def make_random_document(num_procs, num_seg_defs, num_segs, num_seg_sums, start_time, end_time, max_len):
"""Create a ligolw document with random segments and segment_summary"""
doc = ligolw.Document()
doc.appendChild(ligolw.LIGO_LW())
# Add some processes
proc_ids = []
seg_def_ids = {}
segment_map = {}
segment_sum_map = {}
for count in range(num_procs):
proc_id = append_process(doc, "Test program %d" % count).process_id
proc_ids.append(proc_id)
seg_def_ids[proc_id] = []
# Add some segment definers
for count in range(num_seg_defs):
proc_id = proc_ids[int(uniform(0,num_procs))]
seg_def_id = add_to_segment_definer(doc, proc_id, "H1", "TEST_SEG_%d" % count, 1)
seg_def_ids[proc_id].append(seg_def_id)
# Add some segments
sgmntlst = random_segments(start_time, end_time, num_segs, max_len)
add_to_segment(doc, proc_id, seg_def_id, sgmntlst)
sgmntlst.coalesce()
segment_map["TEST_SEG_%d" % count] = sgmntlst
# Add some segment summaries
sgmntlst = random_segments(start_time, end_time, num_segs, max_len)
add_to_segment_summary(doc, proc_id, seg_def_id, sgmntlst)
sgmntlst.coalesce()
segment_sum_map["TEST_SEG_%d" % count] = sgmntlst
return doc, segment_map, segment_sum_map
def add_segment_info_ns(doc, proc_id, segdefs, segments, segment_summaries):
for i in range(len(segdefs)):
ifo, name, version, start_time, end_time, start_pad, end_pad = segdefs[i]
seg_def_id = segmentdb_utils.add_to_segment_definer(doc, proc_id, ifo, name, version)
add_to_segment_summary_ns(doc, proc_id, seg_def_id, segment_summaries[i])
if segments:
add_to_segment_ns(doc, proc_id, seg_def_id, segments[i])
def run_segment_operation(outdoc, filenames, segments, use_segment_table, operation, result_name = 'RESULT', preserve = True):
"""
Performs an operation (intersect or union) across a set of segments.
That is, given a set of files each with segment definers DMT-FLAG1,
DMT-FLAG2 etc and a list of segments DMT-FLAG1,DMT-FLAG1 this returns
RESULT = (table 1's DMT-FLAG1 union table 2's DMT-FLAG1 union ...)
operation
(table 1's DMT-FLAG2 union table 2's DMT-FLAG2 union ...)
operation
etc
"""
proc_id = table.get_table(outdoc, lsctables.ProcessTable.tableName)[0].process_id
if preserve:
indoc = ligolw_add.ligolw_add(outdoc, filenames)
else:
indoc = ligolw_add.ligolw_add(ligolw.Document(), filenames)
# Start with a segment covering all of time, then
# intersect with each of the fields of interest
keys = segments.split(',')
if operation == INTERSECT:
sgmntlist = glue.segments.segmentlist([glue.segments.segment(-glue.segments.infinity(), glue.segments.infinity())])
for key in keys:
sgmntlist &= find_segments(indoc, key, use_segment_table)
elif operation == UNION:
sgmntlist = glue.segments.segmentlist([])
for key in keys:
sgmntlist |= find_segments(indoc, key, use_segment_table)
elif operation == DIFF:
sgmntlist = find_segments(indoc, keys[0], use_segment_table)
for key in keys[1:]:
sgmntlist -= find_segments(indoc, key, use_segment_table)
else:
raise NameError("%s is not a known operation (intersect, union or diff)" % operation)
# Add a segment definer and segments
seg_def_id = add_to_segment_definer(outdoc, proc_id, '', result_name, 1)
if use_segment_table:
add_to_segment(outdoc, proc_id, seg_def_id, sgmntlist)
else:
add_to_segment_summary(outdoc, proc_id, seg_def_id, sgmntlist)
return outdoc, abs(sgmntlist)
def run_segment_operation(outdoc, filenames, segments, use_segment_table, operation, result_name = 'RESULT', preserve = True):
"""
Performs an operation (intersect or union) across a set of segments.
