def movies_content(request):
domain = django_settings.SITE_URL
projectName = request.GET.get('p', None)
path_files = django_settings.ABSOLUTE_URL + '/resources_movies/img/'
command = "rsync -av --port 3333 USER_FOLDER/ %s::mws/%s" % (domain,
projectName)
manager = getServiceManager('movies')
project = manager.loadProject(projectName,
protocolsConf=manager.protocols,
hostsConf=manager.hosts)
daysLeft = prettyDelta(project.getLeftTime())
context = contentContext(request, project)
context.update({
# MODE
'formUrl': 'mov_form',
'mode': 'service',
# IMAGES
'importMovies': path_files + 'importMovies.png',
'movieAlignment': path_files + 'movieAlignment.png',
'protMovieAlign': path_files + 'protMovieAlign.png',
'summary': path_files + 'summary.png',
'showj': path_files + 'showj.png',
'download': path_files + 'download.png',
'command': command,
'daysLeft': daysLeft,
})
return render_to_response('movies_content.html', context)
def resmap_content(request):
projectName = request.GET.get('p', None)
path_files = getAbsoluteURL('resources_myresmap/img/')
# Get info about when the project was created
manager = getServiceManager(MYRESMAP_SERVICE)
project = manager.loadProject(projectName,
protocolsConf=manager.protocols,
hostsConf=manager.hosts,
chdir=False)
daysLeft = prettyDelta(project.getLeftTime())
context = contentContext(request, project, serviceName=MYRESMAP_SERVICE)
context.update({
'importVolumes': path_files + 'importVolumes.png',
'useResMap': path_files + 'useResMap.png',
'protResMap': path_files + 'protResMap.png',
'analyzeResults': path_files + 'analyzeResults.png',
'formUrl': 'r_form',
'mode': MODE_SERVICE,
'daysLeft': daysLeft
})
return render_to_response('resmap_content.html', context)
def resmap_content(request):
projectName = request.GET.get('p', None)
path_files = django_settings.ABSOLUTE_URL + '/resources_myresmap/img/'
# Get info about when the project was created
manager = getServiceManager('myresmap')
project = manager.loadProject(projectName,
protocolsConf=manager.protocols,
hostsConf=manager.hosts)
project.getSettings().setLifeTime(336) # 14 days * 24 hours
project.saveSettings()
daysLeft = prettyDelta(project.getLeftTime())
context = contentContext(request, project)
context.update({'importVolumes': path_files + 'importVolumes.png',
'useResMap': path_files + 'useResMap.png',
'protResMap': path_files + 'protResMap.png',
'analyzeResults': path_files + 'analyzeResults.png',
'formUrl': 'r_form',
'mode':'service',
'daysLeft': daysLeft,
})
return render_to_response('resmap_content.html', context)
def movies_content(request):
projectName = request.GET.get('p', None)
path_files = django_settings.ABSOLUTE_URL + '/resources_movies/img/'
command = "rsync -av --port 3333 USER_FOLDER/ scipion.cnb.csic.es::mws/" + projectName
manager = getServiceManager('movies')
project = manager.loadProject(projectName,
protocolsConf=manager.protocols,
hostsConf=manager.hosts)
daysLeft = prettyDelta(project.getLeftTime())
context = contentContext(request, project)
context.update({
# MODE
'formUrl': 'mov_form',
'mode':'service',
# IMAGES
'importMovies': path_files + 'importMovies.png',
'movieAlignment': path_files + 'movieAlignment.png',
'protMovieAlign': path_files + 'protMovieAlign.png',
'summary': path_files + 'summary.png',
'showj': path_files + 'showj.png',
'download': path_files + 'download.png',
'command' : command,
'daysLeft': daysLeft,
})
return render_to_response('movies_content.html', context)
def resmap_content(request):
projectName = request.GET.get('p', None)
path_files = django_settings.ABSOLUTE_URL + '/resources_myresmap/img/'
# Get info about when the project was created
manager = getServiceManager('myresmap')
project = manager.loadProject(projectName,
