def parse(self):
"""
parse options from command line
"""
parser = optparse.OptionParser()
parser.add_option("-V", "--version", dest="version", action="store_true",
help="print version of the program and quit", metavar="FILE", default=False)
parser.add_option("-v", "--verbose",
action="store_true", dest="debug", default=False,
help="switch to debug/verbose mode")
parser.add_option("-m", "--mask", dest="mask",
help="file containing the mask (for image reconstruction)", default=None)
parser.add_option("-M", "--mode", dest="mode",
help="Mode can be online/offline/all", default="offline")
parser.add_option("-o", "--out", dest="output",
help="file for log", default=None)
parser.add_option("-w", "--wavelength", dest="wavelength", type="float",
help="wavelength of the X-Ray beam in Angstrom", default=None)
parser.add_option("-e", "--energy", dest="energy", type="float",
help="energy of the X-Ray beam in keV (hc=%skeV.A)" % self.hc, default=None)
parser.add_option("-t", "--template", dest="template", type="str",
help="template XML file", default=None)
parser.add_option("-n", "--nbcpu", dest="nbcpu", type="int",
help="template XML file", default=self.nbcpu)
(options, args) = parser.parse_args()
# Analyse aruments and options
if options.version:
print("BioSaxs Azimuthal integration version %s" % __version__)
sys.exit(0)
if options.debug:
EDVerbose.setVerboseDebugOn()
self.debug = True
if options.output:
EDVerbose.setLogFileName(options.output)
if options.mask and os.path.isfile(options.mask):
self.maskfile = options.mask
if options.template and os.path.isfile(options.template):
self.xml = open(options.template).read()
if options.wavelength:
self.wavelength = 1e-10 * options.wavelength
elif options.energy:
self.wavelength = 1e-10 * self.hc / options.energy
if options.mode=="offline":
self.mode = "offline"
self.newerOnly = False
elif options.mode=="online":
self.mode = "dirwarch"
self.newerOnly = True
elif options.mode=="dirwatch":
self.mode = "dirwarch"
self.newerOnly = False
self.cpu_sem = Semaphore(options.nbcpu)
self.nbcpu = options.nbcpu
self.dataFiles = [f for f in args if os.path.isfile(f)]
if not self.dataFiles:
raise RuntimeError("Please provide datafiles or read the --help")
def __init__(self, _strPluginName, _functXMLin, \
_functXMLout=None, _functXMLerr=None, \
_iNbThreads=None, _fDelay=1.0, _bVerbose=None, _bDebug=None):
"""
This is the constructor of the edna plugin launcher.
@param _strPluginName: the name of the ENDA plugin
@type _strPluginName: python string
@param _functXMLin: a function taking a path in input and returning the XML string for input in the EDNA plugin.
@type _functXMLin: python function
@param _functXMLOut: a function to be called each time a plugin gas finished his job sucessfully, it should take two option: strXMLin an strXMLout
@type _functXMLOut: python function
@param _functXMLErr: a function to be called each time a plugin gas finished his job and crashed, it should take ONE option: strXMLin
@type _functXMLErr: python function
@param _iNbThreads: The number of parallel threads to be used by EDNA, usually the number of Cores of the computer. If 0 or None, the number of cores will be auto-detected.
@type _iNbThreads: python integer
@param _fDelay: The delay in seconds between two directories analysis
@type _fDelay: python float
@param _bVerbose: Do you want the EDNA plugin execution to be verbose ?
@type _bVerbose: boolean
@param _bDebug: Do you want EDNA plugin execution debug output (OBS! very verbose) ?
