nullpol 0.1.1__py3-none-any.whl

nullpol/.gitignore

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+_version.py

nullpol/__init__.py

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+from __future__ import annotations
+
+from . import (asimov, calibration, clustering, detector, injection,
+               job_creation, likelihood, null_stream, prior, result, source,
+               time_frequency_transform, utils)
+from .utils import logger
+
+__version__ = '0.1.1'
+
+
+def get_version_information() -> str:
+    """Get version information.
+
+    Returns:
+        str: Version information.
+    """
+    return __version__
+
+
+def log_version_information():
+    """Log version information.
+    """
+    logger.info(f"Running nullpol: {__version__}")
+
+
+__all__ = [
+    'asimov',
+    'calibration',
+    'clustering',
+    'detector',
+    'injection',
+    'job_creation',
+    'likelihood',
+    'null_stream',
+    'prior',
+    'result',
+    'source',
+    'time_frequency_transform',
+    'utils',
+    '__version__',
+    'get_version_information',
+    'log_version_information',
+]

nullpol/asimov/analysis_defaults.yaml

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+kind: configuration
+hooks:
+   postmonitor:
+     tgrflow:
+       library location:
+   applicator:
+     tgrflow:
+       library location:
+data:
+  channels:
+    H1: H1:GDS-CALIB_STRAIN_CLEAN
+    L1: L1:GDS-CALIB_STRAIN_CLEAN
+    V1: V1:Hrec_hoft_16384Hz
+  frame types:
+    H1: H1_HOFT_C00
+    L1: L1_HOFT_C00
+    V1: V1Online
+pipelines:
+  gwdata:
+    scheduler:
+      accounting group: ligo.prod.o4.cbc.testgr.tiger
+      request cpus: 1
+  peconfigurator:
+    scheduler:
+      accounting group: ligo.prod.o4.cbc.testgr.tiger
+      request cpus: 1
+  nullpol:
+    tgr schema section: PolAnalyses
+    quality:
+      state vector:
+        L1: L1:GDS-CALIB_STRAIN_CLEAN
+        H1: H1:GDS-CALIB_STRAIN_CLEAN
+        V1: V1:Hrec_hoft_16384Hz
+    sampler:
+      sampler: dynesty
+      parallel jobs: 4
+    scheduler:
+      accounting group: ligo.prod.o4.cbc.testgr.tiger
+      request cpus: 4
+      request disk: 8
+      request memory: 12
+      scitoken issuer: igwn
+quality:
+  minimum frequency:
+    H1: 20
+    L1: 20
+    V1: 20
+    G1: 20
+    K1: 20
+priors:
+    dec:
+        type: Cosine
+    psi:
+        type: Uniform
+    ra:
+        type: Uniform

