lalsuite 7.26.2.dev20251210__cp312-cp312-macosx_12_0_arm64.whl

lalsuite-7.26.2.dev20251210.data/scripts/lalpulsar_MakeSFTDAG

@@ -0,0 +1,1142 @@
+#!python
+# Copyright (C) 2013, 2014, 2020--2024 Evan Goetz
+# Copyright (C) 2011, 2021, 2022 Karl Wette
+# Copyright (C) 2005, 2007 Gregory Mendell
+#
+# 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 2 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 with program; see the file COPYING. If not, write to the
+# Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
+# MA  02110-1301  USA
+
+## \file
+## \ingroup lalpulsar_bin_SFTTools
+"""Creates DAGs to run jobs that generates SFTs"""
+
+import math
+import argparse
+import os
+import re
+from pathlib import Path
+from urllib.parse import urlparse
+
+from gwdatafind import find_urls
+from gwdatafind.utils import filename_metadata, file_segment
+
+from igwn_segments import segment, segmentlist
+
+from lalpulsar import (
+    git_version,
+    SFTFilenameSpec,
+    FillSFTFilenameSpecStrings,
+    BuildSFTFilenameFromSpec,
+)
+
+__author__ = "Evan Goetz <evan.goetz@ligo.org>, Greg Mendell"
+__version__ = git_version.id
+__date__ = git_version.date
+
+cache_re = re.compile(r"^([A-Z])(\s+)(\w+)(\s+)(\d+)(\s+)(\d+)(\s+)(.+gwf)")
+
+
+# REVISIONS:
+# 12/02/05 gam; generate datafind.sub and MakeSFTs.sub as well as dag file in
+#               PWD, with log files based subLogPath and dag filename.
+# 12/28/05 gam; Add option --make-gps-dirs, -D <num>, to make directory based
+#               on this many GPS digits.
+# 12/28/05 gam; Add option --misc-desc, -X <string> giving misc. part of the
+#               SFT description field in the filename.
+# 12/28/05 gam; Add options --start-freq -F and --band -B options to enter
+#               these.
+# 12/28/05 gam; Add in --window-type, -w options; 0 = no window, 1 = default =
+#               Matlab style Tukey window; 2 = make_sfts.c Tukey window; 3 =
+#               Hann window.
+# 12/28/05 gam; Add option --overlap-fraction -P (for use with windows; e.g.,
+#               use -P 0.5 with -w 3 Hann windows; default is 0.0)
+# 12/28/05 gam; Add --sft-version, -v option to select output SFT version (1 =
+#               default is version 1 SFTs; 2 = version 2 SFTs.
+# 12/28/05 gam; Add --comment-field, -c option, for comment for version 2 SFTs.
+# 12/28/05 gam; Remove sample rate option
+# 01/09/06 gam; Add -Z option; write SFT to .*.tmp file, then move to final
+#               file name.
+# 01/14/07 gam; Add -u option to specify frame struct and type; add -i option
+#               to specify IFO name.
+# 07/24/07 gam; Add in -q option to read in list of nodes on which to output
+#               SFTs, -Q option to give node path, and -R option for number of
+#               jobs per node.
+# 04/XX/13 eag; Add -y option to synchronize the start times of SFTs.
+# 07/24/14 eag; Change default to version 2 SFTs
+# 12/2020  eag; Update script to conform to modern python3 and pep8
+# 10/2020  kww; Pass args directly to writeToDag(), use Python f-strings
+# 10/2022  kww; Deprecate options that have been removed from MakeSFTs
+# 10/2022  kww; Parse window type as a string, parameter separated by colon
+# 10/2022  kww; Merge -O and -o log path options to free up -O option
+# 10/2022  kww; Implement public SFT file naming convention
+# 11/2022  kww; -R command line option now used for --observing-revision
+#               instead of --output-jobs-per-node, which now uses -r
+# 11/2022  kww; --datafind-path and --makesfts-path accept executable names
+# 03/2023  eag; Allow user to pass a frame cache file --cache-file
+# 04/2023  kww; Improve documentation of --window-type argument
+# 05/2023  eag; Add the --gaps flag to gw_data_find
+# 08/2023  eag; Allow for multiple channel names to be provided
+# 09/2023  eag; Modify use of environment variables
+# 01/2024  eag; Allow skipping of channels if not in frames or too low data
+#               rate
+# 10/2024  eag; Modify workflow for version 3 SFTs and HTCondor file transfer
+#               workflow
+# 12/2024  eag; Modify workflow to use lalpulsar_MoveSFTs script instead of
+#               remapping files
+# 03/2025  eag; Rewrite to generate cache files running lalpulsar_MakeSFTDAG
