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Fixing codeclimate issues
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Bhooshan Gadre committed Jul 11, 2023
1 parent a81bbf3 commit 7dc2efc
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Showing 2 changed files with 97 additions and 81 deletions.
154 changes: 82 additions & 72 deletions pycbc/psd/__init__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -21,13 +21,14 @@
from pycbc.psd.analytical_space import *
from pycbc.psd.estimate import *
from pycbc.psd.variation import *
from pycbc.types import float32,float64
from pycbc.types import float32, float64
from pycbc.types import MultiDetOptionAppendAction, MultiDetOptionAction
from pycbc.types import DictOptionAction, MultiDetDictOptionAction
from pycbc.types import copy_opts_for_single_ifo
from pycbc.types import required_opts, required_opts_multi_ifo
from pycbc.types import ensure_one_opt, ensure_one_opt_multi_ifo


def from_cli(opt, length, delta_f, low_frequency_cutoff,
strain=None, dyn_range_factor=1, precision=None):
"""Parses the CLI options related to the noise PSD and returns a
Expand Down Expand Up @@ -66,7 +67,7 @@ def from_cli(opt, length, delta_f, low_frequency_cutoff,
The frequency series containing the PSD.
"""
f_low = low_frequency_cutoff
sample_rate = (length -1) * 2 * delta_f
sample_rate = (length - 1) * 2 * delta_f

try:
psd_estimation = opt.psd_estimation is not None
Expand Down Expand Up @@ -125,9 +126,10 @@ def from_cli(opt, length, delta_f, low_frequency_cutoff,

if opt.psd_inverse_length:
psd = inverse_spectrum_truncation(psd,
int(opt.psd_inverse_length * sample_rate),
low_frequency_cutoff=f_low,
trunc_method=opt.invpsd_trunc_method)
int(opt.psd_inverse_length *
sample_rate),
low_frequency_cutoff=f_low,
trunc_method=opt.invpsd_trunc_method)

if hasattr(opt, 'psd_output') and opt.psd_output:
(psd.astype(float64) / (dyn_range_factor ** 2)).save(opt.psd_output)
Expand All @@ -140,18 +142,20 @@ def from_cli(opt, length, delta_f, low_frequency_cutoff,
return psd.astype(float64)
else:
err_msg = "If provided the precision kwarg must be either 'single' "
err_msg += "or 'double'. You provided %s." %(precision)
err_msg += "or 'double'. You provided %s." % (precision)
raise ValueError(err_msg)


def from_cli_single_ifo(opt, length, delta_f, low_frequency_cutoff, ifo,
**kwargs):
**kwargs):
"""
Get the PSD for a single ifo when using the multi-detector CLI
"""
single_det_opt = copy_opts_for_single_ifo(opt, ifo)
return from_cli(single_det_opt, length, delta_f, low_frequency_cutoff,
**kwargs)


def from_cli_multi_ifos(opt, length_dict, delta_f_dict,
low_frequency_cutoff_dict, ifos, strain_dict=None,
**kwargs):
Expand All @@ -169,6 +173,7 @@ def from_cli_multi_ifos(opt, length_dict, delta_f_dict,
strain=strain, **kwargs)
return psd


def insert_psd_option_group(parser, output=True, include_data_options=True):
"""
Adds the options used to call the pycbc.psd.from_cli function to an
Expand All @@ -181,9 +186,9 @@ def insert_psd_option_group(parser, output=True, include_data_options=True):
OptionParser instance.
"""
psd_options = parser.add_argument_group(
"Options to select the method of PSD generation",
"The options --psd-model, --psd-file, --asd-file, "
"and --psd-estimation are mutually exclusive.")
"Options to select the method of PSD generation",
"The options --psd-model, --psd-file, --asd-file, "
"and --psd-estimation are mutually exclusive.")
psd_options.add_argument("--psd-model",
help="Get PSD from given analytical model. ",
choices=get_psd_model_list())
Expand Down Expand Up @@ -241,19 +246,14 @@ def insert_psd_option_group(parser, output=True, include_data_options=True):
psd_options.add_argument("--psdvar-high-freq", type=float, metavar="HERTZ",
help="Maximum frequency to consider in strain "
"bandpass.")