@type _bDebug: boolean
"""
self.__iNbThreads = EDUtilsParallel.detectNumberOfCPUs(_iNbThreads)
EDUtilsParallel.initializeNbThread(self.__iNbThreads)
self.__semaphoreOut = threading.Semaphore()
self.__semaphoreErr = threading.Semaphore()
self.__strPluginName = _strPluginName
self.__functXMLin = _functXMLin
self.__functXMLout = _functXMLout
self.__functXMLerr = _functXMLerr
self.__strCurrWorkDir = os.getcwd()
self.__strTempDir = None
self.__listInputPaths = []
if _bVerbose is not None:
if _bVerbose:
EDVerbose.setVerboseDebugOn()
else:
EDVerbose.setVerboseOff()
if _bDebug is not None:
if _bDebug:
EDVerbose.setVerboseDebugOn()
else:
EDVerbose.setVerboseDebugOff()
self.__fDelay = _fDelay #default delay between two directory checks.
self.__bQuit = False # To check if we should quit the application
self.__bIsFirstExecute = True
signal.signal(signal.SIGTERM, self.handleKill)
signal.signal(signal.SIGINT, self.handleKill)
def __init__(self, _strPluginName, _functXMLin, \
_functXMLout=None, _functXMLerr=None, \
_iNbThreads=None, _fDelay=1.0, _bVerbose=None, _bDebug=None):
"""
This is the constructor of the edna plugin launcher.
@param _strPluginName: the name of the ENDA plugin
@type _strPluginName: python string
@param _functXMLin: a function taking a path in input and returning the XML string for input in the EDNA plugin.
@type _functXMLin: python function
@param _functXMLOut: a function to be called each time a plugin gas finished his job sucessfully, it should take two option: strXMLin an strXMLout
@type _functXMLOut: python function
@param _functXMLErr: a function to be called each time a plugin gas finished his job and crashed, it should take ONE option: strXMLin
@type _functXMLErr: python function
@param _iNbThreads: The number of parallel threads to be used by EDNA, usually the number of Cores of the computer. If 0 or None, the number of cores will be auto-detected.
@type _iNbThreads: python integer
@param _fDelay: The delay in seconds between two directories analysis
@type _fDelay: python float
@param _bVerbose: Do you want the EDNA plugin execution to be verbose ?
@type _bVerbose: boolean
@param _bDebug: Do you want EDNA plugin execution debug output (OBS! very verbose) ?
@type _bDebug: boolean
"""
self.__iNbThreads = EDUtilsParallel.detectNumberOfCPUs(_iNbThreads)
EDUtilsParallel.initializeNbThread(self.__iNbThreads)
self.__semaphoreOut = threading.Semaphore()
self.__semaphoreErr = threading.Semaphore()
self.__strPluginName = _strPluginName
self.__functXMLin = _functXMLin
self.__functXMLout = _functXMLout
self.__functXMLerr = _functXMLerr
self.__strCurrWorkDir = os.getcwd()
self.__strTempDir = None
self.__listInputPaths = []
if _bVerbose is not None:
if _bVerbose:
EDVerbose.setVerboseDebugOn()
else:
EDVerbose.setVerboseOff()
if _bDebug is not None:
if _bDebug:
EDVerbose.setVerboseDebugOn()
else:
EDVerbose.setVerboseDebugOff()
self.__fDelay = _fDelay #default delay between two directory checks.
self.__bQuit = False # To check if we should quit the application
self.__bIsFirstExecute = True
signal.signal(signal.SIGTERM, self.handleKill)
signal.signal(signal.SIGINT, self.handleKill)
def processCommandLineDebugVerboseLogFile(self):
EDVerbose.DEBUG("EDApplication.processCommandLineDebugVerboseLogFile")
EDVerbose.setVerboseOff()
# Check if no log file
if (self.__edCommandLine.existCommand(EDApplication.NO_LOG_LABEL)):
EDVerbose.setLogFileOff()
EDVerbose.DEBUG("Log file output switched off")
# Check if debug mode
if (self.__edCommandLine.existCommand(EDApplication.DEBUG_PARAM_LABEL_1) or
self.__edCommandLine.existCommand(EDApplication.DEBUG_PARAM_LABEL_2)):
EDVerbose.setVerboseDebugOn()
EDVerbose.DEBUG("Debug Mode [ON]")
# Check if verbose
if (self.__edCommandLine.existCommand(EDApplication.VERBOSE_MODE_LABEL)):
EDVerbose.setVerboseOn()
def preProcess(self):
"""
Scans the command line.
