pyreduce-astro 0.6.0__cp314-cp314-win_amd64.whl → 0.7a2__cp314-cp314-win_amd64.whl

pyreduce/__main__.py

@@ -1,106 +1,206 @@
 """
-This is used when pyreduce is used as a script
+PyReduce command-line interface.
+
+Usage:
+    uv run reduce --help
+    uv run reduce run UVES HD132205 --night 2010-04-01
+    uv run reduce run UVES HD132205 --steps bias,flat,orders
+    uv run reduce bias UVES HD132205
+    uv run reduce combine --output combined.fits *.final.fits
 """
 
-import argparse
-import sys
+import click
 
-from .reduce import main
+from . import datasets
+from .configuration import get_configuration_for_instrument
+from .reduce import main as reduce_main
 from .tools.combine import combine as tools_combine
 
-scripts = ["reduce", "combine"]
-
-
-def help():
-    parser = argparse.ArgumentParser(
-        description="PyReduce script tools interface", prog="python -m pyreduce"
-    )
-    parser.add_argument("script", help="which script to execute", choices=scripts)
-    parser.print_help()
-
-
-def reduce():
-    parser = argparse.ArgumentParser(
-        description="PyReduce script tools interface", prog="python -m pyreduce"
-    )
-    parser.add_argument("script", help="which script to execute", choices=["reduce"])
-
-    parser.add_argument("-b", "--bias", action="store_true", help="Create master bias")
-    parser.add_argument("-f", "--flat", action="store_true", help="Create master flat")
-    parser.add_argument("-o", "--orders", action="store_true", help="Trace orders")
-    parser.add_argument("-n", "--norm_flat", action="store_true", help="Normalize flat")
-    parser.add_argument(
-        "-w", "--wavecal", action="store_true", help="Prepare wavelength calibration"
-    )
-    parser.add_argument(
-        "-s", "--science", action="store_true", help="Extract science spectrum"
-    )
-    parser.add_argument(
-        "-c", "--continuum", action="store_true", help="Normalize continuum"
-    )
-
-    parser.add_argument("instrument", type=str, help="instrument used")
-    parser.add_argument("target", type=str, help="target star")
-
-    args = parser.parse_args()
-    instrument = args.instrument.upper()
-    target = args.target.upper()
-
-    steps_to_take = {
-        "bias": args.bias,
-        "flat": args.flat,
-        "orders": args.orders,
-        "norm_flat": args.norm_flat,
-        "wavecal": args.wavecal,
-        "science": args.science,
-        "continuum": args.continuum,
-    }
-    steps_to_take = [k for k, v in steps_to_take.items() if v]
-
-    # if no steps are specified use all
-    if len(steps_to_take) == 0:
-        steps_to_take = "all"
-
-    main(instrument=instrument, target=target, steps=steps_to_take)
-
-
-def combine():
-    parser = argparse.ArgumentParser(
-        description="PyReduce script tools interface", prog="python -m pyreduce"
-    )
-    parser.add_argument("script", help="which script to execute", choices=["combine"])
-
-    parser.add_argument(
-        "--output", help="destination of the combined file", default="./combined.ech"
-    )
-    parser.add_argument(
-        "--plot", type=int, help="plot the results of the desired order"
-    )
-
-    parser.add_argument(
-        "input", nargs="+", help="input files to use", default="./*.final.ech"
+ALL_STEPS = (
+    "bias",
+    "flat",
+    "orders",
+    "curvature",
+    "scatter",
+    "norm_flat",
+    "wavecal_master",
+    "wavecal_init",
+    "wavecal",
+    "freq_comb_master",
+    "freq_comb",
+    "science",
+    "continuum",
+    "finalize",
+)
+
+
+@click.group()
+@click.version_option(package_name="pyreduce-astro")
+def cli():
+    """PyReduce - Echelle spectrograph data reduction pipeline."""
+    pass
+
+
+@cli.command()
+@click.argument("instrument")
+@click.argument("target")
+@click.option("--night", "-n", default=None, help="Observation night (YYYY-MM-DD)")
+@click.option("--arm", "-a", default=None, help="Instrument arm/detector")
+@click.option(
+    "--steps",
+    "-s",
+    default=None,
+    help="Comma-separated steps to run (default: all)",
+)
+@click.option(
+    "--base-dir",
+    "-b",
+    default=None,
+    help="Base directory for data (default: $REDUCE_DATA or ~/REDUCE_DATA)",
+)
+@click.option(
+    "--input-dir", "-i", default="raw", help="Input directory relative to base"
+)
+@click.option(
+    "--output-dir", "-o", default="reduced", help="Output directory relative to base"
+)
+@click.option(
+    "--plot", "-p", default=0, help="Plot level (0=none, 1=save, 2=interactive)"
+)
+@click.option(
+    "--order-range",
+    default=None,
+    help="Order range to process (e.g., '1,21')",
+)
+def run(
+    instrument,
+    target,
+    night,
+    arm,
+    steps,
+    base_dir,
+    input_dir,
+    output_dir,
+    plot,
+    order_range,
+):
+    """Run the reduction pipeline.
+
+    INSTRUMENT: Name of the instrument (e.g., UVES, HARPS, XSHOOTER)
+    TARGET: Target star name or regex pattern
+    """
+    # Parse steps
+    if steps:
+        steps = tuple(s.strip() for s in steps.split(","))
+    else:
+        steps = "all"
+
+    # Parse order range
+    if order_range:
+        parts = order_range.split(",")
+        order_range = (int(parts[0]), int(parts[1]))
+
+    # Load configuration
+    config = get_configuration_for_instrument(instrument)
+
+    # Run reduction
+    reduce_main(
+        instrument=instrument,
+        target=target,
+        night=night,
+        arms=arm,
+        steps=steps,
+        base_dir=base_dir or "",
+        input_dir=input_dir,
+        output_dir=output_dir,
+        configuration=config,
+        order_range=order_range,
+        plot=plot,
     )
 
