SpecProc 1.0.0__py3-none-any.whl

specproc/main.py

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+"""
+SpecProc: Main application entry point.
+
+PyQt-based GUI for echelle spectrograph FITS data reduction.
+"""
+# 提供图形界面与命令行程序入口。
+
+import sys
+import argparse
+import logging
+import shutil
+import time
+from logging.handlers import RotatingFileHandler
+from pathlib import Path
+from typing import Dict, List, Optional, Tuple
+
+from astropy.io import fits
+
+from specproc.config.config_manager import (
+    ConfigManager,
+    list_telescope_profiles,
+    resolve_telescope_profile,
+)
+from specproc.core.processing_pipeline import ProcessingPipeline
+
+
+COPY_DEFAULT_CONFIG_SENTINEL = '__COPY_DEFAULT_CONFIG__'
+
+
+# 设置文件与控制台日志输出。
+def setup_logging(log_file: str = 'specproc.log'):
+    """Setup application logging."""
+    logger = logging.getLogger()
+    logger.setLevel(logging.INFO)  # Set to INFO to reduce debug noise
+
+    # Reduce matplotlib logging - set more specific loggers
+    logging.getLogger('matplotlib').setLevel(logging.WARNING)
+    logging.getLogger('matplotlib.font_manager').setLevel(logging.WARNING)
+    logging.getLogger('matplotlib.pyplot').setLevel(logging.WARNING)
+    logging.getLogger('PIL').setLevel(logging.WARNING)
+    
+    # Also disable font manager's verbose output
+    import matplotlib
+    matplotlib.rcParams['font.family'] = 'sans-serif'
+    matplotlib.rcParams['font.sans-serif'] = ['DejaVu Sans']
+    matplotlib.rcParams['axes.unicode_minus'] = False
+
+    # File handler
+    file_handler = RotatingFileHandler(
+        log_file, maxBytes=10*1024*1024, backupCount=5
+    )
+    file_handler.setLevel(logging.INFO)  # File also at INFO level
+
+    # Console handler
+    console_handler = logging.StreamHandler(sys.stdout)
+    console_handler.setLevel(logging.INFO)
+
+    # Formatter
+    formatter = logging.Formatter(
+        '%(asctime)s - %(name)s - %(levelname)s - %(message)s'
+    )
+    file_handler.setFormatter(formatter)
+    console_handler.setFormatter(formatter)
+
+    # Add handlers
+    logger.addHandler(file_handler)
+    logger.addHandler(console_handler)
+
+    logger.info("=" * 60)
+    logger.info("SpecProc Application Started")
+    logger.info("=" * 60)
+
+
+# 从输入文件或目录收集FITS图像。
+def _collect_input_fits_files(inputs: List[str]) -> List[str]:
+    """Collect FITS files from positional CLI inputs (files and/or directories)."""
+    paths = inputs if inputs else ['.']
+    discovered: List[Path] = []
+
+    for item in paths:
+        p = Path(item).expanduser()
+        if p.is_dir():
+            # Recursively scan directory and subdirectories for FITS files.
+            for pattern in ('*.fits', '*.fit', '*.FITS', '*.FIT'):
+                discovered.extend(sorted(p.rglob(pattern)))
+        elif p.is_file() and p.suffix.lower() in ('.fits', '.fit'):
+            discovered.append(p)
+
+    # Remove duplicates while preserving deterministic order.
+    unique_files: List[str] = []
+    seen = set()
+    for file_path in sorted(discovered):
+        key = str(file_path.resolve())
+        if key not in seen:
+            seen.add(key)
+            unique_files.append(str(file_path.resolve()))
+
+    return unique_files
+
+
+# 读取FITS头中的帧类型与曝光时间。
+def _read_frame_type_hint(fits_path: str) -> Tuple[str, Optional[float]]:
+    """Read frame-type hints and exposure time from FITS headers."""
