isgri 0.3.0__py3-none-any.whl → 0.5.0__py3-none-any.whl

isgri/utils/file_loaders.py

@@ -1,159 +1,392 @@
-from astropy.io import fits
-from .pif import apply_pif_mask, coding_fraction, estimate_active_modules
-import numpy as np
-import os
-
-
-def verify_events_path(path):
-    """
-    Verifies and resolves the events file path.
-
-    Args:
-        path (str): File path or directory path containing events file.
-
-    Returns:
-        str: Resolved path to valid events file.
-
-    Raises:
-        FileNotFoundError: If path doesn't exist, no events file found, or multiple events files found.
-        ValueError: If ISGR-EVTS-ALL extension not found in file.
-
-    """
-    if os.path.isfile(path):
-        resolved_path = path
-    elif os.path.isdir(path):
-        candidate_files = [f for f in os.listdir(path) if "isgri_events" in f]
-        if len(candidate_files) == 0:
-            raise FileNotFoundError("No isgri_events file found in the provided directory.")
-        elif len(candidate_files) > 1:
-            raise FileNotFoundError(
-                f"Multiple isgri_events files found in the provided directory: {path}.",
-                "\nPlease specify the exact file paths.",
-            )
-        else:
-            resolved_path = os.path.join(path, candidate_files[0])
-    else:
-        raise FileNotFoundError(f"Path does not exist: {path}")
-
-    with fits.open(resolved_path) as hdu:
-        if "ISGR-EVTS-ALL" not in hdu:
-            raise ValueError(f"Invalid events file: ISGR-EVTS-ALL extension not found in {resolved_path}")
-    return resolved_path
-
-
-def load_isgri_events(events_path):
-    """
-    Loads ISGRI events from FITS file.
-
-    Args:
-        events_path (str): Path to events file or directory.
-
-    Returns:
-        tuple: (events, gtis, metadata) where:
-            - events: Structured numpy array with TIME, ISGRI_ENERGY, DETY, DETZ fields
-            - gtis: (N, 2) array of Good Time Interval [start, stop] pairs (IJD)
-            - metadata: Dictionary with header info (REVOL, SWID, TSTART, etc.)
-
-    """
-    confirmed_path = verify_events_path(events_path)
-    with fits.open(confirmed_path) as hdu:
-        events = np.array(hdu["ISGR-EVTS-ALL"].data)
-        header = hdu["ISGR-EVTS-ALL"].header
-        metadata = {
-            "REVOL": header.get("REVOL"),
-            "SWID": header.get("SWID"),
-            "TSTART": header.get("TSTART"),
-            "TSTOP": header.get("TSTOP"),
-            "TELAPSE": header.get("TELAPSE"),
-            "OBT_TSTART": header.get("OBTSTART"),
-            "OBT_TSTOP": header.get("OBTEND"),
-            "RA_SCX": header.get("RA_SCX"),
-            "DEC_SCX": header.get("DEC_SCX"),
-            "RA_SCZ": header.get("RA_SCZ"),
-            "DEC_SCZ": header.get("DEC_SCZ"),
-        }
-        try:
-            gtis = np.array(hdu["IBIS-GNRL-GTI"].data)
-            gtis = np.array([gtis["START"], gtis["STOP"]]).T
-        except:
-            gtis = np.array([events["TIME"][0], events["TIME"][-1]]).reshape(1, 2)
-    events = events[events["SELECT_FLAG"] == 0]  # Filter out bad events
-    return events, gtis, metadata
-
-
-def default_pif_metadata():
-    """
-    Creates default PIF metadata dictionary for cases without PIF file.
-
-    Returns:
-        dict: Default PIF metadata with all 8 modules active, no source info.
-    """
-    return {
-        "SWID": None,
-        "SRC_RA": None,
-        "SRC_DEC": None,
-        "Source_Name": None,
-        "cod": None,
-        "No_Modules": [1] * 8,
-    }
-
-
-def merge_metadata(events_metadata, pif_metadata):
-    """
-    Merges events and PIF metadata dictionaries.
