def _defineParams(self, form):
#ProtMonitor._defineParams(self, form)
form.addSection(label='Input')
form.addParam('inputProtocol', params.PointerParam,
label="Input protocols", important=True,
pointerClass='ProtCTFFind, XmippProtCTFMicrographs',
help="this protocol will be monitorized")
form.addParam('samplingInterval', params.IntParam,default=60,
label="Sampling Interval (sec)",
pointerClass='EMProtocol',
help="Take one sample each SamplinInteval seconds")
form.addParam('maxDefocus', params.FloatParam,default=40000,
label="Raise Alarm if maximum defocus (A) >",
help="Raise alarm if defocus is greater than given value")
form.addParam('minDefocus', params.FloatParam,default=1000,
label="Raise Alarm if minimum defocus (A) <",
help="Raise alarm if defocus is smaller than given value")
form.addParam('astigmatism', params.FloatParam,default=2000,
label="Raise Alarm if astigmatism (A) >",
help="Raise alarm if astigmatism is greater than given value")
form.addParam('monitorTime', params.FloatParam, default=300,
label="Total Logging time (min)",
help="Log during this interval")
ProtMonitor._sendMailParams(self, form)
def _defineParams(self, form):
ProtMonitor._defineParams(self, form)
form.addParam('transferMethod',
params.EnumParam,
default=0,
choices=['scp', 'bbcp'],
label='Transfer method')
form.addParam('compress',
params.BooleanParam,
default=True,
label='Compress before transfer?')
form.addParam('destinationHost',
params.StringParam,
default=None,
label='Destination host')
form.addParam('destinationDirectory',
params.StringParam,
default=None,
label='Destination directory')
form.addParam('destinationUser',
params.StringParam,
default=None,
label='Destination user name')
def _defineParams(self, form):
# ProtMonitor._defineParams(self, form)
form.addSection(label='Input')
form.addParam('inputProtocol', params.PointerParam,
label="Input protocol", important=True,
pointerClass='XmippProtMovieGain',
help="This protocol will be monitorized")
form.addParam('stddevValue', params.FloatParam, default=0.04,
label="Raise Alarm if residual gain standard "
"deviation >",
help="Raise alarm if residual gain standard deviation "
"is greater than given value")
form.addParam('ratio1Value', params.FloatParam, default=1.15,
label="Raise Alarm if the ratio between the 97.5 and "
"2.5 percentiles >",
help="Raise alarm if the ratio between the 97.5 and "
"2.5 percentiles is greater than given value")
form.addParam('ratio2Value', params.FloatParam, default=4.5,
label="Raise Alarm if the ratio between the maximum "
"gain value and the 97.5 percentile >",
help="Raise alarm if the ratio between the maximum "
"gain value and the 97.5 percentile is greater "
"than given value")
form.addParam('monitorTime', params.FloatParam, default=300,
label="Total Logging time (min)",
help="Log during this interval")
form.addParam('samplingInterval', params.IntParam, default=60,
label="Sampling Interval (sec)",
pointerClass='EMProtocol',
help="Take one sample each SamplinInteval seconds")
ProtMonitor._sendMailParams(self, form)
def _defineParams(self, form):
ProtMonitor._defineParams(self, form)
form.addParam('cpuAlert', params.FloatParam, default=101,
label="Raise Alarm if CPU > XX%",
help="Raise alarm if memory allocated is greater "
"than given percentage")
form.addParam('memAlert', params.FloatParam, default=101,
label="Raise Alarm if Memory > XX%",
help="Raise alarm if cpu allocated is greater "
"than given percentage")
form.addParam('swapAlert', params.FloatParam, default=101,
label="Raise Alarm if Swap > XX%",
help="Raise alarm if swap allocated is greater "
"than given percentage")
form.addParam('monitorTime', params.FloatParam, default=300,
label="Total Logging time (min)",
help="Log during this interval")
ProtMonitor._sendMailParams(self, form)
group = form.addGroup('GPU')
group.addParam('doGpu', params.BooleanParam, default=False,
label="Check GPU",
help="Set to true if you want to monitor the GPU")
group.addParam('gpusToUse', params.StringParam, default='0',