+    collected: List[str] = []
+    exposure_value: Optional[float] = None
+
+    with fits.open(fits_path) as hdul:
+        for idx in range(len(hdul)):
+            header = getattr(hdul[idx], 'header', None)
+            if header is None:
+                continue
+
+            # Prioritize dedicated type keywords.
+            for key in ('OBSTYPE', 'IMAGETYP', 'OBJECT'):
+                value = str(header.get(key, '')).strip()
+                if value:
+                    collected.append(value)
+
+            if exposure_value is None:
+                raw_exptime = header.get('EXPTIME', header.get('EXPOSURE', None))
+                try:
+                    if raw_exptime is not None:
+                        exposure_value = float(raw_exptime)
+                except (TypeError, ValueError):
+                    pass
+
+            # Some observatories store frame type only in COMMENT.
+            comments = header.get('COMMENT', [])
+            if isinstance(comments, str):
+                if comments.strip():
+                    collected.append(comments.strip())
+            else:
+                for comment in comments:
+                    c = str(comment).strip()
+                    if c:
+                        collected.append(c)
+
+    # Deduplicate while preserving order.
+    seen = set()
+    unique_values: List[str] = []
+    for value in collected:
+        key = value.lower()
+        if key not in seen:
+            seen.add(key)
+            unique_values.append(value)
+
+    return ' | '.join(unique_values), exposure_value
+
+
+# 根据头信息判断观测帧类别。
+def _classify_obstype(obstype: str) -> Optional[str]:
+    """Map header type hints to one of: bias, flat, calib, science."""
+    normalized = obstype.strip().lower().replace('_', ' ')
+    if not normalized:
+        return None
+
+    bias_tokens = {'bias', 'zero'}
+    flat_tokens = {'flat', 'quartz', 'halogen', 'continuum', 'tungsten'}
+    calib_tokens = {'thar', 'lamp', 'arc', 'comparison', 'comp', 'fear', 'ne', 'ar', 'he'}
+    science_tokens = {'science', 'object', 'target', 'star', 'source'}
+
+    if any(tok in normalized for tok in bias_tokens):
+        return 'bias'
+    if any(tok in normalized for tok in flat_tokens):
+        return 'flat'
+    if any(tok in normalized for tok in calib_tokens):
+        return 'calib'
+    if any(tok in normalized for tok in science_tokens):
+        return 'science'
+
+    return None
+
+
+# 分类输入图像并运行命令行归约流程。
+def run_cli_mode(config_path: Optional[str], inputs: List[str]) -> Dict:
+    """Run full pipeline in CLI mode using OBSTYPE-based FITS classification."""
+    logger = logging.getLogger(__name__)
+    started_at = time.perf_counter()
+    fits_files = _collect_input_fits_files(inputs)
+    if not fits_files:
+        raise FileNotFoundError(
+            'No FITS files found. Provide FITS files or directories, e.g. '\
+            'specproc --mode cli 20241102_hrs'
+        )
+
+    config = ConfigManager(config_path)
+    grouped: Dict[str, List[str]] = {
+        'bias': [],
+        'flat': [],
+        'calib': [],
+        'science': [],
+    }
+    unknown: List[Tuple[str, str]] = []
+    by_filename = config.get('data', 'frame_type_source', 'header').strip().lower() == 'filename'
+    is_slit = config.get('telescope', 'instrument', '').strip().lower() == 'slit'
+
+    # 读取并规范化帧类型匹配关键词。
+    def _keywords(key: str, default: str) -> List[str]:
+        return [k.strip().lower() for k in config.get('data', key, default).split(',') if k.strip()]
+
+    kw = {
+        'bias': _keywords('bias_keywords', 'bias'),
+        'flat': _keywords('flat_keywords', 'flat'),
+        'calib': _keywords('lamp_keywords', 'fear'),
+        'dark': _keywords('dark_keywords', 'dark'),
+    }
+
+    for file_path in fits_files:
+        try:
+            if by_filename:
+                fname = Path(file_path).name.lower()
+                category = 'science'
+                for cat in ('bias', 'flat', 'calib', 'dark'):
+                    if any(k in fname for k in kw[cat]):
+                        category = cat
+                        break
+                if category == 'dark':
+                    logger.info(f"Dark frame not used: {Path(file_path).name}")
+                    continue
+                grouped[category].append(file_path)
+                continue
+
+            obstype, exposure_value = _read_frame_type_hint(file_path)
+            category = _classify_obstype(obstype)
+            if category is None and exposure_value is not None and exposure_value > 0:
+                category = 'science'
+
+            if category is None:
+                unknown.append((file_path, obstype))
+                continue
+            grouped[category].append(file_path)
+        except Exception as exc:
+            logger.warning(f"Skip unreadable FITS file {file_path}: {exc}")
+
+    if unknown:
+        for file_path, obstype in unknown:
+            logger.warning(
+                f"Unrecognized frame type for {Path(file_path).name}: '{obstype}'. File is skipped."
