def save_veto_definer(cp, out_dir, tags=None):
""" Retrieve the veto definer file and save it locally
Parameters
-----------
cp : ConfigParser instance
out_dir : path
tags : list of strings
Used to retrieve subsections of the ini file for
configuration options.
"""
if tags is None:
tags = []
make_analysis_dir(out_dir)
veto_def_url = cp.get_opt_tags("workflow-segments",
"segments-veto-definer-url", tags)
veto_def_base_name = os.path.basename(veto_def_url)
veto_def_new_path = os.path.abspath(
os.path.join(out_dir, veto_def_base_name))
# Don't need to do this if already done
resolve_url(veto_def_url, out_dir)
# and update location
cp.set("workflow-segments", "segments-veto-definer-file",
veto_def_new_path)
return veto_def_new_path
def setup_psd_pregenerated(workflow, tags=None):
'''
Setup CBC workflow to use pregenerated psd files.
The file given in cp.get('workflow','pregenerated-psd-file-(ifo)') will
be used as the --psd-file argument to geom_nonspinbank, geom_aligned_bank
and pycbc_plot_psd_file.
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
--------
psd_files : pycbc.workflow.core.FileList
The FileList holding the gating files
'''
if tags is None:
tags = []
psd_files = FileList([])
cp = workflow.cp
global_seg = workflow.analysis_time
user_tag = "PREGEN_PSD"
# Check for one psd for all ifos
try:
pre_gen_file = cp.get_opt_tags('workflow-psd',
'psd-pregenerated-file', tags)
pre_gen_file = resolve_url(pre_gen_file)
file_url = urljoin('file:', pathname2url(pre_gen_file))
curr_file = File(workflow.ifos, user_tag, global_seg, file_url,
tags=tags)
curr_file.PFN(file_url, site='local')
psd_files.append(curr_file)
except ConfigParser.Error:
# Check for one psd per ifo
for ifo in workflow.ifos:
try:
pre_gen_file = cp.get_opt_tags('workflow-psd',
'psd-pregenerated-file-%s' % ifo.lower(),
tags)
pre_gen_file = resolve_url(pre_gen_file)
file_url = urljoin('file:', pathname2url(pre_gen_file))
curr_file = File(ifo, user_tag, global_seg, file_url,
tags=tags)
curr_file.PFN(file_url, site='local')
psd_files.append(curr_file)
except ConfigParser.Error:
# It's unlikely, but not impossible, that only some ifos
# will have pregenerated PSDs
logging.warn("No psd file specified for IFO %s." % (ifo,))
pass
return psd_files
def setup_psd_pregenerated(workflow, tags=[]):
'''
Setup CBC workflow to use pregenerated psd files.
The file given in cp.get('workflow','pregenerated-psd-file-(ifo)') will
be used as the --psd-file argument to geom_nonspinbank, geom_aligned_bank
and pycbc_plot_psd_file.
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
--------
psd_files : pycbc.workflow.core.FileList
The FileList holding the gating files
'''
psd_files = FileList([])
cp = workflow.cp
global_seg = workflow.analysis_time
user_tag = "PREGEN_PSD"
# Check for one psd for all ifos
try:
pre_gen_file = cp.get_opt_tags('workflow-psd',
'psd-pregenerated-file', tags)
pre_gen_file = resolve_url(pre_gen_file)
file_url = urlparse.urljoin('file:',
urllib.pathname2url(pre_gen_file))
curr_file = File(workflow.ifos, user_tag, global_seg, file_url,
tags=tags)
curr_file.PFN(file_url, site='local')
psd_files.append(curr_file)
except ConfigParser.Error:
# Check for one psd per ifo
for ifo in workflow.ifos:
try:
pre_gen_file = cp.get_opt_tags('workflow-psd',
'psd-pregenerated-file-%s' % ifo.lower(),
tags)
pre_gen_file = resolve_url(pre_gen_file)
file_url = urlparse.urljoin('file:',
urllib.pathname2url(pre_gen_file))
curr_file = File(ifo, user_tag, global_seg, file_url,
tags=tags)
curr_file.PFN(file_url, site='local')
psd_files.append(curr_file)
except ConfigParser.Error:
# It's unlikely, but not impossible, that only some ifos
# will have pregenerated PSDs
logging.warn("No psd file specified for IFO %s." % (ifo,))
pass
return psd_files
def get_ipn_sky_files(workflow, file_url, tags=None):
'''
Retreive the sky point files for searching over the IPN error box and
populating it with injections.