+#               enabling frame files on /home or OSDF
+
+
+def sft_name_from_vars(
+    obs,
+    gpsstart,
+    Tsft,
+    channel=None,
+    kind=None,
+    rev=None,
+    window="unknown",
+    par=None,
+    miscstr=None,
+):
+    """Create SFT file name from specification"""
+
+    spec = SFTFilenameSpec()
+
+    FillSFTFilenameSpecStrings(
+        spec=spec,
+        path=None,
+        extn=None,
+        detector=channel[:2],
+        window_type=window,
+        privMisc=miscstr,
+        pubObsKind=kind,
+        pubChannel=channel,
+    )
+    spec.pubObsRun = obs or 0
+    spec.pubRevision = rev or 0
+    spec.window_param = par or 0
+    spec.numSFTs = 1  # MakeSFTDAG will only ever generate 1 SFT per file
+    spec.SFTtimebase = Tsft
+    spec.gpsStart = gpsstart
+    spec.SFTspan = Tsft  # MakeSFTDAG will only ever generate 1 SFT per file
+
+    return BuildSFTFilenameFromSpec(spec)
+
+
+def get_urls(args):
+    """Get frame file URL list from gwdatafind or cache file"""
+
+    if not args.cache_file:
+        urls = find_urls(
+            site,
+            args.input_data_type,
+            segList[0][0],
+            segList[-1][-1],
+            match=args.datafind_match,
+            urltype=args.datafind_urltype,
+        )
+    else:
+        urls = []
+        with open(args.cache_file, "r") as f:
+            for line in f:
+                m = cache_re.match(line)
+                if m:
+                    framefile = m.group(9)
+                    urls.append(framefile)
+
+    # sort the urls by gps time since find_urls() may not return a sorted list
+    sorted_urls = sorted(urls, key=lambda x: file_segment(x)[0])
+
+    return sorted_urls
+
+
+def make_cache(
+    urls,
+    job_seg,
+):
+    """Make a frame list and cache list from a list of URLs"""
+
+    cache = []  # list of lines for the cache file
+    frames = []  # list of frame filenames used in the job
+    for idx, url in enumerate(urls):
+        obs, desc, dataseg = filename_metadata(url)
+        dataseg = segment(dataseg)
+        if dataseg.disjoint(job_seg) < 0:
+            continue
+        if dataseg.disjoint(job_seg) > 0:
+            break
+        if dataseg.intersects(job_seg):
+            framefileurl = urlparse(url)
+            framefilepath = Path(framefileurl.path)
+
+            # list in cache file if files not visible on execute node
+            # otherwise use file url
+            if "/home" in str(framefilepath.parent) or "osdf" in framefileurl.scheme:
+                newcache = (
+                    f"{obs}\t{desc}\t{dataseg[0]}\t{abs(dataseg)}\t{framefilepath.name}"
+                )
+            else:
+                newcache = f"{obs}\t{desc}\t{dataseg[0]}\t{abs(dataseg)}\t{url}"
+            cache.append(newcache)
+
+            if "/home" in str(framefilepath.parent):
+                frames.append(framefilepath)
+            else:
+                frames.append(url)
+
+    return frames, cache
+
+
+def writeToDag(dagFID, nodeCount, startTimeThisNode, endTimeThisNode, urls, args):
+    """Write one job to DAG file"""
+
+    MakeSFTs = f"MakeSFTs_{nodeCount}"
+    tagStringOut = f"{args.tag_string}_{nodeCount}"
+
+    job_segment = segment(
+        startTimeThisNode - args.extra_datafind_time,
+        endTimeThisNode + args.extra_datafind_time,
+    )
+
+    frames, cache = make_cache(urls, job_segment)
+
+    obs, desc, dataseg = filename_metadata(urls[0])
+    cacheFile = args.cache_path / f"{obs}-{job_segment[0]}-{job_segment[1]}.cache"
+    with open(cacheFile, "w") as f:
+        for l in cache:
+            f.write(f"{l}\n")
+
+    argList = []
+    argList.append(f"-O {args.observing_run}")
+    if args.observing_run > 0:
+        argList.append(f"-K {args.observing_kind}")
+        argList.append(f"-R {args.observing_revision}")
+    elif args.misc_desc:
+        argList.append(f"-X {args.misc_desc}")
+    argList.append(f"-f {args.filter_knee_freq}")
+    argList.append(f"-t {args.time_baseline}")
+    # To work with the condor file transfer protocol, we save everything to the
+    # scratch directory because the files will have unique names. Since
+    # lalpulsar_MakeSFTs wants to have a path to save the file to, we provide .