"""
EDVerbose.DEBUG("EDTestLauncher.preProcess")
edCommandLine = EDCommandLine(sys.argv)
EDVerbose.log(self.getEdCommandLine().getCommandLine())
self.processCommandLineDebugVerboseLogFile()
bContinue = True
strTestName = edCommandLine.getArgument(EDTestLauncher.TEST_LABEL)
EDVerbose.DEBUG("EDTestLauncher.preProcess: test name = %r" % strTestName)
if (strTestName is None):
EDVerbose.screen("ERROR - no --test argument found")
bContinue = False
else:
self.__edTestCase = EDUtilsTest.getFactoryPluginTest().loadPlugin(strTestName)
if (bContinue):
# Determine the base directory
if(self.getBaseDir() is None):
self.processCommandLineBaseDirectory()
# Create the application working directory
strApplicationInstanceName = strTestName + "_" + time.strftime("%Y%m%d-%H%M%S", time.localtime())
if(self.getWorkingDir() is None):
self.setWorkingDir(strApplicationInstanceName)
self.createApplicationWorkingDirectory()
# Set the name of the log file
EDVerbose.setLogFileName(os.path.join(self.getBaseDir(), strApplicationInstanceName + ".log"))
# The check for --quiet and --DEBUG should ideally be placed elsewhere,
# for example in EDApplication.
if (edCommandLine.existCommand(EDTestLauncher.QUIET_LABEL)):
EDVerbose.setVerboseOff()
EDVerbose.setTestOff()
if (edCommandLine.existCommand(EDApplication.DEBUG_PARAM_LABEL_1) or \
edCommandLine.existCommand(EDApplication.DEBUG_PARAM_LABEL_2)):
EDVerbose.setVerboseDebugOn()
EDVerbose.DEBUG("EDTestLauncher.preProcess: Debug mode")
from EDVerbose import EDVerbose
from EDFactoryPluginStatic import EDFactoryPluginStatic
EDFactoryPluginStatic.loadModule("EDPluginControlPyarchThumbnailGeneratorv1_0")
from XSDataCommon import XSDataFile
from XSDataCommon import XSDataString
from XSDataCommon import XSDataInteger
from XSDataCommon import XSDataTime
from EDPluginControlPyarchThumbnailGeneratorv1_0 import EDPluginControlPyarchThumbnailGeneratorv1_0
from XSDataPyarchThumbnailGeneratorv1_0 import XSDataInputPyarchThumbnailGenerator
if __name__ == '__main__':
EDVerbose.setVerboseDebugOn()
# Sleep a random time 0-2s in order to avoid problems if many instances started at the same time
fSleepTime = random.random()*2.0
EDVerbose.DEBUG("Sleeping for %.2f s" % fSleepTime)
time.sleep(fSleepTime)
# Popolate input data
EDVerbose.screen("Starting id29_create_thumbnail")
# If no arguments stop
if len(sys.argv) <= 2:
EDVerbose.screen("Usage: id29_create_thumbnail image_directory_path image1 [image2]" )
sys.exit(1)
EDVerbose.screen("Arguments: %r" % sys.argv)
strPathToTempDir = tempfile.mkdtemp(prefix="id29_create_thumbnail_")
os.chdir(strPathToTempDir)
EDVerbose.setLogFileName(os.path.join(strPathToTempDir, "id29_create_thumbnail.log"))
strImageDirectory = sys.argv[1]
#
"""EDNA external libraries builder and installer, useful for PIL, numpy, scipy, Fabio, ... """
__contact__ = "*****@*****.**"
__author__ = "Jerome Kieffer"
__license__ = "GPLv3+"
__copyright__ = "European Synchrotron Radiation Facility, Grenoble, France"
import os, shutil, sys, zipfile, tarfile, urllib2, threading
from EDVerbose import EDVerbose
from EDUtilsPlatform import EDUtilsPlatform
from EDUtilsPath import EDUtilsPath
for strOneArg in sys.argv:
if strOneArg.lower() in ["-d", "--debug"]:
EDVerbose.setVerboseDebugOn()
class EDUtilsLibraryInstaller:
"""
This class helps to install to install an external library within EDNA
"""
iMAX_DOWNLOAD_TIME = 60 #in seconds
def __init__(self,
_strLibraryDirectory,
_strArchiveName=None,
_strSourceDir=None):
"""
Constructor of the class EDUtilsLibraryInstaller,
def __init__(self, cl, name): PyTango.Device_3Impl.__init__(self, cl, name) EDTangoServer.init_device(self) # Initialise the plugin factory self.m_edFactoryPlugin = EDApplication.getFactoryPlugin() EDVerbose.setVerboseDebugOn()
def runEdnaPlugin(execPath, pluginName, isDebug, xml, additionalPaths=None):
'''
execPath - path to run plugin in
pluginName - plugin name
isDebug - True if should run edna in debug mode
xml - xml input to edna
additionalPaths - list of other python path locations
You must set EDNA_HOME to use this method
This method blocks until the EDJob has reached a final status
'''
if (not 'EDNA_HOME' in os.environ):
raise Exception("Cannot locate EDNA_HOME. Please set before running Edna plugins.")