That is, given a set of files each with segment definers DMT-FLAG1,
DMT-FLAG2 etc and a list of segments DMT-FLAG1,DMT-FLAG1 this returns
RESULT = (table 1's DMT-FLAG1 union table 2's DMT-FLAG1 union ...)
operation
(table 1's DMT-FLAG2 union table 2's DMT-FLAG2 union ...)
operation
etc
"""
proc_id = lsctables.ProcessTable.get_table(outdoc)[0].process_id
if preserve:
indoc = ligolw_add.ligolw_add(outdoc, filenames)
else:
indoc = ligolw_add.ligolw_add(ligolw.Document(), filenames)
# Start with a segment covering all of time, then
# intersect with each of the fields of interest
keys = segments.split(',')
if operation == INTERSECT:
sgmntlist = glue.segments.segmentlist([glue.segments.segment(-glue.segments.infinity(), glue.segments.infinity())])
for key in keys:
sgmntlist &= find_segments(indoc, key, use_segment_table)
elif operation == UNION:
sgmntlist = glue.segments.segmentlist([])
for key in keys:
sgmntlist |= find_segments(indoc, key, use_segment_table)
elif operation == DIFF:
sgmntlist = find_segments(indoc, keys[0], use_segment_table)
for key in keys[1:]:
sgmntlist -= find_segments(indoc, key, use_segment_table)
else:
raise NameError("%s is not a known operation (intersect, union or diff)" % operation)
# Add a segment definer and segments
seg_def_id = add_to_segment_definer(outdoc, proc_id, '', result_name, 1)
if use_segment_table:
add_to_segment(outdoc, proc_id, seg_def_id, sgmntlist)
else:
add_to_segment_summary(outdoc, proc_id, seg_def_id, sgmntlist)
return outdoc, abs(sgmntlist)
def add_segment_info_ns(doc, proc_id, segdefs, segments, segment_summaries):
for i in range(len(segdefs)):
ifo, name, version, start_time, end_time, start_pad, end_pad = segdefs[
i]
seg_def_id = segmentdb_utils.add_to_segment_definer(
doc, proc_id, ifo, name, version)
add_to_segment_summary_ns(doc, proc_id, seg_def_id,
segment_summaries[i])
if segments:
add_to_segment_ns(doc, proc_id, seg_def_id, segments[i])
def make_random_document(num_procs, num_seg_defs, num_segs, num_seg_sums,
start_time, end_time, max_len):
"""Create a ligolw document with random segments and segment_summary"""
doc = ligolw.Document()
doc.appendChild(ligolw.LIGO_LW())
# Add some processes
proc_ids = []
seg_def_ids = {}
segment_map = {}
segment_sum_map = {}
for count in range(num_procs):
proc_id = append_process(doc, "Test program %d" % count).process_id
proc_ids.append(proc_id)
seg_def_ids[proc_id] = []
# Add some segment definers
for count in range(num_seg_defs):
proc_id = proc_ids[int(uniform(0, num_procs))]
seg_def_id = add_to_segment_definer(doc, proc_id, "H1",
"TEST_SEG_%d" % count, 1)
seg_def_ids[proc_id].append(seg_def_id)
# Add some segments
sgmntlst = random_segments(start_time, end_time, num_segs, max_len)
add_to_segment(doc, proc_id, seg_def_id, sgmntlst)
sgmntlst.coalesce()
segment_map["TEST_SEG_%d" % count] = sgmntlst
# Add some segment summaries
sgmntlst = random_segments(start_time, end_time, num_segs, max_len)
add_to_segment_summary(doc, proc_id, seg_def_id, sgmntlst)
sgmntlst.coalesce()
segment_sum_map["TEST_SEG_%d" % count] = sgmntlst
return doc, segment_map, segment_sum_map
sciokSegFile = segIfoFiles.find_output_with_tag('SCIENCE_OK')