-
-    Args:
-        events_metadata (dict): Metadata from events file.
-        pif_metadata (dict): Metadata from PIF file.
-
-    Returns:
-        dict: Combined metadata (PIF metadata overwrites events metadata except SWID).
-
-    """
-    merged_metadata = events_metadata.copy()
-    for key in pif_metadata:
-        if key == "SWID":
-            continue
-        merged_metadata[key] = pif_metadata[key]
-    return merged_metadata
-
-
-def load_isgri_pif(pif_path, events, pif_threshold=0.5, pif_extension=-1):
-    """
-    Loads ISGRI PIF (Pixel Illumination Fraction) file and applies mask to events.
-
-    Args:
-        pif_path (str): Path to PIF FITS file.
-        events (ndarray): Events array from load_isgri_events().
-        pif_threshold (float, optional): PIF threshold value (0-1). Defaults to 0.5.
-        pif_extension (int, optional): PIF file extension index. Defaults to -1.
-
-    Returns:
-        tuple: (piffed_events, pif, metadata_pif) where:
-            - piffed_events: Filtered events array with PIF mask applied
-            - pif: PIF values for filtered events
-            - metadata_pif: Dictionary with source info, coding fraction, active modules
-    Raises:
-        ValueError: If PIF file shape is invalid. Usually indicates empty or corrupted file.
-
-    """
-    with fits.open(pif_path) as hdu:
-        pif_file = np.array(hdu[pif_extension].data)
-        header = hdu[pif_extension].header
-
-    if pif_file.shape != (134, 130):
-        raise ValueError(f"Invalid PIF file shape: expected (134, 130), got {pif_file.shape}")
-
-    metadata_pif = {
-        "SWID": header.get("SWID"),
-        "Source_ID": header.get("SOURCEID"),
-        "Source_Name": header.get("NAME"),
-        "SRC_RA": header.get("RA_OBJ"),
-        "SRC_DEC": header.get("DEC_OBJ"),
-    }
-    metadata_pif["cod"] = coding_fraction(pif_file, events)
-    metadata_pif["No_Modules"] = estimate_active_modules(pif_file)
-
-    piffed_events, pif = apply_pif_mask(pif_file, events, pif_threshold)
-
-    return piffed_events, pif, metadata_pif
+"""
+ISGRI Data File Loaders
+========================
+
+Load INTEGRAL/ISGRI event files and detector response (PIF) files.
+
+Functions
+---------
+load_isgri_events : Load photon events from FITS file
+load_isgri_pif : Load and apply detector response (PIF) file
+verify_events_path : Validate and resolve events file path
+default_pif_metadata : Create default PIF metadata
+merge_metadata : Combine events and PIF metadata
+
+Examples
+--------
+>>> from isgri.utils import load_isgri_events, load_isgri_pif
+>>>
+>>> # Load events
+>>> events, gtis, metadata = load_isgri_events("isgri_events.fits")
+>>> print(f"Loaded {len(events)} events")
+>>>
+>>> # Apply PIF weighting
+>>> filtered_events, pif_weights, pif_meta = load_isgri_pif(
+...     "pif_model.fits",
+...     events,
+...     pif_threshold=0.5
+... )
+>>> print(f"Kept {len(filtered_events)}/{len(events)} events")
+>>> print(f"Coding fraction: {pif_meta['cod']:.2%}")
+
+Notes
+-----
+- Events files contain photon arrival times, energies, and detector positions
+- PIF files contain detector response maps for specific source positions
+- PIF weighting corrects for shadowing by the coded mask
+"""
+
+from astropy.io import fits
+from astropy.table import Table
+import numpy as np
+from numpy.typing import NDArray
+from typing import Tuple, Dict, Optional, Union
+from pathlib import Path
+import os
+from .pif import apply_pif_mask, coding_fraction, estimate_active_modules
+
+
+def verify_events_path(path: Union[str, Path]) -> str:
+    """
+    Verify and resolve the events file path.