+    argList.append(f"-p {','.join(['.' for p in args.output_sft_path])}")
+    # To work with the condor file transfer protocol, the cache file is saved
+    # to the scratch directory on transfer so we just need the name, not the
+    # full path
+    argList.append(f"-C {cacheFile.name}")
+    argList.append(f"-s {startTimeThisNode}")
+    argList.append(f"-e {endTimeThisNode}")
+    argList.append(f"-N {','.join(args.channel_name)}")
+    argList.append(f"-F {args.start_freq}")
+    argList.append(f"-B {args.band}")
+    if args.comment_field:
+        argList.append(f"-c {args.comment_field}")
+    if ":" in args.window_type:
+        window_type, window_param = args.window_type.split(":")
+        window_param = float(window_param)
+        argList.append(f"-w {window_type} -r {window_param}")
+    else:
+        window_type = args.window_type
+        window_param = None
+        argList.append(f"-w {window_type}")
+    if args.overlap_fraction:
+        argList.append(f"-P {args.overlap_fraction}")
+    if args.allow_skipping:
+        argList.append("--allow-skipping TRUE")
+    argStr = " ".join(argList)
+
+    # The files are going to go to specific directories, so we need to map
+    # the files to their output directories
+    outputfiles = []
+    remap = []
+    sft_start = startTimeThisNode
+    sft_end = sft_start + args.time_baseline
+    # loop over start times
+    while sft_end <= endTimeThisNode:
+        # loop over channels
+        for idx, c in enumerate(args.channel_name):
+            filename = sft_name_from_vars(
+                args.observing_run,
+                sft_start,
+                args.time_baseline,
+                c,
+                kind=args.observing_kind,
+                rev=args.observing_revision,
+                window=window_type,
+                par=window_param,
+                miscstr=args.misc_desc,
+            )
+            outputfiles.append(filename)
+            remap.append(f"{filename}={args.output_sft_path[idx]/filename}")
+
+        # update start and end times
+        if args.overlap_fraction:
+            sft_start += int(round((1 - args.overlap_fraction) * args.time_baseline))
+        else:
+            sft_start += args.time_baseline
+        sft_end = sft_start + args.time_baseline
+
+    # MakeSFT job
+    dagFID.write(f"JOB {MakeSFTs} {Path(dagFID.name).parent / 'MakeSFTs.sub'}\n")
+    dagFID.write(f"RETRY {MakeSFTs} 1\n")
+    dagFID.write(f'VARS {MakeSFTs} argList="{argStr}" cachefile="{cacheFile}" ')
+    if args.transfer_frame_files:
+        framefiles = ",".join([str(fr) for fr in frames])
+        dagFID.write(f'framefiles="{framefiles}" ')
+    dagFID.write(f'tagstring="{tagStringOut}"\n')
+
+
+#
+# MAIN CODE START HERE
+#
+
+parser = argparse.ArgumentParser(
+    description="This script creates MakeSFTs.sub, MoveSFTs.sub, and a dag \
+                 file that generates SFTs based on the options given.",
+    fromfile_prefix_chars="@",
+)
+
+dag_group = parser.add_argument_group(
+    "DAG organization", "Options for workflow control"
+)
+datafind_group = parser.add_argument_group(
+    "Datafind", "Options for locating frame files"
+)
+makesfts_group = parser.add_argument_group(
+    "SFT creation", "Options for SFT creation and output"
+)
+deprecated_group = parser.add_argument_group("DEPRECATED")
+
+dag_group.add_argument(
+    "-f",
+    "--dag-file",
+    required=True,
+    type=Path,
+    help="filename for .dag file (should end in .dag)",
+)
+dag_group.add_argument(
+    "-G",
+    "--tag-string",
+    required=True,
+    type=str,
+    help="tag string used in names of various files unique to \
+          jobs that will run under the DAG",
+)
+dag_group.add_argument(
+    "-a",
+    "--analysis-start-time",
+    type=int,
+    help="GPS start time of data from which to generate \
+          SFTs (optional and unused if a segment file is given)",
+)
+dag_group.add_argument(
+    "-b",
+    "--analysis-end-time",
+    type=int,
+    help="GPS end time of data from which to generate SFTs \
+          (optional and unused if a segment file is given)",
+)
+dag_group.add_argument(
+    "-L",
+    "--max-length-all-jobs",
+    type=int,
+    help="maximum total amount of data to process, in seconds \
+          (optional and unused if a segment file is given)",
+)
+dag_group.add_argument(
+    "-g",
+    "--segment-file",
+    type=Path,
+    help="alternative file with segments to use, rather than \
+          the input times",
+)
+dag_group.add_argument(
+    "-l",
+    "--min-seg-length",
+    type=int,
+    default=0,
+    help="minimum length segments to process in seconds (used \
+          only if a segment file is given)",
+)
+dag_group.add_argument(
+    "-y",
+    "--synchronize-start",
+    action="store_true",
+    help="synchronize the start times of the SFTs so that the \
+          start times are synchronized when there are gaps in the \
+          data",
+)
+dag_group.add_argument(
+    "-o",
+    "--log-path",
+    type=Path,
+    default="logs",
+    help="path to log, output, and error files (default \
+          is $PWD/logs; this directory is created if it does not \
+          exist and usually should be under a local file system)",