if (not 'EDNA_SITE' in os.environ):
raise Exception(" Please set EDNA_SITE before running Edna plugins.")
'''
Add edna to path
'''
ednaKernelPath = os.environ['EDNA_HOME']+"/kernel/src"
sys.path.insert(0, ednaKernelPath)
'''
If there are any additional paths such as fabio, add these
'''
if (not additionalPaths is None and len(additionalPaths)>0):
for path in additionalPaths:
sys.path.append(path)
os.chdir(execPath)
from EDVerbose import EDVerbose
if (isDebug):
EDVerbose.setVerboseDebugOn()
else:
EDVerbose.setVerboseOn()
EDVerbose.setVerboseDebugOff()
from EDJob import EDJob
EDVerbose.setLogFileName(execPath+"/"+pluginName+".log")
edJob = EDJob(pluginName)
edJob.setDataInput(xml)
edJob.execute()
edJob.synchronize() # In theory should mean that the following loop is not needed
# Unhelpful way of waiting for EDJob to be finished
# TODO Fix this in EDJob some time
while(True):
status = edJob.getStatus()
if (status is None):
time.sleep(0.2) # 200 ms
continue
if ("failure" == status):
raise Exception("EDJob failed! ")
if ("success" == status):
break
ret = edJob.getDataOutput()
return str(ret)
def __init__(self, cl, name):
PyTango.Device_3Impl.__init__(self, cl, name)
EDTangoServer.init_device(self)
# Initialise the plugin factory
self.m_edFactoryPlugin = EDApplication.getFactoryPlugin()
EDVerbose.setVerboseDebugOn()
def runEdnaPlugin(execPath, pluginName, isDebug, xml, additionalPaths=None):
'''
execPath - path to run plugin in
pluginName - plugin name
isDebug - True if should run edna in debug mode
xml - xml input to edna
additionalPaths - list of other python path locations
You must set EDNA_HOME to use this method
This method blocks until the EDJob has reached a final status
'''
if (not 'EDNA_HOME' in os.environ):
raise Exception(
"Cannot locate EDNA_HOME. Please set before running Edna plugins.")
if (not 'EDNA_SITE' in os.environ):
raise Exception(" Please set EDNA_SITE before running Edna plugins.")
'''
Add edna to path
'''
ednaKernelPath = os.environ['EDNA_HOME'] + "/kernel/src"
sys.path.insert(0, ednaKernelPath)
'''
If there are any additional paths such as fabio, add these
'''
if (not additionalPaths is None and len(additionalPaths) > 0):
for path in additionalPaths:
sys.path.append(path)
os.chdir(execPath)
from EDVerbose import EDVerbose
if (isDebug):
EDVerbose.setVerboseDebugOn()
else:
EDVerbose.setVerboseOn()
EDVerbose.setVerboseDebugOff()
from EDJob import EDJob
EDVerbose.setLogFileName(execPath + "/" + pluginName + ".log")
edJob = EDJob(pluginName)
edJob.setDataInput(xml)
edJob.execute()
edJob.synchronize(
) # In theory should mean that the following loop is not needed
# Unhelpful way of waiting for EDJob to be finished
# TODO Fix this in EDJob some time
while (True):
status = edJob.getStatus()
if (status is None):
time.sleep(0.2) # 200 ms
continue
if ("failure" == status):
raise Exception("EDJob failed! ")
if ("success" == status):
break
ret = edJob.getDataOutput()
return str(ret)
