bat-glimpse 0.1.0__tar.gz

bat_glimpse-0.1.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: bat-glimpse
+Version: 0.1.0
+Summary: Swift BAT GUANO imaging and mosaic pipeline.
+Requires-Python: >=3.9
+Description-Content-Type: text/markdown
+Requires-Dist: BatAnalysis==2.1.0
+Requires-Dist: astroquery>=0.4.10
+Requires-Dist: astropy>=4.3.1
+Requires-Dist: dpath>=2.1.4
+Requires-Dist: emcee
+Requires-Dist: healpy>=1.16.6
+Requires-Dist: histpy>=2.0.2
+Requires-Dist: joblib>=1.1.0
+Requires-Dist: ligo-gracedb
+Requires-Dist: ligo.skymap>=2.1.2
+Requires-Dist: matplotlib>=3.4.2
+Requires-Dist: mhealpy>=0.3.5
+Requires-Dist: numpy>=1.24.4
+Requires-Dist: pandas
+Requires-Dist: reproject>=0.13.1
+Requires-Dist: requests>=2.20
+Requires-Dist: scipy>=1.7.2
+Requires-Dist: setuptools>=58.0.4
+Requires-Dist: swiftbat>=0.1.5
+Requires-Dist: swifttools==3.0.22
+Requires-Dist: tqdm
+Requires-Dist: astro-gdt-swift>=1.0.1
+Requires-Dist: astro-gdt-fermi
+Requires-Dist: scikit-learn
+
+# BAT Glimpse
+
+## Install
+
+After publishing to PyPI:
+
+```bash
+python -m pip install bat-glimpse
+```
+
+From the repository root before publishing:
+
+```bash
+python -m pip install .
+```
+
+## Developer Mode
+
+```bash
+git clone <repository-url>
+cd BAT-GLIMPSE
+python3.10 -m venv .venv
+source .venv/bin/activate
+python -m pip install --upgrade pip
+python -m pip install -e .
+```
+
+Editable mode links the installed command to this checkout, so changes under
+`batglimpse/` are picked up without reinstalling the package.
+
+Run the local checkout with:
+
+```bash
+bat-glimpse --workdir /path/to/workdir --trigtime 2026-01-01T00:00:00.000
+```
+
+or:
+
+```bash
+python -m batglimpse --workdir /path/to/workdir --trigtime 2026-01-01T00:00:00.000
+```
+
+The pipeline also expects the Swift/BAT analysis environment required by
+`batanalysis` to be configured, including HEASoft/CALDB where applicable.
+BAT Glimpse uses `BatAnalysis==2.1.0` and requires Python 3.10 or newer.
+
+## Run
+
+```bash
+bat-glimpse --workdir /path/to/workdir --trigtime 2026-01-01T00:00:00.000
+```
+
+You can also run the package module directly:
+
+```bash
+python -m batglimpse --workdir /path/to/workdir --trigtime 2026-01-01T00:00:00.000
+```
+
+If `--trigtime` is omitted, BAT Glimpse reads `trigtime` from
+`<workdir>/config.json`.
+
+## Main options
+
+- `--workdir`: required working directory for inputs and outputs.
+- `--trigtime`: trigger time in `YYYY-MM-DDTHH:MM:SS.sss` format.
+- `--tmin` and `--tmax`: explicit ad-hoc analysis window.
+- `--pipe`: `imaging` or `mosaic` for ad-hoc analysis.
+- `--ext_obsid`: override the GUANO obsid.
+- `--healpix_nside`: mosaic HEALPix resolution.
+- `--skyview_nprocs`: processes used while creating skyviews.
+- `--mosaic_nprocs`: processes used while mosaicing.
+
+## Outputs
+
+BAT Glimpse writes logs, CSV detections, maps, and diagnostic plots into the
+working directory. The main detection tables are `imaging.csv` and
+`mosaic.csv`.
+
+## Authentication
+
+Set `ECHO_API_TOKEN` if Echo trigger metadata is required:
+
+```bash
+export ECHO_API_TOKEN=your-token
+```