# psd_options.add_argument("--use-precomputed-psd", action="store_true", default=False,
# help='Use precomputed MERGE psd files to compute match. This requires --precomputed-psd-file to work')
# FIXME: We may need to use multiple files based on chunk if those are not
# generated in the workflow.
# psd_options.add_argument('--psd-files', metavar='FILE', nargs='*',
# help='PSDs from the given HDF5 files and pick the appropriate '
# 'PSD for each injection')
psd_options.add_argument("--precomputed-psd-file", metavar='FILE', type=str,
help='Given HDF5 MERGE PSD file as the option, appropriate '
'PSD for each strain segment will be chosen and use which is precomputed. PSD from the strain data wil not be computed when this option is provided.')

if include_data_options :
psd_options.add_argument("--precomputed-psd-file", metavar='FILE',
type=str, help='Given HDF5 MERGE PSD file '
'as the option, appropriate PSD for each strain '
'segment will be chosen and use which is '
'precomputed. PSD from the strain data wil not '
'be computed when this option is provided.')

if include_data_options:
psd_options.add_argument("--psd-estimation",
help="Measure PSD from the data, using "
"given average method.",
Expand All @@ -276,10 +276,11 @@ def insert_psd_option_group(parser, output=True, include_data_options=True):
"is given, the code will fail.")
if output:
psd_options.add_argument("--psd-output",
help="(Optional) Write PSD to specified file")
help="(Optional) Write PSD to specified file")

return psd_options


def insert_psd_option_group_multi_ifo(parser):
"""
Adds the options used to call the pycbc.psd.from_cli function to an
Expand All @@ -292,59 +293,59 @@ def insert_psd_option_group_multi_ifo(parser):
OptionParser instance.
"""
psd_options = parser.add_argument_group(
"Options to select the method of PSD generation",
"The options --psd-model, --psd-file, --asd-file, "
"and --psd-estimation are mutually exclusive.")
"Options to select the method of PSD generation",
"The options --psd-model, --psd-file, --asd-file, "
"and --psd-estimation are mutually exclusive.")
psd_options.add_argument("--psd-model", nargs="+",
action=MultiDetOptionAction, metavar='IFO:MODEL',
help="Get PSD from given analytical model. "
"Choose from %s" %(', '.join(get_psd_model_list()),))
action=MultiDetOptionAction, metavar='IFO:MODEL',
help="Get PSD from given analytical model. "
"Choose from %s" % (', '.join(get_psd_model_list()),))
psd_options.add_argument("--psd-extra-args",
nargs='+', action=MultiDetDictOptionAction,
metavar='DETECTOR:PARAM:VALUE', default={},
type=float, help="(optional) Extra arguments "
"passed to the PSD models.")
psd_options.add_argument("--psd-file", nargs="+",
action=MultiDetOptionAction, metavar='IFO:FILE',
help="Get PSD using given PSD ASCII file")
action=MultiDetOptionAction, metavar='IFO:FILE',
help="Get PSD using given PSD ASCII file")
psd_options.add_argument("--asd-file", nargs="+",
action=MultiDetOptionAction, metavar='IFO:FILE',
help="Get PSD using given ASD ASCII file")
action=MultiDetOptionAction, metavar='IFO:FILE',
help="Get PSD using given ASD ASCII file")
psd_options.add_argument("--psd-estimation", nargs="+",
action=MultiDetOptionAction, metavar='IFO:FILE',
help="Measure PSD from the data, using given "
"average method. Choose from "
"mean, median or median-mean.")
action=MultiDetOptionAction, metavar='IFO:FILE',
help="Measure PSD from the data, using given "
"average method. Choose from "
"mean, median or median-mean.")
psd_options.add_argument("--psd-segment-length", type=float, nargs="+",
action=MultiDetOptionAction, metavar='IFO:LENGTH',
help="(Required for --psd-estimation) The segment "
"length for PSD estimation (s)")
action=MultiDetOptionAction, metavar='IFO:LENGTH',
help="(Required for --psd-estimation) The segment "
"length for PSD estimation (s)")
psd_options.add_argument("--psd-segment-stride", type=float, nargs="+",
action=MultiDetOptionAction, metavar='IFO:STRIDE',
help="(Required for --psd-estimation) The separation"
" between consecutive segments (s)")
action=MultiDetOptionAction, metavar='IFO:STRIDE',
help="(Required for --psd-estimation) The separation"
" between consecutive segments (s)")
psd_options.add_argument("--psd-num-segments", type=int, nargs="+",
default=None,
action=MultiDetOptionAction, metavar='IFO:NUM',
help="(Optional, used only with --psd-estimation). "
"If given PSDs will be estimated using only "
"this number of segments. If more data is "
"given than needed to make this number of "
"segments than excess data will not be used in "
"the PSD estimate. If not enough data is given "
"the code will fail.")
default=None,
action=MultiDetOptionAction, metavar='IFO:NUM',
help="(Optional, used only with --psd-estimation). "
"If given PSDs will be estimated using only "
"this number of segments. If more data is "
"given than needed to make this number of "
"segments than excess data will not be used in "
"the PSD estimate. If not enough data is given "
"the code will fail.")
psd_options.add_argument("--psd-inverse-length", type=float, nargs="+",
action=MultiDetOptionAction, metavar='IFO:LENGTH',
help="(Optional) The maximum length of the impulse"
" response of the overwhitening filter (s)")
action=MultiDetOptionAction, metavar='IFO:LENGTH',
help="(Optional) The maximum length of the impulse"
" response of the overwhitening filter (s)")
psd_options.add_argument("--invpsd-trunc-method", default=None,
choices=["hann"],
help="(Optional) What truncation method to use "
"when applying psd-inverse-length. If not "
"provided, a hard truncation will be used.")
psd_options.add_argument("--psd-output", nargs="+",
action=MultiDetOptionAction, metavar='IFO:FILE',
help="(Optional) Write PSD to specified file")
action=MultiDetOptionAction, metavar='IFO:FILE',
help="(Optional) Write PSD to specified file")