+
+    Parameters
+    ----------
+    path : str or Path
+        File path or directory path containing events file.
+        If directory, searches for files containing 'isgri_events'.
+
+    Returns
+    -------
+    resolved_path : str
+        Resolved absolute path to valid events file.
+
+    Raises
+    ------
+    FileNotFoundError
+        If path doesn't exist, no events file found, or multiple
+        candidates found in directory.
+    ValueError
+        If ISGR-EVTS-ALL extension not found in file.
+
+    Examples
+    --------
+    >>> # Direct file path
+    >>> path = verify_events_path("isgri_events.fits")
+
+    >>> # Directory with single events file
+    >>> path = verify_events_path("/data/scw/0234/001200340010.001")
+
+    >>> # Will raise error if multiple files
+    >>> verify_events_path("/data/scw/")  # Multiple SCWs present
+    FileNotFoundError: Multiple isgri_events files found...
+    """
+    path = Path(path)
+
+    if path.is_file():
+        resolved_path = str(path)
+    elif path.is_dir():
+        candidate_files = [f for f in os.listdir(path) if "isgri_events" in f]
+
+        if len(candidate_files) == 0:
+            raise FileNotFoundError(f"No isgri_events file found in directory: {path}")
+        elif len(candidate_files) > 1:
+            raise FileNotFoundError(
+                f"Multiple isgri_events files found in directory: {path}\n"
+                f"Found: {candidate_files}\n"
+                "Please specify the exact file path."
+            )
+        else:
+            resolved_path = str(path / candidate_files[0])
+    else:
+        raise FileNotFoundError(f"Path does not exist: {path}")
+
+    # Verify FITS structure
+    try:
+        with fits.open(resolved_path) as hdu:
+            if "ISGR-EVTS-ALL" not in hdu:
+                raise ValueError(f"Invalid events file: ISGR-EVTS-ALL extension not found in {resolved_path}")
+    except Exception as e:
+        if isinstance(e, (FileNotFoundError, ValueError)):
+            raise
+        raise ValueError(f"Cannot open FITS file {resolved_path}: {e}")
+
+    return resolved_path
+
+
+def load_isgri_events(events_path: Union[str, Path]) -> Tuple[Table, NDArray[np.float64], Dict]:
+    """
+    Load ISGRI photon events from FITS file.
+
+    Parameters
+    ----------
+    events_path : str or Path
+        Path to events FITS file or directory containing it.
+
+    Returns
+    -------
+    events : Table
+        Astropy Table with columns:
+        - TIME : Event time in IJD
+        - ISGRI_ENERGY : Energy in keV
+        - DETY : Y detector coordinate (0-129)
+        - DETZ : Z detector coordinate (0-133)
+    gtis : ndarray, shape (N, 2) or None
+        Good Time Intervals [start, stop] pairs in IJD.
+        If no GTI extension found, returns None.
+    metadata : dict
+        Header metadata with keys:
+        - REVOL : Revolution number
+        - SWID : Science Window ID
+        - TSTART, TSTOP : Start/stop times (IJD)
+        - RA_SCX, DEC_SCX : Pointing axis coordinates
+        - RA_SCZ, DEC_SCZ : Z-axis coordinates
+        - NoEVTS : Number of events in file
+
+    Raises
+    ------
+    FileNotFoundError
+        If events file not found or invalid.
+    ValueError
+        If required FITS extension missing.