-    args = parser.parse_args()
-
-    files = args.input
-    output = args.output
-    plot = args.plot
 
-    tools_combine(files, output, plot=plot)
+@cli.command()
+@click.argument("files", nargs=-1, required=True)
+@click.option("--output", "-o", default="combined.fits", help="Output filename")
+@click.option("--plot", "-p", default=None, type=int, help="Plot specific order")
+def combine(files, output, plot):
+    """Combine multiple reduced spectra.
+
+    FILES: Input .final.fits files to combine
+    """
+    tools_combine(list(files), output, plot=plot)
+
+
+@cli.command()
+@click.argument("instrument")
+def download(instrument):
+    """Download sample dataset for an instrument.
+
+    INSTRUMENT: Name of the instrument (e.g., UVES, HARPS)
+    """
+    instrument = instrument.upper()
+    dataset_func = getattr(datasets, instrument, None)
+    if dataset_func is None:
+        available = [
+            name
+            for name in dir(datasets)
+            if name.isupper() and not name.startswith("_")
+        ]
+        raise click.ClickException(
+            f"Unknown instrument '{instrument}'. Available: {', '.join(available)}"
+        )
+    path = dataset_func()
+    click.echo(f"Dataset downloaded to: {path}")
+
+
+@cli.command("list-steps")
+def list_steps():
+    """List all available reduction steps."""
+    click.echo("Available reduction steps:")
+    for step in ALL_STEPS:
+        click.echo(f"  - {step}")
+
+
+def make_step_command(step_name):
+    """Factory to create a command for a single step."""
+
+    @click.command(name=step_name)
+    @click.argument("instrument")
+    @click.argument("target")
+    @click.option("--night", "-n", default=None, help="Observation night")
+    @click.option("--arm", "-a", default=None, help="Instrument arm")
+    @click.option("--base-dir", "-b", default=None, help="Base directory")
+    @click.option("--input-dir", "-i", default="raw", help="Input directory")
+    @click.option("--output-dir", "-o", default="reduced", help="Output directory")
+    @click.option("--plot", "-p", default=0, help="Plot level")
+    def cmd(instrument, target, night, arm, base_dir, input_dir, output_dir, plot):
+        config = get_configuration_for_instrument(instrument)
+        reduce_main(
+            instrument=instrument,
+            target=target,
+            night=night,
+            arms=arm,
+            steps=(step_name,),
+            base_dir=base_dir or "",
+            input_dir=input_dir,
+            output_dir=output_dir,
+            configuration=config,
+            plot=plot,
+        )
+
+    cmd.__doc__ = f"Run the '{step_name}' step."
+    return cmd
+
+
+# Register individual step commands
+for _step in ALL_STEPS:
+    cli.add_command(make_step_command(_step))
+
+
+def main():
+    """Entry point for the CLI."""
+    cli()
 