label='Which GPUs to use:', condition='doGpu',
help='Providing a list of which GPUs '
'(0,1,2,3, etc). Default is monitor GPU 0 only')
group = form.addGroup('GPU')
group.addParam('doGpu', params.BooleanParam, default=False,
label="Check GPU",
help="Set to true if you want to monitor the GPU")
group.addParam('gpusToUse', params.StringParam, default='0',
label='Which GPUs to use:', condition='doGpu',
help='Providing a list of which GPUs '
'(0,1,2,3, etc). Default is monitor GPU 0 only')
group = form.addGroup('NETWORK')
group.addParam('doNetwork', params.BooleanParam, default=False,
label="Check Network",
help="Set to true if you want to monitor the Network")
group.addParam('netInterfaces', params.EnumParam,
choices=self.nifsNameList,
default=1, # usually 0 is the loopback
label="Interface", condition='doNetwork',
help="Name of the network interface to be checked")
group = form.addGroup('Disk')
group.addParam('doDiskIO', params.BooleanParam, default=False,
label="Check Disk IO",
help="Set to true if you want to monitor the Disk "
"Access")
def _defineParams(self, form):
# ProtMonitor._defineParams(self, form)
form.addSection(label='Input')
form.addParam('inputProtocol',
params.PointerParam,
label="Input protocol",
important=True,
pointerClass='XmippProtMovieGain',
help="This protocol will be monitorized")
form.addParam('stddevValue',
params.FloatParam,
default=0.04,
label="Raise Alarm if residual gain standard "
"deviation >",
help="Raise alarm if residual gain standard deviation "
"is greater than given value")
form.addParam('ratio1Value',
params.FloatParam,
default=1.15,
label="Raise Alarm if the ratio between the 97.5 and "
"2.5 percentiles >",
help="Raise alarm if the ratio between the 97.5 and "
"2.5 percentiles is greater than given value")
form.addParam('ratio2Value',
params.FloatParam,
default=4.5,
label="Raise Alarm if the ratio between the maximum "
"gain value and the 97.5 percentile >",
help="Raise alarm if the ratio between the maximum "
"gain value and the 97.5 percentile is greater "
"than given value")
form.addParam('monitorTime',
params.FloatParam,
default=300,
label="Total Logging time (min)",
help="Log during this interval")
form.addParam('samplingInterval',
params.IntParam,
default=60,
label="Sampling Interval (sec)",
pointerClass='EMProtocol',
help="Take one sample each SamplinInteval seconds")
ProtMonitor._sendMailParams(self, form)
def _defineParams(self, form):
#ProtMonitor._defineParams(self, form)
form.addSection(label='Input')
form.addParam('inputProtocol',
params.PointerParam,
label="Input protocols",
important=True,
pointerClass='ProtCTFFind, XmippProtCTFMicrographs',
help="this protocol will be monitorized")
form.addParam('samplingInterval',
params.IntParam,
default=60,
label="Sampling Interval (sec)",
pointerClass='EMProtocol',
help="Take one sample each SamplinInteval seconds")
form.addParam(
'maxDefocus',
params.FloatParam,
default=40000,
label="Raise Alarm if maximum defocus (A) >",
help="Raise alarm if defocus is greater than given value")
form.addParam(
'minDefocus',
params.FloatParam,
default=1000,
label="Raise Alarm if minimum defocus (A) <",
help="Raise alarm if defocus is smaller than given value")
form.addParam(
'astigmatism',
params.FloatParam,
default=2000,
label="Raise Alarm if astigmatism (A) >",
help="Raise alarm if astigmatism is greater than given value")
form.addParam('monitorTime',
params.FloatParam,
default=300,
label="Total Logging time (min)",
help="Log during this interval")
ProtMonitor._sendMailParams(self, form)
def _defineParams(self, form):
ProtMonitor._defineParams(self, form)
form.addParam('cpuAlert', params.FloatParam,default=101,
label="Raise Alarm if CPU > XX%",
help="Raise alarm if memory allocated is greater "
"than given percentage")
form.addParam('memAlert', params.FloatParam,default=101,
label="Raise Alarm if Memory > XX%",
help="Raise alarm if cpu allocated is greater "
"than given percentage")
form.addParam('swapAlert', params.FloatParam,default=101,