nullpol/asimov/asimov.py

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+"""Nullpol Pipeline specification."""
+
+from __future__ import annotations
+
+import glob
+import os
+import subprocess
+import time
+
+import pkg_resources
+from asimov import config
+from asimov.pipeline import Pipeline, PipelineException, PipelineLogger
+from asimov.pipelines.bilby import Bilby
+
+from .pesummary import PESummaryPipeline
+
+
+class Nullpol(Bilby):
+    """
+    The nullpol pipeline.
+
+    Parameters
+    ----------
+    production : :class:`asimov.Production`
+       The production object.
+    category : str, optional
+        The category of the job.
+        Defaults to "C01_offline".
+    """
+
+    name = "nullpol"
+    STATUS = {"wait", "stuck", "stopped", "running", "finished"}
+
+    @property
+    def config_template(self):
+        return pkg_resources.resource_filename('nullpol.asimov', 'nullpol.ini')
+
+    def __init__(self, production, category=None):
+        Pipeline.__init__(self, production=production, category=category)
+        self.logger.info("Using the nullpol pipeline")
+
+        if not production.pipeline.lower() == "nullpol":
+            raise PipelineException(f'Pipeline {production.pipeline.lower()} '
+                                    'is not recognized.')
+
+    def detect_completion(self):
+        """
+        Check for the production of the posterior file to signal that the job has completed.
+        """
+        self.logger.info("Checking if the nullpol job has completed")
+        results_dir = glob.glob(f"{self.production.rundir}/result")
+        config = self.read_ini(self.config_file_path)
+        expected_number_of_result_files = len(self.production.meta['likelihood']['polarization modes'])
+        if len(results_dir) > 0:  # dynesty_merge_result.json
+            results_files = glob.glob(
+                os.path.join(results_dir[0], "*merge*_result.hdf5")
+            )
+            results_files += glob.glob(
+                os.path.join(results_dir[0], "*merge*_result.json")
+            )
+            self.logger.debug(f"results files {results_files}")
+            if len(results_files) == expected_number_of_result_files:
+                self.logger.info(f"{len(results_files)} result files found, the job is finished.")
+                return True
+            elif len(results_files) > 0:
+                self.logger.info(f"{len(results_files)} < {expected_number_of_result_files} result files found, the job is not finished.")
+            else:
+                self.logger.info("No results files found.")
+                return False
+        else:
+            self.logger.info("No results directory found")
+            return False
+
+    def subrun_samples(self, subrun_label, absolute=False):
+        """
+        Collect the combined samples file for PESummary.
+        """
+
+        if absolute:
+            rundir = os.path.abspath(self.production.rundir)
+        else:
+            rundir = self.production.rundir
+        self.logger.info(f"Rundir for samples: {rundir}")
+        return glob.glob(
+            os.path.join(rundir, "result", f"*_{subrun_label}_merge*_result.hdf5")
+        ) + glob.glob(os.path.join(rundir, "result", f"*_{subrun_label}_merge*_result.json"))
+
+    def after_completion(self):
+        post_pipeline = PESummaryPipeline(production=self.production)
+        self.logger.info("Job has completed. Running PE Summary.")
+        cluster = post_pipeline.submit_dag()
+        self.production.meta["job id"] = int(cluster)
+        self.production.status = "processing"
+        self.production.event.update_data()
+
+    @property
+    def config_file_path(self):
+        """Path of the configuration file.
+
+        Returns:
+            str: Path of the configuration file.
+        """
+        cwd = os.getcwd()
+        if self.production.event.repository:
+            ini = self.production.event.repository.find_prods(
+                self.production.name, self.category
+            )[0]
+            ini = os.path.join(cwd, ini)
+        else:
+            ini = f"{self.production.name}.ini"
+        return ini
+
+    def build_dag(self, psds=None, user=None, clobber_psd=False, dryrun=False):
+        """
+        Construct a DAG file in order to submit a production to the
+        condor scheduler using nullpol_pipe.
+
+        Args:
+            production (str): The production name.
+        psds (dict, optional): The PSDs which should be used for this DAG. If no PSDs are
+           provided the PSD files specified in the ini file will be used
+           instead.
+        user (str): The user accounting tag which should be used to run the job.
+        dryrun (bool): If set to true the commands will not be run, but will be printed to
+           standard output. Defaults to False.
+
+        Raises:
+            PipelineException: Raised if the construction of the DAG fails.
+        """
+
+        cwd = os.getcwd()
+
+        self.logger.info(f"Working in {cwd}")
+
+        if self.production.rundir:
+            rundir = self.production.rundir
+        else:
+            rundir = os.path.join(
+                os.path.expanduser("~"),
+                self.production.event.name,
+                self.production.name,
+            )
+            self.production.rundir = rundir
+
+        if "job label" in self.production.meta:
+            job_label = self.production.meta["job label"]
+        else:
+            job_label = self.production.name
+
+        command = [
+            os.path.join(config.get("pipelines", "environment"),
+                         "bin",
+                         "nullpol_pipe"),
+            self.config_file_path,
+            "--label",
+            job_label,
+            "--outdir",
+            f"{os.path.abspath(self.production.rundir)}",
+        ]
+
+        if "accounting group" in self.production.meta:
+            command += [
+                "--accounting",
+                f"{self.production.meta['scheduler']['accounting group']}",
+            ]
+        else:
+            self.logger.warning(
+                "This nullpol Job does not supply any accounting"
+                " information, which may prevent it running"
+                " on some clusters."
+            )
+
+        if dryrun:
+            print(" ".join(command))
+        else:
+            self.logger.info(" ".join(command))
+            pipe = subprocess.Popen(
+                command, stdout=subprocess.PIPE, stderr=subprocess.STDOUT
+            )
+            out, err = pipe.communicate()
+            self.logger.info(out)
+
+            expected_out = 'DAG generation complete, to submit jobs'
+            if err or expected_out not in str(out):
+                self.production.status = "stuck"
+                self.logger.error(err)
+                raise PipelineException(
+                    (f'DAG file could not be created.\n'
+                     f'{command}\n{out}\n\n{err}'),
+                    production=self.production.name,
+                )
+            else:
+                time.sleep(10)
+                return PipelineLogger(message=out,
+                                      production=self.production.name)