 
 if __name__ == "__main__":
-    # Determine which script to run
-    if len(sys.argv) == 1:
-        script = "help"
-    else:
-        script = sys.argv[1]
-
-    # Run the chosen script
-    if script == "reduce":
-        reduce()
-    elif script == "combine":
-        combine()
-    else:
-        help()
+    main()

pyreduce/cli.py

@@ -0,0 +1,342 @@
+"""Click-based CLI for PyReduce.
+
+Usage:
+    uv run reduce --help
+    uv run reduce bias INSTRUMENT --files bias/*.fits --output output/
+    uv run reduce run reduction.yaml
+"""
+
+from __future__ import annotations
+
+from glob import glob
+from pathlib import Path
+
+import click
+
+from . import datasets
+from .instruments.instrument_info import load_instrument
+from .pipeline import Pipeline
+
+# Map CLI names to dataset functions
+AVAILABLE_DATASETS = {
+    "UVES": datasets.UVES,
+    "HARPS": datasets.HARPS,
+    "XSHOOTER": datasets.XSHOOTER,
+    "NIRSPEC": datasets.KECK_NIRSPEC,
+    "JWST_NIRISS": datasets.JWST_NIRISS,
+    "JWST_MIRI": datasets.JWST_MIRI,
+    "LICK_APF": datasets.LICK_APF,
+    "MCDONALD": datasets.MCDONALD,
+}
+
+
+@click.group()
+@click.version_option(package_name="pyreduce-astro")
+def cli():
+    """PyReduce echelle spectrograph reduction pipeline."""
+    pass
+
+
+@cli.command()
+@click.argument("instrument")
+@click.option(
+    "--output",
+    "-o",
+    default=None,
+    help="Output directory (default: $REDUCE_DATA or ~/REDUCE_DATA)",
+)
+def download(instrument: str, output: str | None):
+    """Download example dataset for an instrument.
+
+    Available instruments: UVES, HARPS, XSHOOTER, NIRSPEC, JWST_NIRISS, JWST_MIRI,
+    LICK_APF, MCDONALD
+
+    Data is saved to $REDUCE_DATA if set, otherwise ~/REDUCE_DATA.
+
+    \b
+    Examples:
+        uv run reduce download UVES
+        uv run reduce download UVES -o ~/data/
+    """
+    instrument_upper = instrument.upper()
+    if instrument_upper not in AVAILABLE_DATASETS:
+        available = ", ".join(sorted(AVAILABLE_DATASETS.keys()))
+        raise click.ClickException(
+            f"Unknown instrument '{instrument}'. Available: {available}"
+        )
+
+    click.echo(f"Downloading {instrument_upper} example dataset...")
+    data_dir = AVAILABLE_DATASETS[instrument_upper](output)
+    click.echo(f"Dataset saved to: {data_dir}")
+
+
+@cli.command("list-datasets")
+def list_datasets():
+    """List available example datasets."""
+    click.echo("Available example datasets:")
+    click.echo()
+    for name in sorted(AVAILABLE_DATASETS.keys()):
+        click.echo(f"  {name}")
+    click.echo()
+    click.echo("Download with: uv run reduce download <INSTRUMENT> -o <DIR>")
+
+
+@cli.command()
+@click.argument("instrument")
+@click.option(
+    "--files",
+    "-f",
+    multiple=True,
+    help="Input FITS files (can use glob patterns)",
+)
+@click.option("--output", "-o", default=".", help="Output directory")
+@click.option("--mode", "-m", default="", help="Instrument mode (e.g., RED, BLUE)")
+@click.option(
+    "--plot", "-p", default=0, type=int, help="Plot level (0=off, 1=basic, 2=detailed)"
+)
+def bias(instrument: str, files: tuple[str, ...], output: str, mode: str, plot: int):
+    """Create master bias from bias frames."""
+    inst = load_instrument(instrument)
+    file_list = _expand_globs(files)
+
+    if not file_list:
+        raise click.ClickException("No input files specified. Use --files option.")
+
+    click.echo(f"Creating master bias from {len(file_list)} files...")
+    Pipeline(inst, output, mode=mode, plot=plot).bias(file_list).run()
+    click.echo(f"Master bias saved to {output}")
+
+
+@cli.command()
+@click.argument("instrument")
+@click.option(
+    "--files",
+    "-f",
+    multiple=True,