Parameters
----------
workflow: pycbc.workflow.core.Workflow
An instanced class that manages the constructed workflow.
file_url : string
The URL of the IPN sky points file.
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
--------
sky_points_file : pycbc.workflow.core.File
File object representing the IPN sky points file.
'''
tags = tags or []
ipn_sky_points = resolve_url(file_url)
sky_points_url = urlparse.urljoin("file:",
urllib.pathname2url(ipn_sky_points))
sky_points_file = File(workflow.ifos,
"IPN_SKY_POINTS",
workflow.analysis_time,
file_url=sky_points_url,
tags=tags)
sky_points_file.PFN(sky_points_url, site="local")
return sky_points_file
def get_ipn_sky_files(workflow, file_url, tags=None):
'''
Retreive the sky point files for searching over the IPN error box and
populating it with injections.
Parameters
----------
workflow: pycbc.workflow.core.Workflow
An instanced class that manages the constructed workflow.
file_url : string
The URL of the IPN sky points file.
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
--------
sky_points_file : pycbc.workflow.core.File
File object representing the IPN sky points file.
'''
tags = tags or []
ipn_sky_points = resolve_url(file_url)
sky_points_url = urlparse.urljoin("file:",
urllib.pathname2url(ipn_sky_points))
sky_points_file = File(workflow.ifos, "IPN_SKY_POINTS",
workflow.analysis_time, file_url=sky_points_url, tags=tags)
sky_points_file.PFN(sky_points_url, site="local")
return sky_points_file
def get_ipn_sky_files(workflow, tags=None):
'''
Retreive the sky point files for searching over the IPN error box and
populating it with injections.
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
--------
cp : pycbc.workflow.core.Workflow
The parsed configuration options for the workflow
ipn_files : pycbc.workflow.core.FileList
FileList holding the details of the IPN sky point files.
'''
if tags is None:
tags = []
cp = workflow.cp
ipn_search_points = cp.get("workflow-inspiral", "ipn-search-points")
ipn_search_points = resolve_url(ipn_search_points)
search_points_url = urlparse.urljoin(
"file:", urllib.pathname2url(ipn_search_points))
search_points_file = File(workflow.ifos,
"SEARCH_POINTS",
workflow.analysis_time,
file_url=search_points_url,
tags=tags)
search_points_file.PFN(search_points_url, site="local")
ipn_sim_points = cp.get("workflow-injections", "ipn-sim-points")
ipn_sim_points = resolve_url(ipn_sim_points)
sim_points_url = urlparse.urljoin("file:",
urllib.pathname2url(ipn_sim_points))
sim_points_file = File(workflow.ifos,
"SIM_POINTS",
workflow.analysis_time,
file_url=sim_points_url,
tags=tags)
sim_points_file.PFN(sim_points_url, site="local")
return search_points_file, sim_points_file
def get_ipn_sky_files(workflow, tags=None):
'''
Retreive the sky point files for searching over the IPN error box and
populating it with injections.
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
--------
cp : pycbc.workflow.core.Workflow
The parsed configuration options for the workflow
ipn_files : pycbc.workflow.core.FileList
FileList holding the details of the IPN sky point files.