assert (len(sciokSegFile) == 1)
sciokSegFile = sciokSegFile[0]
sciokSegs = sciokSegFile.segmentList
# SCIENCE_AVAILABLE
sciavailableSegFile = segIfoFiles.find_output_with_tag('SCIENCE_AVAILABLE')
assert (len(sciavailableSegFile) == 1)
sciavailableSegFile = sciavailableSegFile[0]
sciavailableSegs = sciavailableSegFile.segmentList
# ANALYSABLE - This one needs to come from inspiral outs
analysableSegs = insps.get_times_covered_by_files()
# And add these to the output file
# Start with the segment summary
summSegs = segments.segmentlist([workflow.analysis_time])
sci_def_id = segmentdb_utils.add_to_segment_definer(
outdoc, proc_id, ifo, "CBC_DAYHOPE_SCIENCE", 0)
sciok_def_id = segmentdb_utils.add_to_segment_definer(
outdoc, proc_id, ifo, "CBC_DAYHOPE_SCIENCE_OK", 0)
sciavailable_def_id = segmentdb_utils.add_to_segment_definer(
outdoc, proc_id, ifo, "CBC_DAYHOPE_SCIENCE_AVAILABLE", 0)
analysable_def_id = segmentdb_utils.add_to_segment_definer(
outdoc, proc_id, ifo, "CBC_DAYHOPE_ANALYSABLE", 0)
segmentdb_utils.add_to_segment(outdoc, proc_id, sci_def_id, sciSegs)
segmentdb_utils.add_to_segment(outdoc, proc_id, sciok_def_id, sciokSegs)
segmentdb_utils.add_to_segment(outdoc, proc_id, sciavailable_def_id,
sciavailableSegs)
segmentdb_utils.add_to_segment(outdoc, proc_id, analysable_def_id,
analysableSegs)
segmentdb_utils.add_to_segment_summary(outdoc,
sciokSegFile = segIfoFiles.find_output_with_tag('SCIENCE_OK')
assert(len(sciokSegFile) == 1)
sciokSegFile = sciokSegFile[0]
sciokSegs = sciokSegFile.segmentList
# SCIENCE_AVAILABLE
sciavailableSegFile = segIfoFiles.find_output_with_tag('SCIENCE_AVAILABLE')
assert(len(sciavailableSegFile) == 1)
sciavailableSegFile = sciavailableSegFile[0]
sciavailableSegs = sciavailableSegFile.segmentList
# ANALYSABLE - This one needs to come from inspiral outs
analysableSegs = insps.get_times_covered_by_files()
# And add these to the output file
# Start with the segment summary
summSegs = segments.segmentlist([workflow.analysis_time])
sci_def_id = segmentdb_utils.add_to_segment_definer(outdoc, proc_id, ifo,
"CBC_DAYHOPE_SCIENCE", 0)
sciok_def_id = segmentdb_utils.add_to_segment_definer(outdoc, proc_id, ifo,
"CBC_DAYHOPE_SCIENCE_OK", 0)
sciavailable_def_id = segmentdb_utils.add_to_segment_definer(outdoc,
proc_id, ifo, "CBC_DAYHOPE_SCIENCE_AVAILABLE", 0)
analysable_def_id = segmentdb_utils.add_to_segment_definer(outdoc, proc_id,
ifo, "CBC_DAYHOPE_ANALYSABLE", 0)
segmentdb_utils.add_to_segment(outdoc, proc_id, sci_def_id, sciSegs)
segmentdb_utils.add_to_segment(outdoc, proc_id, sciok_def_id, sciokSegs)
segmentdb_utils.add_to_segment(outdoc, proc_id, sciavailable_def_id,
sciavailableSegs)
segmentdb_utils.add_to_segment(outdoc, proc_id, analysable_def_id,
analysableSegs)
segmentdb_utils.add_to_segment_summary(outdoc, proc_id, sci_def_id,
def run_file_operation(outdoc,
filenames,
use_segment_table,
operation,
preserve=True):
"""
Performs an operation (intersect or union) across a set of files.
That is, given a set of files each with segment definers DMT-FLAG1,
DMT-FLAG2 etc the result is a file where
DMT-FLAG1 = (file 1's DMT-FLAG1 operation file 2's DMT-FLAG1 operation ...)