nullpol/asimov/nullpol.ini

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+{%- if production.event.repository -%}
+{%- assign repo_dir = production.event.repository.directory -%}
+{%- else -%}
+{%- assign repo_dir = '.' -%}
+{%- endif -%}
+{%- if production.meta['likelihood'] contains 'calibration' -%}
+{%- assign calibration_on = production.meta['likelihood']['calibration']['sample'] -%}
+{%- else -%}
+{%- assign calibration_on = True %}
+{%- endif -%}
+{%- assign meta = production.meta -%}
+{%- assign sampler = production.meta['sampler'] -%}
+{%- assign scheduler = production.meta['scheduler'] -%}
+{%- assign likelihood = production.meta['likelihood'] -%}
+{%- assign priors = production.meta['priors'] -%}
+{%- assign data = production.meta['data'] -%}
+{%- assign quality = production.meta['quality'] -%}
+{%- assign ifos = production.meta['interferometers'] -%}
+{%- assign gr_pe_info = production.meta['gr pe info'] -%}
+
+{%- if data contains 'calibration' %}
+{%- if calibration_on %}
+{%- if data['calibration'] contains ifos[0] %}
+################################################################################
+## Calibration arguments
+################################################################################
+calibration-model=CubicSpline
+spline-calibration-envelope-dict={ {% for ifo in ifos %}{{ifo}}:{{data['calibration'][ifo]}},{% endfor %} }
+spline-calibration-nodes=10
+spline-calibration-amplitude-uncertainty-dict=None
+spline-calibration-phase-uncertainty-dict=None
+calibration-correction-type=data
+{%- if priors contains 'calibration' %}
+calibration-prior-boundary={{ priors['calibration']['boundary'] | default: reflective }}
+{%- endif %}
+{%- endif %}
+{%- endif %}
+{%- endif %}
+
+################################################################################
+## Data generation arguments
+################################################################################
+
+ignore-gwpy-data-quality-check=True
+gps-tuple=None
+gps-file=None
+timeslide-file=None
+timeslide-dict=None
+trigger-time={{ production.meta['event time'] }}
+gaussian-noise=False
+n-simulation=0
+{%- if data['data files'].size > 0 %}
+data-dict={ {% for ifo in ifos %}{{ifo}}:{{data['data files'][ifo]}},{% endfor %} }
+{%- else %}
+data-dict=None
+{%- endif %}
+data-format={{ data['format'] | default: 'gwf' }}
+channel-dict={ {% for ifo in ifos %}{{ifo}}:{{data['channels'][ifo]}},{% endfor %} }
+{%- if data contains 'frame types' %}
+frame-type-dict={ {% for ifo in ifos %}{{ifo}}:{{data['frame types'][ifo]}},{% endfor %} }
+{%- endif %}
+
+################################################################################
+## Detector arguments
+################################################################################
+
+detectors={{ ifos }}
+duration={{ data['segment length'] }}
+generation-seed=42
+psd-dict={ {% for ifo in ifos %}{{ifo}}:{{production.psds[ifo]}},{% endfor %} }
+psd-fractional-overlap=0.5
+post-trigger-duration={{ likelihood['post trigger time'] | default: 2.0 }}
+sampling-frequency={{ likelihood['sample rate'] | round }}
+psd-length={{ likelihood['psd length'] | round }}
+psd-maximum-duration=1024
+psd-method=median
+psd-start-time=None
+minimum-frequency={ {% for ifo in ifos %}{{ifo}}:{{quality['minimum frequency'][ifo]}},{% endfor %}{% if likelihood contains 'start frequency'%} waveform: {{ likelihood['start frequency'] }} {% endif %} }
+maximum-frequency={ {% for ifo in ifos %}{{ifo}}:{{quality['maximum frequency'][ifo]}},{% endfor %} }
+zero-noise=False
+tukey-roll-off={{ likelihood['roll off time'] | default: 0.4 }}
+resampling-method=lal
+
+################################################################################
+## Injection arguments
+################################################################################
+
+injection=False
+injection-dict=None
+injection-file=None
+injection-numbers=None
+injection-waveform-approximant=None
