# Copyright (C) 2013 Ian Harry
#
# This program is free software; you can redistribute it and/or modify it
# under the terms of the GNU General Public License as published by the
# Free Software Foundation; either version 3 of the License, or (at your
# option) any later version.
#
# This program is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General
# Public License for more details.
#
# You should have received a copy of the GNU General Public License along
# with this program; if not, write to the Free Software Foundation, Inc.,
# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
#
# =============================================================================
#
# Preamble
#
# =============================================================================
#
"""
This module is responsible for setting up the template bank stage of CBC
workflows. For details about this module and its capabilities see here:
https://ldas-jobs.ligo.caltech.edu/~cbc/docs/pycbc/ahope/template_bank.html
"""
import os
import logging
import configparser as ConfigParser
import pycbc
from pycbc.workflow.core import FileList
from pycbc.workflow.core import make_analysis_dir, resolve_url_to_file
from pycbc.workflow.jobsetup import select_tmpltbank_class, sngl_ifo_job_setup
logger = logging.getLogger('pycbc.workflow.tmpltbank')
[docs]def setup_tmpltbank_workflow(workflow, science_segs, datafind_outs,
output_dir=None, psd_files=None, tags=None,
return_format=None):
'''
Setup template bank section of CBC workflow. This function is responsible
for deciding which of the various template bank workflow generation
utilities should be used.
Parameters
----------
workflow: pycbc.workflow.core.Workflow
An instanced class that manages the constructed workflow.
science_segs : Keyed dictionary of ligo.segments.segmentlist objects
scienceSegs[ifo] holds the science segments to be analysed for each
ifo.
datafind_outs : pycbc.workflow.core.FileList
The file list containing the datafind files.
output_dir : path string
The directory where data products will be placed.
psd_files : pycbc.workflow.core.FileList
The file list containing predefined PSDs, if provided.
tags : list of strings
If given these tags are used to uniquely name and identify output files
that would be produced in multiple calls to this function.
Returns
--------
tmplt_banks : pycbc.workflow.core.FileList
The FileList holding the details of all the template bank jobs.
'''
if tags is None:
tags = []
logger.info("Entering template bank generation module.")
make_analysis_dir(output_dir)
cp = workflow.cp
# Parse for options in ini file
tmpltbankMethod = cp.get_opt_tags("workflow-tmpltbank", "tmpltbank-method",
tags)
# There can be a large number of different options here, for e.g. to set
# up fixed bank, or maybe something else
if tmpltbankMethod == "PREGENERATED_BANK":
logger.info("Setting template bank from pre-generated bank(s).")
tmplt_banks = setup_tmpltbank_pregenerated(workflow, tags=tags)
# Else we assume template banks will be generated in the workflow
elif tmpltbankMethod == "WORKFLOW_INDEPENDENT_IFOS":
logger.info("Adding template bank jobs to workflow.")
tmplt_banks = setup_tmpltbank_dax_generated(workflow, science_segs,
datafind_outs, output_dir, tags=tags,
psd_files=psd_files)
elif tmpltbankMethod == "WORKFLOW_INDEPENDENT_IFOS_NODATA":
logger.info("Adding template bank jobs to workflow.")
tmplt_banks = setup_tmpltbank_without_frames(workflow, output_dir,
tags=tags, independent_ifos=True,
psd_files=psd_files)
elif tmpltbankMethod == "WORKFLOW_NO_IFO_VARIATION_NODATA":
logger.info("Adding template bank jobs to workflow.")
tmplt_banks = setup_tmpltbank_without_frames(workflow, output_dir,
tags=tags, independent_ifos=False,
psd_files=psd_files)
else:
errMsg = "Template bank method not recognized. Must be either "
errMsg += "PREGENERATED_BANK, WORKFLOW_INDEPENDENT_IFOS "
errMsg += "or WORKFLOW_INDEPENDENT_IFOS_NODATA."