protocolsConf=manager.protocols,
hostsConf=manager.hosts)
project.getSettings().setLifeTime(14)
project.saveSettings()
daysLeft = prettyDelta(project.getLeftTime())
context = contentContext(request, project)
context.update({'importVolumes': path_files + 'importVolumes.png',
'useResMap': path_files + 'useResMap.png',
'protResMap': path_files + 'protResMap.png',
'analyzeResults': path_files + 'analyzeResults.png',
'formUrl': 'r_form',
'mode':'service',
'daysLeft': daysLeft,
})
return render_to_response('resmap_content.html', context)
def service_content(request):
projectName = request.GET.get('p', None)
path_files = django_settings.ABSOLUTE_URL + '/resources_myfirstmap/img/'
# Get info about when the project was created
manager = getServiceManager('myfirstmap')
project = manager.loadProject(projectName,
protocolsConf=manager.protocols,
hostsConf=manager.hosts)
daysLeft = prettyDelta(project.getLeftTime())
context = contentContext(request, project)
context.update({'importAverages': path_files + 'importAverages.png',
'useProtocols': path_files + 'useProtocols.png',
'protForm': path_files + 'protForm.png',
'summary': path_files + 'summary.png',
'showj': path_files + 'showj.png',
'alignVol': path_files + 'alignVol.png',
'validateVols': path_files + 'validateVols.png',
'download': path_files + 'download.png',
'formUrl': 'my_form',
'mode':'service',
'daysLeft': daysLeft,
})
return render_to_response('service_content.html', context)
def service_content(request):
projectName = request.GET.get('p', None)
path_files = django_settings.ABSOLUTE_URL + '/resources_myfirstmap/img/'
# Get info about when the project was created
manager = getServiceManager('myfirstmap')
project = manager.loadProject(projectName,
protocolsConf=manager.protocols,
hostsConf=manager.hosts)
daysLeft = prettyDelta(project.getLeftTime())
context = contentContext(request, project)
context.update({
'importAverages': path_files + 'importAverages.png',
'useProtocols': path_files + 'useProtocols.png',
'protForm': path_files + 'protForm.png',
'summary': path_files + 'summary.png',
'showj': path_files + 'showj.png',
'alignVol': path_files + 'alignVol.png',
'download': path_files + 'download.png',
'formUrl': 'my_form',
'mode': 'service',
'daysLeft': daysLeft,
})
return render_to_response('service_content.html', context)
def movies_content(request):
projectName = request.GET.get('p', None)
path_files = getAbsoluteURL('resources_movies/img/')
command = getSyncCommand(request)
manager = getServiceManager(MOVIES_SERVICE)
project = manager.loadProject(projectName,
protocolsConf=manager.protocols,
hostsConf=manager.hosts,
chdir=False)
daysLeft = prettyDelta(project.getLeftTime())
context = contentContext(request, project, serviceName=MOVIES_SERVICE)
context.update({
# MODE
'formUrl': 'mov_form',
'mode': MODE_SERVICE,
# IMAGES
'importMovies': path_files + 'importMovies.png',
'movieAlignment': path_files + 'movieAlignment.png',
'protMovieAlign': path_files + 'protMovieAlign.png',
'summary': path_files + 'summary.png',
'showj': path_files + 'showj.png',
'download': path_files + 'download.png',
'command': command,
'daysLeft': daysLeft
})
return render_to_response('movies_content.html', context)
def service_content(request):
projectName = request.GET.get('p', None)
path_files = getAbsoluteURL('resources_myfirstmap/img/')
# Get info about when the project was created
manager = getServiceManager(MYFIRSTMAP_SERVICE)
project = manager.loadProject(projectName,
protocolsConf=manager.protocols,
hostsConf=manager.hosts,
chdir=False)
daysLeft = prettyDelta(project.getLeftTime())
context = contentContext(request, project, serviceName=MYFIRSTMAP_SERVICE)
context.update({'importAverages': path_files + 'importAverages.png',
