lightstack 0.1.0__tar.gz

lightstack-0.1.0/PKG-INFO

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+Metadata-Version: 2.1
+Name: lightstack
+Version: 0.1.0
+Summary: Tools for building and processing multi-filter astrophysical datacubes
+Author: Andressa Wille, Thallis Pessi
+Requires-Dist: numpy
+Requires-Dist: astropy
+Requires-Dist: matplotlib
+Requires-Dist: reproject
+Requires-Dist: regions
+Requires-Dist: scipy
+Requires-Dist: photutils

lightstack-0.1.0/README.md

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+<img src="images/logo.png" width="120">
+
+# Lightstack
+
+
+This is a code with functions for:
+- cropping FITS images
+- building photometric datacubes
+- PSF matching
+
+(only JWST and HST for now)
+
+pip install git+https://github.com/AndressaWille/lightstack.git
+
+
+Documentation: https://lightstack.readthedocs.io/en/latest/
+
+See the tutorial notebook!

lightstack-0.1.0/pyproject.toml

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+[project]
+name = "lightstack"
+version = "0.1.0"
+description = "Tools for building and processing multi-filter astrophysical datacubes"
+authors = [{name = "Andressa Wille"}, {name="Thallis Pessi"}]
+dependencies = [
+    "numpy",
+    "astropy",
+    "matplotlib",
+    "reproject",
+    "regions",
+    "scipy",
+    "photutils"
+]
+license = {file = "LICENSE"}
+
+[build-system]
+requires = ["setuptools", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[tool.setuptools.packages.find]
+where = ["src"]

lightstack-0.1.0/setup.cfg

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+[egg_info]
+tag_build = 
+tag_date = 0
+

lightstack-0.1.0/src/lightstack/__init__.py

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+"""
+Lightstack: Tools for processing, PSF matching, and visualization
+of multi-filter photometric datacubes using astronomical imaging (HST and JWST).
+
+Main functionalities include:
+- Crop regions
+- Image alignment and photometric datacube construction
+- PSF matching using convolution kernels
+- Visualization of FITS images and datacubes
+"""
+
+# =========================
+# Cropping 
+# =========================
+from .crop import (
+    get_sky_bbox_from_cutout,
+    crop_from_radec,
+    crop_using_reference,
+    crop_reg,
+    cut_region_2d,
+)
+
+
+# =========================
+# Datacube / alignment
+# =========================
+from .datacube import (
+    align_reproject_fits,
+    build_datacube,
+    cut_region_datacube,
+    build_valid_datacube,
+    remove_filter,
+    update_cube_header,
+)
+
+# =========================
+# PSF matching
+# =========================
+from .psf import (
+    build_kernel,
+    save_kernel,
+    apply_kernel,
+    psf_match_datacube,
+)
+
+# =========================
+# Visualization
+# =========================
+from .plot import (
+    visualize_fits,
+    plot_datacube_filters,
+    plot_psf_grid,
+)
+
+# =========================
+# Utils 
+# =========================
+from .utils import (
+    find_ext,
+    infer_filter,
+)
+
+# =========================
+# Public API
+# =========================
+__all__ = [
+    # crop
+    "get_sky_bbox_from_cutout",
+    "crop_from_radec",
+    "crop_using_reference",
+    "crop_reg",
+    "cut_region_2d",
+    
+    # datacube
+    "align_reproject_fits",
+    "build_datacube",
+    "cut_region_datacube",
+    "build_valid_datacube",
+    "remove_filter",
+    "update_cube_header",
+
+    # psf
+    "build_kernel",
+    "save_kernel",
+    "apply_kernel",
+    "psf_match_datacube",
+
+    # plot
+    "visualize_fits",
+    "plot_datacube_filters",
+    "plot_psf_grid",
+
+    # utils
+    "find_ext",
+    "infer_filter",
+    "pick_folder",
+    "get_filter",
+    "filter_id",
+    "save_fits",
+    "sort_fits",
+    "MJy_sr_to_jy",
+    "get_pixel_scale",
+    
+]