raise ValueError(errMsg)
# Check the format of the input template bank file and return it in
# the format requested as per return_format, provided a conversion
# between the two specific formats has been implemented. Currently,
# a conversion from xml.gz or xml to hdf is supported, but not vice
# versa. If a return_format is not specified the function returns
# the bank in the format as it was inputted.
tmplt_bank_filename=tmplt_banks[0].name
ext = tmplt_bank_filename.split('.', 1)[1]
logger.info("Input bank is a %s file", ext)
if return_format is None :
tmplt_banks_return = tmplt_banks
elif return_format in ('hdf', 'h5', 'hdf5'):
if ext in ('hdf', 'h5', 'hdf5') or ext in ('xml.gz' , 'xml'):
tmplt_banks_return = pycbc.workflow.convert_bank_to_hdf(workflow,
tmplt_banks, "bank")
else :
if ext == return_format:
tmplt_banks_return = tmplt_banks
else:
raise NotImplementedError("{0} to {1} conversion is not "
"supported.".format(ext, return_format))
logger.info("Leaving template bank generation module.")
return tmplt_banks_return
[docs]def setup_tmpltbank_dax_generated(workflow, science_segs, datafind_outs,
output_dir, tags=None,
psd_files=None):
'''
Setup template bank jobs that are generated as part of the CBC workflow.
This function will add numerous jobs to the CBC workflow using
configuration options from the .ini file. The following executables are
currently supported:
* lalapps_tmpltbank
* pycbc_geom_nonspin_bank
Parameters
----------
workflow: pycbc.workflow.core.Workflow
An instanced class that manages the constructed workflow.
science_segs : Keyed dictionary of ligo.segments.segmentlist objects
scienceSegs[ifo] holds the science segments to be analysed for each
ifo.
datafind_outs : pycbc.workflow.core.FileList
The file list containing the datafind files.
output_dir : path string
The directory where data products will be placed.
tags : list of strings
If given these tags are used to uniquely name and identify output files
that would be produced in multiple calls to this function.
psd_file : pycbc.workflow.core.FileList
The file list containing predefined PSDs, if provided.
Returns
--------
tmplt_banks : pycbc.workflow.core.FileList
The FileList holding the details of all the template bank jobs.
'''
if tags is None:
tags = []
cp = workflow.cp
# Need to get the exe to figure out what sections are analysed, what is
# discarded etc. This should *not* be hardcoded, so using a new executable
# will require a bit of effort here ....
ifos = science_segs.keys()
tmplt_bank_exe = os.path.basename(cp.get('executables', 'tmpltbank'))
# Select the appropriate class
exe_class = select_tmpltbank_class(tmplt_bank_exe)
# Set up class for holding the banks
tmplt_banks = FileList([])
for ifo in ifos:
job_instance = exe_class(workflow.cp, 'tmpltbank', ifo=ifo,
out_dir=output_dir,
tags=tags)
# Check for the write_psd flag
if cp.has_option_tags("workflow-tmpltbank", "tmpltbank-write-psd-file", tags):
job_instance.write_psd = True
else:
job_instance.write_psd = False
sngl_ifo_job_setup(workflow, ifo, tmplt_banks, job_instance,
science_segs[ifo], datafind_outs,
allow_overlap=True)
return tmplt_banks
[docs]def setup_tmpltbank_without_frames(workflow, output_dir,
tags=None, independent_ifos=False,
psd_files=None):
'''
Setup CBC workflow to use a template bank (or banks) that are generated in
the workflow, but do not use the data to estimate a PSD, and therefore do
not vary over the duration of the workflow. This can either generate one
bank that is valid for all ifos at all times, or multiple banks that are
valid only for a single ifo at all times (one bank per ifo).
Parameters
----------
workflow: pycbc.workflow.core.Workflow
An instanced class that manages the constructed workflow.
output_dir : path string
The directory where the template bank outputs will be placed.
tags : list of strings
If given these tags are used to uniquely name and identify output files
that would be produced in multiple calls to this function.
independent_ifos : Boolean, optional (default=False)
If given this will produce one template bank per ifo. If not given
there will be on template bank to cover all ifos.
psd_file : pycbc.workflow.core.FileList
The file list containing predefined PSDs, if provided.