DMT-FLAG2 = (file 1's DMT-FLAG2 operation file 2's DMT-FLAG2 operation ...)
etc
"""
proc_id = table.get_table(outdoc,
lsctables.ProcessTable.tableName)[0].process_id
# load up the files into individual documents
xmldocs = [
ligolw_add.ligolw_add(ligolw.Document(), [fname])
for fname in filenames
]
# Get the list of dinstinct segment_definers across all docs
segment_definers = {}
def register_definer(seg_def):
key = (seg_def.ifos, seg_def.name, seg_def.version)
segment_definers[key] = True
return key
for xmldoc in xmldocs:
seg_def_table = table.get_table(xmldoc,
lsctables.SegmentDefTable.tableName)
map(register_definer, seg_def_table)
# For each unique segment definer, find the intersection
for ifo, name, version in segment_definers:
if operation == INTERSECT:
# If I were feeling especially functional-ist I'd write this
# with reduce()
result = glue.segments.segmentlist([
glue.segments.segment(-glue.segments.infinity(),
glue.segments.infinity())
])
for xmldoc in xmldocs:
result &= find_segments(xmldoc,
'%s:%s:%d' % (ifo, name, version),
use_segment_table)
elif operation == UNION:
result = glue.segments.segmentlist([])
for xmldoc in xmldocs:
result |= find_segments(xmldoc,
'%s:%s:%d' % (ifo, name, version),
use_segment_table)
elif operation == DIFF:
result = find_segments(xmldocs[0],
'%s:%s:%d' % (ifo, name, version),
use_segment_table)
for xmldoc in xmldocs[1:]:
result -= find_segments(xmldoc,
'%s:%s:%d' % (ifo, name, version),
use_segment_table)
else:
raise NameError(
"%s is not a known operation (intersect, union or diff)" %
operation)
# Add a segment definer for the result
seg_def_id = add_to_segment_definer(outdoc, proc_id, ifo, name,
version)
# Add the segments
if use_segment_table:
add_to_segment(outdoc, proc_id, seg_def_id, result)
else:
add_to_segment_summary(outdoc, proc_id, seg_def_id, result)
# If we're preserving, also load up everything into the output document.
if preserve:
# Add them to the output document
map(lambda x: outdoc.appendChild(x.childNodes[0]), xmldocs)
# Merge the ligolw elements and tables
ligolw_add.merge_ligolws(outdoc)
ligolw_add.merge_compatible_tables(outdoc)
return outdoc, abs(result)
def run_file_operation(outdoc, filenames, use_segment_table, operation, preserve = True):
"""
Performs an operation (intersect or union) across a set of files.
That is, given a set of files each with segment definers DMT-FLAG1,
DMT-FLAG2 etc the result is a file where
DMT-FLAG1 = (file 1's DMT-FLAG1 operation file 2's DMT-FLAG1 operation ...)
DMT-FLAG2 = (file 1's DMT-FLAG2 operation file 2's DMT-FLAG2 operation ...)
etc
"""
proc_id = table.get_table(outdoc, lsctables.ProcessTable.tableName)[0].process_id
# load up the files into individual documents
xmldocs = [ligolw_add.ligolw_add(ligolw.Document(), [fname]) for fname in filenames]
# Get the list of dinstinct segment_definers across all docs
segment_definers = {}
def register_definer(seg_def):
key = (seg_def.ifos, seg_def.name, seg_def.version)
segment_definers[key] = True
return key
for xmldoc in xmldocs:
seg_def_table = table.get_table(xmldoc, lsctables.SegmentDefTable.tableName)
map (register_definer, seg_def_table)
# For each unique segment definer, find the intersection
for ifo, name, version in segment_definers:
if operation == INTERSECT:
# If I were feeling especially functional-ist I'd write this
# with reduce()
result = glue.segments.segmentlist([glue.segments.segment(-glue.segments.infinity(), glue.segments.infinity())])
for xmldoc in xmldocs:
result &= find_segments(xmldoc, '%s:%s:%d' % (ifo, name, version), use_segment_table)
elif operation == UNION:
result = glue.segments.segmentlist([])
for xmldoc in xmldocs:
result |= find_segments(xmldoc, '%s:%s:%d' % (ifo, name, version), use_segment_table)
elif operation == DIFF:
result = find_segments(xmldocs[0], '%s:%s:%d' % (ifo, name, version), use_segment_table)
for xmldoc in xmldocs[1:]:
result -= find_segments(xmldoc, '%s:%s:%d' % (ifo, name, version), use_segment_table)
else:
raise NameError ("%s is not a known operation (intersect, union or diff)" % operation)
# Add a segment definer for the result
seg_def_id = add_to_segment_definer(outdoc, proc_id, ifo, name, version)
# Add the segments
if use_segment_table:
add_to_segment(outdoc, proc_id, seg_def_id, result)
else:
add_to_segment_summary(outdoc, proc_id, seg_def_id, result)