+    help="Input FITS files (can use glob patterns)",
+)
+@click.option("--output", "-o", default=".", help="Output directory")
+@click.option("--mode", "-m", default="", help="Instrument mode")
+@click.option(
+    "--plot", "-p", default=0, type=int, help="Plot level (0=off, 1=basic, 2=detailed)"
+)
+def flat(instrument: str, files: tuple[str, ...], output: str, mode: str, plot: int):
+    """Create master flat from flat frames."""
+    inst = load_instrument(instrument)
+    file_list = _expand_globs(files)
+
+    if not file_list:
+        raise click.ClickException("No input files specified. Use --files option.")
+
+    click.echo(f"Creating master flat from {len(file_list)} files...")
+    Pipeline(inst, output, mode=mode, plot=plot).flat(file_list).run()
+    click.echo(f"Master flat saved to {output}")
+
+
+@cli.command()
+@click.argument("instrument")
+@click.option(
+    "--files",
+    "-f",
+    multiple=True,
+    help="Flat files for tracing (optional if flat already exists)",
+)
+@click.option("--output", "-o", default=".", help="Output directory")
+@click.option("--mode", "-m", default="", help="Instrument mode")
+@click.option(
+    "--plot", "-p", default=0, type=int, help="Plot level (0=off, 1=basic, 2=detailed)"
+)
+def trace(instrument: str, files: tuple[str, ...], output: str, mode: str, plot: int):
+    """Trace echelle orders on flat field."""
+    inst = load_instrument(instrument)
+    file_list = _expand_globs(files) if files else None
+
+    click.echo("Tracing echelle orders...")
+    pipe = Pipeline(inst, output, mode=mode, plot=plot)
+    if file_list:
+        pipe = pipe.flat(file_list)
+    pipe.trace_orders(file_list).run()
+    click.echo(f"Order trace saved to {output}")
+
+
+@cli.command()
+@click.argument("instrument")
+@click.option(
+    "--files",
+    "-f",
+    multiple=True,
+    required=True,
+    help="Wavelength calibration files (ThAr, etc.)",
+)
+@click.option("--output", "-o", default=".", help="Output directory")
+@click.option("--mode", "-m", default="", help="Instrument mode")
+@click.option(
+    "--plot", "-p", default=0, type=int, help="Plot level (0=off, 1=basic, 2=detailed)"
+)
+def wavecal(instrument: str, files: tuple[str, ...], output: str, mode: str, plot: int):
+    """Perform wavelength calibration."""
+    inst = load_instrument(instrument)
+    file_list = _expand_globs(files)
+
+    if not file_list:
+        raise click.ClickException("No input files specified. Use --files option.")
+
+    click.echo(f"Running wavelength calibration with {len(file_list)} files...")
+    Pipeline(inst, output, mode=mode, plot=plot).wavelength_calibration(file_list).run()
+    click.echo(f"Wavelength calibration saved to {output}")
+
+
+@cli.command()
+@click.argument("instrument")
+@click.option(
+    "--files",
+    "-f",
+    multiple=True,
+    required=True,
+    help="Science observation files",
+)
+@click.option("--output", "-o", default=".", help="Output directory")
+@click.option("--mode", "-m", default="", help="Instrument mode")
+@click.option("--target", "-t", default="", help="Target name")
+@click.option(
+    "--plot", "-p", default=0, type=int, help="Plot level (0=off, 1=basic, 2=detailed)"
+)
+def extract(
+    instrument: str,
+    files: tuple[str, ...],
+    output: str,
+    mode: str,
+    target: str,
+    plot: int,
+):
+    """Extract spectra from science frames."""
+    inst = load_instrument(instrument)
+    file_list = _expand_globs(files)
+
+    if not file_list:
+        raise click.ClickException("No input files specified. Use --files option.")
+
+    click.echo(f"Extracting spectra from {len(file_list)} files...")
+    Pipeline(inst, output, mode=mode, target=target, plot=plot).extract(file_list).run()
+    click.echo(f"Extracted spectra saved to {output}")
