Python Node.add_opt方法代码示例

# 需要导入模块: from pycbc.workflow.core import Node [as 别名]
# 或者: from pycbc.workflow.core.Node import add_opt [as 别名]
    def create_node(self, parent, tags=None):
        import Pegasus.DAX3 as dax
        if tags is None:
            tags = []
        node = Node(self)

        # Set input / output options
        node.add_opt('--trig-file', '%s' % parent.storage_path)
        #node._dax_node.uses(parent, link=dax.Link.INPUT, register=False,
        #                    transfer=False)
        #node._inputs += [parent]

        node.add_opt('--output-dir', self.out_dir)

        node.add_profile('condor', 'request_cpus', self.num_threads)

        # Adding output files as pycbc.workflow.core.File objects
        out_file = File(self.ifos, 'INSPIRAL', parent.segment,
                        directory=self.out_dir, extension='xml.gz',
                        tags=[parent.tag_str, 'CLUSTERED'],
                        store_file=self.retain_files)
        out_file.PFN(out_file.cache_entry.path, site="local")
        #node._dax_node.uses(out_file, link=dax.Link.OUTPUT, register=False,
        #                    transfer=False)
        #node._outputs += [out_file]
        out_file.node = node
        #node._add_output(out_file)

        return node, FileList([out_file])

# 需要导入模块: from pycbc.workflow.core import Node [as 别名]
# 或者: from pycbc.workflow.core.Node import add_opt [as 别名]
 def create_node(self, inj_coinc_file, inj_xml_file, veto_file, veto_name, tags=[]):
     node = Node(self)        
     node.add_input_list_opt('--trigger-file', inj_coinc_file)
     node.add_input_list_opt('--injection-file', inj_xml_file)
     if veto_name is not None:
         node.add_input_opt('--veto-file', veto_file)
     node.add_opt('--segment-name', veto_name)
     node.new_output_file_opt(inj_xml_file[0].segment, '.hdf', '--output-file', 
                              tags=tags)
     return node

# 需要导入模块: from pycbc.workflow.core import Node [as 别名]
# 或者: from pycbc.workflow.core.Node import add_opt [as 别名]
 def create_node(self, trig_file, bank_file, veto_file, veto_name):
     node = Node(self)
     # Executable objects are initialized with ifo information
     node.add_opt('--ifo', self.ifo_string)
     node.add_input_opt('--trigger-file', trig_file)
     node.add_input_opt('--template-file', bank_file)
     node.add_input_opt('--veto-file', veto_file)
     node.add_opt('--veto-segment-name', veto_name)
     node.new_output_file_opt(trig_file.segment, '.hdf', '--output')
     return node

# 需要导入模块: from pycbc.workflow.core import Node [as 别名]
# 或者: from pycbc.workflow.core.Node import add_opt [as 别名]
    def create_node(self, coinc_files, ifos, tags=None):
        if tags is None:
            tags = []
        segs = coinc_files.get_times_covered_by_files()
        seg = segments.segment(segs[0][0], segs[-1][1])

        node = Node(self)
        node.set_memory(5000)
        node.add_input_list_opt('--coinc-files', coinc_files)
        node.add_opt('--ifos', ifos)
        node.new_output_file_opt(seg, '.hdf', '--output-file', tags=tags)
        return node

# 需要导入模块: from pycbc.workflow.core import Node [as 别名]
# 或者: from pycbc.workflow.core.Node import add_opt [as 别名]
    def create_node(self, parent, inj_trigs, inj_string, max_inc, segment):
        node = Node(self)

        trig_name = self.cp.get('workflow', 'trigger-name')
        node.add_opt('--inj-string', inj_string)
        node.add_opt('--max-inclination', max_inc)
        node.add_opt('--inj-cache', '%s' % parent.storage_path)

        out_files = FileList([])
        for inj_trig in inj_trigs:
            out_file_tag = [
                inj_string, "FILTERED", max_inc,
                inj_trig.tag_str.rsplit('_', 1)[-1]
            ]
            out_file = File(
                self.ifos,
                inj_trig.description,
                inj_trig.segment,
                extension="xml",
                directory=self.out_dir,
                tags=out_file_tag)
            out_file.PFN(out_file.cache_entry.path, site="local")
            out_files.append(out_file)

        node.add_opt('--output-dir', self.out_dir)

        return node, out_files

# 需要导入模块: from pycbc.workflow.core import Node [as 别名]
# 或者: from pycbc.workflow.core.Node import add_opt [as 别名]
    def create_node(self, parent, inj_trigs, inj_string, max_inc, segment):
        node = Node(self)

