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Commit 08b6098d authored by Patrick Godwin's avatar Patrick Godwin
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gstlal_feature_extractor: add dot graph for documentation, added separate... 

gstlal_feature_extractor: add dot graph for documentation, added separate groups for command line options, move imports around for aesthetics, change comment blocks (e.g. main) for documentation
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gstlal-ugly/bin/gstlal_feature_extractor
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#!/usr/bin/env python
# Copyright (C) 2017 Sydney J. Chamberlin, Patrick Godwin, Chad Hanna, Duncan Meacher
# Copyright (C) 2017-2018 Sydney J. Chamberlin, Patrick Godwin, Chad Hanna, Duncan Meacher
#
# 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
......@@ -18,26 +18,128 @@
####################
# =============================
#
# preamble
# preamble
#
####################
# =============================
### A program to extract features from auxiliary channel data in real time or in offline mode
###
### .. graphviz::
###
### digraph llpipe {
### labeljust = "r";
### label="gstlal_feature_extractor"
### rankdir=LR;
### graph [fontname="Roman", fontsize=24];
### edge [ fontname="Roman", fontsize=10 ];
### node [fontname="Roman", shape=box, fontsize=11];
###
###
### subgraph clusterNodeN {
###
### style=rounded;
### label="gstreamer pipeline";
### labeljust = "r";
### fontsize = 14;
###
### H1L1src [label="H1(L1) data source:\n mkbasicmultisrc()", color=red4];
###
### Aux1 [label="Auxiliary channel 1", color=red4];
### Aux2 [label="Auxiliary channel 2", color=green4];
### AuxN [label="Auxiliary channel N", color=magenta4];
###
### Multirate1 [label="Auxiliary channel 1 whitening and downsampling:\nmkwhitened_multirate_src()", color=red4];
### Multirate2 [label="Auxiliary channel 2 whitening and downsampling:\nmkwhitened_multirate_src()", color=green4];
### MultirateN [label="Auxiliary channel N whitening and downsampling:\nmkwhitened_multirate_src()", color=magenta4];
###
### FilterBankAux1Rate1 [label="Auxiliary Channel 1:\nGlitch Filter Bank", color=red4];
### FilterBankAux1Rate2 [label="Auxiliary Channel 1:\nGlitch Filter Bank", color=red4];
### FilterBankAux1RateN [label="Auxiliary Channel 1:\nGlitch Filter Bank", color=red4];
### FilterBankAux2Rate1 [label="Auxiliary Channel 2:\nGlitch Filter Bank", color=green4];
### FilterBankAux2Rate2 [label="Auxiliary Channel 2:\nGlitch Filter Bank", color=green4];
### FilterBankAux2RateN [label="Auxiliary Channel 2:\nGlitch Filter Bank", color=green4];
### FilterBankAuxNRate1 [label="Auxiliary Channel N:\nGlitch Filter Bank", color=magenta4];
### FilterBankAuxNRate2 [label="Auxiliary Channel N:\nGlitch Filter Bank", color=magenta4];
### FilterBankAuxNRateN [label="Auxiliary Channel N:\nGlitch Filter Bank", color=magenta4];
###
### TriggerAux1Rate1 [label="Auxiliary Channel 1:\nTrigger Max (1 sec)", color=red4];
### TriggerAux1Rate2 [label="Auxiliary Channel 1:\nTrigger Max (1 sec)", color=red4];
### TriggerAux1RateN [label="Auxiliary Channel 1:\nTrigger Max (1 sec)", color=red4];
### TriggerAux2Rate1 [label="Auxiliary Channel 2:\nTrigger Max (1 sec)", color=green4];
### TriggerAux2Rate2 [label="Auxiliary Channel 2:\nTrigger Max (1 sec)", color=green4];
### TriggerAux2RateN [label="Auxiliary Channel 2:\nTrigger Max (1 sec)", color=green4];
### TriggerAuxNRate1 [label="Auxiliary Channel N:\nTrigger Max (1 sec)", color=magenta4];
### TriggerAuxNRate2 [label="Auxiliary Channel N:\nTrigger Max (1 sec)", color=magenta4];
### TriggerAuxNRateN [label="Auxiliary Channel N:\nTrigger Max (1 sec)", color=magenta4];
###
### H1L1src -> Aux1;
### H1L1src -> Aux2;
### H1L1src -> AuxN;
###
### Aux1 -> Multirate1;
### Aux2 -> Multirate2;
### AuxN -> MultirateN;
###
### Multirate1 -> FilterBankAux1Rate1 [label="Aux 1 4096Hz"];
### Multirate2 -> FilterBankAux2Rate1 [label="Aux 2 4096Hz"];
### MultirateN -> FilterBankAuxNRate1 [label="Aux N 4096Hz"];
### Multirate1 -> FilterBankAux1Rate2 [label="Aux 1 2048Hz"];
### Multirate2 -> FilterBankAux2Rate2 [label="Aux 2 2048Hz"];
### MultirateN -> FilterBankAuxNRate2 [label="Aux N 2048Hz"];
### Multirate1 -> FilterBankAux1RateN [label="Aux 1 Nth-pow-of-2 Hz"];
### Multirate2 -> FilterBankAux2RateN [label="Aux 2 Nth-pow-of-2 Hz"];
### MultirateN -> FilterBankAuxNRateN [label="Aux N Nth-pow-of-2 Hz"];
###
### FilterBankAux1Rate1 -> TriggerAux1Rate1;
### FilterBankAux1Rate2 -> TriggerAux1Rate2;
### FilterBankAux1RateN -> TriggerAux1RateN;
### FilterBankAux2Rate1 -> TriggerAux2Rate1;
### FilterBankAux2Rate2 -> TriggerAux2Rate2;
### FilterBankAux2RateN -> TriggerAux2RateN;
### FilterBankAuxNRate1 -> TriggerAuxNRate1;
### FilterBankAuxNRate2 -> TriggerAuxNRate2;
### FilterBankAuxNRateN -> TriggerAuxNRateN;
### }
###
###
### Synchronize [label="Synchronize buffers by timestamp"];
### Extract [label="Extract features from buffer"];
### Save [label="Save triggers to disk"];
### Kafka [label="Push features to queue"];
###
### TriggerAux1Rate1 -> Synchronize;
### TriggerAux1Rate2 -> Synchronize;
### TriggerAux1RateN -> Synchronize;
### TriggerAux2Rate1 -> Synchronize;
### TriggerAux2Rate2 -> Synchronize;
### TriggerAux2RateN -> Synchronize;
### TriggerAuxNRate1 -> Synchronize;
### TriggerAuxNRate2 -> Synchronize;
### TriggerAuxNRateN -> Synchronize;
###
### Synchronize -> Extract;
###
### Extract -> Save [label="Option 1"];
### Extract -> Kafka [label="Option 2"];
###
### }
###
from optparse import OptionParser
from collections import deque, namedtuple
import json
import math
from optparse import OptionParser, OptionGroup
import os
import sys
import socket
import resource
import StringIO
import socket
import sys
import tempfile
import threading
import shutil
import traceback
import shutil
import h5py
import numpy
......@@ -60,18 +162,18 @@ from glue.ligolw import utils as ligolw_utils
from glue.ligolw.utils import process as ligolw_process
from glue.ligolw.utils import segments as ligolw_segments
from gstlal import aggregator
from gstlal import auxcache
from gstlal import pipeio
from gstlal import bottle
from gstlal import datasource
from gstlal import httpinterface
from gstlal import idq_multirate_datasource
from gstlal import idq_utils
from gstlal import multichannel_datasource
from gstlal import sngltriggertable
from gstlal import pipeio
from gstlal import pipeparts
from gstlal import simplehandler
from gstlal import aggregator
from gstlal import idq_utils
from gstlal import httpinterface
from gstlal import bottle
from gstlal import sngltriggertable
#
# Make sure we have sufficient resources
......@@ -94,11 +196,11 @@ setrlimit(resource.RLIMIT_RSS, None)
setrlimit(resource.RLIMIT_STACK, 1024 * 1024) # 1 MiB per thread
####################
# =============================
#
# classes
# classes
#
####################
# =============================
class MultiChannelHandler(simplehandler.Handler):
......@@ -501,40 +603,49 @@ class LinkedAppSync(pipeparts.AppSync):
self.appsinks[elem] = None
self.appsink_new_buffer(elem, self.sink_dict)
###############################
# =============================
#
# command line parser
# command line parser
#
###############################
# =============================
def parse_command_line():
parser = OptionParser(description = __doc__)
#
# First append the datasource common options
#
multichannel_datasource.append_options(parser)
parser.add_option("--local-frame-caching", action = "store_true", help = "Pre-reads frame data and stores to local filespace.")
parser.add_option("--out-path", metavar = "path", default = ".", help = "Write to this path. Default = .")
parser.add_option("--description", metavar = "string", default = "GSTLAL_IDQ_TRIGGERS", help = "Set the filename description in which to save the output.")
parser.add_option("--cadence", type = "int", default = 32, help = "Rate at which to write trigger files to disk. Default = 32 seconds.")
parser.add_option("--persist-cadence", type = "int", default = 320, help = "Rate at which to persist trigger files to disk, used with hdf5 files. Only used for live data, and needs to be a multiple of save cadence. Default = 320 seconds.")
parser.add_option("--disable-web-service", action = "store_true", help = "If set, disables web service that allows monitoring of PSDS of aux channels.")
parser.add_option("-v", "--verbose", action = "store_true", help = "Be verbose.")
parser.add_option("--save-format", metavar = "string", default = "hdf5", help = "Specifies the save format (ascii or hdf5) of features written to disk. Default = hdf5")
parser.add_option("--use-kafka", action = "store_true", default = False, help = "If set, will output feature vector subsets to a Kafka topic.")
parser.add_option("--kafka-partition", metavar = "string", help = "If using Kafka, sets the partition that this feature extractor is assigned to.")
