Python plotting.PlotExecutable类代码示例

def make_inference_corner_plot(workflow, mcmc_file, output_dir, config_file,
                    name="mcmc_corner", analysis_seg=None, tags=None):
    """ Sets up the corner plot of the posteriors in the workflow.

    Parameters
    ----------
    workflow: pycbc.workflow.Workflow
        The core workflow instance we are populating
    mcmc_file: pycbc.workflow.File
        The file with MCMC samples.
    output_dir: str
        The directory to store result plots and files.
    config_file: str
        The path to the inference configuration file that has a
        [variable_args] section.
    name: str
        The name in the [executables] section of the configuration file
        to use.
    analysis_segs: {None, glue.segments.Segment}
       The segment this job encompasses. If None then use the total analysis
       time from the workflow.
    tags: {None, optional}
        Tags to add to the minifollowups executables.

    Returns
    -------
    pycbc.workflow.FileList
        A list of result and output files. 
    """

    # default values
    tags = [] if tags is None else tags
    analysis_seg = workflow.analysis_time \
                       if analysis_seg is None else analysis_seg

    # read config file to get variables that vary
    cp = WorkflowConfigParser([config_file])
    variable_args = cp.options("variable_args")

    # add derived mass parameters if mass1 and mass2 in variable_args
    if "mass1" in variable_args and "mass2" in variable_args:
        variable_args += ["mchirp", "eta"]

    # make the directory that will contain the output files
    makedir(output_dir)

    # make a node for plotting the posterior as a corner plot
    node = PlotExecutable(workflow.cp, name, ifos=workflow.ifos,
                      out_dir=output_dir, universe="local",
                      tags=tags).create_node()

    # add command line options
    node.add_input_opt("--input-file", mcmc_file)
    node.new_output_file_opt(analysis_seg, ".png", "--output-file")

    # add node to workflow
    workflow += node

    return node.output_files

def make_trigger_timeseries(workflow,
                            singles,
                            ifo_times,
                            out_dir,
                            special_tids,
                            exclude=None,
                            require=None,
                            tags=None):
    tags = [] if tags is None else tags
    makedir(out_dir)
    name = 'plot_trigger_timeseries'
    secs = requirestr(workflow.cp.get_subsections(name), require)
    secs = excludestr(secs, exclude)
    files = FileList([])
    for tag in secs:
        node = PlotExecutable(
            workflow.cp,
            name,
            ifos=workflow.ifos,
            out_dir=out_dir,
            tags=[tag] + tags).create_node()
        node.add_multiifo_input_list_opt('--single-trigger-files', singles)
        node.add_opt('--times', ifo_times)
        node.new_output_file_opt(workflow.analysis_time, '.png',
                                 '--output-file')

        if special_tids is not None:
            node.add_opt('--special-trigger-ids', special_tids)

        workflow += node
        files += node.output_files
    return files

def make_inference_inj_plots(workflow, inference_files, output_dir,
                             parameters, name="inference_recovery",
                             analysis_seg=None, tags=None):
    """ Sets up the recovered versus injected parameter plot in the workflow.

    Parameters
    ----------
    workflow: pycbc.workflow.Workflow
        The core workflow instance we are populating
    inference_files: pycbc.workflow.FileList
        The files with posterior samples.
    output_dir: str
        The directory to store result plots and files.
    parameters : list
        A ``list`` of parameters. Each parameter gets its own plot.
    name: str
        The name in the [executables] section of the configuration file
        to use.
    analysis_segs: {None, ligo.segments.Segment}
       The segment this job encompasses. If None then use the total analysis
       time from the workflow.
    tags: {None, optional}
        Tags to add to the inference executables.

    Returns
    -------
    pycbc.workflow.FileList
        A list of result and output files.
    """

    # default values
    tags = [] if tags is None else tags
    analysis_seg = workflow.analysis_time \
                       if analysis_seg is None else analysis_seg
    output_files = FileList([])

    # make the directory that will contain the output files
    makedir(output_dir)

    # add command line options
    for (ii, param) in enumerate(parameters):
        plot_exe = PlotExecutable(workflow.cp, name, ifos=workflow.ifos,
                                  out_dir=output_dir,
                                  tags=tags+['param{}'.format(ii)])
        node = plot_exe.create_node()
        node.add_input_list_opt("--input-file", inference_files)
        node.new_output_file_opt(analysis_seg, ".png", "--output-file")
        node.add_opt("--parameters", param)
        workflow += node
        output_files += node.output_files

    return output_files

def make_inference_acceptance_rate_plot(workflow, mcmc_file, output_dir,
                    name="mcmc_rate", analysis_seg=None, tags=None):
    """ Sets up the acceptance rate plot in the workflow.