+
+    Examples
+    --------
+    >>> events, gtis, meta = load_isgri_events("isgri_events.fits")
+    >>> print(f"Loaded {len(events)} events")
+    >>> print(f"Time range: {meta['TSTART']:.1f} - {meta['TSTOP']:.1f} IJD")
+    >>> print(f"GTIs: {len(gtis)} intervals")
+
+    >>> # Check energy range
+    >>> print(f"Energy: {events['ISGRI_ENERGY'].min():.1f} - "
+    ...       f"{events['ISGRI_ENERGY'].max():.1f} keV")
+
+    See Also
+    --------
+    load_isgri_pif : Apply detector response weighting
+    """
+    confirmed_path = verify_events_path(events_path)
+
+    with fits.open(confirmed_path) as hdu:
+        # Load events
+        events_data = hdu["ISGR-EVTS-ALL"].data
+        header = hdu["ISGR-EVTS-ALL"].header
+
+        # Extract metadata
+        metadata = {
+            "REVOL": header.get("REVOL"),
+            "SWID": header.get("SWID"),
+            "TSTART": header.get("TSTART"),
+            "TSTOP": header.get("TSTOP"),
+            "TELAPSE": header.get("TELAPSE"),
+            "OBT_TSTART": header.get("OBTSTART"),
+            "OBT_TSTOP": header.get("OBTEND"),
+            "RA_SCX": header.get("RA_SCX"),
+            "DEC_SCX": header.get("DEC_SCX"),
+            "RA_SCZ": header.get("RA_SCZ"),
+            "DEC_SCZ": header.get("DEC_SCZ"),
+            "NoEVTS": header.get("NAXIS2"),
+        }
+
+        # Load GTIs
+        try:
+            gti_data = hdu["IBIS-GNRL-GTI"].data
+            gtis = np.column_stack([gti_data["START"], gti_data["STOP"]])
+        except (KeyError, IndexError):
+            # No GTI extension - return empty GTI
+            # t_start = events_data["TIME"][0]
+            # t_stop = events_data["TIME"][-1]
+            # gtis = np.array([[t_start, t_stop]])
+            gtis = None
+
+    # Filter bad events (SELECT_FLAG != 0)
+    good_mask = events_data["SELECT_FLAG"] == 0
+    events = Table(events_data[good_mask])
+
+    return events, gtis, metadata
+
+
+def default_pif_metadata() -> Dict:
+    """
+    Create default PIF metadata for cases without PIF file.
+
+    Used when no PIF weighting is applied. All modules are
+    considered active with unit weight.
+
+    Returns
+    -------
+    metadata : dict
+        Default PIF metadata with:
+        - SWID : None
+        - SRC_RA, SRC_DEC : None (no source position)
+        - Source_Name : None
+        - cod : None (no coding fraction)
+        - No_Modules : [True]*8 (all modules active)
+
+    Examples
+    --------
+    >>> meta = default_pif_metadata()
+    >>> print(meta['No_Modules'])
+    [True, True, True, True, True, True, True, True]
+    """
+    return {
+        "SWID": None,
+        "SRC_RA": None,
+        "SRC_DEC": None,
+        "Source_Name": None,
+        "cod": None,
+        "No_Modules": [True] * 8,  # All modules active
+    }
+
+
+def merge_metadata(events_metadata: Dict, pif_metadata: Dict) -> Dict:
+    """
+    Merge events and PIF metadata dictionaries.
+
+    PIF metadata takes precedence except for SWID, which is
+    preserved from events metadata.
+
+    Parameters
+    ----------
+    events_metadata : dict
+        Metadata from events file.
+    pif_metadata : dict
+        Metadata from PIF file.
+
+    Returns
+    -------
+    merged : dict
+        Combined metadata with PIF values overwriting events values
+        (except SWID).
+
+    Examples
+    --------
+    >>> events_meta = {'SWID': '023400100010', 'TSTART': 3000.0}
+    >>> pif_meta = {'SWID': '999999999999', 'SRC_RA': 83.63, 'SRC_DEC': 22.01}
+    >>> merged = merge_metadata(events_meta, pif_meta)
+    >>> print(merged['SWID'])  # Preserved from events
+    023400100010
+    >>> print(merged['SRC_RA'])  # From PIF
+    83.63
+    """
+    merged = events_metadata.copy()
+
+    for key, value in pif_metadata.items():
+        if key != "SWID":  # Preserve SWID from events
+            merged[key] = value
+
+    return merged
+
+
+def load_isgri_pif(
+    pif_path: Union[str, Path],
+    events: Table,
+    pif_threshold: float = 0.5,
+    pif_extension: int = -1,
+) -> Tuple[Table, NDArray[np.float64], Dict]:
+    """
+    Load PIF (Pixel Illumination Fraction) file and apply to events.