Returns
--------
tmplt_banks : pycbc.workflow.core.FileList
The FileList holding the details of the template bank(s).
'''
if tags is None:
tags = []
cp = workflow.cp
# Need to get the exe to figure out what sections are analysed, what is
# discarded etc. This should *not* be hardcoded, so using a new executable
# will require a bit of effort here ....
ifos = workflow.ifos
fullSegment = workflow.analysis_time
tmplt_bank_exe = os.path.basename(cp.get('executables','tmpltbank'))
# Can not use lalapps_template bank with this
if tmplt_bank_exe == 'lalapps_tmpltbank':
errMsg = "Lalapps_tmpltbank cannot be used to generate template banks "
errMsg += "without using frames. Try another code."
raise ValueError(errMsg)
# Select the appropriate class
exe_instance = select_tmpltbank_class(tmplt_bank_exe)
tmplt_banks = FileList([])
# Make the distinction between one bank for all ifos and one bank per ifo
if independent_ifos:
ifoList = [ifo for ifo in ifos]
else:
ifoList = [[ifo for ifo in ifos]]
# Check for the write_psd flag
if cp.has_option_tags("workflow-tmpltbank", "tmpltbank-write-psd-file", tags):
exe_instance.write_psd = True
else:
exe_instance.write_psd = False
for ifo in ifoList:
job_instance = exe_instance(workflow.cp, 'tmpltbank', ifo=ifo,
out_dir=output_dir,
tags=tags,
psd_files=psd_files)
node = job_instance.create_nodata_node(fullSegment)
workflow.add_node(node)
tmplt_banks += node.output_files
return tmplt_banks
[docs]def setup_tmpltbank_pregenerated(workflow, tags=None):
'''
Setup CBC workflow to use a pregenerated template bank.
The bank given in cp.get('workflow','pregenerated-template-bank') will be used
as the input file for all matched-filtering jobs. If this option is
present, workflow will assume that it should be used and not generate
template banks within the workflow.
Parameters
----------
workflow: pycbc.workflow.core.Workflow
An instanced class that manages the constructed workflow.
tags : list of strings
If given these tags are used to uniquely name and identify output files
that would be produced in multiple calls to this function.
Returns
--------
tmplt_banks : pycbc.workflow.core.FileList
The FileList holding the details of the template bank.
'''
if tags is None:
tags = []
# Currently this uses the *same* fixed bank for all ifos.
# Maybe we want to add capability to analyse separate banks in all ifos?
# Set up class for holding the banks
tmplt_banks = FileList([])
cp = workflow.cp
global_seg = workflow.analysis_time
file_attrs = {'segs' : global_seg, 'tags' : tags}
try:
# First check if we have a bank for all ifos
pre_gen_bank = cp.get_opt_tags('workflow-tmpltbank',
'tmpltbank-pregenerated-bank', tags)
file_attrs['ifos'] = workflow.ifos
curr_file = resolve_url_to_file(pre_gen_bank, attrs=file_attrs)
tmplt_banks.append(curr_file)
except ConfigParser.Error:
# Okay then I must have banks for each ifo
for ifo in workflow.ifos:
try:
pre_gen_bank = cp.get_opt_tags('workflow-tmpltbank',
'tmpltbank-pregenerated-bank-%s' % ifo.lower(),
tags)
file_attrs['ifos'] = [ifo]
curr_file = resolve_url_to_file(pre_gen_bank, attrs=file_attrs)
tmplt_banks.append(curr_file)
except ConfigParser.Error:
err_msg = "Cannot find pregerated template bank in section "
err_msg += "[workflow-tmpltbank] or any tagged sections. "
if tags:
tagged_secs = " ".join("[workflow-tmpltbank-%s]" \
%(ifo,) for ifo in workflow.ifos)
err_msg += "Tagged sections are %s. " %(tagged_secs,)
err_msg += "I looked for 'tmpltbank-pregenerated-bank' option "
err_msg += "and 'tmpltbank-pregenerated-bank-%s'." %(ifo,)
raise ConfigParser.Error(err_msg)
return tmplt_banks