def getAttrTestFile(key):
if(key == "ribosome"):
riboDataset = DataSet.getDataSet('riboMovies')
riboFiles = riboDataset.getFile("allMovies")
attr = {#"filesPath" : "/services/scipion/data/scipionweb/movies_testdata/80S_ribosome/",
"path": riboDataset.getPath(),
"filesPath" : riboFiles,
"voltage" : 300.0,
"sphericalAberration" : 2.7,
"amplitudeContrast" : 0.1,
"magnification" : 59000,
"samplingRate": 1.77}
if(key == "falcon"):
jmbFalconDataset = DataSet.getDataSet('jmbFalconMovies')
jmbFalconFiles = jmbFalconDataset.getFile("allMovies")
attr = {#"path" : "/services/scipion/data/scipionweb/movies_testdata/JMB_2015/",
"path": jmbFalconDataset.getPath(),
"filesPath" : jmbFalconFiles,
"voltage" : 300.0,
"sphericalAberration" : 2.7,
"amplitudeContrast" : 0.1,
"magnification" : 59000,
"samplingRate": 1.34}
return attr
def getAttrTestFile(key):
if (key == "ribosome"):
riboDataset = DataSet.getDataSet('riboMovies')
riboFiles = riboDataset.getFile("allMovies")
attr = { #"filesPath" : "/services/scipion/data/scipionweb/movies_testdata/80S_ribosome/",
"path": riboDataset.getPath(),
"filesPath": riboFiles,
"voltage": 300.0,
"sphericalAberration": 2.7,
"amplitudeContrast": 0.1,
"magnification": 59000,
"samplingRate": 1.77
}
if (key == "falcon"):
jmbFalconDataset = DataSet.getDataSet('jmbFalconMovies')
jmbFalconFiles = jmbFalconDataset.getFile("allMovies")
attr = { #"path" : "/services/scipion/data/scipionweb/movies_testdata/JMB_2015/",
"path": jmbFalconDataset.getPath(),
"filesPath": jmbFalconFiles,
"voltage": 300.0,
"sphericalAberration": 2.7,
"amplitudeContrast": 0.1,
"magnification": 59000,
"samplingRate": 1.34
}
return attr
def getAttrTestFile(key):
if key == "ribosome":
riboDataset = DataSet.getDataSet('riboMovies')
riboFiles = riboDataset.getFile("allMovies")
attr = {
"path": riboDataset.getPath(),
"filesPath": riboFiles,
"voltage": 300.0,
"sphericalAberration": 2.7,
"amplitudeContrast": 0.1,
"magnification": 59000,
"samplingRate": 1.77
}
if key == "falcon":
jmbFalconDataset = DataSet.getDataSet('jmbFalconMovies')
jmbFalconFiles = jmbFalconDataset.getFile("allMovies")
attr = {
"path": jmbFalconDataset.getPath(),
"filesPath": jmbFalconFiles,
"voltage": 300.0,
"sphericalAberration": 2.7,
"amplitudeContrast": 0.1,
"magnification": 59000,
"samplingRate": 1.34
}
return attr
def getAttrTestFile(key):
resmap = DataSet.getDataSet('resmap')
if key == "fcv":
attr = {
"file": resmap.getFile("fcv"),
"samplingRate": 2.33,
}
if key == "mito_ribosome":
attr = {
"file": resmap.getFile("mito_ribo"),
"samplingRate": 1.34,
}
if key == "t20s_proteasome":
attr = {
"file": resmap.getFile("t20s"),
"samplingRate": 0.98,
}
return attr
def getAttrTestFile(key, projectPath):
pval = DataSet.getDataSet('particle_validation')
attr = None
if key == "betagal":
attr = {
"path": pval.getPath(),
"volume": pval.getFile("betagal_volume"),
"samplingRate": 3.98,
"particles": pval.getFile("betagal_particles"),
"metaFile": pval.getFile("betagal_meta"),
"microscopeVoltage": 300,
"sphericalAberration": 2,
"amplitudeContrast": 0.1,
"magnificationRate": 50000,
"particlesSamplingRate": 3.98,
"symmetry": 'd2',
"numberOfParticles": '10 20 50 100 200 500 1000 2000',
"importFrom": ProtImportParticles.IMPORT_FROM_RELION
}
linkTestData(pval.getFile('betagal_optimizer'), projectPath)
linkTestData(pval.getFile('betagal_half1'), projectPath)
linkTestData(pval.getFile('betagal_half2'), projectPath)
linkTestData(pval.getFile('betagal_sampling'), projectPath)
elif key == "10004":
attr = {
"path": pval.getPath(),
"volume": pval.getFile("10004_volume"),
"samplingRate": 4.32,
"particles": pval.getFile("10004_particles"),
"metaFile": pval.getFile("10004_meta"),
"microscopeVoltage": 80,
"sphericalAberration": 2,
"amplitudeContrast": 0.1,
"magnificationRate": 75000,
"particlesSamplingRate": 4.32,
"symmetry": 'c3',
"numberOfParticles": '10 20 50 100 200 500 1000 2000',
"importFrom": ProtImportParticles.IMPORT_FROM_RELION
}
linkTestData(pval.getFile('10004_optimizer'), projectPath)
linkTestData(pval.getFile('10004_half1'), projectPath)
linkTestData(pval.getFile('10004_half2'), projectPath)
linkTestData(pval.getFile('10004_sampling'), projectPath)
elif key == "10008":
attr = {
"path": pval.getPath(),
"volume": pval.getFile("10008_volume"),
"samplingRate": 3.00,
"particles": pval.getFile("10008_particles"),
"metaFile": pval.getFile("10008_meta"),
"microscopeVoltage": 200,
"sphericalAberration": 2,
"amplitudeContrast": 0.1,
"magnificationRate": 50000,
"particlesSamplingRate": 3.00,
"symmetry": 'c3',
"numberOfParticles": '10 20 50 100 200 500 1000 2000',
"importFrom": ProtImportParticles.IMPORT_FROM_SCIPION
}
return attr
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 get_testdata(request):
# Filename to use as test data
testDataKey = request.GET.get('testData')
dsMDA = DataSet.getDataSet('initial_volume')
fn = dsMDA.getFile(testDataKey)
return HttpResponse(fn, 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 get_testdata(request):
# Filename to use as test data
testDataKey = request.GET.get('testData')
dsMDA = DataSet.getDataSet('initial_volume')
fn = dsMDA.getFile(testDataKey)
return HttpResponse(fn, mimetype='application/javascript')
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')
