newProtocol(XmippProtReconstructSignificant)
protSignificant.setObjLabel('xmipp - significant')
protSignificant.inputSet.set(protImport)
protSignificant.inputSet.setExtended('outputAverages')
if testDataKey :
setProtocolParams(protSignificant, testDataKey)
project.saveProtocol(protSignificant)
# 3. Join result volumes
p1 = Pointer()
p1.set(protRansac)
p1.setExtended('outputVolumes')
p2 = Pointer()
p2.set(protEmanInitVol)
p2.setExtended('outputVolumes')
p3 = Pointer()
p3.set(protSignificant)
p3.setExtended('outputVolume')
protJoin = project.newProtocol(XmippProtAlignVolumeForWeb)
protJoin.setObjLabel('align volumes')
protJoin.inputVolumes.append(p1)
protJoin.inputVolumes.append(p2)
protJoin.inputVolumes.append(p3)
# protJoin.inputVolumes.append(p4)
project.saveProtocol(protJoin)
protValidate = project.newProtocol(XmippProtValidateNonTilt)
protValidate.setObjLabel('validate nontilt')
protValidate.inputVolumes.set(protJoin)
protValidate.inputVolumes.setExtended('outputVolumes')
protValidate.inputParticles.set(protImport)
protValidate.inputParticles.setExtended('outputAverages')
protValidate.numberOfThreads.set(8)
if testDataKey :
setProtocolParams(protValidate, testDataKey)
# protJoin.inputVolumes.append(p4)
project.saveProtocol(protValidate)
return HttpResponse(mimetype='application/javascript')
def create_service_project(request):
if request.is_ajax():
import os
from pyworkflow.object import Pointer
from pyworkflow.em.protocol import ProtUnionSet, ProtImportAverages
from pyworkflow.em.packages.xmipp3 import XmippProtRansac, XmippProtReconstructSignificant, XmippProtAlignVolumeForWeb
from pyworkflow.em.packages.eman2 import EmanProtInitModel
from pyworkflow.em.packages.simple import ProtPrime
# Create a new project
projectName = request.GET.get('projectName')
# Filename to use as test data
testDataKey = request.GET.get('testData')
#customMenu = os.path.join(os.path.dirname(os.environ['SCIPION_PROTOCOLS']), 'menu_initvolume.conf')
manager = getServiceManager('myfirstmap')
writeCustomMenu(manager.protocols)
project = manager.createProject(projectName,
runsView=1,
hostsConf=manager.hosts,
protocolsConf=manager.protocols)
project.getSettings().setLifeTime(336) # 14 days * 24 hours
project.saveSettings()
#copyFile(customMenu, project.getPath('.config', 'protocols.conf'))
# 1. Import averages
# If using test data execute the import averages run
# options are set in 'project_utils.js'
dsMDA = DataSet.getDataSet('initial_volume')
if testDataKey:
fn = dsMDA.getFile(testDataKey)
newFn = join(project.uploadPath, basename(fn))
copyFile(fn, newFn)
label_import = 'import averages (' + testDataKey + ')'
protImport = project.newProtocol(ProtImportAverages,
objLabel=label_import)
protImport.filesPath.set(newFn)
protImport.samplingRate.set(1.)
project.launchProtocol(protImport, wait=True)
else:
protImport = project.newProtocol(ProtImportAverages,
objLabel='import averages')
project.saveProtocol(protImport)
# 2a. Ransac
protRansac = project.newProtocol(XmippProtRansac)
protRansac.setObjLabel('xmipp - ransac')
protRansac.inputSet.set(protImport)
protRansac.inputSet.setExtended('outputAverages')
if testDataKey:
setProtocolParams(protRansac, testDataKey)
project.saveProtocol(protRansac)
# 2b. Eman
protEmanInitVol = project.newProtocol(EmanProtInitModel)
protEmanInitVol.setObjLabel('eman - initial vol')
protEmanInitVol.inputSet.set(protImport)
protEmanInitVol.inputSet.setExtended('outputAverages')
if testDataKey:
setProtocolParams(protEmanInitVol, testDataKey)
project.saveProtocol(protEmanInitVol)
# 2c. Significant
protSignificant = project.newProtocol(XmippProtReconstructSignificant)
protSignificant.setObjLabel('xmipp - significant')
protSignificant.inputSet.set(protImport)
protSignificant.inputSet.setExtended('outputAverages')
if testDataKey:
setProtocolParams(protSignificant, testDataKey)
project.saveProtocol(protSignificant)
# 3. Join result volumes
p1 = Pointer()
p1.set(protRansac)
p1.setExtended('outputVolumes')
p2 = Pointer()
p2.set(protEmanInitVol)
p2.setExtended('outputVolumes')
p3 = Pointer()
p3.set(protSignificant)