lightstack-0.1.0/src/lightstack/crop.py

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+import numpy as np
+
+from astropy.io import fits
+from astropy.wcs import WCS
+from astropy.wcs.utils import proj_plane_pixel_scales, skycoord_to_pixel
+from astropy.coordinates import SkyCoord
+import astropy.units as u
+
+from .utils import find_ext
+
+def get_sky_bbox_from_cutout(fits_cut):
+    """
+    Get sky bounding box (RA, Dec) from a FITS cutout.
+
+    Parameters
+    ----------
+    fits_cut : str
+        Path to FITS file
+
+    Returns
+    -------
+    ra, dec : arrays
+        RA and Dec of the four corners
+    """
+    # Read FITS
+    with fits.open(fits_cut) as hdul:
+        ext = find_ext(hdul)
+        if ext is None:
+            raise ValueError(f"No 2D image found in {fits_cut}")
+
+        data = hdul[ext].data
+        header = hdul[ext].header
+
+        wcs = WCS(header)
+
+    ny, nx = data.shape
+
+    # Define pixel coordinates of the four corners
+    corners_pix = np.array([
+        [0, 0],
+        [nx-1, 0],
+        [0, ny-1],
+        [nx-1, ny-1]])
+
+    # Convert pixel coordinates to sky (RA, Dec)
+    ra, dec = wcs.wcs_pix2world(
+        corners_pix[:, 0],
+        corners_pix[:, 1],
+        0  # origin = 0 (Python convention)
+    )
+
+    return ra, dec
+
+
+def crop_from_radec(fits_path, ra, dec, size_arcsec, output_path=None):
+    """
+    Extract a square cutout from a FITS image centered on a given sky position.
+
+    Parameters
+    ----------
+    fits_path : str
+        Path to the FITS image.
+
+    ra : float
+        Right Ascension of the center (in degrees).
+
+    dec : float
+        Declination of the center (in degrees).
+
+    size_arcsec : float
+        Size of the cutout (in arcseconds). The cutout is square.
+
+    Returns
+    -------
+    data_cut : 2D numpy array
+        Cropped image data.
+
+    header_cut : FITS header
+        Updated header with corrected WCS reference (CRPIX).
+    """
+
+    # Open FITS
+    with fits.open(fits_path) as hdul:
+        ext = find_ext(hdul)
+        if ext is None:
+            raise ValueError(f"No 2D image data found in {fits_path}")
+
+        data = hdul[ext].data
+        header = hdul[ext].header
+        wcs = WCS(header)
+
+    # Convert sky coordinates (RA, Dec) to pixel coordinates
+    coord = SkyCoord(ra=ra * u.deg, dec=dec * u.deg)
+    x_center, y_center = skycoord_to_pixel(coord, wcs)
+
+    # Get pixel scale (arcsec/pixel)
+    pixel_scales = proj_plane_pixel_scales(wcs) * 3600.0  # deg → arcsec
+
+    pixscale = np.mean(pixel_scales)
+
+    # Convert size from arcsec to pixels
+    half_size_pix = (size_arcsec / pixscale) / 2.0
+
+    # Define integer pixel bounds
+    x_min = int(np.floor(x_center - half_size_pix))
+    x_max = int(np.ceil(x_center + half_size_pix))
+    y_min = int(np.floor(y_center - half_size_pix))
+    y_max = int(np.ceil(y_center + half_size_pix))
+
+    ny, nx = data.shape
+    x_min = max(0, x_min)
+    x_max = min(nx, x_max)
+    y_min = max(0, y_min)
+    y_max = min(ny, y_max)
+
+    # Extract cutout
+    data_cut = data[y_min:y_max, x_min:x_max]
+
+    # Update WCS
+    header_cut = header.copy()
+    header_cut['CRPIX1'] -= x_min
+    header_cut['CRPIX2'] -= y_min
+
+    if output_path is not None:
+        fits.PrimaryHDU(data_cut, header=header_cut).writeto(
+        output_path,
+        overwrite=True)
+    
+    return data_cut, header_cut
+
+
+def crop_using_reference(fits_path, ref_cutout, output_path=None):
+    """
+    Crop a FITS image using the sky footprint of a reference cutout.
+
+    This function extracts a region from a target image such that it matches
+    the sky coverage (RA/Dec bounding box) of a reference FITS cutout.
+
+    Parameters
+    ----------
+    fits_path : str
+        Path to the target FITS image to be cropped.
+
+    ref_cutout : str
+        Path to the reference FITS cutout defining the sky region.
+
+    output_path : str, optional
+        If provided, saves the cropped FITS to this path.
+
+    Returns
+    -------
+    data_cut : 2D numpy array
+        Cropped image data.
+
+    header_cut : FITS header
+        Updated header with corrected WCS reference (CRPIX).