# If we're preserving, also load up everything into the output document.
if preserve:
# Add them to the output document
map(lambda x: outdoc.appendChild(x.childNodes[0]), xmldocs)
# Merge the ligolw elements and tables
ligolw_add.merge_ligolws(outdoc)
ligolw_add.merge_compatible_tables(outdoc)
return outdoc, abs(result)
def run_query_segments(doc, process_id, engine, gps_start_time, gps_end_time, include_segments, exclude_segments, result_name):
segdefs = []
for included in include_segments.split(','):
spec = included.split(':')
if len(spec) < 2 or len(spec) > 3:
print("Included segements must be of the form ifo:name:version or ifo:name:*", file=sys.stderr)
sys.exit(1)
ifo = spec[0]
name = spec[1]
if len(spec) is 3 and spec[2] is not '*':
version = int(spec[2])
if version < 1:
print("Segment version numbers must be greater than zero", file=sys.stderr)
sys.exit(1)
else:
version = '*'
segdefs += segmentdb_utils.expand_version_number(engine, (ifo, name, version, gps_start_time, gps_end_time, 0, 0) )
found_segments = segmentdb_utils.query_segments(engine, 'segment', segdefs)
found_segments = reduce(operator.or_, found_segments).coalesce()
# We could also do:
segment_summaries = segmentdb_utils.query_segments(engine, 'segment_summary', segdefs)
# And we could write out everything we found
segmentdb_utils.add_segment_info(doc, process_id, segdefs, None, segment_summaries)
# Do the same for excluded
if exclude_segments:
ex_segdefs = []
for excluded in exclude_segments.split(','):
spec = excluded.split(':')
if len(spec) < 2:
print("Excluded segements must be of the form ifo:name:version or ifo:name:*", file=sys.stderr)
sys.exit(1)
ifo = spec[0]
name = spec[1]
version = len(spec) > 2 and spec[2] or '*'
ex_segdefs += segmentdb_utils.expand_version_number(engine, (ifo, name, version, gps_start_time, gps_end_time, 0, 0) )
excluded_segments = segmentdb_utils.query_segments(engine, 'segment', ex_segdefs)
excluded_segments = reduce(operator.or_, excluded_segments).coalesce()
found_segments.coalesce()
found_segments -= excluded_segments
# Add the result type to the segment definer table
seg_name = result_name
seg_def_id = segmentdb_utils.add_to_segment_definer(doc, process_id, ifo, seg_name, 1)
# and segment summary
segmentdb_utils.add_to_segment_summary(doc, process_id, seg_def_id, [[gps_start_time, gps_end_time]])
# and store the segments
segmentdb_utils.add_to_segment(doc, process_id, seg_def_id, found_segments)
print("Made it to the end of the query code")
print(doc)
def run_query_segments(doc, process_id, engine, gps_start_time, gps_end_time,
include_segments, exclude_segments, result_name):
segdefs = []
for included in include_segments.split(','):
spec = included.split(':')
if len(spec) < 2 or len(spec) > 3:
print >> sys.stderr, "Included segements must be of the form ifo:name:version or ifo:name:*"
sys.exit(1)
ifo = spec[0]
name = spec[1]
if len(spec) is 3 and spec[2] is not '*':
version = int(spec[2])
if version < 1:
print >> sys.stderr, "Segment version numbers must be greater than zero"
sys.exit(1)
else:
version = '*'
segdefs += segmentdb_utils.expand_version_number(
engine, (ifo, name, version, gps_start_time, gps_end_time, 0, 0))
found_segments = segmentdb_utils.query_segments(engine, 'segment', segdefs)
found_segments = reduce(operator.or_, found_segments).coalesce()
# We could also do:
segment_summaries = segmentdb_utils.query_segments(engine,
'segment_summary',
segdefs)
# And we could write out everything we found
segmentdb_utils.add_segment_info(doc, process_id, segdefs, None,
segment_summaries)
# Do the same for excluded
if exclude_segments:
ex_segdefs = []
for excluded in exclude_segments.split(','):
spec = excluded.split(':')