'useProtocols': path_files + 'useProtocols.png',
'protForm': path_files + 'protForm.png',
'summary': path_files + 'summary.png',
'showj': path_files + 'showj.png',
'alignVol': path_files + 'alignVol.png',
'download': path_files + 'download.png',
'formUrl': 'my_form',
'mode': MODE_SERVICE,
'daysLeft': daysLeft
})
return render_to_response('service_content.html', context)
def create_resmap_project(request):
if request.is_ajax():
import os
from pyworkflow.em.protocol import ProtImportVolumes
from pyworkflow.em.packages.resmap.protocol_resmap import ProtResMap
# Create a new project
projectName = request.GET.get(PROJECT_NAME)
# Filename to use as test data
testDataKey = request.GET.get('testData')
manager = getServiceManager(MYRESMAP_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()
projectPath = manager.getProjectPath(projectName)
# 1. Import maps
if testDataKey:
attr = getAttrTestFile(testDataKey)
source = attr['file']
dest = os.path.join(projectPath, 'Uploads', basename(source))
pwutils.createLink(source, dest)
label_import = "import volumes (" + testDataKey + ")"
protImport = project.newProtocol(ProtImportVolumes,
objLabel=label_import)
protImport.filesPath.set(dest)
protImport.samplingRate.set(attr['samplingRate'])
project.launchProtocol(protImport, wait=True, chdir=False)
else:
protImport = project.newProtocol(ProtImportVolumes,
objLabel='import volumes')
project.saveProtocol(protImport)
# 2. ResMap
protResMap = project.newProtocol(ProtResMap)
protResMap.setObjLabel('resmap - local resolution')
protResMap.inputVolume.set(protImport)
protResMap.inputVolume.setExtended('outputVolume')
loadProtocolConf(protResMap)
project.saveProtocol(protResMap)
return HttpResponse(content_type='application/javascript')
def create_resmap_project(request):
if request.is_ajax():
import os
from pyworkflow.object import Pointer
from pyworkflow.em.protocol import ProtImportVolumes
from pyworkflow.em.packages.resmap.protocol_resmap import ProtResMap
# Create a new project
projectName = request.GET.get('projectName')
# Filename to use as test data
testDataKey = request.GET.get('testData')
manager = getServiceManager('myresmap')
writeCustomMenu(manager.protocols)
project = manager.createProject(projectName, runsView=1,
hostsConf=manager.hosts,
protocolsConf=manager.protocols
)
project.getSettings().setLifeTime(14)
project.saveSettings()
projectPath = manager.getProjectPath(projectName)
# 1. Import movies
if testDataKey :
attr = getAttrTestFile(testDataKey)
source = attr['path'] + attr['file']
dest = os.path.join(projectPath,'Uploads', attr['file'])
pwutils.createLink(source, dest)
label_import = "import volumes ("+ testDataKey +")"
protImport = project.newProtocol(ProtImportVolumes, objLabel=label_import)
protImport.filesPath.set(dest)
protImport.samplingRate.set(attr['samplingRate'])
project.launchProtocol(protImport, wait=True)
else:
protImport = project.newProtocol(ProtImportVolumes, objLabel='import volumes')
project.saveProtocol(protImport)
# 2. ResMap
protResMap = project.newProtocol(ProtResMap)
protResMap.setObjLabel('resmap - local resolution')
protResMap.inputVolume.set(protImport)
protResMap.inputVolume.setExtendedAttribute('outputVolume')
project.saveProtocol(protResMap)
return HttpResponse(mimetype='application/javascript')
def particleValidation_content(request):
projectName = request.GET.get('p', None)
path_files = getAbsoluteURL('resources_mypval/img/')
# Get info about when the project was created
manager = getServiceManager(MYPVAL_SERVICE)
project = manager.loadProject(projectName,
protocolsConf=manager.protocols,
hostsConf=manager.hosts,
chdir=False)
daysLeft = prettyDelta(project.getLeftTime())
context = contentContext(request, project, serviceName=MYPVAL_SERVICE)