+            )
+
+    required = ('bias', 'science') if is_slit else ('bias', 'flat', 'calib', 'science')
+    missing = [name for name in required if not grouped[name]]
+    if missing:
+        counts = ', '.join([f"{key}={len(val)}" for key, val in grouped.items()])
+        raise RuntimeError(
+            f"Frame classification incomplete ({counts}). Missing: {', '.join(missing)}."
+        )
+
+    logger.info(
+        "CLI classification result: "
+        f"bias={len(grouped['bias'])}, flat={len(grouped['flat'])}, "
+        f"calib={len(grouped['calib'])}, science={len(grouped['science'])}"
+    )
+
+    processed_files = grouped['bias'] + grouped['flat'] + grouped['calib'] + grouped['science']
+    total_bytes = sum(Path(file_path).stat().st_size for file_path in processed_files if Path(file_path).exists())
+    total_mb = total_bytes / (1024.0 * 1024.0)
+
+    pipeline = ProcessingPipeline(config)
+    result = pipeline.run_full_pipeline(
+        raw_image_paths=grouped['science'],
+        bias_filenames=grouped['bias'],
+        flat_filenames=grouped['flat'],
+        calib_filenames=grouped['calib'],
+    )
+
+    elapsed_minutes = (time.perf_counter() - started_at) / 60.0
+    speed = total_mb / elapsed_minutes if elapsed_minutes > 0 else 0.0
+    logger.info(
+        f"CLI processing summary: elapsed={elapsed_minutes:.2f} min, "
+        f"input_size={total_mb:.2f} MB, throughput={speed:.2f} MB/min"
+    )
+
+    return result
+
+
+# 将所选默认配置复制到当前目录。
+def copy_default_config_to_cwd(target_filename: str = 'specproc.cfg',
+                                profile: Optional[str] = None) -> Path:
+    """Copy a packaged default config into the current working directory.
+
+    Args:
+        target_filename: Name of the file to create in the current directory.
+        profile: Optional telescope profile name (e.g. 'XL216_hrs' for the
+            Xinglong 2.16m HRS, 'MSTG193_slit' for the Muztagh-Ata 1.93m slit
+            spectrograph). If omitted, the generic default_config.cfg is used.
+    """
+    if profile:
+        default_config = resolve_telescope_profile(profile)
+        if default_config is None:
+            available = ', '.join(sorted(list_telescope_profiles())) or '(none)'
+            raise FileNotFoundError(
+                f"Unknown telescope profile '{profile}'. Available profiles: {available}"
+            )
+    else:
+        default_config = Path(__file__).parent / 'config' / 'default_config.cfg'
+        if not default_config.exists():
+            raise FileNotFoundError(f'Default config file not found: {default_config}')
+
+    target_path = Path.cwd() / target_filename
+    if target_path.exists():
+        print(f'Config already exists: {target_path}')
+        return target_path
+
+    shutil.copyfile(default_config, target_path)
+    suffix = f' (telescope profile: {profile})' if profile else ''
+    print(f'Default config copied to: {target_path}{suffix}')
+    return target_path
+
+
+# 解析启动参数并选择程序运行模式。
+def main(config_path: Optional[str] = None, mode: Optional[str] = None):
+    """Main application entry point.