parser.add_option("--kafka-topic", metavar = "string", help = "If using Kafka, sets the topic name that this feature extractor publishes feature vector subsets to.")
parser.add_option("--kafka-server", metavar = "string", help = "If using Kafka, sets the server url that the kafka topic is hosted on.")
parser.add_option("--job-id", type = "string", default = "0001", help = "Sets the job identication of the feature extractor with a 4 digit integer string code, padded with zeros. Default = 0001")
parser.add_option("--nxydump-segment", metavar = "start:stop", help = "Set the time interval to dump from nxydump elements (optional).")
parser.add_option("-m", "--mismatch", type = "float", default = 0.2, help = "Mismatch between templates, mismatch = 1 - minimal match. Default = 0.2.")
parser.add_option("-q", "--qhigh", type = "float", default = 20, help = "Q high value for half sine-gaussian waveforms. Default = 20.")
parser.add_option("--waveform", metavar = "string", default = "half_sine_gaussian", help = "Specifies the waveform used for matched filtering. Possible options: (half_sine_gaussian, sine_gaussian). Default = half_sine_gaussian")
parser.add_option("--trigger-start-time", type = "int", metavar = "seconds", help = "Set the start time of the segment to output triggers in GPS seconds. Required unless --data-source=lvshm")
parser.add_option("--trigger-end-time", type = "int", metavar = "seconds", help = "Set the end time of the segment to output triggers in GPS seconds. Required unless --data-source=lvshm")
group = OptionGroup(parser, "Waveform Options", "Adjust waveforms/parameter space used for feature extraction")
group.add_option("-m", "--mismatch", type = "float", default = 0.2, help = "Mismatch between templates, mismatch = 1 - minimal match. Default = 0.2.")
group.add_option("-q", "--qhigh", type = "float", default = 20, help = "Q high value for half sine-gaussian waveforms. Default = 20.")
group.add_option("--waveform", metavar = "string", default = "half_sine_gaussian", help = "Specifies the waveform used for matched filtering. Possible options: (half_sine_gaussian, sine_gaussian). Default = half_sine_gaussian")
parser.add_option_group(group)
group = OptionGroup(parser, "Saving Options", "Adjust parameters used for saving/persisting features to disk as well as directories specified")
group.add_option("--out-path", metavar = "path", default = ".", help = "Write to this path. Default = .")
group.add_option("--description", metavar = "string", default = "GSTLAL_IDQ_TRIGGERS", help = "Set the filename description in which to save the output.")
group.add_option("--save-format", metavar = "string", default = "hdf5", help = "Specifies the save format (ascii or hdf5) of features written to disk. Default = hdf5")
group.add_option("--cadence", type = "int", default = 32, help = "Rate at which to write trigger files to disk. Default = 32 seconds.")
group.add_option("--persist-cadence", type = "int", default = 320, help = "Rate at which to persist trigger files to disk, used with hdf5 files. Only used for live data, and needs to be a multiple of save cadence. Default = 320 seconds.")
parser.add_option_group(group)
group = OptionGroup(parser, "Kafka Options", "Adjust settings used for pushing extracted features to a Kafka topic.")
group.add_option("--use-kafka", action = "store_true", default = False, help = "If set, will output feature vector subsets to a Kafka topic.")
group.add_option("--kafka-partition", metavar = "string", help = "If using Kafka, sets the partition that this feature extractor is assigned to.")
group.add_option("--kafka-topic", metavar = "string", help = "If using Kafka, sets the topic name that this feature extractor publishes feature vector subsets to.")
group.add_option("--kafka-server", metavar = "string", help = "If using Kafka, sets the server url that the kafka topic is hosted on.")
group.add_option("--job-id", type = "string", default = "0001", help = "Sets the job identication of the feature extractor with a 4 digit integer string code, padded with zeros. Default = 0001")
parser.add_option_group(group)
group = OptionGroup(parser, "Program Behavior")
group.add_option("--local-frame-caching", action = "store_true", help = "Pre-reads frame data and stores to local filespace.")
group.add_option("--disable-web-service", action = "store_true", help = "If set, disables web service that allows monitoring of PSDS of aux channels.")
group.add_option("-v", "--verbose", action = "store_true", help = "Be verbose.")
group.add_option("--nxydump-segment", metavar = "start:stop", help = "Set the time interval to dump from nxydump elements (optional).")
group.add_option("--trigger-start-time", type = "int", metavar = "seconds", help = "Set the start time of the segment to output triggers in GPS seconds. Required unless --data-source=lvshm")
group.add_option("--trigger-end-time", type = "int", metavar = "seconds", help = "Set the end time of the segment to output triggers in GPS seconds. Required unless --data-source=lvshm")
parser.add_option_group(group)
#
# parse the arguments and sanity check
......@@ -566,11 +677,11 @@ def parse_command_line():
return options, filenames
####################
# =============================
#
# main
# main
#
####################
# =============================
#
# parsing and setting up some core structures
......
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