def fromXML(self, xmlObj):
"""
fromXML : Assigns values to result attributes from XML object
@param xmlObj: A xml object
@author: chen
"""
from lxml.etree import _Element
if xmlObj.__class__ != _Element:
from pytom.basic.exceptions import ParameterError
raise ParameterError(
'Is not a lxml.etree._Element! You must provide a valid XML-PeakResultMsg object.'
)
from pytom.localization.peak_job import PeakResult
if xmlObj.tag == "PeakResultMsg":
main = xmlObj
else:
main = xmlObj.xpath('PeakResultMsg')
if len(main) == 0:
from pytom.parallel.messages import MessageError
raise MessageError("This message is not a PeakResultMsg")
main = main[0]
message = main.xpath('Message')
message = message[0]
self._sender = message.get('Sender')
self._recipient = message.get('Recipient')
self._timestamp = message.get('Timestamp')
res = main.xpath('Result')[0]
self.result = PeakResult()
self.result.fromXML(res)
def PeakResultMsg_Test(self):
from pytom.localization.peak_job_msg import PeakResultMsg
from pytom.localization.peak_job import PeakResult
from pytom.localization.structures import Volume, Orientation
v = Volume(self.testfilename)
o = Orientation(self.testfilename)
r = PeakResult(v, o)
a = PeakResultMsg(str(1), str(0))
a.setResult(r)
xmlObj = a.toXML()
b = PeakResultMsg()
b.fromXML(xmlObj)
self.assertTrue(b.getSender() == a.getSender(), msg='')
self.assertTrue(b.getRecipient() == a.getRecipient(), msg='')
def PeakResult_Test(self):
from pytom.localization.peak_job import PeakResult
from pytom.localization.structures import Volume, Orientation
v = Volume(self.testfilename)
o = Orientation(self.testfilename)
a = PeakResult(v, o, 2)
xmlObj = a.toXML()
b = PeakResult()
b.fromXML(xmlObj)
self.assertTrue(b.jobID == a.jobID, msg='')
self.assertTrue(b.result.getFilename() == a.result.getFilename(),
msg='')
self.assertTrue(b.orient.getFilename() == a.orient.getFilename(),
msg='')
def writeRes(self, resV, orientV, jobID=None):
"""
writeRes: Write the result back to the disk, and return the PeakJobResult.
@param resV: result volume
@type resV: L{pytom_volume.vol}
@param orientV: orientation volume
@type orientV: L{pytom_volume.vol}
@param jobID: ID of job
@type jobID: integer
@rtype: L{pytom.localization.peak_job.PeakResult}
"""
from pytom.tompy.io import read, write
if jobID != None:
resFilename = self.dstDir + self.name + '_job' + str(
jobID) + '_res.em'
orientFilename = self.dstDir + self.name + '_job' + str(
jobID) + '_orient.em'
else:
resFilename = self.dstDir + self.name + '_res.em'
orientFilename = self.dstDir + self.name + '_orient.em'
try:
resV.write(resFilename)
orientV.write(orientFilename)
except:
print(resFilename, orientFilename)
write(resFilename, resV)
write(orientFilename, orientV)
from pytom.localization.structures import Volume, Orientation
res = Volume(resFilename)
orient = Orientation(orientFilename)
# construct the result
from pytom.localization.peak_job import PeakResult
result = PeakResult(res, orient, jobID)
return result
def parallelRun(self, verbose=True, **kwargs):
'''
parallelRun: Run the worker in parallel status and send the result message back
@param verbose: verbose mode
@type verbose: boolean
'''
from pytom.parallel.messages import StatusMessage, MessageError
from pytom.basic.exceptions import ParameterError
from pytom.basic.structures import PyTomClassError
end = False
while not end:
# get the message string
mpi_msgString = getMsgStr()
try:
msg = self.getJobMsg(mpi_msgString)
self.jobFromMsg(msg)
if verbose == True:
print(self.name + ': running...')
[resV, orientV, sumV, sqrV] = self.run(verbose, moreInfo=True)
# write the result volume back to the disk
resFilename = self.name + '_job' + str(self.jobID) + '_res.em'
orientFilename = self.name + '_job' + str(
self.jobID) + '_orient.em'
resV.write(resFilename)
orientV.write(orientFilename)
if sumV and sqrV:
sumFilename = self.name + '_job' + str(
self.jobID) + '_sum.em'
sqrFilename = self.name + '_job' + str(
self.jobID) + '_sqr.em'
sumV.write(sumFilename)
sqrV.write(sqrFilename)
from pytom.localization.structures import Volume, Orientation
res = Volume(resFilename, self.volume.subregion)
orient = Orientation(orientFilename)
# construct the result
from pytom.localization.peak_job import PeakResult
result = PeakResult(res, orient, self.jobID)
# sent the result back
if verbose == True:
print(self.name + ': sending back result')
result.send(self.mpi_id, self.backTo)
except (MessageError, PyTomClassError, ParameterError):
try:
# get the message as StatusMessage and finish
msg = StatusMessage('', '')
msg.fromStr(mpi_msgString)
if msg.getStatus() == 'End':
end = True
if verbose == True:
print(self.name + ': ending...')
except (MessageError, PyTomClassError, ParameterError):
print(
'Error parsing message. Message either unknown or invalid.'
)
assert False
class PeakResultMsg(Message):
result = -1
def setResult(self, result):
"""
@param result: result
@type result: L{pytom.localization.peak_job.PeakResult}
"""
self.result = result
def getResult(self):
return self.result
def fromXML(self, xmlObj):
"""
fromXML : Assigns values to result attributes from XML object
@param xmlObj: A xml object
@author: chen
"""
from lxml.etree import _Element
if xmlObj.__class__ != _Element:
from pytom.basic.exceptions import ParameterError
raise ParameterError(
'Is not a lxml.etree._Element! You must provide a valid XML-PeakResultMsg object.'
)
from pytom.localization.peak_job import PeakResult
if xmlObj.tag == "PeakResultMsg":
main = xmlObj
else:
main = xmlObj.xpath('PeakResultMsg')
if len(main) == 0:
from pytom.parallel.messages import MessageError
raise MessageError("This message is not a PeakResultMsg")
main = main[0]
message = main.xpath('Message')
message = message[0]
self._sender = message.get('Sender')
self._recipient = message.get('Recipient')
self._timestamp = message.get('Timestamp')
res = main.xpath('Result')[0]
self.result = PeakResult()
self.result.fromXML(res)
def toXML(self):
from lxml import etree
resMsg = etree.Element("PeakResultMsg")
messageElement = etree.Element("Message",
Sender=self._sender,
Recipient=self._recipient,
Timestamp=self._timestamp.__str__())
resMsg.append(messageElement)
resultElement = self.result.toXML()
resMsg.append(resultElement)
return resMsg