+)
+dag_group.add_argument(
+    "-m",
+    "--max-num-per-node",
+    type=int,
+    default=1,
+    help="maximum number of SFTs to generate on one node",
+)
+dag_group.add_argument(
+    "-J",
+    "--makesfts-path",
+    type=Path,
+    help="string specifying the lalpulsar_MakeSFTs executable, \
+          or a path to it; if not set, will use \
+          MAKESFTS_PATH env variable or system default (in that \
+          order)",
+)
+dag_group.add_argument(
+    "--movesfts-path",
+    type=Path,
+    help="string specifying the lalpulsar_MoveSFTs executable, \
+          or a path to it; if not set, will use \
+          MOVESFTS_PATH env variable or system default (in that \
+          order)",
+)
+dag_group.add_argument(
+    "-Y",
+    "--request-memory",
+    type=int,
+    default=4096,
+    help="memory allocation in MB to request from condor for \
+          lalpulsar_MakeSFTs step",
+)
+dag_group.add_argument(
+    "-s",
+    "--request-disk",
+    type=int,
+    default=4096,
+    help="disk space allocation in MB to request from condor \
+          for lalpulsar_MakeSFTs step",
+)
+dag_group.add_argument(
+    "-A",
+    "--accounting-group",
+    required=True,
+    type=str,
+    help="Condor tag for the production of SFTs",
+)
+dag_group.add_argument(
+    "-U",
+    "--accounting-group-user",
+    required=True,
+    type=str,
+    help="albert.einstein username (do not add @LIGO.ORG)",
+)
+dag_group.add_argument(
+    "-t",
+    "--transfer-frame-files",
+    action="store_true",
+    help="Transfer frame files via HTCondor file transfer system. \
+          This should be specified if frames are not visible to the \
+          compute node file system. Ex. this should be specified if \
+          frames are on /home or running on the open science grid. \
+          Usually frame files are visible on CIT, LHO, LLO clusters \
+          so that this does not need to be specified in that case.",
+)
+
+datafind_group.add_argument(
+    "-d",
+    "--input-data-type",
+    required=True,
+    type=str,
+    help="input data type for use with the gw_data_find --type \
+          option",
+)
+datafind_group.add_argument(
+    "-x",
+    "--extra-datafind-time",
+    type=int,
+    default=0,
+    help="extra time to subtract/add from/to start/end time \
+          arguments of gw_data_find",
+)
+datafind_group.add_argument(
+    "-M",
+    "--datafind-match",
+    type=str,
+    help="string to use with the gw_data_find --match option",
+)
+datafind_group.add_argument(
+    "--datafind-urltype",
+    type=str,
+    default="file",
+    choices=["file", "osdf"],
+    help="String for the gw_data_find --urltype option. \
+          Use 'file' if creating SFTs on a local LDG cluster. \
+          Use 'osdf' if creating SFTs on the open science grid",
+)
+datafind_group.add_argument(
+    "-e",
+    "--cache-file",
+    type=Path,
+    help="path and filename to frame cache file to use instead \
+          of gw_data_find",
+)
+
+makesfts_group.add_argument(
+    "-O",
+    "--observing-run",
+    required=True,
+    type=int,
+    help="For public SFTs, observing run data the SFTs are generated from, or \
+          (in the case of mock data challenge data) the observing \
+          run on which the data is most closely based",
+)
+makesfts_group.add_argument(
+    "-K",
+    "--observing-kind",
+    type=str,
+    choices=["RUN", "AUX", "SIM", "DEV"],
+    help='For public SFTs, one of: "RUN" for production SFTs of h(t) channels; \
+          "AUX" for SFTs of non-h(t) channels; \
+          "SIM" for mock data challenge or other simulated data; or \
+          "DEV" for development/testing purposes',
+)
+makesfts_group.add_argument(
+    "-R",
+    "--observing-revision",
+    type=int,
+    help="For public SFTs: revision number starts at 1, and should be incremented once \
+          SFTs have been widely distributed across clusters, advertised \
+          as being ready for use, etc.  For example, if mistakes are found \
+          in the initial SFT production run after they have been published, \
+          regenerated SFTs should have a revision number of at least 2",
+)
+makesfts_group.add_argument(
+    "-X",
+    "--misc-desc",
+    type=str,
+    help="For private SFTs, miscellaneous part of the SFT \
+          description field in the filename",
+)
+makesfts_group.add_argument(
+    "-k",
+    "--filter-knee-freq",
+    required=True,
+    type=float,
+    help="high pass filter knee frequency used on time domain \
+          data before generating SFTs",
+)
+makesfts_group.add_argument(
+    "-T",
+    "--time-baseline",
+    required=True,
+    type=int,
+    help="time baseline of SFTs  (e.g., 60 or 1800 seconds)",
+)
+makesfts_group.add_argument(
+    "-p",
+    "--output-sft-path",
+    nargs="+",
+    type=Path,
+    help="Path where to save the SFT files. Can specify multiple options, \
+          If specifying multiple options then it is required to specify the \
+          same number of output-sft-path options as the number of channels. \
+          The first listed channel will have the SFTs go into the first \
+          listed output-sft-path. Otherwise specify only one output path. \