label="Raise Alarm if Swap > XX%",
help="Raise alarm if swap allocated is greater "
"than given percentage")
form.addParam('monitorTime', params.FloatParam,default=300,
label="Total Logging time (min)",
help="Log during this interval")
ProtMonitor._sendMailParams(self, form)
def __init__(self, **kwargs):
ProtMonitor.__init__(self, **kwargs)
self._runIds = pwobj.CsvList(pType=int)
def _defineParams(self, form):
ProtMonitor._defineParams(self, form)
form.addSection('MovieGain Monitor')
form.addParam('stddevValue', params.FloatParam, default=0.04,
label="Raise Alarm if residual gain standard "
"deviation >",
help="Raise alarm if residual gain standard deviation "
"is greater than given value")
form.addParam('ratio1Value', params.FloatParam, default=1.15,
label="Raise Alarm if the ratio between the 97.5 "
"and 2.5 percentiles >",
help="Raise alarm if the ratio between the 97.5 "
"and 2.5 percentiles is greater than given value")
form.addParam('ratio2Value', params.FloatParam, default=4.5,
label="Raise Alarm if the ratio between the maximum "
"gain value and the 97.5 percentile >",
help="Raise alarm if the ratio between the maximum "
"gain value and the 97.5 percentile is greater "
"than given value")
form.addSection('CTF Monitor')
form.addParam('maxDefocus', params.FloatParam, default=40000,
label="Raise Alarm if maximum defocus (A) >",
help="Raise alarm if defocus is greater than given "
"value")
form.addParam('minDefocus', params.FloatParam, default=1000,
label="Raise Alarm if minimum defocus (A) <",
help="Raise alarm if defocus is smaller than given "
"value")
form.addParam('astigmatism', params.FloatParam, default=1000,
label="Raise Alarm if astigmatism >",
help="Raise alarm if astigmatism (defocusU-defocusV)is greater than given "
"value")
form.addParam('monitorTime', params.FloatParam, default=30000,
label="Total Logging time (min)",
help="Log during this interval")
form.addSection('System Monitor')
form.addParam('cpuAlert', params.FloatParam, default=101,
label="Raise Alarm if CPU > XX%",
help="Raise alarm if memory allocated is greater "
"than given percentage")
form.addParam('memAlert', params.FloatParam, default=101,
label="Raise Alarm if Memory > XX%",
help="Raise alarm if cpu allocated is greater "
"than given percentage")
form.addParam('swapAlert', params.FloatParam, default=101,
label="Raise Alarm if Swap > XX%",
help="Raise alarm if swap allocated is greater "
"than given percentage")
group = form.addGroup('GPU')
group.addParam('doGpu', params.BooleanParam, default=False,
label="Check GPU",
help="Set to true if you want to monitor the GPU")
group.addParam('gpusToUse', params.StringParam, default='0',
label='Which GPUs to use:', condition='doGpu',
help='Provide a list of GPUs '
'(e.g. "0 1 2 3"). Default is to monitor GPU 0 only')
group = form.addGroup('NETWORK')
group.addParam('doNetwork', params.BooleanParam, default=False,
label="Check Network",
help="Set to true if you want to monitor the Network")
group.addParam('netInterfaces', params.EnumParam,
choices=self.nifsNameList,
default=1, # usually 0 is the loopback
label="Interface", condition='doNetwork',
help="Name of the network interface to be checked")
group = form.addGroup('Disk')
group.addParam('doDiskIO', params.BooleanParam, default=False,
label="Check Disk IO",
help="Set to true if you want to monitor the Disk "
"Acces")
form.addSection('Mail settings')
ProtMonitor._sendMailParams(self, form)
form.addSection('HTML Report')
form.addParam('publishCmd', params.StringParam, default='',
label="Publish command",
help="Specify a command to publish the template. "
"You can use the special token %(REPORT_FOLDER)s "
"that will be replaced with the report folder. "
"For example: \n"
"rsync -avL %(REPORT_FOLDER)s "
"scipion@webserver:public_html/")
def __init__(self, **kwargs):
ProtMonitor.__init__(self, **kwargs)
self.reportDir = ''
self.reportPath = ''
def _defineParams(self, form):
ProtMonitor._defineParams(self, form)
form.addParam('cpuAlert',
params.FloatParam,