'''
if tags is None:
tags = []
cp = workflow.cp
ipn_search_points = cp.get("workflow-inspiral", "ipn-search-points")
ipn_search_points = resolve_url(ipn_search_points)
search_points_url = urlparse.urljoin("file:",
urllib.pathname2url(ipn_search_points))
search_points_file = File(workflow.ifos, "SEARCH_POINTS",
workflow.analysis_time, file_url=search_points_url, tags=tags)
search_points_file.PFN(search_points_url, site="local")
ipn_sim_points = cp.get("workflow-injections", "ipn-sim-points")
ipn_sim_points = resolve_url(ipn_sim_points)
sim_points_url = urlparse.urljoin("file:",
urllib.pathname2url(ipn_sim_points))
sim_points_file = File(workflow.ifos, "SIM_POINTS", workflow.analysis_time,
file_url=sim_points_url, tags=tags)
sim_points_file.PFN(sim_points_url, site="local")
return search_points_file, sim_points_file
def setup_gate_pregenerated(workflow, output_dir=None, tags=None):
'''
Setup CBC workflow to use pregenerated gating files.
The file given in cp.get('workflow','gating-file-(ifo)') will
be used as the --gating-file for all jobs for that ifo.
Parameters
----------
workflow: pycbc.workflow.core.Workflow
An instanced class that manages the constructed workflow.
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.
Returns
--------
gate_files : pycbc.workflow.core.FileList
The FileList holding the gating files
'''
if tags is None:
tags = []
gate_files = FileList([])
cp = workflow.cp
global_seg = workflow.analysis_time
user_tag = "PREGEN_GATE"
for ifo in workflow.ifos:
try:
pre_gen_file = cp.get_opt_tags('workflow-gating',
'gating-file-%s' % ifo.lower(),
tags)
pre_gen_file = resolve_url(pre_gen_file,
os.path.join(os.getcwd(),output_dir))
file_url = urlparse.urljoin('file:',
urllib.pathname2url(pre_gen_file))
curr_file = File(ifo, user_tag, global_seg, file_url,
tags=tags)
curr_file.PFN(file_url, site='local')
gate_files.append(curr_file)
logging.info("Using gating file %s for %s", file_url, ifo)
except ConfigParser.Error:
logging.info("No gating file specified for %s", ifo)
return gate_files
def setup_gate_pregenerated(workflow, output_dir=None, tags=None):
'''
Setup CBC workflow to use pregenerated gating files.
The file given in cp.get('workflow','gating-file-(ifo)') will
be used as the --gating-file for all jobs for that ifo.
Parameters
----------
workflow: pycbc.workflow.core.Workflow
An instanced class that manages the constructed workflow.
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.
Returns
--------
gate_files : pycbc.workflow.core.FileList
The FileList holding the gating files
'''
if tags is None:
tags = []
gate_files = FileList([])
cp = workflow.cp
global_seg = workflow.analysis_time
user_tag = "PREGEN_GATE"
for ifo in workflow.ifos:
try:
pre_gen_file = cp.get_opt_tags('workflow-gating',
'gating-file-%s' % ifo.lower(),
tags)
pre_gen_file = resolve_url(pre_gen_file,
os.path.join(os.getcwd(), output_dir))
file_url = urlparse.urljoin('file:',
urllib.pathname2url(pre_gen_file))
curr_file = File(ifo, user_tag, global_seg, file_url, tags=tags)
curr_file.PFN(file_url, site='local')
gate_files.append(curr_file)
logging.info("Using gating file %s for %s", file_url, ifo)
except ConfigParser.Error:
logging.info("No gating file specified for %s", ifo)
return gate_files
def setup_gate_pregenerated(workflow, tags=None):
'''
Setup CBC workflow to use pregenerated gating files.
The file given in cp.get('workflow','pregenerated-gating-file-(ifo)') will
be used as the --gating-file for all matched-filtering jobs for that ifo.
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
--------
gate_files : pycbc.workflow.core.FileList
The FileList holding the gating files
'''
if tags is None:
tags = []
gate_files = FileList([])
cp = workflow.cp
global_seg = workflow.analysis_time
user_tag = "PREGEN_GATE"
for ifo in workflow.ifos:
try:
pre_gen_file = cp.get_opt_tags(
'workflow-gating', 'gating-pregenerated-file-%s' % ifo.lower(),
tags)
pre_gen_file = resolve_url(pre_gen_file)
file_url = urlparse.urljoin('file:',
urllib.pathname2url(pre_gen_file))
curr_file = File(ifo, user_tag, global_seg, file_url, tags=tags)
curr_file.PFN(file_url, site='local')
gate_files.append(curr_file)
except ConfigParser.Error:
# It's unlikely, but not impossible, that only some ifos
# will be gated
logging.warn("No gating file specified for IFO %s." % (ifo, ))
pass
return gate_files
def setup_gate_pregenerated(workflow, tags=[]):
'''
Setup CBC workflow to use pregenerated gating files.