    Parameters
    ----------
    workflow: pycbc.workflow.Workflow
        The core workflow instance we are populating
    mcmc_file: pycbc.workflow.File
        The file with MCMC samples.
    output_dir: str
        The directory to store result plots and files.
    name: str
        The name in the [executables] section of the configuration file
        to use.
    analysis_segs: {None, glue.segments.Segment}
       The segment this job encompasses. If None then use the total analysis
       time from the workflow.
    tags: {None, optional}
        Tags to add to the minifollowups executables.

    Returns
    -------
    pycbc.workflow.FileList
        A list of result and output files. 
    """

    # default values
    tags = [] if tags is None else tags
    analysis_seg = workflow.analysis_time \
                       if analysis_seg is None else analysis_seg

    # make the directory that will contain the output files
    makedir(output_dir)

    # make a node for plotting the acceptance rate
    node = PlotExecutable(workflow.cp, name, ifos=workflow.ifos,
                      out_dir=output_dir, tags=tags).create_node()

    # add command line options
    node.add_input_opt("--input-file", mcmc_file)
    node.new_output_file_opt(analysis_seg, ".png", "--output-file")

    # add node to workflow
    workflow += node

    return node.output_files

def make_inj_info(workflow, injection_file, injection_index, num, out_dir, tags=None):
    tags = [] if tags is None else tags
    makedir(out_dir)
    name = "page_injinfo"
    files = FileList([])
    node = PlotExecutable(workflow.cp, name, ifos=workflow.ifos, out_dir=out_dir, tags=tags).create_node()
    node.add_input_opt("--injection-file", injection_file)
    node.add_opt("--injection-index", str(injection_index))
    node.add_opt("--n-nearest", str(num))
    node.new_output_file_opt(workflow.analysis_time, ".html", "--output-file")
    workflow += node
    files += node.output_files
    return files

def make_inference_samples_plot(
                    workflow, inference_file, output_dir, parameters=None,
                    name="inference_samples", analysis_seg=None, tags=None):
    # default values
    tags = [] if tags is None else tags
    analysis_seg = workflow.analysis_time \
                       if analysis_seg is None else analysis_seg

    # make the directory that will contain the output files
    makedir(output_dir)

    # make a node for plotting the posterior as a corner plot
    node = PlotExecutable(workflow.cp, name, ifos=workflow.ifos,
                      out_dir=output_dir, universe="local",
                      tags=tags).create_node()

    # add command line options
    node.add_input_opt("--input-file", inference_file)
    node.new_output_file_opt(analysis_seg, ".png", "--output-file")
    node.add_opt("--parameters", " ".join(parameters))

    # add node to workflow
    workflow += node

    return node.output_files

def make_inference_corner_plot(workflow, inference_file, output_dir,
                    variable_args=None,
                    name="inference_posterior", analysis_seg=None, tags=None):
    """ Sets up the corner plot of the posteriors in the workflow.

    Parameters
    ----------
    workflow: pycbc.workflow.Workflow
        The core workflow instance we are populating
    inference_file: pycbc.workflow.File
        The file with posterior samples.
    output_dir: str
        The directory to store result plots and files.
    config_file: str
        The path to the inference configuration file that has a
        [variable_args] section.
    variable_args : list
        A list of parameters to use instead of [variable_args].
    name: str
        The name in the [executables] section of the configuration file
        to use.
    analysis_segs: {None, glue.segments.Segment}
       The segment this job encompasses. If None then use the total analysis
       time from the workflow.
    tags: {None, optional}
        Tags to add to the minifollowups executables.

    Returns
    -------
    pycbc.workflow.FileList
        A list of result and output files. 
    """

    # default values
    tags = [] if tags is None else tags
    analysis_seg = workflow.analysis_time \
                       if analysis_seg is None else analysis_seg

    # make the directory that will contain the output files
    makedir(output_dir)

    # make a node for plotting the posterior as a corner plot
    node = PlotExecutable(workflow.cp, name, ifos=workflow.ifos,
                      out_dir=output_dir, universe="local",
                      tags=tags).create_node()

    # add command line options
    node.add_input_opt("--input-file", inference_file)
    node.new_output_file_opt(analysis_seg, ".png", "--output-file")
    node.add_opt("--variable-args", " ".join(variable_args))