+          If one path is specified and more than 1 channels are specified \
+          then --observing-run must be >= 1 and --observing-kind and \
+          --observing-revision must be set",
+)
+makesfts_group.add_argument(
+    "-C",
+    "--cache-path",
+    type=Path,
+    default="cache",
+    help="path to cache files that will be produced by \
+          gw_data_find (default is $PWD/cache; this directory is \
+          created if it does not exist and must agree with that \
+          given in .sub files)",
+)
+makesfts_group.add_argument(
+    "-N",
+    "--channel-name",
+    nargs="+",
+    type=str,
+    help="Name of input time-domain channel to read from frames. \
+          Can specify multiple options. The number of channels must be \
+          equal to the number of output-sft-path options given. The \
+          first listed channel will have the SFTs go to the first listed \
+          output-sft-path. Can only specify one channel when generating \
+          private SFTs (--observing-run=0)",
+)
+makesfts_group.add_argument(
+    "-c", "--comment-field", type=str, help="comment for SFT header"
+)
+makesfts_group.add_argument(
+    "-F", "--start-freq", type=int, default=10, help="start frequency of the SFTs"
+)
+makesfts_group.add_argument(
+    "-B", "--band", type=int, default=1990, help="frequency band of the SFTs"
+)
+makesfts_group.add_argument(
+    "-w",
+    "--window-type",
+    type=str,
+    default="tukey:0.001",
+    help='type of windowing of time-domain to do \
+          before generating SFTs, e.g. "rectangular", \
+          "hann", "tukey:<beta in [0,1], required>"; \
+          (default is "tukey:0.001", standard choice for LVK production SFTs)',
+)
+makesfts_group.add_argument(
+    "-P",
+    "--overlap-fraction",
+    type=float,
+    default=0,
+    help="overlap fraction (for use with windows; e.g., use \
+          --overlap-fraction 0.5 with --window-type hann windows)",
+)
+makesfts_group.add_argument(
+    "--allow-skipping",
+    action="store_true",
+    help="allow channels to be skipped if not in frames or too low sampling \
+          frequency",
+)
+makesfts_group.add_argument(
+    "--no-validate",
+    dest="validate",
+    action="store_false",
+    help="do not validate created SFTs",
+)
+
+##### DEPRECATED OPTIONS #####
+class DeprecateAction(argparse.Action):
+    def __call__(self, parser, namespace, values, option_string=None):
+        parser.error(
+            f"Argument {self.option_strings} has been deprecated in lalpulsar_MakeSFTs"
+        )
+
+
+deprecated_group.add_argument(
+    "-u",
+    "--frame-struct-type",
+    nargs=0,
+    action=DeprecateAction,
+    help="DEPRECATED. No longer required; \
+          the frame channel type is determined automatically",
+)
+deprecated_group.add_argument(
+    "-H",
+    "--use-hoft",
+    nargs=0,
+    action=DeprecateAction,
+    help="DEPRECATED. No longer required; \
+          the frame channel type is determined automatically",
+)
+deprecated_group.add_argument(
+    "-i",
+    "--ifo",
+    nargs=0,
+    action=DeprecateAction,
+    help="DEPRECATED. No longer required; \
+          the detector prefix is deduced from the channel name",
+)
+deprecated_group.add_argument(
+    "-D",
+    "--make-gps-dirs",
+    nargs=0,
+    action=DeprecateAction,
+    help="DEPRECATED. No longer supported",
+)
+deprecated_group.add_argument(
+    "-Z",
+    "--make-tmp-file",
+    nargs=0,
+    action=DeprecateAction,
+    help="DEPRECATED. Default behaviour",
+)
+deprecated_group.add_argument(
+    "-v",
+    "--sft-version",
+    nargs=0,
+    action=DeprecateAction,
+    help="DEPRECATED. No longer supported",
+)
+deprecated_group.add_argument(
+    "-S",
+    "--use-single",
+    nargs=0,
+    action=DeprecateAction,
+    help="DEPRECATED. No longer supported",
+)
+deprecated_group.add_argument(
+    "-q",
+    "--list-of-nodes",
+    type=str,
+    action=DeprecateAction,
+    help="DEPCRECATED. No longer supported",
+)
+deprecated_group.add_argument(
+    "-Q",
+    "--node-path",
+    type=Path,
+    action=DeprecateAction,
+    help="DEPCRECATED. No longer supported",
+)
+deprecated_group.add_argument(
+    "-r",
+    "--output-jobs-per-node",
+    type=int,
+    default=0,
+    action=DeprecateAction,
+    help="DEPRECATED. No longer supported",
+)
+
+args = parser.parse_args()
+
+# Some basic argument value checking
+if args.observing_run < 0:
+    raise parser.error("--observing-run must be >= 0")
+
+if args.observing_run > 0 and not args.observing_kind:
+    raise parser.error("--observing-run requires --observing-kind")
+
+if args.observing_run > 0 and not args.observing_revision:
+    raise parser.error("--observing-run requires --observing-revision")
+
+if args.observing_revision and args.observing_revision <= 0:
+    raise parser.error("--observing-revision must be > 0")
+
+if args.observing_run > 0 and args.misc_desc:
+    raise parser.error(
+        f"--observing-run={args.observing_run} incompatible with --misc-desc"
+    )
+
+if args.misc_desc and not re.compile(r"^[A-Za-z0-9]+$").match(args.misc_desc):
+    raise parser.error("--misc-desc may only contain A-Z, a-z, 0-9 characters")
+
+if args.extra_datafind_time < 0:
+    raise parser.error("--extra-datafind-time must be >= 0")
+
+if args.filter_knee_freq < 0:
+    raise parser.error("--filter-knee-freq must be >= 0")
+
+if args.time_baseline <= 0:
+    raise parser.error("--time-baseline must be > 0")
+
+if args.overlap_fraction < 0.0 or args.overlap_fraction >= 1.0:
+    raise parser.error("--overlap-fraction must be in the range [0,1)")
+
+if args.start_freq < 0.0 or args.start_freq >= 7192.0:
+    raise parser.error("--start-freq must be in the range [0,7192)")
+
+if args.band <= 0 or args.band >= 8192.0:
+    raise parser.error("--band must be in the range (0,8192)")
+
+if args.start_freq + args.band >= 8192.0:
+    raise parser.error("--start-freq + --band must be < 8192")
+
+if args.max_num_per_node <= 0:
+    raise parser.error("--max-num-per-node must be > 0")
+
+if (
+    len(args.channel_name) != len(args.output_sft_path)
+    and len(args.output_sft_path) != 1
+):
+    raise parser.error(
+        "--channel-name and --output-sft-path must be the "
+        "same length or --output-sft-path must be length of 1"
+    )
+
+if len(args.channel_name) > 1 and args.observing_run == 0:
+    raise parser.error(
+        "When creating SFTs from multiple channels, public SFT naming "
+        "convention must be used: --observing-run > 0 and set "
+        "--observing-kind and --observing-revision"
+    )
+
+if args.datafind_urltype == "osdf" and not args.transfer_frame_files:
+    raise parser.error(
+        "--transfer-frame-files must be specified when --datafind-urltype=osdf"
+    )
+
+# Set executables for lalpulsar_MakeSFTs, and lalpulsar_MoveSFTs
+makeSFTsExe = "lalpulsar_MakeSFTs"
+if args.makesfts_path:
+    if args.makesfts_path.is_file():
+        makeSFTsExe = args.makesfts_path
+    else:
+        makeSFTsExe = args.makesfts_path / makeSFTsExe
+elif "MAKESFTS_PATH" in os.environ:
+    makeSFTsExe = Path("$ENV(MAKESFTS_PATH)") / makeSFTsExe
+else:
+    makeSFTsExe = Path("/Users/gitlab/builds/JjyQBtwP4/0/lscsoft/lalsuite/wheel/build/inst/bin") / makeSFTsExe
+
+moveSFTsExe = "lalpulsar_MoveSFTs"
+if args.movesfts_path:
+    if args.movesfts_path.is_file():
+        moveSFTsExe = args.movesfts_path
+    else:
+        moveSFTsExe = args.movesfts_path / moveSFTsExe
+elif "MOVESFTS_PATH" in os.environ:
+    moveSFTsExe = Path("$ENV(MOVESFTS_PATH)") / moveSFTsExe
+else:
+    moveSFTsExe = Path("/Users/gitlab/builds/JjyQBtwP4/0/lscsoft/lalsuite/wheel/build/inst/bin") / moveSFTsExe
+
+# make directories to store the cache files, job logs, and SFTs
+args.log_path.mkdir(exist_ok=True)
+args.cache_path.mkdir(exist_ok=True)
+for p in args.output_sft_path:
+    p.mkdir(exist_ok=True)
+
+# Check if segment file was given, else set up one segment from the command line
+segList = segmentlist()
+adjustSegExtraTime = False
+if args.segment_file is not None:
+    if args.min_seg_length < 0:
+        raise parser.error("--min-seg-length must be >= 0")
+
+    # the next flag causes extra time that cannot be processes to be trimmed
+    # from the start and end of a segment
+    adjustSegExtraTime = True
+
+    with open(args.segment_file) as fp_segfile:
+        for idx, line in enumerate(fp_segfile):
+            splitLine = line.split()
+            oneSeg = segment(int(splitLine[0]), int(splitLine[1]))
+            if abs(oneSeg) >= args.min_seg_length:
+                segList.append(oneSeg)
+
+    if len(segList) < 1:
+        raise ValueError(f"No segments found in segment file: {args.segment_file}")
+else:
+    if args.analysis_start_time is None:
+        raise parser.error(
+            "--analysis-start-time must be specified if no segment file is " "given"
+        )
+
+    if args.analysis_end_time is None:
+        raise parser.error(
+            "--analysis-start-time must be specified if no segment file is " "given"
+        )
+
+    if args.max_length_all_jobs is None:
+        raise parser.error(
+            "--max-length-all-jobs must be specified if no segment file is " "given"
+        )
+
+    # Make sure not to exceed maximum allow analysis
+    if args.analysis_end_time > (args.analysis_start_time + args.max_length_all_jobs):
+        args.analysis_end_time = args.analysis_start_time + args.max_length_all_jobs
+
+    oneSeg = segment(args.analysis_start_time, args.analysis_end_time)
+    segList.append(oneSeg)
+# END if (args.segment_file != None)
+segList.coalesce()
+
+# Get the IFO site, which is the first letter of the channel name.
+site = args.channel_name[0][0]
+
+# Get the frame file URL list
+urls = get_urls(args)
+
+# Basic check that the frame file url list are traditionally visible on EPs
+if not args.transfer_frame_files:
+    for f in urls:
+        if "/home" in f:
+            raise parser.error(
+                "--transfer-frame-files must be specified when frame files are in /home"
+            )
+
+# data segments created from the list of frame URLs
+dataSegs = segmentlist()
+for url in urls:
+    dataSegs.append(file_segment(url))
+dataSegs.coalesce()
+
+# intersection of segList with dataSegs
+segList &= dataSegs
+segList.coalesce()  # just in case
+
+# initialize count of nodes
+nodeCount = 0
+
+# Create .sub files
+path_to_dag_file = args.dag_file.parent