# Options for PSD variation
psd_options.add_argument("--psdvar-segment", type=float,
Expand Down Expand Up @@ -372,10 +373,12 @@ def insert_psd_option_group_multi_ifo(parser):

return psd_options


ensure_one_opt_groups = []
ensure_one_opt_groups.append(['--psd-file', '--psd-model',
'--psd-estimation', '--asd-file'])


def verify_psd_options(opt, parser):
"""Parses the CLI options and verifies that they are consistent and
reasonable.
Expand All @@ -400,7 +403,8 @@ def verify_psd_options(opt, parser):
if psd_estimation:
required_opts(opt, parser,
['--psd-segment-stride', '--psd-segment-length'],
required_by = "--psd-estimation")
required_by="--psd-estimation")


def verify_psd_options_multi_ifo(opt, parser, ifos):
"""Parses the CLI options and verifies that they are consistent and
Expand All @@ -421,8 +425,10 @@ def verify_psd_options_multi_ifo(opt, parser, ifos):

if opt.psd_estimation[ifo]:
required_opts_multi_ifo(opt, parser, ifo,
['--psd-segment-stride', '--psd-segment-length'],
required_by = "--psd-estimation")
['--psd-segment-stride',
'--psd-segment-length'],
required_by="--psd-estimation")


def generate_overlapping_psds(opt, gwstrain, flen, delta_f, flow,
dyn_range_factor=1., precision=None):
Expand Down Expand Up @@ -466,7 +472,7 @@ def generate_overlapping_psds(opt, gwstrain, flen, delta_f, flow,
if not opt.psd_estimation:
psd = from_cli(opt, flen, delta_f, flow, strain=gwstrain,
dyn_range_factor=dyn_range_factor, precision=precision)
psds_and_times = [ (0, len(gwstrain), psd) ]
psds_and_times = [(0, len(gwstrain), psd)]
return psds_and_times