bat_glimpse-0.1.0/README.md

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+# BAT Glimpse
+
+## Install
+
+After publishing to PyPI:
+
+```bash
+python -m pip install bat-glimpse
+```
+
+From the repository root before publishing:
+
+```bash
+python -m pip install .
+```
+
+## Developer Mode
+
+```bash
+git clone <repository-url>
+cd BAT-GLIMPSE
+python3.10 -m venv .venv
+source .venv/bin/activate
+python -m pip install --upgrade pip
+python -m pip install -e .
+```
+
+Editable mode links the installed command to this checkout, so changes under
+`batglimpse/` are picked up without reinstalling the package.
+
+Run the local checkout with:
+
+```bash
+bat-glimpse --workdir /path/to/workdir --trigtime 2026-01-01T00:00:00.000
+```
+
+or:
+
+```bash
+python -m batglimpse --workdir /path/to/workdir --trigtime 2026-01-01T00:00:00.000
+```
+
+The pipeline also expects the Swift/BAT analysis environment required by
+`batanalysis` to be configured, including HEASoft/CALDB where applicable.
+BAT Glimpse uses `BatAnalysis==2.1.0` and requires Python 3.10 or newer.
+
+## Run
+
+```bash
+bat-glimpse --workdir /path/to/workdir --trigtime 2026-01-01T00:00:00.000
+```
+
+You can also run the package module directly:
+
+```bash
+python -m batglimpse --workdir /path/to/workdir --trigtime 2026-01-01T00:00:00.000
+```
+
+If `--trigtime` is omitted, BAT Glimpse reads `trigtime` from
+`<workdir>/config.json`.
+
+## Main options
+
+- `--workdir`: required working directory for inputs and outputs.
+- `--trigtime`: trigger time in `YYYY-MM-DDTHH:MM:SS.sss` format.
+- `--tmin` and `--tmax`: explicit ad-hoc analysis window.
+- `--pipe`: `imaging` or `mosaic` for ad-hoc analysis.
+- `--ext_obsid`: override the GUANO obsid.
+- `--healpix_nside`: mosaic HEALPix resolution.
+- `--skyview_nprocs`: processes used while creating skyviews.
+- `--mosaic_nprocs`: processes used while mosaicing.
+
+## Outputs
+
+BAT Glimpse writes logs, CSV detections, maps, and diagnostic plots into the
+working directory. The main detection tables are `imaging.csv` and
+`mosaic.csv`.
+
+## Authentication
+
+Set `ECHO_API_TOKEN` if Echo trigger metadata is required:
+
+```bash
+export ECHO_API_TOKEN=your-token
+```

bat_glimpse-0.1.0/bat_glimpse.egg-info/PKG-INFO

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+Metadata-Version: 2.4
+Name: bat-glimpse
+Version: 0.1.0
+Summary: Swift BAT GUANO imaging and mosaic pipeline.
+Requires-Python: >=3.9
+Description-Content-Type: text/markdown
+Requires-Dist: BatAnalysis==2.1.0
+Requires-Dist: astroquery>=0.4.10
+Requires-Dist: astropy>=4.3.1
+Requires-Dist: dpath>=2.1.4
+Requires-Dist: emcee
+Requires-Dist: healpy>=1.16.6
+Requires-Dist: histpy>=2.0.2
+Requires-Dist: joblib>=1.1.0
+Requires-Dist: ligo-gracedb
+Requires-Dist: ligo.skymap>=2.1.2
+Requires-Dist: matplotlib>=3.4.2
+Requires-Dist: mhealpy>=0.3.5
+Requires-Dist: numpy>=1.24.4
+Requires-Dist: pandas
+Requires-Dist: reproject>=0.13.1
+Requires-Dist: requests>=2.20
+Requires-Dist: scipy>=1.7.2
+Requires-Dist: setuptools>=58.0.4
+Requires-Dist: swiftbat>=0.1.5
+Requires-Dist: swifttools==3.0.22
+Requires-Dist: tqdm
+Requires-Dist: astro-gdt-swift>=1.0.1
+Requires-Dist: astro-gdt-fermi
+Requires-Dist: scikit-learn
+
+# BAT Glimpse
+
+## Install
+
+After publishing to PyPI:
+
+```bash
+python -m pip install bat-glimpse
+```
+
+From the repository root before publishing:
+
+```bash
+python -m pip install .
+```
+
+## Developer Mode
+
+```bash
+git clone <repository-url>
+cd BAT-GLIMPSE
+python3.10 -m venv .venv
+source .venv/bin/activate
+python -m pip install --upgrade pip
+python -m pip install -e .
+```
+
+Editable mode links the installed command to this checkout, so changes under
+`batglimpse/` are picked up without reinstalling the package.
+
+Run the local checkout with:
+
+```bash
+bat-glimpse --workdir /path/to/workdir --trigtime 2026-01-01T00:00:00.000
+```
+
+or:
+
+```bash
+python -m batglimpse --workdir /path/to/workdir --trigtime 2026-01-01T00:00:00.000
+```
+
+The pipeline also expects the Swift/BAT analysis environment required by
+`batanalysis` to be configured, including HEASoft/CALDB where applicable.
+BAT Glimpse uses `BatAnalysis==2.1.0` and requires Python 3.10 or newer.
+
+## Run
+
+```bash
+bat-glimpse --workdir /path/to/workdir --trigtime 2026-01-01T00:00:00.000
+```
+
+You can also run the package module directly:
+
+```bash
+python -m batglimpse --workdir /path/to/workdir --trigtime 2026-01-01T00:00:00.000
+```
+
+If `--trigtime` is omitted, BAT Glimpse reads `trigtime` from
+`<workdir>/config.json`.
+
+## Main options
+
+- `--workdir`: required working directory for inputs and outputs.
+- `--trigtime`: trigger time in `YYYY-MM-DDTHH:MM:SS.sss` format.
+- `--tmin` and `--tmax`: explicit ad-hoc analysis window.
+- `--pipe`: `imaging` or `mosaic` for ad-hoc analysis.
+- `--ext_obsid`: override the GUANO obsid.
+- `--healpix_nside`: mosaic HEALPix resolution.
+- `--skyview_nprocs`: processes used while creating skyviews.
+- `--mosaic_nprocs`: processes used while mosaicing.
+
+## Outputs
+
+BAT Glimpse writes logs, CSV detections, maps, and diagnostic plots into the
+working directory. The main detection tables are `imaging.csv` and
+`mosaic.csv`.
+
+## Authentication
+
+Set `ECHO_API_TOKEN` if Echo trigger metadata is required:
+
+```bash
+export ECHO_API_TOKEN=your-token
+```