    # add node to workflow
    workflow += node

    return node.output_files

def make_trigger_timeseries(workflow, singles, coinc, num, out_dir,
                            exclude=None, require=None, tags=None):
    tags = [] if tags is None else tags
    makedir(out_dir)
    name = 'plot_trigger_timeseries'
    secs = requirestr(workflow.cp.get_subsections(name), require)  
    secs = excludestr(secs, exclude)
    files = FileList([])
    for tag in secs:
        node = PlotExecutable(workflow.cp, name, ifos=workflow.ifos,
                              out_dir=out_dir, tags=[tag] + tags).create_node()
        node.add_input_list_opt('--single-trigger-files', singles)
        node.add_input_opt('--statmap-file', coinc)
        node.add_opt('--n-loudest', str(num))
        node.new_output_file_opt(workflow.analysis_time, '.png', '--output-file')
        workflow += node
        files += node.output_files
    return files

def make_inference_prior_plot(workflow, config_file, output_dir,
                    sections=None, name="inference_prior",
                    analysis_seg=None, tags=None):
    """ Sets up the corner plot of the priors in the workflow.

    Parameters
    ----------
    workflow: pycbc.workflow.Workflow
        The core workflow instance we are populating
    config_file: pycbc.workflow.File
        The WorkflowConfigParser parasable inference configuration file..
    output_dir: str
        The directory to store result plots and files.
    sections : list
        A list of subsections to use.
    name: str
        The name in the [executables] section of the configuration file
        to use.
    analysis_segs: {None, ligo.segments.Segment}
       The segment this job encompasses. If None then use the total analysis
       time from the workflow.
    tags: {None, optional}
        Tags to add to the inference executables.

    Returns
    -------
    pycbc.workflow.FileList
        A list of result and output files.
    """

    # default values
    tags = [] if tags is None else tags
    analysis_seg = workflow.analysis_time \
                       if analysis_seg is None else analysis_seg

    # make the directory that will contain the output files
    makedir(output_dir)

    # make a node for plotting the posterior as a corner plot
    node = PlotExecutable(workflow.cp, name, ifos=workflow.ifos,
                      out_dir=output_dir, universe="local",
                      tags=tags).create_node()

    # add command line options
    node.add_input_opt("--config-file", config_file)
    node.new_output_file_opt(analysis_seg, ".png", "--output-file")
    if sections is not None:
        node.add_opt("--sections", " ".join(sections))

    # add node to workflow
    workflow += node

    return node.output_files

def make_singles_timefreq(workflow, single, bank_file, start, end, out_dir,
                          veto_file=None, tags=None):
    tags = [] if tags is None else tags
    makedir(out_dir)
    name = 'plot_singles_timefreq'

    node = PlotExecutable(workflow.cp, name, ifos=[single.ifo],
                          out_dir=out_dir, tags=tags).create_node()
    node.add_input_opt('--trig-file', single)
    node.add_input_opt('--bank-file', bank_file)
    node.add_opt('--gps-start-time', int(start))
    node.add_opt('--gps-end-time', int(end))
    
    if veto_file:
        node.add_input_opt('--veto-file', veto_file)
        
    node.add_opt('--detector', single.ifo)
    node.new_output_file_opt(workflow.analysis_time, '.png', '--output-file')
    workflow += node
    return node.output_files

def make_sngl_ifo(workflow, sngl_file, bank_file, num, out_dir, ifo,
                  veto_file=None, veto_segment_name=None, tags=None):
    """Setup a job to create sngl detector sngl ifo html summary snippet.
    """
    tags = [] if tags is None else tags
    makedir(out_dir)
    name = 'page_snglinfo'
    files = FileList([])
    node = PlotExecutable(workflow.cp, name, ifos=[ifo],
                              out_dir=out_dir, tags=tags).create_node()
    node.add_input_opt('--single-trigger-file', sngl_file)
    node.add_input_opt('--bank-file', bank_file)
    if veto_file is not None:
        assert(veto_segment_name is not None)
        node.add_input_opt('--veto-file', veto_file)
        node.add_opt('--veto-segment-name', veto_segment_name)
    node.add_opt('--n-loudest', str(num))
    node.add_opt('--instrument', ifo)
    node.new_output_file_opt(workflow.analysis_time, '.html', '--output-file')
    workflow += node
    files += node.output_files
    return files