The file given in cp.get('workflow','pregenerated-gating-file-(ifo)') will
be used as the --gating-file for all matched-filtering jobs for that ifo.
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
--------
gate_files : pycbc.workflow.core.FileList
The FileList holding the gating files
'''
gate_files = FileList([])
cp = workflow.cp
global_seg = workflow.analysis_time
user_tag = "PREGEN_GATE"
for ifo in workflow.ifos:
try:
pre_gen_file = cp.get_opt_tags('workflow-gating',
'gating-pregenerated-file-%s' % ifo.lower(),
tags)
pre_gen_file = resolve_url(pre_gen_file)
file_url = urlparse.urljoin('file:',
urllib.pathname2url(pre_gen_file))
curr_file = File(ifo, user_tag, global_seg, file_url,
tags=tags)
curr_file.PFN(file_url, site='local')
gate_files.append(curr_file)
except ConfigParser.Error:
# It's unlikely, but not impossible, that only some ifos
# will be gated
logging.warn("No gating file specified for IFO %s." % (ifo,))
pass
return gate_files
def get_segments_file(workflow, name, option_name, out_dir):
"""Get cumulative segments from option name syntax for each ifo.
Use syntax of configparser string to define the resulting segment_file
e.x. option_name = +up_flag1,+up_flag2,+up_flag3,-down_flag1,-down_flag2
Each ifo may have a different string and is stored separately in the file.
Flags which add time must precede flags which subtract time.
Parameters
----------
workflow: pycbc.workflow.Workflow
name: string
Name of the segment list being created
option_name: str
Name of option in the associated config parser to get the flag list
returns
--------
seg_file: pycbc.workflow.SegFile
SegFile intance that points to the segment xml file on disk.
"""
from pycbc.dq import query_str
make_analysis_dir(out_dir)
cp = workflow.cp
start = workflow.analysis_time[0]
end = workflow.analysis_time[1]
# Check for veto definer file
veto_definer = None
if cp.has_option("workflow-segments", "segments-veto-definer-url"):
veto_definer = save_veto_definer(workflow.cp, out_dir, [])
# Check for provided server
server = "https://segments.ligo.org"
if cp.has_option("workflow-segments", "segments-database-url"):
server = cp.get("workflow-segments", "segments-database-url")
source = "any"
if cp.has_option("workflow-segments", "segments-source"):
source = cp.get("workflow-segments", "segments-source")
if source == "file":
local_file_path = \
resolve_url(cp.get("workflow-segments", option_name+"-file"))
pfn = os.path.join(out_dir, os.path.basename(local_file_path))
shutil.move(local_file_path, pfn)
return SegFile.from_segment_xml(pfn)
segs = {}
for ifo in workflow.ifos:
flag_str = cp.get_opt_tags("workflow-segments", option_name, [ifo])
key = ifo + ':' + name
segs[key] = query_str(ifo,
flag_str,
start,
end,
source=source,
server=server,
veto_definer=veto_definer)
logging.info("%s: got %s flags", ifo, option_name)
return SegFile.from_segment_list_dict(name,
segs,
extension='.xml',
valid_segment=workflow.analysis_time,
directory=out_dir)
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
user_tag = "PREGEN_TMPLTBANK"
try:
# First check if we have a bank for all ifos
pre_gen_bank = cp.get_opt_tags('workflow-tmpltbank',
'tmpltbank-pregenerated-bank', tags)
pre_gen_bank = resolve_url(pre_gen_bank)
file_url = urlparse.urljoin('file:', urllib.pathname2url(pre_gen_bank))
curr_file = File(workflow.ifos,
user_tag,
global_seg,
file_url,
tags=tags)
curr_file.PFN(file_url, site='local')
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)
pre_gen_bank = resolve_url(pre_gen_bank)
file_url = urlparse.urljoin('file:',
urllib.pathname2url(pre_gen_bank))
curr_file = File(ifo,
user_tag,
global_seg,
file_url,
tags=tags)
curr_file.PFN(file_url, site='local')
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
def setup_injection_workflow(workflow,
output_dir=None,
inj_section_name='injections',
exttrig_file=None,
tags=None):
"""
This function is the gateway for setting up injection-generation jobs in a
workflow. It should be possible for this function to support a number
of different ways/codes that could be used for doing this, however as this
will presumably stay as a single call to a single code (which need not be
inspinj) there are currently no subfunctions in this moudle.