if len(spec) < 2:
print >> sys.stderr, "Excluded segements must be of the form ifo:name:version or ifo:name:*"
sys.exit(1)
ifo = spec[0]
name = spec[1]
version = len(spec) > 2 and spec[2] or '*'
ex_segdefs += segmentdb_utils.expand_version_number(
engine,
(ifo, name, version, gps_start_time, gps_end_time, 0, 0))
excluded_segments = segmentdb_utils.query_segments(
engine, 'segment', ex_segdefs)
excluded_segments = reduce(operator.or_, excluded_segments).coalesce()
found_segments.coalesce()
found_segments -= excluded_segments
# Add the result type to the segment definer table
seg_name = result_name
seg_def_id = segmentdb_utils.add_to_segment_definer(
doc, process_id, ifo, seg_name, 1)
# and segment summary
segmentdb_utils.add_to_segment_summary(doc, process_id, seg_def_id,
[[gps_start_time, gps_end_time]])
# and store the segments
segmentdb_utils.add_to_segment(doc, process_id, seg_def_id, found_segments)
print "Made it to the end of the query code"
print doc
def setup_analysislogging(workflow, segs_list, insps, args, output_dir,
program_name="workflow", tags=[]):
"""
This module sets up the analysis logging xml file that contains the
following information:
* Command line arguments that the code was run with
* Segment list of times marked as SCIENCE
* Segment list of times marked as SCIENCE and "OK" ie. not CAT_1 vetoed
* Segment list of times marked as SCIENCE_OK and present on the cluster
* The times that will be analysed by the matched-filter jobs
Parameters
-----------
workflow : pycbc.workflow.core.Workflow
The Workflow instance.
segs_list : pycbc.workflow.core.FileList
A list of Files containing the information needed to generate the
segments above. For segments generated at run time the associated
segmentlist is a property of this object.
insps : pycbc.workflow.core.FileList
The output files from the matched-filtering module. Used to identify
what times have been analysed in this workflow.
output_dir : path
Directory to output any files to.
program_name : string (optional, default = "workflow")
The program name to stick in the process/process_params tables.
tags : list (optional, default = [])
If given restrict to considering inspiral and segment files that
are tagged with all tags in this list.
"""
logging.info("Entering analysis logging module.")
make_analysis_dir(output_dir)
# Construct the summary XML file
outdoc = ligolw.Document()
outdoc.appendChild(ligolw.LIGO_LW())
# Add process and process_params tables
proc_id = process.register_to_xmldoc(outdoc, program_name,
vars(args) ).process_id
# Now add the various segment lists to this file
summ_segs = segmentlist([workflow.analysis_time])
# If tags is given filter by tags
if tags:
for tag in tags:
segs_list = segs_list.find_output_with_tag(tag)
insps = insps.find_output_with_tag(tag)
for ifo in workflow.ifos:
# Lets get the segment lists we need
seg_ifo_files = segs_list.find_output_with_ifo(ifo)
# SCIENCE
sci_seg_file = seg_ifo_files.find_output_with_tag('SCIENCE')
if len(sci_seg_file) == 1:
sci_seg_file = sci_seg_file[0]
print sci_seg_file.segment_dict.keys()
sci_segs = sci_seg_file.segment_dict['%s:%s' %(ifo, 'RESULT')]
sci_def_id = segmentdb_utils.add_to_segment_definer(outdoc, proc_id,
ifo, "CBC_WORKFLOW_SCIENCE", 0)
segmentdb_utils.add_to_segment(outdoc, proc_id, sci_def_id,
sci_segs)
segmentdb_utils.add_to_segment_summary(outdoc, proc_id, sci_def_id,
summ_segs, comment='')
elif sci_seg_file:
# FIXME: While the segment module is still fractured (#127) this
# may not work. Please update when #127 is resolved
pass
#err_msg = "Got %d files matching %s and %s. Expected 1 or 0." \
# %(len(sci_seg_file), ifo, 'SCIENCE')
#raise ValueError(err_msg)