# Figure out the data length used for PSD generation
Expand All @@ -489,15 +495,16 @@ def generate_overlapping_psds(opt, gwstrain, flen, delta_f, flow,
if input_data_len < psd_data_len:
err_msg = "Input data length must be longer than data length needed "
err_msg += "to estimate a PSD. You specified that a PSD should be "
err_msg += "estimated with %d seconds. " %(psd_data_len)
err_msg += "Input data length is %d seconds. " %(input_data_len)
err_msg += "estimated with %d seconds. " % (psd_data_len)
err_msg += "Input data length is %d seconds. " % (input_data_len)
raise ValueError(err_msg)
elif input_data_len == psd_data_len:
num_psd_measurements = 1
psd_stride = 0
else:
num_psd_measurements = int(2 * (input_data_len-1) / psd_data_len)
psd_stride = int((input_data_len - psd_data_len) / num_psd_measurements)
psd_stride = int((input_data_len - psd_data_len) /
num_psd_measurements)

for idx in range(num_psd_measurements):
if idx == (num_psd_measurements - 1):
Expand All @@ -509,9 +516,10 @@ def generate_overlapping_psds(opt, gwstrain, flen, delta_f, flow,
strain_part = gwstrain[start_idx:end_idx]
psd = from_cli(opt, flen, delta_f, flow, strain=strain_part,
dyn_range_factor=dyn_range_factor, precision=precision)
psds_and_times.append( (start_idx, end_idx, psd) )
psds_and_times.append((start_idx, end_idx, psd))
return psds_and_times


def associate_psds_to_segments(opt, fd_segments, gwstrain, flen, delta_f, flow,
dyn_range_factor=1., precision=None):
"""Generate a set of overlapping PSDs covering the data in GWstrain.
Expand Down Expand Up @@ -555,22 +563,22 @@ def associate_psds_to_segments(opt, fd_segments, gwstrain, flen, delta_f, flow,
inp_seg = segments.segment(fd_segment.start_time,
fd_segment.end_time)
best_psd = tpsd.assosiate_psd_to_inspiral_segment(inp_seg,
delta_f=fd_segment.delta_f)
delta_f=fd_segment.delta_f)
if best_psd is None:
err_msg = "No PSDs found intersecting segment!"
raise ValueError(err_msg)
fd_segment.psd = best_psd

else:
psds_and_times = generate_overlapping_psds(opt, gwstrain, flen, delta_f,
flow, dyn_range_factor=dyn_range_factor,
precision=precision)
flow, dyn_range_factor=dyn_range_factor,
precision=precision)

for fd_segment in fd_segments:
best_psd = None
psd_overlap = 0
inp_seg = segments.segment(fd_segment.seg_slice.start,
fd_segment.seg_slice.stop)
fd_segment.seg_slice.stop)
for start_idx, end_idx, psd in psds_and_times:
psd_seg = segments.segment(start_idx, end_idx)
if psd_seg.intersects(inp_seg):
Expand All @@ -583,6 +591,7 @@ def associate_psds_to_segments(opt, fd_segments, gwstrain, flen, delta_f, flow,
raise ValueError(err_msg)
fd_segment.psd = best_psd


def associate_psds_to_single_ifo_segments(opt, fd_segments, gwstrain, flen,
delta_f, flow, ifo,
dyn_range_factor=1., precision=None):
Expand All @@ -595,6 +604,7 @@ def associate_psds_to_single_ifo_segments(opt, fd_segments, gwstrain, flen,
delta_f, flow, dyn_range_factor=dyn_range_factor,
precision=precision)


def associate_psds_to_multi_ifo_segments(opt, fd_segments, gwstrain, flen,
delta_f, flow, ifos,
dyn_range_factor=1., precision=None):
Expand All @@ -613,5 +623,5 @@ def associate_psds_to_multi_ifo_segments(opt, fd_segments, gwstrain, flen,
segments = None

associate_psds_to_single_ifo_segments(opt, segments, strain, flen,
delta_f, flow, ifo, dyn_range_factor=dyn_range_factor,
precision=precision)
delta_f, flow, ifo, dyn_range_factor=dyn_range_factor,
precision=precision)
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