Parameters
-----------
workflow : pycbc.workflow.core.Workflow
The Workflow instance that the coincidence jobs will be added to.
output_dir : path
The directory in which injection files will be stored.
inj_section_name : string (optional, default='injections')
The string that corresponds to the option describing the exe location
in the [executables] section of the .ini file and that corresponds to
the section (and sub-sections) giving the options that will be given to
the code at run time.
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. This will be used in output names.
Returns
--------
inj_files : pycbc.workflow.core.FileList
The list of injection files created by this call.
inj_tags : list of strings
The tag corresponding to each injection file and used to uniquely
identify them. The FileList class contains functions to search
based on tags.
"""
if tags is None:
tags = []
logging.info("Entering injection module.")
make_analysis_dir(output_dir)
# Get full analysis segment for output file naming
full_segment = workflow.analysis_time
ifos = workflow.ifos
# Identify which injections to do by presence of sub-sections in
# the configuration file
inj_tags = []
inj_files = FileList([])
for section in workflow.cp.get_subsections(inj_section_name):
inj_tag = section.upper()
curr_tags = tags + [inj_tag]
# FIXME: Remove once fixed in pipedown
# TEMPORARILY we require inj tags to end in "INJ"
if not inj_tag.endswith("INJ"):
err_msg = "Currently workflow requires injection names to end with "
err_msg += "a inj suffix. Ie. bnslininj or bbhinj. "
err_msg += "%s is not good." % (inj_tag.lower())
raise ValueError(err_msg)
# Parse for options in ini file
injection_method = workflow.cp.get_opt_tags("workflow-injections",
"injections-method",
curr_tags)
if injection_method in ["IN_WORKFLOW", "AT_RUNTIME"]:
# FIXME: Add ability to specify different exes
inj_job = LalappsInspinjExecutable(workflow.cp,
inj_section_name,
out_dir=output_dir,
ifos='HL',
tags=curr_tags)
node = inj_job.create_node(full_segment)
if injection_method == "AT_RUNTIME":
workflow.execute_node(node)
else:
workflow.add_node(node)
inj_file = node.output_files[0]
inj_files.append(inj_file)
elif injection_method == "PREGENERATED":
injectionFilePath = workflow.cp.get_opt_tags(
"workflow-injections", "injections-pregenerated-file",
curr_tags)
injectionFilePath = resolve_url(injectionFilePath)
file_url = urlparse.urljoin('file:',
urllib.pathname2url(injectionFilePath))
inj_file = File('HL',
'PREGEN_inj_file',
full_segment,
file_url,
tags=curr_tags)
inj_file.PFN(injectionFilePath, site='local')
inj_files.append(inj_file)
elif injection_method in ["IN_COH_PTF_WORKFLOW", "AT_COH_PTF_RUNTIME"]:
inj_job = LalappsInspinjExecutable(workflow.cp,
inj_section_name,
out_dir=output_dir,
ifos=ifos,
tags=curr_tags)
node = inj_job.create_node(full_segment, exttrig_file)
if injection_method == "AT_COH_PTF_RUNTIME":
workflow.execute_node(node)
else:
workflow.add_node(node)
inj_file = node.output_files[0]
if workflow.cp.has_option("workflow-injections", "em-bright-only"):
em_filter_job = PycbcDarkVsBrightInjectionsExecutable(
workflow.cp,
'em_bright_filter',
tags=curr_tags,
out_dir=output_dir,
ifos=ifos)
node = em_filter_job.create_node(inj_file, full_segment,
curr_tags)
if injection_method == "AT_COH_PTF_RUNTIME":