# Resources for the help - guide, to be done.
context.update({
'formUrl': MYPVAL_FORM_URL,
'mode': MODE_SERVICE,
'daysLeft': daysLeft
})
return render_to_response('pval_content.html', context)
def create_movies_project(request):
if request.is_ajax():
import os
from pyworkflow.object import Pointer
from pyworkflow.em.protocol import ProtImportMovies
from pyworkflow.em.packages.xmipp3 import ProtMovieAlignment
# Create a new project
projectName = request.GET.get('projectName')
# Filename to use as test data
testDataKey = request.GET.get('testData')
manager = getServiceManager('movies')
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'))
# Create symbolic link for uploads
projectPath = manager.getProjectPath(projectName)
dest = os.path.join(projectPath,'Uploads')
# @todo: this path to uploads dir should be configurable outside the code...
source = "/services/scipion/data/uploads/"+ projectName
pwutils.path.makePath(source)
pwutils.createLink(source, dest)
# 1. Import movies
if testDataKey :
attr = getAttrTestFile(testDataKey)
path_test = attr['path']
for f in os.listdir(path_test):
# Create a symbolic link for each file
file_path = os.path.join(path_test, f)
source_file = os.path.join(source, f)
pwutils.createAbsLink(file_path, source_file)
label_import = "import movies ("+ testDataKey +")"
protImport = project.newProtocol(ProtImportMovies, objLabel=label_import)
protImport.filesPath.set(attr["filesPath"])
protImport.voltage.set(attr['voltage'])
protImport.sphericalAberration.set(attr['sphericalAberration'])
protImport.amplitudeContrast.set(attr['amplitudeContrast'])
protImport.magnification.set(attr['magnification'])
protImport.samplingRate.set(attr['samplingRate'])
project.launchProtocol(protImport, wait=True)
else:
protImport = project.newProtocol(ProtImportMovies, objLabel='import movies')
project.saveProtocol(protImport)
# 2. Movie Alignment
protMovAlign = project.newProtocol(ProtMovieAlignment)
protMovAlign.setObjLabel('xmipp - movie alignment')
protMovAlign.inputMovies.set(protImport)
protMovAlign.inputMovies.setExtended('outputMovies')
project.saveProtocol(protMovAlign)
return HttpResponse(mimetype='application/javascript')
def create_particleValidation_project(request):
if request.is_ajax():
from pyworkflow.em.protocol import ProtImportVolumes
from pyworkflow.em.protocol import ProtImportParticles
# Create a new project
projectName = request.GET.get(PROJECT_NAME)
# Filename to use as test data
testDataKey = request.GET.get('testData')
manager = getServiceManager(MYPVAL_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()
projectPath = manager.getProjectPath(projectName)
# If we need to import test data...
if testDataKey:
# Get test data attributes
attr = getAttrTestFile(testDataKey, projectPath)
# 1. Import volumes
source = attr['volume']
dest = os.path.join(projectPath, 'Uploads', basename(source))
pwutils.createLink(source, dest)
label_import = "import volumes (" + testDataKey + ")"
protImportVol = project.newProtocol(ProtImportVolumes,
objLabel=label_import)
protImportVol.filesPath.set(dest)
protImportVol.samplingRate.set(attr['samplingRate'])
project.launchProtocol(protImportVol, wait=True, chdir=False)
# 2. Import particles
binary = linkTestData(attr['particles'], projectPath)
metaFile = linkTestData(attr['metaFile'], projectPath)
label_import = "import particles (" + testDataKey + ")"
protImportParticles = project.newProtocol(ProtImportParticles,
objLabel=label_import)
protImportParticles.filesPath.set(binary)
# Set import particle attributes
protImportParticles.importFrom.set(attr["importFrom"])
# RELION Datasets
if attr["importFrom"] == ProtImportParticles.IMPORT_FROM_RELION:
protImportParticles.starFile.set(metaFile)
else:
protImportParticles.sqliteFile.set(metaFile)
protImportParticles.voltage.set(attr["microscopeVoltage"])
protImportParticles.sphericalAberration.set(
attr["sphericalAberration"])
protImportParticles.amplitudeContrast.set(
attr["amplitudeContrast"])
protImportParticles.magnification.set(attr["magnificationRate"])
protImportParticles.samplingRate.set(attr["particlesSamplingRate"])
project.launchProtocol(protImportParticles, wait=True, chdir=False)