+dag_filename = args.dag_file.name
+makesfts_sub = path_to_dag_file / "MakeSFTs.sub"
+movesfts_sub = path_to_dag_file / "MoveSFTs.sub"
+
+# create MakeSFTs.sub
+with open(makesfts_sub, "w") as MakeSFTsFID:
+    MakeSFTsLogFile = f"{args.log_path}/MakeSFTs_{dag_filename}.log"
+    MakeSFTsFID.write("universe = vanilla\n")
+    MakeSFTsFID.write(f"executable = {makeSFTsExe}\n")
+    MakeSFTsFID.write("arguments = $(argList)\n")
+    MakeSFTsFID.write(f"accounting_group = {args.accounting_group}\n")
+    MakeSFTsFID.write(f"accounting_group_user = {args.accounting_group_user}\n")
+    MakeSFTsFID.write(f"log = {MakeSFTsLogFile}\n")
+    MakeSFTsFID.write(f"error = {args.log_path}/MakeSFTs_$(tagstring).err\n")
+    MakeSFTsFID.write(f"output = {args.log_path}/MakeSFTs_$(tagstring).out\n")
+    MakeSFTsFID.write("notification = never\n")
+    MakeSFTsFID.write(f"request_memory = {args.request_memory}MB\n")
+    MakeSFTsFID.write(f"request_disk = {args.request_disk}MB\n")
+    MakeSFTsFID.write("RequestCpus = 1\n")
+    MakeSFTsFID.write("should_transfer_files = yes\n")
+    if args.transfer_frame_files:
+        MakeSFTsFID.write("transfer_input_files = $(cachefile),$(framefiles)\n")
+    else:
+        MakeSFTsFID.write("transfer_input_files = $(cachefile)\n")
+    if "MAKESFTS_PATH" in os.environ and not args.makesfts_path:
+        MakeSFTsFID.write("getenv = MAKESFTS_PATH\n")
+    if args.datafind_urltype == "osdf":
+        MakeSFTsFID.write("use_oauth_services = scitokens\n")
+        MakeSFTsFID.write(
+            "environment = BEARER_TOKEN_FILE=$$(CondorScratchDir)/.condor_creds/scitokens.use\n"
+        )
+    MakeSFTsFID.write("queue 1\n")
+
+# create MoveSFTs.sub
+with open(movesfts_sub, "w") as MoveSFTsFID:
+    MoveSFTsLogFile = f"{args.log_path}/MoveSFTs_{dag_filename}.log"
+    MoveSFTsFID.write("universe = local\n")
+    MoveSFTsFID.write(f"executable = {moveSFTsExe}\n")
+    MoveSFTsFID.write("arguments = ")
+    if not args.validate:
+        MoveSFTsFID.write("$(opts) ")
+    MoveSFTsFID.write("-s $(sourcedirectory) -c $(channels) -d $(destdirectory)\n")
+    MoveSFTsFID.write(f"accounting_group = {args.accounting_group}\n")
+    MoveSFTsFID.write(f"accounting_group_user = {args.accounting_group_user}\n")
+    MoveSFTsFID.write(f"log = {MoveSFTsLogFile}\n")
+    MoveSFTsFID.write(f"error = {args.log_path}/MoveSFTs.err\n")
+    MoveSFTsFID.write(f"output = {args.log_path}/MoveSFTs.out\n")
+    MoveSFTsFID.write("notification = never\n")
+    MoveSFTsFID.write(f"request_memory = 1GB\n")
+    MoveSFTsFID.write(f"request_disk = 10MB\n")
+    MoveSFTsFID.write("RequestCpus = 1\n")
+    if "MOVESFTS_PATH" in os.environ and not args.movesfts_path:
+        MoveSFTsFID.write("getenv = MOVESFTS_PATH\n")
+    MoveSFTsFID.write("queue 1\n")
+
+# create the DAG file with the jobs to run
+with open(args.dag_file, "w") as dagFID:
+    startTimeAllNodes = None
+    firstSFTstartTime = 0  # need this for the synchronized start option
+
+    # Loop over the segment list to generate the SFTs for each segment
+    for seg in segList:
+        # Each segment in the segList runs on one or more nodes;
+        # initialize the number SFTs produced by the current node:
+        numThisNode = 0
+        numThisSeg = 0
+
+        # Case 1: a segment file was given but the SFTs do not need their
+        # start times to be synchronized
+        if adjustSegExtraTime and not args.synchronize_start:
+            segStartTime = seg[0]
+            segEndTime = seg[1]
+
+            # First we figure out how much extra time is in the segment so that
+            # SFTs are fit within the segment:
+            # |..<SFT><SFT><SFT>..|
+            # where the .. represent the extra time in the segment
+            # The amount of extra time in a segment is given as the remainder
+            # of (total segment time) / (SFT time baseline)
+            segExtraTime = (segEndTime - segStartTime) % args.time_baseline
+
+            # If there is overlap of SFTs requested, then we compute the extra
+            # time as:
+            # the remainder of (end - start - Tsft) / (non-overlap time)
+            # provided there was at least one SFT that is in the segment
+            if args.overlap_fraction != 0.0:
+                if (segEndTime - segStartTime) > args.time_baseline:
+                    segExtraTime = (
+                        segEndTime - segStartTime - args.time_baseline
+                    ) % int((1.0 - args.overlap_fraction) * args.time_baseline)
+
+            # We'll add half the extra time to the start of the SFTs to be
+            # created in this segment and half at the end
+            segExtraStart = int(segExtraTime / 2)
+            segExtraEnd = segExtraTime - segExtraStart
+            args.analysis_start_time = segStartTime + segExtraStart
+
+            # This shift may have pushed past the end time of the segment. In
+            # that case, just fix the start time to the end time of the segment
+            if args.analysis_start_time > segEndTime:
+                args.analysis_start_time = segEndTime
+
+            # shifting the end time by the other portion of the extra time
+            # amount ...