workflow.execute_node(node)
else:
workflow.add_node(node)
inj_file = node.output_files[0]
if workflow.cp.has_option("workflow-injections",
"do-jitter-skyloc"):
jitter_job = LigolwCBCJitterSkylocExecutable(
workflow.cp,
'jitter_skyloc',
tags=curr_tags,
out_dir=output_dir,
ifos=ifos)
node = jitter_job.create_node(inj_file, full_segment,
curr_tags)
if injection_method == "AT_COH_PTF_RUNTIME":
workflow.execute_node(node)
else:
workflow.add_node(node)
inj_file = node.output_files[0]
if workflow.cp.has_option("workflow-injections",
"do-align-total-spin"):
align_job = LigolwCBCAlignTotalSpinExecutable(
workflow.cp,
'align_total_spin',
tags=curr_tags,
out_dir=output_dir,
ifos=ifos)
node = align_job.create_node(inj_file, full_segment, curr_tags)
if injection_method == "AT_COH_PTF_RUNTIME":
workflow.execute_node(node)
else:
workflow.add_node(node)
inj_file = node.output_files[0]
inj_files.append(inj_file)
else:
err = "Injection method must be one of IN_WORKFLOW, "
err += "AT_RUNTIME or PREGENERATED. Got %s." % (injection_method)
raise ValueError(err)
inj_tags.append(inj_tag)
logging.info("Leaving injection module.")
return inj_files, inj_tags
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
user_tag = "PREGEN_TMPLTBANK"
try:
# First check if we have a bank for all ifos
pre_gen_bank = cp.get_opt_tags('workflow-tmpltbank',
'tmpltbank-pregenerated-bank', tags)
pre_gen_bank = resolve_url(pre_gen_bank)
file_url = urlparse.urljoin('file:', urllib.pathname2url(pre_gen_bank))
curr_file = File(workflow.ifos, user_tag, global_seg, file_url,
tags=tags)
curr_file.PFN(file_url, site='local')
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)
pre_gen_bank = resolve_url(pre_gen_bank)
file_url = urlparse.urljoin('file:',
urllib.pathname2url(pre_gen_bank))
curr_file = File(ifo, user_tag, global_seg, file_url,
tags=tags)
curr_file.PFN(file_url, site='local')
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
def setup_injection_workflow(workflow, output_dir=None,
inj_section_name='injections', exttrig_file=None,
tags =None):
"""
This function is the gateway for setting up injection-generation jobs in a
workflow. It should be possible for this function to support a number
of different ways/codes that could be used for doing this, however as this
will presumably stay as a single call to a single code (which need not be
inspinj) there are currently no subfunctions in this moudle.
Parameters
-----------
workflow : pycbc.workflow.core.Workflow
The Workflow instance that the coincidence jobs will be added to.
output_dir : path
The directory in which injection files will be stored.
inj_section_name : string (optional, default='injections')
The string that corresponds to the option describing the exe location
in the [executables] section of the .ini file and that corresponds to
the section (and sub-sections) giving the options that will be given to
the code at run time.
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. This will be used in output names.
Returns
--------
inj_files : pycbc.workflow.core.FileList
The list of injection files created by this call.
inj_tags : list of strings
The tag corresponding to each injection file and used to uniquely
identify them. The FileList class contains functions to search
based on tags.
