def config(self, cfgdata=None):
if cfgdata is None:
self.LogError('Please provide configuration file!')
Daisy.CfgParser(self, cfgdata, self.cfg)
self.foname = self.cfg['outputfile_name']
self.dspath = self.cfg['hdf5dataset_path']
return True
def initialize(self, default_init=None):
super().createSvc("PyDataStoreSvc/DataStore")
self.snoopy = self.Snoopy()
self.snoopy.config()
self.snoopy.initialize()
self.datastore = self.find("DataMemSvc").find('DataStore').data()
if default_init is not None:
self.LogDebug(
str(type(default_init)) + ' value ' + str(default_init))
init_cfg = Daisy.CfgParser(self, default_init)
for key in init_cfg.keys():
alg_name = key
alg_class = init_cfg[key]['class_name']
alg = self.createAlg(alg_class + '/' + alg_name)
try:
algParas = init_cfg[key]['init_paras']
self.LogDebug('name: ' + str(alg_name) + ' class: ' +
str(alg_class) + " parameters: " +
str(algParas) + ' type of ' +
str(type(algParas)))
self[alg_name].initialize(default_init=algParas)
except KeyError as error:
self.LogDebug(error)
self[alg_name].initialize()
def config(self, cfgdata=None):
if cfgdata is None:
self.LogError('Please provide configuration file!')
Daisy.CfgParser(self, cfgdata, self.cfg)
self.ai.setFit2D(directDist=self.cfg['directDist'], centerX=self.cfg['centerX'], \
centerY=self.cfg['centerY'], tilt=self.cfg['tilt'], \
tiltPlanRotation=self.cfg['PlanRotation'], pixelX=self.cfg['pixelX'],\
pixelY=self.cfg['pixelY'], splineFile=None)
return True
def config(self, cfgdata=None):
if cfgdata is None:
self.LogError('Please provide configuration file!')
Daisy.CfgParser(self, cfgdata, self.cfg)
self.ipath = self.cfg['input_path']
if os.path.isdir(self.ipath):
self.LogInfo("initialized, read TIF Files in Path: " + self.ipath)
return True
else:
self.LogError('initiallized, Path ' + self.ipath +
' does not exist')
return False
def initialize(self, default_init=None):
#self.addSvc(datasvc)
#self.createSvc("PyDataStoreSvc/Operators")
self.snoopy = self.Snoopy()
self.snoopy.config()
self.snoopy.initialize()
#p=PyMQDataStore.PyMQDataStore('DataStore')
#self.operators['DataStore'] = p
#self.datastore = p.data()
self.operators['DataStore'] = Daisy.Base.PyMQDataStore.PyMQDataStore('DataStore')
self.datastore = self.operators['DataStore'].data()
if default_init is not None:
init_cfg = Daisy.CfgParser(self, default_init)
for key in init_cfg.keys():
alg_name = key
alg_class = init_cfg[key]['class_name']
alg = self.createAlg(alg_class+'/'+alg_name)
self[alg_name].initialize(default_init=init_cfg[key]['init_paras'])
def initialize(self,
workflow_engine=None,
default_init=None,
workflow_environment={},
algorithms_cfg={}):
#print(self.objName()+' workflow_environment type of '+str(type(workflow_environment))+" value: "+str(workflow_environment))
#print(self.objName()+' default_init type of '+str(type(default_init))+" value: "+str(default_init))
if default_init is not None:
if workflow_engine is None:
if 'workflow_engine' in default_init:
workflow_engine = default_init['workflow_engine']
else:
self.LogError('Please enter Workflow Engine name!')
if 'workflow_environment' in default_init:
workflow_environment = default_init['workflow_environment']
elif workflow_engine is None:
self.LogError('Please enter Workflow Engin name!')
self.engine = Daisy.CreateWorkflowEngine(class_name=workflow_engine,
name=self.objName())
self.engine.initialize(default_init=workflow_environment)
self.engine.config(default_cfg=algorithms_cfg)
def config(self, cfgdata=None):
if cfgdata is None:
self.LogError('Please provide configuration file!')
Daisy.CfgParser(self, cfgdata, self.cfg)
self.finame = self.cfg['inputfile_name']
#with h5py.File(self.finame, 'r') as handle:
# print(handle)
# self.hdf5 = handle
# self.LogInfo("initialized, read HDF5 File: "+self.finame)
#return True
#if default_init is not None:
# if inputfile_name is None:
# if 'inputfile_name' in default_init:
# inputfile_name = default_init['inputfile_name']
# else:
# self.LogError('Please enter Input File name!')
#elif inputfile_name is None:
# self.LogError('Please enter Input File name!')
#self.finame = inputfile_name
self.hdf5 = h5py.File(self.finame, 'r')
self.LogInfo("initialized, read HDF5 File: "+self.finame)
return True
def config(self, cfgdata=None):
if cfgdata is None:
self.LogError('Please provide configuration file!')
Daisy.CfgParser(self, cfgdata, self.cfg)
self.cmd = self.cfg['shell_command']
try:
if self.cfg['shell'].upper() == 'TRUE':
self.shell = True
except:
pass
ret = self.__shell.run(['which', self.cmd],
stdout=subprocess.PIPE,
stderr=subprocess.PIPE)
if ret.returncode == 0:
self.LogInfo("Find " + self.cmd + ' at ' +
ret.stdout.decode()[:-1])
return True
else:
self.LogError("Can not find " + self.cmd + ' error message: ' +
ret.stderr.decode()[:-1])
return False
#!/usr/bin/env python
# -*- coding:utf-8 -*-
# author: tianhl
# using the new Workflow Engine for data analysis.
import Daisy
init_dict = {
'ls' :{'class_name':'PyAlgorithms.AlgCommandline' },\
'pwd':{'class_name':'PyAlgorithms.AlgCommandline' },\
}
cfg_dict = {
'ls':{'shell_command':'ls' },\
'pwd':{'shell_command':'pwd' },\
}
if __name__ == "__main__":
wf = Daisy.CreateWorkflowEngine(class_name='PyWorkflowEngine',
name='workflow')
wf.initialize(default_init=init_dict)
wf.config(default_cfg=cfg_dict)
wf.setLogLevel(3)
wf['pwd'].execute()
wf['ls'].execute(parameters=['-al'])
wf.finalize()
def config(self, default_cfg=None):
if default_cfg is not None:
cfg = Daisy.CfgParser(self, default_cfg)
for key in cfg.keys():
self.LogTest(key + ' configure with dict ' + str(cfg[key]))
self[key].config(cfg[key])