+    """
+
+    # Get RA/Dec bounding box from reference cutout
+    ra, dec = get_sky_bbox_from_cutout(ref_cutout)
+
+    # Open FITS
+    with fits.open(fits_path) as hdul:
+        ext = find_ext(hdul)
+        if ext is None:
+            raise ValueError(f"No 2D image found in {fits_path}")
+
+        data = hdul[ext].data
+        header = hdul[ext].header
+        wcs = WCS(header)
+
+    # Convert sky coordinates (RA/Dec) to pixel coordinates 
+    x, y = wcs.wcs_world2pix(ra, dec, 0)
+
+    # Define bounding box in pixel space
+    x_min = int(np.floor(np.min(x)))
+    x_max = int(np.ceil(np.max(x)))
+    y_min = int(np.floor(np.min(y)))
+    y_max = int(np.ceil(np.max(y)))
+
+    ny, nx = data.shape
+    x_min = max(0, x_min)
+    x_max = min(nx, x_max)
+    y_min = max(0, y_min)
+    y_max = min(ny, y_max)
+
+    # Extract cutout
+    data_cut = data[y_min:y_max, x_min:x_max]
+
+    # Update WCS
+    header_cut = header.copy()
+    header_cut['CRPIX1'] -= x_min
+    header_cut['CRPIX2'] -= y_min
+
+    # Save 
+    if output_path is not None:
+        fits.PrimaryHDU(data_cut, header=header_cut).writeto(
+            output_path,
+            overwrite=True)
+
+    return data_cut, header_cut
+    
+
+def crop_reg(fits_path, region):
+    """
+    Crops a FITS image using a DS9 region.
+
+    Parameters
+    ----------
+    fits_path : str
+        Path to the FITS file.
+    region : regions.Region
+        Region object read from a DS9 region file.
+
+    Returns
+    -------
+    data_cut : numpy.ndarray
+        Cropped image data.
+    header_cut : astropy.io.fits.Header
+        Updated FITS header with adjusted CRPIX keywords.
+
+    Raises
+    ------
+    ValueError
+        If no image data extension is found in the FITS file.
+    """
+    # Open fits
+    with fits.open(fits_path) as hdul:
+        ext = find_ext(hdul)
+        if ext is None:
+            raise ValueError(f"No image data found in {fits_path}")
+
+        data = hdul[ext].data
+        header = hdul[ext].header
+        wcs = WCS(header)
+    
+    # Define region limits
+    pix_region = region.to_pixel(wcs)
+    bbox = pix_region.bounding_box
+
+    x_min, x_max = int(bbox.ixmin), int(bbox.ixmax)
+    y_min, y_max = int(bbox.iymin), int(bbox.iymax)
+
+    # Crop the image
+    data_cut = data[y_min:y_max, x_min:x_max]
+
+    # Update reference pixel in the header
+    header_cut = header.copy()
+    header_cut['CRPIX1'] -= x_min
+    header_cut['CRPIX2'] -= y_min
+
+    return data_cut, header_cut
+    
+    
+def cut_region_2d(fits_file, x_start, x_end, y_start, y_end, output_path):
+    """
+    Cuts a spatial region from a 2D fits image.
+
+    Parameters
+    ----------
+    fits_file : str
+        Path to the input 2D fits image.
+    x_start, x_end : int
+        Pixel indices for the x axis.
+    y_start, y_end : int
+        Pixel indices for the y axis.
+    output_path : str
+        Path to the output fits file.
+
+    Returns
+    -------
+    None
+        Saves the cut fits image.
+    """
+    # Open FITS
+    with fits.open(fits_file) as hdul:
+        ext = find_ext(hdul)
+        if ext is None:
+            raise ValueError(f"No image data found in {fits_path}")
+
+        data = hdul[ext].data
+        header = hdul[ext].header
+
+        # Cut the data
+        cut_data = data[y_start:y_end, x_start:x_end]
+
+        # Update WCS
+        wcs_2d = WCS(header)
+        wcs_2d.wcs.crpix[0] -= x_start
+        wcs_2d.wcs.crpix[1] -= y_start
+
+        # Build new header
+        new_header = wcs_2d.to_header()
+        new_header['NAXIS'] = 2
+        new_header['NAXIS1'] = x_end - x_start
+        new_header['NAXIS2'] = y_end - y_start
+
+        # Preserve unit if exists
+        if 'BUNIT' in header:
+            new_header['BUNIT'] = header['BUNIT']
+
+        # Optional: store crop info
+        new_header['XMINPIX'] = x_start
+        new_header['XMAXPIX'] = x_end
+        new_header['YMINPIX'] = y_start
+        new_header['YMAXPIX'] = y_end
+
+        # Save cut image
+        fits.PrimaryHDU(cut_data, header=new_header).writeto(output_path, overwrite=True)
+        print(f"Cut 2D fits saved to '{output_path}'")