default=101,
label="Raise Alarm if CPU > XX%",
help="Raise alarm if memory allocated is greater "
"than given percentage")
form.addParam('memAlert',
params.FloatParam,
default=101,
label="Raise Alarm if Memory > XX%",
help="Raise alarm if cpu allocated is greater "
"than given percentage")
form.addParam('swapAlert',
params.FloatParam,
default=101,
label="Raise Alarm if Swap > XX%",
help="Raise alarm if swap allocated is greater "
"than given percentage")
form.addParam('monitorTime',
params.FloatParam,
default=300,
label="Total Logging time (min)",
help="Log during this interval")
ProtMonitor._sendMailParams(self, form)
group = form.addGroup('GPU')
group.addParam('doGpu',
params.BooleanParam,
default=False,
label="Check GPU",
help="Set to true if you want to monitor the GPU")
group.addParam('gpusToUse',
params.StringParam,
default='0',
label='Which GPUs to use:',
condition='doGpu',
help='Providing a list of which GPUs '
'(0,1,2,3, etc). Default is monitor GPU 0 only')
group = form.addGroup('GPU')
group.addParam('doGpu',
params.BooleanParam,
default=False,
label="Check GPU",
help="Set to true if you want to monitor the GPU")
group.addParam('gpusToUse',
params.StringParam,
default='0',
label='Which GPUs to use:',
condition='doGpu',
help='Providing a list of which GPUs '
'(0,1,2,3, etc). Default is monitor GPU 0 only')
group = form.addGroup('NETWORK')
group.addParam('doNetwork',
params.BooleanParam,
default=False,
label="Check Network",
help="Set to true if you want to monitor the Network")
group.addParam(
'netInterfaces',
params.EnumParam,
choices=self.nifsNameList,
default=1, # usually 0 is the loopback
label="Interface",
condition='doNetwork',
help="Name of the network interface to be checked")
group = form.addGroup('Disk')
group.addParam('doDiskIO',
params.BooleanParam,
default=False,
label="Check Disk IO",
help="Set to true if you want to monitor the Disk "
"Access")
def __init__(self, **kwargs):
ProtMonitor.__init__(self, **kwargs)
self.dataBase = 'log.sqlite'
self.tableName = 'log'
def __init__(self, **kwargs):
ProtMonitor.__init__(self, **kwargs)
self.dataBase = 'log.sqlite'
self.tableName = 'log'
def _defineParams(self, form):
ProtMonitor._defineParams(self, form)
form.addSection('CTF Monitor')
form.addParam(
'maxDefocus',
params.FloatParam,
default=40000,
label="Raise Alarm if maximum defocus (A) >",
help="Raise alarm if defocus is greater than given value")
form.addParam(
'minDefocus',
params.FloatParam,
default=1000,
label="Raise Alarm if minimum defocus (A) <",
help="Raise alarm if defocus is smaller than given value")
form.addParam(
'astigmatism',
params.FloatParam,
default=0.2,
label="Raise Alarm if astigmatism >",
help="Raise alarm if astigmatism is greater than given value")
form.addParam('monitorTime',
params.FloatParam,
default=30000,
label="Total Logging time (min)",
help="Log during this interval")
form.addSection('System Monitor')
form.addParam('cpuAlert',
params.FloatParam,
default=101,
label="Raise Alarm if CPU > XX%",
help="Raise alarm if memory allocated is greater "
"than given percentage")
form.addParam('memAlert',
params.FloatParam,
default=101,
label="Raise Alarm if Memory > XX%",
help="Raise alarm if cpu allocated is greater "
"than given percentage")
form.addParam('swapAlert',
params.FloatParam,
default=101,
label="Raise Alarm if Swap > XX%",
help="Raise alarm if swap allocated is greater "
"than given percentage")
form.addSection('Mail settings')
ProtMonitor._sendMailParams(self, form)
form.addSection('HTML Report')
form.addParam(
'publishCmd',
params.StringParam,
default='',
label="Publish command",
help="Specify a command to publish the template. "
"You can use the special token %(REPORT_FOLDER)s "
"that will be replaced with the report folder. "
"For example: \n"
"rsync -av %(REPORT_FOLDER)s scipion@webserver:public_html/")
def __init__(self, **kwargs):
ProtMonitor.__init__(self, **kwargs)
self._runIds = pwobj.CsvList(pType=int)
def _defineParams(self, form):
ProtMonitor._defineParams(self, form)