def make_coinc_info(workflow, singles, bank, coinc, num, out_dir, tags=None):
    tags = [] if tags is None else tags
    makedir(out_dir)
    name = 'page_coincinfo'
    files = FileList([])
    node = PlotExecutable(workflow.cp, name, ifos=workflow.ifos,
                              out_dir=out_dir, tags=tags).create_node()
    node.add_input_list_opt('--single-trigger-files', singles)
    node.add_input_opt('--statmap-file', coinc)
    node.add_input_opt('--bank-file', bank)
    node.add_opt('--n-loudest', str(num))
    node.new_output_file_opt(workflow.analysis_time, '.html', '--output-file')
    workflow += node
    files += node.output_files
    return files

def make_plot_waveform_plot(workflow, params, out_dir, ifos, exclude=None,
                            require=None, tags=None):
    """ Add plot_waveform jobs to the workflow.
    """
    tags = [] if tags is None else tags
    makedir(out_dir)
    name = 'single_template_plot'
    secs = requirestr(workflow.cp.get_subsections(name), require)
    secs = excludestr(secs, exclude)
    files = FileList([])
    for tag in secs:
        node = PlotExecutable(workflow.cp, 'plot_waveform', ifos=ifos,
                              out_dir=out_dir, tags=[tag] + tags).create_node()
        node.add_opt('--mass1', "%.6f" % params['mass1'])
        node.add_opt('--mass2', "%.6f" % params['mass2'])
        node.add_opt('--spin1z',"%.6f" % params['spin1z'])
        node.add_opt('--spin2z',"%.6f" % params['spin2z'])
        if params.has_key('u_vals'):
            # Precessing options
            node.add_opt('--spin1x',"%.6f" % params['spin1x'])
            node.add_opt('--spin2x',"%.6f" % params['spin2x'])
            node.add_opt('--spin1y',"%.6f" % params['spin1y'])
            node.add_opt('--spin2y',"%.6f" % params['spin2y'])
            node.add_opt('--inclination',"%.6f" % params['inclination'])
            node.add_opt('--u-val', "%.6f" % params['u_vals'])
        node.new_output_file_opt(workflow.analysis_time, '.png',
                                     '--output-file')
        workflow += node
        files += node.output_files
    return files

def make_coinc_info(workflow, singles, bank, coinc, out_dir,
                    n_loudest=None, trig_id=None, file_substring=None,
                    tags=None):
    tags = [] if tags is None else tags
    makedir(out_dir)
    name = 'page_coincinfo'
    files = FileList([])
    node = PlotExecutable(workflow.cp, name, ifos=workflow.ifos,
                              out_dir=out_dir, tags=tags).create_node()
    node.add_input_list_opt('--single-trigger-files', singles)
    node.add_input_opt('--statmap-file', coinc)
    node.add_input_opt('--bank-file', bank)
    if n_loudest is not None:
        node.add_opt('--n-loudest', str(n_loudest))
    if trig_id is not None:
        node.add_opt('--trigger-id', str(trig_id))
    if file_substring is not None:
        node.add_opt('--statmap-file-subspace-name', file_substring)
    node.new_output_file_opt(workflow.analysis_time, '.html', '--output-file')
    workflow += node
    files += node.output_files
    return files

def make_single_template_plots(workflow, segs, seg_name, coinc, bank, num, out_dir, 
                               exclude=None, require=None, tags=None):
    tags = [] if tags is None else tags
    makedir(out_dir)
    name = 'single_template_plot'
    secs = requirestr(workflow.cp.get_subsections(name), require)  
    secs = excludestr(secs, exclude)
    files = FileList([])
    for tag in secs:
        for ifo in workflow.ifos:
            # Reanalyze the time around the trigger in each detector
            node = PlotExecutable(workflow.cp, 'single_template', ifos=[ifo],
                                 out_dir=out_dir, tags=[tag] + tags).create_node()
            node.add_input_opt('--statmap-file', coinc)
            node.add_opt('--n-loudest', str(num))
            node.add_input_opt('--inspiral-segments', segs[ifo])
            node.add_opt('--segment-name', seg_name)
            node.add_input_opt('--bank-file', bank)
            node.new_output_file_opt(workflow.analysis_time, '.hdf', '--output-file')
            data = node.output_files[0]
            workflow += node
            
            # Make the plot for this trigger and detector
            node = PlotExecutable(workflow.cp, name, ifos=[ifo],
                                  out_dir=out_dir, tags=[tag] + tags).create_node()
            node.add_input_opt('--single-template-file', data)
            node.new_output_file_opt(workflow.analysis_time, '.png', '--output-file')
            workflow += node
            files += node.output_files
    return files