# SCIENCE_OK
sci_ok_seg_file = seg_ifo_files.find_output_with_tag('SCIENCE_OK')
if len(sci_ok_seg_file) == 1:
sci_ok_seg_file = sci_ok_seg_file[0]
sci_ok_segs = \
sci_ok_seg_file.segment_dict['%s:%s' %(ifo,'SCIENCE_OK')]
sci_ok_def_id = segmentdb_utils.add_to_segment_definer(outdoc,
proc_id, ifo, "CBC_WORKFLOW_SCIENCE_OK", 0)
segmentdb_utils.add_to_segment(outdoc, proc_id, sci_ok_def_id,
sci_ok_segs)
segmentdb_utils.add_to_segment_summary(outdoc, proc_id,
sci_ok_def_id, summ_segs, comment='')
elif sci_ok_seg_file:
# FIXME: While the segment module is still fractured (#127) this
# may not work. Please update when #127 is resolved
pass
#err_msg = "Got %d files matching %s and %s. Expected 1 or 0." \
# %(len(sci_ok_seg_file), ifo, 'SCIENCE_OK')
#raise ValueError(err_msg)
# SCIENCE_AVAILABLE
sci_available_seg_file = seg_ifo_files.find_output_with_tag(\
'SCIENCE_AVAILABLE')
if len(sci_available_seg_file) == 1:
sci_available_seg_file = sci_available_seg_file[0]
sci_available_segs = sci_available_seg_file.segment_dict
sci_available_segs = \
sci_available_segs['%s:%s' %(ifo, 'SCIENCE_AVAILABLE')]
sci_available_def_id = segmentdb_utils.add_to_segment_definer(\
outdoc, proc_id, ifo, "CBC_WORKFLOW_SCIENCE_AVAILABLE", 0)
segmentdb_utils.add_to_segment(outdoc, proc_id,
sci_available_def_id, sci_available_segs)
segmentdb_utils.add_to_segment_summary(outdoc, proc_id,
sci_available_def_id, summ_segs, comment='')
elif sci_available_seg_file:
# FIXME: While the segment module is still fractured (#127) this
# may not work. Please update when #127 is resolved
pass
#err_msg = "Got %d files matching %s and %s. Expected 1 or 0." \
# %(len(sci_available_seg_file), ifo, 'SCIENCE_AVAILABLE')
#raise ValueError(err_msg)
# ANALYSABLE - This one needs to come from inspiral outs
ifo_insps = insps.find_output_with_ifo(ifo)
analysable_segs = ifo_insps.get_times_covered_by_files()
analysable_def_id = segmentdb_utils.add_to_segment_definer(outdoc,
proc_id, ifo, "CBC_WORKFLOW_ANALYSABLE", 0)
segmentdb_utils.add_to_segment(outdoc, proc_id, analysable_def_id,
analysable_segs)
segmentdb_utils.add_to_segment_summary(outdoc, proc_id,
analysable_def_id, summ_segs, comment='')
summ_file = File(workflow.ifos, "WORKFLOW_SUMMARY",
workflow.analysis_time, extension=".xml",
directory=output_dir)
summ_file.PFN(summ_file.storage_path, site='local')
utils.write_filename(outdoc, summ_file.storage_path)
return FileList([summ_file])
def setup_analysislogging(workflow, segs_list, insps, args, output_dir,
program_name="workflow", tags=[]):
"""
This module sets up the analysis logging xml file that contains the
following information:
* Command line arguments that the code was run with
* Segment list of times marked as SCIENCE
* Segment list of times marked as SCIENCE and "OK" ie. not CAT_1 vetoed
* Segment list of times marked as SCIENCE_OK and present on the cluster
* The times that will be analysed by the matched-filter jobs
Parameters
-----------
workflow : pycbc.workflow.core.Workflow
The Workflow instance.
segs_list : pycbc.workflow.core.FileList
A list of Files containing the information needed to generate the
segments above. For segments generated at run time the associated
segmentlist is a property of this object.
insps : pycbc.workflow.core.FileList
The output files from the matched-filtering module. Used to identify
what times have been analysed in this workflow.
output_dir : path
Directory to output any files to.
program_name : string (optional, default = "workflow")
The program name to stick in the process/process_params tables.
tags : list (optional, default = [])
If given restrict to considering inspiral and segment files that
are tagged with all tags in this list.