p3.setExtended('outputVolume')
protJoin = project.newProtocol(XmippProtAlignVolumeForWeb)
protJoin.setObjLabel('align volumes')
protJoin.inputVolumes.append(p1)
protJoin.inputVolumes.append(p2)
protJoin.inputVolumes.append(p3)
# protJoin.inputVolumes.append(p4)
project.saveProtocol(protJoin)
# protValidate = project.newProtocol(XmippProtValidateNonTilt)
# protValidate.setObjLabel('validate nontilt')
# protValidate.inputVolumes.set(protJoin)
# protValidate.inputVolumes.setExtended('outputVolumes')
# protValidate.inputParticles.set(protImport)
# protValidate.inputParticles.setExtended('outputAverages')
# protValidate.numberOfThreads.set(8)
# if testDataKey :
# setProtocolParams(protValidate, testDataKey)
# # protJoin.inputVolumes.append(p4)
# project.saveProtocol(protValidate)
return HttpResponse(mimetype='application/javascript')
def getInputMicrographsPointer(self):
ptr = Pointer()
ptr.set(self.getInputMicrographs())
return ptr
def create_service_project(request):
if request.is_ajax():
# Create a new project
projectName = getVarFromRequest(request, PROJECT_NAME)
# Filename to use as test data
testDataKey = request.GET.get('testData')
manager = getServiceManager(MYFIRSTMAP_SERVICE)
writeCustomMenu(manager.protocols)
project = manager.createProject(projectName, runsView=1,
hostsConf=manager.hosts,
protocolsConf=manager.protocols,
chdir=False)
project.getSettings().setLifeTime(336) # 14 days * 24 hours
project.saveSettings()
#copyFile(customMenu, project.getPath('.config', 'protocols.conf'))
# 1. Import averages
# If using test data execute the import averages run
# options are set in 'project_utils.js'
dsMDA = DataSet.getDataSet('initial_volume')
if testDataKey :
fn = dsMDA.getFile(testDataKey)
newFn = getImageFullPath(project.path, join(project.uploadPath, basename(fn)))
copyFile(fn, newFn)
label_import = 'import averages ('+ testDataKey +')'
protImport = project.newProtocol(ProtImportAverages, objLabel=label_import)
protImport.filesPath.set(newFn)
protImport.samplingRate.set(1.)
project.launchProtocol(protImport, wait=True, chdir=False)
else:
protImport = project.newProtocol(ProtImportAverages, objLabel='import averages')
project.saveProtocol(protImport)
# 2a. Ransac
protRansac = project.newProtocol(XmippProtRansac)
protRansac.setObjLabel('xmipp - ransac')
protRansac.inputSet.set(protImport)
protRansac.inputSet.setExtended('outputAverages')
setProtocolParams(protRansac, testDataKey)
project.saveProtocol(protRansac)
# 2b. Eman
protEmanInitVol = project.newProtocol(EmanProtInitModel)
protEmanInitVol.setObjLabel('eman - initial vol')
protEmanInitVol.inputSet.set(protImport)
protEmanInitVol.inputSet.setExtended('outputAverages')
setProtocolParams(protEmanInitVol, testDataKey)
project.saveProtocol(protEmanInitVol)
# 2c. Significant
protSignificant = project.newProtocol(XmippProtReconstructSignificant)
protSignificant.setObjLabel('xmipp - significant')
protSignificant.inputSet.set(protImport)
protSignificant.inputSet.setExtended('outputAverages')
setProtocolParams(protSignificant, testDataKey)
project.saveProtocol(protSignificant)
# 3. Join result volumes
p1 = Pointer()
p1.set(protRansac)
p1.setExtended('outputVolumes')
p2 = Pointer()
p2.set(protEmanInitVol)
p2.setExtended('outputVolumes')
p3 = Pointer()
p3.set(protSignificant)
p3.setExtended('outputVolume')
protJoin = project.newProtocol(XmippProtAlignVolumeForWeb)
protJoin.setObjLabel('align volumes')
protJoin.inputVolumes.append(p1)
protJoin.inputVolumes.append(p2)
protJoin.inputVolumes.append(p3)
project.saveProtocol(protJoin)
# protValidate = project.newProtocol(XmippProtValidateNonTilt)
# protValidate.setObjLabel('validate nontilt')
# protValidate.inputVolumes.set(protJoin)
# protValidate.inputVolumes.setExtended('outputVolumes')
# protValidate.inputParticles.set(protImport)
# protValidate.inputParticles.setExtended('outputAverages')
# protValidate.numberOfThreads.set(8)
# if testDataKey :
# setProtocolParams(protValidate, testDataKey)
# # protJoin.inputVolumes.append(p4)
# project.saveProtocol(protValidate)
return HttpResponse(content_type='application/javascript')