bat_glimpse-0.1.0/bat_glimpse.egg-info/SOURCES.txt

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+README.md
+pyproject.toml
+bat_glimpse.egg-info/PKG-INFO
+bat_glimpse.egg-info/SOURCES.txt
+bat_glimpse.egg-info/dependency_links.txt
+bat_glimpse.egg-info/entry_points.txt
+bat_glimpse.egg-info/requires.txt
+bat_glimpse.egg-info/top_level.txt
+batglimpse/__init__.py
+batglimpse/__main__.py
+batglimpse/bat_glimpse.py
+batglimpse/bat_glimpse_helpers.py
+batglimpse/bat_glimpse_pipeline.py
+batglimpse/bat_glimpse_plotting.py
+batglimpse/bat_glimpse_utils.py

bat_glimpse-0.1.0/bat_glimpse.egg-info/dependency_links.txt

@@ -0,0 +1 @@
+

bat_glimpse-0.1.0/bat_glimpse.egg-info/entry_points.txt

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+[console_scripts]
+bat-glimpse = batglimpse.bat_glimpse:main
+batglimpse = batglimpse.bat_glimpse:main

bat_glimpse-0.1.0/bat_glimpse.egg-info/requires.txt

@@ -0,0 +1,24 @@
+BatAnalysis==2.1.0
+astroquery>=0.4.10
+astropy>=4.3.1
+dpath>=2.1.4
+emcee
+healpy>=1.16.6
+histpy>=2.0.2
+joblib>=1.1.0
+ligo-gracedb
+ligo.skymap>=2.1.2
+matplotlib>=3.4.2
+mhealpy>=0.3.5
+numpy>=1.24.4
+pandas
+reproject>=0.13.1
+requests>=2.20
+scipy>=1.7.2
+setuptools>=58.0.4
+swiftbat>=0.1.5
+swifttools==3.0.22
+tqdm
+astro-gdt-swift>=1.0.1
+astro-gdt-fermi
+scikit-learn

bat_glimpse-0.1.0/bat_glimpse.egg-info/top_level.txt

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+batglimpse

bat_glimpse-0.1.0/batglimpse/__init__.py

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+"""BAT Glimpse package."""
+
+__version__ = "0.1.0"

bat_glimpse-0.1.0/batglimpse/__main__.py

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+from .bat_glimpse import main
+
+
+if __name__ == "__main__":
+    main()