        trig_name = self.cp.get("workflow", "trigger-name")
        node.add_opt("--inj-string", inj_string)
        node.add_opt("--max-inclination", max_inc)
        node.add_opt("--inj-cache", "%s" % parent.storage_path)

        out_files = FileList([])
        for inj_trig in inj_trigs:
            out_string = inj_string.split(max_inc)[0]
            out_file_tag = [out_string, "FILTERED", max_inc, inj_trig.tag_str.rsplit("_", 1)[-1]]
            out_file = File(
                self.ifos,
                inj_trig.description,
                inj_trig.segment,
                extension="xml",
                directory=self.out_dir,
                tags=out_file_tag,
            )
            out_file.PFN(out_file.cache_entry.path, site="local")
            out_files.append(out_file)

        node.add_opt("--output-dir", self.out_dir)

        return node, out_files

# 需要导入模块: from pycbc.workflow.core import Node [as 别名]
# 或者: from pycbc.workflow.core.Node import add_opt [as 别名]
    def create_node(self, data_seg, valid_seg, parent=None, inj_file=None,
                    dfParents=None, bankVetoBank=None, ipn_file=None, tags=[]):
        node = Node(self)

        if not dfParents:
            raise ValueError("%s must be supplied with frame files"
                              % self.name)

        # If doing single IFO search, make sure slides are disabled
        if len(self.ifo_list) < 2 and \
                ('--do-short-slides' in node._options or \
                 '--short-slide-offset' in node._options):
            raise ValueError("Cannot run with time slides in a single IFO "
                             "configuration! Please edit your configuration "
                             "file accordingly.")

        pad_data = self.get_opt('pad-data')
        if pad_data is None:
            raise ValueError("The option pad-data is a required option of "
                             "%s. Please check the ini file." % self.name)

        # Feed in bank_veto_bank.xml
        if self.cp.has_option('inspiral', 'do-bank-veto'):
            if not bankVetoBank:
                raise ValueError("%s must be given a bank veto file if the "
                                 "argument 'do-bank-veto' is given"
                                 % self.name)
            node.add_input_opt('--bank-veto-templates', bankVetoBank)

        # Set time options
        node.add_opt('--gps-start-time', data_seg[0] + int(pad_data))
        node.add_opt('--gps-end-time', data_seg[1] - int(pad_data))
        node.add_opt('--trig-start-time', valid_seg[0])
        node.add_opt('--trig-end-time', valid_seg[1])

        node.add_profile('condor', 'request_cpus', self.num_threads)

        # Set the input and output files
        node.new_output_file_opt(data_seg, '.xml.gz', '--output-file',
                                 tags=tags, store_file=self.retain_files)
        node.add_input_opt('--non-spin-bank', parent, )

        for frameCache in dfParents:
            node.add_input_opt('--%s-frame-cache' % frameCache.ifo.lower(),
                               frameCache)
            node.add_arg('--%s-data' % frameCache.ifo.lower())

        if ipn_file is not None:
            node.add_input_opt('--sky-positions-file', ipn_file)

        if inj_file is not None:
            if ('--do-short-slides' in node._options or \
                    '--short-slide-offset' in node._options):
                raise ValueError("Cannot run with short slides in an "
                                 "injection job. Please edit your "
                                 "configuration file accordingly.")
            node.add_input_opt('--injection-file', inj_file)

        return node

# 需要导入模块: from pycbc.workflow.core import Node [as 别名]
# 或者: from pycbc.workflow.core.Node import add_opt [as 别名]
    def create_node(self, zerolag, full_data,
                    injfull, fullinj, ifos, tags=None):
        if tags is None:
            tags = []
        segs = zerolag.get_times_covered_by_files()
        seg = segments.segment(segs[0][0], segs[-1][1])

        node = Node(self)
        node.set_memory(5000)
        node.add_input_list_opt('--zero-lag-coincs', zerolag)
        node.add_input_list_opt('--full-data-background', full_data)
        node.add_input_list_opt('--mixed-coincs-inj-full', injfull)
        node.add_input_list_opt('--mixed-coincs-full-inj', fullinj)
        node.add_opt('--ifos', ifos)
        node.new_output_file_opt(seg, '.hdf', '--output-file', tags=tags)
        return node

# 需要导入模块: from pycbc.workflow.core import Node [as 别名]
# 或者: from pycbc.workflow.core.Node import add_opt [as 别名]
    def create_node(self, data_seg, valid_seg, parent=None, inj_file=None,
                    dfParents=None, bankVetoBank=None, tags=[]):
        node = Node(self)

        if not dfParents:
            raise ValueError("%s must be supplied with frame files"
                              % self.name)

        pad_data = self.get_opt('pad-data')
        if pad_data is None:
            raise ValueError("The option pad-data is a required option of "
                             "%s. Please check the ini file." % self.name)
        
