pyreduce-astro 0.7a4__cp314-cp314-win_amd64.whl

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()

pyreduce/clib/build_extract.py

@@ -0,0 +1,75 @@
+#!/usr/bin/env python3
+"""Builds the C library that contains the extraction algorithm
+
+This module prepares and builds the C libary containing the curved
+(and vertical) extraction algorithm using CFFI.
+It also prepares the ffibuilder objects for setup.py,
+so that the library is compiled on installation.
+
+
+The user can also call the Module as a script to compile the
+C libraries again.
+
+Attributes
+----------
+ffi_builder_vertical : FFI
+    CFFI Builder for the vertical extraction algorithm
+ffi_builder_curved : FFI
+    CFFI Builder for the curved extraction algorithm
+"""
+
+import logging
+import os
+
+from cffi import FFI
+
+logger = logging.getLogger(__name__)
+
+
+CWD = os.path.dirname(__file__)
+CWD = os.path.abspath(CWD)
+release_path = os.path.join(CWD, "Release")
+
+print("Include dir: ", CWD)
+print("Release dir: ", release_path)
+
+
+ffibuilder_vertical = FFI()
+with open(os.path.join(CWD, "slit_func_bd.h")) as f:
+    ffibuilder_vertical.cdef(f.read())
+with open(os.path.join(CWD, "slit_func_bd.c")) as f:
+    ffibuilder_vertical.set_source(
+        "_slitfunc_bd",
+        f.read(),
+        include_dirs=[CWD, release_path],
+        depends=["slit_func_bd.h"],
+    )
+
+ffibuilder_curved = FFI()
+with open(os.path.join(CWD, "slit_func_2d_xi_zeta_bd.h")) as f:
+    ffibuilder_curved.cdef(f.read())
+with open(os.path.join(CWD, "slit_func_2d_xi_zeta_bd.c")) as f:
+    ffibuilder_curved.set_source(
+        "_slitfunc_2d",
+        f.read(),
+        include_dirs=[CWD, release_path],
+        depends=["slit_func_2d_xi_zeta_bd.h"],
+    )
+
+
+def build():
+    """Builds the C slitfunc library"""
+    logger.info("Building required C libraries, this might take a few seconds")
+
+    old_cwd = os.getcwd()
+    path = os.path.abspath(CWD)
+    os.chdir(path)
+
+    ffibuilder_vertical.compile(verbose=True, debug=False)
+    ffibuilder_curved.compile(verbose=True, debug=False)
+
+    os.chdir(old_cwd)
+
+
+if __name__ == "__main__":  # pragma: no cover
+    build()