"""
logging.info("Entering analysis logging module.")
make_analysis_dir(output_dir)
# Construct the summary XML file
outdoc = ligolw.Document()
outdoc.appendChild(ligolw.LIGO_LW())
# Add process and process_params tables
proc_id = process.register_to_xmldoc(outdoc, program_name,
vars(args) ).process_id
# Now add the various segment lists to this file
summ_segs = segmentlist([workflow.analysis_time])
# If tags is given filter by tags
if tags:
for tag in tags:
segs_list = segs_list.find_output_with_tag(tag)
insps = insps.find_output_with_tag(tag)
for ifo in workflow.ifos:
# Lets get the segment lists we need
seg_ifo_files = segs_list.find_output_with_ifo(ifo)
# SCIENCE
sci_seg_file = seg_ifo_files.find_output_with_tag('SCIENCE')
if len(sci_seg_file) == 1:
sci_seg_file = sci_seg_file[0]
sci_segs = sci_seg_file.segmentList
sci_def_id = segmentdb_utils.add_to_segment_definer(outdoc, proc_id,
ifo, "CBC_WORKFLOW_SCIENCE", 0)
segmentdb_utils.add_to_segment(outdoc, proc_id, sci_def_id,
sci_segs)
segmentdb_utils.add_to_segment_summary(outdoc, proc_id, sci_def_id,
summ_segs, comment='')
elif sci_seg_file:
# FIXME: While the segment module is still fractured (#127) this
# may not work. Please update when #127 is resolved
pass
#err_msg = "Got %d files matching %s and %s. Expected 1 or 0." \
# %(len(sci_seg_file), ifo, 'SCIENCE')
#raise ValueError(err_msg)
# SCIENCE_OK
sci_ok_seg_file = seg_ifo_files.find_output_with_tag('SCIENCE_OK')
if len(sci_ok_seg_file) == 1:
sci_ok_seg_file = sci_ok_seg_file[0]
sci_ok_segs = sci_ok_seg_file.segmentList
sci_ok_def_id = segmentdb_utils.add_to_segment_definer(outdoc,
proc_id, ifo, "CBC_WORKFLOW_SCIENCE_OK", 0)
segmentdb_utils.add_to_segment(outdoc, proc_id, sci_ok_def_id,
sci_ok_segs)
segmentdb_utils.add_to_segment_summary(outdoc, proc_id,
sci_ok_def_id, summ_segs, comment='')
elif sci_ok_seg_file:
# FIXME: While the segment module is still fractured (#127) this
# may not work. Please update when #127 is resolved
pass
#err_msg = "Got %d files matching %s and %s. Expected 1 or 0." \
# %(len(sci_ok_seg_file), ifo, 'SCIENCE_OK')
#raise ValueError(err_msg)
# SCIENCE_AVAILABLE
sci_available_seg_file = seg_ifo_files.find_output_with_tag(\
'SCIENCE_AVAILABLE')
if len(sci_available_seg_file) == 1:
sci_available_seg_file = sci_available_seg_file[0]
sci_available_segs = sci_available_seg_file.segmentList
sci_available_def_id = segmentdb_utils.add_to_segment_definer(\
outdoc, proc_id, ifo, "CBC_WORKFLOW_SCIENCE_AVAILABLE", 0)
segmentdb_utils.add_to_segment(outdoc, proc_id,
sci_available_def_id, sci_available_segs)
segmentdb_utils.add_to_segment_summary(outdoc, proc_id,
sci_available_def_id, summ_segs, comment='')
elif sci_available_seg_file:
# FIXME: While the segment module is still fractured (#127) this
# may not work. Please update when #127 is resolved
pass
#err_msg = "Got %d files matching %s and %s. Expected 1 or 0." \
# %(len(sci_available_seg_file), ifo, 'SCIENCE_AVAILABLE')
#raise ValueError(err_msg)
# ANALYSABLE - This one needs to come from inspiral outs
ifo_insps = insps.find_output_with_ifo(ifo)
analysable_segs = ifo_insps.get_times_covered_by_files()
analysable_def_id = segmentdb_utils.add_to_segment_definer(outdoc,
proc_id, ifo, "CBC_WORKFLOW_ANALYSABLE", 0)
segmentdb_utils.add_to_segment(outdoc, proc_id, analysable_def_id,
analysable_segs)
segmentdb_utils.add_to_segment_summary(outdoc, proc_id,
analysable_def_id, summ_segs, comment='')
summ_file = File(workflow.ifos, "WORKFLOW_SUMMARY",
workflow.analysis_time, extension=".xml",
directory=output_dir)
summ_file.PFN(summ_file.storage_path, site='local')
utils.write_filename(outdoc, summ_file.storage_path)
return FileList([summ_file])