+            args.analysis_end_time = segEndTime - segExtraEnd
+
+            # Again, this shift could have pushed the end time beyond the start
+            # of the segment, so just fix the end time to the segment start
+            if args.analysis_end_time < segStartTime:
+                args.analysis_end_time = segStartTime
+
+        # Case 2: SFTs need a synchronized start. This is a special case for
+        # methods like TwoSpect, where signal periodicity spacing must be
+        # maintained
+        elif args.synchronize_start:
+            segStartTime = seg[0]
+            segEndTime = seg[1]
+
+            # If we haven't set the first SFT start time, then set it equal to
+            # the start time of the first segment
+            if firstSFTstartTime == 0:
+                firstSFTstartTime = segStartTime
+
+            # This is a tricky bit of math to set the start time based on when
+            # the first SFT start time of all the segments
+            args.analysis_start_time = (
+                int(
+                    round(
+                        math.ceil(
+                            (segStartTime - firstSFTstartTime)
+                            / ((1.0 - args.overlap_fraction) * args.time_baseline)
+                        )
+                        * (1.0 - args.overlap_fraction)
+                        * args.time_baseline
+                    )
+                )
+                + firstSFTstartTime
+            )
+
+            # This shift may have pushed past the end time of the segment. In
+            # that case, just fix the start time to the end time of the segment
+            if args.analysis_start_time > segEndTime:
+                args.analysis_start_time = segEndTime
+
+            # This is a tricky bit of math to set the end time based on when
+            # the first SFT start time of all the segments
+            args.analysis_end_time = (
+                int(
+                    round(
+                        math.floor(
+                            (segEndTime - args.analysis_start_time - args.time_baseline)
+                            / ((1.0 - args.overlap_fraction) * args.time_baseline)
+                        )
+                        * (1.0 - args.overlap_fraction)
+                        * args.time_baseline
+                    )
+                )
+                + args.time_baseline
+                + args.analysis_start_time
+            )
+
+            # Again, this shift could have pushed the end time beyond the start
+            # of the segment, so just fix the end time to the segment start
+            if args.analysis_end_time < segStartTime:
+                args.analysis_end_time = segStartTime
+
+        # If no segment file given and no synchronized starts, just set the
+        # start time and end time to the segment start and end
+        else:
+            args.analysis_start_time = seg[0]
+            args.analysis_end_time = seg[1]
+
+        # Loop through the analysis time; make sure no more than
+        # args.max_num_per_node SFTs are produced by any one node
+        startTimeThisNode = args.analysis_start_time
+        endTimeThisNode = args.analysis_start_time
+        endTimeAllNodes = args.analysis_start_time
+        while endTimeAllNodes < args.analysis_end_time:
+            # increment endTimeAllNodes by the args.time_baseline until we get
+            # past the args.analysis_end_time
+            if args.overlap_fraction != 0.0:
+                # handle overlap
+                if numThisSeg == 0:
+                    endTimeAllNodes = endTimeAllNodes + args.time_baseline
+                else:
+                    endTimeAllNodes = endTimeAllNodes + int(
+                        (1.0 - args.overlap_fraction) * args.time_baseline
+                    )
+            else:
+                # default case, no overlap
+                endTimeAllNodes = endTimeAllNodes + args.time_baseline
+            if endTimeAllNodes <= args.analysis_end_time:
+                # increment the number of SFTs output from this node, and
+                # update the end time this node.
+                numThisNode = numThisNode + 1
+                numThisSeg = numThisSeg + 1
+                endTimeThisNode = endTimeAllNodes
+                if numThisNode < args.max_num_per_node:
+                    continue
+                else:
+                    # write jobs to dag for this node
+                    nodeCount = nodeCount + 1
+
+                    if nodeCount == 1:
+                        startTimeAllNodes = startTimeThisNode
+                    writeToDag(
+                        dagFID,
+                        nodeCount,
+                        startTimeThisNode,
+                        endTimeThisNode,
+                        urls,
+                        args,
+                    )
+                    # Update for next node
+                    numThisNode = 0
+                    if args.overlap_fraction != 0.0:
+                        # handle overlap
+                        startTimeThisNode = endTimeThisNode - int(
+                            (args.overlap_fraction) * args.time_baseline
+                        )
+                    else:
+                        # default case, no overlap
+                        startTimeThisNode = endTimeThisNode
+        else:
+            # we are at or past the args.analysis_end_time; output job for last
+            # node if needed.
+            if numThisNode > 0:
+                # write jobs to dag for this node
+                nodeCount = nodeCount + 1
+
+                if nodeCount == 1:
+                    startTimeAllNodes = startTimeThisNode
+                writeToDag(
+                    dagFID, nodeCount, startTimeThisNode, endTimeThisNode, urls, args
+                )
+        # END while (endTimeAllNodes < args.analysis_end_time)
+    # END for seg in segList
+
+    # Write the move SFTs job to the DAG
+    # Move SFTs
+    dagFID.write(f"JOB MoveSFTs {Path(dagFID.name).parent / 'MoveSFTs.sub'}\n")
+    dagFID.write(f"RETRY MoveSFTs 1\n")
+    dagFID.write(f"VARS MoveSFTs ")
+    if not args.validate:
+        dagFID.write('opts="--no-validate" ')
+    dagFID.write(
+        f'sourcedirectory="." '
+        f"channels=\"{' '.join(args.channel_name)}\" "
+        f"destdirectory=\"{' '.join([str(p) for p in args.output_sft_path])}\"\n"
+    )
+    dagFID.write(
+        f"PARENT {' '.join([f'MakeSFTs_{n}' for n in range(1, nodeCount+1)])} CHILD MoveSFTs\n"
+    )
+
+# Close the DAG file
+
+# Update actual end time of the last job and print out the times all jobs will run on:
+endTimeAllNodes = endTimeThisNode
+
+if startTimeAllNodes is None:
+    raise Exception("The startTimeAllNodes == none; the DAG file contains no jobs!")
+
+if endTimeAllNodes <= startTimeAllNodes:
+    raise Exception(
+        "The endTimeAllNodes <= startTimeAllNodes; the DAG file contains no jobs!"
+    )
+
+print(startTimeAllNodes, endTimeAllNodes)