+
+
+@cli.command()
+@click.argument("config_file", type=click.Path(exists=True))
+@click.option(
+    "--steps",
+    "-s",
+    default="all",
+    help="Steps to run (comma-separated, or 'all')",
+)
+@click.option("--skip-existing", is_flag=True, help="Skip steps with existing output")
+@click.option(
+    "--plot", "-p", default=0, type=int, help="Plot level (0=off, 1=basic, 2=detailed)"
+)
+def run(config_file: str, steps: str, skip_existing: bool, plot: int):
+    """Run full reduction pipeline from config file.
+
+    CONFIG_FILE should be a YAML file with instrument, files, and output settings.
+
+    Example config.yaml:
+
+    \b
+        instrument: UVES
+        output: /data/reduced/
+        mode: RED
+        files:
+          bias: /data/raw/bias/*.fits
+          flat: /data/raw/flat/*.fits
+          wavecal: /data/raw/thar/*.fits
+          science: /data/raw/science/*.fits
+        steps: [bias, flat, trace, wavecal, extract]
+    """
+    import yaml
+
+    with open(config_file) as f:
+        config = yaml.safe_load(f)
+
+    instrument_name = config.get("instrument")
+    if not instrument_name:
+        raise click.ClickException("Config file must specify 'instrument'")
+
+    inst = load_instrument(instrument_name)
+    output = config.get("output", ".")
+    mode = config.get("mode", "")
+    target = config.get("target", "")
+    files = config.get("files", {})
+    config_steps = config.get("steps", [])
+
+    # Parse steps
+    if steps != "all":
+        config_steps = [s.strip() for s in steps.split(",")]
+    elif not config_steps:
+        config_steps = ["bias", "flat", "trace", "wavecal", "extract"]
+
+    click.echo(f"Running pipeline for {instrument_name}")
+    click.echo(f"Steps: {', '.join(config_steps)}")
+    click.echo(f"Output: {output}")
+
+    pipe = Pipeline(inst, output, mode=mode, target=target, plot=plot)
+
+    # Add steps based on config
+    if "bias" in config_steps and files.get("bias"):
+        pipe = pipe.bias(_expand_globs(files["bias"]))
+
+    if "flat" in config_steps and files.get("flat"):
+        pipe = pipe.flat(_expand_globs(files["flat"]))
+
+    if "trace" in config_steps:
+        trace_files = files.get("orders") or files.get("flat")
+        pipe = pipe.trace_orders(_expand_globs(trace_files) if trace_files else None)
+
+    if "scatter" in config_steps:
+        pipe = pipe.scatter()
+
+    if "norm_flat" in config_steps:
+        pipe = pipe.normalize_flat()
+
+    if "wavecal" in config_steps and files.get("wavecal"):
+        pipe = pipe.wavelength_calibration(_expand_globs(files["wavecal"]))
+
+    if "curvature" in config_steps:
+        curv_files = files.get("curvature") or files.get("wavecal")
+        pipe = pipe.curvature(_expand_globs(curv_files) if curv_files else None)
+
+    if "extract" in config_steps and files.get("science"):
+        pipe = pipe.extract(_expand_globs(files["science"]))
+
+    if "continuum" in config_steps:
+        pipe = pipe.continuum()
+
+    if "finalize" in config_steps:
+        pipe = pipe.finalize()
+
+    pipe.run(skip_existing=skip_existing)
+    click.echo("Pipeline complete!")
+
+
+def _expand_globs(patterns) -> list[str]:
+    """Expand glob patterns to file list."""
+    if isinstance(patterns, str):
+        patterns = [patterns]
+
+    files = []
+    for pattern in patterns:
+        expanded = glob(pattern)
+        if expanded:
+            files.extend(expanded)
+        else:
+            # If no glob match, treat as literal path
+            if Path(pattern).exists():
+                files.append(pattern)
+    return sorted(set(files))
+
+
+def main():
+    """Entry point for the CLI."""
+    cli()
+
+
+if __name__ == "__main__":
+    main()