        # Feed in bank_veto_bank.xml
        if self.cp.has_option('inspiral', 'do-bank-veto'):
            if not bankVetoBank:
                raise ValueError("%s must be given a bank veto file if the"
                                 "argument 'do-bank-veto' is given"
                                 % self.name)
            node.add_input_opt('--bank-veto-templates', bankVetoBank)
        
        node.add_opt('--gps-start-time', data_seg[0] + int(pad_data))
        node.add_opt('--gps-end-time', data_seg[1] - int(pad_data))
        node.add_opt('--trig-start-time', valid_seg[0])
        node.add_opt('--trig-end-time', valid_seg[1])

        node.add_profile('condor', 'request_cpus', self.num_threads)

        # Set the input and output files
        node.new_output_file_opt(data_seg, '.xml.gz', '--output-file',
                                 tags=tags, store_file=self.retain_files)
        node.add_input_opt('--non-spin-bank', parent, )

        for frameCache in dfParents:
            node.add_input_opt('--%s-frame-cache' % frameCache.ifo.lower(),
                               frameCache)
            node.add_arg('--%s-data' % frameCache.ifo.lower())
            node.add_opt('--%s-channel-name' % frameCache.ifo.lower(),
                         self.cp.get('workflow',
                                     '%s-channel-name' %frameCache.ifo.lower()))

        if inj_file is not None:
            node.add_input_opt('--injection-file', inj_file)

        return node

# 需要导入模块: from pycbc.workflow.core import Node [as 别名]
# 或者: from pycbc.workflow.core.Node import add_opt [as 别名]
    def create_node(self, segment, coinc_file, tmpltbank_file, data_type, loudest_event_number):
        ''' Creates a node for the loudest_event_number-th loudest event in the
        coinc_file. '''

        # make a node
        node = Node(self)

        # add input files
        node.add_input_opt('--coinc-file', coinc_file)
        node.add_input_opt('--tmpltbank-file', tmpltbank_file)

        # add options
        node.add_opt('--data-type', data_type)
        node.add_opt('--loudest-event-number', loudest_event_number)

        # add output file
        node.new_output_file_opt(segment, '.html', '--output-file',
                                 store_file=self.retain_files)

        return node

# 需要导入模块: from pycbc.workflow.core import Node [as 别名]
# 或者: from pycbc.workflow.core.Node import add_opt [as 别名]
def setup_plotthinca(workflow, input_files, cache_filename, coinc_cachepattern,
                     slide_cachepattern, output_dir, tags=[], **kwargs):
    """
    This function sets up the nodes that will generate summary from a list of
    thinca files.

    Parameters
    -----------
    Workflow : ahope.Workflow
        The ahope workflow instance that the coincidence jobs will be added to.
    input_files : ahope.FileList
        An FileList of files that are used as input at this stage.
    cache_filename : str
        Filename of the ihope cache.
    coinc_cachepattern : str
        The pattern that will be used to find zero-lag coincidence filenames in the cache.
    slide_cachepattern : str
        The pattern that will be used to find time slide filenames in the cache.
    output_dir : path
        The directory in which output files will be stored.
    tags : list of strings (optional, default = [])
        A list of the tagging strings that will be used for all jobs created
        by this call to the workflow. An example might be ['full_data'].
        This will be used in output names and directories.

    Returns
    --------
    plot_files : ahope.FileList
        A list of the output files from this stage.
    """

    plot_files = FileList([])

    # create executable
    plotthinca_job = Executable(workflow.cp, 'plotthinca', 'vanilla',
                                workflow.ifos, output_dir, tags)

    # get all ifo combinations of at least 2 coincident ifos
    ifo_combos = []
    for n in xrange(len(plotthinca_job.ifo_list)+1):
        for ifo_list in itertools.combinations(plotthinca_job.ifo_list, n+2):
            ifo_combos.append(ifo_list)

    for tag in tags:
        for ifo_list in ifo_combos:
            ifo_string = ''.join(ifo_list)

            # create node
            node = Node(plotthinca_job)
            node.add_opt('--gps-start-time', workflow.analysis_time[0])
            node.add_opt('--gps-end-time', workflow.analysis_time[1])
            node.add_opt('--cache-file', cache_filename)
            node.add_opt('--ifo-times', ifo_string)
            node.add_opt('--ifo-tag', 'SECOND_'+ifo_string)
            for ifo in ifo_list:
                node.add_opt('--%s-triggers'%ifo.lower(), '')
            node.add_opt('--user-tag', tag.upper()+'_SUMMARY_PLOTS')
            node.add_opt('--output-path', output_dir)
            node.add_opt('--coinc-pattern', coinc_cachepattern)
            node.add_opt('--slide-pattern', slide_cachepattern)
            node.add_opt('--enable-output')