inputVolumeProtocol = protImportVol
inputVolumeExtended = 'outputVolume'
inputParticlesProtocol = protImportParticles
inputParticlesExtended = 'outputParticles'
else:
# Empty import volumes protocol
protImportVol = project.newProtocol(ProtImportVolumes,
objLabel='import volume')
project.saveProtocol(protImportVol)
# Empty import particles protocol
protImportParticles = project.newProtocol(
ProtImportParticles, objLabel='import particles')
project.saveProtocol(protImportParticles)
inputVolumeProtocol = protImportVol
inputVolumeExtended = 'outputVolume'
inputParticlesProtocol = protImportParticles
inputParticlesExtended = 'outputParticles'
# 3a. Validate non tilt
protNonTilt = project.newProtocol(XmippProtValidateNonTilt)
protNonTilt.setObjLabel('alignment reliability (validate non tilt)')
# link Input volumes
protNonTilt.inputVolumes.set(inputVolumeProtocol)
protNonTilt.inputVolumes.setExtended(inputVolumeExtended)
# Input particles
protNonTilt.inputParticles.set(inputParticlesProtocol)
protNonTilt.inputParticles.setExtended(inputParticlesExtended)
# Attributes
if testDataKey:
protNonTilt.symmetryGroup.set(attr['symmetry'])
# Load additional configuration
loadProtocolConf(protNonTilt)
project.saveProtocol(protNonTilt)
# 3b. Validation overfitting
protValidation = project.newProtocol(XmippProtValidateOverfitting)
protValidation.setObjLabel('BSOFT/xmipp3 - validate overfitting')
# link Input volumes
protValidation.input3DReference.set(inputVolumeProtocol)
protValidation.input3DReference.setExtended(inputVolumeExtended)
# Input particles
protValidation.inputParticles.set(inputParticlesProtocol)
protValidation.inputParticles.setExtended(inputParticlesExtended)
# Attributes
if testDataKey:
protValidation.symmetryGroup.set(attr['symmetry'])
protValidation.numberOfParticles.set(attr['numberOfParticles'])
# Load additional configuration
loadProtocolConf(protValidation)
project.saveProtocol(protValidation)
return HttpResponse(content_type='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(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 create_movies_project(request):
if request.is_ajax():
import os
from pyworkflow.object import Pointer
from pyworkflow.em.protocol import ProtImportMovies
from pyworkflow.em.packages.xmipp3 import ProtMovieAlignment
# Create a new project
projectName = request.GET.get('projectName')
# Filename to use as test data
testDataKey = request.GET.get('testData')
manager = getServiceManager('movies')
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'))
# Create symbolic link for uploads
projectPath = manager.getProjectPath(projectName)
dest = os.path.join(projectPath, 'Uploads')
os.rmdir(dest) #in movies uploads is created as a link
# @todo: this path to uploads dir should be configurable outside the code...
source = "/services/scipion/data/uploads/" + projectName
pwutils.path.makePath(source)
pwutils.createLink(source, dest)
# 1. Import movies
if testDataKey:
attr = getAttrTestFile(testDataKey)
path_test = attr['path']
for f in os.listdir(path_test):
# Create a symbolic link for each file
file_path = os.path.join(path_test, f)
source_file = os.path.join(source, f)
pwutils.createAbsLink(file_path, source_file)
label_import = "import movies (" + testDataKey + ")"
protImport = project.newProtocol(ProtImportMovies,
objLabel=label_import)
protImport.filesPath.set(attr["filesPath"])
protImport.voltage.set(attr['voltage'])
protImport.sphericalAberration.set(attr['sphericalAberration'])
protImport.amplitudeContrast.set(attr['amplitudeContrast'])
protImport.magnification.set(attr['magnification'])
protImport.samplingRate.set(attr['samplingRate'])
project.launchProtocol(protImport, wait=True)
else:
protImport = project.newProtocol(ProtImportMovies,
objLabel='import movies')
project.saveProtocol(protImport)
# 2. Movie Alignment
protMovAlign = project.newProtocol(ProtMovieAlignment)
protMovAlign.setObjLabel('xmipp - movie alignment')
protMovAlign.inputMovies.set(protImport)
protMovAlign.inputMovies.setExtended('outputMovies')
project.saveProtocol(protMovAlign)
return HttpResponse(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')