+injection-frequency-domain-source-model=None
+injection-waveform-arguments=None
+
+################################################################################
+## Job submission arguments
+################################################################################
+
+{%- if scheduler contains 'accounting group' %}
+accounting={{ scheduler['accounting group'] }}
+accounting-user = {{ scheduler['accounting user'] }}
+{%- else %}
+accounting=not.required.here
+accounting-user = {{ config['condor']['user'] }}
+{%- endif %}
+label={{ production.name }}
+local=False
+local-generation={{ scheduler['local generation'] | default: False }}
+local-plot=False
+outdir={{ production.rundir }}
+periodic-restart-time={{ scheduler['periodic restart time'] | default: 28800 }}
+request-memory={{ scheduler['request memory'] | default: 4.0}}
+request-memory-generation={{ scheduler['request generation memory'] | default: None }}
+request-cpus={{ scheduler['request cpus'] | default: 1 }}
+request-disk={{ scheduler['request disk'] | default: 1 }}
+scheduler={{ scheduler['type'] | default: 'condor' }}
+scheduler-args=None
+scheduler-module=None
+scheduler-env=None
+transfer-files={% if scheduler['osg'] %}True{% else %}{{ scheduler['transfer files'] | default: True }}{% endif %}
+log-directory=None
+getenv=[GWDATAFIND_SERVER]
+online-pe=False
+osg={{ scheduler['osg'] | default: False }}
+desired-sites={{ scheduler['desired sites'] | default: None }}
+analysis-executable={{ config['pipelines']['environment'] }}/bin/nullpol_pipe_analysis
+environment-variables={{ scheduler['environment variables'] | default: "{'HDF5_USE_FILE_LOCKING': False, 'OMP_NUM_THREADS'=1, 'OMP_PROC_BIND'=False}" }}
+
+################################################################################
+## Likelihood arguments
+################################################################################
+
+reference-frame=sky
+time-reference=geocent
+number-of-response-curves=1000
+extra-likelihood-kwargs={{ likelihood['kwargs'] | default: 'None' }}
+likelihood-type={{ likelihood['type'] | default: 'FractionalProjectionTimeFrequencyLikelihood' }}
+polarization-modes={{ likelihood['polarization modes'] | default: '[pc, b, xy, pcb, pcxy, xyb, pcbxy, pc, xy, pcb, pcxy, xyb, pcbxy]' }}
+polarization-basis={{ likelihood['polarization basis'] | default: '[p, b, x, p, p, x, p, pc, xy, pb, px, xb, pb]' }}
+wavelet-frequency-resolution={{ likelihood['wavelet frequency resolution'] | default: 16.0 }}
+wavelet-nx={{ likelihood['wavelet nx'] | default: 4.0 }}
+
+################################################################################
+## Output arguments
+################################################################################
+
+plot-trace=False
+plot-data=False
+plot-injection=False
+plot-spectrogram=False
+plot-calibration=False
+plot-corner=False
+plot-marginal=False
+plot-skymap=True
+plot-waveform=False
+plot-format=png
+create-summary=False
+email=None
+notification=Error
+queue=None
+existing-dir=None
+webdir={{ config['general']['webroot'] }}/{{ production.event.name }}/{{ production.name }}
+summarypages-arguments=None
+result-format=hdf5
+final-result=True
+final-result-nsamples=20000
+
+################################################################################
+## Prior arguments
+################################################################################
+
+deltaT=0.2
+prior-file=None
+{%- if production.meta contains 'priors' %}
+prior-dict={
+{%- assign priors_keys = priors.keys() -%}
+{%- if priors_keys contains 'ra' or priors_keys contains 'dec' or priors_keys contains 'amplitude_' or priors_keys contains 'phase_' -%}
+{%- assign mode_list = "p,c,b,l,x,y" | split: "," -%}
+{%- assign prior_parameter_list = "amplitude_,phase_" | split: "," -%}
+{%- assign found_prior = false -%}
+{%- if priors_keys contains 'ra' and priors['ra'].keys() contains 'type' -%}
+{%- if priors['ra']['type'] contains 'DeltaFunction' and priors['ra'].keys() contains 'peak' %}