            # add node to workflow
            workflow.add_node(node)

            # make all input_files parents
            #for f in input_files:
            #    dep = dax.Dependency(parent=f.node._dax_node, child=node._dax_node)
            #    workflow._adag.addDependency(dep)

    return plot_files

# 需要导入模块: from pycbc.workflow.core import Node [as 别名]
# 或者: from pycbc.workflow.core.Node import add_opt [as 别名]
def get_veto_segs(workflow, ifo, category, start_time, end_time, out_dir, 
                  vetoGenJob, tag=None, execute_now=False):
    """
    Obtain veto segments for the selected ifo and veto category and add the job
    to generate this to the workflow.

    Parameters
    -----------
    workflow: pycbc.workflow.core.Workflow
        An instance of the Workflow class that manages the workflow.
    ifo : string
        The string describing the ifo to generate vetoes for.
    category : int
        The veto category to generate vetoes for.
    start_time : gps time (either int/LIGOTimeGPS)
        The time at which to begin searching for segments.
    end_time : gps time (either int/LIGOTimeGPS)
        The time at which to stop searching for segments.
    out_dir : path
        The directory in which output will be stored.    
    vetoGenJob : Job
        The veto generation Job class that will be used to create the Node.
    tag : string, optional (default=None)
        Use this to specify a tag. This can be used if this module is being
        called more than once to give call specific configuration (by setting
        options in [workflow-datafind-${TAG}] rather than [workflow-datafind]). This
        is also used to tag the Files returned by the class to uniqueify
        the Files and uniqueify the actual filename.
        FIXME: Filenames may not be unique with current codes!
    execute_now : boolean, optional
        If true, jobs are executed immediately. If false, they are added to the
        workflow to be run later.

    Returns
    --------
    veto_def_file : pycbc.workflow.core.OutSegFile
        The workflow File object corresponding to this DQ veto file.
    """
    segValidSeg = segments.segment([start_time,end_time])
    node = Node(vetoGenJob)
    node.add_opt('--veto-categories', str(category))
    node.add_opt('--ifo-list', ifo)
    node.add_opt('--gps-start-time', str(start_time))
    node.add_opt('--gps-end-time', str(end_time))
    vetoXmlFileName = "%s-VETOTIME_CAT%d-%d-%d.xml" \
                         %(ifo, category, start_time, end_time-start_time)
    vetoXmlFilePath = os.path.abspath(os.path.join(out_dir, vetoXmlFileName))
    currUrl = urlparse.urlunparse(['file', 'localhost',
                                   vetoXmlFilePath, None, None, None])
    if tag:
        currTags = [tag, 'VETO_CAT%d' %(category)]
    else:
        currTags = ['VETO_CAT%d' %(category)]

    vetoXmlFile = OutSegFile(ifo, 'SEGMENTS', segValidSeg, currUrl,
                                  tags=currTags)
    node._add_output(vetoXmlFile)
    
    if execute_now:
        if file_needs_generating(vetoXmlFile.cache_entry.path):
            workflow.execute_node(node)
        else:
            node.executed = True
            for fil in node._outputs:
                fil.node = None
                fil.PFN(fil.storage_path, site='local')
    else:
        workflow.add_node(node)
    return vetoXmlFile

# 需要导入模块: from pycbc.workflow.core import Node [as 别名]
# 或者: from pycbc.workflow.core.Node import add_opt [as 别名]
def setup_hardware_injection_page(workflow, input_files, cache_filename,
                         inspiral_cachepattern, output_dir, tags=[], **kwargs):
    """
    This function sets up the nodes that will create the hardware injection page.

    Parameters
    -----------
    Workflow : ahope.Workflow
        The ahope workflow instance that the coincidence jobs will be added to.
    input_files : ahope.FileList
        An FileList of files that are used as input at this stage.
    cache_filename : str
        Filename of the ihope cache.
    inspiral_cachepattern : str
        The pattern that will be used to find inspiral filenames in the cache.
    output_dir : path
        The directory in which output files will be stored.
    tags : list of strings (optional, default = [])
        A list of the tagging strings that will be used for all jobs created
        by this call to the workflow. An example might be ['full_data'].
        This will be used to search the cache.