"""
if tags is None:
tags = []
logging.info("Entering injection module.")
make_analysis_dir(output_dir)
# Get full analysis segment for output file naming
full_segment = workflow.analysis_time
ifos = workflow.ifos
# Identify which injections to do by presence of sub-sections in
# the configuration file
inj_tags = []
inj_files = FileList([])
for section in workflow.cp.get_subsections(inj_section_name):
inj_tag = section.upper()
curr_tags = tags + [inj_tag]
# FIXME: Remove once fixed in pipedown
# TEMPORARILY we require inj tags to end in "INJ"
if not inj_tag.endswith("INJ"):
err_msg = "Currently workflow requires injection names to end with "
err_msg += "a inj suffix. Ie. bnslininj or bbhinj. "
err_msg += "%s is not good." %(inj_tag.lower())
raise ValueError(err_msg)
# Parse for options in ini file
injection_method = workflow.cp.get_opt_tags("workflow-injections",
"injections-method",
curr_tags)
if injection_method in ["IN_WORKFLOW", "AT_RUNTIME"]:
# FIXME: Add ability to specify different exes
inj_job = LalappsInspinjExecutable(workflow.cp, inj_section_name,
out_dir=output_dir, ifos='HL',
tags=curr_tags)
node = inj_job.create_node(full_segment)
if injection_method == "AT_RUNTIME":
workflow.execute_node(node)
else:
workflow.add_node(node)
inj_file = node.output_files[0]
inj_files.append(inj_file)
elif injection_method == "PREGENERATED":
injectionFilePath = workflow.cp.get_opt_tags("workflow-injections",
"injections-pregenerated-file", curr_tags)
injectionFilePath = resolve_url(injectionFilePath)
file_url = urlparse.urljoin('file:',
urllib.pathname2url(injectionFilePath))
inj_file = File('HL', 'PREGEN_inj_file', full_segment, file_url,
tags=curr_tags)
inj_file.PFN(injectionFilePath, site='local')
inj_files.append(inj_file)
elif injection_method in ["IN_COH_PTF_WORKFLOW", "AT_COH_PTF_RUNTIME"]:
inj_job = LalappsInspinjExecutable(workflow.cp, inj_section_name,
out_dir=output_dir, ifos=ifos,
tags=curr_tags)
node = inj_job.create_node(full_segment, exttrig_file)
if injection_method == "AT_COH_PTF_RUNTIME":
workflow.execute_node(node)
else:
workflow.add_node(node)
inj_file = node.output_files[0]
if workflow.cp.has_option("workflow-injections",
"em-bright-only"):
em_filter_job = PycbcDarkVsBrightInjectionsExecutable(
workflow.cp,
'em_bright_filter',
tags=curr_tags,
out_dir=output_dir,
ifos=ifos)
node = em_filter_job.create_node(inj_file, full_segment,
curr_tags)
if injection_method == "AT_COH_PTF_RUNTIME":
workflow.execute_node(node)
else:
workflow.add_node(node)
inj_file = node.output_files[0]
if workflow.cp.has_option("workflow-injections",
"do-jitter-skyloc"):
jitter_job = LigolwCBCJitterSkylocExecutable(workflow.cp,
'jitter_skyloc',
tags=curr_tags,
out_dir=output_dir,
ifos=ifos)
node = jitter_job.create_node(inj_file, full_segment, curr_tags)
if injection_method == "AT_COH_PTF_RUNTIME":
workflow.execute_node(node)
else:
workflow.add_node(node)
inj_file = node.output_files[0]
if workflow.cp.has_option("workflow-injections",
"do-align-total-spin"):
align_job = LigolwCBCAlignTotalSpinExecutable(workflow.cp,
'align_total_spin', tags=curr_tags, out_dir=output_dir,
ifos=ifos)
node = align_job.create_node(inj_file, full_segment, curr_tags)
if injection_method == "AT_COH_PTF_RUNTIME":
workflow.execute_node(node)
else:
workflow.add_node(node)
inj_file = node.output_files[0]
inj_files.append(inj_file)
else:
err = "Injection method must be one of IN_WORKFLOW, "
err += "AT_RUNTIME or PREGENERATED. Got %s." % (injection_method)
raise ValueError(err)
inj_tags.append(inj_tag)
logging.info("Leaving injection module.")
return inj_files, inj_tags