+    ra={{priors['ra']['peak']}},
+{%- elsif priors['ra']['type'] contains 'Uniform' and priors['ra'].keys() contains 'minimum' and priors['ra'].keys() contains 'maximum' %}
+    ra=Uniform(minimum={{priors['ra']['minimum']}}, maximum={{priors['ra']['maximum']}}, name='ra'),
+{%- endif -%}
+{%- endif -%}
+{%- if priors_keys contains 'dec' and priors['dec'].keys() contains 'type' %}
+{%- if priors['dec']['type'] contains 'DeltaFunction' and priors['dec'].keys() contains 'peak' %}
+    dec={{priors['dec']['peak']}},
+{%- elsif priors['dec']['type'] contains 'Uniform' and priors['dec'].keys() contains 'minimum' and priors['dec'].keys() contains 'maximum' %}
+    dec=Uniform(minimum={{priors['dec']['minimum']}}, maximum={{priors['dec']['maximum']}}, name='dec'),
+{%- endif -%}
+{%- endif -%}
+{%- for i in mode_list -%}
+{%- for j in mode_list -%}
+{%- for prior_parameter in prior_parameter_list -%}
+{%- assign parameter_name = prior_parameter | append: i | append: j -%}
+{%- if priors_keys contains parameter_name -%}
+{%- if priors[parameter_name] contains 'type' -%}
+{%- if priors[parameter_name]['type'] contains 'Uniform' and priors[parameter_name] contains 'minimum' and priors[parameter_name] contains 'maximum' %}
+    {{parameter_name}}=Uniform(minimum={{priors[parameter_name]['minimum']}}, maximum={{priors[parameter_name]['maximum']}}, name='{{parameter_name}}'),
+{%- endif -%}
+{%- endif -%}
+{%- endif -%}
+{%- endfor -%}
+{%- endfor -%}
+{%- endfor -%}
+{%- endif %}
+}
+{%- endif %}
+enforce-signal-duration={{ production.meta['waveform']['enforce signal duration'] | default: False }}
+default-prior=PolarizationPriorDict
+
+
+################################################################################
+## Post processing arguments
+################################################################################
+
+postprocessing-executable=None
+postprocessing-arguments=None
+single-postprocessing-executable=None
+single-postprocessing-arguments=None
+
+################################################################################
+## Sampler arguments
+################################################################################
+
+sampler={{sampler['sampler'] | default: 'dynesty' }}
+sampling-seed={{sampler['seed'] | default: 1 }}
+n-parallel={{ sampler['parallel jobs'] | default: 2 }}
+sampler-kwargs={{ sampler['sampler kwargs'] |  default: "{'nlive': 1000, 'naccept': 60, 'check_point_plot': True, 'check_point_delta_t': 1800, 'print_method': 'interval-60', 'sample': 'acceptance-walk'}"  }}
+
+################################################################################
+## Time-frequency clustering
+################################################################################
+
+time-frequency-clustering-method={{ likelihood['time frequency clustering method'] | default: 'maxL' }}
+time-frequency-clustering-injection-parameters-filename={{ likelihood['time frequency clustering injection parameters filename'] | default: None}}
+time-frequency-clustering-pe-samples-filename={{ likelihood['time frequency clustering pe samples filename'] | default: gr_pe_info['result file path']}}
+time-frequency-clustering-threshold={{ likelihood['time frequency clustering threshold'] | default: 1.0 }}
+time-frequency-clustering-threshold-type={{ likelihood['time frequency clustering threshold type'] | default: 'variance' }}
+time-frequency-clustering-time-padding={{ likelihood['time frequency clustering time padding'] | default: 0.1 }}
+time-frequency-clustering-frequency-padding={{ likelihood['time frequency clustering frequency padding'] | default: 1.0 }}
+time-frequency-clustering-skypoints={{ likelihood['time frequency clustering skypoints'] | default: 100 }}

nullpol/asimov/nullpol_analysis.yaml

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+kind: analysis
+name: Prod0
+pipeline: nullpol
+comment: nullpol analysis with the default settings