+
+    Filters events by PIF threshold and returns PIF weights for
+    detector response correction.
+
+    Parameters
+    ----------
+    pif_path : str or Path
+        Path to PIF FITS file.
+    events : Table
+        Events table from load_isgri_events() with DETZ, DETY columns.
+    pif_threshold : float, default 0.5
+        Minimum PIF value to keep event (0.0-1.0).
+        Higher values = only well-illuminated pixels.
+    pif_extension : int, default -1
+        FITS extension index containing PIF data.
+        -1 = last extension (typical).
+
+    Returns
+    -------
+    filtered_events : Table
+        Events with PIF >= threshold.
+    pif_weights : ndarray
+        PIF value for each filtered event (for response correction).
+    pif_metadata : dict
+        Metadata with keys:
+        - SWID : Science Window ID
+        - Source_ID, Source_Name : Source identifiers
+        - SRC_RA, SRC_DEC : Source position (degrees)
+        - cod : Coding fraction (0.0-1.0)
+        - No_Modules : Array of active module flags
+
+    Raises
+    ------
+    ValueError
+        If PIF file has invalid shape (must be 134×130).
+    FileNotFoundError
+        If PIF file not found.
+
+    Examples
+    --------
+    >>> events, gtis, meta = load_isgri_events("events.fits")
+    >>> filtered, weights, pif_meta = load_isgri_pif(
+    ...     "pif_model.fits",
+    ...     events,
+    ...     pif_threshold=0.5
+    ... )
+    >>>
+    >>> print(f"Filtered: {len(filtered)}/{len(events)} events")
+    >>> print(f"Coding fraction: {pif_meta['cod']:.2%}")
+    >>> print(f"Active modules: {np.sum(pif_meta['No_Modules'])}/8")
+
+    >>> # Use for light curve with response correction
+    >>> from isgri.utils import LightCurve
+    >>> lc = LightCurve(
+    ...     time=filtered['TIME'],
+    ...     energies=filtered['ISGRI_ENERGY'],
+    ...     dety=filtered['DETY'],
+    ...     detz=filtered['DETZ'],
+    ...     weights=weights,
+    ...     gtis=gtis,
+    ...     metadata={**meta, **pif_meta}
+    ... )
+
+    See Also
+    --------
+    load_isgri_events : Load event data
+    apply_pif_mask : Apply PIF filtering
+    coding_fraction : Calculate coded fraction
+    """
+    if not (0 <= pif_threshold <= 1):
+        raise ValueError(f"pif_threshold must be in [0, 1], got {pif_threshold}")
+
+    pif_path = Path(pif_path)
+    if not pif_path.exists():
+        raise FileNotFoundError(f"PIF file not found: {pif_path}")
+
+    # Load PIF file
+    with fits.open(pif_path) as hdu:
+        pif_file = np.array(hdu[pif_extension].data)
+        header = hdu[pif_extension].header
+
+    # Validate shape
+    if pif_file.shape != (134, 130):
+        raise ValueError(
+            f"Invalid PIF file shape: expected (134, 130), got {pif_file.shape}. " "File may be empty or corrupted."
+        )
+
+    # Extract metadata
+    pif_metadata = {
+        "SWID": header.get("SWID"),
+        "Source_ID": header.get("SOURCEID"),
+        "Source_Name": header.get("NAME"),
+        "SRC_RA": header.get("RA_OBJ"),
+        "SRC_DEC": header.get("DEC_OBJ"),
+    }
+
+    # Compute quality metrics
+    pif_metadata["cod"] = coding_fraction(pif_file, events)
+    pif_metadata["No_Modules"] = estimate_active_modules(pif_file)
+
+    # Apply PIF mask
+    filtered_events, pif_weights = apply_pif_mask(pif_file, events, pif_threshold)
+
+    return filtered_events, pif_weights, pif_metadata