+    
+    Args:
+        config_path: Path to configuration file (optional)
+        mode: Run mode ('gui' or 'cli')
+    """
+    # Parse command line arguments first (before QApplication)
+    telescope_profiles = sorted(list_telescope_profiles())
+    profiles_hint = ', '.join(telescope_profiles) if telescope_profiles else '(none packaged)'
+    parser = argparse.ArgumentParser(
+        description='SpecProc - Spectral Processing Tool for Echelle Spectrographs',
+        epilog='Examples:\n  specproc                        # Start GUI mode\n  specproc 20241102_hrs           # Auto CLI mode with directory input\n  specproc --config               # Copy default config to current directory\n  specproc --mode cli 20241102_hrs\n  specproc --mode cli --config custom.cfg ./raw_data\n  specproc --mode cli --config XL216_hrs 20241102_hrs      # Process with a packaged telescope profile\n  specproc --config MSTG193_slit  # Copy a packaged telescope profile to ./specproc.cfg\n\n'
+               f'Available telescope profiles: {profiles_hint}',
+        formatter_class=argparse.RawDescriptionHelpFormatter
+    )
+    parser.add_argument('--mode', choices=['gui', 'cli'], default=None,
+                        help='Run mode: gui or cli (auto: cli when inputs are provided, otherwise gui)')
+    parser.add_argument('--config', nargs='?', const=COPY_DEFAULT_CONFIG_SENTINEL, default=None,
+                        help='Path to configuration file, or the name of a packaged telescope '
+                             f'profile ({profiles_hint}). With inputs, the profile/config is used '
+                             'directly for processing; without inputs, it is copied to ./specproc.cfg. '
+                             'Pass --config without a value to copy the generic default config.')
+    parser.add_argument('inputs', nargs='*',
+                        help='FITS files or directories (CLI mode). If omitted, current directory is used.')
+    parser.add_argument('--version', action='version', version='SpecProc 1.0.0')
+    args = parser.parse_args()
+
+    # Override with function arguments if provided
+    if config_path is not None:
+        args.config = config_path
+    if mode is not None:
+        args.mode = mode
+
+    if args.config == COPY_DEFAULT_CONFIG_SENTINEL:
+        copy_default_config_to_cwd()
+        return
+
+    # If --config was given a value that is not an existing file path, try
+    # resolving it as a packaged telescope profile name (e.g. 'XL216_hrs',
+    # 'MSTG193_slit'). With inputs provided, use the profile directly for
+    # processing; without inputs, bootstrap ./specproc.cfg from it (mirrors
+    # the no-value --config behavior above, but for a specific telescope).
+    if args.config and not Path(args.config).expanduser().exists():
+        profile_path = resolve_telescope_profile(args.config)
+        if profile_path is not None:
+            if args.inputs:
+                args.config = str(profile_path)
+            else:
+                copy_default_config_to_cwd(profile=args.config)
+                return
+
+    # Auto mode selection:
+    # - If positional inputs are provided, default to CLI
+    # - Otherwise default to GUI
+    if args.mode is None:
+        args.mode = 'cli' if args.inputs else 'gui'
+
+    # Setup logging
+    setup_logging()
+
+    if args.mode == 'cli':
+        run_cli_mode(args.config, args.inputs)
+    else:
+        # GUI mode
+        from PyQt5.QtWidgets import QApplication
+        from specproc.gui.main_window import MainWindow
+
+        config = ConfigManager(args.config)
+        app = QApplication(sys.argv)
+        window = MainWindow(config)
+        window.show()
+        sys.exit(app.exec_())
+
+
+if __name__ == '__main__':
+    main()

specproc/plotting/__init__.py

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+"""Plotting and visualization modules."""