bat_glimpse-0.1.0/batglimpse/bat_glimpse.py

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+import argparse
+import json
+import logging
+import multiprocessing
+import os
+import time
+import warnings
+from pathlib import Path
+
+from swifttools.swift_too import Clock
+
+try:
+    from EchoAPI import API
+except ModuleNotFoundError:
+    API = None
+
+from . import bat_glimpse_helpers as helpers
+from .bat_glimpse_pipeline import guano_query
+
+
+DEFAULT_API_TOKEN = os.getenv("ECHO_API_TOKEN")
+
+
+def parse_args():
+    parser = argparse.ArgumentParser(description="Process some time.")
+    parser.add_argument("--trigtime", required=False, type=str, help="Time in the format YYYY-MM-DDTHH:MM:SS.sss")
+    parser.add_argument("--workdir", required=True, type=str, help="work directory")
+    parser.add_argument("--tmin", required=False, type=str, help="min time to start")
+    parser.add_argument("--tmax", required=False, type=str, help="max time to start")
+    parser.add_argument("--ext_obsid", required=False, type=str, help="obsid")
+    parser.add_argument("--pipe", required=False, type=str, help="pipeline, either imaging or mosaic")
+    parser.add_argument("--healpix_nside", type=int, default=512, help="Nside of mosaic healpix map")
+    parser.add_argument("--skyview_nprocs", type=int, default=8, help="Number of processes to use when creating skyviews in parallel")
+    parser.add_argument("--mosaic_nprocs", type=int, default=8, help="Number of processes to use when creating mosaic in parallel. NOTE: ALLOCATE ~10GB OF MEMORY PER PROCESS.")
+    return parser.parse_args()
+
+
+def load_trigger_metadata(trigid):
+    if API is None:
+        logging.warning("EchoAPI is not available; continuing without external trigger metadata.")
+        return [], []
+    api = API(api_token=DEFAULT_API_TOKEN)
+    parsed_results = [json.loads(entry) for entry in api.get_trigs()]
+    match_ = next((entry for entry in parsed_results if entry.get("trigid") == float(trigid)), None)
+    if match_ is None:
+        logging.error(f"No matching trigger found for trigid {trigid}.")
+        return [], []
+    return match_["event_name"], match_["trigger_instruments"]
+
+
+def prepare_runtime(args):
+    # Normalize path to avoid empty basename when a trailing slash is used.
+    workdir = os.path.abspath(os.path.normpath(args.workdir))
+    trigid = os.path.basename(workdir)[:9]
+    if not trigid:
+        raise ValueError(f"Unable to derive trigid from workdir: {workdir}")
+    os.makedirs(workdir, exist_ok=True)
+    warnings.filterwarnings("ignore")
+    log_path = os.path.join(workdir, "batglimpse.log")
+    logging.basicConfig(
+        filename=log_path,
+        level=logging.INFO,
+        format="%(asctime)s - %(levelname)s - %(message)s",
+        filemode="w",
+        force=True,
+    )
+    ext_trig, trig_instr = load_trigger_metadata(trigid)
+    helpers.set_runtime_context(workdir=workdir, trigid=trigid, ext_trig=ext_trig, trig_instr=trig_instr)
+    return workdir, trigid, ext_trig, trig_instr
+
+
+def create_nitrates_config(
+    trigger_time,
+    output_file="config.json",
+    trigger_id=0,
+    queue_id=0,
+):
+
+    config = {
+        "ERRORS": [],
+        "WARNINGS": [],
+        "config": {
+            "BkgPost": "true",
+            "BkgPre": "true",
+            "BkgSrcPosFit": "null",
+            "Epeaks": [97.7, 212.1, 460.6],
+            "Gammas": [0.1, 0.6, 1.1],
+            "MaxDT": 20.48,
+            "MaxDur": 16.384,
+            "MinDT": -20.48,
+            "MinDur": 0.128,
+            "id": 99,
+            "minSNR": 2.5,
+            "name": "Default",
+            "version": "0.0.0",
+        },
+        "queueID": queue_id,
+        "triggerID": trigger_id,
+        "trigtime": trigger_time,
+    }
+
+    with open(output_file, "w") as f:
+        json.dump(config, f, indent=4)
+
+
+def main():
+    start_time = time.time()
+    print(f"Number of CPU cores available: {multiprocessing.cpu_count()}")
+    args = parse_args()
+    workdir, trigid, ext_trig, trig_instr = prepare_runtime(args)
+
+    create_nitrates_config(
+        trigger_time=args.trigtime,
+        output_file=os.path.join(args.workdir, "config.json"),
+    )
+
+    triggertime = args.trigtime
+    tmin = args.tmin
+    tmax = args.tmax
+    ext_obsid = args.ext_obsid
+    pipe = args.pipe
+    healpix_nside = args.healpix_nside
+    skyview_nprocs = args.skyview_nprocs
+    mosaic_nprocs = args.mosaic_nprocs
+
+    if triggertime is not None:
+        logging.info("Trying using already existing data")
+        with open(os.path.join(workdir, "config.json"), "r", encoding="utf-8") as handle:
+            config = json.load(handle)
+        triggertime = config.get("trigtime")
+        fail = False
+        start_time_try = time.time()
+        helpers.search_ext_maps(triggertime, workdir)
+        guano_query(triggertime, ext_obsid, workdir, tmin, tmax, pipe, healpix_nside, skyview_nprocs, mosaic_nprocs)
+
+    logging.info(f"Time spent: {time.time() - start_time} seconds")
+    try:
+        log_file = os.path.join(workdir, "batglimpse.log")
+        name_id = os.path.basename(workdir)
+    except Exception:
+        logging.error(f"Error in copying log file: {helpers.traceback.format_exc()}")

bat_glimpse-0.1.0/batglimpse/bat_glimpse_helpers.py

@@ -0,0 +1 @@
+from .bat_glimpse_utils import *