    Returns
    --------
    plot_files : ahope.FileList
        A list of the output files from this stage.
    """

    logging.info("Entering hardware injection page setup.")

    out_files = FileList([])

    # check if hardware injection section exists
    # if not then do not do add hardware injection job to the workflow
    if not workflow.cp.has_section('workflow-hardware-injections'):
      msg  = "There is no workflow-hardware-injections section. "
      msg += "The hardware injection page will not be added to the workflow."
      logging.info(msg)
      logging.info("Leaving hardware injection page setup.")
      return out_files

    # make the output dir
    if not os.path.exists(output_dir):
        os.makedirs(output_dir)

    # create executable
    hwinjpage_job = Executable(workflow.cp, 'hardware_injection_page',
                                    'vanilla', workflow.ifos, output_dir, tags)

    # retrieve hardware injection file
    hwinjDefUrl = workflow.cp.get_opt_tags('workflow-hardware-injections',
                                                     'hwinj-definer-url', tags)
    hwinjDefBaseName = os.path.basename(hwinjDefUrl)
    hwinjDefNewPath = os.path.join(output_dir, hwinjDefBaseName)
    urllib.urlretrieve (hwinjDefUrl, hwinjDefNewPath)

    # update hwinj definer file location
    workflow.cp.set("workflow-hardware-injections", "hwinj-definer-file",
                                                               hwinjDefNewPath)

    # query for the hardware injection segments
    get_hardware_injection_segment_files(workflow, output_dir, hwinjDefNewPath)

    # create node
    node = Node(hwinjpage_job)
    node.add_opt('--gps-start-time', workflow.analysis_time[0])
    node.add_opt('--gps-end-time', workflow.analysis_time[1])
    node.add_opt('--source-xml', hwinjDefNewPath)
    node.add_opt('--segment-dir', output_dir)
    node.add_opt('--cache-file', cache_filename)
    node.add_opt('--cache-pattern', inspiral_cachepattern)
    node.add_opt('--analyze-injections', '')
    for ifo in workflow.ifos:
        node.add_opt('--%s-injections'%ifo.lower(), '')
    outfile = File(node.executable.ifo_string, 'HWINJ_SUMMARY',
                workflow.analysis_time, extension='html', directory=output_dir)
    node.add_opt('--outfile', outfile.storage_path)

    # add node to workflow
    workflow.add_node(node)

    # make all input_files parents
    #for f in input_files:
    #    dep = dax.Dependency(parent=f.node._dax_node, child=node._dax_node)
    #    workflow._adag.addDependency(dep)

    out_files += node.output_files

    logging.info("Leaving hardware injection page setup.")

    return out_files

# 需要导入模块: from pycbc.workflow.core import Node [as 别名]
# 或者: from pycbc.workflow.core.Node import add_opt [as 别名]
def setup_plotnumtemplates(workflow, input_files, cache_filename,
                           tmpltbank_cachepattern, output_dir, tags=[],
                           **kwargs):
    """
    This function sets up the nodes that will generate a plot of the number
    of templates against time.

    Parameters
    -----------
    Workflow : ahope.Workflow
        The ahope workflow instance that the coincidence jobs will be added to.
    input_files : ahope.FileList
        An FileList of files that are used as input at this stage.
    cache_filename : str
        Filename of the ihope cache.
    tmpltbank_cachepattern : str
        The pattern that will be used to find template_bank filenames in the cache.
    output_dir : path
        The directory in which output files will be stored.
    tags : list of strings (optional, default = [])
        A list of the tagging strings that will be used for all jobs created
        by this call to the workflow. An example might be ['full_data'].
        This will be used in output names and directories.

    Returns
    --------
    plot_files : ahope.FileList
        A list of the output files from this stage.
    """

    plot_files = FileList([])

    # create executable
    plotnumtemplates_job = Executable(workflow.cp, 'plotnumtemplates',
                                  'vanilla', workflow.ifos, output_dir, tags)

    for tag in tags:
        # create node
        node = Node(plotnumtemplates_job)
        node.add_opt('--gps-start-time', workflow.analysis_time[0])
        node.add_opt('--gps-end-time', workflow.analysis_time[1])
        node.add_opt('--cache-file', cache_filename)
        node.add_opt('--ifo-times', node.executable.ifo_string)
        node.add_opt('--user-tag', tag.upper()+'_SUMMARY_PLOTS')
        node.add_opt('--output-path', output_dir)
        node.add_opt('--bank-pattern', tmpltbank_cachepattern)
        node.add_opt('--enable-output')

        # add node to workflow
        workflow.add_node(node)

        # make all input_files parents
        #for f in input_files:
        #    dep = dax.Dependency(parent=f.node._dax_node, child=node._dax_node)
        #    workflow._adag.addDependency(dep)

    return plot_files